Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01009074.1 Corchorus capsularis cultivar CVL-1 contig09095, 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: 40578
ACGTcount: A:0.34, C:0.19, G:0.17, T:0.31
Found at i:6288 original size:2 final size:2
Alignment explanation
Indices: 6281--6328 Score: 96
Period size: 2 Copynumber: 24.0 Consensus size: 2
6271 GTGCGCTTGT
6281 GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA
1 GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA
6323 GA GA GA
1 GA GA GA
6329 ACCTGCTAAG
Statistics
Matches: 46, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 46 1.00
ACGTcount: A:0.50, C:0.00, G:0.50, T:0.00
Consensus pattern (2 bp):
GA
Found at i:9516 original size:2 final size:2
Alignment explanation
Indices: 9511--9561 Score: 102
Period size: 2 Copynumber: 25.5 Consensus size: 2
9501 TATATACATT
9511 AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC
1 AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC
9553 AC AC AC AC A
1 AC AC AC AC A
9562 TATATAGGAA
Statistics
Matches: 49, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 49 1.00
ACGTcount: A:0.51, C:0.49, G:0.00, T:0.00
Consensus pattern (2 bp):
AC
Found at i:9973 original size:36 final size:37
Alignment explanation
Indices: 9909--9978 Score: 124
Period size: 36 Copynumber: 1.9 Consensus size: 37
9899 GAATATCGTG
*
9909 AATAAAATGTGTCTTGGGATTCACTCACTCCCACACT
1 AATAAAATGTGTCTTGAGATTCACTCACTCCCACACT
9946 AATAAAATGTGTCTT-AGATTCACTCACTCCCAC
1 AATAAAATGTGTCTTGAGATTCACTCACTCCCAC
9979 GCTTTCTCTA
Statistics
Matches: 32, Mismatches: 1, Indels: 1
0.94 0.03 0.03
Matches are distributed among these distances:
36 17 0.53
37 15 0.47
ACGTcount: A:0.31, C:0.27, G:0.11, T:0.30
Consensus pattern (37 bp):
AATAAAATGTGTCTTGAGATTCACTCACTCCCACACT
Found at i:11519 original size:19 final size:18
Alignment explanation
Indices: 11490--11546 Score: 57
Period size: 19 Copynumber: 3.2 Consensus size: 18
11480 CGATTGGCCA
11490 AAAAGAAAGAAAGAGAGAG
1 AAAA-AAAGAAAGAGAGAG
11509 AAGAAAAAGAAA-A-AG-G
1 AA-AAAAAGAAAGAGAGAG
*
11525 AAAGAAAGAAAGAAGAGAG
1 AAAAAAAGAAAG-AGAGAG
11544 AAA
1 AAA
11547 CTACCTGTGG
Statistics
Matches: 32, Mismatches: 1, Indels: 10
0.74 0.02 0.23
Matches are distributed among these distances:
15 8 0.25
16 3 0.09
17 3 0.09
18 3 0.09
19 13 0.41
20 2 0.06
ACGTcount: A:0.72, C:0.00, G:0.28, T:0.00
Consensus pattern (18 bp):
AAAAAAAGAAAGAGAGAG
Found at i:13573 original size:24 final size:24
Alignment explanation
Indices: 13546--13595 Score: 100
Period size: 24 Copynumber: 2.1 Consensus size: 24
13536 TATATATATC
13546 ATAACATATATATTAAAGTTGAAA
1 ATAACATATATATTAAAGTTGAAA
13570 ATAACATATATATTAAAGTTGAAA
1 ATAACATATATATTAAAGTTGAAA
13594 AT
1 AT
13596 GAAATTATCC
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
24 26 1.00
ACGTcount: A:0.54, C:0.04, G:0.08, T:0.34
Consensus pattern (24 bp):
ATAACATATATATTAAAGTTGAAA
Found at i:16195 original size:34 final size:34
Alignment explanation
Indices: 16149--16270 Score: 103
Period size: 32 Copynumber: 3.7 Consensus size: 34
16139 TCTTAAAGTG
*
16149 AACGCCGCCATATAGGGGCGTTTATGTCAAGTAA
1 AACGCCGACATATAGGGGCGTTTATGTCAAGTAA
* *
16183 AACGCCGGCATATGGGGGCGTTGTA-G-CAA-TAGA
1 AACGCCGACATATAGGGGCGTT-TATGTCAAGTA-A
* * ** *
16216 AACACCGTA-ATTTAGGGGCGTTTATGTTTAG--G
1 AACGCCG-ACATATAGGGGCGTTTATGTCAAGTAA
16248 AACGCCGACATATAGGGGCGTTT
1 AACGCCGACATATAGGGGCGTTT
16271 GATAAGTTGA
Statistics
Matches: 70, Mismatches: 11, Indels: 16
0.72 0.11 0.16
Matches are distributed among these distances:
31 1 0.01
32 23 0.33
33 22 0.31
34 22 0.31
35 2 0.03
ACGTcount: A:0.27, C:0.18, G:0.30, T:0.25
Consensus pattern (34 bp):
AACGCCGACATATAGGGGCGTTTATGTCAAGTAA
Found at i:17817 original size:222 final size:222
Alignment explanation
Indices: 17421--17990 Score: 856
Period size: 222 Copynumber: 2.6 Consensus size: 222
17411 GCAAAGGATT
** * ** *
17421 CATCCAATTCAGCCATCAAACC-AAGATCACATATTCTGATTTTGCTAATGTTTTTTAAGCTAAA
1 CATCCAATTCAGCCATC-AACCAAAGATCACATATTCTGA-TTTAATCACATTTTTCAAGCTAAA
* *
17485 TTGAGCCAAAACTCAACACCATATCAAACACAATGCATCAACCAACAAAACAAAACTTTTTTGCA
64 CTGAGCCAAAACTCAACACCATCTCAAACACAATGCATCAACCAACAAAACAAAACTTTTTTGCA
* *
17550 ATAATTTTGTATCTCCTAAGATGCATTTAAACAACTCTCAATCACACAAGCACGATCATAATATA
129 ATAATTCTGTATCTCCTAAGATGCATTTAAACAACTCACAATCACACAAGCACGATCATAATATA
* *
17615 CTACTCAGGTCCAATAAAGGACTGAACAA
194 CTACTCAAGTCCAACAAAGGACTGAACAA
* *
17644 CATTCAATTCAGCCATCAACCAAAGATCACATATTCTGATTTAATCACATTATTCAAGCTAAACT
1 CATCCAATTCAGCCATCAACCAAAGATCACATATTCTGATTTAATCACATTTTTCAAGCTAAACT
* *
17709 GAGCCAAAACTCAACACCATCTCAAACACAATGCATCAACCAACAAAACAAACCTTTTTTGTAAT
66 GAGCCAAAACTCAACACCATCTCAAACACAATGCATCAACCAACAAAACAAAACTTTTTTGCAAT
* * *
17774 AATTCTGTATCATGCT-ATATGCATTTAAACAACTCAGAATCACACAAGCACGATCATAATATAC
131 AATTCTGTATC-TCCTAAGATGCATTTAAACAACTCACAATCACACAAGCACGATCATAATATAC
* *
17838 TACTCAAGTCCAGCAAAGGATTGAACAA
195 TACTCAAGTCCAACAAAGGACTGAACAA
* * * *
17866 CATCCAATTTAGCCATCAAGCAAAGATCACATATTCTCATTTAAGCACATTTTTCAAGCTAAACT
1 CATCCAATTCAGCCATCAACCAAAGATCACATATTCTGATTTAATCACATTTTTCAAGCTAAACT
* *
17931 GAGTCAAAACTCAACACCATCTCAAACACAATGCATCAACCAAGAAAACAAAACTTTTTT
66 GAGCCAAAACTCAACACCATCTCAAACACAATGCATCAACCAACAAAACAAAACTTTTTT
17991 CAGAAAATTG
Statistics
Matches: 315, Mismatches: 30, Indels: 5
0.90 0.09 0.01
Matches are distributed among these distances:
222 279 0.89
223 36 0.11
ACGTcount: A:0.41, C:0.25, G:0.08, T:0.26
Consensus pattern (222 bp):
CATCCAATTCAGCCATCAACCAAAGATCACATATTCTGATTTAATCACATTTTTCAAGCTAAACT
GAGCCAAAACTCAACACCATCTCAAACACAATGCATCAACCAACAAAACAAAACTTTTTTGCAAT
AATTCTGTATCTCCTAAGATGCATTTAAACAACTCACAATCACACAAGCACGATCATAATATACT
ACTCAAGTCCAACAAAGGACTGAACAA
Found at i:25329 original size:20 final size:21
Alignment explanation
Indices: 25304--25342 Score: 71
Period size: 21 Copynumber: 1.9 Consensus size: 21
25294 ACTAGCGTTG
25304 GGCG-CCCATGTGGTTTGCTT
1 GGCGCCCCATGTGGTTTGCTT
25324 GGCGCCCCATGTGGTTTGC
1 GGCGCCCCATGTGGTTTGC
25343 CTCGCAACCC
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
20 4 0.22
21 14 0.78
ACGTcount: A:0.05, C:0.28, G:0.36, T:0.31
Consensus pattern (21 bp):
GGCGCCCCATGTGGTTTGCTT
Found at i:25353 original size:21 final size:21
Alignment explanation
Indices: 25308--25356 Score: 62
Period size: 21 Copynumber: 2.3 Consensus size: 21
25298 GCGTTGGGCG
* * **
25308 CCCATGTGGTTTGCTTGGCGC
1 CCCATGTGGTTTGCCTCGCAA
25329 CCCATGTGGTTTGCCTCGCAA
1 CCCATGTGGTTTGCCTCGCAA
25350 CCCATGT
1 CCCATGT
25357 ACTCCAGTGC
Statistics
Matches: 24, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
21 24 1.00
ACGTcount: A:0.10, C:0.33, G:0.27, T:0.31
Consensus pattern (21 bp):
CCCATGTGGTTTGCCTCGCAA
Found at i:26436 original size:5 final size:5
Alignment explanation
Indices: 26426--26465 Score: 52
Period size: 5 Copynumber: 8.8 Consensus size: 5
26416 AATTAATATT
26426 TTTTA TTTTA TTTTA -TTTA -TTTA -TTTA -TTTA TTTTA TTTT
1 TTTTA TTTTA TTTTA TTTTA TTTTA TTTTA TTTTA TTTTA TTTT
26466 TTTAAGCAAG
Statistics
Matches: 34, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
4 16 0.47
5 18 0.53
ACGTcount: A:0.20, C:0.00, G:0.00, T:0.80
Consensus pattern (5 bp):
TTTTA
Found at i:26446 original size:4 final size:4
Alignment explanation
Indices: 26422--26469 Score: 53
Period size: 4 Copynumber: 11.5 Consensus size: 4
26412 GATTAATTAA
*
26422 TATT T-TT TATTT TATTT TATT TATT TATT TATT TATTT TATT TTTT TA
1 TATT TATT TA-TT TA-TT TATT TATT TATT TATT TA-TT TATT TATT TA
26470 AGCAAGAAAA
Statistics
Matches: 39, Mismatches: 2, Indels: 6
0.83 0.04 0.13
Matches are distributed among these distances:
3 3 0.08
4 23 0.59
5 13 0.33
ACGTcount: A:0.21, C:0.00, G:0.00, T:0.79
Consensus pattern (4 bp):
TATT
Found at i:26452 original size:17 final size:18
Alignment explanation
Indices: 26422--26469 Score: 59
Period size: 17 Copynumber: 2.8 Consensus size: 18
26412 GATTAATTAA
26422 TATTT-TTTATTTTATTT
1 TATTTATTTATTTTATTT
26439 TATTTATTTA-TTTA-TT
1 TATTTATTTATTTTATTT
26455 TATTTTATTT-TTTTA
1 TA-TTTATTTATTTTA
26470 AGCAAGAAAA
Statistics
Matches: 28, Mismatches: 0, Indels: 6
0.82 0.00 0.18
Matches are distributed among these distances:
16 4 0.14
17 20 0.71
18 4 0.14
ACGTcount: A:0.21, C:0.00, G:0.00, T:0.79
Consensus pattern (18 bp):
TATTTATTTATTTTATTT
Found at i:26456 original size:21 final size:22
Alignment explanation
Indices: 26422--26469 Score: 73
Period size: 21 Copynumber: 2.3 Consensus size: 22
26412 GATTAATTAA
26422 TATTT-TTTATTTTATTTTATT
1 TATTTATTTATTTTATTTTATT
26443 TATTTATTTA-TTTATTTTATT
1 TATTTATTTATTTTATTTTATT
*
26464 TTTTTA
1 TATTTA
26470 AGCAAGAAAA
Statistics
Matches: 25, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
21 21 0.84
22 4 0.16
ACGTcount: A:0.21, C:0.00, G:0.00, T:0.79
Consensus pattern (22 bp):
TATTTATTTATTTTATTTTATT
Found at i:33588 original size:21 final size:21
Alignment explanation
Indices: 33543--33591 Score: 62
Period size: 21 Copynumber: 2.3 Consensus size: 21
33533 GCGTTGGGCG
* * * *
33543 CCCATGTGGTTTGCTTGGCGC
1 CCCATGTGGTTAGCCTCGCGA
33564 CCCATGTGGTTAGCCTCGCGA
1 CCCATGTGGTTAGCCTCGCGA
33585 CCCATGT
1 CCCATGT
33592 ACTCCAGTGC
Statistics
Matches: 24, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
21 24 1.00
ACGTcount: A:0.10, C:0.33, G:0.29, T:0.29
Consensus pattern (21 bp):
CCCATGTGGTTAGCCTCGCGA
Found at i:34598 original size:19 final size:20
Alignment explanation
Indices: 34561--34598 Score: 51
Period size: 20 Copynumber: 1.9 Consensus size: 20
34551 TATTATAATT
* *
34561 AAAATCAATCTCATGTTTCA
1 AAAATAAATCTCATATTTCA
34581 AAAATAAATCTCA-ATTTC
1 AAAATAAATCTCATATTTC
34599 TAGATGGATA
Statistics
Matches: 16, Mismatches: 2, Indels: 1
0.84 0.11 0.05
Matches are distributed among these distances:
19 4 0.25
20 12 0.75
ACGTcount: A:0.45, C:0.18, G:0.03, T:0.34
Consensus pattern (20 bp):
AAAATAAATCTCATATTTCA
Found at i:36843 original size:68 final size:70
Alignment explanation
Indices: 36759--36908 Score: 232
Period size: 68 Copynumber: 2.1 Consensus size: 70
36749 CCATAATTAA
* *
36759 CAAATTAAAGTCACGTTAGTGGTATATATGTGTGATGATCTATAACGTTTATT-A-ATTTCTAAA
1 CAAATTAAAGTAACGTTAGTGGTATATATATGTGATGATCTATAACGTTTATTAAGATTTCTAAA
36822 TAATT
66 TAATT
*
36827 CAAATTAGAGTAACGTTAGTGGTATATATATGTGATGATCTATAACGTTTATTAAAGGATTTCTA
1 CAAATTAAAGTAACGTTAGTGGTATATATATGTGATGATCTATAACGTTTATT-AA-GATTTCTA
36892 AATAATT
64 AATAATT
*
36899 GAAATTAAAG
1 CAAATTAAAG
36909 GATTAAAGAG
Statistics
Matches: 73, Mismatches: 5, Indels: 4
0.89 0.06 0.05
Matches are distributed among these distances:
68 50 0.68
70 1 0.01
72 22 0.30
ACGTcount: A:0.38, C:0.07, G:0.16, T:0.39
Consensus pattern (70 bp):
CAAATTAAAGTAACGTTAGTGGTATATATATGTGATGATCTATAACGTTTATTAAGATTTCTAAA
TAATT
Found at i:36976 original size:2 final size:2
Alignment explanation
Indices: 36969--37012 Score: 72
Period size: 2 Copynumber: 22.5 Consensus size: 2
36959 TCAAAAATAC
*
36969 AT AT AT AT AT AT AT TT AT A- 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 AT AT AT AT AT
37010 AT A
1 AT A
37013 GATAGATAGA
Statistics
Matches: 39, Mismatches: 2, Indels: 2
0.91 0.05 0.05
Matches are distributed among these distances:
1 1 0.03
2 38 0.97
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:37984 original size:32 final size:32
Alignment explanation
Indices: 37938--37999 Score: 106
Period size: 32 Copynumber: 1.9 Consensus size: 32
37928 AAATGATATG
*
37938 ACATGAAATCTAAACCCTAAGTGAGATAAAAT
1 ACATGAAATATAAACCCTAAGTGAGATAAAAT
*
37970 ACATGATATATAAACCCTAAGTGAGATAAA
1 ACATGAAATATAAACCCTAAGTGAGATAAA
38000 GAAATGCCCC
Statistics
Matches: 28, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
32 28 1.00
ACGTcount: A:0.50, C:0.15, G:0.13, T:0.23
Consensus pattern (32 bp):
ACATGAAATATAAACCCTAAGTGAGATAAAAT
Done.