Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01012020.1 Corchorus capsularis cultivar CVL-1 contig12041, 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: 31741
ACGTcount: A:0.34, C:0.18, G:0.17, T:0.32
Found at i:251 original size:15 final size:15
Alignment explanation
Indices: 208--276 Score: 66
Period size: 15 Copynumber: 4.5 Consensus size: 15
198 TGGGTGCCCA
*
208 AACCCGAGATTACCCG
1 AACCCGA-ATGACCCG
* * *
224 AATCCAAACGACCCG
1 AACCCGAATGACCCG
*
239 AACCCGAATGACCCA
1 AACCCGAATGACCCG
*
254 AACCCAAAATGACCCG
1 AACCC-GAATGACCCG
270 AACCCGA
1 AACCCGA
277 TCAACCCGAC
Statistics
Matches: 41, Mismatches: 11, Indels: 3
0.75 0.20 0.05
Matches are distributed among these distances:
15 23 0.56
16 18 0.44
ACGTcount: A:0.39, C:0.39, G:0.14, T:0.07
Consensus pattern (15 bp):
AACCCGAATGACCCG
Found at i:539 original size:7 final size:7
Alignment explanation
Indices: 527--553 Score: 54
Period size: 7 Copynumber: 3.9 Consensus size: 7
517 GTTCCATTAA
527 TTGAAAG
1 TTGAAAG
534 TTGAAAG
1 TTGAAAG
541 TTGAAAG
1 TTGAAAG
548 TTGAAA
1 TTGAAA
554 CTATACTATT
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 20 1.00
ACGTcount: A:0.44, C:0.00, G:0.26, T:0.30
Consensus pattern (7 bp):
TTGAAAG
Found at i:1319 original size:2 final size:2
Alignment explanation
Indices: 1307--1345 Score: 53
Period size: 2 Copynumber: 19.0 Consensus size: 2
1297 GAAAGTCTAT
1307 TA TA T- TA TA TA TA TA TA TA TA TA GTA TA TA TA TA GTA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA -TA TA TA TA TA -TA TA
1346 AATCAGCAAC
Statistics
Matches: 34, Mismatches: 0, Indels: 6
0.85 0.00 0.15
Matches are distributed among these distances:
1 1 0.03
2 29 0.85
3 4 0.12
ACGTcount: A:0.46, C:0.00, G:0.05, T:0.49
Consensus pattern (2 bp):
TA
Found at i:1334 original size:11 final size:11
Alignment explanation
Indices: 1312--1345 Score: 61
Period size: 11 Copynumber: 3.2 Consensus size: 11
1302 TCTATTATAT
1312 TATATATA-TA
1 TATATATAGTA
1322 TATATATAGTA
1 TATATATAGTA
1333 TATATATAGTA
1 TATATATAGTA
1344 TA
1 TA
1346 AATCAGCAAC
Statistics
Matches: 23, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
10 8 0.35
11 15 0.65
ACGTcount: A:0.47, C:0.00, G:0.06, T:0.47
Consensus pattern (11 bp):
TATATATAGTA
Found at i:1745 original size:15 final size:15
Alignment explanation
Indices: 1691--1747 Score: 53
Period size: 15 Copynumber: 3.6 Consensus size: 15
1681 TCCAAACCGT
*
1691 ATGACCCGAAACCGAAA
1 ATGACCCG-AACC-CAA
*
1708 ACGACCC-AACCCAGA
1 ATGACCCGAACCCA-A
1723 ATTGACCCGAACCCAA
1 A-TGACCCGAACCCAA
1739 ATGACCCGA
1 ATGACCCGA
1748 CATTTCATCG
Statistics
Matches: 34, Mismatches: 3, Indels: 8
0.76 0.07 0.18
Matches are distributed among these distances:
14 1 0.03
15 14 0.41
16 7 0.21
17 12 0.35
ACGTcount: A:0.40, C:0.37, G:0.16, T:0.07
Consensus pattern (15 bp):
ATGACCCGAACCCAA
Found at i:4494 original size:153 final size:157
Alignment explanation
Indices: 4295--4611 Score: 437
Period size: 161 Copynumber: 2.0 Consensus size: 157
4285 CTTTTTTTTT
4295 AGGAATACAATATTCAAAATCTCATTACAATCAAATAATTCCTTATATGCCGTTATAAAAAAAAA
1 AGGAATACAATATTCAAAATCTCATTACAATCAAATAATTCCTTATATGCCGTTAT-AAAAAAAA
* * *
4360 T-TTCT-T-ATATCCAATGAGAAATGACCAAATAAACAAACTATAATAAACATAATAAAACCAAC
65 TCTTATGTCACATCCAATGAGAAATGACCAAATAAACAAACTATAATAAACATAACAAAACCAAC
*
4422 -AAACCCACATGCATTGAATACGATGGG
130 AAAACCCACATACATTGAATACGATGGG
* **
4449 AGGAATACATTATTC-AAATCTCATTACAATCAAATAATTCCTTATATGTTGTTATAAAAAAAAT
1 AGGAATACAATATTCAAAATCTCATTACAATCAAATAATTCCTTATATGCCGTTATAAAAAAAAT
* *
4513 CCTTATGTGCCCAAACATCCAATGAGAAATGACCACATAAACAAACTATAATAAATATAACAAAA
66 -CTTATGT---C--ACATCCAATGAGAAATGACCAAATAAACAAACTATAATAAACATAACAAAA
* *
4578 CTAACAAAAGCCACATACATTGAATACGATGGG
125 CCAACAAAACCCACATACATTGAATACGATGGG
4611 A
1 A
4612 CTCAACCCTG
Statistics
Matches: 142, Mismatches: 11, Indels: 12
0.86 0.07 0.07
Matches are distributed among these distances:
152 9 0.06
153 38 0.27
154 17 0.12
155 1 0.01
161 51 0.36
162 26 0.18
ACGTcount: A:0.48, C:0.18, G:0.09, T:0.26
Consensus pattern (157 bp):
AGGAATACAATATTCAAAATCTCATTACAATCAAATAATTCCTTATATGCCGTTATAAAAAAAAT
CTTATGTCACATCCAATGAGAAATGACCAAATAAACAAACTATAATAAACATAACAAAACCAACA
AAACCCACATACATTGAATACGATGGG
Found at i:4752 original size:2 final size:2
Alignment explanation
Indices: 4745--4770 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
4735 ATTTGACTCA
4745 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
4771 CAATTTAAGT
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):
AT
Found at i:8740 original size:20 final size:20
Alignment explanation
Indices: 8715--8757 Score: 77
Period size: 20 Copynumber: 2.1 Consensus size: 20
8705 TAATAATTTT
8715 TTAATGATAATTACTATTAG
1 TTAATGATAATTACTATTAG
*
8735 TTAATGATAATTATTATTAG
1 TTAATGATAATTACTATTAG
8755 TTA
1 TTA
8758 TGGTCGATAT
Statistics
Matches: 22, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
20 22 1.00
ACGTcount: A:0.40, C:0.02, G:0.09, T:0.49
Consensus pattern (20 bp):
TTAATGATAATTACTATTAG
Found at i:10053 original size:18 final size:19
Alignment explanation
Indices: 10022--10061 Score: 55
Period size: 18 Copynumber: 2.2 Consensus size: 19
10012 GTCGTAGCAT
10022 TTATTATTAATGTTA-TTA
1 TTATTATTAATGTTATTTA
* *
10040 TTATTTTTAGTGTTATTTA
1 TTATTATTAATGTTATTTA
10059 TTA
1 TTA
10062 GTCTATGCAT
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
18 13 0.68
19 6 0.32
ACGTcount: A:0.28, C:0.00, G:0.07, T:0.65
Consensus pattern (19 bp):
TTATTATTAATGTTATTTA
Found at i:12145 original size:49 final size:49
Alignment explanation
Indices: 12073--12171 Score: 173
Period size: 49 Copynumber: 2.0 Consensus size: 49
12063 ACCCCATTTT
*
12073 ACAAATACAAATGTATAAATGTTATATA-GAAGAAATGAAAATAGAAATC
1 ACAAATACAAATGTATAAATGTTATATACG-AGAAATGAAAATACAAATC
12122 ACAAATACAAATGTATAAATGTTATATACGAGAAATGAAAATACAAATC
1 ACAAATACAAATGTATAAATGTTATATACGAGAAATGAAAATACAAATC
12171 A
1 A
12172 GTCGGCCAAA
Statistics
Matches: 48, Mismatches: 1, Indels: 2
0.94 0.02 0.04
Matches are distributed among these distances:
49 47 0.98
50 1 0.02
ACGTcount: A:0.57, C:0.08, G:0.11, T:0.24
Consensus pattern (49 bp):
ACAAATACAAATGTATAAATGTTATATACGAGAAATGAAAATACAAATC
Found at i:14622 original size:61 final size:59
Alignment explanation
Indices: 14524--14642 Score: 157
Period size: 61 Copynumber: 2.0 Consensus size: 59
14514 AAAATTTGAG
* *
14524 GTTTTAGTTTGAAGGGTAGAGGATTTGAAGCTAGAAAGCTTGAAGAAAATGAAGTAAAA
1 GTTTTAGTTTGAAGGGTAAAGGATTTGAAGCTAGAAAGCTTAAAGAAAATGAAGTAAAA
* * * * *
14583 GTTTTAGTTTGAAGGTTTTAAAGGATTTGAAGTTGGAAAGTTTAAAGAAAATGAGGTAAA
1 GTTTTAGTTTGAAGG--GTAAAGGATTTGAAGCTAGAAAGCTTAAAGAAAATGAAGTAAA
14643 GGGTAAAAGG
Statistics
Matches: 51, Mismatches: 7, Indels: 2
0.85 0.12 0.03
Matches are distributed among these distances:
59 15 0.29
61 36 0.71
ACGTcount: A:0.39, C:0.02, G:0.28, T:0.31
Consensus pattern (59 bp):
GTTTTAGTTTGAAGGGTAAAGGATTTGAAGCTAGAAAGCTTAAAGAAAATGAAGTAAAA
Found at i:15490 original size:4 final size:4
Alignment explanation
Indices: 15475--15532 Score: 53
Period size: 4 Copynumber: 14.0 Consensus size: 4
15465 CTCATAGTAT
* * * * *
15475 TACA TGCA TACA TACA TACA TACC TACC TATA TATCA TACA TACA TATA
1 TACA TACA TACA TACA TACA TACA TACA TACA TA-CA TACA TACA TACA
15524 TATCA TACA
1 TA-CA TACA
15533 GATATCAGCT
Statistics
Matches: 44, Mismatches: 8, Indels: 4
0.79 0.14 0.07
Matches are distributed among these distances:
4 38 0.86
5 6 0.14
ACGTcount: A:0.43, C:0.24, G:0.02, T:0.31
Consensus pattern (4 bp):
TACA
Found at i:15523 original size:17 final size:17
Alignment explanation
Indices: 15481--15532 Score: 70
Period size: 17 Copynumber: 3.1 Consensus size: 17
15471 GTATTACATG
*
15481 CATACATACATA-CATA
1 CATACATATATATCATA
* *
15497 CCTACCTATATATCATA
1 CATACATATATATCATA
15514 CATACATATATATCATA
1 CATACATATATATCATA
15531 CA
1 CA
15533 GATATCAGCT
Statistics
Matches: 30, Mismatches: 5, Indels: 1
0.83 0.14 0.03
Matches are distributed among these distances:
16 9 0.30
17 21 0.70
ACGTcount: A:0.44, C:0.25, G:0.00, T:0.31
Consensus pattern (17 bp):
CATACATATATATCATA
Found at i:15530 original size:13 final size:15
Alignment explanation
Indices: 15481--15539 Score: 50
Period size: 13 Copynumber: 3.9 Consensus size: 15
15471 GTATTACATG
*
15481 CATACATACATACATA
1 CATACATATAT-CATA
*
15497 CCTACCTATATATCATA
1 CATA-C-ATATATCATA
15514 CATACATATAT-AT-
1 CATACATATATCATA
*
15527 CATACAGATATCA
1 CATACATATATCA
15540 GCTATATATA
Statistics
Matches: 36, Mismatches: 4, Indels: 8
0.75 0.08 0.17
Matches are distributed among these distances:
13 10 0.28
14 3 0.08
15 6 0.17
16 4 0.11
17 8 0.22
18 5 0.14
ACGTcount: A:0.44, C:0.24, G:0.02, T:0.31
Consensus pattern (15 bp):
CATACATATATCATA
Found at i:30860 original size:55 final size:53
Alignment explanation
Indices: 30777--30883 Score: 144
Period size: 55 Copynumber: 2.0 Consensus size: 53
30767 AATCTGTAAA
* * *
30777 TAGTATCTAGGAGGAAGCAACTTCTACATTTATAAAGGTGATAGAATTA-ATAAT
1 TAGTATCTAAGAGGAAGCAACTTCTACATTCAT-AAGGTAATA-AATTATATAAT
*
30831 TAGTACTCTAAGAGGAAGCAGCTTCTACATTCATAAGGTAATAAATTATATAA
1 TAGTA-TCTAAGAGGAAGCAACTTCTACATTCATAAGGTAATAAATTATATAA
30884 AGAGGACTTT
Statistics
Matches: 47, Mismatches: 4, Indels: 4
0.85 0.07 0.07
Matches are distributed among these distances:
53 5 0.11
54 17 0.36
55 25 0.53
ACGTcount: A:0.41, C:0.11, G:0.17, T:0.31
Consensus pattern (53 bp):
TAGTATCTAAGAGGAAGCAACTTCTACATTCATAAGGTAATAAATTATATAAT
Found at i:31586 original size:16 final size:16
Alignment explanation
Indices: 31562--31632 Score: 52
Period size: 16 Copynumber: 4.1 Consensus size: 16
31552 CAAGCAGTTT
*
31562 TTTCAGGTCATTCGGG
1 TTTCGGGTCATTCGGG
* *
31578 TTTCTGGTCATTTGGG
1 TTTCGGGTCATTCGGG
31594 TTCGGGTTTCGGGTCATTCGGG
1 -T----TT-CGGGTCATTCGGG
*
31616 TCTCGGGTCATTCGGG
1 TTTCGGGTCATTCGGG
31632 T
1 T
31633 CAGGCAGTTT
Statistics
Matches: 44, Mismatches: 5, Indels: 12
0.72 0.08 0.20
Matches are distributed among these distances:
16 28 0.64
17 2 0.05
21 3 0.07
22 11 0.25
ACGTcount: A:0.07, C:0.18, G:0.35, T:0.39
Consensus pattern (16 bp):
TTTCGGGTCATTCGGG
Found at i:31597 original size:22 final size:22
Alignment explanation
Indices: 31572--31634 Score: 81
Period size: 22 Copynumber: 2.7 Consensus size: 22
31562 TTTCAGGTCA
* *
31572 TTCGGGTTTCTGGTCATTTGGG
1 TTCGGGTTTCGGGTCATTCGGG
31594 TTCGGGTTTCGGGTCATTCGGG
1 TTCGGGTTTCGGGTCATTCGGG
31616 TCTCGGGTCATTCGGGTCA
1 T-TCGGGT--TTCGGGTCA
31635 GGCAGTTTTT
Statistics
Matches: 36, Mismatches: 2, Indels: 3
0.88 0.05 0.07
Matches are distributed among these distances:
22 21 0.58
23 6 0.17
25 9 0.25
ACGTcount: A:0.06, C:0.19, G:0.37, T:0.38
Consensus pattern (22 bp):
TTCGGGTTTCGGGTCATTCGGG
Found at i:31633 original size:16 final size:16
Alignment explanation
Indices: 31594--31633 Score: 71
Period size: 16 Copynumber: 2.5 Consensus size: 16
31584 GTCATTTGGG
*
31594 TTCGGGTTTCGGGTCA
1 TTCGGGTCTCGGGTCA
31610 TTCGGGTCTCGGGTCA
1 TTCGGGTCTCGGGTCA
31626 TTCGGGTC
1 TTCGGGTC
31634 AGGCAGTTTT
Statistics
Matches: 23, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
16 23 1.00
ACGTcount: A:0.05, C:0.23, G:0.38, T:0.35
Consensus pattern (16 bp):
TTCGGGTCTCGGGTCA
Found at i:31633 original size:81 final size:77
Alignment explanation
Indices: 31512--31658 Score: 197
Period size: 81 Copynumber: 1.9 Consensus size: 77
31502 CGGGTTTGGG
*
31512 GGGTTCGGGTCCGGGTCATTTGGGTTCGGGTCAAATGGGTCAAGCAGTTTTTTCAGGTCATTCGG
1 GGGTTCGGGTCCGGGTCATTCGGGTTCGGGTCAAATGGGTCAAGCAGTTTTTTCAGGTC--TCGG
31577 GTTTCTGGTCATTT
64 GTTTCTGGTCATTT
* * * *
31591 GGGTTCGGGTTTCGGGTCATTCGGGTCTCGGGTC-ATTCGGGTCAGGCAGTTTTTTCGGGTCTCG
1 GGGTTCGGG-TCCGGGTCATTCGGGT-TCGGGTCAAAT-GGGTCAAGCAGTTTTTTCAGGTCTCG
31655 GGTT
63 GGTT
31659 GGGCGGGTTC
Statistics
Matches: 60, Mismatches: 5, Indels: 6
0.85 0.07 0.08
Matches are distributed among these distances:
79 16 0.27
80 16 0.27
81 28 0.47
ACGTcount: A:0.10, C:0.18, G:0.37, T:0.36
Consensus pattern (77 bp):
GGGTTCGGGTCCGGGTCATTCGGGTTCGGGTCAAATGGGTCAAGCAGTTTTTTCAGGTCTCGGGT
TTCTGGTCATTT
Done.