Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01011544.1 Corchorus capsularis cultivar CVL-1 contig11565, 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: 46832
ACGTcount: A:0.31, C:0.17, G:0.18, T:0.33
Found at i:195 original size:16 final size:16
Alignment explanation
Indices: 153--198 Score: 55
Period size: 16 Copynumber: 3.1 Consensus size: 16
143 AAAAAAATTT
153 AAGAAAAAATTAAGAA
1 AAGAAAAAATTAAGAA
*
169 AAG--GAAA--AAGAA
1 AAGAAAAAATTAAGAA
181 AAGAAAAAATTAAGAA
1 AAGAAAAAATTAAGAA
197 AA
1 AA
199 AAAGGTGAAA
Statistics
Matches: 24, Mismatches: 2, Indels: 8
0.71 0.06 0.24
Matches are distributed among these distances:
12 8 0.33
14 6 0.25
16 10 0.42
ACGTcount: A:0.76, C:0.00, G:0.15, T:0.09
Consensus pattern (16 bp):
AAGAAAAAATTAAGAA
Found at i:201 original size:19 final size:19
Alignment explanation
Indices: 179--219 Score: 55
Period size: 19 Copynumber: 2.2 Consensus size: 19
169 AAGGAAAAAG
179 AAAAGAAAAAATTAAGAAA
1 AAAAGAAAAAATTAAGAAA
***
198 AAAAGGTGAAATTAAGAAA
1 AAAAGAAAAAATTAAGAAA
217 AAA
1 AAA
220 TATACAACGT
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
19 19 1.00
ACGTcount: A:0.73, C:0.00, G:0.15, T:0.12
Consensus pattern (19 bp):
AAAAGAAAAAATTAAGAAA
Found at i:2645 original size:3 final size:3
Alignment explanation
Indices: 2637--2669 Score: 66
Period size: 3 Copynumber: 11.0 Consensus size: 3
2627 TTATTCCTAT
2637 ATC ATC ATC ATC ATC ATC ATC ATC ATC ATC ATC
1 ATC ATC ATC ATC ATC ATC ATC ATC ATC ATC ATC
2670 TTTCTCCTTT
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 30 1.00
ACGTcount: A:0.33, C:0.33, G:0.00, T:0.33
Consensus pattern (3 bp):
ATC
Found at i:10511 original size:25 final size:25
Alignment explanation
Indices: 10477--10531 Score: 101
Period size: 25 Copynumber: 2.2 Consensus size: 25
10467 TGAGAACAAT
*
10477 TTCTCACATTCTTCATATTTTATTG
1 TTCTCACATTCTTCATATTTTATTC
10502 TTCTCACATTCTTCATATTTTATTC
1 TTCTCACATTCTTCATATTTTATTC
10527 TTCTC
1 TTCTC
10532 CATATTCTAT
Statistics
Matches: 29, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
25 29 1.00
ACGTcount: A:0.18, C:0.24, G:0.02, T:0.56
Consensus pattern (25 bp):
TTCTCACATTCTTCATATTTTATTC
Found at i:15107 original size:34 final size:32
Alignment explanation
Indices: 15045--15108 Score: 85
Period size: 34 Copynumber: 1.9 Consensus size: 32
15035 CAAGAAGCAG
15045 CCAGAAGTCAACAACAAAGAAGTTCAACCATC
1 CCAGAAGTCAACAACAAAGAAGTTCAACCATC
*
15077 CCAGAAGATCAACCAACCAAGCAA-TTCAACCA
1 CCAGAAG-TCAA-CAACAAAG-AAGTTCAACCA
15109 AGAAGCAAGA
Statistics
Matches: 28, Mismatches: 1, Indels: 4
0.85 0.03 0.12
Matches are distributed among these distances:
32 7 0.25
33 4 0.14
34 15 0.54
35 2 0.07
ACGTcount: A:0.47, C:0.31, G:0.11, T:0.11
Consensus pattern (32 bp):
CCAGAAGTCAACAACAAAGAAGTTCAACCATC
Found at i:24449 original size:86 final size:89
Alignment explanation
Indices: 24348--24521 Score: 237
Period size: 89 Copynumber: 2.0 Consensus size: 89
24338 ATCTCGCAAA
* * * **
24348 AAAAAAGCATGAATATTTATAACAAACCTCCATAA-TCAAA-AT-ATATAATACTAATAATGATA
1 AAAAAAGCATGAATATTTAAAACAAAACTCCATAATTAAAATATAATATAATACTAATAAAAATA
*
24410 CTTCTACAATTATAATATTTTTAC
66 CTACTACAATTATAATATTTTTAC
* * *
24434 AAAATAGCATGAATATTTAAAATAAAACTCCATAATTAAAATATAATATAATACTAGTAAAAATA
1 AAAAAAGCATGAATATTTAAAACAAAACTCCATAATTAAAATATAATATAATACTAATAAAAATA
*
24499 CTACTACAATTCTAATATTTTTA
66 CTACTACAATTATAATATTTTTA
24522 TTTTTATAAT
Statistics
Matches: 75, Mismatches: 10, Indels: 3
0.85 0.11 0.03
Matches are distributed among these distances:
86 31 0.41
87 4 0.05
88 2 0.03
89 38 0.51
ACGTcount: A:0.51, C:0.12, G:0.03, T:0.34
Consensus pattern (89 bp):
AAAAAAGCATGAATATTTAAAACAAAACTCCATAATTAAAATATAATATAATACTAATAAAAATA
CTACTACAATTATAATATTTTTAC
Found at i:25914 original size:68 final size:66
Alignment explanation
Indices: 25612--25988 Score: 379
Period size: 66 Copynumber: 5.7 Consensus size: 66
25602 AAATTGAACG
* * * * * **
25612 TAAACTTAGATGCACAAGACAAAAATGATCCTTCGACC-AGAAGGGTA-TTTTTAGAAATGAAAA
1 TAAACTTAAATGCAAAAGACGAAAATGACCCTTCCACCGA-AAGGGTACTTTTGGGAAA-GAAAA
25675 TAC
64 TAC
* * * * ** * *
25678 TAAACTTGAATACAAAAGA-TAATATTGACCCTTTGACCGAAAGGGTA-TTCTTGGGAATGAGAA
1 TAAACTTAAATGCAAAAGACGAA-AATGACCCTTCCACCGAAAGGGTACTT-TTGGGAAAGAAAA
25741 TAC
64 TAC
* * * ** * *
25744 TAAACTTGAATGCAAGAGAC-AATACTGACCCTTTGACCGAAAGGGTATTTTTGGGAAA-AAGAT
1 TAAACTTAAATGCAAAAGACGAA-AATGACCCTTCCACCGAAAGGGTACTTTTGGGAAAGAAAAT
25807 AC
65 AC
25809 TAAACTTAAATGCAAAAGACGAAAATGACCCTTCCACCGAAAGGGTACTTTTGGGTAAAGAAAAT
1 TAAACTTAAATGCAAAAGACGAAAATGACCCTTCCACCGAAAGGGTACTTTTGGG-AAAGAAAAT
25874 AC
65 AC
* * *
25876 TAAACTTAAATGCGAAAGGACGAAAATGACCCTCCCACCGAAAGGGTACTTTTTGGAAAAAGAAA
1 TAAACTTAAATGC-AAAAGACGAAAATGACCCTTCCACCGAAAGGGTAC-TTTTGG-GAAAGAAA
*
25941 GTAC
63 ATAC
* *
25945 TAAACTCAAATGCAAAAGATGAAAATGACCCTTCCACCGAAAGG
1 TAAACTTAAATGCAAAAGACGAAAATGACCCTTCCACCGAAAGG
25989 ATATTTTCGT
Statistics
Matches: 267, Mismatches: 33, Indels: 20
0.83 0.10 0.06
Matches are distributed among these distances:
65 53 0.20
66 98 0.37
67 27 0.10
68 61 0.23
69 28 0.10
ACGTcount: A:0.42, C:0.17, G:0.19, T:0.22
Consensus pattern (66 bp):
TAAACTTAAATGCAAAAGACGAAAATGACCCTTCCACCGAAAGGGTACTTTTGGGAAAGAAAATA
C
Found at i:29512 original size:42 final size:42
Alignment explanation
Indices: 29465--29559 Score: 165
Period size: 42 Copynumber: 2.3 Consensus size: 42
29455 TTAATTAATC
*
29465 AATGAACTAAATTGAACTTAAATTACCTGATTAAAAATACTA
1 AATGAACTAAATTGAACTTAAACTACCTGATTAAAAATACTA
29507 AATGAACTAAATTGAACTTAAACTACCTGATTAAAAATACTA
1 AATGAACTAAATTGAACTTAAACTACCTGATTAAAAATACTA
*
29549 AAT-TACTAAAT
1 AATGAACTAAAT
29560 GAAGCTAAGA
Statistics
Matches: 51, Mismatches: 2, Indels: 1
0.94 0.04 0.02
Matches are distributed among these distances:
41 7 0.14
42 44 0.86
ACGTcount: A:0.51, C:0.13, G:0.06, T:0.31
Consensus pattern (42 bp):
AATGAACTAAATTGAACTTAAACTACCTGATTAAAAATACTA
Found at i:35904 original size:18 final size:18
Alignment explanation
Indices: 35883--35917 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
35873 CGAATCTGCT
* *
35883 TTTATTCTCTGTTTTCTG
1 TTTACTCTCTGCTTTCTG
35901 TTTACTCTCTGCTTTCT
1 TTTACTCTCTGCTTTCT
35918 TACTCTGCTT
Statistics
Matches: 15, Mismatches: 2, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
18 15 1.00
ACGTcount: A:0.06, C:0.23, G:0.09, T:0.63
Consensus pattern (18 bp):
TTTACTCTCTGCTTTCTG
Found at i:45187 original size:13 final size:13
Alignment explanation
Indices: 45169--45206 Score: 62
Period size: 13 Copynumber: 3.1 Consensus size: 13
45159 TTTGATTGAT
45169 TGATGTTTGACTA
1 TGATGTTTGACTA
45182 TGATGTTTGA-T-
1 TGATGTTTGACTA
45193 TGATGTTTGACTA
1 TGATGTTTGACTA
45206 T
1 T
45207 TTATAATGCT
Statistics
Matches: 23, Mismatches: 0, Indels: 4
0.85 0.00 0.15
Matches are distributed among these distances:
11 10 0.43
12 2 0.09
13 11 0.48
ACGTcount: A:0.21, C:0.05, G:0.24, T:0.50
Consensus pattern (13 bp):
TGATGTTTGACTA
Found at i:45196 original size:11 final size:11
Alignment explanation
Indices: 45164--45202 Score: 60
Period size: 11 Copynumber: 3.4 Consensus size: 11
45154 ACTCTTTTGA
45164 TTGATTGATGT
1 TTGATTGATGT
45175 TTGACTATGATGT
1 TTGA-T-TGATGT
45188 TTGATTGATGT
1 TTGATTGATGT
45199 TTGA
1 TTGA
45203 CTATTTATAA
Statistics
Matches: 26, Mismatches: 0, Indels: 4
0.87 0.00 0.13
Matches are distributed among these distances:
11 14 0.54
12 2 0.08
13 10 0.38
ACGTcount: A:0.21, C:0.03, G:0.26, T:0.51
Consensus pattern (11 bp):
TTGATTGATGT
Done.