Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01015182.1 Corchorus olitorius cultivar O-4 contig15215, 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: 10189
ACGTcount: A:0.34, C:0.15, G:0.17, T:0.34
Found at i:479 original size:11 final size:12
Alignment explanation
Indices: 459--490 Score: 64
Period size: 12 Copynumber: 2.7 Consensus size: 12
449 AAATTACCCA
459 TCCAAAAAAACC
1 TCCAAAAAAACC
471 TCCAAAAAAACC
1 TCCAAAAAAACC
483 TCCAAAAA
1 TCCAAAAA
491 CTACTCACAT
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 20 1.00
ACGTcount: A:0.59, C:0.31, G:0.00, T:0.09
Consensus pattern (12 bp):
TCCAAAAAAACC
Found at i:692 original size:48 final size:48
Alignment explanation
Indices: 636--730 Score: 190
Period size: 48 Copynumber: 2.0 Consensus size: 48
626 TCAACTTCGA
636 TATTGATCACTTTATAAATAAATCCTTTTCAATTTGAGTCAAATTGTG
1 TATTGATCACTTTATAAATAAATCCTTTTCAATTTGAGTCAAATTGTG
684 TATTGATCACTTTATAAATAAATCCTTTTCAATTTGAGTCAAATTGT
1 TATTGATCACTTTATAAATAAATCCTTTTCAATTTGAGTCAAATTGT
731 TCACACAATG
Statistics
Matches: 47, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
48 47 1.00
ACGTcount: A:0.34, C:0.13, G:0.09, T:0.44
Consensus pattern (48 bp):
TATTGATCACTTTATAAATAAATCCTTTTCAATTTGAGTCAAATTGTG
Found at i:4226 original size:72 final size:72
Alignment explanation
Indices: 4109--4243 Score: 243
Period size: 72 Copynumber: 1.9 Consensus size: 72
4099 GGGATAATAT
* *
4109 TAGTATTGAATTTTATTAATGCTATGAAAGTTTACTAAAAACTTCAAATTTATTTGGTTTGATTT
1 TAGTATTGAATTCTATTAATGCTATGAAAGTTTACTAAAAACTTCAAATTTATCTGGTTTGATTT
4174 TGGATGA
66 TGGATGA
*
4181 TAGTATTGAATTCTATTAATGCTATGAAATTTTACTAAAAACTTCAAATTTATCTGGTTTGAT
1 TAGTATTGAATTCTATTAATGCTATGAAAGTTTACTAAAAACTTCAAATTTATCTGGTTTGAT
4244 GATGGTGATT
Statistics
Matches: 60, Mismatches: 3, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
72 60 1.00
ACGTcount: A:0.34, C:0.07, G:0.13, T:0.45
Consensus pattern (72 bp):
TAGTATTGAATTCTATTAATGCTATGAAAGTTTACTAAAAACTTCAAATTTATCTGGTTTGATTT
TGGATGA
Found at i:4915 original size:2 final size:2
Alignment explanation
Indices: 4908--4934 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
4898 AAGGCAAACC
4908 TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA T
4935 GTGTGTGTGA
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 25 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:6346 original size:1 final size:1
Alignment explanation
Indices: 6340--6369 Score: 60
Period size: 1 Copynumber: 30.0 Consensus size: 1
6330 ATCATCATGG
6340 TTTTTTTTTTTTTTTTTTTTTTTTTTTTTT
1 TTTTTTTTTTTTTTTTTTTTTTTTTTTTTT
6370 ACTTCGAAAA
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
1 29 1.00
ACGTcount: A:0.00, C:0.00, G:0.00, T:1.00
Consensus pattern (1 bp):
T
Found at i:6604 original size:2 final size:2
Alignment explanation
Indices: 6597--6622 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
6587 TGGCGTTGAA
6597 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
6623 TATGAGTATT
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 24 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:7263 original size:273 final size:272
Alignment explanation
Indices: 6763--7264 Score: 632
Period size: 274 Copynumber: 1.8 Consensus size: 272
6753 CGGTACAGTG
* ** * * *
6763 TTGCATGATTTTTGGCGCTGAGACTCCTTGCAATATCTATATTCATCTAACCAAATCTCAGCCAC
1 TTGCATGATTTTTGACGCCAAGACTCCTTGCAATATCCATATTCATCTAACCAAATATCAGCAAC
* *
6828 ATTGGATTTAAGGATTTCTAAAACAAACATCTGAATCATGTTTCGATTTAATCAAAAATTAATTT
66 ATTGGATTTAAGAATTTCTAAAACAAACATCTGAATCATGTTTCAATTTAATCAAAAATTAATTT
* * * *
6893 GAAAAATAATAGGAAAAACGATATTAGAAGCATGAAAAGCCCTTCAATCTTATTGGCTTTGAATT
131 GAAAAATAAT--GAAAAACGATATTAAAAGCATGAAAAGCCCTCCAATCTTATTGGCATTAAATT
* * *
6958 ATATAATTTTAATGAGTGTTGTGGCTAAAAATTGAGGGAATAACTTTCGAGTAAATTTTTGTAAA
194 ATATAATTTTAATGAGTATTGTAGCCAAAAATTGAGGGAATAACTTTCGAGTAAATTTTTGTAAA
7023 TTAATTAATGAGTT
259 TTAATTAATGAGTT
* * *
7037 TTGCATGATTTTTGACGCCAAGACTCTTTG-AGATATCCATATTCATTTAATCAAATATCAGCAA
1 TTGCATGATTTTTGACGCCAAGACTCCTTGCA-ATATCCATATTCATCTAACCAAATATCAGCAA
* *** ** * * * *
7101 CATTGGATTTAAGAATTTGTTTTTATGAGCCTCTGAATCTTGTTTCAATTTAATTAAAAATTAAT
65 CATTGGATTTAAGAATTT-CTAAAACAAACATCTGAATCATGTTTCAATTTAATCAAAAATTAAT
* ** *
7166 TTAGAAAAATAAT-AAAAACGATATTAAAAGCGTGAAAAGTTCTCCAATCTTTTTGGCATTAAAT
129 TT-GAAAAATAATGAAAAACGATATTAAAAGCATGAAAAGCCCTCCAATCTTATTGGCATTAAAT
*
7230 TATATATATTTT-ATGAGTATTTTAGCCAAAAATTG
193 TATATA-ATTTTAATGAGTATTGTAGCCAAAAATTG
7265 TCAGAAAATT
Statistics
Matches: 191, Mismatches: 33, Indels: 9
0.82 0.14 0.04
Matches are distributed among these distances:
273 69 0.36
274 75 0.39
275 37 0.19
276 10 0.05
ACGTcount: A:0.37, C:0.12, G:0.14, T:0.37
Consensus pattern (272 bp):
TTGCATGATTTTTGACGCCAAGACTCCTTGCAATATCCATATTCATCTAACCAAATATCAGCAAC
ATTGGATTTAAGAATTTCTAAAACAAACATCTGAATCATGTTTCAATTTAATCAAAAATTAATTT
GAAAAATAATGAAAAACGATATTAAAAGCATGAAAAGCCCTCCAATCTTATTGGCATTAAATTAT
ATAATTTTAATGAGTATTGTAGCCAAAAATTGAGGGAATAACTTTCGAGTAAATTTTTGTAAATT
AATTAATGAGTT
Found at i:8643 original size:330 final size:329
Alignment explanation
Indices: 7033--8933 Score: 1983
Period size: 332 Copynumber: 5.7 Consensus size: 329
7023 TTAATTAATG
* * * * * *
7033 AGTTTTGCATGATTTTTGACGCCAAGACTCTTTGAGATATCCATATTCATTTAATCAAATATCAG
1 AGTTTTGCATGATTTTTGGCGCCAAGACTCCTTGAAATATCTATATTCATCTAA-CAAATCTCAG
* * * * * *
7098 CAACATTGGATTTAAGAATTTGTTTTTATGAGCCTCTGAATCTTGTTTCAATTTAATTAAAAATT
65 CCACATT-GATTTAAGGATTTGTTTTTACGAGCATCTGAATCTTGTTTCGATTTAATTAGAAATT
* * * *
7163 AATTTAG-AAAAATAATAAAAACGATATTAAAAGCGTGAAAAGTTCTCCAATCTTTTTGGCATTA
129 AATTCAGAAAAAATAAGAAAAACGATATTAAAAGCGTGAAAAGTCCTCCAATCTTTTTGGCATTG
* * *
7227 AATTATATATATTTTATGAGTATTTTAGCCAAAAATTGTCA-GAAAATTTTTTTTGGGTCAATTT
194 AATTATATATATTTTATGAGTATTTTAGTCAAAAATTG--AGGAAAA-ATTTTTCGGGTCAATTT
* * ** * *
7291 TTGCATAA-TTTAGCCGAAATTGTGTACTAACCATCATGGTTTTTGGCTAAAAACGCGTTTCGAG
256 TTGCAAAATTTTAGCCGAAATCGTGTACTAACCATCACAGTTTTTGGCTAAAAACGCGTTCCGGG
** *
7355 ACCCAGGCTT
321 GTCC-GGCTC
* * * * *
7365 AGTTTTGCATGATTTTTTGCGCCGAGACTTCTTGAAATATCTTTATTCATCTAATCAAATTTCAG
1 AGTTTTGCATGATTTTTGGCGCCAAGACTCCTTGAAATATCTATATTCATCTAA-CAAATCTCAG
* * * *
7430 CCACATTGAATTTAAGGATTTGCTTTTACGAGCCTATGAATCTTGTTTCAATTTAATTAGAAATT
65 CCACATTG-ATTTAAGGATTTGTTTTTACGAGCATCTGAATCTTGTTTCGATTTAATTAGAAATT
* * * **
7495 AATTCAG-AAAAATATGAAAAACGATATTAAAAGCGTGAAAAGTGCTCCAGTCTTTTTGGTGTTG
129 AATTCAGAAAAAATAAGAAAAACGATATTAAAAGCGTGAAAAGTCCTCCAATCTTTTTGGCATTG
* * * * * *
7559 AATTATATATATTTTATGAGTGTTGT-GGCTAAAAATTGA-GACCAAATATTTCGAGTCAATTTT
194 AATTATATATATTTTATGAGTATTTTAGTC-AAAAATTGAGGA-AAAATTTTTCGGGTCAATTTT
7622 TGCAAAATTTTAGCCGAAATCGTG---T-ACCATCACAGTTTTTTGGCTAAAAACGCGTTCCGGG
257 TGCAAAATTTTAGCCGAAATCGTGTACTAACCATCACAG-TTTTTGGCTAAAAACGCGTTCCGGG
*
7683 GCTCCGGGTC
321 G-TCCGGCTC
* * ** * * * *
7693 AATTTTGCATGATTTTTGGTGGAAAAAATCCTTGAAATATCTTTATTCATCTAACCAAATCTTAG
1 AGTTTTGCATGATTTTTGGCGCCAAGACTCCTTGAAATATCTATATTCATCTAA-CAAATCTCAG
* * * *
7758 CCACACTTGATTTAAGGATTTGTTTTTGCGAGCATCTGAATCATGTTTTGATTTAATTAGAAATG
65 CCACA-TTGATTTAAGGATTTGTTTTTACGAGCATCTGAATCTTGTTTCGATTTAATTAGAAATT
* * * * * * * *
7823 AATTTGAAAAAAAATAGGAAAAACGATATTAGAAGCGTGAGAAGCCCTTCAATCTTTTTGGCGTT
129 AA-TTCAGAAAAAATAAGAAAAACGATATTAAAAGCGTGAAAAGTCCTCCAATCTTTTTGGCATT
* * * * * *
7888 GAATTATATATTTTTTTATGAGTATTGT-GGCTAAACATTGA-GAAAAATATTTCGGGTTAATTT
193 GAATTATATA-TATTTTATGAGTATTTTAGTC-AAAAATTGAGGAAAAATTTTTCGGGTCAATTT
* *****
7951 TTGCAAAATTTTAGCCGAAATCGTGTACT-ATCATTGTTTTTTTTGGCTAAAAACGCGTTCCGGG
256 TTGCAAAATTTTAGCCGAAATCGTGTACTAACCATCACAGTTTTTGGCTAAAAACGCGTTCCGGG
** *
8015 GTTTTGGGTC
321 G-TCCGGCTC
* *
8025 AGTTTTGCATGATTTTTGGCGTCAAGACT-CTTAAAATATATCTATATTCATCTAACCAAATCTC
1 AGTTTTGCATGATTTTTGGCGCCAAGACTCCTT-GAA-ATATCTATATTCATCTAA-CAAATCTC
* *** * *
8089 AGCCACATTGTATTTAAGGATTTATTTTTACGAATTTCTAAATCTTGTTTTGATTTAATTAGAAA
63 AGCCACATTG-ATTTAAGGATTTGTTTTTACGAGCATCTGAATCTTGTTTCGATTTAATTAGAAA
* ** * ** * * * * *
8154 TTAGTTTGGAAAGAAAATAAGTAAAACGATATTTGAAGCGTGAAAAAGGCTTTCATTTTTTTTGG
127 TTAATTCAG-AA-AAAATAAGAAAAACGATATTAAAAGCGTG-AAAAGTCCTCCAATCTTTTTGG
* * * *
8219 CATTTAATTATATAT-TTTTATGAGTATTTTTG-CTAGAAATCGAGGAAAAATTTTTCGGGTCAA
189 CATTGAATTATATATATTTTATGAGTATTTTAGTC-AAAAATTGAGGAAAAATTTTTCGGGTCAA
* * * * *
8282 TTTTTGGAAAATTTTAGCTGAAATCGTGTACTAACCATCACAATTTTCGGCTAAAAACGCGTTTC
253 TTTTTGCAAAATTTTAGCCGAAATCGTGTACTAACCATCACAGTTTTTGGCTAAAAACGCGTTCC
*
8347 GGGGTCCTGCTC
318 GGGGTCCGGCTC
* * * *
8359 AGTTTTGCATGATTTTTGGTGTCAAGACTCCTTGAAATATCTATATTCATTTAACGAAATCTTAG
1 AGTTTTGCATGATTTTTGGCGCCAAGACTCCTTGAAATATCTATATTCATCTAAC-AAATCTCAG
* * * *
8424 CCACATTAGATTTAAAGATTTGTTTTTATGAGCATTTGAATCTTGTTTCGATTTAATT-GGAATT
65 CCACATT-GATTTAAGGATTTGTTTTTACGAGCATCTGAATCTTGTTTCGATTTAATTAGAAATT
* * * * * * **
8488 GAATTCAGAAAGAAATAGGAAAAACAATATTAGAAGCGTTAAAAGCCCTTCAATCTTTTTGATAT
129 -AATTCAGAAA-AAATAAGAAAAACGATATTAAAAGCGTGAAAAGTCCTCCAATCTTTTTGGCAT
* * *
8553 CGAATCATATAT-TTTTATGAGTATTTTAGTC-AAAATTGAGGAAATATTTTTCGGGTCAATTTT
192 TGAATTATATATATTTTATGAGTATTTTAGTCAAAAATTGAGGAAAAATTTTTCGGGTCAATTTT
* * * **
8616 TGCAAAATTTTAGCCAAAATCGTGTACTAACCATCACGGTTTTTGGTTAAAAACGCGTTCCAAGG
257 TGCAAAATTTTAGCCGAAATCGTGTACTAACCATCACAGTTTTTGGCTAAAAACGCGTTCCGGGG
* *
8681 CCACAGCTC
322 TC-CGGCTC
* * *
8690 TGTTTTGCATGATTTTTGGCGCCAAGACTCCTTGAAATATCTTTATTCATCTAATAAAATCTCAG
1 AGTTTTGCATGATTTTTGGCGCCAAGACTCCTTGAAATATCTATATTCATCTAA-CAAATCTCAG
* * * *
8755 CCACATTGGATTTAACGATTTGTTTTTATGTGCATCT-AATCTTGTATCGATTTAATTAGAAATT
65 CCACATT-GATTTAAGGATTTGTTTTTACGAGCATCTGAATCTTGTTTCGATTTAATTAGAAATT
* * * *
8819 AATTCAGAAAAAAT--GAAAAACAATATTAAAAGCGTGAAAAATCCTCCAATGTTTTTGGCGTTG
129 AATTCAGAAAAAATAAGAAAAACGATATTAAAAGCGTGAAAAGTCCTCCAATCTTTTTGGCATTG
* *
8882 AATTATATATATTTTATGAGTATTTTTGTCAAAAATTGAGGAAAAATCTTTC
194 AATTATATATATTTTATGAGTATTTTAGTCAAAAATTGAGGAAAAATTTTTC
8934 AGTCATTTTT
Statistics
Matches: 1324, Mismatches: 212, Indels: 69
0.82 0.13 0.04
Matches are distributed among these distances:
327 56 0.04
328 153 0.12
329 31 0.02
330 237 0.18
331 197 0.15
332 294 0.22
333 186 0.14
334 110 0.08
335 60 0.05
ACGTcount: A:0.32, C:0.13, G:0.16, T:0.38
Consensus pattern (329 bp):
AGTTTTGCATGATTTTTGGCGCCAAGACTCCTTGAAATATCTATATTCATCTAACAAATCTCAGC
CACATTGATTTAAGGATTTGTTTTTACGAGCATCTGAATCTTGTTTCGATTTAATTAGAAATTAA
TTCAGAAAAAATAAGAAAAACGATATTAAAAGCGTGAAAAGTCCTCCAATCTTTTTGGCATTGAA
TTATATATATTTTATGAGTATTTTAGTCAAAAATTGAGGAAAAATTTTTCGGGTCAATTTTTGCA
AAATTTTAGCCGAAATCGTGTACTAACCATCACAGTTTTTGGCTAAAAACGCGTTCCGGGGTCCG
GCTC
Done.