Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01016188.1 Corchorus capsularis cultivar CVL-1 contig16209, whole genome shotgun sequence
Parameters: 2 7 7 80 10 50 1000
Pmatch=0.80,Pindel=0.10
tuple sizes 0,4,5,7
tuple distances 0, 29, 159, 1000
Length: 5879
ACGTcount: A:0.36, C:0.13, G:0.14, T:0.37
Found at i:522 original size:199 final size:196
Alignment explanation
Indices: 1--1030 Score: 1095
Period size: 199 Copynumber: 5.3 Consensus size: 196
* * *
1 GGTTGACATGTGTCCCC-TAGGGGAAGATGTATTGATATTAAATATTTAATTAATTATGAAATGG
1 GGTTGACATGTGTCCCCTTA-GAGAATATGTATT-ATATTAAATATTTAATTAATTATGAAATGA
* * ** *
65 GGTATCTGTCAACTTCTTAACCTGTTTATGGAGTTTAAATTTTACACTGACAGTGTATTGTATAA
64 GGTATATGTCAACTTCTTAACC-GCTTATGGAGTCCAAAATTTACACTGACAGTGTATTGTATAA
*
130 TAATCCTATAAGAAAAATAATATAATACACCGTCAGTAGATTTTAGCATACTGCACGTGCAGGGT
128 TAATCCTATAAGAAAAATAATATAATACACCGTCAGTAGATTTTAGCAGACTGCACGTGCAGGGT
*
195 TAAG
193 TAAA
* * * *
199 GGTTGACATGTGTCCCATAAGAGAATATGTA--ATATTATATATTTAATTAATGATGAAATGAGG
1 GGTTGACATGTGTCCCCTTAGAGAATATGTATTATATTAAATATTTAATTAATTATGAAATGAGG
* * * *
262 TATGTGTCAACTTCTTAACACGCTTATAGAGTCCAAAATTTACACTGATAGTGTGTTGTATAATA
66 TATATGTCAACTTCTTAAC-CGCTTATGGAGTCCAAAATTTACACTGACAGTGTATTGTATAATA
* * * * * * *
327 ATTCTATAAGGAAAATTATATAATACACCGTCAGTGGATTTTAGGAGGCTGCACGTGCGGGGTTT
130 ATCCTATAAGAAAAATAATATAATACACCGTCAGTAGATTTTAGCAGACTGCACGTGCAGGG-TT
392 AAA
194 AAA
*
395 GGTTGACATGTGTCCCCTTAGAGAATATGTATTACTATTAAATATTTAATTAATTATGAAATGCG
1 GGTTGACATGTGTCCCCTTAGAGAATATGTATTA-TATTAAATATTTAATTAATTATGAAATGAG
* * * *
460 GTATATGTCAACTTCTTAATCCACTTATGGCGTCCAAAATTTACATTGACAGTTTATTGTATAAT
65 GTATATGTCAACTTCTTAA-CCGCTTATGGAGTCCAAAATTTACACTGACAGTGTATTGTATAAT
* * * * *
525 AATCCTACACAG--------T-CAAT-----G---G-AG--TTTAGCAGGCTGCACATGC-GGTC
129 AATCCTATA-AGAAAAATAATATAATACACCGTCAGTAGATTTTAGCAGACTGCACGTGCAGG-G
*
569 TTTAA
192 TTAAA
* * *
574 GAATTGACATGTGTCCCCTTAGGGAATATGTATTAATATTAAATATTTTATTAATTATGAAATGA
1 G-GTTGACATGTGTCCCCTTAGAGAATATGTATT-ATATTAAATATTTAATTAATTATGAAATGA
* *
639 GGTATGTGTCAACTTCTTAATCCGCTTACGGAGTCCAAAATTTACACTGACAGTGTATTGTATAA
64 GGTATATGTCAACTTCTTAA-CCGCTTATGGAGTCCAAAATTTACACTGACAGTGTATTGTATAA
* * * * * *
704 TAATCCTATAAGAAAAATTATAGT-ATACACCGTCAATCGAGTTTAGAAGACTGTACGTGCAGGG
128 TAATCCTATAAGAAAAATAATA-TAATACACCGTCAGTAGATTTTAGCAGACTGCACGTGCAGGG
*
768 TTTAA
192 TTAAA
* * *
773 GTGTTAACATGTATCCCCTTA-AGGAATATGTATTAATATTAAATATTTAATTAATTATCAAATG
1 G-GTTGACATGTGTCCCCTTAGA-GAATATGTATT-ATATTAAATATTTAATTAATTATGAAATG
* ** * * *
837 GGGTATGCGTGAACTTCTTAACCCGCTTATGGAGTCCAAAATTTACATTGACAGTTTATTGTATA
63 AGGTATATGTCAACTTCTTAA-CCGCTTATGGAGTCCAAAATTTACACTGACAGTGTATTGTATA
* * * * * * * *
902 ATAATCATATAAGAACAATTATACAATACATCGTCACTGGAGTTTAGCAGACTGCACGTGCAGGG
127 ATAATCCTATAAGAAAAATAATATAATACACCGTCAGTAGATTTTAGCAGACTGCACGTGCAGGG
*
967 TTTAAG
192 -TTAAA
* *
973 GGTTGACATGTGTCCCCTTAGGGAATATGTATTGATATTAAATATTTTATTAATTATG
1 GGTTGACATGTGTCCCCTTAGAGAATATGTATT-ATATTAAATATTTAATTAATTATG
1031 TCCCCAAGGG
Statistics
Matches: 701, Mismatches: 94, Indels: 73
0.81 0.11 0.08
Matches are distributed among these distances:
179 9 0.01
180 142 0.20
181 1 0.00
182 1 0.00
183 1 0.00
186 1 0.00
187 1 0.00
188 2 0.00
191 3 0.00
192 1 0.00
193 1 0.00
195 138 0.20
196 34 0.05
197 1 0.00
198 26 0.04
199 330 0.47
200 9 0.01
ACGTcount: A:0.33, C:0.13, G:0.18, T:0.35
Consensus pattern (196 bp):
GGTTGACATGTGTCCCCTTAGAGAATATGTATTATATTAAATATTTAATTAATTATGAAATGAGG
TATATGTCAACTTCTTAACCGCTTATGGAGTCCAAAATTTACACTGACAGTGTATTGTATAATAA
TCCTATAAGAAAAATAATATAATACACCGTCAGTAGATTTTAGCAGACTGCACGTGCAGGGTTAA
A
Found at i:677 original size:180 final size:180
Alignment explanation
Indices: 350--711 Score: 546
Period size: 180 Copynumber: 2.0 Consensus size: 180
340 AATTATATAA
* * * * * * *
350 TACACCGTCAGTGGATTTTAGGAGGCTGCACGTGCGGGGTTTAAAGGTTGACATGTGTCCCCTTA
1 TACACAGTCAATGGAGTTTAGCAGGCTGCACATGCGGGCTTTAAAGATTGACATGTGTCCCCTTA
* *
415 GAGAATATGTATTACTATTAAATATTTAATTAATTATGAAATGCGGTATATGTCAACTTCTTAAT
66 GAGAATATGTATTAATATTAAATATTTAATTAATTATGAAATGAGGTATATGTCAACTTCTTAAT
* * * *
480 CCACTTATGGCGTCCAAAATTTACATTGACAGTTTATTGTATAATAATCC
131 CCACTTACGGAGTCCAAAATTTACACTGACAGTGTATTGTATAATAATCC
*
530 TACACAGTCAATGGAGTTTAGCAGGCTGCACATGCGGTCTTT-AAGAATTGACATGTGTCCCCTT
1 TACACAGTCAATGGAGTTTAGCAGGCTGCACATGCGGGCTTTAAAG-ATTGACATGTGTCCCCTT
* * *
594 AGGGAATATGTATTAATATTAAATATTTTATTAATTATGAAATGAGGTATGTGTCAACTTCTTAA
65 AGAGAATATGTATTAATATTAAATATTTAATTAATTATGAAATGAGGTATATGTCAACTTCTTAA
*
659 TCCGCTTACGGAGTCCAAAATTTACACTGACAGTGTATTGTATAATAATCC
130 TCCACTTACGGAGTCCAAAATTTACACTGACAGTGTATTGTATAATAATCC
710 TA
1 TA
712 TAAGAAAAAT
Statistics
Matches: 163, Mismatches: 18, Indels: 2
0.89 0.10 0.01
Matches are distributed among these distances:
179 3 0.02
180 160 0.98
ACGTcount: A:0.31, C:0.15, G:0.19, T:0.35
Consensus pattern (180 bp):
TACACAGTCAATGGAGTTTAGCAGGCTGCACATGCGGGCTTTAAAGATTGACATGTGTCCCCTTA
GAGAATATGTATTAATATTAAATATTTAATTAATTATGAAATGAGGTATATGTCAACTTCTTAAT
CCACTTACGGAGTCCAAAATTTACACTGACAGTGTATTGTATAATAATCC
Found at i:1606 original size:199 final size:200
Alignment explanation
Indices: 1187--1658 Score: 644
Period size: 199 Copynumber: 2.4 Consensus size: 200
1177 GTAGCAAAAA
1187 AAATATTTTATTAATTATGAAATAGGGTATGTGTCAACTTCTTAACCCGCTTATGGAG-TCTAAA
1 AAATATTTTATTAATTATGAAATAGGGTATGTGTCAACTTCTTAACCCGCTTATGGAGTTC-AAA
** * * * *
1251 ATTTACACTGAGTGTGTATTGTATAATAATGCTATAAAAAAAAATTATACAATACACCGTCAGTC
65 ATTTACACTGACAGTGTATTATATAATAATCCTATAAAAAAAAATTAAACAATACACCGTAAGTC
** ** * *
1316 GAGTTTAGCAAACTGCACTTGCGGGGTTTAAGAGTTTACATGTGCCCCCTTAAAGAATATGTATT
130 GAGTTTAGCAAACTGCAAGTGCGGACTTTAAGAGTTGACATATGCCCCCTTAAAGAATATGTATT
1381 AATATT
195 AATATT
* * * *
1387 AAATATTTAATTTATTATGAAATAAGGTATGTGTCAACTTCTTAACCCGTTTATGGAGTTCAAAA
1 AAATATTTTATTAATTATGAAATAGGGTATGTGTCAACTTCTTAACCCGCTTATGGAGTTCAAAA
* * * *
1452 TTTACACTGACAGTTTATTATATAATAATCCTAT-AAGAAAAATTAAACTATACACCGTAAGTGG
66 TTTACACTGACAGTGTATTATATAATAATCCTATAAAAAAAAATTAAACAATACACCGTAAGTCG
* * **
1516 AGTTTAGCAGACTGCAAGTGCGGACTTTAA-AGGTTGACATATGTCCCCTTAGGGAATATGTATT
131 AGTTTAGCAAACTGCAAGTGCGGACTTTAAGA-GTTGACATATGCCCCCTTAAAGAATATGTATT
1580 AATATT
195 AATATT
* * * *
1586 AAATATTTTATTAATTATGAAATGGGGTATGTGTGAACTTCTTAACCCGCTTATAGAGTCCAAAA
1 AAATATTTTATTAATTATGAAATAGGGTATGTGTCAACTTCTTAACCCGCTTATGGAGTTCAAAA
*
1651 TGTACACT
66 TTTACACT
1659 ACGAGAATGG
Statistics
Matches: 237, Mismatches: 33, Indels: 5
0.86 0.12 0.02
Matches are distributed among these distances:
198 1 0.00
199 147 0.62
200 87 0.37
201 2 0.01
ACGTcount: A:0.35, C:0.14, G:0.16, T:0.35
Consensus pattern (200 bp):
AAATATTTTATTAATTATGAAATAGGGTATGTGTCAACTTCTTAACCCGCTTATGGAGTTCAAAA
TTTACACTGACAGTGTATTATATAATAATCCTATAAAAAAAAATTAAACAATACACCGTAAGTCG
AGTTTAGCAAACTGCAAGTGCGGACTTTAAGAGTTGACATATGCCCCCTTAAAGAATATGTATTA
ATATT
Found at i:2177 original size:2 final size:2
Alignment explanation
Indices: 2170--2197 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
2160 TATAATTACA
2170 AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT
2198 CATTCCATTA
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:4606 original size:26 final size:24
Alignment explanation
Indices: 4577--4645 Score: 66
Period size: 26 Copynumber: 2.7 Consensus size: 24
4567 TCTTAATATC
4577 AATGAAATGTTACTAAAATTTCTAA
1 AATGAAA-GTTACTAAAATTTCTAA
* * *
4602 GAATGCAAGGTTATTGAAATTTCTAA
1 -AATG-AAAGTTACTAAAATTTCTAA
4628 AGATGAGAAGTTACTAAA
1 A-ATGA-AAGTTACTAAA
4646 TTTATGTAAA
Statistics
Matches: 34, Mismatches: 6, Indels: 6
0.74 0.13 0.13
Matches are distributed among these distances:
25 2 0.06
26 30 0.88
27 2 0.06
ACGTcount: A:0.45, C:0.07, G:0.16, T:0.32
Consensus pattern (24 bp):
AATGAAAGTTACTAAAATTTCTAA
Found at i:4917 original size:26 final size:26
Alignment explanation
Indices: 4862--4920 Score: 66
Period size: 26 Copynumber: 2.3 Consensus size: 26
4852 GAAACATTAC
* * **
4862 TAAAATTTCTAACAATGTAGTGTTTC
1 TAAATTTTCTAAAAATGTAGTGTTAA
4888 TAAATTTTCTAAAAATGTGAG-GTTAA
1 TAAATTTTCTAAAAATGT-AGTGTTAA
4914 TAAATTT
1 TAAATTT
4921 ATGTAGAAAC
Statistics
Matches: 28, Mismatches: 4, Indels: 2
0.82 0.12 0.06
Matches are distributed among these distances:
26 26 0.93
27 2 0.07
ACGTcount: A:0.39, C:0.07, G:0.12, T:0.42
Consensus pattern (26 bp):
TAAATTTTCTAAAAATGTAGTGTTAA
Found at i:5482 original size:26 final size:26
Alignment explanation
Indices: 5452--5515 Score: 83
Period size: 26 Copynumber: 2.5 Consensus size: 26
5442 ATATTGACGA
* *
5452 AAGGTTACTAAAATTTGTAAGAATGC
1 AAGGTTACTAAAAATTATAAGAATGC
*
5478 AAGGTTATTAAAAATTATAAGAATGC
1 AAGGTTACTAAAAATTATAAGAATGC
* *
5504 GAGATTACTAAA
1 AAGGTTACTAAA
5516 TTTATGTATT
Statistics
Matches: 32, Mismatches: 6, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
26 32 1.00
ACGTcount: A:0.47, C:0.06, G:0.17, T:0.30
Consensus pattern (26 bp):
AAGGTTACTAAAAATTATAAGAATGC
Found at i:5740 original size:2 final size:2
Alignment explanation
Indices: 5733--5764 Score: 64
Period size: 2 Copynumber: 16.0 Consensus size: 2
5723 AGAGCTTTCA
5733 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
5765 GTGTGTATAT
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 30 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Done.