Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01012336.1 Corchorus capsularis cultivar CVL-1 contig12357, 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: 13714
ACGTcount: A:0.34, C:0.15, G:0.18, T:0.33
Found at i:1441 original size:30 final size:30
Alignment explanation
Indices: 1384--1442 Score: 75
Period size: 30 Copynumber: 2.0 Consensus size: 30
1374 TTGGACAAAA
* *
1384 GGAAATAAATTAATTACTTTAGGTTGATTG
1 GGAAATAAATTAATCACTTTAGATTGATTG
*
1414 GGAAATATATTAATCACATTT-GATTGATT
1 GGAAATAAATTAATCAC-TTTAGATTGATT
1443 AATTAGTTGA
Statistics
Matches: 25, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
30 22 0.88
31 3 0.12
ACGTcount: A:0.37, C:0.05, G:0.17, T:0.41
Consensus pattern (30 bp):
GGAAATAAATTAATCACTTTAGATTGATTG
Found at i:1721 original size:192 final size:191
Alignment explanation
Indices: 1386--1764 Score: 634
Period size: 192 Copynumber: 2.0 Consensus size: 191
1376 GGACAAAAGG
* *
1386 AAATAAATTAATTACTTTAGGTTGATTGGGAAATATATTAATCACATTTGATTGATTAATTAGTT
1 AAATAAATTAATTACTTCAGGTTGATTAGGAAATATATTAATCACATTTGATTGATTAATTAGTT
* *
1451 GATTTGAATAATTTGATGAATTAAAATCAATTAGTAATAATTCTATTTAATTAATTGTTAAATGA
66 GATTTGAATAATTTGATCAATTAAAATCAATTAGTAATAATTCTATTCAATTAATTGTTAAATGA
* *
1516 AAATTTTGATCAATTACAACCAATTAACATTAATGCTATTTAGTTGTTAATTACTAATATT
131 AAATTTTGATCAATTACAACCAATTAACATTAATGCCATTTAGCTGTTAATTACTAATATT
* ** *
1577 AAATTAATT-ATTACTTCAGGTTGATTAGGAAATATATTAATTTCTTTTGATTGATTAATTAGTT
1 AAATAAATTAATTACTTCAGGTTGATTAGGAAATATATTAATCACATTTGATTGATTAATTAGTT
1641 GATTTTTGAATAATTTGATCAATTAAAATCAATTAGTAATAATTCTATTCAATTAATTGTTAAAT
66 GA--TTTGAATAATTTGATCAATTAAAATCAATTAGTAATAATTCTATTCAATTAATTGTTAAAT
*
1706 GAAAATTTTGATCAATTACAATCAATTAACATTAATGCCATTTAGCTGTTAATTACTAA
129 GAAAATTTTGATCAATTACAACCAATTAACATTAATGCCATTTAGCTGTTAATTACTAA
1765 AATAACCCTA
Statistics
Matches: 175, Mismatches: 11, Indels: 3
0.93 0.06 0.02
Matches are distributed among these distances:
190 52 0.30
191 8 0.05
192 115 0.66
ACGTcount: A:0.40, C:0.07, G:0.10, T:0.43
Consensus pattern (191 bp):
AAATAAATTAATTACTTCAGGTTGATTAGGAAATATATTAATCACATTTGATTGATTAATTAGTT
GATTTGAATAATTTGATCAATTAAAATCAATTAGTAATAATTCTATTCAATTAATTGTTAAATGA
AAATTTTGATCAATTACAACCAATTAACATTAATGCCATTTAGCTGTTAATTACTAATATT
Found at i:2068 original size:19 final size:20
Alignment explanation
Indices: 2044--2081 Score: 60
Period size: 20 Copynumber: 1.9 Consensus size: 20
2034 TTAGTATGGC
*
2044 AAAA-TTTTTATTTTTTTAG
1 AAAATTTTTTATTTATTTAG
2063 AAAATTTTTTATTTATTTA
1 AAAATTTTTTATTTATTTA
2082 AGAACTTATA
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
19 4 0.24
20 13 0.76
ACGTcount: A:0.34, C:0.00, G:0.03, T:0.63
Consensus pattern (20 bp):
AAAATTTTTTATTTATTTAG
Found at i:3278 original size:140 final size:141
Alignment explanation
Indices: 3105--3437 Score: 508
Period size: 141 Copynumber: 2.4 Consensus size: 141
3095 AAGTTAGTGA
* * *
3105 TCGTTAGTTAATTTTGCCAATCAAAGTCGTAATTGATTGATAATTATTTAATTTTACCAT-AAAT
1 TCGTTAGTTAATTTTGCCAATCAAAGTTGTAATTGATTGATGATTATATAATTTTACCATAAAAT
* * *
3169 CGCTACCAAAAAAATTTAACATAGAGAAATAAATCAATTAGTAA-TATGTTACCAAAAAAATAAA
66 AGCCACCAAAAAAA-TTAACATAAAGAAATAAATCAATTAGTAATTATGTTACCAAAAAAATAAA
3233 TTATTGAACATG
130 TTATTGAACATG
* * * * *
3245 TCGTTAGTTAATTTTGTCAGTCAAGGTTATAATTAATTGATGATTATATAATTTTACCATAAAAT
1 TCGTTAGTTAATTTTGCCAATCAAAGTTGTAATTGATTGATGATTATATAATTTTACCATAAAAT
* *
3310 AGCCACCAAAAAAATTACCATAAATAAATAAATCAATTAGTAATTATGTTACCAAAAAAATAAAT
66 AGCCACCAAAAAAATTAACATAAAGAAATAAATCAATTAGTAATTATGTTACCAAAAAAATAAAT
*
3375 TATTGAATATG
131 TATTGAACATG
*
3386 TCGTTAGTTAATTTTGCCAATCAAAGTTGTAATTGATTGATGATTATGTAAT
1 TCGTTAGTTAATTTTGCCAATCAAAGTTGTAATTGATTGATGATTATATAAT
3438 CAAAGTTGTA
Statistics
Matches: 171, Mismatches: 20, Indels: 3
0.88 0.10 0.02
Matches are distributed among these distances:
140 78 0.46
141 93 0.54
ACGTcount: A:0.43, C:0.10, G:0.11, T:0.36
Consensus pattern (141 bp):
TCGTTAGTTAATTTTGCCAATCAAAGTTGTAATTGATTGATGATTATATAATTTTACCATAAAAT
AGCCACCAAAAAAATTAACATAAAGAAATAAATCAATTAGTAATTATGTTACCAAAAAAATAAAT
TATTGAACATG
Found at i:10306 original size:13 final size:13
Alignment explanation
Indices: 10284--10323 Score: 53
Period size: 13 Copynumber: 3.1 Consensus size: 13
10274 CAGATAATAT
10284 TATCAACAGAAGA
1 TATCAACAGAAGA
*
10297 TATCATCAGAAGA
1 TATCAACAGAAGA
* *
10310 TTTCAACTGAAGA
1 TATCAACAGAAGA
10323 T
1 T
10324 TATCTGGAGA
Statistics
Matches: 23, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
13 23 1.00
ACGTcount: A:0.45, C:0.15, G:0.15, T:0.25
Consensus pattern (13 bp):
TATCAACAGAAGA
Found at i:10336 original size:11 final size:11
Alignment explanation
Indices: 10316--10346 Score: 53
Period size: 11 Copynumber: 2.8 Consensus size: 11
10306 AAGATTTCAA
10316 CTGAAGATTAT
1 CTGAAGATTAT
*
10327 CTGGAGATTAT
1 CTGAAGATTAT
10338 CTGAAGATT
1 CTGAAGATT
10347 TAAGTAGATT
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
11 18 1.00
ACGTcount: A:0.32, C:0.10, G:0.23, T:0.35
Consensus pattern (11 bp):
CTGAAGATTAT
Found at i:10763 original size:41 final size:41
Alignment explanation
Indices: 10717--10885 Score: 180
Period size: 41 Copynumber: 4.1 Consensus size: 41
10707 AAATTACCTT
* *
10717 TGACACCCGAAGTTGTCATTTTGGTAAATTAAAATTACTAC
1 TGACACCAGAAGTTGTCACTTTGGTAAATTAAAATTACTAC
* * * **
10758 TGACACTAGAAGTTGTCACCTTGGTAAATTAAAATTATTTT
1 TGACACCAGAAGTTGTCACTTTGGTAAATTAAAATTACTAC
*
10799 TGACACCAGAAGTTGTCACTTTGGTAAATTAAAATTACCT-T
1 TGACACCAGAAGTTGTCACTTTGGTAAATTAAAATTA-CTAC
* * * ** * *
10840 TAACAGCAGAAG-TGTTACTCCGGTAAATTATAATTACTAT
1 TGACACCAGAAGTTGTCACTTTGGTAAATTAAAATTACTAC
10880 TGACAC
1 TGACAC
10886 ACCAAAAATT
Statistics
Matches: 108, Mismatches: 18, Indels: 5
0.82 0.14 0.04
Matches are distributed among these distances:
39 2 0.02
40 25 0.23
41 80 0.74
42 1 0.01
ACGTcount: A:0.35, C:0.16, G:0.15, T:0.34
Consensus pattern (41 bp):
TGACACCAGAAGTTGTCACTTTGGTAAATTAAAATTACTAC
Done.