Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01006727.1 Corchorus capsularis cultivar CVL-1 contig06748, 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: 12644
ACGTcount: A:0.35, C:0.17, G:0.18, T:0.30
Found at i:105 original size:50 final size:50
Alignment explanation
Indices: 34--324 Score: 390
Period size: 50 Copynumber: 5.8 Consensus size: 50
24 TCCTCTTATT
34 CCAAAATGCCCCTTCCCGGTCGGAAGGTCCCTGTTTTCTTTGTTTGCTTC
1 CCAAAATGCCCCTTCCCGGTCGGAAGGTCCCTGTTTTCTTTGTTTGCTTC
* * * *
84 CCAAAATGCCCATTCCCGGTCGGAAGGTCCTTGTTTTCTTTATTTGTTTC
1 CCAAAATGCCCCTTCCCGGTCGGAAGGTCCCTGTTTTCTTTGTTTGCTTC
* *
134 CAAAAATGCCCCTTCCCGGTCGGAAGGTCCTCGTTTTTTCTTTGTTTG-TTC
1 CCAAAATGCCCCTTCCCGGTCGGAAGGTCC-C-TGTTTTCTTTGTTTGCTTC
* *
185 ACCAAAAATGCCCCTTCCCGGTCGGAAGGT-CCTCGTTTTCTTTTTTTGCTTA
1 -CC-AAAATGCCCCTTCCCGGTCGGAAGGTCCCT-GTTTTCTTTGTTTGCTTC
* * * *
237 CCAAAATGCCCCTTCCTGGTCGGAAGATCCTTGTTTTCTTTGTTTGTTTC
1 CCAAAATGCCCCTTCCCGGTCGGAAGGTCCCTGTTTTCTTTGTTTGCTTC
* *
287 CCAAAATGCCCCTTCCCGCTCGGAAGGT-CCAGTTTTCT
1 CCAAAATGCCCCTTCCCGGTCGGAAGGTCCCTGTTTTCT
325 CTTCACATTT
Statistics
Matches: 210, Mismatches: 24, Indels: 15
0.84 0.10 0.06
Matches are distributed among these distances:
49 8 0.04
50 139 0.66
51 20 0.10
52 17 0.08
53 26 0.12
ACGTcount: A:0.15, C:0.29, G:0.19, T:0.37
Consensus pattern (50 bp):
CCAAAATGCCCCTTCCCGGTCGGAAGGTCCCTGTTTTCTTTGTTTGCTTC
Found at i:314 original size:153 final size:153
Alignment explanation
Indices: 36--316 Score: 474
Period size: 153 Copynumber: 1.8 Consensus size: 153
26 CTCTTATTCC
*
36 AAAATGCCCCTTCCCGGTCGGAAGGTCCCTGTTTTCTTTGTTTGCTTCCCAAAATGCCCATTCCC
1 AAAATGCCCCTTCCCGGTCGGAAGGTCCCTGTTTTCTTTGTTTGCTTACCAAAATGCCCATTCCC
* *
101 GGTCGGAAGGTCCTTGTTTTCTTTATTTGTTTCCAAAAATGCCCCTTCCCGGTCGGAAGGTCCTC
66 GGTCGGAAGATCCTTGTTTTCTTTATTTGTTTCCAAAAATGCCCCTTCCCGCTCGGAAGGTCCTC
166 GTTTTTTCTTTGTTTGTTCACCA
131 GTTTTTTCTTTGTTTGTTCACCA
* *
189 AAAATGCCCCTTCCCGGTCGGAAGGT-CCTCGTTTTCTTTTTTTGCTTACCAAAATGCCCCTTCC
1 AAAATGCCCCTTCCCGGTCGGAAGGTCCCT-GTTTTCTTTGTTTGCTTACCAAAATGCCCATTCC
* * *
253 TGGTCGGAAGATCCTTGTTTTCTTTGTTTGTTTCCCAAAATGCCCCTTCCCGCTCGGAAGGTCC
65 CGGTCGGAAGATCCTTGTTTTCTTTATTTGTTTCCAAAAATGCCCCTTCCCGCTCGGAAGGTCC
317 AGTTTTCTCT
Statistics
Matches: 119, Mismatches: 8, Indels: 2
0.92 0.06 0.02
Matches are distributed among these distances:
152 3 0.03
153 116 0.97
ACGTcount: A:0.15, C:0.29, G:0.19, T:0.37
Consensus pattern (153 bp):
AAAATGCCCCTTCCCGGTCGGAAGGTCCCTGTTTTCTTTGTTTGCTTACCAAAATGCCCATTCCC
GGTCGGAAGATCCTTGTTTTCTTTATTTGTTTCCAAAAATGCCCCTTCCCGCTCGGAAGGTCCTC
GTTTTTTCTTTGTTTGTTCACCA
Found at i:2412 original size:94 final size:95
Alignment explanation
Indices: 2222--2413 Score: 305
Period size: 94 Copynumber: 2.0 Consensus size: 95
2212 AATCATTATA
* * * *
2222 TTTTGAATCTTTAGCATGTAGGATTGCATTGTGTTAATGATGGTTAAAAATTGTTGCACGTTCAT
1 TTTTGAATCTTTAACATGTAGGATTGCATTGTGTTAATAACGGTTAAAAATTGTTGCACATTCAT
2287 TAATTGAATTAAGAAAATAAAATTCCGTTG
66 TAATTGAATTAAGAAAATAAAATTCCGTTG
* *
2317 TTTTGAATCTTTAATATGTAGGATTGCATTGTGTTAATAACGGTT-AAAATTGTTTCACATTCAT
1 TTTTGAATCTTTAACATGTAGGATTGCATTGTGTTAATAACGGTTAAAAATTGTTGCACATTCAT
* *
2381 TAATTGACTTAAGAAAATAAAGTTCCGTTG
66 TAATTGAATTAAGAAAATAAAATTCCGTTG
2411 TTT
1 TTT
2414 ACAAAATGAA
Statistics
Matches: 89, Mismatches: 8, Indels: 1
0.91 0.08 0.01
Matches are distributed among these distances:
94 48 0.54
95 41 0.46
ACGTcount: A:0.32, C:0.09, G:0.17, T:0.42
Consensus pattern (95 bp):
TTTTGAATCTTTAACATGTAGGATTGCATTGTGTTAATAACGGTTAAAAATTGTTGCACATTCAT
TAATTGAATTAAGAAAATAAAATTCCGTTG
Found at i:3108 original size:14 final size:14
Alignment explanation
Indices: 3089--3126 Score: 51
Period size: 14 Copynumber: 2.7 Consensus size: 14
3079 TTCAAAAATT
3089 GTTTTCAAGAAAAG-
1 GTTTTCAA-AAAAGA
*
3103 GTTTTCAAAAATGA
1 GTTTTCAAAAAAGA
3117 GTTTTCAAAA
1 GTTTTCAAAA
3127 GGTTTTGGGT
Statistics
Matches: 22, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
13 4 0.18
14 18 0.82
ACGTcount: A:0.42, C:0.08, G:0.16, T:0.34
Consensus pattern (14 bp):
GTTTTCAAAAAAGA
Found at i:10144 original size:28 final size:28
Alignment explanation
Indices: 10069--10132 Score: 94
Period size: 27 Copynumber: 2.3 Consensus size: 28
10059 AGAATAAAAG
* *
10069 AAAAAAAAGAGAAGAGAAGAGAGTTTGAA
1 AAAAAAAAGA-AAAAGAAGAGAGTCTGAA
10098 AAAAAAAAGAAAAAGAAGAGA-TCTGAA
1 AAAAAAAAGAAAAAGAAGAGAGTCTGAA
10125 AAAAAAAA
1 AAAAAAAA
10133 CGTAGAAGAA
Statistics
Matches: 33, Mismatches: 2, Indels: 2
0.89 0.05 0.05
Matches are distributed among these distances:
27 13 0.39
28 10 0.30
29 10 0.30
ACGTcount: A:0.70, C:0.02, G:0.20, T:0.08
Consensus pattern (28 bp):
AAAAAAAAGAAAAAGAAGAGAGTCTGAA
Found at i:12187 original size:51 final size:51
Alignment explanation
Indices: 12115--12436 Score: 292
Period size: 51 Copynumber: 6.4 Consensus size: 51
12105 AAGATTTGGA
* * *
12115 TTTTAAAGTAATTTGTAAATAAAGATTGAATCTTTATGTTGAAAGA-TGAAGC
1 TTTT-AAGTAATTTGTAAATAAAGATTGAATCTTTAAG-TAAAAGATTGAATC
* * * *
12167 TTTTACGTGATTTGTTAATAAAGATTGAAT-TCTTAAGTAAAAAAATTGAATC
1 TTTTAAGTAATTTGTAAATAAAGATTGAATCT-TTAAGT-AAAAGATTGAATC
* * * *
12219 TTTTAAGTAGTTTGTAAATAAGGATTGAATCTTT-A-T----G-GTGAAAC
1 TTTTAAGTAATTTGTAAATAAAGATTGAATCTTTAAGTAAAAGATTGAATC
* * * * * *
12263 TTTTAAGTGATTTGTAAATGAATATTGGATCTTTAAGTGAAAGATTAAATC
1 TTTTAAGTAATTTGTAAATAAAGATTGAATCTTTAAGTAAAAGATTGAATC
* * *
12314 TTTTAAGTAATTTGTGAATAAAGATTGAATTTTTAATTAAAAGATTGAA-C
1 TTTTAAGTAATTTGTAAATAAAGATTGAATCTTTAAGTAAAAGATTGAATC
*
12364 TTTTAAGTAAATTTTGTAAATAAAGATTGAATCCTTAAGTAAAAGA-TGAAATC
1 TTTTAAGT-AA-TTTGTAAATAAAGATTGAATCTTTAAGTAAAAGATTG-AATC
*
12417 TTTGAA-TAATTTG-AAATAAA
1 TTTTAAGTAATTTGTAAATAAA
12437 AGTGGAATTT
Statistics
Matches: 217, Mismatches: 38, Indels: 33
0.75 0.13 0.11
Matches are distributed among these distances:
44 33 0.15
45 1 0.00
46 1 0.00
49 7 0.03
50 17 0.08
51 82 0.38
52 69 0.32
53 7 0.03
ACGTcount: A:0.41, C:0.04, G:0.16, T:0.40
Consensus pattern (51 bp):
TTTTAAGTAATTTGTAAATAAAGATTGAATCTTTAAGTAAAAGATTGAATC
Found at i:12334 original size:95 final size:99
Alignment explanation
Indices: 12115--12436 Score: 302
Period size: 103 Copynumber: 3.2 Consensus size: 99
12105 AAGATTTGGA
* *
12115 TTTTAAAGTAATTTGTAAATAAAGATTGAATCTTTATGTTGAAAGATGAAGCTTTTACGTGATTT
1 TTTT-AAGTAATTTGTAAATAAAGATTGAATCTTTA--TTG--AGATGAAACTTTTAAGTGATTT
* *
12180 GTTAATAAAGATTGAATTCTTAAGTAAAAAAATTGAATC
61 GTAAATAAAGATTGAATTCTTAAGTAAAAAAATTAAATC
* *
12219 TTTTAAGTAGTTTGTAAATAAGGATTGAATCTTTA-TG-G-TGAAACTTTTAAGTGATTTGTAAA
1 TTTTAAGTAATTTGTAAATAAAGATTGAATCTTTATTGAGATGAAACTTTTAAGTGATTTGTAAA
* * * * *
12281 TGAATATTGGA-TCTTTAAGT-GAAAGATTAAATC
66 TAAAGATTGAATTC-TTAAGTAAAAAAATTAAATC
* * * *
12314 TTTTAAGTAATTTGTGAATAAAGATTGAATTTTTAATTAAAAGATTG-AACTTTTAAGTAAATTT
1 TTTTAAGTAATTTGTAAATAAAGATTGAATCTTT-ATT--GAGA-TGAAACTTTTAAGT-GA-TT
* * *
12378 TGTAAATAAAGATTGAATCCTTAAGT-AAAAGATGAAATC
60 TGTAAATAAAGATTGAATTCTTAAGTAAAAAAATTAAATC
*
12417 TTTGAA-TAATTTG-AAATAAA
1 TTTTAAGTAATTTGTAAATAAA
12437 AGTGGAATTT
Statistics
Matches: 182, Mismatches: 25, Indels: 25
0.78 0.11 0.11
Matches are distributed among these distances:
95 42 0.23
96 36 0.20
97 2 0.01
100 3 0.02
101 17 0.09
102 10 0.05
103 67 0.37
104 5 0.03
ACGTcount: A:0.41, C:0.04, G:0.16, T:0.40
Consensus pattern (99 bp):
TTTTAAGTAATTTGTAAATAAAGATTGAATCTTTATTGAGATGAAACTTTTAAGTGATTTGTAAA
TAAAGATTGAATTCTTAAGTAAAAAAATTAAATC
Found at i:12355 original size:147 final size:147
Alignment explanation
Indices: 12115--12396 Score: 372
Period size: 147 Copynumber: 1.9 Consensus size: 147
12105 AAGATTTGGA
* * * *
12115 TTTTAAAGTAATTTGTAAATAAAGATTGAATCTTTATGTTGAAAGATGAAGCTTTTACGTGATTT
1 TTTTAAAGTAATTTGTAAATAAAGATTGAATCTTTAAGTTGAAAGATAAAGCTTTTAAGTAATTT
* *
12180 GTTAATAAAGATTGAATTCTTAAGTAAAAAAATTGAATCTTTTAAGT-AGTTTGTAAATAAGGAT
66 GTGAATAAAGATTGAATTCTTAAGT-AAAAAATTGAA-CTTTTAAGTAAGTTTGTAAATAAAGAT
12244 TGAATCTTTATGGTGAAAC
129 TGAATCTTTATGGTGAAAC
* * * * *
12263 TTTT-AAGTGATTTGTAAATGAATATTGGATCTTTAAG-TGAAAGATTAAATCTTTTAAGTAATT
1 TTTTAAAGTAATTTGTAAATAAAGATTGAATCTTTAAGTTGAAAGA-TAAAGCTTTTAAGTAATT
* * * *
12326 TGTGAATAAAGATTGAATTTTTAATTAAAAGATTGAACTTTTAAGTAAATTTTGTAAATAAAGAT
65 TGTGAATAAAGATTGAATTCTTAAGTAAAAAATTGAACTTTTAAGT-AAGTTTGTAAATAAAGAT
12391 TGAATC
129 TGAATC
12397 CTTAAGTAAA
Statistics
Matches: 116, Mismatches: 15, Indels: 7
0.84 0.11 0.05
Matches are distributed among these distances:
145 9 0.08
146 17 0.15
147 86 0.74
148 4 0.03
ACGTcount: A:0.39, C:0.04, G:0.16, T:0.41
Consensus pattern (147 bp):
TTTTAAAGTAATTTGTAAATAAAGATTGAATCTTTAAGTTGAAAGATAAAGCTTTTAAGTAATTT
GTGAATAAAGATTGAATTCTTAAGTAAAAAATTGAACTTTTAAGTAAGTTTGTAAATAAAGATTG
AATCTTTATGGTGAAAC
Found at i:12358 original size:20 final size:20
Alignment explanation
Indices: 12333--12374 Score: 66
Period size: 20 Copynumber: 2.1 Consensus size: 20
12323 ATTTGTGAAT
* *
12333 AAAGATTGAATTTTTAATTA
1 AAAGATTGAACTTTTAAGTA
12353 AAAGATTGAACTTTTAAGTA
1 AAAGATTGAACTTTTAAGTA
12373 AA
1 AA
12375 TTTTGTAAAT
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
20 20 1.00
ACGTcount: A:0.48, C:0.02, G:0.12, T:0.38
Consensus pattern (20 bp):
AAAGATTGAACTTTTAAGTA
Done.