Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01024599.1 Corchorus olitorius cultivar O-4 contig24632, 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: 19639
ACGTcount: A:0.34, C:0.16, G:0.16, T:0.34
Found at i:282 original size:117 final size:114
Alignment explanation
Indices: 74--450 Score: 515
Period size: 117 Copynumber: 3.2 Consensus size: 114
64 TTTCTAATCA
*
74 ATATATCAATATAATGAATATTAAAATTAATTAGAGACATGTGTCGAGATTTGGAGGCCTCAACA
1 ATATAT-AATATAATGAATATT-AAATTAATTAGAGACACGTGTCGAGATTTGGAGGCCTCAACA
139 TTTAAAGAGTTTCCATATTTGTAGTGTACATTGTTATCATTATATATATAT
64 TTTAAAGAGTTTCCATATTTGTAGTGTACATTGTTATCATTATATATATAT
*
190 ATGATATCAATATAATGAATATTAGAATTAATTAGAGACAGGTGTCGAGATTTGGAGGCCTCAAC
1 AT-ATAT-AATATAATGAATATTA-AATTAATTAGAGACACGTGTCGAGATTTGGAGGCCTCAAC
255 ATTTAAAGAGTTTCCATATTTGTAGTGTACATTGTTATCATTATATATATAT
63 ATTTAAAGAGTTTCCATATTTGTAGTGTACATTGTTATCATTATATATATAT
* * * * *
307 GATATATGATTTAAT-AA-ATTAAATTCAATAAAAAAGCATGCCACTTGTCGAGATTTGGAGGCC
1 -ATATATAATATAATGAATATTAAATT-AAT----TAG-A-GACACGTGTCGAGATTTGGAGGCC
*
370 TCAATATTTAAAGAGTTTCCATATTTGTAGTGTACATTGTTATCATATATATATATAT
58 TCAACATTTAAAGAGTTTCCATATTTGTAGTGTACATTGTTATCAT-TATATATATAT
428 ATATATATATATATATGATATAT
1 ATATATA-ATATA-ATGA-ATAT
451 GATTAGAGCC
Statistics
Matches: 235, Mismatches: 10, Indels: 23
0.88 0.04 0.09
Matches are distributed among these distances:
113 4 0.02
114 7 0.03
115 2 0.01
116 9 0.04
117 115 0.49
118 4 0.02
119 1 0.00
120 72 0.31
121 15 0.06
122 2 0.01
123 1 0.00
124 1 0.00
125 2 0.01
ACGTcount: A:0.37, C:0.09, G:0.15, T:0.39
Consensus pattern (114 bp):
ATATATAATATAATGAATATTAAATTAATTAGAGACACGTGTCGAGATTTGGAGGCCTCAACATT
TAAAGAGTTTCCATATTTGTAGTGTACATTGTTATCATTATATATATAT
Found at i:421 original size:2 final size:2
Alignment explanation
Indices: 414--450 Score: 65
Period size: 2 Copynumber: 18.0 Consensus size: 2
404 CATTGTTATC
414 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT GAT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT -AT AT AT
451 GATTAGAGCC
Statistics
Matches: 34, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
2 32 0.94
3 2 0.06
ACGTcount: A:0.49, C:0.00, G:0.03, T:0.49
Consensus pattern (2 bp):
AT
Found at i:3342 original size:34 final size:34
Alignment explanation
Indices: 3299--3367 Score: 138
Period size: 34 Copynumber: 2.0 Consensus size: 34
3289 TCTATTTTGA
3299 TTCCAAATTAAAGAGTTATTATTTGATCCACCGC
1 TTCCAAATTAAAGAGTTATTATTTGATCCACCGC
3333 TTCCAAATTAAAGAGTTATTATTTGATCCACCGC
1 TTCCAAATTAAAGAGTTATTATTTGATCCACCGC
3367 T
1 T
3368 GATGGAATTT
Statistics
Matches: 35, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
34 35 1.00
ACGTcount: A:0.32, C:0.20, G:0.12, T:0.36
Consensus pattern (34 bp):
TTCCAAATTAAAGAGTTATTATTTGATCCACCGC
Found at i:11498 original size:7 final size:7
Alignment explanation
Indices: 11488--11525 Score: 51
Period size: 7 Copynumber: 5.3 Consensus size: 7
11478 TAACAACTAA
11488 ATCATAT
1 ATCATAT
11495 ATCATAT
1 ATCATAT
11502 ATCATATGT
1 ATCATA--T
11511 ATCATAT
1 ATCATAT
11518 AT-ATAT
1 ATCATAT
11524 AT
1 AT
11526 ATAATGATAA
Statistics
Matches: 29, Mismatches: 0, Indels: 5
0.85 0.00 0.15
Matches are distributed among these distances:
6 6 0.21
7 16 0.55
9 7 0.24
ACGTcount: A:0.42, C:0.11, G:0.03, T:0.45
Consensus pattern (7 bp):
ATCATAT
Found at i:11515 original size:16 final size:15
Alignment explanation
Indices: 11494--11523 Score: 51
Period size: 16 Copynumber: 1.9 Consensus size: 15
11484 CTAAATCATA
11494 TATCATATATCATATG
1 TATCATATAT-ATATG
11510 TATCATATATATAT
1 TATCATATATATAT
11524 ATATAATGAT
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 4 0.29
16 10 0.71
ACGTcount: A:0.40, C:0.10, G:0.03, T:0.47
Consensus pattern (15 bp):
TATCATATATATATG
Found at i:17523 original size:198 final size:197
Alignment explanation
Indices: 17029--17623 Score: 870
Period size: 198 Copynumber: 3.0 Consensus size: 197
17019 ATAAGTTTAT
*
17029 TATAAGAAAAATTATACAATACACTGTCAGTGGAGTTTAGCAGACTGCACGTGCGGGGTTTAAGG
1 TATAA-AAAAATTATACAATACACTGTCAGTGGAGTTTAGCAGACTGCACGTGC-AGGTTTAAGG
*
17094 GTTGACATGTATCCCCTTAGGGAATATGTATTAATATTGAATATTTAATTAATTATGAAATGGGG
64 GTTGACATGTATCCCCTTAGGGAATATGTATTAATATTAAATATTTAATTAATTATGAAATGGGG
* * *
17159 TATGTGTCAACTTCTTAACTCGTTTATGGAGTCCAAAATTTACATTGACA-TGTATTGTACAATA
129 TATGTGTCAACTTCTTAACCCGCTTATGGAGTCCAAAATTTACATTGACAGTGTATTGTATAATA
*
17223 ATCA
194 ATCC
* * * * *
17227 TAT-AAAAAATTGTACAATACATTGTGAGTGGAGTTTAGCAGACTGCACGCGCGAGGTTTTAGGG
1 TATAAAAAAATTATACAATACACTGTCAGTGGAGTTTAGCAGACTGCACGTGC-AGGTTTAAGGG
* ** ** * * *
17291 TTGACATGTGTCATCTTAGGGAATATGTATTAATATTTTATATCTAATTAATGATGAAATAGGGT
65 TTGACATGTATCCCCTTAGGGAATATGTATTAATATTAAATATTTAATTAATTATGAAATGGGGT
* * * *
17356 ATGTGTCAACTTCTTAACCCGGTTATGAAGTTCAAAATTTACACTGACAGTGTATTGTATAATAA
130 ATGTGTCAACTTCTTAACCCGCTTATGGAGTCCAAAATTTACATTGACAGTGTATTGTATAATAA
17421 TCC
195 TCC
* * *
17424 TATAAAAAAATTATACAATACACCGTCAGTGGAGTTTAGCAGGCTGTACGTGCATGGTTTAAGGG
1 TATAAAAAAATTATACAATACACTGTCAGTGGAGTTTAGCAGACTGCACGTGCA-GGTTTAAGGG
*
17489 TTGACATGTATCCCCTTAGGGAATATGTATTAATATCAAATATTTAATTAATTATGAAATGGGGT
65 TTGACATGTATCCCCTTAGGGAATATGTATTAATATTAAATATTTAATTAATTATGAAATGGGGT
* *
17554 ATGTGTCAACTTCTTAACCAGCTTATGGAGTCCAAAATTTACATTGACAGTGTATTTGTATACTA
130 ATGTGTCAACTTCTTAACCCGCTTATGGAGTCCAAAATTTACATTGACAGTGTA-TTGTATAATA
17619 ATCC
194 ATCC
17623 T
1 T
17624 TATTATAAAG
Statistics
Matches: 349, Mismatches: 44, Indels: 7
0.87 0.11 0.02
Matches are distributed among these distances:
196 155 0.44
197 21 0.06
198 159 0.46
199 14 0.04
ACGTcount: A:0.33, C:0.13, G:0.19, T:0.35
Consensus pattern (197 bp):
TATAAAAAAATTATACAATACACTGTCAGTGGAGTTTAGCAGACTGCACGTGCAGGTTTAAGGGT
TGACATGTATCCCCTTAGGGAATATGTATTAATATTAAATATTTAATTAATTATGAAATGGGGTA
TGTGTCAACTTCTTAACCCGCTTATGGAGTCCAAAATTTACATTGACAGTGTATTGTATAATAAT
CC
Found at i:18583 original size:2 final size:2
Alignment explanation
Indices: 18576--18611 Score: 72
Period size: 2 Copynumber: 18.0 Consensus size: 2
18566 CCTAGTAATA
18576 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
18612 CATTTCCATC
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 34 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Done.