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

Sequence source file: "/data/brick1/zmahmoud/africandsi-megassr/megassr-v3/results/hub_GCA_002093615.1/fasta/hub_GCA_002093615.1_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:              3256
Total size of examined sequences (bp):           9040186
Total number of identified SSRs:                 1819
Number of SSR containing sequences:              664
Number of sequences containing more than 1 SSR:  324
Number of SSRs present in compound formation:    351


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

Unit size	Number of SSRs
1	67
2	373
3	856
4	113
5	118
6	292

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	total
A	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	3	2	2	5	2	4						2	1	4	1		1					1								1	29
T	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	11	5	5	3		6	1	2	1	1		1					1		1												38
AC	-	-	-	1																																												1
AG	-	-	-	4	2	3							1																																			10
AT	-	-	-	62	27	25	29	14	14	13	14	7	5	6	7	4	1	3																														231
CT	-	-	-	1							1																																					2
GA	-	-	-	2	1		1	1																																								5
GC	-	-	-	3																																												3
GT	-	-	-					1																																								1
TA	-	-	-	27	13	10	13	7	8	5	4	3	4	11	1	2			1		1	3																										113
TC	-	-	-	5	1																																											6
TG	-	-	-		1																																											1
AAC	-	-	1			1																																										2
AAG	-	-	6	1	1			1																																								9
AAT	-	-	28	20	17	12	6	3	4		3	1	3	3		1																																101
ACA	-	-	2	4		2																																										8
ACT	-	-	8	3	4	3	2	2																																								22
AGA	-	-	1	3	1				1																																							6
AGG	-	-	1		1				1																																							3
AGT	-	-	5	1		1				1																																						8
ATA	-	-	14	10	11	8	5	1	1	2		1																																				53
ATC	-	-	9		2	1	1	1																																								14
ATG	-	-	4	4	3				1																																							12
ATT	-	-	27	13	11	12	5	1	4	4	2	1	1																																			81
CAA	-	-	4	2	3																																											9
CAC	-	-	1				1				1																																					3
CAG	-	-			1																																											1
CAT	-	-	4	2	1	1		1																																								9
CCA	-	-	2																																													2
CCT	-	-	4	1				1	1																																							7
CTA	-	-	6	2	3	1	1																																									13
CTC	-	-	2	1	1																																											4
CTG	-	-	1																																													1
CTT	-	-	2	2	1	1					1																																					7
GAA	-	-	12	5	2	2	2	1			1																																					25
GAG	-	-	1		1	1			1																																							4
GAT	-	-	9	7	1	1		2	2	1			1																																			24
GCA	-	-		1				1																																								2
GCT	-	-	3			1																																										4
GGA	-	-	1	1	1	1	1																																									5
GGT	-	-				1																																										1
GTA	-	-	11	6	4	1	1	1					1			1																																26
GTG	-	-	3																																													3
GTT	-	-	8	4	5	3							1	1																																		22
TAA	-	-	26	18	4	9	5	5		1	1	1		2	1					1																												74
TAC	-	-	2	1	1		1	1																																								6
TAG	-	-	6	3		1	2						1	1																																		14
TAT	-	-	31	12	14	8	6	4	7	3	4	1	2		1				1																													94
TCA	-	-	16	4	1	5		1	1																																							28
TCC	-	-	3	4	1			2																																								10
TCT	-	-	3	5	4	1	1	1				1																																				16
TGA	-	-	10	2	1	2					1																																					16
TGC	-	-	1				1																																									2
TGG	-	-	2	2																																												4
TGT	-	-	13	1	3	1	1																																									19
TTA	-	-	26	13	8	6	2	3	2	1																																						61
TTC	-	-	8	1				1																																								10
TTG	-	-	7	1	3																																											11
AAAG	-	1																																														1
AAAT	-	8	3	2	1																																											14
AACA	-	1																																														1
AAGG	-	1																																														1
AATA	-	5	4																																													9
AATT	-	2	2			1																																										5
ATAA	-	2	1																																													3
ATGA	-	1																																														1
ATGC	-	7	2																																													9
ATGT	-			1																																												1
ATTA	-	3																																														3
ATTG	-	1			1																																											2
ATTT	-	5																																														5
CATG	-	1																																														1
CTTC	-	1																																														1
CTTT	-	1					1																																									2
GAAA	-	2																																														2
TAAA	-	5																																														5
TAAT	-	3																																														3
TAGA	-	1																																														1
TATT	-	8	1		1			1																																								11
TCTA	-		1																																													1
TGCA	-	6		1	1																																											8
TTAA	-	3	1																																													4
TTAT	-	5	1																																													6
TTCT	-	1																																														1
TTGA	-	1																																														1
TTTA	-	8			1																																											9
TTTC	-	1																																														1
TTTG	-	1																																														1
AAAAC	4																																															4
AAAAG	1																																															1
AAAAT	6	2																																														8
AAAGA	3																																															3
AAAGG	1	1																																														2
AAATA	3																																															3
AAATT	3																																															3
AAGAA	1																																															1
AAGAG	1																																															1
AATAA	2																																															2
AATAT	3																																															3
AATCA	1																																															1
AATCC	1																																															1
AATTA	1																																															1
AATTT	4																																															4
AGAAA	1																																															1
AGACG	1																																															1
ATAAT	4																																															4
ATATA	2																																															2
ATATC	1																																															1
ATATT	3																																															3
ATCAA	1																																															1
ATTAA	3																																															3
ATTGT	1																																															1
ATTTC	1																																															1
ATTTT	1																																															1
CAAAA	1																																															1
CAATT	1																																															1
CGAGA	1																																															1
CGTCT	1																																															1
CTATA	1																																															1
CTTTC	1																																															1
CTTTT	2																																															2
GAAAA	2																																															2
GAATT	2																																															2
GATTG	1																																															1
TAAAA	1	1																																														2
TAAAT	2																																															2
TATAA	1		1																																													2
TATAT	1																																															1
TATTA	1																																															1
TATTG	1																																															1
TATTT	3																																															3
TCATA	1																																															1
TCTTT	1																																															1
TGAAT	1																																															1
TGTTA								1																																								1
TGTTG		1																																														1
TTAAA	3																																															3
TTAAG	1																																															1
TTAAT	4																																															4
TTATA	1																																															1
TTATG	1																																															1
TTATT	4																																															4
TTCCC	1																																															1
TTCTC	1																																															1
TTGAT	3																																															3
TTTAC	1																																															1
TTTAT	2	1																																														3
TTTCT	1																																															1
TTTTA	3	1																																														4
TTTTC	2																																															2
TTTTG	1																																															1
AAAAAT	1																																															1
AAAATA	1	1																																														2
AAACCT	1	1	2	1																																												5
AAAGAC		1																																														1
AAAGGA	1																																															1
AAATGA		1																																														1
AACAAG	1					2																																										3
AACCTA		1																																														1
AACCTG		1																																														1
AAGAAA	1																																															1
AAGATG	1																																															1
AATAAA	1																																															1
AATACT	1																																															1
AATAGC	1																																															1
AATATA			1																																													1
AATATT	2																																															2
AATCCA	1																																															1
AATCTG	1																																															1
AATGAA	1																																															1
AATGAT		1																																														1
ACAACT	2																																															2
ACTACC	1	2	1																																													4
ACTTCA	1	1																																														2
AGAAAA		1																																														1
AGAAAG	1																																															1
AGAAAT	1																																															1
AGAAGT	1																																															1
AGAATC			1																																													1
AGAGAA	1																																															1
AGAGAT										1																																						1
AGATCC	1		1																																													2
AGGAAT	2																																															2
AGGAGT		1																																														1
AGGATT				1																																												1
ATAAAA	1																																															1
ATAAAT	1																																															1
ATAATC		1																																														1
ATACAT	1																																															1
ATAGGC		1																																														1
ATATTT	3																																															3
ATCAAA		2																																														2
ATCAAG	2																																															2
ATCAGA		1																																														1
ATCATG	1																																															1
ATCTAA	1																																															1
ATGACC		1																																														1
ATGATA	1																																															1
ATGCCA		1																																														1
ATGTCC	1																																															1
ATTATC		1																																														1
ATTATG	1																																															1
ATTCCC		1																																														1
ATTGTA	1																																															1
ATTTAT	1																																															1
ATTTTT	2																																															2
CAAAAG	1																																															1
CAAAGC	1																																															1
CAACAT	1																																															1
CAAGAA					1																																											1
CAAGAT	2																																															2
CAATAA	1																																															1
CAATAC	1																																															1
CACATC	1																																															1
CAGAAC					1																																											1
CAGAAT	1																																															1
CAGCAA	2																																															2
CAGGAA	1		1		1																																											3
CAGGAT							1																																									1
CATCTA		1																																														1
CATCTT	1																																															1
CATTGG		1																																														1
CCAACA			1																																													1
CCACCT	1	1																																														2
CCATCA	1																																															1
CCTAAA	2	1	3	1																																												7
CCTGAG	1																																															1
CCTGAT	1																																															1
CCTGTT	1																																															1
CCTTTC	1																																															1
CGATGA		1																																														1
CGTTCT					1																																											1
CTAAAC		1																																														1
CTAAAG	1																																															1
CTACAT	1																																															1
CTAGAT		1																																														1
CTATTA	1																																															1
CTGAAA		1																																														1
CTGAGC			1																																													1
CTGCAG	1																																															1
CTGCTC					1																																											1
CTGGTC	1	1																																														2
CTTCAT		1																																														1
CTTGAA		1																																														1
CTTGAT			1																																													1
CTTGTT	1																																															1
CTTTCT				1																																												1
GAAAGA		1																																														1
GAAATA	1																																															1
GAACAA	2																																															2
GAACCT	1																																															1
GAAGAG	1																																															1
GAATCT		1	2																																													3
GAGGAT				1																																												1
GAGGCT	1																																															1
GATAAT		1																																														1
GATCAA		1																																														1
GATCAC			1																																													1
GATCAG	1																																															1
GATCCT		1																																														1
GATCTG			1																																													1
GATCTT	1																																															1
GATTCT		1																																														1
GATTTG			1																																													1
GCAGCT	1																																															1
GCAGGA	1																																															1
GCAGTT	1																																															1
GCCTGA			1																																													1
GCTCCA	1																																															1
GCTCCT		1																																														1
GCTCTG						1																																										1
GCTTGA		1																																														1
GGAGCT	1																																															1
GGATCT		1																																														1
GGATGA			1																																													1
GGCTCT				1																																												1
GGGAGG	1																																															1
GGTTTA	3	5	2																																													10
GGTTTT		1																																														1
GTAATG	1																																															1
GTACTT	1																																															1
GTAGAA	1																																															1
GTAGTG						1		1																																								2
GTAGTT	3		1																																													4
GTCCTT			1																																													1
GTGATT		1																																														1
GTGGTA	1		1																																													2
GTGGTT			1																																													1
GTTCTA		1																																														1
GTTGTA	1																																															1
GTTGTG	1		1																																													2
GTTTAG	1																																															1
GTTTTG	1																																															1
TAAATA		1																																														1
TAACAA	1																																															1
TAATAC	1																																															1
TAATAT	1																																															1
TACTAT		1																																														1
TAGTAT		1																																														1
TATAAA	2																																															2
TATAAC		1																																														1
TATATT	2																																															2
TATCAT	2																																															2
TATTAG	1																																															1
TATTCA	1																																															1
TATTTA	2																																															2
TCAAGA	1																																															1
TCAAGT	1																																															1
TCACGT			1																																													1
TCAGAT	2																																															2
TCAGGG		1																																														1
TCATCT	1		1		1																																											3
TCATGA	1																																															1
TCATTA						1																																										1
TCCAAT	1																																															1
TCCAGA		1																																														1
TCCAGC	1					1																																										2
TCCTCT	1																																															1
TCCTGT			1																																													1
TCTCTA		1																																														1
TCTCTT		1																																														1
TCTGAA		1																																														1
TCTTCA	1																																															1
TCTTCC	3																																															3
TCTTGA		1	1																																													2
TCTTGT	1																																															1
TGAACC	1																																															1
TGACGA	1																																															1
TGACTT	1																																															1
TGAGCC			1		1																																											2
TGAGGA		1																																														1
TGATCT		1																																														1
TGCATG	1																																															1
TGCTGT			1																																													1
TGGAAT	2																																															2
TGGAGC	1																																															1
TGGTAA	1																																															1
TGGTTT	1																																															1
TGTAGT	1																																															1
TGTTAC		1																																														1
TGTTAT		1																																														1
TGTTCC	1																																															1
TTAATA	2																																															2
TTACCA	1																																															1
TTAGGT	1	1																																														2
TTATGA	1																																															1
TTATTG	1																																															1
TTATTT	1																																															1
TTCAAA		1																																														1
TTCACG			1																																													1
TTCATC	1																																															1
TTCCAG	1	1																																														2
TTCCTG	1																																															1
TTCTCG			1																																													1
TTCTGA		1																																														1
TTCTTG			1																																													1
TTGAAC	1		1																																													2
TTGTTC	1	1																																														2
TTTAGG	4	3	2	2																																												11
TTTCAA	1																																															1
TTTCAT			1																																													1
TTTCTG	1																																															1
TTTGTT	1																																															1
TTTTCT	1																																															1
TTTTGG		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	total
A/T	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	14	7	7	8	2	10	1	2	1	1		3	1	4	1		2		1			1								1	67
AC/GT	-	-	-	1	1			1																																								3
AG/CT	-	-	-	12	4	3	1	1			1		1																																			23
AT/AT	-	-	-	89	40	35	42	21	22	18	18	10	9	17	8	6	1	3	1		1	3																										344
CG/CG	-	-	-	3																																												3
AAC/GTT	-	-	35	12	14	7	1						1	1																																		71
AAG/CTT	-	-	32	17	9	4	3	4	1		2	1																																				73
AAT/ATT	-	-	152	86	65	55	29	17	18	11	10	5	6	5	2	1			1	1																												464
ACC/GGT	-	-	8	2		1	1				1																																					13
ACT/AGT	-	-	38	16	12	7	7	4		1			2	1		1																																89
AGC/CTG	-	-	5	1	1	1	1	1																																								10
AGG/CCT	-	-	12	7	5	2	1	3	3																																							33
ATC/ATG	-	-	52	19	9	10	1	5	4	1	1		1																																			103
AAAC/GTTT	-	2																																														2
AAAG/CTTT	-	6					1																																									7
AAAT/ATTT	-	46	10	2	3			1																																								62
AAGG/CCTT	-	2																																														2
AATC/ATTG	-	2			1																																											3
AATG/ATTC	-	1																																														1
AATT/AATT	-	11	3			1																																										15
ACAT/ATGT	-			1																																												1
AGAT/ATCT	-	1	1																																													2
ATGC/ATGC	-	14	2	1	1																																											18
AAAAC/GTTTT	6																																															6
AAAAG/CTTTT	14																																															14
AAAAT/ATTTT	25	5																																														30
AAAGG/CCTTT	2	1																																														3
AAAGT/ACTTT	1																																															1
AAATC/ATTTG	5																																															5
AAATG/ATTTC	1																																															1
AAATT/AATTT	20																																															20
AACAC/GTGTT		1																																														1
AACAT/ATGTT	1							1																																								2
AACTT/AAGTT	1																																															1
AAGAG/CTCTT	2																																															2
AAGGG/CCCTT	1																																															1
AATAC/ATTGT	2																																															2
AATAT/ATATT	16		1																																													17
AATCC/ATTGG	2																																															2
AATTC/AATTG	4																																															4
ACGAG/CGTCT	3																																															3
ACTAT/AGTAT	1																																															1
ATATC/ATATG	2																																															2
AAAAAC/GTTTTT	1																																															1
AAAAAG/CTTTTT	2	1																																														3
AAAAAT/ATTTTT	7	1																																														8
AAAACC/GGTTTT	2	2																																														4
AAAAGC/CTTTTG	1																																															1
AAAAGG/CCTTTT	1																																															1
AAAATC/ATTTTG		2																																														2
AAAATG/ATTTTC	1	1	1																																													3
AAACAG/CTGTTT	1																																															1
AAACCT/AGGTTT	12	13	9	4																																												38
AAACTG/AGTTTC		1																																														1
AAAGAC/CTTTGT		1																																														1
AAAGAG/CTCTTT	2	2		1																																												5
AAAGCC/CTTTGG	1																																															1
AAAGCT/AGCTTT	1																																															1
AAAGGG/CCCTTT	1																																															1
AAAGTC/ACTTTG	1																																															1
AAATAG/ATTTCT	2																																															2
AAATAT/ATATTT	11	1	1																																													13
AAATCC/ATTTGG	1		1																																													2
AAATCT/AGATTT	1																																															1
AAATTC/AATTTG		1																																														1
AAATTG/AATTTC	1																																															1
AACAAG/CTTGTT	6	1	1		1	2																																										11
AACAAT/ATTGTT	3	1																																														4
AACACC/GGTGTT			1																																													1
AACAGC/CTGTTG	2		1																																													3
AACAGG/CCTGTT	4		2		1																																											7
AACAGT/ACTGTT		1																																														1
AACATC/ATGTTG	1																																															1
AACCAC/GGTTGT	1		2																																													3
AACCAG/CTGGTT					1																																											1
AACCTG/AGGTTC	2	1																																														3
AACGAG/CGTTCT			1		1																																											2
AACGTG/ACGTTC			2																																													2
AACTAC/AGTTGT	7		1																																													8
AACTAG/AGTTCT		1																																														1
AACTAT/AGTTAT		1																																														1
AACTGC/AGTTGC	1																																															1
AACTGG/AGTTCC	1	1																																														2
AACTTC/AAGTTG	1	1																																														2
AACTTG/AAGTTC	2	1	1																																													4
AAGAGG/CCTCTT	5																																															5
AAGATC/ATCTTG	6	3	2																																													11
AAGATG/ATCTTC	5	1	1		1																																											8
AAGCTC/AGCTTG		1																																														1
AAGGAC/CCTTGT			1																																													1
AAGTAC/ACTTGT	1																																															1
AAGTAG/ACTTCT	2																																															2
AATACC/ATTGGT	1																																															1
AATACT/AGTATT	3	1																																														4
AATAGC/ATTGCT	1																																															1
AATAGG/ATTCCT	2																																															2
AATAGT/ACTATT	1	1																																														2
AATATG/ATATTC	1																																															1
AATATT/AATATT	5																																															5
AATCAC/ATTGTG		1																																														1
AATCAG/ATTCTG	1	3	1																																													5
AATCAT/ATGATT	2	1																																														3
AATCCT/AGGATT				1																																												1
AATCTG/AGATTC	3	2	2																																													7
AATGAT/ATCATT	3	3				1																																										7
AATGCC/ATTGGC		2																																														2
AATGGG/ATTCCC		1																																														1
AATGGT/ACCATT	3																																															3
AATTAC/AATTGT	1																																															1
AATTCC/AATTGG	3																																															3
ACATAT/ATATGT	1																																															1
ACATCC/ATGTGG	1																																															1
ACATCT/AGATGT	1	1																																														2
ACATGC/ATGTGC	1																																															1
ACATGG/ATGTCC	1																																															1
ACCACT/AGTGGT	2	2	2			1		1																																								8
ACCAGG/CCTGGT	1	1																																														2
ACCATC/ATGGTG	1																																															1
ACCATG/ATGGTC		1																																														1
ACCCTG/AGGGTC		1																																														1
ACCTCC/AGGTGG	1	1																																														2
ACGATC/ATCGTG			1																																													1
ACGATG/ATCGTC	1	1																																														2
ACTCCT/AGGAGT		1																																														1
AGAGAT/ATCTCT		1								1																																						2
AGAGCC/CTCTGG				1		1																																										2
AGATCC/ATCTGG	1	2	2																																													5
AGATCT/AGATCT		1																																														1
AGCAGG/CCTGCT	1	1			1																																											3
AGCCTC/AGGCTG	1																																															1
AGCCTG/AGGCTC	1		3		1																																											5
AGCTCC/AGCTGG	4					1																																										5
AGCTGC/AGCTGC	2																																															2
AGGATC/ATCCTG	2	1					1																																									4
AGGATG/ATCCTC		1	1	1																																												3
AGGCAT/ATGCCT		1																																														1
AGGGGG/CCCCCT	1																																															1
ATCATG/ATCATG	2																																															2
