Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01006902.1 Corchorus capsularis cultivar CVL-1 contig06923, 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: 31749
ACGTcount: A:0.35, C:0.19, G:0.16, T:0.30
Found at i:3416 original size:2 final size:2
Alignment explanation
Indices: 3409--3461 Score: 69
Period size: 2 Copynumber: 28.5 Consensus size: 2
3399 GTAAAAGCAA
3409 AT AT AT AT AT AT AT AT AT AT AT -T A- AT -T AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
*
3448 AT AT -T AT AT TT AT A
1 AT AT AT AT AT AT AT A
3462 ATACCCATAA
Statistics
Matches: 45, Mismatches: 2, Indels: 8
0.82 0.04 0.15
Matches are distributed among these distances:
1 4 0.09
2 41 0.91
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (2 bp):
AT
Found at i:3438 original size:21 final size:22
Alignment explanation
Indices: 3409--3461 Score: 83
Period size: 21 Copynumber: 2.5 Consensus size: 22
3399 GTAAAAGCAA
3409 ATATATATATATATATATATATT
1 ATAT-TATATATATATATATATT
3432 A-ATTATATATATATATATATT
1 ATATTATATATATATATATATT
3453 ATATT-TATA
1 ATATTATATA
3462 ATACCCATAA
Statistics
Matches: 29, Mismatches: 0, Indels: 4
0.88 0.00 0.12
Matches are distributed among these distances:
21 23 0.79
22 5 0.17
23 1 0.03
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (22 bp):
ATATTATATATATATATATATT
Found at i:3440 original size:17 final size:17
Alignment explanation
Indices: 3409--3461 Score: 76
Period size: 15 Copynumber: 3.3 Consensus size: 17
3399 GTAAAAGCAA
3409 ATATATATATA-TATAT
1 ATATATATATATTATAT
3425 ATATAT-TA-ATTATAT
1 ATATATATATATTATAT
3440 ATATATATATATTATAT
1 ATATATATATATTATAT
*
3457 TTATA
1 ATATA
3462 ATACCCATAA
Statistics
Matches: 33, Mismatches: 1, Indels: 5
0.85 0.03 0.13
Matches are distributed among these distances:
14 1 0.03
15 13 0.39
16 8 0.24
17 11 0.33
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (17 bp):
ATATATATATATTATAT
Found at i:5104 original size:31 final size:31
Alignment explanation
Indices: 5053--5137 Score: 125
Period size: 31 Copynumber: 2.7 Consensus size: 31
5043 TTGTATATAT
* * *
5053 ATTAGCGGCGCCTGGTTTCCAAGCGCCGCAG
1 ATTAGCGGCGTCTGGATTCCAAACGCCGCAG
*
5084 ATTAGAGGCGTCTGGATTCCAAACGCCGCAG
1 ATTAGCGGCGTCTGGATTCCAAACGCCGCAG
*
5115 ATTAGCGGCGTCTGGAGTCCAAA
1 ATTAGCGGCGTCTGGATTCCAAA
5138 TGCCACTATT
Statistics
Matches: 48, Mismatches: 6, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
31 48 1.00
ACGTcount: A:0.22, C:0.27, G:0.31, T:0.20
Consensus pattern (31 bp):
ATTAGCGGCGTCTGGATTCCAAACGCCGCAG
Found at i:5734 original size:31 final size:31
Alignment explanation
Indices: 5699--5765 Score: 100
Period size: 31 Copynumber: 2.2 Consensus size: 31
5689 TCTTATCTAA
5699 ACGCCACTAAATAGCGGCACCTGAAT-TTAAG
1 ACGCCACTAAATAGCGGCACCT-AATATTAAG
**
5730 ACGCCACTAAATAGCGGCGTCTAATATTAAG
1 ACGCCACTAAATAGCGGCACCTAATATTAAG
5761 ACGCC
1 ACGCC
5766 GCTATCTTCA
Statistics
Matches: 33, Mismatches: 2, Indels: 2
0.89 0.05 0.05
Matches are distributed among these distances:
30 3 0.09
31 30 0.91
ACGTcount: A:0.34, C:0.27, G:0.19, T:0.19
Consensus pattern (31 bp):
ACGCCACTAAATAGCGGCACCTAATATTAAG
Found at i:9267 original size:18 final size:19
Alignment explanation
Indices: 9238--9276 Score: 55
Period size: 18 Copynumber: 2.1 Consensus size: 19
9228 ATTACTTCAT
9238 TTTCCTTTAATTAT-CATAA
1 TTTCCTTTAATT-TCCATAA
9257 TTTCC-TTAATTTCCATAA
1 TTTCCTTTAATTTCCATAA
9275 TT
1 TT
9277 AAATTCGGAT
Statistics
Matches: 19, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
17 1 0.05
18 13 0.68
19 5 0.26
ACGTcount: A:0.28, C:0.18, G:0.00, T:0.54
Consensus pattern (19 bp):
TTTCCTTTAATTTCCATAA
Found at i:11990 original size:84 final size:78
Alignment explanation
Indices: 11831--12076 Score: 341
Period size: 78 Copynumber: 3.1 Consensus size: 78
11821 GTTTTTTAAT
**
11831 TAAAATAGTAAAATTTTAAAATATAATAGTTATAAGGATATTAGATTTAATTATATAAAAATAGA
1 TAAAATAGTAAAATAGTAAAATATAATAGTTATAAGGATATTAGATTTAATTATATAAAAATAGA
*
11896 TTTTTTAGTTGAG
66 GTTTTTAGTTGAG
* *
11909 TAAAATAGTAAAATGGTAAAATATAATAGTCATAAGGATTCACTCATTAGATTTAATTATATAAA
1 TAAAATAGTAAAATAGTAAAATATAATAGTTATAAGG----A-T-ATTAGATTTAATTATATAAA
11974 AATAGAGTTTTTAGTTGAG
60 AATAGAGTTTTTAGTTGAG
* * * *
11993 TAAAATAGTAACATAGTAAAATAAAATAGTTATGAA-GATATTATATTTAATTAAATAAAAATAG
1 TAAAATAGTAAAATAGTAAAATATAATAGTTAT-AAGGATATTAGATTTAATTATATAAAAATAG
12057 AGTTTTTAGTTGAG
65 AGTTTTTAGTTGAG
12071 TAAAAT
1 TAAAAT
12077 TATAAAAACC
Statistics
Matches: 151, Mismatches: 10, Indels: 14
0.86 0.06 0.08
Matches are distributed among these distances:
78 77 0.51
79 1 0.01
80 1 0.01
82 1 0.01
83 1 0.01
84 68 0.45
85 2 0.01
ACGTcount: A:0.48, C:0.02, G:0.13, T:0.37
Consensus pattern (78 bp):
TAAAATAGTAAAATAGTAAAATATAATAGTTATAAGGATATTAGATTTAATTATATAAAAATAGA
GTTTTTAGTTGAG
Found at i:14006 original size:30 final size:30
Alignment explanation
Indices: 13952--14010 Score: 84
Period size: 30 Copynumber: 2.0 Consensus size: 30
13942 GTTTGGAAGT
*
13952 TTCTATAGAAAGTAAAAAGGTAGAAAGTTC
1 TTCTATAGAAAGTAAAAAGCTAGAAAGTTC
*
13982 TTCTATAGAAAGTTTAAAA-CTAGAAAGTT
1 TTCTATAGAAAG-TAAAAAGCTAGAAAGTT
14011 TTTTCTTCAG
Statistics
Matches: 26, Mismatches: 2, Indels: 2
0.87 0.07 0.07
Matches are distributed among these distances:
30 21 0.81
31 5 0.19
ACGTcount: A:0.46, C:0.07, G:0.17, T:0.31
Consensus pattern (30 bp):
TTCTATAGAAAGTAAAAAGCTAGAAAGTTC
Found at i:15465 original size:15 final size:15
Alignment explanation
Indices: 15445--15479 Score: 54
Period size: 15 Copynumber: 2.3 Consensus size: 15
15435 TGGTGAATGA
15445 AAAGAGT-CTCGAAGC
1 AAAGAGTCCT-GAAGC
15460 AAAGAGTCCTGAAGC
1 AAAGAGTCCTGAAGC
15475 AAAGA
1 AAAGA
15480 CTAATTAGTA
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
15 17 0.89
16 2 0.11
ACGTcount: A:0.46, C:0.17, G:0.26, T:0.11
Consensus pattern (15 bp):
AAAGAGTCCTGAAGC
Found at i:16666 original size:484 final size:465
Alignment explanation
Indices: 15700--17048 Score: 1539
Period size: 484 Copynumber: 2.8 Consensus size: 465
15690 GACCTAAGCT
* * * *
15700 GCTTCCAAAAATAAATTTTGACTCAGATT-TTCAAAATCAGACAACGAT-TATCATGTGACAATC
1 GCTTCCAAATATAAATTTTTACTTAGATTCTT-AAAATCAGACAACGATATATCACGTGACAATC
* * * * *
15763 AAACGTTTACAAAA-TCCAAACAATTAATAAAATAGAACAACTAGCTTTGGAATCCTGGAGCCCT
65 AAAC-ATTACAAAATTCAAAACAATTAATAAAAGA-AACAACTAGCTTTGGAGTCCTGGAGCCAT
* *
15827 AGACCTTGATTTCCATGCATGTACCATCCAATTTTTTCCTTTTATAATCTAATTGAAAATTTTGA
128 AGACC-TGATTT---T-CATGTACCATCC----TTTT--TTTTATAATCAAATTGAAAAATTTG-
* *
15892 AAAAGAAATGTGTTATCATTATGTCG----GGATTGTCTTCCATAGTATATGAAAGAGCCCTTAA
181 -AAAGAAATGTGTTATCATTATGTCGACTCGGATTGTCTTCCATGGTAAATGAAAGAGCCC-TAA
*
15953 GCACGGACTAATTCGTGCAATTAGGATTTTGAATTTGTAGGAGAGTTTTTGAATGACAATTTATA
244 GCAC--A--GA---GT--AATTAGGATTTTGAATTTGTAGGAGAGTTTTTGAATGACAATTTATA
* * * *
16018 GGACATTTATGGCGATATGAACAATGTTACTATAATTTTAAACATTATTAATAAGAAAAGAAAAA
300 GGAGAATTATGGCGATATGAACAATGTTACTATAATTTTAAACATTATAAAAAAGAAAAGAAAAA
* * *
16083 CGCATTTTCATGTTATTTACAAATTAACCAATGAAATTTTCATTTTTTAAATTGTAAAAAAATCA
365 CACATTTTCATGTCATTTACAAATTAACCAATGAAATTTTCATTTTTAAAATTGTAAAAAAATCA
* * *
16148 CCCTCACGTGACGTTTAAGCGTTACTAAACACCTAG
430 CCCTCACGTGACATTTAAGCATTACTAAACACCTAA
* *
16184 GCTTCCAAATATAAAATTTTTACTTAGATTCTTAAAATCAAACAACGATATATCACGTGACATTC
1 GCTTCCAAATAT-AAATTTTTACTTAGATTCTTAAAATCAGACAACGATATATCACGTGACAATC
* * *
16249 AGACATTACAAAATTCAAAACAATTAATAAAAGAAAACAACTAGATTTGGAGTCCTGGAGCCTGT
65 AAACATTACAAAATTCAAAACAATTAATAAAAG-AAACAACTAGCTTTGGAGTCCTGGAGCC-AT
*
16314 AGAACCTGATTTTCATGCACCATCC-TTTTTTT-TAATCAAATTGAAAAATTTGAAAGAAATGTG
128 AG-ACCTGATTTTCATGTACCATCCTTTTTTTTATAATCAAATTGAAAAATTTGAAAGAAATGTG
16377 TTATCATTATGTCGAACTCTGGATTGTCTTCCATGGTAAATGAAAGAGCCCTGAAGCACAGAGTA
192 TTATCATTATGTCG-ACTC-GGATTGTCTTCCATGGTAAATGAAAGAGCCCT-AAGCACAGAGTA
* *
16442 ATTAAGATTTTGAATTTGTAAGAGAGTTTTTGAATGACAATTTATTTATAGGAGAATTATGGCGA
254 ATTAGGATTTTGAATTTGTAGGAGAGTTTTTGAATGAC-A---ATTTATAGGAGAATTATGGCGA
16507 TATGAACAATGTTACTATAATTTTAAACATTATAAAAAAGAAAAGAAAAGAAAAATAATAACACA
315 TATGAACAATGTTACTATAATTTTAAACATTAT----AA-AAAAGAAAAG----A-AA-AACACA
* * *
16572 TTTTCATGTCATTTACAAATTAACCAATGGAA-TTTCATTTTTAAAATTGTAAAAAAATCATCGT
369 TTTTCATGTCATTTACAAATTAACCAATGAAATTTTCATTTTTAAAATTGTAAAAAAATCACCCT
* *
16636 TACGTTACATTTAAGCATTACTAAACACCTAA
434 CACGTGACATTTAAGCATTACTAAACACCTAA
* * * *
16668 ACTTCCAAATATAAATTTTTACTTAGATTCTT-AAGTTAGACAATGATATATCACGTGACAATCA
1 GCTTCCAAATATAAATTTTTACTTAGATTCTTAAAATCAGACAACGATATATCACGTGACAATCA
* *
16732 AACATTACAAAATTCAAAACAATTAATAAAAG--AGAACTAGCTTTGGAGTCTTGGAGCCCATAG
66 AACATTACAAAATTCAAAACAATTAATAAAAGAAACAACTAGCTTTGGAGTCCTGGAG-CCATAG
* *
16795 -CCTGATTTTCATGTACCATCCTTCTTTTTTCTAATCAAATTGAAAAATTTGAAAGAAATTTGTT
130 ACCTGATTTTCATGTACCATCCTT-TTTTTTATAATCAAATTGAAAAATTTGAAAGAAATGTGTT
* ** ** *
16859 ATCATTATGTTGGACTCCGGATCATCTTCCATGGTAAATGAAAGAGCCCT-A-TTC-GTGTAATT
194 ATCATTATG-TCGACT-CGGATTGTCTTCCATGGTAAATGAAAGAGCCCTAAGCACAGAGTAATT
* * *
16921 AGGATTTTGAATTTGTAGGAGAGTTTTTTAATGGCAATTTATAGGAGAGTTATGGCGATATGAAC
257 AGGATTTTGAATTTGTAGGAGAGTTTTTGAATGACAATTTATAGGAGAATTATGGCGATATGAAC
* ** * * *
16986 AATGTTACTATAGTTTTAAATGTTA-AAAAACAAAAAAAAAAAACACAATTTT-ATGTTATTTAC
322 AATGTTACTATAATTTTAAACATTATAAAAA-AGAAAAGAAAAACAC-ATTTTCATGTCATTTAC
17049 TGTAGTTTTC
Statistics
Matches: 762, Mismatches: 66, Indels: 97
0.82 0.07 0.10
Matches are distributed among these distances:
461 15 0.02
462 7 0.01
463 1 0.00
466 3 0.00
467 7 0.01
470 37 0.05
471 1 0.00
472 52 0.07
473 25 0.03
474 53 0.07
475 20 0.03
476 42 0.06
477 22 0.03
478 7 0.01
479 74 0.10
480 76 0.10
481 3 0.00
482 58 0.08
483 32 0.04
484 81 0.11
485 73 0.10
486 60 0.08
487 10 0.01
488 3 0.00
ACGTcount: A:0.39, C:0.14, G:0.14, T:0.34
Consensus pattern (465 bp):
GCTTCCAAATATAAATTTTTACTTAGATTCTTAAAATCAGACAACGATATATCACGTGACAATCA
AACATTACAAAATTCAAAACAATTAATAAAAGAAACAACTAGCTTTGGAGTCCTGGAGCCATAGA
CCTGATTTTCATGTACCATCCTTTTTTTTATAATCAAATTGAAAAATTTGAAAGAAATGTGTTAT
CATTATGTCGACTCGGATTGTCTTCCATGGTAAATGAAAGAGCCCTAAGCACAGAGTAATTAGGA
TTTTGAATTTGTAGGAGAGTTTTTGAATGACAATTTATAGGAGAATTATGGCGATATGAACAATG
TTACTATAATTTTAAACATTATAAAAAAGAAAAGAAAAACACATTTTCATGTCATTTACAAATTA
ACCAATGAAATTTTCATTTTTAAAATTGTAAAAAAATCACCCTCACGTGACATTTAAGCATTACT
AAACACCTAA
Found at i:19450 original size:33 final size:33
Alignment explanation
Indices: 19413--19519 Score: 103
Period size: 33 Copynumber: 3.2 Consensus size: 33
19403 CGCCAAGCGA
*
19413 TGGCCGGTTG-TGGCCGGACATGTCCATGTCGCG
1 TGGCCGGTTGATGGCCGGACATCTCCA-GTCGCG
*
19446 TGGCCGG-TGATGGCCGGGCATCTCCGAGTCGCG
1 TGGCCGGTTGATGGCCGGACATCTCC-AGTCGCG
* * * * *
19479 TGGCC-GATGTTGGCCGGTCTTCTCCAAGTCGCA
1 TGGCCGGTTGATGGCCGGACATCTCC-AGTCGCG
19512 TGGCCGGT
1 TGGCCGGT
19520 CACTCGCACC
Statistics
Matches: 62, Mismatches: 8, Indels: 7
0.81 0.10 0.09
Matches are distributed among these distances:
32 3 0.05
33 57 0.92
34 2 0.03
ACGTcount: A:0.09, C:0.29, G:0.38, T:0.23
Consensus pattern (33 bp):
TGGCCGGTTGATGGCCGGACATCTCCAGTCGCG
Found at i:24863 original size:6 final size:5
Alignment explanation
Indices: 24831--24865 Score: 54
Period size: 5 Copynumber: 7.0 Consensus size: 5
24821 TCTGGTCAAA
24831 ATTTT -TTTT ATTTT ATTTT ATTTT ATTTAT ATTTT
1 ATTTT ATTTT ATTTT ATTTT ATTTT ATTT-T ATTTT
24866 TCGATATAAC
Statistics
Matches: 28, Mismatches: 0, Indels: 4
0.88 0.00 0.12
Matches are distributed among these distances:
4 4 0.14
5 19 0.68
6 5 0.18
ACGTcount: A:0.20, C:0.00, G:0.00, T:0.80
Consensus pattern (5 bp):
ATTTT
Found at i:25973 original size:33 final size:33
Alignment explanation
Indices: 25936--26039 Score: 113
Period size: 33 Copynumber: 3.2 Consensus size: 33
25926 CACCAAGCGA
*
25936 TGGCCGGTTG-TGGCCGGACATGTCC-ATGTCGCG
1 TGGCCGG-TGATGGCCGGACATCTCCGA-GTCGCG
*
25969 TGGCCGGTGATGGCCGGGCATCTCCGAGTCGCG
1 TGGCCGGTGATGGCCGGACATCTCCGAGTCGCG
* * * * *
26002 TGGCCGGTGTTGGCCGGTCTTCTCCAAGTCGCA
1 TGGCCGGTGATGGCCGGACATCTCCGAGTCGCG
26035 TGGCC
1 TGGCC
26040 AGTCACTTGC
Statistics
Matches: 62, Mismatches: 7, Indels: 4
0.85 0.10 0.05
Matches are distributed among these distances:
32 2 0.03
33 59 0.95
34 1 0.02
ACGTcount: A:0.09, C:0.30, G:0.38, T:0.23
Consensus pattern (33 bp):
TGGCCGGTGATGGCCGGACATCTCCGAGTCGCG
Found at i:28169 original size:18 final size:17
Alignment explanation
Indices: 28135--28168 Score: 50
Period size: 17 Copynumber: 2.0 Consensus size: 17
28125 TTTTATTTAT
* *
28135 TTTTTTATTTTTGAAAA
1 TTTTTTAATGTTGAAAA
28152 TTTTTTAATGTTGAAAA
1 TTTTTTAATGTTGAAAA
28169 AAATCGTAAG
Statistics
Matches: 15, Mismatches: 2, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
17 15 1.00
ACGTcount: A:0.32, C:0.00, G:0.09, T:0.59
Consensus pattern (17 bp):
TTTTTTAATGTTGAAAA
Done.