Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: A03
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: 108673976
ACGTcount: A:0.31, C:0.17, G:0.16, T:0.31
Warning! 5040000 characters in sequence are not A, C, G, or T
File 133 of 333
Found at i:43211261 original size:49 final size:50
Alignment explanation
Indices: 43211195--43211340 Score: 195
Period size: 51 Copynumber: 2.9 Consensus size: 50
43211185 TAGCCAAAGC
* * *
43211195 TATCTGGTACGCATAGTAGCCTGCACTTGGTACTACACATGCGACCAA-T
1 TATCAGGTACACATAGTAGCCTGCACTTAGTACTACACATGCGACCAAGT
* * * * *
43211244 TATCCGGTACACGTAGTAGCCTGCACTTAGTACTACACACGTGATCGAAGT
1 TATCAGGTACACATAGTAGCCTGCACTTAGTACTACACATGCGA-CCAAGT
*
43211295 TATCAGGTACGCATAGTAGCCTGCACTTAGTACTACACATGCGACC
1 TATCAGGTACACATAGTAGCCTGCACTTAGTACTACACATGCGACC
43211341 TTACAATAGA
Statistics
Matches: 82, Mismatches: 13, Indels: 3
0.84 0.13 0.03
Matches are distributed among these distances:
49 38 0.46
50 4 0.05
51 40 0.49
ACGTcount: A:0.27, C:0.27, G:0.21, T:0.25
Consensus pattern (50 bp):
TATCAGGTACACATAGTAGCCTGCACTTAGTACTACACATGCGACCAAGT
Found at i:43230315 original size:10 final size:10
Alignment explanation
Indices: 43230300--43230325 Score: 52
Period size: 10 Copynumber: 2.6 Consensus size: 10
43230290 TTTAATGAGA
43230300 TATTTATTAT
1 TATTTATTAT
43230310 TATTTATTAT
1 TATTTATTAT
43230320 TATTTA
1 TATTTA
43230326 GTATATAAGG
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 16 1.00
ACGTcount: A:0.31, C:0.00, G:0.00, T:0.69
Consensus pattern (10 bp):
TATTTATTAT
Found at i:43231988 original size:31 final size:32
Alignment explanation
Indices: 43231950--43232040 Score: 132
Period size: 32 Copynumber: 2.9 Consensus size: 32
43231940 GTACAACTAG
43231950 AAAAGGAAATGTACA-TGTGTGTGTACACTTA
1 AAAAGGAAATGTACACTGTGTGTGTACACTTA
* *
43231981 AAAAGGAAATGTACACTTTGTGTGTACACTTG
1 AAAAGGAAATGTACACTGTGTGTGTACACTTA
*
43232013 AAAAGGAAATGTACGCCT-TGTGTGTACA
1 AAAAGGAAATGTAC-ACTGTGTGTGTACA
43232041 ATGTGAAAAG
Statistics
Matches: 55, Mismatches: 3, Indels: 3
0.90 0.05 0.05
Matches are distributed among these distances:
31 15 0.27
32 38 0.69
33 2 0.04
ACGTcount: A:0.36, C:0.12, G:0.23, T:0.29
Consensus pattern (32 bp):
AAAAGGAAATGTACACTGTGTGTGTACACTTA
Found at i:43232080 original size:31 final size:31
Alignment explanation
Indices: 43232043--43232159 Score: 180
Period size: 31 Copynumber: 3.8 Consensus size: 31
43232033 TGTGTACAAT
*
43232043 GTGAAAAGTGGTAGCTTCGGCTACCTAATCA
1 GTGAAAAGTGGTAGCTTCAGCTACCTAATCA
* *
43232074 GTGAAAAGTGGTAGCTTCGGCTACCTAATTA
1 GTGAAAAGTGGTAGCTTCAGCTACCTAATCA
* *
43232105 GTGAAAAGTGGTAGCTCCAGCTACCTGATCA
1 GTGAAAAGTGGTAGCTTCAGCTACCTAATCA
*
43232136 GTGAATAGTGGTAGCTTCAGCTAC
1 GTGAAAAGTGGTAGCTTCAGCTAC
43232160 AAGTGACAAG
Statistics
Matches: 79, Mismatches: 7, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
31 79 1.00
ACGTcount: A:0.28, C:0.19, G:0.26, T:0.26
Consensus pattern (31 bp):
GTGAAAAGTGGTAGCTTCAGCTACCTAATCA
Found at i:43232282 original size:27 final size:27
Alignment explanation
Indices: 43232251--43232315 Score: 103
Period size: 27 Copynumber: 2.4 Consensus size: 27
43232241 TAGTTGAACT
*
43232251 ATGGCAAAGTGATAAAGTGTGCCAATC
1 ATGGCAAAGTGATAAAGTGTGCCAAAC
*
43232278 ATGGCAAAGTGATATAGTGTGCCAAAC
1 ATGGCAAAGTGATAAAGTGTGCCAAAC
*
43232305 ATAGCAAAGTG
1 ATGGCAAAGTG
43232316 TTCAGTGATC
Statistics
Matches: 35, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
27 35 1.00
ACGTcount: A:0.38, C:0.14, G:0.26, T:0.22
Consensus pattern (27 bp):
ATGGCAAAGTGATAAAGTGTGCCAAAC
Found at i:43232395 original size:34 final size:34
Alignment explanation
Indices: 43232364--43232442 Score: 97
Period size: 34 Copynumber: 2.4 Consensus size: 34
43232354 TGATCCATGG
43232364 CAAAG-TGTGAAAAGTAGGTATGGTATTTCCATA
1 CAAAGTTGTGAAAAGTAGGTATGGTATTTCCATA
** * *
43232397 CCGAGTTGTGAAACGTAGGTATGGTGTTTCCATA
1 CAAAGTTGTGAAAAGTAGGTATGGTATTTCCATA
**
43232431 CTGAGTTGTGAA
1 CAAAGTTGTGAA
43232443 TCGTGGCACG
Statistics
Matches: 40, Mismatches: 5, Indels: 1
0.87 0.11 0.02
Matches are distributed among these distances:
33 3 0.08
34 37 0.93
ACGTcount: A:0.29, C:0.11, G:0.28, T:0.32
Consensus pattern (34 bp):
CAAAGTTGTGAAAAGTAGGTATGGTATTTCCATA
Found at i:43233483 original size:20 final size:21
Alignment explanation
Indices: 43233449--43233489 Score: 75
Period size: 20 Copynumber: 2.0 Consensus size: 21
43233439 TACATGTATG
43233449 AATGTTATGTGAAGCGAAATT
1 AATGTTATGTGAAGCGAAATT
43233470 AATGTTAT-TGAAGCGAAATT
1 AATGTTATGTGAAGCGAAATT
43233490 CTGTTAAATG
Statistics
Matches: 20, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
20 12 0.60
21 8 0.40
ACGTcount: A:0.39, C:0.05, G:0.22, T:0.34
Consensus pattern (21 bp):
AATGTTATGTGAAGCGAAATT
Found at i:43239026 original size:40 final size:40
Alignment explanation
Indices: 43238837--43239062 Score: 298
Period size: 40 Copynumber: 5.7 Consensus size: 40
43238827 TTGAATGATG
* * * *
43238837 TCCGGGCTAAGTCCCGAAGGC-TTTGTGCTAAGTGACCATA
1 TCCGGGCTAAGTCCCGAAGGCATTTGTGC-GAGTTACTAAA
*
43238877 TCCGGACTAAGAT-CCGAAGGCATTTGTGCGAGTTACTAAA
1 TCCGGGCTAAG-TCCCGAAGGCATTTGTGCGAGTTACTAAA
*
43238917 TCCGGACTAAGAT-CCGAAGGCATTTGTGCGAGTTACTAAA
1 TCCGGGCTAAG-TCCCGAAGGCATTTGTGCGAGTTACTAAA
*
43238957 TCCGGGTTAAGTCCCGAAGGCATTTGTGCGAGTTACTAAA
1 TCCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTAAA
*
43238997 TCCGGGTTAAGTCCCGAAGGCATTTGTGCGAGTTACTATAA
1 TCCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTA-AA
* *
43239038 -CCGGGCTATGTCCCGAAGACATTTG
1 TCCGGGCTAAGTCCCGAAGGCATTTG
43239063 AATGAGTAGC
Statistics
Matches: 172, Mismatches: 10, Indels: 8
0.91 0.05 0.04
Matches are distributed among these distances:
39 1 0.01
40 161 0.94
41 10 0.06
ACGTcount: A:0.26, C:0.22, G:0.27, T:0.26
Consensus pattern (40 bp):
TCCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTAAA
Found at i:43239080 original size:80 final size:79
Alignment explanation
Indices: 43238848--43239095 Score: 236
Period size: 80 Copynumber: 3.1 Consensus size: 79
43238838 CCGGGCTAAG
* * * * * * **
43238848 TCCCGAAGGC-TTTGTGCTAAGTGACCATATCCGGACTAAGAT-CCGAAGGCATTTGTGCGAGTT
1 TCCCGAAGGCATTTGTGC-GAGTTACTAAATCCGGGCTAAG-TCCCGAAGACATTTGAACGAGTT
*
43238911 ACTAAATCCGGACTAAGA
64 ACTAAATCCGG-TTAA-A
* * **
43238929 T-CCGAAGGCATTTGTGCGAGTTACTAAATCCGGGTTAAGTCCCGAAGGCATTTGTGCGAGTTAC
1 TCCCGAAGGCATTTGTGCGAGTTACTAAATCCGGGCTAAGTCCCGAAGACATTTGAACGAGTTAC
*
43238993 TAAATCCGGGTTAAG
66 TAAATCC-GGTTAAA
* *
43239008 TCCCGAAGGCATTTGTGCGAGTTACTATAA-CCGGGCTATGTCCCGAAGACATTTGAATGAG-TA
1 TCCCGAAGGCATTTGTGCGAGTTACTA-AATCCGGGCTAAGTCCCGAAGACATTTGAACGAGTTA
*
43239071 GCTATATCCGGTTAAA
65 -CTAAATCCGGTTAAA
*
43239087 TTCCGAAGG
1 TCCCGAAGG
43239096 TACGTGATTT
Statistics
Matches: 144, Mismatches: 17, Indels: 14
0.82 0.10 0.08
Matches are distributed among these distances:
79 18 0.12
80 114 0.79
81 12 0.08
ACGTcount: A:0.27, C:0.21, G:0.26, T:0.27
Consensus pattern (79 bp):
TCCCGAAGGCATTTGTGCGAGTTACTAAATCCGGGCTAAGTCCCGAAGACATTTGAACGAGTTAC
TAAATCCGGTTAAA
Found at i:43239080 original size:120 final size:120
Alignment explanation
Indices: 43238837--43239095 Score: 287
Period size: 120 Copynumber: 2.2 Consensus size: 120
43238827 TTGAATGATG
* *
43238837 TCCGGGCTAAGTCCCGAAGGCTTTGTGCTAAGTGACCATATCCGGACTAAGATCCGAAGGCATTT
1 TCCGGGTTAAGTCCCGAAGGCTTTGTGCTAAGTGACCAAATCCGGACTAAGATCCGAAGGCATTT
* **
43238902 GTGCGAGTTACTAAATCCGGACTAAGATCCGAAGGCATTTGTGCGAGTTACTAAA
66 GTGCGAGTTACTAAATCCGGACTAAGATCCGAAGACATTTGAACGAGTTACTAAA
* * * **
43238957 TCCGGGTTAAGTCCCGAAGGCATTTGTGC-GAGTTACTAAATCCGGGTTAAG-TCCCGAAGGCAT
1 TCCGGGTTAAGTCCCGAAGGC-TTTGTGCTAAGTGACCAAATCCGGACTAAGAT-CCGAAGGCAT
* * * *
43239020 TTGTGCGAGTTACTATAA-CCGGGCTATG-TCCCGAAGACATTTGAATGAG-TAGCTATA
64 TTGTGCGAGTTACTA-AATCCGGACTAAGAT-CCGAAGACATTTGAACGAGTTA-CTAAA
* *
43239077 TCC-GGTTAAATTCCGAAGG
1 TCCGGGTTAAGTCCCGAAGG
43239096 TACGTGATTT
Statistics
Matches: 118, Mismatches: 16, Indels: 11
0.81 0.11 0.08
Matches are distributed among these distances:
119 18 0.15
120 91 0.77
121 9 0.08
ACGTcount: A:0.27, C:0.21, G:0.26, T:0.26
Consensus pattern (120 bp):
TCCGGGTTAAGTCCCGAAGGCTTTGTGCTAAGTGACCAAATCCGGACTAAGATCCGAAGGCATTT
GTGCGAGTTACTAAATCCGGACTAAGATCCGAAGACATTTGAACGAGTTACTAAA
Found at i:43244665 original size:37 final size:39
Alignment explanation
Indices: 43244618--43244820 Score: 245
Period size: 39 Copynumber: 5.3 Consensus size: 39
43244608 GGACTAAGAT
43244618 CCGAAGGCATTTGTGCGAGATACAAATCCGGGTTAAG-C
1 CCGAAGGCATTTGTGCGAGATACAAATCCGGGTTAAGTC
43244656 CC-AAGGCATTTGTGCGAGATAC-AATCCGGGTTAAG-C
1 CCGAAGGCATTTGTGCGAGATACAAATCCGGGTTAAGTC
*
43244692 CCGAAGGCCTTTGTGCGAGATACTAAATCCGGGTTAAGTC
1 CCGAAGGCATTTGTGCGAGATAC-AAATCCGGGTTAAGTC
* * *** *
43244732 CCGAAGGCATTCGTGCGAGTTGTTAATCCGGGTTATGTC
1 CCGAAGGCATTTGTGCGAGATACAAATCCGGGTTAAGTC
* * * * *
43244771 CCGAAGGCA-TTGTGTGAGTTACTAAAACCGGGCTATGTC
1 CCGAAGGCATTTGTGCGAGATAC-AAATCCGGGTTAAGTC
43244810 CCGAAGGCATT
1 CCGAAGGCATT
43244821 GAACGAGGAG
Statistics
Matches: 144, Mismatches: 15, Indels: 10
0.85 0.09 0.06
Matches are distributed among these distances:
36 16 0.11
37 39 0.27
38 11 0.08
39 58 0.40
40 20 0.14
ACGTcount: A:0.25, C:0.22, G:0.29, T:0.25
Consensus pattern (39 bp):
CCGAAGGCATTTGTGCGAGATACAAATCCGGGTTAAGTC
Found at i:43244760 original size:39 final size:39
Alignment explanation
Indices: 43244565--43244820 Score: 215
Period size: 39 Copynumber: 6.6 Consensus size: 39
43244555 TTGAATGCTG
* * ** *
43244565 TCCGGGCTAAGTCCCGAAGGC-TTTGTGCTAAGTGAATATA
1 TCCGGGTTAAGTCCCGAAGGCATTTGTGC-GAGT-TCTAAA
** *
43244605 TCCGGACTAAGAT-CCGAAGGCATTTGTGCGAGATAC-AAA
1 TCCGGGTTAAG-TCCCGAAGGCATTTGTGCGAG-TTCTAAA
*
43244644 TCCGGGTTAAG-CCC-AAGGCATTTGTGCGAG--ATACAA
1 TCCGGGTTAAGTCCCGAAGGCATTTGTGCGAGTTCTA-AA
* *
43244680 TCCGGGTTAAG-CCCGAAGGCCTTTGTGCGAGATACTAAA
1 TCCGGGTTAAGTCCCGAAGGCATTTGTGCGAG-TTCTAAA
* * *
43244719 TCCGGGTTAAGTCCCGAAGGCATTCGTGCGAGTTGTTAA
1 TCCGGGTTAAGTCCCGAAGGCATTTGTGCGAGTTCTAAA
* *
43244758 TCCGGGTTATGTCCCGAAGGCA-TTGTGTGAGTTACTAAA
1 TCCGGGTTAAGTCCCGAAGGCATTTGTGCGAGTT-CTAAA
* * *
43244797 ACCGGGCTATGTCCCGAAGGCATT
1 TCCGGGTTAAGTCCCGAAGGCATT
43244821 GAACGAGGAG
Statistics
Matches: 182, Mismatches: 21, Indels: 26
0.79 0.09 0.11
Matches are distributed among these distances:
35 1 0.01
36 16 0.09
37 31 0.17
38 11 0.06
39 72 0.40
40 42 0.23
41 9 0.05
ACGTcount: A:0.25, C:0.21, G:0.28, T:0.25
Consensus pattern (39 bp):
TCCGGGTTAAGTCCCGAAGGCATTTGTGCGAGTTCTAAA
Found at i:43244839 original size:78 final size:78
Alignment explanation
Indices: 43244618--43244853 Score: 195
Period size: 78 Copynumber: 3.1 Consensus size: 78
43244608 GGACTAAGAT
* * * ** *
43244618 CCGAAGG-CATTTGTGCGAGATAC-AAATCCGGGTTAAG-CCC-AAGGCATTTGTGCGA-GATAC
1 CCGAAGGCCA-TTGTGCGAGATACTAAAACCGGGCTAAGTCCCGAAGGCATTCGAACGAGGA-GC
43244678 -AATCCGGGTTAAG-C
64 TAATCCGGGTT-AGTC
* * * ** ** *
43244692 CCGAAGGCCTTTGTGCGAGATACTAAATCCGGGTTAAGTCCCGAAGGCATTCGTGCGAGTTGTTA
1 CCGAAGGCCATTGTGCGAGATACTAAAACCGGGCTAAGTCCCGAAGGCATTCGAACGAGGAGCTA
43244757 ATCCGGGTTATGTC
66 ATCCGGGTTA-GTC
* * *
43244771 CCGAAGG-CATTGTGTGAGTTACTAAAACCGGGCTATGTCCCGAAGGCATT-GAACGAGGAGCTA
1 CCGAAGGCCATTGTGCGAGATACTAAAACCGGGCTAAGTCCCGAAGGCATTCGAACGAGGAGCTA
*
43244834 TATCC-GGTTAATC
66 -ATCCGGGTTAGTC
43244847 CCGAAGG
1 CCGAAGG
43244854 TACGTGATTG
Statistics
Matches: 135, Mismatches: 18, Indels: 16
0.80 0.11 0.09
Matches are distributed among these distances:
74 20 0.15
75 15 0.11
76 12 0.09
77 28 0.21
78 52 0.39
79 8 0.06
ACGTcount: A:0.26, C:0.22, G:0.29, T:0.24
Consensus pattern (78 bp):
CCGAAGGCCATTGTGCGAGATACTAAAACCGGGCTAAGTCCCGAAGGCATTCGAACGAGGAGCTA
ATCCGGGTTAGTC
Found at i:43252701 original size:39 final size:39
Alignment explanation
Indices: 43252458--43252717 Score: 233
Period size: 40 Copynumber: 6.6 Consensus size: 39
43252448 TTGAATGCTG
* * * * *
43252458 TCCGGGCTAAGTCCCGAAGGCTTTGTGCTA-AGTGAATATA
1 TCCGGGTTAAGTCCCGAAGGCATTGTGCGAGA-T-ACTAAA
**
43252498 TCCGGACTAAGAT-CCGAAGGCATTTGTGCGAGATAC-AAA
1 TCCGGGTTAAG-TCCCGAAGGCA-TTGTGCGAGATACTAAA
*
43252537 TTCCGGTTTAAG-CCCGAAGGCATTTGTGCGAGATAC-AAA
1 -TCCGGGTTAAGTCCCGAAGGCA-TTGTGCGAGATACTAAA
* *
43252576 TTCCGGGTTAAGCCCCGAAGGCCTTTGTGCGAGATACTAAA
1 -TCCGGGTTAAGTCCCGAAGG-CATTGTGCGAGATACTAAA
* **
43252617 TCCGGGTTAAGTCCCGAAGGCATTCGTGCGAGTTGTTAAA
1 TCCGGGTTAAGTCCCGAAGGCATT-GTGCGAGATACTAAA
* * *
43252657 TCCGGGTTATGTCCCGAAGGCATTGTGTGAGTTACTAAA
1 TCCGGGTTAAGTCCCGAAGGCATTGTGCGAGATACTAAA
* * *
43252696 ACCGGGCTATGTCCCGAAGGCA
1 TCCGGGTTAAGTCCCGAAGGCA
43252718 ATTGAACGAG
Statistics
Matches: 191, Mismatches: 20, Indels: 19
0.83 0.09 0.08
Matches are distributed among these distances:
39 74 0.39
40 103 0.54
41 13 0.07
42 1 0.01
ACGTcount: A:0.26, C:0.22, G:0.28, T:0.25
Consensus pattern (39 bp):
TCCGGGTTAAGTCCCGAAGGCATTGTGCGAGATACTAAA
Found at i:43252739 original size:79 final size:80
Alignment explanation
Indices: 43252577--43252754 Score: 191
Period size: 79 Copynumber: 2.2 Consensus size: 80
43252567 AGATACAAAT
* * * *
43252577 TCCGGGTTAAGCCCCGAAGGCCTTTGTGCGAGATACTAAATCCGGGTTAAGTCCCGAAGGCATTC
1 TCCGGGTTAAGTCCCGAAGGCCATTGTGCGAGATACTAAAACCGGGCTAAGTCCCGAAGGCATTC
** ** *
43252642 GTGCGAGTTGTTAAA
66 GAACGAGGAGCTAAA
* * * *
43252657 TCCGGGTTATGTCCCGAAGG-CATTGTGTGAGTTACTAAAACCGGGCTATGTCCCGAAGGCAATT
1 TCCGGGTTAAGTCCCGAAGGCCATTGTGCGAGATACTAAAACCGGGCTAAGTCCCGAAGGC-ATT
*
43252721 -GAACGAGGAGCTATA
65 CGAACGAGGAGCTAAA
*
43252736 TCC-GGTTAAATCCCGAAGG
1 TCCGGGTTAAGTCCCGAAGG
43252755 TACGTGATTT
Statistics
Matches: 81, Mismatches: 16, Indels: 4
0.80 0.16 0.04
Matches are distributed among these distances:
78 14 0.17
79 46 0.57
80 21 0.26
ACGTcount: A:0.25, C:0.22, G:0.29, T:0.24
Consensus pattern (80 bp):
TCCGGGTTAAGTCCCGAAGGCCATTGTGCGAGATACTAAAACCGGGCTAAGTCCCGAAGGCATTC
GAACGAGGAGCTAAA
Found at i:43257020 original size:43 final size:44
Alignment explanation
Indices: 43256971--43257121 Score: 209
Period size: 43 Copynumber: 3.5 Consensus size: 44
43256961 GTTTACCGAG
*
43256971 ATGTGATTACATGTAAGACCATGTTTGGGACATTGGCATTGTAT
1 ATGTGATTACATGTAAGACCATGTTTGGGACATTGGCATAGTAT
* *
43257015 -TGTGATTACGTGTAAGACCATGTCTGGGACATTGGCATAGT-T
1 ATGTGATTACATGTAAGACCATGTTTGGGACATTGGCATAGTAT
* * * *
43257057 ATATGATTTCGTGTAAGACCATGTTTGGGACATTGGCATCG-AT
1 ATGTGATTACATGTAAGACCATGTTTGGGACATTGGCATAGTAT
*
43257100 ATGTGATAACATGTAAGACCAT
1 ATGTGATTACATGTAAGACCAT
43257122 ATTTAGGATA
Statistics
Matches: 94, Mismatches: 11, Indels: 5
0.85 0.10 0.05
Matches are distributed among these distances:
42 1 0.01
43 93 0.99
ACGTcount: A:0.28, C:0.13, G:0.25, T:0.34
Consensus pattern (44 bp):
ATGTGATTACATGTAAGACCATGTTTGGGACATTGGCATAGTAT
Found at i:43258950 original size:26 final size:26
Alignment explanation
Indices: 43258900--43258952 Score: 70
Period size: 26 Copynumber: 2.0 Consensus size: 26
43258890 ATTGGGATCC
* * *
43258900 CCATGTTTACTGTCCTGGCAAACTAT
1 CCATGTTTAATGTCCCGACAAACTAT
*
43258926 CCATGTTTAATGTCCCGACAGACTAT
1 CCATGTTTAATGTCCCGACAAACTAT
43258952 C
1 C
43258953 TATGATGCCA
Statistics
Matches: 23, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
26 23 1.00
ACGTcount: A:0.25, C:0.28, G:0.15, T:0.32
Consensus pattern (26 bp):
CCATGTTTAATGTCCCGACAAACTAT
Found at i:43260929 original size:23 final size:23
Alignment explanation
Indices: 43260902--43260945 Score: 63
Period size: 23 Copynumber: 1.9 Consensus size: 23
43260892 TAAGAGAATA
43260902 TAAAATAA-AAAAAAGAAAAAAGT
1 TAAAA-AACAAAAAAGAAAAAAGT
*
43260925 TAAAAAACATAAAAGAAAAAA
1 TAAAAAACAAAAAAGAAAAAA
43260946 ATTTAAATTA
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
22 2 0.11
23 17 0.89
ACGTcount: A:0.80, C:0.02, G:0.07, T:0.11
Consensus pattern (23 bp):
TAAAAAACAAAAAAGAAAAAAGT
Found at i:43272303 original size:50 final size:49
Alignment explanation
Indices: 43272140--43272319 Score: 170
Period size: 49 Copynumber: 3.7 Consensus size: 49
43272130 GGTGTAATGC
* * * * * *
43272140 CGATGCCATGTCCCAGATATGGCCTTACATTGGCTTA-TC-CAT-CAAGT
1 CGATGCCATGTCCCAGAAATGGTCTTACACTGAC-TACTCAAATCCAGGT
* * * * *
43272187 CGATGCCATGTCCCAGACATGGTCTTACACTGACTATTGAAATCGAGGC
1 CGATGCCATGTCCCAGAAATGGTCTTACACTGACTACTCAAATCCAGGT
* * * *
43272236 CGACGCCATGTCCCAGAAATGGTCTTACACTGGCT-CTCACATCTCCGTGT
1 CGATGCCATGTCCCAGAAATGGTCTTACACTGACTACTCAAATC-CAG-GT
43272286 CGATGCCATGTCCCAGAAATGGTCTTACACTGAC
1 CGATGCCATGTCCCAGAAATGGTCTTACACTGAC
43272320 ACATCTCATA
Statistics
Matches: 108, Mismatches: 20, Indels: 7
0.80 0.15 0.05
Matches are distributed among these distances:
46 2 0.02
47 31 0.29
48 7 0.06
49 35 0.32
50 33 0.31
ACGTcount: A:0.24, C:0.29, G:0.21, T:0.26
Consensus pattern (49 bp):
CGATGCCATGTCCCAGAAATGGTCTTACACTGACTACTCAAATCCAGGT
Found at i:43272753 original size:27 final size:27
Alignment explanation
Indices: 43272695--43272753 Score: 109
Period size: 27 Copynumber: 2.2 Consensus size: 27
43272685 TTTTCCCCAG
*
43272695 TCTAGGCCCAAATTTTGTAATTCTTGA
1 TCTATGCCCAAATTTTGTAATTCTTGA
43272722 TCTATGCCCAAATTTTGTAATTCTTGA
1 TCTATGCCCAAATTTTGTAATTCTTGA
43272749 TCTAT
1 TCTAT
43272754 AATGATAAAA
Statistics
Matches: 31, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
27 31 1.00
ACGTcount: A:0.25, C:0.19, G:0.12, T:0.44
Consensus pattern (27 bp):
TCTATGCCCAAATTTTGTAATTCTTGA
Found at i:43275256 original size:20 final size:20
Alignment explanation
Indices: 43275233--43275282 Score: 64
Period size: 20 Copynumber: 2.5 Consensus size: 20
43275223 TACACTTCAA
43275233 TGTCCTTGTTCGCACTACGG
1 TGTCCTTGTTCGCACTACGG
* * *
43275253 TGTCCCTGTTTGCACTTCGG
1 TGTCCTTGTTCGCACTACGG
*
43275273 TGCCCTTGTT
1 TGTCCTTGTT
43275283 ATACATCTAT
Statistics
Matches: 25, Mismatches: 5, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
20 25 1.00
ACGTcount: A:0.06, C:0.30, G:0.24, T:0.40
Consensus pattern (20 bp):
TGTCCTTGTTCGCACTACGG
Found at i:43276306 original size:20 final size:20
Alignment explanation
Indices: 43276281--43276318 Score: 58
Period size: 20 Copynumber: 1.9 Consensus size: 20
43276271 ATCGATTTTT
*
43276281 AATTAAGTATCGATACCACA
1 AATTAAGTATCAATACCACA
*
43276301 AATTAATTATCAATACCA
1 AATTAAGTATCAATACCA
43276319 TTATTTTTAT
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 16 1.00
ACGTcount: A:0.47, C:0.18, G:0.05, T:0.29
Consensus pattern (20 bp):
AATTAAGTATCAATACCACA
Found at i:43277581 original size:19 final size:19
Alignment explanation
Indices: 43277549--43277608 Score: 86
Period size: 19 Copynumber: 3.2 Consensus size: 19
43277539 ATATGAGTTT
43277549 ATGCACTT-ATGTGCTAGG
1 ATGCACTTCATGTGCTAGG
43277567 ATGCACTTCATGTGCTAGG
1 ATGCACTTCATGTGCTAGG
* * *
43277586 ATGCATTTCATTTGCTAAG
1 ATGCACTTCATGTGCTAGG
43277605 ATGC
1 ATGC
43277609 GTTTTATGCT
Statistics
Matches: 38, Mismatches: 3, Indels: 1
0.90 0.07 0.02
Matches are distributed among these distances:
18 8 0.21
19 30 0.79
ACGTcount: A:0.23, C:0.18, G:0.23, T:0.35
Consensus pattern (19 bp):
ATGCACTTCATGTGCTAGG
Found at i:43280790 original size:27 final size:27
Alignment explanation
Indices: 43280760--43280937 Score: 205
Period size: 27 Copynumber: 6.6 Consensus size: 27
43280750 ATATTGAGTC
* * * *
43280760 CGCACACTCAGTGCTATATAATCAACT
1 CGCACACTTAGTGCTACATAGTCAAAT
* *
43280787 CGCACACTTAGTGCTACGTAATCAAAT
1 CGCACACTTAGTGCTACATAGTCAAAT
43280814 CGCACACTTAGTGCTACATAGTCAAACT
1 CGCACACTTAGTGCTACATAGTCAAA-T
** * *
43280842 CGCACACTTAGTGCCGCATGGTCAATT
1 CGCACACTTAGTGCTACATAGTCAAAT
* **
43280869 CGCACACTTAGTGC-ATCATATTCATTT
1 CGCACACTTAGTGCTA-CATAGTCAAAT
*
43280896 CGCACACTTAGTGCAACATAGTCAAAT
1 CGCACACTTAGTGCTACATAGTCAAAT
43280923 CGCACACTTAGTGCT
1 CGCACACTTAGTGCT
43280938 GTACAATTTA
Statistics
Matches: 130, Mismatches: 18, Indels: 6
0.84 0.12 0.04
Matches are distributed among these distances:
27 106 0.82
28 24 0.18
ACGTcount: A:0.30, C:0.28, G:0.15, T:0.27
Consensus pattern (27 bp):
CGCACACTTAGTGCTACATAGTCAAAT
Found at i:43280899 original size:82 final size:81
Alignment explanation
Indices: 43280781--43280936 Score: 233
Period size: 82 Copynumber: 1.9 Consensus size: 81
43280771 TGCTATATAA
* *
43280781 TCAACTCGCACACTTAGTGCTACGTAATCAAATCGCACACTTAGTGCTACATAGTCAAACTCGCA
1 TCAACTCGCACACTTAGTGCTACATAATCAAATCGCACACTTAGTGCAACATAGTCAAA-TCGCA
43280846 CACTTAGTGCCGCATGG
65 CACTTAGTGCCGCATGG
* * **
43280863 TCAATTCGCACACTTAGTGC-ATCATATTCATTTCGCACACTTAGTGCAACATAGTCAAATCGCA
1 TCAACTCGCACACTTAGTGCTA-CATAATCAAATCGCACACTTAGTGCAACATAGTCAAATCGCA
43280927 CACTTAGTGC
65 CACTTAGTGC
43280937 TGTACAATTT
Statistics
Matches: 67, Mismatches: 6, Indels: 3
0.88 0.08 0.04
Matches are distributed among these distances:
81 16 0.24
82 51 0.76
ACGTcount: A:0.29, C:0.28, G:0.15, T:0.27
Consensus pattern (81 bp):
TCAACTCGCACACTTAGTGCTACATAATCAAATCGCACACTTAGTGCAACATAGTCAAATCGCAC
ACTTAGTGCCGCATGG
Found at i:43281436 original size:12 final size:12
Alignment explanation
Indices: 43281419--43281445 Score: 54
Period size: 12 Copynumber: 2.2 Consensus size: 12
43281409 ATGGCATACT
43281419 TATGTATATATA
1 TATGTATATATA
43281431 TATGTATATATA
1 TATGTATATATA
43281443 TAT
1 TAT
43281446 ACTTCGGAAT
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 15 1.00
ACGTcount: A:0.41, C:0.00, G:0.07, T:0.52
Consensus pattern (12 bp):
TATGTATATATA
Found at i:43288810 original size:27 final size:27
Alignment explanation
Indices: 43288780--43288957 Score: 205
Period size: 27 Copynumber: 6.6 Consensus size: 27
43288770 ATATTGAGTC
* * * *
43288780 CGCACACTCAGTGCTATATAATCAACT
1 CGCACACTTAGTGCTACATAGTCAAAT
* *
43288807 CGCACACTTAGTGCTACGTAATCAAAT
1 CGCACACTTAGTGCTACATAGTCAAAT
43288834 CGCACACTTAGTGCTACATAGTCAAACT
1 CGCACACTTAGTGCTACATAGTCAAA-T
** * *
43288862 CGCACACTTAGTGCCGCATGGTCAATT
1 CGCACACTTAGTGCTACATAGTCAAAT
* **
43288889 CGCACACTTAGTGC-ATCATATTCATTT
1 CGCACACTTAGTGCTA-CATAGTCAAAT
*
43288916 CGCACACTTAGTGCAACATAGTCAAAT
1 CGCACACTTAGTGCTACATAGTCAAAT
43288943 CGCACACTTAGTGCT
1 CGCACACTTAGTGCT
43288958 GTACAATTTA
Statistics
Matches: 130, Mismatches: 18, Indels: 6
0.84 0.12 0.04
Matches are distributed among these distances:
27 106 0.82
28 24 0.18
ACGTcount: A:0.30, C:0.28, G:0.15, T:0.27
Consensus pattern (27 bp):
CGCACACTTAGTGCTACATAGTCAAAT
Found at i:43288919 original size:82 final size:81
Alignment explanation
Indices: 43288801--43288956 Score: 233
Period size: 82 Copynumber: 1.9 Consensus size: 81
43288791 TGCTATATAA
* *
43288801 TCAACTCGCACACTTAGTGCTACGTAATCAAATCGCACACTTAGTGCTACATAGTCAAACTCGCA
1 TCAACTCGCACACTTAGTGCTACATAATCAAATCGCACACTTAGTGCAACATAGTCAAA-TCGCA
43288866 CACTTAGTGCCGCATGG
65 CACTTAGTGCCGCATGG
* * **
43288883 TCAATTCGCACACTTAGTGC-ATCATATTCATTTCGCACACTTAGTGCAACATAGTCAAATCGCA
1 TCAACTCGCACACTTAGTGCTA-CATAATCAAATCGCACACTTAGTGCAACATAGTCAAATCGCA
43288947 CACTTAGTGC
65 CACTTAGTGC
43288957 TGTACAATTT
Statistics
Matches: 67, Mismatches: 6, Indels: 3
0.88 0.08 0.04
Matches are distributed among these distances:
81 16 0.24
82 51 0.76
ACGTcount: A:0.29, C:0.28, G:0.15, T:0.27
Consensus pattern (81 bp):
TCAACTCGCACACTTAGTGCTACATAATCAAATCGCACACTTAGTGCAACATAGTCAAATCGCAC
ACTTAGTGCCGCATGG
Found at i:43289460 original size:12 final size:12
Alignment explanation
Indices: 43289443--43289469 Score: 54
Period size: 12 Copynumber: 2.2 Consensus size: 12
43289433 ATGGCATACT
43289443 TATGTATATATA
1 TATGTATATATA
43289455 TATGTATATATA
1 TATGTATATATA
43289467 TAT
1 TAT
43289470 ACTTCGGAAT
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 15 1.00
ACGTcount: A:0.41, C:0.00, G:0.07, T:0.52
Consensus pattern (12 bp):
TATGTATATATA
Found at i:43291626 original size:24 final size:23
Alignment explanation
Indices: 43291589--43291633 Score: 63
Period size: 24 Copynumber: 1.9 Consensus size: 23
43291579 AACCCTTTCC
*
43291589 CTCTCAGCTCCTTATGTCTCCTT
1 CTCTCACCTCCTTATGTCTCCTT
*
43291612 CTCTCACCTTCCTTATTTCTCC
1 CTCTCACC-TCCTTATGTCTCC
43291634 ACATAGGAAG
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
23 7 0.37
24 12 0.63
ACGTcount: A:0.09, C:0.42, G:0.04, T:0.44
Consensus pattern (23 bp):
CTCTCACCTCCTTATGTCTCCTT
Found at i:43292951 original size:43 final size:42
Alignment explanation
Indices: 43292854--43292973 Score: 170
Period size: 43 Copynumber: 2.8 Consensus size: 42
43292844 CGGGTTACTA
* *
43292854 AGATTACGTGTAAGACCATATCTGGGATATGGCATCTATATG
1 AGATTACGTGTAAGACCATATCTGGGATATGGCATCAATACG
* *
43292896 AGACTT-TGTGTAAGACCATAGCTGGGATATTGGCATCAATACG
1 AGA-TTACGTGTAAGACCATATCTGGGATA-TGGCATCAATACG
*
43292939 AGATTACATGTAAGACCATATCTGGGATATGGCAT
1 AGATTACGTGTAAGACCATATCTGGGATATGGCAT
43292974 TGGTATGGTA
Statistics
Matches: 68, Mismatches: 7, Indels: 6
0.84 0.09 0.07
Matches are distributed among these distances:
42 32 0.47
43 36 0.53
ACGTcount: A:0.32, C:0.15, G:0.24, T:0.29
Consensus pattern (42 bp):
AGATTACGTGTAAGACCATATCTGGGATATGGCATCAATACG
Found at i:43295087 original size:5 final size:6
Alignment explanation
Indices: 43295072--43295101 Score: 51
Period size: 6 Copynumber: 4.8 Consensus size: 6
43295062 AAATGACAAG
43295072 AAAAAT AAAAAT AAAAAT AAAAAT ATAAAA
1 AAAAAT AAAAAT AAAAAT AAAAAT A-AAAA
43295102 CAAATTTTCT
Statistics
Matches: 23, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
6 19 0.83
7 4 0.17
ACGTcount: A:0.83, C:0.00, G:0.00, T:0.17
Consensus pattern (6 bp):
AAAAAT
Found at i:43296970 original size:21 final size:22
Alignment explanation
Indices: 43296925--43296974 Score: 66
Period size: 21 Copynumber: 2.3 Consensus size: 22
43296915 TGTAGGGCTC
* *
43296925 ACACGCCCGTGTGGTCCGAGGG
1 ACACGCCCGTGTGGACCCAGGG
*
43296947 ACACGCCCGTGT-GACCCTGGG
1 ACACGCCCGTGTGGACCCAGGG
43296968 ACACGCC
1 ACACGCC
43296975 GGTGCTAGAG
Statistics
Matches: 25, Mismatches: 3, Indels: 1
0.86 0.10 0.03
Matches are distributed among these distances:
21 13 0.52
22 12 0.48
ACGTcount: A:0.16, C:0.38, G:0.34, T:0.12
Consensus pattern (22 bp):
ACACGCCCGTGTGGACCCAGGG
Found at i:43299444 original size:40 final size:40
Alignment explanation
Indices: 43299400--43299587 Score: 304
Period size: 40 Copynumber: 4.7 Consensus size: 40
43299390 GCAAACACAT
* * *
43299400 TTGCCTTCGGGTCTTAACCCGGACATATCAACTTGCATAA
1 TTGCCTTCGGGTCTTAGCCCGGATATATCAACTCGCATAA
* *
43299440 TTGCCTTCGGGTCTTAACCCGGATATATCAACTTGCATAA
1 TTGCCTTCGGGTCTTAGCCCGGATATATCAACTCGCATAA
43299480 TTGCCTTCGGGTCTTAGCCCGGATATATCAACTCGCATAA
1 TTGCCTTCGGGTCTTAGCCCGGATATATCAACTCGCATAA
* * *
43299520 TTGCCTTCGGGTCATAGCCCGAATATATCAACTCGCGTAA
1 TTGCCTTCGGGTCTTAGCCCGGATATATCAACTCGCATAA
43299560 TTGCCTTCGGGTCTTAGCCCGGATATAT
1 TTGCCTTCGGGTCTTAGCCCGGATATAT
43299588 TCCAGTGCTC
Statistics
Matches: 140, Mismatches: 8, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
40 140 1.00
ACGTcount: A:0.23, C:0.27, G:0.20, T:0.31
Consensus pattern (40 bp):
TTGCCTTCGGGTCTTAGCCCGGATATATCAACTCGCATAA
Found at i:43307069 original size:40 final size:40
Alignment explanation
Indices: 43307025--43307172 Score: 260
Period size: 40 Copynumber: 3.7 Consensus size: 40
43307015 GCAAACACAT
* *
43307025 TTGCCTTCGGGTCTTAACCCGGACATATCAACTTGCATAA
1 TTGCCTTCGGGTCTTAGCCCGGATATATCAACTTGCATAA
43307065 TTGCCTTCGGGTCTTAGCCCGGATATATCAACTTGCATAA
1 TTGCCTTCGGGTCTTAGCCCGGATATATCAACTTGCATAA
* *
43307105 TTGCCTTCGGGTCTTAGCCCGGATATATCAACTCGCGTAA
1 TTGCCTTCGGGTCTTAGCCCGGATATATCAACTTGCATAA
43307145 TTGCCTTCGGGTCTTAGCCCGGATATAT
1 TTGCCTTCGGGTCTTAGCCCGGATATAT
43307173 TCCAATGCTC
Statistics
Matches: 104, Mismatches: 4, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
40 104 1.00
ACGTcount: A:0.21, C:0.26, G:0.21, T:0.32
Consensus pattern (40 bp):
TTGCCTTCGGGTCTTAGCCCGGATATATCAACTTGCATAA
Found at i:43310446 original size:39 final size:39
Alignment explanation
Indices: 43310390--43310513 Score: 176
Period size: 39 Copynumber: 3.2 Consensus size: 39
43310380 CAGTGATGTT
* *
43310390 TATCCGGCCTTAGGGTCCGCAGGCTATGTGCTGGAATTA
1 TATCCGGACTTAAGGTCCGCAGGCTATGTGCTGGAATTA
*
43310429 TATCCGGACTTAAGGTCCGCAGGCTATGTGATGGAATTA
1 TATCCGGACTTAAGGTCCGCAGGCTATGTGCTGGAATTA
* ** *
43310468 TAACCGGACTTAAGGTCCGCAGGCTACATGCTGGAAATA
1 TATCCGGACTTAAGGTCCGCAGGCTATGTGCTGGAATTA
*
43310507 TGTCCGG
1 TATCCGG
43310514 GCTAGTCCCG
Statistics
Matches: 75, Mismatches: 10, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
39 75 1.00
ACGTcount: A:0.23, C:0.22, G:0.29, T:0.26
Consensus pattern (39 bp):
TATCCGGACTTAAGGTCCGCAGGCTATGTGCTGGAATTA
Found at i:43314516 original size:11 final size:11
Alignment explanation
Indices: 43314500--43314531 Score: 57
Period size: 11 Copynumber: 3.0 Consensus size: 11
43314490 TCTATAAACA
43314500 CATATCATATT
1 CATATCATATT
43314511 CATATCATATT
1 CATATCATATT
43314522 CAT-TCATATT
1 CATATCATATT
43314532 TATGTTTCCA
Statistics
Matches: 21, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
10 7 0.33
11 14 0.67
ACGTcount: A:0.34, C:0.19, G:0.00, T:0.47
Consensus pattern (11 bp):
CATATCATATT
Found at i:43318588 original size:31 final size:33
Alignment explanation
Indices: 43318550--43318612 Score: 87
Period size: 33 Copynumber: 2.0 Consensus size: 33
43318540 AGCAGTGGGT
43318550 ACTGGGCC-GAG-CCCTTTTCAGA-ATACAGTAA
1 ACTGGGCCTGAGCCCCTTTTCAGATA-ACAGTAA
*
43318581 ACTGGGCCTTAGCCCCTTTTCAGATAACAGTA
1 ACTGGGCCTGAGCCCCTTTTCAGATAACAGTA
43318613 TGGCCCGTAG
Statistics
Matches: 28, Mismatches: 1, Indels: 4
0.85 0.03 0.12
Matches are distributed among these distances:
31 8 0.29
32 2 0.07
33 17 0.61
34 1 0.04
ACGTcount: A:0.27, C:0.27, G:0.21, T:0.25
Consensus pattern (33 bp):
ACTGGGCCTGAGCCCCTTTTCAGATAACAGTAA
Found at i:43322997 original size:8 final size:8
Alignment explanation
Indices: 43322984--43323018 Score: 61
Period size: 8 Copynumber: 4.4 Consensus size: 8
43322974 TATAAGTTGA
43322984 GAAATGTG
1 GAAATGTG
43322992 GAAATGTG
1 GAAATGTG
*
43323000 TAAATGTG
1 GAAATGTG
43323008 GAAATGTG
1 GAAATGTG
43323016 GAA
1 GAA
43323019 TGAAATGAAA
Statistics
Matches: 25, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
8 25 1.00
ACGTcount: A:0.40, C:0.00, G:0.34, T:0.26
Consensus pattern (8 bp):
GAAATGTG
Found at i:43323439 original size:37 final size:36
Alignment explanation
Indices: 43323389--43323527 Score: 142
Period size: 37 Copynumber: 3.8 Consensus size: 36
43323379 CATGTGAGTA
*
43323389 CGTGTAAGACCATAGCTGGGTTATGGCATCGTAATAG
1 CGTGTAAGACCATAGCTGGGCTATGGCATCGT-ATAG
***
43323426 CGTGTAAGACCATAGCTGGGCTATGGCATCGTGCGG
1 CGTGTAAGACCATAGCTGGGCTATGGCATCGTATAG
*
43323462 ACATGTAAGACCATAGCTGGGCTATGGCA-CTGTGATA-
1 -CGTGTAAGACCATAGCTGGGCTATGGCATC-GT-ATAG
*
43323499 CGTGTAGGACCAT-GTCTGGGAC-ATGGCAT
1 CGTGTAAGACCATAG-CTGGG-CTATGGCAT
43323528 TAATATGAGA
Statistics
Matches: 86, Mismatches: 10, Indels: 12
0.80 0.09 0.11
Matches are distributed among these distances:
35 1 0.01
36 24 0.28
37 61 0.71
ACGTcount: A:0.24, C:0.19, G:0.32, T:0.24
Consensus pattern (36 bp):
CGTGTAAGACCATAGCTGGGCTATGGCATCGTATAG
Found at i:43323479 original size:74 final size:73
Alignment explanation
Indices: 43323391--43323527 Score: 190
Period size: 74 Copynumber: 1.9 Consensus size: 73
43323381 TGTGAGTACG
*
43323391 TGTAAGACCATAGCTGGGTTATGGCA-TCGTAATAGCGTGTAAGACCATAG-CTGGG-CTATGGC
1 TGTAAGACCATAGCTGGGCTATGGCACT-GTAATA-CGTGTAAGACCAT-GTCTGGGAC-ATGGC
43323453 ATCGTGCGGACA
62 ATCGTGCGGACA
* *
43323465 TGTAAGACCATAGCTGGGCTATGGCACTGTGATACGTGTAGGACCATGTCTGGGACATGGCAT
1 TGTAAGACCATAGCTGGGCTATGGCACTGTAATACGTGTAAGACCATGTCTGGGACATGGCAT
43323528 TAATATGAGA
Statistics
Matches: 57, Mismatches: 3, Indels: 7
0.85 0.04 0.10
Matches are distributed among these distances:
72 1 0.02
73 24 0.42
74 31 0.54
75 1 0.02
ACGTcount: A:0.25, C:0.19, G:0.31, T:0.25
Consensus pattern (73 bp):
TGTAAGACCATAGCTGGGCTATGGCACTGTAATACGTGTAAGACCATGTCTGGGACATGGCATCG
TGCGGACA
Found at i:43332055 original size:21 final size:20
Alignment explanation
Indices: 43332027--43332065 Score: 51
Period size: 21 Copynumber: 1.9 Consensus size: 20
43332017 GTTTCATGAT
*
43332027 GAAATTTTCTAAGTTTTCTC
1 GAAATTTTCAAAGTTTTCTC
*
43332047 GAAAGTTTTCAAATTTTTC
1 GAAA-TTTTCAAAGTTTTC
43332066 AGTTTAATCC
Statistics
Matches: 16, Mismatches: 2, Indels: 1
0.84 0.11 0.05
Matches are distributed among these distances:
20 4 0.25
21 12 0.75
ACGTcount: A:0.28, C:0.13, G:0.10, T:0.49
Consensus pattern (20 bp):
GAAATTTTCAAAGTTTTCTC
Found at i:43334642 original size:10 final size:10
Alignment explanation
Indices: 43334629--43334663 Score: 52
Period size: 10 Copynumber: 3.5 Consensus size: 10
43334619 AAGCTCCGTC
*
43334629 CAGCTCAATT
1 CAGCTCATTT
43334639 CAGCTCATTT
1 CAGCTCATTT
*
43334649 GAGCTCATTT
1 CAGCTCATTT
43334659 CAGCT
1 CAGCT
43334664 TGTTTGAGCT
Statistics
Matches: 22, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
10 22 1.00
ACGTcount: A:0.23, C:0.29, G:0.14, T:0.34
Consensus pattern (10 bp):
CAGCTCATTT
Found at i:43334653 original size:20 final size:20
Alignment explanation
Indices: 43334630--43334676 Score: 67
Period size: 20 Copynumber: 2.4 Consensus size: 20
43334620 AGCTCCGTCC
43334630 AGCTCAATTCAGCTCATTTG
1 AGCTCAATTCAGCTCATTTG
* **
43334650 AGCTCATTTCAGCTTGTTTG
1 AGCTCAATTCAGCTCATTTG
43334670 AGCTCAA
1 AGCTCAA
43334677 CCGAGCTTAC
Statistics
Matches: 23, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
20 23 1.00
ACGTcount: A:0.23, C:0.23, G:0.17, T:0.36
Consensus pattern (20 bp):
AGCTCAATTCAGCTCATTTG
Found at i:43334901 original size:22 final size:22
Alignment explanation
Indices: 43334876--43334921 Score: 92
Period size: 22 Copynumber: 2.1 Consensus size: 22
43334866 TATTTATGAA
43334876 GTCTAGTTAATGTTCTTAACAT
1 GTCTAGTTAATGTTCTTAACAT
43334898 GTCTAGTTAATGTTCTTAACAT
1 GTCTAGTTAATGTTCTTAACAT
43334920 GT
1 GT
43334922 TCAGCTGAAC
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 24 1.00
ACGTcount: A:0.26, C:0.13, G:0.15, T:0.46
Consensus pattern (22 bp):
GTCTAGTTAATGTTCTTAACAT
Found at i:43338483 original size:27 final size:27
Alignment explanation
Indices: 43338452--43338629 Score: 205
Period size: 27 Copynumber: 6.6 Consensus size: 27
43338442 TAAATTGTAC
43338452 AGCACTAAGTGTGCGATTTGACTATGT
1 AGCACTAAGTGTGCGATTTGACTATGT
* ** *
43338479 TGCACTAAGTGTGCGAAATGAATATG-
1 AGCACTAAGTGTGCGATTTGACTATGT
* * *
43338505 ATGCACTAAGTGTGCGAATTGACCATGC
1 A-GCACTAAGTGTGCGATTTGACTATGT
*
43338533 GGCACTAAGTGTGCGAGTTTGACTATGT
1 AGCACTAAGTGTGCGA-TTTGACTATGT
* *
43338561 AGCACTAAGTGTGCGATTTGATTACGT
1 AGCACTAAGTGTGCGATTTGACTATGT
* * *
43338588 AGCACTAAGTGTGCGAGTTGATTATAT
1 AGCACTAAGTGTGCGATTTGACTATGT
*
43338615 AGCACTGAGTGTGCG
1 AGCACTAAGTGTGCG
43338630 GACTCAATAT
Statistics
Matches: 129, Mismatches: 19, Indels: 6
0.84 0.12 0.04
Matches are distributed among these distances:
27 106 0.82
28 23 0.18
ACGTcount: A:0.27, C:0.15, G:0.28, T:0.30
Consensus pattern (27 bp):
AGCACTAAGTGTGCGATTTGACTATGT
Found at i:43338566 original size:82 final size:81
Alignment explanation
Indices: 43338453--43338608 Score: 233
Period size: 82 Copynumber: 1.9 Consensus size: 81
43338443 AAATTGTACA
* *
43338453 GCACTAAGTGTGCGATTTGACTATGTTGCACTAAGTGTGCGAAATGAATATG-ATGCACTAAGTG
1 GCACTAAGTGTGCGATTTGACTATGTAGCACTAAGTGTGCGAAATGAATACGTA-GCACTAAGTG
43338517 TGCGAATTGACCATGCG
65 TGCGAATTGACCATGCG
** *
43338534 GCACTAAGTGTGCGAGTTTGACTATGTAGCACTAAGTGTGCGATTTGATTACGTAGCACTAAGTG
1 GCACTAAGTGTGCGA-TTTGACTATGTAGCACTAAGTGTGCGAAATGAATACGTAGCACTAAGTG
*
43338599 TGCGAGTTGA
65 TGCGAATTGA
43338609 TTATATAGCA
Statistics
Matches: 67, Mismatches: 6, Indels: 3
0.88 0.08 0.04
Matches are distributed among these distances:
81 15 0.22
82 51 0.76
83 1 0.01
ACGTcount: A:0.27, C:0.15, G:0.28, T:0.29
Consensus pattern (81 bp):
GCACTAAGTGTGCGATTTGACTATGTAGCACTAAGTGTGCGAAATGAATACGTAGCACTAAGTGT
GCGAATTGACCATGCG
Found at i:43338620 original size:82 final size:81
Alignment explanation
Indices: 43338449--43338629 Score: 229
Period size: 82 Copynumber: 2.2 Consensus size: 81
43338439 GATTAAATTG
* *
43338449 TACAGCACTAAGTGTGCGATTTGACTATGTTGCACTAAGTGTGCGAAATGAATATGATGCACTAA
1 TACAGCACTAAGTGTGCGATTTGACTATGTAGCACTAAGTGTGCGAAATGAATACGATGCACTAA
43338514 GTGTGCGAATTGACCA
66 GTGTGCGAATTGACCA
* * ** *
43338530 TGCGGCACTAAGTGTGCGAGTTTGACTATGTAGCACTAAGTGTGCGATTTGATTACG-TAGCACT
1 TACAGCACTAAGTGTGCGA-TTTGACTATGTAGCACTAAGTGTGCGAAATGAATACGAT-GCACT
* **
43338594 AAGTGTGCGAGTTGATTA
64 AAGTGTGCGAATTGACCA
* *
43338612 TATAGCACTGAGTGTGCG
1 TACAGCACTAAGTGTGCG
43338630 GACTCAATAT
Statistics
Matches: 84, Mismatches: 14, Indels: 3
0.83 0.14 0.03
Matches are distributed among these distances:
81 18 0.21
82 66 0.79
ACGTcount: A:0.27, C:0.15, G:0.28, T:0.30
Consensus pattern (81 bp):
TACAGCACTAAGTGTGCGATTTGACTATGTAGCACTAAGTGTGCGAAATGAATACGATGCACTAA
GTGTGCGAATTGACCA
Found at i:43346879 original size:27 final size:27
Alignment explanation
Indices: 43346846--43347023 Score: 196
Period size: 27 Copynumber: 6.6 Consensus size: 27
43346836 TAAATTGTAC
43346846 AGCACTAAGTGTGCGATTTGACTATGT
1 AGCACTAAGTGTGCGATTTGACTATGT
* * ** *
43346873 TGTACTAAGTGTGCGAAATGAATATG-
1 AGCACTAAGTGTGCGATTTGACTATGT
* * *
43346899 ATGCACTAAGTGTGCGAATTGACCATGC
1 A-GCACTAAGTGTGCGATTTGACTATGT
*
43346927 GGCACTAAGTGTGCGAGTTTGACTATGT
1 AGCACTAAGTGTGCGA-TTTGACTATGT
* *
43346955 AGCACTAAGTGTGCGATTTGATTACGT
1 AGCACTAAGTGTGCGATTTGACTATGT
* * *
43346982 AGCACTAAGTGTGCGAGTTGATTATAT
1 AGCACTAAGTGTGCGATTTGACTATGT
*
43347009 AGCACTGAGTGTGCG
1 AGCACTAAGTGTGCG
43347024 GACTCAATAT
Statistics
Matches: 127, Mismatches: 21, Indels: 6
0.82 0.14 0.04
Matches are distributed among these distances:
27 104 0.82
28 23 0.18
ACGTcount: A:0.27, C:0.15, G:0.28, T:0.30
Consensus pattern (27 bp):
AGCACTAAGTGTGCGATTTGACTATGT
Found at i:43346962 original size:82 final size:81
Alignment explanation
Indices: 43346847--43347002 Score: 224
Period size: 82 Copynumber: 1.9 Consensus size: 81
43346837 AAATTGTACA
* * *
43346847 GCACTAAGTGTGCGATTTGACTATGTTGTACTAAGTGTGCGAAATGAATATG-ATGCACTAAGTG
1 GCACTAAGTGTGCGATTTGACTATGTAGCACTAAGTGTGCGAAATGAATACGTA-GCACTAAGTG
43346911 TGCGAATTGACCATGCG
65 TGCGAATTGACCATGCG
** *
43346928 GCACTAAGTGTGCGAGTTTGACTATGTAGCACTAAGTGTGCGATTTGATTACGTAGCACTAAGTG
1 GCACTAAGTGTGCGA-TTTGACTATGTAGCACTAAGTGTGCGAAATGAATACGTAGCACTAAGTG
*
43346993 TGCGAGTTGA
65 TGCGAATTGA
43347003 TTATATAGCA
Statistics
Matches: 66, Mismatches: 7, Indels: 3
0.87 0.09 0.04
Matches are distributed among these distances:
81 15 0.23
82 50 0.76
83 1 0.02
ACGTcount: A:0.27, C:0.15, G:0.28, T:0.30
Consensus pattern (81 bp):
GCACTAAGTGTGCGATTTGACTATGTAGCACTAAGTGTGCGAAATGAATACGTAGCACTAAGTGT
GCGAATTGACCATGCG
Found at i:43347014 original size:82 final size:81
Alignment explanation
Indices: 43346843--43347023 Score: 220
Period size: 82 Copynumber: 2.2 Consensus size: 81
43346833 GATTAAATTG
* * *
43346843 TACAGCACTAAGTGTGCGATTTGACTATGTTGTACTAAGTGTGCGAAATGAATATGATGCACTAA
1 TACAGCACTAAGTGTGCGATTTGACTATGTAGCACTAAGTGTGCGAAATGAATACGATGCACTAA
43346908 GTGTGCGAATTGACCA
66 GTGTGCGAATTGACCA
* * ** *
43346924 TGCGGCACTAAGTGTGCGAGTTTGACTATGTAGCACTAAGTGTGCGATTTGATTACG-TAGCACT
1 TACAGCACTAAGTGTGCGA-TTTGACTATGTAGCACTAAGTGTGCGAAATGAATACGAT-GCACT
* **
43346988 AAGTGTGCGAGTTGATTA
64 AAGTGTGCGAATTGACCA
* *
43347006 TATAGCACTGAGTGTGCG
1 TACAGCACTAAGTGTGCG
43347024 GACTCAATAT
Statistics
Matches: 83, Mismatches: 15, Indels: 3
0.82 0.15 0.03
Matches are distributed among these distances:
81 18 0.22
82 65 0.78
ACGTcount: A:0.27, C:0.15, G:0.28, T:0.30
Consensus pattern (81 bp):
TACAGCACTAAGTGTGCGATTTGACTATGTAGCACTAAGTGTGCGAAATGAATACGATGCACTAA
GTGTGCGAATTGACCA
Found at i:43354384 original size:18 final size:18
Alignment explanation
Indices: 43354361--43354397 Score: 74
Period size: 18 Copynumber: 2.1 Consensus size: 18
43354351 GTCTGGGATG
43354361 TTGACATCGTATTTGATT
1 TTGACATCGTATTTGATT
43354379 TTGACATCGTATTTGATT
1 TTGACATCGTATTTGATT
43354397 T
1 T
43354398 CATGTAAGAC
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 19 1.00
ACGTcount: A:0.22, C:0.11, G:0.16, T:0.51
Consensus pattern (18 bp):
TTGACATCGTATTTGATT
Found at i:43361271 original size:39 final size:39
Alignment explanation
Indices: 43361217--43361497 Score: 427
Period size: 39 Copynumber: 7.2 Consensus size: 39
43361207 GAAATGTGTA
43361217 TGGAAATATATCCGGGCTAAAGACCCGCAGGCTTTGTGC
1 TGGAAATATATCCGGGCTAAAGACCCGCAGGCTTTGTGC
*
43361256 TGGAAATATATCCGGGCCAAAGACCCGCAGGCTTTGTGC
1 TGGAAATATATCCGGGCTAAAGACCCGCAGGCTTTGTGC
* * * *
43361295 TGGAAATGTATCCGGGCTAAAGTCCCACAGGCTTTGCGC
1 TGGAAATATATCCGGGCTAAAGACCCGCAGGCTTTGTGC
* * *
43361334 TGGAAACATATCCGGGCTAAAGACCCGTAGGCTTCGTGC
1 TGGAAATATATCCGGGCTAAAGACCCGCAGGCTTTGTGC
*
43361373 TGGAAATATATCCGGGCTAAAGACCCGCAGGCTTCGTGC
1 TGGAAATATATCCGGGCTAAAGACCCGCAGGCTTTGTGC
* *
43361412 TGGAAATGTATCCAGGCTAAAGACCCGCAGGCTTTGTGC
1 TGGAAATATATCCGGGCTAAAGACCCGCAGGCTTTGTGC
* * *
43361451 TGGAAATGTATCTGGGCTAAAGTCCCGCAGGCTTTGTGC
1 TGGAAATATATCCGGGCTAAAGACCCGCAGGCTTTGTGC
*
43361490 TGGTAATA
1 TGGAAATA
43361498 AAATTTCAGG
Statistics
Matches: 219, Mismatches: 23, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
39 219 1.00
ACGTcount: A:0.25, C:0.23, G:0.28, T:0.23
Consensus pattern (39 bp):
TGGAAATATATCCGGGCTAAAGACCCGCAGGCTTTGTGC
Found at i:43365515 original size:14 final size:15
Alignment explanation
Indices: 43365496--43365526 Score: 55
Period size: 14 Copynumber: 2.1 Consensus size: 15
43365486 TCTATGTTTG
43365496 TTATATGTG-AAATA
1 TTATATGTGAAAATA
43365510 TTATATGTGAAAATA
1 TTATATGTGAAAATA
43365525 TT
1 TT
43365527 GTGTTTTGAT
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
14 9 0.56
15 7 0.44
ACGTcount: A:0.42, C:0.00, G:0.13, T:0.45
Consensus pattern (15 bp):
TTATATGTGAAAATA
Found at i:43367295 original size:39 final size:39
Alignment explanation
Indices: 43367241--43367560 Score: 532
Period size: 39 Copynumber: 8.2 Consensus size: 39
43367231 GAAATGTGTA
43367241 TGGAAATATATCCGGGCTAAAGACCCGCAGGCTTTGTGC
1 TGGAAATATATCCGGGCTAAAGACCCGCAGGCTTTGTGC
*
43367280 TGGAAATATATCCGGGCCAAAGACCCGCAGGCTTTGTGC
1 TGGAAATATATCCGGGCTAAAGACCCGCAGGCTTTGTGC
43367319 TGGAAATATATCCGGGCTAAAGACCCGCAGGCTTTGTGC
1 TGGAAATATATCCGGGCTAAAGACCCGCAGGCTTTGTGC
* * *
43367358 TGGAAATGTATCCGGGCTAAAGTCCCGCAGGCTTTGCGC
1 TGGAAATATATCCGGGCTAAAGACCCGCAGGCTTTGTGC
* *
43367397 TGGAAATATATCCGGGCTAAAGACCCGCAGGCTTCGTGT
1 TGGAAATATATCCGGGCTAAAGACCCGCAGGCTTTGTGC
*
43367436 TGGAAATATATCCGGGCTAAAGACCCGCAGGCTTCGTGC
1 TGGAAATATATCCGGGCTAAAGACCCGCAGGCTTTGTGC
* *
43367475 TGGAAATGTATCCAGGCTAAAGACCCGCAGGCTTTGTGC
1 TGGAAATATATCCGGGCTAAAGACCCGCAGGCTTTGTGC
* *
43367514 TGGAAATGTATCCGGGCTAAAGTCCCGCAGGCTTTGTGC
1 TGGAAATATATCCGGGCTAAAGACCCGCAGGCTTTGTGC
*
43367553 TGGTAATA
1 TGGAAATA
43367561 AAATTTCGGG
Statistics
Matches: 263, Mismatches: 18, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
39 263 1.00
ACGTcount: A:0.25, C:0.23, G:0.29, T:0.23
Consensus pattern (39 bp):
TGGAAATATATCCGGGCTAAAGACCCGCAGGCTTTGTGC
Found at i:43371618 original size:27 final size:27
Alignment explanation
Indices: 43371588--43371765 Score: 196
Period size: 27 Copynumber: 6.6 Consensus size: 27
43371578 ATATTGAGTC
* * * *
43371588 CGCACACTCAGTGCTATATAATCAACT
1 CGCACACTTAGTGCTACATAGTCAAAT
* *
43371615 CGCACACTTAGTGCTACGTAATCAAAT
1 CGCACACTTAGTGCTACATAGTCAAAT
43371642 CGCACACTTAGTGCTACATAGTCAAACT
1 CGCACACTTAGTGCTACATAGTCAAA-T
* ** * *
43371670 CGCACACATAGTGCCGCATGGTCAATT
1 CGCACACTTAGTGCTACATAGTCAAAT
* **
43371697 CGCACACTTAGTGC-ATCATATTCATTT
1 CGCACACTTAGTGCTA-CATAGTCAAAT
*
43371724 CGCACACTTAGTGCAACATAGTCAAAT
1 CGCACACTTAGTGCTACATAGTCAAAT
43371751 CGCACACTTAGTGCT
1 CGCACACTTAGTGCT
43371766 GTACAATTTA
Statistics
Matches: 128, Mismatches: 20, Indels: 6
0.83 0.13 0.04
Matches are distributed among these distances:
27 105 0.82
28 23 0.18
ACGTcount: A:0.30, C:0.28, G:0.15, T:0.26
Consensus pattern (27 bp):
CGCACACTTAGTGCTACATAGTCAAAT
Found at i:43371727 original size:82 final size:81
Alignment explanation
Indices: 43371609--43371764 Score: 224
Period size: 82 Copynumber: 1.9 Consensus size: 81
43371599 TGCTATATAA
* *
43371609 TCAACTCGCACACTTAGTGCTACGTAATCAAATCGCACACTTAGTGCTACATAGTCAAACTCGCA
1 TCAACTCGCACACTTAGTGCTACATAATCAAATCGCACACTTAGTGCAACATAGTCAAA-TCGCA
43371674 CACATAGTGCCGCATGG
65 CACATAGTGCCGCATGG
* * **
43371691 TCAATTCGCACACTTAGTGC-ATCATATTCATTTCGCACACTTAGTGCAACATAGTCAAATCGCA
1 TCAACTCGCACACTTAGTGCTA-CATAATCAAATCGCACACTTAGTGCAACATAGTCAAATCGCA
*
43371755 CACTTAGTGC
65 CACATAGTGC
43371765 TGTACAATTT
Statistics
Matches: 66, Mismatches: 7, Indels: 3
0.87 0.09 0.04
Matches are distributed among these distances:
81 15 0.23
82 51 0.77
ACGTcount: A:0.30, C:0.28, G:0.15, T:0.26
Consensus pattern (81 bp):
TCAACTCGCACACTTAGTGCTACATAATCAAATCGCACACTTAGTGCAACATAGTCAAATCGCAC
ACATAGTGCCGCATGG
Found at i:43394077 original size:37 final size:37
Alignment explanation
Indices: 43394009--43394131 Score: 144
Period size: 37 Copynumber: 3.4 Consensus size: 37
43393999 TGTCCCAGAC
* *
43394009 ATGGTCCTACACG-TATCAC-AGTGCCATAGCCCAGCT
1 ATGGTCTTACACGCTAGCACGA-TGCCATAGCCCAGCT
* *
43394045 ATGGTCTTACATG-TCCGCACGATGCCATAGCCCAGCT
1 ATGGTCTTACACGCT-AGCACGATGCCATAGCCCAGCT
** *
43394082 ATGGTCTTACACGCTATTACGATGCCATAACCCAGCT
1 ATGGTCTTACACGCTAGCACGATGCCATAGCCCAGCT
43394119 ATGGTCTTACACG
1 ATGGTCTTACACG
43394132 TACTCACATG
Statistics
Matches: 75, Mismatches: 9, Indels: 5
0.84 0.10 0.06
Matches are distributed among these distances:
36 12 0.16
37 61 0.81
38 2 0.03
ACGTcount: A:0.24, C:0.31, G:0.20, T:0.25
Consensus pattern (37 bp):
ATGGTCTTACACGCTAGCACGATGCCATAGCCCAGCT
Found at i:43394515 original size:8 final size:8
Alignment explanation
Indices: 43394502--43394536 Score: 61
Period size: 8 Copynumber: 4.4 Consensus size: 8
43394492 TTTCATTTCA
43394502 TTCCACAT
1 TTCCACAT
43394510 TTCCACAT
1 TTCCACAT
*
43394518 TTACACAT
1 TTCCACAT
43394526 TTCCACAT
1 TTCCACAT
43394534 TTC
1 TTC
43394537 TCAACTTATA
Statistics
Matches: 25, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
8 25 1.00
ACGTcount: A:0.26, C:0.34, G:0.00, T:0.40
Consensus pattern (8 bp):
TTCCACAT
Found at i:43407723 original size:39 final size:39
Alignment explanation
Indices: 43407607--43407730 Score: 135
Period size: 39 Copynumber: 3.2 Consensus size: 39
43407597 GGACTTTAGC
* * * * * *
43407607 CCGGACATACTTCCAACACGTAGCCTGCAGACCTTAAGT
1 CCGGATATAATTCCAGCACATAGCCTACGGACCTTAAGT
43407646 CC-GATTATAATTCCAGCACATAGCCTACGGACCTTAAGT
1 CCGGA-TATAATTCCAGCACATAGCCTACGGACCTTAAGT
* * *
43407685 CTGGATATAATTCCAGCACATAGCCTGCGTATCC-TAAGT
1 CCGGATATAATTCCAGCACATAGCCTACGGA-CCTTAAGT
43407724 CCGGATA
1 CCGGATA
43407731 AACATCACTG
Statistics
Matches: 72, Mismatches: 10, Indels: 6
0.82 0.11 0.07
Matches are distributed among these distances:
38 2 0.03
39 66 0.92
40 4 0.06
ACGTcount: A:0.29, C:0.29, G:0.18, T:0.24
Consensus pattern (39 bp):
CCGGATATAATTCCAGCACATAGCCTACGGACCTTAAGT
Found at i:43412388 original size:48 final size:48
Alignment explanation
Indices: 43412297--43412388 Score: 141
Period size: 48 Copynumber: 1.9 Consensus size: 48
43412287 CTTACCGAAG
*
43412297 CCATATCCCAGATATGGTCTTACACGTAATCTCATATCGATGCCGATT
1 CCATATCCCAGATATGGTCTTACACGTAATCTCATATCAATGCCGATT
* *
43412345 CCATATCCCAGATATGGTCTTACACAG-GATCTCATATTAATGCC
1 CCATATCCCAGATATGGTCTTACAC-GTAATCTCATATCAATGCC
43412389 ATGTCCCAGA
Statistics
Matches: 40, Mismatches: 3, Indels: 2
0.89 0.07 0.04
Matches are distributed among these distances:
48 39 0.98
49 1 0.03
ACGTcount: A:0.28, C:0.27, G:0.14, T:0.30
Consensus pattern (48 bp):
CCATATCCCAGATATGGTCTTACACGTAATCTCATATCAATGCCGATT
Found at i:43412469 original size:37 final size:37
Alignment explanation
Indices: 43412384--43412523 Score: 171
Period size: 37 Copynumber: 3.8 Consensus size: 37
43412374 TCTCATATTA
*
43412384 ATGCCAT-GTCCCAGAC-ATGGTCTTACACGT-ATCACA
1 ATGCCATAG-CCCAG-CTATGGTCTTACACGTCATCACG
* *
43412420 ATGCCATAGCCCAGCTATGGTCTTACATGTCCTCACG
1 ATGCCATAGCCCAGCTATGGTCTTACACGTCATCACG
* *
43412457 ATGCCATAGCCCAACTATGGTCTTACACG-CTATTACG
1 ATGCCATAGCCCAGCTATGGTCTTACACGTC-ATCACG
*
43412494 ATGCCATAACCCAGCTATGGTCTTACACGT
1 ATGCCATAGCCCAGCTATGGTCTTACACGT
43412524 ACTCACATGT
Statistics
Matches: 90, Mismatches: 9, Indels: 8
0.84 0.08 0.07
Matches are distributed among these distances:
35 1 0.01
36 26 0.29
37 63 0.70
ACGTcount: A:0.26, C:0.31, G:0.17, T:0.26
Consensus pattern (37 bp):
ATGCCATAGCCCAGCTATGGTCTTACACGTCATCACG
Found at i:43412514 original size:74 final size:73
Alignment explanation
Indices: 43412384--43412529 Score: 206
Period size: 74 Copynumber: 2.0 Consensus size: 73
43412374 TCTCATATTA
* *
43412384 ATGCCATGTCCCAGACATGGTCTTACACGTATCACAATGCCATAGCCCAGCTATGGTCTTACATG
1 ATGCCATGTCCCAGACATGGTCTTACACGTATCACAATGCCATAACCCAGCTATGGTCTTACACG
*
43412449 TCCTCACG
66 TACTCACG
* *
43412457 ATGCCATAG-CCCA-ACTATGGTCTTACACGCTATTACGATGCCATAACCCAGCTATGGTCTTAC
1 ATGCCAT-GTCCCAGAC-ATGGTCTTACACG-TATCACAATGCCATAACCCAGCTATGGTCTTAC
43412520 ACGTACTCAC
63 ACGTACTCAC
43412530 ATGTATTGCC
Statistics
Matches: 65, Mismatches: 5, Indels: 5
0.87 0.07 0.07
Matches are distributed among these distances:
72 2 0.03
73 24 0.37
74 39 0.60
ACGTcount: A:0.26, C:0.32, G:0.16, T:0.26
Consensus pattern (73 bp):
ATGCCATGTCCCAGACATGGTCTTACACGTATCACAATGCCATAACCCAGCTATGGTCTTACACG
TACTCACG
Found at i:43412908 original size:8 final size:8
Alignment explanation
Indices: 43412895--43412921 Score: 54
Period size: 8 Copynumber: 3.4 Consensus size: 8
43412885 TTTCATTTCA
43412895 TTCCACAT
1 TTCCACAT
43412903 TTCCACAT
1 TTCCACAT
43412911 TTCCACAT
1 TTCCACAT
43412919 TTC
1 TTC
43412922 TCAACTTATA
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
8 19 1.00
ACGTcount: A:0.22, C:0.37, G:0.00, T:0.41
Consensus pattern (8 bp):
TTCCACAT
Found at i:43416446 original size:64 final size:64
Alignment explanation
Indices: 43416365--43416550 Score: 189
Period size: 67 Copynumber: 2.9 Consensus size: 64
43416355 AGACATTATG
* * * *
43416365 ATGTAGCTAGGTCGCATGGGTGATACTATGTGTACACCATATAGACAAGAGAGCTACGGGATAT
1 ATGTAGCTAGGTCGCATGGGTGGTACTATGTGTACACCATGTAGACAAGAGAGCTACGAGATAA
* * * * * *
43416429 ATGTAGCTAGGTCGCATGTGTGGTTCCAGGTGAAGGACACCATGTAGACAAGAGAGCTATGAGAT
1 ATGTAGCTAGGTCGCATGGGTGGTACTA--TG-TGTACACCATGTAGACAAGAGAGCTACGAGAT
43416494 AA
63 AA
* * *
43416496 ACTG--GCTAGGTCACATGGGTGGTACTAAGTGTCCACCATGT-GTACAAGAGAGCTA
1 A-TGTAGCTAGGTCGCATGGGTGGTACTATGTGTACACCATGTAG-ACAAGAGAGCTA
43416551 AACTATATGA
Statistics
Matches: 99, Mismatches: 18, Indels: 11
0.77 0.14 0.09
Matches are distributed among these distances:
62 1 0.01
63 21 0.21
64 25 0.25
66 21 0.21
67 29 0.29
68 2 0.02
ACGTcount: A:0.30, C:0.17, G:0.30, T:0.24
Consensus pattern (64 bp):
ATGTAGCTAGGTCGCATGGGTGGTACTATGTGTACACCATGTAGACAAGAGAGCTACGAGATAA
Found at i:43443468 original size:46 final size:46
Alignment explanation
Indices: 43443408--43443727 Score: 489
Period size: 46 Copynumber: 7.0 Consensus size: 46
43443398 TTTGACATGA
* * * * * * *
43443408 TGCCATAGTGTCTTTAAACTATGGTCTTACTCATTTTC-TGTCATGT
1 TGCCATGGTATCTTTCAACCATGGTCTTACACA-TTTCATATCAGGT
** * * *
43443454 TGCCATGGTATCTTTCAACCATGGTCTTATTCTTTTCATGTCATGT
1 TGCCATGGTATCTTTCAACCATGGTCTTACACATTTCATATCAGGT
**
43443500 TGCCATGGTATCTTTCAACCATGGTCTTATTCATTTCATATCAGGT
1 TGCCATGGTATCTTTCAACCATGGTCTTACACATTTCATATCAGGT
43443546 TGCCATGGTATCTTTCAACCATGGTCTTACACATTTCATATCAGGT
1 TGCCATGGTATCTTTCAACCATGGTCTTACACATTTCATATCAGGT
*
43443592 TGCCATGGTATCTTTCAACCATGGTCTTACACATTTCATATCAGGC
1 TGCCATGGTATCTTTCAACCATGGTCTTACACATTTCATATCAGGT
43443638 TGCCATGGTATCTTTCAACCATGGTCTTACACATTTCATATCAGGT
1 TGCCATGGTATCTTTCAACCATGGTCTTACACATTTCATATCAGGT
43443684 TGCCATGGTATCTTTCAACCATGGTCTTACACATTTCATATCAG
1 TGCCATGGTATCTTTCAACCATGGTCTTACACATTTCATATCAG
43443728 AGAGCACACT
Statistics
Matches: 260, Mismatches: 13, Indels: 2
0.95 0.05 0.01
Matches are distributed among these distances:
45 4 0.02
46 256 0.98
ACGTcount: A:0.22, C:0.23, G:0.15, T:0.40
Consensus pattern (46 bp):
TGCCATGGTATCTTTCAACCATGGTCTTACACATTTCATATCAGGT
Found at i:43445824 original size:11 final size:11
Alignment explanation
Indices: 43445808--43445855 Score: 51
Period size: 11 Copynumber: 4.2 Consensus size: 11
43445798 CTTTATATAC
43445808 TAATAAAATAA
1 TAATAAAATAA
*
43445819 TAATAAAATATCT
1 TAATAAAATA--A
* *
43445832 TATTAAAATAT
1 TAATAAAATAA
43445843 TAATAAAATAA
1 TAATAAAATAA
43445854 TA
1 TA
43445856 TTTATCTAAT
Statistics
Matches: 31, Mismatches: 4, Indels: 4
0.79 0.10 0.10
Matches are distributed among these distances:
11 22 0.71
13 9 0.29
ACGTcount: A:0.62, C:0.02, G:0.00, T:0.35
Consensus pattern (11 bp):
TAATAAAATAA
Found at i:43446817 original size:55 final size:55
Alignment explanation
Indices: 43446749--43446883 Score: 202
Period size: 55 Copynumber: 2.5 Consensus size: 55
43446739 CGTGCCTTTA
* * *
43446749 GCCCGTGTGCAACACTGACTTTAAAACACGACCATGACACACGCCTGTGTGGCTT
1 GCCCGTGTACAACACTGACTTTAAAACACGACCATGACACACGCCCGTGTGGCCT
*
43446804 GCCCGTGTACAACACTGACTTTAAAACACGGCCATGACACACGCCCGTGTGGCCT
1 GCCCGTGTACAACACTGACTTTAAAACACGACCATGACACACGCCCGTGTGGCCT
*
43446859 ACCCGTGTACTAA-ACTGAC-TTAAAA
1 GCCCGTGTAC-AACACTGACTTTAAAA
43446884 TTTTAAGTGC
Statistics
Matches: 74, Mismatches: 5, Indels: 3
0.90 0.06 0.04
Matches are distributed among these distances:
54 6 0.08
55 66 0.89
56 2 0.03
ACGTcount: A:0.28, C:0.31, G:0.20, T:0.21
Consensus pattern (55 bp):
GCCCGTGTACAACACTGACTTTAAAACACGACCATGACACACGCCCGTGTGGCCT
Found at i:43447895 original size:138 final size:142
Alignment explanation
Indices: 43447630--43447900 Score: 342
Period size: 140 Copynumber: 1.9 Consensus size: 142
43447620 GATAAGTTGT
*
43447630 CGATGCCATGTCCCAGACATGGTCTCACATAGGCTATCATCATCAAGGCCGATGCCATGTCCCAG
1 CGATGCCATGTCCCAGACATGGTCTCACATAGGCTATCATCATCAACGCCGATGCCATGTCCCAG
* * * *
43447695 ACATGGTCTTATACTAGCTCTAGTATATACGTGCTGATGCATGTCCCGGACATGCCTTACACTAG
66 ACATGGTCTTACACTAGCACTAGTATATA-GTGCCGATGCATGTCCCAGACATGCCTTACACTAG
43447760 CACGACTCTTAGC
130 CACGACTCTTAGC
* * *
43447773 CGATG-CATGTCCCAGACAT-GTCTTACACT-GGC-ACTCATC-TCTACGCTGATGCCATGTCCC
1 CGATGCCATGTCCCAGACATGGTCTCACA-TAGGCTA-TCATCATCAACGCCGATGCCATGTCCC
* * *
43447833 AGACATGGTCTTACACTGGCACTCA-TA-AT-GTGCCCGATGTATGTCCCAGACATGTCTTACAC
64 AGACATGGTCTTACACTAGCACT-AGTATATAGTG-CCGATGCATGTCCCAGACATGCCTTACAC
43447895 TAGCAC
127 TAGCAC
43447901 ACAAGAAATC
Statistics
Matches: 113, Mismatches: 11, Indels: 13
0.82 0.08 0.09
Matches are distributed among these distances:
137 3 0.03
138 31 0.27
139 2 0.02
140 41 0.36
141 16 0.14
142 15 0.13
143 5 0.04
ACGTcount: A:0.24, C:0.30, G:0.20, T:0.26
Consensus pattern (142 bp):
CGATGCCATGTCCCAGACATGGTCTCACATAGGCTATCATCATCAACGCCGATGCCATGTCCCAG
ACATGGTCTTACACTAGCACTAGTATATAGTGCCGATGCATGTCCCAGACATGCCTTACACTAGC
ACGACTCTTAGC
Found at i:43449361 original size:40 final size:42
Alignment explanation
Indices: 43449280--43449361 Score: 114
Period size: 42 Copynumber: 2.0 Consensus size: 42
43449270 CGGGTAAATC
* * *
43449280 CAACAACCCATGTTTATCTTTTCCTCTTTTTAAATTCTTTTT
1 CAACAACCCAAGATTATCTTCTCCTCTTTTTAAATTCTTTTT
*
43449322 CAACAACCCAAGATTATCTTCT-C-CTTTTTAAATTTTTTTT
1 CAACAACCCAAGATTATCTTCTCCTCTTTTTAAATTCTTTTT
43449362 AAGATAAAAC
Statistics
Matches: 36, Mismatches: 4, Indels: 2
0.86 0.10 0.05
Matches are distributed among these distances:
40 16 0.44
41 1 0.03
42 19 0.53
ACGTcount: A:0.24, C:0.23, G:0.02, T:0.50
Consensus pattern (42 bp):
CAACAACCCAAGATTATCTTCTCCTCTTTTTAAATTCTTTTT
Found at i:43452252 original size:34 final size:33
Alignment explanation
Indices: 43452204--43452277 Score: 96
Period size: 34 Copynumber: 2.2 Consensus size: 33
43452194 TTTATGCATT
43452204 ATTGATACTGTACTG-AATTGGGCTAAGGCCTAC
1 ATTGATACTGTACTGTAA-TGGGCTAAGGCCTAC
* *
43452237 ATTGTTACTGCTACTGTAATGGGCTAAGGCCCAC
1 ATTGATACTG-TACTGTAATGGGCTAAGGCCTAC
*
43452271 ACTGATA
1 ATTGATA
43452278 TGTGAACATG
Statistics
Matches: 35, Mismatches: 4, Indels: 3
0.83 0.10 0.07
Matches are distributed among these distances:
33 9 0.26
34 24 0.69
35 2 0.06
ACGTcount: A:0.27, C:0.20, G:0.23, T:0.30
Consensus pattern (33 bp):
ATTGATACTGTACTGTAATGGGCTAAGGCCTAC
Found at i:43462429 original size:18 final size:18
Alignment explanation
Indices: 43462401--43462440 Score: 55
Period size: 18 Copynumber: 2.2 Consensus size: 18
43462391 TTTGGGCTTA
43462401 ATGGGCCACATGAG-CGT
1 ATGGGCCACATGAGCCGT
*
43462418 ATGGGCCCACATGGGCCGT
1 ATGGG-CCACATGAGCCGT
43462437 ATGG
1 ATGG
43462441 TAGGCTTGGG
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
17 5 0.25
18 8 0.40
19 7 0.35
ACGTcount: A:0.20, C:0.25, G:0.38, T:0.17
Consensus pattern (18 bp):
ATGGGCCACATGAGCCGT
Found at i:43466127 original size:55 final size:55
Alignment explanation
Indices: 43466038--43466162 Score: 223
Period size: 55 Copynumber: 2.3 Consensus size: 55
43466028 TGCTAAGGTT
*
43466038 TATAATGGCATGTATAGGGTGATTTGTGATGGTATTATGGTGTATGTGTTAATAG
1 TATATTGGCATGTATAGGGTGATTTGTGATGGTATTATGGTGTATGTGTTAATAG
*
43466093 TATATTGGCATGTATAGGGTGCTTTGTGATGGTATTATGGTGTATGTGTTAATAG
1 TATATTGGCATGTATAGGGTGATTTGTGATGGTATTATGGTGTATGTGTTAATAG
*
43466148 TGTATTGGCATGTAT
1 TATATTGGCATGTAT
43466163 TAGCTTTGGA
Statistics
Matches: 67, Mismatches: 3, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
55 67 1.00
ACGTcount: A:0.23, C:0.03, G:0.30, T:0.43
Consensus pattern (55 bp):
TATATTGGCATGTATAGGGTGATTTGTGATGGTATTATGGTGTATGTGTTAATAG
Found at i:43469240 original size:41 final size:41
Alignment explanation
Indices: 43469172--43469253 Score: 112
Period size: 42 Copynumber: 2.0 Consensus size: 41
43469162 TACAGGGGTT
* * *
43469172 TTCACACGGCCGAGCACATGCTGGTGTCCTTGGCCCGTGTCC
1 TTCACACGGCCGAGCACATGCTCGTGT-CGTCGCCCGTGTCC
*
43469214 TTCACACGGCCTAG-ACATGCTCGTGTCGTCGCCCGTGTCC
1 TTCACACGGCCGAGCACATGCTCGTGTCGTCGCCCGTGTCC
43469254 AAAAACCTGA
Statistics
Matches: 36, Mismatches: 4, Indels: 2
0.86 0.10 0.05
Matches are distributed among these distances:
40 12 0.33
41 11 0.31
42 13 0.36
ACGTcount: A:0.12, C:0.37, G:0.27, T:0.24
Consensus pattern (41 bp):
TTCACACGGCCGAGCACATGCTCGTGTCGTCGCCCGTGTCC
Found at i:43475001 original size:44 final size:44
Alignment explanation
Indices: 43474917--43475001 Score: 102
Period size: 44 Copynumber: 1.9 Consensus size: 44
43474907 TACAGTATCG
* * *
43474917 CATCCATTATGAACTAGGACCAATTCAACGAGTTCGGATGCTCC
1 CATCCATTATGAACTAGAACCAACTCAACGAGTTCAGATGCTCC
*
43474961 CATCCA-TAGTGAACTCGAACCAACTCAACGAGCTT-AGATGC
1 CATCCATTA-TGAACTAGAACCAACTCAACGAG-TTCAGATGC
43475002 CTCATATATA
Statistics
Matches: 35, Mismatches: 4, Indels: 4
0.81 0.09 0.09
Matches are distributed among these distances:
43 2 0.06
44 31 0.89
45 2 0.06
ACGTcount: A:0.32, C:0.28, G:0.18, T:0.22
Consensus pattern (44 bp):
CATCCATTATGAACTAGAACCAACTCAACGAGTTCAGATGCTCC
Found at i:43475279 original size:69 final size:69
Alignment explanation
Indices: 43475168--43475307 Score: 280
Period size: 69 Copynumber: 2.0 Consensus size: 69
43475158 CGTAGTATCA
43475168 ATTACTCATTCATAGCATAATAAGGCATAACTCAAATAGCAAATAAGCTTTTAAGAATTTATATA
1 ATTACTCATTCATAGCATAATAAGGCATAACTCAAATAGCAAATAAGCTTTTAAGAATTTATATA
43475233 ACAT
66 ACAT
43475237 ATTACTCATTCATAGCATAATAAGGCATAACTCAAATAGCAAATAAGCTTTTAAGAATTTATATA
1 ATTACTCATTCATAGCATAATAAGGCATAACTCAAATAGCAAATAAGCTTTTAAGAATTTATATA
43475302 ACAT
66 ACAT
43475306 AT
1 AT
43475308 ATCACATATT
Statistics
Matches: 71, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
69 71 1.00
ACGTcount: A:0.45, C:0.14, G:0.09, T:0.32
Consensus pattern (69 bp):
ATTACTCATTCATAGCATAATAAGGCATAACTCAAATAGCAAATAAGCTTTTAAGAATTTATATA
ACAT
Found at i:43476853 original size:54 final size:54
Alignment explanation
Indices: 43476771--43476877 Score: 205
Period size: 54 Copynumber: 2.0 Consensus size: 54
43476761 CCACTTTATG
43476771 ATACATCACTGGAAATCATGAATTTCTTGCCCATTGTAGGCCAAGACAAATCTT
1 ATACATCACTGGAAATCATGAATTTCTTGCCCATTGTAGGCCAAGACAAATCTT
*
43476825 ATACATCACTGGAAATCATGAATTTCTTGCCCATTGTAGGCCAAGCCAAATCT
1 ATACATCACTGGAAATCATGAATTTCTTGCCCATTGTAGGCCAAGACAAATCT
43476878 AACATTTCGG
Statistics
Matches: 52, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
54 52 1.00
ACGTcount: A:0.33, C:0.23, G:0.15, T:0.29
Consensus pattern (54 bp):
ATACATCACTGGAAATCATGAATTTCTTGCCCATTGTAGGCCAAGACAAATCTT
Found at i:43478185 original size:17 final size:17
Alignment explanation
Indices: 43478163--43478196 Score: 68
Period size: 17 Copynumber: 2.0 Consensus size: 17
43478153 TAACTGTGAC
43478163 ATGGCATAGTTTGAATG
1 ATGGCATAGTTTGAATG
43478180 ATGGCATAGTTTGAATG
1 ATGGCATAGTTTGAATG
43478197 GTCTTTCAAA
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 17 1.00
ACGTcount: A:0.29, C:0.06, G:0.29, T:0.35
Consensus pattern (17 bp):
ATGGCATAGTTTGAATG
Found at i:43480829 original size:44 final size:44
Alignment explanation
Indices: 43480742--43480829 Score: 117
Period size: 44 Copynumber: 2.0 Consensus size: 44
43480732 ATTACATGTA
* *
43480742 TCGCATCCATTATGAACTAGGACCAATTCAACGAGTTCGGATGC
1 TCGCATCCATTATGAACTAGGACCAACTCAACGAGTTCAGATGC
*
43480786 TCGCATCCA-TAGTGAACTCGGACCAACTCAACGAGCTT-AGATGC
1 TCGCATCCATTA-TGAACTAGGACCAACTCAACGAG-TTCAGATGC
43480830 CTCATATATA
Statistics
Matches: 39, Mismatches: 3, Indels: 4
0.85 0.07 0.09
Matches are distributed among these distances:
43 2 0.05
44 35 0.90
45 2 0.05
ACGTcount: A:0.30, C:0.27, G:0.20, T:0.23
Consensus pattern (44 bp):
TCGCATCCATTATGAACTAGGACCAACTCAACGAGTTCAGATGC
Found at i:43493280 original size:43 final size:43
Alignment explanation
Indices: 43493215--43493355 Score: 255
Period size: 43 Copynumber: 3.3 Consensus size: 43
43493205 GCTGGTATTA
* *
43493215 TATTCGGGCCTTCGTGCTTAGCAGGCTTTGTGCCGGTGATGTG
1 TATTCGGGCCTTCGTGCCTAGCAGGCTTCGTGCCGGTGATGTG
*
43493258 TATTCGGGCCTTCGTGCCTAGCAGGCTTCGTGCCAGTGATGTG
1 TATTCGGGCCTTCGTGCCTAGCAGGCTTCGTGCCGGTGATGTG
43493301 TATTCGGGCCTTCGTGCCTAGCAGGCTTCGTGCCGGTGATGTG
1 TATTCGGGCCTTCGTGCCTAGCAGGCTTCGTGCCGGTGATGTG
43493344 TATTCGGGCCTT
1 TATTCGGGCCTT
43493356 TGAGCCTTGC
Statistics
Matches: 94, Mismatches: 4, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
43 94 1.00
ACGTcount: A:0.10, C:0.24, G:0.33, T:0.33
Consensus pattern (43 bp):
TATTCGGGCCTTCGTGCCTAGCAGGCTTCGTGCCGGTGATGTG
Found at i:43496417 original size:13 final size:13
Alignment explanation
Indices: 43496399--43496424 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
43496389 AATATATTTC
43496399 ACCTAAACCAAAA
1 ACCTAAACCAAAA
43496412 ACCTAAACCAAAA
1 ACCTAAACCAAAA
43496425 CTAATAATTA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.62, C:0.31, G:0.00, T:0.08
Consensus pattern (13 bp):
ACCTAAACCAAAA
Found at i:43497613 original size:25 final size:25
Alignment explanation
Indices: 43497585--43497635 Score: 102
Period size: 25 Copynumber: 2.0 Consensus size: 25
43497575 AATCACATTA
43497585 ATTCATTGATAATTCTCATTCGGCT
1 ATTCATTGATAATTCTCATTCGGCT
43497610 ATTCATTGATAATTCTCATTCGGCT
1 ATTCATTGATAATTCTCATTCGGCT
43497635 A
1 A
43497636 ACATACTAAT
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
25 26 1.00
ACGTcount: A:0.25, C:0.20, G:0.12, T:0.43
Consensus pattern (25 bp):
ATTCATTGATAATTCTCATTCGGCT
Found at i:43507367 original size:12 final size:12
Alignment explanation
Indices: 43507350--43507374 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
43507340 ATTTGGCATA
43507350 GCCTAGCACACG
1 GCCTAGCACACG
43507362 GCCTAGCACACG
1 GCCTAGCACACG
43507374 G
1 G
43507375 ACGTGTGGTT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.24, C:0.40, G:0.28, T:0.08
Consensus pattern (12 bp):
GCCTAGCACACG
Found at i:43509079 original size:49 final size:47
Alignment explanation
Indices: 43509017--43509182 Score: 128
Period size: 49 Copynumber: 3.4 Consensus size: 47
43509007 TCGATACTGC
*
43509017 GTCCCAAATAGGTCTTACACTGACTTTTGTATATCGAGGCCTATGCCAT
1 GTCCCAAACAGGTCTTACACTGAC-TTTGTATATCGAGG-CTATGCCAT
* * ** *
43509066 GTCCCAGACAGGTCTTACACTGGCTCTCATCTATC-AGTG-TAAATGCCAT
1 GTCCCAAACAGGTCTTACACTGACT-TTGTATATCGAG-GCT--ATGCCAT
43509115 GTCCCAAACAGGTCTTACACT-AGC-TTGTATATCCCGAGGCTGATG-CAT
1 GTCCCAAACAGGTCTTACACTGA-CTTTGTATAT--CGAGGCT-ATGCCAT
* *
43509163 -TCCCAGACATGTCTTACACT
1 GTCCCAAACAGGTCTTACACT
43509183 AGATCTCGTC
Statistics
Matches: 94, Mismatches: 14, Indels: 20
0.73 0.11 0.16
Matches are distributed among these distances:
47 24 0.26
48 6 0.06
49 61 0.65
50 3 0.03
ACGTcount: A:0.25, C:0.28, G:0.18, T:0.30
Consensus pattern (47 bp):
GTCCCAAACAGGTCTTACACTGACTTTGTATATCGAGGCTATGCCAT
Found at i:43509221 original size:46 final size:45
Alignment explanation
Indices: 43509156--43509284 Score: 149
Period size: 46 Copynumber: 2.8 Consensus size: 45
43509146 TCCCGAGGCT
*
43509156 GATGCAT-TCCCAGACATGTCTTACACTAGATCTCGTC-TCAA-TA-TC
1 GATGCATGTCCCAGACATGTCTTACACTAG--CTC-TCAT-AAGTAGCC
* *
43509201 GATGCATGTCCCAGGCATGTCTTACACTTGCTCTCATAATGTAGCC
1 GATGCATGTCCCAGACATGTCTTACACTAGCTCTCATAA-GTAGCC
*
43509247 GATGCATGTCCCAGACATGTCTTACACTAGCTCACATA
1 GATGCATGTCCCAGACATGTCTTACACTAGCTCTCATA
43509285 CCACCCAATG
Statistics
Matches: 73, Mismatches: 6, Indels: 9
0.83 0.07 0.10
Matches are distributed among these distances:
43 4 0.05
44 4 0.05
45 9 0.12
46 56 0.77
ACGTcount: A:0.26, C:0.29, G:0.16, T:0.29
Consensus pattern (45 bp):
GATGCATGTCCCAGACATGTCTTACACTAGCTCTCATAAGTAGCC
Found at i:43513230 original size:26 final size:26
Alignment explanation
Indices: 43513201--43513253 Score: 72
Period size: 26 Copynumber: 2.0 Consensus size: 26
43513191 TCAAACATGC
43513201 ATTTAGGTCAATTTA-CTCCTAGGGGT
1 ATTTAGGT-AATTTATCTCCTAGGGGT
* *
43513227 ATTTCGGTACTTTATCTCCTAGGGGT
1 ATTTAGGTAATTTATCTCCTAGGGGT
43513253 A
1 A
43513254 AAACTGTAAA
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
25 5 0.21
26 19 0.79
ACGTcount: A:0.21, C:0.17, G:0.23, T:0.40
Consensus pattern (26 bp):
ATTTAGGTAATTTATCTCCTAGGGGT
Found at i:43514544 original size:24 final size:24
Alignment explanation
Indices: 43514507--43514605 Score: 135
Period size: 24 Copynumber: 4.1 Consensus size: 24
43514497 AATTCTTGCT
* *
43514507 CTTTGATCAACTCCTAAATCTTCTC
1 CTTT-ATCAGCTCCTAAATCCTCTC
43514532 CTTTATCAGCTCCTAAATCCTCTC
1 CTTTATCAGCTCCTAAATCCTCTC
* *
43514556 CCTTATCAGCTCCTAAATCCTCCC
1 CTTTATCAGCTCCTAAATCCTCTC
* *
43514580 CCTTATCAGCTCCTAAATCTTCTC
1 CTTTATCAGCTCCTAAATCCTCTC
43514604 CT
1 CT
43514606 GGCATCCTTT
Statistics
Matches: 67, Mismatches: 7, Indels: 1
0.89 0.09 0.01
Matches are distributed among these distances:
24 63 0.94
25 4 0.06
ACGTcount: A:0.21, C:0.38, G:0.04, T:0.36
Consensus pattern (24 bp):
CTTTATCAGCTCCTAAATCCTCTC
Found at i:43521156 original size:24 final size:24
Alignment explanation
Indices: 43521114--43521219 Score: 149
Period size: 24 Copynumber: 4.4 Consensus size: 24
43521104 GCTGGCCAAC
*
43521114 TCCTGCTCCTTGATCAGCTCCTAAA
1 TCCT-CTCCTTTATCAGCTCCTAAA
* *
43521139 TCTTCTCCTTTATTAGCTCCTAAA
1 TCCTCTCCTTTATCAGCTCCTAAA
*
43521163 TCCTCTCCCTTATCAGCTCCTAAA
1 TCCTCTCCTTTATCAGCTCCTAAA
*
43521187 TCCTCTCCCTTATCAGCTCCTAAA
1 TCCTCTCCTTTATCAGCTCCTAAA
*
43521211 TCTTCTCCT
1 TCCTCTCCT
43521220 GACAGCCTTT
Statistics
Matches: 73, Mismatches: 8, Indels: 1
0.89 0.10 0.01
Matches are distributed among these distances:
24 70 0.96
25 3 0.04
ACGTcount: A:0.19, C:0.38, G:0.06, T:0.38
Consensus pattern (24 bp):
TCCTCTCCTTTATCAGCTCCTAAA
Found at i:43524658 original size:47 final size:47
Alignment explanation
Indices: 43524592--43524948 Score: 334
Period size: 47 Copynumber: 8.1 Consensus size: 47
43524582 GAAATGATAG
43524592 TAAGGCCTAATGGCCGATGTGATGAATGTGAAAGTGTATATATGTGA
1 TAAGGCCTAATGGCCGATGTGATGAATGTGAAAGTGTATATATGTGA
*
43524639 TAAGGCCTAATGGCCGATGTGATGAATGTGAAAATGTATATATGTGA
1 TAAGGCCTAATGGCCGATGTGATGAATGTGAAAGTGTATATATGTGA
*
43524686 TAAGGCCTAATGGCCGATGTGATGAATGTGAAATTGTATATATGTGA
1 TAAGGCCTAATGGCCGATGTGATGAATGTGAAAGTGTATATATGTGA
43524733 TAAGGCCTAAT-GCCGATGTGATGAATGTG--A-TG-A-ATATGTGA
1 TAAGGCCTAATGGCCGATGTGATGAATGTGAAAGTGTATATATGTGA
* * * *
43524774 T-A-G--TAAT-G--GATGT-ATG-ATGTG--TGTATATATTAAG-GCC
1 TAAGGCCTAATGGCCGATGTGATGAATGTGAAAGTGTATA-TATGTG-A
* *
43524811 TAATGGCC---G-----ATGTGATGAATGTAAAAGTGTATATATGTGA
1 TAA-GGCCTAATGGCCGATGTGATGAATGTGAAAGTGTATATATGTGA
*
43524851 TAAGGCATAATGGCCGATGTGATGAATGTGAAAGTGTATATATGTGA
1 TAAGGCCTAATGGCCGATGTGATGAATGTGAAAGTGTATATATGTGA
*** * * * * * * *
43524898 CGGGGCCGAGTGGCCAACGTGATGGATGTGAAAGTGCATAAATGTGA
1 TAAGGCCTAATGGCCGATGTGATGAATGTGAAAGTGTATATATGTGA
43524945 TAAG
1 TAAG
43524949 TCCTGAAGGG
Statistics
Matches: 258, Mismatches: 29, Indels: 46
0.77 0.09 0.14
Matches are distributed among these distances:
33 5 0.02
34 4 0.02
35 6 0.02
36 2 0.01
37 13 0.05
38 4 0.02
39 8 0.03
40 8 0.03
41 16 0.06
42 1 0.00
43 2 0.01
44 1 0.00
46 18 0.07
47 170 0.66
ACGTcount: A:0.32, C:0.08, G:0.30, T:0.30
Consensus pattern (47 bp):
TAAGGCCTAATGGCCGATGTGATGAATGTGAAAGTGTATATATGTGA
Found at i:43525120 original size:37 final size:37
Alignment explanation
Indices: 43525064--43525142 Score: 115
Period size: 37 Copynumber: 2.1 Consensus size: 37
43525054 TATCCGAGTA
* *
43525064 AAGACCCGATGACTACGTGTGG-GAATTTTGTCCGGGT
1 AAGACCCGATAACTACGTGTGGAG-ATTATGTCCGGGT
*
43525101 AAGACCCGATAACTTCGTGTGGAGATTATGTCCGGGT
1 AAGACCCGATAACTACGTGTGGAGATTATGTCCGGGT
43525138 AAGAC
1 AAGAC
43525143 TTCGTAATAA
Statistics
Matches: 38, Mismatches: 3, Indels: 2
0.88 0.07 0.05
Matches are distributed among these distances:
37 37 0.97
38 1 0.03
ACGTcount: A:0.25, C:0.19, G:0.30, T:0.25
Consensus pattern (37 bp):
AAGACCCGATAACTACGTGTGGAGATTATGTCCGGGT
Found at i:43527044 original size:43 final size:43
Alignment explanation
Indices: 43526996--43527098 Score: 197
Period size: 43 Copynumber: 2.4 Consensus size: 43
43526986 TTGGTTTTCA
43526996 GCACTAAGTGTGCGGGCAATAAGTGTTCACGGTTGTGAGATTG
1 GCACTAAGTGTGCGGGCAATAAGTGTTCACGGTTGTGAGATTG
43527039 GCACTAAGTGTGCGGGCAATAAGTGTTCACGGTTGTGAGATTG
1 GCACTAAGTGTGCGGGCAATAAGTGTTCACGGTTGTGAGATTG
*
43527082 TCACTAAGTGTGCGGGC
1 GCACTAAGTGTGCGGGC
43527099 TTGAAATGCA
Statistics
Matches: 59, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
43 59 1.00
ACGTcount: A:0.22, C:0.16, G:0.35, T:0.27
Consensus pattern (43 bp):
GCACTAAGTGTGCGGGCAATAAGTGTTCACGGTTGTGAGATTG
Found at i:43527118 original size:29 final size:29
Alignment explanation
Indices: 43527083--43527153 Score: 99
Period size: 29 Copynumber: 2.4 Consensus size: 29
43527073 GTGAGATTGT
* *
43527083 CACTAAGTGTGCGGGCTTGAAA-TGCATGG
1 CACTAAGTGTGCGAG-TTGAAAGTACATGG
*
43527112 CACTAAGTGTGCGAGTTTAAAGTACATGG
1 CACTAAGTGTGCGAGTTGAAAGTACATGG
43527141 CACTAAGTGTGCG
1 CACTAAGTGTGCG
43527154 TGGTTGATTA
Statistics
Matches: 38, Mismatches: 3, Indels: 2
0.88 0.07 0.05
Matches are distributed among these distances:
28 5 0.13
29 33 0.87
ACGTcount: A:0.27, C:0.17, G:0.31, T:0.25
Consensus pattern (29 bp):
CACTAAGTGTGCGAGTTGAAAGTACATGG
Found at i:43527587 original size:40 final size:40
Alignment explanation
Indices: 43527464--43527659 Score: 166
Period size: 40 Copynumber: 4.9 Consensus size: 40
43527454 TCGAATGATG
** *
43527464 TCCGGGCTAAGTCCCGAAG-GC-TTTGTGCTAAGTGACCATA
1 TCCGGGCTAAGTCCCGAAGAGCATTCATGCT-AGTGA-TATA
* ** * * *
43527504 TCCGGACTAAGAT-CCGAAG-GCATTGGTGCGAGTTACTAAA
1 TCCGGGCTAAG-TCCCGAAGAGCATTCATGCTAGTGA-TATA
*
43527544 TCCGGGCTAAGTCCCGAAGAGCATTCATGCTAGTGATGTA
1 TCCGGGCTAAGTCCCGAAGAGCATTCATGCTAGTGATATA
* ** *
43527584 TCCGGGCTATGTTTCGAAGAGCATTCGTGCTAGTGATATA
1 TCCGGGCTAAGTCCCGAAGAGCATTCATGCTAGTGATATA
* * * *
43527624 TCCGTGCTAAATCCCGAAGAGCAATCATGCTGGTGA
1 TCCGGGCTAAGTCCCGAAGAGCATTCATGCTAGTGA
43527660 CGTGTATTCG
Statistics
Matches: 126, Mismatches: 26, Indels: 8
0.79 0.16 0.05
Matches are distributed among these distances:
39 1 0.01
40 106 0.84
41 19 0.15
ACGTcount: A:0.26, C:0.22, G:0.27, T:0.26
Consensus pattern (40 bp):
TCCGGGCTAAGTCCCGAAGAGCATTCATGCTAGTGATATA
Found at i:43527602 original size:80 final size:81
Alignment explanation
Indices: 43527464--43527660 Score: 204
Period size: 80 Copynumber: 2.5 Consensus size: 81
43527454 TCGAATGATG
**
43527464 TCCGGGCTAAGTCCCGAAG-GC-TTTGTGCTAAGTGACCATATCCGGACTAAGATCCGAAG-GCA
1 TCCGGGCTAAGTCCCGAAGAGCATTCATGCT-AGTGACCATATCCGGACTAAGATCCGAAGAGCA
* *
43527526 TTGGTGCGAGTTACTAAA
65 TTCGTGCGAGTGA-TAAA
** * * * *
43527544 TCCGGGCTAAGTCCCGAAGAGCATTCATGCTAGTGA-TGTATCCGGGCTATGTTTCGAAGAGCAT
1 TCCGGGCTAAGTCCCGAAGAGCATTCATGCTAGTGACCATATCCGGACTAAGATCCGAAGAGCAT
* *
43527608 TCGTGCTAGTGATATA
66 TCGTGCGAGTGATAAA
* * * *
43527624 TCCGTGCTAAATCCCGAAGAGCAATCATGCTGGTGAC
1 TCCGGGCTAAGTCCCGAAGAGCATTCATGCTAGTGAC
43527661 GTGTATTCGG
Statistics
Matches: 97, Mismatches: 16, Indels: 7
0.81 0.13 0.06
Matches are distributed among these distances:
80 71 0.73
81 20 0.21
82 6 0.06
ACGTcount: A:0.25, C:0.22, G:0.27, T:0.25
Consensus pattern (81 bp):
TCCGGGCTAAGTCCCGAAGAGCATTCATGCTAGTGACCATATCCGGACTAAGATCCGAAGAGCAT
TCGTGCGAGTGATAAA
Found at i:43531127 original size:47 final size:47
Alignment explanation
Indices: 43531061--43531440 Score: 625
Period size: 47 Copynumber: 8.1 Consensus size: 47
43531051 GAAATGATAG
43531061 TAAGGCCTAATGGCCGATGTGATGAATGTGAAAGTGTATATATGTGA
1 TAAGGCCTAATGGCCGATGTGATGAATGTGAAAGTGTATATATGTGA
43531108 TAAGGCCTAATGGCCGATGTGATGAATGTGAAAGTGTATATATGTGA
1 TAAGGCCTAATGGCCGATGTGATGAATGTGAAAGTGTATATATGTGA
*
43531155 TAAGGCCTAATGGCTGATGTGATGAATGTGAAAGTGTATATATGTGA
1 TAAGGCCTAATGGCCGATGTGATGAATGTGAAAGTGTATATATGTGA
* *
43531202 TAAGACCTAATAGCCGATGTGATGAATGTGAAAGTGTATATATGTGA
1 TAAGGCCTAATGGCCGATGTGATGAATGTGAAAGTGTATATATGTGA
*
43531249 TAAGGCCTAATGGCCGATGTGATGAATGTGAAAGTGTATATATGTAA
1 TAAGGCCTAATGGCCGATGTGATGAATGTGAAAGTGTATATATGTGA
43531296 TAAGGCCTAATGGCCGATGTGATGAATGTGAAAGTGTATATATGTGA
1 TAAGGCCTAATGGCCGATGTGATGAATGTGAAAGTGTATATATGTGA
*
43531343 TAAGGCCTAATGGCCGATGTGATGAGTGTGAAAGTGTATATATGTGA
1 TAAGGCCTAATGGCCGATGTGATGAATGTGAAAGTGTATATATGTGA
*** * * * * * * *
43531390 CGGGGCCGAGTGGCCAACGTGATGGATGTGAAAGTGCATAAATGTGA
1 TAAGGCCTAATGGCCGATGTGATGAATGTGAAAGTGTATATATGTGA
43531437 TAAG
1 TAAG
43531441 TCCCGAAGGG
Statistics
Matches: 310, Mismatches: 23, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
47 310 1.00
ACGTcount: A:0.32, C:0.09, G:0.30, T:0.29
Consensus pattern (47 bp):
TAAGGCCTAATGGCCGATGTGATGAATGTGAAAGTGTATATATGTGA
Found at i:43531615 original size:37 final size:37
Alignment explanation
Indices: 43531559--43531637 Score: 115
Period size: 37 Copynumber: 2.1 Consensus size: 37
43531549 CCGAGCTCTA
* *
43531559 AAGACCCGATGACTACGTGTGG-GAATTTTGTCCGGGT
1 AAGACCCGATAACTACGTGTGGAG-ATTATGTCCGGGT
*
43531596 AAGACCCGATAACTTCGTGTGGAGATTATGTCCGGGT
1 AAGACCCGATAACTACGTGTGGAGATTATGTCCGGGT
43531633 AAGAC
1 AAGAC
43531638 TTCGTAATAA
Statistics
Matches: 38, Mismatches: 3, Indels: 2
0.88 0.07 0.05
Matches are distributed among these distances:
37 37 0.97
38 1 0.03
ACGTcount: A:0.25, C:0.19, G:0.30, T:0.25
Consensus pattern (37 bp):
AAGACCCGATAACTACGTGTGGAGATTATGTCCGGGT
Found at i:43548263 original size:39 final size:40
Alignment explanation
Indices: 43548146--43548330 Score: 216
Period size: 40 Copynumber: 4.7 Consensus size: 40
43548136 GCTACTCGTT
*
43548146 CAAATGCCTTCGGGACATAGCCCGG-TTATAGTAACTCGCA
1 CAAATGCCTTCGGGACTTAGCCCGGATT-TAGTAACTCGCA
*
43548186 CAAATGCCTTCGGGACTTAACCCGGATTTAGTAACTCGCA
1 CAAATGCCTTCGGGACTTAGCCCGGATTTAGTAACTCGCA
* * *
43548226 CCAATGCCTTCGGG-CTTAGCCCGGAATTAGTATCTCGCA
1 CAAATGCCTTCGGGACTTAGCCCGGATTTAGTAACTCGCA
** * * * *
43548265 CAAATGCCTTC-GGATCTTAGTTCGGATATGGTCACTTAGCA
1 CAAATGCCTTCGGGA-CTTAGCCCGGATTTAGTAAC-TCGCA
43548306 CAAA-GCCTTCGGGACTTAGCCCGGA
1 CAAATGCCTTCGGGACTTAGCCCGGA
43548331 CATCATTCGA
Statistics
Matches: 123, Mismatches: 17, Indels: 10
0.82 0.11 0.07
Matches are distributed among these distances:
38 2 0.02
39 32 0.26
40 76 0.62
41 13 0.11
ACGTcount: A:0.25, C:0.28, G:0.23, T:0.25
Consensus pattern (40 bp):
CAAATGCCTTCGGGACTTAGCCCGGATTTAGTAACTCGCA
Found at i:43548291 original size:79 final size:81
Alignment explanation
Indices: 43548148--43548330 Score: 214
Period size: 79 Copynumber: 2.3 Consensus size: 81
43548138 TACTCGTTCA
* *
43548148 AATGCCTTCGGGACATAGCCCGG-TTATAGTAACTCGCACAAATGCCTTCGGGACTTAACCCGGA
1 AATGCCTTCGGGACTTAGCCCGGAATATAGTAACTCGCACAAATGCCTTCGGGACTTAACCCGGA
* *
43548212 TTTAGTAAC-TCGCACC
66 TATAGTAACTTAGCA-C
* ***
43548228 AATGCCTTCGGG-CTTAGCCCGGAAT-TAGTATCTCGCACAAATGCCTTC-GGATCTTAGTTCGG
1 AATGCCTTCGGGACTTAGCCCGGAATATAGTAACTCGCACAAATGCCTTCGGGA-CTTAACCCGG
* *
43548290 ATATGGTCACTTAGCAC
65 ATATAGTAACTTAGCAC
*
43548307 AAAGCCTTCGGGACTTAGCCCGGA
1 AATGCCTTCGGGACTTAGCCCGGA
43548331 CATCATTCGA
Statistics
Matches: 88, Mismatches: 11, Indels: 8
0.82 0.10 0.07
Matches are distributed among these distances:
78 3 0.03
79 57 0.65
80 28 0.32
ACGTcount: A:0.25, C:0.27, G:0.23, T:0.25
Consensus pattern (81 bp):
AATGCCTTCGGGACTTAGCCCGGAATATAGTAACTCGCACAAATGCCTTCGGGACTTAACCCGGA
TATAGTAACTTAGCAC
Found at i:43564452 original size:17 final size:17
Alignment explanation
Indices: 43564430--43564472 Score: 50
Period size: 17 Copynumber: 2.5 Consensus size: 17
43564420 AAATATAACT
*
43564430 AAATTAAATAAAAAATA
1 AAATTAAATAAAAAACA
* *
43564447 AAATTAATTTAAAAACA
1 AAATTAAATAAAAAACA
*
43564464 AAATCAAAT
1 AAATTAAAT
43564473 TACACCAAAT
Statistics
Matches: 21, Mismatches: 5, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
17 21 1.00
ACGTcount: A:0.70, C:0.05, G:0.00, T:0.26
Consensus pattern (17 bp):
AAATTAAATAAAAAACA
Found at i:43564458 original size:22 final size:22
Alignment explanation
Indices: 43564433--43564474 Score: 59
Period size: 22 Copynumber: 1.9 Consensus size: 22
43564423 TATAACTAAA
43564433 TTAAATAA-AAAATAAAATTAAT
1 TTAAA-AACAAAATAAAATTAAT
*
43564455 TTAAAAACAAAATCAAATTA
1 TTAAAAACAAAATAAAATTA
43564475 CACCAAATTA
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
21 2 0.11
22 16 0.89
ACGTcount: A:0.67, C:0.05, G:0.00, T:0.29
Consensus pattern (22 bp):
TTAAAAACAAAATAAAATTAAT
Found at i:43569889 original size:49 final size:49
Alignment explanation
Indices: 43569716--43569889 Score: 210
Period size: 49 Copynumber: 3.5 Consensus size: 49
43569706 ATGAACAAAT
* * *
43569716 GAGTTAC-TAATGCATGAC-TTCATTTAAAGATGCAAATTTTAACTAACATGG
1 GAGTTACATAATGCATGACATT-ATTT-ATGATGC--ATCTTAACTAACATGA
* *
43569767 GAGTTACATAATACATGACATAATTTATGATGCATCTTAACTAACATGA
1 GAGTTACATAATGCATGACATTATTTATGATGCATCTTAACTAACATGA
*
43569816 GAGTTACATAATGCATGTCATTATTTATGATGCATAC-TAACTAACATGA
1 GAGTTACATAATGCATGACATTATTTATGATGCAT-CTTAACTAACATGA
* *
43569865 AAGTTACATAATGCATGACGTTATT
1 GAGTTACATAATGCATGACATTATT
43569890 AAATGCAAAA
Statistics
Matches: 109, Mismatches: 11, Indels: 8
0.85 0.09 0.06
Matches are distributed among these distances:
49 80 0.73
50 1 0.01
51 13 0.12
52 14 0.13
53 1 0.01
ACGTcount: A:0.38, C:0.14, G:0.14, T:0.34
Consensus pattern (49 bp):
GAGTTACATAATGCATGACATTATTTATGATGCATCTTAACTAACATGA
Found at i:43573555 original size:39 final size:39
Alignment explanation
Indices: 43573512--43573589 Score: 147
Period size: 39 Copynumber: 2.0 Consensus size: 39
43573502 TTTTGGAGTA
*
43573512 AACTGTAGGCCCAGATAACTGATCAAACAAATCTTCAAT
1 AACTGTAGGCCCAGATAACTAATCAAACAAATCTTCAAT
43573551 AACTGTAGGCCCAGATAACTAATCAAACAAATCTTCAAT
1 AACTGTAGGCCCAGATAACTAATCAAACAAATCTTCAAT
43573590 CATGGGCAGA
Statistics
Matches: 38, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
39 38 1.00
ACGTcount: A:0.42, C:0.23, G:0.12, T:0.23
Consensus pattern (39 bp):
AACTGTAGGCCCAGATAACTAATCAAACAAATCTTCAAT
Found at i:43576209 original size:30 final size:30
Alignment explanation
Indices: 43576175--43576235 Score: 77
Period size: 30 Copynumber: 2.0 Consensus size: 30
43576165 TTCCCGAGCC
*
43576175 TAGGGGAAAAAGTGTAAATATGTAAAAGTT
1 TAGGGGAAAAAGTGTAAATATGCAAAAGTT
* * * *
43576205 TAGGGGCAAAATTGTAATTTTGCAAAAGTT
1 TAGGGGAAAAAGTGTAAATATGCAAAAGTT
43576235 T
1 T
43576236 GAGTTAAGGA
Statistics
Matches: 26, Mismatches: 5, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
30 26 1.00
ACGTcount: A:0.41, C:0.03, G:0.25, T:0.31
Consensus pattern (30 bp):
TAGGGGAAAAAGTGTAAATATGCAAAAGTT
Found at i:43576818 original size:68 final size:68
Alignment explanation
Indices: 43576746--43576897 Score: 177
Period size: 67 Copynumber: 2.2 Consensus size: 68
43576736 CATCATGTGT
** *
43576746 ACAAGAGAGCTACGAGACATTATGATGTAGCTAGGTCGCATGGGTGATACTA-TG-TGCACACCA
1 ACAAGAGAGCTACGAGACA-TAT-ATGTAGCTAGGTCGCATGCATGATACTAGTGAAGCACACCA
43576809 TGTAG
64 TGTAG
* * * * *
43576814 ACAAGAGAGCTACG-G-GATATATGTAGCTAGGTCGCATGCATGGTTCTAGGTGAAGGACACCGT
1 ACAAGAGAGCTACGAGACATATATGTAGCTAGGTCGCATGCATGATACTA-GTGAAGCACACCAT
43576877 GTAG
65 GTAG
43576881 ACAAGAGAGCTACGAGA
1 ACAAGAGAGCTACGAGA
43576898 TAAACTGGAT
Statistics
Matches: 71, Mismatches: 8, Indels: 9
0.81 0.09 0.10
Matches are distributed among these distances:
64 24 0.34
65 3 0.04
66 3 0.04
67 26 0.37
68 15 0.21
ACGTcount: A:0.32, C:0.17, G:0.30, T:0.21
Consensus pattern (68 bp):
ACAAGAGAGCTACGAGACATATATGTAGCTAGGTCGCATGCATGATACTAGTGAAGCACACCATG
TAG
Found at i:43580011 original size:30 final size:30
Alignment explanation
Indices: 43579977--43580037 Score: 86
Period size: 30 Copynumber: 2.0 Consensus size: 30
43579967 TTCCCGAGCC
43579977 TAGGGGCAAAAGTGTAAATATGCAAAAGTT
1 TAGGGGCAAAAGTGTAAATATGCAAAAGTT
* * * *
43580007 TAGGGGCAAAATTGTAATTTTTCAAAAGTT
1 TAGGGGCAAAAGTGTAAATATGCAAAAGTT
43580037 T
1 T
43580038 GAGTTAAGGA
Statistics
Matches: 27, Mismatches: 4, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
30 27 1.00
ACGTcount: A:0.39, C:0.07, G:0.23, T:0.31
Consensus pattern (30 bp):
TAGGGGCAAAAGTGTAAATATGCAAAAGTT
Found at i:43584785 original size:12 final size:12
Alignment explanation
Indices: 43584768--43584792 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
43584758 CAAAAATGTA
43584768 AAAATCATCAAG
1 AAAATCATCAAG
43584780 AAAATCATCAAG
1 AAAATCATCAAG
43584792 A
1 A
43584793 TCACTTACAT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.60, C:0.16, G:0.08, T:0.16
Consensus pattern (12 bp):
AAAATCATCAAG
Found at i:43589955 original size:31 final size:32
Alignment explanation
Indices: 43589912--43589975 Score: 121
Period size: 31 Copynumber: 2.0 Consensus size: 32
43589902 TATATGAAAA
43589912 AAAAACAATTTATAATCATCAGGAATCGTCAG
1 AAAAACAATTTATAATCATCAGGAATCGTCAG
43589944 AAAAA-AATTTATAATCATCAGGAATCGTCAG
1 AAAAACAATTTATAATCATCAGGAATCGTCAG
43589975 A
1 A
43589976 CTATCACTAT
Statistics
Matches: 32, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
31 27 0.84
32 5 0.16
ACGTcount: A:0.48, C:0.14, G:0.12, T:0.25
Consensus pattern (32 bp):
AAAAACAATTTATAATCATCAGGAATCGTCAG
Found at i:43591484 original size:47 final size:47
Alignment explanation
Indices: 43591416--43591588 Score: 181
Period size: 47 Copynumber: 3.7 Consensus size: 47
43591406 CGCTCAGTCA
* *
43591416 ATGCATGTCCCAGACACGTCTTACACTGGCTA-TCATCATCGAGGCCG
1 ATGCATGTCCCAAACAAGTCTTACACTGGC-ACTCATCATCGAGGCCG
* ***
43591463 ATGCATGTCCCAAACAAGTCTTACACTGGCACTCATC-TCTACATCG
1 ATGCATGTCCCAAACAAGTCTTACACTGGCACTCATCATCGAGGCCG
* * * * *
43591509 ATGCCATGTCCCAGACATGGTCTTACACTGGCACTCATAAT-GTGGCCA
1 ATG-CATGTCCCAAACA-AGTCTTACACTGGCACTCATCATCGAGGCCG
* *
43591557 ATGCATGTTCCAAACATGTCTTACACTGGCAC
1 ATGCATGTCCCAAACAAGTCTTACACTGGCAC
43591589 ATAAGTAATC
Statistics
Matches: 104, Mismatches: 18, Indels: 9
0.79 0.14 0.07
Matches are distributed among these distances:
46 24 0.23
47 56 0.54
48 23 0.22
49 1 0.01
ACGTcount: A:0.26, C:0.31, G:0.18, T:0.25
Consensus pattern (47 bp):
ATGCATGTCCCAAACAAGTCTTACACTGGCACTCATCATCGAGGCCG
Found at i:43591541 original size:48 final size:47
Alignment explanation
Indices: 43591320--43591546 Score: 180
Period size: 47 Copynumber: 4.8 Consensus size: 47
43591310 GATAAGTTGC
* * * * * *
43591320 CGATGCCATGTCCCAGACATGGTCTTACACTAGCTCTCGTATATACGT
1 CGATG-CATGTCCCAGACATGGTCTTACACTGGCACTCATCTCTACAT
* * * *
43591368 GCTGATGCATGTCCCAGACAT-GTCTTACACT--AACACAACGCT-CAGT
1 -C-GATGCATGTCCCAGACATGGTCTTACACTGGCACTCATCTCTACA-T
* * * ***
43591414 CAATGCATGTCCCAGACA-CGTCTTACACTGGCTA-TCATCATCGAGGC
1 CGATGCATGTCCCAGACATGGTCTTACACTGGC-ACTCATC-TCTACAT
* *
43591461 CGATGCATGTCCCAAACA-AGTCTTACACTGGCACTCATCTCTACAT
1 CGATGCATGTCCCAGACATGGTCTTACACTGGCACTCATCTCTACAT
43591507 CGATGCCATGTCCCAGACATGGTCTTACACTGGCACTCAT
1 CGATG-CATGTCCCAGACATGGTCTTACACTGGCACTCAT
43591547 AATGTGGCCA
Statistics
Matches: 140, Mismatches: 27, Indels: 23
0.74 0.14 0.12
Matches are distributed among these distances:
44 26 0.19
45 2 0.01
46 16 0.11
47 48 0.34
48 29 0.21
49 15 0.11
50 4 0.03
ACGTcount: A:0.26, C:0.31, G:0.18, T:0.26
Consensus pattern (47 bp):
CGATGCATGTCCCAGACATGGTCTTACACTGGCACTCATCTCTACAT
Found at i:43591570 original size:94 final size:94
Alignment explanation
Indices: 43591320--43591589 Score: 293
Period size: 94 Copynumber: 2.9 Consensus size: 94
43591310 GATAAGTTGC
* * * *
43591320 CGATGCCATGTCCCAGACATGGTCTTACACTAGCTCTCGTATATACGT-GCTGATGCATGTCCCA
1 CGATGCCATGTCCCAGACATGGTCTTACACTGGCACTC--ATA-ATGTGGCCGATGCATGTCCCA
* *
43591384 GACATGTCTTACACT--AACACAACGCTCAGT
63 AACATGTCTTACACTGGCACACAACGCTCAGT
* * * *
43591414 CAATG-CATGTCCCAGACA-CGTCTTACACTGGCTA-TCATCATCGAGGCCGATGCATGTCCCAA
1 CGATGCCATGTCCCAGACATGGTCTTACACTGGC-ACTCATAAT-GTGGCCGATGCATGTCCCAA
* * * *
43591476 ACAAGTCTTACACTGGCACTCATCTCTACA-T
64 ACATGTCTTACACTGGCACACAACGCT-CAGT
* *
43591507 CGATGCCATGTCCCAGACATGGTCTTACACTGGCACTCATAATGTGGCCAATGCATGTTCCAAAC
1 CGATGCCATGTCCCAGACATGGTCTTACACTGGCACTCATAATGTGGCCGATGCATGTCCCAAAC
43591572 ATGTCTTACACTGGCACA
66 ATGTCTTACACTGGCACA
43591590 TAAGTAATCC
Statistics
Matches: 145, Mismatches: 22, Indels: 18
0.78 0.12 0.10
Matches are distributed among these distances:
89 1 0.01
90 3 0.02
91 28 0.19
92 14 0.10
93 25 0.17
94 55 0.38
95 19 0.13
ACGTcount: A:0.26, C:0.30, G:0.18, T:0.26
Consensus pattern (94 bp):
CGATGCCATGTCCCAGACATGGTCTTACACTGGCACTCATAATGTGGCCGATGCATGTCCCAAAC
ATGTCTTACACTGGCACACAACGCTCAGT
Found at i:43597076 original size:27 final size:26
Alignment explanation
Indices: 43597032--43597083 Score: 68
Period size: 27 Copynumber: 2.0 Consensus size: 26
43597022 CTTACTGCAA
*
43597032 TCTGGTGGCCTCGCCACATATATCTGT
1 TCTGGTGACCTCGCCACA-ATATCTGT
* *
43597059 TCTGGTGACTTCGTCACAATATCTG
1 TCTGGTGACCTCGCCACAATATCTG
43597084 GCAGCCTTGC
Statistics
Matches: 22, Mismatches: 3, Indels: 1
0.85 0.12 0.04
Matches are distributed among these distances:
26 7 0.32
27 15 0.68
ACGTcount: A:0.17, C:0.27, G:0.21, T:0.35
Consensus pattern (26 bp):
TCTGGTGACCTCGCCACAATATCTGT
Found at i:43602489 original size:31 final size:31
Alignment explanation
Indices: 43602451--43602513 Score: 126
Period size: 31 Copynumber: 2.0 Consensus size: 31
43602441 GCTTGTCCTC
43602451 AAGCAAAATCCTCAAGTTATAATCAAAATAA
1 AAGCAAAATCCTCAAGTTATAATCAAAATAA
43602482 AAGCAAAATCCTCAAGTTATAATCAAAATAA
1 AAGCAAAATCCTCAAGTTATAATCAAAATAA
43602513 A
1 A
43602514 TCCTTCTCAA
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
31 32 1.00
ACGTcount: A:0.56, C:0.16, G:0.06, T:0.22
Consensus pattern (31 bp):
AAGCAAAATCCTCAAGTTATAATCAAAATAA
Found at i:43609329 original size:12 final size:13
Alignment explanation
Indices: 43609305--43609334 Score: 53
Period size: 12 Copynumber: 2.4 Consensus size: 13
43609295 GAAAAAGAAG
43609305 AATTAGTAATAAA
1 AATTAGTAATAAA
43609318 AATTAG-AATAAA
1 AATTAGTAATAAA
43609330 AATTA
1 AATTA
43609335 AATTGCAGTA
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
12 11 0.65
13 6 0.35
ACGTcount: A:0.63, C:0.00, G:0.07, T:0.30
Consensus pattern (13 bp):
AATTAGTAATAAA
Found at i:43612840 original size:28 final size:28
Alignment explanation
Indices: 43612809--43612863 Score: 74
Period size: 28 Copynumber: 2.0 Consensus size: 28
43612799 CAGTATTGTC
* * *
43612809 TGGGCCTTAGCCCTATATAGTAACAGTG
1 TGGGCCTAAGCCCAATACAGTAACAGTG
*
43612837 TGGGCCTAAGCCCAATACAGTATCAGT
1 TGGGCCTAAGCCCAATACAGTAACAGT
43612864 ACAGTGTAAT
Statistics
Matches: 23, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
28 23 1.00
ACGTcount: A:0.27, C:0.24, G:0.24, T:0.25
Consensus pattern (28 bp):
TGGGCCTAAGCCCAATACAGTAACAGTG
Found at i:43618073 original size:55 final size:55
Alignment explanation
Indices: 43617960--43618094 Score: 144
Period size: 55 Copynumber: 2.5 Consensus size: 55
43617950 CACCACGACA
* * * * * ** *
43617960 AACCTACCCAAACAACACGGGCGTGCGAGACGCCCGTGCCTTGAAATGGTGGCCG
1 AACCTGCCAAAACAACACGGGCATGCGACACACCCGTGCCAAGAAATCGTGGCCG
* ** * **
43618015 AACCTGTCAAATTAACACGGGCATGCGACACACCCGTGCCAAGCAATCGTGGGTG
1 AACCTGCCAAAACAACACGGGCATGCGACACACCCGTGCCAAGAAATCGTGGCCG
43618070 AACCTGCCAAAACAACACGGGCATG
1 AACCTGCCAAAACAACACGGGCATG
43618095 GGCCTACATA
Statistics
Matches: 63, Mismatches: 17, Indels: 0
0.79 0.21 0.00
Matches are distributed among these distances:
55 63 1.00
ACGTcount: A:0.30, C:0.31, G:0.26, T:0.13
Consensus pattern (55 bp):
AACCTGCCAAAACAACACGGGCATGCGACACACCCGTGCCAAGAAATCGTGGCCG
Found at i:43630522 original size:20 final size:21
Alignment explanation
Indices: 43630497--43630537 Score: 66
Period size: 20 Copynumber: 2.0 Consensus size: 21
43630487 ACACCTATTA
*
43630497 TTTATTTTTA-CTTTTTTTAT
1 TTTATTTTTATCTTTATTTAT
43630517 TTTATTTTTATCTTTATTTAT
1 TTTATTTTTATCTTTATTTAT
43630538 CTTTTGAAAT
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
20 10 0.53
21 9 0.47
ACGTcount: A:0.17, C:0.05, G:0.00, T:0.78
Consensus pattern (21 bp):
TTTATTTTTATCTTTATTTAT
Found at i:43630532 original size:12 final size:12
Alignment explanation
Indices: 43630497--43630535 Score: 50
Period size: 11 Copynumber: 3.6 Consensus size: 12
43630487 ACACCTATTA
43630497 TTTATTTTTA-C
1 TTTATTTTTATC
43630508 -TT-TTTTTAT-
1 TTTATTTTTATC
43630517 TTTATTTTTATC
1 TTTATTTTTATC
43630529 TTTATTT
1 TTTATTT
43630536 ATCTTTTGAA
Statistics
Matches: 24, Mismatches: 0, Indels: 7
0.77 0.00 0.23
Matches are distributed among these distances:
9 6 0.25
10 4 0.17
11 7 0.29
12 7 0.29
ACGTcount: A:0.15, C:0.05, G:0.00, T:0.79
Consensus pattern (12 bp):
TTTATTTTTATC
Found at i:43633981 original size:50 final size:49
Alignment explanation
Indices: 43633805--43634041 Score: 215
Period size: 50 Copynumber: 4.8 Consensus size: 49
43633795 ATTATGAATA
* * * * ** * *
43633805 CACGTGAGTAGTACTAAGTGCAGGCTACTATGTGTACCATACTATTAAGA
1 CACGTGTGTAGTACTAAGTGCAGGCTACTACGTGTATCAGA-TGGTAGGT
* * * * * * *
43633855 CGCATGTGTAGTACTAAGTGCAGGCTACTATGCGTACTCA-ATGACTTCGAT
1 CACGTGTGTAGTACTAAGTGCAGGCTACTACGTGTA-TCAGATG--GTAGGT
43633906 CACGTGTGTAGTACTAAGTGCAGGCTACTACGTGTATCAGATGGTGAGGT
1 CACGTGTGTAGTACTAAGTGCAGGCTACTACGTGTATCAGATGGT-AGGT
** * * *
43633956 CACGTGTGTAGTACTAAGTAAAGGCTACTACGTGTATCGGATTGTTGGT
1 CACGTGTGTAGTACTAAGTGCAGGCTACTACGTGTATCAGATGGTAGGT
* * *
43634005 CACATGTGTAGTACTAAGTGCAGGCTATTATGTGTAT
1 CACGTGTGTAGTACTAAGTGCAGGCTACTACGTGTAT
43634042 AAGACAGCTT
Statistics
Matches: 155, Mismatches: 27, Indels: 11
0.80 0.14 0.06
Matches are distributed among these distances:
49 37 0.24
50 79 0.51
51 39 0.25
ACGTcount: A:0.27, C:0.17, G:0.26, T:0.30
Consensus pattern (49 bp):
CACGTGTGTAGTACTAAGTGCAGGCTACTACGTGTATCAGATGGTAGGT
Found at i:43633981 original size:101 final size:98
Alignment explanation
Indices: 43633805--43634046 Score: 245
Period size: 101 Copynumber: 2.4 Consensus size: 98
43633795 ATTATGAATA
* * * * *
43633805 CACGTGAGTAGTACTAAGTGCAGGCTACTATGTGTACCATACTATTAAGACGCATGTGTAGTACT
1 CACGTGTGTAGTACTAAGTGCAGGCTACTATGTGTATCAGACTATGAAGACACATGTGTAGTACT
** *
43633870 AAGTGCAGGCTACTATGCGTACTC-AATGACTTCGAT
66 AAGTAAAGGCTACTACGCGTA-TCGAATG--TT-GAT
* * * * *
43633906 CACGTGTGTAGTACTAAGTGCAGGCTACTACGTGTATCAGA-TGGTGAGGTCACGTGTGTAGTAC
1 CACGTGTGTAGTACTAAGTGCAGGCTACTATGTGTATCAGACT-ATGAAGACACATGTGTAGTAC
* * *
43633970 TAAGTAAAGGCTACTACGTGTATCGGATTGTTGGT
65 TAAGTAAAGGCTACTACGCGTATC-GAATGTTGAT
* * *
43634005 CACATGTGTAGTACTAAGTGCAGGCTATTATGTGTATAAGAC
1 CACGTGTGTAGTACTAAGTGCAGGCTACTATGTGTATCAGAC
43634047 AGCTTCGACT
Statistics
Matches: 117, Mismatches: 20, Indels: 9
0.80 0.14 0.06
Matches are distributed among these distances:
99 39 0.33
100 5 0.04
101 70 0.60
102 3 0.03
ACGTcount: A:0.27, C:0.17, G:0.26, T:0.30
Consensus pattern (98 bp):
CACGTGTGTAGTACTAAGTGCAGGCTACTATGTGTATCAGACTATGAAGACACATGTGTAGTACT
AAGTAAAGGCTACTACGCGTATCGAATGTTGAT
Found at i:43634164 original size:27 final size:26
Alignment explanation
Indices: 43634134--43634185 Score: 70
Period size: 26 Copynumber: 2.0 Consensus size: 26
43634124 GGGAAAATCG
43634134 ATAAAGTGGTAATATGTG-AAATTTATT
1 ATAAAGTGG--ATATGTGCAAATTTATT
*
43634161 ATAAGGTGGATATGTGCAAATTTAT
1 ATAAAGTGGATATGTGCAAATTTAT
43634186 GTTTATGAAA
Statistics
Matches: 23, Mismatches: 1, Indels: 3
0.85 0.04 0.11
Matches are distributed among these distances:
25 7 0.30
26 8 0.35
27 8 0.35
ACGTcount: A:0.38, C:0.02, G:0.21, T:0.38
Consensus pattern (26 bp):
ATAAAGTGGATATGTGCAAATTTATT
Done.