Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01007038.1 Corchorus capsularis cultivar CVL-1 contig07059, 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: 50567
ACGTcount: A:0.32, C:0.19, G:0.17, T:0.32
Found at i:15114 original size:36 final size:35
Alignment explanation
Indices: 15074--15141 Score: 127
Period size: 36 Copynumber: 1.9 Consensus size: 35
15064 TTTTTTTCGC
15074 AAACCTTTTTTTTTTTAGAAAAAATCGGAAAAAGTA
1 AAACCTTTTTTTTTTTAGAAAAAA-CGGAAAAAGTA
15110 AAACCTTTTTTTTTTTAGAAAAAACGGAAAAA
1 AAACCTTTTTTTTTTTAGAAAAAACGGAAAAA
15142 CAAAAACTAA
Statistics
Matches: 32, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
35 8 0.25
36 24 0.75
ACGTcount: A:0.46, C:0.09, G:0.10, T:0.35
Consensus pattern (35 bp):
AAACCTTTTTTTTTTTAGAAAAAACGGAAAAAGTA
Found at i:17886 original size:21 final size:21
Alignment explanation
Indices: 17862--17903 Score: 57
Period size: 21 Copynumber: 2.0 Consensus size: 21
17852 CCCTGTAATC
* *
17862 ATCATTCCTGTATCTTTCTCT
1 ATCATTCCTGAATCTGTCTCT
*
17883 ATCATTTCTGAATCTGTCTCT
1 ATCATTCCTGAATCTGTCTCT
17904 TTTGTAGCCT
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
21 18 1.00
ACGTcount: A:0.17, C:0.26, G:0.07, T:0.50
Consensus pattern (21 bp):
ATCATTCCTGAATCTGTCTCT
Found at i:20772 original size:21 final size:21
Alignment explanation
Indices: 20722--20761 Score: 62
Period size: 21 Copynumber: 1.9 Consensus size: 21
20712 TTTGGATAAG
*
20722 TAAATTATTTTACTTAATTAA
1 TAAATAATTTTACTTAATTAA
*
20743 TAAATAATTTTATTTAATT
1 TAAATAATTTTACTTAATT
20762 GAATGAAAAT
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
21 17 1.00
ACGTcount: A:0.42, C:0.03, G:0.00, T:0.55
Consensus pattern (21 bp):
TAAATAATTTTACTTAATTAA
Found at i:22773 original size:14 final size:15
Alignment explanation
Indices: 22744--22775 Score: 57
Period size: 15 Copynumber: 2.2 Consensus size: 15
22734 CCGCTGTTCT
22744 TTTTTTTTTTCTTTC
1 TTTTTTTTTTCTTTC
22759 TTTTTTTTTTC-TTC
1 TTTTTTTTTTCTTTC
22773 TTT
1 TTT
22776 AAAGGCTTTT
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
14 6 0.35
15 11 0.65
ACGTcount: A:0.00, C:0.12, G:0.00, T:0.88
Consensus pattern (15 bp):
TTTTTTTTTTCTTTC
Found at i:23491 original size:125 final size:126
Alignment explanation
Indices: 23214--23581 Score: 564
Period size: 125 Copynumber: 2.9 Consensus size: 126
23204 ATTTTGTTAC
23214 AAAATAGGATATTGTTTTTCATAAGGTTTAGCCCCAAATTAATTAAATGAAAGAAATTATAGGGT
1 AAAATAGGATATTGTTTTTCATAAGGTTTAGCCCCAAATTAATTAAATGAAAGAAATTATAGGGT
*
23279 TGATCATTTTTTGAAATATTTATAGGACTAGGGTTTTAGATTTTTTATTAAAAAACTCCTT
66 TGGTCATTTTTTGAAATATTTATAGGACTAGGGTTTTAGATTTTTTATTAAAAAACTCCTT
* *
23340 AAAATAGGATATTGTTTTTTAGAAGGTTTAGCCCCAAATTAATTAAATGAAAGAAATTATAGGGT
1 AAAATAGGATATTGTTTTTCATAAGGTTTAGCCCCAAATTAATTAAATGAAAGAAATTATAGGGT
*
23405 TGGT-ATTTTTTGAAATATTTATAGGACTAGGGTTTTAGATTTTTTATTAAAAAGCTCCTT
66 TGGTCATTTTTTGAAATATTTATAGGACTAGGGTTTTAGATTTTTTATTAAAAAACTCCTT
* * * *
23465 AAAATAGGATATAGTTTTTCATAAGGTTTAACCCCAAATTAA-TATAAGGAAATAAATTATAGGG
1 AAAATAGGATATTGTTTTTCATAAGGTTTAGCCCCAAATTAATTA-AATGAAAGAAATTATAGGG
** * * * * *
23529 TAAGTCCTATTTTG--ATATATATAGAACTAGGGTTTTAGATTATTTATTAAAAA
65 TTGGTCATTTTTTGAAATATTTATAGGACTAGGGTTTTAGATTTTTTATTAAAAA
23582 TTTTAAATTA
Statistics
Matches: 223, Mismatches: 17, Indels: 6
0.91 0.07 0.02
Matches are distributed among these distances:
124 38 0.17
125 113 0.51
126 72 0.32
ACGTcount: A:0.38, C:0.07, G:0.16, T:0.39
Consensus pattern (126 bp):
AAAATAGGATATTGTTTTTCATAAGGTTTAGCCCCAAATTAATTAAATGAAAGAAATTATAGGGT
TGGTCATTTTTTGAAATATTTATAGGACTAGGGTTTTAGATTTTTTATTAAAAAACTCCTT
Found at i:26592 original size:21 final size:20
Alignment explanation
Indices: 26543--26602 Score: 68
Period size: 19 Copynumber: 3.0 Consensus size: 20
26533 TAAAATGTAG
26543 TCACTATTTGGTGTAAT-AA
1 TCACTATTTGGTGTAATGAA
* *
26562 TCACAATTTGGTGTAATGGTA
1 TCACTATTTGGTGTAAT-GAA
* *
26583 TCACTTTTTGGTATAATGAA
1 TCACTATTTGGTGTAATGAA
26603 AATTATCATG
Statistics
Matches: 33, Mismatches: 6, Indels: 3
0.79 0.14 0.07
Matches are distributed among these distances:
19 16 0.48
20 2 0.06
21 15 0.45
ACGTcount: A:0.30, C:0.10, G:0.18, T:0.42
Consensus pattern (20 bp):
TCACTATTTGGTGTAATGAA
Found at i:30439 original size:1 final size:1
Alignment explanation
Indices: 30433--30471 Score: 78
Period size: 1 Copynumber: 39.0 Consensus size: 1
30423 ATATCTTCTG
30433 TTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTT
1 TTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTT
30472 ATCTTTTCGA
Statistics
Matches: 38, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
1 38 1.00
ACGTcount: A:0.00, C:0.00, G:0.00, T:1.00
Consensus pattern (1 bp):
T
Found at i:34175 original size:58 final size:58
Alignment explanation
Indices: 34061--34175 Score: 158
Period size: 58 Copynumber: 2.0 Consensus size: 58
34051 GGAGCCGATC
* *
34061 GACATCATTCATTATCGGCAATAAGACCCCACGGGCTATAAGACCGATCGACGCACAT
1 GACATCATCCATTATCGGCAATAAGACCCCACGGGCTATAAGACCGATCAACGCACAT
* * ** * *
34119 GACATCATCCATTGTCGGCAATAAGACCTCATTGGCTATAAGACCGTTCAATGCACA
1 GACATCATCCATTATCGGCAATAAGACCCCACGGGCTATAAGACCGATCAACGCACA
34176 CGACTCAGTT
Statistics
Matches: 49, Mismatches: 8, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
58 49 1.00
ACGTcount: A:0.32, C:0.28, G:0.18, T:0.22
Consensus pattern (58 bp):
GACATCATCCATTATCGGCAATAAGACCCCACGGGCTATAAGACCGATCAACGCACAT
Found at i:36906 original size:20 final size:20
Alignment explanation
Indices: 36859--36899 Score: 82
Period size: 20 Copynumber: 2.0 Consensus size: 20
36849 GACAGTGTAC
36859 TACTACAAATATTAATCACT
1 TACTACAAATATTAATCACT
36879 TACTACAAATATTAATCACT
1 TACTACAAATATTAATCACT
36899 T
1 T
36900 GGTACAATGA
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 21 1.00
ACGTcount: A:0.44, C:0.20, G:0.00, T:0.37
Consensus pattern (20 bp):
TACTACAAATATTAATCACT
Found at i:38345 original size:2 final size:2
Alignment explanation
Indices: 38340--38373 Score: 68
Period size: 2 Copynumber: 17.0 Consensus size: 2
38330 TACTCATAAT
38340 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
38374 CTTTGAGGGG
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 32 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:39872 original size:28 final size:28
Alignment explanation
Indices: 39841--39894 Score: 108
Period size: 28 Copynumber: 1.9 Consensus size: 28
39831 GCTTAAAACG
39841 TTTTAGTTTACATAAATAGGATTTGACA
1 TTTTAGTTTACATAAATAGGATTTGACA
39869 TTTTAGTTTACATAAATAGGATTTGA
1 TTTTAGTTTACATAAATAGGATTTGA
39895 GTAATTTTGG
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
28 26 1.00
ACGTcount: A:0.35, C:0.06, G:0.15, T:0.44
Consensus pattern (28 bp):
TTTTAGTTTACATAAATAGGATTTGACA
Found at i:41867 original size:16 final size:15
Alignment explanation
Indices: 41848--41877 Score: 51
Period size: 15 Copynumber: 1.9 Consensus size: 15
41838 GATAAAAAAA
41848 CAAAAAGGAAAAAACT
1 CAAAAA-GAAAAAACT
41864 CAAAAAGAAAAAAC
1 CAAAAAGAAAAAAC
41878 AACAAACAAA
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 8 0.57
16 6 0.43
ACGTcount: A:0.73, C:0.13, G:0.10, T:0.03
Consensus pattern (15 bp):
CAAAAAGAAAAAACT
Found at i:41883 original size:16 final size:16
Alignment explanation
Indices: 41841--41892 Score: 56
Period size: 16 Copynumber: 3.3 Consensus size: 16
41831 GATAAGAGAT
41841 AAAAA-AACAAAAAGGA
1 AAAAACAACAAAAA-GA
*
41857 AAAAAC-TCAAAAAGA
1 AAAAACAACAAAAAGA
41872 AAAAACAACAAACAA-A
1 AAAAACAACAAA-AAGA
41888 AAAAA
1 AAAAA
41893 ATATAAAAAT
Statistics
Matches: 31, Mismatches: 2, Indels: 6
0.79 0.05 0.15
Matches are distributed among these distances:
15 8 0.26
16 21 0.68
17 2 0.06
ACGTcount: A:0.81, C:0.12, G:0.06, T:0.02
Consensus pattern (16 bp):
AAAAACAACAAAAAGA
Found at i:44341 original size:51 final size:51
Alignment explanation
Indices: 44282--44392 Score: 186
Period size: 51 Copynumber: 2.2 Consensus size: 51
44272 TGGATTTTTA
* *
44282 AAATAAAGATTAAATGTTTAAGTGGAAGATTTAATCTTTTAAGTAATTTGT
1 AAATAAAGATTAAATGTTTAAGTGAAAGATTGAATCTTTTAAGTAATTTGT
*
44333 AAATAAAGATTAAATGTTTAAGTGAAAGATTGAATCTTTTAGGTAATTTGT
1 AAATAAAGATTAAATGTTTAAGTGAAAGATTGAATCTTTTAAGTAATTTGT
*
44384 GAATAAAGA
1 AAATAAAGA
44393 CTGAATTTTT
Statistics
Matches: 56, Mismatches: 4, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
51 56 1.00
ACGTcount: A:0.43, C:0.02, G:0.17, T:0.38
Consensus pattern (51 bp):
AAATAAAGATTAAATGTTTAAGTGAAAGATTGAATCTTTTAAGTAATTTGT
Found at i:44392 original size:31 final size:30
Alignment explanation
Indices: 44357--44450 Score: 74
Period size: 31 Copynumber: 3.2 Consensus size: 30
44347 TGTTTAAGTG
44357 AAAGATTGAATCTTTTAGGTAATTTGTGAAT
1 AAAGATTGAATCTTTTA-GTAATTTGTGAAT
* * *
44388 AAAGACTGAAT-TTTT--T-CTTT-TGAGT
1 AAAGATTGAATCTTTTAGTAATTTGTGAAT
*
44413 GAAA-ATTTGAATCTTTTAAGTAATTAGTGAAT
1 -AAAGA-TTGAATCTTTT-AGTAATTTGTGAAT
44445 AAAGAT
1 AAAGAT
44451 GTAACCTTTG
Statistics
Matches: 47, Mismatches: 7, Indels: 18
0.65 0.10 0.25
Matches are distributed among these distances:
25 5 0.11
26 11 0.23
27 5 0.11
30 5 0.11
31 16 0.34
32 5 0.11
ACGTcount: A:0.37, C:0.04, G:0.17, T:0.41
Consensus pattern (30 bp):
AAAGATTGAATCTTTTAGTAATTTGTGAAT
Found at i:44474 original size:51 final size:49
Alignment explanation
Indices: 44406--44580 Score: 142
Period size: 50 Copynumber: 3.5 Consensus size: 49
44396 AATTTTTTCT
* *
44406 TTTGAGTGAAAA-TTTGAATCTTTTAAGTAATTAGTGAATAAAGATGTAACC
1 TTTGAGT-AAAAGATTGAA-CTTTTAAGTAATTTGTGAATAAAGATG-AACC
* * * *
44457 TTTGAGTAAAAGATTGAACTTTTAAGTGA-TTG-GAAGATAAAAATGCCATC
1 TTTGAGTAAAAGATTGAACTTTTAAGTAATTTGTG-A-ATAAAGATG-AACC
** * *
44507 TTTGAGTAAAA-ATTGAACTTTTAAGCGATTTGTAAATAAAAAATGAGACC
1 TTTGAGTAAAAGATTGAACTTTTAAGTAATTTGTGAAT-AAAGATGA-ACC
*
44557 TTTGAATTAAAAGATTGAACTTTT
1 TTTG-AGTAAAAGATTGAACTTTT
44581 GATGAAAATG
Statistics
Matches: 103, Mismatches: 12, Indels: 17
0.78 0.09 0.13
Matches are distributed among these distances:
48 1 0.01
49 21 0.20
50 52 0.50
51 18 0.17
52 11 0.11
ACGTcount: A:0.41, C:0.07, G:0.17, T:0.35
Consensus pattern (49 bp):
TTTGAGTAAAAGATTGAACTTTTAAGTAATTTGTGAATAAAGATGAACC
Found at i:44497 original size:50 final size:49
Alignment explanation
Indices: 44442--44580 Score: 156
Period size: 50 Copynumber: 2.8 Consensus size: 49
44432 GTAATTAGTG
* *
44442 AATAAAGATGTAACCTTTGAGTAAAAGATTGAACTTTTAAGTGA-TTGGA
1 AATAAAAATG-AACCTTTGAGTAAAAGATTGAACTTTTAAGCGATTTGGA
* * *
44491 AGATAAAAATGCCATCTTTGAGTAAAA-ATTGAACTTTTAAGCGATTTGTA
1 A-ATAAAAATG-AACCTTTGAGTAAAAGATTGAACTTTTAAGCGATTTGGA
*
44541 AATAAAAAATGAGACCTTTGAATTAAAAGATTGAACTTTT
1 AAT-AAAAATGA-ACCTTTG-AGTAAAAGATTGAACTTTT
44581 GATGAAAATG
Statistics
Matches: 75, Mismatches: 9, Indels: 9
0.81 0.10 0.10
Matches are distributed among these distances:
49 19 0.25
50 39 0.52
51 6 0.08
52 11 0.15
ACGTcount: A:0.42, C:0.08, G:0.17, T:0.33
Consensus pattern (49 bp):
AATAAAAATGAACCTTTGAGTAAAAGATTGAACTTTTAAGCGATTTGGA
Found at i:45452 original size:49 final size:49
Alignment explanation
Indices: 45321--45805 Score: 629
Period size: 49 Copynumber: 10.0 Consensus size: 49
45311 TTCCCAATTT
* * * **
45321 GCCCTTCCTAGACGGAAGCCATTTA-TTTTACCTGCTATTTCCCAAAAT
1 GCCCTTCCCAGACGGAAGCCATTCATTTTTACTTGCTATTTCCCAAAGC
* *
45369 GCCCTTCCCACAGACGGAAGCCATTTATTTTTACTTTCTATTTCCCAAAGC
1 GCCCTT-CC-CAGACGGAAGCCATTCATTTTTACTTGCTATTTCCCAAAGC
* *
45420 GCCCTTCCTAGACGGAAGCCATGCATTTTTACTTGCTATTTCCCAAAGC
1 GCCCTTCCCAGACGGAAGCCATTCATTTTTACTTGCTATTTCCCAAAGC
* *
45469 GCTCTTCCCAGACGGAAGCCATTTATTTTTACTTGCTATTTCCCAAAGC
1 GCCCTTCCCAGACGGAAGCCATTCATTTTTACTTGCTATTTCCCAAAGC
* * *
45518 GCCCTTCCCAGACGGAAGCCATTTATTTTTGCTTGCTATTTCCCAAAAC
1 GCCCTTCCCAGACGGAAGCCATTCATTTTTACTTGCTATTTCCCAAAGC
* * * * *
45567 GCCCTTCCTAGACGGAAGCCATTCATCTTTACTTTCTATCTCCCAAAAC
1 GCCCTTCCCAGACGGAAGCCATTCATTTTTACTTGCTATTTCCCAAAGC
* *
45616 ACCCTTCCCAGATGGAAGCCATTCATTTTTACTTGCTATTTCCCAAAGC
1 GCCCTTCCCAGACGGAAGCCATTCATTTTTACTTGCTATTTCCCAAAGC
*
45665 GCCCTTCCCAGATGGAAGCCATTCATTTTTACTTGCTATTTCCCAAAGC
1 GCCCTTCCCAGACGGAAGCCATTCATTTTTACTTGCTATTTCCCAAAGC
* * *
45714 GCCCTTCCCAGATGGAAGCCATT--TATTT--TTGCTATTTCCCAAAAC
1 GCCCTTCCCAGACGGAAGCCATTCATTTTTACTTGCTATTTCCCAAAGC
* ** * * * *
45759 ACCCTTCCCAGACGGAAGGTATTTATTCTTACCTGCCATTTCCCAAA
1 GCCCTTCCCAGACGGAAGCCATTCATTTTTACTTGCTATTTCCCAAA
45806 ATGCCTTTTC
Statistics
Matches: 390, Mismatches: 40, Indels: 13
0.88 0.09 0.03
Matches are distributed among these distances:
45 35 0.09
47 7 0.02
48 6 0.02
49 299 0.77
50 18 0.05
51 25 0.06
ACGTcount: A:0.24, C:0.31, G:0.13, T:0.32
Consensus pattern (49 bp):
GCCCTTCCCAGACGGAAGCCATTCATTTTTACTTGCTATTTCCCAAAGC
Found at i:47497 original size:17 final size:17
Alignment explanation
Indices: 47477--47512 Score: 72
Period size: 17 Copynumber: 2.1 Consensus size: 17
47467 ACTAAATTTG
47477 GCTAAATTATTAATTCA
1 GCTAAATTATTAATTCA
47494 GCTAAATTATTAATTCA
1 GCTAAATTATTAATTCA
47511 GC
1 GC
47513 CCATCGAATT
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 19 1.00
ACGTcount: A:0.39, C:0.14, G:0.08, T:0.39
Consensus pattern (17 bp):
GCTAAATTATTAATTCA
Found at i:48781 original size:2 final size:2
Alignment explanation
Indices: 48774--48886 Score: 79
Period size: 2 Copynumber: 61.5 Consensus size: 2
48764 CTTTTGACAG
48774 AT AT AT AT AT AT AT AT AT -T AT AT -T AT AT AT -T AT A- AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
* * * * *
48812 AT AT -T AC AT AT -T AT AT AT -T AT AT ACC CT A- ACC CT A- AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT A-T AT AT A-T AT AT AT AT
48851 AT A- AT AT AT AT -T AT A- 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
48887 ATGGAATAAA
Statistics
Matches: 88, Mismatches: 9, Indels: 28
0.70 0.07 0.22
Matches are distributed among these distances:
1 12 0.14
2 76 0.86
ACGTcount: A:0.47, C:0.06, G:0.00, T:0.47
Consensus pattern (2 bp):
AT
Found at i:48811 original size:26 final size:26
Alignment explanation
Indices: 48774--48833 Score: 90
Period size: 26 Copynumber: 2.4 Consensus size: 26
48764 CTTTTGACAG
48774 ATATA-TATATATATATATT--ATATT
1 ATATATTATA-ATATATATTACATATT
48798 ATATATTATAATATATATTACATATT
1 ATATATTATAATATATATTACATATT
48824 ATATATTATA
1 ATATATTATA
48834 TACCCTAACC
Statistics
Matches: 33, Mismatches: 0, Indels: 4
0.89 0.00 0.11
Matches are distributed among these distances:
24 14 0.42
25 4 0.12
26 15 0.45
ACGTcount: A:0.47, C:0.02, G:0.00, T:0.52
Consensus pattern (26 bp):
ATATATTATAATATATATTACATATT
Found at i:49045 original size:34 final size:35
Alignment explanation
Indices: 48987--49055 Score: 104
Period size: 34 Copynumber: 2.0 Consensus size: 35
48977 ATTATAGAAA
*
48987 AGAAAACCCAACCCTTTGAAATTTACAATACAAAT
1 AGAAAACCCAACCCTTTCAAATTTACAATACAAAT
* *
49022 AGAAAACTCAA-CTTTTCAAATTTACAATACAAAT
1 AGAAAACCCAACCCTTTCAAATTTACAATACAAAT
49056 TGCAAAAAAT
Statistics
Matches: 31, Mismatches: 3, Indels: 1
0.89 0.09 0.03
Matches are distributed among these distances:
34 21 0.68
35 10 0.32
ACGTcount: A:0.49, C:0.20, G:0.04, T:0.26
Consensus pattern (35 bp):
AGAAAACCCAACCCTTTCAAATTTACAATACAAAT
Done.