Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01012804.1 Corchorus capsularis cultivar CVL-1 contig12825, 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: 41607
ACGTcount: A:0.33, C:0.18, G:0.17, T:0.32
Found at i:50 original size:2 final size:2
Alignment explanation
Indices: 43--73 Score: 53
Period size: 2 Copynumber: 15.5 Consensus size: 2
33 TTTAAATTGA
*
43 AT AT AT AT AT AT AT TT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
74 AACATTGTAT
Statistics
Matches: 27, Mismatches: 2, Indels: 0
0.93 0.07 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):
AT
Found at i:7824 original size:167 final size:167
Alignment explanation
Indices: 7470--7913 Score: 560
Period size: 167 Copynumber: 2.7 Consensus size: 167
7460 TGAGTCATTT
* *
7470 GTCAATTGAGAAATGA-CAAAAAAGTTTAGTTATTTAATCCCCTCAAGAATCAAAAGTTAGGACA
1 GTCAATTGAGAAATGACCAAAAAA-ATTAGTTATTTAATCACCTCAAGAATCAAAAGTTAGGACA
* * * * ** * *
7534 TTTAAGTAATCTGTC-AAGTA-GATAAACACGAAAAAAATTAGTTTTCTAGCTCATCATCAATCC
65 TTTAAGTAATCTGACAAAGTAGGA-AAAGACGAAAAAAATTAGTTCTCTAACTCAAAAGCAAGCC
* * *
7597 TTGATGGGGATCTTTTATTAATTCCACTACTCTATTCAA
129 TTGATAGGGATCTTTTAGTAATTCCACTACTCTATTAAA
* * * *
7636 GTCTATTGAGAAATGACCAAAAAAATTACTTATTTAATCTCCTCAAAAATCAAAAGTTAGGACAT
1 GTCAATTGAGAAATGACCAAAAAAATTAGTTATTTAATCACCTCAAGAATCAAAAGTTAGGACAT
* *
7701 TTAAATAATCT-ACAAAGTAGGAAAAGACGAAAAAAATAAGTTCTCTAACTCCAAAAGCAAGCCT
66 TTAAGTAATCTGACAAAGTAGGAAAAGACGAAAAAAATTAGTTCTCTAACT-CAAAAGCAAGCCT
* *
7765 TGGTAGGGATCTTTTAGTAATTCCACTACTTTATTAAA
130 TGATAGGGATCTTTTAGTAATTCCACTACTCTATTAAA
* *
7803 GTCAATTGAGAAATAACC-AAAAAGTCTAGTTATTTAATCACCTCAAGAATCAAAAGTTAGGACA
1 GTCAATTGAGAAATGACCAAAAAAAT-TAGTTATTTAATCACCTCAAGAATCAAAAGTTAGGACA
** *
7867 TTTAAGTAAT-TGGTAAAGT-GTGAAAAGATGAAAAAAATTAGTTCTCT
65 TTTAAGTAATCTGACAAAGTAG-GAAAAGACGAAAAAAATTAGTTCTCT
7914 CGCTCCTCAT
Statistics
Matches: 240, Mismatches: 31, Indels: 13
0.85 0.11 0.05
Matches are distributed among these distances:
165 1 0.00
166 99 0.41
167 140 0.58
ACGTcount: A:0.41, C:0.15, G:0.14, T:0.30
Consensus pattern (167 bp):
GTCAATTGAGAAATGACCAAAAAAATTAGTTATTTAATCACCTCAAGAATCAAAAGTTAGGACAT
TTAAGTAATCTGACAAAGTAGGAAAAGACGAAAAAAATTAGTTCTCTAACTCAAAAGCAAGCCTT
GATAGGGATCTTTTAGTAATTCCACTACTCTATTAAA
Found at i:8624 original size:54 final size:54
Alignment explanation
Indices: 8565--8695 Score: 176
Period size: 54 Copynumber: 2.4 Consensus size: 54
8555 ATTTGACTCC
*
8565 AACAAGATTAGTCATAAAAATAACATATAAGCATTTAGGGCAGACTTTGCCTT-G
1 AACAAGATTAGTCATAAAAATAACATATAAGCATTTAGGACAGAC-TTGCCTTAG
* * **
8619 AACAAGATTAGTTATAAAAATAACTTATAAGCATTTAGGATTGACTTGCCTTAG
1 AACAAGATTAGTCATAAAAATAACATATAAGCATTTAGGACAGACTTGCCTTAG
*
8673 AACAAG-TTCAGTCGTAAAAATAA
1 AACAAGATT-AGTCATAAAAATAA
8696 GAGCATTTGT
Statistics
Matches: 68, Mismatches: 7, Indels: 4
0.86 0.09 0.05
Matches are distributed among these distances:
53 9 0.13
54 59 0.87
ACGTcount: A:0.43, C:0.13, G:0.15, T:0.29
Consensus pattern (54 bp):
AACAAGATTAGTCATAAAAATAACATATAAGCATTTAGGACAGACTTGCCTTAG
Found at i:33539 original size:109 final size:110
Alignment explanation
Indices: 33386--33680 Score: 427
Period size: 109 Copynumber: 2.7 Consensus size: 110
33376 TAAATTAAAA
** * *
33386 TGGTAAAAATAAAAAAAATTATATAAAATATT-GAATTTAATTAAATGAAAATAGAGTTTTTAGT
1 TGGTAAAAAT-AAAGTAATTATA-AAGATATTAGTATTTAATTAAATGAAAATAGAGTTTTTAGT
33450 AGAATAAAATTGTATATTAGAAAAAATTTTAATATATCCAAATTTTT
64 AGAATAAAATTGTATATTAGAAAAAATTTTAATATATCCAAATTTTT
33497 TGGTAAAAATAAAGTAATTATAAAGATATTAG-ATTTAATTAAATGAAAATAGAGTTTTTAGTAG
1 TGGTAAAAATAAAGTAATTATAAAGATATTAGTATTTAATTAAATGAAAATAGAGTTTTTAGTAG
*
33561 AATAAAATTGTATATTAGAAAAAATTTTAGTATATCCAAATTTTT
66 AATAAAATTGTATATTAGAAAAAATTTTAATATATCCAAATTTTT
* * *
33606 T--TAAAAAATAAAGTAATTATAAAGATATTAGATTTTATTTAATTGAATAAAAATAGAGTTTCT
1 TGGT-AAAAATAAAGTAATTATAAAGATATTAG----TATTTAATTAAATGAAAATAGAGTTTTT
33669 AGTAGAATAAAA
61 AGTAGAATAAAA
33681 CTATAATAGT
Statistics
Matches: 170, Mismatches: 7, Indels: 12
0.90 0.04 0.06
Matches are distributed among these distances:
107 1 0.01
108 28 0.16
109 84 0.49
110 11 0.06
111 10 0.06
113 36 0.21
ACGTcount: A:0.50, C:0.02, G:0.11, T:0.38
Consensus pattern (110 bp):
TGGTAAAAATAAAGTAATTATAAAGATATTAGTATTTAATTAAATGAAAATAGAGTTTTTAGTAG
AATAAAATTGTATATTAGAAAAAATTTTAATATATCCAAATTTTT
Found at i:36825 original size:6 final size:6
Alignment explanation
Indices: 36814--36848 Score: 61
Period size: 6 Copynumber: 5.8 Consensus size: 6
36804 TCTGGCAGTG
*
36814 CAGAGC CAGAGC CAGAGC CAGAGC CAAAGC CAGAG
1 CAGAGC CAGAGC CAGAGC CAGAGC CAGAGC CAGAG
36849 GAAGAACAAA
Statistics
Matches: 27, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
6 27 1.00
ACGTcount: A:0.37, C:0.31, G:0.31, T:0.00
Consensus pattern (6 bp):
CAGAGC
Done.