Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01015633.1 Corchorus capsularis cultivar CVL-1 contig15654, 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: 40027
ACGTcount: A:0.34, C:0.18, G:0.16, T:0.33
Warning! 2 characters in sequence are not A, C, G, or T
Found at i:11128 original size:14 final size:14
Alignment explanation
Indices: 11111--11140 Score: 51
Period size: 14 Copynumber: 2.1 Consensus size: 14
11101 ATTTTTTTAA
11111 TAAAAAATAAAATT
1 TAAAAAATAAAATT
*
11125 TAAAAATTAAAATT
1 TAAAAAATAAAATT
11139 TA
1 TA
11141 TATAAAATCT
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
14 15 1.00
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (14 bp):
TAAAAAATAAAATT
Found at i:13276 original size:13 final size:13
Alignment explanation
Indices: 13243--13288 Score: 58
Period size: 12 Copynumber: 3.5 Consensus size: 13
13233 GTCTCCAATT
13243 TATTAAAATTAAAA
1 TATTAAAA-TAAAA
**
13257 TGGTAAAATAAAA
1 TATTAAAATAAAA
13270 TATT-AAATAAAA
1 TATTAAAATAAAA
13282 TATTAAA
1 TATTAAA
13289 TTTAATTAAA
Statistics
Matches: 27, Mismatches: 4, Indels: 3
0.79 0.12 0.09
Matches are distributed among these distances:
12 12 0.44
13 9 0.33
14 6 0.22
ACGTcount: A:0.63, C:0.00, G:0.04, T:0.33
Consensus pattern (13 bp):
TATTAAAATAAAA
Found at i:13537 original size:93 final size:93
Alignment explanation
Indices: 13432--13604 Score: 319
Period size: 93 Copynumber: 1.9 Consensus size: 93
13422 TATTAGTAAT
13432 ATGGTAAAAATAAAATAGGTATAAGGATATTAGATTTAATTAAATAAAAATAGAGTTTTTAGTTG
1 ATGGTAAAAATAAAATAGGTATAAGGATATTAGATTTAATTAAATAAAAATAGAGTTTTTAGTTG
*
13497 AGTAAAACTATAAAAGTAAAATAGCAAA
66 ACTAAAACTATAAAAGTAAAATAGCAAA
*
13525 ATGGTAAAAATAAAATAGTTATAAGGATATTAGATTTAATTAAATAAAAATAGAGTTTTTAGTTG
1 ATGGTAAAAATAAAATAGGTATAAGGATATTAGATTTAATTAAATAAAAATAGAGTTTTTAGTTG
*
13590 ACTAAATCTATAAAA
66 ACTAAAACTATAAAA
13605 ATTTAAACAA
Statistics
Matches: 77, Mismatches: 3, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
93 77 1.00
ACGTcount: A:0.51, C:0.02, G:0.14, T:0.32
Consensus pattern (93 bp):
ATGGTAAAAATAAAATAGGTATAAGGATATTAGATTTAATTAAATAAAAATAGAGTTTTTAGTTG
ACTAAAACTATAAAAGTAAAATAGCAAA
Found at i:14802 original size:70 final size:72
Alignment explanation
Indices: 14728--14870 Score: 247
Period size: 73 Copynumber: 2.0 Consensus size: 72
14718 AGGGTTCAAT
14728 TCCTAACAATTTC-AA-AAAAAAAA-TGTTACGATAATATGTTTTGAACGCAATTAATTATAAAA
1 TCCTAACAATTTCAAATAAAAAAAATTGTTACGATAATATGTTTTGAACGCAATTAATTAT-AAA
14790 TTTTAGAA
65 TTTTAGAA
*
14798 TCCTAACAATTTCAAATAAAAAAAATTGTTACGATGATATGTTTTGAACGCAATTAATTATAAAT
1 TCCTAACAATTTCAAATAAAAAAAATTGTTACGATAATATGTTTTGAACGCAATTAATTATAAAT
14863 TTTAGAA
66 TTTAGAA
14870 T
1 T
14871 TCTACATTTT
Statistics
Matches: 69, Mismatches: 1, Indels: 4
0.93 0.01 0.05
Matches are distributed among these distances:
70 13 0.19
71 2 0.03
72 20 0.29
73 34 0.49
ACGTcount: A:0.45, C:0.10, G:0.09, T:0.36
Consensus pattern (72 bp):
TCCTAACAATTTCAAATAAAAAAAATTGTTACGATAATATGTTTTGAACGCAATTAATTATAAAT
TTTAGAA
Found at i:15359 original size:19 final size:19
Alignment explanation
Indices: 15332--15387 Score: 94
Period size: 19 Copynumber: 2.9 Consensus size: 19
15322 TGTTTAGTAC
*
15332 ACCGTTTCACTACCGTTTG
1 ACCGTTTCACCACCGTTTG
*
15351 ACTGTTTCACCACCGTTTG
1 ACCGTTTCACCACCGTTTG
15370 ACCGTTTCACCACCGTTT
1 ACCGTTTCACCACCGTTT
15388 TGGGTCCAAA
Statistics
Matches: 34, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
19 34 1.00
ACGTcount: A:0.16, C:0.34, G:0.14, T:0.36
Consensus pattern (19 bp):
ACCGTTTCACCACCGTTTG
Found at i:15463 original size:21 final size:19
Alignment explanation
Indices: 15438--15495 Score: 80
Period size: 19 Copynumber: 2.9 Consensus size: 19
15428 GCTGCTCTAA
15438 TAATCTCATCTGTACAGTACC
1 TAATCTCATCTGTACAGT--C
* *
15459 TAATCTAATCTGTACAGTG
1 TAATCTCATCTGTACAGTC
15478 TAATCTCATCTGTACAGT
1 TAATCTCATCTGTACAGT
15496 TGTTAAACAG
Statistics
Matches: 34, Mismatches: 3, Indels: 2
0.87 0.08 0.05
Matches are distributed among these distances:
19 17 0.50
21 17 0.50
ACGTcount: A:0.29, C:0.22, G:0.12, T:0.36
Consensus pattern (19 bp):
TAATCTCATCTGTACAGTC
Found at i:15929 original size:31 final size:31
Alignment explanation
Indices: 15887--15947 Score: 95
Period size: 31 Copynumber: 2.0 Consensus size: 31
15877 GAACTAACTC
*
15887 AAACATCCAAGATCCAAAGATCTGGAGACTG
1 AAACATCCAAGATCCAAAGATCTGAAGACTG
* *
15918 AAACATTCAAGATCTAAAGATCTGAAGACT
1 AAACATCCAAGATCCAAAGATCTGAAGACT
15948 AAAAACCCAA
Statistics
Matches: 27, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
31 27 1.00
ACGTcount: A:0.44, C:0.20, G:0.16, T:0.20
Consensus pattern (31 bp):
AAACATCCAAGATCCAAAGATCTGAAGACTG
Found at i:16216 original size:103 final size:103
Alignment explanation
Indices: 15884--16199 Score: 614
Period size: 103 Copynumber: 3.1 Consensus size: 103
15874 ATTGAACTAA
*
15884 CTCAAACATCCAAGATCCAAAGATCTGGAGACTGAAACATTCAAGATCTAAAGATCTGAAGACTA
1 CTCAAACATCCAAGATCCAAAGATCTGGAGATTGAAACATTCAAGATCTAAAGATCTGAAGACTA
15949 AAAACCCAAACAGATTAACAGATATGTGGGACTTTATT
66 AAAACCCAAACAGATTAACAGATATGTGGGACTTTATT
15987 CTCAAACATCCAAGATCCAAAGATCTGGAGATTGAAACATTCAAGATCTAAAGATCTGAAGACTA
1 CTCAAACATCCAAGATCCAAAGATCTGGAGATTGAAACATTCAAGATCTAAAGATCTGAAGACTA
16052 AAAACCCAAACAGATTAACAGATATGTGGGACTTTATT
66 AAAACCCAAACAGATTAACAGATATGTGGGACTTTATT
16090 CTCAAACATCCAAGATCCAAAGATCTGGAGATTGAAACATTCAAGATCTAAAGATCTGAAGACTA
1 CTCAAACATCCAAGATCCAAAGATCTGGAGATTGAAACATTCAAGATCTAAAGATCTGAAGACTA
16155 AAAACCCAAACAGATTAACAGATATGTGGGACTTTATT
66 AAAACCCAAACAGATTAACAGATATGTGGGACTTTATT
*
16193 CTAAAAC
1 CTCAAAC
16200 TAAATAAAAA
Statistics
Matches: 211, Mismatches: 2, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
103 211 1.00
ACGTcount: A:0.43, C:0.19, G:0.15, T:0.23
Consensus pattern (103 bp):
CTCAAACATCCAAGATCCAAAGATCTGGAGATTGAAACATTCAAGATCTAAAGATCTGAAGACTA
AAAACCCAAACAGATTAACAGATATGTGGGACTTTATT
Found at i:16897 original size:2 final size:2
Alignment explanation
Indices: 16890--16922 Score: 66
Period size: 2 Copynumber: 16.5 Consensus size: 2
16880 ATGCCTCATA
16890 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
16923 AGGTAAATAA
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 31 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:17959 original size:61 final size:61
Alignment explanation
Indices: 17840--17960 Score: 161
Period size: 61 Copynumber: 2.0 Consensus size: 61
17830 TGCTATCAAT
* * *
17840 TGCAAGAAAGAATGTTTCCCATGATCATAATTCAAATCTTAATAATTTTCCGTCAAAAAAA
1 TGCAAGAAAGAATGTTTCCCATGATCATAATTCAAATCCTAATAATTTTCCATAAAAAAAA
* * * * **
17901 TGCAAGATAGAATGTTTCCGATGATTATAATTCAAATCCTGATAATTTTTTATAAAAAAA
1 TGCAAGAAAGAATGTTTCCCATGATCATAATTCAAATCCTAATAATTTTCCATAAAAAAA
17961 TGGAGTGAAG
Statistics
Matches: 51, Mismatches: 9, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
61 51 1.00
ACGTcount: A:0.42, C:0.13, G:0.11, T:0.34
Consensus pattern (61 bp):
TGCAAGAAAGAATGTTTCCCATGATCATAATTCAAATCCTAATAATTTTCCATAAAAAAAA
Found at i:27587 original size:12 final size:12
Alignment explanation
Indices: 27559--27588 Score: 51
Period size: 12 Copynumber: 2.5 Consensus size: 12
27549 CACTCTTAAC
*
27559 CTTCATCTTTTT
1 CTTCTTCTTTTT
27571 CTTCTTCTTTTT
1 CTTCTTCTTTTT
27583 CTTCTT
1 CTTCTT
27589 TTTCTCCTCA
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
12 17 1.00
ACGTcount: A:0.03, C:0.27, G:0.00, T:0.70
Consensus pattern (12 bp):
CTTCTTCTTTTT
Found at i:27645 original size:33 final size:33
Alignment explanation
Indices: 27607--27672 Score: 123
Period size: 33 Copynumber: 2.0 Consensus size: 33
27597 CAACTTCAAC
27607 TTCCCTCTCTTCTATTTCATCTTCCTCTTGCTT
1 TTCCCTCTCTTCTATTTCATCTTCCTCTTGCTT
*
27640 TTCCCTCTCTTCTATTTCATTTTCCTCTTGCTT
1 TTCCCTCTCTTCTATTTCATCTTCCTCTTGCTT
27673 CTCTGGTTGA
Statistics
Matches: 32, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
33 32 1.00
ACGTcount: A:0.06, C:0.35, G:0.03, T:0.56
Consensus pattern (33 bp):
TTCCCTCTCTTCTATTTCATCTTCCTCTTGCTT
Found at i:27657 original size:15 final size:15
Alignment explanation
Indices: 27607--27657 Score: 50
Period size: 15 Copynumber: 3.2 Consensus size: 15
27597 CAACTTCAAC
27607 TTCCCTCTCTTCTAT
1 TTCCCTCTCTTCTAT
*
27622 TTCATCTTCCTCTTGCT-T
1 TTC--CCT-CTCTT-CTAT
27640 TTCCCTCTCTTCTAT
1 TTCCCTCTCTTCTAT
27655 TTC
1 TTC
27658 ATTTTCCTCT
Statistics
Matches: 29, Mismatches: 2, Indels: 10
0.71 0.05 0.24
Matches are distributed among these distances:
14 2 0.07
15 12 0.41
16 2 0.07
17 2 0.07
18 9 0.31
19 2 0.07
ACGTcount: A:0.06, C:0.37, G:0.02, T:0.55
Consensus pattern (15 bp):
TTCCCTCTCTTCTAT
Found at i:30642 original size:28 final size:25
Alignment explanation
Indices: 30592--30649 Score: 64
Period size: 27 Copynumber: 2.2 Consensus size: 25
30582 TAGAATAGAG
*
30592 AAAAAAAAAACAGAAATACAAAACACA
1 AAAAAAAAAAAAGAAATACAAAA-A-A
*
30619 AAAAAAAAAGAAAGAAA-ATAAAAAA
1 AAAAAAAAA-AAAGAAATACAAAAAA
30644 AAAAAA
1 AAAAAA
30650 CAGGGAGAGT
Statistics
Matches: 28, Mismatches: 2, Indels: 4
0.82 0.06 0.12
Matches are distributed among these distances:
25 7 0.25
26 1 0.04
27 14 0.50
28 6 0.21
ACGTcount: A:0.84, C:0.07, G:0.05, T:0.03
Consensus pattern (25 bp):
AAAAAAAAAAAAGAAATACAAAAAA
Found at i:30645 original size:24 final size:24
Alignment explanation
Indices: 30592--30649 Score: 64
Period size: 24 Copynumber: 2.5 Consensus size: 24
30582 TAGAATAGAG
* * *
30592 AAAAAAAAAACAGAAATACAAAAC
1 AAAAAAAAAAAAGAAAGACAAAAA
* *
30616 ACAAAAAAAAAAGAAAGA-AAATA
1 AAAAAAAAAAAAGAAAGACAAAAA
30639 AAAAAAAAAAA
1 AAAAAAAAAAA
30650 CAGGGAGAGT
Statistics
Matches: 28, Mismatches: 6, Indels: 1
0.80 0.17 0.03
Matches are distributed among these distances:
23 13 0.46
24 15 0.54
ACGTcount: A:0.84, C:0.07, G:0.05, T:0.03
Consensus pattern (24 bp):
AAAAAAAAAAAAGAAAGACAAAAA
Found at i:32221 original size:49 final size:49
Alignment explanation
Indices: 32039--32767 Score: 749
Period size: 49 Copynumber: 14.9 Consensus size: 49
32029 TCTTTCAATT
* * * * *
32039 TTCAGTTTTTACCTGCTTTTTCCCAAAACACCCTTCCCGGACGGAAGGCA
1 TTCA-TTTTTACTTGCTATTTCCCAAAACGCCCTTCCCAGACGGAAGCCA
* * * * ** *
32089 CTCAATTTTTATTTGCTTTTTCCCTAAACGCCCTTCCTGGACGGAAGGCA
1 TTC-ATTTTTACTTGCTATTTCCCAAAACGCCCTTCCCAGACGGAAGCCA
* * * * *
32139 CTTC--TTTTATTTGCTTTTTCCTAAAATGCCCTTCCCAAACGGAAGCCA
1 -TTCATTTTTACTTGCTATTTCCCAAAACGCCCTTCCCAGACGGAAGCCA
* * * *
32187 TTTATTTTTGCTAGCTATTTCCCAAAACGCCCTTCTCAGACGGAAGCCA
1 TTCATTTTTACTTGCTATTTCCCAAAACGCCCTTCCCAGACGGAAGCCA
**
32236 TTCATTTTTACTTGCTATTTCCCAAAACGCTATTCCCAGACGGAAGCCA
1 TTCATTTTTACTTGCTATTTCCCAAAACGCCCTTCCCAGACGGAAGCCA
* * *
32285 TTCATCTTTACTTGCTATTTCCCAAAACGCCATTCCCAGACAGAAGCCA
1 TTCATTTTTACTTGCTATTTCCCAAAACGCCCTTCCCAGACGGAAGCCA
* *
32334 TTCATTTTTACTTGCTATTTCCCAAAGCG-CCTT-CCAGATGGAAGCCA
1 TTCATTTTTACTTGCTATTTCCCAAAACGCCCTTCCCAGACGGAAGCCA
* **
32381 TTCATCTTTACTTGCTATTTCCCAAAACGCTATTCCCAGACGGAAGCCA
1 TTCATTTTTACTTGCTATTTCCCAAAACGCCCTTCCCAGACGGAAGCCA
* * * *
32430 TTCATCTTTATTTGCTATCTCCCAAAACACCCTTCCCAGACGGAAGCCA
1 TTCATTTTTACTTGCTATTTCCCAAAACGCCCTTCCCAGACGGAAGCCA
* *
32479 CTT-A-TTTTACTTGCTATTTCCCAAAGCGCCATTCCCAGACGGAAGCCA
1 -TTCATTTTTACTTGCTATTTCCCAAAACGCCCTTCCCAGACGGAAGCCA
* ** * *
32527 TTTATTTTCGCTTGCTATTTCCCAAAGCGCCCTTCCCAGACGAAAGCCA
1 TTCATTTTTACTTGCTATTTCCCAAAACGCCCTTCCCAGACGGAAGCCA
* * * * *
32576 TTTATTTTTACTAGCTATCTCCCCAAAACGCCCTTCCCGGACGGAAGCCG
1 TTCATTTTTACTTGCTAT-TTCCCAAAACGCCCTTCCCAGACGGAAGCCA
* ** *
32626 TTTATTTTTACTTGCTATTTCCCAAAACGCCCTTCCTGGACGGAAGGCA
1 TTCATTTTTACTTGCTATTTCCCAAAACGCCCTTCCCAGACGGAAGCCA
* * * * * * *
32675 CTGATTATTACCTG-T-TTCTCCCAAAACACCCTTCCCGGACGGAAGGCA
1 TTCATTTTTACTTGCTATT-TCCCAAAACGCCCTTCCCAGACGGAAGCCA
* * * * * *
32723 CT-AGTTTTTACCTG-TTTTTCCTAAAACGCCCTTCCCGGACAGAAG
1 TTCA-TTTTTACTTGCTATTTCCCAAAACGCCCTTCCCAGACGGAAG
32768 GCACCATTCT
Statistics
Matches: 586, Mismatches: 80, Indels: 28
0.84 0.12 0.04
Matches are distributed among these distances:
47 46 0.08
48 146 0.25
49 304 0.52
50 87 0.15
51 3 0.01
ACGTcount: A:0.24, C:0.31, G:0.14, T:0.31
Consensus pattern (49 bp):
TTCATTTTTACTTGCTATTTCCCAAAACGCCCTTCCCAGACGGAAGCCA
Found at i:34479 original size:22 final size:22
Alignment explanation
Indices: 34451--34501 Score: 102
Period size: 22 Copynumber: 2.3 Consensus size: 22
34441 CGAAACCGAT
34451 ATGACCCGACCTCAAATCCTTA
1 ATGACCCGACCTCAAATCCTTA
34473 ATGACCCGACCTCAAATCCTTA
1 ATGACCCGACCTCAAATCCTTA
34495 ATGACCC
1 ATGACCC
34502 AAACCTGAAT
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 29 1.00
ACGTcount: A:0.31, C:0.37, G:0.10, T:0.22
Consensus pattern (22 bp):
ATGACCCGACCTCAAATCCTTA
Found at i:36713 original size:10 final size:10
Alignment explanation
Indices: 36698--36738 Score: 57
Period size: 10 Copynumber: 4.2 Consensus size: 10
36688 AAACCGACTA
36698 ATCGGTTTTG
1 ATCGGTTTTG
*
36708 ATCGGTTTCG
1 ATCGGTTTTG
*
36718 GTCGGTTTTG
1 ATCGGTTTTG
36728 -TCGGTTTTG
1 ATCGGTTTTG
36737 AT
1 AT
36739 TTATATTTCT
Statistics
Matches: 27, Mismatches: 3, Indels: 2
0.84 0.09 0.06
Matches are distributed among these distances:
9 9 0.33
10 18 0.67
ACGTcount: A:0.07, C:0.12, G:0.32, T:0.49
Consensus pattern (10 bp):
ATCGGTTTTG
Found at i:37072 original size:14 final size:14
Alignment explanation
Indices: 37053--37082 Score: 51
Period size: 14 Copynumber: 2.1 Consensus size: 14
37043 TCGGTGCTAT
*
37053 GTCGGTTTTGGTCG
1 GTCGGTTTCGGTCG
37067 GTCGGTTTCGGTCG
1 GTCGGTTTCGGTCG
37081 GT
1 GT
37083 TTTAGGCGGT
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
14 15 1.00
ACGTcount: A:0.00, C:0.17, G:0.43, T:0.40
Consensus pattern (14 bp):
GTCGGTTTCGGTCG
Found at i:37607 original size:10 final size:10
Alignment explanation
Indices: 37592--37621 Score: 60
Period size: 10 Copynumber: 3.0 Consensus size: 10
37582 CATGAGGCGC
37592 CAACCGGCCA
1 CAACCGGCCA
37602 CAACCGGCCA
1 CAACCGGCCA
37612 CAACCGGCCA
1 CAACCGGCCA
37622 TCGCATGGGC
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 20 1.00
ACGTcount: A:0.30, C:0.50, G:0.20, T:0.00
Consensus pattern (10 bp):
CAACCGGCCA
Found at i:39647 original size:6 final size:6
Alignment explanation
Indices: 39636--39674 Score: 78
Period size: 6 Copynumber: 6.5 Consensus size: 6
39626 ATTAATATGC
39636 TTTAGA TTTAGA TTTAGA TTTAGA TTTAGA TTTAGA TTT
1 TTTAGA TTTAGA TTTAGA TTTAGA TTTAGA TTTAGA TTT
39675 GCTTTGCTTT
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 33 1.00
ACGTcount: A:0.31, C:0.00, G:0.15, T:0.54
Consensus pattern (6 bp):
TTTAGA
Done.