Specifications
==============

Sequence source file: "/data/brick1/zmahmoud/africandsi-megassr/megassr-v3/results/hub_GCA_018244995.1/fasta/hub_GCA_018244995.1_genomic.fa"

Definement of microsatellites (unit size / minimum number of repeats):
(1/20) (2/6) (3/5) (4/4) (5/3) (6/3) 

Maximal number of bases interrupting 2 SSRs in a compound microsatellite:  100



RESULTS OF MICROSATELLITE SEARCH
================================

Total number of sequences examined:              20517
Total size of examined sequences (bp):           6374276
Total number of identified SSRs:                 647
Number of SSR containing sequences:              539
Number of sequences containing more than 1 SSR:  54
Number of SSRs present in compound formation:    87


Distribution to different repeat type classes
---------------------------------------------

Unit size	Number of SSRs
1	51
2	212
3	70
4	96
5	167
6	51

Frequency of identified SSR motifs
----------------------------------

Repeats	3	4	5	6	7	8	9	10	11	12	13	14	15	16	17	18	19	20	21	22	23	24	25	26	27	28	29	30	31	32	33	34	35	36	37	38	39	40	41	42	43	44	45	46	47	48	49	50	51	52	53	54	55	56	57	58	59	60	61	62	63	64	65	66	67	68	69	70	71	72	73	74	75	76	77	total
A	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	2	3		1							2	1						1												1																					1								12
C	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	1		1					1				1				1					1																					1																	7
G	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	1		2	1	1		1			2	1		1		1							1																													1								13
T	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	1	3	1	1	2	4						2													1	1														1						1												1	19
AC	-	-	-	10	3	1					1	1																																																																16
AG	-	-	-	5	1	2	1																																																																					9
AT	-	-	-	17	5	10	4	3	3			1																																																																43
CA	-	-	-	3	5	1	1				1																																																																	11
CG	-	-	-	3	1																																																																							4
CT	-	-	-	3		1	1	1	2	1		1																																																																10
GA	-	-	-	4	2		1	1																																																																				8
GC	-	-	-	3																																																																								3
GT	-	-	-	2	2	2			2	1	1					1																																																												11
TA	-	-	-	17	5	9	4	1	5	2				1																																																														44
TC	-	-	-	8	5	6	3	3	3	1	2	1		1																						1	1																																							35
TG	-	-	-	4	5	4	1	1		1			1																							1																																								18
AAC	-	-	1																																																																									1
AAG	-	-	1	1																																																																								2
AAT	-	-	2	1																																																																								3
ACT	-	-	1																																																																									1
ATA	-	-	3	2																																																																								5
ATC	-	-	1																																																																									1
ATG	-	-	1																																																																									1
ATT	-	-	5		1				1																																																																			7
CAG	-	-	1																																																																									1
CAT	-	-	1																																																																									1
CCA	-	-	1		1																																																																							2
CCG	-	-	2																																																																									2
CGC	-	-	1																																																																									1
CGG	-	-	1																																																																									1
CTA	-	-	1																																																																									1
CTT	-	-	2																																																																									2
GAA	-	-			1																																																																							1
GAT	-	-	1																																																																									1
GCG	-	-	1	1																																																																								2
GCT	-	-	1																																																																									1
GGC	-	-					1																																																																					1
GTG	-	-	1																																																																									1
GTT	-	-	1																																																																									1
TAA	-	-	1																																																																									1
TAC	-	-	1																																																																									1
TAG	-	-	2																																																																									2
TAT	-	-	1	2			1																																																																					4
TCA	-	-	2		1																																																																							3
TCT	-	-	4																																																																									4
TGA	-	-	1																																																																									1
TGC	-	-	2																																																																									2
TGG	-	-	1	1																																																																								2
TTA	-	-	4	1																																																																								5
TTC	-	-	4	1																																																																								5
AAAC	-	1																																																																										1
AAAT	-	2																																																																										2
AACA	-	1																																																																										1
AAGA	-	1																																																																										1
AATA	-		1	1	1																																																																							3
AATT	-	1																																																																										1
ACAA	-	1		1																																																																								2
ACGA	-	1																																																																										1
ACTG	-		1																																																																									1
AGAC	-	1																																																																										1
AGTC	-	1																																																																										1
ATAA	-	2	1																																																																									3
ATAC	-	2	1		1																																																																							4
ATAG	-	2																																																																										2
ATCA	-	1																																																																										1
ATGA	-	1																																																																										1
ATTT	-	1																																																																										1
CAAA	-	3																																																																										3
CAGA	-	1																																																																										1
CAGT	-	1																																																																										1
CCAT	-	1																																																																										1
CCTA	-	1																																																																										1
CTAC	-	1																																																																										1
GAAG	-	1																																																																										1
GATA	-		1																																																																									1
GATT	-	1																																																																										1
GGTC	-	1																																																																										1
GTAG	-	2																																																																										2
GTGC	-	1																																																																										1
GTTG	-	1																																																																										1
GTTT	-			1																																																																								1
TAAA	-	7	1	2																																																																								10
TACA	-	2	1																																																																									3
TATC	-	1																																																																										1
TATG	-	1		1			1																																																																					3
TATT	-		1																																																																									1
TCGG	-	1																																																																										1
TCGT	-	1																																																																										1
TCTA	-	1	1	1																																																																								3
TGAC	-	2		1																																																																								3
TGTA	-	3	2		1	2																																																																						8
TGTT	-	1																																																																										1
TTAA	-	1																																																																										1
TTAT	-	2	2	1	1																																																																							6
TTCA	-	2																																																																										2
TTGG	-		1																																																																									1
TTTA	-	3		1																																																																								4
TTTC	-	1	1			1																																																																						3
AAAAC	1																																																																											1
AAAAT	1																																																																											1
AAACT	1																																																																											1
AAAGT	1																																																																											1
AAATA	1																																																																											1
AAATT	1																																																																											1
AACAT	1																																																																											1
AACCT	2																																																																											2
AACTA	1																																																																											1
AAGGA	1																																																																											1
AATAA	1																																																																											1
AATAC	1																																																																											1
AATCA	1																																																																											1
AATTT	2																																																																											2
ACCGA	1																																																																											1
ACCTA				1	2				1																																																																			4
ACGAA	1																																																																											1
ACGGG	1																																																																											1
ACTAC	1																																																																											1
ACTTA	1																																																																											1
AGAAC				1																																																																								1
AGAAG	2																																																																											2
AGAGA	1																																																																											1
AGGTT	1	1																																																																										2
AGTAA		1																																																																										1
AGTTG	1																																																																											1
ATAAA	3																																																																											3
ATACG	1																																																																											1
ATAGA				1																																																																								1
ATATA	1																																																																											1
ATATC	1																																																																											1
ATGTA	1																																																																											1
ATTAA	3																																																																											3
ATTCT	1																																																																											1
ATTTT	1																																																																											1
CAGTC	1																																																																											1
CATTA	1																																																																											1
CCCGC	1																																																																											1
CCGCG	1																																																																											1
CCGGC	1																																																																											1
CCTAA	1							2			1																																																																	4
CCTTG							1																																																																					1
CGATA	1																																																																											1
CGCCG	2																																																																											2
CGGGA		1																																																																										1
CGGTT	1																																																																											1
CGTCC	2																																																																											2
CTAAC	1	1																																																																										2
CTAAT	1																																																																											1
CTATA	1																																																																											1
CTCCT	1																																																																											1
CTCTT	1																																																																											1
GAAAA				1																																																																								1
GAATA	1																																																																											1
GACAA	2																																																																											2
GACGG	1	1																																																																										2
GACTT	1																																																																											1
GAGAT							1																																																																					1
GAGGT	1																																																																											1
GATGT	1																																																																											1
GCTAT	1																																																																											1
GCTCA	1																																																																											1
GGACT	1																																																																											1
GGAGA	1																																																																											1
GGATA		1																																																																										1
GGATG		1																																																																										1
GGCGC	1																																																																											1
GGTTA	1		1	1	2		1	1								1																																																												8
GTCAT	1																																																																											1
GTGTG	1																																																																											1
GTTAG	1				2				1		1																																																																	5
GTTCA	1																																																																											1
GTTTG	1																																																																											1
GTTTT	1																																																																											1
TAAAA	1																																																																											1
TAAAT	1																																																																											1
TAACC		1	1	1																																																																								3
TAAGA	1																																																																											1
TAATT	1																																																																											1
TACAG	1																																																																											1
TACTG	1																																																																											1
TAGGT	1	1	1																																																																									3
TATAT	1																																																																											1
TATCA	1																																																																											1
TATTG	2																																																																											2
TATTT	1																																																																											1
TCAAA	1																																																																											1
TCCCA	1																																																																											1
TCCCG	1																																																																											1
TCTAA	1																																																																											1
TCTAG	1																																																																											1
TCTAT	2																																																																											2
TCTTC	1																																																																											1
TCTTT	1																																																																											1
TGATT	1																																																																											1
TGTAT	2																																																																											2
TGTCA		1																																																																										1
TGTGG	1																																																																											1
TTAAA	1																																																																											1
TTAAG	1																																																																											1
TTAGA	1																																																																											1
TTAGG	1	2	2							2																																																																		7
TTATA	1																																																																											1
TTCAT	1																																																																											1
TTCCT	1																																																																											1
TTGAA	1																																																																											1
TTGAG	1																																																																											1
TTGCC	1		1					1				1																																																																4
TTGGA	1																																																																											1
TTGGT	1																																																																											1
TTGTA	1																																																																											1
TTTAC	1																																																																											1
TTTAT	2																																																																											2
TTTCA	1																																																																											1
TTTGT	2																																																																											2
TTTTA	2																																																																											2
TTTTC	1																																																																											1
TTTTG	1																																																																											1
AAAGCG	1																																																																											1
AACCAG	1																																																																											1
AATTCA			1																																																																									1
ACAGTG		1																																																																										1
ACTAAC		1																																																																										1
ACTGAA	4	1																																																																										5
AGTTTT	1																																																																											1
ATCTTG		1																																																																										1
ATTCTG	1																																																																											1
CAAAGA	1																																																																											1
CAAGAC		1																																																																										1
CACAGG						1																																																																						1
CAGTAG	1																																																																											1
CCCCTT	1																																																																											1
CCTTTT	1																																																																											1
CGACAC	1																																																																											1
CGGAGA						1																																																																						1
CGGTGT	1																																																																											1
CTCTTG							1																																																																					1
CTGACA		1																																																																										1
CTGCGG		1																																																																										1
CTGTAA	1																																																																											1
GCACTG	1																																																																											1
GCCACC	2																																																																											2
GCCGCT	1																																																																											1
GCGACA	1																																																																											1
GTAGGA		1																																																																										1
GTCTCG		1																																																																										1
GTGACA			1																																																																									1
GTGCCT								1																																																																				1
GTGTAT		1																																																																										1
GTGTGC	1	1																																																																										2
GTTGCA	1																																																																											1
TACGAT	1																																																																											1
TCACTG	1																																																																											1
TCTTGA							1				1																																																																	2
TCTTGC		1																																																																										1
TGCCGC	1																																																																											1
TGCGCG	1																																																																											1
TGTATG				1																																																																								1
TGTCAA	1																																																																											1
TGTCAC	1																																																																											1
TTTATA	1																																																																											1
TTTTAA	1																																																																											1

Frequency of classified repeat types (considering sequence complementary)
-------------------------------------------------------------------------

Repeats	3	4	5	6	7	8	9	10	11	12	13	14	15	16	17	18	19	20	21	22	23	24	25	26	27	28	29	30	31	32	33	34	35	36	37	38	39	40	41	42	43	44	45	46	47	48	49	50	51	52	53	54	55	56	57	58	59	60	61	62	63	64	65	66	67	68	69	70	71	72	73	74	75	76	77	total
A/T	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	3	6	1	2	2	4					2	3						1							1	1				1										1						1					1							1	31
C/G	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	2		3	1	1		1	1		2	1	1	1		1	1					1	1																				1									1								20
AC/GT	-	-	-	19	15	8	2	1	2	2	3	1	1			1																				1																																								56
AG/CT	-	-	-	20	8	9	6	5	5	2	2	2		1																						1	1																																							62
AT/AT	-	-	-	34	10	19	8	4	8	2		1		1																																																														87
CG/CG	-	-	-	6	1																																																																							7
AAC/GTT	-	-	2																																																																									2
AAG/CTT	-	-	11	2	1																																																																							14
AAT/ATT	-	-	16	6	1		1		1																																																																			25
ACC/GGT	-	-	3	1	1																																																																							5
ACT/AGT	-	-	5																																																																									5
AGC/CTG	-	-	4																																																																									4
ATC/ATG	-	-	7		1																																																																							8
CCG/CGG	-	-	5	1			1																																																																					7
AAAC/GTTT	-	7		2																																																																								9
AAAG/CTTT	-	2	1			1																																																																						4
AAAT/ATTT	-	17	6	5	2																																																																							30
AACC/GGTT	-	1	1																																																																									2
AACG/CGTT	-	2																																																																										2
AAGG/CCTT	-	1																																																																										1
AATC/ATTG	-	2																																																																										2
AATG/ATTC	-	3																																																																										3
AATT/AATT	-	2																																																																										2
ACAG/CTGT	-	2																																																																										2
ACAT/ATGT	-	8	4	1	2	2	1																																																																					18
ACCG/CGGT	-	2																																																																										2
ACCT/AGGT	-	4																																																																										4
ACGC/CGTG	-	1																																																																										1
ACTG/AGTC	-	4	1	1																																																																								6
AGAT/ATCT	-	4	2	1																																																																								7
ATCC/ATGG	-	1																																																																										1
AAAAC/GTTTT	5																																																																											5
AAAAG/CTTTT	2			1																																																																								3
AAAAT/ATTTT	13																																																																											13
AAACC/GGTTT	2																																																																											2
AAACG/CGTTT	1																																																																											1
AAACT/AGTTT	2																																																																											2
AAAGG/CCTTT	2																																																																											2
AAAGT/ACTTT	2	1																																																																										3
AAATC/ATTTG	3																																																																											3
AAATG/ATTTC	2																																																																											2
AAATT/AATTT	9																																																																											9
AACAG/CTGTT				1																																																																								1
AACAT/ATGTT	1																																																																											1
AACCG/CGGTT	2																																																																											2
AACCT/AGGTT	9	6	5	3	6		1	3	2	2	2					1																																																												40
AACTC/AGTTG	2																																																																											2
AACTG/AGTTC	1																																																																											1
AACTT/AAGTT	2																																																																											2
AAGAC/CTTGT	2																																																																											2
AAGAG/CTCTT	5																																																																											5
AAGAT/ATCTT	1																																																																											1
AAGGC/CCTTG	1		1				1	1				1																																																																5
AAGTC/ACTTG	1																																																																											1
AATAC/ATTGT	6																																																																											6
AATAG/ATTCT	4			1																																																																								5
AATAT/ATATT	3																																																																											3
AATCC/ATTGG	1																																																																											1
AATCT/AGATT	3																																																																											3
AATGT/ACATT	2																																																																											2
AATTC/AATTG	1																																																																											1
ACACC/GGTGT	2																																																																											2
ACACT/AGTGT	1																																																																											1
ACAGT/ACTGT	2																																																																											2
ACATC/ATGTG	1																																																																											1
ACATG/ATGTC	1	1																																																																										2
ACCTC/AGGTG	1																																																																											1
ACGAT/ATCGT	2																																																																											2
ACGGG/CCCGT	5	2																																																																										7
ACTAG/AGTCT	1																																																																											1
ACTAT/AGTAT	1																																																																											1
ACTGG/AGTCC	2																																																																											2
AGAGG/CCTCT	2																																																																											2
AGATG/ATCTC							1																																																																					1
AGCAT/ATGCT	1																																																																											1
AGCTC/AGCTG	1																																																																											1
AGGAT/ATCCT		1																																																																										1
ATATC/ATATG	2																																																																											2
ATCCC/ATGGG	1	1																																																																										2
CCCCG/CGGGG	1																																																																											1
CCCGG/CCGGG	1																																																																											1
CCGCG/CGCGG	4																																																																											4
AAAACT/AGTTTT	1																																																																											1
AAAAGG/CCTTTT	1																																																																											1
AAAATT/AATTTT	1																																																																											1
AAACTG/AGTTTC	4	1																																																																										5
AAAGAC/CTTTGT	1																																																																											1
AAAGCG/CGCTTT	1																																																																											1
AAATAT/ATATTT	1																																																																											1
AAATTC/AATTTG			1																																																																									1
AACACT/AGTGTT		1																																																																										1
AACCAG/CTGGTT	1																																																																											1
AACTGC/AGTTGC	1																																																																											1
AACTGT/ACAGTT	1																																																																											1
AAGACC/CTTGGT		1																																																																										1
AAGAGC/CTCTTG		1					1																																																																					2
AAGATC/ATCTTG		1					1				1																																																																	3
AAGGGG/CCCCTT	1																																																																											1
AATCAG/ATTCTG	1																																																																											1
AATCGT/ACGATT	1																																																																											1
AATGTC/ACATTG	1																																																																											1
ACACAT/ATGTGT		1		1																																																																								2
ACACCG/CGGTGT	2																																																																											2
ACACGC/CGTGTG	1	1																																																																										2
ACACTG/AGTGTC		1																																																																										1
ACAGCG/CGCTGT	1																																																																											1
ACAGGC/CCTGTG						1		1																																																																				2
ACAGTG/ACTGTC	2	1	1																																																																									4
ACCGAG/CGGTCT		1																																																																										1
ACCGCC/CGGTGG	2																																																																											2
ACGCGC/CGCGTG	1																																																																											1
ACGGAG/CCGTCT						1																																																																						1
ACTCCT/AGGAGT		1																																																																										1
ACTGCT/AGCAGT	1																																																																											1
ACTGGC/AGTGCC	1																																																																											1
AGCCGC/CGGCTG		1																																																																										1
AGCGGC/CCGCTG	2																																																																											2
