Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01008818.1 Corchorus capsularis cultivar CVL-1 contig08839, 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: 14471
ACGTcount: A:0.32, C:0.19, G:0.18, T:0.31
Found at i:1350 original size:17 final size:16
Alignment explanation
Indices: 1328--1362 Score: 52
Period size: 16 Copynumber: 2.1 Consensus size: 16
1318 CGCAATTGGA
1328 AAGAAGAAGGAAGGAAG
1 AAGAAGAA-GAAGGAAG
*
1345 AAGAAGAAGAAGGGAG
1 AAGAAGAAGAAGGAAG
1361 AA
1 AA
1363 CTAGAGAGGC
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
16 9 0.53
17 8 0.47
ACGTcount: A:0.60, C:0.00, G:0.40, T:0.00
Consensus pattern (16 bp):
AAGAAGAAGAAGGAAG
Found at i:3162 original size:2 final size:2
Alignment explanation
Indices: 3151--3202 Score: 97
Period size: 2 Copynumber: 26.5 Consensus size: 2
3141 AATAGTGTCT
3151 CA CA -A CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA
1 CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA
3192 CA CA CA CA CA C
1 CA CA CA CA CA C
3203 TTATTTACCA
Statistics
Matches: 49, Mismatches: 0, Indels: 2
0.96 0.00 0.04
Matches are distributed among these distances:
1 1 0.02
2 48 0.98
ACGTcount: A:0.50, C:0.50, G:0.00, T:0.00
Consensus pattern (2 bp):
CA
Found at i:7701 original size:13 final size:13
Alignment explanation
Indices: 7683--7717 Score: 61
Period size: 13 Copynumber: 2.7 Consensus size: 13
7673 AATCTAAATC
*
7683 TAAAGCAGATTAA
1 TAAAGCAAATTAA
7696 TAAAGCAAATTAA
1 TAAAGCAAATTAA
7709 TAAAGCAAA
1 TAAAGCAAA
7718 CAATAATTAT
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
13 21 1.00
ACGTcount: A:0.60, C:0.09, G:0.11, T:0.20
Consensus pattern (13 bp):
TAAAGCAAATTAA
Found at i:7994 original size:554 final size:537
Alignment explanation
Indices: 6939--8010 Score: 1424
Period size: 554 Copynumber: 2.0 Consensus size: 537
6929 CGTCAGCAAT
*
6939 CATAAAAATAATCCCCAAAAGAACTAACTAAACTAGCTAGGGCAAGTAGGGGTCGAATCCCATAG
1 CATAAAAATAATCCCCAAAAGAACTAACTAAACTAGCTAGGGCAAGTAGGGGTCGAATCCCACAG
** ** * * * *
7004 AGAAGGGTTATAATTGTGAAGGTCTTTTCCAAAGAATATATCTTTTCCAAAAATCACTTAGAAAG
66 AGAAGGGTTATAATTGTGAAGAACAATTCAAAAGAAAAGATCTTTTCCAAAAATCACTTAGAAAC
* * * * * *
7069 AGGGGATTAATTATATCAATTATAAAGAAAACAATTAACCTAAAAATAAAGTAAAGTAAAGTAAA
131 AGGGGATTAATAATAACAATTATAAAGAAAACAATTAAACTAAAAATAAAGCAAAGCAAACTAAA
* * *
7134 TCTAGATCTAAGACAAATTGTAAAGCAAACAATAATTATAAAGCATACTTCTTCTCCGATGGTAT
196 TCTAAATCTAAGACAAATTATAAAGCAAACAATAATTATAAAGCATACTTCTTCACCGATGGTAT
* * * *
7199 GATTCAATCAGATTAACTATGTATCATTGATTTAAAAGGTGAATTTAGCATCTTATTCTTGACTG
261 CATTCAATCAAATTAACTATGGATCATAGATTTAAAAGGTGAATTTAGCATCTTATTCTTGACTG
* * * *
7264 ACAACTGGTATAGGAAATTCCAACATGTATATTAGATAAGAGGCCGATCAAAGCTGTATTTATCC
326 ACAACTGATATAGG-AATTCCAACATGTATATTAGATAAGAGGCCGATCAAAGCTGCAGTTAACC
* * **
7329 CTTTTATTCCTTCAGCAATCGATTACTTTCTCAGGGCTTAAAGATTGCTTGAGAACAAAGCATTA
390 CTATTATTCCTTCAACAATCGATTACTTTCTCAGGGCTTAAAGATCACTTGAGAACAAAGCATTA
* *
7394 AGATCAATTAATTTTACACACATGCCTACAAGTAGAACCATACGAAGAGAAATTTCTCGCCCTTT
455 AGAACAATTAATTTTACACACATGCCTACAAATAGAACCATACGAAGAGAAATTTCTCGCCCTTT
7459 GATCGTGTCGTCTATGAC
520 GATCGTGTCGTCTATGAC
*
7477 CATAAAAATAATCCCCACAAATAACTAACTAGAA-TAGCTAGGGCAAGTAGGGGTCGAATCCCAC
1 CATAAAAATAATCCCCA-AAAGAACTAACTA-AACTAGCTAGGGCAAGTAGGGGTCGAATCCCAC
*
7541 AGAGAA-GGTT-T-A-TGTGATGAACAATT-AAAAGATAGAAAGATCTTTTCCAAAAATCGA-TT
64 AGAGAAGGGTTATAATTGTGAAGAACAATTCAAAAG--A-AAAGATCTTTTCCAAAAATC-ACTT
7600 AGAAAACAGGGGATTAAATAAATAACAATTATAAAGAAAACAATTAAACTAAAAATAAAGCAAAG
125 AG-AAACAGGGGATT-AAT-AATAACAATTATAAAGAAAACAATTAAACTAAAAATAAAGCAAAG
7665 CAAATCTAAATCTAAATCTAAAGCAGATTAATAAAGCAAATTAATAAAGCAAACAATAATTATAA
187 CAAA-CTAAATCTAAATCT--A--AG--------A-CAAATT-ATAAAGCAAACAATAATTATAA
* *
7730 AGCATACTTCTTCACC-AGTGGTATCCTTCAATCAAATTAACTATGGATCCTAGATTTAAAAGGT
237 AGCATACTTCTTCACCGA-TGGTATCATTCAATCAAATTAACTATGGATCATAGATTTAAAAGGT
* * *
7794 GAATTTCGCATCTTATTCTTGACTGACAACTGATATAGG-TTTCCCAACATGTATTTTAGATAAG
301 GAATTTAGCATCTTATTCTTGACTGACAACTGATATAGGAATT-CCAACATGTATATTAGATAAG
* * ** *
7858 AGGCCGATTAGAGCTGCAGTTAACCCTATTATTCCTTCAATGATCGATTACTTTCTTAGGGCTTA
365 AGGCCGATCAAAGCTGCAGTTAACCCTATTATTCCTTCAACAATCGATTACTTTCTCAGGGCTTA
* *
7923 AAGATCACTTGAGAACAAAGCATTAAGAACAGTTAATTTTACACACATGCCTATAAATAGAACCA
430 AAGATCACTTGAGAACAAAGCATTAAGAACAATTAATTTTACACACATGCCTACAAATAGAACCA
7988 TACGAAGAGAAATTTCTCGCCCT
495 TACGAAGAGAAATTTCTCGCCCT
8011 CCGGTAGACA
Statistics
Matches: 462, Mismatches: 46, Indels: 36
0.85 0.08 0.07
Matches are distributed among these distances:
534 4 0.01
535 9 0.02
536 2 0.00
537 23 0.05
538 33 0.07
539 50 0.11
540 46 0.10
541 12 0.03
543 1 0.00
545 2 0.00
553 3 0.01
554 164 0.35
555 113 0.24
ACGTcount: A:0.40, C:0.17, G:0.15, T:0.28
Consensus pattern (537 bp):
CATAAAAATAATCCCCAAAAGAACTAACTAAACTAGCTAGGGCAAGTAGGGGTCGAATCCCACAG
AGAAGGGTTATAATTGTGAAGAACAATTCAAAAGAAAAGATCTTTTCCAAAAATCACTTAGAAAC
AGGGGATTAATAATAACAATTATAAAGAAAACAATTAAACTAAAAATAAAGCAAAGCAAACTAAA
TCTAAATCTAAGACAAATTATAAAGCAAACAATAATTATAAAGCATACTTCTTCACCGATGGTAT
CATTCAATCAAATTAACTATGGATCATAGATTTAAAAGGTGAATTTAGCATCTTATTCTTGACTG
ACAACTGATATAGGAATTCCAACATGTATATTAGATAAGAGGCCGATCAAAGCTGCAGTTAACCC
TATTATTCCTTCAACAATCGATTACTTTCTCAGGGCTTAAAGATCACTTGAGAACAAAGCATTAA
GAACAATTAATTTTACACACATGCCTACAAATAGAACCATACGAAGAGAAATTTCTCGCCCTTTG
ATCGTGTCGTCTATGAC
Found at i:11279 original size:11 final size:11
Alignment explanation
Indices: 11263--11291 Score: 58
Period size: 11 Copynumber: 2.6 Consensus size: 11
11253 GGTGTCGATG
11263 GCCGGGCTGCA
1 GCCGGGCTGCA
11274 GCCGGGCTGCA
1 GCCGGGCTGCA
11285 GCCGGGC
1 GCCGGGC
11292 ATACTGGATT
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 18 1.00
ACGTcount: A:0.07, C:0.38, G:0.48, T:0.07
Consensus pattern (11 bp):
GCCGGGCTGCA
Done.