Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01007604.1 Corchorus capsularis cultivar CVL-1 contig07625, 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: 58217
ACGTcount: A:0.32, C:0.17, G:0.17, T:0.33
Found at i:541 original size:29 final size:30
Alignment explanation
Indices: 509--578 Score: 88
Period size: 30 Copynumber: 2.4 Consensus size: 30
499 CACTAACAGT
*
509 CAAATAAGTCCCTGAACT-TCAATTTTGAC
1 CAAATAAGTCCCTGAACTATCAATTTCGAC
** *
538 CAAATAAACCCCTGAACTATCAATTTCGGC
1 CAAATAAGTCCCTGAACTATCAATTTCGAC
*
568 CAGATAAGTCC
1 CAAATAAGTCC
579 TTTATGAGAA
Statistics
Matches: 33, Mismatches: 7, Indels: 1
0.80 0.17 0.02
Matches are distributed among these distances:
29 16 0.48
30 17 0.52
ACGTcount: A:0.36, C:0.27, G:0.11, T:0.26
Consensus pattern (30 bp):
CAAATAAGTCCCTGAACTATCAATTTCGAC
Found at i:11989 original size:5 final size:5
Alignment explanation
Indices: 11979--12009 Score: 53
Period size: 5 Copynumber: 6.0 Consensus size: 5
11969 AACTTTATAC
11979 ATTTT ATTTT ATTTT ATTTT ATTTT AGTTTT
1 ATTTT ATTTT ATTTT ATTTT ATTTT A-TTTT
12010 TGGCAGTAAA
Statistics
Matches: 25, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
5 21 0.84
6 4 0.16
ACGTcount: A:0.19, C:0.00, G:0.03, T:0.77
Consensus pattern (5 bp):
ATTTT
Found at i:13197 original size:33 final size:34
Alignment explanation
Indices: 13139--13211 Score: 98
Period size: 36 Copynumber: 2.2 Consensus size: 34
13129 CTAAATTTTG
*
13139 TTTTCTTTTTTAATAAACAATTCATTTTTTCCTTCT
1 TTTTTTTTTTTAATAAACAATTCA-TTTTT-CTTCT
13175 TTTTTTTTTTTAA-AAA-AA-TCATTTTTCTTCT
1 TTTTTTTTTTTAATAAACAATTCATTTTTCTTCT
13206 TTTTTT
1 TTTTTT
13212 AAATCTCGTG
Statistics
Matches: 36, Mismatches: 1, Indels: 5
0.86 0.02 0.12
Matches are distributed among these distances:
31 11 0.31
32 5 0.14
33 3 0.08
34 2 0.06
35 3 0.08
36 12 0.33
ACGTcount: A:0.22, C:0.12, G:0.00, T:0.66
Consensus pattern (34 bp):
TTTTTTTTTTTAATAAACAATTCATTTTTCTTCT
Found at i:14968 original size:30 final size:30
Alignment explanation
Indices: 14932--15005 Score: 116
Period size: 29 Copynumber: 2.5 Consensus size: 30
14922 CGCTAAGCTA
14932 AGGGGGCAAAACGTCCCAAAATTGAAGTTC
1 AGGGGGCAAAACGTCCCAAAATTGAAGTTC
* *
14962 AGGGGGCAAAATGT-CCAAAATTTAAGTTC
1 AGGGGGCAAAACGTCCCAAAATTGAAGTTC
14991 A-GGGGCAAAACGTCC
1 AGGGGGCAAAACGTCC
15006 AAACGCTACA
Statistics
Matches: 40, Mismatches: 3, Indels: 3
0.87 0.07 0.07
Matches are distributed among these distances:
28 11 0.28
29 16 0.40
30 13 0.32
ACGTcount: A:0.36, C:0.19, G:0.27, T:0.18
Consensus pattern (30 bp):
AGGGGGCAAAACGTCCCAAAATTGAAGTTC
Found at i:15005 original size:28 final size:29
Alignment explanation
Indices: 14932--15008 Score: 120
Period size: 28 Copynumber: 2.7 Consensus size: 29
14922 CGCTAAGCTA
14932 AGGGGGCAAAACGTCCCAAAATTGAAGTTC
1 AGGGGGCAAAACGT-CCAAAATTGAAGTTC
* *
14962 AGGGGGCAAAATGTCCAAAATTTAAGTTC
1 AGGGGGCAAAACGTCCAAAATTGAAGTTC
14991 A-GGGGCAAAACGTCCAAA
1 AGGGGGCAAAACGTCCAAA
15009 CGCTACAAGT
Statistics
Matches: 44, Mismatches: 3, Indels: 2
0.90 0.06 0.04
Matches are distributed among these distances:
28 16 0.36
29 15 0.34
30 13 0.30
ACGTcount: A:0.39, C:0.18, G:0.26, T:0.17
Consensus pattern (29 bp):
AGGGGGCAAAACGTCCAAAATTGAAGTTC
Found at i:16394 original size:23 final size:23
Alignment explanation
Indices: 16364--16408 Score: 81
Period size: 23 Copynumber: 2.0 Consensus size: 23
16354 ATAGGTTTAA
*
16364 TATGTTTGAGTTTTGCTTGCTAG
1 TATGTTTGAGTTTTGCCTGCTAG
16387 TATGTTTGAGTTTTGCCTGCTA
1 TATGTTTGAGTTTTGCCTGCTA
16409 CTTGAGATGT
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:0.13, C:0.11, G:0.24, T:0.51
Consensus pattern (23 bp):
TATGTTTGAGTTTTGCCTGCTAG
Found at i:19416 original size:11 final size:10
Alignment explanation
Indices: 19398--19431 Score: 50
Period size: 11 Copynumber: 3.2 Consensus size: 10
19388 AATAGTATTC
19398 AAATCTTCAA
1 AAATCTTCAA
19408 AATATCTTCAA
1 AA-ATCTTCAA
19419 GAAATCTTCAA
1 -AAATCTTCAA
19430 AA
1 AA
19432 CACGAACTTC
Statistics
Matches: 22, Mismatches: 0, Indels: 4
0.85 0.00 0.15
Matches are distributed among these distances:
10 4 0.18
11 16 0.73
12 2 0.09
ACGTcount: A:0.50, C:0.18, G:0.03, T:0.29
Consensus pattern (10 bp):
AAATCTTCAA
Found at i:29906 original size:2 final size:2
Alignment explanation
Indices: 29899--29931 Score: 66
Period size: 2 Copynumber: 16.5 Consensus size: 2
29889 ATTAGGTACT
29899 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
29932 TCAAATCAAT
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 31 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:38272 original size:107 final size:107
Alignment explanation
Indices: 38100--38363 Score: 406
Period size: 107 Copynumber: 2.5 Consensus size: 107
38090 AATTTAGCCT
* *
38100 TAATTTCACTAAGTTTAGCCCCAAATTAAAATTTTATTTTTATTTTAAGGGTAAATTTCAAAATT
1 TAATTTCACTAAGTTTAGGCCCAAATTAAAATTTTATTTTTATTTTAAGGGTAAATTCCAAAATT
*
38165 AATAATTTATTGTTATAGGGTTTTAGAAATATAATACAAAAC
66 AATAATTTATTGTTATAGGGTTTTAGAAATAAAATACAAAAC
* *
38207 TAATTTTACTAAGTTTAGGCCCAAATTAAAATTTTATTTTTATTTTAAGGGTAAATTCCATAATT
1 TAATTTCACTAAGTTTAGGCCCAAATTAAAATTTTATTTTTATTTTAAGGGTAAATTCCAAAATT
* * *
38272 AATAGTTTATTGTTATAGGGTTTTAGAAATAAAATATATAAC
66 AATAATTTATTGTTATAGGGTTTTAGAAATAAAATACAAAAC
* ** *
38314 TAA-TTCATTAAGTTTA-GCCCAAATTAAAATTAAAATTTTATTTTAAGGGT
1 TAATTTCACTAAGTTTAGGCCCAAATTAAAATTTTATTTTTATTTTAAGGGT
38364 TAGAAAAATT
Statistics
Matches: 144, Mismatches: 13, Indels: 2
0.91 0.08 0.01
Matches are distributed among these distances:
105 31 0.22
106 11 0.08
107 102 0.71
ACGTcount: A:0.39, C:0.08, G:0.10, T:0.43
Consensus pattern (107 bp):
TAATTTCACTAAGTTTAGGCCCAAATTAAAATTTTATTTTTATTTTAAGGGTAAATTCCAAAATT
AATAATTTATTGTTATAGGGTTTTAGAAATAAAATACAAAAC
Found at i:41121 original size:28 final size:29
Alignment explanation
Indices: 41085--41142 Score: 73
Period size: 28 Copynumber: 2.0 Consensus size: 29
41075 AAAAATGACA
* *
41085 CGTGGCATGTGGCATTTTTG-ACATGTGG
1 CGTGCCATGTGGCATTTTTGTACACGTGG
* *
41113 CGTGCCATGTGTCCTTTTTGTACACGTGG
1 CGTGCCATGTGGCATTTTTGTACACGTGG
41142 C
1 C
41143 ATTTTTTGTA
Statistics
Matches: 25, Mismatches: 4, Indels: 1
0.83 0.13 0.03
Matches are distributed among these distances:
28 17 0.68
29 8 0.32
ACGTcount: A:0.12, C:0.21, G:0.31, T:0.36
Consensus pattern (29 bp):
CGTGCCATGTGGCATTTTTGTACACGTGG
Found at i:41150 original size:18 final size:18
Alignment explanation
Indices: 41127--41162 Score: 54
Period size: 18 Copynumber: 2.0 Consensus size: 18
41117 CCATGTGTCC
41127 TTTTTGTACACGTGGCAT
1 TTTTTGTACACGTGGCAT
* *
41145 TTTTTGTATATGTGGCAT
1 TTTTTGTACACGTGGCAT
41163 GCCACATCGG
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
18 16 1.00
ACGTcount: A:0.17, C:0.11, G:0.22, T:0.50
Consensus pattern (18 bp):
TTTTTGTACACGTGGCAT
Found at i:46127 original size:32 final size:31
Alignment explanation
Indices: 46091--46163 Score: 85
Period size: 32 Copynumber: 2.3 Consensus size: 31
46081 TTCAGGGCCC
*
46091 ATTTTGTCTTATTTAATCAAAATTTGAAG-GTT
1 ATTTTGTCTT-TTTAATCAAAA-TTGAAGAGAT
**
46123 ATTTTGTCATTTTTTGTCAAAATTGAAGAGAT
1 ATTTTGTC-TTTTTAATCAAAATTGAAGAGAT
46155 ATTTTGTCT
1 ATTTTGTCT
46164 ATCAATTTGT
Statistics
Matches: 36, Mismatches: 3, Indels: 5
0.82 0.07 0.11
Matches are distributed among these distances:
31 7 0.19
32 27 0.75
33 2 0.06
ACGTcount: A:0.29, C:0.07, G:0.14, T:0.51
Consensus pattern (31 bp):
ATTTTGTCTTTTTAATCAAAATTGAAGAGAT
Found at i:46642 original size:6 final size:6
Alignment explanation
Indices: 46631--46679 Score: 55
Period size: 6 Copynumber: 8.2 Consensus size: 6
46621 GCCCAAAGTA
* **
46631 AAAAAG AAAAAGG AAAAAC AAATGG AAAAAG AAAAAG AAAAA- AAAAAG
1 AAAAAG AAAAA-G AAAAAG AAAAAG AAAAAG AAAAAG AAAAAG AAAAAG
46679 A
1 A
46680 GATCCTCTCT
Statistics
Matches: 35, Mismatches: 6, Indels: 4
0.78 0.13 0.09
Matches are distributed among these distances:
5 5 0.14
6 24 0.69
7 6 0.17
ACGTcount: A:0.80, C:0.02, G:0.16, T:0.02
Consensus pattern (6 bp):
AAAAAG
Found at i:47897 original size:20 final size:20
Alignment explanation
Indices: 47868--47906 Score: 60
Period size: 20 Copynumber: 1.9 Consensus size: 20
47858 ATCTCCTTTT
*
47868 ATTTTCTTTTTCTTTTTTCC
1 ATTTTCTTTTTCCTTTTTCC
*
47888 ATTTTGTTTTTCCTTTTTC
1 ATTTTCTTTTTCCTTTTTC
47907 TTTTTACTTT
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.05, C:0.18, G:0.03, T:0.74
Consensus pattern (20 bp):
ATTTTCTTTTTCCTTTTTCC
Found at i:47916 original size:13 final size:13
Alignment explanation
Indices: 47869--47916 Score: 53
Period size: 13 Copynumber: 3.7 Consensus size: 13
47859 TCTCCTTTTA
47869 TTTT-CTTTTTCTT
1 TTTTCCTTTTTC-T
* *
47882 TTTTCCATTTTGT
1 TTTTCCTTTTTCT
47895 TTTTCCTTTTTCT
1 TTTTCCTTTTTCT
*
47908 TTTTACTTT
1 TTTTCCTTT
47917 GGGCGGGATG
Statistics
Matches: 29, Mismatches: 5, Indels: 2
0.81 0.14 0.06
Matches are distributed among these distances:
13 24 0.83
14 5 0.17
ACGTcount: A:0.04, C:0.17, G:0.02, T:0.77
Consensus pattern (13 bp):
TTTTCCTTTTTCT
Found at i:49115 original size:112 final size:112
Alignment explanation
Indices: 48987--49197 Score: 386
Period size: 112 Copynumber: 1.9 Consensus size: 112
48977 AGAAAATTAT
* * * *
48987 ATTATATACAAATTAAATTACTAGTTCCATATTCTACTATATTTTGTATATTTTCTAACTATATA
1 ATTATATACAAATTAAATTACTAATTCCATATTCTACTATATTTTGCATATTATCTAACTAAATA
49052 AAACAACATCATAATTGACAAATAATTTATACTAAATTAATGAGAAA
66 AAACAACATCATAATTGACAAATAATTTATACTAAATTAATGAGAAA
49099 ATTATATACAAATTAAATTACTAATTCCATATTCTACTATATTTTGCATATTATCTAACTAAATA
1 ATTATATACAAATTAAATTACTAATTCCATATTCTACTATATTTTGCATATTATCTAACTAAATA
49164 AAACAACATCATAATTGACAAATAATTTATACTA
66 AAACAACATCATAATTGACAAATAATTTATACTA
49198 TTTTCTTCAA
Statistics
Matches: 95, Mismatches: 4, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
112 95 1.00
ACGTcount: A:0.45, C:0.13, G:0.03, T:0.39
Consensus pattern (112 bp):
ATTATATACAAATTAAATTACTAATTCCATATTCTACTATATTTTGCATATTATCTAACTAAATA
AAACAACATCATAATTGACAAATAATTTATACTAAATTAATGAGAAA
Found at i:50846 original size:20 final size:20
Alignment explanation
Indices: 50821--50862 Score: 84
Period size: 20 Copynumber: 2.1 Consensus size: 20
50811 ATTAGACTCT
50821 TATTACTATTAATTAAGCTA
1 TATTACTATTAATTAAGCTA
50841 TATTACTATTAATTAAGCTA
1 TATTACTATTAATTAAGCTA
50861 TA
1 TA
50863 AATTTTGAGC
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 22 1.00
ACGTcount: A:0.40, C:0.10, G:0.05, T:0.45
Consensus pattern (20 bp):
TATTACTATTAATTAAGCTA
Found at i:53251 original size:13 final size:13
Alignment explanation
Indices: 53233--53262 Score: 60
Period size: 13 Copynumber: 2.3 Consensus size: 13
53223 TGTAAATAAT
53233 ATATACAGAGAGG
1 ATATACAGAGAGG
53246 ATATACAGAGAGG
1 ATATACAGAGAGG
53259 ATAT
1 ATAT
53263 TTTACAGATT
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 17 1.00
ACGTcount: A:0.47, C:0.07, G:0.27, T:0.20
Consensus pattern (13 bp):
ATATACAGAGAGG
Done.