Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01012361.1 Corchorus capsularis cultivar CVL-1 contig12382, 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: 24526
ACGTcount: A:0.35, C:0.17, G:0.17, T:0.32
Found at i:243 original size:21 final size:22
Alignment explanation
Indices: 205--257 Score: 74
Period size: 22 Copynumber: 2.5 Consensus size: 22
195 AAGGTATCTA
*
205 AAAAAGTAAAATGGTAATCAGT
1 AAAAAGTAAAATGATAATCAGT
227 AAAAAGTAAAA-GATAATCAGT
1 AAAAAGTAAAATGATAATCAGT
*
248 -AAGAGTAAAA
1 AAAAAGTAAAA
258 CAGTAATCGG
Statistics
Matches: 29, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
20 9 0.31
21 9 0.31
22 11 0.38
ACGTcount: A:0.60, C:0.04, G:0.17, T:0.19
Consensus pattern (22 bp):
AAAAAGTAAAATGATAATCAGT
Found at i:264 original size:21 final size:21
Alignment explanation
Indices: 209--278 Score: 70
Period size: 21 Copynumber: 3.3 Consensus size: 21
199 TATCTAAAAA
** *
209 AGTAAAATGGTAATCAGTAAAA
1 AGTAAAACAGTAATCAGT-AAG
*
231 AGTAAAAGA-TAATCAGTAAG
1 AGTAAAACAGTAATCAGTAAG
*
251 AGTAAAACAGTAATCGGTAAG
1 AGTAAAACAGTAATCAGTAAG
*
272 AGCAAAA
1 AGTAAAA
279 GCGATAATAG
Statistics
Matches: 41, Mismatches: 6, Indels: 3
0.82 0.12 0.06
Matches are distributed among these distances:
20 10 0.24
21 24 0.59
22 7 0.17
ACGTcount: A:0.54, C:0.07, G:0.20, T:0.19
Consensus pattern (21 bp):
AGTAAAACAGTAATCAGTAAG
Found at i:395 original size:29 final size:28
Alignment explanation
Indices: 370--434 Score: 89
Period size: 27 Copynumber: 2.4 Consensus size: 28
360 GTAAAAAGTG
370 GTAATAAATAAAAGAGAGTAAGAAAAGA
1 GTAATAAATAAAAGAGAGTAAGAAAAGA
***
398 GTAATTGGTAAAA-AGAGTAAGAAAAGA
1 GTAATAAATAAAAGAGAGTAAGAAAAGA
425 GTAA-AAATAA
1 GTAATAAATAA
435 TAAAAGTAGC
Statistics
Matches: 31, Mismatches: 6, Indels: 2
0.79 0.15 0.05
Matches are distributed among these distances:
26 3 0.10
27 18 0.58
28 10 0.32
ACGTcount: A:0.62, C:0.00, G:0.22, T:0.17
Consensus pattern (28 bp):
GTAATAAATAAAAGAGAGTAAGAAAAGA
Found at i:1545 original size:2 final size:2
Alignment explanation
Indices: 1538--1576 Score: 78
Period size: 2 Copynumber: 19.5 Consensus size: 2
1528 ATCCTAAGGC
1538 AT AT AT 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 AT AT AT A
1577 ACTAAACTGA
Statistics
Matches: 37, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 37 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:6356 original size:16 final size:16
Alignment explanation
Indices: 6337--6370 Score: 52
Period size: 16 Copynumber: 2.1 Consensus size: 16
6327 TTTCTATCCC
6337 TTTTC-TTTTAAATTTT
1 TTTTCGTTTT-AATTTT
6353 TTTTCGTTTTAATTTT
1 TTTTCGTTTTAATTTT
6369 TT
1 TT
6371 GCAATTTTAT
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
16 13 0.76
17 4 0.24
ACGTcount: A:0.15, C:0.06, G:0.03, T:0.76
Consensus pattern (16 bp):
TTTTCGTTTTAATTTT
Found at i:8002 original size:48 final size:48
Alignment explanation
Indices: 7950--8266 Score: 463
Period size: 48 Copynumber: 6.6 Consensus size: 48
7940 AAATCTAGCG
* * * * *
7950 CCTTCCGACCGAGAAGGGCAAAACAGGAAAGAGACACTGAAGACTGCA
1 CCTTCCGACCGGGAAGGGCAAAACTGGAAATAAACACCGAAGACTGCA
*
7998 CCTTCCGACCGGGAAGGGAAAAACTGGAAATAAACACCGAAGACTGCA
1 CCTTCCGACCGGGAAGGGCAAAACTGGAAATAAACACCGAAGACTGCA
*
8046 CCTTCCGACCGGGAAGGGCTAAACTGGAAATAAACACCGAAGACTGCA
1 CCTTCCGACCGGGAAGGGCAAAACTGGAAATAAACACCGAAGACTGCA
*
8094 CCTTCCGACCGGGAAGGGCTAAACTGGAAATAAACACCGAAGACTGCA
1 CCTTCCGACCGGGAAGGGCAAAACTGGAAATAAACACCGAAGACTGCA
* * * * *
8142 CCTTCCGACTGGGAAGGGCAAAAATGGAAATAGACACTGAAGACGGCA
1 CCTTCCGACCGGGAAGGGCAAAACTGGAAATAAACACCGAAGACTGCA
* * *
8190 CCTTCCGACCGGGAAGGGCAAAATTGGAAATAAACACTGAAAACTGCA
1 CCTTCCGACCGGGAAGGGCAAAACTGGAAATAAACACCGAAGACTGCA
* * *
8238 CCTTCTGTCCGGGAAGGGCAAAACGGGAA
1 CCTTCCGACCGGGAAGGGCAAAACTGGAA
8267 TAAGCGGATT
Statistics
Matches: 246, Mismatches: 23, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
48 246 1.00
ACGTcount: A:0.37, C:0.25, G:0.26, T:0.12
Consensus pattern (48 bp):
CCTTCCGACCGGGAAGGGCAAAACTGGAAATAAACACCGAAGACTGCA
Found at i:8816 original size:51 final size:50
Alignment explanation
Indices: 8761--8867 Score: 126
Period size: 50 Copynumber: 2.1 Consensus size: 50
8751 AGGTTGCACT
* * * *
8761 TTTATT-TCAAGTTTATCAAAATTTAAGCCTTTCTAAACTAAAGATTGTATC
1 TTTATTGTCAA-TTTACCAAAACTCAAG-CTTTCTAAACCAAAGATTGTATC
* * *
8812 TTTATTGTCAATTTACCAAAACTCAAGCTTTTTAAGCCAAAGATTGTATT
1 TTTATTGTCAATTTACCAAAACTCAAGCTTTCTAAACCAAAGATTGTATC
8862 TTTATT
1 TTTATT
8868 ATCGACTCAC
Statistics
Matches: 48, Mismatches: 7, Indels: 3
0.83 0.12 0.05
Matches are distributed among these distances:
50 25 0.52
51 19 0.40
52 4 0.08
ACGTcount: A:0.34, C:0.14, G:0.08, T:0.44
Consensus pattern (50 bp):
TTTATTGTCAATTTACCAAAACTCAAGCTTTCTAAACCAAAGATTGTATC
Found at i:8860 original size:50 final size:51
Alignment explanation
Indices: 8800--8919 Score: 143
Period size: 51 Copynumber: 2.4 Consensus size: 51
8790 TTTCTAAACT
* * * * *
8800 AAAGATTGTATCTTTATTGTCAATTTACCAAAA-CTCAAGCTTTTTAAGCC
1 AAAGATTGTATTTTTATTATCAACTCACCAAAATCTAAAGCTTTTTAAGCC
* * *
8850 AAAGATTGTATTTTTATTATCGACTCACCAAAATTTAAAGTTTTTTAAGCC
1 AAAGATTGTATTTTTATTATCAACTCACCAAAATCTAAAGCTTTTTAAGCC
**
8901 AAAGGGTGTATTTTTATTA
1 AAAGATTGTATTTTTATTA
8920 CAAACCTATC
Statistics
Matches: 59, Mismatches: 10, Indels: 1
0.84 0.14 0.01
Matches are distributed among these distances:
50 28 0.47
51 31 0.53
ACGTcount: A:0.34, C:0.13, G:0.12, T:0.41
Consensus pattern (51 bp):
AAAGATTGTATTTTTATTATCAACTCACCAAAATCTAAAGCTTTTTAAGCC
Found at i:13639 original size:2 final size:2
Alignment explanation
Indices: 13632--13702 Score: 124
Period size: 2 Copynumber: 35.5 Consensus size: 2
13622 ACTCTTTTAA
*
13632 AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AT 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
*
13674 AC AT AC AC AC AC AC AC AC AC AC AC AC AC A
1 AC AC AC AC AC AC AC AC AC AC AC AC AC AC A
13703 TATATATATA
Statistics
Matches: 65, Mismatches: 4, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
2 65 1.00
ACGTcount: A:0.51, C:0.46, G:0.00, T:0.03
Consensus pattern (2 bp):
AC
Found at i:17465 original size:42 final size:43
Alignment explanation
Indices: 17418--17507 Score: 119
Period size: 45 Copynumber: 2.1 Consensus size: 43
17408 TATTACCTAA
* * *
17418 ATTCTA-CTACGTCTCTAGGTAATTCATCAAAATAAAGTTAAT
1 ATTCTACCTACATCTCTAGATAATTCATCAAAATAAAGATAAT
*
17460 ATTCTACTCCTCCATCTCTAGATAATTCATCAAAATAAAGATAAT
1 ATTCTA--CCTACATCTCTAGATAATTCATCAAAATAAAGATAAT
17505 ATT
1 ATT
17508 AATTGTTGCT
Statistics
Matches: 41, Mismatches: 4, Indels: 3
0.85 0.08 0.06
Matches are distributed among these distances:
42 6 0.15
45 35 0.85
ACGTcount: A:0.39, C:0.19, G:0.07, T:0.36
Consensus pattern (43 bp):
ATTCTACCTACATCTCTAGATAATTCATCAAAATAAAGATAAT
Found at i:19174 original size:2 final size:2
Alignment explanation
Indices: 19169--19196 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
19159 TTATCTTTCA
19169 AT 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 AT
19197 TATTTTGAGA
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:19370 original size:16 final size:16
Alignment explanation
Indices: 19349--19383 Score: 52
Period size: 16 Copynumber: 2.2 Consensus size: 16
19339 GCCCAAACAT
*
19349 AAACTACCTGCCTACC
1 AAACTACCTACCTACC
*
19365 AAACTACTTACCTACC
1 AAACTACCTACCTACC
19381 AAA
1 AAA
19384 TAAACAAACA
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
16 17 1.00
ACGTcount: A:0.40, C:0.37, G:0.03, T:0.20
Consensus pattern (16 bp):
AAACTACCTACCTACC
Found at i:19530 original size:2 final size:2
Alignment explanation
Indices: 19525--19565 Score: 50
Period size: 2 Copynumber: 21.0 Consensus size: 2
19515 TTTTGATAGA
*
19525 AT AT AT AT AT AT AT AT AT AT TT AT AT -T AT A- AT ACT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A-T AT AT AT
19566 GAAGTAATTT
Statistics
Matches: 34, Mismatches: 2, Indels: 6
0.81 0.05 0.14
Matches are distributed among these distances:
1 2 0.06
2 30 0.88
3 2 0.06
ACGTcount: A:0.46, C:0.02, G:0.00, T:0.51
Consensus pattern (2 bp):
AT
Found at i:20774 original size:16 final size:15
Alignment explanation
Indices: 20706--20775 Score: 59
Period size: 16 Copynumber: 4.4 Consensus size: 15
20696 GTGGGCTCGA
*
20706 GTTCGGGATTTTTTGG
1 GTTCGGG-TTTTTCGG
*
20722 GTTCGGGTTTATTCAG
1 GTTCGGGTTT-TTCGG
* *
20738 GTTCAGGTTCTGTCGG
1 GTTCGGGTT-TTTCGG
*
20754 ATTCGGGTATTTTCGG
1 GTTCGGGT-TTTTCGG
20770 GTTCGG
1 GTTCGG
20776 TCTCGGCTAG
Statistics
Matches: 42, Mismatches: 9, Indels: 6
0.74 0.16 0.11
Matches are distributed among these distances:
15 3 0.07
16 37 0.88
17 2 0.05
ACGTcount: A:0.09, C:0.13, G:0.36, T:0.43
Consensus pattern (15 bp):
GTTCGGGTTTTTCGG
Found at i:20961 original size:13 final size:14
Alignment explanation
Indices: 20936--20966 Score: 55
Period size: 13 Copynumber: 2.3 Consensus size: 14
20926 AAGTTTATTG
20936 ATAATATATATAAT
1 ATAATATATATAAT
20950 ATAATA-ATATAAT
1 ATAATATATATAAT
20963 ATAA
1 ATAA
20967 CATGATTAAC
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
13 11 0.65
14 6 0.35
ACGTcount: A:0.61, C:0.00, G:0.00, T:0.39
Consensus pattern (14 bp):
ATAATATATATAAT
Found at i:20980 original size:22 final size:19
Alignment explanation
Indices: 20938--20994 Score: 55
Period size: 22 Copynumber: 2.9 Consensus size: 19
20928 GTTTATTGAT
* *
20938 AATATATAT-AATA-TAAT
1 AATATATATAAAGATTAAC
20955 AATATAATATAACATGATTAAC
1 AATAT-ATATAA-A-GATTAAC
20977 AATATATATAAAGATTAA
1 AATATATATAAAGATTAA
20995 ATAATTGTTA
Statistics
Matches: 33, Mismatches: 2, Indels: 8
0.77 0.05 0.19
Matches are distributed among these distances:
17 5 0.15
18 4 0.12
19 7 0.21
20 2 0.06
21 7 0.21
22 8 0.24
ACGTcount: A:0.58, C:0.04, G:0.04, T:0.35
Consensus pattern (19 bp):
AATATATATAAAGATTAAC
Found at i:23084 original size:2 final size:2
Alignment explanation
Indices: 23077--23106 Score: 60
Period size: 2 Copynumber: 15.0 Consensus size: 2
23067 ACCGGGTCAC
23077 AT AT 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 AT AT
23107 CGGGTCATTT
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 28 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:24420 original size:33 final size:33
Alignment explanation
Indices: 24378--24440 Score: 99
Period size: 33 Copynumber: 1.9 Consensus size: 33
24368 GATGGTTCAG
*
24378 CCACGGCGGAGCCTCCACATTGGGGAGGCTCAA
1 CCACGGCGGAGCCTCCACACTGGGGAGGCTCAA
* *
24411 CCACGGCGGAGCCTCCCCACTGGGGCGGCT
1 CCACGGCGGAGCCTCCACACTGGGGAGGCT
24441 TCGCCATGGC
Statistics
Matches: 27, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
33 27 1.00
ACGTcount: A:0.16, C:0.38, G:0.35, T:0.11
Consensus pattern (33 bp):
CCACGGCGGAGCCTCCACACTGGGGAGGCTCAA
Found at i:24475 original size:32 final size:32
Alignment explanation
Indices: 24434--24523 Score: 153
Period size: 32 Copynumber: 2.8 Consensus size: 32
24424 TCCCCACTGG
* *
24434 GGCGGCTTCGCCATGGCAAGCCGCCCTCATGA
1 GGCGGCTTCGCCACGGCAGGCCGCCCTCATGA
24466 GGCGGCTTCGCCACGGCAGGCCGCCCTCATGA
1 GGCGGCTTCGCCACGGCAGGCCGCCCTCATGA
*
24498 GGCGGCTTTGCCACGGCAGGCCGCCC
1 GGCGGCTTCGCCACGGCAGGCCGCCC
24524 CGG
Statistics
Matches: 55, Mismatches: 3, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
32 55 1.00
ACGTcount: A:0.12, C:0.40, G:0.34, T:0.13
Consensus pattern (32 bp):
GGCGGCTTCGCCACGGCAGGCCGCCCTCATGA
Done.