Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01019109.1 Corchorus olitorius cultivar O-4 contig19142, 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: 18443
ACGTcount: A:0.33, C:0.16, G:0.17, T:0.34
Found at i:2075 original size:15 final size:15
Alignment explanation
Indices: 2056--2093 Score: 53
Period size: 14 Copynumber: 2.7 Consensus size: 15
2046 TCAAAACATA
2056 ATTTTT-TAAAATTT
1 ATTTTTATAAAATTT
*
2070 ATTTTTATATAATTT
1 ATTTTTATAAAATTT
2085 A-TTTTATAA
1 ATTTTTATAA
2094 TTAAAGGTCA
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
14 13 0.62
15 8 0.38
ACGTcount: A:0.37, C:0.00, G:0.00, T:0.63
Consensus pattern (15 bp):
ATTTTTATAAAATTT
Found at i:8746 original size:20 final size:20
Alignment explanation
Indices: 8723--8762 Score: 55
Period size: 20 Copynumber: 2.0 Consensus size: 20
8713 AAAATGTGGC
8723 AGAAACTGTCAAGAAC-CCCA
1 AGAAACT-TCAAGAACTCCCA
*
8743 AGAATCTTCAAGAACTCCCA
1 AGAAACTTCAAGAACTCCCA
8763 TCGCCCGCCA
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
19 8 0.44
20 10 0.56
ACGTcount: A:0.42, C:0.30, G:0.12, T:0.15
Consensus pattern (20 bp):
AGAAACTTCAAGAACTCCCA
Found at i:15425 original size:13 final size:13
Alignment explanation
Indices: 15407--15435 Score: 58
Period size: 13 Copynumber: 2.2 Consensus size: 13
15397 ATTGAAGTGA
15407 TTTCAAGTATTGT
1 TTTCAAGTATTGT
15420 TTTCAAGTATTGT
1 TTTCAAGTATTGT
15433 TTT
1 TTT
15436 TCTTATATTT
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 16 1.00
ACGTcount: A:0.21, C:0.07, G:0.14, T:0.59
Consensus pattern (13 bp):
TTTCAAGTATTGT
Found at i:18402 original size:320 final size:320
Alignment explanation
Indices: 17361--18440 Score: 1120
Period size: 320 Copynumber: 3.3 Consensus size: 320
17351 GTTTTTGCAA
* * *
17361 ACGACTCAGTTTTGCATGGTTTTTGGCATAAAGTCTCCTTGAAATATCTATATTCATCTAACCAA
1 ACGACTCAGTTTTGCATGGTTTTTGGCATAAAGACTCCTTAAAATATCTATATTCATCGAACCAA
* * * * * * *
17426 ATTTCAGCCACATTGGATTTAATGATTTTTTTTTATGAGCATCTGAATTTTGTTTCGATTTAATT
66 ATCTCAGCCACATTCGATTTAAGGATTTGTTTTTACGAGTATCTGAATCTTGTTTCGATTTAATT
* * * * * * * *
17491 AGAAATAAATTCAGAAAAAAAATTGAAAAACAATATTAGAAACGAGAAAAACCCTTTAATTTTTT
131 AGAAATTAATT-TGGAAAAAAATGGAAAAACGATATTAGAAGCGTGAAAAA-CC-TTCATTTTTT
* * * ** *
17556 TCGTG-TTGAATTATATATTTTTTCTCAGTATTGTGGCAAGTAATTGAGAAAAAAAT-TTTCGGG
193 TTGTGATTGAATTATATATTTTTTCTTAGTATTGTGACAAAAAATTGAG--AAAAATCTTTCGGC
* * ***** * *
17619 TTAGTTTTTG-CGAAACTTTAGCCGAAATCGTGTTTTTTGCAGGGCCAGTATTGTGGCTAAAAAC
256 TCAGTTTTTGCCGAAA--TTAG-CG-TA-C-T-AACCAT-CA----CGGT-TTTTGGCTAAAAAC
*
17683 GTGTTTCAGGGCC
308 GAGTTTCAGGGCC
* * * * * *
17696 ACGACTCAGTTTTTCATGATTTTTGACGTAAAGACTTCTTAAAATATCTATATTCAACGAACCAA
1 ACGACTCAGTTTTGCATGGTTTTTGGCATAAAGACTCCTTAAAATATCTATATTCATCGAACCAA
* * *** * *
17761 TTCACAGCCACATTCGATTTACTTATTTGTTTTTACGAGTATCTAAATCTTGTTTCGATTTTATT
66 ATCTCAGCCACATTCGATTTAAGGATTTGTTTTTACGAGTATCTGAATCTTGTTTCGATTTAATT
* * * *
17826 AGAAATTAATTTGGAAAAAAATGGAAAAACGATATTAGAAGCGTTAAAAACTATTCAATATTTTT
131 AGAAATTAATTTGGAAAAAAATGGAAAAACGATATTAGAAGCGTGAAAAAC-CTTCATTTTTTTT
* * * **
17891 G-GCATTGTATTATATATTTTTTCTTTGTATTGT-AGCAAAAAATTGAGAAAAAACTTTTCTACT
195 GTG-ATTGAATTATATATTTTTTCTTAGTATTGTGA-CAAAAAATTGAGAAAAATC-TTTCGGCT
* * * * * **
17954 CAGTTTTTAGCCGAAA-TCGTGTACTAACCATCACGGTTTTTGACAAAAAACGCGTTTTGGGGCC
257 CAGTTTTT-GCCGAAATTAGCGTACTAACCATCACGGTTTTTGGCTAAAAACGAGTTTCAGGGCC
* * * * * *
18018 CCGACTCAATTTTGCAT-GATTTTGGCGTAAAGAGTTCTTAAAATATCTATATTCATCGAACCAA
1 ACGACTCAGTTTTGCATGGTTTTTGGCATAAAGACTCCTTAAAATATCTATATTCATCGAACCAA
* *
18082 ATCCCAACCACATTCGATTTAAGGATTTGTTTTTACGAGTATCTGAATCTTGTTTCGATTTAATT
66 ATCTCAGCCACATTCGATTTAAGGATTTGTTTTTACGAGTATCTGAATCTTGTTTCGATTTAATT
18147 AGAAATTAATTTGGAAAAAAA-GGAAAAACGATATTAGAAGCGTGAAAAATCCTTCATTCTTTTT
131 AGAAATTAATTTGGAAAAAAATGGAAAAACGATATTAGAAGCGTGAAAAA-CCTTCATT-TTTTT
* *
18211 TGTGATT-AATTATATATTTTTT-TATAATACTGTGACAAAAAATTGAGAAAAATCTTTCGGCTC
194 TGTGATTGAATTATATATTTTTTCT-TAGTATTGTGACAAAAAATTGAGAAAAATCTTTCGGCTC
*
18274 AGTGTTTTGCCGAAATTAG-GTACTAACCATCACGGTTTTTGGCTAAAAACGAATTTCAGGGCC
258 AGT-TTTTGCCGAAATTAGCGTACTAACCATCACGGTTTTTGGCTAAAAACGAGTTTCAGGGCC
* * * * *
18337 TCGACTCAGTTTTGCATGGTTTTTCGCATAAAGACTCCTTGAAATATCTATATTCGTCTAACCAA
1 ACGACTCAGTTTTGCATGGTTTTTGGCATAAAGACTCCTTAAAATATCTATATTCATCGAACCAA
*
18402 ATCTCAGCCACATTGGATTTAAGGATTTGTTTTTACGAG
66 ATCTCAGCCACATTCGATTTAAGGATTTGTTTTTACGAG
18441 CAT
Statistics
Matches: 622, Mismatches: 107, Indels: 47
0.80 0.14 0.06
Matches are distributed among these distances:
319 71 0.11
320 151 0.24
321 131 0.21
322 36 0.06
323 3 0.00
327 2 0.00
328 1 0.00
329 1 0.00
330 1 0.00
331 1 0.00
332 7 0.01
333 12 0.02
334 80 0.13
335 120 0.19
336 5 0.01
ACGTcount: A:0.33, C:0.15, G:0.16, T:0.37
Consensus pattern (320 bp):
ACGACTCAGTTTTGCATGGTTTTTGGCATAAAGACTCCTTAAAATATCTATATTCATCGAACCAA
ATCTCAGCCACATTCGATTTAAGGATTTGTTTTTACGAGTATCTGAATCTTGTTTCGATTTAATT
AGAAATTAATTTGGAAAAAAATGGAAAAACGATATTAGAAGCGTGAAAAACCTTCATTTTTTTTG
TGATTGAATTATATATTTTTTCTTAGTATTGTGACAAAAAATTGAGAAAAATCTTTCGGCTCAGT
TTTTGCCGAAATTAGCGTACTAACCATCACGGTTTTTGGCTAAAAACGAGTTTCAGGGCC
Done.