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 132 of 427
Found at i:35472157 original size:14 final size:14
Alignment explanation
Indices: 35472140--35472181 Score: 57
Period size: 14 Copynumber: 3.0 Consensus size: 14
35472130 TTTTATAATA
35472140 TTTCATGTATATAT
1 TTTCATGTATATAT
*
35472154 TTTCATGCATATAT
1 TTTCATGTATATAT
* *
35472168 TTTCTTTTATATAT
1 TTTCATGTATATAT
35472182 CGTGTACATA
Statistics
Matches: 24, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
14 24 1.00
ACGTcount: A:0.26, C:0.10, G:0.05, T:0.60
Consensus pattern (14 bp):
TTTCATGTATATAT
Found at i:35484730 original size:54 final size:54
Alignment explanation
Indices: 35484648--35484815 Score: 309
Period size: 54 Copynumber: 3.1 Consensus size: 54
35484638 TTTTTATTTC
*
35484648 TCAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCATTTTAATTTCTGTTTT
1 TCAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTTTTAATTTCTGTTTT
*
35484702 TCAAAAGTCAACTCATATTGCGAGAGGTGAGTTGAGCCTTTTAATTTCTGTTTT
1 TCAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTTTTAATTTCTGTTTT
*
35484756 TCAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCCTTTAATTTCTGTTTT
1 TCAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTTTTAATTTCTGTTTT
35484810 TCAAAA
1 TCAAAA
35484816 TCTACCTTTC
Statistics
Matches: 110, Mismatches: 4, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
54 110 1.00
ACGTcount: A:0.29, C:0.15, G:0.18, T:0.38
Consensus pattern (54 bp):
TCAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTTTTAATTTCTGTTTT
Found at i:35486066 original size:14 final size:14
Alignment explanation
Indices: 35486043--35486073 Score: 53
Period size: 14 Copynumber: 2.2 Consensus size: 14
35486033 TTAAGGTGAA
*
35486043 TTTTCTATTTTTAT
1 TTTTCAATTTTTAT
35486057 TTTTCAATTTTTAT
1 TTTTCAATTTTTAT
35486071 TTT
1 TTT
35486074 CGAATCTATT
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
14 16 1.00
ACGTcount: A:0.16, C:0.06, G:0.00, T:0.77
Consensus pattern (14 bp):
TTTTCAATTTTTAT
Found at i:35486769 original size:3 final size:3
Alignment explanation
Indices: 35486752--35486823 Score: 128
Period size: 3 Copynumber: 24.3 Consensus size: 3
35486742 AATACTCTTG
*
35486752 TTA TTG TTA -TA 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
35486799 TTA TTA TTA TTA TTA TTA TTA TTA T
1 TTA TTA TTA TTA TTA TTA TTA TTA T
35486824 GCATTAGTTT
Statistics
Matches: 66, Mismatches: 2, Indels: 2
0.94 0.03 0.03
Matches are distributed among these distances:
2 2 0.03
3 64 0.97
ACGTcount: A:0.32, C:0.00, G:0.01, T:0.67
Consensus pattern (3 bp):
TTA
Found at i:35487159 original size:25 final size:25
Alignment explanation
Indices: 35487129--35487188 Score: 68
Period size: 25 Copynumber: 2.4 Consensus size: 25
35487119 ATATTTTACA
35487129 TATATATTATCATGTATATACTTTTT
1 TATATATTATCATGTATATA-TTTTT
* * *
35487155 T-TATATCATTATTTATATATTTTT
1 TATATATTATCATGTATATATTTTT
*
35487179 TATACATTAT
1 TATATATTAT
35487189 TTCGTGAATA
Statistics
Matches: 28, Mismatches: 5, Indels: 3
0.78 0.14 0.08
Matches are distributed among these distances:
24 6 0.21
25 21 0.75
26 1 0.04
ACGTcount: A:0.32, C:0.07, G:0.02, T:0.60
Consensus pattern (25 bp):
TATATATTATCATGTATATATTTTT
Found at i:35487171 original size:12 final size:12
Alignment explanation
Indices: 35487154--35487190 Score: 51
Period size: 11 Copynumber: 3.2 Consensus size: 12
35487144 ATATACTTTT
35487154 TTTATATCATTA
1 TTTATATCATTA
*
35487166 TTTATAT-ATTT
1 TTTATATCATTA
35487177 TTTATA-CATTA
1 TTTATATCATTA
35487188 TTT
1 TTT
35487191 CGTGAATATA
Statistics
Matches: 22, Mismatches: 2, Indels: 3
0.81 0.07 0.11
Matches are distributed among these distances:
11 15 0.68
12 7 0.32
ACGTcount: A:0.30, C:0.05, G:0.00, T:0.65
Consensus pattern (12 bp):
TTTATATCATTA
Found at i:35487250 original size:14 final size:14
Alignment explanation
Indices: 35487233--35487274 Score: 57
Period size: 14 Copynumber: 3.0 Consensus size: 14
35487223 TTTTATAATA
35487233 TTTCATGTATATAT
1 TTTCATGTATATAT
*
35487247 TTTCATGCATATAT
1 TTTCATGTATATAT
* *
35487261 TTTCTTTTATATAT
1 TTTCATGTATATAT
35487275 CGTGTACATA
Statistics
Matches: 24, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
14 24 1.00
ACGTcount: A:0.26, C:0.10, G:0.05, T:0.60
Consensus pattern (14 bp):
TTTCATGTATATAT
Found at i:35492006 original size:32 final size:34
Alignment explanation
Indices: 35491970--35492034 Score: 80
Period size: 34 Copynumber: 2.0 Consensus size: 34
35491960 TAACAGTGGT
*
35491970 ACTGGACCAGAG-CCCTT-TTCAGATTACAATAA
1 ACTGGACCAGAGCCCCTTATTCAGATAACAATAA
* **
35492002 ACTGGGCCTTAGCCCCTTATTCAGATAACAATA
1 ACTGGACCAGAGCCCCTTATTCAGATAACAATA
35492035 TGGCCCATAG
Statistics
Matches: 27, Mismatches: 4, Indels: 2
0.82 0.12 0.06
Matches are distributed among these distances:
32 9 0.33
33 5 0.19
34 13 0.48
ACGTcount: A:0.32, C:0.26, G:0.15, T:0.26
Consensus pattern (34 bp):
ACTGGACCAGAGCCCCTTATTCAGATAACAATAA
Found at i:35492191 original size:64 final size:64
Alignment explanation
Indices: 35491981--35492191 Score: 142
Period size: 64 Copynumber: 3.2 Consensus size: 64
35491971 CTGGACCAGA
* *
35491981 GCCCTTTTCAGATTACAATAAACTGGGCCTTAGCCCCTTATTCAGATAACAATATGGCCCATAG
1 GCCCATTTCAGATTACAATAAACTGGGCCTTAGCCCCTTATTCAGATAACAGTATGGCCCATAG
* * * *** * ** *
35492045 GCCCATTTCAAAATAC-ATGCAACATCAGTAAACATATGCAAGCCC--ATTTGGGTAACAGTGGT
1 GCCCATTTCAGATTACAAT--AA-A-CTG-GGCCTTA-GC---CCCTTATTCAGATAACA---GT
* *
35492107 ACTGGGCCAGA-
54 A-TGGCCCATAG
*
35492118 GCCCTTTTCAGATTACAATAAACTGGGCCTTAGCCCCTTATTCAGATAACAGTATGGCCCATAG
1 GCCCATTTCAGATTACAATAAACTGGGCCTTAGCCCCTTATTCAGATAACAGTATGGCCCATAG
35492182 GCCCATTTCA
1 GCCCATTTCA
35492192 AAATACATGC
Statistics
Matches: 102, Mismatches: 28, Indels: 34
0.62 0.17 0.21
Matches are distributed among these distances:
63 9 0.09
64 25 0.25
65 5 0.05
66 1 0.01
67 11 0.11
68 5 0.05
69 5 0.05
70 11 0.11
71 1 0.01
72 5 0.05
73 15 0.15
74 9 0.09
ACGTcount: A:0.30, C:0.26, G:0.18, T:0.26
Consensus pattern (64 bp):
GCCCATTTCAGATTACAATAAACTGGGCCTTAGCCCCTTATTCAGATAACAGTATGGCCCATAG
Found at i:35492193 original size:137 final size:137
Alignment explanation
Indices: 35491947--35492233 Score: 538
Period size: 137 Copynumber: 2.1 Consensus size: 137
35491937 TATTGGGCCT
**
35491947 AAGCCCATTCAGGTAACAGTGGTACTGGACCAGAGCCCTTTTCAGATTACAATAAACTGGGCCTT
1 AAGCCCATTTGGGTAACAGTGGTACTGGACCAGAGCCCTTTTCAGATTACAATAAACTGGGCCTT
35492012 AGCCCCTTATTCAGATAACAATATGGCCCATAGGCCCATTTCAAAATACATGCAACATCAGTAAA
66 AGCCCCTTATTCAGATAACAATATGGCCCATAGGCCCATTTCAAAATACATGCAACATCAGTAAA
35492077 CATATGC
131 CATATGC
*
35492084 AAGCCCATTTGGGTAACAGTGGTACTGGGCCAGAGCCCTTTTCAGATTACAATAAACTGGGCCTT
1 AAGCCCATTTGGGTAACAGTGGTACTGGACCAGAGCCCTTTTCAGATTACAATAAACTGGGCCTT
*
35492149 AGCCCCTTATTCAGATAACAGTATGGCCCATAGGCCCATTTCAAAATACATGCAACATCAGTAAA
66 AGCCCCTTATTCAGATAACAATATGGCCCATAGGCCCATTTCAAAATACATGCAACATCAGTAAA
35492214 CATATGC
131 CATATGC
35492221 AAGCCCATTTGGG
1 AAGCCCATTTGGG
35492234 GAGACTACTC
Statistics
Matches: 146, Mismatches: 4, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
137 146 1.00
ACGTcount: A:0.32, C:0.25, G:0.18, T:0.24
Consensus pattern (137 bp):
AAGCCCATTTGGGTAACAGTGGTACTGGACCAGAGCCCTTTTCAGATTACAATAAACTGGGCCTT
AGCCCCTTATTCAGATAACAATATGGCCCATAGGCCCATTTCAAAATACATGCAACATCAGTAAA
CATATGC
Found at i:35494053 original size:26 final size:26
Alignment explanation
Indices: 35494017--35494100 Score: 150
Period size: 26 Copynumber: 3.2 Consensus size: 26
35494007 CATGAAATTC
35494017 TTATCATGAAACATTTACCTAACCCA
1 TTATCATGAAACATTTACCTAACCCA
35494043 TTATCATGAAACATTTACCTAACCCA
1 TTATCATGAAACATTTACCTAACCCA
* *
35494069 TTATCATGGAACATTTACCTAACCTA
1 TTATCATGAAACATTTACCTAACCCA
35494095 TTATCA
1 TTATCA
35494101 ATTTGTATCA
Statistics
Matches: 56, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
26 56 1.00
ACGTcount: A:0.37, C:0.25, G:0.05, T:0.33
Consensus pattern (26 bp):
TTATCATGAAACATTTACCTAACCCA
Found at i:35497967 original size:20 final size:20
Alignment explanation
Indices: 35497942--35497984 Score: 77
Period size: 20 Copynumber: 2.1 Consensus size: 20
35497932 TAATTACTTG
*
35497942 TAAAAATATCATGGAATTGA
1 TAAAAATAGCATGGAATTGA
35497962 TAAAAATAGCATGGAATTGA
1 TAAAAATAGCATGGAATTGA
35497982 TAA
1 TAA
35497985 TGCTTATAAA
Statistics
Matches: 22, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
20 22 1.00
ACGTcount: A:0.51, C:0.05, G:0.16, T:0.28
Consensus pattern (20 bp):
TAAAAATAGCATGGAATTGA
Found at i:35503331 original size:27 final size:26
Alignment explanation
Indices: 35503294--35503360 Score: 82
Period size: 26 Copynumber: 2.5 Consensus size: 26
35503284 AAGACCTCGT
*
35503294 TTTGTAAAATTA-CCAAAGTACCCCCAG
1 TTTGTAAAATTATCCAAA-TA-CCCAAG
* *
35503321 TTTGTAAAATTATCGAAATACTCAAG
1 TTTGTAAAATTATCCAAATACCCAAG
35503347 TTTGTAAAATTATC
1 TTTGTAAAATTATC
35503361 GGATTTCCCT
Statistics
Matches: 36, Mismatches: 3, Indels: 3
0.86 0.07 0.07
Matches are distributed among these distances:
26 18 0.50
27 14 0.39
28 4 0.11
ACGTcount: A:0.39, C:0.16, G:0.10, T:0.34
Consensus pattern (26 bp):
TTTGTAAAATTATCCAAATACCCAAG
Found at i:35503401 original size:27 final size:27
Alignment explanation
Indices: 35503349--35503410 Score: 72
Period size: 27 Copynumber: 2.3 Consensus size: 27
35503339 TACTCAAGTT
* * *
35503349 TGTAAAATTATCGGATTTCCCTTGTAG
1 TGTAAAATTACCGAATATCCCTTGTAG
35503376 TGTAAAATTACCGAAATATCCC-TGTAG
1 TGTAAAATTACCG-AATATCCCTTGTAG
*
35503403 GGTAAAAT
1 TGTAAAAT
35503411 GACTGTTTTG
Statistics
Matches: 30, Mismatches: 4, Indels: 2
0.83 0.11 0.06
Matches are distributed among these distances:
27 24 0.80
28 6 0.20
ACGTcount: A:0.34, C:0.15, G:0.18, T:0.34
Consensus pattern (27 bp):
TGTAAAATTACCGAATATCCCTTGTAG
Found at i:35503593 original size:26 final size:27
Alignment explanation
Indices: 35503530--35503595 Score: 98
Period size: 27 Copynumber: 2.5 Consensus size: 27
35503520 AAGACCCTAT
* **
35503530 TTTGTAAAATTACCAAAATACCCCTGA
1 TTTGTAAAATTATCAAAATACCCAAGA
35503557 TTTGTAAAATTATCAAAATACCCAAG-
1 TTTGTAAAATTATCAAAATACCCAAGA
35503583 TTTGTAAAATTAT
1 TTTGTAAAATTAT
35503596 TGGATTACCC
Statistics
Matches: 36, Mismatches: 3, Indels: 1
0.90 0.08 0.03
Matches are distributed among these distances:
26 13 0.36
27 23 0.64
ACGTcount: A:0.42, C:0.15, G:0.08, T:0.35
Consensus pattern (27 bp):
TTTGTAAAATTATCAAAATACCCAAGA
Found at i:35503631 original size:27 final size:26
Alignment explanation
Indices: 35503532--35503646 Score: 72
Period size: 27 Copynumber: 4.3 Consensus size: 26
35503522 GACCCTATTT
*
35503532 TGTAAAATTACCAAAATACCCC-TGATT
1 TGTAAAATTACCAAAATACCCCGT-A-G
* * *
35503559 TGTAAAATTATCAAAATACCCAAGT-T
1 TGTAAAATTACCAAAATACCC-CGTAG
**** *
35503585 TGTAAAATTATTGGATTACCCTCGTAG
1 TGTAAAATTACCAAAATACCC-CGTAG
*
35503612 TGTAAAATTACCGAAATACCCCTGTAG
1 TGTAAAATTACCAAAATACCCC-GTAG
*
35503639 GGTAAAAT
1 TGTAAAAT
35503647 GACTGTTTTA
Statistics
Matches: 70, Mismatches: 14, Indels: 8
0.76 0.15 0.09
Matches are distributed among these distances:
26 21 0.30
27 48 0.69
29 1 0.01
ACGTcount: A:0.39, C:0.17, G:0.13, T:0.30
Consensus pattern (26 bp):
TGTAAAATTACCAAAATACCCCGTAG
Found at i:35503691 original size:236 final size:240
Alignment explanation
Indices: 35503278--35503750 Score: 733
Period size: 236 Copynumber: 2.0 Consensus size: 240
35503268 CTTCTGTCGA
* * * *
35503278 GTCGTTAAGACCTCGTTTTGTAAAATTACCAAAGTACCCCCAGTTTGTAAAATTATCGAAATACT
1 GTCGTTAAGACCTCATTTTGTAAAATTACCAAAATACCCCCAGTTTGTAAAATTATCAAAATACC
* * *
35503343 CAAGTTTGTAAAATTATCGGATTTCCCTTGTAGTGTAAAATTACCGAAATATCCCTGTAGGGTAA
66 CAAGTTTGTAAAATTATCGGATTACCCTCGTAGTGTAAAATTACCGAAATACCCCTGTAGGGTAA
*
35503408 AATGACTGTTTTGCCTTGTAGGTAAATGACTGACTTGGAC-T-A-TGA-ATTTGACTGTGATTGT
131 AATGACTGTTTTACCTTGTAGGTAAATGACTGACTTGGACATAATTGACATTTGACTGTGATTGT
* *
35503469 ACGACTGTGATTTAACTGCTTGACGGTGGTTGTACGATCTGTTGG
196 ACGACTATGATTTAACTGCTTGACAGTGGTTGTACGATCTGTTGG
*
35503514 GTCGTTAAGACC-CTATTTTGTAAAATTACCAAAATA-CCCCTGATTTGTAAAATTATCAAAATA
1 GTCGTTAAGACCTC-ATTTTGTAAAATTACCAAAATACCCCCAG-TTTGTAAAATTATCAAAATA
*
35503577 CCCAAGTTTGTAAAATTATTGGATTACCCTCGTAGTGTAAAATTACCGAAATACCCCTGTAGGGT
64 CCCAAGTTTGTAAAATTATCGGATTACCCTCGTAGTGTAAAATTACCGAAATACCCCTGTAGGGT
35503642 AAAATGACTGTTTTACCTTGTAGGTAAATGACTGACTTGGACTATGAATTTGACTGATTTGACTG
129 AAAATGACTGTTTTACCTTGTAGGTAAATGACTGACTTGGAC-AT-AA-TTGAC--ATTTGACTG
35503707 TGATTGTACGACTATGATTTAACTGCTTGACAGTGGTTGTACGA
189 TGATTGTACGACTATGATTTAACTGCTTGACAGTGGTTGTACGA
35503751 CTGATATGCT
Statistics
Matches: 214, Mismatches: 12, Indels: 13
0.90 0.05 0.05
Matches are distributed among these distances:
235 6 0.03
236 152 0.71
238 1 0.00
240 1 0.00
242 3 0.01
245 51 0.24
ACGTcount: A:0.30, C:0.16, G:0.20, T:0.35
Consensus pattern (240 bp):
GTCGTTAAGACCTCATTTTGTAAAATTACCAAAATACCCCCAGTTTGTAAAATTATCAAAATACC
CAAGTTTGTAAAATTATCGGATTACCCTCGTAGTGTAAAATTACCGAAATACCCCTGTAGGGTAA
AATGACTGTTTTACCTTGTAGGTAAATGACTGACTTGGACATAATTGACATTTGACTGTGATTGT
ACGACTATGATTTAACTGCTTGACAGTGGTTGTACGATCTGTTGG
Found at i:35503747 original size:33 final size:35
Alignment explanation
Indices: 35503681--35503752 Score: 94
Period size: 33 Copynumber: 2.1 Consensus size: 35
35503671 GACTGACTTG
* * *
35503681 GACTATGAATTTGACTGATTTGACTGTGATTGTAC
1 GACTATGAATTTAACTGACTTGACAGTGATTGTAC
*
35503716 GACTATG-ATTTAACTG-CTTGACAGTGGTTGTAC
1 GACTATGAATTTAACTGACTTGACAGTGATTGTAC
35503749 GACT
1 GACT
35503753 GATATGCTTT
Statistics
Matches: 33, Mismatches: 4, Indels: 2
0.85 0.10 0.05
Matches are distributed among these distances:
33 18 0.55
34 8 0.24
35 7 0.21
ACGTcount: A:0.25, C:0.14, G:0.24, T:0.38
Consensus pattern (35 bp):
GACTATGAATTTAACTGACTTGACAGTGATTGTAC
Found at i:35504242 original size:3 final size:3
Alignment explanation
Indices: 35504234--35504283 Score: 100
Period size: 3 Copynumber: 16.7 Consensus size: 3
35504224 ATCTTAGATT
35504234 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
35504282 TT
1 TT
35504284 TGATTTAAAA
Statistics
Matches: 47, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 47 1.00
ACGTcount: A:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (3 bp):
TTA
Found at i:35505778 original size:29 final size:27
Alignment explanation
Indices: 35505702--35505782 Score: 92
Period size: 27 Copynumber: 2.9 Consensus size: 27
35505692 AATGCCTTAT
* * *
35505702 TGGTGTCTTAGGGAGGATATACTATAC
1 TGGTGTGTTATGGAGGATATATTATAC
*
35505729 TGGTGTGTT-TGGGAGGCTATATTATAC
1 TGGTGTGTTAT-GGAGGATATATTATAC
35505756 TGGTGTGTTATGGAGGATTTATATTAT
1 TGGTGTGTTATGGAGGA--TATATTAT
35505783 TCCGGGTGTG
Statistics
Matches: 45, Mismatches: 5, Indels: 6
0.80 0.09 0.11
Matches are distributed among these distances:
27 36 0.80
28 1 0.02
29 8 0.18
ACGTcount: A:0.22, C:0.06, G:0.31, T:0.41
Consensus pattern (27 bp):
TGGTGTGTTATGGAGGATATATTATAC
Found at i:35512876 original size:13 final size:14
Alignment explanation
Indices: 35512847--35512879 Score: 50
Period size: 13 Copynumber: 2.4 Consensus size: 14
35512837 TATGATTAGT
35512847 GTTAATTAGACTTA
1 GTTAATTAGACTTA
*
35512861 GTTAATTA-AGTTA
1 GTTAATTAGACTTA
35512874 GTTAAT
1 GTTAAT
35512880 ATTAATTATA
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
13 10 0.56
14 8 0.44
ACGTcount: A:0.36, C:0.03, G:0.15, T:0.45
Consensus pattern (14 bp):
GTTAATTAGACTTA
Found at i:35513190 original size:46 final size:46
Alignment explanation
Indices: 35513097--35513198 Score: 134
Period size: 46 Copynumber: 2.2 Consensus size: 46
35513087 TTGATTTTCA
* * *
35513097 TAACATATGATTCAATACTAAAATTATTCCAAACTAATATGGTAAG
1 TAACATATGACTCAATACTAAAATCATTCCAAACTAATATGATAAG
* * *
35513143 TAATATATGACTCAATACTAAAATCATTCCCAACTAGTAT-ATCAAG
1 TAACATATGACTCAATACTAAAATCATTCCAAACTAATATGAT-AAG
35513189 TAACATATGA
1 TAACATATGA
35513199 TAAAAAATGT
Statistics
Matches: 48, Mismatches: 7, Indels: 2
0.84 0.12 0.04
Matches are distributed among these distances:
45 1 0.02
46 47 0.98
ACGTcount: A:0.45, C:0.16, G:0.08, T:0.31
Consensus pattern (46 bp):
TAACATATGACTCAATACTAAAATCATTCCAAACTAATATGATAAG
Found at i:35519058 original size:6 final size:6
Alignment explanation
Indices: 35519047--35519071 Score: 50
Period size: 6 Copynumber: 4.2 Consensus size: 6
35519037 AGCAAGAGAG
35519047 AAAGAA AAAGAA AAAGAA AAAGAA A
1 AAAGAA AAAGAA AAAGAA AAAGAA A
35519072 GAGAGAGAAC
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 19 1.00
ACGTcount: A:0.84, C:0.00, G:0.16, T:0.00
Consensus pattern (6 bp):
AAAGAA
Found at i:35522687 original size:2 final size:2
Alignment explanation
Indices: 35522682--35522707 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
35522672 ATAAAAAGTA
35522682 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
35522708 TTAAATGAGT
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:35524353 original size:12 final size:12
Alignment explanation
Indices: 35524338--35524372 Score: 52
Period size: 12 Copynumber: 2.9 Consensus size: 12
35524328 AACCTAACCC
35524338 AAAAAAAAAACA
1 AAAAAAAAAACA
*
35524350 AAAAAAAAAAGA
1 AAAAAAAAAACA
*
35524362 AAAAGAAAAAC
1 AAAAAAAAAAC
35524373 TTACCCCAAA
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
12 20 1.00
ACGTcount: A:0.89, C:0.06, G:0.06, T:0.00
Consensus pattern (12 bp):
AAAAAAAAAACA
Found at i:35524386 original size:16 final size:16
Alignment explanation
Indices: 35524367--35524403 Score: 56
Period size: 16 Copynumber: 2.3 Consensus size: 16
35524357 AAAGAAAAAG
*
35524367 AAAAACTTACCCCAAA
1 AAAAACTAACCCCAAA
*
35524383 AAAACCTAACCCCAAA
1 AAAAACTAACCCCAAA
35524399 AAAAA
1 AAAAA
35524404 AAAAGAAAAA
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
16 18 1.00
ACGTcount: A:0.62, C:0.30, G:0.00, T:0.08
Consensus pattern (16 bp):
AAAAACTAACCCCAAA
Found at i:35525233 original size:11 final size:11
Alignment explanation
Indices: 35525215--35525244 Score: 51
Period size: 11 Copynumber: 2.7 Consensus size: 11
35525205 GTGTATATTG
35525215 TATATATTATA
1 TATATATTATA
*
35525226 TTTATATTATA
1 TATATATTATA
35525237 TATATATT
1 TATATATT
35525245 CTTAATGTTA
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
11 17 1.00
ACGTcount: A:0.40, C:0.00, G:0.00, T:0.60
Consensus pattern (11 bp):
TATATATTATA
Found at i:35530839 original size:20 final size:20
Alignment explanation
Indices: 35530814--35530860 Score: 53
Period size: 20 Copynumber: 2.4 Consensus size: 20
35530804 TTAAATTAAA
* *
35530814 TATTAAGA-TAATAATTTTAG
1 TATTAAGATTAATAA-ATTAC
35530834 TATTAA-ATTAATAAATTAC
1 TATTAAGATTAATAAATTAC
35530853 TATTAAGA
1 TATTAAGA
35530861 AAAGTATTAA
Statistics
Matches: 23, Mismatches: 2, Indels: 4
0.79 0.07 0.14
Matches are distributed among these distances:
19 10 0.43
20 13 0.57
ACGTcount: A:0.49, C:0.02, G:0.06, T:0.43
Consensus pattern (20 bp):
TATTAAGATTAATAAATTAC
Found at i:35530979 original size:128 final size:128
Alignment explanation
Indices: 35530829--35531077 Score: 410
Period size: 128 Copynumber: 1.9 Consensus size: 128
35530819 AGATAATAAT
* *
35530829 TTTAGTATTAAATTAATAAATTACTATTAAGAAAAGTATTAAGTTAAATTTAATATTAAAATATT
1 TTTAATATTAAATTAATAAATTACTATTAAGAAAAGTATTAACTTAAATTTAATATTAAAATATT
*
35530894 AAAATATTATTTTTTTTG-GAATAATTAATCTGAAATCAAATTCTCGGGTAGAATCCAGTTCAC
66 AAAATATTATTATTTTTGAG-ATAATTAATCTGAAATCAAATTCTCGGGTAGAATCCAGTTCAC
* * * *
35530957 TTTAATATTAAATTAATGAATTACTATTAAGATAAGTATTAACTTTAATTTAATATTAAATTATT
1 TTTAATATTAAATTAATAAATTACTATTAAGAAAAGTATTAACTTAAATTTAATATTAAAATATT
*
35531022 AAAATATTATTATTTTTGAGATAATTAATCTGAAATCAAATTCTCTGGTAGAATCC
66 AAAATATTATTATTTTTGAGATAATTAATCTGAAATCAAATTCTCGGGTAGAATCC
35531078 CAATAAGAGT
Statistics
Matches: 112, Mismatches: 8, Indels: 2
0.92 0.07 0.02
Matches are distributed among these distances:
128 111 0.99
129 1 0.01
ACGTcount: A:0.43, C:0.07, G:0.08, T:0.42
Consensus pattern (128 bp):
TTTAATATTAAATTAATAAATTACTATTAAGAAAAGTATTAACTTAAATTTAATATTAAAATATT
AAAATATTATTATTTTTGAGATAATTAATCTGAAATCAAATTCTCGGGTAGAATCCAGTTCAC
Found at i:35537389 original size:34 final size:34
Alignment explanation
Indices: 35537351--35537415 Score: 112
Period size: 34 Copynumber: 1.9 Consensus size: 34
35537341 AACATCTCTC
*
35537351 TATAAACCCAGGAAAAAAACCCTTTTCCTCTCGT
1 TATAAACCCAGAAAAAAAACCCTTTTCCTCTCGT
*
35537385 TATAAACCCAGAAAAAAAACTCTTTTCCTCT
1 TATAAACCCAGAAAAAAAACCCTTTTCCTCT
35537416 TGTAATGTAT
Statistics
Matches: 29, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
34 29 1.00
ACGTcount: A:0.38, C:0.28, G:0.06, T:0.28
Consensus pattern (34 bp):
TATAAACCCAGAAAAAAAACCCTTTTCCTCTCGT
Found at i:35540762 original size:4 final size:4
Alignment explanation
Indices: 35540753--35540783 Score: 62
Period size: 4 Copynumber: 7.8 Consensus size: 4
35540743 GAGTATAGTT
35540753 TTTA TTTA TTTA TTTA TTTA TTTA TTTA TTT
1 TTTA TTTA TTTA TTTA TTTA TTTA TTTA TTT
35540784 TAATTATCAA
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 27 1.00
ACGTcount: A:0.23, C:0.00, G:0.00, T:0.77
Consensus pattern (4 bp):
TTTA
Found at i:35542118 original size:28 final size:28
Alignment explanation
Indices: 35542084--35542160 Score: 77
Period size: 28 Copynumber: 2.7 Consensus size: 28
35542074 GGTTTTTTAA
*
35542084 TTTATTTTATCTTTATATAAAATTAATT-
1 TTTATTTTATATTT-TATAAAATTAATTG
* * *
35542112 TTTATTTTTTATTTTTTAAAATTATTTG
1 TTTATTTTATATTTTATAAAATTAATTG
35542140 TTTATTTGGTATATTTT-TAAA
1 TTTATTT--TATATTTTATAAA
35542161 TTTTATATAT
Statistics
Matches: 41, Mismatches: 5, Indels: 5
0.80 0.10 0.10
Matches are distributed among these distances:
27 11 0.27
28 19 0.46
29 4 0.10
30 7 0.17
ACGTcount: A:0.30, C:0.01, G:0.04, T:0.65
Consensus pattern (28 bp):
TTTATTTTATATTTTATAAAATTAATTG
Found at i:35542135 original size:27 final size:29
Alignment explanation
Indices: 35542101--35542160 Score: 79
Period size: 27 Copynumber: 2.1 Consensus size: 29
35542091 TATCTTTATA
**
35542101 TAAAATTAATT-TTTATTTTTTAT-TTTT
1 TAAAATTAATTGTTTATTTGGTATATTTT
*
35542128 TAAAATTATTTGTTTATTTGGTATATTTT
1 TAAAATTAATTGTTTATTTGGTATATTTT
35542157 TAAA
1 TAAA
35542161 TTTTATATAT
Statistics
Matches: 28, Mismatches: 3, Indels: 2
0.85 0.09 0.06
Matches are distributed among these distances:
27 10 0.36
28 10 0.36
29 8 0.29
ACGTcount: A:0.32, C:0.00, G:0.05, T:0.63
Consensus pattern (29 bp):
TAAAATTAATTGTTTATTTGGTATATTTT
Found at i:35542249 original size:22 final size:23
Alignment explanation
Indices: 35542202--35542249 Score: 57
Period size: 21 Copynumber: 2.2 Consensus size: 23
35542192 TTTTTTTATT
* *
35542202 TTTA-TATATATTTTAAGATATA
1 TTTATTATATATTTTAAAAAATA
35542224 -TTATTATAT-TTTTAAAAAATA
1 TTTATTATATATTTTAAAAAATA
35542245 TTTAT
1 TTTAT
35542250 GTATTTATAT
Statistics
Matches: 22, Mismatches: 2, Indels: 4
0.79 0.07 0.14
Matches are distributed among these distances:
21 13 0.59
22 9 0.41
ACGTcount: A:0.42, C:0.00, G:0.02, T:0.56
Consensus pattern (23 bp):
TTTATTATATATTTTAAAAAATA
Found at i:35542644 original size:18 final size:20
Alignment explanation
Indices: 35542607--35542672 Score: 73
Period size: 19 Copynumber: 3.2 Consensus size: 20
35542597 TCTTTCAACA
*
35542607 AAAAATACAAAATAATTTTT
1 AAAAATTCAAAATAATTTTT
35542627 -AAAATTCAAAAT-ATTTTT
1 AAAAATTCAAAATAATTTTT
*
35542645 AAAAATTCTAAAATTTATCTTTT
1 AAAAATTC-AAAA-TAAT-TTTT
35542668 AAAAA
1 AAAAA
35542673 AAAATATAAA
Statistics
Matches: 40, Mismatches: 1, Indels: 7
0.83 0.02 0.15
Matches are distributed among these distances:
18 6 0.15
19 18 0.45
20 4 0.10
21 1 0.03
22 2 0.05
23 9 0.22
ACGTcount: A:0.55, C:0.06, G:0.00, T:0.39
Consensus pattern (20 bp):
AAAAATTCAAAATAATTTTT
Found at i:35543359 original size:2 final size:2
Alignment explanation
Indices: 35543352--35543376 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
35543342 AATTACATTA
35543352 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 A
35543377 ATCAATATTT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:35543959 original size:16 final size:15
Alignment explanation
Indices: 35543938--35543967 Score: 51
Period size: 15 Copynumber: 1.9 Consensus size: 15
35543928 AGAAAGGACA
35543938 AACAAAGAAAACAAAT
1 AACAAAG-AAACAAAT
35543954 AACAAAGAAACAAA
1 AACAAAGAAACAAA
35543968 AAATAGAAAT
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 7 0.50
16 7 0.50
ACGTcount: A:0.77, C:0.13, G:0.07, T:0.03
Consensus pattern (15 bp):
AACAAAGAAACAAAT
Found at i:35545163 original size:27 final size:26
Alignment explanation
Indices: 35545034--35545379 Score: 149
Period size: 26 Copynumber: 13.8 Consensus size: 26
35545024 TTAAACTATT
35545034 TTATTTATTTTAAA---TTTTATATA
1 TTATTTATTTTAAATTGTTTTATATA
** * * *
35545057 TTAAACTGTTTTAAATTTTTTTAGATA
1 TT-ATTTATTTTAAATTGTTTTATATA
* *
35545084 -TA-TTATTTTAAATTATTTCATATA
1 TTATTTATTTTAAATTGTTTTATATA
* * * * *
35545108 CTATATACTTTAAATTGCTTTATACA
1 TTATTTATTTTAAATTGTTTTATATA
*
35545134 TTATTTATTTTAAATTTGTTTTATGTA
1 TTATTTATTTTAAA-TTGTTTTATATA
*
35545161 TTATTCATTTTAAATTG-TTTAT-TA
1 TTATTTATTTTAAATTGTTTTATATA
* *
35545185 TTACTTTA----AAAAT-TTTCATATA
1 TTA-TTTATTTTAAATTGTTTTATATA
** *
35545207 TTATCAATTTCAAA-T-TTTTATAT-
1 TTATTTATTTTAAATTGTTTTATATA
* *
35545230 GTA-TTA-TCT--ATT-TTTTATATA
1 TTATTTATTTTAAATTGTTTTATATA
** *
35545251 CCATTTATTTTTTAAGA-TGTTTTTTATA
1 TTATTTA--TTTTAA-ATTGTTTTATATA
* * *
35545279 TTACTTATTTTAAATTTCTTTTTACATA
1 TTATTTATTTTAAA-TT-GTTTTATATA
* * ** *
35545307 ATATTTATTTTAAACTCATTTATACA
1 TTATTTATTTTAAATTGTTTTATATA
* * *
35545333 TTATTTATCTTAAATTATTTTACATA
1 TTATTTATTTTAAATTGTTTTATATA
*
35545359 TTATTTATTTTAAATTTTTTT
1 TTATTTATTTTAAATTGTTTT
35545380 CCCCTCTTAT
Statistics
Matches: 237, Mismatches: 59, Indels: 51
0.68 0.17 0.15
Matches are distributed among these distances:
19 1 0.00
20 9 0.04
21 12 0.05
22 9 0.04
23 4 0.02
24 39 0.16
25 17 0.07
26 81 0.34
27 33 0.14
28 32 0.14
ACGTcount: A:0.32, C:0.06, G:0.03, T:0.59
Consensus pattern (26 bp):
TTATTTATTTTAAATTGTTTTATATA
Found at i:35545300 original size:26 final size:26
Alignment explanation
Indices: 35545271--35545514 Score: 91
Period size: 26 Copynumber: 8.9 Consensus size: 26
35545261 TTTAAGATGT
*
35545271 TTTTTATATTACTTATTTTAAATTTC
1 TTTTTATATTATTTATTTTAAATTTC
* *
35545297 TTTTTACATAATATTTATTTTAAA-CTC
1 TTTTT--ATATTATTTATTTTAAATTTC
* * *
35545324 ATTTATACATTATTTATCTTAAATTAT-
1 -TTTTTATATTATTTATTTTAAATT-TC
** *
35545351 TTTACATATTATTTATTTTAAATTTTT
1 TTTTTATATTATTTATTTTAAA-TTTC
*
35545378 TTCCCCTCTTATATTATTTATTTCAAACTTTC
1 TT----T-TTATATTATTTATTTTAAA-TTTC
*** ** *
35545410 -GCCTATATTACCTATTTTAAATTTT
1 TTTTTATATTATTTATTTTAAATTTC
* * *
35545435 TTTTTACATATAATCTATTTTTAATTGT-
1 TTTTT--ATATTATTTATTTTAAATT-TC
* ** * *
35545463 TTTGTATATTGCTGATATTAAATTTC
1 TTTTTATATTATTTATTTTAAATTTC
*
35545489 TTTTTTCACATTATTTATTTTAAATT
1 -TTTTT-ATATTATTTATTTTAAATT
35545515 CATTTATTAT
Statistics
Matches: 156, Mismatches: 43, Indels: 36
0.66 0.18 0.15
Matches are distributed among these distances:
25 4 0.03
26 67 0.43
27 10 0.06
28 54 0.35
29 1 0.01
31 1 0.01
32 19 0.12
ACGTcount: A:0.29, C:0.11, G:0.02, T:0.59
Consensus pattern (26 bp):
TTTTTATATTATTTATTTTAAATTTC
Found at i:35545570 original size:49 final size:48
Alignment explanation
Indices: 35545498--35545602 Score: 122
Period size: 49 Copynumber: 2.2 Consensus size: 48
35545488 CTTTTTTCAC
* *
35545498 ATTATTTATTTTAAATTCATTTATTATCATTTTAAAATTTGTTTTACAT
1 ATTATTTATTTTAAATTCATTTATAATCATTTTAAAA-TTGTTATACAT
* * ** *
35545547 TTTATTTATTTTAATTTGC-TTTATAATTTTTTTAAAATTGTTATATAT
1 ATTATTTATTTTAAATT-CATTTATAATCATTTTAAAATTGTTATACAT
35545595 ATTATTTA
1 ATTATTTA
35545603 ATTCATTTGT
Statistics
Matches: 47, Mismatches: 8, Indels: 3
0.81 0.14 0.05
Matches are distributed among these distances:
48 16 0.34
49 30 0.64
50 1 0.02
ACGTcount: A:0.31, C:0.04, G:0.03, T:0.62
Consensus pattern (48 bp):
ATTATTTATTTTAAATTCATTTATAATCATTTTAAAATTGTTATACAT
Found at i:35560960 original size:18 final size:18
Alignment explanation
Indices: 35560939--35560975 Score: 56
Period size: 18 Copynumber: 2.1 Consensus size: 18
35560929 GGTTCTCAAG
35560939 AATTAAAAAAATTCAAAA
1 AATTAAAAAAATTCAAAA
**
35560957 AATTAAAAATTTTCAAAA
1 AATTAAAAAAATTCAAAA
35560975 A
1 A
35560976 TTTATTTTAA
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
18 17 1.00
ACGTcount: A:0.68, C:0.05, G:0.00, T:0.27
Consensus pattern (18 bp):
AATTAAAAAAATTCAAAA
Found at i:35560976 original size:17 final size:17
Alignment explanation
Indices: 35560934--35560977 Score: 52
Period size: 18 Copynumber: 2.5 Consensus size: 17
35560924 TAAAAGGTTC
*
35560934 TCAAGAATTAAAAAAAT
1 TCAAAAATTAAAAAAAT
**
35560951 TCAAAAAATTAAAAATTT
1 TC-AAAAATTAAAAAAAT
35560969 TCAAAAATT
1 TCAAAAATT
35560978 TATTTTAAAA
Statistics
Matches: 23, Mismatches: 3, Indels: 2
0.82 0.11 0.07
Matches are distributed among these distances:
17 9 0.39
18 14 0.61
ACGTcount: A:0.61, C:0.07, G:0.02, T:0.30
Consensus pattern (17 bp):
TCAAAAATTAAAAAAAT
Found at i:35562934 original size:12 final size:12
Alignment explanation
Indices: 35562917--35562959 Score: 50
Period size: 12 Copynumber: 3.5 Consensus size: 12
35562907 TTGAAAGTAT
35562917 TGATGATTGATA
1 TGATGATTGATA
* *
35562929 TGATGAATCGATC
1 TGATG-ATTGATA
*
35562942 TTATGATTGATA
1 TGATGATTGATA
35562954 TGATGA
1 TGATGA
35562960 ATCGATCTTA
Statistics
Matches: 24, Mismatches: 6, Indels: 2
0.75 0.19 0.06
Matches are distributed among these distances:
12 15 0.62
13 9 0.38
ACGTcount: A:0.33, C:0.05, G:0.23, T:0.40
Consensus pattern (12 bp):
TGATGATTGATA
Found at i:35562947 original size:25 final size:25
Alignment explanation
Indices: 35562919--35562970 Score: 104
Period size: 25 Copynumber: 2.1 Consensus size: 25
35562909 GAAAGTATTG
35562919 ATGATTGATATGATGAATCGATCTT
1 ATGATTGATATGATGAATCGATCTT
35562944 ATGATTGATATGATGAATCGATCTT
1 ATGATTGATATGATGAATCGATCTT
35562969 AT
1 AT
35562971 TGGTGTTGGC
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:0.33, C:0.08, G:0.19, T:0.40
Consensus pattern (25 bp):
ATGATTGATATGATGAATCGATCTT
Found at i:35564426 original size:307 final size:304
Alignment explanation
Indices: 35563872--35564466 Score: 734
Period size: 307 Copynumber: 1.9 Consensus size: 304
35563862 GATCACCTCC
* * * *
35563872 GATAAATAAGATTGGCCTTGACATCCAAGTCAATGTTAGGTTTAGTAATATCTTATTGTTTGGGA
1 GATAAATAAGATTGGCCTTGACATCCAAGTCAATATTAGATTTAGTAATATCTTATTATTTAGGA
* ** *
35563937 ATTAAATTTCACATGTATGTGCACGAATTGTACTTTGACCTTGAGATCAAATCTAATTTATGGAT
66 ATCAAATTTCACATGTATGTGCACGAACCGTACTTTAACCTTGAGATCAAATCTAATTTATGGAT
* ** * * *
35564002 ATGCTTTTCAAGGAATCTTGGGCATAGGTTTTGTGGAGAATTAAATCCCACGAAAAACTTGACAC
131 ATGCTTTTCAAGAAATCTTGAACATAGATTTTGTAGAGAATTAAATCCCACGAAAAAATTGACAC
* * * * *
35564067 CTATGAGTGTCGAGATTTACCTATAAAAAAGAGCATATATTGACAGATAATGAAAAAAAAAAGTT
196 CTATGAGTATCGAAATTTACCTATAAAAAAGAGCATACATAGACAAATAATG---AAAAAAAGTT
* * *
35564132 TTGAAAAAGAACTACAATGTTCTCCTCAAAACCATTAAGAGATTTTT
258 TTAAAAAAGAACTACAATGTTCACCACAAAACCATTAAGAGATTTTT
** * **
35564179 GATAAATAAGATTGGCCTTGACATCCTGGTCGATATTAGATTTAGTCGTATCTTATTATTTAGGA
1 GATAAATAAGATTGGCCTTGACATCCAAGTCAATATTAGATTTAGTAATATCTTATTATTTAGGA
* * *
35564244 ATCAAATTTCACATGTATGTGCACGAACCGTACTTTAACTTTGAGATCAAGTCTAATCTT-TGTA
66 ATCAAATTTCACATGTATGTGCACGAACCGTACTTTAACCTTGAGATCAAATCTAAT-TTATGGA
* * *
35564308 TATGTTTTTTAAGAAATCTTGAATATAGATTTTGTAGAGAATTAAATCCCAC-AAAAAATTGAAC
130 TATGCTTTTCAAGAAATCTTGAACATAGATTTTGTAGAGAATTAAATCCCACGAAAAAATTG-AC
* * * *
35564372 ACCTATGAGTATCGAAATTTTTCCCTA-AAATGAA-A-C-TACATCAGATAAATAATGAAAAAGA
194 ACCTATGAGTATCGAAA--TTTACCTATAAA-AAAGAGCATACAT-AGACAAATAATGAAAAAAA
35564433 GTTTTAAAAAAGAACTACAATGTTCACCACAAAA
255 GTTTTAAAAAAGAACTACAATGTTCACCACAAAA
35564467 TGTTGAATGT
Statistics
Matches: 245, Mismatches: 37, Indels: 15
0.82 0.12 0.05
Matches are distributed among these distances:
304 37 0.15
306 12 0.05
307 181 0.74
308 6 0.02
309 9 0.04
ACGTcount: A:0.38, C:0.14, G:0.16, T:0.33
Consensus pattern (304 bp):
GATAAATAAGATTGGCCTTGACATCCAAGTCAATATTAGATTTAGTAATATCTTATTATTTAGGA
ATCAAATTTCACATGTATGTGCACGAACCGTACTTTAACCTTGAGATCAAATCTAATTTATGGAT
ATGCTTTTCAAGAAATCTTGAACATAGATTTTGTAGAGAATTAAATCCCACGAAAAAATTGACAC
CTATGAGTATCGAAATTTACCTATAAAAAAGAGCATACATAGACAAATAATGAAAAAAAGTTTTA
AAAAAGAACTACAATGTTCACCACAAAACCATTAAGAGATTTTT
Found at i:35564727 original size:6 final size:6
Alignment explanation
Indices: 35564716--35564753 Score: 76
Period size: 6 Copynumber: 6.3 Consensus size: 6
35564706 TCCAAAAATA
35564716 ATTTAT ATTTAT ATTTAT ATTTAT ATTTAT ATTTAT AT
1 ATTTAT ATTTAT ATTTAT ATTTAT ATTTAT ATTTAT AT
35564754 AGCTTTAGGA
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 32 1.00
ACGTcount: A:0.34, C:0.00, G:0.00, T:0.66
Consensus pattern (6 bp):
ATTTAT
Found at i:35569046 original size:40 final size:40
Alignment explanation
Indices: 35568964--35569147 Score: 205
Period size: 40 Copynumber: 4.6 Consensus size: 40
35568954 TATTCGAATG
* * *
35568964 ATATCCGGGCTAAG-TCCCGAAGGCTTTTATGCTAGTGACT
1 ATATTCGGGCTAAGAT-CCGAAGGCATTTGTGCTAGTGACT
* *
35569004 ATATTCGGACTAAGATCCGAAGGCATTTGTGCAAGTTG-CT
1 ATATTCGGGCTAAGATCCGAAGGCATTTGTGCTAG-TGACT
* * *
35569044 ATATCCGGGCTAAGACCCGAAGGCATTTGTGCTAGCGACT
1 ATATTCGGGCTAAGATCCGAAGGCATTTGTGCTAGTGACT
* *
35569084 ATATTCGGGCTAAG-TCCCGAAGGCATTTATGCTAGTGACC
1 ATATTCGGGCTAAGAT-CCGAAGGCATTTGTGCTAGTGACT
*
35569124 ATA-TCTGGGCTAAGACCCGAAGGC
1 ATATTC-GGGCTAAGATCCGAAGGC
35569148 CTTGTGCGAG
Statistics
Matches: 122, Mismatches: 16, Indels: 12
0.81 0.11 0.08
Matches are distributed among these distances:
39 3 0.02
40 116 0.95
41 3 0.02
ACGTcount: A:0.26, C:0.22, G:0.26, T:0.26
Consensus pattern (40 bp):
ATATTCGGGCTAAGATCCGAAGGCATTTGTGCTAGTGACT
Found at i:35569097 original size:80 final size:80
Alignment explanation
Indices: 35568964--35569147 Score: 255
Period size: 80 Copynumber: 2.3 Consensus size: 80
35568954 TATTCGAATG
* * *
35568964 ATATCCGGGCTAAGTCCCGAAGGCTTTTATGCTAGTGACTATATTCGGACTAAGAT-CCGAAGGC
1 ATATCCGGGCTAAGACCCGAAGGCATTTATGCTAGCGACTATATTCGGACTAAG-TCCCGAAGGC
* *
35569028 ATTTGTGCAAGTTG-CT
65 ATTTATGCAAG-TGACC
* *
35569044 ATATCCGGGCTAAGACCCGAAGGCATTTGTGCTAGCGACTATATTCGGGCTAAGTCCCGAAGGCA
1 ATATCCGGGCTAAGACCCGAAGGCATTTATGCTAGCGACTATATTCGGACTAAGTCCCGAAGGCA
*
35569109 TTTATGCTAGTGACC
66 TTTATGCAAGTGACC
*
35569124 ATATCTGGGCTAAGACCCGAAGGC
1 ATATCCGGGCTAAGACCCGAAGGC
35569148 CTTGTGCGAG
Statistics
Matches: 93, Mismatches: 9, Indels: 4
0.88 0.08 0.04
Matches are distributed among these distances:
79 3 0.03
80 90 0.97
ACGTcount: A:0.26, C:0.22, G:0.26, T:0.26
Consensus pattern (80 bp):
ATATCCGGGCTAAGACCCGAAGGCATTTATGCTAGCGACTATATTCGGACTAAGTCCCGAAGGCA
TTTATGCAAGTGACC
Found at i:35576283 original size:40 final size:40
Alignment explanation
Indices: 35576221--35576404 Score: 212
Period size: 40 Copynumber: 4.6 Consensus size: 40
35576211 TATTCGAATG
*
35576221 ATATCCGGGCTAAG-TCCCGAAGGCTTTTATGCTAGTGACT
1 ATATCCGGGCTAAGAT-CCGAAGGCATTTATGCTAGTGACT
* * * *
35576261 ATATCCGGACTAAGATCTGAAGGCATTTGTGCGAGTTG-CT
1 ATATCCGGGCTAAGATCCGAAGGCATTTATGCTAG-TGACT
* * *
35576301 ATATCCGGGCTAAGACCCGAAGGCATTTGTGCTAGCGACT
1 ATATCCGGGCTAAGATCCGAAGGCATTTATGCTAGTGACT
* *
35576341 ATATTCGGGCTAAG-TCCCGAAGGCATTTATGCTAGTGACC
1 ATATCCGGGCTAAGAT-CCGAAGGCATTTATGCTAGTGACT
* *
35576381 ATATCTGGGCTAAGACCCGAAGGC
1 ATATCCGGGCTAAGATCCGAAGGC
35576405 CTTGTGCGAG
Statistics
Matches: 121, Mismatches: 18, Indels: 10
0.81 0.12 0.07
Matches are distributed among these distances:
39 1 0.01
40 117 0.97
41 3 0.02
ACGTcount: A:0.25, C:0.22, G:0.27, T:0.26
Consensus pattern (40 bp):
ATATCCGGGCTAAGATCCGAAGGCATTTATGCTAGTGACT
Found at i:35576354 original size:80 final size:80
Alignment explanation
Indices: 35576221--35576404 Score: 237
Period size: 80 Copynumber: 2.3 Consensus size: 80
35576211 TATTCGAATG
* * * *
35576221 ATATCCGGGCTAAGTCCCGAAGGCTTTTATGCTAGTGACTATATCCGGACTAAGAT-CTGAAGGC
1 ATATCCGGGCTAAGACCCGAAGGCATTTATGCTAGCGACTATATCCGGACTAAG-TCCCGAAGGC
* *
35576285 ATTTGTGCGAGTTG-CT
65 ATTTATGCGAG-TGACC
* * *
35576301 ATATCCGGGCTAAGACCCGAAGGCATTTGTGCTAGCGACTATATTCGGGCTAAGTCCCGAAGGCA
1 ATATCCGGGCTAAGACCCGAAGGCATTTATGCTAGCGACTATATCCGGACTAAGTCCCGAAGGCA
*
35576366 TTTATGCTAGTGACC
66 TTTATGCGAGTGACC
*
35576381 ATATCTGGGCTAAGACCCGAAGGC
1 ATATCCGGGCTAAGACCCGAAGGC
35576405 CTTGTGCGAG
Statistics
Matches: 91, Mismatches: 11, Indels: 4
0.86 0.10 0.04
Matches are distributed among these distances:
79 3 0.03
80 88 0.97
ACGTcount: A:0.25, C:0.22, G:0.27, T:0.26
Consensus pattern (80 bp):
ATATCCGGGCTAAGACCCGAAGGCATTTATGCTAGCGACTATATCCGGACTAAGTCCCGAAGGCA
TTTATGCGAGTGACC
Found at i:35579269 original size:63 final size:62
Alignment explanation
Indices: 35579168--35579298 Score: 174
Period size: 63 Copynumber: 2.1 Consensus size: 62
35579158 ATCTTTGCTT
* *
35579168 ATTTGCAAATGAATTCATTTCTCATTTTCATTTTCATTTCCATTTT-GAGAAAACCACATTC
1 ATTTCCAAATGAATTCATTTCTCATTTTCATTTTCATTTCCATTTTGGAGAAAACCACAATC
* * ** *
35579229 ATTTCCAAATGATTTTATTTTCTCCATTTTCATTTTCATTTTGATTTTGGAGAAAACCATAATC
1 ATTTCCAAATGAATTCA-TTTCT-CATTTTCATTTTCATTTCCATTTTGGAGAAAACCACAATC
35579293 ATTTCC
1 ATTTCC
35579299 TGAATGTTTT
Statistics
Matches: 60, Mismatches: 7, Indels: 3
0.86 0.10 0.04
Matches are distributed among these distances:
61 14 0.23
62 5 0.08
63 22 0.37
64 19 0.32
ACGTcount: A:0.28, C:0.18, G:0.07, T:0.47
Consensus pattern (62 bp):
ATTTCCAAATGAATTCATTTCTCATTTTCATTTTCATTTCCATTTTGGAGAAAACCACAATC
Found at i:35581642 original size:48 final size:45
Alignment explanation
Indices: 35581542--35581663 Score: 149
Period size: 47 Copynumber: 2.6 Consensus size: 45
35581532 AGTTATCGTG
*
35581542 AGCTAGTGTAAGACATGTCTGGGACAT-GCATCGGTCACATTATGAG
1 AGCTAGTGTAAGACATGTCTGGGACATGGCATCGG--ACATTATGAA
*
35581588 AGCTAGTGTAAGACCATGTCTAGGACATGGCATCGG-CATTGAGATGAA
1 AGCTAGTGTAAGA-CATGTCTGGGACATGGCATCGGACATT---ATGAA
*
35581636 AGCTAGTGTAAGACTTGTCTGGGACATG
1 AGCTAGTGTAAGACATGTCTGGGACATG
35581664 CATTGGCCTC
Statistics
Matches: 67, Mismatches: 4, Indels: 9
0.84 0.05 0.11
Matches are distributed among these distances:
45 4 0.06
46 13 0.19
47 26 0.39
48 24 0.36
ACGTcount: A:0.29, C:0.16, G:0.30, T:0.25
Consensus pattern (45 bp):
AGCTAGTGTAAGACATGTCTGGGACATGGCATCGGACATTATGAA
Found at i:35581683 original size:36 final size:36
Alignment explanation
Indices: 35581642--35581719 Score: 156
Period size: 36 Copynumber: 2.2 Consensus size: 36
35581632 TGAAAGCTAG
35581642 TGTAAGACTTGTCTGGGACATGCATTGGCCTCGAGA
1 TGTAAGACTTGTCTGGGACATGCATTGGCCTCGAGA
35581678 TGTAAGACTTGTCTGGGACATGCATTGGCCTCGAGA
1 TGTAAGACTTGTCTGGGACATGCATTGGCCTCGAGA
35581714 TGTAAG
1 TGTAAG
35581720 CTAGTGTAAG
Statistics
Matches: 42, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
36 42 1.00
ACGTcount: A:0.23, C:0.18, G:0.31, T:0.28
Consensus pattern (36 bp):
TGTAAGACTTGTCTGGGACATGCATTGGCCTCGAGA
Found at i:35581742 original size:82 final size:84
Alignment explanation
Indices: 35581594--35581748 Score: 224
Period size: 82 Copynumber: 1.9 Consensus size: 84
35581584 TGAGAGCTAG
* *
35581594 TGTAAGACCATGTCTAGGACATGGCATCGGCATTGAGATGAAAGCTAGTGTAAGACTTGTCTGGG
1 TGTAAGACCATGTCTAGGACATGGCATCGGCATCGAGATGAAAGCTAGTGTAAGACATGTCTGGG
35581659 ACATGCATTGGCCTCGAGA
66 ACATGCATTGGCCTCGAGA
* * * * * *
35581678 TGTAAGA-CTTGTCTGGGACAT-GCATTGGCCTCGAGATGTAAGCTAGTGTAAGACATGTTTGGG
1 TGTAAGACCATGTCTAGGACATGGCATCGGCATCGAGATGAAAGCTAGTGTAAGACATGTCTGGG
35581741 ACATGCAT
66 ACATGCAT
35581749 CGTCTACGAG
Statistics
Matches: 63, Mismatches: 8, Indels: 2
0.86 0.11 0.03
Matches are distributed among these distances:
82 44 0.70
83 12 0.19
84 7 0.11
ACGTcount: A:0.26, C:0.17, G:0.30, T:0.27
Consensus pattern (84 bp):
TGTAAGACCATGTCTAGGACATGGCATCGGCATCGAGATGAAAGCTAGTGTAAGACATGTCTGGG
ACATGCATTGGCCTCGAGA
Found at i:35582335 original size:2 final size:2
Alignment explanation
Indices: 35582328--35582369 Score: 84
Period size: 2 Copynumber: 21.0 Consensus size: 2
35582318 ATATTCATTT
35582328 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
35582370 AAAGATGTTA
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):
TA
Found at i:35584271 original size:19 final size:19
Alignment explanation
Indices: 35584228--35584271 Score: 61
Period size: 19 Copynumber: 2.3 Consensus size: 19
35584218 TACAAGCAAC
*
35584228 ACAACATTAATCCAAATAA
1 ACAACATTAATCCAAAAAA
*
35584247 ACAACATTAGTCCAAAAAA
1 ACAACATTAATCCAAAAAA
*
35584266 ATAACA
1 ACAACA
35584272 AAAAAAATAC
Statistics
Matches: 22, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
19 22 1.00
ACGTcount: A:0.59, C:0.20, G:0.02, T:0.18
Consensus pattern (19 bp):
ACAACATTAATCCAAAAAA
Found at i:35587660 original size:37 final size:37
Alignment explanation
Indices: 35587598--35587681 Score: 141
Period size: 37 Copynumber: 2.2 Consensus size: 37
35587588 ATCATATGAG
*
35587598 AATTTACTAATTACAACTTGAACCAGTAATACAAAATT
1 AATTAACT-ATTACAACTTGAACCAGTAATACAAAATT
*
35587636 AATTAACTATTACAACTTGGACCAGTAATACAAAATT
1 AATTAACTATTACAACTTGAACCAGTAATACAAAATT
35587673 AATTAACTA
1 AATTAACTA
35587682 AGTTTTAAAA
Statistics
Matches: 44, Mismatches: 2, Indels: 1
0.94 0.04 0.02
Matches are distributed among these distances:
37 37 0.84
38 7 0.16
ACGTcount: A:0.48, C:0.15, G:0.06, T:0.31
Consensus pattern (37 bp):
AATTAACTATTACAACTTGAACCAGTAATACAAAATT
Found at i:35594246 original size:46 final size:46
Alignment explanation
Indices: 35594072--35594292 Score: 195
Period size: 46 Copynumber: 4.8 Consensus size: 46
35594062 GAGTTATCGT
* * * *
35594072 GAGCTAGTGTAAGACATGTTTGGGACATGCATCGGCCAC-ATTATGA
1 GAGCTAGTGTAAGACATGTCTGGGACATGCATCGACCTCGA-GATGA
* * * * *
35594118 GAGCTAGTGTAAGATTATGTCTGGGACATGGCA-CCAGCATTGAGACGA
1 GAGCTAGTGTAAGA-CATGTCTGGGACAT-GCATCGA-CCTCGAGATGA
*
35594166 GAGCTAGTGTAAGACATGTCTGAGACATGCATCGACCTCGAGATGTA
1 GAGCTAGTGTAAGACATGTCTGGGACATGCATCGACCTCGAGATG-A
* *
35594213 -AGCTAGTGTAAGACATGTTTGGGACATGTATCGA-CTACGAGAT-A
1 GAGCTAGTGTAAGACATGTCTGGGACATGCATCGACCT-CGAGATGA
* *
35594257 G-TC-AGTGTAAGACTATGTCTGGAACATGGCATCGAC
1 GAGCTAGTGTAAGAC-ATGTCTGGGACAT-GCATCGAC
35594293 ATTCTACCCC
Statistics
Matches: 142, Mismatches: 22, Indels: 22
0.76 0.12 0.12
Matches are distributed among these distances:
43 10 0.07
44 13 0.09
45 8 0.06
46 61 0.43
47 28 0.20
48 21 0.15
49 1 0.01
ACGTcount: A:0.29, C:0.17, G:0.29, T:0.25
Consensus pattern (46 bp):
GAGCTAGTGTAAGACATGTCTGGGACATGCATCGACCTCGAGATGA
Found at i:35604903 original size:69 final size:70
Alignment explanation
Indices: 35604771--35604903 Score: 214
Period size: 69 Copynumber: 1.9 Consensus size: 70
35604761 TAGTTTATTA
* * * * *
35604771 CTAATTAATTTGCTGCTGTAATGCTGTAAATTATTGGCTGTCCAAATTAGGACAAATTTATGGTA
1 CTAATTAATATGCTGCTATAATACTGTAAATTATTGGCTGTCCAAATTAGGACAAAATCATGGTA
35604836 CTTAG
66 CTTAG
35604841 CTAATTAATATGCTGCTATAATACT-TAAATTATTGGCTGTCCAAATTAGGACAAAATCATGGT
1 CTAATTAATATGCTGCTATAATACTGTAAATTATTGGCTGTCCAAATTAGGACAAAATCATGGT
35604904 GTTATGTGCT
Statistics
Matches: 58, Mismatches: 5, Indels: 1
0.91 0.08 0.02
Matches are distributed among these distances:
69 36 0.62
70 22 0.38
ACGTcount: A:0.33, C:0.14, G:0.17, T:0.37
Consensus pattern (70 bp):
CTAATTAATATGCTGCTATAATACTGTAAATTATTGGCTGTCCAAATTAGGACAAAATCATGGTA
CTTAG
Found at i:35606210 original size:48 final size:48
Alignment explanation
Indices: 35606139--35606380 Score: 403
Period size: 48 Copynumber: 5.0 Consensus size: 48
35606129 CAAGATAAAT
* *
35606139 ATATGTATATGTGGTAAGGCCGAATGGCTAATGTGAAATATGTATGGG
1 ATATGTATATGTGGTAAAGCCGAATGGCTAATGTGAAATATGTATGAG
*
35606187 ATATGTATTTGTGGTAAAGCCGAATGGCTAATGTGAAATATGTATGAG
1 ATATGTATATGTGGTAAAGCCGAATGGCTAATGTGAAATATGTATGAG
35606235 ATATGTATATGTGGTAAAGCCGAATGGCTAATGTGAAATATGTATGAG
1 ATATGTATATGTGGTAAAGCCGAATGGCTAATGTGAAATATGTATGAG
*
35606283 ATATGTATATGTGGTAAAGCTGAATGGCTAATGTGAAATATGTATGAG
1 ATATGTATATGTGGTAAAGCCGAATGGCTAATGTGAAATATGTATGAG
* * * * *
35606331 ATACGTATACGTGGTAAAGCCGAAGGGCTAGTGTGAAATATGTAGGAG
1 ATATGTATATGTGGTAAAGCCGAATGGCTAATGTGAAATATGTATGAG
35606379 AT
1 AT
35606381 GTGTGTATAT
Statistics
Matches: 183, Mismatches: 11, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
48 183 1.00
ACGTcount: A:0.34, C:0.07, G:0.29, T:0.31
Consensus pattern (48 bp):
ATATGTATATGTGGTAAAGCCGAATGGCTAATGTGAAATATGTATGAG
Found at i:35606666 original size:37 final size:37
Alignment explanation
Indices: 35606521--35606665 Score: 245
Period size: 37 Copynumber: 3.9 Consensus size: 37
35606511 GGAAATATAT
35606521 TCCGGGTAAGACCCGATGACTACGTGTGGAGATTATG
1 TCCGGGTAAGACCCGATGACTACGTGTGGAGATTATG
35606558 TCCGGGTAAGACCCGATGACTACGTGTGGAGATTATG
1 TCCGGGTAAGACCCGATGACTACGTGTGGAGATTATG
* * *
35606595 TCCGGGTAAGACCCGATGACCACGTGTAGAGATTTTG
1 TCCGGGTAAGACCCGATGACTACGTGTGGAGATTATG
* *
35606632 TCCGGGTAAGACCCGATAACTTCGTGTGGAGATT
1 TCCGGGTAAGACCCGATGACTACGTGTGGAGATT
35606666 TCATCTGAGC
Statistics
Matches: 101, Mismatches: 7, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
37 101 1.00
ACGTcount: A:0.24, C:0.20, G:0.31, T:0.25
Consensus pattern (37 bp):
TCCGGGTAAGACCCGATGACTACGTGTGGAGATTATG
Found at i:35616369 original size:40 final size:40
Alignment explanation
Indices: 35616325--35616415 Score: 155
Period size: 40 Copynumber: 2.3 Consensus size: 40
35616315 TGACTAAATC
35616325 GTAATAAATTGGACTAAATCAAATAGAACTAAGAACTTAA
1 GTAATAAATTGGACTAAATCAAATAGAACTAAGAACTTAA
* * *
35616365 GTAATAAATTGGACTAAATCGAATATAACTAAGAACTTAG
1 GTAATAAATTGGACTAAATCAAATAGAACTAAGAACTTAA
35616405 GTAATAAATTG
1 GTAATAAATTG
35616416 AACCAAGGAC
Statistics
Matches: 48, Mismatches: 3, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
40 48 1.00
ACGTcount: A:0.49, C:0.09, G:0.14, T:0.27
Consensus pattern (40 bp):
GTAATAAATTGGACTAAATCAAATAGAACTAAGAACTTAA
Found at i:35618623 original size:40 final size:40
Alignment explanation
Indices: 35618457--35618641 Score: 180
Period size: 40 Copynumber: 4.6 Consensus size: 40
35618447 TTCGAATGAT
* * *
35618457 ATCCGGGCTAAGTCCCGAAGGC-TTTGTGCTAAGTGACTAA
1 ATCCGGGCTAAGTCCCGAAGGCATTCGTGC-GAGTTACTAA
** * *
35618497 ATCCGGAATAAGAT-CCGACGGCATACGTGCGAGTTACTAA
1 ATCCGGGCTAAG-TCCCGAAGGCATTCGTGCGAGTTACTAA
* * * *
35618537 ATCCGGACTAAGAT-CCGAAGGCTTTCGAGCGAGCTACTAA
1 ATCCGGGCTAAG-TCCCGAAGGCATTCGTGCGAGTTACTAA
* *
35618577 ATCCGGGTTAAGTCCCGAAGGCATTCGTGCGAGTTACTGTA
1 ATCCGGGCTAAGTCCCGAAGGCATTCGTGCGAGTTACT-AA
*
35618618 A-CCGGGCTATGTCCCGAAGGCATT
1 ATCCGGGCTAAGTCCCGAAGGCATT
35618642 TGAATGTGTA
Statistics
Matches: 120, Mismatches: 21, Indels: 8
0.81 0.14 0.05
Matches are distributed among these distances:
39 1 0.01
40 111 0.93
41 8 0.07
ACGTcount: A:0.26, C:0.24, G:0.27, T:0.23
Consensus pattern (40 bp):
ATCCGGGCTAAGTCCCGAAGGCATTCGTGCGAGTTACTAA
Found at i:35618635 original size:80 final size:80
Alignment explanation
Indices: 35618457--35618644 Score: 206
Period size: 80 Copynumber: 2.3 Consensus size: 80
35618447 TTCGAATGAT
* *
35618457 ATCCGGGCTAAGTCCCGAAGGCTTTGTGCTAAGTGACTAAATCCGGAATAAGATCCGACGGCATA
1 ATCCGGGCTAAGTCCCGAAGGCTTTGAGCTAAGTGACTAAATCCGGAATAAGATCCGAAGGCATA
35618522 CGTGCGAGTTACTAA
66 CGTGCGAGTTACTAA
* * **
35618537 ATCCGGACTAAGAT-CCGAAGGCTTTCGAGC-GAGCT-ACTAAATCCGGGTTAAG-TCCCGAAGG
1 ATCCGGGCTAAG-TCCCGAAGGCTTT-GAGCTAAG-TGACTAAATCCGGAATAAGAT-CCGAAGG
* *
35618598 CATTCGTGCGAGTTACTGTA
62 CATACGTGCGAGTTACT-AA
*
35618618 A-CCGGGCTATGTCCCGAAGGCATTTGA
1 ATCCGGGCTAAGTCCCGAAGGC-TTTGA
35618645 ATGTGTAGCC
Statistics
Matches: 91, Mismatches: 10, Indels: 14
0.79 0.09 0.12
Matches are distributed among these distances:
79 2 0.02
80 79 0.87
81 10 0.11
ACGTcount: A:0.27, C:0.23, G:0.27, T:0.23
Consensus pattern (80 bp):
ATCCGGGCTAAGTCCCGAAGGCTTTGAGCTAAGTGACTAAATCCGGAATAAGATCCGAAGGCATA
CGTGCGAGTTACTAA
Found at i:35626603 original size:40 final size:40
Alignment explanation
Indices: 35626437--35626621 Score: 180
Period size: 40 Copynumber: 4.6 Consensus size: 40
35626427 TTCGAATGAT
* * *
35626437 ATCCGGGCTAAGTCCCGAAGGC-TTTGTGCTAAGTGACTAA
1 ATCCGGGCTAAGTCCCGAAGGCATTCGTGC-GAGTTACTAA
** * *
35626477 ATCCGGAATAAGAT-CCGACGGCATACGTGCGAGTTACTAA
1 ATCCGGGCTAAG-TCCCGAAGGCATTCGTGCGAGTTACTAA
* * * *
35626517 ATCCGGACTAAGAT-CCGAAGGCTTTCGAGCGAGCTACTAA
1 ATCCGGGCTAAG-TCCCGAAGGCATTCGTGCGAGTTACTAA
* *
35626557 ATCCGGGTTAAGTCCCGAAGGCATTCGTGCGAGTTACTGTA
1 ATCCGGGCTAAGTCCCGAAGGCATTCGTGCGAGTTACT-AA
*
35626598 A-CCGGGCTATGTCCCGAAGGCATT
1 ATCCGGGCTAAGTCCCGAAGGCATT
35626622 TGAATGTGTA
Statistics
Matches: 120, Mismatches: 21, Indels: 8
0.81 0.14 0.05
Matches are distributed among these distances:
39 1 0.01
40 111 0.93
41 8 0.07
ACGTcount: A:0.26, C:0.24, G:0.27, T:0.23
Consensus pattern (40 bp):
ATCCGGGCTAAGTCCCGAAGGCATTCGTGCGAGTTACTAA
Found at i:35626615 original size:80 final size:80
Alignment explanation
Indices: 35626437--35626624 Score: 206
Period size: 80 Copynumber: 2.3 Consensus size: 80
35626427 TTCGAATGAT
* *
35626437 ATCCGGGCTAAGTCCCGAAGGCTTTGTGCTAAGTGACTAAATCCGGAATAAGATCCGACGGCATA
1 ATCCGGGCTAAGTCCCGAAGGCTTTGAGCTAAGTGACTAAATCCGGAATAAGATCCGAAGGCATA
35626502 CGTGCGAGTTACTAA
66 CGTGCGAGTTACTAA
* * **
35626517 ATCCGGACTAAGAT-CCGAAGGCTTTCGAGC-GAGCT-ACTAAATCCGGGTTAAG-TCCCGAAGG
1 ATCCGGGCTAAG-TCCCGAAGGCTTT-GAGCTAAG-TGACTAAATCCGGAATAAGAT-CCGAAGG
* *
35626578 CATTCGTGCGAGTTACTGTA
62 CATACGTGCGAGTTACT-AA
*
35626598 A-CCGGGCTATGTCCCGAAGGCATTTGA
1 ATCCGGGCTAAGTCCCGAAGGC-TTTGA
35626625 ATGTGTAGCC
Statistics
Matches: 91, Mismatches: 10, Indels: 14
0.79 0.09 0.12
Matches are distributed among these distances:
79 2 0.02
80 79 0.87
81 10 0.11
ACGTcount: A:0.27, C:0.23, G:0.27, T:0.23
Consensus pattern (80 bp):
ATCCGGGCTAAGTCCCGAAGGCTTTGAGCTAAGTGACTAAATCCGGAATAAGATCCGAAGGCATA
CGTGCGAGTTACTAA
Found at i:35630299 original size:26 final size:26
Alignment explanation
Indices: 35630265--35630318 Score: 90
Period size: 26 Copynumber: 2.1 Consensus size: 26
35630255 TTCTTTCTAC
* *
35630265 TTGTGGTAGCCTGGAGACCTTATTCT
1 TTGTAGTAGCCTAGAGACCTTATTCT
35630291 TTGTAGTAGCCTAGAGACCTTATTCT
1 TTGTAGTAGCCTAGAGACCTTATTCT
35630317 TT
1 TT
35630319 CCTCTCTTAG
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
26 26 1.00
ACGTcount: A:0.19, C:0.19, G:0.22, T:0.41
Consensus pattern (26 bp):
TTGTAGTAGCCTAGAGACCTTATTCT
Found at i:35634521 original size:5 final size:5
Alignment explanation
Indices: 35634506--35634535 Score: 51
Period size: 5 Copynumber: 5.8 Consensus size: 5
35634496 AACAAGTGTG
35634506 TAAAA TAAAAA TAAAA TAAAA TAAAA TAAA
1 TAAAA T-AAAA TAAAA TAAAA TAAAA TAAA
35634536 GAACACACAG
Statistics
Matches: 24, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
5 19 0.79
6 5 0.21
ACGTcount: A:0.80, C:0.00, G:0.00, T:0.20
Consensus pattern (5 bp):
TAAAA
Found at i:35640113 original size:23 final size:25
Alignment explanation
Indices: 35640087--35640134 Score: 64
Period size: 25 Copynumber: 2.0 Consensus size: 25
35640077 AATTAAAAAA
*
35640087 TAATGTAA-T-TAAAAATATTTAAT
1 TAATGTAATTATAAAAATAATTAAT
*
35640110 TAATTTAATTATAAAAATAATTAAT
1 TAATGTAATTATAAAAATAATTAAT
35640135 ATTAAAATTC
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
23 7 0.33
24 1 0.05
25 13 0.62
ACGTcount: A:0.54, C:0.00, G:0.02, T:0.44
Consensus pattern (25 bp):
TAATGTAATTATAAAAATAATTAAT
Found at i:35646778 original size:18 final size:19
Alignment explanation
Indices: 35646732--35646788 Score: 64
Period size: 19 Copynumber: 2.9 Consensus size: 19
35646722 TATAGTTTTC
35646732 CATTAAAAATATATAAAAAAAT
1 CATTAAAAATAT-T--AAAAAT
35646754 CATT-AAAATGATTAAAAAT
1 CATTAAAAAT-ATTAAAAAT
35646773 CA-TAAAAATATTAAAA
1 CATTAAAAATATTAAAA
35646789 TTTATATAAT
Statistics
Matches: 33, Mismatches: 0, Indels: 8
0.80 0.00 0.20
Matches are distributed among these distances:
18 8 0.24
19 13 0.39
21 6 0.18
22 6 0.18
ACGTcount: A:0.65, C:0.05, G:0.02, T:0.28
Consensus pattern (19 bp):
CATTAAAAATATTAAAAAT
Found at i:35646799 original size:17 final size:19
Alignment explanation
Indices: 35646779--35646813 Score: 56
Period size: 17 Copynumber: 1.9 Consensus size: 19
35646769 AAATCATAAA
35646779 AATATTA-AAAT-TTATAT
1 AATATTATAAATATTATAT
35646796 AATATTATAAATATTATA
1 AATATTATAAATATTATA
35646814 AAATTTCTAA
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
17 7 0.44
18 4 0.25
19 5 0.31
ACGTcount: A:0.54, C:0.00, G:0.00, T:0.46
Consensus pattern (19 bp):
AATATTATAAATATTATAT
Found at i:35646805 original size:28 final size:28
Alignment explanation
Indices: 35646769--35646893 Score: 87
Period size: 28 Copynumber: 4.4 Consensus size: 28
35646759 AAATGATTAA
*
35646769 AAATCATAAAAA-TATTAAAATTTAT-AT
1 AAATTATAAAAATTA-TAAAATTTATAAT
* *
35646796 AATATTATAAATATTATAAAATTTCTAAT
1 AA-ATTATAAAAATTATAAAATTTATAAT
** *
35646825 AAATTATAAATTTTTATAAAATTAATAA-
1 AAATTATAAA-AATTATAAAATTTATAAT
* *
35646853 AACATATTTAAAATAGTTA-AAATTTTATAAT
1 AA-AT-TATAAAA-A-TTATAAAATTTATAAT
35646884 AAATTATAAA
1 AAATTATAAA
35646894 TAAATAATAA
Statistics
Matches: 77, Mismatches: 12, Indels: 16
0.73 0.11 0.15
Matches are distributed among these distances:
27 2 0.03
28 27 0.35
29 27 0.35
30 16 0.21
31 5 0.06
ACGTcount: A:0.56, C:0.02, G:0.01, T:0.41
Consensus pattern (28 bp):
AAATTATAAAAATTATAAAATTTATAAT
Found at i:35646810 original size:9 final size:9
Alignment explanation
Indices: 35646778--35646815 Score: 53
Period size: 9 Copynumber: 4.3 Consensus size: 9
35646768 AAAATCATAA
35646778 AAATATTA-
1 AAATATTAT
35646786 AAAT-TTAT
1 AAATATTAT
35646794 ATAATATTAT
1 A-AATATTAT
35646804 AAATATTAT
1 AAATATTAT
35646813 AAA
1 AAA
35646816 ATTTCTAATA
Statistics
Matches: 27, Mismatches: 0, Indels: 5
0.84 0.00 0.16
Matches are distributed among these distances:
7 3 0.11
8 5 0.19
9 14 0.52
10 5 0.19
ACGTcount: A:0.58, C:0.00, G:0.00, T:0.42
Consensus pattern (9 bp):
AAATATTAT
Found at i:35646817 original size:10 final size:10
Alignment explanation
Indices: 35646757--35646893 Score: 66
Period size: 10 Copynumber: 14.4 Consensus size: 10
35646747 AAAAAATCAT
35646757 TAAAATGATTA
1 TAAAAT-ATTA
35646768 -AAAATCA-TA
1 TAAAAT-ATTA
35646777 -AAAATA-T-
1 TAAAATATTA
35646784 TAAAAT-TTA
1 TAAAATATTA
*
35646793 TATAATATTA
1 TAAAATATTA
35646803 T-AAATATTA
1 TAAAATATTA
*
35646812 TAAAAT-TTC
1 TAAAATATTA
35646821 TAATAA-ATTA
1 TAA-AATATTA
* *
35646831 TAAATTTTTA
1 TAAAATATTA
*
35646841 TAAAAT-TAA
1 TAAAATATTA
35646850 TAAAACATATT-
1 T-AAA-ATATTA
*
35646861 TAAAATAGT-
1 TAAAATATTA
*
35646870 TAAAATTTTA
1 TAAAATATTA
35646880 TAATAA-ATTA
1 TAA-AATATTA
35646890 TAAA
1 TAAA
35646894 TAAATAATAA
Statistics
Matches: 99, Mismatches: 14, Indels: 28
0.70 0.10 0.20
Matches are distributed among these distances:
8 8 0.08
9 41 0.41
10 44 0.44
11 5 0.05
12 1 0.01
ACGTcount: A:0.56, C:0.02, G:0.01, T:0.40
Consensus pattern (10 bp):
TAAAATATTA
Found at i:35646842 original size:29 final size:28
Alignment explanation
Indices: 35646784--35646895 Score: 88
Period size: 29 Copynumber: 3.9 Consensus size: 28
35646774 ATAAAAATAT
35646784 TAAAATTTATATAATATTATAAATATTA
1 TAAAATTTATATAATATTATAAATATTA
* *
35646812 TAAAATTTCTAATAA-ATTATAAATTTTTA
1 TAAAATTTAT-ATAATATTATAAA-TATTA
* * *
35646841 TAAAATTAATAAAACATATT-TAAAATAGT-
1 TAAAATTTAT-ATA-ATATTAT-AAATATTA
35646870 TAAAATTT-TATAATAAATTATAAATA
1 TAAAATTTATATAAT--ATTATAAATA
35646896 AATAATAAAT
Statistics
Matches: 67, Mismatches: 9, Indels: 16
0.73 0.10 0.17
Matches are distributed among these distances:
26 2 0.03
27 2 0.03
28 26 0.39
29 27 0.40
30 4 0.06
31 6 0.09
ACGTcount: A:0.54, C:0.02, G:0.01, T:0.43
Consensus pattern (28 bp):
TAAAATTTATATAATATTATAAATATTA
Found at i:35646846 original size:18 final size:18
Alignment explanation
Indices: 35646800--35646853 Score: 56
Period size: 18 Copynumber: 2.8 Consensus size: 18
35646790 TTATATAATA
35646800 TTATAAATATTATAAAATTT
1 TTATAAA-ATTAT-AAATTT
*
35646820 CTA-ATAAATTATAAATTT
1 TTATA-AAATTATAAATTT
35646838 TTATAAAATTAATAAA
1 TTATAAAATT-ATAAA
35646854 ACATATTTAA
Statistics
Matches: 29, Mismatches: 2, Indels: 7
0.76 0.05 0.18
Matches are distributed among these distances:
18 13 0.45
19 12 0.41
20 4 0.14
ACGTcount: A:0.54, C:0.02, G:0.00, T:0.44
Consensus pattern (18 bp):
TTATAAAATTATAAATTT
Found at i:35646897 original size:11 final size:11
Alignment explanation
Indices: 35646877--35646917 Score: 50
Period size: 11 Copynumber: 3.9 Consensus size: 11
35646867 AGTTAAAATT
35646877 TTAT-AATAAA
1 TTATAAATAAA
35646887 TTATAAATAAA
1 TTATAAATAAA
*
35646898 TAATAAAT-AA
1 TTATAAATAAA
*
35646908 TTACAAATAA
1 TTATAAATAA
35646918 TAGAAATTTT
Statistics
Matches: 26, Mismatches: 3, Indels: 3
0.81 0.09 0.09
Matches are distributed among these distances:
10 12 0.46
11 14 0.54
ACGTcount: A:0.63, C:0.02, G:0.00, T:0.34
Consensus pattern (11 bp):
TTATAAATAAA
Found at i:35647668 original size:19 final size:19
Alignment explanation
Indices: 35647640--35647958 Score: 116
Period size: 19 Copynumber: 16.7 Consensus size: 19
35647630 GATTTAATAA
35647640 ATAT-TTTTTATAATTTTT
1 ATATATTTTTATAATTTTT
*
35647658 ATATA-TTTT-TAATATCTT
1 ATATATTTTTATAAT-TTTT
* * ** *
35647676 ATAAATTTATTAAAAAATAT
1 ATATATTT-TTATAATTTTT
*
35647696 A-ATTTTATTTATAATTTATT
1 ATATATT-TTTATAATTT-TT
* * *
35647716 AGA-ACTTATTATGATTTTT
1 ATATA-TTTTTATAATTTTT
* * *
35647735 -TATAAGTTTTATAATTAATG
1 ATAT-ATTTTTATAATT-TTT
*
35647755 ATA-ATTTTTATAATTTGT
1 ATATATTTTTATAATTTTT
35647773 ATGATGATTTATTATAACTTTTT
1 AT-AT-ATTT-TTATAA-TTTTT
* *
35647796 AGA-ATTTTTATAAGCTTTT
1 ATATATTTTTATAA-TTTTT
* *
35647815 ATA-ATATTTATAAGTTTTG
1 ATATATTTTTATAA-TTTTT
*
35647834 ATGA-ATTCTTTATAAGTTTT
1 AT-ATATT-TTTATAATTTTT
*
35647854 AAATA-TTTTA-AATATTTT
1 ATATATTTTTATAAT-TTTT
* *
35647872 TTA-ATTTTTATTATTTTT
1 ATATATTTTTATAATTTTT
35647890 AT-TATTTTTATAATTTATT
1 ATATATTTTTATAATTT-TT
* *
35647909 AGA-ATTTTTATAA-GTTT
1 ATATATTTTTATAATTTTT
35647926 ATATAATTTTTA-AATTTTT
1 ATAT-ATTTTTATAATTTTT
*
35647945 -TATGTATTTTATAA
1 ATATAT-TTTTATAA
35647959 AAATTTTTAA
Statistics
Matches: 220, Mismatches: 49, Indels: 63
0.66 0.15 0.19
Matches are distributed among these distances:
17 12 0.05
18 60 0.27
19 89 0.40
20 29 0.13
21 18 0.08
22 7 0.03
23 5 0.02
ACGTcount: A:0.35, C:0.02, G:0.05, T:0.58
Consensus pattern (19 bp):
ATATATTTTTATAATTTTT
Found at i:35647767 original size:9 final size:9
Alignment explanation
Indices: 35647703--35647944 Score: 157
Period size: 9 Copynumber: 25.3 Consensus size: 9
35647693 TATAATTTTA
35647703 TTTATAATT
1 TTTATAATT
*
35647712 TATTAGAACTT
1 T-TTATAA-TT
* *
35647723 ATTATGATTT
1 TTTAT-AATT
*
35647733 TTTATAAGT
1 TTTATAATT
35647742 TTTATAATT
1 TTTATAATT
* *
35647751 AATGATAATT
1 -TTTATAATT
35647761 TTTATAATT
1 TTTATAATT
*
35647770 TGTATGATGATT
1 T-T-T-ATAATT
35647782 TATTATAACTT
1 T-TTATAA-TT
*
35647793 TTTAGAATT
1 TTTATAATT
*
35647802 TTTATAAGCT
1 TTTATAA-TT
*
35647812 TTTATAATA
1 TTTATAATT
35647821 TTTATAAGTT
1 TTTATAA-TT
*
35647831 TTGATGAATT
1 TTTAT-AATT
*
35647841 CTTTATAAGT
1 -TTTATAATT
35647851 TTTA-AATAT
1 TTTATAAT-T
35647860 TTTA-AATAT
1 TTTATAAT-T
*
35647869 TTTTTAATT
1 TTTATAATT
*
35647878 TTTATTATT
1 TTTATAATT
*
35647887 TTTATTATT
1 TTTATAATT
35647896 TTTATAATT
1 TTTATAATT
*
35647905 TATTAGAATT
1 T-TTATAATT
35647915 TTTATAAGTT
1 TTTATAA-TT
*
35647925 TATATAATT
1 TTTATAATT
35647934 TTTA-AATT
1 TTTATAATT
35647942 TTT
1 TTT
35647945 TATGTATTTT
Statistics
Matches: 184, Mismatches: 33, Indels: 33
0.74 0.13 0.13
Matches are distributed among these distances:
8 9 0.05
9 87 0.47
10 67 0.36
11 14 0.08
12 7 0.04
ACGTcount: A:0.33, C:0.02, G:0.06, T:0.59
Consensus pattern (9 bp):
TTTATAATT
Found at i:35647955 original size:37 final size:38
Alignment explanation
Indices: 35647732--35647958 Score: 177
Period size: 37 Copynumber: 6.0 Consensus size: 38
35647722 TATTATGATT
* ** *
35647732 TTTTATAAGTTTTATAATTAATGAT-AATTTTTATAA-
1 TTTTATAATTTTTATAATTTTTTATGAATTTTTATAAG
*
35647768 TTTGTATGATGATTTATTATAACTTTTTA-GAATTTTTATAAG
1 TTT-TAT-A--ATTT-TTATAATTTTTTATGAATTTTTATAAG
* * *
35647810 CTTTTATAATATTTATAAGTTTTGATGAATTCTTTATAAG
1 -TTTTATAATTTTTATAATTTTTTATGAATT-TTTATAAG
* *
35647850 TTTTA-AATATTTTA-AATATTTTT-T-AATTTTTATTAT
1 TTTTATAAT-TTTTATAAT-TTTTTATGAATTTTTATAAG
* *
35647886 TTTTATTATTTTTATAATTTATTA-GAATTTTTATAAG
1 TTTTATAATTTTTATAATTTTTTATGAATTTTTATAAG
*
35647923 TTTATATAATTTTTA-AATTTTTTATGTA-TTTTATAA
1 TTT-TATAATTTTTATAATTTTTTATGAATTTTTATAA
35647959 AAATTTTTAA
Statistics
Matches: 153, Mismatches: 20, Indels: 35
0.74 0.10 0.17
Matches are distributed among these distances:
36 23 0.15
37 41 0.27
38 30 0.20
39 21 0.14
40 11 0.07
41 21 0.14
42 3 0.02
43 3 0.02
ACGTcount: A:0.33, C:0.01, G:0.06, T:0.59
Consensus pattern (38 bp):
TTTTATAATTTTTATAATTTTTTATGAATTTTTATAAG
Found at i:35652496 original size:12 final size:12
Alignment explanation
Indices: 35652479--35652504 Score: 52
Period size: 12 Copynumber: 2.2 Consensus size: 12
35652469 TTTCCTGATT
35652479 TTGCCTTACCAA
1 TTGCCTTACCAA
35652491 TTGCCTTACCAA
1 TTGCCTTACCAA
35652503 TT
1 TT
35652505 CAACAGGCAC
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:0.23, C:0.31, G:0.08, T:0.38
Consensus pattern (12 bp):
TTGCCTTACCAA
Found at i:35658310 original size:192 final size:194
Alignment explanation
Indices: 35657809--35658460 Score: 992
Period size: 192 Copynumber: 3.3 Consensus size: 194
35657799 TTCTCTTCAC
35657809 CTTCTACCTCATCCTTCTTCATTTCTTTCTTCTTCTC-CTTTGCCTCTTTGTCTTTCTTCTTTTC
1 CTTCTACCTCATCCTTC-T--TTTCTTTCTTCTTCTCTCTTTGCCTCTTTGTCTTTCTTCTTTTC
*
35657873 TTTCTTTCCCTCTTCTAATTCTTCAGCTTC-T-TCTACCTCATCCTTCTTCTTCTTTTCTTTCTT
63 TTTCTTTCCCTCTTCTAATTCTTCATCTTCATCTCTACCTCATCCTTCTTCTTCTTTTCTTTCTT
* *
35657936 CTTCTCCTTTGCCTCTTTGTCTTTCTTCTTTTCTTTCTTTCCCTCTTCTGATTCTTCATCTTCAT
128 CTTCTCCTTTGCTTCTTTGTCTTTCTTCTTTTCTTTCTTTCCCTCTTCTAATTCTT-ATCTTCAT
35658001 CTT
192 CTT
35658004 CTTCTACCTCATCCTTCTTCTTCTTTTCTTTCTTCTTCTCCTTTGCCTCTTTGTCTTTCTTCTTT
1 CTTCTACCTCATCCTTCTT-TTC-TTTC-TTCTTC-TCT-CTTTGCCTCTTTGTCTTTCTTCTTT
*
35658069 TCTTTCTTTCCCTCTTCTAATTCTTCATCTTCATCTTCTACCTCATCCTTGTTCTTCTTTTCTTT
61 TCTTTCTTTCCCTCTTCTAATTCTTCATCTTCATC-TCTACCTCATCCTTCTTCTTCTTTTCTTT
*
35658134 CTTCTTCTCCTTTGCTTCTTTGTCTTTCTTCTTTTCTTTTTTTCCCTCTTCTAATTC-T-TCTTC
125 CTTCTTCTCCTTTGCTTCTTTGTCTTTCTTCTTTTCTTTCTTTCCCTCTTCTAATTCTTATCTTC
35658197 ATCTT
190 ATCTT
*
35658202 CTTCTACCTCATCCTTCTTTTCTTTCTTCTTCTCT-TTTGCCTCTTTGTCTTTCTCCTTTTCTTT
1 CTTCTACCTCATCCTTCTTTTCTTTCTTCTTCTCTCTTTGCCTCTTTGTCTTTCTTCTTTTCTTT
* *
35658266 CTTTCCCTCTTCTAATTCTTCATCTTCATCTCCTACATCATCCTTCTTCTTCTTCTCTTTCTTCT
66 CTTTCCCTCTTCTAATTCTTCATCTTCATCT-CTACCTCATCCTTCTTCTTCTTTTCTTTCTTCT
* *
35658331 TTTCCTTTGCTTCTTTGTCTTTCTTCTTTTCTTTCTTTCCCTCTTCTATTTCTTCATCTTCATCT
130 TCTCCTTTGCTTCTTTGTCTTTCTTCTTTTCTTTCTTTCCCTCTTCTAATTCTT-ATCTTCATCT
*
35658396 C
194 T
* *
35658397 CTTCTACTTTATCCTTATTCTTTTCTTTCTTCTTCTCCTCCTTTGCCTCTTTGTCTTTCTTCTT
1 CTTCTACCTCATCC---TTCTTTTCTTTCTTCTTCT-CT-CTTTGCCTCTTTGTCTTTCTTCTT
35658461 CTCTGTCTCT
Statistics
Matches: 422, Mismatches: 16, Indels: 32
0.90 0.03 0.07
Matches are distributed among these distances:
191 1 0.00
192 138 0.33
193 4 0.01
194 8 0.02
195 50 0.12
196 6 0.01
197 3 0.01
198 104 0.25
199 3 0.01
200 1 0.00
201 104 0.25
ACGTcount: A:0.06, C:0.33, G:0.03, T:0.59
Consensus pattern (194 bp):
CTTCTACCTCATCCTTCTTTTCTTTCTTCTTCTCTCTTTGCCTCTTTGTCTTTCTTCTTTTCTTT
CTTTCCCTCTTCTAATTCTTCATCTTCATCTCTACCTCATCCTTCTTCTTCTTTTCTTTCTTCTT
CTCCTTTGCTTCTTTGTCTTTCTTCTTTTCTTTCTTTCCCTCTTCTAATTCTTATCTTCATCTT
Found at i:35658493 original size:102 final size:102
Alignment explanation
Indices: 35657809--35658460 Score: 958
Period size: 99 Copynumber: 6.6 Consensus size: 102
35657799 TTCTCTTCAC
*
35657809 CTTCTACCTCAT-C--CTTCTTCATTTCTTTCTTCTTCTCCTTTGCCTCTTTGTCTTTCTTCTTT
1 CTTCTACCTCATCCTTCTTCTTCTTTTCTTTCTTCTTCTCCTTTGCCTCTTTGTCTTTCTTCTTT
*
35657871 TCTTTCTTTCCCTCTTCTAA----T--TCTTCAGCTT
66 TCTTTCTTTCCCTCTTCTAATTCTTCATCTTCATCTT
35657902 CTTCTACCTCATCCTTCTTCTTCTTTTCTTTCTTCTTCTCCTTTGCCTCTTTGTCTTTCTTCTTT
1 CTTCTACCTCATCCTTCTTCTTCTTTTCTTTCTTCTTCTCCTTTGCCTCTTTGTCTTTCTTCTTT
*
35657967 TCTTTCTTTCCCTCTTCTGATTCTTCATCTTCATCTT
66 TCTTTCTTTCCCTCTTCTAATTCTTCATCTTCATCTT
35658004 CTTCTACCTCATCCTTCTTCTTCTTTTCTTTCTTCTTCTCCTTTGCCTCTTTGTCTTTCTTCTTT
1 CTTCTACCTCATCCTTCTTCTTCTTTTCTTTCTTCTTCTCCTTTGCCTCTTTGTCTTTCTTCTTT
35658069 TCTTTCTTTCCCTCTTCTAATTCTTCATCTTCA---T
66 TCTTTCTTTCCCTCTTCTAATTCTTCATCTTCATCTT
* *
35658103 CTTCTACCTCATCCTTGTTCTTCTTTTCTTTCTTCTTCTCCTTTGCTTCTTTGTCTTTCTTCTTT
1 CTTCTACCTCATCCTTCTTCTTCTTTTCTTTCTTCTTCTCCTTTGCCTCTTTGTCTTTCTTCTTT
*
35658168 TCTTTTTTTCCCTCTTCTAATTC-T--TCTTCATCTT
66 TCTTTCTTTCCCTCTTCTAATTCTTCATCTTCATCTT
*
35658202 CTTCTACCTCATCCTTCTT-TTC-TTTC-TTCTTC-TCT--TTTGCCTCTTTGTCTTTCTCCTTT
1 CTTCTACCTCATCCTTCTTCTTCTTTTCTTTCTTCTTCTCCTTTGCCTCTTTGTCTTTCTTCTTT
35658261 TCTTTCTTTCCCTCTTCTAATTCTTCATCTTCATC-T
66 TCTTTCTTTCCCTCTTCTAATTCTTCATCTTCATCTT
* * * *
35658297 C--CTACATCATCCTTCTTCTTCTTCTCTTTCTTCTTTTCCTTTGCTTCTTTGTCTTTCTTCTTT
1 CTTCTACCTCATCCTTCTTCTTCTTTTCTTTCTTCTTCTCCTTTGCCTCTTTGTCTTTCTTCTTT
* *
35658360 TCTTTCTTTCCCTCTTCTATTTCTTCATCTTCATCTC
66 TCTTTCTTTCCCTCTTCTAATTCTTCATCTTCATCTT
* * * * *
35658397 CTTCTACTTTATCCTTATTCTTTTCTTTC-TTCTTCTCCTCCTTTGCCTCTTTGTCTTTCTTCTT
1 CTTCTACCTCATCCTTCTTCTTCT-TTTCTTTCTTCTTCTCCTTTGCCTCTTTGTCTTTCTTCTT
35658461 CTCTGTCTCT
Statistics
Matches: 508, Mismatches: 26, Indels: 41
0.88 0.05 0.07
Matches are distributed among these distances:
93 71 0.14
94 5 0.01
95 8 0.02
96 93 0.18
97 6 0.01
98 4 0.01
99 161 0.32
100 2 0.00
102 155 0.31
103 3 0.01
ACGTcount: A:0.06, C:0.33, G:0.03, T:0.59
Consensus pattern (102 bp):
CTTCTACCTCATCCTTCTTCTTCTTTTCTTTCTTCTTCTCCTTTGCCTCTTTGTCTTTCTTCTTT
TCTTTCTTTCCCTCTTCTAATTCTTCATCTTCATCTT
Found at i:35658702 original size:18 final size:17
Alignment explanation
Indices: 35658679--35658727 Score: 53
Period size: 18 Copynumber: 2.8 Consensus size: 17
35658669 TCTCCTTTTG
* *
35658679 CTTCTTTTCTTTTTTCTT
1 CTTCTTCTCTTCTTTC-T
35658697 CTTCTTCTCTTCTTTCT
1 CTTCTTCTCTTCTTTCT
*
35658714 CTTCATCATCTTCT
1 CTTCTTC-TCTTCT
35658728 ACCACCTCTT
Statistics
Matches: 27, Mismatches: 3, Indels: 2
0.84 0.09 0.06
Matches are distributed among these distances:
17 7 0.26
18 20 0.74
ACGTcount: A:0.04, C:0.31, G:0.00, T:0.65
Consensus pattern (17 bp):
CTTCTTCTCTTCTTTCT
Found at i:35663753 original size:12 final size:12
Alignment explanation
Indices: 35663708--35663758 Score: 54
Period size: 12 Copynumber: 4.5 Consensus size: 12
35663698 TGTGTTAAAA
*
35663708 TATATATTAAAT
1 TATATATTATAT
35663720 TAT-TATTATA-
1 TATATATTATAT
**
35663730 T-TATGGTATAT
1 TATATATTATAT
35663741 TATATATTATAT
1 TATATATTATAT
35663753 TATATA
1 TATATA
35663759 AATAAGTAAA
Statistics
Matches: 31, Mismatches: 5, Indels: 6
0.74 0.12 0.14
Matches are distributed among these distances:
9 1 0.03
10 6 0.19
11 7 0.23
12 17 0.55
ACGTcount: A:0.41, C:0.00, G:0.04, T:0.55
Consensus pattern (12 bp):
TATATATTATAT
Found at i:35663784 original size:10 final size:10
Alignment explanation
Indices: 35663769--35663816 Score: 53
Period size: 10 Copynumber: 4.7 Consensus size: 10
35663759 AATAAGTAAA
35663769 GAAACAGAAT
1 GAAACAGAAT
35663779 GAAACAGAAT
1 GAAACAGAAT
*
35663789 GAAAGCA-AAC
1 GAAA-CAGAAT
*
35663799 GAAACAGAGAA
1 GAAACAGA-AT
35663810 GAAACAG
1 GAAACAG
35663817 GGGAGAAAGA
Statistics
Matches: 33, Mismatches: 2, Indels: 5
0.82 0.05 0.12
Matches are distributed among these distances:
9 2 0.06
10 21 0.64
11 10 0.30
ACGTcount: A:0.60, C:0.12, G:0.23, T:0.04
Consensus pattern (10 bp):
GAAACAGAAT
Found at i:35665097 original size:18 final size:19
Alignment explanation
Indices: 35665076--35665114 Score: 62
Period size: 18 Copynumber: 2.1 Consensus size: 19
35665066 ATATATAGAT
35665076 ATATATATTGAATA-TTGA
1 ATATATATTGAATATTTGA
*
35665094 ATATATATTGATTATTTGA
1 ATATATATTGAATATTTGA
35665113 AT
1 AT
35665115 TGAATTGAAA
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
18 13 0.68
19 6 0.32
ACGTcount: A:0.41, C:0.00, G:0.10, T:0.49
Consensus pattern (19 bp):
ATATATATTGAATATTTGA
Found at i:35665465 original size:39 final size:39
Alignment explanation
Indices: 35665355--35665489 Score: 112
Period size: 39 Copynumber: 3.4 Consensus size: 39
35665345 GACCTCGAGT
* * * *
35665355 CGATGAGACACTGGGTGTCACTATATTTCTTCGGATAGATT
1 CGATGAGACACTGGGTGTCA-AATATTACTTCGGCTAG-TC
** ** * *
35665396 CGATGAGGTACTGGGTACCAACT-TTACTTCGGCTAGGC
1 CGATGAGACACTGGGTGTCAAATATTACTTCGGCTAGTC
* *
35665434 CGATGAGACACTGGGTGTCAAATATTGCTTCGAACTA-TC
1 CGATGAGACACTGGGTGTCAAATATTACTTCG-GCTAGTC
*
35665473 CGATGAGGCACTGGGTG
1 CGATGAGACACTGGGTG
35665490 CCATATTGGT
Statistics
Matches: 73, Mismatches: 19, Indels: 6
0.74 0.19 0.06
Matches are distributed among these distances:
38 18 0.25
39 35 0.48
40 4 0.05
41 16 0.22
ACGTcount: A:0.24, C:0.20, G:0.28, T:0.28
Consensus pattern (39 bp):
CGATGAGACACTGGGTGTCAAATATTACTTCGGCTAGTC
Found at i:35665633 original size:18 final size:19
Alignment explanation
Indices: 35665612--35665652 Score: 59
Period size: 19 Copynumber: 2.2 Consensus size: 19
35665602 AATGAAATGA
35665612 GAAATTGA-AT-TGAGAATT
1 GAAATTGAGATATGAG-ATT
35665630 GAAATTGAGATATGAGATT
1 GAAATTGAGATATGAGATT
35665649 GAAA
1 GAAA
35665653 ACATGAACCA
Statistics
Matches: 21, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
18 8 0.38
19 9 0.43
20 4 0.19
ACGTcount: A:0.46, C:0.00, G:0.24, T:0.29
Consensus pattern (19 bp):
GAAATTGAGATATGAGATT
Found at i:35666431 original size:18 final size:17
Alignment explanation
Indices: 35666408--35666501 Score: 68
Period size: 18 Copynumber: 5.4 Consensus size: 17
35666398 GGGCGTTACA
35666408 ATTATTGT-CTAATATATT
1 ATTATTGTACT-AT-TATT
35666426 ATTATTGTACTATTATT
1 ATTATTGTACTATTATT
* *
35666443 ATTACTT-TACTATTGTA
1 ATTA-TTGTACTATTATT
* *
35666460 ATTTATGGTATTATTATT
1 A-TTATTGTACTATTATT
*
35666478 ATTACTCT-TATTATTATT
1 ATTA-T-TGTACTATTATT
35666496 ATTATT
1 ATTATT
35666502 ATTAGTGACC
Statistics
Matches: 63, Mismatches: 7, Indels: 14
0.75 0.08 0.17
Matches are distributed among these distances:
16 1 0.02
17 22 0.35
18 38 0.60
19 2 0.03
ACGTcount: A:0.30, C:0.06, G:0.05, T:0.59
Consensus pattern (17 bp):
ATTATTGTACTATTATT
Found at i:35666476 original size:3 final size:3
Alignment explanation
Indices: 35666468--35666713 Score: 171
Period size: 3 Copynumber: 80.7 Consensus size: 3
35666458 TAATTTATGG
* * * *
35666468 TAT TAT TAT TAT TAC TCT TAT TAT TAT TAT TAT TAT TAGT GACC TAT
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TA-T TA-T TAT
* * * * *
35666515 TAC TAT TCT TAT TAG CA- TAC TAT TAT T-T CCTAT T-T TA- TAT TAT
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT --TAT TAT TAT TAT TAT
* * * * * * **
35666558 TAT TGT TAT CAA CAT ATAT TAT TAT CAT TAAT GTAT TGT TAT TCCC TAT
1 TAT TAT TAT TAT TAT -TAT TAT TAT TAT T-AT -TAT TAT TAT T-AT TAT
*
35666607 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TCT TAT
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
* * *
35666655 TAT TAC TAC TAT T-T TAT TCCT T-T TAT TATT TAT TAT TAT TAT TAT
1 TAT TAT TAT TAT TAT TAT T-AT TAT TAT TA-T TAT TAT TAT TAT TAT
35666700 TAT TAT TAT TAT TA
1 TAT TAT TAT TAT TA
35666714 ATAACGTTCT
Statistics
Matches: 192, Mismatches: 36, Indels: 30
0.74 0.14 0.12
Matches are distributed among these distances:
2 10 0.05
3 164 0.85
4 16 0.08
5 2 0.01
ACGTcount: A:0.30, C:0.09, G:0.02, T:0.59
Consensus pattern (3 bp):
TAT
Found at i:35666767 original size:3 final size:3
Alignment explanation
Indices: 35666759--35666818 Score: 57
Period size: 3 Copynumber: 19.0 Consensus size: 3
35666749 TTATTTAACA
* * *
35666759 TAT TAT TAT TAT TAT TAAT TTT TAT TAT CAT TAT TAC TAT CGTAT TAT
1 TAT TAT TAT TAT TAT T-AT TAT TAT TAT TAT TAT TAT TAT --TAT TAT
*
35666807 TAT TAC TAT TAT
1 TAT TAT TAT TAT
35666819 ATTTTCATTT
Statistics
Matches: 46, Mismatches: 8, Indels: 6
0.77 0.13 0.10
Matches are distributed among these distances:
3 40 0.87
4 3 0.07
5 3 0.07
ACGTcount: A:0.32, C:0.07, G:0.02, T:0.60
Consensus pattern (3 bp):
TAT
Found at i:35666870 original size:16 final size:16
Alignment explanation
Indices: 35666849--35666879 Score: 62
Period size: 16 Copynumber: 1.9 Consensus size: 16
35666839 TATTGTTATT
35666849 TATCTATTTATATTTC
1 TATCTATTTATATTTC
35666865 TATCTATTTATATTT
1 TATCTATTTATATTT
35666880 TCGTTGTTAT
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 15 1.00
ACGTcount: A:0.26, C:0.10, G:0.00, T:0.65
Consensus pattern (16 bp):
TATCTATTTATATTTC
Found at i:35666935 original size:22 final size:22
Alignment explanation
Indices: 35666910--35666951 Score: 59
Period size: 22 Copynumber: 1.9 Consensus size: 22
35666900 GCATTATATC
35666910 TATATTATCAT-TTCATTATTGT
1 TATATTATCATATT-ATTATTGT
*
35666932 TATATTTTCATATTATTATT
1 TATATTATCATATTATTATT
35666952 ATCACTACTA
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
22 16 0.89
23 2 0.11
ACGTcount: A:0.29, C:0.07, G:0.02, T:0.62
Consensus pattern (22 bp):
TATATTATCATATTATTATTGT
Found at i:35669421 original size:3 final size:3
Alignment explanation
Indices: 35669413--35669446 Score: 61
Period size: 3 Copynumber: 11.7 Consensus size: 3
35669403 TCTCTTAATT
35669413 TTC TTC TTC TTC TTC TTC TTC TTC TTC TT- TTC TT
1 TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TT
35669447 TTACCTCTTT
Statistics
Matches: 30, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
2 2 0.07
3 28 0.93
ACGTcount: A:0.00, C:0.29, G:0.00, T:0.71
Consensus pattern (3 bp):
TTC
Found at i:35670990 original size:6 final size:6
Alignment explanation
Indices: 35670979--35671003 Score: 50
Period size: 6 Copynumber: 4.2 Consensus size: 6
35670969 ATTTTATAAT
35670979 TTTTTA TTTTTA TTTTTA TTTTTA T
1 TTTTTA TTTTTA TTTTTA TTTTTA T
35671004 CAATTTTTAA
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 19 1.00
ACGTcount: A:0.16, C:0.00, G:0.00, T:0.84
Consensus pattern (6 bp):
TTTTTA
Found at i:35688236 original size:79 final size:80
Alignment explanation
Indices: 35688117--35688300 Score: 176
Period size: 79 Copynumber: 2.3 Consensus size: 80
35688107 GCTACTCGTT
* * * * *
35688117 CAAACGCCTTCGGGACATAGCCCGGATATGGTAACCCGCACCAAGGCCTACGGGACTTAACCCGG
1 CAAATGCCTTCGGGTCTTAGCCCGGATATGATAACCCGCACCAAGGCCTACGGGACTTAACCCAG
* *
35688182 ATATCA-CGA-TTGCA
66 ATAT-AGCCACTAGCA
* * * * * * *
35688196 CAAATGCCTTCGGGTCTTAGCCCGGATA-GAATGACTCGCACGAATGCCTTCGGGTCTTAGCCCA
1 CAAATGCCTTCGGGTCTTAGCCCGGATATG-ATAACCCGCACCAAGGCCTACGGGACTTAACCCA
35688260 GATATAGCCACTAGCA
65 GATATAGCCACTAGCA
* * *
35688276 CCATTGCCTTCGGGTCTTAACCCGG
1 CAAATGCCTTCGGGTCTTAGCCCGG
35688301 TTATAATTTC
Statistics
Matches: 85, Mismatches: 17, Indels: 5
0.79 0.16 0.05
Matches are distributed among these distances:
78 2 0.02
79 57 0.67
80 26 0.31
ACGTcount: A:0.24, C:0.31, G:0.24, T:0.21
Consensus pattern (80 bp):
CAAATGCCTTCGGGTCTTAGCCCGGATATGATAACCCGCACCAAGGCCTACGGGACTTAACCCAG
ATATAGCCACTAGCA
Found at i:35688245 original size:40 final size:40
Alignment explanation
Indices: 35688193--35688300 Score: 126
Period size: 40 Copynumber: 2.7 Consensus size: 40
35688183 TATCACGATT
** *
35688193 GCACAAATGCCTTCGGGTCTTAGCCCGGATAGAATGACTC
1 GCACAAATGCCTTCGGGTCTTAGCCCGGATAGAACCACTA
* * * *
35688233 GCACGAATGCCTTCGGGTCTTAGCCCAGATATAGCCACTA
1 GCACAAATGCCTTCGGGTCTTAGCCCGGATAGAACCACTA
* * *
35688273 GCACCATTGCCTTCGGGTCTTAACCCGG
1 GCACAAATGCCTTCGGGTCTTAGCCCGG
35688301 TTATAATTTC
Statistics
Matches: 57, Mismatches: 11, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
40 57 1.00
ACGTcount: A:0.22, C:0.31, G:0.24, T:0.23
Consensus pattern (40 bp):
GCACAAATGCCTTCGGGTCTTAGCCCGGATAGAACCACTA
Found at i:35691137 original size:14 final size:14
Alignment explanation
Indices: 35691118--35691144 Score: 54
Period size: 14 Copynumber: 1.9 Consensus size: 14
35691108 TATTAAGGCA
35691118 ATAATTAAGAACAC
1 ATAATTAAGAACAC
35691132 ATAATTAAGAACA
1 ATAATTAAGAACA
35691145 AGAACAAGTA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 13 1.00
ACGTcount: A:0.59, C:0.11, G:0.07, T:0.22
Consensus pattern (14 bp):
ATAATTAAGAACAC
Found at i:35693366 original size:18 final size:17
Alignment explanation
Indices: 35693345--35693406 Score: 79
Period size: 18 Copynumber: 3.5 Consensus size: 17
35693335 AATAAAGTTC
35693345 AAAATAAAAAAAACAAAA
1 AAAATAAAAAAAA-AAAA
35693363 AAAATAAAAAAATAAAAA
1 AAAATAAAAAAA-AAAAA
* *
35693381 AAAATAAACATAAAAATA
1 AAAATAAA-AAAAAAAAA
35693399 AAAATAAA
1 AAAATAAA
35693407 CATAAAGATA
Statistics
Matches: 40, Mismatches: 2, Indels: 4
0.87 0.04 0.09
Matches are distributed among these distances:
18 36 0.90
19 4 0.10
ACGTcount: A:0.85, C:0.03, G:0.00, T:0.11
Consensus pattern (17 bp):
AAAATAAAAAAAAAAAA
Found at i:35693393 original size:6 final size:6
Alignment explanation
Indices: 35693345--35693418 Score: 71
Period size: 6 Copynumber: 12.3 Consensus size: 6
35693335 AATAAAGTTC
* * *
35693345 AAAATA AAAA-A AACAAAA AAAATA AAAA-A ATAAAAA AAAATA AACATA
1 AAAATA AAAATA AA-AATA AAAATA AAAATA A-AAATA AAAATA AAAATA
* *
35693393 AAAATA AAAATA AACATA AAGATA AA
1 AAAATA AAAATA AAAATA AAAATA AA
35693419 TGGACTCAAT
Statistics
Matches: 58, Mismatches: 6, Indels: 8
0.81 0.08 0.11
Matches are distributed among these distances:
5 5 0.09
6 48 0.83
7 5 0.09
ACGTcount: A:0.82, C:0.04, G:0.01, T:0.12
Consensus pattern (6 bp):
AAAATA
Found at i:35693407 original size:18 final size:17
Alignment explanation
Indices: 35693345--35693418 Score: 84
Period size: 16 Copynumber: 4.5 Consensus size: 17
35693335 AATAAAGTTC
35693345 AAAATAAAAAAAACA-A
1 AAAATAAAAAAAACATA
35693361 AAAA-AATAAAAAA-ATA
1 AAAATAA-AAAAAACATA
*
35693377 AAAA-AAAATAAACATA
1 AAAATAAAAAAAACATA
35693393 AAAATAAAAATAAACATA
1 AAAATAAAAA-AAACATA
*
35693411 AAGATAAA
1 AAAATAAA
35693419 TGGACTCAAT
Statistics
Matches: 50, Mismatches: 3, Indels: 8
0.82 0.05 0.13
Matches are distributed among these distances:
15 8 0.16
16 24 0.48
17 4 0.08
18 14 0.28
ACGTcount: A:0.82, C:0.04, G:0.01, T:0.12
Consensus pattern (17 bp):
AAAATAAAAAAAACATA
Found at i:35695078 original size:3 final size:3
Alignment explanation
Indices: 35695070--35695471 Score: 274
Period size: 3 Copynumber: 131.3 Consensus size: 3
35695060 TAATGAAAAT
35695070 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
* *
35695118 ATA ATA ATA ATA ATAA ATA ACA ATA ATA ATA ACA ATA ATA ATA A-A
1 ATA ATA ATA ATA AT-A ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA
* * *
35695163 A-A ATA ACA ATA ATAA ATA ACA ATA ATA ATA A-A A-A ATA ACA ATA
1 ATA ATA ATA ATA AT-A ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA
* * * * * *
35695206 AGA ATAA ATA ACA ATA AGA ATAA ATA ACA ATA AGA ATAA ATA ACA ATA
1 ATA AT-A ATA ATA ATA ATA AT-A ATA ATA ATA ATA AT-A ATA ATA ATA
* * * * * * *
35695254 AGA ATAA ATA AGA ATA AGA ATAA ATA AGA ATA AGA ATA AGA ATA AGA
1 ATA AT-A ATA ATA ATA ATA AT-A ATA ATA ATA ATA ATA ATA ATA ATA
* * * * * * *
35695301 ATAA ATA AGA ATT AGA ATA AGA ATAA ATA AGA ATA AGA ATA AGA ATA
1 AT-A ATA ATA ATA ATA ATA ATA AT-A ATA ATA ATA ATA ATA ATA ATA
* * * * * * *
35695348 AGA ATA AGA ATA AGA ATAA ATA ACA ATA ACA ATA ACA ATA ACA ATA
1 ATA ATA ATA ATA ATA AT-A ATA ATA ATA ATA ATA ATA ATA ATA ATA
* * * * * * * *
35695394 ACA ATA ACA ATA ACA ATA ACA ATA ACA ATA ACA ATA ACA ATA ACA AT-
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA
**
35695441 ATGGA CCA ATA ATA GATA ATA ATA ATA ATA A
1 AT--A ATA ATA ATA -ATA ATA ATA ATA ATA A
35695472 CAAAGAAAAA
Statistics
Matches: 299, Mismatches: 84, Indels: 32
0.72 0.20 0.08
Matches are distributed among these distances:
2 10 0.03
3 256 0.86
4 33 0.11
ACGTcount: A:0.67, C:0.05, G:0.05, T:0.22
Consensus pattern (3 bp):
ATA
Found at i:35700195 original size:24 final size:24
Alignment explanation
Indices: 35700163--35700211 Score: 98
Period size: 24 Copynumber: 2.0 Consensus size: 24
35700153 GGTTGGTAGC
35700163 TTGTTTTGAAGAATAGCTGAACAT
1 TTGTTTTGAAGAATAGCTGAACAT
35700187 TTGTTTTGAAGAATAGCTGAACAT
1 TTGTTTTGAAGAATAGCTGAACAT
35700211 T
1 T
35700212 CCTTGTTGAG
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
24 25 1.00
ACGTcount: A:0.33, C:0.08, G:0.20, T:0.39
Consensus pattern (24 bp):
TTGTTTTGAAGAATAGCTGAACAT
Found at i:35705546 original size:6 final size:6
Alignment explanation
Indices: 35705531--35705575 Score: 81
Period size: 6 Copynumber: 7.5 Consensus size: 6
35705521 GCAAATGGAT
*
35705531 CATTTC CATTTT CATTTC CATTTC CATTTC CATTTC CATTTC CAT
1 CATTTC CATTTC CATTTC CATTTC CATTTC CATTTC CATTTC CAT
35705576 ATTTGGAAAC
Statistics
Matches: 37, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
6 37 1.00
ACGTcount: A:0.18, C:0.31, G:0.00, T:0.51
Consensus pattern (6 bp):
CATTTC
Found at i:35708067 original size:12 final size:12
Alignment explanation
Indices: 35708050--35708077 Score: 56
Period size: 12 Copynumber: 2.3 Consensus size: 12
35708040 TTATACCTTT
35708050 TTTTTCTTTTTA
1 TTTTTCTTTTTA
35708062 TTTTTCTTTTTA
1 TTTTTCTTTTTA
35708074 TTTT
1 TTTT
35708078 CCTTCTTCTT
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 16 1.00
ACGTcount: A:0.07, C:0.07, G:0.00, T:0.86
Consensus pattern (12 bp):
TTTTTCTTTTTA
Found at i:35713097 original size:21 final size:21
Alignment explanation
Indices: 35713068--35713108 Score: 64
Period size: 21 Copynumber: 2.0 Consensus size: 21
35713058 AAATATGCCA
*
35713068 AACAGAAGCTCATAAGAGCTT
1 AACAAAAGCTCATAAGAGCTT
*
35713089 AACAAAAGCTTATAAGAGCT
1 AACAAAAGCTCATAAGAGCT
35713109 GATCCACCCG
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
21 18 1.00
ACGTcount: A:0.46, C:0.17, G:0.17, T:0.20
Consensus pattern (21 bp):
AACAAAAGCTCATAAGAGCTT
Found at i:35714879 original size:29 final size:29
Alignment explanation
Indices: 35714847--35714925 Score: 77
Period size: 29 Copynumber: 2.7 Consensus size: 29
35714837 ATACCCTCCG
** *
35714847 AGCTCGCACACCCAGTGCCGTATTTTTCC
1 AGCTCGCACACCCAGTGCCAAATATTTCC
* **
35714876 AGCTTGCACACTTAGTGCCAAATATTTCC
1 AGCTCGCACACCCAGTGCCAAATATTTCC
* **
35714905 AGCACGCACACTTAGTGCCAA
1 AGCTCGCACACCCAGTGCCAA
35714926 TCTCGTCACC
Statistics
Matches: 42, Mismatches: 8, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
29 42 1.00
ACGTcount: A:0.25, C:0.33, G:0.16, T:0.25
Consensus pattern (29 bp):
AGCTCGCACACCCAGTGCCAAATATTTCC
Found at i:35716792 original size:29 final size:29
Alignment explanation
Indices: 35716760--35716838 Score: 77
Period size: 29 Copynumber: 2.7 Consensus size: 29
35716750 ATACCCTCCG
** *
35716760 AGCTCGCACACCCAGTGCCGTATTTTTCC
1 AGCTCGCACACCCAGTGCCAAATATTTCC
* **
35716789 AGCTTGCACACTTAGTGCCAAATATTTCC
1 AGCTCGCACACCCAGTGCCAAATATTTCC
* **
35716818 AGCACGCACACTTAGTGCCAA
1 AGCTCGCACACCCAGTGCCAA
35716839 TCTCGTCACC
Statistics
Matches: 42, Mismatches: 8, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
29 42 1.00
ACGTcount: A:0.25, C:0.33, G:0.16, T:0.25
Consensus pattern (29 bp):
AGCTCGCACACCCAGTGCCAAATATTTCC
Found at i:35718703 original size:29 final size:28
Alignment explanation
Indices: 35718642--35718749 Score: 83
Period size: 29 Copynumber: 3.8 Consensus size: 28
35718632 ACGTAATTTA
* **
35718642 AGCTCGCACACACAGTGCC-ATACCCTCC
1 AGCTCGCACACCCAGTGCCAATA-TTTCC
* *
35718670 GAGCTCGCACACCCAGTGCCGTATTTTTCC
1 -AGCTCGCACACCCAGTGCC-AATATTTCC
* **
35718700 AGCTTGCACACTTAGTGCCAATATTTCC
1 AGCTCGCACACCCAGTGCCAATATTTCC
* **
35718728 AGCACGCACACTTAGTGCCAAT
1 AGCTCGCACACCCAGTGCCAAT
35718750 CTCGTCACCA
Statistics
Matches: 66, Mismatches: 11, Indels: 5
0.80 0.13 0.06
Matches are distributed among these distances:
28 27 0.41
29 34 0.52
30 3 0.05
31 2 0.03
ACGTcount: A:0.24, C:0.36, G:0.17, T:0.23
Consensus pattern (28 bp):
AGCTCGCACACCCAGTGCCAATATTTCC
Found at i:35718736 original size:28 final size:28
Alignment explanation
Indices: 35718695--35718749 Score: 92
Period size: 28 Copynumber: 2.0 Consensus size: 28
35718685 GTGCCGTATT
**
35718695 TTTCCAGCTTGCACACTTAGTGCCAATA
1 TTTCCAGCACGCACACTTAGTGCCAATA
35718723 TTTCCAGCACGCACACTTAGTGCCAAT
1 TTTCCAGCACGCACACTTAGTGCCAAT
35718750 CTCGTCACCA
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:0.25, C:0.31, G:0.15, T:0.29
Consensus pattern (28 bp):
TTTCCAGCACGCACACTTAGTGCCAATA
Found at i:35726704 original size:29 final size:29
Alignment explanation
Indices: 35726672--35726750 Score: 77
Period size: 29 Copynumber: 2.7 Consensus size: 29
35726662 ATACCCTCCG
** *
35726672 AGCTCGCACACCCAGTGCCGTATTTTTCC
1 AGCTCGCACACCCAGTGCCAAATATTTCC
* **
35726701 AGCTTGCACACTTAGTGCCAAATATTTCC
1 AGCTCGCACACCCAGTGCCAAATATTTCC
* **
35726730 AGCACGCACACTTAGTGCCAA
1 AGCTCGCACACCCAGTGCCAA
35726751 TCTCGTCACC
Statistics
Matches: 42, Mismatches: 8, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
29 42 1.00
ACGTcount: A:0.25, C:0.33, G:0.16, T:0.25
Consensus pattern (29 bp):
AGCTCGCACACCCAGTGCCAAATATTTCC
Found at i:35729611 original size:2 final size:2
Alignment explanation
Indices: 35729606--35729632 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
35729596 AAAACCTTTA
35729606 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
35729633 AATTAATTAA
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:35729752 original size:17 final size:16
Alignment explanation
Indices: 35729730--35729776 Score: 51
Period size: 17 Copynumber: 2.9 Consensus size: 16
35729720 AAATTTTAAG
*
35729730 AAAAATCTATAAAATAT
1 AAAAATATATAAAAT-T
*
35729747 AAAAATATATACAATT
1 AAAAATATATAAAATT
35729763 -AAAATATATTAAAA
1 AAAAATATA-TAAAA
35729777 GCTTATAATA
Statistics
Matches: 26, Mismatches: 3, Indels: 3
0.81 0.09 0.09
Matches are distributed among these distances:
15 8 0.31
16 5 0.19
17 13 0.50
ACGTcount: A:0.66, C:0.04, G:0.00, T:0.30
Consensus pattern (16 bp):
AAAAATATATAAAATT
Found at i:35730195 original size:11 final size:11
Alignment explanation
Indices: 35730168--35730206 Score: 53
Period size: 11 Copynumber: 3.5 Consensus size: 11
35730158 ATTTAAAACT
*
35730168 TTTAAAA-TAA
1 TTTAAAATTTA
35730178 TTATAAAATTTA
1 TT-TAAAATTTA
35730190 TTTAAAATTTA
1 TTTAAAATTTA
35730201 TTTAAA
1 TTTAAA
35730207 TTATTCTTAA
Statistics
Matches: 26, Mismatches: 1, Indels: 3
0.87 0.03 0.10
Matches are distributed among these distances:
10 2 0.08
11 20 0.77
12 4 0.15
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (11 bp):
TTTAAAATTTA
Found at i:35732232 original size:39 final size:39
Alignment explanation
Indices: 35732178--35732437 Score: 265
Period size: 39 Copynumber: 7.0 Consensus size: 39
35732168 ATTACACTAA
* *
35732178 CACACAGCCTACTAGGCACATAGACCGAATAATCACCGG
1 CACACAGCCTGCTAGGCACATAGCCCGAATAATCACCGG
* ** *
35732217 CACACAGCCTGCTAGGCACATTGCTTGAATAATCATCGG
1 CACACAGCCTGCTAGGCACATAGCCCGAATAATCACCGG
* * *
35732256 CACACAGCTTACTAGGCACATAGCCCGAATAATCACCAG
1 CACACAGCCTGCTAGGCACATAGCCCGAATAATCACCGG
*
35732295 CATACAGCCTGCTAGGCACATAGCCCG---AAT------
1 CACACAGCCTGCTAGGCACATAGCCCGAATAATCACCGG
* * * *
35732325 -A-ACAGCTTGCTAGGTACATAGCTCGAATAATCACCGA
1 CACACAGCCTGCTAGGCACATAGCCCGAATAATCACCGG
* *
35732362 CACACAACCTGCTAGGCACATAGCCCGAATAATCACCAG
1 CACACAGCCTGCTAGGCACATAGCCCGAATAATCACCGG
* **
35732401 CACACAGCCTGCTAGGCATATAATCCGAATAAT-ACCG
1 CACACAGCCTGCTAGGCACATAGCCCGAATAATCACCG
35732438 TATTTCTATT
Statistics
Matches: 180, Mismatches: 30, Indels: 23
0.77 0.13 0.10
Matches are distributed among these distances:
28 21 0.12
29 1 0.01
31 3 0.02
36 3 0.02
38 4 0.02
39 148 0.82
ACGTcount: A:0.34, C:0.31, G:0.18, T:0.17
Consensus pattern (39 bp):
CACACAGCCTGCTAGGCACATAGCCCGAATAATCACCGG
Found at i:35732338 original size:28 final size:28
Alignment explanation
Indices: 35732298--35732354 Score: 87
Period size: 28 Copynumber: 2.0 Consensus size: 28
35732288 TCACCAGCAT
35732298 ACAGCCTGCTAGGCACATAGCCCGAATA
1 ACAGCCTGCTAGGCACATAGCCCGAATA
* * *
35732326 ACAGCTTGCTAGGTACATAGCTCGAATA
1 ACAGCCTGCTAGGCACATAGCCCGAATA
35732354 A
1 A
35732355 TCACCGACAC
Statistics
Matches: 26, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
28 26 1.00
ACGTcount: A:0.33, C:0.26, G:0.21, T:0.19
Consensus pattern (28 bp):
ACAGCCTGCTAGGCACATAGCCCGAATA
Found at i:35732373 original size:67 final size:67
Alignment explanation
Indices: 35732259--35732393 Score: 209
Period size: 67 Copynumber: 2.0 Consensus size: 67
35732249 TCATCGGCAC
* *
35732259 ACAGCTTACTAGGCACATAGCCCGAATAATCACCAGCATACAGCCTGCTAGGCACATAGCCCGAA
1 ACAGCTTACTAGGCACATAGCCCGAATAATCACCAGCACACAACCTGCTAGGCACATAGCCCGAA
35732324 TA
66 TA
* * *
35732326 ACAGCTTGCTAGGTACATAGCTCGAATAATCACC-GACACACAACCTGCTAGGCACATAGCCCGA
1 ACAGCTTACTAGGCACATAGCCCGAATAATCACCAG-CACACAACCTGCTAGGCACATAGCCCGA
35732390 ATA
65 ATA
35732393 A
1 A
35732394 TCACCAGCAC
Statistics
Matches: 62, Mismatches: 5, Indels: 2
0.90 0.07 0.03
Matches are distributed among these distances:
66 1 0.02
67 61 0.98
ACGTcount: A:0.35, C:0.30, G:0.18, T:0.17
Consensus pattern (67 bp):
ACAGCTTACTAGGCACATAGCCCGAATAATCACCAGCACACAACCTGCTAGGCACATAGCCCGAA
TA
Found at i:35732408 original size:106 final size:106
Alignment explanation
Indices: 35732220--35732432 Score: 309
Period size: 106 Copynumber: 2.0 Consensus size: 106
35732210 TCACCGGCAC
* * * * * *
35732220 ACAGCCTGCTAGGCACATTGCTTGAATAATCATCGGCACACAGCTTACTAGGCACATAGCCCGAA
1 ACAGCCTGCTAGGCACATAGCTCGAATAATCACCGACACACAACCTACTAGGCACATAGCCCGAA
* *
35732285 TAATCACCAGCATACAGCCTGCTAGGCACATAGCCCGAATA
66 TAATCACCAGCACACAGCCTGCTAGGCACATAACCCGAATA
* * *
35732326 ACAGCTTGCTAGGTACATAGCTCGAATAATCACCGACACACAACCTGCTAGGCACATAGCCCGAA
1 ACAGCCTGCTAGGCACATAGCTCGAATAATCACCGACACACAACCTACTAGGCACATAGCCCGAA
* *
35732391 TAATCACCAGCACACAGCCTGCTAGGCATATAATCCGAATA
66 TAATCACCAGCACACAGCCTGCTAGGCACATAACCCGAATA
35732432 A
1 A
35732433 TACCGTATTT
Statistics
Matches: 94, Mismatches: 13, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
106 94 1.00
ACGTcount: A:0.34, C:0.30, G:0.18, T:0.18
Consensus pattern (106 bp):
ACAGCCTGCTAGGCACATAGCTCGAATAATCACCGACACACAACCTACTAGGCACATAGCCCGAA
TAATCACCAGCACACAGCCTGCTAGGCACATAACCCGAATA
Found at i:35737404 original size:20 final size:21
Alignment explanation
Indices: 35737333--35737406 Score: 75
Period size: 20 Copynumber: 3.7 Consensus size: 21
35737323 ATTTAGTCAT
* *
35737333 ATAATA-AA-TTAATAATATA
1 ATAATATAATTTAATATTTTA
*
35737352 ATAAGTATAATTTATTATTTTA
1 ATAA-TATAATTTAATATTTTA
*
35737374 ATAA-ATTATTTAATATTTTA
1 ATAATATAATTTAATATTTTA
35737394 ATAATA-AATTTAA
1 ATAATATAATTTAA
35737407 AATAATAATT
Statistics
Matches: 45, Mismatches: 6, Indels: 7
0.78 0.10 0.12
Matches are distributed among these distances:
19 4 0.09
20 26 0.58
21 3 0.07
22 12 0.27
ACGTcount: A:0.51, C:0.00, G:0.01, T:0.47
Consensus pattern (21 bp):
ATAATATAATTTAATATTTTA
Done.