Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01006176.1 Corchorus capsularis cultivar CVL-1 contig06194, 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: 25524
ACGTcount: A:0.34, C:0.16, G:0.16, T:0.33
Found at i:215 original size:2 final size:2
Alignment explanation
Indices: 210--244 Score: 70
Period size: 2 Copynumber: 17.5 Consensus size: 2
200 TTTGGTGAAA
210 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
245 AAATTAAGAT
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 33 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:2992 original size:74 final size:74
Alignment explanation
Indices: 2903--3054 Score: 236
Period size: 74 Copynumber: 2.1 Consensus size: 74
2893 ATTAAGGAAT
* * *
2903 GTGTAATTACGAAAAATGGTAGAAGGAAAAGGAAT-GTGGGAAACTCATAGAGGGGTTTTTTAGT
1 GTGTAATTACAAAAAAGGGTAGAAGGAAAAGGAATAG-GGGAAACTCATAGAGGGGCTTTTTAGT
2967 CATCC-GAAAA
65 CA-CCTGAAAA
*
2977 GTGTAATTACAAAAAAGGGTAGAAGGCAAAGGAATAGGGGAAACTCATAGAGGGGCTTTTTAGTC
1 GTGTAATTACAAAAAAGGGTAGAAGGAAAAGGAATAGGGGAAACTCATAGAGGGGCTTTTTAGTC
3042 ACCTGAAAA
66 ACCTGAAAA
3051 GTGT
1 GTGT
3055 GAAAAGACCA
Statistics
Matches: 72, Mismatches: 4, Indels: 4
0.90 0.05 0.05
Matches are distributed among these distances:
73 2 0.03
74 69 0.96
75 1 0.01
ACGTcount: A:0.39, C:0.09, G:0.29, T:0.23
Consensus pattern (74 bp):
GTGTAATTACAAAAAAGGGTAGAAGGAAAAGGAATAGGGGAAACTCATAGAGGGGCTTTTTAGTC
ACCTGAAAA
Found at i:4521 original size:17 final size:18
Alignment explanation
Indices: 4499--4540 Score: 50
Period size: 17 Copynumber: 2.3 Consensus size: 18
4489 AATGCACATG
4499 AATAATATCTAGTT-ATC
1 AATAATATCTAGTTAATC
* *
4516 AATAATCTTTAGTTCAATC
1 AATAATATCTAGTT-AATC
4535 AATAAT
1 AATAAT
4541 CTAGTGGAAT
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
17 12 0.57
19 9 0.43
ACGTcount: A:0.43, C:0.12, G:0.05, T:0.40
Consensus pattern (18 bp):
AATAATATCTAGTTAATC
Found at i:6805 original size:2 final size:2
Alignment explanation
Indices: 6800--6829 Score: 53
Period size: 2 Copynumber: 15.5 Consensus size: 2
6790 CTCTCCTAAT
6800 TA TA TA TA TA TA TA TA TA TA TA T- TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
6830 GTAAAAGATA
Statistics
Matches: 27, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
1 1 0.04
2 26 0.96
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (2 bp):
TA
Found at i:9954 original size:31 final size:27
Alignment explanation
Indices: 9886--9939 Score: 108
Period size: 27 Copynumber: 2.0 Consensus size: 27
9876 TGTTTTCCAG
9886 TATTATATTAATCTACCATTGATCATT
1 TATTATATTAATCTACCATTGATCATT
9913 TATTATATTAATCTACCATTGATCATT
1 TATTATATTAATCTACCATTGATCATT
9940 CTACCATTAT
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
27 27 1.00
ACGTcount: A:0.33, C:0.15, G:0.04, T:0.48
Consensus pattern (27 bp):
TATTATATTAATCTACCATTGATCATT
Found at i:10151 original size:132 final size:132
Alignment explanation
Indices: 9909--10176 Score: 527
Period size: 132 Copynumber: 2.0 Consensus size: 132
9899 TACCATTGAT
*
9909 CATTTATTATATTAATCTACCATTGATCATTCTACCATTATATTAAATATGTATAAGAAACTCAC
1 CATTGATTATATTAATCTACCATTGATCATTCTACCATTATATTAAATATGTATAAGAAACTCAC
9974 CAAAGTTACTTGAGAGAGGATGAGAAATCTATTATTCTCCTTACTCGGATATACAAGGTAAAGGA
66 CAAAGTTACTTGAGAGAGGATGAGAAATCTATTATTCTCCTTACTCGGATATACAAGGTAAAGGA
10039 CA
131 CA
10041 CATTGATTATATTAATCTACCATTGATCATTCTACCATTATATTAAATATGTATAAGAAACTCAC
1 CATTGATTATATTAATCTACCATTGATCATTCTACCATTATATTAAATATGTATAAGAAACTCAC
10106 CAAAGTTACTTGAGAGAGGATGAGAAATCTATTATTCTCCTTACTCGGATATACAAGGTAAAGGA
66 CAAAGTTACTTGAGAGAGGATGAGAAATCTATTATTCTCCTTACTCGGATATACAAGGTAAAGGA
10171 CA
131 CA
10173 CATT
1 CATT
10177 AAAATCTTGA
Statistics
Matches: 135, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
132 135 1.00
ACGTcount: A:0.38, C:0.16, G:0.13, T:0.33
Consensus pattern (132 bp):
CATTGATTATATTAATCTACCATTGATCATTCTACCATTATATTAAATATGTATAAGAAACTCAC
CAAAGTTACTTGAGAGAGGATGAGAAATCTATTATTCTCCTTACTCGGATATACAAGGTAAAGGA
CA
Found at i:12598 original size:21 final size:25
Alignment explanation
Indices: 12564--12612 Score: 70
Period size: 23 Copynumber: 2.1 Consensus size: 25
12554 ATATGATATC
12564 AATATATGACATAATAAT-ATAA-G
1 AATATATGACATAATAATAATAATG
12587 AATATAT-A-ATAATAATAATAATG
1 AATATATGACATAATAATAATAATG
12610 AAT
1 AAT
12613 TCTCTATATT
Statistics
Matches: 24, Mismatches: 0, Indels: 4
0.86 0.00 0.14
Matches are distributed among these distances:
21 8 0.33
22 5 0.21
23 11 0.46
ACGTcount: A:0.59, C:0.02, G:0.06, T:0.33
Consensus pattern (25 bp):
AATATATGACATAATAATAATAATG
Found at i:12746 original size:20 final size:20
Alignment explanation
Indices: 12721--12772 Score: 86
Period size: 20 Copynumber: 2.6 Consensus size: 20
12711 AAAAAATTAC
12721 TAAGGTTGAGCTACAAATAA
1 TAAGGTTGAGCTACAAATAA
* *
12741 TAAGGTTAAGTTACAAATAA
1 TAAGGTTGAGCTACAAATAA
12761 TAAGGTTGAGCT
1 TAAGGTTGAGCT
12773 TCATTTAAGT
Statistics
Matches: 28, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
20 28 1.00
ACGTcount: A:0.42, C:0.08, G:0.21, T:0.29
Consensus pattern (20 bp):
TAAGGTTGAGCTACAAATAA
Found at i:14745 original size:16 final size:16
Alignment explanation
Indices: 14724--14758 Score: 70
Period size: 16 Copynumber: 2.2 Consensus size: 16
14714 TCCTCCTTTT
14724 ATTGTTTTGTATAATG
1 ATTGTTTTGTATAATG
14740 ATTGTTTTGTATAATG
1 ATTGTTTTGTATAATG
14756 ATT
1 ATT
14759 TCTACTGTGA
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 19 1.00
ACGTcount: A:0.26, C:0.00, G:0.17, T:0.57
Consensus pattern (16 bp):
ATTGTTTTGTATAATG
Found at i:16685 original size:37 final size:37
Alignment explanation
Indices: 16644--16714 Score: 124
Period size: 37 Copynumber: 1.9 Consensus size: 37
16634 AATCAAGGGA
16644 TTTACCCTCAAACTATCCATATTTATAACTAGGGGGC
1 TTTACCCTCAAACTATCCATATTTATAACTAGGGGGC
* *
16681 TTTACCCTCAAACTCTCCATATTTATAATTAGGG
1 TTTACCCTCAAACTATCCATATTTATAACTAGGG
16715 CTAAACCTGA
Statistics
Matches: 32, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
37 32 1.00
ACGTcount: A:0.30, C:0.24, G:0.11, T:0.35
Consensus pattern (37 bp):
TTTACCCTCAAACTATCCATATTTATAACTAGGGGGC
Found at i:16770 original size:41 final size:41
Alignment explanation
Indices: 16711--16790 Score: 124
Period size: 41 Copynumber: 2.0 Consensus size: 41
16701 ATTTATAATT
*
16711 AGGGCTAAACCTGAATTTAATTTCTTACCTTAATTATTAGA
1 AGGGCTAAACCTGAATTTAATTTATTACCTTAATTATTAGA
* * *
16752 AGGGCTAAACTTGGATTTAATTTATTTCCTTAATTATTA
1 AGGGCTAAACCTGAATTTAATTTATTACCTTAATTATTA
16791 TGAGGATCAA
Statistics
Matches: 35, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
41 35 1.00
ACGTcount: A:0.33, C:0.12, G:0.12, T:0.42
Consensus pattern (41 bp):
AGGGCTAAACCTGAATTTAATTTATTACCTTAATTATTAGA
Found at i:19123 original size:20 final size:21
Alignment explanation
Indices: 19098--19138 Score: 75
Period size: 21 Copynumber: 2.0 Consensus size: 21
19088 TAGTACTATT
19098 AATTTGAA-TTTTTTTGCTAC
1 AATTTGAATTTTTTTTGCTAC
19118 AATTTGAATTTTTTTTGCTAC
1 AATTTGAATTTTTTTTGCTAC
19139 TTCAATTAAT
Statistics
Matches: 20, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
20 8 0.40
21 12 0.60
ACGTcount: A:0.24, C:0.10, G:0.10, T:0.56
Consensus pattern (21 bp):
AATTTGAATTTTTTTTGCTAC
Found at i:20701 original size:5 final size:5
Alignment explanation
Indices: 20691--20718 Score: 56
Period size: 5 Copynumber: 5.6 Consensus size: 5
20681 ATTTGGTCAT
20691 ATCTA ATCTA ATCTA ATCTA ATCTA ATC
1 ATCTA ATCTA ATCTA ATCTA ATCTA ATC
20719 AACCCTTTAT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 23 1.00
ACGTcount: A:0.39, C:0.21, G:0.00, T:0.39
Consensus pattern (5 bp):
ATCTA
Found at i:21661 original size:2 final size:2
Alignment explanation
Indices: 21654--21692 Score: 78
Period size: 2 Copynumber: 19.5 Consensus size: 2
21644 TTCATTCCCT
21654 CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA C
1 CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA C
21693 TATTGAATCT
Statistics
Matches: 37, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 37 1.00
ACGTcount: A:0.49, C:0.51, G:0.00, T:0.00
Consensus pattern (2 bp):
CA
Done.