Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01007996.1 Corchorus capsularis cultivar CVL-1 contig08017, 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: 23323
ACGTcount: A:0.31, C:0.17, G:0.21, T:0.31
Found at i:5997 original size:924 final size:928
Alignment explanation
Indices: 3340--7485 Score: 6999
Period size: 927 Copynumber: 4.5 Consensus size: 928
3330 ACGACCAATC
3340 ACATAGTGGCATAAGCCCAATATCATTAGTTATCTTTGTTTGGGCTTAATTCTATCTTAGATTAG
1 ACATAGTGGCATAAGCCCAATATCATTAGTTATCTTTGTTTGGGCTTAATTCTATCTTAGATTAG
*
3405 CTTATTTTTAAGTTTGGATGTTATTTGGGTTGGGCCTTGTTTGACTAAGTCCAATCCTTGTTTAA
66 CTTATTTTTAAGTTTGGATGTTATTTGGGTTGGGCCTTGTTTGAATAAGTCCAATCCTTGTTTAA
*
3470 TTATGCTTTTATTTACCTTTCCTAGTTGGGCTTGGACTAGTTTTTCCCTAGCCCTTATATTTGGA
131 TTATGCTTTTATTTCCCTTTCCTAGTTGGGCTTGGACTAGTTTTTCCCTAGCCCTTATATTTGGA
*
3535 CGAAAATTAGGATTTATTTTAAGATTTTGGTTGACCCTATCACTATATAAGGCCACCAATATCTC
196 CGAAAATTAGGATTTATTTTAGGATTTTGGTTGACCCTATCACTATATAAGGCCACCAATATCTC
3600 TTGTAAAAGTGGAAGTTGAGTTGATTAATAAAATTGAGGTTTATTCTCCCAAATTGATTATCTTG
261 TTGTAAAAGTGGAAGTTGAGTTGATTAATAAAATTGAGGTTTATTCTCCCAAATTGATTATCTTG
*
3665 GCTTCATTGTTCTAGTTTGAGCAAACTTAGGGTTCTTCAATATTGTAGAGTCCTAGCAAACAATT
326 GCTTCATTGTTCTAGTTTGAGCAAACTTAGGGTTCTTCAATCTTGTAGAGTCCTAGCAAACAATT
*
3730 AGGTTGTGTGATGCTTAATGGTTTGTGAATCTTGTGATCTTAGGTATTCAATTGCAGGTCTAATT
391 AGGTTGTGTGATGCTTAATTGTTTGTGAATCTTGTGATCTTAGGTATTCAATTGCAGGTCTAATT
* * * * *
3795 GAAGACTTCA-GTTTGACGAACAAAGAGTGATTGCTTTGTGAAGCTTGTCGACATACTTGTCTAG
456 GAAGACTTAAGGTCTGACGAACGAAGAGAGATTGCTTTGTGAAGGTTGTCGACATACTTGTCTAG
*
3859 AAGTTGAAGAAGTTCAAGTAGATTCTTGGCAGGTCTCAAGGATAGATTTTATCATGGAGGGCCAA
521 AAGTTGAAGAAGTTCAAGTAGATTCATGGCAGGTCTCAAGGATAGATTTTATCATGGAGGGCCAA
*
3924 GGACTTATCATGGTCTTGAAGACAAGCATTGAGAGCATGGAAAGGATGTGCATGGGCTACAAGGA
586 GGACTTATCATGGTCTTGAAGACAAGCATGGAGAGCATGGAAAGGATGTGCATGGGCTACAAGGA
* *
3989 AGCATGGAGATGCTTGAAGATTATCGAGATATTGATAAGCATGTTCCAAGCACCAAAAAGCTGCT
651 AGCATGGAGATGCATGAAGATTATCGAGATATTGATAAGCATGTTCCAAGCACCAAAAAGATGCT
* *
4054 ATTCGATTCATTGAAGATGCCTACTAGTCCGATGACAAGAGCAAGAGCTAAGAGATTCAAGGATG
716 AATCGATTCATTGAAGATGCCTATTAGTCCGATGACAAGAGCAAGAGCTAAGAGATTCAAGGATG
4119 CACTCATGGGCCTTGTTCGAACTCATCTTGAAGACTTGAAGACCATTCAAGTTCAATTGAAGAGC
781 CACTCATGGGCCTTGTTCGAACTCATCTTGAAGACTTGAAGACCATTCAAGTTCAATTGAAGAGC
4184 TTTGATGATGATTTGAGCAAGAAAACA-TCAATCAATTACAAGTTCATCACTTTGCTTGCTATTG
846 TTTGATGATGATTTGAGCAAGAAAACACT-AATCAATTACAAGTTCATCACTTTGCTTGCTATTG
4248 ATTCTAAATGGCCGGATTG
910 ATTCTAAATGGCCGGATTG
* * *
4267 ACATAGTGGCATAAGCCCAATATCGTTAGTTTTCTTTGTATGGGCTTAATTCTATCTTAGATTAG
1 ACATAGTGGCATAAGCCCAATATCATTAGTTATCTTTGTTTGGGCTTAATTCTATCTTAGATTAG
** * *
4332 CTTATTTTTAAGTTTGGATAATATTTGGGTTGGGCCTTGTTTGACTAAGTCTAATCCTTGTTTAA
66 CTTATTTTTAAGTTTGGATGTTATTTGGGTTGGGCCTTGTTTGAATAAGTCCAATCCTTGTTTAA
*
4397 TTATGCTTTTATTTCCCTTTCCTAGTTGGGCTTGGACTAGTTTGTCCCTAGCCCTTATATTTGGA
131 TTATGCTTTTATTTCCCTTTCCTAGTTGGGCTTGGACTAGTTTTTCCCTAGCCCTTATATTTGGA
4462 CGAAAATTAGGATTTATTTTAGGATTTTGGTTGACCCTATCACTATATAAGGCCACCAATATCTC
196 CGAAAATTAGGATTTATTTTAGGATTTTGGTTGACCCTATCACTATATAAGGCCACCAATATCTC
4527 TTGTAAAAGTGGAAGTTGAGTTGATTAATAAAATTGAGGTTTATTCTCCCAAATTGATTATCTTG
261 TTGTAAAAGTGGAAGTTGAGTTGATTAATAAAATTGAGGTTTATTCTCCCAAATTGATTATCTTG
** *
4592 GCTTCATTGTTCTAACTTGAGCAAACTTAGGGTTCTTCAAACTTGTAGAGTCCTAGCAAACAATT
326 GCTTCATTGTTCTAGTTTGAGCAAACTTAGGGTTCTTCAATCTTGTAGAGTCCTAGCAAACAATT
* * *
4657 AGGTTGTGTGATGCTTAATTTTTTGTGAATATTGTGATCCTAGGTATTCAATTGCAGGTCTAATT
391 AGGTTGTGTGATGCTTAATTGTTTGTGAATCTTGTGATCTTAGGTATTCAATTGCAGGTCTAATT
* *
4722 GAAGACTTAAGG-CTGACGAAAGAAGAGAGATTGCTTTGTGAAGGTTGTTGACATACTTGTCTAG
456 GAAGACTTAAGGTCTGACGAACGAAGAGAGATTGCTTTGTGAAGGTTGTCGACATACTTGTCTAG
*
4786 AAGTTGAAGAAGTTCAAGTAGATTCCTGGCAGGTCTCAAGGATAGATTTTATCATGGAGGGCCAA
521 AAGTTGAAGAAGTTCAAGTAGATTCATGGCAGGTCTCAAGGATAGATTTTATCATGGAGGGCCAA
*
4851 GGACTTATCATGGTCTTGAAGACAAGCATGGAGAGCATTGAAAGGATGTGCATGGGCTACAAGGA
586 GGACTTATCATGGTCTTGAAGACAAGCATGGAGAGCATGGAAAGGATGTGCATGGGCTACAAGGA
*
4916 AGCATGGAGATGCATGAAGATTATCGAGATATTGATAAGCATGTTCCAAGCACCAAAAAGATCCT
651 AGCATGGAGATGCATGAAGATTATCGAGATATTGATAAGCATGTTCCAAGCACCAAAAAGATGCT
* * * *
4981 AATAGATCCATTGAAGATGCCTATTAGTCCGATGACAAGAGCAACAGCTAAGAGATTCAAGGAGG
716 AATCGATTCATTGAAGATGCCTATTAGTCCGATGACAAGAGCAAGAGCTAAGAGATTCAAGGATG
*
5046 CACTCATGGGCCTTGTTCGAACTCATCTTGAAGACTTGAAGACCATTCAAGTTCAATTAAAGAGC
781 CACTCATGGGCCTTGTTCGAACTCATCTTGAAGACTTGAAGACCATTCAAGTTCAATTGAAGAGC
* * *
5111 TTTGATGATGATTTTAGCAAGAAAACACTAATCAATTACAAGTTCATCACTTTGCTTGTTGTTGA
846 TTTGATGATGATTTGAGCAAGAAAACACTAATCAATTACAAGTTCATCACTTTGCTTGCTATTGA
5176 TTCTAAATGGCCGGATTG
911 TTCTAAATGGCCGGATTG
* * * * ***
5194 ACATAGTGGCATGAGCCCAATATCATTAGTTCTCTTTCTTTGGTCTTAATTCTATCTTAGGCCAG
1 ACATAGTGGCATAAGCCCAATATCATTAGTTATCTTTGTTTGGGCTTAATTCTATCTTAGATTAG
**
5259 CTTATTTTTAAGTTTAAATGTTATTTGGGTTGGGCCTTGTTTGAATAAGTCCAATCCTTGTTTAA
66 CTTATTTTTAAGTTTGGATGTTATTTGGGTTGGGCCTTGTTTGAATAAGTCCAATCCTTGTTTAA
* * * *
5324 TTATGCTTTTATTTCCTTTTCCTAGTTGGACTTGGACTAG-ATTTCGCTAGCCCTTATATTTGGA
131 TTATGCTTTTATTTCCCTTTCCTAGTTGGGCTTGGACTAGTTTTTCCCTAGCCCTTATATTTGGA
* * *
5388 CGAAAATTAGGATTTATTTTAGGATTTTGGTTGACCCTGTCACTATCTAAGGCCACGAATATCTC
196 CGAAAATTAGGATTTATTTTAGGATTTTGGTTGACCCTATCACTATATAAGGCCACCAATATCTC
*
5453 TTGTAAAAGTGGAAGTTGAGTTGATTAATAAAATTGAGGTTTATTCTTCCAAATTGATTATCTTG
261 TTGTAAAAGTGGAAGTTGAGTTGATTAATAAAATTGAGGTTTATTCTCCCAAATTGATTATCTTG
* * * * *
5518 GCATCATTGTTATAGTTTAAGCAAACTTAAGGTTCTTCAATCTTGTAGTGTCCTAGCAAACAATT
326 GCTTCATTGTTCTAGTTTGAGCAAACTTAGGGTTCTTCAATCTTGTAGAGTCCTAGCAAACAATT
*
5583 AGGTTGTGTGATGCTTAATTGTTTGTGAATATTGTGATCTTAGGTATTCAATTGCAGGTCTAATT
391 AGGTTGTGTGATGCTTAATTGTTTGTGAATCTTGTGATCTTAGGTATTCAATTGCAGGTCTAATT
*
5648 GAAGACTTAAGGTC-GACGAACGAAGAGAGATTGC-TT-TGAAGGTTGTTC-ACATACTTGTGTA
456 GAAGACTTAAGGTCTGACGAACGAAGAGAGATTGCTTTGTGAAGGTTG-TCGACATACTTGTCTA
5709 GAAGTTGAAGAAGTTCAAGTAGATTCATGGCAGGTCTCAAGGATAGATTTTATCATGGAGGGCCA
520 GAAGTTGAAGAAGTTCAAGTAGATTCATGGCAGGTCTCAAGGATAGATTTTATCATGGAGGGCCA
* * * *
5774 AGGACTTTTCATGGTCTTCAAGACAAGCATGGAGAGCATGGAAAGGATGTGCATAGGCTGCAAGG
585 AGGACTTATCATGGTCTTGAAGACAAGCATGGAGAGCATGGAAAGGATGTGCATGGGCTACAAGG
*
5839 AAGCATGGAGATGCATGAAGATTATCGAGATATTAATAAGCAT-TTCCCAAGCACCAAAAAGATG
650 AAGCATGGAGATGCATGAAGATTATCGAGATATTGATAAGCATGTT-CCAAGCACCAAAAAGATG
* *
5903 CTAATCGATTCATTGAAGATGCCTGTTAGTCCGGTGACAAGAGCAAGAGCTAAGAGATTCAAGGA
714 CTAATCGATTCATTGAAGATGCCTATTAGTCCGATGACAAGAGCAAGAGCTAAGAGATTCAAGGA
* *
5968 TGCACTCATGGGCCTTGTACGAACTCATCTTGCAGACTTGAAGACCATTCAAGTTCAATTGAAGA
779 TGCACTCATGGGCCTTGTTCGAACTCATCTTGAAGACTTGAAGACCATTCAAGTTCAATTGAAGA
* *
6033 GCTTTGATGATGATTTGAGCAAGAAAACACCAATCAATTACAAGTTCATCACTTTGCTTGCTGTT
844 GCTTTGATGATGATTTGAGCAAGAAAACACTAATCAATTACAAGTTCATCACTTTGCTTGCTATT
*
6098 GATTCTAAATGGTCGGATTG
909 GATTCTAAATGGCCGGATTG
* * * *
6118 ACATAGTGGCATGAA--CCATATATCATTAGTTCTCTTTCTTTGGGCTTAATTCTATCTTAGGTC
1 ACATAGTGGCAT-AAGCCCA-ATATCATTAGTTATCTTTGTTTGGGCTTAATTCTATCTTAGATT
** *
6181 AGCTTATTTTTAAGTTTAAATGTTATTTGGGTTGGGCCTTGTTTGAATAAGTCCAATCCTTGTCT
64 AGCTTATTTTTAAGTTTGGATGTTATTTGGGTTGGGCCTTGTTTGAATAAGTCCAATCCTTGTTT
* * *
6246 AATTATGCTTTTATTTCCTTTTCCTAGTTGGACTTGGACTAGTTTTTTCCTAGCCCTTATATTTG
129 AATTATGCTTTTATTTCCCTTTCCTAGTTGGGCTTGGACTAGTTTTTCCCTAGCCCTTATATTTG
* * *
6311 GACGAAAATTAGGATTTATTTTAGGATTTTTGTTGACCATATCACTATATAAGTCCACCAATATC
194 GACGAAAATTAGGATTTATTTTAGGATTTTGGTTGACCCTATCACTATATAAGGCCACCAATATC
6376 TCTTGTAAAAGTGGAAGTTGAGTTGATTAATAAAATTGAGGTTTATTCTCCCAAATTGATTATCT
259 TCTTGTAAAAGTGGAAGTTGAGTTGATTAATAAAATTGAGGTTTATTCTCCCAAATTGATTATCT
* *
6441 TGGCATCATTGTTCTAGTTTGAGCAAACTTAGGGTTTTTCAATCTTGTAGAGTCCTAGCAAACAA
324 TGGCTTCATTGTTCTAGTTTGAGCAAACTTAGGGTTCTTCAATCTTGTAGAGTCCTAGCAAACAA
6506 TTAGGTTGTGTGATGCTTAATTGTTTGTGAATCTTGTGATCTTAGGTATTCAATTGCAGGTCTAA
389 TTAGGTTGTGTGATGCTTAATTGTTTGTGAATCTTGTGATCTTAGGTATTCAATTGCAGGTCTAA
* *
6571 TTGAAGACTTAA-GACTGACGAACGAAGAGAGATTGCTTTGTGAAGGTTGTCGACATACTTGTAT
454 TTGAAGACTTAAGGTCTGACGAACGAAGAGAGATTGCTTTGTGAAGGTTGTCGACATACTTGTCT
* * *
6635 AGAAGTTGAAGAAGTTCAAGTATATTCGTGGCAGGTCTCAAGGATAGATTTTATCGTGGAGGGCC
519 AGAAGTTGAAGAAGTTCAAGTAGATTCATGGCAGGTCTCAAGGATAGATTTTATCATGGAGGGCC
*
6700 AAGGACTTATCATAGTCTTGAAG---A-C----A-AGCATGGAAAGGATGTGCATGGGCTACAAG
584 AAGGACTTATCATGGTCTTGAAGACAAGCATGGAGAGCATGGAAAGGATGTGCATGGGCTACAAG
*
6756 GAAGCATGGAGATGCATGAAGATTATCGAGATATTGATAAGCATGTTCCAAGCACCAAAAAGATA
649 GAAGCATGGAGATGCATGAAGATTATCGAGATATTGATAAGCATGTTCCAAGCACCAAAAAGATG
*
6821 CTAATCGATTCATTGAAGATGCGTATTAGTCCGATGACAAGAGCAAGAGCTAAGAGATTCAAGGA
714 CTAATCGATTCATTGAAGATGCCTATTAGTCCGATGACAAGAGCAAGAGCTAAGAGATTCAAGGA
* * *
6886 TGCACTCATGGGCCTTATTCGAACTCAACTTGAAGACTTGAAGACCATTCAAGTTCAATTGAAGG
779 TGCACTCATGGGCCTTGTTCGAACTCATCTTGAAGACTTGAAGACCATTCAAGTTCAATTGAAGA
* *
6951 GCTTAGATGATGATTTGAGCAAGAAAACACTAATCAATTACAAGTTCATCGCTTTGCTTGCTATT
844 GCTTTGATGATGATTTGAGCAAGAAAACACTAATCAATTACAAGTTCATCACTTTGCTTGCTATT
7016 GATTCTAAATGGCCGGATTG
909 GATTCTAAATGGCCGGATTG
7036 ACATAGTGGCATAAGCCCAATATCATTAGTTATCTTTGTTTGGGCTTAATTCTATCTTAGATTAG
1 ACATAGTGGCATAAGCCCAATATCATTAGTTATCTTTGTTTGGGCTTAATTCTATCTTAGATTAG
* *
7101 CTTATTTTTAAGTTTGGATGTTATTTGGGTTGGGCCTTGTTGGAATAAGTCCAATTCTTGTTTAA
66 CTTATTTTTAAGTTTGGATGTTATTTGGGTTGGGCCTTGTTTGAATAAGTCCAATCCTTGTTTAA
*
7166 TTATGCTTTTATTTCCCTTTCCTAGTTGGGCTTGGACTAGTTTTTCCCTAACCCTTATATTTGGA
131 TTATGCTTTTATTTCCCTTTCCTAGTTGGGCTTGGACTAGTTTTTCCCTAGCCCTTATATTTGGA
7231 CG---A--A--A---A--TTAGGATTTTGGTTGACCCTATCACTATATAAGGCCACCAATATCTC
196 CGAAAATTAGGATTTATTTTAGGATTTTGGTTGACCCTATCACTATATAAGGCCACCAATATCTC
* *
7284 TTGTAAAAGTGGAAGTTGAGTTGATTAATGAAATTGAGGTTTATTCTCCCAAATTGATTGTCTTG
261 TTGTAAAAGTGGAAGTTGAGTTGATTAATAAAATTGAGGTTTATTCTCCCAAATTGATTATCTTG
*
7349 GCTTCATTGTTCTAGTTTGAGCAAACTCAGGGTTCTTCAATCTTGTAGAGTCCTAGCAAACAATT
326 GCTTCATTGTTCTAGTTTGAGCAAACTTAGGGTTCTTCAATCTTGTAGAGTCCTAGCAAACAATT
7414 AGGTTGTGTGATGCTTAATTGTTTGTGAATCTTGTGATCTTAGGTATTCAATTGCAGGTCTAATT
391 AGGTTGTGTGATGCTTAATTGTTTGTGAATCTTGTGATCTTAGGTATTCAATTGCAGGTCTAATT
7479 GAAGACT
456 GAAGACT
7486 GTTGGACTTT
Statistics
Matches: 3040, Mismatches: 164, Indels: 51
0.93 0.05 0.02
Matches are distributed among these distances:
906 241 0.08
908 1 0.00
911 1 0.00
913 1 0.00
915 1 0.00
917 2 0.00
918 467 0.15
919 6 0.00
923 6 0.00
924 569 0.19
925 302 0.10
926 302 0.10
927 1139 0.37
928 2 0.00
ACGTcount: A:0.29, C:0.15, G:0.21, T:0.35
Consensus pattern (928 bp):
ACATAGTGGCATAAGCCCAATATCATTAGTTATCTTTGTTTGGGCTTAATTCTATCTTAGATTAG
CTTATTTTTAAGTTTGGATGTTATTTGGGTTGGGCCTTGTTTGAATAAGTCCAATCCTTGTTTAA
TTATGCTTTTATTTCCCTTTCCTAGTTGGGCTTGGACTAGTTTTTCCCTAGCCCTTATATTTGGA
CGAAAATTAGGATTTATTTTAGGATTTTGGTTGACCCTATCACTATATAAGGCCACCAATATCTC
TTGTAAAAGTGGAAGTTGAGTTGATTAATAAAATTGAGGTTTATTCTCCCAAATTGATTATCTTG
GCTTCATTGTTCTAGTTTGAGCAAACTTAGGGTTCTTCAATCTTGTAGAGTCCTAGCAAACAATT
AGGTTGTGTGATGCTTAATTGTTTGTGAATCTTGTGATCTTAGGTATTCAATTGCAGGTCTAATT
GAAGACTTAAGGTCTGACGAACGAAGAGAGATTGCTTTGTGAAGGTTGTCGACATACTTGTCTAG
AAGTTGAAGAAGTTCAAGTAGATTCATGGCAGGTCTCAAGGATAGATTTTATCATGGAGGGCCAA
GGACTTATCATGGTCTTGAAGACAAGCATGGAGAGCATGGAAAGGATGTGCATGGGCTACAAGGA
AGCATGGAGATGCATGAAGATTATCGAGATATTGATAAGCATGTTCCAAGCACCAAAAAGATGCT
AATCGATTCATTGAAGATGCCTATTAGTCCGATGACAAGAGCAAGAGCTAAGAGATTCAAGGATG
CACTCATGGGCCTTGTTCGAACTCATCTTGAAGACTTGAAGACCATTCAAGTTCAATTGAAGAGC
TTTGATGATGATTTGAGCAAGAAAACACTAATCAATTACAAGTTCATCACTTTGCTTGCTATTGA
TTCTAAATGGCCGGATTG
Found at i:8064 original size:33 final size:34
Alignment explanation
Indices: 7983--8064 Score: 82
Period size: 33 Copynumber: 2.4 Consensus size: 34
7973 CCGCGCAACA
*
7983 CTGGCCACAAGACCGGCCACGCGACTTGGAAATGTC
1 CTGGCCAC-A-ACCGGCCACGCGACTAGGAAATGTC
*
8019 C-GGCCATC-ACCGGCCACGCGA-TAAGGACATG-C
1 CTGGCCA-CAACCGGCCACGCGACT-AGGAAATGTC
8051 CTGGCCACAACCGG
1 CTGGCCACAACCGG
8065 TCAAACGACT
Statistics
Matches: 40, Mismatches: 2, Indels: 11
0.75 0.04 0.21
Matches are distributed among these distances:
32 4 0.10
33 29 0.73
35 5 0.12
36 2 0.05
ACGTcount: A:0.24, C:0.37, G:0.28, T:0.11
Consensus pattern (34 bp):
CTGGCCACAACCGGCCACGCGACTAGGAAATGTC
Found at i:10561 original size:40 final size:40
Alignment explanation
Indices: 10482--10566 Score: 100
Period size: 40 Copynumber: 2.1 Consensus size: 40
10472 AATTGAGGAT
* * * *
10482 TTAATTCATAGAAATTAAGTAAAGATAGTACTCAGAAGAC
1 TTAATTCATAGAAATTAAGTAAAAACAGCACTCAAAAGAC
**
10522 TTAATTCATCA-AAATTAAGTAAAAACAGCGGTCAAAAGAC
1 TTAATTCAT-AGAAATTAAGTAAAAACAGCACTCAAAAGAC
10562 TTAAT
1 TTAAT
10567 AGAAATTAAA
Statistics
Matches: 38, Mismatches: 6, Indels: 2
0.83 0.13 0.04
Matches are distributed among these distances:
40 37 0.97
41 1 0.03
ACGTcount: A:0.48, C:0.12, G:0.13, T:0.27
Consensus pattern (40 bp):
TTAATTCATAGAAATTAAGTAAAAACAGCACTCAAAAGAC
Found at i:10702 original size:11 final size:11
Alignment explanation
Indices: 10686--10749 Score: 74
Period size: 11 Copynumber: 5.8 Consensus size: 11
10676 TTAGGCAAAG
10686 TTAGACTGAAA
1 TTAGACTGAAA
10697 TTAGACTGAAA
1 TTAGACTGAAA
** *
10708 AAAGACTGATA
1 TTAGACTGAAA
*
10719 TTAAACTGAAA
1 TTAGACTGAAA
* *
10730 TCAAACTGAAA
1 TTAGACTGAAA
10741 TTAGACTGA
1 TTAGACTGA
10750 TAAAAGACTG
Statistics
Matches: 43, Mismatches: 10, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
11 43 1.00
ACGTcount: A:0.48, C:0.11, G:0.16, T:0.25
Consensus pattern (11 bp):
TTAGACTGAAA
Found at i:10714 original size:22 final size:22
Alignment explanation
Indices: 10688--10759 Score: 92
Period size: 22 Copynumber: 3.3 Consensus size: 22
10678 AGGCAAAGTT
10688 AGACTGAAATTAGACTGAAAAA
1 AGACTGAAATTAGACTGAAAAA
* * *
10710 AGACTGATATTAAACTGAAATCA
1 AGACTGAAATTAGACTGAAA-AA
*
10733 A-ACTGAAATTAGACTGATAAA
1 AGACTGAAATTAGACTGAAAAA
10754 AGACTG
1 AGACTG
10760 GCTTAGTTTC
Statistics
Matches: 41, Mismatches: 7, Indels: 4
0.79 0.13 0.08
Matches are distributed among these distances:
21 2 0.05
22 37 0.90
23 2 0.05
ACGTcount: A:0.50, C:0.11, G:0.17, T:0.22
Consensus pattern (22 bp):
AGACTGAAATTAGACTGAAAAA
Found at i:10806 original size:36 final size:35
Alignment explanation
Indices: 10752--11547 Score: 922
Period size: 36 Copynumber: 22.7 Consensus size: 35
10742 TAGACTGATA
*
10752 AAAGACTGGCTTAGTTTCAAGGAAGCTAGGTAAAG
1 AAAGACTGGCTTAGTTTCAAGGAAACTAGGTAAAG
* * *
10787 AATAGACTGGCTTAATTTCAAGGAAATTAAGTAAA-
1 AA-AGACTGGCTTAGTTTCAAGGAAACTAGGTAAAG
10822 ACAAGACTGGCTTAGTTTCAAGGAAACTAGGTAAAG
1 A-AAGACTGGCTTAGTTTCAAGGAAACTAGGTAAAG
* * * * *
10858 ATAGACTGGCTTAATTTCAAGAAAATTAAGTAAA-
1 AAAGACTGGCTTAGTTTCAAGGAAACTAGGTAAAG
10892 AAAGAACTGGCTTAGTTTCAAGGAAACTAGGTAAAG
1 AAAG-ACTGGCTTAGTTTCAAGGAAACTAGGTAAAG
*
10928 TAAAGACTGGCTTAGTTTCAAGGAAACTAGGTGAAG
1 -AAAGACTGGCTTAGTTTCAAGGAAACTAGGTAAAG
10964 AAAAGACTGGCTTAGTTTCAAGGAAACTAGGTAAAG
1 -AAAGACTGGCTTAGTTTCAAGGAAACTAGGTAAAG
*
11000 AAAAGACTGGCTTAGTTTCATGGAAACTAGGTAAAG
1 -AAAGACTGGCTTAGTTTCAAGGAAACTAGGTAAAG
* * *
11036 -AAGACTGGCTTAATTTCAAGGAAATTAAGTAAA-
1 AAAGACTGGCTTAGTTTCAAGGAAACTAGGTAAAG
*
11069 ACAAGACTGGCTTAGTTTCAAGGAAACTAGGTGAAG
1 A-AAGACTGGCTTAGTTTCAAGGAAACTAGGTAAAG
* *
11105 AAAAAACTGGCTTAGTTTCAAGGAAACTAGGTGAAG
1 -AAAGACTGGCTTAGTTTCAAGGAAACTAGGTAAAG
11141 AAAAGACTGGCTTAGTTTCAAGGAAACTAGGTAAAG
1 -AAAGACTGGCTTAGTTTCAAGGAAACTAGGTAAAG
*
11177 AAAAGACTGGCTTAGTTTCAAGGAAACTAAGTAAAG
1 -AAAGACTGGCTTAGTTTCAAGGAAACTAGGTAAAG
* *
11213 AAAAGACTGGCTTAATTTCAAGGAAATTAGGTAAAG
1 -AAAGACTGGCTTAGTTTCAAGGAAACTAGGTAAAG
* * * *
11249 ATAGATTGGC-----TT-AA--AAATTAAGTAAA-
1 AAAGACTGGCTTAGTTTCAAGGAAACTAGGTAAAG
11275 AAAGAACTGGCTTAGTTTCAAGGAAACTAGGTAAAG
1 AAAG-ACTGGCTTAGTTTCAAGGAAACTAGGTAAAG
*
11311 AAAAGACTGGCTTAGTTTCAAGAAAACTAGGTAAAG
1 -AAAGACTGGCTTAGTTTCAAGGAAACTAGGTAAAG
* * * *
11347 ATAGACTGACTTAATTTCAAGGAAATTAGGTAAAG
1 AAAGACTGGCTTAGTTTCAAGGAAACTAGGTAAAG
* * * * *
11382 ATAGACTGGCTTAATTTCAAGGGAATTAAGTAAA-
1 AAAGACTGGCTTAGTTTCAAGGAAACTAGGTAAAG
* * *
11416 AAAGGACTGGCTTAGTTTCAAGGAAATTAGATAAAAA
1 AAA-GACTGGCTTAGTTTCAAGGAAACTAGGT-AAAG
* *
11453 AAAGACTGGCTTAATTTCAAGGAAATTAGGTAAAGG
1 AAAGACTGGCTTAGTTTCAAGGAAACTAGGTAAA-G
* * *
11489 AAAGACTGGCTTAATTTCAAGGAAATTAAGTAAA-
1 AAAGACTGGCTTAGTTTCAAGGAAACTAGGTAAAG
* * *
11523 AAGACACAGGCTTAATTTC-AGGAAA
1 AA-AGACTGGCTTAGTTTCAAGGAAA
11548 GGAAATTAAG
Statistics
Matches: 672, Mismatches: 63, Indels: 53
0.85 0.08 0.07
Matches are distributed among these distances:
26 3 0.00
27 16 0.02
29 2 0.00
30 2 0.00
32 2 0.00
33 2 0.00
34 42 0.06
35 235 0.35
36 356 0.53
37 12 0.02
ACGTcount: A:0.42, C:0.10, G:0.23, T:0.25
Consensus pattern (35 bp):
AAAGACTGGCTTAGTTTCAAGGAAACTAGGTAAAG
Found at i:11048 original size:177 final size:177
Alignment explanation
Indices: 10751--11547 Score: 1084
Period size: 177 Copynumber: 4.6 Consensus size: 177
10741 TTAGACTGAT
* * * *
10751 AAAAGACTGGCTTAGTTTCAAGGAAGCTAGGTAAAGAATAGACTGGCTTAATTTCAAGGAAATTA
1 AAAAGACTGGCTTAGTTTCAAGGAAACTAGGTAAAGAAAAGACTGGCTTAGTTTCAAGGAAACTA
* * *
10816 AGTAAA-ACAAGACTGGCTTAGTTTCAAGGAAACTAGGTAAAGATAGACTGGCTTAATTTCAAGA
66 GGTAAAGAAAAGACTGGCTTAGTTTCAAGGAAACTAGGTAAAGATAGACTGGCTTAATTTCAAGG
10880 AAATTAAGTAAAAAAGAACTGGCTTAGTTTCAAGGAAACTAGGTAAAG
131 AAATTAAGTAAAAAAG-ACTGGCTTAGTTTCAAGGAAACTAGGTAAAG
* *
10928 TAAAGACTGGCTTAGTTTCAAGGAAACTAGGTGAAGAAAAGACTGGCTTAGTTTCAAGGAAACTA
1 AAAAGACTGGCTTAGTTTCAAGGAAACTAGGTAAAGAAAAGACTGGCTTAGTTTCAAGGAAACTA
*
10993 GGTAAAGAAAAGACTGGCTTAGTTTCATGGAAACTAGGTAAAGA-AGACTGGCTTAATTTCAAGG
66 GGTAAAGAAAAGACTGGCTTAGTTTCAAGGAAACTAGGTAAAGATAGACTGGCTTAATTTCAAGG
*
11057 AAATTAAGTAAAACAAGACTGGCTTAGTTTCAAGGAAACTAGGTGAAG
131 AAATTAAGTAAAA-AAGACTGGCTTAGTTTCAAGGAAACTAGGTAAAG
* *
11105 AAAAAACTGGCTTAGTTTCAAGGAAACTAGGTGAAGAAAAGACTGGCTTAGTTTCAAGGAAACTA
1 AAAAGACTGGCTTAGTTTCAAGGAAACTAGGTAAAGAAAAGACTGGCTTAGTTTCAAGGAAACTA
* *
11170 GGTAAAGAAAAGACTGGCTTAGTTTCAAGGAAACTAAGTAAAGAAAAGACTGGCTTAATTTCAAG
66 GGTAAAGAAAAGACTGGCTTAGTTTCAAGGAAACTAGGTAAAG-ATAGACTGGCTTAATTTCAAG
* * * * *
11235 GAAATTAGGTAAAGATAGATTGGC-----TT-AA--AAATTAAGT-AA-
130 GAAATTAAGTAAA-AAAGACTGGCTTAGTTTCAAGGAAACTAGGTAAAG
*
11274 AAAAGAACTGGCTTAGTTTCAAGGAAACTAGGTAAAGAAAAGACTGGCTTAGTTTCAAGAAAACT
1 AAAAG-ACTGGCTTAGTTTCAAGGAAACTAGGTAAAGAAAAGACTGGCTTAGTTTCAAGGAAACT
* * * *
11339 AGGTAAAG-ATAGACTGACTTAATTTCAAGGAAATTAGGTAAAGATAGACTGGCTTAATTTCAAG
65 AGGTAAAGAAAAGACTGGCTTAGTTTCAAGGAAACTAGGTAAAGATAGACTGGCTTAATTTCAAG
* * * *
11403 GGAATTAAGTAAAAAAGGACTGGCTTAGTTTCAAGGAAATTAGATAAAA
130 GAAATTAAGTAAAAAA-GACTGGCTTAGTTTCAAGGAAACTAGGTAAAG
* * * * *
11452 AAAAGACTGGCTTAATTTCAAGGAAATTAGGTAAAGGAAAGACTGGCTTAATTTCAAGGAAATTA
1 AAAAGACTGGCTTAGTTTCAAGGAAACTAGGTAAAGAAAAGACTGGCTTAGTTTCAAGGAAACTA
* * * * *
11517 AGTAAA-AAGACACAGGCTTAATTTC-AGGAAA
66 GGTAAAGAAAAGACTGGCTTAGTTTCAAGGAAA
11548 GGAAATTAAG
Statistics
Matches: 556, Mismatches: 46, Indels: 37
0.87 0.07 0.06
Matches are distributed among these distances:
167 2 0.00
168 37 0.07
169 34 0.06
170 67 0.12
171 7 0.01
173 4 0.01
174 4 0.01
176 13 0.02
177 305 0.55
178 44 0.08
179 38 0.07
180 1 0.00
ACGTcount: A:0.43, C:0.10, G:0.23, T:0.25
Consensus pattern (177 bp):
AAAAGACTGGCTTAGTTTCAAGGAAACTAGGTAAAGAAAAGACTGGCTTAGTTTCAAGGAAACTA
GGTAAAGAAAAGACTGGCTTAGTTTCAAGGAAACTAGGTAAAGATAGACTGGCTTAATTTCAAGG
AAATTAAGTAAAAAAGACTGGCTTAGTTTCAAGGAAACTAGGTAAAG
Found at i:11118 original size:213 final size:212
Alignment explanation
Indices: 10751--11547 Score: 1007
Period size: 213 Copynumber: 3.8 Consensus size: 212
10741 TTAGACTGAT
* * *
10751 AAAAGACTGGCTTAGTTTCAAGGAAGCTAGGTAAAGAATAGACTGGCTTAATTTCAAGGAAATTA
1 AAAAGACTGGCTTAGTTTCAAGGAAACTAAGTAAAGAAAAGACTGGCTTAATTTCAAGGAAATTA
* * * * * * *
10816 AGTAAAACAAGACTGGCTTAGTTTCAAGGAAACTAGGTAAAGATAGACTGGCTTAATTTCAAGAA
66 GGTAAAAGAAGACTGGCTTAATTTCAAGGAAATTAAGTAAAGAAAGACTGGCTTAATTTCAAGGA
* *
10881 AATTAAGTAA-AAAAGAACTGGCTTAGTTTCAAGGAAACTAGGTAAAGTAAAGACTGGCTTAGTT
131 AACTAGGTAAGAAAA-AACTGGCTTAGTTTCAAGGAAACTAGGTAAAG-AAAGACTGGCTTAGTT
*
10945 TCAAGGAAACTAGGTGAAG
194 TCAAGGAAACTAGGTAAAG
* * * *
10964 AAAAGACTGGCTTAGTTTCAAGGAAACTAGGTAAAGAAAAGACTGGCTTAGTTTCATGGAAACTA
1 AAAAGACTGGCTTAGTTTCAAGGAAACTAAGTAAAGAAAAGACTGGCTTAATTTCAAGGAAATTA
*
11029 GGT-AAAGAAGACTGGCTTAATTTCAAGGAAATTAAGTAAA-ACAAGACTGGCTTAGTTTCAAGG
66 GGTAAAAGAAGACTGGCTTAATTTCAAGGAAATTAAGTAAAGA-AAGACTGGCTTAATTTCAAGG
*
11092 AAACTAGGTGAAGAAAAAACTGGCTTAGTTTCAAGGAAACTAGGTGAAGAAAAGACTGGCTTAGT
130 AAACTAGGT-AAGAAAAAACTGGCTTAGTTTCAAGGAAACTAGGTAAAG-AAAGACTGGCTTAGT
11157 TTCAAGGAAACTAGGTAAAG
193 TTCAAGGAAACTAGGTAAAG
11177 AAAAGACTGGCTTAGTTTCAAGGAAACTAAGTAAAGAAAAGACTGGCTTAATTTCAAGGAAATTA
1 AAAAGACTGGCTTAGTTTCAAGGAAACTAAGTAAAGAAAAGACTGGCTTAATTTCAAGGAAATTA
* *
11242 GGT-AAAGATAGATTGGC-----TT-AA--AAATTAAGTAAA-AAAGAACTGGCTTAGTTTCAAG
66 GGTAAAAGA-AGACTGGCTTAATTTCAAGGAAATTAAGTAAAGAAAG-ACTGGCTTAATTTCAAG
* * * * *
11297 GAAACTAGGTAAAGAAAAGACTGGCTTAGTTTCAAGAAAACTAGGTAAAGATAGACTGACTTAAT
129 GAAACTAGGT-AAGAAAAAACTGGCTTAGTTTCAAGGAAACTAGGTAAAGAAAGACTGGCTTAGT
*
11362 TTCAAGGAAATTAGGTAAAG
193 TTCAAGGAAACTAGGTAAAG
* * * * * *
11382 -ATAGACTGGCTTAATTTCAAGGGAATTAAGTAAA-AAAGGACTGGCTTAGTTTCAAGGAAATTA
1 AAAAGACTGGCTTAGTTTCAAGGAAACTAAGTAAAGAAAAGACTGGCTTAATTTCAAGGAAATTA
* * *
11445 GATAAAAAAAAGACTGGCTTAATTTCAAGGAAATTAGGTAAAGGAAAGACTGGCTTAATTTCAAG
66 GGT-AAAAGAAGACTGGCTTAATTTCAAGGAAATTAAGTAAA-GAAAGACTGGCTTAATTTCAAG
* * * * *
11510 GAAATTAAGTAA-AAAGACACAGGCTTAATTTC-AGGAAA
129 GAAACTAGGTAAGAAA-AAACTGGCTTAGTTTCAAGGAAA
11548 GGAAATTAAG
Statistics
Matches: 518, Mismatches: 48, Indels: 38
0.86 0.08 0.06
Matches are distributed among these distances:
203 29 0.06
204 37 0.07
205 38 0.07
206 76 0.15
208 2 0.00
209 4 0.01
210 2 0.00
211 9 0.02
212 84 0.16
213 222 0.43
214 15 0.03
ACGTcount: A:0.43, C:0.10, G:0.23, T:0.25
Consensus pattern (212 bp):
AAAAGACTGGCTTAGTTTCAAGGAAACTAAGTAAAGAAAAGACTGGCTTAATTTCAAGGAAATTA
GGTAAAAGAAGACTGGCTTAATTTCAAGGAAATTAAGTAAAGAAAGACTGGCTTAATTTCAAGGA
AACTAGGTAAGAAAAAACTGGCTTAGTTTCAAGGAAACTAGGTAAAGAAAGACTGGCTTAGTTTC
AAGGAAACTAGGTAAAG
Found at i:11351 original size:98 final size:100
Alignment explanation
Indices: 10751--11547 Score: 687
Period size: 106 Copynumber: 7.6 Consensus size: 100
10741 TTAGACTGAT
* * * *
10751 AAAAGACTGGCTTAGTTTCAAGGAAGCTAGGTAAAGAATAGACTGGCTTAATTTCAAGGAAATTA
1 AAAAGACTGGCTTAGTTTCAAGGAAACTAGGTAAAGAAAAGACTGGCTTAGTTTCAAGGAAACTA
* * * *
10816 AGTAAA-ACAAGACTGGCTTAGTTTCAAGGAAACTAGGTAA
66 GGTAAAGA-TAGACTGGC----TTTCAA-GAAATTAAGTAA
* * * * *
10856 AGATAGACTGGCTTAATTTCAAGAAAATTAAGT-AA-AAAAGAACTGGCTTAGTTTCAAGGAAAC
1 A-AAAGACTGGCTTAGTTTCAAGGAAACTAGGTAAAGAAAAG-ACTGGCTTAGTTTCAAGGAAAC
* * *
10919 TAGGTAAAGTAAAGACTGGCTTAGTTTCAAGGAAACTAGGTGAA
64 TAGGTAAAG-ATAGACTGGC----TTTCAA-GAAATTAAGT-AA
*
10963 GAAAAGACTGGCTTAGTTTCAAGGAAACTAGGTAAAGAAAAGACTGGCTTAGTTTCATGGAAACT
1 -AAAAGACTGGCTTAGTTTCAAGGAAACTAGGTAAAGAAAAGACTGGCTTAGTTTCAAGGAAACT
11028 AGGTAAAGA-AGACTGGCTTAATTTCAAGGAAATTAAGTAA
65 AGGTAAAGATAGACTGGC----TTTCAA-GAAATTAAGTAA
* *
11068 AACAAGACTGGCTTAGTTTCAAGGAAACTAGGTGAAGAAAAAACTGGCTTAGTTTCAAGGAAACT
1 AA-AAGACTGGCTTAGTTTCAAGGAAACTAGGTAAAGAAAAGACTGGCTTAGTTTCAAGGAAACT
* * * *
11133 AGGTGAAGAAAAGACTGGCTTAGTTTCAAGGAAACTAGGTAAA
65 AGGTAAAG-ATAGACTGGC----TTTCAA-GAAATTAAGT-AA
* * *
11176 GAAAAGACTGGCTTAGTTTCAAGGAAACTAAGTAAAGAAAAGACTGGCTTAATTTCAAGGAAATT
1 -AAAAGACTGGCTTAGTTTCAAGGAAACTAGGTAAAGAAAAGACTGGCTTAGTTTCAAGGAAACT
*
11241 AGGTAAAGATAGATTGGC-TT-AA-AAATTAAGTAA
65 AGGTAAAGATAGACTGGCTTTCAAGAAATTAAGTAA
*
11274 AAAAGAACTGGCTTAGTTTCAAGGAAACTAGGTAAAGAAAAGACTGGCTTAGTTTCAAGAAAACT
1 AAAAG-ACTGGCTTAGTTTCAAGGAAACTAGGTAAAGAAAAGACTGGCTTAGTTTCAAGGAAACT
* *
11339 AGGTAAAGATAGACTGACTTAATTTCAAGGAAATTAGGTAA
65 AGGTAAAGATAGACTGGC----TTTCAA-GAAATTAAGTAA
* * * * * * *
11380 AGATAGACTGGCTTAATTTCAAGGGAATTAAGTAAA-AAAGGACTGGCTTAGTTTCAAGGAAATT
1 A-AAAGACTGGCTTAGTTTCAAGGAAACTAGGTAAAGAAAAGACTGGCTTAGTTTCAAGGAAACT
* * * *
11444 AGATAAAAAAAAGACTGGCTTAATTTCAAGGAAATTAGGTAA
65 AGGT-AAAGATAGACTGGC----TTTCAA-GAAATTAAGTAA
* * * * * * *
11486 AGGAAAGACTGGCTTAATTTCAAGGAAATTAAGTAAA-AAGACACAGGCTTAATTTC-AGGAAA
1 A--AAAGACTGGCTTAGTTTCAAGGAAACTAGGTAAAGAAAAGACTGGCTTAGTTTCAAGGAAA
11548 GGAAATTAAG
Statistics
Matches: 605, Mismatches: 62, Indels: 49
0.84 0.09 0.07
Matches are distributed among these distances:
97 5 0.01
98 73 0.12
99 7 0.01
101 2 0.00
102 2 0.00
103 2 0.00
104 8 0.01
105 126 0.21
106 160 0.26
107 114 0.19
108 99 0.16
109 7 0.01
ACGTcount: A:0.43, C:0.10, G:0.23, T:0.25
Consensus pattern (100 bp):
AAAAGACTGGCTTAGTTTCAAGGAAACTAGGTAAAGAAAAGACTGGCTTAGTTTCAAGGAAACTA
GGTAAAGATAGACTGGCTTTCAAGAAATTAAGTAA
Found at i:11588 original size:32 final size:32
Alignment explanation
Indices: 11551--11657 Score: 117
Period size: 32 Copynumber: 3.2 Consensus size: 32
11541 CAGGAAAGGA
11551 AATTAAGTAAAATAAAGAACTTAATTCAGGGT
1 AATTAAGTAAAATAAAGAACTTAATTCAGGGT
* *
11583 AATTAAGTGGAAGTCAATAAA-AGGCTTAATTCAGAGT
1 AATTAAGT--AA---AATAAAGA-ACTTAATTCAGGGT
* *
11620 AATTAAGTAGAATAAAGAACTTAATTCAAGGT
1 AATTAAGTAAAATAAAGAACTTAATTCAGGGT
11652 AATTAA
1 AATTAA
11658 AGGAAGTCAA
Statistics
Matches: 62, Mismatches: 6, Indels: 14
0.76 0.07 0.17
Matches are distributed among these distances:
32 31 0.50
33 1 0.02
34 2 0.03
35 1 0.02
36 1 0.02
37 26 0.42
ACGTcount: A:0.49, C:0.07, G:0.17, T:0.28
Consensus pattern (32 bp):
AATTAAGTAAAATAAAGAACTTAATTCAGGGT
Found at i:11602 original size:37 final size:37
Alignment explanation
Indices: 11561--11673 Score: 132
Period size: 37 Copynumber: 3.2 Consensus size: 37
11551 AATTAAGTAA
11561 AATAAAGAACTTAATTCAGGGTAATTAAGTGGAAGTC
1 AATAAAGAACTTAATTCAGGGTAATTAAGTGGAAGTC
* *
11598 AATAAA-AGGCTTAATTCAGAGTAATTAAGT---AG--
1 AATAAAGA-ACTTAATTCAGGGTAATTAAGTGGAAGTC
* *
11630 AATAAAGAACTTAATTCAAGGTAATTAA-AGGAAGTC
1 AATAAAGAACTTAATTCAGGGTAATTAAGTGGAAGTC
11666 AATAAAGA
1 AATAAAGA
11674 GTTTAATCTA
Statistics
Matches: 63, Mismatches: 6, Indels: 15
0.75 0.07 0.18
Matches are distributed among these distances:
32 23 0.37
33 1 0.02
34 4 0.06
36 9 0.14
37 26 0.41
ACGTcount: A:0.49, C:0.07, G:0.19, T:0.26
Consensus pattern (37 bp):
AATAAAGAACTTAATTCAGGGTAATTAAGTGGAAGTC
Found at i:12770 original size:18 final size:18
Alignment explanation
Indices: 12706--12771 Score: 69
Period size: 18 Copynumber: 3.7 Consensus size: 18
12696 GGATTCAGAG
* *
12706 GATGATGTTTACCTAGAT
1 GATGATCTTGACCTAGAT
* * *
12724 GATGGTGTTGACCCAGAT
1 GATGATCTTGACCTAGAT
* *
12742 GATGATTTTGATCTAGAT
1 GATGATCTTGACCTAGAT
12760 GATGATCTTGAC
1 GATGATCTTGAC
12772 GAGGATTTTG
Statistics
Matches: 39, Mismatches: 9, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
18 39 1.00
ACGTcount: A:0.26, C:0.12, G:0.26, T:0.36
Consensus pattern (18 bp):
GATGATCTTGACCTAGAT
Found at i:12771 original size:36 final size:36
Alignment explanation
Indices: 12701--12771 Score: 90
Period size: 36 Copynumber: 2.0 Consensus size: 36
12691 GATTCGGATT
* *
12701 CAGAGGATGATGTTTACCTAGATGATGGTGTTGACC
1 CAGAGGATGATGTTTACCTAGATGATGATCTTGACC
* *
12737 CAGATGATGAT-TTTGATCTAGATGATGATCTTGAC
1 CAGAGGATGATGTTT-ACCTAGATGATGATCTTGAC
12772 GAGGATTTTG
Statistics
Matches: 30, Mismatches: 4, Indels: 2
0.83 0.11 0.06
Matches are distributed among these distances:
35 3 0.10
36 27 0.90
ACGTcount: A:0.27, C:0.13, G:0.27, T:0.34
Consensus pattern (36 bp):
CAGAGGATGATGTTTACCTAGATGATGATCTTGACC
Found at i:12779 original size:30 final size:30
Alignment explanation
Indices: 12745--12806 Score: 79
Period size: 30 Copynumber: 2.1 Consensus size: 30
12735 CCCAGATGAT
* * *
12745 GATTTTGATCTAGATGATGATCTTGACGAG
1 GATTTTGACCTAGATGAGGATCCTGACGAG
* *
12775 GATTTTGACCTGGATGAGGATCCTGATGAG
1 GATTTTGACCTAGATGAGGATCCTGACGAG
12805 GA
1 GA
12807 CTTTCATCCA
Statistics
Matches: 27, Mismatches: 5, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
30 27 1.00
ACGTcount: A:0.26, C:0.11, G:0.31, T:0.32
Consensus pattern (30 bp):
GATTTTGACCTAGATGAGGATCCTGACGAG
Found at i:12931 original size:15 final size:15
Alignment explanation
Indices: 12898--12931 Score: 50
Period size: 15 Copynumber: 2.3 Consensus size: 15
12888 TCAGACGACA
*
12898 AGGAAGTCGACTGCG
1 AGGAAGTCGACGGCG
*
12913 AGGAAGTCGACGGCT
1 AGGAAGTCGACGGCG
12928 AGGA
1 AGGA
12932 TGTCCGTCAT
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
15 17 1.00
ACGTcount: A:0.29, C:0.18, G:0.41, T:0.12
Consensus pattern (15 bp):
AGGAAGTCGACGGCG
Found at i:20949 original size:411 final size:410
Alignment explanation
Indices: 20203--20960 Score: 1198
Period size: 410 Copynumber: 1.8 Consensus size: 410
20193 AAGCATGGAG
* * * * *
20203 AGCATGGAAAGGATGTGCATGGGCTGCAAGGAAGCATGGAGATGAATGAAGATTATCGAGATATT
1 AGCATGGAAAGGACGTGCAAGGGCTGCAAGGAAGCATGGAGATGAATGAAGATCATAGAGATATC
* * * *
20268 GATAAGCATGCTCTAAGCACCAAAAAGATGCTTATCGATTCATTGAAGATGCCTATTTGTCAGAT
66 GATAAGCATGCTCCAAGCACCAAAAAGATGCTTATCGATCCATTGAAGATGCCTAATAGTCAGAT
20333 GACAAGAGCAAGAGCTAAGAGATTCAAGGATGCACTCATGTGCCTTGTCCGACTCATCTTGAAGA
131 GACAAGAGCAAGAGCTAAGAGATTCAAGGATGCACTCATGTGCCTTGTCCGACTCATCTTGAAGA
* *
20398 CTTCAAGACCATTCAAGTTCAATTGAAGAGCTTTGATGGTGATTTGAGCAAGAAAACACCAATCA
196 CTTCAAGACCATTCAAGTTCAATTGAAGAGCTTTGATGATGATTTGAGCAAGAAAACACAAATCA
* *
20463 ATTACAAGTTCATCACTTTGCTTGCTGTTGATTCTAAATGGCCGGATTGACATAGTGGCATGAGC
261 ATTACAAGTTCATCACATTGCTTGCTATTGATTCTAAATGGCCGGATTGACATAGTGGCATGAGC
*
20528 CCAATATCATTAGTTCTCTTTGATGCGCCCAAGCCTTATCATGGAAGGAATTATGCGCCAAGGAC
326 CCAATATCATTAGTTATCTTTGATGCGCCCAAGCCTTATCATGGAAGGAATTATGCGCCAAGGAC
20593 TTATTATGGCCTTGAAGACA
391 TTATTATGGCCTTGAAGACA
*
20613 AGCATGGAAAGGACGTGCAAGGGCTGCAAGGAAGCATGGAGATGTATGAAGATCATAGAGATATC
1 AGCATGGAAAGGACGTGCAAGGGCTGCAAGGAAGCATGGAGATGAATGAAGATCATAGAGATATC
* * * * *
20678 GTTGAGCATGTTCCAAGCTCCAAAAAGATGC-TATTCGATCCATTGAAGATGCCTAATAGTCCGA
66 GATAAGCATGCTCCAAGCACCAAAAAGATGCTTA-TCGATCCATTGAAGATGCCTAATAGTCAGA
*
20742 TGACAAGAGCAAGAGCTAAGAGATTCAAGGATGCACTCATG-GACCTTGTTCGAACTCATCTTGA
130 TGACAAGAGCAAGAGCTAAGAGATTCAAGGATGCACTCATGTG-CCTTGTCCG-ACTCATCTTGA
* * * * **
20806 AGACTTGAAGACCATTGAAGTTCAATTGAAGAGCTTTGGTGATGATTTGGGCAAGAAATTACAAA
193 AGACTTCAAGACCATTCAAGTTCAATTGAAGAGCTTTGATGATGATTTGAGCAAGAAAACACAAA
*
20871 TCAATTACAAGTTCATCACATTGCTTGCTATTGATTCTAGATGGCCGGATTGACATCA-TGGCAT
258 TCAATTACAAGTTCATCACATTGCTTGCTATTGATTCTAAATGGCCGGATTGACAT-AGTGGCAT
*
20935 GAGCCCATTATCATTAGTTATCTTTG
322 GAGCCCAATATCATTAGTTATCTTTG
20961 TTTGGGCTTA
Statistics
Matches: 315, Mismatches: 29, Indels: 7
0.90 0.08 0.02
Matches are distributed among these distances:
409 3 0.01
410 160 0.51
411 151 0.48
412 1 0.00
ACGTcount: A:0.32, C:0.18, G:0.23, T:0.27
Consensus pattern (410 bp):
AGCATGGAAAGGACGTGCAAGGGCTGCAAGGAAGCATGGAGATGAATGAAGATCATAGAGATATC
GATAAGCATGCTCCAAGCACCAAAAAGATGCTTATCGATCCATTGAAGATGCCTAATAGTCAGAT
GACAAGAGCAAGAGCTAAGAGATTCAAGGATGCACTCATGTGCCTTGTCCGACTCATCTTGAAGA
CTTCAAGACCATTCAAGTTCAATTGAAGAGCTTTGATGATGATTTGAGCAAGAAAACACAAATCA
ATTACAAGTTCATCACATTGCTTGCTATTGATTCTAAATGGCCGGATTGACATAGTGGCATGAGC
CCAATATCATTAGTTATCTTTGATGCGCCCAAGCCTTATCATGGAAGGAATTATGCGCCAAGGAC
TTATTATGGCCTTGAAGACA
Done.