Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01007384.1 Corchorus capsularis cultivar CVL-1 contig07405, 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: 24359
ACGTcount: A:0.33, C:0.20, G:0.17, T:0.30
Found at i:1432 original size:21 final size:21
Alignment explanation
Indices: 1408--1456 Score: 62
Period size: 21 Copynumber: 2.3 Consensus size: 21
1398 CAGCTGGGGG
* * *
1408 CCCATGTGGTATGCTTGGCGC
1 CCCATGTGGTATGCCTCGCGA
*
1429 CCCATGTGGTTTGCCTCGCGA
1 CCCATGTGGTATGCCTCGCGA
1450 CCCATGT
1 CCCATGT
1457 CCTCCAGTGC
Statistics
Matches: 24, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
21 24 1.00
ACGTcount: A:0.10, C:0.33, G:0.29, T:0.29
Consensus pattern (21 bp):
CCCATGTGGTATGCCTCGCGA
Found at i:16534 original size:30 final size:30
Alignment explanation
Indices: 16493--16555 Score: 92
Period size: 30 Copynumber: 2.1 Consensus size: 30
16483 TCGCATGCAG
16493 CATCACATGGGGCAACCG-GCCACAACCGGC
1 CATCACATGGGGCAACCGCG-CACAACCGGC
* *
16523 CATCGCATGGGGCATCCGCGCACAACCGGC
1 CATCACATGGGGCAACCGCGCACAACCGGC
16553 CAT
1 CAT
16556 TTGATCCTTT
Statistics
Matches: 30, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
30 29 0.97
31 1 0.03
ACGTcount: A:0.24, C:0.40, G:0.27, T:0.10
Consensus pattern (30 bp):
CATCACATGGGGCAACCGCGCACAACCGGC
Found at i:19463 original size:30 final size:30
Alignment explanation
Indices: 19411--19472 Score: 81
Period size: 30 Copynumber: 2.1 Consensus size: 30
19401 GTCTTGAAGA
* * *
19411 CCATTATAAGTCCTTGGGGCATCTTTCCCT
1 CCATGATAAGTCCTTGGCGCATCATTCCCT
19441 CCATGATAAG-CCTTAGGCGCATCATTCCCT
1 CCATGATAAGTCCTT-GGCGCATCATTCCCT
19471 CC
1 CC
19473 CCCTTGAAGA
Statistics
Matches: 28, Mismatches: 3, Indels: 2
0.85 0.09 0.06
Matches are distributed among these distances:
29 4 0.14
30 24 0.86
ACGTcount: A:0.19, C:0.34, G:0.16, T:0.31
Consensus pattern (30 bp):
CCATGATAAGTCCTTGGCGCATCATTCCCT
Found at i:20000 original size:33 final size:33
Alignment explanation
Indices: 19956--20043 Score: 115
Period size: 33 Copynumber: 2.7 Consensus size: 33
19946 CTAAAAAAGA
* * *
19956 TTTAGTGTCATTGTAAAGC-ACACTTAAATTAGG
1 TTTAGTATCATTGCAAA-CAACACTCAAATTAGG
19989 TTTAGTATCATTGCAAACAACACTCAAATTAGG
1 TTTAGTATCATTGCAAACAACACTCAAATTAGG
* *
20022 TTTAATATCATCGCAAACAACA
1 TTTAGTATCATTGCAAACAACA
20044 TCTAAAACAC
Statistics
Matches: 49, Mismatches: 5, Indels: 2
0.88 0.09 0.04
Matches are distributed among these distances:
32 1 0.02
33 48 0.98
ACGTcount: A:0.39, C:0.17, G:0.12, T:0.32
Consensus pattern (33 bp):
TTTAGTATCATTGCAAACAACACTCAAATTAGG
Found at i:23555 original size:927 final size:928
Alignment explanation
Indices: 21520--24359 Score: 5283
Period size: 927 Copynumber: 3.1 Consensus size: 928
21510 TATTAGATTC
* *
21520 AAATCTATCATTGAGACCTGCCAAGAATCTACTTGGACTTCTTCAGCTTCTAGACAAGTATGTCG
1 AAATCTATCCTTGAGACCTGCCAAGAATCTACTTGGACTTCTTCAGCTTGTAGACAAGTATGTCG
21585 ACAACCTTCACAAAGCAATCTCTCTTCGTTCGTCGGCCTTAAGTCTTCAATTAGACCTGCAATTG
66 ACAACCTTCACAAAGCAATCTCTCTTCGTTCGTCGGCCTTAAGTCTTCAATTAGACCTGCAATTG
21650 AATAACCTAAGATCACAAGATTCACAAACAATTAAGCATCACACAACCTAATTGTTTGCTAGGAC
131 AATAACCTAAGATCACAAGATTCACAAACAATTAAGCATCACACAACCTAATTGTTTGCTAGGAC
21715 TCTACAAGATTGAAGAACCCTAAGTTTCCTCGAACTAGAACAATGAAGCCAAGATATTCAATTTG
196 TCTACAAGATTGAAGAACCCTAAGTTTCCTCGAACTAGAACAATGAAGCCAAGATATTCAATTTG
21780 GGAGAATCAACCTCAATTTTATTAATCAACTCAACTTCCACTTTTTACAAGAGATATTCGTGGCC
261 GGAGAATCAACCTCAATTTTATTAATCAACTCAACTTCCAC-TTTTACAAGAGATATTCGTGGCC
21845 TTATATAGTGATAGGGTCAACGAAAATCCTAAAATAAATCCTAATTTTCGTCCAAATATAAGGGC
325 TTATATAGTGATAGGGTCAACGAAAATCCTAAAATAAATCCTAATTTTCGTCCAAATATAAGGGC
21910 TAGGGAAAAACTAGTCCAAGCCCAACTAGGAAAAGGAAATAAAAGTATAATTAAACAAGGATTGG
390 TAGGGAAAAACTAGTCCAAGCCCAACTAGGAAAAGGAAATAAAAGTATAATTAAACAAGGATTGG
*
21975 ACTTAGTCAAACAAGGCCAAATCCAAATAACATCCAAACTTAAAGATAAGCTAATCTAAGATAGA
455 ACTTAGTCAAACAAGGCCAAATCCAAATAACATCCAAACTTAAAAATAAGCTAATCTAAGATAGA
22040 ATTAAGCCCAAACAAAGATAACTGAGCATATTGGGCTCATGCCACTATGTCAATCCGGCCATTTA
520 ATTAAGCCCAAACAAAGATAACTGAGCATATTGGGCTCATGCCACTATGTCAATCCGGCCATTTA
22105 GAATCAATAGCAAGCAAAGTGATGAACTTGTAATTCATTGGTGTTTTCTTGCTCAAATCATCATC
585 GAATCAATAGCAAGCAAAGTGATGAACTTGTAATTCATTGGTGTTTTCTTGCTCAAATCATCATC
* *
22170 AAAGCTCTTCAATCGAACTTGAATGGTCTTCAAGTCTTCAAGATGGGTTCGAACAAGGCTCATGA
650 AAAGCTCTTCAATTGAACTTGAATGGTCTTCAAGTCTTCAAGATGAGTTCGAACAAGGCTCATGA
*
22235 GTGCATCCCTGAATCTCTTAGCTCTTGCCCTTGTCATCGGGCTAATAGGCATCTTCAATGAATCG
715 GTGCATCCCTGAATCTCTTAGCTCTTGCTCTTGTCATCGGGCTAATAGGCATCTTCAATGAATCG
* *
22300 AACAACATCTTTTTAGTGCTTGGAACATGCTTATCAATATCTCGATAATCTTCATGCATCTCCAT
780 AATAACATCTTTTTGGTGCTTGGAACATGCTTATCAATATCTCGATAATCTTCATGCATCTCCAT
22365 GCTTCCTTGCAGCCCATGCACATCCTTTCTATGGTCTCCATGCTTGTCTCCAAGACCATGAGAAG
845 GCTTCCTTGCAGCCCATGCACATCCTTTCTATGGTCTCCATGCTTGTCTCCAAGACCATGAGAAG
22430 TCCTTGGACCTCCATGATA
910 TCCTTGGACCTCCATGATA
22449 AAATCTATCCTTGAGACCTGCCAAGAATCTACTTGGACTTCTTCAGCTTGTAGACAAGTATGTCG
1 AAATCTATCCTTGAGACCTGCCAAGAATCTACTTGGACTTCTTCAGCTTGTAGACAAGTATGTCG
*
22514 ACAACCTTCACAAAGCAATCTCTCTTCGTTCGTCAGCCTTAAGTCTTCAATTAGACCTGCAATTG
66 ACAACCTTCACAAAGCAATCTCTCTTCGTTCGTCGGCCTTAAGTCTTCAATTAGACCTGCAATTG
*
22579 AATAACCTAAGATCACAAGATTCACAAACAATTAAGCATCACTCAACCTAATTGTTTGCTAGGAC
131 AATAACCTAAGATCACAAGATTCACAAACAATTAAGCATCACACAACCTAATTGTTTGCTAGGAC
* * *
22644 TTTACAAGATCGAAGAACCCTAAGTTTCCTCGAACTAGAACAATGAAGCCAAGATAATCAATTTG
196 TCTACAAGATTGAAGAACCCTAAGTTTCCTCGAACTAGAACAATGAAGCCAAGATATTCAATTTG
22709 GGAGAATCAACCTCAATTTTATTAATCAACTCAACTTCCACTTTTACAAGAGATATTCGTGGCCT
261 GGAGAATCAACCTCAATTTTATTAATCAACTCAACTTCCACTTTTACAAGAGATATTCGTGGCCT
*
22774 TATATAGTGATAGGGTCAACGAAAATCCTAAAATAAATCCTAATTTTCGTCCAAATATAAGGGAT
326 TATATAGTGATAGGGTCAACGAAAATCCTAAAATAAATCCTAATTTTCGTCCAAATATAAGGGCT
* * *
22839 AGCGAAAAACTAGTCCAAGCCAAACTAGGAAAAGGAAATAAAAGCATAATTAAACAAGGATTGGA
391 AGGGAAAAACTAGTCCAAGCCCAACTAGGAAAAGGAAATAAAAGTATAATTAAACAAGGATTGGA
* * *
22904 CTTAGACAAACAAGGCCCAACCCAAATAACATCCAAACTTAAAAATAAGCTAATCTAAGATAGAA
456 CTTAGTCAAACAAGGCCAAATCCAAATAACATCCAAACTTAAAAATAAGCTAATCTAAGATAGAA
*
22969 TTAAGCCCAAACAAAGATAACTGATG-ATATTGGGCTTATGCCACTATGTCAATCCGGCCATTTA
521 TTAAGCCCAAACAAAGATAACTGA-GCATATTGGGCTCATGCCACTATGTCAATCCGGCCATTTA
*
23033 GAATCAATAGCAAGCAAAGTGATGAACTTGTAATTCATTGATGTTTTCTTGCTCAAATCATCATC
585 GAATCAATAGCAAGCAAAGTGATGAACTTGTAATTCATTGGTGTTTTCTTGCTCAAATCATCATC
*
23098 AAAGCTCTTCAATTGAACTTGAATGGTCTTCAAGTCTTCAAGATGAGTTCG-ATAAGGCTCATGA
650 AAAGCTCTTCAATTGAACTTGAATGGTCTTCAAGTCTTCAAGATGAGTTCGAACAAGGCTCATGA
*
23162 GTGCATCCCTGAATCTCTTAGCTCTTGCTCTTGTCATCGGGCTAATAGGAATCTTCAATGAATCG
715 GTGCATCCCTGAATCTCTTAGCTCTTGCTCTTGTCATCGGGCTAATAGGCATCTTCAATGAATCG
* * *
23227 AATAGCATCTTTTTGGTGCTTGGAACATGCTTATCAATATCTCGATAATCTTCTTGCATCTGCAT
780 AATAACATCTTTTTGGTGCTTGGAACATGCTTATCAATATCTCGATAATCTTCATGCATCTCCAT
* * * *
23292 ACTTCCTTGCAGCCCATGCACATCCTTTCCATGCTCTCCATGCTTGTCT-AAGAGACCATGAGAA
845 GCTTCCTTGCAGCCCATGCACATCCTTTCTATGGTCTCCATGCTTGTCTCCA-AGACCATGAGAA
23356 GTCCTTGGACCTCCATGATA
909 GTCCTTGGACCTCCATGATA
*
23376 AAATCTATCCTTGAGACCTGCCAAGAATCTACTTGGACTTCTTCTGCTTGTAGACAAGTATGTCG
1 AAATCTATCCTTGAGACCTGCCAAGAATCTACTTGGACTTCTTCAGCTTGTAGACAAGTATGTCG
*
23441 ACAACCTTCACAAAGCAATCTCTCTTCGTTCGTCGGCCTTAAGTCTTCAATTAGACCTGAAATTG
66 ACAACCTTCACAAAGCAATCTCTCTTCGTTCGTCGGCCTTAAGTCTTCAATTAGACCTGCAATTG
23506 AATAACCTAAGATCACAAGATTCACAAACAATTAAGCATCACACAACCTAATTGTTTGCTAGGAC
131 AATAACCTAAGATCACAAGATTCACAAACAATTAAGCATCACACAACCTAATTGTTTGCTAGGAC
*
23571 TCTACAAGATTGAAGAACCCTAAGTTTCCTCGAACTAGAACAATAAAGCCAAGATATTCAATTTG
196 TCTACAAGATTGAAGAACCCTAAGTTTCCTCGAACTAGAACAATGAAGCCAAGATATTCAATTTG
23636 GGAGAATCAACCTCAATTTTATTAATCAACTCAACTTCCACTTTTACAAGAGATATTCGTGGCCT
261 GGAGAATCAACCTCAATTTTATTAATCAACTCAACTTCCACTTTTACAAGAGATATTCGTGGCCT
23701 TATATAGTGATAGGGTCAACGAAAATCCTAAAATAAATCCTAATTTTCGTCCAAATATAAGGGCT
326 TATATAGTGATAGGGTCAACGAAAATCCTAAAATAAATCCTAATTTTCGTCCAAATATAAGGGCT
23766 AGGGAAAAACTAGTCCAAGCCCAACTAGGAAAAGGAAATAAAAGTATAATTAAACAAGGATTGGA
391 AGGGAAAAACTAGTCCAAGCCCAACTAGGAAAAGGAAATAAAAGTATAATTAAACAAGGATTGGA
23831 CTTAGTCAAACAAGGCCAAATCCAAATAACATCCAAACTTAAAAATAAGCTAATCTAAGATAGAA
456 CTTAGTCAAACAAGGCCAAATCCAAATAACATCCAAACTTAAAAATAAGCTAATCTAAGATAGAA
* *
23896 TTAAACCCAAACAAAGATAACTGAGCATATTGGGCTCATGCCACTACGTCAATCCGGCCATTTAG
521 TTAAGCCCAAACAAAGATAACTGAGCATATTGGGCTCATGCCACTATGTCAATCCGGCCATTTAG
23961 AATCAATAGCAAGCAAAGTGATGAACTTGTAATTCATTGGTGTTTTCTTGCTCAAATCATCATCA
586 AATCAATAGCAAGCAAAGTGATGAACTTGTAATTCATTGGTGTTTTCTTGCTCAAATCATCATCA
24026 AAGCTCTTCAATTGAACTTGAATGGTCTTCAAGTCTTCAAGATGAGTTCGAACAAGGCTCATGAG
651 AAGCTCTTCAATTGAACTTGAATGGTCTTCAAGTCTTCAAGATGAGTTCGAACAAGGCTCATGAG
24091 TGCATCCCTGAATCTCTTAGCTCTTGCTCTTGTCATCGGGCTAATAGGCATCTTCAATGAATCGA
716 TGCATCCCTGAATCTCTTAGCTCTTGCTCTTGTCATCGGGCTAATAGGCATCTTCAATGAATCGA
24156 ATAACATC-TTTTGGTGCTTGGAACATGCTTATCAATATCTCGATAATCTTCATGCATCTCCATG
781 ATAACATCTTTTTGGTGCTTGGAACATGCTTATCAATATCTCGATAATCTTCATGCATCTCCATG
* *
24220 CTTCCTTGCAGTCCATGCACATCCTTTCTATGGTCTCCATGCTTGTCTCCAAGACCAGGAGAAGT
846 CTTCCTTGCAGCCCATGCACATCCTTTCTATGGTCTCCATGCTTGTCTCCAAGACCATGAGAAGT
24285 CCTTGGACCTCCATGATA
911 CCTTGGACCTCCATGATA
24303 AAATCTATCCTTGAGACCTGCCAAGAATCTACTTGGACTTCTTCAGCTTGTAGACAA
1 AAATCTATCCTTGAGACCTGCCAAGAATCTACTTGGACTTCTTCAGCTTGTAGACAA
Statistics
Matches: 1844, Mismatches: 62, Indels: 12
0.96 0.03 0.01
Matches are distributed among these distances:
926 2 0.00
927 1077 0.58
928 470 0.25
929 295 0.16
ACGTcount: A:0.34, C:0.22, G:0.16, T:0.28
Consensus pattern (928 bp):
AAATCTATCCTTGAGACCTGCCAAGAATCTACTTGGACTTCTTCAGCTTGTAGACAAGTATGTCG
ACAACCTTCACAAAGCAATCTCTCTTCGTTCGTCGGCCTTAAGTCTTCAATTAGACCTGCAATTG
AATAACCTAAGATCACAAGATTCACAAACAATTAAGCATCACACAACCTAATTGTTTGCTAGGAC
TCTACAAGATTGAAGAACCCTAAGTTTCCTCGAACTAGAACAATGAAGCCAAGATATTCAATTTG
GGAGAATCAACCTCAATTTTATTAATCAACTCAACTTCCACTTTTACAAGAGATATTCGTGGCCT
TATATAGTGATAGGGTCAACGAAAATCCTAAAATAAATCCTAATTTTCGTCCAAATATAAGGGCT
AGGGAAAAACTAGTCCAAGCCCAACTAGGAAAAGGAAATAAAAGTATAATTAAACAAGGATTGGA
CTTAGTCAAACAAGGCCAAATCCAAATAACATCCAAACTTAAAAATAAGCTAATCTAAGATAGAA
TTAAGCCCAAACAAAGATAACTGAGCATATTGGGCTCATGCCACTATGTCAATCCGGCCATTTAG
AATCAATAGCAAGCAAAGTGATGAACTTGTAATTCATTGGTGTTTTCTTGCTCAAATCATCATCA
AAGCTCTTCAATTGAACTTGAATGGTCTTCAAGTCTTCAAGATGAGTTCGAACAAGGCTCATGAG
TGCATCCCTGAATCTCTTAGCTCTTGCTCTTGTCATCGGGCTAATAGGCATCTTCAATGAATCGA
ATAACATCTTTTTGGTGCTTGGAACATGCTTATCAATATCTCGATAATCTTCATGCATCTCCATG
CTTCCTTGCAGCCCATGCACATCCTTTCTATGGTCTCCATGCTTGTCTCCAAGACCATGAGAAGT
CCTTGGACCTCCATGATA
Done.