Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Chr08 129432109
Parameters: 2 7 7 80 10 50 1000
Pmatch=0.80,Pindel=0.10
tuple sizes 0,4,5,7
tuple distances 0, 29, 159, 1000
Length: 129432109
ACGTcount: A:0.32, C:0.18, G:0.18, T:0.32
Warning! 350 characters in sequence are not A, C, G, or T
File 178 of 425
Found at i:53875079 original size:40 final size:40
Alignment explanation
Indices: 53874952--53875081 Score: 138
Period size: 40 Copynumber: 3.2 Consensus size: 40
53874942 ATGCTGGAAA
* * * *
53874952 TTATATCCGGGTTAAGACCCGAAGGCAATTGTGCTAGTGG
1 TTATATCCGGGCTAAGACCCGAAGGCATTTGTGCGAATGG
* * * **
53874992 CTACATCCGGGCTAAGACCCGAAGGCATTCGTGCGAGA-CA
1 TTATATCCGGGCTAAGACCCGAAGGCATTTGTGCGA-ATGG
*
53875032 TTCTATCCGGGCTAAGACCCGAAGGCATTTGTGC-ACATGG
1 TTATATCCGGGCTAAGACCCGAAGGCATTTGTGCGA-ATGG
53875072 TTATATCCGG
1 TTATATCCGG
53875082 TTATGTTCCG
Statistics
Matches: 71, Mismatches: 17, Indels: 4
0.77 0.18 0.04
Matches are distributed among these distances:
39 2 0.03
40 69 0.97
ACGTcount: A:0.25, C:0.24, G:0.28, T:0.24
Consensus pattern (40 bp):
TTATATCCGGGCTAAGACCCGAAGGCATTTGTGCGAATGG
Found at i:53884660 original size:40 final size:38
Alignment explanation
Indices: 53884611--53884718 Score: 128
Period size: 40 Copynumber: 2.7 Consensus size: 38
53884601 ATCACGATTT
*
53884611 GCACAAATGCCTTCGGGTCTTAGCCCGGATAGAATG-ACTC
1 GCAC-AATGCCTTCGGGTCTTAGCCCGGAT-GAA-GCACTA
*
53884651 GCACGAATGCCTTCGGGTCTTAGCCCGGATGTAGCCACTA
1 GCAC-AATGCCTTCGGGTCTTAGCCCGGATGAAG-CACTA
*
53884691 GCACAATTGCCTTCGGGTCTTAACCCGG
1 GCACAA-TGCCTTCGGGTCTTAGCCCGG
53884719 TTATAATTTC
Statistics
Matches: 61, Mismatches: 4, Indels: 6
0.86 0.06 0.08
Matches are distributed among these distances:
38 1 0.02
39 4 0.07
40 56 0.92
ACGTcount: A:0.21, C:0.30, G:0.26, T:0.23
Consensus pattern (38 bp):
GCACAATGCCTTCGGGTCTTAGCCCGGATGAAGCACTA
Found at i:53884678 original size:80 final size:80
Alignment explanation
Indices: 53884570--53884718 Score: 183
Period size: 80 Copynumber: 1.9 Consensus size: 80
53884560 TATGGTAACC
* * * *
53884570 CGCACCAAGGCCTACGGGACTTAACCCGGATATCA-CGATTTGCACAAATGCCTTCGGGTCTTAG
1 CGCACCAAGGCCTACGGGACTTAACCCGGATAT-AGCCACTAGCACAAATGCCTTCGGGTCTTAA
53884634 CCCGGATAGAATGACT
65 CCCGGATAGAATGACT
* * * * * * *
53884650 CGCACGAATGCCTTCGGGTCTTAGCCCGGATGTAGCCACTAGCACAATTGCCTTCGGGTCTTAAC
1 CGCACCAAGGCCTACGGGACTTAACCCGGATATAGCCACTAGCACAAATGCCTTCGGGTCTTAAC
53884715 CCGG
66 CCGG
53884719 TTATAATTTC
Statistics
Matches: 57, Mismatches: 11, Indels: 2
0.81 0.16 0.03
Matches are distributed among these distances:
79 1 0.02
80 56 0.98
ACGTcount: A:0.23, C:0.30, G:0.25, T:0.22
Consensus pattern (80 bp):
CGCACCAAGGCCTACGGGACTTAACCCGGATATAGCCACTAGCACAAATGCCTTCGGGTCTTAAC
CCGGATAGAATGACT
Found at i:53892796 original size:46 final size:46
Alignment explanation
Indices: 53892746--53892921 Score: 216
Period size: 46 Copynumber: 3.8 Consensus size: 46
53892736 TGGTTGAGCA
53892746 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAATG
1 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAATG
* * *
53892792 TCCGAACTCGTTGAGTTGAGTCCGAGTTC-GTGA--GATG-TAACTAGG
1 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAA-T--G
*
53892837 CATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAACG
1 --TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAATG
* * *
53892885 CCCGAGCTCGTTGAGTTGAGTCCGAGTTCGCTTATGG
1 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGG
53892922 GCGGGTTACA
Statistics
Matches: 111, Mismatches: 10, Indels: 18
0.80 0.07 0.13
Matches are distributed among these distances:
42 2 0.02
43 5 0.05
45 3 0.03
46 63 0.57
47 29 0.26
48 3 0.03
50 4 0.04
51 2 0.02
ACGTcount: A:0.20, C:0.21, G:0.30, T:0.29
Consensus pattern (46 bp):
TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAATG
Found at i:53892902 original size:93 final size:93
Alignment explanation
Indices: 53892743--53892914 Score: 317
Period size: 93 Copynumber: 1.8 Consensus size: 93
53892733 GGATGGTTGA
* *
53892743 GCATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAATGTCCGAACTCGTTGAGT
1 GCATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAACGCCCGAACTCGTTGAGT
53892808 TGAGTCCGAGTTCGTGAGATGTAACTAG
66 TGAGTCCGAGTTCGTGAGATGTAACTAG
*
53892836 GCATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAACGCCCGAGCTCGTTGAGT
1 GCATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAACGCCCGAACTCGTTGAGT
53892901 TGAGTCCGAGTTCG
66 TGAGTCCGAGTTCG
53892915 CTTATGGGCG
Statistics
Matches: 76, Mismatches: 3, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
93 76 1.00
ACGTcount: A:0.21, C:0.22, G:0.30, T:0.28
Consensus pattern (93 bp):
GCATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAACGCCCGAACTCGTTGAGT
TGAGTCCGAGTTCGTGAGATGTAACTAG
Found at i:53900006 original size:28 final size:28
Alignment explanation
Indices: 53899974--53900039 Score: 89
Period size: 28 Copynumber: 2.4 Consensus size: 28
53899964 TTTTCCTTCA
*
53899974 CACACTTAGTGCTCGA-TAATCAAACTCG
1 CACACTTAGTGCTC-ATTAACCAAACTCG
*
53900002 TACACTTAGTGCTCATTAACCAAACTCG
1 CACACTTAGTGCTCATTAACCAAACTCG
*
53900030 CACGCTTAGT
1 CACACTTAGT
53900040 AAAATTTTCA
Statistics
Matches: 33, Mismatches: 4, Indels: 2
0.85 0.10 0.05
Matches are distributed among these distances:
27 1 0.03
28 32 0.97
ACGTcount: A:0.30, C:0.29, G:0.14, T:0.27
Consensus pattern (28 bp):
CACACTTAGTGCTCATTAACCAAACTCG
Found at i:53911613 original size:55 final size:55
Alignment explanation
Indices: 53911525--53911779 Score: 232
Period size: 55 Copynumber: 4.8 Consensus size: 55
53911515 CATTAGGGTT
* *
53911525 TAAGGATACCATGTAAGACCATGCCAAGGCATGGCAATTGGTAAGGTTTC-TAAGG
1 TAAGGATACCATGTAAGACCATGTCAAGACATGGCAATTGGTAA-GTTTCATAAGG
* *
53911580 TAAGGATATCATGTAAGACCATGTCAAGACATGGC-ATTGATAAGTTTCTATAAGG
1 TAAGGATACCATGTAAGACCATGTCAAGACATGGCAATTGGTAAGTTTC-ATAAGG
* * * * * *
53911635 CAAAGG-TCCCATGTAAGACCATG-CGAAGGCACGGC-ATGGGTGAG-TTCATAAGG
1 -TAAGGATACCATGTAAGACCATGTC-AAGACATGGCAATTGGTAAGTTTCATAAGG
* *
53911688 CAAGGATACCATGTAAGACCATGTCGAGACATGGCAA-TGGTAAGTTTC--AA--
1 TAAGGATACCATGTAAGACCATGTCAAGACATGGCAATTGGTAAGTTTCATAAGG
* * * *
53911738 -AAGGATACCACGTAAGA-CATGACAAGTCATGG-AAATGGTAAG
1 TAAGGATACCATGTAAGACCATGTCAAGACATGGCAATTGGTAAG
53911780 GTACCCGTGT
Statistics
Matches: 168, Mismatches: 23, Indels: 25
0.78 0.11 0.12
Matches are distributed among these distances:
47 2 0.01
48 19 0.11
49 16 0.10
52 6 0.04
53 39 0.23
54 16 0.10
55 66 0.39
56 4 0.02
ACGTcount: A:0.35, C:0.16, G:0.26, T:0.22
Consensus pattern (55 bp):
TAAGGATACCATGTAAGACCATGTCAAGACATGGCAATTGGTAAGTTTCATAAGG
Found at i:53911732 original size:108 final size:110
Alignment explanation
Indices: 53911533--53911735 Score: 295
Period size: 108 Copynumber: 1.9 Consensus size: 110
53911523 TTTAAGGATA
* * * *
53911533 CCATGTAAGACCATGCCAAGGCATGGCAATTGGTAAGGTTTCTAAGGTAAGGATATCATGTAAGA
1 CCATGTAAGACCATGCCAAGGCACGGCAATGGGTAAGGTTTCTAAGGCAAGGATACCATGTAAGA
*
53911598 CCATGTCAAGACATGGCATTGATAAGTTTCTATAAGGCAAAGGTC
66 CCATGTCAAGACATGGCAATGATAAGTTTCTATAAGGCAAAGGTC
* *
53911643 CCATGTAAGACCATGCGAAGGCACGGC-ATGGGTGA-G-TTCATAAGGCAAGGATACCATGTAAG
1 CCATGTAAGACCATGCCAAGGCACGGCAATGGGTAAGGTTTC-TAAGGCAAGGATACCATGTAAG
* *
53911705 ACCATGTCGAGACATGGCAATGGTAAGTTTC
65 ACCATGTCAAGACATGGCAATGATAAGTTTC
53911736 AAAAGGATAC
Statistics
Matches: 83, Mismatches: 9, Indels: 4
0.86 0.09 0.04
Matches are distributed among these distances:
107 3 0.04
108 49 0.59
109 6 0.07
110 25 0.30
ACGTcount: A:0.33, C:0.18, G:0.27, T:0.23
Consensus pattern (110 bp):
CCATGTAAGACCATGCCAAGGCACGGCAATGGGTAAGGTTTCTAAGGCAAGGATACCATGTAAGA
CCATGTCAAGACATGGCAATGATAAGTTTCTATAAGGCAAAGGTC
Found at i:53914956 original size:38 final size:38
Alignment explanation
Indices: 53914885--53915014 Score: 156
Period size: 38 Copynumber: 3.4 Consensus size: 38
53914875 ATTTGATGTG
* *
53914885 TATCCGGGCTTAAATACCCTCAGGCTAT-ATGCTGGAATTA
1 TATCCGGG-TTAAAT-CCCGCAGGCT-TCGTGCTGGAATTA
53914925 TATCCGGGTTAAATCCCGCAGGCTTCGTGCTGGTAA-TA
1 TATCCGGGTTAAATCCCGCAGGCTTCGTGCTGG-AATTA
* * *
53914963 TATCCGGGTTAAATCCCGCAGACTTCGTGTTGGTATTA
1 TATCCGGGTTAAATCCCGCAGGCTTCGTGCTGGAATTA
*
53915001 TATCCAGGTTAAAT
1 TATCCGGGTTAAAT
53915015 GCCTAGTGCT
Statistics
Matches: 81, Mismatches: 6, Indels: 8
0.85 0.06 0.08
Matches are distributed among these distances:
37 2 0.02
38 63 0.78
39 8 0.10
40 8 0.10
ACGTcount: A:0.25, C:0.22, G:0.22, T:0.32
Consensus pattern (38 bp):
TATCCGGGTTAAATCCCGCAGGCTTCGTGCTGGAATTA
Found at i:53916049 original size:16 final size:16
Alignment explanation
Indices: 53916028--53916058 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
53916018 ATAAATTTGA
53916028 TTAAGTAAGTAAGTAT
1 TTAAGTAAGTAAGTAT
*
53916044 TTAAGTAAGTGAGTA
1 TTAAGTAAGTAAGTA
53916059 AGTGAAGAAG
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:0.42, C:0.00, G:0.23, T:0.35
Consensus pattern (16 bp):
TTAAGTAAGTAAGTAT
Found at i:53917608 original size:40 final size:39
Alignment explanation
Indices: 53917563--53917692 Score: 136
Period size: 40 Copynumber: 3.3 Consensus size: 39
53917553 CGGAATATAA
53917563 CCGGATATAACCATGTGCACAAATGCCTTCGGGTCTTAGC
1 CCGGATATAACCAT-TGCACAAATGCCTTCGGGTCTTAGC
* * * *
53917603 CCGGATAGAATGTC-TCGCACGAATGCCTTCGGGTCTTAGC
1 CCGGATATAA--CCATTGCACAAATGCCTTCGGGTCTTAGC
* * * * *
53917643 CCGGATGTAGCCACTAGCACAATTGCCTTCGGGTCTTAAC
1 CCGGATATAACCA-TTGCACAAATGCCTTCGGGTCTTAGC
53917683 CCGGATATAA
1 CCGGATATAA
53917693 TTTCCAGCAT
Statistics
Matches: 72, Mismatches: 14, Indels: 8
0.77 0.15 0.09
Matches are distributed among these distances:
38 1 0.01
40 69 0.96
41 1 0.01
42 1 0.01
ACGTcount: A:0.24, C:0.28, G:0.24, T:0.25
Consensus pattern (39 bp):
CCGGATATAACCATTGCACAAATGCCTTCGGGTCTTAGC
Found at i:53917707 original size:40 final size:40
Alignment explanation
Indices: 53917579--53917730 Score: 148
Period size: 40 Copynumber: 3.8 Consensus size: 40
53917569 ATAACCATGT
* * *
53917579 GCACAAATGCCTTCGGGTCTTAGCCCGGATAGAATGTCTC-
1 GCACAATTGCCTTCGGGTCTTAGCCCGGATATAATCTC-CA
* ** * *
53917619 GCACGAA-TGCCTTCGGGTCTTAGCCCGGATGTAGCCACTA
1 GCAC-AATTGCCTTCGGGTCTTAGCCCGGATATAATCTCCA
* *
53917659 GCACAATTGCCTTCGGGTCTTAACCCGGATATAATTTCCA
1 GCACAATTGCCTTCGGGTCTTAGCCCGGATATAATCTCCA
* *
53917699 GCATAATTGTCTTCGGGAT-TTAGCCCGGATAT
1 GCACAATTGCCTTCGGG-TCTTAGCCCGGATAT
53917731 CATTCAATTT
Statistics
Matches: 91, Mismatches: 17, Indels: 8
0.78 0.15 0.07
Matches are distributed among these distances:
39 2 0.02
40 86 0.95
41 3 0.03
ACGTcount: A:0.22, C:0.26, G:0.24, T:0.28
Consensus pattern (40 bp):
GCACAATTGCCTTCGGGTCTTAGCCCGGATATAATCTCCA
Found at i:53917713 original size:80 final size:80
Alignment explanation
Indices: 53917579--53917728 Score: 198
Period size: 80 Copynumber: 1.9 Consensus size: 80
53917569 ATAACCATGT
*
53917579 GCACAAATGCCTTCGGGTCTTAGCCCGGATAGAATGTCTCGCACGAATGCCTTCGGG-TCTTAGC
1 GCACAAATGCCTTCGGGTCTTAACCCGGATAGAATGTCTCGCACGAATGCCTTCGGGAT-TTAGC
53917643 CCGGATGTAGCCACTA
65 CCGGATGTAGCCACTA
* * * * *
53917659 GCACAATTGCCTTCGGGTCTTAACCCGGATATAATTTC-CAGCA-TAATTGTCTTCGGGATTTAG
1 GCACAAATGCCTTCGGGTCTTAACCCGGATAGAATGTCTC-GCACGAA-TGCCTTCGGGATTTAG
53917722 CCCGGAT
64 CCCGGAT
53917729 ATCATTCAAT
Statistics
Matches: 61, Mismatches: 6, Indels: 6
0.84 0.08 0.08
Matches are distributed among these distances:
79 3 0.05
80 57 0.93
81 1 0.02
ACGTcount: A:0.22, C:0.27, G:0.24, T:0.27
Consensus pattern (80 bp):
GCACAAATGCCTTCGGGTCTTAACCCGGATAGAATGTCTCGCACGAATGCCTTCGGGATTTAGCC
CGGATGTAGCCACTA
Found at i:53925624 original size:40 final size:39
Alignment explanation
Indices: 53925579--53925708 Score: 136
Period size: 40 Copynumber: 3.3 Consensus size: 39
53925569 CGGAATATAA
53925579 CCGGATATAACCATGTGCACAAATGCCTTCGGGTCTTAGC
1 CCGGATATAACCAT-TGCACAAATGCCTTCGGGTCTTAGC
* * * *
53925619 CCGGATAGAATGTC-TCGCACGAATGCCTTCGGGTCTTAGC
1 CCGGATATAA--CCATTGCACAAATGCCTTCGGGTCTTAGC
* * * * *
53925659 CCGGATGTAGCCACTAGCACAATTGCCTTCGGGTCTTAAC
1 CCGGATATAACCA-TTGCACAAATGCCTTCGGGTCTTAGC
53925699 CCGGATATAA
1 CCGGATATAA
53925709 TTTCCAGCAT
Statistics
Matches: 72, Mismatches: 14, Indels: 8
0.77 0.15 0.09
Matches are distributed among these distances:
38 1 0.01
40 69 0.96
41 1 0.01
42 1 0.01
ACGTcount: A:0.24, C:0.28, G:0.24, T:0.25
Consensus pattern (39 bp):
CCGGATATAACCATTGCACAAATGCCTTCGGGTCTTAGC
Found at i:53925723 original size:40 final size:40
Alignment explanation
Indices: 53925595--53925746 Score: 148
Period size: 40 Copynumber: 3.8 Consensus size: 40
53925585 ATAACCATGT
* * *
53925595 GCACAAATGCCTTCGGGTCTTAGCCCGGATAGAATGTCTC-
1 GCACAATTGCCTTCGGGTCTTAGCCCGGATATAATCTC-CA
* ** * *
53925635 GCACGAA-TGCCTTCGGGTCTTAGCCCGGATGTAGCCACTA
1 GCAC-AATTGCCTTCGGGTCTTAGCCCGGATATAATCTCCA
* *
53925675 GCACAATTGCCTTCGGGTCTTAACCCGGATATAATTTCCA
1 GCACAATTGCCTTCGGGTCTTAGCCCGGATATAATCTCCA
* *
53925715 GCATAATTGTCTTCGGGAT-TTAGCCCGGATAT
1 GCACAATTGCCTTCGGG-TCTTAGCCCGGATAT
53925747 CATTCAATTT
Statistics
Matches: 91, Mismatches: 17, Indels: 8
0.78 0.15 0.07
Matches are distributed among these distances:
39 2 0.02
40 86 0.95
41 3 0.03
ACGTcount: A:0.22, C:0.26, G:0.24, T:0.28
Consensus pattern (40 bp):
GCACAATTGCCTTCGGGTCTTAGCCCGGATATAATCTCCA
Found at i:53925729 original size:80 final size:80
Alignment explanation
Indices: 53925595--53925744 Score: 198
Period size: 80 Copynumber: 1.9 Consensus size: 80
53925585 ATAACCATGT
*
53925595 GCACAAATGCCTTCGGGTCTTAGCCCGGATAGAATGTCTCGCACGAATGCCTTCGGG-TCTTAGC
1 GCACAAATGCCTTCGGGTCTTAACCCGGATAGAATGTCTCGCACGAATGCCTTCGGGAT-TTAGC
53925659 CCGGATGTAGCCACTA
65 CCGGATGTAGCCACTA
* * * * *
53925675 GCACAATTGCCTTCGGGTCTTAACCCGGATATAATTTC-CAGCA-TAATTGTCTTCGGGATTTAG
1 GCACAAATGCCTTCGGGTCTTAACCCGGATAGAATGTCTC-GCACGAA-TGCCTTCGGGATTTAG
53925738 CCCGGAT
64 CCCGGAT
53925745 ATCATTCAAT
Statistics
Matches: 61, Mismatches: 6, Indels: 6
0.84 0.08 0.08
Matches are distributed among these distances:
79 3 0.05
80 57 0.93
81 1 0.02
ACGTcount: A:0.22, C:0.27, G:0.24, T:0.27
Consensus pattern (80 bp):
GCACAAATGCCTTCGGGTCTTAACCCGGATAGAATGTCTCGCACGAATGCCTTCGGGATTTAGCC
CGGATGTAGCCACTA
Found at i:53931386 original size:2 final size:2
Alignment explanation
Indices: 53931379--53931407 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
53931369 ACATCAGCTA
53931379 AT AT 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 AT AT A
53931408 ATAGGATGAA
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 27 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:53945521 original size:48 final size:48
Alignment explanation
Indices: 53945459--53945739 Score: 499
Period size: 48 Copynumber: 5.9 Consensus size: 48
53945449 TATATATGTG
53945459 TGTGGTAAAGCCGAATGGCTAATGTGAAATATGTATGAGATATGTATA
1 TGTGGTAAAGCCGAATGGCTAATGTGAAATATGTATGAGATATGTATA
* *
53945507 TATGGTAAAGCCGAATGGCTAGTGTGAAATATGTATGAGATATGTATA
1 TGTGGTAAAGCCGAATGGCTAATGTGAAATATGTATGAGATATGTATA
* *
53945555 TGTGGTAAAGCCGAATGGCTAATGTTAAATATATATGAGATATGTATA
1 TGTGGTAAAGCCGAATGGCTAATGTGAAATATGTATGAGATATGTATA
53945603 TGTGGTAAAGCCGAATGGCTAATGTGAAATATGTATGAGATATGTATA
1 TGTGGTAAAGCCGAATGGCTAATGTGAAATATGTATGAGATATGTATA
*
53945651 TGTGGTAAAGCCGAATGGCTAGTGTGAAATATGTATGAGATATGTATA
1 TGTGGTAAAGCCGAATGGCTAATGTGAAATATGTATGAGATATGTATA
* *
53945699 TGTGGTAAAGCCGAATGGCTAGTGTGAAATATGTAGGAGAT
1 TGTGGTAAAGCCGAATGGCTAATGTGAAATATGTATGAGAT
53945740 GTGTGTATAT
Statistics
Matches: 223, Mismatches: 10, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
48 223 1.00
ACGTcount: A:0.35, C:0.06, G:0.28, T:0.31
Consensus pattern (48 bp):
TGTGGTAAAGCCGAATGGCTAATGTGAAATATGTATGAGATATGTATA
Found at i:53945955 original size:36 final size:37
Alignment explanation
Indices: 53945880--53945976 Score: 160
Period size: 36 Copynumber: 2.6 Consensus size: 37
53945870 GGAAATATAT
53945880 TCCGGGTAAGACCCGATGACTACGTGTGGAGATTATG
1 TCCGGGTAAGACCCGATGACTACGTGTGGAGATTATG
* *
53945917 TCCGGGTAAGACCTGATGACTA-GTGTGGAGATTTTG
1 TCCGGGTAAGACCCGATGACTACGTGTGGAGATTATG
*
53945953 TCCGGGTAAGACCCGATAACTACG
1 TCCGGGTAAGACCCGATGACTACG
53945977 CGTTGGGACT
Statistics
Matches: 55, Mismatches: 4, Indels: 2
0.90 0.07 0.03
Matches are distributed among these distances:
36 33 0.60
37 22 0.40
ACGTcount: A:0.25, C:0.20, G:0.31, T:0.25
Consensus pattern (37 bp):
TCCGGGTAAGACCCGATGACTACGTGTGGAGATTATG
Found at i:53947407 original size:2 final size:2
Alignment explanation
Indices: 53947390--53947423 Score: 54
Period size: 2 Copynumber: 18.0 Consensus size: 2
53947380 TTTTGGTTTG
53947390 TA TA T- TA TA T- TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
53947424 CGTCAATGGT
Statistics
Matches: 30, Mismatches: 0, Indels: 4
0.88 0.00 0.12
Matches are distributed among these distances:
1 2 0.07
2 28 0.93
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (2 bp):
TA
Found at i:53954782 original size:2 final size:2
Alignment explanation
Indices: 53954772--53954806 Score: 54
Period size: 2 Copynumber: 18.0 Consensus size: 2
53954762 TTTTGGTTTG
*
53954772 TA TA T- TA TA TA TA TA TA TA TA TA CA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
53954807 CGTCAATGGT
Statistics
Matches: 30, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
1 1 0.03
2 29 0.97
ACGTcount: A:0.49, C:0.03, G:0.00, T:0.49
Consensus pattern (2 bp):
TA
Found at i:53962331 original size:46 final size:46
Alignment explanation
Indices: 53962263--53962399 Score: 184
Period size: 46 Copynumber: 3.0 Consensus size: 46
53962253 TATATATACA
* * * * *
53962263 CATCTCATACATATCTCACATTAGCCATTTGGCTTTACCGCATGTC
1 CATCTCATACACATTTCGCATTAGCCATTCGGCTTTACCGCATATC
* * *
53962309 CATCTCATACACGTTTCGCATTATCCATTCGGCTTTACCTCATATC
1 CATCTCATACACATTTCGCATTAGCCATTCGGCTTTACCGCATATC
* *
53962355 CATCTCATACACATTTTGCATTAGCCATTCGGCTTTACCACATAT
1 CATCTCATACACATTTCGCATTAGCCATTCGGCTTTACCGCATAT
53962400 ATACACTTCC
Statistics
Matches: 79, Mismatches: 12, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
46 79 1.00
ACGTcount: A:0.24, C:0.31, G:0.09, T:0.36
Consensus pattern (46 bp):
CATCTCATACACATTTCGCATTAGCCATTCGGCTTTACCGCATATC
Found at i:53962444 original size:47 final size:47
Alignment explanation
Indices: 53962373--53962824 Score: 690
Period size: 47 Copynumber: 9.6 Consensus size: 47
53962363 ACACATTTTG
* * * * * *
53962373 CATTAGCCATTCGGCTTTACCACATATATACACT-TCCACGTTCATCA
1 CATTGGCCATTCGGCCTTATCACATATATGCA-TGTTCACATTCATCA
* *
53962420 CATTGGCCATTCAGCCTTGTCACATATATGCATGTTCACATTCATCA
1 CATTGGCCATTCGGCCTTATCACATATATGCATGTTCACATTCATCA
* *
53962467 CATTGGCCATTCGACCTTATCACATATATGCAAGTTCACATTCATCA
1 CATTGGCCATTCGGCCTTATCACATATATGCATGTTCACATTCATCA
* * * *
53962514 CATTGGCCATTTGGCCTTATCACACATACGCATGTTCACATTAATCA
1 CATTGGCCATTCGGCCTTATCACATATATGCATGTTCACATTCATCA
* *
53962561 CATTGGCCATTCGGCCTTATCACACATATGCATGTTTACATTCATCA
1 CATTGGCCATTCGGCCTTATCACATATATGCATGTTCACATTCATCA
*
53962608 CATTGGCCATTCGGCCTTATCACACATATGCATGTTCACATTCATCA
1 CATTGGCCATTCGGCCTTATCACATATATGCATGTTCACATTCATCA
53962655 CATTGGCCATTCGGCCTTATCACATATATGCATGTTCACATTCATCA
1 CATTGGCCATTCGGCCTTATCACATATATGCATGTTCACATTCATCA
*
53962702 CATTGGCCCTTCGGCCTTATCACATATATGCATGTTCACATTCATCA
1 CATTGGCCATTCGGCCTTATCACATATATGCATGTTCACATTCATCA
* *
53962749 CATTGGCTATTCGGCCTTATCTCATATATGCATGTTCACATTCATCA
1 CATTGGCCATTCGGCCTTATCACATATATGCATGTTCACATTCATCA
* *
53962796 CATTTGCCATTCGGCCTTATCTCATATAT
1 CATTGGCCATTCGGCCTTATCACATATAT
53962825 ACACATAAAC
Statistics
Matches: 374, Mismatches: 30, Indels: 2
0.92 0.07 0.00
Matches are distributed among these distances:
46 1 0.00
47 373 1.00
ACGTcount: A:0.26, C:0.28, G:0.12, T:0.34
Consensus pattern (47 bp):
CATTGGCCATTCGGCCTTATCACATATATGCATGTTCACATTCATCA
Found at i:53966680 original size:25 final size:25
Alignment explanation
Indices: 53966643--53966695 Score: 70
Period size: 25 Copynumber: 2.1 Consensus size: 25
53966633 GTTGAAGAAC
* * *
53966643 TTGCACTCTTAGTGCCTCTAATCAT
1 TTGCACACATAGTGCCCCTAATCAT
*
53966668 TTGCACACATAGTGCCCCTATTCAT
1 TTGCACACATAGTGCCCCTAATCAT
53966693 TTG
1 TTG
53966696 TTGTTACACA
Statistics
Matches: 24, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
25 24 1.00
ACGTcount: A:0.21, C:0.28, G:0.13, T:0.38
Consensus pattern (25 bp):
TTGCACACATAGTGCCCCTAATCAT
Found at i:53966914 original size:40 final size:40
Alignment explanation
Indices: 53966859--53967094 Score: 436
Period size: 40 Copynumber: 5.9 Consensus size: 40
53966849 GAATACACAT
* *
53966859 CACCAGCATGAATGCTCTTCGGGACTTAGCCCGGATATAA
1 CACCAGCACGTATGCTCTTCGGGACTTAGCCCGGATATAA
*
53966899 CACCAGTACGTATGCTCTTCGGGACTTAGCCCGGATATAA
1 CACCAGCACGTATGCTCTTCGGGACTTAGCCCGGATATAA
53966939 CACCAGCACGTATGCTCTTCGGGACTTAGCCCGGATATAA
1 CACCAGCACGTATGCTCTTCGGGACTTAGCCCGGATATAA
53966979 CACCAGCACGTATGCTCTTCGGGACTTAGCCCGGATATAA
1 CACCAGCACGTATGCTCTTCGGGACTTAGCCCGGATATAA
53967019 CACCAGCACGTATGCTCTTCGGGACTTAGCCCGGATATAA
1 CACCAGCACGTATGCTCTTCGGGACTTAGCCCGGATATAA
*
53967059 CTCCAGCACGTATGCTCTTCGGGACTTAGCCCGGAT
1 CACCAGCACGTATGCTCTTCGGGACTTAGCCCGGAT
53967095 CATATATAAC
Statistics
Matches: 191, Mismatches: 5, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
40 191 1.00
ACGTcount: A:0.24, C:0.30, G:0.23, T:0.23
Consensus pattern (40 bp):
CACCAGCACGTATGCTCTTCGGGACTTAGCCCGGATATAA
Found at i:53967814 original size:19 final size:19
Alignment explanation
Indices: 53967790--53967829 Score: 55
Period size: 19 Copynumber: 2.1 Consensus size: 19
53967780 AGCTCCCATG
53967790 TAGCTC-CACACCAGCTCAT
1 TAGCTCGCA-ACCAGCTCAT
*
53967809 TAGCTCGGAACCAGCTCAT
1 TAGCTCGCAACCAGCTCAT
53967828 TA
1 TA
53967830 TCAGCTCACG
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
19 18 0.95
20 1 0.05
ACGTcount: A:0.28, C:0.35, G:0.15, T:0.23
Consensus pattern (19 bp):
TAGCTCGCAACCAGCTCAT
Found at i:53969090 original size:14 final size:14
Alignment explanation
Indices: 53969068--53969115 Score: 60
Period size: 14 Copynumber: 3.4 Consensus size: 14
53969058 ACCTAAACCG
* *
53969068 ACCAATTTGTTCAT
1 ACCATTTTGTTCCT
53969082 ACCATTTTGTTCCT
1 ACCATTTTGTTCCT
* *
53969096 ACCCTTTCGTTCCT
1 ACCATTTTGTTCCT
53969110 ACCATT
1 ACCATT
53969116 CCATTCGTAC
Statistics
Matches: 29, Mismatches: 5, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
14 29 1.00
ACGTcount: A:0.19, C:0.31, G:0.06, T:0.44
Consensus pattern (14 bp):
ACCATTTTGTTCCT
Found at i:53969522 original size:12 final size:12
Alignment explanation
Indices: 53969507--53969550 Score: 70
Period size: 12 Copynumber: 3.7 Consensus size: 12
53969497 TAAAAAAAAT
53969507 AAAAAAAATTCG
1 AAAAAAAATTCG
53969519 AAAAAAAATTCG
1 AAAAAAAATTCG
* *
53969531 AAAAAAAAATAG
1 AAAAAAAATTCG
53969543 AAAAAAAA
1 AAAAAAAA
53969551 AAAAAGAGTG
Statistics
Matches: 30, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
12 30 1.00
ACGTcount: A:0.77, C:0.05, G:0.07, T:0.11
Consensus pattern (12 bp):
AAAAAAAATTCG
Found at i:53969551 original size:12 final size:12
Alignment explanation
Indices: 53969498--53969551 Score: 67
Period size: 12 Copynumber: 4.7 Consensus size: 12
53969488 TATACAAGTT
53969498 AAAAAAAAT--A
1 AAAAAAAATCGA
*
53969508 AAAAAAATTCGA
1 AAAAAAAATCGA
*
53969520 AAAAAAATTCGA
1 AAAAAAAATCGA
*
53969532 AAAAAAAATAGA
1 AAAAAAAATCGA
53969544 AAAAAAAA
1 AAAAAAAA
53969552 AAAAGAGTGA
Statistics
Matches: 39, Mismatches: 3, Indels: 2
0.89 0.07 0.05
Matches are distributed among these distances:
10 8 0.21
12 31 0.79
ACGTcount: A:0.80, C:0.04, G:0.06, T:0.11
Consensus pattern (12 bp):
AAAAAAAATCGA
Found at i:53972582 original size:15 final size:15
Alignment explanation
Indices: 53972562--53972592 Score: 62
Period size: 15 Copynumber: 2.1 Consensus size: 15
53972552 AAAAGTGTTC
53972562 ATTTTGCACTGATAA
1 ATTTTGCACTGATAA
53972577 ATTTTGCACTGATAA
1 ATTTTGCACTGATAA
53972592 A
1 A
53972593 GTTGTGTTTT
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 16 1.00
ACGTcount: A:0.35, C:0.13, G:0.13, T:0.39
Consensus pattern (15 bp):
ATTTTGCACTGATAA
Found at i:53976235 original size:25 final size:25
Alignment explanation
Indices: 53976206--53976253 Score: 69
Period size: 25 Copynumber: 1.9 Consensus size: 25
53976196 TTATAATATG
* * *
53976206 AAAATGACCGTTTTGCCCCTAGGTA
1 AAAATGACCATTATACCCCTAGGTA
53976231 AAAATGACCATTATACCCCTAGG
1 AAAATGACCATTATACCCCTAGG
53976254 GTTTATGTAT
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
25 20 1.00
ACGTcount: A:0.33, C:0.25, G:0.17, T:0.25
Consensus pattern (25 bp):
AAAATGACCATTATACCCCTAGGTA
Found at i:53976322 original size:20 final size:20
Alignment explanation
Indices: 53976297--53976355 Score: 100
Period size: 20 Copynumber: 3.0 Consensus size: 20
53976287 TAAATATGGT
53976297 ATGTATGATATGCACATGAA
1 ATGTATGATATGCACATGAA
* *
53976317 ATGTATGATACGCACATGAT
1 ATGTATGATATGCACATGAA
53976337 ATGTATGATATGCACATGA
1 ATGTATGATATGCACATGA
53976356 GGTAATCATA
Statistics
Matches: 36, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
20 36 1.00
ACGTcount: A:0.37, C:0.12, G:0.20, T:0.31
Consensus pattern (20 bp):
ATGTATGATATGCACATGAA
Found at i:53976475 original size:47 final size:48
Alignment explanation
Indices: 53976406--53976524 Score: 172
Period size: 47 Copynumber: 2.5 Consensus size: 48
53976396 GAGGAAGTGA
53976406 AAAAGGGCTTATGCCCCAGTTATCGAAAGGGCTTAT-GCCCCAGTTA-T
1 AAAAGGGCTTATGCCCCAGTTATCGAAAGGGCTT-TGGCCCCAGTTATT
*
53976453 AAAAGGGCTTATGCCCCAGTTATTGAAAGGGCTTTGGCCCCAGTTATT
1 AAAAGGGCTTATGCCCCAGTTATCGAAAGGGCTTTGGCCCCAGTTATT
*
53976501 AAAAGAGGC-TAGGCCTCCAGTTAT
1 AAAAG-GGCTTATGCC-CCAGTTAT
53976525 ATGATAAAGC
Statistics
Matches: 66, Mismatches: 2, Indels: 6
0.89 0.03 0.08
Matches are distributed among these distances:
46 1 0.02
47 43 0.65
48 11 0.17
49 11 0.17
ACGTcount: A:0.28, C:0.22, G:0.24, T:0.26
Consensus pattern (48 bp):
AAAAGGGCTTATGCCCCAGTTATCGAAAGGGCTTTGGCCCCAGTTATT
Found at i:53976500 original size:24 final size:24
Alignment explanation
Indices: 53976406--53976524 Score: 154
Period size: 24 Copynumber: 5.0 Consensus size: 24
53976396 GAGGAAGTGA
*
53976406 AAAAGGGCTTATGCCCCAGTTATC
1 AAAAGGGCTTATGCCCCAGTTATT
*
53976430 GAAAGGGCTTATGCCCCAGTTA-T
1 AAAAGGGCTTATGCCCCAGTTATT
53976453 AAAAGGGCTTATGCCCCAGTTATT
1 AAAAGGGCTTATGCCCCAGTTATT
*
53976477 GAAAGGGCTT-TGGCCCCAGTTATT
1 AAAAGGGCTTAT-GCCCCAGTTATT
*
53976501 AAAAGAGGC-TAGGCCTCCAGTTAT
1 AAAAG-GGCTTATGCC-CCAGTTAT
53976525 ATGATAAAGC
Statistics
Matches: 84, Mismatches: 6, Indels: 9
0.85 0.06 0.09
Matches are distributed among these distances:
23 22 0.26
24 51 0.61
25 11 0.13
ACGTcount: A:0.28, C:0.22, G:0.24, T:0.26
Consensus pattern (24 bp):
AAAAGGGCTTATGCCCCAGTTATT
Found at i:53976751 original size:31 final size:31
Alignment explanation
Indices: 53976716--53976816 Score: 130
Period size: 31 Copynumber: 3.1 Consensus size: 31
53976706 CGTTTACAGT
53976716 AAAGGCTTCGGCCCAGTAATATGAAATATGA
1 AAAGGCTTCGGCCCAGTAATATGAAATATGA
*
53976747 AAAGGCTTCGGCCCAGTATTATGAATATGAAACATGA
1 AAAGGCTTCGGCCCAG-----T-AATATGAAATATGA
*
53976784 AAAGGCTTCGGCCCAGTATTATGAAATATGA
1 AAAGGCTTCGGCCCAGTAATATGAAATATGA
53976815 AA
1 AA
53976817 TATGAAAAGG
Statistics
Matches: 61, Mismatches: 3, Indels: 12
0.80 0.04 0.16
Matches are distributed among these distances:
31 30 0.49
32 1 0.02
36 1 0.02
37 29 0.48
ACGTcount: A:0.39, C:0.16, G:0.22, T:0.24
Consensus pattern (31 bp):
AAAGGCTTCGGCCCAGTAATATGAAATATGA
Found at i:53976784 original size:37 final size:38
Alignment explanation
Indices: 53976733--53976839 Score: 180
Period size: 37 Copynumber: 2.8 Consensus size: 38
53976723 TCGGCCCAGT
53976733 AATATGAAATATGAAAAGGCTTCGGCCCAGTATTATG-
1 AATATGAAATATGAAAAGGCTTCGGCCCAGTATTATGA
*
53976770 AATATGAAACATGAAAAGGCTTCGGCCCAGTATTATGA
1 AATATGAAATATGAAAAGGCTTCGGCCCAGTATTATGA
*
53976808 AATATGAAATATGAAAAGGGCTACGGCCCAGT
1 AATATGAAATATGAAAA-GGCTTCGGCCCAGT
53976840 GCATGATTGA
Statistics
Matches: 65, Mismatches: 3, Indels: 2
0.93 0.04 0.03
Matches are distributed among these distances:
37 36 0.55
38 16 0.25
39 13 0.20
ACGTcount: A:0.39, C:0.15, G:0.22, T:0.23
Consensus pattern (38 bp):
AATATGAAATATGAAAAGGCTTCGGCCCAGTATTATGA
Found at i:53984653 original size:20 final size:20
Alignment explanation
Indices: 53984628--53984686 Score: 100
Period size: 20 Copynumber: 3.0 Consensus size: 20
53984618 TAAATATGGT
53984628 ATGTATGATATGCACATGAA
1 ATGTATGATATGCACATGAA
* *
53984648 ATGTATGATACGCACATGAT
1 ATGTATGATATGCACATGAA
53984668 ATGTATGATATGCACATGA
1 ATGTATGATATGCACATGA
53984687 GGTAATCATA
Statistics
Matches: 36, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
20 36 1.00
ACGTcount: A:0.37, C:0.12, G:0.20, T:0.31
Consensus pattern (20 bp):
ATGTATGATATGCACATGAA
Found at i:53984806 original size:47 final size:48
Alignment explanation
Indices: 53984737--53984855 Score: 172
Period size: 47 Copynumber: 2.5 Consensus size: 48
53984727 GAGGAAGTGA
53984737 AAAAGGGCTTATGCCCCAGTTATCGAAAGGGCTTAT-GCCCCAGTTA-T
1 AAAAGGGCTTATGCCCCAGTTATCGAAAGGGCTT-TGGCCCCAGTTATT
*
53984784 AAAAGGGCTTATGCCCCAGTTATTGAAAGGGCTTTGGCCCCAGTTATT
1 AAAAGGGCTTATGCCCCAGTTATCGAAAGGGCTTTGGCCCCAGTTATT
*
53984832 AAAAGAGGC-TAGGCCTCCAGTTAT
1 AAAAG-GGCTTATGCC-CCAGTTAT
53984856 ATGATAAAGC
Statistics
Matches: 66, Mismatches: 2, Indels: 6
0.89 0.03 0.08
Matches are distributed among these distances:
46 1 0.02
47 43 0.65
48 11 0.17
49 11 0.17
ACGTcount: A:0.28, C:0.22, G:0.24, T:0.26
Consensus pattern (48 bp):
AAAAGGGCTTATGCCCCAGTTATCGAAAGGGCTTTGGCCCCAGTTATT
Found at i:53984831 original size:24 final size:24
Alignment explanation
Indices: 53984737--53984855 Score: 154
Period size: 24 Copynumber: 5.0 Consensus size: 24
53984727 GAGGAAGTGA
*
53984737 AAAAGGGCTTATGCCCCAGTTATC
1 AAAAGGGCTTATGCCCCAGTTATT
*
53984761 GAAAGGGCTTATGCCCCAGTTA-T
1 AAAAGGGCTTATGCCCCAGTTATT
53984784 AAAAGGGCTTATGCCCCAGTTATT
1 AAAAGGGCTTATGCCCCAGTTATT
*
53984808 GAAAGGGCTT-TGGCCCCAGTTATT
1 AAAAGGGCTTAT-GCCCCAGTTATT
*
53984832 AAAAGAGGC-TAGGCCTCCAGTTAT
1 AAAAG-GGCTTATGCC-CCAGTTAT
53984856 ATGATAAAGC
Statistics
Matches: 84, Mismatches: 6, Indels: 9
0.85 0.06 0.09
Matches are distributed among these distances:
23 22 0.26
24 51 0.61
25 11 0.13
ACGTcount: A:0.28, C:0.22, G:0.24, T:0.26
Consensus pattern (24 bp):
AAAAGGGCTTATGCCCCAGTTATT
Found at i:53985082 original size:31 final size:31
Alignment explanation
Indices: 53985047--53985148 Score: 123
Period size: 31 Copynumber: 3.1 Consensus size: 31
53985037 CATTTACAGT
53985047 AAAGGCTTCGGCCCAGTAATATGAAATATGA
1 AAAGGCTTCGGCCCAGTAATATGAAATATGA
*
53985078 AAAGGCTTCGGCCCAGTATTATGAAATATGAAACATGA
1 AAAGGCTTCGGCCCAG-----T--AATATGAAATATGA
*
53985116 AAAGGCTTCGGCCCAGTATTATGAAATATGA
1 AAAGGCTTCGGCCCAGTAATATGAAATATGA
53985147 AA
1 AA
53985149 TATGAAAAGG
Statistics
Matches: 61, Mismatches: 3, Indels: 14
0.78 0.04 0.18
Matches are distributed among these distances:
31 30 0.49
33 1 0.02
36 1 0.02
38 29 0.48
ACGTcount: A:0.39, C:0.16, G:0.22, T:0.24
Consensus pattern (31 bp):
AAAGGCTTCGGCCCAGTAATATGAAATATGA
Found at i:53985116 original size:38 final size:38
Alignment explanation
Indices: 53985064--53985171 Score: 189
Period size: 38 Copynumber: 2.8 Consensus size: 38
53985054 TCGGCCCAGT
53985064 AATATGAAATATGAAAAGGCTTCGGCCCAGTATTATGA
1 AATATGAAATATGAAAAGGCTTCGGCCCAGTATTATGA
*
53985102 AATATGAAACATGAAAAGGCTTCGGCCCAGTATTATGA
1 AATATGAAATATGAAAAGGCTTCGGCCCAGTATTATGA
*
53985140 AATATGAAATATGAAAAGGGCTACGGCCCAGT
1 AATATGAAATATGAAAA-GGCTTCGGCCCAGT
53985172 GCATGATTGA
Statistics
Matches: 66, Mismatches: 3, Indels: 1
0.94 0.04 0.01
Matches are distributed among these distances:
38 53 0.80
39 13 0.20
ACGTcount: A:0.40, C:0.15, G:0.22, T:0.23
Consensus pattern (38 bp):
AATATGAAATATGAAAAGGCTTCGGCCCAGTATTATGA
Found at i:53986244 original size:21 final size:21
Alignment explanation
Indices: 53986218--53986265 Score: 62
Period size: 21 Copynumber: 2.3 Consensus size: 21
53986208 ATTCCCCACA
53986218 TGGAGTGTAG-GGCTGGTAGGG
1 TGGAGTGTAGTGGCTGGT-GGG
*
53986239 TGGAGTGTAGTGGTTGGTGGG
1 TGGAGTGTAGTGGCTGGTGGG
*
53986260 TTGAGT
1 TGGAGT
53986266 AGTCTCCCCA
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
21 18 0.75
22 6 0.25
ACGTcount: A:0.12, C:0.02, G:0.54, T:0.31
Consensus pattern (21 bp):
TGGAGTGTAGTGGCTGGTGGG
Found at i:53989978 original size:12 final size:12
Alignment explanation
Indices: 53989961--53989995 Score: 52
Period size: 12 Copynumber: 2.8 Consensus size: 12
53989951 ATGAATAAAG
*
53989961 AAGATAAATGGA
1 AAGATAAATGAA
53989973 AAGATAAATGAA
1 AAGATAAATGAA
53989985 AAGATAGAATG
1 AAGATA-AATG
53989996 TGGCGTGTAG
Statistics
Matches: 21, Mismatches: 1, Indels: 1
0.91 0.04 0.04
Matches are distributed among these distances:
12 17 0.81
13 4 0.19
ACGTcount: A:0.60, C:0.00, G:0.23, T:0.17
Consensus pattern (12 bp):
AAGATAAATGAA
Found at i:53993618 original size:16 final size:17
Alignment explanation
Indices: 53993599--53993635 Score: 51
Period size: 15 Copynumber: 2.3 Consensus size: 17
53993589 ATTTTTTTAT
53993599 TTTTTATTTTTTCGTA-
1 TTTTTATTTTTTCGTAC
*
53993615 -TTTTATTTTTTTGTAC
1 TTTTTATTTTTTCGTAC
53993631 TTTTT
1 TTTTT
53993636 TGATCACCTT
Statistics
Matches: 18, Mismatches: 1, Indels: 3
0.82 0.05 0.14
Matches are distributed among these distances:
15 14 0.78
17 4 0.22
ACGTcount: A:0.11, C:0.05, G:0.05, T:0.78
Consensus pattern (17 bp):
TTTTTATTTTTTCGTAC
Found at i:53995768 original size:25 final size:25
Alignment explanation
Indices: 53995740--53995791 Score: 86
Period size: 25 Copynumber: 2.1 Consensus size: 25
53995730 TTTATTTCTC
*
53995740 ATTTTTATCTTTGTCTTTAATTTTA
1 ATTTTAATCTTTGTCTTTAATTTTA
*
53995765 ATTTTAATCTTTGTTTTTAATTTTA
1 ATTTTAATCTTTGTCTTTAATTTTA
53995790 AT
1 AT
53995792 GTGAGTTTTA
Statistics
Matches: 25, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
25 25 1.00
ACGTcount: A:0.23, C:0.06, G:0.04, T:0.67
Consensus pattern (25 bp):
ATTTTAATCTTTGTCTTTAATTTTA
Found at i:53995775 original size:19 final size:19
Alignment explanation
Indices: 53995753--53995791 Score: 60
Period size: 19 Copynumber: 2.1 Consensus size: 19
53995743 TTTATCTTTG
53995753 TCTTTAATTTTAATTTTAA
1 TCTTTAATTTTAATTTTAA
**
53995772 TCTTTGTTTTTAATTTTAA
1 TCTTTAATTTTAATTTTAA
53995791 T
1 T
53995792 GTGAGTTTTA
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
19 18 1.00
ACGTcount: A:0.26, C:0.05, G:0.03, T:0.67
Consensus pattern (19 bp):
TCTTTAATTTTAATTTTAA
Found at i:53995799 original size:19 final size:19
Alignment explanation
Indices: 53995760--53995800 Score: 55
Period size: 19 Copynumber: 2.2 Consensus size: 19
53995750 TTGTCTTTAA
**
53995760 TTTTAATTTTAATCTTTGT
1 TTTTAATTTTAATCTGAGT
*
53995779 TTTTAATTTTAATGTGAGT
1 TTTTAATTTTAATCTGAGT
53995798 TTT
1 TTT
53995801 ATTTATTTTA
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
19 19 1.00
ACGTcount: A:0.22, C:0.02, G:0.10, T:0.66
Consensus pattern (19 bp):
TTTTAATTTTAATCTGAGT
Found at i:53998691 original size:31 final size:31
Alignment explanation
Indices: 53998620--53998693 Score: 89
Period size: 30 Copynumber: 2.4 Consensus size: 31
53998610 TAATAAGAGC
53998620 AAATAAAAGAG-TGCTCAAAGTCTCAAAAAAA
1 AAATAAAA-AGTTGCTCAAAGTCTCAAAAAAA
* * **
53998651 AAAT-CAAAGTTGCTCAAAGTTTGGAAAAAA
1 AAATAAAAAGTTGCTCAAAGTCTCAAAAAAA
53998681 AAATAAAAAGTTG
1 AAATAAAAAGTTG
53998694 AGCATGAGTT
Statistics
Matches: 36, Mismatches: 5, Indels: 4
0.80 0.11 0.09
Matches are distributed among these distances:
29 2 0.06
30 23 0.64
31 11 0.31
ACGTcount: A:0.55, C:0.09, G:0.15, T:0.20
Consensus pattern (31 bp):
AAATAAAAAGTTGCTCAAAGTCTCAAAAAAA
Found at i:53999400 original size:18 final size:20
Alignment explanation
Indices: 53999363--53999406 Score: 56
Period size: 19 Copynumber: 2.3 Consensus size: 20
53999353 TAAAATGACC
*
53999363 TAAAAAACATAGAACGTCA-
1 TAAAAAACATAGAACATCAT
*
53999382 TAAAAAATATAGAA-ATCAT
1 TAAAAAACATAGAACATCAT
53999401 TAAAAA
1 TAAAAA
53999407 CAAGCTTGAA
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
18 3 0.14
19 19 0.86
ACGTcount: A:0.64, C:0.09, G:0.07, T:0.20
Consensus pattern (20 bp):
TAAAAAACATAGAACATCAT
Found at i:54000911 original size:24 final size:23
Alignment explanation
Indices: 54000879--54000987 Score: 137
Period size: 24 Copynumber: 4.6 Consensus size: 23
54000869 ACCAAACGTT
* **
54000879 GCACACATAGTGCTTATTATGTTC
1 GCACACATAGTGCTTAGTA-AATC
*
54000903 GCACACATAGTGCCATAGTAAATC
1 GCACACATAGTG-CTTAGTAAATC
54000927 GCACACATAGTGCTATAGTAAATC
1 GCACACATAGTGCT-TAGTAAATC
*
54000951 GCACACATAGTGCCATAGTAAATC
1 GCACACATAGTG-CTTAGTAAATC
54000975 GCACACATAGTGC
1 GCACACATAGTGC
54000988 ATTTGAGATT
Statistics
Matches: 76, Mismatches: 6, Indels: 7
0.85 0.07 0.08
Matches are distributed among these distances:
23 2 0.03
24 68 0.89
25 6 0.08
ACGTcount: A:0.34, C:0.24, G:0.17, T:0.25
Consensus pattern (23 bp):
GCACACATAGTGCTTAGTAAATC
Found at i:54000935 original size:48 final size:48
Alignment explanation
Indices: 54000879--54000987 Score: 175
Period size: 48 Copynumber: 2.3 Consensus size: 48
54000869 ACCAAACGTT
* **
54000879 GCACACATAGTGCT-TATTATGTTCGCACACATAGTGCCATAGTAAATC
1 GCACACATAGTGCTATAGTA-AATCGCACACATAGTGCCATAGTAAATC
54000927 GCACACATAGTGCTATAGTAAATCGCACACATAGTGCCATAGTAAATC
1 GCACACATAGTGCTATAGTAAATCGCACACATAGTGCCATAGTAAATC
54000975 GCACACATAGTGC
1 GCACACATAGTGC
54000988 ATTTGAGATT
Statistics
Matches: 57, Mismatches: 3, Indels: 2
0.92 0.05 0.03
Matches are distributed among these distances:
48 53 0.93
49 4 0.07
ACGTcount: A:0.34, C:0.24, G:0.17, T:0.25
Consensus pattern (48 bp):
GCACACATAGTGCTATAGTAAATCGCACACATAGTGCCATAGTAAATC
Found at i:54003964 original size:43 final size:42
Alignment explanation
Indices: 54003848--54003970 Score: 140
Period size: 43 Copynumber: 2.9 Consensus size: 42
54003838 GACTTATGAT
* ** *
54003848 TTACATGTAAGACCATGTCTGGGACATCAGCATCGTATTTGA
1 TTACATGTAAGACCATGTCTGGGACGTTGGCATTGTATTTGA
* * *
54003890 TTTCGTGTAAGACCTTGTCTGGGACAG-TGGCATTGATATTTGA
1 TTACATGTAAGACCATGTCTGGGAC-GTTGGCATTG-TATTTGA
* *
54003933 TTACATGTAAGACCACGCCTGGGACGTTGGCATTGTAT
1 TTACATGTAAGACCATGTCTGGGACGTTGGCATTGTAT
54003971 GAGCTTTTCG
Statistics
Matches: 66, Mismatches: 12, Indels: 6
0.79 0.14 0.07
Matches are distributed among these distances:
42 31 0.47
43 35 0.53
ACGTcount: A:0.24, C:0.18, G:0.25, T:0.33
Consensus pattern (42 bp):
TTACATGTAAGACCATGTCTGGGACGTTGGCATTGTATTTGA
Found at i:54004675 original size:34 final size:34
Alignment explanation
Indices: 54004610--54004675 Score: 80
Period size: 34 Copynumber: 1.9 Consensus size: 34
54004600 AATAGTCAAT
* * *
54004610 TTGGTAAATTTATGATATGAGCTTATTTGAAGAA
1 TTGGTAAATTCATGATATGAGATTATATGAAGAA
*
54004644 TTGGTAAGTTCATGATATGAGATTGA-ATGAAG
1 TTGGTAAATTCATGATATGAGATT-ATATGAAG
54004676 TGTATAAGGT
Statistics
Matches: 27, Mismatches: 4, Indels: 2
0.82 0.12 0.06
Matches are distributed among these distances:
34 26 0.96
35 1 0.04
ACGTcount: A:0.35, C:0.03, G:0.24, T:0.38
Consensus pattern (34 bp):
TTGGTAAATTCATGATATGAGATTATATGAAGAA
Found at i:54007297 original size:7 final size:7
Alignment explanation
Indices: 54007285--54007309 Score: 50
Period size: 7 Copynumber: 3.6 Consensus size: 7
54007275 GTTGTCTTCT
54007285 TGTTTGA
1 TGTTTGA
54007292 TGTTTGA
1 TGTTTGA
54007299 TGTTTGA
1 TGTTTGA
54007306 TGTT
1 TGTT
54007310 GTGGTGATGA
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 18 1.00
ACGTcount: A:0.12, C:0.00, G:0.28, T:0.60
Consensus pattern (7 bp):
TGTTTGA
Found at i:54008239 original size:27 final size:28
Alignment explanation
Indices: 54008183--54008252 Score: 115
Period size: 27 Copynumber: 2.5 Consensus size: 28
54008173 AAATTTGTAC
54008183 AGCACTAAGTGTGCGAGTTTGATTATAT
1 AGCACTAAGTGTGCGAGTTTGATTATAT
* *
54008211 AGCACTAGGTGTGCGAG-TTGATTTTAT
1 AGCACTAAGTGTGCGAGTTTGATTATAT
54008238 AGCACTAAGTGTGCG
1 AGCACTAAGTGTGCG
54008253 GACTCACTAT
Statistics
Matches: 39, Mismatches: 3, Indels: 1
0.91 0.07 0.02
Matches are distributed among these distances:
27 23 0.59
28 16 0.41
ACGTcount: A:0.26, C:0.13, G:0.29, T:0.33
Consensus pattern (28 bp):
AGCACTAAGTGTGCGAGTTTGATTATAT
Found at i:54017380 original size:66 final size:68
Alignment explanation
Indices: 54017251--54017380 Score: 149
Period size: 66 Copynumber: 1.9 Consensus size: 68
54017241 GGGATGTATC
* * *
54017251 CCATGTAGACAAAGAGCTACGGGAGAGGATAAATGTAGCTAGGTCGCATGTGTGATTCCAAGTGA
1 CCATGTAGACAAAGAGCTAC--G-GAGGATAAATGTAGCTAGGTCACATGGGTGATACCAAGTGA
54017316 AGGACA
63 AGGACA
* * *
54017322 CCATGTAGACAAAAGAGCTAC-GA-GATAAAT-TGGCTAGGTCACATGGGTGGTACTAAGTG
1 CCATGTAGAC-AAAGAGCTACGGAGGATAAATGTAGCTAGGTCACATGGGTGATACCAAGTG
54017381 TTCACCATGT
Statistics
Matches: 52, Mismatches: 6, Indels: 7
0.80 0.09 0.11
Matches are distributed among these distances:
66 23 0.44
67 7 0.13
68 2 0.04
71 10 0.19
72 10 0.19
ACGTcount: A:0.34, C:0.15, G:0.30, T:0.21
Consensus pattern (68 bp):
CCATGTAGACAAAGAGCTACGGAGGATAAATGTAGCTAGGTCACATGGGTGATACCAAGTGAAGG
ACA
Found at i:54018648 original size:20 final size:20
Alignment explanation
Indices: 54018625--54018666 Score: 66
Period size: 20 Copynumber: 2.1 Consensus size: 20
54018615 TCGGTGACGG
*
54018625 ATACGGGTAAGGGGTGTTAC
1 ATACCGGTAAGGGGTGTTAC
*
54018645 ATACCGGTTAGGGGTGTTAC
1 ATACCGGTAAGGGGTGTTAC
54018665 AT
1 AT
54018667 TTGGTTCGTA
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
20 20 1.00
ACGTcount: A:0.24, C:0.12, G:0.36, T:0.29
Consensus pattern (20 bp):
ATACCGGTAAGGGGTGTTAC
Found at i:54020684 original size:43 final size:44
Alignment explanation
Indices: 54020586--54020684 Score: 127
Period size: 42 Copynumber: 2.3 Consensus size: 44
54020576 AACTTTTGTT
*
54020586 TTACATTTAAGA-CTATGTCTGGGACATCGGCATCGTATTTGAG
1 TTACATGTAAGACCTATGTCTGGGACATCGGCATCGTATTTGAG
*
54020629 TT-CATGTAAGACCT-TGTCTGGGACAAT-GGCATCGATGTTTGA-
1 TTACATGTAAGACCTATGTCTGGGAC-ATCGGCATCG-TATTTGAG
54020671 TTACATGTAAGACC
1 TTACATGTAAGACC
54020685 ACGTCTAGGA
Statistics
Matches: 50, Mismatches: 2, Indels: 8
0.83 0.03 0.13
Matches are distributed among these distances:
42 27 0.54
43 23 0.46
ACGTcount: A:0.26, C:0.17, G:0.23, T:0.33
Consensus pattern (44 bp):
TTACATGTAAGACCTATGTCTGGGACATCGGCATCGTATTTGAG
Found at i:54020702 original size:43 final size:42
Alignment explanation
Indices: 54020547--54020703 Score: 147
Period size: 43 Copynumber: 3.7 Consensus size: 42
54020537 TGTGATTTCG
* * *
54020547 TGTAAGACCACGTTTGGGACATTGGCATCAACTTTTGTTTTACA
1 TGTAAGACCACGTCTGGGACATTGGCATCGA-TTTTG-ATTACA
* * * *
54020591 TTTAAGACTATGTCTGGGACATCGGCATCG-TATTTGAGTT-CA
1 TGTAAGACCACGTCTGGGACATTGGCATCGAT-TTTGA-TTACA
** *
54020633 TGTAAGACCTTGTCTGGGACAATGGCATCGATGTTTGATTACA
1 TGTAAGACCACGTCTGGGACATTGGCATCGAT-TTTGATTACA
* *
54020676 TGTAAGACCACGTCTAGGACGTTGGCAT
1 TGTAAGACCACGTCTGGGACATTGGCAT
54020704 TGTATATGTT
Statistics
Matches: 91, Mismatches: 18, Indels: 9
0.77 0.15 0.08
Matches are distributed among these distances:
42 30 0.33
43 37 0.41
44 24 0.26
ACGTcount: A:0.25, C:0.18, G:0.24, T:0.33
Consensus pattern (42 bp):
TGTAAGACCACGTCTGGGACATTGGCATCGATTTTGATTACA
Found at i:54023372 original size:23 final size:23
Alignment explanation
Indices: 54023346--54023395 Score: 68
Period size: 23 Copynumber: 2.2 Consensus size: 23
54023336 ACCCCATGCA
54023346 ATGCAACATA-ATATTATACATGG-
1 ATGCAACATACATA-TA-ACATGGC
54023369 ATGCAACATACATATAACATGGC
1 ATGCAACATACATATAACATGGC
54023392 ATGC
1 ATGC
54023396 TCAAATATAG
Statistics
Matches: 25, Mismatches: 0, Indels: 4
0.86 0.00 0.14
Matches are distributed among these distances:
22 6 0.24
23 16 0.64
24 3 0.12
ACGTcount: A:0.42, C:0.18, G:0.14, T:0.26
Consensus pattern (23 bp):
ATGCAACATACATATAACATGGC
Found at i:54023531 original size:27 final size:27
Alignment explanation
Indices: 54023430--54023535 Score: 108
Period size: 27 Copynumber: 3.9 Consensus size: 27
54023420 GAACAAATTT
** *
54023430 GTCATTTTACCTTACCAGGGTATTAT-A
1 GTCATTTTACCTTATGAGGGTATT-TCG
*
54023457 GTCATTTTACCATAT-AGGGGTATTTCG
1 GTCATTTTACCTTATGA-GGGTATTTCG
* * *
54023484 GTCATTCTACCCTATGGGGGTATTTCG
1 GTCATTTTACCTTATGAGGGTATTTCG
*
54023511 GTCATTTTACCTTTTGAGGGTATTT
1 GTCATTTTACCTTATGAGGGTATTT
54023536 TTATCATTTT
Statistics
Matches: 66, Mismatches: 10, Indels: 6
0.80 0.12 0.07
Matches are distributed among these distances:
26 2 0.03
27 64 0.97
ACGTcount: A:0.20, C:0.17, G:0.21, T:0.42
Consensus pattern (27 bp):
GTCATTTTACCTTATGAGGGTATTTCG
Found at i:54030897 original size:14 final size:15
Alignment explanation
Indices: 54030857--54030896 Score: 62
Period size: 15 Copynumber: 2.7 Consensus size: 15
54030847 CATAAATCAC
*
54030857 TTTTTTTTTTTTGAA
1 TTTTTTTTTTTCGAA
*
54030872 TTTTTTTTTTTCGGA
1 TTTTTTTTTTTCGAA
54030887 TTTTTTTTTT
1 TTTTTTTTTT
54030897 CAAACTTGTA
Statistics
Matches: 23, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
15 23 1.00
ACGTcount: A:0.07, C:0.03, G:0.07, T:0.82
Consensus pattern (15 bp):
TTTTTTTTTTTCGAA
Found at i:54040175 original size:56 final size:56
Alignment explanation
Indices: 54040089--54040217 Score: 249
Period size: 56 Copynumber: 2.3 Consensus size: 56
54040079 TCTTACATGT
54040089 AATCACATATCGATGCCACTATCCCAAATAGGGTCTTACTTGCACACAAATATTGG
1 AATCACATATCGATGCCACTATCCCAAATAGGGTCTTACTTGCACACAAATATTGG
*
54040145 AATCACATATCGATGCCACTGTCCCAAATAGGGTCTTACTTGCACACAAATATTGG
1 AATCACATATCGATGCCACTATCCCAAATAGGGTCTTACTTGCACACAAATATTGG
54040201 AATCACATATCGATGCC
1 AATCACATATCGATGCC
54040218 GTGGTCTGTA
Statistics
Matches: 72, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
56 72 1.00
ACGTcount: A:0.33, C:0.26, G:0.15, T:0.26
Consensus pattern (56 bp):
AATCACATATCGATGCCACTATCCCAAATAGGGTCTTACTTGCACACAAATATTGG
Found at i:54041268 original size:54 final size:54
Alignment explanation
Indices: 54041109--54041407 Score: 379
Period size: 54 Copynumber: 5.5 Consensus size: 54
54041099 CCAAAGTACT
* * *
54041109 CTCGATTTACAAAATTACCGTTTTACCCTCAATTTACAGAATTACCGTTTTACC
1 CTCGATTTACAGAATTACTGTTTTACCCTCAGTTTACAGAATTACCGTTTTACC
* *** *
54041163 CTCAATTTTTTGAAATTACCGTTTTACCCTCAGTTTACAGAATTACCGTTTTACC
1 CTCGATTTACAG-AATTACTGTTTTACCCTCAGTTTACAGAATTACCGTTTTACC
*
54041218 CTCGATTTACAGAATTACTGTTTTACCCTCAGTTTACAGAATTACTGTTTTACC
1 CTCGATTTACAGAATTACTGTTTTACCCTCAGTTTACAGAATTACCGTTTTACC
* * * *
54041272 CTCGATTTACAGAATTACTATTTTACGCTCGATTTGTA-A-AATTACCATTTTACC
1 CTCGATTTACAGAATTACTGTTTTACCCTC-AGTT-TACAGAATTACCGTTTTACC
* * * * *
54041326 CTTGA-TTACAGAATTTCTGGTTTACCCTCAGTTTACAAAATTATCGTTTTACC
1 CTCGATTTACAGAATTACTGTTTTACCCTCAGTTTACAGAATTACCGTTTTACC
*
54041379 CTCGATTTATAGAATTACTGTTTTACCCT
1 CTCGATTTACAGAATTACTGTTTTACCCT
54041408 TGATTGTGAA
Statistics
Matches: 210, Mismatches: 29, Indels: 12
0.84 0.12 0.05
Matches are distributed among these distances:
51 2 0.01
52 4 0.02
53 37 0.18
54 112 0.53
55 53 0.25
56 2 0.01
ACGTcount: A:0.27, C:0.22, G:0.10, T:0.41
Consensus pattern (54 bp):
CTCGATTTACAGAATTACTGTTTTACCCTCAGTTTACAGAATTACCGTTTTACC
Found at i:54041303 original size:81 final size:81
Alignment explanation
Indices: 54041114--54041407 Score: 349
Period size: 80 Copynumber: 3.6 Consensus size: 81
54041104 GTACTCTCGA
* * ***
54041114 TTTACAAAATTACCGTTTTACCCTCAATTTACAGAATTACCGTTTTACCCTCAATTTTTTGAAAT
1 TTTACAAAATTACCGTTTTACCCTCGATTTACAGAATTACCGTTTTACCCTCAGTTTACAG-AAT
*
54041179 TACCGTTTTACCCTCAG
65 TACTGTTTTACCCTCAG
* *
54041196 TTTACAGAATTACCGTTTTACCCTCGATTTACAGAATTACTGTTTTACCCTCAGTTTACAGAATT
1 TTTACAAAATTACCGTTTTACCCTCGATTTACAGAATTACCGTTTTACCCTCAGTTTACAGAATT
54041261 ACTGTTTTACCCTC-G
66 ACTGTTTTACCCTCAG
* ** * ** * * * *
54041276 ATTTACAGAATTACTATTTTACGCTCGATTTGTAAAATTACCATTTTACCCT-TGATTACAGAAT
1 -TTTACAAAATTACCGTTTTACCCTCGATTTACAGAATTACCGTTTTACCCTCAGTTTACAGAAT
* *
54041340 TTCTGGTTTACCCTCAG
65 TACTGTTTTACCCTCAG
* * *
54041357 TTTACAAAATTATCGTTTTACCCTCGATTTATAGAATTACTGTTTTACCCT
1 TTTACAAAATTACCGTTTTACCCTCGATTTACAGAATTACCGTTTTACCCT
54041408 TGATTGTGAA
Statistics
Matches: 181, Mismatches: 29, Indels: 6
0.84 0.13 0.03
Matches are distributed among these distances:
80 66 0.36
81 61 0.34
82 54 0.30
ACGTcount: A:0.27, C:0.22, G:0.10, T:0.41
Consensus pattern (81 bp):
TTTACAAAATTACCGTTTTACCCTCGATTTACAGAATTACCGTTTTACCCTCAGTTTACAGAATT
ACTGTTTTACCCTCAG
Found at i:54041368 original size:107 final size:107
Alignment explanation
Indices: 54041080--54041422 Score: 388
Period size: 109 Copynumber: 3.2 Consensus size: 107
54041070 TACTGAAATG
*** * * * * *
54041080 CCCTCGACTTGTAAAATTACCAAAGTACTCTCGATTTACAAAATTACCGTTTTACCCTCAATTTA
1 CCCTCGA-TTGTAAAATTACCATTTTACCCTCGATTTACAGAATTACTGGTTTACCCTCAGTTTA
* * * * *
54041145 CAGAATTACCGTTTTACCCTCAATTTTTTGAAATTACCGTTTTA
65 CAGAATTACTGTTTTACCCTCGATTTATAG-AATTACTGTTTTA
* *
54041189 CCCTC-AGTT-TACAGAATTACCGTTTTACCCTCGATTTACAGAATTACTGTTTTACCCTCAGTT
1 CCCTCGA-TTGTA-A-AATTACCATTTTACCCTCGATTTACAGAATTACTGGTTTACCCTCAGTT
* *
54041252 TACAGAATTACTGTTTTACCCTCGATTTACAGAATTACTATTTTA
63 TACAGAATTACTGTTTTACCCTCGATTTATAGAATTACTGTTTTA
* * *
54041297 CGCTCGATTTGTAAAATTACCATTTTACCCTTGA-TTACAGAATTTCTGGTTTACCCTCAGTTTA
1 CCCTCGA-TTGTAAAATTACCATTTTACCCTCGATTTACAGAATTACTGGTTTACCCTCAGTTTA
*
54041361 CAAAATTA-TCGTTTTACCCTCGATTTATAGAATTACTGTTTTA
65 CAGAATTACT-GTTTTACCCTCGATTTATAGAATTACTGTTTTA
* *
54041404 CCCTTGATTGTGAAATTAC
1 CCCTCGATTGTAAAATTAC
54041423 TGAAATACCC
Statistics
Matches: 201, Mismatches: 28, Indels: 13
0.83 0.12 0.05
Matches are distributed among these distances:
106 12 0.06
107 73 0.36
108 37 0.18
109 77 0.38
110 2 0.01
ACGTcount: A:0.28, C:0.22, G:0.10, T:0.40
Consensus pattern (107 bp):
CCCTCGATTGTAAAATTACCATTTTACCCTCGATTTACAGAATTACTGGTTTACCCTCAGTTTAC
AGAATTACTGTTTTACCCTCGATTTATAGAATTACTGTTTTA
Found at i:54041412 original size:27 final size:27
Alignment explanation
Indices: 54041109--54041412 Score: 321
Period size: 27 Copynumber: 11.3 Consensus size: 27
54041099 CCAAAGTACT
* *
54041109 CTCGATTTACAAAATTACCGTTTTACC
1 CTCGATTTACAGAATTACTGTTTTACC
* *
54041136 CTCAATTTACAGAATTACCGTTTTACC
1 CTCGATTTACAGAATTACTGTTTTACC
* *** *
54041163 CTCAATTTTTTGAAATTACCGTTTTACC
1 CTCGATTTACAG-AATTACTGTTTTACC
*
54041191 CTC-AGTTTACAGAATTACCGTTTTACC
1 CTCGA-TTTACAGAATTACTGTTTTACC
54041218 CTCGATTTACAGAATTACTGTTTTACC
1 CTCGATTTACAGAATTACTGTTTTACC
54041245 CTC-AGTTTACAGAATTACTGTTTTACC
1 CTCGA-TTTACAGAATTACTGTTTTACC
* *
54041272 CTCGATTTACAGAATTACTATTTTACG
1 CTCGATTTACAGAATTACTGTTTTACC
** * **
54041299 CTCGATTTGTAAAATTACCATTTTACC
1 CTCGATTTACAGAATTACTGTTTTACC
* * *
54041326 CTTGA-TTACAGAATTTCTGGTTTACC
1 CTCGATTTACAGAATTACTGTTTTACC
*
54041352 CTC-AGTTTACAAAATTA-TCGTTTTACC
1 CTCGA-TTTACAGAATTACT-GTTTTACC
*
54041379 CTCGATTTATAGAATTACTGTTTTACC
1 CTCGATTTACAGAATTACTGTTTTACC
*
54041406 CTTGATT
1 CTCGATT
54041413 GTGAAATTAC
Statistics
Matches: 236, Mismatches: 31, Indels: 20
0.82 0.11 0.07
Matches are distributed among these distances:
25 1 0.00
26 18 0.08
27 191 0.81
28 26 0.11
ACGTcount: A:0.27, C:0.22, G:0.10, T:0.41
Consensus pattern (27 bp):
CTCGATTTACAGAATTACTGTTTTACC
Found at i:54041446 original size:107 final size:107
Alignment explanation
Indices: 54041226--54041451 Score: 260
Period size: 107 Copynumber: 2.1 Consensus size: 107
54041216 CCCTCGATTT
* * *
54041226 ACAGAATTACTGTTTTACCCTCAGTTTACAGAATTACTGTTTTACCCTCGATTTACAGAATTACT
1 ACAGAATTTCTGGTTTACCCTCAGTTTACAAAATTACTGTTTTACCCTCGATTTACAGAATTACT
* ** * **
54041291 ATTTTACGCTCGATTTGTAAAATTACCATTTTACCCTTGATT
66 ATTTTACCCTCGATTTGTAAAATTACCATAATACCCCTGAGG
*
54041333 ACAGAATTTCTGGTTTACCCTCAGTTTACAAAATTA-TCGTTTTACCCTCGATTTATAGAATTAC
1 ACAGAATTTCTGGTTTACCCTCAGTTTACAAAATTACT-GTTTTACCCTCGATTTACAGAATTAC
* * * *
54041397 TGTTTTACCCTTGA-TTGTGAAATTACTGA-AATACCCCTGTAGG
65 TATTTTACCCTCGATTTGTAAAATTAC-CATAATACCCCTG-AGG
**
54041440 GTAGAATTTCTG
1 ACAGAATTTCTG
54041452 AAATACCCCT
Statistics
Matches: 100, Mismatches: 16, Indels: 6
0.82 0.13 0.05
Matches are distributed among these distances:
106 19 0.19
107 81 0.81
ACGTcount: A:0.28, C:0.19, G:0.13, T:0.40
Consensus pattern (107 bp):
ACAGAATTTCTGGTTTACCCTCAGTTTACAAAATTACTGTTTTACCCTCGATTTACAGAATTACT
ATTTTACCCTCGATTTGTAAAATTACCATAATACCCCTGAGG
Found at i:54041447 original size:27 final size:27
Alignment explanation
Indices: 54041417--54041611 Score: 230
Period size: 27 Copynumber: 7.2 Consensus size: 27
54041407 TTGATTGTGA
54041417 AATTACTGAAATACCCCTGTAGGGTAG
1 AATTACTGAAATACCCCTGTAGGGTAG
* * *
54041444 AATTTCTGAAATACCCCTATAAGGTAG
1 AATTACTGAAATACCCCTGTAGGGTAG
* * *
54041471 AATTACTGAAATACCCTTATAGGATAG
1 AATTACTGAAATACCCCTGTAGGGTAG
*
54041498 AATTACTAAAATACCCCTGTAGGGTAG
1 AATTACTGAAATACCCCTGTAGGGTAG
*
54041525 AATTA-TCGAAATACCCTTGTAGGGTAG
1 AATTACT-GAAATACCCCTGTAGGGTAG
* **
54041552 AAATACCAAAATACCCCTGTAGGGTAG
1 AATTACTGAAATACCCCTGTAGGGTAG
* * * * *
54041579 AATTACCGAGATACCCTTGTGGGGTAA
1 AATTACTGAAATACCCCTGTAGGGTAG
54041606 AATTAC
1 AATTAC
54041612 CATTTTGCCC
Statistics
Matches: 143, Mismatches: 23, Indels: 4
0.84 0.14 0.02
Matches are distributed among these distances:
26 1 0.01
27 142 0.99
ACGTcount: A:0.36, C:0.18, G:0.19, T:0.27
Consensus pattern (27 bp):
AATTACTGAAATACCCCTGTAGGGTAG
Found at i:54041485 original size:54 final size:54
Alignment explanation
Indices: 54041417--54041611 Score: 257
Period size: 54 Copynumber: 3.6 Consensus size: 54
54041407 TTGATTGTGA
* * * * *
54041417 AATTACTGAAATACCCCTGTAGGGTAGAATTTCTGAAATACCCCTATAAGGTAG
1 AATTACTGAAATACCCTTGTAGGGTAGAATTACTAAAATACCCCTGTAGGGTAG
* *
54041471 AATTACTGAAATACCCTTATAGGATAGAATTACTAAAATACCCCTGTAGGGTAG
1 AATTACTGAAATACCCTTGTAGGGTAGAATTACTAAAATACCCCTGTAGGGTAG
* *
54041525 AATTA-TCGAAATACCCTTGTAGGGTAGAAATACCAAAATACCCCTGTAGGGTAG
1 AATTACT-GAAATACCCTTGTAGGGTAGAATTACTAAAATACCCCTGTAGGGTAG
* * * *
54041579 AATTACCGAGATACCCTTGTGGGGTAAAATTAC
1 AATTACTGAAATACCCTTGTAGGGTAGAATTAC
54041612 CATTTTGCCC
Statistics
Matches: 123, Mismatches: 16, Indels: 4
0.86 0.11 0.03
Matches are distributed among these distances:
53 1 0.01
54 122 0.99
ACGTcount: A:0.36, C:0.18, G:0.19, T:0.27
Consensus pattern (54 bp):
AATTACTGAAATACCCTTGTAGGGTAGAATTACTAAAATACCCCTGTAGGGTAG
Found at i:54041986 original size:22 final size:22
Alignment explanation
Indices: 54041954--54042012 Score: 64
Period size: 22 Copynumber: 2.7 Consensus size: 22
54041944 CCCGTTATTA
*
54041954 ATGGCTCTGTGCCAACCTAAAT
1 ATGGCTTTGTGCCAACCTAAAT
* * * *
54041976 ATGGCTTTGTGCCATCTTGACT
1 ATGGCTTTGTGCCAACCTAAAT
*
54041998 ATGGCTTCGTGCCAA
1 ATGGCTTTGTGCCAA
54042013 ACGTATTTAC
Statistics
Matches: 30, Mismatches: 7, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
22 30 1.00
ACGTcount: A:0.20, C:0.25, G:0.22, T:0.32
Consensus pattern (22 bp):
ATGGCTTTGTGCCAACCTAAAT
Found at i:54042199 original size:27 final size:27
Alignment explanation
Indices: 54042177--54042250 Score: 89
Period size: 27 Copynumber: 2.8 Consensus size: 27
54042167 TAGGTGGGTT
*
54042177 TGCCACATTATCTG-ATTCTGGTGGCTC
1 TGCCACAATATCTGTA-TCTGGTGGCTC
*
54042204 TGCCACAATATCTGTATCTGGTGACTC
1 TGCCACAATATCTGTATCTGGTGGCTC
* *
54042231 TGTCACGATATCTGT-TCTGG
1 TGCCACAATATCTGTATCTGG
54042251 CAGCCATGCT
Statistics
Matches: 42, Mismatches: 4, Indels: 3
0.86 0.08 0.06
Matches are distributed among these distances:
26 5 0.12
27 36 0.86
28 1 0.02
ACGTcount: A:0.18, C:0.24, G:0.22, T:0.36
Consensus pattern (27 bp):
TGCCACAATATCTGTATCTGGTGGCTC
Found at i:54042377 original size:6 final size:6
Alignment explanation
Indices: 54042368--54042444 Score: 88
Period size: 6 Copynumber: 12.8 Consensus size: 6
54042358 TTGCATTCAC
* *
54042368 ATTCTG ATTCTG ATTTTG ATTCTG -TTACTA ATAT-TG ATTCTG ATTCTG
1 ATTCTG ATTCTG ATTCTG ATTCTG ATT-CTG AT-TCTG ATTCTG ATTCTG
54042416 ATTCTG -TTACTG ATTCTG ATTCTG ATTCT
1 ATTCTG ATT-CTG ATTCTG ATTCTG ATTCT
54042445 CATTTTGGTT
Statistics
Matches: 61, Mismatches: 4, Indels: 12
0.79 0.05 0.16
Matches are distributed among these distances:
5 5 0.08
6 52 0.85
7 3 0.05
8 1 0.02
ACGTcount: A:0.19, C:0.14, G:0.14, T:0.52
Consensus pattern (6 bp):
ATTCTG
Found at i:54042465 original size:30 final size:30
Alignment explanation
Indices: 54042368--54042444 Score: 120
Period size: 30 Copynumber: 2.6 Consensus size: 30
54042358 TTGCATTCAC
*
54042368 ATTCTGATTCTGATTTTGATTCTGTTACTA
1 ATTCTGATTCTGATTCTGATTCTGTTACTA
*
54042398 ATAT-TGATTCTGATTCTGATTCTGTTACTG
1 AT-TCTGATTCTGATTCTGATTCTGTTACTA
54042428 ATTCTGATTCTGATTCT
1 ATTCTGATTCTGATTCT
54042445 CATTTTGGTT
Statistics
Matches: 43, Mismatches: 2, Indels: 4
0.88 0.04 0.08
Matches are distributed among these distances:
29 1 0.02
30 41 0.95
31 1 0.02
ACGTcount: A:0.19, C:0.14, G:0.14, T:0.52
Consensus pattern (30 bp):
ATTCTGATTCTGATTCTGATTCTGTTACTA
Found at i:54050271 original size:43 final size:43
Alignment explanation
Indices: 54050205--54050759 Score: 545
Period size: 43 Copynumber: 13.0 Consensus size: 43
54050195 ATATCGTACA
* * * *
54050205 ATGCCAATGTCCCAAATGTGGTCTTACATGTAATCACATATCG
1 ATGCCACTGTCCCAGACGTGGTCTTACACGTAATCACATATCG
* * * * * * *
54050248 ATGCCACTATCCTAAATAG-GGTCTTAAAC-AAATCAAATA-CG
1 ATGCCACTGTCCCAGA-CGTGGTCTTACACGTAATCACATATCG
** * * * * *
54050289 ATATCAATGTCCTAGACATGGTCATACACATAATCACATATCG
1 ATGCCACTGTCCCAGACGTGGTCTTACACGTAATCACATATCG
* * * *
54050332 ATGCCAAC-ATCTCAGACGTCGTCTTACATGTAATCACATATCG
1 ATGCC-ACTGTCCCAGACGTGGTCTTACACGTAATCACATATCG
* ** * *
54050375 ATGCCAAC-ATCCCAGACGTCATCTTACATGTAATCACATATGG
1 ATGCC-ACTGTCCCAGACGTGGTCTTACACGTAATCACATATCG
* * *
54050418 ATGCCAATGTCCCAGACGTTGTCTTACATGTAATCACATATCG
1 ATGCCACTGTCCCAGACGTGGTCTTACACGTAATCACATATCG
* * * * *
54050461 ACGCCAATGTCCTAGACGTTGTCCTACACGTAATCACATATCG
1 ATGCCACTGTCCCAGACGTGGTCTTACACGTAATCACATATCG
* * *
54050504 ATGCCAATGTCCTAGACGTGGTCTTACACGTAATCACATATTG
1 ATGCCACTGTCCCAGACGTGGTCTTACACGTAATCACATATCG
* *
54050547 ATGCCAAC-GTCCCAGACGTGGTCTTACATGTAATCACTTATCG
1 ATGCC-ACTGTCCCAGACGTGGTCTTACACGTAATCACATATCG
* * * *
54050590 ATGCCAAC-ATCCAAGACATGGTCTTACACATAATCACATATCG
1 ATGCC-ACTGTCCCAGACGTGGTCTTACACGTAATCACATATCG
*
54050633 ATGCCAAC-GTCCCAGACGGGGTCTTACACGTAATCACATATCG
1 ATGCC-ACTGTCCCAGACGTGGTCTTACACGTAATCACATATCG
*
54050676 ATGCCACTGTCCCAGACAG-GGTCTTACACGTAATCACATATAG
1 ATGCCACTGTCCCAGAC-GTGGTCTTACACGTAATCACATATCG
*
54050719 ATGCCAAC-GTCCCAGACGTGGTCTTACACATAATCACATAT
1 ATGCC-ACTGTCCCAGACGTGGTCTTACACGTAATCACATAT
54050760 TGAAATCACA
Statistics
Matches: 437, Mismatches: 64, Indels: 22
0.84 0.12 0.04
Matches are distributed among these distances:
41 21 0.05
42 20 0.05
43 390 0.89
44 6 0.01
ACGTcount: A:0.31, C:0.27, G:0.16, T:0.26
Consensus pattern (43 bp):
ATGCCACTGTCCCAGACGTGGTCTTACACGTAATCACATATCG
Found at i:54050494 original size:129 final size:129
Alignment explanation
Indices: 54050293--54050759 Score: 605
Period size: 129 Copynumber: 3.6 Consensus size: 129
54050283 AATACGATAT
* * * ** *
54050293 CAATGTCCTAGACATGGTCATACACATAATCACATATCGATGCCAACAT-CTCAGACGTCGTCTT
1 CAATGTCCCAGACGTGGTCTTACATGTAATCACATATCGATGCCAACATCCT-AGACGTGGTCTT
** * ** * *
54050357 ACATGTAATCACATATCGATGCCAACATCCCAGACGTCATCTTACATGTAATCACATATGGATGC
65 ACACATAATCACATATCGATGCCAACGTCCCAGACGTGGTCTTACACGTAATCACATATCGATGC
* * ** * *
54050422 CAATGTCCCAGACGTTGTCTTACATGTAATCACATATCGACGCCAATGTCCTAGACGTTGTCCTA
1 CAATGTCCCAGACGTGGTCTTACATGTAATCACATATCGATGCCAACATCCTAGACGTGGTCTTA
* * * *
54050487 CACGTAATCACATATCGATGCCAATGTCCTAGACGTGGTCTTACACGTAATCACATATTGATGC
66 CACATAATCACATATCGATGCCAACGTCCCAGACGTGGTCTTACACGTAATCACATATCGATGC
* * * *
54050551 CAACGTCCCAGACGTGGTCTTACATGTAATCACTTATCGATGCCAACATCCAAGACATGGTCTTA
1 CAATGTCCCAGACGTGGTCTTACATGTAATCACATATCGATGCCAACATCCTAGACGTGGTCTTA
*
54050616 CACATAATCACATATCGATGCCAACGTCCCAGACGGGGTCTTACACGTAATCACATATCGATGC
66 CACATAATCACATATCGATGCCAACGTCCCAGACGTGGTCTTACACGTAATCACATATCGATGC
* * * * *
54050680 CACTGTCCCAGACAG-GGTCTTACACGTAATCACATATAGATGCCAACGTCCCAGACGTGGTCTT
1 CAATGTCCCAGAC-GTGGTCTTACATGTAATCACATATCGATGCCAACATCCTAGACGTGGTCTT
54050744 ACACATAATCACATAT
65 ACACATAATCACATAT
54050760 TGAAATCACA
Statistics
Matches: 294, Mismatches: 42, Indels: 4
0.86 0.12 0.01
Matches are distributed among these distances:
129 291 0.99
130 3 0.01
ACGTcount: A:0.30, C:0.28, G:0.16, T:0.26
Consensus pattern (129 bp):
CAATGTCCCAGACGTGGTCTTACATGTAATCACATATCGATGCCAACATCCTAGACGTGGTCTTA
CACATAATCACATATCGATGCCAACGTCCCAGACGTGGTCTTACACGTAATCACATATCGATGC
Found at i:54058986 original size:40 final size:40
Alignment explanation
Indices: 54058942--54059062 Score: 179
Period size: 40 Copynumber: 3.0 Consensus size: 40
54058932 AGAATTGAGA
* * *
54058942 GTTATATCCGGGTTAAGTCCCGAAGAGCATTCATGCTGGT
1 GTTATATCTGGGCTAAGTCCCGAAGAGCATTCGTGCTGGT
54058982 GTTATATCTGGGCTAAGTCCCGAAGAGCATTCGTGCTGGT
1 GTTATATCTGGGCTAAGTCCCGAAGAGCATTCGTGCTGGT
* * * *
54059022 GTTACATCTGGGCTAAGTCCTGAAGGGCATTCGTGCCGGT
1 GTTATATCTGGGCTAAGTCCCGAAGAGCATTCGTGCTGGT
54059062 G
1 G
54059063 ATGTGTATTC
Statistics
Matches: 74, Mismatches: 7, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
40 74 1.00
ACGTcount: A:0.20, C:0.21, G:0.31, T:0.29
Consensus pattern (40 bp):
GTTATATCTGGGCTAAGTCCCGAAGAGCATTCGTGCTGGT
Found at i:54059112 original size:43 final size:43
Alignment explanation
Indices: 54059051--54059138 Score: 140
Period size: 43 Copynumber: 2.0 Consensus size: 43
54059041 CTGAAGGGCA
*
54059051 TTCGTGCCGGTGATGTGTATTCGGGCCTTCGTTCCTAGCAGGC
1 TTCGTGCCGGTGATGTGTATTCGGGCCTTCGTGCCTAGCAGGC
* * *
54059094 TTCGTGCCGGTGATGTGTATTTGGGTCTTCGTGCTTAGCAGGC
1 TTCGTGCCGGTGATGTGTATTCGGGCCTTCGTGCCTAGCAGGC
54059137 TT
1 TT
54059139 AATGCCGATG
Statistics
Matches: 41, Mismatches: 4, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
43 41 1.00
ACGTcount: A:0.09, C:0.22, G:0.33, T:0.36
Consensus pattern (43 bp):
TTCGTGCCGGTGATGTGTATTCGGGCCTTCGTGCCTAGCAGGC
Found at i:54059145 original size:43 final size:43
Alignment explanation
Indices: 54059055--54059150 Score: 129
Period size: 43 Copynumber: 2.2 Consensus size: 43
54059045 AGGGCATTCG
* **
54059055 TGCCGGTGATGTGTATTCGGGCCTTCGTTCCTAGCAGGCTTCG
1 TGCCGGTGATGTGTATTCGGGCCTTCGTGCCTAGCAGGCTTAA
* * *
54059098 TGCCGGTGATGTGTATTTGGGTCTTCGTGCTTAGCAGGCTTAA
1 TGCCGGTGATGTGTATTCGGGCCTTCGTGCCTAGCAGGCTTAA
*
54059141 TGCCGATGAT
1 TGCCGGTGAT
54059151 TCGAGCAAAG
Statistics
Matches: 46, Mismatches: 7, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
43 46 1.00
ACGTcount: A:0.12, C:0.21, G:0.32, T:0.34
Consensus pattern (43 bp):
TGCCGGTGATGTGTATTCGGGCCTTCGTGCCTAGCAGGCTTAA
Found at i:54059308 original size:25 final size:25
Alignment explanation
Indices: 54059269--54059323 Score: 85
Period size: 25 Copynumber: 2.2 Consensus size: 25
54059259 TGTGTAATAA
54059269 CGAATGAATATAGGCACTATGGGTG
1 CGAATGAATATAGGCACTATGGGTG
*
54059294 CGAATGAAT-TGAGGCACTATGTGTG
1 CGAATGAATAT-AGGCACTATGGGTG
54059319 CGAAT
1 CGAAT
54059324 TCTTTAATCG
Statistics
Matches: 28, Mismatches: 1, Indels: 2
0.90 0.03 0.06
Matches are distributed among these distances:
24 1 0.04
25 27 0.96
ACGTcount: A:0.31, C:0.13, G:0.31, T:0.25
Consensus pattern (25 bp):
CGAATGAATATAGGCACTATGGGTG
Found at i:54059342 original size:28 final size:28
Alignment explanation
Indices: 54059307--54059405 Score: 103
Period size: 28 Copynumber: 3.5 Consensus size: 28
54059297 ATGAATTGAG
54059307 GCACTATGTGTGCGAATTCTTTAATCGA
1 GCACTATGTGTGCGAATTCTTTAATCGA
* * * *
54059335 GCACTATGTGTGCGAGA-TCAGTCAGT-GG
1 GCACTATGTGTGCGA-ATTC-TTTAATCGA
* *
54059363 GCACTGTGTGTGCGAATTCTTTAACCGA
1 GCACTATGTGTGCGAATTCTTTAATCGA
*
54059391 GCAATATGTGTGCGA
1 GCACTATGTGTGCGA
54059406 GATCGTCAGT
Statistics
Matches: 55, Mismatches: 12, Indels: 8
0.73 0.16 0.11
Matches are distributed among these distances:
27 3 0.05
28 48 0.87
29 4 0.07
ACGTcount: A:0.23, C:0.18, G:0.28, T:0.30
Consensus pattern (28 bp):
GCACTATGTGTGCGAATTCTTTAATCGA
Found at i:54059373 original size:56 final size:55
Alignment explanation
Indices: 54059306--54059431 Score: 216
Period size: 56 Copynumber: 2.3 Consensus size: 55
54059296 AATGAATTGA
* * *
54059306 GGCACTATGTGTGCGAATTCTTTAATCGAGCACTATGTGTGCGAGATCAGTCAGTG
1 GGCACTGTGTGTGCGAATTCTTTAACCGAGCAATATGTGTGCGAGATC-GTCAGTG
54059362 GGCACTGTGTGTGCGAATTCTTTAACCGAGCAATATGTGTGCGAGATCGTCAGTG
1 GGCACTGTGTGTGCGAATTCTTTAACCGAGCAATATGTGTGCGAGATCGTCAGTG
54059417 GGCACTGTGTGTGCG
1 GGCACTGTGTGTGCG
54059432 GATTTCGTTT
Statistics
Matches: 67, Mismatches: 3, Indels: 1
0.94 0.04 0.01
Matches are distributed among these distances:
55 22 0.33
56 45 0.67
ACGTcount: A:0.21, C:0.18, G:0.32, T:0.29
Consensus pattern (55 bp):
GGCACTGTGTGTGCGAATTCTTTAACCGAGCAATATGTGTGCGAGATCGTCAGTG
Found at i:54067895 original size:43 final size:42
Alignment explanation
Indices: 54067822--54067944 Score: 176
Period size: 43 Copynumber: 2.9 Consensus size: 42
54067812 TCTAAACTCA
* **
54067822 TTCACCGGCATT-TCGCTGCTAGGCTTGAAGCCCGATATCAT
1 TTCACCGGCATTATAGCTGCTAGGCCCGAAGCCCGATATCAT
*
54067863 TTCACCGGCATTATAGCTTGCTAGGCCCGAAGCCCGATATTAT
1 TTCACCGGCATTATAGC-TGCTAGGCCCGAAGCCCGATATCAT
*
54067906 CTCACCGGCATTATAGCCTGCTAGGCCCGAAGCCCGATA
1 TTCACCGGCATTATAG-CTGCTAGGCCCGAAGCCCGATA
54067945 ATATTATTCA
Statistics
Matches: 74, Mismatches: 5, Indels: 4
0.89 0.06 0.05
Matches are distributed among these distances:
41 12 0.16
42 3 0.04
43 58 0.78
44 1 0.01
ACGTcount: A:0.22, C:0.31, G:0.22, T:0.25
Consensus pattern (42 bp):
TTCACCGGCATTATAGCTGCTAGGCCCGAAGCCCGATATCAT
Found at i:54069662 original size:14 final size:15
Alignment explanation
Indices: 54069633--54069662 Score: 53
Period size: 15 Copynumber: 2.1 Consensus size: 15
54069623 CAAAATTTAG
54069633 ACATGATACTTTCAC
1 ACATGATACTTTCAC
54069648 ACATGATAC-TTCAC
1 ACATGATACTTTCAC
54069662 A
1 A
54069663 TATAATAAAC
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
14 6 0.40
15 9 0.60
ACGTcount: A:0.37, C:0.27, G:0.07, T:0.30
Consensus pattern (15 bp):
ACATGATACTTTCAC
Found at i:54073516 original size:42 final size:43
Alignment explanation
Indices: 54073413--54073539 Score: 136
Period size: 42 Copynumber: 3.0 Consensus size: 43
54073403 ATGTGTCTTC
* * * *
54073413 GTGTAAGACCACATCTGGGA-TGTTGGCATCGACT-TATGATTTAC
1 GTGTAAGACCATATCTGGGACAG-TGGCATCGA-TATTTGATTT-T
*
54073457 GTGTAAGACCATGTCTGGGACA-TCGGCATC-ATATTTGATTTT
1 GTGTAAGACCATATCTGGGACAGT-GGCATCGATATTTGATTTT
*
54073499 GTGTAAGACCCTATCTGGGACAGTGGCATCGATATTTGATT
1 GTGTAAGACCATATCTGGGACAGTGGCATCGATATTTGATT
54073540 ACATGTAAGA
Statistics
Matches: 71, Mismatches: 7, Indels: 11
0.80 0.08 0.12
Matches are distributed among these distances:
42 27 0.38
43 20 0.28
44 24 0.34
ACGTcount: A:0.24, C:0.17, G:0.25, T:0.33
Consensus pattern (43 bp):
GTGTAAGACCATATCTGGGACAGTGGCATCGATATTTGATTTT
Found at i:54073569 original size:43 final size:43
Alignment explanation
Indices: 54073412--54073570 Score: 155
Period size: 43 Copynumber: 3.7 Consensus size: 43
54073402 TATGTGTCTT
* *
54073412 CGTGTAAGACCACATCTGGGATGTTGGCATCGACT-TATGATTTA
1 CGTGTAAGACCACATCTGGGACGTTGGCATCGA-TATTTGA-TTA
** * * *
54073456 CGTGTAAGACCATGTCTGGGACATCGGCATC-ATATTTGATTT
1 CGTGTAAGACCACATCTGGGACGTTGGCATCGATATTTGATTA
*
54073498 TGTGTAAGACC-CTATCTGGGACAG-TGGCATCGATATTTGATTA
1 CGTGTAAGACCAC-ATCTGGGAC-GTTGGCATCGATATTTGATTA
* * *
54073541 CATGTAAGACCACGTCTGGAACGTTGGCAT
1 CGTGTAAGACCACATCTGGGACGTTGGCAT
54073571 TGTATGAGCT
Statistics
Matches: 92, Mismatches: 17, Indels: 13
0.75 0.14 0.11
Matches are distributed among these distances:
42 28 0.30
43 37 0.40
44 27 0.29
ACGTcount: A:0.25, C:0.19, G:0.25, T:0.31
Consensus pattern (43 bp):
CGTGTAAGACCACATCTGGGACGTTGGCATCGATATTTGATTA
Found at i:54075566 original size:40 final size:40
Alignment explanation
Indices: 54075483--54075646 Score: 179
Period size: 40 Copynumber: 4.1 Consensus size: 40
54075473 CGGAATTTAG
* ** *
54075483 CCGGATATAACCACAAGCA-AAATTGCCTTTGGGTCTTAAC
1 CCGGATATAACAACTCGCACAAA-TGCCTTCGGGTCTTAAC
* * * *
54075523 CCGGGTATAGCAACTCGTACAAATGCCTTCGGGTCTTAGC
1 CCGGATATAACAACTCGCACAAATGCCTTCGGGTCTTAAC
54075563 CCGGATATAACAACTCGCACAAATGCCTTCGGGTCTTAAC
1 CCGGATATAACAACTCGCACAAATGCCTTCGGGTCTTAAC
* * * * *
54075603 CCGGATATAATC-ACTAGCATAAATGTCTTCGGGGCTTAGC
1 CCGGATATAA-CAACTCGCACAAATGCCTTCGGGTCTTAAC
54075643 CCGG
1 CCGG
54075647 GTATCATTCA
Statistics
Matches: 105, Mismatches: 17, Indels: 4
0.83 0.13 0.03
Matches are distributed among these distances:
40 101 0.96
41 4 0.04
ACGTcount: A:0.27, C:0.27, G:0.21, T:0.24
Consensus pattern (40 bp):
CCGGATATAACAACTCGCACAAATGCCTTCGGGTCTTAAC
Found at i:54075602 original size:80 final size:80
Alignment explanation
Indices: 54075479--54075646 Score: 198
Period size: 80 Copynumber: 2.1 Consensus size: 80
54075469 TCTTCGGAAT
* * * * *
54075479 TTAG-CCGGATATAACCACAAGCAAAATTGCCTTTGGGTCTTAACCCGGGTAT-AGCAACTCGTA
1 TTAGCCCGGATATAACAACAAGCAAAATTGCCTTCGGGTCTTAACCCGGATATAAGC-ACTAGCA
*
54075542 CAAATGCCTTCGGGTC
65 CAAATGCCTTCGGGGC
** *
54075558 TTAGCCCGGATATAACAACTCGCACAAA-TGCCTTCGGGTCTTAACCCGGATATAATCACTAGCA
1 TTAGCCCGGATATAACAACAAGCA-AAATTGCCTTCGGGTCTTAACCCGGATATAAGCACTAGCA
* *
54075622 TAAATGTCTTCGGGGC
65 CAAATGCCTTCGGGGC
54075638 TTAGCCCGG
1 TTAGCCCGG
54075647 GTATCATTCA
Statistics
Matches: 75, Mismatches: 11, Indels: 5
0.82 0.12 0.05
Matches are distributed among these distances:
79 4 0.05
80 66 0.88
81 5 0.07
ACGTcount: A:0.27, C:0.26, G:0.21, T:0.25
Consensus pattern (80 bp):
TTAGCCCGGATATAACAACAAGCAAAATTGCCTTCGGGTCTTAACCCGGATATAAGCACTAGCAC
AAATGCCTTCGGGGC
Found at i:54077969 original size:40 final size:40
Alignment explanation
Indices: 54077861--54078070 Score: 305
Period size: 40 Copynumber: 5.2 Consensus size: 40
54077851 CGGGATTTAA
* * * * *
54077861 CCGGATATAGCGACTCGCACGATTGCCTTCGGGTCATAAC
1 CCGGATATATCAACTCGCACGAATGCCTTCGGGTCTTAGC
* * * * * *
54077901 CCGGATTTGGT-GACTTGCACAAAGGCCTTCGGGTCTTAGC
1 CCGGATAT-ATCAACTCGCACGAATGCCTTCGGGTCTTAGC
54077941 CCGGATATATCAACTCGCACGAATGCCTTCGGGTCTTAGC
1 CCGGATATATCAACTCGCACGAATGCCTTCGGGTCTTAGC
54077981 CCGGATATATCAACTCGCACGAATGCCTTCGGGTCTTAGC
1 CCGGATATATCAACTCGCACGAATGCCTTCGGGTCTTAGC
54078021 CCGGATATATCAACTCGCACGAATGCCTTCGGGTCTTAGC
1 CCGGATATATCAACTCGCACGAATGCCTTCGGGTCTTAGC
54078061 CCGGATATAT
1 CCGGATATAT
54078071 TTCCAATGTT
Statistics
Matches: 153, Mismatches: 15, Indels: 4
0.89 0.09 0.02
Matches are distributed among these distances:
39 1 0.01
40 152 0.99
ACGTcount: A:0.22, C:0.29, G:0.24, T:0.25
Consensus pattern (40 bp):
CCGGATATATCAACTCGCACGAATGCCTTCGGGTCTTAGC
Found at i:54086099 original size:40 final size:40
Alignment explanation
Indices: 54085991--54086200 Score: 305
Period size: 40 Copynumber: 5.2 Consensus size: 40
54085981 CGGGATTTAA
* * * * *
54085991 CCGGATATAGCGACTCGCACGATTGCCTTCGGGTCATAAC
1 CCGGATATATCAACTCGCACGAATGCCTTCGGGTCTTAGC
* * * * * *
54086031 CCGGATTTGGT-GACTTGCACAAAGGCCTTCGGGTCTTAGC
1 CCGGATAT-ATCAACTCGCACGAATGCCTTCGGGTCTTAGC
54086071 CCGGATATATCAACTCGCACGAATGCCTTCGGGTCTTAGC
1 CCGGATATATCAACTCGCACGAATGCCTTCGGGTCTTAGC
54086111 CCGGATATATCAACTCGCACGAATGCCTTCGGGTCTTAGC
1 CCGGATATATCAACTCGCACGAATGCCTTCGGGTCTTAGC
54086151 CCGGATATATCAACTCGCACGAATGCCTTCGGGTCTTAGC
1 CCGGATATATCAACTCGCACGAATGCCTTCGGGTCTTAGC
54086191 CCGGATATAT
1 CCGGATATAT
54086201 TTCCAATGTT
Statistics
Matches: 153, Mismatches: 15, Indels: 4
0.89 0.09 0.02
Matches are distributed among these distances:
39 1 0.01
40 152 0.99
ACGTcount: A:0.22, C:0.29, G:0.24, T:0.25
Consensus pattern (40 bp):
CCGGATATATCAACTCGCACGAATGCCTTCGGGTCTTAGC
Found at i:54094122 original size:28 final size:29
Alignment explanation
Indices: 54094026--54094156 Score: 140
Period size: 29 Copynumber: 4.6 Consensus size: 29
54094016 TACTCGATTT
** * *
54094026 CGCACACTTAGTGCCATGCGATTT-AAGCC
1 CGCACACTTAGTGCCAT-ATATTTCCAGCA
* *** * *
54094055 CGCACACATAGTGCCATACCCTTCGAGCT
1 CGCACACTTAGTGCCATATATTTCCAGCA
54094084 CGCACACTTAGTGCCATATA-TTCCAGCA
1 CGCACACTTAGTGCCATATATTTCCAGCA
*
54094112 TGCACACTTAGTGCCATATATTTCCAGCA
1 CGCACACTTAGTGCCATATATTTCCAGCA
54094141 CGCACACTTAGTGCCA
1 CGCACACTTAGTGCCA
54094157 ATCTCGTCAC
Statistics
Matches: 86, Mismatches: 14, Indels: 4
0.83 0.13 0.04
Matches are distributed among these distances:
28 27 0.31
29 59 0.69
ACGTcount: A:0.26, C:0.33, G:0.17, T:0.24
Consensus pattern (29 bp):
CGCACACTTAGTGCCATATATTTCCAGCA
Found at i:54098067 original size:49 final size:49
Alignment explanation
Indices: 54097995--54098220 Score: 210
Period size: 49 Copynumber: 4.6 Consensus size: 49
54097985 TCTGATACGT
*
54097995 ATAGTAGTCTGCACTTAGTACTACACATGCGA-TAAACAATCCAG-TACAC
1 ATAGTAGCCTGCACTTAGTACTACACATGCGACTAAAC-AT-CAGATACAC
* * * *
54098044 ATAGTAGCCTGCACTTAGTACTACACATGTGACCTCATCATCTGATACAC
1 ATAGTAGCCTGCACTTAGTACTACACATGCGA-CTAAACATCAGATACAC
* * * * * * *
54098094 -TAGTAGCCTGCACTTAGTACTATACACGTGATCGAAGTCAT-TGAGTACGC
1 ATAGTAGCCTGCACTTAGTACTACACATGCGA-CTAA-ACATCAGA-TACAC
*
54098144 ATAGTAGCCTGCACTTAGTACTACACATGCGACTTAACAGT-ATGATACAC
1 ATAGTAGCCTGCACTTAGTACTACACATGCGACTAAACA-TCA-GATACAC
* *
54098194 GTAGTAGCCTACACTTAGTACTACACA
1 ATAGTAGCCTGCACTTAGTACTACACA
54098221 CGTGTATTCA
Statistics
Matches: 148, Mismatches: 21, Indels: 15
0.80 0.11 0.08
Matches are distributed among these distances:
49 68 0.46
50 47 0.32
51 33 0.22
ACGTcount: A:0.32, C:0.25, G:0.16, T:0.27
Consensus pattern (49 bp):
ATAGTAGCCTGCACTTAGTACTACACATGCGACTAAACATCAGATACAC
Found at i:54098156 original size:100 final size:101
Alignment explanation
Indices: 54098037--54098224 Score: 290
Period size: 100 Copynumber: 1.9 Consensus size: 101
54098027 TAAACAATCC
* * *
54098037 AGTACACATAGTAGCCTGCACTTAGTACTACACATGTGACCTCATCA-TCTGATACAC-TAGTAG
1 AGTACACATAGTAGCCTGCACTTAGTACTACACATGCGA-CTCAACAGTATGATACACGTAGTAG
* *
54098100 CCTGCACTTAGTACTATACACGTGATCGAAGTCATTG
65 CCTACACTTAGTACTACACACGTGATCGAAGTCATTG
* *
54098137 AGTACGCATAGTAGCCTGCACTTAGTACTACACATGCGACTTAACAGTATGATACACGTAGTAGC
1 AGTACACATAGTAGCCTGCACTTAGTACTACACATGCGACTCAACAGTATGATACACGTAGTAGC
54098202 CTACACTTAGTACTACACACGTG
66 CTACACTTAGTACTACACACGTG
54098225 TATTCACAAT
Statistics
Matches: 79, Mismatches: 7, Indels: 3
0.89 0.08 0.03
Matches are distributed among these distances:
99 5 0.06
100 46 0.58
101 28 0.35
ACGTcount: A:0.31, C:0.25, G:0.18, T:0.27
Consensus pattern (101 bp):
AGTACACATAGTAGCCTGCACTTAGTACTACACATGCGACTCAACAGTATGATACACGTAGTAGC
CTACACTTAGTACTACACACGTGATCGAAGTCATTG
Found at i:54100087 original size:24 final size:24
Alignment explanation
Indices: 54100058--54100105 Score: 96
Period size: 24 Copynumber: 2.0 Consensus size: 24
54100048 CACTTGTGAC
54100058 CATACAATGCTCCGTACGATGCCA
1 CATACAATGCTCCGTACGATGCCA
54100082 CATACAATGCTCCGTACGATGCCA
1 CATACAATGCTCCGTACGATGCCA
54100106 TCTGTTTACT
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
24 24 1.00
ACGTcount: A:0.29, C:0.33, G:0.17, T:0.21
Consensus pattern (24 bp):
CATACAATGCTCCGTACGATGCCA
Found at i:54102802 original size:34 final size:34
Alignment explanation
Indices: 54102764--54102838 Score: 143
Period size: 34 Copynumber: 2.2 Consensus size: 34
54102754 CAAACATAAG
54102764 AATGAGTAGATCCAGGATCAATCAATGCAATGAC
1 AATGAGTAGATCCAGGATCAATCAATGCAATGAC
54102798 AATGAGTAGATCCAGGATCAATCAATGCAATGAC
1 AATGAGTAGATCCAGGATCAATCAATGCAATGAC
54102832 AAT-AGTA
1 AATGAGTA
54102839 TCATAAAGAG
Statistics
Matches: 41, Mismatches: 0, Indels: 1
0.98 0.00 0.02
Matches are distributed among these distances:
33 4 0.10
34 37 0.90
ACGTcount: A:0.43, C:0.16, G:0.20, T:0.21
Consensus pattern (34 bp):
AATGAGTAGATCCAGGATCAATCAATGCAATGAC
Found at i:54104426 original size:21 final size:21
Alignment explanation
Indices: 54104402--54104443 Score: 84
Period size: 21 Copynumber: 2.0 Consensus size: 21
54104392 CTCTAATTTG
54104402 AACAAAAATAGATAAAATTAA
1 AACAAAAATAGATAAAATTAA
54104423 AACAAAAATAGATAAAATTAA
1 AACAAAAATAGATAAAATTAA
54104444 CAGATATACA
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 21 1.00
ACGTcount: A:0.71, C:0.05, G:0.05, T:0.19
Consensus pattern (21 bp):
AACAAAAATAGATAAAATTAA
Found at i:54108162 original size:27 final size:28
Alignment explanation
Indices: 54108132--54108231 Score: 121
Period size: 27 Copynumber: 3.5 Consensus size: 28
54108122 ATAGTGAGTC
54108132 CGCACACTTAGTGCTATAAAATC-AACT
1 CGCACACTTAGTGCTATAAAATCAAACT
* *
54108159 CGCACACCTAGTGCTATATAATCAAACT
1 CGCACACTTAGTGCTATAAAATCAAACT
* * *
54108187 CGCACACTTAGTGCTGTACAAATTTAAAACC
1 CGCACACTTAGTGCTATA-AAA--TCAAACT
54108218 CGCACACTTAGTGC
1 CGCACACTTAGTGC
54108232 AATCTCATGA
Statistics
Matches: 62, Mismatches: 7, Indels: 4
0.85 0.10 0.05
Matches are distributed among these distances:
27 21 0.34
28 20 0.32
29 2 0.03
31 19 0.31
ACGTcount: A:0.34, C:0.28, G:0.13, T:0.25
Consensus pattern (28 bp):
CGCACACTTAGTGCTATAAAATCAAACT
Found at i:54109089 original size:7 final size:7
Alignment explanation
Indices: 54109079--54109103 Score: 50
Period size: 7 Copynumber: 3.6 Consensus size: 7
54109069 TCATCACCAC
54109079 AACATCA
1 AACATCA
54109086 AACATCA
1 AACATCA
54109093 AACATCA
1 AACATCA
54109100 AACA
1 AACA
54109104 AGATGACAAC
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 18 1.00
ACGTcount: A:0.60, C:0.28, G:0.00, T:0.12
Consensus pattern (7 bp):
AACATCA
Found at i:54126878 original size:44 final size:46
Alignment explanation
Indices: 54126809--54126944 Score: 186
Period size: 44 Copynumber: 3.0 Consensus size: 46
54126799 AGGAGTGTTA
*
54126809 CAATATATATATAGCCGAAGCTATCTCAATCACGCACACTAAGTGC
1 CAATATATATATAGCCGAAGCTATCTCAATCTCGCACACTAAGTGC
* ** *
54126855 C-A-ATATATATAGCCGAAGATATCTCGGTCTCGCATACTAAGTGC
1 CAATATATATATAGCCGAAGCTATCTCAATCTCGCACACTAAGTGC
* * *
54126899 CAATATATATATAGTCGAAGCTATTTCAATCTCGCACACCAAGTGC
1 CAATATATATATAGCCGAAGCTATCTCAATCTCGCACACTAAGTGC
54126945 AAATTCATAA
Statistics
Matches: 76, Mismatches: 12, Indels: 4
0.83 0.13 0.04
Matches are distributed among these distances:
44 38 0.50
45 2 0.03
46 36 0.47
ACGTcount: A:0.35, C:0.24, G:0.15, T:0.26
Consensus pattern (46 bp):
CAATATATATATAGCCGAAGCTATCTCAATCTCGCACACTAAGTGC
Found at i:54135864 original size:30 final size:30
Alignment explanation
Indices: 54135830--54135890 Score: 77
Period size: 30 Copynumber: 2.0 Consensus size: 30
54135820 TTCCTGAGCC
*
54135830 TAGGGGAAAAAGTGTAAATATGCAAAAGTT
1 TAGGGGAAAAAGTATAAATATGCAAAAGTT
* * * *
54135860 TAGGGGCAAAATTATAAATTTTCAAAAGTT
1 TAGGGGAAAAAGTATAAATATGCAAAAGTT
54135890 T
1 T
54135891 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:0.44, C:0.05, G:0.21, T:0.30
Consensus pattern (30 bp):
TAGGGGAAAAAGTATAAATATGCAAAAGTT
Found at i:54136782 original size:24 final size:24
Alignment explanation
Indices: 54136755--54136830 Score: 59
Period size: 25 Copynumber: 3.1 Consensus size: 24
54136745 TTCAATCACA
54136755 TATGTAGTACTAAGTGCAGGCTAC
1 TATGTAGTACTAAGTGCAGGCTAC
* *
54136779 TATGT-GTA-TCAGATAGTTAGGAC-AC
1 TATGTAGTACTAAG-T-G-CAGG-CTAC
*
54136804 ATGTGTAGTACTAAGTGCAGGCTAC
1 -TATGTAGTACTAAGTGCAGGCTAC
54136829 TA
1 TA
54136831 CGTGTACCAG
Statistics
Matches: 38, Mismatches: 6, Indels: 16
0.63 0.10 0.27
Matches are distributed among these distances:
22 3 0.08
23 4 0.11
24 8 0.21
25 10 0.26
26 6 0.16
27 4 0.11
28 3 0.08
ACGTcount: A:0.30, C:0.14, G:0.25, T:0.30
Consensus pattern (24 bp):
TATGTAGTACTAAGTGCAGGCTAC
Found at i:54136891 original size:99 final size:101
Alignment explanation
Indices: 54136702--54136895 Score: 268
Period size: 99 Copynumber: 1.9 Consensus size: 101
54136692 AGCTAGGTCG
*
54136702 CATGTGTAGTACTAAGTGCAGGCTACTATGCATACCCAATAACTTCAATCACATATGTAGTACTA
1 CATGTGTAGTACTAAGTGCAGGCTACTACGCATACCCAATAACTTCAATCACATATGTAGTACTA
* *
54136767 AGTGCAGGCTACTATGTGTATCAGATAGTTAGGACA
66 AGTGCAGGCTACTATGCGTACCAGATAGTTAGGACA
** ** * *
54136803 CATGTGTAGTACTAAGTGCAGGCTACTACGTGTA-CCAGATAA-TT-GGTCGCATGTGTAGTACT
1 CATGTGTAGTACTAAGTGCAGGCTACTACGCATACCCA-ATAACTTCAATCACATATGTAGTACT
*
54136865 AAGTGTAGGCTACTATGCGTACCAGATAGTT
65 AAGTGCAGGCTACTATGCGTACCAGATAGTT
54136896 TGGCTACATA
Statistics
Matches: 82, Mismatches: 10, Indels: 4
0.85 0.10 0.04
Matches are distributed among these distances:
99 42 0.51
100 5 0.06
101 35 0.43
ACGTcount: A:0.30, C:0.18, G:0.23, T:0.29
Consensus pattern (101 bp):
CATGTGTAGTACTAAGTGCAGGCTACTACGCATACCCAATAACTTCAATCACATATGTAGTACTA
AGTGCAGGCTACTATGCGTACCAGATAGTTAGGACA
Found at i:54138819 original size:78 final size:78
Alignment explanation
Indices: 54138710--54138916 Score: 308
Period size: 78 Copynumber: 2.7 Consensus size: 78
54138700 CTTAAGGCGA
* * * *
54138710 ATAGGATTTGACCTGAAAAGGTAATCTTGATTTGCTATGGTTACATGATATATGATTCATTATGG
1 ATAGGATTTGACCTGAAAAGGTAATCTTGATTCGCTACGATTACATGATATATGATTCATTATGA
54138775 TAACCTAAGGTGG
66 TAACCTAAGGTGG
* *
54138788 ATAGGATTTGACCTGAAAAGGTAATCCTGATTCGCTACGATTACATGATATATGATTCCTTATGA
1 ATAGGATTTGACCTGAAAAGGTAATCTTGATTCGCTACGATTACATGATATATGATTCATTATGA
*
54138853 TAACTTAAGGTGG
66 TAACCTAAGGTGG
* * *
54138866 GTAGGATTTGACCTGAAAAGGTAATCTTGATCCACTAC-AGTTACATGATAT
1 ATAGGATTTGACCTGAAAAGGTAATCTTGATTCGCTACGA-TTACATGATAT
54138917 GTGACTTGAG
Statistics
Matches: 117, Mismatches: 11, Indels: 2
0.90 0.08 0.02
Matches are distributed among these distances:
77 1 0.01
78 116 0.99
ACGTcount: A:0.32, C:0.13, G:0.21, T:0.34
Consensus pattern (78 bp):
ATAGGATTTGACCTGAAAAGGTAATCTTGATTCGCTACGATTACATGATATATGATTCATTATGA
TAACCTAAGGTGG
Found at i:54139122 original size:24 final size:23
Alignment explanation
Indices: 54139076--54139122 Score: 58
Period size: 23 Copynumber: 2.0 Consensus size: 23
54139066 CAAGAATTAT
** *
54139076 AATATGAAAAGAATGTTACATGA
1 AATATGAAAAGAATACTAAATGA
54139099 AATATGAAAATGAATACTAAATGA
1 AATATGAAAA-GAATACTAAATGA
54139123 TATAAATTAA
Statistics
Matches: 20, Mismatches: 3, Indels: 1
0.83 0.12 0.04
Matches are distributed among these distances:
23 10 0.50
24 10 0.50
ACGTcount: A:0.55, C:0.04, G:0.15, T:0.26
Consensus pattern (23 bp):
AATATGAAAAGAATACTAAATGA
Found at i:54143581 original size:40 final size:38
Alignment explanation
Indices: 54143500--54143636 Score: 145
Period size: 40 Copynumber: 3.5 Consensus size: 38
54143490 GAGTCACGTA
*
54143500 CCTTCGGGAT-TTAA-CCGGATATAACCACAAGCACAATTG
1 CCTTCGGG-TCTTAACCCGGATATAA-CACTAGCACAA-TG
*
54143539 CCTTCGGGTCTTAACCCGGATATAACAACTCGCACGAATG
1 CCTTCGGGTCTTAACCCGGATATAAC-ACTAGCAC-AATG
* *
54143579 CCTTCGGGTCTTAGCCCGGATATAATCACTAGCATAAATG
1 CCTTCGGGTCTTAACCCGGATATAA-CACTAGCA-CAATG
*
54143619 CCTTCGGG-ATTAACCCGG
1 CCTTCGGGTCTTAACCCGG
54143637 GTATCATTCA
Statistics
Matches: 85, Mismatches: 7, Indels: 12
0.82 0.07 0.12
Matches are distributed among these distances:
38 1 0.01
39 21 0.25
40 60 0.71
41 3 0.04
ACGTcount: A:0.28, C:0.28, G:0.20, T:0.24
Consensus pattern (38 bp):
CCTTCGGGTCTTAACCCGGATATAACACTAGCACAATG
Found at i:54150193 original size:26 final size:26
Alignment explanation
Indices: 54150131--54150183 Score: 106
Period size: 26 Copynumber: 2.0 Consensus size: 26
54150121 TTTATTTGTC
54150131 AAAATCGATTTGATTCTATAAAAAAA
1 AAAATCGATTTGATTCTATAAAAAAA
54150157 AAAATCGATTTGATTCTATAAAAAAA
1 AAAATCGATTTGATTCTATAAAAAAA
54150183 A
1 A
54150184 CCCTTCATTT
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
26 27 1.00
ACGTcount: A:0.55, C:0.08, G:0.08, T:0.30
Consensus pattern (26 bp):
AAAATCGATTTGATTCTATAAAAAAA
Found at i:54150790 original size:22 final size:22
Alignment explanation
Indices: 54150764--54150805 Score: 59
Period size: 22 Copynumber: 1.9 Consensus size: 22
54150754 AATTCTATAA
*
54150764 AAATTACTATA-ATGACATTTTG
1 AAATTAATATATAT-ACATTTTG
54150786 AAATTAATATATATACATTT
1 AAATTAATATATATACATTT
54150806 ACTTGATAGT
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
22 16 0.89
23 2 0.11
ACGTcount: A:0.45, C:0.07, G:0.05, T:0.43
Consensus pattern (22 bp):
AAATTAATATATATACATTTTG
Found at i:54153270 original size:14 final size:14
Alignment explanation
Indices: 54153251--54153278 Score: 56
Period size: 14 Copynumber: 2.0 Consensus size: 14
54153241 AAGAAAATAT
54153251 GACCCTAAAGACAG
1 GACCCTAAAGACAG
54153265 GACCCTAAAGACAG
1 GACCCTAAAGACAG
54153279 TCAATCCATT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 14 1.00
ACGTcount: A:0.43, C:0.29, G:0.21, T:0.07
Consensus pattern (14 bp):
GACCCTAAAGACAG
Found at i:54154655 original size:15 final size:16
Alignment explanation
Indices: 54154635--54154668 Score: 52
Period size: 15 Copynumber: 2.2 Consensus size: 16
54154625 ATATTAATAA
*
54154635 TAATTTTTTAAA-ATT
1 TAATTTTTAAAATATT
54154650 TAATTTTTAAAATATT
1 TAATTTTTAAAATATT
54154666 TAA
1 TAA
54154669 AATAATAAAA
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
15 11 0.65
16 6 0.35
ACGTcount: A:0.44, C:0.00, G:0.00, T:0.56
Consensus pattern (16 bp):
TAATTTTTAAAATATT
Found at i:54155217 original size:18 final size:17
Alignment explanation
Indices: 54155170--54155224 Score: 65
Period size: 18 Copynumber: 3.1 Consensus size: 17
54155160 CATTGGTTAT
* *
54155170 TATTAAATATATATAATA
1 TATTAATTAT-TATAAAA
*
54155188 TATTAGTTATTATAAAA
1 TATTAATTATTATAAAA
54155205 TATTATATTATTATAAAA
1 TATTA-ATTATTATAAAA
54155223 TA
1 TA
54155225 AATTTCGGTT
Statistics
Matches: 32, Mismatches: 4, Indels: 2
0.84 0.11 0.05
Matches are distributed among these distances:
17 11 0.34
18 21 0.66
ACGTcount: A:0.51, C:0.00, G:0.02, T:0.47
Consensus pattern (17 bp):
TATTAATTATTATAAAA
Found at i:54158465 original size:27 final size:27
Alignment explanation
Indices: 54158435--54158490 Score: 112
Period size: 27 Copynumber: 2.1 Consensus size: 27
54158425 AGGGAAGTGG
54158435 ACAACTTCTTATAAGAGATGGAACAAT
1 ACAACTTCTTATAAGAGATGGAACAAT
54158462 ACAACTTCTTATAAGAGATGGAACAAT
1 ACAACTTCTTATAAGAGATGGAACAAT
54158489 AC
1 AC
54158491 TTCCGTACCA
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
27 29 1.00
ACGTcount: A:0.45, C:0.16, G:0.14, T:0.25
Consensus pattern (27 bp):
ACAACTTCTTATAAGAGATGGAACAAT
Found at i:54169019 original size:15 final size:15
Alignment explanation
Indices: 54169001--54169037 Score: 58
Period size: 15 Copynumber: 2.5 Consensus size: 15
54168991 AAAACAATGT
54169001 GAAGAA-AACGAAGGA
1 GAAGAAGAA-GAAGGA
54169016 GAAGAAGAAGAAGGA
1 GAAGAAGAAGAAGGA
54169031 GAAGAAG
1 GAAGAAG
54169038 GCGGAGGTAA
Statistics
Matches: 21, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
15 19 0.90
16 2 0.10
ACGTcount: A:0.59, C:0.03, G:0.38, T:0.00
Consensus pattern (15 bp):
GAAGAAGAAGAAGGA
Found at i:54173260 original size:12 final size:12
Alignment explanation
Indices: 54173243--54173268 Score: 52
Period size: 12 Copynumber: 2.2 Consensus size: 12
54173233 CCTCACACGC
54173243 CCGTGTGCTAGG
1 CCGTGTGCTAGG
54173255 CCGTGTGCTAGG
1 CCGTGTGCTAGG
54173267 CC
1 CC
54173269 ATGTAACTGA
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:0.08, C:0.31, G:0.38, T:0.23
Consensus pattern (12 bp):
CCGTGTGCTAGG
Found at i:54175044 original size:46 final size:46
Alignment explanation
Indices: 54174994--54175169 Score: 216
Period size: 46 Copynumber: 3.8 Consensus size: 46
54174984 TGGTTGAGCA
54174994 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAATG
1 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAATG
* * *
54175040 TCCGAACTCGTTGAGTTGAGTCCGAGTTC-GTGA--GATG-TAACTAGG
1 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAA-T--G
*
54175085 CATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAACG
1 --TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAATG
* * *
54175133 CCCGAGCTCGTTGAGTTGAGTCCGAGTTCGCTTATGG
1 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGG
54175170 GCGGGTTACA
Statistics
Matches: 111, Mismatches: 10, Indels: 18
0.80 0.07 0.13
Matches are distributed among these distances:
42 2 0.02
43 5 0.05
45 3 0.03
46 63 0.57
47 29 0.26
48 3 0.03
50 4 0.04
51 2 0.02
ACGTcount: A:0.20, C:0.21, G:0.30, T:0.29
Consensus pattern (46 bp):
TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAATG
Found at i:54175150 original size:93 final size:93
Alignment explanation
Indices: 54174991--54175162 Score: 317
Period size: 93 Copynumber: 1.8 Consensus size: 93
54174981 GGATGGTTGA
* *
54174991 GCATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAATGTCCGAACTCGTTGAGT
1 GCATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAACGCCCGAACTCGTTGAGT
54175056 TGAGTCCGAGTTCGTGAGATGTAACTAG
66 TGAGTCCGAGTTCGTGAGATGTAACTAG
*
54175084 GCATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAACGCCCGAGCTCGTTGAGT
1 GCATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAACGCCCGAACTCGTTGAGT
54175149 TGAGTCCGAGTTCG
66 TGAGTCCGAGTTCG
54175163 CTTATGGGCG
Statistics
Matches: 76, Mismatches: 3, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
93 76 1.00
ACGTcount: A:0.21, C:0.22, G:0.30, T:0.28
Consensus pattern (93 bp):
GCATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAACGCCCGAACTCGTTGAGT
TGAGTCCGAGTTCGTGAGATGTAACTAG
Found at i:54184974 original size:30 final size:30
Alignment explanation
Indices: 54184917--54184975 Score: 73
Period size: 30 Copynumber: 2.0 Consensus size: 30
54184907 TTTACTAGCC
* * *
54184917 TAGGGGCAAAAGCGTAATTTTGGCAAAATT
1 TAGGGGCAAAAGCATAAATTTGCCAAAATT
**
54184947 TAGGGGCAAAATTATAAATTTGCCAAAAT
1 TAGGGGCAAAAGCATAAATTTGCCAAAAT
54184976 ATGATTTTTG
Statistics
Matches: 24, Mismatches: 5, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
30 24 1.00
ACGTcount: A:0.41, C:0.10, G:0.22, T:0.27
Consensus pattern (30 bp):
TAGGGGCAAAAGCATAAATTTGCCAAAATT
Found at i:54185496 original size:47 final size:48
Alignment explanation
Indices: 54185442--54185569 Score: 158
Period size: 47 Copynumber: 2.7 Consensus size: 48
54185432 AATATGTGTG
*
54185442 TGCTAGTGTAAGACATGTCTGGGACATGCATCGGCCACACTATGA-A-A
1 TGCTAGTGTAAGACATGTCTGGGACATGCATCGG-CACACTAAGACAGA
* * *
54185489 TGCTAGTGTAACACATGTCTAGGACATGCATC-G-ACATTAAGACGAGA
1 TGCTAGTGTAAGACATGTCTGGGACATGCATCGGCACACTAAGAC-AGA
*
54185536 -GCCAGTGTAAGACATGTCTGGGACATGCATCGGC
1 TGCTAGTGTAAGACATGTCTGGGACATGCATCGGC
54185570 TACGAGATGT
Statistics
Matches: 69, Mismatches: 7, Indels: 9
0.81 0.08 0.11
Matches are distributed among these distances:
44 7 0.10
46 30 0.43
47 32 0.46
ACGTcount: A:0.30, C:0.21, G:0.27, T:0.23
Consensus pattern (48 bp):
TGCTAGTGTAAGACATGTCTGGGACATGCATCGGCACACTAAGACAGA
Found at i:54185560 original size:46 final size:45
Alignment explanation
Indices: 54185446--54185567 Score: 140
Period size: 46 Copynumber: 2.6 Consensus size: 45
54185436 TGTGTGTGCT
* *
54185446 AGTGTAAGACATGTCTGGGACATGCATCGGCCACACTATGAAATGCT
1 AGTGTAAGACATGTCTGGGACATGCATC-G-CACACTAAGAAATGCC
* * *
54185493 AGTGTAACACATGTCTAGGACATGCATCG-ACATTAAGACGAGA-GCC
1 AGTGTAAGACATGTCTGGGACATGCATCGCACACTAAGA--A-ATGCC
54185539 AGTGTAAGACATGTCTGGGACATGCATCG
1 AGTGTAAGACATGTCTGGGACATGCATCG
54185568 GCTACGAGAT
Statistics
Matches: 65, Mismatches: 7, Indels: 7
0.82 0.09 0.09
Matches are distributed among these distances:
44 7 0.11
46 31 0.48
47 27 0.42
ACGTcount: A:0.31, C:0.20, G:0.26, T:0.22
Consensus pattern (45 bp):
AGTGTAAGACATGTCTGGGACATGCATCGCACACTAAGAAATGCC
Found at i:54190033 original size:29 final size:30
Alignment explanation
Indices: 54189977--54190033 Score: 71
Period size: 29 Copynumber: 1.9 Consensus size: 30
54189967 GTTCAATTGC
* * *
54189977 TTTTGGTTGAGTCTTGTTAGTGTCATTAGT
1 TTTTGGTTGAATCTTGTTAATGTAATTAGT
*
54190007 TTTTGGTTGAAT-TTGTTAATTTAATTA
1 TTTTGGTTGAATCTTGTTAATGTAATTA
54190034 CATTCATGGT
Statistics
Matches: 23, Mismatches: 4, Indels: 1
0.82 0.14 0.04
Matches are distributed among these distances:
29 12 0.52
30 11 0.48
ACGTcount: A:0.19, C:0.04, G:0.21, T:0.56
Consensus pattern (30 bp):
TTTTGGTTGAATCTTGTTAATGTAATTAGT
Found at i:54196556 original size:24 final size:24
Alignment explanation
Indices: 54196504--54196669 Score: 230
Period size: 24 Copynumber: 7.0 Consensus size: 24
54196494 GCTTTATCAT
*
54196504 ATAACTGGAGGCCT-AGCCTCTTTTA
1 ATAACTGG-GGCATAAGCC-CTTTTA
* *
54196529 ATAACTGGGGCAAAAGCCCTTTTT
1 ATAACTGGGGCATAAGCCCTTTTA
54196553 ATAACTGGGGCATAAGCCC-TTTA
1 ATAACTGGGGCATAAGCCCTTTTA
* *
54196576 ATAACTGGGGCGTAAGCCCTTTTG
1 ATAACTGGGGCATAAGCCCTTTTA
* *
54196600 ATAACTGGGGCGTAAGCCCTTTTG
1 ATAACTGGGGCATAAGCCCTTTTA
54196624 ATAACTGGGGCATAAGCCC-TTTA
1 ATAACTGGGGCATAAGCCCTTTTA
54196647 ATAACTGGGGCATAAGCCCTTTT
1 ATAACTGGGGCATAAGCCCTTTT
54196670 GCACTTCCTC
Statistics
Matches: 129, Mismatches: 9, Indels: 7
0.89 0.06 0.05
Matches are distributed among these distances:
23 43 0.33
24 74 0.57
25 12 0.09
ACGTcount: A:0.26, C:0.22, G:0.23, T:0.29
Consensus pattern (24 bp):
ATAACTGGGGCATAAGCCCTTTTA
Done.