Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: A04
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: 82679320
ACGTcount: A:0.31, C:0.17, G:0.17, T:0.31
Warning! 4050000 characters in sequence are not A, C, G, or T
File 163 of 255
Found at i:53444145 original size:19 final size:19
Alignment explanation
Indices: 53444121--53444159 Score: 69
Period size: 19 Copynumber: 2.1 Consensus size: 19
53444111 TATAAATAAT
*
53444121 AATGATGTTAGAAATATAC
1 AATGATATTAGAAATATAC
53444140 AATGATATTAGAAATATAC
1 AATGATATTAGAAATATAC
53444159 A
1 A
53444160 TAAAATAGTA
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
19 19 1.00
ACGTcount: A:0.51, C:0.05, G:0.13, T:0.31
Consensus pattern (19 bp):
AATGATATTAGAAATATAC
Found at i:53444401 original size:19 final size:19
Alignment explanation
Indices: 53444365--53444403 Score: 53
Period size: 19 Copynumber: 2.1 Consensus size: 19
53444355 ATATACATAA
*
53444365 ATATATTAAAAACATATAC
1 ATATATTAAAAAAATATAC
53444384 ATATA-TAAAAAAATTATAC
1 ATATATTAAAAAAA-TATAC
53444403 A
1 A
53444404 CTAATATATA
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
18 7 0.39
19 11 0.61
ACGTcount: A:0.62, C:0.08, G:0.00, T:0.31
Consensus pattern (19 bp):
ATATATTAAAAAAATATAC
Found at i:53444559 original size:3 final size:3
Alignment explanation
Indices: 53444553--53444690 Score: 86
Period size: 3 Copynumber: 46.0 Consensus size: 3
53444543 CATACTGATG
*
53444553 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATAA ATA A-A TTA ATA A-A
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA AT-A ATA ATA ATA ATA ATA
* * * * * * * * *
53444597 AGGA ATA AAA ACA ATG TTA ATA ACA AGA ATA TTA ATA ATA GTA ATA
1 A-TA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA
* * * *
53444643 ATA AT- CTAA ATA ATA ATA TTA ATA ATA CTA GA-A ATG ATA ATA ATA
1 ATA ATA AT-A ATA ATA ATA ATA ATA ATA ATA -ATA ATA ATA ATA ATA
53444688 ATA
1 ATA
53444691 TTTAATAAAG
Statistics
Matches: 102, Mismatches: 25, Indels: 16
0.71 0.17 0.11
Matches are distributed among these distances:
2 5 0.05
3 91 0.89
4 6 0.06
ACGTcount: A:0.62, C:0.03, G:0.05, T:0.30
Consensus pattern (3 bp):
ATA
Found at i:53444702 original size:27 final size:29
Alignment explanation
Indices: 53444650--53444712 Score: 76
Period size: 27 Copynumber: 2.2 Consensus size: 29
53444640 ATAATAATCT
* *
53444650 AAATAATAATATTAATAATACTAGAAATGA
1 AAATAATAATATT-ATAATACAAGAAACGA
*
53444680 TAATAATAATATT-TAATA-AAGAAACGA
1 AAATAATAATATTATAATACAAGAAACGA
53444707 AAATAA
1 AAATAA
53444713 AAAAAAGGAC
Statistics
Matches: 29, Mismatches: 4, Indels: 3
0.81 0.11 0.08
Matches are distributed among these distances:
27 12 0.41
28 5 0.17
30 12 0.41
ACGTcount: A:0.62, C:0.03, G:0.06, T:0.29
Consensus pattern (29 bp):
AAATAATAATATTATAATACAAGAAACGA
Found at i:53445806 original size:34 final size:35
Alignment explanation
Indices: 53445751--53445819 Score: 122
Period size: 34 Copynumber: 2.0 Consensus size: 35
53445741 AATTGTAAAT
*
53445751 GGGTCATAGGGCAAAATTGGGCTATAATATACTTC
1 GGGTCATAGGGCAAAATTGGGCTATAACATACTTC
53445786 GGGTCATAGGG-AAAATTGGGCTATAACATACTTC
1 GGGTCATAGGGCAAAATTGGGCTATAACATACTTC
53445820 TCACTAAGGA
Statistics
Matches: 33, Mismatches: 1, Indels: 1
0.94 0.03 0.03
Matches are distributed among these distances:
34 22 0.67
35 11 0.33
ACGTcount: A:0.32, C:0.14, G:0.26, T:0.28
Consensus pattern (35 bp):
GGGTCATAGGGCAAAATTGGGCTATAACATACTTC
Found at i:53457879 original size:5 final size:5
Alignment explanation
Indices: 53457869--53457924 Score: 60
Period size: 5 Copynumber: 11.2 Consensus size: 5
53457859 TATTTATATT
* * * *
53457869 AATAA AATAA AATAA AATAA AATAAA AATAT ATTAA ATTAA ATTAA AAT-A
1 AATAA AATAA AATAA AATAA AAT-AA AATAA AATAA AATAA AATAA AATAA
53457919 AATAA A
1 AATAA A
53457925 CACGTAAATA
Statistics
Matches: 45, Mismatches: 4, Indels: 4
0.85 0.08 0.08
Matches are distributed among these distances:
4 4 0.09
5 36 0.80
6 5 0.11
ACGTcount: A:0.73, C:0.00, G:0.00, T:0.27
Consensus pattern (5 bp):
AATAA
Found at i:53458838 original size:10 final size:10
Alignment explanation
Indices: 53458823--53458847 Score: 50
Period size: 10 Copynumber: 2.5 Consensus size: 10
53458813 TATCAAATTA
53458823 CAAACACACC
1 CAAACACACC
53458833 CAAACACACC
1 CAAACACACC
53458843 CAAAC
1 CAAAC
53458848 CTCACAATCT
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 15 1.00
ACGTcount: A:0.52, C:0.48, G:0.00, T:0.00
Consensus pattern (10 bp):
CAAACACACC
Found at i:53459320 original size:23 final size:23
Alignment explanation
Indices: 53459292--53459337 Score: 92
Period size: 23 Copynumber: 2.0 Consensus size: 23
53459282 GAAGGTTAAA
53459292 ATTGGTTGAATCTCTAAAAAATT
1 ATTGGTTGAATCTCTAAAAAATT
53459315 ATTGGTTGAATCTCTAAAAAATT
1 ATTGGTTGAATCTCTAAAAAATT
53459338 TTGTTAAAAT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
23 23 1.00
ACGTcount: A:0.39, C:0.09, G:0.13, T:0.39
Consensus pattern (23 bp):
ATTGGTTGAATCTCTAAAAAATT
Found at i:53463702 original size:47 final size:46
Alignment explanation
Indices: 53463648--53463767 Score: 141
Period size: 47 Copynumber: 2.5 Consensus size: 46
53463638 GATTTTATGA
*
53463648 GATGAATGTGAATGTGTATATATGTGATAAGGCCGAATGGCCAATGT
1 GATGAATGTGAA-GTGTATATATGTGATAAGGCAGAATGGCCAATGT
* * * * *
53463695 GATGAATGTGAACATGCATATGTGTGATAAGGTAGAATGGCTAATGT
1 GATGAATGTGAA-GTGTATATATGTGATAAGGCAGAATGGCCAATGT
* *
53463742 GATAAACGTGGAAGTGTATATATGTG
1 GATGAATGT-GAAGTGTATATATGTG
53463768 GCGAAGCCAA
Statistics
Matches: 60, Mismatches: 12, Indels: 2
0.81 0.16 0.03
Matches are distributed among these distances:
47 57 0.95
48 3 0.05
ACGTcount: A:0.33, C:0.07, G:0.30, T:0.30
Consensus pattern (46 bp):
GATGAATGTGAAGTGTATATATGTGATAAGGCAGAATGGCCAATGT
Found at i:53478406 original size:38 final size:39
Alignment explanation
Indices: 53478364--53478458 Score: 102
Period size: 39 Copynumber: 2.5 Consensus size: 39
53478354 ATTCACTTTT
* * **
53478364 AAGCATATATCACATTACACATAT-ATTACATAATGTTC
1 AAGCATATATCACAATACACATATAATCACATAACATTC
* ** * *
53478402 AAGCACATATTGCAATACTCATATAATCGCATAACATTC
1 AAGCATATATCACAATACACATATAATCACATAACATTC
53478441 AAGCATATATCACAATAC
1 AAGCATATATCACAATAC
53478459 TCAAAAACAT
Statistics
Matches: 44, Mismatches: 12, Indels: 1
0.77 0.21 0.02
Matches are distributed among these distances:
38 19 0.43
39 25 0.57
ACGTcount: A:0.43, C:0.21, G:0.06, T:0.29
Consensus pattern (39 bp):
AAGCATATATCACAATACACATATAATCACATAACATTC
Found at i:53480931 original size:40 final size:40
Alignment explanation
Indices: 53480883--53481150 Score: 455
Period size: 40 Copynumber: 6.7 Consensus size: 40
53480873 GCAAACACAT
* *
53480883 TTGCCTTCGGGTCTTAACCCGGATATATCAACTTGCATAA
1 TTGCCTTCGGGTCTTAGCCCGGATATATCAACTCGCATAA
*
53480923 TTGCCTTCGGGTCTTAGCCCGGATATATCATCTCGCATAA
1 TTGCCTTCGGGTCTTAGCCCGGATATATCAACTCGCATAA
* * *
53480963 TTGCCTTCGGGTCATAGCCCGGACATATTAACTCGCATAA
1 TTGCCTTCGGGTCTTAGCCCGGATATATCAACTCGCATAA
53481003 TTGCCTTCGGGTCTTAGCCCGGATATATCAACTCGCATAA
1 TTGCCTTCGGGTCTTAGCCCGGATATATCAACTCGCATAA
* *
53481043 TTGCCTTCGGGTCTTAGCCCAGATATATTAACTCGCATAA
1 TTGCCTTCGGGTCTTAGCCCGGATATATCAACTCGCATAA
*
53481083 TTGCCTTCGGGTCTTAGCCCGGATATATCATCTCGCATAA
1 TTGCCTTCGGGTCTTAGCCCGGATATATCAACTCGCATAA
53481123 TTGCCTTCGGGTCTTAGCCCGGATATAT
1 TTGCCTTCGGGTCTTAGCCCGGATATAT
53481151 TCCAATGCTC
Statistics
Matches: 213, Mismatches: 15, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
40 213 1.00
ACGTcount: A:0.22, C:0.26, G:0.20, T:0.32
Consensus pattern (40 bp):
TTGCCTTCGGGTCTTAGCCCGGATATATCAACTCGCATAA
Found at i:53494962 original size:42 final size:42
Alignment explanation
Indices: 53494901--53495027 Score: 161
Period size: 42 Copynumber: 3.0 Consensus size: 42
53494891 CTTCGTTTTC
** *
53494901 TCGATGCCATAGTTCAACTATGGTCTTACACATCTTCACATAA
1 TCGATGCCATAGCCCAACTATGGTCTTACACATATTCACAT-A
*
53494944 T-GATGCCATAGCCCAACTATGGTCTTACACATATTCATATA
1 TCGATGCCATAGCCCAACTATGGTCTTACACATATTCACATA
* *
53494985 TCGATGCCATAGCCTAGCTATGGTCTTACACGA-A-TCACATA
1 TCGATGCCATAGCCCAACTATGGTCTTACAC-ATATTCACATA
53495026 TC
1 TC
53495028 TCACTGATGC
Statistics
Matches: 75, Mismatches: 7, Indels: 6
0.85 0.08 0.07
Matches are distributed among these distances:
41 10 0.13
42 63 0.84
43 2 0.03
ACGTcount: A:0.30, C:0.26, G:0.13, T:0.31
Consensus pattern (42 bp):
TCGATGCCATAGCCCAACTATGGTCTTACACATATTCACATA
Found at i:53495087 original size:47 final size:46
Alignment explanation
Indices: 53494986--53495109 Score: 158
Period size: 47 Copynumber: 2.7 Consensus size: 46
53494976 ATTCATATAT
* * * * * *
53494986 CGATGCCATAGCCTAGCTATGGTCTTACACGAATCACATATCTCAC
1 CGATGCCATATCCCAGATATGGTCTTATACGAAGCACATATCACAC
* * *
53495032 TGATGCCATATCCCAGATATGGTCTTATACAGTAGCATATATCACAC
1 CGATGCCATATCCCAGATATGGTCTTATAC-GAAGCACATATCACAC
53495079 CGATGCCATATCCCAGATATGGTCTTATACG
1 CGATGCCATATCCCAGATATGGTCTTATACG
53495110 GAAATCACTT
Statistics
Matches: 67, Mismatches: 10, Indels: 2
0.85 0.13 0.03
Matches are distributed among these distances:
46 26 0.39
47 41 0.61
ACGTcount: A:0.29, C:0.27, G:0.16, T:0.28
Consensus pattern (46 bp):
CGATGCCATATCCCAGATATGGTCTTATACGAAGCACATATCACAC
Found at i:53495169 original size:31 final size:31
Alignment explanation
Indices: 53495134--53495251 Score: 161
Period size: 31 Copynumber: 3.8 Consensus size: 31
53495124 CTTGCCACTT
*
53495134 GTAGCCGAAGCTACCACTATTCACTGATCAG
1 GTAGCCGAAGCTACCACTTTTCACTGATCAG
53495165 GTAGCC-AGAGCTACCA-TTTGTCACTGATCAG
1 GTAGCCGA-AGCTACCACTTT-TCACTGATCAG
* *
53495196 GTAGCCGGAGCTACCACTTTTCACTGGTCAG
1 GTAGCCGAAGCTACCACTTTTCACTGATCAG
53495227 GTAGCCGGAA-CTACCACTTTTCACT
1 GTAGCC-GAAGCTACCACTTTTCACT
53495252 TGTCATTTGT
Statistics
Matches: 78, Mismatches: 4, Indels: 10
0.85 0.04 0.11
Matches are distributed among these distances:
30 3 0.04
31 70 0.90
32 5 0.06
ACGTcount: A:0.25, C:0.29, G:0.21, T:0.25
Consensus pattern (31 bp):
GTAGCCGAAGCTACCACTTTTCACTGATCAG
Found at i:53495331 original size:50 final size:51
Alignment explanation
Indices: 53495227--53495355 Score: 192
Period size: 50 Copynumber: 2.5 Consensus size: 51
53495217 CACTGGTCAG
* *
53495227 GTAGCCGGAA-CTACCACTTTTCACTTGTCATTTGTCATTGATCAGATAAGT
1 GTAGCC-GAAGCTATCACTTATCACTTGTCATTTGTCATTGATCAGATAAGT
*
53495278 GTAGCCGAAGCTATCACTTATCACTT-TCACTTT-TCCTTGATCAGATAAGT
1 GTAGCCGAAGCTATCACTTATCACTTGTCA-TTTGTCATTGATCAGATAAGT
53495328 GTAGCCGAAGCTATCACTTATCACTTGT
1 GTAGCCGAAGCTATCACTTATCACTTGT
53495356 TGCCATGCTC
Statistics
Matches: 72, Mismatches: 3, Indels: 6
0.89 0.04 0.07
Matches are distributed among these distances:
50 48 0.67
51 24 0.33
ACGTcount: A:0.26, C:0.23, G:0.16, T:0.35
Consensus pattern (51 bp):
GTAGCCGAAGCTATCACTTATCACTTGTCATTTGTCATTGATCAGATAAGT
Found at i:53499656 original size:42 final size:42
Alignment explanation
Indices: 53499607--53499716 Score: 154
Period size: 42 Copynumber: 2.6 Consensus size: 42
53499597 CATAGTTCAA
*
53499607 CTATGGTCTTACACATCTTCACATAAT-GATGCCATAGCCCAG
1 CTATGGTCTTACACATATTCACAT-ATCGATGCCATAGCCCAG
* *
53499649 CTATGGTCTTACACATATTCATATATCGATGCCATAGCCTAG
1 CTATGGTCTTACACATATTCACATATCGATGCCATAGCCCAG
53499691 CTATGGTCTTACACGA-A-TCACATATC
1 CTATGGTCTTACAC-ATATTCACATATC
53499717 TCACTGATGC
Statistics
Matches: 62, Mismatches: 4, Indels: 5
0.87 0.06 0.07
Matches are distributed among these distances:
41 10 0.16
42 51 0.82
43 1 0.02
ACGTcount: A:0.29, C:0.26, G:0.14, T:0.31
Consensus pattern (42 bp):
CTATGGTCTTACACATATTCACATATCGATGCCATAGCCCAG
Found at i:53499776 original size:47 final size:46
Alignment explanation
Indices: 53499675--53499798 Score: 158
Period size: 47 Copynumber: 2.7 Consensus size: 46
53499665 ATTCATATAT
* * * * * *
53499675 CGATGCCATAGCCTAGCTATGGTCTTACACGAATCACATATCTCAC
1 CGATGCCATATCCCAGATATGGTCTTATACGAAGCACATATCACAC
* * *
53499721 TGATGCCATATCCCAGATATGGTCTTATACAGTAGCATATATCACAC
1 CGATGCCATATCCCAGATATGGTCTTATAC-GAAGCACATATCACAC
53499768 CGATGCCATATCCCAGATATGGTCTTATACG
1 CGATGCCATATCCCAGATATGGTCTTATACG
53499799 GAAATCACTT
Statistics
Matches: 67, Mismatches: 10, Indels: 2
0.85 0.13 0.03
Matches are distributed among these distances:
46 26 0.39
47 41 0.61
ACGTcount: A:0.29, C:0.27, G:0.16, T:0.28
Consensus pattern (46 bp):
CGATGCCATATCCCAGATATGGTCTTATACGAAGCACATATCACAC
Found at i:53499867 original size:31 final size:31
Alignment explanation
Indices: 53499827--53499940 Score: 149
Period size: 31 Copynumber: 3.7 Consensus size: 31
53499817 TCACTTGTAA
* *
53499827 CCGACGCTACCACTATTCACTGATCAGGTAG
1 CCGAAGCTACCACTTTTCACTGATCAGGTAG
* *
53499858 CCGAAGCTACCATTTTTCATTGATCAGGTAG
1 CCGAAGCTACCACTTTTCACTGATCAGGTAG
* *
53499889 CCGGAGCTACCACTTTTCACTGATCAGGTAA
1 CCGAAGCTACCACTTTTCACTGATCAGGTAG
*
53499920 CCGGAA-CTACGACTTTTCACT
1 CC-GAAGCTACCACTTTTCACT
53499941 TGTCATTTGT
Statistics
Matches: 72, Mismatches: 10, Indels: 2
0.86 0.12 0.02
Matches are distributed among these distances:
31 70 0.97
32 2 0.03
ACGTcount: A:0.25, C:0.29, G:0.18, T:0.27
Consensus pattern (31 bp):
CCGAAGCTACCACTTTTCACTGATCAGGTAG
Found at i:53500012 original size:50 final size:51
Alignment explanation
Indices: 53499931--53500044 Score: 187
Period size: 50 Copynumber: 2.3 Consensus size: 51
53499921 CGGAACTACG
53499931 ACTTTTCACTTGTCATTTGTCATTGATCAGATAAGTGTAGCCGAAGCTATC
1 ACTTTTCACTTGTCATTTGTCATTGATCAGATAAGTGTAGCCGAAGCTATC
* *
53499982 ACTTATCACTT-TCACTTT-TCCTTGATCAGATAAGTGTAGCCGAAGCTATC
1 ACTTTTCACTTGTCA-TTTGTCATTGATCAGATAAGTGTAGCCGAAGCTATC
53500032 ACTTTTCACTTGT
1 ACTTTTCACTTGT
53500045 TTCCATGGTC
Statistics
Matches: 58, Mismatches: 3, Indels: 4
0.89 0.05 0.06
Matches are distributed among these distances:
50 44 0.76
51 14 0.24
ACGTcount: A:0.25, C:0.22, G:0.15, T:0.39
Consensus pattern (51 bp):
ACTTTTCACTTGTCATTTGTCATTGATCAGATAAGTGTAGCCGAAGCTATC
Found at i:53505291 original size:57 final size:58
Alignment explanation
Indices: 53505228--53505352 Score: 234
Period size: 58 Copynumber: 2.2 Consensus size: 58
53505218 TACCTCCACG
53505228 ATTAACCCTTTGTAAACCCCTTTGAGCCT-ACAAGTCATTCCTTGTATTACCCTCAAT
1 ATTAACCCTTTGTAAACCCCTTTGAGCCTAACAAGTCATTCCTTGTATTACCCTCAAT
*
53505285 ATTAACCCTTTGTATACCCCTTTGAGCCTAACAAGTCATTCCTTGTATTACCCTCAAT
1 ATTAACCCTTTGTAAACCCCTTTGAGCCTAACAAGTCATTCCTTGTATTACCCTCAAT
53505343 ATTAACCCTT
1 ATTAACCCTT
53505353 AACCCATTAT
Statistics
Matches: 66, Mismatches: 1, Indels: 1
0.97 0.01 0.01
Matches are distributed among these distances:
57 28 0.42
58 38 0.58
ACGTcount: A:0.26, C:0.30, G:0.08, T:0.36
Consensus pattern (58 bp):
ATTAACCCTTTGTAAACCCCTTTGAGCCTAACAAGTCATTCCTTGTATTACCCTCAAT
Found at i:53512168 original size:7 final size:6
Alignment explanation
Indices: 53512121--53512167 Score: 58
Period size: 6 Copynumber: 7.5 Consensus size: 6
53512111 ATAATTTAAT
* *
53512121 AAATAA AAATAA AAATCTAA AACTAA AACTAA AAATAA AAATAA AAA
1 AAATAA AAATAA AAA--TAA AAATAA AAATAA AAATAA AAATAA AAA
53512168 ACATATAATT
Statistics
Matches: 37, Mismatches: 2, Indels: 4
0.86 0.05 0.09
Matches are distributed among these distances:
6 32 0.86
8 5 0.14
ACGTcount: A:0.77, C:0.06, G:0.00, T:0.17
Consensus pattern (6 bp):
AAATAA
Found at i:53512201 original size:9 final size:9
Alignment explanation
Indices: 53512187--53512272 Score: 118
Period size: 9 Copynumber: 9.6 Consensus size: 9
53512177 TTTATACAAA
53512187 TAATTCGGT
1 TAATTCGGT
53512196 TAATTCGGT
1 TAATTCGGT
* *
53512205 TAATTTGGG
1 TAATTCGGT
*
53512214 TAATTCGGA
1 TAATTCGGT
*
53512223 TAATTCAGT
1 TAATTCGGT
53512232 TAATTCGGT
1 TAATTCGGT
*
53512241 TAATTCGAT
1 TAATTCGGT
*
53512250 TAACTCGGT
1 TAATTCGGT
53512259 TAATTCGGT
1 TAATTCGGT
53512268 TAATT
1 TAATT
53512273 TTATACTTAT
Statistics
Matches: 66, Mismatches: 11, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
9 66 1.00
ACGTcount: A:0.27, C:0.10, G:0.20, T:0.43
Consensus pattern (9 bp):
TAATTCGGT
Found at i:53533143 original size:20 final size:19
Alignment explanation
Indices: 53533104--53533148 Score: 54
Period size: 20 Copynumber: 2.3 Consensus size: 19
53533094 AACTCTTTTT
* **
53533104 TCTTTCTAATTTGAGGAGC
1 TCTTTCTAACTTGAAAAGC
53533123 TCGTTTCTAACTTGAAAAGC
1 TC-TTTCTAACTTGAAAAGC
53533143 TCTTTC
1 TCTTTC
53533149 GGCGTGCCCT
Statistics
Matches: 22, Mismatches: 3, Indels: 2
0.81 0.11 0.07
Matches are distributed among these distances:
19 6 0.27
20 16 0.73
ACGTcount: A:0.22, C:0.20, G:0.16, T:0.42
Consensus pattern (19 bp):
TCTTTCTAACTTGAAAAGC
Found at i:53542674 original size:13 final size:14
Alignment explanation
Indices: 53542656--53542687 Score: 50
Period size: 12 Copynumber: 2.4 Consensus size: 14
53542646 TGTTTTATAG
53542656 ATTTTTTAAAA-TT
1 ATTTTTTAAAAGTT
53542669 A-TTTTTAAAAGTT
1 ATTTTTTAAAAGTT
53542682 ATTTTT
1 ATTTTT
53542688 AATAAAACAA
Statistics
Matches: 17, Mismatches: 0, Indels: 3
0.85 0.00 0.15
Matches are distributed among these distances:
12 9 0.53
13 4 0.24
14 4 0.24
ACGTcount: A:0.34, C:0.00, G:0.03, T:0.62
Consensus pattern (14 bp):
ATTTTTTAAAAGTT
Found at i:53542675 original size:12 final size:13
Alignment explanation
Indices: 53542658--53542689 Score: 57
Period size: 13 Copynumber: 2.5 Consensus size: 13
53542648 TTTTATAGAT
53542658 TTTTTAAAA-TTA
1 TTTTTAAAAGTTA
53542670 TTTTTAAAAGTTA
1 TTTTTAAAAGTTA
53542683 TTTTTAA
1 TTTTTAA
53542690 TAAAACAAAT
Statistics
Matches: 19, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
12 9 0.47
13 10 0.53
ACGTcount: A:0.38, C:0.00, G:0.03, T:0.59
Consensus pattern (13 bp):
TTTTTAAAAGTTA
Found at i:53542862 original size:12 final size:12
Alignment explanation
Indices: 53542845--53542869 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
53542835 ATCTTATATT
53542845 ATATATATATAC
1 ATATATATATAC
53542857 ATATATATATAC
1 ATATATATATAC
53542869 A
1 A
53542870 CACACGAGGG
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:0.52, C:0.08, G:0.00, T:0.40
Consensus pattern (12 bp):
ATATATATATAC
Found at i:53544384 original size:22 final size:22
Alignment explanation
Indices: 53544359--53544402 Score: 79
Period size: 22 Copynumber: 2.0 Consensus size: 22
53544349 CATATGGATC
*
53544359 ACTCAAAAGCTTTATGAATGCA
1 ACTCAAAAACTTTATGAATGCA
53544381 ACTCAAAAACTTTATGAATGCA
1 ACTCAAAAACTTTATGAATGCA
53544403 TTTATATTTG
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
22 21 1.00
ACGTcount: A:0.43, C:0.18, G:0.11, T:0.27
Consensus pattern (22 bp):
ACTCAAAAACTTTATGAATGCA
Found at i:53544984 original size:13 final size:12
Alignment explanation
Indices: 53544965--53544998 Score: 50
Period size: 13 Copynumber: 2.8 Consensus size: 12
53544955 AAATTTTTTG
53544965 TTTTCTTTTCCC
1 TTTTCTTTTCCC
*
53544977 TATTTCTTCTCCC
1 T-TTTCTTTTCCC
53544990 TTTTCTTTT
1 TTTTCTTTT
53544999 TCATCTTCTT
Statistics
Matches: 19, Mismatches: 2, Indels: 2
0.83 0.09 0.09
Matches are distributed among these distances:
12 8 0.42
13 11 0.58
ACGTcount: A:0.03, C:0.29, G:0.00, T:0.68
Consensus pattern (12 bp):
TTTTCTTTTCCC
Found at i:53547512 original size:46 final size:46
Alignment explanation
Indices: 53547462--53547637 Score: 205
Period size: 46 Copynumber: 3.8 Consensus size: 46
53547452 TGGTTGAGCA
*
53547462 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAATG
1 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCAAATG
* * * * *
53547508 TCCGAACTCGTTGAGTTGAGTCCGAGTTC-GTGA--AATGTAACTAGG
1 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCAA--ATG
* *
53547553 CATCCGAGCTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCAAACG
1 --TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCAAATG
* *
53547601 TCCGAGCTCGTTGAGTTGAATCCGAGTTCACTTATGG
1 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGG
53547638 GCGGGTTACA
Statistics
Matches: 110, Mismatches: 13, Indels: 14
0.80 0.09 0.10
Matches are distributed among these distances:
43 4 0.04
45 4 0.04
46 65 0.59
47 28 0.25
48 4 0.04
50 5 0.05
ACGTcount: A:0.22, C:0.20, G:0.28, T:0.30
Consensus pattern (46 bp):
TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCAAATG
Found at i:53547618 original size:93 final size:93
Alignment explanation
Indices: 53547459--53547629 Score: 297
Period size: 93 Copynumber: 1.8 Consensus size: 93
53547449 GGATGGTTGA
* *
53547459 GCATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAATGTCCGAACTCGTTGAGT
1 GCATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCAAACGTCCGAACTCGTTGAGT
*
53547524 TGAGTCCGAGTTCGTGAAATGTAACTAG
66 TGAATCCGAGTTCGTGAAATGTAACTAG
* *
53547552 GCATCCGAGCTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCAAACGTCCGAGCTCGTTGAGT
1 GCATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCAAACGTCCGAACTCGTTGAGT
53547617 TGAATCCGAGTTC
66 TGAATCCGAGTTC
53547630 ACTTATGGGC
Statistics
Matches: 73, Mismatches: 5, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
93 73 1.00
ACGTcount: A:0.22, C:0.21, G:0.28, T:0.29
Consensus pattern (93 bp):
GCATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCAAACGTCCGAACTCGTTGAGT
TGAATCCGAGTTCGTGAAATGTAACTAG
Found at i:53550330 original size:18 final size:18
Alignment explanation
Indices: 53550309--53550343 Score: 61
Period size: 18 Copynumber: 1.9 Consensus size: 18
53550299 CATATACATG
53550309 TGCGAACCTATATGTATT
1 TGCGAACCTATATGTATT
*
53550327 TGCGAGCCTATATGTAT
1 TGCGAACCTATATGTAT
53550344 GTGCAAACTC
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
18 16 1.00
ACGTcount: A:0.26, C:0.17, G:0.20, T:0.37
Consensus pattern (18 bp):
TGCGAACCTATATGTATT
Found at i:53550548 original size:18 final size:18
Alignment explanation
Indices: 53550525--53550586 Score: 79
Period size: 18 Copynumber: 3.4 Consensus size: 18
53550515 GTCTTATGCA
* *
53550525 AACCTAGATGCATGTGCG
1 AACCTATATGCATGTGTG
*
53550543 AACCTATATGCTATATGTG
1 AACCTATATGC-ATGTGTG
*
53550562 AACCTATATGTATGTGTG
1 AACCTATATGCATGTGTG
53550580 AACCTAT
1 AACCTAT
53550587 TTGAAGTATG
Statistics
Matches: 38, Mismatches: 5, Indels: 2
0.84 0.11 0.04
Matches are distributed among these distances:
18 23 0.61
19 15 0.39
ACGTcount: A:0.31, C:0.18, G:0.19, T:0.32
Consensus pattern (18 bp):
AACCTATATGCATGTGTG
Found at i:53553255 original size:29 final size:29
Alignment explanation
Indices: 53553213--53553269 Score: 71
Period size: 29 Copynumber: 2.0 Consensus size: 29
53553203 TATCCGCTTC
*
53553213 TCCCAAATTAGTA-CTTATGGTTTTTTTTG
1 TCCCAAATTAGTACCTTA-GCTTTTTTTTG
* *
53553242 TCCCAGATTGGTACCTTAGCTTTTTTTT
1 TCCCAAATTAGTACCTTAGCTTTTTTTT
53553270 TCCGTCAACT
Statistics
Matches: 24, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
29 20 0.83
30 4 0.17
ACGTcount: A:0.18, C:0.18, G:0.14, T:0.51
Consensus pattern (29 bp):
TCCCAAATTAGTACCTTAGCTTTTTTTTG
Found at i:53564943 original size:9 final size:9
Alignment explanation
Indices: 53564931--53564963 Score: 57
Period size: 9 Copynumber: 3.7 Consensus size: 9
53564921 GAATTATTCG
53564931 AATCGAGTT
1 AATCGAGTT
53564940 AATCGAGTT
1 AATCGAGTT
*
53564949 AATCGAATT
1 AATCGAGTT
53564958 AATCGA
1 AATCGA
53564964 ATCAACTCGA
Statistics
Matches: 23, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
9 23 1.00
ACGTcount: A:0.39, C:0.12, G:0.18, T:0.30
Consensus pattern (9 bp):
AATCGAGTT
Found at i:53564964 original size:9 final size:9
Alignment explanation
Indices: 53564931--53564976 Score: 56
Period size: 9 Copynumber: 5.0 Consensus size: 9
53564921 GAATTATTCG
*
53564931 AATCGAGTT
1 AATCGAATT
*
53564940 AATCGAGTT
1 AATCGAATT
53564949 AATCGAATT
1 AATCGAATT
*
53564958 AATCGAATC
1 AATCGAATT
53564967 AACTCGAATT
1 AA-TCGAATT
53564977 TTTTTTCGAA
Statistics
Matches: 33, Mismatches: 3, Indels: 1
0.89 0.08 0.03
Matches are distributed among these distances:
9 27 0.82
10 6 0.18
ACGTcount: A:0.39, C:0.15, G:0.15, T:0.30
Consensus pattern (9 bp):
AATCGAATT
Found at i:53567082 original size:30 final size:30
Alignment explanation
Indices: 53567048--53567114 Score: 125
Period size: 30 Copynumber: 2.2 Consensus size: 30
53567038 CTATCTATTT
*
53567048 TTAATTTATGCTATTGTACTATTATATTAA
1 TTAATTTATGCTATTATACTATTATATTAA
53567078 TTAATTTATGCTATTATACTATTATATTAA
1 TTAATTTATGCTATTATACTATTATATTAA
53567108 TTAATTT
1 TTAATTT
53567115 TTAATTTAAC
Statistics
Matches: 36, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
30 36 1.00
ACGTcount: A:0.34, C:0.06, G:0.04, T:0.55
Consensus pattern (30 bp):
TTAATTTATGCTATTATACTATTATATTAA
Found at i:53571737 original size:6 final size:7
Alignment explanation
Indices: 53571720--53571744 Score: 50
Period size: 7 Copynumber: 3.6 Consensus size: 7
53571710 AGGGCTGTGT
53571720 TTTTTTC
1 TTTTTTC
53571727 TTTTTTC
1 TTTTTTC
53571734 TTTTTTC
1 TTTTTTC
53571741 TTTT
1 TTTT
53571745 CCCACATAAT
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:0.00, C:0.12, G:0.00, T:0.88
Consensus pattern (7 bp):
TTTTTTC
Found at i:53575666 original size:25 final size:25
Alignment explanation
Indices: 53575637--53575684 Score: 96
Period size: 25 Copynumber: 1.9 Consensus size: 25
53575627 ACAAGGTCAG
53575637 AATGATTTCGGGTTCCCCTATTCAA
1 AATGATTTCGGGTTCCCCTATTCAA
53575662 AATGATTTCGGGTTCCCCTATTC
1 AATGATTTCGGGTTCCCCTATTC
53575685 TGACTTTGTA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
25 23 1.00
ACGTcount: A:0.21, C:0.25, G:0.17, T:0.38
Consensus pattern (25 bp):
AATGATTTCGGGTTCCCCTATTCAA
Found at i:53576547 original size:50 final size:50
Alignment explanation
Indices: 53576464--53576640 Score: 273
Period size: 50 Copynumber: 3.5 Consensus size: 50
53576454 CCATGGCAAC
*
53576464 AAGTGATAAGTGATAGCTTCGGCTACTCTTATCTGATCAAGGACAAATGA
1 AAGTGATAAGTGATAGCTTCGGCTACACTTATCTGATCAAGGACAAATGA
* * * *
53576514 AAGTGATAAGTAATAGCTTCGACTACACATATCTGATCAAGGACAAGTGA
1 AAGTGATAAGTGATAGCTTCGGCTACACTTATCTGATCAAGGACAAATGA
*
53576564 AAGTGATAAGTGATAGCTTCGGCTACACTTATCTGATCAAGTACAAATGA
1 AAGTGATAAGTGATAGCTTCGGCTACACTTATCTGATCAAGGACAAATGA
* *
53576614 CAAGTGAAAAGTGGTAGCTTCGGCTAC
1 -AAGTGATAAGTGATAGCTTCGGCTAC
53576641 TTGATCAGTG
Statistics
Matches: 114, Mismatches: 12, Indels: 1
0.90 0.09 0.01
Matches are distributed among these distances:
50 90 0.79
51 24 0.21
ACGTcount: A:0.36, C:0.16, G:0.22, T:0.26
Consensus pattern (50 bp):
AAGTGATAAGTGATAGCTTCGGCTACACTTATCTGATCAAGGACAAATGA
Found at i:53576654 original size:31 final size:31
Alignment explanation
Indices: 53576616--53576764 Score: 226
Period size: 31 Copynumber: 4.8 Consensus size: 31
53576606 ACAAATGACA
*
53576616 AGTGAAAAGTGGTAGCTTCGGCTACTTGATC
1 AGTGAAAAGTGGTAGCTTCGGCTACCTGATC
**
53576647 AGTGAAAAGTGGTAGCTTCTACTACCTGATC
1 AGTGAAAAGTGGTAGCTTCGGCTACCTGATC
* *
53576678 AGTGAAAAGTGGTAGCTCCGGCTACCTAATC
1 AGTGAAAAGTGGTAGCTTCGGCTACCTGATC
* *
53576709 AGTGAAAAATGGTAGCTCCGGCTACCTGATC
1 AGTGAAAAGTGGTAGCTTCGGCTACCTGATC
*
53576740 AGTGAATAGTGGTAGCTTCGGCTAC
1 AGTGAAAAGTGGTAGCTTCGGCTAC
53576765 AAGTGACAAG
Statistics
Matches: 106, Mismatches: 12, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
31 106 1.00
ACGTcount: A:0.28, C:0.19, G:0.27, T:0.26
Consensus pattern (31 bp):
AGTGAAAAGTGGTAGCTTCGGCTACCTGATC
Found at i:53576852 original size:47 final size:46
Alignment explanation
Indices: 53576782--53576903 Score: 145
Period size: 47 Copynumber: 2.6 Consensus size: 46
53576772 AAGTGATTTC
* * *
53576782 CGTATAAGACCATATCTGGGATATGGCATCGGTGTGATATATGCTA
1 CGTATAAGACCATATCTGGGATATGGCATCAGTGAGATATATGATA
* * * *
53576828 CTGTATAAGACCATATCTGAGATATGACATCAGTGAGATATGTGATT
1 C-GTATAAGACCATATCTGGGATATGGCATCAGTGAGATATATGATA
* * *
53576875 CGTGTAAGACCATAGCTGGGCTATGGCAT
1 CGTATAAGACCATATCTGGGATATGGCAT
53576904 TGATACATGG
Statistics
Matches: 63, Mismatches: 12, Indels: 2
0.82 0.16 0.03
Matches are distributed among these distances:
46 24 0.38
47 39 0.62
ACGTcount: A:0.30, C:0.16, G:0.25, T:0.30
Consensus pattern (46 bp):
CGTATAAGACCATATCTGGGATATGGCATCAGTGAGATATATGATA
Found at i:53577016 original size:31 final size:31
Alignment explanation
Indices: 53576978--53577086 Score: 155
Period size: 31 Copynumber: 3.5 Consensus size: 31
53576968 TGTAAGACCA
* *
53576978 TGGTAGCTTCTGCTACCTGATCAGTGAAAAG
1 TGGTAGCTCCGGCTACCTGATCAGTGAAAAG
* *
53577009 TGGTAGCTCCGGCTACCTAATCAGTGAAAAA
1 TGGTAGCTCCGGCTACCTGATCAGTGAAAAG
*
53577040 TGGTAGCTCCGGCTACCTGATCAGTGAATAG
1 TGGTAGCTCCGGCTACCTGATCAGTGAAAAG
* *
53577071 TAGTAGCTTCGGCTAC
1 TGGTAGCTCCGGCTAC
53577087 AAGTGACAAG
Statistics
Matches: 69, Mismatches: 9, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
31 69 1.00
ACGTcount: A:0.26, C:0.22, G:0.26, T:0.27
Consensus pattern (31 bp):
TGGTAGCTCCGGCTACCTGATCAGTGAAAAG
Found at i:53577174 original size:47 final size:46
Alignment explanation
Indices: 53577104--53577318 Score: 145
Period size: 47 Copynumber: 4.7 Consensus size: 46
53577094 AAGTGATTTC
* * *
53577104 CGTATAAGACCATATCTGGGATATGGCATCGGTGTGATATATGCTA
1 CGTATAAGACCATATCTGGGATATGGCATCAGTGAGATATATGATA
* * * *
53577150 CTGTATAAGACCATATCTGAGATATGACATCAGTGAGATATGTGATT
1 C-GTATAAGACCATATCTGGGATATGGCATCAGTGAGATATATGATA
* * * * * *
53577197 CGTGTAAGACCATAGCTGGGCTATGGCAT-TGATACATGATATGTGATTA
1 CGTATAAGACCATATCTGGGATATGGCATCAG-T-GA-GATATATGA-TA
* * * *
53577246 TGTGTAAGACCATAGCTGGGCTATGGCATC-----GATATATGAATA
1 CGTATAAGACCATATCTGGGATATGGCATCAGTGAGATATATG-ATA
* * * *
53577288 TGTGTAAGACCATAGCTGGGCTATGGCATCA
1 CGTATAAGACCATATCTGGGATATGGCATCA
53577319 TTATGTGAAG
Statistics
Matches: 144, Mismatches: 17, Indels: 19
0.80 0.09 0.11
Matches are distributed among these distances:
42 39 0.27
43 1 0.01
45 1 0.01
46 25 0.17
47 40 0.28
48 9 0.06
49 29 0.20
ACGTcount: A:0.30, C:0.15, G:0.26, T:0.30
Consensus pattern (46 bp):
CGTATAAGACCATATCTGGGATATGGCATCAGTGAGATATATGATA
Found at i:53577242 original size:322 final size:322
Alignment explanation
Indices: 53576656--53577300 Score: 1245
Period size: 322 Copynumber: 2.0 Consensus size: 322
53576646 CAGTGAAAAG
53576656 TGGTAGCTTCTACTACCTGATCAGTGAAAAGTGGTAGCTCCGGCTACCTAATCAGTGAAAAATGG
1 TGGTAGCTTCTACTACCTGATCAGTGAAAAGTGGTAGCTCCGGCTACCTAATCAGTGAAAAATGG
*
53576721 TAGCTCCGGCTACCTGATCAGTGAATAGTGGTAGCTTCGGCTACAAGTGACAAGTGATTTCCGTA
66 TAGCTCCGGCTACCTGATCAGTGAATAGTAGTAGCTTCGGCTACAAGTGACAAGTGATTTCCGTA
53576786 TAAGACCATATCTGGGATATGGCATCGGTGTGATATATGCTACTGTATAAGACCATATCTGAGAT
131 TAAGACCATATCTGGGATATGGCATCGGTGTGATATATGCTACTGTATAAGACCATATCTGAGAT
*
53576851 ATGACATCAGTGAGATATGTGATTCGTGTAAGACCATAGCTGGGCTATGGCATTGATACATGGTA
196 ATGACATCAGTGAGATATGTGATTCGTGTAAGACCATAGCTGGGCTATGGCATTGATACATGATA
53576916 TGTGATTACGTGTAAGACCATAGCTGGGCTATGGCATCGATATATAAATATGTGTAAGACCA
261 TGTGATTACGTGTAAGACCATAGCTGGGCTATGGCATCGATATATAAATATGTGTAAGACCA
*
53576978 TGGTAGCTTCTGCTACCTGATCAGTGAAAAGTGGTAGCTCCGGCTACCTAATCAGTGAAAAATGG
1 TGGTAGCTTCTACTACCTGATCAGTGAAAAGTGGTAGCTCCGGCTACCTAATCAGTGAAAAATGG
53577043 TAGCTCCGGCTACCTGATCAGTGAATAGTAGTAGCTTCGGCTACAAGTGACAAGTGATTTCCGTA
66 TAGCTCCGGCTACCTGATCAGTGAATAGTAGTAGCTTCGGCTACAAGTGACAAGTGATTTCCGTA
53577108 TAAGACCATATCTGGGATATGGCATCGGTGTGATATATGCTACTGTATAAGACCATATCTGAGAT
131 TAAGACCATATCTGGGATATGGCATCGGTGTGATATATGCTACTGTATAAGACCATATCTGAGAT
53577173 ATGACATCAGTGAGATATGTGATTCGTGTAAGACCATAGCTGGGCTATGGCATTGATACATGATA
196 ATGACATCAGTGAGATATGTGATTCGTGTAAGACCATAGCTGGGCTATGGCATTGATACATGATA
* *
53577238 TGTGATTATGTGTAAGACCATAGCTGGGCTATGGCATCGATATATGAATATGTGTAAGACCA
261 TGTGATTACGTGTAAGACCATAGCTGGGCTATGGCATCGATATATAAATATGTGTAAGACCA
53577300 T
1 T
53577301 AGCTGGGCTA
Statistics
Matches: 318, Mismatches: 5, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
322 318 1.00
ACGTcount: A:0.29, C:0.17, G:0.25, T:0.29
Consensus pattern (322 bp):
TGGTAGCTTCTACTACCTGATCAGTGAAAAGTGGTAGCTCCGGCTACCTAATCAGTGAAAAATGG
TAGCTCCGGCTACCTGATCAGTGAATAGTAGTAGCTTCGGCTACAAGTGACAAGTGATTTCCGTA
TAAGACCATATCTGGGATATGGCATCGGTGTGATATATGCTACTGTATAAGACCATATCTGAGAT
ATGACATCAGTGAGATATGTGATTCGTGTAAGACCATAGCTGGGCTATGGCATTGATACATGATA
TGTGATTACGTGTAAGACCATAGCTGGGCTATGGCATCGATATATAAATATGTGTAAGACCA
Found at i:53577257 original size:49 final size:44
Alignment explanation
Indices: 53577186--53577358 Score: 178
Period size: 42 Copynumber: 3.9 Consensus size: 44
53577176 ACATCAGTGA
*
53577186 GATATGTGATT-CGTGTAAGACCATAGCTGGGCTATGGCATTGATAC
1 GATATGTGATTATGTGTAAGACCATAGCTGGGCTATGGCA-T-AT-C
53577232 ATGATATGTGATTATGTGTAAGACCATAGCTGGGCTATGGC--ATC
1 --GATATGTGATTATGTGTAAGACCATAGCTGGGCTATGGCATATC
* *
53577276 GATATATGAATATGTGTAAGACCATAGCTGGGCTATGGC--ATC
1 GATATGTGATTATGTGTAAGACCATAGCTGGGCTATGGCATATC
** * **
53577318 -ATTATGTGAAGATGTGTAAGACCATAGTTGAACTATGGCAT
1 GA-TATGTGATTATGTGTAAGACCATAGCTGGGCTATGGCAT
53577359 CGAGAAAATA
Statistics
Matches: 113, Mismatches: 8, Indels: 12
0.85 0.06 0.09
Matches are distributed among these distances:
41 1 0.01
42 72 0.64
44 1 0.01
45 2 0.02
48 11 0.10
49 26 0.23
ACGTcount: A:0.29, C:0.13, G:0.27, T:0.31
Consensus pattern (44 bp):
GATATGTGATTATGTGTAAGACCATAGCTGGGCTATGGCATATC
Found at i:53577293 original size:42 final size:42
Alignment explanation
Indices: 53577234--53577361 Score: 186
Period size: 42 Copynumber: 3.0 Consensus size: 42
53577224 ATTGATACAT
*
53577234 GATATGTGATTATGTGTAAGACCATAGCTGGGCTATGGCATC
1 GATATGTGAATATGTGTAAGACCATAGCTGGGCTATGGCATC
*
53577276 GATATATGAATATGTGTAAGACCATAGCTGGGCTATGGCATC
1 GATATGTGAATATGTGTAAGACCATAGCTGGGCTATGGCATC
* * **
53577318 -ATTATGTGAAGATGTGTAAGACCATAGTTGAACTATGGCATC
1 GA-TATGTGAATATGTGTAAGACCATAGCTGGGCTATGGCATC
53577360 GA
1 GA
53577362 GAAAATAAAG
Statistics
Matches: 77, Mismatches: 7, Indels: 3
0.89 0.08 0.03
Matches are distributed among these distances:
41 1 0.01
42 75 0.97
43 1 0.01
ACGTcount: A:0.30, C:0.13, G:0.27, T:0.30
Consensus pattern (42 bp):
GATATGTGAATATGTGTAAGACCATAGCTGGGCTATGGCATC
Found at i:53583624 original size:30 final size:30
Alignment explanation
Indices: 53583590--53583650 Score: 95
Period size: 30 Copynumber: 2.0 Consensus size: 30
53583580 TCCTTAACTC
53583590 AAACTTTTGCAAAATTACAATTTTGCCCCT
1 AAACTTTTGCAAAATTACAATTTTGCCCCT
* * *
53583620 AAACTTTTGCATATTTACACTTTTGCCCCT
1 AAACTTTTGCAAAATTACAATTTTGCCCCT
53583650 A
1 A
53583651 GGCTCGGGAA
Statistics
Matches: 28, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
30 28 1.00
ACGTcount: A:0.30, C:0.25, G:0.07, T:0.39
Consensus pattern (30 bp):
AAACTTTTGCAAAATTACAATTTTGCCCCT
Found at i:53589194 original size:26 final size:26
Alignment explanation
Indices: 53589158--53589267 Score: 166
Period size: 26 Copynumber: 4.2 Consensus size: 26
53589148 TGATACAAAT
53589158 TGATAATAGGTTAGGTAAATGTTCCA
1 TGATAATAGGTTAGGTAAATGTTCCA
53589184 TGATAATAGGTTAGGTAAATGTTCCA
1 TGATAATAGGTTAGGTAAATGTTCCA
* *
53589210 TGATAATGGGTTAGGTAAATGTTTCA
1 TGATAATAGGTTAGGTAAATGTTCCA
* * * *
53589236 TGATAATGGGCTAGATAAATGTTTCA
1 TGATAATAGGTTAGGTAAATGTTCCA
53589262 TGATAA
1 TGATAA
53589268 GAATTTCATG
Statistics
Matches: 80, Mismatches: 4, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
26 80 1.00
ACGTcount: A:0.35, C:0.06, G:0.24, T:0.35
Consensus pattern (26 bp):
TGATAATAGGTTAGGTAAATGTTCCA
Found at i:53593316 original size:41 final size:41
Alignment explanation
Indices: 53593259--53593436 Score: 295
Period size: 41 Copynumber: 4.4 Consensus size: 41
53593249 GTTATATGAC
*
53593259 TTTTAGCGGCGTTTTACTAAAAGCGCCGCTAATGCTCTGGT
1 TTTTAGCGGCGTTTTACCAAAAGCGCCGCTAATGCTCTGGT
* *
53593300 TTTTAGCAGTGTTTTACCAAAAGCGCCGCTAATGCTCTGGT
1 TTTTAGCGGCGTTTTACCAAAAGCGCCGCTAATGCTCTGGT
53593341 TTTTAGCGGCGTTTTACCAAAAGCGCCGCTAATGCTCTGGT
1 TTTTAGCGGCGTTTTACCAAAAGCGCCGCTAATGCTCTGGT
* *
53593382 TTTTAGCGGCGTATTACCTAAAGCGCCGCTAATGCTCT-GT
1 TTTTAGCGGCGTTTTACCAAAAGCGCCGCTAATGCTCTGGT
*
53593422 TTTTAGCGGTGTTTT
1 TTTTAGCGGCGTTTT
53593437 TTGTAAAACG
Statistics
Matches: 128, Mismatches: 9, Indels: 1
0.93 0.07 0.01
Matches are distributed among these distances:
40 15 0.12
41 113 0.88
ACGTcount: A:0.19, C:0.22, G:0.24, T:0.35
Consensus pattern (41 bp):
TTTTAGCGGCGTTTTACCAAAAGCGCCGCTAATGCTCTGGT
Found at i:53597546 original size:99 final size:101
Alignment explanation
Indices: 53597429--53597635 Score: 391
Period size: 100 Copynumber: 2.1 Consensus size: 101
53597419 AACGATAGAA
*
53597429 GGTAAAAAGAGAGAGCCAACTAGTGCCCTAACCTCC-CAAAAAAAAATGAAAGATTACTACTTTA
1 GGTAAAAAGAGAGAGCCAACTAGTGCCCTAACCTCCAAAAAAAAAAATGAAAGATTACTACTTTA
53597493 GTCTCCCAAGATTTATAAAATCTTAAGTTAATATAT
66 GTCTCCCAAGATTTATAAAATCTTAAGTTAATATAT
53597529 GGTAAAAA-AGAGAGCCAACTAGTGCCCTAACCTCCAAAAAAAAAAATGAAAGATTACTACTTTA
1 GGTAAAAAGAGAGAGCCAACTAGTGCCCTAACCTCCAAAAAAAAAAATGAAAGATTACTACTTTA
53597593 GTCTCCCAAGATTTATAAAATCTTAAGTTAATATAT
66 GTCTCCCAAGATTTATAAAATCTTAAGTTAATATAT
53597629 GGTAAAA
1 GGTAAAA
53597636 TTATAATTTC
Statistics
Matches: 105, Mismatches: 1, Indels: 2
0.97 0.01 0.02
Matches are distributed among these distances:
99 27 0.26
100 78 0.74
ACGTcount: A:0.44, C:0.17, G:0.13, T:0.26
Consensus pattern (101 bp):
GGTAAAAAGAGAGAGCCAACTAGTGCCCTAACCTCCAAAAAAAAAAATGAAAGATTACTACTTTA
GTCTCCCAAGATTTATAAAATCTTAAGTTAATATAT
Found at i:53600904 original size:38 final size:38
Alignment explanation
Indices: 53600817--53600941 Score: 169
Period size: 38 Copynumber: 3.3 Consensus size: 38
53600807 ATTACGAAAC
* **
53600817 ACATGTTAAGCATGCCTACTACTACTATTGAACCCCAAT
1 ACATGTTAAGCATGCCTACTGCTACTATTGAA-CTGAAT
** *
53600856 ACATGTTAAGCATATCTACTGTTACTATTGAACTGAAT
1 ACATGTTAAGCATGCCTACTGCTACTATTGAACTGAAT
* *
53600894 ACATGTTAAGCATGCCTAATGCTACTATTGAACTGAAA
1 ACATGTTAAGCATGCCTACTGCTACTATTGAACTGAAT
53600932 ACATGTTAAG
1 ACATGTTAAG
53600942 TATGTTAATT
Statistics
Matches: 75, Mismatches: 11, Indels: 1
0.86 0.13 0.01
Matches are distributed among these distances:
38 47 0.63
39 28 0.37
ACGTcount: A:0.35, C:0.20, G:0.14, T:0.31
Consensus pattern (38 bp):
ACATGTTAAGCATGCCTACTGCTACTATTGAACTGAAT
Found at i:53602766 original size:45 final size:43
Alignment explanation
Indices: 53602703--53602834 Score: 142
Period size: 45 Copynumber: 3.0 Consensus size: 43
53602693 CATAGGATTT
* **
53602703 TCGATATGTGTTCTCGTGTAAGACCACGTCTGGGACGTTGGCA
1 TCGATATGTGATAGCGTGTAAGACCACGTCTGGGACGTTGGCA
* *
53602746 TCGATATATGTGGTTA-CGTGTAAGACCATGTCTGGGACAG-TGGCA
1 TCG--ATATGT-GATAGCGTGTAAGACCACGTCTGGGAC-GTTGGCA
* * *
53602791 TCGATATGTGATAGCATGTAAGACCGCGTCTAGGACGTTGGCA
1 TCGATATGTGATAGCGTGTAAGACCACGTCTGGGACGTTGGCA
53602834 T
1 T
53602835 TGTATGACAT
Statistics
Matches: 76, Mismatches: 7, Indels: 12
0.80 0.07 0.13
Matches are distributed among these distances:
42 4 0.05
43 33 0.43
45 35 0.46
46 4 0.05
ACGTcount: A:0.23, C:0.18, G:0.30, T:0.29
Consensus pattern (43 bp):
TCGATATGTGATAGCGTGTAAGACCACGTCTGGGACGTTGGCA
Found at i:53602812 original size:43 final size:44
Alignment explanation
Indices: 53602719--53602834 Score: 139
Period size: 43 Copynumber: 2.6 Consensus size: 44
53602709 TGTGTTCTCG
* *
53602719 TGTAAGACCACGTCTGGGACGTTGGCATCGATATATGTGGTTACG
1 TGTAAGACCACGTCTGGGACGTTGGCATCGA-ATATGTGGATACA
*
53602764 TGTAAGACCATGTCTGGGACAG-TGGCATCG-ATATGT-GATAGCA
1 TGTAAGACCACGTCTGGGAC-GTTGGCATCGAATATGTGGATA-CA
* *
53602807 TGTAAGACCGCGTCTAGGACGTTGGCAT
1 TGTAAGACCACGTCTGGGACGTTGGCAT
53602835 TGTATGACAT
Statistics
Matches: 62, Mismatches: 6, Indels: 8
0.82 0.08 0.11
Matches are distributed among these distances:
42 4 0.06
43 30 0.48
45 27 0.44
46 1 0.02
ACGTcount: A:0.24, C:0.18, G:0.31, T:0.27
Consensus pattern (44 bp):
TGTAAGACCACGTCTGGGACGTTGGCATCGAATATGTGGATACA
Found at i:53606833 original size:32 final size:32
Alignment explanation
Indices: 53606792--53606857 Score: 132
Period size: 32 Copynumber: 2.1 Consensus size: 32
53606782 TTAGATAATT
53606792 TTATGTTAGTTTAATTAATTCATTTTAATTTG
1 TTATGTTAGTTTAATTAATTCATTTTAATTTG
53606824 TTATGTTAGTTTAATTAATTCATTTTAATTTG
1 TTATGTTAGTTTAATTAATTCATTTTAATTTG
53606856 TT
1 TT
53606858 TTTTGTAATA
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
32 34 1.00
ACGTcount: A:0.27, C:0.03, G:0.09, T:0.61
Consensus pattern (32 bp):
TTATGTTAGTTTAATTAATTCATTTTAATTTG
Found at i:53608248 original size:18 final size:18
Alignment explanation
Indices: 53608222--53608258 Score: 65
Period size: 18 Copynumber: 2.1 Consensus size: 18
53608212 CTTGATTGGT
*
53608222 AATAGTTTCTCGACCATA
1 AATAATTTCTCGACCATA
53608240 AATAATTTCTCGACCATA
1 AATAATTTCTCGACCATA
53608258 A
1 A
53608259 TCAGGAAAGC
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
18 18 1.00
ACGTcount: A:0.38, C:0.22, G:0.08, T:0.32
Consensus pattern (18 bp):
AATAATTTCTCGACCATA
Found at i:53611271 original size:41 final size:42
Alignment explanation
Indices: 53611208--53611292 Score: 154
Period size: 41 Copynumber: 2.0 Consensus size: 42
53611198 CTTTTAAGAT
53611208 CATTGTTTAATGAGGATGATAGTAAAGCCATTACTCTTATCC
1 CATTGTTTAATGAGGATGATAGTAAAGCCATTACTCTTATCC
*
53611250 CATTTTTTAATGA-GATGATAGTAAAGCCATTACTCTTATCC
1 CATTGTTTAATGAGGATGATAGTAAAGCCATTACTCTTATCC
53611291 CA
1 CA
53611293 ATTGGAAGAC
Statistics
Matches: 42, Mismatches: 1, Indels: 1
0.95 0.02 0.02
Matches are distributed among these distances:
41 30 0.71
42 12 0.29
ACGTcount: A:0.32, C:0.18, G:0.14, T:0.36
Consensus pattern (42 bp):
CATTGTTTAATGAGGATGATAGTAAAGCCATTACTCTTATCC
Found at i:53614577 original size:21 final size:22
Alignment explanation
Indices: 53614548--53614594 Score: 78
Period size: 21 Copynumber: 2.2 Consensus size: 22
53614538 CAGAAGGAGT
*
53614548 GAGTAGTACTTCGCAGCAGGTG
1 GAGTAGTACTCCGCAGCAGGTG
53614570 GAGT-GTACTCCGCAGCAGGTG
1 GAGTAGTACTCCGCAGCAGGTG
53614591 GAGT
1 GAGT
53614595 TTGAGCAGAG
Statistics
Matches: 24, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
21 20 0.83
22 4 0.17
ACGTcount: A:0.21, C:0.19, G:0.38, T:0.21
Consensus pattern (22 bp):
GAGTAGTACTCCGCAGCAGGTG
Found at i:53618835 original size:14 final size:14
Alignment explanation
Indices: 53618816--53618847 Score: 55
Period size: 14 Copynumber: 2.3 Consensus size: 14
53618806 AGTTTGGATT
*
53618816 TCAAATTATTCGAA
1 TCAAATTAATCGAA
53618830 TCAAATTAATCGAA
1 TCAAATTAATCGAA
53618844 TCAA
1 TCAA
53618848 TTCAAATTTT
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
14 17 1.00
ACGTcount: A:0.47, C:0.16, G:0.06, T:0.31
Consensus pattern (14 bp):
TCAAATTAATCGAA
Found at i:53621000 original size:36 final size:36
Alignment explanation
Indices: 53620976--53621051 Score: 152
Period size: 36 Copynumber: 2.1 Consensus size: 36
53620966 AGATGAGATG
53620976 TATCTGACTTTCAAGACATCCTTATCAAGCATTGGC
1 TATCTGACTTTCAAGACATCCTTATCAAGCATTGGC
53621012 TATCTGACTTTCAAGACATCCTTATCAAGCATTGGC
1 TATCTGACTTTCAAGACATCCTTATCAAGCATTGGC
53621048 TATC
1 TATC
53621052 ATCTTTCCAA
Statistics
Matches: 40, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
36 40 1.00
ACGTcount: A:0.28, C:0.25, G:0.13, T:0.34
Consensus pattern (36 bp):
TATCTGACTTTCAAGACATCCTTATCAAGCATTGGC
Found at i:53623980 original size:93 final size:93
Alignment explanation
Indices: 53623872--53624044 Score: 328
Period size: 93 Copynumber: 1.9 Consensus size: 93
53623862 CGCCTATAAG
*
53623872 CGAACTCGGACTCAACTCAACGAGCTCGGGCGTTCGCATCCATAAGTGAACTCGGACTCAACTCA
1 CGAACTCGGACTCAACTCAACGAGCTCGGACGTTCGCATCCATAAGTGAACTCGGACTCAACTCA
53623937 ACGAGCTCGGATGCCTAGTTACATCTCA
66 ACGAGCTCGGATGCCTAGTTACATCTCA
*
53623965 CGAACTCGGACTCAACTCAACGAGTTCGGACGTTCGCATCCATAAGTGAACTCGGACTCAACTCA
1 CGAACTCGGACTCAACTCAACGAGCTCGGACGTTCGCATCCATAAGTGAACTCGGACTCAACTCA
53624030 ACGAGCTCGGATGCC
66 ACGAGCTCGGATGCC
53624045 AAAATATCCG
Statistics
Matches: 78, Mismatches: 2, Indels: 0
0.98 0.03 0.00
Matches are distributed among these distances:
93 78 1.00
ACGTcount: A:0.27, C:0.31, G:0.22, T:0.20
Consensus pattern (93 bp):
CGAACTCGGACTCAACTCAACGAGCTCGGACGTTCGCATCCATAAGTGAACTCGGACTCAACTCA
ACGAGCTCGGATGCCTAGTTACATCTCA
Found at i:53624040 original size:46 final size:46
Alignment explanation
Indices: 53623867--53624040 Score: 221
Period size: 46 Copynumber: 3.8 Consensus size: 46
53623857 TAACCCGCCT
*
53623867 ATAAGCGAACTCGGACTCAACTCAACGAGCTCGGGCGTTCGCATCC
1 ATAAGCGAACTCGGACTCAACTCAACGAGCTCGGACGTTCGCATCC
* *
53623913 ATAAGTGAACTCGGACTCAACTCAACGAGCTCGGATGCCTAGTT-ACAT-C
1 ATAAGCGAACTCGGACTCAACTCAACGAGCTCGGA---C--GTTCGCATCC
* *
53623962 -TCA-CGAACTCGGACTCAACTCAACGAGTTCGGACGTTCGCATCC
1 ATAAGCGAACTCGGACTCAACTCAACGAGCTCGGACGTTCGCATCC
*
53624006 ATAAGTGAACTCGGACTCAACTCAACGAGCTCGGA
1 ATAAGCGAACTCGGACTCAACTCAACGAGCTCGGA
53624041 TGCCAAAATA
Statistics
Matches: 109, Mismatches: 10, Indels: 18
0.80 0.07 0.13
Matches are distributed among these distances:
42 3 0.03
43 3 0.03
44 2 0.02
45 2 0.02
46 61 0.56
47 28 0.26
48 2 0.02
49 2 0.02
50 3 0.03
51 3 0.03
ACGTcount: A:0.29, C:0.30, G:0.22, T:0.20
Consensus pattern (46 bp):
ATAAGCGAACTCGGACTCAACTCAACGAGCTCGGACGTTCGCATCC
Found at i:53625938 original size:13 final size:14
Alignment explanation
Indices: 53625920--53625949 Score: 53
Period size: 13 Copynumber: 2.2 Consensus size: 14
53625910 TAATTGGTTA
53625920 TAATTAAG-TTAAT
1 TAATTAAGTTTAAT
53625933 TAATTAAGTTTAAT
1 TAATTAAGTTTAAT
53625947 TAA
1 TAA
53625950 AACTAAACAA
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
13 8 0.50
14 8 0.50
ACGTcount: A:0.47, C:0.00, G:0.07, T:0.47
Consensus pattern (14 bp):
TAATTAAGTTTAAT
Found at i:53626982 original size:19 final size:19
Alignment explanation
Indices: 53626954--53627009 Score: 67
Period size: 19 Copynumber: 2.9 Consensus size: 19
53626944 GCACTTACGC
*
53626954 GCCAGGATGCACTTCGTGA
1 GCCAGGATGCACTTTGTGA
* * *
53626973 GCCAGTATGCGCTTTGTGC
1 GCCAGGATGCACTTTGTGA
*
53626992 GCTAGGATGCACTTTGTG
1 GCCAGGATGCACTTTGTG
53627010 TACTAGTATG
Statistics
Matches: 30, Mismatches: 7, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
19 30 1.00
ACGTcount: A:0.16, C:0.23, G:0.32, T:0.29
Consensus pattern (19 bp):
GCCAGGATGCACTTTGTGA
Found at i:53627015 original size:19 final size:18
Alignment explanation
Indices: 53626957--53627024 Score: 55
Period size: 19 Copynumber: 3.6 Consensus size: 18
53626947 CTTACGCGCC
* *
53626957 AGGATGCACTTCGTGAGCC
1 AGGATGCACTTTGTGA-CT
* * *
53626976 AGTATGCGCTTTGTGCGCT
1 AGGATGCACTTTGTG-ACT
53626995 AGGATGCACTTTGTGTACT
1 AGGATGCACTTTGTG-ACT
*
53627014 AGTATGCACTT
1 AGGATGCACTT
53627025 ACATGCTAGC
Statistics
Matches: 38, Mismatches: 10, Indels: 2
0.76 0.20 0.04
Matches are distributed among these distances:
19 38 1.00
ACGTcount: A:0.19, C:0.21, G:0.28, T:0.32
Consensus pattern (18 bp):
AGGATGCACTTTGTGACT
Found at i:53638535 original size:21 final size:21
Alignment explanation
Indices: 53638455--53638554 Score: 80
Period size: 21 Copynumber: 4.8 Consensus size: 21
53638445 TTCCTTCTTA
* *
53638455 AATTTTCAATCTTCAATCTTT
1 AATTATCAATCTTCAATTTTT
* * *
53638476 AA-TACCCATTTTCCAA-TTTT
1 AATTATCAATCTT-CAATTTTT
*
53638496 ATATTTTCAATCTTCAATTTTT
1 A-ATTATCAATCTTCAATTTTT
53638518 AATTATCAAT-TTCAAATTTTT
1 AATTATCAATCTTC-AATTTTT
* *
53638539 AATTCTCAATCCTCAA
1 AATTATCAATCTTCAA
53638555 CTATTATTTT
Statistics
Matches: 61, Mismatches: 12, Indels: 12
0.72 0.14 0.14
Matches are distributed among these distances:
20 13 0.21
21 35 0.57
22 13 0.21
ACGTcount: A:0.32, C:0.19, G:0.00, T:0.49
Consensus pattern (21 bp):
AATTATCAATCTTCAATTTTT
Found at i:53638536 original size:42 final size:42
Alignment explanation
Indices: 53638455--53638554 Score: 114
Period size: 42 Copynumber: 2.4 Consensus size: 42
53638445 TTCCTTCTTA
* *
53638455 AATTTTCAATCTTCAATCTTTAATACCCATTTTCCAA-TTTT
1 AATTTTCAATCTTCAATCTTTAATACCCAATTTCAAATTTTT
* *
53638496 ATATTTTCAATCTTCAATTTTTAATTA-TCAATTTCAAATTTTT
1 A-ATTTTCAATCTTCAATCTTTAA-TACCCAATTTCAAATTTTT
* *
53638539 AATTCTCAATCCTCAA
1 AATTTTCAATCTTCAA
53638555 CTATTATTTT
Statistics
Matches: 50, Mismatches: 6, Indels: 5
0.82 0.10 0.08
Matches are distributed among these distances:
41 1 0.02
42 42 0.84
43 7 0.14
ACGTcount: A:0.32, C:0.19, G:0.00, T:0.49
Consensus pattern (42 bp):
AATTTTCAATCTTCAATCTTTAATACCCAATTTCAAATTTTT
Found at i:53640947 original size:13 final size:13
Alignment explanation
Indices: 53640929--53640957 Score: 58
Period size: 13 Copynumber: 2.2 Consensus size: 13
53640919 ACTCATTTAG
53640929 AATGTACAAAACA
1 AATGTACAAAACA
53640942 AATGTACAAAACA
1 AATGTACAAAACA
53640955 AAT
1 AAT
53640958 TTATTAAATT
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 16 1.00
ACGTcount: A:0.62, C:0.14, G:0.07, T:0.17
Consensus pattern (13 bp):
AATGTACAAAACA
Found at i:53641019 original size:20 final size:19
Alignment explanation
Indices: 53640994--53641035 Score: 57
Period size: 19 Copynumber: 2.2 Consensus size: 19
53640984 AATCAAGTTG
53640994 CGAGTTTAAAATTTACAATT
1 CGAG-TTAAAATTTACAATT
* *
53641014 CGAGTTGAATTTTACAATT
1 CGAGTTAAAATTTACAATT
53641033 CGA
1 CGA
53641036 ATAACTCGAA
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
19 16 0.80
20 4 0.20
ACGTcount: A:0.36, C:0.12, G:0.14, T:0.38
Consensus pattern (19 bp):
CGAGTTAAAATTTACAATT
Found at i:53641087 original size:10 final size:10
Alignment explanation
Indices: 53641072--53641113 Score: 50
Period size: 10 Copynumber: 4.2 Consensus size: 10
53641062 TTTTATATGT
53641072 AAAATTATAA
1 AAAATTATAA
*
53641082 AAAATT-CAA
1 AAAATTATAA
*
53641091 AAAATTCTAA
1 AAAATTATAA
53641101 AAAATATATAA
1 AAAAT-TATAA
53641112 AA
1 AA
53641114 TTCGAAGGAG
Statistics
Matches: 27, Mismatches: 3, Indels: 3
0.82 0.09 0.09
Matches are distributed among these distances:
9 8 0.30
10 13 0.48
11 6 0.22
ACGTcount: A:0.69, C:0.05, G:0.00, T:0.26
Consensus pattern (10 bp):
AAAATTATAA
Found at i:53641092 original size:9 final size:10
Alignment explanation
Indices: 53641072--53641105 Score: 52
Period size: 10 Copynumber: 3.5 Consensus size: 10
53641062 TTTTATATGT
*
53641072 AAAATTATAA
1 AAAATTCTAA
53641082 AAAATTC-AA
1 AAAATTCTAA
53641091 AAAATTCTAA
1 AAAATTCTAA
53641101 AAAAT
1 AAAAT
53641106 ATATAAAATT
Statistics
Matches: 22, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
9 9 0.41
10 13 0.59
ACGTcount: A:0.68, C:0.06, G:0.00, T:0.26
Consensus pattern (10 bp):
AAAATTCTAA
Found at i:53641113 original size:19 final size:19
Alignment explanation
Indices: 53641066--53641116 Score: 59
Period size: 19 Copynumber: 2.7 Consensus size: 19
53641056 AACAGATTTT
* *
53641066 ATATGTAAAATTATAAAAA
1 ATATATAAAATTCTAAAAA
*
53641085 AT-TCAAAAAATTCTAAAAA
1 ATAT-ATAAAATTCTAAAAA
53641104 ATATATAAAATTC
1 ATATATAAAATTC
53641117 GAAGGAGTGT
Statistics
Matches: 26, Mismatches: 4, Indels: 4
0.76 0.12 0.12
Matches are distributed among these distances:
18 1 0.04
19 24 0.92
20 1 0.04
ACGTcount: A:0.61, C:0.06, G:0.02, T:0.31
Consensus pattern (19 bp):
ATATATAAAATTCTAAAAA
Found at i:53641578 original size:29 final size:29
Alignment explanation
Indices: 53641545--53641604 Score: 84
Period size: 29 Copynumber: 2.1 Consensus size: 29
53641535 CAAGTTAACA
*
53641545 AAGGTTATGCCGTTAAGGGATAAAGCATG
1 AAGGTTATGCCATTAAGGGATAAAGCATG
* **
53641574 AAGGTTATGCTATTAAGGGATGGAGCATG
1 AAGGTTATGCCATTAAGGGATAAAGCATG
53641603 AA
1 AA
53641605 TGGGGCCATA
Statistics
Matches: 27, Mismatches: 4, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
29 27 1.00
ACGTcount: A:0.35, C:0.08, G:0.32, T:0.25
Consensus pattern (29 bp):
AAGGTTATGCCATTAAGGGATAAAGCATG
Found at i:53642146 original size:112 final size:110
Alignment explanation
Indices: 53642004--53642222 Score: 402
Period size: 112 Copynumber: 2.0 Consensus size: 110
53641994 AACTTGGACC
*
53642004 TTGAGATGAAACACAATTTGACTTCCCAGTAGATGACTCTATACTCACATGGTAGATGAAATTTG
1 TTGAGATGAAACACAATTCGACTTCCCAGTAGATGACTCTATACTCACATGGTAGATGAAATTTG
53642069 TAGGTTACCCAGGTCCATGGCACTATCATAAATTCAAACATTCCAAG
66 TAGGTTACCCAGGTCCATGGCACTA--ATAAATTCAAACATTCCAAG
53642116 TTGAGATGAAACACAATTCGACTTCCCAGTAGATGACTCTATACTCACATGGTAGATGAAATTTG
1 TTGAGATGAAACACAATTCGACTTCCCAGTAGATGACTCTATACTCACATGGTAGATGAAATTTG
*
53642181 TAGGTTACCCAGGTCCATGGCACTAGTAAATTCAAACATTCC
66 TAGGTTACCCAGGTCCATGGCACTAATAAATTCAAACATTCC
53642223 TTAAAACTAT
Statistics
Matches: 105, Mismatches: 2, Indels: 2
0.96 0.02 0.02
Matches are distributed among these distances:
110 16 0.15
112 89 0.85
ACGTcount: A:0.33, C:0.21, G:0.17, T:0.28
Consensus pattern (110 bp):
TTGAGATGAAACACAATTCGACTTCCCAGTAGATGACTCTATACTCACATGGTAGATGAAATTTG
TAGGTTACCCAGGTCCATGGCACTAATAAATTCAAACATTCCAAG
Found at i:53644424 original size:40 final size:40
Alignment explanation
Indices: 53644354--53644571 Score: 316
Period size: 40 Copynumber: 5.5 Consensus size: 40
53644344 AAGCCAAGTA
* * * * *
53644354 CCTTCGGGATTTA-ACCGGATATAGCT-ACTCGCTCGAATA
1 CCTTCGGGACTTAGCCCGGATATAG-TAACTCGCACAAATG
*
53644393 CCTTCGGGACATAGCCCGGATATAGTAACTCGCACAAATG
1 CCTTCGGGACTTAGCCCGGATATAGTAACTCGCACAAATG
53644433 CCTTCGGGACTTAGCCCGGATATAGTAACTCGCACAAATG
1 CCTTCGGGACTTAGCCCGGATATAGTAACTCGCACAAATG
53644473 CCTTCGGGACTTAGCCCGGATATAGTAACTCGCACAAATG
1 CCTTCGGGACTTAGCCCGGATATAGTAACTCGCACAAATG
* * *
53644513 CCTTCGGGACTTAGCCCGGA-ACTAGTCACTAGCGCAAATG
1 CCTTCGGGACTTAGCCCGGATA-TAGTAACTCGCACAAATG
53644553 CCTTCGGGACTTAGCCCGG
1 CCTTCGGGACTTAGCCCGG
53644572 TTATCATCCA
Statistics
Matches: 166, Mismatches: 10, Indels: 5
0.92 0.06 0.03
Matches are distributed among these distances:
39 13 0.08
40 153 0.92
ACGTcount: A:0.26, C:0.28, G:0.23, T:0.22
Consensus pattern (40 bp):
CCTTCGGGACTTAGCCCGGATATAGTAACTCGCACAAATG
Found at i:53645893 original size:53 final size:52
Alignment explanation
Indices: 53645818--53645942 Score: 187
Period size: 53 Copynumber: 2.4 Consensus size: 52
53645808 CTCAAAGCTC
* * * *
53645818 TTTTTCCTTCCTTTTCTTTCTTCTATTCGGCCAAGAACAACATGAGAGCTTTT
1 TTTTTTCTTCTTTTTCTTTCTTCTATTCAGCCAAGAAAAACATGAGAGC-TTT
53645871 TTTTTTCTTCTTTTTCTTTCTTCTATTCAGCCAAGAAAAACATGAGAGCTTT
1 TTTTTTCTTCTTTTTCTTTCTTCTATTCAGCCAAGAAAAACATGAGAGCTTT
*
53645923 TTTTTTCTTTCTTTTCCTTT
1 TTTTTTC-TTCTTTTTCTTT
53645943 TTTCATCATC
Statistics
Matches: 66, Mismatches: 5, Indels: 2
0.90 0.07 0.03
Matches are distributed among these distances:
52 10 0.15
53 56 0.85
ACGTcount: A:0.18, C:0.22, G:0.09, T:0.52
Consensus pattern (52 bp):
TTTTTTCTTCTTTTTCTTTCTTCTATTCAGCCAAGAAAAACATGAGAGCTTT
Found at i:53647336 original size:25 final size:24
Alignment explanation
Indices: 53647308--53647354 Score: 60
Period size: 26 Copynumber: 1.9 Consensus size: 24
53647298 ATGGAAAATA
53647308 AAGA-AAAACAAAAGAAAGTTAAAAG
1 AAGATAAAACAAAA-AAA-TTAAAAG
*
53647333 AAGATAAAAGAAAAAAATTAAA
1 AAGATAAAACAAAAAAATTAAA
53647355 TTACTGAAAA
Statistics
Matches: 20, Mismatches: 1, Indels: 3
0.83 0.04 0.12
Matches are distributed among these distances:
24 5 0.25
25 7 0.35
26 8 0.40
ACGTcount: A:0.74, C:0.02, G:0.13, T:0.11
Consensus pattern (24 bp):
AAGATAAAACAAAAAAATTAAAAG
Found at i:53647514 original size:31 final size:28
Alignment explanation
Indices: 53647479--53647552 Score: 76
Period size: 31 Copynumber: 2.5 Consensus size: 28
53647469 AACGGCTCAA
*
53647479 TGACTAGAATGTTACAATACGATAACATAAG
1 TGACTA-AATGTAACAATAC-A-AACATAAG
* * *
53647510 TGACTAAAACGTAACATTTCAAACATAAG
1 TGACT-AAATGTAACAATACAAACATAAG
53647539 TGACTAAATGTAAC
1 TGACTAAATGTAAC
53647553 CTGAGGCAAA
Statistics
Matches: 37, Mismatches: 5, Indels: 5
0.79 0.11 0.11
Matches are distributed among these distances:
28 8 0.22
29 13 0.35
30 1 0.03
31 14 0.38
32 1 0.03
ACGTcount: A:0.46, C:0.15, G:0.14, T:0.26
Consensus pattern (28 bp):
TGACTAAATGTAACAATACAAACATAAG
Found at i:53651370 original size:30 final size:30
Alignment explanation
Indices: 53651336--53651396 Score: 95
Period size: 30 Copynumber: 2.0 Consensus size: 30
53651326 TTCCTGAGTC
53651336 TAGGGGCAAAAGTGTAAATATGCAAAAGTT
1 TAGGGGCAAAAGTGTAAATATGCAAAAGTT
* * *
53651366 TAGGGGCAAAATTGTAATTTTGCAAAAGTT
1 TAGGGGCAAAAGTGTAAATATGCAAAAGTT
53651396 T
1 T
53651397 GAGTTAAGGA
Statistics
Matches: 28, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
30 28 1.00
ACGTcount: A:0.39, C:0.07, G:0.25, T:0.30
Consensus pattern (30 bp):
TAGGGGCAAAAGTGTAAATATGCAAAAGTT
Found at i:53651974 original size:68 final size:66
Alignment explanation
Indices: 53651888--53652240 Score: 242
Period size: 67 Copynumber: 5.4 Consensus size: 66
53651878 TAATACGGGA
* *
53651888 TGTATACCATGT-GTACAAGAGAGCTACGAGACATTATGAGGTAGCTAGGTTGCATGGGTGATAC
1 TGTACACCATGTAG-ACAAGAGAGCTACGAGACA-TAT-AGGTAGCTAGGTCGCATGGGTGATAC
53651952 TATG
63 TATG
* *
53651956 TGTACACCATGTAGACAAGAGAGCTACG-G-GATATATGTAGCTAGGTCGCATGGGTGATACTAT
1 TGTACACCATGTAGACAAGAGAGCTACGAGACATATAGGTAGCTAGGTCGCATGGGTGATACTAT
53652019 G
66 G
* * * * * * * *
53652020 TGTACACCATGTAGACAAGATAGCTACGAG--ATAAATGTAGCTAGGTTGCATGTGTGGTTCCAA
1 TGTACACCATGTAGACAAGAGAGCTACGAGACATATAGGTAGCTAGGTCGCATGGGT-GATACTA
53652083 GTG
65 -TG
* * * * * * * * * * *
53652086 AAGGACACCATGTAAACAAGAGAGCTACGAG--GTAAATGTAGCTAGGTTGCATGTGTGGTTCCA
1 -TGTACACCATGTAGACAAGAGAGCTACGAGACATATAGGTAGCTAGGTCGCATGGGTGATACTA
53652149 GGTG
65 --TG
* * * * * * *
53652153 AAGGACACCATGTAAACAAGAGAGCTACGAG--ATA-AAGTGGCTAGGTCACATGGGTGGTACTA
1 -TGTACACCATGTAGACAAGAGAGCTACGAGACATATAGGTAGCTAGGTCGCATGGGTGATACTA
*
53652215 AG
65 TG
* *
53652217 TGTTCACCATCT-GTACAAGAGAGC
1 TGTACACCATGTAG-ACAAGAGAGC
53652241 CAAAATTATG
Statistics
Matches: 245, Mismatches: 33, Indels: 19
0.82 0.11 0.06
Matches are distributed among these distances:
63 18 0.07
64 78 0.32
65 8 0.03
66 28 0.11
67 87 0.36
68 25 0.10
69 1 0.00
ACGTcount: A:0.31, C:0.16, G:0.29, T:0.24
Consensus pattern (66 bp):
TGTACACCATGTAGACAAGAGAGCTACGAGACATATAGGTAGCTAGGTCGCATGGGTGATACTAT
G
Found at i:53652013 original size:64 final size:64
Alignment explanation
Indices: 53651928--53652240 Score: 299
Period size: 67 Copynumber: 4.8 Consensus size: 64
53651918 ACATTATGAG
*
53651928 GTAGCTAGGTTGCATGGGTGATACTATGTGTACACCATGTAGACAAGAGAGCTACGGGATATAT
1 GTAGCTAGGTTGCATGGGTGATACTATGTGTACACCATGTAGACAAGAGAGCTACGGGATAAAT
* * *
53651992 GTAGCTAGGTCGCATGGGTGATACTATGTGTACACCATGTAGACAAGATAGCTACGAGATAAAT
1 GTAGCTAGGTTGCATGGGTGATACTATGTGTACACCATGTAGACAAGAGAGCTACGGGATAAAT
* * * * * * *
53652056 GTAGCTAGGTTGCATGTGTGGTTCCAAGTGAAGGACACCATGTAAACAAGAGAGCTACGAGG-TA
1 GTAGCTAGGTTGCATGGGT-GATACTA-TG-TGTACACCATGTAGACAAGAGAGCTACG-GGATA
53652120 AAT
62 AAT
* * * * * * * *
53652123 GTAGCTAGGTTGCATGTGTGGTTCCAGGTGAAGGACACCATGTAAACAAGAGAGCTACGAGATAA
1 GTAGCTAGGTTGCATGGGTGATACTA--TG-TGTACACCATGTAGACAAGAGAGCTACGGGATAA
53652188 A-
63 AT
* ** * * * *
53652189 GTGGCTAGGTCACATGGGTGGTACTAAGTGTTCACCATCT-GTACAAGAGAGC
1 GTAGCTAGGTTGCATGGGTGATACTATGTGTACACCATGTAG-ACAAGAGAGC
53652241 CAAAATTATG
Statistics
Matches: 212, Mismatches: 30, Indels: 15
0.82 0.12 0.06
Matches are distributed among these distances:
63 18 0.08
64 78 0.37
65 4 0.02
66 27 0.13
67 84 0.40
68 1 0.00
ACGTcount: A:0.31, C:0.16, G:0.29, T:0.24
Consensus pattern (64 bp):
GTAGCTAGGTTGCATGGGTGATACTATGTGTACACCATGTAGACAAGAGAGCTACGGGATAAAT
Found at i:53652099 original size:131 final size:132
Alignment explanation
Indices: 53651959--53652198 Score: 324
Period size: 131 Copynumber: 1.8 Consensus size: 132
53651949 TACTATGTGT
* * * *
53651959 ACACCATGTAGACAAGAGAGCTACG-GGATATATGTAGCTAGGTCGCATGGGTGATACTA-TG-T
1 ACACCATGTAAACAAGAGAGCTACGAGG-TAAATGTAGCTAGGTCGCATGGGTGATACCAGTGAA
* * *
53652021 GTACACCATGTAGACAAGATAGCTACGAGATAAATGTAGCTAGGTTGCATGTGTGGTTCCAAGTG
65 GGACACCATGTAAACAAGAGAGCTACGAGATAAA-GTAGCTAGGTTGCATGTGTGGTTCCAAGTG
53652086 AAGG
129 AAGG
* * * *
53652090 ACACCATGTAAACAAGAGAGCTACGAGGTAAATGTAGCTAGGTTGCATGTGTGGTTCCAGGTGAA
1 ACACCATGTAAACAAGAGAGCTACGAGGTAAATGTAGCTAGGTCGCATGGGTGATACCA-GTGAA
*
53652155 GGACACCATGTAAACAAGAGAGCTACGAGATAAAGTGGCTAGGT
65 GGACACCATGTAAACAAGAGAGCTACGAGATAAAGTAGCTAGGT
53652199 CACATGGGTG
Statistics
Matches: 93, Mismatches: 12, Indels: 6
0.84 0.11 0.05
Matches are distributed among these distances:
131 49 0.53
132 2 0.02
133 11 0.12
134 31 0.33
ACGTcount: A:0.33, C:0.15, G:0.29, T:0.23
Consensus pattern (132 bp):
ACACCATGTAAACAAGAGAGCTACGAGGTAAATGTAGCTAGGTCGCATGGGTGATACCAGTGAAG
GACACCATGTAAACAAGAGAGCTACGAGATAAAGTAGCTAGGTTGCATGTGTGGTTCCAAGTGAA
GG
Found at i:53652112 original size:67 final size:67
Alignment explanation
Indices: 53651959--53652198 Score: 317
Period size: 67 Copynumber: 3.6 Consensus size: 67
53651949 TACTATGTGT
* * * * * * * * *
53651959 ACACCATGTAGACAAGAGAGCTACGGGATATATGTAGCTAGGTCGCATGGGT-GATACTA-TG-T
1 ACACCATGTAAACAAGAGAGCTACGAGATAAATGTAGCTAGGTTGCATGTGTGGTTCCAAGTGAA
*
53652021 GT
66 GG
* *
53652023 ACACCATGTAGACAAGATAGCTACGAGATAAATGTAGCTAGGTTGCATGTGTGGTTCCAAGTGAA
1 ACACCATGTAAACAAGAGAGCTACGAGATAAATGTAGCTAGGTTGCATGTGTGGTTCCAAGTGAA
53652088 GG
66 GG
* *
53652090 ACACCATGTAAACAAGAGAGCTACGAGGTAAATGTAGCTAGGTTGCATGTGTGGTTCCAGGTGAA
1 ACACCATGTAAACAAGAGAGCTACGAGATAAATGTAGCTAGGTTGCATGTGTGGTTCCAAGTGAA
53652155 GG
66 GG
*
53652157 ACACCATGTAAACAAGAGAGCTACGAGATAAA-GTGGCTAGGT
1 ACACCATGTAAACAAGAGAGCTACGAGATAAATGTAGCTAGGT
53652199 CACATGGGTG
Statistics
Matches: 157, Mismatches: 16, Indels: 4
0.89 0.09 0.02
Matches are distributed among these distances:
64 47 0.30
65 4 0.03
66 11 0.07
67 95 0.61
ACGTcount: A:0.33, C:0.15, G:0.29, T:0.23
Consensus pattern (67 bp):
ACACCATGTAAACAAGAGAGCTACGAGATAAATGTAGCTAGGTTGCATGTGTGGTTCCAAGTGAA
GG
Found at i:53657248 original size:68 final size:64
Alignment explanation
Indices: 53657183--53657390 Score: 213
Period size: 67 Copynumber: 3.2 Consensus size: 64
53657173 CATCATGTGT
* *
53657183 ACAAGAAAGCTACGAGACATTATGATGTAGCTAGGTCGCATGGGTGATACTATGTGTACACCATG
1 ACAAGAGAGCTACGAG--A-TAT-ATGTAGCTAGGTCGCATGGGTGGTACTATGTGTACACCATG
53657248 TAG
62 TAG
* * * * * *
53657251 ACAAGAGAGCTACGGGATATATGTAGCTAGGTCGCATGCGTGGTTCCAGGTGAAGGACACCATGT
1 ACAAGAGAGCTACGAGATATATGTAGCTAGGTCGCATGGGTGGTACTA--TG-TGTACACCATGT
53657316 AG
63 AG
* * * * *
53657318 ACAAGAGAGCTACGAGATAAAT-TGGCTAGGTCACATGGGTGGTACTAAGTGTTCACCATGT-G
1 ACAAGAGAGCTACGAGATATATGTAGCTAGGTCGCATGGGTGGTACTATGTGTACACCATGTAG
53657380 TACAAGAGAGC
1 -ACAAGAGAGC
53657391 CACAATTATG
Statistics
Matches: 117, Mismatches: 19, Indels: 13
0.79 0.13 0.09
Matches are distributed among these distances:
62 1 0.01
63 19 0.16
64 25 0.21
65 3 0.03
66 23 0.20
67 32 0.27
68 14 0.12
ACGTcount: A:0.31, C:0.17, G:0.29, T:0.23
Consensus pattern (64 bp):
ACAAGAGAGCTACGAGATATATGTAGCTAGGTCGCATGGGTGGTACTATGTGTACACCATGTAG
Found at i:53657495 original size:25 final size:25
Alignment explanation
Indices: 53657461--53657510 Score: 100
Period size: 25 Copynumber: 2.0 Consensus size: 25
53657451 TGTACAAGAA
53657461 AGCTTCGATTTTAAAGGTGGGCTGT
1 AGCTTCGATTTTAAAGGTGGGCTGT
53657486 AGCTTCGATTTTAAAGGTGGGCTGT
1 AGCTTCGATTTTAAAGGTGGGCTGT
53657511 GTGCGATAGC
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
25 25 1.00
ACGTcount: A:0.20, C:0.12, G:0.32, T:0.36
Consensus pattern (25 bp):
AGCTTCGATTTTAAAGGTGGGCTGT
Found at i:53661803 original size:39 final size:39
Alignment explanation
Indices: 53661713--53661963 Score: 335
Period size: 39 Copynumber: 6.5 Consensus size: 39
53661703 TGGGACTTTA
* ** * *
53661713 AGCCCGGATATAATACCAGCAC-AAACCCTGCGGGACTTT
1 AGCCCGGATATAACACCAGCACGAATGCCTTCAGGAC-TT
* * * *
53661752 AG-CCAGATATAACACCAACACGAATGCCTTCGGGGCTT
1 AGCCCGGATATAACACCAGCACGAATGCCTTCAGGACTT
53661790 AGCCCGGATATAACACCAGCACGAATGCCTTCAGGACTT
1 AGCCCGGATATAACACCAGCACGAATGCCTTCAGGACTT
* *
53661829 AGCCCGGATATAACACCAGCAGGAATGCCTTCGGGACTT
1 AGCCCGGATATAACACCAGCACGAATGCCTTCAGGACTT
* *
53661868 AGCCCGGATATAACACCAGTAGGAATGCCTTCAGGACTT
1 AGCCCGGATATAACACCAGCACGAATGCCTTCAGGACTT
*
53661907 AGCCCGGATATAACACCAGCAGGAATGCCTTCAGGACTT
1 AGCCCGGATATAACACCAGCACGAATGCCTTCAGGACTT
**
53661946 AGCTTGGATATAACACCA
1 AGCCCGGATATAACACCA
53661964 TTATAAAGTC
Statistics
Matches: 192, Mismatches: 18, Indels: 4
0.90 0.08 0.02
Matches are distributed among these distances:
38 20 0.10
39 172 0.90
ACGTcount: A:0.31, C:0.28, G:0.22, T:0.19
Consensus pattern (39 bp):
AGCCCGGATATAACACCAGCACGAATGCCTTCAGGACTT
Found at i:53662069 original size:28 final size:28
Alignment explanation
Indices: 53662036--53662117 Score: 92
Period size: 28 Copynumber: 2.9 Consensus size: 28
53662026 ATTTAATCAT
** *
53662036 TCAATATTTTTCACACTAAGTGTCATTC
1 TCAATATTTCGCACACTAAGTGCCATTC
* *
53662064 TCAATATCTCGCACATTAAGTGCCATTC
1 TCAATATTTCGCACACTAAGTGCCATTC
* * *
53662092 TCAATATTTCGTACACTGAGTACCAT
1 TCAATATTTCGCACACTAAGTGCCAT
53662118 ATTTGATTGC
Statistics
Matches: 44, Mismatches: 10, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
28 44 1.00
ACGTcount: A:0.29, C:0.24, G:0.10, T:0.37
Consensus pattern (28 bp):
TCAATATTTCGCACACTAAGTGCCATTC
Found at i:53666839 original size:30 final size:30
Alignment explanation
Indices: 53666796--53666853 Score: 73
Period size: 30 Copynumber: 1.9 Consensus size: 30
53666786 CATGAGCTGC
*
53666796 CACATGGGAGTGTGGCT-AGCCCATGTGGCT
1 CACACGGGAGTGT-GCTCAGCCCATGTGGCT
* *
53666826 CACACGGGTGTGTGCTCAGCCCGTGTGG
1 CACACGGGAGTGTGCTCAGCCCATGTGG
53666854 AAATGGTCTT
Statistics
Matches: 24, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
29 3 0.12
30 21 0.88
ACGTcount: A:0.14, C:0.26, G:0.38, T:0.22
Consensus pattern (30 bp):
CACACGGGAGTGTGCTCAGCCCATGTGGCT
Found at i:53670294 original size:32 final size:32
Alignment explanation
Indices: 53670219--53670306 Score: 87
Period size: 32 Copynumber: 2.8 Consensus size: 32
53670209 GAAATAGTGA
*
53670219 AATAAT-AATAATAAT-AATAAT-AAAATAAT
1 AATAATGAATAATAATGAATAATAAAAATAAG
** *
53670248 AATAATGACCAATAATGAATAATAAAAATACG
1 AATAATGAATAATAATGAATAATAAAAATAAG
53670280 AATAA-GAAATAATAATGAAATAA-AAAA
1 AATAATG-AATAATAATG-AATAATAAAA
53670307 CTGAAAATGG
Statistics
Matches: 48, Mismatches: 6, Indels: 7
0.79 0.10 0.11
Matches are distributed among these distances:
29 6 0.12
30 7 0.15
31 7 0.15
32 23 0.48
33 5 0.10
ACGTcount: A:0.67, C:0.03, G:0.06, T:0.24
Consensus pattern (32 bp):
AATAATGAATAATAATGAATAATAAAAATAAG
Found at i:53670295 original size:3 final size:3
Alignment explanation
Indices: 53670219--53670277 Score: 66
Period size: 3 Copynumber: 19.3 Consensus size: 3
53670209 GAAATAGTGA
**
53670219 AAT AAT AAT AAT AAT AAT AAT AA- AAT AAT AAT AAT GACC AAT AAT
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT -AAT AAT AAT
*
53670264 GAAT AAT AAA AAT A
1 -AAT AAT AAT AAT A
53670278 CGAATAAGAA
Statistics
Matches: 47, Mismatches: 6, Indels: 6
0.80 0.10 0.10
Matches are distributed among these distances:
2 2 0.04
3 41 0.87
4 4 0.09
ACGTcount: A:0.66, C:0.03, G:0.03, T:0.27
Consensus pattern (3 bp):
AAT
Found at i:53671325 original size:18 final size:18
Alignment explanation
Indices: 53671302--53671340 Score: 53
Period size: 18 Copynumber: 2.2 Consensus size: 18
53671292 AATTTAAAAG
*
53671302 AAATAATATGAAAT-AAAT
1 AAATAA-ATAAAATCAAAT
53671320 AAATAAATAAAATCAAAT
1 AAATAAATAAAATCAAAT
53671338 AAA
1 AAA
53671341 AATGAGGAAA
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
17 6 0.32
18 13 0.68
ACGTcount: A:0.72, C:0.03, G:0.03, T:0.23
Consensus pattern (18 bp):
AAATAAATAAAATCAAAT
Found at i:53679539 original size:30 final size:30
Alignment explanation
Indices: 53679505--53679572 Score: 136
Period size: 30 Copynumber: 2.3 Consensus size: 30
53679495 TTTCAGAGTC
53679505 ACAAAATCTTAAACATATCTAAAACCTATA
1 ACAAAATCTTAAACATATCTAAAACCTATA
53679535 ACAAAATCTTAAACATATCTAAAACCTATA
1 ACAAAATCTTAAACATATCTAAAACCTATA
53679565 ACAAAATC
1 ACAAAATC
53679573 CAATCTTCGT
Statistics
Matches: 38, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
30 38 1.00
ACGTcount: A:0.54, C:0.21, G:0.00, T:0.25
Consensus pattern (30 bp):
ACAAAATCTTAAACATATCTAAAACCTATA
Found at i:53680226 original size:43 final size:43
Alignment explanation
Indices: 53680158--53680243 Score: 109
Period size: 43 Copynumber: 2.0 Consensus size: 43
53680148 TAACGAGCAC
** *
53680158 CATCACTTAAGCTCGTATGGAGAGCTTTGCTAATACACAGCTT
1 CATCACTTAAGCTCACATGGAGAGCTTCGCTAATACACAGCTT
* * * *
53680201 CATCACTTAAGCTCACGTGGGGAGCTTCGCTGATACATAGCTT
1 CATCACTTAAGCTCACATGGAGAGCTTCGCTAATACACAGCTT
53680244 GTCCTTAACT
Statistics
Matches: 36, Mismatches: 7, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
43 36 1.00
ACGTcount: A:0.26, C:0.24, G:0.21, T:0.29
Consensus pattern (43 bp):
CATCACTTAAGCTCACATGGAGAGCTTCGCTAATACACAGCTT
Found at i:53680336 original size:40 final size:40
Alignment explanation
Indices: 53680273--53680395 Score: 158
Period size: 40 Copynumber: 3.1 Consensus size: 40
53680263 GATTTGCTGG
*
53680273 TACACAACTTATCCATAAGCTCACAGAGGAACTTTGTTGA
1 TACAAAACTTATCCATAAGCTCACAGAGGAACTTTGTTGA
*
53680313 TACAAAAGTTATCCATAAGCTCACA-AGGGAACTTTGTTGA
1 TACAAAACTTATCCATAAGCTCACAGA-GGAACTTTGTTGA
* * * * * *
53680353 TACACAACTTATCCATAAACTCATAGGGGAGCTTTGCTGA
1 TACAAAACTTATCCATAAGCTCACAGAGGAACTTTGTTGA
53680393 TAC
1 TAC
53680396 GCAGCTTGAA
Statistics
Matches: 72, Mismatches: 9, Indels: 4
0.85 0.11 0.05
Matches are distributed among these distances:
39 1 0.01
40 71 0.99
ACGTcount: A:0.35, C:0.21, G:0.16, T:0.28
Consensus pattern (40 bp):
TACAAAACTTATCCATAAGCTCACAGAGGAACTTTGTTGA
Found at i:53683051 original size:20 final size:20
Alignment explanation
Indices: 53683026--53683075 Score: 59
Period size: 20 Copynumber: 2.5 Consensus size: 20
53683016 TTCCCAAGGG
53683026 AAAGAAAGGAAA-ATATAAAA
1 AAAGAAAGGAAAGATA-AAAA
*
53683046 AAAGAAAGCAAAGATAAAAA
1 AAAGAAAGGAAAGATAAAAA
*
53683066 ATA-AAAGGAA
1 AAAGAAAGGAA
53683076 GAAGAAAAGT
Statistics
Matches: 26, Mismatches: 3, Indels: 3
0.81 0.09 0.09
Matches are distributed among these distances:
19 6 0.23
20 17 0.65
21 3 0.12
ACGTcount: A:0.74, C:0.02, G:0.16, T:0.08
Consensus pattern (20 bp):
AAAGAAAGGAAAGATAAAAA
Found at i:53683064 original size:19 final size:20
Alignment explanation
Indices: 53683026--53683080 Score: 60
Period size: 19 Copynumber: 2.8 Consensus size: 20
53683016 TTCCCAAGGG
*
53683026 AAAGAAAGGAAAATATAAAA
1 AAAGAAAGGAAAAGATAAAA
*
53683046 AAAGAAA-GCAAAGATAAAA
1 AAAGAAAGGAAAAGATAAAA
53683065 AATA-AAAGGAAGAAGA
1 AA-AGAAAGGAA-AAGA
53683081 AAAGTGCGTC
Statistics
Matches: 29, Mismatches: 3, Indels: 5
0.78 0.08 0.14
Matches are distributed among these distances:
19 15 0.52
20 10 0.34
21 4 0.14
ACGTcount: A:0.73, C:0.02, G:0.18, T:0.07
Consensus pattern (20 bp):
AAAGAAAGGAAAAGATAAAA
Found at i:53694835 original size:31 final size:30
Alignment explanation
Indices: 53694794--53694853 Score: 93
Period size: 31 Copynumber: 2.0 Consensus size: 30
53694784 AAATGTACCA
*
53694794 AAATTATTATAGTTTATTGTCTTTTCAAAAG
1 AAATTATTATAGTTTATTGTATTTT-AAAAG
*
53694825 AAATTGTTATAGTTTATTGTATTTTAAAA
1 AAATTATTATAGTTTATTGTATTTTAAAA
53694854 TTTTATTTTA
Statistics
Matches: 27, Mismatches: 2, Indels: 1
0.90 0.07 0.03
Matches are distributed among these distances:
30 4 0.15
31 23 0.85
ACGTcount: A:0.37, C:0.03, G:0.10, T:0.50
Consensus pattern (30 bp):
AAATTATTATAGTTTATTGTATTTTAAAAG
Found at i:53696723 original size:22 final size:22
Alignment explanation
Indices: 53696695--53696737 Score: 86
Period size: 22 Copynumber: 2.0 Consensus size: 22
53696685 CCTGCACATC
53696695 ACAATTGGGTTATAATAGGCCT
1 ACAATTGGGTTATAATAGGCCT
53696717 ACAATTGGGTTATAATAGGCC
1 ACAATTGGGTTATAATAGGCC
53696738 CATCACCCTA
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 21 1.00
ACGTcount: A:0.33, C:0.14, G:0.23, T:0.30
Consensus pattern (22 bp):
ACAATTGGGTTATAATAGGCCT
Found at i:53699949 original size:20 final size:22
Alignment explanation
Indices: 53699924--53699976 Score: 74
Period size: 20 Copynumber: 2.5 Consensus size: 22
53699914 AAGTTACGTA
53699924 GGTATCGATACTACCTTT-A-T
1 GGTATCGATACTACCTTTAAGT
* *
53699944 GGTATCGATATTTCCTTTAAGT
1 GGTATCGATACTACCTTTAAGT
53699966 GGTATCGATAC
1 GGTATCGATAC
53699977 CATTTGGAAA
Statistics
Matches: 28, Mismatches: 3, Indels: 2
0.85 0.09 0.06
Matches are distributed among these distances:
20 16 0.57
21 1 0.04
22 11 0.39
ACGTcount: A:0.25, C:0.17, G:0.19, T:0.40
Consensus pattern (22 bp):
GGTATCGATACTACCTTTAAGT
Found at i:53700743 original size:10 final size:10
Alignment explanation
Indices: 53700725--53700756 Score: 55
Period size: 10 Copynumber: 3.2 Consensus size: 10
53700715 ATGTATTAAC
53700725 CACATATAAT
1 CACATATAAT
*
53700735 CACAAATAAT
1 CACATATAAT
53700745 CACATATAAT
1 CACATATAAT
53700755 CA
1 CA
53700757 TATTTAGTCA
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
10 20 1.00
ACGTcount: A:0.53, C:0.22, G:0.00, T:0.25
Consensus pattern (10 bp):
CACATATAAT
Found at i:53705229 original size:26 final size:27
Alignment explanation
Indices: 53705180--53705230 Score: 68
Period size: 26 Copynumber: 1.9 Consensus size: 27
53705170 GATTTTTTTA
* * *
53705180 AAATTTTTATAATTTTTTTGAAAATAT
1 AAATTTTGATAATTTTTATAAAAATAT
53705207 AAATTTTGA-AATTTTTATAAAAAT
1 AAATTTTGATAATTTTTATAAAAAT
53705231 TTTGAAAATT
Statistics
Matches: 21, Mismatches: 3, Indels: 1
0.84 0.12 0.04
Matches are distributed among these distances:
26 13 0.62
27 8 0.38
ACGTcount: A:0.45, C:0.00, G:0.04, T:0.51
Consensus pattern (27 bp):
AAATTTTGATAATTTTTATAAAAATAT
Found at i:53705436 original size:17 final size:17
Alignment explanation
Indices: 53705414--53705448 Score: 52
Period size: 17 Copynumber: 2.1 Consensus size: 17
53705404 TTATTCAAGT
53705414 TAACTCAAAAAATTGAA
1 TAACTCAAAAAATTGAA
* *
53705431 TAACTCGAATAATTGAA
1 TAACTCAAAAAATTGAA
53705448 T
1 T
53705449 TCGATTAACT
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
17 16 1.00
ACGTcount: A:0.51, C:0.11, G:0.09, T:0.29
Consensus pattern (17 bp):
TAACTCAAAAAATTGAA
Found at i:53707638 original size:31 final size:31
Alignment explanation
Indices: 53707594--53707656 Score: 78
Period size: 31 Copynumber: 2.0 Consensus size: 31
53707584 AGTTACAAGA
53707594 TGGTCACCTAACTATT-AATAATTT-TCTTTTT
1 TGGTCACCTAACTATTCAAT--TTTGTCTTTTT
53707625 TGGTCATCC-AACTATTCAATTTTGTCTTTTT
1 TGGTCA-CCTAACTATTCAATTTTGTCTTTTT
53707656 T
1 T
53707657 TTCAACAACT
Statistics
Matches: 29, Mismatches: 0, Indels: 6
0.83 0.00 0.17
Matches are distributed among these distances:
30 3 0.10
31 21 0.72
32 5 0.17
ACGTcount: A:0.22, C:0.17, G:0.08, T:0.52
Consensus pattern (31 bp):
TGGTCACCTAACTATTCAATTTTGTCTTTTT
Found at i:53713501 original size:23 final size:23
Alignment explanation
Indices: 53713457--53713501 Score: 56
Period size: 23 Copynumber: 2.0 Consensus size: 23
53713447 ACCGACAACA
**
53713457 CTCTCTCTCACCTTTAGTTTCAT
1 CTCTCTCTCACCTTTAAATTCAT
53713480 CTCTCCTCTC-CCTTTAAATTCA
1 CTCT-CTCTCACCTTTAAATTCA
53713502 GACATCAACA
Statistics
Matches: 19, Mismatches: 2, Indels: 2
0.83 0.09 0.09
Matches are distributed among these distances:
23 14 0.74
24 5 0.26
ACGTcount: A:0.16, C:0.38, G:0.02, T:0.44
Consensus pattern (23 bp):
CTCTCTCTCACCTTTAAATTCAT
Found at i:53721804 original size:25 final size:25
Alignment explanation
Indices: 53721776--53721834 Score: 68
Period size: 24 Copynumber: 2.4 Consensus size: 25
53721766 GGATGTTACA
53721776 TTCTCAGCTCG-TCAAAGCTTACTGT
1 TTCTCAGCTCGAT-AAAGCTTACTGT
* *
53721801 TTCT-AGTTCGATAGAGCTTACTGT
1 TTCTCAGCTCGATAAAGCTTACTGT
*
53721825 TTATCAGCTC
1 TTCTCAGCTC
53721835 AGGAGGAGCT
Statistics
Matches: 28, Mismatches: 4, Indels: 4
0.78 0.11 0.11
Matches are distributed among these distances:
24 19 0.68
25 9 0.32
ACGTcount: A:0.20, C:0.24, G:0.17, T:0.39
Consensus pattern (25 bp):
TTCTCAGCTCGATAAAGCTTACTGT
Found at i:53722905 original size:12 final size:12
Alignment explanation
Indices: 53722888--53722917 Score: 51
Period size: 12 Copynumber: 2.5 Consensus size: 12
53722878 TCAGAAAGTT
53722888 ACATGGGGTAGG
1 ACATGGGGTAGG
*
53722900 ACATGGGTTAGG
1 ACATGGGGTAGG
53722912 ACATGG
1 ACATGG
53722918 CCATGTGCTC
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
12 17 1.00
ACGTcount: A:0.27, C:0.10, G:0.43, T:0.20
Consensus pattern (12 bp):
ACATGGGGTAGG
Found at i:53743743 original size:31 final size:31
Alignment explanation
Indices: 53743705--53743779 Score: 141
Period size: 31 Copynumber: 2.4 Consensus size: 31
53743695 ATGGTTACTA
53743705 GGCCGAAGCCTTTTCATAAATCATATCACTG
1 GGCCGAAGCCTTTTCATAAATCATATCACTG
53743736 GGCCGAAGCCTTTTCATAAATCATATCACTG
1 GGCCGAAGCCTTTTCATAAATCATATCACTG
*
53743767 CGCCGAAGCCTTT
1 GGCCGAAGCCTTT
53743780 ACTGTAAACG
Statistics
Matches: 43, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
31 43 1.00
ACGTcount: A:0.27, C:0.28, G:0.17, T:0.28
Consensus pattern (31 bp):
GGCCGAAGCCTTTTCATAAATCATATCACTG
Found at i:53743850 original size:42 final size:42
Alignment explanation
Indices: 53743803--53743894 Score: 148
Period size: 42 Copynumber: 2.2 Consensus size: 42
53743793 TGGCCCTTAG
* ** *
53743803 GCCCATTTCAATATCACATGTAATGTCAATGGATGTATGCAA
1 GCCCATTTCAATATCACATGAAATACCAATGAATGTATGCAA
53743845 GCCCATTTCAATATCACATGAAATACCAATGAATGTATGCAA
1 GCCCATTTCAATATCACATGAAATACCAATGAATGTATGCAA
53743887 GCCCATTT
1 GCCCATTT
53743895 GGGGAGACTA
Statistics
Matches: 46, Mismatches: 4, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
42 46 1.00
ACGTcount: A:0.35, C:0.22, G:0.14, T:0.29
Consensus pattern (42 bp):
GCCCATTTCAATATCACATGAAATACCAATGAATGTATGCAA
Found at i:53744067 original size:24 final size:26
Alignment explanation
Indices: 53744031--53744086 Score: 71
Period size: 25 Copynumber: 2.2 Consensus size: 26
53744021 GGAGGCCCAA
*
53744031 CCTTTTTTAAT-AACTGGGGCAAAG-
1 CCTTTTCTAATAAACTGGGGCAAAGC
* *
53744055 CCTTTTCTGATAAACTGGGGCAGAGC
1 CCTTTTCTAATAAACTGGGGCAAAGC
53744081 CCTTTT
1 CCTTTT
53744087 AGCACTTCCT
Statistics
Matches: 27, Mismatches: 3, Indels: 2
0.84 0.09 0.06
Matches are distributed among these distances:
24 9 0.33
25 12 0.44
26 6 0.22
ACGTcount: A:0.23, C:0.21, G:0.21, T:0.34
Consensus pattern (26 bp):
CCTTTTCTAATAAACTGGGGCAAAGC
Found at i:53745055 original size:27 final size:26
Alignment explanation
Indices: 53745007--53745062 Score: 69
Period size: 27 Copynumber: 2.1 Consensus size: 26
53744997 GTAAATCTAC
*
53745007 AAACCAATGGTATTTCAGTAATTTTGT
1 AAACCAATGGTATTCCAGTAATTTT-T
*
53745034 AAACTAATGGTATTCCTA-TAATTTTT
1 AAACCAATGGTATTCC-AGTAATTTTT
53745060 AAA
1 AAA
53745063 AAAGTCAAGG
Statistics
Matches: 26, Mismatches: 2, Indels: 3
0.84 0.06 0.10
Matches are distributed among these distances:
26 4 0.15
27 21 0.81
28 1 0.04
ACGTcount: A:0.38, C:0.11, G:0.11, T:0.41
Consensus pattern (26 bp):
AAACCAATGGTATTCCAGTAATTTTT
Found at i:53745111 original size:27 final size:26
Alignment explanation
Indices: 53745071--53745167 Score: 104
Period size: 27 Copynumber: 3.6 Consensus size: 26
53745061 AAAAAGTCAA
* *
53745071 GGGTATTTTTGTAATTTTGTAAATTAG
1 GGGTATTTTGGTAATTTT-CAAATTAG
*
53745098 GGGTATTTTGGTAATTTTACAAATTAA
1 GGGTATTTTGGTAATTTT-CAAATTAG
* **
53745125 GGGTATTTCGGTAATTTCTCAAACCAG
1 GGGTATTTTGGTAATTT-TCAAATTAG
*
53745152 TGGTATTTTGGTAATT
1 GGGTATTTTGGTAATT
53745168 CTATCCTACA
Statistics
Matches: 59, Mismatches: 10, Indels: 2
0.83 0.14 0.03
Matches are distributed among these distances:
27 58 0.98
28 1 0.02
ACGTcount: A:0.27, C:0.06, G:0.22, T:0.45
Consensus pattern (26 bp):
GGGTATTTTGGTAATTTTCAAATTAG
Found at i:53745282 original size:27 final size:27
Alignment explanation
Indices: 53745199--53745290 Score: 114
Period size: 27 Copynumber: 3.4 Consensus size: 27
53745189 GTAATTTCAC
53745199 AATCGAGGGTAAAACGGTAATTTTGTA
1 AATCGAGGGTAAAACGGTAATTTTGTA
* * *
53745226 AA-CTAAGGGTAAAATGGTAATTTTGCA
1 AATC-GAGGGTAAAACGGTAATTTTGTA
* * *
53745253 AATCGAGGGTAAAACGATAATTCTATA
1 AATCGAGGGTAAAACGGTAATTTTGTA
53745280 AATCGAGGGTA
1 AATCGAGGGTA
53745291 TTTCAATAAT
Statistics
Matches: 54, Mismatches: 9, Indels: 4
0.81 0.13 0.06
Matches are distributed among these distances:
26 1 0.02
27 52 0.96
28 1 0.02
ACGTcount: A:0.40, C:0.09, G:0.24, T:0.27
Consensus pattern (27 bp):
AATCGAGGGTAAAACGGTAATTTTGTA
Found at i:53747071 original size:94 final size:92
Alignment explanation
Indices: 53746902--53747124 Score: 265
Period size: 94 Copynumber: 2.4 Consensus size: 92
53746892 ATATTTGTGT
* * *
53746902 GCTAGTGTAAGACATGTTTGGGACATGCATCGGCCACATTATGAGAGCCCGTGTAAGACCATGTT
1 GCTAGTGTAAGACATGTTTGGGACATGCATTGGCCACATTATGAGAGCCAGTGTAAGACCATGTC
53746967 TGAGAAATGGCATCAGTA-TTGAGAC-GAGA
66 TGAGAAATGGCATC-G-ACTT-A-ACGGAGA
* *
53746996 GCTAGTGTAAGACATGTTTGGGACATGCATTGGCCTC-TTGATGTA-AGTCAGTGTAAGACCATG
1 GCTAGTGTAAGACATGTTTGGGACATGCATTGGCCACATT-ATG-AGAGCCAGTGTAAGACCATG
* *
53747059 TCTGGGACATGGCATCGACTTAACGTGAGA
64 TCTGAGAAATGGCATCGACTTAACG-GAGA
*
53747089 GCTAGTGTAAGACCATGTCTGGGACATGGCATTGGC
1 GCTAGTGTAAGA-CATGTTTGGGACAT-GCATTGGC
53747125 ATTATACCCT
Statistics
Matches: 114, Mismatches: 8, Indels: 13
0.84 0.06 0.10
Matches are distributed among these distances:
91 2 0.02
92 2 0.02
93 21 0.18
94 80 0.70
95 9 0.08
ACGTcount: A:0.27, C:0.17, G:0.30, T:0.26
Consensus pattern (92 bp):
GCTAGTGTAAGACATGTTTGGGACATGCATTGGCCACATTATGAGAGCCAGTGTAAGACCATGTC
TGAGAAATGGCATCGACTTAACGGAGA
Found at i:53755773 original size:20 final size:20
Alignment explanation
Indices: 53755748--53755794 Score: 76
Period size: 20 Copynumber: 2.4 Consensus size: 20
53755738 TGGTCCGCAA
* *
53755748 GCCCATTGGGCCCAGTTTTG
1 GCCCATCGGGCCCAATTTTG
53755768 GCCCATCGGGCCCAATTTTG
1 GCCCATCGGGCCCAATTTTG
53755788 GCCCATC
1 GCCCATC
53755795 TGACCCCTTT
Statistics
Matches: 25, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
20 25 1.00
ACGTcount: A:0.13, C:0.36, G:0.26, T:0.26
Consensus pattern (20 bp):
GCCCATCGGGCCCAATTTTG
Found at i:53755806 original size:20 final size:20
Alignment explanation
Indices: 53755748--53755800 Score: 61
Period size: 20 Copynumber: 2.6 Consensus size: 20
53755738 TGGTCCGCAA
* * *
53755748 GCCCATTGGGCCCAGTTTTG
1 GCCCATCGGACCCAATTTTG
*
53755768 GCCCATCGGGCCCAATTTTG
1 GCCCATCGGACCCAATTTTG
*
53755788 GCCCATCTGACCC
1 GCCCATCGGACCC
53755801 CTTTTTCCGA
Statistics
Matches: 29, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
20 29 1.00
ACGTcount: A:0.13, C:0.38, G:0.25, T:0.25
Consensus pattern (20 bp):
GCCCATCGGACCCAATTTTG
Found at i:53775523 original size:40 final size:40
Alignment explanation
Indices: 53775479--53775743 Score: 360
Period size: 40 Copynumber: 6.7 Consensus size: 40
53775469 GCTCCTCGTT
* * * *
53775479 CAAATGCCTTTGGGACATAGCCCGG-TTATAGTAATTCGCA
1 CAAATGCCTTCGGGACTTAACCCGGATT-TAGTAACTCGCA
*
53775519 CAAATGCCTTCGGGACTTAACCCGGATTTAGTAACTTGCA
1 CAAATGCCTTCGGGACTTAACCCGGATTTAGTAACTCGCA
53775559 CAAATGCCTTCGGGACTTAACCCGGATTTAGTAACTCGCA
1 CAAATGCCTTCGGGACTTAACCCGGATTTAGTAACTCGCA
53775599 CAAATGCCTTCGGGACTTAACCCGGATTTAGTAACTCGCA
1 CAAATGCCTTCGGGACTTAACCCGGATTTAGTAACTCGCA
*
53775639 CAAATGCCTTCGGGACTTAACCTGGATTTAGTAACTCGCA
1 CAAATGCCTTCGGGACTTAACCCGGATTTAGTAACTCGCA
** * *
53775679 CAAATGCCTTC-GGATCTTAGTCCGGATATT-GTCACTTAGCA
1 CAAATGCCTTCGGGA-CTTAACCCGGAT-TTAGTAAC-TCGCA
*
53775720 C-AA-GCCTTCGGGACTTAGCCCGGA
1 CAAATGCCTTCGGGACTTAACCCGGA
53775744 CAGCATTCAA
Statistics
Matches: 207, Mismatches: 13, Indels: 11
0.90 0.06 0.05
Matches are distributed among these distances:
39 19 0.09
40 179 0.86
41 9 0.04
ACGTcount: A:0.26, C:0.26, G:0.21, T:0.26
Consensus pattern (40 bp):
CAAATGCCTTCGGGACTTAACCCGGATTTAGTAACTCGCA
Found at i:53777644 original size:40 final size:40
Alignment explanation
Indices: 53777585--53777729 Score: 193
Period size: 40 Copynumber: 3.6 Consensus size: 40
53777575 CATTTGAATG
* *
53777585 ATATCCGGGCTAAGTCCCGAAGGCATTTATGCTAG-TGATT
1 ATATCCGGGCTAAGACCCGAAGGCATTTATGCGAGTTGA-T
* *
53777625 TTATCCGGGCTAAGACCCGAAGGCATTTGTGCGAGTTGAT
1 ATATCCGGGCTAAGACCCGAAGGCATTTATGCGAGTTGAT
* * *
53777665 ATATCCGGGCTAAGACCCGAAGGCATTTGTGCGACTTGCT
1 ATATCCGGGCTAAGACCCGAAGGCATTTATGCGAGTTGAT
* *
53777705 ATACCCGGGTTAAGACCCGAAGGCA
1 ATATCCGGGCTAAGACCCGAAGGCA
53777730 ATTGTGCTTG
Statistics
Matches: 95, Mismatches: 9, Indels: 2
0.90 0.08 0.02
Matches are distributed among these distances:
40 92 0.97
41 3 0.03
ACGTcount: A:0.25, C:0.23, G:0.28, T:0.25
Consensus pattern (40 bp):
ATATCCGGGCTAAGACCCGAAGGCATTTATGCGAGTTGAT
Found at i:53777748 original size:80 final size:80
Alignment explanation
Indices: 53777585--53777756 Score: 204
Period size: 80 Copynumber: 2.2 Consensus size: 80
53777575 CATTTGAATG
* * * * *
53777585 ATATCCGGGCTAAGTCCCGAAGGCATTTATGCTAGTGATTTTATCCGGGCTAAGACCCGAAGGCA
1 ATATCCGGGCTAAGACCCGAAGGCATTTATGCGAGTGACTATACCCGGGCTAAGACCCGAAGGCA
* *
53777650 TTTGTGCGAGTTGAT
66 ATTGTGCGAGTGGAT
* * *
53777665 ATATCCGGGCTAAGACCCGAAGGCATTTGTGCGACTTG-CTATACCCGGGTTAAGACCCGAAGGC
1 ATATCCGGGCTAAGACCCGAAGGCATTTATGCGA-GTGACTATACCCGGGCTAAGACCCGAAGGC
** *
53777729 AATTGTGCTTGTGGTT
65 AATTGTGCGAGTGGAT
53777745 ATATCC-GGCTAA
1 ATATCCGGGCTAA
53777757 ATTCCGAAGA
Statistics
Matches: 78, Mismatches: 13, Indels: 3
0.83 0.14 0.03
Matches are distributed among these distances:
79 6 0.08
80 70 0.90
81 2 0.03
ACGTcount: A:0.24, C:0.22, G:0.27, T:0.27
Consensus pattern (80 bp):
ATATCCGGGCTAAGACCCGAAGGCATTTATGCGAGTGACTATACCCGGGCTAAGACCCGAAGGCA
ATTGTGCGAGTGGAT
Found at i:53781855 original size:46 final size:46
Alignment explanation
Indices: 53781786--53781954 Score: 166
Period size: 46 Copynumber: 3.7 Consensus size: 46
53781776 TGTAACCCGC
* *
53781786 CCATAAGCGAACTCGGACACAACTCAACGAGATCGGGCGTTCGCAT
1 CCATAAGTGAACTCGGACTCAACTCAACGAGATCGGGCGTTCGCAT
* * *
53781832 CCATAAGTAAACTCGGACTCAACTCAACGAGCTCGGATGCCTAGTT-ACAT
1 CCATAAGTGAACTCGGACTCAACTCAACGAGATCGG--G-C--GTTCGCAT
* * * * *
53781882 -C-TCA-CGAACTCGGACTCAACTCAACGAGTTCGGACGCTCGCAT
1 CCATAAGTGAACTCGGACTCAACTCAACGAGATCGGGCGTTCGCAT
*
53781925 CCATAAGTGAACTCTGACTCAACTCAACGA
1 CCATAAGTGAACTCGGACTCAACTCAACGA
53781955 ATTCGGATGC
Statistics
Matches: 99, Mismatches: 15, Indels: 18
0.75 0.11 0.14
Matches are distributed among these distances:
42 2 0.02
43 3 0.03
44 2 0.02
45 2 0.02
46 53 0.54
47 26 0.26
48 3 0.03
49 2 0.02
50 3 0.03
51 3 0.03
ACGTcount: A:0.31, C:0.31, G:0.20, T:0.19
Consensus pattern (46 bp):
CCATAAGTGAACTCGGACTCAACTCAACGAGATCGGGCGTTCGCAT
Found at i:53781907 original size:93 final size:93
Alignment explanation
Indices: 53781793--53781965 Score: 274
Period size: 93 Copynumber: 1.9 Consensus size: 93
53781783 CGCCCATAAG
* *
53781793 CGAACTCGGACACAACTCAACGAGATCGGGCGTTCGCATCCATAAGTAAACTCGGACTCAACTCA
1 CGAACTCGGACACAACTCAACGAGATCGGACGCTCGCATCCATAAGTAAACTCGGACTCAACTCA
*
53781858 ACGAGCTCGGATGCCTAGTTACATCTCA
66 ACGAACTCGGATGCCTAGTTACATCTCA
* * * *
53781886 CGAACTCGGACTCAACTCAACGAGTTCGGACGCTCGCATCCATAAGTGAACTCTGACTCAACTCA
1 CGAACTCGGACACAACTCAACGAGATCGGACGCTCGCATCCATAAGTAAACTCGGACTCAACTCA
*
53781951 ACGAATTCGGATGCC
66 ACGAACTCGGATGCC
53781966 CAAATATCCC
Statistics
Matches: 72, Mismatches: 8, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
93 72 1.00
ACGTcount: A:0.29, C:0.31, G:0.20, T:0.20
Consensus pattern (93 bp):
CGAACTCGGACACAACTCAACGAGATCGGACGCTCGCATCCATAAGTAAACTCGGACTCAACTCA
ACGAACTCGGATGCCTAGTTACATCTCA
Found at i:53785131 original size:50 final size:50
Alignment explanation
Indices: 53785056--53785281 Score: 217
Period size: 50 Copynumber: 4.5 Consensus size: 50
53785046 TGAATACACG
* * *
53785056 TGTGTAGTACTAAGTGCAGGCTACTACGTGTACCATACTGTTAAGTCGCA
1 TGTGTAGTACTAAGTGTAGGCTACTACGTGTACCAGACTGTTAAGTCACA
* ** ** *
53785106 TGTGTAGTACTAAGTGTAGGCTACTATGCATACTCAATGACT-TCGA-TCACG
1 TGTGTAGTACTAAGTGTAGGCTACTACGTGTAC-C-A-GACTGTTAAGTCACA
* * * * *
53785157 TGTGTAGTACTAAGTGCAGGCTACTACGTGTATCAGA-TGGTGAGGTCACG
1 TGTGTAGTACTAAGTGTAGGCTACTACGTGTACCAGACT-GTTAAGTCACA
* * * * *
53785207 TGTGTAGTACTAAGTGTAGGCTACTACATGTACCGGATTGTT-GGTCGCA
1 TGTGTAGTACTAAGTGTAGGCTACTACGTGTACCAGACTGTTAAGTCACA
53785256 TGTGTAGTACTAAGTGTAGGCTACTA
1 TGTGTAGTACTAAGTGTAGGCTACTA
53785282 TATCAAATAG
Statistics
Matches: 145, Mismatches: 24, Indels: 15
0.79 0.13 0.08
Matches are distributed among these distances:
47 1 0.01
48 2 0.01
49 33 0.23
50 70 0.48
51 33 0.23
52 3 0.02
53 3 0.02
ACGTcount: A:0.25, C:0.17, G:0.27, T:0.31
Consensus pattern (50 bp):
TGTGTAGTACTAAGTGTAGGCTACTACGTGTACCAGACTGTTAAGTCACA
Done.