Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01006442.1 Corchorus capsularis cultivar CVL-1 contig06463, 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: 19213
ACGTcount: A:0.30, C:0.18, G:0.17, T:0.34
Found at i:11 original size:2 final size:2
Alignment explanation
Indices: 5--46 Score: 57
Period size: 2 Copynumber: 21.0 Consensus size: 2
1 TATC
* * *
5 TA TA TA TA TA TA TC TA TC TA TG 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 TA TA TA TA
47 ATTTTTTTTT
Statistics
Matches: 34, Mismatches: 6, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
2 34 1.00
ACGTcount: A:0.43, C:0.05, G:0.02, T:0.50
Consensus pattern (2 bp):
TA
Found at i:375 original size:55 final size:55
Alignment explanation
Indices: 291--419 Score: 249
Period size: 55 Copynumber: 2.3 Consensus size: 55
281 TGGATTAGTA
*
291 ATAAAATTTAATTTGATTAGCAATTATTACCTAACTAGACTACTACTCTTACTAT
1 ATAAAATTTAATTTGATTAGCAATTATTACCTAACAAGACTACTACTCTTACTAT
346 ATAAAATTTAATTTGATTAGCAATTATTACCTAACAAGACTACTACTCTTACTAT
1 ATAAAATTTAATTTGATTAGCAATTATTACCTAACAAGACTACTACTCTTACTAT
401 ATAAAATTTAATTTGATTA
1 ATAAAATTTAATTTGATTA
420 ATACTACTCT
Statistics
Matches: 73, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
55 73 1.00
ACGTcount: A:0.40, C:0.14, G:0.05, T:0.40
Consensus pattern (55 bp):
ATAAAATTTAATTTGATTAGCAATTATTACCTAACAAGACTACTACTCTTACTAT
Found at i:6564 original size:14 final size:14
Alignment explanation
Indices: 6545--6581 Score: 60
Period size: 14 Copynumber: 2.8 Consensus size: 14
6535 TCTATAATTT
6545 TTATTGGGTTAAAG
1 TTATTGGGTTAAAG
6559 TTATTGGGTT-AAG
1 TTATTGGGTTAAAG
6572 -TATTGGGTTA
1 TTATTGGGTTA
6582 TAATTAATTG
Statistics
Matches: 22, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
12 9 0.41
13 3 0.14
14 10 0.45
ACGTcount: A:0.24, C:0.00, G:0.30, T:0.46
Consensus pattern (14 bp):
TTATTGGGTTAAAG
Found at i:6576 original size:26 final size:27
Alignment explanation
Indices: 6546--6600 Score: 78
Period size: 27 Copynumber: 2.1 Consensus size: 27
6536 CTATAATTTT
*
6546 TATTGGGTTA-AAGTT-ATTGGGTTAAG
1 TATTGGGTTATAA-TTAATTGGATTAAG
6572 TATTGGGTTATAATTAATTGGATTAAG
1 TATTGGGTTATAATTAATTGGATTAAG
6599 TA
1 TA
6601 GAGGTCTTTT
Statistics
Matches: 26, Mismatches: 1, Indels: 3
0.87 0.03 0.10
Matches are distributed among these distances:
26 12 0.46
27 14 0.54
ACGTcount: A:0.31, C:0.00, G:0.25, T:0.44
Consensus pattern (27 bp):
TATTGGGTTATAATTAATTGGATTAAG
Found at i:6577 original size:12 final size:13
Alignment explanation
Indices: 6545--6581 Score: 58
Period size: 12 Copynumber: 2.8 Consensus size: 13
6535 TCTATAATTT
6545 TTATTGGGTTAAAG
1 TTATTGGGTT-AAG
6559 TTATTGGGTTAAG
1 TTATTGGGTTAAG
6572 -TATTGGGTTA
1 TTATTGGGTTA
6582 TAATTAATTG
Statistics
Matches: 23, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
12 10 0.43
13 3 0.13
14 10 0.43
ACGTcount: A:0.24, C:0.00, G:0.30, T:0.46
Consensus pattern (13 bp):
TTATTGGGTTAAG
Found at i:8660 original size:87 final size:88
Alignment explanation
Indices: 8507--8667 Score: 227
Period size: 87 Copynumber: 1.8 Consensus size: 88
8497 TGATAAGAAT
* * ***
8507 TAATAATGAGAATATTTTCTAAATCTTGCCAAATTGTGGAGGGTTTAGGAGATATTTTAAGAAAA
1 TAATAATGAGAATATTTTCTAAATCTTGCCAAATTGTGGAGGATTTAGAAGATATAAAAAGAAAA
8572 TA-AATAAATTATAAAGATTGAA
66 TATAATAAATTATAAAGATTGAA
* * *
8594 TAATAATGAGGATATTTTCTAAATCTTGTCAAATTGTGG-GAGATTTAGAAGATATAAAAAGGAA
1 TAATAATGAGAATATTTTCTAAATCTTGCCAAATTGTGGAG-GATTTAGAAGATATAAAAAGAAA
8658 ATATAATAAA
65 ATATAATAAA
8668 AATTAAATAA
Statistics
Matches: 64, Mismatches: 8, Indels: 3
0.85 0.11 0.04
Matches are distributed among these distances:
86 1 0.02
87 57 0.89
88 6 0.09
ACGTcount: A:0.45, C:0.04, G:0.17, T:0.34
Consensus pattern (88 bp):
TAATAATGAGAATATTTTCTAAATCTTGCCAAATTGTGGAGGATTTAGAAGATATAAAAAGAAAA
TATAATAAATTATAAAGATTGAA
Found at i:10502 original size:37 final size:37
Alignment explanation
Indices: 10461--10537 Score: 136
Period size: 37 Copynumber: 2.1 Consensus size: 37
10451 TTCTTTTTTT
*
10461 TTCTTGCTTAAGAGCGTTGCAACATTTATTTCATAGG
1 TTCTTGCTTAAGAGCGTTGCAACATTTATTTCATAAG
*
10498 TTCTTGCTTAGGAGCGTTGCAACATTTATTTCATAAG
1 TTCTTGCTTAAGAGCGTTGCAACATTTATTTCATAAG
10535 TTC
1 TTC
10538 AGAGTGAGCA
Statistics
Matches: 38, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
37 38 1.00
ACGTcount: A:0.23, C:0.17, G:0.18, T:0.42
Consensus pattern (37 bp):
TTCTTGCTTAAGAGCGTTGCAACATTTATTTCATAAG
Found at i:13649 original size:36 final size:35
Alignment explanation
Indices: 13586--13654 Score: 102
Period size: 36 Copynumber: 1.9 Consensus size: 35
13576 TCCTTTTGAT
13586 TCAGATTTGCTTTGTTGATGGAAAAGAAATTTGTC
1 TCAGATTTGCTTTGTTGATGGAAAAGAAATTTGTC
* * *
13621 TCAGATTTGTTTTGCTTGATGGAGAAGAACTTTG
1 TCAGATTTGCTTTG-TTGATGGAAAAGAAATTTG
13655 CCTTTGAACT
Statistics
Matches: 30, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
35 13 0.43
36 17 0.57
ACGTcount: A:0.26, C:0.09, G:0.25, T:0.41
Consensus pattern (35 bp):
TCAGATTTGCTTTGTTGATGGAAAAGAAATTTGTC
Found at i:14242 original size:21 final size:21
Alignment explanation
Indices: 14218--14260 Score: 86
Period size: 21 Copynumber: 2.0 Consensus size: 21
14208 CATTATAATA
14218 AATAATCTTAAGTAAGTTATT
1 AATAATCTTAAGTAAGTTATT
14239 AATAATCTTAAGTAAGTTATT
1 AATAATCTTAAGTAAGTTATT
14260 A
1 A
14261 GATTATTTAT
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 22 1.00
ACGTcount: A:0.44, C:0.05, G:0.09, T:0.42
Consensus pattern (21 bp):
AATAATCTTAAGTAAGTTATT
Found at i:14925 original size:12 final size:12
Alignment explanation
Indices: 14908--14949 Score: 59
Period size: 12 Copynumber: 3.6 Consensus size: 12
14898 TTCTTCAAAG
*
14908 CATTTTTGTTGC
1 CATTTTTCTTGC
*
14920 CATTTTTCTTAC
1 CATTTTTCTTGC
14932 C-TTTTTCTTGC
1 CATTTTTCTTGC
14943 CATTTTT
1 CATTTTT
14950 TCCCTTTTTT
Statistics
Matches: 26, Mismatches: 3, Indels: 2
0.84 0.10 0.06
Matches are distributed among these distances:
11 10 0.38
12 16 0.62
ACGTcount: A:0.10, C:0.21, G:0.07, T:0.62
Consensus pattern (12 bp):
CATTTTTCTTGC
Found at i:14948 original size:22 final size:23
Alignment explanation
Indices: 14910--14963 Score: 67
Period size: 22 Copynumber: 2.4 Consensus size: 23
14900 CTTCAAAGCA
*
14910 TTTTTGTTGCCATTTTTCTTACC-
1 TTTTTCTTGCCATTTTT-TTACCT
*
14933 TTTTTCTTGCCA-TTTTTTCCCT
1 TTTTTCTTGCCATTTTTTTACCT
14955 TTTTTCTTG
1 TTTTTCTTG
14964 TCATAGATTT
Statistics
Matches: 28, Mismatches: 2, Indels: 3
0.85 0.06 0.09
Matches are distributed among these distances:
21 4 0.14
22 13 0.46
23 11 0.39
ACGTcount: A:0.06, C:0.22, G:0.07, T:0.65
Consensus pattern (23 bp):
TTTTTCTTGCCATTTTTTTACCT
Found at i:15383 original size:21 final size:20
Alignment explanation
Indices: 15357--15414 Score: 82
Period size: 19 Copynumber: 2.9 Consensus size: 20
15347 TTTGAAGTTT
15357 CATTACACCTAATAGTGATAC
1 CATTACACCTAATAGTGA-AC
*
15378 CATTACACCTAAAAG-GAAC
1 CATTACACCTAATAGTGAAC
*
15397 CATTACACCAAATAGTGA
1 CATTACACCTAATAGTGA
15415 CAACATTTCA
Statistics
Matches: 33, Mismatches: 3, Indels: 3
0.85 0.08 0.08
Matches are distributed among these distances:
19 15 0.45
20 4 0.12
21 14 0.42
ACGTcount: A:0.43, C:0.24, G:0.10, T:0.22
Consensus pattern (20 bp):
CATTACACCTAATAGTGAAC
Found at i:15400 original size:19 final size:21
Alignment explanation
Indices: 15357--15414 Score: 77
Period size: 21 Copynumber: 2.9 Consensus size: 21
15347 TTTGAAGTTT
*
15357 CATTACACCTAATAGTGATAC
1 CATTACACCTAAAAGTGATAC
15378 CATTACACCTAAAAG-GA-AC
1 CATTACACCTAAAAGTGATAC
15397 CATTACACC-AAATAGTGA
1 CATTACACCTAAA-AGTGA
15415 CAACATTTCA
Statistics
Matches: 34, Mismatches: 1, Indels: 5
0.85 0.03 0.12
Matches are distributed among these distances:
18 3 0.09
19 13 0.38
20 4 0.12
21 14 0.41
ACGTcount: A:0.43, C:0.24, G:0.10, T:0.22
Consensus pattern (21 bp):
CATTACACCTAAAAGTGATAC
Found at i:16049 original size:64 final size:63
Alignment explanation
Indices: 15906--16062 Score: 179
Period size: 64 Copynumber: 2.5 Consensus size: 63
15896 GATAAAACTG
* * * * * *
15906 ACCCTTTGTCCGAAAGGGTATTTTGGGAAAACTAAACTTAAATGCAGGAATGTGACGAAACTA
1 ACCCTTTGTCCGAAAGGGCATTTTAGGAAAACTAAACTTAAATGCAAGAATATGACAAAACCA
* * * * *
15969 GCCTTTTGTTCAAAAGGGCGTTTTAGGAAAACTAGAACTTAAATGCAAGAATATGACAAAACCA
1 ACCCTTTGTCCGAAAGGGCATTTTAGGAAAACTA-AACTTAAATGCAAGAATATGACAAAACCA
* * *
16033 ACCCTTGGTCCGAAAGGGTATTTTGGGAAA
1 ACCCTTTGTCCGAAAGGGCATTTTAGGAAA
16063 TAGCAAGTAA
Statistics
Matches: 74, Mismatches: 19, Indels: 1
0.79 0.20 0.01
Matches are distributed among these distances:
63 27 0.36
64 47 0.64
ACGTcount: A:0.36, C:0.16, G:0.22, T:0.25
Consensus pattern (63 bp):
ACCCTTTGTCCGAAAGGGCATTTTAGGAAAACTAAACTTAAATGCAAGAATATGACAAAACCA
Found at i:16150 original size:49 final size:49
Alignment explanation
Indices: 16046--16452 Score: 628
Period size: 49 Copynumber: 8.4 Consensus size: 49
16036 CTTGGTCCGA
* * **
16046 AAGGGTATTTTGGGAAATAGCA-AGT-AAAATAAGTATCTTCCGTCCGGG
1 AAGGGCATTTTGGGAAATAGCAGA-TAAAAACAAGTGCCTTCCGTCCGGG
*
16094 AAGGGCATTTTGGGAAGTAGCAGATAAAAACAAGTGCCTTCCGTCCGGG
1 AAGGGCATTTTGGGAAATAGCAGATAAAAACAAGTGCCTTCCGTCCGGG
*
16143 AAGGGCATTTTGGGAAGTAGCAGATAAAAACAAGTGCCTTCCGTCCGGG
1 AAGGGCATTTTGGGAAATAGCAGATAAAAACAAGTGCCTTCCGTCCGGG
* *
16192 AATGGCA-TTTGGG-AATAGCAGATAAAAACAGGTGCCTTCCGTCCGGG
1 AAGGGCATTTTGGGAAATAGCAGATAAAAACAAGTGCCTTCCGTCCGGG
16239 AAGGGCATTTTGGGAAATAGCAGATAAAAACAAGTGCCTTCCGTCCGGG
1 AAGGGCATTTTGGGAAATAGCAGATAAAAACAAGTGCCTTCCGTCCGGG
* *
16288 AATGGCATTTTGGGAAATAGCAGATAAAAACAGGTGCCTTCCGTCCGGG
1 AAGGGCATTTTGGGAAATAGCAGATAAAAACAAGTGCCTTCCGTCCGGG
*
16337 AAGGGCATTTTGGGAAATAGCAGAT-AAAACAAGTGCCTTCCATCCGGG
1 AAGGGCATTTTGGGAAATAGCAGATAAAAACAAGTGCCTTCCGTCCGGG
* *
16385 AAGGGCATTTTGGGAAATAGCAGATGAAAACCAA-TGCCTTCCGCCCGGG
1 AAGGGCATTTTGGGAAATAGCAGAT-AAAAACAAGTGCCTTCCGTCCGGG
16434 AAGGGCATTTTTGGGAAAT
1 AAGGGCA-TTTTGGGAAAT
16453 GTAAAATTTG
Statistics
Matches: 334, Mismatches: 18, Indels: 12
0.92 0.05 0.03
Matches are distributed among these distances:
47 38 0.11
48 79 0.24
49 200 0.60
50 17 0.05
ACGTcount: A:0.31, C:0.18, G:0.29, T:0.22
Consensus pattern (49 bp):
AAGGGCATTTTGGGAAATAGCAGATAAAAACAAGTGCCTTCCGTCCGGG
Found at i:16303 original size:145 final size:146
Alignment explanation
Indices: 16046--16452 Score: 633
Period size: 145 Copynumber: 2.8 Consensus size: 146
16036 CTTGGTCCGA
* * **
16046 AAGGGTATTTTGGGAAATAGCA-AGTAAAATAAGTATCTTCCGTCCGGGAAGGGCATTTTGGGAA
1 AAGGGCATTTTGGGAAATAGCAGA-TAAAACAAGTGCCTTCCGTCCGGGAAGGGCATTTTGGGAA
* *
16110 GTAGCAGATAAAAACAAGTGCCTTCCGTCCGGGAAGGGCATTTTGGGAAGTAGCAGATAAAAACA
65 ATAGCAGATAAAAACAAGTGCCTTCCGTCCGGGAAGGGCATTTTGGGAAATAGCAGATAAAAACA
16175 AGTGCCTTCCGTCCGGG
130 AGTGCCTTCCGTCCGGG
* *
16192 AATGGCA-TTTGGG-AATAGCAGATAAAAACAGGTGCCTTCCGTCCGGGAAGGGCATTTTGGGAA
1 AAGGGCATTTTGGGAAATAGCAGAT-AAAACAAGTGCCTTCCGTCCGGGAAGGGCATTTTGGGAA
*
16255 ATAGCAGATAAAAACAAGTGCCTTCCGTCCGGGAATGGCATTTTGGGAAATAGCAGATAAAAACA
65 ATAGCAGATAAAAACAAGTGCCTTCCGTCCGGGAAGGGCATTTTGGGAAATAGCAGATAAAAACA
*
16320 GGTGCCTTCCGTCCGGG
130 AGTGCCTTCCGTCCGGG
*
16337 AAGGGCATTTTGGGAAATAGCAGATAAAACAAGTGCCTTCCATCCGGGAAGGGCATTTTGGGAAA
1 AAGGGCATTTTGGGAAATAGCAGATAAAACAAGTGCCTTCCGTCCGGGAAGGGCATTTTGGGAAA
* *
16402 TAGCAGATGAAAACCAA-TGCCTTCCGCCCGGGAAGGGCATTTTTGGGAAAT
66 TAGCAGAT-AAAAACAAGTGCCTTCCGTCCGGGAAGGGCA-TTTTGGGAAAT
16453 GTAAAATTTG
Statistics
Matches: 239, Mismatches: 16, Indels: 11
0.90 0.06 0.04
Matches are distributed among these distances:
144 8 0.03
145 126 0.53
146 77 0.32
147 28 0.12
ACGTcount: A:0.31, C:0.18, G:0.29, T:0.22
Consensus pattern (146 bp):
AAGGGCATTTTGGGAAATAGCAGATAAAACAAGTGCCTTCCGTCCGGGAAGGGCATTTTGGGAAA
TAGCAGATAAAAACAAGTGCCTTCCGTCCGGGAAGGGCATTTTGGGAAATAGCAGATAAAAACAA
GTGCCTTCCGTCCGGG
Done.