Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Gbar_D13
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: 60343961
ACGTcount: A:0.33, C:0.16, G:0.16, T:0.33
Warning! 596159 characters in sequence are not A, C, G, or T
File 182 of 204
Found at i:53859625 original size:16 final size:16
Alignment explanation
Indices: 53859606--53859638 Score: 57
Period size: 16 Copynumber: 2.1 Consensus size: 16
53859596 GTGAGAAAAA
53859606 ATATAAATATACATAT
1 ATATAAATATACATAT
*
53859622 ATATAAATATATATAT
1 ATATAAATATACATAT
53859638 A
1 A
53859639 AAATGAGTAT
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 16 1.00
ACGTcount: A:0.58, C:0.03, G:0.00, T:0.39
Consensus pattern (16 bp):
ATATAAATATACATAT
Found at i:53859793 original size:3 final size:3
Alignment explanation
Indices: 53859775--53859845 Score: 97
Period size: 3 Copynumber: 23.7 Consensus size: 3
53859765 AATGATAGTC
* * * **
53859775 ATA ATA GTA TTA ATA ATA ATA CTA AGG ATA ATA ATA ATA ATA ATA ATA
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA
53859823 ATA ATA ATA ATA ATA ATA ATA AT
1 ATA ATA ATA ATA ATA ATA ATA AT
53859846 TGATTAAACA
Statistics
Matches: 59, Mismatches: 9, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
3 59 1.00
ACGTcount: A:0.61, C:0.01, G:0.04, T:0.34
Consensus pattern (3 bp):
ATA
Found at i:53862361 original size:18 final size:17
Alignment explanation
Indices: 53862328--53862366 Score: 53
Period size: 18 Copynumber: 2.2 Consensus size: 17
53862318 TTTTATAAAT
53862328 TGTGAATTATATTTGATA
1 TGTGAATTATATTTGA-A
53862346 TGTGAATTA-ATATTGAA
1 TGTGAATTATAT-TTGAA
53862363 TGTG
1 TGTG
53862367 GAAGGAAAAT
Statistics
Matches: 20, Mismatches: 0, Indels: 3
0.87 0.00 0.13
Matches are distributed among these distances:
17 7 0.35
18 13 0.65
ACGTcount: A:0.33, C:0.00, G:0.21, T:0.46
Consensus pattern (17 bp):
TGTGAATTATATTTGAA
Found at i:53862626 original size:23 final size:23
Alignment explanation
Indices: 53862591--53862661 Score: 115
Period size: 23 Copynumber: 3.1 Consensus size: 23
53862581 AGTGTTATTG
*
53862591 ATCAGTGGTAGCTTCGGCTACAT
1 ATCAATGGTAGCTTCGGCTACAT
*
53862614 TTCAATGGTAGCTTCGGCTACAT
1 ATCAATGGTAGCTTCGGCTACAT
*
53862637 ATCAGTGGTAGCTTCGGCTACAT
1 ATCAATGGTAGCTTCGGCTACAT
53862660 AT
1 AT
53862662 TAGTGTGGCA
Statistics
Matches: 44, Mismatches: 4, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
23 44 1.00
ACGTcount: A:0.23, C:0.21, G:0.24, T:0.32
Consensus pattern (23 bp):
ATCAATGGTAGCTTCGGCTACAT
Found at i:53874610 original size:21 final size:22
Alignment explanation
Indices: 53874571--53874611 Score: 66
Period size: 22 Copynumber: 1.9 Consensus size: 22
53874561 AAATAGGGAG
*
53874571 AAAACAACAAGAGAATAGCATT
1 AAAACAACAAGAAAATAGCATT
53874593 AAAACAACAA-AAAATAGCA
1 AAAACAACAAGAAAATAGCA
53874612 ATTTTTTTCC
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
21 8 0.44
22 10 0.56
ACGTcount: A:0.66, C:0.15, G:0.10, T:0.10
Consensus pattern (22 bp):
AAAACAACAAGAAAATAGCATT
Found at i:53875765 original size:21 final size:21
Alignment explanation
Indices: 53875731--53875793 Score: 65
Period size: 21 Copynumber: 3.0 Consensus size: 21
53875721 TAGAAATTAT
*
53875731 AAAAGATCATTAAAAATATTTA
1 AAAAAATCA-TAAAAATATTTA
* *
53875753 AAAAAATCATAAAAAAAGTTA
1 AAAAAATCATAAAAATATTTA
* *
53875774 TAAAAATCATAAGAAT-TTTA
1 AAAAAATCATAAAAATATTTA
53875794 TCAAAATGCT
Statistics
Matches: 34, Mismatches: 7, Indels: 2
0.79 0.16 0.05
Matches are distributed among these distances:
20 3 0.09
21 23 0.68
22 8 0.24
ACGTcount: A:0.62, C:0.05, G:0.05, T:0.29
Consensus pattern (21 bp):
AAAAAATCATAAAAATATTTA
Found at i:53875997 original size:23 final size:21
Alignment explanation
Indices: 53875945--53875997 Score: 63
Period size: 21 Copynumber: 2.4 Consensus size: 21
53875935 TGAAATATAT
*
53875945 ATAATATCTATTGTTTAAAAA
1 ATAATATTTATTGTTTAAAAA
53875966 AT-ATCATTTATTGTTTAACAAA
1 ATAAT-ATTTATTGTTTAA-AAA
53875988 ATTAATATTT
1 A-TAATATTT
53875998 TTGAAGTTTT
Statistics
Matches: 27, Mismatches: 1, Indels: 6
0.79 0.03 0.18
Matches are distributed among these distances:
20 2 0.07
21 14 0.52
22 4 0.15
23 5 0.19
24 2 0.07
ACGTcount: A:0.43, C:0.06, G:0.04, T:0.47
Consensus pattern (21 bp):
ATAATATTTATTGTTTAAAAA
Found at i:53877310 original size:34 final size:35
Alignment explanation
Indices: 53877266--53877332 Score: 102
Period size: 34 Copynumber: 1.9 Consensus size: 35
53877256 CAGTAAAATG
53877266 TTTTCCGTAAAATGATTT-CTTG-AAAATATTTTAC
1 TTTTCCGTAAAATGATTTAC-TGAAAAATATTTTAC
*
53877300 TTTTCTGTAAAATGATTTACTGAAAAATATTTT
1 TTTTCCGTAAAATGATTTACTGAAAAATATTTT
53877333 CTGGTGTTTG
Statistics
Matches: 30, Mismatches: 1, Indels: 3
0.88 0.03 0.09
Matches are distributed among these distances:
34 19 0.63
35 11 0.37
ACGTcount: A:0.34, C:0.09, G:0.09, T:0.48
Consensus pattern (35 bp):
TTTTCCGTAAAATGATTTACTGAAAAATATTTTAC
Found at i:53877391 original size:32 final size:32
Alignment explanation
Indices: 53877323--53877397 Score: 89
Period size: 32 Copynumber: 2.3 Consensus size: 32
53877313 GATTTACTGA
* **
53877323 AAAATATTTTCTGGTGTTTGATTGAATTGTGT
1 AAAATATTTTCTGCTGTTTGACAGAATTGTGT
* *
53877355 AAAATATTTTCTGCTGTTTGACAGATTTCT-T
1 AAAATATTTTCTGCTGTTTGACAGAATTGTGT
53877386 GAAAATATTTTC
1 -AAAATATTTTC
53877398 CGGAAAAGTT
Statistics
Matches: 37, Mismatches: 5, Indels: 2
0.84 0.11 0.05
Matches are distributed among these distances:
31 1 0.03
32 36 0.97
ACGTcount: A:0.28, C:0.08, G:0.16, T:0.48
Consensus pattern (32 bp):
AAAATATTTTCTGCTGTTTGACAGAATTGTGT
Found at i:53931695 original size:35 final size:35
Alignment explanation
Indices: 53931656--53931726 Score: 142
Period size: 35 Copynumber: 2.0 Consensus size: 35
53931646 GTGCAAATAA
53931656 TTATTCATAAATTTATACTTTGTATATTTCTTTGG
1 TTATTCATAAATTTATACTTTGTATATTTCTTTGG
53931691 TTATTCATAAATTTATACTTTGTATATTTCTTTGG
1 TTATTCATAAATTTATACTTTGTATATTTCTTTGG
53931726 T
1 T
53931727 GTATCCCCAT
Statistics
Matches: 36, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
35 36 1.00
ACGTcount: A:0.25, C:0.08, G:0.08, T:0.58
Consensus pattern (35 bp):
TTATTCATAAATTTATACTTTGTATATTTCTTTGG
Found at i:53936895 original size:44 final size:44
Alignment explanation
Indices: 53936832--53937052 Score: 167
Period size: 44 Copynumber: 4.8 Consensus size: 44
53936822 CTGAAGAAGA
* *
53936832 AATCTTATCTCCCTTAGATTATAGCGGAGCAGATTGAAGCTAGT
1 AATCTTATCTCCCTGAGATTACAGCGGAGCAGATTGAAGCTAGT
* * ** *
53936876 AATCCTATCTCCCTGAGATTACAGTGGAGCAGATT-AAAATAAAT
1 AATCTTATCTCCCTGAGATTACAGCGGAGCAGATTGAAGCT-AGT
* * * * *
53936920 GATCTTATCTCTCTGA-AGTTACAGTAGAGTAGATCGCATCAGGTTGAAGCTAGA
1 AATCTTATCTCCCTGAGA-TTAC---AGCG--GA--G---CAGATTGAAGCTAGT
* *
53936974 AAGCTTATCTCCCTGAGATTACAGCGGAGCAGATTGAAGTTAGT
1 AATCTTATCTCCCTGAGATTACAGCGGAGCAGATTGAAGCTAGT
* * *
53937018 AATCCTATCTCCCTGAGATTACAGTGGAGCGGATT
1 AATCTTATCTCCCTGAGATTACAGCGGAGCAGATT
53937053 AAAACAAAGG
Statistics
Matches: 136, Mismatches: 27, Indels: 28
0.71 0.14 0.15
Matches are distributed among these distances:
43 4 0.03
44 93 0.68
47 4 0.03
49 4 0.03
51 4 0.03
54 23 0.17
55 4 0.03
ACGTcount: A:0.31, C:0.19, G:0.22, T:0.29
Consensus pattern (44 bp):
AATCTTATCTCCCTGAGATTACAGCGGAGCAGATTGAAGCTAGT
Found at i:53937040 original size:98 final size:98
Alignment explanation
Indices: 53936865--53937042 Score: 241
Period size: 98 Copynumber: 1.8 Consensus size: 98
53936855 GCGGAGCAGA
* * * * *
53936865 TTGAAGCTAGTAATCCTATCTCCCTGAGATTACAGTGGAGCAGATTAAAATAAATGATCTTATCT
1 TTGAAGCTAGAAAGCCTATCTCCCTGAGATTACAGCGGAGCAGATTAAAATAAATAATCCTATCT
*
53936930 CTCTGAAGTTACAGTAGAGTAGATCGCATCAGG
66 CCCTGAAGTTACAGTAGAGTAGATCGCATCAGG
* * * * *
53936963 TTGAAGCTAGAAAGCTTATCTCCCTGAGATTACAGCGGAGCAGATTGAAGTTAGTAATCCTATCT
1 TTGAAGCTAGAAAGCCTATCTCCCTGAGATTACAGCGGAGCAGATTAAAATAAATAATCCTATCT
53937028 CCCTG-AGATTACAGT
66 CCCTGAAG-TTACAGT
53937043 GGAGCGGATT
Statistics
Matches: 68, Mismatches: 11, Indels: 2
0.84 0.14 0.02
Matches are distributed among these distances:
97 2 0.03
98 66 0.97
ACGTcount: A:0.31, C:0.19, G:0.21, T:0.29
Consensus pattern (98 bp):
TTGAAGCTAGAAAGCCTATCTCCCTGAGATTACAGCGGAGCAGATTAAAATAAATAATCCTATCT
CCCTGAAGTTACAGTAGAGTAGATCGCATCAGG
Found at i:53937071 original size:44 final size:44
Alignment explanation
Indices: 53936977--53937095 Score: 107
Period size: 44 Copynumber: 2.7 Consensus size: 44
53936967 AGCTAGAAAG
* * ***
53936977 CTTATCTCCCTGAGATTACAGCGGAGCAGATTGAAGTTAGTAAT
1 CTTATCTCCCTGAGATTACAGTGGAGCAGATTAAACAAAGTAAT
* * *
53937021 CCTATCTCCCTGAGATTACAGTGGAGCGGATTAAAACAAAG-GAT
1 CTTATCTCCCTGAGATTACAGTGGAGCAGATT-AAACAAAGTAAT
* * *
53937065 CTTATCTCTCTGA-AGTTACAGTAGAGTAGAT
1 CTTATCTCCCTGAGA-TTACAGTGGAGCAGAT
53937096 CGCATCAGAT
Statistics
Matches: 60, Mismatches: 13, Indels: 4
0.78 0.17 0.05
Matches are distributed among these distances:
43 1 0.02
44 55 0.92
45 4 0.07
ACGTcount: A:0.31, C:0.18, G:0.22, T:0.29
Consensus pattern (44 bp):
CTTATCTCCCTGAGATTACAGTGGAGCAGATTAAACAAAGTAAT
Found at i:53937085 original size:142 final size:142
Alignment explanation
Indices: 53936829--53937111 Score: 494
Period size: 142 Copynumber: 2.0 Consensus size: 142
53936819 AGACTGAAGA
* * *
53936829 AGAAATCTTATCTCCCTTAGATTATAGCGGAGCAGATTGAAGCTAGTAATCCTATCTCCCTGAGA
1 AGAAAGCTTATCTCCCTGAGATTACAGCGGAGCAGATTGAAGCTAGTAATCCTATCTCCCTGAGA
* *
53936894 TTACAGTGGAGCAGATTAAAATAAATGATCTTATCTCTCTGAAGTTACAGTAGAGTAGATCGCAT
66 TTACAGTGGAGCAGATTAAAACAAAGGATCTTATCTCTCTGAAGTTACAGTAGAGTAGATCGCAT
*
53936959 CAGGTTGAAGCT
131 CAGATTGAAGCT
*
53936971 AGAAAGCTTATCTCCCTGAGATTACAGCGGAGCAGATTGAAGTTAGTAATCCTATCTCCCTGAGA
1 AGAAAGCTTATCTCCCTGAGATTACAGCGGAGCAGATTGAAGCTAGTAATCCTATCTCCCTGAGA
*
53937036 TTACAGTGGAGCGGATTAAAACAAAGGATCTTATCTCTCTGAAGTTACAGTAGAGTAGATCGCAT
66 TTACAGTGGAGCAGATTAAAACAAAGGATCTTATCTCTCTGAAGTTACAGTAGAGTAGATCGCAT
53937101 CAGATTGAAGC
131 CAGATTGAAGC
53937112 CAGGAATCTT
Statistics
Matches: 133, Mismatches: 8, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
142 133 1.00
ACGTcount: A:0.33, C:0.18, G:0.22, T:0.28
Consensus pattern (142 bp):
AGAAAGCTTATCTCCCTGAGATTACAGCGGAGCAGATTGAAGCTAGTAATCCTATCTCCCTGAGA
TTACAGTGGAGCAGATTAAAACAAAGGATCTTATCTCTCTGAAGTTACAGTAGAGTAGATCGCAT
CAGATTGAAGCT
Found at i:53944921 original size:4 final size:4
Alignment explanation
Indices: 53944912--53945034 Score: 246
Period size: 4 Copynumber: 30.8 Consensus size: 4
53944902 TTCTTGGAAT
53944912 ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC
1 ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC
53944960 ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC
1 ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC
53945008 ATAC ATAC ATAC ATAC ATAC ATAC ATA
1 ATAC ATAC ATAC ATAC ATAC ATAC ATA
53945035 AATCATGGTT
Statistics
Matches: 119, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 119 1.00
ACGTcount: A:0.50, C:0.24, G:0.00, T:0.25
Consensus pattern (4 bp):
ATAC
Found at i:53945748 original size:16 final size:16
Alignment explanation
Indices: 53945727--53945782 Score: 80
Period size: 16 Copynumber: 3.6 Consensus size: 16
53945717 TATTGCCTTA
53945727 TTTTTAAAAGTTTTCT
1 TTTTTAAAAGTTTTCT
*
53945743 TTTTTAAAA-TTCTT-A
1 TTTTTAAAAGTT-TTCT
53945758 TTTTTAAAAGTTTTCT
1 TTTTTAAAAGTTTTCT
53945774 TTTTTAAAA
1 TTTTTAAAA
53945783 TTGGGGAAAA
Statistics
Matches: 35, Mismatches: 2, Indels: 6
0.81 0.05 0.14
Matches are distributed among these distances:
15 13 0.37
16 22 0.63
ACGTcount: A:0.30, C:0.05, G:0.04, T:0.61
Consensus pattern (16 bp):
TTTTTAAAAGTTTTCT
Found at i:53945758 original size:31 final size:31
Alignment explanation
Indices: 53945723--53945784 Score: 124
Period size: 31 Copynumber: 2.0 Consensus size: 31
53945713 TGAATATTGC
53945723 CTTATTTTTAAAAGTTTTCTTTTTTAAAATT
1 CTTATTTTTAAAAGTTTTCTTTTTTAAAATT
53945754 CTTATTTTTAAAAGTTTTCTTTTTTAAAATT
1 CTTATTTTTAAAAGTTTTCTTTTTTAAAATT
53945785 GGGGAAAATT
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
31 31 1.00
ACGTcount: A:0.29, C:0.06, G:0.03, T:0.61
Consensus pattern (31 bp):
CTTATTTTTAAAAGTTTTCTTTTTTAAAATT
Found at i:53948162 original size:22 final size:22
Alignment explanation
Indices: 53948130--53948171 Score: 57
Period size: 22 Copynumber: 1.9 Consensus size: 22
53948120 TATACATGTA
* *
53948130 ATATTACTTGAATAGTTATGAG
1 ATATTAATTGAATAATTATGAG
*
53948152 ATATTAATTGAGTAATTATG
1 ATATTAATTGAATAATTATG
53948172 TCTCCTTTAA
Statistics
Matches: 17, Mismatches: 3, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
22 17 1.00
ACGTcount: A:0.38, C:0.02, G:0.17, T:0.43
Consensus pattern (22 bp):
ATATTAATTGAATAATTATGAG
Found at i:53953204 original size:108 final size:107
Alignment explanation
Indices: 53952983--53953260 Score: 280
Period size: 108 Copynumber: 2.6 Consensus size: 107
53952973 CAATCAGAGT
* * * *
53952983 CTTTGTCTCGTTGAGTATATAATACCCAACCAAACTCATAGAGGAGCACGCGCTTTGGGACATAT
1 CTTTGTCTCGTTGAGTACATAATACCCAACCAAACTCACAGAGGAGCACGCACTTTGAGACATAT
* * *
53953048 CACATTAGCTCATATACAGAGCTGGTTTCACTCAGTAGAAAA
66 CACATTAGCTCATATACAGAGCGGGCTTCACTAAGTAGAAAA
* * * * * *
53953090 CATTGTCTTGTTGAGTACATAATTACCCATCCGAACTCACAGAGGAGCATGTACTTTGAGACATA
1 CTTTGTCTCGTTGAGTACATAA-TACCCAACCAAACTCACAGAGGAGCACGCACTTTGAGACATA
* *
53953155 TCACTTTAGCTCATATACAGAGCCGGGCTT-ACTAAAG-AGCAAA
65 TCACATTAGCTCATATACAGAG-CGGGCTTCACT-AAGTAGAAAA
* * * * ** **
53953198 CTTTGTCTCATTGAG--CAT-AT-CCCAACCGAACTCACAAAAGAGCATACGTTTTGAGACATAT
1 CTTTGTCTCGTTGAGTACATAATACCCAACCAAACTCACAGAGGAGCACGCACTTTGAGACATAT
53953259 CA
66 CA
53953261 TGAGTGAGTA
Statistics
Matches: 143, Mismatches: 25, Indels: 10
0.80 0.14 0.06
Matches are distributed among these distances:
103 36 0.25
104 1 0.01
105 1 0.01
106 3 0.02
107 19 0.13
108 76 0.53
109 7 0.05
ACGTcount: A:0.32, C:0.23, G:0.18, T:0.27
Consensus pattern (107 bp):
CTTTGTCTCGTTGAGTACATAATACCCAACCAAACTCACAGAGGAGCACGCACTTTGAGACATAT
CACATTAGCTCATATACAGAGCGGGCTTCACTAAGTAGAAAA
Found at i:53954368 original size:67 final size:67
Alignment explanation
Indices: 53954258--53954558 Score: 354
Period size: 67 Copynumber: 4.5 Consensus size: 67
53954248 CACGTCAAGA
* * * * * *
53954258 CATTAAACATGGGGTATGATGTATAAAATCATAGCTCGACTATAACAACATAGAGAGCCCGCTAG
1 CATTAAACATGGGGTATGATGTGTAAGACCATAGCTCGGCTATAACAACATAAAGAGCTCGCTAG
53954323 GG
66 GG
*
53954325 CATTAAACATGGGGTATGATGCGTAAGACCATAGCTCGGCTATAACAACATAAAGAGCTCGCTAG
1 CATTAAACATGGGGTATGATGTGTAAGACCATAGCTCGGCTATAACAACATAAAGAGCTCGCTAG
*
53954390 GA
66 GG
* * * * * *
53954392 CATTAAACATGTGGTATGATGTGTAAGGCCATAGCTCAGCTATGACAACATAAAGAGTTCG-TCG
1 CATTAAACATGGGGTATGATGTGTAAGACCATAGCTCGGCTATAACAACATAAAGAGCTCGCTAG
53954456 GG
66 GG
* * * *
53954458 ACATTAAACATGGGGTATGATGTGTAAGACCATAACTCGGCTATGACAACATAAAAAG-TCCACT
1 -CATTAAACATGGGGTATGATGTGTAAGACCATAGCTCGGCTATAACAACATAAAGAGCT-CGCT
**
53954522 AGAA
64 AGGG
** **
53954526 CATTAAATGTAAGGTATGATGTGTAAGACCATA
1 CATTAAACATGGGGTATGATGTGTAAGACCATA
53954559 ACTCAGTTTT
Statistics
Matches: 202, Mismatches: 29, Indels: 6
0.85 0.12 0.03
Matches are distributed among these distances:
66 4 0.02
67 196 0.97
68 2 0.01
ACGTcount: A:0.37, C:0.17, G:0.23, T:0.24
Consensus pattern (67 bp):
CATTAAACATGGGGTATGATGTGTAAGACCATAGCTCGGCTATAACAACATAAAGAGCTCGCTAG
GG
Found at i:53955437 original size:9 final size:9
Alignment explanation
Indices: 53955415--53955447 Score: 50
Period size: 9 Copynumber: 3.8 Consensus size: 9
53955405 GGCCTATTTG
53955415 TTTATTTA-
1 TTTATTTAT
53955423 TTTATTTAT
1 TTTATTTAT
*
53955432 TTTATTTCT
1 TTTATTTAT
53955441 TTTATTT
1 TTTATTT
53955448 TGAAAGAAAA
Statistics
Matches: 23, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
8 8 0.35
9 15 0.65
ACGTcount: A:0.18, C:0.03, G:0.00, T:0.79
Consensus pattern (9 bp):
TTTATTTAT
Found at i:53956389 original size:25 final size:25
Alignment explanation
Indices: 53956356--53956404 Score: 80
Period size: 25 Copynumber: 2.0 Consensus size: 25
53956346 TATACCTTTG
53956356 TTTTAAAATCTATTATGTATTATTT
1 TTTTAAAATCTATTATGTATTATTT
* *
53956381 TTTTGAAATTTATTATGTATTATT
1 TTTTAAAATCTATTATGTATTATT
53956405 CACTATTATA
Statistics
Matches: 22, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
25 22 1.00
ACGTcount: A:0.31, C:0.02, G:0.06, T:0.61
Consensus pattern (25 bp):
TTTTAAAATCTATTATGTATTATTT
Found at i:53956633 original size:4 final size:4
Alignment explanation
Indices: 53956626--53956652 Score: 54
Period size: 4 Copynumber: 6.8 Consensus size: 4
53956616 TTCATTATAT
53956626 ATAC ATAC ATAC ATAC ATAC ATAC ATA
1 ATAC ATAC ATAC ATAC ATAC ATAC ATA
53956653 ATCTATTGTA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 23 1.00
ACGTcount: A:0.52, C:0.22, G:0.00, T:0.26
Consensus pattern (4 bp):
ATAC
Found at i:53960905 original size:30 final size:29
Alignment explanation
Indices: 53960843--53960905 Score: 90
Period size: 29 Copynumber: 2.1 Consensus size: 29
53960833 CCATTTTGGC
*
53960843 AAAATACAAAGGCAATAAAATTTCCTTCA
1 AAAATACAAAGGCAATAAAATTTCCTTAA
**
53960872 AAAATACAAAGGCAATAAGTTATTCCTTAA
1 AAAATACAAAGGCAATAAAAT-TTCCTTAA
53960902 AAAA
1 AAAA
53960906 GCCAATAAAT
Statistics
Matches: 30, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
29 19 0.63
30 11 0.37
ACGTcount: A:0.54, C:0.14, G:0.08, T:0.24
Consensus pattern (29 bp):
AAAATACAAAGGCAATAAAATTTCCTTAA
Found at i:53968520 original size:34 final size:34
Alignment explanation
Indices: 53968477--53968543 Score: 125
Period size: 34 Copynumber: 2.0 Consensus size: 34
53968467 TTTAAGCCCC
53968477 CTTACTTACTATAAGTTTGGAAAACTACTCAACA
1 CTTACTTACTATAAGTTTGGAAAACTACTCAACA
*
53968511 CTTATTTACTATAAGTTTGGAAAACTACTCAAC
1 CTTACTTACTATAAGTTTGGAAAACTACTCAAC
53968544 TAGAAAGAAA
Statistics
Matches: 32, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
34 32 1.00
ACGTcount: A:0.37, C:0.19, G:0.09, T:0.34
Consensus pattern (34 bp):
CTTACTTACTATAAGTTTGGAAAACTACTCAACA
Found at i:53979541 original size:29 final size:28
Alignment explanation
Indices: 53979468--53979541 Score: 76
Period size: 29 Copynumber: 2.5 Consensus size: 28
53979458 TGCGAGTTGT
*
53979468 AAAGTTGCAAGCTTGTTGAAGACAATGAGC
1 AAAG-TGCAAGC-TGTTGAAGACAATAAGC
* * *
53979498 AAAGTACGAGCCTGTTGAAGACAGTAAGC
1 AAAGTGCAAG-CTGTTGAAGACAATAAGC
53979527 AAAGTGCAAGTCTGT
1 AAAGTGCAAG-CTGT
53979542 CAAAGTGTGA
Statistics
Matches: 36, Mismatches: 7, Indels: 3
0.78 0.15 0.07
Matches are distributed among these distances:
29 31 0.86
30 5 0.14
ACGTcount: A:0.36, C:0.15, G:0.27, T:0.22
Consensus pattern (28 bp):
AAAGTGCAAGCTGTTGAAGACAATAAGC
Found at i:53979611 original size:44 final size:44
Alignment explanation
Indices: 53979563--53979658 Score: 138
Period size: 44 Copynumber: 2.2 Consensus size: 44
53979553 CCTATCAAAT
*
53979563 TGCAAGCCGAAGTGGTGGACAGTCTAAATGCAAACCCGAATGGG
1 TGCAAGCCGAAGTGGAGGACAGTCTAAATGCAAACCCGAATGGG
* * * * *
53979607 TGCAACCCGAAGTGGAGGACGGTCTAAATGCAAGCTCGAGTGGG
1 TGCAAGCCGAAGTGGAGGACAGTCTAAATGCAAACCCGAATGGG
53979651 TGCAAGCC
1 TGCAAGCC
53979659 AAAATGGCAG
Statistics
Matches: 45, Mismatches: 7, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
44 45 1.00
ACGTcount: A:0.29, C:0.22, G:0.33, T:0.16
Consensus pattern (44 bp):
TGCAAGCCGAAGTGGAGGACAGTCTAAATGCAAACCCGAATGGG
Found at i:53982078 original size:24 final size:23
Alignment explanation
Indices: 53982022--53982078 Score: 62
Period size: 25 Copynumber: 2.3 Consensus size: 23
53982012 AAGAACTTCT
*
53982022 ATTTTATTAAAAATATAAAAATA
1 ATTTTATTAAAAATATAAAAACA
53982045 ATTTACTATT-AAAATATTAAAAACA
1 ATTT--TATTAAAAATA-TAAAAACA
53982070 ACTTTTATT
1 A-TTTTATT
53982079 TTATTAAATG
Statistics
Matches: 29, Mismatches: 1, Indels: 7
0.78 0.03 0.19
Matches are distributed among these distances:
23 4 0.14
24 10 0.34
25 12 0.41
26 3 0.10
ACGTcount: A:0.53, C:0.05, G:0.00, T:0.42
Consensus pattern (23 bp):
ATTTTATTAAAAATATAAAAACA
Found at i:53983793 original size:730 final size:730
Alignment explanation
Indices: 53982564--53984751 Score: 4117
Period size: 730 Copynumber: 3.0 Consensus size: 730
53982554 GGGCCCGGTG
53982564 ATTGTATAGGCGTTGTTGATGGGTCCATGCTGTCATCCTTTCTCCTTGGATTTAAAGGGCCTCAT
1 ATTGTATAGGCGTTGTTGATGGGTCCATGCTGTCATCCTTTCTCCTTGGATTTAAAGGGCCTCAT
*
53982629 TGTTCCCTTTTGACATGGATTTGCCGACACCTCTGCTCTTCCGGCAACAAATATGGCTTGTCATG
66 TGTTCCCTTTTGACATGGATTTGCCGACACCTCTGCTCTTCCGGTAACAAATATGGCTTGTCATG
*
53982694 GATCTTAAACCATTGCATGTAATCCGGCGCGCATGCTAACTCTAGGACGATGATCAGTTCGCGAA
131 GATCTTAAACCATTGCATGTAATCCGGCGCGCATGCTAACTCTAGGACGATGATCAGTTCGCGAG
* *
53982759 CAAGTATATGATCATATCGATTTTTCAAATTTTTGATATATTCTGAGAAGAATACCAGTCAATTC
196 CAAGTATATGATCATACCGATTTTTCAAATTTTCGATATATTCTGAGAAGAATACCAGTCAATTC
53982824 GTATTTTTTTGCCATAAGTCGATTTTGTGCTCTTTATTGATCACCTCAGGTGCCTCGGGAATTGG
261 GTATTTTTTTGCCATAAGTCGATTTTGTGCTCTTTATTGATCACCTCAGGTGCCTCGGGAATTGG
*
53982889 TTTTTAGAATCTAAATTACTGCAACACTCTATCCGTCTGATGCATCTCGACAGTAACATAGTTGA
326 TTTTTAGAATCTAAATTACCGCAACACTCTATCCGTCTGATGCATCTCGACAGTAACATAGTTGA
53982954 CCAATGAGACCTTAACATGCCAAATGTTCAGATTTTGAAAGAACTCATCCGGAATTACTGCCCGA
391 CCAATGAGACCTTAACATGCCAAATGTTCAGATTTTGAAAGAACTCATCCGGAATTACTGCCCGA
53983019 ATTACCGGATCCTCGTATGGTGTCCATTGAAACTATGTGAACGAGATAAAAATATTAGTTATATA
456 ATTACCGGATCCTCGTATGGTGTCCATTGAAACTATGTGAACGAGATAAAAATATTAGTTATATA
53983084 CATAATACTAAATACTAAATATGAAACAACTATTTTATGTATATATATTTTATTTAATACTTACT
521 CATAATACTAAATACTAAATATGAAACAACTATTTTATGTATATATATTTTATTTAATACTTACT
53983149 TGCGCTTCTGACTGTTGGTCTAATAGAAGCCGTATATCTTCAAGAGCGGTAGGCATTCCAACATA
586 TGCGCTTCTGACTGTTGGTCTAATAGAAGCCGTATATCTTCAAGAGCGGTAGGCATTCCAACATA
53983214 ACTCGCCAGATGGTTCCACCAAATTAAATAAATTTTTAGCATACAATTTTGTTTTAAATCTATGT
651 ACTCGCCAGATGGTTCCACCAAATTAAATAAATTTTTAGCATACAATTTTGTTTTAAATCTATGT
53983279 AATAATTGTAAAAAC
716 AATAATTGTAAAAAC
* *
53983294 ATTGTATAGGCGTTGTTGATGGGTCCATGATGTCATCATTTCTCCTTGGATTTAAAGGGCCTCAT
1 ATTGTATAGGCGTTGTTGATGGGTCCATGCTGTCATCCTTTCTCCTTGGATTTAAAGGGCCTCAT
53983359 TGTTCCCTTTTGACATGGATTTGCCGACACCTCTGCTCTTCCGGTAACAAATATGGCTTGTCATG
66 TGTTCCCTTTTGACATGGATTTGCCGACACCTCTGCTCTTCCGGTAACAAATATGGCTTGTCATG
*
53983424 GATCTTAAACCATTGTATGTAATCCGGCGCGCATGCTAACTCTAGGACGATGATCAGTTCGCGAG
131 GATCTTAAACCATTGCATGTAATCCGGCGCGCATGCTAACTCTAGGACGATGATCAGTTCGCGAG
* *
53983489 CAAGTATATGATCATACCGAATTTTCAAATTTTCGATATATTCTGATAAGAATACCAGTCAATTC
196 CAAGTATATGATCATACCGATTTTTCAAATTTTCGATATATTCTGAGAAGAATACCAGTCAATTC
*
53983554 GTATTTTTTTGCCATAAGTCAATTTTGTGCTCTTTATTGATCACCTCAGGTGCCTCGGGAATTGG
261 GTATTTTTTTGCCATAAGTCGATTTTGTGCTCTTTATTGATCACCTCAGGTGCCTCGGGAATTGG
53983619 TTTTTAGAATCTAAATTACCGCAACACTCTATCCGTCTGATGCATCTCGACAGTAACATAGTTGA
326 TTTTTAGAATCTAAATTACCGCAACACTCTATCCGTCTGATGCATCTCGACAGTAACATAGTTGA
53983684 CCAATGAGACCTTAACATGCCAAATGTTCAGATTTTGAAAGAACTCATCCGGAATTACTGCCCGA
391 CCAATGAGACCTTAACATGCCAAATGTTCAGATTTTGAAAGAACTCATCCGGAATTACTGCCCGA
53983749 ATTACCGGATCCTCGTATGGTGTCCATTGAAACTATGTGAACGAGATAAAAATATTAGTTATATA
456 ATTACCGGATCCTCGTATGGTGTCCATTGAAACTATGTGAACGAGATAAAAATATTAGTTATATA
53983814 CATAATACTAAATACTAAATATGAAACAACTATTTTATGTATATATATTTTATTTAATACTTACT
521 CATAATACTAAATACTAAATATGAAACAACTATTTTATGTATATATATTTTATTTAATACTTACT
*
53983879 TGCGCTTCTGACTGTTGGTCTAATAGAAGCCGTATATCTTCAAAAGCGGTAGGCATTCCAACATA
586 TGCGCTTCTGACTGTTGGTCTAATAGAAGCCGTATATCTTCAAGAGCGGTAGGCATTCCAACATA
53983944 ACTCGCCAGATGGTTCCACCAAATTAAATAAATTTTTAGCATACAATTTTGTTTTAAATCTATGT
651 ACTCGCCAGATGGTTCCACCAAATTAAATAAATTTTTAGCATACAATTTTGTTTTAAATCTATGT
53984009 AATAATTGTAAAAAC
716 AATAATTGTAAAAAC
* * *
53984024 ATTGTGTAGGCGTTGTTGATGGGTCCATGCTGTCATCCTTTCTCCTTGGATTTAGAGGGCCTTAT
1 ATTGTATAGGCGTTGTTGATGGGTCCATGCTGTCATCCTTTCTCCTTGGATTTAAAGGGCCTCAT
53984089 TGTTCCCTTTTGACATGGATTTGCCGACACCTCTGCTCTTCC-GTCAACAAATATGGCTTGTCAT
66 TGTTCCCTTTTGACATGGATTTGCCGACACCTCTGCTCTTCCGGT-AACAAATATGGCTTGTCAT
*
53984153 GGATCTTAAACCATTGCATGTAATCCGGCGCGCATGCTAACTCTAGGATGATGATCAGTTCGCGA
130 GGATCTTAAACCATTGCATGTAATCCGGCGCGCATGCTAACTCTAGGACGATGATCAGTTCGCGA
*
53984218 GCAAGTATATGATCATACCGATTTTTCAAATTTTCGATATATTCTAAGAAGAATACCAGTCAATT
195 GCAAGTATATGATCATACCGATTTTTCAAATTTTCGATATATTCTGAGAAGAATACCAGTCAATT
* *
53984283 CTTATTTTTTTGCCATAAGTCGATTTTGTGCTCTTTATTGAGCACCTCAGGTGCCTCGGGAATTG
260 CGTATTTTTTTGCCATAAGTCGATTTTGTGCTCTTTATTGATCACCTCAGGTGCCTCGGGAATTG
53984348 GTTTTTAGAATCTAAATTACCGCAACACTCTATCCGTCTGATGCATCTCGACAGTAACATAGTTG
325 GTTTTTAGAATCTAAATTACCGCAACACTCTATCCGTCTGATGCATCTCGACAGTAACATAGTTG
*
53984413 ACCAATGAGACCTTAACATGCCAAATGTTCAGATTTTGAAAGAATTCATCCGGAATTACTGCCCG
390 ACCAATGAGACCTTAACATGCCAAATGTTCAGATTTTGAAAGAACTCATCCGGAATTACTGCCCG
* **
53984478 AATTACTGGATCCTCGTATGGTGTCCATTGAAACTATGTGAAATAGATAAAAATATTAGTTATAT
455 AATTACCGGATCCTCGTATGGTGTCCATTGAAACTATGTGAACGAGATAAAAATATTAGTTATAT
53984543 ACATAATACTAAATACTAAATATGAAACAACTATTTTATGTATATATATTTTATTTAATACTTAC
520 ACATAATACTAAATACTAAATATGAAACAACTATTTTATGTATATATATTTTATTTAATACTTAC
* *
53984608 TTGCGCTTCTGACTGTTGGTCTAATAGAAGCTGTATATCTTCAAGAGCGGTAGGCATTCTAACAT
585 TTGCGCTTCTGACTGTTGGTCTAATAGAAGCCGTATATCTTCAAGAGCGGTAGGCATTCCAACAT
* *
53984673 AACTCGCCAGATGGTTCCACCTAATTAAATAAGTTTTTAGCATACAATTTTGTTTTAAATCTATG
650 AACTCGCCAGATGGTTCCACCAAATTAAATAAATTTTTAGCATACAATTTTGTTTTAAATCTATG
53984738 TAATAATTGTAAAA
715 TAATAATTGTAAAA
53984752 TCAAATAAAA
Statistics
Matches: 1423, Mismatches: 34, Indels: 2
0.98 0.02 0.00
Matches are distributed among these distances:
729 2 0.00
730 1421 1.00
ACGTcount: A:0.30, C:0.19, G:0.17, T:0.35
Consensus pattern (730 bp):
ATTGTATAGGCGTTGTTGATGGGTCCATGCTGTCATCCTTTCTCCTTGGATTTAAAGGGCCTCAT
TGTTCCCTTTTGACATGGATTTGCCGACACCTCTGCTCTTCCGGTAACAAATATGGCTTGTCATG
GATCTTAAACCATTGCATGTAATCCGGCGCGCATGCTAACTCTAGGACGATGATCAGTTCGCGAG
CAAGTATATGATCATACCGATTTTTCAAATTTTCGATATATTCTGAGAAGAATACCAGTCAATTC
GTATTTTTTTGCCATAAGTCGATTTTGTGCTCTTTATTGATCACCTCAGGTGCCTCGGGAATTGG
TTTTTAGAATCTAAATTACCGCAACACTCTATCCGTCTGATGCATCTCGACAGTAACATAGTTGA
CCAATGAGACCTTAACATGCCAAATGTTCAGATTTTGAAAGAACTCATCCGGAATTACTGCCCGA
ATTACCGGATCCTCGTATGGTGTCCATTGAAACTATGTGAACGAGATAAAAATATTAGTTATATA
CATAATACTAAATACTAAATATGAAACAACTATTTTATGTATATATATTTTATTTAATACTTACT
TGCGCTTCTGACTGTTGGTCTAATAGAAGCCGTATATCTTCAAGAGCGGTAGGCATTCCAACATA
ACTCGCCAGATGGTTCCACCAAATTAAATAAATTTTTAGCATACAATTTTGTTTTAAATCTATGT
AATAATTGTAAAAAC
Found at i:53985750 original size:30 final size:30
Alignment explanation
Indices: 53985716--53985784 Score: 102
Period size: 30 Copynumber: 2.3 Consensus size: 30
53985706 ATTAATTAAA
53985716 GAGAGTTTTGAGAAATTTAAAGAGAAATTT
1 GAGAGTTTTGAGAAATTTAAAGAGAAATTT
**
53985746 GAGAGTTTTGAGAAATTTAGGGAGAAATTT
1 GAGAGTTTTGAGAAATTTAAAGAGAAATTT
* *
53985776 AAGATTTTT
1 GAGAGTTTT
53985785 TTGCTAAAAT
Statistics
Matches: 35, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
30 35 1.00
ACGTcount: A:0.39, C:0.00, G:0.25, T:0.36
Consensus pattern (30 bp):
GAGAGTTTTGAGAAATTTAAAGAGAAATTT
Found at i:53988194 original size:16 final size:16
Alignment explanation
Indices: 53988175--53988206 Score: 55
Period size: 16 Copynumber: 2.0 Consensus size: 16
53988165 TTAAGCACGA
*
53988175 GGAAGGATTAGCACCC
1 GGAAGGATTAACACCC
53988191 GGAAGGATTAACACCC
1 GGAAGGATTAACACCC
53988207 TCGATACGCC
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 15 1.00
ACGTcount: A:0.34, C:0.25, G:0.28, T:0.12
Consensus pattern (16 bp):
GGAAGGATTAACACCC
Found at i:53989005 original size:26 final size:26
Alignment explanation
Indices: 53988880--53989005 Score: 98
Period size: 26 Copynumber: 4.9 Consensus size: 26
53988870 AAAGAAAATG
*
53988880 AAATAAAATAATATAT-AGAACAATTTG
1 AAAT-AAATAATATATCA-AACAATTTA
* * *
53988907 AAGTAAATAGTATA--AAATAATTTA
1 AAATAAATAATATATCAAACAATTTA
* * * *
53988931 AAGTAAATAATATGTAAAACAAATTA
1 AAATAAATAATATATCAAACAATTTA
*
53988957 AAATAAATAATACA-CAAAGCAATTTA
1 AAATAAATAATATATCAAA-CAATTTA
* *
53988983 AAATAAATAACATATCAGACAAT
1 AAATAAATAATATATCAAACAAT
53989006 AAAAAGTTTA
Statistics
Matches: 79, Mismatches: 16, Indels: 9
0.76 0.15 0.09
Matches are distributed among these distances:
24 19 0.24
25 4 0.05
26 50 0.63
27 6 0.08
ACGTcount: A:0.60, C:0.06, G:0.06, T:0.27
Consensus pattern (26 bp):
AAATAAATAATATATCAAACAATTTA
Found at i:53989062 original size:28 final size:27
Alignment explanation
Indices: 53988927--53989149 Score: 98
Period size: 26 Copynumber: 7.9 Consensus size: 27
53988917 TATAAAATAA
* **
53988927 TTTAAAGTAAATAATATGTAAAACAAA-
1 TTTAAAATAAATAATATACAAAA-AAAG
* **
53988954 -TTAAAATAAATAATACACAAAGCAA-
1 TTTAAAATAAATAATATACAAAAAAAG
53988979 TTTAAAATAAATAACATATCAGACAATAAAAAG
1 TTTAAAATAAAT-A-ATAT---ACAA-AAAAAG
* **
53989012 TTTAAAATAAATTATATGTAAAAAGAAG
1 TTTAAAATAAATAATATACAAAAA-AAG
* *
53989040 TTTCAAATAAATAATATAC-AAAATAG
1 TTTAAAATAAATAATATACAAAAAAAG
* * *
53989066 TTTTAAAAAATAAATGATGTATATATAAATAA-
1 -TTT--AAAATAAAT-A-ATATACA-AAAAAAG
* * * *
53989098 TTCAAAATAAATAATATA-TATAACAG
1 TTTAAAATAAATAATATACAAAAAAAG
*
53989124 TTTAAAAATAAATAATATATAAAAAA
1 TTT-AAAATAAATAATATACAAAAAA
53989150 TGGATAATAG
Statistics
Matches: 145, Mismatches: 32, Indels: 37
0.68 0.15 0.17
Matches are distributed among these distances:
25 5 0.03
26 32 0.22
27 30 0.21
28 27 0.19
29 17 0.12
30 1 0.01
31 14 0.10
32 3 0.02
33 16 0.11
ACGTcount: A:0.60, C:0.05, G:0.05, T:0.30
Consensus pattern (27 bp):
TTTAAAATAAATAATATACAAAAAAAG
Found at i:53989080 original size:29 final size:27
Alignment explanation
Indices: 53989004--53989147 Score: 107
Period size: 27 Copynumber: 5.2 Consensus size: 27
53988994 ATATCAGACA
*
53989004 ATAAAA-AGTTT-AAAATAAATTATAT
1 ATAAAATAGTTTAAAAATAAATAATAT
* * *
53989029 GTAAAAAGAAGTTT-CAAATAAATAATAT
1 AT-AAAA-TAGTTTAAAAATAAATAATAT
* *
53989057 ACAAAATAGTTTTAAAAAATAAATGATGTAT
1 ATAAAATAG-TTT-AAAAATAAAT-A-ATAT
* *
53989088 ATATAAATA-ATTCAAAATAAATAATAT
1 ATA-AAATAGTTTAAAAATAAATAATAT
* *
53989115 ATATAACAGTTTAAAAATAAATAATAT
1 ATAAAATAGTTTAAAAATAAATAATAT
53989142 ATAAAA
1 ATAAAA
53989148 AATGGATAAT
Statistics
Matches: 92, Mismatches: 17, Indels: 18
0.72 0.13 0.14
Matches are distributed among these distances:
25 1 0.01
26 9 0.10
27 34 0.37
28 18 0.20
29 17 0.18
30 3 0.03
31 5 0.05
32 5 0.05
ACGTcount: A:0.60, C:0.03, G:0.06, T:0.32
Consensus pattern (27 bp):
ATAAAATAGTTTAAAAATAAATAATAT
Found at i:53989249 original size:27 final size:25
Alignment explanation
Indices: 53989198--53989254 Score: 71
Period size: 25 Copynumber: 2.2 Consensus size: 25
53989188 TGGAAACTTG
*
53989198 AAATAAATAATAATAAAACAATTTA
1 AAATAAATAATAATAAAAAAATTTA
53989223 AAATAAATAAT-ATAAGAAAAAGGTTTA
1 AAATAAATAATAATAA-AAAAA--TTTA
53989250 AAATA
1 AAATA
53989255 TAAATGAAAA
Statistics
Matches: 28, Mismatches: 1, Indels: 4
0.85 0.03 0.12
Matches are distributed among these distances:
24 4 0.14
25 15 0.54
27 9 0.32
ACGTcount: A:0.67, C:0.02, G:0.05, T:0.26
Consensus pattern (25 bp):
AAATAAATAATAATAAAAAAATTTA
Found at i:53990856 original size:19 final size:19
Alignment explanation
Indices: 53990832--53990870 Score: 53
Period size: 19 Copynumber: 2.1 Consensus size: 19
53990822 TAATAACATA
53990832 AAAATAA-AATAAGTTAATC
1 AAAATAATAATAA-TTAATC
*
53990851 AAAATAATTATAATTAATC
1 AAAATAATAATAATTAATC
53990870 A
1 A
53990871 TGAATTAGCT
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
19 14 0.78
20 4 0.22
ACGTcount: A:0.62, C:0.05, G:0.03, T:0.31
Consensus pattern (19 bp):
AAAATAATAATAATTAATC
Found at i:53991457 original size:20 final size:20
Alignment explanation
Indices: 53991432--53991469 Score: 60
Period size: 20 Copynumber: 1.9 Consensus size: 20
53991422 TATGTTTGAA
53991432 ACGTTA-CGTTTTAGTTACTT
1 ACGTTATCGTTTT-GTTACTT
53991452 ACGTTATCGTTTTGTTAC
1 ACGTTATCGTTTTGTTAC
53991470 AAAGTGGTCA
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
20 11 0.65
21 6 0.35
ACGTcount: A:0.18, C:0.16, G:0.16, T:0.50
Consensus pattern (20 bp):
ACGTTATCGTTTTGTTACTT
Found at i:54000520 original size:11 final size:11
Alignment explanation
Indices: 54000479--54000518 Score: 55
Period size: 11 Copynumber: 3.6 Consensus size: 11
54000469 CTCTAATATT
54000479 CTCTCAATTTC
1 CTCTCAATTTC
54000490 CTCTCAATTTC
1 CTCTCAATTTC
*
54000501 CTCTGAAATTT-
1 CTCT-CAATTTC
54000512 CTCTCAA
1 CTCTCAA
54000519 ATCCCTATTT
Statistics
Matches: 26, Mismatches: 2, Indels: 3
0.84 0.06 0.10
Matches are distributed among these distances:
10 2 0.08
11 19 0.73
12 5 0.19
ACGTcount: A:0.23, C:0.33, G:0.03, T:0.42
Consensus pattern (11 bp):
CTCTCAATTTC
Found at i:54002387 original size:18 final size:18
Alignment explanation
Indices: 54002364--54002406 Score: 59
Period size: 18 Copynumber: 2.4 Consensus size: 18
54002354 TGCCAGGTGC
* *
54002364 GTATCCTAGCCCTTTTAT
1 GTATCCTAACCCTTATAT
54002382 GTATCCTAACCCTTATAT
1 GTATCCTAACCCTTATAT
*
54002400 GTTTCCT
1 GTATCCT
54002407 TTTTCGAGTC
Statistics
Matches: 22, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
18 22 1.00
ACGTcount: A:0.19, C:0.28, G:0.09, T:0.44
Consensus pattern (18 bp):
GTATCCTAACCCTTATAT
Found at i:54002674 original size:21 final size:21
Alignment explanation
Indices: 54002647--54002694 Score: 62
Period size: 21 Copynumber: 2.3 Consensus size: 21
54002637 CCAACACCAA
54002647 CAACCAG-ATACCCTACCGGAG
1 CAACCAGAAT-CCCTACCGGAG
* *
54002668 GAACCAGAATCCTTACCGGAG
1 CAACCAGAATCCCTACCGGAG
54002689 CAACCA
1 CAACCA
54002695 CAACCCCCGC
Statistics
Matches: 23, Mismatches: 3, Indels: 2
0.82 0.11 0.07
Matches are distributed among these distances:
21 21 0.91
22 2 0.09
ACGTcount: A:0.35, C:0.35, G:0.19, T:0.10
Consensus pattern (21 bp):
CAACCAGAATCCCTACCGGAG
Found at i:54003060 original size:7 final size:7
Alignment explanation
Indices: 54003045--54003091 Score: 58
Period size: 7 Copynumber: 6.7 Consensus size: 7
54003035 TAACATATTG
54003045 TAAACCC
1 TAAACCC
*
54003052 TAAATCC
1 TAAACCC
54003059 TAAACCC
1 TAAACCC
*
54003066 TAAACCT
1 TAAACCC
**
54003073 TAAACAT
1 TAAACCC
54003080 TAAACCC
1 TAAACCC
54003087 TAAAC
1 TAAAC
54003092 TTGTACCGAA
Statistics
Matches: 34, Mismatches: 6, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
7 34 1.00
ACGTcount: A:0.47, C:0.32, G:0.00, T:0.21
Consensus pattern (7 bp):
TAAACCC
Found at i:54004334 original size:125 final size:126
Alignment explanation
Indices: 54004115--54004379 Score: 390
Period size: 125 Copynumber: 2.1 Consensus size: 126
54004105 GCCACTGTAG
* *
54004115 CAAAAGC-ACGTCCACGTGGGAGCTTCTTTCAGTACTTCTGCTGACAAAGCATCTTGCTTAAACC
1 CAAAAGCGA-GTCCACGTGGGAGCTTCTTTCAATACTTCTGCTGACAAAGCATCCTGCTTAAACC
* * *
54004179 GTTTTTGACACTATTTGCTCAGAAATGTCTACTCG-AATTATTTTTTCAAGAGCTACTATAG
65 GTTTTTGACACTATTTGCTCAAAAACGTCTACTCGAAATTATTTTTTCAAGAGCTACTATAA
* * *
54004240 CAAAGGCGAGTCCACGTGGGAGCTTTTTTCAATACTTCTGCTGACAAAGCATCCTGCTTAAAGCG
1 CAAAAGCGAGTCCACGTGGGAGCTTCTTTCAATACTTCTGCTGACAAAGCATCCTGCTTAAACCG
* * * *
54004305 TTTTTGACACTTTTTGCTCAAAAACGTCTACTCGAAATTATTTTTTTAGGAGCTACTGTAA
66 TTTTTGACACTATTTGCTCAAAAACGTCTACTCGAAATTATTTTTTCAAGAGCTACTATAA
*
54004366 CAAAAGCGCGTCCA
1 CAAAAGCGAGTCCA
54004380 ACCCTAATCT
Statistics
Matches: 124, Mismatches: 14, Indels: 3
0.88 0.10 0.02
Matches are distributed among these distances:
125 89 0.72
126 35 0.28
ACGTcount: A:0.28, C:0.22, G:0.18, T:0.32
Consensus pattern (126 bp):
CAAAAGCGAGTCCACGTGGGAGCTTCTTTCAATACTTCTGCTGACAAAGCATCCTGCTTAAACCG
TTTTTGACACTATTTGCTCAAAAACGTCTACTCGAAATTATTTTTTCAAGAGCTACTATAA
Found at i:54005147 original size:21 final size:19
Alignment explanation
Indices: 54005109--54005155 Score: 60
Period size: 19 Copynumber: 2.5 Consensus size: 19
54005099 TTGTAAATTT
54005109 TATTTTTAAAAATTATATA
1 TATTTTTAAAAATTATATA
*
54005128 TATTTTTATAATATT-TATA
1 TATTTTTA-AAAATTATATA
*
54005147 TACTTTTAA
1 TATTTTTAA
54005156 TAAAAAATTA
Statistics
Matches: 25, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
18 1 0.04
19 19 0.76
20 5 0.20
ACGTcount: A:0.40, C:0.02, G:0.00, T:0.57
Consensus pattern (19 bp):
TATTTTTAAAAATTATATA
Found at i:54005166 original size:21 final size:21
Alignment explanation
Indices: 54005115--54005166 Score: 54
Period size: 20 Copynumber: 2.5 Consensus size: 21
54005105 ATTTTATTTT
*
54005115 TAAAAATTATATATATTTTTA
1 TAAAAATTATATATATTTTAA
*
54005136 T-AATATT-TATATACTTTTAA
1 TAAAAATTATATATA-TTTTAA
54005156 TAAAAAATTAT
1 T-AAAAATTAT
54005167 TTATTTATTT
Statistics
Matches: 24, Mismatches: 3, Indels: 6
0.73 0.09 0.18
Matches are distributed among these distances:
19 6 0.25
20 11 0.46
21 1 0.04
22 5 0.21
23 1 0.04
ACGTcount: A:0.48, C:0.02, G:0.00, T:0.50
Consensus pattern (21 bp):
TAAAAATTATATATATTTTAA
Found at i:54006519 original size:6 final size:6
Alignment explanation
Indices: 54006508--54006571 Score: 110
Period size: 6 Copynumber: 10.7 Consensus size: 6
54006498 AGTAGCAATG
54006508 GCAGGA GCAGGA GCAGGA GCAGGA GCAGGA GCAGGA GCAGGA GCAGGA
1 GCAGGA GCAGGA GCAGGA GCAGGA GCAGGA GCAGGA GCAGGA GCAGGA
* *
54006556 GAAGAA GCAGGA GCAG
1 GCAGGA GCAGGA GCAG
54006572 TCGCAGGCCC
Statistics
Matches: 54, Mismatches: 4, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
6 54 1.00
ACGTcount: A:0.36, C:0.16, G:0.48, T:0.00
Consensus pattern (6 bp):
GCAGGA
Found at i:54009889 original size:23 final size:23
Alignment explanation
Indices: 54009863--54009912 Score: 55
Period size: 23 Copynumber: 2.2 Consensus size: 23
54009853 TCTTGCTCTC
*
54009863 TTTTTTTACCCTTTTTTTTACTA
1 TTTTCTTACCCTTTTTTTTACTA
****
54009886 TTTTCTTGTTGTTTTTTTTACTA
1 TTTTCTTACCCTTTTTTTTACTA
54009909 TTTT
1 TTTT
54009913 GCTACTATTT
Statistics
Matches: 22, Mismatches: 5, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
23 22 1.00
ACGTcount: A:0.10, C:0.12, G:0.04, T:0.74
Consensus pattern (23 bp):
TTTTCTTACCCTTTTTTTTACTA
Found at i:54022089 original size:11 final size:11
Alignment explanation
Indices: 54022073--54022098 Score: 52
Period size: 11 Copynumber: 2.4 Consensus size: 11
54022063 ATTTTTTTAA
54022073 TTTTAAAATAC
1 TTTTAAAATAC
54022084 TTTTAAAATAC
1 TTTTAAAATAC
54022095 TTTT
1 TTTT
54022099 TTTTTAATTT
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 15 1.00
ACGTcount: A:0.38, C:0.08, G:0.00, T:0.54
Consensus pattern (11 bp):
TTTTAAAATAC
Found at i:54022109 original size:42 final size:40
Alignment explanation
Indices: 54022063--54022150 Score: 131
Period size: 42 Copynumber: 2.1 Consensus size: 40
54022053 TATTATTATT
*
54022063 ATTTTTTTAATTTTAAAATACTTTTAAAATACTTTTTTTTTA
1 ATTTTTTTAATTTTAAAATACTTTTAAAAT--TTTTGTTTTA
**
54022105 ATTTTTTTAATTTTAAAATACTTTTTTAATTTTTGTTTTA
1 ATTTTTTTAATTTTAAAATACTTTTAAAATTTTTGTTTTA
54022145 ATTTTT
1 ATTTTT
54022151 AAAATAAATT
Statistics
Matches: 43, Mismatches: 3, Indels: 2
0.90 0.06 0.04
Matches are distributed among these distances:
40 15 0.35
42 28 0.65
ACGTcount: A:0.30, C:0.03, G:0.01, T:0.66
Consensus pattern (40 bp):
ATTTTTTTAATTTTAAAATACTTTTAAAATTTTTGTTTTA
Found at i:54022119 original size:31 final size:31
Alignment explanation
Indices: 54022084--54022156 Score: 96
Period size: 31 Copynumber: 2.3 Consensus size: 31
54022074 TTTAAAATAC
*
54022084 TTTTAAAATACTTTTTT-TTTAATTTTTTTAA-
1 TTTTAAAATACTTTTTTATTT--TTGTTTTAAT
54022115 TTTTAAAATACTTTTTTAATTTTTGTTTTAAT
1 TTTTAAAATACTTTTTT-ATTTTTGTTTTAAT
54022147 TTTTAAAATA
1 TTTTAAAATA
54022157 AATTTTTGGT
Statistics
Matches: 38, Mismatches: 1, Indels: 5
0.86 0.02 0.11
Matches are distributed among these distances:
31 25 0.66
32 10 0.26
33 3 0.08
ACGTcount: A:0.32, C:0.03, G:0.01, T:0.64
Consensus pattern (31 bp):
TTTTAAAATACTTTTTTATTTTTGTTTTAAT
Found at i:54022680 original size:20 final size:20
Alignment explanation
Indices: 54022623--54022686 Score: 64
Period size: 19 Copynumber: 3.3 Consensus size: 20
54022613 TTTTTTAAAT
*
54022623 ATTTTTT-ATATTTAATTTA
1 ATTTTTTAATATATAATTTA
*
54022642 A-TTATTAAT-TATTATATTTA
1 ATTTTTTAATATA-TA-ATTTA
54022662 ATTTTTTAATATATAATTT-
1 ATTTTTTAATATATAATTTA
54022681 ATTTTT
1 ATTTTT
54022687 ATATGACATT
Statistics
Matches: 37, Mismatches: 3, Indels: 10
0.74 0.06 0.20
Matches are distributed among these distances:
18 5 0.14
19 11 0.30
20 10 0.27
21 9 0.24
22 2 0.05
ACGTcount: A:0.34, C:0.00, G:0.00, T:0.66
Consensus pattern (20 bp):
ATTTTTTAATATATAATTTA
Found at i:54023791 original size:3 final size:3
Alignment explanation
Indices: 54023783--54023823 Score: 82
Period size: 3 Copynumber: 13.7 Consensus size: 3
54023773 ATTCAAATAC
54023783 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT AT
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT AT
54023824 CTTTTAATTA
Statistics
Matches: 38, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 38 1.00
ACGTcount: A:0.34, C:0.00, G:0.00, T:0.66
Consensus pattern (3 bp):
ATT
Found at i:54024121 original size:11 final size:11
Alignment explanation
Indices: 54024105--54024234 Score: 91
Period size: 11 Copynumber: 12.4 Consensus size: 11
54024095 ATTTTTTTAA
*
54024105 TTTTAAAATGT
1 TTTTAAAATAT
54024116 TTTTAAAATACT
1 TTTTAAAATA-T
*
54024128 TTTT-TAA-A-
1 TTTTAAAATAT
54024136 TTTTAAAATAT
1 TTTTAAAATAT
54024147 TTTTAAAATAT
1 TTTTAAAATAT
54024158 TTTTAAAATACT
1 TTTTAAAATA-T
*
54024170 TTTT-TAAT-T
1 TTTTAAAATAT
* *
54024179 TTTT---TTAA
1 TTTTAAAATAT
54024187 TTTTAAAATAT
1 TTTTAAAATAT
54024198 TTTTAAAATACT
1 TTTTAAAATA-T
**
54024210 TTTT-TTA-AT
1 TTTTAAAATAT
54024219 TTTTAAAATAAT
1 TTTTAAAAT-AT
54024231 TTTT
1 TTTT
54024235 TGGTATTTAT
Statistics
Matches: 94, Mismatches: 12, Indels: 25
0.72 0.09 0.19
Matches are distributed among these distances:
7 1 0.01
8 8 0.09
9 12 0.13
10 4 0.04
11 48 0.51
12 21 0.22
ACGTcount: A:0.38, C:0.02, G:0.01, T:0.59
Consensus pattern (11 bp):
TTTTAAAATAT
Found at i:54024138 original size:31 final size:30
Alignment explanation
Indices: 54024094--54024166 Score: 110
Period size: 31 Copynumber: 2.4 Consensus size: 30
54024084 TAAATATATT
* *
54024094 TATTTTTTTAATTTTAAAATGTTTTTAAAA
1 TATTTTTTAAATTTTAAAATATTTTTAAAA
54024124 TACTTTTTTAAATTTTAAAATATTTTTAAAA
1 TA-TTTTTTAAATTTTAAAATATTTTTAAAA
*
54024155 TATTTTTAAAAT
1 TATTTTTTAAAT
54024167 ACTTTTTTAA
Statistics
Matches: 39, Mismatches: 3, Indels: 2
0.89 0.07 0.05
Matches are distributed among these distances:
30 11 0.28
31 28 0.72
ACGTcount: A:0.40, C:0.01, G:0.01, T:0.58
Consensus pattern (30 bp):
TATTTTTTAAATTTTAAAATATTTTTAAAA
Found at i:54029964 original size:17 final size:17
Alignment explanation
Indices: 54029942--54029981 Score: 55
Period size: 17 Copynumber: 2.4 Consensus size: 17
54029932 TAAATTTTTT
* *
54029942 TATATAATTTTTAAAAA
1 TATATAATATATAAAAA
54029959 TATATAATATATAAAAA
1 TATATAATATATAAAAA
54029976 TA-ATAA
1 TATATAA
54029982 AAATATTAAA
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
16 4 0.19
17 17 0.81
ACGTcount: A:0.60, C:0.00, G:0.00, T:0.40
Consensus pattern (17 bp):
TATATAATATATAAAAA
Found at i:54029987 original size:17 final size:18
Alignment explanation
Indices: 54029953--54029995 Score: 54
Period size: 17 Copynumber: 2.5 Consensus size: 18
54029943 ATATAATTTT
*
54029953 TAAAAAT-ATATAATATA
1 TAAAAATAATATAAAATA
54029970 TAAAAATAATA-AAAATA
1 TAAAAATAATATAAAATA
*
54029987 TTAAAATAA
1 TAAAAATAA
54029996 ATATTTCTCA
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
17 20 0.87
18 3 0.13
ACGTcount: A:0.70, C:0.00, G:0.00, T:0.30
Consensus pattern (18 bp):
TAAAAATAATATAAAATA
Found at i:54030252 original size:20 final size:21
Alignment explanation
Indices: 54030210--54030255 Score: 76
Period size: 21 Copynumber: 2.2 Consensus size: 21
54030200 AAGAAAATAG
54030210 CAATAAAACAATAAAATACAA
1 CAATAAAACAATAAAATACAA
*
54030231 CAATAAAGCAATAAAA-ACAA
1 CAATAAAACAATAAAATACAA
54030251 CAATA
1 CAATA
54030256 GTTTTTGTTT
Statistics
Matches: 24, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
20 9 0.38
21 15 0.62
ACGTcount: A:0.70, C:0.15, G:0.02, T:0.13
Consensus pattern (21 bp):
CAATAAAACAATAAAATACAA
Found at i:54035329 original size:13 final size:13
Alignment explanation
Indices: 54035311--54035366 Score: 64
Period size: 13 Copynumber: 4.5 Consensus size: 13
54035301 TAGATTTTTC
54035311 CTAAATATTATCA
1 CTAAATATTATCA
*
54035324 CTAAATATTATAA
1 CTAAATATTATCA
* *
54035337 GTAAATA--AT-T
1 CTAAATATTATCA
54035347 CTAAATATTATCA
1 CTAAATATTATCA
54035360 CTAAATA
1 CTAAATA
54035367 ATTCTAAATT
Statistics
Matches: 35, Mismatches: 5, Indels: 6
0.76 0.11 0.13
Matches are distributed among these distances:
10 6 0.17
11 2 0.06
12 2 0.06
13 25 0.71
ACGTcount: A:0.50, C:0.11, G:0.02, T:0.38
Consensus pattern (13 bp):
CTAAATATTATCA
Found at i:54035352 original size:23 final size:23
Alignment explanation
Indices: 54035324--54035375 Score: 86
Period size: 23 Copynumber: 2.3 Consensus size: 23
54035314 AATATTATCA
*
54035324 CTAAATATTATAAGTAAATAATT
1 CTAAATATTATAACTAAATAATT
*
54035347 CTAAATATTATCACTAAATAATT
1 CTAAATATTATAACTAAATAATT
54035370 CTAAAT
1 CTAAAT
54035376 TTAAAAATCA
Statistics
Matches: 27, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
23 27 1.00
ACGTcount: A:0.50, C:0.10, G:0.02, T:0.38
Consensus pattern (23 bp):
CTAAATATTATAACTAAATAATT
Found at i:54035388 original size:23 final size:23
Alignment explanation
Indices: 54035324--54035388 Score: 69
Period size: 23 Copynumber: 2.8 Consensus size: 23
54035314 AATATTATCA
* *
54035324 CTAAATATTATAAGTAAATAATT
1 CTAAATATTAAAAATAAATAATT
** *
54035347 CTAAATATTATCACTAAATAATT
1 CTAAATATTAAAAATAAATAATT
54035370 CTAAAT-TTAAAAATCAAAT
1 CTAAATATTAAAAAT-AAAT
54035389 TTAAACTAAT
Statistics
Matches: 36, Mismatches: 5, Indels: 2
0.84 0.12 0.05
Matches are distributed among these distances:
22 5 0.14
23 31 0.86
ACGTcount: A:0.52, C:0.09, G:0.02, T:0.37
Consensus pattern (23 bp):
CTAAATATTAAAAATAAATAATT
Found at i:54036908 original size:15 final size:14
Alignment explanation
Indices: 54036879--54036912 Score: 50
Period size: 15 Copynumber: 2.4 Consensus size: 14
54036869 CTAAAACTCA
*
54036879 AAATTAAATGAAAT
1 AAATAAAATGAAAT
54036893 AAATAAAATAGAAAT
1 AAATAAAAT-GAAAT
54036908 AAATA
1 AAATA
54036913 TGGGTTGCCT
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
14 8 0.44
15 10 0.56
ACGTcount: A:0.71, C:0.00, G:0.06, T:0.24
Consensus pattern (14 bp):
AAATAAAATGAAAT
Found at i:54039799 original size:18 final size:19
Alignment explanation
Indices: 54039761--54039797 Score: 56
Period size: 19 Copynumber: 1.9 Consensus size: 19
54039751 ACTTGAAATT
54039761 ATAAAAAAAAATAAAGGGG
1 ATAAAAAAAAATAAAGGGG
* *
54039780 ATAAACAAAAATATAGGG
1 ATAAAAAAAAATAAAGGG
54039798 ATTTTTATGA
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
19 16 1.00
ACGTcount: A:0.65, C:0.03, G:0.19, T:0.14
Consensus pattern (19 bp):
ATAAAAAAAAATAAAGGGG
Found at i:54039936 original size:13 final size:13
Alignment explanation
Indices: 54039920--54039944 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
54039910 ATAATACTTT
54039920 TTATATTTAATTA
1 TTATATTTAATTA
54039933 TTATATTTAATT
1 TTATATTTAATT
54039945 TTAAAAATAT
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.36, C:0.00, G:0.00, T:0.64
Consensus pattern (13 bp):
TTATATTTAATTA
Found at i:54041590 original size:50 final size:50
Alignment explanation
Indices: 54041515--54041707 Score: 350
Period size: 50 Copynumber: 3.9 Consensus size: 50
54041505 GATAATAACA
* * *
54041515 TGCCAAAGCCATGTCCCAGACATGGTCTTATAGGGGACCTCTCATCTCGG
1 TGCCAATGCCATGTCCCAGACATGGTCTTACATGGGACCTCTCATCTCGG
*
54041565 TGCCAACGCCATGTCCCAGACATGGTCTTACATGGGACCTCTCATCTCGG
1 TGCCAATGCCATGTCCCAGACATGGTCTTACATGGGACCTCTCATCTCGG
54041615 TGCCAATGCCATGTCCCAGACATGGTCTTACATGGGACCTCTCATCTCGG
1 TGCCAATGCCATGTCCCAGACATGGTCTTACATGGGACCTCTCATCTCGG
54041665 TGCCAATGCCATGTCCCAGACATGGTCTTACATGGGACCTCTC
1 TGCCAATGCCATGTCCCAGACATGGTCTTACATGGGACCTCTC
54041708 GGTACCAATT
Statistics
Matches: 139, Mismatches: 4, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
50 139 1.00
ACGTcount: A:0.21, C:0.32, G:0.22, T:0.25
Consensus pattern (50 bp):
TGCCAATGCCATGTCCCAGACATGGTCTTACATGGGACCTCTCATCTCGG
Found at i:54048491 original size:50 final size:50
Alignment explanation
Indices: 54048376--54048619 Score: 398
Period size: 50 Copynumber: 4.9 Consensus size: 50
54048366 GATAATAACA
* ** * *
54048376 TGCCAAAGCCATGTCCCAGACATGGTCTTACATGGGATGTTCTCATGTTGG
1 TGCCAATGCCATGTCCCAGACATGGTCTTACATGGGA-CCTCTCATCTCGG
* * *
54048427 TGCCCATGCCATGTCCCAGACATGGTCTTATAGGGGACCTCTCATCTCGG
1 TGCCAATGCCATGTCCCAGACATGGTCTTACATGGGACCTCTCATCTCGG
*
54048477 TGCCAACGCCATGTCCCAGACATGGTCTTACATGGGACCTCTCATCTCGG
1 TGCCAATGCCATGTCCCAGACATGGTCTTACATGGGACCTCTCATCTCGG
54048527 TGCCAATGCCATGTCCCAGACATGGTCTTACATGGGACCTCTCATCTCGG
1 TGCCAATGCCATGTCCCAGACATGGTCTTACATGGGACCTCTCATCTCGG
54048577 TGCCAATGCCATGTCCCAGACATGGTCTTACATGGGACCTCTC
1 TGCCAATGCCATGTCCCAGACATGGTCTTACATGGGACCTCTC
54048620 GGTACCAATT
Statistics
Matches: 180, Mismatches: 13, Indels: 1
0.93 0.07 0.01
Matches are distributed among these distances:
50 147 0.82
51 33 0.18
ACGTcount: A:0.20, C:0.31, G:0.23, T:0.26
Consensus pattern (50 bp):
TGCCAATGCCATGTCCCAGACATGGTCTTACATGGGACCTCTCATCTCGG
Found at i:54056415 original size:20 final size:20
Alignment explanation
Indices: 54056377--54056415 Score: 51
Period size: 20 Copynumber: 1.9 Consensus size: 20
54056367 GGTTCATGCC
* *
54056377 TTTCAGTTACGTATTTCATA
1 TTTCAGTTACATATATCATA
*
54056397 TTTCAGTTATATATATCAT
1 TTTCAGTTACATATATCAT
54056416 TCATGTCACA
Statistics
Matches: 16, Mismatches: 3, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
20 16 1.00
ACGTcount: A:0.28, C:0.13, G:0.08, T:0.51
Consensus pattern (20 bp):
TTTCAGTTACATATATCATA
Found at i:54060734 original size:48 final size:48
Alignment explanation
Indices: 54060652--54060745 Score: 129
Period size: 48 Copynumber: 2.0 Consensus size: 48
54060642 TTTCTTGGCT
* * *
54060652 TAAAAACGCCTAAGTCAGCCTAACTTCCACCAATAATGGATTCAACCG
1 TAAAAACGCCTAAATCAGCCTAACTTCCAACAATAAAGGATTCAACCG
54060700 TAAAAACGCCTAAATCAG-CTCAAC-TCGCAACAATAAAGGATTCAAC
1 TAAAAACGCCTAAATCAGCCT-AACTTC-CAACAATAAAGGATTCAAC
54060746 AGAATTCCCT
Statistics
Matches: 41, Mismatches: 3, Indels: 4
0.85 0.06 0.08
Matches are distributed among these distances:
47 4 0.10
48 37 0.90
ACGTcount: A:0.41, C:0.28, G:0.12, T:0.19
Consensus pattern (48 bp):
TAAAAACGCCTAAATCAGCCTAACTTCCAACAATAAAGGATTCAACCG
Found at i:54063246 original size:48 final size:48
Alignment explanation
Indices: 54063164--54063257 Score: 129
Period size: 48 Copynumber: 2.0 Consensus size: 48
54063154 TTTCTTGGCT
* * *
54063164 TAAAAACGCCTAAGTCAGCCTAACTTCCACCAATAATGGATTCAACCG
1 TAAAAACGCCTAAATCAGCCTAACTTCCAACAATAAAGGATTCAACCG
54063212 TAAAAACGCCTAAATCAG-CTCAAC-TCGCAACAATAAAGGATTCAAC
1 TAAAAACGCCTAAATCAGCCT-AACTTC-CAACAATAAAGGATTCAAC
54063258 AGAATTCCCT
Statistics
Matches: 41, Mismatches: 3, Indels: 4
0.85 0.06 0.08
Matches are distributed among these distances:
47 4 0.10
48 37 0.90
ACGTcount: A:0.41, C:0.28, G:0.12, T:0.19
Consensus pattern (48 bp):
TAAAAACGCCTAAATCAGCCTAACTTCCAACAATAAAGGATTCAACCG
Found at i:54088117 original size:30 final size:31
Alignment explanation
Indices: 54088075--54088144 Score: 90
Period size: 31 Copynumber: 2.3 Consensus size: 31
54088065 CGTCAAAGGG
* *
54088075 CAAACC-TTTCAAAA-TGATTAAATAATGGC
1 CAAACCTTTTCAAAATTGATCAAACAATGGC
* *
54088104 CAAATCTTTTCAAAATTGCTCAAACAATGGC
1 CAAACCTTTTCAAAATTGATCAAACAATGGC
54088135 CAAACCTTTT
1 CAAACCTTTT
54088145 TGAAAGTACT
Statistics
Matches: 34, Mismatches: 5, Indels: 2
0.83 0.12 0.05
Matches are distributed among these distances:
29 5 0.15
30 8 0.24
31 21 0.62
ACGTcount: A:0.40, C:0.21, G:0.09, T:0.30
Consensus pattern (31 bp):
CAAACCTTTTCAAAATTGATCAAACAATGGC
Found at i:54088157 original size:31 final size:31
Alignment explanation
Indices: 54088098--54088158 Score: 77
Period size: 31 Copynumber: 2.0 Consensus size: 31
54088088 ATGATTAAAT
* * *
54088098 AATGGCCAAATCTTTTCAAAATTGCTCAAAC
1 AATGGCCAAACCTTTTCAAAAGTACTCAAAC
**
54088129 AATGGCCAAACCTTTTTGAAAGTACTCAAA
1 AATGGCCAAACCTTTTCAAAAGTACTCAAA
54088159 TAAGGATTAT
Statistics
Matches: 25, Mismatches: 5, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
31 25 1.00
ACGTcount: A:0.39, C:0.21, G:0.11, T:0.28
Consensus pattern (31 bp):
AATGGCCAAACCTTTTCAAAAGTACTCAAAC
Found at i:54088362 original size:14 final size:14
Alignment explanation
Indices: 54088343--54088369 Score: 54
Period size: 14 Copynumber: 1.9 Consensus size: 14
54088333 CAAAACTACC
54088343 CATGAACTTTGATG
1 CATGAACTTTGATG
54088357 CATGAACTTTGAT
1 CATGAACTTTGAT
54088370 TTGGTGCAAT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 13 1.00
ACGTcount: A:0.30, C:0.15, G:0.19, T:0.37
Consensus pattern (14 bp):
CATGAACTTTGATG
Found at i:54090004 original size:23 final size:23
Alignment explanation
Indices: 54089955--54090005 Score: 61
Period size: 22 Copynumber: 2.3 Consensus size: 23
54089945 TGATATGTAA
* *
54089955 ATTTTTTATTTTGATTGAAAAGT
1 ATTTTTTATTTTGACTAAAAAGT
54089978 -TTTTATTATTTT-ACTAAAAAGT
1 ATTTT-TTATTTTGACTAAAAAGT
54090000 ATTTTT
1 ATTTTT
54090006 GTAAAAAAGT
Statistics
Matches: 24, Mismatches: 2, Indels: 5
0.77 0.06 0.16
Matches are distributed among these distances:
22 13 0.54
23 11 0.46
ACGTcount: A:0.31, C:0.02, G:0.08, T:0.59
Consensus pattern (23 bp):
ATTTTTTATTTTGACTAAAAAGT
Found at i:54090701 original size:24 final size:24
Alignment explanation
Indices: 54090669--54090715 Score: 76
Period size: 24 Copynumber: 2.0 Consensus size: 24
54090659 ATGTAAACAC
54090669 CCTTCAATTGAGCTATACATGATT
1 CCTTCAATTGAGCTATACATGATT
* *
54090693 CCTTTAATTGAGCTTTACATGAT
1 CCTTCAATTGAGCTATACATGAT
54090716 GCATTATCTT
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
24 21 1.00
ACGTcount: A:0.28, C:0.19, G:0.13, T:0.40
Consensus pattern (24 bp):
CCTTCAATTGAGCTATACATGATT
Found at i:54095669 original size:18 final size:18
Alignment explanation
Indices: 54095628--54095675 Score: 62
Period size: 18 Copynumber: 2.7 Consensus size: 18
54095618 TTATGTTCCA
*
54095628 AAAAATAATTTTTTTTGT
1 AAAATTAATTTTTTTTGT
**
54095646 TCAATTAATTTTTTTTGT
1 AAAATTAATTTTTTTTGT
54095664 AAAATT-ATTTTT
1 AAAATTAATTTTT
54095676 CGAAAAATTA
Statistics
Matches: 25, Mismatches: 5, Indels: 1
0.81 0.16 0.03
Matches are distributed among these distances:
17 6 0.24
18 19 0.76
ACGTcount: A:0.33, C:0.02, G:0.04, T:0.60
Consensus pattern (18 bp):
AAAATTAATTTTTTTTGT
Found at i:54096706 original size:14 final size:14
Alignment explanation
Indices: 54096687--54096716 Score: 60
Period size: 14 Copynumber: 2.1 Consensus size: 14
54096677 GATTAGTTAC
54096687 TTAATTCTTTAAAT
1 TTAATTCTTTAAAT
54096701 TTAATTCTTTAAAT
1 TTAATTCTTTAAAT
54096715 TT
1 TT
54096717 TTATAACATT
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 16 1.00
ACGTcount: A:0.33, C:0.07, G:0.00, T:0.60
Consensus pattern (14 bp):
TTAATTCTTTAAAT
Found at i:54098290 original size:21 final size:21
Alignment explanation
Indices: 54098266--54098311 Score: 51
Period size: 21 Copynumber: 2.2 Consensus size: 21
54098256 AAAAGCGTAA
54098266 ATTAAAACAA-CAAAATTTATT
1 ATTAAAACAATC-AAATTTATT
* *
54098287 ATTATACCAATCAAATTTATT
1 ATTAAAACAATCAAATTTATT
54098308 -TTAA
1 ATTAA
54098312 TTGATAAAAA
Statistics
Matches: 21, Mismatches: 3, Indels: 3
0.78 0.11 0.11
Matches are distributed among these distances:
20 3 0.14
21 17 0.81
22 1 0.05
ACGTcount: A:0.50, C:0.11, G:0.00, T:0.39
Consensus pattern (21 bp):
ATTAAAACAATCAAATTTATT
Found at i:54098339 original size:63 final size:62
Alignment explanation
Indices: 54098248--54098366 Score: 193
Period size: 63 Copynumber: 1.9 Consensus size: 62
54098238 ATCATGATTA
* *
54098248 AATTGATAAAAAGCGTAAATTAAAACAACAAAATTTATTATTATACCAATCAAATTTATTTT
1 AATTGATAAAAAACGTAAAATAAAACAACAAAATTTATTATTATACCAATCAAATTTATTTT
* *
54098310 AATTGATAAAAACACGTAAAATATAACAACCAAATTTATTATTATACCAATCAAATT
1 AATTGATAAAAA-ACGTAAAATAAAACAACAAAATTTATTATTATACCAATCAAATT
54098367 GACCGAAATC
Statistics
Matches: 52, Mismatches: 4, Indels: 1
0.91 0.07 0.02
Matches are distributed among these distances:
62 12 0.23
63 40 0.77
ACGTcount: A:0.51, C:0.12, G:0.04, T:0.33
Consensus pattern (62 bp):
AATTGATAAAAAACGTAAAATAAAACAACAAAATTTATTATTATACCAATCAAATTTATTTT
Found at i:54101161 original size:20 final size:20
Alignment explanation
Indices: 54101133--54101170 Score: 58
Period size: 20 Copynumber: 1.9 Consensus size: 20
54101123 TGAAAGTCAA
*
54101133 AAGTCTTGGGCAATAGAAAG
1 AAGTCTTGGGCAAGAGAAAG
*
54101153 AAGTTTTGGGCAAGAGAA
1 AAGTCTTGGGCAAGAGAA
54101171 TTTAAAAGAA
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:0.39, C:0.08, G:0.32, T:0.21
Consensus pattern (20 bp):
AAGTCTTGGGCAAGAGAAAG
Found at i:54102462 original size:29 final size:30
Alignment explanation
Indices: 54102429--54102487 Score: 93
Period size: 29 Copynumber: 2.0 Consensus size: 30
54102419 TATGGTTCAA
54102429 TGTGTAATTATATATATG-AATTTTAATTT
1 TGTGTAATTATATATATGAAATTTTAATTT
* *
54102458 TGTGTAATTTTATATATGAAATTTTGATTT
1 TGTGTAATTATATATATGAAATTTTAATTT
54102488 GATCCAATTC
Statistics
Matches: 27, Mismatches: 2, Indels: 1
0.90 0.07 0.03
Matches are distributed among these distances:
29 17 0.63
30 10 0.37
ACGTcount: A:0.32, C:0.00, G:0.12, T:0.56
Consensus pattern (30 bp):
TGTGTAATTATATATATGAAATTTTAATTT
Found at i:54104545 original size:3 final size:3
Alignment explanation
Indices: 54104537--54104564 Score: 56
Period size: 3 Copynumber: 9.3 Consensus size: 3
54104527 TGGGATGCAT
54104537 GCA GCA GCA GCA GCA GCA GCA GCA GCA G
1 GCA GCA GCA GCA GCA GCA GCA GCA GCA G
54104565 AGACTTTAGG
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 25 1.00
ACGTcount: A:0.32, C:0.32, G:0.36, T:0.00
Consensus pattern (3 bp):
GCA
Found at i:54111540 original size:21 final size:22
Alignment explanation
Indices: 54111510--54111551 Score: 59
Period size: 21 Copynumber: 2.0 Consensus size: 22
54111500 ATTTTAAAGT
54111510 TTTTTAAATAACAAAATAATTC
1 TTTTTAAATAACAAAATAATTC
* *
54111532 TTTTT-AATAATACAATAATT
1 TTTTTAAATAACAAAATAATT
54111552 AAATTATTCC
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
21 13 0.72
22 5 0.28
ACGTcount: A:0.48, C:0.07, G:0.00, T:0.45
Consensus pattern (22 bp):
TTTTTAAATAACAAAATAATTC
Found at i:54113717 original size:18 final size:17
Alignment explanation
Indices: 54113679--54113727 Score: 55
Period size: 17 Copynumber: 2.9 Consensus size: 17
54113669 ATACTCTCTC
*
54113679 TTTTTCTAATTTTCATA
1 TTTTTCTAATTTTAATA
54113696 TTTTTCTAAATTTTAAT-
1 TTTTTCT-AATTTTAATA
* *
54113713 TTTTTATTATTTTAA
1 TTTTTCTAATTTTAA
54113728 AATATTTTTA
Statistics
Matches: 28, Mismatches: 3, Indels: 3
0.82 0.09 0.09
Matches are distributed among these distances:
16 7 0.25
17 13 0.46
18 8 0.29
ACGTcount: A:0.27, C:0.06, G:0.00, T:0.67
Consensus pattern (17 bp):
TTTTTCTAATTTTAATA
Found at i:54119491 original size:51 final size:50
Alignment explanation
Indices: 54119433--54119619 Score: 250
Period size: 51 Copynumber: 3.7 Consensus size: 50
54119423 TCAGTTCACA
*
54119433 TAGTAGCCTGCACATAGTACTACACATGTGACCATTACCATTCGATACACG
1 TAGTAGCCTGCACATAGTACTACACACGTGACCA-TACCATTCGATACACG
* * * * *
54119484 TAGTAGCCTGCACATAGTACTACACACGTGACCGAAACTATCCGATACGCA
1 TAGTAGCCTGCACATAGTACTACACACGTGACC-ATACCATTCGATACACG
* * * *
54119535 TAGTAGCCTGCACATAGTACTACACATGCGACC-TATCATTCCGGTACACG
1 TAGTAGCCTGCACATAGTACTACACACGTGACCATACCATT-CGATACACG
54119585 TAGTAGCCTGCACATAGTACTACACACGTGACCAT
1 TAGTAGCCTGCACATAGTACTACACACGTGACCAT
54119620 CACTTTCACT
Statistics
Matches: 116, Mismatches: 17, Indels: 6
0.83 0.12 0.04
Matches are distributed among these distances:
49 3 0.03
50 37 0.32
51 75 0.65
52 1 0.01
ACGTcount: A:0.31, C:0.29, G:0.17, T:0.23
Consensus pattern (50 bp):
TAGTAGCCTGCACATAGTACTACACACGTGACCATACCATTCGATACACG
Found at i:54119608 original size:101 final size:101
Alignment explanation
Indices: 54119431--54119617 Score: 322
Period size: 101 Copynumber: 1.8 Consensus size: 101
54119421 GTTCAGTTCA
*
54119431 CATAGTAGCCTGCACATAGTACTACACATGTGACCATTACCATTCGATACACGTAGTAGCCTGCA
1 CATAGTAGCCTGCACATAGTACTACACATGCGACCA-TACCATTCGATACACGTAGTAGCCTGCA
54119496 CATAGTACTACACACGTGACCGAAACTATCCGATACG
65 CATAGTACTACACACGTGACCGAAACTATCCGATACG
* *
54119533 CATAGTAGCCTGCACATAGTACTACACATGCGACC-TATCATTCCGGTACACGTAGTAGCCTGCA
1 CATAGTAGCCTGCACATAGTACTACACATGCGACCATACCATT-CGATACACGTAGTAGCCTGCA
54119597 CATAGTACTACACACGTGACC
65 CATAGTACTACACACGTGACC
54119618 ATCACTTTCA
Statistics
Matches: 81, Mismatches: 3, Indels: 3
0.93 0.03 0.03
Matches are distributed among these distances:
100 6 0.07
101 41 0.51
102 34 0.42
ACGTcount: A:0.31, C:0.29, G:0.17, T:0.22
Consensus pattern (101 bp):
CATAGTAGCCTGCACATAGTACTACACATGCGACCATACCATTCGATACACGTAGTAGCCTGCAC
ATAGTACTACACACGTGACCGAAACTATCCGATACG
Found at i:54120169 original size:16 final size:16
Alignment explanation
Indices: 54120148--54120184 Score: 74
Period size: 16 Copynumber: 2.3 Consensus size: 16
54120138 TTTTAAATGA
54120148 TATTTTATTATTTTAT
1 TATTTTATTATTTTAT
54120164 TATTTTATTATTTTAT
1 TATTTTATTATTTTAT
54120180 TATTT
1 TATTT
54120185 AGTATATATA
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 21 1.00
ACGTcount: A:0.24, C:0.00, G:0.00, T:0.76
Consensus pattern (16 bp):
TATTTTATTATTTTAT
Found at i:54122150 original size:57 final size:57
Alignment explanation
Indices: 54122042--54122183 Score: 187
Period size: 57 Copynumber: 2.4 Consensus size: 57
54122032 AATTGACGGT
*
54122042 AAAAAGGATCTAGCCCGGACGGGTGATCCTATCTTGATATAGCCCTCCCGAAGAATGTGTGTG
1 AAAAA-GATCTAGCCCGGACGGGTG---C-ATCTTGATATAGCCCTCCCGAAGAATATGTG-G
54122105 AAAAAGATCTAGCCCGGACGGGTG-ATCTTGATATAGCCCTCCCGAAGAATATGTGG
1 AAAAAGATCTAGCCCGGACGGGTGCATCTTGATATAGCCCTCCCGAAGAATATGTGG
** *
54122161 AAATGGATTTAGCCCGGACGGGT
1 AAAAAGATCTAGCCCGGACGGGT
54122184 AATCCAAATT
Statistics
Matches: 75, Mismatches: 4, Indels: 7
0.87 0.05 0.08
Matches are distributed among these distances:
56 21 0.28
57 30 0.40
62 19 0.25
63 5 0.07
ACGTcount: A:0.28, C:0.21, G:0.28, T:0.23
Consensus pattern (57 bp):
AAAAAGATCTAGCCCGGACGGGTGCATCTTGATATAGCCCTCCCGAAGAATATGTGG
Found at i:54127146 original size:28 final size:30
Alignment explanation
Indices: 54127125--54127186 Score: 79
Period size: 30 Copynumber: 2.0 Consensus size: 30
54127115 CAAAACATTC
54127125 ATTTAACAGAGATAGTCACAAAAGCATCCT
1 ATTTAACAGAGATAGTCACAAAAGCATCCT
* ** *
54127155 TTTTAAGGGAGATAGTCACAAAGGACATCCT
1 ATTTAACAGAGATAGTCACAAAAG-CATCCT
54127186 A
1 A
54127187 ATTATAAGCT
Statistics
Matches: 26, Mismatches: 5, Indels: 1
0.81 0.16 0.03
Matches are distributed among these distances:
30 20 0.77
31 6 0.23
ACGTcount: A:0.40, C:0.18, G:0.18, T:0.24
Consensus pattern (30 bp):
ATTTAACAGAGATAGTCACAAAAGCATCCT
Found at i:54129563 original size:13 final size:11
Alignment explanation
Indices: 54129527--54129557 Score: 53
Period size: 11 Copynumber: 2.8 Consensus size: 11
54129517 CCGCCCGTAT
54129527 TAATTTTTATA
1 TAATTTTTATA
*
54129538 TTATTTTTATA
1 TAATTTTTATA
54129549 TAATTTTTA
1 TAATTTTTA
54129558 GATATATATT
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
11 18 1.00
ACGTcount: A:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (11 bp):
TAATTTTTATA
Found at i:54129569 original size:22 final size:22
Alignment explanation
Indices: 54129527--54129572 Score: 58
Period size: 22 Copynumber: 2.1 Consensus size: 22
54129517 CCGCCCGTAT
* *
54129527 TAATTTTTATATTATTTTTATA
1 TAATTTTTAGATTATTATTATA
54129549 TAATTTTTAGA-TATATATTATA
1 TAATTTTTAGATTAT-TATTATA
54129571 TA
1 TA
54129573 TCAAAAATAC
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
21 3 0.14
22 18 0.86
ACGTcount: A:0.37, C:0.00, G:0.02, T:0.61
Consensus pattern (22 bp):
TAATTTTTAGATTATTATTATA
Found at i:54132179 original size:6 final size:6
Alignment explanation
Indices: 54132168--54132193 Score: 52
Period size: 6 Copynumber: 4.3 Consensus size: 6
54132158 CTTAGCATCT
54132168 TTACTA TTACTA TTACTA TTACTA TT
1 TTACTA TTACTA TTACTA TTACTA TT
54132194 GGATTTCTAG
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 20 1.00
ACGTcount: A:0.31, C:0.15, G:0.00, T:0.54
Consensus pattern (6 bp):
TTACTA
Found at i:54132590 original size:18 final size:18
Alignment explanation
Indices: 54132567--54132603 Score: 56
Period size: 18 Copynumber: 2.1 Consensus size: 18
54132557 TATGTTGTAC
* *
54132567 ATAAAATTATCTTATAAA
1 ATAAAATAATCCTATAAA
54132585 ATAAAATAATCCTATAAA
1 ATAAAATAATCCTATAAA
54132603 A
1 A
54132604 ATATCTTATG
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
18 17 1.00
ACGTcount: A:0.59, C:0.08, G:0.00, T:0.32
Consensus pattern (18 bp):
ATAAAATAATCCTATAAA
Found at i:54133398 original size:12 final size:12
Alignment explanation
Indices: 54133381--54133405 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
54133371 GGTGTTCATT
54133381 CGGTTAACCGAC
1 CGGTTAACCGAC
54133393 CGGTTAACCGAC
1 CGGTTAACCGAC
54133405 C
1 C
54133406 CGAAATAATA
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:0.36, G:0.24, T:0.16
Consensus pattern (12 bp):
CGGTTAACCGAC
Found at i:54133580 original size:9 final size:9
Alignment explanation
Indices: 54133566--54133623 Score: 80
Period size: 9 Copynumber: 6.4 Consensus size: 9
54133556 TTTAGTGAAA
54133566 AATTAACCG
1 AATTAACCG
*
54133575 AATTAATCG
1 AATTAACCG
* *
54133584 GATTACCCG
1 AATTAACCG
54133593 AATTAACCG
1 AATTAACCG
54133602 AATTAACCG
1 AATTAACCG
*
54133611 AAATAACCG
1 AATTAACCG
54133620 AATT
1 AATT
54133624 GAATCACTAC
Statistics
Matches: 41, Mismatches: 8, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
9 41 1.00
ACGTcount: A:0.43, C:0.21, G:0.12, T:0.24
Consensus pattern (9 bp):
AATTAACCG
Found at i:54133766 original size:18 final size:18
Alignment explanation
Indices: 54133726--54133769 Score: 61
Period size: 18 Copynumber: 2.4 Consensus size: 18
54133716 AATTTTTATG
**
54133726 ATTGGGTTGGGTTGGGTA
1 ATTGGGTTGGGTTGAATA
54133744 ATTGGGTTGGGTTGAATA
1 ATTGGGTTGGGTTGAATA
*
54133762 CTTGGGTT
1 ATTGGGTT
54133770 TGGATTGGGT
Statistics
Matches: 23, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
18 23 1.00
ACGTcount: A:0.14, C:0.02, G:0.43, T:0.41
Consensus pattern (18 bp):
ATTGGGTTGGGTTGAATA
Found at i:54140537 original size:27 final size:27
Alignment explanation
Indices: 54140497--54140555 Score: 111
Period size: 27 Copynumber: 2.2 Consensus size: 27
54140487 ATTATATTAA
54140497 GTGC-TTAAAATCATTCTAGATATGTC
1 GTGCTTTAAAATCATTCTAGATATGTC
54140523 GTGCTTTAAAATCATTCTAGATATGTC
1 GTGCTTTAAAATCATTCTAGATATGTC
54140550 GTGCTT
1 GTGCTT
54140556 GAGTTGTGAT
Statistics
Matches: 32, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
26 4 0.12
27 28 0.88
ACGTcount: A:0.27, C:0.15, G:0.17, T:0.41
Consensus pattern (27 bp):
GTGCTTTAAAATCATTCTAGATATGTC
Found at i:54142760 original size:4 final size:4
Alignment explanation
Indices: 54142753--54142823 Score: 58
Period size: 4 Copynumber: 17.2 Consensus size: 4
54142743 AACCCTTGCG
* *
54142753 TCTT TCTT TCTT T-TT TCTT T-TT TCTT TCTT TAATT TCTG T-TT TCGTT
1 TCTT TCTT TCTT TCTT TCTT TCTT TCTT TCTT T-CTT TCTT TCTT TC-TT
54142800 TGGCTT TCTTT TCTT TCTT TCTT T
1 T--CTT TC-TT TCTT TCTT TCTT T
54142824 TTTATTTGTT
Statistics
Matches: 55, Mismatches: 4, Indels: 16
0.73 0.05 0.21
Matches are distributed among these distances:
3 8 0.15
4 33 0.60
5 10 0.18
6 3 0.05
7 1 0.02
ACGTcount: A:0.03, C:0.18, G:0.06, T:0.73
Consensus pattern (4 bp):
TCTT
Found at i:54142790 original size:27 final size:27
Alignment explanation
Indices: 54142759--54142819 Score: 68
Period size: 27 Copynumber: 2.3 Consensus size: 27
54142749 TGCGTCTTTC
* **
54142759 TTTCTTTTTTCTTTTTTCTTTCTTTAA
1 TTTCTTTTTTCGTTTGGCTTTCTTTAA
* **
54142786 TTTCTGTTTTCGTTTGGCTTTCTTTTC
1 TTTCTTTTTTCGTTTGGCTTTCTTTAA
54142813 TTTCTTT
1 TTTCTTT
54142820 CTTTTTTATT
Statistics
Matches: 27, Mismatches: 7, Indels: 0
0.79 0.21 0.00
Matches are distributed among these distances:
27 27 1.00
ACGTcount: A:0.03, C:0.16, G:0.07, T:0.74
Consensus pattern (27 bp):
TTTCTTTTTTCGTTTGGCTTTCTTTAA
Found at i:54142795 original size:22 final size:18
Alignment explanation
Indices: 54142755--54142826 Score: 65
Period size: 20 Copynumber: 3.8 Consensus size: 18
54142745 CCCTTGCGTC
54142755 TTTCTTTCTTTTTTCTTT
1 TTTCTTTCTTTTTTCTTT
*
54142773 TTTCTTTCTTTAATTTCTGT
1 TTTCTTTCTTT--TTTCTTT
* *
54142793 TTTCGTTTGGCTTTCTT-TTC
1 TTTC-TTT--CTTTTTTCTTT
54142813 TTTCTTTCTTTTTT
1 TTTCTTTCTTTTTT
54142827 ATTTGTTTTA
Statistics
Matches: 44, Mismatches: 5, Indels: 11
0.73 0.08 0.18
Matches are distributed among these distances:
17 6 0.14
18 11 0.25
19 3 0.07
20 15 0.34
21 5 0.11
23 4 0.09
ACGTcount: A:0.03, C:0.17, G:0.06, T:0.75
Consensus pattern (18 bp):
TTTCTTTCTTTTTTCTTT
Found at i:54151235 original size:30 final size:31
Alignment explanation
Indices: 54151190--54151252 Score: 110
Period size: 30 Copynumber: 2.1 Consensus size: 31
54151180 ATAGAAACTA
*
54151190 ATATCAGTTAACTGATTCTTAGGAAATTAGG
1 ATATCAATTAACTGATTCTTAGGAAATTAGG
54151221 ATATCAATT-ACTGATTCTTAGGAAATTAGG
1 ATATCAATTAACTGATTCTTAGGAAATTAGG
54151251 AT
1 AT
54151253 TTATTTCCTT
Statistics
Matches: 31, Mismatches: 1, Indels: 1
0.94 0.03 0.03
Matches are distributed among these distances:
30 23 0.74
31 8 0.26
ACGTcount: A:0.37, C:0.10, G:0.17, T:0.37
Consensus pattern (31 bp):
ATATCAATTAACTGATTCTTAGGAAATTAGG
Found at i:54155892 original size:30 final size:31
Alignment explanation
Indices: 54155847--54155909 Score: 110
Period size: 30 Copynumber: 2.1 Consensus size: 31
54155837 ATAGAAACTA
*
54155847 ATATCAGTTAACTGATTCTTAGGAAATTAGG
1 ATATCAATTAACTGATTCTTAGGAAATTAGG
54155878 ATATCAATT-ACTGATTCTTAGGAAATTAGG
1 ATATCAATTAACTGATTCTTAGGAAATTAGG
54155908 AT
1 AT
54155910 TTATTTACTT
Statistics
Matches: 31, Mismatches: 1, Indels: 1
0.94 0.03 0.03
Matches are distributed among these distances:
30 23 0.74
31 8 0.26
ACGTcount: A:0.37, C:0.10, G:0.17, T:0.37
Consensus pattern (31 bp):
ATATCAATTAACTGATTCTTAGGAAATTAGG
Found at i:54161913 original size:16 final size:16
Alignment explanation
Indices: 54161892--54161927 Score: 63
Period size: 16 Copynumber: 2.2 Consensus size: 16
54161882 TTTGGTTCGC
54161892 TGTATTAGATTAGAGG
1 TGTATTAGATTAGAGG
*
54161908 TGTATTGGATTAGAGG
1 TGTATTAGATTAGAGG
54161924 TGTA
1 TGTA
54161928 ATAGTAAATT
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
16 19 1.00
ACGTcount: A:0.28, C:0.00, G:0.33, T:0.39
Consensus pattern (16 bp):
TGTATTAGATTAGAGG
Found at i:54162155 original size:16 final size:16
Alignment explanation
Indices: 54162118--54162159 Score: 52
Period size: 15 Copynumber: 2.7 Consensus size: 16
54162108 TTAATCATAT
*
54162118 TTAAACATA-ATTATTA
1 TTAAA-ATATATTATAA
54162134 TT-AAATATATTATAA
1 TTAAAATATATTATAA
54162149 TTAAAATATAT
1 TTAAAATATAT
54162160 AATTTAATAA
Statistics
Matches: 23, Mismatches: 1, Indels: 4
0.82 0.04 0.14
Matches are distributed among these distances:
14 3 0.13
15 10 0.43
16 10 0.43
ACGTcount: A:0.52, C:0.02, G:0.00, T:0.45
Consensus pattern (16 bp):
TTAAAATATATTATAA
Found at i:54162166 original size:14 final size:15
Alignment explanation
Indices: 54162127--54162168 Score: 52
Period size: 15 Copynumber: 2.9 Consensus size: 15
54162117 TTTAAACATA
*
54162127 ATTATTATTAAATAT
1 ATTATAATTAAATAT
54162142 ATTATAATTAAA-AT
1 ATTATAATTAAATAT
*
54162156 A-TATAATTTAATA
1 ATTATAATTAAATA
54162169 AAATTCTTAA
Statistics
Matches: 24, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
13 9 0.38
14 4 0.17
15 11 0.46
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (15 bp):
ATTATAATTAAATAT
Found at i:54183216 original size:14 final size:14
Alignment explanation
Indices: 54183179--54183216 Score: 51
Period size: 14 Copynumber: 2.6 Consensus size: 14
54183169 CAAAAATAAT
54183179 ATAATATATAAATAC
1 ATAATAT-TAAATAC
54183194 ATCAA-ATTAAATAC
1 AT-AATATTAAATAC
54183208 ATAATATTA
1 ATAATATTA
54183217 CTCAATTATT
Statistics
Matches: 21, Mismatches: 0, Indels: 5
0.81 0.00 0.19
Matches are distributed among these distances:
13 2 0.10
14 13 0.62
15 4 0.19
16 2 0.10
ACGTcount: A:0.58, C:0.08, G:0.00, T:0.34
Consensus pattern (14 bp):
ATAATATTAAATAC
Found at i:54196281 original size:50 final size:50
Alignment explanation
Indices: 54196177--54196415 Score: 221
Period size: 50 Copynumber: 4.7 Consensus size: 50
54196167 AAAAAGATCT
* * *
54196177 CATGTAAGACCATGTCTGGGACATGGAATTGGCATCATTGAGGTTATGAGAGGTCT
1 CATGTAAGACCATGTCTGGGACATGGCATTGGCA-C--CGA-G--ATGAGAGGTCC
* *
54196233 CATGTAAGACCATGTCTGGGATATGGCGTTGGCACCGAGATGAGAGGTCC
1 CATGTAAGACCATGTCTGGGACATGGCATTGGCACCGAGATGAGAGGTCC
** * * **
54196283 CCCGTAAGACCATGTCTGGGACATGGCATGGGCACCGATATGAGAACTCC
1 CATGTAAGACCATGTCTGGGACATGGCATTGGCACCGAGATGAGAGGTCC
* * * * * **
54196333 CATGTAAGACCATATCTGGGATATGGCATTGGCA--GTACAAGAAACATCC
1 CATGTAAGACCATGTCTGGGACATGGCATTGGCACCG-AGATGAGAGGTCC
* *
54196382 CATGTAAGACCATGTCTGGGACGTGGCTTTGGCA
1 CATGTAAGACCATGTCTGGGACATGGCATTGGCA
54196416 TGTTATCATC
Statistics
Matches: 155, Mismatches: 27, Indels: 9
0.81 0.14 0.05
Matches are distributed among these distances:
48 1 0.01
49 38 0.25
50 81 0.52
52 1 0.01
53 2 0.01
55 1 0.01
56 31 0.20
ACGTcount: A:0.27, C:0.21, G:0.29, T:0.23
Consensus pattern (50 bp):
CATGTAAGACCATGTCTGGGACATGGCATTGGCACCGAGATGAGAGGTCC
Found at i:54197535 original size:19 final size:19
Alignment explanation
Indices: 54197494--54197580 Score: 102
Period size: 19 Copynumber: 4.3 Consensus size: 19
54197484 AACCAAAAAT
*
54197494 TCTTAGATATGATATATTCAA
1 TCTTAGATATGATAT-GT-AA
54197515 TCTTAGATATGATATGTAA
1 TCTTAGATATGATATGTAA
*
54197534 TCTTAGAAGATATGATTTTGTAA
1 TCTT---AGATATGA-TATGTAA
54197557 TCTTAGATATGATATGTAA
1 TCTTAGATATGATATGTAA
54197576 TCTTA
1 TCTTA
54197581 AAAGATATGA
Statistics
Matches: 59, Mismatches: 3, Indels: 10
0.82 0.04 0.14
Matches are distributed among these distances:
19 17 0.29
20 9 0.15
21 15 0.25
22 8 0.14
23 10 0.17
ACGTcount: A:0.36, C:0.07, G:0.14, T:0.44
Consensus pattern (19 bp):
TCTTAGATATGATATGTAA
Found at i:54197547 original size:22 final size:23
Alignment explanation
Indices: 54197519--54197605 Score: 103
Period size: 23 Copynumber: 4.0 Consensus size: 23
54197509 ATTCAATCTT
54197519 AGATATGA-TATGTAATCTTAGA
1 AGATATGATTATGTAATCTTAGA
*
54197541 AGATATGATTTTGTAATCTT---
1 AGATATGATTATGTAATCTTAGA
*
54197561 AGATATGA-TATGTAATCTTAAA
1 AGATATGATTATGTAATCTTAGA
* *
54197583 AGATATGATTTTGTAATATTAGA
1 AGATATGATTATGTAATCTTAGA
54197606 GATTTAATTT
Statistics
Matches: 55, Mismatches: 5, Indels: 9
0.80 0.07 0.13
Matches are distributed among these distances:
19 10 0.18
20 8 0.15
22 16 0.29
23 21 0.38
ACGTcount: A:0.39, C:0.03, G:0.16, T:0.41
Consensus pattern (23 bp):
AGATATGATTATGTAATCTTAGA
Found at i:54197563 original size:42 final size:42
Alignment explanation
Indices: 54197513--54197605 Score: 168
Period size: 42 Copynumber: 2.2 Consensus size: 42
54197503 TGATATATTC
*
54197513 AATCTTAGATATGATATGTAATCTTAGAAGATATGATTTTGT
1 AATCTTAGATATGATATGTAATCTTAAAAGATATGATTTTGT
54197555 AATCTTAGATATGATATGTAATCTTAAAAGATATGATTTTGT
1 AATCTTAGATATGATATGTAATCTTAAAAGATATGATTTTGT
*
54197597 AATATTAGA
1 AATCTTAGA
54197606 GATTTAATTT
Statistics
Matches: 49, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
42 49 1.00
ACGTcount: A:0.39, C:0.04, G:0.15, T:0.42
Consensus pattern (42 bp):
AATCTTAGATATGATATGTAATCTTAAAAGATATGATTTTGT
Found at i:54197608 original size:22 final size:21
Alignment explanation
Indices: 54197498--54197608 Score: 95
Period size: 22 Copynumber: 5.2 Consensus size: 21
54197488 AAAAATTCTT
*
54197498 AGATATGATATATTCAATCTT--
1 AGATATGATAT-GT-AATCTTAG
54197519 AGATATGATATGTAATCTTAG
1 AGATATGATATGTAATCTTAG
*
54197540 AAGATATGATTTTGTAATCTT--
1 -AGATATGA-TATGTAATCTTAG
*
54197561 AGATATGATATGTAATCTTAAA
1 AGATATGATATGTAATCTT-AG
* *
54197583 AGATATGATTTTGTAATATTAG
1 AGATATGA-TATGTAATCTTAG
54197605 AGAT
1 AGAT
54197609 TTAATTTGTA
Statistics
Matches: 76, Mismatches: 6, Indels: 15
0.78 0.06 0.15
Matches are distributed among these distances:
19 16 0.21
20 9 0.12
21 11 0.14
22 21 0.28
23 19 0.25
ACGTcount: A:0.39, C:0.05, G:0.15, T:0.41
Consensus pattern (21 bp):
AGATATGATATGTAATCTTAG
Found at i:54197804 original size:19 final size:21
Alignment explanation
Indices: 54197780--54197818 Score: 55
Period size: 19 Copynumber: 2.0 Consensus size: 21
54197770 TACTATTTTC
*
54197780 TTTTTTTCTT-TTT-CGATTA
1 TTTTTTACTTATTTACGATTA
54197799 TTTTTTACTTATTTACGATT
1 TTTTTTACTTATTTACGATT
54197819 TTAAAAAAGG
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
19 9 0.53
20 3 0.18
21 5 0.29
ACGTcount: A:0.15, C:0.10, G:0.05, T:0.69
Consensus pattern (21 bp):
TTTTTTACTTATTTACGATTA
Found at i:54198047 original size:3 final size:3
Alignment explanation
Indices: 54198039--54198073 Score: 61
Period size: 3 Copynumber: 11.3 Consensus size: 3
54198029 ATTAATTTTG
54198039 TTA TTA TTA TTA TTA TTA TTA TTA TATA TTA TTA T
1 TTA TTA TTA TTA TTA TTA TTA TTA T-TA TTA TTA T
54198074 ACCTACATAT
Statistics
Matches: 31, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
3 28 0.90
4 3 0.10
ACGTcount: A:0.34, C:0.00, G:0.00, T:0.66
Consensus pattern (3 bp):
TTA
Found at i:54201658 original size:54 final size:54
Alignment explanation
Indices: 54201589--54201697 Score: 191
Period size: 54 Copynumber: 2.0 Consensus size: 54
54201579 TTCTTAAATC
*
54201589 TAAATTGATAGTCTTACTCTTTATAGTCTTCTTATTATTTTTCTCTCTTGGTGG
1 TAAATTAATAGTCTTACTCTTTATAGTCTTCTTATTATTTTTCTCTCTTGGTGG
* *
54201643 TAAATTAATATTCTTACTCTTTATAGTTTTCTTATTATTTTTCTCTCTTGGTGG
1 TAAATTAATAGTCTTACTCTTTATAGTCTTCTTATTATTTTTCTCTCTTGGTGG
54201697 T
1 T
54201698 TATGAAAACT
Statistics
Matches: 52, Mismatches: 3, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
54 52 1.00
ACGTcount: A:0.19, C:0.14, G:0.11, T:0.56
Consensus pattern (54 bp):
TAAATTAATAGTCTTACTCTTTATAGTCTTCTTATTATTTTTCTCTCTTGGTGG
Found at i:54201916 original size:29 final size:26
Alignment explanation
Indices: 54201864--54201917 Score: 63
Period size: 26 Copynumber: 2.0 Consensus size: 26
54201854 CTATTAATTA
* *
54201864 AATAATAAAATATCTTATATTAAAAT
1 AATAATAAAATATCTTACAATAAAAT
54201890 AATAATAAAATAATCTTAACCAATAAAA
1 AATAATAAAAT-ATCTT-A-CAATAAAA
54201918 ATCTAACACC
Statistics
Matches: 23, Mismatches: 2, Indels: 3
0.82 0.07 0.11
Matches are distributed among these distances:
26 11 0.48
27 5 0.22
28 1 0.04
29 6 0.26
ACGTcount: A:0.61, C:0.07, G:0.00, T:0.31
Consensus pattern (26 bp):
AATAATAAAATATCTTACAATAAAAT
Found at i:54208005 original size:22 final size:22
Alignment explanation
Indices: 54207975--54208020 Score: 58
Period size: 22 Copynumber: 2.1 Consensus size: 22
54207965 AAAAGAGATT
*
54207975 AATTGGGAGCGAAGAA-AAGAAG
1 AATTAGGAG-GAAGAAGAAGAAG
*
54207997 AATTAGGAGGAAGAAGAGGAAG
1 AATTAGGAGGAAGAAGAAGAAG
54208019 AA
1 AA
54208021 AAAGATCAGA
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
21 6 0.29
22 15 0.71
ACGTcount: A:0.52, C:0.02, G:0.37, T:0.09
Consensus pattern (22 bp):
AATTAGGAGGAAGAAGAAGAAG
Found at i:54209877 original size:100 final size:100
Alignment explanation
Indices: 54209689--54209880 Score: 276
Period size: 100 Copynumber: 1.9 Consensus size: 100
54209679 ATTGAACATT
* * *
54209689 AACATCATTTACAGTCTTGAGCAATTAGTTTGAATGCCCCTAATATTTAACATTCCACCTTTCTG
1 AACATCATTTACAGTCTTGAACAATTAGTCTGAATGCCCCTAATATTTAAAATTCCACCTTTCTG
* *
54209754 AGCTGAAAACTTAAATGGGGATTTAAATTGTGATC
66 AGCTGAAAACTCAAATGGAGATTTAAATTGTGATC
* * * * *
54209789 AACATCATTTTCAGTCTTTAACAATTAGTCTGAATGCCCTTAATATTTAAAATTCTACCTTTTTG
1 AACATCATTTACAGTCTTGAACAATTAGTCTGAATGCCCCTAATATTTAAAATTCCACCTTTCTG
* *
54209854 AGCTGACAACTCAATTGGAGATTTAAA
66 AGCTGAAAACTCAAATGGAGATTTAAA
54209881 GTGCAATCAA
Statistics
Matches: 80, Mismatches: 12, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
100 80 1.00
ACGTcount: A:0.33, C:0.18, G:0.13, T:0.36
Consensus pattern (100 bp):
AACATCATTTACAGTCTTGAACAATTAGTCTGAATGCCCCTAATATTTAAAATTCCACCTTTCTG
AGCTGAAAACTCAAATGGAGATTTAAATTGTGATC
Found at i:54216822 original size:12 final size:11
Alignment explanation
Indices: 54216795--54216863 Score: 56
Period size: 11 Copynumber: 6.4 Consensus size: 11
54216785 ATTTTTTTAA
54216795 TTTTAAAATAT
1 TTTTAAAATAT
54216806 TTTTAAAATACT
1 TTTTAAAATA-T
* *
54216818 TTTTATTATTAT
1 TTTTA-AAATAT
*
54216830 TTTT----TAA
1 TTTTAAAATAT
54216837 TTTTAAAATAT
1 TTTTAAAATAT
54216848 TTTTAAAATACT
1 TTTTAAAATA-T
54216860 TTTT
1 TTTT
54216864 TTAATTTTTA
Statistics
Matches: 47, Mismatches: 4, Indels: 13
0.73 0.06 0.20
Matches are distributed among these distances:
7 6 0.13
11 22 0.47
12 16 0.34
13 3 0.06
ACGTcount: A:0.36, C:0.03, G:0.00, T:0.61
Consensus pattern (11 bp):
TTTTAAAATAT
Found at i:54216841 original size:31 final size:31
Alignment explanation
Indices: 54216804--54216878 Score: 91
Period size: 31 Copynumber: 2.4 Consensus size: 31
54216794 ATTTTAAAAT
* *
54216804 ATTTTTAAAATACTTTTTATTATTA-TTTTTTA
1 ATTTTTAAAATA-TTTTTA-AAATACTTTTTTA
54216836 A-TTTTAAAATATTTTTAAAATACTTTTTTTA
1 ATTTTTAAAATATTTTTAAAATAC-TTTTTTA
54216867 ATTTTTAAAATA
1 ATTTTTAAAATA
54216879 AATTTTTAGT
Statistics
Matches: 38, Mismatches: 2, Indels: 6
0.83 0.04 0.13
Matches are distributed among these distances:
29 3 0.08
30 6 0.16
31 18 0.47
32 11 0.29
ACGTcount: A:0.37, C:0.03, G:0.00, T:0.60
Consensus pattern (31 bp):
ATTTTTAAAATATTTTTAAAATACTTTTTTA
Found at i:54216853 original size:17 final size:17
Alignment explanation
Indices: 54216778--54216811 Score: 59
Period size: 17 Copynumber: 2.0 Consensus size: 17
54216768 TATATTTATT
*
54216778 TTTTAAAATTTTTTTAA
1 TTTTAAAATATTTTTAA
54216795 TTTTAAAATATTTTTAA
1 TTTTAAAATATTTTTAA
54216812 AATACTTTTT
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
17 16 1.00
ACGTcount: A:0.38, C:0.00, G:0.00, T:0.62
Consensus pattern (17 bp):
TTTTAAAATATTTTTAA
Found at i:54216884 original size:21 final size:21
Alignment explanation
Indices: 54216846--54216885 Score: 62
Period size: 21 Copynumber: 1.9 Consensus size: 21
54216836 ATTTTAAAAT
**
54216846 ATTTTTAAAATACTTTTTTTA
1 ATTTTTAAAATAAATTTTTTA
54216867 ATTTTTAAAATAAATTTTT
1 ATTTTTAAAATAAATTTTT
54216886 AGTATTTATT
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
21 17 1.00
ACGTcount: A:0.38, C:0.03, G:0.00, T:0.60
Consensus pattern (21 bp):
ATTTTTAAAATAAATTTTTTA
Found at i:54217911 original size:22 final size:24
Alignment explanation
Indices: 54217886--54217933 Score: 73
Period size: 22 Copynumber: 2.1 Consensus size: 24
54217876 TTTTACTTTT
54217886 AATAAATAAATATA-TAAA-TAAA
1 AATAAATAAATATACTAAACTAAA
*
54217908 AATAAATTAATATACTAAACTAAA
1 AATAAATAAATATACTAAACTAAA
54217932 AA
1 AA
54217934 AATTATTCTT
Statistics
Matches: 23, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
22 13 0.57
23 4 0.17
24 6 0.26
ACGTcount: A:0.69, C:0.04, G:0.00, T:0.27
Consensus pattern (24 bp):
AATAAATAAATATACTAAACTAAA
Found at i:54221598 original size:306 final size:306
Alignment explanation
Indices: 54221045--54221656 Score: 1224
Period size: 306 Copynumber: 2.0 Consensus size: 306
54221035 TGGAAGTTTT
54221045 ATGTTTAGTTGTTGTTAAAAACATATTATCTATTTCATTTTCTGTTTGTGTTGTGGCTTGGAGAC
1 ATGTTTAGTTGTTGTTAAAAACATATTATCTATTTCATTTTCTGTTTGTGTTGTGGCTTGGAGAC
54221110 GAACGGGAATTCAGCTTCATTTGAATGGGCACTAAAACTATTTGTGTCATGGTTTCCGTGTTCGG
66 GAACGGGAATTCAGCTTCATTTGAATGGGCACTAAAACTATTTGTGTCATGGTTTCCGTGTTCGG
54221175 ATGTTATGGTATGCTGTATCCTATCCTGTATTTAACAGGCAACGCTTGCTTGTGAGCTGAGTTAC
131 ATGTTATGGTATGCTGTATCCTATCCTGTATTTAACAGGCAACGCTTGCTTGTGAGCTGAGTTAC
54221240 TTTAGTATAACGATGAAACTAATGATCTTTTGGGGTGTAAGTCGTCAAATGCATCCACCGCAGTT
196 TTTAGTATAACGATGAAACTAATGATCTTTTGGGGTGTAAGTCGTCAAATGCATCCACCGCAGTT
54221305 CACAGCCAAAACGAAAGGAGGAATCTCATGCGCAATGGAAATGTTA
261 CACAGCCAAAACGAAAGGAGGAATCTCATGCGCAATGGAAATGTTA
54221351 ATGTTTAGTTGTTGTTAAAAACATATTATCTATTTCATTTTCTGTTTGTGTTGTGGCTTGGAGAC
1 ATGTTTAGTTGTTGTTAAAAACATATTATCTATTTCATTTTCTGTTTGTGTTGTGGCTTGGAGAC
54221416 GAACGGGAATTCAGCTTCATTTGAATGGGCACTAAAACTATTTGTGTCATGGTTTCCGTGTTCGG
66 GAACGGGAATTCAGCTTCATTTGAATGGGCACTAAAACTATTTGTGTCATGGTTTCCGTGTTCGG
54221481 ATGTTATGGTATGCTGTATCCTATCCTGTATTTAACAGGCAACGCTTGCTTGTGAGCTGAGTTAC
131 ATGTTATGGTATGCTGTATCCTATCCTGTATTTAACAGGCAACGCTTGCTTGTGAGCTGAGTTAC
54221546 TTTAGTATAACGATGAAACTAATGATCTTTTGGGGTGTAAGTCGTCAAATGCATCCACCGCAGTT
196 TTTAGTATAACGATGAAACTAATGATCTTTTGGGGTGTAAGTCGTCAAATGCATCCACCGCAGTT
54221611 CACAGCCAAAACGAAAGGAGGAATCTCATGCGCAATGGAAATGTTA
261 CACAGCCAAAACGAAAGGAGGAATCTCATGCGCAATGGAAATGTTA
54221657 CACGGTGAAG
Statistics
Matches: 306, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
306 306 1.00
ACGTcount: A:0.26, C:0.16, G:0.23, T:0.35
Consensus pattern (306 bp):
ATGTTTAGTTGTTGTTAAAAACATATTATCTATTTCATTTTCTGTTTGTGTTGTGGCTTGGAGAC
GAACGGGAATTCAGCTTCATTTGAATGGGCACTAAAACTATTTGTGTCATGGTTTCCGTGTTCGG
ATGTTATGGTATGCTGTATCCTATCCTGTATTTAACAGGCAACGCTTGCTTGTGAGCTGAGTTAC
TTTAGTATAACGATGAAACTAATGATCTTTTGGGGTGTAAGTCGTCAAATGCATCCACCGCAGTT
CACAGCCAAAACGAAAGGAGGAATCTCATGCGCAATGGAAATGTTA
Done.