Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01006014.1 Corchorus capsularis cultivar CVL-1 contig06032, 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: 27484
ACGTcount: A:0.32, C:0.18, G:0.17, T:0.33
Found at i:1108 original size:17 final size:17
Alignment explanation
Indices: 1088--1143 Score: 57
Period size: 17 Copynumber: 3.4 Consensus size: 17
1078 TTTTTTTAAT
1088 TATTTTTATTTTCTAAA
1 TATTTTTATTTTCTAAA
1105 TATTTTTAATATTT-T---
1 TATTTTT-AT-TTTCTAAA
*
1120 CATTTTTATTTTCTAAA
1 TATTTTTATTTTCTAAA
1137 TATTTTT
1 TATTTTT
1144 TAATATTTTC
Statistics
Matches: 31, Mismatches: 2, Indels: 12
0.69 0.04 0.27
Matches are distributed among these distances:
13 3 0.10
14 3 0.10
15 6 0.19
17 13 0.42
18 3 0.10
19 3 0.10
ACGTcount: A:0.27, C:0.05, G:0.00, T:0.68
Consensus pattern (17 bp):
TATTTTTATTTTCTAAA
Found at i:1125 original size:32 final size:34
Alignment explanation
Indices: 1088--1165 Score: 133
Period size: 32 Copynumber: 2.4 Consensus size: 34
1078 TTTTTTTAAT
1088 TATTTTTATTTTCTAAATA-TTTTTAATATTTTC
1 TATTTTTATTTTCTAAATATTTTTTAATATTTTC
1121 -ATTTTTATTTTCTAAATATTTTTTAATATTTTC
1 TATTTTTATTTTCTAAATATTTTTTAATATTTTC
*
1154 TTTTTTTATTTT
1 TATTTTTATTTT
1166 TCTCGTCTTT
Statistics
Matches: 42, Mismatches: 1, Indels: 3
0.91 0.02 0.07
Matches are distributed among these distances:
32 18 0.43
33 14 0.33
34 10 0.24
ACGTcount: A:0.24, C:0.05, G:0.00, T:0.71
Consensus pattern (34 bp):
TATTTTTATTTTCTAAATATTTTTTAATATTTTC
Found at i:9774 original size:73 final size:74
Alignment explanation
Indices: 9680--9826 Score: 269
Period size: 73 Copynumber: 2.0 Consensus size: 74
9670 ACCTTTTATC
*
9680 TTTTCATTTTTGTTATTTTTCTCATTATATTACATTTATATTGACCT-AAATTTTTTTTTATCAG
1 TTTTCATTTTTGTTATTTTTCTCATTATATTACATTTATATTGACCTAAAATATTTTTTTATCAG
9744 TATAATAAA
66 TATAATAAA
*
9753 TTTTTATTTTTGTTATTTTTCTCATTATATTACATTTATATTGACCTAAAATATTTTTTTATCAG
1 TTTTCATTTTTGTTATTTTTCTCATTATATTACATTTATATTGACCTAAAATATTTTTTTATCAG
9818 TATAATAAA
66 TATAATAAA
9827 AGGTGCCGCA
Statistics
Matches: 71, Mismatches: 2, Indels: 1
0.96 0.03 0.01
Matches are distributed among these distances:
73 46 0.65
74 25 0.35
ACGTcount: A:0.30, C:0.09, G:0.04, T:0.57
Consensus pattern (74 bp):
TTTTCATTTTTGTTATTTTTCTCATTATATTACATTTATATTGACCTAAAATATTTTTTTATCAG
TATAATAAA
Found at i:10972 original size:95 final size:95
Alignment explanation
Indices: 10809--10999 Score: 364
Period size: 95 Copynumber: 2.0 Consensus size: 95
10799 CAAGCCAACA
* *
10809 ATCCTGGCTCCGTCCCTGATTCTGCCCCTGCCCGTACTGGACTCTTATATCTAATCCACGTAGTC
1 ATCCTGGCTCCGCCCCTGATTCCGCCCCTGCCCGTACTGGACTCTTATATCTAATCCACGTAGTC
10874 GTTACATGAGTTTGTGCATATATTTGAGTC
66 GTTACATGAGTTTGTGCATATATTTGAGTC
10904 ATCCTGGCTCCGCCCCTGATTCCGCCCCTGCCCGTACTGGACTCTTATATCTAATCCACGTAGTC
1 ATCCTGGCTCCGCCCCTGATTCCGCCCCTGCCCGTACTGGACTCTTATATCTAATCCACGTAGTC
10969 GTTACATGAGTTTGTGCATATATTTGAGTC
66 GTTACATGAGTTTGTGCATATATTTGAGTC
10999 A
1 A
11000 ATTGATTGAT
Statistics
Matches: 94, Mismatches: 2, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
95 94 1.00
ACGTcount: A:0.18, C:0.29, G:0.19, T:0.34
Consensus pattern (95 bp):
ATCCTGGCTCCGCCCCTGATTCCGCCCCTGCCCGTACTGGACTCTTATATCTAATCCACGTAGTC
GTTACATGAGTTTGTGCATATATTTGAGTC
Found at i:16859 original size:27 final size:27
Alignment explanation
Indices: 16821--16874 Score: 99
Period size: 27 Copynumber: 2.0 Consensus size: 27
16811 GCAACAAACC
16821 ACATCTCCTAGTAGGCTGTAGAATATG
1 ACATCTCCTAGTAGGCTGTAGAATATG
*
16848 ACATCTCCTAGTAGGCTGTGGAATATG
1 ACATCTCCTAGTAGGCTGTAGAATATG
16875 CAGAAGCTTT
Statistics
Matches: 26, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
27 26 1.00
ACGTcount: A:0.28, C:0.19, G:0.24, T:0.30
Consensus pattern (27 bp):
ACATCTCCTAGTAGGCTGTAGAATATG
Found at i:19960 original size:9 final size:9
Alignment explanation
Indices: 19946--20004 Score: 56
Period size: 9 Copynumber: 7.1 Consensus size: 9
19936 ATCGTCACAT
19946 TTTTTACAC
1 TTTTTACAC
19955 TTTTTACAC
1 TTTTTACAC
*
19964 -TTTTA-TC
1 TTTTTACAC
19971 -TTTTAC-C
1 TTTTTACAC
*
19978 -TTTTGCAC
1 TTTTTACAC
*
19986 TTTTTGCAC
1 TTTTTACAC
19995 TTTTTACAC
1 TTTTTACAC
20004 T
1 T
20005 AGTCTCCCCA
Statistics
Matches: 44, Mismatches: 3, Indels: 6
0.83 0.06 0.11
Matches are distributed among these distances:
7 12 0.27
8 6 0.14
9 26 0.59
ACGTcount: A:0.17, C:0.22, G:0.03, T:0.58
Consensus pattern (9 bp):
TTTTTACAC
Found at i:20052 original size:33 final size:33
Alignment explanation
Indices: 20008--20085 Score: 111
Period size: 33 Copynumber: 2.4 Consensus size: 33
19998 TTACACTAGT
**
20008 CTCCCCACTAGGACGGCTCTGCCACGGCGGAGC
1 CTCCCCACTAGGACGGCTCAACCACGGCGGAGC
* *
20041 CTCCCCTCTAGGACGGCTCAACCATGGCGGAGC
1 CTCCCCACTAGGACGGCTCAACCACGGCGGAGC
*
20074 CGCCCCACTAGG
1 CTCCCCACTAGG
20086 CAACTAGGCA
Statistics
Matches: 39, Mismatches: 6, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
33 39 1.00
ACGTcount: A:0.17, C:0.42, G:0.28, T:0.13
Consensus pattern (33 bp):
CTCCCCACTAGGACGGCTCAACCACGGCGGAGC
Found at i:20429 original size:21 final size:22
Alignment explanation
Indices: 20399--20443 Score: 65
Period size: 21 Copynumber: 2.1 Consensus size: 22
20389 GCAAAAGCGT
*
20399 AAAAAGTGGGGCGGTGTATAGC
1 AAAAAGTGGGGCGGTATATAGC
*
20421 AAAAA-TGGGGCGGTATTTAGC
1 AAAAAGTGGGGCGGTATATAGC
20442 AA
1 AA
20444 TTCAGATTTT
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
21 16 0.76
22 5 0.24
ACGTcount: A:0.36, C:0.09, G:0.36, T:0.20
Consensus pattern (22 bp):
AAAAAGTGGGGCGGTATATAGC
Found at i:23284 original size:29 final size:29
Alignment explanation
Indices: 23251--23331 Score: 162
Period size: 29 Copynumber: 2.8 Consensus size: 29
23241 ATTTTATAAT
23251 AAGTAACATGTATTACAACCCTTAGCAGG
1 AAGTAACATGTATTACAACCCTTAGCAGG
23280 AAGTAACATGTATTACAACCCTTAGCAGG
1 AAGTAACATGTATTACAACCCTTAGCAGG
23309 AAGTAACATGTATTACAACCCTT
1 AAGTAACATGTATTACAACCCTT
23332 TGAATATAGA
Statistics
Matches: 52, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
29 52 1.00
ACGTcount: A:0.38, C:0.21, G:0.15, T:0.26
Consensus pattern (29 bp):
AAGTAACATGTATTACAACCCTTAGCAGG
Done.