Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01009731.1 Corchorus capsularis cultivar CVL-1 contig09752, 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: 111450
ACGTcount: A:0.33, C:0.18, G:0.17, T:0.32
Warning! 1 characters in sequence are not A, C, G, or T
Found at i:77 original size:29 final size:29
Alignment explanation
Indices: 35--91 Score: 96
Period size: 29 Copynumber: 2.0 Consensus size: 29
25 AACTCTTGCT
* *
35 TGTTTTTGAACAATTGACAAAACAATAAC
1 TGTTTTTAAACAATGGACAAAACAATAAC
64 TGTTTTTAAACAATGGACAAAACAATAA
1 TGTTTTTAAACAATGGACAAAACAATAA
92 TAAAAAACTA
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
29 26 1.00
ACGTcount: A:0.47, C:0.12, G:0.11, T:0.30
Consensus pattern (29 bp):
TGTTTTTAAACAATGGACAAAACAATAAC
Found at i:386 original size:170 final size:173
Alignment explanation
Indices: 64--394 Score: 472
Period size: 170 Copynumber: 1.9 Consensus size: 173
54 AAACAATAAC
64 TGTTTTTAAACAATGGACAAAACAATAATAAAAAACTATTTTAAACAAAGAAAATTATAACTTAT
1 TGTTTTTAAACAATGGACAAAACAATAATAAAAAACTATTTTAAACAAAG--AA-TATAACTTAT
* *
129 AAGCCCCTACGGGGTGGTATAGTGGCAGGAAGCCGAGTGTAAGGTTCCTATAGGTGTGATCATGG
63 AAGCCCCTACGGGGTGGTATAGTGGCAGGAAGCCGAGTGTAAGGTTCCTACAGGTGCGATCATGG
*
194 GTTCGAGTTTGAATAAACACAATGTTTTCTCACATAGATTCTTTCT
128 GTTCGAGTCTGAATAAACACAATGTTTTCTCACATAGATTCTTTCT
* *
240 TGTTTTTGAACAATTGACAAAACAATAATAAAAAACTATTTTAAACAAAG-A-A-AA-TTATAAG
1 TGTTTTTAAACAATGGACAAAACAATAATAAAAAACTATTTTAAACAAAGAATATAACTTATAAG
* * * * * *
301 CCCTTACGGGGGTGGTTTAGTGGCAGGAAGTCGAGTGTAAGGTTCTTGCAGGTGCGGTCATGGGT
66 CCCCTAC-GGGGTGGTATAGTGGCAGGAAGCCGAGTGTAAGGTTCCTACAGGTGCGATCATGGGT
* * *
366 TTGAGTCTGAGTTAACACAATGTTTTCTC
130 TCGAGTCTGAATAAACACAATGTTTTCTC
395 GGTTTAGTGG
Statistics
Matches: 140, Mismatches: 14, Indels: 8
0.86 0.09 0.05
Matches are distributed among these distances:
169 13 0.09
170 77 0.55
171 1 0.01
173 1 0.01
176 48 0.34
ACGTcount: A:0.34, C:0.14, G:0.21, T:0.31
Consensus pattern (173 bp):
TGTTTTTAAACAATGGACAAAACAATAATAAAAAACTATTTTAAACAAAGAATATAACTTATAAG
CCCCTACGGGGTGGTATAGTGGCAGGAAGCCGAGTGTAAGGTTCCTACAGGTGCGATCATGGGTT
CGAGTCTGAATAAACACAATGTTTTCTCACATAGATTCTTTCT
Found at i:453 original size:81 final size:81
Alignment explanation
Indices: 314--475 Score: 234
Period size: 81 Copynumber: 2.0 Consensus size: 81
304 TTACGGGGGT
* * * * * * *
314 GGTTTAGTGGCAGGAAGTCGAGTGTAAGGTTCTTGCAGGTGCGGTCATGGGTTTGAGTCTGAGTT
1 GGTTTAGTGGCAGGAAGCCGAGTGTAAAGTTCCTGCAGGTGCGATCATAGGTTCGAGTCTGAGTA
379 AACACAATGTTTTCTC
66 AACACAATGTTTTCTC
* *
395 GGTTTAGTGGCAGGAAGCCGAGTGTAAAGTTCCTGCATGTGTGATCATAGGTTCGAGTCTGAGTA
1 GGTTTAGTGGCAGGAAGCCGAGTGTAAAGTTCCTGCAGGTGCGATCATAGGTTCGAGTCTGAGTA
*
460 AACGCAATGTTTTCTC
66 AACACAATGTTTTCTC
476 ACATAGACTC
Statistics
Matches: 71, Mismatches: 10, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
81 71 1.00
ACGTcount: A:0.22, C:0.15, G:0.31, T:0.32
Consensus pattern (81 bp):
GGTTTAGTGGCAGGAAGCCGAGTGTAAAGTTCCTGCAGGTGCGATCATAGGTTCGAGTCTGAGTA
AACACAATGTTTTCTC
Found at i:633 original size:248 final size:251
Alignment explanation
Indices: 148--641 Score: 805
Period size: 248 Copynumber: 2.0 Consensus size: 251
138 CGGGGTGGTA
* * * *
148 TAGTGGCAGGAAGCCGAGTGTAAGGTTCCTATAGGTGTGATCATGGGTTCGAGTTTGAATAAACA
1 TAGTGGCAGGAAGCCGAGTGTAAAGTTCCTACAGGTGTGATCATAGGTTCGAGTCTGAATAAACA
*
213 CAATGTTTTCTCACATAGATTCTTTCTTGTTTTTGAACAATTGACAAAACAATAATAAAAAACTA
66 CAATGTTTTCTCACATAGACTCTTTCTTGTTTTTGAACAATTGACAAAACAATAATAAAAAACTA
* *
278 TTTTAAACAAAGAAAATTATAAGCCCTTACGGGGGTGGTTTAGTGGCAGGAAGTCGAGTGTAAGG
131 TTTTAAACAAAGAAAATTATAAGCCCCTACGGGGGTGGTTTAGTGACAGGAAGTCGAGTGTAAGG
* * *
343 TTCTTGCAGGTGCGGTCATGGGTTTGAGTCTGAGTTAACACAATGTTTTCTCGGTT
196 TTCCTGCAGGTGCGGTCATGGGTTCGAGTCTGAGTAAACACAATGTTTTCTCGGTT
* * * *
399 TAGTGGCAGGAAGCCGAGTGTAAAGTTCCTGCATGTGTGATCATAGGTTCGAGTCTGAGTAAACG
1 TAGTGGCAGGAAGCCGAGTGTAAAGTTCCTACAGGTGTGATCATAGGTTCGAGTCTGAATAAACA
*
464 CAATGTTTTCTCACATAGACTC-TT-TTGTTTTTGAACAATTTACAAAACAATAATAAAAAACTA
66 CAATGTTTTCTCACATAGACTCTTTCTTGTTTTTGAACAATTGACAAAACAATAATAAAAAACTA
*
527 TTTTAAACAAAGAAAATTATAAGCCCCTGC-GGGGTGGTTTAGTGACAGGAAGTCGAGTGTAAGG
131 TTTTAAACAAAGAAAATTATAAGCCCCTACGGGGGTGGTTTAGTGACAGGAAGTCGAGTGTAAGG
* *
591 TTCCTGCAGGTGTGGTCATGTGTTCGAGTCTGAGTAAACACAATGTTTTCT
196 TTCCTGCAGGTGCGGTCATGGGTTCGAGTCTGAGTAAACACAATGTTTTCT
642 GGCATAGATT
Statistics
Matches: 225, Mismatches: 18, Indels: 3
0.91 0.07 0.01
Matches are distributed among these distances:
248 79 0.35
249 66 0.29
250 2 0.01
251 78 0.35
ACGTcount: A:0.30, C:0.14, G:0.24, T:0.32
Consensus pattern (251 bp):
TAGTGGCAGGAAGCCGAGTGTAAAGTTCCTACAGGTGTGATCATAGGTTCGAGTCTGAATAAACA
CAATGTTTTCTCACATAGACTCTTTCTTGTTTTTGAACAATTGACAAAACAATAATAAAAAACTA
TTTTAAACAAAGAAAATTATAAGCCCCTACGGGGGTGGTTTAGTGACAGGAAGTCGAGTGTAAGG
TTCCTGCAGGTGCGGTCATGGGTTCGAGTCTGAGTAAACACAATGTTTTCTCGGTT
Found at i:728 original size:169 final size:167
Alignment explanation
Indices: 395--812 Score: 640
Period size: 167 Copynumber: 2.5 Consensus size: 167
385 ATGTTTTCTC
* * *
395 GGTTTAGTGGCAGGAAGCCGAGTGTAAAGTTCCTGCATGTGTGATCATAGGTTCGAGTCTGAGTA
1 GGTTTAGTGGCAGGAAGTCGAGTGTAAGGTTCCTGCAGGTGTGATCAT-GGTTCGAGTCTGAGTA
* * *
460 AACGCAATGTTTTCTCACATAGACTCTTTTGTTTTTGAACAATTTACAAAACAATAATAAAAAAC
65 AACGCAATGTTTTCTCACATAGACTCTTTCGTTTTCGAACAATTGACAAAACAATAATAAAAAAC
525 TATTTTAAACAAAGAAAATTATAAGCCCCTGC-GGGGT
130 TATTTTAAACAAAGAAAATTATAAGCCCCTGCGGGGGT
* *
562 GGTTTAGTGACAGGAAGTCGAGTGTAAGGTTCCTGCAGGTGTGGTCATGTGTTCGAGTCTGAGTA
1 GGTTTAGTGGCAGGAAGTCGAGTGTAAGGTTCCTGCAGGTGTGATCATG-GTTCGAGTCTGAGTA
* ** *
627 AACACAATGTTTTCTGGCATAGATTCTTGCTCGTTTTCGAACAATTGACAAAACAATAATAAAAA
65 AACGCAATGTTTTCTCACATAGACTCTT--TCGTTTTCGAACAATTGACAAAACAATAATAAAAA
692 ACTATTTTAAACAAAGAAAATTATAAGCCCCTGCGGGGGT
128 ACTATTTTAAACAAAGAAAATTATAAGCCCCTGCGGGGGT
* * * *
732 GGCTTAGTGGCAGGAAGTCGAGTGTAAGGTTCCTGCAGGTGTGACCATGGTTTCGAATCTGAATA
1 GGTTTAGTGGCAGGAAGTCGAGTGTAAGGTTCCTGCAGGTGTGATCATGG-TTCGAGTCTGAGTA
797 AACGCAATGTTTTCTC
65 AACGCAATGTTTTCTC
813 GGCTTAGTAG
Statistics
Matches: 226, Mismatches: 20, Indels: 7
0.89 0.08 0.03
Matches are distributed among these distances:
166 1 0.00
167 82 0.36
169 67 0.30
170 76 0.34
ACGTcount: A:0.31, C:0.16, G:0.23, T:0.30
Consensus pattern (167 bp):
GGTTTAGTGGCAGGAAGTCGAGTGTAAGGTTCCTGCAGGTGTGATCATGGTTCGAGTCTGAGTAA
ACGCAATGTTTTCTCACATAGACTCTTTCGTTTTCGAACAATTGACAAAACAATAATAAAAAACT
ATTTTAAACAAAGAAAATTATAAGCCCCTGCGGGGGT
Found at i:848 original size:418 final size:422
Alignment explanation
Indices: 64--902 Score: 1276
Period size: 418 Copynumber: 2.0 Consensus size: 422
54 AAACAATAAC
64 TGTTTTTAAACAATGGACAAAACAATAATAAAAAACTATTTTAAACAAAGAAAATTATAACTTAT
1 TGTTTTTAAACAATGGACAAAACAATAATAAAAAACTATTTTAAACAAAG--AA-TATAACTTAT
* *
129 AAGCCCCTACGGGGTGGTATAGTGGCAGGAAGCCGAGTGTAAGGTTCCTATAGGTGTGATCATGG
63 AAGCCCCTACGGGGTGGTATAGTGACAGGAAGCCGAGTGTAAGGTTCCTACAGGTGTGATCATGG
* * * *
194 GTTCGAGTTTGAATAAACACAATGTTTTCTCACATAGATTCTTTCTTGTTTTTGAACAATTGACA
128 GTTCGAGTCTGAATAAACACAATGTTTTCTCACATAGATTCTTGCTCGTTTTCGAACAATTGACA
* *
259 AAACAATAATAAAAAACTATTTTAAACAAAGAAAATTATAAGCCCTTACGGGGGTGGTTTAGTGG
193 AAACAATAATAAAAAACTATTTTAAACAAAGAAAATTATAAGCCCCTACGGGGGTGGCTTAGTGG
* ** * * *
324 CAGGAAGTCGAGTGTAAGGTTCTTGCAGGTGCGGTCATGGGTTTGAGTCTGAGTTAACACAATGT
258 CAGGAAGTCGAGTGTAAGGTTCCTGCAGGTGCGACCATGGGTTTGAATCTGAATAAACACAATGT
* * * *
389 TTTCTCGGTTTAGTGGCAGGAAGCCGAGTGTAAAGTTCCTGCATGTGTGATCATAGG-TTCGAGT
323 TTTCTCGGCTTAGTAGCAAGAAGCCGAGTGTAAAGTTCCTGCAGGTGTGATCAT-GGATTCGAGT
453 CTGAGTAAACGCAATGTTTTCTCACATAGACTCTTT
387 CTGAGTAAACGCAATGTTTTCTCACATAGACTCTTT
* **
489 TGTTTTTGAACAATTTACAAAACAATAATAAAAAACTATTTTAAACAAAG-A-A-AA-TTATAAG
1 TGTTTTTAAACAATGGACAAAACAATAATAAAAAACTATTTTAAACAAAGAATATAACTTATAAG
* * * * * *
550 CCCCTGCGGGGTGGTTTAGTGACAGGAAGTCGAGTGTAAGGTTCCTGCAGGTGTGGTCATGTGTT
66 CCCCTACGGGGTGGTATAGTGACAGGAAGCCGAGTGTAAGGTTCCTACAGGTGTGATCATGGGTT
* **
615 CGAGTCTGAGTAAACACAATGTTTTCTGGCATAGATTCTTGCTCGTTTTCGAACAATTGACAAAA
131 CGAGTCTGAATAAACACAATGTTTTCTCACATAGATTCTTGCTCGTTTTCGAACAATTGACAAAA
*
680 CAATAATAAAAAACTATTTTAAACAAAGAAAATTATAAGCCCCTGCGGGGGTGGCTTAGTGGCAG
196 CAATAATAAAAAACTATTTTAAACAAAGAAAATTATAAGCCCCTACGGGGGTGGCTTAGTGGCAG
* *
745 GAAGTCGAGTGTAAGGTTCCTGCAGGTGTGACCAT-GGTTTCGAATCTGAATAAACGCAATGTTT
261 GAAGTCGAGTGTAAGGTTCCTGCAGGTGCGACCATGGGTTT-GAATCTGAATAAACACAATGTTT
*
809 TCTCGGCTTAGTAGCAAGAAGCCGAGTGTAAGGTTCCTGCAGGTGTGATCATGGATTCGAGTCTG
325 TCTCGGCTTAGTAGCAAGAAGCCGAGTGTAAAGTTCCTGCAGGTGTGATCATGGATTCGAGTCTG
*
874 AGTAAATGCAATGTTTTCTCACATAGACT
390 AGTAAACGCAATGTTTTCTCACATAGACT
903 TTTGCTTGTC
Statistics
Matches: 377, Mismatches: 35, Indels: 11
0.89 0.08 0.03
Matches are distributed among these distances:
417 7 0.02
418 319 0.85
419 2 0.01
420 1 0.00
422 1 0.00
425 47 0.12
ACGTcount: A:0.32, C:0.15, G:0.23, T:0.30
Consensus pattern (422 bp):
TGTTTTTAAACAATGGACAAAACAATAATAAAAAACTATTTTAAACAAAGAATATAACTTATAAG
CCCCTACGGGGTGGTATAGTGACAGGAAGCCGAGTGTAAGGTTCCTACAGGTGTGATCATGGGTT
CGAGTCTGAATAAACACAATGTTTTCTCACATAGATTCTTGCTCGTTTTCGAACAATTGACAAAA
CAATAATAAAAAACTATTTTAAACAAAGAAAATTATAAGCCCCTACGGGGGTGGCTTAGTGGCAG
GAAGTCGAGTGTAAGGTTCCTGCAGGTGCGACCATGGGTTTGAATCTGAATAAACACAATGTTTT
CTCGGCTTAGTAGCAAGAAGCCGAGTGTAAAGTTCCTGCAGGTGTGATCATGGATTCGAGTCTGA
GTAAACGCAATGTTTTCTCACATAGACTCTTT
Found at i:868 original size:81 final size:81
Alignment explanation
Indices: 732--893 Score: 252
Period size: 81 Copynumber: 2.0 Consensus size: 81
722 CTGCGGGGGT
* * * *
732 GGCTTAGTGGCAGGAAGTCGAGTGTAAGGTTCCTGCAGGTGTGACCATGGTTTCGAATCTGAATA
1 GGCTTAGTAGCAAGAAGCCGAGTGTAAGGTTCCTGCAGGTGTGACCATGGATTCGAATCTGAATA
797 AACGCAATGTTTTCTC
66 AACGCAATGTTTTCTC
* * *
813 GGCTTAGTAGCAAGAAGCCGAGTGTAAGGTTCCTGCAGGTGTGATCATGGATTCGAGTCTGAGTA
1 GGCTTAGTAGCAAGAAGCCGAGTGTAAGGTTCCTGCAGGTGTGACCATGGATTCGAATCTGAATA
*
878 AATGCAATGTTTTCTC
66 AACGCAATGTTTTCTC
894 ACATAGACTT
Statistics
Matches: 73, Mismatches: 8, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
81 73 1.00
ACGTcount: A:0.24, C:0.17, G:0.30, T:0.30
Consensus pattern (81 bp):
GGCTTAGTAGCAAGAAGCCGAGTGTAAGGTTCCTGCAGGTGTGACCATGGATTCGAATCTGAATA
AACGCAATGTTTTCTC
Found at i:942 original size:42 final size:42
Alignment explanation
Indices: 883--962 Score: 142
Period size: 42 Copynumber: 1.9 Consensus size: 42
873 GAGTAAATGC
*
883 AATGTTTTCTCACATAGACTTTTGCTTGTCCCCTCCCTACAT
1 AATGTTTTCTCACATAGACTCTTGCTTGTCCCCTCCCTACAT
*
925 AATGTTTTTTCACATAGACTCTTGCTTGTCCCCTCCCT
1 AATGTTTTCTCACATAGACTCTTGCTTGTCCCCTCCCT
963 GTGTTAAGAT
Statistics
Matches: 36, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
42 36 1.00
ACGTcount: A:0.17, C:0.31, G:0.10, T:0.41
Consensus pattern (42 bp):
AATGTTTTCTCACATAGACTCTTGCTTGTCCCCTCCCTACAT
Found at i:5115 original size:26 final size:26
Alignment explanation
Indices: 5065--5116 Score: 70
Period size: 26 Copynumber: 2.0 Consensus size: 26
5055 TTAGTAGAAT
*
5065 AATTGTAAAAGTTTATTTCTAAAAAA
1 AATTGTAAAAGTATATTTCTAAAAAA
5091 AATTGTAAAAGAATATATTT-TAAAAA
1 AATTGTAAAAG--TATATTTCTAAAAA
5117 TTCTAATATG
Statistics
Matches: 23, Mismatches: 1, Indels: 3
0.85 0.04 0.11
Matches are distributed among these distances:
26 11 0.48
27 6 0.26
28 6 0.26
ACGTcount: A:0.54, C:0.02, G:0.08, T:0.37
Consensus pattern (26 bp):
AATTGTAAAAGTATATTTCTAAAAAA
Found at i:5802 original size:2 final size:2
Alignment explanation
Indices: 5795--5859 Score: 62
Period size: 2 Copynumber: 33.0 Consensus size: 2
5785 CTCGTACTTT
* * *
5795 TA TA TA TA GTA TA GA TA TA TA TA TA TA TA TA TA TA TT TT TA TA
1 TA TA TA TA -TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
* *
5838 TA TA T- TA TT TA T- TA TT TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA
5860 ATAATAATGG
Statistics
Matches: 52, Mismatches: 8, Indels: 6
0.79 0.12 0.09
Matches are distributed among these distances:
1 2 0.04
2 48 0.92
3 2 0.04
ACGTcount: A:0.42, C:0.00, G:0.03, T:0.55
Consensus pattern (2 bp):
TA
Found at i:12852 original size:4 final size:4
Alignment explanation
Indices: 12843--12869 Score: 54
Period size: 4 Copynumber: 6.8 Consensus size: 4
12833 CCAAAAAGGA
12843 AAAG AAAG AAAG AAAG AAAG AAAG AAA
1 AAAG AAAG AAAG AAAG AAAG AAAG AAA
12870 CCCACCAGAG
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 23 1.00
ACGTcount: A:0.78, C:0.00, G:0.22, T:0.00
Consensus pattern (4 bp):
AAAG
Found at i:18990 original size:31 final size:30
Alignment explanation
Indices: 18901--18977 Score: 113
Period size: 29 Copynumber: 2.6 Consensus size: 30
18891 ATACTGTACA
18901 GGTCCCTCTACTTACAAAAA-TGAATCAATTT
1 GGTCCCTCTACTTACAAAAACTG--TCAATTT
*
18932 GGTCCCCCTAC-TACAAAAACTGTCAATTT
1 GGTCCCTCTACTTACAAAAACTGTCAATTT
18961 GGTCCCTCTACTTACAA
1 GGTCCCTCTACTTACAA
18978 TTTATTGTCA
Statistics
Matches: 42, Mismatches: 2, Indels: 5
0.86 0.04 0.10
Matches are distributed among these distances:
29 17 0.40
30 13 0.31
31 12 0.29
ACGTcount: A:0.31, C:0.29, G:0.10, T:0.30
Consensus pattern (30 bp):
GGTCCCTCTACTTACAAAAACTGTCAATTT
Found at i:19638 original size:12 final size:13
Alignment explanation
Indices: 19606--19640 Score: 54
Period size: 13 Copynumber: 2.8 Consensus size: 13
19596 GAGTTTTGCT
19606 ACTTGACCCTCCA
1 ACTTGACCCTCCA
*
19619 ATTTGACCCTCC-
1 ACTTGACCCTCCA
19631 ACTTGACCCT
1 ACTTGACCCT
19641 ACTGATGTGT
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
12 9 0.45
13 11 0.55
ACGTcount: A:0.20, C:0.43, G:0.09, T:0.29
Consensus pattern (13 bp):
ACTTGACCCTCCA
Found at i:23450 original size:21 final size:22
Alignment explanation
Indices: 23406--23451 Score: 58
Period size: 21 Copynumber: 2.1 Consensus size: 22
23396 ATTATAATCA
* *
23406 GACAATTTCATCAATTTGGGATT
1 GACAATTTCA-CAAATTAGGATT
23429 GACAATTTCA-AAATTAGGATT
1 GACAATTTCACAAATTAGGATT
23450 GA
1 GA
23452 GGAATCAAAT
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
21 11 0.52
23 10 0.48
ACGTcount: A:0.37, C:0.11, G:0.17, T:0.35
Consensus pattern (22 bp):
GACAATTTCACAAATTAGGATT
Found at i:36953 original size:13 final size:13
Alignment explanation
Indices: 36935--36973 Score: 51
Period size: 16 Copynumber: 2.8 Consensus size: 13
36925 TTAAAGAGAA
36935 GCAAGATGTGTTT
1 GCAAGATGTGTTT
36948 GCAAGATTTGGTGTTT
1 GCAAGA--T-GTGTTT
36964 GCAAGATGTG
1 GCAAGATGTG
36974 CAGCAAATAC
Statistics
Matches: 23, Mismatches: 0, Indels: 6
0.79 0.00 0.21
Matches are distributed among these distances:
13 9 0.39
14 1 0.04
15 1 0.04
16 12 0.52
ACGTcount: A:0.23, C:0.08, G:0.33, T:0.36
Consensus pattern (13 bp):
GCAAGATGTGTTT
Found at i:38868 original size:50 final size:47
Alignment explanation
Indices: 38808--38905 Score: 160
Period size: 50 Copynumber: 2.0 Consensus size: 47
38798 ACATCCAGAT
*
38808 TCTGCATTGCATAATCAAAGTCGAGTTGATTGAAAACATAAACAAAATTA
1 TCTGCATTGCATAATCAAAAT-GAGTTGATTGAAAACAT--ACAAAATTA
38858 TCTGCATTGCATAATCAAAATGAGTTGATTGAAAACATACAAAATTA
1 TCTGCATTGCATAATCAAAATGAGTTGATTGAAAACATACAAAATTA
38905 T
1 T
38906 ATATAATGAC
Statistics
Matches: 47, Mismatches: 1, Indels: 3
0.92 0.02 0.06
Matches are distributed among these distances:
47 10 0.21
49 17 0.36
50 20 0.43
ACGTcount: A:0.44, C:0.13, G:0.13, T:0.30
Consensus pattern (47 bp):
TCTGCATTGCATAATCAAAATGAGTTGATTGAAAACATACAAAATTA
Found at i:51415 original size:60 final size:60
Alignment explanation
Indices: 51317--51477 Score: 270
Period size: 60 Copynumber: 2.7 Consensus size: 60
51307 GCTAATTGCT
* * *
51317 CAAATAAGGGTCTAACGTTTGTC-AAAATGCTCAAATAAGGGTCCGATCTTTTAATTTGGC
1 CAAATAAGGGCCTAACG-TTATCGAAAATGCTCAAATAAGGGTCCGATCTTTTAATTTAGC
*
51377 CAAAAAAGGGCCTAACGTTATCGAAAATGCTCAAATAAGGGTCCGATCTTTTAATTTAGC
1 CAAATAAGGGCCTAACGTTATCGAAAATGCTCAAATAAGGGTCCGATCTTTTAATTTAGC
51437 CAAATAAGGGCCTAACGTTATCGAAAATGCTCAAATAAGGG
1 CAAATAAGGGCCTAACGTTATCGAAAATGCTCAAATAAGGG
51478 CCCGGTGTCA
Statistics
Matches: 95, Mismatches: 5, Indels: 2
0.93 0.05 0.02
Matches are distributed among these distances:
59 4 0.04
60 91 0.96
ACGTcount: A:0.36, C:0.17, G:0.20, T:0.27
Consensus pattern (60 bp):
CAAATAAGGGCCTAACGTTATCGAAAATGCTCAAATAAGGGTCCGATCTTTTAATTTAGC
Found at i:51441 original size:29 final size:28
Alignment explanation
Indices: 51348--51446 Score: 83
Period size: 29 Copynumber: 3.4 Consensus size: 28
51338 TCAAAATGCT
51348 CAAATAAGGGTCCGATCTTTTAATTTGGC
1 CAAATAAGGGTCCGATCTTTTAATTT-GC
* * * * **
51377 CAAAAAAGGG-CCTAACGTTATCGAAAATGC
1 CAAATAAGGGTCCGATC-TT-T-TAATTTGC
51407 TCAAATAAGGGTCCGATCTTTTAATTTAGC
1 -CAAATAAGGGTCCGATCTTTTAATTT-GC
51437 CAAATAAGGG
1 CAAATAAGGG
51447 CCTAACGTTA
Statistics
Matches: 52, Mismatches: 12, Indels: 12
0.68 0.16 0.16
Matches are distributed among these distances:
28 4 0.08
29 24 0.46
30 6 0.12
31 14 0.27
32 4 0.08
ACGTcount: A:0.35, C:0.17, G:0.20, T:0.27
Consensus pattern (28 bp):
CAAATAAGGGTCCGATCTTTTAATTTGC
Found at i:51475 original size:31 final size:30
Alignment explanation
Indices: 51313--51479 Score: 105
Period size: 31 Copynumber: 5.5 Consensus size: 30
51303 CTTGGCTAAT
*
51313 TGCTCAAATAAGGGTCTAACGTTT-GTCAAAA
1 TGCTCAAATAAGGGCCTAACGTTTCG--AAAA
* * * **
51344 TGCTCAAATAAGGGTCCGATC-TTT-TAATT
1 TGCTCAAATAAGGG-CCTAACGTTTCGAAAA
*
51373 TGGC-CAAAAAAGGGCCTAACGTTATCGAAAA
1 T-GCTCAAATAAGGGCCTAACGTT-TCGAAAA
* * * **
51404 TGCTCAAATAAGGGTCCGATC-TTT-TAATT
1 TGCTCAAATAAGGG-CCTAACGTTTCGAAAA
51433 TAGC-CAAATAAGGGCCTAACGTTATCGAAAA
1 T-GCTCAAATAAGGGCCTAACGTT-TCGAAAA
51464 TGCTCAAATAAGGGCC
1 TGCTCAAATAAGGGCC
51480 CGGTGTCAGT
Statistics
Matches: 101, Mismatches: 23, Indels: 24
0.68 0.16 0.16
Matches are distributed among these distances:
28 8 0.08
29 29 0.29
30 11 0.11
31 46 0.46
32 7 0.07
ACGTcount: A:0.35, C:0.19, G:0.20, T:0.27
Consensus pattern (30 bp):
TGCTCAAATAAGGGCCTAACGTTTCGAAAA
Found at i:51542 original size:31 final size:29
Alignment explanation
Indices: 51507--51611 Score: 97
Period size: 31 Copynumber: 3.5 Consensus size: 29
51497 ACTCGTGAGA
51507 TAGGCCCTTATTTGAGCATTTTGGCAAATGT
1 TAGGCCCTTATTTGAGCATTTT-GCAAA-GT
** *
51538 TAGGCCCTTATTT-AGCCAAATT-CAAAGG
1 TAGGCCCTTATTTGAG-CATTTTGCAAAGT
*
51566 TGGGACCCTTATTTGAGCATTTTAGCAAACGT
1 TAGG-CCCTTATTTGAGCATTTT-GCAAA-GT
*
51598 TAAGCCCTTATTTG
1 TAGGCCCTTATTTG
51612 GCCAAATTAA
Statistics
Matches: 59, Mismatches: 9, Indels: 12
0.74 0.11 0.15
Matches are distributed among these distances:
28 4 0.07
29 17 0.29
30 4 0.07
31 31 0.53
32 3 0.05
ACGTcount: A:0.26, C:0.19, G:0.20, T:0.35
Consensus pattern (29 bp):
TAGGCCCTTATTTGAGCATTTTGCAAAGT
Found at i:51579 original size:60 final size:60
Alignment explanation
Indices: 51509--51670 Score: 209
Period size: 60 Copynumber: 2.7 Consensus size: 60
51499 TCGTGAGATA
* * *
51509 GGCCCTTATTTGAGCATTTTGGCAAATGTTAGGCCCTTATTTAGCCAAATTCAAAGGT-G
1 GGCCCTTATTTGAGCATTTTGGCAAATGTTAAGCCCTTATTTAGCCAAATTAAAAGATCG
* * *
51568 GGACCCTTATTTGAGCATTTTAGCAAACGTTAAGCCCTTATTTGGCCAAATTAAAAGATCG
1 GG-CCCTTATTTGAGCATTTTGGCAAATGTTAAGCCCTTATTTAGCCAAATTAAAAGATCG
* ** * *
51629 GGCTCTTATTTGAATATTTTGTCAAATGTTAAACCCTTATTT
1 GGCCCTTATTTGAGCATTTTGGCAAATGTTAAGCCCTTATTT
51671 GAGCAATTAG
Statistics
Matches: 88, Mismatches: 13, Indels: 3
0.85 0.12 0.03
Matches are distributed among these distances:
59 2 0.02
60 83 0.94
61 3 0.03
ACGTcount: A:0.28, C:0.18, G:0.18, T:0.36
Consensus pattern (60 bp):
GGCCCTTATTTGAGCATTTTGGCAAATGTTAAGCCCTTATTTAGCCAAATTAAAAGATCG
Found at i:68687 original size:29 final size:30
Alignment explanation
Indices: 68625--68698 Score: 105
Period size: 29 Copynumber: 2.5 Consensus size: 30
68615 TTGATAACGG
* *
68625 AGGGTGCAAAGTGGAACAAAAATAAAACATT
1 AGGGTGCAAAGT-GAACAAAAATAAAAAAGT
*
68656 AGGGTGCAAAGTGATC-AAAATAAAAAAGT
1 AGGGTGCAAAGTGAACAAAAATAAAAAAGT
68685 AGGGTGCAAAGTGA
1 AGGGTGCAAAGTGA
68699 CCGTCCATAA
Statistics
Matches: 40, Mismatches: 3, Indels: 2
0.89 0.07 0.04
Matches are distributed among these distances:
29 25 0.62
30 3 0.08
31 12 0.30
ACGTcount: A:0.49, C:0.08, G:0.27, T:0.16
Consensus pattern (30 bp):
AGGGTGCAAAGTGAACAAAAATAAAAAAGT
Found at i:83934 original size:29 final size:28
Alignment explanation
Indices: 83901--83999 Score: 83
Period size: 29 Copynumber: 3.4 Consensus size: 28
83891 CTAATTGTTT
83901 AAATAAGGGTCCGATCTTTTAATTTGGTC
1 AAATAAGGGTCC-ATCTTTTAATTTGGTC
* ** * *
83930 AAATAAGGGTCTCA-CGTATTGAAAATGCTT
1 AAATAAGGGTC-CATC-T-TTTAATTTGGTC
* *
83960 AAATAAGGGTCAAATATTTTAATTTGGTC
1 AAATAAGGGTC-CATCTTTTAATTTGGTC
83989 AAATAAGGGTC
1 AAATAAGGGTC
84000 TAACATCATC
Statistics
Matches: 53, Mismatches: 13, Indels: 8
0.72 0.18 0.11
Matches are distributed among these distances:
28 1 0.02
29 31 0.58
30 21 0.40
ACGTcount: A:0.35, C:0.11, G:0.20, T:0.33
Consensus pattern (28 bp):
AAATAAGGGTCCATCTTTTAATTTGGTC
Found at i:84168 original size:61 final size:60
Alignment explanation
Indices: 84072--84203 Score: 151
Period size: 61 Copynumber: 2.2 Consensus size: 60
84062 CGACGCCAGG
* * * * * *
84072 CCCTTATTTGGCTAAATTAAAAGATCGAGCACTTATTTGAGCATTTCCGA-TAACATTAGGA
1 CCCTTATTTGACCAAATTAAAAAATCGAGCACTTATCTGAGCATTT-CGACAAACATTA-AA
* *
84133 CCCTTATTTGACCAAATTAAAAAATC-AGACTCTTATCTGAGCATTTTGACAAACATTAAA
1 CCCTTATTTGACCAAATTAAAAAATCGAG-CACTTATCTGAGCATTTCGACAAACATTAAA
84193 CCCTTATTTGA
1 CCCTTATTTGA
84204 GCAATCAGCC
Statistics
Matches: 61, Mismatches: 8, Indels: 5
0.82 0.11 0.07
Matches are distributed among these distances:
60 16 0.26
61 45 0.74
ACGTcount: A:0.35, C:0.20, G:0.12, T:0.33
Consensus pattern (60 bp):
CCCTTATTTGACCAAATTAAAAAATCGAGCACTTATCTGAGCATTTCGACAAACATTAAA
Found at i:86130 original size:2 final size:2
Alignment explanation
Indices: 86123--86147 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
86113 ATAAATTGTA
86123 AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT A
86148 ATTGGGGTTA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Done.