Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01013519.1 Corchorus capsularis cultivar CVL-1 contig13540, 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: 23884
ACGTcount: A:0.32, C:0.20, G:0.18, T:0.30
Found at i:170 original size:2 final size:2
Alignment explanation
Indices: 163--199 Score: 74
Period size: 2 Copynumber: 18.5 Consensus size: 2
153 AACCACATGG
163 TA TA TA TA TA 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 TA TA TA TA TA T
200 TACTTTCAAC
Statistics
Matches: 35, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 35 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:749 original size:15 final size:15
Alignment explanation
Indices: 729--760 Score: 55
Period size: 15 Copynumber: 2.1 Consensus size: 15
719 TACTAAATAA
*
729 ATAATAATTATTTTT
1 ATAATAATTATTATT
744 ATAATAATTATTATT
1 ATAATAATTATTATT
759 AT
1 AT
761 TCAATATGTG
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 16 1.00
ACGTcount: A:0.44, C:0.00, G:0.00, T:0.56
Consensus pattern (15 bp):
ATAATAATTATTATT
Found at i:6371 original size:30 final size:30
Alignment explanation
Indices: 6335--6391 Score: 105
Period size: 30 Copynumber: 1.9 Consensus size: 30
6325 GGGCCACTAA
*
6335 CACATCACACACACTAAAAGAGGCCCAATG
1 CACATCACACACACTAAAAGAGACCCAATG
6365 CACATCACACACACTAAAAGAGACCCA
1 CACATCACACACACTAAAAGAGACCCA
6392 TGAATTTCAC
Statistics
Matches: 26, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
30 26 1.00
ACGTcount: A:0.46, C:0.35, G:0.11, T:0.09
Consensus pattern (30 bp):
CACATCACACACACTAAAAGAGACCCAATG
Found at i:14383 original size:27 final size:27
Alignment explanation
Indices: 14326--14404 Score: 77
Period size: 27 Copynumber: 2.9 Consensus size: 27
14316 TTCGCGTGGC
* * ** **
14326 AACCCAAAATCGCAAAGTTGTTGCAGC
1 AACCCAAAATTGCAAAATTGCCGCAAA
14353 AACCCAAAATTGCAAAATTGCCGCAAA
1 AACCCAAAATTGCAAAATTGCCGCAAA
* * *
14380 AACCCGAAATTGAAAAACTGCCGCA
1 AACCCAAAATTGCAAAATTGCCGCA
14405 GCGAGCCAAA
Statistics
Matches: 43, Mismatches: 9, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
27 43 1.00
ACGTcount: A:0.43, C:0.27, G:0.15, T:0.15
Consensus pattern (27 bp):
AACCCAAAATTGCAAAATTGCCGCAAA
Found at i:18201 original size:15 final size:15
Alignment explanation
Indices: 18183--18213 Score: 53
Period size: 15 Copynumber: 2.1 Consensus size: 15
18173 TTACTTTTGC
*
18183 TACTTTTATCATTTT
1 TACTTTTACCATTTT
18198 TACTTTTACCATTTT
1 TACTTTTACCATTTT
18213 T
1 T
18214 CTTACTCTTT
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.19, C:0.16, G:0.00, T:0.65
Consensus pattern (15 bp):
TACTTTTACCATTTT
Found at i:18213 original size:24 final size:24
Alignment explanation
Indices: 18168--18240 Score: 65
Period size: 24 Copynumber: 2.9 Consensus size: 24
18158 TACTGATTAC
* * *
18168 CATTTTTACTTTTGCTACTTTTAT
1 CATTTTTACTTTTACCATTTTTAT
*
18192 CATTTTTACTTTTACCATTTTTCT
1 CATTTTTACTTTTACCATTTTTAT
* *
18216 TACTCTTTTACTTAATACCATTTTT
1 CA-T-TTTTACTT-TTACCATTTTT
18241 TGACTTTCTT
Statistics
Matches: 40, Mismatches: 6, Indels: 3
0.82 0.12 0.06
Matches are distributed among these distances:
24 21 0.52
25 1 0.03
26 8 0.20
27 10 0.25
ACGTcount: A:0.19, C:0.19, G:0.01, T:0.60
Consensus pattern (24 bp):
CATTTTTACTTTTACCATTTTTAT
Found at i:18234 original size:27 final size:26
Alignment explanation
Indices: 18194--18267 Score: 80
Period size: 26 Copynumber: 2.8 Consensus size: 26
18184 ACTTTTATCA
* *
18194 TTTTTACTT-TTACCATTTTTCTTAC
1 TTTTTACTTAATACCATTTTTCTGAC
18219 TCTTTTACTTAATACCATTTTT-TGAC
1 T-TTTTACTTAATACCATTTTTCTGAC
* *
18245 TTTCTTACTCAATACCATATTTC
1 TTT-TTACTTAATACCATTTTTC
18268 ACTTGATACC
Statistics
Matches: 41, Mismatches: 4, Indels: 6
0.80 0.08 0.12
Matches are distributed among these distances:
25 3 0.07
26 28 0.68
27 10 0.24
ACGTcount: A:0.22, C:0.22, G:0.01, T:0.55
Consensus pattern (26 bp):
TTTTTACTTAATACCATTTTTCTGAC
Found at i:18292 original size:42 final size:42
Alignment explanation
Indices: 18225--18337 Score: 199
Period size: 42 Copynumber: 2.7 Consensus size: 42
18215 TTACTCTTTT
* *
18225 ACTTAATACCATTTTTTGACTTTCTTACTCAATACCATATTTC
1 ACTTGATACCA-TTTTTGACCTTCTTACTCAATACCATATTTC
18268 ACTTGATACCATTTTTGACCTTCTTACTCAATACCATATTTC
1 ACTTGATACCATTTTTGACCTTCTTACTCAATACCATATTTC
18310 ACTTGATACCATTTTTGACCTTCTTACT
1 ACTTGATACCATTTTTGACCTTCTTACT
18338 GATTACTTTT
Statistics
Matches: 68, Mismatches: 2, Indels: 1
0.96 0.03 0.01
Matches are distributed among these distances:
42 58 0.85
43 10 0.15
ACGTcount: A:0.26, C:0.25, G:0.04, T:0.45
Consensus pattern (42 bp):
ACTTGATACCATTTTTGACCTTCTTACTCAATACCATATTTC
Found at i:18832 original size:38 final size:38
Alignment explanation
Indices: 18770--18868 Score: 126
Period size: 38 Copynumber: 2.6 Consensus size: 38
18760 TACTGATTAC
* * * *
18770 TATTTTTACCTTGACTCTTGATTATCAATTTTACTGAT
1 TATTATTACTTTGACTCTTAATTATCAACTTTACTGAT
* *
18808 TATTCTTACTTTGACTCTTAATTATTAACTTTACTGAT
1 TATTATTACTTTGACTCTTAATTATCAACTTTACTGAT
* *
18846 TACTAATACTTTGACTCTTAATT
1 TATTATTACTTTGACTCTTAATT
18869 TTATTGGGGT
Statistics
Matches: 53, Mismatches: 8, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
38 53 1.00
ACGTcount: A:0.26, C:0.16, G:0.06, T:0.52
Consensus pattern (38 bp):
TATTATTACTTTGACTCTTAATTATCAACTTTACTGAT
Found at i:22525 original size:29 final size:29
Alignment explanation
Indices: 22492--22566 Score: 100
Period size: 27 Copynumber: 2.7 Consensus size: 29
22482 AGGTGAACTT
* *
22492 AAAAATGACTAAGATGCCCCCCTAAGTGC
1 AAAAATGACCAAAATGCCCCCCTAAGTGC
**
22521 AAAAATGACCAAAATG--CCCCTGGGTGC
1 AAAAATGACCAAAATGCCCCCCTAAGTGC
22548 AAAAATGACCAAAATGCCC
1 AAAAATGACCAAAATGCCC
22567 TTGGGCGACC
Statistics
Matches: 40, Mismatches: 4, Indels: 4
0.83 0.08 0.08
Matches are distributed among these distances:
27 25 0.62
29 15 0.38
ACGTcount: A:0.41, C:0.27, G:0.17, T:0.15
Consensus pattern (29 bp):
AAAAATGACCAAAATGCCCCCCTAAGTGC
Found at i:22548 original size:27 final size:27
Alignment explanation
Indices: 22517--22571 Score: 101
Period size: 27 Copynumber: 2.0 Consensus size: 27
22507 GCCCCCCTAA
22517 GTGCAAAAATGACCAAAATGCCCCTGG
1 GTGCAAAAATGACCAAAATGCCCCTGG
*
22544 GTGCAAAAATGACCAAAATGCCCTTGG
1 GTGCAAAAATGACCAAAATGCCCCTGG
22571 G
1 G
22572 CGACCCTAAT
Statistics
Matches: 27, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
27 27 1.00
ACGTcount: A:0.36, C:0.24, G:0.24, T:0.16
Consensus pattern (27 bp):
GTGCAAAAATGACCAAAATGCCCCTGG
Found at i:22702 original size:31 final size:33
Alignment explanation
Indices: 22661--22727 Score: 93
Period size: 31 Copynumber: 2.1 Consensus size: 33
22651 TCGAACTAAA
* *
22661 AAAATGTTAATTAGTTAA-T-TAAAATACCCTT
1 AAAATCTTAATTAGTCAATTATAAAATACCCTT
22692 AAAATCTTAATTAGTCAATTACTAAAATACCCTT
1 AAAATCTTAATTAGTCAATTA-TAAAATACCCTT
22726 AA
1 AA
22728 TATTATATAG
Statistics
Matches: 31, Mismatches: 2, Indels: 3
0.86 0.06 0.08
Matches are distributed among these distances:
31 16 0.52
32 1 0.03
34 14 0.45
ACGTcount: A:0.46, C:0.13, G:0.04, T:0.36
Consensus pattern (33 bp):
AAAATCTTAATTAGTCAATTATAAAATACCCTT
Done.