Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01015090.1 Corchorus capsularis cultivar CVL-1 contig15111, 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: 36758
ACGTcount: A:0.33, C:0.19, G:0.18, T:0.29
Found at i:2465 original size:35 final size:35
Alignment explanation
Indices: 2399--2465 Score: 91
Period size: 35 Copynumber: 1.9 Consensus size: 35
2389 CATGGACCCG
* * *
2399 GGTCGCGACGCGGGTCGCAGCCTACTGCATGGCTT
1 GGTCGCGACGCGAGTCGCAGCCTAATCCATGGCTT
2434 GGTCGCGACGCGAGTCGC-GACCTAATCCATGG
1 GGTCGCGACGCGAGTCGCAG-CCTAATCCATGG
2466 GCAGGCTGCG
Statistics
Matches: 28, Mismatches: 3, Indels: 2
0.85 0.09 0.06
Matches are distributed among these distances:
34 1 0.04
35 27 0.96
ACGTcount: A:0.15, C:0.31, G:0.36, T:0.18
Consensus pattern (35 bp):
GGTCGCGACGCGAGTCGCAGCCTAATCCATGGCTT
Found at i:5154 original size:2 final size:2
Alignment explanation
Indices: 5147--5174 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
5137 GAAAGGGGCC
5147 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
5175 GTTTTGCCAG
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:7625 original size:436 final size:432
Alignment explanation
Indices: 6610--7627 Score: 1202
Period size: 436 Copynumber: 2.3 Consensus size: 432
6600 CAATCGGAAT
* * * * *
6610 CACAAAATTTCAAAAGTATTTTTTAGAATTGAAACATAAAAATTAGCTTTTTAGTCTTTCATGAA
1 CACAAAATTTCGAAAGCATTTTTTAGAATTAAAACATAAAAATTAGCTTTTGAGTCATTCATGAA
** * *
6675 AATTGTAGATCACAAAATTACCTTTTAATAAACACATGAATTACCTTAATTGGACAAATATAACA
66 AATTGTAGATCATGAAATTACCTTTTAATAGACACATGAATCACCTTAATTGGAC-AA-ATAA-A
* *
6740 AGGAAAATAAAAAA-ATAAGCGTAAAATCAAATAAGATAGAATTTGTAAATGACTAAATAGCATA
128 A-GAAAATAAAAAATA-AAGCGTAAAATCAAATAAGATAGAATTTGTAAAGGAATAAATAGCATA
* * * *
6804 AAATAGAAAAGTATGAGGATCATTTGATAACTAATTCAAATAAGAAAATATTTCGTAATGGATAT
191 AAATAGAAAAATATGAGGATCATTTGATAAATAATTCAAATAAGAAAATATTTCGTAATAGAGAT
* * * * *
6869 CTTGAAACATAAAAATTCGCTTTTGAACCCTTTATGAAACTCGTAGATCAAATTAACTTTCGGGT
256 CTAGAAACATAAAAATTCCCTTTTGAACCCTTCATGAAACTCGTAGATCAAATTAACTTTCAGAT
** * * * * * *
6934 TGTTCATGAAAGTCGTAGATCATACAGTAACCTTTTAACCGATACTTGAATAACTTTAATCGGAC
321 CCTTCATGAAAGTCATAAATCATACAATAACCTTTTAACCGACACTTCAATAACTTCAATCGGAC
* * * * *
6999 ATGTGGATCGAAAATTATATGGTATTAAATAGACCAACAATCGAAAC
386 ATGTGGAACAAAAATTATACGATATTAAATAGACCAACAATCAAAAC
* * * * * *
7046 GACAAAATTTAGAAAGCATTTTTTTGAATTAAAATATAAAAATTTGCTTTTGAGTCATTCTTGAA
1 CACAAAATTTCGAAAGCATTTTTTAGAATTAAAACATAAAAATTAGCTTTTGAGTCATTCATGAA
* * *
7111 AGTTGTAGATCATGAAATTACCTTTTAATAGACACATGAATCAACTTAATTGGACAAATAAAACA
66 AATTGTAGATCATGAAATTACCTTTTAATAGACACATGAATCACCTTAATTGGACAAATAAAAGA
* * * * * * *
7176 AAGGATAAAAAATAAATCTTAAACATTAGATTAAGATAGGATTTGTAAAGGAATAAGTAGTATAA
131 AA--ATAAAAAATAAAGCGTAAA-ATCA-AATAAGATAGAATTTGTAAAGGAATAAATAGCATAA
* * *
7241 AGTAGAAAAATATGAGGGTCATTTGATAAATAATTCAAATAAGAAAATGTTT-GTTAATAGAGAT
192 AATAGAAAAATATGAGGATCATTTGATAAATAATTCAAATAAGAAAATATTTCG-TAATAGAGAT
* * *
7305 CTAGAAGCATAAAAATTCCCTTTTGAATCCTTCATGAAACTCGTAGATCAAATTTAGCTTTCAGA
256 CTAGAAACATAAAAATTCCCTTTTGAACCCTTCATGAAACTCGTAGATCAAA-TTAACTTTCAGA
* * *
7370 TCCTTTATGAAAGTCATAAATCGTGCAATAACCTTTT-ACCTGACACTTCAATAACTTCAATCGG
320 TCCTTCATGAAAGTCATAAATCATACAATAACCTTTTAACC-GACACTTCAATAACTTCAATCGG
* * **
7434 ACATGT-GAACAAAAAATTGTACGATATTAAATTGACCGGCAATCAAAAC
384 ACATGTGGAAC-AAAAATTATACGATATTAAATAGACCAACAATCAAAAC
* * * * *
7483 CACAAAATTTCGGAAGCATGTTTTAGAATCAAAACATTAAAATTGGCTTTTGAGTTC-TTCATGA
1 CACAAAATTTCGAAAGCATTTTTTAGAATTAAAACATAAAAATTAGCTTTTGAG-TCATTCATGA
* * * * *
7547 AAATTGTAGATAATGAAATTACCTTTTATTAGACACTTGAATCACCTTAATCGGATAAATAGAAA
65 AAATTGTAGATCATGAAATTACCTTTTAATAGACACATGAATCACCTTAATTGGACAAATA-AAA
7612 -AAAATACAAAAATAAA
129 GAAAATA-AAAAATAAA
7628 AGTCAACGCG
Statistics
Matches: 491, Mismatches: 79, Indels: 24
0.83 0.13 0.04
Matches are distributed among these distances:
432 3 0.01
433 2 0.00
434 19 0.04
435 10 0.02
436 250 0.51
437 202 0.41
438 5 0.01
ACGTcount: A:0.43, C:0.12, G:0.13, T:0.31
Consensus pattern (432 bp):
CACAAAATTTCGAAAGCATTTTTTAGAATTAAAACATAAAAATTAGCTTTTGAGTCATTCATGAA
AATTGTAGATCATGAAATTACCTTTTAATAGACACATGAATCACCTTAATTGGACAAATAAAAGA
AAATAAAAAATAAAGCGTAAAATCAAATAAGATAGAATTTGTAAAGGAATAAATAGCATAAAATA
GAAAAATATGAGGATCATTTGATAAATAATTCAAATAAGAAAATATTTCGTAATAGAGATCTAGA
AACATAAAAATTCCCTTTTGAACCCTTCATGAAACTCGTAGATCAAATTAACTTTCAGATCCTTC
ATGAAAGTCATAAATCATACAATAACCTTTTAACCGACACTTCAATAACTTCAATCGGACATGTG
GAACAAAAATTATACGATATTAAATAGACCAACAATCAAAAC
Found at i:8556 original size:6 final size:6
Alignment explanation
Indices: 8545--8582 Score: 67
Period size: 6 Copynumber: 6.3 Consensus size: 6
8535 CAGGCTGCAC
*
8545 CACAAT CACAAT CACAGT CACAAT CACAAT CACAAT CA
1 CACAAT CACAAT CACAAT CACAAT CACAAT CACAAT CA
8583 TCCGTTAACA
Statistics
Matches: 30, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
6 30 1.00
ACGTcount: A:0.47, C:0.34, G:0.03, T:0.16
Consensus pattern (6 bp):
CACAAT
Found at i:9848 original size:18 final size:19
Alignment explanation
Indices: 9821--9856 Score: 56
Period size: 18 Copynumber: 1.9 Consensus size: 19
9811 AGTTATATCG
*
9821 AAAAATATAAAAA-AAATC
1 AAAAAAATAAAAACAAATC
9839 AAAAAAATAAAAACAAAT
1 AAAAAAATAAAAACAAAT
9857 TCGACCAGAA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
18 12 0.75
19 4 0.25
ACGTcount: A:0.81, C:0.06, G:0.00, T:0.14
Consensus pattern (19 bp):
AAAAAAATAAAAACAAATC
Found at i:31457 original size:66 final size:66
Alignment explanation
Indices: 31353--31821 Score: 775
Period size: 66 Copynumber: 7.1 Consensus size: 66
31343 AAAAGTTAAT
* *
31353 TAAACGATCCTTGAATCGTAAACTTAAATAAGATGAACGTCTCCCTCGAGACCATTTTATCAAAA
1 TAAACGATCCTTGAATCGTAAACTTAAATAAGACGAACGTCTCCCTCGAGACCGTTTTATCAAAA
31418 C
66 C
* *
31419 TAAACGATCCTTGAATCGTAAATTTAAATAGGACGAACGTCTCCCTCGAGACCGTTTTATCAAAA
1 TAAACGATCCTTGAATCGTAAACTTAAATAAGACGAACGTCTCCCTCGAGACCGTTTTATCAAAA
*
31484 T
66 C
31485 TAAACGATCCTTGAATCGTAAACTTAAATAAGACGAACGTCTCCCTCGAGACCGTTTTATCAAAA
1 TAAACGATCCTTGAATCGTAAACTTAAATAAGACGAACGTCTCCCTCGAGACCGTTTTATCAAAA
31550 C
66 C
*
31551 TAAACGATCCTTGAATCGTAAACATAAA-ATAGACGAACGTCTCCCTCGAGACCGTTTTATCAAA
1 TAAACGATCCTTGAATCGTAAACTTAAATA-AGACGAACGTCTCCCTCGAGACCGTTTTATCAAA
31615 A-
65 AC
31616 TAAACGATCCTTGAATCGTAAACTTAAATAAGACGAACGTCTCCCTCGAGACCGTTTTATCAAAA
1 TAAACGATCCTTGAATCGTAAACTTAAATAAGACGAACGTCTCCCTCGAGACCGTTTTATCAAAA
31681 C
66 C
*
31682 TAAACGATCCTTGAATCGTAAACTTAAATAAGACGAACGTCTCCCTCGAGACCGTTTGATCAAAA
1 TAAACGATCCTTGAATCGTAAACTTAAATAAGACGAACGTCTCCCTCGAGACCGTTTTATCAAAA
31747 -
66 C
* * *
31747 TAAAACGATCCTCGAATCGTAAAACTTAAGTAAGACGAGCGTCTCCACT-GAGACCGTTTTATCA
1 T-AAACGATCCTTGAATCGT-AAACTTAAATAAGACGAACGTCTCC-CTCGAGACCGTTTTATCA
*
31811 AAAT
63 AAAC
31815 TAAACGA
1 TAAACGA
31822 CCATCGCGTC
Statistics
Matches: 381, Mismatches: 15, Indels: 13
0.93 0.04 0.03
Matches are distributed among these distances:
65 64 0.17
66 268 0.70
67 46 0.12
68 3 0.01
ACGTcount: A:0.37, C:0.23, G:0.14, T:0.26
Consensus pattern (66 bp):
TAAACGATCCTTGAATCGTAAACTTAAATAAGACGAACGTCTCCCTCGAGACCGTTTTATCAAAA
C
Found at i:31689 original size:197 final size:198
Alignment explanation
Indices: 31353--31821 Score: 768
Period size: 197 Copynumber: 2.4 Consensus size: 198
31343 AAAAGTTAAT
* *
31353 TAAACGATCCTTGAATCGTAAAC-TTAAATAAGATGAACGTCTCCCTCGAGACCATTTTATCAAA
1 TAAACGATCCTTGAATCGTAAACATTAAATAAGACGAACGTCTCCCTCGAGACCGTTTTATCAAA
* *
31417 ACTAAACGATCCTTGAATCGTAAATTTAAATAGGACGAACGTCTCCCTCGAGACCGTTTTATCAA
66 ACTAAACGATCCTTGAATCGTAAACTTAAATAAGACGAACGTCTCCCTCGAGACCGTTTTATCAA
* *
31482 AATTAAACGATCCTTGAATCGTAAACTTAAATAAGACGAACGTCTCCCTCGAGACCGTTTTATCA
131 AACTAAACGATCCTTGAATCGTAAACTTAAATAAGACGAACGTCTCCCTCGAGACCGTTTGATCA
31547 AAA
196 AAA
*
31550 CTAAACGATCCTTGAATCGTAAACATAAAAT-AGACGAACGTCTCCCTCGAGACCGTTTTATCAA
1 -TAAACGATCCTTGAATCGTAAACATTAAATAAGACGAACGTCTCCCTCGAGACCGTTTTATCAA
31614 AA-TAAACGATCCTTGAATCGTAAACTTAAATAAGACGAACGTCTCCCTCGAGACCGTTTTATCA
65 AACTAAACGATCCTTGAATCGTAAACTTAAATAAGACGAACGTCTCCCTCGAGACCGTTTTATCA
31678 AAACTAAACGATCCTTGAATCGTAAACTTAAATAAGACGAACGTCTCCCTCGAGACCGTTTGATC
130 AAACTAAACGATCCTTGAATCGTAAACTTAAATAAGACGAACGTCTCCCTCGAGACCGTTTGATC
31743 AAAA
195 AAAA
* * *
31747 TAAAACGATCCTCGAATCGTAAA-ACTTAAGTAAGACGAGCGTCTCCACT-GAGACCGTTTTATC
1 T-AAACGATCCTTGAATCGTAAACA-TTAAATAAGACGAACGTCTCC-CTCGAGACCGTTTTATC
*
31810 AAAATTAAACGA
63 AAAACTAAACGA
31822 CCATCGCGTC
Statistics
Matches: 254, Mismatches: 11, Indels: 11
0.92 0.04 0.04
Matches are distributed among these distances:
196 2 0.01
197 151 0.59
198 87 0.34
199 14 0.06
ACGTcount: A:0.37, C:0.23, G:0.14, T:0.26
Consensus pattern (198 bp):
TAAACGATCCTTGAATCGTAAACATTAAATAAGACGAACGTCTCCCTCGAGACCGTTTTATCAAA
ACTAAACGATCCTTGAATCGTAAACTTAAATAAGACGAACGTCTCCCTCGAGACCGTTTTATCAA
AACTAAACGATCCTTGAATCGTAAACTTAAATAAGACGAACGTCTCCCTCGAGACCGTTTGATCA
AAA
Done.