Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: A11
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: 114316535
ACGTcount: A:0.31, C:0.16, G:0.16, T:0.31
Warning! 4920000 characters in sequence are not A, C, G, or T
File 347 of 356
Found at i:111047743 original size:18 final size:19
Alignment explanation
Indices: 111047720--111047774 Score: 58
Period size: 18 Copynumber: 2.8 Consensus size: 19
111047710 CAGCTCTGAT
111047720 GAGCTTCAGTTAGCCTT-C
1 GAGCTTCAGTTAGCCTTAC
* *
111047738 GAGCTTCCGTTTAGCACTTAT
1 GAGCTTCAG-TTAGC-CTTAC
*
111047759 GTGCTTCAGTTAGCCT
1 GAGCTTCAGTTAGCCT
111047775 CTGGGCTTCC
Statistics
Matches: 30, Mismatches: 4, Indels: 5
0.77 0.10 0.13
Matches are distributed among these distances:
18 8 0.27
19 7 0.23
20 8 0.27
21 7 0.23
ACGTcount: A:0.16, C:0.25, G:0.22, T:0.36
Consensus pattern (19 bp):
GAGCTTCAGTTAGCCTTAC
Found at i:111047804 original size:38 final size:39
Alignment explanation
Indices: 111047722--111047805 Score: 136
Period size: 39 Copynumber: 2.2 Consensus size: 39
111047712 GCTCTGATGA
111047722 GCTTCAGTTAGCCTTCGAGCTTCCGTTTAGCACTTATGT
1 GCTTCAGTTAGCCTTCGAGCTTCCGTTTAGCACTTATGT
*
111047761 GCTTCAGTTAGCC-TCTGGGCTTCCGTTTAG-ACTTATGT
1 GCTTCAGTTAGCCTTC-GAGCTTCCGTTTAGCACTTATGT
111047799 GCTTCAG
1 GCTTCAG
111047806 CTAGATTTCG
Statistics
Matches: 43, Mismatches: 1, Indels: 3
0.91 0.02 0.06
Matches are distributed among these distances:
38 17 0.40
39 26 0.60
ACGTcount: A:0.14, C:0.25, G:0.23, T:0.38
Consensus pattern (39 bp):
GCTTCAGTTAGCCTTCGAGCTTCCGTTTAGCACTTATGT
Found at i:111047819 original size:38 final size:38
Alignment explanation
Indices: 111047722--111047821 Score: 121
Period size: 38 Copynumber: 2.6 Consensus size: 38
111047712 GCTCTGATGA
* *
111047722 GCTTCAGTTAGCCTTCGAGCTTCCGTTTAGCACTTATGT
1 GCTTCAGCTAG-CTTCGGGCTTCCGTTTAGCACTTATGT
* *
111047761 GCTTCAGTTAGCCTCTGGGCTTCCGTTTAG-ACTTATGT
1 GCTTCAGCTAGCTTC-GGGCTTCCGTTTAGCACTTATGT
*
111047799 GCTTCAGCTAGATTTCGGGCTTC
1 GCTTCAGCTAG-CTTCGGGCTTC
111047822 AGATCACGAT
Statistics
Matches: 54, Mismatches: 5, Indels: 5
0.84 0.08 0.08
Matches are distributed among these distances:
38 28 0.52
39 26 0.48
ACGTcount: A:0.14, C:0.25, G:0.23, T:0.38
Consensus pattern (38 bp):
GCTTCAGCTAGCTTCGGGCTTCCGTTTAGCACTTATGT
Found at i:111049125 original size:12 final size:12
Alignment explanation
Indices: 111049108--111049133 Score: 52
Period size: 12 Copynumber: 2.2 Consensus size: 12
111049098 TATTTGAGTC
111049108 AACTCAAATAAG
1 AACTCAAATAAG
111049120 AACTCAAATAAG
1 AACTCAAATAAG
111049132 AA
1 AA
111049134 ATTTTGGATT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 14 1.00
ACGTcount: A:0.62, C:0.15, G:0.08, T:0.15
Consensus pattern (12 bp):
AACTCAAATAAG
Found at i:111049287 original size:19 final size:19
Alignment explanation
Indices: 111049263--111049312 Score: 77
Period size: 18 Copynumber: 2.7 Consensus size: 19
111049253 TCTCTCTTAA
111049263 CAAAAATTACAAAAAAAAT
1 CAAAAATTACAAAAAAAAT
111049282 CAAAAATTA-AAAAAAAAT
1 CAAAAATTACAAAAAAAAT
*
111049300 TAAAAATT-CAAAA
1 CAAAAATTACAAAA
111049313 TATTTATAAA
Statistics
Matches: 29, Mismatches: 1, Indels: 3
0.88 0.03 0.09
Matches are distributed among these distances:
18 20 0.69
19 9 0.31
ACGTcount: A:0.74, C:0.08, G:0.00, T:0.18
Consensus pattern (19 bp):
CAAAAATTACAAAAAAAAT
Found at i:111050876 original size:18 final size:18
Alignment explanation
Indices: 111050842--111050876 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
111050832 TTTATAATTC
*
111050842 TATATATTATGTTATTTT
1 TATATATTATGTAATTTT
*
111050860 TATATATTTTGTAATTT
1 TATATATTATGTAATTT
111050877 AGAACACGAT
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:0.29, C:0.00, G:0.06, T:0.66
Consensus pattern (18 bp):
TATATATTATGTAATTTT
Found at i:111052688 original size:4 final size:4
Alignment explanation
Indices: 111052675--111052739 Score: 78
Period size: 4 Copynumber: 16.0 Consensus size: 4
111052665 AACAAACAAC
111052675 CACT CAACT CACT CACT CACT CACT CACT CACT CACT CACT C-CTT CACT
1 CACT C-ACT CACT CACT CACT CACT CACT CACT CACT CACT CAC-T CACT
* * *
111052724 CGCT CGCT CGCT CACT
1 CACT CACT CACT CACT
111052740 TCCATTGATA
Statistics
Matches: 56, Mismatches: 2, Indels: 6
0.88 0.03 0.09
Matches are distributed among these distances:
3 1 0.02
4 50 0.89
5 5 0.09
ACGTcount: A:0.20, C:0.49, G:0.05, T:0.26
Consensus pattern (4 bp):
CACT
Found at i:111053645 original size:170 final size:174
Alignment explanation
Indices: 111053431--111053763 Score: 478
Period size: 176 Copynumber: 1.9 Consensus size: 174
111053421 CATCATCAAC
*
111053431 ATCATCATCTTTTTGTTGGATTTCTTTTGGTAGCTTTTGGAAATTAAGTTCTGTTGAAATCTGC-
1 ATCATCATCTTTTTGTTGGATTTCTTTTGGTAGCTTTCGGAAATTAAGTTCTGTTGAAATCTGCA
* * *
111053495 A-T-TGC-T-CTCTGTTAATATTTGAATACCTTGTATATTAGATCGCAAATATGTGGATATGTTT
66 ATTCTGCATCCTCTGTTAA-ATTTGAATACCTTGGATATTAGATCGCAAATATCTGGATATATTT
*
111053556 AGTATTTCGATCTGAAGCATCGCATATTCACTCGATGTTTTCTTT
130 AGTATTTAGATCTGAAGCATCGCATATTCACTCGATGTTTTCTTT
* *
111053601 ATCATCATCTTTTTGTTGGATTTCTTTTGGTGGCTTTCGGAAATTAAGTTTTGTTGAAATCTGCA
1 ATCATCATCTTTTTGTTGGATTTCTTTTGGTAGCTTTCGGAAATTAAGTTCTGTTGAAATCTGCA
* * * *
111053666 ATTCTTCATTGCCTCTGTTAAATTTGAATTCCTTGGATATTAGATCGCAAATCTCTGTATATATT
66 ATTCTGCA-T-CCTCTGTTAAATTTGAATACCTTGGATATTAGATCGCAAATATCTGGATATATT
* * *
111053731 TAGTATTTAGATCTGAATCATTGCATTTTCACT
129 TAGTATTTAGATCTGAAGCATCGCATATTCACT
111053764 TTACTTTTTT
Statistics
Matches: 142, Mismatches: 14, Indels: 8
0.87 0.09 0.05
Matches are distributed among these distances:
170 61 0.43
171 1 0.01
172 1 0.01
173 2 0.01
175 1 0.01
176 67 0.47
177 9 0.06
ACGTcount: A:0.24, C:0.14, G:0.16, T:0.46
Consensus pattern (174 bp):
ATCATCATCTTTTTGTTGGATTTCTTTTGGTAGCTTTCGGAAATTAAGTTCTGTTGAAATCTGCA
ATTCTGCATCCTCTGTTAAATTTGAATACCTTGGATATTAGATCGCAAATATCTGGATATATTTA
GTATTTAGATCTGAAGCATCGCATATTCACTCGATGTTTTCTTT
Found at i:111056277 original size:18 final size:20
Alignment explanation
Indices: 111056240--111056279 Score: 57
Period size: 21 Copynumber: 2.0 Consensus size: 20
111056230 TAACTTCAAG
111056240 TTATTTTGAATTACTTTTAAT
1 TTATTTTGAA-TACTTTTAAT
111056261 TTATTTTGAA-A-TTTTAAT
1 TTATTTTGAATACTTTTAAT
111056279 T
1 T
111056280 GTTTTTAATT
Statistics
Matches: 19, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
18 8 0.42
19 1 0.05
21 10 0.53
ACGTcount: A:0.30, C:0.03, G:0.05, T:0.62
Consensus pattern (20 bp):
TTATTTTGAATACTTTTAAT
Found at i:111056304 original size:28 final size:29
Alignment explanation
Indices: 111056254--111056310 Score: 75
Period size: 28 Copynumber: 2.0 Consensus size: 29
111056244 TTTGAATTAC
111056254 TTTTAATTTATTTTGAAATTTTA-ATTGT
1 TTTTAATTTATTTTGAAATTTTATATTGT
111056282 TTTTAATTTA-TTT-AAATAATTTATATTGT
1 TTTTAATTTATTTTGAAAT--TTTATATTGT
111056311 AATTTAAATG
Statistics
Matches: 26, Mismatches: 0, Indels: 5
0.84 0.00 0.16
Matches are distributed among these distances:
26 4 0.15
27 3 0.12
28 14 0.54
29 5 0.19
ACGTcount: A:0.32, C:0.00, G:0.05, T:0.63
Consensus pattern (29 bp):
TTTTAATTTATTTTGAAATTTTATATTGT
Found at i:111056871 original size:28 final size:26
Alignment explanation
Indices: 111056830--111056897 Score: 73
Period size: 28 Copynumber: 2.5 Consensus size: 26
111056820 AAATTCAAAA
* *
111056830 AAAAATATAAAAAATTATTTTAAAAATT
1 AAAAATAT-TAAAATTATTAT-AAAATT
*
111056858 AAAAATCATTAAAATTATTATAAAGTT
1 AAAAAT-ATTAAAATTATTATAAAATT
*
111056885 ATAAATATTAAAA
1 AAAAATATTAAAA
111056898 ATTAATTAAA
Statistics
Matches: 35, Mismatches: 4, Indels: 4
0.81 0.09 0.09
Matches are distributed among these distances:
26 7 0.20
27 10 0.29
28 16 0.46
29 2 0.06
ACGTcount: A:0.62, C:0.01, G:0.01, T:0.35
Consensus pattern (26 bp):
AAAAATATTAAAATTATTATAAAATT
Found at i:111056898 original size:27 final size:28
Alignment explanation
Indices: 111056830--111056901 Score: 85
Period size: 27 Copynumber: 2.6 Consensus size: 28
111056820 AAATTCAAAA
* *
111056830 AAAAATATAAAAAATTATTTTAAAAATT
1 AAAAATATTAAAAATTATTATAAAAATT
*
111056858 AAAAATCATT-AAAATTATTAT-AAAGTT
1 AAAAAT-ATTAAAAATTATTATAAAAATT
*
111056885 ATAAATATTAAAAATTA
1 AAAAATATTAAAAATTA
111056902 ATTAAATGTT
Statistics
Matches: 38, Mismatches: 4, Indels: 5
0.81 0.09 0.11
Matches are distributed among these distances:
26 3 0.08
27 17 0.45
28 16 0.42
29 2 0.05
ACGTcount: A:0.61, C:0.01, G:0.01, T:0.36
Consensus pattern (28 bp):
AAAAATATTAAAAATTATTATAAAAATT
Found at i:111059582 original size:53 final size:53
Alignment explanation
Indices: 111059456--111059606 Score: 198
Period size: 53 Copynumber: 2.8 Consensus size: 53
111059446 ATAAGTGCGC
* * **
111059456 CCGTTTAAGACCATAGCTAGGCTATGGCATCGGTGCAATGTGATAATGTGACT
1 CCGTATAAGACCATAGCTGGGCTATGGCATCGGTATAATGTGATAATGTGACT
*
111059509 CCGTATAAGACCATAGCTGGGCTATGGCATCGGTATAATGTGATAATGTGATT
1 CCGTATAAGACCATAGCTGGGCTATGGCATCGGTATAATGTGATAATGTGACT
*
111059562 CCGTATAAGACCAT-GTCTGGGAC-ATGGCTTCGGTATGATATGTGA
1 CCGTATAAGACCATAG-CTGGG-CTATGGCATCGGTAT-A-ATGTGA
111059607 ACCGTGTAAG
Statistics
Matches: 88, Mismatches: 6, Indels: 6
0.88 0.06 0.06
Matches are distributed among these distances:
52 1 0.01
53 79 0.90
54 2 0.02
55 6 0.07
ACGTcount: A:0.26, C:0.17, G:0.27, T:0.29
Consensus pattern (53 bp):
CCGTATAAGACCATAGCTGGGCTATGGCATCGGTATAATGTGATAATGTGACT
Found at i:111067075 original size:53 final size:53
Alignment explanation
Indices: 111066949--111067099 Score: 189
Period size: 53 Copynumber: 2.8 Consensus size: 53
111066939 ATAAGTGCGC
* * **
111066949 CCGTTTAAGACCATAGCTAGGCTATGGCATCGGTGCAATGTGATAATGTGACT
1 CCGTATAAGACCATAGCTGGGCTATGGCATCGGTATAATGTGATAATGTGACT
*
111067002 CCGTATAAGACCATAGCTGGGCTATGGCATCGGTATAATGTGATAATGTGATT
1 CCGTATAAGACCATAGCTGGGCTATGGCATCGGTATAATGTGATAATGTGACT
* *
111067055 CCGTATAAGATCAT-GTCTGGGAC-ATGGCTTCGGTATGATATGTGA
1 CCGTATAAGACCATAG-CTGGG-CTATGGCATCGGTAT-A-ATGTGA
111067100 ACCGTGTAAG
Statistics
Matches: 87, Mismatches: 7, Indels: 6
0.87 0.07 0.06
Matches are distributed among these distances:
52 1 0.01
53 78 0.90
54 2 0.02
55 6 0.07
ACGTcount: A:0.26, C:0.17, G:0.27, T:0.30
Consensus pattern (53 bp):
CCGTATAAGACCATAGCTGGGCTATGGCATCGGTATAATGTGATAATGTGACT
Found at i:111069998 original size:47 final size:47
Alignment explanation
Indices: 111069896--111070155 Score: 346
Period size: 46 Copynumber: 5.6 Consensus size: 47
111069886 TGATGTCATA
* * *
111069896 GTATCTTTCAACTATGGTTTTACTCGTTTT-CTGTCATGTTGCCATG
1 GTATCTTTCAACCATGGTCTTACTCATTTTCCTGTCATGTTGCCATG
* *
111069942 GTATCTTTCAACCATGGTCTTATTCATTTTCCCGTCATGTTGCCATG
1 GTATCTTTCAACCATGGTCTTACTCATTTTCCTGTCATGTTGCCATG
* * *
111069989 GTATATTTCAACCATGGTCTTACTCA-TTTCATGTCAGGTTGCCATG
1 GTATCTTTCAACCATGGTCTTACTCATTTTCCTGTCATGTTGCCATG
* * * *
111070035 ATATCTTTCAACCATGGTCTTATTCATTTTCCCGTCTTGTTGCCATG
1 GTATCTTTCAACCATGGTCTTACTCATTTTCCTGTCATGTTGCCATG
* * * *
111070082 GTATCTTTCAACCATGGTCTTACACA-TTTCATATCAGGTTGCCATG
1 GTATCTTTCAACCATGGTCTTACTCATTTTCCTGTCATGTTGCCATG
*
111070128 GTATCTTTCAACCATGGTCTTACACATT
1 GTATCTTTCAACCATGGTCTTACTCATT
111070156 CTATATCAGA
Statistics
Matches: 186, Mismatches: 25, Indels: 5
0.86 0.12 0.02
Matches are distributed among these distances:
46 107 0.58
47 79 0.42
ACGTcount: A:0.20, C:0.23, G:0.15, T:0.42
Consensus pattern (47 bp):
GTATCTTTCAACCATGGTCTTACTCATTTTCCTGTCATGTTGCCATG
Found at i:111070060 original size:93 final size:93
Alignment explanation
Indices: 111069896--111070149 Score: 411
Period size: 93 Copynumber: 2.7 Consensus size: 93
111069886 TGATGTCATA
* * * *
111069896 GTATCTTTCAACTATGGTTTTACTCGTTTTC-TGTCATGTTGCCATGGTATCTTTCAACCATGGT
1 GTATCTTTCAACCATGGTCTTACTC-ATTTCATGTCAGGTTGCCATGGTATCTTTCAACCATGGT
111069960 CTTATTCATTTTCCCGTCATGTTGCCATG
65 CTTATTCATTTTCCCGTCATGTTGCCATG
* *
111069989 GTATATTTCAACCATGGTCTTACTCATTTCATGTCAGGTTGCCATGATATCTTTCAACCATGGTC
1 GTATCTTTCAACCATGGTCTTACTCATTTCATGTCAGGTTGCCATGGTATCTTTCAACCATGGTC
*
111070054 TTATTCATTTTCCCGTCTTGTTGCCATG
66 TTATTCATTTTCCCGTCATGTTGCCATG
* *
111070082 GTATCTTTCAACCATGGTCTTACACATTTCATATCAGGTTGCCATGGTATCTTTCAACCATGGTC
1 GTATCTTTCAACCATGGTCTTACTCATTTCATGTCAGGTTGCCATGGTATCTTTCAACCATGGTC
111070147 TTA
66 TTA
111070150 CACATTCTAT
Statistics
Matches: 149, Mismatches: 11, Indels: 2
0.92 0.07 0.01
Matches are distributed among these distances:
92 4 0.03
93 145 0.97
ACGTcount: A:0.19, C:0.23, G:0.15, T:0.42
Consensus pattern (93 bp):
GTATCTTTCAACCATGGTCTTACTCATTTCATGTCAGGTTGCCATGGTATCTTTCAACCATGGTC
TTATTCATTTTCCCGTCATGTTGCCATG
Found at i:111081468 original size:18 final size:16
Alignment explanation
Indices: 111081432--111081478 Score: 60
Period size: 18 Copynumber: 2.9 Consensus size: 16
111081422 CATCATTCTA
111081432 TTTATTTTA-TTTTAT
1 TTTATTTTATTTTTAT
111081447 TTTATTTTATTTTTAAAT
1 TTTATTTTATTTTT--AT
*
111081465 TTTATTTAATTTTT
1 TTTATTTTATTTTT
111081479 TCATTATCAC
Statistics
Matches: 28, Mismatches: 1, Indels: 3
0.88 0.03 0.09
Matches are distributed among these distances:
15 9 0.32
16 4 0.14
18 15 0.54
ACGTcount: A:0.23, C:0.00, G:0.00, T:0.77
Consensus pattern (16 bp):
TTTATTTTATTTTTAT
Found at i:111081471 original size:5 final size:5
Alignment explanation
Indices: 111081432--111081459 Score: 56
Period size: 5 Copynumber: 5.6 Consensus size: 5
111081422 CATCATTCTA
111081432 TTTAT TTTAT TTTAT TTTAT TTTAT TTT
1 TTTAT TTTAT TTTAT TTTAT TTTAT TTT
111081460 TAAATTTTAT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 23 1.00
ACGTcount: A:0.18, C:0.00, G:0.00, T:0.82
Consensus pattern (5 bp):
TTTAT
Found at i:111081757 original size:13 final size:13
Alignment explanation
Indices: 111081741--111081767 Score: 54
Period size: 13 Copynumber: 2.1 Consensus size: 13
111081731 TAAAATTTTT
111081741 AATCTGATCATTA
1 AATCTGATCATTA
111081754 AATCTGATCATTA
1 AATCTGATCATTA
111081767 A
1 A
111081768 TATTTTTATT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 14 1.00
ACGTcount: A:0.41, C:0.15, G:0.07, T:0.37
Consensus pattern (13 bp):
AATCTGATCATTA
Found at i:111082208 original size:15 final size:15
Alignment explanation
Indices: 111082187--111082224 Score: 58
Period size: 15 Copynumber: 2.5 Consensus size: 15
111082177 TTCCGACAAA
111082187 TACAAAACCGAACAC
1 TACAAAACCGAACAC
* *
111082202 TATAAAACCGAACCC
1 TACAAAACCGAACAC
111082217 TACAAAAC
1 TACAAAAC
111082225 ACTCAACTCA
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
15 20 1.00
ACGTcount: A:0.53, C:0.32, G:0.05, T:0.11
Consensus pattern (15 bp):
TACAAAACCGAACAC
Found at i:111085549 original size:99 final size:101
Alignment explanation
Indices: 111085395--111085579 Score: 302
Period size: 99 Copynumber: 1.9 Consensus size: 101
111085385 AACTTAGTTA
111085395 AGAATCCTCCAAAAAGAACTATCATTGAAACAAACCCCAAAAAGGCAATTCGTTAAAAACCAGTA
1 AGAATCCTCCAAAAAGAACTATCATTGAAACAAACCCCAAAAAGGCAATTCGTTAAAAACCAGTA
*
111085460 TTCAACACTCACATTCGAATCTGAATAACATTTTTT
66 TTCAACACTCACACTCGAATCTGAATAACATTTTTT
* * *
111085496 AGAATCCTCCAAAGA-AACTATCATTGAAACAAACCCC-CAAAGGCAATTCGTTAAAAACCGGTA
1 AGAATCCTCCAAAAAGAACTATCATTGAAACAAACCCCAAAAAGGCAATTCGTTAAAAACCAGTA
* *
111085559 TTTAACGCTCACACTCGAATC
66 TTCAACACTCACACTCGAATC
111085580 CAAATGAATC
Statistics
Matches: 78, Mismatches: 6, Indels: 2
0.91 0.07 0.02
Matches are distributed among these distances:
99 42 0.54
100 22 0.28
101 14 0.18
ACGTcount: A:0.42, C:0.25, G:0.10, T:0.23
Consensus pattern (101 bp):
AGAATCCTCCAAAAAGAACTATCATTGAAACAAACCCCAAAAAGGCAATTCGTTAAAAACCAGTA
TTCAACACTCACACTCGAATCTGAATAACATTTTTT
Found at i:111085764 original size:97 final size:97
Alignment explanation
Indices: 111085647--111085837 Score: 242
Period size: 97 Copynumber: 2.0 Consensus size: 97
111085637 TAAATAAACA
* *
111085647 CTCACACTCAAATCCAAATAAC-CTAGTTAAAAGAATCCTACAAAGAAACTATCAATAAAAAACT
1 CTCACACTCAAATCCAAATAACTC-AGTCAAAAGAATCCTACAAAGAAACTATAAATAAAAAACT
** * *
111085711 ATCATGCAAT-ATGTTTAAAACTGATATTCATCC
65 ATCACCCAATGA-GTTAAAAACCGATATTCATCC
* * * * * *
111085744 CTCACACTCGAATCCGAATAATTCAGTCAAAAGAATCCTCCAAAGAAACTATAAATCAAAATCTA
1 CTCACACTCAAATCCAAATAACTCAGTCAAAAGAATCCTACAAAGAAACTATAAATAAAAAACTA
111085809 TCACCCAATGAGTTAAAAACCGATATTCA
66 TCACCCAATGAGTTAAAAACCGATATTCA
111085838 ACTCAGAATA
Statistics
Matches: 80, Mismatches: 12, Indels: 4
0.83 0.12 0.04
Matches are distributed among these distances:
97 78 0.98
98 2 0.03
ACGTcount: A:0.46, C:0.23, G:0.07, T:0.24
Consensus pattern (97 bp):
CTCACACTCAAATCCAAATAACTCAGTCAAAAGAATCCTACAAAGAAACTATAAATAAAAAACTA
TCACCCAATGAGTTAAAAACCGATATTCATCC
Found at i:111114312 original size:12 final size:13
Alignment explanation
Indices: 111114295--111114327 Score: 50
Period size: 13 Copynumber: 2.6 Consensus size: 13
111114285 TTTGGAAATT
*
111114295 GAAAATTTA-AAA
1 GAAAATATATAAA
111114307 GAAAATATATAAA
1 GAAAATATATAAA
111114320 GAAAATAT
1 GAAAATAT
111114328 TTAATGTACT
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
12 8 0.42
13 11 0.58
ACGTcount: A:0.67, C:0.00, G:0.09, T:0.24
Consensus pattern (13 bp):
GAAAATATATAAA
Found at i:111122564 original size:13 final size:14
Alignment explanation
Indices: 111122546--111122574 Score: 51
Period size: 13 Copynumber: 2.1 Consensus size: 14
111122536 CTAAATAGCT
111122546 AACTTTTTT-TTAA
1 AACTTTTTTATTAA
111122559 AACTTTTTTATTAA
1 AACTTTTTTATTAA
111122573 AA
1 AA
111122575 TATTGAATGC
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
13 9 0.60
14 6 0.40
ACGTcount: A:0.38, C:0.07, G:0.00, T:0.55
Consensus pattern (14 bp):
AACTTTTTTATTAA
Found at i:111132350 original size:290 final size:295
Alignment explanation
Indices: 111131677--111132351 Score: 875
Period size: 300 Copynumber: 2.3 Consensus size: 295
111131667 GAGTGTTCAG
* * **
111131677 TTTGAAAGTTAAAAATGGAACAGTTAGGTATTGTTTGGTAAATGATAAGCGATTCTCAATGCGTT
1 TTTGAATGTTAAAAATGGAACAGTTAGGTGTTGTTTGGTAAATGATAAGTAATTCTCAATGCGTT
* *
111131742 TGGTTTCTCATTTTGGAGATTAAGCTTGACTGATTGTTTTCAATAATATATACTACTTATGAGTT
66 TGGTTTCTCATTTTGGAGATTAAGCTTGAATGATTATTTTCAATAATATATACTACTTATGAGTT
*
111131807 AAAGCAATGCTACTTTTTTCCCGTCATTTGACCACTATGAGCTCACTTCCTGTTTGGTTACCGAG
131 AAAGCAATGCTA-TTTTTTCCCATCATTTGACCACTATGAGCTCACTTCCTGTTTGGTTACCGAG
* ** * *
111131872 AAAGTGAAGGAGCATGGAAAGTTGAAACATTGTTTCACCGTGCAAAAGAACCTGGTTTTGTCATC
195 AAAATGAAGGAAAATGGAAAGTTGAAACATTGTTTAACCGTGCAAAAGAACCTGGCTTTGTCATC
*
111131937 TGAGTGTTCGGTAGAGGGTAGTATTTTTGTTTCCATTGTT
260 TGA----TCGGTAGAGGGTAGTATTTTTGTTTCCATTGGT
* * *
111131977 TTTGAATGTTAAAAATGGAACAGTTAGGTGTTGTTTGGTTAACGATAAGTAACTCTCAATGCGTT
1 TTTGAATGTTAAAAATGGAACAGTTAGGTGTTGTTTGGTAAATGATAAGTAATTCTCAATGCGTT
* *
111132042 TGGTTTCTTATTTTGGAGATTAAGCTT-AATGAATTATTTTCAATAATATATACTACTTAATGTG
66 TGGTTTCTCATTTTGGAGATTAAGCTTGAATG-ATTATTTTCAATAATATATACTACTT-ATGAG
** * ** *
111132106 TTACGGCAATG-T-TTTCTTT-TCATCATTTGACTTCTATGAGTTCACTTCCTGTTTGGTTACCG
129 TTAAAGCAATGCTATTT-TTTCCCATCATTTGACCACTATGAGCTCACTTCCTGTTTGGTTACCG
* * * * *
111132168 AGAAAATGAAGGAAAATGGAAAGTTGAAATGATTGTTTAACTGTTCACAAGAACCT-GCTTTGTT
193 AGAAAATGAAGGAAAATGGAAAGTTGAAA-CATTGTTTAACCGTGCAAAAGAACCTGGCTTTGTC
*
111132232 ATCTGA-C-TTA-AGGGTAGTATTTTAT-TTT-CATTGGT
257 ATCTGATCGGTAGAGGGTAGTATTTT-TGTTTCCATTGGT
* * *
111132267 TTTGAATGTTAAAAATGGAACGGTTAGGGGTTGTTTGGTAAATGATAAGTAATTCTCAATGCATT
1 TTTGAATGTTAAAAATGGAACAGTTAGGTGTTGTTTGGTAAATGATAAGTAATTCTCAATGCGTT
**
111132332 TGGTTTCTCAAATTGGAGAT
66 TGGTTTCTCATTTTGGAGAT
111132352 AAGTTTTATT
Statistics
Matches: 331, Mismatches: 39, Indels: 20
0.85 0.10 0.05
Matches are distributed among these distances:
290 82 0.25
291 16 0.05
292 3 0.01
293 1 0.00
298 79 0.24
299 27 0.08
300 110 0.33
301 13 0.04
ACGTcount: A:0.28, C:0.12, G:0.21, T:0.39
Consensus pattern (295 bp):
TTTGAATGTTAAAAATGGAACAGTTAGGTGTTGTTTGGTAAATGATAAGTAATTCTCAATGCGTT
TGGTTTCTCATTTTGGAGATTAAGCTTGAATGATTATTTTCAATAATATATACTACTTATGAGTT
AAAGCAATGCTATTTTTTCCCATCATTTGACCACTATGAGCTCACTTCCTGTTTGGTTACCGAGA
AAATGAAGGAAAATGGAAAGTTGAAACATTGTTTAACCGTGCAAAAGAACCTGGCTTTGTCATCT
GATCGGTAGAGGGTAGTATTTTTGTTTCCATTGGT
Found at i:111136903 original size:14 final size:14
Alignment explanation
Indices: 111136881--111136930 Score: 55
Period size: 14 Copynumber: 3.6 Consensus size: 14
111136871 TATTTTTTAT
111136881 ATTTTAATAGTTAA
1 ATTTTAATAGTTAA
* * *
111136895 ATTTAAATAATCAA
1 ATTTTAATAGTTAA
* *
111136909 ATTTTAATTGTTTA
1 ATTTTAATAGTTAA
111136923 ATTTTAAT
1 ATTTTAAT
111136931 TTGTCAAGTT
Statistics
Matches: 28, Mismatches: 8, Indels: 0
0.78 0.22 0.00
Matches are distributed among these distances:
14 28 1.00
ACGTcount: A:0.42, C:0.02, G:0.04, T:0.52
Consensus pattern (14 bp):
ATTTTAATAGTTAA
Found at i:111137416 original size:5 final size:5
Alignment explanation
Indices: 111137406--111137430 Score: 50
Period size: 5 Copynumber: 5.0 Consensus size: 5
111137396 AATAATTAAG
111137406 TATAT TATAT TATAT TATAT TATAT
1 TATAT TATAT TATAT TATAT TATAT
111137431 ATAAAAGAAA
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 20 1.00
ACGTcount: A:0.40, C:0.00, G:0.00, T:0.60
Consensus pattern (5 bp):
TATAT
Found at i:111137500 original size:31 final size:30
Alignment explanation
Indices: 111137465--111137525 Score: 70
Period size: 30 Copynumber: 2.0 Consensus size: 30
111137455 GAAACAGAAT
*
111137465 GAAAGCAAACGAAAC-AGAGAAGAACAGGGGA
1 GAAAG-AAACGAAACAAGA-AAGAAAAGGGGA
* *
111137496 GAAAGAAAGGAAAGAAGAAAGAAAAGGGGA
1 GAAAGAAACGAAACAAGAAAGAAAAGGGGA
111137526 AATAAGGTTT
Statistics
Matches: 26, Mismatches: 3, Indels: 3
0.81 0.09 0.09
Matches are distributed among these distances:
30 18 0.69
31 8 0.31
ACGTcount: A:0.59, C:0.07, G:0.34, T:0.00
Consensus pattern (30 bp):
GAAAGAAACGAAACAAGAAAGAAAAGGGGA
Found at i:111139072 original size:39 final size:39
Alignment explanation
Indices: 111138965--111139099 Score: 123
Period size: 39 Copynumber: 3.4 Consensus size: 39
111138955 GACCTCGAGT
* * *
111138965 CGATGAGACACTGGGTGTC-ACTATATTTCTTCGGATAGATT
1 CGATGAGACACTGGGTGTCAAC--TATTACTTCGGCTAG-TC
** ** *
111139006 CGATGAGGTACTGGGTACCAACT-TTACTTCGGCTAGGC
1 CGATGAGACACTGGGTGTCAACTATTACTTCGGCTAGTC
*
111139044 CGATGAGACACTGGGTGTCAACTATTACTTCGAACTA-TC
1 CGATGAGACACTGGGTGTCAACTATTACTTCG-GCTAGTC
*
111139083 CGATGAGGCACTGGGTG
1 CGATGAGACACTGGGTG
111139100 CCATATTGGT
Statistics
Matches: 76, Mismatches: 15, Indels: 8
0.77 0.15 0.08
Matches are distributed among these distances:
38 19 0.25
39 36 0.47
40 4 0.05
41 15 0.20
42 2 0.03
ACGTcount: A:0.24, C:0.21, G:0.27, T:0.28
Consensus pattern (39 bp):
CGATGAGACACTGGGTGTCAACTATTACTTCGGCTAGTC
Found at i:111145244 original size:31 final size:30
Alignment explanation
Indices: 111145209--111145269 Score: 70
Period size: 30 Copynumber: 2.0 Consensus size: 30
111145199 GAAACAGAAT
*
111145209 GAAAGCAAACGAAAC-AGAGAAGAATAGGGGA
1 GAAAG-AAACGAAACAAGA-AAGAAAAGGGGA
* *
111145240 GAAAGAAAGGAAAGAAGAAAGAAAAGGGGA
1 GAAAGAAACGAAACAAGAAAGAAAAGGGGA
111145270 AATAAGGTTT
Statistics
Matches: 26, Mismatches: 3, Indels: 3
0.81 0.09 0.09
Matches are distributed among these distances:
30 18 0.69
31 8 0.31
ACGTcount: A:0.59, C:0.05, G:0.34, T:0.02
Consensus pattern (30 bp):
GAAAGAAACGAAACAAGAAAGAAAAGGGGA
Found at i:111146816 original size:39 final size:40
Alignment explanation
Indices: 111146709--111146818 Score: 109
Period size: 38 Copynumber: 2.8 Consensus size: 40
111146699 GACCTCGAGT
* **
111146709 CGATGAGACACTGGGTGTC-ACTATATTTCTTCGGATAGATT
1 CGATGAGACACTGGGTGTCAAC--TATTACTTCGGATAGAGC
** ** *
111146750 CGATGAGGTACTGGGTACCAACT-TTACTTCGGCTAG-GC
1 CGATGAGACACTGGGTGTCAACTATTACTTCGGATAGAGC
111146788 CGATGAGACACTGGGTGTCAACTATTACTTC
1 CGATGAGACACTGGGTGTCAACTATTACTTC
111146819 AAACTATCCG
Statistics
Matches: 55, Mismatches: 12, Indels: 6
0.75 0.16 0.08
Matches are distributed among these distances:
38 19 0.35
39 18 0.33
40 1 0.02
41 15 0.27
42 2 0.04
ACGTcount: A:0.24, C:0.21, G:0.25, T:0.30
Consensus pattern (40 bp):
CGATGAGACACTGGGTGTCAACTATTACTTCGGATAGAGC
Found at i:111156058 original size:2 final size:2
Alignment explanation
Indices: 111156051--111156075 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
111156041 ATATCAATAG
111156051 AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT A
111156076 GTGTAGGAAT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:111159397 original size:20 final size:21
Alignment explanation
Indices: 111159364--111159403 Score: 55
Period size: 20 Copynumber: 2.0 Consensus size: 21
111159354 TATAATATTT
111159364 TAAAAAATACAAATTGTATAC
1 TAAAAAATACAAATTGTATAC
* *
111159385 TAAAATATA-AAATTTTATA
1 TAAAAAATACAAATTGTATA
111159404 TTTTTGTATT
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
20 9 0.53
21 8 0.47
ACGTcount: A:0.57, C:0.05, G:0.03, T:0.35
Consensus pattern (21 bp):
TAAAAAATACAAATTGTATAC
Found at i:111160443 original size:15 final size:16
Alignment explanation
Indices: 111160425--111160454 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
111160415 TTATGTTGGT
111160425 GATT-AATGAAAATTG
1 GATTAAATGAAAATTG
111160440 GATTAAATGAAAATT
1 GATTAAATGAAAATT
111160455 TCAATATTAT
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 4 0.29
16 10 0.71
ACGTcount: A:0.50, C:0.00, G:0.17, T:0.33
Consensus pattern (16 bp):
GATTAAATGAAAATTG
Found at i:111160924 original size:51 final size:51
Alignment explanation
Indices: 111160869--111160966 Score: 196
Period size: 51 Copynumber: 1.9 Consensus size: 51
111160859 TCATCAAATC
111160869 AACTCTAAAACCCGAATTAAACATTAAAAAATTAACACAGATACCCGAATT
1 AACTCTAAAACCCGAATTAAACATTAAAAAATTAACACAGATACCCGAATT
111160920 AACTCTAAAACCCGAATTAAACATTAAAAAATTAACACAGATACCCG
1 AACTCTAAAACCCGAATTAAACATTAAAAAATTAACACAGATACCCG
111160967 TTAACAAAAA
Statistics
Matches: 47, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
51 47 1.00
ACGTcount: A:0.51, C:0.22, G:0.06, T:0.20
Consensus pattern (51 bp):
AACTCTAAAACCCGAATTAAACATTAAAAAATTAACACAGATACCCGAATT
Found at i:111163768 original size:26 final size:26
Alignment explanation
Indices: 111163717--111163768 Score: 61
Period size: 26 Copynumber: 2.0 Consensus size: 26
111163707 AGTTTATCTC
* * *
111163717 TTTTGTCACTTTGGCCTAATTACTTT
1 TTTTATCACTTTAGCCTAAATACTTT
111163743 TTTTATCACTTTAGCCTTAAAT-CTTT
1 TTTTATCACTTTAGCC-TAAATACTTT
111163769 AAAATTTAGT
Statistics
Matches: 22, Mismatches: 3, Indels: 2
0.81 0.11 0.07
Matches are distributed among these distances:
26 18 0.82
27 4 0.18
ACGTcount: A:0.19, C:0.19, G:0.08, T:0.54
Consensus pattern (26 bp):
TTTTATCACTTTAGCCTAAATACTTT
Found at i:111166343 original size:238 final size:238
Alignment explanation
Indices: 111165743--111166413 Score: 833
Period size: 238 Copynumber: 2.8 Consensus size: 238
111165733 CATATACTAT
* *
111165743 TCTTTCTACATATGACAAGTTGACAACGAAACAATATATTAACTCCCAGACTCATCCCCTTCCTA
1 TCTTTCCACATATGACAAGTTGACAACGAAACAATATATTAACTCCCAGACTCGTCCCCTTCCTA
* * * *
111165808 TACTTATAACGAACATAAAAAGCCACGAATTCTGCTTCGCTCATCTTAGAATTGCAAACTCGAAG
66 TACTTATAATGAACATAAAAAACCA-GAATTCTCCTTCGCCCATCTTAGAATTGCAAACTCGAAG
*
111165873 TGCACTCAGAGACAGGCAATTATTGAATAT-A--ATACAACCTTAACACCTACAAA-GGAGAATA
130 TGCACTCAGAGACAGGCAATTATTGAATATAACCATACAACCTTAACACCTACAAAGGGAAAATA
* * * * *
111165934 ATAACGGTTCTATATCACGATGCGAACCTTTCAGCCAACATATATGA
195 AGAAAGGTTCTAAAACACGATGAGAACCTTTCAGCCAAC--A-ATGA
* * *
111165981 TTCTTTCCACATATGACAAGTTGACAACGAAACAATATATTAACTTCCACACTCGTCTCCTTCCT
1 -TCTTTCCACATATGACAAGTTGACAACGAAACAATATATTAACTCCCAGACTCGTCCCCTTCCT
* * * *
111166046 ATACTTATAACT-AACATAAAAGTAA-CA-AATTCTCCTTCGCCTATCTCAAAATGGCAAACTCG
65 ATACTTATAA-TGAACATAAAA--AACCAGAATTCTCCTTCGCCCATCTTAGAATTGCAAACTCG
*
111166108 AAGTGCACTCAGAGACGGGCAATTATTGAATATAACCATACAACCTTAACACCTACAAAGGGAAA
127 AAGTGCACTCAGAGACAGGCAATTATTGAATATAACCATACAACCTTAACACCTACAAAGGGAAA
* ** *
111166173 ATAAAGGAAAGGCTT-TAAAACATGATGAGAACCTTTTGGTCAAC-AT-A
192 AT-AA-GAAAGG-TTCTAAAACACGATGAGAACCTTTCAGCCAACAATGA
* * * * *
111166220 -CTTTCCACATATGACAAGCTGATAACGAAACAATACATTAACTCCCAGACTTGTCCCCCTCCTA
1 TCTTTCCACATATGACAAGTTGACAACGAAACAATATATTAACTCCCAGACTCGTCCCCTTCCTA
111166284 TACTTATAATGAACATAAAAAACCATGAATTCTCCTTCGCCCATCTTAGAATTGCAAACTCGAAG
66 TACTTATAATGAACATAAAAAACCA-GAATTCTCCTTCGCCCATCTTAGAATTGCAAACTCGAAG
* * * * * *
111166349 TGCAATCAGAGACAGGTAACTATTGAACATATCCATACAACCTTAACACCTACAGAGGAGAAAAT
130 TGCACTCAGAGACAGGCAATTATTGAATATAACCATACAACCTTAACACCTACAAAGG-GAAAAT
111166414 TAATGGTTCT
Statistics
Matches: 374, Mismatches: 43, Indels: 30
0.84 0.10 0.07
Matches are distributed among these distances:
235 2 0.01
236 3 0.01
237 74 0.20
238 146 0.39
239 86 0.23
240 4 0.01
241 23 0.06
242 6 0.02
243 2 0.01
244 26 0.07
245 2 0.01
ACGTcount: A:0.38, C:0.24, G:0.12, T:0.25
Consensus pattern (238 bp):
TCTTTCCACATATGACAAGTTGACAACGAAACAATATATTAACTCCCAGACTCGTCCCCTTCCTA
TACTTATAATGAACATAAAAAACCAGAATTCTCCTTCGCCCATCTTAGAATTGCAAACTCGAAGT
GCACTCAGAGACAGGCAATTATTGAATATAACCATACAACCTTAACACCTACAAAGGGAAAATAA
GAAAGGTTCTAAAACACGATGAGAACCTTTCAGCCAACAATGA
Found at i:111169891 original size:5 final size:5
Alignment explanation
Indices: 111169881--111169915 Score: 61
Period size: 5 Copynumber: 7.0 Consensus size: 5
111169871 ATTTAACATT
*
111169881 TAAAA TAAAA TAAAA CAAAA TAAAA TAAAA TAAAA
1 TAAAA TAAAA TAAAA TAAAA TAAAA TAAAA TAAAA
111169916 AGAAACCAAA
Statistics
Matches: 28, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
5 28 1.00
ACGTcount: A:0.80, C:0.03, G:0.00, T:0.17
Consensus pattern (5 bp):
TAAAA
Found at i:111169926 original size:20 final size:20
Alignment explanation
Indices: 111169882--111169929 Score: 62
Period size: 20 Copynumber: 2.4 Consensus size: 20
111169872 TTTAACATTT
*
111169882 AAAATAAAATAAAACAAAAT
1 AAAATAAAATAAAACAAAAC
111169902 AAAATAAAATAAAA-AGAAAC
1 AAAATAAAATAAAACA-AAAC
*
111169922 CAAATAAA
1 AAAATAAA
111169930 TACTAACACT
Statistics
Matches: 25, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
19 1 0.04
20 24 0.96
ACGTcount: A:0.79, C:0.06, G:0.02, T:0.12
Consensus pattern (20 bp):
AAAATAAAATAAAACAAAAC
Found at i:111172161 original size:20 final size:21
Alignment explanation
Indices: 111172120--111172160 Score: 73
Period size: 21 Copynumber: 2.0 Consensus size: 21
111172110 GAATAACAAA
111172120 AATAACCCTTTCATTTTTTTT
1 AATAACCCTTTCATTTTTTTT
*
111172141 AATAACCCTTTTATTTTTTT
1 AATAACCCTTTCATTTTTTT
111172161 ATCTTTTTTA
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
21 19 1.00
ACGTcount: A:0.24, C:0.17, G:0.00, T:0.59
Consensus pattern (21 bp):
AATAACCCTTTCATTTTTTTT
Found at i:111176379 original size:17 final size:18
Alignment explanation
Indices: 111176357--111176391 Score: 54
Period size: 17 Copynumber: 2.0 Consensus size: 18
111176347 AGAAGAAAAT
111176357 TATTTTTTATT-AAATAA
1 TATTTTTTATTCAAATAA
*
111176374 TATTTTTTTTTCAAATAA
1 TATTTTTTATTCAAATAA
111176392 AAACTAAAAT
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
17 10 0.62
18 6 0.38
ACGTcount: A:0.37, C:0.03, G:0.00, T:0.60
Consensus pattern (18 bp):
TATTTTTTATTCAAATAA
Found at i:111176713 original size:30 final size:29
Alignment explanation
Indices: 111176653--111176713 Score: 70
Period size: 29 Copynumber: 2.1 Consensus size: 29
111176643 AAACTTAAAG
* *
111176653 TTTAGTCCCTATACTTTTATTTTTAGAAA
1 TTTAGTCCCTATACTTTTAATTTCAGAAA
*
111176682 TTTAGTCCCTTTACTTTTTAGATTTCA-AAA
1 TTTAGTCCCTATAC-TTTTA-ATTTCAGAAA
111176712 TT
1 TT
111176714 AATGTCTATT
Statistics
Matches: 27, Mismatches: 3, Indels: 3
0.82 0.09 0.09
Matches are distributed among these distances:
29 13 0.48
30 10 0.37
31 4 0.15
ACGTcount: A:0.26, C:0.15, G:0.07, T:0.52
Consensus pattern (29 bp):
TTTAGTCCCTATACTTTTAATTTCAGAAA
Found at i:111177086 original size:20 final size:20
Alignment explanation
Indices: 111177063--111177101 Score: 51
Period size: 20 Copynumber: 1.9 Consensus size: 20
111177053 TAACAAAAGA
111177063 AAAAAGAAAAAATATTAAAT
1 AAAAAGAAAAAATATTAAAT
* * *
111177083 AAAAATAACATATATTAAA
1 AAAAAGAAAAAATATTAAA
111177102 AAATAATATG
Statistics
Matches: 16, Mismatches: 3, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
20 16 1.00
ACGTcount: A:0.72, C:0.03, G:0.03, T:0.23
Consensus pattern (20 bp):
AAAAAGAAAAAATATTAAAT
Found at i:111186888 original size:9 final size:9
Alignment explanation
Indices: 111186874--111186992 Score: 55
Period size: 9 Copynumber: 12.6 Consensus size: 9
111186864 GGCCTCTCTA
111186874 AAAAAAATT
1 AAAAAAATT
111186883 -AAAAAATT
1 AAAAAAATT
*
111186891 CAAAATAATTT
1 -AAAA-AAATT
**
111186902 TTAAAAA-T
1 AAAAAAATT
*
111186910 AAAAATATT
1 AAAAAAATT
* *
111186919 TATAAAATT
1 AAAAAAATT
**
111186928 CTAAAAATT
1 AAAAAAATT
111186937 ATAAAAAATTCT
1 A-AAAAAA-T-T
111186949 AAAAAAATT
1 AAAAAAATT
111186958 CAAAATAACA-T
1 -AAAA-AA-ATT
111186969 ATAAAAAATT
1 A-AAAAAATT
*
111186979 TAAAAAATT
1 AAAAAAATT
111186988 AAAAA
1 AAAAA
111186993 CTTTATAGAA
Statistics
Matches: 81, Mismatches: 17, Indels: 24
0.66 0.14 0.20
Matches are distributed among these distances:
8 13 0.16
9 29 0.36
10 19 0.23
11 17 0.21
12 3 0.04
ACGTcount: A:0.66, C:0.04, G:0.00, T:0.29
Consensus pattern (9 bp):
AAAAAAATT
Found at i:111186900 original size:18 final size:19
Alignment explanation
Indices: 111186874--111186987 Score: 58
Period size: 20 Copynumber: 5.9 Consensus size: 19
111186864 GGCCTCTCTA
111186874 AAAAAAATTAAAAAATTC-
1 AAAAAAATTAAAAAATTCT
* *
111186892 AAAATAATTTTTAAAAA---T
1 AAAA-AA-ATTAAAAAATTCT
* *
111186910 AAAAATATTTATAAAATTCT
1 AAAAA-AATTAAAAAATTCT
*
111186930 -AAAAATTATAAAAAATTCT
1 AAAAAAAT-TAAAAAATTCT
* *
111186949 AAAAAAATTCAAAATAACATAT
1 AAAAAAATT-AAAA-AA-TTCT
*
111186971 AAAAAATTTAAAAAATT
1 AAAAAAATTAAAAAATT
111186988 AAAAACTTTA
Statistics
Matches: 74, Mismatches: 10, Indels: 23
0.69 0.09 0.21
Matches are distributed among these distances:
17 8 0.11
18 12 0.16
19 18 0.24
20 20 0.27
21 6 0.08
22 10 0.14
ACGTcount: A:0.65, C:0.04, G:0.00, T:0.31
Consensus pattern (19 bp):
AAAAAAATTAAAAAATTCT
Found at i:111186907 original size:19 final size:18
Alignment explanation
Indices: 111186885--111186942 Score: 57
Period size: 19 Copynumber: 3.2 Consensus size: 18
111186875 AAAAAATTAA
*
111186885 AAAATTCAAAATAATTTTT
1 AAAATTCAAAAT-ATTTAT
* *
111186904 AAAAATAAAAATATTTAT
1 AAAATTCAAAATATTTAT
111186922 AAAATTCTAAAA-A-TTAT
1 AAAATTC-AAAATATTTAT
111186939 AAAA
1 AAAA
111186943 AATTCTAAAA
Statistics
Matches: 33, Mismatches: 5, Indels: 4
0.79 0.12 0.10
Matches are distributed among these distances:
17 8 0.24
18 11 0.33
19 14 0.42
ACGTcount: A:0.62, C:0.03, G:0.00, T:0.34
Consensus pattern (18 bp):
AAAATTCAAAATATTTAT
Found at i:111186984 original size:30 final size:28
Alignment explanation
Indices: 111186874--111186992 Score: 100
Period size: 28 Copynumber: 4.2 Consensus size: 28
111186864 GGCCTCTCTA
* *
111186874 AAAAAAAT-TAAAAAATTCAAAATAATTT
1 AAAAAAATATAAAAAATTTAAAA-AATTC
** * *
111186902 TTAAAAATA-AAAATATTTATAAAATTC
1 AAAAAAATATAAAAAATTTAAAAAATTC
* *
111186929 TAAAAATTATAAAAAATTCTAAAAAAATTC
1 AAAAAAATATAAAAAATT-T-AAAAAATTC
111186959 AAAATAACATATAAAAAATTTAAAAAATT-
1 AAAA-AA-ATATAAAAAATTTAAAAAATTC
111186988 AAAAA
1 AAAAA
111186993 CTTTATAGAA
Statistics
Matches: 73, Mismatches: 12, Indels: 12
0.75 0.12 0.12
Matches are distributed among these distances:
27 11 0.15
28 24 0.33
29 5 0.07
30 19 0.26
31 3 0.04
32 11 0.15
ACGTcount: A:0.66, C:0.04, G:0.00, T:0.29
Consensus pattern (28 bp):
AAAAAAATATAAAAAATTTAAAAAATTC
Found at i:111187107 original size:16 final size:16
Alignment explanation
Indices: 111187086--111187116 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
111187076 TTGAATAAGC
111187086 TTTCAAATATATATGG
1 TTTCAAATATATATGG
*
111187102 TTTCAAATTTATATG
1 TTTCAAATATATATG
111187117 CTTCAACATG
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
16 14 1.00
ACGTcount: A:0.35, C:0.06, G:0.10, T:0.48
Consensus pattern (16 bp):
TTTCAAATATATATGG
Found at i:111190228 original size:17 final size:16
Alignment explanation
Indices: 111190197--111190239 Score: 52
Period size: 17 Copynumber: 2.7 Consensus size: 16
111190187 CCACCAATTT
111190197 ATAAATAT-TTATTAA
1 ATAAATATATTATTAA
*
111190212 CTAAATATATTATTTAA
1 ATAAATATATTA-TTAA
*
111190229 AAAAATATATT
1 ATAAATATATT
111190240 GCTATATTCG
Statistics
Matches: 23, Mismatches: 3, Indels: 2
0.82 0.11 0.07
Matches are distributed among these distances:
15 7 0.30
16 3 0.13
17 13 0.57
ACGTcount: A:0.53, C:0.02, G:0.00, T:0.44
Consensus pattern (16 bp):
ATAAATATATTATTAA
Found at i:111204317 original size:18 final size:18
Alignment explanation
Indices: 111204247--111204327 Score: 53
Period size: 18 Copynumber: 4.6 Consensus size: 18
111204237 ATATAATAAC
*
111204247 TATA-AAAATATAAAAAT
1 TATATAAAATATTAAAAT
* * *
111204264 T-TACAAAGTATTAAAAA
1 TATATAAAATATTAAAAT
* *
111204281 CATA-AACAATTATTCAAAT
1 TATATAA-AA-TATTAAAAT
111204300 T-TATTAAAATATTAAAAT
1 TATA-TAAAATATTAAAAT
111204318 TATATAAAAT
1 TATATAAAAT
111204328 CTAAATAAAA
Statistics
Matches: 48, Mismatches: 9, Indels: 13
0.69 0.13 0.19
Matches are distributed among these distances:
16 2 0.04
17 13 0.27
18 20 0.42
19 11 0.23
20 2 0.04
ACGTcount: A:0.59, C:0.05, G:0.01, T:0.35
Consensus pattern (18 bp):
TATATAAAATATTAAAAT
Found at i:111204363 original size:10 final size:9
Alignment explanation
Indices: 111204222--111204381 Score: 55
Period size: 8 Copynumber: 17.2 Consensus size: 9
111204212 TAAAACTATG
111204222 AAAAATTATT
1 AAAAATTA-T
111204232 AACAAA-TAT
1 AA-AAATTAT
* *
111204241 AATAACTAT
1 AAAAATTAT
111204250 AAAAA-TAT
1 AAAAATTAT
111204258 AAAAATT-T
1 AAAAATTAT
* *
111204266 ACAAAGTATT
1 AAAAATTA-T
*
111204276 AAAAA-CAT
1 AAAAATTAT
111204284 AAACAATTATT
1 AAA-AATTA-T
* *
111204295 CAAATTTAT
1 AAAAATTAT
*
111204304 TAAAA-TAT
1 AAAAATTAT
*
111204312 TAAAATTAT
1 AAAAATTAT
*
111204321 ATAAAATCTAA
1 A-AAAAT-TAT
111204332 ATAAAATCTA-
1 A-AAAAT-TAT
* *
111204342 AAAACTTGT
1 AAAAATTAT
111204351 AAAGAATTAT
1 AAA-AATTAT
111204361 AAAAA-TAT
1 AAAAATTAT
111204369 AAATAAATTAT
1 -AA-AAATTAT
111204380 AA
1 AA
111204382 TAAAATTAAA
Statistics
Matches: 117, Mismatches: 17, Indels: 32
0.70 0.10 0.19
Matches are distributed among these distances:
8 32 0.27
9 32 0.27
10 32 0.27
11 21 0.18
ACGTcount: A:0.61, C:0.06, G:0.02, T:0.32
Consensus pattern (9 bp):
AAAAATTAT
Found at i:111204377 original size:19 final size:19
Alignment explanation
Indices: 111204314--111204381 Score: 57
Period size: 20 Copynumber: 3.5 Consensus size: 19
111204304 TAAAATATTA
*
111204314 AAATTATATAAAATCTAAAT
1 AAATTATA-AAAATATAAAT
* * *
111204334 AAAATCTAAAAACTTGTAAA-
1 AAATTATAAAAA--TATAAAT
*
111204354 GAATTATAAAAATATAAAT
1 AAATTATAAAAATATAAAT
111204373 AAATTATAA
1 AAATTATAA
111204382 TAAAATTAAA
Statistics
Matches: 37, Mismatches: 8, Indels: 7
0.71 0.15 0.13
Matches are distributed among these distances:
18 5 0.14
19 12 0.32
20 15 0.41
21 5 0.14
ACGTcount: A:0.62, C:0.04, G:0.03, T:0.31
Consensus pattern (19 bp):
AAATTATAAAAATATAAAT
Found at i:111209912 original size:29 final size:30
Alignment explanation
Indices: 111209853--111209910 Score: 80
Period size: 30 Copynumber: 1.9 Consensus size: 30
111209843 TCCGAGCCTT
**
111209853 GGGGCAAAAATGTAATTATGTAAAAGTTTA
1 GGGGCAAAAATGTAATTATAAAAAAGTTTA
* *
111209883 GGGGCAAAATTGTAATTTTAAAAAAGTT
1 GGGGCAAAAATGTAATTATAAAAAAGTT
111209911 AGAGTCGAGG
Statistics
Matches: 24, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
30 24 1.00
ACGTcount: A:0.43, C:0.03, G:0.22, T:0.31
Consensus pattern (30 bp):
GGGGCAAAAATGTAATTATAAAAAAGTTTA
Found at i:111210140 original size:13 final size:13
Alignment explanation
Indices: 111210122--111210153 Score: 55
Period size: 13 Copynumber: 2.5 Consensus size: 13
111210112 TTTCTAGCAA
111210122 TTATGAATTTATT
1 TTATGAATTTATT
111210135 TTATGAATTTATT
1 TTATGAATTTATT
*
111210148 TGATGA
1 TTATGA
111210154 TGATCCAAGC
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
13 18 1.00
ACGTcount: A:0.31, C:0.00, G:0.12, T:0.56
Consensus pattern (13 bp):
TTATGAATTTATT
Found at i:111210361 original size:50 final size:50
Alignment explanation
Indices: 111210248--111210489 Score: 297
Period size: 50 Copynumber: 4.7 Consensus size: 50
111210238 ATTTGGGTAA
* * *
111210248 AGAGATCCCATGTAAGACCATGTCTGGGACATGGCATTGGCATCCTTAAGATCATG
1 AGAGGTCCCATGTAAGACCATGTCTGGGACATGGCATGGGCA-CC--GAGA-C--G
*
111210304 AGAGGTCCCCTGTAAGACCATGTCTGGGACATGGCATGGGCACCGAGACG
1 AGAGGTCCCATGTAAGACCATGTCTGGGACATGGCATGGGCACCGAGACG
* * *
111210354 AGAGGTCCCATGTAAGACCATGTCTGGGACATGGCGTTGGCACCGAGATG
1 AGAGGTCCCATGTAAGACCATGTCTGGGACATGGCATGGGCACCGAGACG
* * *
111210404 AGAGGTCCCCTATAAGACCATGTCTGGGACATGGCATGGGCACC-ATCACG
1 AGAGGTCCCATGTAAGACCATGTCTGGGACATGGCATGGGCACCGA-GACG
**
111210454 AGAACATCCCATGTAAGACCATGTCTGGGACATGGC
1 AG-AGGTCCCATGTAAGACCATGTCTGGGACATGGC
111210490 TTTGGCATGT
Statistics
Matches: 166, Mismatches: 18, Indels: 9
0.86 0.09 0.05
Matches are distributed among these distances:
49 1 0.01
50 91 0.55
51 29 0.17
52 1 0.01
53 3 0.02
55 2 0.01
56 39 0.23
ACGTcount: A:0.26, C:0.24, G:0.29, T:0.20
Consensus pattern (50 bp):
AGAGGTCCCATGTAAGACCATGTCTGGGACATGGCATGGGCACCGAGACG
Found at i:111210437 original size:100 final size:103
Alignment explanation
Indices: 111210248--111210497 Score: 364
Period size: 100 Copynumber: 2.4 Consensus size: 103
111210238 ATTTGGGTAA
111210248 AGAGATCCCATGTAAGACCATGTCTGGGACATGGCATTGGCATCCTTAAGATCATGAGAGGTCCC
1 AGAGATCCCATGTAAGACCATGTCTGGGACATGGCATTGGCATCC---AGATCATGAGAGGTCCC
* *
111210313 CTGTAAGACCATGTCTGGGACATGGCATGGGCACCGA-GACG
63 CTATAAGACCATGTCTGGGACATGGCATGGGCACC-ATCACG
* * *
111210354 AGAGGTCCCATGTAAGACCATGTCTGGGACATGGCGTTGGCA-CC-GA-GATGAGAGGTCCCCTA
1 AGAGATCCCATGTAAGACCATGTCTGGGACATGGCATTGGCATCCAGATCATGAGAGGTCCCCTA
111210416 TAAGACCATGTCTGGGACATGGCATGGGCACCATCACG
66 TAAGACCATGTCTGGGACATGGCATGGGCACCATCACG
* *
111210454 AGAACATCCCATGTAAGACCATGTCTGGGACATGGCTTTGGCAT
1 AG-AGATCCCATGTAAGACCATGTCTGGGACATGGCATTGGCAT
111210498 GTTATTATCA
Statistics
Matches: 133, Mismatches: 8, Indels: 10
0.88 0.05 0.07
Matches are distributed among these distances:
99 1 0.01
100 51 0.38
101 39 0.29
105 2 0.02
106 40 0.30
ACGTcount: A:0.26, C:0.24, G:0.29, T:0.21
Consensus pattern (103 bp):
AGAGATCCCATGTAAGACCATGTCTGGGACATGGCATTGGCATCCAGATCATGAGAGGTCCCCTA
TAAGACCATGTCTGGGACATGGCATGGGCACCATCACG
Found at i:111212565 original size:20 final size:20
Alignment explanation
Indices: 111212528--111212565 Score: 51
Period size: 20 Copynumber: 1.9 Consensus size: 20
111212518 GTAAAACTAG
*
111212528 TATGAAAATATAAGATTAAA
1 TATGAAAATATAAAATTAAA
111212548 TATGAAAA-ATTAAAATTA
1 TATGAAAATA-TAAAATTA
111212566 GTCTCGGTTT
Statistics
Matches: 16, Mismatches: 1, Indels: 2
0.84 0.05 0.11
Matches are distributed among these distances:
19 1 0.06
20 15 0.94
ACGTcount: A:0.61, C:0.00, G:0.08, T:0.32
Consensus pattern (20 bp):
TATGAAAATATAAAATTAAA
Found at i:111212918 original size:25 final size:25
Alignment explanation
Indices: 111212870--111212918 Score: 62
Period size: 25 Copynumber: 2.0 Consensus size: 25
111212860 CATAATTGAA
* * *
111212870 ATGAAATGGATTGATTTTGTATATT
1 ATGAAATAGATTGATTATGAATATT
*
111212895 ATGAAATATATTGATTATGAATAT
1 ATGAAATAGATTGATTATGAATAT
111212919 ATGTGTATTG
Statistics
Matches: 20, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
25 20 1.00
ACGTcount: A:0.39, C:0.00, G:0.16, T:0.45
Consensus pattern (25 bp):
ATGAAATAGATTGATTATGAATATT
Found at i:111217354 original size:34 final size:34
Alignment explanation
Indices: 111217311--111217378 Score: 127
Period size: 34 Copynumber: 2.0 Consensus size: 34
111217301 GTGTAGTTAG
111217311 ATTGCCAATAATTCTTCAACTTTTTAAATTTATT
1 ATTGCCAATAATTCTTCAACTTTTTAAATTTATT
*
111217345 ATTGCCAATAATTCTTCAACTTTTTAGATTTATT
1 ATTGCCAATAATTCTTCAACTTTTTAAATTTATT
111217379 CTTCTTTTGT
Statistics
Matches: 33, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
34 33 1.00
ACGTcount: A:0.31, C:0.15, G:0.04, T:0.50
Consensus pattern (34 bp):
ATTGCCAATAATTCTTCAACTTTTTAAATTTATT
Found at i:111224028 original size:17 final size:17
Alignment explanation
Indices: 111224008--111224041 Score: 59
Period size: 17 Copynumber: 2.0 Consensus size: 17
111223998 AAATAGATTT
111224008 TTAATTAAAAATTTTAA
1 TTAATTAAAAATTTTAA
*
111224025 TTAATTAAAATTTTTAA
1 TTAATTAAAAATTTTAA
111224042 ACCTAAACCT
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
17 16 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (17 bp):
TTAATTAAAAATTTTAA
Found at i:111224203 original size:17 final size:17
Alignment explanation
Indices: 111224183--111224216 Score: 59
Period size: 17 Copynumber: 2.0 Consensus size: 17
111224173 AGGTTTAGGT
111224183 TTAAAAATTTTAATTAA
1 TTAAAAATTTTAATTAA
*
111224200 TTAAAATTTTTAATTAA
1 TTAAAAATTTTAATTAA
111224217 AAATCTATTT
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
17 16 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (17 bp):
TTAAAAATTTTAATTAA
Found at i:111224270 original size:18 final size:20
Alignment explanation
Indices: 111224233--111224270 Score: 62
Period size: 18 Copynumber: 2.0 Consensus size: 20
111224223 ATTTTCGTCT
111224233 CATTTAGAAATCTAAGTTGG
1 CATTTAGAAATCTAAGTTGG
111224253 CATTTA-AAATCT-AGTTGG
1 CATTTAGAAATCTAAGTTGG
111224271 ACTGTCACGT
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
18 6 0.33
19 6 0.33
20 6 0.33
ACGTcount: A:0.34, C:0.11, G:0.18, T:0.37
Consensus pattern (20 bp):
CATTTAGAAATCTAAGTTGG
Found at i:111224556 original size:17 final size:18
Alignment explanation
Indices: 111224514--111224556 Score: 54
Period size: 17 Copynumber: 2.5 Consensus size: 18
111224504 ATATTAAAAA
111224514 TATAA-TTTTATCATTTT
1 TATAATTTTTATCATTTT
* *
111224531 AATAGTTTTTAT-ATTTT
1 TATAATTTTTATCATTTT
111224548 TATAATTTT
1 TATAATTTT
111224557 AACGGATTGG
Statistics
Matches: 21, Mismatches: 4, Indels: 2
0.78 0.15 0.07
Matches are distributed among these distances:
17 15 0.71
18 6 0.29
ACGTcount: A:0.30, C:0.02, G:0.02, T:0.65
Consensus pattern (18 bp):
TATAATTTTTATCATTTT
Found at i:111228054 original size:9 final size:10
Alignment explanation
Indices: 111228043--111228107 Score: 51
Period size: 12 Copynumber: 5.9 Consensus size: 10
111228033 GGTATAAATA
111228043 AATAAATAA-
1 AATAAATAAT
*
111228052 AATGTAATAAT
1 AAT-AAATAAT
111228063 AATAATGATAAT
1 AATAA--ATAAT
111228075 AATAATAATAAT
1 AAT-A-AATAAT
111228087 AATAAATTCAAT
1 AATAAA-T-AAT
111228099 AATAAATAA
1 AATAAATAA
111228108 AATGACAGGA
Statistics
Matches: 46, Mismatches: 2, Indels: 15
0.73 0.03 0.24
Matches are distributed among these distances:
9 3 0.07
10 10 0.22
11 6 0.13
12 25 0.54
13 1 0.02
14 1 0.02
ACGTcount: A:0.65, C:0.02, G:0.03, T:0.31
Consensus pattern (10 bp):
AATAAATAAT
Found at i:111228103 original size:3 final size:3
Alignment explanation
Indices: 111228056--111228091 Score: 63
Period size: 3 Copynumber: 12.0 Consensus size: 3
111228046 AAATAAAATG
*
111228056 TAA TAA TAA TAA TGA TAA TAA TAA TAA TAA TAA TAA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
111228092 ATTCAATAAT
Statistics
Matches: 31, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
3 31 1.00
ACGTcount: A:0.64, C:0.00, G:0.03, T:0.33
Consensus pattern (3 bp):
TAA
Found at i:111234133 original size:8 final size:8
Alignment explanation
Indices: 111234120--111234144 Score: 50
Period size: 8 Copynumber: 3.1 Consensus size: 8
111234110 TTCGCTGTGT
111234120 TTCAAAAC
1 TTCAAAAC
111234128 TTCAAAAC
1 TTCAAAAC
111234136 TTCAAAAC
1 TTCAAAAC
111234144 T
1 T
111234145 CTTTGCCTCC
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
8 17 1.00
ACGTcount: A:0.48, C:0.24, G:0.00, T:0.28
Consensus pattern (8 bp):
TTCAAAAC
Found at i:111258406 original size:9 final size:10
Alignment explanation
Indices: 111258395--111258456 Score: 56
Period size: 12 Copynumber: 5.9 Consensus size: 10
111258385 GGTATAAATA
111258395 AATAAATAA-
1 AATAAATAAT
*
111258404 AATGTAATAAT
1 AAT-AAATAAT
111258415 AATAATGATAAT
1 AATAA--ATAAT
111258427 AAT-AATAAT
1 AATAAATAAT
111258436 AATAAATTCAAT
1 AATAAA-T-AAT
111258448 AATAAATAA
1 AATAAATAA
111258457 AATGACAGGA
Statistics
Matches: 44, Mismatches: 2, Indels: 13
0.75 0.03 0.22
Matches are distributed among these distances:
9 11 0.25
10 10 0.23
11 6 0.14
12 17 0.39
ACGTcount: A:0.65, C:0.02, G:0.03, T:0.31
Consensus pattern (10 bp):
AATAAATAAT
Found at i:111258452 original size:3 final size:3
Alignment explanation
Indices: 111258408--111258440 Score: 57
Period size: 3 Copynumber: 11.0 Consensus size: 3
111258398 AAATAAAATG
*
111258408 TAA TAA TAA TAA TGA TAA TAA TAA TAA TAA TAA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
111258441 ATTCAATAAT
Statistics
Matches: 28, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
3 28 1.00
ACGTcount: A:0.64, C:0.00, G:0.03, T:0.33
Consensus pattern (3 bp):
TAA
Found at i:111260171 original size:11 final size:11
Alignment explanation
Indices: 111260155--111260181 Score: 54
Period size: 11 Copynumber: 2.5 Consensus size: 11
111260145 CGTTCAATAT
111260155 AGAAACAAAAA
1 AGAAACAAAAA
111260166 AGAAACAAAAA
1 AGAAACAAAAA
111260177 AGAAA
1 AGAAA
111260182 TGCTGTATAC
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 16 1.00
ACGTcount: A:0.81, C:0.07, G:0.11, T:0.00
Consensus pattern (11 bp):
AGAAACAAAAA
Found at i:111260322 original size:12 final size:12
Alignment explanation
Indices: 111260301--111260330 Score: 51
Period size: 12 Copynumber: 2.5 Consensus size: 12
111260291 ATCCACGGCG
*
111260301 GCGGCGGCAACA
1 GCGGCAGCAACA
111260313 GCGGCAGCAACA
1 GCGGCAGCAACA
111260325 GCGGCA
1 GCGGCA
111260331 ACACCAGTAA
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:0.27, C:0.33, G:0.40, T:0.00
Consensus pattern (12 bp):
GCGGCAGCAACA
Found at i:111262937 original size:22 final size:21
Alignment explanation
Indices: 111262912--111262955 Score: 52
Period size: 22 Copynumber: 2.0 Consensus size: 21
111262902 AACGTGTCCT
* *
111262912 AAATTACATAATATATATATAA
1 AAATAACATAAAATAT-TATAA
*
111262934 AAATAATATAAAATATTATAA
1 AAATAACATAAAATATTATAA
111262955 A
1 A
111262956 CTTAAAAATG
Statistics
Matches: 19, Mismatches: 3, Indels: 1
0.83 0.13 0.04
Matches are distributed among these distances:
21 6 0.32
22 13 0.68
ACGTcount: A:0.64, C:0.02, G:0.00, T:0.34
Consensus pattern (21 bp):
AAATAACATAAAATATTATAA
Found at i:111263549 original size:28 final size:29
Alignment explanation
Indices: 111263504--111263562 Score: 111
Period size: 28 Copynumber: 2.1 Consensus size: 29
111263494 ATATATATAT
111263504 TCATAAAAAAAAGAGAGTGACTAAGTTAA
1 TCATAAAAAAAAGAGAGTGACTAAGTTAA
111263533 TCATAAAAAAAA-AGAGTGACTAAGTTAA
1 TCATAAAAAAAAGAGAGTGACTAAGTTAA
111263561 TC
1 TC
111263563 CTTTAAAGCA
Statistics
Matches: 30, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
28 18 0.60
29 12 0.40
ACGTcount: A:0.54, C:0.08, G:0.15, T:0.22
Consensus pattern (29 bp):
TCATAAAAAAAAGAGAGTGACTAAGTTAA
Found at i:111263611 original size:49 final size:50
Alignment explanation
Indices: 111263567--111263670 Score: 185
Period size: 49 Copynumber: 2.1 Consensus size: 50
111263557 TTAATCCTTT
*
111263567 AAAGCAGAGATGGTAAGTGAAAAAGTATTAATAAACAATATAAT-CTGCA
1 AAAGAAGAGATGGTAAGTGAAAAAGTATTAATAAACAATATAATCCTGCA
111263616 AAAGAAGAGATGGTAAGTGAAAAAGTATTAATAAACAATATAAT-CTGCA
1 AAAGAAGAGATGGTAAGTGAAAAAGTATTAATAAACAATATAATCCTGCA
111263665 AAAGAA
1 AAAGAA
111263671 TATTCTCCAT
Statistics
Matches: 54, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
49 54 1.00
ACGTcount: A:0.54, C:0.07, G:0.18, T:0.21
Consensus pattern (50 bp):
AAAGAAGAGATGGTAAGTGAAAAAGTATTAATAAACAATATAATCCTGCA
Found at i:111264417 original size:16 final size:17
Alignment explanation
Indices: 111264386--111264419 Score: 52
Period size: 16 Copynumber: 2.1 Consensus size: 17
111264376 TCCAGTTTTC
*
111264386 TTTAAATTTTATAAAAA
1 TTTAAATTTAATAAAAA
111264403 TTTAAA-TTAATAAAAA
1 TTTAAATTTAATAAAAA
111264419 T
1 T
111264420 AACTTTTAAA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
16 10 0.62
17 6 0.38
ACGTcount: A:0.56, C:0.00, G:0.00, T:0.44
Consensus pattern (17 bp):
TTTAAATTTAATAAAAA
Found at i:111273407 original size:224 final size:218
Alignment explanation
Indices: 111272972--111273414 Score: 638
Period size: 224 Copynumber: 2.0 Consensus size: 218
111272962 GATATCAGAT
* * **
111272972 AATTCCTAACCTAGTTAGATTGAAAAAAAATGTCATTTTTTAAACAACCAACCATGTCATTAGAA
1 AATTCCCAACCTAGTTAGATTGAAAAAAAATGTCATTTTTAAAACAACCAACCACCTCATTAGAA
*
111273037 TCATTTTTAAGATATTCCGCTTCGACGCAGGATAATCTGCTAGTCAGTTCCTCGATTTGTGTCTT
66 TCATTTTTAAGATATTCCGCTTCGACGCAGGATAATCTGCTAGTCAGTTCCTCGATATGTGTCTT
* *
111273102 TAGTTTATCCCTTTCTCTTGAAATGTACAGAAGTTGATCTTTAAGATTCTGCAAAGAATGAAATA
131 TAGTTCATCCCTTTCTCTTGAAATGTACAGAAGTTGATCTTTAAGAATCTGCAAAGAATGAAATA
111273167 AACTTTTCAGTCTCTAAGAAATA
196 AACTTTTCAGTCTCTAAGAAATA
*
111273190 AATTCCCAACCTAGTTAGATTGCTAGCAAGAAAAGA-GTCATTTTTAAAAATAACCAACCACCTC
1 AATTCCCAACCTAGTTAGATTG--A--AA-AAAA-ATGTCATTTTT-AAAACAACCAACCACCTC
* * ** * * *
111273254 ATTAGAATCGTTTTTAAGATTTTCCTTTTCGAGGCAGGATAATTTGCTGGTCAGTTCCTCGATAT
59 ATTAGAATCATTTTTAAGATATTCCGCTTCGACGCAGGATAATCTGCTAGTCAGTTCCTCGATAT
* *
111273319 GTGTCTTTAGTTCATCCCTTTCTGTTGAAATGTCCAGAAGTTGAT-TTTGAAGAATCTGCAAAGA
124 GTGTCTTTAGTTCATCCCTTTCTCTTGAAATGTACAGAAGTTGATCTTT-AAGAATCTGCAAAGA
*
111273383 ATGAATTAAACTTTTCAGTCTCTAAGAAATA
188 ATGAAATAAACTTTTCAGTCTCTAAGAAATA
111273414 A
1 A
111273415 TTACCAGTTC
Statistics
Matches: 199, Mismatches: 18, Indels: 10
0.88 0.08 0.04
Matches are distributed among these distances:
218 21 0.11
220 1 0.01
222 2 0.01
223 16 0.08
224 159 0.80
ACGTcount: A:0.33, C:0.17, G:0.15, T:0.35
Consensus pattern (218 bp):
AATTCCCAACCTAGTTAGATTGAAAAAAAATGTCATTTTTAAAACAACCAACCACCTCATTAGAA
TCATTTTTAAGATATTCCGCTTCGACGCAGGATAATCTGCTAGTCAGTTCCTCGATATGTGTCTT
TAGTTCATCCCTTTCTCTTGAAATGTACAGAAGTTGATCTTTAAGAATCTGCAAAGAATGAAATA
AACTTTTCAGTCTCTAAGAAATA
Found at i:111284470 original size:29 final size:29
Alignment explanation
Indices: 111284436--111284491 Score: 85
Period size: 29 Copynumber: 1.9 Consensus size: 29
111284426 TGTTTGTCTC
* *
111284436 ATGTTACATTTTAGTTACTTATGTTTGAA
1 ATGTTACATTTTAGTCACTTATATTTGAA
*
111284465 ATGTTACGTTTTAGTCACTTATATTTG
1 ATGTTACATTTTAGTCACTTATATTTG
111284492 TGTTGTAATA
Statistics
Matches: 24, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
29 24 1.00
ACGTcount: A:0.25, C:0.09, G:0.14, T:0.52
Consensus pattern (29 bp):
ATGTTACATTTTAGTCACTTATATTTGAA
Found at i:111285965 original size:9 final size:9
Alignment explanation
Indices: 111285951--111285993 Score: 52
Period size: 9 Copynumber: 4.8 Consensus size: 9
111285941 TATAAACTGA
111285951 AAAAAAAAG
1 AAAAAAAAG
*
111285960 AAAAAAAGG
1 AAAAAAAAG
*
111285969 AAAAGAAAG
1 AAAAAAAAG
111285978 AAAAAGAAA-
1 AAAAA-AAAG
111285987 AAAAAAA
1 AAAAAAA
111285994 TATAAACTGA
Statistics
Matches: 29, Mismatches: 4, Indels: 3
0.81 0.11 0.08
Matches are distributed among these distances:
8 2 0.07
9 24 0.83
10 3 0.10
ACGTcount: A:0.86, C:0.00, G:0.14, T:0.00
Consensus pattern (9 bp):
AAAAAAAAG
Found at i:111289660 original size:19 final size:20
Alignment explanation
Indices: 111289632--111289675 Score: 74
Period size: 19 Copynumber: 2.3 Consensus size: 20
111289622 AATTGGACAC
111289632 CTAT-TTATCTAGATCCA-T
1 CTATATTATCTAGATCCATT
111289650 CTATATTATCTAGATCCATT
1 CTATATTATCTAGATCCATT
111289670 CTATAT
1 CTATAT
111289676 GTATTTTTAA
Statistics
Matches: 24, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
18 4 0.17
19 13 0.54
20 7 0.29
ACGTcount: A:0.30, C:0.20, G:0.05, T:0.45
Consensus pattern (20 bp):
CTATATTATCTAGATCCATT
Found at i:111289864 original size:30 final size:28
Alignment explanation
Indices: 111289817--111289880 Score: 69
Period size: 30 Copynumber: 2.2 Consensus size: 28
111289807 TATAAGAATA
111289817 TTAATTATTAAGAATTTATTAAATATATAT-
1 TTAATTATTAAGAATTTA-T-AATA-ATATG
*
111289847 TTAATTA-TAATATATTTATAATAATATG
1 TTAATTATTAAGA-ATTTATAATAATATG
111289875 TTAATT
1 TTAATT
111289881 TATATTTATA
Statistics
Matches: 31, Mismatches: 1, Indels: 6
0.82 0.03 0.16
Matches are distributed among these distances:
27 4 0.13
28 10 0.32
29 5 0.16
30 12 0.39
ACGTcount: A:0.45, C:0.00, G:0.03, T:0.52
Consensus pattern (28 bp):
TTAATTATTAAGAATTTATAATAATATG
Found at i:111289879 original size:28 final size:27
Alignment explanation
Indices: 111289807--111289997 Score: 74
Period size: 28 Copynumber: 6.7 Consensus size: 27
111289797 TCCAAATTCA
* *
111289807 TATAAGAATA-TTAATTATTAAGA-ATT
1 TATAATAATATTTAATTA-TAATATATT
111289833 TATTAAATATATATTTAATTATAATATATT
1 TA-T-AATA-ATATTTAATTATAATATATT
* *
111289863 TATAATAATATGTTAATT-TATATTTATAG
1 TATAATAATAT-TTAATTATA-ATATAT-T
* * * *
111289892 TATCAT-ATATTATGATT-TGAGTAAATT
1 TATAATAATATT-TAATTAT-AATATATT
* *
111289919 CATATAAGAATA-TTGATTATAATA-ATTT
1 --TATAATAATATTTAATTATAATATA-TT
*
111289947 TATTAAATTAATGTATTAATTATAATATATT
1 TA-T-AA-TAATAT-TTAATTATAATATATT
111289978 T-TAATAATATGTTAATTATA
1 TATAATAATAT-TTAATTATA
111289998 TTTAAGTATC
Statistics
Matches: 126, Mismatches: 18, Indels: 41
0.68 0.10 0.22
Matches are distributed among these distances:
26 4 0.03
27 24 0.19
28 44 0.35
29 24 0.19
30 15 0.12
31 14 0.11
32 1 0.01
ACGTcount: A:0.45, C:0.01, G:0.06, T:0.49
Consensus pattern (27 bp):
TATAATAATATTTAATTATAATATATT
Found at i:111289920 original size:114 final size:110
Alignment explanation
Indices: 111289800--111290096 Score: 416
Period size: 114 Copynumber: 2.7 Consensus size: 110
111289790 TCATTTATCC
*
111289800 AAATTCATATAAGAATATTAATTATTAAGAATTTATTAAATATATATTTAATTATAATATATTTA
1 AAATTCATATAAGAATATTGATTA-TAA-AATTTATTAAATATATATTTAATTATAATATATTTA
*
111289865 TAATAATATGTTAATTTATATTTATAGTATCATATATTATGATTTGAGT
64 TAATAATATGTTAATTTATATTTA-AGTATCATATAATAT-ATTTGAGT
*
111289914 AAATTCATATAAGAATATTGATTATAATAATTTTATTAAAT-TAATGTATTAATTATAATATATT
1 AAATTCATATAAGAATATTGATTATAA-AA-TTTATTAAATAT-ATAT-TTAATTATAATATATT
111289978 T-TAATAATATGTTAA-TTATATTTAAGTATCATATAATATATTTGAGT
62 TATAATAATATGTTAATTTATATTTAAGTATCATATAATATATTTGAGT
111290025 AAATTCATATAAG-A-A-TGA-TATAAAATTTATTAAATATATATTTTAA-T-TAA-ATATTTAT
1 AAATTCATATAAGAATATTGATTATAAAATTTATTAAATATATA-TTTAATTATAATATATTTAT
111290083 AATAATATGTTAAT
65 AATAATATGTTAAT
111290097 ATGATAAATT
Statistics
Matches: 171, Mismatches: 5, Indels: 24
0.86 0.03 0.12
Matches are distributed among these distances:
102 6 0.04
103 17 0.10
104 1 0.01
105 16 0.09
106 4 0.02
107 5 0.03
108 3 0.02
109 1 0.01
110 1 0.01
111 21 0.12
112 14 0.08
113 15 0.09
114 50 0.29
115 17 0.10
ACGTcount: A:0.45, C:0.02, G:0.06, T:0.47
Consensus pattern (110 bp):
AAATTCATATAAGAATATTGATTATAAAATTTATTAAATATATATTTAATTATAATATATTTATA
ATAATATGTTAATTTATATTTAAGTATCATATAATATATTTGAGT
Found at i:111291275 original size:15 final size:15
Alignment explanation
Indices: 111291229--111291280 Score: 54
Period size: 15 Copynumber: 3.5 Consensus size: 15
111291219 CATACATAAC
111291229 AAATA-TAATTATAT
1 AAATATTAATTATAT
*
111291243 AAATTTTAGATTAT-T
1 AAATATTA-ATTATAT
*
111291258 AAATATTAATTGTAT
1 AAATATTAATTATAT
*
111291273 AAAAATTA
1 AAATATTA
111291281 TGAAAGATGT
Statistics
Matches: 31, Mismatches: 4, Indels: 5
0.77 0.10 0.12
Matches are distributed among these distances:
14 8 0.26
15 18 0.58
16 5 0.16
ACGTcount: A:0.52, C:0.00, G:0.04, T:0.44
Consensus pattern (15 bp):
AAATATTAATTATAT
Found at i:111298541 original size:20 final size:20
Alignment explanation
Indices: 111298516--111298566 Score: 84
Period size: 20 Copynumber: 2.5 Consensus size: 20
111298506 AGAAAAGGAA
111298516 AAATGCATGCAAAAATGAAG
1 AAATGCATGCAAAAATGAAG
111298536 AAATGCATGCAAAAATGAAG
1 AAATGCATGCAAAAATGAAG
* *
111298556 ACACGCATGCA
1 AAATGCATGCA
111298567 CACATTAAAG
Statistics
Matches: 29, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
20 29 1.00
ACGTcount: A:0.51, C:0.16, G:0.20, T:0.14
Consensus pattern (20 bp):
AAATGCATGCAAAAATGAAG
Found at i:111306745 original size:12 final size:12
Alignment explanation
Indices: 111306732--111306763 Score: 50
Period size: 10 Copynumber: 2.8 Consensus size: 12
111306722 AGACAGCACT
111306732 TTTTTCTTTT-C
1 TTTTTCTTTTGC
111306743 -TTTTCTTTTGC
1 TTTTTCTTTTGC
111306754 TTTTTCTTTT
1 TTTTTCTTTT
111306764 ACCTAATTCA
Statistics
Matches: 19, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
10 9 0.47
11 1 0.05
12 9 0.47
ACGTcount: A:0.00, C:0.16, G:0.03, T:0.81
Consensus pattern (12 bp):
TTTTTCTTTTGC
Found at i:111329846 original size:40 final size:41
Alignment explanation
Indices: 111329800--111329977 Score: 256
Period size: 40 Copynumber: 4.4 Consensus size: 41
111329790 TCCAATTTCT
*
111329800 AGCACAAAGCCTGCGGGATTTAA-CCCGAATATCTATTACC
1 AGCACAAAGCCTGCGGGATTTAACCCCGGATATCTATTACC
111329840 AGCACAAAGCCTGCGGGATTTAA-CCCGGATATCTATTACC
1 AGCACAAAGCCTGCGGGATTTAACCCCGGATATCTATTACC
* * *
111329880 AGCACAAAACCTGCGGGATTTAACCCGGCGGACATCTATTATC
1 AGCACAAAGCCTGCGGGATTTAACCC--CGGATATCTATTACC
* *
111329923 AGCAC-AAGCCTACGGGATTTAACCCC-GATATCTATTGCC
1 AGCACAAAGCCTGCGGGATTTAACCCCGGATATCTATTACC
111329962 AGCACAAAGCCTGCGG
1 AGCACAAAGCCTGCGG
111329978 ACTATAAGTC
Statistics
Matches: 124, Mismatches: 10, Indels: 8
0.87 0.07 0.06
Matches are distributed among these distances:
39 15 0.12
40 71 0.57
41 2 0.02
42 18 0.15
43 18 0.15
ACGTcount: A:0.30, C:0.29, G:0.20, T:0.21
Consensus pattern (41 bp):
AGCACAAAGCCTGCGGGATTTAACCCCGGATATCTATTACC
Found at i:111329955 original size:82 final size:80
Alignment explanation
Indices: 111329800--111329977 Score: 259
Period size: 82 Copynumber: 2.2 Consensus size: 80
111329790 TCCAATTTCT
* *
111329800 AGCACAAAGCCTGCGGGATTTAACCCGAATATCTATTACCAGCACAAAGCCTGCGGGATTTAACC
1 AGCACAAAGCCTGCGGGATTTAACCCGAACATCTATTACCAGCACAAAGCCTACGGGATTTAACC
*
111329865 CGGATATCTATTACC
66 CCGATATCTATTACC
* * *
111329880 AGCACAAAACCTGCGGGATTTAACCCGGCGGACATCTATTATCAGCAC-AAGCCTACGGGATTTA
1 AGCACAAAGCCTGCGGGATTTAA-CC--CGAACATCTATTACCAGCACAAAGCCTACGGGATTTA
*
111329944 ACCCCGATATCTATTGCC
63 ACCCCGATATCTATTACC
111329962 AGCACAAAGCCTGCGG
1 AGCACAAAGCCTGCGG
111329978 ACTATAAGTC
Statistics
Matches: 87, Mismatches: 8, Indels: 4
0.88 0.08 0.04
Matches are distributed among these distances:
80 22 0.25
81 2 0.02
82 46 0.53
83 17 0.20
ACGTcount: A:0.30, C:0.29, G:0.20, T:0.21
Consensus pattern (80 bp):
AGCACAAAGCCTGCGGGATTTAACCCGAACATCTATTACCAGCACAAAGCCTACGGGATTTAACC
CCGATATCTATTACC
Found at i:111353033 original size:11 final size:11
Alignment explanation
Indices: 111353001--111353034 Score: 52
Period size: 11 Copynumber: 3.2 Consensus size: 11
111352991 TTCTCTGATC
111353001 TTCTTTATTTT
1 TTCTTTATTTT
*
111353012 CTCTTTATTTT
1 TTCTTTATTTT
111353023 TTCTTT-TTTT
1 TTCTTTATTTT
111353033 TT
1 TT
111353035 GCCTTTTAAT
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
10 6 0.29
11 15 0.71
ACGTcount: A:0.06, C:0.12, G:0.00, T:0.82
Consensus pattern (11 bp):
TTCTTTATTTT
Found at i:111353883 original size:234 final size:229
Alignment explanation
Indices: 111353418--111353927 Score: 779
Period size: 234 Copynumber: 2.2 Consensus size: 229
111353408 TTGTGTTCGG
* * * * *
111353418 TGAAATTAGATGAATTTGAGGCAGTATAATCTTTTGTTTTAATCGAATCTTTTGTTTGCATGATC
1 TGAAATTAGATGACTTTGAGGCAATTTAATCTCTTGTTTTAATCGAATCTTGTGTTTGCATGATC
*
111353483 ATATAATCGAGTTTTGTTTGTCAAAGTTTTCCCCCCTTATTTGATAAGTTTGATGTTCTATTATT
66 ATATAATCGAGTTTTGTTTGTCAAAGTTTTCCCCCCTTATTTGATAAATTTGATGTTCTATTATT
* * * *
111353548 GGAAAAATATGATTAGGAAAATGAAAGATGAATAATTTTAGAAAATTCTTTAATTCCGTTGTTTC
131 GGAAAAAAATGATTAGGAAAATGAAAGATGAATAATTGTAGAAAATTCTTTAACTACGTTGTTTC
111353613 ATGCTGATCACCGCTTTAAATTAGAAGTGCTAGA
196 ATGCTGATCACCGCTTTAAATTAGAAGTGCTAGA
* * *
111353647 TGAAATTAGATGACTTTGAGGCAATTTAATCTCTTGTTTTGATCTAATGTTGTGTTTGCATGATC
1 TGAAATTAGATGACTTTGAGGCAATTTAATCTCTTGTTTTAATCGAATCTTGTGTTTGCATGATC
* **
111353712 ATATAATCGAGTTTTGTTTGTCAATGTTCTTTTTCCCCTTATTTGATAAATTTG-TGGTTCTATT
66 ATATAATCGAGTTTTGTTTGTCAAAG-T-TTTCCCCCCTTATTTGATAAATTTGAT-GTTCTATT
*
111353776 ATTGGAAAAAAAATTGATTAGGAAAATGAAAAGATTAATAATTGTAGAAAATTCTTTAACTACGT
128 ATTGG-AAAAAAA-TGATTAGGAAAATG-AAAGATGAATAATTGTAGAAAATTCTTTAACTACGT
* *
111353841 TGTTTCATGCTGATCACTGCTTTAAATTAGTAGTGCTAGA
190 TGTTTCATGCTGATCACCGCTTTAAATTAGAAGTGCTAGA
*
111353881 TGAAATTAGATGACTTTGAGGCAATTTAATCTCTTATTTTAATCGAA
1 TGAAATTAGATGACTTTGAGGCAATTTAATCTCTTGTTTTAATCGAA
111353928 CCCAAGTTTT
Statistics
Matches: 253, Mismatches: 22, Indels: 7
0.90 0.08 0.02
Matches are distributed among these distances:
229 82 0.32
230 2 0.01
231 35 0.14
232 6 0.02
233 14 0.06
234 114 0.45
ACGTcount: A:0.31, C:0.11, G:0.17, T:0.42
Consensus pattern (229 bp):
TGAAATTAGATGACTTTGAGGCAATTTAATCTCTTGTTTTAATCGAATCTTGTGTTTGCATGATC
ATATAATCGAGTTTTGTTTGTCAAAGTTTTCCCCCCTTATTTGATAAATTTGATGTTCTATTATT
GGAAAAAAATGATTAGGAAAATGAAAGATGAATAATTGTAGAAAATTCTTTAACTACGTTGTTTC
ATGCTGATCACCGCTTTAAATTAGAAGTGCTAGA
Found at i:111354337 original size:231 final size:234
Alignment explanation
Indices: 111353952--111354466 Score: 631
Period size: 231 Copynumber: 2.2 Consensus size: 234
111353942 GTCAAGTGAA
* * * * *
111353952 TTTTTTCCTTATTTAATAATTTTGCTGTTAAATTATTAATGAAAAATTT-ATCAGTAAAAAGAGA
1 TTTTTTTCTTATTTTATAATTTTGCTGTTAAATTATTGATG-AAAATTTGATCAGGAAAAAGAAA
* *
111354016 AGATGAATAATTGTTGAAATTTTTTTAGTTATGTTGTTTCATGTGGATCACTGCTTTAAACTCGT
65 AGATGAATAATTGTTGAAATTTCTTTAGTTATATTGTTTCATGTGGATCACTGCTTTAAACTCGT
* ** * * *
111354081 AGTGTTTTATGAAATTAAGTGACTTTGAGG-TGATTTAATCTATTGTTTTAA-CTGAATCTTGTG
130 AGTGCTAGATGAAATTAAGTGACTTTGAGGCAG-TTAAATCTATTGTTTTAATCT-AATCTTCTG
* *
111354144 TTTGCATGATCAAATAATCAAGTT-TTACT-TGTAAAGTT-CT
193 TTTGCATGATCAAATAATCAAGTTCTT-CTCTGCAAAGTTAAT
* * *
111354184 TTTTTTT-TT-TTGTTGATAATTTTGATGTTAAATTATTGATGAAAATTTGATCAGGGAGAAGAA
1 TTTTTTTCTTATT-TT-ATAATTTTGCTGTTAAATTATTGATGAAAATTTGATCAGGAAAAAGAA
* *
111354247 AAGATTAATAGTTGTTGAGAA-TTCTTTA-TTATATTGTTTCATGTTGG-TCACTGCTTTAAACT
64 AAGATGAATAATTGTTGA-AATTTCTTTAGTTATATTGTTTCATG-TGGATCACTGCTTTAAACT
* *
111354309 TGTAGTGCTAGATGAAATT-AGATGACTTTGAGGCAGTTAAATCTCTTGTTTTAATCTAATCTTC
127 CGTAGTGCTAGATGAAATTAAG-TGACTTTGAGGCAGTTAAATCTATTGTTTTAATCTAATCTTC
* * *
111354373 TGTTTGCATGATCATATAATCAAGTTCTTGTCTGCCAAGTTAAT
191 TGTTTGCATGATCAAATAATCAAGTTCTTCTCTGCAAAGTTAAT
*
111354417 TTTTTTTCTTATTTTATAATTTTGCTGTTAAATTATTGATGAAAAATTGA
1 TTTTTTTCTTATTTTATAATTTTGCTGTTAAATTATTGATGAAAATTTGA
111354467 GCAAGAGTGA
Statistics
Matches: 243, Mismatches: 27, Indels: 25
0.82 0.09 0.08
Matches are distributed among these distances:
230 4 0.02
231 113 0.47
232 77 0.32
233 43 0.18
234 4 0.02
235 2 0.01
ACGTcount: A:0.30, C:0.08, G:0.16, T:0.46
Consensus pattern (234 bp):
TTTTTTTCTTATTTTATAATTTTGCTGTTAAATTATTGATGAAAATTTGATCAGGAAAAAGAAAA
GATGAATAATTGTTGAAATTTCTTTAGTTATATTGTTTCATGTGGATCACTGCTTTAAACTCGTA
GTGCTAGATGAAATTAAGTGACTTTGAGGCAGTTAAATCTATTGTTTTAATCTAATCTTCTGTTT
GCATGATCAAATAATCAAGTTCTTCTCTGCAAAGTTAAT
Found at i:111354608 original size:86 final size:86
Alignment explanation
Indices: 111354463--111354636 Score: 339
Period size: 86 Copynumber: 2.0 Consensus size: 86
111354453 TGATGAAAAA
111354463 TTGAGCAAGAGTGAATCGTATAAGGATATTAATTTACTTATGCTTGAATATGTATATTTTTGTAT
1 TTGAGCAAGAGTGAATCGTATAAGGATATTAATTTACTTATGCTTGAATATGTATATTTTTGTAT
*
111354528 TTGTTGTCAAATTGTGTTTAT
66 TTGTTGTCAAACTGTGTTTAT
111354549 TTGAGCAAGAGTGAATCGTATAAGGATATTAATTTACTTATGCTTGAATATGTATATTTTTGTAT
1 TTGAGCAAGAGTGAATCGTATAAGGATATTAATTTACTTATGCTTGAATATGTATATTTTTGTAT
111354614 TTGTTGTCAAACTGTGTTTAT
66 TTGTTGTCAAACTGTGTTTAT
111354635 TT
1 TT
111354637 TCAGGTATGG
Statistics
Matches: 87, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
86 87 1.00
ACGTcount: A:0.29, C:0.06, G:0.18, T:0.47
Consensus pattern (86 bp):
TTGAGCAAGAGTGAATCGTATAAGGATATTAATTTACTTATGCTTGAATATGTATATTTTTGTAT
TTGTTGTCAAACTGTGTTTAT
Found at i:111359388 original size:21 final size:21
Alignment explanation
Indices: 111359364--111359406 Score: 86
Period size: 21 Copynumber: 2.0 Consensus size: 21
111359354 GAATATTGGA
111359364 TGGTTTTATATATTCTGGTTT
1 TGGTTTTATATATTCTGGTTT
111359385 TGGTTTTATATATTCTGGTTT
1 TGGTTTTATATATTCTGGTTT
111359406 T
1 T
111359407 ATATTTGTTT
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 22 1.00
ACGTcount: A:0.14, C:0.05, G:0.19, T:0.63
Consensus pattern (21 bp):
TGGTTTTATATATTCTGGTTT
Found at i:111359461 original size:17 final size:17
Alignment explanation
Indices: 111359435--111359468 Score: 59
Period size: 17 Copynumber: 2.0 Consensus size: 17
111359425 TTGCTCTAAA
111359435 TATGTAGTCAAATTATG
1 TATGTAGTCAAATTATG
*
111359452 TATGTGGTCAAATTATG
1 TATGTAGTCAAATTATG
111359469 GTGCCAGTTA
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
17 16 1.00
ACGTcount: A:0.32, C:0.06, G:0.21, T:0.41
Consensus pattern (17 bp):
TATGTAGTCAAATTATG
Found at i:111367954 original size:54 final size:54
Alignment explanation
Indices: 111367848--111367964 Score: 128
Period size: 54 Copynumber: 2.2 Consensus size: 54
111367838 TACAATAGTA
* * * * *
111367848 GTCATTTAATTATTAGTATCTTTTTGTTACCTAATTATGAAAAGTTATAAAATG
1 GTCATTCAACTATTAGTATCTTTTTGTCACCTAACTATGAAAAGTTACAAAATG
* **
111367902 GTCATTCAACTATTAGTATTTTTTTGTCAGCC-AACTATGAAGCGTTACAAAATG
1 GTCATTCAACTATTAGTATCTTTTTGTCA-CCTAACTATGAAAAGTTACAAAATG
* *
111367956 ATTATTCAA
1 GTCATTCAA
111367965 TTTTATCTTT
Statistics
Matches: 52, Mismatches: 10, Indels: 2
0.81 0.16 0.03
Matches are distributed among these distances:
54 50 0.96
55 2 0.04
ACGTcount: A:0.34, C:0.12, G:0.12, T:0.42
Consensus pattern (54 bp):
GTCATTCAACTATTAGTATCTTTTTGTCACCTAACTATGAAAAGTTACAAAATG
Found at i:111368368 original size:32 final size:32
Alignment explanation
Indices: 111368331--111368394 Score: 119
Period size: 32 Copynumber: 2.0 Consensus size: 32
111368321 AATAAAAGTA
*
111368331 TACTTACTTTATAAAAGGAAATATCTTTTGAT
1 TACTTACTTTATAAAAGAAAATATCTTTTGAT
111368363 TACTTACTTTATAAAAGAAAATATCTTTTGAT
1 TACTTACTTTATAAAAGAAAATATCTTTTGAT
111368395 GATTTTTAAT
Statistics
Matches: 31, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
32 31 1.00
ACGTcount: A:0.39, C:0.09, G:0.08, T:0.44
Consensus pattern (32 bp):
TACTTACTTTATAAAAGAAAATATCTTTTGAT
Found at i:111377060 original size:187 final size:182
Alignment explanation
Indices: 111376783--111377115 Score: 517
Period size: 187 Copynumber: 1.8 Consensus size: 182
111376773 TTGAAACATA
*
111376783 CTGTATATAGCTTTGTTTCCAGTGATAATTCTTAATGAATCTACTCTTTTAGAGGCTTATGATGA
1 CTGTATATAGCTTTGTTTCCAGTGATAATTATTAATGAATCTACTCTTTTAGAGGCTTATGATGA
*
111376848 TTAAGAATTGCCTACATTGTCAGATCTTTACTCTGATGACAATAAAA-TAAACAAAATCTGAGGC
66 TTAAGAATTGCCTACATTGTCAGATCATTACTCTGATGACAATAAAAGT-AAC-AAATCTGAGGC
111376912 CTAAAGTTGCTGGTCATAACTTAAAAACTTATTTGCAACGGACATGCATGTAAT
129 CTAAAGTTGCTGGTCATAACTTAAAAACTTATTTGCAACGGACATGCATGTAAT
* **
111376966 CTGTGTATAGCTTTGTTTTTGAGTGATGTAATTATTAATGAATCTA-TGCTTTTACGAGGCTTAT
1 CTGTATATAGCTTTG-TTTCCAGTGA--TAATTATTAATGAATCTACT-CTTTTA-GAGGCTTAT
* *
111377030 GATGATTGAGAATTGCCTACATTGTCAGATCATTACTTTGATGACAATAAAAGTAACAAATCTGA
61 GATGATTAAGAATTGCCTACATTGTCAGATCATTACTCTGATGACAATAAAAGTAACAAATCTGA
*
111377095 GGCCTTAAGTTGCTGGTCATA
126 GGCCTAAAGTTGCTGGTCATA
111377116 TAGAGTGTGA
Statistics
Matches: 136, Mismatches: 8, Indels: 9
0.89 0.05 0.06
Matches are distributed among these distances:
183 14 0.10
184 8 0.06
185 1 0.01
186 51 0.38
187 61 0.45
188 1 0.01
ACGTcount: A:0.32, C:0.14, G:0.18, T:0.36
Consensus pattern (182 bp):
CTGTATATAGCTTTGTTTCCAGTGATAATTATTAATGAATCTACTCTTTTAGAGGCTTATGATGA
TTAAGAATTGCCTACATTGTCAGATCATTACTCTGATGACAATAAAAGTAACAAATCTGAGGCCT
AAAGTTGCTGGTCATAACTTAAAAACTTATTTGCAACGGACATGCATGTAAT
Found at i:111390360 original size:16 final size:16
Alignment explanation
Indices: 111390339--111390379 Score: 73
Period size: 16 Copynumber: 2.6 Consensus size: 16
111390329 ACTAAATACT
111390339 AACCCATAAATAAATA
1 AACCCATAAATAAATA
111390355 AACCCATAAATAAATA
1 AACCCATAAATAAATA
*
111390371 AACCAATAA
1 AACCCATAA
111390380 TTTTATTTTC
Statistics
Matches: 24, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
16 24 1.00
ACGTcount: A:0.63, C:0.20, G:0.00, T:0.17
Consensus pattern (16 bp):
AACCCATAAATAAATA
Found at i:111390629 original size:17 final size:17
Alignment explanation
Indices: 111390603--111390650 Score: 78
Period size: 17 Copynumber: 2.8 Consensus size: 17
111390593 TTTGTCAATT
*
111390603 TAATTACTCTAATTAAA
1 TAATTGCTCTAATTAAA
111390620 TAATTGCTCTAATTAAA
1 TAATTGCTCTAATTAAA
*
111390637 TAATTGCTCGAATT
1 TAATTGCTCTAATT
111390651 GATCCATTAA
Statistics
Matches: 29, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
17 29 1.00
ACGTcount: A:0.40, C:0.12, G:0.06, T:0.42
Consensus pattern (17 bp):
TAATTGCTCTAATTAAA
Found at i:111392928 original size:59 final size:59
Alignment explanation
Indices: 111392864--111393014 Score: 141
Period size: 59 Copynumber: 2.6 Consensus size: 59
111392854 AGTTGGGCCA
** * * *
111392864 AAAAAAAATTTTAGGCC-CAAATGTG-GTAATAATTGCCAAGTGCAAGTG-CTAACTTTGAC
1 AAAAAAAATTCCAGGCCTC-AATGTGCG-AACAATTGCCAAGTGC-AGGGACTAACTTAGAC
* * *
111392923 AAAAAAAAGTCCAGGCCTCAATTTGCGAACAATTGCCAAGTTCAGGGACTAACTTAGAC
1 AAAAAAAATTCCAGGCCTCAATGTGCGAACAATTGCCAAGTGCAGGGACTAACTTAGAC
* *
111392982 AAAAAAAATT-CAAGCAC-CAATGTGGGAACAATT
1 AAAAAAAATTCCAGGC-CTCAATGTGCGAACAATT
111393015 ATTAAGTCCA
Statistics
Matches: 76, Mismatches: 12, Indels: 9
0.78 0.12 0.09
Matches are distributed among these distances:
58 21 0.28
59 53 0.70
60 2 0.03
ACGTcount: A:0.42, C:0.18, G:0.18, T:0.23
Consensus pattern (59 bp):
AAAAAAAATTCCAGGCCTCAATGTGCGAACAATTGCCAAGTGCAGGGACTAACTTAGAC
Found at i:111402410 original size:24 final size:24
Alignment explanation
Indices: 111402370--111402415 Score: 58
Period size: 24 Copynumber: 1.9 Consensus size: 24
111402360 TTATATTCTT
* *
111402370 GTTAATTTAATTCTTATTCTTTTA
1 GTTAATTTAACTCTTATCCTTTTA
111402394 GTTAA-TTAACTCTTTATCCTTT
1 GTTAATTTAACTC-TTATCCTTT
111402416 GAAAGAGTCA
Statistics
Matches: 19, Mismatches: 2, Indels: 2
0.83 0.09 0.09
Matches are distributed among these distances:
23 6 0.32
24 13 0.68
ACGTcount: A:0.24, C:0.13, G:0.04, T:0.59
Consensus pattern (24 bp):
GTTAATTTAACTCTTATCCTTTTA
Found at i:111409016 original size:14 final size:14
Alignment explanation
Indices: 111408997--111409063 Score: 71
Period size: 14 Copynumber: 4.7 Consensus size: 14
111408987 GTTTGCAGGT
*
111408997 AAAATGTTTTCTGA
1 AAAATGATTTCTGA
* *
111409011 AAAATGACTTCTGG
1 AAAATGATTTCTGA
* *
111409025 AAAATAATTTCTTGG
1 AAAATGATTTC-TGA
*
111409040 AAAATAATTTCTGA
1 AAAATGATTTCTGA
111409054 AAAATGATTT
1 AAAATGATTT
111409064 ACTTTTCTGG
Statistics
Matches: 45, Mismatches: 7, Indels: 2
0.83 0.13 0.04
Matches are distributed among these distances:
14 31 0.69
15 14 0.31
ACGTcount: A:0.42, C:0.07, G:0.13, T:0.37
Consensus pattern (14 bp):
AAAATGATTTCTGA
Found at i:111409040 original size:15 final size:15
Alignment explanation
Indices: 111409022--111409051 Score: 60
Period size: 15 Copynumber: 2.0 Consensus size: 15
111409012 AAATGACTTC
111409022 TGGAAAATAATTTCT
1 TGGAAAATAATTTCT
111409037 TGGAAAATAATTTCT
1 TGGAAAATAATTTCT
111409052 GAAAAATGAT
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:0.07, G:0.13, T:0.40
Consensus pattern (15 bp):
TGGAAAATAATTTCT
Found at i:111410373 original size:129 final size:129
Alignment explanation
Indices: 111410142--111410380 Score: 424
Period size: 129 Copynumber: 1.9 Consensus size: 129
111410132 CATTTTACAT
111410142 AAAAAGCAAGCAATTTTACCCGTGTTCCTGAAAATGTTTTCCGTAGGTAAAATGTTTTCAGGTTA
1 AAAAAGCAAGCAATTTTACCCGTGTTCCTGAAAATGTTTTCCGTAGGTAAAATGTTTTCAGGTTA
* *
111410207 CCAAATAACATAAAACCAGGAAAATATTTTCCAGAAAATGTTTTCCTGGTTGCCAAACGGAGCC
66 CCAAACAACATAAAACCAGGAAAACATTTTCCAGAAAATGTTTTCCTGGTTGCCAAACGGAGCC
*
111410271 AAAAAGCAGGCAATTTTACCCGTGTTCCTGAAAATGTTTTCCGTAGGTAAAATGTTTTCAGGTTA
1 AAAAAGCAAGCAATTTTACCCGTGTTCCTGAAAATGTTTTCCGTAGGTAAAATGTTTTCAGGTTA
* * *
111410336 CCAAACAACGTAAAATCAGGAAAACATTTTCCGGAAAATGTTTTC
66 CCAAACAACATAAAACCAGGAAAACATTTTCCAGAAAATGTTTTC
111410381 AGGTTACCAA
Statistics
Matches: 104, Mismatches: 6, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
129 104 1.00
ACGTcount: A:0.36, C:0.18, G:0.17, T:0.29
Consensus pattern (129 bp):
AAAAAGCAAGCAATTTTACCCGTGTTCCTGAAAATGTTTTCCGTAGGTAAAATGTTTTCAGGTTA
CCAAACAACATAAAACCAGGAAAACATTTTCCAGAAAATGTTTTCCTGGTTGCCAAACGGAGCC
Found at i:111410381 original size:51 final size:51
Alignment explanation
Indices: 111410319--111410431 Score: 172
Period size: 51 Copynumber: 2.2 Consensus size: 51
111410309 TTCCGTAGGT
*
111410319 AAAATGTTTTCAGGTTACCAAACAACGTAAAATCAGGAAAACATTTTCCGG
1 AAAATGTTTTCAGGTTACCAAACAACGTAAAACCAGGAAAACATTTTCCGG
* ** * *
111410370 AAAATGTTTTCAGGTTACCAATCAATTTCAAACCAGGAAAATATTTTCCGG
1 AAAATGTTTTCAGGTTACCAAACAACGTAAAACCAGGAAAACATTTTCCGG
111410421 AAAATGTTTTC
1 AAAATGTTTTC
111410432 CTGGTTGCCA
Statistics
Matches: 56, Mismatches: 6, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
51 56 1.00
ACGTcount: A:0.39, C:0.17, G:0.14, T:0.30
Consensus pattern (51 bp):
AAAATGTTTTCAGGTTACCAAACAACGTAAAACCAGGAAAACATTTTCCGG
Found at i:111411249 original size:21 final size:19
Alignment explanation
Indices: 111411211--111411248 Score: 67
Period size: 19 Copynumber: 2.0 Consensus size: 19
111411201 TGTGAAGTTC
111411211 ATTGATGAATATTTATATA
1 ATTGATGAATATTTATATA
*
111411230 ATTGATGAATATTTTTATA
1 ATTGATGAATATTTATATA
111411249 TTTAAAGTTT
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
19 18 1.00
ACGTcount: A:0.39, C:0.00, G:0.11, T:0.50
Consensus pattern (19 bp):
ATTGATGAATATTTATATA
Found at i:111416861 original size:18 final size:18
Alignment explanation
Indices: 111416840--111416874 Score: 61
Period size: 18 Copynumber: 1.9 Consensus size: 18
111416830 TTTATTGTTT
*
111416840 TTAAATATTTTTTAAATA
1 TTAAATATTTTTGAAATA
111416858 TTAAATATTTTTGAAAT
1 TTAAATATTTTTGAAAT
111416875 CTATACGTAT
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
18 16 1.00
ACGTcount: A:0.43, C:0.00, G:0.03, T:0.54
Consensus pattern (18 bp):
TTAAATATTTTTGAAATA
Found at i:111418684 original size:3 final size:3
Alignment explanation
Indices: 111418608--111418665 Score: 82
Period size: 3 Copynumber: 19.7 Consensus size: 3
111418598 AATTAAAATA
* * *
111418608 AAT AAT AAC AAA AAT AAT AAT AAT AA- AAT AAT AAC AAT AAT AAT AAT
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
111418655 AAT AAT AAT AA
1 AAT AAT AAT AA
111418666 GCCAAAGTAG
Statistics
Matches: 49, Mismatches: 5, Indels: 2
0.88 0.09 0.04
Matches are distributed among these distances:
2 2 0.04
3 47 0.96
ACGTcount: A:0.71, C:0.03, G:0.00, T:0.26
Consensus pattern (3 bp):
AAT
Found at i:111418878 original size:3 final size:3
Alignment explanation
Indices: 111418870--111419173 Score: 158
Period size: 3 Copynumber: 99.7 Consensus size: 3
111418860 TAATACTAAG
* * * *
111418870 ATA ATA ATA ATA GTA ATA GAGA GTA ACA ATA CATTA ATA ATA ATA AT-
1 ATA ATA ATA ATA ATA ATA -ATA ATA ATA ATA -A-TA ATA ATA ATA ATA
* * * * *
111418917 ATG TTA ATA ACA ATA ATA ATA ATA TATA A-A AGGGA ATA ATA ATA GT-
1 ATA ATA ATA ATA ATA ATA ATA ATA -ATA ATA A--TA ATA ATA ATA ATA
* * * * *
111418963 ATA GTA AAA ATA ATA AT- GTA TTA ATA ATA ATG ATA ATA ATA A-A ATGA
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA AT-A
* * * * *
111419010 GATT ATA ATA ATA ATA TTA ATA AAA ATA GACGTA A-A AGAA ATA GTA
1 -ATA ATA ATA ATA ATA ATA ATA ATA ATA -A--TA ATA A-TA ATA ATA
* * * * *
111419056 ATA ATA GTA ATA ATA ATA GTA ATA AT- ATAA ATA ATA ATA TATG TTT
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA AT-A ATA ATA ATA -ATA ATA
** ** *
111419102 GCA A-A ATA ACG ATA GTA A-A ATA ATA ATA ATA ATA ATA ATA ATA ATA
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA
111419148 ATA ATA ATA ATA ATA ATA ATA ATA AT
1 ATA ATA ATA ATA ATA ATA ATA ATA AT
111419174 GGCATTAGAA
Statistics
Matches: 227, Mismatches: 51, Indels: 46
0.70 0.16 0.14
Matches are distributed among these distances:
2 16 0.07
3 187 0.82
4 15 0.07
5 7 0.03
6 2 0.01
ACGTcount: A:0.59, C:0.02, G:0.08, T:0.31
Consensus pattern (3 bp):
ATA
Found at i:111418977 original size:23 final size:22
Alignment explanation
Indices: 111418905--111418979 Score: 66
Period size: 23 Copynumber: 3.4 Consensus size: 22
111418895 ACAATACATT
*
111418905 AATAATAATAATATGT-TAATAAC
1 AATAATAATAATA-GTAT-ATAAA
111418928 AATAATAATAATA-TATA-AAA
1 AATAATAATAATAGTATATAAA
***
111418948 GGGAATAATAATAGTATAGTAAA
1 AATAATAATAATAGTATA-TAAA
111418971 AATAATAAT
1 AATAATAAT
111418980 GTATTAATAA
Statistics
Matches: 41, Mismatches: 7, Indels: 8
0.73 0.12 0.14
Matches are distributed among these distances:
20 12 0.29
21 6 0.15
22 1 0.02
23 22 0.54
ACGTcount: A:0.60, C:0.01, G:0.08, T:0.31
Consensus pattern (22 bp):
AATAATAATAATAGTATATAAA
Found at i:111421078 original size:17 final size:17
Alignment explanation
Indices: 111421056--111421088 Score: 57
Period size: 17 Copynumber: 1.9 Consensus size: 17
111421046 ATAATTATTA
*
111421056 TTTTTTAATTTAGTCTT
1 TTTTTTAATTGAGTCTT
111421073 TTTTTTAATTGAGTCT
1 TTTTTTAATTGAGTCT
111421089 ATAATTCACT
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:0.18, C:0.06, G:0.09, T:0.67
Consensus pattern (17 bp):
TTTTTTAATTGAGTCTT
Found at i:111421605 original size:23 final size:22
Alignment explanation
Indices: 111421536--111421605 Score: 68
Period size: 23 Copynumber: 3.0 Consensus size: 22
111421526 TTTATTGACT
*
111421536 TGTTCGTGAACATGTACAATTATA
1 TGTTCGTGAACATGTTC-ATTA-A
**
111421560 TGTTTATGAACATGTTCATTTAA
1 TGTTCGTGAACATGTTCA-TTAA
*
111421583 TGTTCGTGAACATATTCGATTAA
1 TGTTCGTGAACATGTTC-ATTAA
111421606 GTTAAATGAA
Statistics
Matches: 38, Mismatches: 6, Indels: 5
0.78 0.12 0.10
Matches are distributed among these distances:
23 20 0.53
24 18 0.47
ACGTcount: A:0.31, C:0.11, G:0.16, T:0.41
Consensus pattern (22 bp):
TGTTCGTGAACATGTTCATTAA
Found at i:111422662 original size:16 final size:16
Alignment explanation
Indices: 111422641--111422672 Score: 64
Period size: 16 Copynumber: 2.0 Consensus size: 16
111422631 CAAGTAAATG
111422641 TCTCTAAAATAGTAAC
1 TCTCTAAAATAGTAAC
111422657 TCTCTAAAATAGTAAC
1 TCTCTAAAATAGTAAC
111422673 AAAATTAACA
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:0.44, C:0.19, G:0.06, T:0.31
Consensus pattern (16 bp):
TCTCTAAAATAGTAAC
Found at i:111430587 original size:62 final size:62
Alignment explanation
Indices: 111430510--111430632 Score: 210
Period size: 62 Copynumber: 2.0 Consensus size: 62
111430500 TTACTGCCAC
*
111430510 ACGGCCTGGACACACGCCTATGTCCTTGGCCGTGTGGTTTTATACCATAAACAGTGAGTTAT
1 ACGGCCTGGACACACGCCTATGTCCTTAGCCGTGTGGTTTTATACCATAAACAGTGAGTTAT
* * *
111430572 ACGGCCTGGGCACACGCCTGTGTCCTTAGCCGTGTGGTTTTATTCCATAAACAGTGAGTTA
1 ACGGCCTGGACACACGCCTATGTCCTTAGCCGTGTGGTTTTATACCATAAACAGTGAGTTA
111430633 CACGATCATT
Statistics
Matches: 57, Mismatches: 4, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
62 57 1.00
ACGTcount: A:0.21, C:0.24, G:0.25, T:0.29
Consensus pattern (62 bp):
ACGGCCTGGACACACGCCTATGTCCTTAGCCGTGTGGTTTTATACCATAAACAGTGAGTTAT
Found at i:111431973 original size:37 final size:37
Alignment explanation
Indices: 111431923--111431994 Score: 144
Period size: 37 Copynumber: 1.9 Consensus size: 37
111431913 TTCTTACATA
111431923 TAAGATTAAACTTAACTGGGTAGTGCATGCTTGTGAG
1 TAAGATTAAACTTAACTGGGTAGTGCATGCTTGTGAG
111431960 TAAGATTAAACTTAACTGGGTAGTGCATGCTTGTG
1 TAAGATTAAACTTAACTGGGTAGTGCATGCTTGTG
111431995 GGTTGGTTCT
Statistics
Matches: 35, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
37 35 1.00
ACGTcount: A:0.29, C:0.11, G:0.26, T:0.33
Consensus pattern (37 bp):
TAAGATTAAACTTAACTGGGTAGTGCATGCTTGTGAG
Found at i:111438878 original size:30 final size:30
Alignment explanation
Indices: 111438842--111438940 Score: 180
Period size: 30 Copynumber: 3.3 Consensus size: 30
111438832 CTAGCCTTTG
111438842 CCACCACCAACTCCACTAGCCACACTTGCT
1 CCACCACCAACTCCACTAGCCACACTTGCT
111438872 CCACCACCAACTCCACTAGCCACACTTGCT
1 CCACCACCAACTCCACTAGCCACACTTGCT
* *
111438902 CCACTACCTACTCCACTAGCCACACTTGCT
1 CCACCACCAACTCCACTAGCCACACTTGCT
111438932 CCACCACCA
1 CCACCACCA
111438941 CTTGTACCTA
Statistics
Matches: 65, Mismatches: 4, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
30 65 1.00
ACGTcount: A:0.26, C:0.51, G:0.06, T:0.17
Consensus pattern (30 bp):
CCACCACCAACTCCACTAGCCACACTTGCT
Found at i:111439514 original size:25 final size:25
Alignment explanation
Indices: 111439486--111439627 Score: 110
Period size: 25 Copynumber: 5.7 Consensus size: 25
111439476 ATTCTAAATT
*
111439486 CTATATTACGTATATATATATTATA
1 CTATATTATGTATATATATATTATA
* *
111439511 CTATTTTATGTATATATCT-TTAATA
1 CTATATTATGTATATATATATT-ATA
*
111439536 CTATATTATTTATATATATATT-TA
1 CTATATTATGTATATATATATTATA
* * * *
111439560 C-ATGTTATCTTATGTATATATTTTAA
1 CTATATTAT-GTATATATATATTAT-A
* * * * *
111439586 TTATATTATGTATGTATTTTTTACA
1 CTATATTATGTATATATATATTATA
*
111439611 CTATATTATGTACATAT
1 CTATATTATGTATATAT
111439628 TTTTAATATT
Statistics
Matches: 93, Mismatches: 18, Indels: 12
0.76 0.15 0.10
Matches are distributed among these distances:
23 6 0.06
24 17 0.18
25 51 0.55
26 13 0.14
27 6 0.06
ACGTcount: A:0.34, C:0.07, G:0.05, T:0.54
Consensus pattern (25 bp):
CTATATTATGTATATATATATTATA
Found at i:111439540 original size:50 final size:49
Alignment explanation
Indices: 111439486--111439635 Score: 144
Period size: 50 Copynumber: 3.0 Consensus size: 49
111439476 ATTCTAAATT
* *
111439486 CTATATTACGTATATATATATTATACTATTTTATGTATATATCTTTAATA
1 CTATATTATGTATATATATATTATACTATATTATGTATATAT-TTTAATA
* *
111439536 CTATATTATTTATATATATATT-TACATGTTATCTTATGTATATATTTTAAT-
1 CTATATTATGTATATATATATTATAC----TATATTATGTATATATTTTAATA
* * * * *
111439587 -TATATTATGTATGTATTTTTTACACTATATTATGTACATATTTTTAATA
1 CTATATTATGTATATATATATTATACTATATTATGTATATA-TTTTAATA
111439636 TTATCACGTA
Statistics
Matches: 83, Mismatches: 10, Indels: 15
0.77 0.09 0.14
Matches are distributed among these distances:
47 13 0.16
48 7 0.08
49 3 0.04
50 37 0.45
51 2 0.02
52 6 0.07
53 15 0.18
ACGTcount: A:0.34, C:0.07, G:0.05, T:0.55
Consensus pattern (49 bp):
CTATATTATGTATATATATATTATACTATATTATGTATATATTTTAATA
Found at i:111439589 original size:22 final size:22
Alignment explanation
Indices: 111439564--111439671 Score: 71
Period size: 22 Copynumber: 4.9 Consensus size: 22
111439554 TATTTACATG
*
111439564 TTATCTTATGTATATATTTTAA
1 TTATATTATGTATATATTTTAA
*
111439586 TTATATTATGTATGTATTTTTTACA
1 TTATATTATGTA--TATATTTTA-A
* *
111439611 CTATATTATGTACATATTTTTAA
1 TTATATTATGTATATA-TTTTAA
* * *
111439634 -TATTATCACGTATTTATTTT--
1 TTA-TATTATGTATATATTTTAA
*
111439654 TTATA-TATGTACATATTT
1 TTATATTATGTATATATTT
111439672 ATGTAGTATT
Statistics
Matches: 67, Mismatches: 13, Indels: 15
0.71 0.14 0.16
Matches are distributed among these distances:
19 9 0.13
20 2 0.03
21 2 0.03
22 17 0.25
23 12 0.18
24 13 0.19
25 12 0.18
ACGTcount: A:0.31, C:0.06, G:0.06, T:0.57
Consensus pattern (22 bp):
TTATATTATGTATATATTTTAA
Found at i:111439638 original size:20 final size:20
Alignment explanation
Indices: 111439613--111439671 Score: 57
Period size: 23 Copynumber: 2.9 Consensus size: 20
111439603 TTTTTACACT
111439613 ATATTATGTACATATTTTTA
1 ATATTATGTACATATTTTTA
** *
111439633 ATATTATCACGTATTTATTTTTT
1 ATATTAT---GTACATATTTTTA
111439656 ATA-TATGTACATATTT
1 ATATTATGTACATATTT
111439672 ATGTAGTATT
Statistics
Matches: 31, Mismatches: 5, Indels: 7
0.72 0.12 0.16
Matches are distributed among these distances:
19 8 0.26
20 7 0.23
22 3 0.10
23 13 0.42
ACGTcount: A:0.32, C:0.07, G:0.05, T:0.56
Consensus pattern (20 bp):
ATATTATGTACATATTTTTA
Found at i:111439810 original size:16 final size:15
Alignment explanation
Indices: 111439786--111439820 Score: 52
Period size: 16 Copynumber: 2.3 Consensus size: 15
111439776 TAATTATTAT
111439786 TATTCTAATATTTTGA
1 TATTCTAATATTTT-A
*
111439802 TATTTTAATATTTTA
1 TATTCTAATATTTTA
111439817 TATT
1 TATT
111439821 ATTCACATCA
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
15 5 0.28
16 13 0.72
ACGTcount: A:0.31, C:0.03, G:0.03, T:0.63
Consensus pattern (15 bp):
TATTCTAATATTTTA
Found at i:111448244 original size:17 final size:17
Alignment explanation
Indices: 111448222--111448256 Score: 61
Period size: 17 Copynumber: 2.1 Consensus size: 17
111448212 AATAAGTTGT
111448222 ACGTTTAGACAATAAGA
1 ACGTTTAGACAATAAGA
*
111448239 ACGTTTAGTCAATAAGA
1 ACGTTTAGACAATAAGA
111448256 A
1 A
111448257 TATAACACAT
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
17 17 1.00
ACGTcount: A:0.46, C:0.11, G:0.17, T:0.26
Consensus pattern (17 bp):
ACGTTTAGACAATAAGA
Done.