Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01010434.1 Corchorus capsularis cultivar CVL-1 contig10455, 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: 49252
ACGTcount: A:0.34, C:0.18, G:0.17, T:0.32
Found at i:3961 original size:92 final size:92
Alignment explanation
Indices: 3804--3989 Score: 372
Period size: 92 Copynumber: 2.0 Consensus size: 92
3794 TTTATTATAT
3804 TTGTATTCATTTAGTTTGGAAAAATCAAAAGACATTCATCCCCTTTTCCTATATAAAATAAATTA
1 TTGTATTCATTTAGTTTGGAAAAATCAAAAGACATTCATCCCCTTTTCCTATATAAAATAAATTA
3869 ATCAAATAATTATAAATTAATTATAAA
66 ATCAAATAATTATAAATTAATTATAAA
3896 TTGTATTCATTTAGTTTGGAAAAATCAAAAGACATTCATCCCCTTTTCCTATATAAAATAAATTA
1 TTGTATTCATTTAGTTTGGAAAAATCAAAAGACATTCATCCCCTTTTCCTATATAAAATAAATTA
3961 ATCAAATAATTATAAATTAATTATAAA
66 ATCAAATAATTATAAATTAATTATAAA
3988 TT
1 TT
3990 TGTTAAGAAT
Statistics
Matches: 94, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
92 94 1.00
ACGTcount: A:0.44, C:0.12, G:0.05, T:0.39
Consensus pattern (92 bp):
TTGTATTCATTTAGTTTGGAAAAATCAAAAGACATTCATCCCCTTTTCCTATATAAAATAAATTA
ATCAAATAATTATAAATTAATTATAAA
Found at i:19900 original size:27 final size:27
Alignment explanation
Indices: 19862--19915 Score: 99
Period size: 27 Copynumber: 2.0 Consensus size: 27
19852 CAGAAGTTAG
*
19862 CTGCTATAGCATTGAAGGAATTTTACT
1 CTGCTATAGCATTAAAGGAATTTTACT
19889 CTGCTATAGCATTAAAGGAATTTTACT
1 CTGCTATAGCATTAAAGGAATTTTACT
19916 TTGTTAATTA
Statistics
Matches: 26, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
27 26 1.00
ACGTcount: A:0.31, C:0.15, G:0.17, T:0.37
Consensus pattern (27 bp):
CTGCTATAGCATTAAAGGAATTTTACT
Found at i:23137 original size:12 final size:11
Alignment explanation
Indices: 23104--23133 Score: 51
Period size: 11 Copynumber: 2.6 Consensus size: 11
23094 CAACAAGTGG
23104 TAAATAATAAAA
1 TAAATAAT-AAA
23116 TAAATAATAAA
1 TAAATAATAAA
23127 TAAATAA
1 TAAATAA
23134 ATAACAATAT
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
11 10 0.56
12 8 0.44
ACGTcount: A:0.73, C:0.00, G:0.00, T:0.27
Consensus pattern (11 bp):
TAAATAATAAA
Found at i:26540 original size:433 final size:432
Alignment explanation
Indices: 25525--26578 Score: 1051
Period size: 436 Copynumber: 2.4 Consensus size: 432
25515 ACATCTGGAT
* * ** * * * *
25525 AAAAAATAATATGATATTAAATAGATTGTCAATCAAAATCACAAAATTTTA-AAAGCATTTTTTA
1 AAAAAATTATACGATATTAAATAGA--CACAATCAAAACCA-AAAAATTTAGGAAGCATTTTTTT
* * * * * *
25589 GAA-CTGAAATATAAAAA-TTAGCTTTTGGGTCTTTCAT-AAAAGTTGTAGATCATAAAATTACC
63 GAATC-AAAACATAAAAATTTA-CTTTTGAGTCCTTAATGAAAA-TTGTAGATCATGAAATTACC
** * * *** * *
25651 TTTTAATAGACACCCGAATTACCTTAATTATACAAATAGAACAAAGAAAATAAAAAAAATGATG-
125 TTTTAATAGACACATGAATCAACTTAATCGGACAAATAG-A-AAA-AAAAT-AAAAAAATAAAGA
* *
25715 TGCTAAATCG--AG--TAAGATAGAATTTGGAAAGGACTAAGTAGTATAAAATAGAAAAATATGA
186 T--TAAA-CGTTAGATTCAGATAGAATTTGGAAAGGACTAAGTAGCATAAAATAGAAAAATATGA
* * * ** *
25776 GGATAATTTGGTAACTAATTCAAATAAGAAAATATTTCTTAATGGAGATCTTGAAACATAAAAAT
248 GGATAATTTGATAAATAATCCAAATAAGAAAATATTTCTTAATAAAGATCTTAAAACATAAAAAT
* * * * * *
25841 TTCCTTTTGAACCCTTCATGAAACTCGCAGATTAAATTAACTTTCGGGTTCTTCATGAAAGTCGT
313 TCCCTTTTGAACCCTTCACGAAACTCACAGATCAAATTAACTTTCGGGTCCTTCATGAAAGTCAT
* * * * *
25906 AGATTATACAGTAATCTTTTAACCGACACTTGAATAACTTTAATTGGACATGCGGAT
378 AAATCATACAATAATCTTTTAACCGACACTT--ATAACTTCAATTGGACATGCGGAC
** * * * **
25963 TGAAAATTATATGGTATTAAATAGACACAATCGAAATGAAAAAATTTAGGAAGCATTTTTTTGAA
1 AAAAAATTATACGATATTAAATAGACACAATCAAAACCAAAAAATTTAGGAAGCATTTTTTTGAA
** * * *
26028 TTGAAACATAAAAATTTGCTTTTGAGTCCTTCATGAAAGTTGTAGATCATGAAATTACCTTTTAA
66 TCAAAACATAAAAATTTACTTTTGAGTCCTTAATGAAAATTGTAGATCATGAAATTACCTTTTAA
* *
26093 TAGACACATGAATCAACTTAATCGGACAAATATAACAAATAATAAAAAAATAAAGATTAAACGTT
131 TAGACACATGAATCAACTTAATCGGACAAATAGAA-AAAAAATAAAAAAATAAAGATTAAACGTT
* * ** * *
26158 AGATTCAGATAGAATTTGTAAAGGACTAAGTAGCATAAAGTAGAAATGTATGAGGGTCATTTGAT
195 AGATTCAGATAGAATTTGGAAAGGACTAAGTAGCATAAAATAGAAAAATATGAGGATAATTTGAT
* * * *
26223 AAATAATCCAGATAAGAAAATGTTTGTTAATAAAGATCTTAAAACGTAAAAATTCCCTTTTGAAC
260 AAATAATCCAAATAAGAAAATATTTCTTAATAAAGATCTTAAAACATAAAAATTCCCTTTTGAAC
* * * * *
26288 CTTTCACGAAACTCATAGATCAAATTTAGCTTTCGGGTCCTTCATGGAAGTCATAAATCATGCAA
325 CCTTCACGAAACTCACAGATCAAA-TTAACTTTCGGGTCCTTCATGAAAGTCATAAATCATACAA
**
26353 TAA-CATTTTAACCGACACTT-T-AC-TCAATTGGACATTTGGAC
389 TAATC-TTTTAACCGACACTTATAACTTCAATTGGACATGCGGAC
* * *
26394 AAAAAATTATACGATATTAAATTA-ACCGGCAATCAAAACCACAAAATTTCGGAAGCATTTTTTA
1 AAAAAATTATACGATATTAAA-TAGA-C-ACAATCAAAACCAAAAAATTTAGGAAGCATTTTTT-
* *
26458 T-AATCAAAACATCAAAATTTACTTTTGAGTTCTTAATGAAAATTGTAGATCATGAAATTA-CTT
62 TGAATCAAAACATAAAAATTTACTTTTGAGTCCTTAATGAAAATTGTAGATCATGAAATTACCTT
* ** *
26521 TTAAATAGACACTTGAATCAGTTTAATCGGACAAATAGAAAAAAAATACAAAAATAAA
127 TT-AATAGACACATGAATCAACTTAATCGGACAAATAGAAAAAAAATAAAAAAATAAA
26579 AGGCAACGCG
Statistics
Matches: 511, Mismatches: 88, Indels: 40
0.80 0.14 0.06
Matches are distributed among these distances:
431 34 0.07
432 30 0.06
433 127 0.25
434 7 0.01
435 138 0.27
436 149 0.29
437 5 0.01
438 21 0.04
ACGTcount: A:0.43, C:0.12, G:0.13, T:0.31
Consensus pattern (432 bp):
AAAAAATTATACGATATTAAATAGACACAATCAAAACCAAAAAATTTAGGAAGCATTTTTTTGAA
TCAAAACATAAAAATTTACTTTTGAGTCCTTAATGAAAATTGTAGATCATGAAATTACCTTTTAA
TAGACACATGAATCAACTTAATCGGACAAATAGAAAAAAAATAAAAAAATAAAGATTAAACGTTA
GATTCAGATAGAATTTGGAAAGGACTAAGTAGCATAAAATAGAAAAATATGAGGATAATTTGATA
AATAATCCAAATAAGAAAATATTTCTTAATAAAGATCTTAAAACATAAAAATTCCCTTTTGAACC
CTTCACGAAACTCACAGATCAAATTAACTTTCGGGTCCTTCATGAAAGTCATAAATCATACAATA
ATCTTTTAACCGACACTTATAACTTCAATTGGACATGCGGAC
Found at i:27230 original size:16 final size:16
Alignment explanation
Indices: 27189--27234 Score: 56
Period size: 16 Copynumber: 2.9 Consensus size: 16
27179 AACTCGTCCG
*
27189 AACCCGAACCTGAAAA
1 AACCCGAACCCGAAAA
* * *
27205 AGCTCAAACCCGAAAA
1 AACCCGAACCCGAAAA
27221 AACCCGAACCCGAA
1 AACCCGAACCCGAA
27235 CCTAAAAAAA
Statistics
Matches: 23, Mismatches: 7, Indels: 0
0.77 0.23 0.00
Matches are distributed among these distances:
16 23 1.00
ACGTcount: A:0.48, C:0.35, G:0.13, T:0.04
Consensus pattern (16 bp):
AACCCGAACCCGAAAA
Found at i:27443 original size:32 final size:32
Alignment explanation
Indices: 27405--27487 Score: 114
Period size: 32 Copynumber: 2.6 Consensus size: 32
27395 GTCAAAACCC
*
27405 ACCCGAACCCGAATTAACCTGACCCAAAATTG
1 ACCCGAACCCGAATTAACCTGACCCAAAATTA
* *
27437 ATCCGAACCCG-ATTCAACCTGACCCAAATTTA
1 ACCCGAACCCGAATT-AACCTGACCCAAAATTA
*
27469 ACCCGAACCCGAATCAACC
1 ACCCGAACCCGAATTAACC
27488 CAACCTAACT
Statistics
Matches: 44, Mismatches: 5, Indels: 4
0.83 0.09 0.08
Matches are distributed among these distances:
31 3 0.07
32 39 0.89
33 2 0.05
ACGTcount: A:0.36, C:0.37, G:0.11, T:0.16
Consensus pattern (32 bp):
ACCCGAACCCGAATTAACCTGACCCAAAATTA
Found at i:37601 original size:48 final size:48
Alignment explanation
Indices: 37506--37602 Score: 115
Period size: 48 Copynumber: 2.0 Consensus size: 48
37496 TCATGTTGAG
* ****
37506 GTGAATGATCAAGCTGCAGATATTGAAGAGCTAGTGGTTGATCAAGAA
1 GTGAATGAACAAGCTGCAGATATTGAAGAGCTAGTGCACAATCAAGAA
* *
37554 GTGAATGAACAAGCTGCAGATATTGGAGAGGCTA-TGCACAATGAAGAA
1 GTGAATGAACAAGCTGCAGATATTGAAGA-GCTAGTGCACAATCAAGAA
37602 G
1 G
37603 AAGTTGACAA
Statistics
Matches: 41, Mismatches: 7, Indels: 2
0.82 0.14 0.04
Matches are distributed among these distances:
48 37 0.90
49 4 0.10
ACGTcount: A:0.37, C:0.11, G:0.30, T:0.22
Consensus pattern (48 bp):
GTGAATGAACAAGCTGCAGATATTGAAGAGCTAGTGCACAATCAAGAA
Found at i:38001 original size:27 final size:27
Alignment explanation
Indices: 37924--38004 Score: 74
Period size: 32 Copynumber: 2.8 Consensus size: 27
37914 ATAGGGATAG
37924 TGCTTTTGATGAAGATTGGTATTACAA
1 TGCTTTTGATGAAGATTGGTATTACAA
* * *
37951 TGAAGAGGTTTTTGGTAAAG-TTGGTATTACAA
1 T------GCTTTTGATGAAGATTGGTATTACAA
37983 TGCTTTTGATGAAGATTGGTAT
1 TGCTTTTGATGAAGATTGGTAT
38005 GTCAATATAA
Statistics
Matches: 41, Mismatches: 6, Indels: 14
0.67 0.10 0.23
Matches are distributed among these distances:
26 10 0.24
27 8 0.20
32 13 0.32
33 10 0.24
ACGTcount: A:0.28, C:0.05, G:0.26, T:0.41
Consensus pattern (27 bp):
TGCTTTTGATGAAGATTGGTATTACAA
Found at i:38835 original size:17 final size:17
Alignment explanation
Indices: 38813--38861 Score: 53
Period size: 18 Copynumber: 2.8 Consensus size: 17
38803 GTATTTAATA
38813 ATTTATTTTTTAATTTC
1 ATTTATTTTTTAATTTC
* *
38830 ATTTATTTATTTTATTTT
1 ATTTATTT-TTTAATTTC
*
38848 ATTTTTTATTTTAA
1 ATTTATT-TTTTAA
38862 AAAAAATCCA
Statistics
Matches: 26, Mismatches: 4, Indels: 3
0.79 0.12 0.09
Matches are distributed among these distances:
17 8 0.31
18 17 0.65
19 1 0.04
ACGTcount: A:0.24, C:0.02, G:0.00, T:0.73
Consensus pattern (17 bp):
ATTTATTTTTTAATTTC
Found at i:40687 original size:19 final size:19
Alignment explanation
Indices: 40676--40712 Score: 58
Period size: 19 Copynumber: 2.0 Consensus size: 19
40666 AATTTTTAAG
40676 TAAAAATATAATATATAAA
1 TAAAAATATAATATATAAA
*
40695 TAAAAATTTAATAT-TAAA
1 TAAAAATATAATATATAAA
40713 ACAATTAATT
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
18 4 0.24
19 13 0.76
ACGTcount: A:0.65, C:0.00, G:0.00, T:0.35
Consensus pattern (19 bp):
TAAAAATATAATATATAAA
Done.