Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01021917.1 Corchorus olitorius cultivar O-4 contig21950, 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: 33574
ACGTcount: A:0.33, C:0.18, G:0.16, T:0.33
Found at i:64 original size:2 final size:2
Alignment explanation
Indices: 57--82 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
47 GAATAGATTG
57 AT 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
83 CTAGAAGTCA
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 24 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:3339 original size:16 final size:18
Alignment explanation
Indices: 3318--3350 Score: 52
Period size: 16 Copynumber: 1.9 Consensus size: 18
3308 TTAAAAATAC
3318 CAATT-ATAAA-CAAAAG
1 CAATTAATAAAGCAAAAG
3334 CAATTAATAAAGCAAAA
1 CAATTAATAAAGCAAAA
3351 TTAAATTAAA
Statistics
Matches: 15, Mismatches: 0, Indels: 2
0.88 0.00 0.12
Matches are distributed among these distances:
16 5 0.33
17 5 0.33
18 5 0.33
ACGTcount: A:0.64, C:0.12, G:0.06, T:0.18
Consensus pattern (18 bp):
CAATTAATAAAGCAAAAG
Found at i:5967 original size:22 final size:22
Alignment explanation
Indices: 5955--6448 Score: 165
Period size: 22 Copynumber: 22.6 Consensus size: 22
5945 ATGATCTCCT
5955 TATGAAATTTTGATAACCTTCC
1 TATGAAATTTTGATAACCTTCC
** *
5977 TATGAAATTTTGATAACGATAC
1 TATGAAATTTTGATAACCTTCC
* ** * ** **
5999 TATGGAATTTCAAGAATATTTT
1 TATGAAATTTTGATAACCTTCC
** *
6021 TAT-AAATTATTTTTAACCTTCT
1 TATGAAATT-TTGATAACCTTCC
*
6043 TATGAAATTTT-ATTAACCTCCC
1 TATGAAATTTTGA-TAACCTTCC
*
6065 TGAAG-AATTTTGA-AGACC-TCAC
1 T-ATGAAATTTTGATA-ACCTTC-C
*
6087 TATGAAATTTTGTTAA-CTTCC
1 TATGAAATTTTGATAACCTTCC
* **
6108 TAATGAAATTTTGATGACCAACAC
1 T-ATGAAATTTTGATAACCTTC-C
* * *
6132 TATGAGATGTTGATAACC-TCTA
1 TATGAAATTTTGATAACCTTC-C
* * * * *
6154 TATGATATATTAATAACC-ACAT
1 TATGAAATTTTGATAACCTTC-C
* * *
6176 TATGAAAATTTAAGAACC-TCC
1 TATGAAATTTTGATAACCTTCC
6197 ATATG-AATTGTT-AGTAA--TTACAC
1 -TATGAAATT-TTGA-TAACCTT-C-C
* * * *
6220 TCTGAAATTTTGATAATCATAC
1 TATGAAATTTTGATAACCTTCC
* *
6242 TATAAAATTGTGATAACC-TCGC
1 TATGAAATTTTGATAACCTTC-C
*
6264 TAAGAAATTTTGATAAACCTTCC
1 TATGAAATTTTGAT-AACCTTCC
* *
6287 TATAAAATTTTGATAAACCTCCC
1 TATGAAATTTTGAT-AACCTTCC
*
6310 TATAAAATTTTGATAA-----C
1 TATGAAATTTTGATAACCTTCC
*
6327 TA-CAAATTTTGATAA-CTTCCC
1 TATGAAATTTTGATAACCTT-CC
*
6348 TATG-AATGTTTGATAACC-TCAT
1 TATGAAAT-TTTGATAACCTTC-C
* *
6370 TATGAAATTTT-ATTAATCTCCC
1 TATGAAATTTTGA-TAACCTTCC
* * *
6392 TATGAAATTTTGATCTA-CATAC
1 TATGAAATTTTGAT-AACCTTCC
* *
6414 TATGAAATTTTGATAACCCTCT
1 TATGAAATTTTGATAACCTTCC
6436 TATGAAATTTTGA
1 TATGAAATTTTGA
6449 AAACTAAACT
Statistics
Matches: 352, Mismatches: 79, Indels: 82
0.69 0.15 0.16
Matches are distributed among these distances:
16 12 0.03
17 3 0.01
21 26 0.07
22 229 0.65
23 77 0.22
24 5 0.01
ACGTcount: A:0.36, C:0.15, G:0.10, T:0.39
Consensus pattern (22 bp):
TATGAAATTTTGATAACCTTCC
Found at i:6291 original size:45 final size:47
Alignment explanation
Indices: 6223--6325 Score: 133
Period size: 46 Copynumber: 2.3 Consensus size: 47
6213 ATTACACTCT
* *
6223 GAAATTTTGAT-AATCATACTATAAAATTGTGAT-AACCTCGCTA-A
1 GAAATTTTGATAAACCATACTATAAAATTGTGATAAACCTCCCTATA
* * *
6267 GAAATTTTGATAAACCTTCCTATAAAATTTTGATAAACCTCCCTATA
1 GAAATTTTGATAAACCATACTATAAAATTGTGATAAACCTCCCTATA
6314 -AAATTTTGATAA
1 GAAATTTTGATAA
6326 CTACAAATTT
Statistics
Matches: 51, Mismatches: 5, Indels: 4
0.85 0.08 0.07
Matches are distributed among these distances:
44 11 0.22
45 18 0.35
46 21 0.41
47 1 0.02
ACGTcount: A:0.41, C:0.15, G:0.09, T:0.36
Consensus pattern (47 bp):
GAAATTTTGATAAACCATACTATAAAATTGTGATAAACCTCCCTATA
Found at i:6342 original size:84 final size:82
Alignment explanation
Indices: 6246--6405 Score: 189
Period size: 82 Copynumber: 1.9 Consensus size: 82
6236 TCATACTATA
*
6246 AAATTGTGATAACCTCGCTAAGAAAT-TTTGATAAACCTTC-CTATAAAATTTTGATAAACCTCC
1 AAATTGTGATAACCTCCCTAAG-AATGTTTGAT-AACC-TCACTATAAAATTTT-ATAAACCTCC
6309 CTATAAAATTTTGATAACTAC
62 CTATAAAATTTTGATAACTAC
* * * * * * *
6330 AAATTTTGATAACTTCCCTATGAATGTTTGATAACCTCATTATGAAATTTTATTAATCTCCCTAT
1 AAATTGTGATAACCTCCCTAAGAATGTTTGATAACCTCACTATAAAATTTTATAAACCTCCCTAT
*
6395 GAAATTTTGAT
66 AAAATTTTGAT
6406 CTACATACTA
Statistics
Matches: 65, Mismatches: 9, Indels: 6
0.81 0.11 0.08
Matches are distributed among these distances:
82 24 0.37
83 17 0.26
84 24 0.37
ACGTcount: A:0.36, C:0.16, G:0.09, T:0.39
Consensus pattern (82 bp):
AAATTGTGATAACCTCCCTAAGAATGTTTGATAACCTCACTATAAAATTTTATAAACCTCCCTAT
AAAATTTTGATAACTAC
Found at i:6360 original size:38 final size:39
Alignment explanation
Indices: 6291--6364 Score: 107
Period size: 38 Copynumber: 1.9 Consensus size: 39
6281 CCTTCCTATA
6291 AAATTTTGATAAACCTCCCTATAAAATTTTGATAACTAC
1 AAATTTTGATAAACCTCCCTATAAAATTTTGATAACTAC
* *
6330 AAATTTTGAT-AACTTCCCTAT-GAATGTTTGATAAC
1 AAATTTTGATAAACCTCCCTATAAAAT-TTTGATAAC
6365 CTCATTATGA
Statistics
Matches: 32, Mismatches: 2, Indels: 3
0.86 0.05 0.08
Matches are distributed among these distances:
37 3 0.09
38 19 0.59
39 10 0.31
ACGTcount: A:0.38, C:0.16, G:0.08, T:0.38
Consensus pattern (39 bp):
AAATTTTGATAAACCTCCCTATAAAATTTTGATAACTAC
Found at i:6667 original size:21 final size:23
Alignment explanation
Indices: 6602--6673 Score: 80
Period size: 22 Copynumber: 3.3 Consensus size: 23
6592 AATCACATTT
* *
6602 TGAAAA-TTTGATAACTTCTTTA
1 TGAAAATTTTGATAACCTCTCTA
6624 TG-AAATTTTGATAACCTCTCTA
1 TGAAAATTTTGATAACCTCTCTA
* *
6646 T-AAAATTTTGTTGACC-CTCTA
1 TGAAAATTTTGATAACCTCTCTA
6667 TGAAAAT
1 TGAAAAT
6674 AATCACATTT
Statistics
Matches: 43, Mismatches: 4, Indels: 6
0.81 0.08 0.11
Matches are distributed among these distances:
21 9 0.21
22 34 0.79
ACGTcount: A:0.35, C:0.14, G:0.10, T:0.42
Consensus pattern (23 bp):
TGAAAATTTTGATAACCTCTCTA
Found at i:6894 original size:22 final size:22
Alignment explanation
Indices: 6845--6983 Score: 128
Period size: 22 Copynumber: 6.4 Consensus size: 22
6835 AAATTGAGAC
6845 TTTT-ATAACCTTCAC-ATGAAA
1 TTTTGATAACC-TCACTATGAAA
*
6866 -TTTGATAACCACACTATGAAA
1 TTTTGATAACCTCACTATGAAA
* *
6887 TTTTGATAACCTCCCCATGAAA
1 TTTTGATAACCTCACTATGAAA
* *
6909 TATT-AGTAACCTTCA-TATGGAA
1 TTTTGA-TAACC-TCACTATGAAA
* *
6931 TTTTGTTAACCACACTATGAAA
1 TTTTGATAACCTCACTATGAAA
*
6953 TTCTT-ATAACCTCACTATGACA
1 TT-TTGATAACCTCACTATGAAA
6975 TTTTGATAA
1 TTTTGATAA
6984 TCTCTTTGAT
Statistics
Matches: 94, Mismatches: 15, Indels: 17
0.75 0.12 0.13
Matches are distributed among these distances:
20 6 0.06
21 17 0.18
22 67 0.71
23 4 0.04
ACGTcount: A:0.36, C:0.19, G:0.09, T:0.36
Consensus pattern (22 bp):
TTTTGATAACCTCACTATGAAA
Found at i:7102 original size:22 final size:22
Alignment explanation
Indices: 7001--7220 Score: 112
Period size: 22 Copynumber: 9.9 Consensus size: 22
6991 GATAACCTTT
* *
7001 CTATAAAATTGTGATAACCACA
1 CTATGAAATTTTGATAACCACA
** *
7023 CTATGAAATTTCAATAACCTTC-
1 CTATGAAATTTTGATAACC-ACA
* **
7045 CTAAGAAATTTAAATAACCTGATC-
1 CTATGAAATTTTGATAACC--A-CA
*
7069 CTATGAAATTTTGGTAACCACA
1 CTATGAAATTTTGATAACCACA
**
7091 CTATGAAATTTTGATAAACTTC-
1 CTATGAAATTTTGAT-AACCACA
* * *
7113 CCATGAAATTTTTATAGCTTC-CA
1 CTATGAAATTTTGATAAC--CACA
*
7136 -TATGAAATTTTGGTAACCACA
1 CTATGAAATTTTGATAACCACA
* *
7157 CTATGGAATTTTGATAACCTC-
1 CTATGAAATTTTGATAACCACA
* *
7178 CTCATGAAATTATAATAACCATC-
1 CT-ATGAAATTTTGATAACCA-CA
* * *
7201 TTATAAAATTTTGATTACCA
1 CTATGAAATTTTGATAACCA
7221 TACAGAGTCA
Statistics
Matches: 150, Mismatches: 36, Indels: 24
0.71 0.17 0.11
Matches are distributed among these distances:
20 1 0.01
21 7 0.05
22 119 0.79
23 7 0.05
24 16 0.11
ACGTcount: A:0.38, C:0.18, G:0.09, T:0.35
Consensus pattern (22 bp):
CTATGAAATTTTGATAACCACA
Found at i:7210 original size:66 final size:65
Alignment explanation
Indices: 7002--7213 Score: 205
Period size: 66 Copynumber: 3.2 Consensus size: 65
6992 ATAACCTTTC
* * ** *
7002 TATAAAATTGTGATAACCACACTATGAAATTTCAATAACCTTCCT-AAGAAATTTAAATAACCTG
1 TATAAAATTTTGGTAACCACACTATGAAATTTTGATAACC-TCCTCATGAAATTT-AATAACC--
*
7066 ATCC
62 ATCA
* * * * *
7070 TATGAAATTTTGGTAACCACACTATGAAATTTTGATAAACTTCC-CATGAAATTT-TTATAGCTT
1 TATAAAATTTTGGTAACCACACTATGAAATTTTGAT-AACCTCCTCATGAAATTTAATA-ACCAT
7133 CCA
64 -CA
* *
7136 TATGAAATTTTGGTAACCACACTATGGAATTTTGATAACCTCCTCATGAAATTATAATAACCATC
1 TATAAAATTTTGGTAACCACACTATGAAATTTTGATAACCTCCTCATGAAATT-TAATAACCATC
*
7201 T
65 A
7202 TATAAAATTTTG
1 TATAAAATTTTG
7214 ATTACCATAC
Statistics
Matches: 119, Mismatches: 18, Indels: 16
0.78 0.12 0.10
Matches are distributed among these distances:
65 7 0.06
66 59 0.50
67 6 0.05
68 44 0.37
69 3 0.03
ACGTcount: A:0.38, C:0.17, G:0.09, T:0.35
Consensus pattern (65 bp):
TATAAAATTTTGGTAACCACACTATGAAATTTTGATAACCTCCTCATGAAATTTAATAACCATCA
Found at i:7421 original size:20 final size:20
Alignment explanation
Indices: 7383--7421 Score: 53
Period size: 20 Copynumber: 1.9 Consensus size: 20
7373 TATTGACATT
7383 TAAAAAATTGAAATTAAAAG
1 TAAAAAATTGAAATTAAAAG
*
7403 TAAAACATT-AAATTCAAAA
1 TAAAAAATTGAAATT-AAAA
7422 AATAATAGTA
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
19 5 0.29
20 12 0.71
ACGTcount: A:0.64, C:0.05, G:0.05, T:0.26
Consensus pattern (20 bp):
TAAAAAATTGAAATTAAAAG
Found at i:8880 original size:164 final size:164
Alignment explanation
Indices: 8590--8919 Score: 581
Period size: 164 Copynumber: 2.0 Consensus size: 164
8580 TTCTTCTTAA
*
8590 ACTTTTATTTAACTTTAACTTTTAAATTTTAATTGGTGGGGAACTTTTATTTAACTTTGATAAAG
1 ACTTTTATTTAACTTTAACTTTTAAATTTTAATTGGTGGGGAACTTTTATTTAACTTTAATAAAG
* *
8655 TAAAAAAATGGGTAATTTGTAATTCATAAAACTTTTACATATTAAAAGAAAAAATTAAATAAAAC
66 -AAAAAAATGGGTAATTCGTAATTCATAAAACTTTTACATATAAAAAGAAAAAATTAAATAAAAC
*
8720 TTTAGAAGATCATGAATGGATGAATTCATTTCAAT
130 TTTAGAAGATCATGAATGGATGAATTAATTTCAAT
*
8755 ACTTTTATTTAACTTTAACTTTTAAATTTTAATTGGTGGGTAACTTTTATTTAACTTTAATAAA-
1 ACTTTTATTTAACTTTAACTTTTAAATTTTAATTGGTGGGGAACTTTTATTTAACTTTAATAAAG
*
8819 AGAAAAAATTGGTAATTCGTAATTCATAAAACTTTTACATATAAAAAGAAAAAATTAAATAAAAC
66 A-AAAAAATGGGTAATTCGTAATTCATAAAACTTTTACATATAAAAAGAAAAAATTAAATAAAAC
8884 TTTAGAAGATCATGAATGGATGAATTAATTTCAAT
130 TTTAGAAGATCATGAATGGATGAATTAATTTCAAT
8919 A
1 A
8920 ATATTCAAAT
Statistics
Matches: 158, Mismatches: 6, Indels: 3
0.95 0.04 0.02
Matches are distributed among these distances:
163 1 0.01
164 95 0.60
165 62 0.39
ACGTcount: A:0.43, C:0.07, G:0.11, T:0.39
Consensus pattern (164 bp):
ACTTTTATTTAACTTTAACTTTTAAATTTTAATTGGTGGGGAACTTTTATTTAACTTTAATAAAG
AAAAAAATGGGTAATTCGTAATTCATAAAACTTTTACATATAAAAAGAAAAAATTAAATAAAACT
TTAGAAGATCATGAATGGATGAATTAATTTCAAT
Found at i:12328 original size:865 final size:865
Alignment explanation
Indices: 10659--12391 Score: 3261
Period size: 865 Copynumber: 2.0 Consensus size: 865
10649 AGTTGGTATT
*
10659 TTCAATAATATAATTGTTGCGCCAAAAATCTCTTGCTAGAGTTTTCGCGGAGAATTCTTTATAAC
1 TTCAATAATATAACTGTTGCGCCAAAAATCTCTTGCTAGAGTTTTCGCGGAGAATTCTTTATAAC
*
10724 AGAATAAGGGCATGCCAGTCAAATTTGCTGAAATTGACAAAGAGGTTGTAAAAACTAGATCTGGT
66 AGAATAAGGGCATGCCAGTCAAATTTGCTGAAATTGACAAAAAGGTTGTAAAAACTAGATCTGGT
*
10789 GCGCGGAGCAGCAGATTAAAAGATCAGAGCGATTTGTGGGGACTAGATCAAAATCACACCGGAGC
131 GCGCGGAGCAGCAGATTAAAAGATCAGAGCGATTTGTGGGGACTAAATCAAAATCACACCGGAGC
*
10854 ATTTAAATTATTGGATCCACAACAAGTTGTTCTTTATAACTGGGCCTTCTTCTTCCTTTTAACTG
196 ATTTAAATCATTGGATCCACAACAAGTTGTTCTTTATAACTGGGCCTTCTTCTTCCTTTTAACTG
*
10919 GATCAGATCTGTGAGATCTGTTTTTGATTGAAATTGAAAGAAAATAACAATTTGATTGTTATTTA
261 GATCAGATCAGTGAGATCTGTTTTTGATTGAAATTGAAAGAAAATAACAATTTGATTGTTATTTA
*
10984 TGAGAGAGAAACACGTGTACAGTGTTTTTGTATCCGGAGACAAGATTGAAATAAGAGGAAAAAAA
326 TGAGAGAGAAACACGTGTACAGTGTTTTTGTATCCGGAGACAAGATTGAAACAAGAGGAAAAAAA
11049 AACTAAAAGAGTGTTTGGGTGTCCTGAGACAAGATCTAAACAAGAAAAATATGAAGAACAAGTAA
391 AACTAAAAGAGTGTTTGGGTGTCCTGAGACAAGATCTAAACAAGAAAAATATGAAGAACAAGTAA
11114 GAACTCGTGATGAACAAAGAGGAAATGGCGCAAAGCCAGAAGAGAAAATAAGCACGAAGCTTGGT
456 GAACTCGTGATGAACAAAGAGGAAATGGCGCAAAGCCAGAAGAGAAAATAAGCACGAAGCTTGGT
*
11179 TTTTTGCGCGGAGCAAGTTTGTAGCTTCAGAAGCTGGTTTTTGAGATGAGTGATATATGTCTAAA
521 TTTTTGCGCGGAACAAGTTTGTAGCTTCAGAAGCTGGTTTTTGAGATGAGTGATATATGTCTAAA
11244 GCCTTGGAATGGCTTCCTTTATATAGGGGGCGGCATGGGTCTTGAATTTAATGGGCTTGACTTGC
586 GCCTTGGAATGGCTTCCTTTATATAGGGGGCGGCATGGGTCTTGAATTTAATGGGCTTGACTTGC
11309 TGAAGAAGGTGAATTCCTCCTCCTAGGTAGATGACAGCTTCTAGGAAGGTGTAGTGAAGCTTCAA
651 TGAAGAAGGTGAATTCCTCCTCCTAGGTAGATGACAGCTTCTAGGAAGGTGTAGTGAAGCTTCAA
11374 TCTTCTTCTGATTGTTTCCAACAACTGAGGAGATGGAAGAAAAGGATGCCAGGGCATCACAGTCT
716 TCTTCTTCTGATTGTTTCCAACAACTGAGGAGATGGAAGAAAAGGATGCCAGGGCATCACAGTCT
11439 TATATGGGAGATGGAAATCTTCCTCCTAGATGGTTGATGGCGAATCCTTCCTTCTTCCTGTCACA
781 TATATGGGAGATGGAAATCTTCCTCCTAGATGGTTGATGGCGAATCCTTCCTTCTTCCTGTCACA
11504 CTTCAGCATGCTTTCGTTGC
846 CTTCAGCATGCTTTCGTTGC
* *
11524 TTCAATAATATAACTGTTGCGCCAAAAATCTCTTGCTAGAGTTTTTGCGGATAATTCTTTATAAC
1 TTCAATAATATAACTGTTGCGCCAAAAATCTCTTGCTAGAGTTTTCGCGGAGAATTCTTTATAAC
*
11589 AGAATAGGGGCATGCCAGTC-AATTTGCTGAAATTGACAAAAAGGTTGTAAAAACTAGATCTGGT
66 AGAATAAGGGCATGCCAGTCAAATTTGCTGAAATTGACAAAAAGGTTGTAAAAACTAGATCTGGT
*
11653 GCGCGGAGCAGCAGATTAAAAGATCAGAGCGATTTGTGGGGACTAAATCAAAGTCACACCGGAGC
131 GCGCGGAGCAGCAGATTAAAAGATCAGAGCGATTTGTGGGGACTAAATCAAAATCACACCGGAGC
11718 ATTTAAATCATTGGATCCACAACAAGTTGTTCTTTATAACTGGGCCTTCTTCTTCCTTTTAACTG
196 ATTTAAATCATTGGATCCACAACAAGTTGTTCTTTATAACTGGGCCTTCTTCTTCCTTTTAACTG
11783 GATCAGATCAGTGAGATCTGTTTTTGATTGAAATTGAAAGAAAATAACAATTTGATTGTTATTTA
261 GATCAGATCAGTGAGATCTGTTTTTGATTGAAATTGAAAGAAAATAACAATTTGATTGTTATTTA
11848 TGAGAGAGAAACACGTGTACAGTGATTTTTGTATCCGGAGACAAGATTGAAACAAGAGGAAAAAA
326 TGAGAGAGAAACACGTGTACAGTG-TTTTTGTATCCGGAGACAAGATTGAAACAAGAGGAAAAAA
* *
11913 AAACTAAAAGAGTGTTTGGGTGTCCTGAGACAGGATCTAAACAAGAAAAATATGAAGAACGAGTA
390 AAACTAAAAGAGTGTTTGGGTGTCCTGAGACAAGATCTAAACAAGAAAAATATGAAGAACAAGTA
* *
11978 AGAACTCGTGATGAACAAAGAGGAAATGGCGCAGAGCCAGAAGAGAAAATAAGCACGGAGCTTGG
455 AGAACTCGTGATGAACAAAGAGGAAATGGCGCAAAGCCAGAAGAGAAAATAAGCACGAAGCTTGG
* *
12043 TTTTTTGCGCGGAACAAGTTTGTAGCTTCAGAAGCTGGTTTTTGAGATGAGTGATATCTGTCTGA
520 TTTTTTGCGCGGAACAAGTTTGTAGCTTCAGAAGCTGGTTTTTGAGATGAGTGATATATGTCTAA
12108 AGCCTTGGAATGGCTTCCTTTATATAGGGGGCGGCATGGGTCTTGAATTTAATGGGCTTGACTTG
585 AGCCTTGGAATGGCTTCCTTTATATAGGGGGCGGCATGGGTCTTGAATTTAATGGGCTTGACTTG
12173 CTGAAGAAGGTGAATTCCTCCTCCTAGGTAGATGACAGCTTCTAGGAAGGTGTAGTGAAGCTTCA
650 CTGAAGAAGGTGAATTCCTCCTCCTAGGTAGATGACAGCTTCTAGGAAGGTGTAGTGAAGCTTCA
* *
12238 ATCTTCTTCTGATTGTTTCCAACTACTGAGGAGATGGAAGAAAAGGATGCCAGGGCGTCACAGTC
715 ATCTTCTTCTGATTGTTTCCAACAACTGAGGAGATGGAAGAAAAGGATGCCAGGGCATCACAGTC
* *
12303 TTATATGGGAGATGGAATTCTTCCTCTTAGATGGTTGATGGCGAATCCTTCCTTCTTCCTGTCAC
780 TTATATGGGAGATGGAAATCTTCCTCCTAGATGGTTGATGGCGAATCCTTCCTTCTTCCTGTCAC
12368 ACTTCAGCATGCTTTCGTTGC
845 ACTTCAGCATGCTTTCGTTGC
12389 TTC
1 TTC
12392 CTTTATGCTG
Statistics
Matches: 846, Mismatches: 21, Indels: 2
0.97 0.02 0.00
Matches are distributed among these distances:
864 258 0.30
865 588 0.70
ACGTcount: A:0.31, C:0.16, G:0.24, T:0.29
Consensus pattern (865 bp):
TTCAATAATATAACTGTTGCGCCAAAAATCTCTTGCTAGAGTTTTCGCGGAGAATTCTTTATAAC
AGAATAAGGGCATGCCAGTCAAATTTGCTGAAATTGACAAAAAGGTTGTAAAAACTAGATCTGGT
GCGCGGAGCAGCAGATTAAAAGATCAGAGCGATTTGTGGGGACTAAATCAAAATCACACCGGAGC
ATTTAAATCATTGGATCCACAACAAGTTGTTCTTTATAACTGGGCCTTCTTCTTCCTTTTAACTG
GATCAGATCAGTGAGATCTGTTTTTGATTGAAATTGAAAGAAAATAACAATTTGATTGTTATTTA
TGAGAGAGAAACACGTGTACAGTGTTTTTGTATCCGGAGACAAGATTGAAACAAGAGGAAAAAAA
AACTAAAAGAGTGTTTGGGTGTCCTGAGACAAGATCTAAACAAGAAAAATATGAAGAACAAGTAA
GAACTCGTGATGAACAAAGAGGAAATGGCGCAAAGCCAGAAGAGAAAATAAGCACGAAGCTTGGT
TTTTTGCGCGGAACAAGTTTGTAGCTTCAGAAGCTGGTTTTTGAGATGAGTGATATATGTCTAAA
GCCTTGGAATGGCTTCCTTTATATAGGGGGCGGCATGGGTCTTGAATTTAATGGGCTTGACTTGC
TGAAGAAGGTGAATTCCTCCTCCTAGGTAGATGACAGCTTCTAGGAAGGTGTAGTGAAGCTTCAA
TCTTCTTCTGATTGTTTCCAACAACTGAGGAGATGGAAGAAAAGGATGCCAGGGCATCACAGTCT
TATATGGGAGATGGAAATCTTCCTCCTAGATGGTTGATGGCGAATCCTTCCTTCTTCCTGTCACA
CTTCAGCATGCTTTCGTTGC
Found at i:19093 original size:11 final size:11
Alignment explanation
Indices: 19077--19136 Score: 52
Period size: 11 Copynumber: 5.5 Consensus size: 11
19067 CTGATTACTA
19077 ATATATAATAT
1 ATATATAATAT
19088 ATATATAATAT
1 ATATATAATAT
*
19099 ATCT-TAA-AT
1 ATATATAATAT
* *
19108 TTATTTAATAT
1 ATATATAATAT
* *
19119 TTATAATAAAAT
1 ATAT-ATAATAT
19131 ATATAT
1 ATATAT
19137 TTGGGTTCTC
Statistics
Matches: 40, Mismatches: 6, Indels: 6
0.77 0.12 0.12
Matches are distributed among these distances:
9 4 0.10
10 6 0.15
11 22 0.55
12 8 0.20
ACGTcount: A:0.50, C:0.02, G:0.00, T:0.48
Consensus pattern (11 bp):
ATATATAATAT
Found at i:26259 original size:28 final size:29
Alignment explanation
Indices: 26212--26272 Score: 88
Period size: 28 Copynumber: 2.1 Consensus size: 29
26202 GCTTCAAGGC
*
26212 AGATTCCACATCTCACAAAACATCTCTCAG
1 AGATTCCACATCT-ACAAAACATCTCCCAG
*
26242 AGATTCCACATCT-CAAAACATTTCCCAG
1 AGATTCCACATCTACAAAACATCTCCCAG
26270 AGA
1 AGA
26273 AATCACTCTT
Statistics
Matches: 29, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
28 16 0.55
30 13 0.45
ACGTcount: A:0.38, C:0.31, G:0.08, T:0.23
Consensus pattern (29 bp):
AGATTCCACATCTACAAAACATCTCCCAG
Found at i:32449 original size:50 final size:48
Alignment explanation
Indices: 32348--32490 Score: 164
Period size: 49 Copynumber: 3.0 Consensus size: 48
32338 CAAGCAATCA
* * ** *
32348 TTTACTTTTCACTGCACTTTTTATCAATTTTTACTACAAAATTGAACT
1 TTTAATTTTCATTGCACTTTTTATCAATTTTTAAGACAAAATTGATCT
* *
32396 TTT-ATTTTTACTTGCATCTTTTTCTCAATTTTTAAAGACAAAATTGATCT
1 TTTAATTTTCA-TTGCA-CTTTTTATCAATTTTT-AAGACAAAATTGATCT
* *
32446 TTTAATTTTCATCGCACTTTTTATCAATTTTT-TGACAAAATTGAT
1 TTTAATTTTCATTGCACTTTTTATCAATTTTTAAGACAAAATTGAT
32491 TGGCACGCTC
Statistics
Matches: 80, Mismatches: 11, Indels: 9
0.80 0.11 0.09
Matches are distributed among these distances:
47 17 0.21
48 7 0.09
49 30 0.38
50 20 0.25
51 6 0.08
ACGTcount: A:0.29, C:0.15, G:0.06, T:0.50
Consensus pattern (48 bp):
TTTAATTTTCATTGCACTTTTTATCAATTTTTAAGACAAAATTGATCT
Found at i:33046 original size:18 final size:18
Alignment explanation
Indices: 33023--33128 Score: 140
Period size: 18 Copynumber: 5.9 Consensus size: 18
33013 CATCAACAAA
**
33023 TCGCACCGCACCAAGTAT
1 TCGCACCGCACCAAGTGG
*
33041 TCGCACCGCACCAAATGG
1 TCGCACCGCACCAAGTGG
* *
33059 TCGCAACACACCAAGTGG
1 TCGCACCGCACCAAGTGG
*
33077 TCGCACCACACCAAGTGG
1 TCGCACCGCACCAAGTGG
*
33095 TCGCACCGCACCCAGTGG
1 TCGCACCGCACCAAGTGG
*
33113 TCGCACCGTACCAAGT
1 TCGCACCGCACCAAGT
33129 TGCCACACTT
Statistics
Matches: 77, Mismatches: 11, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
18 77 1.00
ACGTcount: A:0.26, C:0.39, G:0.22, T:0.13
Consensus pattern (18 bp):
TCGCACCGCACCAAGTGG
Done.