Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Chr02 99090824
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: 99090824
ACGTcount: A:0.32, C:0.18, G:0.18, T:0.32
Warning! 317 characters in sequence are not A, C, G, or T
File 171 of 318
Found at i:53126642 original size:20 final size:20
Alignment explanation
Indices: 53126603--53126642 Score: 53
Period size: 20 Copynumber: 2.0 Consensus size: 20
53126593 AAATATTGAG
*
53126603 ATTTTATTTTCTAAGTATAA
1 ATTTTATTTTCTAAGAATAA
* *
53126623 ATTTTATTTTTTGAGAATAA
1 ATTTTATTTTCTAAGAATAA
53126643 CAAATCTACT
Statistics
Matches: 17, Mismatches: 3, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.35, C:0.03, G:0.07, T:0.55
Consensus pattern (20 bp):
ATTTTATTTTCTAAGAATAA
Found at i:53126877 original size:12 final size:12
Alignment explanation
Indices: 53126860--53126885 Score: 52
Period size: 12 Copynumber: 2.2 Consensus size: 12
53126850 ATTGCTATAA
53126860 ATATCACAAACT
1 ATATCACAAACT
53126872 ATATCACAAACT
1 ATATCACAAACT
53126884 AT
1 AT
53126886 CTCAATTTTT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 14 1.00
ACGTcount: A:0.50, C:0.23, G:0.00, T:0.27
Consensus pattern (12 bp):
ATATCACAAACT
Found at i:53132242 original size:17 final size:18
Alignment explanation
Indices: 53132222--53132262 Score: 50
Period size: 17 Copynumber: 2.3 Consensus size: 18
53132212 TATTATATAT
53132222 TTTTATATAA-CTATTAA-
1 TTTTA-ATAATCTATTAAC
*
53132239 TTTTAATAATTTATTAAC
1 TTTTAATAATCTATTAAC
53132257 TTTTAA
1 TTTTAA
53132263 CATTTATTAT
Statistics
Matches: 21, Mismatches: 1, Indels: 3
0.84 0.04 0.12
Matches are distributed among these distances:
16 4 0.19
17 11 0.52
18 6 0.29
ACGTcount: A:0.39, C:0.05, G:0.00, T:0.56
Consensus pattern (18 bp):
TTTTAATAATCTATTAAC
Found at i:53132267 original size:17 final size:17
Alignment explanation
Indices: 53132233--53132271 Score: 53
Period size: 17 Copynumber: 2.3 Consensus size: 17
53132223 TTTATATAAC
53132233 TATTAATTTTAATAATT
1 TATTAATTTTAATAATT
*
53132250 TATTAACTTTTAA-CATT
1 TATTAA-TTTTAATAATT
53132267 TATTA
1 TATTA
53132272 TACATATATA
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
17 14 0.70
18 6 0.30
ACGTcount: A:0.38, C:0.05, G:0.00, T:0.56
Consensus pattern (17 bp):
TATTAATTTTAATAATT
Found at i:53132601 original size:8 final size:8
Alignment explanation
Indices: 53132588--53132616 Score: 58
Period size: 8 Copynumber: 3.6 Consensus size: 8
53132578 TCGATCATTG
53132588 AATTTGAA
1 AATTTGAA
53132596 AATTTGAA
1 AATTTGAA
53132604 AATTTGAA
1 AATTTGAA
53132612 AATTT
1 AATTT
53132617 TTATTTGAAG
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
8 21 1.00
ACGTcount: A:0.48, C:0.00, G:0.10, T:0.41
Consensus pattern (8 bp):
AATTTGAA
Found at i:53137753 original size:39 final size:39
Alignment explanation
Indices: 53137695--53137838 Score: 182
Period size: 39 Copynumber: 3.7 Consensus size: 39
53137685 GATATTGATG
* * *
53137695 TATATCCGGACTTAGGGTCCGCAGGCTATGTGCTGGAAT
1 TATATCCGGACTTAAGGTCCGCAGGCTACGTGCTGGAAA
*
53137734 TATATCCGGACTTAAGGTCCGCAAGCTACGTGCTGGAAA
1 TATATCCGGACTTAAGGTCCGCAGGCTACGTGCTGGAAA
* * *
53137773 TATGTCCGGGCTTAAGGTCCGCAGGCTACGTGCTGAAAA
1 TATATCCGGACTTAAGGTCCGCAGGCTACGTGCTGGAAA
* * *
53137812 TATGTCCGGGC-TAAAGTCTCGCAGGCT
1 TATATCCGGACTTAAGGTC-CGCAGGCT
53137839 TCGAGTTGGT
Statistics
Matches: 95, Mismatches: 9, Indels: 2
0.90 0.08 0.02
Matches are distributed among these distances:
38 6 0.06
39 89 0.94
ACGTcount: A:0.23, C:0.23, G:0.29, T:0.25
Consensus pattern (39 bp):
TATATCCGGACTTAAGGTCCGCAGGCTACGTGCTGGAAA
Found at i:53138751 original size:2 final size:2
Alignment explanation
Indices: 53138744--53138775 Score: 64
Period size: 2 Copynumber: 16.0 Consensus size: 2
53138734 TTGGCGATGC
53138744 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
53138776 TATTGCGTAT
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 30 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:53139414 original size:21 final size:20
Alignment explanation
Indices: 53139388--53139436 Score: 66
Period size: 21 Copynumber: 2.5 Consensus size: 20
53139378 AAGGATGAAT
53139388 AAATAATAA-TAAATAAATAA
1 AAATAATAAGTAAATAAAT-A
53139408 CAAATAA-AAGTAAATAAATA
1 -AAATAATAAGTAAATAAATA
53139428 AAATAATAA
1 AAATAATAA
53139437 AAAAATGTGA
Statistics
Matches: 26, Mismatches: 0, Indels: 5
0.84 0.00 0.16
Matches are distributed among these distances:
19 6 0.23
20 5 0.19
21 15 0.58
ACGTcount: A:0.73, C:0.02, G:0.02, T:0.22
Consensus pattern (20 bp):
AAATAATAAGTAAATAAATA
Found at i:53140081 original size:3 final size:3
Alignment explanation
Indices: 53140073--53140126 Score: 108
Period size: 3 Copynumber: 18.0 Consensus size: 3
53140063 CTTTTCCCTC
53140073 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
53140121 TAT TAT
1 TAT TAT
53140127 ATATGTGTGA
Statistics
Matches: 51, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 51 1.00
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (3 bp):
TAT
Found at i:53142889 original size:2 final size:2
Alignment explanation
Indices: 53142882--53142920 Score: 53
Period size: 2 Copynumber: 19.5 Consensus size: 2
53142872 ATAAATACTA
*
53142882 AT AT AT AT AT AT AT AT AT AT AT A- AT AT AA AT AGT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A-T AT AT A
53142921 ATTTAATAAA
Statistics
Matches: 33, Mismatches: 2, Indels: 4
0.85 0.05 0.10
Matches are distributed among these distances:
1 1 0.03
2 30 0.91
3 2 0.06
ACGTcount: A:0.54, C:0.00, G:0.03, T:0.44
Consensus pattern (2 bp):
AT
Found at i:53143913 original size:310 final size:310
Alignment explanation
Indices: 53143349--53143928 Score: 729
Period size: 310 Copynumber: 1.9 Consensus size: 310
53143339 TGGAAATTAC
* * * *
53143349 GTATTTAAAATATAGATGTGTGCTTAAAAATAACATAAGATAAATAATGAAACGTATGATTTGAA
1 GTATTTAAAATACAAATGTGTGCTTAAAAATAACATAAAATAAATAATAAAACGTATGATTTGAA
* * * *
53143414 ACTAACTAATAATAACATGTGAAATATATACGATATTAAAATAAGAAAAATTAGATTTAATTGTG
66 ACTAAATAATAATAACATGTGAAATATATACGATATTAAAATAAGAAAAATTAGATTAAATTATA
* ** * * *
53143479 AGTAAAATGAAATTTAAACACAAAAATACATCACGCTAAGAATACTAAATGAATATAATTGTTTA
131 AGTAAAACGAAATCCAAACACAAAAATACATCACGCTAAGAATACTAAATAAATACAATTATTTA
* * * ** * * *
53143544 TGATGGTGTTATCATCAATCCTGAGTTCGTGTCGAGTTAATTTGTGATATCAACTCAATCAACAA
196 TCATGGTGCTATCATCAATCCTAAGTAAGTGTCGAGTTAACTTGTGACACCAACTCAATCAACAA
53143609 CATTATTAATGCTAGAAAGTTTATCACACATGTATGCATGTGGAACTCAT
261 CATTATTAATGCTAGAAAGTTTATCACACATGTATGCATGTGGAACTCAT
* * * * * *
53143659 GTATTTAAAATACAAATTTGTGTTTAAACATAGCGTAAAATAAATAATAAAATGTATGATTTGAA
1 GTATTTAAAATACAAATGTGTGCTTAAAAATAACATAAAATAAATAATAAAACGTATGATTTGAA
* *
53143724 ACTAATTAATAATAATAACATGTGAAATATGTATGATATTAAAATAA-AAAAA-T-GATTAAATT
66 ACT-A--AATAATAATAACATGTGAAATATATACGATATTAAAATAAGAAAAATTAGATTAAATT
* * * *
53143786 ATAAGTAAAACGAAATCCAAACA-AATGAATACATCA-GATTAAGACTACTAAATAAATACGATT
128 ATAAGTAAAACGAAATCCAAACACAA-AAATACATCACG-CTAAGAATACTAAATAAATACAATT
* * * *
53143849 ATTTATCTTGGTGCTGTCATCAATCCTAAGTAAGTGTTGAGTTAACTTGTGACACCATCTCAATC
191 ATTTATCATGGTGCTATCATCAATCCTAAGTAAGTGTCGAGTTAACTTGTGACACCAACTCAATC
*
53143914 AACAATATTATTAAT
256 AACAACATTATTAAT
53143929 ATATACAATT
Statistics
Matches: 226, Mismatches: 39, Indels: 10
0.82 0.14 0.04
Matches are distributed among these distances:
309 3 0.01
310 179 0.79
311 2 0.01
312 5 0.02
313 37 0.16
ACGTcount: A:0.44, C:0.11, G:0.13, T:0.32
Consensus pattern (310 bp):
GTATTTAAAATACAAATGTGTGCTTAAAAATAACATAAAATAAATAATAAAACGTATGATTTGAA
ACTAAATAATAATAACATGTGAAATATATACGATATTAAAATAAGAAAAATTAGATTAAATTATA
AGTAAAACGAAATCCAAACACAAAAATACATCACGCTAAGAATACTAAATAAATACAATTATTTA
TCATGGTGCTATCATCAATCCTAAGTAAGTGTCGAGTTAACTTGTGACACCAACTCAATCAACAA
CATTATTAATGCTAGAAAGTTTATCACACATGTATGCATGTGGAACTCAT
Found at i:53157345 original size:356 final size:357
Alignment explanation
Indices: 53156678--53157392 Score: 1166
Period size: 356 Copynumber: 2.0 Consensus size: 357
53156668 CACATCGAGA
* * *
53156678 TCGATCATCACTTTATTCGAGAAAAAGTCCTAGATAGTATACTGCATGTCAATTATGTCCCGTCC
1 TCGATCATCACTTCATTCGAGAAAAAGTCCCAGATAGTATACTACATGTCAATTATGTCCCGTCC
* ** *
53156743 TCAAAATAGATTGCTGATGTACTTACCAAACTCATTTCACCAAAACAATTTGAGTCATTTCGACA
66 TCAAAATAGATTGCTAATGTACTTAAAAAACCCATTTCACCAAAACAATTTGAGTCATTTCGACA
* *
53156808 AGCTCTTCAAGTGCTACCACCAACCACAGAATCTATAAAAGTTCAAACACTGACAAAACTAGAAG
131 AGCTCTTCAAGTACTACCACCAACCACAGAATCTATAAAAGTTCAAACACTGACAAAACCAGAAG
* *
53156873 AATGTTAGAATAACAGTTGTTACGGTTAATCTGATACTTCTATTAAGGAAAAATGTTAAGCAGTT
196 AATGTTAGAATAACAGTTGTTACAGTTAACCTGATACTTCTATTAAGGAAAAATGTTAAGCAGTT
53156938 AGAGATTGGTTAGACAATTCCTTTAAATATGTTCAGTGTTCATGCATTAAAAAATACAATTGATA
261 AGAGATTGGTTAGACAATTCCTTTAAATATGTTCAGTGTTCATGCATTAAAAAATACAATTGATA
53157003 AATAAAGTTCTCTTGATGTTTGA-TTTATGCT
326 AATAAAGTTCTCTTGATGTTTGATTTTATGCT
* * * *
53157034 TCGATCGTCACTTCATTCGAGAAAAAGTCCCCGATGGTATACTACATGTCAATTATGTCTCGTCC
1 TCGATCATCACTTCATTCGAGAAAAAGTCCCAGATAGTATACTACATGTCAATTATGTCCCGTCC
** * *
53157099 TTGAAATAGATTGCTAATGTACTTAAAAAACCCATTTCACCAAAACAATTTGAGTTATTTTGACA
66 TCAAAATAGATTGCTAATGTACTTAAAAAACCCATTTCACCAAAACAATTTGAGTCATTTCGACA
* *
53157164 AGCTCTTCAAGTACTACCACCAACCACA-ACATCTATAAAAGTTGAAACACTGACAAAACCAGGA
131 AGCTCTTCAAGTACTACCACCAACCACAGA-ATCTATAAAAGTTCAAACACTGACAAAACCAGAA
* *
53157228 GAATGTTAGAATAACAGTTGTTACAGTTAACCT-ATTACTTCTGTTAAGGAAAATTGTTAAGCAG
195 GAATGTTAGAATAACAGTTGTTACAGTTAACCTGA-TACTTCTATTAAGGAAAAATGTTAAGCAG
53157292 TTAGAGATTGGTTAGACAATTCCTTTAAATATGTTCAGTGTTCATGCATTAAAAAATACAATTGA
259 TTAGAGATTGGTTAGACAATTCCTTTAAATATGTTCAGTGTTCATGCATTAAAAAATACAATTGA
* *
53157357 TAAATAAAGTTTTCTTGATTTTTGATTTTATGCT
324 TAAATAAAGTTCTCTTGATGTTTGATTTTATGCT
53157391 TC
1 TC
53157393 AGTGGTAACT
Statistics
Matches: 331, Mismatches: 25, Indels: 5
0.92 0.07 0.01
Matches are distributed among these distances:
355 2 0.01
356 319 0.96
357 10 0.03
ACGTcount: A:0.36, C:0.17, G:0.14, T:0.33
Consensus pattern (357 bp):
TCGATCATCACTTCATTCGAGAAAAAGTCCCAGATAGTATACTACATGTCAATTATGTCCCGTCC
TCAAAATAGATTGCTAATGTACTTAAAAAACCCATTTCACCAAAACAATTTGAGTCATTTCGACA
AGCTCTTCAAGTACTACCACCAACCACAGAATCTATAAAAGTTCAAACACTGACAAAACCAGAAG
AATGTTAGAATAACAGTTGTTACAGTTAACCTGATACTTCTATTAAGGAAAAATGTTAAGCAGTT
AGAGATTGGTTAGACAATTCCTTTAAATATGTTCAGTGTTCATGCATTAAAAAATACAATTGATA
AATAAAGTTCTCTTGATGTTTGATTTTATGCT
Found at i:53158512 original size:17 final size:17
Alignment explanation
Indices: 53158492--53158527 Score: 72
Period size: 17 Copynumber: 2.1 Consensus size: 17
53158482 TGTTTATTCA
53158492 TTCAAGTGGTTTTCACG
1 TTCAAGTGGTTTTCACG
53158509 TTCAAGTGGTTTTCACG
1 TTCAAGTGGTTTTCACG
53158526 TT
1 TT
53158528 TAACGCTTGC
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 19 1.00
ACGTcount: A:0.17, C:0.17, G:0.22, T:0.44
Consensus pattern (17 bp):
TTCAAGTGGTTTTCACG
Found at i:53164946 original size:3 final size:3
Alignment explanation
Indices: 53164938--53165093 Score: 75
Period size: 3 Copynumber: 52.3 Consensus size: 3
53164928 TCCCATTTCT
* * * * * *
53164938 TTA TTA TTA CTA TTA TCA TTA TTA TTTG TTGC TTA ATA -TA TTA TTG
1 TTA TTA TTA TTA TTA TTA TTA TTA -TTA TT-A TTA TTA TTA TTA TTA
* ** * * * *
53164984 TTA TTA TTT TTA TCC TCA TCA TTA TTA TTA TTA TTA TTA TTA ATA ATA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
* * * * * *
53165032 TTA TTA TTA TTA TT- TGA -TA CTA TCA TTA CTA TTA TTA TTC TAA TTA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
** *
53165078 CCA TTA TTA CTA TTA T
1 TTA TTA TTA TTA TTA T
53165094 ATATATACAT
Statistics
Matches: 113, Mismatches: 35, Indels: 10
0.72 0.22 0.06
Matches are distributed among these distances:
2 4 0.04
3 105 0.93
4 4 0.04
ACGTcount: A:0.31, C:0.09, G:0.03, T:0.57
Consensus pattern (3 bp):
TTA
Found at i:53165155 original size:87 final size:86
Alignment explanation
Indices: 53165056--53165254 Score: 278
Period size: 87 Copynumber: 2.3 Consensus size: 86
53165046 TGATACTATC
* * *
53165056 ATTACTATTATTATTCTAATTACCA-TT-ATTACTATTATATATATACATACCTTTTATTATTAT
1 ATTACCATTATTATT-T--TTACCACTTAATGACTATTATATATATACATACCTTTTACTATTAT
53165119 TCATGTACATATATTTTAAATATT
63 TCATGTACATATATTTTAAATATT
* **
53165143 ATTACCATTATTATTTTTATCACTTACATGGTTATTATATATATACATACCTTTTACTATTATTC
1 ATTACCATTATTATTTTTACCACTTA-ATGACTATTATATATATACATACCTTTTACTATTATTC
53165208 ATGTACATATATTTTAAATATT
65 ATGTACATATATTTTAAATATT
*
53165230 ATTACCATTATTA-TTTTATCACTTA
1 ATTACCATTATTATTTTTACCACTTA
53165255 CATGGTTATT
Statistics
Matches: 103, Mismatches: 6, Indels: 7
0.89 0.05 0.06
Matches are distributed among these distances:
84 5 0.05
85 2 0.02
86 13 0.13
87 83 0.81
ACGTcount: A:0.34, C:0.13, G:0.02, T:0.51
Consensus pattern (86 bp):
ATTACCATTATTATTTTTACCACTTAATGACTATTATATATATACATACCTTTTACTATTATTCA
TGTACATATATTTTAAATATT
Found at i:53165306 original size:87 final size:85
Alignment explanation
Indices: 53165088--53165266 Score: 288
Period size: 87 Copynumber: 2.1 Consensus size: 85
53165078 CCATTATTAC
* *
53165088 TATTATATATATACATACCTTTTATTATTATTCATGTACATATATTTTAAATATTATTACCATTA
1 TATTATATATATACATA-C-TATACTATTATTCATGTACATATATTTTAAATATTATTACCATTA
53165153 TTATTTTTATCACTTACATGGT
64 TTATTTTTATCACTTACATGGT
*
53165175 TATTATATATATACATACCTTTTACTATTATTCATGTACATATATTTTAAATATTATTACCATTA
1 TATTATATATATACATA-C-TATACTATTATTCATGTACATATATTTTAAATATTATTACCATTA
53165240 TTA-TTTTATCACTTACATGGT
64 TTATTTTTATCACTTACATGGT
53165261 TATTAT
1 TATTAT
53165267 TATTCTATTA
Statistics
Matches: 91, Mismatches: 1, Indels: 1
0.98 0.01 0.01
Matches are distributed among these distances:
86 24 0.26
87 67 0.74
ACGTcount: A:0.34, C:0.12, G:0.03, T:0.51
Consensus pattern (85 bp):
TATTATATATATACATACTATACTATTATTCATGTACATATATTTTAAATATTATTACCATTATT
ATTTTTATCACTTACATGGT
Found at i:53166580 original size:19 final size:19
Alignment explanation
Indices: 53166556--53166594 Score: 78
Period size: 19 Copynumber: 2.1 Consensus size: 19
53166546 CGTTCTTTTG
53166556 AGCAAATTTTTTCTCCAAC
1 AGCAAATTTTTTCTCCAAC
53166575 AGCAAATTTTTTCTCCAAC
1 AGCAAATTTTTTCTCCAAC
53166594 A
1 A
53166595 ATCTCTTAAA
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 20 1.00
ACGTcount: A:0.33, C:0.26, G:0.05, T:0.36
Consensus pattern (19 bp):
AGCAAATTTTTTCTCCAAC
Found at i:53170967 original size:26 final size:26
Alignment explanation
Indices: 53170936--53171043 Score: 189
Period size: 26 Copynumber: 4.2 Consensus size: 26
53170926 TGAAATGCCC
*
53170936 ATCATGGAACATTTACCTAAACCATT
1 ATCATGGAACATTTACCTAACCCATT
53170962 ATCATGGAACATTTACCTAACCCATT
1 ATCATGGAACATTTACCTAACCCATT
* *
53170988 ATCATGGAATATTTACCTAATCCATT
1 ATCATGGAACATTTACCTAACCCATT
53171014 ATCATGGAACATTTACCTAACCCATT
1 ATCATGGAACATTTACCTAACCCATT
53171040 ATCA
1 ATCA
53171044 ATTTGTACCA
Statistics
Matches: 77, Mismatches: 5, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
26 77 1.00
ACGTcount: A:0.36, C:0.24, G:0.07, T:0.32
Consensus pattern (26 bp):
ATCATGGAACATTTACCTAACCCATT
Found at i:53182661 original size:28 final size:28
Alignment explanation
Indices: 53182625--53182679 Score: 92
Period size: 28 Copynumber: 2.0 Consensus size: 28
53182615 AAGGGTAAGG
*
53182625 CTTCGATCAGGAAAAAGAACAAAATTTT
1 CTTCAATCAGGAAAAAGAACAAAATTTT
*
53182653 CTTCAATCAGGAAAAGGAACAAAATTT
1 CTTCAATCAGGAAAAAGAACAAAATTT
53182680 GCAAACATGA
Statistics
Matches: 25, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
28 25 1.00
ACGTcount: A:0.47, C:0.15, G:0.15, T:0.24
Consensus pattern (28 bp):
CTTCAATCAGGAAAAAGAACAAAATTTT
Found at i:53188983 original size:21 final size:21
Alignment explanation
Indices: 53188957--53188997 Score: 82
Period size: 21 Copynumber: 2.0 Consensus size: 21
53188947 CATATCAAAC
53188957 ACCGATTAAGTGACTAAATTA
1 ACCGATTAAGTGACTAAATTA
53188978 ACCGATTAAGTGACTAAATT
1 ACCGATTAAGTGACTAAATT
53188998 TACAAATTCG
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 20 1.00
ACGTcount: A:0.41, C:0.15, G:0.15, T:0.29
Consensus pattern (21 bp):
ACCGATTAAGTGACTAAATTA
Found at i:53189799 original size:25 final size:25
Alignment explanation
Indices: 53189765--53189812 Score: 62
Period size: 25 Copynumber: 1.9 Consensus size: 25
53189755 ATTGCCAAAG
53189765 CAACAATATTCTAT-TCATAATTAAA
1 CAACAATATT-TATATCATAATTAAA
* *
53189790 CAACACTATTTATATGATAATTA
1 CAACAATATTTATATCATAATTA
53189813 TCAATAAAAT
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
24 3 0.15
25 17 0.85
ACGTcount: A:0.46, C:0.15, G:0.02, T:0.38
Consensus pattern (25 bp):
CAACAATATTTATATCATAATTAAA
Found at i:53194332 original size:27 final size:27
Alignment explanation
Indices: 53194292--53194579 Score: 330
Period size: 27 Copynumber: 10.8 Consensus size: 27
53194282 GCGTACCTGA
*
53194292 ACCCTTATGTGATAAAATGACAATTTT
1 ACCCTTATGTGATAAAATGACGATTTT
* *
53194319 ATCCTTATGTGATAAAATGACGATATT
1 ACCCTTATGTGATAAAATGACGATTTT
* *
53194346 GCCCTTATGTGAT-AAATGATGATTTT
1 ACCCTTATGTGATAAAATGACGATTTT
* *
53194372 ACCTTTATGTGATAAAATGACAATTTT
1 ACCCTTATGTGATAAAATGACGATTTT
* * * * *
53194399 GCCCTCATATGATAAATTGACAATTTT
1 ACCCTTATGTGATAAAATGACGATTTT
* *
53194426 ACCTTTATGTGATAAAATGACGATATT
1 ACCCTTATGTGATAAAATGACGATTTT
* *
53194453 GCCCTTTTGTGATAAAATGACGATTTT
1 ACCCTTATGTGATAAAATGACGATTTT
* * *
53194480 AGCCTAATATGAT-AAATGACGATTTT
1 ACCCTTATGTGATAAAATGACGATTTT
* **
53194506 GCCCAAATGTGATAAAATGACGATTTT
1 ACCCTTATGTGATAAAATGACGATTTT
* *
53194533 -GCCTTATGTGATAAAATGATGATTTT
1 ACCCTTATGTGATAAAATGACGATTTT
*
53194559 TCCCTTATGTGATAAAATGAC
1 ACCCTTATGTGATAAAATGAC
53194580 CGAAATACCC
Statistics
Matches: 216, Mismatches: 42, Indels: 6
0.82 0.16 0.02
Matches are distributed among these distances:
26 66 0.31
27 150 0.69
ACGTcount: A:0.34, C:0.13, G:0.15, T:0.38
Consensus pattern (27 bp):
ACCCTTATGTGATAAAATGACGATTTT
Found at i:53194380 original size:53 final size:53
Alignment explanation
Indices: 53194293--53194579 Score: 371
Period size: 53 Copynumber: 5.4 Consensus size: 53
53194283 CGTACCTGAA
* *
53194293 CCCTTATGTGATAAAATGACAATTTTATCCTTATGTGATAAAATGACGATATTG
1 CCCTTATGTGATAAAATGACGATTTTA-CCTTATGTGATAAAATGACGATTTTG
* *
53194347 CCCTTATGTGAT-AAATGATGATTTTACCTTTATGTGATAAAATGACAATTTTG
1 CCCTTATGTGATAAAATGACGATTTTACC-TTATGTGATAAAATGACGATTTTG
* * * * *
53194400 CCCTCATATGATAAATTGACAATTTTACCTTTATGTGATAAAATGACGATATTG
1 CCCTTATGTGATAAAATGACGATTTTACC-TTATGTGATAAAATGACGATTTTG
* * *
53194454 CCCTTTTGTGATAAAATGACGATTTTAGCCTAATATGAT-AAATGACGATTTTG
1 CCCTTATGTGATAAAATGACGATTTTA-CCTTATGTGATAAAATGACGATTTTG
** * * *
53194507 CCCAAATGTGATAAAATGACGATTTTGCCTTATGTGATAAAATGATGATTTTT
1 CCCTTATGTGATAAAATGACGATTTTACCTTATGTGATAAAATGACGATTTTG
53194560 CCCTTATGTGATAAAATGAC
1 CCCTTATGTGATAAAATGAC
53194580 CGAAATACCC
Statistics
Matches: 200, Mismatches: 29, Indels: 9
0.84 0.12 0.04
Matches are distributed among these distances:
52 11 0.05
53 110 0.55
54 77 0.38
55 2 0.01
ACGTcount: A:0.34, C:0.13, G:0.15, T:0.38
Consensus pattern (53 bp):
CCCTTATGTGATAAAATGACGATTTTACCTTATGTGATAAAATGACGATTTTG
Found at i:53194497 original size:107 final size:107
Alignment explanation
Indices: 53194301--53194579 Score: 384
Period size: 107 Copynumber: 2.6 Consensus size: 107
53194291 AACCCTTATG
53194301 TGATAAAATGACAATTTTATCCTTATGTGATAAAATGACGATATTGCCCTTATGTGAT-AAATGA
1 TGATAAAATGACAATTTTA-CCTTATGTGATAAAATGACGATATTGCCCTTATGTGATAAAATGA
* * * **
53194365 TGATTTTACCTTTATGTGATAAAATGACAATTTTGCCCTCATA
65 CGATTTTACCTTAATATGATAAAATGACAATTTTGCCCAAATA
* *
53194408 TGATAAATTGACAATTTTACCTTTATGTGATAAAATGACGATATTGCCCTTTTGTGATAAAATGA
1 TGATAAAATGACAATTTTACC-TTATGTGATAAAATGACGATATTGCCCTTATGTGATAAAATGA
* *
53194473 CGATTTTAGCC-TAATATGAT-AAATGACGATTTTGCCCAAATG
65 CGATTTTA-CCTTAATATGATAAAATGACAATTTTGCCCAAATA
* * * * *
53194515 TGATAAAATGACGATTTTGCCTTATGTGATAAAATGATGATTTTTCCCTTATGTGATAAAATGAC
1 TGATAAAATGACAATTTTACCTTATGTGATAAAATGACGATATTGCCCTTATGTGATAAAATGAC
53194580 CGAAATACCC
Statistics
Matches: 153, Mismatches: 16, Indels: 7
0.87 0.09 0.04
Matches are distributed among these distances:
106 42 0.27
107 89 0.58
108 20 0.13
109 2 0.01
ACGTcount: A:0.34, C:0.13, G:0.15, T:0.38
Consensus pattern (107 bp):
TGATAAAATGACAATTTTACCTTATGTGATAAAATGACGATATTGCCCTTATGTGATAAAATGAC
GATTTTACCTTAATATGATAAAATGACAATTTTGCCCAAATA
Found at i:53194590 original size:27 final size:26
Alignment explanation
Indices: 53194560--53194660 Score: 80
Period size: 27 Copynumber: 3.7 Consensus size: 26
53194550 GATGATTTTT
53194560 CCCTTATGTGATAAAATGACCGAAATA
1 CCCTTATG-GATAAAATGACCGAAATA
* * * *
53194587 CCCTCATAGGGTAAGATGATCGAAATA
1 CCCTTAT-GGATAAAATGACCGAAATA
* *
53194614 CCCTCGTA-GGGTAGAATGACCGAAATA
1 CCCT--TATGGATAAAATGACCGAAATA
53194641 TCCCTGTATGG-TAAAATGAC
1 -CCCT-TATGGATAAAATGAC
53194661 TTTAATACCC
Statistics
Matches: 60, Mismatches: 9, Indels: 10
0.76 0.11 0.13
Matches are distributed among these distances:
27 52 0.87
28 7 0.12
29 1 0.02
ACGTcount: A:0.36, C:0.20, G:0.21, T:0.24
Consensus pattern (26 bp):
CCCTTATGGATAAAATGACCGAAATA
Found at i:53196431 original size:44 final size:44
Alignment explanation
Indices: 53196364--53196493 Score: 149
Period size: 43 Copynumber: 3.0 Consensus size: 44
53196354 CATAGGATTC
*
53196364 CGATATGTGATTT-CGTGTAAGACCATGTTTGGGACGTTGGCAT
1 CGATATGTGATTTACGTGTAAGACCATGTCTGGGACGTTGGCAT
* * * *
53196407 CGATTTGTGATTTACGTGTAAGACCCTGTCTGGGATAG-TGGCAA
1 CGATATGTGATTTACGTGTAAGACCATGTCTGGGA-CGTTGGCAT
* * * *
53196451 CAATATGTGA-TTACATGTAAGACCACGTCTAGGACGTTGGCAT
1 CGATATGTGATTTACGTGTAAGACCATGTCTGGGACGTTGGCAT
53196494 TGTACGAGCT
Statistics
Matches: 71, Mismatches: 13, Indels: 6
0.79 0.14 0.07
Matches are distributed among these distances:
42 1 0.01
43 37 0.52
44 32 0.45
45 1 0.01
ACGTcount: A:0.25, C:0.16, G:0.28, T:0.32
Consensus pattern (44 bp):
CGATATGTGATTTACGTGTAAGACCATGTCTGGGACGTTGGCAT
Found at i:53196492 original size:43 final size:43
Alignment explanation
Indices: 53196366--53196492 Score: 132
Period size: 44 Copynumber: 2.9 Consensus size: 43
53196356 TAGGATTCCG
* * * * *
53196366 ATATGTGATTTCGTGTAAGACCATGTTTGGGACGTTGGCATCG
1 ATATGTGATTACGTGTAAGACCACGTCTGGGACGTTGGCAACA
* *
53196409 ATTTGTGATTTACGTGTAAGACC-CTGTCTGGGATAG-TGGCAACA
1 ATATGTGA-TTACGTGTAAGACCAC-GTCTGGGA-CGTTGGCAACA
* *
53196453 ATATGTGATTACATGTAAGACCACGTCTAGGACGTTGGCA
1 ATATGTGATTACGTGTAAGACCACGTCTGGGACGTTGGCA
53196493 TTGTACGAGC
Statistics
Matches: 68, Mismatches: 11, Indels: 10
0.76 0.12 0.11
Matches are distributed among these distances:
42 1 0.01
43 32 0.47
44 34 0.50
45 1 0.01
ACGTcount: A:0.25, C:0.16, G:0.28, T:0.31
Consensus pattern (43 bp):
ATATGTGATTACGTGTAAGACCACGTCTGGGACGTTGGCAACA
Found at i:53198202 original size:22 final size:21
Alignment explanation
Indices: 53198173--53198235 Score: 76
Period size: 20 Copynumber: 3.0 Consensus size: 21
53198163 GTTACACGTA
53198173 TGTT-GCCTTTATGGCATAGTT
1 TGTTAGCCTTTATGGCATA-TT
*
53198194 TGTTAGCCTTTATGGCAT-TC
1 TGTTAGCCTTTATGGCATATT
* *
53198214 TGCTAGCCTTTTTGGCATATT
1 TGTTAGCCTTTATGGCATATT
53198235 T
1 T
53198236 TGTAAGTCAC
Statistics
Matches: 36, Mismatches: 4, Indels: 4
0.82 0.09 0.09
Matches are distributed among these distances:
20 17 0.47
21 6 0.17
22 13 0.36
ACGTcount: A:0.14, C:0.17, G:0.21, T:0.48
Consensus pattern (21 bp):
TGTTAGCCTTTATGGCATATT
Found at i:53200115 original size:20 final size:19
Alignment explanation
Indices: 53200072--53200120 Score: 62
Period size: 20 Copynumber: 2.5 Consensus size: 19
53200062 AAAGAACAAT
*
53200072 GTATCGATACCCTTGTAAA
1 GTATCGATACCCTAGTAAA
* *
53200091 GTATCAATACCCTGAGTAGA
1 GTATCGATACCCT-AGTAAA
53200111 GTATCGATAC
1 GTATCGATAC
53200121 TTTGATTGGG
Statistics
Matches: 25, Mismatches: 4, Indels: 1
0.83 0.13 0.03
Matches are distributed among these distances:
19 12 0.48
20 13 0.52
ACGTcount: A:0.33, C:0.20, G:0.18, T:0.29
Consensus pattern (19 bp):
GTATCGATACCCTAGTAAA
Found at i:53205345 original size:29 final size:29
Alignment explanation
Indices: 53205312--53205393 Score: 155
Period size: 29 Copynumber: 2.8 Consensus size: 29
53205302 TGACGAGATA
*
53205312 GGCACTAAGTGTGCGTGCTGGAAATATAT
1 GGCACTAAGTGTGCATGCTGGAAATATAT
53205341 GGCACTAAGTGTGCATGCTGGAAATATAT
1 GGCACTAAGTGTGCATGCTGGAAATATAT
53205370 GGCACTAAGTGTGCATGCTGGAAA
1 GGCACTAAGTGTGCATGCTGGAAA
53205394 AAAAAATAAT
Statistics
Matches: 52, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
29 52 1.00
ACGTcount: A:0.29, C:0.15, G:0.30, T:0.26
Consensus pattern (29 bp):
GGCACTAAGTGTGCATGCTGGAAATATAT
Found at i:53207999 original size:15 final size:15
Alignment explanation
Indices: 53207979--53208007 Score: 58
Period size: 15 Copynumber: 1.9 Consensus size: 15
53207969 GTAAATGATA
53207979 GTGATGGATGACTTT
1 GTGATGGATGACTTT
53207994 GTGATGGATGACTT
1 GTGATGGATGACTT
53208008 GATCACTATT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.21, C:0.07, G:0.34, T:0.38
Consensus pattern (15 bp):
GTGATGGATGACTTT
Found at i:53212247 original size:30 final size:30
Alignment explanation
Indices: 53212213--53212273 Score: 77
Period size: 30 Copynumber: 2.0 Consensus size: 30
53212203 TCCTTAACTC
53212213 AAACTTTGGAAAAATTACAATTTTGCCCCT
1 AAACTTTGGAAAAATTACAATTTTGCCCCT
* * * * *
53212243 AAACTTTTGCATATTTACACTTTTGCCCCT
1 AAACTTTGGAAAAATTACAATTTTGCCCCT
53212273 A
1 A
53212274 GGCTCGGGAA
Statistics
Matches: 26, Mismatches: 5, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
30 26 1.00
ACGTcount: A:0.31, C:0.23, G:0.08, T:0.38
Consensus pattern (30 bp):
AAACTTTGGAAAAATTACAATTTTGCCCCT
Found at i:53214662 original size:48 final size:48
Alignment explanation
Indices: 53214493--53214675 Score: 186
Period size: 48 Copynumber: 3.8 Consensus size: 48
53214483 CATAGTAGGG
* * * * * * *
53214493 TGCCAATGCTATATCCCAGATATGGTCTTATATAGGACCACTTATTGA
1 TGCCAATGCCATATCCCAGACATGGTCTTACATGGGATCACATATCGA
* * *
53214541 TGCCAATGCCATGTCCCAGACATGGTCTTACATGGGATCACATAACAA
1 TGCCAATGCCATATCCCAGACATGGTCTTACATGGGATCACATATCGA
* *
53214589 TGCCAATGCCATGTCTCAGACATGGTCTTACATGGGATCACATATCGA
1 TGCCAATGCCATATCCCAGACATGGTCTTACATGGGATCACATATCGA
* * * * * * * *
53214637 TGTCGATACAATATCCCAAATATGGTCTTATACGGGATC
1 TGCCAATGCCATATCCCAGACATGGTCTTACATGGGATC
53214676 TCATCAACCC
Statistics
Matches: 112, Mismatches: 23, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
48 112 1.00
ACGTcount: A:0.30, C:0.23, G:0.19, T:0.28
Consensus pattern (48 bp):
TGCCAATGCCATATCCCAGACATGGTCTTACATGGGATCACATATCGA
Found at i:53216749 original size:40 final size:40
Alignment explanation
Indices: 53216712--53216896 Score: 243
Period size: 40 Copynumber: 4.7 Consensus size: 40
53216702 GCTACTCGTT
*
53216712 CAAATGCCTTCGGGACATAGCCCGG-TTATAGTAACTCGCA
1 CAAATGCCTTCGGGACTTAGCCCGGATT-TAGTAACTCGCA
*
53216752 CAAATGCCTTCGGGACTTAACCCGGATTTAGTAACTCGCA
1 CAAATGCCTTCGGGACTTAGCCCGGATTTAGTAACTCGCA
* *
53216792 CAAATGCCTTC-GGACTTAACCCGGATTTAGTAACTCACA
1 CAAATGCCTTCGGGACTTAGCCCGGATTTAGTAACTCGCA
* * * *
53216831 CAAATGCCTTC-GGATCTTAGTCCGGATATAGTCACTTAGCA
1 CAAATGCCTTCGGGA-CTTAGCCCGGATTTAGTAAC-TCGCA
53216872 CAAA-GCCTTCGGGACTTAGCCCGGA
1 CAAATGCCTTCGGGACTTAGCCCGGA
53216897 CATCATTCGA
Statistics
Matches: 131, Mismatches: 10, Indels: 8
0.88 0.07 0.05
Matches are distributed among these distances:
39 41 0.31
40 78 0.60
41 12 0.09
ACGTcount: A:0.28, C:0.28, G:0.21, T:0.24
Consensus pattern (40 bp):
CAAATGCCTTCGGGACTTAGCCCGGATTTAGTAACTCGCA
Found at i:53216824 original size:79 final size:82
Alignment explanation
Indices: 53216712--53216896 Score: 247
Period size: 79 Copynumber: 2.3 Consensus size: 82
53216702 GCTACTCGTT
* *
53216712 CAAATGCCTTCGGGACATAGCCCGG-TTATAGTAACTCGCACAAATGCCTTCGGGA-CTTAACCC
1 CAAATGCCTTCGGGACTTAGCCCGGATTATAGTAACTCACACAAATGCCTTC-GGATCTTAACCC
* *
53216775 GGATTTAGTAAC-TCGCA
65 GGATATAGTAACTTAGCA
* **
53216792 CAAATGCCTTC-GGACTTAACCCGGATT-TAGTAACTCACACAAATGCCTTCGGATCTTAGTCCG
1 CAAATGCCTTCGGGACTTAGCCCGGATTATAGTAACTCACACAAATGCCTTCGGATCTTAACCCG
*
53216855 GATATAGTCACTTAGCA
66 GATATAGTAACTTAGCA
53216872 CAAA-GCCTTCGGGACTTAGCCCGGA
1 CAAATGCCTTCGGGACTTAGCCCGGA
53216897 CATCATTCGA
Statistics
Matches: 92, Mismatches: 9, Indels: 8
0.84 0.08 0.07
Matches are distributed among these distances:
78 3 0.03
79 55 0.60
80 34 0.37
ACGTcount: A:0.28, C:0.28, G:0.21, T:0.24
Consensus pattern (82 bp):
CAAATGCCTTCGGGACTTAGCCCGGATTATAGTAACTCACACAAATGCCTTCGGATCTTAACCCG
GATATAGTAACTTAGCA
Found at i:53219439 original size:60 final size:60
Alignment explanation
Indices: 53219345--53219558 Score: 178
Period size: 60 Copynumber: 3.6 Consensus size: 60
53219335 AGGTTTCCAG
* * * * * * *
53219345 AAAGGCTTACCTTTCCA-AGGTTTTGCCACGAAGGCATTCTTTTCATTCAGTAGTCGCCAT
1 AAAGGCTTTCCTATCCAGA-GTTTTTCCACAAAGGCATCCTTTACATTCAGTACTCGCCAT
* * * * ** * * *
53219405 AAAGGCTTTCCTGTCTAGAGTTTTTCCATAAAGGCATCCATTGGATTCATTACTCACCAC
1 AAAGGCTTTCCTATCCAGAGTTTTTCCACAAAGGCATCCTTTACATTCAGTACTCGCCAT
* * * *
53219465 AAAGGCTTTCCTATCCAGATTTTTTCCACAAATGCATCCTTTACATTCAGAACTCGCTAT
1 AAAGGCTTTCCTATCCAGAGTTTTTCCACAAAGGCATCCTTTACATTCAGTACTCGCCAT
* ** * * *
53219525 AAAGGCTCTATTGTCCAGATTTTTTCCGCAAAGG
1 AAAGGCTTTCCTATCCAGAGTTTTTCCACAAAGG
53219559 TGTCTTTTAC
Statistics
Matches: 120, Mismatches: 33, Indels: 2
0.77 0.21 0.01
Matches are distributed among these distances:
60 119 0.99
61 1 0.01
ACGTcount: A:0.26, C:0.25, G:0.15, T:0.34
Consensus pattern (60 bp):
AAAGGCTTTCCTATCCAGAGTTTTTCCACAAAGGCATCCTTTACATTCAGTACTCGCCAT
Found at i:53227729 original size:20 final size:20
Alignment explanation
Indices: 53227704--53227748 Score: 63
Period size: 20 Copynumber: 2.2 Consensus size: 20
53227694 AGGGACTAAA
* *
53227704 ATGAAAAGTTGTAAAATTTG
1 ATGAAAAATTCTAAAATTTG
*
53227724 ATGAAAAATTCTAAAATTTT
1 ATGAAAAATTCTAAAATTTG
53227744 ATGAA
1 ATGAA
53227749 TACATGTGTT
Statistics
Matches: 22, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
20 22 1.00
ACGTcount: A:0.49, C:0.02, G:0.13, T:0.36
Consensus pattern (20 bp):
ATGAAAAATTCTAAAATTTG
Found at i:53229668 original size:22 final size:21
Alignment explanation
Indices: 53229614--53229668 Score: 56
Period size: 21 Copynumber: 2.6 Consensus size: 21
53229604 ACGGCCTCCA
**
53229614 ACACGGGCGTGTCCCAGGGTC
1 ACACGGGCGTGTCCCAGGACC
* * *
53229635 AGACGGGTGTGTCCCTTGGACC
1 ACACGGGCGTGTCCC-AGGACC
53229657 ACACGGGCGTGT
1 ACACGGGCGTGT
53229669 GAGCCATGCA
Statistics
Matches: 26, Mismatches: 7, Indels: 1
0.76 0.21 0.03
Matches are distributed among these distances:
21 13 0.50
22 13 0.50
ACGTcount: A:0.15, C:0.29, G:0.38, T:0.18
Consensus pattern (21 bp):
ACACGGGCGTGTCCCAGGACC
Found at i:53230671 original size:22 final size:22
Alignment explanation
Indices: 53230645--53230698 Score: 72
Period size: 22 Copynumber: 2.5 Consensus size: 22
53230635 TAACTCTCTC
*
53230645 TTAACTTAGCAAGAGTATCATT
1 TTAACTTAACAAGAGTATCATT
* *
53230667 TTAACTTAACAAGAGTTTCCTT
1 TTAACTTAACAAGAGTATCATT
*
53230689 TAAACTTAAC
1 TTAACTTAAC
53230699 TCAAGTCTTT
Statistics
Matches: 28, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
22 28 1.00
ACGTcount: A:0.37, C:0.17, G:0.09, T:0.37
Consensus pattern (22 bp):
TTAACTTAACAAGAGTATCATT
Found at i:53235090 original size:2 final size:2
Alignment explanation
Indices: 53235074--53235107 Score: 52
Period size: 2 Copynumber: 17.5 Consensus size: 2
53235064 ATTTGAGTGT
*
53235074 TA TA T- TA TG TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
53235108 TTCCAATGTG
Statistics
Matches: 29, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
1 1 0.03
2 28 0.97
ACGTcount: A:0.44, C:0.00, G:0.03, T:0.53
Consensus pattern (2 bp):
TA
Found at i:53245989 original size:40 final size:40
Alignment explanation
Indices: 53245902--53246051 Score: 123
Period size: 40 Copynumber: 3.8 Consensus size: 40
53245892 AATTGAATGA
* * * **
53245902 TATCCGGGCTAAGCCCCGAAGACAATTATGCTG-GAAATTA-
1 TATCCGGGCTAAGACCCGAAGGCAATTGTGC-GAGTCA-TAC
* * *
53245942 TAACCGGGTTAAGACCCGAAGGCAATTGTGCTAGTGGC-TAC
1 TATCCGGGCTAAGACCCGAAGGCAATTGTGCGAGT--CATAC
*
53245983 -ATCCGGGCTAAGACCCGAAGGC-ATTCGTGCGAGTCATTC
1 TATCCGGGCTAAGACCCGAAGGCAATT-GTGCGAGTCATAC
*
53246022 TATCC-GGCTAAGACCCGAAGGCATTTGTGC
1 TATCCGGGCTAAGACCCGAAGGCAATTGTGC
53246052 AAATCGTGAT
Statistics
Matches: 89, Mismatches: 13, Indels: 17
0.75 0.11 0.14
Matches are distributed among these distances:
38 1 0.01
39 26 0.29
40 62 0.70
ACGTcount: A:0.27, C:0.25, G:0.27, T:0.22
Consensus pattern (40 bp):
TATCCGGGCTAAGACCCGAAGGCAATTGTGCGAGTCATAC
Found at i:53246065 original size:39 final size:38
Alignment explanation
Indices: 53245951--53246067 Score: 117
Period size: 39 Copynumber: 3.0 Consensus size: 38
53245941 ATAACCGGGT
* * * *
53245951 TAAGACCCGAAGGCAATTGTGCTAGTGGCTACATCCGGGC
1 TAAGACCCGAAGGCATTTGTGCAAGTCG-TATATCC-GGC
* * * *
53245991 TAAGACCCGAAGGCATTCGTGCGAGTCATTCTATCCGGC
1 TAAGACCCGAAGGCATTTGTGCAAGTC-GTATATCCGGC
*
53246030 TAAGACCCGAAGGCATTTGTGCAAATCGTGATATCCGG
1 TAAGACCCGAAGGCATTTGTGCAAGTCGT-ATATCCGG
53246068 GTTAAGTCCC
Statistics
Matches: 63, Mismatches: 12, Indels: 5
0.79 0.15 0.06
Matches are distributed among these distances:
38 1 0.02
39 34 0.54
40 28 0.44
ACGTcount: A:0.26, C:0.25, G:0.27, T:0.22
Consensus pattern (38 bp):
TAAGACCCGAAGGCATTTGTGCAAGTCGTATATCCGGC
Found at i:53254068 original size:40 final size:39
Alignment explanation
Indices: 53253906--53254086 Score: 129
Period size: 40 Copynumber: 4.6 Consensus size: 39
53253896 AAATTGAATG
* *
53253906 ATATCCGGGCTAAG-CCCGAAGACAATTATGCTGGAAAT--T
1 ATATCCGGGCTAAGACCCGAAGGC-ATT-TG-TGCAAATCGT
* * * * *
53253945 ATAACCGGGTTAAGACCCGAAGGCAATTGTGC-TATGGCT
1 ATATCCGGGCTAAGACCCGAAGGCATTTGTGCAAATCG-T
* * * * *
53253984 ACATCC-GGCTAAGACCCGAAGGCATTCGTGCGAGTCATT
1 ATATCCGGGCTAAGACCCGAAGGCATTTGTGCAAATC-GT
*
53254023 CTATCCGGGCTAAGACCCGAAGGCATTTGTGCAAATCGT
1 ATATCCGGGCTAAGACCCGAAGGCATTTGTGCAAATCGT
* * *
53254062 GATATCCGGGTTAAGTCCCGTAGGC
1 -ATATCCGGGCTAAGACCCGAAGGC
53254087 CTTGGTGCGG
Statistics
Matches: 109, Mismatches: 25, Indels: 15
0.73 0.17 0.10
Matches are distributed among these distances:
36 2 0.02
37 2 0.02
38 24 0.22
39 26 0.24
40 55 0.50
ACGTcount: A:0.27, C:0.24, G:0.27, T:0.23
Consensus pattern (39 bp):
ATATCCGGGCTAAGACCCGAAGGCATTTGTGCAAATCGT
Found at i:53262353 original size:29 final size:29
Alignment explanation
Indices: 53262320--53262393 Score: 139
Period size: 29 Copynumber: 2.6 Consensus size: 29
53262310 CCTTCGAGCT
53262320 CGCACACTTAGTGCCATATATTTCCAGCA
1 CGCACACTTAGTGCCATATATTTCCAGCA
*
53262349 TGCACACTTAGTGCCATATATTTCCAGCA
1 CGCACACTTAGTGCCATATATTTCCAGCA
53262378 CGCACACTTAGTGCCA
1 CGCACACTTAGTGCCA
53262394 ATCTCGTCAC
Statistics
Matches: 43, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
29 43 1.00
ACGTcount: A:0.27, C:0.31, G:0.15, T:0.27
Consensus pattern (29 bp):
CGCACACTTAGTGCCATATATTTCCAGCA
Found at i:53262354 original size:58 final size:58
Alignment explanation
Indices: 53262261--53262393 Score: 133
Period size: 58 Copynumber: 2.3 Consensus size: 58
53262251 ATACTCGATT
* * * * *
53262261 TCGCACACTTAGTGCCATGCGATTTAAGCCCGCACACACAGTGCCATGCCCTTCGAGC
1 TCGCACACTTAGTGCCATGAGATTTAAGCACGCACACACAGTGCCATACACTTCCAGC
* * * ** * *
53262319 TCGCACACTTAGTGCCAT-ATATTTCCAGCATGCACACTTAGTGCCATATATTTCCAGC
1 TCGCACACTTAGTGCCATGAGATTT-AAGCACGCACACACAGTGCCATACACTTCCAGC
*
53262377 ACGCACACTTAGTGCCA
1 TCGCACACTTAGTGCCA
53262394 ATCTCGTCAC
Statistics
Matches: 61, Mismatches: 13, Indels: 2
0.80 0.17 0.03
Matches are distributed among these distances:
57 4 0.07
58 57 0.93
ACGTcount: A:0.25, C:0.33, G:0.17, T:0.25
Consensus pattern (58 bp):
TCGCACACTTAGTGCCATGAGATTTAAGCACGCACACACAGTGCCATACACTTCCAGC
Found at i:53264039 original size:27 final size:28
Alignment explanation
Indices: 53263977--53264040 Score: 69
Period size: 27 Copynumber: 2.4 Consensus size: 28
53263967 CAGTCACTTG
*
53263977 CCCACAAGGGCAAAACAGTCATTTAACA
1 CCCACAAGGGCAAAACAGTAATTTAACA
* ** *
53264005 CCC-TAAGGGCAAAATGGTAATTTTAC-
1 CCCACAAGGGCAAAACAGTAATTTAACA
53264031 CCCACAAGGG
1 CCCACAAGGG
53264041 TATCTCGGTA
Statistics
Matches: 29, Mismatches: 6, Indels: 3
0.76 0.16 0.08
Matches are distributed among these distances:
26 3 0.10
27 23 0.79
28 3 0.10
ACGTcount: A:0.38, C:0.27, G:0.19, T:0.17
Consensus pattern (28 bp):
CCCACAAGGGCAAAACAGTAATTTAACA
Found at i:53264050 original size:27 final size:27
Alignment explanation
Indices: 53264020--53264825 Score: 823
Period size: 27 Copynumber: 29.9 Consensus size: 27
53264010 AGGGCAAAAT
* * *
53264020 GGTAATTTTACCCCACAAGGGTATCTC
1 GGTAATTCTACCCTACAAGGGTATTTC
* *
53264047 GGTAATCCTACCCTACAGGGGTATTTC
1 GGTAATTCTACCCTACAAGGGTATTTC
* *
53264074 AGTAATTCTACCTTACAAGGGTATTTC
1 GGTAATTCTACCCTACAAGGGTATTTC
53264101 GGTAATTCTACCCTAC-AGGGCTATTTC
1 GGTAATTCTACCCTACAAGGG-TATTTC
*
53264128 AGTAATTCTACCCTAC-AGGGATATTTC
1 GGTAATTCTACCCTACAAGGG-TATTTC
* *
53264155 AGTAATTCTACCCTACAGGGGTATTTC
1 GGTAATTCTACCCTACAAGGGTATTTC
* * * *
53264182 AGTAATTCTACCCTATAGGGGTATTTT
1 GGTAATTCTACCCTACAAGGGTATTTC
* * *
53264209 GGTATTTCTACCCTACAAGGGTATATA
1 GGTAATTCTACCCTACAAGGGTATTTC
* * * * * *
53264236 GATAATTCTAACATATAGGGGTATTTT
1 GGTAATTCTACCCTACAAGGGTATTTC
* *
53264263 AGTAATTCTACCCTACAGGGGTATTTC
1 GGTAATTCTACCCTACAAGGGTATTTC
* *
53264290 AGTAACTCTACCCTAC-AGGGTATTTC
1 GGTAATTCTACCCTACAAGGGTATTTC
53264316 GGTAATTCTACCCTACAAGGGTATTTC
1 GGTAATTCTACCCTACAAGGGTATTTC
* ** *
53264343 AGTAATTCTATTCTA-TAGGGTATTTC
1 GGTAATTCTACCCTACAAGGGTATTTC
*
53264369 GGTAATTCTACCCTACAGGGGTATTTC
1 GGTAATTCTACCCTACAAGGGTATTTC
* * *
53264396 GATAATTCTACCCTATAGGGGTATTTC
1 GGTAATTCTACCCTACAAGGGTATTTC
*
53264423 GGTAATTCTACCCTACAAGAGTA-TTC
1 GGTAATTCTACCCTACAAGGGTATTTC
* *
53264449 GGCAATTCTACCCTACAGGGGTATTTC
1 GGTAATTCTACCCTACAAGGGTATTTC
* * *** ****
53264476 GGTAATTTTACCCTATTCTACCCTACAGG
1 GGTAATTCTACCCTA--CAAGGGTATTTC
* **
53264505 GGTATTTCGGTAATTCTATCCTACAGGGGTATTTC
1 GGTAATTC--T-ACCCTA--C-A-AGGG-TATTTC
* * *
53264540 AGTAACTCTACCCTACAGGGGTATTTC
1 GGTAATTCTACCCTACAAGGGTATTTC
*
53264567 GATAATTCTACCCTACAAGGGTATTTC
1 GGTAATTCTACCCTACAAGGGTATTTC
**
53264594 GGTAATTCTATTCTACAAGGGTATTTC
1 GGTAATTCTACCCTACAAGGGTATTTC
53264621 GGTAATTCTACCCTACAAGGGTATTTC
1 GGTAATTCTACCCTACAAGGGTATTTC
*
53264648 GGTAATTCTACCCTACAGGGGTATTTC
1 GGTAATTCTACCCTACAAGGGTATTTC
53264675 GGTAATTCTACCCTACAAGGGTATTTC
1 GGTAATTCTACCCTACAAGGGTATTTC
* *
53264702 AGTAATTCTACCCTACAGGGGTATTTC
1 GGTAATTCTACCCTACAAGGGTATTTC
* **
53264729 AGTAATTCTACCCTTGAAGGGTATTTC
1 GGTAATTCTACCCTACAAGGGTATTTC
53264756 GGTAATTCTACCCTAC-A-GG------
1 GGTAATTCTACCCTACAAGGGTATTTC
53264775 GGT-ATTCTACCCTACAGA-GGTATTTC
1 GGTAATTCTACCCTACA-AGGGTATTTC
*
53264801 GGTAATTCTACCCTACAGGGGTATT
1 GGTAATTCTACCCTACAAGGGTATT
53264826 CTACCCTACA
Statistics
Matches: 648, Mismatches: 108, Indels: 46
0.81 0.13 0.06
Matches are distributed among these distances:
18 12 0.02
19 3 0.00
20 3 0.00
25 2 0.00
26 76 0.12
27 515 0.79
28 6 0.01
29 10 0.02
30 1 0.00
31 1 0.00
32 10 0.02
33 1 0.00
34 1 0.00
35 7 0.01
ACGTcount: A:0.26, C:0.21, G:0.19, T:0.34
Consensus pattern (27 bp):
GGTAATTCTACCCTACAAGGGTATTTC
Found at i:53264079 original size:54 final size:54
Alignment explanation
Indices: 53264021--53264905 Score: 1023
Period size: 54 Copynumber: 16.6 Consensus size: 54
53264011 GGGCAAAATG
* * * *
53264021 GTAATTTTACCCCACAAGGGTATCTCGGTAATCCTACCCTACAGGGGTATTTCA
1 GTAATTCTACCCTACAAGGGTATTTCGGTAATTCTACCCTACAGGGGTATTTCA
* *
53264075 GTAATTCTACCTTACAAGGGTATTTCGGTAATTCTACCCTACAGGGCTATTTCA
1 GTAATTCTACCCTACAAGGGTATTTCGGTAATTCTACCCTACAGGGGTATTTCA
*
53264129 GTAATTCTACCCTAC-AGGGATATTTCAGTAATTCTACCCTACAGGGGTATTTCA
1 GTAATTCTACCCTACAAGGG-TATTTCGGTAATTCTACCCTACAGGGGTATTTCA
* * * * * *
53264183 GTAATTCTACCCTATAGGGGTATTTTGGTATTTCTACCCTACAAGGGTATAT-A
1 GTAATTCTACCCTACAAGGGTATTTCGGTAATTCTACCCTACAGGGGTATTTCA
* * * * **
53264236 GATAATTCTAACATATAGGGGTATTTTAGTAATTCTACCCTACAGGGGTATTTCA
1 G-TAATTCTACCCTACAAGGGTATTTCGGTAATTCTACCCTACAGGGGTATTTCA
* *
53264291 GTAACTCTACCCTAC-AGGGTATTTCGGTAATTCTACCCTACAAGGGTATTTCA
1 GTAATTCTACCCTACAAGGGTATTTCGGTAATTCTACCCTACAGGGGTATTTCA
** *
53264344 GTAATTCTATTCTA-TAGGGTATTTCGGTAATTCTACCCTACAGGGGTATTTC-
1 GTAATTCTACCCTACAAGGGTATTTCGGTAATTCTACCCTACAGGGGTATTTCA
* * * * *
53264396 GATAATTCTACCCTATAGGGGTATTTCGGTAATTCTACCCTACAAGAGTA-TTCG
1 G-TAATTCTACCCTACAAGGGTATTTCGGTAATTCTACCCTACAGGGGTATTTCA
* * *
53264450 GCAATTCTACCCTACAGGGGTATTTCGGTAATTTTACCCTATTCTACCCTACAGGGGTATTTCG
1 GTAATTCTACCCTACAAGGGTATTTCGG------TA----ATTCTACCCTACAGGGGTATTTCA
* * * *
53264514 GTAATTCTATCCTACAGGGGTATTTCAGTAACTCTACCCTACAGGGGTATTTC-
1 GTAATTCTACCCTACAAGGGTATTTCGGTAATTCTACCCTACAGGGGTATTTCA
** * *
53264567 GATAATTCTACCCTACAAGGGTATTTCGGTAATTCTATTCTACAAGGGTATTTCG
1 G-TAATTCTACCCTACAAGGGTATTTCGGTAATTCTACCCTACAGGGGTATTTCA
*
53264622 GTAATTCTACCCTACAAGGGTATTTCGGTAATTCTACCCTACAGGGGTATTTCG
1 GTAATTCTACCCTACAAGGGTATTTCGGTAATTCTACCCTACAGGGGTATTTCA
*
53264676 GTAATTCTACCCTACAAGGGTATTTCAGTAATTCTACCCTACAGGGGTATTTCA
1 GTAATTCTACCCTACAAGGGTATTTCGGTAATTCTACCCTACAGGGGTATTTCA
**
53264730 GTAATTCTACCCTTGAAGGGTATTTCGGTAATTCTACCCTACA-GGG-------
1 GTAATTCTACCCTACAAGGGTATTTCGGTAATTCTACCCTACAGGGGTATTTCA
53264776 GT-ATTCTACCCTAC-AGAGGTATTTCGGTAATTCTACCCTACA-GGG-------
1 GTAATTCTACCCTACAAG-GGTATTTCGGTAATTCTACCCTACAGGGGTATTTCA
* *
53264821 GT-ATTCTACCCTAC-AGGGTATTTCGATAATTCTACCCTACAGGGGTATTTCG
1 GTAATTCTACCCTACAAGGGTATTTCGGTAATTCTACCCTACAGGGGTATTTCA
*
53264873 GTAATTCTACCCTACAAGGGTATTTTGGTAATT
1 GTAATTCTACCCTACAAGGGTATTTCGGTAATT
53264906 TTACAAACCA
Statistics
Matches: 731, Mismatches: 68, Indels: 64
0.85 0.08 0.07
Matches are distributed among these distances:
44 26 0.04
45 57 0.08
46 2 0.00
52 3 0.00
53 142 0.19
54 445 0.61
55 6 0.01
58 2 0.00
59 2 0.00
63 17 0.02
64 29 0.04
ACGTcount: A:0.26, C:0.21, G:0.19, T:0.34
Consensus pattern (54 bp):
GTAATTCTACCCTACAAGGGTATTTCGGTAATTCTACCCTACAGGGGTATTTCA
Found at i:53264144 original size:81 final size:80
Alignment explanation
Indices: 53264020--53264905 Score: 1018
Period size: 81 Copynumber: 11.1 Consensus size: 80
53264010 AGGGCAAAAT
* * * * *
53264020 GGTAATTTTACCCCACAAGGGTATCTCGGTAATCCTACCCTACAGGGGTATTTCAGTAATTCTAC
1 GGTAATTCTACCCTAC-AGGGTATTTCGGTAATTCTACCCTACAGGGGTATTTCGGTAATTCTAC
*
53264085 CTTACAAGGGTATTTC
65 CCTACAAGGGTATTTC
* * *
53264101 GGTAATTCTACCCTACAGGGCTATTTCAGTAATTCTACCCTACAGGGATATTTCAGTAATTCTAC
1 GGTAATTCTACCCTACAGGG-TATTTCGGTAATTCTACCCTACAGGGGTATTTCGGTAATTCTAC
*
53264166 CCTACAGGGGTATTTC
65 CCTACAAGGGTATTTC
* * * * * * * * *
53264182 AGTAATTCTACCCTATAGGGGTATTTTGGTATTTCTACCCTACAAGGGTATATAGATAATTCTAA
1 GGTAATTCTACCCTACA-GGGTATTTCGGTAATTCTACCCTACAGGGGTATTTCGGTAATTCTAC
* * * *
53264247 CATATAGGGGTATTTT
65 CCTACAAGGGTATTTC
* * *
53264263 AGTAATTCTACCCTACAGGGGTATTTCAGTAACTCTACCCTACA-GGGTATTTCGGTAATTCTAC
1 GGTAATTCTACCCTACA-GGGTATTTCGGTAATTCTACCCTACAGGGGTATTTCGGTAATTCTAC
53264327 CCTACAAGGGTATTTC
65 CCTACAAGGGTATTTC
* ** * *
53264343 AGTAATTCTATTCTATAGGGTATTTCGGTAATTCTACCCTACAGGGGTATTTCGATAATTCTACC
1 GGTAATTCTACCCTACAGGGTATTTCGGTAATTCTACCCTACAGGGGTATTTCGGTAATTCTACC
* *
53264408 CTATAGGGGTATTTC
66 CTACAAGGGTATTTC
* *
53264423 GGTAATTCTACCCTACAAGAGTA-TTCGGCAATTCTACCCTACAGGGGTATTTCGGTAATTTTAC
1 GGTAATTCTACCCTAC-AGGGTATTTCGGTAATTCTACCCTACAGGGGTATTTCGG------TA-
*
53264487 CCTATTCTACCCTACAGGGGTATTTC
58 ---ATTCTACCCTACAAGGGTATTTC
* * * *
53264513 GGTAATTCTATCCTACAGGGGTATTTCAGTAACTCTACCCTACAGGGGTATTTCGATAATTCTAC
1 GGTAATTCTACCCTACA-GGGTATTTCGGTAATTCTACCCTACAGGGGTATTTCGGTAATTCTAC
53264578 CCTACAAGGGTATTTC
65 CCTACAAGGGTATTTC
** *
53264594 GGTAATTCTATTCTACAAGGGTATTTCGGTAATTCTACCCTACAAGGGTATTTCGGTAATTCTAC
1 GGTAATTCTACCCTAC-AGGGTATTTCGGTAATTCTACCCTACAGGGGTATTTCGGTAATTCTAC
*
53264659 CCTACAGGGGTATTTC
65 CCTACAAGGGTATTTC
* *
53264675 GGTAATTCTACCCTACAAGGGTATTTCAGTAATTCTACCCTACAGGGGTATTTCAGTAATTCTAC
1 GGTAATTCTACCCTAC-AGGGTATTTCGGTAATTCTACCCTACAGGGGTATTTCGGTAATTCTAC
**
53264740 CCTTGAAGGGTATTTC
65 CCTACAAGGGTATTTC
*
53264756 GGTAATTCTACCCTACA-GG------GGT-ATTCTACCCTACAGAGGTATTTCGGTAATTCTACC
1 GGTAATTCTACCCTACAGGGTATTTCGGTAATTCTACCCTACAGGGGTATTTCGGTAATTCTACC
53264813 CTAC-A-GG------
66 CTACAAGGGTATTTC
*
53264820 GGT-ATTCTACCCTACAGGGTATTTCGATAATTCTACCCTACAGGGGTATTTCGGTAATTCTACC
1 GGTAATTCTACCCTACAGGGTATTTCGGTAATTCTACCCTACAGGGGTATTTCGGTAATTCTACC
*
53264884 CTACAAGGGTATTTT
66 CTACAAGGGTATTTC
53264899 GGTAATT
1 GGTAATT
53264906 TTACAAACCA
Statistics
Matches: 691, Mismatches: 80, Indels: 69
0.82 0.10 0.08
Matches are distributed among these distances:
63 13 0.02
64 5 0.01
70 4 0.01
71 39 0.06
72 36 0.05
73 4 0.01
79 29 0.04
80 125 0.18
81 358 0.52
82 4 0.01
85 2 0.00
86 2 0.00
89 1 0.00
90 41 0.06
91 28 0.04
ACGTcount: A:0.26, C:0.21, G:0.19, T:0.34
Consensus pattern (80 bp):
GGTAATTCTACCCTACAGGGTATTTCGGTAATTCTACCCTACAGGGGTATTTCGGTAATTCTACC
CTACAAGGGTATTTC
Found at i:53264797 original size:45 final size:44
Alignment explanation
Indices: 53264733--53264869 Score: 231
Period size: 45 Copynumber: 3.1 Consensus size: 44
53264723 TATTTCAGTA
53264733 ATTCTACCCTTGA-AGGGTATTTCGGTAATTCTACCCTACAGGGGT
1 ATTCTACCC-T-ACAGGGTATTTCGGTAATTCTACCCTACAGGGGT
53264778 ATTCTACCCTACAGAGGTATTTCGGTAATTCTACCCTACAGGGGT
1 ATTCTACCCTACAG-GGTATTTCGGTAATTCTACCCTACAGGGGT
*
53264823 ATTCTACCCTACAGGGTATTTCGATAATTCTACCCTACAGGGGT
1 ATTCTACCCTACAGGGTATTTCGGTAATTCTACCCTACAGGGGT
53264867 ATT
1 ATT
53264870 TCGGTAATTC
Statistics
Matches: 89, Mismatches: 1, Indels: 5
0.94 0.01 0.05
Matches are distributed among these distances:
43 1 0.01
44 35 0.39
45 53 0.60
ACGTcount: A:0.24, C:0.23, G:0.20, T:0.33
Consensus pattern (44 bp):
ATTCTACCCTACAGGGTATTTCGGTAATTCTACCCTACAGGGGT
Found at i:53264841 original size:17 final size:18
Alignment explanation
Indices: 53264760--53264842 Score: 78
Period size: 18 Copynumber: 4.2 Consensus size: 18
53264750 TATTTCGGTA
53264760 ATTCTACCCTACAGGGGT
1 ATTCTACCCTACAGGGGT
53264778 ATTCTACCCTACAGAGGTATTTCGGT
1 ATTCTACCCTAC--AGG------GGT
53264804 AATTCTACCCTACAGGGGT
1 -ATTCTACCCTACAGGGGT
53264823 ATTCTACCCTACA-GGGT
1 ATTCTACCCTACAGGGGT
53264840 ATT
1 ATT
53264843 TCGATAATTC
Statistics
Matches: 56, Mismatches: 0, Indels: 19
0.75 0.00 0.25
Matches are distributed among these distances:
17 7 0.12
18 25 0.45
19 3 0.05
20 3 0.05
25 3 0.05
26 3 0.05
27 12 0.21
ACGTcount: A:0.24, C:0.25, G:0.19, T:0.31
Consensus pattern (18 bp):
ATTCTACCCTACAGGGGT
Found at i:53264877 original size:27 final size:27
Alignment explanation
Indices: 53264823--53264932 Score: 134
Period size: 27 Copynumber: 4.1 Consensus size: 27
53264813 CTACAGGGGT
*
53264823 ATTCTACCCTACA-GGGTATTTCGATA
1 ATTCTACCCTACAGGGGTATTTCGGTA
53264849 ATTCTACCCTACAGGGGTATTTCGGTA
1 ATTCTACCCTACAGGGGTATTTCGGTA
* *
53264876 ATTCTACCCTACAAGGGTATTTTGGTA
1 ATTCTACCCTACAGGGGTATTTCGGTA
* ** *
53264903 ATTTTA-CAAACCAGGGGTATTTTGGTA
1 ATTCTACCCTA-CAGGGGTATTTCGGTA
53264930 ATT
1 ATT
53264933 TTATAAACAA
Statistics
Matches: 75, Mismatches: 7, Indels: 3
0.88 0.08 0.04
Matches are distributed among these distances:
26 15 0.20
27 60 0.80
ACGTcount: A:0.26, C:0.18, G:0.19, T:0.36
Consensus pattern (27 bp):
ATTCTACCCTACAGGGGTATTTCGGTA
Found at i:53264918 original size:54 final size:53
Alignment explanation
Indices: 53264860--53265094 Score: 263
Period size: 54 Copynumber: 4.4 Consensus size: 53
53264850 TTCTACCCTA
* *
53264860 CAGGGGTATTTCGGTAATTCTACCCTACAAGGGTATTTTGGTAATTTTACAAAC
1 CAGGGGTATTTTGGTAATTCTA-CCAACAAGGGTATTTTGGTAATTTTACAAAC
* ** *
53264914 CAGGGGTATTTTGGTAATTTTATAAACAAAGGGTATTTTAGTAATTTTACAAAC
1 CAGGGGTATTTTGGTAATTCTACCAAC-AAGGGTATTTTGGTAATTTTACAAAC
* * ***
53264968 CAAGGGTATTTTGGTAATTTTGTAAACCAAGGGTATTTTGGTAATTTTACAAAC
1 CAGGGGTATTTTGGTAATTCTACCAA-CAAGGGTATTTTGGTAATTTTACAAAC
* * * * ** * *
53265022 TAGGGTTATTTTGGTGATTTTATAAACCAAAGGTATTTTAGTAATTTTACAAAC
1 CAGGGGTATTTTGGTAATTCTACCAA-CAAGGGTATTTTGGTAATTTTACAAAC
53265076 CAGGGGTATTTTGGTAATT
1 CAGGGGTATTTTGGTAATT
53265095 TGGTAAACTA
Statistics
Matches: 160, Mismatches: 19, Indels: 4
0.87 0.10 0.02
Matches are distributed among these distances:
53 2 0.01
54 157 0.98
55 1 0.01
ACGTcount: A:0.31, C:0.10, G:0.20, T:0.39
Consensus pattern (53 bp):
CAGGGGTATTTTGGTAATTCTACCAACAAGGGTATTTTGGTAATTTTACAAAC
Found at i:53265102 original size:27 final size:27
Alignment explanation
Indices: 53264887--53265095 Score: 294
Period size: 27 Copynumber: 7.7 Consensus size: 27
53264877 TTCTACCCTA
53264887 CAAGGGTATTTTGGTAATTTTACAAAC
1 CAAGGGTATTTTGGTAATTTTACAAAC
* *
53264914 CAGGGGTATTTTGGTAATTTTATAAAC
1 CAAGGGTATTTTGGTAATTTTACAAAC
* *
53264941 AAAGGGTATTTTAGTAATTTTACAAAC
1 CAAGGGTATTTTGGTAATTTTACAAAC
**
53264968 CAAGGGTATTTTGGTAATTTTGTAAAC
1 CAAGGGTATTTTGGTAATTTTACAAAC
53264995 CAAGGGTATTTTGGTAATTTTACAAA-
1 CAAGGGTATTTTGGTAATTTTACAAAC
* * *
53265021 CTAGGGTTATTTTGGTGATTTTATAAAC
1 CAAGGG-TATTTTGGTAATTTTACAAAC
* *
53265049 CAAAGGTATTTTAGTAATTTTACAAAC
1 CAAGGGTATTTTGGTAATTTTACAAAC
*
53265076 CAGGGGTATTTTGGTAATTT
1 CAAGGGTATTTTGGTAATTT
53265096 GGTAAACTAA
Statistics
Matches: 157, Mismatches: 23, Indels: 4
0.85 0.12 0.02
Matches are distributed among these distances:
26 5 0.03
27 148 0.94
28 4 0.03
ACGTcount: A:0.32, C:0.08, G:0.20, T:0.40
Consensus pattern (27 bp):
CAAGGGTATTTTGGTAATTTTACAAAC
Found at i:53268217 original size:45 final size:45
Alignment explanation
Indices: 53268157--53268356 Score: 133
Period size: 45 Copynumber: 4.5 Consensus size: 45
53268147 ATCTTGTTTC
*
53268157 CCTGAAATTGCAGTGAAGCAGATCGAAGACGGTGAATCTTGGCTT
1 CCTGAAGTTGCAGTGAAGCAGATCGAAGACGGTGAATCTTGGCTT
* ** **** * * *
53268202 CCTGAAGTTGTAGTGAAGCAGATTTAAG-CCACCAA-CCTAGCTC
1 CCTGAAGTTGCAGTGAAGCAGATCGAAGACGGTGAATCTTGGCTT
* * * * * ** * *
53268245 CCTAAAGTTGTAGTGGAGTAGGCTC-AA-A-TTTTAGATCTT-GTTT
1 CCTGAAGTTGCAGTGAAGCA-GATCGAAGACGGTGA-ATCTTGGCTT
* *
53268288 CCCAGAAATTGCAGTGAAGCAGATCGAAGACGGTGAATCTTGGCTT
1 -CCTGAAGTTGCAGTGAAGCAGATCGAAGACGGTGAATCTTGGCTT
53268334 CCTGAAGTTGCAGTGAAGCAGAT
1 CCTGAAGTTGCAGTGAAGCAGAT
53268357 TTAAGCCACC
Statistics
Matches: 110, Mismatches: 36, Indels: 18
0.67 0.22 0.11
Matches are distributed among these distances:
42 1 0.01
43 30 0.27
44 23 0.21
45 51 0.46
46 5 0.05
ACGTcount: A:0.29, C:0.18, G:0.26, T:0.27
Consensus pattern (45 bp):
CCTGAAGTTGCAGTGAAGCAGATCGAAGACGGTGAATCTTGGCTT
Found at i:53268250 original size:132 final size:132
Alignment explanation
Indices: 53268013--53269191 Score: 1831
Period size: 132 Copynumber: 8.9 Consensus size: 132
53268003 CAAATCCTAC
* * * * *
53268013 AGATCTTGTTTCCCTGAAGTTGCAGTGAGGCAAATTGAAGACGGCGAATCTTGGCTTCCTGAAGT
1 AGATCTTGTTTCCCTGAAATTGCAGTGAAGCAGATCGAAGACGGTGAATCTTGGCTTCCTGAAGT
* * *
53268078 TACAGTGAAGCAGATTTAAGCCACCAACCTAGGTCCCTAAAGTTGTAGTGGAGTAGGCTCAAATT
66 TGCAGTGAAGCAGATTTAAGCCACCAACCTAGCTCCCTAAAGTTGTAGTGGAGTAGGCTGAAATT
53268143 TT
131 TT
53268145 AGATCTTGTTTCCCTGAAATTGCAGTGAAGCAGATCGAAGACGGTGAATCTTGGCTTCCTGAAGT
1 AGATCTTGTTTCCCTGAAATTGCAGTGAAGCAGATCGAAGACGGTGAATCTTGGCTTCCTGAAGT
* *
53268210 TGTAGTGAAGCAGATTTAAGCCACCAACCTAGCTCCCTAAAGTTGTAGTGGAGTAGGCTCAAATT
66 TGCAGTGAAGCAGATTTAAGCCACCAACCTAGCTCCCTAAAGTTGTAGTGGAGTAGGCTGAAATT
53268275 TT
131 TT
*
53268277 AGATCTTGTTTCCCAGAAATTGCAGTGAAGCAGATCGAAGACGGTGAATCTTGGCTTCCTGAAGT
1 AGATCTTGTTTCCCTGAAATTGCAGTGAAGCAGATCGAAGACGGTGAATCTTGGCTTCCTGAAGT
53268342 TGCAGTGAAGCAGATTTAAGCCACCAACCTAGCTCCCTAAAGTTGTAGTGGAGTAGGCTGAAATT
66 TGCAGTGAAGCAGATTTAAGCCACCAACCTAGCTCCCTAAAGTTGTAGTGGAGTAGGCTGAAATT
53268407 TT
131 TT
* * *
53268409 AGATCTTGTTTCCTTAAAATTGCAGTGAAGCAGATCGAAGACGGCGAATCTTGGCTT-CTAGAAG
1 AGATCTTGTTTCCCTGAAATTGCAGTGAAGCAGATCGAAGACGGTGAATCTTGGCTTCCT-GAAG
*
53268473 TTGCAGTGAAGCAGATTTAAGCCACCATCCTAGCTCCCTAAAGTTGTAGTGGAGTAGGCTGAAAT
65 TTGCAGTGAAGCAGATTTAAGCCACCAACCTAGCTCCCTAAAGTTGTAGTGGAGTAGGCTGAAAT
53268538 TTT
130 TTT
* * * * * * *
53268541 AGATCTCGTTTCCCTGAAGTTACAGTGGAGCAGATCAAAGATGGTGAATCTAGGCTTCCTGAAGT
1 AGATCTTGTTTCCCTGAAATTGCAGTGAAGCAGATCGAAGACGGTGAATCTTGGCTTCCTGAAGT
* * *
53268606 TGTAGTGAAGCAGATTTAAGCCACCGACCTAGCTCCCTAAAGTTGTAGTGGAGTAGGCTAAAATT
66 TGCAGTGAAGCAGATTTAAGCCACCAACCTAGCTCCCTAAAGTTGTAGTGGAGTAGGCTGAAATT
53268671 TT
131 TT
* *
53268673 AGATCTTGTTTCCCTGAAATTGCAGTGAAACAGATCGAAGACGGTGAATTTTGGCTTCCTGAAGT
1 AGATCTTGTTTCCCTGAAATTGCAGTGAAGCAGATCGAAGACGGTGAATCTTGGCTTCCTGAAGT
53268738 TGCAGTGAAGCAGATTTAAGCCACCAACCTAGCTCCCTAAAGTTGTAGTGGAGTAGGCTGAAATT
66 TGCAGTGAAGCAGATTTAAGCCACCAACCTAGCTCCCTAAAGTTGTAGTGGAGTAGGCTGAAATT
53268803 TT
131 TT
*
53268805 AGATCTTGTTTCCCTGAAATTGCAGTGAAGCAGATCGAAGA-GGCGAATCTTGGCTTCCTGAAGT
1 AGATCTTGTTTCCCTGAAATTGCAGTGAAGCAGATCGAAGACGGTGAATCTTGGCTTCCTGAAGT
* * *
53268869 TGCAGTGAAGCAGATTTAAGCTACCATCCTAGCTCCCTAAAGTTGTAGTGGAGTAGGCTAAAATT
66 TGCAGTGAAGCAGATTTAAGCCACCAACCTAGCTCCCTAAAGTTGTAGTGGAGTAGGCTGAAATT
53268934 TT
131 TT
* * * * * * ** *
53268936 AGATCTCGTTTCCCTGAAGTTGCAGTGGAGCAAATTGAAGATGACGAATCTTGGCTTCCAGAAGT
1 AGATCTTGTTTCCCTGAAATTGCAGTGAAGCAGATCGAAGACGGTGAATCTTGGCTTCCTGAAGT
* *
53269001 TGCAGTGAAGTAGATTTAAGCCACCAACCTAGCTTCCTAAAGTTGTAGTGGAGTAGGCTGAAGAT
66 TGCAGTGAAGCAGATTTAAGCCACCAACCTAGCTCCCTAAAGTTGTAGTGGAGTAGGCTGAA-AT
**
53269066 AGT
130 TTT
* * * * * * * * *
53269069 AGATTTTATCTCCATGAAGTTGTAGTGAAGCAGATTGAAGACGATGAATCTTGGCTTACTGAAGT
1 AGATCTTGTTTCCCTGAAATTGCAGTGAAGCAGATCGAAGACGGTGAATCTTGGCTTCCTGAAGT
* *
53269134 TGCAGTGAAGCAGATTTAAGCCACCAACCTAGCTCCCCAAAGTTGTAGTAGAGTAGGC
66 TGCAGTGAAGCAGATTTAAGCCACCAACCTAGCTCCCTAAAGTTGTAGTGGAGTAGGC
53269192 CGAAGATCGC
Statistics
Matches: 965, Mismatches: 78, Indels: 7
0.92 0.07 0.01
Matches are distributed among these distances:
131 123 0.13
132 730 0.76
133 112 0.12
ACGTcount: A:0.29, C:0.18, G:0.25, T:0.28
Consensus pattern (132 bp):
AGATCTTGTTTCCCTGAAATTGCAGTGAAGCAGATCGAAGACGGTGAATCTTGGCTTCCTGAAGT
TGCAGTGAAGCAGATTTAAGCCACCAACCTAGCTCCCTAAAGTTGTAGTGGAGTAGGCTGAAATT
TT
Found at i:53270662 original size:20 final size:20
Alignment explanation
Indices: 53270621--53270662 Score: 50
Period size: 20 Copynumber: 2.1 Consensus size: 20
53270611 ATAGATTCAT
* *
53270621 TTCATGTTATTTTTATCTTA
1 TTCATGTTATATTTACCTTA
53270641 TTCATGTT-TATTTACCTGTA
1 TTCATGTTATATTTACCT-TA
53270661 TT
1 TT
53270663 AATTACATTA
Statistics
Matches: 19, Mismatches: 2, Indels: 2
0.83 0.09 0.09
Matches are distributed among these distances:
19 7 0.37
20 12 0.63
ACGTcount: A:0.19, C:0.12, G:0.07, T:0.62
Consensus pattern (20 bp):
TTCATGTTATATTTACCTTA
Found at i:53272007 original size:130 final size:130
Alignment explanation
Indices: 53271774--53272173 Score: 602
Period size: 130 Copynumber: 3.1 Consensus size: 130
53271764 AAACTCTTCA
*
53271774 AAACGAAGATGAGATTTGATGTTTGGCAATTCGCGGAATCGTGCCCTAACGTGTTGGGTTGCAAT
1 AAACGAAGACGAGATTTGATGTTTGGCAATTCGCGGAATCGTGCCCTAACGTGTTGGGTTGCAAT
53271839 TTCGCGTTTGCTCAAAATAATCGAATATCACTTCAAAATTTCACTCATGTCTTTTAAAATCCCTT
66 TTCGCGTTTGCTCAAAATAATCGAATATCACTTCAAAATTTCACTCATGTCTTTTAAAATCCCTT
*
53271904 AAACGAAGACGAGATTTGATGTTTGGCAATTCGCGGTATCGTGCCCTAACGTGTTGGGTTGCAAT
1 AAACGAAGACGAGATTTGATGTTTGGCAATTCGCGGAATCGTGCCCTAACGTGTTGGGTTGCAAT
* *
53271969 TTCGCGTTTGCTCAAAATAATTGAATATCACTTCAAAATTTCACTCATGCCTTTTAAAATCCCTT
66 TTCGCGTTTGCTCAAAATAATCGAATATCACTTCAAAATTTCACTCATGTCTTTTAAAATCCCTT
* * ** * * *
53272034 AAACGAAGGCGATATGCGATATTTGGCAATTCGTGGAATCGTGCCCTAACGTATTGGGTTGCAAT
1 AAACGAAGACGAGATTTGATGTTTGGCAATTCGCGGAATCGTGCCCTAACGTGTTGGGTTGCAAT
* * * * * * * * *
53272099 TTCCCATTTGTTTAAAATAATCAAATATCCCTTCAAAATTTCACTCAGGTCTTCTAAAAATCCTT
66 TTCGCGTTTGCTCAAAATAATCGAATATCACTTCAAAATTTCACTCATGTCTT-TTAAAATCCCT
53272164 T
130 T
53272165 AAAACGAAG
1 -AAACGAAG
53272174 GTAATAGTTG
Statistics
Matches: 245, Mismatches: 23, Indels: 2
0.91 0.09 0.01
Matches are distributed among these distances:
130 227 0.93
131 10 0.04
132 8 0.03
ACGTcount: A:0.30, C:0.20, G:0.18, T:0.33
Consensus pattern (130 bp):
AAACGAAGACGAGATTTGATGTTTGGCAATTCGCGGAATCGTGCCCTAACGTGTTGGGTTGCAAT
TTCGCGTTTGCTCAAAATAATCGAATATCACTTCAAAATTTCACTCATGTCTTTTAAAATCCCTT
Found at i:53272626 original size:13 final size:14
Alignment explanation
Indices: 53272608--53272637 Score: 53
Period size: 14 Copynumber: 2.2 Consensus size: 14
53272598 CTATAAATAG
53272608 TTTAAA-TTTGATT
1 TTTAAATTTTGATT
53272621 TTTAAATTTTGATT
1 TTTAAATTTTGATT
53272635 TTT
1 TTT
53272638 TTAGTTGATA
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
13 6 0.38
14 10 0.62
ACGTcount: A:0.27, C:0.00, G:0.07, T:0.67
Consensus pattern (14 bp):
TTTAAATTTTGATT
Found at i:53289353 original size:36 final size:36
Alignment explanation
Indices: 53289308--53289392 Score: 170
Period size: 36 Copynumber: 2.4 Consensus size: 36
53289298 ACATAACATC
53289308 AAAATAAGCCAAATCACATGGCTTAACTTATACACA
1 AAAATAAGCCAAATCACATGGCTTAACTTATACACA
53289344 AAAATAAGCCAAATCACATGGCTTAACTTATACACA
1 AAAATAAGCCAAATCACATGGCTTAACTTATACACA
53289380 AAAATAAGCCAAA
1 AAAATAAGCCAAA
53289393 GTCTTAATAT
Statistics
Matches: 49, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
36 49 1.00
ACGTcount: A:0.51, C:0.21, G:0.08, T:0.20
Consensus pattern (36 bp):
AAAATAAGCCAAATCACATGGCTTAACTTATACACA
Found at i:53290006 original size:22 final size:23
Alignment explanation
Indices: 53289941--53290020 Score: 92
Period size: 23 Copynumber: 3.5 Consensus size: 23
53289931 TAAGTTGATG
* *
53289941 AACAATAAGCTCTATTAAGCTGA
1 AACAGTAAGCTCTATCAAGCTGA
53289964 AACAGTAAGCTCTATCAAGCTG-
1 AACAGTAAGCTCTATCAAGCTGA
* *
53289986 AACAGTAAGCT-TATACGAGCTAA
1 AACAGTAAGCTCTAT-CAAGCTGA
*
53290009 AACGGTAAGCTC
1 AACAGTAAGCTC
53290021 CAATGAGATA
Statistics
Matches: 49, Mismatches: 5, Indels: 5
0.83 0.08 0.08
Matches are distributed among these distances:
21 3 0.06
22 16 0.33
23 30 0.61
ACGTcount: A:0.40, C:0.20, G:0.17, T:0.23
Consensus pattern (23 bp):
AACAGTAAGCTCTATCAAGCTGA
Found at i:53295189 original size:32 final size:32
Alignment explanation
Indices: 53295153--53295217 Score: 103
Period size: 32 Copynumber: 2.0 Consensus size: 32
53295143 ATCTGAAAAG
* * *
53295153 ACCAACTACGGAACTAGATTGAGGAAAGTAAA
1 ACCAACTACGGAACTAGATCGAAGAAAGCAAA
53295185 ACCAACTACGGAACTAGATCGAAGAAAGCAAA
1 ACCAACTACGGAACTAGATCGAAGAAAGCAAA
53295217 A
1 A
53295218 GGTTTCGGAT
Statistics
Matches: 30, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
32 30 1.00
ACGTcount: A:0.49, C:0.18, G:0.20, T:0.12
Consensus pattern (32 bp):
ACCAACTACGGAACTAGATCGAAGAAAGCAAA
Found at i:53302747 original size:40 final size:40
Alignment explanation
Indices: 53302688--53302832 Score: 213
Period size: 40 Copynumber: 3.6 Consensus size: 40
53302678 CGGATGATAA
*
53302688 CCGGGCTAAGTCCCGAAGGCATTTGTGCTAGTGACTA-ATT
1 CCGGGCTAAGTCCCGAAGGCATTTGTGCTAGTTACTATA-T
* *
53302728 CCGGGCTAAGTCCCTAAGGCATTTGTGCGAGTTACTATAT
1 CCGGGCTAAGTCCCGAAGGCATTTGTGCTAGTTACTATAT
*
53302768 CCGGGCTAAGTCCCGAAGGCATTTGTG-TGAGTTACTATAA
1 CCGGGCTAAGTCCCGAAGGCATTTGTGCT-AGTTACTATAT
*
53302808 CCAGGCTAAGTCCCGAAGGCATTTG
1 CCGGGCTAAGTCCCGAAGGCATTTG
53302833 AGCAAGTAGT
Statistics
Matches: 96, Mismatches: 7, Indels: 4
0.90 0.07 0.04
Matches are distributed among these distances:
40 95 0.99
41 1 0.01
ACGTcount: A:0.23, C:0.23, G:0.27, T:0.27
Consensus pattern (40 bp):
CCGGGCTAAGTCCCGAAGGCATTTGTGCTAGTTACTATAT
Found at i:53303132 original size:22 final size:21
Alignment explanation
Indices: 53303091--53303134 Score: 54
Period size: 22 Copynumber: 2.0 Consensus size: 21
53303081 GAATGTGCAT
53303091 ATATGAAGTTATCCATTTAGCC
1 ATATGAAGTTATCCA-TTAGCC
53303113 ATATGAATGTTATACC-TTAGCC
1 ATATGAA-GTTAT-CCATTAGCC
53303135 GAAACTAATT
Statistics
Matches: 20, Mismatches: 0, Indels: 4
0.83 0.00 0.17
Matches are distributed among these distances:
22 13 0.65
23 5 0.25
24 2 0.10
ACGTcount: A:0.32, C:0.18, G:0.14, T:0.36
Consensus pattern (21 bp):
ATATGAAGTTATCCATTAGCC
Found at i:53304285 original size:19 final size:19
Alignment explanation
Indices: 53304248--53304295 Score: 64
Period size: 19 Copynumber: 2.6 Consensus size: 19
53304238 TTTATATCAT
*
53304248 TTATCATTTA--TCGGGCA
1 TTATCATTTATTTCAGGCA
53304265 TTATCATTTATTTCAGGCA
1 TTATCATTTATTTCAGGCA
*
53304284 TTATCACTTATT
1 TTATCATTTATT
53304296 GGGCTTCGTC
Statistics
Matches: 27, Mismatches: 2, Indels: 2
0.87 0.06 0.06
Matches are distributed among these distances:
17 10 0.37
19 17 0.63
ACGTcount: A:0.25, C:0.17, G:0.10, T:0.48
Consensus pattern (19 bp):
TTATCATTTATTTCAGGCA
Found at i:53309328 original size:29 final size:29
Alignment explanation
Indices: 53309266--53309368 Score: 111
Period size: 29 Copynumber: 3.6 Consensus size: 29
53309256 GTGACGAGAT
* * *
53309266 TGGCACTGAGTGTGCGAGCTTGTAATGTA
1 TGGCACTAAGTGTGCGAGCTTGGAATATA
* * *
53309295 CGGCACTAAGTGTGCGAGTTTGGACTATA
1 TGGCACTAAGTGTGCGAGCTTGGAATATA
*
53309324 TGGCACTATGTGTGC-AGGCTT-GAATCATA
1 TGGCACTAAGTGTGCGA-GCTTGGAAT-ATA
53309353 TGGCACTAAGTGTGCG
1 TGGCACTAAGTGTGCG
53309369 TGATTGAGTA
Statistics
Matches: 60, Mismatches: 11, Indels: 5
0.79 0.14 0.07
Matches are distributed among these distances:
28 4 0.07
29 56 0.93
ACGTcount: A:0.22, C:0.17, G:0.32, T:0.29
Consensus pattern (29 bp):
TGGCACTAAGTGTGCGAGCTTGGAATATA
Found at i:53312378 original size:25 final size:26
Alignment explanation
Indices: 53312343--53312418 Score: 73
Period size: 25 Copynumber: 2.9 Consensus size: 26
53312333 AAAAAAGTCT
* * *
53312343 AAAAAAAAAAAAAAATAACTAAAAAC
1 AAAAATAAAAAGAAATAAATAAAAAC
* * *
53312369 AAGATTAAAAAGAAA-AAATAAAAAT
1 AAAAATAAAAAGAAATAAATAAAAAC
*
53312394 AAAAATAAAAATAAATAAAATAAAA
1 AAAAATAAAAAGAAAT-AAATAAAA
53312419 TTAGTGATCT
Statistics
Matches: 39, Mismatches: 9, Indels: 3
0.76 0.18 0.06
Matches are distributed among these distances:
25 20 0.51
26 11 0.28
27 8 0.21
ACGTcount: A:0.82, C:0.03, G:0.03, T:0.13
Consensus pattern (26 bp):
AAAAATAAAAAGAAATAAATAAAAAC
Found at i:53312391 original size:6 final size:6
Alignment explanation
Indices: 53312382--53312408 Score: 54
Period size: 6 Copynumber: 4.5 Consensus size: 6
53312372 ATTAAAAAGA
53312382 AAAAAT AAAAAT AAAAAT AAAAAT AAA
1 AAAAAT AAAAAT AAAAAT AAAAAT AAA
53312409 TAAAATAAAA
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 21 1.00
ACGTcount: A:0.85, C:0.00, G:0.00, T:0.15
Consensus pattern (6 bp):
AAAAAT
Found at i:53316665 original size:17 final size:18
Alignment explanation
Indices: 53316637--53316678 Score: 77
Period size: 17 Copynumber: 2.4 Consensus size: 18
53316627 CCTAGCCCCG
53316637 TTTTTAATGCTCTTCATA
1 TTTTTAATGCTCTTCATA
53316655 TTTTTAA-GCTCTTCATA
1 TTTTTAATGCTCTTCATA
53316672 TTTTTAA
1 TTTTTAA
53316679 AATCCTCGTA
Statistics
Matches: 24, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
17 17 0.71
18 7 0.29
ACGTcount: A:0.24, C:0.14, G:0.05, T:0.57
Consensus pattern (18 bp):
TTTTTAATGCTCTTCATA
Found at i:53323269 original size:93 final size:92
Alignment explanation
Indices: 53323111--53323280 Score: 313
Period size: 93 Copynumber: 1.8 Consensus size: 92
53323101 GCCCCTAAGT
*
53323111 GAACTCGGACTCAACTCAACGAGCTCGGCGTTCGCATCCATAAGTGAACTCGGACTCAACTCAAC
1 GAACTCGGACTCAACTCAACGAGCTCGGCATTCGCATCCATAAGTGAACTCGGACTCAACTCAAC
53323176 GAGTTCGGATGCCTAGTTACATTTCAC
66 GAGTTCGGATGCCTAGTTACATTTCAC
*
53323203 GAACTCGGACTCAACTCAACGAGTTCGGACATTCGCATCCATAAGTGAACTCGGACTCAACTCAA
1 GAACTCGGACTCAACTCAACGAGCTCGG-CATTCGCATCCATAAGTGAACTCGGACTCAACTCAA
53323268 CGAGTTCGGATGC
65 CGAGTTCGGATGC
53323281 TCAACCATCC
Statistics
Matches: 75, Mismatches: 2, Indels: 1
0.96 0.03 0.01
Matches are distributed among these distances:
92 27 0.36
93 48 0.64
ACGTcount: A:0.28, C:0.29, G:0.21, T:0.22
Consensus pattern (92 bp):
GAACTCGGACTCAACTCAACGAGCTCGGCATTCGCATCCATAAGTGAACTCGGACTCAACTCAAC
GAGTTCGGATGCCTAGTTACATTTCAC
Found at i:53323296 original size:46 final size:46
Alignment explanation
Indices: 53323105--53323289 Score: 159
Period size: 45 Copynumber: 4.0 Consensus size: 46
53323095 TAACCCGCCC
* * * * *
53323105 CTAAGTGAACTCGGACTCAACTCAACGAGCTCGGCGTTCGCATCCA-
1 CTAAGTGAACTCGGACTCAACTCAACGAGTTCGG-ATGCTCAACCAT
53323151 -TAAGTGAACTCGGACTCAACTCAACGAGTTCGGATGC-CTAGTTA-CAT
1 CTAAGTGAACTCGGACTCAACTCAACGAGTTCGGATGCTC-A---ACCAT
* * * * * *
53323198 TTCA-CGAACTCGGACTCAACTCAACGAGTTCGGACATTCGCATCCA-
1 CTAAGTGAACTCGGACTCAACTCAACGAGTTCGG--ATGCTCAACCAT
53323244 -TAAGTGAACTCGGACTCAACTCAACGAGTTCGGATGCTCAACCAT
1 CTAAGTGAACTCGGACTCAACTCAACGAGTTCGGATGCTCAACCAT
53323289 C
1 C
53323290 CTAGTGACAT
Statistics
Matches: 113, Mismatches: 13, Indels: 26
0.74 0.09 0.17
Matches are distributed among these distances:
43 1 0.01
44 11 0.10
45 34 0.30
46 30 0.27
47 30 0.27
48 2 0.02
49 4 0.04
50 1 0.01
ACGTcount: A:0.29, C:0.29, G:0.20, T:0.22
Consensus pattern (46 bp):
CTAAGTGAACTCGGACTCAACTCAACGAGTTCGGATGCTCAACCAT
Found at i:53323660 original size:30 final size:30
Alignment explanation
Indices: 53323626--53323685 Score: 93
Period size: 30 Copynumber: 2.0 Consensus size: 30
53323616 ATTTAATACG
53323626 AACTTTGGAAAAATTACACTTTTGCCCCTA
1 AACTTTGGAAAAATTACACTTTTGCCCCTA
* * *
53323656 AACTTTTGCATAATTACACTTTTGCCCCTA
1 AACTTTGGAAAAATTACACTTTTGCCCCTA
53323686 GGCTCGGGAA
Statistics
Matches: 27, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
30 27 1.00
ACGTcount: A:0.30, C:0.25, G:0.08, T:0.37
Consensus pattern (30 bp):
AACTTTGGAAAAATTACACTTTTGCCCCTA
Found at i:53330691 original size:90 final size:89
Alignment explanation
Indices: 53330589--53330753 Score: 267
Period size: 90 Copynumber: 1.8 Consensus size: 89
53330579 CCCTAAGTGA
* * * *
53330589 ACTCGACTCAACTCAATGAGCTCGGGCGTTCGCATCCATAAGTGAACTCAGACTCAACTCAACGA
1 ACTCGACTCAACTCAACGAGCTCAGACATTCGCATCCATAAGTGAACTCAGACTCAACTCAACGA
53330654 GTTCGGATGCCTAGAATTTTCACG
66 GTTCGGATGCCTAGAATTTTCACG
* *
53330678 ACTCGGACTCAACTCAACGAGTTCAGACATTCGCATCCATAAGTGAACTCGGACTCAACTCAACG
1 ACTC-GACTCAACTCAACGAGCTCAGACATTCGCATCCATAAGTGAACTCAGACTCAACTCAACG
53330743 AGTTCGGATGC
65 AGTTCGGATGC
53330754 TCAACCATCC
Statistics
Matches: 69, Mismatches: 6, Indels: 1
0.91 0.08 0.01
Matches are distributed among these distances:
89 4 0.06
90 65 0.94
ACGTcount: A:0.29, C:0.28, G:0.20, T:0.22
Consensus pattern (89 bp):
ACTCGACTCAACTCAACGAGCTCAGACATTCGCATCCATAAGTGAACTCAGACTCAACTCAACGA
GTTCGGATGCCTAGAATTTTCACG
Found at i:53330769 original size:46 final size:43
Alignment explanation
Indices: 53330584--53330761 Score: 117
Period size: 46 Copynumber: 4.0 Consensus size: 43
53330574 CCCGCCCCTA
* * * * * *
53330584 AGTGAACTC-GACTCAACTCAATGAGCTCGGGCGTTCGCATCCATA
1 AGTGAACTCGGACTCAACTCAACGAGTTC-GG-ATGC-CAACCATT
* * **
53330629 AGTGAACTCAGACTCAACTCAACGAGTTCGGATGCCTAGAATT
1 AGTGAACTCGGACTCAACTCAACGAGTTCGGATGCCAACCATT
* * * * * *
53330672 -TTCACGACTCGGACTCAACTCAACGAGTTCAGACATTCGCATCCATA
1 AGTGA--ACTCGGACTCAACTCAACGAGTTC-G-GATGC-CAACCATT
53330719 AGTGAACTCGGACTCAACTCAACGAGTTCGGATGCTCAACCAT
1 AGTGAACTCGGACTCAACTCAACGAGTTCGGATGC-CAACCAT
53330762 CCTAGTGACA
Statistics
Matches: 101, Mismatches: 25, Indels: 15
0.72 0.18 0.11
Matches are distributed among these distances:
42 2 0.02
43 3 0.03
44 34 0.34
45 13 0.13
46 44 0.44
47 3 0.03
48 2 0.02
ACGTcount: A:0.30, C:0.28, G:0.20, T:0.22
Consensus pattern (43 bp):
AGTGAACTCGGACTCAACTCAACGAGTTCGGATGCCAACCATT
Found at i:53331207 original size:30 final size:30
Alignment explanation
Indices: 53331173--53331232 Score: 93
Period size: 30 Copynumber: 2.0 Consensus size: 30
53331163 ATTTAATACG
53331173 AACTTTGGAAAAATTACACTTTTGCCCCTA
1 AACTTTGGAAAAATTACACTTTTGCCCCTA
* * *
53331203 AACTTTTGCATAATTACACTTTTGCCCCTA
1 AACTTTGGAAAAATTACACTTTTGCCCCTA
53331233 GGCTCGGGAA
Statistics
Matches: 27, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
30 27 1.00
ACGTcount: A:0.30, C:0.25, G:0.08, T:0.37
Consensus pattern (30 bp):
AACTTTGGAAAAATTACACTTTTGCCCCTA
Found at i:53335809 original size:36 final size:37
Alignment explanation
Indices: 53335709--53335813 Score: 167
Period size: 37 Copynumber: 2.9 Consensus size: 37
53335699 CGAATAGTCC
* * * *
53335709 CCACACGAAGTTATCGGGTCTTACCCAGACAAAATCT
1 CCACACGTAGTCATCGGGTCTTACCCGGACATAATCT
53335746 CCACACGTAGTCATCGGGTCTTACCCGGACATAATCT
1 CCACACGTAGTCATCGGGTCTTACCCGGACATAATCT
53335783 CCACACGTAGTCATC-GGTCTTACCCGGACAT
1 CCACACGTAGTCATCGGGTCTTACCCGGACAT
53335814 CGGGTCTTAC
Statistics
Matches: 64, Mismatches: 4, Indels: 1
0.93 0.06 0.01
Matches are distributed among these distances:
36 16 0.25
37 48 0.75
ACGTcount: A:0.27, C:0.32, G:0.18, T:0.23
Consensus pattern (37 bp):
CCACACGTAGTCATCGGGTCTTACCCGGACATAATCT
Found at i:53335816 original size:17 final size:18
Alignment explanation
Indices: 53335794--53335831 Score: 69
Period size: 18 Copynumber: 2.2 Consensus size: 18
53335784 CACACGTAGT
53335794 CATC-GGTCTTACCCGGA
1 CATCGGGTCTTACCCGGA
53335811 CATCGGGTCTTACCCGGA
1 CATCGGGTCTTACCCGGA
53335829 CAT
1 CAT
53335832 AATCTCCACA
Statistics
Matches: 20, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
17 4 0.20
18 16 0.80
ACGTcount: A:0.18, C:0.34, G:0.24, T:0.24
Consensus pattern (18 bp):
CATCGGGTCTTACCCGGA
Found at i:53335839 original size:54 final size:55
Alignment explanation
Indices: 53335757--53335865 Score: 211
Period size: 54 Copynumber: 2.0 Consensus size: 55
53335747 CACACGTAGT
53335757 CATCGGGTCTTACCCGGACATAATCTCCACACGTAGTCATC-GGTCTTACCCGGA
1 CATCGGGTCTTACCCGGACATAATCTCCACACGTAGTCATCGGGTCTTACCCGGA
53335811 CATCGGGTCTTACCCGGACATAATCTCCACACGTAGTCATCGGGTCTTACCCGGA
1 CATCGGGTCTTACCCGGACATAATCTCCACACGTAGTCATCGGGTCTTACCCGGA
53335866 ATATATTTCC
Statistics
Matches: 54, Mismatches: 0, Indels: 1
0.98 0.00 0.02
Matches are distributed among these distances:
54 41 0.76
55 13 0.24
ACGTcount: A:0.22, C:0.33, G:0.21, T:0.24
Consensus pattern (55 bp):
CATCGGGTCTTACCCGGACATAATCTCCACACGTAGTCATCGGGTCTTACCCGGA
Found at i:53336063 original size:48 final size:48
Alignment explanation
Indices: 53336005--53336342 Score: 595
Period size: 48 Copynumber: 7.0 Consensus size: 48
53335995 ATATACACAC
*
53336005 ATCTCCTACATATTTCACACTAGCCATTCGGCTTTACCACATATACAT
1 ATCTCATACATATTTCACACTAGCCATTCGGCTTTACCACATATACAT
*
53336053 ATCTCATACATATTTCACACTAGCCATTCGGCTTTACAACATATACAT
1 ATCTCATACATATTTCACACTAGCCATTCGGCTTTACCACATATACAT
* *
53336101 ATCTCATATATATTTCACATTAGCCATTCGGCTTTACCACATATACAT
1 ATCTCATACATATTTCACACTAGCCATTCGGCTTTACCACATATACAT
* *
53336149 ATCTCATACATATTTCACATTAGCCGTTCGGCTTTACCACATATACAT
1 ATCTCATACATATTTCACACTAGCCATTCGGCTTTACCACATATACAT
53336197 ATCTCATACATATTTCACACTAGCCATTCGGCTTTACCACATATACAT
1 ATCTCATACATATTTCACACTAGCCATTCGGCTTTACCACATATACAT
*
53336245 ATCTCATACATATTTCACACTAGCCATTCGGCTTTACCACATATAAAT
1 ATCTCATACATATTTCACACTAGCCATTCGGCTTTACCACATATACAT
* *
53336293 ATCTCATACATATTTCACACTAGCCATTCGGCTTTACCACACATATAT
1 ATCTCATACATATTTCACACTAGCCATTCGGCTTTACCACATATACAT
53336341 AT
1 AT
53336343 ATTTATCTTG
Statistics
Matches: 278, Mismatches: 12, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
48 278 1.00
ACGTcount: A:0.31, C:0.28, G:0.07, T:0.34
Consensus pattern (48 bp):
ATCTCATACATATTTCACACTAGCCATTCGGCTTTACCACATATACAT
Found at i:53339697 original size:57 final size:57
Alignment explanation
Indices: 53339635--53339795 Score: 232
Period size: 57 Copynumber: 2.8 Consensus size: 57
53339625 CTGACTGATT
** * *
53339635 TCGCACACATAGCACTCGATTAAAGAACTTGCACACATAGTGCCTCAATTACCAATC
1 TCGCACACATAGTGCTCGATTGAAGAACTTGCACACATAGTGCCTCAACTACCAATC
* **
53339692 TCGCACACATAGTGCTCGATTGAAGAACTCGCACACATAGTGCCTCAACTACTGATC
1 TCGCACACATAGTGCTCGATTGAAGAACTTGCACACATAGTGCCTCAACTACCAATC
* * *
53339749 TGGCACACATAGTGCTCGGTTGAAGAACTTGCACACACAGTGCCTCA
1 TCGCACACATAGTGCTCGATTGAAGAACTTGCACACATAGTGCCTCA
53339796 TAACTCCAGC
Statistics
Matches: 93, Mismatches: 11, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
57 93 1.00
ACGTcount: A:0.31, C:0.29, G:0.17, T:0.22
Consensus pattern (57 bp):
TCGCACACATAGTGCTCGATTGAAGAACTTGCACACATAGTGCCTCAACTACCAATC
Found at i:53339698 original size:29 final size:29
Alignment explanation
Indices: 53339665--53339763 Score: 112
Period size: 29 Copynumber: 3.4 Consensus size: 29
53339655 TAAAGAACTT
53339665 GCACACATAGTGCCTCAATTACCAATCTC
1 GCACACATAGTGCCTCAATTACCAATCTC
* **
53339694 GCACACATAGTG-CTCGATTGAAGAA-CTC
1 GCACACATAGTGCCTCAATT-ACCAATCTC
* ** *
53339722 GCACACATAGTGCCTCAACTACTGATCTG
1 GCACACATAGTGCCTCAATTACCAATCTC
53339751 GCACACATAGTGC
1 GCACACATAGTGC
53339764 TCGGTTGAAG
Statistics
Matches: 58, Mismatches: 9, Indels: 6
0.79 0.12 0.08
Matches are distributed among these distances:
28 23 0.40
29 35 0.60
ACGTcount: A:0.30, C:0.30, G:0.17, T:0.22
Consensus pattern (29 bp):
GCACACATAGTGCCTCAATTACCAATCTC
Found at i:53339731 original size:28 final size:27
Alignment explanation
Indices: 53339635--53339791 Score: 125
Period size: 28 Copynumber: 5.6 Consensus size: 27
53339625 CTGACTGATT
**
53339635 TCGCACACATAGCACTCGATTAAAGAAC
1 TCGCACACATAGTGCTCGATT-AAGAAC
* * **
53339663 TTGCACACATAGTGCCTCAATTACCAATC
1 TCGCACACATAGTG-CTCGATTAAGAA-C
53339692 TCGCACACATAGTGCTCGATTGAAGAAC
1 TCGCACACATAGTGCTCGATT-AAGAAC
* * * *
53339720 TCGCACACATAGTGCCTCAACTACTGATC
1 TCGCACACATAGTG-CTCGATTA-AGAAC
* *
53339749 TGGCACACATAGTGCTCGGTTGAAGAAC
1 TCGCACACATAGTGCTCGATT-AAGAAC
* *
53339777 TTGCACACACAGTGC
1 TCGCACACATAGTGC
53339792 CTCATAACTC
Statistics
Matches: 101, Mismatches: 22, Indels: 12
0.75 0.16 0.09
Matches are distributed among these distances:
28 56 0.55
29 45 0.45
ACGTcount: A:0.31, C:0.29, G:0.18, T:0.22
Consensus pattern (27 bp):
TCGCACACATAGTGCTCGATTAAGAAC
Found at i:53339867 original size:40 final size:40
Alignment explanation
Indices: 53339823--53340074 Score: 416
Period size: 40 Copynumber: 6.3 Consensus size: 40
53339813 CCTTCGAGGT
*
53339823 TTAGCCCGGATATATCACTAGCACGAATGCTCTTCGGAAC
1 TTAGCCCGGATACATCACTAGCACGAATGCTCTTCGGAAC
* *
53339863 TTAGCCCGGATACATTACTAGCATGAATGCTCTTCGGAAC
1 TTAGCCCGGATACATCACTAGCACGAATGCTCTTCGGAAC
53339903 TTAGCCCGGATACATCACTAGCACGAATGCTCTTCGGAAC
1 TTAGCCCGGATACATCACTAGCACGAATGCTCTTCGGAAC
*
53339943 TTAGCCCGGATACATCACTAGCACGAATGCTCTT-TGAGAC
1 TTAGCCCGGATACATCACTAGCACGAATGCTCTTCGGA-AC
* *
53339983 TTAGCCCGGATACATCACTAGCACGAATGTTCTTCGGGAC
1 TTAGCCCGGATACATCACTAGCACGAATGCTCTTCGGAAC
* *
53340023 TTAGCCCGGATACATTACTAGCACGAATGCTCTTCGGGAC
1 TTAGCCCGGATACATCACTAGCACGAATGCTCTTCGGAAC
53340063 TTAGCCCGGATA
1 TTAGCCCGGATA
53340075 TATATAACTC
Statistics
Matches: 199, Mismatches: 11, Indels: 4
0.93 0.05 0.02
Matches are distributed among these distances:
39 2 0.01
40 196 0.98
41 1 0.01
ACGTcount: A:0.27, C:0.27, G:0.21, T:0.25
Consensus pattern (40 bp):
TTAGCCCGGATACATCACTAGCACGAATGCTCTTCGGAAC
Found at i:53341412 original size:37 final size:37
Alignment explanation
Indices: 53341359--53341458 Score: 173
Period size: 37 Copynumber: 2.7 Consensus size: 37
53341349 CGAATAGTCC
*
53341359 CCACACGTAGTTATCGGGTCTTACCCGAACAAAATCT
1 CCACACGTAGTCATCGGGTCTTACCCGAACAAAATCT
* *
53341396 CCACACGTAGTCATCGGGTCTTACCCGGACATAATCT
1 CCACACGTAGTCATCGGGTCTTACCCGAACAAAATCT
53341433 CCACACGTAGTCATCGGGTCTTACCC
1 CCACACGTAGTCATCGGGTCTTACCC
53341459 AGACATCGGG
Statistics
Matches: 60, Mismatches: 3, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
37 60 1.00
ACGTcount: A:0.25, C:0.33, G:0.18, T:0.24
Consensus pattern (37 bp):
CCACACGTAGTCATCGGGTCTTACCCGAACAAAATCT
Found at i:53341467 original size:18 final size:18
Alignment explanation
Indices: 53341444--53341482 Score: 69
Period size: 18 Copynumber: 2.2 Consensus size: 18
53341434 CACACGTAGT
53341444 CATCGGGTCTTACCCAGA
1 CATCGGGTCTTACCCAGA
*
53341462 CATCGGGTCTTACCCGGA
1 CATCGGGTCTTACCCAGA
53341480 CAT
1 CAT
53341483 AATCTCCATA
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
18 20 1.00
ACGTcount: A:0.21, C:0.33, G:0.23, T:0.23
Consensus pattern (18 bp):
CATCGGGTCTTACCCAGA
Found at i:53341512 original size:37 final size:37
Alignment explanation
Indices: 53341462--53341553 Score: 166
Period size: 37 Copynumber: 2.5 Consensus size: 37
53341452 CTTACCCAGA
*
53341462 CATCGGGTCTTACCCGGACATAATCTCCATACGTAGT
1 CATCGGGTCTTACCCGGACATAATCTCCACACGTAGT
*
53341499 CATCGGGTCTTACCTGGACATAATCTCCACACGTAGT
1 CATCGGGTCTTACCCGGACATAATCTCCACACGTAGT
53341536 CATCGGGTCTTACCCGGA
1 CATCGGGTCTTACCCGGA
53341554 ATATATTTCC
Statistics
Matches: 52, Mismatches: 3, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
37 52 1.00
ACGTcount: A:0.23, C:0.30, G:0.21, T:0.26
Consensus pattern (37 bp):
CATCGGGTCTTACCCGGACATAATCTCCACACGTAGT
Found at i:53341519 original size:55 final size:55
Alignment explanation
Indices: 53341407--53341512 Score: 203
Period size: 55 Copynumber: 1.9 Consensus size: 55
53341397 CACACGTAGT
53341407 CATCGGGTCTTACCCGGACATAATCTCCACACGTAGTCATCGGGTCTTACCCAGA
1 CATCGGGTCTTACCCGGACATAATCTCCACACGTAGTCATCGGGTCTTACCCAGA
*
53341462 CATCGGGTCTTACCCGGACATAATCTCCATACGTAGTCATCGGGTCTTACC
1 CATCGGGTCTTACCCGGACATAATCTCCACACGTAGTCATCGGGTCTTACC
53341513 TGGACATAAT
Statistics
Matches: 50, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
55 50 1.00
ACGTcount: A:0.23, C:0.32, G:0.20, T:0.25
Consensus pattern (55 bp):
CATCGGGTCTTACCCGGACATAATCTCCACACGTAGTCATCGGGTCTTACCCAGA
Found at i:53341528 original size:92 final size:92
Alignment explanation
Indices: 53341371--53341550 Score: 324
Period size: 92 Copynumber: 2.0 Consensus size: 92
53341361 ACACGTAGTT
53341371 ATCGGGTCTTACCCGAACAAAATCTCCACACGTAGTCATCGGGTCTTACCCGGACATAATCTCCA
1 ATCGGGTCTTACCCGAACAAAATCTCCACACGTAGTCATCGGGTCTTACCCGGACATAATCTCCA
53341436 CACGTAGTCATCGGGTCTTACCCAGAC
66 CACGTAGTCATCGGGTCTTACCCAGAC
* * * *
53341463 ATCGGGTCTTACCCGGACATAATCTCCATACGTAGTCATCGGGTCTTACCTGGACATAATCTCCA
1 ATCGGGTCTTACCCGAACAAAATCTCCACACGTAGTCATCGGGTCTTACCCGGACATAATCTCCA
53341528 CACGTAGTCATCGGGTCTTACCC
66 CACGTAGTCATCGGGTCTTACCC
53341551 GGAATATATT
Statistics
Matches: 84, Mismatches: 4, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
92 84 1.00
ACGTcount: A:0.24, C:0.32, G:0.19, T:0.25
Consensus pattern (92 bp):
ATCGGGTCTTACCCGAACAAAATCTCCACACGTAGTCATCGGGTCTTACCCGGACATAATCTCCA
CACGTAGTCATCGGGTCTTACCCAGAC
Found at i:53341751 original size:48 final size:48
Alignment explanation
Indices: 53341693--53341903 Score: 377
Period size: 48 Copynumber: 4.4 Consensus size: 48
53341683 ATATACACAC
*
53341693 ATCTCCTACATATTTCACACTAGCCATTCGGCTTTACCACATATACAT
1 ATCTCATACATATTTCACACTAGCCATTCGGCTTTACCACATATACAT
53341741 ATCTCATACATATTTCACACTAGCCATTCGGCTTTACCACATATACAT
1 ATCTCATACATATTTCACACTAGCCATTCGGCTTTACCACATATACAT
* ** *
53341789 ATCTCATATATATTTCACGTTAGCCATTTGGCTTTACCACATATACAT
1 ATCTCATACATATTTCACACTAGCCATTCGGCTTTACCACATATACAT
53341837 ATCTCATACATATTTCACACTAGCCATTCGGCTTTACCACATATACAT
1 ATCTCATACATATTTCACACTAGCCATTCGGCTTTACCACATATACAT
53341885 ATCTCATACATATTTCACA
1 ATCTCATACATATTTCACA
53341904 TATACATATC
Statistics
Matches: 154, Mismatches: 9, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
48 154 1.00
ACGTcount: A:0.31, C:0.28, G:0.06, T:0.35
Consensus pattern (48 bp):
ATCTCATACATATTTCACACTAGCCATTCGGCTTTACCACATATACAT
Found at i:53341910 original size:26 final size:26
Alignment explanation
Indices: 53341874--53341929 Score: 112
Period size: 26 Copynumber: 2.2 Consensus size: 26
53341864 TCGGCTTTAC
53341874 CACATATACATATCTCATACATATTT
1 CACATATACATATCTCATACATATTT
53341900 CACATATACATATCTCATACATATTT
1 CACATATACATATCTCATACATATTT
53341926 CACA
1 CACA
53341930 CTAGCCATTC
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
26 30 1.00
ACGTcount: A:0.39, C:0.25, G:0.00, T:0.36
Consensus pattern (26 bp):
CACATATACATATCTCATACATATTT
Found at i:53352051 original size:40 final size:40
Alignment explanation
Indices: 53351950--53352140 Score: 242
Period size: 40 Copynumber: 4.8 Consensus size: 40
53351940 TGGATGATAA
* * * * **
53351950 CCGGGCTAAGTCCCGAAGGCATCTGCGCTAGTGACTAGTT
1 CCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTAAAT
*
53351990 CCGTGC-AAGTCCCGAAGGCATTTGTGCGAGTTACTAAAT
1 CCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTAAAT
*
53352029 CCGGGCTAAGTCCCGAAGGCATTTGTGTGAGTTACTAAAT
1 CCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTAAAT
* *
53352069 CCGGGCTAAGTCCCGAAGGCAATTGTGCGAGTTACTCTAA-
1 CCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACT-AAAT
* * *
53352109 CCGGCCTATGTCCCGAAGGCATTTGAGCGAGT
1 CCGGGCTAAGTCCCGAAGGCATTTGTGCGAGT
53352141 AGCTATATCC
Statistics
Matches: 133, Mismatches: 16, Indels: 4
0.87 0.10 0.03
Matches are distributed among these distances:
39 32 0.24
40 99 0.74
41 2 0.02
ACGTcount: A:0.23, C:0.25, G:0.28, T:0.24
Consensus pattern (40 bp):
CCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTAAAT
Found at i:53356618 original size:39 final size:40
Alignment explanation
Indices: 53356569--53356712 Score: 166
Period size: 39 Copynumber: 3.6 Consensus size: 40
53356559 AATGTTCGAG
*
53356569 TGATACCCGGGCTAAG-CCCGAAGGCAATTGTGCGAGTTA
1 TGATATCCGGGCTAAGTCCCGAAGGCAATTGTGCGAGTTA
* * *
53356608 TGATATCCGGGCTAAG-CCCGAAGGCAATTGTGCAAATTG
1 TGATATCCGGGCTAAGTCCCGAAGGCAATTGTGCGAGTTA
* ** *
53356647 TGATATCCGGGTTAAGTCCCGAAGGCCTTTGTGCGGGTTA
1 TGATATCCGGGCTAAGTCCCGAAGGCAATTGTGCGAGTTA
** * *
53356687 CCATAACCGGGCTATGTCCCGAAGGC
1 TGATATCCGGGCTAAGTCCCGAAGGC
53356713 GTTTGAACGA
Statistics
Matches: 88, Mismatches: 16, Indels: 1
0.84 0.15 0.01
Matches are distributed among these distances:
39 50 0.57
40 38 0.43
ACGTcount: A:0.24, C:0.24, G:0.30, T:0.23
Consensus pattern (40 bp):
TGATATCCGGGCTAAGTCCCGAAGGCAATTGTGCGAGTTA
Found at i:53361973 original size:13 final size:13
Alignment explanation
Indices: 53361955--53361981 Score: 54
Period size: 13 Copynumber: 2.1 Consensus size: 13
53361945 TTGGCCGAAT
53361955 AGAAGAAAAAAAA
1 AGAAGAAAAAAAA
53361968 AGAAGAAAAAAAA
1 AGAAGAAAAAAAA
53361981 A
1 A
53361982 AGCTCTCATG
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 14 1.00
ACGTcount: A:0.85, C:0.00, G:0.15, T:0.00
Consensus pattern (13 bp):
AGAAGAAAAAAAA
Found at i:53362031 original size:53 final size:53
Alignment explanation
Indices: 53361906--53362031 Score: 207
Period size: 53 Copynumber: 2.4 Consensus size: 53
53361896 GATGATGAAA
*
53361906 AAAAAGAAAAGAAAGAAAAAAAAAGCTCTCATGTTGTTCTTGGCCGAATAGAAG
1 AAAAA-AAAAGAAGGAAAAAAAAAGCTCTCATGTTGTTCTTGGCCGAATAGAAG
*
53361960 AAAAAAAAAGAAGAAAAAAAAAAGCTCTCATGTTGTTCTTGGCCGAATAGAAG
1 AAAAAAAAAGAAGGAAAAAAAAAGCTCTCATGTTGTTCTTGGCCGAATAGAAG
* *
53362013 AAAGAAAAAGATGGAAAAA
1 AAAAAAAAAGAAGGAAAAA
53362032 GAGCTTTGAG
Statistics
Matches: 67, Mismatches: 5, Indels: 1
0.92 0.07 0.01
Matches are distributed among these distances:
53 62 0.93
54 5 0.07
ACGTcount: A:0.54, C:0.10, G:0.20, T:0.17
Consensus pattern (53 bp):
AAAAAAAAAGAAGGAAAAAAAAAGCTCTCATGTTGTTCTTGGCCGAATAGAAG
Found at i:53362566 original size:40 final size:40
Alignment explanation
Indices: 53362467--53362657 Score: 251
Period size: 40 Copynumber: 4.8 Consensus size: 40
53362457 TGGATGATAA
* * * * * **
53362467 CCGGGCTAAGTCCCAAAGGCATCTGCGCTAGTGACTAGTT
1 CCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTAAAT
53362507 CCGGGC-AAGTCCCGAAGGCATTTGTGCGAGTTACTAAAT
1 CCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTAAAT
*
53362546 CCGGGCTAAGTCTCGAAGGCATTTGTGCGAGTTACTAAAT
1 CCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTAAAT
* *
53362586 CCGGGCTAAGTCCCGAAGGCAATTGTGCGAGTTACTCTAA-
1 CCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACT-AAAT
* *
53362626 CCGGGCTATGTCCCGAAGGCATTTGAGCGAGT
1 CCGGGCTAAGTCCCGAAGGCATTTGTGCGAGT
53362658 AGCTATATTC
Statistics
Matches: 135, Mismatches: 14, Indels: 4
0.88 0.09 0.03
Matches are distributed among these distances:
39 32 0.24
40 101 0.75
41 2 0.01
ACGTcount: A:0.24, C:0.24, G:0.29, T:0.24
Consensus pattern (40 bp):
CCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTAAAT
Found at i:53366400 original size:46 final size:46
Alignment explanation
Indices: 53366350--53366521 Score: 217
Period size: 46 Copynumber: 3.7 Consensus size: 46
53366340 GGTTGAGCAT
53366350 CCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAATGC
1 CCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAATGC
* * *
53366396 CCGAACTCGTTGAGTTGAGTCCGAGTTC-GTGA--GATG-TAACTAGGC
1 CCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAA-T--GC
* *
53366441 ATCCGAACTCGTTGAGTTGAGTCCGAGTTCATTTATGGATGCGAACGC
1 --CCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAATGC
*
53366489 CCGAGCTCGTTGAGTTGAGTCCGAGTTCACTTA
1 CCGAACTCGTTGAGTTGAGTCCGAGTTCACTTA
53366522 GGGGCGGGTT
Statistics
Matches: 108, Mismatches: 9, Indels: 18
0.80 0.07 0.13
Matches are distributed among these distances:
42 2 0.02
43 5 0.05
45 4 0.04
46 59 0.55
47 28 0.26
48 4 0.04
50 4 0.04
51 2 0.02
ACGTcount: A:0.22, C:0.22, G:0.28, T:0.28
Consensus pattern (46 bp):
CCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAATGC
Found at i:53366505 original size:93 final size:93
Alignment explanation
Indices: 53366346--53366516 Score: 315
Period size: 93 Copynumber: 1.8 Consensus size: 93
53366336 GGATGGTTGA
*
53366346 GCATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAATGCCCGAACTCGTTGAGT
1 GCATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAACGCCCGAACTCGTTGAGT
53366411 TGAGTCCGAGTTCGTGAGATGTAACTAG
66 TGAGTCCGAGTTCGTGAGATGTAACTAG
* *
53366439 GCATCCGAACTCGTTGAGTTGAGTCCGAGTTCATTTATGGATGCGAACGCCCGAGCTCGTTGAGT
1 GCATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAACGCCCGAACTCGTTGAGT
53366504 TGAGTCCGAGTTC
66 TGAGTCCGAGTTC
53366517 ACTTAGGGGC
Statistics
Matches: 75, Mismatches: 3, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
93 75 1.00
ACGTcount: A:0.21, C:0.22, G:0.29, T:0.28
Consensus pattern (93 bp):
GCATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAACGCCCGAACTCGTTGAGT
TGAGTCCGAGTTCGTGAGATGTAACTAG
Found at i:53366781 original size:19 final size:20
Alignment explanation
Indices: 53366746--53366783 Score: 53
Period size: 19 Copynumber: 1.9 Consensus size: 20
53366736 ATAAGGTGGT
53366746 AAGATAATGAATGATGTTTA
1 AAGATAATGAATGATGTTTA
53366766 AAGAT-ATGATAT-ATGTTT
1 AAGATAATGA-ATGATGTTT
53366784 TGGTGGTACC
Statistics
Matches: 17, Mismatches: 0, Indels: 3
0.85 0.00 0.15
Matches are distributed among these distances:
19 10 0.59
20 7 0.41
ACGTcount: A:0.42, C:0.00, G:0.18, T:0.39
Consensus pattern (20 bp):
AAGATAATGAATGATGTTTA
Found at i:53372589 original size:2 final size:2
Alignment explanation
Indices: 53372582--53372616 Score: 70
Period size: 2 Copynumber: 17.5 Consensus size: 2
53372572 GGCCAACAAG
53372582 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
53372617 AAGAGGAAAA
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 33 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:53373413 original size:2 final size:2
Alignment explanation
Indices: 53373406--53373432 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
53373396 TCATACATAC
53373406 AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT A
53373433 CCAGAATTGC
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 25 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:53380917 original size:9 final size:9
Alignment explanation
Indices: 53380903--53380933 Score: 53
Period size: 9 Copynumber: 3.3 Consensus size: 9
53380893 GATTAAGTAA
53380903 AATTAAATT
1 AATTAAATT
53380912 AATTAAATT
1 AATTAAATT
53380921 AATTGAAATT
1 AATT-AAATT
53380931 AAT
1 AAT
53380934 ATGATATTTT
Statistics
Matches: 21, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
9 13 0.62
10 8 0.38
ACGTcount: A:0.55, C:0.00, G:0.03, T:0.42
Consensus pattern (9 bp):
AATTAAATT
Found at i:53381376 original size:17 final size:19
Alignment explanation
Indices: 53381329--53381377 Score: 57
Period size: 20 Copynumber: 2.6 Consensus size: 19
53381319 AATAGTATTT
*
53381329 TATTAATTTAATATTAAAG
1 TATTATTTTAATATTAAAG
*
53381348 TGATTATCTTAATATTAAA-
1 T-ATTATTTTAATATTAAAG
53381367 T-TTATTTTAAT
1 TATTATTTTAAT
53381378 GTTTATATTG
Statistics
Matches: 26, Mismatches: 3, Indels: 4
0.79 0.09 0.12
Matches are distributed among these distances:
17 9 0.35
19 2 0.08
20 15 0.58
ACGTcount: A:0.41, C:0.02, G:0.04, T:0.53
Consensus pattern (19 bp):
TATTATTTTAATATTAAAG
Found at i:53384291 original size:41 final size:41
Alignment explanation
Indices: 53384234--53384315 Score: 164
Period size: 41 Copynumber: 2.0 Consensus size: 41
53384224 TCAACTAAAT
53384234 GGTTGGGAGGCACGTGCTTTGTCAATTGTAGGAAGAGTCAC
1 GGTTGGGAGGCACGTGCTTTGTCAATTGTAGGAAGAGTCAC
53384275 GGTTGGGAGGCACGTGCTTTGTCAATTGTAGGAAGAGTCAC
1 GGTTGGGAGGCACGTGCTTTGTCAATTGTAGGAAGAGTCAC
53384316 TCTTACAAAA
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:0.22, C:0.15, G:0.37, T:0.27
Consensus pattern (41 bp):
GGTTGGGAGGCACGTGCTTTGTCAATTGTAGGAAGAGTCAC
Found at i:53386801 original size:60 final size:58
Alignment explanation
Indices: 53386727--53386859 Score: 151
Period size: 60 Copynumber: 2.3 Consensus size: 58
53386717 ATTTAAGCCC
* * * * *
53386727 GCACACATAGTGCCATACCCTTCGAGC-TCGCACACCCAGTGCCGTATTTTTTTCCAGCAT
1 GCACACTTAGTGCCATACACTTCCAGCAT-GCACACCCAGTGCC--ATATATTTCCAGCAT
* * **
53386787 GCACACTTAGTGCCATATATTTCCAGCATGCACACTTAGTGCCATATATTTCCAGCAT
1 GCACACTTAGTGCCATACACTTCCAGCATGCACACCCAGTGCCATATATTTCCAGCAT
53386845 GCACACTTAGTGCCA
1 GCACACTTAGTGCCA
53386860 ATCTCGTCAC
Statistics
Matches: 63, Mismatches: 9, Indels: 4
0.83 0.12 0.05
Matches are distributed among these distances:
58 28 0.44
60 34 0.54
61 1 0.02
ACGTcount: A:0.25, C:0.32, G:0.16, T:0.28
Consensus pattern (58 bp):
GCACACTTAGTGCCATACACTTCCAGCATGCACACCCAGTGCCATATATTTCCAGCAT
Found at i:53386817 original size:29 final size:29
Alignment explanation
Indices: 53386777--53386859 Score: 166
Period size: 29 Copynumber: 2.9 Consensus size: 29
53386767 GCCGTATTTT
53386777 TTTCCAGCATGCACACTTAGTGCCATATA
1 TTTCCAGCATGCACACTTAGTGCCATATA
53386806 TTTCCAGCATGCACACTTAGTGCCATATA
1 TTTCCAGCATGCACACTTAGTGCCATATA
53386835 TTTCCAGCATGCACACTTAGTGCCA
1 TTTCCAGCATGCACACTTAGTGCCA
53386860 ATCTCGTCAC
Statistics
Matches: 54, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
29 54 1.00
ACGTcount: A:0.27, C:0.29, G:0.14, T:0.30
Consensus pattern (29 bp):
TTTCCAGCATGCACACTTAGTGCCATATA
Found at i:53388054 original size:21 final size:18
Alignment explanation
Indices: 53388019--53388067 Score: 57
Period size: 18 Copynumber: 2.7 Consensus size: 18
53388009 GAACGAACAC
53388019 TTTTTTTTTTC-T-TTTCT
1 TTTTTTTTTTCATATTT-T
*
53388036 TTGTTTTTCTTCATATTTT
1 TT-TTTTTTTTCATATTTT
53388055 TTTTTTTTTTCAT
1 TTTTTTTTTTCAT
53388068 TTCTTTATTC
Statistics
Matches: 27, Mismatches: 2, Indels: 5
0.79 0.06 0.15
Matches are distributed among these distances:
17 2 0.07
18 18 0.67
19 4 0.15
20 3 0.11
ACGTcount: A:0.06, C:0.10, G:0.02, T:0.82
Consensus pattern (18 bp):
TTTTTTTTTTCATATTTT
Found at i:53388079 original size:33 final size:32
Alignment explanation
Indices: 53388019--53388080 Score: 90
Period size: 32 Copynumber: 1.9 Consensus size: 32
53388009 GAACGAACAC
*
53388019 TTTTTTTTTTCTTTTCTTTGTTTTTCTTCATA
1 TTTTTTTTTTCTTTTCTTTCTTTTTCTTCATA
53388051 TTTTTTTTTT-TTTTCATTTCTTTATTCTTC
1 TTTTTTTTTTCTTTTC-TTTCTTT-TTCTTC
53388081 CTACATAATC
Statistics
Matches: 27, Mismatches: 1, Indels: 3
0.87 0.03 0.10
Matches are distributed among these distances:
31 5 0.19
32 16 0.59
33 6 0.22
ACGTcount: A:0.06, C:0.13, G:0.02, T:0.79
Consensus pattern (32 bp):
TTTTTTTTTTCTTTTCTTTCTTTTTCTTCATA
Found at i:53389688 original size:19 final size:19
Alignment explanation
Indices: 53389643--53389681 Score: 69
Period size: 19 Copynumber: 2.1 Consensus size: 19
53389633 TTGATAACTC
*
53389643 ACACAAAGTGCCAATACAT
1 ACACGAAGTGCCAATACAT
53389662 ACACGAAGTGCCAATACAT
1 ACACGAAGTGCCAATACAT
53389681 A
1 A
53389682 GCCGAAGCTA
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:0.46, C:0.26, G:0.13, T:0.15
Consensus pattern (19 bp):
ACACGAAGTGCCAATACAT
Found at i:53391394 original size:15 final size:15
Alignment explanation
Indices: 53391362--53391390 Score: 51
Period size: 14 Copynumber: 2.0 Consensus size: 15
53391352 ATTTTCTGTG
53391362 TTTATTATGTGTGAA
1 TTTATTATGTGTGAA
53391377 TTTA-TATGTGTGAA
1 TTTATTATGTGTGAA
53391391 ATTTTTGTGC
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
14 10 0.71
15 4 0.29
ACGTcount: A:0.28, C:0.00, G:0.21, T:0.52
Consensus pattern (15 bp):
TTTATTATGTGTGAA
Found at i:53392550 original size:45 final size:45
Alignment explanation
Indices: 53392486--53392596 Score: 186
Period size: 45 Copynumber: 2.5 Consensus size: 45
53392476 TAGGATTCCA
53392486 ATATGTGATTTTGTGTAAGACCACGTCTAGGACATTGGCATCGAT
1 ATATGTGATTTTGTGTAAGACCACGTCTAGGACATTGGCATCGAT
* *
53392531 ATATGTGATTTTGTGTAAGACCACGTCTGGGACATTGTCATCGAT
1 ATATGTGATTTTGTGTAAGACCACGTCTAGGACATTGGCATCGAT
* *
53392576 ATATGTGGTTATGTGTAAGAC
1 ATATGTGATTTTGTGTAAGAC
53392597 ATTGTTTAGA
Statistics
Matches: 62, Mismatches: 4, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
45 62 1.00
ACGTcount: A:0.26, C:0.14, G:0.25, T:0.35
Consensus pattern (45 bp):
ATATGTGATTTTGTGTAAGACCACGTCTAGGACATTGGCATCGAT
Found at i:53393297 original size:14 final size:14
Alignment explanation
Indices: 53393278--53393306 Score: 58
Period size: 14 Copynumber: 2.1 Consensus size: 14
53393268 AGCTCGAGGA
53393278 TCGTCAGTAAAGTC
1 TCGTCAGTAAAGTC
53393292 TCGTCAGTAAAGTC
1 TCGTCAGTAAAGTC
53393306 T
1 T
53393307 ATCACACTAT
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 15 1.00
ACGTcount: A:0.28, C:0.21, G:0.21, T:0.31
Consensus pattern (14 bp):
TCGTCAGTAAAGTC
Found at i:53395351 original size:40 final size:39
Alignment explanation
Indices: 53395287--53395453 Score: 151
Period size: 40 Copynumber: 4.2 Consensus size: 39
53395277 TCTTCAGAAT
* **
53395287 TTAG-CCGGATATAACCACAAGCACAATTGCCTTCGGGTC
1 TTAGCCCGGATATAACAACTCGCACAA-TGCCTTCGGGTC
* * *** *
53395326 TTAACCCGGATTTGGTAACTTGCACAAATGCCTTCGGGTC
1 TTAGCCCGGATATAACAACTCGCAC-AATGCCTTCGGGTC
53395366 TTAGCCCGGATATAACAACTCGCACGAATGCCTTCGGGTC
1 TTAGCCCGGATATAACAACTCGCAC-AATGCCTTCGGGTC
* * *
53395406 TTAGCCCGGATGTAATC-ACTAGCATAAATGCCTTCGAGG-C
1 TTAGCCCGGATATAA-CAACTCGCA-CAATGCCTTCG-GGTC
53395446 TTAGCCCG
1 TTAGCCCG
53395454 TGTATCATTC
Statistics
Matches: 105, Mismatches: 18, Indels: 9
0.80 0.14 0.07
Matches are distributed among these distances:
39 3 0.03
40 97 0.92
41 5 0.05
ACGTcount: A:0.25, C:0.28, G:0.22, T:0.25
Consensus pattern (39 bp):
TTAGCCCGGATATAACAACTCGCACAATGCCTTCGGGTC
Found at i:53395435 original size:80 final size:80
Alignment explanation
Indices: 53395287--53395453 Score: 205
Period size: 80 Copynumber: 2.1 Consensus size: 80
53395277 TCTTCAGAAT
* * ** *
53395287 TTAG-CCGGATATAACCACAAGCACAATTGCCTTCGGGTCTTAACCCGGATTTGGTAACTTGCAC
1 TTAGCCCGGATATAACAACAAGCACAATTGCCTTCGGGTCTTAACCCGGATGTAATAACTAGCAC
53395351 AAATGCCTTCG-GGTC
66 AAATGCCTTCGAGG-C
** * *
53395366 TTAGCCCGGATATAACAACTCGCACGAA-TGCCTTCGGGTCTTAGCCCGGATGTAATCACTAGCA
1 TTAGCCCGGATATAACAACAAGCAC-AATTGCCTTCGGGTCTTAACCCGGATGTAATAACTAGCA
*
53395430 TAAATGCCTTCGAGGC
65 CAAATGCCTTCGAGGC
53395446 TTAGCCCG
1 TTAGCCCG
53395454 TGTATCATTC
Statistics
Matches: 75, Mismatches: 10, Indels: 5
0.83 0.11 0.06
Matches are distributed among these distances:
79 4 0.05
80 67 0.89
81 4 0.05
ACGTcount: A:0.25, C:0.28, G:0.22, T:0.25
Consensus pattern (80 bp):
TTAGCCCGGATATAACAACAAGCACAATTGCCTTCGGGTCTTAACCCGGATGTAATAACTAGCAC
AAATGCCTTCGAGGC
Found at i:53399208 original size:48 final size:48
Alignment explanation
Indices: 53399091--53399306 Score: 140
Period size: 48 Copynumber: 4.6 Consensus size: 48
53399081 TAGTAAGATG
* * * * *
53399091 CAATGCCATATCCCAGATATGGTCTTACATGGGATCATAGATTGA-AG
1 CAATGCCATATCCCAGATATGGTCTTACACGAGATCAAATATTGATAC
* * ** * **
53399138 C--T--AATAGCCCATCTATGGTCTTATACGATG-TCTCATATTGATAC
1 CAATGCCATATCCCAGATATGGTCTTACACGA-GATCAAATATTGATAC
* *
53399182 TAATGCCATATCCCAGATATGGTCTTACATGAGATCAAATATTGATAC
1 CAATGCCATATCCCAGATATGGTCTTACACGAGATCAAATATTGATAC
* * * * * * *
53399230 CAATGCCATGTCCCAGACATGGTTTTACATGGGATCACAAT-TCGATGC
1 CAATGCCATATCCCAGATATGGTCTTACACGAGATCA-AATATTGATAC
** **
53399278 CAATGCCATGCCCCAGACCTGGTCTTACA
1 CAATGCCATATCCCAGATATGGTCTTACA
53399307 TGGGATCACA
Statistics
Matches: 131, Mismatches: 30, Indels: 15
0.74 0.17 0.09
Matches are distributed among these distances:
43 27 0.21
44 2 0.02
45 1 0.01
46 1 0.01
47 2 0.02
48 95 0.73
49 3 0.02
ACGTcount: A:0.30, C:0.24, G:0.18, T:0.29
Consensus pattern (48 bp):
CAATGCCATATCCCAGATATGGTCTTACACGAGATCAAATATTGATAC
Found at i:53399307 original size:48 final size:49
Alignment explanation
Indices: 53399183--53399364 Score: 217
Period size: 48 Copynumber: 3.8 Consensus size: 49
53399173 TATTGATACT
* * * * *
53399183 AATGCCATATCCCAGATATGGTCTTACATGAGATCA-AATATTGATACC
1 AATGCCATGTCCCAGACATGGTCTTACATGGGATCACAATATCGATGCC
*
53399231 AATGCCATGTCCCAGACATGGTTTTACATGGGATCACAAT-TCGATGCC
1 AATGCCATGTCCCAGACATGGTCTTACATGGGATCACAATATCGATGCC
* * * *
53399279 AATGCCATGCCCCAGACCTGGTCTTACATGGGATCAC-ATATCAATGTC
1 AATGCCATGTCCCAGACATGGTCTTACATGGGATCACAATATCGATGCC
* * * *
53399327 AATGCCATGTCCCTGACATGCTCTTTCCTGGGATCACA
1 AATGCCATGTCCCAGACATGGTCTTACATGGGATCACA
53399365 TATAACCCTA
Statistics
Matches: 114, Mismatches: 17, Indels: 5
0.84 0.12 0.04
Matches are distributed among these distances:
47 2 0.02
48 109 0.96
49 3 0.03
ACGTcount: A:0.28, C:0.26, G:0.18, T:0.27
Consensus pattern (49 bp):
AATGCCATGTCCCAGACATGGTCTTACATGGGATCACAATATCGATGCC
Found at i:53412001 original size:79 final size:81
Alignment explanation
Indices: 53411918--53412067 Score: 225
Period size: 79 Copynumber: 1.9 Consensus size: 81
53411908 TTATAATGAT
* * *
53411918 TCGCACAATTGCCTTCGGGAATT-AGCCCGGATTTAGTAAC-TCGCA-AAATGCCTTCGGGACTT
1 TCGCACAAATGCCTTCGGGAATTGA-CCCGGATTTAGTAACTTAGCACAAAAGCCTTCGGGACTT
53411980 AACCCGGTTTTGGTAAC
65 AACCCGGTTTTGGTAAC
*
53411997 TCGCACAAATGCCTTCGGGAATTGACCCGGATTTAGTCACTTAGCACAAAAGCCTTCGGGACTTA
1 TCGCACAAATGCCTTCGGGAATTGACCCGGATTTAGTAACTTAGCACAAAAGCCTTCGGGACTTA
*
53412062 GCCCGG
66 ACCCGG
53412068 ATATCATTCG
Statistics
Matches: 63, Mismatches: 5, Indels: 4
0.88 0.07 0.06
Matches are distributed among these distances:
79 36 0.57
80 5 0.08
81 22 0.35
ACGTcount: A:0.25, C:0.27, G:0.23, T:0.25
Consensus pattern (81 bp):
TCGCACAAATGCCTTCGGGAATTGACCCGGATTTAGTAACTTAGCACAAAAGCCTTCGGGACTTA
ACCCGGTTTTGGTAAC
Found at i:53412067 original size:41 final size:40
Alignment explanation
Indices: 53411918--53412069 Score: 191
Period size: 39 Copynumber: 3.8 Consensus size: 40
53411908 TTATAATGAT
*
53411918 TCGCACAATTGCCTTCGGGAATTAGCCCGGATTTAGTAAC
1 TCGCACAAATGCCTTCGGGAATTAGCCCGGATTTAGTAAC
* * * *
53411958 TCGCA-AAATGCCTTCGGGACTTAACCCGGTTTTGGTAAC
1 TCGCACAAATGCCTTCGGGAATTAGCCCGGATTTAGTAAC
*
53411997 TCGCACAAATGCCTTCGGGAATT-GACCCGGATTTAGTCAC
1 TCGCACAAATGCCTTCGGGAATTAG-CCCGGATTTAGTAAC
* * *
53412037 TTAGCACAAAAGCCTTCGGGACTTAGCCCGGAT
1 -TCGCACAAATGCCTTCGGGAATTAGCCCGGAT
53412070 ATCATTCGAA
Statistics
Matches: 95, Mismatches: 13, Indels: 7
0.83 0.11 0.06
Matches are distributed among these distances:
39 34 0.36
40 33 0.35
41 27 0.28
42 1 0.01
ACGTcount: A:0.25, C:0.26, G:0.23, T:0.26
Consensus pattern (40 bp):
TCGCACAAATGCCTTCGGGAATTAGCCCGGATTTAGTAAC
Found at i:53416357 original size:15 final size:17
Alignment explanation
Indices: 53416322--53416361 Score: 57
Period size: 18 Copynumber: 2.4 Consensus size: 17
53416312 GTAACGGATA
53416322 TTTATTCTTTATCGTCAC
1 TTTATTCTTTA-CGTCAC
53416340 TTTATTCTTTA-G-CAC
1 TTTATTCTTTACGTCAC
53416355 TTTATTC
1 TTTATTC
53416362 AGCTGACGAT
Statistics
Matches: 22, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
15 10 0.45
16 1 0.05
18 11 0.50
ACGTcount: A:0.17, C:0.20, G:0.05, T:0.57
Consensus pattern (17 bp):
TTTATTCTTTACGTCAC
Found at i:53426357 original size:40 final size:40
Alignment explanation
Indices: 53426320--53426545 Score: 255
Period size: 40 Copynumber: 5.7 Consensus size: 40
53426310 GCTACTCGTT
*
53426320 CAAATGCCTTCGGGA-CATAGCCCGG-TTATAGTAACTCGCA
1 CAAATGCCTTC-GGATCTTAGCCCGGATT-TAGTAACTCGCA
* *
53426360 CAGATGCCTTCGGGA-CTTAACCCGGATTTAGTAACTCGCA
1 CAAATGCCTTC-GGATCTTAGCCCGGATTTAGTAACTCGCA
*
53426400 CAAATGCCTTCGGATCTTAGTCCGGATTTAGTAACTCGCA
1 CAAATGCCTTCGGATCTTAGCCCGGATTTAGTAACTCGCA
* * *
53426440 CGAATGCCTTCGGATCTTAGTCCGGATTTAGTAACTCACA
1 CAAATGCCTTCGGATCTTAGCCCGGATTTAGTAACTCGCA
* * * * *
53426480 CGAATGCCTTCGGATCTTAGTCCGGATATAGTCACTTAGCA
1 CAAATGCCTTCGGATCTTAGCCCGGATTTAGTAAC-TCGCA
*
53426521 CAAA-GCCTTCGGGA-CATAGCCCGGA
1 CAAATGCCTTC-GGATCTTAGCCCGGA
53426546 CATCATTCGA
Statistics
Matches: 167, Mismatches: 15, Indels: 8
0.88 0.08 0.04
Matches are distributed among these distances:
39 3 0.02
40 153 0.92
41 11 0.07
ACGTcount: A:0.26, C:0.27, G:0.22, T:0.26
Consensus pattern (40 bp):
CAAATGCCTTCGGATCTTAGCCCGGATTTAGTAACTCGCA
Found at i:53433148 original size:40 final size:40
Alignment explanation
Indices: 53433093--53433287 Score: 302
Period size: 40 Copynumber: 4.9 Consensus size: 40
53433083 GGATATAGCT
*
53433093 ACTCGCTCAAATGCCTTCGGGACTTAGCCCGGTTATAGTA
1 ACTCGCACAAATGCCTTCGGGACTTAGCCCGGTTATAGTA
*
53433133 ACTCGCACAATTGCCTTCGGGACTTAGCCCGGTTATAGTA
1 ACTCGCACAAATGCCTTCGGGACTTAGCCCGGTTATAGTA
* * * *
53433173 ACTCACACAATTGCCTTCAGGACTTGGCCCGGTTATAGTA
1 ACTCGCACAAATGCCTTCGGGACTTAGCCCGGTTATAGTA
* *
53433213 ACTCGCACAAATGCCTTCGGGACTTAGCCCGGATATATTA
1 ACTCGCACAAATGCCTTCGGGACTTAGCCCGGTTATAGTA
*
53433253 ACTCGCACAAATGCCTTCGGG-CTTAGCCTGGTTAT
1 ACTCGCACAAATGCCTTCGGGACTTAGCCCGGTTAT
53433288 CAATCCGAAT
Statistics
Matches: 142, Mismatches: 13, Indels: 1
0.91 0.08 0.01
Matches are distributed among these distances:
39 12 0.08
40 130 0.92
ACGTcount: A:0.24, C:0.28, G:0.22, T:0.27
Consensus pattern (40 bp):
ACTCGCACAAATGCCTTCGGGACTTAGCCCGGTTATAGTA
Done.