Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01014275.1 Corchorus capsularis cultivar CVL-1 contig14296, 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: 16135
ACGTcount: A:0.34, C:0.17, G:0.15, T:0.35
Warning! 1 characters in sequence are not A, C, G, or T
Found at i:559 original size:46 final size:47
Alignment explanation
Indices: 477--568 Score: 127
Period size: 46 Copynumber: 2.0 Consensus size: 47
467 AATCTTTTAA
477 CCAAACCCCATCCTCTCAAAAGAAAGATAAACCAGATTTGAAGGAAT
1 CCAAACCCCATCCTCTCAAAAGAAAGATAAACCAGATTTGAAGGAAT
* *
524 CCAAA-CCCATCCTCTTAAGAG-AAGAATGAAA-CAGATTTGAAGGAA
1 CCAAACCCCATCCTCTCAAAAGAAAG-AT-AAACCAGATTTGAAGGAA
569 CAATAGAATT
Statistics
Matches: 41, Mismatches: 2, Indels: 5
0.85 0.04 0.10
Matches are distributed among these distances:
45 3 0.07
46 30 0.73
47 8 0.20
ACGTcount: A:0.45, C:0.23, G:0.15, T:0.17
Consensus pattern (47 bp):
CCAAACCCCATCCTCTCAAAAGAAAGATAAACCAGATTTGAAGGAAT
Found at i:4212 original size:14 final size:14
Alignment explanation
Indices: 4178--4212 Score: 54
Period size: 14 Copynumber: 2.6 Consensus size: 14
4168 TTCTTCAATC
*
4178 TTCTTTGTCTTTTT
1 TTCTTTTTCTTTTT
4192 TTCTTTTTCTTTTT
1 TTCTTTTTCTTTTT
4206 TT-TTTTT
1 TTCTTTTT
4213 AAATTTTTCC
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
13 5 0.25
14 15 0.75
ACGTcount: A:0.00, C:0.11, G:0.03, T:0.86
Consensus pattern (14 bp):
TTCTTTTTCTTTTT
Found at i:9878 original size:7 final size:6
Alignment explanation
Indices: 9846--9879 Score: 50
Period size: 6 Copynumber: 5.5 Consensus size: 6
9836 AATTCATATA
*
9846 TATCGT TATCTT TATCTT TATCTT TATTCTT TAT
1 TATCTT TATCTT TATCTT TATCTT TA-TCTT TAT
9880 ATTTTATAAT
Statistics
Matches: 26, Mismatches: 1, Indels: 2
0.90 0.03 0.07
Matches are distributed among these distances:
6 20 0.77
7 6 0.23
ACGTcount: A:0.18, C:0.15, G:0.03, T:0.65
Consensus pattern (6 bp):
TATCTT
Found at i:9970 original size:27 final size:25
Alignment explanation
Indices: 9932--9987 Score: 60
Period size: 26 Copynumber: 2.2 Consensus size: 25
9922 TAAAATATCC
*
9932 TTTTTAATTTTAAATAT-TAAATTTAA
1 TTTTTAAGTTT-AATATGT-AATTTAA
*
9958 TTTTTAAGGTTTAATATGTAATTTTA
1 TTTTTAA-GTTTAATATGTAATTTAA
9984 TTTT
1 TTTT
9988 GAATATATTT
Statistics
Matches: 26, Mismatches: 2, Indels: 4
0.81 0.06 0.12
Matches are distributed among these distances:
26 22 0.85
27 4 0.15
ACGTcount: A:0.34, C:0.00, G:0.05, T:0.61
Consensus pattern (25 bp):
TTTTTAAGTTTAATATGTAATTTAA
Found at i:10385 original size:114 final size:110
Alignment explanation
Indices: 10236--10466 Score: 374
Period size: 110 Copynumber: 2.1 Consensus size: 110
10226 TTGATTTATA
*
10236 TATGTGTAAATCAAGGTAGTTCACGTTTTAATTAAAATTAAAAAAGTGTAAAAACTTTTTTTTAA
1 TATGTGTAAATCAAGGTAGTTCACATTTTAATTAAAATTAAAAAAGTGTAAAAAC----TTTTAA
*
10301 AAAAAATCCTAGATTATTCTATTTTATCGAAATAAAGTACCTAAACATT
62 AAAAAATCCTAGATTATTCTATTTTATCGAAATAAAGTACATAAACATT
*
10350 TATGTGTAGATCAAGGTAGTTCACATTTTAATTAAAATTAAAAAAGTGTAAAAACTTTTAAAAAA
1 TATGTGTAAATCAAGGTAGTTCACATTTTAATTAAAATTAAAAAAGTGTAAAAACTTTTAAAAAA
* *
10415 AATCTTAGATTATTCTATTTTATCGAAATAAAGTACATAAACGTT
66 AATCCTAGATTATTCTATTTTATCGAAATAAAGTACATAAACATT
10460 TAT-TGTA
1 TATGTGTA
10467 CTTGAGTAAG
Statistics
Matches: 112, Mismatches: 5, Indels: 5
0.92 0.04 0.04
Matches are distributed among these distances:
109 4 0.04
110 55 0.49
114 53 0.47
ACGTcount: A:0.43, C:0.09, G:0.10, T:0.38
Consensus pattern (110 bp):
TATGTGTAAATCAAGGTAGTTCACATTTTAATTAAAATTAAAAAAGTGTAAAAACTTTTAAAAAA
AATCCTAGATTATTCTATTTTATCGAAATAAAGTACATAAACATT
Found at i:12688 original size:3 final size:3
Alignment explanation
Indices: 12680--12704 Score: 50
Period size: 3 Copynumber: 8.3 Consensus size: 3
12670 ATATCAAAAT
12680 ATA ATA ATA ATA ATA ATA ATA ATA A
1 ATA ATA ATA ATA ATA ATA ATA ATA A
12705 AATTTGTTGA
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 22 1.00
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.32
Consensus pattern (3 bp):
ATA
Found at i:13861 original size:335 final size:336
Alignment explanation
Indices: 13240--13896 Score: 849
Period size: 335 Copynumber: 1.9 Consensus size: 336
13230 ACAAAAATGC
* * * * ** *
13240 AAGGTTATTGAATTAGTTGTTAATACTATACATCTTTTATGATCATTATAGGTTTTTTAATAACT
1 AAGGTCATTGAATTAGTTGATAATACCATACATCTTTTATAAAAATTATAGGTTTTTCAATAACT
* *
13305 TTTGAGAAAAAAAAGGGTAAATATTCACCATTGATGAAAGTTTAGTCATGTTATTAAGAATGTAA
66 TTTGAGAAAAAAAAGGGTAAATATTCACCATTGATGAAAGTTTACTAATG-T-TT---AATGTAA
* * *
13370 GGATTAGTAAATACAATTTTAATTTACTTTTATAGCTTTTTTAGTAAACTTAAGTAATAAAATTG
126 GGATTAGTAAATACAATTTTAATTAACTTTTATAGCTGTTTCAGTAAACTTAAGTAATAAAATTG
** * ** *
13435 GTAACTTTTATTAATGATAAAAAGTTACTAAACTTAATAAGAACGTGTAAGGTTATTTCAATCTA
191 GTAACTTCCATTAATGATAAAAAGTTACTAAAATTAATAAGAAC-TGTAAAATTACTTCAATCTA
* *
13500 GATAGTACTATAAAGTTTTTCATAACCTTTATAACCTTTTAAGTAATCTTAGATAAGAAAATCAG
255 GATAGAACTATAAAGTTTTCCATAACCTTTATAA-C-TTTAAGTAATCTTAGATAAGAAAATCAG
13565 TACTTTACCTTTATAATAT
318 TACTTTACCTTTATAATAT
* * * *
13584 AAGGTCATTGAATTAGTTGATAGTACCATACCTTTTTTATAAAAATTATAGGTTTTTCAGTAACT
1 AAGGTCATTGAATTAGTTGATAATACCATACATCTTTTATAAAAATTATAGGTTTTTCAATAACT
* * *
13649 TTTGAGAGAAAAAA-GGTAAATCTTTACCATTGATGAAAGTTTACTAATG-TT-AT-TAAGGATT
66 TTTGAGAAAAAAAAGGGTAAATATTCACCATTGATGAAAGTTTACTAATGTTTAATGTAAGGATT
* * *
13710 GGTAAATACAATTTTAA-TAACTTTTATGGGTGTTTCAGTAGATCACTTAAGTAATAAAATTGGT
131 AGTAAATACAATTTTAATTAACTTTTATAGCTGTTTCAGTA-A--ACTTAAGTAATAAAATTGGT
* * * * *
13774 AACTTCCATTATTGATTAAAAGTTACTAAAATTAATAAGGA-TGTAAAATTACTTGAATGTAGAT
193 AACTTCCATTAATGATAAAAAGTTACTAAAATTAATAAGAACTGTAAAATTACTTCAATCTAGAT
*
13838 AGAACTATAATGTTTTCCATAACCTTTATAACTTTAAGTAATCTTAGATAAGAAAATCA
258 AGAACTATAAAGTTTTCCATAACCTTTATAACTTTAAGTAATCTTAGATAAGAAAATCA
13897 ATAACCAATA
Statistics
Matches: 274, Mismatches: 36, Indels: 17
0.84 0.11 0.05
Matches are distributed among these distances:
333 27 0.10
334 19 0.07
335 71 0.26
336 2 0.01
337 55 0.20
340 2 0.01
343 31 0.11
344 67 0.24
ACGTcount: A:0.39, C:0.09, G:0.13, T:0.39
Consensus pattern (336 bp):
AAGGTCATTGAATTAGTTGATAATACCATACATCTTTTATAAAAATTATAGGTTTTTCAATAACT
TTTGAGAAAAAAAAGGGTAAATATTCACCATTGATGAAAGTTTACTAATGTTTAATGTAAGGATT
AGTAAATACAATTTTAATTAACTTTTATAGCTGTTTCAGTAAACTTAAGTAATAAAATTGGTAAC
TTCCATTAATGATAAAAAGTTACTAAAATTAATAAGAACTGTAAAATTACTTCAATCTAGATAGA
ACTATAAAGTTTTCCATAACCTTTATAACTTTAAGTAATCTTAGATAAGAAAATCAGTACTTTAC
CTTTATAATAT
Found at i:14605 original size:21 final size:20
Alignment explanation
Indices: 14572--14615 Score: 52
Period size: 21 Copynumber: 2.1 Consensus size: 20
14562 GTGGAAAGCA
*
14572 TTATAGCTATTTTAATAACTT
1 TTATAACTATTTTAATAA-TT
* *
14593 TTATAACTTTTTTAGTAATT
1 TTATAACTATTTTAATAATT
14613 TTA
1 TTA
14616 GATTACAAGA
Statistics
Matches: 20, Mismatches: 3, Indels: 1
0.83 0.12 0.04
Matches are distributed among these distances:
20 5 0.25
21 15 0.75
ACGTcount: A:0.32, C:0.07, G:0.05, T:0.57
Consensus pattern (20 bp):
TTATAACTATTTTAATAATT
Found at i:14708 original size:2 final size:2
Alignment explanation
Indices: 14701--14732 Score: 64
Period size: 2 Copynumber: 16.0 Consensus size: 2
14691 TGATTAGGAC
14701 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
14733 ATCTTCACAA
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 30 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:14917 original size:21 final size:21
Alignment explanation
Indices: 14892--14933 Score: 59
Period size: 21 Copynumber: 2.0 Consensus size: 21
14882 CTTATAATAC
14892 TATAACATTTTCTA-TAACCTT
1 TATAAC-TTTTCTAGTAACCTT
*
14913 TATAACTTTTTTAGTAACCTT
1 TATAACTTTTCTAGTAACCTT
14934 AAAGAAGAAC
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
20 6 0.32
21 13 0.68
ACGTcount: A:0.31, C:0.17, G:0.02, T:0.50
Consensus pattern (21 bp):
TATAACTTTTCTAGTAACCTT
Done.