Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: A09
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: 81831061
ACGTcount: A:0.31, C:0.16, G:0.16, T:0.31
Warning! 3560000 characters in sequence are not A, C, G, or T
File 164 of 259
Found at i:53315828 original size:40 final size:40
Alignment explanation
Indices: 53315773--53315852 Score: 160
Period size: 40 Copynumber: 2.0 Consensus size: 40
53315763 ACAAGTAGTT
53315773 AACTAGAATTCTTGGTTGCATGTTGGTTGCTTAAGAATCA
1 AACTAGAATTCTTGGTTGCATGTTGGTTGCTTAAGAATCA
53315813 AACTAGAATTCTTGGTTGCATGTTGGTTGCTTAAGAATCA
1 AACTAGAATTCTTGGTTGCATGTTGGTTGCTTAAGAATCA
53315853 CTTAGTTCTC
Statistics
Matches: 40, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
40 40 1.00
ACGTcount: A:0.28, C:0.12, G:0.23, T:0.38
Consensus pattern (40 bp):
AACTAGAATTCTTGGTTGCATGTTGGTTGCTTAAGAATCA
Found at i:53321888 original size:16 final size:17
Alignment explanation
Indices: 53321855--53321890 Score: 56
Period size: 17 Copynumber: 2.2 Consensus size: 17
53321845 TTATGGGGGT
*
53321855 TTAAAATATTTATTTAA
1 TTAAAATATATATTTAA
53321872 TTAAAATATAT-TTTAA
1 TTAAAATATATATTTAA
53321888 TTA
1 TTA
53321891 TATTTAAAAG
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
16 8 0.44
17 10 0.56
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (17 bp):
TTAAAATATATATTTAA
Found at i:53322598 original size:64 final size:65
Alignment explanation
Indices: 53322469--53322598 Score: 253
Period size: 64 Copynumber: 2.0 Consensus size: 65
53322459 CAGGTTCCTT
53322469 TGTTTGTTTCATGCTTCTTCTCGTGCCTTTTTTTTTGTAATTTTTTATGAGTTTTAATATTTATG
1 TGTTTGTTTCATGCTTCTTCTCGTGCCTTTTTTTTTGTAATTTTTTATGAGTTTTAATATTTATG
53322534 TGTTTGTTTCATGCTTCTTCTCGTGCC-TTTTTTTTGTAATTTTTTATGAGTTTTAATATTTATG
1 TGTTTGTTTCATGCTTCTTCTCGTGCCTTTTTTTTTGTAATTTTTTATGAGTTTTAATATTTATG
53322598 T
1 T
53322599 TCCGTTGCTG
Statistics
Matches: 65, Mismatches: 0, Indels: 1
0.98 0.00 0.02
Matches are distributed among these distances:
64 38 0.58
65 27 0.42
ACGTcount: A:0.14, C:0.11, G:0.14, T:0.62
Consensus pattern (65 bp):
TGTTTGTTTCATGCTTCTTCTCGTGCCTTTTTTTTTGTAATTTTTTATGAGTTTTAATATTTATG
Found at i:53328624 original size:19 final size:20
Alignment explanation
Indices: 53328580--53328618 Score: 64
Period size: 19 Copynumber: 2.0 Consensus size: 20
53328570 TATTTAAGTT
53328580 TAAAAATAATTAAAATATTA
1 TAAAAATAATTAAAATATTA
53328600 TAAAAA-AATTAAAAT-TTA
1 TAAAAATAATTAAAATATTA
53328618 T
1 T
53328619 GGAAAATCTA
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
18 4 0.21
19 9 0.47
20 6 0.32
ACGTcount: A:0.64, C:0.00, G:0.00, T:0.36
Consensus pattern (20 bp):
TAAAAATAATTAAAATATTA
Found at i:53328810 original size:22 final size:21
Alignment explanation
Indices: 53328748--53328847 Score: 71
Period size: 21 Copynumber: 4.7 Consensus size: 21
53328738 ATTTTTAAAC
* * *
53328748 ATTATAAAAAACTATTAA-AT
1 ATTATAAAATATTAATAAGAT
*
53328768 ATTATAAAATATTATTAAGAT
1 ATTATAAAATATTAATAAGAT
*
53328789 CTTATGAAAATATTAA-ATAGAT
1 ATTAT-AAAATATTAATA-AGAT
* * *
53328811 ATTATAAAAAATTTAGAAGAT
1 ATTATAAAATATTAATAAGAT
53328832 -TATATAAAATAATTAA
1 AT-TATAAAAT-ATTAA
53328848 AATTATAAAA
Statistics
Matches: 65, Mismatches: 9, Indels: 10
0.77 0.11 0.12
Matches are distributed among these distances:
20 17 0.26
21 26 0.40
22 22 0.34
ACGTcount: A:0.56, C:0.02, G:0.05, T:0.37
Consensus pattern (21 bp):
ATTATAAAATATTAATAAGAT
Found at i:53328831 original size:43 final size:43
Alignment explanation
Indices: 53328766--53328848 Score: 100
Period size: 43 Copynumber: 1.9 Consensus size: 43
53328756 AAACTATTAA
* *
53328766 ATATTATAAAATATTATTAAGATCT-TATGAAAAT-ATTAAATAG
1 ATATTATAAAAAATTATGAAGAT-TATAT-AAAATAATTAAATAG
53328809 ATATTATAAAAAATT-TAGAAGATTATATAAAATAATTAAA
1 ATATTATAAAAAATTAT-GAAGATTATATAAAATAATTAAA
53328849 ATTATAAAAG
Statistics
Matches: 35, Mismatches: 2, Indels: 6
0.81 0.05 0.14
Matches are distributed among these distances:
42 7 0.20
43 28 0.80
ACGTcount: A:0.55, C:0.01, G:0.06, T:0.37
Consensus pattern (43 bp):
ATATTATAAAAAATTATGAAGATTATATAAAATAATTAAATAG
Found at i:53329115 original size:12 final size:12
Alignment explanation
Indices: 53329095--53329130 Score: 54
Period size: 12 Copynumber: 3.0 Consensus size: 12
53329085 TAGAACTACT
*
53329095 AGAATATTATAA
1 AGAAAATTATAA
53329107 AGAAAATTATAA
1 AGAAAATTATAA
*
53329119 AAAAAATTATAA
1 AGAAAATTATAA
53329131 GTTATTAAAA
Statistics
Matches: 22, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
12 22 1.00
ACGTcount: A:0.67, C:0.00, G:0.06, T:0.28
Consensus pattern (12 bp):
AGAAAATTATAA
Found at i:53331271 original size:31 final size:31
Alignment explanation
Indices: 53331221--53331280 Score: 86
Period size: 31 Copynumber: 1.9 Consensus size: 31
53331211 GAATAATTTG
53331221 GGTAATGAAGTATAATTTAGGTATCACTTTA
1 GGTAATGAAGTATAATTTAGGTATCACTTTA
* *
53331252 GGTAATGGAA-TATATTTTAGGTATTACTT
1 GGTAAT-GAAGTATAATTTAGGTATCACTT
53331281 GTGAAAAAAA
Statistics
Matches: 26, Mismatches: 2, Indels: 2
0.87 0.07 0.07
Matches are distributed among these distances:
31 23 0.88
32 3 0.12
ACGTcount: A:0.33, C:0.05, G:0.20, T:0.42
Consensus pattern (31 bp):
GGTAATGAAGTATAATTTAGGTATCACTTTA
Found at i:53333008 original size:10 final size:10
Alignment explanation
Indices: 53332995--53333031 Score: 56
Period size: 10 Copynumber: 3.6 Consensus size: 10
53332985 AAAAAGGCAA
53332995 AAAAAAAAAG
1 AAAAAAAAAG
53333005 AAAAAAAAAG
1 AAAAAAAAAG
*
53333015 AAAAAGAAAG
1 AAAAAAAAAG
53333025 AAGAAAA
1 AA-AAAA
53333032 CTTTAAAAAT
Statistics
Matches: 24, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
10 21 0.88
11 3 0.12
ACGTcount: A:0.86, C:0.00, G:0.14, T:0.00
Consensus pattern (10 bp):
AAAAAAAAAG
Found at i:53333012 original size:16 final size:16
Alignment explanation
Indices: 53332993--53333023 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
53332983 TAAAAAAGGC
53332993 AAAAAAAAAAAGAAAA
1 AAAAAAAAAAAGAAAA
*
53333009 AAAAAGAAAAAGAAA
1 AAAAAAAAAAAGAAA
53333024 GAAGAAAACT
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:0.90, C:0.00, G:0.10, T:0.00
Consensus pattern (16 bp):
AAAAAAAAAAAGAAAA
Found at i:53333012 original size:23 final size:23
Alignment explanation
Indices: 53332984--53333031 Score: 62
Period size: 23 Copynumber: 2.1 Consensus size: 23
53332974 CTAACTGGAT
*
53332984 AAAAAAGGCAAAAA-AAAAAAGAA
1 AAAAAAAG-AAAAAGAAAAAAGAA
*
53333007 AAAAAAAGAAAAAGAAAGAAGAA
1 AAAAAAAGAAAAAGAAAAAAGAA
53333030 AA
1 AA
53333032 CTTTAAAAAT
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
22 5 0.23
23 17 0.77
ACGTcount: A:0.83, C:0.02, G:0.15, T:0.00
Consensus pattern (23 bp):
AAAAAAAGAAAAAGAAAAAAGAA
Found at i:53336862 original size:22 final size:22
Alignment explanation
Indices: 53336823--53336864 Score: 66
Period size: 22 Copynumber: 1.9 Consensus size: 22
53336813 GTGAGATGAC
*
53336823 AGCAAAACAATGATAAAACAGT
1 AGCAAAACAATGAGAAAACAGT
*
53336845 AGCAAAACAATGGGAAAACA
1 AGCAAAACAATGAGAAAACA
53336865 AGAATATAAT
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
22 18 1.00
ACGTcount: A:0.60, C:0.14, G:0.17, T:0.10
Consensus pattern (22 bp):
AGCAAAACAATGAGAAAACAGT
Found at i:53340814 original size:11 final size:11
Alignment explanation
Indices: 53340800--53340836 Score: 56
Period size: 11 Copynumber: 3.4 Consensus size: 11
53340790 AAATAGTGAT
53340800 AAAACAACAAG
1 AAAACAACAAG
* *
53340811 AAAATAACAAC
1 AAAACAACAAG
53340822 AAAACAACAAG
1 AAAACAACAAG
53340833 AAAA
1 AAAA
53340837 TAAAGTAGTT
Statistics
Matches: 22, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
11 22 1.00
ACGTcount: A:0.76, C:0.16, G:0.05, T:0.03
Consensus pattern (11 bp):
AAAACAACAAG
Found at i:53343053 original size:21 final size:21
Alignment explanation
Indices: 53343028--53343185 Score: 178
Period size: 21 Copynumber: 7.6 Consensus size: 21
53343018 CATATTTTAC
* *
53343028 TTTCTGTTTAGCTCTTACGAG
1 TTTCTGTTCAACTCTTACGAG
* * *
53343049 CTTCTGTTAAACTCTTATGAG
1 TTTCTGTTCAACTCTTACGAG
53343070 TTTCTGTT-AAGCTCTTACGAG
1 TTTCTGTTCAA-CTCTTACGAG
*
53343091 TTTCTGTTCAACTCTTATGAG
1 TTTCTGTTCAACTCTTACGAG
* *
53343112 TTTCTTTTCAGCTCTTACGAG
1 TTTCTGTTCAACTCTTACGAG
*
53343133 CTTCTGTTCAACTCTTA--AG
1 TTTCTGTTCAACTCTTACGAG
* *
53343152 TTTTTGTTCAACTCTTATGAG
1 TTTCTGTTCAACTCTTACGAG
*
53343173 CTTCTGTTCAACT
1 TTTCTGTTCAACT
53343186 TTCAAGCTTC
Statistics
Matches: 116, Mismatches: 17, Indels: 8
0.82 0.12 0.06
Matches are distributed among these distances:
19 17 0.15
20 2 0.02
21 95 0.82
22 2 0.02
ACGTcount: A:0.18, C:0.21, G:0.15, T:0.46
Consensus pattern (21 bp):
TTTCTGTTCAACTCTTACGAG
Found at i:53343076 original size:42 final size:42
Alignment explanation
Indices: 53343028--53343185 Score: 223
Period size: 42 Copynumber: 3.8 Consensus size: 42
53343018 CATATTTTAC
*
53343028 TTTCTGTTTAGCTCTTACGAGCTTCTGTTAAACTCTTATGAG
1 TTTCTGTTTAGCTCTTACGAGCTTCTGTTCAACTCTTATGAG
* *
53343070 TTTCTGTTAAGCTCTTACGAGTTTCTGTTCAACTCTTATGAG
1 TTTCTGTTTAGCTCTTACGAGCTTCTGTTCAACTCTTATGAG
53343112 TTTCT-TTTCAGCTCTTACGAGCTTCTGTTCAACTCTTA--AG
1 TTTCTGTTT-AGCTCTTACGAGCTTCTGTTCAACTCTTATGAG
* * * *
53343152 TTTTTGTTCAACTCTTATGAGCTTCTGTTCAACT
1 TTTCTGTTTAGCTCTTACGAGCTTCTGTTCAACT
53343186 TTCAAGCTTC
Statistics
Matches: 105, Mismatches: 9, Indels: 6
0.88 0.08 0.05
Matches are distributed among these distances:
40 29 0.28
41 4 0.04
42 72 0.69
ACGTcount: A:0.18, C:0.21, G:0.15, T:0.46
Consensus pattern (42 bp):
TTTCTGTTTAGCTCTTACGAGCTTCTGTTCAACTCTTATGAG
Found at i:53343138 original size:63 final size:61
Alignment explanation
Indices: 53343028--53343199 Score: 197
Period size: 63 Copynumber: 2.8 Consensus size: 61
53343018 CATATTTTAC
* * * * * *
53343028 TTTCTGTTTAGCTCTTACGAGCTTCTGTTAAACTCTTATGAGTTTCTGTT-AAGCTCTTACGAG
1 TTTCTGTTCAACTCTTATGAGCTTCTGTTCAACTCTTACGAGCTTCTGTTCAA-CTCTTA--AG
* * *
53343091 TTTCTGTTCAACTCTTATGAGTTTCTTTTCAGCTCTTACGAGCTTCTGTTCAACTCTTAAG
1 TTTCTGTTCAACTCTTATGAGCTTCTGTTCAACTCTTACGAGCTTCTGTTCAACTCTTAAG
* *
53343152 TTTTTGTTCAACTCTTATGAGCTTCTGTTCAACT-TT-CAAGCTTCTGTT
1 TTTCTGTTCAACTCTTATGAGCTTCTGTTCAACTCTTACGAGCTTCTGTT
53343200 GTCATATCTG
Statistics
Matches: 94, Mismatches: 14, Indels: 6
0.82 0.12 0.05
Matches are distributed among these distances:
59 11 0.12
60 2 0.02
61 32 0.34
63 47 0.50
64 2 0.02
ACGTcount: A:0.18, C:0.21, G:0.15, T:0.47
Consensus pattern (61 bp):
TTTCTGTTCAACTCTTATGAGCTTCTGTTCAACTCTTACGAGCTTCTGTTCAACTCTTAAG
Found at i:53351383 original size:16 final size:16
Alignment explanation
Indices: 53351364--53351394 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
53351354 AAAAAAGTAT
*
53351364 TAAATATAAAATAAAA
1 TAAAAATAAAATAAAA
53351380 TAAAAATAAAATAAA
1 TAAAAATAAAATAAA
53351395 TATTTTTAAA
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:0.77, C:0.00, G:0.00, T:0.23
Consensus pattern (16 bp):
TAAAAATAAAATAAAA
Found at i:53354450 original size:52 final size:48
Alignment explanation
Indices: 53354431--53354633 Score: 265
Period size: 46 Copynumber: 4.3 Consensus size: 48
53354421 TGACAAGTGG
* *
53354431 AAAGTGATAAGTAATAGCTTCGGCTATACTTATCTGATCAAGTGAC--
1 AAAGTGATAAGTGATAGCTTCGGCTACACTTATCTGATCAAGTGACAA
53354477 AAAGTGATAAGTGATAGCTTCGGCTACACTTATCTGATCAAGTGACAAGTGA
1 AAAGTGATAAGTGATAGCTTCGGCTACACTTATCTGATCAAGTGAC-A---A
* *
53354529 AAAGTGATAAGTGATAGCTTCGGCTATACTTATCTGATCAAGAGAC--
1 AAAGTGATAAGTGATAGCTTCGGCTACACTTATCTGATCAAGTGACAA
** *
53354575 AAAGTGATAAGTGATAGCTTTAGCTACACTTATCTGATCAAGAGAC--
1 AAAGTGATAAGTGATAGCTTCGGCTACACTTATCTGATCAAGTGACAA
53354621 AAAGTGATAAGTG
1 AAAGTGATAAGTG
53354634 GCTACACTTA
Statistics
Matches: 144, Mismatches: 7, Indels: 12
0.88 0.04 0.07
Matches are distributed among these distances:
46 100 0.69
52 44 0.31
ACGTcount: A:0.36, C:0.14, G:0.22, T:0.28
Consensus pattern (48 bp):
AAAGTGATAAGTGATAGCTTCGGCTACACTTATCTGATCAAGTGACAA
Found at i:53354485 original size:98 final size:98
Alignment explanation
Indices: 53354365--53354633 Score: 457
Period size: 98 Copynumber: 2.7 Consensus size: 98
53354355 TTTGAGTACT
*
53354365 TCTGATCAAGTGACAAAGTGATAAGTGGTAGCTTTAGCTACACTTATCTGATCAAGTGACAAGTG
1 TCTGATCAAGTGACAAAGTGATAAGTGATAGCTTTAGCTACACTTATCTGATCAAGTGACAAGTG
*
53354430 GAAAGTGATAAGTAATAGCTTCGGCTATACTTA
66 AAAAGTGATAAGTAATAGCTTCGGCTATACTTA
**
53354463 TCTGATCAAGTGACAAAGTGATAAGTGATAGCTTCGGCTACACTTATCTGATCAAGTGACAAGTG
1 TCTGATCAAGTGACAAAGTGATAAGTGATAGCTTTAGCTACACTTATCTGATCAAGTGACAAGTG
*
53354528 AAAAGTGATAAGTGATAGCTTCGGCTATACTTA
66 AAAAGTGATAAGTAATAGCTTCGGCTATACTTA
* *
53354561 TCTGATCAAGAGACAAAGTGATAAGTGATAGCTTTAGCTACACTTATCTGATCAAGAGACAAAGT
1 TCTGATCAAGTGACAAAGTGATAAGTGATAGCTTTAGCTACACTTATCTGATCAAGTGAC-AAGT
*
53354626 GATAAGTG
65 GAAAAGTG
53354634 GCTACACTTA
Statistics
Matches: 160, Mismatches: 10, Indels: 1
0.94 0.06 0.01
Matches are distributed among these distances:
98 149 0.93
99 11 0.07
ACGTcount: A:0.35, C:0.14, G:0.22, T:0.28
Consensus pattern (98 bp):
TCTGATCAAGTGACAAAGTGATAAGTGATAGCTTTAGCTACACTTATCTGATCAAGTGACAAGTG
AAAAGTGATAAGTAATAGCTTCGGCTATACTTA
Found at i:53354641 original size:37 final size:37
Alignment explanation
Indices: 53354597--53354742 Score: 233
Period size: 37 Copynumber: 4.0 Consensus size: 37
53354587 GATAGCTTTA
*
53354597 GCTACACTTATCTGATCAAGAGACAAAGTGATAAGTG
1 GCTACACTTATCTGATCAAGAAACAAAGTGATAAGTG
*
53354634 GCTACACTTATCTGATCAATAAACAAAGTGATAAGTG
1 GCTACACTTATCTGATCAAGAAACAAAGTGATAAGTG
*
53354671 GCTACACTTATCTGATCAAGAAACAAAGTGATAGGTG
1 GCTACACTTATCTGATCAAGAAACAAAGTGATAAGTG
**
53354708 GCTACACTTATCTGATC-AGGGAC-AAGTGATAAGTG
1 GCTACACTTATCTGATCAAGAAACAAAGTGATAAGTG
53354743 ATCATACGTA
Statistics
Matches: 102, Mismatches: 7, Indels: 2
0.92 0.06 0.02
Matches are distributed among these distances:
35 11 0.11
36 4 0.04
37 87 0.85
ACGTcount: A:0.37, C:0.16, G:0.21, T:0.25
Consensus pattern (37 bp):
GCTACACTTATCTGATCAAGAAACAAAGTGATAAGTG
Found at i:53355533 original size:3 final size:3
Alignment explanation
Indices: 53355515--53355559 Score: 58
Period size: 3 Copynumber: 15.3 Consensus size: 3
53355505 TTTAATGAAA
*
53355515 TAT T-T TAT TAT T-T TAT TAT TAT TAT TAT TATT TAT TAT TTT TAT
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TA-T TAT TAT TAT TAT
53355559 T
1 T
53355560 TAGTATAAAA
Statistics
Matches: 37, Mismatches: 2, Indels: 6
0.82 0.04 0.13
Matches are distributed among these distances:
2 4 0.11
3 30 0.81
4 3 0.08
ACGTcount: A:0.27, C:0.00, G:0.00, T:0.73
Consensus pattern (3 bp):
TAT
Found at i:53355548 original size:19 final size:20
Alignment explanation
Indices: 53355515--53355559 Score: 67
Period size: 19 Copynumber: 2.4 Consensus size: 20
53355505 TTTAATGAAA
53355515 TATT-TTATTATTTTATTAT
1 TATTATTATTATTTTATTAT
53355534 TATTATTATTA-TTTATTAT
1 TATTATTATTATTTTATTAT
*
53355553 TTTTATT
1 TATTATT
53355560 TAGTATAAAA
Statistics
Matches: 24, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
19 18 0.75
20 6 0.25
ACGTcount: A:0.27, C:0.00, G:0.00, T:0.73
Consensus pattern (20 bp):
TATTATTATTATTTTATTAT
Found at i:53356841 original size:51 final size:51
Alignment explanation
Indices: 53356765--53356872 Score: 216
Period size: 51 Copynumber: 2.1 Consensus size: 51
53356755 AAGTTATCTA
53356765 GATGAAATATGAAGCTCTTGTTGAAGCTAGAGCAACAAAGTAATAATTCTG
1 GATGAAATATGAAGCTCTTGTTGAAGCTAGAGCAACAAAGTAATAATTCTG
53356816 GATGAAATATGAAGCTCTTGTTGAAGCTAGAGCAACAAAGTAATAATTCTG
1 GATGAAATATGAAGCTCTTGTTGAAGCTAGAGCAACAAAGTAATAATTCTG
53356867 GATGAA
1 GATGAA
53356873 GTACGAAGTA
Statistics
Matches: 57, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
51 57 1.00
ACGTcount: A:0.40, C:0.11, G:0.22, T:0.27
Consensus pattern (51 bp):
GATGAAATATGAAGCTCTTGTTGAAGCTAGAGCAACAAAGTAATAATTCTG
Found at i:53357742 original size:46 final size:46
Alignment explanation
Indices: 53357675--53357878 Score: 309
Period size: 46 Copynumber: 4.4 Consensus size: 46
53357665 GCTTTTTGAA
* *
53357675 ATGAAATATGTAAGACTATGGTTGAAAGATACCATGGCAACATGAT
1 ATGAAATGTGTAAGACCATGGTTGAAAGATACCATGGCAACATGAT
* *
53357721 ATGAATTGTGTAAGACCATGGTTGAATGATACCATGGCAACATGAT
1 ATGAAATGTGTAAGACCATGGTTGAAAGATACCATGGCAACATGAT
* * *
53357767 ATGAAATATGTAAGACCATGGTTGAAAGATAACATGGAAACATGAT
1 ATGAAATGTGTAAGACCATGGTTGAAAGATACCATGGCAACATGAT
* *
53357813 ATGAAATGTGTAAGACCATGGTTGAAAGATACCATGGCAACGTGAC
1 ATGAAATGTGTAAGACCATGGTTGAAAGATACCATGGCAACATGAT
**
53357859 ATGAAATGAATAAGACCATG
1 ATGAAATGTGTAAGACCATG
53357879 ACAACATGAC
Statistics
Matches: 142, Mismatches: 16, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
46 142 1.00
ACGTcount: A:0.41, C:0.12, G:0.23, T:0.25
Consensus pattern (46 bp):
ATGAAATGTGTAAGACCATGGTTGAAAGATACCATGGCAACATGAT
Found at i:53357877 original size:30 final size:30
Alignment explanation
Indices: 53357843--53357907 Score: 87
Period size: 30 Copynumber: 2.2 Consensus size: 30
53357833 GTTGAAAGAT
* *
53357843 ACCATGGCAACGTGACATG-AAATGAATAAG
1 ACCATGACAACATGACA-GAAAATGAATAAG
*
53357873 ACCATGACAACATGACAGAAAATGAGTAAG
1 ACCATGACAACATGACAGAAAATGAATAAG
53357903 ACCAT
1 ACCAT
53357908 AGTTGAAAGA
Statistics
Matches: 31, Mismatches: 3, Indels: 2
0.86 0.08 0.06
Matches are distributed among these distances:
29 1 0.03
30 30 0.97
ACGTcount: A:0.46, C:0.18, G:0.20, T:0.15
Consensus pattern (30 bp):
ACCATGACAACATGACAGAAAATGAATAAG
Found at i:53359406 original size:26 final size:26
Alignment explanation
Indices: 53359377--53359484 Score: 180
Period size: 26 Copynumber: 4.2 Consensus size: 26
53359367 TGGTACAAAT
53359377 TGATAATGGGTTAGGTAAATGTTCCA
1 TGATAATGGGTTAGGTAAATGTTCCA
* *
53359403 TGATAATGGATTAGGTAAATATTCCA
1 TGATAATGGGTTAGGTAAATGTTCCA
53359429 TGATAATGGGTTAGGTAAATGTTCCA
1 TGATAATGGGTTAGGTAAATGTTCCA
* *
53359455 TGATAATGGCTTAGGTAAATGTTTCA
1 TGATAATGGGTTAGGTAAATGTTCCA
53359481 TGAT
1 TGAT
53359485 GGGCATTTCA
Statistics
Matches: 76, Mismatches: 6, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
26 76 1.00
ACGTcount: A:0.32, C:0.07, G:0.24, T:0.36
Consensus pattern (26 bp):
TGATAATGGGTTAGGTAAATGTTCCA
Found at i:53367117 original size:12 final size:11
Alignment explanation
Indices: 53367092--53367139 Score: 51
Period size: 12 Copynumber: 4.2 Consensus size: 11
53367082 AAATTAAGAT
**
53367092 AATAAAATTGA
1 AATAAAATAAA
53367103 AATGAAAATAAA
1 AAT-AAAATAAA
*
53367115 AATAAAAAATAA
1 AATAAAATA-AA
53367127 AATAAAATAAA
1 AATAAAATAAA
53367138 AA
1 AA
53367140 GAATAAAAAG
Statistics
Matches: 31, Mismatches: 4, Indels: 4
0.79 0.10 0.10
Matches are distributed among these distances:
11 12 0.39
12 19 0.61
ACGTcount: A:0.77, C:0.00, G:0.04, T:0.19
Consensus pattern (11 bp):
AATAAAATAAA
Found at i:53372499 original size:13 final size:13
Alignment explanation
Indices: 53372477--53372509 Score: 50
Period size: 13 Copynumber: 2.6 Consensus size: 13
53372467 AAGGGTTTGT
53372477 TTAT-TAAACTAA
1 TTATCTAAACTAA
53372489 TTATCTAAACTAA
1 TTATCTAAACTAA
*
53372502 TTAACTAA
1 TTATCTAA
53372510 TTTAATTAAA
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
12 4 0.21
13 15 0.79
ACGTcount: A:0.48, C:0.12, G:0.00, T:0.39
Consensus pattern (13 bp):
TTATCTAAACTAA
Found at i:53382554 original size:21 final size:21
Alignment explanation
Indices: 53382529--53382632 Score: 85
Period size: 21 Copynumber: 5.2 Consensus size: 21
53382519 TAGCCTTCGG
53382529 GCTTCCGTTTAGCACTTATGT
1 GCTTCCGTTTAGCACTTATGT
* ** *
53382550 GCTTCAG-TTAGC-C-TCCGG
1 GCTTCCGTTTAGCACTTATGT
*
53382568 GCTTCCATTTAGCACTTATGT
1 GCTTCCGTTTAGCACTTATGT
* * *
53382589 GCTTCAG-TTAGC-CTT-CGG
1 GCTTCCGTTTAGCACTTATGT
*
53382607 GCTTCCGTTTAGCACGTATGT
1 GCTTCCGTTTAGCACTTATGT
53382628 GCTTC
1 GCTTC
53382633 AGCTAGATTT
Statistics
Matches: 60, Mismatches: 17, Indels: 12
0.67 0.19 0.13
Matches are distributed among these distances:
18 14 0.23
19 14 0.23
20 13 0.22
21 19 0.32
ACGTcount: A:0.13, C:0.27, G:0.22, T:0.38
Consensus pattern (21 bp):
GCTTCCGTTTAGCACTTATGT
Found at i:53382559 original size:39 final size:39
Alignment explanation
Indices: 53382511--53382650 Score: 217
Period size: 39 Copynumber: 3.6 Consensus size: 39
53382501 GCTCTAATGA
*
53382511 GCTTTAGTTAGCCTTCGGGCTTCCGTTTAGCACTTATGT
1 GCTTCAGTTAGCCTTCGGGCTTCCGTTTAGCACTTATGT
* *
53382550 GCTTCAGTTAGCCTCCGGGCTTCCATTTAGCACTTATGT
1 GCTTCAGTTAGCCTTCGGGCTTCCGTTTAGCACTTATGT
*
53382589 GCTTCAGTTAGCCTTCGGGCTTCCGTTTAGCACGTATGT
1 GCTTCAGTTAGCCTTCGGGCTTCCGTTTAGCACTTATGT
* **
53382628 GCTTCAGCTAGATTTCGGGCTTC
1 GCTTCAGTTAGCCTTCGGGCTTC
53382651 AGATCACAAT
Statistics
Matches: 92, Mismatches: 9, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
39 92 1.00
ACGTcount: A:0.14, C:0.26, G:0.24, T:0.37
Consensus pattern (39 bp):
GCTTCAGTTAGCCTTCGGGCTTCCGTTTAGCACTTATGT
Found at i:53384109 original size:33 final size:32
Alignment explanation
Indices: 53383968--53384146 Score: 161
Period size: 31 Copynumber: 5.4 Consensus size: 32
53383958 GTGAAAAGTA
* * *
53383968 GTAGCTTCGGCTACCTGATCAGT-GAAAAGTG
1 GTAGCTCCGGCTACCTGATCAGTAAAAAAATG
53383999 GTAGCTCCGGCTACCTGAT-AGATAAAAAAATG
1 GTAGCTCCGGCTACCTGATCAG-TAAAAAAATG
*
53384031 GTCA-CTCTGGCTACCTGATCAGTGAATAGTGAAAAGTG
1 GT-AGCTCCGGCTACCTGATCAGT-AA-A---AAAA-TG
53384069 GTAGCTCCGGCTACCTGAT-AGATAAAAAAAATG
1 GTAGCTCCGGCTACCTGATCAG-T-AAAAAAATG
* * *
53384102 GTAGCTCCGGCTACCTGATCAGT-GAATAGTG
1 GTAGCTCCGGCTACCTGATCAGTAAAAAAATG
*
53384133 GTAGCTTCGGCTAC
1 GTAGCTCCGGCTAC
53384147 AAGTGACAAG
Statistics
Matches: 125, Mismatches: 10, Indels: 26
0.78 0.06 0.16
Matches are distributed among these distances:
30 2 0.02
31 37 0.30
32 23 0.18
33 27 0.22
34 7 0.06
37 8 0.06
38 21 0.17
ACGTcount: A:0.30, C:0.20, G:0.26, T:0.25
Consensus pattern (32 bp):
GTAGCTCCGGCTACCTGATCAGTAAAAAAATG
Found at i:53384243 original size:46 final size:47
Alignment explanation
Indices: 53384169--53384262 Score: 109
Period size: 46 Copynumber: 2.0 Consensus size: 47
53384159 ACAATTGGTT
* *
53384169 TCCGTATAAGACCATATCTGGGATATGGCATC-AGTGTGATATGTGA
1 TCCGTATAAGACCATAGCTGGGACATGGCATCGAGTGTGATATGTGA
* * * * *
53384215 TCCGTGTAAGACCATGGCTGGGCCATGGCTTCGGTGTGTGATATGTGA
1 TCCGTATAAGACCATAGCTGGGACATGGCATC-GAGTGTGATATGTGA
53384263 CTATGCGCAA
Statistics
Matches: 39, Mismatches: 7, Indels: 2
0.81 0.15 0.04
Matches are distributed among these distances:
46 26 0.67
48 13 0.33
ACGTcount: A:0.22, C:0.17, G:0.31, T:0.30
Consensus pattern (47 bp):
TCCGTATAAGACCATAGCTGGGACATGGCATCGAGTGTGATATGTGA
Found at i:53385665 original size:17 final size:17
Alignment explanation
Indices: 53385643--53385683 Score: 82
Period size: 17 Copynumber: 2.4 Consensus size: 17
53385633 AAAAAGAACT
53385643 AAATTGTATCAAATGCA
1 AAATTGTATCAAATGCA
53385660 AAATTGTATCAAATGCA
1 AAATTGTATCAAATGCA
53385677 AAATTGT
1 AAATTGT
53385684 GGGAAATGAT
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 24 1.00
ACGTcount: A:0.46, C:0.10, G:0.12, T:0.32
Consensus pattern (17 bp):
AAATTGTATCAAATGCA
Found at i:53387646 original size:39 final size:39
Alignment explanation
Indices: 53387507--53387630 Score: 203
Period size: 39 Copynumber: 3.2 Consensus size: 39
53387497 GCTCTGATGA
* * **
53387507 GCTTCGGTTAGCCTTCGGGCTTCCGTTTAGTGCTTATGT
1 GCTTCAGTTAGCCTCCGGGCTTCCGTTTAGAACTTATGT
*
53387546 GCTTCAGTTAGCCTCCGGGCTTCCGTTTAGCACTTATGT
1 GCTTCAGTTAGCCTCCGGGCTTCCGTTTAGAACTTATGT
53387585 GCTTCAGTTAGCCTCCGGGCTTCCGTTTAGAACTTATGT
1 GCTTCAGTTAGCCTCCGGGCTTCCGTTTAGAACTTATGT
53387624 GCTTCAG
1 GCTTCAG
53387631 CTAGATTTCG
Statistics
Matches: 80, Mismatches: 5, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
39 80 1.00
ACGTcount: A:0.12, C:0.26, G:0.25, T:0.37
Consensus pattern (39 bp):
GCTTCAGTTAGCCTCCGGGCTTCCGTTTAGAACTTATGT
Found at i:53394210 original size:26 final size:26
Alignment explanation
Indices: 53394138--53394214 Score: 68
Period size: 26 Copynumber: 2.9 Consensus size: 26
53394128 ACATATTTTC
* *
53394138 TCAAAATTTTA-TCAGGGATATAATCA
1 TCAAAATTTTACTGAGGG-TAAAATCA
* * *
53394164 TCAAAAAATTTACCG-GAGGTAAAATCG
1 TC-AAAATTTTACTGAG-GGTAAAATCA
53394191 TCAAAATTTTACTGAGGGTAAAAT
1 TCAAAATTTTACTGAGGGTAAAAT
53394215 AGGGATGAGA
Statistics
Matches: 40, Mismatches: 7, Indels: 8
0.73 0.13 0.15
Matches are distributed among these distances:
26 20 0.50
27 18 0.45
28 2 0.05
ACGTcount: A:0.43, C:0.12, G:0.16, T:0.30
Consensus pattern (26 bp):
TCAAAATTTTACTGAGGGTAAAATCA
Found at i:53411259 original size:18 final size:20
Alignment explanation
Indices: 53411214--53411260 Score: 62
Period size: 19 Copynumber: 2.5 Consensus size: 20
53411204 AATTGGTATA
53411214 AAGTGCATATCTGGCACATG
1 AAGTGCATATCTGGCACATG
* *
53411234 AGGTGCAT-TTTGGCACAT-
1 AAGTGCATATCTGGCACATG
53411252 AAGTGCATA
1 AAGTGCATA
53411261 ATCCTATACA
Statistics
Matches: 23, Mismatches: 3, Indels: 3
0.79 0.10 0.10
Matches are distributed among these distances:
18 7 0.30
19 9 0.39
20 7 0.30
ACGTcount: A:0.30, C:0.17, G:0.26, T:0.28
Consensus pattern (20 bp):
AAGTGCATATCTGGCACATG
Found at i:53420863 original size:24 final size:24
Alignment explanation
Indices: 53420829--53420875 Score: 76
Period size: 24 Copynumber: 2.0 Consensus size: 24
53420819 ATTAATTGTA
* *
53420829 AAAAAATTATATACTGGATCCAAT
1 AAAAAACTATATACCGGATCCAAT
53420853 AAAAAACTATATACCGGATCCAA
1 AAAAAACTATATACCGGATCCAA
53420876 GATTTTTTTG
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:0.51, C:0.17, G:0.09, T:0.23
Consensus pattern (24 bp):
AAAAAACTATATACCGGATCCAAT
Found at i:53421332 original size:27 final size:27
Alignment explanation
Indices: 53421279--53421335 Score: 78
Period size: 27 Copynumber: 2.1 Consensus size: 27
53421269 AAAACAATTA
* *
53421279 AGTGGAGGGTGTCAGGTAGATGACACC
1 AGTGGAGGGTGTCAAGTAGACGACACC
* *
53421306 AGTGGAGGGTGTCAAGTAGGCGGCACC
1 AGTGGAGGGTGTCAAGTAGACGACACC
53421333 AGT
1 AGT
53421336 TGTGCCTATC
Statistics
Matches: 26, Mismatches: 4, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
27 26 1.00
ACGTcount: A:0.25, C:0.16, G:0.42, T:0.18
Consensus pattern (27 bp):
AGTGGAGGGTGTCAAGTAGACGACACC
Found at i:53421681 original size:27 final size:27
Alignment explanation
Indices: 53421646--53421697 Score: 77
Period size: 27 Copynumber: 1.9 Consensus size: 27
53421636 AAAATTTTTT
* *
53421646 AATATATTTGATATTATTAGAAATAAC
1 AATAAATTTAATATTATTAGAAATAAC
*
53421673 AATAAATTTAATATTGTTAGAAATA
1 AATAAATTTAATATTATTAGAAATA
53421698 GACTATTATC
Statistics
Matches: 22, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
27 22 1.00
ACGTcount: A:0.50, C:0.02, G:0.08, T:0.40
Consensus pattern (27 bp):
AATAAATTTAATATTATTAGAAATAAC
Found at i:53424583 original size:64 final size:64
Alignment explanation
Indices: 53424485--53424641 Score: 271
Period size: 64 Copynumber: 2.5 Consensus size: 64
53424475 TGAGCTTATG
* *
53424485 TAATTTATATAAAA-AAATTATATTACAAAATTTGTTCCAATTAGATTATGGTTGTAATGTATT
1 TAATTTATATAAAATAATTTATATTACAAAATTTGTTCCAATTAGATTATGGTTGTAATGAATT
*
53424548 TAATTTATATAAAATAATTTATATTACAAACTTTGTTCCAATTAGATTATGGTTGTAATGAATT
1 TAATTTATATAAAATAATTTATATTACAAAATTTGTTCCAATTAGATTATGGTTGTAATGAATT
*
53424612 TAATTTATATAACATAATTTATATTACAAA
1 TAATTTATATAAAATAATTTATATTACAAA
53424642 GCTAAGTTTG
Statistics
Matches: 89, Mismatches: 4, Indels: 1
0.95 0.04 0.01
Matches are distributed among these distances:
63 14 0.16
64 75 0.84
ACGTcount: A:0.42, C:0.06, G:0.08, T:0.45
Consensus pattern (64 bp):
TAATTTATATAAAATAATTTATATTACAAAATTTGTTCCAATTAGATTATGGTTGTAATGAATT
Found at i:53427140 original size:114 final size:110
Alignment explanation
Indices: 53426989--53427207 Score: 309
Period size: 107 Copynumber: 2.0 Consensus size: 110
53426979 CCACATTAAA
*
53426989 ATATTAAAATACTAAAAATAATATGCCAATAAAAAAAATAAAAAACATAACATAAACGATACATA
1 ATATTAAAATACTAAAAATAACATGCCAAT------AA-AAAAAACATAACATAAACGATACATA
* *
53427054 ATAAATATG-A-ATTTTT-TTATTATTTTAAAATGATAATAAGTAAATTTTT
59 ATAAATACGAATATTTTTATTATTACTTTAAAATGATAATAAGTAAATTTTT
* *
53427103 ATATTAAAATACTAAAAATAACATGCCAATAACAAAAACATAACTTAAACGATACATAATAAATA
1 ATATTAAAATACTAAAAATAACATGCCAATAAAAAAAACATAACATAAACGATACATAATAAATA
53427168 CGAATATTTTTATTATTACTTTAAAATGATAATAAGTAAA
66 CGAATATTTTTATTATTACTTTAAAATGATAATAAGTAAA
53427208 CATTTTTGGT
Statistics
Matches: 97, Mismatches: 5, Indels: 10
0.87 0.04 0.09
Matches are distributed among these distances:
107 32 0.33
108 3 0.03
109 6 0.06
110 27 0.28
114 29 0.30
ACGTcount: A:0.55, C:0.08, G:0.05, T:0.32
Consensus pattern (110 bp):
ATATTAAAATACTAAAAATAACATGCCAATAAAAAAAACATAACATAAACGATACATAATAAATA
CGAATATTTTTATTATTACTTTAAAATGATAATAAGTAAATTTTT
Found at i:53428590 original size:20 final size:18
Alignment explanation
Indices: 53428562--53428615 Score: 63
Period size: 20 Copynumber: 2.8 Consensus size: 18
53428552 GGTTTAGGGT
*
53428562 TTTTTTATATTTTTAAGTA
1 TTTTTTATATTTTTAA-AA
53428581 TTTTTATATATATTTTAAAA
1 TTTTT-TATAT-TTTTAAAA
53428601 TTTTTTATAATTTTT
1 TTTTTTAT-ATTTTT
53428616 TGAGTTGTAA
Statistics
Matches: 31, Mismatches: 1, Indels: 6
0.82 0.03 0.16
Matches are distributed among these distances:
19 12 0.39
20 13 0.42
21 6 0.19
ACGTcount: A:0.30, C:0.00, G:0.02, T:0.69
Consensus pattern (18 bp):
TTTTTTATATTTTTAAAA
Found at i:53429160 original size:14 final size:16
Alignment explanation
Indices: 53429137--53429169 Score: 52
Period size: 15 Copynumber: 2.2 Consensus size: 16
53429127 TTTTTGGTCA
53429137 TTTCTATCTTTTTC-T
1 TTTCTATCTTTTTCAT
53429152 TTTCT-TCTTTTTCAT
1 TTTCTATCTTTTTCAT
53429167 TTT
1 TTT
53429170 GATTATTTTG
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
14 8 0.47
15 9 0.53
ACGTcount: A:0.06, C:0.18, G:0.00, T:0.76
Consensus pattern (16 bp):
TTTCTATCTTTTTCAT
Found at i:53442216 original size:13 final size:12
Alignment explanation
Indices: 53442198--53442260 Score: 51
Period size: 13 Copynumber: 5.2 Consensus size: 12
53442188 AGTAATAATT
53442198 TTATTTATATATA
1 TTATTTATAT-TA
53442211 TTATTTATATTA
1 TTATTTATATTA
* *
53442223 TTAAATTAAATT-
1 TT-ATTTATATTA
53442235 TCATATTT-TA-TA
1 T--TATTTATATTA
53442247 TTATTTATATTA
1 TTATTTATATTA
53442259 TT
1 TT
53442261 GAATTTGTTT
Statistics
Matches: 40, Mismatches: 4, Indels: 13
0.70 0.07 0.23
Matches are distributed among these distances:
10 5 0.12
11 3 0.08
12 11 0.28
13 20 0.50
14 1 0.03
ACGTcount: A:0.37, C:0.02, G:0.00, T:0.62
Consensus pattern (12 bp):
TTATTTATATTA
Found at i:53442219 original size:9 final size:9
Alignment explanation
Indices: 53442197--53442260 Score: 55
Period size: 9 Copynumber: 7.2 Consensus size: 9
53442187 TAGTAATAAT
53442197 TTTAT-TTA
1 TTTATATTA
*
53442205 TATATATTA
1 TTTATATTA
53442214 TTTATATTA
1 TTTATATTA
*
53442223 -TTAAATTAAA
1 TTTATATT--A
53442233 TTTCATA-T-
1 TTT-ATATTA
53442241 TTTATATTA
1 TTTATATTA
53442250 TTTATATTA
1 TTTATATTA
53442259 TT
1 TT
53442261 GAATTTGTTT
Statistics
Matches: 45, Mismatches: 4, Indels: 13
0.73 0.06 0.21
Matches are distributed among these distances:
7 3 0.07
8 14 0.31
9 22 0.49
10 1 0.02
11 3 0.07
12 2 0.04
ACGTcount: A:0.36, C:0.02, G:0.00, T:0.62
Consensus pattern (9 bp):
TTTATATTA
Found at i:53446547 original size:113 final size:113
Alignment explanation
Indices: 53446349--53446572 Score: 412
Period size: 113 Copynumber: 2.0 Consensus size: 113
53446339 CTTATAAACT
53446349 ACTACAGGAGGCTAATTCGGGTCCTAGTGATAATTTTTTACAGGCCAAGACTAGAGATTTCTGTA
1 ACTACAGGAGGCTAATTCGGGTCCTAGTGATAATTTTTTACAGGCCAAGACTAGAGATTTCTGTA
53446414 GGAAATTATGGAATATACATCTCCCTTCAAAAATTAAATTAACAATAA
66 GGAAATTATGGAATATACATCTCCCTTCAAAAATTAAATTAACAATAA
* * **
53446462 ACTACAGGAGGCTAATTTGGGTCCTAGTGATAATTTTTTATAGGCGGAGACTAGAGATTTCTGTA
1 ACTACAGGAGGCTAATTCGGGTCCTAGTGATAATTTTTTACAGGCCAAGACTAGAGATTTCTGTA
53446527 GGAAATTATGGAATATACATCTCCCTTCAAAAATTAAATTAACAAT
66 GGAAATTATGGAATATACATCTCCCTTCAAAAATTAAATTAACAAT
53446573 TTGGAGAATT
Statistics
Matches: 107, Mismatches: 4, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
113 107 1.00
ACGTcount: A:0.36, C:0.15, G:0.18, T:0.31
Consensus pattern (113 bp):
ACTACAGGAGGCTAATTCGGGTCCTAGTGATAATTTTTTACAGGCCAAGACTAGAGATTTCTGTA
GGAAATTATGGAATATACATCTCCCTTCAAAAATTAAATTAACAATAA
Found at i:53449092 original size:30 final size:30
Alignment explanation
Indices: 53449058--53449116 Score: 109
Period size: 30 Copynumber: 2.0 Consensus size: 30
53449048 TGTTTTATTG
53449058 TTAATTTTGTTATTATTTTAGAAGCATTTC
1 TTAATTTTGTTATTATTTTAGAAGCATTTC
*
53449088 TTAATTTTGTTATTATTTTAGAGGCATTT
1 TTAATTTTGTTATTATTTTAGAAGCATTT
53449117 GTTTGTTAAG
Statistics
Matches: 28, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
30 28 1.00
ACGTcount: A:0.25, C:0.05, G:0.12, T:0.58
Consensus pattern (30 bp):
TTAATTTTGTTATTATTTTAGAAGCATTTC
Found at i:53456283 original size:22 final size:22
Alignment explanation
Indices: 53456239--53456283 Score: 54
Period size: 22 Copynumber: 2.0 Consensus size: 22
53456229 AGAAATAAGT
* * * *
53456239 CCAAAAACAAAAATATAATAAA
1 CCAAAAAAAAAAACAAAAAAAA
53456261 CCAAAAAAAAAAACAAAAAAAA
1 CCAAAAAAAAAAACAAAAAAAA
53456283 C
1 C
53456284 GAAGTCCAAG
Statistics
Matches: 19, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
22 19 1.00
ACGTcount: A:0.78, C:0.16, G:0.00, T:0.07
Consensus pattern (22 bp):
CCAAAAAAAAAAACAAAAAAAA
Found at i:53456428 original size:19 final size:19
Alignment explanation
Indices: 53456401--53456437 Score: 65
Period size: 19 Copynumber: 1.9 Consensus size: 19
53456391 ATAATCTTCA
*
53456401 ATGATATGCAATCTTAGAT
1 ATGAAATGCAATCTTAGAT
53456420 ATGAAATGCAATCTTAGA
1 ATGAAATGCAATCTTAGA
53456438 AGATATGATT
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
19 17 1.00
ACGTcount: A:0.41, C:0.11, G:0.16, T:0.32
Consensus pattern (19 bp):
ATGAAATGCAATCTTAGAT
Found at i:53456470 original size:22 final size:22
Alignment explanation
Indices: 53456429--53456474 Score: 58
Period size: 21 Copynumber: 2.1 Consensus size: 22
53456419 TATGAAATGC
*
53456429 AATCTTAGAAGATATGATTTTGT
1 AATCTTAGAAGATAT-AATTTGT
*
53456452 AATCTTAG-AGATTTAATTTGT
1 AATCTTAGAAGATATAATTTGT
53456473 AA
1 AA
53456475 ATACCTTTTA
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
21 8 0.38
22 5 0.24
23 8 0.38
ACGTcount: A:0.37, C:0.04, G:0.15, T:0.43
Consensus pattern (22 bp):
AATCTTAGAAGATATAATTTGT
Found at i:53456473 original size:21 final size:23
Alignment explanation
Indices: 53456416--53456474 Score: 61
Period size: 22 Copynumber: 2.7 Consensus size: 23
53456406 ATGCAATCTT
* *
53456416 AGATATGAA-ATGCAATCTTAGA
1 AGATATGAATTTGTAATCTTAGA
*
53456438 AGATATGATTTTGTAATCTTAG-
1 AGATATGAATTTGTAATCTTAGA
*
53456460 AGAT-TTAATTTGTAA
1 AGATATGAATTTGTAA
53456475 ATACCTTTTA
Statistics
Matches: 31, Mismatches: 5, Indels: 3
0.79 0.13 0.08
Matches are distributed among these distances:
21 9 0.29
22 12 0.39
23 10 0.32
ACGTcount: A:0.39, C:0.05, G:0.17, T:0.39
Consensus pattern (23 bp):
AGATATGAATTTGTAATCTTAGA
Found at i:53461586 original size:9 final size:9
Alignment explanation
Indices: 53461584--53461616 Score: 50
Period size: 9 Copynumber: 3.7 Consensus size: 9
53461574 AAAAAAGGAA
53461584 AAAAGAAAAG
1 AAAA-AAAAG
53461594 AAAAAAAAG
1 AAAAAAAAG
53461603 -AAAAAAAG
1 AAAAAAAAG
53461611 AAAAAA
1 AAAAAA
53461617 TGGAGAGGCC
Statistics
Matches: 22, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
8 8 0.36
9 10 0.45
10 4 0.18
ACGTcount: A:0.88, C:0.00, G:0.12, T:0.00
Consensus pattern (9 bp):
AAAAAAAAG
Found at i:53461587 original size:8 final size:7
Alignment explanation
Indices: 53461574--53461616 Score: 52
Period size: 7 Copynumber: 5.9 Consensus size: 7
53461564 TCTATTTCGA
53461574 AAAAAAGG
1 AAAAAA-G
53461582 AAAAAAG
1 AAAAAAG
53461589 AAAAGAA-
1 AAAA-AAG
53461596 AAAAAAG
1 AAAAAAG
53461603 AAAAAAAG
1 -AAAAAAG
53461611 AAAAAA
1 AAAAAA
53461617 TGGAGAGGCC
Statistics
Matches: 32, Mismatches: 0, Indels: 7
0.82 0.00 0.18
Matches are distributed among these distances:
6 2 0.06
7 15 0.47
8 15 0.47
ACGTcount: A:0.86, C:0.00, G:0.14, T:0.00
Consensus pattern (7 bp):
AAAAAAG
Found at i:53461601 original size:22 final size:22
Alignment explanation
Indices: 53461573--53461614 Score: 75
Period size: 22 Copynumber: 1.9 Consensus size: 22
53461563 TTCTATTTCG
*
53461573 AAAAAAAGGAAAAAAGAAAAGA
1 AAAAAAAGAAAAAAAGAAAAGA
53461595 AAAAAAAGAAAAAAAGAAAA
1 AAAAAAAGAAAAAAAGAAAA
53461615 AATGGAGAGG
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
22 19 1.00
ACGTcount: A:0.86, C:0.00, G:0.14, T:0.00
Consensus pattern (22 bp):
AAAAAAAGAAAAAAAGAAAAGA
Found at i:53462623 original size:44 final size:43
Alignment explanation
Indices: 53462564--53463127 Score: 291
Period size: 44 Copynumber: 12.9 Consensus size: 43
53462554 GATCCAAGAT
* *
53462564 GATTTGGCGTCTCTGTATTGTCAGGGAGCAGATCGAAGATGACA
1 GATTTGGCATCTCTGTATTGGCAGGGAGCAGATCGAAGAT-ACA
**
53462608 GATTTGGCATCTCTGTATTGGCAAAGAGCAGATCGAAGATAACA
1 GATTTGGCATCTCTGTATTGGCAGGGAGCAGATCGAAGAT-ACA
* *
53462652 GATTTGGCATCTCTGTATTGGCAGGGAGCAGATCAAAGACATAACT
1 GATTTGGCATCTCTGTATTGGCAGGGAGCAGATCGAAG--AT-ACA
* * * * * * * *
53462698 GATTTAGCTTTCACGTGT-TT-ACATTGAAGCAAATCCAAGAT---
1 GATTTGGC-ATCTC-TGTATTGGCA-GGGAGCAGATCGAAGATACA
** * *
53462739 GATTTGGTGTCTCTGTATTGTCAGAGAGCAGATCGAAGATAGCA
1 GATTTGGCATCTCTGTATTGGCAGGGAGCAGATCGAAGATA-CA
* * *
53462783 GATTTGGCATCTTTGTATTGGCAGAGAGCAGATCGAAGACAGCA
1 GATTTGGCATCTCTGTATTGGCAGGGAGCAGATCGAAGATA-CA
* * *
53462827 GATTTGGCATCTCTATATTGGCAGGGAGCAGATCGAGGTCATAGCT
1 GATTTGGCATCTCTGTATTGGCAGGGAGCAGATCGAAG--ATA-CA
* * * * * *
53462873 GATTTGGCTTTCACGTGT-TT-AC-GTTGAAGCAAATCTAAGAT---
1 GATTTGGC-ATCTC-TGTATTGGCAG--GGAGCAGATCGAAGATACA
* * *
53462914 GATTTGGCGTCTCTGTATTGGCAGGGAGCAGATCGAAGACATGGCT
1 GATTTGGCATCTCTGTATTGGCAGGGAGCAGATCGAAG--AT-ACA
* * * * * *
53462960 GATTTGGCTTTTACGTGT-TT-AC-GTTGAAGCAAATCTAAGAT---
1 GATTTGGCATCT-C-TGTATTGGCAG--GGAGCAGATCGAAGATACA
* * * * * *
53463001 GATTTGACATCTCTGTATTGGCA-GAATGCAAATTGAAGACAGA
1 GATTTGGCATCTCTGTATTGGCAGGGA-GCAGATCGAAGATACA
* * ** *
53463044 TGATTTGGCGTCTCTGTATTGTCAATGAGCAGATCGAATATACCA
1 -GATTTGGCATCTCTGTATTGGCAGGGAGCAGATCGAAGATA-CA
* *
53463089 GATTTGGCGTCTCTGTATTGGCAAGGAGCAGATCGAAGA
1 GATTTGGCATCTCTGTATTGGCAGGGAGCAGATCGAAGA
53463128 CATAGCTTTC
Statistics
Matches: 402, Mismatches: 78, Indels: 80
0.72 0.14 0.14
Matches are distributed among these distances:
39 12 0.03
40 46 0.11
41 27 0.07
42 3 0.01
44 213 0.53
45 10 0.02
46 38 0.09
47 45 0.11
48 8 0.02
ACGTcount: A:0.28, C:0.16, G:0.27, T:0.29
Consensus pattern (43 bp):
GATTTGGCATCTCTGTATTGGCAGGGAGCAGATCGAAGATACA
Found at i:53462768 original size:87 final size:87
Alignment explanation
Indices: 53462540--53463294 Score: 626
Period size: 87 Copynumber: 8.7 Consensus size: 87
53462530 CCTTCAAGTA
* * * *
53462540 TTTACACTGAAGCAGATCCAAGATGATTTGGCGTCTCTGTATTGTCAGGGAGCAGATCGAAG--A
1 TTTACATTGAAGCAAATCTAAGATGATTTGGCGTCTCTGTATTGGCAGGGAGCAGATCGAAGACA
* * * *
53462603 TGACAGATTTGGC-ATCTC-TG
66 TAACTGATTTGGCTTTCACGTG
* ** * * * *
53462623 TATTGGCAAAG-AGCAGATCGAAGATAACAGATTTGGCATCTCTGTATTGGCAGGGAGCAGATCA
1 T-TT-ACATTGAAGCAAATCTAAGAT----GATTTGGCGTCTCTGTATTGGCAGGGAGCAGATCG
*
53462687 AAGACATAACTGATTTAGCTTTCACGTG
60 AAGACATAACTGATTTGGCTTTCACGTG
* * * *
53462715 TTTACATTGAAGCAAATCCAAGATGATTTGGTGTCTCTGTATTGTCAGAGAGCAGATCGAAG--A
1 TTTACATTGAAGCAAATCTAAGATGATTTGGCGTCTCTGTATTGGCAGGGAGCAGATCGAAGACA
* * * *
53462778 TAGCAGATTTGGCATCTT--TGTA
66 TAACTGATTTGGC-T-TTCACGTG
** * * * * *
53462800 TTGGCA--GAGAGCAGATCGAAGACAGCAGATTTGGCATCTCTATATTGGCAGGGAGCAGATCGA
1 TTTACATTGA-AGCAAATCTAAG--A--TGATTTGGCGTCTCTGTATTGGCAGGGAGCAGATCGA
* * *
53462863 GGTCATAGCTGATTTGGCTTTCACGTG
61 AGACATAACTGATTTGGCTTTCACGTG
*
53462890 TTTACGTTGAAGCAAATCTAAGATGATTTGGCGTCTCTGTATTGGCAGGGAGCAGATCGAAGACA
1 TTTACATTGAAGCAAATCTAAGATGATTTGGCGTCTCTGTATTGGCAGGGAGCAGATCGAAGACA
** *
53462955 TGGCTGATTTGGCTTTTACGTG
66 TAACTGATTTGGCTTTCACGTG
* * * * * *
53462977 TTTACGTTGAAGCAAATCTAAGATGATTTGACATCTCTGTATTGGCA-GAATGCAAATTGAAGAC
1 TTTACATTGAAGCAAATCTAAGATGATTTGGCGTCTCTGTATTGGCAGGGA-GCAGATCGAAGAC
* * *
53463041 A-GA-TGATTTGGC-GTCTC-TG
65 ATAACTGATTTGGCTTTCACGTG
* * * * * *
53463060 TATTGTCAATG-AGCAGATCGAATATACCAGATTTGGCGTCTCTGTATTGGCAAGGAGCAGATCG
1 T-TT-ACATTGAAGCAAATCTAAGAT----GATTTGGCGTCTCTGTATTGGCAGGGAGCAGATCG
53463124 AAGAC---A-T-A----GCTTTCACGTG
60 AAGACATAACTGATTTGGCTTTCACGTG
*
53463143 TTTACGTTGAAGCAAATCTAAGATGATTTGGCGTCTCTGTATTGGCAGGGAGCAGATCGAAGACA
1 TTTACATTGAAGCAAATCTAAGATGATTTGGCGTCTCTGTATTGGCAGGGAGCAGATCGAAGACA
*
53463208 TAGCTGATTTGGCTTTCACGTG
66 TAACTGATTTGGCTTTCACGTG
* * *
53463230 TTTACGTTGAAGCAAATCTAAGATGATTTGGCGTCTCTGTATTGGCAGAGAGCAGATTGAAGACA
1 TTTACATTGAAGCAAATCTAAGATGATTTGGCGTCTCTGTATTGGCAGGGAGCAGATCGAAGACA
53463295 GATGATTTGG
Statistics
Matches: 543, Mismatches: 85, Indels: 84
0.76 0.12 0.12
Matches are distributed among these distances:
78 39 0.07
81 5 0.01
82 17 0.03
83 10 0.02
84 40 0.07
85 33 0.06
86 7 0.01
87 223 0.41
88 101 0.19
89 4 0.01
90 32 0.06
91 27 0.05
92 5 0.01
ACGTcount: A:0.28, C:0.16, G:0.26, T:0.30
Consensus pattern (87 bp):
TTTACATTGAAGCAAATCTAAGATGATTTGGCGTCTCTGTATTGGCAGGGAGCAGATCGAAGACA
TAACTGATTTGGCTTTCACGTG
Found at i:53462838 original size:175 final size:173
Alignment explanation
Indices: 53462540--53463384 Score: 757
Period size: 175 Copynumber: 4.9 Consensus size: 173
53462530 CCTTCAAGTA
* * * *
53462540 TTTACACTGAAGCAGATCCAAGATGATTTGGCGTCTCTGTATTGTCAGGGAGCAGATCGAAGAT-
1 TTTACATTGAAGCAAATCCAAGATGATTTGGCGTCTCTGTATTGGCAGAGAGCAGATCGAAGATA
* * *
53462604 GACAGATTTGGCATCTCTGTATTGGCAAAGAGCAGATCGAAGATAACAGATTTGGCATCTCTGTA
66 G-CAGATTTGGCATCTTTGTATTGGCAGAGAGCAAATCGAAG--AACAGATTTGGCATCTCTGTA
* *
53462669 TTGGCAGGGAGCAGATCAAAGACATAACTGATTTAGCTTTCACGTG
128 TTGGCAGGGAGCAGATCGAAGACATAACTGATTTGGCTTTCACGTG
* *
53462715 TTTACATTGAAGCAAATCCAAGATGATTTGGTGTCTCTGTATTGTCAGAGAGCAGATCGAAGATA
1 TTTACATTGAAGCAAATCCAAGATGATTTGGCGTCTCTGTATTGGCAGAGAGCAGATCGAAGATA
* *
53462780 GCAGATTTGGCATCTTTGTATTGGCAGAGAGCAGATCGAAGACAGCAGATTTGGCATCTCTATAT
66 GCAGATTTGGCATCTTTGTATTGGCAGAGAGCAAATCGAAGA-A-CAGATTTGGCATCTCTGTAT
* * *
53462845 TGGCAGGGAGCAGATCGAGGTCATAGCTGATTTGGCTTTCACGTG
129 TGGCAGGGAGCAGATCGAAGACATAACTGATTTGGCTTTCACGTG
* * *
53462890 TTTACGTTGAAGCAAATCTAAGATGATTTGGCGTCTCTGTATTGGCAGGGAGCAGATCGAAGACA
1 TTTACATTGAAGCAAATCCAAGATGATTTGGCGTCTCTGTATTGGCAGAGAGCAGATCGAAG--A
* * * ** * * * *
53462955 TGGCTGATTTGGC-T-TTTACGTGTTTAC-GTTGAAGCAAATCTAAG-A-TGATTTGACATCTCT
64 TAGCAGATTTGGCATCTTT--GTATTGGCAG-AG-AGCAAATCGAAGAACAGATTTGGCATCTCT
* * * * * *
53463015 GTATTGGCA-GAATGCAAATTGAAGACA-GA-TGATTTGGC-GTCTC-TG
125 GTATTGGCAGGGA-GCAGATCGAAGACATAACTGATTTGGCTTTCACGTG
* * * * *
53463060 TATTGTCAATG-AGCAGATCGAATATACCAGATTTGGCGTCTCTGTATTGGCA-AGGAGCAGATC
1 T-TT-ACATTGAAGCAAATCCAAGAT----GATTTGGCGTCTCTGTATTGGCAGA-GAGCAGATC
* * * * * ** * * *
53463123 GAAGACA-TAGCTTT--CA-C-GTGT-TTACGTTGA-AGCAAATCTAAG-A-TGATTTGGCGTCT
59 GAAGATAGCAGATTTGGCATCTTTGTATT-GGCAGAGAGCAAATCGAAGAACAGATTTGGCATCT
*
53463179 CTGTATTGGCAGGGAGCAGATCGAAGACATAGCTGATTTGGCTTTCACGTG
123 CTGTATTGGCAGGGAGCAGATCGAAGACATAACTGATTTGGCTTTCACGTG
* * * *
53463230 TTTACGTTGAAGCAAATCTAAGATGATTTGGCGTCTCTGTATTGGCAGAGAGCAGATTGAAGACA
1 TTTACATTGAAGCAAATCCAAGATGATTTGGCGTCTCTGTATTGGCAGAGAGCAGATCGAAGATA
* * * * **
53463295 G-ATGATTTGGTATCTTTGTATTGTCAGAGAACAAATTGAAGAAACAGATTTGGCATCTCCATAT
66 GCA-GATTTGGCATCTTTGTATTGGCAGAGAGCAAATCGAAG-AACAGATTTGGCATCTCTGTAT
*
53463359 TCG-ACGGAGAGCAGATCGAAGACATA
129 TGGCA-GG-GAGCAGATCGAAGACATA
53463385 GCAGATCTAA
Statistics
Matches: 544, Mismatches: 85, Indels: 82
0.77 0.12 0.12
Matches are distributed among these distances:
165 39 0.07
166 52 0.10
167 4 0.01
168 15 0.03
169 18 0.03
170 13 0.02
171 27 0.05
172 16 0.03
173 6 0.01
174 51 0.09
175 271 0.50
176 4 0.01
177 18 0.03
178 10 0.02
ACGTcount: A:0.29, C:0.16, G:0.26, T:0.29
Consensus pattern (173 bp):
TTTACATTGAAGCAAATCCAAGATGATTTGGCGTCTCTGTATTGGCAGAGAGCAGATCGAAGATA
GCAGATTTGGCATCTTTGTATTGGCAGAGAGCAAATCGAAGAACAGATTTGGCATCTCTGTATTG
GCAGGGAGCAGATCGAAGACATAACTGATTTGGCTTTCACGTG
Found at i:53463119 original size:262 final size:253
Alignment explanation
Indices: 53462652--53463386 Score: 1003
Period size: 253 Copynumber: 2.9 Consensus size: 253
53462642 GAAGATAACA
* * * *
53462652 GATTTGGCATCTCTGTATTGGCAGGGAGCAGATCAAAGACATAACTGATTTAGCTTTCACGTGTT
1 GATTTGGCGTCTCTGTATTGGCAGGGAGCAGATCGAAGACATAGCTGATTTGGCTTTCACGTGTT
* * * * * *
53462717 TACATTGAAGCAAATCCAAGATGATTTGGTGTCTCTGTATTGTCAGAGAGCAGATCGAAGATAGC
66 TACGTTGAAGCAAATCTAAGATGATTTGGCGTCTCTGTATTGGCAGAGAGCAGATTGAAGACAG-
* *
53462782 A-GATTTGGCATCTTTGTATTGGCAGAGAGCAGATCGAAGACAGCAGATTTGGCATCTCTATATT
130 ATGATTTGGCATCTTTGTATTGTCAGAGAGCAGATCGAAGACACCAGATTTGGCATCTCTATATT
* * *
53462846 GGCAGGGAGCAGATCGAGGTCATAGCTGATTTGGCTTTCACGTGTTTACGTTGAAGCAAATCTAA
195 GGCAAGGAGCAGATCGA----AGA-C--A--TAGCTTTCACGTGTTTACGTTGAAGCAAATCTAA
53462911 GAT
251 GAT
* *
53462914 GATTTGGCGTCTCTGTATTGGCAGGGAGCAGATCGAAGACATGGCTGATTTGGCTTTTACGTGTT
1 GATTTGGCGTCTCTGTATTGGCAGGGAGCAGATCGAAGACATAGCTGATTTGGCTTTCACGTGTT
* * *
53462979 TACGTTGAAGCAAATCTAAGATGATTTGACATCTCTGTATTGGCAGA-ATGCAAATTGAAGACAG
66 TACGTTGAAGCAAATCTAAGATGATTTGGCGTCTCTGTATTGGCAGAGA-GCAGATTGAAGACAG
* * * * * *
53463043 ATGATTTGGCGTCTCTGTATTGTCA-ATGAGCAGATCGAATATACCAGATTTGGCGTCTCTGTAT
130 ATGATTTGGCATCTTTGTATTGTCAGA-GAGCAGATCGAAGACACCAGATTTGGCATCTCTATAT
53463107 TGGCAAGGAGCAGATCGAAGACATAGCTTTCACGTGTTTACGTTGAAGCAAATCTAAGAT
194 TGGCAAGGAGCAGATCGAAGACATAGCTTTCACGTGTTTACGTTGAAGCAAATCTAAGAT
53463167 GATTTGGCGTCTCTGTATTGGCAGGGAGCAGATCGAAGACATAGCTGATTTGGCTTTCACGTGTT
1 GATTTGGCGTCTCTGTATTGGCAGGGAGCAGATCGAAGACATAGCTGATTTGGCTTTCACGTGTT
53463232 TACGTTGAAGCAAATCTAAGATGATTTGGCGTCTCTGTATTGGCAGAGAGCAGATTGAAGACAGA
66 TACGTTGAAGCAAATCTAAGATGATTTGGCGTCTCTGTATTGGCAGAGAGCAGATTGAAGACAGA
* * * * * * *
53463297 TGATTTGGTATCTTTGTATTGTCAGAGAACAAATTGAAGA-AACAGATTTGGCATCTCCATATTC
131 TGATTTGGCATCTTTGTATTGTCAGAGAGCAGATCGAAGACACCAGATTTGGCATCTCTATATTG
*
53463361 G-ACGGAGAGCAGATCGAAGACATAGC
196 GCA-AG-GAGCAGATCGAAGACATAGC
53463387 AGATCTAACC
Statistics
Matches: 422, Mismatches: 44, Indels: 23
0.86 0.09 0.05
Matches are distributed among these distances:
251 1 0.00
252 21 0.05
253 210 0.50
254 2 0.00
255 1 0.00
257 1 0.00
258 2 0.00
261 3 0.01
262 181 0.43
ACGTcount: A:0.28, C:0.16, G:0.26, T:0.30
Consensus pattern (253 bp):
GATTTGGCGTCTCTGTATTGGCAGGGAGCAGATCGAAGACATAGCTGATTTGGCTTTCACGTGTT
TACGTTGAAGCAAATCTAAGATGATTTGGCGTCTCTGTATTGGCAGAGAGCAGATTGAAGACAGA
TGATTTGGCATCTTTGTATTGTCAGAGAGCAGATCGAAGACACCAGATTTGGCATCTCTATATTG
GCAAGGAGCAGATCGAAGACATAGCTTTCACGTGTTTACGTTGAAGCAAATCTAAGAT
Found at i:53463315 original size:44 final size:44
Alignment explanation
Indices: 53463250--53463353 Score: 129
Period size: 44 Copynumber: 2.4 Consensus size: 44
53463240 AGCAAATCTA
* * *
53463250 AGATGATTTGGCGTCTCTGTATTGGCAGAGAGCAGATTGAAGAC
1 AGATGATTTGGCATCTCTGTATTGGCAGAGAACAAATTGAAGAC
* * * *
53463294 AGATGATTTGGTATCTTTGTATTGTCAGAGAACAAATTGAAGAA
1 AGATGATTTGGCATCTCTGTATTGGCAGAGAACAAATTGAAGAC
*
53463338 ACA-GATTTGGCATCTC
1 AGATGATTTGGCATCTC
53463354 CATATTCGAC
Statistics
Matches: 50, Mismatches: 10, Indels: 1
0.82 0.16 0.02
Matches are distributed among these distances:
43 11 0.22
44 39 0.78
ACGTcount: A:0.31, C:0.12, G:0.26, T:0.31
Consensus pattern (44 bp):
AGATGATTTGGCATCTCTGTATTGGCAGAGAACAAATTGAAGAC
Found at i:53463568 original size:44 final size:43
Alignment explanation
Indices: 53463520--53463783 Score: 196
Period size: 44 Copynumber: 6.0 Consensus size: 43
53463510 GATTTTAACA
*
53463520 TGGCATCCCTGTGTTTATAGGGAACA-AGTTGAAGATAGCAGATT
1 TGGCATCCCTGTGTTTACAGGGAACAGA-TTGAAGATAGCAGA-T
53463564 TGGCATCCCTGTGTTTACAGGGAACAGATTGAAGACATAGCAGAT
1 TGGCATCCCTGTGTTTACAGGGAACAGATTGAAG--ATAGCAGAT
** * * * * * ***
53463609 CTGATATTCTTGTGCTTACAGCGAAACAGATCGAAGATTTTAGCA-
1 -TGGCATCCCTGTGTTTACAG-GGAACAGATTGAAGATAGCAG-AT
* *
53463654 TGGCATCCCTGTGTTTATAGGGAACAGATCGAAGACATAGCAGAT
1 TGGCATCCCTGTGTTTACAGGGAACAGATTGAAG--ATAGCAGAT
* * * * **
53463699 CTGACATTCCTGTGCTTACAGCGAAGCAGATTGAAGATTTCAGCA-
1 -TGGCATCCCTGTGTTTACAGGGAA-CAGATTGAAGATAGCAG-AT
*
53463744 TGGCATCCCTGTGTTTATAGGGAACA-AGTTGAAGA-AGCAG
1 TGGCATCCCTGTGTTTACAGGGAACAGA-TTGAAGATAGCAG
53463784 GTTTGGCGTC
Statistics
Matches: 171, Mismatches: 36, Indels: 28
0.73 0.15 0.12
Matches are distributed among these distances:
42 4 0.02
43 22 0.13
44 65 0.38
45 15 0.09
46 44 0.26
47 21 0.12
ACGTcount: A:0.30, C:0.17, G:0.25, T:0.27
Consensus pattern (43 bp):
TGGCATCCCTGTGTTTACAGGGAACAGATTGAAGATAGCAGAT
Found at i:53463623 original size:134 final size:136
Alignment explanation
Indices: 53463460--53463735 Score: 396
Period size: 134 Copynumber: 2.0 Consensus size: 136
53463450 AGAGCAAATC
***
53463460 GAAGACATAGCAGATCTGACATTCCTGTGCTTACAGCGAGGTAGATCAAAGATTTTAACATGGCA
1 GAAGACATAGCAGATCTGACATTCCTGTGCTTACAGCGAAACAGATCAAAGATTTTAACATGGCA
* * * * *
53463525 TCCCTGTGTTTATAGGGAACA-AGTTGAAG-ATAGCAGATTTGGCATCCCTGTGTTTACAGGGAA
66 TCCCTGTGTTTATAGGGAACAGA-TCGAAGAATAGCAGATCTGACATCCCTGTGCTTACAGCGAA
53463588 -CAGATT
130 GCAGATT
* * * *
53463594 GAAGACATAGCAGATCTGATATTCTTGTGCTTACAGCGAAACAGATCGAAGATTTTAGCATGGCA
1 GAAGACATAGCAGATCTGACATTCCTGTGCTTACAGCGAAACAGATCAAAGATTTTAACATGGCA
*
53463659 TCCCTGTGTTTATAGGGAACAGATCGAAGACATAGCAGATCTGACATTCCTGTGCTTACAGCGAA
66 TCCCTGTGTTTATAGGGAACAGATCGAAGA-ATAGCAGATCTGACATCCCTGTGCTTACAGCGAA
53463724 GCAGATT
130 GCAGATT
53463731 GAAGA
1 GAAGA
53463736 TTTCAGCATG
Statistics
Matches: 125, Mismatches: 13, Indels: 5
0.87 0.09 0.03
Matches are distributed among these distances:
134 84 0.67
135 1 0.01
136 29 0.23
137 11 0.09
ACGTcount: A:0.32, C:0.18, G:0.24, T:0.26
Consensus pattern (136 bp):
GAAGACATAGCAGATCTGACATTCCTGTGCTTACAGCGAAACAGATCAAAGATTTTAACATGGCA
TCCCTGTGTTTATAGGGAACAGATCGAAGAATAGCAGATCTGACATCCCTGTGCTTACAGCGAAG
CAGATT
Found at i:53463628 original size:46 final size:46
Alignment explanation
Indices: 53463457--53463735 Score: 175
Period size: 44 Copynumber: 6.2 Consensus size: 46
53463447 CAAAGAGCAA
* **
53463457 ATCGAAGACATAGCAGATCTGACATTCCTGTGCTTACAGCGAGGTAG
1 ATCGAAGACATAGCAGATCTGACATTCCTGTGCTTACAGGGA-ACAG
* *** * * * *
53463504 ATC-AA-AGATTTTA-A-CATGGCATCCCTGTGTTTATAGGGAACA-
1 ATCGAAGACATAGCAGATC-TGACATTCCTGTGCTTACAGGGAACAG
* * * * *
53463546 AGTTGAAG--ATAGCAGATTTGGCATCCCTGTGTTTACAGGGAACAG
1 A-TCGAAGACATAGCAGATCTGACATTCCTGTGCTTACAGGGAACAG
* * * *
53463591 ATTGAAGACATAGCAGATCTGATATTCTTGTGCTTACAGCGAAACAG
1 ATCGAAGACATAGCAGATCTGACATTCCTGTGCTTACAG-GGAACAG
** * * * *
53463638 ATCGAAGATTTTAGC--A--TGGCATCCCTGTGTTTATAGGGAACAG
1 ATCGAAGA-CATAGCAGATCTGACATTCCTGTGCTTACAGGGAACAG
*
53463681 ATCGAAGACATAGCAGATCTGACATTCCTGTGCTTACAGCGAAGCAG
1 ATCGAAGACATAGCAGATCTGACATTCCTGTGCTTACAGGGAA-CAG
*
53463728 ATTGAAGA
1 ATCGAAGA
53463736 TTTCAGCATG
Statistics
Matches: 174, Mismatches: 42, Indels: 32
0.70 0.17 0.13
Matches are distributed among these distances:
42 5 0.03
43 20 0.11
44 68 0.39
45 5 0.03
46 46 0.26
47 26 0.15
48 4 0.02
ACGTcount: A:0.32, C:0.18, G:0.24, T:0.27
Consensus pattern (46 bp):
ATCGAAGACATAGCAGATCTGACATTCCTGTGCTTACAGGGAACAG
Found at i:53463670 original size:90 final size:90
Alignment explanation
Indices: 53463564--53463778 Score: 351
Period size: 90 Copynumber: 2.4 Consensus size: 90
53463554 ATAGCAGATT
* * *
53463564 TGGCATCCCTGTGTTTACAGGGAACAGATTGAAGACATAGCAGATCTGATATTCTTGTGCTTACA
1 TGGCATCCCTGTGTTTATAGGGAACAGATTGAAGACATAGCAGATCTGACATTCCTGTGCTTACA
*
53463629 GCGAAACAGATCGAAGATTTTAGCA
66 GCGAAACAGATCGAAGATTTCAGCA
*
53463654 TGGCATCCCTGTGTTTATAGGGAACAGATCGAAGACATAGCAGATCTGACATTCCTGTGCTTACA
1 TGGCATCCCTGTGTTTATAGGGAACAGATTGAAGACATAGCAGATCTGACATTCCTGTGCTTACA
* *
53463719 GCGAAGCAGATTGAAGATTTCAGCA
66 GCGAAACAGATCGAAGATTTCAGCA
53463744 TGGCATCCCTGTGTTTATAGGGAACA-AGTTGAAGA
1 TGGCATCCCTGTGTTTATAGGGAACAGA-TTGAAGA
53463779 AGCAGGTTTG
Statistics
Matches: 116, Mismatches: 8, Indels: 2
0.92 0.06 0.02
Matches are distributed among these distances:
89 1 0.01
90 115 0.99
ACGTcount: A:0.30, C:0.18, G:0.25, T:0.27
Consensus pattern (90 bp):
TGGCATCCCTGTGTTTATAGGGAACAGATTGAAGACATAGCAGATCTGACATTCCTGTGCTTACA
GCGAAACAGATCGAAGATTTCAGCA
Found at i:53464250 original size:19 final size:19
Alignment explanation
Indices: 53464226--53464316 Score: 152
Period size: 19 Copynumber: 4.9 Consensus size: 19
53464216 ATAATCTTCA
53464226 ATGATATGCAATCTTAGAT
1 ATGATATGCAATCTTAGAT
53464245 ATGATATGCAATCTTAGAT
1 ATGATATGCAATCTTAGAT
53464264 ATGATA--CAATCTTAGAT
1 ATGATATGCAATCTTAGAT
53464281 ATGAT-TGCAATCTTAGAT
1 ATGATATGCAATCTTAGAT
*
53464299 ATGAAATGCAATCTTAGA
1 ATGATATGCAATCTTAGA
53464317 AGATATGATT
Statistics
Matches: 68, Mismatches: 1, Indels: 6
0.91 0.01 0.08
Matches are distributed among these distances:
17 16 0.24
18 15 0.22
19 37 0.54
ACGTcount: A:0.38, C:0.11, G:0.15, T:0.35
Consensus pattern (19 bp):
ATGATATGCAATCTTAGAT
Found at i:53464297 original size:35 final size:37
Alignment explanation
Indices: 53464234--53464323 Score: 134
Period size: 35 Copynumber: 2.5 Consensus size: 37
53464224 CAATGATATG
53464234 CAATCTTAGATATGATATGCAATCTTAGATATG-ATA
1 CAATCTTAGATATGATATGCAATCTTAGATATGAATA
*
53464270 CAATCTTAGATATGAT-TGCAATCTTAGATATGAAATG
1 CAATCTTAGATATGATATGCAATCTTAGATATG-AATA
53464307 CAATCTTAGA-A-GATATG
1 CAATCTTAGATATGATATG
53464324 ATTTTGTAAT
Statistics
Matches: 50, Mismatches: 1, Indels: 6
0.88 0.02 0.11
Matches are distributed among these distances:
35 19 0.38
36 19 0.38
37 12 0.24
ACGTcount: A:0.39, C:0.11, G:0.16, T:0.34
Consensus pattern (37 bp):
CAATCTTAGATATGATATGCAATCTTAGATATGAATA
Found at i:53466349 original size:8 final size:9
Alignment explanation
Indices: 53466311--53466351 Score: 50
Period size: 9 Copynumber: 4.6 Consensus size: 9
53466301 TTTTAAATTT
53466311 TTTTTGAAT-
1 TTTTT-AATA
53466320 TTTTTATATA
1 TTTTTA-ATA
53466330 TTTTTAATA
1 TTTTTAATA
53466339 TTTTTAA-A
1 TTTTTAATA
53466347 TTTTT
1 TTTTT
53466352 TGTTGATATA
Statistics
Matches: 30, Mismatches: 0, Indels: 5
0.86 0.00 0.14
Matches are distributed among these distances:
8 7 0.23
9 17 0.57
10 6 0.20
ACGTcount: A:0.27, C:0.00, G:0.02, T:0.71
Consensus pattern (9 bp):
TTTTTAATA
Found at i:53469086 original size:31 final size:33
Alignment explanation
Indices: 53469051--53469112 Score: 85
Period size: 31 Copynumber: 1.9 Consensus size: 33
53469041 GATTCATCCA
*
53469051 TGGAAA-ATAAAATTAAAA-AAA-ATGATAAAAT
1 TGGAAAGATAAAA-AAAAATAAAGATGATAAAAT
53469082 TGGAAAGATAAAAAAAAATAAAGATGATAAA
1 TGGAAAGATAAAAAAAAATAAAGATGATAAA
53469113 TAATAAAAAG
Statistics
Matches: 27, Mismatches: 1, Indels: 4
0.84 0.03 0.12
Matches are distributed among these distances:
31 10 0.37
32 9 0.33
33 8 0.30
ACGTcount: A:0.68, C:0.00, G:0.13, T:0.19
Consensus pattern (33 bp):
TGGAAAGATAAAAAAAAATAAAGATGATAAAAT
Found at i:53472677 original size:20 final size:20
Alignment explanation
Indices: 53472654--53472718 Score: 53
Period size: 21 Copynumber: 3.1 Consensus size: 20
53472644 ACTTAAGTTG
53472654 AAAAAATAATTTAATTAAAT
1 AAAAAATAATTTAATTAAAT
* *
53472674 AAAATAATATTTTGA-T-AAT
1 AAAA-AATAATTTAATTAAAT
53472693 AAAAAATTAATTATTAAGTTAAAT
1 AAAAAA-TAA-T-TTAA-TTAAAT
53472717 AA
1 AA
53472719 TTATATGAGT
Statistics
Matches: 34, Mismatches: 4, Indels: 10
0.71 0.08 0.21
Matches are distributed among these distances:
18 2 0.06
19 9 0.26
20 6 0.18
21 11 0.32
23 1 0.03
24 5 0.15
ACGTcount: A:0.60, C:0.00, G:0.03, T:0.37
Consensus pattern (20 bp):
AAAAAATAATTTAATTAAAT
Found at i:53474022 original size:25 final size:26
Alignment explanation
Indices: 53473990--53474044 Score: 103
Period size: 25 Copynumber: 2.2 Consensus size: 26
53473980 AAAGTTTATG
53473990 AAAATTTTAAAATTTCACCATGCAA-
1 AAAATTTTAAAATTTCACCATGCAAC
53474015 AAAATTTTAAAATTTCACCATGCAAC
1 AAAATTTTAAAATTTCACCATGCAAC
53474041 AAAA
1 AAAA
53474045 CTCATTTTTG
Statistics
Matches: 29, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
25 25 0.86
26 4 0.14
ACGTcount: A:0.51, C:0.16, G:0.04, T:0.29
Consensus pattern (26 bp):
AAAATTTTAAAATTTCACCATGCAAC
Found at i:53477719 original size:6 final size:6
Alignment explanation
Indices: 53477708--53477748 Score: 64
Period size: 6 Copynumber: 6.5 Consensus size: 6
53477698 ATAATTTAAT
53477708 AAATAA AAATAA AAATATA AAACTAA AAATAA AAATAA AAA
1 AAATAA AAATAA AAATA-A AAA-TAA AAATAA AAATAA AAA
53477749 ACATATAATT
Statistics
Matches: 33, Mismatches: 0, Indels: 4
0.89 0.00 0.11
Matches are distributed among these distances:
6 23 0.70
7 8 0.24
8 2 0.06
ACGTcount: A:0.80, C:0.02, G:0.00, T:0.17
Consensus pattern (6 bp):
AAATAA
Found at i:53477736 original size:20 final size:20
Alignment explanation
Indices: 53477711--53477750 Score: 71
Period size: 20 Copynumber: 2.0 Consensus size: 20
53477701 ATTTAATAAA
*
53477711 TAAAAATAAAAATATAAAAC
1 TAAAAATAAAAATAAAAAAC
53477731 TAAAAATAAAAATAAAAAAC
1 TAAAAATAAAAATAAAAAAC
53477751 ATATAATTTT
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
20 19 1.00
ACGTcount: A:0.78, C:0.05, G:0.00, T:0.17
Consensus pattern (20 bp):
TAAAAATAAAAATAAAAAAC
Found at i:53477782 original size:9 final size:9
Alignment explanation
Indices: 53477768--53477826 Score: 64
Period size: 9 Copynumber: 6.6 Consensus size: 9
53477758 TTTATACAAA
*
53477768 TAATTTGGT
1 TAATTCGGT
* *
53477777 TAATTTGGG
1 TAATTCGGT
*
53477786 TAATTCGGG
1 TAATTCGGT
53477795 TAATTCGGT
1 TAATTCGGT
*
53477804 TAATTCGAT
1 TAATTCGGT
*
53477813 TAATTCGAT
1 TAATTCGGT
53477822 TAATT
1 TAATT
53477827 TTATACTTAT
Statistics
Matches: 46, Mismatches: 4, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
9 46 1.00
ACGTcount: A:0.27, C:0.07, G:0.20, T:0.46
Consensus pattern (9 bp):
TAATTCGGT
Found at i:53486612 original size:6 final size:6
Alignment explanation
Indices: 53486596--53486639 Score: 61
Period size: 6 Copynumber: 7.3 Consensus size: 6
53486586 ACAATGTTGG
* * *
53486596 AAATGA TAATGA CAATGA CAATGA AAATGA AAATGA AAATGA AA
1 AAATGA AAATGA AAATGA AAATGA AAATGA AAATGA AAATGA AA
53486640 GGTGCAGTGA
Statistics
Matches: 35, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
6 35 1.00
ACGTcount: A:0.61, C:0.05, G:0.16, T:0.18
Consensus pattern (6 bp):
AAATGA
Found at i:53488384 original size:27 final size:27
Alignment explanation
Indices: 53488330--53488386 Score: 71
Period size: 27 Copynumber: 2.1 Consensus size: 27
53488320 GTTCTATAAT
* * *
53488330 AAGGTTAATATAGTAAATTATAAAATA
1 AAGGTTAATATAATAAAATAAAAAATA
53488357 AAGGTTAAT-TAATAAAATAAAAACATA
1 AAGGTTAATATAATAAAATAAAAA-ATA
53488384 AAG
1 AAG
53488387 ATGAGTTTCA
Statistics
Matches: 26, Mismatches: 3, Indels: 2
0.84 0.10 0.06
Matches are distributed among these distances:
26 11 0.42
27 15 0.58
ACGTcount: A:0.60, C:0.02, G:0.11, T:0.28
Consensus pattern (27 bp):
AAGGTTAATATAATAAAATAAAAAATA
Found at i:53497513 original size:44 final size:44
Alignment explanation
Indices: 53497465--53497655 Score: 238
Period size: 44 Copynumber: 4.3 Consensus size: 44
53497455 CGTTTTTTAG
* * *
53497465 AAAAAAATGCCGCCAAAGACCAGGACCTTTAGCGGCGCTTTTGT
1 AAAAAAACGCCGCTATAGACCAGGACCTTTAGCGGCGCTTTTGT
* *
53497509 AAAAAAACGCCGCTATAGACCAAGAACTTTAGCGGCGCTTTTGT
1 AAAAAAACGCCGCTATAGACCAGGACCTTTAGCGGCGCTTTTGT
* ** * * *
53497553 AAAAAAATGCCGCTATAGACTTGTACTTTTAGCGGCGCTTTTTT
1 AAAAAAACGCCGCTATAGACCAGGACCTTTAGCGGCGCTTTTGT
* * * *
53497597 AAAAAAACGCCGCTATAGACCTGTACTTTTAGCGGCGCTTTTTT
1 AAAAAAACGCCGCTATAGACCAGGACCTTTAGCGGCGCTTTTGT
*
53497641 GAAAAAACGCCGCTA
1 AAAAAAACGCCGCTA
53497656 ATTTGCCCAG
Statistics
Matches: 131, Mismatches: 16, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
44 131 1.00
ACGTcount: A:0.31, C:0.23, G:0.20, T:0.26
Consensus pattern (44 bp):
AAAAAAACGCCGCTATAGACCAGGACCTTTAGCGGCGCTTTTGT
Found at i:53499909 original size:14 final size:14
Alignment explanation
Indices: 53499890--53499919 Score: 60
Period size: 14 Copynumber: 2.1 Consensus size: 14
53499880 AAAAACTTGT
53499890 TTAATCGAGAGAAA
1 TTAATCGAGAGAAA
53499904 TTAATCGAGAGAAA
1 TTAATCGAGAGAAA
53499918 TT
1 TT
53499920 CACCATTGTA
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:0.47, C:0.07, G:0.20, T:0.27
Consensus pattern (14 bp):
TTAATCGAGAGAAA
Found at i:53501743 original size:21 final size:21
Alignment explanation
Indices: 53501719--53501758 Score: 71
Period size: 21 Copynumber: 1.9 Consensus size: 21
53501709 AAATTAATTC
*
53501719 ATACTTAAGTTGAATCAAATA
1 ATACTTAAGTTGAACCAAATA
53501740 ATACTTAAGTTGAACCAAA
1 ATACTTAAGTTGAACCAAA
53501759 ATATAAAAAC
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
21 18 1.00
ACGTcount: A:0.47, C:0.12, G:0.10, T:0.30
Consensus pattern (21 bp):
ATACTTAAGTTGAACCAAATA
Found at i:53504125 original size:133 final size:133
Alignment explanation
Indices: 53503824--53504342 Score: 975
Period size: 133 Copynumber: 3.9 Consensus size: 133
53503814 GAATTCAACA
*
53503824 ATATAAAACGTGAGCAACAAGACAGCAATAAACTCTTAAATCAATCTAAGTCCACACTAAACACA
1 ATATAAAACGTGAGCAACAAGACAACAATAAACTCTTAAATCAATCTAAGTCCACACTAAACACA
*
53503889 TAAGTTGGATAGAAACATGAAAAACAGACCAAAAGAACATCTAAATAACCAAAATACAACAATTT
66 TAAGTTGGATAGAAACATG-AAAACAGACCAAAAGAACATCTAAATAACCAAAATATAACAATTT
53503954 TATT
130 TATT
* *
53503958 ATATAATACGTGAGCAACAAGACAGCAATAAACTCTTAAATCAATCTAAGTCCACACTAAACACA
1 ATATAAAACGTGAGCAACAAGACAACAATAAACTCTTAAATCAATCTAAGTCCACACTAAACACA
53504023 TAAGTTGGATAGAAACATGAAAACAGACCAAAAGAACATCTAAATAACCAAAATATAACAATTTT
66 TAAGTTGGATAGAAACATGAAAACAGACCAAAAGAACATCTAAATAACCAAAATATAACAATTTT
53504088 ATT
131 ATT
53504091 ATATAAAACGTGAGCAACAAGACAACAATAAACTCTTAAATCAATCTAAGTCCACACTAAACACA
1 ATATAAAACGTGAGCAACAAGACAACAATAAACTCTTAAATCAATCTAAGTCCACACTAAACACA
53504156 TAAGTTGGATAGAAACATGAAAACAGACCAAAAGAACATCTAAATAACCAAAATATAACAATTTT
66 TAAGTTGGATAGAAACATGAAAACAGACCAAAAGAACATCTAAATAACCAAAATATAACAATTTT
53504221 ATT
131 ATT
* *
53504224 ATATAAAATGTGAGCAACAAGACAACAATAAACTATTAAATCAATCTAAGTCCACACTAAACACA
1 ATATAAAACGTGAGCAACAAGACAACAATAAACTCTTAAATCAATCTAAGTCCACACTAAACACA
53504289 TAAGTTGGATAGAAACATGAAAACAGACCAAAAGAACATCTAAATAACCAAAAT
66 TAAGTTGGATAGAAACATGAAAACAGACCAAAAGAACATCTAAATAACCAAAAT
53504343 GGAATCACCA
Statistics
Matches: 379, Mismatches: 6, Indels: 1
0.98 0.02 0.00
Matches are distributed among these distances:
133 296 0.78
134 83 0.22
ACGTcount: A:0.52, C:0.18, G:0.10, T:0.20
Consensus pattern (133 bp):
ATATAAAACGTGAGCAACAAGACAACAATAAACTCTTAAATCAATCTAAGTCCACACTAAACACA
TAAGTTGGATAGAAACATGAAAACAGACCAAAAGAACATCTAAATAACCAAAATATAACAATTTT
ATT
Found at i:53507109 original size:10 final size:11
Alignment explanation
Indices: 53507092--53507138 Score: 58
Period size: 12 Copynumber: 4.0 Consensus size: 11
53507082 CCACTTTTCA
53507092 TATATATATATT
1 TATATATAT-TT
53507104 TATATATATTT
1 TATATATATTT
*
53507115 TAAAATAATATTT
1 T-ATAT-ATATTT
53507128 TATATATATTT
1 TATATATATTT
53507139 ATCTTATATA
Statistics
Matches: 31, Mismatches: 2, Indels: 5
0.82 0.05 0.13
Matches are distributed among these distances:
11 9 0.29
12 15 0.48
13 7 0.23
ACGTcount: A:0.43, C:0.00, G:0.00, T:0.57
Consensus pattern (11 bp):
TATATATATTT
Found at i:53507147 original size:15 final size:15
Alignment explanation
Indices: 53507127--53507158 Score: 55
Period size: 15 Copynumber: 2.1 Consensus size: 15
53507117 AAATAATATT
*
53507127 TTATATATATTTATC
1 TTATATACATTTATC
53507142 TTATATACATTTATC
1 TTATATACATTTATC
53507157 TT
1 TT
53507159 CTAAATTAAA
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 16 1.00
ACGTcount: A:0.31, C:0.09, G:0.00, T:0.59
Consensus pattern (15 bp):
TTATATACATTTATC
Found at i:53508031 original size:14 final size:14
Alignment explanation
Indices: 53508012--53508045 Score: 52
Period size: 14 Copynumber: 2.4 Consensus size: 14
53508002 ATTAAACCTG
53508012 CTTAAACCATATAT-
1 CTTAAACCATA-ATC
53508026 CTTAAACCATAATC
1 CTTAAACCATAATC
53508040 CTTAAA
1 CTTAAA
53508046 ATATAATGAT
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
13 2 0.11
14 17 0.89
ACGTcount: A:0.44, C:0.24, G:0.00, T:0.32
Consensus pattern (14 bp):
CTTAAACCATAATC
Found at i:53508273 original size:41 final size:41
Alignment explanation
Indices: 53508210--53508347 Score: 143
Period size: 41 Copynumber: 3.4 Consensus size: 41
53508200 GTTATAGGGT
* ** *
53508210 TTTTAGCGGCATTTTACCTAAAGCGCCGCTAATGCTCTGGG
1 TTTTAGCGGCGTTTTAGATAAAGCGCCGCTAATGCTCTAGG
* * * *
53508251 TTTTAGCGGCGCTTTAGGTAAAGTGCCGCTAATGCTCTAGT
1 TTTTAGCGGCGTTTTAGATAAAGCGCCGCTAATGCTCTAGG
* * * *
53508292 TTTTAGCGGCGTTTTAGAAAAAAACGCCGCTAATGCTAT-GT
1 TTTTAGCGGCGTTTTAG-ATAAAGCGCCGCTAATGCTCTAGG
*
53508333 TTTTACCGGCGTTTT
1 TTTTAGCGGCGTTTT
53508348 TTTGGAACGC
Statistics
Matches: 82, Mismatches: 14, Indels: 2
0.84 0.14 0.02
Matches are distributed among these distances:
41 66 0.80
42 16 0.20
ACGTcount: A:0.21, C:0.20, G:0.24, T:0.35
Consensus pattern (41 bp):
TTTTAGCGGCGTTTTAGATAAAGCGCCGCTAATGCTCTAGG
Found at i:53513026 original size:17 final size:18
Alignment explanation
Indices: 53512996--53513029 Score: 61
Period size: 17 Copynumber: 1.9 Consensus size: 18
53512986 GATATGAGGA
53512996 AATTGAGAAATGATGATG
1 AATTGAGAAATGATGATG
53513014 AATTGAG-AATGATGAT
1 AATTGAGAAATGATGAT
53513030 ATGTGAATTG
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
17 9 0.56
18 7 0.44
ACGTcount: A:0.44, C:0.00, G:0.26, T:0.29
Consensus pattern (18 bp):
AATTGAGAAATGATGATG
Found at i:53514639 original size:27 final size:27
Alignment explanation
Indices: 53514601--53514654 Score: 108
Period size: 27 Copynumber: 2.0 Consensus size: 27
53514591 GGGAAGGTAG
53514601 AACCTTTGTTGAATTGTAGATATTTAT
1 AACCTTTGTTGAATTGTAGATATTTAT
53514628 AACCTTTGTTGAATTGTAGATATTTAT
1 AACCTTTGTTGAATTGTAGATATTTAT
53514655 CTCAAATAGA
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
27 27 1.00
ACGTcount: A:0.30, C:0.07, G:0.15, T:0.48
Consensus pattern (27 bp):
AACCTTTGTTGAATTGTAGATATTTAT
Found at i:53515102 original size:6 final size:6
Alignment explanation
Indices: 53515084--53515137 Score: 63
Period size: 6 Copynumber: 8.8 Consensus size: 6
53515074 GCAAATGGAT
* * * *
53515084 CATTTCC CATTTT CATTTT CATTTT CATTTC CGTTTC CATTTC CATTTC
1 CATTT-C CATTTC CATTTC CATTTC CATTTC CATTTC CATTTC CATTTC
53515133 CATTT
1 CATTT
53515138 TTGAGAAACA
Statistics
Matches: 43, Mismatches: 4, Indels: 1
0.90 0.08 0.02
Matches are distributed among these distances:
6 38 0.88
7 5 0.12
ACGTcount: A:0.15, C:0.28, G:0.02, T:0.56
Consensus pattern (6 bp):
CATTTC
Found at i:53517845 original size:20 final size:22
Alignment explanation
Indices: 53517806--53517856 Score: 65
Period size: 20 Copynumber: 2.5 Consensus size: 22
53517796 GAAAGTAATG
53517806 AAAATT-TATTTTCTTAGAA-T
1 AAAATTCTATTTTCTTAGAATT
53517826 -AAATTCTATTTTC-TAGGAATT
1 AAAATTCTATTTTCTTA-GAATT
53517847 AAAATTCTAT
1 AAAATTCTAT
53517857 CGGTTTCTAT
Statistics
Matches: 27, Mismatches: 0, Indels: 6
0.82 0.00 0.18
Matches are distributed among these distances:
19 7 0.26
20 10 0.37
21 1 0.04
22 9 0.33
ACGTcount: A:0.39, C:0.08, G:0.06, T:0.47
Consensus pattern (22 bp):
AAAATTCTATTTTCTTAGAATT
Found at i:53519835 original size:18 final size:19
Alignment explanation
Indices: 53519807--53519851 Score: 58
Period size: 18 Copynumber: 2.4 Consensus size: 19
53519797 TGAATTTGTG
53519807 TAAAAAAATAA-ATA-AAA
1 TAAAAAAATAACATAGAAA
*
53519824 TATAAAATATAACATAGAAA
1 TA-AAAAAATAACATAGAAA
53519844 TAAAAAAA
1 TAAAAAAA
53519852 AGGTAATGGA
Statistics
Matches: 23, Mismatches: 2, Indels: 4
0.79 0.07 0.14
Matches are distributed among these distances:
17 2 0.09
18 8 0.35
19 8 0.35
20 5 0.22
ACGTcount: A:0.76, C:0.02, G:0.02, T:0.20
Consensus pattern (19 bp):
TAAAAAAATAACATAGAAA
Found at i:53523480 original size:12 final size:12
Alignment explanation
Indices: 53523463--53523499 Score: 58
Period size: 12 Copynumber: 3.1 Consensus size: 12
53523453 AGACAAACAA
53523463 ATAAAATAATAT
1 ATAAAATAATAT
53523475 ATAAAATAATA-
1 ATAAAATAATAT
53523486 ATAATAATAATAT
1 ATAA-AATAATAT
53523499 A
1 A
53523500 GTAACATATG
Statistics
Matches: 23, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
11 4 0.17
12 18 0.78
13 1 0.04
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.32
Consensus pattern (12 bp):
ATAAAATAATAT
Found at i:53523906 original size:21 final size:21
Alignment explanation
Indices: 53523882--53523926 Score: 56
Period size: 21 Copynumber: 2.1 Consensus size: 21
53523872 ATAATGTATA
53523882 ATATAA-ATAAATATATAAGAT
1 ATATAAGATAAA-ATATAAGAT
* *
53523903 ATATAAGTTAAAATATAATAT
1 ATATAAGATAAAATATAAGAT
53523924 ATA
1 ATA
53523927 ATAATAATTT
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
21 17 0.81
22 4 0.19
ACGTcount: A:0.60, C:0.00, G:0.04, T:0.36
Consensus pattern (21 bp):
ATATAAGATAAAATATAAGAT
Found at i:53523972 original size:12 final size:12
Alignment explanation
Indices: 53523950--53523983 Score: 61
Period size: 12 Copynumber: 2.9 Consensus size: 12
53523940 ACTTTTGAAA
53523950 ATATA-AATAAT
1 ATATATAATAAT
53523961 ATATATAATAAT
1 ATATATAATAAT
53523973 ATATATAATAA
1 ATATATAATAA
53523984 ATTAAAAATA
Statistics
Matches: 22, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
11 5 0.23
12 17 0.77
ACGTcount: A:0.62, C:0.00, G:0.00, T:0.38
Consensus pattern (12 bp):
ATATATAATAAT
Found at i:53524338 original size:17 final size:18
Alignment explanation
Indices: 53524285--53524445 Score: 202
Period size: 17 Copynumber: 8.9 Consensus size: 18
53524275 AATCATATCT
*
53524285 TCTAAGATTGTATATCATA
1 TCTAAGATTG-CTATCATA
*
53524304 TCTAAGATTGCAATCATA
1 TCTAAGATTGCTATCATA
*
53524322 CCTAAGATTG-TATCATA
1 TCTAAGATTGCTATCATA
*
53524339 TCTAAGATTGCAATCATA
1 TCTAAGATTGCTATCATA
*
53524357 TTTAAGATTG-TATCATA
1 TCTAAGATTGCTATCATA
*
53524374 TCTAAGATTGCAATCATA
1 TCTAAGATTGCTATCATA
*
53524392 TCTATGATTG-TATCATA
1 TCTAAGATTGCTATCATA
*
53524409 TCTAAGATTGCATATCACA
1 TCTAAGATTGC-TATCATA
53524428 TCTAAGATTGCATATCAT
1 TCTAAGATTGC-TATCAT
53524446 TGAAGATTAT
Statistics
Matches: 123, Mismatches: 15, Indels: 8
0.84 0.10 0.05
Matches are distributed among these distances:
17 45 0.37
18 45 0.37
19 33 0.27
ACGTcount: A:0.36, C:0.15, G:0.11, T:0.38
Consensus pattern (18 bp):
TCTAAGATTGCTATCATA
Found at i:53524343 original size:35 final size:35
Alignment explanation
Indices: 53524285--53524437 Score: 243
Period size: 35 Copynumber: 4.3 Consensus size: 35
53524275 AATCATATCT
53524285 TCTAAGATTGTATATCATATCTAAGATTGCAATCATA
1 TCTAAGATTG--TATCATATCTAAGATTGCAATCATA
*
53524322 CCTAAGATTGTATCATATCTAAGATTGCAATCATA
1 TCTAAGATTGTATCATATCTAAGATTGCAATCATA
*
53524357 TTTAAGATTGTATCATATCTAAGATTGCAATCATA
1 TCTAAGATTGTATCATATCTAAGATTGCAATCATA
* *
53524392 TCTATGATTGTATCATATCTAAGATTGCATATCACA
1 TCTAAGATTGTATCATATCTAAGATTGCA-ATCATA
53524428 TCTAAGATTG
1 TCTAAGATTG
53524438 CATATCATTG
Statistics
Matches: 108, Mismatches: 7, Indels: 3
0.92 0.06 0.03
Matches are distributed among these distances:
35 85 0.79
36 14 0.13
37 9 0.08
ACGTcount: A:0.36, C:0.14, G:0.12, T:0.38
Consensus pattern (35 bp):
TCTAAGATTGTATCATATCTAAGATTGCAATCATA
Found at i:53525811 original size:33 final size:33
Alignment explanation
Indices: 53525774--53525840 Score: 134
Period size: 33 Copynumber: 2.0 Consensus size: 33
53525764 TTAAATTGGT
53525774 AAACATCTATGTTTTGGTTGTGAATTGATAGAC
1 AAACATCTATGTTTTGGTTGTGAATTGATAGAC
53525807 AAACATCTATGTTTTGGTTGTGAATTGATAGAC
1 AAACATCTATGTTTTGGTTGTGAATTGATAGAC
53525840 A
1 A
53525841 CATAATTTTG
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
33 34 1.00
ACGTcount: A:0.31, C:0.09, G:0.21, T:0.39
Consensus pattern (33 bp):
AAACATCTATGTTTTGGTTGTGAATTGATAGAC
Found at i:53537002 original size:41 final size:41
Alignment explanation
Indices: 53536957--53537038 Score: 164
Period size: 41 Copynumber: 2.0 Consensus size: 41
53536947 CAATAAAGAA
53536957 AAAAAATTGAAGGCCTCAGTTTCAAAATGGCTTCAATGAGG
1 AAAAAATTGAAGGCCTCAGTTTCAAAATGGCTTCAATGAGG
53536998 AAAAAATTGAAGGCCTCAGTTTCAAAATGGCTTCAATGAGG
1 AAAAAATTGAAGGCCTCAGTTTCAAAATGGCTTCAATGAGG
53537039 CTCCTTGCAA
Statistics
Matches: 41, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
41 41 1.00
ACGTcount: A:0.39, C:0.15, G:0.22, T:0.24
Consensus pattern (41 bp):
AAAAAATTGAAGGCCTCAGTTTCAAAATGGCTTCAATGAGG
Found at i:53539217 original size:21 final size:22
Alignment explanation
Indices: 53539193--53539235 Score: 63
Period size: 21 Copynumber: 2.0 Consensus size: 22
53539183 TTTATTTTTA
53539193 AAAATATT-TAAATATT-AATAT
1 AAAATATTAT-AATATTCAATAT
53539214 AAAATATTATAATATTCAATAT
1 AAAATATTATAATATTCAATAT
53539236 TATTAAAAAA
Statistics
Matches: 20, Mismatches: 0, Indels: 3
0.87 0.00 0.13
Matches are distributed among these distances:
21 14 0.70
22 6 0.30
ACGTcount: A:0.56, C:0.02, G:0.00, T:0.42
Consensus pattern (22 bp):
AAAATATTATAATATTCAATAT
Found at i:53542453 original size:36 final size:37
Alignment explanation
Indices: 53542375--53542456 Score: 96
Period size: 36 Copynumber: 2.3 Consensus size: 37
53542365 ATATTCCAAC
**
53542375 CAAAACACA-TCAGATGCTCATAAAATCTAATCCATT
1 CAAAACACACTCAGATGCTCATAAAAGATAATCCATT
** * *
53542411 TGAAACACACT-AGATGCTCATAACAGATAATTCATT
1 CAAAACACACTCAGATGCTCATAAAAGATAATCCATT
53542447 CAAAACACAC
1 CAAAACACAC
53542457 CAATAGCTCA
Statistics
Matches: 37, Mismatches: 8, Indels: 2
0.79 0.17 0.04
Matches are distributed among these distances:
36 36 0.97
37 1 0.03
ACGTcount: A:0.45, C:0.24, G:0.07, T:0.23
Consensus pattern (37 bp):
CAAAACACACTCAGATGCTCATAAAAGATAATCCATT
Found at i:53547422 original size:6 final size:6
Alignment explanation
Indices: 53547411--53547438 Score: 56
Period size: 6 Copynumber: 4.7 Consensus size: 6
53547401 GTGAGTAGTT
53547411 TTTTAA TTTTAA TTTTAA TTTTAA TTTT
1 TTTTAA TTTTAA TTTTAA TTTTAA TTTT
53547439 TGTTAGTTCT
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 22 1.00
ACGTcount: A:0.29, C:0.00, G:0.00, T:0.71
Consensus pattern (6 bp):
TTTTAA
Found at i:53551850 original size:21 final size:22
Alignment explanation
Indices: 53551826--53551868 Score: 63
Period size: 21 Copynumber: 2.0 Consensus size: 22
53551816 TTTATTTTTA
53551826 AAAATATT-TAAATATT-AATAT
1 AAAATATTAT-AATATTCAATAT
53551847 AAAATATTATAATATTCAATAT
1 AAAATATTATAATATTCAATAT
53551869 TATTAAAAAA
Statistics
Matches: 20, Mismatches: 0, Indels: 3
0.87 0.00 0.13
Matches are distributed among these distances:
21 14 0.70
22 6 0.30
ACGTcount: A:0.56, C:0.02, G:0.00, T:0.42
Consensus pattern (22 bp):
AAAATATTATAATATTCAATAT
Found at i:53551861 original size:15 final size:16
Alignment explanation
Indices: 53551838--53551884 Score: 55
Period size: 15 Copynumber: 3.1 Consensus size: 16
53551828 AATATTTAAA
53551838 TATTAATATAAAATAT
1 TATTAATATAAAATAT
**
53551854 TA-TAATATTCAATAT
1 TATTAATATAAAATAT
53551869 TATTAA-A-AAAATAT
1 TATTAATATAAAATAT
53551883 TA
1 TA
53551885 GTTATTTACA
Statistics
Matches: 26, Mismatches: 4, Indels: 4
0.76 0.12 0.12
Matches are distributed among these distances:
14 7 0.27
15 14 0.54
16 5 0.19
ACGTcount: A:0.55, C:0.02, G:0.00, T:0.43
Consensus pattern (16 bp):
TATTAATATAAAATAT
Found at i:53554515 original size:23 final size:23
Alignment explanation
Indices: 53554485--53554564 Score: 96
Period size: 23 Copynumber: 3.7 Consensus size: 23
53554475 AAACACAACA
53554485 TTGCATTAACACATCATTCATAT
1 TTGCATTAACACATCATTCATAT
* *
53554508 TTGCATTAA-A-A-CA-TCTTAC
1 TTGCATTAACACATCATTCATAT
*
53554527 CTGCATTAACACATCATTCATAT
1 TTGCATTAACACATCATTCATAT
*
53554550 TTGCATTAAAACATC
1 TTGCATTAACACATC
53554565 TTACCTCATT
Statistics
Matches: 46, Mismatches: 7, Indels: 8
0.75 0.11 0.13
Matches are distributed among these distances:
19 12 0.26
20 3 0.07
21 2 0.04
22 3 0.07
23 26 0.57
ACGTcount: A:0.36, C:0.23, G:0.05, T:0.36
Consensus pattern (23 bp):
TTGCATTAACACATCATTCATAT
Found at i:53554532 original size:42 final size:42
Alignment explanation
Indices: 53554486--53554574 Score: 171
Period size: 42 Copynumber: 2.1 Consensus size: 42
53554476 AACACAACAT
53554486 TGCATTAACACATCATTCATATTTGCATTAAAACATCTTACC
1 TGCATTAACACATCATTCATATTTGCATTAAAACATCTTACC
53554528 TGCATTAACACATCATTCATATTTGCATTAAAACATCTTACC
1 TGCATTAACACATCATTCATATTTGCATTAAAACATCTTACC
53554570 T-CATT
1 TGCATT
53554575 CTTATATATG
Statistics
Matches: 47, Mismatches: 0, Indels: 1
0.98 0.00 0.02
Matches are distributed among these distances:
41 4 0.09
42 43 0.91
ACGTcount: A:0.35, C:0.24, G:0.04, T:0.37
Consensus pattern (42 bp):
TGCATTAACACATCATTCATATTTGCATTAAAACATCTTACC
Found at i:53554533 original size:19 final size:19
Alignment explanation
Indices: 53554509--53554574 Score: 62
Period size: 19 Copynumber: 3.3 Consensus size: 19
53554499 CATTCATATT
53554509 TGCATTAAAACATCTTACC
1 TGCATTAAAACATCTTACC
* **
53554528 TGCATTAACACATCATTCATATT
1 TGCATTAA-A-A-CA-TCTTACC
53554551 TGCATTAAAACATCTTACC
1 TGCATTAAAACATCTTACC
53554570 T-CATT
1 TGCATT
53554575 CTTATATATG
Statistics
Matches: 37, Mismatches: 6, Indels: 9
0.71 0.12 0.17
Matches are distributed among these distances:
18 4 0.11
19 13 0.35
20 3 0.08
21 2 0.05
22 3 0.08
23 12 0.32
ACGTcount: A:0.35, C:0.24, G:0.05, T:0.36
Consensus pattern (19 bp):
TGCATTAAAACATCTTACC
Found at i:53555092 original size:36 final size:36
Alignment explanation
Indices: 53555036--53555156 Score: 122
Period size: 36 Copynumber: 3.4 Consensus size: 36
53555026 TATTCCAACC
*
53555036 AAAACACATCAAATGCTCATAAGAGCTAATCCATCT
1 AAAACACACCAAATGCTCATAAGAGCTAATCCATCT
* *
53555072 AAAACACACCAGATGTTCATAAGAGCTAATCCATCCT
1 AAAACACACCAAATGCTCATAAGAGCTAATCCAT-CT
* ** *
53555109 -AAGCACACC-AATGGCTCCGAAGAGCTAGTCCAAT-T
1 AAAACACACCAAAT-GCTCATAAGAGCTAATCC-ATCT
*
53555144 GAAACACACCAAA
1 AAAACACACCAAA
53555157 AGAAGGAGTA
Statistics
Matches: 70, Mismatches: 10, Indels: 9
0.79 0.11 0.10
Matches are distributed among these distances:
35 3 0.04
36 61 0.87
37 6 0.09
ACGTcount: A:0.42, C:0.27, G:0.12, T:0.18
Consensus pattern (36 bp):
AAAACACACCAAATGCTCATAAGAGCTAATCCATCT
Found at i:53558988 original size:24 final size:24
Alignment explanation
Indices: 53558956--53559014 Score: 82
Period size: 24 Copynumber: 2.5 Consensus size: 24
53558946 ATGTACGCTT
* * *
53558956 ACACGAGCTGTTATTAAAATGCTC
1 ACACGAGCTATAATCAAAATGCTC
*
53558980 ACACGAGCTATAATCATAATGCTC
1 ACACGAGCTATAATCAAAATGCTC
53559004 ACACGAGCTAT
1 ACACGAGCTAT
53559015 GAAAATGGGC
Statistics
Matches: 31, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
24 31 1.00
ACGTcount: A:0.36, C:0.24, G:0.15, T:0.25
Consensus pattern (24 bp):
ACACGAGCTATAATCAAAATGCTC
Found at i:53561027 original size:26 final size:27
Alignment explanation
Indices: 53560991--53561045 Score: 94
Period size: 27 Copynumber: 2.1 Consensus size: 27
53560981 CATATAAACA
*
53560991 TTTCATATAAT-AGTTCATATAATTAT
1 TTTCATATAATCAATTCATATAATTAT
53561017 TTTCATATAATCAATTCATATAATTAT
1 TTTCATATAATCAATTCATATAATTAT
53561044 TT
1 TT
53561046 CATTTCTCTA
Statistics
Matches: 27, Mismatches: 1, Indels: 1
0.93 0.03 0.03
Matches are distributed among these distances:
26 11 0.41
27 16 0.59
ACGTcount: A:0.38, C:0.09, G:0.02, T:0.51
Consensus pattern (27 bp):
TTTCATATAATCAATTCATATAATTAT
Found at i:53561040 original size:13 final size:13
Alignment explanation
Indices: 53560981--53561048 Score: 75
Period size: 13 Copynumber: 5.2 Consensus size: 13
53560971 CATATCTATC
*
53560981 CATATAAACATTT
1 CATATAATCATTT
*
53560994 CATATAAT-AGTT
1 CATATAATCATTT
*
53561006 CATATAATTATTTT
1 CATATAATCA-TTT
*
53561020 CATATAATCAATT
1 CATATAATCATTT
*
53561033 CATATAATTATTT
1 CATATAATCATTT
53561046 CAT
1 CAT
53561049 TTCTCTATTT
Statistics
Matches: 46, Mismatches: 7, Indels: 4
0.81 0.12 0.07
Matches are distributed among these distances:
12 11 0.24
13 24 0.52
14 11 0.24
ACGTcount: A:0.41, C:0.12, G:0.01, T:0.46
Consensus pattern (13 bp):
CATATAATCATTT
Found at i:53564272 original size:13 final size:13
Alignment explanation
Indices: 53564238--53564281 Score: 54
Period size: 13 Copynumber: 3.3 Consensus size: 13
53564228 GGCTTAGCAT
53564238 TCTGTATATCTGT-
1 TCTGT-TATCTGTA
*
53564251 TCTGCTTATTTGTA
1 TCTG-TTATCTGTA
53564265 TCTGTTATCTGTA
1 TCTGTTATCTGTA
53564278 TCTG
1 TCTG
53564282 AAATTATGAC
Statistics
Matches: 27, Mismatches: 2, Indels: 4
0.82 0.06 0.12
Matches are distributed among these distances:
13 22 0.81
14 5 0.19
ACGTcount: A:0.14, C:0.16, G:0.16, T:0.55
Consensus pattern (13 bp):
TCTGTTATCTGTA
Found at i:53566592 original size:38 final size:38
Alignment explanation
Indices: 53566550--53566678 Score: 197
Period size: 38 Copynumber: 3.4 Consensus size: 38
53566540 ACAGGCTATA
*
53566550 TGCTGAAATTATATCCGGGTTAAATCCCGCAGGCTTCG
1 TGCTGGAATTATATCCGGGTTAAATCCCGCAGGCTTCG
53566588 TGCTGGTAA-TATATCCGGGTTAAATCCCGCAGGCTTCG
1 TGCTGG-AATTATATCCGGGTTAAATCCCGCAGGCTTCG
* * *
53566626 TGCTGGTATTATATCCGGGTTAAATCCCGCAGGCCTAG
1 TGCTGGAATTATATCCGGGTTAAATCCCGCAGGCTTCG
*
53566664 TGCTGGTATTATATC
1 TGCTGGAATTATATC
53566679 TGAGCTTAAA
Statistics
Matches: 85, Mismatches: 4, Indels: 4
0.91 0.04 0.04
Matches are distributed among these distances:
37 1 0.01
38 82 0.96
39 2 0.02
ACGTcount: A:0.22, C:0.22, G:0.25, T:0.31
Consensus pattern (38 bp):
TGCTGGAATTATATCCGGGTTAAATCCCGCAGGCTTCG
Found at i:53568488 original size:94 final size:94
Alignment explanation
Indices: 53568327--53568522 Score: 322
Period size: 94 Copynumber: 2.1 Consensus size: 94
53568317 GTAAAGTTAC
* *
53568327 CAGTCTAGCTAAACTTTTAAAATGACAACGAATTACCAGTTCAAGCTAAATCTGTATCACATGTA
1 CAGTCTAGCTAAACTTTTAAAATGACAACAAATTACCAGTTCAAGCTAAATCCGTATCACATGTA
*
53568392 TATCTGAGTCCACAACAAATGCT-GAAGCT
66 TATCTGAATCCACAACAAATGCTAG-AGCT
* * *
53568421 CAGTCTAGCTAAACTTTTAAAATGACAACAAATTACCAGTTCAGGCTAAATCCGTGTCACGTGTA
1 CAGTCTAGCTAAACTTTTAAAATGACAACAAATTACCAGTTCAAGCTAAATCCGTATCACATGTA
53568486 TATCTGAATCCACAACAAATGCTAGAGCT
66 TATCTGAATCCACAACAAATGCTAGAGCT
53568515 CAGTCTAG
1 CAGTCTAG
53568523 AATGGGAATC
Statistics
Matches: 95, Mismatches: 6, Indels: 2
0.92 0.06 0.02
Matches are distributed among these distances:
94 94 0.99
95 1 0.01
ACGTcount: A:0.36, C:0.22, G:0.15, T:0.27
Consensus pattern (94 bp):
CAGTCTAGCTAAACTTTTAAAATGACAACAAATTACCAGTTCAAGCTAAATCCGTATCACATGTA
TATCTGAATCCACAACAAATGCTAGAGCT
Found at i:53570702 original size:21 final size:22
Alignment explanation
Indices: 53570678--53570718 Score: 57
Period size: 21 Copynumber: 1.9 Consensus size: 22
53570668 AACAAGAGTC
*
53570678 AAATTTAATTA-AATTTTTTTT
1 AAATCTAATTATAATTTTTTTT
*
53570699 AAATCTAATTATTATTTTTT
1 AAATCTAATTATAATTTTTT
53570719 AATAAAAAAT
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
21 10 0.59
22 7 0.41
ACGTcount: A:0.37, C:0.02, G:0.00, T:0.61
Consensus pattern (22 bp):
AAATCTAATTATAATTTTTTTT
Found at i:53578134 original size:55 final size:55
Alignment explanation
Indices: 53578069--53578178 Score: 202
Period size: 55 Copynumber: 2.0 Consensus size: 55
53578059 GAGTTCACCA
53578069 ACACCCTTTTACAATAAACCTATAGAAATTTATTTGAGTGGACCTTTATAAATAT
1 ACACCCTTTTACAATAAACCTATAGAAATTTATTTGAGTGGACCTTTATAAATAT
* *
53578124 ACACCCTTTTACAATAATCCTATAGCAATTTATTTGAGTGGACCTTTATAAATAT
1 ACACCCTTTTACAATAAACCTATAGAAATTTATTTGAGTGGACCTTTATAAATAT
53578179 GTAATCCAAG
Statistics
Matches: 53, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
55 53 1.00
ACGTcount: A:0.36, C:0.17, G:0.09, T:0.37
Consensus pattern (55 bp):
ACACCCTTTTACAATAAACCTATAGAAATTTATTTGAGTGGACCTTTATAAATAT
Found at i:53584179 original size:14 final size:14
Alignment explanation
Indices: 53584160--53584187 Score: 56
Period size: 14 Copynumber: 2.0 Consensus size: 14
53584150 TATACCTCTA
53584160 TTTAATTGCTTAAC
1 TTTAATTGCTTAAC
53584174 TTTAATTGCTTAAC
1 TTTAATTGCTTAAC
53584188 CATTAATATA
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:0.29, C:0.14, G:0.07, T:0.50
Consensus pattern (14 bp):
TTTAATTGCTTAAC
Found at i:53586568 original size:31 final size:31
Alignment explanation
Indices: 53586533--53586593 Score: 86
Period size: 31 Copynumber: 2.0 Consensus size: 31
53586523 TTTTATTTGG
53586533 TCATTAAACTATTCAAAAGTTTTCATTTAAT
1 TCATTAAACTATTCAAAAGTTTTCATTTAAT
* ** *
53586564 TCATTGAACTATTTGAAAGTTTTTATTTAA
1 TCATTAAACTATTCAAAAGTTTTCATTTAA
53586594 GCCAGGACTA
Statistics
Matches: 26, Mismatches: 4, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
31 26 1.00
ACGTcount: A:0.36, C:0.10, G:0.07, T:0.48
Consensus pattern (31 bp):
TCATTAAACTATTCAAAAGTTTTCATTTAAT
Found at i:53587750 original size:24 final size:24
Alignment explanation
Indices: 53587712--53587764 Score: 63
Period size: 24 Copynumber: 2.2 Consensus size: 24
53587702 ATTTCTAGAT
* *
53587712 ATTTTT-AAACTTTTAGAAAGCTCA
1 ATTTTTAAAAATTTAAGAAA-CTCA
*
53587736 ATTTTTAAAAATTTAAGAAACTTA
1 ATTTTTAAAAATTTAAGAAACTCA
53587760 ATTTT
1 ATTTT
53587765 GAAAGATTAT
Statistics
Matches: 25, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
24 14 0.56
25 11 0.44
ACGTcount: A:0.42, C:0.08, G:0.06, T:0.45
Consensus pattern (24 bp):
ATTTTTAAAAATTTAAGAAACTCA
Found at i:53589887 original size:6 final size:7
Alignment explanation
Indices: 53589867--53589891 Score: 50
Period size: 7 Copynumber: 3.6 Consensus size: 7
53589857 TAAAATCACA
53589867 TTATTTT
1 TTATTTT
53589874 TTATTTT
1 TTATTTT
53589881 TTATTTT
1 TTATTTT
53589888 TTAT
1 TTAT
53589892 ATAATATTAT
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:0.16, C:0.00, G:0.00, T:0.84
Consensus pattern (7 bp):
TTATTTT
Found at i:53589899 original size:14 final size:14
Alignment explanation
Indices: 53589868--53589919 Score: 50
Period size: 14 Copynumber: 3.5 Consensus size: 14
53589858 AAAATCACAT
**
53589868 TATTTTTTATTTTT
1 TATTTTTTATTTAA
*
53589882 TATTTTTTATATAA
1 TATTTTTTATTTAA
53589896 TATTATTTTTAGTTTAA
1 TA-T-TTTTTA-TTTAA
53589913 TATTTTT
1 TATTTTT
53589920 ATTAAAGTTA
Statistics
Matches: 31, Mismatches: 4, Indels: 5
0.77 0.10 0.12
Matches are distributed among these distances:
14 13 0.42
15 5 0.16
16 7 0.23
17 6 0.19
ACGTcount: A:0.25, C:0.00, G:0.02, T:0.73
Consensus pattern (14 bp):
TATTTTTTATTTAA
Found at i:53590972 original size:22 final size:23
Alignment explanation
Indices: 53590944--53590992 Score: 64
Period size: 23 Copynumber: 2.2 Consensus size: 23
53590934 AATATAAATT
*
53590944 AAAATAAAT-TGAATAAAACATA
1 AAAATAAATCTGAAAAAAACATA
* *
53590966 AAAATAAATCTTAAAAAAATATA
1 AAAATAAATCTGAAAAAAACATA
53590989 AAAA
1 AAAA
53590993 GTTTAAACAT
Statistics
Matches: 23, Mismatches: 3, Indels: 1
0.85 0.11 0.04
Matches are distributed among these distances:
22 9 0.39
23 14 0.61
ACGTcount: A:0.71, C:0.04, G:0.02, T:0.22
Consensus pattern (23 bp):
AAAATAAATCTGAAAAAAACATA
Found at i:53597696 original size:3 final size:3
Alignment explanation
Indices: 53597688--53597729 Score: 84
Period size: 3 Copynumber: 14.0 Consensus size: 3
53597678 TTCTTGATCC
53597688 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT
53597730 CTACCTTTCC
Statistics
Matches: 39, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 39 1.00
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (3 bp):
ATT
Found at i:53600869 original size:21 final size:21
Alignment explanation
Indices: 53600845--53600884 Score: 71
Period size: 21 Copynumber: 1.9 Consensus size: 21
53600835 GATTATATTT
*
53600845 ATATATTTTAAATATTATAAA
1 ATATATTTAAAATATTATAAA
53600866 ATATATTTAAAATATTATA
1 ATATATTTAAAATATTATA
53600885 GATCTGTGGA
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
21 18 1.00
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (21 bp):
ATATATTTAAAATATTATAAA
Found at i:53605080 original size:20 final size:20
Alignment explanation
Indices: 53605015--53605082 Score: 59
Period size: 20 Copynumber: 3.4 Consensus size: 20
53605005 CCACATTTAC
*
53605015 TAAATTTTATTTTTTATTTGT
1 TAAATTTT-CTTTTTATTTGT
* * *
53605036 TTAATTTCCTTTTTCTTT-T
1 TAAATTTTCTTTTTATTTGT
53605055 TAAATTTTCTTTATT-TTTGT
1 TAAATTTTCTTT-TTATTTGT
*
53605075 TGAATTTT
1 TAAATTTT
53605083 TTTCACCACA
Statistics
Matches: 38, Mismatches: 7, Indels: 5
0.76 0.14 0.10
Matches are distributed among these distances:
19 14 0.37
20 18 0.47
21 6 0.16
ACGTcount: A:0.19, C:0.06, G:0.04, T:0.71
Consensus pattern (20 bp):
TAAATTTTCTTTTTATTTGT
Done.