Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01014539.1 Corchorus capsularis cultivar CVL-1 contig14560, 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: 39440
ACGTcount: A:0.31, C:0.18, G:0.17, T:0.34
Found at i:3053 original size:18 final size:18
Alignment explanation
Indices: 3030--3065 Score: 63
Period size: 18 Copynumber: 2.0 Consensus size: 18
3020 ACCGGCCGGT
*
3030 TTTGAAGAAGAAGGAGAA
1 TTTGAAGAAGAAGAAGAA
3048 TTTGAAGAAGAAGAAGAA
1 TTTGAAGAAGAAGAAGAA
3066 GTGATTAGCT
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
18 17 1.00
ACGTcount: A:0.53, C:0.00, G:0.31, T:0.17
Consensus pattern (18 bp):
TTTGAAGAAGAAGAAGAA
Found at i:10178 original size:14 final size:14
Alignment explanation
Indices: 10155--10189 Score: 61
Period size: 14 Copynumber: 2.4 Consensus size: 14
10145 CCTAGCCGCT
10155 CCTCTCCCCCTTCTC
1 CCTCT-CCCCTTCTC
10170 CCTCTCCCCTTCTC
1 CCTCTCCCCTTCTC
10184 CCTCTC
1 CCTCTC
10190 TAGTTCTCGT
Statistics
Matches: 20, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
14 15 0.75
15 5 0.25
ACGTcount: A:0.00, C:0.66, G:0.00, T:0.34
Consensus pattern (14 bp):
CCTCTCCCCTTCTC
Found at i:13660 original size:174 final size:174
Alignment explanation
Indices: 13366--13713 Score: 678
Period size: 174 Copynumber: 2.0 Consensus size: 174
13356 CCCATTTGTA
13366 TATACATAGGATTTTACTATCAAAATAACAAAAGAAATTATCACACACAAAGAAAAATATTAACA
1 TATACATAGGATTTTACTATCAAAATAACAAAAGAAATTATCACACACAAAGAAAAATATTAACA
13431 AAGTAAAACAACAAATTTAAACCTACAACAAAAGTTACATTTATCAAGAAAAAAATAAATTATAA
66 AAGTAAAACAACAAATTTAAACCTACAACAAAAGTTACATTTATCAAGAAAAAAATAAATTATAA
13496 GTCAAATAAAATAATTACACGTCAGGGAAATAATACATTTTAAT
131 GTCAAATAAAATAATTACACGTCAGGGAAATAATACATTTTAAT
*
13540 TATACATAGGATTTTACTATCAAAGTAACAAAAGAAATTATCACACACAAAGAAAAATATTAACA
1 TATACATAGGATTTTACTATCAAAATAACAAAAGAAATTATCACACACAAAGAAAAATATTAACA
*
13605 AAGTAAAACAACAAATTTAAACCTACAACAAAAGTTACATTTATCAAGCAAAAAATAAATTATAA
66 AAGTAAAACAACAAATTTAAACCTACAACAAAAGTTACATTTATCAAGAAAAAAATAAATTATAA
13670 GTCAAATAAAATAATTACACGTCAGGGAAATAATACATTTTAAT
131 GTCAAATAAAATAATTACACGTCAGGGAAATAATACATTTTAAT
13714 CATGATAAAT
Statistics
Matches: 172, Mismatches: 2, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
174 172 1.00
ACGTcount: A:0.55, C:0.13, G:0.07, T:0.25
Consensus pattern (174 bp):
TATACATAGGATTTTACTATCAAAATAACAAAAGAAATTATCACACACAAAGAAAAATATTAACA
AAGTAAAACAACAAATTTAAACCTACAACAAAAGTTACATTTATCAAGAAAAAAATAAATTATAA
GTCAAATAAAATAATTACACGTCAGGGAAATAATACATTTTAAT
Found at i:13665 original size:87 final size:87
Alignment explanation
Indices: 13395--13667 Score: 252
Period size: 87 Copynumber: 3.1 Consensus size: 87
13385 TCAAAATAAC
13395 AAAAGAAATTATCACACACAAAGAAAAATATTAACAAAGTAAAACAACAAATTTAAACCTACAAC
1 AAAAGAAATTATCACACACAAAGAAAAATATTAACAAAGTAAAACAACAAATTTAAACCTACAAC
13460 AAAAGTTACATTTATCAAGAAA
66 AAAAGTTACATTTATCAAGAAA
* ** * ** ** * * * * *
13482 AAAATAAATTAT-A-AGTCAAA-TAAAATAATTACACGTCAGGGAAATAATACATTTTAA-TTA-
1 AAAAGAAATTATCACACACAAAGAAAAAT-ATTA-AC-AAAGTAAAACAACAAATTTAAACCTAC
* * * ** * *
13542 TACATAGGATTTTA-CTATCAAAGTAAC
63 AACAAAAG-TTACATTTATC-AAG-AAA
13569 AAAAGAAATTATCACACACAAAGAAAAATATTAACAAAGTAAAACAACAAATTTAAACCTACAAC
1 AAAAGAAATTATCACACACAAAGAAAAATATTAACAAAGTAAAACAACAAATTTAAACCTACAAC
*
13634 AAAAGTTACATTTATCAAGCAA
66 AAAAGTTACATTTATCAAGAAA
*
13656 AAAATAAATTAT
1 AAAAGAAATTAT
13668 AAGTCAAATA
Statistics
Matches: 132, Mismatches: 42, Indels: 24
0.67 0.21 0.12
Matches are distributed among these distances:
84 5 0.04
85 18 0.14
86 11 0.08
87 64 0.48
88 11 0.08
89 18 0.14
90 5 0.04
ACGTcount: A:0.56, C:0.13, G:0.07, T:0.24
Consensus pattern (87 bp):
AAAAGAAATTATCACACACAAAGAAAAATATTAACAAAGTAAAACAACAAATTTAAACCTACAAC
AAAAGTTACATTTATCAAGAAA
Found at i:15731 original size:17 final size:17
Alignment explanation
Indices: 15709--15744 Score: 54
Period size: 17 Copynumber: 2.1 Consensus size: 17
15699 CTATATAACC
*
15709 TCCAGTCTACTATGCAG
1 TCCAGTCTACTACGCAG
*
15726 TCCAGTCTAGTACGCAG
1 TCCAGTCTACTACGCAG
15743 TC
1 TC
15745 TCAAGATTCA
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
17 17 1.00
ACGTcount: A:0.22, C:0.31, G:0.19, T:0.28
Consensus pattern (17 bp):
TCCAGTCTACTACGCAG
Found at i:19188 original size:29 final size:31
Alignment explanation
Indices: 19128--19199 Score: 94
Period size: 29 Copynumber: 2.4 Consensus size: 31
19118 GCTAAATACC
* * *
19128 CAAAAAAATCTCTTATGTTTTTCTTTTGGGA
1 CAAAATAATCCCTTATGTTTTTCTTTCGGGA
19159 CAAAATAATCCCTTATG-TTTT-TTTCGGGA
1 CAAAATAATCCCTTATGTTTTTCTTTCGGGA
*
19188 CAAATTAATCCC
1 CAAAATAATCCC
19200 ATACGTTTCA
Statistics
Matches: 37, Mismatches: 4, Indels: 2
0.86 0.09 0.05
Matches are distributed among these distances:
29 18 0.49
30 4 0.11
31 15 0.41
ACGTcount: A:0.31, C:0.18, G:0.11, T:0.40
Consensus pattern (31 bp):
CAAAATAATCCCTTATGTTTTTCTTTCGGGA
Found at i:19207 original size:29 final size:28
Alignment explanation
Indices: 19151--19207 Score: 78
Period size: 29 Copynumber: 2.0 Consensus size: 28
19141 TATGTTTTTC
* *
19151 TTTTGGGACAAAATAATCCCTTATGTTT
1 TTTTGGGACAAAATAATCCCATACGTTT
*
19179 TTTTCGGGACAAATTAATCCCATACGTTT
1 TTTT-GGGACAAAATAATCCCATACGTTT
19208 CAAAAATGAG
Statistics
Matches: 25, Mismatches: 3, Indels: 1
0.86 0.10 0.03
Matches are distributed among these distances:
28 4 0.16
29 21 0.84
ACGTcount: A:0.28, C:0.18, G:0.14, T:0.40
Consensus pattern (28 bp):
TTTTGGGACAAAATAATCCCATACGTTT
Found at i:20086 original size:180 final size:177
Alignment explanation
Indices: 19784--20135 Score: 551
Period size: 180 Copynumber: 2.0 Consensus size: 177
19774 TTGATGATTA
*** * * *
19784 TACCCTTATTTTTCGGTTATATTTATTAAATACCATTGTTTAAATTTTTATAGTTTTACTCAACT
1 TACCCTTATTTTTCAAATATATTTATTAAATACCATTGTTTAAACTTTTACAATTTTACTCAACT
* **
19849 AAAAACTCTATTTTTATTTAATTTAATATAATATATTTATAAATATTTTATTTTTACCATTTTAC
66 AAAAAATCTATTTTTATTTAATCAAATATAATATATTTATAAATATTTTATTTTTACCATTTTAC
19914 TATTTTAATTAAAAATTTTAGATATATTAGAATTTTTTAAATATACTTCT
131 TATTTTAATTAAAAA--TTAGATATATTAGAA-TTTTTAAATATACTTCT
* **
19964 TACCCTTATTTTTCAAATATATTTCTTAAATACCATTGTTTAAACTTTTACAATTTTACTCAGTT
1 TACCCTTATTTTTCAAATATATTTATTAAATACCATTGTTTAAACTTTTACAATTTTACTCAACT
* *
20029 AAAAAATCTATTTTTATTTAATCAAATCTAATATATTTATAACTATTTTATTTTTACCATTTTAC
66 AAAAAATCTATTTTTATTTAATCAAATATAATATATTTATAAATATTTTATTTTTACCATTTTAC
20094 TATTTTAATTAAAAATTAGATATATTAGAATTTTTAAATATA
131 TATTTTAATTAAAAATTAGATATATTAGAATTTTTAAATATA
20136 TTTTTTAAAA
Statistics
Matches: 158, Mismatches: 14, Indels: 3
0.90 0.08 0.02
Matches are distributed among these distances:
177 12 0.08
178 15 0.09
180 131 0.83
ACGTcount: A:0.36, C:0.10, G:0.03, T:0.51
Consensus pattern (177 bp):
TACCCTTATTTTTCAAATATATTTATTAAATACCATTGTTTAAACTTTTACAATTTTACTCAACT
AAAAAATCTATTTTTATTTAATCAAATATAATATATTTATAAATATTTTATTTTTACCATTTTAC
TATTTTAATTAAAAATTAGATATATTAGAATTTTTAAATATACTTCT
Found at i:20225 original size:31 final size:30
Alignment explanation
Indices: 20190--20283 Score: 136
Period size: 31 Copynumber: 3.1 Consensus size: 30
20180 ACTAAATACT
*
20190 AAAAAAATCCCTTATGTTTTTCTTTTGGAAC
1 AAAAAAATCTCTTATGTTTTTCTTTTGG-AC
20221 AAAAAAATCTCTTATGTTTTTCTTTTGGGAC
1 AAAAAAATCTCTTATGTTTTTCTTTT-GGAC
* *
20252 AAAAAAATCTCTTATATATTT-TTTTGGAC
1 AAAAAAATCTCTTATGTTTTTCTTTTGGAC
20281 AAA
1 AAA
20284 TTAGTCCATT
Statistics
Matches: 59, Mismatches: 3, Indels: 4
0.89 0.05 0.06
Matches are distributed among these distances:
29 7 0.12
30 4 0.07
31 46 0.78
32 2 0.03
ACGTcount: A:0.35, C:0.13, G:0.10, T:0.43
Consensus pattern (30 bp):
AAAAAAATCTCTTATGTTTTTCTTTTGGAC
Found at i:20439 original size:29 final size:29
Alignment explanation
Indices: 20363--20442 Score: 88
Period size: 29 Copynumber: 2.7 Consensus size: 29
20353 CTCATTTTTG
* * * *
20363 AAACGTAAGAGATTAATTTGTCCCGAAAA
1 AAACATAAGGGATTATTTTGTCCCAAAAA
20392 AAACATAAGGGATTATTTTGTCCCAAAAGCA
1 AAACATAAGGGATTATTTTGTCCCAAAA--A
* *
20423 AAACATAATGGATTTTTTTG
1 AAACATAAGGGATTATTTTG
20443 AGTATTTAGC
Statistics
Matches: 43, Mismatches: 6, Indels: 2
0.84 0.12 0.04
Matches are distributed among these distances:
29 24 0.56
31 19 0.44
ACGTcount: A:0.41, C:0.12, G:0.16, T:0.30
Consensus pattern (29 bp):
AAACATAAGGGATTATTTTGTCCCAAAAA
Found at i:28851 original size:32 final size:27
Alignment explanation
Indices: 28790--28846 Score: 114
Period size: 27 Copynumber: 2.1 Consensus size: 27
28780 ACGATCTCTC
28790 TCTTGTGTTTCCTTTCCAGTTGACTAA
1 TCTTGTGTTTCCTTTCCAGTTGACTAA
28817 TCTTGTGTTTCCTTTCCAGTTGACTAA
1 TCTTGTGTTTCCTTTCCAGTTGACTAA
28844 TCT
1 TCT
28847 AATCTCGGGT
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
27 30 1.00
ACGTcount: A:0.14, C:0.23, G:0.14, T:0.49
Consensus pattern (27 bp):
TCTTGTGTTTCCTTTCCAGTTGACTAA
Done.