Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01007937.1 Corchorus capsularis cultivar CVL-1 contig07958, 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: 46630
ACGTcount: A:0.31, C:0.17, G:0.18, T:0.34
Found at i:2257 original size:21 final size:23
Alignment explanation
Indices: 2231--2279 Score: 59
Period size: 21 Copynumber: 2.3 Consensus size: 23
2221 AGGTGTAAGC
*
2231 TTCAAAATTG-TTACCTAACCA-
1 TTCAAAATTGATTACATAACCAT
*
2252 TTC-AAATTGATTTCATAACCAT
1 TTCAAAATTGATTACATAACCAT
2274 TTCAAA
1 TTCAAA
2280 TGTTTACTCC
Statistics
Matches: 23, Mismatches: 2, Indels: 4
0.79 0.07 0.14
Matches are distributed among these distances:
20 6 0.26
21 12 0.52
22 3 0.13
23 2 0.09
ACGTcount: A:0.39, C:0.20, G:0.04, T:0.37
Consensus pattern (23 bp):
TTCAAAATTGATTACATAACCAT
Found at i:13810 original size:2 final size:2
Alignment explanation
Indices: 13803--13833 Score: 62
Period size: 2 Copynumber: 15.5 Consensus size: 2
13793 TCTCCAATCA
13803 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
13834 GTTCCACAGA
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 29 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:15390 original size:2 final size:2
Alignment explanation
Indices: 15323--15370 Score: 60
Period size: 2 Copynumber: 23.5 Consensus size: 2
15313 ACTTTGACAC
* * *
15323 AT AT AT AT AT AT AT AT AT AT GGT AT AT AT AT AT GT TT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT -AT AT AT AT AT AT AT AT AT AT AT
15366 AT AT A
1 AT AT A
15371 CAAAAAATTT
Statistics
Matches: 40, Mismatches: 5, Indels: 2
0.85 0.11 0.04
Matches are distributed among these distances:
2 39 0.98
3 1 0.03
ACGTcount: A:0.44, C:0.00, G:0.06, T:0.50
Consensus pattern (2 bp):
AT
Found at i:32572 original size:2 final size:2
Alignment explanation
Indices: 32565--32602 Score: 76
Period size: 2 Copynumber: 19.0 Consensus size: 2
32555 GGCAGAAGAA
32565 AT 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 AT
32603 CATCTTTTCT
Statistics
Matches: 36, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 36 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:37745 original size:6 final size:6
Alignment explanation
Indices: 37734--37765 Score: 64
Period size: 6 Copynumber: 5.3 Consensus size: 6
37724 CATTACTATA
37734 TATATG TATATG TATATG TATATG TATATG TA
1 TATATG TATATG TATATG TATATG TATATG TA
37766 AAGGATGCAT
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 26 1.00
ACGTcount: A:0.34, C:0.00, G:0.16, T:0.50
Consensus pattern (6 bp):
TATATG
Found at i:41627 original size:1 final size:1
Alignment explanation
Indices: 41621--41662 Score: 84
Period size: 1 Copynumber: 42.0 Consensus size: 1
41611 TTAAGCATAC
41621 TTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTT
1 TTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTT
41663 AAACTGCAAA
Statistics
Matches: 41, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
1 41 1.00
ACGTcount: A:0.00, C:0.00, G:0.00, T:1.00
Consensus pattern (1 bp):
T
Found at i:45781 original size:332 final size:332
Alignment explanation
Indices: 44870--46630 Score: 2704
Period size: 332 Copynumber: 5.3 Consensus size: 332
44860 AAAATGATAT
44870 ATATAATGAAAGATCACCCACTTTGGAATTAAGGATTTGTTTTTACGAGCATCTCAATCCGGTTT
1 ATATAATGAAAGATCACCCACTTTGGAATTAAGGATTTGTTTTTACGAGCATCTCAATCCGGTTT
* *
44935 CGATTTAATCAGAAACTAATTCGAAAAAAATAAGAAAAAT-ATTATTACATGCGTGAGAAGCCCT
66 CGATTTAATCAGAAACTACTTCGAAAAAAATAGGAAAAATGA-TATTACATGCGTGAGAAGCCCT
* * * *
44999 TCAATCTTTTTTGTGTTGAGTTGTATATTTTTCATGAGTATTTATGGCCGAAAATTGAGGAGAAC
130 TCAATCTTTTTGGCGTTGAGTTGTATATTTTTCATGAGTATTTATGGCCAAAAATTGAGGAGAAA
* * * *
45064 TGTTTCGGGTCAAATTTTGCAAAATTTTAGCCAAAATCATGTACTAACCATCACTGTTTTTTGAC
195 TGTTTCGGGCCAAATTTTTCAAAATTTTAGCCGAAATCATGTACTAACCATCAC-GGTTTTTG-C
* * *
45129 TAAAAACGCATTCCGGGGGCCAGGCTCAGTTTTGCATGATTTTTGGCAACAAGATTCATTGCAAT
258 TAAAAACGCGTTCCGGGGGCCCGGCTCAGTTTTGCATGATTTTTGGCAACAAGACTCATTGCAAT
45194 ATCTATATTC
323 ATCTATATTC
45204 ATATAATGAAAGATCACCCACTTTGGAATTAAGGATTTGTTTTTACGAGCATCTCAATCCGGTTT
1 ATATAATGAAAGATCACCCACTTTGGAATTAAGGATTTGTTTTTACGAGCATCTCAATCCGGTTT
*
45269 CGATTTAATCAGAAACTACTTCGAAAAAAATAGGAAAAATGATATTACATGCGTGAGAAGCCCAT
66 CGATTTAATCAGAAACTACTTCGAAAAAAATAGGAAAAATGATATTACATGCGTGAGAAGCCCTT
*
45334 CAATCTTTTTGGCGTTGAGTTGTATATTTTTCATGAGTATTTATGGCCAAAAATTGAGAAGAAAT
131 CAATCTTTTTGGCGTTGAGTTGTATATTTTTCATGAGTATTTATGGCCAAAAATTGAGGAGAAAT
* * *
45399 GTTACGGACTAAATTTTTCAAAATTTTAGCCGAAATCATGTACTAACCATCACGGTTTTTGCTAA
196 GTTTCGGGCCAAATTTTTCAAAATTTTAGCCGAAATCATGTACTAACCATCACGGTTTTTGCTAA
* * *
45464 AAACGCGTTCCGGGGGCCCGGCTCAGTTTTGCATGATTTTT-TCAATAAGACTCACTGCAATATC
261 AAACGCGTTCCGGGGGCCCGGCTCAGTTTTGCATGATTTTTGGCAACAAGACTCATTGCAATATC
45528 TATATTC
326 TATATTC
*
45535 ATATAATGAAAGATCACCCACTTTGGAATTAAGGATTTGTTTTTACGAGCATCTCAATCCAGTTT
1 ATATAATGAAAGATCACCCACTTTGGAATTAAGGATTTGTTTTTACGAGCATCTCAATCCGGTTT
* **
45600 CGGTTTAATCAGAAACTACTTCGAAAAAAATAGGAAAAATGATATTACATTAGTGAGAAGCCCTT
66 CGATTTAATCAGAAACTACTTCGAAAAAAATAGGAAAAATGATATTACATGCGTGAGAAGCCCTT
* * * *
45665 CAATCTTTTTTGCGTTGAGTTGTATATTTTTCCATGAGCATTTATGGCCGAAAATTGAGGATAAA
131 CAATCTTTTTGGCGTTGAGTTGTATATTTTT-CATGAGTATTTATGGCCAAAAATTGAGGAGAAA
* * *
45730 TGTTTCGGGTCAAATTTTTCTAAATTTTAGCCGAAATCATGTACTAACCATCACTGTTTTTTGAC
195 TGTTTCGGGCCAAATTTTTCAAAATTTTAGCCGAAATCATGTACTAACCATCAC-GGTTTTTG-C
* * * *
45795 TATAAACGCGTTCCGGGGGCCCGACTTAGTTTTGCATGATTTTTGGCAACAAGACTCATTGAAAT
258 TAAAAACGCGTTCCGGGGGCCCGGCTCAGTTTTGCATGATTTTTGGCAACAAGACTCATTGCAAT
45860 ATCTATATTC
323 ATCTATATTC
* * * * *
45870 ATATGATGAAAGGTCACCCACTTTGGAATTAATGATTTGTTTTTACGAGTATCTCAATCCAGTTT
1 ATATAATGAAAGATCACCCACTTTGGAATTAAGGATTTGTTTTTACGAGCATCTCAATCCGGTTT
45935 CGATTTAATCAGAAACTACTTCGAAAAAAATAGGAAAAATGATATTACATGCGTGAGAAGCCCTT
66 CGATTTAATCAGAAACTACTTCGAAAAAAATAGGAAAAATGATATTACATGCGTGAGAAGCCCTT
46000 CAATCTTTTTGGCGTTGAGTTGTATATTTTTCATGAGTATTTATGGCCAAAAATTGAGGAGAAAT
131 CAATCTTTTTGGCGTTGAGTTGTATATTTTTCATGAGTATTTATGGCCAAAAATTGAGGAGAAAT
* * * *
46065 GTTTCAGACCAAAATTTTCAAAATTTTAGCCGAAATCATGTACTAACCATCACGGTTTTTAACTA
196 GTTTCGGGCCAAATTTTTCAAAATTTTAGCCGAAATCATGTACTAACCATCACGGTTTTT-GCTA
*
46130 AAAACGCGTTCC-GGGGCCCGGCCCAGTTTTGCATGATTTTTGGCAACAAGACTCATTGCAATAT
260 AAAACGCGTTCCGGGGGCCCGGCTCAGTTTTGCATGATTTTTGGCAACAAGACTCATTGCAATAT
*
46194 CTATAATC
325 CTATATTC
* *
46202 ATATTATGAAAGATCACCCACTTTGGAACTAAGGATTTGTTTTTACGAGCATCTCAATCCGGTTT
1 ATATAATGAAAGATCACCCACTTTGGAATTAAGGATTTGTTTTTACGAGCATCTCAATCCGGTTT
* * *
46267 CGGTTTAATCAGAAACTACTTCTACAAAAATAGGAAAAATGATATTACATGCGTGAGAAGCCCTT
66 CGATTTAATCAGAAACTACTTCGAAAAAAATAGGAAAAATGATATTACATGCGTGAGAAGCCCTT
* *
46332 CAATCTTTTTGGCGTTGAGTTGTATATTTTTCATGAGTATTTATGGCAAAAAATTGAGGTGAAAT
131 CAATCTTTTTGGCGTTGAGTTGTATATTTTTCATGAGTATTTATGGCCAAAAATTGAGGAGAAAT
* *
46397 GTTTCGGACCAAATTTTTCAAGATTTTAGCCGAAATCATG---------T-A---------CTAA
196 GTTTCGGGCCAAATTTTTCAAAATTTTAGCCGAAATCATGTACTAACCATCACGGTTTTTGCTAA
* *
46443 AAACGCGTTCCGGGGGCCCGGCTCAGTTTTGCATGACTTTTTGGCTATAAGACTCATTGCAATAT
261 AAACGCGTTCCGGGGGCCCGGCTCAGTTTTGCATGA-TTTTTGGCAACAAGACTCATTGCAATAT
*
46508 ACTTATATTT
325 -C-TATATTC
46518 ATATAATGAAAGATCACCCACTTTGGAATTAAGGTATTTG-TTTTACGAGCATCTCAATCCGGTT
1 ATATAATGAAAGATCACCCACTTTGGAATTAAGG-ATTTGTTTTTACGAGCATCTCAATCCGGTT
*
46582 TCGGTTTAATCAGAAACTACTTCGAAAAAAATAAGGAAAAATAGATATT
65 TCGATTTAATCAGAAACTACTTCGAAAAAAAT-AGGAAAAAT-GATATT
Statistics
Matches: 1323, Mismatches: 91, Indels: 42
0.91 0.06 0.03
Matches are distributed among these distances:
312 15 0.01
313 23 0.02
314 26 0.02
315 1 0.00
316 91 0.07
317 14 0.01
318 6 0.00
322 1 0.00
323 1 0.00
331 181 0.14
332 397 0.30
333 34 0.03
334 353 0.27
335 180 0.14
ACGTcount: A:0.32, C:0.16, G:0.18, T:0.34
Consensus pattern (332 bp):
ATATAATGAAAGATCACCCACTTTGGAATTAAGGATTTGTTTTTACGAGCATCTCAATCCGGTTT
CGATTTAATCAGAAACTACTTCGAAAAAAATAGGAAAAATGATATTACATGCGTGAGAAGCCCTT
CAATCTTTTTGGCGTTGAGTTGTATATTTTTCATGAGTATTTATGGCCAAAAATTGAGGAGAAAT
GTTTCGGGCCAAATTTTTCAAAATTTTAGCCGAAATCATGTACTAACCATCACGGTTTTTGCTAA
AAACGCGTTCCGGGGGCCCGGCTCAGTTTTGCATGATTTTTGGCAACAAGACTCATTGCAATATC
TATATTC
Found at i:46148 original size:666 final size:664
Alignment explanation
Indices: 44870--46630 Score: 2780
Period size: 666 Copynumber: 2.7 Consensus size: 664
44860 AAAATGATAT
44870 ATATAATGAAAGATCACCCACTTTGGAATTAAGGATTTGTTTTTACGAGCATCTCAATCCGGTTT
1 ATATAATGAAAGATCACCCACTTTGGAATTAAGGATTTGTTTTTACGAGCATCTCAATCCGGTTT
* * *
44935 CGATTTAATCAGAAACTAATTCGAAAAAAATAAGAAAAAT-ATTATTACATGCGTGAGAAGCCCT
66 CGGTTTAATCAGAAACTACTTCGAAAAAAATAGGAAAAATGA-TATTACATGCGTGAGAAGCCCT
* * *
44999 TCAATCTTTTTTGTGTTGAGTTGTATATTTTTCATGAGTATTTATGGCCGAAAATTGAGGAGAAC
130 TCAATCTTTTTTGCGTTGAGTTGTATATTTTTCATGAGTATTTATGGCCGAAAATTGAGGATAAA
* *
45064 TGTTTCGGGTCAAATTTTGCAAAATTTTAGCCAAAATCATGTACTAACCATCACTGTTTTTTGAC
195 TGTTTCGGGTCAAATTTTTC-AAATTTTAGCCGAAATCATGTACTAACCATCACTGTTTTTTGAC
* * *
45129 TAAAAACGCATTCCGGGGGCCAGGCTCAGTTTTGCATGATTTTTGGCAACAAGATTCATTGCAAT
259 T-AAAACGCGTTCCGGGGGCCCGGCTCAGTTTTGCATGATTTTTGGCAACAAGACTCATTGCAAT
45194 ATCTATATTCATATAATGAAAGATCACCCACTTTGGAATTAAGGATTTGTTTTTACGAGCATCTC
323 ATCTATATTCATATAATGAAAGATCACCCACTTTGGAATTAAGGATTTGTTTTTACGAGCATCTC
45259 AATCCGGTTTCGATTTAATCAGAAACTACTTCGAAAAAAATAGGAAAAATGATATTACATGCGTG
388 AATCCGGTTTCGATTTAATCAGAAACTACTTCGAAAAAAATAGGAAAAATGATATTACATGCGTG
45324 AGAAGCCCATCAATCTTTTTGGCGTTGAGTTGTATATTTTTCATGAGTATTTATGGCCAAAAATT
453 AGAAGCCCATCAATCTTTTTGGCGTTGAGTTGTATATTTTTCATGAGTATTTATGGCCAAAAATT
* * *
45389 GAGAAGAAATGTTACGGACTAAATTTTTCAAAATTTTAGCCGAAATCATGTACTAACCATCACGG
518 GAGAAGAAATGTTACAGACCAAAATTTTCAAAATTTTAGCCGAAATCATGTACTAACCATCACGG
* * * *
45454 TTTTTGCTAAAAACGCGTTCCGGGGGCCCGGCTCAGTTTTGCATGATTTTT-TCAATAAGACTCA
583 TTTTTACTAAAAACGCGTTCCGGGGGCCCGGCCCAGTTTTGCATGATTTTTGGCAACAAGACTCA
*
45518 CTGCAATATCTATATTC
648 CTGCAATATCTATAATC
*
45535 ATATAATGAAAGATCACCCACTTTGGAATTAAGGATTTGTTTTTACGAGCATCTCAATCCAGTTT
1 ATATAATGAAAGATCACCCACTTTGGAATTAAGGATTTGTTTTTACGAGCATCTCAATCCGGTTT
**
45600 CGGTTTAATCAGAAACTACTTCGAAAAAAATAGGAAAAATGATATTACATTAGTGAGAAGCCCTT
66 CGGTTTAATCAGAAACTACTTCGAAAAAAATAGGAAAAATGATATTACATGCGTGAGAAGCCCTT
*
45665 CAATCTTTTTTGCGTTGAGTTGTATATTTTTCCATGAGCATTTATGGCCGAAAATTGAGGATAAA
131 CAATCTTTTTTGCGTTGAGTTGTATATTTTT-CATGAGTATTTATGGCCGAAAATTGAGGATAAA
45730 TGTTTCGGGTCAAATTTTTCTAAATTTTAGCCGAAATCATGTACTAACCATCACTGTTTTTTGAC
195 TGTTTCGGGTCAAATTTTTC-AAATTTTAGCCGAAATCATGTACTAACCATCACTGTTTTTTGAC
* * *
45795 TATAAACGCGTTCCGGGGGCCCGACTTAGTTTTGCATGATTTTTGGCAACAAGACTCATTGAAAT
259 TA-AAACGCGTTCCGGGGGCCCGGCTCAGTTTTGCATGATTTTTGGCAACAAGACTCATTGCAAT
* * * *
45860 ATCTATATTCATATGATGAAAGGTCACCCACTTTGGAATTAATGATTTGTTTTTACGAGTATCTC
323 ATCTATATTCATATAATGAAAGATCACCCACTTTGGAATTAAGGATTTGTTTTTACGAGCATCTC
*
45925 AATCCAGTTTCGATTTAATCAGAAACTACTTCGAAAAAAATAGGAAAAATGATATTACATGCGTG
388 AATCCGGTTTCGATTTAATCAGAAACTACTTCGAAAAAAATAGGAAAAATGATATTACATGCGTG
*
45990 AGAAGCCCTTCAATCTTTTTGGCGTTGAGTTGTATATTTTTCATGAGTATTTATGGCCAAAAATT
453 AGAAGCCCATCAATCTTTTTGGCGTTGAGTTGTATATTTTTCATGAGTATTTATGGCCAAAAATT
* *
46055 GAGGAGAAATGTTTCAGACCAAAATTTTCAAAATTTTAGCCGAAATCATGTACTAACCATCACGG
518 GAGAAGAAATGTTACAGACCAAAATTTTCAAAATTTTAGCCGAAATCATGTACTAACCATCACGG
46120 TTTTTAACTAAAAACGCGTTCC-GGGGCCCGGCCCAGTTTTGCATGATTTTTGGCAACAAGACTC
583 TTTTT-ACTAAAAACGCGTTCCGGGGGCCCGGCCCAGTTTTGCATGATTTTTGGCAACAAGACTC
*
46184 ATTGCAATATCTATAATC
647 ACTGCAATATCTATAATC
* *
46202 ATATTATGAAAGATCACCCACTTTGGAACTAAGGATTTGTTTTTACGAGCATCTCAATCCGGTTT
1 ATATAATGAAAGATCACCCACTTTGGAATTAAGGATTTGTTTTTACGAGCATCTCAATCCGGTTT
* *
46267 CGGTTTAATCAGAAACTACTTCTACAAAAATAGGAAAAATGATATTACATGCGTGAGAAGCCCTT
66 CGGTTTAATCAGAAACTACTTCGAAAAAAATAGGAAAAATGATATTACATGCGTGAGAAGCCCTT
* **
46332 CAATCTTTTTGGCGTTGAGTTGTATATTTTTCATGAGTATTTATGGCAAAAAATTGAGG-TGAAA
131 CAATCTTTTTTGCGTTGAGTTGTATATTTTTCATGAGTATTTATGGCCGAAAATTGAGGAT-AAA
**
46396 TGTTTCGGACCAAATTTTTCAAGATTTTAGCCGAAATCATG---------T-AC-------T-A-
195 TGTTTCGGGTCAAATTTTTCAA-ATTTTAGCCGAAATCATGTACTAACCATCACTGTTTTTTGAC
* *
46442 -AAAACGCGTTCCGGGGGCCCGGCTCAGTTTTGCATGACTTTTTGGCTATAAGACTCATTGCAAT
259 TAAAACGCGTTCCGGGGGCCCGGCTCAGTTTTGCATGA-TTTTTGGCAACAAGACTCATTGCAAT
*
46506 ATACTTATATTTATATAATGAAAGATCACCCACTTTGGAATTAAGGTATTTG-TTTTACGAGCAT
323 AT-C-TATATTCATATAATGAAAGATCACCCACTTTGGAATTAAGG-ATTTGTTTTTACGAGCAT
*
46570 CTCAATCCGGTTTCGGTTTAATCAGAAACTACTTCGAAAAAAATAAGGAAAAATAGATATT
385 CTCAATCCGGTTTCGATTTAATCAGAAACTACTTCGAAAAAAAT-AGGAAAAAT-GATATT
Statistics
Matches: 1022, Mismatches: 61, Indels: 41
0.91 0.05 0.04
Matches are distributed among these distances:
645 34 0.03
646 26 0.03
647 1 0.00
648 91 0.09
649 15 0.01
650 6 0.01
656 2 0.00
657 1 0.00
665 156 0.15
666 496 0.49
667 194 0.19
ACGTcount: A:0.32, C:0.16, G:0.18, T:0.34
Consensus pattern (664 bp):
ATATAATGAAAGATCACCCACTTTGGAATTAAGGATTTGTTTTTACGAGCATCTCAATCCGGTTT
CGGTTTAATCAGAAACTACTTCGAAAAAAATAGGAAAAATGATATTACATGCGTGAGAAGCCCTT
CAATCTTTTTTGCGTTGAGTTGTATATTTTTCATGAGTATTTATGGCCGAAAATTGAGGATAAAT
GTTTCGGGTCAAATTTTTCAAATTTTAGCCGAAATCATGTACTAACCATCACTGTTTTTTGACTA
AAACGCGTTCCGGGGGCCCGGCTCAGTTTTGCATGATTTTTGGCAACAAGACTCATTGCAATATC
TATATTCATATAATGAAAGATCACCCACTTTGGAATTAAGGATTTGTTTTTACGAGCATCTCAAT
CCGGTTTCGATTTAATCAGAAACTACTTCGAAAAAAATAGGAAAAATGATATTACATGCGTGAGA
AGCCCATCAATCTTTTTGGCGTTGAGTTGTATATTTTTCATGAGTATTTATGGCCAAAAATTGAG
AAGAAATGTTACAGACCAAAATTTTCAAAATTTTAGCCGAAATCATGTACTAACCATCACGGTTT
TTACTAAAAACGCGTTCCGGGGGCCCGGCCCAGTTTTGCATGATTTTTGGCAACAAGACTCACTG
CAATATCTATAATC
Done.