Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Chr08 129432109
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: 129432109
ACGTcount: A:0.32, C:0.18, G:0.18, T:0.32
Warning! 350 characters in sequence are not A, C, G, or T
File 310 of 425
Found at i:96433427 original size:80 final size:81
Alignment explanation
Indices: 96433286--96433460 Score: 237
Period size: 80 Copynumber: 2.2 Consensus size: 81
96433276 CGAATGGTAT
* *
96433286 CCGGGCTAAGTCCCGAAGGCTTTTGTGCTAAGTGACTAAATCCGGGTCAATTCCCGAAGGCATTT
1 CCGGGCTAAGTCCCGAAGGCATTTGTGCTAAGTGACTAAATCCGGGTCAATTCCCGAAGGCAATT
96433351 GTGCGAGTTACCAAAA
66 GTGCGAGTTACCAAAA
* * *
96433367 CCGGGTTAAGTCCCGAAGGCATTTGTGC-GAGTTACTAAATCCGGG-CTAATTCCCGAAGGCAAT
1 CCGGGCTAAGTCCCGAAGGCATTTGTGCTAAGTGACTAAATCCGGGTC-AATTCCCGAAGGCAAT
* * * *
96433430 TGTGCGAATCACTATAA
65 TGTGCGAGTTACCAAAA
*
96433447 CCGGGCTATGTCCC
1 CCGGGCTAAGTCCC
96433461 AAGACAATCG
Statistics
Matches: 82, Mismatches: 11, Indels: 3
0.85 0.11 0.03
Matches are distributed among these distances:
79 1 0.01
80 55 0.67
81 26 0.32
ACGTcount: A:0.25, C:0.25, G:0.26, T:0.25
Consensus pattern (81 bp):
CCGGGCTAAGTCCCGAAGGCATTTGTGCTAAGTGACTAAATCCGGGTCAATTCCCGAAGGCAATT
GTGCGAGTTACCAAAA
Found at i:96441701 original size:40 final size:40
Alignment explanation
Indices: 96441623--96441846 Score: 265
Period size: 40 Copynumber: 5.5 Consensus size: 40
96441613 ACACAAGTAT
* * *
96441623 CTTCGGGATTTAG-CCGGATATA-ACAACTCGCACAAATGC
1 CTTCGGGACTTAGCCCGGATATAGTC-ACTAGCACAAATGC
* **
96441662 CTTCGGGTCTTAGCCCGGATATAGTCACTAGCATGAATGC
1 CTTCGGGACTTAGCCCGGATATAGTCACTAGCACAAATGC
*
96441702 CTTCGAGACTTAGCCCGGATATAGTCACTAGCACAAATGC
1 CTTCGGGACTTAGCCCGGATATAGTCACTAGCACAAATGC
* *
96441742 CTTCGGGACTTAGCCCGGGTATAG-CAACTACTCACTCAAATGC
1 CTTCGGGACTTAGCCCGGATATAGTC-ACTA-GCA--CAAATGC
* * *
96441785 CTTCGGGACTTAGCCTGGATATAGTAACTTGCACAAATGC
1 CTTCGGGACTTAGCCCGGATATAGTCACTAGCACAAATGC
*
96441825 CTTTGGGACTTAGCCCGGATAT
1 CTTCGGGACTTAGCCCGGATAT
96441847 CATCCGAATA
Statistics
Matches: 158, Mismatches: 20, Indels: 13
0.83 0.10 0.07
Matches are distributed among these distances:
39 12 0.08
40 109 0.69
41 3 0.02
42 2 0.01
43 32 0.20
ACGTcount: A:0.26, C:0.26, G:0.22, T:0.25
Consensus pattern (40 bp):
CTTCGGGACTTAGCCCGGATATAGTCACTAGCACAAATGC
Found at i:96441835 original size:123 final size:119
Alignment explanation
Indices: 96441623--96441846 Score: 304
Period size: 123 Copynumber: 1.8 Consensus size: 119
96441613 ACACAAGTAT
* * *
96441623 CTTCGGGATTTAGCCGGATATAACAACTCGCACAAATGCCTTCGGGTCTTAGCCCGGATATAGTC
1 CTTCGGGACTTAGCCGGATATAACAACTCGCACAAATGCCTTCGGGACTTAGCCCGGATATAGTA
**
96441688 ACTAGCATGAATGCCTTCGAGACTTAGCCCGGATATAGTCACTAGCACAAATGC
66 ACTAGCACAAATGCCTTCGAGACTTAGCCCGGATATAGTCACTAGCACAAATGC
* * * *
96441742 CTTCGGGACTTAGCCCGGGTATAGCAACTACTCACTCAAATGCCTTCGGGACTTAGCCTGGATAT
1 CTTCGGGACTTAG-CCGGATATAACAACT-CGCA--CAAATGCCTTCGGGACTTAGCCCGGATAT
* * *
96441807 AGTAACTTGCACAAATGCCTTTGGGACTTAGCCCGGATAT
62 AGTAACTAGCACAAATGCCTTCGAGACTTAGCCCGGATAT
96441847 CATCCGAATA
Statistics
Matches: 89, Mismatches: 12, Indels: 4
0.85 0.11 0.04
Matches are distributed among these distances:
119 12 0.13
120 13 0.15
121 3 0.03
123 61 0.69
ACGTcount: A:0.26, C:0.26, G:0.22, T:0.25
Consensus pattern (119 bp):
CTTCGGGACTTAGCCGGATATAACAACTCGCACAAATGCCTTCGGGACTTAGCCCGGATATAGTA
ACTAGCACAAATGCCTTCGAGACTTAGCCCGGATATAGTCACTAGCACAAATGC
Found at i:96442447 original size:2 final size:2
Alignment explanation
Indices: 96442442--96442469 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
96442432 ATATTCACAC
96442442 AT 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 AT
96442470 TATGCCATTT
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:96444752 original size:78 final size:78
Alignment explanation
Indices: 96444623--96444777 Score: 267
Period size: 78 Copynumber: 2.0 Consensus size: 78
96444613 GAATGAACAA
* *
96444623 GGAGGAGAGATGTTAAGTGTTGGGGCATCAACAAAGTATTTTGGATCTCTGAAACACATATCAAG
1 GGAGGAGAGATGCTAAGTCTTGGGGCATCAACAAAGTATTTTGGATCTCTGAAACACATATCAAG
96444688 TTCAAAAGGGTCC
66 TTCAAAAGGGTCC
*
96444701 GGAGGAGAGATGCTACA-TCTTGGGGTATCAACAAAGTATTTTGGATCTCTGAAACACATATCAA
1 GGAGGAGAGATGCTA-AGTCTTGGGGCATCAACAAAGTATTTTGGATCTCTGAAACACATATCAA
96444765 GTTCAAAAGGGTC
65 GTTCAAAAGGGTC
96444778 TTCGAGAAGT
Statistics
Matches: 73, Mismatches: 3, Indels: 2
0.94 0.04 0.03
Matches are distributed among these distances:
78 72 0.99
79 1 0.01
ACGTcount: A:0.34, C:0.15, G:0.26, T:0.26
Consensus pattern (78 bp):
GGAGGAGAGATGCTAAGTCTTGGGGCATCAACAAAGTATTTTGGATCTCTGAAACACATATCAAG
TTCAAAAGGGTCC
Found at i:96445513 original size:44 final size:44
Alignment explanation
Indices: 96445450--96446211 Score: 466
Period size: 44 Copynumber: 16.9 Consensus size: 44
96445440 TATAATAGTG
* *
96445450 AATCTTATCTCCCTAAAGTTGCAGTGGAACAGATTGAAGCCACT
1 AATCTTATCTCCCTGAAGTTGCAGTGGAGCAGATTGAAGCCACT
* * * * * * * *** *
96445494 AATCTCATATCTCTGAAGTTGTAGTAGAGTAGATTTAATATAACA
1 AATCTTATCTCCCTGAAGTTGCAGTGGAGCAGATTGAA-GCCACT
* * *
96445539 AATCTTAT-TCCCCTAAAGTTGCAGTGG-GACAGGTTGAAGCTATCAT
1 AATCTTATCT-CCCTGAAGTTGCAGTGGAG-CAGATTGAAGCCA-C-T
*
96445585 GGCAGATCTTATCTCCCTGAAGTTGCAGTGGAGTAGATTGAAGCCACT
1 ---A-ATCTTATCTCCCTGAAGTTGCAGTGGAGCAGATTGAAGCCACT
* * * *
96445633 AATCTCATTTCCCTGAAGTTGCAGT-GAGACAGGTTGAAGCAATCATGGCG
1 AATCTTATCTCCCTGAAGTTGCAGTGGAG-CAGATTGAAGC---CA---CT
* * * *
96445683 GATCTTATCTCCCTAAAGTTGTAGTGGAGTAGATTGAAGCCACT
1 AATCTTATCTCCCTGAAGTTGCAGTGGAGCAGATTGAAGCCACT
* *
96445727 AA-CATTATCTCCCTGAAGTTGCAGTAGAGTAGATTGAAGCCACT
1 AATC-TTATCTCCCTGAAGTTGCAGTGGAGCAGATTGAAGCCACT
* * * * **
96445771 AATCTTATCTCCCTAAAGTTGTAGTGGAACAGGTTGAAGTTAC-
1 AATCTTATCTCCCTGAAGTTGCAGTGGAGCAGATTGAAGCCACT
* * **
96445814 AAGTCTTATCTCCCAGAAGTTGCAGTGGAGCAAATTGAAGCCAAA
1 AA-TCTTATCTCCCTGAAGTTGCAGTGGAGCAGATTGAAGCCACT
* * ** *
96445859 AATCTTATCTCCCTGAAGTTGCAGTGGAGTAGATTAAAGATAGCA
1 AATCTTATCTCCCTGAAGTTGCAGTGGAGCAGATTGAAGCCA-CT
* *
96445904 AATCTTAT-TCTCCTGAAGTTGCAATGG-GACA-AGTTGAAGCTATCAT
1 AATCTTATCTC-CCTGAAGTTGCAGTGGAG-CAGA-TTGAAGCCA-C-T
*
96445950 GGCAGATCTTATCTCCCTGAAGTTGCAGTGGAGTAGATTGAAGCCACT
1 ---A-ATCTTATCTCCCTGAAGTTGCAGTGGAGCAGATTGAAGCCACT
* * * * * ** *
96445998 -ACCTCATCTCCTTAAAGTTGTAGTGGAGCA-AGTTGAAGTTA-A
1 AATCTTATCTCCCTGAAGTTGCAGTGGAGCAGA-TTGAAGCCACT
* ** *
96446040 AAGTCTTATCTCCCTGAAGTTGTAGTGGAGCAGATTGAAGATAGT
1 AA-TCTTATCTCCCTGAAGTTGCAGTGGAGCAGATTGAAGCCACT
* * ** * * ** *
96446085 GAATATTATCTCCCCGAAGTTATAGTGGAGTAGATTAAAGTAACA
1 -AATCTTATCTCCCTGAAGTTGCAGTGGAGCAGATTGAAGCCACT
* * ** * *** *
96446130 AATCTTATCTCTCTGAAGTTACAGTGGAATATATTGAAATTACA
1 AATCTTATCTCCCTGAAGTTGCAGTGGAGCAGATTGAAGCCACT
* * *
96446174 AATCTTATCTCCCTGAAGTTGTAGTGGGGTAGATTGAA
1 AATCTTATCTCCCTGAAGTTGCAGTGGAGCAGATTGAA
96446212 ACAACAAATT
Statistics
Matches: 559, Mismatches: 118, Indels: 82
0.74 0.16 0.11
Matches are distributed among these distances:
42 1 0.00
43 38 0.07
44 305 0.55
45 100 0.18
46 2 0.00
47 4 0.01
48 2 0.00
49 4 0.01
50 94 0.17
51 9 0.02
ACGTcount: A:0.31, C:0.17, G:0.22, T:0.30
Consensus pattern (44 bp):
AATCTTATCTCCCTGAAGTTGCAGTGGAGCAGATTGAAGCCACT
Found at i:96446016 original size:226 final size:227
Alignment explanation
Indices: 96445731--96446149 Score: 628
Period size: 226 Copynumber: 1.9 Consensus size: 227
96445721 GCCACTAACA
* *
96445731 TTATCTCCCTGAAGTTGCAGTAGAGTAGATTGAAGCCACTAATCTTATCTCCCTAAAGTTGTAGT
1 TTATCTCCCTGAAGTTGCAGTAGAGTAGATTGAAGCCACTAACCTCATCTCCCTAAAGTTGTAGT
* * *
96445796 GGAACAGGTTGAAGTTACAAGTCTTATCTCCCAGAAGTTGCAGTGGAGCAAATTGAAGCCA-AAA
66 GGAACAAGTTGAAGTTAAAAGTCTTATCTCCCAGAAGTTGCAGTGGAGCAAATTGAAGACAGAAA
* * * *
96445860 ATCTTATCTCCCTGAAGTTGCAGTGGAGTAGATTAAAGATAGCAAATCTTAT-TCTCCTGAAGTT
131 ATATTATCTCCCCGAAGTTACAGTGGAGTAGATTAAAG-TAACAAATCTTATCTCT-CTGAAGTT
96445924 GCAATGGGACAAGTTGAAGCTATCATGGCAGATC
194 GCAATGGGACAAGTTGAAGCTATCATGGCAGATC
* *
96445958 TTATCTCCCTGAAGTTGCAGTGGAGTAGATTGAAGCCACT-ACCTCATCTCCTTAAAGTTGTAGT
1 TTATCTCCCTGAAGTTGCAGTAGAGTAGATTGAAGCCACTAACCTCATCTCCCTAAAGTTGTAGT
* * * * * **
96446022 GGAGCAAGTTGAAGTTAAAAGTCTTATCTCCCTGAAGTTGTAGTGGAGCAGATTGAAGATAGTGA
66 GGAACAAGTTGAAGTTAAAAGTCTTATCTCCCAGAAGTTGCAGTGGAGCAAATTGAAGACAGAAA
*
96446087 ATATTATCTCCCCGAAGTTATAGTGGAGTAGATTAAAGTAACAAATCTTATCTCTCTGAAGTT
131 ATATTATCTCCCCGAAGTTACAGTGGAGTAGATTAAAGTAACAAATCTTATCTCTCTGAAGTT
96446150 ACAGTGGAAT
Statistics
Matches: 171, Mismatches: 19, Indels: 5
0.88 0.10 0.03
Matches are distributed among these distances:
226 94 0.55
227 77 0.45
ACGTcount: A:0.31, C:0.17, G:0.22, T:0.30
Consensus pattern (227 bp):
TTATCTCCCTGAAGTTGCAGTAGAGTAGATTGAAGCCACTAACCTCATCTCCCTAAAGTTGTAGT
GGAACAAGTTGAAGTTAAAAGTCTTATCTCCCAGAAGTTGCAGTGGAGCAAATTGAAGACAGAAA
ATATTATCTCCCCGAAGTTACAGTGGAGTAGATTAAAGTAACAAATCTTATCTCTCTGAAGTTGC
AATGGGACAAGTTGAAGCTATCATGGCAGATC
Found at i:96448940 original size:23 final size:23
Alignment explanation
Indices: 96448857--96448993 Score: 102
Period size: 23 Copynumber: 5.8 Consensus size: 23
96448847 CTCATCACAA
*
96448857 CTCGTATGAGCTTACTGATATATCAG
1 CTCGTATGAGCTTACTG-T-T-TTAG
* *
96448883 CTCGTAAGAGCTTACTATTTTCAG
1 CTCGTATGAGCTTACTGTTTT-AG
* *
96448907 CTCAT-TGGAGCTTACCGTTTTAG
1 CTCGTAT-GAGCTTACTGTTTTAG
96448930 CTCGTATGAGCTTACTG-TTTAG
1 CTCGTATGAGCTTACTGTTTTAG
** *
96448952 CTCG-ATAGAGCTTACCATTTCAG
1 CTCGTAT-GAGCTTACTGTTTTAG
*
96448975 CTCAT-TAGAGCTTACTGTT
1 CTCGTAT-GAGCTTACTGTT
96448994 CATCAGCTCA
Statistics
Matches: 90, Mismatches: 15, Indels: 15
0.75 0.12 0.12
Matches are distributed among these distances:
21 2 0.02
22 17 0.19
23 35 0.39
24 20 0.22
25 1 0.01
26 15 0.17
ACGTcount: A:0.23, C:0.21, G:0.19, T:0.37
Consensus pattern (23 bp):
CTCGTATGAGCTTACTGTTTTAG
Found at i:96448977 original size:45 final size:46
Alignment explanation
Indices: 96448879--96449003 Score: 130
Period size: 45 Copynumber: 2.7 Consensus size: 46
96448869 TACTGATATA
* * * *
96448879 TCAGCTCGTAAGAGCTTACTATTTTCAGCTCATTGGAGCTTACCGTT
1 TCAGCTCGTATGAGCTTACT-GTTTCAGCTCATTAGAGCTTACCATT
*
96448926 TTAGCTCGTATGAGCTTACTGTTT-AGCTCGA-TAGAGCTTACCATT
1 TCAGCTCGTATGAGCTTACTGTTTCAGCTC-ATTAGAGCTTACCATT
*
96448971 TCAGCTCAT-TAGAGCTTACTGTTCATCAGCTCA
1 TCAGCTCGTAT-GAGCTTACTGTT--TCAGCTCA
96449004 AGAGGAGCTT
Statistics
Matches: 66, Mismatches: 7, Indels: 10
0.80 0.08 0.12
Matches are distributed among these distances:
44 1 0.02
45 36 0.55
46 4 0.06
47 20 0.30
48 5 0.08
ACGTcount: A:0.22, C:0.23, G:0.18, T:0.36
Consensus pattern (46 bp):
TCAGCTCGTATGAGCTTACTGTTTCAGCTCATTAGAGCTTACCATT
Found at i:96451959 original size:8 final size:8
Alignment explanation
Indices: 96451945--96451974 Score: 51
Period size: 8 Copynumber: 3.8 Consensus size: 8
96451935 TAGTATAGTT
96451945 GATATATA
1 GATATATA
*
96451953 TATATATA
1 GATATATA
96451961 GATATATA
1 GATATATA
96451969 GATATA
1 GATATA
96451975 CATATTCAGC
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
8 20 1.00
ACGTcount: A:0.50, C:0.00, G:0.10, T:0.40
Consensus pattern (8 bp):
GATATATA
Found at i:96452653 original size:29 final size:29
Alignment explanation
Indices: 96452618--96452691 Score: 105
Period size: 29 Copynumber: 2.6 Consensus size: 29
96452608 GGTTGGAGAT
* *
96452618 TGGCACTAAGTGTGCGGGCTTGAAA-TGCA
1 TGGCACTAAGTGTGCGAG-TTGAAAGTACA
*
96452647 TGGCACTAAGTGTGCGAGTTTAAAGTACA
1 TGGCACTAAGTGTGCGAGTTGAAAGTACA
96452676 TGGCACTAAGTGTGCG
1 TGGCACTAAGTGTGCG
96452692 TGGTTGATTA
Statistics
Matches: 41, Mismatches: 3, Indels: 2
0.89 0.07 0.04
Matches are distributed among these distances:
28 5 0.12
29 36 0.88
ACGTcount: A:0.26, C:0.16, G:0.32, T:0.26
Consensus pattern (29 bp):
TGGCACTAAGTGTGCGAGTTGAAAGTACA
Found at i:96455931 original size:80 final size:80
Alignment explanation
Indices: 96455847--96455995 Score: 183
Period size: 80 Copynumber: 1.9 Consensus size: 80
96455837 TATGGTAACC
* * * *
96455847 CGCACCAAGGCCTACGGGACTTAACCCGGATATCA-CGATTTGCACAAATGCCTTCGGGTCTTAG
1 CGCACCAAGGCCTACGGGACTTAACCCGGATAT-AGCCACTAGCACAAATGCCTTCGGGTCTTAA
96455911 CCCGGATAGAATGACT
65 CCCGGATAGAATGACT
* * * * * * *
96455927 CGCACGAATGCCTTCGGGTCTTAGCCCGGATGTAGCCACTAGCACAATTGCCTTCGGGTCTTAAC
1 CGCACCAAGGCCTACGGGACTTAACCCGGATATAGCCACTAGCACAAATGCCTTCGGGTCTTAAC
96455992 CCGG
66 CCGG
96455996 TTATAATTTC
Statistics
Matches: 57, Mismatches: 11, Indels: 2
0.81 0.16 0.03
Matches are distributed among these distances:
79 1 0.02
80 56 0.98
ACGTcount: A:0.23, C:0.30, G:0.25, T:0.22
Consensus pattern (80 bp):
CGCACCAAGGCCTACGGGACTTAACCCGGATATAGCCACTAGCACAAATGCCTTCGGGTCTTAAC
CCGGATAGAATGACT
Found at i:96455937 original size:40 final size:38
Alignment explanation
Indices: 96455888--96455995 Score: 128
Period size: 40 Copynumber: 2.7 Consensus size: 38
96455878 ATCACGATTT
*
96455888 GCACAAATGCCTTCGGGTCTTAGCCCGGATAGAATG-ACTC
1 GCAC-AATGCCTTCGGGTCTTAGCCCGGAT-GAA-GCACTA
*
96455928 GCACGAATGCCTTCGGGTCTTAGCCCGGATGTAGCCACTA
1 GCAC-AATGCCTTCGGGTCTTAGCCCGGATGAAG-CACTA
*
96455968 GCACAATTGCCTTCGGGTCTTAACCCGG
1 GCACAA-TGCCTTCGGGTCTTAGCCCGG
96455996 TTATAATTTC
Statistics
Matches: 61, Mismatches: 4, Indels: 6
0.86 0.06 0.08
Matches are distributed among these distances:
38 1 0.02
39 4 0.07
40 56 0.92
ACGTcount: A:0.21, C:0.30, G:0.26, T:0.23
Consensus pattern (38 bp):
GCACAATGCCTTCGGGTCTTAGCCCGGATGAAGCACTA
Found at i:96464048 original size:80 final size:80
Alignment explanation
Indices: 96463964--96464112 Score: 183
Period size: 80 Copynumber: 1.9 Consensus size: 80
96463954 TATGGTAACC
* * * *
96463964 CGCACCAAGGCCTACGGGACTTAACCCGGATATCA-CGATTTGCACAAATGCCTTCGGGTCTTAG
1 CGCACCAAGGCCTACGGGACTTAACCCGGATAT-AGCCACTAGCACAAATGCCTTCGGGTCTTAA
96464028 CCCGGATAGAATGACT
65 CCCGGATAGAATGACT
* * * * * * *
96464044 CGCACGAATGCCTTCGGGTCTTAGCCCGGATGTAGCCACTAGCACAATTGCCTTCGGGTCTTAAC
1 CGCACCAAGGCCTACGGGACTTAACCCGGATATAGCCACTAGCACAAATGCCTTCGGGTCTTAAC
96464109 CCGG
66 CCGG
96464113 TTATAATTTC
Statistics
Matches: 57, Mismatches: 11, Indels: 2
0.81 0.16 0.03
Matches are distributed among these distances:
79 1 0.02
80 56 0.98
ACGTcount: A:0.23, C:0.30, G:0.25, T:0.22
Consensus pattern (80 bp):
CGCACCAAGGCCTACGGGACTTAACCCGGATATAGCCACTAGCACAAATGCCTTCGGGTCTTAAC
CCGGATAGAATGACT
Found at i:96464054 original size:40 final size:38
Alignment explanation
Indices: 96464005--96464112 Score: 128
Period size: 40 Copynumber: 2.7 Consensus size: 38
96463995 ATCACGATTT
*
96464005 GCACAAATGCCTTCGGGTCTTAGCCCGGATAGAATG-ACTC
1 GCAC-AATGCCTTCGGGTCTTAGCCCGGAT-GAA-GCACTA
*
96464045 GCACGAATGCCTTCGGGTCTTAGCCCGGATGTAGCCACTA
1 GCAC-AATGCCTTCGGGTCTTAGCCCGGATGAAG-CACTA
*
96464085 GCACAATTGCCTTCGGGTCTTAACCCGG
1 GCACAA-TGCCTTCGGGTCTTAGCCCGG
96464113 TTATAATTTC
Statistics
Matches: 61, Mismatches: 4, Indels: 6
0.86 0.06 0.08
Matches are distributed among these distances:
38 1 0.02
39 4 0.07
40 56 0.92
ACGTcount: A:0.21, C:0.30, G:0.26, T:0.23
Consensus pattern (38 bp):
GCACAATGCCTTCGGGTCTTAGCCCGGATGAAGCACTA
Found at i:96469348 original size:80 final size:80
Alignment explanation
Indices: 96469264--96469412 Score: 183
Period size: 80 Copynumber: 1.9 Consensus size: 80
96469254 TATGGTAACC
* * * *
96469264 CGCACCAAGGCCTACGGGACTTAACCCGGATATCA-CGATTTGCACAAATGCCTTCGGGTCTTAG
1 CGCACCAAGGCCTACGGGACTTAACCCGGATAT-AGCCACTAGCACAAATGCCTTCGGGTCTTAA
96469328 CCCGGATAGAATGACT
65 CCCGGATAGAATGACT
* * * * * * *
96469344 CGCACGAATGCCTTCGGGTCTTAGCCCGGATGTAGCCACTAGCACAATTGCCTTCGGGTCTTAAC
1 CGCACCAAGGCCTACGGGACTTAACCCGGATATAGCCACTAGCACAAATGCCTTCGGGTCTTAAC
96469409 CCGG
66 CCGG
96469413 TTATAATTTC
Statistics
Matches: 57, Mismatches: 11, Indels: 2
0.81 0.16 0.03
Matches are distributed among these distances:
79 1 0.02
80 56 0.98
ACGTcount: A:0.23, C:0.30, G:0.25, T:0.22
Consensus pattern (80 bp):
CGCACCAAGGCCTACGGGACTTAACCCGGATATAGCCACTAGCACAAATGCCTTCGGGTCTTAAC
CCGGATAGAATGACT
Found at i:96469354 original size:40 final size:38
Alignment explanation
Indices: 96469305--96469412 Score: 128
Period size: 40 Copynumber: 2.7 Consensus size: 38
96469295 ATCACGATTT
*
96469305 GCACAAATGCCTTCGGGTCTTAGCCCGGATAGAATG-ACTC
1 GCAC-AATGCCTTCGGGTCTTAGCCCGGAT-GAA-GCACTA
*
96469345 GCACGAATGCCTTCGGGTCTTAGCCCGGATGTAGCCACTA
1 GCAC-AATGCCTTCGGGTCTTAGCCCGGATGAAG-CACTA
*
96469385 GCACAATTGCCTTCGGGTCTTAACCCGG
1 GCACAA-TGCCTTCGGGTCTTAGCCCGG
96469413 TTATAATTTC
Statistics
Matches: 61, Mismatches: 4, Indels: 6
0.86 0.06 0.08
Matches are distributed among these distances:
38 1 0.02
39 4 0.07
40 56 0.92
ACGTcount: A:0.21, C:0.30, G:0.26, T:0.23
Consensus pattern (38 bp):
GCACAATGCCTTCGGGTCTTAGCCCGGATGAAGCACTA
Found at i:96477464 original size:80 final size:80
Alignment explanation
Indices: 96477380--96477528 Score: 183
Period size: 80 Copynumber: 1.9 Consensus size: 80
96477370 TATGGTAACC
* * * *
96477380 CGCACCAAGGCCTACGGGACTTAACCCGGATATCA-CGATTTGCACAAATGCCTTCGGGTCTTAG
1 CGCACCAAGGCCTACGGGACTTAACCCGGATAT-AGCCACTAGCACAAATGCCTTCGGGTCTTAA
96477444 CCCGGATAGAATGACT
65 CCCGGATAGAATGACT
* * * * * * *
96477460 CGCACGAATGCCTTCGGGTCTTAGCCCGGATGTAGCCACTAGCACAATTGCCTTCGGGTCTTAAC
1 CGCACCAAGGCCTACGGGACTTAACCCGGATATAGCCACTAGCACAAATGCCTTCGGGTCTTAAC
96477525 CCGG
66 CCGG
96477529 TTATAATTTC
Statistics
Matches: 57, Mismatches: 11, Indels: 2
0.81 0.16 0.03
Matches are distributed among these distances:
79 1 0.02
80 56 0.98
ACGTcount: A:0.23, C:0.30, G:0.25, T:0.22
Consensus pattern (80 bp):
CGCACCAAGGCCTACGGGACTTAACCCGGATATAGCCACTAGCACAAATGCCTTCGGGTCTTAAC
CCGGATAGAATGACT
Found at i:96477470 original size:40 final size:38
Alignment explanation
Indices: 96477421--96477528 Score: 128
Period size: 40 Copynumber: 2.7 Consensus size: 38
96477411 ATCACGATTT
*
96477421 GCACAAATGCCTTCGGGTCTTAGCCCGGATAGAATG-ACTC
1 GCAC-AATGCCTTCGGGTCTTAGCCCGGAT-GAA-GCACTA
*
96477461 GCACGAATGCCTTCGGGTCTTAGCCCGGATGTAGCCACTA
1 GCAC-AATGCCTTCGGGTCTTAGCCCGGATGAAG-CACTA
*
96477501 GCACAATTGCCTTCGGGTCTTAACCCGG
1 GCACAA-TGCCTTCGGGTCTTAGCCCGG
96477529 TTATAATTTC
Statistics
Matches: 61, Mismatches: 4, Indels: 6
0.86 0.06 0.08
Matches are distributed among these distances:
38 1 0.02
39 4 0.07
40 56 0.92
ACGTcount: A:0.21, C:0.30, G:0.26, T:0.23
Consensus pattern (38 bp):
GCACAATGCCTTCGGGTCTTAGCCCGGATGAAGCACTA
Found at i:96483872 original size:16 final size:18
Alignment explanation
Indices: 96483841--96483873 Score: 52
Period size: 16 Copynumber: 1.9 Consensus size: 18
96483831 AACTCGTCAC
96483841 ACTATCTATCGTTTTGGT
1 ACTATCTATCGTTTTGGT
96483859 ACTAT-TAT-GTTTTGG
1 ACTATCTATCGTTTTGG
96483874 AATTTGTATG
Statistics
Matches: 15, Mismatches: 0, Indels: 2
0.88 0.00 0.12
Matches are distributed among these distances:
16 7 0.47
17 3 0.20
18 5 0.33
ACGTcount: A:0.18, C:0.12, G:0.18, T:0.52
Consensus pattern (18 bp):
ACTATCTATCGTTTTGGT
Found at i:96491409 original size:16 final size:18
Alignment explanation
Indices: 96491378--96491410 Score: 52
Period size: 16 Copynumber: 1.9 Consensus size: 18
96491368 AACTCGTCAC
96491378 ACTATCTATCGTTTTGGT
1 ACTATCTATCGTTTTGGT
96491396 ACTAT-TAT-GTTTTGG
1 ACTATCTATCGTTTTGG
96491411 AATTTGTATG
Statistics
Matches: 15, Mismatches: 0, Indels: 2
0.88 0.00 0.12
Matches are distributed among these distances:
16 7 0.47
17 3 0.20
18 5 0.33
ACGTcount: A:0.18, C:0.12, G:0.18, T:0.52
Consensus pattern (18 bp):
ACTATCTATCGTTTTGGT
Found at i:96499533 original size:53 final size:51
Alignment explanation
Indices: 96499456--96499563 Score: 126
Period size: 53 Copynumber: 2.1 Consensus size: 51
96499446 TAATTCTGTT
* * ***
96499456 ATTTATTTATTCATCTACTTGTTTATTTATTCCTTATTCCATTTACTTTATTC
1 ATTTATCTATTCATCTACTCGTTTATTTATAAATTATT-CATTTA-TTTATTC
* * *
96499509 ATTTATCTGTTCATTTACTCGTTTATTTATAAATTATTCATTTATTTATTT
1 ATTTATCTATTCATCTACTCGTTTATTTATAAATTATTCATTTATTTATTC
96499560 ATTT
1 ATTT
96499564 TTGTTTCAAT
Statistics
Matches: 47, Mismatches: 8, Indels: 2
0.82 0.14 0.04
Matches are distributed among these distances:
51 10 0.21
52 6 0.13
53 31 0.66
ACGTcount: A:0.23, C:0.13, G:0.03, T:0.61
Consensus pattern (51 bp):
ATTTATCTATTCATCTACTCGTTTATTTATAAATTATTCATTTATTTATTC
Found at i:96499889 original size:6 final size:6
Alignment explanation
Indices: 96499878--96499937 Score: 52
Period size: 6 Copynumber: 9.5 Consensus size: 6
96499868 GGCATCTAGC
96499878 ATTTTT ATTTTT CATTTTTT ATTTTTT ATTTTT A--TTT ATTTTT ATTACTTT
1 ATTTTT ATTTTT -A-TTTTT A-TTTTT ATTTTT ATTTTT ATTTTT ATT--TTT
*
96499929 ATTTAT ATT
1 ATTTTT ATT
96499938 ATACCATGGA
Statistics
Matches: 47, Mismatches: 1, Indels: 12
0.78 0.02 0.20
Matches are distributed among these distances:
4 4 0.09
6 23 0.49
7 9 0.19
8 11 0.23
ACGTcount: A:0.20, C:0.03, G:0.00, T:0.77
Consensus pattern (6 bp):
ATTTTT
Found at i:96499889 original size:7 final size:7
Alignment explanation
Indices: 96499879--96499914 Score: 56
Period size: 7 Copynumber: 5.3 Consensus size: 7
96499869 GCATCTAGCA
96499879 TTTTTAT
1 TTTTTAT
*
96499886 TTTTCAT
1 TTTTTAT
96499893 TTTTTAT
1 TTTTTAT
96499900 TTTTTA-
1 TTTTTAT
96499906 TTTTTAT
1 TTTTTAT
96499913 TT
1 TT
96499915 ATTTTTATTA
Statistics
Matches: 26, Mismatches: 2, Indels: 2
0.87 0.07 0.07
Matches are distributed among these distances:
6 6 0.23
7 20 0.77
ACGTcount: A:0.14, C:0.03, G:0.00, T:0.83
Consensus pattern (7 bp):
TTTTTAT
Found at i:96499929 original size:18 final size:16
Alignment explanation
Indices: 96499881--96499934 Score: 58
Period size: 16 Copynumber: 3.3 Consensus size: 16
96499871 ATCTAGCATT
96499881 TTTATTTTTCATTTTT-
1 TTTATTTTT-ATTTTTA
*
96499897 TAT-TTTTTATTTTTA
1 TTTATTTTTATTTTTA
96499912 TTTATTTTTATTACTTTA
1 TTTATTTTTATT--TTTA
96499930 TTTAT
1 TTTAT
96499935 ATTATACCAT
Statistics
Matches: 32, Mismatches: 2, Indels: 6
0.80 0.05 0.15
Matches are distributed among these distances:
14 6 0.19
15 7 0.22
16 10 0.31
18 9 0.28
ACGTcount: A:0.19, C:0.04, G:0.00, T:0.78
Consensus pattern (16 bp):
TTTATTTTTATTTTTA
Found at i:96499939 original size:23 final size:23
Alignment explanation
Indices: 96499893--96499937 Score: 63
Period size: 24 Copynumber: 1.9 Consensus size: 23
96499883 TATTTTTCAT
* *
96499893 TTTTTATTTTTTATTTTTATTTA
1 TTTTTATTCTTTATTTATATTTA
96499916 TTTTTATTACTTTATTTATATT
1 TTTTTATT-CTTTATTTATATT
96499938 ATACCATGGA
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
23 8 0.42
24 11 0.58
ACGTcount: A:0.20, C:0.02, G:0.00, T:0.78
Consensus pattern (23 bp):
TTTTTATTCTTTATTTATATTTA
Found at i:96502029 original size:20 final size:20
Alignment explanation
Indices: 96502006--96502044 Score: 69
Period size: 20 Copynumber: 1.9 Consensus size: 20
96501996 TGAAGGAAGA
96502006 TTATAGAAAAATCATGATTT
1 TTATAGAAAAATCATGATTT
*
96502026 TTATAGAAGAATCATGATT
1 TTATAGAAAAATCATGATT
96502045 AAAGTTTGCT
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
20 18 1.00
ACGTcount: A:0.44, C:0.05, G:0.13, T:0.38
Consensus pattern (20 bp):
TTATAGAAAAATCATGATTT
Found at i:96511044 original size:15 final size:15
Alignment explanation
Indices: 96511024--96511052 Score: 58
Period size: 15 Copynumber: 1.9 Consensus size: 15
96511014 ACTCTGTTAC
96511024 TTTTTTTACTTTTTT
1 TTTTTTTACTTTTTT
96511039 TTTTTTTACTTTTT
1 TTTTTTTACTTTTT
96511053 CTACTCTTGT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.07, C:0.07, G:0.00, T:0.86
Consensus pattern (15 bp):
TTTTTTTACTTTTTT
Found at i:96511134 original size:13 final size:12
Alignment explanation
Indices: 96511113--96511147 Score: 52
Period size: 13 Copynumber: 2.8 Consensus size: 12
96511103 GTCTTTTATC
96511113 TTTATTTATTTTA
1 TTTA-TTATTTTA
96511126 TTTACTTATTTTA
1 TTTA-TTATTTTA
96511139 TTTATTATT
1 TTTATTATT
96511148 AATTTTAAAA
Statistics
Matches: 21, Mismatches: 1, Indels: 1
0.91 0.04 0.04
Matches are distributed among these distances:
12 5 0.24
13 16 0.76
ACGTcount: A:0.23, C:0.03, G:0.00, T:0.74
Consensus pattern (12 bp):
TTTATTATTTTA
Found at i:96511217 original size:44 final size:44
Alignment explanation
Indices: 96511162--96511249 Score: 158
Period size: 44 Copynumber: 2.0 Consensus size: 44
96511152 TTAAAAAAAT
96511162 TTGAAATGTATATTTGAAATGTTGTATAATATATAATTTTTAAA
1 TTGAAATGTATATTTGAAATGTTGTATAATATATAATTTTTAAA
* *
96511206 TTGAAATGTATATTTGAAATGTTTTATAATATATATTTTTTAAA
1 TTGAAATGTATATTTGAAATGTTGTATAATATATAATTTTTAAA
96511250 AATTTTAAAT
Statistics
Matches: 42, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
44 42 1.00
ACGTcount: A:0.40, C:0.00, G:0.10, T:0.50
Consensus pattern (44 bp):
TTGAAATGTATATTTGAAATGTTGTATAATATATAATTTTTAAA
Found at i:96511240 original size:23 final size:23
Alignment explanation
Indices: 96511170--96511243 Score: 66
Period size: 23 Copynumber: 3.3 Consensus size: 23
96511160 ATTTGAAATG
*
96511170 TATATTTGAAATGTTGTATAATA
1 TATATTTGAAATGTTTTATAATA
* * *
96511193 TATAATTTTTAAA---TTGA-AATG
1 TAT-A-TTTGAAATGTTTTATAATA
96511214 TATATTTGAAATGTTTTATAATA
1 TATATTTGAAATGTTTTATAATA
96511237 TATATTT
1 TATATTT
96511244 TTTAAAAATT
Statistics
Matches: 38, Mismatches: 7, Indels: 12
0.67 0.12 0.21
Matches are distributed among these distances:
19 6 0.16
20 1 0.03
21 6 0.16
22 5 0.13
23 13 0.34
24 1 0.03
25 6 0.16
ACGTcount: A:0.39, C:0.00, G:0.09, T:0.51
Consensus pattern (23 bp):
TATATTTGAAATGTTTTATAATA
Found at i:96511307 original size:21 final size:20
Alignment explanation
Indices: 96511274--96511344 Score: 79
Period size: 21 Copynumber: 3.4 Consensus size: 20
96511264 ATTTCTGAAA
96511274 TTATTTTTCTAAATTTTAAAT
1 TTATTTTT-TAAATTTTAAAT
*
96511295 GTTATTTTTTAAACTTTAAAT
1 -TTATTTTTTAAATTTTAAAT
* *
96511316 ATCAATTTTTAAATTTTAAAT
1 -TTATTTTTTAAATTTTAAAT
*
96511337 ATATTTTT
1 TTATTTTT
96511345 AATAATATAA
Statistics
Matches: 41, Mismatches: 8, Indels: 2
0.80 0.16 0.04
Matches are distributed among these distances:
20 5 0.12
21 28 0.68
22 8 0.20
ACGTcount: A:0.35, C:0.04, G:0.01, T:0.59
Consensus pattern (20 bp):
TTATTTTTTAAATTTTAAAT
Found at i:96511437 original size:123 final size:127
Alignment explanation
Indices: 96511273--96511568 Score: 324
Period size: 134 Copynumber: 2.3 Consensus size: 127
96511263 TATTTCTGAA
*
96511273 ATTATTTTTCTAA-ATTTTAAATGTTATTTTTTAAACT-TTAAATA-TCAA-TTTT-TAA-ATTT
1 ATTA-TTTTATAATATTTTAAATG-TATTTTTTAAA-TATTAAATATTCAATTTTTATAATATTT
96511332 TAAA-TAT-ATTTTT-AATAATATAAAACAT-TTAAATATTTTAAAGATATGACCTTTCAAATCT
63 TAAATTATGATTTTTAAATAATATAAAACATATT--AT-TTTTAAAGATATGACCTTTCAAATCT
96511393 ATT
125 ATT
*
96511396 ATTAGTTTTATAATATTTTAAATGTATTTTTTAAATATTAAATATTTTTTAATTTCTTTTATAAT
1 ATTA-TTTTATAATATTTTAAATGTATTTTTTAAATATTAAATA---TTCAA--T-TTTTATAAT
* * * *
96511461 ATTTTAAATTATGATTTTTAAATTATTTAAAATATATTATTTTTAAAGATATGACCTTTCAAATT
59 ATTTTAAATTATGATTTTTAAATAATATAAAACATATTATTTTTAAAGATATGACCTTTCAAATC
96511526 TATT
124 TATT
* *
96511530 ATTTATTTTATAATATTTTAAATATATATTTTAAATATT
1 A-TTATTTTATAATATTTTAAATGTATTTTTTAAATATT
96511569 TTTTAAATTT
Statistics
Matches: 147, Mismatches: 9, Indels: 23
0.82 0.05 0.13
Matches are distributed among these distances:
122 1 0.01
123 29 0.20
124 10 0.07
127 3 0.02
131 4 0.03
132 3 0.02
133 8 0.05
134 64 0.44
135 11 0.07
136 12 0.08
137 2 0.01
ACGTcount: A:0.39, C:0.04, G:0.03, T:0.54
Consensus pattern (127 bp):
ATTATTTTATAATATTTTAAATGTATTTTTTAAATATTAAATATTCAATTTTTATAATATTTTAA
ATTATGATTTTTAAATAATATAAAACATATTATTTTTAAAGATATGACCTTTCAAATCTATT
Found at i:96511487 original size:24 final size:24
Alignment explanation
Indices: 96511452--96511507 Score: 69
Period size: 24 Copynumber: 2.3 Consensus size: 24
96511442 TTTTAATTTC
*
96511452 TTTTATAATATTTTAAAT-TATGAT
1 TTTTA-AATATTTAAAATATATGAT
*
96511476 TTTTAAATTATTTAAAATATATTAT
1 TTTTAAA-TATTTAAAATATATGAT
96511501 TTTTAAA
1 TTTTAAA
96511508 GATATGACCT
Statistics
Matches: 28, Mismatches: 2, Indels: 3
0.85 0.06 0.09
Matches are distributed among these distances:
23 2 0.07
24 14 0.50
25 12 0.43
ACGTcount: A:0.41, C:0.00, G:0.02, T:0.57
Consensus pattern (24 bp):
TTTTAAATATTTAAAATATATGAT
Found at i:96511560 original size:13 final size:13
Alignment explanation
Indices: 96511542--96511576 Score: 56
Period size: 13 Copynumber: 2.8 Consensus size: 13
96511532 TTATTTTATA
96511542 ATATTTTAAATAT
1 ATATTTTAAATAT
96511555 ATATTTTAAATAT
1 ATATTTTAAATAT
96511568 -T-TTTTAAAT
1 ATATTTTAAAT
96511577 TTTAAATATA
Statistics
Matches: 22, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
11 8 0.36
12 1 0.05
13 13 0.59
ACGTcount: A:0.43, C:0.00, G:0.00, T:0.57
Consensus pattern (13 bp):
ATATTTTAAATAT
Found at i:96511580 original size:31 final size:31
Alignment explanation
Indices: 96511533--96511623 Score: 93
Period size: 31 Copynumber: 3.0 Consensus size: 31
96511523 ATTTATTATT
96511533 TATTTTATAATATTTTAAATATATATTTTAAA
1 TATTTTATAATATTTTAAATATA-ATTTTAAA
*
96511565 TATTTTTTAA-ATTTTAAATATAATTTTTATAA
1 TATTTTATAATATTTTAAATATAA-TTTTA-AA
* *
96511597 -ATTAT-TAAT-TTTAAAAT-TAATTTTAAA
1 TATTTTATAATATTTTAAATATAATTTTAAA
96511624 GATATTCAAA
Statistics
Matches: 53, Mismatches: 3, Indels: 11
0.79 0.04 0.16
Matches are distributed among these distances:
27 2 0.04
28 5 0.09
29 3 0.06
30 11 0.21
31 21 0.40
32 11 0.21
ACGTcount: A:0.44, C:0.00, G:0.00, T:0.56
Consensus pattern (31 bp):
TATTTTATAATATTTTAAATATAATTTTAAA
Found at i:96511745 original size:19 final size:19
Alignment explanation
Indices: 96511711--96511789 Score: 108
Period size: 19 Copynumber: 4.1 Consensus size: 19
96511701 ATTATAAAAC
96511711 AATTT-AAAAAATAATATTTA
1 AATTTAAAAAAAT-A-ATTTA
96511731 AATTTTAAAAAAATAATTTA
1 AA-TTTAAAAAAATAATTTA
*
96511751 AATTTAAGAAAATAATTTA
1 AATTTAAAAAAATAATTTA
96511770 AATTT-AAAAAATAATTTA
1 AATTTAAAAAAATAATTTA
96511788 AA
1 AA
96511790 AAATAATATT
Statistics
Matches: 55, Mismatches: 2, Indels: 6
0.87 0.03 0.10
Matches are distributed among these distances:
18 14 0.25
19 21 0.38
20 9 0.16
21 4 0.07
22 7 0.13
ACGTcount: A:0.61, C:0.00, G:0.01, T:0.38
Consensus pattern (19 bp):
AATTTAAAAAAATAATTTA
Found at i:96511749 original size:34 final size:34
Alignment explanation
Indices: 96511706--96511848 Score: 168
Period size: 34 Copynumber: 4.1 Consensus size: 34
96511696 TTAATATTAT
*
96511706 AAAACAATTTAAAAAATAATATTT-AAATTTTAAA
1 AAAATAATTTAAAAAATAATATTTAAAATTTT-AA
*
96511740 AAAATAATTTAAATTTAAGAAAATAATTT-AAA-TTTAA
1 AAAATAATTTAAA---AA-ATAAT-ATTTAAAATTTTAA
96511777 AAAATAATTTAAAAAATAATATTTAAAATTTT-A
1 AAAATAATTTAAAAAATAATATTTAAAATTTTAA
*
96511810 AAAATAATTTCAAAAATATATATTTAAAATTTTAA
1 AAAATAATTTAAAAAATA-ATATTTAAAATTTTAA
96511845 AAAA
1 AAAA
96511849 ATATATTATA
Statistics
Matches: 96, Mismatches: 4, Indels: 17
0.82 0.03 0.15
Matches are distributed among these distances:
32 4 0.04
33 25 0.26
34 31 0.32
35 5 0.05
37 17 0.18
38 7 0.07
39 7 0.07
ACGTcount: A:0.61, C:0.01, G:0.01, T:0.37
Consensus pattern (34 bp):
AAAATAATTTAAAAAATAATATTTAAAATTTTAA
Found at i:96511800 original size:14 final size:12
Alignment explanation
Indices: 96511770--96511838 Score: 65
Period size: 12 Copynumber: 5.8 Consensus size: 12
96511760 AAATAATTTA
96511770 AATTTAAAAAAT
1 AATTTAAAAAAT
96511782 AATTTAAAAAAT
1 AATTTAAAAAAT
*
96511794 AATATT-TAAAAT
1 AAT-TTAAAAAAT
96511806 --TTT-AAAAAT
1 AATTTAAAAAAT
96511815 AATTTCAAAAATAT
1 AATTT-AAAAA-AT
96511829 ATATTTAAAA
1 A-ATTTAAAA
96511839 TTTTAAAAAA
Statistics
Matches: 48, Mismatches: 2, Indels: 12
0.77 0.03 0.19
Matches are distributed among these distances:
9 7 0.15
10 1 0.02
11 3 0.06
12 20 0.42
13 6 0.12
14 7 0.15
15 4 0.08
ACGTcount: A:0.61, C:0.01, G:0.00, T:0.38
Consensus pattern (12 bp):
AATTTAAAAAAT
Found at i:96511825 original size:21 final size:21
Alignment explanation
Indices: 96511782--96511826 Score: 56
Period size: 21 Copynumber: 2.1 Consensus size: 21
96511772 TTTAAAAAAT
*
96511782 AATTTAAAAAATAATATTTAA
1 AATTTAAAAAATAATATTAAA
*
96511803 AATTTTAAAAATAAT-TTCAAA
1 AATTTAAAAAATAATATT-AAA
96511824 AAT
1 AAT
96511827 ATATATTTAA
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
20 2 0.10
21 19 0.90
ACGTcount: A:0.60, C:0.02, G:0.00, T:0.38
Consensus pattern (21 bp):
AATTTAAAAAATAATATTAAA
Found at i:96511969 original size:23 final size:21
Alignment explanation
Indices: 96511943--96511991 Score: 64
Period size: 23 Copynumber: 2.2 Consensus size: 21
96511933 AACTTAACAA
96511943 AAAAAAAG-TAAAAGAAACAATAT
1 AAAAAAAGTTAAAA-AAA-AAT-T
96511966 AAAAAAAGTTAAAAAAAAATT
1 AAAAAAAGTTAAAAAAAAATT
96511987 AAAAA
1 AAAAA
96511992 GTAACAGGGT
Statistics
Matches: 25, Mismatches: 0, Indels: 4
0.86 0.00 0.14
Matches are distributed among these distances:
21 6 0.24
22 3 0.12
23 11 0.44
24 5 0.20
ACGTcount: A:0.78, C:0.02, G:0.06, T:0.14
Consensus pattern (21 bp):
AAAAAAAGTTAAAAAAAAATT
Found at i:96517387 original size:11 final size:10
Alignment explanation
Indices: 96517352--96517430 Score: 59
Period size: 11 Copynumber: 7.4 Consensus size: 10
96517342 GGTATTTTTT
96517352 TAAAGAAATTA
1 TAAA-AAATTA
*
96517363 TAATAAAATAA
1 TAA-AAAATTA
96517374 TAAAAAATTCA
1 TAAAAAATT-A
* *
96517385 TAAAACATTG
1 TAAAAAATTA
*
96517395 TAAAAATTTA
1 TAAAAAATTA
*
96517405 TTTAAAAATATA
1 -TAAAAAAT-TA
*
96517417 TAGAAAATTA
1 TAAAAAATTA
96517427 TAAA
1 TAAA
96517431 CATTAATAAA
Statistics
Matches: 52, Mismatches: 12, Indels: 9
0.71 0.16 0.12
Matches are distributed among these distances:
10 17 0.33
11 32 0.62
12 3 0.06
ACGTcount: A:0.62, C:0.03, G:0.04, T:0.32
Consensus pattern (10 bp):
TAAAAAATTA
Found at i:96517389 original size:10 final size:9
Alignment explanation
Indices: 96517357--96517539 Score: 59
Period size: 9 Copynumber: 19.2 Consensus size: 9
96517347 TTTTTTAAAG
96517357 AAATTATAATA
1 AAATTAT-A-A
*
96517368 AAATAATAAA
1 AAATTAT-AA
96517378 AAATTCATAA
1 AAATT-ATAA
*
96517388 AACATTGTAA
1 AA-ATTATAA
96517398 AAATTTATTTAA
1 AAA-TTA--TAA
96517410 AAATATATAGA
1 AAAT-TATA-A
96517421 AAATTATAA
1 AAATTATAA
*
96517430 ACATTAATAA
1 AAATT-ATAA
* *
96517440 AAATGACAA
1 AAATTATAA
*
96517449 ATCATTATAA
1 A-AATTATAA
* *
96517459 AAAATACAA
1 AAATTATAA
* *
96517468 AAGA-AAGAA
1 AA-ATTATAA
*
96517477 AAA-TATTA
1 AAATTATAA
96517485 AAA--ATAA
1 AAATTATAA
*
96517492 AAACTATAA
1 AAATTATAA
*
96517501 AAATTATTA
1 AAATTATAA
* *
96517510 GAATTATTTA
1 AAATTA-TAA
*
96517520 AAATTAAAA
1 AAATTATAA
*
96517529 AAATAATAA
1 AAATTATAA
96517538 AA
1 AA
96517540 CAAATTAAAA
Statistics
Matches: 131, Mismatches: 28, Indels: 28
0.70 0.15 0.15
Matches are distributed among these distances:
7 6 0.05
8 6 0.05
9 48 0.37
10 44 0.34
11 19 0.15
12 8 0.06
ACGTcount: A:0.64, C:0.04, G:0.03, T:0.28
Consensus pattern (9 bp):
AAATTATAA
Found at i:96517908 original size:29 final size:27
Alignment explanation
Indices: 96517871--96517971 Score: 89
Period size: 29 Copynumber: 3.6 Consensus size: 27
96517861 AATTGAAAAT
96517871 ATTTTTATAATTTTTTGTAATCTTATATA
1 ATTTTTATAATTTTTT-T-ATCTTATATA
* * *
96517900 ATTTTTATAATTTTTTATTTTTTAAAATA
1 ATTTTTATAATTTTTT-TATCTT-ATATA
* *
96517929 ATATTTATAATTTTTTTCA-CTT-TTTA
1 ATTTTTATAATTTTTTT-ATCTTATATA
96517955 TATTTTTATAATTTTTT
1 -ATTTTTATAATTTTTT
96517972 AATAATTGCA
Statistics
Matches: 59, Mismatches: 10, Indels: 8
0.77 0.13 0.10
Matches are distributed among these distances:
26 2 0.03
27 15 0.25
28 6 0.10
29 36 0.61
ACGTcount: A:0.30, C:0.03, G:0.01, T:0.66
Consensus pattern (27 bp):
ATTTTTATAATTTTTTTATCTTATATA
Found at i:96517960 original size:8 final size:9
Alignment explanation
Indices: 96517871--96518027 Score: 86
Period size: 10 Copynumber: 16.6 Consensus size: 9
96517861 AATTGAAAAT
96517871 ATTTTTATA
1 ATTTTTATA
*
96517880 ATTTTTTGTA
1 A-TTTTTATA
*
96517890 ATCTTATATA
1 AT-TTTTATA
96517900 ATTTTTATA
1 ATTTTTATA
96517909 ATTTTT-TA
1 ATTTTTATA
*
96517917 TTTTTTAAAATA
1 ATTTTT---ATA
*
96517929 ATATTTATA
1 ATTTTTATA
*
96517938 ATTTTTTTCA
1 ATTTTTAT-A
*
96517948 CTTTTTAT-
1 ATTTTTATA
96517956 ATTTTTATA
1 ATTTTTATA
96517965 ATTTTTTAATA
1 A-TTTTT-ATA
***
96517976 ATTGCAAT-
1 ATTTTTATA
* *
96517984 GTTTTTTTA
1 ATTTTTATA
96517993 ATCTTTTATGA
1 AT-TTTTAT-A
*
96518004 AATTTTATAA
1 ATTTTTAT-A
96518014 ATTTTTATA
1 ATTTTTATA
96518023 ATTTT
1 ATTTT
96518028 GTAATGATAT
Statistics
Matches: 110, Mismatches: 25, Indels: 26
0.68 0.16 0.16
Matches are distributed among these distances:
8 17 0.15
9 33 0.30
10 48 0.44
11 6 0.05
12 6 0.05
ACGTcount: A:0.31, C:0.03, G:0.03, T:0.63
Consensus pattern (9 bp):
ATTTTTATA
Found at i:96518085 original size:29 final size:29
Alignment explanation
Indices: 96518052--96518108 Score: 96
Period size: 29 Copynumber: 2.0 Consensus size: 29
96518042 GAATTTTTAA
96518052 AAGGAAAATACCAATTTTCACAACGTGAG
1 AAGGAAAATACCAATTTTCACAACGTGAG
* *
96518081 AAGGAAAATATCAATTTTCACAAGGTGA
1 AAGGAAAATACCAATTTTCACAACGTGA
96518109 AACAATACTA
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:0.46, C:0.14, G:0.18, T:0.23
Consensus pattern (29 bp):
AAGGAAAATACCAATTTTCACAACGTGAG
Found at i:96518209 original size:1 final size:1
Alignment explanation
Indices: 96518203--96518237 Score: 70
Period size: 1 Copynumber: 35.0 Consensus size: 1
96518193 AAAGATATGG
96518203 TTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTT
1 TTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTT
96518238 AGAAAAATCA
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
1 34 1.00
ACGTcount: A:0.00, C:0.00, G:0.00, T:1.00
Consensus pattern (1 bp):
T
Found at i:96519742 original size:29 final size:27
Alignment explanation
Indices: 96519681--96519734 Score: 72
Period size: 27 Copynumber: 1.9 Consensus size: 27
96519671 TTCGCTATTT
* *
96519681 AAAACTACATTGGTGAATATTGTAAAA
1 AAAACTACAATGGTGAACATTGTAAAA
96519708 AAAACTACAATGGTGAAGCCATTGTAA
1 AAAACTACAATGGTGAA--CATTGTAA
96519735 GAATAACTGC
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
27 16 0.70
29 7 0.30
ACGTcount: A:0.46, C:0.11, G:0.17, T:0.26
Consensus pattern (27 bp):
AAAACTACAATGGTGAACATTGTAAAA
Found at i:96526124 original size:19 final size:19
Alignment explanation
Indices: 96526078--96526125 Score: 55
Period size: 19 Copynumber: 2.6 Consensus size: 19
96526068 GTATATATTT
96526078 TAAA-TTTATTTAGGTAGA
1 TAAATTTTATTTAGGTAGA
*
96526096 TAAATCTTATTT-GGATAGA
1 TAAATTTTATTTAGG-TAGA
*
96526115 TAAGTTTTATT
1 TAAATTTTATT
96526126 CATATTCTAG
Statistics
Matches: 25, Mismatches: 3, Indels: 3
0.81 0.10 0.10
Matches are distributed among these distances:
18 6 0.24
19 19 0.76
ACGTcount: A:0.35, C:0.02, G:0.15, T:0.48
Consensus pattern (19 bp):
TAAATTTTATTTAGGTAGA
Found at i:96530861 original size:19 final size:19
Alignment explanation
Indices: 96530815--96530862 Score: 55
Period size: 19 Copynumber: 2.6 Consensus size: 19
96530805 GTATATATTT
96530815 TAAA-TTTATTTAGGTAGA
1 TAAATTTTATTTAGGTAGA
*
96530833 TAAATCTTATTT-GGATAGA
1 TAAATTTTATTTAGG-TAGA
*
96530852 TAAGTTTTATT
1 TAAATTTTATT
96530863 CATATTCTAG
Statistics
Matches: 25, Mismatches: 3, Indels: 3
0.81 0.10 0.10
Matches are distributed among these distances:
18 6 0.24
19 19 0.76
ACGTcount: A:0.35, C:0.02, G:0.15, T:0.48
Consensus pattern (19 bp):
TAAATTTTATTTAGGTAGA
Found at i:96530934 original size:41 final size:43
Alignment explanation
Indices: 96530882--96530964 Score: 134
Period size: 43 Copynumber: 2.0 Consensus size: 43
96530872 GAAATTTTTA
96530882 TTTTATCTTTTAGTA-TTTACTA-AATAAGGGAACTATTTTCT
1 TTTTATCTTTTAGTAGTTTACTAGAATAAGGGAACTATTTTCT
* *
96530923 TTTTATGTTTTAGTAGTTTATTAGAATAAGGGAACTATTTTC
1 TTTTATCTTTTAGTAGTTTACTAGAATAAGGGAACTATTTTC
96530965 CCAATTAGGA
Statistics
Matches: 38, Mismatches: 2, Indels: 2
0.90 0.05 0.05
Matches are distributed among these distances:
41 14 0.37
42 6 0.16
43 18 0.47
ACGTcount: A:0.29, C:0.07, G:0.13, T:0.51
Consensus pattern (43 bp):
TTTTATCTTTTAGTAGTTTACTAGAATAAGGGAACTATTTTCT
Found at i:96532741 original size:12 final size:13
Alignment explanation
Indices: 96532719--96532750 Score: 50
Period size: 12 Copynumber: 2.6 Consensus size: 13
96532709 GCTGTTTGCA
96532719 TTTCTTTTCTTTC
1 TTTCTTTTCTTTC
96532732 TTTC-TTTCTTTC
1 TTTCTTTTCTTTC
96532744 TTT-TTTT
1 TTTCTTTT
96532751 TAAATTTTCC
Statistics
Matches: 18, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
12 14 0.78
13 4 0.22
ACGTcount: A:0.00, C:0.19, G:0.00, T:0.81
Consensus pattern (13 bp):
TTTCTTTTCTTTC
Found at i:96539002 original size:17 final size:16
Alignment explanation
Indices: 96538974--96539016 Score: 50
Period size: 17 Copynumber: 2.6 Consensus size: 16
96538964 AAAAGTTTAA
* *
96538974 TTTAATTAAATTCATT
1 TTTAATTTAATTCAAT
*
96538990 TTATAATTTAATTTAAT
1 TT-TAATTTAATTCAAT
96539007 TTTAATTTAA
1 TTTAATTTAA
96539017 AAGTATCATG
Statistics
Matches: 23, Mismatches: 3, Indels: 2
0.82 0.11 0.07
Matches are distributed among these distances:
16 10 0.43
17 13 0.57
ACGTcount: A:0.40, C:0.02, G:0.00, T:0.58
Consensus pattern (16 bp):
TTTAATTTAATTCAAT
Found at i:96540334 original size:18 final size:19
Alignment explanation
Indices: 96540281--96540337 Score: 64
Period size: 19 Copynumber: 3.1 Consensus size: 19
96540271 AATTACAAAA
*
96540281 AAAAAATCAAAATAATTT-T
1 AAAAATTCAAAAT-ATTTAT
*
96540300 TAAAATTCAAAATATTTAT
1 AAAAATTCAAAATATTTAT
*
96540319 AAAAATTCTAAA-ATTTAT
1 AAAAATTCAAAATATTTAT
96540337 A
1 A
96540338 CTTTTTAAAA
Statistics
Matches: 33, Mismatches: 4, Indels: 3
0.82 0.10 0.08
Matches are distributed among these distances:
18 11 0.33
19 22 0.67
ACGTcount: A:0.58, C:0.05, G:0.00, T:0.37
Consensus pattern (19 bp):
AAAAATTCAAAATATTTAT
Found at i:96540375 original size:19 final size:19
Alignment explanation
Indices: 96540339--96540376 Score: 58
Period size: 19 Copynumber: 2.0 Consensus size: 19
96540329 AAATTTATAC
*
96540339 TTTTTAAAAAATTATAAAA
1 TTTTTAAAAAAATATAAAA
*
96540358 TTTTTAAAAAAATCTAAAA
1 TTTTTAAAAAAATATAAAA
96540377 ATATATATTA
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
19 17 1.00
ACGTcount: A:0.58, C:0.03, G:0.00, T:0.39
Consensus pattern (19 bp):
TTTTTAAAAAAATATAAAA
Found at i:96543248 original size:24 final size:24
Alignment explanation
Indices: 96543203--96543249 Score: 60
Period size: 24 Copynumber: 2.0 Consensus size: 24
96543193 GAAGGTGATG
* *
96543203 AAGATGAAAACGGAGGTGGAGATA
1 AAGATAAAAACGGAGGTCGAGATA
96543227 AAGATAAAAAC-GATGGTCGAGAT
1 AAGATAAAAACGGA-GGTCGAGAT
96543250 GAATATGTGT
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
23 2 0.10
24 18 0.90
ACGTcount: A:0.47, C:0.06, G:0.32, T:0.15
Consensus pattern (24 bp):
AAGATAAAAACGGAGGTCGAGATA
Found at i:96548487 original size:15 final size:15
Alignment explanation
Indices: 96548467--96548496 Score: 60
Period size: 15 Copynumber: 2.0 Consensus size: 15
96548457 ATAGATAAAA
96548467 AATTTAATATATGTT
1 AATTTAATATATGTT
96548482 AATTTAATATATGTT
1 AATTTAATATATGTT
96548497 GATGTCTATA
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.40, C:0.00, G:0.07, T:0.53
Consensus pattern (15 bp):
AATTTAATATATGTT
Found at i:96554905 original size:16 final size:16
Alignment explanation
Indices: 96554884--96554915 Score: 64
Period size: 16 Copynumber: 2.0 Consensus size: 16
96554874 CAATTGAAGC
96554884 ATTTTCCTTGAAATTT
1 ATTTTCCTTGAAATTT
96554900 ATTTTCCTTGAAATTT
1 ATTTTCCTTGAAATTT
96554916 TTACTTTTTT
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 16 1.00
ACGTcount: A:0.25, C:0.12, G:0.06, T:0.56
Consensus pattern (16 bp):
ATTTTCCTTGAAATTT
Found at i:96556367 original size:83 final size:83
Alignment explanation
Indices: 96556236--96556478 Score: 246
Period size: 85 Copynumber: 2.9 Consensus size: 83
96556226 TAAGTCTTCG
* * * * **
96556236 TTTGGAAATAAATC-AAGATCAAATAATATTTGTTAAACGACGAAAATAAATCCTGAAACAGATT
1 TTTGGAGATAAAACAAAGATGAAATAAAATTTGTTAAACGACGGGAATAAATCC-GAAACA-ATT
*
96556300 TTATTTAATTTTAATTTCTC-
64 TTATTTAATTTTAA-TACTCA
* *
96556320 TGTTGGCA-AT-AAA-AAA-ATGAAATAAAATTTGTTGAACGGCGGGAATAAATACCGAAACAAT
1 T-TTGG-AGATAAAACAAAGATGAAATAAAATTTGTTAAACGACGGGAATAAAT-CCGAAACAAT
*
96556381 TTTTTTTAATTTTAATACTCA
63 TTTATTTAATTTTAATACTCA
* *
96556402 TTTGGAGATAAAATCAAAGATGAAATAAAGTCTGTTAAACGACGGGAATAAATCCCGAAACAAAT
1 TTTGGAGATAAAA-CAAAGATGAAATAAAATTTGTTAAACGACGGGAATAAAT-CCGAAAC-AAT
*
96556467 TTTATTCAATTT
63 TTTATTTAATTT
96556479 AAAATTTTGT
Statistics
Matches: 132, Mismatches: 16, Indels: 20
0.79 0.10 0.12
Matches are distributed among these distances:
80 1 0.01
81 10 0.08
82 20 0.15
83 34 0.26
84 10 0.08
85 43 0.33
86 14 0.11
ACGTcount: A:0.43, C:0.11, G:0.13, T:0.33
Consensus pattern (83 bp):
TTTGGAGATAAAACAAAGATGAAATAAAATTTGTTAAACGACGGGAATAAATCCGAAACAATTTT
ATTTAATTTTAATACTCA
Found at i:96556480 original size:85 final size:83
Alignment explanation
Indices: 96556174--96556478 Score: 268
Period size: 82 Copynumber: 3.7 Consensus size: 83
96556164 AATTAAATCA
* * * * *
96556174 AAATAAAATCTATTAAACAACAGAAATAAATCCCGAAACAAA-ATTATTTGA--TTAAGTCTTCG
1 AAATAAAATCTGTTAAACGACGGAAATAAATCCCGAAACAAATTTTATTTAATTTTAAGTC-TC-
*
96556236 TTTGGAAATAAATC-AAGATC
64 TTTGG-AATAAATCAAAGATG
* * * * * *
96556256 AAATAATATTTGTTAAACGACGAAAATAAATCCTGAAACAGATTTTATTTAATTTTAATTTCTCT
1 AAATAAAATCTGTTAAACGACGGAAATAAATCCCGAAACAAATTTTATTTAATTTTAA-GTCTCT
96556321 GTTGGCAATAAA--AAA-ATG
65 -TTGG-AATAAATCAAAGATG
* * * * * *
96556339 AAATAAAATTTGTTGAACGGCGGGAATAAATACCGAAAC-AATTTTTTTTAATTTTAA-TACTCA
1 AAATAAAATCTGTTAAACGACGGAAATAAATCCCGAAACAAATTTTATTTAATTTTAAGT-CTC-
96556402 TTTGGAGATAAAATCAAAGATG
64 TTTGGA-AT-AAATCAAAGATG
* * *
96556424 AAATAAAGTCTGTTAAACGACGGGAATAAATCCCGAAACAAATTTTATTCAATTT
1 AAATAAAATCTGTTAAACGACGGAAATAAATCCCGAAACAAATTTTATTTAATTT
96556479 AAAATTTTGT
Statistics
Matches: 180, Mismatches: 29, Indels: 24
0.77 0.12 0.10
Matches are distributed among these distances:
80 2 0.01
81 9 0.05
82 54 0.30
83 41 0.23
84 6 0.03
85 53 0.29
86 15 0.08
ACGTcount: A:0.45, C:0.11, G:0.12, T:0.32
Consensus pattern (83 bp):
AAATAAAATCTGTTAAACGACGGAAATAAATCCCGAAACAAATTTTATTTAATTTTAAGTCTCTT
TGGAATAAATCAAAGATG
Found at i:96560827 original size:39 final size:39
Alignment explanation
Indices: 96560717--96560910 Score: 262
Period size: 39 Copynumber: 4.9 Consensus size: 39
96560707 TCGTTCAAAC
* * * * * *
96560717 GCCTTCGGGATATAGCCCGGTTATGATAACCCGCACAAAT
1 GCCTTCGGGCT-TAGCCCGGATATCACAACTCGCACAATT
* *
96560757 GCCTGCGGGACTTAACCCGGATATCACAACTCGCACAATT
1 GCCTTCGGG-CTTAGCCCGGATATCACAACTCGCACAATT
*
96560797 GCCTTCGGGCTTAGCCCGGATATCATAACTCGCACAATT
1 GCCTTCGGGCTTAGCCCGGATATCACAACTCGCACAATT
*
96560836 GCCTTCGGGCTTAGCCCGGATATCACAATTCGCACAATT
1 GCCTTCGGGCTTAGCCCGGATATCACAACTCGCACAATT
* *
96560875 GCCTTCGGGCTTAGCCCAGATATCACAATTCGCACA
1 GCCTTCGGGCTTAGCCCGGATATCACAACTCGCACA
96560911 TTCATACACA
Statistics
Matches: 139, Mismatches: 14, Indels: 3
0.89 0.09 0.02
Matches are distributed among these distances:
39 100 0.72
40 38 0.27
41 1 0.01
ACGTcount: A:0.25, C:0.31, G:0.21, T:0.23
Consensus pattern (39 bp):
GCCTTCGGGCTTAGCCCGGATATCACAACTCGCACAATT
Found at i:96566742 original size:14 final size:16
Alignment explanation
Indices: 96566724--96566760 Score: 53
Period size: 13 Copynumber: 2.5 Consensus size: 16
96566714 AAATAAATCA
96566724 AAAATATAAAATTT-G
1 AAAATATAAAATTTAG
96566739 -AAATA-AAAATTTAG
1 AAAATATAAAATTTAG
96566753 AAAATATA
1 AAAATATA
96566761 TAAAATTTAA
Statistics
Matches: 19, Mismatches: 0, Indels: 5
0.79 0.00 0.21
Matches are distributed among these distances:
13 7 0.37
14 6 0.32
15 5 0.26
16 1 0.05
ACGTcount: A:0.65, C:0.00, G:0.05, T:0.30
Consensus pattern (16 bp):
AAAATATAAAATTTAG
Found at i:96577443 original size:13 final size:13
Alignment explanation
Indices: 96577425--96577450 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
96577415 CGTATTGGTG
96577425 CACACGACCGTGT
1 CACACGACCGTGT
96577438 CACACGACCGTGT
1 CACACGACCGTGT
96577451 TCTACTTCAT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.23, C:0.38, G:0.23, T:0.15
Consensus pattern (13 bp):
CACACGACCGTGT
Found at i:96577537 original size:25 final size:25
Alignment explanation
Indices: 96577491--96577538 Score: 60
Period size: 25 Copynumber: 1.9 Consensus size: 25
96577481 TTCCAATGCG
***
96577491 CACGCCCGTGTTGTTTTATCAGTCA
1 CACGCCCGTGTTAAATTATCAGTCA
*
96577516 CACGCCCGTGTTAAATTCTCAGT
1 CACGCCCGTGTTAAATTATCAGT
96577539 TTCAACCACG
Statistics
Matches: 19, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
25 19 1.00
ACGTcount: A:0.19, C:0.29, G:0.19, T:0.33
Consensus pattern (25 bp):
CACGCCCGTGTTAAATTATCAGTCA
Found at i:96583159 original size:41 final size:41
Alignment explanation
Indices: 96583114--96583229 Score: 94
Period size: 41 Copynumber: 3.1 Consensus size: 41
96583104 TGAAAGATAA
96583114 ATGTAGCTAGGTCGCATGCGTGATTCCAAGTGAAGGACACC
1 ATGTAGCTAGGTCGCATGCGTGATTCCAAGTGAAGGACACC
* * * * *
96583155 ATGTAGAC-AAG-AG-A-GC-T-A---C--GTGAAAGATA-A
1 ATGTAG-CTAGGTCGCATGCGTGATTCCAAGTGAAGGACACC
96583185 ATGTAGCTAGGTCGCATGCGTGATTCCAAGTGAAGGACACC
1 ATGTAGCTAGGTCGCATGCGTGATTCCAAGTGAAGGACACC
96583226 ATGT
1 ATGT
96583230 GACAAGAGAG
Statistics
Matches: 52, Mismatches: 10, Indels: 26
0.59 0.11 0.30
Matches are distributed among these distances:
29 1 0.02
30 8 0.15
31 9 0.17
32 1 0.02
33 3 0.06
34 1 0.02
35 1 0.02
36 1 0.02
37 1 0.02
38 3 0.06
39 1 0.02
40 9 0.17
41 12 0.23
42 1 0.02
ACGTcount: A:0.32, C:0.18, G:0.28, T:0.22
Consensus pattern (41 bp):
ATGTAGCTAGGTCGCATGCGTGATTCCAAGTGAAGGACACC
Found at i:96583170 original size:71 final size:71
Alignment explanation
Indices: 96583082--96583244 Score: 319
Period size: 71 Copynumber: 2.3 Consensus size: 71
96583072 GAGATGTATC
96583082 CCATGTAGACAAGAGAGCTACGTGAAAGATAAATGTAGCTAGGTCGCATGCGTGATTCCAAGTGA
1 CCATGTAGACAAGAGAGCTACGTGAAAGATAAATGTAGCTAGGTCGCATGCGTGATTCCAAGTGA
96583147 AGGACA
66 AGGACA
96583153 CCATGTAGACAAGAGAGCTACGTGAAAGATAAATGTAGCTAGGTCGCATGCGTGATTCCAAGTGA
1 CCATGTAGACAAGAGAGCTACGTGAAAGATAAATGTAGCTAGGTCGCATGCGTGATTCCAAGTGA
96583218 AGGACA
66 AGGACA
96583224 CCATGT-GACAAGAGAGCTACG
1 CCATGTAGACAAGAGAGCTACG
96583245 AGACAAATCG
Statistics
Matches: 92, Mismatches: 0, Indels: 1
0.99 0.00 0.01
Matches are distributed among these distances:
70 15 0.16
71 77 0.84
ACGTcount: A:0.35, C:0.18, G:0.28, T:0.19
Consensus pattern (71 bp):
CCATGTAGACAAGAGAGCTACGTGAAAGATAAATGTAGCTAGGTCGCATGCGTGATTCCAAGTGA
AGGACA
Found at i:96583281 original size:65 final size:68
Alignment explanation
Indices: 96583082--96583267 Score: 254
Period size: 71 Copynumber: 2.7 Consensus size: 68
96583072 GAGATGTATC
*
96583082 CCATGTAGACAAGAGAGCTACGTGAAAGATAAATGTAGCTAGGTCGCATGCGTGATTCCAAGTGA
1 CCATGTAGACAAGAGAGCTACG-G-AAGACAAATG-AGCTAGGTCGCATGCGTGATTCCAAGTGA
96583147 AGGACA
63 AGGACA
*
96583153 CCATGTAGACAAGAGAGCTACGTGAAAGATAAATGTAGCTAGGTCGCATGCGTGATTCCAAGTGA
1 CCATGTAGACAAGAGAGCTACG-G-AAGACAAATG-AGCTAGGTCGCATGCGTGATTCCAAGTGA
96583218 AGGACA
63 AGGACA
*
96583224 CCATGT-GACAAGAGAGCTAC-G-AGACAAATCG-GTTAGGTCGCATG
1 CCATGTAGACAAGAGAGCTACGGAAGACAAAT-GAGCTAGGTCGCATG
96583268 AGTGGTACTA
Statistics
Matches: 112, Mismatches: 2, Indels: 8
0.92 0.02 0.07
Matches are distributed among these distances:
65 12 0.11
66 7 0.06
67 1 0.01
68 1 0.01
70 14 0.12
71 77 0.69
ACGTcount: A:0.34, C:0.18, G:0.28, T:0.19
Consensus pattern (68 bp):
CCATGTAGACAAGAGAGCTACGGAAGACAAATGAGCTAGGTCGCATGCGTGATTCCAAGTGAAGG
ACA
Found at i:96590227 original size:41 final size:41
Alignment explanation
Indices: 96590182--96590297 Score: 94
Period size: 41 Copynumber: 3.1 Consensus size: 41
96590172 TGAAAGATAA
96590182 ATGTAGCTAGGTCGCATGCGTGATTCCAAGTGAAGGACACC
1 ATGTAGCTAGGTCGCATGCGTGATTCCAAGTGAAGGACACC
* * * * *
96590223 ATGTAGAC-AAG-AG-A-GC-T-A---C--GTGAAAGATA-A
1 ATGTAG-CTAGGTCGCATGCGTGATTCCAAGTGAAGGACACC
96590253 ATGTAGCTAGGTCGCATGCGTGATTCCAAGTGAAGGACACC
1 ATGTAGCTAGGTCGCATGCGTGATTCCAAGTGAAGGACACC
96590294 ATGT
1 ATGT
96590298 GGACAAGAGA
Statistics
Matches: 52, Mismatches: 10, Indels: 26
0.59 0.11 0.30
Matches are distributed among these distances:
29 1 0.02
30 8 0.15
31 9 0.17
32 1 0.02
33 3 0.06
34 1 0.02
35 1 0.02
36 1 0.02
37 1 0.02
38 3 0.06
39 1 0.02
40 9 0.17
41 12 0.23
42 1 0.02
ACGTcount: A:0.32, C:0.18, G:0.28, T:0.22
Consensus pattern (41 bp):
ATGTAGCTAGGTCGCATGCGTGATTCCAAGTGAAGGACACC
Found at i:96590238 original size:71 final size:71
Alignment explanation
Indices: 96590150--96590313 Score: 319
Period size: 71 Copynumber: 2.3 Consensus size: 71
96590140 GAGATGTATC
96590150 CCATGTAGACAAGAGAGCTACGTGAAAGATAAATGTAGCTAGGTCGCATGCGTGATTCCAAGTGA
1 CCATGTAGACAAGAGAGCTACGTGAAAGATAAATGTAGCTAGGTCGCATGCGTGATTCCAAGTGA
96590215 AGGACA
66 AGGACA
96590221 CCATGTAGACAAGAGAGCTACGTGAAAGATAAATGTAGCTAGGTCGCATGCGTGATTCCAAGTGA
1 CCATGTAGACAAGAGAGCTACGTGAAAGATAAATGTAGCTAGGTCGCATGCGTGATTCCAAGTGA
96590286 AGGACA
66 AGGACA
*
96590292 CCATGTGGACAAGAGAGCTACG
1 CCATGTAGACAAGAGAGCTACG
96590314 AGACAAATCG
Statistics
Matches: 92, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
71 92 1.00
ACGTcount: A:0.35, C:0.18, G:0.29, T:0.19
Consensus pattern (71 bp):
CCATGTAGACAAGAGAGCTACGTGAAAGATAAATGTAGCTAGGTCGCATGCGTGATTCCAAGTGA
AGGACA
Found at i:96593210 original size:39 final size:39
Alignment explanation
Indices: 96593141--96593300 Score: 248
Period size: 39 Copynumber: 4.1 Consensus size: 39
96593131 GGTAACCCGT
* *
96593141 ACAAATGCCTTCGGGACTTAACCCGGATATCACAACTCGC
1 ACAATTGCCTTCGGG-CTTAGCCCGGATATCACAACTCGC
***
96593181 ACAATTGCCTTCGGGCTTAGCCCGGATATCATGGCTCGC
1 ACAATTGCCTTCGGGCTTAGCCCGGATATCACAACTCGC
*
96593220 ACCATTGCCTTCGGGCTTAGCCCGGATATCACAACTCGC
1 ACAATTGCCTTCGGGCTTAGCCCGGATATCACAACTCGC
*
96593259 ACAATTGCCTTCGGGCTTAGCCCGGATATCACAATTCGC
1 ACAATTGCCTTCGGGCTTAGCCCGGATATCACAACTCGC
96593298 ACA
1 ACA
96593301 TTCATACACA
Statistics
Matches: 109, Mismatches: 11, Indels: 1
0.90 0.09 0.01
Matches are distributed among these distances:
39 95 0.87
40 14 0.13
ACGTcount: A:0.24, C:0.33, G:0.21, T:0.23
Consensus pattern (39 bp):
ACAATTGCCTTCGGGCTTAGCCCGGATATCACAACTCGC
Found at i:96599732 original size:20 final size:20
Alignment explanation
Indices: 96599707--96599750 Score: 79
Period size: 20 Copynumber: 2.2 Consensus size: 20
96599697 GTGTGGTCAC
96599707 ACACGTCCGTGTGGCTTGGG
1 ACACGTCCGTGTGGCTTGGG
*
96599727 ACACGTCCTTGTGGCTTGGG
1 ACACGTCCGTGTGGCTTGGG
96599747 ACAC
1 ACAC
96599751 ACCCGTGTCC
Statistics
Matches: 23, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
20 23 1.00
ACGTcount: A:0.14, C:0.27, G:0.34, T:0.25
Consensus pattern (20 bp):
ACACGTCCGTGTGGCTTGGG
Found at i:96610037 original size:46 final size:45
Alignment explanation
Indices: 96609963--96610123 Score: 134
Period size: 46 Copynumber: 3.5 Consensus size: 45
96609953 GATGCCATGC
* * *
96609963 CCCAGTCATGGTCTTACACTGACACATCTCGTAGTCGATGCATAT
1 CCCAGACATAGTCTTACACTGGCACATCTCGTAGTCGATGCATAT
* * *
96610008 CCCAGACAT-GTCTTACACTGGCTTACATCTTG-AGGCCGATGCATGT
1 CCCAGACATAGTCTTACACTGGC--ACATCTCGTA-GTCGATGCATAT
* * *
96610054 CCCAAACATA-TCTTACACTAGCAC-TCGTC-TCAATGCAGATGCCATAT
1 CCCAGACATAGTCTTACACTGGCACATC-TCGT-AGT-C-GATG-CATAT
96610101 CCCAGACATAGTCTTACACTGGC
1 CCCAGACATAGTCTTACACTGGC
96610124 TCTCATAATG
Statistics
Matches: 92, Mismatches: 13, Indels: 19
0.74 0.10 0.15
Matches are distributed among these distances:
43 2 0.02
44 15 0.16
45 11 0.12
46 40 0.43
47 13 0.14
48 11 0.12
ACGTcount: A:0.26, C:0.30, G:0.17, T:0.27
Consensus pattern (45 bp):
CCCAGACATAGTCTTACACTGGCACATCTCGTAGTCGATGCATAT
Found at i:96610143 original size:48 final size:47
Alignment explanation
Indices: 96609998--96610144 Score: 128
Period size: 46 Copynumber: 3.1 Consensus size: 47
96609988 ATCTCGTAGT
** *
96609998 CGATGCATATCCCAGACAT-GTCTTACACTGGCT-TACATCTTGAGGC
1 CGATGCATATCCCAGACATAGTCTTACACTGGCTCT-CATAATGTGGC
* * *
96610044 CGATGCATGTCCCAAACATA-TCTTACACTAGCACTCGTC-TCAA--T-GC
1 CGATGCATATCCCAGACATAGTCTTACACT-G-GCTC-TCAT-AATGTGGC
*
96610090 AGATGCCATATCCCAGACATAGTCTTACACTGGCTCTCATAATGTGGC
1 CGATG-CATATCCCAGACATAGTCTTACACTGGCTCTCATAATGTGGC
96610138 CGATGCA
1 CGATGCA
96610145 CATGTCTTAC
Statistics
Matches: 78, Mismatches: 11, Indels: 23
0.70 0.10 0.21
Matches are distributed among these distances:
45 4 0.05
46 36 0.46
47 18 0.23
48 18 0.23
49 1 0.01
50 1 0.01
ACGTcount: A:0.27, C:0.29, G:0.18, T:0.27
Consensus pattern (47 bp):
CGATGCATATCCCAGACATAGTCTTACACTGGCTCTCATAATGTGGC
Found at i:96612881 original size:6 final size:7
Alignment explanation
Indices: 96612864--96612891 Score: 56
Period size: 7 Copynumber: 4.0 Consensus size: 7
96612854 GATTGGGAGA
96612864 AAAAAAG
1 AAAAAAG
96612871 AAAAAAG
1 AAAAAAG
96612878 AAAAAAG
1 AAAAAAG
96612885 AAAAAAG
1 AAAAAAG
96612892 TGTGTGAGCT
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 21 1.00
ACGTcount: A:0.86, C:0.00, G:0.14, T:0.00
Consensus pattern (7 bp):
AAAAAAG
Found at i:96624856 original size:13 final size:13
Alignment explanation
Indices: 96624838--96624865 Score: 56
Period size: 13 Copynumber: 2.2 Consensus size: 13
96624828 AAACCACCTC
96624838 AAAATGAATTAAT
1 AAAATGAATTAAT
96624851 AAAATGAATTAAT
1 AAAATGAATTAAT
96624864 AA
1 AA
96624866 GTTAATGTTT
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 15 1.00
ACGTcount: A:0.64, C:0.00, G:0.07, T:0.29
Consensus pattern (13 bp):
AAAATGAATTAAT
Found at i:96625451 original size:17 final size:18
Alignment explanation
Indices: 96625431--96625466 Score: 56
Period size: 17 Copynumber: 2.1 Consensus size: 18
96625421 CTAAAGTTTT
96625431 ATTTTAATGTTA-TATAC
1 ATTTTAATGTTATTATAC
*
96625448 ATTTTAATTTTATTATAC
1 ATTTTAATGTTATTATAC
96625466 A
1 A
96625467 CATTTTATTG
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
17 11 0.65
18 6 0.35
ACGTcount: A:0.36, C:0.06, G:0.03, T:0.56
Consensus pattern (18 bp):
ATTTTAATGTTATTATAC
Found at i:96628251 original size:42 final size:42
Alignment explanation
Indices: 96628195--96628276 Score: 155
Period size: 42 Copynumber: 2.0 Consensus size: 42
96628185 AAAAAATAAT
96628195 AAAAAGTTACAAATGTTAAGATTTAAACCCCACGTCATCATA
1 AAAAAGTTACAAATGTTAAGATTTAAACCCCACGTCATCATA
*
96628237 AAAAAGTTACAAATGTTAAGATTTATACCCCACGTCATCA
1 AAAAAGTTACAAATGTTAAGATTTAAACCCCACGTCATCA
96628277 ATATTTATTT
Statistics
Matches: 39, Mismatches: 1, Indels: 0
0.98 0.03 0.00
Matches are distributed among these distances:
42 39 1.00
ACGTcount: A:0.44, C:0.20, G:0.10, T:0.27
Consensus pattern (42 bp):
AAAAAGTTACAAATGTTAAGATTTAAACCCCACGTCATCATA
Found at i:96628431 original size:35 final size:31
Alignment explanation
Indices: 96628352--96628432 Score: 110
Period size: 31 Copynumber: 2.6 Consensus size: 31
96628342 CTAAATTTTT
*
96628352 AAAGTGGCAAATCAATCACTAACATTTATGA
1 AAAGTGACAAATCAATCACTAACATTTATGA
* *
96628383 AAAGTGACAAATCAATCACTAACGTTT-TCTA
1 AAAGTGACAAATCAATCACTAACATTTAT-GA
*
96628414 AAAGTGACAAACCAATCAC
1 AAAGTGACAAATCAATCAC
96628433 CTAAGCCCAT
Statistics
Matches: 45, Mismatches: 4, Indels: 2
0.88 0.08 0.04
Matches are distributed among these distances:
30 1 0.02
31 44 0.98
ACGTcount: A:0.46, C:0.20, G:0.11, T:0.23
Consensus pattern (31 bp):
AAAGTGACAAATCAATCACTAACATTTATGA
Found at i:96628446 original size:35 final size:31
Alignment explanation
Indices: 96628339--96628432 Score: 106
Period size: 31 Copynumber: 3.1 Consensus size: 31
96628329 AAAATTTCAG
* *
96628339 TCACTAA-ATTTT-T-AAAGTGGCAAATCAA
1 TCACTAACATTTTCTAAAAGTGACAAACCAA
* *
96628367 TCACTAACATTTAT-GAAAAGTGACAAATCAA
1 TCACTAACATTT-TCTAAAAGTGACAAACCAA
*
96628398 TCACTAACGTTTTCTAAAAGTGACAAACCAA
1 TCACTAACATTTTCTAAAAGTGACAAACCAA
96628429 TCAC
1 TCAC
96628433 CTAAGCCCAT
Statistics
Matches: 57, Mismatches: 5, Indels: 5
0.85 0.07 0.07
Matches are distributed among these distances:
28 7 0.12
29 4 0.07
30 2 0.04
31 44 0.77
ACGTcount: A:0.44, C:0.19, G:0.10, T:0.28
Consensus pattern (31 bp):
TCACTAACATTTTCTAAAAGTGACAAACCAA
Found at i:96630628 original size:46 final size:46
Alignment explanation
Indices: 96630578--96630750 Score: 208
Period size: 46 Copynumber: 3.7 Consensus size: 46
96630568 TGGTTGAGCA
*
96630578 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCAAATG
1 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCAAACG
* * * * *
96630624 TCCGAACTCGTTGAGTTGAGTTCGAGTTC-GTGA--GATGTAACTAGGCA
1 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCAA--A--CG
* *
96630671 TCCGAACTCGTTGAGTTGAGTCCGAGTTCATTTATGGATGCGAACG
1 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCAAACG
*
96630717 TCCGAGCTCGTTGAGTTGAGTCCGAGTTCACTTA
1 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTA
96630751 GGGGCGGGTT
Statistics
Matches: 106, Mismatches: 14, Indels: 14
0.79 0.10 0.10
Matches are distributed among these distances:
43 6 0.06
45 3 0.03
46 61 0.58
47 28 0.26
48 3 0.03
50 5 0.05
ACGTcount: A:0.22, C:0.20, G:0.28, T:0.31
Consensus pattern (46 bp):
TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCAAACG
Found at i:96630734 original size:93 final size:93
Alignment explanation
Indices: 96630575--96630745 Score: 297
Period size: 93 Copynumber: 1.8 Consensus size: 93
96630565 GGATGGTTGA
*
96630575 GCATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCAAATGTCCGAACTCGTTGAGT
1 GCATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCAAACGTCCGAACTCGTTGAGT
*
96630640 TGAGTTCGAGTTCGTGAGATGTAACTAG
66 TGAGTCCGAGTTCGTGAGATGTAACTAG
* * *
96630668 GCATCCGAACTCGTTGAGTTGAGTCCGAGTTCATTTATGGATGCGAACGTCCGAGCTCGTTGAGT
1 GCATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCAAACGTCCGAACTCGTTGAGT
96630733 TGAGTCCGAGTTC
66 TGAGTCCGAGTTC
96630746 ACTTAGGGGC
Statistics
Matches: 73, Mismatches: 5, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
93 73 1.00
ACGTcount: A:0.22, C:0.20, G:0.29, T:0.30
Consensus pattern (93 bp):
GCATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCAAACGTCCGAACTCGTTGAGT
TGAGTCCGAGTTCGTGAGATGTAACTAG
Found at i:96638463 original size:49 final size:48
Alignment explanation
Indices: 96638221--96638539 Score: 273
Period size: 46 Copynumber: 6.7 Consensus size: 48
96638211 AGATATGTGT
* *
96638221 GCTAGTGTAAGACATGCCTGGGACATGCATCAGACA-C-ATTG-TGAGA
1 GCTAGTGTAAGACATGTCTGGGACATGCATC-GACATCGATAGATGAGA
* * *
96638267 GCCAGTGTAAGACATGTCTAGGACATGCATCGACCA-C-AT-TATGAGA
1 GCTAGTGTAAGACATGTCTGGGACATGCATCGA-CATCGATAGATGAGA
* * * *
96638313 GCTAGTGTAAGACATGTCTGGGACATGTATTGGCATTG--AGATGAGA
1 GCTAGTGTAAGACATGTCTGGGACATGCATCGACATCGATAGATGAGA
* * * *
96638359 GCTAGTGTAAGACATGTCTGGGACATGCATC-ATCCTCGAGATAT-ACAA
1 GCTAGTGTAAGACATGTCTGGGACATGCATCGA-CATCGATAGATGA-GA
*
96638407 GCTAGTGTAAGACCTGTCTGGGACATGGCATCGACATCGATAGATGAGA
1 GCTAGTGTAAGACATGTCTGGGACAT-GCATCGACATCGATAGATGAGA
* * * * * * *
96638456 GCTAGTGTAAGACCTATCTGGGACATGACATTGGCCTTGAT-GTATGAAA
1 GCTAGTGTAAGACATGTCTGGGACATG-CATCGACATCGATAG-ATGAGA
* * *
96638505 GTTAGTGTAAGACCTATCTGGGACATGGCATCGAC
1 GCTAGTGTAAGACATGTCTGGGACAT-GCATCGAC
96638540 TTTGATGTGC
Statistics
Matches: 226, Mismatches: 32, Indels: 27
0.79 0.11 0.09
Matches are distributed among these distances:
45 4 0.02
46 104 0.46
47 1 0.00
48 31 0.14
49 83 0.37
50 3 0.01
ACGTcount: A:0.29, C:0.18, G:0.28, T:0.25
Consensus pattern (48 bp):
GCTAGTGTAAGACATGTCTGGGACATGCATCGACATCGATAGATGAGA
Found at i:96638545 original size:49 final size:49
Alignment explanation
Indices: 96638306--96638547 Score: 212
Period size: 49 Copynumber: 5.0 Consensus size: 49
96638296 TCGACCACAT
* * * * * *
96638306 TATGAGAGCTAGTGTAAGACATGTCTGGGACAT-GTATTGGCATTGA-G
1 TATGAAAGCTAGTGTAAGACCTATCTGGGACATGGCATCGACATTGATG
* * * * *
96638353 -ATGAGAGCTAGTGTAAGACATGTCTGGGACAT-GCATC-ATCCTCGA-G
1 TATGAAAGCTAGTGTAAGACCTATCTGGGACATGGCATCGA-CATTGATG
* *
96638399 ATAT-ACAAGCTAGTGTAAGACCTGTCTGGGACATGGCATCGACATCGATAG
1 -TATGA-AAGCTAGTGTAAGACCTATCTGGGACATGGCATCGACATTGAT-G
* * * * *
96638450 -ATGAGAGCTAGTGTAAGACCTATCTGGGACATGACATTGGCCTTGATG
1 TATGAAAGCTAGTGTAAGACCTATCTGGGACATGGCATCGACATTGATG
* *
96638498 TATGAAAGTTAGTGTAAGACCTATCTGGGACATGGCATCGACTTTGATG
1 TATGAAAGCTAGTGTAAGACCTATCTGGGACATGGCATCGACATTGATG
96638547 T
1 T
96638548 GCTTGCCAGT
Statistics
Matches: 164, Mismatches: 21, Indels: 18
0.81 0.10 0.09
Matches are distributed among these distances:
46 40 0.24
47 1 0.01
48 29 0.18
49 91 0.55
50 2 0.01
51 1 0.01
ACGTcount: A:0.29, C:0.16, G:0.28, T:0.27
Consensus pattern (49 bp):
TATGAAAGCTAGTGTAAGACCTATCTGGGACATGGCATCGACATTGATG
Found at i:96642588 original size:32 final size:32
Alignment explanation
Indices: 96642535--96642604 Score: 81
Period size: 32 Copynumber: 2.2 Consensus size: 32
96642525 TACATCCACA
* *
96642535 TGAATTTGGACAAATGGTTATTTAGGTTCA-CT
1 TGAATTTGGACAAAT-GTTATTCAAGTTCATCT
96642567 TGAATTTGGACAACCAT-TTATTCAAGTTCATCT
1 TGAATTTGGACAA--ATGTTATTCAAGTTCATCT
96642600 TGAAT
1 TGAAT
96642605 GTGGTTTTTT
Statistics
Matches: 33, Mismatches: 2, Indels: 5
0.82 0.05 0.12
Matches are distributed among these distances:
32 24 0.73
33 7 0.21
34 2 0.06
ACGTcount: A:0.30, C:0.13, G:0.17, T:0.40
Consensus pattern (32 bp):
TGAATTTGGACAAATGTTATTCAAGTTCATCT
Found at i:96642714 original size:29 final size:29
Alignment explanation
Indices: 96642671--96642731 Score: 81
Period size: 29 Copynumber: 2.1 Consensus size: 29
96642661 ATTTATTTTA
*
96642671 AAATTATAAATAATTA-TATCAAATTAGTT
1 AAATTATAAATAATTACT-TAAAATTAGTT
96642700 AAATTATTAAA-AATTACTTAAAATTAGTT
1 AAATTA-TAAATAATTACTTAAAATTAGTT
96642729 AAA
1 AAA
96642732 AATTAGTATT
Statistics
Matches: 29, Mismatches: 1, Indels: 4
0.85 0.03 0.12
Matches are distributed among these distances:
29 24 0.83
30 5 0.17
ACGTcount: A:0.54, C:0.03, G:0.03, T:0.39
Consensus pattern (29 bp):
AAATTATAAATAATTACTTAAAATTAGTT
Found at i:96642722 original size:11 final size:10
Alignment explanation
Indices: 96642630--96642736 Score: 57
Period size: 10 Copynumber: 10.8 Consensus size: 10
96642620 AATAACTAAA
*
96642630 AAAAATTA-A
1 AAAAATTATT
96642639 AAAAATTA-T
1 AAAAATTATT
*
96642648 AAAAATTATG
1 AAAAATTATT
* *
96642658 GAAATTTATTT
1 AAAAATTA-TT
*
96642669 TAAAATTA-T
1 AAAAATTATT
96642678 AAATAATTA-T
1 AAA-AATTATT
*
96642688 ATCAAATTAGTT
1 A-AAAATTA-TT
96642700 --AAATTATT
1 AAAAATTATT
96642708 AAAAATTACTT
1 AAAAATTA-TT
96642719 -AAAATTAGTT
1 AAAAATTA-TT
96642729 AAAAATTA
1 AAAAATTA
96642737 GTATTAAAAA
Statistics
Matches: 78, Mismatches: 10, Indels: 18
0.74 0.09 0.17
Matches are distributed among these distances:
8 2 0.03
9 25 0.32
10 33 0.42
11 17 0.22
12 1 0.01
ACGTcount: A:0.56, C:0.02, G:0.04, T:0.38
Consensus pattern (10 bp):
AAAAATTATT
Found at i:96642745 original size:13 final size:11
Alignment explanation
Indices: 96642691--96642748 Score: 61
Period size: 10 Copynumber: 5.5 Consensus size: 11
96642681 TAATTATATC
96642691 AAATTAGTT--
1 AAATTAGTTAA
96642700 AAATTA-TTAA
1 AAATTAGTTAA
*
96642710 AAATTACTT-A
1 AAATTAGTTAA
96642720 AAATTAGTTAA
1 AAATTAGTTAA
96642731 AAATTAGTATTAA
1 AAATTAG--TTAA
96642744 AAATT
1 AAATT
96642749 TCAAATACAC
Statistics
Matches: 42, Mismatches: 1, Indels: 8
0.82 0.02 0.16
Matches are distributed among these distances:
8 2 0.05
9 6 0.14
10 15 0.36
11 10 0.24
13 9 0.21
ACGTcount: A:0.53, C:0.02, G:0.05, T:0.40
Consensus pattern (11 bp):
AAATTAGTTAA
Found at i:96644205 original size:27 final size:27
Alignment explanation
Indices: 96644175--96644239 Score: 87
Period size: 27 Copynumber: 2.4 Consensus size: 27
96644165 TCAGGGTATG
96644175 CCACAAAGGC-AGTTCTCTCAGAGTTCA
1 CCACAAAGGCTA-TTCTCTCAGAGTTCA
* * *
96644202 CCACAAAGGCTATTCTTTTAGAGTTCG
1 CCACAAAGGCTATTCTCTCAGAGTTCA
96644229 CCACAAAGGCT
1 CCACAAAGGCT
96644240 CACAAAATGA
Statistics
Matches: 34, Mismatches: 3, Indels: 2
0.87 0.08 0.05
Matches are distributed among these distances:
27 33 0.97
28 1 0.03
ACGTcount: A:0.29, C:0.28, G:0.18, T:0.25
Consensus pattern (27 bp):
CCACAAAGGCTATTCTCTCAGAGTTCA
Found at i:96644926 original size:26 final size:26
Alignment explanation
Indices: 96644909--96644962 Score: 108
Period size: 26 Copynumber: 2.1 Consensus size: 26
96644899 AATTAGTGTA
96644909 AGGGGCTTAAATGGGAAATATACCTT
1 AGGGGCTTAAATGGGAAATATACCTT
96644935 AGGGGCTTAAATGGGAAATATACCTT
1 AGGGGCTTAAATGGGAAATATACCTT
96644961 AG
1 AG
96644963 TTATGTGATT
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
26 28 1.00
ACGTcount: A:0.35, C:0.11, G:0.28, T:0.26
Consensus pattern (26 bp):
AGGGGCTTAAATGGGAAATATACCTT
Found at i:96647365 original size:21 final size:22
Alignment explanation
Indices: 96647336--96647379 Score: 56
Period size: 21 Copynumber: 2.0 Consensus size: 22
96647326 GATTTTTACC
96647336 ATTTCTGG-ATTTAAGTATCGAT
1 ATTTCTGGAATTT-AGTATCGAT
*
96647358 ATTT-TGGAATTTTGTATCGAT
1 ATTTCTGGAATTTAGTATCGAT
96647379 A
1 A
96647380 GTCGACTACA
Statistics
Matches: 20, Mismatches: 1, Indels: 3
0.83 0.04 0.12
Matches are distributed among these distances:
21 12 0.60
22 8 0.40
ACGTcount: A:0.27, C:0.07, G:0.18, T:0.48
Consensus pattern (22 bp):
ATTTCTGGAATTTAGTATCGAT
Found at i:96662613 original size:40 final size:40
Alignment explanation
Indices: 96662557--96662724 Score: 175
Period size: 40 Copynumber: 4.2 Consensus size: 40
96662547 CAATTGAATG
* * *
96662557 ATATCCGGGTTAAGACCTGAAGGCAATTGTGCTAGTGACTT
1 ATATCCGGGCTAAGACCCGAAGGCAATTGTGCAAGTG-CTT
96662598 -TATCCGGGCTAAGACCCGAAGGC-ATTCGTGCAAGTTG-TT
1 ATATCCGGGCTAAGACCCGAAGGCAATT-GTGCAAG-TGCTT
* * *
96662637 ATATCCGGGCTAATACCCGAAGGCATTTGTGCGAGT-CGTT
1 ATATCCGGGCTAAGACCCGAAGGCAATTGTGCAAGTGC-TT
** *
96662677 ATATCCGGGCTAAGACCCGAAGGC-ATTCGTGCGTGTGGTT
1 ATATCCGGGCTAAGACCCGAAGGCAATT-GTGCAAGTGCTT
96662717 ATATCCGG
1 ATATCCGG
96662725 TTGTATTCCG
Statistics
Matches: 109, Mismatches: 10, Indels: 17
0.80 0.07 0.12
Matches are distributed among these distances:
39 8 0.07
40 97 0.89
41 4 0.04
ACGTcount: A:0.23, C:0.21, G:0.29, T:0.27
Consensus pattern (40 bp):
ATATCCGGGCTAAGACCCGAAGGCAATTGTGCAAGTGCTT
Found at i:96662690 original size:80 final size:79
Alignment explanation
Indices: 96662557--96662724 Score: 230
Period size: 80 Copynumber: 2.1 Consensus size: 79
96662547 CAATTGAATG
* * *
96662557 ATATCCGGGTTAAGACCTGAAGGCAATTGTGCTAGTGACTTTATCCGGGCTAAGACCCGAAGGCA
1 ATATCCGGGCTAAGACCCGAAGGCAATTGTGCGAGTGA-TTTATCCGGGCTAAGACCCGAAGGCA
*
96662622 TTCGTGCAAGTTGTT
65 TTCGTGCAAGTGGTT
* *
96662637 ATATCCGGGCTAATACCCGAAGGCATTTGTGCGAGTCG-TTATATCCGGGCTAAGACCCGAAGGC
1 ATATCCGGGCTAAGACCCGAAGGCAATTGTGCGAGT-GATT-TATCCGGGCTAAGACCCGAAGGC
**
96662701 ATTCGTGCGTGTGGTT
64 ATTCGTGCAAGTGGTT
96662717 ATATCCGG
1 ATATCCGG
96662725 TTGTATTCCG
Statistics
Matches: 78, Mismatches: 8, Indels: 4
0.87 0.09 0.04
Matches are distributed among these distances:
79 2 0.03
80 75 0.96
81 1 0.01
ACGTcount: A:0.23, C:0.21, G:0.29, T:0.27
Consensus pattern (79 bp):
ATATCCGGGCTAAGACCCGAAGGCAATTGTGCGAGTGATTTATCCGGGCTAAGACCCGAAGGCAT
TCGTGCAAGTGGTT
Found at i:96677839 original size:8 final size:8
Alignment explanation
Indices: 96677826--96677856 Score: 53
Period size: 8 Copynumber: 3.8 Consensus size: 8
96677816 TTTTTAAAGA
96677826 TATTTTAT
1 TATTTTAT
96677834 TATTTTAT
1 TATTTTAT
96677842 TATTATTAT
1 TATT-TTAT
96677851 TATTTT
1 TATTTT
96677857 TTAGTATAAA
Statistics
Matches: 22, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
8 14 0.64
9 8 0.36
ACGTcount: A:0.26, C:0.00, G:0.00, T:0.74
Consensus pattern (8 bp):
TATTTTAT
Found at i:96679822 original size:60 final size:60
Alignment explanation
Indices: 96679729--96679849 Score: 154
Period size: 60 Copynumber: 2.0 Consensus size: 60
96679719 ATTGACGGTA
* * * *
96679729 AAAAGGATATAGCCCAGATAGGTGATCTTAATGATATAGCCC-TCTCGAAGAATATGAGTG
1 AAAAGGATATAGCCCAGACAGGTGATCCTAATGATATAACCCTTC-CAAAGAATATGAGTG
* * * *
96679789 AAAAGGATCTAGCCCGGACGGGTGATCCTAATGATATAACCCTTCCAAAGAATATGTGTG
1 AAAAGGATATAGCCCAGACAGGTGATCCTAATGATATAACCCTTCCAAAGAATATGAGTG
96679849 A
1 A
96679850 GTCTGGATTT
Statistics
Matches: 52, Mismatches: 8, Indels: 2
0.84 0.13 0.03
Matches are distributed among these distances:
60 50 0.96
61 2 0.04
ACGTcount: A:0.36, C:0.17, G:0.23, T:0.24
Consensus pattern (60 bp):
AAAAGGATATAGCCCAGACAGGTGATCCTAATGATATAACCCTTCCAAAGAATATGAGTG
Found at i:96680069 original size:67 final size:67
Alignment explanation
Indices: 96679961--96680089 Score: 170
Period size: 67 Copynumber: 1.9 Consensus size: 67
96679951 AGCATATGTT
* ** * *
96679961 ACAGGGGATTTAGCTTGGACTAGTAATCCTGCTGTAAGAAATGAGGTT-GACAGGAGTGTGCTCT
1 ACAGGGGATTTAGCCTGGACTAGTAATCCCACTATAAGAAATAAGGTTCG-CAGGAGTGTGCTCT
96680025 CTC
65 CTC
* * *
96680028 ACAGGGGATTTAGCCTGGACTGGTAATCCCACTATGAGAAATAAGGTTCGCGGGAGTGTGCT
1 ACAGGGGATTTAGCCTGGACTAGTAATCCCACTATAAGAAATAAGGTTCGCAGGAGTGTGCT
96680090 ATCTAAAATG
Statistics
Matches: 53, Mismatches: 8, Indels: 2
0.84 0.13 0.03
Matches are distributed among these distances:
67 52 0.98
68 1 0.02
ACGTcount: A:0.26, C:0.17, G:0.31, T:0.26
Consensus pattern (67 bp):
ACAGGGGATTTAGCCTGGACTAGTAATCCCACTATAAGAAATAAGGTTCGCAGGAGTGTGCTCTC
TC
Found at i:96680241 original size:20 final size:23
Alignment explanation
Indices: 96680211--96680255 Score: 69
Period size: 20 Copynumber: 2.1 Consensus size: 23
96680201 ATAGAAAATG
96680211 ATAAGAACTTGAAAT-CA-AGAA
1 ATAAGAACTTGAAATACATAGAA
96680232 ATAA-AACTTGAAATACATAGAA
1 ATAAGAACTTGAAATACATAGAA
96680254 AT
1 AT
96680256 GATAATTATT
Statistics
Matches: 22, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
20 10 0.45
21 6 0.27
22 6 0.27
ACGTcount: A:0.58, C:0.09, G:0.11, T:0.22
Consensus pattern (23 bp):
ATAAGAACTTGAAATACATAGAA
Found at i:96681248 original size:41 final size:41
Alignment explanation
Indices: 96681189--96681270 Score: 146
Period size: 41 Copynumber: 2.0 Consensus size: 41
96681179 TTGGTGTCTA
*
96681189 AACATCTCTGATTGCGAATCAGGTGTGGGTTTCAAAACTTT
1 AACATCTCTGATTACGAATCAGGTGTGGGTTTCAAAACTTT
*
96681230 AACATCTCTGATTACGAATCAGGTGTGGGTTTCGAAACTTT
1 AACATCTCTGATTACGAATCAGGTGTGGGTTTCAAAACTTT
96681271 CTATTTTTTG
Statistics
Matches: 39, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
41 39 1.00
ACGTcount: A:0.27, C:0.17, G:0.22, T:0.34
Consensus pattern (41 bp):
AACATCTCTGATTACGAATCAGGTGTGGGTTTCAAAACTTT
Found at i:96687469 original size:27 final size:26
Alignment explanation
Indices: 96687425--96687476 Score: 68
Period size: 27 Copynumber: 2.0 Consensus size: 26
96687415 CTCGCTGCAA
*
96687425 TCTGGTGGCCTCGCCACATATATCTGT
1 TCTGGTGACCTCGCCACA-ATATCTGT
* *
96687452 TCTGGTGACTTCGTCACAATATCTG
1 TCTGGTGACCTCGCCACAATATCTG
96687477 GCAGCCTCGC
Statistics
Matches: 22, Mismatches: 3, Indels: 1
0.85 0.12 0.04
Matches are distributed among these distances:
26 7 0.32
27 15 0.68
ACGTcount: A:0.17, C:0.27, G:0.21, T:0.35
Consensus pattern (26 bp):
TCTGGTGACCTCGCCACAATATCTGT
Found at i:96687529 original size:65 final size:66
Alignment explanation
Indices: 96687406--96687571 Score: 259
Period size: 65 Copynumber: 2.5 Consensus size: 66
96687396 GAGGAAGTGT
*
96687406 TCTGGCAGCCTCGCTGCAATCTGGTGGCCTCGCCACATATATCTGTTCTGGTGACTTCGTCACAA
1 TCTGGCAGCCTCGCTGCAATCTGGTGG-CTTGCCACATATATCTGTTCTGGTGACTTCGTCACAA
96687471 TA
65 TA
*
96687473 TCTGGCAGCCTCGCTGCAATCTGGTGG-TTGCCACATATATCTGTTTTGGTGACTTCGTCACAAT
1 TCTGGCAGCCTCGCTGCAATCTGGTGGCTTGCCACATATATCTGTTCTGGTGACTTCGTCACAAT
96687537 A
66 A
*
96687538 TCTGGCA---TCGCTGTAATCTGGTGGCTTCGCCACA
1 TCTGGCAGCCTCGCTGCAATCTGGTGGCTT-GCCACA
96687572 CACACACATA
Statistics
Matches: 94, Mismatches: 3, Indels: 7
0.90 0.03 0.07
Matches are distributed among these distances:
62 16 0.17
63 2 0.02
64 6 0.06
65 43 0.46
67 27 0.29
ACGTcount: A:0.17, C:0.28, G:0.23, T:0.31
Consensus pattern (66 bp):
TCTGGCAGCCTCGCTGCAATCTGGTGGCTTGCCACATATATCTGTTCTGGTGACTTCGTCACAAT
A
Found at i:96696664 original size:27 final size:26
Alignment explanation
Indices: 96696612--96696671 Score: 75
Period size: 27 Copynumber: 2.3 Consensus size: 26
96696602 ATATATATAT
*
96696612 ATATCTGTTCTGGTGGCCTAGCCACA
1 ATATCTGTTCTGGTGACCTAGCCACA
* * *
96696638 ATATCTGTATCTGGTGACTTCGTCACA
1 ATATCTGT-TCTGGTGACCTAGCCACA
96696665 ATATCTG
1 ATATCTG
96696672 GCAGCCTAGC
Statistics
Matches: 29, Mismatches: 4, Indels: 1
0.85 0.12 0.03
Matches are distributed among these distances:
26 8 0.28
27 21 0.72
ACGTcount: A:0.22, C:0.23, G:0.20, T:0.35
Consensus pattern (26 bp):
ATATCTGTTCTGGTGACCTAGCCACA
Found at i:96699367 original size:23 final size:22
Alignment explanation
Indices: 96699328--96699376 Score: 55
Period size: 23 Copynumber: 2.2 Consensus size: 22
96699318 GTGATTCATA
* *
96699328 TGAATGTATTTTGATTATGATTG
1 TGAATGAATTTTGATTAAG-TTG
96699351 TGAATGAATGTTT-ATTAAGTTG
1 TGAATGAAT-TTTGATTAAGTTG
96699373 TGAA
1 TGAA
96699377 ATGTTAGTTA
Statistics
Matches: 23, Mismatches: 2, Indels: 3
0.82 0.07 0.11
Matches are distributed among these distances:
22 7 0.30
23 13 0.57
24 3 0.13
ACGTcount: A:0.31, C:0.00, G:0.22, T:0.47
Consensus pattern (22 bp):
TGAATGAATTTTGATTAAGTTG
Found at i:96704866 original size:40 final size:40
Alignment explanation
Indices: 96704821--96704986 Score: 183
Period size: 40 Copynumber: 4.2 Consensus size: 40
96704811 CGGAATATAA
96704821 CCGGATATAATCACGT-GCACAAATGCCTTCGGGTCTTAGC
1 CCGGATATAATCAC-TAGCACAAATGCCTTCGGGTCTTAGC
* * * * *
96704861 CCGGATAGAATAACTCGCACGAATGCCTTCGGGCCTTAGC
1 CCGGATATAATCACTAGCACAAATGCCTTCGGGTCTTAGC
* * *
96704901 CCGGATATAACCACTAGCACAATTGCCTTCGGGTCTTAAC
1 CCGGATATAATCACTAGCACAAATGCCTTCGGGTCTTAGC
** * * * *
96704941 CCGGATATAATTTCCAGCATAATTGTCTTCGGG-CTTAGC
1 CCGGATATAATCACTAGCACAAATGCCTTCGGGTCTTAGC
96704980 CCGGATA
1 CCGGATA
96704987 ATTCAAATAC
Statistics
Matches: 106, Mismatches: 19, Indels: 3
0.83 0.15 0.02
Matches are distributed among these distances:
39 13 0.12
40 93 0.88
ACGTcount: A:0.25, C:0.28, G:0.22, T:0.25
Consensus pattern (40 bp):
CCGGATATAATCACTAGCACAAATGCCTTCGGGTCTTAGC
Found at i:96704971 original size:80 final size:79
Alignment explanation
Indices: 96704821--96704986 Score: 203
Period size: 80 Copynumber: 2.1 Consensus size: 79
96704811 CGGAATATAA
* *
96704821 CCGGATATAATCACGTGCACAAATGCCTTCGGGTCTTAGCCCGGATAGAATAACTCGCACGAATG
1 CCGGATATAACCACGTGCACAAATGCCTTCGGGTCTTAACCCGGATAGAATAACTCGCACGAATG
96704886 CCTTCGGGCCTTAGC
66 CCTTCGGG-CTTAGC
* * ** *
96704901 CCGGATATAACCAC-TAGCACAATTGCCTTCGGGTCTTAACCCGGATATAATTTC-CAGCA-TAA
1 CCGGATATAACCACGT-GCACAAATGCCTTCGGGTCTTAACCCGGATAGAATAACTC-GCACGAA
*
96704963 TTGTCTTCGGGCTTAGC
64 -TGCCTTCGGGCTTAGC
96704980 CCGGATA
1 CCGGATA
96704987 ATTCAAATAC
Statistics
Matches: 75, Mismatches: 8, Indels: 7
0.83 0.09 0.08
Matches are distributed among these distances:
79 17 0.23
80 58 0.77
ACGTcount: A:0.25, C:0.28, G:0.22, T:0.25
Consensus pattern (79 bp):
CCGGATATAACCACGTGCACAAATGCCTTCGGGTCTTAACCCGGATAGAATAACTCGCACGAATG
CCTTCGGGCTTAGC
Found at i:96705709 original size:17 final size:19
Alignment explanation
Indices: 96705686--96705731 Score: 53
Period size: 17 Copynumber: 2.5 Consensus size: 19
96705676 AAGAAGCATG
96705686 AATCATGCTCAAGAATG-C
1 AATCATGCTCAAGAATGAC
*
96705704 -ATCATGGC-CAAGTATGAC
1 AATCAT-GCTCAAGAATGAC
96705722 AATCATGCTC
1 AATCATGCTC
96705732 CTTTTCAACT
Statistics
Matches: 23, Mismatches: 1, Indels: 7
0.74 0.03 0.23
Matches are distributed among these distances:
17 12 0.52
18 5 0.22
19 6 0.26
ACGTcount: A:0.35, C:0.24, G:0.17, T:0.24
Consensus pattern (19 bp):
AATCATGCTCAAGAATGAC
Found at i:96712745 original size:40 final size:40
Alignment explanation
Indices: 96712700--96712869 Score: 191
Period size: 40 Copynumber: 4.3 Consensus size: 40
96712690 CGGAATATAA
96712700 CCGGATATAATCACGT-GCACAAATGCCTTCGGGTCTTAGC
1 CCGGATATAATCAC-TAGCACAAATGCCTTCGGGTCTTAGC
* * * * *
96712740 CCGGATAGAATAACTCGCACGAATGCCTTCGGGCCTTAGC
1 CCGGATATAATCACTAGCACAAATGCCTTCGGGTCTTAGC
* * *
96712780 CCGGATATAACCACTAGCACAATTGCCTTCGGGTCTTAAC
1 CCGGATATAATCACTAGCACAAATGCCTTCGGGTCTTAGC
** * * * *
96712820 CCGGATATAATTTCCAGCATAATTGTCTTCGGG-CTTAGC
1 CCGGATATAATCACTAGCACAAATGCCTTCGGGTCTTAGC
96712859 CCGGATATAAT
1 CCGGATATAAT
96712870 TCAAATACTC
Statistics
Matches: 110, Mismatches: 19, Indels: 3
0.83 0.14 0.02
Matches are distributed among these distances:
39 17 0.15
40 93 0.85
ACGTcount: A:0.26, C:0.27, G:0.21, T:0.26
Consensus pattern (40 bp):
CCGGATATAATCACTAGCACAAATGCCTTCGGGTCTTAGC
Found at i:96713591 original size:17 final size:19
Alignment explanation
Indices: 96713568--96713613 Score: 53
Period size: 17 Copynumber: 2.5 Consensus size: 19
96713558 AAGAAGCATG
96713568 AATCATGCTCAAGAATG-C
1 AATCATGCTCAAGAATGAC
*
96713586 -ATCATGGC-CAAGTATGAC
1 AATCAT-GCTCAAGAATGAC
96713604 AATCATGCTC
1 AATCATGCTC
96713614 CTTTTCAACT
Statistics
Matches: 23, Mismatches: 1, Indels: 7
0.74 0.03 0.23
Matches are distributed among these distances:
17 12 0.52
18 5 0.22
19 6 0.26
ACGTcount: A:0.35, C:0.24, G:0.17, T:0.24
Consensus pattern (19 bp):
AATCATGCTCAAGAATGAC
Found at i:96718100 original size:29 final size:29
Alignment explanation
Indices: 96718066--96718167 Score: 186
Period size: 29 Copynumber: 3.5 Consensus size: 29
96718056 AATCGATCAT
* *
96718066 GCACACTTAGTGCCATGTGATTTAAGCTC
1 GCACACTTAGTGCCATATAATTTAAGCTC
96718095 GCACACTTAGTGCCATATAATTTAAGCTC
1 GCACACTTAGTGCCATATAATTTAAGCTC
96718124 GCACACTTAGTGCCATATAATTTAAGCTC
1 GCACACTTAGTGCCATATAATTTAAGCTC
96718153 GCACACTTAGTGCCA
1 GCACACTTAGTGCCA
96718168 ATCTCGTCAC
Statistics
Matches: 71, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
29 71 1.00
ACGTcount: A:0.28, C:0.25, G:0.17, T:0.29
Consensus pattern (29 bp):
GCACACTTAGTGCCATATAATTTAAGCTC
Found at i:96726014 original size:18 final size:18
Alignment explanation
Indices: 96725991--96726027 Score: 74
Period size: 18 Copynumber: 2.1 Consensus size: 18
96725981 ATTAATGAGT
96725991 ATATTTTCATATAAAAGA
1 ATATTTTCATATAAAAGA
96726009 ATATTTTCATATAAAAGA
1 ATATTTTCATATAAAAGA
96726027 A
1 A
96726028 ACAGAGCAAG
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 19 1.00
ACGTcount: A:0.51, C:0.05, G:0.05, T:0.38
Consensus pattern (18 bp):
ATATTTTCATATAAAAGA
Found at i:96726665 original size:2 final size:2
Alignment explanation
Indices: 96726658--96726693 Score: 72
Period size: 2 Copynumber: 18.0 Consensus size: 2
96726648 TCATGACATG
96726658 TA TA 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 TA TA
96726694 ACTAGTCTCA
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 34 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:96735119 original size:24 final size:25
Alignment explanation
Indices: 96735091--96735139 Score: 82
Period size: 24 Copynumber: 2.0 Consensus size: 25
96735081 GCCATTGTTG
*
96735091 ATAGCTTGTGATTTTT-TTTTTTGA
1 ATAGCTTGTGATTTTTGTTGTTTGA
96735115 ATAGCTTGTGATTTTTGTTGTTTGA
1 ATAGCTTGTGATTTTTGTTGTTTGA
96735140 TGATGAAAAA
Statistics
Matches: 23, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
24 16 0.70
25 7 0.30
ACGTcount: A:0.16, C:0.04, G:0.20, T:0.59
Consensus pattern (25 bp):
ATAGCTTGTGATTTTTGTTGTTTGA
Found at i:96737103 original size:12 final size:12
Alignment explanation
Indices: 96737086--96737115 Score: 51
Period size: 12 Copynumber: 2.5 Consensus size: 12
96737076 CGACTACTTG
*
96737086 ATATATATATAC
1 ATATATATATAA
96737098 ATATATATATAA
1 ATATATATATAA
96737110 ATATAT
1 ATATAT
96737116 TTGATGTTTA
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
12 17 1.00
ACGTcount: A:0.53, C:0.03, G:0.00, T:0.43
Consensus pattern (12 bp):
ATATATATATAA
Found at i:96743698 original size:20 final size:18
Alignment explanation
Indices: 96743648--96743699 Score: 54
Period size: 20 Copynumber: 2.8 Consensus size: 18
96743638 ATATAAGATA
96743648 AACATTAAATTAA-ATTT
1 AACATTAAATTAATATTT
96743665 AACATTAAGA-TAATCACTTT
1 AACATTAA-ATTAAT-A-TTT
*
96743685 AATATTAAATTAATA
1 AACATTAAATTAATA
96743700 AAATACTAGT
Statistics
Matches: 29, Mismatches: 1, Indels: 8
0.76 0.03 0.21
Matches are distributed among these distances:
17 11 0.38
18 1 0.03
19 3 0.10
20 14 0.48
ACGTcount: A:0.52, C:0.08, G:0.02, T:0.38
Consensus pattern (18 bp):
AACATTAAATTAATATTT
Found at i:96752823 original size:40 final size:40
Alignment explanation
Indices: 96752760--96752860 Score: 103
Period size: 40 Copynumber: 2.5 Consensus size: 40
96752750 TGAATGATAT
* * * * * *
96752760 CCGGGCTAAGCCCCAAAGACAATTATGCTGGAAATTATAA
1 CCGGGCTAAGACCCGAAGGCAATTATGCTAGAAACTACAA
* * ** *
96752800 CCGGGTTAAGACCCGAAGGCAATTGTGCTAGTGACTACAT
1 CCGGGCTAAGACCCGAAGGCAATTATGCTAGAAACTACAA
96752840 CCGGGCTAAGACCCGAAGGCA
1 CCGGGCTAAGACCCGAAGGCA
96752861 TTCGTGCGAG
Statistics
Matches: 49, Mismatches: 12, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
40 49 1.00
ACGTcount: A:0.32, C:0.25, G:0.26, T:0.18
Consensus pattern (40 bp):
CCGGGCTAAGACCCGAAGGCAATTATGCTAGAAACTACAA
Found at i:96752882 original size:40 final size:39
Alignment explanation
Indices: 96752800--96752907 Score: 137
Period size: 40 Copynumber: 2.7 Consensus size: 39
96752790 GAAATTATAA
* * *
96752800 CCGGGTTAAGACCCGAAGGCAATTGTGCTAGTGACTACAT
1 CCGGGCTAAGACCCGAAGGC-ATTGTGCGAGTCACTACAT
*
96752840 CCGGGCTAAGACCCGAAGGCATTCGTGCGAGTCA-TTCTAT
1 CCGGGCTAAGACCCGAAGGCATT-GTGCGAGTCACTAC-AT
96752880 CCGGGCTAAGACCCGAAGGCATTTGTGC
1 CCGGGCTAAGACCCGAAGGCA-TTGTGC
96752908 AAATCGTGAT
Statistics
Matches: 61, Mismatches: 4, Indels: 6
0.86 0.06 0.08
Matches are distributed among these distances:
39 5 0.08
40 54 0.89
41 2 0.03
ACGTcount: A:0.24, C:0.26, G:0.29, T:0.21
Consensus pattern (39 bp):
CCGGGCTAAGACCCGAAGGCATTGTGCGAGTCACTACAT
Found at i:96752921 original size:40 final size:38
Alignment explanation
Indices: 96752800--96752922 Score: 113
Period size: 40 Copynumber: 3.1 Consensus size: 38
96752790 GAAATTATAA
* * *
96752800 CCGGGTTAAGACCCGAAGGCAATTGTGC-TAGTGACTACAT
1 CCGGGCTAAGACCCGAAGGCATTTGTGCATCGTGA-T--AT
* * **
96752840 CCGGGCTAAGACCCGAAGGCATTCGTGCGAGTCATTCTAT
1 CCGGGCTAAGACCCGAAGGCATTTGTGC-A-TCGTGATAT
96752880 CCGGGCTAAGACCCGAAGGCATTTGTGCAAATCGTGATAT
1 CCGGGCTAAGACCCGAAGGCATTTGTGC--ATCGTGATAT
96752920 CCG
1 CCG
96752923 AGTTAAGTCC
Statistics
Matches: 67, Mismatches: 12, Indels: 8
0.77 0.14 0.09
Matches are distributed among these distances:
40 63 0.94
41 1 0.01
42 1 0.01
43 2 0.03
ACGTcount: A:0.25, C:0.25, G:0.28, T:0.22
Consensus pattern (38 bp):
CCGGGCTAAGACCCGAAGGCATTTGTGCATCGTGATAT
Found at i:96759455 original size:42 final size:42
Alignment explanation
Indices: 96759345--96759513 Score: 139
Period size: 43 Copynumber: 4.0 Consensus size: 42
96759335 AAATGCTAAT
* * * *
96759345 AATCAAGTACAATGCCGACGTCCCACAC-GTGGTCTTACATGTA
1 AATCAA-TACGATGCCGATGTCCCAGACAG-GGTCTTACACGTA
* **
96759388 ATTCAATATCGATGCCTTTGTCCCAGACAGGGTCTTACACG-A
1 AATCAATA-CGATGCCGATGTCCCAGACAGGGTCTTACACGTA
* *
96759430 AATCAGATACGATGCCGATGTCCCAGACATGGTCTTATACGTA
1 AATCA-ATACGATGCCGATGTCCCAGACAGGGTCTTACACGTA
* * *
96759473 AATCTCAAT-CGAGGCCTG-TGTCCCAGACACGGTATTACACG
1 AA--TCAATACGATGCC-GATGTCCCAGACAGGGTCTTACACG
96759514 ATGTCATAGA
Statistics
Matches: 103, Mismatches: 16, Indels: 14
0.77 0.12 0.11
Matches are distributed among these distances:
42 35 0.34
43 61 0.59
44 4 0.04
45 3 0.03
ACGTcount: A:0.28, C:0.27, G:0.20, T:0.25
Consensus pattern (42 bp):
AATCAATACGATGCCGATGTCCCAGACAGGGTCTTACACGTA
Found at i:96759495 original size:85 final size:85
Alignment explanation
Indices: 96759356--96759514 Score: 205
Period size: 85 Copynumber: 1.9 Consensus size: 85
96759346 ATCAAGTACA
* * * * *
96759356 ATGCCGACGTCCCACACGTGGTCTTACATGTAATTCAATATCGATGCCTTTGTCCCAGACAGGGT
1 ATGCCGACGTCCCACACATGGTCTTACACGTAATTCAATATCGAGGCCTGTGTCCCAGACACGGT
*
96759421 CTTACACGAAATCAGATACG
66 ATTACACGAAATCAGATACG
* * *
96759441 ATGCCGATGTCCCAGACATGGTCTTATACGTAAATCTC-A-ATCGAGGCCTGTGTCCCAGACACG
1 ATGCCGACGTCCCACACATGGTCTTACACGT-AAT-TCAATATCGAGGCCTGTGTCCCAGACACG
96759504 GTATTACACGA
64 GTATTACACGA
96759515 TGTCATAGAC
Statistics
Matches: 63, Mismatches: 9, Indels: 4
0.83 0.12 0.05
Matches are distributed among these distances:
85 57 0.90
86 4 0.06
87 2 0.03
ACGTcount: A:0.27, C:0.27, G:0.21, T:0.25
Consensus pattern (85 bp):
ATGCCGACGTCCCACACATGGTCTTACACGTAATTCAATATCGAGGCCTGTGTCCCAGACACGGT
ATTACACGAAATCAGATACG
Found at i:96767759 original size:13 final size:13
Alignment explanation
Indices: 96767736--96767770 Score: 61
Period size: 13 Copynumber: 2.6 Consensus size: 13
96767726 TGCTTTAACA
96767736 TTTAGCACTCAACT
1 TTTA-CACTCAACT
96767750 TTTACACTCAACT
1 TTTACACTCAACT
96767763 TTTACACT
1 TTTACACT
96767771 TTACGTGGTT
Statistics
Matches: 21, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
13 17 0.81
14 4 0.19
ACGTcount: A:0.29, C:0.29, G:0.03, T:0.40
Consensus pattern (13 bp):
TTTACACTCAACT
Found at i:96770576 original size:19 final size:19
Alignment explanation
Indices: 96770540--96770578 Score: 51
Period size: 19 Copynumber: 2.1 Consensus size: 19
96770530 TTTTCATCAT
* *
96770540 AGTAAAATAAAATAATAAA
1 AGTAAAACAAAACAATAAA
*
96770559 AGTAAAACAAAACCATAAA
1 AGTAAAACAAAACAATAAA
96770578 A
1 A
96770579 ATAATTAAAA
Statistics
Matches: 17, Mismatches: 3, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
19 17 1.00
ACGTcount: A:0.72, C:0.08, G:0.05, T:0.15
Consensus pattern (19 bp):
AGTAAAACAAAACAATAAA
Found at i:96771128 original size:28 final size:28
Alignment explanation
Indices: 96771042--96771131 Score: 94
Period size: 27 Copynumber: 3.2 Consensus size: 28
96771032 GTGACAGAGT
* *
96771042 CACCAGATATAGATATTTTGTGGCAGTA-C
1 CACCAGA-ACAGATAATTTGTGGCA-TAGC
** **
96771071 CACCAGAACAGAT-ATACGTGGCAGGGC
1 CACCAGAACAGATAATTTGTGGCATAGC
96771098 CACCAGAACAGATAATTTGTGGCATAGC
1 CACCAGAACAGATAATTTGTGGCATAGC
96771126 CACCAG
1 CACCAG
96771132 GACGCTTCCT
Statistics
Matches: 49, Mismatches: 10, Indels: 5
0.77 0.16 0.08
Matches are distributed among these distances:
27 21 0.43
28 21 0.43
29 7 0.14
ACGTcount: A:0.33, C:0.23, G:0.23, T:0.20
Consensus pattern (28 bp):
CACCAGAACAGATAATTTGTGGCATAGC
Done.