Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01007229.1 Corchorus capsularis cultivar CVL-1 contig07250, 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: 65597
ACGTcount: A:0.32, C:0.18, G:0.18, T:0.32
Found at i:370 original size:2 final size:2
Alignment explanation
Indices: 365--401 Score: 58
Period size: 2 Copynumber: 19.0 Consensus size: 2
355 TAAAATAATC
*
365 AT AT AT AT AT -T TT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
402 TTCAACACCA
Statistics
Matches: 33, Mismatches: 1, Indels: 2
0.92 0.03 0.06
Matches are distributed among these distances:
1 1 0.03
2 32 0.97
ACGTcount: A:0.46, C:0.00, G:0.00, T:0.54
Consensus pattern (2 bp):
AT
Found at i:703 original size:358 final size:355
Alignment explanation
Indices: 24--724 Score: 837
Period size: 354 Copynumber: 2.0 Consensus size: 355
14 TACTCATAAA
* *
24 ATATATATATTATATATTTTTAAAGCCAAAAAGATTGAAGGGCTTGTTTCACGCTTCTAATATCG
1 ATATATATATTATATATTTTCAAAGCCAAAAAGATTGAAGGGCGTGTTTCACGCTTCTAATATCG
* * * * * *
89 ATTTTTCCATTTTTTTTTTACAAATTAATTTCTAATTAAATCGAAACATGATTCAGATGCTTGTA
66 ATTTTACC--TTATTTTTTACAAATTAATTTATAATTAAATCAAAACAAGATTCAGATGCTCGTA
* * *
154 AAAACAAATTCTTAAATCAATATGACTGAGATTTGATTAGATGAATATGGATATCTTAAGGAGTC
129 AAAACAAATCCTTAAATCAATATGACTGAGATTTGATTAGATGAATATAGATATCTTAAGGAGCC
* * * * * * *
219 TTAGCATCAAAAATAATGCAAAACTGAGTCGGGGCCCTAGAACGCTTTTTTAGCCAAAAACTGTG
194 TTAGCAGCAAAAATAATGCAAAACTGAGACGGCGCCCTAGAACGCGTTTTGAGCCAAAAACCGTA
* ** * *
284 ATGGTTATTATACGATTTCGTCTAAAATTTTGTAAAAATTGACCCGAAAGATATTTCCTCAATTT
259 ATGGTTATTATACGATTTCGGCTAAAATTTTACAAAAATTAACACGAAAGATATTTCCTCAA-TT
349 TTTGGCTAAAATAATCATATATATATTTTATAT
323 TTTGGCTAAAATAATCATATATATATTTTATAT
* * *
382 ATATATATATATATATATATTTCAACA-CCAAAAATATTGAAGGG-GT-TTTGACGTTTCTAATA
1 ATATATATAT-TATATAT-TTTCAA-AGCCAAAAAGATTGAAGGGCGTGTTTCACGCTTCTAATA
* *
444 TC-ATTTTACC-TATTTTTTCCGAATTAATTTAT-ATATAAATCAAAACAAGATTCAGATGCTCG
63 TCGATTTTACCTTATTTTTTACAAATTAATTTATAAT-TAAATCAAAACAAGATTCAGATGCTCG
* * *
506 TAAAAACAAATCCTTAGATCCAATGTGACTGAGATTTGATTAGATGAATATAGATAT-TTCAAGT
127 TAAAAACAAATCCTTAAAT-CAATATGACTGAGATTTGATTAGATGAATATAGATATCTT-AAGG
* * * * * * *
570 AGCCTT-GGAGGCAAAAATCATGCAAAATTGCGACGGCTCCC-CGAACGCGTTTTGAGTCAAAAA
190 AGCCTTAGCA-GCAAAAATAATGCAAAACTGAGACGGCGCCCTAGAACGCGTTTTGAGCCAAAAA
*
633 CCGTAATGGTTAGTTAGTACATGATTTCGGCTAAAATTTTACGAAAATTAACACGAAAGAT-TTC
254 CCGTAATGGTTA-TTA-TAC--GATTTCGGCTAAAATTTTACAAAAATTAACACGAAAGATATT-
*
697 TCCTCAATTTTTGGCTAAAATACTCATA
314 TCCTCAATTTTTGGCTAAAATAATCATA
725 AAAATATATG
Statistics
Matches: 291, Mismatches: 40, Indels: 25
0.82 0.11 0.07
Matches are distributed among these distances:
353 2 0.01
354 91 0.31
355 70 0.24
356 3 0.01
357 29 0.10
358 66 0.23
359 8 0.03
360 21 0.07
361 1 0.00
ACGTcount: A:0.36, C:0.14, G:0.14, T:0.36
Consensus pattern (355 bp):
ATATATATATTATATATTTTCAAAGCCAAAAAGATTGAAGGGCGTGTTTCACGCTTCTAATATCG
ATTTTACCTTATTTTTTACAAATTAATTTATAATTAAATCAAAACAAGATTCAGATGCTCGTAAA
AACAAATCCTTAAATCAATATGACTGAGATTTGATTAGATGAATATAGATATCTTAAGGAGCCTT
AGCAGCAAAAATAATGCAAAACTGAGACGGCGCCCTAGAACGCGTTTTGAGCCAAAAACCGTAAT
GGTTATTATACGATTTCGGCTAAAATTTTACAAAAATTAACACGAAAGATATTTCCTCAATTTTT
GGCTAAAATAATCATATATATATTTTATAT
Found at i:11939 original size:2 final size:2
Alignment explanation
Indices: 11929--11958 Score: 53
Period size: 2 Copynumber: 15.5 Consensus size: 2
11919 CTCACTTTAA
11929 TC TC T- TC TC TC TC TC TC TC TC TC TC TC TC T
1 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC T
11959 TACTTGTTGG
Statistics
Matches: 27, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
1 1 0.04
2 26 0.96
ACGTcount: A:0.00, C:0.47, G:0.00, T:0.53
Consensus pattern (2 bp):
TC
Found at i:12059 original size:1 final size:1
Alignment explanation
Indices: 12055--12079 Score: 50
Period size: 1 Copynumber: 25.0 Consensus size: 1
12045 TCCCCCCAAA
12055 TTTTTTTTTTTTTTTTTTTTTTTTT
1 TTTTTTTTTTTTTTTTTTTTTTTTT
12080 AAATTACAGG
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
1 24 1.00
ACGTcount: A:0.00, C:0.00, G:0.00, T:1.00
Consensus pattern (1 bp):
T
Found at i:20860 original size:2 final size:2
Alignment explanation
Indices: 20853--20881 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
20843 TTAACTAAAT
20853 TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
20882 TTGAGTATAT
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 27 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:28852 original size:6 final size:6
Alignment explanation
Indices: 28841--28891 Score: 59
Period size: 6 Copynumber: 8.5 Consensus size: 6
28831 CGAACACTGG
* * *
28841 CTCCAT CTCCAT CTCCAT ATCCAT ATCCAT CTCC-T CTTCCAT TTCCAT
1 CTCCAT CTCCAT CTCCAT CTCCAT CTCCAT CTCCAT C-TCCAT CTCCAT
28889 CTC
1 CTC
28892 TCTCTAAAAC
Statistics
Matches: 39, Mismatches: 4, Indels: 4
0.83 0.09 0.09
Matches are distributed among these distances:
5 2 0.05
6 36 0.92
7 1 0.03
ACGTcount: A:0.18, C:0.45, G:0.00, T:0.37
Consensus pattern (6 bp):
CTCCAT
Found at i:29281 original size:26 final size:28
Alignment explanation
Indices: 29245--29306 Score: 110
Period size: 28 Copynumber: 2.3 Consensus size: 28
29235 TTTCTTTTTT
29245 GTTTTTGTTTTTG-T-TATAGCGCCCAG
1 GTTTTTGTTTTTGTTATATAGCGCCCAG
29271 GTTTTTGTTTTTGTTATATAGCGCCCAG
1 GTTTTTGTTTTTGTTATATAGCGCCCAG
29299 GTTTTTGT
1 GTTTTTGT
29307 AACGATCCAA
Statistics
Matches: 34, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
26 13 0.38
27 1 0.03
28 20 0.59
ACGTcount: A:0.11, C:0.13, G:0.23, T:0.53
Consensus pattern (28 bp):
GTTTTTGTTTTTGTTATATAGCGCCCAG
Found at i:33676 original size:76 final size:76
Alignment explanation
Indices: 33550--33701 Score: 286
Period size: 76 Copynumber: 2.0 Consensus size: 76
33540 TGGTTAGAAT
* *
33550 CACCCCATATCACTAGTGATCTAAAATTACCAGTGATGTAAGATCACCGGTGATCAAAGATTACA
1 CACCCCATATCACTAGTGATCTAAAATCACCAGTGATGCAAGATCACCGGTGATCAAAGATTACA
33615 TGGGTTTATGG
66 TGGGTTTATGG
33626 CACCCCATATCACTAGTGATCTAAAATCACCAGTGATGCAAGATCACCGGTGATCAAAGATTACA
1 CACCCCATATCACTAGTGATCTAAAATCACCAGTGATGCAAGATCACCGGTGATCAAAGATTACA
33691 TGGGTTTATGG
66 TGGGTTTATGG
33702 TGGTAATCCA
Statistics
Matches: 74, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
76 74 1.00
ACGTcount: A:0.33, C:0.21, G:0.20, T:0.26
Consensus pattern (76 bp):
CACCCCATATCACTAGTGATCTAAAATCACCAGTGATGCAAGATCACCGGTGATCAAAGATTACA
TGGGTTTATGG
Found at i:33685 original size:17 final size:17
Alignment explanation
Indices: 33634--33686 Score: 56
Period size: 17 Copynumber: 3.1 Consensus size: 17
33624 GGCACCCCAT
*
33634 ATCACTAGTGATCTAAA-
1 ATCACCAGTGATC-AAAG
33651 ATCACCAGTGATGC-AAG
1 ATCACCAGTGAT-CAAAG
*
33668 ATCACCGGTGATCAAAG
1 ATCACCAGTGATCAAAG
33685 AT
1 AT
33687 TACATGGGTT
Statistics
Matches: 31, Mismatches: 2, Indels: 6
0.79 0.05 0.15
Matches are distributed among these distances:
16 3 0.10
17 27 0.87
18 1 0.03
ACGTcount: A:0.38, C:0.21, G:0.19, T:0.23
Consensus pattern (17 bp):
ATCACCAGTGATCAAAG
Found at i:34586 original size:31 final size:31
Alignment explanation
Indices: 34551--34643 Score: 85
Period size: 28 Copynumber: 3.2 Consensus size: 31
34541 AGATTAGAAC
34551 AATATTTCATTTGTCATTAAATTATTATTGA
1 AATATTTCATTTGTCATTAAATTATTATTGA
* * *
34582 AATATTATCA--TG--GTTAGATTA-GA---A
1 AATATT-TCATTTGTCATTAAATTATTATTGA
34606 CAATATTTCATTTGTCATTAAATTATTATTGA
1 -AATATTTCATTTGTCATTAAATTATTATTGA
34638 AATATT
1 AATATT
34644 ATCGTGTAAG
Statistics
Matches: 46, Mismatches: 6, Indels: 20
0.64 0.08 0.28
Matches are distributed among these distances:
24 4 0.09
25 6 0.13
26 2 0.04
27 1 0.02
28 14 0.30
29 1 0.02
30 2 0.04
31 12 0.26
32 4 0.09
ACGTcount: A:0.38, C:0.06, G:0.09, T:0.47
Consensus pattern (31 bp):
AATATTTCATTTGTCATTAAATTATTATTGA
Found at i:34594 original size:56 final size:56
Alignment explanation
Indices: 34532--34646 Score: 230
Period size: 56 Copynumber: 2.1 Consensus size: 56
34522 GCTCTTTCTC
34532 ATCATGGTTAGATTAGAACAATATTTCATTTGTCATTAAATTATTATTGAAATATT
1 ATCATGGTTAGATTAGAACAATATTTCATTTGTCATTAAATTATTATTGAAATATT
34588 ATCATGGTTAGATTAGAACAATATTTCATTTGTCATTAAATTATTATTGAAATATT
1 ATCATGGTTAGATTAGAACAATATTTCATTTGTCATTAAATTATTATTGAAATATT
34644 ATC
1 ATC
34647 GTGTAAGCGT
Statistics
Matches: 59, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
56 59 1.00
ACGTcount: A:0.37, C:0.08, G:0.10, T:0.44
Consensus pattern (56 bp):
ATCATGGTTAGATTAGAACAATATTTCATTTGTCATTAAATTATTATTGAAATATT
Found at i:39608 original size:30 final size:31
Alignment explanation
Indices: 39562--39620 Score: 93
Period size: 30 Copynumber: 1.9 Consensus size: 31
39552 ACTCAAATCT
39562 TTTAGTGGGGTCAATATCTTAAAACTTTCAA
1 TTTAGTGGGGTCAATATCTTAAAACTTTCAA
* *
39593 TTTA-TGGGGTTAATATCTTAAAATTTTC
1 TTTAGTGGGGTCAATATCTTAAAACTTTC
39621 TTTGAATTGA
Statistics
Matches: 26, Mismatches: 2, Indels: 1
0.90 0.07 0.03
Matches are distributed among these distances:
30 22 0.85
31 4 0.15
ACGTcount: A:0.31, C:0.10, G:0.15, T:0.44
Consensus pattern (31 bp):
TTTAGTGGGGTCAATATCTTAAAACTTTCAA
Done.