Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01015374.1 Corchorus capsularis cultivar CVL-1 contig15395, 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: 41294
ACGTcount: A:0.32, C:0.17, G:0.17, T:0.33
Found at i:5168 original size:31 final size:31
Alignment explanation
Indices: 5110--5169 Score: 93
Period size: 31 Copynumber: 1.9 Consensus size: 31
5100 CTCTCCCAAA
*
5110 GGCTCAAACTCTCTTCCTCCCAGAGATTTAT
1 GGCTCAAACTCTCTTCCTCCCACAGATTTAT
* *
5141 GGCTCAAACTCTCTTCCTCTCTCAGATTT
1 GGCTCAAACTCTCTTCCTCCCACAGATTT
5170 CTAGTTTCAT
Statistics
Matches: 26, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
31 26 1.00
ACGTcount: A:0.20, C:0.33, G:0.12, T:0.35
Consensus pattern (31 bp):
GGCTCAAACTCTCTTCCTCCCACAGATTTAT
Found at i:18431 original size:33 final size:33
Alignment explanation
Indices: 18384--18460 Score: 111
Period size: 33 Copynumber: 2.3 Consensus size: 33
18374 AATAAGTTGG
*
18384 TTAACTGAAACCAATTGCTAG-AAGGCTCTGCTA
1 TTAAATGAAACCAATTGCTAGAAAGG-TCTGCTA
* *
18417 TTAAATGAAACCAATTGCTAGAAAGGTCTGTTG
1 TTAAATGAAACCAATTGCTAGAAAGGTCTGCTA
18450 TTAAATGAAAC
1 TTAAATGAAAC
18461 AAAACGAGAC
Statistics
Matches: 40, Mismatches: 3, Indels: 2
0.89 0.07 0.04
Matches are distributed among these distances:
33 36 0.90
34 4 0.10
ACGTcount: A:0.38, C:0.16, G:0.18, T:0.29
Consensus pattern (33 bp):
TTAAATGAAACCAATTGCTAGAAAGGTCTGCTA
Found at i:23163 original size:443 final size:434
Alignment explanation
Indices: 22343--23298 Score: 1105
Period size: 443 Copynumber: 2.2 Consensus size: 434
22333 ATAACCTTTT
* * * * *
22343 AAAGTTGTAGATCATGAAATTAC--CTAATAGACACCTAAATTACCTTAATTAGATAAATAGAAC
1 AAAGTTGTAGATCATGAAATTACTTTTAATAGACACCTGAATCACCTTAATCAGATAAACA-AAC
* *
22406 AAAAACAAATAAAGTTGAAACATTAAATCGATTAAGATAGAATTAGTAAAGGATTAAGTTGTATA
65 AAAAA-AAATAAAGTTGAAACATTAAATCGATTAAGATAGAATTAGTAAAGGACTAAGTAGTATA
* * * *
22471 AAATAGAAAAAATATTAGGGTCATTTGATACATATCCAAATAAGAAAATATTTGTTAGTGGAGAT
129 AAATAGAAAAAATATTAGGATCATTGGATAAATATCCAAATAAGAAAATATTTGTTAGTGGAAAT
* * * * *
22536 CTTGAAACATAAAAATTTCTTTTTGAGCCCTCCATGAAACTTGTAGATTAAATTTAGCTTTCGAG
194 CTTGAAACATAAAAATTTCGTTTTGAGCCCTCCATAAAACTCGTAGATCAAATTTAGCTTCCGAG
* * *
22601 CCCTTTATGAAAGTCATAGACCATGCAATAACCCTTTAACCAACACTTGAATATTTTTAATCGGA
259 CCCTTCATGAAAGTCATAGACCATGCAATAACACTTTAACCAACACTTGAATAATTTTAATCGGA
** * * * * * * * * * *
22666 CATGTAGATTGAAAATTGTTTGCTATTAAATAGGCCGGCAATCGAAACCACCAAATTTTAAAAGC
324 CATACAAATCGAAAATTATATGATATGAAATAGACCGACAATCGAAAACACCAAATTTCAAAAGC
* * *
22731 ATTTTTTTAGAACTAAAACATAAAAATTGACTTTTGACTTCTTCA-A
389 AATTTTTT-GAACTAAAACATAAAAATTGACTTTTAACTCCTTCACA
* * *
22777 GAAAGTTGTAAATCATTAAATTATCTTTTAATAGACACCTGAATCACCTTAATCGGATAAACAAA
1 -AAAGTTGTAGATCATGAAATTA-CTTTTAATAGACACCTGAATCACCTTAATCAGATAAACAAA
* *
22842 -AGAAAAAATAAAGTTGAAACGTTAAATCGATTAAGATAGAATTAGTAAAGGACTAAGTAGTATA
64 CAAAAAAAATAAAGTTGAAACATTAAATCGATTAAGATAGAATTAGTAAAGGACTAAGTAGTATA
* * * *
22906 AAATATATATATATATATATATGATGATCATTGGATAAATAATCCAAATGAGAAAATGTTTGTT-
129 AAATAGA-A-A-A-A-ATAT-T-AGGATCATTGGATAAAT-ATCCAAATAAGAAAATATTTGTTA
* * * * *
22970 GATGGAAATTTTGAAACATTAAAATTAT-GTTTTGAGCTCTTCATAAAACTCGTATATCAAATTT
186 G-TGGAAATCTTGAAACATAAAAATT-TCGTTTTGAGCCCTCCATAAAACTCGTAGATCAAATTT
* * * * * * **
23034 AGCTTCCGGGTCCTTCATGAAAGTCGTAGATCATGTAATAACATTTTAACGGACACTTGAATAAT
249 AGCTTCCGAGCCCTTCATGAAAGTCATAGACCATGCAATAACACTTTAACCAACACTTGAATAAT
* *
23099 TTTAATCGGACATACAAATCGAAAATTATATGATATGAAATAGACTGACAATGGAAAACACCAAA
314 TTTAATCGGACATACAAATCGAAAATTATATGATATGAAATAGACCGACAATCGAAAACACCAAA
* ** * * *
23164 TTTCAGAATTAATTTTTTGAATTAAAACATTAAAATTGACTTTTAAGTCCTTCACA
379 TTTCAAAAGCAATTTTTTGAACTAAAACATAAAAATTGACTTTTAACTCCTTCACA
* * * *
23220 AAAGTTGTAGATCATGAGATTACCTTTTAATAGACACATGAATCACCTTAATCTGACAAACAAAC
1 AAAGTTGTAGATCATGAAATTA-CTTTTAATAGACACCTGAATCACCTTAATCAGATAAACAAAC
23285 AAAAGAAAATAAAG
65 AAAA-AAAATAAAG
23299 AAAATAAAAC
Statistics
Matches: 433, Mismatches: 72, Indels: 23
0.82 0.14 0.04
Matches are distributed among these distances:
435 82 0.19
436 6 0.01
437 3 0.01
438 31 0.07
439 1 0.00
440 4 0.01
441 1 0.00
442 102 0.24
443 193 0.45
444 10 0.02
ACGTcount: A:0.42, C:0.13, G:0.13, T:0.31
Consensus pattern (434 bp):
AAAGTTGTAGATCATGAAATTACTTTTAATAGACACCTGAATCACCTTAATCAGATAAACAAACA
AAAAAAATAAAGTTGAAACATTAAATCGATTAAGATAGAATTAGTAAAGGACTAAGTAGTATAAA
ATAGAAAAAATATTAGGATCATTGGATAAATATCCAAATAAGAAAATATTTGTTAGTGGAAATCT
TGAAACATAAAAATTTCGTTTTGAGCCCTCCATAAAACTCGTAGATCAAATTTAGCTTCCGAGCC
CTTCATGAAAGTCATAGACCATGCAATAACACTTTAACCAACACTTGAATAATTTTAATCGGACA
TACAAATCGAAAATTATATGATATGAAATAGACCGACAATCGAAAACACCAAATTTCAAAAGCAA
TTTTTTGAACTAAAACATAAAAATTGACTTTTAACTCCTTCACA
Found at i:24771 original size:31 final size:31
Alignment explanation
Indices: 24709--24776 Score: 84
Period size: 31 Copynumber: 2.2 Consensus size: 31
24699 CGCGGCCTTA
**
24709 CCACGTGGCATTTTGGTCAAATGTGGCATTG
1 CCACGTGGCATTTTGGTCAAACATGGCATTG
**
24740 CCACGTGGCATTTTTGGTCCGACATGG-ATTG
1 CCACGTGGCA-TTTTGGTCAAACATGGCATTG
24771 CCACGT
1 CCACGT
24777 CAGCAATACC
Statistics
Matches: 32, Mismatches: 4, Indels: 2
0.84 0.11 0.05
Matches are distributed among these distances:
31 20 0.62
32 12 0.38
ACGTcount: A:0.18, C:0.24, G:0.28, T:0.31
Consensus pattern (31 bp):
CCACGTGGCATTTTGGTCAAACATGGCATTG
Found at i:24819 original size:34 final size:35
Alignment explanation
Indices: 24776--24850 Score: 107
Period size: 38 Copynumber: 2.1 Consensus size: 35
24766 GATTGCCACG
*
24776 TCAGCAATACCGT-TTATATAATTCAATCAATTAA
1 TCAGCAATACCCTATTATATAATTCAATCAATTAA
24810 TCAGCAATACCCTAACCTTATATAATTCAATCAATTAA
1 TCAGCAATACCCT-A--TTATATAATTCAATCAATTAA
24848 TCA
1 TCA
24851 AGCACCACTT
Statistics
Matches: 36, Mismatches: 1, Indels: 4
0.88 0.02 0.10
Matches are distributed among these distances:
34 12 0.33
38 24 0.67
ACGTcount: A:0.41, C:0.21, G:0.04, T:0.33
Consensus pattern (35 bp):
TCAGCAATACCCTATTATATAATTCAATCAATTAA
Found at i:26918 original size:22 final size:23
Alignment explanation
Indices: 26893--26944 Score: 70
Period size: 23 Copynumber: 2.3 Consensus size: 23
26883 CGCGACATAG
*
26893 GTTTATCAAA-ATTTCATAATGA
1 GTTTATCAAATATTTCATAAGGA
*
26915 GTTTATCAAATTTTTCATAAGGA
1 GTTTATCAAATATTTCATAAGGA
*
26938 GATTATC
1 GTTTATC
26945 GCAATTTGAT
Statistics
Matches: 26, Mismatches: 3, Indels: 1
0.87 0.10 0.03
Matches are distributed among these distances:
22 10 0.38
23 16 0.62
ACGTcount: A:0.37, C:0.10, G:0.12, T:0.42
Consensus pattern (23 bp):
GTTTATCAAATATTTCATAAGGA
Found at i:28898 original size:12 final size:12
Alignment explanation
Indices: 28881--28906 Score: 52
Period size: 12 Copynumber: 2.2 Consensus size: 12
28871 GTCTTGACGA
28881 GTAAGAAAGCGT
1 GTAAGAAAGCGT
28893 GTAAGAAAGCGT
1 GTAAGAAAGCGT
28905 GT
1 GT
28907 GTGCACTCTG
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 14 1.00
ACGTcount: A:0.38, C:0.08, G:0.35, T:0.19
Consensus pattern (12 bp):
GTAAGAAAGCGT
Found at i:29321 original size:2 final size:2
Alignment explanation
Indices: 29314--29343 Score: 60
Period size: 2 Copynumber: 15.0 Consensus size: 2
29304 TTACGATTTA
29314 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
29344 GTTTTAGGGT
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 28 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:32023 original size:17 final size:17
Alignment explanation
Indices: 31997--32037 Score: 55
Period size: 17 Copynumber: 2.4 Consensus size: 17
31987 TGTTGAAGGG
* *
31997 TTTTTTTTTTCTTTTTC
1 TTTTTGTTTTCGTTTTC
32014 TTTTTGTTTTCGTTTTC
1 TTTTTGTTTTCGTTTTC
32031 TTGTTTG
1 TT-TTTG
32038 GGGTGGGGGG
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
17 17 0.81
18 4 0.19
ACGTcount: A:0.00, C:0.10, G:0.10, T:0.80
Consensus pattern (17 bp):
TTTTTGTTTTCGTTTTC
Found at i:38953 original size:34 final size:34
Alignment explanation
Indices: 38904--38969 Score: 96
Period size: 34 Copynumber: 1.9 Consensus size: 34
38894 ATTGATTTCT
* * *
38904 AAAATGGTTTCTTTTTTTTTCTTACTAAACAAAA
1 AAAATGATTTCTTTTTCTTTCCTACTAAACAAAA
*
38938 AAAATGATTTTTTTTTCTTTCCTACTAAACAA
1 AAAATGATTTCTTTTTCTTTCCTACTAAACAA
38970 GAAGAAGAAA
Statistics
Matches: 28, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
34 28 1.00
ACGTcount: A:0.35, C:0.14, G:0.05, T:0.47
Consensus pattern (34 bp):
AAAATGATTTCTTTTTCTTTCCTACTAAACAAAA
Done.