Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01008193.1 Corchorus capsularis cultivar CVL-1 contig08214, 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: 50837
ACGTcount: A:0.33, C:0.19, G:0.17, T:0.32
Found at i:237 original size:13 final size:13
Alignment explanation
Indices: 213--247 Score: 52
Period size: 13 Copynumber: 2.7 Consensus size: 13
203 AATCTAAATC
*
213 TAAAGCAGATTAA
1 TAAAGCAAATTAA
*
226 TACAGCAAATTAA
1 TAAAGCAAATTAA
239 TAAAGCAAA
1 TAAAGCAAA
248 CAATAATTAT
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
13 19 1.00
ACGTcount: A:0.57, C:0.11, G:0.11, T:0.20
Consensus pattern (13 bp):
TAAAGCAAATTAA
Found at i:16689 original size:25 final size:25
Alignment explanation
Indices: 16661--16708 Score: 71
Period size: 25 Copynumber: 2.0 Consensus size: 25
16651 TTGTTAACCA
*
16661 TTTTATCA-ATAATAATAGAAGTTT
1 TTTTTTCAGATAATAATAGAAGTTT
*
16685 TTTTTTGAGATAATAATAGAAGTT
1 TTTTTTCAGATAATAATAGAAGTT
16709 ATTAAATTTA
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
24 6 0.29
25 15 0.71
ACGTcount: A:0.40, C:0.02, G:0.12, T:0.46
Consensus pattern (25 bp):
TTTTTTCAGATAATAATAGAAGTTT
Found at i:17985 original size:22 final size:23
Alignment explanation
Indices: 17955--18001 Score: 69
Period size: 22 Copynumber: 2.1 Consensus size: 23
17945 TCCAATGTAG
*
17955 AAATATTGATAACCACATTTTGA
1 AAATATTGATAACCACATTATGA
*
17978 AAAT-TTGATAACCTCATTATGA
1 AAATATTGATAACCACATTATGA
18000 AA
1 AA
18002 TTTCAATAAC
Statistics
Matches: 22, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
22 18 0.82
23 4 0.18
ACGTcount: A:0.45, C:0.13, G:0.09, T:0.34
Consensus pattern (23 bp):
AAATATTGATAACCACATTATGA
Found at i:18010 original size:22 final size:22
Alignment explanation
Indices: 17963--18034 Score: 65
Period size: 22 Copynumber: 3.3 Consensus size: 22
17953 AGAAATATTG
* * *
17963 ATAACCACATTTTGAAAATTTG
1 ATAACCTCATTATGAAAATTTA
17985 ATAACCTCATTATG-AAATTTCA
1 ATAACCTCATTATGAAAATTT-A
** * *
18007 ATAACCTCCCTAAGAAAATTTG
1 ATAACCTCATTATGAAAATTTA
18029 ATAACC
1 ATAACC
18035 ATTTGGTAAC
Statistics
Matches: 41, Mismatches: 7, Indels: 4
0.79 0.13 0.08
Matches are distributed among these distances:
21 6 0.15
22 29 0.71
23 6 0.15
ACGTcount: A:0.42, C:0.19, G:0.07, T:0.32
Consensus pattern (22 bp):
ATAACCTCATTATGAAAATTTA
Found at i:18066 original size:22 final size:22
Alignment explanation
Indices: 18036--18087 Score: 77
Period size: 22 Copynumber: 2.4 Consensus size: 22
18026 TTGATAACCA
*
18036 TTTGGTAACCACACTGTGAAAT
1 TTTGATAACCACACTGTGAAAT
* *
18058 TTTGATAACCTCAGTGTGAAAT
1 TTTGATAACCACACTGTGAAAT
18080 TTTGATAA
1 TTTGATAA
18088 TCTGCCTATA
Statistics
Matches: 27, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
22 27 1.00
ACGTcount: A:0.33, C:0.13, G:0.17, T:0.37
Consensus pattern (22 bp):
TTTGATAACCACACTGTGAAAT
Found at i:18305 original size:22 final size:22
Alignment explanation
Indices: 18277--18464 Score: 127
Period size: 22 Copynumber: 8.5 Consensus size: 22
18267 CCTCCCTCCC
*
18277 TATGAAATTTTGTTAACTTTCA
1 TATGAAATTTTGATAACTTTCA
* *
18299 TATGAAATTTT-ATTAACATTCC
1 TATGAAATTTTGA-TAACTTTCA
* * * *
18321 TAAGAAATTTTGGTTACCTTT-T
1 TATGAAATTTT-GATAACTTTCA
* *
18343 TATGAAATTTTGGTAAC-CTCTA
1 TATGAAATTTTGATAACTTTC-A
* * *
18365 TATAAAATTTTGATAAC-TACGC
1 TATGAAATTTTGATAACTTTC-A
* *
18387 TATGAAGTTTTGATAACTTCCA
1 TATGAAATTTTGATAACTTTCA
* *
18409 TATGAAATTTTGGTAAC-TACA
1 TATGAAATTTTGATAACTTTCA
18430 CTATGAAATTTTGATAACCTTTC-
1 -TATGAAATTTTGATAA-CTTTCA
*
18453 TATGTAATTTTG
1 TATGAAATTTTG
18465 GTTTGATTGT
Statistics
Matches: 128, Mismatches: 29, Indels: 18
0.73 0.17 0.10
Matches are distributed among these distances:
20 1 0.01
21 7 0.05
22 110 0.86
23 8 0.06
24 2 0.02
ACGTcount: A:0.33, C:0.12, G:0.11, T:0.44
Consensus pattern (22 bp):
TATGAAATTTTGATAACTTTCA
Found at i:18398 original size:66 final size:65
Alignment explanation
Indices: 18277--18447 Score: 161
Period size: 66 Copynumber: 2.6 Consensus size: 65
18267 CCTCCCTCCC
* * * * *
18277 TATGAAATTTTGTTAACTTTCATATGAAATTTT-ATTAACATTCCTAAGAAATTTTGGTTACCTT
1 TATGAAATTTTGGTAACTCT-ATATGAAATTTTGA-TAACATACCTAAGAAATTTT-GATAACTT
**
18341 -TT
63 CCA
* * *
18343 TATGAAATTTTGGTAACCTCTATATAAAATTTTGATAAC-TACGCTATGAAGTTTTGATAACTTC
1 TATGAAATTTTGGTAA-CTCTATATGAAATTTTGATAACATAC-CTAAGAAATTTTGATAACTTC
18407 CA
64 CA
18409 TATGAAATTTTGGTAACTAC-ACTATGAAATTTTGATAAC
1 TATGAAATTTTGGTAACT-CTA-TATGAAATTTTGATAAC
18448 CTTTCTATGT
Statistics
Matches: 88, Mismatches: 11, Indels: 12
0.79 0.10 0.11
Matches are distributed among these distances:
65 11 0.12
66 73 0.83
67 4 0.05
ACGTcount: A:0.35, C:0.12, G:0.11, T:0.43
Consensus pattern (65 bp):
TATGAAATTTTGGTAACTCTATATGAAATTTTGATAACATACCTAAGAAATTTTGATAACTTCCA
Found at i:18462 original size:44 final size:44
Alignment explanation
Indices: 18276--18466 Score: 156
Period size: 44 Copynumber: 4.3 Consensus size: 44
18266 ACCTCCCTCC
* * * *
18276 CTATGAAATTTTGTTAACTTTCA-TATGAAATTTT-ATTAACATTC
1 CTATGAAATTTTGGTAAC-TACACTATGAAATTTTGA-TAACCTTT
* * *** * *
18320 CTAAGAAATTTTGGTTACCT-TTTTATGAAATTTTGGTAACCTCT
1 CTATGAAATTTTGG-TAACTACACTATGAAATTTTGATAACCTTT
* * * * * *
18364 ATATAAAATTTTGATAACTACGCTATGAAGTTTTGATAA-CTTC
1 CTATGAAATTTTGGTAACTACACTATGAAATTTTGATAACCTTT
18407 CATATGAAATTTTGGTAACTACACTATGAAATTTTGATAACCTTT
1 C-TATGAAATTTTGGTAACTACACTATGAAATTTTGATAACCTTT
*
18452 CTATGTAATTTTGGT
1 CTATGAAATTTTGGT
18467 TTGATTGTGA
Statistics
Matches: 113, Mismatches: 28, Indels: 12
0.74 0.18 0.08
Matches are distributed among these distances:
43 6 0.05
44 100 0.88
45 7 0.06
ACGTcount: A:0.32, C:0.12, G:0.12, T:0.44
Consensus pattern (44 bp):
CTATGAAATTTTGGTAACTACACTATGAAATTTTGATAACCTTT
Found at i:26625 original size:24 final size:24
Alignment explanation
Indices: 26593--26648 Score: 76
Period size: 24 Copynumber: 2.3 Consensus size: 24
26583 ATTTTTCATT
26593 CACTGACAATGTATAAGATTAATA
1 CACTGACAATGTATAAGATTAATA
* **
26617 CACTTACAATGTATTGGATTAATA
1 CACTGACAATGTATAAGATTAATA
*
26641 TACTGACA
1 CACTGACA
26649 GTGCATCAAA
Statistics
Matches: 27, Mismatches: 5, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
24 27 1.00
ACGTcount: A:0.41, C:0.14, G:0.12, T:0.32
Consensus pattern (24 bp):
CACTGACAATGTATAAGATTAATA
Found at i:30756 original size:31 final size:32
Alignment explanation
Indices: 30721--30781 Score: 106
Period size: 31 Copynumber: 1.9 Consensus size: 32
30711 GGGCCCGAAC
*
30721 CCGAAAATACTCGAACCCGAAAA-ACCCGAGG
1 CCGAAAATACCCGAACCCGAAAATACCCGAGG
30752 CCGAAAATACCCGAACCCGAAAATACCCGA
1 CCGAAAATACCCGAACCCGAAAATACCCGA
30782 ACTTGCCAAA
Statistics
Matches: 28, Mismatches: 1, Indels: 1
0.93 0.03 0.03
Matches are distributed among these distances:
31 22 0.79
32 6 0.21
ACGTcount: A:0.43, C:0.34, G:0.16, T:0.07
Consensus pattern (32 bp):
CCGAAAATACCCGAACCCGAAAATACCCGAGG
Found at i:30757 original size:15 final size:16
Alignment explanation
Indices: 30714--30783 Score: 106
Period size: 16 Copynumber: 4.4 Consensus size: 16
30704 CCGACCCGGG
30714 CCCGAACCCGAAAATA
1 CCCGAACCCGAAAATA
*
30730 CTCGAACCCGAAAA-A
1 CCCGAACCCGAAAATA
**
30745 CCCGAGGCCGAAAATA
1 CCCGAACCCGAAAATA
30761 CCCGAACCCGAAAATA
1 CCCGAACCCGAAAATA
30777 CCCGAAC
1 CCCGAAC
30784 TTGCCAAATT
Statistics
Matches: 47, Mismatches: 6, Indels: 2
0.85 0.11 0.04
Matches are distributed among these distances:
15 12 0.26
16 35 0.74
ACGTcount: A:0.41, C:0.37, G:0.16, T:0.06
Consensus pattern (16 bp):
CCCGAACCCGAAAATA
Found at i:31797 original size:37 final size:37
Alignment explanation
Indices: 31756--31850 Score: 118
Period size: 37 Copynumber: 2.6 Consensus size: 37
31746 ATCTAAGCCC
* * *
31756 AAATAGGACGTTGGAGATAAAGACAAAAAACAAAATT
1 AAATAGGACATTGGAAACAAAGACAAAAAACAAAATT
** **
31793 AAATACAACATTGGAAACAAAGACAAAAGGCAAAATT
1 AAATAGGACATTGGAAACAAAGACAAAAAACAAAATT
*
31830 AAATAGGACATTGAAAACAAA
1 AAATAGGACATTGGAAACAAA
31851 AAGCAAAATT
Statistics
Matches: 48, Mismatches: 10, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
37 48 1.00
ACGTcount: A:0.59, C:0.11, G:0.16, T:0.15
Consensus pattern (37 bp):
AAATAGGACATTGGAAACAAAGACAAAAAACAAAATT
Found at i:32016 original size:27 final size:26
Alignment explanation
Indices: 31961--32013 Score: 65
Period size: 27 Copynumber: 2.0 Consensus size: 26
31951 ATGGTAAAAA
31961 AATAATGGAATAATTAAAATATTATTT
1 AATAATGGAAT-ATTAAAATATTATTT
31988 AATAATGGCAAT-TTAGAAATA-TATTT
1 AATAATGG-AATATTA-AAATATTATTT
32014 TAAGAAAAAG
Statistics
Matches: 24, Mismatches: 0, Indels: 5
0.83 0.00 0.17
Matches are distributed among these distances:
26 8 0.33
27 13 0.54
28 3 0.12
ACGTcount: A:0.49, C:0.02, G:0.09, T:0.40
Consensus pattern (26 bp):
AATAATGGAATATTAAAATATTATTT
Found at i:32118 original size:17 final size:17
Alignment explanation
Indices: 32096--32130 Score: 70
Period size: 17 Copynumber: 2.1 Consensus size: 17
32086 TATTCGTACT
32096 TTTATATATAGTATAGA
1 TTTATATATAGTATAGA
32113 TTTATATATAGTATAGA
1 TTTATATATAGTATAGA
32130 T
1 T
32131 ATAGATAGGA
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 18 1.00
ACGTcount: A:0.40, C:0.00, G:0.11, T:0.49
Consensus pattern (17 bp):
TTTATATATAGTATAGA
Found at i:32162 original size:17 final size:17
Alignment explanation
Indices: 32142--32180 Score: 69
Period size: 17 Copynumber: 2.3 Consensus size: 17
32132 TAGATAGGAG
*
32142 AAGATAAGAGATAAGAT
1 AAGATAAAAGATAAGAT
32159 AAGATAAAAGATAAGAT
1 AAGATAAAAGATAAGAT
32176 AAGAT
1 AAGAT
32181 GATTACTCAT
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
17 21 1.00
ACGTcount: A:0.62, C:0.00, G:0.21, T:0.18
Consensus pattern (17 bp):
AAGATAAAAGATAAGAT
Found at i:32175 original size:12 final size:12
Alignment explanation
Indices: 32142--32177 Score: 54
Period size: 12 Copynumber: 3.0 Consensus size: 12
32132 TAGATAGGAG
* *
32142 AAGATAAGAGAT
1 AAGATAAGATAA
32154 AAGATAAGATAA
1 AAGATAAGATAA
32166 AAGATAAGATAA
1 AAGATAAGATAA
32178 GATGATTACT
Statistics
Matches: 22, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
12 22 1.00
ACGTcount: A:0.64, C:0.00, G:0.19, T:0.17
Consensus pattern (12 bp):
AAGATAAGATAA
Found at i:40153 original size:165 final size:165
Alignment explanation
Indices: 39881--40181 Score: 575
Period size: 165 Copynumber: 1.8 Consensus size: 165
39871 GAGACCTTCA
*
39881 ATCAGCTCAACAGCTGGTGATAGGAGTAGTTTAATGCTTGGAGGAAAGTTCAAATTAATTTCTCA
1 ATCAGCTCAACAGCTGGTGATAGGAGTAGTTTAATGCTCGGAGGAAAGTTCAAATTAATTTCTCA
*
39946 TCCTAAACAAATGAAAAGAGAATATTAAATGTATATATAAGCGGCAATGATAAAATTGGTTTTAA
66 TCCTAAACAAATGAAAAGAGAATATTAAATGAATATATAAGCGGCAATGATAAAATTGGTTTTAA
40011 TCACGGTAATATTAAAGTTCAAACTAATTCCTATC
131 TCACGGTAATATTAAAGTTCAAACTAATTCCTATC
40046 ATCAGCTCAACAGCTGGTGATAGGAGTAGTTTAATGCTCGGAGGAAAGTTCAAATTAATTTCTCA
1 ATCAGCTCAACAGCTGGTGATAGGAGTAGTTTAATGCTCGGAGGAAAGTTCAAATTAATTTCTCA
*
40111 TCCTAAACAAATGAAAGGAGAATATTAAATGAATATATAAGCGGCAATGATAAAATTGGTTTTAA
66 TCCTAAACAAATGAAAAGAGAATATTAAATGAATATATAAGCGGCAATGATAAAATTGGTTTTAA
40176 TCACGG
131 TCACGG
40182 CAATGGTATA
Statistics
Matches: 133, Mismatches: 3, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
165 133 1.00
ACGTcount: A:0.39, C:0.13, G:0.19, T:0.30
Consensus pattern (165 bp):
ATCAGCTCAACAGCTGGTGATAGGAGTAGTTTAATGCTCGGAGGAAAGTTCAAATTAATTTCTCA
TCCTAAACAAATGAAAAGAGAATATTAAATGAATATATAAGCGGCAATGATAAAATTGGTTTTAA
TCACGGTAATATTAAAGTTCAAACTAATTCCTATC
Found at i:40182 original size:27 final size:27
Alignment explanation
Indices: 40152--40204 Score: 88
Period size: 27 Copynumber: 2.0 Consensus size: 27
40142 AATATATAAG
40152 CGGCAATGATAAAATTGGTTTTAATCA
1 CGGCAATGATAAAATTGGTTTTAATCA
* *
40179 CGGCAATGGTATAATTGGTTTTAATC
1 CGGCAATGATAAAATTGGTTTTAATC
40205 GAATTAAACA
Statistics
Matches: 24, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
27 24 1.00
ACGTcount: A:0.32, C:0.11, G:0.21, T:0.36
Consensus pattern (27 bp):
CGGCAATGATAAAATTGGTTTTAATCA
Found at i:40651 original size:27 final size:27
Alignment explanation
Indices: 40611--40662 Score: 86
Period size: 27 Copynumber: 1.9 Consensus size: 27
40601 TATATAAGCG
40611 GCAATGATAAAATTGGTTTTAATCACA
1 GCAATGATAAAATTGGTTTTAATCACA
* *
40638 GCAATGGTATAATTGGTTTTAATCA
1 GCAATGATAAAATTGGTTTTAATCA
40663 AATTAAACAT
Statistics
Matches: 23, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
27 23 1.00
ACGTcount: A:0.37, C:0.10, G:0.17, T:0.37
Consensus pattern (27 bp):
GCAATGATAAAATTGGTTTTAATCACA
Found at i:40914 original size:24 final size:24
Alignment explanation
Indices: 40872--40923 Score: 61
Period size: 24 Copynumber: 2.2 Consensus size: 24
40862 TTTGTCTTTC
* *
40872 TACTTTTTTACTTGAATTTAGTCA
1 TACTATTTTACTTCAATTTAGTCA
* *
40896 TACTATTTTACTTCTATTTATTCA
1 TACTATTTTACTTCAATTTAGTCA
40920 -ACTA
1 TACTA
40924 AGAGAATATA
Statistics
Matches: 24, Mismatches: 4, Indels: 1
0.83 0.14 0.03
Matches are distributed among these distances:
23 4 0.17
24 20 0.83
ACGTcount: A:0.27, C:0.15, G:0.04, T:0.54
Consensus pattern (24 bp):
TACTATTTTACTTCAATTTAGTCA
Found at i:45039 original size:20 final size:21
Alignment explanation
Indices: 45014--45052 Score: 71
Period size: 21 Copynumber: 1.9 Consensus size: 21
45004 ACTAGCGCTG
45014 GGCG-CCCATGTGGTTTGCTT
1 GGCGCCCCATGTGGTTTGCTT
45034 GGCGCCCCATGTGGTTTGC
1 GGCGCCCCATGTGGTTTGC
45053 CTCGCGACCC
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:45063 original size:21 final size:21
Alignment explanation
Indices: 45018--45064 Score: 67
Period size: 21 Copynumber: 2.2 Consensus size: 21
45008 GCGCTGGGCG
* * *
45018 CCCATGTGGTTTGCTTGGCGC
1 CCCATGTGGTTTGCCTCGCGA
45039 CCCATGTGGTTTGCCTCGCGA
1 CCCATGTGGTTTGCCTCGCGA
45060 CCCAT
1 CCCAT
45065 TTACTCCAGT
Statistics
Matches: 23, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
21 23 1.00
ACGTcount: A:0.09, C:0.34, G:0.28, T:0.30
Consensus pattern (21 bp):
CCCATGTGGTTTGCCTCGCGA
Done.