Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold25
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: 9553305
ACGTcount: A:0.34, C:0.16, G:0.16, T:0.34
Warning! 6276 characters in sequence are not A, C, G, or T
File 32 of 56
Found at i:5414811 original size:13 final size:13
Alignment explanation
Indices: 5414793--5414817 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
5414783 ATTACTCAAA
5414793 TGTATCGATACAT
1 TGTATCGATACAT
5414806 TGTATCGATACA
1 TGTATCGATACA
5414818 CTGATCTTTG
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.32, C:0.16, G:0.16, T:0.36
Consensus pattern (13 bp):
TGTATCGATACAT
Found at i:5414869 original size:52 final size:50
Alignment explanation
Indices: 5414806--5414954 Score: 208
Period size: 52 Copynumber: 2.9 Consensus size: 50
5414796 ATCGATACAT
*
5414806 TGTATCGATACACTGATCTTTGTATCGATACATGCAGGCAAATTTGCCCAGA
1 TGTATCGATACACT-AT-TATGTATCGATACATGCAGGCAAATTTGCCCAGA
* *
5414858 TGTATCGATACATTATAAAATGTATCGATACATGCAGGCAAATTTGCCCAGA
1 TGTATCGATACACTAT--TATGTATCGATACATGCAGGCAAATTTGCCCAGA
*
5414910 TGTATCGATACACTATTAAATGTATCGATACATGCAGGTAAATTT
1 TGTATCGATACACTATT--ATGTATCGATACATGCAGGCAAATTT
5414955 TCATATTTCG
Statistics
Matches: 87, Mismatches: 7, Indels: 6
0.87 0.07 0.06
Matches are distributed among these distances:
51 2 0.02
52 85 0.98
ACGTcount: A:0.34, C:0.17, G:0.17, T:0.32
Consensus pattern (50 bp):
TGTATCGATACACTATTATGTATCGATACATGCAGGCAAATTTGCCCAGA
Found at i:5419909 original size:23 final size:24
Alignment explanation
Indices: 5419857--5419911 Score: 69
Period size: 24 Copynumber: 2.3 Consensus size: 24
5419847 GGTGACTTGT
5419857 TACATGAACCCTATTAAATATCTA
1 TACATGAACCCTATTAAATATCTA
* *
5419881 TACATGTACCCTAATT-AAT-TTTA
1 TACATGAACCCT-ATTAAATATCTA
5419904 TACATGAA
1 TACATGAA
5419912 TTACATGGAT
Statistics
Matches: 27, Mismatches: 3, Indels: 3
0.82 0.09 0.09
Matches are distributed among these distances:
23 10 0.37
24 14 0.52
25 3 0.11
ACGTcount: A:0.40, C:0.18, G:0.05, T:0.36
Consensus pattern (24 bp):
TACATGAACCCTATTAAATATCTA
Found at i:5421008 original size:16 final size:15
Alignment explanation
Indices: 5420969--5421018 Score: 59
Period size: 15 Copynumber: 3.4 Consensus size: 15
5420959 TCAAACTTTG
**
5420969 AATTATTTTTTAATA
1 AATTATTTTAAAATA
5420984 AATTA--TTAAAATA
1 AATTATTTTAAAATA
5420997 ATATTATTTTAAAATA
1 A-ATTATTTTAAAATA
5421013 AATTAT
1 AATTAT
5421019 CAAATTGTTA
Statistics
Matches: 30, Mismatches: 2, Indels: 6
0.79 0.05 0.16
Matches are distributed among these distances:
13 7 0.23
14 4 0.13
15 10 0.33
16 9 0.30
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (15 bp):
AATTATTTTAAAATA
Found at i:5422178 original size:193 final size:193
Alignment explanation
Indices: 5421862--5422868 Score: 511
Period size: 195 Copynumber: 5.3 Consensus size: 193
5421852 AAGCATCCGG
* * * * ** * *
5421862 TATATTAAGATTTTCATGAGTGCTTGCACTAAG-GAGGAGCAAATCACGATT-TTATGTAAATAT
1 TATATTAAGATTTCCTTGAGTGGTTACACTAAGAG-GGAATAAATCACCATTGTT-CGTAAATAT
* ** * ** * * *
5421925 TAGAGCACATGTGAAGTGTGGGAAAGAGT-TTAGGTATATTATGATTTCCTTGAGTGGTTACCCT
64 TAGAGCATATGTGAAGCATGGGAAAAAGTCCGA-GTATATTAAGATTTCCTTAAATGGTTACCCT
**
5421989 ATGGAA-GAACT-GATCACCATTGTCCACAAATATTGGAGCATACATGAAGCTAA-GGAAGAGTC
128 A-AAAAGGAA-TAGATCACCATTGTCCACAAATATTGGAGCATACATGAAGC-AAGGGAAGAGTC
5422051 CAAA
190 CAAA
5422055 TATATTAAGATTTCCTTGAGTGGTTACACTAAGAGGGAATAAATCACCATTGTTCGTAAATATTA
1 TATATTAAGATTTCCTTGAGTGGTTACACTAAGAGGGAATAAATCACCATTGTTCGTAAATATTA
* * *
5422120 GAGCATATGTGAAGCATGGGAAAAAGTCCGAGTACATTAAGAGTTCCTTAAATGGTTACCTTAAA
66 GAGCATATGTGAAGCATGGGAAAAAGTCCGAGTATATTAAGATTTCCTTAAATGGTTACCCTAAA
* ** * **
5422185 AAGGAATAGATCACCATTGTTCGTAAATATTGGAGTATATGTGAAGCAAGGGGGAAGAGTCCAAA
131 AAGGAATAGATCACCATTGTCCACAAATATTGGAGCATACATGAAGCAA--GGGAAGAGTCCAAA
* * * * * * * **
5422250 TATATGAAGATTTCCTTGAATGGTTACATTAAAGAGGAGCAT--ATCATCATTGTCCATGTATAT
1 TATATTAAGATTTCCTTGAGTGGTTACACT-AAGAGG-GAATAAATCACCATTGTTCGTAAATAT
* * * * ** *
5422313 TGGAGCATATGTGAAGCATGGGGAGAAGTCCGAGTATATTAAGATTTCCTTGAACAGTTACACTA
64 TAGAGCATATGTGAAGCATGGGAAAAAGTCCGAGTATATTAAGATTTCCTTAAATGGTTACCCTA
* ** * * ** ** *** * *
5422378 AGAAGGAGCAGATCACCATTG-CCTATAAATATTAGAATATATGTGAAGTGTGGGGAGAAGTCTA
129 AAAAGGAATAGATCACCATTGTCC-ACAAATATTGGAGCATACATGAAGCAAGGGAAG-AGTCCA
**
5422442 CG
192 AA
* * *
5422444 TATATTAAGATTTCCATGAG-GAGTTACACT-A-AGGAAATGCAAATTACCATTG-TCGATAAAT
1 TATATTAAGATTTCCTTGAGTG-GTTACACTAAGAGGGAAT--AAATCACCATTGTTCG-TAAAT
* ** * *
5422505 ATTAGAACATATGTGAATTATGGG-----G--C----------AGATTTCCTTGAATGGTTACAC
62 ATTAGAGCATATGTGAAGCATGGGAAAAAGTCCGAGTATATTAAGATTTCCTTAAATGGTTACCC
* * * * * ** * ** *
5422553 TAAAAAAGAATAGATCACCATTGTGCATATATATTAGAGCATATGTGAAGCATGAAAAGAGTGCA
127 TAAAAAGGAATAGATCACCATTGTCCACAAATATTGGAGCATACATGAAGCAAGGGAAGAGTCCA
*
5422618 AG
192 AA
* * * * * * * *
5422620 TGTATT-AGAATTACCTTGAATGGTTACACTAA-AGAGGAGTAAATCATCGTTATTTGTAAATAT
1 TATATTAAG-ATTTCCTTGAGTGGTTACACTAAGAG-GGAATAAATCACCATTGTTCGTAAATAT
* * * * ** * * * * *
5422683 TAAAGCATATGGGAAGAATGGGGAAGAA-TTTGGGTATATTAAGATTTCTTTGAGTGGTTACACT
64 TAGAGCATATGTGAAGCAT-GGGAAAAAGTCCGAGTATATTAAGATTTCCTTAAATGGTTACCCT
* * * ** * * * * * *
5422747 AAGGAA-GAGTAGATCACTATTGTCCGTAAATATTGGATCATACGGTTAAGCATAAGAAAGATTC
128 AA-AAAGGAATAGATCACCATTGTCCACAAATATTGGAGCATAC-ATGAAGCA-AGGGAAGAGTC
*
5422811 CAAG
190 CAAA
* * * *
5422815 TATATAAAGATTTTCTTAAATGGTTACACTAAG-GAGGAA-AATATCACCATTGTT
1 TATATTAAGATTTCCTTGAGTGGTTACACTAAGAG-GGAATAA-ATCACCATTGTT
5422869 ATTTTAGGTC
Statistics
Matches: 628, Mismatches: 138, Indels: 94
0.73 0.16 0.11
Matches are distributed among these distances:
175 2 0.00
176 55 0.09
177 73 0.12
178 4 0.01
187 1 0.00
189 1 0.00
190 2 0.00
191 3 0.00
192 6 0.01
193 196 0.31
194 76 0.12
195 198 0.32
196 8 0.01
197 3 0.00
ACGTcount: A:0.36, C:0.12, G:0.22, T:0.30
Consensus pattern (193 bp):
TATATTAAGATTTCCTTGAGTGGTTACACTAAGAGGGAATAAATCACCATTGTTCGTAAATATTA
GAGCATATGTGAAGCATGGGAAAAAGTCCGAGTATATTAAGATTTCCTTAAATGGTTACCCTAAA
AAGGAATAGATCACCATTGTCCACAAATATTGGAGCATACATGAAGCAAGGGAAGAGTCCAAA
Found at i:5422192 original size:97 final size:97
Alignment explanation
Indices: 5421958--5422458 Score: 377
Period size: 97 Copynumber: 5.2 Consensus size: 97
5421948 AAGAGTTTAG
* * * ** * * **
5421958 GTATATTATGATTTCCTTGAGTGGTTACCCTATGGAA-GAACT-GATCACCATTGTCCACAAATA
1 GTATATTAAGATTTCCTTGAATGGTTACCTTA-AAAAGGAA-TAAATCACCATTGTTCGTAAATA
** ** * *
5422021 TTGGAGCATACATGAAGC-TAAGGAAGAGTCCAA
64 TTGGAGCATATGTGAAGCATGGGGAAAAGTCCGA
* * * *
5422054 ATATATTAAGATTTCCTTGAGTGGTTACAC-TAAGAGGGAATAAATCACCATTGTTCGTAAATAT
1 GTATATTAAGATTTCCTTGAATGGTTAC-CTTAAAAAGGAATAAATCACCATTGTTCGTAAATAT
* *
5422118 TAGAGCATATGTGAAGCATGGGAAAAAGTCCGA
65 TGGAGCATATGTGAAGCATGGGGAAAAGTCCGA
* * * *
5422151 GTACATTAAGAGTTCCTTAAATGGTTACCTTAAAAAGGAATAGATCACCATTGTTCGTAAATATT
1 GTATATTAAGATTTCCTTGAATGGTTACCTTAAAAAGGAATAAATCACCATTGTTCGTAAATATT
* * * *
5422216 GGAGTATATGTGAAGCAAGGGGGAAGAGTCCAA
66 GGAGCATATGTGAAGC-ATGGGGAAAAGTCCGA
* * * * ** * * * * **
5422249 ATATATGAAGATTTCCTTGAATGGTTACATTAAAGAGGAGCATATCATCATTGTCCATGTATATT
1 GTATATTAAGATTTCCTTGAATGGTTACCTTAAAAAGGAATAAATCACCATTGTTCGTAAATATT
*
5422314 GGAGCATATGTGAAGCATGGGGAGAAGTCCGA
66 GGAGCATATGTGAAGCATGGGGAAAAGTCCGA
** * ** * * *
5422346 GTATATTAAGATTTCCTTGAACAGTTACAC-TAAGAAGGAGCAGATCACCATTG-CCTATAAATA
1 GTATATTAAGATTTCCTTGAATGGTTAC-CTTAAAAAGGAATAAATCACCATTGTTC-GTAAATA
* ** ** * *
5422409 TTAGAATATATGTGAAGTGTGGGGAGAAGT-CTA
64 TTGGAGCATATGTGAAGCATGGGGAAAAGTCCGA
5422442 CGTATATTAAGATTTCC
1 -GTATATTAAGATTTCC
5422459 ATGAGGAGTT
Statistics
Matches: 329, Mismatches: 67, Indels: 17
0.80 0.16 0.04
Matches are distributed among these distances:
95 3 0.01
96 68 0.21
97 181 0.55
98 77 0.23
ACGTcount: A:0.35, C:0.14, G:0.22, T:0.29
Consensus pattern (97 bp):
GTATATTAAGATTTCCTTGAATGGTTACCTTAAAAAGGAATAAATCACCATTGTTCGTAAATATT
GGAGCATATGTGAAGCATGGGGAAAAGTCCGA
Found at i:5422529 original size:97 final size:96
Alignment explanation
Indices: 5422055--5422529 Score: 300
Period size: 97 Copynumber: 4.9 Consensus size: 96
5422045 AGAGTCCAAA
* *** * ** *
5422055 TATATTAAGATTTCCTTGAGTGGTTACACTAAGAGGGAATAAATCACCATTGTTCG-TAAATATT
1 TATATTAAGATTTCCATGAACAGTTACACTAAGA-AGAGCAAATCACCATTG-CCGATAAATATT
* * * *
5422119 AGAGCATATGTGAAGCATGGGAAAAAGTCCGAG
64 AGAACATATGTGAAGTATGGGGAGAAGTCCGAG
* * * * ** * * *
5422152 TACATTAAGAGTTCCTTAAATGGTTAC-CTTAAAAAG-GAATAGATCACCATTGTTCG-TAAATA
1 TATATTAAGATTTCCATGAACAGTTACAC-TAAGAAGAGCA-A-ATCACCATTG-CCGATAAATA
* ** * * * *
5422214 TTGGAGTATATGTGAAGCAAGGGG-GAAGAGTCCAAA
62 TTAGAACATATGTGAAGTATGGGGAG-A-AGTCCGAG
* * ** * * * * **
5422250 TATATGAAGATTTCCTTGAATGGTTACATTAAAGAGGAGCATATCATCATTGTCC-ATGTATATT
1 TATATTAAGATTTCCATGAACAGTTACACT-AAGAAGAGCAAATCACCATTG-CCGATAAATATT
* * *
5422314 GGAGCATATGTGAAGCATGGGGAGAAGTCCGAG
64 AGAACATATGTGAAGTATGGGGAGAAGTCCGAG
* * *
5422347 TATATTAAGATTTCCTTGAACAGTTACACTAAGAAGGAGCAGATCACCATTGCCTATAAATATTA
1 TATATTAAGATTTCCATGAACAGTTACACTAAGAA-GAGCAAATCACCATTGCCGATAAATATTA
* * *
5422412 GAATATATGTGAAGTGTGGGGAGAAGT-CTACG
65 GAACATATGTGAAGTATGGGGAGAAGTCCGA-G
** * *
5422444 TATATTAAGATTTCCATGAGGAGTTACACTAAGGAA-ATGCAAATTACCATTGTCGATAAATATT
1 TATATTAAGATTTCCATGAACAGTTACACTAA-GAAGA-GCAAATCACCATTGCCGATAAATATT
*
5422508 AGAACATATGTGAATTATGGGG
64 AGAACATATGTGAAGTATGGGG
5422530 CAGATTTCCT
Statistics
Matches: 306, Mismatches: 57, Indels: 30
0.78 0.15 0.08
Matches are distributed among these distances:
95 1 0.00
96 12 0.04
97 215 0.70
98 71 0.23
99 5 0.02
100 2 0.01
ACGTcount: A:0.36, C:0.12, G:0.23, T:0.29
Consensus pattern (96 bp):
TATATTAAGATTTCCATGAACAGTTACACTAAGAAGAGCAAATCACCATTGCCGATAAATATTAG
AACATATGTGAAGTATGGGGAGAAGTCCGAG
Found at i:5424057 original size:20 final size:21
Alignment explanation
Indices: 5424018--5424057 Score: 64
Period size: 21 Copynumber: 2.0 Consensus size: 21
5424008 TTGTGATGGT
*
5424018 ATTTTTGTCACGAATTTTTAA
1 ATTTTTGTCACGAATATTTAA
5424039 ATTTTTGTCAC-AATATTTA
1 ATTTTTGTCACGAATATTTA
5424058 GTTAATTTGA
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
20 7 0.39
21 11 0.61
ACGTcount: A:0.30, C:0.10, G:0.07, T:0.53
Consensus pattern (21 bp):
ATTTTTGTCACGAATATTTAA
Found at i:5424188 original size:37 final size:37
Alignment explanation
Indices: 5424147--5424255 Score: 101
Period size: 37 Copynumber: 3.1 Consensus size: 37
5424137 TTACAAAATT
5424147 ATATTCTATTACAAACTTACTGTCATAATTTTTTCCC
1 ATATTCTATTACAAACTTACTGTCATAATTTTTTCCC
* *
5424184 ATATTCTATTACTAAATTTTA-T-TACA-AA---ATT---
1 ATATTCTATTAC-AAA-CTTACTGT-CATAATTTTTTCCC
*
5424215 ATATTTTATTACAAACTTACTGTCATAATTTTTTCCC
1 ATATTCTATTACAAACTTACTGTCATAATTTTTTCCC
5424252 ATAT
1 ATAT
5424256 AAATTCCTTT
Statistics
Matches: 55, Mismatches: 5, Indels: 24
0.65 0.06 0.29
Matches are distributed among these distances:
29 3 0.05
30 6 0.11
31 14 0.25
34 4 0.07
37 19 0.35
38 6 0.11
39 3 0.05
ACGTcount: A:0.34, C:0.17, G:0.02, T:0.48
Consensus pattern (37 bp):
ATATTCTATTACAAACTTACTGTCATAATTTTTTCCC
Found at i:5424207 original size:68 final size:68
Alignment explanation
Indices: 5424124--5424255 Score: 246
Period size: 68 Copynumber: 1.9 Consensus size: 68
5424114 ACTATTTTTG
5424124 TTACTAAATTCTATTACAAAATTATATTCTATTACAAACTTACTGTCATAATTTTTTCCCATATT
1 TTACTAAATTCTATTACAAAATTATATTCTATTACAAACTTACTGTCATAATTTTTTCCCATATT
5424189 CTA
66 CTA
* *
5424192 TTACTAAATTTTATTACAAAATTATATTTTATTACAAACTTACTGTCATAATTTTTTCCCATAT
1 TTACTAAATTCTATTACAAAATTATATTCTATTACAAACTTACTGTCATAATTTTTTCCCATAT
5424256 AAATTCCTTT
Statistics
Matches: 62, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
68 62 1.00
ACGTcount: A:0.36, C:0.16, G:0.02, T:0.47
Consensus pattern (68 bp):
TTACTAAATTCTATTACAAAATTATATTCTATTACAAACTTACTGTCATAATTTTTTCCCATATT
CTA
Found at i:5435291 original size:20 final size:20
Alignment explanation
Indices: 5435245--5435302 Score: 62
Period size: 20 Copynumber: 2.8 Consensus size: 20
5435235 TCACGTAAAA
* *
5435245 TAAATAATAATTAAAATATAT
1 TAAA-AATAATTAAAAAATAC
5435266 TAAAAATAATTAAAAAATAC
1 TAAAAATAATTAAAAAATAC
* *
5435286 TGAAAATGGATTAAAAA
1 TAAAAAT-AATTAAAAA
5435303 CAAAGTTTCA
Statistics
Matches: 32, Mismatches: 4, Indels: 2
0.84 0.11 0.05
Matches are distributed among these distances:
20 20 0.62
21 12 0.38
ACGTcount: A:0.64, C:0.02, G:0.05, T:0.29
Consensus pattern (20 bp):
TAAAAATAATTAAAAAATAC
Found at i:5436370 original size:21 final size:18
Alignment explanation
Indices: 5436343--5436392 Score: 55
Period size: 21 Copynumber: 2.6 Consensus size: 18
5436333 TTACTTTTAA
5436343 TTTATTTTTTTTAAAAAT
1 TTTATTTTTTTTAAAAAT
**
5436361 ATGTTAATTTTTAATAAAAAT
1 -T-TT-ATTTTTTTTAAAAAT
5436382 TTTATTTTTTT
1 TTTATTTTTTT
5436393 CATCTTAAGA
Statistics
Matches: 25, Mismatches: 4, Indels: 5
0.74 0.12 0.15
Matches are distributed among these distances:
18 6 0.24
19 3 0.12
20 3 0.12
21 13 0.52
ACGTcount: A:0.34, C:0.00, G:0.02, T:0.64
Consensus pattern (18 bp):
TTTATTTTTTTTAAAAAT
Found at i:5438741 original size:41 final size:44
Alignment explanation
Indices: 5438658--5438741 Score: 113
Period size: 41 Copynumber: 2.0 Consensus size: 44
5438648 TAATTCTTGT
*
5438658 AATTTTATTATTATAAAATATTAAATATATTATATATTTATATA
1 AATTTTAATATTATAAAATATTAAATATATTATATATTTATATA
*
5438702 AATTTTAAT-TTATGAAAT-TTAAA-ATAATT-TATATTTATAT
1 AATTTTAATATTATAAAATATTAAATAT-ATTATATATTTATAT
5438742 TATATGAATA
Statistics
Matches: 37, Mismatches: 2, Indels: 5
0.84 0.05 0.11
Matches are distributed among these distances:
41 13 0.35
42 8 0.22
43 8 0.22
44 8 0.22
ACGTcount: A:0.46, C:0.00, G:0.01, T:0.52
Consensus pattern (44 bp):
AATTTTAATATTATAAAATATTAAATATATTATATATTTATATA
Found at i:5440884 original size:2 final size:2
Alignment explanation
Indices: 5440879--5440910 Score: 64
Period size: 2 Copynumber: 16.0 Consensus size: 2
5440869 ATAATCACAC
5440879 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
5440911 CGTAACATGA
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 30 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:5447855 original size:13 final size:13
Alignment explanation
Indices: 5447837--5447861 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
5447827 CATAAAATGT
5447837 TGTATCGATACAA
1 TGTATCGATACAA
5447850 TGTATCGATACA
1 TGTATCGATACA
5447862 TTTGTTTTTG
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.36, C:0.16, G:0.16, T:0.32
Consensus pattern (13 bp):
TGTATCGATACAA
Found at i:5447942 original size:13 final size:13
Alignment explanation
Indices: 5447924--5447948 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
5447914 ATTACTCAAA
5447924 TGTATCGATACAT
1 TGTATCGATACAT
5447937 TGTATCGATACA
1 TGTATCGATACA
5447949 CTGATCTTTA
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.32, C:0.16, G:0.16, T:0.36
Consensus pattern (13 bp):
TGTATCGATACAT
Found at i:5451310 original size:20 final size:19
Alignment explanation
Indices: 5451260--5451310 Score: 57
Period size: 20 Copynumber: 2.6 Consensus size: 19
5451250 GGTAAAAAGA
5451260 CATAATGTATCGATACATT
1 CATAATGTATCGATACATT
* * *
5451279 GTAGAATATATCGATACATT
1 -CATAATGTATCGATACATT
5451299 CATACATGTATC
1 CATA-ATGTATC
5451311 TATATTGAAA
Statistics
Matches: 24, Mismatches: 6, Indels: 2
0.75 0.19 0.06
Matches are distributed among these distances:
19 2 0.08
20 22 0.92
ACGTcount: A:0.37, C:0.16, G:0.12, T:0.35
Consensus pattern (19 bp):
CATAATGTATCGATACATT
Found at i:5451946 original size:32 final size:32
Alignment explanation
Indices: 5451890--5452641 Score: 1135
Period size: 32 Copynumber: 23.7 Consensus size: 32
5451880 TTTTTAAAAA
** * *
5451890 AAAAGGG-TGCCACTAACTTATGTGGGCCTTG
1 AAAAGGGTTGCCACCGACTTGTGTGGGCTTTG
** *
5451921 AAAAGAATTGCCACCGACTCGTGTGGGCTTTG
1 AAAAGGGTTGCCACCGACTTGTGTGGGCTTTG
*
5451953 AAATGGGTTGCCACCGACTTGTGTGGGCTTT-
1 AAAAGGGTTGCCACCGACTTGTGTGGGCTTTG
*
5451984 --AAGGG--GCAACCGACTTGTGTGGGCTTTG
1 AAAAGGGTTGCCACCGACTTGTGTGGGCTTTG
5452012 AAAAGGGTTGCCACCGACTTGTGTGGGCTTTG
1 AAAAGGGTTGCCACCGACTTGTGTGGGCTTTG
5452044 AAAAGGGTTGCCACCGACTTGTGTGGGCTTTG
1 AAAAGGGTTGCCACCGACTTGTGTGGGCTTTG
* *
5452076 AAATGGGTTGCCACCGACTTGTGTGAGCTTT-
1 AAAAGGGTTGCCACCGACTTGTGTGGGCTTTG
* *
5452107 AGAATGGGTTGCCACTGACTTGTGTGGGCTTTG
1 A-AAAGGGTTGCCACCGACTTGTGTGGGCTTTG
5452140 AAAAGGGTTGCCACCGACTTGTGTGGGCTTTG
1 AAAAGGGTTGCCACCGACTTGTGTGGGCTTTG
* *
5452172 AAATGGGTTGCCACCGACTTATGTGGGCTTTG
1 AAAAGGGTTGCCACCGACTTGTGTGGGCTTTG
* *
5452204 GAATGGGTTGCCACCGACTTGTGTGGGCTTTG
1 AAAAGGGTTGCCACCGACTTGTGTGGGCTTTG
*
5452236 AAATGGGTTGCCACCGACTTGTGTGGGCTTT-
1 AAAAGGGTTGCCACCGACTTGTGTGGGCTTTG
*
5452267 AGAATGGGTTGCCACCGACTTGTGTGGGCTTTG
1 A-AAAGGGTTGCCACCGACTTGTGTGGGCTTTG
5452300 AAAAGGGTTGCCACCGACTTGTGTGGGCTTTG
1 AAAAGGGTTGCCACCGACTTGTGTGGGCTTTG
*
5452332 AAAATGGTTGCCACCGACTTGTGTGGGCTTTG
1 AAAAGGGTTGCCACCGACTTGTGTGGGCTTTG
* * *
5452364 AAATGGGTTGCCATCGACTTGTGTCGGCTTTG
1 AAAAGGGTTGCCACCGACTTGTGTGGGCTTTG
*
5452396 AAAAGGGTTGCCACCGACTTGTGTAGGCTTTG
1 AAAAGGGTTGCCACCGACTTGTGTGGGCTTTG
5452428 AAAAGGGTTGCCACCGACTTGTGTGGGCTTTG
1 AAAAGGGTTGCCACCGACTTGTGTGGGCTTTG
*
5452460 AAAATGGTTGCCACCGACTTGTGTGGGCTTTG
1 AAAAGGGTTGCCACCGACTTGTGTGGGCTTTG
*
5452492 AAATGGGTTGCCACCGACTTGTGTGGGCTTTG
1 AAAAGGGTTGCCACCGACTTGTGTGGGCTTTG
*
5452524 AAAAAGGTTGCCACCGACTTGTGTGGGCTTTG
1 AAAAGGGTTGCCACCGACTTGTGTGGGCTTTG
*
5452556 AAATGGGTTGCCACCGACTTGTGTGGGCTTTG
1 AAAAGGGTTGCCACCGACTTGTGTGGGCTTTG
*
5452588 AAATGGGTTGCCACCGACTTGTGTGGGCTTTG
1 AAAAGGGTTGCCACCGACTTGTGTGGGCTTTG
* * *
5452620 AAATGGG-TGCCACAGAGTTGTG
1 AAAAGGGTTGCCACCGACTTGTG
5452642 GATTTTAAAA
Statistics
Matches: 667, Mismatches: 44, Indels: 20
0.91 0.06 0.03
Matches are distributed among these distances:
27 21 0.03
29 4 0.01
30 5 0.01
31 20 0.03
32 615 0.92
33 2 0.00
ACGTcount: A:0.18, C:0.19, G:0.33, T:0.30
Consensus pattern (32 bp):
AAAAGGGTTGCCACCGACTTGTGTGGGCTTTG
Found at i:5452721 original size:27 final size:27
Alignment explanation
Indices: 5452624--5453663 Score: 1630
Period size: 27 Copynumber: 38.0 Consensus size: 27
5452614 GCTTTGAAAT
* *
5452624 GGGTGCCACAGAGTTGTGGATTTTAAAA
1 GGGTGCCACGGAGTTGTGGA-CTTAAAA
*
5452652 GGGTGCCACAGAGTTGTGGACTTAAAA
1 GGGTGCCACGGAGTTGTGGACTTAAAA
* * *
5452679 GAGATGCCATGGAGTTATGGACTTAAAA
1 G-GGTGCCACGGAGTTGTGGACTTAAAA
*
5452707 GGGTGCCACGGAGTTGTGGTCTTAAAA
1 GGGTGCCACGGAGTTGTGGACTTAAAA
5452734 GGGTGCCACGGAGTTGTGGACTTAAAA
1 GGGTGCCACGGAGTTGTGGACTTAAAA
*
5452761 GGGTGCCACGGAGTTGTGGTCTTAAAA
1 GGGTGCCACGGAGTTGTGGACTTAAAA
5452788 GGGATGCCACGGAGTTGTGGACTTAAAA
1 GGG-TGCCACGGAGTTGTGGACTTAAAA
*
5452816 GGGTGCCGCGGAGTTGTGGACTTAAAA
1 GGGTGCCACGGAGTTGTGGACTTAAAA
**
5452843 GGGTGCCACGGAGTTGTGGTTTTAAAA
1 GGGTGCCACGGAGTTGTGGACTTAAAA
*
5452870 GGGATGCCACGGAGTTGTGGAATTAAAA
1 GGG-TGCCACGGAGTTGTGGACTTAAAA
* *
5452898 GGGTGTCGCGGAGTTGTGGACTTAAAA
1 GGGTGCCACGGAGTTGTGGACTTAAAA
*
5452925 GGGTGCCACGGAGTTGTTGACTTAAAA
1 GGGTGCCACGGAGTTGTGGACTTAAAA
5452952 GGGTGCCACGGAGTTGTGGACTTAAAA
1 GGGTGCCACGGAGTTGTGGACTTAAAA
* *
5452979 GGATGCCACGAAGTTGTGGACTTAAAA
1 GGGTGCCACGGAGTTGTGGACTTAAAA
*
5453006 GGGATGCCACAGAGTTGTGGACTTAAAA
1 GGG-TGCCACGGAGTTGTGGACTTAAAA
5453034 GGGTGCCACGGAGTTGTGGACTTAAAA
1 GGGTGCCACGGAGTTGTGGACTTAAAA
5453061 GGGTGCCACGGAGTTGTGGACTTAAAA
1 GGGTGCCACGGAGTTGTGGACTTAAAA
5453088 GGGTGCCACGGAGTTGTGGACTTTAAAA
1 GGGTGCCACGGAGTTGTGGAC-TTAAAA
*
5453116 GGGTGCCACAGAGTTGTGGACTTAAAA
1 GGGTGCCACGGAGTTGTGGACTTAAAA
**
5453143 GATATGCCACGGAGTTGTGGACTTAAAA
1 G-GGTGCCACGGAGTTGTGGACTTAAAA
*
5453171 GGGTGTCACGGAGTTGTGGACTTAAAA
1 GGGTGCCACGGAGTTGTGGACTTAAAA
*
5453198 GGGTGCCACGGAGTTGTGGTCTTAAAA
1 GGGTGCCACGGAGTTGTGGACTTAAAA
5453225 GGGATGCCACGGAGTTGTGGACTTAAAA
1 GGG-TGCCACGGAGTTGTGGACTTAAAA
* * *
5453253 GGGTGCCGCGAAGTTATGGACTTAAAA
1 GGGTGCCACGGAGTTGTGGACTTAAAA
5453280 GGGTGCCACGGAGTTGTGGACTTAAAA
1 GGGTGCCACGGAGTTGTGGACTTAAAA
5453307 GGGTGCCACGGAGTTGTGGACTTAAAAA
1 GGGTGCCACGGAGTTGTGGACTT-AAAA
5453335 GGGTGCCACGGAGTTGTGGACTTAAAA
1 GGGTGCCACGGAGTTGTGGACTTAAAA
* *
5453362 GAGATGCCACGGAGTTATGGACTTAAAA
1 G-GGTGCCACGGAGTTGTGGACTTAAAA
*
5453390 GGGTGCCACGGAGTTGTGGTCTTAAAA
1 GGGTGCCACGGAGTTGTGGACTTAAAA
*
5453417 GGGATGCCACAGAGTTGTGGACTTAAAA
1 GGG-TGCCACGGAGTTGTGGACTTAAAA
*
5453445 GGGTGCCACGGAGTTATGGACTTAAAA
1 GGGTGCCACGGAGTTGTGGACTTAAAA
5453472 GGGTGCCACGGAGTTGTGGACTTAAAA
1 GGGTGCCACGGAGTTGTGGACTTAAAA
**
5453499 GAATGCCACGGAGTTGTGGACTTTAAAA
1 GGGTGCCACGGAGTTGTGGAC-TTAAAA
* *
5453527 GGATGCCACGAAGTTGTGGACTTAAAA
1 GGGTGCCACGGAGTTGTGGACTTAAAA
5453554 GGGATGCCACGGAGTTGTGGACTTAAAA
1 GGG-TGCCACGGAGTTGTGGACTTAAAA
5453582 GGGTGCCACGGAGTTGTGGACTTAAAA
1 GGGTGCCACGGAGTTGTGGACTTAAAA
5453609 GGGTGCCACGGAGTTGTGGACTTAAAA
1 GGGTGCCACGGAGTTGTGGACTTAAAA
* *
5453636 GGGTGCCACGGAGTTGTGGGCTTTAAA
1 GGGTGCCACGGAGTTGTGGACTTAAAA
5453663 G
1 G
5453664 AGGTCACACT
Statistics
Matches: 935, Mismatches: 65, Indels: 25
0.91 0.06 0.02
Matches are distributed among these distances:
27 612 0.65
28 323 0.35
ACGTcount: A:0.28, C:0.14, G:0.35, T:0.23
Consensus pattern (27 bp):
GGGTGCCACGGAGTTGTGGACTTAAAA
Found at i:5452796 original size:82 final size:81
Alignment explanation
Indices: 5452624--5453663 Score: 1630
Period size: 82 Copynumber: 12.7 Consensus size: 81
5452614 GCTTTGAAAT
* * * * *
5452624 GGGTGCCACAGAGTTGTGGATTTTAAAAGGGTGCCACAGAGTTGTGGACTTAAAAGAGATGCCAT
1 GGGTGCCACGGAGTTGTGGA-CTTAAAAGGGTGCCACGGAGTTGTGGACTTAAAAG-GGTGCCAC
*
5452689 GGAGTTATGGACTTAAAA
64 GGAGTTGTGGACTTAAAA
*
5452707 GGGTGCCACGGAGTTGTGGTCTTAAAAGGGTGCCACGGAGTTGTGGACTTAAAAGGGTGCCACGG
1 GGGTGCCACGGAGTTGTGGACTTAAAAGGGTGCCACGGAGTTGTGGACTTAAAAGGGTGCCACGG
*
5452772 AGTTGTGGTCTTAAAA
66 AGTTGTGGACTTAAAA
*
5452788 GGGATGCCACGGAGTTGTGGACTTAAAAGGGTGCCGCGGAGTTGTGGACTTAAAAGGGTGCCACG
1 GGG-TGCCACGGAGTTGTGGACTTAAAAGGGTGCCACGGAGTTGTGGACTTAAAAGGGTGCCACG
**
5452853 GAGTTGTGGTTTTAAAA
65 GAGTTGTGGACTTAAAA
* * *
5452870 GGGATGCCACGGAGTTGTGGAATTAAAAGGGTGTCGCGGAGTTGTGGACTTAAAAGGGTGCCACG
1 GGG-TGCCACGGAGTTGTGGACTTAAAAGGGTGCCACGGAGTTGTGGACTTAAAAGGGTGCCACG
*
5452935 GAGTTGTTGACTTAAAA
65 GAGTTGTGGACTTAAAA
* * *
5452952 GGGTGCCACGGAGTTGTGGACTTAAAAGGATGCCACGAAGTTGTGGACTTAAAAGGGATGCCACA
1 GGGTGCCACGGAGTTGTGGACTTAAAAGGGTGCCACGGAGTTGTGGACTTAAAAGGG-TGCCACG
5453017 GAGTTGTGGACTTAAAA
65 GAGTTGTGGACTTAAAA
5453034 GGGTGCCACGGAGTTGTGGACTTAAAAGGGTGCCACGGAGTTGTGGACTTAAAAGGGTGCCACGG
1 GGGTGCCACGGAGTTGTGGACTTAAAAGGGTGCCACGGAGTTGTGGACTTAAAAGGGTGCCACGG
5453099 AGTTGTGGACTTTAAAA
66 AGTTGTGGAC-TTAAAA
* ** *
5453116 GGGTGCCACAGAGTTGTGGACTTAAAAGATATGCCACGGAGTTGTGGACTTAAAAGGGTGTCACG
1 GGGTGCCACGGAGTTGTGGACTTAAAAG-GGTGCCACGGAGTTGTGGACTTAAAAGGGTGCCACG
5453181 GAGTTGTGGACTTAAAA
65 GAGTTGTGGACTTAAAA
* *
5453198 GGGTGCCACGGAGTTGTGGTCTTAAAAGGGATGCCACGGAGTTGTGGACTTAAAAGGGTGCCGCG
1 GGGTGCCACGGAGTTGTGGACTTAAAAGGG-TGCCACGGAGTTGTGGACTTAAAAGGGTGCCACG
* *
5453263 AAGTTATGGACTTAAAA
65 GAGTTGTGGACTTAAAA
5453280 GGGTGCCACGGAGTTGTGGACTTAAAAGGGTGCCACGGAGTTGTGGACTTAAAAAGGGTGCCACG
1 GGGTGCCACGGAGTTGTGGACTTAAAAGGGTGCCACGGAGTTGTGGACTT-AAAAGGGTGCCACG
5453345 GAGTTGTGGACTTAAAA
65 GAGTTGTGGACTTAAAA
* * *
5453362 GAGATGCCACGGAGTTATGGACTTAAAAGGGTGCCACGGAGTTGTGGTCTTAAAAGGGATGCCAC
1 G-GGTGCCACGGAGTTGTGGACTTAAAAGGGTGCCACGGAGTTGTGGACTTAAAAGGG-TGCCAC
*
5453427 AGAGTTGTGGACTTAAAA
64 GGAGTTGTGGACTTAAAA
* **
5453445 GGGTGCCACGGAGTTATGGACTTAAAAGGGTGCCACGGAGTTGTGGACTTAAAAGAATGCCACGG
1 GGGTGCCACGGAGTTGTGGACTTAAAAGGGTGCCACGGAGTTGTGGACTTAAAAGGGTGCCACGG
5453510 AGTTGTGGACTTTAAAA
66 AGTTGTGGAC-TTAAAA
* *
5453527 GGATGCCACGAAGTTGTGGACTTAAAAGGGATGCCACGGAGTTGTGGACTTAAAAGGGTGCCACG
1 GGGTGCCACGGAGTTGTGGACTTAAAAGGG-TGCCACGGAGTTGTGGACTTAAAAGGGTGCCACG
5453592 GAGTTGTGGACTTAAAA
65 GAGTTGTGGACTTAAAA
* *
5453609 GGGTGCCACGGAGTTGTGGACTTAAAAGGGTGCCACGGAGTTGTGGGCTTTAAAG
1 GGGTGCCACGGAGTTGTGGACTTAAAAGGGTGCCACGGAGTTGTGGACTTAAAAG
5453664 AGGTCACACT
Statistics
Matches: 887, Mismatches: 60, Indels: 22
0.92 0.06 0.02
Matches are distributed among these distances:
81 151 0.17
82 561 0.63
83 175 0.20
ACGTcount: A:0.28, C:0.14, G:0.35, T:0.23
Consensus pattern (81 bp):
GGGTGCCACGGAGTTGTGGACTTAAAAGGGTGCCACGGAGTTGTGGACTTAAAAGGGTGCCACGG
AGTTGTGGACTTAAAA
Found at i:5452816 original size:109 final size:109
Alignment explanation
Indices: 5452624--5453663 Score: 1647
Period size: 109 Copynumber: 9.5 Consensus size: 109
5452614 GCTTTGAAAT
* * * * *
5452624 GGGTGCCACAGAGTTGTGGATTTTAAAAGGGTGCCACAGAGTTGTGGACTTAAAAGAGATGCCAT
1 GGGTGCCACGGAGTTGTGGA-CTTAAAAGGGTGCCACGGAGTTGTGGACTTAAAAGGGATGCCAC
* *
5452689 GGAGTTATGGACTTAAAAGGGTGCCACGGAGTTGTGGTCTTAAAA
65 GGAGTTGTGGACTTAAAAGGGTGCCACGGAGTTGTGGACTTAAAA
*
5452734 GGGTGCCACGGAGTTGTGGACTTAAAAGGGTGCCACGGAGTTGTGGTCTTAAAAGGGATGCCACG
1 GGGTGCCACGGAGTTGTGGACTTAAAAGGGTGCCACGGAGTTGTGGACTTAAAAGGGATGCCACG
*
5452799 GAGTTGTGGACTTAAAAGGGTGCCGCGGAGTTGTGGACTTAAAA
66 GAGTTGTGGACTTAAAAGGGTGCCACGGAGTTGTGGACTTAAAA
** * * *
5452843 GGGTGCCACGGAGTTGTGGTTTTAAAAGGGATGCCACGGAGTTGTGGAATTAAAAGGG-TGTCGC
1 GGGTGCCACGGAGTTGTGGACTTAAAAGGG-TGCCACGGAGTTGTGGACTTAAAAGGGATGCCAC
*
5452907 GGAGTTGTGGACTTAAAAGGGTGCCACGGAGTTGTTGACTTAAAA
65 GGAGTTGTGGACTTAAAAGGGTGCCACGGAGTTGTGGACTTAAAA
* * *
5452952 GGGTGCCACGGAGTTGTGGACTTAAAAGGATGCCACGAAGTTGTGGACTTAAAAGGGATGCCACA
1 GGGTGCCACGGAGTTGTGGACTTAAAAGGGTGCCACGGAGTTGTGGACTTAAAAGGGATGCCACG
5453017 GAGTTGTGGACTTAAAAGGGTGCCACGGAGTTGTGGACTTAAAA
66 GAGTTGTGGACTTAAAAGGGTGCCACGGAGTTGTGGACTTAAAA
5453061 GGGTGCCACGGAGTTGTGGACTTAAAAGGGTGCCACGGAGTTGTGGACTTTAAAAGGG-TGCCAC
1 GGGTGCCACGGAGTTGTGGACTTAAAAGGGTGCCACGGAGTTGTGGAC-TTAAAAGGGATGCCAC
* **
5453125 AGAGTTGTGGACTTAAAAGATATGCCACGGAGTTGTGGACTTAAAA
65 GGAGTTGTGGACTTAAAAG-GGTGCCACGGAGTTGTGGACTTAAAA
* *
5453171 GGGTGTCACGGAGTTGTGGACTTAAAAGGGTGCCACGGAGTTGTGGTCTTAAAAGGGATGCCACG
1 GGGTGCCACGGAGTTGTGGACTTAAAAGGGTGCCACGGAGTTGTGGACTTAAAAGGGATGCCACG
* * *
5453236 GAGTTGTGGACTTAAAAGGGTGCCGCGAAGTTATGGACTTAAAA
66 GAGTTGTGGACTTAAAAGGGTGCCACGGAGTTGTGGACTTAAAA
5453280 GGGTGCCACGGAGTTGTGGACTTAAAAGGGTGCCACGGAGTTGTGGACTTAAAAAGGG-TGCCAC
1 GGGTGCCACGGAGTTGTGGACTTAAAAGGGTGCCACGGAGTTGTGGACTT-AAAAGGGATGCCAC
* *
5453344 GGAGTTGTGGACTTAAAAGAGATGCCACGGAGTTATGGACTTAAAA
65 GGAGTTGTGGACTTAAAAG-GGTGCCACGGAGTTGTGGACTTAAAA
* *
5453390 GGGTGCCACGGAGTTGTGGTCTTAAAAGGGATGCCACAGAGTTGTGGACTTAAAAGGG-TGCCAC
1 GGGTGCCACGGAGTTGTGGACTTAAAAGGG-TGCCACGGAGTTGTGGACTTAAAAGGGATGCCAC
*
5453454 GGAGTTATGGACTTAAAAGGGTGCCACGGAGTTGTGGACTTAAAA
65 GGAGTTGTGGACTTAAAAGGGTGCCACGGAGTTGTGGACTTAAAA
** * *
5453499 GAATGCCACGGAGTTGTGGACTTTAAAAGGATGCCACGAAGTTGTGGACTTAAAAGGGATGCCAC
1 GGGTGCCACGGAGTTGTGGAC-TTAAAAGGGTGCCACGGAGTTGTGGACTTAAAAGGGATGCCAC
5453564 GGAGTTGTGGACTTAAAAGGGTGCCACGGAGTTGTGGACTTAAAA
65 GGAGTTGTGGACTTAAAAGGGTGCCACGGAGTTGTGGACTTAAAA
* *
5453609 GGGTGCCACGGAGTTGTGGACTTAAAAGGGTGCCACGGAGTTGTGGGCTTTAAAG
1 GGGTGCCACGGAGTTGTGGACTTAAAAGGGTGCCACGGAGTTGTGGACTTAAAAG
5453664 AGGTCACACT
Statistics
Matches: 859, Mismatches: 61, Indels: 21
0.91 0.06 0.02
Matches are distributed among these distances:
108 25 0.03
109 501 0.58
110 314 0.37
111 19 0.02
ACGTcount: A:0.28, C:0.14, G:0.35, T:0.23
Consensus pattern (109 bp):
GGGTGCCACGGAGTTGTGGACTTAAAAGGGTGCCACGGAGTTGTGGACTTAAAAGGGATGCCACG
GAGTTGTGGACTTAAAAGGGTGCCACGGAGTTGTGGACTTAAAA
Found at i:5454986 original size:23 final size:23
Alignment explanation
Indices: 5454938--5454989 Score: 63
Period size: 23 Copynumber: 2.3 Consensus size: 23
5454928 CATGTCCTCA
*
5454938 TTTTTTTTATTTTTGTTGTTCCC
1 TTTTTTTTATTTTTGTTGTTCAC
5454961 TTTTTTTTA-TTTTGCTT-TTGCAC
1 TTTTTTTTATTTTTG-TTGTT-CAC
5454984 TTTTTT
1 TTTTTT
5454990 CTTTTCATCT
Statistics
Matches: 26, Mismatches: 1, Indels: 4
0.84 0.03 0.13
Matches are distributed among these distances:
22 7 0.27
23 19 0.73
ACGTcount: A:0.06, C:0.12, G:0.08, T:0.75
Consensus pattern (23 bp):
TTTTTTTTATTTTTGTTGTTCAC
Found at i:5454988 original size:15 final size:16
Alignment explanation
Indices: 5454970--5455012 Score: 54
Period size: 15 Copynumber: 2.8 Consensus size: 16
5454960 CTTTTTTTTA
5454970 TTTTGCTTTTGCA-CT
1 TTTTGCTTTTGCATCT
*
5454985 TTTTTCTTTT-CATCT
1 TTTTGCTTTTGCATCT
5455000 TTTGTGCTTTTGC
1 TTT-TGCTTTTGC
5455013 TTTTGACTTT
Statistics
Matches: 23, Mismatches: 2, Indels: 4
0.79 0.07 0.14
Matches are distributed among these distances:
14 2 0.09
15 14 0.61
16 6 0.26
17 1 0.04
ACGTcount: A:0.05, C:0.19, G:0.12, T:0.65
Consensus pattern (16 bp):
TTTTGCTTTTGCATCT
Found at i:5461161 original size:23 final size:23
Alignment explanation
Indices: 5461135--5461183 Score: 98
Period size: 23 Copynumber: 2.1 Consensus size: 23
5461125 TGGACATGTT
5461135 AAAAATGCATGAAACATAATAAA
1 AAAAATGCATGAAACATAATAAA
5461158 AAAAATGCATGAAACATAATAAA
1 AAAAATGCATGAAACATAATAAA
5461181 AAA
1 AAA
5461184 TGCATGGTCA
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
23 26 1.00
ACGTcount: A:0.67, C:0.08, G:0.08, T:0.16
Consensus pattern (23 bp):
AAAAATGCATGAAACATAATAAA
Found at i:5461183 original size:21 final size:22
Alignment explanation
Indices: 5461135--5461189 Score: 94
Period size: 23 Copynumber: 2.5 Consensus size: 22
5461125 TGGACATGTT
5461135 AAAAATGCATGAAACATAATAAA
1 AAAAATGCATGAAACATAAT-AA
5461158 AAAAATGCATGAAACATAAT-A
1 AAAAATGCATGAAACATAATAA
5461179 AAAAATGCATG
1 AAAAATGCATG
5461190 GTCAAAGGCT
Statistics
Matches: 32, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
21 12 0.38
23 20 0.62
ACGTcount: A:0.62, C:0.09, G:0.11, T:0.18
Consensus pattern (22 bp):
AAAAATGCATGAAACATAATAA
Found at i:5462150 original size:20 final size:20
Alignment explanation
Indices: 5462103--5462177 Score: 71
Period size: 20 Copynumber: 3.8 Consensus size: 20
5462093 AAAAAGACAT
*
5462103 AATGTATCGATACATT-GTA
1 AATGTATCGATACATTCATA
*
5462122 GAATATATCGATACATTCATA
1 -AATGTATCGATACATTCATA
* * * * *
5462143 CATGTATCAATATATTGAAA
1 AATGTATCGATACATTCATA
5462163 AATGTATCGATACAT
1 AATGTATCGATACAT
5462178 CAAGGTAAAA
Statistics
Matches: 43, Mismatches: 11, Indels: 2
0.77 0.20 0.04
Matches are distributed among these distances:
20 41 0.95
21 2 0.05
ACGTcount: A:0.41, C:0.12, G:0.12, T:0.35
Consensus pattern (20 bp):
AATGTATCGATACATTCATA
Found at i:5462171 original size:40 final size:39
Alignment explanation
Indices: 5462100--5462177 Score: 102
Period size: 40 Copynumber: 2.0 Consensus size: 39
5462090 GGTAAAAAGA
* * *
5462100 CATAATGTATCGATACATTGTAGAATATATCGATACATT
1 CATAATGTATCAATACATTGAAAAATATATCGATACATT
* *
5462139 CATACATGTATCAATATATTGAAAAATGTATCGATACAT
1 CATA-ATGTATCAATACATTGAAAAATATATCGATACAT
5462178 CAAGGTAAAA
Statistics
Matches: 33, Mismatches: 5, Indels: 1
0.85 0.13 0.03
Matches are distributed among these distances:
39 4 0.12
40 29 0.88
ACGTcount: A:0.41, C:0.13, G:0.12, T:0.35
Consensus pattern (39 bp):
CATAATGTATCAATACATTGAAAAATATATCGATACATT
Found at i:5465915 original size:70 final size:70
Alignment explanation
Indices: 5465784--5465918 Score: 189
Period size: 70 Copynumber: 1.9 Consensus size: 70
5465774 TTGTTGCACC
* ** *
5465784 AAAATTTATCCACCATGTCTATCTAAGTATCAAAGTCAAATTACCCTCAGAATGAATAAAATTAA
1 AAAATTTATCCACCATGTCTATCTAAGTATCAAAGTCAAATTACCCTCAAAACAAACAAAATTAA
5465849 GAAGT
66 GAAGT
* * * **
5465854 AAAATTTATCCACCATGTTTGTTTAAGTATTGAAGTCAAATTACCCTCAAAACAAACAAAATTAA
1 AAAATTTATCCACCATGTCTATCTAAGTATCAAAGTCAAATTACCCTCAAAACAAACAAAATTAA
5465919 AAAGCATACC
Statistics
Matches: 56, Mismatches: 9, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
70 56 1.00
ACGTcount: A:0.44, C:0.17, G:0.09, T:0.30
Consensus pattern (70 bp):
AAAATTTATCCACCATGTCTATCTAAGTATCAAAGTCAAATTACCCTCAAAACAAACAAAATTAA
GAAGT
Found at i:5467312 original size:17 final size:18
Alignment explanation
Indices: 5467276--5467322 Score: 60
Period size: 17 Copynumber: 2.7 Consensus size: 18
5467266 TCGAGGTTGG
5467276 TTTAGTTCATTTCAACA-
1 TTTAGTTCATTTCAACAT
**
5467293 TTTAGTTCATTTCAGTAT
1 TTTAGTTCATTTCAACAT
*
5467311 TTTAGTTGATTT
1 TTTAGTTCATTT
5467323 TTAATTTATT
Statistics
Matches: 26, Mismatches: 3, Indels: 1
0.87 0.10 0.03
Matches are distributed among these distances:
17 15 0.58
18 11 0.42
ACGTcount: A:0.23, C:0.11, G:0.11, T:0.55
Consensus pattern (18 bp):
TTTAGTTCATTTCAACAT
Found at i:5467333 original size:29 final size:29
Alignment explanation
Indices: 5467293--5467387 Score: 118
Period size: 29 Copynumber: 3.3 Consensus size: 29
5467283 CATTTCAACA
* *
5467293 TTTAGTTCATTTCAGTATTTTAGTTGATT
1 TTTAATTCATTTCAGTATTTTAGTTGACT
* ** *
5467322 TTTAATTTATTTTTGTGTTTTAGTTGACT
1 TTTAATTCATTTCAGTATTTTAGTTGACT
* *
5467351 TTTAATTCCTTTCAGTATTTTAATTGACT
1 TTTAATTCATTTCAGTATTTTAGTTGACT
5467380 TTTAATTC
1 TTTAATTC
5467388 TTTTTTGTGT
Statistics
Matches: 54, Mismatches: 12, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
29 54 1.00
ACGTcount: A:0.21, C:0.08, G:0.11, T:0.60
Consensus pattern (29 bp):
TTTAATTCATTTCAGTATTTTAGTTGACT
Found at i:5467393 original size:58 final size:58
Alignment explanation
Indices: 5467293--5467419 Score: 175
Period size: 58 Copynumber: 2.2 Consensus size: 58
5467283 CATTTCAACA
* * * * * *
5467293 TTTAGTTCATTTCAGTATTTTAGTTGATTTTTAATTTATTTTTGTGTTTTAGTTGACT
1 TTTAATTCCTTTCAGTATTTTAATTGACTTTTAATTTATTTTTGTGTTTAAGGTGACT
*
5467351 TTTAATTCCTTTCAGTATTTTAATTGACTTTTAATTCT-TTTTTGTGTTTAAGGTGATT
1 TTTAATTCCTTTCAGTATTTTAATTGACTTTTAATT-TATTTTTGTGTTTAAGGTGACT
5467409 TTTAATTCCTT
1 TTTAATTCCTT
5467420 AGCTTTATAT
Statistics
Matches: 61, Mismatches: 7, Indels: 2
0.87 0.10 0.03
Matches are distributed among these distances:
58 60 0.98
59 1 0.02
ACGTcount: A:0.20, C:0.08, G:0.12, T:0.61
Consensus pattern (58 bp):
TTTAATTCCTTTCAGTATTTTAATTGACTTTTAATTTATTTTTGTGTTTAAGGTGACT
Found at i:5467411 original size:29 final size:29
Alignment explanation
Indices: 5467314--5467416 Score: 102
Period size: 29 Copynumber: 3.6 Consensus size: 29
5467304 TCAGTATTTT
* *
5467314 AGTTGATTTTTAATT-TATTTTTGTGTTTT
1 AGTTGACTTTTAATTCT-TTTTTGTGTTTA
* ** *
5467343 AGTTGACTTTTAATTCCTTTCAGTATTTTA
1 AGTTGACTTTTAATTCTTTTTTGT-GTTTA
5467373 A-TTGACTTTTAATTCTTTTTTGTGTTTA
1 AGTTGACTTTTAATTCTTTTTTGTGTTTA
* *
5467401 AGGTGATTTTTAATTC
1 AGTTGACTTTTAATTC
5467417 CTTAGCTTTA
Statistics
Matches: 59, Mismatches: 12, Indels: 6
0.77 0.16 0.08
Matches are distributed among these distances:
28 5 0.08
29 50 0.85
30 4 0.07
ACGTcount: A:0.20, C:0.07, G:0.13, T:0.60
Consensus pattern (29 bp):
AGTTGACTTTTAATTCTTTTTTGTGTTTA
Found at i:5468878 original size:13 final size:13
Alignment explanation
Indices: 5468860--5468884 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
5468850 GAAGATATTC
5468860 ATATAACATGTGG
1 ATATAACATGTGG
5468873 ATATAACATGTG
1 ATATAACATGTG
5468885 AAGTTATCGA
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.40, C:0.08, G:0.20, T:0.32
Consensus pattern (13 bp):
ATATAACATGTGG
Found at i:5469553 original size:14 final size:14
Alignment explanation
Indices: 5469523--5469551 Score: 51
Period size: 13 Copynumber: 2.1 Consensus size: 14
5469513 TAAAATACCG
5469523 TTATTAAATTTATT
1 TTATTAAATTTATT
5469537 TTATT-AATTTATT
1 TTATTAAATTTATT
5469550 TT
1 TT
5469552 TAACAGTAAT
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
13 10 0.67
14 5 0.33
ACGTcount: A:0.31, C:0.00, G:0.00, T:0.69
Consensus pattern (14 bp):
TTATTAAATTTATT
Found at i:5469853 original size:30 final size:30
Alignment explanation
Indices: 5469819--5469875 Score: 71
Period size: 30 Copynumber: 1.9 Consensus size: 30
5469809 AATTTAATTT
*
5469819 ATTATATATACTTTTAAAT-ATTATATTTTA
1 ATTATATATA-TATTAAATAATTATATTTTA
* *
5469849 ATTATTTTTATATTAAATAATTATATT
1 ATTATATATATATTAAATAATTATATT
5469876 AAATTTAAAA
Statistics
Matches: 23, Mismatches: 3, Indels: 2
0.82 0.11 0.07
Matches are distributed among these distances:
29 7 0.30
30 16 0.70
ACGTcount: A:0.40, C:0.02, G:0.00, T:0.58
Consensus pattern (30 bp):
ATTATATATATATTAAATAATTATATTTTA
Found at i:5470115 original size:2 final size:2
Alignment explanation
Indices: 5470110--5470141 Score: 64
Period size: 2 Copynumber: 16.0 Consensus size: 2
5470100 TTTGAAAACA
5470110 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
5470142 TTTTGAAAGA
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 30 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:5470713 original size:3 final size:3
Alignment explanation
Indices: 5470705--5470748 Score: 88
Period size: 3 Copynumber: 14.7 Consensus size: 3
5470695 CGCTCATTGG
5470705 CTT CTT CTT CTT CTT CTT CTT CTT CTT CTT CTT CTT CTT CTT CT
1 CTT CTT CTT CTT CTT CTT CTT CTT CTT CTT CTT CTT CTT CTT CT
5470749 CTGTTTATTA
Statistics
Matches: 41, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 41 1.00
ACGTcount: A:0.00, C:0.34, G:0.00, T:0.66
Consensus pattern (3 bp):
CTT
Found at i:5483123 original size:20 final size:21
Alignment explanation
Indices: 5483098--5483137 Score: 64
Period size: 20 Copynumber: 2.0 Consensus size: 21
5483088 TAAATATATT
5483098 ATTTAAAAATAAAAA-TAAAA
1 ATTTAAAAATAAAAACTAAAA
*
5483118 ATTTAAATATAAAAACTAAA
1 ATTTAAAAATAAAAACTAAA
5483138 TATAATTAAT
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
20 14 0.78
21 4 0.22
ACGTcount: A:0.70, C:0.03, G:0.00, T:0.28
Consensus pattern (21 bp):
ATTTAAAAATAAAAACTAAAA
Found at i:5483150 original size:13 final size:13
Alignment explanation
Indices: 5483101--5483142 Score: 50
Period size: 14 Copynumber: 3.2 Consensus size: 13
5483091 ATATATTATT
*
5483101 TAAAAA-TAAAAA
1 TAAAAACTAAATA
*
5483113 TAAAAATTTAAATA
1 TAAAAA-CTAAATA
5483127 TAAAAACTAAATA
1 TAAAAACTAAATA
5483140 TAA
1 TAA
5483143 TTAATAAAAT
Statistics
Matches: 26, Mismatches: 2, Indels: 3
0.84 0.06 0.10
Matches are distributed among these distances:
12 6 0.23
13 9 0.35
14 11 0.42
ACGTcount: A:0.71, C:0.02, G:0.00, T:0.26
Consensus pattern (13 bp):
TAAAAACTAAATA
Found at i:5484155 original size:7 final size:7
Alignment explanation
Indices: 5484120--5484154 Score: 52
Period size: 7 Copynumber: 4.9 Consensus size: 7
5484110 AAAAAATGAT
5484120 ATTTAAAA
1 ATTT-AAA
5484128 ATTTAAA
1 ATTTAAA
5484135 ATTTAAA
1 ATTTAAA
*
5484142 ATTTAAT
1 ATTTAAA
5484149 ATTTAA
1 ATTTAA
5484155 TTTTTTTTTT
Statistics
Matches: 26, Mismatches: 1, Indels: 1
0.93 0.04 0.04
Matches are distributed among these distances:
7 22 0.85
8 4 0.15
ACGTcount: A:0.54, C:0.00, G:0.00, T:0.46
Consensus pattern (7 bp):
ATTTAAA
Found at i:5484184 original size:8 final size:7
Alignment explanation
Indices: 5484173--5484227 Score: 58
Period size: 8 Copynumber: 7.3 Consensus size: 7
5484163 TTATTTTTAA
5484173 ATTATGAT
1 ATTAT-AT
5484181 ATTATAT
1 ATTATAT
5484188 A-TATAT
1 ATTATAT
5484194 ATATATAT
1 AT-TATAT
5484202 ATATATAT
1 AT-TATAT
5484210 ATATATAT
1 AT-TATAT
5484218 ATATATAT
1 AT-TATAT
5484226 AT
1 AT
5484228 AAAGGTAATG
Statistics
Matches: 45, Mismatches: 0, Indels: 4
0.92 0.00 0.08
Matches are distributed among these distances:
6 6 0.13
7 3 0.07
8 36 0.80
ACGTcount: A:0.47, C:0.00, G:0.02, T:0.51
Consensus pattern (7 bp):
ATTATAT
Found at i:5484190 original size:2 final size:2
Alignment explanation
Indices: 5484179--5484228 Score: 93
Period size: 2 Copynumber: 25.5 Consensus size: 2
5484169 TTAAATTATG
5484179 AT AT -T AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
5484220 AT AT AT AT A
1 AT AT AT AT A
5484229 AAGGTAATGA
Statistics
Matches: 47, Mismatches: 0, Indels: 2
0.96 0.00 0.04
Matches are distributed among these distances:
1 1 0.02
2 46 0.98
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:5484381 original size:2 final size:2
Alignment explanation
Indices: 5484376--5484400 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
5484366 ATGTTTTCAA
5484376 AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT A
5484401 AATGTTCAAT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:5491691 original size:6 final size:6
Alignment explanation
Indices: 5491680--5491709 Score: 53
Period size: 6 Copynumber: 5.2 Consensus size: 6
5491670 TATTGTAACC
5491680 TAAATA TAAATA TAAATA TAAATA -AAATA T
1 TAAATA TAAATA TAAATA TAAATA TAAATA T
5491710 TTATGCGTTT
Statistics
Matches: 23, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
5 5 0.22
6 18 0.78
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (6 bp):
TAAATA
Found at i:5492382 original size:24 final size:23
Alignment explanation
Indices: 5492355--5492426 Score: 85
Period size: 23 Copynumber: 3.1 Consensus size: 23
5492345 TTTGGGATAC
5492355 CTTAGATAAATATTTTTGGAAATT
1 CTTAGATAAATATTTTT-GAAATT
* *
5492379 CTTA-ACATATATGTTTTGAAATT
1 CTTAGATAAATAT-TTTTGAAATT
5492402 CTTAGATAAATA-TTTTGATAATT
1 CTTAGATAAATATTTTTGA-AATT
5492425 CT
1 CT
5492427 GTTAAAATTT
Statistics
Matches: 41, Mismatches: 4, Indels: 7
0.79 0.08 0.13
Matches are distributed among these distances:
22 6 0.15
23 22 0.54
24 13 0.32
ACGTcount: A:0.36, C:0.07, G:0.10, T:0.47
Consensus pattern (23 bp):
CTTAGATAAATATTTTTGAAATT
Found at i:5492558 original size:25 final size:25
Alignment explanation
Indices: 5492529--5492577 Score: 80
Period size: 25 Copynumber: 2.0 Consensus size: 25
5492519 ATAAGAGTGA
*
5492529 ATAAATAAGATTTATTAAATATAAT
1 ATAAAAAAGATTTATTAAATATAAT
*
5492554 ATAAAAAAGATTTATTAAGTATAA
1 ATAAAAAAGATTTATTAAATATAA
5492578 AATTTGATTT
Statistics
Matches: 22, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
25 22 1.00
ACGTcount: A:0.57, C:0.00, G:0.06, T:0.37
Consensus pattern (25 bp):
ATAAAAAAGATTTATTAAATATAAT
Found at i:5492773 original size:2 final size:2
Alignment explanation
Indices: 5492768--5492797 Score: 60
Period size: 2 Copynumber: 15.0 Consensus size: 2
5492758 TAAATGTGAA
5492768 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
5492798 CTCAATACGT
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 28 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:5496373 original size:66 final size:66
Alignment explanation
Indices: 5496262--5496394 Score: 212
Period size: 66 Copynumber: 2.0 Consensus size: 66
5496252 AGCATTTGGG
* *
5496262 AACCCATTCTCTTTCTTGTATTGGCATGTATACATATATACATATATTATAATATTCAATACGTA
1 AACCCATTCTCTTTCTTGTATTGGCATATATACATATATACATATATTACAATATTCAATACGTA
5496327 T
66 T
* * * *
5496328 AACCCATTCTCTTTCTTGTATTGGCATATGTACATATATATATATATTACAATATTGAATATGTA
1 AACCCATTCTCTTTCTTGTATTGGCATATATACATATATACATATATTACAATATTCAATACGTA
5496393 T
66 T
5496394 A
1 A
5496395 TATATTCTAT
Statistics
Matches: 61, Mismatches: 6, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
66 61 1.00
ACGTcount: A:0.34, C:0.15, G:0.08, T:0.43
Consensus pattern (66 bp):
AACCCATTCTCTTTCTTGTATTGGCATATATACATATATACATATATTACAATATTCAATACGTA
T
Found at i:5496886 original size:2 final size:2
Alignment explanation
Indices: 5496879--5496916 Score: 58
Period size: 2 Copynumber: 19.0 Consensus size: 2
5496869 TTAAGGTTAC
* *
5496879 AT AT AT AT AT AT AT AT AT AT AT GT AT AT AT AT AC AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
5496917 TCACTTTCCA
Statistics
Matches: 32, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
2 32 1.00
ACGTcount: A:0.47, C:0.03, G:0.03, T:0.47
Consensus pattern (2 bp):
AT
Found at i:5501022 original size:26 final size:26
Alignment explanation
Indices: 5500993--5501044 Score: 86
Period size: 26 Copynumber: 2.0 Consensus size: 26
5500983 CCAGATCATG
*
5500993 CATTTGTCAAGCTTTATGTATATTGT
1 CATTGGTCAAGCTTTATGTATATTGT
*
5501019 CATTGGTCAAGCTTTGTGTATATTGT
1 CATTGGTCAAGCTTTATGTATATTGT
5501045 TATATCTATT
Statistics
Matches: 24, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
26 24 1.00
ACGTcount: A:0.21, C:0.12, G:0.19, T:0.48
Consensus pattern (26 bp):
CATTGGTCAAGCTTTATGTATATTGT
Found at i:5502162 original size:20 final size:19
Alignment explanation
Indices: 5502115--5502165 Score: 57
Period size: 19 Copynumber: 2.6 Consensus size: 19
5502105 TCGATATATT
* * *
5502115 GTATCGATACATGTTCATA
1 GTATCGATACATCTTAAAA
*
5502134 GTATTGATACATCTTGAAAA
1 GTATCGATACATCTT-AAAA
5502154 GTATCGATACAT
1 GTATCGATACAT
5502166 GAAACTGGCA
Statistics
Matches: 26, Mismatches: 5, Indels: 1
0.81 0.16 0.03
Matches are distributed among these distances:
19 13 0.50
20 13 0.50
ACGTcount: A:0.35, C:0.14, G:0.16, T:0.35
Consensus pattern (19 bp):
GTATCGATACATCTTAAAA
Found at i:5503609 original size:12 final size:12
Alignment explanation
Indices: 5503592--5503616 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
5503582 TACACCAAGT
5503592 ATGTATCGATAC
1 ATGTATCGATAC
5503604 ATGTATCGATAC
1 ATGTATCGATAC
5503616 A
1 A
5503617 CAAAAATTGT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.36, C:0.16, G:0.16, T:0.32
Consensus pattern (12 bp):
ATGTATCGATAC
Found at i:5503612 original size:31 final size:31
Alignment explanation
Indices: 5503574--5503636 Score: 92
Period size: 31 Copynumber: 2.0 Consensus size: 31
5503564 TAGCCAAACT
* *
5503574 TGTATCGATACAC-CAAGTATGTATCGATACA
1 TGTATCGATACACAAAAAT-TGTATCGATACA
5503605 TGTATCGATACACAAAAATTGTATCGATACA
1 TGTATCGATACACAAAAATTGTATCGATACA
5503636 T
1 T
5503637 TGGCTTGTAA
Statistics
Matches: 29, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
31 26 0.90
32 3 0.10
ACGTcount: A:0.38, C:0.17, G:0.14, T:0.30
Consensus pattern (31 bp):
TGTATCGATACACAAAAATTGTATCGATACA
Found at i:5505870 original size:21 final size:21
Alignment explanation
Indices: 5505837--5505881 Score: 56
Period size: 21 Copynumber: 2.1 Consensus size: 21
5505827 TTGCAAGTTG
*
5505837 AAATAAAGAAGTTGGCTAATGA
1 AAATAAAGAAGTTAGCTAA-GA
*
5505859 AAATAATG-AGTTAGCTAAGA
1 AAATAAAGAAGTTAGCTAAGA
5505879 AAA
1 AAA
5505882 ATGAAAACTT
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
20 5 0.24
21 9 0.43
22 7 0.33
ACGTcount: A:0.53, C:0.04, G:0.20, T:0.22
Consensus pattern (21 bp):
AAATAAAGAAGTTAGCTAAGA
Found at i:5507705 original size:15 final size:15
Alignment explanation
Indices: 5507685--5507715 Score: 62
Period size: 15 Copynumber: 2.1 Consensus size: 15
5507675 TAAAAATGTC
5507685 CAAAATGAAGAAGCT
1 CAAAATGAAGAAGCT
5507700 CAAAATGAAGAAGCT
1 CAAAATGAAGAAGCT
5507715 C
1 C
5507716 CAAACGAAAT
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 16 1.00
ACGTcount: A:0.52, C:0.16, G:0.19, T:0.13
Consensus pattern (15 bp):
CAAAATGAAGAAGCT
Found at i:5509813 original size:13 final size:13
Alignment explanation
Indices: 5509795--5509820 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
5509785 CATTTTTTCT
5509795 TTGTATCGATACA
1 TTGTATCGATACA
5509808 TTGTATCGATACA
1 TTGTATCGATACA
5509821 GGGTGATTAT
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:0.31, C:0.15, G:0.15, T:0.38
Consensus pattern (13 bp):
TTGTATCGATACA
Found at i:5512382 original size:13 final size:13
Alignment explanation
Indices: 5512364--5512389 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
5512354 TACACCAAGT
5512364 ATGTATCGATACA
1 ATGTATCGATACA
5512377 ATGTATCGATACA
1 ATGTATCGATACA
5512390 CAAAAAATTG
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:0.38, C:0.15, G:0.15, T:0.31
Consensus pattern (13 bp):
ATGTATCGATACA
Found at i:5512387 original size:32 final size:33
Alignment explanation
Indices: 5512346--5512409 Score: 94
Period size: 32 Copynumber: 2.0 Consensus size: 33
5512336 TAGCCAAACT
* **
5512346 TGTATCGATACACCAAGTA-TGTATCGATACAA
1 TGTATCGATACACAAAAAATTGTATCGATACAA
5512378 TGTATCGATACACAAAAAATTGTATCGATACA
1 TGTATCGATACACAAAAAATTGTATCGATACA
5512410 TTGGCTTGTA
Statistics
Matches: 28, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
32 16 0.57
33 12 0.43
ACGTcount: A:0.41, C:0.17, G:0.14, T:0.28
Consensus pattern (33 bp):
TGTATCGATACACAAAAAATTGTATCGATACAA
Found at i:5519976 original size:33 final size:33
Alignment explanation
Indices: 5519928--5519990 Score: 92
Period size: 33 Copynumber: 1.9 Consensus size: 33
5519918 CCCAGATGTA
5519928 TCGATACTGCATTCTTAATATCGATACATAATG
1 TCGATACTGCATTCTTAATATCGATACATAATG
**
5519961 TCGATACTG-AGTTCTTTGTATCGATACATA
1 TCGATACTGCA-TTCTTAATATCGATACATA
5519991 GAGTACTATT
Statistics
Matches: 27, Mismatches: 2, Indels: 2
0.87 0.06 0.06
Matches are distributed among these distances:
32 1 0.04
33 26 0.96
ACGTcount: A:0.30, C:0.17, G:0.14, T:0.38
Consensus pattern (33 bp):
TCGATACTGCATTCTTAATATCGATACATAATG
Found at i:5523622 original size:20 final size:20
Alignment explanation
Indices: 5523597--5523651 Score: 76
Period size: 20 Copynumber: 2.8 Consensus size: 20
5523587 AAAAAGACAT
*
5523597 AATGTATCGATACATTGA-A
1 AATGTATCGATACATTCATA
5523616 GAATGTATCGATACATTCATA
1 -AATGTATCGATACATTCATA
*
5523637 CATGTATCGATACAT
1 AATGTATCGATACAT
5523652 CTGGGTAAAA
Statistics
Matches: 32, Mismatches: 2, Indels: 2
0.89 0.06 0.06
Matches are distributed among these distances:
20 31 0.97
21 1 0.03
ACGTcount: A:0.38, C:0.15, G:0.15, T:0.33
Consensus pattern (20 bp):
AATGTATCGATACATTCATA
Found at i:5525015 original size:28 final size:27
Alignment explanation
Indices: 5524602--5525009 Score: 492
Period size: 28 Copynumber: 14.5 Consensus size: 27
5524592 CGCCGACTTG
** *
5524602 TGTGGGCTTTGAAAAGGTGCCACCAATT
1 TGTGGGCTTTG-AAAGGTGCCACTGACT
5524630 TGTGGGCTTTGAAAGGGTATGCCACTGACT
1 TGTGGGCTTTGAAA-GG--TGCCACTGACT
5524660 TGTGGGCTTTGAAAGGGTGCCACTGACT
1 TGTGGGCTTTGAAA-GGTGCCACTGACT
5524688 TGTGGGCTTTGAAAGGGTGCCACTGACT
1 TGTGGGCTTTGAAA-GGTGCCACTGACT
* *
5524716 TGTGGGCTTTGAAGGCGTACCACTGACT
1 TGTGGGCTTTGAAAG-GTGCCACTGACT
* * *
5524744 TATGGGCTTTGAAGGGGTGCCGCTGACT
1 TGTGGGCTTTGAA-AGGTGCCACTGACT
5524772 TGTGGGCTTTGAAAGGGTGCCACTGACT
1 TGTGGGCTTTGAAA-GGTGCCACTGACT
* * *
5524800 TGTGAGCTTTGGAAGGGTGCCACCGACT
1 TGTGGGCTTT-GAAAGGTGCCACTGACT
5524828 TGTGGGCTTTGAAGAGGTGCCACTGACT
1 TGTGGGCTTTGAA-AGGTGCCACTGACT
*
5524856 TGTGGGCTTTGAAAGGATGCCACTAACT
1 TGTGGGCTTTGAAAGG-TGCCACTGACT
* *
5524884 TGTGGGCTTTGAAAGGATGCTACTAACT
1 TGTGGGCTTTGAAAGG-TGCCACTGACT
5524912 TGTGGGCTTTGAAACAGGTGCCACTGACT
1 TGTGGGCTTTG-AA-AGGTGCCACTGACT
* * *
5524941 TGTGGGCTTTGAAAAGATGTCACTAACT
1 TGTGGGCTTTG-AAAGGTGCCACTGACT
* *
5524969 TGTGGGCTTTGAAAGGATGCCACTAACC
1 TGTGGGCTTTGAAAGG-TGCCACTGACT
5524997 TGTGGGCTTTGAA
1 TGTGGGCTTTGAA
5525010 GAGATGAACG
Statistics
Matches: 341, Mismatches: 27, Indels: 24
0.87 0.07 0.06
Matches are distributed among these distances:
27 14 0.04
28 269 0.79
29 30 0.09
30 28 0.08
ACGTcount: A:0.21, C:0.18, G:0.33, T:0.29
Consensus pattern (27 bp):
TGTGGGCTTTGAAAGGTGCCACTGACT
Found at i:5526267 original size:4 final size:4
Alignment explanation
Indices: 5526258--5526295 Score: 51
Period size: 4 Copynumber: 9.8 Consensus size: 4
5526248 GGACCCCTTT
* *
5526258 TTTG TTTG TTTG TTTT TTTG TTTG TTT- TTTT TTTG TTT
1 TTTG TTTG TTTG TTTG TTTG TTTG TTTG TTTG TTTG TTT
5526296 TTGGTTCTTT
Statistics
Matches: 30, Mismatches: 3, Indels: 2
0.86 0.09 0.06
Matches are distributed among these distances:
3 3 0.10
4 27 0.90
ACGTcount: A:0.00, C:0.00, G:0.16, T:0.84
Consensus pattern (4 bp):
TTTG
Found at i:5526296 original size:8 final size:8
Alignment explanation
Indices: 5526255--5526332 Score: 72
Period size: 8 Copynumber: 10.0 Consensus size: 8
5526245 TTTGGACCCC
5526255 TTTTTTGT
1 TTTTTTGT
*
5526263 TTGTTTGT
1 TTTTTTGT
5526271 TTTTTTGT
1 TTTTTTGT
*
5526279 TTGTTT-T
1 TTTTTTGT
5526286 TTTTTTG-
1 TTTTTTGT
*
5526293 -TTTTTGG
1 TTTTTTGT
*
5526300 TTCTTTGT
1 TTTTTTGT
*
5526308 TTTTTCTAT
1 TTTTT-TGT
*
5526317 TTTTTTAT
1 TTTTTTGT
5526325 TTTTTTGT
1 TTTTTTGT
5526333 ACGAAGGATG
Statistics
Matches: 57, Mismatches: 9, Indels: 8
0.77 0.12 0.11
Matches are distributed among these distances:
6 6 0.11
7 6 0.11
8 38 0.67
9 7 0.12
ACGTcount: A:0.03, C:0.03, G:0.13, T:0.82
Consensus pattern (8 bp):
TTTTTTGT
Found at i:5526298 original size:37 final size:39
Alignment explanation
Indices: 5526256--5526332 Score: 104
Period size: 37 Copynumber: 2.0 Consensus size: 39
5526246 TTGGACCCCT
* * *
5526256 TTTTTGTTTGTTTGTTTTTT-TGTTTGTTT-TTTTTTTG
1 TTTTTGGTTCTTTGTTTTTTCTATTTGTTTATTTTTTTG
*
5526293 TTTTTGGTTCTTTGTTTTTTCTATTTTTTTATTTTTTTG
1 TTTTTGGTTCTTTGTTTTTTCTATTTGTTTATTTTTTTG
5526332 T
1 T
5526333 ACGAAGGATG
Statistics
Matches: 34, Mismatches: 4, Indels: 2
0.85 0.10 0.05
Matches are distributed among these distances:
37 18 0.53
38 7 0.21
39 9 0.26
ACGTcount: A:0.03, C:0.03, G:0.13, T:0.82
Consensus pattern (39 bp):
TTTTTGGTTCTTTGTTTTTTCTATTTGTTTATTTTTTTG
Found at i:5526314 original size:11 final size:12
Alignment explanation
Indices: 5526266--5526312 Score: 60
Period size: 12 Copynumber: 3.8 Consensus size: 12
5526256 TTTTTGTTTG
*
5526266 TTTGTTTTTTTG
1 TTTGTTTTTTTC
5526278 TTTGTTTTTTT-
1 TTTGTTTTTTTC
5526289 TTTGTTTTTGGTTC
1 TTTGTTTTT--TTC
5526303 TTTGTTTTTT
1 TTTGTTTTTT
5526313 CTATTTTTTT
Statistics
Matches: 32, Mismatches: 0, Indels: 6
0.84 0.00 0.16
Matches are distributed among these distances:
11 9 0.28
12 12 0.38
13 2 0.06
14 9 0.28
ACGTcount: A:0.00, C:0.02, G:0.15, T:0.83
Consensus pattern (12 bp):
TTTGTTTTTTTC
Found at i:5542793 original size:22 final size:21
Alignment explanation
Indices: 5542745--5542806 Score: 63
Period size: 22 Copynumber: 2.9 Consensus size: 21
5542735 TATCAAAGAC
* *
5542745 GTTTTAGAGATAAATATAAAT
1 GTTTTAAAGATAAAAATAAAT
*
5542766 GTTTTTAAAGATAAAAATCATAT
1 G-TTTTAAAGATAAAAAT-AAAT
*
5542789 GTTTTCAAG-TAAAAATAA
1 GTTTTAAAGATAAAAATAA
5542807 TCCAAAGTAT
Statistics
Matches: 34, Mismatches: 5, Indels: 5
0.77 0.11 0.11
Matches are distributed among these distances:
20 1 0.03
21 8 0.24
22 21 0.62
23 4 0.12
ACGTcount: A:0.48, C:0.03, G:0.11, T:0.37
Consensus pattern (21 bp):
GTTTTAAAGATAAAAATAAAT
Found at i:5542924 original size:19 final size:20
Alignment explanation
Indices: 5542881--5542952 Score: 74
Period size: 20 Copynumber: 3.6 Consensus size: 20
5542871 AACCCTAGAA
*
5542881 AGTATCGATACATATTGCTT
1 AGTATCGATACATATTGCAT
* *
5542901 AGTATCGATGCATGTT-CAT
1 AGTATCGATACATATTGCAT
** * *
5542920 AGTATCGATACACCTTGAAA
1 AGTATCGATACATATTGCAT
5542940 AGTATCGATACAT
1 AGTATCGATACAT
5542953 GAAACTGGCA
Statistics
Matches: 42, Mismatches: 9, Indels: 2
0.79 0.17 0.04
Matches are distributed among these distances:
19 15 0.36
20 27 0.64
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
Consensus pattern (20 bp):
AGTATCGATACATATTGCAT
Found at i:5549871 original size:79 final size:79
Alignment explanation
Indices: 5549681--5550061 Score: 360
Period size: 79 Copynumber: 4.8 Consensus size: 79
5549671 AAAAATAGTG
* *
5549681 TTGGAGTAT-CCTAGAGATGAGAAATTCAATGTTTTAGAAGTAAAA-ATGGGGTTAAAGTATCCC
1 TTGGAGTATCCCCAGAGATGAAAAATTCAATGTTTTAGAAGTAAAACA--GGGTTAAAGTATCCC
*
5549744 CTCGAAGATGGTGGGG
64 CTCGAAGATGGTGGGA
* * * * * * * * *
5549760 TTGAAATATCCCCATAGATAAAAAATTTAATGTTTTAGAAGTAAAACAGGATTAAATTATTCTCT
1 TTGGAGTATCCCCAGAGATGAAAAATTCAATGTTTTAGAAGTAAAACAGGGTTAAAGTATCCCCT
*
5549825 CGGAGATGGTGGGA
66 CGAAGATGGTGGGA
* * *
5549839 TTGGAGTATACCCTA-AGATGAAAAATTCAATGTTTTAGAAGTAAAA-ATGGGGTTAGAGTATCT
1 TTGGAGTAT-CCCCAGAGATGAAAAATTCAATGTTTTAGAAGTAAAACA--GGGTTAAAGTATCC
* * *
5549902 CTTCAAAGATTGT-GGA
63 CCTCGAAGATGGTGGGA
* * * * *
5549918 GTTAGAGTATCCCCAGAGATAAAAAAATTCAGTGTTTTAGAAGTAAAACGGGGTTAGAGTATCCC
1 -TTGGAGTATCCCCAGAGAT-GAAAAATTCAATGTTTTAGAAGTAAAACAGGGTTAAAGTATCCC
* *
5549983 CTTGAAGATGGTGGGG
64 CTCGAAGATGGTGGGA
* * *** *
5549999 TTGGAGTA-CCTCCAAAGATGAAAATTTTGGTGTTTTAGAAGTAAAACAGGGTTGAAGTATCCC
1 TTGGAGTATCC-CCAGAGATGAAAAATTCAATGTTTTAGAAGTAAAACAGGGTTAAAGTATCCC
5550062 TTTTGGATTG
Statistics
Matches: 243, Mismatches: 48, Indels: 22
0.78 0.15 0.07
Matches are distributed among these distances:
78 1 0.00
79 114 0.47
80 100 0.41
81 28 0.12
ACGTcount: A:0.35, C:0.11, G:0.25, T:0.29
Consensus pattern (79 bp):
TTGGAGTATCCCCAGAGATGAAAAATTCAATGTTTTAGAAGTAAAACAGGGTTAAAGTATCCCCT
CGAAGATGGTGGGA
Found at i:5550043 original size:160 final size:159
Alignment explanation
Indices: 5549681--5550061 Score: 430
Period size: 159 Copynumber: 2.4 Consensus size: 159
5549671 AAAAATAGTG
* * *
5549681 TTGGAGTAT-CCTAGAGATGAGAAATTCAATGTTTTAGAAGTAAAAATGGGGTTAAAGTATCCCC
1 TTGGAGTATACCCAAAGATGAAAAATTCAATGTTTTAGAAGTAAAAATGGGGTTAAAGTATCCCC
* * * *
5549745 TCGAAGATGGTGGGGTTGAAATATCCCCATAGATAAAAAATTTAATGTTTTAGAAGTAAAACAGG
66 TCAAAGATGGTGGAGTTGAAATATCCCCAGAGATAAAAAATTCAATGTTTTAGAAGTAAAACAGG
* * * *
5549810 ATTAAATTATTCTCTCGGAGATGGTGGGA
131 ATTAAAGTATCCCCTCGAAGATGGTGGGA
* * * *
5549839 TTGGAGTATACCCTAAGATGAAAAATTCAATGTTTTAGAAGTAAAAATGGGGTTAGAGTATCTCT
1 TTGGAGTATACCCAAAGATGAAAAATTCAATGTTTTAGAAGTAAAAATGGGGTTAAAGTATCCCC
* * * *
5549904 TCAAAGATTGTGGAGTT-AGAGTATCCCCAGAGATAAAAAAATTCAGTGTTTTAGAAGTAAAACG
66 TCAAAGATGGTGGAGTTGA-AATATCCCCAGAGAT-AAAAAATTCAATGTTTTAGAAGTAAAACA
* * * *
5549968 GGGTTAGAGTATCCCCTTGAAGATGGTGGGG
129 GGATTAAAGTATCCCCTCGAAGATGGTGGGA
* * *** *
5549999 TTGGAGTA-CCTCCAAAGATGAAAATTTTGGTGTTTTAGAAGTAAAACA--GGGTTGAAGTATCC
1 TTGGAGTATAC-CCAAAGATGAAAAATTCAATGTTTTAGAAGTAAAA-ATGGGGTTAAAGTATCC
5550061 C
64 C
5550062 TTTTGGATTG
Statistics
Matches: 186, Mismatches: 32, Indels: 9
0.82 0.14 0.04
Matches are distributed among these distances:
158 10 0.05
159 88 0.47
160 87 0.47
161 1 0.01
ACGTcount: A:0.35, C:0.11, G:0.25, T:0.29
Consensus pattern (159 bp):
TTGGAGTATACCCAAAGATGAAAAATTCAATGTTTTAGAAGTAAAAATGGGGTTAAAGTATCCCC
TCAAAGATGGTGGAGTTGAAATATCCCCAGAGATAAAAAATTCAATGTTTTAGAAGTAAAACAGG
ATTAAAGTATCCCCTCGAAGATGGTGGGA
Found at i:5552870 original size:2 final size:2
Alignment explanation
Indices: 5552863--5552906 Score: 88
Period size: 2 Copynumber: 22.0 Consensus size: 2
5552853 ATTTGTTTAC
5552863 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
5552905 AT
1 AT
5552907 CTTCGATCTC
Statistics
Matches: 42, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 42 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:5555502 original size:14 final size:14
Alignment explanation
Indices: 5555483--5555511 Score: 58
Period size: 14 Copynumber: 2.1 Consensus size: 14
5555473 TCCTGCACTC
5555483 GTAGCAGAAGCTAG
1 GTAGCAGAAGCTAG
5555497 GTAGCAGAAGCTAG
1 GTAGCAGAAGCTAG
5555511 G
1 G
5555512 AAGCGTTTCA
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 15 1.00
ACGTcount: A:0.34, C:0.14, G:0.38, T:0.14
Consensus pattern (14 bp):
GTAGCAGAAGCTAG
Found at i:5556887 original size:16 final size:16
Alignment explanation
Indices: 5556866--5556916 Score: 51
Period size: 16 Copynumber: 3.6 Consensus size: 16
5556856 TAACAAAATA
5556866 ATTTAAATTTAAATTT
1 ATTTAAATTTAAATTT
5556882 ATTT-AA---AAA-TT
1 ATTTAAATTTAAATTT
*
5556893 -TTTGAATTTAAATTT
1 ATTTAAATTTAAATTT
5556908 ATTTAAATT
1 ATTTAAATT
5556917 GATTTAATAA
Statistics
Matches: 28, Mismatches: 1, Indels: 12
0.68 0.02 0.29
Matches are distributed among these distances:
10 3 0.11
11 4 0.14
12 3 0.11
14 3 0.11
15 4 0.14
16 11 0.39
ACGTcount: A:0.43, C:0.00, G:0.02, T:0.55
Consensus pattern (16 bp):
ATTTAAATTTAAATTT
Found at i:5557873 original size:22 final size:20
Alignment explanation
Indices: 5557822--5557875 Score: 54
Period size: 22 Copynumber: 2.5 Consensus size: 20
5557812 AAAATATATA
*
5557822 TATGAAATATTTTAAAATCAT
1 TATGAAA-ATTTTAATATCAT
*
5557843 TGATAAAAATTTTCAATATCAT
1 T-ATGAAAATTTT-AATATCAT
5557865 GTATGAAAATT
1 -TATGAAAATT
5557876 ATTTTCTATT
Statistics
Matches: 27, Mismatches: 3, Indels: 5
0.77 0.09 0.14
Matches are distributed among these distances:
21 6 0.22
22 20 0.74
23 1 0.04
ACGTcount: A:0.46, C:0.06, G:0.07, T:0.41
Consensus pattern (20 bp):
TATGAAAATTTTAATATCAT
Found at i:5558678 original size:19 final size:19
Alignment explanation
Indices: 5558654--5558699 Score: 65
Period size: 19 Copynumber: 2.4 Consensus size: 19
5558644 CTACTTATAT
* * *
5558654 TATTTTTTATATTTTAATA
1 TATTTTTAATAATTAAATA
5558673 TATTTTTAATAATTAAATA
1 TATTTTTAATAATTAAATA
5558692 TATTTTTA
1 TATTTTTA
5558700 TTAAGTTTTT
Statistics
Matches: 24, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
19 24 1.00
ACGTcount: A:0.37, C:0.00, G:0.00, T:0.63
Consensus pattern (19 bp):
TATTTTTAATAATTAAATA
Found at i:5559745 original size:23 final size:23
Alignment explanation
Indices: 5559729--5559772 Score: 61
Period size: 23 Copynumber: 1.9 Consensus size: 23
5559719 ATTTAAGTTT
*
5559729 TAAAATTATAAATATTTGATATC
1 TAAAATTATAAATATTTAATATC
* *
5559752 TAAAATTTTAAATATTAAATA
1 TAAAATTATAAATATTTAATA
5559773 AATATAAAAA
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
23 18 1.00
ACGTcount: A:0.52, C:0.02, G:0.02, T:0.43
Consensus pattern (23 bp):
TAAAATTATAAATATTTAATATC
Found at i:5560026 original size:85 final size:85
Alignment explanation
Indices: 5559883--5560061 Score: 297
Period size: 85 Copynumber: 2.1 Consensus size: 85
5559873 AAAAGAAAAC
* * *
5559883 ATTAAATTGGCTTAAGAAGCAAATAAGTGAAAATATTTTAAAAAAATAAAATACCAAATTCTTTT
1 ATTAAATTGGCTCAAGAAGCAAATAAGTGAAAATATTTTAAAAAAACAAAATACCAAATTCGTTT
5559948 ACCAACTACTATGGATCGGT
66 ACCAACTACTATGGATCGGT
*
5559968 ATTAAATTGGCTCAAGAAGCAAATAGGTGAAAATATTTTAAAAAAACAAAATACCAAATTCGTTT
1 ATTAAATTGGCTCAAGAAGCAAATAAGTGAAAATATTTTAAAAAAACAAAATACCAAATTCGTTT
*
5560033 ACCAACTACTATGGATGGGT
66 ACCAACTACTATGGATCGGT
*
5560053 A-CAAATTGG
1 ATTAAATTGG
5560062 TATGTTGAAA
Statistics
Matches: 88, Mismatches: 6, Indels: 1
0.93 0.06 0.01
Matches are distributed among these distances:
84 7 0.08
85 81 0.92
ACGTcount: A:0.45, C:0.12, G:0.14, T:0.28
Consensus pattern (85 bp):
ATTAAATTGGCTCAAGAAGCAAATAAGTGAAAATATTTTAAAAAAACAAAATACCAAATTCGTTT
ACCAACTACTATGGATCGGT
Found at i:5561192 original size:22 final size:23
Alignment explanation
Indices: 5561148--5561194 Score: 60
Period size: 24 Copynumber: 2.0 Consensus size: 23
5561138 AGATAAAAGC
**
5561148 ATATTTTTTTTTATTTTACATTAA
1 ATATTTTTAATTATTTTA-ATTAA
5561172 ATATTTTTAATTATTTT-ATTAA
1 ATATTTTTAATTATTTTAATTAA
5561194 A
1 A
5561195 AATAATAATA
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
22 6 0.29
24 15 0.71
ACGTcount: A:0.34, C:0.02, G:0.00, T:0.64
Consensus pattern (23 bp):
ATATTTTTAATTATTTTAATTAA
Found at i:5563254 original size:29 final size:28
Alignment explanation
Indices: 5563222--5563284 Score: 65
Period size: 29 Copynumber: 2.2 Consensus size: 28
5563212 TTAAAATATT
5563222 ATTTAATAAATAAAAATATTTT-TAATTTA
1 ATTTAA-AAATAAAAAT-TTTTATAATTTA
* **
5563251 ATTTTAAAATATTAATTTTTAATAATTTA
1 ATTTAAAAATAAAAATTTTT-ATAATTTA
5563280 ATTTA
1 ATTTA
5563285 TTTTTAAAAA
Statistics
Matches: 28, Mismatches: 4, Indels: 4
0.78 0.11 0.11
Matches are distributed among these distances:
27 4 0.14
28 8 0.29
29 16 0.57
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (28 bp):
ATTTAAAAATAAAAATTTTTATAATTTA
Found at i:5563272 original size:15 final size:15
Alignment explanation
Indices: 5563244--5563283 Score: 57
Period size: 15 Copynumber: 2.7 Consensus size: 15
5563234 AAAATATTTT
5563244 TAATTTAA-TTTTAA
1 TAATTTAATTTTTAA
5563258 -AATATTAATTTTTAA
1 TAAT-TTAATTTTTAA
5563273 TAATTTAATTT
1 TAATTTAATTT
5563284 ATTTTTAAAA
Statistics
Matches: 23, Mismatches: 0, Indels: 5
0.82 0.00 0.18
Matches are distributed among these distances:
13 3 0.13
14 4 0.17
15 13 0.57
16 3 0.13
ACGTcount: A:0.42, C:0.00, G:0.00, T:0.57
Consensus pattern (15 bp):
TAATTTAATTTTTAA
Found at i:5564208 original size:2 final size:2
Alignment explanation
Indices: 5564201--5564231 Score: 62
Period size: 2 Copynumber: 15.5 Consensus size: 2
5564191 AAATCTATTC
5564201 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
5564232 AAATTAAAAA
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 29 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:5574120 original size:6 final size:6
Alignment explanation
Indices: 5574111--5574135 Score: 50
Period size: 6 Copynumber: 4.2 Consensus size: 6
5574101 TTATCTTTTT
5574111 CATTTA CATTTA CATTTA CATTTA C
1 CATTTA CATTTA CATTTA CATTTA C
5574136 TGAAAATCAA
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 19 1.00
ACGTcount: A:0.32, C:0.20, G:0.00, T:0.48
Consensus pattern (6 bp):
CATTTA
Found at i:5577371 original size:28 final size:26
Alignment explanation
Indices: 5577340--5577401 Score: 79
Period size: 26 Copynumber: 2.3 Consensus size: 26
5577330 AGAATTTGAC
5577340 TAATTTTAATACATAAAATATAATTAAA
1 TAATTTTAATACAT--AATATAATTAAA
* *
5577368 TAATTTTATTGCATAATATAATTAAA
1 TAATTTTAATACATAATATAATTAAA
*
5577394 TAACTTTA
1 TAATTTTA
5577402 TTAAATTAAA
Statistics
Matches: 31, Mismatches: 3, Indels: 2
0.86 0.08 0.06
Matches are distributed among these distances:
26 19 0.61
28 12 0.39
ACGTcount: A:0.50, C:0.05, G:0.02, T:0.44
Consensus pattern (26 bp):
TAATTTTAATACATAATATAATTAAA
Found at i:5578207 original size:4 final size:4
Alignment explanation
Indices: 5578198--5578232 Score: 70
Period size: 4 Copynumber: 8.8 Consensus size: 4
5578188 AGCTGAGGAA
5578198 GTAT GTAT GTAT GTAT GTAT GTAT GTAT GTAT GTA
1 GTAT GTAT GTAT GTAT GTAT GTAT GTAT GTAT GTA
5578233 AATCATAATT
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 31 1.00
ACGTcount: A:0.26, C:0.00, G:0.26, T:0.49
Consensus pattern (4 bp):
GTAT
Found at i:5580108 original size:19 final size:18
Alignment explanation
Indices: 5580073--5580120 Score: 51
Period size: 18 Copynumber: 2.6 Consensus size: 18
5580063 TTATTTTAAT
* *
5580073 TTTAATAATTTTTAAATA
1 TTTATTAATTTTCAAATA
5580091 TTTATTAATTTCTCAAATA
1 TTTATTAATTT-TCAAATA
*
5580110 TATTATAAATT
1 T-TTATTAATT
5580121 CTATTTTATA
Statistics
Matches: 25, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
18 10 0.40
19 7 0.28
20 8 0.32
ACGTcount: A:0.42, C:0.04, G:0.00, T:0.54
Consensus pattern (18 bp):
TTTATTAATTTTCAAATA
Found at i:5584500 original size:18 final size:18
Alignment explanation
Indices: 5584479--5584514 Score: 54
Period size: 18 Copynumber: 2.0 Consensus size: 18
5584469 TTTTTTTTAA
*
5584479 TTAAAAAATTTTGAAATT
1 TTAAAAAATTTTAAAATT
*
5584497 TTAAATAATTTTAAAATT
1 TTAAAAAATTTTAAAATT
5584515 ATTTTAATTT
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
18 16 1.00
ACGTcount: A:0.50, C:0.00, G:0.03, T:0.47
Consensus pattern (18 bp):
TTAAAAAATTTTAAAATT
Found at i:5584546 original size:22 final size:22
Alignment explanation
Indices: 5584519--5584568 Score: 91
Period size: 22 Copynumber: 2.3 Consensus size: 22
5584509 AAAATTATTT
5584519 TAATTTTTATTAAATTAAATTG
1 TAATTTTTATTAAATTAAATTG
*
5584541 TAATTTTTATTAAATTAAATTT
1 TAATTTTTATTAAATTAAATTG
5584563 TAATTT
1 TAATTT
5584569 AAATATATAT
Statistics
Matches: 27, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
22 27 1.00
ACGTcount: A:0.40, C:0.00, G:0.02, T:0.58
Consensus pattern (22 bp):
TAATTTTTATTAAATTAAATTG
Found at i:5584622 original size:22 final size:22
Alignment explanation
Indices: 5584565--5584675 Score: 69
Period size: 21 Copynumber: 5.3 Consensus size: 22
5584555 TTAAATTTTA
5584565 ATTTAAATATATATTAA--A-T
1 ATTTAAATATATATTAATTATT
* *
5584584 ATTTAAA-ATTTATT--TT-TA
1 ATTTAAATATATATTAATTATT
5584602 ATTTAAATATATATTAATT-TT
1 ATTTAAATATATATTAATTATT
** * *
5584623 GAGATAAATATATTATATTATTGTT
1 -ATTTAAATATA-TAT-TAATTATT
*
5584648 ATTTAAA-ATAAATTAATTATT
1 ATTTAAATATATATTAATTATT
5584669 ATTTAAA
1 ATTTAAA
5584676 AAATAAACAA
Statistics
Matches: 70, Mismatches: 12, Indels: 18
0.70 0.12 0.18
Matches are distributed among these distances:
18 13 0.19
19 13 0.19
21 16 0.23
22 11 0.16
23 6 0.09
24 9 0.13
25 2 0.03
ACGTcount: A:0.46, C:0.00, G:0.03, T:0.51
Consensus pattern (22 bp):
ATTTAAATATATATTAATTATT
Found at i:5584882 original size:16 final size:16
Alignment explanation
Indices: 5584830--5584888 Score: 66
Period size: 16 Copynumber: 3.7 Consensus size: 16
5584820 GTTTAGGTTG
*
5584830 AATTTTAATTATTTTA
1 AATTTGAATTATTTTA
*
5584846 AA-TTCATATTATTTTA
1 AATTTGA-ATTATTTTA
*
5584862 TATTTGAATTATTTTA
1 AATTTGAATTATTTTA
*
5584878 AATTTGGATTA
1 AATTTGAATTA
5584889 GGCTTGGATA
Statistics
Matches: 36, Mismatches: 5, Indels: 4
0.80 0.11 0.09
Matches are distributed among these distances:
15 3 0.08
16 30 0.83
17 3 0.08
ACGTcount: A:0.36, C:0.02, G:0.05, T:0.58
Consensus pattern (16 bp):
AATTTGAATTATTTTA
Found at i:5588082 original size:24 final size:24
Alignment explanation
Indices: 5588037--5588082 Score: 65
Period size: 24 Copynumber: 1.9 Consensus size: 24
5588027 CAAAAGCATA
* **
5588037 TTTTTGGACTTTTTTATTTGTTTT
1 TTTTTAGACTTTTTTACCTGTTTT
5588061 TTTTTAGACTTTTTTACCTGTT
1 TTTTTAGACTTTTTTACCTGTT
5588083 CTTTAAGGAT
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
24 19 1.00
ACGTcount: A:0.11, C:0.09, G:0.11, T:0.70
Consensus pattern (24 bp):
TTTTTAGACTTTTTTACCTGTTTT
Found at i:5590995 original size:21 final size:20
Alignment explanation
Indices: 5590963--5591004 Score: 57
Period size: 21 Copynumber: 2.0 Consensus size: 20
5590953 AAGAATGGAA
* *
5590963 AAAATAAAAAATATTTTTAT
1 AAAACAAAAAATATATTTAT
5590983 AAAACAAATAAATATATTTAT
1 AAAACAAA-AAATATATTTAT
5591004 A
1 A
5591005 TAATTTATTT
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
20 7 0.37
21 12 0.63
ACGTcount: A:0.62, C:0.02, G:0.00, T:0.36
Consensus pattern (20 bp):
AAAACAAAAAATATATTTAT
Found at i:5592148 original size:20 final size:21
Alignment explanation
Indices: 5592111--5592150 Score: 55
Period size: 20 Copynumber: 2.0 Consensus size: 21
5592101 ATCATAAAAA
*
5592111 TTTAATTAATTTTAAAATTAT
1 TTTAATTAATTATAAAATTAT
*
5592132 TTTAATT-ATTATCAAATTA
1 TTTAATTAATTATAAAATTA
5592151 AATTACATTA
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
20 10 0.59
21 7 0.41
ACGTcount: A:0.42, C:0.03, G:0.00, T:0.55
Consensus pattern (21 bp):
TTTAATTAATTATAAAATTAT
Found at i:5592908 original size:30 final size:30
Alignment explanation
Indices: 5592867--5592929 Score: 83
Period size: 30 Copynumber: 2.1 Consensus size: 30
5592857 TATCACTTAC
* **
5592867 TAAATTTTTTAATTATTTATAATTAATTT-T
1 TAAAATTTTTAAAAATTTAT-ATTAATTTAT
5592897 TAAAATTTTTAAAAATTTATATTAATTTAT
1 TAAAATTTTTAAAAATTTATATTAATTTAT
5592927 TAA
1 TAA
5592930 TAAAATATTA
Statistics
Matches: 29, Mismatches: 3, Indels: 2
0.85 0.09 0.06
Matches are distributed among these distances:
29 8 0.28
30 21 0.72
ACGTcount: A:0.43, C:0.00, G:0.00, T:0.57
Consensus pattern (30 bp):
TAAAATTTTTAAAAATTTATATTAATTTAT
Found at i:5592934 original size:23 final size:23
Alignment explanation
Indices: 5592901--5592952 Score: 58
Period size: 23 Copynumber: 2.3 Consensus size: 23
5592891 AATTTTTAAA
5592901 ATTTTT-A-AAAAT-TTATATTA-
1 ATTTTTAATAAAATATTAT-TTAT
5592921 ATTTATTAATAAAATATTATTTAT
1 ATTT-TTAATAAAATATTATTTAT
5592945 ATTTTTAA
1 ATTTTTAA
5592953 AAATTCACTT
Statistics
Matches: 27, Mismatches: 0, Indels: 7
0.79 0.00 0.21
Matches are distributed among these distances:
20 4 0.15
21 2 0.07
22 1 0.04
23 12 0.44
24 8 0.30
ACGTcount: A:0.44, C:0.00, G:0.00, T:0.56
Consensus pattern (23 bp):
ATTTTTAATAAAATATTATTTAT
Found at i:5609070 original size:52 final size:52
Alignment explanation
Indices: 5609009--5609107 Score: 162
Period size: 52 Copynumber: 1.9 Consensus size: 52
5608999 TAACTGCTCA
* *
5609009 TGTTCGCCACCATGGCATTCTCATTATCAGTGACACCAAGTCACCCTAACCT
1 TGTTCGCCACCATGCCATCCTCATTATCAGTGACACCAAGTCACCCTAACCT
**
5609061 TGTTCGCCACCATGCCATCCTCATTATCAGTGATGCCAAGTCACCCT
1 TGTTCGCCACCATGCCATCCTCATTATCAGTGACACCAAGTCACCCT
5609108 TATTAGCTTT
Statistics
Matches: 43, Mismatches: 4, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
52 43 1.00
ACGTcount: A:0.23, C:0.35, G:0.14, T:0.27
Consensus pattern (52 bp):
TGTTCGCCACCATGCCATCCTCATTATCAGTGACACCAAGTCACCCTAACCT
Found at i:5612694 original size:21 final size:21
Alignment explanation
Indices: 5612656--5612696 Score: 55
Period size: 21 Copynumber: 2.0 Consensus size: 21
5612646 TCCTGATCGT
* * *
5612656 CAATAACTTTTCTGACTGCCC
1 CAATAACCTCTCTAACTGCCC
5612677 CAATAACCTCTCTAACTGCC
1 CAATAACCTCTCTAACTGCC
5612697 AGAAGACTGG
Statistics
Matches: 17, Mismatches: 3, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
21 17 1.00
ACGTcount: A:0.27, C:0.37, G:0.07, T:0.29
Consensus pattern (21 bp):
CAATAACCTCTCTAACTGCCC
Found at i:5614264 original size:71 final size:71
Alignment explanation
Indices: 5614155--5614313 Score: 187
Period size: 71 Copynumber: 2.2 Consensus size: 71
5614145 ATTGTATCCT
* * * * * *
5614155 TTTCAATTTTTATAAGATTCGTTGTCCATGAATGTTCATTAATCACATCTAGTGGTAATAT-AAT
1 TTTCCATTTTTATAAGTTTAGTTGTACATGAATATTCATTAACCACAT-TAGTGGTAATATAAAT
*
5614219 TTCACTTC
65 TGCA-TTC
* * *
5614227 TTTCCA-TTTTATAAGTTTAGTTGTACGTGAATATTCATTAACCATATTGGTGGTAATATAAATT
1 TTTCCATTTTTATAAGTTTAGTTGTACATGAATATTCATTAACCACATTAGTGGTAATATAAATT
*
5614291 GGATTC
66 GCATTC
5614297 TTTCCATTTTTATAAGT
1 TTTCCATTTTTATAAGT
5614314 ATCATTCTAC
Statistics
Matches: 74, Mismatches: 11, Indels: 5
0.82 0.12 0.06
Matches are distributed among these distances:
70 20 0.27
71 49 0.66
72 5 0.07
ACGTcount: A:0.29, C:0.13, G:0.13, T:0.46
Consensus pattern (71 bp):
TTTCCATTTTTATAAGTTTAGTTGTACATGAATATTCATTAACCACATTAGTGGTAATATAAATT
GCATTC
Found at i:5614344 original size:2 final size:2
Alignment explanation
Indices: 5614337--5614371 Score: 63
Period size: 2 Copynumber: 18.0 Consensus size: 2
5614327 TGTTAAACTA
5614337 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT -T AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
5614372 CACATACTAA
Statistics
Matches: 32, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
1 1 0.03
2 31 0.97
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
AT
Found at i:5614999 original size:14 final size:14
Alignment explanation
Indices: 5614937--5615000 Score: 51
Period size: 15 Copynumber: 4.6 Consensus size: 14
5614927 ATGAATATGA
5614937 AATAAC-AT-AAAT
1 AATAACTATAAAAT
* * *
5614949 ACTAAATAAAAAAT
1 AATAACTATAAAAT
*
5614963 AATAAAATATAAACAT
1 AAT-AACTATAAA-AT
*
5614979 AAGAACTATAAAAT
1 AATAACTATAAAAT
5614993 AATAACTA
1 AATAACTA
5615001 GTAACTTATA
Statistics
Matches: 40, Mismatches: 8, Indels: 6
0.74 0.15 0.11
Matches are distributed among these distances:
12 4 0.10
13 1 0.03
14 15 0.38
15 16 0.40
16 4 0.10
ACGTcount: A:0.67, C:0.08, G:0.02, T:0.23
Consensus pattern (14 bp):
AATAACTATAAAAT
Found at i:5615552 original size:16 final size:15
Alignment explanation
Indices: 5615494--5615563 Score: 52
Period size: 16 Copynumber: 4.5 Consensus size: 15
5615484 CAAATATACA
*
5615494 AATATCATAAAATTT
1 AATATAATAAAATTT
*
5615509 -ATAAAATACAAATTATT
1 AATATAATA-AAA-T-TT
*
5615526 AATATATTAAAATTT
1 AATATAATAAAATTT
**
5615541 AATTATAATAAAAAAT
1 AA-TATAATAAAATTT
5615557 AATATAA
1 AATATAA
5615564 ATACAAAATA
Statistics
Matches: 43, Mismatches: 7, Indels: 10
0.72 0.12 0.17
Matches are distributed among these distances:
14 6 0.14
15 12 0.28
16 14 0.33
17 5 0.12
18 6 0.14
ACGTcount: A:0.60, C:0.03, G:0.00, T:0.37
Consensus pattern (15 bp):
AATATAATAAAATTT
Found at i:5615877 original size:25 final size:24
Alignment explanation
Indices: 5615822--5615877 Score: 58
Period size: 25 Copynumber: 2.2 Consensus size: 24
5615812 TAAATATAAT
5615822 TATAATATAAAAATATAATTTAAAA
1 TATAA-ATAAAAATATAATTTAAAA
* * * *
5615847 TTTAAATTAAAATATTATTATAAAC
1 TATAAATAAAAATATAATT-TAAAA
5615872 TATAAA
1 TATAAA
5615878 AATTATCTCA
Statistics
Matches: 25, Mismatches: 5, Indels: 2
0.78 0.16 0.06
Matches are distributed among these distances:
24 12 0.48
25 13 0.52
ACGTcount: A:0.59, C:0.02, G:0.00, T:0.39
Consensus pattern (24 bp):
TATAAATAAAAATATAATTTAAAA
Found at i:5616090 original size:13 final size:13
Alignment explanation
Indices: 5616045--5616094 Score: 59
Period size: 13 Copynumber: 3.8 Consensus size: 13
5616035 CAACATAAAC
5616045 ATAATATTAAAAA-
1 ATAATA-TAAAAAT
5616058 ATAATA-AAAATAT
1 ATAATATAAAA-AT
5616071 GATAATATAAAAAT
1 -ATAATATAAAAAT
5616085 ATAATATAAA
1 ATAATATAAA
5616095 CAAGACACAA
Statistics
Matches: 33, Mismatches: 0, Indels: 8
0.80 0.00 0.20
Matches are distributed among these distances:
11 4 0.12
12 1 0.03
13 16 0.48
14 8 0.24
15 4 0.12
ACGTcount: A:0.68, C:0.00, G:0.02, T:0.30
Consensus pattern (13 bp):
ATAATATAAAAAT
Found at i:5618360 original size:2 final size:2
Alignment explanation
Indices: 5618353--5618382 Score: 60
Period size: 2 Copynumber: 15.0 Consensus size: 2
5618343 TTCTTCTGTA
5618353 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
5618383 GTATGTATAA
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 28 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:5618990 original size:14 final size:14
Alignment explanation
Indices: 5618967--5619013 Score: 58
Period size: 14 Copynumber: 3.4 Consensus size: 14
5618957 TCAAATAGAA
5618967 ATATAAATATAAAT
1 ATATAAATATAAAT
* *
5618981 ATATATATATATAT
1 ATATAAATATAAAT
**
5618995 ATATAGCTATAAAT
1 ATATAAATATAAAT
5619009 ATATA
1 ATATA
5619014 GCGATATAGC
Statistics
Matches: 28, Mismatches: 5, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
14 28 1.00
ACGTcount: A:0.55, C:0.02, G:0.02, T:0.40
Consensus pattern (14 bp):
ATATAAATATAAAT
Found at i:5626956 original size:18 final size:20
Alignment explanation
Indices: 5626933--5626975 Score: 72
Period size: 20 Copynumber: 2.2 Consensus size: 20
5626923 GTATTACAAG
5626933 TAAATTTTTA-T-TATTTTA
1 TAAATTTTTATTATATTTTA
5626951 TAAATTTTTATTATATTTTA
1 TAAATTTTTATTATATTTTA
5626971 TAAAT
1 TAAAT
5626976 AAATAAAATT
Statistics
Matches: 23, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
18 10 0.43
19 1 0.04
20 12 0.52
ACGTcount: A:0.37, C:0.00, G:0.00, T:0.63
Consensus pattern (20 bp):
TAAATTTTTATTATATTTTA
Found at i:5628291 original size:11 final size:11
Alignment explanation
Indices: 5628275--5628301 Score: 54
Period size: 11 Copynumber: 2.5 Consensus size: 11
5628265 AATACATATT
5628275 TAAAAATAAAA
1 TAAAAATAAAA
5628286 TAAAAATAAAA
1 TAAAAATAAAA
5628297 TAAAA
1 TAAAA
5628302 GCTTATTTTT
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 16 1.00
ACGTcount: A:0.81, C:0.00, G:0.00, T:0.19
Consensus pattern (11 bp):
TAAAAATAAAA
Found at i:5628371 original size:205 final size:204
Alignment explanation
Indices: 5628019--5628428 Score: 741
Period size: 205 Copynumber: 2.0 Consensus size: 204
5628009 GATACAGATT
*
5628019 TGAAATTAATTTATAAGTTAATATGTGAATTAATTACTTTAAATACATATTTAAAAATAAAACAA
1 TGAAATTAATTTATAAGTTAATATATGAATTAATTACTTTAAATACATATTTAAAAATAAAACAA
*
5628084 AAATAAAATAAAAACTTATTTTTCTCAACTGAGTTAAGAACAAATACTAAATCAACTCAAATATA
66 AAATAAAATAAAAACTTATTTTTCTCAACTAAGTTAAGAACAAATACTAAATCAACTCAAATATA
*
5628149 CAAATTAATTTTTTTAAATAAATCATTTGAAAATAAAATTTTTTTCTAAGCA-GATTAGATATAT
131 CAAATTAATTTTTTTAAATAAATCATTTGAAAATAAAATTTTTTTCTAAGCAGGA-TACATATAT
5628213 CTTAACTCAAC
195 -TTAACTCAAC
*
5628224 TGAAATTAATTTATAAGTTAATATATGAATTAATTACTTTAAATACATATTTAAAAATAAAATAA
1 TGAAATTAATTTATAAGTTAATATATGAATTAATTACTTTAAATACATATTTAAAAATAAAACAA
*
5628289 AAATAAAATAAAAGCTTATTTTTCTCAACTAAGTTAAGAACAAATACTAAATCAACTCAAATATA
66 AAATAAAATAAAAACTTATTTTTCTCAACTAAGTTAAGAACAAATACTAAATCAACTCAAATATA
*
5628354 CAAATTAATTTTTTTAAATAAATCATTTGAAAATAAAATTTTTTTCTAAGCAGGATACATATCTT
131 CAAATTAATTTTTTTAAATAAATCATTTGAAAATAAAATTTTTTTCTAAGCAGGATACATATATT
5628419 TAACTCAAC
196 TAACTCAAC
5628428 T
1 T
5628429 TGCAAGTGAA
Statistics
Matches: 198, Mismatches: 6, Indels: 3
0.96 0.03 0.01
Matches are distributed among these distances:
204 11 0.06
205 185 0.93
206 2 0.01
ACGTcount: A:0.48, C:0.10, G:0.05, T:0.37
Consensus pattern (204 bp):
TGAAATTAATTTATAAGTTAATATATGAATTAATTACTTTAAATACATATTTAAAAATAAAACAA
AAATAAAATAAAAACTTATTTTTCTCAACTAAGTTAAGAACAAATACTAAATCAACTCAAATATA
CAAATTAATTTTTTTAAATAAATCATTTGAAAATAAAATTTTTTTCTAAGCAGGATACATATATT
TAACTCAAC
Found at i:5628917 original size:2 final size:2
Alignment explanation
Indices: 5628910--5628944 Score: 70
Period size: 2 Copynumber: 17.5 Consensus size: 2
5628900 TTCTATGTAT
5628910 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
5628945 GTTATGGATC
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 33 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:5629671 original size:11 final size:11
Alignment explanation
Indices: 5629657--5629732 Score: 51
Period size: 11 Copynumber: 7.5 Consensus size: 11
5629647 TAAAATATTT
*
5629657 TCAAAACTATA
1 TCAAAAGTATA
*
5629668 TCAAAGGT-T-
1 TCAAAAGTATA
5629677 T-AAAA-TATA
1 TCAAAAGTATA
5629686 TC-AAAGT-TA
1 TCAAAAGTATA
5629695 TCAAAA-TCATA
1 TCAAAAGT-ATA
5629706 TCAAAAGT-TA
1 TCAAAAGTATA
* *
5629716 TCAAAATTATT
1 TCAAAAGTATA
5629727 TCAAAA
1 TCAAAA
5629733 ATTCCTAACA
Statistics
Matches: 51, Mismatches: 5, Indels: 18
0.69 0.07 0.24
Matches are distributed among these distances:
7 1 0.02
8 4 0.08
9 10 0.20
10 14 0.27
11 21 0.41
12 1 0.02
ACGTcount: A:0.51, C:0.12, G:0.05, T:0.32
Consensus pattern (11 bp):
TCAAAAGTATA
Found at i:5629687 original size:18 final size:19
Alignment explanation
Indices: 5629657--5629722 Score: 82
Period size: 21 Copynumber: 3.4 Consensus size: 19
5629647 TAAAATATTT
5629657 TCAAAACTATATCAAAGGTT-
1 TCAAAA-TATATCAAA-GTTA
5629677 T-AAAATATATCAAAGTTA
1 TCAAAATATATCAAAGTTA
5629695 TCAAAATCATATCAAAAGTTA
1 TCAAAAT-ATATC-AAAGTTA
5629716 TCAAAAT
1 TCAAAAT
5629723 TATTTCAAAA
Statistics
Matches: 42, Mismatches: 0, Indels: 7
0.86 0.00 0.14
Matches are distributed among these distances:
17 3 0.07
18 10 0.24
19 9 0.21
20 6 0.14
21 14 0.33
ACGTcount: A:0.52, C:0.12, G:0.06, T:0.30
Consensus pattern (19 bp):
TCAAAATATATCAAAGTTA
Found at i:5629698 original size:9 final size:9
Alignment explanation
Indices: 5629678--5629725 Score: 51
Period size: 9 Copynumber: 4.9 Consensus size: 9
5629668 TCAAAGGTTT
5629678 AAAATATATC
1 AAAAT-TATC
*
5629688 AAAGTTATC
1 AAAATTATC
5629697 AAAATCATATC
1 AAAAT--TATC
5629708 AAAAGTTATC
1 AAAA-TTATC
5629718 AAAATTAT
1 AAAATTAT
5629726 TTCAAAAATT
Statistics
Matches: 33, Mismatches: 2, Indels: 7
0.79 0.05 0.17
Matches are distributed among these distances:
9 12 0.36
10 12 0.36
11 8 0.24
12 1 0.03
ACGTcount: A:0.54, C:0.10, G:0.04, T:0.31
Consensus pattern (9 bp):
AAAATTATC
Found at i:5629714 original size:21 final size:21
Alignment explanation
Indices: 5629657--5629732 Score: 81
Period size: 21 Copynumber: 3.8 Consensus size: 21
5629647 TAAAATATTT
*
5629657 TCAAAA-CTATATCAAAGGTT-
1 TCAAAATC-ATATCAAAAGTTA
5629677 T-AAAAT-ATATC-AAAGTTA
1 TCAAAATCATATCAAAAGTTA
5629695 TCAAAATCATATCAAAAGTTA
1 TCAAAATCATATCAAAAGTTA
* *
5629716 TCAAAATTATTTCAAAA
1 TCAAAATCATATCAAAA
5629733 ATTCCTAACA
Statistics
Matches: 48, Mismatches: 3, Indels: 9
0.80 0.05 0.15
Matches are distributed among these distances:
17 5 0.10
18 6 0.12
19 9 0.19
20 6 0.12
21 22 0.46
ACGTcount: A:0.51, C:0.12, G:0.05, T:0.32
Consensus pattern (21 bp):
TCAAAATCATATCAAAAGTTA
Found at i:5629761 original size:21 final size:21
Alignment explanation
Indices: 5629665--5629763 Score: 75
Period size: 21 Copynumber: 4.9 Consensus size: 21
5629655 TTTCAAAACT
*
5629665 ATATCAAAGGTT--TAAAAT-
1 ATATCAAAAGTTACTAAAATA
*
5629683 ATATC-AAAGTTA-TCAAAATC
1 ATATCAAAAGTTACT-AAAATA
*
5629703 ATATCAAAAGTTA-TCAAAATT
1 ATATCAAAAGTTACT-AAAATA
* * * *
5629724 ATTTCAAAAATTCCTAACATA
1 ATATCAAAAGTTACTAAAATA
5629745 ATATCAAAAGTTACTAAAA
1 ATATCAAAAGTTACTAAAA
5629764 GGATACCCAA
Statistics
Matches: 65, Mismatches: 11, Indels: 7
0.78 0.13 0.08
Matches are distributed among these distances:
17 5 0.08
18 6 0.09
19 5 0.08
20 5 0.08
21 43 0.66
22 1 0.02
ACGTcount: A:0.52, C:0.12, G:0.05, T:0.31
Consensus pattern (21 bp):
ATATCAAAAGTTACTAAAATA
Found at i:5629877 original size:11 final size:11
Alignment explanation
Indices: 5629861--5629919 Score: 54
Period size: 11 Copynumber: 5.6 Consensus size: 11
5629851 TTATGAATGT
5629861 TATCAAAATTA
1 TATCAAAATTA
5629872 TATC-AAA-TA
1 TATCAAAATTA
*
5629881 TTATCAAATTTA
1 -TATCAAAATTA
*
5629893 TATC-AAAGT-
1 TATCAAAATTA
*
5629902 TATCACAATTA
1 TATCAAAATTA
5629913 TATCAAA
1 TATCAAA
5629920 GGTTACTCAA
Statistics
Matches: 37, Mismatches: 6, Indels: 10
0.70 0.11 0.19
Matches are distributed among these distances:
9 6 0.16
10 13 0.35
11 16 0.43
12 2 0.05
ACGTcount: A:0.49, C:0.12, G:0.02, T:0.37
Consensus pattern (11 bp):
TATCAAAATTA
Found at i:5629884 original size:21 final size:21
Alignment explanation
Indices: 5629860--5630038 Score: 156
Period size: 21 Copynumber: 8.6 Consensus size: 21
5629850 TTTATGAATG
*
5629860 TTATCAAAATTATATCAAATA
1 TTATCAAAATTATATCAAAGA
*
5629881 TTATCAAATTTATATCAAAG-
1 TTATCAAAATTATATCAAAGA
* *
5629901 TTATCACAATTATATCAAAGG
1 TTATCAAAATTATATCAAAGA
* *
5629922 TTACTCAAAATCATATAAAATG-
1 TTA-TCAAAATTATATCAAA-GA
* * *
5629944 TTA-CTGAAATTATATAAAAAA
1 TTATC-AAAATTATATCAAAGA
*
5629965 TTA-CAAAAATTAT-T-TAAGA
1 TTATC-AAAATTATATCAAAGA
*
5629984 TTATCTAAATTAT-TACAAAGA
1 TTATCAAAATTATAT-CAAAGA
*
5630005 TTATCAAAATTATATTAAAGA
1 TTATCAAAATTATATCAAAGA
5630026 TTATCAAAATTAT
1 TTATCAAAATTAT
5630039 TTTTAATTAT
Statistics
Matches: 131, Mismatches: 18, Indels: 18
0.78 0.11 0.11
Matches are distributed among these distances:
19 14 0.11
20 21 0.16
21 78 0.60
22 17 0.13
23 1 0.01
ACGTcount: A:0.50, C:0.09, G:0.04, T:0.37
Consensus pattern (21 bp):
TTATCAAAATTATATCAAAGA
Found at i:5629987 original size:31 final size:31
Alignment explanation
Indices: 5629950--5630055 Score: 90
Period size: 31 Copynumber: 3.5 Consensus size: 31
5629940 AATGTTACTG
5629950 AAATTATATAAAAAATTACAAAAATTATTTA
1 AAATTATATAAAAAATTACAAAAATTATTTA
* * ** * *
5629981 AGATTATCTAAATTATTACAAAGATTA-TCA
1 AAATTATATAAAAAATTACAAAAATTATTTA
* * *
5630011 AAATTATATTAAAGATTATC-AAAATTATTTT
1 AAATTATATAAAAAATTA-CAAAAATTATTTA
* *
5630042 TAATTATATTAAAA
1 AAATTATATAAAAA
5630056 CTATTTTATC
Statistics
Matches: 57, Mismatches: 16, Indels: 4
0.74 0.21 0.05
Matches are distributed among these distances:
30 21 0.37
31 36 0.63
ACGTcount: A:0.53, C:0.05, G:0.03, T:0.40
Consensus pattern (31 bp):
AAATTATATAAAAAATTACAAAAATTATTTA
Found at i:5630315 original size:20 final size:20
Alignment explanation
Indices: 5630261--5630318 Score: 57
Period size: 20 Copynumber: 3.0 Consensus size: 20
5630251 TAAAACTATT
* *
5630261 ATAAAA-AATTATCAAAATT
1 ATAAAAGAATTATTAAAATC
* *
5630280 ATATAAAG-GTTGTTAAAATC
1 ATA-AAAGAATTATTAAAATC
5630300 ATAAAAGAATTATTAAAAT
1 ATAAAAGAATTATTAAAAT
5630319 TATATTAAAT
Statistics
Matches: 30, Mismatches: 6, Indels: 5
0.73 0.15 0.12
Matches are distributed among these distances:
19 7 0.23
20 23 0.77
ACGTcount: A:0.57, C:0.03, G:0.07, T:0.33
Consensus pattern (20 bp):
ATAAAAGAATTATTAAAATC
Found at i:5630321 original size:9 final size:10
Alignment explanation
Indices: 5630258--5630338 Score: 51
Period size: 10 Copynumber: 8.1 Consensus size: 10
5630248 TACTAAAACT
*
5630258 ATTATAAAAA
1 ATTATATAAA
*
5630268 ATTAT-CAAA
1 ATTATATAAA
5630277 ATTATATAAA
1 ATTATATAAA
* *
5630287 GGTTGT-TAAA
1 -ATTATATAAA
* *
5630297 ATCATAAAAGA
1 ATTATATAA-A
5630308 ATTAT-TAAA
1 ATTATATAAA
*
5630317 ATTATATTAA
1 ATTATATAAA
5630327 ATTATATCAAA
1 ATTATAT-AAA
5630338 A
1 A
5630339 GTTACCAAAA
Statistics
Matches: 53, Mismatches: 12, Indels: 11
0.70 0.16 0.14
Matches are distributed among these distances:
9 16 0.30
10 26 0.49
11 11 0.21
ACGTcount: A:0.56, C:0.04, G:0.05, T:0.36
Consensus pattern (10 bp):
ATTATATAAA
Found at i:5630349 original size:21 final size:21
Alignment explanation
Indices: 5630325--5630370 Score: 74
Period size: 21 Copynumber: 2.2 Consensus size: 21
5630315 AAATTATATT
5630325 AAATTATATCAAAAGTTACCA
1 AAATTATATCAAAAGTTACCA
* *
5630346 AAATTATATCTAAAGTTATCA
1 AAATTATATCAAAAGTTACCA
5630367 AAAT
1 AAAT
5630371 CAAAATTATA
Statistics
Matches: 23, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
21 23 1.00
ACGTcount: A:0.52, C:0.11, G:0.04, T:0.33
Consensus pattern (21 bp):
AAATTATATCAAAAGTTACCA
Found at i:5630374 original size:27 final size:27
Alignment explanation
Indices: 5630344--5630397 Score: 81
Period size: 27 Copynumber: 2.0 Consensus size: 27
5630334 CAAAAGTTAC
* * *
5630344 CAAAATTATATCTAAAGTTATCAAAAT
1 CAAAATTATACCAAAAGTTAACAAAAT
5630371 CAAAATTATACCAAAAGTTAACAAAAT
1 CAAAATTATACCAAAAGTTAACAAAAT
5630398 TATATAAAAA
Statistics
Matches: 24, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
27 24 1.00
ACGTcount: A:0.56, C:0.13, G:0.04, T:0.28
Consensus pattern (27 bp):
CAAAATTATACCAAAAGTTAACAAAAT
Found at i:5630386 original size:48 final size:48
Alignment explanation
Indices: 5630325--5630418 Score: 143
Period size: 48 Copynumber: 2.0 Consensus size: 48
5630315 AAATTATATT
* * **
5630325 AAATTATATCAAAAGTTACCAAAATTATATCTAAAGTTATCAAAATCA
1 AAATTATACCAAAAGTTAACAAAATTATATAAAAAGTTATCAAAATCA
*
5630373 AAATTATACCAAAAGTTAACAAAATTATATAAAAAGTTATTAAAAT
1 AAATTATACCAAAAGTTAACAAAATTATATAAAAAGTTATCAAAAT
5630419 TCTATTAAAT
Statistics
Matches: 41, Mismatches: 5, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
48 41 1.00
ACGTcount: A:0.55, C:0.10, G:0.04, T:0.31
Consensus pattern (48 bp):
AAATTATACCAAAAGTTAACAAAATTATATAAAAAGTTATCAAAATCA
Done.