Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01014361.1 Corchorus olitorius cultivar O-4 contig14394, 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: 10625
ACGTcount: A:0.33, C:0.16, G:0.15, T:0.36
Found at i:6146 original size:1 final size:1
Alignment explanation
Indices: 6135--6170 Score: 63
Period size: 1 Copynumber: 36.0 Consensus size: 1
6125 GTTAAGTTAG
*
6135 AAAATAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA
1 AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA
6171 CAGAGGAAGT
Statistics
Matches: 33, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
1 33 1.00
ACGTcount: A:0.97, C:0.00, G:0.00, T:0.03
Consensus pattern (1 bp):
A
Found at i:7572 original size:158 final size:159
Alignment explanation
Indices: 7282--7601 Score: 615
Period size: 158 Copynumber: 2.0 Consensus size: 159
7272 TTGTCTTACT
7282 ATCTTACTATCTTACTACTATATAAAAAATCACGAACTCAAAAATTCTAATTGGAAAATTTCATA
1 ATCTTACTATCTTACTACTATAT-AAAAATCACGAACTCAAAAATTCTAATTGGAAAATTTCATA
7347 AATACCCTTGTAATATAATATAATAATTTTTTAATCAGTATCCTTTTTAGTCATTAAACTTTTTT
65 AATACCCTTGTAATATAATATAATAATTTTTTAATCAGTATCCTTTTTAGTCATTAAACTTTTTT
7412 TATTAATTATGGAAAGATGTTGTAAATCTA
130 TATTAATTATGGAAAGATGTTGTAAATCTA
*
7442 ATCTTACTATCTTACTACTATAT-AAAATCACGAACTCAAAAATTCTAATTGGGAAATTTCATAA
1 ATCTTACTATCTTACTACTATATAAAAATCACGAACTCAAAAATTCTAATTGGAAAATTTCATAA
7506 ATACCCTTGTAATATAATATAATAATTTTTTAATCAGTATCCTTTTTAGTCATTAAACTTTTTTT
66 ATACCCTTGTAATATAATATAATAATTTTTTAATCAGTATCCTTTTTAGTCATTAAACTTTTTTT
7571 ATTAATTATGGAAAGATGTTGTAAATCTA
131 ATTAATTATGGAAAGATGTTGTAAATCTA
7600 AT
1 AT
7602 ATTTTAATTT
Statistics
Matches: 159, Mismatches: 1, Indels: 2
0.98 0.01 0.01
Matches are distributed among these distances:
158 136 0.86
160 23 0.14
ACGTcount: A:0.39, C:0.12, G:0.07, T:0.42
Consensus pattern (159 bp):
ATCTTACTATCTTACTACTATATAAAAATCACGAACTCAAAAATTCTAATTGGAAAATTTCATAA
ATACCCTTGTAATATAATATAATAATTTTTTAATCAGTATCCTTTTTAGTCATTAAACTTTTTTT
ATTAATTATGGAAAGATGTTGTAAATCTA
Found at i:9340 original size:22 final size:22
Alignment explanation
Indices: 9314--9364 Score: 66
Period size: 22 Copynumber: 2.3 Consensus size: 22
9304 TGCGGTTACC
* **
9314 AATTTTATAGCGTGATTATCAA
1 AATTTCATAGCGAAATTATCAA
*
9336 AATTTCATAGGGAAATTATCAA
1 AATTTCATAGCGAAATTATCAA
9358 AATTTCA
1 AATTTCA
9365 CACTGAGAGG
Statistics
Matches: 25, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
22 25 1.00
ACGTcount: A:0.41, C:0.10, G:0.12, T:0.37
Consensus pattern (22 bp):
AATTTCATAGCGAAATTATCAA
Found at i:9443 original size:44 final size:44
Alignment explanation
Indices: 9329--9517 Score: 141
Period size: 44 Copynumber: 4.2 Consensus size: 44
9319 TATAGCGTGA
** * *
9329 TTATCAAAATTT-CATAGGGAAATTATCAAAATTTCACACTGAGAGG
1 TTATC-AAATTTGCATAGGGAGGTTATCAAAATTCCACAAT--GAGG
* * * *
9375 TTATCAGAA-TTG-ATTAGTGTGGTTATCAAAATTCCACAGTGTGG
1 TTATCA-AATTTGCA-TAGGGAGGTTATCAAAATTCCACAATGAGG
* * * *
9419 TTATCAAATTTGCATAGGGAGGTTATCGAAATTTCATAATGAAG
1 TTATCAAATTTGCATAGGGAGGTTATCAAAATTCCACAATGAGG
* * *** * *
9463 TTATCAAATTTTCACAAATAGGTTATCAAAATTTCATAATGAGG
1 TTATCAAATTTGCATAGGGAGGTTATCAAAATTCCACAATGAGG
9507 TTATCAAATTT
1 TTATCAAATTT
9518 TCACAGTGCG
Statistics
Matches: 116, Mismatches: 22, Indels: 12
0.77 0.15 0.08
Matches are distributed among these distances:
43 2 0.02
44 82 0.71
45 5 0.04
46 27 0.23
ACGTcount: A:0.37, C:0.11, G:0.16, T:0.35
Consensus pattern (44 bp):
TTATCAAATTTGCATAGGGAGGTTATCAAAATTCCACAATGAGG
Found at i:9518 original size:44 final size:44
Alignment explanation
Indices: 9395--9522 Score: 157
Period size: 44 Copynumber: 2.9 Consensus size: 44
9385 TGATTAGTGT
* * * * * * **
9395 GGTTATCAAAATTCCACAGTGTGGTTATCAAATTTGCATAGGGA
1 GGTTATCAAAATTTCATAATGAGGTTATCAAATTTTCACAAAGA
* * *
9439 GGTTATCGAAATTTCATAATGAAGTTATCAAATTTTCACAAATA
1 GGTTATCAAAATTTCATAATGAGGTTATCAAATTTTCACAAAGA
9483 GGTTATCAAAATTTCATAATGAGGTTATCAAATTTTCACA
1 GGTTATCAAAATTTCATAATGAGGTTATCAAATTTTCACA
9523 GTGCGATTGT
Statistics
Matches: 71, Mismatches: 13, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
44 71 1.00
ACGTcount: A:0.37, C:0.12, G:0.16, T:0.35
Consensus pattern (44 bp):
GGTTATCAAAATTTCATAATGAGGTTATCAAATTTTCACAAAGA
Found at i:9519 original size:22 final size:22
Alignment explanation
Indices: 9417--9520 Score: 122
Period size: 22 Copynumber: 4.7 Consensus size: 22
9407 TCCACAGTGT
* **
9417 GGTTATCAAATTTGCATAGGGA
1 GGTTATCAAATTTTCATAATGA
9439 GGTTATCGAAA-TTTCATAATGA
1 GGTTATC-AAATTTTCATAATGA
* *
9461 AGTTATCAAATTTTCACAAAT-A
1 GGTTATCAAATTTTCA-TAATGA
*
9483 GGTTATCAAAATTTCATAATGA
1 GGTTATCAAATTTTCATAATGA
9505 GGTTATCAAATTTTCA
1 GGTTATCAAATTTTCA
9521 CAGTGCGATT
Statistics
Matches: 69, Mismatches: 9, Indels: 8
0.80 0.10 0.09
Matches are distributed among these distances:
21 6 0.09
22 57 0.83
23 6 0.09
ACGTcount: A:0.38, C:0.11, G:0.15, T:0.37
Consensus pattern (22 bp):
GGTTATCAAATTTTCATAATGA
Done.