Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01007214.1 Corchorus capsularis cultivar CVL-1 contig07235, 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: 45407
ACGTcount: A:0.31, C:0.19, G:0.18, T:0.31
Found at i:13900 original size:156 final size:156
Alignment explanation
Indices: 13616--13922 Score: 578
Period size: 156 Copynumber: 2.0 Consensus size: 156
13606 CTCAAGCCTT
* *
13616 ACTTCGAACCATTAACAATAGCGTTGATTGAAGAAATTAAATTGGAGGATCCTATTTATCTTCCA
1 ACTTCAAACCATTAACAATAGCATTGATTGAAGAAATTAAATTGGAGGATCCTATTTATCTTCCA
*
13681 ATTTAGGGTCGAAGAAAGGAAGAGTCAAGCTAATGACTTTAAACAAGCGCTTATTGGGAGGCAAC
66 ATTTAGGGTCGAAGAAAGGAAGAGTCAAGCTAATGACTTTAAACAAGCGCTTATTAGGAGGCAAC
13746 CCAATTTTAATTTTAAATTTTTGAAG
131 CCAATTTTAATTTTAAATTTTTGAAG
*
13772 ACTTCAAACCATTAACAATAGCATTGATTGAAGGAATTAAATTGGAGGATCCTATTTATCTTCCA
1 ACTTCAAACCATTAACAATAGCATTGATTGAAGAAATTAAATTGGAGGATCCTATTTATCTTCCA
13837 ATTTAGGGTCGAAGAAAGGAAGAGTCAAGCTAATGACTTTAAACAAGCGCTTATTAGGAGGCAAC
66 ATTTAGGGTCGAAGAAAGGAAGAGTCAAGCTAATGACTTTAAACAAGCGCTTATTAGGAGGCAAC
13902 CCAATTTTAATTTTAAATTTT
131 CCAATTTTAATTTTAAATTTT
13923 GAATTTTTAT
Statistics
Matches: 147, Mismatches: 4, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
156 147 1.00
ACGTcount: A:0.36, C:0.14, G:0.18, T:0.31
Consensus pattern (156 bp):
ACTTCAAACCATTAACAATAGCATTGATTGAAGAAATTAAATTGGAGGATCCTATTTATCTTCCA
ATTTAGGGTCGAAGAAAGGAAGAGTCAAGCTAATGACTTTAAACAAGCGCTTATTAGGAGGCAAC
CCAATTTTAATTTTAAATTTTTGAAG
Found at i:15714 original size:24 final size:23
Alignment explanation
Indices: 15687--15733 Score: 60
Period size: 24 Copynumber: 2.0 Consensus size: 23
15677 AGTTATTTAG
*
15687 TTTATGCTT-TATCTTTAATTTTTC
1 TTTAT-CTTATATCTCT-ATTTTTC
15711 TTTATCTTATATCTCTATTTTTC
1 TTTATCTTATATCTCTATTTTTC
15734 AAGTTTCATT
Statistics
Matches: 21, Mismatches: 1, Indels: 3
0.84 0.04 0.12
Matches are distributed among these distances:
23 10 0.48
24 11 0.52
ACGTcount: A:0.17, C:0.15, G:0.02, T:0.66
Consensus pattern (23 bp):
TTTATCTTATATCTCTATTTTTC
Found at i:18201 original size:33 final size:33
Alignment explanation
Indices: 18164--18248 Score: 125
Period size: 33 Copynumber: 2.6 Consensus size: 33
18154 TCTTTCCATT
*
18164 CAAAACAGAATTATTTTCAATGCTATGATCAAC
1 CAAAACAGAATTATTTTCAATGATATGATCAAC
* *
18197 CAAAACAAAATTATTTTTAATGATATGATCAAC
1 CAAAACAGAATTATTTTCAATGATATGATCAAC
* *
18230 CAAAACAGATTTGTTTTCA
1 CAAAACAGAATTATTTTCA
18249 TCACAATTAG
Statistics
Matches: 45, Mismatches: 7, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
33 45 1.00
ACGTcount: A:0.44, C:0.15, G:0.08, T:0.33
Consensus pattern (33 bp):
CAAAACAGAATTATTTTCAATGATATGATCAAC
Found at i:18306 original size:33 final size:33
Alignment explanation
Indices: 18264--18366 Score: 107
Period size: 33 Copynumber: 3.1 Consensus size: 33
18254 ATTAGCATCC
* * * *
18264 AAAACAGATTTTGTTTCATCACAAACAACACCT
1 AAAATAGATTTAGTATCATCGCAAACAACACCT
* * *
18297 AAAATAGATTTAGTGTCATTGCAAACAACACCC
1 AAAATAGATTTAGTATCATCGCAAACAACACCT
* * * *
18330 AAATTAGGTTTAGTATCATCGCAAATAACATCT
1 AAAATAGATTTAGTATCATCGCAAACAACACCT
18363 AAAA
1 AAAA
18367 CACTCTTTTC
Statistics
Matches: 56, Mismatches: 14, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
33 56 1.00
ACGTcount: A:0.44, C:0.19, G:0.10, T:0.27
Consensus pattern (33 bp):
AAAATAGATTTAGTATCATCGCAAACAACACCT
Found at i:22799 original size:19 final size:18
Alignment explanation
Indices: 22762--22801 Score: 53
Period size: 19 Copynumber: 2.2 Consensus size: 18
22752 TTCTTGAAAT
*
22762 AATTCTTCAATGGTCTTC
1 AATTCTTCAATGATCTTC
*
22780 AATTCTTCGAATTATCTTC
1 AATTCTTC-AATGATCTTC
22799 AAT
1 AAT
22802 AAATCTTCAA
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
18 8 0.42
19 11 0.58
ACGTcount: A:0.28, C:0.20, G:0.07, T:0.45
Consensus pattern (18 bp):
AATTCTTCAATGATCTTC
Found at i:28024 original size:69 final size:69
Alignment explanation
Indices: 27849--28222 Score: 423
Period size: 69 Copynumber: 5.2 Consensus size: 69
27839 TAGGATAGTA
* * * *
27849 TAAAGACAAGGTGACAGACATAATGCTCAATCACCAATGCCTTGCCATAAAGTGGACTTTTTGTA
1 TAAAGACAAGGTGAGAGACATAATGCTCAATCACCATTGCCTTGCCACAAAGTGGACATTTTGT-
27914 AATAG
65 AATAG
* *
27919 TAAAGGCAAGGTGAGAGACATAATGCTCAATTACCATTGCCTTGCCACAAAGTGGACATTTTGTA
1 TAAAGACAAGGTGAGAGACATAATGCTCAATCACCATTGCCTTGCCACAAAGTGGACATTTTGTA
27984 ATAG
66 ATAG
* * * * *
27988 TAATGACAAGTTGAGAGACATAATGATCTATCACCATTGCCTTGCCACAAAGTGGACCTTTTGTA
1 TAAAGACAAGGTGAGAGACATAATGCTCAATCACCATTGCCTTGCCACAAAGTGGACATTTTGTA
28053 ATAG
66 ATAG
* *
28057 TAAAGACAAGGTAAGAGACCTAATGCTCAA-CAACCATTGCCTTGCCACAAAGTTGCCACAAAGT
1 TAAAGACAAGGTGAGAGACATAATGCTCAATC-ACCA-----TTG-C-C----TTGCCACAAAGT
*
28121 GGACCTTTTGTAATAG
54 GGACATTTTGTAATAG
* *
28137 TAAAGACAAGGTAAGAGACATAATGCTCAATTACCATTGCCTTGCCACATAA-TGGTAC--TTTG
1 TAAAGACAAGGTGAGAGACATAATGCTCAATCACCATTGCCTTGCCACA-AAGTGG-ACATTTTG
28199 TAAATAG
64 T-AATAG
*
28206 TAAAGACAAGCTGAGAG
1 TAAAGACAAGGTGAGAG
28223 GCATTGATCA
Statistics
Matches: 265, Mismatches: 23, Indels: 33
0.83 0.07 0.10
Matches are distributed among these distances:
68 6 0.02
69 126 0.48
70 62 0.23
73 1 0.00
74 4 0.02
75 4 0.02
76 1 0.00
80 61 0.23
ACGTcount: A:0.36, C:0.19, G:0.20, T:0.25
Consensus pattern (69 bp):
TAAAGACAAGGTGAGAGACATAATGCTCAATCACCATTGCCTTGCCACAAAGTGGACATTTTGTA
ATAG
Found at i:28162 original size:80 final size:80
Alignment explanation
Indices: 28029--28185 Score: 287
Period size: 80 Copynumber: 2.0 Consensus size: 80
28019 CACCATTGCC
*
28029 TTGCCACAAAGTGGACCTTTTGTAATAGTAAAGACAAGGTAAGAGACCTAATGCTCAACAACCAT
1 TTGCCACAAAGTGGACCTTTTGTAATAGTAAAGACAAGGTAAGAGACATAATGCTCAACAACCAT
28094 TGCCTTGCCACAAAG
66 TGCCTTGCCACAAAG
**
28109 TTGCCACAAAGTGGACCTTTTGTAATAGTAAAGACAAGGTAAGAGACATAATGCTCAATTACCAT
1 TTGCCACAAAGTGGACCTTTTGTAATAGTAAAGACAAGGTAAGAGACATAATGCTCAACAACCAT
28174 TGCCTTGCCACA
66 TGCCTTGCCACA
28186 TAATGGTACT
Statistics
Matches: 74, Mismatches: 3, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
80 74 1.00
ACGTcount: A:0.36, C:0.22, G:0.18, T:0.24
Consensus pattern (80 bp):
TTGCCACAAAGTGGACCTTTTGTAATAGTAAAGACAAGGTAAGAGACATAATGCTCAACAACCAT
TGCCTTGCCACAAAG
Found at i:40245 original size:6 final size:6
Alignment explanation
Indices: 40209--40237 Score: 58
Period size: 6 Copynumber: 4.8 Consensus size: 6
40199 TCACAAATCA
40209 TACACT TACACT TACACT TACACT TACAC
1 TACACT TACACT TACACT TACACT TACAC
40238 ACTTACACAA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 23 1.00
ACGTcount: A:0.34, C:0.34, G:0.00, T:0.31
Consensus pattern (6 bp):
TACACT
Found at i:41999 original size:20 final size:20
Alignment explanation
Indices: 41974--42014 Score: 82
Period size: 20 Copynumber: 2.0 Consensus size: 20
41964 TCTACGTCTT
41974 AGGCTATATATCGATTTGGG
1 AGGCTATATATCGATTTGGG
41994 AGGCTATATATCGATTTGGG
1 AGGCTATATATCGATTTGGG
42014 A
1 A
42015 TAATGTATGA
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 21 1.00
ACGTcount: A:0.27, C:0.10, G:0.29, T:0.34
Consensus pattern (20 bp):
AGGCTATATATCGATTTGGG
Found at i:43169 original size:19 final size:18
Alignment explanation
Indices: 43145--43180 Score: 54
Period size: 19 Copynumber: 1.9 Consensus size: 18
43135 TGAAGATATC
43145 TTGAAGATAATTTGAAGAT
1 TTGAAGATAA-TTGAAGAT
*
43164 TTGAAGATCATTGAAGA
1 TTGAAGATAATTGAAGA
43181 ATTATTTCAA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
18 7 0.44
19 9 0.56
ACGTcount: A:0.42, C:0.03, G:0.22, T:0.33
Consensus pattern (18 bp):
TTGAAGATAATTGAAGAT
Done.