Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: At_chr8
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: 78745976
ACGTcount: A:0.31, C:0.17, G:0.17, T:0.31
Warning! 2640508 characters in sequence are not A, C, G, or T
File 158 of 235
Found at i:53208535 original size:40 final size:40
Alignment explanation
Indices: 53208459--53208535 Score: 100
Period size: 40 Copynumber: 1.9 Consensus size: 40
53208449 GCCGATGCCA
*
53208459 TGTCCCAAACAGGTCTTACACTAACTTTCATATATCGACG
1 TGTCCCAAACAGGTCTTACACTAACTCTCATATATCGACG
* * ** *
53208499 TGTCCCAGATAGGTCTTACACTGGCTCTCATTTATCG
1 TGTCCCAAACAGGTCTTACACTAACTCTCATATATCG
53208536 GTGTCGATGC
Statistics
Matches: 31, Mismatches: 6, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
40 31 1.00
ACGTcount: A:0.25, C:0.27, G:0.16, T:0.32
Consensus pattern (40 bp):
TGTCCCAAACAGGTCTTACACTAACTCTCATATATCGACG
Found at i:53208561 original size:89 final size:89
Alignment explanation
Indices: 53208408--53208572 Score: 276
Period size: 89 Copynumber: 1.9 Consensus size: 89
53208398 AGGCCGATGC
* *
53208408 CGTGTCCCAGATAGTTCTTACACTGGCTCTTATCTATCAGTGCCGATGCCATGTCCCAAACAGGT
1 CGTGTCCCAGATAGGTCTTACACTGGCTCTCATCTATCAGTGCCGATGCCATGTCCCAAACAGGT
53208473 CTTACACTAACTTTCATATATCGA
66 CTTACACTAACTTTCATATATCGA
* * * *
53208497 CGTGTCCCAGATAGGTCTTACACTGGCTCTCATTTATCGGTGTCGATGCCATGTCCCAAGCAGGT
1 CGTGTCCCAGATAGGTCTTACACTGGCTCTCATCTATCAGTGCCGATGCCATGTCCCAAACAGGT
53208562 CTTACACTAAC
66 CTTACACTAAC
53208573 ACACAACAAA
Statistics
Matches: 70, Mismatches: 6, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
89 70 1.00
ACGTcount: A:0.23, C:0.28, G:0.18, T:0.30
Consensus pattern (89 bp):
CGTGTCCCAGATAGGTCTTACACTGGCTCTCATCTATCAGTGCCGATGCCATGTCCCAAACAGGT
CTTACACTAACTTTCATATATCGA
Found at i:53208656 original size:48 final size:48
Alignment explanation
Indices: 53208590--53208804 Score: 190
Period size: 46 Copynumber: 4.6 Consensus size: 48
53208580 AAACTGACGC
* *
53208590 CATGTCCCAGATAGGTCTTACACTAGCTTGTATATCTTGAGGTCGATG
1 CATGTCCCAGACATGTCTTACACTAGCTTGTATATCTTGAGGTCGATG
* ** ** *
53208638 CATGTCCCAGACATGTCTTACACTAG-TTCT-CGTCTCAATGTCGATG
1 CATGTCCCAGACATGTCTTACACTAGCTTGTATATCTTGAGGTCGATG
* * * * * *
53208684 CATGTCCCAGACATGTCTTACACTGGCTGGTATATC-TCAGGGCATATA
1 CATGTCCCAGACATGTCTTACACTAGCTTGTATATCTTGAGGTC-GATG
* * * * *
53208732 CATGTCCCAAACATGTCTTACACTGGCTCT-CA-AT-ATGTGGTCGATG
1 CATGTCCCAGACATGTCTTACACTAGCT-TGTATATCTTGAGGTCGATG
*
53208778 CATGTCCCAAACATGTCTTACACTAGC
1 CATGTCCCAGACATGTCTTACACTAGC
53208805 ACATATCACC
Statistics
Matches: 134, Mismatches: 28, Indels: 12
0.77 0.16 0.07
Matches are distributed among these distances:
46 64 0.48
47 14 0.10
48 56 0.42
ACGTcount: A:0.24, C:0.26, G:0.19, T:0.31
Consensus pattern (48 bp):
CATGTCCCAGACATGTCTTACACTAGCTTGTATATCTTGAGGTCGATG
Found at i:53208692 original size:187 final size:185
Alignment explanation
Indices: 53208155--53208711 Score: 466
Period size: 196 Copynumber: 2.9 Consensus size: 185
53208145 AACACATCAA
* * * ** * *** * *
53208155 GTCGATGTCATGTCCCAGATAGGTCTTACACTGACTTTCATATATCGAGGTCGATGCCGTGTCCC
1 GTCGATGCCATGTCCAAGACAGGTCTTACACT-A-AATCACATATCGAAACCGACGCCATGTCCC
* * * * * **
53208220 AGATAGGTTTTACACTAGCTCTCATCTATCAGTGTCGATGCCATGTCCCAGACATGTCTTATGCT
64 AGATAGGTCTTACACTAGCTCTTATCTATCAGTGCCGATGCCATGTCCCAAACAGGTCTTACACT
*
53208285 GACTTTCATATATCGAGGCCGATGTTGTGTCCCAGACAAGTCTTACACTGGCTCTCATCTATCAG
129 AACTTTCATATATCGA---C-A-----TGTCCCAGACAAGTCTTACACTGGCTCTCATCTATCAG
53208350 T
185 T
* * ** * *
53208351 GTCGATGCCATGTCCTAGACAGGTCTTACACTAAATTTCATATATCGAGGCCGATGCCGTGTCCC
1 GTCGATGCCATGTCCAAGACAGGTCTTACACTAAA--TCACATATCGAAACCGACGCCATGTCCC
* *
53208416 AGATAGTTCTTACACTGGCTCTTATCTATCAGTGCCGATGCCATGTCCCAAACAGGTCTTACACT
64 AGATAGGTCTTACACTAGCTCTTATCTATCAGTGCCGATGCCATGTCCCAAACAGGTCTTACACT
* * * * *
53208481 AACTTTCATATATCGACGTGTCCCAGATAGGTCTTACACTGGCTCTCATTTATCGGT
129 AACTTTCATATATCGACATGTCCCAGACAAGTCTTACACTGGCTCTCATCTATCAGT
*
53208538 GTCGATGCCATGTCCCAAG-CAGGTCTTACACTAACA-CACA-A-C-AAACTGACGCCATGTCCC
1 GTCGATGCCATGT-CCAAGACAGGTCTTACACTAA-ATCACATATCGAAACCGACGCCATGTCCC
* * * * *
53208598 AGATAGGTCTTACACTAGCTTGTATATCT-TGAG-GTCGATG-CATGTCCCAGACATGTCTTACA
64 AGATAGGTCTTACACTAGC-TCT-TATCTATCAGTGCCGATGCCATGTCCCAAACAGGTCTTACA
* * *
53208660 CTAGTTCTCGTCTCA-ATGTCGATGCATGTCCCAGACATGTCTTACACTGGCT
127 CTA--ACT--T-TCATATATCGA--CATGTCCCAGACAAGTCTTACACTGGCT
53208712 GGTATATCTC
Statistics
Matches: 308, Mismatches: 40, Indels: 35
0.80 0.10 0.09
Matches are distributed among these distances:
181 23 0.07
182 36 0.12
183 8 0.03
184 6 0.02
185 10 0.03
186 3 0.01
187 88 0.29
188 5 0.02
193 1 0.00
195 1 0.00
196 127 0.41
ACGTcount: A:0.24, C:0.27, G:0.19, T:0.30
Consensus pattern (185 bp):
GTCGATGCCATGTCCAAGACAGGTCTTACACTAAATCACATATCGAAACCGACGCCATGTCCCAG
ATAGGTCTTACACTAGCTCTTATCTATCAGTGCCGATGCCATGTCCCAAACAGGTCTTACACTAA
CTTTCATATATCGACATGTCCCAGACAAGTCTTACACTGGCTCTCATCTATCAGT
Found at i:53208706 original size:94 final size:94
Alignment explanation
Indices: 53208590--53208804 Score: 247
Period size: 94 Copynumber: 2.3 Consensus size: 94
53208580 AAACTGACGC
* * * * * * *
53208590 CATGTCCCAGATAGGTCTTACACTAGCTTGTATATCTTGAGGTC-GATGCATGTCCCAGACATGT
1 CATGTCCCAGACATGTCTTACACTAGCTGGTATATC-TCAGGGCAGATACATGTCCCAAACATGT
* * *
53208654 CTTACACTAGTTCTC-GTCTCAAT-GTCGATG
65 CTTACACTAGCTCTCAATAT--ATGGTCGATG
* *
53208684 CATGTCCCAGACATGTCTTACACTGGCTGGTATATCTCAGGGCATATACATGTCCCAAACATGTC
1 CATGTCCCAGACATGTCTTACACTAGCTGGTATATCTCAGGGCAGATACATGTCCCAAACATGTC
* *
53208749 TTACACTGGCTCTCAATATGTGGTCGATG
66 TTACACTAGCTCTCAATATATGGTCGATG
*
53208778 CATGTCCCAAACATGTCTTACACTAGC
1 CATGTCCCAGACATGTCTTACACTAGC
53208805 ACATATCACC
Statistics
Matches: 102, Mismatches: 16, Indels: 6
0.82 0.13 0.05
Matches are distributed among these distances:
93 6 0.06
94 94 0.92
95 2 0.02
ACGTcount: A:0.24, C:0.26, G:0.19, T:0.31
Consensus pattern (94 bp):
CATGTCCCAGACATGTCTTACACTAGCTGGTATATCTCAGGGCAGATACATGTCCCAAACATGTC
TTACACTAGCTCTCAATATATGGTCGATG
Found at i:53215075 original size:25 final size:25
Alignment explanation
Indices: 53215041--53215110 Score: 122
Period size: 25 Copynumber: 2.8 Consensus size: 25
53215031 CAGGCCTATT
53215041 TTCACAGCTCGTGTGAGCATTCTAA
1 TTCACAGCTCGTGTGAGCATTCTAA
* *
53215066 TTCACAGCTCGTCTGAGCATTCTGA
1 TTCACAGCTCGTGTGAGCATTCTAA
53215091 TTCACAGCTCGTGTGAGCAT
1 TTCACAGCTCGTGTGAGCAT
53215111 ACATGTACAG
Statistics
Matches: 42, Mismatches: 3, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
25 42 1.00
ACGTcount: A:0.21, C:0.26, G:0.21, T:0.31
Consensus pattern (25 bp):
TTCACAGCTCGTGTGAGCATTCTAA
Found at i:53217119 original size:17 final size:17
Alignment explanation
Indices: 53217099--53217132 Score: 50
Period size: 17 Copynumber: 2.0 Consensus size: 17
53217089 GTCTCAATCG
* *
53217099 TGTGTGACACACGGCCA
1 TGTGTAACACACAGCCA
53217116 TGTGTAACACACAGCCA
1 TGTGTAACACACAGCCA
53217133 GACGAAACGG
Statistics
Matches: 15, Mismatches: 2, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
17 15 1.00
ACGTcount: A:0.29, C:0.29, G:0.24, T:0.18
Consensus pattern (17 bp):
TGTGTAACACACAGCCA
Found at i:53219187 original size:68 final size:68
Alignment explanation
Indices: 53219062--53219190 Score: 197
Period size: 67 Copynumber: 1.9 Consensus size: 68
53219052 ACATCTCGTC
* * *
53219062 TGAGCAGCATCATGTAGCTAACATTCTGACCTACAGCTCATATGAGCAAGCCCATTTCACAACTC
1 TGAGCAGCATCATGTAGCTAACATTCAGACCCACAGCTCATATGAGAAAGCCCATTTCACAACTC
53219127 ATA
66 ATA
* *
53219130 TGAGTAGCATCATG-AGCTAACATTCAGACCCACAGCTCATGTGAGAAAAGCCCATTTCACA
1 TGAGCAGCATCATGTAGCTAACATTCAGACCCACAGCTCATATGAG-AAAGCCCATTTCACA
53219191 GCTTGTGTGA
Statistics
Matches: 55, Mismatches: 5, Indels: 2
0.89 0.08 0.03
Matches are distributed among these distances:
67 28 0.51
68 27 0.49
ACGTcount: A:0.33, C:0.27, G:0.16, T:0.23
Consensus pattern (68 bp):
TGAGCAGCATCATGTAGCTAACATTCAGACCCACAGCTCATATGAGAAAGCCCATTTCACAACTC
ATA
Found at i:53220773 original size:42 final size:42
Alignment explanation
Indices: 53220653--53220779 Score: 123
Period size: 42 Copynumber: 3.0 Consensus size: 42
53220643 GATGGGTTAG
*
53220653 GGGTGTTACAGAGATAGGT-TAAAAGTTGTTGATGAAGGTTTATG
1 GGGTGTT--AGAGATA-GTATAAAAGTTGTTGATGAAGGTTTATA
* * * **
53220697 GGGTGTTAGATATAGTCTAAAAGCTACT-AGTGAAGGTTTATA
1 GGGTGTTAGAGATAGTATAAAAGTTGTTGA-TGAAGGTTTATA
* * *
53220739 GGGTGTTGGAGATGGTATAGAAGTTGTTGATGAAGGTTTAT
1 GGGTGTTAGAGATAGTATAAAAGTTGTTGATGAAGGTTTAT
53220780 GTAACACCCA
Statistics
Matches: 67, Mismatches: 13, Indels: 8
0.76 0.15 0.09
Matches are distributed among these distances:
41 3 0.04
42 56 0.84
43 1 0.01
44 7 0.10
ACGTcount: A:0.29, C:0.03, G:0.33, T:0.35
Consensus pattern (42 bp):
GGGTGTTAGAGATAGTATAAAAGTTGTTGATGAAGGTTTATA
Found at i:53222463 original size:28 final size:28
Alignment explanation
Indices: 53222432--53222498 Score: 91
Period size: 28 Copynumber: 2.4 Consensus size: 28
53222422 TCTTAATGAC
*
53222432 AATTTTAAAGTTGGATTAT-TGATTCCAT
1 AATTTGAAAGTTGGATTATAT-ATTCCAT
53222460 AATTTGAAAGTTGGATTATATATTCCAT
1 AATTTGAAAGTTGGATTATATATTCCAT
* *
53222488 ACTCTGAAAGT
1 AATTTGAAAGT
53222499 ATTTGATAAT
Statistics
Matches: 35, Mismatches: 3, Indels: 2
0.88 0.08 0.05
Matches are distributed among these distances:
28 34 0.97
29 1 0.03
ACGTcount: A:0.34, C:0.09, G:0.15, T:0.42
Consensus pattern (28 bp):
AATTTGAAAGTTGGATTATATATTCCAT
Found at i:53224888 original size:29 final size:29
Alignment explanation
Indices: 53224837--53224893 Score: 78
Period size: 29 Copynumber: 2.0 Consensus size: 29
53224827 AAGGAAGAGT
* * * *
53224837 GAAGAAAGGAGGGAGTTTGAAGGTTAAAA
1 GAAGAAAGGAGAGAGTATAAAGGCTAAAA
53224866 GAAGAAAGGAGAGAGTATAAAGGCTAAA
1 GAAGAAAGGAGAGAGTATAAAGGCTAAA
53224894 GGCAGTCTTG
Statistics
Matches: 24, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
29 24 1.00
ACGTcount: A:0.49, C:0.02, G:0.35, T:0.14
Consensus pattern (29 bp):
GAAGAAAGGAGAGAGTATAAAGGCTAAAA
Found at i:53226999 original size:43 final size:42
Alignment explanation
Indices: 53226938--53227047 Score: 134
Period size: 43 Copynumber: 2.6 Consensus size: 42
53226928 CAATGCCAAC
*
53226938 GTCCCAGACGTGATCTTACATGTAATCAAATATCGATACC-ACT
1 GTCCCAGACGTGGTCTTACATGTAATCAAATAT-GATACCTA-T
* *
53226981 GTCCCAGACAG-GGTCTTACATGAAATCAAATATGATGCCTAT
1 GTCCCAGAC-GTGGTCTTACATGTAATCAAATATGATACCTAT
* *
53227023 GTCCCAGATGTGGTCTTACACGTAA
1 GTCCCAGACGTGGTCTTACATGTAA
53227048 ATCATAAGTC
Statistics
Matches: 58, Mismatches: 6, Indels: 7
0.82 0.08 0.10
Matches are distributed among these distances:
41 1 0.02
42 26 0.45
43 30 0.52
44 1 0.02
ACGTcount: A:0.31, C:0.24, G:0.18, T:0.27
Consensus pattern (42 bp):
GTCCCAGACGTGGTCTTACATGTAATCAAATATGATACCTAT
Found at i:53227050 original size:43 final size:42
Alignment explanation
Indices: 53226938--53227087 Score: 121
Period size: 43 Copynumber: 3.5 Consensus size: 42
53226928 CAATGCCAAC
* * *
53226938 GTCCCAGACGTGATCTTACATGT-AATCAAATATCGATACCACT
1 GTCCCAGATGTGGTCTTACACGTAAATCAAATAT-GATACCA-T
* * *
53226981 GTCCCAGACAG-GGTCTTACATG-AAATCAAATATGATGCCTAT
1 GTCCCAGA-TGTGGTCTTACACGTAAATCAAATATGATACC-AT
*
53227023 GTCCCAGATGTGGTCTTACACGTAAATCATAAGTCA--ATTCCAAT
1 GTCCCAGATGTGGTCTTACACGTAAATCA-AA-T-ATGATACC-AT
*
53227067 GTCCCAGATGTGGGCTTACAC
1 GTCCCAGATGTGGTCTTACAC
53227088 AATAACACAT
Statistics
Matches: 91, Mismatches: 8, Indels: 15
0.80 0.07 0.13
Matches are distributed among these distances:
41 1 0.01
42 24 0.26
43 35 0.38
44 29 0.32
45 1 0.01
46 1 0.01
ACGTcount: A:0.31, C:0.24, G:0.18, T:0.27
Consensus pattern (42 bp):
GTCCCAGATGTGGTCTTACACGTAAATCAAATATGATACCAT
Found at i:53239739 original size:46 final size:46
Alignment explanation
Indices: 53239689--53239864 Score: 173
Period size: 46 Copynumber: 3.8 Consensus size: 46
53239679 TGGTTGAGCA
*
53239689 TCCGAACTCGTTGAGTTGAGTTCGAGTTCACTTATGGATGCGAATG
1 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAATG
* * * * *
53239735 TCCGAACTCGTTGAGTTGAGTTCGAGTTC-GTGA--AATG-TAACTAGG
1 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAA-T--G
*
53239780 CATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAACG
1 --TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAATG
* * *
53239828 -CCCAAGCTCATTGAGTTGAGTCCGAGTTCGCTTATGG
1 TCCGAA-CTCGTTGAGTTGAGTCCGAGTTCACTTATGG
53239865 GCGGGTTACA
Statistics
Matches: 107, Mismatches: 13, Indels: 20
0.76 0.09 0.14
Matches are distributed among these distances:
42 2 0.02
43 4 0.04
45 7 0.07
46 58 0.54
47 28 0.26
48 3 0.03
50 3 0.03
51 2 0.02
ACGTcount: A:0.22, C:0.20, G:0.28, T:0.30
Consensus pattern (46 bp):
TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAATG
Found at i:53239798 original size:93 final size:93
Alignment explanation
Indices: 53239686--53239857 Score: 283
Period size: 93 Copynumber: 1.8 Consensus size: 93
53239676 GGATGGTTGA
* * * *
53239686 GCATCCGAACTCGTTGAGTTGAGTTCGAGTTCACTTATGGATGCGAATGTCCGAA-CTCGTTGAG
1 GCATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAACG-CCCAAGCTCATTGAG
*
53239750 TTGAGTTCGAGTTCGTGAAATGTAACTAG
65 TTGAGTCCGAGTTCGTGAAATGTAACTAG
53239779 GCATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAACGCCCAAGCTCATTGAGT
1 GCATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAACGCCCAAGCTCATTGAGT
53239844 TGAGTCCGAGTTCG
66 TGAGTCCGAGTTCG
53239858 CTTATGGGCG
Statistics
Matches: 73, Mismatches: 5, Indels: 2
0.91 0.06 0.03
Matches are distributed among these distances:
92 4 0.05
93 69 0.95
ACGTcount: A:0.23, C:0.20, G:0.28, T:0.29
Consensus pattern (93 bp):
GCATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAACGCCCAAGCTCATTGAGT
TGAGTCCGAGTTCGTGAAATGTAACTAG
Found at i:53241324 original size:29 final size:29
Alignment explanation
Indices: 53241292--53241384 Score: 80
Period size: 29 Copynumber: 3.2 Consensus size: 29
53241282 AATTTGATAA
53241292 TGAAAGTTGAAAGAAGGAAGTAGGGAGCT
1 TGAAAGTTGAAAGAAGGAAGTAGGGAGCT
* ** ** * *
53241321 TGAAGGAAGAGTGAA-GAAATGAGGGAGTT
1 TGAAAGTTGAAAGAAGGAAGT-AGGGAGCT
* * *
53241350 TGAAGGTTGAAAGAAGAAAGCAGGGAGCT
1 TGAAAGTTGAAAGAAGGAAGTAGGGAGCT
53241379 TGAAAG
1 TGAAAG
53241385 CTAAAAGTAG
Statistics
Matches: 46, Mismatches: 16, Indels: 4
0.70 0.24 0.06
Matches are distributed among these distances:
28 4 0.09
29 40 0.87
30 2 0.04
ACGTcount: A:0.42, C:0.03, G:0.39, T:0.16
Consensus pattern (29 bp):
TGAAAGTTGAAAGAAGGAAGTAGGGAGCT
Found at i:53241391 original size:29 final size:29
Alignment explanation
Indices: 53241333--53241391 Score: 66
Period size: 29 Copynumber: 2.0 Consensus size: 29
53241323 AAGGAAGAGT
* * * *
53241333 GAAGAAATGAGGGAGTTTGAAGGTTGAAA
1 GAAGAAATGAGGGAGCTTGAAAGCTAAAA
53241362 GAAGAAA-GCAGGGAGCTTGAAAGCTAAAA
1 GAAGAAATG-AGGGAGCTTGAAAGCTAAAA
53241391 G
1 G
53241392 TAGTTATGTG
Statistics
Matches: 25, Mismatches: 4, Indels: 2
0.81 0.13 0.06
Matches are distributed among these distances:
28 1 0.04
29 24 0.96
ACGTcount: A:0.44, C:0.05, G:0.36, T:0.15
Consensus pattern (29 bp):
GAAGAAATGAGGGAGCTTGAAAGCTAAAA
Found at i:53245809 original size:29 final size:26
Alignment explanation
Indices: 53245773--53245841 Score: 75
Period size: 29 Copynumber: 2.4 Consensus size: 26
53245763 AGAAAGTAGT
53245773 GAGCTTGAAGGAACACTGAAGAAATGAGG
1 GAGCTTGAAGGAA-A--GAAGAAATGAGG
*
53245802 GAGTTTGAAAGTTGAAAGAAGAAATGAGG
1 GAGCTTG-AAG--GAAAGAAGAAATGAGG
53245831 GAGCTTGAAGG
1 GAGCTTGAAGG
53245842 CTAAATGCAG
Statistics
Matches: 35, Mismatches: 2, Indels: 9
0.76 0.04 0.20
Matches are distributed among these distances:
26 1 0.03
28 3 0.09
29 24 0.69
30 3 0.09
31 1 0.03
32 3 0.09
ACGTcount: A:0.41, C:0.06, G:0.36, T:0.17
Consensus pattern (26 bp):
GAGCTTGAAGGAAAGAAGAAATGAGG
Found at i:53246466 original size:29 final size:29
Alignment explanation
Indices: 53246430--53246514 Score: 107
Period size: 29 Copynumber: 2.9 Consensus size: 29
53246420 AATGAAAGTG
*
53246430 GAAAGAAGAAAGTAGGGAGCTTGAAGGAA
1 GAAAGAAGAAAGGAGGGAGCTTGAAGGAA
** * **
53246459 GAGTGAAGAAAGGAGGGAGTTTGAAGGTT
1 GAAAGAAGAAAGGAGGGAGCTTGAAGGAA
*
53246488 GAAAGAAGAAAGGAGGGAGCATGAAGG
1 GAAAGAAGAAAGGAGGGAGCTTGAAGG
53246515 CTAAAGGTAG
Statistics
Matches: 46, Mismatches: 10, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
29 46 1.00
ACGTcount: A:0.44, C:0.02, G:0.42, T:0.12
Consensus pattern (29 bp):
GAAAGAAGAAAGGAGGGAGCTTGAAGGAA
Found at i:53247067 original size:627 final size:636
Alignment explanation
Indices: 53245518--53249659 Score: 3305
Period size: 668 Copynumber: 6.4 Consensus size: 636
53245508 GGATGTTACA
* * *
53245518 GGAACAAATAACCAGAAAGGAGAATCAACTCCCAAATAGGGAACATAATAGGACCATAATACCAT
1 GGAACAAATAACCAG--AGGAGAATCAACTGCCAAATAGAGAACATAATAGGACCATAACACCAT
* * * * * * *
53245583 GGACTCATCAAGACTTTAAATAGATTTACTCCTAAAGCAG-ATGTGCGAGAAAGTAAAGAATCGT
64 GGACTCATAAAGACTTTAAACAGCTTTTCTCCTAAATCAGAATGTGCGAGAAGGTAGAGAATC-T
* * * * * * **
53245647 TGTATAAGCGATTATAAAAAGGGCTGACAATGCAAGAGTTTTTATTCCAAACATGTTAAAGTAAA
128 TGTATAAGCGGTTATAAAAAGGGCTAACCATGCAAGAGTTTCTATTCCAAACATTTTAGAGTCGA
* * *
53245712 AAATAAGTAAA-AATGAAAAGGAT-AGGAAATGTGATGATGAGAGATGAAGGAAGAAAGTAGTGA
193 AAATAAGTAAACAATGAAAAGGATGA-GAAATATGATGATGAGAGTTGAAGGAAGAAAGTAGGGA
* * * * * *
53245775 GCTTGAAGGAACACTGAAGAAATGAGGGAGTTTGAAAGTTGAAAGAAGAAATGAGGGAGCTTGAA
257 GCTTGAAGGAAGAGTGAAGAAAGGAGGGAGTTTGAAGGTTGAAAGAAGAAAGGAGGGAGCATGAA
* * *
53245840 GGCTAAATGCAGTCTTGTGATTTTTGTGTAATTTTTGTAGGTGTAATTTTCATTTTTTTTTCATT
322 GGCTAAAGGCAGTCTTGTGATTTTTGTGTAATTTTCG-A---GTAA---TC-----CTTTTCATT
* ** * *
53245905 TTGTCTTATTCTAAATAAAAAAGTAAAACTATATTAGTGCAACGAAGACCACAATATAACCATTT
375 TTGTCTTATT-T-AAT-AAAAA--AAAATTATATTAGTGGGACTAAAACCACAATATAACCATTT
*
53245970 TTTATATTGAAAATGCTAACTGTTGTTATTGTTTTATATTACTAATCACCATATTTACTCGTATT
435 TTTATATTGAAAATGCTAACTGTTGTTATGGTTTTATATTACTAATCACCATATTTACTCGTATT
* * * **
53246035 ATTATAGTATTTGAATTCAATTTTTTTGATAAGAGACTTTGTTGGAGGTTGCATTATAGGTTATT
500 ATTATAGTATTTGGATTCAATTTTTTCGATAAGAGACTTTGTTGGAGGTGGCATTGCAGGTTATT
* * * *
53246100 GTGATCAATTTTAGATGTAATGAATTTGAGACGTGCATGTCATTACTATAACACCATATTTCCCC
565 GTGATC------A-AT-T--T-AA--T-AGACGTACATATCTTTACTATAATACCATATTTCCCC
* *
53246165 AAAATA-ATGTGTAAAAATTAGCAT
616 AAAA-ACA--TGT-AACATTAGCAG
* * * *
53246189 GGAACAATTAACTAGA-GAGGAAATTAACTGCCAAAATA-AGGAACATAATAGGACCATAATACC
1 GGAACAAATAACCAGAGGA-G-AATCAACTGCC-AAATAGA-GAACATAATAGGACCATAACACC
* * ** * *
53246252 ATGGACTCATAAAGAATTTAAACAACTTTTGACCTAAAGCAGAACGTGCGAGAAGGTAGAGAATC
62 ATGGACTCATAAAGACTTTAAACAGCTTTTCTCCTAAATCAGAATGTGCGAGAAGGTAGAGAATC
* *
53246317 ATTGTTTAAGCGATTATAAAAAGGGCTAACCATGCAAGAGTTTCTATTCCAAACATTTTAGAGTC
127 -TTGTATAAGCGGTTATAAAAAGGGCTAACCATGCAAGAGTTTCTATTCCAAACATTTTAGAGTC
* * * * * *
53246382 GAAAATAAGTAAGCAATGAAAAGGATGAGAAATTTGATAATGAAAGTGGAAAGAAGAAAGTAGGG
191 GAAAATAAGTAAACAATGAAAAGGATGAGAAATATGATGATGAGAGTTGAAGGAAGAAAGTAGGG
53246447 AGCTTGAAGGAAGAGTGAAGAAAGGAGGGAGTTTGAAGGTTGAAAGAAGAAAGGAGGGAGCATGA
256 AGCTTGAAGGAAGAGTGAAGAAAGGAGGGAGTTTGAAGGTTGAAAGAAGAAAGGAGGGAGCATGA
*
53246512 AGGCTAAAGGTAGTCTTGTGATTTTTGTGTAATTTTC-A-T-ATCCTTTTCATTTTGTCTTA-TT
321 AGGCTAAAGGCAGTCTTGTGATTTTTGTGTAATTTTCGAGTAATCCTTTTCATTTTGTCTTATTT
*
53246573 -AT-AAAAAAAATTATATTAGTGGGACTAAAACCACAATCTAACCATTTTTTATATTGAAAATGC
386 AATAAAAAAAAATTATATTAGTGGGACTAAAACCACAATATAACCATTTTTTATATTGAAAATGC
* * * * **
53246636 TAACTATTGTTATGGTTTTATATTACTAATCACCATATTTGCTCATATTATTATAATATTTATAT
451 TAACTGTTGTTATGGTTTTATATTACTAATCACCATATTTACTCGTATTATTATAGTATTTGGAT
* *
53246701 TCAATTTTTTCGACAAGAGACTTTGTTGGAGGTGGCATTGCAGGTTATTTTGATCAATTT-A-AG
516 TCAATTTTTTCGATAAGAGACTTTGTTGGAGGTGGCATTGCAGGTTATTGTGATCAATTTAATAG
*
53246764 ACGTACATATCTTTACTATAATACCATATTCCCCCAAAAACATG-AACATTAGCAG
581 ACGTACATATCTTTACTATAATACCATATTTCCCCAAAAACATGTAACATTAGCAG
* * *
53246819 GGAACAAATAACCAGAGGAGAATCAACTTCCAAATAGAGAACATAATAGGAACATAATACCATGG
1 GGAACAAATAACCAGAGGAGAATCAACTGCCAAATAGAGAACATAATAGGACCATAACACCATGG
*
53246884 ACTCATAAAGACTTTAAACAGCTTTTCTCCTAAATCAAAATGTGCGAG-AGGTAGAGAATCTCTG
66 ACTCATAAAGACTTTAAACAGCTTTTCTCCTAAATCAGAATGTGCGAGAAGGTAGAGAATCT-TG
* * * * * **
53246948 TATAAGCGGTTATAAAAAGGCCTAACCATTCGAGAGATTCTATTCAAAATGTTTTAGAGTCGAAA
130 TATAAGCGGTTATAAAAAGGGCTAACCATGCAAGAGTTTCTATTCCAAACATTTTAGAGTCGAAA
*
53247013 ATAAGTAAACAATGAAAAGGATGAGAAATATAATGATGAGAGTTGAAGGAAGAAA-TGAGGGAGC
195 ATAAGTAAACAATGAAAAGGATGAGAAATATGATGATGAGAGTTGAAGGAAGAAAGT-AGGGAGC
* **** * ** * ***** * *
53247077 TTGAAGGCTAA-AG-GCAG--TCTTGTGA-TTT--TTG-TGTAA-TTTTCA-TA-GGTG--T-AA
259 TTGAAGG--AAGAGTGAAGAAAGGAGGGAGTTTGAAGGTTGAAAGAAGAAAGGAGGGAGCATGAA
** ** * * * * * * ** **** * **
53247128 -TTTTTA-G-ATTCTTAT-AATTTTGTCT--TATTCTAAAAAAAAATTT-ATATTAG----ATGG
322 GGCTAAAGGCAGTCTTGTGATTTTTGTGTAATTTTCGAGTAATCCTTTTCAT-TTTGTCTTATTT
* * * * * **** * *** * * ** * *
53247182 ACTAAAACCACAA-TATAATCGT-TTTTTATATTGAAAATTCTAACTGTTGTTTTCAT-TT-TAT
386 AATAAAA-AAAAATTATATTAGTGGGACTAAAACCACAA-TATAACCATT-TTTT-ATATTGAAA
* * * * * *
53247243 AT--T-AC------TA-----AT-----------CACCAAATTTGCTCGTTTTATTAAACTATTT
447 ATGCTAACTGTTGTTATGGTTTTATATTACTAATCACCATATTTACTCGTATTATTATAGTATTT
*
53247283 GGATTCAATTTTTTCGATAAGAGACATTT-TTTGAGGTGGCATTGCAGGTTATTGTGATCAATTT
512 GGATTCAATTTTTTCGATAAGAGAC-TTTGTTGGAGGTGGCATTGCAGGTTATTGTGATCAA--T
* * * *
53247347 GAGACGTAATGAAATTGAGATGTACATGTCTTTATTATAATACCATATTTCCCCAAAAACGTGTA
574 ------T--T--AA-T-AGACGTACATATCTTTACTATAATACCATATTTCCCCAAAAACATGT-
53247412 AACATTAGCAG
626 AACATTAGCAG
* * * *
53247423 GGAACAAATAACAAAAGAGGAGAATAAACTGCCAAATAGGGAACATAATAGGACCATAAAACCAT
1 GGAACAAATAAC--CAGAGGAGAATCAACTGCCAAATAGAGAACATAATAGGACCATAACACCAT
* * * *
53247488 GGACTCAAAAAGATTTTAAACAACTTTTCTCCTAAATCAGAATGTGCGAGAAGGTAGAGAATCGC
64 GGACTCATAAAGACTTTAAACAGCTTTTCTCCTAAATCAGAATGTGCGAGAAGGTAGAGAATC-T
* * * * ** *
53247553 TATAGAAGCGGTTGTAAAAAGGGTTCCCCATGCAAGAGTCTCTATTCCAAACATTTTAGAGTTC-
128 TGTATAAGCGGTTATAAAAAGGGCTAACCATGCAAGAGTTTCTATTCCAAACATTTTAGAG-TCG
* * * * *
53247617 AAAATAAGTAAACAGTGAAAAGGATGAGAAATATAATGACGAAAGTTCAAGGAAGAAAGTAGGGA
192 AAAATAAGTAAACAATGAAAAGGATGAGAAATATGATGATGAGAGTTGAAGGAAGAAAGTAGGGA
* * *
53247682 GCTTGAAGGAAAAGTGAAGAAATGAGGGAGTTTGAAGGTTGAAAGAAGAAAGGAGGGTGCATGAA
257 GCTTGAAGGAAGAGTGAAGAAAGGAGGGAGTTTGAAGGTTGAAAGAAGAAAGGAGGGAGCATGAA
* * *
53247747 GGCTAAAGGCAGTCTTGTGAATTTTGTGTAATTTTCGTACGTGTAATTTTCAGATTCCTGTGATT
322 GGCTAAAGGCAGTCTTGTGATTTTTGTGTAATTTTCG-A---GTAA---TC--CTT--T-TCATT
** * *
53247812 TTGTCTTATTCTAAATAAAAAAGAAAAATTATATTAGTGGGACTAAAACCACGGTTTAACTATTT
375 TTGTCTTATT-T-AAT--AAAA-AAAAATTATATTAGTGGGACTAAAACCACAATATAACCATTT
* * *
53247877 TCTATATTTAAAATGCTAACTGTTGATATGG-TTTATATTACTAATCACCATATTTACTCGTATT
435 TTTATATTGAAAATGCTAACTGTTGTTATGGTTTTATATTACTAATCACCATATTTACTCGTATT
* * *
53247941 ATTATAGTATTT-GATTCAATTTTTTCGATAAGAGACTTT-TTTGATGTGGCATTACAGGTTATT
500 ATTATAGTATTTGGATTCAATTTTTTCGATAAGAGACTTTGTTGGAGGTGGCATTGCAGGTTATT
* * * * *
53248004 GTAATCAATTTGAGACGTAATGAATTTGAGACATACATGTCTTTATTATAATACCATAATTCCCC
565 GTGATCAA--T------T--T-AA--T-AGACGTACATATCTTTACTATAATACCATATTTCCCC
*
53248069 AAAAACGTGTAAACATTAGCAG
616 AAAAACATGT-AACATTAGCAG
* * *
53248091 GGAACAAATAACCAGAAAGCAAAATCAACTACCAAATATG-GAACATAATAGGACCATAACACCA
1 GGAACAAATAACCAG--AGGAGAATCAACTGCCAAATA-GAGAACATAATAGGACCATAACACCA
* * * * *
53248155 TGGACTTATAAAGGCTTTAAACAGATTTTCTCCTAAATCAAAATGTGCGAGAAGGT-GCATAATC
63 TGGACTCATAAAGACTTTAAACAGCTTTTCTCCTAAATCAGAATGTGCGAGAAGGTAG-AGAATC
* * * * * *
53248219 TTTATATAAGGGGTTATAAAAAGGGCTGACCATTCAACAGTTTCTATTCCAAACATTTTAGAGTA
127 -TTGTATAAGCGGTTATAAAAAGGGCTAACCATGCAAGAGTTTCTATTCCAAACATTTTAGAGTC
* * * * *
53248284 AAAAATAAGTAAACAATGAAAAGGATGAGAAATATGATTATGAGAGTTGAAAGAGGAAATTAGGG
191 GAAAATAAGTAAACAATGAAAAGGATGAGAAATATGATGATGAGAGTTGAAGGAAGAAAGTAGGG
* ** * *** *
53248349 AGCTCGAAGGAAGAGTGTTGAAAGGAGGGAGTTTGAAGGTTGAAAGAAAAAAGGACAAAGCTTGA
256 AGCTTGAAGGAAGAGTGAAGAAAGGAGGGAGTTTGAAGGTTGAAAGAAGAAAGGAGGGAGCATGA
* * *
53248414 AGGCTAAAGGCAATCTTGTGATTTTTGTGTAATTTTCGTAGGTGTAATTTTTAGATCCTTGTGAT
321 AGGCTAAAGGCAGTCTTGTGATTTTTGTGTAATTTTCG-A---G-------TA-ATCCTTTTCAT
* ** * *
53248479 TTTGTCTTATTTTAAATAAAAAAAAGAAAGAAAAATTATATTAGTAGGACTAAGGCCATAGTATA
374 TTTGTCTTA-TTT-AAT-------A-AAA-AAAAATTATATTAGTGGGACTAAAACCACAATATA
* * *
53248544 ACCATTTTTTATATTGAAAATGTTAACTGTTGTTATGGTTTTATATTTCTAATCACCATATTTGC
428 ACCATTTTTTATATTGAAAATGCTAACTGTTGTTATGGTTTTATATTACTAATCACCATATTTAC
* * * * *
53248609 TCGTATTATTATAGTATTTGGATTCAATTATTTCAATAAGAGATTTTGTTGAAGGTGGCATTGTA
493 TCGTATTATTATAGTATTTGGATTCAATTTTTTCGATAAGAGACTTTGTTGGAGGTGGCATTGCA
* * *
53248674 GGTTATTGTCATAAATTTGAGGCATAATGAATTTGAGACGTACATGTCTTTACTATAATACCATA
558 GGTTATTGTGATCAA--T------T--T-AA--T-AGACGTACATATCTTTACTATAATACCATA
* * * *
53248739 TTTCTCCAAGAACGTGTAACATTAGTAG
609 TTTCCCCAAAAACATGTAACATTAGCAG
* *
53248767 GGAACAAATAACTCGAGTGGAGAATCAACTGCCAAATATG-GAACATAATAAGACCATAACACCA
1 GGAACAAATAAC-C-AGAGGAGAATCAACTGCCAAATA-GAGAACATAATAGGACCATAACACCA
* * * ** * *
53248831 TTGACTCAT-AAGACTTTAAACAG-TTTTCTCTTAAAGCAGAATGTATGAGAAGGTACAAAATCG
63 TGGACTCATAAAGACTTTAAACAGCTTTTCTCCTAAATCAGAATGTGCGAGAAGGTAGAGAATC-
* * * * *
53248894 ATGTATAAACGGTTATAAAAAGGGCTGACCATGCAATAGTTTCTATTCCAAACATTATAGAGTCG
127 TTGTATAAGCGGTTATAAAAAGGGCTAACCATGCAAGAGTTTCTATTCCAAACATTTTAGAGTCG
* *
53248959 AAAATAAGTAAACAATGAAAAGAATGAGAAACATGATGATGAGAGTTGAAGGAAGAAAGTAGGGA
192 AAAATAAGTAAACAATGAAAAGGATGAGAAATATGATGATGAGAGTTGAAGGAAGAAAGTAGGGA
*
53249024 GCTTGAAGGAAGAGTGAAGAAAGGAGGGAGTTTGAAGGTTGAAAGAAGAAATGAGGGAGCATGAA
257 GCTTGAAGGAAGAGTGAAGAAAGGAGGGAGTTTGAAGGTTGAAAGAAGAAAGGAGGGAGCATGAA
* *
53249089 GGCTAAAGGCTGTCTTGTGATTTTTGTGTAATTTTCGTAGTGTAAT--TTTTAGATTCTTGTGAT
322 GGCTAAAGGCAGTCTTGTGATTTTTGTGTAATTTTCG-A--GTAATCCTTTT-CA-T-TT-TG-T
* * * * * *
53249152 TTTATCTTATTCTTAAAAAAATTTATATTAGTGGGACTAAAACCACAATAAAACCGTTTTTTATA
379 CTTAT-TTA--ATAAAAAAAAATTATATTAGTGGGACTAAAACCACAATATAACCATTTTTTATA
* *
53249217 TTGAAAATGTTAACTGTTGATATGG-TTTATATTACTAATCACCATATTTACTCGTATTATTATA
441 TTGAAAATGCTAACTGTTGTTATGGTTTTATATTACTAATCACCATATTTACTCGTATTATTATA
* * * **
53249281 GTATTTGGATTCAATTATTTCGATAATAGACTTTGTTAGAGGTGAAATTGCAGGTTATTGTGATC
506 GTATTTGGATTCAATTTTTTCGATAAGAGACTTTGTTGGAGGTGGCATTGCAGGTTATTGTGATC
* * * *** * ** * *
53249346 AATTT--GAGACGTA-ATGAAT-TTGA-GA-CGGA-CATGTCTTTACTATAATACCA--T-A-AT
571 AATTTAATAGACGTACAT--ATCTTTACTATAATACCATAT-TTCCCCA-AA-AACATGTAACAT
53249400 T--C--
631 TAGCAG
** * * * *
53249402 ----CTCA-AA--A-AGCAGAATCAACTACCAAATATAGAACATAATAAGACCATAACACCATGG
1 GGAACAAATAACCAGAGGAGAATCAACTGCCAAATAGAGAACATAATAGGACCATAACACCATGG
* * * * *
53249459 GCTCATAAAGACTTTAAACAGCTTTTCTCCTAAATCAGAATGTGTGAGAAGGTACAGAATTTTTA
66 ACTCATAAAGACTTTAAACAGCTTTTCTCCTAAATCAGAATGTGCGAGAAGGTAGAGAA-TCTTG
*
53249524 TATAAGCGGTTATAAAAAGGACTAACCATGCAAGAGTTTCTATTCCAAACATTTTAGAGTCGAAA
130 TATAAGCGGTTATAAAAAGGGCTAACCATGCAAGAGTTTCTATTCCAAACATTTTAGAGTCGAAA
* *
53249589 ATAAGTAAACAATGAAAAGGATGAGAAATATGATGATAAGAGTTGAAGGAAGAAAGGAGGGAGCT
195 ATAAGTAAACAATGAAAAGGATGAGAAATATGATGATGAGAGTTGAAGGAAGAAAGTAGGGAGCT
53249654 TGAAGG
260 TGAAGG
53249660 CTAAAGGCGT
Statistics
Matches: 2860, Mismatches: 448, Indels: 370
0.78 0.12 0.10
Matches are distributed among these distances:
586 78 0.03
587 3 0.00
588 1 0.00
594 1 0.00
596 1 0.00
597 1 0.00
599 1 0.00
602 43 0.02
604 23 0.01
605 2 0.00
606 93 0.03
607 130 0.05
608 6 0.00
609 8 0.00
610 11 0.00
611 31 0.01
612 23 0.01
613 7 0.00
614 3 0.00
615 3 0.00
616 5 0.00
618 4 0.00
619 3 0.00
620 3 0.00
621 5 0.00
622 7 0.00
623 9 0.00
624 3 0.00
625 56 0.02
626 18 0.01
627 296 0.10
628 75 0.03
629 14 0.00
630 26 0.01
631 4 0.00
632 2 0.00
633 1 0.00
634 39 0.01
636 1 0.00
637 4 0.00
638 3 0.00
639 3 0.00
640 6 0.00
641 8 0.00
642 5 0.00
643 16 0.01
644 4 0.00
645 12 0.00
646 18 0.01
647 4 0.00
648 1 0.00
649 3 0.00
650 158 0.06
651 1 0.00
652 4 0.00
654 2 0.00
655 2 0.00
656 1 0.00
657 2 0.00
658 16 0.01
659 95 0.03
660 64 0.02
661 3 0.00
663 5 0.00
664 2 0.00
665 3 0.00
666 7 0.00
667 9 0.00
668 438 0.15
669 30 0.01
670 35 0.01
671 78 0.03
672 87 0.03
673 143 0.05
674 306 0.11
675 58 0.02
676 96 0.03
677 86 0.03
678 2 0.00
ACGTcount: A:0.38, C:0.12, G:0.19, T:0.31
Consensus pattern (636 bp):
GGAACAAATAACCAGAGGAGAATCAACTGCCAAATAGAGAACATAATAGGACCATAACACCATGG
ACTCATAAAGACTTTAAACAGCTTTTCTCCTAAATCAGAATGTGCGAGAAGGTAGAGAATCTTGT
ATAAGCGGTTATAAAAAGGGCTAACCATGCAAGAGTTTCTATTCCAAACATTTTAGAGTCGAAAA
TAAGTAAACAATGAAAAGGATGAGAAATATGATGATGAGAGTTGAAGGAAGAAAGTAGGGAGCTT
GAAGGAAGAGTGAAGAAAGGAGGGAGTTTGAAGGTTGAAAGAAGAAAGGAGGGAGCATGAAGGCT
AAAGGCAGTCTTGTGATTTTTGTGTAATTTTCGAGTAATCCTTTTCATTTTGTCTTATTTAATAA
AAAAAAATTATATTAGTGGGACTAAAACCACAATATAACCATTTTTTATATTGAAAATGCTAACT
GTTGTTATGGTTTTATATTACTAATCACCATATTTACTCGTATTATTATAGTATTTGGATTCAAT
TTTTTCGATAAGAGACTTTGTTGGAGGTGGCATTGCAGGTTATTGTGATCAATTTAATAGACGTA
CATATCTTTACTATAATACCATATTTCCCCAAAAACATGTAACATTAGCAG
Found at i:53248029 original size:16 final size:16
Alignment explanation
Indices: 53248004--53248035 Score: 55
Period size: 16 Copynumber: 2.0 Consensus size: 16
53247994 ACAGGTTATT
53248004 GTAATCAATTTGAGAC
1 GTAATCAATTTGAGAC
*
53248020 GTAATGAATTTGAGAC
1 GTAATCAATTTGAGAC
53248036 ATACATGTCT
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 15 1.00
ACGTcount: A:0.38, C:0.09, G:0.22, T:0.31
Consensus pattern (16 bp):
GTAATCAATTTGAGAC
Found at i:53249071 original size:29 final size:29
Alignment explanation
Indices: 53249003--53249090 Score: 95
Period size: 29 Copynumber: 3.0 Consensus size: 29
53248993 GATGATGAGA
* *
53249003 GTTGAAGGAAGAAAGTAGGGAGCTTGAAG
1 GTTGAAAGAAGAAAGGAGGGAGCTTGAAG
** ** *
53249032 GAAGAGTGAAGAAAGGAGGGAGTTTGAAG
1 GTTGAAAGAAGAAAGGAGGGAGCTTGAAG
* *
53249061 GTTGAAAGAAGAAATGAGGGAGCATGAAG
1 GTTGAAAGAAGAAAGGAGGGAGCTTGAAG
53249090 G
1 G
53249091 CTAAAGGCTG
Statistics
Matches: 46, Mismatches: 13, Indels: 0
0.78 0.22 0.00
Matches are distributed among these distances:
29 46 1.00
ACGTcount: A:0.41, C:0.02, G:0.42, T:0.15
Consensus pattern (29 bp):
GTTGAAAGAAGAAAGGAGGGAGCTTGAAG
Found at i:53252361 original size:14 final size:15
Alignment explanation
Indices: 53252344--53252374 Score: 55
Period size: 15 Copynumber: 2.1 Consensus size: 15
53252334 GAATATGATA
53252344 AAATA-TTAAAAAAT
1 AAATATTTAAAAAAT
53252358 AAATATTTAAAAAAT
1 AAATATTTAAAAAAT
53252373 AA
1 AA
53252375 CTAATAGTTG
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
14 5 0.31
15 11 0.69
ACGTcount: A:0.71, C:0.00, G:0.00, T:0.29
Consensus pattern (15 bp):
AAATATTTAAAAAAT
Found at i:53258219 original size:23 final size:22
Alignment explanation
Indices: 53258177--53258220 Score: 54
Period size: 23 Copynumber: 2.0 Consensus size: 22
53258167 TCTTAATAAT
*
53258177 ATTATTAATTAGTGATATTTAG
1 ATTATTAATTAATGATATTTAG
53258199 ATTATATAATTAAT-ATAATTTA
1 ATTAT-TAATTAATGAT-ATTTA
53258221 CAAATATTAT
Statistics
Matches: 19, Mismatches: 1, Indels: 3
0.83 0.04 0.13
Matches are distributed among these distances:
22 7 0.37
23 12 0.63
ACGTcount: A:0.43, C:0.00, G:0.07, T:0.50
Consensus pattern (22 bp):
ATTATTAATTAATGATATTTAG
Found at i:53260869 original size:6 final size:6
Alignment explanation
Indices: 53260858--53260890 Score: 66
Period size: 6 Copynumber: 5.5 Consensus size: 6
53260848 AATTAATTGC
53260858 GGTTCT GGTTCT GGTTCT GGTTCT GGTTCT GGT
1 GGTTCT GGTTCT GGTTCT GGTTCT GGTTCT GGT
53260891 AGCTGCTATA
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 27 1.00
ACGTcount: A:0.00, C:0.15, G:0.36, T:0.48
Consensus pattern (6 bp):
GGTTCT
Found at i:53270903 original size:37 final size:37
Alignment explanation
Indices: 53270827--53270905 Score: 106
Period size: 37 Copynumber: 2.1 Consensus size: 37
53270817 TTATTACGAA
* * *
53270827 GTCTTACCCGGACATAATCTCCACACGAAGTTATCGG
1 GTCTTACCCGGACAAAATCCCCACACGAAGTCATCGG
*
53270864 GTCTTACCCGGACAAAATCCCCACAC-ATAGTCATTGG
1 GTCTTACCCGGACAAAATCCCCACACGA-AGTCATCGG
53270901 GTCTT
1 GTCTT
53270906 TAGAGCTCGG
Statistics
Matches: 37, Mismatches: 4, Indels: 2
0.86 0.09 0.05
Matches are distributed among these distances:
36 1 0.03
37 36 0.97
ACGTcount: A:0.27, C:0.30, G:0.18, T:0.25
Consensus pattern (37 bp):
GTCTTACCCGGACAAAATCCCCACACGAAGTCATCGG
Found at i:53271051 original size:47 final size:47
Alignment explanation
Indices: 53270997--53271457 Score: 825
Period size: 47 Copynumber: 9.8 Consensus size: 47
53270987 CTCGGCCCTG
53270997 ACATTCGTCACATCGGCCATTAGGCCTTATCACATATATACACTTTC
1 ACATTCGTCACATCGGCCATTAGGCCTTATCACATATATACACTTTC
53271044 ACATTCGTCACATCGGCCATTAGGCCTTATCACATATATACACTTTC
1 ACATTCGTCACATCGGCCATTAGGCCTTATCACATATATACACTTTC
53271091 ACATTCGTCACATCGGCCATTAGGCCTTATCACATATATACACTTTC
1 ACATTCGTCACATCGGCCATTAGGCCTTATCACATATATACACTTTC
53271138 ACATTCGTCACATCGGCCATTAGGCCTTATCACACATATATACACTTTC
1 ACATTCGTCACATCGGCCATTAGGCCTTAT--CACATATATACACTTTC
* *
53271187 ACATTCATCACATCGGCCATTAGGCCTTATTACATATATACACTTTC
1 ACATTCGTCACATCGGCCATTAGGCCTTATCACATATATACACTTTC
*
53271234 ACATTCATCACATCGGCCATTAGGCCTTATCACATATATACACTTTC
1 ACATTCGTCACATCGGCCATTAGGCCTTATCACATATATACACTTTC
53271281 ACATT-GATCACATCGGCCATTAGGCCTTATCACATATATACACTTTC
1 ACATTCG-TCACATCGGCCATTAGGCCTTATCACATATATACACTTTC
53271328 ACATTCGTCACATCGGCCATTAGGCCTTATCACATATATACACTTTC
1 ACATTCGTCACATCGGCCATTAGGCCTTATCACATATATACACTTTC
* *
53271375 ACATTCATCACATCGGCTATTAGGCCTTATCACATATATACACTTTC
1 ACATTCGTCACATCGGCCATTAGGCCTTATCACATATATACACTTTC
**
53271422 ACATTTATCACATCGGCCATTAGGCCTTATCACATA
1 ACATTCGTCACATCGGCCATTAGGCCTTATCACATA
53271458 GAATCCTAAA
Statistics
Matches: 402, Mismatches: 8, Indels: 8
0.96 0.02 0.02
Matches are distributed among these distances:
47 355 0.88
48 1 0.00
49 46 0.11
ACGTcount: A:0.29, C:0.29, G:0.10, T:0.32
Consensus pattern (47 bp):
ACATTCGTCACATCGGCCATTAGGCCTTATCACATATATACACTTTC
Found at i:53281143 original size:40 final size:41
Alignment explanation
Indices: 53281059--53281152 Score: 113
Period size: 40 Copynumber: 2.3 Consensus size: 41
53281049 ATCTGTATCG
* * *
53281059 CACACATAGTGCC-TTCTATAGCCGAAGCTATGCCAACTCG
1 CACACTTAGTGCCATTCTATAGCCGAAGCTATGCAAACTCA
**
53281099 CACACTTAGTGCCATT-TATAGCCGAAGCTATATTAAAC-CA
1 CACACTTAGTGCCATTCTATAGCCGAAGCTAT-GCAAACTCA
53281139 CACACTTAGTGCCA
1 CACACTTAGTGCCA
53281153 ATCATAGTCA
Statistics
Matches: 47, Mismatches: 5, Indels: 4
0.84 0.09 0.07
Matches are distributed among these distances:
40 42 0.89
41 5 0.11
ACGTcount: A:0.31, C:0.30, G:0.15, T:0.24
Consensus pattern (41 bp):
CACACTTAGTGCCATTCTATAGCCGAAGCTATGCAAACTCA
Found at i:53283419 original size:41 final size:40
Alignment explanation
Indices: 53283366--53283535 Score: 152
Period size: 41 Copynumber: 4.2 Consensus size: 40
53283356 AGTCCGACTC
*
53283366 TTAG-CACCGGCTCAAAAGCCCTTCGAGACCAAGCTCGGA
1 TTAGACACTGGCTCAAAAGCCCTTCGAGACCAAGCTCGGA
* * *
53283405 TTAGACTACTGGCTCGAAGGCCCTTCG-GAACTAAG-TCCGG-
1 TTAGAC-ACTGGCTCAAAAGCCCTTCGAG-ACCAAGCT-CGGA
* * * *
53283445 TTATGACACTGGCTCTAAAAAGCCCTTCAAAACTAAGTTCGGTTA
1 TTA-GACACTGGCTC--AAAAGCCCTTCGAGACCAAGCTCGG--A
53283490 TTAG-CACTGGCTCAAAAGCCCTTCGAGACCAAGCTCGGA
1 TTAGACACTGGCTCAAAAGCCCTTCGAGACCAAGCTCGGA
53283529 TTTAGAC
1 -TTAGAC
53283536 CCCGATTAGC
Statistics
Matches: 105, Mismatches: 12, Indels: 26
0.73 0.08 0.18
Matches are distributed among these distances:
39 5 0.05
40 18 0.17
41 50 0.48
42 18 0.17
43 10 0.10
44 1 0.01
45 3 0.03
ACGTcount: A:0.28, C:0.28, G:0.22, T:0.22
Consensus pattern (40 bp):
TTAGACACTGGCTCAAAAGCCCTTCGAGACCAAGCTCGGA
Found at i:53291005 original size:40 final size:40
Alignment explanation
Indices: 53290922--53291184 Score: 325
Period size: 40 Copynumber: 6.6 Consensus size: 40
53290912 TTGAATGCTG
* * * * * *
53290922 TCCGGGCTAAGTCCCGAAGGC-TTTGTGCTAAGTGAATATA
1 TCCGGGTTAAGTCCCGAAGGCATTCGTGC-GAGTTATTAAA
* * * * *
53290962 TCCGGATTAAGAT-CCGAAGGCCTTTGTGCGAGATACTAAA
1 TCCGGGTTAAG-TCCCGAAGGCATTCGTGCGAGTTATTAAA
53291002 TCCGGGTTAAGTCCCGAAGGCATTCGTGCGAGTTATTAAA
1 TCCGGGTTAAGTCCCGAAGGCATTCGTGCGAGTTATTAAA
53291042 TCCGGGTTAAGTCCCGAAGGCATTCGTGCGAGTTATTAAA
1 TCCGGGTTAAGTCCCGAAGGCATTCGTGCGAGTTATTAAA
*
53291082 TCCGGGTTAAGTCCCGAAGGCATTCGTGCGAGTTGTTAAA
1 TCCGGGTTAAGTCCCGAAGGCATTCGTGCGAGTTATTAAA
* * *
53291122 TCCGGGTTATGTCCCGAAGGCATT-GTGTGAGTTACTAAA
1 TCCGGGTTAAGTCCCGAAGGCATTCGTGCGAGTTATTAAA
* * *
53291161 ACCGGGCTATGTCCCGAAGGCATT
1 TCCGGGTTAAGTCCCGAAGGCATT
53291185 TGAACGAGGA
Statistics
Matches: 201, Mismatches: 19, Indels: 7
0.89 0.08 0.03
Matches are distributed among these distances:
39 35 0.17
40 158 0.79
41 8 0.04
ACGTcount: A:0.25, C:0.21, G:0.28, T:0.27
Consensus pattern (40 bp):
TCCGGGTTAAGTCCCGAAGGCATTCGTGCGAGTTATTAAA
Found at i:53291204 original size:79 final size:80
Alignment explanation
Indices: 53290961--53291219 Score: 256
Period size: 80 Copynumber: 3.3 Consensus size: 80
53290951 AAGTGAATAT
* * * * * *
53290961 ATCCGGATTAAGAT-CCGAAGGCCTTTGTGCGAGATACTAAATCCGGGTTAAGTCCCGAAGGCAT
1 ATCCGGGTTAAG-TCCCGAAGGCATTCGTGCGAGTTACTAAAACCGGGCTAAGTCCCGAAGGCAT
** * *
53291025 TCGTGCGAGTTA-TTAA
65 TCGAACGAG-GAGCTAA
* * *
53291041 ATCCGGGTTAAGTCCCGAAGGCATTCGTGCGAGTTATTAAATCCGGGTTAAGTCCCGAAGGCATT
1 ATCCGGGTTAAGTCCCGAAGGCATTCGTGCGAGTTACTAAAACCGGGCTAAGTCCCGAAGGCATT
** ** *
53291106 CGTGCGAGTTGTTAA
66 CGAACGAGGAGCTAA
* * *
53291121 ATCCGGGTTATGTCCCGAAGGCATT-GTGTGAGTTACTAAAACCGGGCTATGTCCCGAAGGCATT
1 ATCCGGGTTAAGTCCCGAAGGCATTCGTGCGAGTTACTAAAACCGGGCTAAGTCCCGAAGGCATT
* *
53291185 TGAACGAGGAGCTAT
66 CGAACGAGGAGCTAA
*
53291200 ATCC-GGTTAAATCCCGAAGG
1 ATCCGGGTTAAGTCCCGAAGG
53291220 TACGTGATTT
Statistics
Matches: 156, Mismatches: 21, Indels: 6
0.85 0.11 0.03
Matches are distributed among these distances:
78 14 0.09
79 48 0.31
80 94 0.60
ACGTcount: A:0.26, C:0.20, G:0.28, T:0.26
Consensus pattern (80 bp):
ATCCGGGTTAAGTCCCGAAGGCATTCGTGCGAGTTACTAAAACCGGGCTAAGTCCCGAAGGCATT
CGAACGAGGAGCTAA
Found at i:53298955 original size:40 final size:40
Alignment explanation
Indices: 53298911--53299134 Score: 308
Period size: 40 Copynumber: 5.6 Consensus size: 40
53298901 AAGTGAATAT
* * * * **
53298911 ATCCGGATTAAGAT-CCGAAGGCCTTTGTGCGAGATACTAA
1 ATCCGGGTTAAG-TCCCGAAGGCATTCGTGCGAGTTGTTAA
53298951 ATCCGGGTTAAGTCCCGAAGGCATTCGTGCGAGTTGTTAA
1 ATCCGGGTTAAGTCCCGAAGGCATTCGTGCGAGTTGTTAA
53298991 ATCCGGGTTAAGTCCCGAAGGCATTCGTGCGAGTTGTTAA
1 ATCCGGGTTAAGTCCCGAAGGCATTCGTGCGAGTTGTTAA
53299031 ATCCGGGTTAAGTCCCGAAGGCATTCGTGCGAGTTGTTAA
1 ATCCGGGTTAAGTCCCGAAGGCATTCGTGCGAGTTGTTAA
* * **
53299071 ATCCGGGTTATGTCCCGAAGGCATT-GTGTGAGTTACTAA
1 ATCCGGGTTAAGTCCCGAAGGCATTCGTGCGAGTTGTTAA
* * *
53299110 AACCGGGCTATGTCCCGAAGGCATT
1 ATCCGGGTTAAGTCCCGAAGGCATT
53299135 TGAACGAGGA
Statistics
Matches: 171, Mismatches: 12, Indels: 3
0.92 0.06 0.02
Matches are distributed among these distances:
39 35 0.20
40 136 0.80
ACGTcount: A:0.24, C:0.21, G:0.29, T:0.27
Consensus pattern (40 bp):
ATCCGGGTTAAGTCCCGAAGGCATTCGTGCGAGTTGTTAA
Found at i:53299009 original size:80 final size:80
Alignment explanation
Indices: 53298872--53299134 Score: 318
Period size: 80 Copynumber: 3.3 Consensus size: 80
53298862 TTGAATGCTG
* * * * *
53298872 TCCGGGCTAAGTCCCGAAGGC-TTTGTGCTAAG-TGAATATATCCGGATTAAGAT-CCGAAGGCC
1 TCCGGGCTAAGTCCCGAAGGCATTCGTGC-GAGTTG-TTAAATCCGGGTTAAG-TCCCGAAGGCC
*
53298934 TTTGTGCGAGATACTAAA
63 TTTGTGCGAGTTACTAAA
* * *
53298952 TCCGGGTTAAGTCCCGAAGGCATTCGTGCGAGTTGTTAAATCCGGGTTAAGTCCCGAAGGCATTC
1 TCCGGGCTAAGTCCCGAAGGCATTCGTGCGAGTTGTTAAATCCGGGTTAAGTCCCGAAGGCCTTT
**
53299017 GTGCGAGTTGTTAAA
66 GTGCGAGTTACTAAA
* * *
53299032 TCCGGGTTAAGTCCCGAAGGCATTCGTGCGAGTTGTTAAATCCGGGTTATGTCCCGAAGG-CATT
1 TCCGGGCTAAGTCCCGAAGGCATTCGTGCGAGTTGTTAAATCCGGGTTAAGTCCCGAAGGCCTTT
*
53299096 GTGTGAGTTACTAAA
66 GTGCGAGTTACTAAA
* *
53299111 ACCGGGCTATGTCCCGAAGGCATT
1 TCCGGGCTAAGTCCCGAAGGCATT
53299135 TGAACGAGGA
Statistics
Matches: 159, Mismatches: 21, Indels: 7
0.85 0.11 0.04
Matches are distributed among these distances:
79 35 0.22
80 116 0.73
81 8 0.05
ACGTcount: A:0.24, C:0.21, G:0.29, T:0.27
Consensus pattern (80 bp):
TCCGGGCTAAGTCCCGAAGGCATTCGTGCGAGTTGTTAAATCCGGGTTAAGTCCCGAAGGCCTTT
GTGCGAGTTACTAAA
Found at i:53299086 original size:120 final size:120
Alignment explanation
Indices: 53298872--53299134 Score: 318
Period size: 120 Copynumber: 2.2 Consensus size: 120
53298862 TTGAATGCTG
* * *
53298872 TCCGGGCTAAGTCCCGAAGGC-TTTGTGCTAAGTGAATATATCCGGATTAAGATCCGAAGGCCTT
1 TCCGGGCTAAGTCCCGAAGGCATTCGTGCTAAGTGAATAAATCCGGATTAAGATCCGAAGGCATT
* **
53298936 TGTGCGAGATACTAAATCCGGGTTAAGTCCCGAAGGCATTCGTGCGAGTTGTTAAA
66 CGTGCGAGATACTAAATCCGGGTTAAGTCCCGAAGGCATT-GTGCGAGTTACTAAA
* * * *
53298992 TCCGGGTTAAGTCCCGAAGGCATTCGTGC-GAGTTG-TTAAATCCGGGTTAAG-TCCCGAAGGCA
1 TCCGGGCTAAGTCCCGAAGGCATTCGTGCTAAG-TGAATAAATCCGGATTAAGAT-CCGAAGGCA
* ** * *
53299054 TTCGTGCGAGTTGTTAAATCCGGGTTATGTCCCGAAGGCATTGTGTGAGTTACTAAA
64 TTCGTGCGAGATACTAAATCCGGGTTAAGTCCCGAAGGCATTGTGCGAGTTACTAAA
* *
53299111 ACCGGGCTATGTCCCGAAGGCATT
1 TCCGGGCTAAGTCCCGAAGGCATT
53299135 TGAACGAGGA
Statistics
Matches: 122, Mismatches: 18, Indels: 7
0.83 0.12 0.05
Matches are distributed among these distances:
119 34 0.28
120 80 0.66
121 8 0.07
ACGTcount: A:0.24, C:0.21, G:0.29, T:0.27
Consensus pattern (120 bp):
TCCGGGCTAAGTCCCGAAGGCATTCGTGCTAAGTGAATAAATCCGGATTAAGATCCGAAGGCATT
CGTGCGAGATACTAAATCCGGGTTAAGTCCCGAAGGCATTGTGCGAGTTACTAAA
Found at i:53303149 original size:40 final size:41
Alignment explanation
Indices: 53303064--53303172 Score: 129
Period size: 40 Copynumber: 2.7 Consensus size: 41
53303054 TAAATCGGTA
*
53303064 TCGCACACTTAGTGCC-TTCTATAGCCGAAGCTATGCCAAC
1 TCGCACACTTAGTGCCATTCTATAGCCGAAGCTATGCAAAC
* *
53303104 TCGCACACTTAGTGCCATT-TATAGTCGAAGCTGTAT-TAAAC
1 TCGCACACTTAGTGCCATTCTATAGCCGAAGC--TATGCAAAC
*
53303145 -CGCACACTTAGTGCCAATC-ATAGCCGAA
1 TCGCACACTTAGTGCCATTCTATAGCCGAA
53303173 TATCATTATA
Statistics
Matches: 60, Mismatches: 5, Indels: 8
0.82 0.07 0.11
Matches are distributed among these distances:
40 52 0.87
41 5 0.08
42 3 0.05
ACGTcount: A:0.28, C:0.28, G:0.17, T:0.26
Consensus pattern (41 bp):
TCGCACACTTAGTGCCATTCTATAGCCGAAGCTATGCAAAC
Found at i:53310114 original size:36 final size:36
Alignment explanation
Indices: 53310074--53310185 Score: 106
Period size: 36 Copynumber: 3.2 Consensus size: 36
53310064 TCGGTTATCT
*
53310074 GACTAGCGCTAGGCACAATAATTTGTCAATTCGTTC
1 GACTAGCACTAGGCACAATAATTTGTCAATTCGTTC
* * * *
53310110 GACTA-CTACTGGGCACAACT-A-TCGTCAATT-ATCC
1 GACTAGC-ACTAGGCACAA-TAATTTGTCAATTCGTTC
* * *
53310144 GACTAGCACTAGGCGCAATAATTTATCGATTCGTTC
1 GACTAGCACTAGGCACAATAATTTGTCAATTCGTTC
53310180 GACTAG
1 GACTAG
53310186 TGCTAGGAAC
Statistics
Matches: 58, Mismatches: 12, Indels: 12
0.71 0.15 0.15
Matches are distributed among these distances:
33 1 0.02
34 17 0.29
35 16 0.28
36 23 0.40
37 1 0.02
ACGTcount: A:0.29, C:0.24, G:0.19, T:0.29
Consensus pattern (36 bp):
GACTAGCACTAGGCACAATAATTTGTCAATTCGTTC
Found at i:53310380 original size:27 final size:27
Alignment explanation
Indices: 53310349--53310404 Score: 112
Period size: 27 Copynumber: 2.1 Consensus size: 27
53310339 AATGTAAATT
53310349 TTCGTTACTAGTTGAAAGTGAGATACA
1 TTCGTTACTAGTTGAAAGTGAGATACA
53310376 TTCGTTACTAGTTGAAAGTGAGATACA
1 TTCGTTACTAGTTGAAAGTGAGATACA
53310403 TT
1 TT
53310405 GAGATCATGA
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
27 29 1.00
ACGTcount: A:0.32, C:0.11, G:0.21, T:0.36
Consensus pattern (27 bp):
TTCGTTACTAGTTGAAAGTGAGATACA
Found at i:53315208 original size:38 final size:38
Alignment explanation
Indices: 53315166--53315260 Score: 120
Period size: 38 Copynumber: 2.5 Consensus size: 38
53315156 ATAGGCTATA
* * *
53315166 TGCTGGAATTATATCCGGGTTAAATCCCGCAGGCTTCG
1 TGCTGGAATTATATCCGGGTTAAATCCCGCAAGCCTAG
*
53315204 TGCTGGTAA-TATATCCAGGTTAAATCCCGCAAGCCTAG
1 TGCTGG-AATTATATCCGGGTTAAATCCCGCAAGCCTAG
* *
53315242 TGCTGGTATTATATTCGGG
1 TGCTGGAATTATATCCGGG
53315261 CCTTCGTGCC
Statistics
Matches: 48, Mismatches: 7, Indels: 4
0.81 0.12 0.07
Matches are distributed among these distances:
37 1 0.02
38 45 0.94
39 2 0.04
ACGTcount: A:0.23, C:0.21, G:0.25, T:0.31
Consensus pattern (38 bp):
TGCTGGAATTATATCCGGGTTAAATCCCGCAAGCCTAG
Found at i:53315329 original size:43 final size:43
Alignment explanation
Indices: 53315251--53315334 Score: 141
Period size: 43 Copynumber: 2.0 Consensus size: 43
53315241 GTGCTGGTAT
* *
53315251 TATATTCGGGCCTTCGTGCCTAGCAGGCTTCATGCCAGTGATG
1 TATATTCGGGCCTTCGTGCCTAGCAGGCGTAATGCCAGTGATG
*
53315294 TATATTCGGGCCTTCGTGCCTAGCAGGCGTAATGCCGGTGA
1 TATATTCGGGCCTTCGTGCCTAGCAGGCGTAATGCCAGTGA
53315335 AATGATATGT
Statistics
Matches: 38, Mismatches: 3, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
43 38 1.00
ACGTcount: A:0.17, C:0.25, G:0.30, T:0.29
Consensus pattern (43 bp):
TATATTCGGGCCTTCGTGCCTAGCAGGCGTAATGCCAGTGATG
Found at i:53318742 original size:50 final size:50
Alignment explanation
Indices: 53318688--53318822 Score: 155
Period size: 52 Copynumber: 2.7 Consensus size: 50
53318678 ATGCATTGTA
* * *
53318688 TAACTCTCATGTTAATTAAGTTTGCATCATAAATTATGACATGCTTTATG
1 TAACTCTCATGTTAATTAAGTTTGCATCATAAATTAAGACATGCATTAAG
* * *
53318738 TAACTCTCATGTTAGTTAAAGTTTGCATAATTAAATTAAGCCATGCATTAAG
1 TAACTCTCATGTTAATT-AAGTTTGCATCA-TAAATTAAGACATGCATTAAG
* * *
53318790 TAACTCATC-TGTTCATTTAGTTTGCATCTTAAA
1 TAACTC-TCATGTTAATTAAGTTTGCATCATAAA
53318823 CCATGCATTT
Statistics
Matches: 71, Mismatches: 11, Indels: 6
0.81 0.12 0.07
Matches are distributed among these distances:
50 20 0.28
51 20 0.28
52 29 0.41
53 2 0.03
ACGTcount: A:0.33, C:0.15, G:0.12, T:0.41
Consensus pattern (50 bp):
TAACTCTCATGTTAATTAAGTTTGCATCATAAATTAAGACATGCATTAAG
Found at i:53318793 original size:52 final size:51
Alignment explanation
Indices: 53318665--53318816 Score: 157
Period size: 50 Copynumber: 3.0 Consensus size: 51
53318655 TGTGTTTTGC
* * * *
53318665 ATTAAATAAAGTCATGCATTGTA-TAACTCTCATGTTAATTAAGTTTGCATC
1 ATTAAATTAAGACATGCATT-AAGTAACTCTCATGTTAATTAAGTTTGCATA
* * * *
53318716 A-TAAATTATGACATGCTTTATGTAACTCTCATGTTAGTTAAAGTTTGCATA
1 ATTAAATTAAGACATGCATTAAGTAACTCTCATGTTAATT-AAGTTTGCATA
* * *
53318767 ATTAAATTAAGCCATGCATTAAGTAACTCATC-TGTTCATTTAGTTTGCAT
1 ATTAAATTAAGACATGCATTAAGTAACTC-TCATGTTAATTAAGTTTGCAT
53318817 CTTAAACCAT
Statistics
Matches: 82, Mismatches: 15, Indels: 8
0.78 0.14 0.08
Matches are distributed among these distances:
50 30 0.37
51 21 0.26
52 29 0.35
53 2 0.02
ACGTcount: A:0.34, C:0.14, G:0.12, T:0.40
Consensus pattern (51 bp):
ATTAAATTAAGACATGCATTAAGTAACTCTCATGTTAATTAAGTTTGCATA
Found at i:53320047 original size:22 final size:23
Alignment explanation
Indices: 53320002--53320050 Score: 64
Period size: 22 Copynumber: 2.2 Consensus size: 23
53319992 TAGAAGTTTC
**
53320002 AAAATATCAAAAAAAAAGTGAAA
1 AAAATATCAAAAAAAAAGCAAAA
*
53320025 AAAAT-TCGAAAAAAAAGCAAAA
1 AAAATATCAAAAAAAAAGCAAAA
53320047 AAAA
1 AAAA
53320051 GTAAAAAAAA
Statistics
Matches: 23, Mismatches: 3, Indels: 1
0.85 0.11 0.04
Matches are distributed among these distances:
22 18 0.78
23 5 0.22
ACGTcount: A:0.76, C:0.06, G:0.08, T:0.10
Consensus pattern (23 bp):
AAAATATCAAAAAAAAAGCAAAA
Found at i:53320060 original size:10 final size:10
Alignment explanation
Indices: 53320011--53320060 Score: 55
Period size: 10 Copynumber: 4.8 Consensus size: 10
53320001 CAAAATATCA
53320011 AAAAAAAAGT
1 AAAAAAAAGT
* *
53320021 GAAAAAAATT
1 AAAAAAAAGT
*
53320031 CGAAAAAAAAGC
1 --AAAAAAAAGT
53320043 AAAAAAAAGT
1 AAAAAAAAGT
53320053 AAAAAAAA
1 AAAAAAAA
53320061 ATTCAAATTT
Statistics
Matches: 32, Mismatches: 6, Indels: 4
0.76 0.14 0.10
Matches are distributed among these distances:
10 25 0.78
12 7 0.22
ACGTcount: A:0.78, C:0.04, G:0.10, T:0.08
Consensus pattern (10 bp):
AAAAAAAAGT
Found at i:53320960 original size:18 final size:19
Alignment explanation
Indices: 53320927--53320999 Score: 68
Period size: 18 Copynumber: 4.1 Consensus size: 19
53320917 AGCGAAAAAT
53320927 AAAAGAAATTGAGAGAAGAAA
1 AAAAGAAATT--GAGAAGAAA
53320948 AAAAGAAA-TGAG-AG--A
1 AAAAGAAATTGAGAAGAAA
53320963 AAAAGAAATTGA-AAGAAA
1 AAAAGAAATTGAGAAGAAA
**
53320981 AAAAGAGCTTGA-AAGAAA
1 AAAAGAAATTGAGAAGAAA
53320999 A
1 A
53321000 GAGAAAGAAA
Statistics
Matches: 46, Mismatches: 2, Indels: 11
0.78 0.03 0.19
Matches are distributed among these distances:
15 9 0.20
16 5 0.11
17 2 0.04
18 21 0.46
20 1 0.02
21 8 0.17
ACGTcount: A:0.67, C:0.01, G:0.22, T:0.10
Consensus pattern (19 bp):
AAAAGAAATTGAGAAGAAA
Found at i:53320967 original size:15 final size:16
Alignment explanation
Indices: 53320947--53321005 Score: 59
Period size: 15 Copynumber: 3.6 Consensus size: 16
53320937 GAGAGAAGAA
*
53320947 AAAAAGAAA-TGAGAG
1 AAAAAGAAATTGAAAG
53320962 AAAAAGAAATTGAAAG
1 AAAAAGAAATTGAAAG
53320978 AAAAA-AAGAGCTTGAAAG
1 AAAAAGAA-A--TTGAAAG
53320996 AAAAGAGAAA
1 AAAA-AGAAA
53321006 GAAAAAGAAT
Statistics
Matches: 37, Mismatches: 1, Indels: 8
0.80 0.02 0.17
Matches are distributed among these distances:
15 11 0.30
16 11 0.30
18 11 0.30
19 2 0.05
20 2 0.05
ACGTcount: A:0.68, C:0.02, G:0.22, T:0.08
Consensus pattern (16 bp):
AAAAAGAAATTGAAAG
Found at i:53320976 original size:21 final size:19
Alignment explanation
Indices: 53320912--53320966 Score: 74
Period size: 21 Copynumber: 2.7 Consensus size: 19
53320902 TAATGAGAGA
*
53320912 AAATGAGCGAAAAATAAAAG
1 AAATGAGAGAAAAA-AAAAG
53320932 AAATTGAGAGAAGAAAAAAAG
1 AAA-TGAGAGAA-AAAAAAAG
53320953 AAATGAGAGAAAAA
1 AAATGAGAGAAAAA
53320967 GAAATTGAAA
Statistics
Matches: 32, Mismatches: 1, Indels: 5
0.84 0.03 0.13
Matches are distributed among these distances:
19 3 0.09
20 11 0.34
21 15 0.47
22 3 0.09
ACGTcount: A:0.67, C:0.02, G:0.22, T:0.09
Consensus pattern (19 bp):
AAATGAGAGAAAAAAAAAG
Found at i:53322997 original size:46 final size:45
Alignment explanation
Indices: 53322944--53323119 Score: 174
Period size: 46 Copynumber: 3.8 Consensus size: 45
53322934 TGTTTGGGCA
*
53322944 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATACAAATG
1 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATAC-AACG
*** * * *
53322990 TCCGAACTCGTTGAGTTGAGTCCGAGTTCGAGAGATGTA-ACTAGGCA
1 TCCGAACTCGTTGAGTTGAGTCCGAGTTC-ACTTATGGATAC-A-ACG
* * * * *
53323037 TCCGAGCTTGTTGAGTTGAGTCCGAGTTCATTTATGGATGCGAACC
1 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATAC-AACG
* *
53323083 CCCGAGCTCGTTGAGTTGAGTCCGAGTTCACTTATGG
1 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGG
53323120 GCGGGTTACA
Statistics
Matches: 106, Mismatches: 21, Indels: 6
0.80 0.16 0.05
Matches are distributed among these distances:
46 72 0.68
47 34 0.32
ACGTcount: A:0.22, C:0.20, G:0.28, T:0.30
Consensus pattern (45 bp):
TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATACAACG
Found at i:53323099 original size:93 final size:93
Alignment explanation
Indices: 53322940--53323111 Score: 263
Period size: 93 Copynumber: 1.8 Consensus size: 93
53322930 AGGATGTTTG
***
53322940 GGCATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATACAAATGTCCGAACTCGTTGAG
1 GGCATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATACAAACCCCCGAACTCGTTGAG
53323005 TTGAGTCCGAGTTCGAGAGATGTAACTA
66 TTGAGTCCGAGTTCGAGAGATGTAACTA
* * * * * *
53323033 GGCATCCGAGCTTGTTGAGTTGAGTCCGAGTTCATTTATGGATGCGAACCCCCGAGCTCGTTGAG
1 GGCATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATACAAACCCCCGAACTCGTTGAG
53323098 TTGAGTCCGAGTTC
66 TTGAGTCCGAGTTC
53323112 ACTTATGGGC
Statistics
Matches: 70, Mismatches: 9, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
93 70 1.00
ACGTcount: A:0.22, C:0.21, G:0.28, T:0.28
Consensus pattern (93 bp):
GGCATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATACAAACCCCCGAACTCGTTGAG
TTGAGTCCGAGTTCGAGAGATGTAACTA
Found at i:53325749 original size:50 final size:50
Alignment explanation
Indices: 53325686--53325848 Score: 181
Period size: 50 Copynumber: 3.3 Consensus size: 50
53325676 CATTATGTGT
*
53325686 TTTGCAT--TAAATAAAGTCACGCATTATGTAACTCTCATGTTAGTTAAG
1 TTTGCATCATAAATAAAGTCATGCATTATGTAACTCTCATGTTAGTTAAG
* * *
53325734 TTTGCATCATAAATAATGACATGCTTTATGTAACTCTCATGTTAGTTAAAG
1 TTTGCATCATAAATAAAGTCATGCATTATGTAACTCTCATGTTAGTT-AAG
* * * *
53325785 TTTGCATAATTAAATTAAGTCATGCATTAAGTAACTCAT-ATGTTCA-TTTAG
1 TTTGCATCA-TAAATAAAGTCATGCATTATGTAACTC-TCATGTT-AGTTAAG
*
53325836 TTTGCATCTTAAA
1 TTTGCATCATAAA
53325849 CCATGCATTT
Statistics
Matches: 96, Mismatches: 13, Indels: 10
0.81 0.11 0.08
Matches are distributed among these distances:
48 7 0.07
50 38 0.40
51 20 0.21
52 29 0.30
53 2 0.02
ACGTcount: A:0.34, C:0.13, G:0.13, T:0.40
Consensus pattern (50 bp):
TTTGCATCATAAATAAAGTCATGCATTATGTAACTCTCATGTTAGTTAAG
Found at i:53329840 original size:19 final size:19
Alignment explanation
Indices: 53329816--53329853 Score: 76
Period size: 19 Copynumber: 2.0 Consensus size: 19
53329806 ATAGAAAGAA
53329816 GACTTAGTTTGAAAATCGT
1 GACTTAGTTTGAAAATCGT
53329835 GACTTAGTTTGAAAATCGT
1 GACTTAGTTTGAAAATCGT
53329854 TTTTGCATAC
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 19 1.00
ACGTcount: A:0.32, C:0.11, G:0.21, T:0.37
Consensus pattern (19 bp):
GACTTAGTTTGAAAATCGT
Found at i:53335617 original size:47 final size:47
Alignment explanation
Indices: 53335586--53336519 Score: 1616
Period size: 47 Copynumber: 19.9 Consensus size: 47
53335576 TAGGGCCGAG
* * * * * * *
53335586 TGGCCAATGTGATGGATGTGAAAGTATATATATGTGATAGGGCCGAG
1 TGGCCAATGTGATGAATGTGAAAGTGTATATATGAGATAAGACCTAA
* * * *
53335633 TGGCCAACGTGATGAATGTGAAAGTGTATATATGTGATAAGGCCGAA
1 TGGCCAATGTGATGAATGTGAAAGTGTATATATGAGATAAGACCTAA
53335680 TGGCCAATGTGATGAATGTGAAAGTGTATATATGAGATAAGACCTAA
1 TGGCCAATGTGATGAATGTGAAAGTGTATATATGAGATAAGACCTAA
53335727 TGGCCAATGTGATGAATGTGAAAGTGTATATATGAGATAAGACCTAA
1 TGGCCAATGTGATGAATGTGAAAGTGTATATATGAGATAAGACCTAA
53335774 TGGCCAATGTGATGAATGTGAAAGTGTATATATGAGATAAGACCTAA
1 TGGCCAATGTGATGAATGTGAAAGTGTATATATGAGATAAGACCTAA
53335821 TGGCCAATGTGATGAATGTGAAAGTGTATATATGAGATAAGACCTAA
1 TGGCCAATGTGATGAATGTGAAAGTGTATATATGAGATAAGACCTAA
53335868 TGGCCAATGTGATGAATGTGAAAGTGTATATATGAGATAAGACCTAA
1 TGGCCAATGTGATGAATGTGAAAGTGTATATATGAGATAAGACCTAA
53335915 TGGCCAATGTGATGAATGTGAAAGTGTATATATGAGATAAGACCTAA
1 TGGCCAATGTGATGAATGTGAAAGTGTATATATGAGATAAGACCTAA
53335962 TGGCCAATGTGATGAATGTGAAAGTGTATATATGAGATAAGACCTAA
1 TGGCCAATGTGATGAATGTGAAAGTGTATATATGAGATAAGACCTAA
53336009 TGGCCAATGTGATGAATGTGAAAGTGTATATATGAGATAAGACCTAA
1 TGGCCAATGTGATGAATGTGAAAGTGTATATATGAGATAAGACCTAA
53336056 TGGCCAATGTGATGAATGTGAAAGTGTATATATGAGATAAGACCTAA
1 TGGCCAATGTGATGAATGTGAAAGTGTATATATGAGATAAGACCTAA
53336103 TGGCCAATGTGATGAATGTGAAAGTGTATATATGAGATAAGACCTAA
1 TGGCCAATGTGATGAATGTGAAAGTGTATATATGAGATAAGACCTAA
53336150 TGGCCAATGTGATGAATGTGAAAGTGTATATATGAGATAAGACCTAA
1 TGGCCAATGTGATGAATGTGAAAGTGTATATATGAGATAAGACCTAA
53336197 TGGCCAATGTGATGAATGTGAAAGTGTATATATGAGATAAGACCTAA
1 TGGCCAATGTGATGAATGTGAAAGTGTATATATGAGATAAGACCTAA
53336244 TGGCCAATGTGATGAATGTGAAAGTGTATATATGAGATAAGACCTAA
1 TGGCCAATGTGATGAATGTGAAAGTGTATATATGAGATAAGACCTAA
* * ** * *
53336291 TGGCCAATGTGATGAATGTGAAAGTGTATATATGTGATAGGGTCGAG
1 TGGCCAATGTGATGAATGTGAAAGTGTATATATGAGATAAGACCTAA
* * * * *
53336338 TGACCAACGTGATGAATGTGAAAGTGTATATATGTGATAAGGCCGAA
1 TGGCCAATGTGATGAATGTGAAAGTGTATATATGAGATAAGACCTAA
53336385 TGGCCAATGTGATGAATGTGAAAGTGTATATATGAGATAAGACCTAA
1 TGGCCAATGTGATGAATGTGAAAGTGTATATATGAGATAAGACCTAA
* * *
53336432 TGGCCAATGTGATGAATGTGAAAGTGTATATATGTGATAAGGCCGAA
1 TGGCCAATGTGATGAATGTGAAAGTGTATATATGAGATAAGACCTAA
* * *
53336479 TGGCCAATGTGATGGATGTGAAAGTGTATAAATGTGATAAG
1 TGGCCAATGTGATGAATGTGAAAGTGTATATATGAGATAAG
53336520 TCCCGAAGGG
Statistics
Matches: 857, Mismatches: 30, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
47 857 1.00
ACGTcount: A:0.37, C:0.08, G:0.27, T:0.28
Consensus pattern (47 bp):
TGGCCAATGTGATGAATGTGAAAGTGTATATATGAGATAAGACCTAA
Found at i:53339059 original size:109 final size:109
Alignment explanation
Indices: 53338933--53339251 Score: 510
Period size: 101 Copynumber: 3.0 Consensus size: 109
53338923 GGAATTAACG
*
53338933 GCCGACCAATATGCATGGATTAATGACTTGAATTATTTATTATGTTTTATGGCATTGTGGTATAC
1 GCCGACCAATATGCATGGATTAATGACTTGAATTATTTATTATGTTTTATGGCATTATGGTATAC
53338998 TTTAATATATGTTAATATATTATATTTAATAAAAGATGAAAGTA
66 TTTAATATATGTTAATATATTATATTTAATAAAAGATGAAAGTA
53339042 GCCGACCAATATGCATGGATTAATGACTTGAATTATTTATTATGTTTTATGGCATTATGGTATAC
1 GCCGACCAATATGCATGGATTAATGACTTGAATTATTTATTATGTTTTATGGCATTATGGTATAC
53339107 -TTAATATATG-T--TA-A-TATA-TT-ATAAAAGATGAAAGTA
66 TTTAATATATGTTAATATATTATATTTAATAAAAGATGAAAGTA
* * *
53339143 GCTGACCAATATGCATGGATTAATGACTTGAATTGTTTATTATATTTTATGGCATTATGGTATAC
1 GCCGACCAATATGCATGGATTAATGACTTGAATTATTTATTATGTTTTATGGCATTATGGTATAC
* * * *
53339208 TTTAATATATGTTAATATATTATGTTTAAGAAGAGAGGAAAGTA
66 TTTAATATATGTTAATATATTATATTTAATAAAAGATGAAAGTA
53339252 TTCATCTTTC
Statistics
Matches: 194, Mismatches: 8, Indels: 16
0.89 0.04 0.07
Matches are distributed among these distances:
101 78 0.40
102 12 0.06
103 5 0.03
104 1 0.01
105 4 0.02
106 1 0.01
107 4 0.02
108 12 0.06
109 77 0.40
ACGTcount: A:0.36, C:0.07, G:0.17, T:0.40
Consensus pattern (109 bp):
GCCGACCAATATGCATGGATTAATGACTTGAATTATTTATTATGTTTTATGGCATTATGGTATAC
TTTAATATATGTTAATATATTATATTTAATAAAAGATGAAAGTA
Found at i:53339654 original size:28 final size:28
Alignment explanation
Indices: 53339614--53339683 Score: 106
Period size: 28 Copynumber: 2.5 Consensus size: 28
53339604 TATGAGATTG
*
53339614 GCACTAAGTGTGCGAGTTTAATT-GTATA
1 GCACTAAGTGTGCGAGTTTAATTATTA-A
*
53339642 GCACTAAGTGTGCGAGTTTGATTATTAA
1 GCACTAAGTGTGCGAGTTTAATTATTAA
53339670 GCACTAAGTGTGCG
1 GCACTAAGTGTGCG
53339684 GACTTACTAT
Statistics
Matches: 39, Mismatches: 2, Indels: 2
0.91 0.05 0.05
Matches are distributed among these distances:
28 37 0.95
29 2 0.05
ACGTcount: A:0.27, C:0.13, G:0.27, T:0.33
Consensus pattern (28 bp):
GCACTAAGTGTGCGAGTTTAATTATTAA
Found at i:53343698 original size:34 final size:35
Alignment explanation
Indices: 53343638--53343724 Score: 88
Period size: 34 Copynumber: 2.5 Consensus size: 35
53343628 GCAGTGTAAA
* * * * *
53343638 CAGTTTGGGCCTAAACCC-TTATCGGTAGCAATAT
1 CAGTATGGGCCTTAGCCCATTATCGGTAACAATAG
*
53343672 CAGTATGGGCCTTAGCCCATTA-CGGTAACAGTAG
1 CAGTATGGGCCTTAGCCCATTATCGGTAACAATAG
* *
53343706 CAGTGTGGACCTTAGCCCA
1 CAGTATGGGCCTTAGCCCA
53343725 ATTCAGTATA
Statistics
Matches: 44, Mismatches: 8, Indels: 2
0.81 0.15 0.04
Matches are distributed among these distances:
34 41 0.93
35 3 0.07
ACGTcount: A:0.25, C:0.25, G:0.24, T:0.25
Consensus pattern (35 bp):
CAGTATGGGCCTTAGCCCATTATCGGTAACAATAG
Found at i:53345220 original size:22 final size:22
Alignment explanation
Indices: 53345193--53345235 Score: 77
Period size: 22 Copynumber: 2.0 Consensus size: 22
53345183 TCAAGAGAAG
53345193 GGGAGATAGCAAGAATCGGTCA
1 GGGAGATAGCAAGAATCGGTCA
*
53345215 GGGAGATAGTAAGAATCGGTC
1 GGGAGATAGCAAGAATCGGTC
53345236 TAACCAAAAA
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
22 20 1.00
ACGTcount: A:0.35, C:0.12, G:0.37, T:0.16
Consensus pattern (22 bp):
GGGAGATAGCAAGAATCGGTCA
Found at i:53355851 original size:56 final size:56
Alignment explanation
Indices: 53355668--53355843 Score: 275
Period size: 56 Copynumber: 3.2 Consensus size: 56
53355658 TCTCAAACAG
*
53355668 GGTCTTACTC-CACACATATAAT-AGAATCACATATCGATGCCAACATATTAAACAT
1 GGTCTTACTCGCACACATAT-ATCAGAATCACATATCGATGCCAACATATTAAACGT
* *
53355723 AGTCTTACTCACACACATATATCAGAATCACATATCGATGCCAACATATTAAACGT
1 GGTCTTACTCGCACACATATATCAGAATCACATATCGATGCCAACATATTAAACGT
* * *
53355779 GGTCTTACTCGCACACATATATCGGAATCACATATCAATGCCAACGTATTAAACGT
1 GGTCTTACTCGCACACATATATCAGAATCACATATCGATGCCAACATATTAAACGT
53355835 GGTCTTACT
1 GGTCTTACT
53355844 TGTACACAAA
Statistics
Matches: 112, Mismatches: 7, Indels: 3
0.92 0.06 0.02
Matches are distributed among these distances:
55 11 0.10
56 101 0.90
ACGTcount: A:0.36, C:0.24, G:0.11, T:0.28
Consensus pattern (56 bp):
GGTCTTACTCGCACACATATATCAGAATCACATATCGATGCCAACATATTAAACGT
Found at i:53357757 original size:20 final size:19
Alignment explanation
Indices: 53357724--53357770 Score: 58
Period size: 20 Copynumber: 2.4 Consensus size: 19
53357714 GTCATTTTGT
* *
53357724 AAAATTTGTAAAATAGGTGG
1 AAAATGTGTAAAATA-ATGG
*
53357744 AAAATGTGTGAAATAATGG
1 AAAATGTGTAAAATAATGG
53357763 AAAATGTG
1 AAAATGTG
53357771 GGTTGTCCTA
Statistics
Matches: 24, Mismatches: 3, Indels: 1
0.86 0.11 0.04
Matches are distributed among these distances:
19 11 0.46
20 13 0.54
ACGTcount: A:0.47, C:0.00, G:0.26, T:0.28
Consensus pattern (19 bp):
AAAATGTGTAAAATAATGG
Found at i:53358367 original size:48 final size:48
Alignment explanation
Indices: 53358315--53358483 Score: 284
Period size: 48 Copynumber: 3.5 Consensus size: 48
53358305 TGATCCCGTA
*
53358315 TAAGACCATGTCTGGGACATGGCATCGGCATCGTTGTGTGAGCCAGTG
1 TAAGACCATGTCTGGGACATGGCATCGGCATCGTTATGTGAGCCAGTG
* * * *
53358363 TAAGACCATGCCTGGGACATGGCATCGGCATCATTACGTGAGCTAGTG
1 TAAGACCATGTCTGGGACATGGCATCGGCATCGTTATGTGAGCCAGTG
*
53358411 TAAGACCATGTCTGGGACATGGCATCGGCATCGTTATGTGAGCCAATG
1 TAAGACCATGTCTGGGACATGGCATCGGCATCGTTATGTGAGCCAGTG
53358459 TAAGACCATGTCTGGGACATGGCAT
1 TAAGACCATGTCTGGGACATGGCAT
53358484 TGGTACGATA
Statistics
Matches: 111, Mismatches: 10, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
48 111 1.00
ACGTcount: A:0.24, C:0.21, G:0.30, T:0.24
Consensus pattern (48 bp):
TAAGACCATGTCTGGGACATGGCATCGGCATCGTTATGTGAGCCAGTG
Found at i:53366086 original size:1 final size:1
Alignment explanation
Indices: 53366080--53366113 Score: 50
Period size: 1 Copynumber: 34.0 Consensus size: 1
53366070 GGAGTAAAGG
* *
53366080 AAAAAAAAAAAAAAAAAAAAAAGAAAGAAAAAAA
1 AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA
53366114 GACCTGTTCA
Statistics
Matches: 29, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
1 29 1.00
ACGTcount: A:0.94, C:0.00, G:0.06, T:0.00
Consensus pattern (1 bp):
A
Found at i:53367185 original size:65 final size:65
Alignment explanation
Indices: 53367116--53367242 Score: 247
Period size: 65 Copynumber: 2.0 Consensus size: 65
53367106 TATTAAAATT
53367116 GGGGGGGGGGGG-GAATAGTTAGATATTAAAATTTTGGGTAAACTATTAAAATAATTATTTTTTG
1 GGGGGGGGGGGGAGAATAGTTAGATATTAAAATTTTGGGTAAACTATTAAAATAATTATTTTTTG
53367180 GGGGGGGGGGGGAGAATAGTTAGATATTAAAATTTTGGGTAAACTATTAAAATAATTATTTTT
1 GGGGGGGGGGGGAGAATAGTTAGATATTAAAATTTTGGGTAAACTATTAAAATAATTATTTTT
53367243 ATTTACCTCA
Statistics
Matches: 62, Mismatches: 0, Indels: 1
0.98 0.00 0.02
Matches are distributed among these distances:
64 12 0.19
65 50 0.81
ACGTcount: A:0.34, C:0.02, G:0.29, T:0.35
Consensus pattern (65 bp):
GGGGGGGGGGGGAGAATAGTTAGATATTAAAATTTTGGGTAAACTATTAAAATAATTATTTTTTG
Found at i:53369326 original size:59 final size:58
Alignment explanation
Indices: 53369208--53369331 Score: 139
Period size: 59 Copynumber: 2.1 Consensus size: 58
53369198 CTTTTTTTTC
* *
53369208 AAAATTAATTAAATTATTTTAAAAATTGATTAAAAACTCTAAAAATTTTAAAAATATAG
1 AAAATTAATTAAATTATTTTAAAAATT-ATTAAAAAATATAAAAATTTTAAAAATATAG
*
53369267 AAAATT-ATTAAAGTTA-TTT-AAAATT-TTCAAAAAATATAAAAACTATTTAAAAGTTATAG
1 AAAATTAATTAAA-TTATTTTAAAAATTATT-AAAAAATATAAAAA-T-TTTAAAA-ATATAG
53369326 AAAATT
1 AAAATT
53369332 GTAAAAGGAA
Statistics
Matches: 57, Mismatches: 3, Indels: 10
0.81 0.04 0.14
Matches are distributed among these distances:
55 2 0.04
56 12 0.21
57 7 0.12
58 16 0.28
59 20 0.35
ACGTcount: A:0.56, C:0.03, G:0.04, T:0.37
Consensus pattern (58 bp):
AAAATTAATTAAATTATTTTAAAAATTATTAAAAAATATAAAAATTTTAAAAATATAG
Found at i:53369329 original size:29 final size:27
Alignment explanation
Indices: 53369247--53369330 Score: 71
Period size: 29 Copynumber: 3.0 Consensus size: 27
53369237 TTAAAAACTC
*
53369247 TAAAAAT-TTTAAAAATATAGAAAATTA
1 TAAAAATATTTAAAATTATAGAAAA-TA
** * *
53369274 TTAAAGTTATTTAAAATTTTCAAAAAATA
1 -TAAAAATATTTAAAATTAT-AGAAAATA
53369303 TAAAAACTATTTAAAAGTTATAGAAAAT
1 TAAAAA-TATTTAAAA-TTATAGAAAAT
53369331 TGTAAAAGGA
Statistics
Matches: 43, Mismatches: 9, Indels: 7
0.73 0.15 0.12
Matches are distributed among these distances:
28 9 0.21
29 26 0.60
30 8 0.19
ACGTcount: A:0.57, C:0.02, G:0.05, T:0.36
Consensus pattern (27 bp):
TAAAAATATTTAAAATTATAGAAAATA
Found at i:53371413 original size:73 final size:72
Alignment explanation
Indices: 53371315--53371460 Score: 231
Period size: 73 Copynumber: 2.0 Consensus size: 72
53371305 GGTTTTATAG
* *
53371315 CAAATAAATCATATTTTCAGAATTTT-GTAGGGAAAGGAGCAAATTGTAAAACAAGGGAAAAGGG
1 CAAATAAACCATATTTTCAGAATTTTAG-AGGAAAAGGAGCAAATTGTAAAACAAGGGAAAAGGG
*
53371379 GGAGTGGC
65 AGAGTGGC
*
53371387 NCAAATAAACCATATTTTCAGAATTTTAGAGGAAAATGAGCAAATTGTAAAACAAGGGAAAAGGG
1 -CAAATAAACCATATTTTCAGAATTTTAGAGGAAAAGGAGCAAATTGTAAAACAAGGGAAAAGGG
53371452 AGAGTGGC
65 AGAGTGGC
53371460 C
1 C
53371461 TGATAGTAAA
Statistics
Matches: 68, Mismatches: 4, Indels: 3
0.91 0.05 0.04
Matches are distributed among these distances:
72 1 0.01
73 66 0.97
74 1 0.01
ACGTcount: A:0.43, C:0.10, G:0.25, T:0.21
Consensus pattern (72 bp):
CAAATAAACCATATTTTCAGAATTTTAGAGGAAAAGGAGCAAATTGTAAAACAAGGGAAAAGGGA
GAGTGGC
Found at i:53384706 original size:40 final size:40
Alignment explanation
Indices: 53384662--53384885 Score: 274
Period size: 40 Copynumber: 5.6 Consensus size: 40
53384652 TCCTCGTTCA
* *
53384662 AATGCCTTCGGGACATAGCCCGGATTTAACAACTCGCACG
1 AATGCCTTCGGGACTTAACCCGGATTTAACAACTCGCACG
53384702 AATGCCTTCGGGACTTAACCCGGATTTAACAACTCGCACG
1 AATGCCTTCGGGACTTAACCCGGATTTAACAACTCGCACG
*
53384742 AATGCCTTCGGGACTTAACCCGGATTTAATAACTCGCACG
1 AATGCCTTCGGGACTTAACCCGGATTTAACAACTCGCACG
** * *
53384782 AATGCCTTCGGGACTTAACCCGGATTTAGTATCTCGCACA
1 AATGCCTTCGGGACTTAACCCGGATTTAACAACTCGCACG
* * * * *
53384822 AAGGCCTTC-GGATCTTAATCCGGATATATTC-ACTTAGCAC-
1 AATGCCTTCGGGA-CTTAACCCGGATTTA-ACAAC-TCGCACG
* *
53384862 AAAGCCTTCGGGACTTAGCCCGGA
1 AATGCCTTCGGGACTTAACCCGGA
53384886 CAGCATTCAA
Statistics
Matches: 164, Mismatches: 16, Indels: 8
0.87 0.09 0.04
Matches are distributed among these distances:
39 3 0.02
40 153 0.93
41 8 0.05
ACGTcount: A:0.27, C:0.28, G:0.21, T:0.24
Consensus pattern (40 bp):
AATGCCTTCGGGACTTAACCCGGATTTAACAACTCGCACG
Found at i:53387709 original size:20 final size:20
Alignment explanation
Indices: 53387677--53387730 Score: 81
Period size: 20 Copynumber: 2.7 Consensus size: 20
53387667 TTTAAGAGCC
*
53387677 ACACGCCCATGTGGCTTGGG
1 ACACGCCCGTGTGGCTTGGG
*
53387697 ACAGGCCCGTGTGGCTTGGG
1 ACACGCCCGTGTGGCTTGGG
*
53387717 ACACACCCGTGTGG
1 ACACGCCCGTGTGG
53387731 GCAGGCCATG
Statistics
Matches: 30, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
20 30 1.00
ACGTcount: A:0.15, C:0.30, G:0.37, T:0.19
Consensus pattern (20 bp):
ACACGCCCGTGTGGCTTGGG
Found at i:53388531 original size:43 final size:42
Alignment explanation
Indices: 53388483--53388621 Score: 130
Period size: 38 Copynumber: 3.4 Consensus size: 42
53388473 TACCAATGCC
*
53388483 ATATCCCAGA-TATGGTATTACATAGAATCTCATATCGGTGGCA
1 ATATCCCA-ACTATGGT-TTACATAGAATCTCATATCGATGGCA
* *
53388526 ATATCCCAACAATGG--T--ATGGAATCTCATATCGATGGCA
1 ATATCCCAACTATGGTTTACATAGAATCTCATATCGATGGCA
* * *
53388564 ATATCCCAACTATGGTCTTACA-CGAATCATCATATTGAT-GCC
1 ATATCCCAACTATGGT-TTACATAGAATC-TCATATCGATGGCA
*
53388606 ATATCCCAAATATGGT
1 ATATCCCAACTATGGT
53388622 CTTATACGTA
Statistics
Matches: 81, Mismatches: 8, Indels: 15
0.78 0.08 0.14
Matches are distributed among these distances:
38 34 0.42
40 1 0.01
41 1 0.01
42 23 0.28
43 22 0.27
ACGTcount: A:0.33, C:0.22, G:0.16, T:0.29
Consensus pattern (42 bp):
ATATCCCAACTATGGTTTACATAGAATCTCATATCGATGGCA
Found at i:53388611 original size:42 final size:42
Alignment explanation
Indices: 53388483--53388637 Score: 142
Period size: 42 Copynumber: 3.7 Consensus size: 42
53388473 TACCAATGCC
* * * *
53388483 ATATCCCAGATATGGTATTACATAGAATCTCATATCGGTGGCA
1 ATATCCCAAATATGGTCTTACA-CGAATCTCATATCGATGGCA
**
53388526 ATATCCCAACA-ATGG---TA-TGGAATCTCATATCGATGGCA
1 ATATCCCAA-ATATGGTCTTACACGAATCTCATATCGATGGCA
* * *
53388564 ATATCCCAACTATGGTCTTACACGAATCATCATATTGAT-GCC
1 ATATCCCAAATATGGTCTTACACGAATC-TCATATCGATGGCA
*
53388606 ATATCCCAAATATGGTCTTATACGTAATCTCA
1 ATATCCCAAATATGGTCTTACACG-AATCTCA
53388638 AATAACCCTA
Statistics
Matches: 93, Mismatches: 11, Indels: 17
0.77 0.09 0.14
Matches are distributed among these distances:
38 31 0.33
40 2 0.02
41 2 0.02
42 32 0.34
43 25 0.27
44 1 0.01
ACGTcount: A:0.33, C:0.22, G:0.15, T:0.30
Consensus pattern (42 bp):
ATATCCCAAATATGGTCTTACACGAATCTCATATCGATGGCA
Found at i:53395022 original size:15 final size:14
Alignment explanation
Indices: 53395002--53395032 Score: 53
Period size: 15 Copynumber: 2.1 Consensus size: 14
53394992 GCTGAAATTT
53395002 CTAGGGTTTCCATAG
1 CTAGGGTTTCCA-AG
53395017 CTAGGGTTTCCAAG
1 CTAGGGTTTCCAAG
53395031 CT
1 CT
53395033 TTCCGAGCTC
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
14 4 0.25
15 12 0.75
ACGTcount: A:0.19, C:0.23, G:0.26, T:0.32
Consensus pattern (14 bp):
CTAGGGTTTCCAAG
Found at i:53412993 original size:44 final size:44
Alignment explanation
Indices: 53412921--53413043 Score: 153
Period size: 44 Copynumber: 2.8 Consensus size: 44
53412911 TACGGTACTA
* * * **
53412921 ATCGGGCCTTTGAGCCTAGCATGTTATAATGCTGGTGAAATGAT
1 ATCGGGCCTTCGAGCCTAGCAGGCTATAATGCCAGTGAAATGAT
* *
53412965 ATCGGGCCTTCAAGCCTAGTAGGCTATAATGCCAGTGAAATGAT
1 ATCGGGCCTTCGAGCCTAGCAGGCTATAATGCCAGTGAAATGAT
53413009 ATCGGG-CTTCGAGCCTAGCAGG-TGA-AATGCCAGTG
1 ATCGGGCCTTCGAGCCTAGCAGGCT-ATAATGCCAGTG
53413044 GATGAATTTG
Statistics
Matches: 69, Mismatches: 9, Indels: 4
0.84 0.11 0.05
Matches are distributed among these distances:
42 11 0.16
43 15 0.22
44 43 0.62
ACGTcount: A:0.26, C:0.20, G:0.28, T:0.26
Consensus pattern (44 bp):
ATCGGGCCTTCGAGCCTAGCAGGCTATAATGCCAGTGAAATGAT
Found at i:53430388 original size:103 final size:103
Alignment explanation
Indices: 53430209--53430407 Score: 344
Period size: 103 Copynumber: 1.9 Consensus size: 103
53430199 AGTCTTATCT
* *
53430209 CCCTGAAGTTGTAGTGGAGCAGACTGAAGATAGCAGATCTTGCCTCCCTGAAGTTGCAGTGAAGT
1 CCCTGAAGTTGCAGTGGAGCAGACTGAAGATAGCAGATCTTGCCTCCCTGAAGTTGCAGTGAAGC
*
53430274 AGATCGAAGCCACAAACCTTATCTCTCTGAAATTGTAG
66 AGATCAAAGCCACAAACCTTATCTCTCTGAAATTGTAG
* *
53430312 CCCTGAAGTTGCAGTGGAGCAGACTGAAGATAGCAGATCTTGTCTCCCTGAAGTTGCAGTGGAGC
1 CCCTGAAGTTGCAGTGGAGCAGACTGAAGATAGCAGATCTTGCCTCCCTGAAGTTGCAGTGAAGC
*
53430377 AGATCAAAGCCACAATCCTTATCTCTCTGAA
66 AGATCAAAGCCACAAACCTTATCTCTCTGAA
53430408 GTTGCAGTTG
Statistics
Matches: 90, Mismatches: 6, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
103 90 1.00
ACGTcount: A:0.29, C:0.23, G:0.24, T:0.25
Consensus pattern (103 bp):
CCCTGAAGTTGCAGTGGAGCAGACTGAAGATAGCAGATCTTGCCTCCCTGAAGTTGCAGTGAAGC
AGATCAAAGCCACAAACCTTATCTCTCTGAAATTGTAG
Found at i:53438269 original size:13 final size:13
Alignment explanation
Indices: 53438244--53438269 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
53438234 CACACAGGCA
53438244 TGTCACACGGTCG
1 TGTCACACGGTCG
53438257 TGTCACACGGTCG
1 TGTCACACGGTCG
53438270 GGTCCCTTTG
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:0.15, C:0.31, G:0.31, T:0.23
Consensus pattern (13 bp):
TGTCACACGGTCG
Found at i:53459613 original size:22 final size:22
Alignment explanation
Indices: 53459571--53459613 Score: 52
Period size: 22 Copynumber: 2.0 Consensus size: 22
53459561 ACACTGAGTT
*
53459571 TCTTCTCCTAGTTAAACTCTAC
1 TCTTCTCCTAGTGAAACTCTAC
*
53459593 TCTTTTCCTAGTCGAAA-TCTA
1 TCTTCTCCTAGT-GAAACTCTA
53459614 ATTAGTCTAA
Statistics
Matches: 18, Mismatches: 2, Indels: 2
0.82 0.09 0.09
Matches are distributed among these distances:
22 15 0.83
23 3 0.17
ACGTcount: A:0.23, C:0.28, G:0.07, T:0.42
Consensus pattern (22 bp):
TCTTCTCCTAGTGAAACTCTAC
Found at i:53464135 original size:20 final size:21
Alignment explanation
Indices: 53464110--53464148 Score: 55
Period size: 21 Copynumber: 1.9 Consensus size: 21
53464100 GTTTAAATAC
53464110 TTTATT-TTC-ATAATATTTAT
1 TTTATTATTCTATAA-ATTTAT
53464130 TTTATTATTCTATAAATTT
1 TTTATTATTCTATAAATTT
53464149 TTATAATTTA
Statistics
Matches: 17, Mismatches: 0, Indels: 3
0.85 0.00 0.15
Matches are distributed among these distances:
20 6 0.35
21 7 0.41
22 4 0.24
ACGTcount: A:0.31, C:0.05, G:0.00, T:0.64
Consensus pattern (21 bp):
TTTATTATTCTATAAATTTAT
Found at i:53464151 original size:23 final size:22
Alignment explanation
Indices: 53464110--53464161 Score: 54
Period size: 23 Copynumber: 2.3 Consensus size: 22
53464100 GTTTAAATAC
53464110 TTTATT-TTCATAATATTTAT-
1 TTTATTATTCATAATATTTATA
*
53464130 TTTATTATTCTATAAATTTTTATAA
1 TTTATTATTC-AT-AATATTTAT-A
53464155 TTTATTA
1 TTTATTA
53464162 GATTTTTATG
Statistics
Matches: 26, Mismatches: 1, Indels: 5
0.81 0.03 0.16
Matches are distributed among these distances:
20 6 0.23
21 3 0.12
22 2 0.08
23 8 0.31
25 7 0.27
ACGTcount: A:0.33, C:0.04, G:0.00, T:0.63
Consensus pattern (22 bp):
TTTATTATTCATAATATTTATA
Found at i:53464152 original size:18 final size:18
Alignment explanation
Indices: 53464129--53464170 Score: 50
Period size: 18 Copynumber: 2.3 Consensus size: 18
53464119 ATAATATTTA
*
53464129 TTTTATTATTCTA-TAAAT
1 TTTTATAATT-TATTAAAT
*
53464147 TTTTATAATTTATTAGAT
1 TTTTATAATTTATTAAAT
53464165 TTTTAT
1 TTTTAT
53464171 GAAAATTTTT
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
17 2 0.10
18 19 0.90
ACGTcount: A:0.31, C:0.02, G:0.02, T:0.64
Consensus pattern (18 bp):
TTTTATAATTTATTAAAT
Found at i:53464183 original size:49 final size:49
Alignment explanation
Indices: 53464129--53464251 Score: 128
Period size: 49 Copynumber: 2.5 Consensus size: 49
53464119 ATAATATTTA
* *
53464129 TTTTATTATTCTATAA-ATTTTTAT-AA-TTTATTAGATTTTTATGAAAATT
1 TTTTATTATT-TATAAGATTTTTATGAATTTTATAAG-TTTTTAT-AAAAGT
*
53464178 TTTTATTATTTATAAGTTTTTTATGAATTTTATAAGTTTTTATAAAAGT
1 TTTTATTATTTATAAGATTTTTATGAATTTTATAAGTTTTTATAAAAGT
* *
53464227 TTTAAATATTT-TAAGTATGTTTTAT
1 TTTTATTATTTATAAG-AT-TTTTAT
53464252 ATGTTTTATT
Statistics
Matches: 63, Mismatches: 6, Indels: 9
0.81 0.08 0.12
Matches are distributed among these distances:
48 9 0.14
49 32 0.51
50 15 0.24
51 7 0.11
ACGTcount: A:0.33, C:0.01, G:0.07, T:0.59
Consensus pattern (49 bp):
TTTTATTATTTATAAGATTTTTATGAATTTTATAAGTTTTTATAAAAGT
Found at i:53464189 original size:31 final size:31
Alignment explanation
Indices: 53464146--53464204 Score: 91
Period size: 31 Copynumber: 1.9 Consensus size: 31
53464136 ATTCTATAAA
*
53464146 TTTTTATAATTTATTAGATTTTTATGAAAAT
1 TTTTTATAATTTATAAGATTTTTATGAAAAT
* *
53464177 TTTTTATTATTTATAAGTTTTTTATGAA
1 TTTTTATAATTTATAAGATTTTTATGAA
53464205 TTTTATAAGT
Statistics
Matches: 25, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
31 25 1.00
ACGTcount: A:0.32, C:0.00, G:0.07, T:0.61
Consensus pattern (31 bp):
TTTTTATAATTTATAAGATTTTTATGAAAAT
Found at i:53471798 original size:23 final size:23
Alignment explanation
Indices: 53471770--53471833 Score: 76
Period size: 23 Copynumber: 2.8 Consensus size: 23
53471760 GAGCTAAAAG
*
53471770 GTAAGCTCCAATGAGCTGAAACA
1 GTAAGCTCCAACGAGCTGAAACA
** *
53471793 GTAAGCTCTTACGAGCTGAATCA
1 GTAAGCTCCAACGAGCTGAAACA
53471816 GTAAGCT-CATACGAGCTG
1 GTAAGCTCCA-ACGAGCTG
53471834 TGGTGAGTTC
Statistics
Matches: 34, Mismatches: 6, Indels: 2
0.81 0.14 0.05
Matches are distributed among these distances:
23 34 1.00
ACGTcount: A:0.33, C:0.22, G:0.23, T:0.22
Consensus pattern (23 bp):
GTAAGCTCCAACGAGCTGAAACA
Found at i:53479060 original size:24 final size:25
Alignment explanation
Indices: 53479033--53479091 Score: 77
Period size: 24 Copynumber: 2.4 Consensus size: 25
53479023 GTAATGTATA
*
53479033 TATTTTTTTGGTT-AATTTAATTCT
1 TATTTTTTTAGTTAAATTTAATTCT
*
53479057 TA-TTTTTTAGTTAAATTTAATTTT
1 TATTTTTTTAGTTAAATTTAATTCT
53479081 TAATTTTTTTA
1 T-ATTTTTTTA
53479092 AAAAAGTTAA
Statistics
Matches: 30, Mismatches: 2, Indels: 4
0.83 0.06 0.11
Matches are distributed among these distances:
23 9 0.30
24 13 0.43
25 1 0.03
26 7 0.23
ACGTcount: A:0.25, C:0.02, G:0.05, T:0.68
Consensus pattern (25 bp):
TATTTTTTTAGTTAAATTTAATTCT
Found at i:53481829 original size:19 final size:19
Alignment explanation
Indices: 53481805--53481842 Score: 67
Period size: 19 Copynumber: 2.0 Consensus size: 19
53481795 TTGAGATTGC
*
53481805 CAACCTATTTGCTTGAAAT
1 CAACCTATTTGCCTGAAAT
53481824 CAACCTATTTGCCTGAAAT
1 CAACCTATTTGCCTGAAAT
53481843 TATTCATTTC
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
19 18 1.00
ACGTcount: A:0.32, C:0.24, G:0.11, T:0.34
Consensus pattern (19 bp):
CAACCTATTTGCCTGAAAT
Found at i:53494169 original size:88 final size:88
Alignment explanation
Indices: 53494020--53494243 Score: 324
Period size: 88 Copynumber: 2.6 Consensus size: 88
53494010 AGCTGAAGAT
* * *
53494020 ATCCAAGATGATTTGGCATTTCTGTATCAGGCAGGGAGCAGATCGAAGACATAGTTGATTTGGCT
1 ATCCAAGATGATTTGGCATCTCTATATCAGGCAGGGAGCAGATCGAAGACATAGCTGATTTGGCT
* *
53494085 TTCACGTGTTTACGTTGAAGTAG
66 TTCACGTGTTTACGTTGAAGCAA
*
53494108 ATCCAAGATGATTTGGCATCTCTATATCAGGCGGGGAGCAGATCGAAGACATAGCTGATTTGGCT
1 ATCCAAGATGATTTGGCATCTCTATATCAGGCAGGGAGCAGATCGAAGACATAGCTGATTTGGCT
*
53494173 TTCATGTGTTTACGTTGAAGCAA
66 TTCACGTGTTTACGTTGAAGCAA
* * * * * *
53494196 ATCCAAGATGATTTGACGTCTCTGTAGC-GGCAGAGAGTAGATCGAAGA
1 ATCCAAGATGATTTGGCATCTCTATATCAGGCAGGGAGCAGATCGAAGA
53494244 TAACAGATTT
Statistics
Matches: 122, Mismatches: 14, Indels: 1
0.89 0.10 0.01
Matches are distributed among these distances:
87 17 0.14
88 105 0.86
ACGTcount: A:0.28, C:0.16, G:0.27, T:0.29
Consensus pattern (88 bp):
ATCCAAGATGATTTGGCATCTCTATATCAGGCAGGGAGCAGATCGAAGACATAGCTGATTTGGCT
TTCACGTGTTTACGTTGAAGCAA
Found at i:53494260 original size:44 final size:44
Alignment explanation
Indices: 53494205--53495993 Score: 2274
Period size: 44 Copynumber: 41.4 Consensus size: 44
53494195 AATCCAAGAT
* * *
53494205 GATTTGACGTCTCTGTAGCGGCAGAGAGTAGATCGAAGATAACA
1 GATTTGGCGTCTCTGTAGCGGCGGAGAGCAGATCGAAGATAACA
* * *
53494249 GATTTGGCGTCTTTGTAACGGCGGAGAGTAGATCGAAGATAACA
1 GATTTGGCGTCTCTGTAGCGGCGGAGAGCAGATCGAAGATAACA
* * *
53494293 GATTTGGCGTCTCTATAGCGACGGAGAGCAGGTCGAAGATAACA
1 GATTTGGCGTCTCTGTAGCGGCGGAGAGCAGATCGAAGATAACA
* * **
53494337 GATTTGGCATCTCTGTAGCGGCAGAGAGCAGATTAAAGATAACA
1 GATTTGGCGTCTCTGTAGCGGCGGAGAGCAGATCGAAGATAACA
** * *
53494381 GATTTGGTATCTCTGTAGCGGCAGAAAGCAGATCGAAGAT----
1 GATTTGGCGTCTCTGTAGCGGCGGAGAGCAGATCGAAGATAACA
* *
53494421 GATTTGGCATCTCTGTAGCGGCAGAGAGCAGATCGAAGATAACA
1 GATTTGGCGTCTCTGTAGCGGCGGAGAGCAGATCGAAGATAACA
*
53494465 GATTTGGCGTCTCTGTAGCGGCGGAGAGCAGATAGAAGATAACA
1 GATTTGGCGTCTCTGTAGCGGCGGAGAGCAGATCGAAGATAACA
*
53494509 GATTTGGCGTCTCTTTAGCGGCGGAGAGCAGATCGAAGATAACA
1 GATTTGGCGTCTCTGTAGCGGCGGAGAGCAGATCGAAGATAACA
* * ** *
53494553 AATTTGGCATCTCTGTAGCGGCAAAGAGTAGATCGAAGAT----
1 GATTTGGCGTCTCTGTAGCGGCGGAGAGCAGATCGAAGATAACA
* * * *
53494593 GATTTGGCATTTCTATAGCGGCGGAGAGCAGATTGAAGAT----
1 GATTTGGCGTCTCTGTAGCGGCGGAGAGCAGATCGAAGATAACA
* * *
53494633 GATTTGGCATCTCTGTAGTGGCGGAAAGCAGATCGAAGATAACA
1 GATTTGGCGTCTCTGTAGCGGCGGAGAGCAGATCGAAGATAACA
* * * *
53494677 GATTTGACATCTCTGTAACGGCGGAGAGCAGATTGAAGATAACA
1 GATTTGGCGTCTCTGTAGCGGCGGAGAGCAGATCGAAGATAACA
* *
53494721 GATTTGGAGTCTCTATAGCGGCGGAGAGCAGATCGAAGATAACA
1 GATTTGGCGTCTCTGTAGCGGCGGAGAGCAGATCGAAGATAACA
* ***
53494765 GATTTGGCATCTCTGTAGCGATAGAGAGCAGATCGAAGATAACA
1 GATTTGGCGTCTCTGTAGCGGCGGAGAGCAGATCGAAGATAACA
* *
53494809 GATTTGGTGTCTCTGTAGCGGCGGAGAGCATATCGAAGATAACA
1 GATTTGGCGTCTCTGTAGCGGCGGAGAGCAGATCGAAGATAACA
* * * ** *
53494853 GATTTAGCATCTCGGTAGCGGTAGAGAGCAGATCGAAGATAGCA
1 GATTTGGCGTCTCTGTAGCGGCGGAGAGCAGATCGAAGATAACA
* *
53494897 AATTTGGCGTCTCTGTAGCGACGGAGAGCAGATCGAAGATAACA
1 GATTTGGCGTCTCTGTAGCGGCGGAGAGCAGATCGAAGATAACA
* * *
53494941 GATTTGGCGTCTCTATTGCGGCGGAGAGCAGATCGAAGATAGCA
1 GATTTGGCGTCTCTGTAGCGGCGGAGAGCAGATCGAAGATAACA
* * **
53494985 GATTTGGCGTCTCTGTAGCGGCAGAGAGTAGATATAAGATAACA
1 GATTTGGCGTCTCTGTAGCGGCGGAGAGCAGATCGAAGATAACA
*
53495029 GATTTGGCGTCTCTGTAGCGGCGGAGAGCAGATAGAAGATAACA
1 GATTTGGCGTCTCTGTAGCGGCGGAGAGCAGATCGAAGATAACA
*
53495073 GATTTGGCGTCTCTTTAGCGGCGGAGAGCAGATCGAAGAT----
1 GATTTGGCGTCTCTGTAGCGGCGGAGAGCAGATCGAAGATAACA
* * * **
53495113 GATTTGGCATTTTTGTAGCGGCAAAGAGCAGATCGAAGAT----
1 GATTTGGCGTCTCTGTAGCGGCGGAGAGCAGATCGAAGATAACA
* * *
53495153 GATTTGGCATCTTTGTAGCGGCGAAGAGCAGATCGAAGATAACA
1 GATTTGGCGTCTCTGTAGCGGCGGAGAGCAGATCGAAGATAACA
* *
53495197 GATTTGGCGTCTCTATAGCGGCGGAGAGCAAATCGAAGATAACA
1 GATTTGGCGTCTCTGTAGCGGCGGAGAGCAGATCGAAGATAACA
* * * *
53495241 GATTTGGCGTCTCTATAGCGGTGGAGAGCAGATCAAAGATAGCA
1 GATTTGGCGTCTCTGTAGCGGCGGAGAGCAGATCGAAGATAACA
* * *
53495285 AATTTGGCGTCTTTGTAGCGGCAGAGAGCAGATCGAAGATAACA
1 GATTTGGCGTCTCTGTAGCGGCGGAGAGCAGATCGAAGATAACA
* * *
53495329 GATTTGGCGTCTCTATTGCGGCGGAGAGCAGATCGAAGATAGCA
1 GATTTGGCGTCTCTGTAGCGGCGGAGAGCAGATCGAAGATAACA
* *
53495373 AATTTGGCGTCTCTGTAGCGGCAGAGAGCAGATCGAAGATAACA
1 GATTTGGCGTCTCTGTAGCGGCGGAGAGCAGATCGAAGATAACA
* * *
53495417 GATTTGGCGTCTCTGTAGCGACGAAGAGCAAATCGAAGATAACA
1 GATTTGGCGTCTCTGTAGCGGCGGAGAGCAGATCGAAGATAACA
53495461 GATTTGGCGTCTCTGTAGCGGCGGAGAGCAGATCGAAGAT----
1 GATTTGGCGTCTCTGTAGCGGCGGAGAGCAGATCGAAGATAACA
* * * *
53495501 GATTTGTCATCTCTGTAACGGCAGAGAGCAGATCGAAGATAACA
1 GATTTGGCGTCTCTGTAGCGGCGGAGAGCAGATCGAAGATAACA
* * * *
53495545 GATTTGGCATCTCTATAGTGGCGGAGAGCAGATCAAAGATAACA
1 GATTTGGCGTCTCTGTAGCGGCGGAGAGCAGATCGAAGATAACA
* * *
53495589 GATTTGGCGTCTTTGTAACGGCGGAGAGTAGATC----ATAACA
1 GATTTGGCGTCTCTGTAGCGGCGGAGAGCAGATCGAAGATAACA
*
53495629 GATTTGGCGTCTCTGTAGCGGCGAAGAGCAGATCGAAGAT----
1 GATTTGGCGTCTCTGTAGCGGCGGAGAGCAGATCGAAGATAACA
* *
53495669 GATTTGGCATCTCTGTAGCGGCAGAGAGCAGATCGAAGATAACA
1 GATTTGGCGTCTCTGTAGCGGCGGAGAGCAGATCGAAGATAACA
* *
53495713 GATTTGGCGTCTCTGTAGCGGCAGAGAGCAAATCGAAGATAACA
1 GATTTGGCGTCTCTGTAGCGGCGGAGAGCAGATCGAAGATAACA
* ** *
53495757 TATTTGGCACCTCCGTAGCGGCGGAGAGCAGATCGAAGATAACA
1 GATTTGGCGTCTCTGTAGCGGCGGAGAGCAGATCGAAGATAACA
* *
53495801 GATTTGGCGTCTCTGTAGCGGCAGAGAGCAAATCGAAGATAACA
1 GATTTGGCGTCTCTGTAGCGGCGGAGAGCAGATCGAAGATAACA
* ** *
53495845 TATTTGGCACCTCCGTAGCGGCGGAGAGCAGATCGAAGATAACA
1 GATTTGGCGTCTCTGTAGCGGCGGAGAGCAGATCGAAGATAACA
* * *
53495889 GATTTGGCATCTCTGTAGCGGTGGAGAGCAGATCAAAGATAACA
1 GATTTGGCGTCTCTGTAGCGGCGGAGAGCAGATCGAAGATAACA
* * *
53495933 GATTTGGTGTCTCTGTAGCAGCGGAGAGCAGATCGAAGATAACG
1 GATTTGGCGTCTCTGTAGCGGCGGAGAGCAGATCGAAGATAACA
*
53495977 GATTTGACGTCTCTGTA
1 GATTTGGCGTCTCTGTA
53495994 TTAGACGGTG
Statistics
Matches: 1520, Mismatches: 201, Indels: 48
0.86 0.11 0.03
Matches are distributed among these distances:
40 287 0.19
44 1233 0.81
ACGTcount: A:0.30, C:0.17, G:0.31, T:0.23
Consensus pattern (44 bp):
GATTTGGCGTCTCTGTAGCGGCGGAGAGCAGATCGAAGATAACA
Found at i:53497280 original size:19 final size:19
Alignment explanation
Indices: 53497256--53497293 Score: 67
Period size: 19 Copynumber: 2.0 Consensus size: 19
53497246 TTGAGATTGC
*
53497256 CAACCTATTTGCTTGAAAT
1 CAACCTATTTGCCTGAAAT
53497275 CAACCTATTTGCCTGAAAT
1 CAACCTATTTGCCTGAAAT
53497294 TATTCATTTC
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
19 18 1.00
ACGTcount: A:0.32, C:0.24, G:0.11, T:0.34
Consensus pattern (19 bp):
CAACCTATTTGCCTGAAAT
Found at i:53499537 original size:26 final size:25
Alignment explanation
Indices: 53499495--53499548 Score: 72
Period size: 26 Copynumber: 2.1 Consensus size: 25
53499485 AATTTTGAGG
*
53499495 ATTAAATTTAGTATTTAATATTAGA
1 ATTAAATTTAATATTTAATATTAGA
* *
53499520 ATTAAATGTTAATGTTTAATATTATA
1 ATTAAAT-TTAATATTTAATATTAGA
53499546 ATT
1 ATT
53499549 TCGTTACACA
Statistics
Matches: 25, Mismatches: 3, Indels: 1
0.86 0.10 0.03
Matches are distributed among these distances:
25 7 0.28
26 18 0.72
ACGTcount: A:0.43, C:0.00, G:0.07, T:0.50
Consensus pattern (25 bp):
ATTAAATTTAATATTTAATATTAGA
Found at i:53502651 original size:15 final size:16
Alignment explanation
Indices: 53502631--53502665 Score: 56
Period size: 15 Copynumber: 2.3 Consensus size: 16
53502621 TATAGAATAT
53502631 AATAAAATAT-TAAAA
1 AATAAAATATATAAAA
53502646 AAT-AAATATATAAAA
1 AATAAAATATATAAAA
53502661 AATAA
1 AATAA
53502666 GACAGTGGCA
Statistics
Matches: 18, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
14 6 0.33
15 11 0.61
16 1 0.06
ACGTcount: A:0.74, C:0.00, G:0.00, T:0.26
Consensus pattern (16 bp):
AATAAAATATATAAAA
Found at i:53521103 original size:37 final size:37
Alignment explanation
Indices: 53521052--53521133 Score: 137
Period size: 37 Copynumber: 2.2 Consensus size: 37
53521042 CATCAAATAA
53521052 TCATATTTCATGTATATCATGTAAATACCAGTAATAGT
1 TCATA-TTCATGTATATCATGTAAATACCAGTAATAGT
* *
53521090 TCATATTCATGTATTTCATGTAAATACCATTAATAGT
1 TCATATTCATGTATATCATGTAAATACCAGTAATAGT
53521127 TCATATT
1 TCATATT
53521134 GAACTCATAT
Statistics
Matches: 42, Mismatches: 2, Indels: 1
0.93 0.04 0.02
Matches are distributed among these distances:
37 37 0.88
38 5 0.12
ACGTcount: A:0.35, C:0.13, G:0.09, T:0.43
Consensus pattern (37 bp):
TCATATTCATGTATATCATGTAAATACCAGTAATAGT
Found at i:53521294 original size:25 final size:25
Alignment explanation
Indices: 53521260--53521309 Score: 75
Period size: 25 Copynumber: 2.0 Consensus size: 25
53521250 TATGCTAATA
53521260 CGAGCTGAAT-ATCGGAAAGCTCATG
1 CGAGCTGAATAAT-GGAAAGCTCATG
*
53521285 CGAGCTGAATAATGGGAAGCTCATG
1 CGAGCTGAATAATGGAAAGCTCATG
53521310 TAAGTTGAGT
Statistics
Matches: 23, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
25 21 0.91
26 2 0.09
ACGTcount: A:0.32, C:0.18, G:0.30, T:0.20
Consensus pattern (25 bp):
CGAGCTGAATAATGGAAAGCTCATG
Found at i:53525066 original size:252 final size:252
Alignment explanation
Indices: 53524621--53525105 Score: 898
Period size: 252 Copynumber: 1.9 Consensus size: 252
53524611 AATTTAGATC
*
53524621 ATTATAGTTCTTTTAGTTTTTTATTCTGGGTTATCTTCAGAAGATGGGCACATTTATTGCATGAA
1 ATTATAGTTCTTTTAATTTTTTATTCTGGGTTATCTTCAGAAGATGGGCACATTTATTGCATGAA
*
53524686 ATGGGGGTAGGGATAATGTCCACAATTTTGGTTGGTGAATTGTGGAAGAATAGTGGGTGCTAATG
66 ATGGGGGTAGGGATAACGTCCACAATTTTGGTTGGTGAATTGTGGAAGAATAGTGGGTGCTAATG
53524751 GTCAAGGGAAGGATTTGGCTTCATCGATTTAGACAAAACAAAGGGAAATGGCAATTGGGATAGAT
131 GTCAAGGGAAGGATTTGGCTTCATCGATTTAGACAAAACAAAGGGAAATGGCAATTGGGATAGAT
* *
53524816 AACAGATCATCCATTTGTCTTCAAAAGGAGAGAGAGAGCAATGTTCATGGAATAAAT
196 AACAGATCATCCATTTGTCTTCAAAAGAAAAGAGAGAGCAATGTTCATGGAATAAAT
* *
53524873 ATTATAGTTCTTTTAATTTTTTATTTTGGGTTATCTTCAGAAGATGGGCACATTTATTTCATGAA
1 ATTATAGTTCTTTTAATTTTTTATTCTGGGTTATCTTCAGAAGATGGGCACATTTATTGCATGAA
53524938 ATGGGGGTAGGGATAACGTCCACAATTTTGGTTGGTGAATTGTGGAAGAATAGTGGGTGCTAATG
66 ATGGGGGTAGGGATAACGTCCACAATTTTGGTTGGTGAATTGTGGAAGAATAGTGGGTGCTAATG
53525003 GTCAAGGGAAGGATTTGGCTTCATCGATTTAGACAAAACAAAGGGAAATGGCAATTGGGATAGAT
131 GTCAAGGGAAGGATTTGGCTTCATCGATTTAGACAAAACAAAGGGAAATGGCAATTGGGATAGAT
* *
53525068 AACAGGTCATCCATTTGTCTTCCAAAGAAAAGAGAGAG
196 AACAGATCATCCATTTGTCTTCAAAAGAAAAGAGAGAG
53525106 AGAGAGAGAG
Statistics
Matches: 225, Mismatches: 8, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
252 225 1.00
ACGTcount: A:0.32, C:0.11, G:0.26, T:0.32
Consensus pattern (252 bp):
ATTATAGTTCTTTTAATTTTTTATTCTGGGTTATCTTCAGAAGATGGGCACATTTATTGCATGAA
ATGGGGGTAGGGATAACGTCCACAATTTTGGTTGGTGAATTGTGGAAGAATAGTGGGTGCTAATG
GTCAAGGGAAGGATTTGGCTTCATCGATTTAGACAAAACAAAGGGAAATGGCAATTGGGATAGAT
AACAGATCATCCATTTGTCTTCAAAAGAAAAGAGAGAGCAATGTTCATGGAATAAAT
Found at i:53526085 original size:41 final size:41
Alignment explanation
Indices: 53525982--53526207 Score: 300
Period size: 40 Copynumber: 5.6 Consensus size: 41
53525972 AAAAATTAAT
* * * *
53525982 AGAT-TGAGTATTAGTGGCGCTTTTAAAAAAAG-GCCGCTAA
1 AGATCTGAGCATTAGCGGCG-TTTTTAAGAAAGCGCCGCTAA
53526022 AGAT-TGAGCATTAGCGGCGTTTTTAAGAAAGCGCCGCTAA
1 AGATCTGAGCATTAGCGGCGTTTTTAAGAAAGCGCCGCTAA
* * *
53526062 AGATCTAAGCATTAGCGGCGTTTTTGAGAAAGCGCTGCTAA
1 AGATCTGAGCATTAGCGGCGTTTTTAAGAAAGCGCCGCTAA
* * *
53526103 AGATC-GAGCACTAGCGACGTTTTTAAGAAAGCGCAGCTAA
1 AGATCTGAGCATTAGCGGCGTTTTTAAGAAAGCGCCGCTAA
*
53526143 AGATCTGAGCATTAGCAGCGTTTTTAAGAAAGCGCCGCTAA
1 AGATCTGAGCATTAGCGGCGTTTTTAAGAAAGCGCCGCTAA
*
53526184 AGATC-GAGCATTAGCGACGTTTTT
1 AGATCTGAGCATTAGCGGCGTTTTT
53526208 TTAAAAATGC
Statistics
Matches: 165, Mismatches: 18, Indels: 6
0.87 0.10 0.03
Matches are distributed among these distances:
39 10 0.06
40 81 0.49
41 74 0.45
ACGTcount: A:0.31, C:0.17, G:0.26, T:0.26
Consensus pattern (41 bp):
AGATCTGAGCATTAGCGGCGTTTTTAAGAAAGCGCCGCTAA
Found at i:53526126 original size:81 final size:81
Alignment explanation
Indices: 53526010--53526207 Score: 317
Period size: 81 Copynumber: 2.5 Consensus size: 81
53526000 GCTTTTAAAA
* * *
53526010 AAAG-GCCGCTAAAGATTGAGCATTAGCGGCGTTTTTAAGAAAGCGCCGCTAAAGATCTAAGCAT
1 AAAGCGCCGCTAAAGATCGAGCATTAGCGACGTTTTTAAGAAAGCGCAGCTAAAGATCTAAGCAT
* *
53526074 TAGCGGCGTTTTTGAG
66 TAGCAGCGTTTTTAAG
* * *
53526090 AAAGCGCTGCTAAAGATCGAGCACTAGCGACGTTTTTAAGAAAGCGCAGCTAAAGATCTGAGCAT
1 AAAGCGCCGCTAAAGATCGAGCATTAGCGACGTTTTTAAGAAAGCGCAGCTAAAGATCTAAGCAT
53526155 TAGCAGCGTTTTTAAG
66 TAGCAGCGTTTTTAAG
53526171 AAAGCGCCGCTAAAGATCGAGCATTAGCGACGTTTTT
1 AAAGCGCCGCTAAAGATCGAGCATTAGCGACGTTTTT
53526208 TTAAAAATGC
Statistics
Matches: 107, Mismatches: 10, Indels: 1
0.91 0.08 0.01
Matches are distributed among these distances:
80 4 0.04
81 103 0.96
ACGTcount: A:0.31, C:0.19, G:0.26, T:0.24
Consensus pattern (81 bp):
AAAGCGCCGCTAAAGATCGAGCATTAGCGACGTTTTTAAGAAAGCGCAGCTAAAGATCTAAGCAT
TAGCAGCGTTTTTAAG
Found at i:53526208 original size:41 final size:40
Alignment explanation
Indices: 53526010--53526207 Score: 283
Period size: 41 Copynumber: 4.9 Consensus size: 40
53526000 GCTTTTAAAA
* *
53526010 AAAG-GCCGCTAAAGATTGAGCATTAGCGGCGTTTTTAAG
1 AAAGCGCCGCTAAAGATCGAGCATTAGCGACGTTTTTAAG
* * *
53526049 AAAGCGCCGCTAAAGATCTAAGCATTAGCGGCGTTTTTGAG
1 AAAGCGCCGCTAAAGATC-GAGCATTAGCGACGTTTTTAAG
* *
53526090 AAAGCGCTGCTAAAGATCGAGCACTAGCGACGTTTTTAAG
1 AAAGCGCCGCTAAAGATCGAGCATTAGCGACGTTTTTAAG
*
53526130 AAAGCGCAGCTAAAGATCTGAGCATTAGC-AGCGTTTTTAAG
1 AAAGCGCCGCTAAAGATC-GAGCATTAGCGA-CGTTTTTAAG
53526171 AAAGCGCCGCTAAAGATCGAGCATTAGCGACGTTTTT
1 AAAGCGCCGCTAAAGATCGAGCATTAGCGACGTTTTT
53526208 TTAAAAATGC
Statistics
Matches: 143, Mismatches: 11, Indels: 9
0.88 0.07 0.06
Matches are distributed among these distances:
39 4 0.03
40 65 0.45
41 74 0.52
ACGTcount: A:0.31, C:0.19, G:0.26, T:0.24
Consensus pattern (40 bp):
AAAGCGCCGCTAAAGATCGAGCATTAGCGACGTTTTTAAG
Found at i:53526228 original size:81 final size:79
Alignment explanation
Indices: 53526010--53526231 Score: 286
Period size: 81 Copynumber: 2.7 Consensus size: 79
53526000 GCTTTTAAAA
* * *
53526010 AAAG-GCCGCTAAAGATTGAGCATTAGCGGCGTTTTTAAGAAAGCGCCGCTAAAGATCTAAGCAT
1 AAAGCGCCGCTAAAGATCGAGCATTAGCGACGTTTTTAAGAAA--GCCACTAAAGATCTAAGCAT
* *
53526074 TAGCGGCGTTTTTGAG
64 TAGCAGCGTTTTTAAG
* * *
53526090 AAAGCGCTGCTAAAGATCGAGCACTAGCGACGTTTTTAAGAAAGCGCAGCTAAAGATCTGAGCAT
1 AAAGCGCCGCTAAAGATCGAGCATTAGCGACGTTTTTAAGAAAGC-CA-CTAAAGATCTAAGCAT
53526155 TAGCAGCGTTTTTAAG
64 TAGCAGCGTTTTTAAG
*
53526171 AAAGCGCCGCTAAAGATCGAGCATTAGCGACGTTTTTTTAA-AAATGCCACTATAGATCTAA
1 AAAGCGCCGCTAAAGATCGAGCATTAGCGACG--TTTTTAAGAAA-GCCACTAAAGATCTAA
53526232 ACTATTTTAA
Statistics
Matches: 124, Mismatches: 12, Indels: 11
0.84 0.08 0.07
Matches are distributed among these distances:
79 2 0.02
80 5 0.04
81 103 0.83
82 5 0.04
83 9 0.07
ACGTcount: A:0.33, C:0.18, G:0.24, T:0.25
Consensus pattern (79 bp):
AAAGCGCCGCTAAAGATCGAGCATTAGCGACGTTTTTAAGAAAGCCACTAAAGATCTAAGCATTA
GCAGCGTTTTTAAG
Found at i:53526864 original size:66 final size:66
Alignment explanation
Indices: 53526778--53526902 Score: 196
Period size: 66 Copynumber: 1.9 Consensus size: 66
53526768 CTCTTAAATC
* * * * *
53526778 AATAACCCTTTAACCCCCAGATCCTAAATCTCTAATCATAAACTCTTAAAACTATAAACACTAAT
1 AATAACCCTTTAAACACCAGACCCTAAATCTCAAATCATAAACCCTTAAAACTATAAACACTAAT
53526843 T
66 T
*
53526844 AATAACTCTTTAAACACCAGACCCTAAATCTCAAATCATAAACCCTTAAAACTATAAAC
1 AATAACCCTTTAAACACCAGACCCTAAATCTCAAATCATAAACCCTTAAAACTATAAAC
53526903 GATAAACCTT
Statistics
Matches: 53, Mismatches: 6, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
66 53 1.00
ACGTcount: A:0.45, C:0.27, G:0.02, T:0.26
Consensus pattern (66 bp):
AATAACCCTTTAAACACCAGACCCTAAATCTCAAATCATAAACCCTTAAAACTATAAACACTAAT
T
Found at i:53526958 original size:22 final size:21
Alignment explanation
Indices: 53526868--53526954 Score: 70
Period size: 22 Copynumber: 4.0 Consensus size: 21
53526858 CACCAGACCC
53526868 TAAATCTCAAATCATAAACCCT
1 TAAATCTCAAATCATAAA-CCT
* *
53526890 TAAAACT-ATAAACGATAAACCT
1 TAAATCTCA-AATC-ATAAACCT
* * * *
53526912 T-AATCCCAACACCCTAAACCC
1 TAAATCTCAA-ATCATAAACCT
53526933 TAAATCTCAAATCATAAACCT
1 TAAATCTCAAATCATAAACCT
53526954 T
1 T
53526955 TAAAACTCCA
Statistics
Matches: 49, Mismatches: 11, Indels: 11
0.69 0.15 0.15
Matches are distributed among these distances:
21 21 0.43
22 23 0.47
23 5 0.10
ACGTcount: A:0.46, C:0.29, G:0.01, T:0.24
Consensus pattern (21 bp):
TAAATCTCAAATCATAAACCT
Found at i:53526980 original size:14 final size:14
Alignment explanation
Indices: 53526957--53527017 Score: 61
Period size: 14 Copynumber: 4.3 Consensus size: 14
53526947 TAAACCTTTA
*
53526957 AAACTCCAACCCTT
1 AAACCCCAACCCTT
*
53526971 AAACCACAACACC-T
1 AAACCCCAAC-CCTT
*
53526985 AAACCCCAATCCTT
1 AAACCCCAACCCTT
*
53526999 AAACCCCAAGCCCTA
1 AAACCCCAA-CCCTT
53527014 AAAC
1 AAAC
53527018 TAACTTTTAA
Statistics
Matches: 38, Mismatches: 6, Indels: 5
0.78 0.12 0.10
Matches are distributed among these distances:
13 2 0.05
14 27 0.71
15 9 0.24
ACGTcount: A:0.43, C:0.43, G:0.02, T:0.13
Consensus pattern (14 bp):
AAACCCCAACCCTT
Found at i:53527278 original size:7 final size:8
Alignment explanation
Indices: 53527265--53527313 Score: 64
Period size: 8 Copynumber: 6.2 Consensus size: 8
53527255 AAAATCTTTA
*
53527265 AAAAAATT
1 AAAAACTT
*
53527273 AAAAATTT
1 AAAAACTT
53527281 AAAAA-TT
1 AAAAACTT
53527288 AAAAACTT
1 AAAAACTT
53527296 AAAAACTT
1 AAAAACTT
*
53527304 AAAAATTT
1 AAAAACTT
53527312 AA
1 AA
53527314 TATTTAATAT
Statistics
Matches: 38, Mismatches: 2, Indels: 2
0.90 0.05 0.05
Matches are distributed among these distances:
7 7 0.18
8 31 0.82
ACGTcount: A:0.67, C:0.04, G:0.00, T:0.29
Consensus pattern (8 bp):
AAAAACTT
Found at i:53527286 original size:15 final size:15
Alignment explanation
Indices: 53527266--53527313 Score: 78
Period size: 15 Copynumber: 3.1 Consensus size: 15
53527256 AAATCTTTAA
53527266 AAAAATTAAAAATTT
1 AAAAATTAAAAATTT
*
53527281 AAAAATTAAAAACTT
1 AAAAATTAAAAATTT
53527296 AAAAACTTAAAAATTT
1 AAAAA-TTAAAAATTT
53527312 AA
1 AA
53527314 TATTTAATAT
Statistics
Matches: 30, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
15 19 0.63
16 11 0.37
ACGTcount: A:0.67, C:0.04, G:0.00, T:0.29
Consensus pattern (15 bp):
AAAAATTAAAAATTT
Found at i:53527320 original size:23 final size:23
Alignment explanation
Indices: 53527265--53527310 Score: 74
Period size: 23 Copynumber: 2.0 Consensus size: 23
53527255 AAAATCTTTA
* *
53527265 AAAAAATTAAAAATTTAAAAATT
1 AAAAACTTAAAAACTTAAAAATT
53527288 AAAAACTTAAAAACTTAAAAATT
1 AAAAACTTAAAAACTTAAAAATT
53527311 TAATATTTAA
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
23 21 1.00
ACGTcount: A:0.67, C:0.04, G:0.00, T:0.28
Consensus pattern (23 bp):
AAAAACTTAAAAACTTAAAAATT
Found at i:53528632 original size:154 final size:154
Alignment explanation
Indices: 53528352--53528659 Score: 562
Period size: 154 Copynumber: 2.0 Consensus size: 154
53528342 AGTAAGATAG
* * *
53528352 ATTGATTTCACTGATTTTAGGCTTGAATTTTACGTTTTTCAAAGAAAAAGTTTGCTTCCTTCATC
1 ATTGATTTCACTGATTTTAGGCTTGAATTTTACATTCTTCAAAGAAAAAATTTGCTTCCTTCATC
*
53528417 AACTGTCATTTTATATGGTAGTAGACATTGATACCTTTGATAGCATTCTGTGGTGTATAGTTTTT
66 AACTGTCATTTTATATGGTAGCAGACATTGATACCTTTGATAGCATTCTGTGGTGTATAGTTTTT
53528482 ATTTTATCTTATATTCTGCAGAAT
131 ATTTTATCTTATATTCTGCAGAAT
53528506 ATTGATTTCACTGATTTTAGGCTTGAATTTTACATTCTTCAAAGAAAAAATTTGCTTCCTTCATC
1 ATTGATTTCACTGATTTTAGGCTTGAATTTTACATTCTTCAAAGAAAAAATTTGCTTCCTTCATC
*
53528571 AACTGTCATTTTATATGGTAGCAGACATTGATACCTTTGATAGCATTCTGTGTTGTATAGTTTTT
66 AACTGTCATTTTATATGGTAGCAGACATTGATACCTTTGATAGCATTCTGTGGTGTATAGTTTTT
*
53528636 ATTTTATCTTATTTTCTGCAGAAT
131 ATTTTATCTTATATTCTGCAGAAT
53528660 GGGGATGATT
Statistics
Matches: 148, Mismatches: 6, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
154 148 1.00
ACGTcount: A:0.26, C:0.14, G:0.15, T:0.45
Consensus pattern (154 bp):
ATTGATTTCACTGATTTTAGGCTTGAATTTTACATTCTTCAAAGAAAAAATTTGCTTCCTTCATC
AACTGTCATTTTATATGGTAGCAGACATTGATACCTTTGATAGCATTCTGTGGTGTATAGTTTTT
ATTTTATCTTATATTCTGCAGAAT
Found at i:53533853 original size:25 final size:25
Alignment explanation
Indices: 53533825--53533877 Score: 79
Period size: 25 Copynumber: 2.1 Consensus size: 25
53533815 TTTATTAAAC
* **
53533825 TTATTATTTATTATTATATTTAATT
1 TTATTATTAATTAAAATATTTAATT
53533850 TTATTATTAATTAAAATATTTAATT
1 TTATTATTAATTAAAATATTTAATT
53533875 TTA
1 TTA
53533878 GAAAATATTT
Statistics
Matches: 25, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
25 25 1.00
ACGTcount: A:0.38, C:0.00, G:0.00, T:0.62
Consensus pattern (25 bp):
TTATTATTAATTAAAATATTTAATT
Found at i:53533918 original size:19 final size:18
Alignment explanation
Indices: 53533882--53533920 Score: 51
Period size: 18 Copynumber: 2.1 Consensus size: 18
53533872 ATTTTAGAAA
*
53533882 ATATTTTTATTGATATTT
1 ATATTTTTATTAATATTT
*
53533900 ATATTTTTTTTAATAATTT
1 ATATTTTTATTAAT-ATTT
53533919 AT
1 AT
53533921 GTAAACTAAC
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
18 12 0.67
19 6 0.33
ACGTcount: A:0.31, C:0.00, G:0.03, T:0.67
Consensus pattern (18 bp):
ATATTTTTATTAATATTT
Found at i:53537001 original size:26 final size:26
Alignment explanation
Indices: 53536972--53537027 Score: 94
Period size: 26 Copynumber: 2.2 Consensus size: 26
53536962 TGATACAAAT
*
53536972 TGATAATGGGTTAGGTAAATGTTCCA
1 TGATAATGGGCTAGGTAAATGTTCCA
*
53536998 TGATAATGGGCTAGGTAAATGTTTCA
1 TGATAATGGGCTAGGTAAATGTTCCA
53537024 TGAT
1 TGAT
53537028 TGGAATTTTA
Statistics
Matches: 28, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
26 28 1.00
ACGTcount: A:0.30, C:0.07, G:0.27, T:0.36
Consensus pattern (26 bp):
TGATAATGGGCTAGGTAAATGTTCCA
Found at i:53540691 original size:30 final size:31
Alignment explanation
Indices: 53540656--53540719 Score: 76
Period size: 30 Copynumber: 2.1 Consensus size: 31
53540646 GAAATAGGGA
* *
53540656 AAAAGAGAGCAAAAATTCAATT-TAATTTGG
1 AAAAGAAAGCAAAAATTCAATTGTAATTAGG
* * *
53540686 AAAAGAAAGCTATAGTTCAATTGTAATTAGG
1 AAAAGAAAGCAAAAATTCAATTGTAATTAGG
53540717 AAA
1 AAA
53540720 TTTTCAAACT
Statistics
Matches: 28, Mismatches: 5, Indels: 1
0.82 0.15 0.03
Matches are distributed among these distances:
30 18 0.64
31 10 0.36
ACGTcount: A:0.50, C:0.06, G:0.17, T:0.27
Consensus pattern (31 bp):
AAAAGAAAGCAAAAATTCAATTGTAATTAGG
Found at i:53541111 original size:20 final size:21
Alignment explanation
Indices: 53541075--53541113 Score: 62
Period size: 21 Copynumber: 1.9 Consensus size: 21
53541065 GACTTAATTG
53541075 GAAACTTTAAGAATTTTTCAC
1 GAAACTTTAAGAATTTTTCAC
*
53541096 GAAATTTTAA-AATTTTTC
1 GAAACTTTAAGAATTTTTC
53541114 CAAAGTGCAG
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
20 8 0.47
21 9 0.53
ACGTcount: A:0.38, C:0.10, G:0.08, T:0.44
Consensus pattern (21 bp):
GAAACTTTAAGAATTTTTCAC
Found at i:53547244 original size:29 final size:30
Alignment explanation
Indices: 53547211--53547272 Score: 81
Period size: 29 Copynumber: 2.1 Consensus size: 30
53547201 TACATCAGAG
*
53547211 TAGTGATAGTAGTTGCGTTTAGTAAAA-AA
1 TAGTGATAATAGTTGCGTTTAGTAAAATAA
* * *
53547240 TAGTGGTAATTGTTGCGTTTGGTAAAATAA
1 TAGTGATAATAGTTGCGTTTAGTAAAATAA
53547270 TAG
1 TAG
53547273 ATTTTAAATC
Statistics
Matches: 28, Mismatches: 4, Indels: 1
0.85 0.12 0.03
Matches are distributed among these distances:
29 23 0.82
30 5 0.18
ACGTcount: A:0.34, C:0.03, G:0.26, T:0.37
Consensus pattern (30 bp):
TAGTGATAATAGTTGCGTTTAGTAAAATAA
Found at i:53550832 original size:48 final size:48
Alignment explanation
Indices: 53550746--53551026 Score: 217
Period size: 48 Copynumber: 5.9 Consensus size: 48
53550736 TGACATTGGG
* * * *
53550746 TGATATGTGTGCCAGTGTAAGACCATGTTTGGTACATGGCATCGGCAA
1 TGATATGAGAGCCAGTGTAAGACCATGTCTGGGACATGGCATCGGCAA
* * * * *
53550794 TGTTATGAGAGCCATTGTAAGACCATGTCCGGGACATGGCATCGACAT
1 TGATATGAGAGCCAGTGTAAGACCATGTCTGGGACATGGCATCGGCAA
* * * * * * *
53550842 TGATAAGTGCGCTAGTGTAAGATCATGTCTGGGACATGGTATCGGC-G
1 TGATATGAGAGCCAGTGTAAGACCATGTCTGGGACATGGCATCGGCAA
* * * * * * * * **
53550889 TCGATATGTGCGCTAGTGCAGGACTATGTCTGGGACACGGTAAAGGCCACA
1 T-GATATGAGAGCCAGTGTAAGACCATGTCTGGGACATGGCATCGG-CA-A
* * *
53550940 T--TATGAGAGCCAATGTAAGACCATGTCTGGGACATGGCATCGACAT
1 TGATATGAGAGCCAGTGTAAGACCATGTCTGGGACATGGCATCGGCAA
* * * *
53550986 TGAGACGAGTGCTAGTGTAAGACCATGTCTGGGACATGGCA
1 TGATATGAGAGCCAGTGTAAGACCATGTCTGGGACATGGCA
53551027 CCAGCAATTT
Statistics
Matches: 180, Mismatches: 47, Indels: 12
0.75 0.20 0.05
Matches are distributed among these distances:
46 1 0.01
47 3 0.02
48 174 0.97
49 1 0.01
51 1 0.01
ACGTcount: A:0.26, C:0.19, G:0.30, T:0.25
Consensus pattern (48 bp):
TGATATGAGAGCCAGTGTAAGACCATGTCTGGGACATGGCATCGGCAA
Found at i:53558566 original size:48 final size:48
Alignment explanation
Indices: 53558514--53558830 Score: 314
Period size: 48 Copynumber: 6.6 Consensus size: 48
53558504 TATGAGAGCC
* * * * *
53558514 AGTGTAAGACCATGTCTGGGAAACGGCATTGGTGTTGATAGGTGTGCT
1 AGTGTAAGACCATGTCTGGGACATGGCATCGGTGTCGATAGGTGCGCT
* *
53558562 AGTGTAAGACCATGTCTGGGACATGGCATCGGTGTCAATATGTGCGCT
1 AGTGTAAGACCATGTCTGGGACATGGCATCGGTGTCGATAGGTGCGCT
* *
53558610 AGTGTAAGACCATGT-TCGGGACATGGCATCGGCGTTGATAGGTGCGCT
1 AGTGTAAGACCATGTCT-GGGACATGGCATCGGTGTCGATAGGTGCGCT
* * * **
53558658 AGTGTAAAACCATGTCTGGGAGATGGCATCGGTGTCGATATGTATGCT
1 AGTGTAAGACCATGTCTGGGACATGGCATCGGTGTCGATAGGTGCGCT
* * *** * * *
53558706 AGTGTAAGACCATGTCTGGGACACGGCAACGGCCAC-ATTATGAGAGCT
1 AGTGTAAGACCATGTCTGGGACATGGCATCGGTGTCGA-TAGGTGCGCT
* * * ** * * * * *
53558754 AGTTTAAGACCATGTCTAGGACATGTCATCGGCATTGAGACGAGAGCT
1 AGTGTAAGACCATGTCTGGGACATGGCATCGGTGTCGATAGGTGCGCT
53558802 AGTGTAAGACCATGTCTGGGACATGGCAT
1 AGTGTAAGACCATGTCTGGGACATGGCAT
53558831 TGGCAATTTA
Statistics
Matches: 224, Mismatches: 41, Indels: 8
0.82 0.15 0.03
Matches are distributed among these distances:
47 2 0.01
48 220 0.98
49 2 0.01
ACGTcount: A:0.25, C:0.18, G:0.32, T:0.26
Consensus pattern (48 bp):
AGTGTAAGACCATGTCTGGGACATGGCATCGGTGTCGATAGGTGCGCT
Found at i:53558715 original size:144 final size:144
Alignment explanation
Indices: 53558466--53558830 Score: 435
Period size: 144 Copynumber: 2.5 Consensus size: 144
53558456 TATGTATGCC
* * * * * * *
53558466 AGTGTAAGACCATGTTTGGAACATGGTATCGGCAATGTTATGAGAGCCAGTGTAAGACCATGTCT
1 AGTGTAAGACCATGTTCGGGACATGGCATCGGCATTGATACGAGAGCTAGTGTAAGACCATGTCT
* * * * * * **
53558531 GGGAAACGGCATTGGTGTTGATAGGTGTGCTAGTGTAAGACCATGTCTGGGACATGGCATCGGTG
66 GGGAAATGGCATCGGTGTCGATAGGTATGCTAGTGTAAGACCATGTCTGGGACACGGCAACGGCC
* * *
53558596 TCAATATGTGCGCT
131 ACAATATGAGAGCT
* * * * *
53558610 AGTGTAAGACCATGTTCGGGACATGGCATCGGCGTTGATAGGTGCGCTAGTGTAAAACCATGTCT
1 AGTGTAAGACCATGTTCGGGACATGGCATCGGCATTGATACGAGAGCTAGTGTAAGACCATGTCT
* *
53558675 GGGAGATGGCATCGGTGTCGATATGTATGCTAGTGTAAGACCATGTCTGGGACACGGCAACGGCC
66 GGGAAATGGCATCGGTGTCGATAGGTATGCTAGTGTAAGACCATGTCTGGGACACGGCAACGGCC
*
53558740 ACATTATGAGAGCT
131 ACAATATGAGAGCT
* * * *
53558754 AGTTTAAGACCATG-TCTAGGACATGTCATCGGCATTGAGACGAGAGCTAGTGTAAGACCATGTC
1 AGTGTAAGACCATGTTC-GGGACATGGCATCGGCATTGATACGAGAGCTAGTGTAAGACCATGTC
*
53558818 TGGGACATGGCAT
65 TGGGAAATGGCAT
53558831 TGGCAATTTA
Statistics
Matches: 185, Mismatches: 35, Indels: 2
0.83 0.16 0.01
Matches are distributed among these distances:
143 2 0.01
144 183 0.99
ACGTcount: A:0.26, C:0.17, G:0.31, T:0.26
Consensus pattern (144 bp):
AGTGTAAGACCATGTTCGGGACATGGCATCGGCATTGATACGAGAGCTAGTGTAAGACCATGTCT
GGGAAATGGCATCGGTGTCGATAGGTATGCTAGTGTAAGACCATGTCTGGGACACGGCAACGGCC
ACAATATGAGAGCT
Found at i:53558755 original size:96 final size:96
Alignment explanation
Indices: 53558466--53558829 Score: 297
Period size: 96 Copynumber: 3.8 Consensus size: 96
53558456 TATGTATGCC
* * * ** * *
53558466 AGTGTAAGACCATGTTTGGAACATGGTATCGGCAAT-GTTATG-AGAGCCAGTGTAAGACCATGT
1 AGTGTAAGACCATGTCTGGGACATGGCATCGG-TGTCGATATGTA-AGCTAGTGTAAGACCATGT
* * ** * *** * *
53558529 CTGGGAAACGGCATTGGTGTTGATAGGTGTGCT
64 CTGGGACATGGCAACGGCGCACATAGGAGAGCT
* **
53558562 AGTGTAAGACCATGTCTGGGACATGGCATCGGTGTCAATATGTGCGCTAGTGTAAGACCATGT-T
1 AGTGTAAGACCATGTCTGGGACATGGCATCGGTGTCGATATGTAAGCTAGTGTAAGACCATGTCT
* *** * *
53558626 CGGGACATGGCATCGGCGTTGATAGGTGCGCT
66 -GGGACATGGCAACGGCGCACATAGGAGAGCT
* * *
53558658 AGTGTAAAACCATGTCTGGGAGATGGCATCGGTGTCGATATGTATGCTAGTGTAAGACCATGTCT
1 AGTGTAAGACCATGTCTGGGACATGGCATCGGTGTCGATATGTAAGCTAGTGTAAGACCATGTCT
* *
53558723 GGGACACGGCAACGGC-CACATTATGAGAGCT
66 GGGACATGGCAACGGCGCACA-TAGGAGAGCT
* * * ** * * *
53558754 AGTTTAAGACCATGTCTAGGACATGTCATCGGCATTGAGACG-AGAGCTAGTGTAAGACCATGTC
1 AGTGTAAGACCATGTCTGGGACATGGCATCGGTGTCGATATGTA-AGCTAGTGTAAGACCATGTC
53558818 TGGGACATGGCA
65 TGGGACATGGCA
53558830 TTGGCAATTT
Statistics
Matches: 222, Mismatches: 40, Indels: 12
0.81 0.15 0.04
Matches are distributed among these distances:
95 4 0.02
96 217 0.98
97 1 0.00
ACGTcount: A:0.26, C:0.17, G:0.31, T:0.26
Consensus pattern (96 bp):
AGTGTAAGACCATGTCTGGGACATGGCATCGGTGTCGATATGTAAGCTAGTGTAAGACCATGTCT
GGGACATGGCAACGGCGCACATAGGAGAGCT
Found at i:53561168 original size:17 final size:17
Alignment explanation
Indices: 53561146--53561187 Score: 75
Period size: 17 Copynumber: 2.5 Consensus size: 17
53561136 CAAGATCGAG
53561146 TGAAAATTGAGAAGAAT
1 TGAAAATTGAGAAGAAT
53561163 TGAAAATTGAGAAGAAT
1 TGAAAATTGAGAAGAAT
*
53561180 GGAAAATT
1 TGAAAATT
53561188 ACCAAATAGC
Statistics
Matches: 24, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
17 24 1.00
ACGTcount: A:0.52, C:0.00, G:0.24, T:0.24
Consensus pattern (17 bp):
TGAAAATTGAGAAGAAT
Found at i:53563321 original size:56 final size:53
Alignment explanation
Indices: 53563242--53563397 Score: 155
Period size: 47 Copynumber: 3.0 Consensus size: 53
53563232 GTGATGTGCG
* *
53563242 AGTAAGACCATGGGATCGATATGTGATTCTGATATATGTGTGCGAGTAAGACC
1 AGTAAAACCATGGCATCGATATGTGATTCTGATATATGTGTGCGAGTAAGACC
* ** * *
53563295 ACGTTTAATACGTTGGCATCGATATGTGATT-TCGATATATGTG-ACGTGT--G---
1 A-G--TAAAACCATGGCATCGATATGTGATTCT-GATATATGTGTGCGAGTAAGACC
*
53563345 AGTAAAACCATGGCATCGATATGTGATTCTGATATATGTGTGCGGGTAAGACC
1 AGTAAAACCATGGCATCGATATGTGATTCTGATATATGTGTGCGAGTAAGACC
53563398 CTGTCTGGGA
Statistics
Matches: 81, Mismatches: 11, Indels: 22
0.71 0.10 0.19
Matches are distributed among these distances:
47 33 0.41
48 5 0.06
49 1 0.01
50 2 0.02
53 2 0.02
54 1 0.01
55 5 0.06
56 32 0.40
ACGTcount: A:0.28, C:0.13, G:0.27, T:0.31
Consensus pattern (53 bp):
AGTAAAACCATGGCATCGATATGTGATTCTGATATATGTGTGCGAGTAAGACC
Found at i:53569143 original size:21 final size:21
Alignment explanation
Indices: 53569101--53569140 Score: 55
Period size: 21 Copynumber: 2.0 Consensus size: 21
53569091 CTCATATTAT
* *
53569101 TTTTAATTTTTATTTAATTTA
1 TTTTAATATTTATATAATTTA
53569122 TTTTAATATTTA-ATAATTT
1 TTTTAATATTTATATAATTT
53569141 TATACATTTT
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
20 6 0.35
21 11 0.65
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.68
Consensus pattern (21 bp):
TTTTAATATTTATATAATTTA
Found at i:53570603 original size:3 final size:3
Alignment explanation
Indices: 53570588--53570626 Score: 62
Period size: 3 Copynumber: 13.0 Consensus size: 3
53570578 GTTATTTTCA
53570588 TAT TAT TGA- TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
1 TAT TAT T-AT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
53570627 GTACTTTTGT
Statistics
Matches: 34, Mismatches: 0, Indels: 4
0.89 0.00 0.11
Matches are distributed among these distances:
2 1 0.03
3 32 0.94
4 1 0.03
ACGTcount: A:0.33, C:0.00, G:0.03, T:0.64
Consensus pattern (3 bp):
TAT
Found at i:53571231 original size:25 final size:22
Alignment explanation
Indices: 53571200--53571257 Score: 71
Period size: 24 Copynumber: 2.5 Consensus size: 22
53571190 ATTATATGTG
53571200 TATATATTATGTAAAATGTTTTAA
1 TATATATTATGT-AAATGTTTT-A
* *
53571224 TATTATATTATATATATGTTTTA
1 TA-TATATTATGTAAATGTTTTA
53571247 TATATATTATG
1 TATATATTATG
53571258 AACATGTATT
Statistics
Matches: 30, Mismatches: 3, Indels: 4
0.81 0.08 0.11
Matches are distributed among these distances:
22 8 0.27
23 3 0.10
24 10 0.33
25 9 0.30
ACGTcount: A:0.38, C:0.00, G:0.07, T:0.55
Consensus pattern (22 bp):
TATATATTATGTAAATGTTTTA
Found at i:53571264 original size:22 final size:23
Alignment explanation
Indices: 53571200--53571264 Score: 71
Period size: 22 Copynumber: 2.8 Consensus size: 23
53571190 ATTATATGTG
53571200 TATATATTATGTAAAATGTTTTAA
1 TATATATTATG-AAAATGTTTTAA
*
53571224 TATTATATTAT-ATATATGTTTT-A
1 TA-TATATTATGA-AAATGTTTTAA
*
53571247 TATATATTATGAACATGT
1 TATATATTATGAAAATGT
53571265 ATTTTCAATA
Statistics
Matches: 36, Mismatches: 2, Indels: 8
0.78 0.04 0.17
Matches are distributed among these distances:
22 13 0.36
23 5 0.14
24 10 0.28
25 8 0.22
ACGTcount: A:0.38, C:0.02, G:0.08, T:0.52
Consensus pattern (23 bp):
TATATATTATGAAAATGTTTTAA
Found at i:53571280 original size:47 final size:46
Alignment explanation
Indices: 53571200--53571301 Score: 104
Period size: 47 Copynumber: 2.2 Consensus size: 46
53571190 ATTATATGTG
*
53571200 TATATATTATGTAAAATGTTTTAATATTATATTA-TATATATGTTTTA
1 TATATATTATGTAAAATGTTTTAATATTATATTAGT-TAAAT-TTTTA
* *
53571247 TATATATTATG-AACATGTATTTTCAATA-T-TATTAGTTAAATTTTTG
1 TATATATTATGTAAAATG--TTTT-AATATTATATTAGTTAAATTTTTA
53571293 TATATATTA
1 TATATATTA
53571302 CCCTATGTAC
Statistics
Matches: 48, Mismatches: 3, Indels: 9
0.80 0.05 0.15
Matches are distributed among these distances:
46 18 0.38
47 20 0.42
48 6 0.12
49 4 0.08
ACGTcount: A:0.37, C:0.02, G:0.07, T:0.54
Consensus pattern (46 bp):
TATATATTATGTAAAATGTTTTAATATTATATTAGTTAAATTTTTA
Found at i:53576913 original size:48 final size:48
Alignment explanation
Indices: 53576861--53577034 Score: 197
Period size: 48 Copynumber: 3.6 Consensus size: 48
53576851 AAACATTGCT
* *
53576861 GATGCCATGTTCCAAACATGGTCTTACACTGGCTCTTATAATGTGGCC
1 GATGCCATGTTCCAAACATGGTCTTACACTGGCTCTCATAATGTGACC
* * * ** ***
53576909 GATGCAATGTCCCAGACATGGTCTTACACTGGCTCTCATAACATTTTC
1 GATGCCATGTTCCAAACATGGTCTTACACTGGCTCTCATAATGTGACC
* * *
53576957 GATGCCATGTTCCAAAGATGATCTTACATTGGCTCTCATAATGTGACC
1 GATGCCATGTTCCAAACATGGTCTTACACTGGCTCTCATAATGTGACC
* *
53577005 AATGCCATG-TCCTAGACATGGTCTTACACT
1 GATGCCATGTTCC-AAACATGGTCTTACACT
53577035 AACACACATA
Statistics
Matches: 100, Mismatches: 25, Indels: 2
0.79 0.20 0.02
Matches are distributed among these distances:
47 3 0.03
48 97 0.97
ACGTcount: A:0.25, C:0.25, G:0.18, T:0.31
Consensus pattern (48 bp):
GATGCCATGTTCCAAACATGGTCTTACACTGGCTCTCATAATGTGACC
Found at i:53576967 original size:96 final size:96
Alignment explanation
Indices: 53576811--53577034 Score: 297
Period size: 96 Copynumber: 2.3 Consensus size: 96
53576801 GTCTCAATGT
* **
53576811 CGATGCCATGTCCCAAGATATGGTCTTACTTTCGCTCTCAAAACATTGCTGATGCCATGTTCCAA
1 CGATGCCATGTCCC-AGACATGGTCTTACACTCGCTCTCAAAACATTGCTGATGCCATGTTCCAA
* * *
53576876 ACATGGTCTTACACTGGCTCTTATAATGTGGC
65 ACATGATCTTACACTGGCTCTCATAATGTGAC
* * * *
53576908 CGATGCAATGTCCCAGACATGGTCTTACACTGGCTCTCATAACATT-TTCGATGCCATGTTCCAA
1 CGATGCCATGTCCCAGACATGGTCTTACACTCGCTCTCAAAACATTGCT-GATGCCATGTTCCAA
* *
53576972 AGATGATCTTACATTGGCTCTCATAATGTGAC
65 ACATGATCTTACACTGGCTCTCATAATGTGAC
* *
53577004 CAATGCCATGTCCTAGACATGGTCTTACACT
1 CGATGCCATGTCCCAGACATGGTCTTACACT
53577035 AACACACATA
Statistics
Matches: 111, Mismatches: 15, Indels: 3
0.86 0.12 0.02
Matches are distributed among these distances:
95 1 0.01
96 97 0.87
97 13 0.12
ACGTcount: A:0.25, C:0.26, G:0.18, T:0.31
Consensus pattern (96 bp):
CGATGCCATGTCCCAGACATGGTCTTACACTCGCTCTCAAAACATTGCTGATGCCATGTTCCAAA
CATGATCTTACACTGGCTCTCATAATGTGAC
Found at i:53584641 original size:48 final size:48
Alignment explanation
Indices: 53584589--53584945 Score: 217
Period size: 48 Copynumber: 7.4 Consensus size: 48
53584579 AGGCCAATGT
* * ** **
53584589 CATGTCTCTAACATGGTCTTATACTAGCTCTCGTCTCAATGTTGATGC
1 CATGTCTCAAACATGGTCTTATACTGGCTCTCGTAACAATGCCGATGC
* *
53584637 CATGTCCCAAACATGGTCTTACT-CTGGCTCTCGTAACATTGCCGATGC
1 CATGTCTCAAACATGGTCTTA-TACTGGCTCTCGTAACAATGCCGATGC
* * ** *
53584685 CATGT-TCCAAACATGGTCTTACACTGGCTCTCATAA-TGTGGCCGATGT
1 CATGTCT-CAAACATGGTCTTATACTGGCTCTCGTAACAAT-GCCGATGC
** * * * * * *
53584733 CATGT-TCCAGGCATAGTCTTACACTGGCTCTCATTACATTGCTGATGC
1 CATGTCT-CAAACATGGTCTTATACTGGCTCTCGTAACAATGCCGATGC
* * ** *
53584781 CATGT-TCCAAACATGGTCTTACACTGGCTCTCATAA-TGTGGTCGATGC
1 CATGTCT-CAAACATGGTCTTATACTGGCTCTCGTAACAAT-GCCGATGC
* * * * * * *
53584829 CATGTCCCAGACATGGTCTTACACTGGCTCTCATAATATTGTCGATGC
1 CATGTCTCAAACATGGTCTTATACTGGCTCTCGTAACAATGCCGATGC
* * * ** *
53584877 CATGT-TCCAAAGATGGTCTTACACTGGCTCTCATAA-TGTGGCCAATGC
1 CATGTCT-CAAACATGGTCTTATACTGGCTCTCGTAACAAT-GCCGATGC
* *
53584925 CATGTCCCAGACATGGTCTTA
1 CATGTCTCAAACATGGTCTTA
53584946 CACTAACACA
Statistics
Matches: 254, Mismatches: 44, Indels: 22
0.79 0.14 0.07
Matches are distributed among these distances:
47 3 0.01
48 248 0.98
49 3 0.01
ACGTcount: A:0.22, C:0.27, G:0.19, T:0.32
Consensus pattern (48 bp):
CATGTCTCAAACATGGTCTTATACTGGCTCTCGTAACAATGCCGATGC
Found at i:53584946 original size:48 final size:48
Alignment explanation
Indices: 53584632--53584949 Score: 415
Period size: 48 Copynumber: 6.6 Consensus size: 48
53584622 TCTCAATGTT
* * * ** *
53584632 GATGCCATGTCCCAAACATGGTCTTACTCTGGCTCTCGTAACATTGCC
1 GATGCCATGTTCCAAACATGGTCTTACACTGGCTCTCATAATGTGGCC
53584680 GATGCCATGTTCCAAACATGGTCTTACACTGGCTCTCATAATGTGGCC
1 GATGCCATGTTCCAAACATGGTCTTACACTGGCTCTCATAATGTGGCC
* ** * *
53584728 GATGTCATGTTCCAGGCATAGTCTTACACTGGCTCTCATTACAT-T-GCT
1 GATGCCATGTTCCAAACATGGTCTTACACTGGCTCTCA-TA-ATGTGGCC
*
53584776 GATGCCATGTTCCAAACATGGTCTTACACTGGCTCTCATAATGTGGTC
1 GATGCCATGTTCCAAACATGGTCTTACACTGGCTCTCATAATGTGGCC
* * * * *
53584824 GATGCCATGTCCCAGACATGGTCTTACACTGGCTCTCATAATATTGTC
1 GATGCCATGTTCCAAACATGGTCTTACACTGGCTCTCATAATGTGGCC
*
53584872 GATGCCATGTTCCAAAGATGGTCTTACACTGGCTCTCATAATGTGGCC
1 GATGCCATGTTCCAAACATGGTCTTACACTGGCTCTCATAATGTGGCC
* * *
53584920 AATGCCATGTCCCAGACATGGTCTTACACT
1 GATGCCATGTTCCAAACATGGTCTTACACT
53584950 AACACACATA
Statistics
Matches: 235, Mismatches: 31, Indels: 8
0.86 0.11 0.03
Matches are distributed among these distances:
46 2 0.01
47 3 0.01
48 225 0.96
49 3 0.01
50 2 0.01
ACGTcount: A:0.23, C:0.27, G:0.20, T:0.31
Consensus pattern (48 bp):
GATGCCATGTTCCAAACATGGTCTTACACTGGCTCTCATAATGTGGCC
Done.