Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01012856.1 Corchorus olitorius cultivar O-4 contig12889, 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: 8601
ACGTcount: A:0.34, C:0.18, G:0.19, T:0.29
Found at i:858 original size:32 final size:31
Alignment explanation
Indices: 818--903 Score: 113
Period size: 32 Copynumber: 2.8 Consensus size: 31
808 TTTCTTAAGC
*
818 AAAT-CCAAAAGAAGATTTTGGAAAATAAGG
1 AAATCCCAAAAGAAGATTTTGGAAAATAAAG
* *
848 TAATCCCCAAAAGGAGATTTTGGAAAATAAAG
1 AAAT-CCCAAAAGAAGATTTTGGAAAATAAAG
*
880 AAATCCGAAAA-AAGATTTTGGAAA
1 AAATCCCAAAAGAAGATTTTGGAAA
904 TTAATAAAAT
Statistics
Matches: 48, Mismatches: 6, Indels: 4
0.83 0.10 0.07
Matches are distributed among these distances:
30 15 0.31
31 6 0.12
32 27 0.56
ACGTcount: A:0.51, C:0.09, G:0.19, T:0.21
Consensus pattern (31 bp):
AAATCCCAAAAGAAGATTTTGGAAAATAAAG
Found at i:3736 original size:14 final size:15
Alignment explanation
Indices: 3712--3749 Score: 51
Period size: 15 Copynumber: 2.5 Consensus size: 15
3702 AGGAAATTGT
3712 TTTCAAGAAAA-AGGC
1 TTTCAA-AAAATAGGC
*
3727 TTTCAAAAAATAGGT
1 TTTCAAAAAATAGGC
3742 TTTCAAAA
1 TTTCAAAA
3750 GGTTTTGGGT
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
14 4 0.19
15 17 0.81
ACGTcount: A:0.47, C:0.11, G:0.13, T:0.29
Consensus pattern (15 bp):
TTTCAAAAAATAGGC
Found at i:4057 original size:12 final size:12
Alignment explanation
Indices: 4042--4066 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
4032 TCATCAAGTG
4042 ATTCAAATCAAA
1 ATTCAAATCAAA
4054 ATTCAAATCAAA
1 ATTCAAATCAAA
4066 A
1 A
4067 GTGAATCAAA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.60, C:0.16, G:0.00, T:0.24
Consensus pattern (12 bp):
ATTCAAATCAAA
Found at i:6264 original size:64 final size:64
Alignment explanation
Indices: 6116--6578 Score: 559
Period size: 64 Copynumber: 7.2 Consensus size: 64
6106 GGAAGATAAC
* * * * *
6116 CGGAAGATGATCTTGTCAAGAAGTACACCAGAAGATGGTTTTCTCAACAATTCTAAGAAGATGAT
1 CGGAAGACGATCTTGTCAAGAACTACACCAGAAGATGG-TTTCTCAACAATTTTCAGAAGTTGAT
* ** * * *
6181 CGGAAGATGATCTTGTCAAGAACTATGCCAGAAGATGGGTTCTCAAAAATTTTTAGAAGTTGAT
1 CGGAAGACGATCTTGTCAAGAACTACACCAGAAGATGGTTTCTCAACAATTTTCAGAAGTTGAT
* * * *
6245 CGGAAGACGAACGTT-TCAAGAAGTACACTAGAAGATGGTTTTCTCAACAATTTTCAGAAGATGA
1 CGGAAGACGATC-TTGTCAAGAACTACACCAGAAGATGG-TTTCTCAACAATTTTCAGAAGTTGA
6309 T
64 T
* * * * *
6310 CGGAAGACGATCTTGTCAAGAACTACTCCAGGAGATGGTTTTCTCAACAATTTTTAAAAGATGAT
1 CGGAAGACGATCTTGTCAAGAACTACACCAGAAGATGG-TTTCTCAACAATTTTCAGAAGTTGAT
* * * * *
6375 CAGAAGACGATCTTGTCAAGAACTACGCCAGAAGATGGGTTCTCAAAAATTTTCAGAAGTCGAT
1 CGGAAGACGATCTTGTCAAGAACTACACCAGAAGATGGTTTCTCAACAATTTTCAGAAGTTGAT
* * * * * *
6439 TGGACGACGATCTTGTCAAGAAGTACACCAGAAGATGGTTTCTTAAGAGTTTTCAGAAGTTGAT
1 CGGAAGACGATCTTGTCAAGAACTACACCAGAAGATGGTTTCTCAACAATTTTCAGAAGTTGAT
* * * *
6503 CGGAAGACGATCTTGTCAAAAATTACACCAGAAGATGGTTTCTCAAGAGTTTTCAGAAGTTGAT
1 CGGAAGACGATCTTGTCAAGAACTACACCAGAAGATGGTTTCTCAACAATTTTCAGAAGTTGAT
*
6567 CGGAAGATGATC
1 CGGAAGACGATC
6579 GAGTCGTTGA
Statistics
Matches: 345, Mismatches: 50, Indels: 7
0.86 0.12 0.02
Matches are distributed among these distances:
64 196 0.57
65 149 0.43
ACGTcount: A:0.35, C:0.16, G:0.22, T:0.27
Consensus pattern (64 bp):
CGGAAGACGATCTTGTCAAGAACTACACCAGAAGATGGTTTCTCAACAATTTTCAGAAGTTGAT
Found at i:6346 original size:129 final size:128
Alignment explanation
Indices: 6116--6578 Score: 581
Period size: 129 Copynumber: 3.6 Consensus size: 128
6106 GGAAGATAAC
* * *
6116 CGGAAGATGATCTTGTCAAGAAGTACACCAGAAGATGGTTTTCTCAACAATTCTAAGAAGATGAT
1 CGGAAGACGATCTTGTCAAGAAGTACACCAGAAGATGG-TTTCTCAACAATTTTCAGAAGATGAT
* *
6181 CGGAAGATGATCTTGTCAAGAACTA-TGCCAGAAGATGGGTTCTCAAAAATTTTTAGAAGTTGAT
65 CGGAAGACGATCTTGTCAAGAACTACT-CCAGAAGATGGTTTCTCAAAAATTTTTAGAAGTTGAT
* *
6245 CGGAAGACGAACGTT-TCAAGAAGTACACTAGAAGATGGTTTTCTCAACAATTTTCAGAAGATGA
1 CGGAAGACGATC-TTGTCAAGAAGTACACCAGAAGATGG-TTTCTCAACAATTTTCAGAAGATGA
* * * *
6309 TCGGAAGACGATCTTGTCAAGAACTACTCCAGGAGATGGTTTTCTCAACAATTTTTAAAAGATGA
64 TCGGAAGACGATCTTGTCAAGAACTACTCCAGAAGATGG-TTTCTCAAAAATTTTTAGAAGTTGA
6374 T
128 T
* * * * *
6375 CAGAAGACGATCTTGTCAAGAACTACGCCAGAAGATGGGTTCTCAAAAATTTTCAGAAG-TCGAT
1 CGGAAGACGATCTTGTCAAGAAGTACACCAGAAGATGGTTTCTCAACAATTTTCAGAAGAT-GAT
* * * * * * * *
6439 TGGACGACGATCTTGTCAAGAAGTACACCAGAAGATGGTTTCTTAAGAGTTTTCAGAAGTTGAT
65 CGGAAGACGATCTTGTCAAGAACTACTCCAGAAGATGGTTTCTCAAAAATTTTTAGAAGTTGAT
* * * * *
6503 CGGAAGACGATCTTGTCAAAAATTACACCAGAAGATGGTTTCTCAAGAGTTTTCAGAAGTTGATC
1 CGGAAGACGATCTTGTCAAGAAGTACACCAGAAGATGGTTTCTCAACAATTTTCAGAAGATGATC
*
6568 GGAAGATGATC
66 GGAAGACGATC
6579 GAGTCGTTGA
Statistics
Matches: 289, Mismatches: 39, Indels: 13
0.85 0.11 0.04
Matches are distributed among these distances:
128 85 0.29
129 149 0.52
130 55 0.19
ACGTcount: A:0.35, C:0.16, G:0.22, T:0.27
Consensus pattern (128 bp):
CGGAAGACGATCTTGTCAAGAAGTACACCAGAAGATGGTTTCTCAACAATTTTCAGAAGATGATC
GGAAGACGATCTTGTCAAGAACTACTCCAGAAGATGGTTTCTCAAAAATTTTTAGAAGTTGAT
Found at i:6460 original size:194 final size:193
Alignment explanation
Indices: 6107--6548 Score: 638
Period size: 194 Copynumber: 2.3 Consensus size: 193
6097 AAGATGATCG
* * * *
6107 GAAGATAACCGGAAGATGATCTTGTCAAGAAGTACACCAGAAGATGGTTTTCTCAACAATTCTAA
1 GAAGATGATCGGAAGACGATCTTGTCAAGAACTACACCAGAAGATGGTTTTCTCAACAATTCTAA
* * * *
6172 GAAGATGATCGGAAGATGATCTTGTCAAGAACTATGCCAGAAGATGGGTTCTCAAAAATTTTTAG
66 GAAGATGATCAGAAGACGATCTTGTCAAGAACTACGCCAGAAGATGGGTTCTCAAAAATTTTCAG
* *
6237 AAGTTGATCGGAAGACGAACGTTTCAAGAAGTACACTAGAAGATGGTTTTCTCAACAATTTTCA
131 AAGTCGATCGGAAGACGAACGTTTCAAGAAGTACACCAGAAGATGG-TTTCTCAACAATTTTCA
* * *
6301 GAAGATGATCGGAAGACGATCTTGTCAAGAACTACTCCAGGAGATGGTTTTCTCAACAATTTTTA
1 GAAGATGATCGGAAGACGATCTTGTCAAGAACTACACCAGAAGATGGTTTTCTCAACAA-TTCTA
6366 A-AAGATGATCAGAAGACGATCTTGTCAAGAACTACGCCAGAAGATGGGTTCTCAAAAATTTTCA
65 AGAAGATGATCAGAAGACGATCTTGTCAAGAACTACGCCAGAAGATGGGTTCTCAAAAATTTTCA
* * * * * *
6430 GAAGTCGATTGGACGACGATC-TTGTCAAGAAGTACACCAGAAGATGGTTTCTTAAGAGTTTTCA
130 GAAGTCGATCGGAAGACGAACGTT-TCAAGAAGTACACCAGAAGATGGTTTCTCAACAATTTTCA
* * *
6494 GAAGTTGATCGGAAGACGATCTTGTCAAAAATTACACCAGAAGATGG-TTTCTCAA
1 GAAGATGATCGGAAGACGATCTTGTCAAGAACTACACCAGAAGATGGTTTTCTCAA
6549 GAGTTTTCAG
Statistics
Matches: 222, Mismatches: 24, Indels: 6
0.88 0.10 0.02
Matches are distributed among these distances:
192 8 0.04
193 58 0.26
194 151 0.68
195 5 0.02
ACGTcount: A:0.36, C:0.16, G:0.22, T:0.27
Consensus pattern (193 bp):
GAAGATGATCGGAAGACGATCTTGTCAAGAACTACACCAGAAGATGGTTTTCTCAACAATTCTAA
GAAGATGATCAGAAGACGATCTTGTCAAGAACTACGCCAGAAGATGGGTTCTCAAAAATTTTCAG
AAGTCGATCGGAAGACGAACGTTTCAAGAAGTACACCAGAAGATGGTTTCTCAACAATTTTCA
Found at i:8570 original size:65 final size:66
Alignment explanation
Indices: 8430--8601 Score: 215
Period size: 65 Copynumber: 2.6 Consensus size: 66
8420 CATTTTGGTT
8430 TGATCAGAAGACGATCTTGTCAAGAACTACACCAGAAGATGGGTTCTCAAAGAAAGTTTCAGAAG
1 TGATCAGAAGACGATCTTGTCAAGAACTACACCAGAAGATGGGTTCTCAAAGAAAGTTTCAGAAG
*
8495 T
66 A
* * * * * * * *
8496 TGAT-TGAAGACGATCTTATCAAGAAGTACACTAGAAGATGGTTTTTTC-AA-CAATTTTCAGAA
1 TGATCAGAAGACGATCTTGTCAAGAACTACACCAGAAGATGG-GTTCTCAAAGAAAGTTTCAGAA
8558 GA
65 GA
* *
8560 TGATCAGAAGACGATCTTGTCAAGAACTACTCCAGGAGATGG
1 TGATCAGAAGACGATCTTGTCAAGAACTACACCAGAAGATGG
Statistics
Matches: 89, Mismatches: 15, Indels: 5
0.82 0.14 0.05
Matches are distributed among these distances:
64 15 0.17
65 66 0.74
66 8 0.09
ACGTcount: A:0.37, C:0.16, G:0.22, T:0.26
Consensus pattern (66 bp):
TGATCAGAAGACGATCTTGTCAAGAACTACACCAGAAGATGGGTTCTCAAAGAAAGTTTCAGAAG
A
Done.