Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Dt_chr10
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: 57797951
ACGTcount: A:0.33, C:0.17, G:0.16, T:0.33
Warning! 1092422 characters in sequence are not A, C, G, or T
File 15 of 187
Found at i:3920119 original size:15 final size:16
Alignment explanation
Indices: 3920091--3920120 Score: 53
Period size: 15 Copynumber: 1.9 Consensus size: 16
3920081 GTTGGACTAA
3920091 ATTGAATGTGAGTTAT
1 ATTGAATGTGAGTTAT
3920107 ATTGAAT-TGAGTTA
1 ATTGAATGTGAGTTA
3920121 AATTTATTCG
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 7 0.50
16 7 0.50
ACGTcount: A:0.33, C:0.00, G:0.23, T:0.43
Consensus pattern (16 bp):
ATTGAATGTGAGTTAT
Found at i:3920145 original size:23 final size:23
Alignment explanation
Indices: 3920119--3920165 Score: 76
Period size: 23 Copynumber: 2.0 Consensus size: 23
3920109 TGAATTGAGT
*
3920119 TAAATTTATTCGTAAAGATTCAG
1 TAAATTCATTCGTAAAGATTCAG
*
3920142 TAAATTCATTCGTACAGATTCAG
1 TAAATTCATTCGTAAAGATTCAG
3920165 T
1 T
3920166 TAGACATCAT
Statistics
Matches: 22, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
23 22 1.00
ACGTcount: A:0.36, C:0.13, G:0.13, T:0.38
Consensus pattern (23 bp):
TAAATTCATTCGTAAAGATTCAG
Found at i:3920457 original size:25 final size:24
Alignment explanation
Indices: 3920429--3920519 Score: 76
Period size: 25 Copynumber: 3.6 Consensus size: 24
3920419 TACCGATTTT
* *
3920429 AGCTCGTATGAGCTTACTGATATTG
1 AGCTCG-AGGAGCTTACTGATATTC
* * * *
3920454 AGCTCGCATGAGCTTACCGTTATTT
1 AGCTCG-AGGAGCTTACTGATATTC
3920479 AGCTCAGAGGAGCTTACT-ATTATTC
1 AGCTC-GAGGAGCTTACTGA-TATTC
3920504 AGCTCGGAGGAGCTTA
1 AGCTC-GAGGAGCTTA
3920520 TCGTTTATAC
Statistics
Matches: 55, Mismatches: 9, Indels: 4
0.81 0.13 0.06
Matches are distributed among these distances:
25 54 0.98
26 1 0.02
ACGTcount: A:0.24, C:0.20, G:0.24, T:0.32
Consensus pattern (24 bp):
AGCTCGAGGAGCTTACTGATATTC
Found at i:3920775 original size:22 final size:24
Alignment explanation
Indices: 3920735--3920779 Score: 76
Period size: 22 Copynumber: 2.0 Consensus size: 24
3920725 GTGATGTTAC
3920735 ATAATACATTGATATATGAAATGA
1 ATAATACATTGATATATGAAATGA
3920759 ATAATACA-TG-TATATGAAATG
1 ATAATACATTGATATATGAAATG
3920780 TGATTACTTG
Statistics
Matches: 21, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
22 11 0.52
23 2 0.10
24 8 0.38
ACGTcount: A:0.49, C:0.04, G:0.13, T:0.33
Consensus pattern (24 bp):
ATAATACATTGATATATGAAATGA
Found at i:3932741 original size:26 final size:26
Alignment explanation
Indices: 3932712--3932791 Score: 66
Period size: 26 Copynumber: 3.3 Consensus size: 26
3932702 ATTAGTCCCA
3932712 AATACTCATGTAATAAAATTTAAAAG
1 AATACTCATGTAATAAAATTTAAAAG
* *
3932738 AATATTCAT-T--T---GTTTAAAA-
1 AATACTCATGTAATAAAATTTAAAAG
* *
3932757 AATACTCGTGTAAAAAAATTTAAAAG
1 AATACTCATGTAATAAAATTTAAAAG
*
3932783 AATATTCAT
1 AATACTCAT
3932792 TTGTTTAAGA
Statistics
Matches: 39, Mismatches: 8, Indels: 14
0.64 0.13 0.23
Matches are distributed among these distances:
19 7 0.18
20 8 0.21
23 1 0.03
25 8 0.21
26 15 0.38
ACGTcount: A:0.50, C:0.07, G:0.07, T:0.35
Consensus pattern (26 bp):
AATACTCATGTAATAAAATTTAAAAG
Found at i:3932775 original size:45 final size:45
Alignment explanation
Indices: 3932711--3932799 Score: 160
Period size: 45 Copynumber: 2.0 Consensus size: 45
3932701 AATTAGTCCC
*
3932711 AAATACTCATGTAATAAAATTTAAAAGAATATTCATTTGTTTAAA
1 AAATACTCATGTAAAAAAATTTAAAAGAATATTCATTTGTTTAAA
*
3932756 AAATACTCGTGTAAAAAAATTTAAAAGAATATTCATTTGTTTAA
1 AAATACTCATGTAAAAAAATTTAAAAGAATATTCATTTGTTTAA
3932800 GATTTAAGAA
Statistics
Matches: 42, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
45 42 1.00
ACGTcount: A:0.48, C:0.07, G:0.08, T:0.37
Consensus pattern (45 bp):
AAATACTCATGTAAAAAAATTTAAAAGAATATTCATTTGTTTAAA
Found at i:3936832 original size:19 final size:19
Alignment explanation
Indices: 3936808--3936858 Score: 84
Period size: 19 Copynumber: 2.7 Consensus size: 19
3936798 CATATCTTCT
3936808 AAGATTGCATATCATATCA
1 AAGATTGCATATCATATCA
* *
3936827 AAGATTACATATCATATCT
1 AAGATTGCATATCATATCA
3936846 AAGATTGCATATC
1 AAGATTGCATATC
3936859 CTTGAAGATT
Statistics
Matches: 29, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
19 29 1.00
ACGTcount: A:0.41, C:0.16, G:0.10, T:0.33
Consensus pattern (19 bp):
AAGATTGCATATCATATCA
Found at i:3943619 original size:19 final size:20
Alignment explanation
Indices: 3943577--3943619 Score: 63
Period size: 19 Copynumber: 2.2 Consensus size: 20
3943567 AGGAAAATAA
*
3943577 TTTTTGTGGCGTTTTTTATC
1 TTTTTGCGGCGTTTTTTATC
3943597 -TTTTGCGGCG-TTTTTATC
1 TTTTTGCGGCGTTTTTTATC
3943615 TTTTT
1 TTTTT
3943620 TATCTTTTGG
Statistics
Matches: 21, Mismatches: 1, Indels: 3
0.84 0.04 0.12
Matches are distributed among these distances:
18 8 0.38
19 13 0.62
ACGTcount: A:0.05, C:0.12, G:0.19, T:0.65
Consensus pattern (20 bp):
TTTTTGCGGCGTTTTTTATC
Found at i:3943637 original size:18 final size:19
Alignment explanation
Indices: 3943578--3943618 Score: 66
Period size: 18 Copynumber: 2.2 Consensus size: 19
3943568 GGAAAATAAT
*
3943578 TTTTGTGGCGTTTTTTATC
1 TTTTGCGGCGTTTTTTATC
3943597 TTTTGCGGCG-TTTTTATC
1 TTTTGCGGCGTTTTTTATC
3943615 TTTT
1 TTTT
3943619 TTATCTTTTG
Statistics
Matches: 21, Mismatches: 1, Indels: 1
0.91 0.04 0.04
Matches are distributed among these distances:
18 12 0.57
19 9 0.43
ACGTcount: A:0.05, C:0.12, G:0.20, T:0.63
Consensus pattern (19 bp):
TTTTGCGGCGTTTTTTATC
Found at i:3943942 original size:87 final size:87
Alignment explanation
Indices: 3943779--3943942 Score: 267
Period size: 87 Copynumber: 1.9 Consensus size: 87
3943769 GCAAAAAATT
* *
3943779 TTTCATTTTGAACAAAATGACGCCATTTTGCTATTCATAAATTTTTATTTTGTTTTTTTATAAAT
1 TTTCATTTTGAACAAAATGACGCCATTTTGCTATTCAAAAATTTTTATTTTATTTTTTTATAAAT
3943844 TGATTTATTTTTTGCGCCGCTA
66 TGATTTATTTTTTGCGCCGCTA
* *
3943866 TTTCATTTTGAACAAAATGACGCCGTTTTGCTATGTTAAAAATTTTTTATTTTATTTTTTTATAA
1 TTTCATTTTGAACAAAATGACGCCATTTTGCTAT-TCAAAAA-TTTTTATTTTATTTTTTTATAA
3943931 ATTGATTT-TTTT
64 ATTGATTTATTTT
3943943 GCGGCATTTT
Statistics
Matches: 71, Mismatches: 4, Indels: 3
0.91 0.05 0.04
Matches are distributed among these distances:
87 33 0.46
88 9 0.13
89 29 0.41
ACGTcount: A:0.26, C:0.10, G:0.10, T:0.54
Consensus pattern (87 bp):
TTTCATTTTGAACAAAATGACGCCATTTTGCTATTCAAAAATTTTTATTTTATTTTTTTATAAAT
TGATTTATTTTTTGCGCCGCTA
Found at i:3944139 original size:106 final size:102
Alignment explanation
Indices: 3944016--3944215 Score: 260
Period size: 103 Copynumber: 1.9 Consensus size: 102
3944006 GCAAAATTTT
* * *
3944016 TTTCATTTTGAACAAAATGATGCCGTTTTGCTATTATAAAAATTTTTTATT-TTGTTTTTTATAA
1 TTTCATTTTGAACAAAATGACGCCGTTTTG-T-TCAGAAAAATTTTTT-TTATT-TTTTTTATAA
3944080 ATTGATTTATTTTTTGCGCCGT-TTTTTATAAAAACGCCGCTA
62 ATTGATTTATTTTTTGCG--GTGTTTTTATAAAAACGCCGCTA
* * ** *
3944122 TTTCATTTTGAACAAAATGACGCTGTTTTGTTCGGCTAAATTTTTTTTATTTTTTTTATATATTG
1 TTTCATTTTGAACAAAATGACGCCGTTTTGTTCAGAAAAATTTTTTTTATTTTTTTTATAAATTG
3944187 ATTTATTTTTTGCGGTGTTTTTATAAAAA
66 ATTTATTTTTTGCGGTGTTTTTATAAAAA
3944216 AATGCCCTAT
Statistics
Matches: 84, Mismatches: 8, Indels: 8
0.84 0.08 0.08
Matches are distributed among these distances:
101 2 0.02
102 12 0.14
103 29 0.35
104 12 0.14
105 1 0.01
106 28 0.33
ACGTcount: A:0.26, C:0.10, G:0.12, T:0.53
Consensus pattern (102 bp):
TTTCATTTTGAACAAAATGACGCCGTTTTGTTCAGAAAAATTTTTTTTATTTTTTTTATAAATTG
ATTTATTTTTTGCGGTGTTTTTATAAAAACGCCGCTA
Found at i:3944318 original size:254 final size:254
Alignment explanation
Indices: 3943858--3944341 Score: 631
Period size: 254 Copynumber: 1.9 Consensus size: 254
3943848 TTATTTTTTG
* * *
3943858 CGCCGCTATTTCATTTTGAACAAAATGACGCCGTTTTGCTATGTTAAAAATTTTTTATTTTATTT
1 CGCCGCTATTTCATTTTGAACAAAATGACGCCGTTTTGCTAGGCT-AAAATTTTTTATTATATTT
* * *
3943923 TTTTATAAATTGATTTTTTTGCGGCATTTTTATGAAAAACGCCGCTATTGCTTACCTTTAGCGGC
65 TTTTATAAATTGATTTTTTTGCGGCATTTTTATAAAAAACGCCGCTATTGCTTACATTTAACGGC
* * * * *
3943988 GTTTTTATGAAAAACGCCGCAAAATTTTTTTCATTTTGAACAAAATGATGCCGTTTTGCTATTAT
130 GTTTTCATGAAAAAC-CCGCAAAAATTATTTCATTTTGAACAAAATGACGCCATTTTGCTATTAT
*
3944053 AAAAATTTTTTATTTTGTTTTTTATAAATTGATTTATTTTTTGCGCCGTTTTTTATAAAAA
194 AAAAATTTTTTATTTTATTTTTTATAAATTGATTTATTTTTTGCGCCGTTTTTTATAAAAA
* * *
3944114 CGCCGCTATTTCATTTTGAACAAAATGACGCTGTTTTGTTCGGCT-AAATTTTTT-TTAT-TTTT
1 CGCCGCTATTTCATTTTGAACAAAATGACGCCGTTTTGCTAGGCTAAAATTTTTTATTATATTTT
* ** * *
3944176 TTTATATATTGATTTATTTTTTGCGGTGTTTTTATAAAAAAATGCC-CTATTGCTTGCATTTAAC
66 TTTATAAATTGA--T-TTTTTTGCGGCATTTTTAT-AAAAAACGCCGCTATTGCTTACATTTAAC
* *
3944240 GGTGTTTGTCAT-AAAAA-CCGCAAAAAATTATTTCATTTTGAACAAAATGACGTCATTTTGCT-
127 GGCGTTT-TCATGAAAAACCCGC-AAAAATTATTTCATTTTGAACAAAATGACGCCATTTTGCTA
*
3944302 TTGCTAAAAATTTTTTATTTTATTTTTTATAAATTGATTT
190 TT-ATAAAAATTTTTTATTTTATTTTTTATAAATTGATTT
3944342 TTTATAAAAT
Statistics
Matches: 198, Mismatches: 23, Indels: 16
0.84 0.10 0.07
Matches are distributed among these distances:
252 15 0.08
253 9 0.05
254 80 0.40
255 43 0.22
256 51 0.26
ACGTcount: A:0.28, C:0.12, G:0.13, T:0.47
Consensus pattern (254 bp):
CGCCGCTATTTCATTTTGAACAAAATGACGCCGTTTTGCTAGGCTAAAATTTTTTATTATATTTT
TTTATAAATTGATTTTTTTGCGGCATTTTTATAAAAAACGCCGCTATTGCTTACATTTAACGGCG
TTTTCATGAAAAACCCGCAAAAATTATTTCATTTTGAACAAAATGACGCCATTTTGCTATTATAA
AAATTTTTTATTTTATTTTTTATAAATTGATTTATTTTTTGCGCCGTTTTTTATAAAAA
Found at i:3944913 original size:15 final size:14
Alignment explanation
Indices: 3944896--3944966 Score: 74
Period size: 15 Copynumber: 4.9 Consensus size: 14
3944886 ATCCCTGAAT
*
3944896 CCCTAAACCTTAAAT
1 CCCTAAACCTT-AAC
3944911 CCCT-AACTCTTAAC
1 CCCTAAAC-CTTAAC
*
3944925 CCCT-AACATCTAAC
1 CCCTAAACCT-TAAC
3944939 CCCTAAACCTCTAAC
1 CCCTAAACCT-TAAC
3944954 CCCTAAACCTTAA
1 CCCTAAACCTTAA
3944967 ATCCCAACCC
Statistics
Matches: 50, Mismatches: 3, Indels: 7
0.83 0.05 0.12
Matches are distributed among these distances:
13 1 0.02
14 23 0.46
15 26 0.52
ACGTcount: A:0.35, C:0.41, G:0.00, T:0.24
Consensus pattern (14 bp):
CCCTAAACCTTAAC
Found at i:3944930 original size:14 final size:14
Alignment explanation
Indices: 3944911--3944959 Score: 57
Period size: 14 Copynumber: 3.4 Consensus size: 14
3944901 AACCTTAAAT
3944911 CCCTAACTCTTAAC
1 CCCTAACTCTTAAC
3944925 CCCTAACATC-TAAC
1 CCCTAAC-TCTTAAC
3944939 CCCTAAAC-CTCTAAC
1 CCCT-AACTCT-TAAC
3944954 CCCTAA
1 CCCTAA
3944960 ACCTTAAATC
Statistics
Matches: 31, Mismatches: 0, Indels: 8
0.79 0.00 0.21
Matches are distributed among these distances:
13 1 0.03
14 17 0.55
15 13 0.42
ACGTcount: A:0.33, C:0.45, G:0.00, T:0.22
Consensus pattern (14 bp):
CCCTAACTCTTAAC
Found at i:3945724 original size:73 final size:73
Alignment explanation
Indices: 3945571--3945725 Score: 190
Period size: 73 Copynumber: 2.1 Consensus size: 73
3945561 AGCATTTTTG
* * *
3945571 GCCGCTAAATCCCCGAAAGCTCAGAAAACGGCGTCGTTGGACTTAGAATTTTTTGCGGTGCTTTC
1 GCCGCTAAATCCCCAAAAGCTCACAAAACGGCGTCGTTGGACTTAGAATTTTTTGCGGCGCTTTC
*
3945636 TTAAAAAT
66 TTAAAAAC
* * *
3945644 GCTGCTAAATCCCCAAAAGCTCACAAAACGGCGTCGTTGGGCTTAG-GTTTTCTTGCGGCG-TTT
1 GCCGCTAAATCCCCAAAAGCTCACAAAACGGCGTCGTTGGACTTAGAATTTT-TTGCGGCGCTTT
*
3945707 -TTGAGAAAGC
65 CTT-A-AAAAC
3945717 GCCGCTAAA
1 GCCGCTAAA
3945726 GCCCTGAGCA
Statistics
Matches: 70, Mismatches: 9, Indels: 6
0.82 0.11 0.07
Matches are distributed among these distances:
71 2 0.03
72 8 0.11
73 60 0.86
ACGTcount: A:0.26, C:0.23, G:0.24, T:0.27
Consensus pattern (73 bp):
GCCGCTAAATCCCCAAAAGCTCACAAAACGGCGTCGTTGGACTTAGAATTTTTTGCGGCGCTTTC
TTAAAAAC
Found at i:3945834 original size:114 final size:114
Alignment explanation
Indices: 3945625--3946066 Score: 611
Period size: 114 Copynumber: 3.9 Consensus size: 114
3945615 AGAATTTTTT
* * * *
3945625 GCGGTGCTTTCTTAAAAATGCTGCTAAATCCCCAAAAGCTCACAAAACGGCGTCGTTGGGCTTAG
1 GCGGCGCTTTCTTAAAAACGCCGCTAAATCCCCGAAAGCTCACAAAACGGCGTCGTTGGGCTTAG
* * * *
3945690 GTTTTCTTGCGGCG-TTTTTGAGAAAGCGCCGCTAAAGCCCTGAGCATTA
66 GTTTTTTTGCGGCGCTTTCTCA-AAAACGCCGCTAAAGCCCTGAGCATTA
* * *
3945739 GCGGCGCTTTCTTAAAAAAGCCGCTAAATCCCCGAAAGCACACAAAACGGCGTCATTGGGCTTAG
1 GCGGCGCTTTCTTAAAAACGCCGCTAAATCCCCGAAAGCTCACAAAACGGCGTCGTTGGGCTTAG
* *
3945804 GTTTTTTTGCGGCGCTTTCTCAAAAACGCCGCTAAAGGCTTGAGCATTA
66 GTTTTTTTGCGGCGCTTTCTCAAAAACGCCGCTAAAGCCCTGAGCATTA
* *
3945853 GCAGCGCTTTCTTAAAAACGCCGCTAAA-CCCTCGAAAGCTCACAAAACGTCGTCGTTGGGCTTA
1 GCGGCGCTTTCTTAAAAACGCCGCTAAATCCC-CGAAAGCTCACAAAACGGCGTCGTTGGGCTTA
* * *
3945917 TGTTTTTTTGCGGCGCTTTCTCAAAAACGCCACTAAAGCCCTGAGCGTTA
65 GGTTTTTTTGCGGCGCTTTCTCAAAAACGCCGCTAAAGCCCTGAGCATTA
* * * * *
3945967 GCGGCGCTTTATTAAAAACGCCGCTAAATCCCCGAAAGCTTACAAAACGGCATTGTTGGGCTTAT
1 GCGGCGCTTTCTTAAAAACGCCGCTAAATCCCCGAAAGCTCACAAAACGGCGTCGTTGGGCTTAG
* * *
3946032 G-TTTTTTGCGGCGCTTTCTTAGAAATGCCGCTAAA
66 GTTTTTTTGCGGCGCTTTCTCAAAAACGCCGCTAAA
3946067 TCCCCGAAAG
Statistics
Matches: 293, Mismatches: 32, Indels: 7
0.88 0.10 0.02
Matches are distributed among these distances:
113 33 0.11
114 252 0.86
115 8 0.03
ACGTcount: A:0.26, C:0.25, G:0.22, T:0.27
Consensus pattern (114 bp):
GCGGCGCTTTCTTAAAAACGCCGCTAAATCCCCGAAAGCTCACAAAACGGCGTCGTTGGGCTTAG
GTTTTTTTGCGGCGCTTTCTCAAAAACGCCGCTAAAGCCCTGAGCATTA
Found at i:3946062 original size:72 final size:72
Alignment explanation
Indices: 3945967--3946110 Score: 198
Period size: 72 Copynumber: 2.0 Consensus size: 72
3945957 CTGAGCGTTA
* * *
3945967 GCGGCGCTTTATTAAAAACGCCGCTAAATCCCCGAAAGCTTACAAAACGGCATTGTTGGGCTTAT
1 GCGGCGCTTTATTAAAAACGCCGCTAAATCCCCGAAAGCTCACAAAACGGCATCGTTGGGCTTAG
3946032 GTTTTTT
66 GTTTTTT
* * * *** *
3946039 GCGGCGCTTTCTTAGAAATGCCGCTAAATCCCCGAAAGCTCGGGAAACGGCGTCGTTGGGCTTAG
1 GCGGCGCTTTATTAAAAACGCCGCTAAATCCCCGAAAGCTCACAAAACGGCATCGTTGGGCTTAG
3946104 GTTTTTT
66 GTTTTTT
3946111 TGCAAAAACG
Statistics
Matches: 62, Mismatches: 10, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
72 62 1.00
ACGTcount: A:0.23, C:0.23, G:0.25, T:0.29
Consensus pattern (72 bp):
GCGGCGCTTTATTAAAAACGCCGCTAAATCCCCGAAAGCTCACAAAACGGCATCGTTGGGCTTAG
GTTTTTT
Found at i:3952756 original size:40 final size:40
Alignment explanation
Indices: 3952701--3952777 Score: 145
Period size: 40 Copynumber: 1.9 Consensus size: 40
3952691 ACTACATTCG
*
3952701 TCTAAAAGCGAAGGTTTCCTAAGGACACGTGAACATAATC
1 TCTAAAAGCGAAGGTTTCATAAGGACACGTGAACATAATC
3952741 TCTAAAAGCGAAGGTTTCATAAGGACACGTGAACATA
1 TCTAAAAGCGAAGGTTTCATAAGGACACGTGAACATA
3952778 GTCTTTTCTT
Statistics
Matches: 36, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
40 36 1.00
ACGTcount: A:0.39, C:0.18, G:0.21, T:0.22
Consensus pattern (40 bp):
TCTAAAAGCGAAGGTTTCATAAGGACACGTGAACATAATC
Found at i:3984876 original size:18 final size:18
Alignment explanation
Indices: 3984849--3984890 Score: 57
Period size: 18 Copynumber: 2.3 Consensus size: 18
3984839 CGCTATAATA
*
3984849 GGGTTTGCATAAACACAT
1 GGGTTCGCATAAACACAT
* *
3984867 GGGTTCGCATAAATATAT
1 GGGTTCGCATAAACACAT
3984885 GGGTTC
1 GGGTTC
3984891 ACACAATTTT
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
18 21 1.00
ACGTcount: A:0.29, C:0.14, G:0.26, T:0.31
Consensus pattern (18 bp):
GGGTTCGCATAAACACAT
Found at i:3985665 original size:49 final size:49
Alignment explanation
Indices: 3985591--3985753 Score: 211
Period size: 49 Copynumber: 3.3 Consensus size: 49
3985581 AACATGCTTA
* * * * *
3985591 CACACTTGTCCTATCAGAATGGTTGAGAAACATAAGATATGTTCTCGCC
1 CACACTTATCTTATCAAAATGGTTGAGGAACATAAAATATGTTCTCGCC
* *
3985640 CACACTTATCTTATCAAAATAGTTGAGGAACATAAAACT-TGTTCTCGCT
1 CACACTTATCTTATCAAAATGGTTGAGGAACATAAAA-TATGTTCTCGCC
* * * *
3985689 CACACTTATCTTATCACAATGGCTGAGGAACATAAAACATGTTCTCACC
1 CACACTTATCTTATCAAAATGGTTGAGGAACATAAAATATGTTCTCGCC
3985738 CACACTTATCTTATCA
1 CACACTTATCTTATCA
3985754 GAATCTGTTG
Statistics
Matches: 99, Mismatches: 13, Indels: 4
0.85 0.11 0.03
Matches are distributed among these distances:
49 98 0.99
50 1 0.01
ACGTcount: A:0.33, C:0.24, G:0.13, T:0.30
Consensus pattern (49 bp):
CACACTTATCTTATCAAAATGGTTGAGGAACATAAAATATGTTCTCGCC
Found at i:3987102 original size:134 final size:134
Alignment explanation
Indices: 3986933--3987564 Score: 659
Period size: 134 Copynumber: 4.7 Consensus size: 134
3986923 TGTCGACTTG
*
3986933 ACGATCATGAACAATTCATTAAGAGTTCATAGATTTACGATCGCAACTCCATTTAAATAGTTCTC
1 ACGATCATGAACAATTCATTAAGAGTTCATCGATTTACGATCGCAACTCCATTTAAATAGTTCTC
* * * * * * *
3986998 TAATTTATGACCACAACTGTCATTTTTCAAGCTCGTTGATTTACGACCACAACTTCAGTTCATTT
66 TGATTTATGATCACAACTATCATTTTTAAAGCTCGTTGATTTACGATCACAACTTCAGTTGATTG
3987063 ATTT
131 ATTT
* ** * * *
3987067 ACGATCATGAACAATTCATTAAGATTTCATCGATTTAAAATCGTAACT-TATTTAAATAATTCAT
1 ACGATCATGAACAATTCATTAAGAGTTCATCGATTTACGATCGCAACTCCATTTAAATAGTTC-T
* * * * *
3987131 -TGATTTACGATCACAATTGTCA-TTTTAAAGGCTCGTTGATTTATGATCACAGCTTCAGTTGAT
65 CTGATTTATGATCACAACTATCATTTTTAAA-GCTCGTTGATTTACGATCACAACTTCAGTTGAT
*
3987194 TGAGTT
129 TGATTT
* * * * * * * *
3987200 ACAATCATGAACAATTCATTAAGACTTCGTCGACTTAC-ATTGCAACTCGATTTAAATAGTACAC
1 ACGATCATGAACAATTCATTAAGAGTTCATCGATTTACGATCGCAACTCCATTTAAATAGTTCTC
* * *
3987264 TGATTTATGATTACAACTATCATTTTTAAAGCTTGTTGATTTACAATCA-AAGCTTCAGTTGATT
66 TGATTTATGATCACAACTATCATTTTTAAAGCTCGTTGATTTACGATCACAA-CTTCAGTTGATT
3987328 GATTT
130 GATTT
* * * * *
3987333 ATGATCATGAACAATTCATTAAGAGTTCACCGACTTACGATCGCAACTCCATTTAAACAGTTCAC
1 ACGATCATGAACAATTCATTAAGAGTTCATCGATTTACGATCGCAACTCCATTTAAATAGTTCTC
** * * ** ** * * * *
3987398 TGATTTATGATCACAGGTATCCTTTTCAAATATCACTAATTAATGAGCACAA-TCTCAGTTGATT
66 TGATTTATGATCACAACTATCATTTTTAAAGCTCGTTGATTTACGATCACAACT-TCAGTTGATT
3987462 GATTT
130 GATTT
* * * * * *
3987467 ACGATCAAGAACAATTCATTAAGAGTCCACCGATTTAAGATCGTAA-TACCATTTCAATAGTTCG
1 ACGATCATGAACAATTCATTAAGAGTTCATCGATTTACGATCGCAACT-CCATTTAAATAGTTC-
*
3987531 T-TGATTTATGATCACAACTATAATTTTTAAAGCT
64 TCTGATTTATGATCACAACTATCATTTTTAAAGCT
3987565 TGCCAATTTA
Statistics
Matches: 409, Mismatches: 78, Indels: 22
0.80 0.15 0.04
Matches are distributed among these distances:
132 14 0.03
133 192 0.47
134 201 0.49
135 2 0.00
ACGTcount: A:0.34, C:0.18, G:0.12, T:0.36
Consensus pattern (134 bp):
ACGATCATGAACAATTCATTAAGAGTTCATCGATTTACGATCGCAACTCCATTTAAATAGTTCTC
TGATTTATGATCACAACTATCATTTTTAAAGCTCGTTGATTTACGATCACAACTTCAGTTGATTG
ATTT
Found at i:3987785 original size:134 final size:134
Alignment explanation
Indices: 3987647--3987890 Score: 323
Period size: 134 Copynumber: 1.8 Consensus size: 134
3987637 GCTTATTTGG
** **
3987647 AATCACA-ATTTGAGTTCATTGATTTACGATCATGA-ACAATTCATTAAGTA-TTTTCTGATTTA
1 AATCACAGATTT-AGTTCATTGATTTACGATCATGAGA-AATTCATTAAG-AGTTCGCCAATTTA
** *
3987709 TGATCACAACTCCATTTAAATAGTTTGTTGATTTACGACCACAACTTTAAGTTTAAAAGCTCATT
63 AAATCACAACTCCATTTAAATAGTTAGTTGATTTACGACCACAACTTTAAGTTTAAAAGCTCATT
3987774 GATTTAC
128 GATTTAC
* * * *
3987781 AATCATAGCTTTAGTTCATTGATTTACGATCATGAGAAATTTATTCAGAGTTCGCCAATTTAAAA
1 AATCACAGATTTAGTTCATTGATTTACGATCATGAGAAATTCATTAAGAGTTCGCCAATTTAAAA
* *
3987846 TCGCAACTCCATTTAAATAGTTAGTTGATTTACGATCACAACTTT
66 TCACAACTCCATTTAAATAGTTAGTTGATTTACGACCACAACTTT
3987891 CACTTTTAAA
Statistics
Matches: 94, Mismatches: 13, Indels: 6
0.83 0.12 0.05
Matches are distributed among these distances:
133 1 0.01
134 89 0.95
135 4 0.04
ACGTcount: A:0.34, C:0.16, G:0.12, T:0.39
Consensus pattern (134 bp):
AATCACAGATTTAGTTCATTGATTTACGATCATGAGAAATTCATTAAGAGTTCGCCAATTTAAAA
TCACAACTCCATTTAAATAGTTAGTTGATTTACGACCACAACTTTAAGTTTAAAAGCTCATTGAT
TTAC
Found at i:3987987 original size:243 final size:243
Alignment explanation
Indices: 3987686--3988140 Score: 578
Period size: 243 Copynumber: 1.9 Consensus size: 243
3987676 TCATGAACAA
* ***
3987686 TTCATTAAGTATTTTCTGATTTATGATCACAACTCCATTTAAATAGTTTGTTGATTTACGACCAC
1 TTCATTAAGTATTTTCTGATTTACGATCACAACTCCATTTAAATAGTTCACTGATTTACGACCAC
* * * * *
3987751 AACTT-TAAGTTTAAAAGCTCATTGATTTACAATCATAGCTTTAGTTCATTGATTTACGATCATG
66 -ACTTGTAAGTTTAAAAGCTCAGTGATTTACAATCACAACTTCAGATCATTGATTTACGATCATG
* * *
3987815 AGA-AATTTATTCAGAGTTCGCCAATTTAAAATCGCAACTCCATTTAAATAGTTAGTTGATTTAC
130 A-ACAATTCATTAAGAGTTCGCCAATTTAAAATCGCAACTCCATTTAAAAAGTTAGTTGATTTAC
* *
3987879 GATCACAACTTTCACTTTTAAAGTTCAGTAATTTACGATTACAACTTCAG
194 CATCACAACTGTCACTTTTAAAGTTCAGTAATTTACGATTACAACTTCAG
*
3987929 TTCATTAAG-AGTTTGT-TGATTTACGATC-CTAACTCCATTTAAATAGTTCACTGATTTACGAT
1 TTCATTAAGTA-TTT-TCTGATTTACGATCAC-AACTCCATTTAAATAGTTCACTGATTTACGAC
* * * * * * *
3987991 CACAGTTGTCATTTTTAAAGCTCGGTGATTTACAATCACAACTTCAGATCATTGATTTACTATTA
63 CACACTTGTAAGTTTAAAAGCTCAGTGATTTACAATCACAACTTCAGATCATTGATTTACGATCA
* * * * *
3988056 TGAACAATTCATTAAGAGTTTGTCGATTTATAATCGCAACTCCATTTAAAAAGTTTGTTGATTTA
128 TGAACAATTCATTAAGAGTTCGCCAATTTAAAATCGCAACTCCATTTAAAAAGTTAGTTGATTTA
*
3988121 CCATCACCACTGTCACTTTT
193 CCATCACAACTGTCACTTTT
3988141 CTTGCAAACT
Statistics
Matches: 179, Mismatches: 28, Indels: 10
0.82 0.13 0.05
Matches are distributed among these distances:
242 6 0.03
243 172 0.96
244 1 0.01
ACGTcount: A:0.32, C:0.17, G:0.12, T:0.39
Consensus pattern (243 bp):
TTCATTAAGTATTTTCTGATTTACGATCACAACTCCATTTAAATAGTTCACTGATTTACGACCAC
ACTTGTAAGTTTAAAAGCTCAGTGATTTACAATCACAACTTCAGATCATTGATTTACGATCATGA
ACAATTCATTAAGAGTTCGCCAATTTAAAATCGCAACTCCATTTAAAAAGTTAGTTGATTTACCA
TCACAACTGTCACTTTTAAAGTTCAGTAATTTACGATTACAACTTCAG
Found at i:3988175 original size:54 final size:54
Alignment explanation
Indices: 3988093--3988196 Score: 199
Period size: 54 Copynumber: 1.9 Consensus size: 54
3988083 TTATAATCGC
3988093 AACTCCATTTAAAAAGTTTGTTGATTTACCATCACCACTGTCACTTTTCTTGCA
1 AACTCCATTTAAAAAGTTTGTTGATTTACCATCACCACTGTCACTTTTCTTGCA
*
3988147 AACTCCATTTAAACAGTTTGTTGATTTACCATCACCACTGTCACTTTTCT
1 AACTCCATTTAAAAAGTTTGTTGATTTACCATCACCACTGTCACTTTTCT
3988197 AGCTCATTAA
Statistics
Matches: 49, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
54 49 1.00
ACGTcount: A:0.27, C:0.25, G:0.09, T:0.39
Consensus pattern (54 bp):
AACTCCATTTAAAAAGTTTGTTGATTTACCATCACCACTGTCACTTTTCTTGCA
Found at i:3990095 original size:71 final size:70
Alignment explanation
Indices: 3989970--3990143 Score: 192
Period size: 71 Copynumber: 2.5 Consensus size: 70
3989960 TCCAACATAA
* * *
3989970 GTTGGGGATTCTTGACAGCTTGAGTGAGCAGCATCGGATCGTTATTAAATGATGGATGAGATCCA
1 GTTGTGGATTCTTGACAGCTTGAGTGAGCAACATCGCATC-TTATTAAATGATGGATGAGATCCA
3990035 ACACGT
65 ACACGT
* *
3990041 GTTGTGGATTCTTGACAGCTTGAGTGAGCAACATCGCAT-TATACTT-TATCGATGGTTGAGATC
1 GTTGTGGATTCTTGACAGCTTGAGTGAGCAACATCGCATCT-TA-TTAAAT-GATGGATGAGATC
* *
3990104 TAGCACGT
63 CAACACGT
* * *
3990112 GTTACT-GATTCTCGACATCTTGAGTGAGCAAC
1 GTT-GTGGATTCTTGACAGCTTGAGTGAGCAAC
3990144 GTCAAATAAA
Statistics
Matches: 89, Mismatches: 10, Indels: 8
0.83 0.09 0.07
Matches are distributed among these distances:
69 1 0.01
70 4 0.04
71 83 0.93
72 1 0.01
ACGTcount: A:0.25, C:0.17, G:0.26, T:0.31
Consensus pattern (70 bp):
GTTGTGGATTCTTGACAGCTTGAGTGAGCAACATCGCATCTTATTAAATGATGGATGAGATCCAA
CACGT
Found at i:3993727 original size:15 final size:15
Alignment explanation
Indices: 3993707--3993736 Score: 51
Period size: 15 Copynumber: 2.0 Consensus size: 15
3993697 AACTAAGAAT
3993707 GAATCAAAAACCTAA
1 GAATCAAAAACCTAA
*
3993722 GAATCAAAACCCTAA
1 GAATCAAAAACCTAA
3993737 AATTGTGTGT
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.57, C:0.23, G:0.07, T:0.13
Consensus pattern (15 bp):
GAATCAAAAACCTAA
Found at i:3998860 original size:70 final size:71
Alignment explanation
Indices: 3998704--3998871 Score: 180
Period size: 70 Copynumber: 2.4 Consensus size: 71
3998694 TAAGTTGGGG
* * * **
3998704 ATTCTCGACAGCTTGAGTGAGCAGCATCAGATCAGTATTTAGCGATGGCTGAGATACAACACGTG
1 ATTCTCGACAGCTTGAGCGAGCAACATCACATCAGTATTTAGCGAAAGCTGAGATACAACACGTG
*
3998769 CTGCGG
66 CTGCGA
* * * * * *
3998775 ATTCTTGACAACTTGAGGGAGCAACATCACCT-A-TACTTTATCGAAAGCTGAGAT-CTAACATG
1 ATTCTCGACAGCTTGAGCGAGCAACATCACATCAGTA-TTTAGCGAAAGCTGAGATAC-AACACG
*
3998837 TGGTGCGA
64 TGCTGCGA
3998845 ATTCTCGACAGCTTGAGCGAGCAACAT
1 ATTCTCGACAGCTTGAGCGAGCAACAT
3998872 TAAATAAAGT
Statistics
Matches: 80, Mismatches: 15, Indels: 5
0.80 0.15 0.05
Matches are distributed among these distances:
69 3 0.04
70 51 0.64
71 26 0.32
ACGTcount: A:0.29, C:0.21, G:0.24, T:0.25
Consensus pattern (71 bp):
ATTCTCGACAGCTTGAGCGAGCAACATCACATCAGTATTTAGCGAAAGCTGAGATACAACACGTG
CTGCGA
Found at i:4010564 original size:34 final size:36
Alignment explanation
Indices: 4010515--4010598 Score: 93
Period size: 36 Copynumber: 2.4 Consensus size: 36
4010505 GAATTTGTCA
* *
4010515 ATTTACGACCGCAACTCT-A-TTTAAACAGTT-CATG
1 ATTTACGATCACAACTCTCATTTTAAA-AGTTCCATG
* * *
4010549 ATTTACGATCACAACTGTCATTTTTAAAGTTCCCTG
1 ATTTACGATCACAACTCTCATTTTAAAAGTTCCATG
4010585 ATTTACGATCACAA
1 ATTTACGATCACAA
4010599 TTTCAATTCA
Statistics
Matches: 42, Mismatches: 5, Indels: 4
0.82 0.10 0.08
Matches are distributed among these distances:
34 15 0.36
35 5 0.12
36 22 0.52
ACGTcount: A:0.32, C:0.23, G:0.11, T:0.35
Consensus pattern (36 bp):
ATTTACGATCACAACTCTCATTTTAAAAGTTCCATG
Found at i:4010744 original size:134 final size:134
Alignment explanation
Indices: 4010473--4011017 Score: 496
Period size: 133 Copynumber: 4.1 Consensus size: 134
4010463 GGGTATTTCA
* * * ** * * * * *
4010473 TCATTGATTTAAGGTCATAAACAATTCATTAAGAA-TTTGTCAATTTACGACCGCAACTCTATTT
1 TCATTGATTTACGATCATGAACAATTCATTAA-AAGTTCATCGATTTACTATCACAACTCCATTT
* ** * *
4010537 AAACAGTTCA-TGATTTACGATCACAACTGTCATTTTTAAAGTTCCCTGATTTACGATCACAATT
65 AAACAGTTCATTGATTTACGATCACAACTGTCACTTTTAAAACTCGCTGATTTACGATCACAACT
*
4010601 TCAAT
130 TCAGT
* * * * * *
4010606 TCATTTATTTACGATCATAAACAATTCATTAAAAGTTTACCGACTT-CTTATTACAACTCCATTT
1 TCATTGATTTACGATCATGAACAATTCATTAAAAGTTCATCGATTTAC-TATCACAACTCCATTT
* * * * *
4010670 AAACAGTTCACTGATTTATGATCACAACTCTCACTTTTAAAACTCGCTAATTTACGATCACAGCT
65 AAACAGTTCATTGATTTACGATCACAACTGTCACTTTTAAAACTCGCTGATTTACGATCACAACT
*
4010735 TGAGT
130 TCAGT
* *
4010740 TCATTGATTTACGATCATGACCAATTCATTAAGAA-TTCATCGATTTACTATCGCAACTCCA-TT
1 TCATTGATTTACGATCATGAACAATTCATTAA-AAGTTCATCGATTTACTATCACAACTCCATTT
* * * * * ** *
4010803 AAGCAGTTCATTGATATA-GAATCATAATTGTCATTTTTAAAACTCATTGGTTTACGA-C-CAAG
65 AAACAGTTCATTGATTTACG-ATCACAACTGTCACTTTTAAAACTCGCTGATTTACGATCACAA-
* *
4010865 GTTTAAGT
128 -CTTCAGT
* * * *
4010873 TCATTGATTTACGATCATGAGCAATTCATTAAGAGTTCATCAATTTACAATCGA-AACTCCATTT
1 TCATTGATTTACGATCATGAACAATTCATTAAAAGTTCATCGATTTACTATC-ACAACTCCATTT
* * * * * * * *
4010937 AAACAATTCGTTGATTTACAATCACAACAGTCACTTTTAAAGCTTGCTTATTTACTATCACAACT
65 AAACAGTTCATTGATTTACGATCACAACTGTCACTTTTAAAACTCGCTGATTTACGATCACAACT
4011002 TCAGT
130 TCAGT
4011007 TCATTGATTTA
1 TCATTGATTTA
4011018 TGATTGCATC
Statistics
Matches: 330, Mismatches: 68, Indels: 27
0.78 0.16 0.06
Matches are distributed among these distances:
131 2 0.01
132 6 0.02
133 161 0.49
134 154 0.47
135 4 0.01
136 3 0.01
ACGTcount: A:0.34, C:0.19, G:0.10, T:0.37
Consensus pattern (134 bp):
TCATTGATTTACGATCATGAACAATTCATTAAAAGTTCATCGATTTACTATCACAACTCCATTTA
AACAGTTCATTGATTTACGATCACAACTGTCACTTTTAAAACTCGCTGATTTACGATCACAACTT
CAGT
Found at i:4010954 original size:267 final size:267
Alignment explanation
Indices: 4010473--4011017 Score: 600
Period size: 267 Copynumber: 2.0 Consensus size: 267
4010463 GGGTATTTCA
* ** *
4010473 TCATTGATTTAAGGTCATAAACAATTCATTAAGAATTTGTCAATTTACGACCGCAACTCTATTTA
1 TCATTGATTTAAGATCATAAACAATTCATTAAGAATTCATCAATTTACGACCGCAACTCCATTTA
* ** *
4010538 AACAGTTCATGATTTACGATCACAACTGTCATTTTTAAAGTTCCCTGATTTACGATCACAATTTC
66 AACAGTTCATGATATACGATCACAACTGTCATTTTTAAAACTCACTGATTTACGATCACAATTTC
* * * * *
4010603 AATTCATTTATTTACGATCATAAACAATTCATTAAAAGTTTACCGACTTCTTATTACAACTCCAT
131 AATTCATTGATTTACGATCATAAACAATTCATTAAAAGTTCACCAACTTCTAATGACAACTCCAT
* ** * *
4010668 TTAAACAGTTCACTGATTTATGATCACAACTCTCACTTTTAAAACTCGCTAATTTACGATCACAG
196 TTAAACAATTCACTGATTTACAATCACAACACTCACTTTTAAAACTCGCTAATTTACGATCACAA
*
4010733 CTTGAGT
261 CTTCAGT
* * * * * *
4010740 TCATTGATTTACGATCATGACCAATTCATTAAGAATTCATCGATTTACTATCGCAACTCCA-TTA
1 TCATTGATTTAAGATCATAAACAATTCATTAAGAATTCATCAATTTACGACCGCAACTCCATTTA
* * * * *
4010804 AGCAGTTCATTGATATA-GAATCATAATTGTCATTTTTAAAACTCATTGGTTTACGA-C-CAAGG
66 AACAGTTCA-TGATATACG-ATCACAACTGTCATTTTTAAAACTCACTGATTTACGATCACAA--
* * * * *
4010866 TTT-AAGTTCATTGATTTACGATCATGAGCAATTCATTAAGAGTTCATCAATTTAC-AATCGA-A
127 TTTCAA-TTCATTGATTTACGATCATAAACAATTCATTAAAAGTTCACCAACTT-CTAAT-GACA
** * * * * *
4010928 ACTCCATTTAAACAATTCGTTGATTTACAATCACAACAGTCACTTTTAAAGCTTGCTTATTTACT
189 ACTCCATTTAAACAATTCACTGATTTACAATCACAACACTCACTTTTAAAACTCGCTAATTTACG
4010993 ATCACAACTTCAGT
254 ATCACAACTTCAGT
4011007 TCATTGATTTA
1 TCATTGATTTA
4011018 TGATTGCATC
Statistics
Matches: 229, Mismatches: 42, Indels: 14
0.80 0.15 0.05
Matches are distributed among these distances:
265 3 0.01
266 15 0.07
267 209 0.91
268 2 0.01
ACGTcount: A:0.34, C:0.19, G:0.10, T:0.37
Consensus pattern (267 bp):
TCATTGATTTAAGATCATAAACAATTCATTAAGAATTCATCAATTTACGACCGCAACTCCATTTA
AACAGTTCATGATATACGATCACAACTGTCATTTTTAAAACTCACTGATTTACGATCACAATTTC
AATTCATTGATTTACGATCATAAACAATTCATTAAAAGTTCACCAACTTCTAATGACAACTCCAT
TTAAACAATTCACTGATTTACAATCACAACACTCACTTTTAAAACTCGCTAATTTACGATCACAA
CTTCAGT
Found at i:4011209 original size:134 final size:134
Alignment explanation
Indices: 4011013--4011277 Score: 352
Period size: 134 Copynumber: 2.0 Consensus size: 134
4011003 CAGTTCATTG
* * * * * * * *
4011013 ATTTATGATTGCATCTCCATTTAAACAGTTTGCTAATTTATGATCACAATTTTTACTTTTAAAGC
1 ATTTATGATCGCAACTCCATTTAAAAAGCTTGCTAATTTACGATCACAAATGTCACTTTTAAAGC
4011078 TCGCTGATGTACGATCACAGCTTCAGTT-ATTTGATTTACAATCATGAACAATTCATTAAGAATT
66 TCGCTGATGTACGATCACAGCTTCAGTTCA-TTGATTTACAATCATGAACAATTCATTAAGAATT
4011142 CGCCA
130 CGCCA
* * * *
4011147 ATTTATGATCGCAACTTCATTTAAAAAGCTTGTTGATTTACGATCACAAATGTCATTTTTAAAGC
1 ATTTATGATCGCAACTCCATTTAAAAAGCTTGCTAATTTACGATCACAAATGTCACTTTTAAAGC
* * * * * *
4011212 TCGTTGATTTACGATCACAGCTTCTGTTCATTGATTTACGATTATGAACAATTCATTAAGAGTTC
66 TCGCTGATGTACGATCACAGCTTCAGTTCATTGATTTACAATCATGAACAATTCATTAAGAATTC
4011277 G
131 G
4011278 TAAATTTACA
Statistics
Matches: 112, Mismatches: 18, Indels: 2
0.85 0.14 0.02
Matches are distributed among these distances:
134 111 0.99
135 1 0.01
ACGTcount: A:0.31, C:0.17, G:0.13, T:0.39
Consensus pattern (134 bp):
ATTTATGATCGCAACTCCATTTAAAAAGCTTGCTAATTTACGATCACAAATGTCACTTTTAAAGC
TCGCTGATGTACGATCACAGCTTCAGTTCATTGATTTACAATCATGAACAATTCATTAAGAATTC
GCCA
Found at i:4017669 original size:26 final size:27
Alignment explanation
Indices: 4017635--4017692 Score: 75
Period size: 27 Copynumber: 2.2 Consensus size: 27
4017625 ATGATTTGGC
* *
4017635 TTTTTATTAT-TTAAATTTTT-ATAAT
1 TTTTTATTATATAAAATTTTTAATAAG
4017660 TTTTTAATTATATAAAATTTTTAATAAG
1 TTTTT-ATTATATAAAATTTTTAATAAG
4017688 TTTTT
1 TTTTT
4017693 CTCGTCCATA
Statistics
Matches: 28, Mismatches: 2, Indels: 3
0.85 0.06 0.09
Matches are distributed among these distances:
25 5 0.18
26 5 0.18
27 9 0.32
28 9 0.32
ACGTcount: A:0.34, C:0.00, G:0.02, T:0.64
Consensus pattern (27 bp):
TTTTTATTATATAAAATTTTTAATAAG
Found at i:4025132 original size:18 final size:18
Alignment explanation
Indices: 4025109--4025143 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
4025099 CAAGAACAGG
4025109 AAGCACCAAAATAGTTTC
1 AAGCACCAAAATAGTTTC
* *
4025127 AAGCACTAAAGTAGTTT
1 AAGCACCAAAATAGTTT
4025144 GACACATCAT
Statistics
Matches: 15, Mismatches: 2, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
18 15 1.00
ACGTcount: A:0.43, C:0.17, G:0.14, T:0.26
Consensus pattern (18 bp):
AAGCACCAAAATAGTTTC
Found at i:4034839 original size:6 final size:6
Alignment explanation
Indices: 4034828--4034860 Score: 66
Period size: 6 Copynumber: 5.5 Consensus size: 6
4034818 ATAATGGCCA
4034828 TTTGTT TTTGTT TTTGTT TTTGTT TTTGTT TTT
1 TTTGTT TTTGTT TTTGTT TTTGTT TTTGTT TTT
4034861 TTTAACTTAC
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 27 1.00
ACGTcount: A:0.00, C:0.00, G:0.15, T:0.85
Consensus pattern (6 bp):
TTTGTT
Found at i:4045785 original size:153 final size:153
Alignment explanation
Indices: 4045507--4045812 Score: 544
Period size: 153 Copynumber: 2.0 Consensus size: 153
4045497 ATATTTCCGA
*
4045507 AGAAAGTTTGAACTGGTCATAGAGGGAGTTGAGAAGAAATCGGTGGAGTGATAATGGGAGAGATT
1 AGAAAGTTTGAACTAGTCATAGAGGGAGTTGAGAAGAAATCGGTGGAGTGATAATGGGAGAGATT
*
4045572 TGAGGAGAGAATATTGAGATTTGGTGAGGTTGTTGTTGTGGAGAGTTATATATATCACATCTCAT
66 TGAGGAGAGAATATTGAGATTTGGTGAGGTTCTTGTTGTGGAGAGTTATATATATCACATCTCAT
*
4045637 TTGTTCTTTGTTCTGAATGGGGG
131 TTGTTCCTTGTTCTGAATGGGGG
4045660 AGAAAGTTTGAACTAGTCATAGAGGGAGTTGAGAAGAAATCGGTGGAGTGATAA-GGCGAGAGAT
1 AGAAAGTTTGAACTAGTCATAGAGGGAGTTGAGAAGAAATCGGTGGAGTGATAATGG-GAGAGAT
*
4045724 TTGAGGAGAGAATATTTAGATTTTGG-GAGGTTCTTGTTGTGGAGAGTTATATATATCACATCTC
65 TTGAGGAGAGAATATTGAGA-TTTGGTGAGGTTCTTGTTGTGGAGAGTTATATATATCACATCTC
4045788 ATTTGTTCCTTGTTCTGAATGGGGG
129 ATTTGTTCCTTGTTCTGAATGGGGG
4045813 GAGATCGGCG
Statistics
Matches: 147, Mismatches: 4, Indels: 4
0.95 0.03 0.03
Matches are distributed among these distances:
152 2 0.01
153 140 0.95
154 5 0.03
ACGTcount: A:0.28, C:0.07, G:0.32, T:0.32
Consensus pattern (153 bp):
AGAAAGTTTGAACTAGTCATAGAGGGAGTTGAGAAGAAATCGGTGGAGTGATAATGGGAGAGATT
TGAGGAGAGAATATTGAGATTTGGTGAGGTTCTTGTTGTGGAGAGTTATATATATCACATCTCAT
TTGTTCCTTGTTCTGAATGGGGG
Found at i:4046687 original size:27 final size:27
Alignment explanation
Indices: 4046394--4046701 Score: 334
Period size: 27 Copynumber: 11.5 Consensus size: 27
4046384 ATACCCCCGA
*
4046394 AGGGTAAAATGACCGTAATGCCCCTGT
1 AGGGTAAAATGACCGTAATGCCCCTAT
* **
4046421 AAGGTAAAATGGTCGTAATGCCCCTAT
1 AGGGTAAAATGACCGTAATGCCCCTAT
* * * * *
4046448 AAGGTAAAATAACTGTAATACCCCTGT
1 AGGGTAAAATGACCGTAATGCCCCTAT
**
4046475 AGGGTAAAATGGTCGTAATGCCCCTAT
1 AGGGTAAAATGACCGTAATGCCCCTAT
*
4046502 AGGGTAAAATGACCGTAATACCCCTAT
1 AGGGTAAAATGACCGTAATGCCCCTAT
* *
4046529 AGGTTAGAATGACCGTAATGCCCCTAT
1 AGGGTAAAATGACCGTAATGCCCCTAT
* * * * *
4046556 AGGGTAAAATAATCGTAAAGCACCTGT
1 AGGGTAAAATGACCGTAATGCCCCTAT
*
4046583 AGGGTAAAATGACCGTAATACCCCTAT
1 AGGGTAAAATGACCGTAATGCCCCTAT
* * *
4046610 AGGATAAAATGACCGTAATGCCCTTGT
1 AGGGTAAAATGACCGTAATGCCCCTAT
* * * *
4046637 AGGGTAAAATGACTGTAATACCCTTGT
1 AGGGTAAAATGACCGTAATGCCCCTAT
*
4046664 AGGATAAAATGACCGTAATG-CCCTAGT
1 AGGGTAAAATGACCGTAATGCCCCTA-T
4046691 -GGG-AAAATGAC
1 AGGGTAAAATGAC
4046702 TATTTTGCCC
Statistics
Matches: 231, Mismatches: 49, Indels: 4
0.81 0.17 0.01
Matches are distributed among these distances:
25 8 0.03
26 5 0.02
27 218 0.94
ACGTcount: A:0.35, C:0.19, G:0.22, T:0.24
Consensus pattern (27 bp):
AGGGTAAAATGACCGTAATGCCCCTAT
Found at i:4046773 original size:24 final size:24
Alignment explanation
Indices: 4046745--4046803 Score: 86
Period size: 24 Copynumber: 2.5 Consensus size: 24
4046735 TCTGTGGTTA
4046745 AATGACTGATTTGTCTGTG-TTTGGT
1 AATGACTGATTTGTCTGTGATTT--T
4046770 -ATGACTGATTTGTCTGTGATTTT
1 AATGACTGATTTGTCTGTGATTTT
4046793 AATGACTGATT
1 AATGACTGATT
4046804 CTGAGCACGG
Statistics
Matches: 32, Mismatches: 0, Indels: 5
0.86 0.00 0.14
Matches are distributed among these distances:
23 1 0.03
24 28 0.88
25 3 0.09
ACGTcount: A:0.20, C:0.08, G:0.24, T:0.47
Consensus pattern (24 bp):
AATGACTGATTTGTCTGTGATTTT
Found at i:4047027 original size:32 final size:32
Alignment explanation
Indices: 4046975--4047285 Score: 152
Period size: 32 Copynumber: 9.7 Consensus size: 32
4046965 ACTGCGATGC
* *
4046975 TACTAATGGCTTTCTGCCGATCATAGTACCAT
1 TACTAATGGCTTTGTGCCGATCATAGTACCGT
* *
4047007 TACTGATGGCTTTGTACCGATCATAGTACCGT
1 TACTAATGGCTTTGTGCCGATCATAGTACCGT
* *
4047039 TACTAATGGCTTTGTGTCGATCATATTACCGT
1 TACTAATGGCTTTGTGCCGATCATAGTACCGT
** * * * * *
4047071 TACCGATGGCTATATGCTGATCAT-TTCACTGT
1 TACTAATGGCTTTGTGCCGATCATAGT-ACCGT
* * **
4047103 TACTGATGG-TTGTGTGCCGATCATATTACTAT
1 TACTAATGGCTT-TGTGCCGATCATAGTACCGT
* * * * *
4047135 TACCAATGGCTGTATGCTGATCAT--TTCGCTGT
1 TACTAATGGCTTTGTGCCGATCATAGTAC-C-GT
* * * * *
4047167 TACTGATGGCTATGTGTCGATCATA-TCACTGC
1 TACTAATGGCTTTGTGCCGATCATAGT-ACCGT
* * * *
4047199 CACTGATGGCTTTATGCTGATCAT-GTTACCGT
1 TACTAATGGCTTTGTGCCGATCATAG-TACCGT
* * * * *
4047231 TACTGATGG-TTGTGTGTCAATCATA-TCACTGC
1 TACTAATGGCTT-TGTGCCGATCATAGT-ACCGT
* *
4047263 TACTGATGGCTTTGTGCCAATCA
1 TACTAATGGCTTTGTGCCGATCA
4047286 CATTACTGTA
Statistics
Matches: 213, Mismatches: 52, Indels: 28
0.73 0.18 0.10
Matches are distributed among these distances:
30 2 0.01
31 6 0.03
32 197 0.92
33 7 0.03
34 1 0.00
ACGTcount: A:0.22, C:0.21, G:0.21, T:0.37
Consensus pattern (32 bp):
TACTAATGGCTTTGTGCCGATCATAGTACCGT
Found at i:4047079 original size:64 final size:63
Alignment explanation
Indices: 4046975--4047275 Score: 266
Period size: 64 Copynumber: 4.7 Consensus size: 63
4046965 ACTGCGATGC
* * * * ** * * *
4046975 TACTAATGGCTTTCTGCCGATCATAGTACCATTACTGATGGCTTTGTACCGATCATAGTACCGT
1 TACTGATGGCTTTGTGTCGATCATATTACTGTTACTGATGGCTTTATGCTGATCAT-GTACCGT
* * * * * *
4047039 TACTAATGGCTTTGTGTCGATCATATTACCGTTACCGATGGCTATATGCTGATCATTTCACTGT
1 TACTGATGGCTTTGTGTCGATCATATTACTGTTACTGATGGCTTTATGCTGATCATGT-ACCGT
* * ** * *
4047103 TACTGATGG-TTGTGTGCCGATCATATTACTATTACCAATGGCTGTATGCTGATCAT-TTCGCTG
1 TACTGATGGCTT-TGTGTCGATCATATTACTGTTACTGATGGCTTTATGCTGATCATGTAC-C-G
4047166 T
63 T
* * **
4047167 TACTGATGGCTATGTGTCGATCATATCACTGCCACTGATGGCTTTATGCTGATCATGTTACCGT
1 TACTGATGGCTTTGTGTCGATCATATTACTGTTACTGATGGCTTTATGCTGATCATG-TACCGT
* * *
4047231 TACTGATGG-TTGTGTGTCAATCATATCACTGCTACTGATGGCTTT
1 TACTGATGGCTT-TGTGTCGATCATATTACTGTTACTGATGGCTTT
4047276 GTGCCAATCA
Statistics
Matches: 197, Mismatches: 32, Indels: 16
0.80 0.13 0.07
Matches are distributed among these distances:
62 1 0.01
63 5 0.03
64 187 0.95
65 2 0.01
66 2 0.01
ACGTcount: A:0.21, C:0.21, G:0.21, T:0.38
Consensus pattern (63 bp):
TACTGATGGCTTTGTGTCGATCATATTACTGTTACTGATGGCTTTATGCTGATCATGTACCGT
Found at i:4047254 original size:96 final size:95
Alignment explanation
Indices: 4047008--4047279 Score: 250
Period size: 96 Copynumber: 2.8 Consensus size: 95
4046998 TAGTACCATT
*
4047008 ACTGATGGCTTTGTACCGATCATAG-TACCGTTACTAATGGCTT-TGTGTCGATCATATTACC-G
1 ACTGATGGCTTTGTGCCGATCAT-GTTACCGTTACTAATGG-TTGTGTGTCGATCAT-TT-CCTG
* * * **
4047070 TTACCGATGGCTATATGCTGATCATTTCACTGTT
62 TTACTGATGGCTATGTGCTGATCATATCACTGCC
* ** * * *
4047104 ACTGATGG-TTGTGTGCCGATCATATTACTATTACCAATGGCTGTATG-CTGATCATTTCGCTGT
1 ACTGATGGCTT-TGTGCCGATCATGTTACCGTTACTAATGGTTGTGTGTC-GATCATTTC-CTGT
4047167 TACTGATGGCTATGTG-TCGATCATATCACTGCC
63 TACTGATGGCTATGTGCT-GATCATATCACTGCC
* * * * * *
4047200 ACTGATGGCTTTATGCTGATCATGTTACCGTTACTGATGGTTGTGTGTCAATCATATCACTGCTA
1 ACTGATGGCTTTGTGCCGATCATGTTACCGTTACTAATGGTTGTGTGTCGATCATTTC-CTGTTA
*
4047265 CTGATGGCTTTGTGC
65 CTGATGGCTATGTGC
4047280 CAATCACATT
Statistics
Matches: 140, Mismatches: 26, Indels: 19
0.76 0.14 0.10
Matches are distributed among these distances:
94 1 0.01
95 8 0.06
96 128 0.91
97 3 0.02
ACGTcount: A:0.21, C:0.20, G:0.22, T:0.38
Consensus pattern (95 bp):
ACTGATGGCTTTGTGCCGATCATGTTACCGTTACTAATGGTTGTGTGTCGATCATTTCCTGTTAC
TGATGGCTATGTGCTGATCATATCACTGCC
Found at i:4047304 original size:31 final size:32
Alignment explanation
Indices: 4047167--4047305 Score: 102
Period size: 32 Copynumber: 4.4 Consensus size: 32
4047157 ATTTCGCTGT
* * * *
4047167 TACTGATGGCTATGTGTCGATCATATCACTGC
1 TACTGATGGCTTTGTGCCAATCACATCACTGC
* * ** ** * * *
4047199 CACTGATGGCTTTATGCTGATCATGTTACCGT
1 TACTGATGGCTTTGTGCCAATCACATCACTGC
* *
4047231 TACTGATGG-TTGTGTGTCAATCATATCACTGC
1 TACTGATGGCTT-TGTGCCAATCACATCACTGC
*
4047263 TACTGATGGCTTTGTGCCAATCACATTACTG-
1 TACTGATGGCTTTGTGCCAATCACATCACTGC
*
4047294 TACTTATGGCTT
1 TACTGATGGCTT
4047306 GTAGCAATTC
Statistics
Matches: 83, Mismatches: 22, Indels: 5
0.75 0.20 0.05
Matches are distributed among these distances:
31 13 0.16
32 68 0.82
33 2 0.02
ACGTcount: A:0.21, C:0.21, G:0.21, T:0.37
Consensus pattern (32 bp):
TACTGATGGCTTTGTGCCAATCACATCACTGC
Found at i:4049170 original size:23 final size:23
Alignment explanation
Indices: 4049144--4049193 Score: 100
Period size: 23 Copynumber: 2.2 Consensus size: 23
4049134 ACAGGCTTTT
4049144 AAGTGTTTTAAAAACACACAAGA
1 AAGTGTTTTAAAAACACACAAGA
4049167 AAGTGTTTTAAAAACACACAAGA
1 AAGTGTTTTAAAAACACACAAGA
4049190 AAGT
1 AAGT
4049194 CATAGGATTG
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
23 27 1.00
ACGTcount: A:0.52, C:0.12, G:0.14, T:0.22
Consensus pattern (23 bp):
AAGTGTTTTAAAAACACACAAGA
Found at i:4055949 original size:17 final size:17
Alignment explanation
Indices: 4055927--4055961 Score: 70
Period size: 17 Copynumber: 2.1 Consensus size: 17
4055917 ACTTGTCCCC
4055927 AGCCTCAAAACGTTACA
1 AGCCTCAAAACGTTACA
4055944 AGCCTCAAAACGTTACA
1 AGCCTCAAAACGTTACA
4055961 A
1 A
4055962 CTTGAAATCA
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 18 1.00
ACGTcount: A:0.43, C:0.29, G:0.11, T:0.17
Consensus pattern (17 bp):
AGCCTCAAAACGTTACA
Found at i:4056385 original size:47 final size:47
Alignment explanation
Indices: 4056319--4056414 Score: 192
Period size: 47 Copynumber: 2.0 Consensus size: 47
4056309 TTAAACTAGT
4056319 TTTCGTACTTTAGGAGCTTGAATATAAGCACTTTGGTTAAGTTTTAG
1 TTTCGTACTTTAGGAGCTTGAATATAAGCACTTTGGTTAAGTTTTAG
4056366 TTTCGTACTTTAGGAGCTTGAATATAAGCACTTTGGTTAAGTTTTAG
1 TTTCGTACTTTAGGAGCTTGAATATAAGCACTTTGGTTAAGTTTTAG
4056413 TT
1 TT
4056415 AACTTTTTGT
Statistics
Matches: 49, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
47 49 1.00
ACGTcount: A:0.25, C:0.10, G:0.21, T:0.44
Consensus pattern (47 bp):
TTTCGTACTTTAGGAGCTTGAATATAAGCACTTTGGTTAAGTTTTAG
Found at i:4059929 original size:24 final size:24
Alignment explanation
Indices: 4059902--4059948 Score: 76
Period size: 24 Copynumber: 2.0 Consensus size: 24
4059892 TTCTATAATC
*
4059902 ATGAATTTGAATTTAATTTATTAT
1 ATGAATTTCAATTTAATTTATTAT
*
4059926 ATGAATTTCAATTTTATTTATTA
1 ATGAATTTCAATTTAATTTATTA
4059949 GGTAAATGTT
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
24 21 1.00
ACGTcount: A:0.36, C:0.02, G:0.06, T:0.55
Consensus pattern (24 bp):
ATGAATTTCAATTTAATTTATTAT
Found at i:4062636 original size:22 final size:22
Alignment explanation
Indices: 4062610--4062652 Score: 68
Period size: 22 Copynumber: 2.0 Consensus size: 22
4062600 GGGTTAGGTT
*
4062610 AATTGGGTTTAGCGTTTGGGCC
1 AATTGGGTTTAGCATTTGGGCC
*
4062632 AATTGGGTTTAGTATTTGGGC
1 AATTGGGTTTAGCATTTGGGC
4062653 TTGGGGTTAG
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
22 19 1.00
ACGTcount: A:0.16, C:0.09, G:0.35, T:0.40
Consensus pattern (22 bp):
AATTGGGTTTAGCATTTGGGCC
Found at i:4062996 original size:44 final size:44
Alignment explanation
Indices: 4062938--4063296 Score: 432
Period size: 44 Copynumber: 8.2 Consensus size: 44
4062928 TATAGAGACT
* * * * **
4062938 AATCTTCCACCTATTCCGCTGTTGGTCAGGGAGATAGGACTTGT
1 AATCTTCAACCTATTCCGCTGCTGGTCTGGGAAATAGGACTTAC
* * * * * *
4062982 AAGCTTCAACCTATTCTGCTGCTAGTCAGGGATATAGGACTTGC
1 AATCTTCAACCTATTCCGCTGCTGGTCTGGGAAATAGGACTTAC
* * *
4063026 AATCCTCAACCTATTCTGCTGCTGGTCTGGGAAATAGGACATAC
1 AATCTTCAACCTATTCCGCTGCTGGTCTGGGAAATAGGACTTAC
*
4063070 AATCTTCGACCTATTCCGCTGCTGGTCTGGGAAATAGGACATT-C
1 AATCTTCAACCTATTCCGCTGCTGGTCTGGGAAATAGGAC-TTAC
* * * *
4063114 AATCTTCAACCTATTTCGCTCCTGGTCTGGGAAATAGGGCATAC
1 AATCTTCAACCTATTCCGCTGCTGGTCTGGGAAATAGGACTTAC
* * *
4063158 AGTCTTCAACCTATTCCGCTGCTGGTCTGGGAAATAGGGCATAC
1 AATCTTCAACCTATTCCGCTGCTGGTCTGGGAAATAGGACTTAC
* ** *
4063202 AATCTTCAACCTATTCCACTATTGGTCTGGGAAATAGGACATAC
1 AATCTTCAACCTATTCCGCTGCTGGTCTGGGAAATAGGACTTAC
* * *
4063246 AATCTTCAACCTATCCCACTGCTGGTCTGGGAAATAGGACTTGC
1 AATCTTCAACCTATTCCGCTGCTGGTCTGGGAAATAGGACTTAC
4063290 AATCTTC
1 AATCTTC
4063297 TACCGGCTTC
Statistics
Matches: 277, Mismatches: 36, Indels: 4
0.87 0.11 0.01
Matches are distributed among these distances:
43 1 0.00
44 275 0.99
45 1 0.00
ACGTcount: A:0.25, C:0.25, G:0.21, T:0.29
Consensus pattern (44 bp):
AATCTTCAACCTATTCCGCTGCTGGTCTGGGAAATAGGACTTAC
Found at i:4077068 original size:22 final size:22
Alignment explanation
Indices: 4077042--4077084 Score: 68
Period size: 22 Copynumber: 2.0 Consensus size: 22
4077032 GGGTTAGGTT
*
4077042 AATTGGGTTTAGCGTTTGGGCC
1 AATTGGGTTTAGCATTTGGGCC
*
4077064 AATTGGGTTTAGTATTTGGGC
1 AATTGGGTTTAGCATTTGGGC
4077085 TTAGGGTTAG
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
22 19 1.00
ACGTcount: A:0.16, C:0.09, G:0.35, T:0.40
Consensus pattern (22 bp):
AATTGGGTTTAGCATTTGGGCC
Found at i:4083876 original size:18 final size:19
Alignment explanation
Indices: 4083853--4083888 Score: 56
Period size: 18 Copynumber: 1.9 Consensus size: 19
4083843 AATTCTTTTA
4083853 AATTTTTTCAAA-AAAAAG
1 AATTTTTTCAAATAAAAAG
*
4083871 AATTTTTTTAAATAAAAA
1 AATTTTTTCAAATAAAAA
4083889 TCAGAAAATT
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
18 11 0.69
19 5 0.31
ACGTcount: A:0.56, C:0.03, G:0.03, T:0.39
Consensus pattern (19 bp):
AATTTTTTCAAATAAAAAG
Found at i:4084063 original size:59 final size:59
Alignment explanation
Indices: 4083971--4084109 Score: 278
Period size: 59 Copynumber: 2.4 Consensus size: 59
4083961 TTTTGAAAGG
4083971 TTGGAGAAGATGAGCTTTTCTGCAAATTTTGGCCTAGGGCTTCAAGTTCTCTCACAACA
1 TTGGAGAAGATGAGCTTTTCTGCAAATTTTGGCCTAGGGCTTCAAGTTCTCTCACAACA
4084030 TTGGAGAAGATGAGCTTTTCTGCAAATTTTGGCCTAGGGCTTCAAGTTCTCTCACAACA
1 TTGGAGAAGATGAGCTTTTCTGCAAATTTTGGCCTAGGGCTTCAAGTTCTCTCACAACA
4084089 TTGGAGAAGATGAGCTTTTCT
1 TTGGAGAAGATGAGCTTTTCT
4084110 ATCTTCTTTC
Statistics
Matches: 80, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
59 80 1.00
ACGTcount: A:0.25, C:0.19, G:0.23, T:0.33
Consensus pattern (59 bp):
TTGGAGAAGATGAGCTTTTCTGCAAATTTTGGCCTAGGGCTTCAAGTTCTCTCACAACA
Found at i:4092033 original size:22 final size:21
Alignment explanation
Indices: 4092008--4092051 Score: 61
Period size: 21 Copynumber: 2.0 Consensus size: 21
4091998 ACTAAAACAG
*
4092008 AATGAGTAAAGGAAACAAAAAA
1 AATGAATAAA-GAAACAAAAAA
*
4092030 AATGAATAAATAAACAAAAAA
1 AATGAATAAAGAAACAAAAAA
4092051 A
1 A
4092052 CGAGATTATT
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
21 11 0.55
22 9 0.45
ACGTcount: A:0.73, C:0.05, G:0.11, T:0.11
Consensus pattern (21 bp):
AATGAATAAAGAAACAAAAAA
Found at i:4093172 original size:15 final size:15
Alignment explanation
Indices: 4093152--4093180 Score: 51
Period size: 14 Copynumber: 2.0 Consensus size: 15
4093142 ATCCTTAAGG
4093152 TTTTTTT-CTTTTAA
1 TTTTTTTCCTTTTAA
4093166 TTTTTTTCCTTTTAA
1 TTTTTTTCCTTTTAA
4093181 GTAGCGAATT
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
14 7 0.50
15 7 0.50
ACGTcount: A:0.14, C:0.10, G:0.00, T:0.76
Consensus pattern (15 bp):
TTTTTTTCCTTTTAA
Found at i:4096807 original size:14 final size:15
Alignment explanation
Indices: 4096775--4096809 Score: 54
Period size: 15 Copynumber: 2.4 Consensus size: 15
4096765 GGGTTAGTTC
*
4096775 TTTATTTTTAAAGAT
1 TTTATTGTTAAAGAT
4096790 TTTATTGTTAAA-AT
1 TTTATTGTTAAAGAT
4096804 TTTATT
1 TTTATT
4096810 TAATTATTAA
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
14 8 0.42
15 11 0.58
ACGTcount: A:0.31, C:0.00, G:0.06, T:0.63
Consensus pattern (15 bp):
TTTATTGTTAAAGAT
Found at i:4103730 original size:21 final size:19
Alignment explanation
Indices: 4103684--4103758 Score: 123
Period size: 19 Copynumber: 3.8 Consensus size: 19
4103674 AATCTTCAAG
4103684 GATATGCAATCTTAGATAT
1 GATATGCAATCTTAGATAT
4103703 GATATGCAATCTTAGATAT
1 GATATGCAATCTTAGATAT
*
4103722 GATATATGCAATCTTGGATAT
1 G--ATATGCAATCTTAGATAT
4103743 GATATGCAATCTTAGA
1 GATATGCAATCTTAGA
4103759 AGATATGATT
Statistics
Matches: 52, Mismatches: 2, Indels: 4
0.90 0.03 0.07
Matches are distributed among these distances:
19 34 0.65
21 18 0.35
ACGTcount: A:0.36, C:0.11, G:0.17, T:0.36
Consensus pattern (19 bp):
GATATGCAATCTTAGATAT
Found at i:4104360 original size:29 final size:27
Alignment explanation
Indices: 4104318--4104394 Score: 84
Period size: 29 Copynumber: 2.8 Consensus size: 27
4104308 CATACATACG
*
4104318 TTTTATAATATATATATTTTTAAATTAA
1 TTTTATAATATATATATTATTAAATT-A
* *
4104346 TTTTGATAATGTATATATTATTCAATTA
1 TTTT-ATAATATATATATTATTAAATTA
*
4104374 TTTT-TAATCTATATATATATT
1 TTTTATAATATATATAT-TATT
4104395 TCTTTTATAT
Statistics
Matches: 43, Mismatches: 4, Indels: 5
0.83 0.08 0.10
Matches are distributed among these distances:
26 11 0.26
27 4 0.09
28 9 0.21
29 19 0.44
ACGTcount: A:0.38, C:0.03, G:0.03, T:0.57
Consensus pattern (27 bp):
TTTTATAATATATATATTATTAAATTA
Found at i:4113286 original size:44 final size:44
Alignment explanation
Indices: 4113062--4113469 Score: 146
Period size: 44 Copynumber: 9.3 Consensus size: 44
4113052 AATAGAAGAT
* *
4113062 CTTGCATTCCTACACCGACAGCGAAGCAGATCAAAGACACCAGC
1 CTTGCCTTCCTGCACCGACAGCGAAGCAGATCAAAGACACCAGC
* *** * * * * * * * *
4113106 CTTGCCTCCCTAG-GTTG-TAGCGGAGCAGGTTAAAAATAGCAGAT
1 CTTGCCTTCCT-GCACCGACAGCGAAGCAGATCAAAGACACCAG-C
*
4113150 CTTGCCTTCCTGCACCGACAGCGAAGCAGATCGAAGACACCAGC
1 CTTGCCTTCCTGCACCGACAGCGAAGCAGATCAAAGACACCAGC
**** * * * * * * *
4113194 CTTGCC-TCCTTGGGTTG-CAGCGGAGCAGGTTAAAAATAGCAGAT
1 CTTGCCTTCC-TGCACCGACAGCGAAGCAGATCAAAGACACCAG-C
* *
4113238 CTTGCCTTCCTGCACCGATAGCGAAGCAGATCGAAGACACCAGC
1 CTTGCCTTCCTGCACCGACAGCGAAGCAGATCAAAGACACCAGC
**** * * * * * * * * *
4113282 CTTG-CTTCCCTGGGTTG-CAACGGAGCTGGTTAAAAATAGCAGAT
1 CTTGCCTT-CCTGCACCGACAGCGAAGCAGATCAAAGACACCAG-C
* * * * *
4113326 CTTACCTTCCTGCACCGGCATCGAAGTAGATCGAAGACACCAGC
1 CTTGCCTTCCTGCACCGACAGCGAAGCAGATCAAAGACACCAGC
* **** * * * * * * *
4113370 CTTGCCTCCCTG-GGTTACAGCGGAGCAGGTTAAAAATAGCAGAT
1 CTTGCCTTCCTGCACCGACAGCGAAGCAGATCAAAGACACCAG-C
* **
4113414 CTTGCCTTCCTGCACCGACAGTGAAGCAGATCGTAGACACCAGC
1 CTTGCCTTCCTGCACCGACAGCGAAGCAGATCAAAGACACCAGC
*
4113458 CTTGCCTCCCTG
1 CTTGCCTTCCTG
4113470 GGTTGCAGCG
Statistics
Matches: 234, Mismatches: 116, Indels: 28
0.62 0.31 0.07
Matches are distributed among these distances:
43 74 0.32
44 88 0.38
45 72 0.31
ACGTcount: A:0.26, C:0.29, G:0.24, T:0.20
Consensus pattern (44 bp):
CTTGCCTTCCTGCACCGACAGCGAAGCAGATCAAAGACACCAGC
Found at i:4113546 original size:88 final size:88
Alignment explanation
Indices: 4113048--4113535 Score: 760
Period size: 88 Copynumber: 5.5 Consensus size: 88
4113038 AGCAGATTAG
* * * *
4113048 TAAAAATAGAAGATCTTGCATTCCTACACCGACAGCGAAGCAGATCAAAGACACCAGCCTTGCCT
1 TAAAAATAGCAGATCTTGCCTTCCTGCACCGACAGCGAAGCAGATCGAAGACACCAGCCTTGCCT
* *
4113113 CCCTAGGTTGTAGCGGAGCAGGT
66 CCCTGGGTTGCAGCGGAGCAGGT
4113136 TAAAAATAGCAGATCTTGCCTTCCTGCACCGACAGCGAAGCAGATCGAAGACACCAGCCTTGCCT
1 TAAAAATAGCAGATCTTGCCTTCCTGCACCGACAGCGAAGCAGATCGAAGACACCAGCCTTGCCT
*
4113201 CCTTGGGTTGCAGCGGAGCAGGT
66 CCCTGGGTTGCAGCGGAGCAGGT
* *
4113224 TAAAAATAGCAGATCTTGCCTTCCTGCACCGATAGCGAAGCAGATCGAAGACACCAGCCTTGCTT
1 TAAAAATAGCAGATCTTGCCTTCCTGCACCGACAGCGAAGCAGATCGAAGACACCAGCCTTGCCT
* *
4113289 CCCTGGGTTGCAACGGAGCTGGT
66 CCCTGGGTTGCAGCGGAGCAGGT
* * * *
4113312 TAAAAATAGCAGATCTTACCTTCCTGCACCGGCATCGAAGTAGATCGAAGACACCAGCCTTGCCT
1 TAAAAATAGCAGATCTTGCCTTCCTGCACCGACAGCGAAGCAGATCGAAGACACCAGCCTTGCCT
*
4113377 CCCTGGGTTACAGCGGAGCAGGT
66 CCCTGGGTTGCAGCGGAGCAGGT
* *
4113400 TAAAAATAGCAGATCTTGCCTTCCTGCACCGACAGTGAAGCAGATCGTAGACACCAGCCTTGCCT
1 TAAAAATAGCAGATCTTGCCTTCCTGCACCGACAGCGAAGCAGATCGAAGACACCAGCCTTGCCT
*
4113465 CCCTGGGTTGCAGCGGAACAGGT
66 CCCTGGGTTGCAGCGGAGCAGGT
* * ** *
4113488 TAAAAATAGCATATATTGCCTTTTTGCACCGACAGCGAAGCATATCGA
1 TAAAAATAGCAGATCTTGCCTTCCTGCACCGACAGCGAAGCAGATCGA
4113536 TGAGCCCAGC
Statistics
Matches: 364, Mismatches: 36, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
88 364 1.00
ACGTcount: A:0.28, C:0.27, G:0.24, T:0.21
Consensus pattern (88 bp):
TAAAAATAGCAGATCTTGCCTTCCTGCACCGACAGCGAAGCAGATCGAAGACACCAGCCTTGCCT
CCCTGGGTTGCAGCGGAGCAGGT
Found at i:4114446 original size:21 final size:19
Alignment explanation
Indices: 4114400--4114474 Score: 123
Period size: 19 Copynumber: 3.8 Consensus size: 19
4114390 AATCTTCAAG
4114400 GATATGCAATCTTAGATAT
1 GATATGCAATCTTAGATAT
4114419 GATATGCAATCTTAGATAT
1 GATATGCAATCTTAGATAT
*
4114438 GATATATGCAATCTTGGATAT
1 G--ATATGCAATCTTAGATAT
4114459 GATATGCAATCTTAGA
1 GATATGCAATCTTAGA
4114475 AGATATGATT
Statistics
Matches: 52, Mismatches: 2, Indels: 4
0.90 0.03 0.07
Matches are distributed among these distances:
19 34 0.65
21 18 0.35
ACGTcount: A:0.36, C:0.11, G:0.17, T:0.36
Consensus pattern (19 bp):
GATATGCAATCTTAGATAT
Found at i:4119281 original size:47 final size:47
Alignment explanation
Indices: 4119197--4119325 Score: 158
Period size: 47 Copynumber: 2.8 Consensus size: 47
4119187 GTTATTTGTA
* * *
4119197 ATATTGTTGTTTTTGTTTAAATGAAAAACCAGCTTATGTGATAGTTG
1 ATATTGTTGTTGTTGTTGAAATGGAAAACCAGCTTATGTGATAGTTG
* * * *
4119244 GTATTGTTGTTGTTGTTGAAATGGAAAATCAGTTTATGTGATTGTTG
1 ATATTGTTGTTGTTGTTGAAATGGAAAACCAGCTTATGTGATAGTTG
4119291 ATATTAG--G--GTTGTTGAAATGGAAAACCAGCTTATG
1 ATATT-GTTGTTGTTGTTGAAATGGAAAACCAGCTTATG
4119326 GTGTTGTTAT
Statistics
Matches: 71, Mismatches: 10, Indels: 5
0.83 0.12 0.06
Matches are distributed among these distances:
44 25 0.35
46 1 0.01
47 44 0.62
48 1 0.01
ACGTcount: A:0.29, C:0.05, G:0.24, T:0.42
Consensus pattern (47 bp):
ATATTGTTGTTGTTGTTGAAATGGAAAACCAGCTTATGTGATAGTTG
Found at i:4123561 original size:41 final size:41
Alignment explanation
Indices: 4123498--4123686 Score: 227
Period size: 41 Copynumber: 4.6 Consensus size: 41
4123488 ATTAATTATA
* *
4123498 CCCTGAATTACACATACGTGCCCCTATTTGTACTTCGGTAC
1 CCCTGAATTACACATACATGCCCCTGTTTGTACTTCGGTAC
** * *
4123539 CATTGAATTACACATATATGCCCTTGTTTGTACTTCGGTAC
1 CCCTGAATTACACATACATGCCCCTGTTTGTACTTCGGTAC
* * **
4123580 CCTTGAATTACACATACGTGCCCCTGTTTGTACTTCAATAC
1 CCCTGAATTACACATACATGCCCCTGTTTGTACTTCGGTAC
* * * *
4123621 CCCTGAGTTGCATATATATGCCCCTGTTTGTACTTCGGTAC
1 CCCTGAATTACACATACATGCCCCTGTTTGTACTTCGGTAC
*
4123662 CCCT-AAATAGCACATACATGCCCCT
1 CCCTGAATTA-CACATACATGCCCCT
4123687 ATTTACACTA
Statistics
Matches: 122, Mismatches: 25, Indels: 2
0.82 0.17 0.01
Matches are distributed among these distances:
40 2 0.02
41 120 0.98
ACGTcount: A:0.23, C:0.29, G:0.14, T:0.33
Consensus pattern (41 bp):
CCCTGAATTACACATACATGCCCCTGTTTGTACTTCGGTAC
Found at i:4123591 original size:82 final size:81
Alignment explanation
Indices: 4123496--4123690 Score: 257
Period size: 82 Copynumber: 2.4 Consensus size: 81
4123486 AAATTAATTA
** *
4123496 TACCCTGAATTACACATACGTGCCCCTATTTGTACTTCGGTACCATTGAATTACACATATATGCC
1 TACCCTGAATTACACATACGTGCCCCTATTTGTACTTCAATACCACTGAATTACACATATATGCC
*
4123561 CTTGTTTGTACTTCGG
66 CCTGTTTGTACTTCGG
* * * * *
4123577 TACCCTTGAATTACACATACGTGCCCCTGTTTGTACTTCAATACCCCTGAGTTGCATATATATGC
1 TACCC-TGAATTACACATACGTGCCCCTATTTGTACTTCAATACCACTGAATTACACATATATGC
4123642 CCCTGTTTGTACTTCGG
65 CCCTGTTTGTACTTCGG
* *
4123659 TACCCCT-AAATAGCACATACATGCCCCTATTT
1 TA-CCCTGAATTA-CACATACGTGCCCCTATTT
4123691 ACACTATGGT
Statistics
Matches: 99, Mismatches: 12, Indels: 5
0.85 0.10 0.04
Matches are distributed among these distances:
81 9 0.09
82 87 0.88
83 3 0.03
ACGTcount: A:0.24, C:0.28, G:0.14, T:0.34
Consensus pattern (81 bp):
TACCCTGAATTACACATACGTGCCCCTATTTGTACTTCAATACCACTGAATTACACATATATGCC
CCTGTTTGTACTTCGG
Found at i:4125233 original size:17 final size:18
Alignment explanation
Indices: 4125208--4125241 Score: 61
Period size: 17 Copynumber: 1.9 Consensus size: 18
4125198 TAATTTTCTT
4125208 ATTTATTTATTTATTTTA
1 ATTTATTTATTTATTTTA
4125226 ATTT-TTTATTTATTTT
1 ATTTATTTATTTATTTT
4125242 TATCCTCTTA
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
17 12 0.75
18 4 0.25
ACGTcount: A:0.24, C:0.00, G:0.00, T:0.76
Consensus pattern (18 bp):
ATTTATTTATTTATTTTA
Found at i:4127174 original size:10 final size:9
Alignment explanation
Indices: 4127146--4127212 Score: 59
Period size: 10 Copynumber: 7.4 Consensus size: 9
4127136 AAAATTGTTA
*
4127146 TTTTAAAAT
1 TTTTATAAT
4127155 TTTT-TAAT
1 TTTTATAAT
4127163 TTTTATATAT
1 TTTTATA-AT
*
4127173 TTTTAGAACT
1 TTTTATAA-T
4127183 TTTTATAA-
1 TTTTATAAT
4127191 -TTTATAAT
1 TTTTATAAT
*
4127199 TTATATAAT
1 TTTTATAAT
4127208 ATTTT
1 -TTTT
4127213 CTAAAATATA
Statistics
Matches: 47, Mismatches: 5, Indels: 11
0.75 0.08 0.17
Matches are distributed among these distances:
7 7 0.15
8 7 0.15
9 14 0.30
10 19 0.40
ACGTcount: A:0.34, C:0.01, G:0.01, T:0.63
Consensus pattern (9 bp):
TTTTATAAT
Found at i:4129488 original size:10 final size:9
Alignment explanation
Indices: 4129460--4129526 Score: 59
Period size: 10 Copynumber: 7.4 Consensus size: 9
4129450 AAAATTGTTA
*
4129460 TTTTAAAAT
1 TTTTATAAT
4129469 TTTT-TAAT
1 TTTTATAAT
4129477 TTTTATATAT
1 TTTTATA-AT
*
4129487 TTTTAGAACT
1 TTTTATAA-T
4129497 TTTTATAA-
1 TTTTATAAT
4129505 -TTTATAAT
1 TTTTATAAT
*
4129513 TTATATAAT
1 TTTTATAAT
4129522 ATTTT
1 -TTTT
4129527 CTAAAATATA
Statistics
Matches: 47, Mismatches: 5, Indels: 11
0.75 0.08 0.17
Matches are distributed among these distances:
7 7 0.15
8 7 0.15
9 14 0.30
10 19 0.40
ACGTcount: A:0.34, C:0.01, G:0.01, T:0.63
Consensus pattern (9 bp):
TTTTATAAT
Found at i:4140290 original size:26 final size:26
Alignment explanation
Indices: 4140259--4140310 Score: 95
Period size: 26 Copynumber: 2.0 Consensus size: 26
4140249 TCGGAGTGTG
4140259 ATTCCTGACGAACCCCAGGTTTGATA
1 ATTCCTGACGAACCCCAGGTTTGATA
*
4140285 ATTCCTGAGGAACCCCAGGTTTGATA
1 ATTCCTGACGAACCCCAGGTTTGATA
4140311 CTTGGCTTTT
Statistics
Matches: 25, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
26 25 1.00
ACGTcount: A:0.27, C:0.25, G:0.21, T:0.27
Consensus pattern (26 bp):
ATTCCTGACGAACCCCAGGTTTGATA
Found at i:4140597 original size:3 final size:3
Alignment explanation
Indices: 4140559--4140586 Score: 56
Period size: 3 Copynumber: 9.3 Consensus size: 3
4140549 CTAATATTTG
4140559 TTA TTA TTA TTA TTA TTA TTA TTA TTA T
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA T
4140587 CGTTTATTAT
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 25 1.00
ACGTcount: A:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (3 bp):
TTA
Found at i:4146071 original size:21 final size:21
Alignment explanation
Indices: 4146047--4146087 Score: 57
Period size: 21 Copynumber: 2.0 Consensus size: 21
4146037 CATGCTTAAA
4146047 CATTCATTAATC-TTTCCCAAT
1 CATTC-TTAATCATTTCCCAAT
*
4146068 CATTCTTAATCATTTTCCAA
1 CATTCTTAATCATTTCCCAA
4146088 ACTTAAAATA
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
20 6 0.33
21 12 0.67
ACGTcount: A:0.29, C:0.27, G:0.00, T:0.44
Consensus pattern (21 bp):
CATTCTTAATCATTTCCCAAT
Found at i:4148560 original size:26 final size:26
Alignment explanation
Indices: 4148520--4148570 Score: 68
Period size: 26 Copynumber: 2.0 Consensus size: 26
4148510 TTCCTTTCTT
* *
4148520 TCCCTTTTTCTTTTCT-TTCTTTTTTC
1 TCCCTATTTCATTTCTATT-TTTTTTC
4148546 TCCCTATTTCATTTCTATTTTTTTT
1 TCCCTATTTCATTTCTATTTTTTTT
4148571 GTTTCTTTTA
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
26 20 0.91
27 2 0.09
ACGTcount: A:0.06, C:0.24, G:0.00, T:0.71
Consensus pattern (26 bp):
TCCCTATTTCATTTCTATTTTTTTTC
Found at i:4148611 original size:7 final size:7
Alignment explanation
Indices: 4148599--4148662 Score: 58
Period size: 7 Copynumber: 8.6 Consensus size: 7
4148589 ATTTACTTAT
4148599 TATAATA
1 TATAATA
4148606 TATAATA
1 TATAATA
4148613 TAATATATA
1 T-ATA-ATA
*
4148622 TTTAATA
1 TATAATA
*
4148629 -ATTAAGA
1 TA-TAATA
4148636 TATAATA
1 TATAATA
4148643 TTATAATA
1 -TATAATA
4148651 TTATAATA
1 -TATAATA
4148659 TATA
1 TATA
4148663 TTTTAACTTG
Statistics
Matches: 48, Mismatches: 4, Indels: 10
0.77 0.06 0.16
Matches are distributed among these distances:
7 23 0.48
8 21 0.44
9 4 0.08
ACGTcount: A:0.53, C:0.00, G:0.02, T:0.45
Consensus pattern (7 bp):
TATAATA
Found at i:4148649 original size:8 final size:8
Alignment explanation
Indices: 4148596--4148659 Score: 64
Period size: 8 Copynumber: 8.4 Consensus size: 8
4148586 TATATTTACT
4148596 TATTATAA
1 TATTATAA
4148604 TA-TATAA
1 TATTATAA
*
4148611 TATAATATA
1 TATTATA-A
4148620 TATT-TAA
1 TATTATAA
*
4148627 TAAT-TAA
1 TATTATAA
*
4148634 GA-TATAA
1 TATTATAA
4148641 TATTATAA
1 TATTATAA
4148649 TATTATAA
1 TATTATAA
4148657 TAT
1 TAT
4148660 ATATTTTAAC
Statistics
Matches: 47, Mismatches: 5, Indels: 8
0.78 0.08 0.13
Matches are distributed among these distances:
6 1 0.02
7 19 0.40
8 23 0.49
9 4 0.09
ACGTcount: A:0.52, C:0.00, G:0.02, T:0.47
Consensus pattern (8 bp):
TATTATAA
Found at i:4162319 original size:4 final size:4
Alignment explanation
Indices: 4162310--4162343 Score: 50
Period size: 4 Copynumber: 8.0 Consensus size: 4
4162300 AAGTTTTATT
4162310 TTTA TTTA TTTA TTTA TTTA TTTTA TTTA GTTTA
1 TTTA TTTA TTTA TTTA TTTA -TTTA TTTA -TTTA
4162344 AATTTTTATA
Statistics
Matches: 28, Mismatches: 0, Indels: 3
0.90 0.00 0.10
Matches are distributed among these distances:
4 20 0.71
5 8 0.29
ACGTcount: A:0.24, C:0.00, G:0.03, T:0.74
Consensus pattern (4 bp):
TTTA
Found at i:4162351 original size:22 final size:22
Alignment explanation
Indices: 4162293--4162352 Score: 61
Period size: 22 Copynumber: 2.7 Consensus size: 22
4162283 AAGTGGCCCA
*
4162293 AGTTGTAAAGTTTTATTTTTATTT
1 AGTT-TAAATTTTTA-TTTTATTT
*
4162317 A-TTT-ATTTATTTATTTTATTT
1 AGTTTAAATT-TTTATTTTATTT
4162338 AGTTTAAATTTTTAT
1 AGTTTAAATTTTTAT
4162353 ATTCAGTCCA
Statistics
Matches: 30, Mismatches: 3, Indels: 8
0.73 0.07 0.20
Matches are distributed among these distances:
21 11 0.37
22 13 0.43
23 5 0.17
24 1 0.03
ACGTcount: A:0.27, C:0.00, G:0.07, T:0.67
Consensus pattern (22 bp):
AGTTTAAATTTTTATTTTATTT
Found at i:4169497 original size:44 final size:44
Alignment explanation
Indices: 4169435--4169544 Score: 159
Period size: 44 Copynumber: 2.5 Consensus size: 44
4169425 CATAGTATTG
* * *
4169435 CAACATCGGTACAAAGTACCTGCTGA-ATATAAATGGCACATAGC
1 CAACATCGGTACATAGTACCTAC-GAGATATAAATGACACATAGC
4169479 CAACATCGGTACATAGTACCTACGAGATATAAATGACACATAGC
1 CAACATCGGTACATAGTACCTACGAGATATAAATGACACATAGC
* *
4169523 CAGCACCGGTACATAGTACCTA
1 CAACATCGGTACATAGTACCTA
4169545 TTACATATAA
Statistics
Matches: 60, Mismatches: 5, Indels: 2
0.90 0.07 0.03
Matches are distributed among these distances:
43 2 0.03
44 58 0.97
ACGTcount: A:0.38, C:0.25, G:0.17, T:0.20
Consensus pattern (44 bp):
CAACATCGGTACATAGTACCTACGAGATATAAATGACACATAGC
Found at i:4170581 original size:17 final size:17
Alignment explanation
Indices: 4170545--4170577 Score: 50
Period size: 17 Copynumber: 2.0 Consensus size: 17
4170535 TTTTTATGTT
*
4170545 TTATTTAACTTATTTTA
1 TTATTTAACTAATTTTA
4170562 TTATTTAAC-AATTTTA
1 TTATTTAACTAATTTTA
4170578 ATTAATAAAA
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
16 6 0.40
17 9 0.60
ACGTcount: A:0.33, C:0.06, G:0.00, T:0.61
Consensus pattern (17 bp):
TTATTTAACTAATTTTA
Found at i:4176518 original size:27 final size:27
Alignment explanation
Indices: 4176471--4176523 Score: 63
Period size: 27 Copynumber: 2.0 Consensus size: 27
4176461 ATTGTTATTC
*
4176471 TTGTGAATTAGTAACTAGCTTTATATG
1 TTGTGAATTAGTAACTAGCTTAATATG
* *
4176498 TTGTGAATTGGTATAGT-GCTTAATAT
1 TTGTGAATTAGTA-ACTAGCTTAATAT
4176524 ATGGTAAGTG
Statistics
Matches: 22, Mismatches: 3, Indels: 2
0.81 0.11 0.07
Matches are distributed among these distances:
27 20 0.91
28 2 0.09
ACGTcount: A:0.28, C:0.06, G:0.21, T:0.45
Consensus pattern (27 bp):
TTGTGAATTAGTAACTAGCTTAATATG
Found at i:4184267 original size:28 final size:28
Alignment explanation
Indices: 4184204--4184261 Score: 80
Period size: 28 Copynumber: 2.1 Consensus size: 28
4184194 AATTAAACTG
* *
4184204 ATAAAATGAATTAAACTAAAATGACCTA
1 ATAAAATTAATTAAACTAAAATAACCTA
* *
4184232 ATAAAATTAATTAACCTAAAATAACGTA
1 ATAAAATTAATTAAACTAAAATAACCTA
4184260 AT
1 AT
4184262 GGAATTTCCT
Statistics
Matches: 26, Mismatches: 4, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
28 26 1.00
ACGTcount: A:0.57, C:0.10, G:0.05, T:0.28
Consensus pattern (28 bp):
ATAAAATTAATTAAACTAAAATAACCTA
Found at i:4185285 original size:19 final size:19
Alignment explanation
Indices: 4185263--4185311 Score: 57
Period size: 18 Copynumber: 2.6 Consensus size: 19
4185253 CAAAGTTACT
4185263 AAAAATAACAAATATAA-AA
1 AAAAATAACAAAT-TAATAA
*
4185282 AAAAATAA-AAATTAATTA
1 AAAAATAACAAATTAATAA
*
4185300 AAAATTAACAAA
1 AAAAATAACAAA
4185312 CAATCGAACT
Statistics
Matches: 26, Mismatches: 2, Indels: 4
0.81 0.06 0.12
Matches are distributed among these distances:
17 3 0.12
18 12 0.46
19 11 0.42
ACGTcount: A:0.76, C:0.04, G:0.00, T:0.20
Consensus pattern (19 bp):
AAAAATAACAAATTAATAA
Found at i:4185302 original size:17 final size:19
Alignment explanation
Indices: 4185262--4185311 Score: 59
Period size: 19 Copynumber: 2.7 Consensus size: 19
4185252 ACAAAGTTAC
4185262 TAAAAATAACAAATATAAA
1 TAAAAATAACAAATATAAA
* *
4185281 AAAAAATAA-AAAT-TAAT
1 TAAAAATAACAAATATAAA
4185298 TAAAAATTAACAAA
1 TAAAAA-TAACAAA
4185312 CAATCGAACT
Statistics
Matches: 26, Mismatches: 3, Indels: 4
0.79 0.09 0.12
Matches are distributed among these distances:
17 8 0.31
18 7 0.27
19 11 0.42
ACGTcount: A:0.74, C:0.04, G:0.00, T:0.22
Consensus pattern (19 bp):
TAAAAATAACAAATATAAA
Found at i:4186222 original size:30 final size:30
Alignment explanation
Indices: 4186188--4186248 Score: 113
Period size: 30 Copynumber: 2.0 Consensus size: 30
4186178 AAAGAGACTG
*
4186188 CTCATTCATAATTAAATTGGAGTGTAGTTT
1 CTCATTCATAATTAAATTGGAGTGCAGTTT
4186218 CTCATTCATAATTAAATTGGAGTGCAGTTT
1 CTCATTCATAATTAAATTGGAGTGCAGTTT
4186248 C
1 C
4186249 GAAACAATCT
Statistics
Matches: 30, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
30 30 1.00
ACGTcount: A:0.30, C:0.13, G:0.16, T:0.41
Consensus pattern (30 bp):
CTCATTCATAATTAAATTGGAGTGCAGTTT
Found at i:4187503 original size:26 final size:27
Alignment explanation
Indices: 4187457--4187523 Score: 84
Period size: 26 Copynumber: 2.5 Consensus size: 27
4187447 GCCTCGCAAG
* *
4187457 TGAGGGTTTGCCAAGATTTAGGTGAAC
1 TGAGGGTTCGCCAAGATTTAGGCGAAC
4187484 T-AGGGGTTCGCCAAGA-TTAGGCGAAC
1 TGA-GGGTTCGCCAAGATTTAGGCGAAC
*
4187510 TGAGGGTTCACCAA
1 TGAGGGTTCGCCAA
4187524 AAGAGTATCT
Statistics
Matches: 35, Mismatches: 3, Indels: 5
0.81 0.07 0.12
Matches are distributed among these distances:
26 21 0.60
27 14 0.40
ACGTcount: A:0.27, C:0.16, G:0.33, T:0.24
Consensus pattern (27 bp):
TGAGGGTTCGCCAAGATTTAGGCGAAC
Found at i:4196135 original size:17 final size:17
Alignment explanation
Indices: 4196115--4196153 Score: 53
Period size: 17 Copynumber: 2.3 Consensus size: 17
4196105 CTCTTTTAGC
*
4196115 ATATTGTAATTG-ACGAA
1 ATATTATAATTGAAC-AA
4196132 ATATTATAATTGAACAA
1 ATATTATAATTGAACAA
4196149 ATATT
1 ATATT
4196154 TATATATATT
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
17 18 0.90
18 2 0.10
ACGTcount: A:0.46, C:0.05, G:0.10, T:0.38
Consensus pattern (17 bp):
ATATTATAATTGAACAA
Found at i:4208876 original size:17 final size:18
Alignment explanation
Indices: 4208842--4208887 Score: 64
Period size: 17 Copynumber: 2.8 Consensus size: 18
4208832 CCGTTATGTC
4208842 CGCGACCGCGA-C--AAA
1 CGCGACCGCGACCGAAAA
4208857 CGCGA-CGCGACCGAAAA
1 CGCGACCGCGACCGAAAA
4208874 CGCGACCGCGACCG
1 CGCGACCGCGACCG
4208888 CAATTTAAAT
Statistics
Matches: 27, Mismatches: 0, Indels: 5
0.84 0.00 0.16
Matches are distributed among these distances:
14 5 0.19
15 6 0.22
17 8 0.30
18 8 0.30
ACGTcount: A:0.28, C:0.41, G:0.30, T:0.00
Consensus pattern (18 bp):
CGCGACCGCGACCGAAAA
Found at i:4218017 original size:75 final size:75
Alignment explanation
Indices: 4217931--4218102 Score: 220
Period size: 75 Copynumber: 2.3 Consensus size: 75
4217921 GCGCCCAGCA
* * * * *
4217931 CTAGTCAGATAAACCGACGAAATAATTAGTGAGCCTAACTTTGGTTGGATAAACCAACAATATTT
1 CTAGTCGGATAAATCGACGAAATAATTAGTGAGCCCAACTCTAGTTGGATAAACCAACAATATTT
*
4217996 GCACCCAATG
66 GCACCCAACG
* * * * *
4218006 CTAGTCGGATAAATCAATGAAATAATTAGTGATCCCAGCTCTAGTTGGATAAACCAACGATATTT
1 CTAGTCGGATAAATCGACGAAATAATTAGTGAGCCCAACTCTAGTTGGATAAACCAACAATATTT
* *
4218071 GCACCTAGCG
66 GCACCCAACG
4218081 CTAGTCGGATAAATCGAC-AAAT
1 CTAGTCGGATAAATCGACGAAAT
4218103 GTGTGCCCAA
Statistics
Matches: 82, Mismatches: 15, Indels: 1
0.84 0.15 0.01
Matches are distributed among these distances:
74 4 0.05
75 78 0.95
ACGTcount: A:0.37, C:0.20, G:0.18, T:0.26
Consensus pattern (75 bp):
CTAGTCGGATAAATCGACGAAATAATTAGTGAGCCCAACTCTAGTTGGATAAACCAACAATATTT
GCACCCAACG
Found at i:4218092 original size:35 final size:35
Alignment explanation
Indices: 4217977--4218093 Score: 101
Period size: 35 Copynumber: 3.2 Consensus size: 35
4217967 AACTTTGGTT
* **
4217977 GGATAAACCAACAATATTTGCACCCAATGCTAGTC
1 GGATAAACCAACGATATTTGCACCCAGCGCTAGTC
* * * *
4218012 GGATAAATCAATGAAATAATTAGTG-ATCCCAGCTCTAGTT
1 GGATAAACCAACG--AT-ATT--TGCA-CCCAGCGCTAGTC
*
4218052 GGATAAACCAACGATATTTGCACCTAGCGCTAGTC
1 GGATAAACCAACGATATTTGCACCCAGCGCTAGTC
4218087 GGATAAA
1 GGATAAA
4218094 TCGACAAATG
Statistics
Matches: 63, Mismatches: 12, Indels: 14
0.71 0.13 0.16
Matches are distributed among these distances:
35 29 0.46
36 1 0.02
37 5 0.08
38 5 0.08
39 1 0.02
40 22 0.35
ACGTcount: A:0.37, C:0.21, G:0.18, T:0.25
Consensus pattern (35 bp):
GGATAAACCAACGATATTTGCACCCAGCGCTAGTC
Found at i:4220604 original size:25 final size:26
Alignment explanation
Indices: 4220576--4220635 Score: 88
Period size: 25 Copynumber: 2.4 Consensus size: 26
4220566 CATAGCTCTT
4220576 ATGAGCTTCCCA-ATACTCAGCTCGC
1 ATGAGCTTCCCAGATACTCAGCTCGC
* *
4220601 ATGAGCTT-CTAGATACTCTGCTCGC
1 ATGAGCTTCCCAGATACTCAGCTCGC
4220626 ATGAGCTTCC
1 ATGAGCTTCC
4220636 TGTTATTCAG
Statistics
Matches: 31, Mismatches: 2, Indels: 3
0.86 0.06 0.08
Matches are distributed among these distances:
24 2 0.06
25 28 0.90
26 1 0.03
ACGTcount: A:0.22, C:0.32, G:0.18, T:0.28
Consensus pattern (26 bp):
ATGAGCTTCCCAGATACTCAGCTCGC
Found at i:4221812 original size:21 final size:21
Alignment explanation
Indices: 4221786--4221825 Score: 62
Period size: 21 Copynumber: 1.9 Consensus size: 21
4221776 ATTATATGAA
*
4221786 ATGTCTAATTAGTTGATCTGT
1 ATGTCTAATTAATTGATCTGT
*
4221807 ATGTCTGATTAATTGATCT
1 ATGTCTAATTAATTGATCT
4221826 ATAAACTTTG
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
21 17 1.00
ACGTcount: A:0.25, C:0.10, G:0.17, T:0.47
Consensus pattern (21 bp):
ATGTCTAATTAATTGATCTGT
Found at i:4237273 original size:45 final size:45
Alignment explanation
Indices: 4237224--4237328 Score: 176
Period size: 45 Copynumber: 2.3 Consensus size: 45
4237214 TTCCATGACG
4237224 TCTTTCAGCCATGGTCTTAGTCC-TATTTATCATGATGCCATGGCT
1 TCTTTCAGCCATGGTCTTAG-CCTTATTTATCATGATGCCATGGCT
*
4237269 TCTTTCAGCCATGGTCTTAGCCTTGTTTATCATGATGCCATGGCT
1 TCTTTCAGCCATGGTCTTAGCCTTATTTATCATGATGCCATGGCT
*
4237314 TTTTTCAGCCATGGT
1 TCTTTCAGCCATGGT
4237329 TTTACTCATT
Statistics
Matches: 57, Mismatches: 2, Indels: 2
0.93 0.03 0.03
Matches are distributed among these distances:
44 2 0.04
45 55 0.96
ACGTcount: A:0.16, C:0.24, G:0.19, T:0.41
Consensus pattern (45 bp):
TCTTTCAGCCATGGTCTTAGCCTTATTTATCATGATGCCATGGCT
Found at i:4237345 original size:45 final size:43
Alignment explanation
Indices: 4237224--4237347 Score: 151
Period size: 45 Copynumber: 2.7 Consensus size: 43
4237214 TTCCATGACG
*
4237224 TCTTTCAGCCATGGTCTTAGTCCTATTTATCATGATGCCATGGCT
1 TCTTTCAGCCATGGTCTTACT-CT-TTTATCATGATGCCATGGCT
4237269 TCTTTCAGCCATGGTCTTAGC-CTTGTTTATCATGATGCCATGGCT
1 TCTTTCAGCCATGGTCTTA-CTC-T-TTTATCATGATGCCATGGCT
* *
4237314 TTTTTCAGCCATGGTTTTACTCATTTATATCATG
1 TCTTTCAGCCATGGTCTTACTC-TTT-TATCATG
4237348 GCGGTATAGC
Statistics
Matches: 70, Mismatches: 5, Indels: 8
0.84 0.06 0.10
Matches are distributed among these distances:
44 4 0.06
45 66 0.94
ACGTcount: A:0.18, C:0.23, G:0.17, T:0.43
Consensus pattern (43 bp):
TCTTTCAGCCATGGTCTTACTCTTTTATCATGATGCCATGGCT
Found at i:4240724 original size:39 final size:38
Alignment explanation
Indices: 4240675--4240771 Score: 131
Period size: 39 Copynumber: 2.5 Consensus size: 38
4240665 TAAATATAAT
** * *
4240675 AATTATAATTACCGTAATTATAATAATGTTTGATCGAAA
1 AATTATAATTACAATAATTATAATAATATTCGATCG-AA
* *
4240714 AATTACAATTACAATAATTATAATAATATTCGATCGTA
1 AATTATAATTACAATAATTATAATAATATTCGATCGAA
4240752 AATTATAATTACAATAATTA
1 AATTATAATTACAATAATTA
4240772 CAACAAGGAT
Statistics
Matches: 51, Mismatches: 7, Indels: 1
0.86 0.12 0.02
Matches are distributed among these distances:
38 20 0.39
39 31 0.61
ACGTcount: A:0.47, C:0.08, G:0.06, T:0.38
Consensus pattern (38 bp):
AATTATAATTACAATAATTATAATAATATTCGATCGAA
Found at i:4241894 original size:90 final size:90
Alignment explanation
Indices: 4241792--4241972 Score: 317
Period size: 90 Copynumber: 2.0 Consensus size: 90
4241782 GTAGAAAAGA
* * *
4241792 AACTGAAATAATAATGGCAATGCCTTATATTAAGAAACGGGGTAAAACAAGTATGTTATTACAAT
1 AACTGAAATAATAATCGCAATACCTTATATTAAGAAACGAGGTAAAACAAGTATGTTATTACAAT
4241857 CATCTCATGATTGGTCTTTGGGCAT
66 CATCTCATGATTGGTCTTTGGGCAT
*
4241882 AACTGAAATAATAATCGCAATACCTTATATTAAGAAATGAGGTAAAACAAGTATGTTATTACAAT
1 AACTGAAATAATAATCGCAATACCTTATATTAAGAAACGAGGTAAAACAAGTATGTTATTACAAT
*
4241947 CATCTTATGATTGGTCTTTGGGCAT
66 CATCTCATGATTGGTCTTTGGGCAT
4241972 A
1 A
4241973 CTCCAATAGT
Statistics
Matches: 86, Mismatches: 5, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
90 86 1.00
ACGTcount: A:0.38, C:0.13, G:0.17, T:0.32
Consensus pattern (90 bp):
AACTGAAATAATAATCGCAATACCTTATATTAAGAAACGAGGTAAAACAAGTATGTTATTACAAT
CATCTCATGATTGGTCTTTGGGCAT
Found at i:4245499 original size:21 final size:21
Alignment explanation
Indices: 4245474--4245517 Score: 88
Period size: 21 Copynumber: 2.1 Consensus size: 21
4245464 ATCTTCGAGG
4245474 ATATGCAATCTTAGATATGAT
1 ATATGCAATCTTAGATATGAT
4245495 ATATGCAATCTTAGATATGAT
1 ATATGCAATCTTAGATATGAT
4245516 AT
1 AT
4245518 GTAATCTTAG
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 23 1.00
ACGTcount: A:0.39, C:0.09, G:0.14, T:0.39
Consensus pattern (21 bp):
ATATGCAATCTTAGATATGAT
Found at i:4245523 original size:19 final size:19
Alignment explanation
Indices: 4245473--4245528 Score: 85
Period size: 21 Copynumber: 2.8 Consensus size: 19
4245463 AATCTTCGAG
4245473 GATATGCAATCTTAGATAT
1 GATATGCAATCTTAGATAT
4245492 GATATATGCAATCTTAGATAT
1 G--ATATGCAATCTTAGATAT
*
4245513 GATATGTAATCTTAGA
1 GATATGCAATCTTAGA
4245529 AGATATGATT
Statistics
Matches: 34, Mismatches: 1, Indels: 4
0.87 0.03 0.10
Matches are distributed among these distances:
19 15 0.44
21 19 0.56
ACGTcount: A:0.38, C:0.09, G:0.16, T:0.38
Consensus pattern (19 bp):
GATATGCAATCTTAGATAT
Found at i:4245535 original size:22 final size:23
Alignment explanation
Indices: 4245486--4245551 Score: 77
Period size: 23 Copynumber: 3.0 Consensus size: 23
4245476 ATGCAATCTT
*
4245486 AGATATGATATATGCAATCTT---
1 AGATATGAT-TATGTAATCTTAGA
4245507 AGATATGA-TATGTAATCTTAGA
1 AGATATGATTATGTAATCTTAGA
*
4245529 AGATATGATTTTGTAATCTTAGA
1 AGATATGATTATGTAATCTTAGA
4245552 GATTTAATTT
Statistics
Matches: 39, Mismatches: 2, Indels: 6
0.83 0.04 0.13
Matches are distributed among these distances:
19 10 0.26
21 8 0.21
22 8 0.21
23 13 0.33
ACGTcount: A:0.38, C:0.06, G:0.17, T:0.39
Consensus pattern (23 bp):
AGATATGATTATGTAATCTTAGA
Found at i:4245561 original size:22 final size:23
Alignment explanation
Indices: 4245517--4245561 Score: 65
Period size: 23 Copynumber: 2.0 Consensus size: 23
4245507 AGATATGATA
*
4245517 TGTAATCTTAGAAGATATGATTT
1 TGTAATCTTAGAAGATATAATTT
*
4245540 TGTAATCTTAG-AGATTTAATTT
1 TGTAATCTTAGAAGATATAATTT
4245562 GTAGATACTC
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
22 9 0.45
23 11 0.55
ACGTcount: A:0.33, C:0.04, G:0.16, T:0.47
Consensus pattern (23 bp):
TGTAATCTTAGAAGATATAATTT
Found at i:4245751 original size:19 final size:21
Alignment explanation
Indices: 4245727--4245765 Score: 55
Period size: 19 Copynumber: 2.0 Consensus size: 21
4245717 TGTTTTCTTT
*
4245727 TTTTTTTCTT-TTT-CGATTA
1 TTTTTTACTTATTTACGATTA
4245746 TTTTTTACTTATTTACGATT
1 TTTTTTACTTATTTACGATT
4245766 TTAAAAAAGG
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
19 9 0.53
20 3 0.18
21 5 0.29
ACGTcount: A:0.15, C:0.10, G:0.05, T:0.69
Consensus pattern (21 bp):
TTTTTTACTTATTTACGATTA
Found at i:4245988 original size:9 final size:9
Alignment explanation
Indices: 4245974--4246015 Score: 54
Period size: 9 Copynumber: 5.0 Consensus size: 9
4245964 TTTTTAGTCT
4245974 ATTTTATTA
1 ATTTTATTA
4245983 ATTTTATTA
1 ATTTTATTA
*
4245992 ATTTTGTT-
1 ATTTTATTA
4246000 A--TTATTA
1 ATTTTATTA
4246007 ATTTTATTA
1 ATTTTATTA
4246016 TTATATTATA
Statistics
Matches: 28, Mismatches: 2, Indels: 6
0.78 0.06 0.17
Matches are distributed among these distances:
6 4 0.14
7 1 0.04
8 1 0.04
9 22 0.79
ACGTcount: A:0.31, C:0.00, G:0.02, T:0.67
Consensus pattern (9 bp):
ATTTTATTA
Found at i:4246006 original size:15 final size:15
Alignment explanation
Indices: 4245986--4246039 Score: 63
Period size: 15 Copynumber: 3.4 Consensus size: 15
4245976 TTTATTAATT
4245986 TTATTAATTTTGTTA
1 TTATTAATTTTGTTA
*
4246001 TTATTAATTTTATTA
1 TTATTAATTTTGTTA
*
4246016 TTATATTATATATTGTTA
1 -T-TATTA-ATTTTGTTA
4246034 TTATTA
1 TTATTA
4246040 TACCTACATA
Statistics
Matches: 33, Mismatches: 3, Indels: 5
0.80 0.07 0.12
Matches are distributed among these distances:
15 14 0.42
16 6 0.18
17 6 0.18
18 7 0.21
ACGTcount: A:0.31, C:0.00, G:0.04, T:0.65
Consensus pattern (15 bp):
TTATTAATTTTGTTA
Found at i:4246014 original size:33 final size:33
Alignment explanation
Indices: 4245974--4246039 Score: 98
Period size: 33 Copynumber: 2.0 Consensus size: 33
4245964 TTTTTAGTCT
* *
4245974 ATTTTATTAATTTTATTA-ATTTTGTTATTATTA
1 ATTTTATT-ATTATATTATATATTGTTATTATTA
4246007 ATTTTATTATTATATTATATATTGTTATTATTA
1 ATTTTATTATTATATTATATATTGTTATTATTA
4246040 TACCTACATA
Statistics
Matches: 30, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
32 8 0.27
33 22 0.73
ACGTcount: A:0.32, C:0.00, G:0.03, T:0.65
Consensus pattern (33 bp):
ATTTTATTATTATATTATATATTGTTATTATTA
Found at i:4246029 original size:24 final size:24
Alignment explanation
Indices: 4245973--4246029 Score: 73
Period size: 24 Copynumber: 2.4 Consensus size: 24
4245963 GTTTTTAGTC
*
4245973 TATT-TTATTAATTTTATTAATTT
1 TATTATTATTAATTTTATTAATTA
*
4245996 TGTTATTATTAATTTTATT-ATTA
1 TATTATTATTAATTTTATTAATTA
4246019 TATTATATATT
1 TATTAT-TATT
4246030 GTTATTATTA
Statistics
Matches: 29, Mismatches: 3, Indels: 3
0.83 0.09 0.09
Matches are distributed among these distances:
23 11 0.38
24 18 0.62
ACGTcount: A:0.32, C:0.00, G:0.02, T:0.67
Consensus pattern (24 bp):
TATTATTATTAATTTTATTAATTA
Found at i:4246287 original size:17 final size:16
Alignment explanation
Indices: 4246265--4246296 Score: 55
Period size: 17 Copynumber: 1.9 Consensus size: 16
4246255 GATTTTTAGG
4246265 ATGTAATTATTATTTTT
1 ATGTAATTATT-TTTTT
4246282 ATGTAATTATTTTTT
1 ATGTAATTATTTTTT
4246297 AATTATATAT
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
16 4 0.27
17 11 0.73
ACGTcount: A:0.28, C:0.00, G:0.06, T:0.66
Consensus pattern (16 bp):
ATGTAATTATTTTTTT
Found at i:4246378 original size:10 final size:10
Alignment explanation
Indices: 4246363--4246400 Score: 51
Period size: 10 Copynumber: 3.9 Consensus size: 10
4246353 ATATTTTTTG
4246363 TATATTTATA
1 TATATTTATA
*
4246373 TATATTCATA
1 TATATTTATA
4246383 TATATTTAT-
1 TATATTTATA
*
4246392 TATTTTTAT
1 TATATTTAT
4246401 GTAGATATTA
Statistics
Matches: 25, Mismatches: 3, Indels: 1
0.86 0.10 0.03
Matches are distributed among these distances:
9 8 0.32
10 17 0.68
ACGTcount: A:0.34, C:0.03, G:0.00, T:0.63
Consensus pattern (10 bp):
TATATTTATA
Found at i:4246833 original size:19 final size:20
Alignment explanation
Indices: 4246792--4246833 Score: 50
Period size: 19 Copynumber: 2.1 Consensus size: 20
4246782 ATTTCCATGC
* *
4246792 CATTGTAATATTTATTATTG
1 CATTGTAATATTTAATATAG
*
4246812 CATTGT-ATATTTAATGTAG
1 CATTGTAATATTTAATATAG
4246831 CAT
1 CAT
4246834 CACATCATTT
Statistics
Matches: 19, Mismatches: 3, Indels: 1
0.83 0.13 0.04
Matches are distributed among these distances:
19 13 0.68
20 6 0.32
ACGTcount: A:0.31, C:0.07, G:0.12, T:0.50
Consensus pattern (20 bp):
CATTGTAATATTTAATATAG
Found at i:4256232 original size:40 final size:39
Alignment explanation
Indices: 4256155--4256236 Score: 103
Period size: 40 Copynumber: 2.1 Consensus size: 39
4256145 CGCACCAGAA
* *
4256155 AGAAGCTCATAGAGCTAATACAACTGAAACACGCCAAAC
1 AGAAGCTCATAGAGCTAATACAACCGAAACACCCCAAAC
* *
4256194 AGAAGCTCATGAGAGCTGATCCAACCGCAAA-ACCCCAAAC
1 AGAAGCTCAT-AGAGCTAATACAACCG-AAACACCCCAAAC
4256234 AGA
1 AGA
4256237 GTATAACACG
Statistics
Matches: 37, Mismatches: 4, Indels: 3
0.84 0.09 0.07
Matches are distributed among these distances:
39 10 0.27
40 24 0.65
41 3 0.08
ACGTcount: A:0.44, C:0.28, G:0.17, T:0.11
Consensus pattern (39 bp):
AGAAGCTCATAGAGCTAATACAACCGAAACACCCCAAAC
Found at i:4257327 original size:17 final size:18
Alignment explanation
Indices: 4257295--4257328 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
4257285 TAAGGAAATC
4257295 CAATTATAATTCTTTAAT
1 CAATTATAATTCTTTAAT
*
4257313 CAATTATCA-TCTTTAA
1 CAATTATAATTCTTTAA
4257329 ATTAATAGTG
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 7 0.47
18 8 0.53
ACGTcount: A:0.38, C:0.15, G:0.00, T:0.47
Consensus pattern (18 bp):
CAATTATAATTCTTTAAT
Found at i:4258141 original size:33 final size:33
Alignment explanation
Indices: 4258079--4258245 Score: 129
Period size: 33 Copynumber: 5.1 Consensus size: 33
4258069 GACTTACCTT
* * * **
4258079 TGTTCTATGTTTATTGTTCTAGCGGACTTTCTC
1 TGTTCTATGTTTATTGTCCCAACAAACTTTCTC
* * *
4258112 TGGTCTGTGTTTATTGTCCCAACAAACTTTATC
1 TGTTCTATGTTTATTGTCCCAACAAACTTTCTC
* **
4258145 TGTTCTATGTTTAGTGTCCCAACCGAC-TTCTC
1 TGTTCTATGTTTATTGTCCCAACAAACTTTCTC
* * * * * * *
4258177 TGTTTTGTGTTTACTATTCCAACAAACTATCTT
1 TGTTCTATGTTTATTGTCCCAACAAACTTTCTC
* ** *
4258210 TGTTTTATGTTTATTGTCTTAACGAACTTTCTC
1 TGTTCTATGTTTATTGTCCCAACAAACTTTCTC
4258243 TGT
1 TGT
4258246 GGATGCTATG
Statistics
Matches: 101, Mismatches: 32, Indels: 2
0.75 0.24 0.01
Matches are distributed among these distances:
32 24 0.24
33 77 0.76
ACGTcount: A:0.18, C:0.20, G:0.14, T:0.48
Consensus pattern (33 bp):
TGTTCTATGTTTATTGTCCCAACAAACTTTCTC
Found at i:4258199 original size:65 final size:66
Alignment explanation
Indices: 4258079--4258244 Score: 165
Period size: 65 Copynumber: 2.5 Consensus size: 66
4258069 GACTTACCTT
* * * * * * *
4258079 TGTTCTATGTTTATTGTTCTAGCGGACTTTCTCTGGTCTGTGTTTATTGTCCCAACAAACTTTAT
1 TGTTCTATGTTTATTGTCCCAACCGACTTTCTCTGGTCTGTGTTTACTATCCCAACAAACTATAT
4258144 C
66 C
* * * * *
4258145 TGTTCTATGTTTAGTGTCCCAACCGAC-TTCTCTGTTTTGTGTTTACTATTCCAACAAACTATCT
1 TGTTCTATGTTTATTGTCCCAACCGACTTTCTCTGGTCTGTGTTTACTATCCCAACAAACTATAT
*
4258209 T
66 C
* **
4258210 TGTTTTATGTTTATTGTCTTAA-CGAACTTTCTCTG
1 TGTTCTATGTTTATTGTCCCAACCG-ACTTTCTCTG
4258245 TGGATGCTAT
Statistics
Matches: 81, Mismatches: 17, Indels: 4
0.79 0.17 0.04
Matches are distributed among these distances:
64 2 0.02
65 50 0.62
66 29 0.36
ACGTcount: A:0.18, C:0.20, G:0.14, T:0.48
Consensus pattern (66 bp):
TGTTCTATGTTTATTGTCCCAACCGACTTTCTCTGGTCTGTGTTTACTATCCCAACAAACTATAT
C
Found at i:4263494 original size:15 final size:15
Alignment explanation
Indices: 4263474--4263581 Score: 87
Period size: 15 Copynumber: 7.2 Consensus size: 15
4263464 TTTATGGAAA
4263474 ATCAAAGATATGGGT
1 ATCAAAGATATGGGT
* **
4263489 ATCAAATA-ATGGAA
1 ATCAAAGATATGGGT
4263503 AGTCAAAGATATGGGT
1 A-TCAAAGATATGGGT
* **
4263519 ATCAAATAT-TGGAA
1 ATCAAAGATATGGGT
4263533 AGTCAAAGATATGGGT
1 A-TCAAAGATATGGGT
* **
4263549 ATCAAATAT-TGGAA
1 ATCAAAGATATGGGT
4263563 AGTCAAAGATATGGGT
1 A-TCAAAGATATGGGT
4263579 ATC
1 ATC
4263582 GAGATATTGG
Statistics
Matches: 69, Mismatches: 18, Indels: 12
0.70 0.18 0.12
Matches are distributed among these distances:
14 13 0.19
15 43 0.62
16 13 0.19
ACGTcount: A:0.44, C:0.07, G:0.23, T:0.26
Consensus pattern (15 bp):
ATCAAAGATATGGGT
Found at i:4263503 original size:30 final size:30
Alignment explanation
Indices: 4263467--4263581 Score: 203
Period size: 30 Copynumber: 3.8 Consensus size: 30
4263457 ATCCATATTT
*
4263467 ATGGAAAATCAAAGATATGGGTATCAAATA
1 ATGGAAAGTCAAAGATATGGGTATCAAATA
4263497 ATGGAAAGTCAAAGATATGGGTATCAAATA
1 ATGGAAAGTCAAAGATATGGGTATCAAATA
*
4263527 TTGGAAAGTCAAAGATATGGGTATCAAATA
1 ATGGAAAGTCAAAGATATGGGTATCAAATA
*
4263557 TTGGAAAGTCAAAGATATGGGTATC
1 ATGGAAAGTCAAAGATATGGGTATC
4263582 GAGATATTGG
Statistics
Matches: 83, Mismatches: 2, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
30 83 1.00
ACGTcount: A:0.44, C:0.07, G:0.23, T:0.25
Consensus pattern (30 bp):
ATGGAAAGTCAAAGATATGGGTATCAAATA
Found at i:4264256 original size:30 final size:30
Alignment explanation
Indices: 4264212--4264304 Score: 159
Period size: 30 Copynumber: 3.1 Consensus size: 30
4264202 TTTATTATGT
*
4264212 CAATATCTCGATACCCATATCTTTGACTTTC
1 CAATAT-TTGATACCCATATCTTTGACTTTC
4264243 CAATATTTGATACCCATATCTTTGACTTTC
1 CAATATTTGATACCCATATCTTTGACTTTC
*
4264273 CAATATTTGATACCCATATCTTTGATTTTC
1 CAATATTTGATACCCATATCTTTGACTTTC
4264303 CA
1 CA
4264305 TAAATATGGA
Statistics
Matches: 60, Mismatches: 2, Indels: 1
0.95 0.03 0.02
Matches are distributed among these distances:
30 54 0.90
31 6 0.10
ACGTcount: A:0.27, C:0.25, G:0.06, T:0.42
Consensus pattern (30 bp):
CAATATTTGATACCCATATCTTTGACTTTC
Found at i:4264266 original size:15 final size:15
Alignment explanation
Indices: 4264221--4264298 Score: 70
Period size: 15 Copynumber: 5.2 Consensus size: 15
4264211 TCAATATCTC
4264221 GATACCCATATCTTT
1 GATACCCATATCTTT
** *
4264236 GACTTTCCA-ATATTT
1 GA-TACCCATATCTTT
4264251 GATACCCATATCTTT
1 GATACCCATATCTTT
** *
4264266 GACTTTCCA-ATATTT
1 GA-TACCCATATCTTT
4264281 GATACCCATATCTTT
1 GATACCCATATCTTT
4264296 GAT
1 GAT
4264299 TTTCCATAAA
Statistics
Matches: 47, Mismatches: 12, Indels: 8
0.70 0.18 0.12
Matches are distributed among these distances:
14 8 0.17
15 31 0.66
16 8 0.17
ACGTcount: A:0.27, C:0.23, G:0.08, T:0.42
Consensus pattern (15 bp):
GATACCCATATCTTT
Found at i:4266119 original size:137 final size:137
Alignment explanation
Indices: 4265922--4266336 Score: 749
Period size: 137 Copynumber: 3.0 Consensus size: 137
4265912 GTTTCAAATT
4265922 CACTCATTCACATAACACTATAACAATTTATTATGTAGGCACGGTACAAAACTCCATCACTCCAA
1 CACTCATTCACATAACACTATAACAATTTATTATGTAGGCACGGTACAAAACTCCATCACTCCAA
4265987 TTACTCTTTTGGAACTCATCACATTTCAATCACACATTCATATTTGCTTGCAATTTCTCATATCC
66 TTACTCTTTTGGAACTCATCACATTTCAATCACACATTCATATTTGCTTGCAATTTCTCATATCC
4266052 CGTTGAA
131 CGTTGAA
* * *
4266059 CACTCATTCACATAACACTATAACAATTTATTATGTCGGCACGGTCCAAAACCCCATCACTCCAA
1 CACTCATTCACATAACACTATAACAATTTATTATGTAGGCACGGTACAAAACTCCATCACTCCAA
4266124 TTACTCTTTTGGAACTCATCACATTTCAATCACACATTCATATTTGCTTGCAATTTCTCATATCC
66 TTACTCTTTTGGAACTCATCACATTTCAATCACACATTCATATTTGCTTGCAATTTCTCATATCC
4266189 CGTTGAA
131 CGTTGAA
*
4266196 CACTCATTCACATAACACTATACCAATTTATTATGTAGGCACGGTACAAAACTCCATCACTCCAA
1 CACTCATTCACATAACACTATAACAATTTATTATGTAGGCACGGTACAAAACTCCATCACTCCAA
* * *
4266261 TTATTATTTTTTTGAACTCATCACATTTCAATCACACATTCATATTTGCTTGCAATTTCTCATAT
66 TTA--CTCTTTTGGAACTCATCACATTTCAATCACACATTCATATTTGCTTGCAATTTCTCATAT
4266326 CCCGTTGAA
129 CCCGTTGAA
4266335 CA
1 CA
4266337 TGTTGGTATA
Statistics
Matches: 266, Mismatches: 10, Indels: 2
0.96 0.04 0.01
Matches are distributed among these distances:
137 198 0.74
139 68 0.26
ACGTcount: A:0.32, C:0.27, G:0.08, T:0.34
Consensus pattern (137 bp):
CACTCATTCACATAACACTATAACAATTTATTATGTAGGCACGGTACAAAACTCCATCACTCCAA
TTACTCTTTTGGAACTCATCACATTTCAATCACACATTCATATTTGCTTGCAATTTCTCATATCC
CGTTGAA
Found at i:4266618 original size:14 final size:14
Alignment explanation
Indices: 4266599--4266645 Score: 80
Period size: 14 Copynumber: 3.5 Consensus size: 14
4266589 GCCGGTTCGA
4266599 TACACATAGTAGCC
1 TACACATAGTAGCC
4266613 TACACATAGTAGCC
1 TACACATAGTAGCC
4266627 TACACATAGTA--C
1 TACACATAGTAGCC
4266639 TACACAT
1 TACACAT
4266646 GTGACCATCA
Statistics
Matches: 33, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
12 8 0.24
14 25 0.76
ACGTcount: A:0.38, C:0.28, G:0.11, T:0.23
Consensus pattern (14 bp):
TACACATAGTAGCC
Found at i:4269092 original size:23 final size:22
Alignment explanation
Indices: 4269049--4269106 Score: 64
Period size: 22 Copynumber: 2.6 Consensus size: 22
4269039 AAAGGGTATC
* *
4269049 TACAAATTAAATC-TCTAAGAT
1 TACAAATCATATCTTCTAAGAT
4269070 TACAAAATCATATCTTCTAAGAT
1 TAC-AAATCATATCTTCTAAGAT
* *
4269093 TGCATATCATATCT
1 TACAAATCATATCT
4269107 AAGATTGCAT
Statistics
Matches: 31, Mismatches: 4, Indels: 3
0.82 0.11 0.08
Matches are distributed among these distances:
21 3 0.10
22 18 0.58
23 10 0.32
ACGTcount: A:0.41, C:0.17, G:0.05, T:0.36
Consensus pattern (22 bp):
TACAAATCATATCTTCTAAGAT
Found at i:4270760 original size:15 final size:15
Alignment explanation
Indices: 4270742--4270799 Score: 50
Period size: 15 Copynumber: 3.9 Consensus size: 15
4270732 TCAATTTAAA
4270742 TTTATAATAATTTAT
1 TTTATAATAATTTAT
4270757 TTTA-AA-AATATT-T
1 TTTATAATAAT-TTAT
* * *
4270770 TTGATAATTATTAAT
1 TTTATAATAATTTAT
4270785 TTTATAATAGATTTA
1 TTTATAATA-ATTTA
4270800 ATCGATTAAG
Statistics
Matches: 32, Mismatches: 6, Indels: 9
0.68 0.13 0.19
Matches are distributed among these distances:
13 7 0.22
14 7 0.22
15 14 0.44
16 4 0.12
ACGTcount: A:0.41, C:0.00, G:0.03, T:0.55
Consensus pattern (15 bp):
TTTATAATAATTTAT
Found at i:4282380 original size:30 final size:30
Alignment explanation
Indices: 4282325--4282381 Score: 78
Period size: 30 Copynumber: 1.9 Consensus size: 30
4282315 AATGAGCATC
*
4282325 ACACATGGCCTAGACACACGGGTGTGTGTG
1 ACACATGGCCTAGACACACGAGTGTGTGTG
* * *
4282355 ACACATGGCCTGGAGACATGAGTGTGT
1 ACACATGGCCTAGACACACGAGTGTGT
4282382 TTTCAGCCAT
Statistics
Matches: 23, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
30 23 1.00
ACGTcount: A:0.25, C:0.21, G:0.33, T:0.21
Consensus pattern (30 bp):
ACACATGGCCTAGACACACGAGTGTGTGTG
Found at i:4283421 original size:6 final size:6
Alignment explanation
Indices: 4283407--4283460 Score: 56
Period size: 6 Copynumber: 8.7 Consensus size: 6
4283397 TCTTATTCTA
* *
4283407 AAAAGAG AAAAAG AAAAAG AAAGAA- AAAAAT AAAAAG AAAGAG AAAAGAG
1 AAAA-AG AAAAAG AAAAAG AAA-AAG AAAAAG AAAAAG AAAAAG AAAA-AG
4283457 AAAA
1 AAAA
4283461 TTAAAAAAAA
Statistics
Matches: 41, Mismatches: 3, Indels: 6
0.82 0.06 0.12
Matches are distributed among these distances:
5 2 0.05
6 27 0.66
7 12 0.29
ACGTcount: A:0.80, C:0.00, G:0.19, T:0.02
Consensus pattern (6 bp):
AAAAAG
Found at i:4283435 original size:18 final size:18
Alignment explanation
Indices: 4283408--4283460 Score: 70
Period size: 18 Copynumber: 2.9 Consensus size: 18
4283398 CTTATTCTAA
*
4283408 AAAGAGAAAAAGAAAAAG
1 AAAGAAAAAAAGAAAAAG
*
4283426 AAAGAAAAAAATAAAAAG
1 AAAGAAAAAAAGAAAAAG
*
4283444 AAAGAGAAAAGAGAAAA
1 AAAGA-AAAAAAGAAAA
4283461 TTAAAAAAAA
Statistics
Matches: 30, Mismatches: 4, Indels: 1
0.86 0.11 0.03
Matches are distributed among these distances:
18 21 0.70
19 9 0.30
ACGTcount: A:0.79, C:0.00, G:0.19, T:0.02
Consensus pattern (18 bp):
AAAGAAAAAAAGAAAAAG
Found at i:4283441 original size:24 final size:25
Alignment explanation
Indices: 4283414--4283467 Score: 74
Period size: 25 Copynumber: 2.2 Consensus size: 25
4283404 CTAAAAAGAG
4283414 AAAAAGAAAAAG-AAAGAAAAAAAT
1 AAAAAGAAAAAGAAAAGAAAAAAAT
* * *
4283438 AAAAAGAAAGAGAAAAGAGAAAATT
1 AAAAAGAAAAAGAAAAGAAAAAAAT
4283463 AAAAA
1 AAAAA
4283468 AAAGTTTATT
Statistics
Matches: 26, Mismatches: 3, Indels: 1
0.87 0.10 0.03
Matches are distributed among these distances:
24 11 0.42
25 15 0.58
ACGTcount: A:0.80, C:0.00, G:0.15, T:0.06
Consensus pattern (25 bp):
AAAAAGAAAAAGAAAAGAAAAAAAT
Found at i:4284505 original size:17 final size:17
Alignment explanation
Indices: 4284483--4284515 Score: 57
Period size: 17 Copynumber: 1.9 Consensus size: 17
4284473 TAAATGAAAA
4284483 AAATGCTAGGGCAATTG
1 AAATGCTAGGGCAATTG
*
4284500 AAATGCTATGGCAATT
1 AAATGCTAGGGCAATT
4284516 CTCAAAGAAC
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
17 15 1.00
ACGTcount: A:0.36, C:0.12, G:0.24, T:0.27
Consensus pattern (17 bp):
AAATGCTAGGGCAATTG
Found at i:4288061 original size:44 final size:45
Alignment explanation
Indices: 4287991--4288081 Score: 157
Period size: 44 Copynumber: 2.0 Consensus size: 45
4287981 TAAATTTGTC
* *
4287991 AAAACTTGGTTGAGTCCTTTAGTTGTCATTATCTTGACAAATTGA
1 AAAACTTGGTTGAGTCCTTCAATTGTCATTATCTTGACAAATTGA
4288036 AAAACTTGG-TGAGTCCTTCAATTGTCATTATCTTGACAAATTGA
1 AAAACTTGGTTGAGTCCTTCAATTGTCATTATCTTGACAAATTGA
4288080 AA
1 AA
4288082 GTGTTCATCA
Statistics
Matches: 44, Mismatches: 2, Indels: 1
0.94 0.04 0.02
Matches are distributed among these distances:
44 35 0.80
45 9 0.20
ACGTcount: A:0.32, C:0.14, G:0.16, T:0.37
Consensus pattern (45 bp):
AAAACTTGGTTGAGTCCTTCAATTGTCATTATCTTGACAAATTGA
Done.