Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Chr11 124536837
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: 124536837
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
Warning! 312 characters in sequence are not A, C, G, or T
File 104 of 427
Found at i:27484519 original size:27 final size:25
Alignment explanation
Indices: 27484489--27484551 Score: 65
Period size: 27 Copynumber: 2.4 Consensus size: 25
27484479 GAGTATTGAT
27484489 TAAAAATAATACTAATAATAG-TAATAG
1 TAAAAATAATA--AATAATAGAT-ATAG
27484516 TAAAATACTAATAAATAATAGATATAG
1 TAAAA-A-TAATAAATAATAGATATAG
*
27484543 TAATAATAA
1 TAAAAATAA
27484552 GAATATATAA
Statistics
Matches: 32, Mismatches: 1, Indels: 8
0.78 0.02 0.20
Matches are distributed among these distances:
25 3 0.09
26 1 0.03
27 21 0.66
28 2 0.06
29 5 0.16
ACGTcount: A:0.60, C:0.03, G:0.06, T:0.30
Consensus pattern (25 bp):
TAAAAATAATAAATAATAGATATAG
Found at i:27484834 original size:16 final size:16
Alignment explanation
Indices: 27484813--27484859 Score: 53
Period size: 15 Copynumber: 3.0 Consensus size: 16
27484803 TATTTAAGAA
27484813 TATAAACATAATATAG
1 TATAAACATAATATAG
27484829 TATAAA-ATATATATA-
1 TATAAACATA-ATATAG
* *
27484844 TATACACGTAATATAG
1 TATAAACATAATATAG
27484860 AATTTAAAAT
Statistics
Matches: 26, Mismatches: 2, Indels: 6
0.76 0.06 0.18
Matches are distributed among these distances:
15 13 0.50
16 13 0.50
ACGTcount: A:0.53, C:0.06, G:0.06, T:0.34
Consensus pattern (16 bp):
TATAAACATAATATAG
Found at i:27484923 original size:15 final size:15
Alignment explanation
Indices: 27484903--27484942 Score: 53
Period size: 15 Copynumber: 2.7 Consensus size: 15
27484893 TATACATAAT
*
27484903 ATAATATTAAGAAAA
1 ATAATATTAACAAAA
*
27484918 ATAATAATAACAAAA
1 ATAATATTAACAAAA
*
27484933 AAAATATTAA
1 ATAATATTAA
27484943 TAATACTATA
Statistics
Matches: 21, Mismatches: 4, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
15 21 1.00
ACGTcount: A:0.70, C:0.03, G:0.03, T:0.25
Consensus pattern (15 bp):
ATAATATTAACAAAA
Found at i:27485016 original size:22 final size:22
Alignment explanation
Indices: 27484997--27485039 Score: 61
Period size: 22 Copynumber: 2.0 Consensus size: 22
27484987 ATACTAATGC
27484997 TAATAAATAAT-AAATATAATAA
1 TAAT-AATAATAAAATATAATAA
*
27485019 TAATAGTAATAAAATATAATA
1 TAATAATAATAAAATATAATA
27485040 GTATTCATAA
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
21 5 0.26
22 14 0.74
ACGTcount: A:0.65, C:0.00, G:0.02, T:0.33
Consensus pattern (22 bp):
TAATAATAATAAAATATAATAA
Found at i:27485515 original size:2 final size:2
Alignment explanation
Indices: 27485508--27485591 Score: 168
Period size: 2 Copynumber: 42.0 Consensus size: 2
27485498 TTGAAAGAAA
27485508 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG
1 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG
27485550 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG
1 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG
27485592 GGGTGGGCGA
Statistics
Matches: 82, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 82 1.00
ACGTcount: A:0.50, C:0.00, G:0.50, T:0.00
Consensus pattern (2 bp):
AG
Found at i:27485742 original size:2 final size:2
Alignment explanation
Indices: 27485737--27485763 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
27485727 TATGCTTTTT
27485737 TA 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 T
27485764 GTGTGTGCAT
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:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:27486588 original size:21 final size:21
Alignment explanation
Indices: 27486563--27486612 Score: 64
Period size: 21 Copynumber: 2.4 Consensus size: 21
27486553 AAGATAAGAT
**
27486563 CTGCAACTTCAATGTGCTCCA
1 CTGCAACTTCAATCAGCTCCA
*
27486584 CTGCAACTTCGATCAGCTCCA
1 CTGCAACTTCAATCAGCTCCA
*
27486605 CTGTAACT
1 CTGCAACT
27486613 GCAAGGCTCT
Statistics
Matches: 25, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
21 25 1.00
ACGTcount: A:0.24, C:0.34, G:0.14, T:0.28
Consensus pattern (21 bp):
CTGCAACTTCAATCAGCTCCA
Found at i:27486915 original size:76 final size:75
Alignment explanation
Indices: 27486787--27487011 Score: 346
Period size: 76 Copynumber: 3.0 Consensus size: 75
27486777 AAAAACAGAA
* *
27486787 TTTGAAAAATAGAAACTGAAAATGCCTCAGCATGTCCTGAGGTTCAACTCACCTCTCGCAATATG
1 TTTGAAAAATAGAAATTGAAAATACCTCAGCATGTCCTGAGGTTCAACTCACCTCTCGCAATATG
27486852 AGCTTGATTTT
66 AG-TTGATTTT
* * *
27486863 TTTGAAAAACAGAAATTGAAAATACCTCAGCATGTCCCGAGGTTCAAATCACCTCTCGCAATATG
1 TTTGAAAAATAGAAATTGAAAATACCTCAGCATGTCCTGAGGTTCAACTCACCTCTCGCAATATG
27486928 AGTTGATTTTT
66 AGTTGA-TTTT
** *
27486939 TTTTCAAAATAGAAATTGAAAATACCTCAGC--GTCCTGAGGCTCAACTCACCTCTCGCAATATG
1 TTTGAAAAATAGAAATTGAAAATACCTCAGCATGTCCTGAGGTTCAACTCACCTCTCGCAATATG
27487002 AGTTGATTTT
66 AGTTGATTTT
27487012 GACGAACATA
Statistics
Matches: 137, Mismatches: 11, Indels: 5
0.90 0.07 0.03
Matches are distributed among these distances:
73 4 0.03
74 35 0.26
75 4 0.03
76 94 0.69
ACGTcount: A:0.32, C:0.21, G:0.16, T:0.31
Consensus pattern (75 bp):
TTTGAAAAATAGAAATTGAAAATACCTCAGCATGTCCTGAGGTTCAACTCACCTCTCGCAATATG
AGTTGATTTT
Found at i:27487050 original size:160 final size:163
Alignment explanation
Indices: 27486864--27487176 Score: 499
Period size: 162 Copynumber: 1.9 Consensus size: 163
27486854 CTTGATTTTT
* * *
27486864 TTGAAAAACAGAAATTGAAAATACCTCAGCATGT-CCCGAGGTTCAAATCACCTCTCGCAATATG
1 TTGAAAAACAGAAACTGAAAATACCTCAACATGTACCCGAGGCTCAAATCACCTCTCGCAATATG
*
27486928 AGTTGATTTTTTTTTCAA-AATAGAAATTGAAAA-TACCTCAGC-GTCCTGAGGCTCAACTCACC
66 AGTTGATTTTTTTTTCAAGAACAGAAATT-AAAATTACCTCAGCAGTCCTGAGGCTCAACTCACC
27486990 TCTCGCAATATGAGTTGATTTTGACGAACATAAA
130 TCTCGCAATATGAGTTGATTTTGACGAACATAAA
* *
27487024 TTGAAAAACAGAAACTGAAAATACCTCAACATGTGAGCCGAGGCTCAACTCACCTCTCGCAATAT
1 TTGAAAAACAGAAACTGAAAATACCTCAACATGT-ACCCGAGGCTCAAATCACCTCTCGCAATAT
*
27487089 GAGTTGATTTTTTTTTTAAGAACAGAAATTAAAATTACCTCAGCATGTCCTGAGGCTCAACTCAC
65 GAGTTGATTTTTTTTTCAAGAACAGAAATTAAAATTACCTCAGCA-GTCCTGAGGCTCAACTCAC
*
27487154 CTCTTGCAATATGAGTTGATTTT
129 CTCTCGCAATATGAGTTGATTTT
27487177 TTTTTTGAAG
Statistics
Matches: 139, Mismatches: 8, Indels: 7
0.90 0.05 0.05
Matches are distributed among these distances:
160 32 0.23
162 48 0.35
163 18 0.13
165 41 0.29
ACGTcount: A:0.34, C:0.21, G:0.16, T:0.29
Consensus pattern (163 bp):
TTGAAAAACAGAAACTGAAAATACCTCAACATGTACCCGAGGCTCAAATCACCTCTCGCAATATG
AGTTGATTTTTTTTTCAAGAACAGAAATTAAAATTACCTCAGCAGTCCTGAGGCTCAACTCACCT
CTCGCAATATGAGTTGATTTTGACGAACATAAA
Found at i:27487156 original size:239 final size:240
Alignment explanation
Indices: 27486736--27487258 Score: 727
Period size: 239 Copynumber: 2.2 Consensus size: 240
27486726 CATGTGACCC
* * *
27486736 GAGGCTCAACTCACCTCTCGCAATATGAGCTGACTTTTGATAAAAACAGAATTTGAAAAATAGAA
1 GAGGCTCAACTCACCTCTCGCAATATGAGTTGA-TTTTGA-AAAAACAGAAATTGAAAAACAGAA
* * *
27486801 ACTGAAAATGCCTCAGCATGTCCTGAGGTTCAACTCACCTCTCGCAATATGAGCTTGATTTTTTT
64 ACTGAAAATACCTCAACATGTCCTGAGGCTCAACTCACCTCTCGCAATATGAGCTTGATTTTTTT
*
27486866 GAAAAACAGAAATTGAAAATACCTCAGCATGTCCCGAGGTTCAAATCACCTCTCGCAATATGAGT
129 GAAAAACAGAAATTGAAAATACCTCAGCATGTCCCGAGGCTCAAATCACCTCTCGCAATATGAGT
*
27486931 TGA-TTTTTTTTTCAAAATAGAAATTGAAAATACCTC-A-GCGTCCT
194 TGATTTTTTTTTTCAAAACAGAAATTGAAAATACCTCAACGCGTCCT
** *
27486975 GAGGCTCAACTCACCTCTCGCAATATGAGTTGATTTTG-ACGAACATAAATTGAAAAACAGAAAC
1 GAGGCTCAACTCACCTCTCGCAATATGAGTTGATTTTGAAAAAACAGAAATTGAAAAACAGAAAC
27487039 TGAAAATACCTCAACATGTGAGCC-GAGGCTCAACTCACCTCTCGCAATATGAG-TTGATTTTTT
66 TGAAAATACCTCAACATGT---CCTGAGGCTCAACTCACCTCTCGCAATATGAGCTTGA--TTTT
* * * * *
27487102 TTTTAAGAACAGAAATT-AAAATTACCTCAGCATGTCCTGAGGCTCAACTCACCTCTTGCAATAT
126 TTTGAAAAACAGAAATTGAAAA-TACCTCAGCATGTCCCGAGGCTCAAATCACCTCTCGCAATAT
* * * *
27487166 GAGTTGATTTTTTTTTTGAAGACAGAAATTGAAAATACCTCAACGTGTCTT
190 GAGTTGATTTTTTTTTTCAAAACAGAAATTGAAAATACCTCAACGCGTCCT
*
27487217 GAGGCTCAACTCACCTCTCTCAATATGAGTTGATTTTTGAAA
1 GAGGCTCAACTCACCTCTCGCAATATGAGTTGA-TTTTGAAA
27487259 CAGAAATAAA
Statistics
Matches: 251, Mismatches: 22, Indels: 17
0.87 0.08 0.06
Matches are distributed among these distances:
236 38 0.15
237 4 0.02
238 37 0.15
239 98 0.39
240 30 0.12
241 1 0.00
242 37 0.15
243 5 0.02
244 1 0.00
ACGTcount: A:0.33, C:0.21, G:0.16, T:0.30
Consensus pattern (240 bp):
GAGGCTCAACTCACCTCTCGCAATATGAGTTGATTTTGAAAAAACAGAAATTGAAAAACAGAAAC
TGAAAATACCTCAACATGTCCTGAGGCTCAACTCACCTCTCGCAATATGAGCTTGATTTTTTTGA
AAAACAGAAATTGAAAATACCTCAGCATGTCCCGAGGCTCAAATCACCTCTCGCAATATGAGTTG
ATTTTTTTTTTCAAAACAGAAATTGAAAATACCTCAACGCGTCCT
Found at i:27487163 original size:77 final size:77
Alignment explanation
Indices: 27486797--27487254 Score: 338
Period size: 77 Copynumber: 5.9 Consensus size: 77
27486787 TTTGAAAAAT
* * * * *
27486797 AGAAACTGAAAATGCCTCAGCATGTCCTGAGGTTCAACTCACCTCTCGCAATATGAGCTTGA---
1 AGAAATTGAAAATACCTCAACATGTCCTGAGGCTCAACTCACCTCTTGCAATATGAG-TTGATTT
*
27486859 TTTTTTTGAAAAAC
65 TTTTTTTG-AAGAC
* * * * *
27486873 AGAAATTGAAAATACCTCAGCATGTCCCGAGGTTCAAATCACCTCTCGCAATATGAGTTGA-TTT
1 AGAAATTGAAAATACCTCAACATGTCCTGAGGCTCAACTCACCTCTTGCAATATGAGTTGATTTT
* * *
27486937 TTTTTTCAAAAT
66 TTTTTTGAAGAC
* *
27486949 AGAAATTGAAAATACCTCAGC--GTCCTGAGGCTCAACTCACCTCTCGCAATATGAGTTGA----
1 AGAAATTGAAAATACCTCAACATGTCCTGAGGCTCAACTCACCTCTTGCAATATGAGTTGATTTT
*
27487008 --TTTTGACGAAC
66 TTTTTTGAAG-AC
* * * * * * *
27487019 ATAAATTGAAAA-ACAGAAACTGAAAATACCTCAACATGTGAGC-CGAGGCTCAACTCACCTCTC
1 AGAAATTGAAAATAC-----CTCAACAT--GTC--C-TGAG-GCTC-A-ACTC-----ACCTCTT
27487082 GCAATATGAGTTGATTTTTTTTTT-AAGAAC
48 GCAATATGAGTTGATTTTTTTTTTGAAG-AC
*
27487112 AGAAATT-AAAATTACCTCAGCATGTCCTGAGGCTCAACTCACCTCTTGCAATATGAGTTGATTT
1 AGAAATTGAAAA-TACCTCAACATGTCCTGAGGCTCAACTCACCTCTTGCAATATGAGTTGATTT
27487176 TTTTTTTGAAGAC
65 TTTTTTTGAAGAC
* *
27487189 AGAAATTGAAAATACCTCAACGTGTCTTGAGGCTCAACTCACCTCTCT-CAATATGAGTTGATTT
1 AGAAATTGAAAATACCTCAACATGTCCTGAGGCTCAACTCACCTCT-TGCAATATGAGTTGATTT
27487253 TT
65 TT
27487255 GAAACAGAAA
Statistics
Matches: 315, Mismatches: 32, Indels: 69
0.76 0.08 0.17
Matches are distributed among these distances:
69 7 0.02
70 12 0.04
74 38 0.12
75 4 0.01
76 78 0.25
77 95 0.30
78 10 0.03
80 1 0.00
81 4 0.01
82 6 0.02
83 6 0.02
84 4 0.01
85 1 0.00
87 2 0.01
88 21 0.07
89 5 0.02
92 4 0.01
93 11 0.03
94 6 0.02
ACGTcount: A:0.33, C:0.21, G:0.16, T:0.31
Consensus pattern (77 bp):
AGAAATTGAAAATACCTCAACATGTCCTGAGGCTCAACTCACCTCTTGCAATATGAGTTGATTTT
TTTTTTGAAGAC
Found at i:27495602 original size:18 final size:18
Alignment explanation
Indices: 27495579--27495613 Score: 61
Period size: 18 Copynumber: 1.9 Consensus size: 18
27495569 GTGCAATGAA
27495579 TGAATAAATGACAAATGT
1 TGAATAAATGACAAATGT
*
27495597 TGAATAAATGACGAATG
1 TGAATAAATGACAAATG
27495614 AATGTTAGTC
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
18 16 1.00
ACGTcount: A:0.49, C:0.06, G:0.20, T:0.26
Consensus pattern (18 bp):
TGAATAAATGACAAATGT
Found at i:27499475 original size:18 final size:17
Alignment explanation
Indices: 27499445--27499479 Score: 52
Period size: 18 Copynumber: 2.0 Consensus size: 17
27499435 ACAAATATAT
*
27499445 TAAAAATAGTAATAATA
1 TAAAAATACTAATAATA
27499462 TAAAAATAACTAATAATA
1 TAAAAAT-ACTAATAATA
27499480 ACGATATATA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
17 7 0.44
18 9 0.56
ACGTcount: A:0.66, C:0.03, G:0.03, T:0.29
Consensus pattern (17 bp):
TAAAAATACTAATAATA
Found at i:27499526 original size:47 final size:47
Alignment explanation
Indices: 27499472--27499607 Score: 122
Period size: 47 Copynumber: 2.9 Consensus size: 47
27499462 TAAAAATAAC
*
27499472 TAATAATAACGATATATAAA-TATATACATA-TATGTATTAAAATATATACA
1 TAATAAT-ACGA-ATAAAAAGTATATACATAGTAT-TA--AAAATATATACA
*
27499522 TAATAATAGGAATAAAAAGTATATACATAGTATTAAAAATATATACA
1 TAATAATACGAATAAAAAGTATATACATAGTATTAAAAATATATACA
* * *
27499569 TACTATATAC-ATATTAAAA-TA-ATA-ATAATATTAAAAATA
1 TAATA-ATACGA-ATAAAAAGTATATACATAGTATTAAAAATA
27499608 GTTATTACAT
Statistics
Matches: 76, Mismatches: 6, Indels: 13
0.80 0.06 0.14
Matches are distributed among these distances:
45 14 0.18
46 3 0.04
47 19 0.25
48 15 0.20
49 15 0.20
50 10 0.13
ACGTcount: A:0.57, C:0.05, G:0.04, T:0.34
Consensus pattern (47 bp):
TAATAATACGAATAAAAAGTATATACATAGTATTAAAAATATATACA
Found at i:27499551 original size:21 final size:20
Alignment explanation
Indices: 27499527--27499570 Score: 61
Period size: 21 Copynumber: 2.1 Consensus size: 20
27499517 ATACATAATA
27499527 ATAGGAATAAAAAGTATATAC
1 ATAGGAATAAAAA-TATATAC
* *
27499548 ATAGTATTAAAAATATATAC
1 ATAGGAATAAAAATATATAC
27499568 ATA
1 ATA
27499571 CTATATACAT
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
20 10 0.48
21 11 0.52
ACGTcount: A:0.57, C:0.05, G:0.09, T:0.30
Consensus pattern (20 bp):
ATAGGAATAAAAATATATAC
Found at i:27499562 original size:27 final size:26
Alignment explanation
Indices: 27499510--27499562 Score: 61
Period size: 27 Copynumber: 2.0 Consensus size: 26
27499500 TATATGTATT
**
27499510 AAAATATATACATAATAATAGGAATA
1 AAAATATATACATAATAATAAAAATA
* *
27499536 AAAAGTATATACATAGTATTAAAAATA
1 AAAA-TATATACATAATAATAAAAATA
27499563 TATACATACT
Statistics
Matches: 22, Mismatches: 4, Indels: 1
0.81 0.15 0.04
Matches are distributed among these distances:
26 4 0.18
27 18 0.82
ACGTcount: A:0.60, C:0.04, G:0.08, T:0.28
Consensus pattern (26 bp):
AAAATATATACATAATAATAAAAATA
Found at i:27499587 original size:49 final size:45
Alignment explanation
Indices: 27499505--27499631 Score: 125
Period size: 47 Copynumber: 2.7 Consensus size: 45
27499495 ATACATATAT
* *
27499505 GTATT-AAAATATATACATAATA-ATAGGA-ATAAAAAGTATATACATA
1 GTATTAAAAATATATACATAATATATA-CATATTAAAA-TA-ATA-ATA
*
27499551 GTATTAAAAATATATACATACTATATACATATTAAAATAATAATA
1 GTATTAAAAATATATACATAATATATACATATTAAAATAATAATA
*
27499596 ATATTAAAAATAGTTATTACATAAATATATACATAT
1 GTATTAAAAATA--TA-TACAT-AATATATACATAT
27499632 ATATATTGAA
Statistics
Matches: 69, Mismatches: 5, Indels: 11
0.81 0.06 0.13
Matches are distributed among these distances:
45 14 0.20
46 8 0.12
47 21 0.30
48 14 0.20
49 12 0.17
ACGTcount: A:0.55, C:0.06, G:0.05, T:0.35
Consensus pattern (45 bp):
GTATTAAAAATATATACATAATATATACATATTAAAATAATAATA
Found at i:27501134 original size:26 final size:26
Alignment explanation
Indices: 27501105--27501157 Score: 63
Period size: 26 Copynumber: 2.0 Consensus size: 26
27501095 TCAAACATGC
27501105 ATTTAAGTCAATTTAAC-CCTAGGGGT
1 ATTTAAGT-AATTTAACTCCTAGGGGT
** *
27501131 ATTTCGGTAATTTATCTCCTAGGGGT
1 ATTTAAGTAATTTAACTCCTAGGGGT
27501157 A
1 A
27501158 AAACTGTAAA
Statistics
Matches: 23, Mismatches: 3, Indels: 2
0.82 0.11 0.07
Matches are distributed among these distances:
25 7 0.30
26 16 0.70
ACGTcount: A:0.26, C:0.15, G:0.21, T:0.38
Consensus pattern (26 bp):
ATTTAAGTAATTTAACTCCTAGGGGT
Found at i:27502167 original size:26 final size:26
Alignment explanation
Indices: 27502136--27502243 Score: 189
Period size: 26 Copynumber: 4.2 Consensus size: 26
27502126 TGAAATGCCC
*
27502136 ATCATGGAACATTTACCTAAACCATT
1 ATCATGGAACATTTACCTAACCCATT
27502162 ATCATGGAACATTTACCTAACCCATT
1 ATCATGGAACATTTACCTAACCCATT
* *
27502188 ATCATGGAATATTTACCTAATCCATT
1 ATCATGGAACATTTACCTAACCCATT
27502214 ATCATGGAACATTTACCTAACCCATT
1 ATCATGGAACATTTACCTAACCCATT
27502240 ATCA
1 ATCA
27502244 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:27502604 original size:25 final size:26
Alignment explanation
Indices: 27502567--27502631 Score: 69
Period size: 27 Copynumber: 2.5 Consensus size: 26
27502557 GGGCGTTACA
**
27502567 ATTAAAATATATATGCAA-TATATAGT
1 ATTAAAA-ATATACACAAGTATATAGT
* *
27502593 ATTAAGAATATACACAATGTATATGGT
1 ATTAAAAATATACACAA-GTATATAGT
27502620 ATTAAAAATATA
1 ATTAAAAATATA
27502632 GTATTAAAAA
Statistics
Matches: 32, Mismatches: 5, Indels: 3
0.80 0.12 0.08
Matches are distributed among these distances:
25 8 0.25
26 6 0.19
27 18 0.56
ACGTcount: A:0.51, C:0.05, G:0.09, T:0.35
Consensus pattern (26 bp):
ATTAAAAATATACACAAGTATATAGT
Found at i:27502870 original size:28 final size:28
Alignment explanation
Indices: 27502817--27502870 Score: 65
Period size: 28 Copynumber: 1.9 Consensus size: 28
27502807 AACATATATA
*
27502817 TATTGAAATTATATATACATAGTATTAG
1 TATTGAAATTATATATACATAATATTAG
* *
27502845 TATTTAAA-TATATATAATATAATATT
1 TATTGAAATTATATAT-ACATAATATT
27502871 TAAGAAAAAC
Statistics
Matches: 22, Mismatches: 3, Indels: 2
0.81 0.11 0.07
Matches are distributed among these distances:
27 7 0.32
28 15 0.68
ACGTcount: A:0.46, C:0.02, G:0.06, T:0.46
Consensus pattern (28 bp):
TATTGAAATTATATATACATAATATTAG
Found at i:27503035 original size:15 final size:15
Alignment explanation
Indices: 27503015--27503054 Score: 53
Period size: 15 Copynumber: 2.7 Consensus size: 15
27503005 TATACATAAT
*
27503015 ATAATATTAAGAAAA
1 ATAATATTAACAAAA
*
27503030 ATAATAATAACAAAA
1 ATAATATTAACAAAA
*
27503045 AAAATATTAA
1 ATAATATTAA
27503055 TAATACTATA
Statistics
Matches: 21, Mismatches: 4, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
15 21 1.00
ACGTcount: A:0.70, C:0.03, G:0.03, T:0.25
Consensus pattern (15 bp):
ATAATATTAACAAAA
Found at i:27503128 original size:22 final size:22
Alignment explanation
Indices: 27503109--27503184 Score: 70
Period size: 22 Copynumber: 3.5 Consensus size: 22
27503099 ATACTAATGC
27503109 TAATAAATAAT-AAATATAATAA
1 TAAT-AATAATAAAATATAATAA
*
27503131 TAATAGTAATAAAATATAATAGTA
1 TAATAATAATAAAATATAATA--A
*
27503155 TACATAATATTAAAAT-TAA-AA
1 TA-ATAATAATAAAATATAATAA
27503176 TAA-AATAAT
1 TAATAATAAT
27503185 GAGAAAAAGT
Statistics
Matches: 46, Mismatches: 4, Indels: 11
0.75 0.07 0.18
Matches are distributed among these distances:
19 5 0.11
20 1 0.02
21 8 0.17
22 14 0.30
23 1 0.02
24 6 0.13
25 11 0.24
ACGTcount: A:0.63, C:0.01, G:0.03, T:0.33
Consensus pattern (22 bp):
TAATAATAATAAAATATAATAA
Found at i:27503149 original size:28 final size:30
Alignment explanation
Indices: 27503096--27503163 Score: 72
Period size: 28 Copynumber: 2.3 Consensus size: 30
27503086 TTAAGCAAAA
*
27503096 ATAATACTAATGCTAATAAATAATAA-A-T
1 ATAATAATAATGCTAATAAATAATAATAGT
27503124 ATAATAATAATAG-TAATAAA-ATATAATAGT
1 ATAATAATAAT-GCTAATAAATA-ATAATAGT
27503154 ATACATAATA
1 ATA-ATAATA
27503164 TTAAAATTAA
Statistics
Matches: 34, Mismatches: 1, Indels: 7
0.81 0.02 0.17
Matches are distributed among these distances:
27 1 0.03
28 21 0.62
29 2 0.06
30 4 0.12
31 6 0.18
ACGTcount: A:0.59, C:0.04, G:0.04, T:0.32
Consensus pattern (30 bp):
ATAATAATAATGCTAATAAATAATAATAGT
Found at i:27505054 original size:29 final size:29
Alignment explanation
Indices: 27505022--27505122 Score: 184
Period size: 29 Copynumber: 3.5 Consensus size: 29
27505012 TTCGAGCTCC
27505022 CACACTTAGTGCCATATATTTCCAGCATG
1 CACACTTAGTGCCATATATTTCCAGCATG
27505051 CACACTTAGTGCCATATATTTCCAGCATG
1 CACACTTAGTGCCATATATTTCCAGCATG
* *
27505080 CACACTCAGTGCCATATTTTTCCAGCATG
1 CACACTTAGTGCCATATATTTCCAGCATG
27505109 CACACTTAGTGCCA
1 CACACTTAGTGCCA
27505123 ATCTCGTCAC
Statistics
Matches: 69, Mismatches: 3, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
29 69 1.00
ACGTcount: A:0.27, C:0.30, G:0.14, T:0.30
Consensus pattern (29 bp):
CACACTTAGTGCCATATATTTCCAGCATG
Found at i:27505054 original size:58 final size:58
Alignment explanation
Indices: 27505000--27505122 Score: 167
Period size: 58 Copynumber: 2.1 Consensus size: 58
27504990 CCGCACACAC
* * *
27505000 AGTGCCATACCCTTCGAGC-TCCCACACTTAGTGCCATATATTTCCAGCATGCACACTT
1 AGTGCCATACACTTCCAGCAT-CCACACTCAGTGCCATATATTTCCAGCATGCACACTT
* * * *
27505058 AGTGCCATATATTTCCAGCATGCACACTCAGTGCCATATTTTTCCAGCATGCACACTT
1 AGTGCCATACACTTCCAGCATCCACACTCAGTGCCATATATTTCCAGCATGCACACTT
27505116 AGTGCCA
1 AGTGCCA
27505123 ATCTCGTCAC
Statistics
Matches: 57, Mismatches: 7, Indels: 2
0.86 0.11 0.03
Matches are distributed among these distances:
58 56 0.98
59 1 0.02
ACGTcount: A:0.25, C:0.32, G:0.15, T:0.28
Consensus pattern (58 bp):
AGTGCCATACACTTCCAGCATCCACACTCAGTGCCATATATTTCCAGCATGCACACTT
Found at i:27508796 original size:8 final size:8
Alignment explanation
Indices: 27508777--27508815 Score: 53
Period size: 8 Copynumber: 4.9 Consensus size: 8
27508767 TACATAATTT
27508777 TTAAATAAA
1 TTAAA-AAA
27508786 TTAAAAAA
1 TTAAAAAA
27508794 TT-AAAAA
1 TTAAAAAA
27508801 TTAAAAAA
1 TTAAAAAA
*
27508809 ATAAAAA
1 TTAAAAA
27508816 GCATAAAAAT
Statistics
Matches: 28, Mismatches: 1, Indels: 3
0.88 0.03 0.09
Matches are distributed among these distances:
7 7 0.25
8 16 0.57
9 5 0.18
ACGTcount: A:0.74, C:0.00, G:0.00, T:0.26
Consensus pattern (8 bp):
TTAAAAAA
Found at i:27508803 original size:15 final size:15
Alignment explanation
Indices: 27508783--27508815 Score: 57
Period size: 15 Copynumber: 2.2 Consensus size: 15
27508773 ATTTTTAAAT
*
27508783 AAATTAAAAAATTAA
1 AAATTAAAAAAATAA
27508798 AAATTAAAAAAATAA
1 AAATTAAAAAAATAA
27508813 AAA
1 AAA
27508816 GCATAAAAAT
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 17 1.00
ACGTcount: A:0.79, C:0.00, G:0.00, T:0.21
Consensus pattern (15 bp):
AAATTAAAAAAATAA
Found at i:27509213 original size:15 final size:14
Alignment explanation
Indices: 27509193--27509226 Score: 50
Period size: 14 Copynumber: 2.4 Consensus size: 14
27509183 CAAAAACCAA
27509193 AAAATAAAATAAACC
1 AAAATAAAA-AAACC
*
27509208 AAAATACAAAAACC
1 AAAATAAAAAAACC
27509222 AAAAT
1 AAAAT
27509227 TAAAGTCCAA
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
14 10 0.56
15 8 0.44
ACGTcount: A:0.74, C:0.15, G:0.00, T:0.12
Consensus pattern (14 bp):
AAAATAAAAAAACC
Found at i:27510742 original size:2 final size:2
Alignment explanation
Indices: 27510735--27510771 Score: 74
Period size: 2 Copynumber: 18.5 Consensus size: 2
27510725 AAATTTTACT
27510735 TA TA TA TA TA TA 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 TA T
27510772 TATTTGTTTC
Statistics
Matches: 35, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 35 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:27513662 original size:26 final size:26
Alignment explanation
Indices: 27513633--27513714 Score: 155
Period size: 26 Copynumber: 3.2 Consensus size: 26
27513623 TGATACAAAT
27513633 TGATAATGGGTTAGGTAAATGTTCCA
1 TGATAATGGGTTAGGTAAATGTTCCA
*
27513659 TGATAATGGGTTAGGTAAATGTTTCA
1 TGATAATGGGTTAGGTAAATGTTCCA
27513685 TGATAATGGGTTAGGTAAATGTTCCA
1 TGATAATGGGTTAGGTAAATGTTCCA
27513711 TGAT
1 TGAT
27513715 GGGAATTTCA
Statistics
Matches: 54, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
26 54 1.00
ACGTcount: A:0.30, C:0.06, G:0.27, T:0.37
Consensus pattern (26 bp):
TGATAATGGGTTAGGTAAATGTTCCA
Found at i:27515226 original size:26 final size:26
Alignment explanation
Indices: 27515197--27515249 Score: 72
Period size: 26 Copynumber: 2.0 Consensus size: 26
27515187 TTTACAGTTT
27515197 TACCCCTAGGAGATAAATT-ACCAAAA
1 TACCCCTAGG-GATAAATTGACCAAAA
* *
27515223 TACCCCTAGGGTTAAATTGACCTAAA
1 TACCCCTAGGGATAAATTGACCAAAA
27515249 T
1 T
27515250 GCATGTTTGA
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
25 7 0.29
26 17 0.71
ACGTcount: A:0.40, C:0.23, G:0.13, T:0.25
Consensus pattern (26 bp):
TACCCCTAGGGATAAATTGACCAAAA
Found at i:27517284 original size:43 final size:43
Alignment explanation
Indices: 27517219--27517324 Score: 144
Period size: 43 Copynumber: 2.5 Consensus size: 43
27517209 TTTTACAAAT
* * *
27517219 GCTAAAGATCATTACCTTTAGCGGCGCTTTTCCCGA-AAACGCC
1 GCTAAAAATCATAACCTTTAGCGGCGCTTTTCAC-ACAAACGCC
*
27517262 GTTAAAAATCATAACCTTTAGCGGCGCTTTTCACACAAACGCC
1 GCTAAAAATCATAACCTTTAGCGGCGCTTTTCACACAAACGCC
27517305 GCTAAAAATCATGAA-CTTTA
1 GCTAAAAATCAT-AACCTTTA
27517325 AAAAAATTAT
Statistics
Matches: 56, Mismatches: 5, Indels: 4
0.86 0.08 0.06
Matches are distributed among these distances:
42 1 0.02
43 53 0.95
44 2 0.04
ACGTcount: A:0.32, C:0.26, G:0.15, T:0.26
Consensus pattern (43 bp):
GCTAAAAATCATAACCTTTAGCGGCGCTTTTCACACAAACGCC
Found at i:27522625 original size:13 final size:13
Alignment explanation
Indices: 27522607--27522631 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
27522597 ACATCAAATG
27522607 TATTAATTCAGTA
1 TATTAATTCAGTA
27522620 TATTAATTCAGT
1 TATTAATTCAGT
27522632 TGTGAAATTA
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.36, C:0.08, G:0.08, T:0.48
Consensus pattern (13 bp):
TATTAATTCAGTA
Found at i:27523423 original size:41 final size:41
Alignment explanation
Indices: 27523361--27523618 Score: 378
Period size: 41 Copynumber: 6.3 Consensus size: 41
27523351 TTATATGACT
* * *
27523361 TTTAGTGGCGTTTTACTAAAAGCGCTGCTAATGCTCTGGTC
1 TTTAGCGGCGTTTTACCAAAAGCGCCGCTAATGCTCTGGTC
27523402 TTTAGCGGCGTTTTACCAAAAGCGCCGCTAATGCTCTGGTC
1 TTTAGCGGCGTTTTACCAAAAGCGCCGCTAATGCTCTGGTC
27523443 TTTAGCGGCGTTTTACCAAAAGCGCCGCTAATGCTCTGG-C
1 TTTAGCGGCGTTTTACCAAAAGCGCCGCTAATGCTCTGGTC
*
27523483 TTTAACGGCGTTTTACCAAAAGCGCCGCTAATGCTCTGGTC
1 TTTAGCGGCGTTTTACCAAAAGCGCCGCTAATGCTCTGGTC
** *
27523524 TTTAGCTACGTTTTACCAAAAGCGCCGCTAATGCTCTGCT-
1 TTTAGCGGCGTTTTACCAAAAGCGCCGCTAATGCTCTGGTC
* * * * *
27523564 TTTAGCGGCGTTTTAACAAAAAACGCCGCTATTGCTC-AGTT
1 TTTAGCGGCGTTTT-ACCAAAAGCGCCGCTAATGCTCTGGTC
27523605 TTTAGCGGCGTTTT
1 TTTAGCGGCGTTTT
27523619 TCTTAAAACG
Statistics
Matches: 199, Mismatches: 15, Indels: 6
0.90 0.07 0.03
Matches are distributed among these distances:
40 52 0.26
41 147 0.74
ACGTcount: A:0.21, C:0.24, G:0.22, T:0.32
Consensus pattern (41 bp):
TTTAGCGGCGTTTTACCAAAAGCGCCGCTAATGCTCTGGTC
Found at i:27523518 original size:81 final size:81
Alignment explanation
Indices: 27523361--27523618 Score: 376
Period size: 81 Copynumber: 3.2 Consensus size: 81
27523351 TTATATGACT
* * *
27523361 TTTAGTGGCGTTTTACTAAAAGCGCTGCTAATGCTCTGGTCTTTAGCGGCGTTTTACCAAAAGCG
1 TTTAGCGGCGTTTTACCAAAAGCGCCGCTAATGCTCTGG-CTTTAGCGGCGTTTTACCAAAAGCG
27523426 CCGCTAATGCTCTGGTC
65 CCGCTAATGCTCTGGTC
*
27523443 TTTAGCGGCGTTTTACCAAAAGCGCCGCTAATGCTCTGGCTTTAACGGCGTTTTACCAAAAGCGC
1 TTTAGCGGCGTTTTACCAAAAGCGCCGCTAATGCTCTGGCTTTAGCGGCGTTTTACCAAAAGCGC
27523508 CGCTAATGCTCTGGTC
66 CGCTAATGCTCTGGTC
** * *
27523524 TTTAGCTACGTTTTACCAAAAGCGCCGCTAATGCTCT-GCTTTTAGCGGCGTTTTAACAAAAAAC
1 TTTAGCGGCGTTTTACCAAAAGCGCCGCTAATGCTCTGGC-TTTAGCGGCGTTTT-ACCAAAAGC
* * *
27523588 GCCGCTATTGCTC-AGTT
64 GCCGCTAATGCTCTGGTC
27523605 TTTAGCGGCGTTTT
1 TTTAGCGGCGTTTT
27523619 TCTTAAAACG
Statistics
Matches: 160, Mismatches: 14, Indels: 5
0.89 0.08 0.03
Matches are distributed among these distances:
80 2 0.01
81 103 0.64
82 55 0.34
ACGTcount: A:0.21, C:0.24, G:0.22, T:0.32
Consensus pattern (81 bp):
TTTAGCGGCGTTTTACCAAAAGCGCCGCTAATGCTCTGGCTTTAGCGGCGTTTTACCAAAAGCGC
CGCTAATGCTCTGGTC
Found at i:27523631 original size:122 final size:122
Alignment explanation
Indices: 27523360--27523634 Score: 392
Period size: 122 Copynumber: 2.3 Consensus size: 122
27523350 GTTATATGAC
* * *
27523360 TTTTAGTGGCGTTTTACTAAAAGCGCTGCTAATGCTCTGGTCTTTAGCGGCGTTTTACCAAAAGC
1 TTTTAGCGGCGTTTTACTAAAAGCGCCGCTAATGCTCTGGTCTTTAGCGACGTTTTACCAAAAGC
* * * *
27523425 GCCGCTAATGCTCTGGTCTTTAGCGGCGTTTTACCAAAAGCGCCGCTAATGCTCTGG
66 GCCGCTAATGCTCTGCTCTTTAGCGGCGTTTTACAAAAAACGCCGCTAATGCTCAGG
* * * *
27523482 CTTTAACGGCGTTTTACCAAAAGCGCCGCTAATGCTCTGGTCTTTAGCTACGTTTTACCAAAAGC
1 TTTTAGCGGCGTTTTACTAAAAGCGCCGCTAATGCTCTGGTCTTTAGCGACGTTTTACCAAAAGC
* *
27523547 GCCGCTAATGCTCTGCT-TTTAGCGGCGTTTTAACAAAAAACGCCGCTATTGCTCAGT
66 GCCGCTAATGCTCTGCTCTTTAGCGGCGTTTT-ACAAAAAACGCCGCTAATGCTCAGG
*
27523604 TTTTAGCGGCGTTTTTCTTAAAA-CGCCGCTA
1 TTTTAGCGGCGTTTTAC-TAAAAGCGCCGCTA
27523635 TTGCCCTGTG
Statistics
Matches: 134, Mismatches: 17, Indels: 4
0.86 0.11 0.03
Matches are distributed among these distances:
121 14 0.10
122 116 0.87
123 4 0.03
ACGTcount: A:0.21, C:0.25, G:0.22, T:0.32
Consensus pattern (122 bp):
TTTTAGCGGCGTTTTACTAAAAGCGCCGCTAATGCTCTGGTCTTTAGCGACGTTTTACCAAAAGC
GCCGCTAATGCTCTGCTCTTTAGCGGCGTTTTACAAAAAACGCCGCTAATGCTCAGG
Found at i:27523649 original size:41 final size:40
Alignment explanation
Indices: 27523360--27523649 Score: 366
Period size: 41 Copynumber: 7.1 Consensus size: 40
27523350 GTTATATGAC
* * *
27523360 TTTTAGTGGCGTTTTACTAAAAGCGCTGCTAATGCTCTGG
1 TTTTAGCGGCGTTTTACCAAAAGCGCCGCTAATGCTCTGG
27523400 TCTTTAGCGGCGTTTTACCAAAAGCGCCGCTAATGCTCTGG
1 T-TTTAGCGGCGTTTTACCAAAAGCGCCGCTAATGCTCTGG
27523441 TCTTTAGCGGCGTTTTACCAAAAGCGCCGCTAATGCTCTGG
1 T-TTTAGCGGCGTTTTACCAAAAGCGCCGCTAATGCTCTGG
* *
27523482 CTTTAACGGCGTTTTACCAAAAGCGCCGCTAATGCTCTGG
1 TTTTAGCGGCGTTTTACCAAAAGCGCCGCTAATGCTCTGG
** *
27523522 TCTTTAGCTACGTTTTACCAAAAGCGCCGCTAATGCTCTGC
1 T-TTTAGCGGCGTTTTACCAAAAGCGCCGCTAATGCTCTGG
* * * * *
27523563 TTTTAGCGGCGTTTTAACAAAAAACGCCGCTATTGCTCAGT
1 TTTTAGCGGCGTTTT-ACCAAAAGCGCCGCTAATGCTCTGG
* * * *
27523604 TTTTAGCGGCGTTTTTCTTAAAA-CGCCGCTATTGCCCTGTG
1 TTTTAGCGGCGTTTTAC-CAAAAGCGCCGCTAATGCTCTG-G
27523645 TTTTA
1 TTTTA
27523650 CAATTTTTGC
Statistics
Matches: 223, Mismatches: 22, Indels: 9
0.88 0.09 0.04
Matches are distributed among these distances:
40 66 0.30
41 157 0.70
ACGTcount: A:0.21, C:0.24, G:0.22, T:0.33
Consensus pattern (40 bp):
TTTTAGCGGCGTTTTACCAAAAGCGCCGCTAATGCTCTGG
Found at i:27525522 original size:25 final size:25
Alignment explanation
Indices: 27525488--27525536 Score: 98
Period size: 25 Copynumber: 2.0 Consensus size: 25
27525478 CTCACTTTGT
27525488 TTGCTTTATTATTTTTTAGGTAATA
1 TTGCTTTATTATTTTTTAGGTAATA
27525513 TTGCTTTATTATTTTTTAGGTAAT
1 TTGCTTTATTATTTTTTAGGTAAT
27525537 CCTCATATTT
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
25 24 1.00
ACGTcount: A:0.22, C:0.04, G:0.12, T:0.61
Consensus pattern (25 bp):
TTGCTTTATTATTTTTTAGGTAATA
Found at i:27527386 original size:20 final size:19
Alignment explanation
Indices: 27527353--27527431 Score: 85
Period size: 20 Copynumber: 4.2 Consensus size: 19
27527343 ATACGTGGGA
27527353 TATGATAT--ACATGATTG
1 TATGATATGCACATGATTG
*
27527370 ATATGATATGCACATGACATG
1 -TATGATATGCACATGA-TTG
27527391 TATGATATGCACATGATATG
1 TATGATATGCACATGAT-TG
27527411 TATGA-AGTGCACATGA-TG
1 TATGATA-TGCACATGATTG
27527429 TAT
1 TAT
27527432 TCATAAATGC
Statistics
Matches: 54, Mismatches: 2, Indels: 10
0.82 0.03 0.15
Matches are distributed among these distances:
18 13 0.24
19 1 0.02
20 38 0.70
21 2 0.04
ACGTcount: A:0.35, C:0.10, G:0.20, T:0.34
Consensus pattern (19 bp):
TATGATATGCACATGATTG
Found at i:27527568 original size:25 final size:26
Alignment explanation
Indices: 27527477--27527599 Score: 187
Period size: 26 Copynumber: 4.8 Consensus size: 26
27527467 GAGGAAGTGC
* **
27527477 AAAAGGGCTTATGCCCTAGTTTATTG
1 AAAAGGGCTTATGCCCCAGTTTACCG
27527503 AAAAGGGCTTATGCCCCAGTTTACCG
1 AAAAGGGCTTATGCCCCAGTTTACCG
* *
27527529 AAAAGGGCTTATGCCCCAGTTTATCA
1 AAAAGGGCTTATGCCCCAGTTTACCG
27527555 AAAAGGGCTT-TGCCCCAGTTTACCG
1 AAAAGGGCTTATGCCCCAGTTTACCG
27527580 AAAAGGGCTT-TGCCCCAGTT
1 AAAAGGGCTTATGCCCCAGTT
27527600 ATTAAAAGAG
Statistics
Matches: 90, Mismatches: 7, Indels: 1
0.92 0.07 0.01
Matches are distributed among these distances:
25 33 0.37
26 57 0.63
ACGTcount: A:0.27, C:0.24, G:0.23, T:0.27
Consensus pattern (26 bp):
AAAAGGGCTTATGCCCCAGTTTACCG
Found at i:27535321 original size:41 final size:41
Alignment explanation
Indices: 27535195--27535331 Score: 129
Period size: 41 Copynumber: 3.4 Consensus size: 41
27535185 GCGTTTCTAG
* * ** *
27535195 ATAGCTTCGGCTAT-ATAAAGCACTTAGTGTGTGA-ACCGGA
1 ATAGCTTCGGCTATGA-AAGGCACTTAGTGTGCGAGATTGAA
* * * *
27535235 ATAGCTTCAGCTAT-ATATGGCACTTAGTGTGCGAGGTTGAG
1 ATAGCTTCGGCTATGA-AAGGCACTTAGTGTGCGAGATTGAA
*
27535276 ATAGCTTTGGCTATGAAAGGCACTTAGTGTGCGAGATT-ATA
1 ATAGCTTCGGCTATGAAAGGCACTTAGTGTGCGAGATTGA-A
27535317 ATAGCTTCGGCTATG
1 ATAGCTTCGGCTATG
27535332 CTTTAGCACT
Statistics
Matches: 79, Mismatches: 15, Indels: 5
0.80 0.15 0.05
Matches are distributed among these distances:
40 31 0.39
41 47 0.59
42 1 0.01
ACGTcount: A:0.27, C:0.15, G:0.27, T:0.31
Consensus pattern (41 bp):
ATAGCTTCGGCTATGAAAGGCACTTAGTGTGCGAGATTGAA
Found at i:27536534 original size:65 final size:65
Alignment explanation
Indices: 27536441--27536562 Score: 156
Period size: 65 Copynumber: 1.9 Consensus size: 65
27536431 ACACACGGGC
* *
27536441 GTGTGACATAAGTCAGTATACCCCCTAAATGGCACATAGCCTAGCACACAGGCGTGTGGTCGGCT
1 GTGTGACACAAGTCAGTATACCCCCTAAATGGCACACAGCCTAGCACACAGGCGTGTGGTCGGCT
* ** * * *
27536506 GTGTGACCCAAGTCAGTA-ACCCCTCTAAATTTCACACGGCCTAGGACACGGGCGTGT
1 GTGTGACACAAGTCAGTATACCCC-CTAAATGGCACACAGCCTAGCACACAGGCGTGT
27536563 TCTCGGCCGC
Statistics
Matches: 48, Mismatches: 8, Indels: 2
0.83 0.14 0.03
Matches are distributed among these distances:
64 5 0.10
65 43 0.90
ACGTcount: A:0.25, C:0.28, G:0.25, T:0.21
Consensus pattern (65 bp):
GTGTGACACAAGTCAGTATACCCCCTAAATGGCACACAGCCTAGCACACAGGCGTGTGGTCGGCT
Found at i:27539207 original size:8 final size:8
Alignment explanation
Indices: 27539194--27539225 Score: 55
Period size: 8 Copynumber: 4.0 Consensus size: 8
27539184 CTAGATCGGC
27539194 AAAAGCCG
1 AAAAGCCG
27539202 AAAAGCCG
1 AAAAGCCG
*
27539210 AAATGCCG
1 AAAAGCCG
27539218 AAAAGCCG
1 AAAAGCCG
27539226 GTATTTTGGG
Statistics
Matches: 22, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
8 22 1.00
ACGTcount: A:0.47, C:0.25, G:0.25, T:0.03
Consensus pattern (8 bp):
AAAAGCCG
Found at i:27539539 original size:28 final size:28
Alignment explanation
Indices: 27539472--27539562 Score: 143
Period size: 28 Copynumber: 3.3 Consensus size: 28
27539462 ATGTACTAGA
27539472 ATACCCCTATGTATGCAAAATTACCA-T
1 ATACCCCTATGTATGCAAAATTACCATT
27539499 -TACCCCTATGTATGCAAAATTACCATT
1 ATACCCCTATGTATGCAAAATTACCATT
*
27539526 ATACCCCTATGTATGCAAAATGACC-TCT
1 ATACCCCTATGTATGCAAAATTACCAT-T
27539554 ATACCCCTA
1 ATACCCCTA
27539563 GGGTTAATTT
Statistics
Matches: 60, Mismatches: 1, Indels: 5
0.91 0.02 0.08
Matches are distributed among these distances:
26 25 0.42
27 2 0.03
28 33 0.55
ACGTcount: A:0.34, C:0.29, G:0.08, T:0.30
Consensus pattern (28 bp):
ATACCCCTATGTATGCAAAATTACCATT
Found at i:27539726 original size:27 final size:28
Alignment explanation
Indices: 27539668--27539757 Score: 112
Period size: 27 Copynumber: 3.2 Consensus size: 28
27539658 AGGAAGCGTC
*
27539668 CTGGTGGCTA-TGCCACAAATTATCTGTT
1 CTGGTGGC-ACTGCCACAAAATATCTGTT
* **
27539696 CTGGTGGCCCTGCCAC-GTATATCTGTT
1 CTGGTGGCACTGCCACAAAATATCTGTT
27539723 CTGGTGGCACTGCCACAAAATATCTGTAT
1 CTGGTGGCACTGCCACAAAATATCTGT-T
27539752 CTGGTG
1 CTGGTG
27539758 ACTCTGTCAC
Statistics
Matches: 52, Mismatches: 7, Indels: 5
0.81 0.11 0.08
Matches are distributed among these distances:
27 23 0.44
28 22 0.42
29 7 0.13
ACGTcount: A:0.19, C:0.24, G:0.24, T:0.32
Consensus pattern (28 bp):
CTGGTGGCACTGCCACAAAATATCTGTT
Found at i:27539768 original size:29 final size:28
Alignment explanation
Indices: 27539678--27539768 Score: 94
Period size: 27 Copynumber: 3.2 Consensus size: 28
27539668 CTGGTGGCTA
* * *
27539678 TGCCACAAATTATCTGTTCTGGTGGCCC
1 TGCCACAAAATATCTGTTCTGGTGACAC
** *
27539706 TGCCAC-GTATATCTGTTCTGGTGGCAC
1 TGCCACAAAATATCTGTTCTGGTGACAC
*
27539733 TGCCACAAAATATCTGTATCTGGTGACTC
1 TGCCACAAAATATCTGT-TCTGGTGACAC
*
27539762 TGTCACA
1 TGCCACA
27539769 TTTTCTGTAT
Statistics
Matches: 52, Mismatches: 9, Indels: 3
0.81 0.14 0.05
Matches are distributed among these distances:
27 23 0.44
28 14 0.27
29 15 0.29
ACGTcount: A:0.21, C:0.26, G:0.21, T:0.32
Consensus pattern (28 bp):
TGCCACAAAATATCTGTTCTGGTGACAC
Found at i:27539776 original size:55 final size:56
Alignment explanation
Indices: 27539668--27539782 Score: 137
Period size: 55 Copynumber: 2.1 Consensus size: 56
27539658 AGGAAGCGTC
* * *
27539668 CTGGTGGCTATGCCACAAATTATCTGTTCTGGTGGCCCTGCCACGTATATCTGT-T
1 CTGGTGGCTATGCCACAAAATATCTGTTCTGGTGACCCTGCCACATATATCTGTAT
* * *
27539723 CTGGTGGC-ACTGCCACAAAATATCTGTATCTGGTGACTCTGTCACAT-TTTCTGTAT
1 CTGGTGGCTA-TGCCACAAAATATCTGT-TCTGGTGACCCTGCCACATATATCTGTAT
27539779 CTGG
1 CTGG
27539783 CAGCCATGCT
Statistics
Matches: 51, Mismatches: 6, Indels: 5
0.82 0.10 0.08
Matches are distributed among these distances:
54 1 0.02
55 30 0.59
56 20 0.39
ACGTcount: A:0.18, C:0.24, G:0.23, T:0.35
Consensus pattern (56 bp):
CTGGTGGCTATGCCACAAAATATCTGTTCTGGTGACCCTGCCACATATATCTGTAT
Found at i:27551033 original size:3 final size:3
Alignment explanation
Indices: 27551027--27551098 Score: 108
Period size: 3 Copynumber: 23.3 Consensus size: 3
27551017 AATTAAAGGT
27551027 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA
* *
27551075 ATA CAAA GATA ATG ATA ATA ATA A
1 ATA -ATA -ATA ATA ATA ATA ATA A
27551099 AAAAAACATT
Statistics
Matches: 63, Mismatches: 5, Indels: 2
0.90 0.07 0.03
Matches are distributed among these distances:
3 59 0.94
4 4 0.06
ACGTcount: A:0.65, C:0.01, G:0.03, T:0.31
Consensus pattern (3 bp):
ATA
Found at i:27552588 original size:40 final size:40
Alignment explanation
Indices: 27552544--27552775 Score: 272
Period size: 40 Copynumber: 5.8 Consensus size: 40
27552534 TATAACCACA
* *
27552544 TGCACGAATGCCTTTGGGTCTTAGCCCGGATAGAGCGACT
1 TGCACGAATGCCTTCGGGTCTTAGCCCGGATAGAGCAACT
* *
27552584 TGCACAAATGCCTTCGGGTCTTAGCCCGGATAGAGCGACT
1 TGCACGAATGCCTTCGGGTCTTAGCCCGGATAGAGCAACT
* * ** *
27552624 TGCACAAATGCCTTCGGGTATTAGCCCGGATTTAACAACT
1 TGCACGAATGCCTTCGGGTCTTAGCCCGGATAGAGCAACT
* ** *
27552664 CGCACGAATGCCTTCGGGTCTTAGCCCGGATTTAACAACT
1 TGCACGAATGCCTTCGGGTCTTAGCCCGGATAGAGCAACT
*
27552704 CGCACGAATGCCTTCGGGTCTTAGCCCGGAT-GTAGTC-ACT
1 TGCACGAATGCCTTCGGGTCTTAGCCCGGATAG-AG-CAACT
* *
27552744 AGCAC-AATTGCCTTCGGGTCTTAACCCGGATA
1 TGCACGAA-TGCCTTCGGGTCTTAGCCCGGATA
27552776 TAATTACCAG
Statistics
Matches: 174, Mismatches: 14, Indels: 7
0.89 0.07 0.04
Matches are distributed among these distances:
39 2 0.01
40 171 0.98
41 1 0.01
ACGTcount: A:0.22, C:0.28, G:0.25, T:0.25
Consensus pattern (40 bp):
TGCACGAATGCCTTCGGGTCTTAGCCCGGATAGAGCAACT
Found at i:27552674 original size:80 final size:78
Alignment explanation
Indices: 27552529--27552816 Score: 270
Period size: 80 Copynumber: 3.6 Consensus size: 78
27552519 CGGAATACGA
* * * * * * *
27552529 CCGGATATAACCACATGCACGAATGCCTTTGGGTCTTAGCCCGGATAGAGCGACTTGCACAAATG
1 CCGGATAGAACAACTTGCACGAATGCCTTCGGGTCTTAGCCCGGATATAAC-ACTAGCAC-AATG
27552594 CCTTCGGGTCTTAGC
64 CCTTCGGGTCTTAGC
* * * * * *
27552609 CCGGATAGAGCGACTTGCACAAATGCCTTCGGGTATTAGCCCGGATTTAACAACTCGCACGAATG
1 CCGGATAGAACAACTTGCACGAATGCCTTCGGGTCTTAGCCCGGATATAAC-ACTAGCAC-AATG
27552674 CCTTCGGGTCTTAGC
64 CCTTCGGGTCTTAGC
** * * *
27552689 CCGGATTTAACAACTCGCACGAATGCCTTCGGGTCTTAGCCCGGATGTAGTCACTAGCACAATTG
1 CCGGATAGAACAACTTGCACGAATGCCTTCGGGTCTTAGCCCGGATATA-ACACTAGCACAA-TG
*
27552754 CCTTCGGGTCTTAAC
64 CCTTCGGGTCTTAGC
* ** ** ** * *
27552769 CCGGATATAATTACCAGCATAAATGTCTTCGGGACTTAGCCCGGATAT
1 CCGGATAGAACAACTTGCACGAATGCCTTCGGGTCTTAGCCCGGATAT
27552817 CATTCAATTG
Statistics
Matches: 172, Mismatches: 34, Indels: 4
0.82 0.16 0.02
Matches are distributed among these distances:
79 2 0.01
80 169 0.98
81 1 0.01
ACGTcount: A:0.24, C:0.27, G:0.24, T:0.25
Consensus pattern (78 bp):
CCGGATAGAACAACTTGCACGAATGCCTTCGGGTCTTAGCCCGGATATAACACTAGCACAATGCC
TTCGGGTCTTAGC
Found at i:27552749 original size:120 final size:120
Alignment explanation
Indices: 27552529--27552815 Score: 339
Period size: 120 Copynumber: 2.4 Consensus size: 120
27552519 CGGAATACGA
* * * * *
27552529 CCGGATATAACCA-CATGCACGAATGCCTTTGGGTCTTAGCCCGGATAGAGCGACTTGCACAAAT
1 CCGGATATAACAACCA-GCACGAATGCCTTCGGGTCTTAGCCCGGATAGAACAACTCGCACAAAT
* *
27552593 GCCTTCGGGTCTTAGCCCGGATAGAGCGACTTGCACAAATGCCTTCGGGTATTAGC
65 GCCTTCGGGTCTTAGCCCGGATAGAGCGACTAGCACAAATGCCTTCGGGTATTAAC
* ** *
27552649 CCGGATTTAACAACTC-GCACGAATGCCTTCGGGTCTTAGCCCGGATTTAACAACTCGCACGAAT
1 CCGGATATAACAAC-CAGCACGAATGCCTTCGGGTCTTAGCCCGGATAGAACAACTCGCACAAAT
* *
27552713 GCCTTCGGGTCTTAGCCCGGAT-GTAGTC-ACTAGCACAATTGCCTTCGGGTCTTAAC
65 GCCTTCGGGTCTTAGCCCGGATAG-AG-CGACTAGCACAAATGCCTTCGGGTATTAAC
** ** * *
27552769 CCGGATATAATTACCAGCATAAATGTCTTCGGGACTTAGCCCGGATA
1 CCGGATATAACAACCAGCACGAATGCCTTCGGGTCTTAGCCCGGATA
27552816 TCATTCAATT
Statistics
Matches: 141, Mismatches: 21, Indels: 10
0.82 0.12 0.06
Matches are distributed among these distances:
119 2 0.01
120 137 0.97
121 1 0.01
122 1 0.01
ACGTcount: A:0.24, C:0.27, G:0.24, T:0.25
Consensus pattern (120 bp):
CCGGATATAACAACCAGCACGAATGCCTTCGGGTCTTAGCCCGGATAGAACAACTCGCACAAATG
CCTTCGGGTCTTAGCCCGGATAGAGCGACTAGCACAAATGCCTTCGGGTATTAAC
Found at i:27552799 original size:40 final size:40
Alignment explanation
Indices: 27552545--27552816 Score: 233
Period size: 40 Copynumber: 6.8 Consensus size: 40
27552535 ATAACCACAT
* * * *** **
27552545 GCACGAATGCCTTTGGGTCTTAGCCCGGATAGAGCGACTT
1 GCACAAATGCCTTCGGGTCTTAGCCCGGATATAATAACCA
* *** **
27552585 GCACAAATGCCTTCGGGTCTTAGCCCGGATAGAGCGACTT
1 GCACAAATGCCTTCGGGTCTTAGCCCGGATATAATAACCA
* * *
27552625 GCACAAATGCCTTCGGGTATTAGCCCGGATTTAACAACTC-
1 GCACAAATGCCTTCGGGTCTTAGCCCGGATATAATAAC-CA
* * *
27552665 GCACGAATGCCTTCGGGTCTTAGCCCGGATTTAACAACTC-
1 GCACAAATGCCTTCGGGTCTTAGCCCGGATATAATAAC-CA
* * * * *
27552705 GCACGAATGCCTTCGGGTCTTAGCCCGGATGTAGTCACTA
1 GCACAAATGCCTTCGGGTCTTAGCCCGGATATAATAACCA
* * *
27552745 GCACAATTGCCTTCGGGTCTTAACCCGGATATAATTACCA
1 GCACAAATGCCTTCGGGTCTTAGCCCGGATATAATAACCA
* * *
27552785 GCATAAATGTCTTCGGGACTTAGCCCGGATAT
1 GCACAAATGCCTTCGGGTCTTAGCCCGGATAT
27552817 CATTCAATTG
Statistics
Matches: 203, Mismatches: 27, Indels: 4
0.87 0.12 0.02
Matches are distributed among these distances:
40 203 1.00
ACGTcount: A:0.24, C:0.27, G:0.24, T:0.25
Consensus pattern (40 bp):
GCACAAATGCCTTCGGGTCTTAGCCCGGATATAATAACCA
Found at i:27554123 original size:25 final size:25
Alignment explanation
Indices: 27554095--27554146 Score: 104
Period size: 25 Copynumber: 2.1 Consensus size: 25
27554085 TTTTTTTGTT
27554095 TCTCTTCCCACATCTAATTATTTTA
1 TCTCTTCCCACATCTAATTATTTTA
27554120 TCTCTTCCCACATCTAATTATTTTA
1 TCTCTTCCCACATCTAATTATTTTA
27554145 TC
1 TC
27554147 ACTTAATACA
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
25 27 1.00
ACGTcount: A:0.23, C:0.29, G:0.00, T:0.48
Consensus pattern (25 bp):
TCTCTTCCCACATCTAATTATTTTA
Found at i:27554157 original size:25 final size:25
Alignment explanation
Indices: 27554103--27554158 Score: 76
Period size: 25 Copynumber: 2.2 Consensus size: 25
27554093 TTTCTCTTCC
* **
27554103 CACATCTAATTATTTTATCTCTTCC
1 CACATCTAATTATTTTATCACTTAA
27554128 CACATCTAATTATTTTATCACTTAA
1 CACATCTAATTATTTTATCACTTAA
*
27554153 TACATC
1 CACATC
27554159 ATGCATTAAC
Statistics
Matches: 27, Mismatches: 4, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
25 27 1.00
ACGTcount: A:0.30, C:0.25, G:0.00, T:0.45
Consensus pattern (25 bp):
CACATCTAATTATTTTATCACTTAA
Found at i:27554762 original size:3 final size:3
Alignment explanation
Indices: 27554754--27554825 Score: 92
Period size: 3 Copynumber: 23.7 Consensus size: 3
27554744 TAAAATATAC
*
27554754 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA CAA TAA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
* *
27554802 TAG TAA -ATA GAA TAA TAAA TAA TA
1 TAA TAA TA-A TAA TAA T-AA TAA TA
27554826 CTTAGAGTAA
Statistics
Matches: 61, Mismatches: 5, Indels: 6
0.85 0.07 0.08
Matches are distributed among these distances:
2 1 0.02
3 56 0.92
4 4 0.07
ACGTcount: A:0.65, C:0.01, G:0.03, T:0.31
Consensus pattern (3 bp):
TAA
Found at i:27565083 original size:50 final size:51
Alignment explanation
Indices: 27565006--27565134 Score: 208
Period size: 50 Copynumber: 2.5 Consensus size: 51
27564996 GACCATGGCA
27565006 ACAAGTGATAAGTGATAGCTTCGGCTACACTTATCTGATCAAGGA-AAAGTG
1 ACAAGTGATAAGTGATAGCTTCGGCTACACTTATCTGATCAAGGACAAA-TG
*
27565057 A-AAGTGATAAGTGATAGCTTCGGCTACACTTATCTGATCAATGACAAATG
1 ACAAGTGATAAGTGATAGCTTCGGCTACACTTATCTGATCAAGGACAAATG
* *
27565107 ACAAGTGAAAAGTGGTAGCTTCGGCTAC
1 ACAAGTGATAAGTGATAGCTTCGGCTAC
27565135 CTGATCAGTG
Statistics
Matches: 73, Mismatches: 3, Indels: 4
0.91 0.04 0.05
Matches are distributed among these distances:
50 45 0.62
51 28 0.38
ACGTcount: A:0.35, C:0.16, G:0.23, T:0.26
Consensus pattern (51 bp):
ACAAGTGATAAGTGATAGCTTCGGCTACACTTATCTGATCAAGGACAAATG
Found at i:27565148 original size:31 final size:31
Alignment explanation
Indices: 27565110--27565196 Score: 113
Period size: 31 Copynumber: 2.8 Consensus size: 31
27565100 ACAAATGACA
*
27565110 AGTGAAAAGTGGTAGCTTCGGCTACCTGATC
1 AGTGAAAAGTGGTAGCTTCGGCTACCTCATC
* *
27565141 AGTGAAAAATGGTAGC-TCTGACTACCTCATC
1 AGTGAAAAGTGGTAGCTTC-GGCTACCTCATC
* *
27565172 AGTGAATAGTGGTAGCTTCCGCTAC
1 AGTGAAAAGTGGTAGCTTCGGCTAC
27565197 AAGTGACAAG
Statistics
Matches: 47, Mismatches: 7, Indels: 4
0.81 0.12 0.07
Matches are distributed among these distances:
30 2 0.04
31 43 0.91
32 2 0.04
ACGTcount: A:0.28, C:0.21, G:0.25, T:0.26
Consensus pattern (31 bp):
AGTGAAAAGTGGTAGCTTCGGCTACCTCATC
Found at i:27565291 original size:47 final size:46
Alignment explanation
Indices: 27565221--27565342 Score: 163
Period size: 47 Copynumber: 2.6 Consensus size: 46
27565211 AAGTGATTTC
* * *
27565221 CGTATAAGACCATATCTGGGATATGGCATCGGTGTGATATATGCTA
1 CGTATAAGACCATATCTGGGATATGGCATCAGTGAGATATATGATA
* *
27565267 CTGTATAAGACCATATCTGGGATATGGCATCAGTGAGATATGTGATT
1 C-GTATAAGACCATATCTGGGATATGGCATCAGTGAGATATATGATA
* * *
27565314 CGTGTAAGACCATAGCTGGGCTATGGCAT
1 CGTATAAGACCATATCTGGGATATGGCAT
27565343 TGATATATGA
Statistics
Matches: 67, Mismatches: 8, Indels: 2
0.87 0.10 0.03
Matches are distributed among these distances:
46 26 0.39
47 41 0.61
ACGTcount: A:0.28, C:0.16, G:0.27, T:0.30
Consensus pattern (46 bp):
CGTATAAGACCATATCTGGGATATGGCATCAGTGAGATATATGATA
Found at i:27565378 original size:42 final size:42
Alignment explanation
Indices: 27565315--27565412 Score: 144
Period size: 42 Copynumber: 2.3 Consensus size: 42
27565305 TATGTGATTC
* * *
27565315 GTGTAAGACCATAGCTGGGCTATGGCATTGA-TATATGAATAT
1 GTGTAAGACCATAGCTAGGCTATGGCA-TCATTATATGAAGAT
*
27565357 GTGTAAGACCATAGCTAGGCTATGGCATCATTATGTGAAGAT
1 GTGTAAGACCATAGCTAGGCTATGGCATCATTATATGAAGAT
27565399 GTGTAAGACCATAG
1 GTGTAAGACCATAG
27565413 TTGAACTATG
Statistics
Matches: 51, Mismatches: 4, Indels: 2
0.89 0.07 0.04
Matches are distributed among these distances:
41 2 0.04
42 49 0.96
ACGTcount: A:0.32, C:0.13, G:0.27, T:0.29
Consensus pattern (42 bp):
GTGTAAGACCATAGCTAGGCTATGGCATCATTATATGAAGAT
Found at i:27565422 original size:42 final size:41
Alignment explanation
Indices: 27565315--27565427 Score: 138
Period size: 42 Copynumber: 2.7 Consensus size: 41
27565305 TATGTGATTC
* * *
27565315 GTGTAAGACCATAGCTGGGCTATGGCATTGATATATGAATAT
1 GTGTAAGACCATAGCTGAGCTATGGCA-TCATATATGAAGAT
*
27565357 GTGTAAGACCATAGCT-AGGCTATGGCATCATTATGTGAAGAT
1 GTGTAAGACCATAGCTGA-GCTATGGCATCA-TATATGAAGAT
* *
27565399 GTGTAAGACCATAGTTGAACTATGGCATC
1 GTGTAAGACCATAGCTGAGCTATGGCATC
27565428 GAGAAAACGA
Statistics
Matches: 62, Mismatches: 6, Indels: 6
0.84 0.08 0.08
Matches are distributed among these distances:
41 2 0.03
42 59 0.95
43 1 0.02
ACGTcount: A:0.31, C:0.14, G:0.26, T:0.29
Consensus pattern (41 bp):
GTGTAAGACCATAGCTGAGCTATGGCATCATATATGAAGAT
Found at i:27571795 original size:47 final size:47
Alignment explanation
Indices: 27571732--27572082 Score: 486
Period size: 47 Copynumber: 7.3 Consensus size: 47
27571722 CCCTTCGGGA
* *
27571732 CTTATCACATTTATACACTTTCACATCCATCACATTGGCCATTCGGC
1 CTTATCACATATATACACTTTCACATTCATCACATTGGCCATTCGGC
* *
27571779 CTTATCACATATATACACTTTCACATTCATCACATTCATCACATTGGCCATTAGGT
1 CTTATCACATATAT--A----CAC-TT--TCACATTCATCACATTGGCCATTCGGC
*
27571835 CTTATCTCATATATACACTTTCACATTCATCACATTGGCCATTCGGC
1 CTTATCACATATATACACTTTCACATTCATCACATTGGCCATTCGGC
* * * *
27571882 CTTATCACATATATACACTTTCACATTCATCACGTTGGTCACTCGAC
1 CTTATCACATATATACACTTTCACATTCATCACATTGGCCATTCGGC
* * * *
27571929 CCTATCACATATATATACTTTCACATTCATCACGTTGGCCACTCGGC
1 CTTATCACATATATACACTTTCACATTCATCACATTGGCCATTCGGC
* *
27571976 CCTATCACATATATATACTTTCACATTCATCACATTGGCCATTCGGC
1 CTTATCACATATATACACTTTCACATTCATCACATTGGCCATTCGGC
27572023 CTTATCACATATATACACTTTCACATTCATCACATTGGCCATTCGGC
1 CTTATCACATATATACACTTTCACATTCATCACATTGGCCATTCGGC
27572070 CTTATCACATATA
1 CTTATCACATATA
27572083 CATATCTTGT
Statistics
Matches: 275, Mismatches: 20, Indels: 18
0.88 0.06 0.06
Matches are distributed among these distances:
47 226 0.82
49 3 0.01
50 3 0.01
53 3 0.01
54 3 0.01
56 37 0.13
ACGTcount: A:0.28, C:0.30, G:0.08, T:0.34
Consensus pattern (47 bp):
CTTATCACATATATACACTTTCACATTCATCACATTGGCCATTCGGC
Found at i:27571813 original size:9 final size:9
Alignment explanation
Indices: 27571799--27571823 Score: 50
Period size: 9 Copynumber: 2.8 Consensus size: 9
27571789 ATATACACTT
27571799 TCACATTCA
1 TCACATTCA
27571808 TCACATTCA
1 TCACATTCA
27571817 TCACATT
1 TCACATT
27571824 GGCCATTAGG
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
9 16 1.00
ACGTcount: A:0.32, C:0.32, G:0.00, T:0.36
Consensus pattern (9 bp):
TCACATTCA
Found at i:27572032 original size:22 final size:22
Alignment explanation
Indices: 27572004--27572079 Score: 64
Period size: 22 Copynumber: 3.3 Consensus size: 22
27571994 TTTCACATTC
27572004 ATCACATTGGCCATTCGGCCTT
1 ATCACATTGGCCATTCGGCCTT
** * * *
27572026 ATCACATATATACACTTTC-ACATT
1 ATCACAT-T-GGC-CATTCGGCCTT
27572050 CATCACATTGGCCATTCGGCCTT
1 -ATCACATTGGCCATTCGGCCTT
27572073 ATCACAT
1 ATCACAT
27572080 ATACATATCT
Statistics
Matches: 39, Mismatches: 10, Indels: 10
0.66 0.17 0.17
Matches are distributed among these distances:
22 18 0.46
23 5 0.13
24 5 0.13
25 11 0.28
ACGTcount: A:0.26, C:0.30, G:0.11, T:0.33
Consensus pattern (22 bp):
ATCACATTGGCCATTCGGCCTT
Found at i:27576562 original size:26 final size:26
Alignment explanation
Indices: 27576533--27576612 Score: 151
Period size: 26 Copynumber: 3.1 Consensus size: 26
27576523 AAATTCCCAA
27576533 CATGGAACATTTACCTAACCCATTAT
1 CATGGAACATTTACCTAACCCATTAT
*
27576559 CATGAAACATTTACCTAACCCATTAT
1 CATGGAACATTTACCTAACCCATTAT
27576585 CATGGAACATTTACCTAACCCATTAT
1 CATGGAACATTTACCTAACCCATTAT
27576611 CA
1 CA
27576613 ATTTGTATCA
Statistics
Matches: 52, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
26 52 1.00
ACGTcount: A:0.36, C:0.28, G:0.06, T:0.30
Consensus pattern (26 bp):
CATGGAACATTTACCTAACCCATTAT
Found at i:27584579 original size:26 final size:26
Alignment explanation
Indices: 27584549--27584675 Score: 187
Period size: 26 Copynumber: 5.2 Consensus size: 26
27584539 TGAAATTCCC
27584549 ATCATGGAACATTTACCTAACCCATT
1 ATCATGGAACATTTACCTAACCCATT
27584575 ATCATGGAACATTTACCTAACCCATT
1 ATCATGGAACATTTACCTAACCCATT
*
27584601 ATCATGAAACATTTACCT-----A--
1 ATCATGGAACATTTACCTAACCCATT
*
27584620 ATCATGAAACATTTACCTAACCCATT
1 ATCATGGAACATTTACCTAACCCATT
27584646 ATCATGGAACATTTACCTAACCCATT
1 ATCATGGAACATTTACCTAACCCATT
27584672 ATCA
1 ATCA
27584676 ATTTGTATCA
Statistics
Matches: 92, Mismatches: 2, Indels: 14
0.85 0.02 0.13
Matches are distributed among these distances:
19 18 0.20
21 1 0.01
24 1 0.01
26 72 0.78
ACGTcount: A:0.37, C:0.26, G:0.06, T:0.31
Consensus pattern (26 bp):
ATCATGGAACATTTACCTAACCCATT
Found at i:27584625 original size:19 final size:19
Alignment explanation
Indices: 27584601--27584639 Score: 78
Period size: 19 Copynumber: 2.1 Consensus size: 19
27584591 CTAACCCATT
27584601 ATCATGAAACATTTACCTA
1 ATCATGAAACATTTACCTA
27584620 ATCATGAAACATTTACCTA
1 ATCATGAAACATTTACCTA
27584639 A
1 A
27584640 CCCATTATCA
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:0.44, C:0.21, G:0.05, T:0.31
Consensus pattern (19 bp):
ATCATGAAACATTTACCTA
Found at i:27584631 original size:45 final size:45
Alignment explanation
Indices: 27584575--27584665 Score: 164
Period size: 45 Copynumber: 2.0 Consensus size: 45
27584565 CTAACCCATT
*
27584575 ATCATGGAACATTTACCTAACCCATTATCATGAAACATTTACCTA
1 ATCATGAAACATTTACCTAACCCATTATCATGAAACATTTACCTA
*
27584620 ATCATGAAACATTTACCTAACCCATTATCATGGAACATTTACCTA
1 ATCATGAAACATTTACCTAACCCATTATCATGAAACATTTACCTA
27584665 A
1 A
27584666 CCCATTATCA
Statistics
Matches: 44, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
45 44 1.00
ACGTcount: A:0.38, C:0.24, G:0.07, T:0.31
Consensus pattern (45 bp):
ATCATGAAACATTTACCTAACCCATTATCATGAAACATTTACCTA
Found at i:27586308 original size:62 final size:62
Alignment explanation
Indices: 27586228--27586414 Score: 322
Period size: 62 Copynumber: 3.0 Consensus size: 62
27586218 ACTTATAGGG
* *
27586228 AAAGTAATTTAGTTCGAAGTATATGAAAGAGATTGCAGCTTGATAAGTGAGTTAACTTAAAT
1 AAAGTAATTTAGTTCGAAGTATATGAGAGAGGTTGCAGCTTGATAAGTGAGTTAACTTAAAT
*
27586290 AAATTAATTTAGTTCGAAGTATATGAGAGAGGTTGCAGCTTGATAAGTGAGTTAACTTAAAT
1 AAAGTAATTTAGTTCGAAGTATATGAGAGAGGTTGCAGCTTGATAAGTGAGTTAACTTAAAT
27586352 AAAGTAATTTAGTTCGAAGTATATGAGAGAGGTTGCAG-TTGTATAAGTGAGTTAAACTTAAAT
1 AAAGTAATTTAGTTCGAAGTATATGAGAGAGGTTGCAGCTTG-ATAAGTGAGTT-AACTTAAAT
27586415 CACACTTGTA
Statistics
Matches: 119, Mismatches: 4, Indels: 3
0.94 0.03 0.02
Matches are distributed among these distances:
61 3 0.03
62 107 0.90
63 9 0.08
ACGTcount: A:0.39, C:0.06, G:0.22, T:0.33
Consensus pattern (62 bp):
AAAGTAATTTAGTTCGAAGTATATGAGAGAGGTTGCAGCTTGATAAGTGAGTTAACTTAAAT
Found at i:27587445 original size:2 final size:2
Alignment explanation
Indices: 27587438--27587470 Score: 66
Period size: 2 Copynumber: 16.5 Consensus size: 2
27587428 ATCCATAAGT
27587438 TA TA TA TA 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 T
27587471 TAATAATGCA
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 31 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:27588818 original size:2 final size:2
Alignment explanation
Indices: 27588813--27588838 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
27588803 TTTTGTACCA
27588813 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
27588839 TGAGATATTT
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 24 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:27601102 original size:30 final size:30
Alignment explanation
Indices: 27601058--27601146 Score: 101
Period size: 30 Copynumber: 3.0 Consensus size: 30
27601048 CAAAGATAAC
27601058 AAGAAAACC-GAATAAAGAAATCCAAGATA
1 AAGAAAACCAGAATAAAGAAATCCAAGATA
* *
27601087 GAGAAACCCAGAATAAAGAAATCC-AGAATA
1 AAGAAAACCAGAATAAAGAAATCCAAG-ATA
* * * *
27601117 AAGAGATCCAGGATAAAGAAACCCAAGATA
1 AAGAAAACCAGAATAAAGAAATCCAAGATA
27601147 CGATACTATG
Statistics
Matches: 50, Mismatches: 7, Indels: 5
0.81 0.11 0.08
Matches are distributed among these distances:
29 9 0.18
30 39 0.78
31 2 0.04
ACGTcount: A:0.57, C:0.16, G:0.17, T:0.10
Consensus pattern (30 bp):
AAGAAAACCAGAATAAAGAAATCCAAGATA
Found at i:27601106 original size:15 final size:15
Alignment explanation
Indices: 27601058--27601137 Score: 92
Period size: 15 Copynumber: 5.4 Consensus size: 15
27601048 CAAAGATAAC
*
27601058 AAGAAAACC-GAATA
1 AAGAAATCCAGAATA
27601072 AAGAAATCCA-AGATA
1 AAGAAATCCAGA-ATA
* *
27601087 GAGAAACCCAGAATA
1 AAGAAATCCAGAATA
27601102 AAGAAATCCAGAATA
1 AAGAAATCCAGAATA
* *
27601117 AAGAGATCCAGGATA
1 AAGAAATCCAGAATA
27601132 AAGAAA
1 AAGAAA
27601138 CCCAAGATAC
Statistics
Matches: 55, Mismatches: 8, Indels: 5
0.81 0.12 0.07
Matches are distributed among these distances:
14 9 0.16
15 45 0.82
16 1 0.02
ACGTcount: A:0.59, C:0.14, G:0.17, T:0.10
Consensus pattern (15 bp):
AAGAAATCCAGAATA
Found at i:27601146 original size:15 final size:15
Alignment explanation
Indices: 27601069--27601146 Score: 79
Period size: 15 Copynumber: 5.2 Consensus size: 15
27601059 AGAAAACCGA
27601069 ATAAAGAAATCCAAG
1 ATAAAGAAATCCAAG
* *
27601084 ATAGAGAAA-CCCAG
1 ATAAAGAAATCCAAG
27601098 AATAAAGAAATCC-AG
1 -ATAAAGAAATCCAAG
* *
27601113 AATAAAGAGATCCAGG
1 -ATAAAGAAATCCAAG
*
27601129 ATAAAGAAACCCAAG
1 ATAAAGAAATCCAAG
27601144 ATA
1 ATA
27601147 CGATACTATG
Statistics
Matches: 52, Mismatches: 8, Indels: 6
0.79 0.12 0.09
Matches are distributed among these distances:
14 4 0.08
15 45 0.87
16 3 0.06
ACGTcount: A:0.56, C:0.15, G:0.17, T:0.12
Consensus pattern (15 bp):
ATAAAGAAATCCAAG
Found at i:27621896 original size:47 final size:46
Alignment explanation
Indices: 27621768--27621944 Score: 201
Period size: 47 Copynumber: 3.8 Consensus size: 46
27621758 GTGCGATTTG
* * *
27621768 CCTTGAGTTGGCTTCGGGACATTGTATAGGTACTCCAAGTAAAGTTA
1 CCTTGAGTTGGCTTCGGGACATGGTATAGGTACTTC-GGTAAAGTTA
* * *
27621815 CGTTGATTTGGCTTCGGGACATTGTATAGGTACTTCGGGTAAAGTTA
1 CCTTGAGTTGGCTTCGGGACATGGTATAGGTACTTC-GGTAAAGTTA
* * *
27621862 CCTTGATTTGGCTTCGGGCCATGGTATAGGTACTTCGGTGATAATTTA
1 CCTTGAGTTGGCTTCGGGACATGGTATAGGTACTTCGGT-A-AAGTTA
* * * *
27621910 CCTTGAGTTAGTTTTGGGCCATGGTATAGGTACTT
1 CCTTGAGTTGGCTTCGGGACATGGTATAGGTACTT
27621945 ATCGTGTGAA
Statistics
Matches: 115, Mismatches: 13, Indels: 3
0.88 0.10 0.02
Matches are distributed among these distances:
46 3 0.03
47 76 0.66
48 36 0.31
ACGTcount: A:0.21, C:0.15, G:0.28, T:0.36
Consensus pattern (46 bp):
CCTTGAGTTGGCTTCGGGACATGGTATAGGTACTTCGGTAAAGTTA
Found at i:27625047 original size:49 final size:49
Alignment explanation
Indices: 27624986--27625133 Score: 296
Period size: 49 Copynumber: 3.0 Consensus size: 49
27624976 ATGTATGAGA
27624986 TATATATATGTGATAAGGCCTAATGGCCGATGTGATGAATGTGAAAGTG
1 TATATATATGTGATAAGGCCTAATGGCCGATGTGATGAATGTGAAAGTG
27625035 TATATATATGTGATAAGGCCTAATGGCCGATGTGATGAATGTGAAAGTG
1 TATATATATGTGATAAGGCCTAATGGCCGATGTGATGAATGTGAAAGTG
27625084 TATATATATGTGATAAGGCCTAATGGCCGATGTGATGAATGTGAAAGTG
1 TATATATATGTGATAAGGCCTAATGGCCGATGTGATGAATGTGAAAGTG
27625133 T
1 T
27625134 GATGAATGTG
Statistics
Matches: 99, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
49 99 1.00
ACGTcount: A:0.32, C:0.08, G:0.28, T:0.31
Consensus pattern (49 bp):
TATATATATGTGATAAGGCCTAATGGCCGATGTGATGAATGTGAAAGTG
Found at i:27625096 original size:98 final size:98
Alignment explanation
Indices: 27624986--27625619 Score: 787
Period size: 98 Copynumber: 6.7 Consensus size: 98
27624976 ATGTATGAGA
27624986 TATATATATGTGATAAGGCCTAATGGCCGATGTGATGAATGTGAAAGTGTATATATATGTGATAA
1 TATATATATGTGATAAGGCCTAATGGCCGATGTGATGAATGTGAAAGTGTATATATATGTGATAA
27625051 GGCCTAATGGCCGATGTGATGAATGTGAAAGTG
66 GGCCTAATGGCCGATGTGATGAATGTGAAAGTG
*
27625084 TATATATATGTGATAAGGCCTAATGGCCGATGTGATGAATGTGAAAGTGTGAT-GA-ATGTGA-A
1 TATATATATGTGATAAGGCCTAATGGCCGATGTGATGAATGTGAAAGTGT-ATATATATGTGATA
** * ***
27625146 AGTG--TATAT---ATATGTGAT-AAGGCCTAA-TG
65 AG-GCCTA-ATGGCCGATGTGATGAATGTGAAAGTG
**** * * *
27625175 ---GCCGATGTGATGAATG--TGAA----AG-TGTGATGAATGTGAAAGTATATATATATGTGAT
1 TATATATATGTGAT-AAGGCCT-AATGGCCGATGTGATGAATGTGAAAGTGTATATATATGTGAT
27625230 AAGGCCTAATGGCCGATGTGATGAATGTGAAAGTG
64 AAGGCCTAATGGCCGATGTGATGAATGTGAAAGTG
* *
27625265 TGTATATATGTGATAAGGCCTAATGGCCGATGTGATGAATGTGAAAGTATATATATATGTGATAA
1 TATATATATGTGATAAGGCCTAATGGCCGATGTGATGAATGTGAAAGTGTATATATATGTGATAA
27625330 GGCCTAATGGCCGATGTGATGAATGTGAAAGTG
66 GGCCTAATGGCCGATGTGATGAATGTGAAAGTG
* *
27625363 TGTATATATGTGATAAGGCCTAATGGCCGATGTGATGAATGTGAAAGTGTGTATATATGTGATAA
1 TATATATATGTGATAAGGCCTAATGGCCGATGTGATGAATGTGAAAGTGTATATATATGTGATAA
*
27625428 GGCCTAATGGCCGATGGGATGAATGTGAAAGTG
66 GGCCTAATGGCCGATGTGATGAATGTGAAAGTG
* *
27625461 TATATATATGTGATAAGGCCTAATGGCCGATGTGATGAATGAGAAGGTGTATATATATGTGATAA
1 TATATATATGTGATAAGGCCTAATGGCCGATGTGATGAATGTGAAAGTGTATATATATGTGATAA
*
27625526 GGCCTAATGGCCAATGTGATGAATGTGAAAGTG
66 GGCCTAATGGCCGATGTGATGAATGTGAAAGTG
* * * * * * *
27625559 --TATATATGTGATAGGGCCGAGT-GCCAAAGTGATGGATGTGGAAGTGTATA-A-ATGTGATAA
1 TATATATATGTGATAAGGCCTAATGGCCGATGTGATGAATGTGAAAGTGTATATATATGTGATAA
27625619 G
66 G
27625620 TCCCGAAGGC
Statistics
Matches: 466, Mismatches: 45, Indels: 55
0.82 0.08 0.10
Matches are distributed among these distances:
82 2 0.00
83 20 0.04
84 8 0.02
85 5 0.01
86 2 0.00
87 1 0.00
88 16 0.03
89 8 0.02
90 2 0.00
91 2 0.00
92 8 0.02
93 26 0.06
94 2 0.00
95 24 0.05
96 24 0.05
97 8 0.02
98 306 0.66
99 2 0.00
ACGTcount: A:0.33, C:0.08, G:0.30, T:0.30
Consensus pattern (98 bp):
TATATATATGTGATAAGGCCTAATGGCCGATGTGATGAATGTGAAAGTGTATATATATGTGATAA
GGCCTAATGGCCGATGTGATGAATGTGAAAGTG
Found at i:27625136 original size:17 final size:17
Alignment explanation
Indices: 27625114--27625214 Score: 79
Period size: 17 Copynumber: 6.1 Consensus size: 17
27625104 TAATGGCCGA
27625114 TGTGATGAATGTGAAAG
1 TGTGATGAATGTGAAAG
27625131 TGTGATGAATGTGAAAG
1 TGTGATGAATGTGAAAG
*
27625148 TGT-ATATATATGTGATAAG
1 TGTGAT-GA-ATGTGA-AAG
** **
27625167 -G-CCT-AATG-G-CCG
1 TGTGATGAATGTGAAAG
27625179 ATGTGATGAATGTGAAAG
1 -TGTGATGAATGTGAAAG
27625197 TGTGATGAATGTGAAAG
1 TGTGATGAATGTGAAAG
27625214 T
1 T
27625215 ATATATATAT
Statistics
Matches: 66, Mismatches: 8, Indels: 20
0.70 0.09 0.21
Matches are distributed among these distances:
12 1 0.02
14 2 0.03
15 4 0.06
16 7 0.11
17 40 0.61
18 9 0.14
19 3 0.05
ACGTcount: A:0.34, C:0.04, G:0.32, T:0.31
Consensus pattern (17 bp):
TGTGATGAATGTGAAAG
Found at i:27625141 original size:66 final size:66
Alignment explanation
Indices: 27625065--27625266 Score: 395
Period size: 66 Copynumber: 3.1 Consensus size: 66
27625055 TAATGGCCGA
27625065 TGTGATGAATGTGAAAGTGTATATATATGTGATAAGGCCTAATGGCCGATGTGATGAATGTGAAA
1 TGTGATGAATGTGAAAGTGTATATATATGTGATAAGGCCTAATGGCCGATGTGATGAATGTGAAA
27625130 G
66 G
27625131 TGTGATGAATGTGAAAGTGTATATATATGTGATAAGGCCTAATGGCCGATGTGATGAATGTGAAA
1 TGTGATGAATGTGAAAGTGTATATATATGTGATAAGGCCTAATGGCCGATGTGATGAATGTGAAA
27625196 G
66 G
*
27625197 TGTGATGAATGTGAAAGTATATATATATGTGATAAGGCCTAATGGCCGATGTGATGAATGTGAAA
1 TGTGATGAATGTGAAAGTGTATATATATGTGATAAGGCCTAATGGCCGATGTGATGAATGTGAAA
27625262 G
66 G
27625263 TGTG
1 TGTG
27625267 TATATATGTG
Statistics
Matches: 135, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
66 135 1.00
ACGTcount: A:0.33, C:0.06, G:0.30, T:0.31
Consensus pattern (66 bp):
TGTGATGAATGTGAAAGTGTATATATATGTGATAAGGCCTAATGGCCGATGTGATGAATGTGAAA
G
Found at i:27625154 original size:115 final size:115
Alignment explanation
Indices: 27625016--27625364 Score: 473
Period size: 115 Copynumber: 3.0 Consensus size: 115
27625006 TAATGGCCGA
27625016 TGTGATGAATGTGAAAGTGTATATATATGTGATAAGGCCTAATGGCCGATGTGATGAATGTGAAA
1 TGTGATGAATGTGAAAGTGTATATATATGTGATAAGGCCTAATGGCCGATGTGATGAATGTGAAA
27625081 GTGTATATATATGTGATAAGGCCTAATGGCCGATGTGATGAATGTGAAAG
66 GTGTATATATATGTGATAAGGCCTAATGGCCGATGTGATGAATGTGAAAG
27625131 TGTGATGAATGTGAAAGTGTATATATATGTGATAAGGCCTAATGGCCGATGTGATGAATGTGAAA
1 TGTGATGAATGTGAAAGTGTATATATATGTGATAAGGCCTAATGGCCGATGTGATGAATGTGAAA
* **** **
27625196 GTGTGAT-GA-ATGTGA-AA-G--TATAT-ATATATGTGATAAGGCCTAATG-G-CCG
66 GTGT-ATATATATGTGATAAGGCCTA-ATGGCCGATGTGAT---G---AATGTGAAAG
*
27625245 ATGTGATGAATGTGAAAGTGTGTATATATGTGATAAGGCCTAATGGCCGATGTGATGAATGTGAA
1 -TGTGATGAATGTGAAAGTGTATATATATGTGATAAGGCCTAATGGCCGATGTGATGAATGTGAA
*
27625310 AGTATATATATATGTGATAAGGCCTAATGGCCGATGTGATGAATGTGAAAG
65 AGTGTATATATATGTGATAAGGCCTAATGGCCGATGTGATGAATGTGAAAG
27625361 TGTG
1 TGTG
27625365 TATATATGTG
Statistics
Matches: 200, Mismatches: 16, Indels: 36
0.79 0.06 0.14
Matches are distributed among these distances:
110 9 0.05
111 2 0.01
112 1 0.00
113 3 0.01
114 13 0.06
115 144 0.72
116 13 0.06
117 3 0.01
118 1 0.00
119 2 0.01
120 9 0.05
ACGTcount: A:0.33, C:0.07, G:0.30, T:0.31
Consensus pattern (115 bp):
TGTGATGAATGTGAAAGTGTATATATATGTGATAAGGCCTAATGGCCGATGTGATGAATGTGAAA
GTGTATATATATGTGATAAGGCCTAATGGCCGATGTGATGAATGTGAAAG
Found at i:27625252 original size:49 final size:49
Alignment explanation
Indices: 27625197--27625619 Score: 667
Period size: 49 Copynumber: 8.7 Consensus size: 49
27625187 AATGTGAAAG
*
27625197 TGTGATGAATGTGAAAGTATATATATATGTGATAAGGCCTAATGGCCGA
1 TGTGATGAATGTGAAAGTGTATATATATGTGATAAGGCCTAATGGCCGA
*
27625246 TGTGATGAATGTGAAAGTGTGTATATATGTGATAAGGCCTAATGGCCGA
1 TGTGATGAATGTGAAAGTGTATATATATGTGATAAGGCCTAATGGCCGA
*
27625295 TGTGATGAATGTGAAAGTATATATATATGTGATAAGGCCTAATGGCCGA
1 TGTGATGAATGTGAAAGTGTATATATATGTGATAAGGCCTAATGGCCGA
*
27625344 TGTGATGAATGTGAAAGTGTGTATATATGTGATAAGGCCTAATGGCCGA
1 TGTGATGAATGTGAAAGTGTATATATATGTGATAAGGCCTAATGGCCGA
*
27625393 TGTGATGAATGTGAAAGTGTGTATATATGTGATAAGGCCTAATGGCCGA
1 TGTGATGAATGTGAAAGTGTATATATATGTGATAAGGCCTAATGGCCGA
*
27625442 TGGGATGAATGTGAAAGTGTATATATATGTGATAAGGCCTAATGGCCGA
1 TGTGATGAATGTGAAAGTGTATATATATGTGATAAGGCCTAATGGCCGA
* * *
27625491 TGTGATGAATGAGAAGGTGTATATATATGTGATAAGGCCTAATGGCCAA
1 TGTGATGAATGTGAAAGTGTATATATATGTGATAAGGCCTAATGGCCGA
* * * *
27625540 TGTGATGAATGTGAAAGTG--TATATATGTGATAGGGCCGAGT-GCCAA
1 TGTGATGAATGTGAAAGTGTATATATATGTGATAAGGCCTAATGGCCGA
* * *
27625586 AGTGATGGATGTGGAAGTGTATA-A-ATGTGATAAG
1 TGTGATGAATGTGAAAGTGTATATATATGTGATAAG
27625620 TCCCGAAGGC
Statistics
Matches: 351, Mismatches: 21, Indels: 7
0.93 0.06 0.02
Matches are distributed among these distances:
46 30 0.09
47 20 0.06
48 2 0.01
49 299 0.85
ACGTcount: A:0.33, C:0.08, G:0.30, T:0.30
Consensus pattern (49 bp):
TGTGATGAATGTGAAAGTGTATATATATGTGATAAGGCCTAATGGCCGA
Found at i:27629579 original size:13 final size:13
Alignment explanation
Indices: 27629561--27629586 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
27629551 GTGAGGCGGC
27629561 ATAATAAAATAAA
1 ATAATAAAATAAA
27629574 ATAATAAAATAAA
1 ATAATAAAATAAA
27629587 GCCATAGAAT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.77, C:0.00, G:0.00, T:0.23
Consensus pattern (13 bp):
ATAATAAAATAAA
Found at i:27631083 original size:20 final size:20
Alignment explanation
Indices: 27631055--27631100 Score: 83
Period size: 20 Copynumber: 2.3 Consensus size: 20
27631045 TATGTAAATA
*
27631055 ATATGAATAATATTATGTTT
1 ATATAAATAATATTATGTTT
27631075 ATATAAATAATATTATGTTT
1 ATATAAATAATATTATGTTT
27631095 ATATAA
1 ATATAA
27631101 TCAACTTACA
Statistics
Matches: 25, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
20 25 1.00
ACGTcount: A:0.46, C:0.00, G:0.07, T:0.48
Consensus pattern (20 bp):
ATATAAATAATATTATGTTT
Found at i:27631665 original size:17 final size:17
Alignment explanation
Indices: 27631639--27631676 Score: 58
Period size: 17 Copynumber: 2.2 Consensus size: 17
27631629 AAGAAAGAAA
*
27631639 GAAAATGAAACAAAAAG
1 GAAAAAGAAACAAAAAG
*
27631656 GAAAAAGAAAGAAAAAG
1 GAAAAAGAAACAAAAAG
27631673 GAAA
1 GAAA
27631677 GAAAGAAGGA
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
17 19 1.00
ACGTcount: A:0.74, C:0.03, G:0.21, T:0.03
Consensus pattern (17 bp):
GAAAAAGAAACAAAAAG
Found at i:27631666 original size:11 final size:10
Alignment explanation
Indices: 27631597--27631680 Score: 50
Period size: 10 Copynumber: 8.2 Consensus size: 10
27631587 ATTATAATAT
*
27631597 AAAACAAAGA
1 AAAAGAAAGA
*
27631607 AATA-AAAGA
1 AAAAGAAAGA
*
27631616 AAATTGAATAG-
1 AAA-AGAA-AGA
27631627 AAAAGAAAGA
1 AAAAGAAAGA
*
27631637 AAGAA-AATGA
1 AA-AAGAAAGA
27631647 AACAA-AAAGGA
1 AA-AAGAAA-GA
27631658 AAAAGAAAGA
1 AAAAGAAAGA
27631668 AAAAGGAAAGA
1 AAAA-GAAAGA
27631679 AA
1 AA
27631681 GAAGGAGAAA
Statistics
Matches: 59, Mismatches: 7, Indels: 15
0.73 0.09 0.19
Matches are distributed among these distances:
9 9 0.15
10 26 0.44
11 22 0.37
12 2 0.03
ACGTcount: A:0.74, C:0.02, G:0.18, T:0.06
Consensus pattern (10 bp):
AAAAGAAAGA
Found at i:27632684 original size:40 final size:40
Alignment explanation
Indices: 27632563--27632700 Score: 147
Period size: 40 Copynumber: 3.5 Consensus size: 40
27632553 CTTCGAGTCA
* * *
27632563 ATGAGACACTAAGTGTCAAATTATTATTTCGGATATATTCG
1 ATGAGACACTGAGTGTCAAATTATTACTTCGGAT-TATCCG
* * * *
27632604 ATGAGGCACTGAGTGTC-AA-T-TTACTTCGGTTTAGCTG
1 ATGAGACACTGAGTGTCAAATTATTACTTCGGATTATCCG
* *
27632641 ATGAGACACTGGGTGTCAAATTATTACTTCGAATTATCCG
1 ATGAGACACTGAGTGTCAAATTATTACTTCGGATTATCCG
* *
27632681 ATGAGACACTGGGTGCCAAA
1 ATGAGACACTGAGTGTCAAA
27632701 CTTGTATATT
Statistics
Matches: 80, Mismatches: 14, Indels: 7
0.79 0.14 0.07
Matches are distributed among these distances:
37 18 0.22
38 11 0.14
39 2 0.03
40 34 0.43
41 15 0.19
ACGTcount: A:0.30, C:0.16, G:0.22, T:0.32
Consensus pattern (40 bp):
ATGAGACACTGAGTGTCAAATTATTACTTCGGATTATCCG
Found at i:27637404 original size:26 final size:26
Alignment explanation
Indices: 27637375--27637456 Score: 164
Period size: 26 Copynumber: 3.2 Consensus size: 26
27637365 TGATACAAAT
27637375 TGATAATGGGTTAGGTAAATGTTCCA
1 TGATAATGGGTTAGGTAAATGTTCCA
27637401 TGATAATGGGTTAGGTAAATGTTCCA
1 TGATAATGGGTTAGGTAAATGTTCCA
27637427 TGATAATGGGTTAGGTAAATGTTCCA
1 TGATAATGGGTTAGGTAAATGTTCCA
27637453 TGAT
1 TGAT
27637457 GGGAATTTCA
Statistics
Matches: 56, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
26 56 1.00
ACGTcount: A:0.30, C:0.07, G:0.27, T:0.35
Consensus pattern (26 bp):
TGATAATGGGTTAGGTAAATGTTCCA
Found at i:27638645 original size:8 final size:8
Alignment explanation
Indices: 27638632--27638668 Score: 56
Period size: 8 Copynumber: 4.6 Consensus size: 8
27638622 CTAGATTGGC
27638632 AAAAGCCG
1 AAAAGCCG
27638640 AAAAGCCG
1 AAAAGCCG
*
27638648 AAATGCCG
1 AAAAGCCG
*
27638656 AAATGCCG
1 AAAAGCCG
27638664 AAAAG
1 AAAAG
27638669 TCGGTATTTT
Statistics
Matches: 27, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
8 27 1.00
ACGTcount: A:0.49, C:0.22, G:0.24, T:0.05
Consensus pattern (8 bp):
AAAAGCCG
Found at i:27639167 original size:54 final size:53
Alignment explanation
Indices: 27639085--27639224 Score: 235
Period size: 54 Copynumber: 2.6 Consensus size: 53
27639075 GGAAGCGTCA
27639085 TGGTGGCTATGCCACAATTATCTGATCTGGTGGCTCTGCCACATATATCTGTTC
1 TGGTGGCTATGCCAC-ATTATCTGATCTGGTGGCTCTGCCACATATATCTGTTC
27639139 TGGTGGCTATGCCACGATTATCTGATCTGGTGGCTCTGCCACATATATCTGTTC
1 TGGTGGCTATGCCAC-ATTATCTGATCTGGTGGCTCTGCCACATATATCTGTTC
* *
27639193 TGGTGGCTCTGCCACAATATCTGTATCTGGTG
1 TGGTGGCTATGCCACATTATCTG-ATCTGGTG
27639225 ACTTCGTCAC
Statistics
Matches: 82, Mismatches: 3, Indels: 2
0.94 0.03 0.02
Matches are distributed among these distances:
53 7 0.09
54 75 0.91
ACGTcount: A:0.17, C:0.24, G:0.24, T:0.35
Consensus pattern (53 bp):
TGGTGGCTATGCCACATTATCTGATCTGGTGGCTCTGCCACATATATCTGTTC
Found at i:27639235 original size:27 final size:27
Alignment explanation
Indices: 27639085--27639242 Score: 191
Period size: 27 Copynumber: 5.9 Consensus size: 27
27639075 GGAAGCGTCA
*
27639085 TGGTGGCTATGCCACAATTATCTG-ATC
1 TGGTGGCTCTGCCACAA-TATCTGTATC
27639112 TGGTGGCTCTGCCACATATATCTGT-TC
1 TGGTGGCTCTGCCACA-ATATCTGTATC
* *
27639139 TGGTGGCTATGCCACGATTATCTG-ATC
1 TGGTGGCTCTGCCAC-AATATCTGTATC
27639166 TGGTGGCTCTGCCACATATATCTGT-TC
1 TGGTGGCTCTGCCACA-ATATCTGTATC
27639193 TGGTGGCTCTGCCACAATATCTGTATC
1 TGGTGGCTCTGCCACAATATCTGTATC
* *
27639220 TGGTGACT-TCGTCACAATATCTG
1 TGGTGGCTCT-GCCACAATATCTG
27639243 GCAGCCTCGC
Statistics
Matches: 116, Mismatches: 7, Indels: 16
0.83 0.05 0.12
Matches are distributed among these distances:
26 10 0.09
27 104 0.90
28 2 0.02
ACGTcount: A:0.18, C:0.24, G:0.23, T:0.35
Consensus pattern (27 bp):
TGGTGGCTCTGCCACAATATCTGTATC
Found at i:27640863 original size:17 final size:16
Alignment explanation
Indices: 27640843--27640895 Score: 56
Period size: 16 Copynumber: 3.3 Consensus size: 16
27640833 TATGGGTACA
27640843 TTTTATTTATTATTGTC
1 TTTTATTTATT-TTGTC
*
27640860 TTTTA-TTATTTTAT-
1 TTTTATTTATTTTGTC
*
27640874 TTTTGTTCTATTTTGTC
1 TTTTATT-TATTTTGTC
27640891 TTTTA
1 TTTTA
27640896 GTGTATTCTT
Statistics
Matches: 29, Mismatches: 4, Indels: 6
0.74 0.10 0.15
Matches are distributed among these distances:
14 4 0.14
15 4 0.14
16 12 0.41
17 9 0.31
ACGTcount: A:0.15, C:0.06, G:0.06, T:0.74
Consensus pattern (16 bp):
TTTTATTTATTTTGTC
Found at i:27640920 original size:3 final size:3
Alignment explanation
Indices: 27640912--27640969 Score: 116
Period size: 3 Copynumber: 19.3 Consensus size: 3
27640902 TCTTGTTCAT
27640912 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
27640960 TTA TTA TTA T
1 TTA TTA TTA T
27640970 ATTTAGCATT
Statistics
Matches: 55, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 55 1.00
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (3 bp):
TTA
Found at i:27646086 original size:20 final size:20
Alignment explanation
Indices: 27646061--27646101 Score: 64
Period size: 20 Copynumber: 2.0 Consensus size: 20
27646051 GTCTTGGCAT
*
27646061 AACTTTACTAATGATGGAAG
1 AACTTTACTAATAATGGAAG
*
27646081 AACTTTGCTAATAATGGAAG
1 AACTTTACTAATAATGGAAG
27646101 A
1 A
27646102 GACATAGTTG
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
20 19 1.00
ACGTcount: A:0.41, C:0.10, G:0.20, T:0.29
Consensus pattern (20 bp):
AACTTTACTAATAATGGAAG
Found at i:27654405 original size:42 final size:42
Alignment explanation
Indices: 27654328--27654407 Score: 124
Period size: 42 Copynumber: 1.9 Consensus size: 42
27654318 CATATGCCAC
*
27654328 ACGGCCTGGACACACACCCATGTCCTTGCCCGTGTGGCTCAT
1 ACGGCCTGGACACACACCCATGTCCCTGCCCGTGTGGCTCAT
* * *
27654370 ACGGCCTGGACACACGCCCATGTCCCTGGCTGTGTGGC
1 ACGGCCTGGACACACACCCATGTCCCTGCCCGTGTGGC
27654408 ATTGACAGTC
Statistics
Matches: 34, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
42 34 1.00
ACGTcount: A:0.15, C:0.38, G:0.28, T:0.20
Consensus pattern (42 bp):
ACGGCCTGGACACACACCCATGTCCCTGCCCGTGTGGCTCAT
Found at i:27660320 original size:16 final size:15
Alignment explanation
Indices: 27660280--27660317 Score: 58
Period size: 15 Copynumber: 2.5 Consensus size: 15
27660270 AAGAGCATAC
*
27660280 CTAAAGCTTTTTCAA
1 CTAAAGCCTTTTCAA
*
27660295 CTGAAGCCTTTTCAA
1 CTAAAGCCTTTTCAA
27660310 CTAAAGCC
1 CTAAAGCC
27660318 CTTGCTTGCG
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
15 20 1.00
ACGTcount: A:0.32, C:0.26, G:0.11, T:0.32
Consensus pattern (15 bp):
CTAAAGCCTTTTCAA
Found at i:27662630 original size:21 final size:22
Alignment explanation
Indices: 27662590--27662639 Score: 59
Period size: 21 Copynumber: 2.3 Consensus size: 22
27662580 AAAAGAAAGT
* *
27662590 TCAATCATAATTCATAATAATTA
1 TCAATTATAATTCACAATAA-TA
27662613 T-AATTATAA-TCACAATAATA
1 TCAATTATAATTCACAATAATA
27662633 TCAATTA
1 TCAATTA
27662640 GTAGATTAGT
Statistics
Matches: 24, Mismatches: 2, Indels: 4
0.80 0.07 0.13
Matches are distributed among these distances:
20 3 0.12
21 13 0.54
22 7 0.29
23 1 0.04
ACGTcount: A:0.50, C:0.12, G:0.00, T:0.38
Consensus pattern (22 bp):
TCAATTATAATTCACAATAATA
Found at i:27670343 original size:81 final size:81
Alignment explanation
Indices: 27670208--27670376 Score: 311
Period size: 81 Copynumber: 2.1 Consensus size: 81
27670198 AAAGAATTAT
*
27670208 TCTTTGGCTTCAGTTCAGTGTCTTTTATTATATTTAAATTGTCACCAAAAATATCATTCATTGGC
1 TCTTTGGCTTCAGTTCAGTGTCTTTTATTATATTTAAATTGTCACCAAAAATATCATTCATGGGC
27670273 TTCAGCTCTGCATCCG
66 TTCAGCTCTGCATCCG
*
27670289 TCTTTGGCTTCAGTTCAGTGTCTTTTATTATATTTAAATTGTCACCAAATATATCATTCATGGGC
1 TCTTTGGCTTCAGTTCAGTGTCTTTTATTATATTTAAATTGTCACCAAAAATATCATTCATGGGC
*
27670354 TTCAGCTCTGCATCCT
66 TTCAGCTCTGCATCCG
27670370 TCTTTGG
1 TCTTTGG
27670377 TTTTAATTTC
Statistics
Matches: 85, Mismatches: 3, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
81 85 1.00
ACGTcount: A:0.22, C:0.21, G:0.14, T:0.43
Consensus pattern (81 bp):
TCTTTGGCTTCAGTTCAGTGTCTTTTATTATATTTAAATTGTCACCAAAAATATCATTCATGGGC
TTCAGCTCTGCATCCG
Found at i:27673234 original size:2 final size:2
Alignment explanation
Indices: 27673221--27673260 Score: 71
Period size: 2 Copynumber: 20.0 Consensus size: 2
27673211 ATTGCCTTAT
*
27673221 AG AG AG AA AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG
1 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG
27673261 TTGTTTGGGG
Statistics
Matches: 36, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
2 36 1.00
ACGTcount: A:0.53, C:0.00, G:0.47, T:0.00
Consensus pattern (2 bp):
AG
Found at i:27674048 original size:16 final size:16
Alignment explanation
Indices: 27674029--27674062 Score: 52
Period size: 16 Copynumber: 2.2 Consensus size: 16
27674019 AATAAAAAAT
*
27674029 AAAAACAA-CAAAATA
1 AAAAACAATCAAAACA
27674044 AAAAACAATCAAAACA
1 AAAAACAATCAAAACA
27674060 AAA
1 AAA
27674063 CCTAAAGACA
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
15 8 0.47
16 9 0.53
ACGTcount: A:0.79, C:0.15, G:0.00, T:0.06
Consensus pattern (16 bp):
AAAAACAATCAAAACA
Found at i:27676216 original size:42 final size:43
Alignment explanation
Indices: 27676165--27676278 Score: 133
Period size: 43 Copynumber: 2.7 Consensus size: 43
27676155 TCTGTTTTAA
*
27676165 GTGTAAGACCATGTCTAGGACATTGGCATC-ATATCTGATT-T
1 GTGTAAGACCATGTCTGGGACATTGGCATCAATATCTGATTAT
* * * * *
27676206 CGTGTAAGACCCTGTCTGGGACAGTGGCATCAATGTTTTATTAT
1 -GTGTAAGACCATGTCTGGGACATTGGCATCAATATCTGATTAT
* *
27676250 ATGTAAGACCACGTCTGGGACATTGGCAT
1 GTGTAAGACCATGTCTGGGACATTGGCAT
27676279 TGTATATGTT
Statistics
Matches: 60, Mismatches: 10, Indels: 3
0.82 0.14 0.04
Matches are distributed among these distances:
42 27 0.45
43 32 0.53
44 1 0.02
ACGTcount: A:0.25, C:0.18, G:0.25, T:0.32
Consensus pattern (43 bp):
GTGTAAGACCATGTCTGGGACATTGGCATCAATATCTGATTAT
Found at i:27680838 original size:75 final size:73
Alignment explanation
Indices: 27680747--27680914 Score: 193
Period size: 75 Copynumber: 2.3 Consensus size: 73
27680737 GGTTTTCCTC
* * **
27680747 ATTGA-AATACCATACCTACATTTTACAACTCAGTATGGGA-AATGCCATACCTACATTTCTTAA
1 ATTGATAAT-CCATACCTACATTTGACAACTCAGTAT-GGATAATACCATACCTACATTTCACAA
27680810 CTCAGTATGG
64 CTCAGTATGG
* * *
27680820 ATTTGATAATTCCATACCTACATTTGACAACTCGGTATGGATGATACCATACCTACTTTTCACAA
1 A-TTGATAA-TCCATACCTACATTTGACAACTCAGTATGGATAATACCATACCTACATTTCACAA
*
27680885 CTCGGTATGG
64 CTCAGTATGG
27680895 A-TGAT-A-CCATACCTACATTT
1 ATTGATAATCCATACCTACATTT
27680915 CACACTTTGC
Statistics
Matches: 83, Mismatches: 8, Indels: 11
0.81 0.08 0.11
Matches are distributed among these distances:
70 14 0.17
72 1 0.01
73 5 0.06
74 7 0.08
75 55 0.66
76 1 0.01
ACGTcount: A:0.32, C:0.23, G:0.12, T:0.33
Consensus pattern (73 bp):
ATTGATAATCCATACCTACATTTGACAACTCAGTATGGATAATACCATACCTACATTTCACAACT
CAGTATGG
Found at i:27680916 original size:35 final size:35
Alignment explanation
Indices: 27680753--27680918 Score: 190
Period size: 35 Copynumber: 4.6 Consensus size: 35
27680743 CCTCATTGAA
* *
27680753 ATACCATACCTACATTTTACAACTCAGTATGGGA-A
1 ATACCATACCTACATTTCACAACTCAGTAT-GGATG
* **
27680788 ATGCCATACCTACATTTCTTAACTCAGTATGGATTTG
1 ATACCATACCTACATTTCACAACTCAGTATGGA--TG
* *
27680825 ATAATTCCATACCTACATTTGACAACTCGGTATGGATG
1 AT-A--CCATACCTACATTTCACAACTCAGTATGGATG
* *
27680863 ATACCATACCTACTTTTCACAACTCGGTATGGATG
1 ATACCATACCTACATTTCACAACTCAGTATGGATG
27680898 ATACCATACCTACATTTCACA
1 ATACCATACCTACATTTCACA
27680919 CTTTGCCATG
Statistics
Matches: 112, Mismatches: 13, Indels: 12
0.82 0.09 0.09
Matches are distributed among these distances:
34 3 0.03
35 76 0.68
37 3 0.03
38 4 0.04
40 26 0.23
ACGTcount: A:0.32, C:0.24, G:0.12, T:0.32
Consensus pattern (35 bp):
ATACCATACCTACATTTCACAACTCAGTATGGATG
Found at i:27683872 original size:2 final size:2
Alignment explanation
Indices: 27683865--27683906 Score: 84
Period size: 2 Copynumber: 21.0 Consensus size: 2
27683855 CAAATGGTGG
27683865 AT AT AT AT AT 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 AT AT AT AT AT
27683907 CCTTCAAATT
Statistics
Matches: 40, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 40 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:27691368 original size:3 final size:3
Alignment explanation
Indices: 27691360--27691423 Score: 119
Period size: 3 Copynumber: 21.3 Consensus size: 3
27691350 CACTCATCTC
27691360 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
*
27691408 AAT AAT AAT AGT AAT A
1 AAT AAT AAT AAT AAT A
27691424 CTTACCTCAA
Statistics
Matches: 59, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
3 59 1.00
ACGTcount: A:0.66, C:0.00, G:0.02, T:0.33
Consensus pattern (3 bp):
AAT
Found at i:27691818 original size:5 final size:5
Alignment explanation
Indices: 27691810--27691886 Score: 58
Period size: 5 Copynumber: 15.8 Consensus size: 5
27691800 TAATTTATTT
* *
27691810 TATAA TATAA TAT-- TATAA TATAA T-TAA TATAAA TTACAA TATAA TAAAA
1 TATAA TATAA TATAA TATAA TATAA TATAA TAT-AA -TATAA TATAA TATAA
27691859 TAATAA TATAA TCA-AA T-TAA -ATAA TATA
1 T-ATAA TATAA T-ATAA TATAA TATAA TATA
27691887 TTTATATAAA
Statistics
Matches: 58, Mismatches: 4, Indels: 20
0.71 0.05 0.24
Matches are distributed among these distances:
3 3 0.05
4 9 0.16
5 35 0.60
6 9 0.16
7 2 0.03
ACGTcount: A:0.60, C:0.03, G:0.00, T:0.38
Consensus pattern (5 bp):
TATAA
Found at i:27691850 original size:21 final size:22
Alignment explanation
Indices: 27691812--27691885 Score: 75
Period size: 21 Copynumber: 3.5 Consensus size: 22
27691802 ATTTATTTTA
*
27691812 TAATATAATATTATAATATAAT
1 TAATATAATATTACAATATAAT
27691834 TAATATAA-ATTACAATATAA-
1 TAATATAATATTACAATATAAT
* * *
27691854 TAAAATAATAATATAATCA-AAT
1 TAATATAATATTACAAT-ATAAT
27691876 TAA-ATAATAT
1 TAATATAATAT
27691886 ATTTATATAA
Statistics
Matches: 44, Mismatches: 5, Indels: 7
0.79 0.09 0.12
Matches are distributed among these distances:
20 7 0.16
21 25 0.57
22 12 0.27
ACGTcount: A:0.59, C:0.03, G:0.00, T:0.38
Consensus pattern (22 bp):
TAATATAATATTACAATATAAT
Found at i:27694683 original size:25 final size:26
Alignment explanation
Indices: 27694655--27694705 Score: 68
Period size: 26 Copynumber: 2.0 Consensus size: 26
27694645 CTTATTTCAT
*
27694655 TAAATAAAAAAT-TTTAAAAATATAA
1 TAAATAAAAAATATTTAAAAACATAA
* *
27694680 TAAATCAAATATATTTAAAAACATAA
1 TAAATAAAAAATATTTAAAAACATAA
27694706 AAACAAATAT
Statistics
Matches: 22, Mismatches: 3, Indels: 1
0.85 0.12 0.04
Matches are distributed among these distances:
25 10 0.45
26 12 0.55
ACGTcount: A:0.65, C:0.04, G:0.00, T:0.31
Consensus pattern (26 bp):
TAAATAAAAAATATTTAAAAACATAA
Found at i:27694697 original size:26 final size:24
Alignment explanation
Indices: 27694667--27694715 Score: 71
Period size: 26 Copynumber: 2.0 Consensus size: 24
27694657 AATAAAAAAT
*
27694667 TTTAAAAATATAATAAATCAAATATA
1 TTTAAAAACATAA-AAA-CAAATATA
27694693 TTTAAAAACATAAAAACAAATAT
1 TTTAAAAACATAAAAACAAATAT
27694716 TAAAACAAAT
Statistics
Matches: 22, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
24 7 0.32
25 3 0.14
26 12 0.55
ACGTcount: A:0.63, C:0.06, G:0.00, T:0.31
Consensus pattern (24 bp):
TTTAAAAACATAAAAACAAATATA
Found at i:27697553 original size:22 final size:22
Alignment explanation
Indices: 27697528--27697577 Score: 57
Period size: 22 Copynumber: 2.3 Consensus size: 22
27697518 ATGTTTGGGT
*
27697528 AATTATCATAATAAGTTTA-AAA
1 AATTATCAT-ACAAGTTTATAAA
*
27697550 AATTATTATACAAGTTTATAAA
1 AATTATCATACAAGTTTATAAA
*
27697572 ACTTAT
1 AATTAT
27697578 TTTTATAAAT
Statistics
Matches: 24, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
21 8 0.33
22 16 0.67
ACGTcount: A:0.50, C:0.06, G:0.04, T:0.40
Consensus pattern (22 bp):
AATTATCATACAAGTTTATAAA
Found at i:27699904 original size:2 final size:2
Alignment explanation
Indices: 27699897--27699929 Score: 66
Period size: 2 Copynumber: 16.5 Consensus size: 2
27699887 AATTGAACCC
27699897 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 A
27699930 ATTTAAAGGA
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 31 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:27701621 original size:22 final size:22
Alignment explanation
Indices: 27701593--27701636 Score: 88
Period size: 22 Copynumber: 2.0 Consensus size: 22
27701583 CTTTACTTAG
27701593 ACTTTTGTATTCGATCAACAAA
1 ACTTTTGTATTCGATCAACAAA
27701615 ACTTTTGTATTCGATCAACAAA
1 ACTTTTGTATTCGATCAACAAA
27701637 GCCATTGCAA
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 22 1.00
ACGTcount: A:0.36, C:0.18, G:0.09, T:0.36
Consensus pattern (22 bp):
ACTTTTGTATTCGATCAACAAA
Found at i:27705572 original size:2 final size:2
Alignment explanation
Indices: 27705559--27705599 Score: 73
Period size: 2 Copynumber: 20.5 Consensus size: 2
27705549 TTTATGGGCT
*
27705559 TC TC TC TT TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC T
1 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC T
27705600 TTTCAACTAA
Statistics
Matches: 37, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
2 37 1.00
ACGTcount: A:0.00, C:0.46, G:0.00, T:0.54
Consensus pattern (2 bp):
TC
Found at i:27706250 original size:352 final size:352
Alignment explanation
Indices: 27705606--27706312 Score: 1378
Period size: 352 Copynumber: 2.0 Consensus size: 352
27705596 CTCTTTTCAA
27705606 CTAAAATATCTTCTCTCTTAAATTTCATGTCTTGCGTATTTTAGGTTATTACCGTCAATGTTTGG
1 CTAAAATATCTTCTCTCTTAAATTTCATGTCTTGCGTATTTTAGGTTATTACCGTCAATGTTTGG
* *
27705671 ATATATGATGTCTAAATATACACTGTTAAAGAGGTCCCAATTGGACGGTCCATTGGCATCTCAAT
66 ATATATGATGTCTAAATATACACTGTTAAAAAGGTCCCAATTCGACGGTCCATTGGCATCTCAAT
*
27705736 CAATAGTAAAAAGAGGTAAATCAAAACATGATGTTTTCCGAGTAGAAGCAATGGCTCTATTAACT
131 CAATAGTAAAAAGAGGTAAATCAAAACATGATGTTTTCCGAGTAAAAGCAATGGCTCTATTAACT
27705801 AGAGTAGTTCATGATGTACTAATAGCAAAAAAGATGGAATAGAGGAAAACTTGTCTTCATGTAAC
196 AGAGTAGTTCATGATGTACTAATAGCAAAAAAGATGGAATAGAGGAAAACTTGTCTTCATGTAAC
27705866 TATATTATTGACCTCATCCTCCTCATTTCCCTATTATTAAATACATGCATGTTTATAGATATCAA
261 TATATTATTGACCTCATCCTCCTCATTTCCCTATTATTAAATACATGCATGTTTATAGATATCAA
*
27705931 TTTTTATTCCAAACCTGAATAGGGCTT
326 TTTTTATTCCAAACCTGAACAGGGCTT
27705958 CTAAAATATCTTCTCTCTTAAATTTCATGTCTTGCGTATTTTAGGTTATTACCGTCAATGTTTGG
1 CTAAAATATCTTCTCTCTTAAATTTCATGTCTTGCGTATTTTAGGTTATTACCGTCAATGTTTGG
27706023 ATATATGATGTCTAAATATACACTGTTAAAAAGGTCCCAATTCGACGGTCCATTGGCATCTCAAT
66 ATATATGATGTCTAAATATACACTGTTAAAAAGGTCCCAATTCGACGGTCCATTGGCATCTCAAT
27706088 CAATAGTAAAAAGAGGTAAATCAAAACATGATGTTTTCCGAGTAAAAGCAATGGCTCTATTAACT
131 CAATAGTAAAAAGAGGTAAATCAAAACATGATGTTTTCCGAGTAAAAGCAATGGCTCTATTAACT
27706153 AGAGTAGTTCATGATGTACTAATAGCAAAAAAGATGGAATAGAGGAAAACTTGTCTTCATGTAAC
196 AGAGTAGTTCATGATGTACTAATAGCAAAAAAGATGGAATAGAGGAAAACTTGTCTTCATGTAAC
27706218 TATATTATTGACCTCATCCTCCTCATTTCCCTATTATTAAATACATGCATGTTTATAGATATCAA
261 TATATTATTGACCTCATCCTCCTCATTTCCCTATTATTAAATACATGCATGTTTATAGATATCAA
27706283 TTTTTATTCCAAACCTGAACAGGGCTT
326 TTTTTATTCCAAACCTGAACAGGGCTT
27706310 CTA
1 CTA
27706313 TACAAAATTG
Statistics
Matches: 351, Mismatches: 4, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
352 351 1.00
ACGTcount: A:0.34, C:0.17, G:0.15, T:0.35
Consensus pattern (352 bp):
CTAAAATATCTTCTCTCTTAAATTTCATGTCTTGCGTATTTTAGGTTATTACCGTCAATGTTTGG
ATATATGATGTCTAAATATACACTGTTAAAAAGGTCCCAATTCGACGGTCCATTGGCATCTCAAT
CAATAGTAAAAAGAGGTAAATCAAAACATGATGTTTTCCGAGTAAAAGCAATGGCTCTATTAACT
AGAGTAGTTCATGATGTACTAATAGCAAAAAAGATGGAATAGAGGAAAACTTGTCTTCATGTAAC
TATATTATTGACCTCATCCTCCTCATTTCCCTATTATTAAATACATGCATGTTTATAGATATCAA
TTTTTATTCCAAACCTGAACAGGGCTT
Found at i:27710143 original size:23 final size:23
Alignment explanation
Indices: 27710114--27710169 Score: 71
Period size: 23 Copynumber: 2.4 Consensus size: 23
27710104 AAATAGAAGA
27710114 TATTATTT-TGTTTTA-TTTAGTTT
1 TATTATTTAT-TTTTATTTTA-TTT
27710137 TATTATTTATTTTTATTTTATTT
1 TATTATTTATTTTTATTTTATTT
27710160 TATTAATTTA
1 TATT-ATTTA
27710170 CGATTAGGTT
Statistics
Matches: 30, Mismatches: 0, Indels: 5
0.86 0.00 0.14
Matches are distributed among these distances:
23 20 0.67
24 10 0.33
ACGTcount: A:0.23, C:0.00, G:0.04, T:0.73
Consensus pattern (23 bp):
TATTATTTATTTTTATTTTATTT
Found at i:27717259 original size:13 final size:13
Alignment explanation
Indices: 27717241--27717280 Score: 53
Period size: 13 Copynumber: 2.9 Consensus size: 13
27717231 GACTCAAAGG
27717241 AAAAAAAAGAAAA
1 AAAAAAAAGAAAA
27717254 AAAAAAGAGAGAAAA
1 AAAAAA-A-AGAAAA
*
27717269 AGAAAAAAGAAA
1 AAAAAAAAGAAA
27717281 TTAAACCCCC
Statistics
Matches: 24, Mismatches: 1, Indels: 4
0.83 0.03 0.14
Matches are distributed among these distances:
13 11 0.46
14 2 0.08
15 11 0.46
ACGTcount: A:0.85, C:0.00, G:0.15, T:0.00
Consensus pattern (13 bp):
AAAAAAAAGAAAA
Found at i:27717751 original size:19 final size:20
Alignment explanation
Indices: 27717719--27717756 Score: 69
Period size: 19 Copynumber: 1.9 Consensus size: 20
27717709 CAACCTAGTC
27717719 GTCGTCGACCACTGCCGTAT
1 GTCGTCGACCACTGCCGTAT
27717739 GTCGTCG-CCACTGCCGTA
1 GTCGTCGACCACTGCCGTA
27717757 CGCCATCGTC
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
19 11 0.61
20 7 0.39
ACGTcount: A:0.13, C:0.37, G:0.26, T:0.24
Consensus pattern (20 bp):
GTCGTCGACCACTGCCGTAT
Found at i:27726483 original size:29 final size:29
Alignment explanation
Indices: 27726441--27726509 Score: 120
Period size: 29 Copynumber: 2.4 Consensus size: 29
27726431 TATGTATACC
*
27726441 ATGTGAAAAGGGATAGCTTCGGCTATCGA
1 ATGTGAAAAGGGATAGCTTCGGCTATCAA
*
27726470 ATGTGAAAAGGGATAGCTTTGGCTATCAA
1 ATGTGAAAAGGGATAGCTTCGGCTATCAA
27726499 ATGTGAAAAGG
1 ATGTGAAAAGG
27726510 TTAGGTATAC
Statistics
Matches: 38, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
29 38 1.00
ACGTcount: A:0.35, C:0.10, G:0.30, T:0.25
Consensus pattern (29 bp):
ATGTGAAAAGGGATAGCTTCGGCTATCAA
Found at i:27726539 original size:33 final size:33
Alignment explanation
Indices: 27726502--27726664 Score: 175
Period size: 33 Copynumber: 5.0 Consensus size: 33
27726492 CTATCAAATG
** *
27726502 TGAAAAGGTTAGGTATACTTTGTTTATACCACA
1 TGAAAAGGAAAGGTATACTTTGTGTATACCACA
** * * * *
27726535 TGAAAAGGTTATGTACACTTTGTGTGTA-CACT
1 TGAAAAGGAAAGGTATACTTTGTGTATACCACA
* * * *
27726567 TGAAAAGGAAATGTATACTTTATGTATGCCATA
1 TGAAAAGGAAAGGTATACTTTGTGTATACCACA
*
27726600 TGAAAAGGAAAGGTATACTTTGTGTATACCATA
1 TGAAAAGGAAAGGTATACTTTGTGTATACCACA
* *
27726633 CGAAAAGGAAAGGTATACTTTGTGTGTACCAC
1 TGAAAAGGAAAGGTATACTTTGTGTATACCAC
27726665 TCAGAAAGAA
Statistics
Matches: 110, Mismatches: 19, Indels: 2
0.84 0.15 0.02
Matches are distributed among these distances:
32 25 0.23
33 85 0.77
ACGTcount: A:0.35, C:0.12, G:0.21, T:0.33
Consensus pattern (33 bp):
TGAAAAGGAAAGGTATACTTTGTGTATACCACA
Found at i:27726583 original size:65 final size:66
Alignment explanation
Indices: 27726503--27726664 Score: 175
Period size: 65 Copynumber: 2.5 Consensus size: 66
27726493 TATCAAATGT
** * ** * *
27726503 GAAAAGGTTAGGTATACTTTGTTTATACCACATGAAAAGGTTATGTACACTTTGTGTGTA-CACT
1 GAAAAGGAAAGGTATACTTTGTGTATACCACATGAAAAGGAAAGGTACACTTTGTGTATACCA-T
*
27726567 -T
65 AC
* * * * *
27726568 GAAAAGGAAATGTATACTTTATGTATGCCATATGAAAAGGAAAGGTATACTTTGTGTATACCATA
1 GAAAAGGAAAGGTATACTTTGTGTATACCACATGAAAAGGAAAGGTACACTTTGTGTATACCATA
27726633 C
66 C
*
27726634 GAAAAGGAAAGGTATACTTTGTGTGTACCAC
1 GAAAAGGAAAGGTATACTTTGTGTATACCAC
27726665 TCAGAAAGAA
Statistics
Matches: 77, Mismatches: 18, Indels: 3
0.79 0.18 0.03
Matches are distributed among these distances:
65 49 0.64
66 28 0.36
ACGTcount: A:0.35, C:0.12, G:0.21, T:0.32
Consensus pattern (66 bp):
GAAAAGGAAAGGTATACTTTGTGTATACCACATGAAAAGGAAAGGTACACTTTGTGTATACCATA
C
Found at i:27736679 original size:61 final size:61
Alignment explanation
Indices: 27736578--27736705 Score: 168
Period size: 61 Copynumber: 2.1 Consensus size: 61
27736568 TGAGAAATCG
* * * * * *
27736578 ACACGGCCTGGACTTCTTTACACGGGTAGAACACATGCCCGTGTAGT-TTTAGCAGACTCTA
1 ACACGGCCTGGACTTCCTTACACAGGTAGAACACACGCCCGTGT-CTATTCAACAGACTCTA
* *
27736639 ACACGGCCTGGACTTCCTTACATAGGTAGACCACACGCCCGTGTCTATTCAACAGACTCTA
1 ACACGGCCTGGACTTCCTTACACAGGTAGAACACACGCCCGTGTCTATTCAACAGACTCTA
27736700 ACACGG
1 ACACGG
27736706 TTCGAAGCAC
Statistics
Matches: 58, Mismatches: 8, Indels: 2
0.85 0.12 0.03
Matches are distributed among these distances:
60 1 0.02
61 57 0.98
ACGTcount: A:0.26, C:0.30, G:0.21, T:0.23
Consensus pattern (61 bp):
ACACGGCCTGGACTTCCTTACACAGGTAGAACACACGCCCGTGTCTATTCAACAGACTCTA
Done.