Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01009236.1 Corchorus capsularis cultivar CVL-1 contig09257, 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: 46371
ACGTcount: A:0.30, C:0.17, G:0.19, T:0.34
Found at i:2640 original size:6 final size:6
Alignment explanation
Indices: 2629--2655 Score: 54
Period size: 6 Copynumber: 4.5 Consensus size: 6
2619 ATTAATCTGT
2629 TTTAGA TTTAGA TTTAGA TTTAGA TTT
1 TTTAGA TTTAGA TTTAGA TTTAGA TTT
2656 GCTTTGCTTT
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 21 1.00
ACGTcount: A:0.30, C:0.00, G:0.15, T:0.56
Consensus pattern (6 bp):
TTTAGA
Found at i:8292 original size:21 final size:21
Alignment explanation
Indices: 8268--8309 Score: 66
Period size: 21 Copynumber: 2.0 Consensus size: 21
8258 TTTTATCATC
* *
8268 ATAAGATTGATTTTCAAGAGT
1 ATAAAATTGACTTTCAAGAGT
8289 ATAAAATTGACTTTCAAGAGT
1 ATAAAATTGACTTTCAAGAGT
8310 TTGAAGCAAA
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
21 19 1.00
ACGTcount: A:0.40, C:0.07, G:0.17, T:0.36
Consensus pattern (21 bp):
ATAAAATTGACTTTCAAGAGT
Found at i:12328 original size:36 final size:33
Alignment explanation
Indices: 12288--12364 Score: 82
Period size: 33 Copynumber: 2.2 Consensus size: 33
12278 GGTTGAAGGG
* *
12288 AAGTGAAGAAGATAATGAGAAGGTTTGGGGTTAGTC
1 AAGTGAAGAACAT-ATG-G-AGGTTTGGCGTTAGTC
* *
12324 AAGTGAAGTACATATGGTGGTTTGGCGTTAGTC
1 AAGTGAAGAACATATGGAGGTTTGGCGTTAGTC
*
12357 AGGTGAAG
1 AAGTGAAG
12365 TAAATACAAT
Statistics
Matches: 36, Mismatches: 5, Indels: 3
0.82 0.11 0.07
Matches are distributed among these distances:
33 21 0.58
34 1 0.03
35 3 0.08
36 11 0.31
ACGTcount: A:0.31, C:0.05, G:0.36, T:0.27
Consensus pattern (33 bp):
AAGTGAAGAACATATGGAGGTTTGGCGTTAGTC
Found at i:12441 original size:22 final size:23
Alignment explanation
Indices: 12410--12452 Score: 70
Period size: 22 Copynumber: 1.9 Consensus size: 23
12400 CCGCTCGAAA
12410 TGGGTGTATTTTCCATTGACTTG
1 TGGGTGTATTTTCCATTGACTTG
*
12433 TGGGT-TATTTTCCGTTGACT
1 TGGGTGTATTTTCCATTGACT
12453 AGTTTATTTT
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
22 14 0.74
23 5 0.26
ACGTcount: A:0.12, C:0.14, G:0.26, T:0.49
Consensus pattern (23 bp):
TGGGTGTATTTTCCATTGACTTG
Found at i:12631 original size:161 final size:161
Alignment explanation
Indices: 12366--12687 Score: 635
Period size: 161 Copynumber: 2.0 Consensus size: 161
12356 CAGGTGAAGT
12366 AAATACAATAATTATGAACAAAGGAAATTGTCTTCCGCTCGAAATGGGTGTATTTTCCATTGACT
1 AAATACAATAATTATGAACAAAGGAAATTGTCTTCCGCTCGAAATGGGTGTATTTTCCATTGACT
12431 TGTGGGTTATTTTCCGTTGACTAGTTTATTTTCTACCAACCAAACACCAGAAAATAAAGAAAATA
66 TGTGGGTTATTTTCCGTTGACTAGTTTATTTTCTACCAACCAAACACCAGAAAATAAAGAAAATA
12496 TTTTCTGGAAGCTATTTTCCGTGAACCAAAC
131 TTTTCTGGAAGCTATTTTCCGTGAACCAAAC
12527 AAATACAATAATTATGAACAAAGGAAATTGTCTTCCGCTCGAAATGGGTGTATTTTCCATTGACT
1 AAATACAATAATTATGAACAAAGGAAATTGTCTTCCGCTCGAAATGGGTGTATTTTCCATTGACT
*
12592 TGTGGGTTATTTTCTGTTGACTAGTTTATTTTCTACCAACCAAACACCAGAAAATAAAGAAAATA
66 TGTGGGTTATTTTCCGTTGACTAGTTTATTTTCTACCAACCAAACACCAGAAAATAAAGAAAATA
12657 TTTTCTGGAAGCTATTTTCCGTGAACCAAAC
131 TTTTCTGGAAGCTATTTTCCGTGAACCAAAC
12688 GGAACCTCAG
Statistics
Matches: 160, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
161 160 1.00
ACGTcount: A:0.34, C:0.17, G:0.16, T:0.33
Consensus pattern (161 bp):
AAATACAATAATTATGAACAAAGGAAATTGTCTTCCGCTCGAAATGGGTGTATTTTCCATTGACT
TGTGGGTTATTTTCCGTTGACTAGTTTATTTTCTACCAACCAAACACCAGAAAATAAAGAAAATA
TTTTCTGGAAGCTATTTTCCGTGAACCAAAC
Found at i:13775 original size:18 final size:18
Alignment explanation
Indices: 13752--13786 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
13742 CCGATTTTTC
*
13752 AAACCGAATCACCCGATA
1 AAACCGAATCAACCGATA
*
13770 AAACCGACTCAACCGAT
1 AAACCGAATCAACCGAT
13787 CCATTTTCAA
Statistics
Matches: 15, Mismatches: 2, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
18 15 1.00
ACGTcount: A:0.43, C:0.34, G:0.11, T:0.11
Consensus pattern (18 bp):
AAACCGAATCAACCGATA
Found at i:14484 original size:27 final size:27
Alignment explanation
Indices: 14437--14489 Score: 63
Period size: 27 Copynumber: 2.0 Consensus size: 27
14427 TAATTAATGT
* *
14437 TTTATTTATTGTATTTGTACTTATTAC
1 TTTATTTATAGTATTTGTACTCATTAC
*
14464 TTTATTTATAGT-TTTATTACTCATTA
1 TTTATTTATAGTATTT-GTACTCATTA
14490 AGTCGGTGAC
Statistics
Matches: 22, Mismatches: 3, Indels: 2
0.81 0.11 0.07
Matches are distributed among these distances:
26 3 0.14
27 19 0.86
ACGTcount: A:0.25, C:0.08, G:0.06, T:0.62
Consensus pattern (27 bp):
TTTATTTATAGTATTTGTACTCATTAC
Found at i:17891 original size:4 final size:4
Alignment explanation
Indices: 17882--17953 Score: 58
Period size: 4 Copynumber: 18.0 Consensus size: 4
17872 TTCTTCACTC
* ** ** *
17882 CTTT CTTT CTTT CTTT CTTT TTTT CCAT CTCTT GATT C-TT C-TT CTCTG
1 CTTT CTTT CTTT CTTT CTTT CTTT CTTT CT-TT CTTT CTTT CTTT CT-TT
17930 CTTT CTTT CTTT CTTT CTTT CTTT
1 CTTT CTTT CTTT CTTT CTTT CTTT
17954 TCCATCTCCT
Statistics
Matches: 54, Mismatches: 11, Indels: 6
0.76 0.15 0.08
Matches are distributed among these distances:
3 6 0.11
4 44 0.81
5 4 0.07
ACGTcount: A:0.03, C:0.26, G:0.03, T:0.68
Consensus pattern (4 bp):
CTTT
Found at i:17974 original size:49 final size:48
Alignment explanation
Indices: 17872--17986 Score: 185
Period size: 49 Copynumber: 2.4 Consensus size: 48
17862 CTCTCCATCA
* * * *
17872 TTCTTCACTCCTTTCTTTCTTTCTTTCTTTTTTTCCATCTCTTGATTC
1 TTCTTCTCTGCTTTCTTTCTTTCTTTCTTTTTTTCCATCTCCTAATTC
17920 TTCTTCTCTGCTTTCTTTCTTTCTTTCTTTCTTTTCCATCTCCTAATTC
1 TTCTTCTCTGCTTTCTTTCTTTCTTTCTTT-TTTTCCATCTCCTAATTC
17969 TTCTTCTCTGCTTTCTTT
1 TTCTTCTCTGCTTTCTTT
17987 TTTTTTTTGT
Statistics
Matches: 62, Mismatches: 4, Indels: 1
0.93 0.06 0.01
Matches are distributed among these distances:
48 28 0.45
49 34 0.55
ACGTcount: A:0.05, C:0.30, G:0.03, T:0.63
Consensus pattern (48 bp):
TTCTTCTCTGCTTTCTTTCTTTCTTTCTTTTTTTCCATCTCCTAATTC
Found at i:18417 original size:46 final size:46
Alignment explanation
Indices: 18366--18458 Score: 159
Period size: 46 Copynumber: 2.0 Consensus size: 46
18356 TTCATTTTTT
*
18366 ATTTTGGATGGCTTTGGGTTCCTCTATTTTTCGTATTTCCCCTTCA
1 ATTTTGGATGGCTTTAGGTTCCTCTATTTTTCGTATTTCCCCTTCA
* *
18412 ATTTTGGATGGCTTTAGGTTCCTCTGTTTTTCTTATTTCCCCTTCA
1 ATTTTGGATGGCTTTAGGTTCCTCTATTTTTCGTATTTCCCCTTCA
18458 A
1 A
18459 ATTCGCCTGT
Statistics
Matches: 44, Mismatches: 3, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
46 44 1.00
ACGTcount: A:0.12, C:0.22, G:0.16, T:0.51
Consensus pattern (46 bp):
ATTTTGGATGGCTTTAGGTTCCTCTATTTTTCGTATTTCCCCTTCA
Found at i:18635 original size:20 final size:20
Alignment explanation
Indices: 18610--18647 Score: 67
Period size: 20 Copynumber: 1.9 Consensus size: 20
18600 AGGTATTCCT
18610 TTTCTCAGCTTATTTGTTCG
1 TTTCTCAGCTTATTTGTTCG
*
18630 TTTCTCAGCTTCTTTGTT
1 TTTCTCAGCTTATTTGTT
18648 GTGATCAGGA
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.08, C:0.21, G:0.13, T:0.58
Consensus pattern (20 bp):
TTTCTCAGCTTATTTGTTCG
Found at i:20228 original size:2 final size:2
Alignment explanation
Indices: 20221--20246 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
20211 ATTCTATAAC
20221 TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA
20247 ATAATTGACC
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 24 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:20540 original size:2 final size:2
Alignment explanation
Indices: 20535--20582 Score: 53
Period size: 2 Copynumber: 22.5 Consensus size: 2
20525 TAATTAAAAA
20535 AT AT AT ACT AT AT AT -T ACT ACT AT AT AT AT AGT AT AT AT AT AT
1 AT AT AT A-T AT AT AT AT A-T A-T AT AT AT AT A-T AT AT AT AT AT
20578 AT AT A
1 AT AT A
20583 GTGGTGTAAT
Statistics
Matches: 42, Mismatches: 0, Indels: 8
0.84 0.00 0.16
Matches are distributed among these distances:
1 1 0.02
2 32 0.76
3 9 0.21
ACGTcount: A:0.46, C:0.06, G:0.02, T:0.46
Consensus pattern (2 bp):
AT
Found at i:20558 original size:13 final size:14
Alignment explanation
Indices: 20535--20578 Score: 58
Period size: 13 Copynumber: 3.4 Consensus size: 14
20525 TAATTAAAAA
20535 ATATA-TACTATAT
1 ATATACTACTATAT
20548 AT-TACTACTATAT
1 ATATACTACTATAT
*
20561 ATATAGTA-TATAT
1 ATATACTACTATAT
20574 ATATA
1 ATATA
20579 TATAGTGGTG
Statistics
Matches: 28, Mismatches: 1, Indels: 4
0.85 0.03 0.12
Matches are distributed among these distances:
12 2 0.07
13 22 0.79
14 4 0.14
ACGTcount: A:0.45, C:0.07, G:0.02, T:0.45
Consensus pattern (14 bp):
ATATACTACTATAT
Found at i:20559 original size:11 final size:11
Alignment explanation
Indices: 20535--20582 Score: 62
Period size: 11 Copynumber: 4.3 Consensus size: 11
20525 TAATTAAAAA
20535 ATATATACTAT
1 ATATATACTAT
20546 ATATTACTACTAT
1 ATA-TA-TACTAT
*
20559 ATATATAGTAT
1 ATATATACTAT
20570 ATATATA-TAT
1 ATATATACTAT
20580 ATA
1 ATA
20583 GTGGTGTAAT
Statistics
Matches: 34, Mismatches: 1, Indels: 5
0.85 0.03 0.12
Matches are distributed among these distances:
10 6 0.18
11 15 0.44
12 4 0.12
13 9 0.26
ACGTcount: A:0.46, C:0.06, G:0.02, T:0.46
Consensus pattern (11 bp):
ATATATACTAT
Found at i:20578 original size:15 final size:15
Alignment explanation
Indices: 20535--20580 Score: 56
Period size: 15 Copynumber: 2.9 Consensus size: 15
20525 TAATTAAAAA
*
20535 ATATATACTATATATT
1 ATATATA-TATATAGT
20551 ACTACTATATATATAGT
1 A-TA-TATATATATAGT
20568 ATATATATATATA
1 ATATATATATATA
20581 TAGTGGTGTA
Statistics
Matches: 27, Mismatches: 1, Indels: 5
0.82 0.03 0.15
Matches are distributed among these distances:
15 10 0.37
16 3 0.11
17 10 0.37
18 4 0.15
ACGTcount: A:0.46, C:0.07, G:0.02, T:0.46
Consensus pattern (15 bp):
ATATATATATATAGT
Found at i:20582 original size:17 final size:16
Alignment explanation
Indices: 20535--20584 Score: 57
Period size: 17 Copynumber: 2.9 Consensus size: 16
20525 TAATTAAAAA
20535 ATATATACTATATA-TT
1 ATATATA-TATATAGTT
20551 ACTACTATATATATAGTAT
1 A-TA-TATATATATAGT-T
20570 ATATATATATATAGT
1 ATATATATATATAGT
20585 GGTGTAATAA
Statistics
Matches: 30, Mismatches: 0, Indels: 7
0.81 0.00 0.19
Matches are distributed among these distances:
16 1 0.03
17 20 0.67
18 7 0.23
19 2 0.07
ACGTcount: A:0.44, C:0.06, G:0.04, T:0.46
Consensus pattern (16 bp):
ATATATATATATAGTT
Found at i:34921 original size:194 final size:194
Alignment explanation
Indices: 34592--34982 Score: 728
Period size: 194 Copynumber: 2.0 Consensus size: 194
34582 CAAAAAAATA
34592 TTAGTTTATGGAGAGAGACCCACAAATAGTAACTTTTTCACAAAATTCCCAAAATACCCTCAATC
1 TTAGTTTATGGAGAGAGACCCACAAATAGTAACTTTTTCACAAAATTCCCAAAATACCCTCAATC
*
34657 ATCAATCCAAATAACGAAAAAACCGAACATGAAAATACCAAAATACCCTTCCTCATTTATTCTTC
66 ATCAATCCAAATAACGAAAAAACCAAACATGAAAATACCAAAATACCCTTCCTCATTTATTCTTC
* *
34722 AACTCATGAGAAGTCAAGGTTGGATTGGTTTTTAGGTAATTTCACTTTCTATTATTATTGTTTC
131 AACTCAAGAGAAGTCAAGGTTGAATTGGTTTTTAGGTAATTTCACTTTCTATTATTATTGTTTC
* *
34786 TTAGTTTATGGAGAGGGACCCACAAATAGTAACTTTTTCACAAAATTCCCAAAATACCCTCAGTC
1 TTAGTTTATGGAGAGAGACCCACAAATAGTAACTTTTTCACAAAATTCCCAAAATACCCTCAATC
34851 ATCAATCCAAATAACGAAAAAACCAAACATGAAAATACCAAAATACCCTTCCTCATTTATTCTTC
66 ATCAATCCAAATAACGAAAAAACCAAACATGAAAATACCAAAATACCCTTCCTCATTTATTCTTC
*
34916 AACTCAAGAGAAGTTAAGGTTGAATTGGTTTTTAGGTAATTTCACTTTCTATTATTATTGTTTC
131 AACTCAAGAGAAGTCAAGGTTGAATTGGTTTTTAGGTAATTTCACTTTCTATTATTATTGTTTC
34980 TTA
1 TTA
34983 TAATATTGTT
Statistics
Matches: 191, Mismatches: 6, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
194 191 1.00
ACGTcount: A:0.36, C:0.20, G:0.11, T:0.33
Consensus pattern (194 bp):
TTAGTTTATGGAGAGAGACCCACAAATAGTAACTTTTTCACAAAATTCCCAAAATACCCTCAATC
ATCAATCCAAATAACGAAAAAACCAAACATGAAAATACCAAAATACCCTTCCTCATTTATTCTTC
AACTCAAGAGAAGTCAAGGTTGAATTGGTTTTTAGGTAATTTCACTTTCTATTATTATTGTTTC
Found at i:35340 original size:11 final size:11
Alignment explanation
Indices: 35324--35355 Score: 55
Period size: 11 Copynumber: 2.9 Consensus size: 11
35314 ACTCGATTAA
35324 TGTTCGTTTAG
1 TGTTCGTTTAG
*
35335 TGTTCGTTTAT
1 TGTTCGTTTAG
35346 TGTTCGTTTA
1 TGTTCGTTTA
35356 ATAGATCGTT
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
11 20 1.00
ACGTcount: A:0.09, C:0.09, G:0.22, T:0.59
Consensus pattern (11 bp):
TGTTCGTTTAG
Found at i:37189 original size:21 final size:20
Alignment explanation
Indices: 37163--37212 Score: 59
Period size: 21 Copynumber: 2.5 Consensus size: 20
37153 AAAGGCACTT
*
37163 TCTCTCTCTTCTTTGAGAGTC
1 TCTCTCTCTTC-ATGAGAGTC
*
37184 TCTCTCTCATCATGAGAGTC
1 TCTCTCTCTTCATGAGAGTC
37204 T-TC-CTCTTC
1 TCTCTCTCTTC
37213 CAGTAAGAGA
Statistics
Matches: 26, Mismatches: 3, Indels: 3
0.81 0.09 0.09
Matches are distributed among these distances:
18 5 0.19
19 2 0.08
20 9 0.35
21 10 0.38
ACGTcount: A:0.12, C:0.32, G:0.12, T:0.44
Consensus pattern (20 bp):
TCTCTCTCTTCATGAGAGTC
Done.