Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01011395.1 Corchorus capsularis cultivar CVL-1 contig11416, 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: 12453
ACGTcount: A:0.32, C:0.18, G:0.17, T:0.33
Found at i:7250 original size:1 final size:1
Alignment explanation
Indices: 7244--7280 Score: 74
Period size: 1 Copynumber: 37.0 Consensus size: 1
7234 GGGATTCTAG
7244 TTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTT
1 TTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTT
7281 AGTTATGGAT
Statistics
Matches: 36, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
1 36 1.00
ACGTcount: A:0.00, C:0.00, G:0.00, T:1.00
Consensus pattern (1 bp):
T
Found at i:8570 original size:42 final size:42
Alignment explanation
Indices: 8489--8573 Score: 143
Period size: 42 Copynumber: 2.0 Consensus size: 42
8479 TTTCGTAATT
* *
8489 ATCATTCAGGTCGGGCTTTTACTAGTTTTGGATTTGATTCGA
1 ATCATTCAAGTCGAGCTTTTACTAGTTTTGGATTTGATTCGA
*
8531 ATCATTCAAGTCGAGCTTTTACTGGTTTTGGATTTGATTCGA
1 ATCATTCAAGTCGAGCTTTTACTAGTTTTGGATTTGATTCGA
8573 A
1 A
8574 AACCAATGAT
Statistics
Matches: 40, Mismatches: 3, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
42 40 1.00
ACGTcount: A:0.21, C:0.14, G:0.22, T:0.42
Consensus pattern (42 bp):
ATCATTCAAGTCGAGCTTTTACTAGTTTTGGATTTGATTCGA
Found at i:10578 original size:12 final size:12
Alignment explanation
Indices: 10561--10597 Score: 65
Period size: 12 Copynumber: 3.1 Consensus size: 12
10551 ATACAAATCA
10561 AATCGAATAGAC
1 AATCGAATAGAC
10573 AATCGAATAGAC
1 AATCGAATAGAC
*
10585 AACCGAATAGAC
1 AATCGAATAGAC
10597 A
1 A
10598 TTCTCCTTGG
Statistics
Matches: 24, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
12 24 1.00
ACGTcount: A:0.51, C:0.19, G:0.16, T:0.14
Consensus pattern (12 bp):
AATCGAATAGAC
Found at i:12389 original size:322 final size:325
Alignment explanation
Indices: 11697--12437 Score: 947
Period size: 322 Copynumber: 2.3 Consensus size: 325
11687 AGGAACAGCG
* * * *
11697 ACAACACTCAGAAAAA-ATCTATAATTTAGCACCAAAAATATTGAAGAGTTTTTTACGCTTCTAA
1 ACAACACTCATAAAAACA-CCATAATTTAACACCAAAAATATTGAAGAGTTTTTCACGCTTCTAA
* *
11761 CATCGTTTTTCTTA-TTTTTTCTGAATTAATTTTTAATTAAATCAAAATAAGATTCAGAAGCTCG
65 TATCGTTTTTCTTATTTTTTTCTGAATTAATTTTTAATTAAATCAAAATAAGATTCAAAAGCTCG
* ** * *
11825 TAAAAATAAATCCTTAAATCCAATTTGACTGAGATTTGGTTATATGATTATAGATAATTGAAGGA
130 TAAAAAGAAATCCTTAAATCCAATGCGACTGAGAATTGG---T-TG----TAGATAATTCAAGGA
* * **
11890 GTCTCGGCACCAAAAATCATGAAAAAGTGAGCCGAGGCCCCAAAACGCGTTTTTAGCCAAAAATC
187 GTCTCAGCACCAAAAATCATGAAAAAGTAAGCCGAGGCCCCAAAACGAATTTTTAGCCAAAAATC
* ** * * * *
11955 GTGATGGTTAATACATGATTTCTGCTAAAATTTTGTAGAAATTGACTCGAAAATTTTTTCCTGAA
252 ATGATAATTAATACATGATTTCGGCTAAAATTTTGCAAAAATTGACCCGAAAATTTTTTCCTGAA
*
12020 GTTTTGGCC
317 GTTTTGGAC
* * * * * *
12029 CCAACACTCATAAAAACTCTATATTTTAACAACAAAAATATT-AACGAGTTTTTCAAGCTTCTAA
1 ACAACACTCATAAAAACACCATAATTTAACACCAAAAATATTGAA-GAGTTTTTCACGCTTCTAA
* * *
12093 TATC-ATTTTCATATTTTTTTCTGAATTAATTTTTAATTAAATCCAAATAAGATTCAAAAGCTCG
65 TATCGTTTTTCTTATTTTTTTCTGAATTAATTTTTAATTAAATCAAAATAAGATTCAAAAGCTCG
* *
12157 TAAAAAGAAATCCTTAAATCCAATGCGACTGAGAATTGG-TG-AGATATTTCAAGGAGTCTTAGC
130 TAAAAAGAAATCCTTAAATCCAATGCGACTGAGAATTGGTTGTAGATAATTCAAGGAGTCTCAGC
* * * * * *
12220 GCCAAAAATCATGCAAAATTAAGCCGGGGCCCCGAAATGAATTTTTAGCCAAAAA-CAATGATAA
195 ACCAAAAATCATGAAAAAGTAAGCCGAGGCCCCAAAACGAATTTTTAGCCAAAAATC-ATGATAA
* *
12284 TTAGTACATGATTTCGGCTAAAATTTTGCAAAAATTGACCCGAAAATTTTTTCCTGAATTTTTGG
259 TTAATACATGATTTCGGCTAAAATTTTGCAAAAATTGACCCGAAAATTTTTTCCTGAAGTTTTGG
12349 AC
324 AC
*
12351 ACATCACTCATAAAAACACCATAATTTAACACCAAAAATATTGAAGAGTTTTTCACGCTTCTAAT
1 ACAACACTCATAAAAACACCATAATTTAACACCAAAAATATTGAAGAGTTTTTCACGCTTCTAAT
12416 ATCGTTTTTCTTATTTTTTTCT
66 ATCGTTTTTCTTATTTTTTTCT
12438 TATTTTTTAA
Statistics
Matches: 354, Mismatches: 49, Indels: 21
0.83 0.12 0.05
Matches are distributed among these distances:
321 1 0.00
322 186 0.53
323 18 0.05
327 2 0.01
331 9 0.03
332 138 0.39
ACGTcount: A:0.37, C:0.16, G:0.13, T:0.34
Consensus pattern (325 bp):
ACAACACTCATAAAAACACCATAATTTAACACCAAAAATATTGAAGAGTTTTTCACGCTTCTAAT
ATCGTTTTTCTTATTTTTTTCTGAATTAATTTTTAATTAAATCAAAATAAGATTCAAAAGCTCGT
AAAAAGAAATCCTTAAATCCAATGCGACTGAGAATTGGTTGTAGATAATTCAAGGAGTCTCAGCA
CCAAAAATCATGAAAAAGTAAGCCGAGGCCCCAAAACGAATTTTTAGCCAAAAATCATGATAATT
AATACATGATTTCGGCTAAAATTTTGCAAAAATTGACCCGAAAATTTTTTCCTGAAGTTTTGGAC
Found at i:12443 original size:10 final size:11
Alignment explanation
Indices: 12420--12445 Score: 52
Period size: 11 Copynumber: 2.4 Consensus size: 11
12410 TCTAATATCG
12420 TTTTTCTTATT
1 TTTTTCTTATT
12431 TTTTTCTTATT
1 TTTTTCTTATT
12442 TTTT
1 TTTT
12446 AATTAAAT
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 15 1.00
ACGTcount: A:0.08, C:0.08, G:0.00, T:0.85
Consensus pattern (11 bp):
TTTTTCTTATT
Done.