Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01014231.1 Corchorus capsularis cultivar CVL-1 contig14252, 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: 23743
ACGTcount: A:0.33, C:0.18, G:0.17, T:0.32
Found at i:942 original size:20 final size:20
Alignment explanation
Indices: 904--942 Score: 53
Period size: 20 Copynumber: 1.9 Consensus size: 20
894 CTCTGTCTTC
*
904 TTCTTTTTTCTTTTCTTTTT
1 TTCTTTTTTCTTGTCTTTTT
924 TTCTTTTTGTCTTGT-TTTT
1 TTCTTTTT-TCTTGTCTTTT
943 GGTAATCTTT
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
20 12 0.71
21 5 0.29
ACGTcount: A:0.00, C:0.13, G:0.05, T:0.82
Consensus pattern (20 bp):
TTCTTTTTTCTTGTCTTTTT
Found at i:2104 original size:31 final size:31
Alignment explanation
Indices: 2066--2133 Score: 102
Period size: 31 Copynumber: 2.2 Consensus size: 31
2056 CAAAAAGTAA
* *
2066 TCAATTTAATCTTTATA-TCCATAAGATTGAG
1 TCAATTTAATCTCTATACT-CACAAGATTGAG
2097 TCAATTTAATCTCTATACTCACAAGATTGAG
1 TCAATTTAATCTCTATACTCACAAGATTGAG
2128 TCAATT
1 TCAATT
2134 AGGTCCTCAA
Statistics
Matches: 34, Mismatches: 2, Indels: 2
0.89 0.05 0.05
Matches are distributed among these distances:
31 33 0.97
32 1 0.03
ACGTcount: A:0.35, C:0.16, G:0.09, T:0.40
Consensus pattern (31 bp):
TCAATTTAATCTCTATACTCACAAGATTGAG
Found at i:2992 original size:24 final size:25
Alignment explanation
Indices: 2958--3004 Score: 87
Period size: 24 Copynumber: 1.9 Consensus size: 25
2948 AGTCATTGTT
2958 TCTTTCTAATTAAATGCATGTTTGA
1 TCTTTCTAATTAAATGCATGTTTGA
2983 TCTTT-TAATTAAATGCATGTTT
1 TCTTTCTAATTAAATGCATGTTT
3005 CAAGAAGGGT
Statistics
Matches: 22, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
24 17 0.77
25 5 0.23
ACGTcount: A:0.28, C:0.11, G:0.11, T:0.51
Consensus pattern (25 bp):
TCTTTCTAATTAAATGCATGTTTGA
Found at i:3087 original size:28 final size:27
Alignment explanation
Indices: 3025--3088 Score: 83
Period size: 27 Copynumber: 2.3 Consensus size: 27
3015 ATTTCTGGAA
* *
3025 AACAAGGGAAAGGGACAATTAAAAGGG
1 AACAAGGGAAAGGAACAATTAAAAAGG
*
3052 AACAAGGGAAATGAACAATTAAAAAGG
1 AACAAGGGAAAGGAACAATTAAAAAGG
*
3079 ATCAGAGGGA
1 AACA-AGGGA
3089 GTATATATGT
Statistics
Matches: 32, Mismatches: 4, Indels: 1
0.86 0.11 0.03
Matches are distributed among these distances:
27 27 0.84
28 5 0.16
ACGTcount: A:0.53, C:0.08, G:0.30, T:0.09
Consensus pattern (27 bp):
AACAAGGGAAAGGAACAATTAAAAAGG
Found at i:6008 original size:78 final size:78
Alignment explanation
Indices: 5878--6058 Score: 211
Period size: 78 Copynumber: 2.3 Consensus size: 78
5868 AAGATCTGAA
* * * * *
5878 TTCTGCAAGGTGTTTGGACCGACGCCATTTAAAGAGTTAGAGTCTAACTCATGGTTTTCAGCAAT
1 TTCTGCAAGGTGTTTGGACCAACACCATGTAAAGAGTTAGAGTCTAACTCATGGCTATCAGCAAT
*
5943 AATGGTATCTGCT
66 AATGGCATCTGCT
* * * * *
5956 TTCTGAAAGGTGTTTGGACCAACACCATGTAGAGAGTTAG-GTTTTAAGTCATGGCTATCAGCTA
1 TTCTGCAAGGTGTTTGGACCAACACCATGTAAAGAGTTAGAG-TCTAACTCATGGCTATCAGCAA
* *
6020 TCATGGCATCTGTT
65 TAATGGCATCTGCT
* *
6034 TTCAGCAAGTTGTTTGGACCAACAC
1 TTCTGCAAGGTGTTTGGACCAACAC
6059 TTTCAAAAGA
Statistics
Matches: 86, Mismatches: 16, Indels: 2
0.83 0.15 0.02
Matches are distributed among these distances:
77 1 0.01
78 85 0.99
ACGTcount: A:0.26, C:0.18, G:0.23, T:0.33
Consensus pattern (78 bp):
TTCTGCAAGGTGTTTGGACCAACACCATGTAAAGAGTTAGAGTCTAACTCATGGCTATCAGCAAT
AATGGCATCTGCT
Found at i:8616 original size:403 final size:402
Alignment explanation
Indices: 7870--8678 Score: 1582
Period size: 403 Copynumber: 2.0 Consensus size: 402
7860 TGAATGATGA
7870 ACAATCATTCTGTCTTTACTTTCTTTCATTAAGGAGCAAATGAACTCTGGCCATCTTCTCCTGAT
1 ACAATCATTCTGTCTTTACTTTCTTTCATTAAGGAGCAAATGAACTCTGGCCATCTTCTCCTGAT
*
7935 ACTTATTTCGAAGGAAAAGTAAGAACTAACCAACCAGAGTTTCTTGGATTTCAAGAAACAGAGAC
66 ACTTATTCCGAAGGAAAAGTAAGAACTAACCAACCAGAGTTTCTTGGATTTCAAGAAACAGAGAC
8000 TCTGCTTGAGTGAACAAAAGATATATTCAAAGATAACTGCTTTAGAAGTTCTCCAGAGTTTCAAA
131 TCTGCTTGAGTGAACAAAAGATATATTCAAAGATAACTGCTTTAGAAGTTCTCCAGAGTTTCAAA
8065 TTCGTAATTATATACGTGCTGATAGCAAAAAAAAAAAAAAAATTTGGACCTCCAAACTTTATAAA
196 TTCGTAATTATATACGTGCTGATAGCAAAAAAAAAAAAAAAATTTGGACCTCCAAACTTTATAAA
8130 AGATCGAAAGTGTTAAGGGAATTTATAAAAGATCGAATGTAGTATCAAGTTATAAAATCAATTAA
261 AGATCGAAAGTGTTAAGGGAATTTATAAAAGATCGAATGTAGTATCAAGTTATAAAATCAATTAA
8195 CATAATTTGATCTAATTACAAAGGAATCCATAAAGGGTTTATATATGATACACCGGCAGTGGAGT
326 CATAATTTGATCTAATTACAAAGGAATCCATAAAGGGTTTATATATGATACACCGGCAGTGGAGT
8260 TTAGCAGACTAC
391 TTAGCAGACTAC
8272 ACAATCATTCTGTCTTTACTTTCTTTCATTAAGGAGCAAATGAACTCTGGCCATCTTCTCCTGAT
1 ACAATCATTCTGTCTTTACTTTCTTTCATTAAGGAGCAAATGAACTCTGGCCATCTTCTCCTGAT
8337 ACTTATTCCGAAGGAAAAGTAAGAACTAACCAACCAGAGTTTCTTGGATTTCAAGAAACAGAGAC
66 ACTTATTCCGAAGGAAAAGTAAGAACTAACCAACCAGAGTTTCTTGGATTTCAAGAAACAGAGAC
8402 TCTGCTTGAGTGAACAAAAGATATATTCAAAAGATAACTGCTTTAGAAGTTCTCCAGAGTTTCAA
131 TCTGCTTGAGTGAACAAAAGATATATTC-AAAGATAACTGCTTTAGAAGTTCTCCAGAGTTTCAA
* *
8467 ATTCGTAATTATATATGTGCTGATAGCAAAAAAAAAAAAAAATTTTGGACCTCCAAACTTTATAA
195 ATTCGTAATTATATACGTGCTGATAGCAAAAAAAAAAAAAAAATTTGGACCTCCAAACTTTATAA
8532 AAGATCGAAAGTGTTAAGGGAATTTATAAAAGATCGAATGTAGTATCAAGTTATAAAATCAATTA
260 AAGATCGAAAGTGTTAAGGGAATTTATAAAAGATCGAATGTAGTATCAAGTTATAAAATCAATTA
8597 ACATAATTTGATCTAATTACAAAGGAATCCATAAAGGGTTTATATATGATACACCGGCAGTGGAG
325 ACATAATTTGATCTAATTACAAAGGAATCCATAAAGGGTTTATATATGATACACCGGCAGTGGAG
8662 TTTAGCAGACTAC
390 TTTAGCAGACTAC
8675 ACAA
1 ACAA
8679 GCGGGTCCTG
Statistics
Matches: 403, Mismatches: 3, Indels: 1
0.99 0.01 0.00
Matches are distributed among these distances:
402 157 0.39
403 246 0.61
ACGTcount: A:0.39, C:0.15, G:0.16, T:0.30
Consensus pattern (402 bp):
ACAATCATTCTGTCTTTACTTTCTTTCATTAAGGAGCAAATGAACTCTGGCCATCTTCTCCTGAT
ACTTATTCCGAAGGAAAAGTAAGAACTAACCAACCAGAGTTTCTTGGATTTCAAGAAACAGAGAC
TCTGCTTGAGTGAACAAAAGATATATTCAAAGATAACTGCTTTAGAAGTTCTCCAGAGTTTCAAA
TTCGTAATTATATACGTGCTGATAGCAAAAAAAAAAAAAAAATTTGGACCTCCAAACTTTATAAA
AGATCGAAAGTGTTAAGGGAATTTATAAAAGATCGAATGTAGTATCAAGTTATAAAATCAATTAA
CATAATTTGATCTAATTACAAAGGAATCCATAAAGGGTTTATATATGATACACCGGCAGTGGAGT
TTAGCAGACTAC
Found at i:21491 original size:15 final size:17
Alignment explanation
Indices: 21470--21518 Score: 59
Period size: 17 Copynumber: 3.1 Consensus size: 17
21460 ATCGTCTAAT
21470 TTTTTACACTTTTGC-C
1 TTTTTACACTTTTGCAC
*
21486 -TTTTAC-CCTTTGCAC
1 TTTTTACACTTTTGCAC
*
21501 TTTTTACACTTTTACAC
1 TTTTTACACTTTTGCAC
21518 T
1 T
21519 GAGCCTCCCC
Statistics
Matches: 27, Mismatches: 3, Indels: 5
0.77 0.09 0.14
Matches are distributed among these distances:
14 6 0.22
15 7 0.26
16 6 0.22
17 8 0.30
ACGTcount: A:0.16, C:0.27, G:0.04, T:0.53
Consensus pattern (17 bp):
TTTTTACACTTTTGCAC
Done.