Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01010731.1 Corchorus capsularis cultivar CVL-1 contig10752, 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: 26994
ACGTcount: A:0.33, C:0.17, G:0.19, T:0.31
Found at i:464 original size:38 final size:38
Alignment explanation
Indices: 432--656 Score: 264
Period size: 38 Copynumber: 6.0 Consensus size: 38
422 AATTAAGGAC
*
432 CAAAGTAATAGTAATCAGTAAAACTGATAATTAAGAGT
1 CAAAGTAATAGTAATCAGTAAAATTGATAATTAAGAGT
470 CAAAGTAATAGTAATCAGTAAAATTGATAATTAAGAGT
1 CAAAGTAATAGTAATCAGTAAAATTGATAATTAAGAGT
* *
508 CAAAGTAAGAGTAATCAATAAAATTGATAATTAAGAGT
1 CAAAGTAATAGTAATCAGTAAAATTGATAATTAAGAGT
* * * *
546 CAAAGTAAGAGTAATCAATAAAATTGATAATCAAGGGT
1 CAAAGTAATAGTAATCAGTAAAATTGATAATTAAGAGT
* *
584 CAAGGTAAAAATAGTAATCAGT-AAA-TCAGTAATTAAGAGT
1 CAAAGT---AATAGTAATCAGTAAAATTGA-TAATTAAGAGT
** *
624 C-AAGGGAT--TAATCAGT-AAATTGATACTTAAGAG
1 CAAAGTAATAGTAATCAGTAAAATTGATAATTAAGAG
657 AGAGAGTAAA
Statistics
Matches: 166, Mismatches: 16, Indels: 14
0.85 0.08 0.07
Matches are distributed among these distances:
34 20 0.12
35 2 0.01
36 2 0.01
38 114 0.69
39 4 0.02
40 13 0.08
41 11 0.07
ACGTcount: A:0.49, C:0.07, G:0.17, T:0.26
Consensus pattern (38 bp):
CAAAGTAATAGTAATCAGTAAAATTGATAATTAAGAGT
Found at i:670 original size:114 final size:113
Alignment explanation
Indices: 422--675 Score: 268
Period size: 114 Copynumber: 2.2 Consensus size: 113
412 ACCCCAATAA
* * *
422 AATTAAG-GACCAAAGTAATAGTAATCAGTAAAACTGATAATTAAGAGTCAAAGTAATAGTAATC
1 AATTAAGAGA-CAAAGTAAGAGTAATCAATAAAACTGATAATCAAGAGTCAAAGTAATAGTAATC
*
486 AGTAAAATTGATAATTAAGAGTCAAAGTAAGAGTAATCAATAAAATTGAT
65 AGTAAAATAGATAATTAAGAGTCAAAG-AAGAGTAATCAATAAAATTGAT
* * * *
536 AATTAAGAGTCAAAGTAAGAGTAATCAATAAAATTGATAATCAAGGGTCAAGGTAAAAATAGTAA
1 AATTAAGAGACAAAGTAAGAGTAATCAATAAAACTGATAATCAAGAGTCAAAGT---AATAGTAA
* * *
601 TCAGT-AAATCAG-TAATTAAGAGTC-AAG-GGATTAATCAGT-AAATTGAT
63 TCAGTAAAAT-AGATAATTAAGAGTCAAAGAAGAGTAATCAATAAAATTGAT
* * *
648 ACTTAAGAGAGAGAGTAAAAGAGTAATC
1 AATTAAGAGACAAAGT--AAGAGTAATC
676 GGTAATTAAG
Statistics
Matches: 118, Mismatches: 15, Indels: 14
0.80 0.10 0.10
Matches are distributed among these distances:
112 20 0.17
113 9 0.08
114 55 0.47
115 4 0.03
116 16 0.14
117 14 0.12
ACGTcount: A:0.50, C:0.07, G:0.18, T:0.25
Consensus pattern (113 bp):
AATTAAGAGACAAAGTAAGAGTAATCAATAAAACTGATAATCAAGAGTCAAAGTAATAGTAATCA
GTAAAATAGATAATTAAGAGTCAAAGAAGAGTAATCAATAAAATTGAT
Found at i:745 original size:33 final size:32
Alignment explanation
Indices: 664--750 Score: 129
Period size: 32 Copynumber: 2.7 Consensus size: 32
654 GAGAGAGAGT
* *
664 AAAAGAGTAATCGGTAATTAAGAAAGGAAGTA
1 AAAAGACTAATCAGTAATTAAGAAAGGAAGTA
*
696 AAAAGATTAATCAGTAATTAAGAAAGGAAGTA
1 AAAAGACTAATCAGTAATTAAGAAAGGAAGTA
728 AAAAGGACTAATCAGTAAATTAA
1 AAAA-GACTAATCAGT-AATTAA
751 TAATTAAGAA
Statistics
Matches: 50, Mismatches: 3, Indels: 2
0.91 0.05 0.04
Matches are distributed among these distances:
32 34 0.68
33 10 0.20
34 6 0.12
ACGTcount: A:0.55, C:0.05, G:0.20, T:0.21
Consensus pattern (32 bp):
AAAAGACTAATCAGTAATTAAGAAAGGAAGTA
Found at i:1016 original size:14 final size:14
Alignment explanation
Indices: 995--1029 Score: 61
Period size: 14 Copynumber: 2.5 Consensus size: 14
985 GTAAAAAGGT
995 AAAGTAATCAGTAA
1 AAAGTAATCAGTAA
*
1009 AGAGTAATCAGTAA
1 AAAGTAATCAGTAA
1023 AAAGTAA
1 AAAGTAA
1030 AAATGGCAAA
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
14 19 1.00
ACGTcount: A:0.57, C:0.06, G:0.17, T:0.20
Consensus pattern (14 bp):
AAAGTAATCAGTAA
Found at i:1169 original size:25 final size:26
Alignment explanation
Indices: 1119--1176 Score: 75
Period size: 26 Copynumber: 2.3 Consensus size: 26
1109 CAAGTGAAAT
*
1119 ATGGTATTGAGTAAGAAGGTCAAAAA
1 ATGGTATTAAGTAAGAAGGTCAAAAA
*
1145 ATGGTGTTAAGTAA-AAGGGTC-AAAA
1 ATGGTATTAAGTAAGAA-GGTCAAAAA
1170 ATGGTAT
1 ATGGTAT
1177 CCATAAGAGA
Statistics
Matches: 28, Mismatches: 3, Indels: 3
0.82 0.09 0.09
Matches are distributed among these distances:
25 12 0.43
26 16 0.57
ACGTcount: A:0.43, C:0.03, G:0.28, T:0.26
Consensus pattern (26 bp):
ATGGTATTAAGTAAGAAGGTCAAAAA
Found at i:1245 original size:15 final size:15
Alignment explanation
Indices: 1225--1254 Score: 51
Period size: 15 Copynumber: 2.0 Consensus size: 15
1215 AAAGAGTAAG
*
1225 AAAAATGGTAAAAGT
1 AAAAATGATAAAAGT
1240 AAAAATGATAAAAGT
1 AAAAATGATAAAAGT
1255 GGCAAAAGTA
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.63, C:0.00, G:0.17, T:0.20
Consensus pattern (15 bp):
AAAAATGATAAAAGT
Found at i:1261 original size:24 final size:24
Alignment explanation
Indices: 1225--1270 Score: 74
Period size: 24 Copynumber: 1.9 Consensus size: 24
1215 AAAGAGTAAG
*
1225 AAAAATGGTAAAAGTAAAAATGAT
1 AAAAATGGCAAAAGTAAAAATGAT
*
1249 AAAAGTGGCAAAAGTAAAAATG
1 AAAAATGGCAAAAGTAAAAATG
1271 GTAATCAGTA
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
24 20 1.00
ACGTcount: A:0.61, C:0.02, G:0.20, T:0.17
Consensus pattern (24 bp):
AAAAATGGCAAAAGTAAAAATGAT
Found at i:4191 original size:31 final size:30
Alignment explanation
Indices: 4155--4223 Score: 84
Period size: 30 Copynumber: 2.3 Consensus size: 30
4145 AAGATTACCA
* *
4155 ATTGACTCTATTAAAATAATAAATTTATAAT
1 ATTGACCCTACTAAAATAA-AAATTTATAAT
* **
4186 TTTGACCCTACTAAAATAAAGTTTTATAAT
1 ATTGACCCTACTAAAATAAAAATTTATAAT
4216 ATTGACCC
1 ATTGACCC
4224 CACTTTTTTT
Statistics
Matches: 32, Mismatches: 6, Indels: 1
0.82 0.15 0.03
Matches are distributed among these distances:
30 16 0.50
31 16 0.50
ACGTcount: A:0.42, C:0.13, G:0.06, T:0.39
Consensus pattern (30 bp):
ATTGACCCTACTAAAATAAAAATTTATAAT
Found at i:13857 original size:22 final size:22
Alignment explanation
Indices: 13832--13892 Score: 61
Period size: 22 Copynumber: 2.8 Consensus size: 22
13822 GGACGTGAAC
13832 AAAATTTCATTGG-GAGGTTATG
1 AAAATTTCA-TGGAGAGGTTATG
* **
13854 AAAATTTTATGGAGAGGTTACC
1 AAAATTTCATGGAGAGGTTATG
* *
13876 AAAATTACATAGAGAGG
1 AAAATTTCATGGAGAGG
13893 ATATCACCGT
Statistics
Matches: 32, Mismatches: 6, Indels: 2
0.80 0.15 0.05
Matches are distributed among these distances:
21 3 0.09
22 29 0.91
ACGTcount: A:0.39, C:0.07, G:0.25, T:0.30
Consensus pattern (22 bp):
AAAATTTCATGGAGAGGTTATG
Found at i:14010 original size:22 final size:22
Alignment explanation
Indices: 13971--14088 Score: 89
Period size: 22 Copynumber: 5.5 Consensus size: 22
13961 CGCAGTTACC
* ** *
13971 AATTTTATAGTGTTATTATCAG
1 AATTTCATAGTGAGATTATCAA
* *
13993 AATTTTATAGGGAGATTATCAA
1 AATTTCATAGTGAGATTATCAA
* * *
14015 AATTTCACACTGAGATTATCAC
1 AATTTCATAGTGAGATTATCAA
*
14037 AATTTCATAGTG-G-TTATAAA
1 AATTTCATAGTGAGATTATCAA
* *
14057 AATTTCACAGT-ATGGTTATCAA
1 AATTTCATAGTGA-GATTATCAA
*
14079 ATTTTCATAG
1 AATTTCATAG
14089 GCAAATAGAG
Statistics
Matches: 76, Mismatches: 17, Indels: 6
0.77 0.17 0.06
Matches are distributed among these distances:
20 15 0.20
21 2 0.03
22 59 0.78
ACGTcount: A:0.36, C:0.10, G:0.14, T:0.40
Consensus pattern (22 bp):
AATTTCATAGTGAGATTATCAA
Found at i:14076 original size:42 final size:42
Alignment explanation
Indices: 13985--14088 Score: 106
Period size: 42 Copynumber: 2.4 Consensus size: 42
13975 TTATAGTGTT
* *
13985 ATTATCAGAATTTT-ATAGGGAGATTATCAAAATTTCACACTGAG
1 ATTATCA-AATTTTCATAGTG-G-TTATAAAAATTTCACACTGAG
*
14029 ATTATCACAA-TTTCATAGTGGTTATAAAAATTTCACAGT-ATG
1 ATTATCA-AATTTTCATAGTGGTTATAAAAATTTCACACTGA-G
*
14071 GTTATCAAATTTTCATAG
1 ATTATCAAATTTTCATAG
14089 GCAAATAGAG
Statistics
Matches: 52, Mismatches: 5, Indels: 8
0.80 0.08 0.12
Matches are distributed among these distances:
41 3 0.06
42 31 0.60
43 4 0.08
44 14 0.27
ACGTcount: A:0.38, C:0.12, G:0.13, T:0.38
Consensus pattern (42 bp):
ATTATCAAATTTTCATAGTGGTTATAAAAATTTCACACTGAG
Found at i:20721 original size:45 final size:45
Alignment explanation
Indices: 20670--20755 Score: 147
Period size: 45 Copynumber: 1.9 Consensus size: 45
20660 AGAGTAGTGG
*
20670 AATTACTAAAAGATCCGTACCTC-GAATTAATGATGAGCTGGGTGA
1 AATTACTAAAAGATCCCTACC-CAGAATTAATGATGAGCTGGGTGA
20715 AATTACTAAAAGATCCCTACCCAGAATTAATGATGAGCTGG
1 AATTACTAAAAGATCCCTACCCAGAATTAATGATGAGCTGG
20756 AGAAGTAATC
Statistics
Matches: 39, Mismatches: 1, Indels: 2
0.93 0.02 0.05
Matches are distributed among these distances:
44 1 0.03
45 38 0.97
ACGTcount: A:0.37, C:0.17, G:0.20, T:0.26
Consensus pattern (45 bp):
AATTACTAAAAGATCCCTACCCAGAATTAATGATGAGCTGGGTGA
Found at i:21430 original size:166 final size:168
Alignment explanation
Indices: 21065--21465 Score: 549
Period size: 168 Copynumber: 2.4 Consensus size: 168
21055 TAAAGTTTAA
* * *
21065 ACTTAAATGTCATAACTTTTGATTCTAGAGGGGATTAAATAACT-ATACTTTTTTGACATTTCTC
1 ACTTAAATGTCATAACTTTTGATTCTTGAGGGGATTAAATAACTAAT-CTTTTTGGTCATTTCTC
* * * * * * * **
21129 AATTGACTTTAATATAGTAGTGGAATTACTAAAAGGTCCCTACCAAGACTTGGTTTTGGAGTTAG
65 AATGGACTTGAATAGAGTAGTGGAATTAATAAAAGATCACTACCAAGACTTGATGATGGAGTTAG
* * *
21194 AGAACTTATTTTTTTCCGTCTTTTCCTACTTGGCAGATT
130 AGAACTTATCTTTTTCCGTCTTTACCTACTTCGCAGATT
* *
21233 ACTTAAATGTCAAAACTTTTGATTCTTGAGGGGATTAAATAAGTAATCTTTTTGGTCATTTCTCA
1 ACTTAAATGTCATAACTTTTGATTCTTGAGGGGATTAAATAACTAATCTTTTTGGTCATTTCTCA
*
21298 ATGGACTTGAATAGAGTAGTGGAATTAATAAAAGATCACTATCAAGGA-TTGATGAT-GAGTTAG
66 ATGGACTTGAATAGAGTAGTGGAATTAATAAAAGATCACTACCAA-GACTTGATGATGGAGTTAG
*
21361 AGAACTTATCTTTTT-CGTCTTTACCTATTTCGCAGATT
130 AGAACTTATCTTTTTCCGTCTTTACCTACTTCGCAGATT
* * * *
21399 ACTTAAATGTCCTAACTTTTGATTTTTGAGGGAATTAAATAACTAAACTTTTTGGTCATTTCTCA
1 ACTTAAATGTCATAACTTTTGATTCTTGAGGGGATTAAATAACTAATCTTTTTGGTCATTTCTCA
21464 AT
66 AT
21466 TGACAAATGA
Statistics
Matches: 206, Mismatches: 25, Indels: 6
0.87 0.11 0.03
Matches are distributed among these distances:
166 81 0.39
167 21 0.10
168 100 0.49
169 4 0.02
ACGTcount: A:0.30, C:0.13, G:0.16, T:0.40
Consensus pattern (168 bp):
ACTTAAATGTCATAACTTTTGATTCTTGAGGGGATTAAATAACTAATCTTTTTGGTCATTTCTCA
ATGGACTTGAATAGAGTAGTGGAATTAATAAAAGATCACTACCAAGACTTGATGATGGAGTTAGA
GAACTTATCTTTTTCCGTCTTTACCTACTTCGCAGATT
Done.