Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01009142.1 Corchorus capsularis cultivar CVL-1 contig09163, 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: 48156
ACGTcount: A:0.33, C:0.16, G:0.17, T:0.33
Found at i:4782 original size:21 final size:21
Alignment explanation
Indices: 4758--4798 Score: 73
Period size: 21 Copynumber: 2.0 Consensus size: 21
4748 CCTTTTTATA
4758 TATATATATAGTCTAGCAGGC
1 TATATATATAGTCTAGCAGGC
*
4779 TATATATGTAGTCTAGCAGG
1 TATATATATAGTCTAGCAGG
4799 TGCAGCGGTT
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
21 19 1.00
ACGTcount: A:0.32, C:0.12, G:0.22, T:0.34
Consensus pattern (21 bp):
TATATATATAGTCTAGCAGGC
Found at i:5319 original size:122 final size:117
Alignment explanation
Indices: 5107--5339 Score: 376
Period size: 122 Copynumber: 1.9 Consensus size: 117
5097 GAAAATCAAG
5107 CTCATGGAAGACTTTGCCATTGCCAAATCAGCATTATGGGTGTAAAAACACAAGTTTTCTAAGCC
1 CTCATGGAAGACTTTGCCATTGCCAAATCAGCATTATGGGTGTAAAAACACAAGTTTTCTAAGCC
* * *
5172 ATTTATCTTCTCTTTTTGTTGAAAATGGCTGATTTTGGCAGAGAATATCAGT
66 ATTTATCTCCTCTCTTTGTTGAAAATGGCTGATTTCGGCAGAGAATATCAGT
* *
5224 CTCATGGAAGACTTTGCCATTATGTGCCAGATCAGGATTATGGGTGTATAAAACACAAGTTTTCT
1 CTCATGGAAGACTTTGCC---AT-TGCCAAATCAGCATTATGGGTGTA-AAAACACAAGTTTTCT
5289 AAGCCATTTATCTCCTCTCTTTGTTGAAAATGGCTGATTTCGGCAGAGAAT
61 AAGCCATTTATCTCCTCTCTTTGTTGAAAATGGCTGATTTCGGCAGAGAAT
5340 TGTTTTCCTA
Statistics
Matches: 106, Mismatches: 5, Indels: 5
0.91 0.04 0.04
Matches are distributed among these distances:
117 18 0.17
120 2 0.02
121 22 0.21
122 64 0.60
ACGTcount: A:0.28, C:0.18, G:0.20, T:0.34
Consensus pattern (117 bp):
CTCATGGAAGACTTTGCCATTGCCAAATCAGCATTATGGGTGTAAAAACACAAGTTTTCTAAGCC
ATTTATCTCCTCTCTTTGTTGAAAATGGCTGATTTCGGCAGAGAATATCAGT
Found at i:11462 original size:22 final size:22
Alignment explanation
Indices: 11420--11462 Score: 59
Period size: 22 Copynumber: 2.0 Consensus size: 22
11410 TTTTTGTTAA
* **
11420 TGTATCTCATTTACAGTTTTGT
1 TGTATCCCATTTACAAATTTGT
11442 TGTATCCCATTTACAAATTTG
1 TGTATCCCATTTACAAATTTG
11463 ATAAAATTTG
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
22 18 1.00
ACGTcount: A:0.23, C:0.16, G:0.12, T:0.49
Consensus pattern (22 bp):
TGTATCCCATTTACAAATTTGT
Found at i:18370 original size:14 final size:14
Alignment explanation
Indices: 18351--18380 Score: 60
Period size: 14 Copynumber: 2.1 Consensus size: 14
18341 AACATCAAAT
18351 TCGTGTTTATACTG
1 TCGTGTTTATACTG
18365 TCGTGTTTATACTG
1 TCGTGTTTATACTG
18379 TC
1 TC
18381 ATTACGTATG
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 16 1.00
ACGTcount: A:0.13, C:0.17, G:0.20, T:0.50
Consensus pattern (14 bp):
TCGTGTTTATACTG
Found at i:18422 original size:72 final size:72
Alignment explanation
Indices: 18305--18440 Score: 272
Period size: 72 Copynumber: 1.9 Consensus size: 72
18295 CGGCCCCTGA
18305 TGTCATTACGTATGTATGATCAAACTATATTTGATAAACATCAAATTCGTGTTTATACTGTCGTG
1 TGTCATTACGTATGTATGATCAAACTATATTTGATAAACATCAAATTCGTGTTTATACTGTCGTG
18370 TTTATAC
66 TTTATAC
18377 TGTCATTACGTATGTATGATCAAACTATATTTGATAAACATCAAATTCGTGTTTATACTGTCGT
1 TGTCATTACGTATGTATGATCAAACTATATTTGATAAACATCAAATTCGTGTTTATACTGTCGT
18441 CTCAAACTTA
Statistics
Matches: 64, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
72 64 1.00
ACGTcount: A:0.31, C:0.14, G:0.14, T:0.41
Consensus pattern (72 bp):
TGTCATTACGTATGTATGATCAAACTATATTTGATAAACATCAAATTCGTGTTTATACTGTCGTG
TTTATAC
Found at i:19146 original size:2 final size:2
Alignment explanation
Indices: 19139--19177 Score: 71
Period size: 2 Copynumber: 20.0 Consensus size: 2
19129 TGTATAACTT
19139 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T- TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
19178 GTTGAAAATG
Statistics
Matches: 36, Mismatches: 0, Indels: 2
0.95 0.00 0.05
Matches are distributed among these distances:
1 1 0.03
2 35 0.97
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:20195 original size:26 final size:27
Alignment explanation
Indices: 20156--20207 Score: 70
Period size: 26 Copynumber: 2.0 Consensus size: 27
20146 GACTATTGTA
*
20156 AATCTAAATTTAAATTAAATAAATAAT
1 AATCTAAATATAAATTAAATAAATAAT
* *
20183 AATCTAAA-ATAAATTCAATAGATAA
1 AATCTAAATATAAATTAAATAAATAA
20208 ATATATTATA
Statistics
Matches: 22, Mismatches: 3, Indels: 1
0.85 0.12 0.04
Matches are distributed among these distances:
26 14 0.64
27 8 0.36
ACGTcount: A:0.60, C:0.06, G:0.02, T:0.33
Consensus pattern (27 bp):
AATCTAAATATAAATTAAATAAATAAT
Found at i:21646 original size:11 final size:11
Alignment explanation
Indices: 21632--21666 Score: 52
Period size: 11 Copynumber: 3.2 Consensus size: 11
21622 CGTTTTTTAT
21632 TTTTGTTTTTG
1 TTTTGTTTTTG
*
21643 TTTTGTTTTCG
1 TTTTGTTTTTG
*
21654 TTTTATTTTTG
1 TTTTGTTTTTG
21665 TT
1 TT
21667 GCGCTGTCAA
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
11 21 1.00
ACGTcount: A:0.03, C:0.03, G:0.14, T:0.80
Consensus pattern (11 bp):
TTTTGTTTTTG
Found at i:22920 original size:25 final size:25
Alignment explanation
Indices: 22891--22943 Score: 106
Period size: 25 Copynumber: 2.1 Consensus size: 25
22881 TTTGAACACT
22891 ATTCTTAGAAAATTGATTAATTTTG
1 ATTCTTAGAAAATTGATTAATTTTG
22916 ATTCTTAGAAAATTGATTAATTTTG
1 ATTCTTAGAAAATTGATTAATTTTG
22941 ATT
1 ATT
22944 TATATATATG
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
25 28 1.00
ACGTcount: A:0.36, C:0.04, G:0.11, T:0.49
Consensus pattern (25 bp):
ATTCTTAGAAAATTGATTAATTTTG
Found at i:23201 original size:97 final size:95
Alignment explanation
Indices: 23084--23275 Score: 357
Period size: 97 Copynumber: 2.0 Consensus size: 95
23074 TACAATTAAT
23084 TTTTAATTTTGTTAATTTGCGTTTAATTAAATCTACGAAATATATATCTCAAATTTACATCAATC
1 TTTTAATTTTGTTAATTTGCGTTTAATTAAATCTACGAAATATATATCTCAAATTTACATCAATC
23149 CAAACTAGAGCAGAAGTTTTTTTTTAGATTTC
66 CAAACTAGAGCAGAAG--TTTTTTTAGATTTC
*
23181 TTTTAATTTTGTTAATTTGCGTTTAATTAAATCTATGAAATATATATCTCAAATTTACATCAATC
1 TTTTAATTTTGTTAATTTGCGTTTAATTAAATCTACGAAATATATATCTCAAATTTACATCAATC
23246 CAAACTAGAGCAGAAGTTTTTTTAGATTTC
66 CAAACTAGAGCAGAAGTTTTTTTAGATTTC
23276 AACTTCTTGA
Statistics
Matches: 94, Mismatches: 1, Indels: 2
0.97 0.01 0.02
Matches are distributed among these distances:
95 14 0.15
97 80 0.85
ACGTcount: A:0.34, C:0.12, G:0.09, T:0.44
Consensus pattern (95 bp):
TTTTAATTTTGTTAATTTGCGTTTAATTAAATCTACGAAATATATATCTCAAATTTACATCAATC
CAAACTAGAGCAGAAGTTTTTTTAGATTTC
Found at i:25538 original size:18 final size:19
Alignment explanation
Indices: 25495--25534 Score: 66
Period size: 19 Copynumber: 2.2 Consensus size: 19
25485 GAGTAAATTT
25495 TAAATAAAAATATAATATA
1 TAAATAAAAATATAATATA
25514 TAAATAAAAAT-TAATAT-
1 TAAATAAAAATATAATATA
25531 TAAA
1 TAAA
25535 ATAATTAATT
Statistics
Matches: 21, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
17 4 0.19
18 6 0.29
19 11 0.52
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.33
Consensus pattern (19 bp):
TAAATAAAAATATAATATA
Found at i:26167 original size:15 final size:16
Alignment explanation
Indices: 26142--26182 Score: 57
Period size: 16 Copynumber: 2.6 Consensus size: 16
26132 TCACGACTAA
26142 AAATAATATTATAAT-T
1 AAAT-ATATTATAATCT
26158 AAATATATTATAATCT
1 AAATATATTATAATCT
*
26174 AAAAATATT
1 AAATATATT
26183 TATTAGAATT
Statistics
Matches: 23, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
15 10 0.43
16 13 0.57
ACGTcount: A:0.56, C:0.02, G:0.00, T:0.41
Consensus pattern (16 bp):
AAATATATTATAATCT
Found at i:26179 original size:18 final size:18
Alignment explanation
Indices: 26138--26185 Score: 59
Period size: 15 Copynumber: 2.8 Consensus size: 18
26128 GGTTTCACGA
26138 CTAAAAATAATATTATAAT
1 CTAAAAAT-ATATTATAAT
26157 -T--AAATATATTATAAT
1 CTAAAAATATATTATAAT
26172 CTAAAAATAT-TTAT
1 CTAAAAATATATTAT
26186 TAGAATTAAA
Statistics
Matches: 26, Mismatches: 0, Indels: 8
0.76 0.00 0.24
Matches are distributed among these distances:
15 10 0.38
16 5 0.19
17 4 0.15
18 7 0.27
ACGTcount: A:0.54, C:0.04, G:0.00, T:0.42
Consensus pattern (18 bp):
CTAAAAATATATTATAAT
Found at i:27533 original size:23 final size:23
Alignment explanation
Indices: 27502--27546 Score: 81
Period size: 23 Copynumber: 2.0 Consensus size: 23
27492 CCCTAAACCC
27502 AATTGTTTTTTAAAAAAATAGCT
1 AATTGTTTTTTAAAAAAATAGCT
*
27525 AATTTTTTTTTAAAAAAATAGC
1 AATTGTTTTTTAAAAAAATAGC
27547 CTTGCCGCCC
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
23 21 1.00
ACGTcount: A:0.44, C:0.04, G:0.07, T:0.44
Consensus pattern (23 bp):
AATTGTTTTTTAAAAAAATAGCT
Found at i:27836 original size:68 final size:68
Alignment explanation
Indices: 27726--27855 Score: 201
Period size: 68 Copynumber: 1.9 Consensus size: 68
27716 AACTAAGGAA
* * *
27726 AAAAATGGTGGGAGCACCATTAATTACATTTCAATGCTAAAATTACATATAAAGATAATGCACCA
1 AAAAATGGTGGCAGCACCATTAATTACATTGCAATGCAAAAATTACATATAAAGATAATGCACCA
27791 AGG
66 AGG
27794 AAAAATGGTAGGCA-CACCATTAATTACA-TGCAAATGCAAAAATTACATATAAAGATAATGCA
1 AAAAATGGT-GGCAGCACCATTAATTACATTGC-AATGCAAAAATTACATATAAAGATAATGCA
27856 TTTCAAGCAA
Statistics
Matches: 57, Mismatches: 3, Indels: 4
0.89 0.05 0.06
Matches are distributed among these distances:
67 2 0.04
68 52 0.91
69 3 0.05
ACGTcount: A:0.47, C:0.15, G:0.15, T:0.24
Consensus pattern (68 bp):
AAAAATGGTGGCAGCACCATTAATTACATTGCAATGCAAAAATTACATATAAAGATAATGCACCA
AGG
Found at i:30545 original size:30 final size:30
Alignment explanation
Indices: 30509--30567 Score: 109
Period size: 30 Copynumber: 2.0 Consensus size: 30
30499 CTTAAAGCAA
30509 CTAAAATCATAAATAGCCATGAATTAATTC
1 CTAAAATCATAAATAGCCATGAATTAATTC
*
30539 CTAAAATCATTAATAGCCATGAATTAATT
1 CTAAAATCATAAATAGCCATGAATTAATT
30568 ACCCTCATTC
Statistics
Matches: 28, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
30 28 1.00
ACGTcount: A:0.46, C:0.15, G:0.07, T:0.32
Consensus pattern (30 bp):
CTAAAATCATAAATAGCCATGAATTAATTC
Found at i:33744 original size:19 final size:19
Alignment explanation
Indices: 33704--33741 Score: 53
Period size: 18 Copynumber: 2.1 Consensus size: 19
33694 AATTTATCCT
33704 ATCTATCTGTTGAATTTGA
1 ATCTATCTGTTGAATTTGA
33723 ATCT-TCTGTTTG-ATTTGA
1 ATCTATCTG-TTGAATTTGA
33741 A
1 A
33742 ATCCTATTTC
Statistics
Matches: 18, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
18 11 0.61
19 7 0.39
ACGTcount: A:0.24, C:0.11, G:0.16, T:0.50
Consensus pattern (19 bp):
ATCTATCTGTTGAATTTGA
Found at i:38110 original size:19 final size:19
Alignment explanation
Indices: 38070--38107 Score: 60
Period size: 18 Copynumber: 2.1 Consensus size: 19
38060 GATTTATCCT
38070 ATCTATCTGTTGAATTTGA
1 ATCTATCTGTTGAATTTGA
*
38089 ATCT-TCTGTTGGATTTGA
1 ATCTATCTGTTGAATTTGA
38107 A
1 A
38108 ATCCTATTTC
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
18 14 0.78
19 4 0.22
ACGTcount: A:0.24, C:0.11, G:0.18, T:0.47
Consensus pattern (19 bp):
ATCTATCTGTTGAATTTGA
Found at i:38526 original size:10 final size:11
Alignment explanation
Indices: 38506--38531 Score: 52
Period size: 11 Copynumber: 2.4 Consensus size: 11
38496 TTTGCTTGTC
38506 AAAAAGAAAAA
1 AAAAAGAAAAA
38517 AAAAAGAAAAA
1 AAAAAGAAAAA
38528 AAAA
1 AAAA
38532 CAGCCAAATC
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 15 1.00
ACGTcount: A:0.92, C:0.00, G:0.08, T:0.00
Consensus pattern (11 bp):
AAAAAGAAAAA
Found at i:38847 original size:21 final size:22
Alignment explanation
Indices: 38823--38867 Score: 65
Period size: 21 Copynumber: 2.1 Consensus size: 22
38813 AAAGCAAACC
*
38823 GAAGAGGAAAGAAA-CAGAGGA
1 GAAGAAGAAAGAAAGCAGAGGA
*
38844 GAAGAAGAAAGAAAGCAGATGA
1 GAAGAAGAAAGAAAGCAGAGGA
38866 GA
1 GA
38868 GATTTTGAAA
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
21 13 0.62
22 8 0.38
ACGTcount: A:0.58, C:0.04, G:0.36, T:0.02
Consensus pattern (22 bp):
GAAGAAGAAAGAAAGCAGAGGA
Found at i:41229 original size:32 final size:32
Alignment explanation
Indices: 41193--41295 Score: 143
Period size: 32 Copynumber: 3.2 Consensus size: 32
41183 CCATCATGTC
* * *
41193 AGGGGACAAATTAGCCTAAATTTCTAAATTTA
1 AGGGGATAAATTGGCCTAAATTTCTAAATTCA
* *
41225 AGGGGGTAAATTGGCCTAAATTTCTAAACTCA
1 AGGGGATAAATTGGCCTAAATTTCTAAATTCA
*
41257 AGGGGGTAAATTGGCCTAAATTTCTAAATTCA
1 AGGGGATAAATTGGCCTAAATTTCTAAATTCA
41289 ATGGGGA
1 A-GGGGA
41296 AAGTGGGACA
Statistics
Matches: 63, Mismatches: 7, Indels: 1
0.89 0.10 0.01
Matches are distributed among these distances:
32 59 0.94
33 4 0.06
ACGTcount: A:0.36, C:0.13, G:0.22, T:0.29
Consensus pattern (32 bp):
AGGGGATAAATTGGCCTAAATTTCTAAATTCA
Found at i:43889 original size:11 final size:11
Alignment explanation
Indices: 43873--43909 Score: 51
Period size: 11 Copynumber: 3.5 Consensus size: 11
43863 CAAAGGATGC
43873 AAGAATGAATG
1 AAGAATGAATG
43884 AAGAATGAA-G
1 AAGAATGAATG
43894 AATGAA-GAATG
1 AA-GAATGAATG
43905 AAGAA
1 AAGAA
43910 AAGGAGCCTG
Statistics
Matches: 24, Mismatches: 0, Indels: 5
0.83 0.00 0.17
Matches are distributed among these distances:
10 9 0.38
11 15 0.62
ACGTcount: A:0.59, C:0.00, G:0.27, T:0.14
Consensus pattern (11 bp):
AAGAATGAATG
Found at i:43891 original size:7 final size:7
Alignment explanation
Indices: 43879--43909 Score: 62
Period size: 7 Copynumber: 4.4 Consensus size: 7
43869 ATGCAAGAAT
43879 GAATGAA
1 GAATGAA
43886 GAATGAA
1 GAATGAA
43893 GAATGAA
1 GAATGAA
43900 GAATGAA
1 GAATGAA
43907 GAA
1 GAA
43910 AAGGAGCCTG
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 24 1.00
ACGTcount: A:0.58, C:0.00, G:0.29, T:0.13
Consensus pattern (7 bp):
GAATGAA
Done.