Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01009450.1 Corchorus capsularis cultivar CVL-1 contig09471, 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: 42016
ACGTcount: A:0.32, C:0.18, G:0.17, T:0.34
Found at i:1594 original size:48 final size:47
Alignment explanation
Indices: 1530--1849 Score: 417
Period size: 48 Copynumber: 6.7 Consensus size: 47
1520 TTTACTTACA
* * * *
1530 TTTTCCCAAAATGCCCTTCCTGGACGGAAGACACTTATTTTACCTGC
1 TTTTTCCAAAACGCCCTTCCCGGACGGAAGGCACTTATTTTACCTGC
* *
1577 TTTTTCGCAAAACGCCCTTCCCAGACGGAAGGCACTTATTTTACTTGC
1 TTTTTC-CAAAACGCCCTTCCCGGACGGAAGGCACTTATTTTACCTGC
* *
1625 TTTTTCCCAAAACGCCCTTCCCAGACGGAAGGCACTTATTTTACTTGC
1 TTTTT-CCAAAACGCCCTTCCCGGACGGAAGGCACTTATTTTACCTGC
* * *
1673 TGTTTCCCAAAACACCCTTCCCGGACGAAAGGCACTT-TTTTACCTGC
1 T-TTTTCCAAAACGCCCTTCCCGGACGGAAGGCACTTATTTTACCTGC
* * * *
1720 TATTTCCAAAAACGCTCTTCCCGGACGGAAGACACTTTTTTTACCTGC
1 TTTTTCC-AAAACGCCCTTCCCGGACGGAAGGCACTTATTTTACCTGC
* *
1768 TATTTCCAAAAACGCCCTTCCCGGACGGAAGGCACTTTTTTTACCTGC
1 TTTTTCC-AAAACGCCCTTCCCGGACGGAAGGCACTTATTTTACCTGC
1816 TTTTTCCAAAAAACGCCCTTCCCGGACGGAAGGC
1 TTTTTCC--AAAACGCCCTTCCCGGACGGAAGGC
1850 GTTAATGTTT
Statistics
Matches: 247, Mismatches: 20, Indels: 10
0.89 0.07 0.04
Matches are distributed among these distances:
46 4 0.02
47 40 0.16
48 173 0.70
49 30 0.12
ACGTcount: A:0.24, C:0.31, G:0.16, T:0.29
Consensus pattern (47 bp):
TTTTTCCAAAACGCCCTTCCCGGACGGAAGGCACTTATTTTACCTGC
Found at i:1780 original size:143 final size:144
Alignment explanation
Indices: 1531--1849 Score: 444
Period size: 143 Copynumber: 2.2 Consensus size: 144
1521 TTACTTACAT
* * * *
1531 TTTCCCAAAATGCCCTTCCTGGACGGAAGACACTTATTTTACCTGCTTTTTCGCAAAACGCCCTT
1 TTTCCCAAAACGCCCTTCCCGGACGGAAGGCACTTATTTTACCTGCTATTTCGCAAAACGCCCTT
* * * *
1596 CCCAGACGGAAGGCACTTATTTTACTTGCTTTTTCCCAAAACGCCCTTCCCAGACGGAAGGCACT
66 CCCAGACGGAAGACACTTATTTTACCTGCTATTTCCAAAAACGCCCTTCCCAGACGGAAGGCACT
*
1661 TATTTTACTTGCTG
131 TATTTTACCTGCTG
* * *
1675 TTTCCCAAAACACCCTTCCCGGACGAAAGGCACTT-TTTTACCTGCTATTTC-CAAAAACGCTCT
1 TTTCCCAAAACGCCCTTCCCGGACGGAAGGCACTTATTTTACCTGCTATTTCGC-AAAACGCCCT
* * *
1738 TCCCGGACGGAAGACACTTTTTTTACCTGCTATTTCCAAAAACGCCCTTCCCGGACGGAAGGCAC
65 TCCCAGACGGAAGACACTTATTTTACCTGCTATTTCCAAAAACGCCCTTCCCAGACGGAAGGCAC
* *
1803 TTTTTTTACCTGCTT
130 TTATTTTACCTGCTG
*
1818 TTTCCAAAAAACGCCCTTCCCGGACGGAAGGC
1 TTTCC-CAAAACGCCCTTCCCGGACGGAAGGC
1850 GTTAATGTTT
Statistics
Matches: 153, Mismatches: 20, Indels: 4
0.86 0.11 0.02
Matches are distributed among these distances:
142 1 0.01
143 99 0.65
144 53 0.35
ACGTcount: A:0.24, C:0.31, G:0.16, T:0.29
Consensus pattern (144 bp):
TTTCCCAAAACGCCCTTCCCGGACGGAAGGCACTTATTTTACCTGCTATTTCGCAAAACGCCCTT
CCCAGACGGAAGACACTTATTTTACCTGCTATTTCCAAAAACGCCCTTCCCAGACGGAAGGCACT
TATTTTACCTGCTG
Found at i:6266 original size:50 final size:50
Alignment explanation
Indices: 6197--6319 Score: 228
Period size: 50 Copynumber: 2.5 Consensus size: 50
6187 TTGACACAAA
* *
6197 CTCTTGACCAATTTCAATCTCAACCAACCTCATCAACGTGATTATTTCTT
1 CTCTTGACCAATTTTAATCTCAACCAACCTCATAAACGTGATTATTTCTT
6247 CTCTTGACCAATTTTAATCTCAACCAACCTCATAAACGTGATTATTTCTT
1 CTCTTGACCAATTTTAATCTCAACCAACCTCATAAACGTGATTATTTCTT
6297 CTCTTGACCAATTTTAATCTCAA
1 CTCTTGACCAATTTTAATCTCAA
6320 TTTTGTTGAG
Statistics
Matches: 71, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
50 71 1.00
ACGTcount: A:0.29, C:0.28, G:0.06, T:0.37
Consensus pattern (50 bp):
CTCTTGACCAATTTTAATCTCAACCAACCTCATAAACGTGATTATTTCTT
Found at i:22038 original size:2 final size:2
Alignment explanation
Indices: 22031--22059 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
22021 TAAATATACT
22031 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 T
22060 CATTGAATCA
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 27 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:22790 original size:105 final size:105
Alignment explanation
Indices: 22497--22857 Score: 542
Period size: 105 Copynumber: 3.5 Consensus size: 105
22487 AGTTTAGTCT
* *
22497 TAATTTCACTAAGTTTAGCCCCAAATTAAAATTTTATTTTTATTTTAAGGGT---TTTCAAAATT
1 TAATTTCACTAAGTTTAGCCCCAAATTAAAATTTTATTTTTATTTTAAGGGTAAATTCCATAATT
*
22559 AATAATTTATTGTTATAGGGTTTTAGAAATAAAATACACAAC
66 AATAA--TATTGTTATAGGGTTTTAGAAATAAAATACAAAAC
22601 TAATTTCACTAAAGTTTAGCCCCAAATT--AA-TTT-TTTTTATTTTAAGGGTAAATTCCATAAT
1 TAATTTCACT-AAGTTTAGCCCCAAATTAAAATTTTATTTTTATTTTAAGGGTAAATTCCATAAT
22662 TAATAATATTGTTATAGGGTTTTAGAAATAAAATACAAAAC
65 TAATAATATTGTTATAGGGTTTTAGAAATAAAATACAAAAC
22703 TAATTTCACTAAGTTTAGCCCCAAATTAAAATTTTATTTTTATTTTAAGGGTAAATTCCATAATT
1 TAATTTCACTAAGTTTAGCCCCAAATTAAAATTTTATTTTTATTTTAAGGGTAAATTCCATAATT
* * * *
22768 AATAATATTGTTATAAGGTTTTAGAAATAAAATATATAAT
66 AATAATATTGTTATAGGGTTTTAGAAATAAAATACAAAAC
** *
22808 TAA-TTCACTAAGTTTAG-CCCAAATTAAAATTAAAATTTTATTTTAAGGGT
1 TAATTTCACTAAGTTTAGCCCCAAATTAAAATTTTATTTTTATTTTAAGGGT
22858 TAGAAAAATT
Statistics
Matches: 239, Mismatches: 10, Indels: 17
0.90 0.04 0.06
Matches are distributed among these distances:
101 33 0.14
102 47 0.20
103 34 0.14
104 40 0.17
105 85 0.36
ACGTcount: A:0.40, C:0.09, G:0.09, T:0.42
Consensus pattern (105 bp):
TAATTTCACTAAGTTTAGCCCCAAATTAAAATTTTATTTTTATTTTAAGGGTAAATTCCATAATT
AATAATATTGTTATAGGGTTTTAGAAATAAAATACAAAAC
Found at i:24130 original size:21 final size:21
Alignment explanation
Indices: 24085--24131 Score: 60
Period size: 20 Copynumber: 2.3 Consensus size: 21
24075 TTCAAAATAA
* * *
24085 AATAAAAACTACCCATTTTAG
1 AATAAAAAATACCCACTATAG
24106 -ATAAAAAATACCCACTATAG
1 AATAAAAAATACCCACTATAG
24126 AATAAA
1 AATAAA
24132 TACAATATTT
Statistics
Matches: 22, Mismatches: 3, Indels: 2
0.81 0.11 0.07
Matches are distributed among these distances:
20 17 0.77
21 5 0.23
ACGTcount: A:0.55, C:0.17, G:0.04, T:0.23
Consensus pattern (21 bp):
AATAAAAAATACCCACTATAG
Found at i:36007 original size:39 final size:38
Alignment explanation
Indices: 35964--36069 Score: 151
Period size: 39 Copynumber: 2.7 Consensus size: 38
35954 TTACCCAATA
35964 ATCAAAGTCCTCAAACACATATAACACAGAGACATCTAT
1 ATCAAAGTCC-CAAACACATATAACACAGAGACATCTAT
*
36003 ATCAAAGTCCCCAAACACATATAACACAGAGGCATCTAT
1 ATCAAAGT-CCCAAACACATATAACACAGAGACATCTAT
*
36042 A-CTAAAGTCCCTAAACACATACAACACA
1 ATC-AAAGTCCC-AAACACATATAACACA
36070 AGGGCAATTT
Statistics
Matches: 62, Mismatches: 2, Indels: 6
0.89 0.03 0.09
Matches are distributed among these distances:
38 4 0.06
39 56 0.90
40 2 0.03
ACGTcount: A:0.46, C:0.28, G:0.08, T:0.18
Consensus pattern (38 bp):
ATCAAAGTCCCAAACACATATAACACAGAGACATCTAT
Found at i:39114 original size:30 final size:29
Alignment explanation
Indices: 39052--39121 Score: 86
Period size: 29 Copynumber: 2.4 Consensus size: 29
39042 ACCGAACCGT
****
39052 CAAATAAGCCCCTGAACTATTATTTCGGC
1 CAAATAAGCCCCTGAACTATTAAAAAGGC
*
39081 CAAATAAGCCCCTGAACTCTTAAAAAAGGC
1 CAAATAAGCCCCTGAACTATT-AAAAAGGC
39111 CAAATAAGCCC
1 CAAATAAGCCC
39122 AGTTGCCAAG
Statistics
Matches: 35, Mismatches: 5, Indels: 1
0.85 0.12 0.02
Matches are distributed among these distances:
29 20 0.57
30 15 0.43
ACGTcount: A:0.39, C:0.29, G:0.13, T:0.20
Consensus pattern (29 bp):
CAAATAAGCCCCTGAACTATTAAAAAGGC
Done.