Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold10
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: 3842500
ACGTcount: A:0.32, C:0.14, G:0.14, T:0.31
Warning! 348197 characters in sequence are not A, C, G, or T
File 18 of 25
Found at i:2869889 original size:15 final size:15
Alignment explanation
Indices: 2869859--2869896 Score: 51
Period size: 15 Copynumber: 2.5 Consensus size: 15
2869849 AAATAGATAA
2869859 TTTATATTTATATTT
1 TTTATATTTATATTT
2869874 TTTATTATTTAT-TTT
1 TTTA-TATTTATATTT
2869889 TTATATAT
1 TT-TATAT
2869897 AGATAATTTA
Statistics
Matches: 21, Mismatches: 0, Indels: 4
0.84 0.00 0.16
Matches are distributed among these distances:
15 12 0.57
16 9 0.43
ACGTcount: A:0.26, C:0.00, G:0.00, T:0.74
Consensus pattern (15 bp):
TTTATATTTATATTT
Found at i:2870076 original size:15 final size:16
Alignment explanation
Indices: 2870056--2870093 Score: 51
Period size: 16 Copynumber: 2.4 Consensus size: 16
2870046 AAATAATATT
2870056 TAAAATT-TAATGAAA
1 TAAAATTCTAATGAAA
* *
2870071 TAAAATTCTAATTAAT
1 TAAAATTCTAATGAAA
2870087 TAAAATT
1 TAAAATT
2870094 AATAAGAACC
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
15 7 0.35
16 13 0.65
ACGTcount: A:0.55, C:0.03, G:0.03, T:0.39
Consensus pattern (16 bp):
TAAAATTCTAATGAAA
Found at i:2870926 original size:15 final size:16
Alignment explanation
Indices: 2870896--2870928 Score: 50
Period size: 15 Copynumber: 2.1 Consensus size: 16
2870886 AAATTAATAA
2870896 AAATAAATATAAAATT
1 AAATAAATATAAAATT
*
2870912 AAATAATTA-AAAATT
1 AAATAAATATAAAATT
2870927 AA
1 AA
2870929 CAAAAGTATA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
15 8 0.50
16 8 0.50
ACGTcount: A:0.70, C:0.00, G:0.00, T:0.30
Consensus pattern (16 bp):
AAATAAATATAAAATT
Found at i:2871381 original size:237 final size:234
Alignment explanation
Indices: 2870973--2871600 Score: 951
Period size: 237 Copynumber: 2.7 Consensus size: 234
2870963 TCACCGAATC
2870973 TACTATGACAACGAAAATAGAAGAACTACCAACAAAATGGTAGGAACCACTAATATCTTCCAAAC
1 TACTATGACAACGAAAATAGAAGAACTACCAACAAAATGGTAGGAACCACTAATATCTTCCAAAC
* *
2871038 GTCCACAAGTAGAAAAAAA-TCCAAAAAGACAAGAATAGATAAAAACAAATAAGAAAAATTAATA
66 GTCCACAAGTAAAAAAAAAGTCCAAAAAGATAAGAATAGATAAAAACAAATAAGAAAAATTAATA
*
2871102 ATATCAAAGTG-TAACTTATCAACATTAAGAGAAAAGCAAGTCCATTAAATAAAAACACCCACTC
131 ATATCAAAGTGCT-ACTTATCAACATTAAGAGAAAAGCAAGTCCATTAAATAAAAACACACACTC
* *
2871166 TTAAAAAAT-CT-AA-GAATAAAAGTCATTTATTAATAAT
195 TTAAAAAATAATAAATAAATAAAAGTCATTTATTAATAAT
* * *
2871203 TACTATGACAACGAAAATAGAAGAACTACTAACAAAATGATAGGAACCACTAATATCTTTCAAAC
1 TACTATGACAACGAAAATAGAAGAACTACCAACAAAATGGTAGGAACCACTAATATCTTCCAAAC
* *
2871268 GTCCGCAAGTAAAAAAAAAAAAAAAGTCCAAAAAGATAAGAATAGATAAAAACAAATAAGAAGAA
66 GTCCACAAGT------AAAAAAAAAGTCCAAAAAGATAAGAATAGATAAAAACAAATAAGAAAAA
* * * *
2871333 TTAATAATATCCAAGTGCTACCTATCAACATTATGAGAAAAGCAAGTCCATTGAATAAAAACACA
125 TTAATAATATCAAAGTGCTACTTATCAACATTAAGAGAAAAGCAAGTCCATTAAATAAAAACACA
* *
2871398 CATTCTTAAAAAATAAATAAATAAATAAAAGTTATTTATTAATAAT
190 CACTCTTAAAAAAT-AATAAATAAATAAAAGTCATTTATTAATAAT
*
2871444 TACTATGACAACGAAAATAGAAGAACTACCAACAAAATGGTAGGAGCCACTAATATCTTCCAAAC
1 TACTATGACAACGAAAATAGAAGAACTACCAACAAAATGGTAGGAACCACTAATATCTTCCAAAC
* * *
2871509 GTCCACAAGTGTAAAAAAAAGTCCAAAAAGATAAGAATAGATAAAAATAAATAAGAAAAATTAAC
66 GTCCACAAGT-AAAAAAAAAGTCCAAAAAGATAAGAATAGATAAAAACAAATAAGAAAAATTAAT
*
2871574 AATATCAAAGTGCAACTTATCAACATT
130 AATATCAAAGTGCTACTTATCAACATT
2871601 GTTGTGACAT
Statistics
Matches: 357, Mismatches: 29, Indels: 18
0.88 0.07 0.04
Matches are distributed among these distances:
230 71 0.20
236 82 0.23
237 108 0.30
238 1 0.00
239 1 0.00
240 2 0.01
241 92 0.26
ACGTcount: A:0.54, C:0.15, G:0.11, T:0.21
Consensus pattern (234 bp):
TACTATGACAACGAAAATAGAAGAACTACCAACAAAATGGTAGGAACCACTAATATCTTCCAAAC
GTCCACAAGTAAAAAAAAAGTCCAAAAAGATAAGAATAGATAAAAACAAATAAGAAAAATTAATA
ATATCAAAGTGCTACTTATCAACATTAAGAGAAAAGCAAGTCCATTAAATAAAAACACACACTCT
TAAAAAATAATAAATAAATAAAAGTCATTTATTAATAAT
Found at i:2872828 original size:7 final size:8
Alignment explanation
Indices: 2872816--2872890 Score: 58
Period size: 8 Copynumber: 10.4 Consensus size: 8
2872806 ACCTTCATAC
2872816 ATAAAT-T
1 ATAAATAT
2872823 ATAAATAT
1 ATAAATAT
2872831 ATAAATAT
1 ATAAATAT
*
2872839 -TATATAT
1 ATAAATAT
2872846 AT-AAT-T
1 ATAAATAT
2872852 ATAAA-A-
1 ATAAATAT
*
2872858 A-AATTAT
1 ATAAATAT
2872865 ATAAATAT
1 ATAAATAT
*
2872873 -TATATAT
1 ATAAATAT
*
2872880 ATATATAT
1 ATAAATAT
2872888 ATA
1 ATA
2872891 CACTCAAATT
Statistics
Matches: 55, Mismatches: 5, Indels: 15
0.73 0.07 0.20
Matches are distributed among these distances:
5 2 0.04
6 5 0.09
7 23 0.42
8 25 0.45
ACGTcount: A:0.57, C:0.00, G:0.00, T:0.43
Consensus pattern (8 bp):
ATAAATAT
Found at i:2872836 original size:15 final size:15
Alignment explanation
Indices: 2872816--2872856 Score: 50
Period size: 15 Copynumber: 2.8 Consensus size: 15
2872806 ACCTTCATAC
2872816 ATAAATTATAAATAT
1 ATAAATTATAAATAT
*
2872831 ATAAA-TAT-TATAT
1 ATAAATTATAAATAT
2872844 ATATAATTATAAA
1 ATA-AATTATAAA
2872857 AAAATTATAT
Statistics
Matches: 21, Mismatches: 2, Indels: 5
0.75 0.07 0.18
Matches are distributed among these distances:
13 7 0.33
14 5 0.24
15 8 0.38
16 1 0.05
ACGTcount: A:0.59, C:0.00, G:0.00, T:0.41
Consensus pattern (15 bp):
ATAAATTATAAATAT
Found at i:2873294 original size:22 final size:21
Alignment explanation
Indices: 2873269--2873341 Score: 67
Period size: 22 Copynumber: 3.2 Consensus size: 21
2873259 ACACAAATAT
2873269 ATATATAATAAAAATAATTAAA
1 ATATA-AATAAAAATAATTAAA
* *
2873291 ATATAATTTAAAATATAA-TATA
1 ATATAA-ATAAAA-ATAATTAAA
2873313 ATATAAATTAAAAATAATATATAA
1 ATATAAA-TAAAAATAAT-TA-AA
2873337 ATATA
1 ATATA
2873342 TAAATTTATT
Statistics
Matches: 41, Mismatches: 4, Indels: 10
0.75 0.07 0.18
Matches are distributed among these distances:
21 5 0.12
22 24 0.59
23 6 0.15
24 6 0.15
ACGTcount: A:0.64, C:0.00, G:0.00, T:0.36
Consensus pattern (21 bp):
ATATAAATAAAAATAATTAAA
Found at i:2873322 original size:34 final size:32
Alignment explanation
Indices: 2873265--2873345 Score: 94
Period size: 33 Copynumber: 2.5 Consensus size: 32
2873255 TAAGACACAA
*
2873265 ATATATATATAATAAAAATAATTAAAATATAAT
1 ATATAAATATAATAAAAATAATTAAAA-ATAAT
* *
2873298 TTA-AAATATAATATAATATAAATTAAAAATAAT
1 ATATAAATATAATA-AAAAT-AATTAAAAATAAT
2873331 ATATAAATAT-ATAAA
1 ATATAAATATAATAAA
2873346 TTTATTTAAA
Statistics
Matches: 41, Mismatches: 4, Indels: 7
0.79 0.08 0.13
Matches are distributed among these distances:
32 11 0.27
33 16 0.39
34 14 0.34
ACGTcount: A:0.64, C:0.00, G:0.00, T:0.36
Consensus pattern (32 bp):
ATATAAATATAATAAAAATAATTAAAAATAAT
Found at i:2873623 original size:16 final size:16
Alignment explanation
Indices: 2873604--2873658 Score: 60
Period size: 16 Copynumber: 3.4 Consensus size: 16
2873594 TCATAATGAT
2873604 TTTAAATATTTTTAAA
1 TTTAAATATTTTTAAA
*
2873620 TTT-AATATTTTTTATA
1 TTTAAATA-TTTTTAAA
*
2873636 TTTAAAT-TTTTATAAC
1 TTTAAATATTTT-TAAA
2873652 TTTAAAT
1 TTTAAAT
2873659 TCTCTACTCT
Statistics
Matches: 33, Mismatches: 3, Indels: 6
0.79 0.07 0.14
Matches are distributed among these distances:
15 8 0.24
16 22 0.67
17 3 0.09
ACGTcount: A:0.38, C:0.02, G:0.00, T:0.60
Consensus pattern (16 bp):
TTTAAATATTTTTAAA
Found at i:2874005 original size:17 final size:16
Alignment explanation
Indices: 2873987--2874023 Score: 60
Period size: 15 Copynumber: 2.4 Consensus size: 16
2873977 AATATTTAAT
2873987 TTATTTTTTTAAATAA
1 TTATTTTTTTAAATAA
2874003 TT-TTTTTTTAAA-AA
1 TTATTTTTTTAAATAA
2874017 TTATTTT
1 TTATTTT
2874024 GAAAGAATAA
Statistics
Matches: 20, Mismatches: 0, Indels: 3
0.87 0.00 0.13
Matches are distributed among these distances:
14 4 0.20
15 14 0.70
16 2 0.10
ACGTcount: A:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (16 bp):
TTATTTTTTTAAATAA
Found at i:2874095 original size:16 final size:16
Alignment explanation
Indices: 2874076--2874113 Score: 58
Period size: 16 Copynumber: 2.4 Consensus size: 16
2874066 TAAAAGGAAA
2874076 GAATTTAAATCTTGAT
1 GAATTTAAATCTTGAT
*
2874092 GAATTCAAATCTTGAT
1 GAATTTAAATCTTGAT
*
2874108 AAATTT
1 GAATTT
2874114 TAAAGAGCGA
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
16 19 1.00
ACGTcount: A:0.39, C:0.08, G:0.11, T:0.42
Consensus pattern (16 bp):
GAATTTAAATCTTGAT
Found at i:2875166 original size:27 final size:28
Alignment explanation
Indices: 2875127--2875193 Score: 82
Period size: 27 Copynumber: 2.4 Consensus size: 28
2875117 CCACCATGTG
* *
2875127 TTTGTCAACAATGGTGGTTAC-TTTGTA
1 TTTGTCAAAAATGGTGATTACTTTTGTA
* * *
2875154 TTTGTCAAAAATGGTGATTCCTTTTTTG
1 TTTGTCAAAAATGGTGATTACTTTTGTA
2875182 TTTGTCAAAAAT
1 TTTGTCAAAAAT
2875194 TATGGCTTGT
Statistics
Matches: 34, Mismatches: 5, Indels: 1
0.85 0.12 0.03
Matches are distributed among these distances:
27 18 0.53
28 16 0.47
ACGTcount: A:0.25, C:0.10, G:0.18, T:0.46
Consensus pattern (28 bp):
TTTGTCAAAAATGGTGATTACTTTTGTA
Found at i:2877462 original size:27 final size:28
Alignment explanation
Indices: 2877423--2877489 Score: 82
Period size: 27 Copynumber: 2.4 Consensus size: 28
2877413 CCACCATGTG
* *
2877423 TTTGTCAACAATGGTGGTTAC-TTTGTA
1 TTTGTCAAAAATGGTGATTACTTTTGTA
* * *
2877450 TTTGTCAAAAATGGTGATTCCTTTTTTG
1 TTTGTCAAAAATGGTGATTACTTTTGTA
2877478 TTTGTCAAAAAT
1 TTTGTCAAAAAT
2877490 TATGGCTTGT
Statistics
Matches: 34, Mismatches: 5, Indels: 1
0.85 0.12 0.03
Matches are distributed among these distances:
27 18 0.53
28 16 0.47
ACGTcount: A:0.25, C:0.10, G:0.18, T:0.46
Consensus pattern (28 bp):
TTTGTCAAAAATGGTGATTACTTTTGTA
Found at i:2879198 original size:52 final size:53
Alignment explanation
Indices: 2879120--2879259 Score: 178
Period size: 52 Copynumber: 2.7 Consensus size: 53
2879110 ATTTACCTGC
* * *
2879120 ATGTATCGATATATTGAAGAATGTATCGATACATTT-GGCTCAAAAACAC-AGA
1 ATGTATCGATATAATGAAAAATGTATCGATACATTTGGGCTCAAAAAC-CTAAA
* * * *
2879172 ATGTATCGATATAATGAAAAATGTATCTATATATTTGGGGTCACAAACCTAAA
1 ATGTATCGATATAATGAAAAATGTATCGATACATTTGGGCTCAAAAACCTAAA
*
2879225 ATGTATCGATACAAT-AAAAATGTATCGATACATTT
1 ATGTATCGATATAATGAAAAATGTATCGATACATTT
2879260 TTATTTCAAA
Statistics
Matches: 76, Mismatches: 10, Indels: 4
0.84 0.11 0.04
Matches are distributed among these distances:
52 51 0.67
53 25 0.33
ACGTcount: A:0.41, C:0.12, G:0.15, T:0.31
Consensus pattern (53 bp):
ATGTATCGATATAATGAAAAATGTATCGATACATTTGGGCTCAAAAACCTAAA
Found at i:2880137 original size:15 final size:15
Alignment explanation
Indices: 2880119--2880147 Score: 58
Period size: 15 Copynumber: 1.9 Consensus size: 15
2880109 ATTAAAATAA
2880119 AATATAAACAAAATT
1 AATATAAACAAAATT
2880134 AATATAAACAAAAT
1 AATATAAACAAAAT
2880148 ATAAATATAT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.69, C:0.07, G:0.00, T:0.24
Consensus pattern (15 bp):
AATATAAACAAAATT
Found at i:2880146 original size:26 final size:24
Alignment explanation
Indices: 2880047--2880152 Score: 87
Period size: 23 Copynumber: 4.4 Consensus size: 24
2880037 AAACTTAATA
2880047 AAAAT-TAACAAAAA-AATTATAAA-
1 AAAATATAA-AAAAATAA-TATAAAT
** * *
2880070 AAAATATAATTACATAACATAAAT
1 AAAATATAAAAAAATAATATAAAT
2880094 AAAATAT-AAAAAATAAT-TAAAAT
1 AAAATATAAAAAAATAATAT-AAAT
*
2880117 AAAATATAAACAAAATTAATATAAAC
1 AAAATATAAA-AAAA-TAATATAAAT
2880143 AAAATATAAA
1 AAAATATAAA
2880153 TATATTAAAA
Statistics
Matches: 66, Mismatches: 9, Indels: 13
0.75 0.10 0.15
Matches are distributed among these distances:
22 1 0.02
23 29 0.44
24 14 0.21
25 4 0.06
26 17 0.26
27 1 0.02
ACGTcount: A:0.71, C:0.05, G:0.00, T:0.25
Consensus pattern (24 bp):
AAAATATAAAAAAATAATATAAAT
Found at i:2880155 original size:6 final size:6
Alignment explanation
Indices: 2880088--2880240 Score: 51
Period size: 6 Copynumber: 26.5 Consensus size: 6
2880078 ATTACATAAC
* * *
2880088 ATAAAT A-AAAT ATAAAAA ATAATT A-AAAT A-AAAT ATAAAC A-AAAT
1 ATAAAT ATAAAT AT-AAAT ATAAAT ATAAAT ATAAAT ATAAAT ATAAAT
* * * *
2880133 -T-AAT ATAAAC A-AAAT ATAAAT AT-ATT A-AAAT TTATATT AATAAAT
1 ATAAAT ATAAAT ATAAAT ATAAAT ATAAAT ATAAAT ATA-AAT -ATAAAT
* * * *
2880178 A-AAATT TTAAAT ATAATT ATAAA- A-AATAT ATAAAT ATTATAT ATATAT
1 ATAAA-T ATAAAT ATAAAT ATAAAT ATAA-AT ATAAAT A-TAAAT ATAAAT
* *
2880226 ATATAT ATATAT ATA
1 ATAAAT ATAAAT ATA
2880241 CACTCAAATT
Statistics
Matches: 111, Mismatches: 19, Indels: 34
0.68 0.12 0.21
Matches are distributed among these distances:
4 5 0.05
5 32 0.29
6 53 0.48
7 19 0.17
8 2 0.02
ACGTcount: A:0.63, C:0.01, G:0.00, T:0.36
Consensus pattern (6 bp):
ATAAAT
Found at i:2880163 original size:31 final size:29
Alignment explanation
Indices: 2880128--2880215 Score: 83
Period size: 31 Copynumber: 3.0 Consensus size: 29
2880118 AAATATAAAC
2880128 AAAATTAATATAAACAAAATATAAATATATT
1 AAAATTAATATAAA-AAAATATAAATAT-TT
* * *
2880159 AAAATTTATATTAATAAATA-AAAT-TTT
1 AAAATTAATATAAAAAAATATAAATATTT
2880186 -AAATATAATTATAAAAAATATATAAATATT
1 AAAAT-TAA-TATAAAAAA-ATATAAATATT
2880216 ATATATATAT
Statistics
Matches: 46, Mismatches: 6, Indels: 10
0.74 0.10 0.16
Matches are distributed among these distances:
26 4 0.09
27 4 0.09
28 8 0.17
29 7 0.15
30 9 0.20
31 14 0.30
ACGTcount: A:0.61, C:0.01, G:0.00, T:0.38
Consensus pattern (29 bp):
AAAATTAATATAAAAAAATATAAATATTT
Found at i:2880169 original size:20 final size:19
Alignment explanation
Indices: 2880146--2880238 Score: 62
Period size: 20 Copynumber: 4.7 Consensus size: 19
2880136 TATAAACAAA
2880146 ATATAAATATATTAAAATTT
1 ATATAAATATA-TAAAATTT
* *
2880166 ATATTAATAAATAAAATTTT
1 ATATAAATATATAAAA-TTT
* **
2880186 AAATATAAT-TATAAAAAAT
1 ATATA-AATATATAAAATTT
* *
2880205 ATATAAATATTATATATATAT
1 ATATAAATA-TATA-AAATTT
*
2880226 ATATATATATATA
1 ATATAAATATATA
2880239 TACACTCAAA
Statistics
Matches: 57, Mismatches: 11, Indels: 10
0.73 0.14 0.13
Matches are distributed among these distances:
18 3 0.05
19 10 0.18
20 29 0.51
21 15 0.26
ACGTcount: A:0.57, C:0.00, G:0.00, T:0.43
Consensus pattern (19 bp):
ATATAAATATATAAAATTT
Found at i:2880188 original size:12 final size:12
Alignment explanation
Indices: 2880059--2880213 Score: 62
Period size: 11 Copynumber: 13.1 Consensus size: 12
2880049 AATTAACAAA
2880059 AAAATTATAAA-
1 AAAATTATAAAT
*
2880070 AAAA-TATAATT
1 AAAATTATAAAT
*
2880081 ACATAA-CATAAAT
1 A-A-AATTATAAAT
*
2880094 AAAA-TATAAAA
1 AAAATTATAAAT
2880105 AATAATTA-AAAT
1 AA-AATTATAAAT
*
2880117 AAAA-TATAAAC
1 AAAATTATAAAT
2880128 AAAATTAATATAA-
1 AAAATT-ATA-AAT
*
2880141 ACAAAATATAAAT
1 A-AAATTATAAAT
*
2880154 -ATATTA-AAATT
1 AAAATTATAAA-T
* *
2880165 TATATTAATAAAT
1 AAAATT-ATAAAT
*
2880178 AAAATTTTAAAT
1 AAAATTATAAAT
*
2880190 ATAATTAT-AA-
1 AAAATTATAAAT
2880200 AAAATATATAAAT
1 AAAAT-TATAAAT
2880213 A
1 A
2880214 TTATATATAT
Statistics
Matches: 110, Mismatches: 16, Indels: 34
0.69 0.10 0.21
Matches are distributed among these distances:
10 14 0.13
11 33 0.30
12 30 0.27
13 24 0.22
14 9 0.08
ACGTcount: A:0.66, C:0.03, G:0.00, T:0.32
Consensus pattern (12 bp):
AAAATTATAAAT
Found at i:2880208 original size:2 final size:2
Alignment explanation
Indices: 2880203--2880240 Score: 60
Period size: 2 Copynumber: 19.5 Consensus size: 2
2880193 ATTATAAAAA
*
2880203 AT AT AT AA AT AT -T AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
2880241 CACTCAAATT
Statistics
Matches: 33, Mismatches: 2, Indels: 2
0.89 0.05 0.05
Matches are distributed among these distances:
1 1 0.03
2 32 0.97
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (2 bp):
AT
Found at i:2880658 original size:26 final size:26
Alignment explanation
Indices: 2880604--2880673 Score: 67
Period size: 25 Copynumber: 2.7 Consensus size: 26
2880594 ATAATAAGAT
**
2880604 ATATATATATAATA-AAAATATTTAAA
1 ATATA-ATATAATATAAAATATAAAAA
2880630 ATATAATATAATATAAAATA-AAAATA
1 ATATAATATAATATAAAATATAAAA-A
2880656 ATAT-ATA-AATATATAAAT
1 ATATAATATAATATA-AAAT
2880674 TTATTTAAAT
Statistics
Matches: 39, Mismatches: 2, Indels: 7
0.81 0.04 0.15
Matches are distributed among these distances:
24 6 0.15
25 17 0.44
26 16 0.41
ACGTcount: A:0.64, C:0.00, G:0.00, T:0.36
Consensus pattern (26 bp):
ATATAATATAATATAAAATATAAAAA
Found at i:2880682 original size:10 final size:10
Alignment explanation
Indices: 2880658--2880724 Score: 59
Period size: 10 Copynumber: 6.8 Consensus size: 10
2880648 TAAAAATAAT
2880658 ATATAAA-T-
1 ATATAAATTA
*
2880666 ATATAAATTT
1 ATATAAATTA
*
2880676 ATTTAAATTA
1 ATATAAATTA
2880686 ATATAAATTA
1 ATATAAATTA
*
2880696 ATTATTAATTA
1 A-TATAAATTA
*
2880707 AT-TATAATTT
1 ATATA-AATTA
2880717 ATATAAAT
1 ATATAAAT
2880725 ATATAATATT
Statistics
Matches: 48, Mismatches: 6, Indels: 8
0.77 0.10 0.13
Matches are distributed among these distances:
8 7 0.15
9 2 0.04
10 28 0.58
11 11 0.23
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (10 bp):
ATATAAATTA
Found at i:2880744 original size:31 final size:31
Alignment explanation
Indices: 2880657--2880746 Score: 91
Period size: 31 Copynumber: 3.0 Consensus size: 31
2880647 ATAAAAATAA
*
2880657 TATATAAATATATAA-A-TTTATTTA-AATT
1 TATATAAATATATAATATTTTAATTATAATT
* *
2880685 AATATAAAT-TA-ATTATTAATTAATTATAATT
1 TATATAAATATATAATATT--TTAATTATAATT
*
2880716 TATATAAATATATAATATTTTAAATATAATT
1 TATATAAATATATAATATTTTAATTATAATT
2880747 ATAAAAAAAA
Statistics
Matches: 49, Mismatches: 6, Indels: 11
0.74 0.09 0.17
Matches are distributed among these distances:
26 1 0.02
27 3 0.06
28 9 0.18
30 6 0.12
31 23 0.47
32 2 0.04
33 5 0.10
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (31 bp):
TATATAAATATATAATATTTTAATTATAATT
Found at i:2880899 original size:16 final size:16
Alignment explanation
Indices: 2880880--2881039 Score: 64
Period size: 16 Copynumber: 9.8 Consensus size: 16
2880870 AATCATATAA
2880880 TTATAATTTAAATTTTTT
1 TTATAATTTAAA--TTTT
2880898 ATTATAAATTTAAA-TTT
1 -TTAT-AATTTAAATTTT
**
2880915 TTATAAATTTTAAATTAA
1 TTAT-AA-TTTAAATTTT
* *
2880933 ATA-AATTTAAATTTA
1 TTATAATTTAAATTTT
* * * *
2880948 TCA-AAATCAAAATTT
1 TTATAATTTAAATTTT
* **
2880963 TTATAATTT-TATATCA
1 TTATAATTTAAAT-TTT
*
2880979 TAATAATTTTAAATATTT
1 TTATAA-TTTAAAT-TTT
2880997 TTA-AATTTAATATTTT
1 TTATAATTTAA-ATTTT
2881013 TTAT-ATTTAAA-TTT
1 TTATAATTTAAATTTT
2881027 TTATAACTTTAAA
1 TTATAA-TTTAAA
2881040 ACCCCTCTTT
Statistics
Matches: 108, Mismatches: 22, Indels: 25
0.70 0.14 0.16
Matches are distributed among these distances:
14 7 0.06
15 23 0.21
16 41 0.38
17 16 0.15
18 9 0.08
19 4 0.04
20 8 0.07
ACGTcount: A:0.44, C:0.03, G:0.00, T:0.54
Consensus pattern (16 bp):
TTATAATTTAAATTTT
Found at i:2880903 original size:19 final size:20
Alignment explanation
Indices: 2880879--2880916 Score: 69
Period size: 20 Copynumber: 1.9 Consensus size: 20
2880869 AAATCATATA
2880879 ATTAT-AATTTAAATTTTTT
1 ATTATAAATTTAAATTTTTT
2880898 ATTATAAATTTAAATTTTT
1 ATTATAAATTTAAATTTTT
2880917 ATAAATTTTA
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
19 5 0.28
20 13 0.72
ACGTcount: A:0.39, C:0.00, G:0.00, T:0.61
Consensus pattern (20 bp):
ATTATAAATTTAAATTTTTT
Found at i:2880917 original size:19 final size:19
Alignment explanation
Indices: 2880879--2880930 Score: 65
Period size: 19 Copynumber: 2.8 Consensus size: 19
2880869 AAATCATATA
2880879 ATTAT-AATTTAAATTTTTT
1 ATTATAAATTTAAA-TTTTT
2880898 ATTATAAATTTAAATTTTT
1 ATTATAAATTTAAATTTTT
*
2880917 A-TA-AATTTTAAATT
1 ATTATAAATTTAAATT
2880931 AAATAAATTT
Statistics
Matches: 31, Mismatches: 1, Indels: 4
0.86 0.03 0.11
Matches are distributed among these distances:
17 10 0.32
18 2 0.06
19 11 0.35
20 8 0.26
ACGTcount: A:0.42, C:0.00, G:0.00, T:0.58
Consensus pattern (19 bp):
ATTATAAATTTAAATTTTT
Found at i:2881432 original size:15 final size:16
Alignment explanation
Indices: 2881398--2881434 Score: 53
Period size: 14 Copynumber: 2.5 Consensus size: 16
2881388 GATATTTAAT
2881398 TTATTTTTTAAAATAA
1 TTATTTTTTAAAATAA
2881414 --ATTTTTTAAAA-AA
1 TTATTTTTTAAAATAA
2881427 TTATTTTT
1 TTATTTTT
2881435 AAATTTAATA
Statistics
Matches: 19, Mismatches: 0, Indels: 5
0.79 0.00 0.21
Matches are distributed among these distances:
13 2 0.11
14 11 0.58
15 6 0.32
ACGTcount: A:0.41, C:0.00, G:0.00, T:0.59
Consensus pattern (16 bp):
TTATTTTTTAAAATAA
Found at i:2882006 original size:17 final size:16
Alignment explanation
Indices: 2881981--2882027 Score: 58
Period size: 17 Copynumber: 2.8 Consensus size: 16
2881971 AAAATAAGTG
*
2881981 TATAATAAATATTTTAA
1 TATATTAAATATTTT-A
2881998 TATATTAAATATTTTA
1 TATATTAAATATTTTA
*
2882014 TAATATTAATTATT
1 T-ATATTAAATATT
2882028 AATTTATAAA
Statistics
Matches: 27, Mismatches: 2, Indels: 2
0.87 0.06 0.06
Matches are distributed among these distances:
16 2 0.07
17 25 0.93
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (16 bp):
TATATTAAATATTTTA
Found at i:2882030 original size:32 final size:34
Alignment explanation
Indices: 2881994--2882070 Score: 81
Period size: 32 Copynumber: 2.3 Consensus size: 34
2881984 AATAAATATT
*
2881994 TTAATATATTAAATATTT-TAT-AATAT-TAATTA
1 TTAATATA-TAAAAATTTATATAAATATATAATTA
* *
2882026 TTAATTTATAAAAATTTATATAAATATATAATATT
1 TTAATATATAAAAATTTATATAAATATATAAT-TA
2882061 TTAA-ATATAA
1 TTAATATATAA
2882071 TTATAATAAA
Statistics
Matches: 37, Mismatches: 4, Indels: 6
0.79 0.09 0.13
Matches are distributed among these distances:
31 8 0.22
32 10 0.27
33 5 0.14
34 9 0.24
35 5 0.14
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (34 bp):
TTAATATATAAAAATTTATATAAATATATAATTA
Found at i:2882063 original size:20 final size:20
Alignment explanation
Indices: 2881995--2882078 Score: 59
Period size: 20 Copynumber: 4.2 Consensus size: 20
2881985 ATAAATATTT
* *
2881995 TAATATATTAAATAT-TTTA
1 TAATATTTTAAATATAATTA
*
2882014 TAATA--TTAATTATTAATTTA
1 TAATATTTTAAATA-TAA-TTA
* * *
2882034 TAAAAATTTATATA-AATATA
1 TAATATTTTAAATATAAT-TA
2882054 TAATATTTTAAATATAATTA
1 TAATATTTTAAATATAATTA
2882074 TAATA
1 TAATA
2882079 AAAAATAATA
Statistics
Matches: 50, Mismatches: 8, Indels: 13
0.70 0.11 0.18
Matches are distributed among these distances:
17 6 0.12
18 1 0.02
19 6 0.12
20 29 0.58
21 3 0.06
22 5 0.10
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (20 bp):
TAATATTTTAAATATAATTA
Found at i:2882093 original size:11 final size:11
Alignment explanation
Indices: 2882073--2882103 Score: 55
Period size: 11 Copynumber: 2.9 Consensus size: 11
2882063 AAATATAATT
2882073 ATAATA-AAAA
1 ATAATATAAAA
2882083 ATAATATAAAA
1 ATAATATAAAA
2882094 ATAATATAAA
1 ATAATATAAA
2882104 TACGTAAATT
Statistics
Matches: 20, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
10 6 0.30
11 14 0.70
ACGTcount: A:0.74, C:0.00, G:0.00, T:0.26
Consensus pattern (11 bp):
ATAATATAAAA
Found at i:2882868 original size:117 final size:116
Alignment explanation
Indices: 2882447--2882914 Score: 530
Period size: 117 Copynumber: 4.0 Consensus size: 116
2882437 TTAATTCAAT
* * * * *
2882447 ATTAAATAGTGAATATATATTTTCTTGCCGTATAAACTCATAAAAGATGAAATTAATTGAGTAAA
1 ATTAAATAGAGAATATATATTTTCTTACCATATAAACTCATAGAAGATAAAATTAATTGAGTAAA
* * * * *
2882512 ATA-TTTAGATACTTTACATTAGATCTATTTAATAATTAATTTTATCTGCTTA
66 ATATTTTA-TTATTTTACATTAGATCTA-TTCATGATTAATTTTATCTACTTA
* *
2882564 ATTAAATAGTGAATATATATTTTCTTACCATATAAACTGATAGAAAGATAAAATTAATTGAGTAA
1 ATTAAATAGAGAATATATATTTTCTTACCATATAAACTCATAG-AAGATAAAATTAATTGAGTAA
* * *
2882629 AATATTTTATTATTTTACGTTAGATCTATTCAGTGATTAATGTTATTTACTTA
65 AATATTTTATTATTTTACATTAGATCTATTCA-TGATTAATTTTATCTACTTA
** * * *
2882682 ATTAAATAG-TTA-ATATATTTTCTTATCATATAAACTCATAGAAGACAAAATTAATTAAGTAAA
1 ATTAAATAGAGAATATATATTTTCTTACCATATAAACTCATAGAAGATAAAATTAATTGAGTAAA
* * * *
2882745 ATATTTTATTATTTTATATTAGATCTATTCGATGATCAATTTTATCAACTTG
66 ATATTTTATTATTTTACATTAGATCTATTC-ATGATTAATTTTATCTACTTA
* * * *
2882797 ATTAAATACAGAATATATATTTTCTTACCATATAAACTTATAGAAGATGAAATTAGTT-ATGTAA
1 ATTAAATAGAGAATATATATTTTCTTACCATATAAACTCATAGAAGATAAAATTAATTGA-GTAA
* ** * * * *
2882861 AATATTTTGTTATTTTATTTTAAATCTATTTAGTCATAAATTTTATCTACTTA
65 AATATTTTATTATTTTACATTAGATCTATTCA-TGATTAATTTTATCTACTTA
2882914 A
1 A
2882915 ATTTAGAAGT
Statistics
Matches: 301, Mismatches: 42, Indels: 16
0.84 0.12 0.04
Matches are distributed among these distances:
115 71 0.24
116 31 0.10
117 130 0.43
118 65 0.22
119 4 0.01
ACGTcount: A:0.40, C:0.08, G:0.08, T:0.44
Consensus pattern (116 bp):
ATTAAATAGAGAATATATATTTTCTTACCATATAAACTCATAGAAGATAAAATTAATTGAGTAAA
ATATTTTATTATTTTACATTAGATCTATTCATGATTAATTTTATCTACTTA
Found at i:2883755 original size:18 final size:20
Alignment explanation
Indices: 2883712--2883777 Score: 64
Period size: 20 Copynumber: 3.3 Consensus size: 20
2883702 ATTAAAATTT
2883712 ATTTATTAAAATATAAAATA
1 ATTTATTAAAATATAAAATA
* *
2883732 AATTATTAATAT-TAAAA-A
1 ATTTATTAAAATATAAAATA
* *
2883750 ATTTATGTAAATACATAATATA
1 ATTTAT-TAAA-ATATAAAATA
2883772 ATTTAT
1 ATTTAT
2883778 ATAATTACAT
Statistics
Matches: 36, Mismatches: 6, Indels: 6
0.75 0.12 0.12
Matches are distributed among these distances:
18 6 0.17
19 8 0.22
20 11 0.31
21 4 0.11
22 7 0.19
ACGTcount: A:0.55, C:0.02, G:0.02, T:0.42
Consensus pattern (20 bp):
ATTTATTAAAATATAAAATA
Found at i:2883774 original size:22 final size:21
Alignment explanation
Indices: 2883749--2883793 Score: 63
Period size: 22 Copynumber: 2.1 Consensus size: 21
2883739 AATATTAAAA
*
2883749 AATTTATGTAAATACATAATAT
1 AATTTATATAAATACAT-ATAT
*
2883771 AATTTATATAATTACATATAT
1 AATTTATATAAATACATATAT
2883792 AA
1 AA
2883794 ATACTAATAA
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
21 6 0.29
22 15 0.71
ACGTcount: A:0.51, C:0.04, G:0.02, T:0.42
Consensus pattern (21 bp):
AATTTATATAAATACATATAT
Found at i:2883946 original size:17 final size:16
Alignment explanation
Indices: 2883913--2883953 Score: 55
Period size: 17 Copynumber: 2.5 Consensus size: 16
2883903 AAAAGTTATA
2883913 TAATATTTAATTAAAT
1 TAATATTTAATTAAAT
*
2883929 TAATATTATAATTTAAT
1 TAATATT-TAATTAAAT
*
2883946 TAAAATTT
1 TAATATTT
2883954 TTAAAATTAA
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
16 8 0.36
17 14 0.64
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (16 bp):
TAATATTTAATTAAAT
Found at i:2884009 original size:22 final size:23
Alignment explanation
Indices: 2883983--2884026 Score: 65
Period size: 22 Copynumber: 2.0 Consensus size: 23
2883973 ATAAAAATTT
2883983 TATATTTA-ATATATTA-ATAATA
1 TATATTTATATA-ATTAGATAATA
2884005 TATATTTATATAATTAGATAAT
1 TATATTTATATAATTAGATAAT
2884027 TTTATTTTAT
Statistics
Matches: 20, Mismatches: 0, Indels: 3
0.87 0.00 0.13
Matches are distributed among these distances:
22 12 0.60
23 8 0.40
ACGTcount: A:0.48, C:0.00, G:0.02, T:0.50
Consensus pattern (23 bp):
TATATTTATATAATTAGATAATA
Found at i:2884147 original size:20 final size:20
Alignment explanation
Indices: 2884117--2884166 Score: 66
Period size: 20 Copynumber: 2.5 Consensus size: 20
2884107 TATCTCGCTA
*
2884117 CTTTTTCTTTCTTTCTTT-TTT
1 CTTTTT-TTTC-TCCTTTCTTT
2884138 CTTTTTTTTCTCCTTTCTTT
1 CTTTTTTTTCTCCTTTCTTT
2884158 CTTTTTTTT
1 CTTTTTTTT
2884167 TCAACTTATT
Statistics
Matches: 27, Mismatches: 1, Indels: 3
0.87 0.03 0.10
Matches are distributed among these distances:
19 5 0.19
20 16 0.59
21 6 0.22
ACGTcount: A:0.00, C:0.20, G:0.00, T:0.80
Consensus pattern (20 bp):
CTTTTTTTTCTCCTTTCTTT
Found at i:2886603 original size:40 final size:41
Alignment explanation
Indices: 2886559--2886655 Score: 108
Period size: 41 Copynumber: 2.4 Consensus size: 41
2886549 ACATTAGTAC
* *
2886559 TAATAATTAAATTTAAATAAAAAT-ATTTTTATTATTTAAA
1 TAATAATTAAATTTAAATAAAAATAATTTTAATTATTAAAA
* *
2886599 TAATAATTTAAA-TTAAATTAAATTAATTTTAATTATTAAAA
1 TAATAA-TTAAATTTAAATAAAAATAATTTTAATTATTAAAA
** *
2886640 TTTTATTTAAATTTAA
1 TAATAATTAAATTTAA
2886656 TTTAATACAA
Statistics
Matches: 47, Mismatches: 7, Indels: 5
0.80 0.12 0.08
Matches are distributed among these distances:
40 21 0.45
41 26 0.55
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (41 bp):
TAATAATTAAATTTAAATAAAAATAATTTTAATTATTAAAA
Found at i:2886628 original size:41 final size:40
Alignment explanation
Indices: 2886559--2886657 Score: 103
Period size: 40 Copynumber: 2.5 Consensus size: 40
2886549 ACATTAGTAC
* * *
2886559 TAATAA-TTAAATTTAAATAAAAATATTTTTATTATTTAAA
1 TAATAATTTAAA-TTAAATTAAAATATTTTAATTATTAAAA
*
2886599 TAATAATTTAAATTAAATTAAATTAATTTTAATTATTAAAA
1 TAATAATTTAAATTAAATTAAAAT-ATTTTAATTATTAAAA
* * *
2886640 T-TTTATTTAAATTTAATT
1 TAATAATTTAAATTAAATT
2886658 TAATACAAAT
Statistics
Matches: 50, Mismatches: 7, Indels: 4
0.82 0.11 0.07
Matches are distributed among these distances:
40 30 0.60
41 20 0.40
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (40 bp):
TAATAATTTAAATTAAATTAAAATATTTTAATTATTAAAA
Found at i:2886658 original size:11 final size:10
Alignment explanation
Indices: 2886592--2886660 Score: 59
Period size: 10 Copynumber: 6.6 Consensus size: 10
2886582 TATTTTTATT
2886592 ATTTAAATAATA
1 ATTTAAAT--TA
2886604 ATTTAAATTA
1 ATTTAAATTA
*
2886614 AATTAAATTA
1 ATTTAAATTA
*
2886624 ATTTTAATT-
1 ATTTAAATTA
* *
2886633 ATTAAAATTTT
1 ATTTAAA-TTA
2886644 ATTTAAATTTA
1 ATTTAAA-TTA
2886655 ATTTAA
1 ATTTAA
2886661 TACAAATTAA
Statistics
Matches: 48, Mismatches: 7, Indels: 5
0.80 0.12 0.08
Matches are distributed among these distances:
9 5 0.10
10 20 0.42
11 15 0.31
12 8 0.17
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (10 bp):
ATTTAAATTA
Found at i:2888359 original size:18 final size:18
Alignment explanation
Indices: 2888325--2888366 Score: 50
Period size: 18 Copynumber: 2.3 Consensus size: 18
2888315 TTCATTATCA
*
2888325 ATATATTATATGAATATT
1 ATATATTATATCAATATT
2888343 ATATATTA-ATCATATATT
1 ATATATTATATCA-ATATT
*
2888361 AAATAT
1 ATATAT
2888367 AAATATTAAT
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
17 3 0.14
18 18 0.86
ACGTcount: A:0.48, C:0.02, G:0.02, T:0.48
Consensus pattern (18 bp):
ATATATTATATCAATATT
Found at i:2888487 original size:17 final size:18
Alignment explanation
Indices: 2888467--2888505 Score: 53
Period size: 17 Copynumber: 2.2 Consensus size: 18
2888457 TTTAAGTTTG
*
2888467 AATTTAATTTA-ATTTAT
1 AATTTAAATTACATTTAT
2888484 AATTTAAATTACTATTTAT
1 AATTTAAATTAC-ATTTAT
2888503 AAT
1 AAT
2888506 ATATTAAAAA
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
17 10 0.53
19 9 0.47
ACGTcount: A:0.44, C:0.03, G:0.00, T:0.54
Consensus pattern (18 bp):
AATTTAAATTACATTTAT
Found at i:2889053 original size:27 final size:28
Alignment explanation
Indices: 2889023--2889117 Score: 88
Period size: 32 Copynumber: 3.3 Consensus size: 28
2889013 TCATATTTAA
2889023 AATAT-TTTATATTTTTATATAAATTTT
1 AATATATTTATATTTTTATATAAATTTT
* *
2889050 AATATGTTAATAATTTATATTATATAAATTTT
1 AATATATTTAT-A-TT-T-TTATATAAATTTT
* *
2889082 AATATATTTTTATATTTATATTAAA-TTT
1 AATATATTTATATTTTTATA-TAAATTTT
2889110 -ATATATTT
1 AATATATTT
2889118 TTTAATATTG
Statistics
Matches: 57, Mismatches: 5, Indels: 12
0.77 0.07 0.16
Matches are distributed among these distances:
27 13 0.23
28 12 0.21
29 6 0.11
30 3 0.05
31 2 0.04
32 21 0.37
ACGTcount: A:0.40, C:0.00, G:0.01, T:0.59
Consensus pattern (28 bp):
AATATATTTATATTTTTATATAAATTTT
Found at i:2889077 original size:32 final size:33
Alignment explanation
Indices: 2889037--2889104 Score: 102
Period size: 32 Copynumber: 2.1 Consensus size: 33
2889027 TTTTATATTT
*
2889037 TTATATAAATTTTAATATGTTAATA-ATTTATA
1 TTATATAAATTTTAATATATTAATATATTTATA
**
2889069 TTATATAAATTTTAATATATTTTTATATTTATA
1 TTATATAAATTTTAATATATTAATATATTTATA
2889102 TTA
1 TTA
2889105 AATTTATATA
Statistics
Matches: 32, Mismatches: 3, Indels: 1
0.89 0.08 0.03
Matches are distributed among these distances:
32 22 0.69
33 10 0.31
ACGTcount: A:0.41, C:0.00, G:0.01, T:0.57
Consensus pattern (33 bp):
TTATATAAATTTTAATATATTAATATATTTATA
Found at i:2889118 original size:27 final size:27
Alignment explanation
Indices: 2888992--2889119 Score: 82
Period size: 32 Copynumber: 4.4 Consensus size: 27
2888982 ATTTTAATTT
*
2888992 ATATATTTTATTATATTATAGT-CATATTTA
1 ATATA-TTT-TTATATTATA-TAAAT-TTTA
* *
2889022 AAATATTTTATATTTTTATATAAATTTTA
1 ATATATTTT-TA-TATTATATAAATTTTA
*
2889051 ATATGTTAATAATTTATATTATATAAATTTTA
1 ATA---T-AT-TTTTATATTATATAAATTTTA
2889083 ATATATTTTTATATTTATATTAAA-TTT-
1 ATATATTTTTATA-TTATA-TAAATTTTA
2889110 ATATATTTTT
1 ATATATTTTT
2889120 TAATATTGTG
Statistics
Matches: 81, Mismatches: 7, Indels: 23
0.73 0.06 0.21
Matches are distributed among these distances:
27 16 0.20
28 11 0.14
29 17 0.21
30 12 0.15
32 19 0.23
33 4 0.05
34 2 0.02
ACGTcount: A:0.39, C:0.01, G:0.02, T:0.59
Consensus pattern (27 bp):
ATATATTTTTATATTATATAAATTTTA
Found at i:2889120 original size:29 final size:29
Alignment explanation
Indices: 2888974--2889126 Score: 81
Period size: 29 Copynumber: 5.3 Consensus size: 29
2888964 TATTTGTGTA
*
2888974 TTTAT-TTTAT-TTTAATTTATATATTTT
1 TTTATATTTATATTAAATTTATATATTTT
* * * * *
2889001 ATTATA-TTATAGTCATATTTA-A-AATAT
1 TTTATATTTATA-TTAAATTTATATATTTT
*
2889028 TTTATATTTTTATATAAATTT-TAATATGTTAAT
1 TTTATATTTATAT-TAAATTTAT-ATAT-TT--T
*
2889061 AATTTATA-TTATA-TAAATTT-TAATATATT
1 --TTTATATTTATATTAAATTTAT-ATATTTT
2889090 TTTATATTTATATTAAATTTATATATTTT
1 TTTATATTTATATTAAATTTATATATTTT
*
2889119 TTAATATT
1 TTTATATT
2889127 GTGTTATTTT
Statistics
Matches: 94, Mismatches: 16, Indels: 30
0.67 0.11 0.21
Matches are distributed among these distances:
27 23 0.24
28 15 0.16
29 28 0.30
30 2 0.02
31 2 0.02
32 13 0.14
33 1 0.01
34 4 0.04
35 6 0.06
ACGTcount: A:0.37, C:0.01, G:0.01, T:0.61
Consensus pattern (29 bp):
TTTATATTTATATTAAATTTATATATTTT
Found at i:2889139 original size:39 final size:39
Alignment explanation
Indices: 2889069--2889144 Score: 91
Period size: 39 Copynumber: 1.9 Consensus size: 39
2889059 ATAATTTATA
*
2889069 TTATATAAATTTTAATATATTTTTATATTTATATTAAAT
1 TTATATAAATTTTAATATATTGTTATATTTATATTAAAT
** * *
2889108 TTATATATTTTTTAATAT-TGTGTTATTTTTATGTTAA
1 TTATATAAATTTTAATATAT-TGTTATATTTATATTAA
2889145 GTTATAATTT
Statistics
Matches: 31, Mismatches: 5, Indels: 2
0.82 0.13 0.05
Matches are distributed among these distances:
38 1 0.03
39 30 0.97
ACGTcount: A:0.34, C:0.00, G:0.04, T:0.62
Consensus pattern (39 bp):
TTATATAAATTTTAATATATTGTTATATTTATATTAAAT
Found at i:2889366 original size:2 final size:2
Alignment explanation
Indices: 2889359--2889385 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
2889349 TGCTACATAC
2889359 AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT A
2889386 AAATACAGAA
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 25 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:2891333 original size:7 final size:7
Alignment explanation
Indices: 2891318--2891350 Score: 59
Period size: 7 Copynumber: 4.9 Consensus size: 7
2891308 ACGTAATATA
2891318 TAAAA-T
1 TAAAATT
2891324 TAAAATT
1 TAAAATT
2891331 TAAAATT
1 TAAAATT
2891338 TAAAATT
1 TAAAATT
2891345 TAAAAT
1 TAAAAT
2891351 AATAAAAAAA
Statistics
Matches: 26, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
6 5 0.19
7 21 0.81
ACGTcount: A:0.61, C:0.00, G:0.00, T:0.39
Consensus pattern (7 bp):
TAAAATT
Found at i:2893245 original size:2 final size:2
Alignment explanation
Indices: 2893238--2893286 Score: 98
Period size: 2 Copynumber: 24.5 Consensus size: 2
2893228 GGCTTGTTTG
2893238 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
2893280 AT AT AT A
1 AT AT AT A
2893287 CATACCTACA
Statistics
Matches: 47, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 47 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:2893291 original size:4 final size:4
Alignment explanation
Indices: 2893284--2893319 Score: 54
Period size: 4 Copynumber: 9.0 Consensus size: 4
2893274 ATATATATAT
* *
2893284 ATAC ATAC CTAC ATAC ATAC AAAC ATAC ATAC ATAC
1 ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC
2893320 TAATCATAAT
Statistics
Matches: 28, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
4 28 1.00
ACGTcount: A:0.50, C:0.28, G:0.00, T:0.22
Consensus pattern (4 bp):
ATAC
Found at i:2895644 original size:20 final size:21
Alignment explanation
Indices: 2895603--2895648 Score: 67
Period size: 21 Copynumber: 2.2 Consensus size: 21
2895593 TTTTTTATTT
* *
2895603 ATTAAATAATTATTATTTTAA
1 ATTAAAAAATTAATATTTTAA
2895624 ATTAAAAAATTAATA-TTTAA
1 ATTAAAAAATTAATATTTTAA
2895644 ATTAA
1 ATTAA
2895649 TTTGTTTCGA
Statistics
Matches: 23, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
20 10 0.43
21 13 0.57
ACGTcount: A:0.54, C:0.00, G:0.00, T:0.46
Consensus pattern (21 bp):
ATTAAAAAATTAATATTTTAA
Found at i:2896658 original size:16 final size:16
Alignment explanation
Indices: 2896615--2896660 Score: 56
Period size: 16 Copynumber: 2.9 Consensus size: 16
2896605 AATATTAAAA
*
2896615 TAAAAAAATAATTTTT
1 TAAAATAATAATTTTT
* **
2896631 TAATATTTTAATTTTT
1 TAAAATAATAATTTTT
2896647 TAAAATAATAATTT
1 TAAAATAATAATTT
2896661 AAATTTATAA
Statistics
Matches: 23, Mismatches: 7, Indels: 0
0.77 0.23 0.00
Matches are distributed among these distances:
16 23 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (16 bp):
TAAAATAATAATTTTT
Found at i:2896661 original size:21 final size:21
Alignment explanation
Indices: 2896631--2896707 Score: 59
Period size: 21 Copynumber: 3.6 Consensus size: 21
2896621 AATAATTTTT
* * *
2896631 TAATATTTTAATTTTTTAAAA
1 TAATAATTTAAATTTATAAAA
*
2896652 TAATAATTTAAATTTATAAAT
1 TAATAATTTAAATTTATAAAA
2896673 TAAATTAAATTTAAATTTA-AACAA
1 T-AA-T-AATTTAAATTTATAA-AA
*
2896697 AAAT-ATTTAAA
1 TAATAATTTAAA
2896708 ATTTTTTTTA
Statistics
Matches: 46, Mismatches: 6, Indels: 9
0.75 0.10 0.15
Matches are distributed among these distances:
20 7 0.15
21 18 0.39
22 3 0.07
23 5 0.11
24 13 0.28
ACGTcount: A:0.53, C:0.01, G:0.00, T:0.45
Consensus pattern (21 bp):
TAATAATTTAAATTTATAAAA
Found at i:2896667 original size:6 final size:6
Alignment explanation
Indices: 2896656--2896693 Score: 51
Period size: 6 Copynumber: 6.3 Consensus size: 6
2896646 TTAAAATAAT
*
2896656 AATTTA AATTTA TAAATTA AA-TTA AATTTA AATTTA AA
1 AATTTA AATTTA -AATTTA AATTTA AATTTA AATTTA AA
2896694 CAAAAATATT
Statistics
Matches: 29, Mismatches: 1, Indels: 4
0.85 0.03 0.12
Matches are distributed among these distances:
5 5 0.17
6 19 0.66
7 5 0.17
ACGTcount: A:0.55, C:0.00, G:0.00, T:0.45
Consensus pattern (6 bp):
AATTTA
Found at i:2897138 original size:35 final size:37
Alignment explanation
Indices: 2897093--2897207 Score: 146
Period size: 37 Copynumber: 3.2 Consensus size: 37
2897083 CCTTTCAATC
*
2897093 CCCCGTTCCACAAGTTAATGTCTACCAT-TCAATC-C-
1 CCCCATTCCACAAGTTAATGTCTACC-TCTCAATCACA
* *
2897128 CCCCATTCCACAAGTTGATGTCTGCCTCTCAATCACA
1 CCCCATTCCACAAGTTAATGTCTACCTCTCAATCACA
* * *
2897165 CCCCATTCCACAAGGTAATGTTTACCTCTCAATCTCA
1 CCCCATTCCACAAGTTAATGTCTACCTCTCAATCACA
2897202 CCCCAT
1 CCCCAT
2897208 GTATAGTTGA
Statistics
Matches: 69, Mismatches: 8, Indels: 4
0.85 0.10 0.05
Matches are distributed among these distances:
34 1 0.01
35 29 0.42
36 1 0.01
37 38 0.55
ACGTcount: A:0.25, C:0.38, G:0.09, T:0.28
Consensus pattern (37 bp):
CCCCATTCCACAAGTTAATGTCTACCTCTCAATCACA
Found at i:2897389 original size:35 final size:34
Alignment explanation
Indices: 2897324--2897468 Score: 157
Period size: 37 Copynumber: 4.1 Consensus size: 34
2897314 AAAAAGCCAA
*
2897324 GTCTACCTCTCAATCCCCCGTTCCACAAGTTAAT
1 GTCTACCTCTCAATCCCCCATTCCACAAGTTAAT
* *
2897358 GTC-AACTACTCAATCCCCCTATTCCACAAGTTGAT
1 GTCTACCT-CTCAATCCCCC-ATTCCACAAGTTAAT
* *
2897393 GTCTACCTCTCAATCATACTCCATTCCACAAGGTAAT
1 GTCTACCTCTCAATC---CCCCATTCCACAAGTTAAT
*
2897430 ATCTACCTCTCAATCCCACCCCATTCCACAAGTTAAT
1 GTCTACCTCTCAAT--C-CCCCATTCCACAAGTTAAT
2897467 GT
1 GT
2897469 ACGACACTTG
Statistics
Matches: 92, Mismatches: 11, Indels: 13
0.79 0.09 0.11
Matches are distributed among these distances:
33 3 0.03
34 14 0.15
35 23 0.25
36 3 0.03
37 45 0.49
38 3 0.03
39 1 0.01
ACGTcount: A:0.28, C:0.36, G:0.08, T:0.29
Consensus pattern (34 bp):
GTCTACCTCTCAATCCCCCATTCCACAAGTTAAT
Found at i:2897396 original size:246 final size:245
Alignment explanation
Indices: 2896963--2897453 Score: 793
Period size: 246 Copynumber: 2.0 Consensus size: 245
2896953 ATGGTGACTG
** *
2896963 GTATAGTTGACTTCTCAACTTTGGGGTAATCTATGCCTTCTTTGATTCGAGTCGTTTTTTATATA
1 GTATAGTTGACTTCTCAACTTTGGAATAATCTATGCCTTCTTTAATTCGAGTCGTTTTTTATATA
* * * *
2897028 GAGGTTACCAAGGCGATCCTTAATATCATGATTGACTTGCAAAAAGCCAAGTTTACCTTTCAATC
66 GAGGTTACCAAGCCGATCCTCAATATCATGATTGACTTGCAAAAAGCCAAGTCTACCTCTCAATC
* * *
2897093 CCCCGTTCCACAAGTTAATGTCTACCATTCAATCCCCCCATTCCACAAGTTGATGTCTGCCTCTC
131 CCCCGTTCCACAAGTTAATGTCAACCACTCAATCCCCCCATTCCACAAGTTGATGTCTACCTCTC
* * *
2897158 AATCACACCCCATTCCACAAGGTAATGTTTACCTCTCAATCTCACCCCAT
196 AATCACACCCCATTCCACAAGGTAATATCTACCTCTCAATCCCACCCCAT
* *
2897208 GTATAGTTGACTTCTCAACTTTGGAATGATCTATGCCTTCTTTAATTCGAGTCATTTTTTTATAT
1 GTATAGTTGACTTCTCAACTTTGGAATAATCTATGCCTTCTTTAATTCGAGTC-GTTTTTTATAT
*
2897273 AGAGGTTACCAAGCCGGTCCTCAATATCATGATTGACTTGCAAAAAGCCAAGTCTACCTCTCAAT
65 AGAGGTTACCAAGCCGATCCTCAATATCATGATTGACTTGCAAAAAGCCAAGTCTACCTCTCAAT
* *
2897338 CCCCCGTTCCACAAGTTAATGTCAACTACTCAATCCCCCTATTCCACAAGTTGATGTCTACCTCT
130 CCCCCGTTCCACAAGTTAATGTCAACCACTCAATCCCCCCATTCCACAAGTTGATGTCTACCTCT
* *
2897403 CAATCATACTCCATTCCACAAGGTAATATCTACCTCTCAATCCCACCCCAT
195 CAATCACACCCCATTCCACAAGGTAATATCTACCTCTCAATCCCACCCCAT
2897454 TCCACAAGTT
Statistics
Matches: 225, Mismatches: 20, Indels: 1
0.91 0.08 0.00
Matches are distributed among these distances:
245 49 0.22
246 176 0.78
ACGTcount: A:0.27, C:0.28, G:0.12, T:0.33
Consensus pattern (245 bp):
GTATAGTTGACTTCTCAACTTTGGAATAATCTATGCCTTCTTTAATTCGAGTCGTTTTTTATATA
GAGGTTACCAAGCCGATCCTCAATATCATGATTGACTTGCAAAAAGCCAAGTCTACCTCTCAATC
CCCCGTTCCACAAGTTAATGTCAACCACTCAATCCCCCCATTCCACAAGTTGATGTCTACCTCTC
AATCACACCCCATTCCACAAGGTAATATCTACCTCTCAATCCCACCCCAT
Found at i:2897443 original size:72 final size:71
Alignment explanation
Indices: 2897324--2897468 Score: 170
Period size: 72 Copynumber: 2.0 Consensus size: 71
2897314 AAAAAGCCAA
* * * *
2897324 GTCTACCTCTCAATCCCCCGTTCCACAAGTTAATGTCAACTACTCAAT-CC-CCCTATTCCACAA
1 GTCTACCTCTCAATCCCCCATTCCACAAGGTAATATCAACTACTCAATCCCACCCCATTCCACAA
*
2897387 GTTGAT
66 GTTAAT
* *
2897393 GTCTACCTCTCAATCATACTCCATTCCACAAGGTAATATCTACCT-CTCAATCCCACCCCATTCC
1 GTCTACCTCTCAATC---CCCCATTCCACAAGGTAATATC-AACTACTCAATCCCACCCCATTCC
2897457 ACAAGTTAAT
62 ACAAGTTAAT
2897467 GT
1 GT
2897469 ACGACACTTG
Statistics
Matches: 63, Mismatches: 7, Indels: 7
0.82 0.09 0.09
Matches are distributed among these distances:
69 15 0.24
72 24 0.38
73 5 0.08
74 19 0.30
ACGTcount: A:0.28, C:0.36, G:0.08, T:0.29
Consensus pattern (71 bp):
GTCTACCTCTCAATCCCCCATTCCACAAGGTAATATCAACTACTCAATCCCACCCCATTCCACAA
GTTAAT
Found at i:2897980 original size:2 final size:2
Alignment explanation
Indices: 2897973--2898005 Score: 66
Period size: 2 Copynumber: 16.5 Consensus size: 2
2897963 ACCATTCTTT
2897973 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
2898006 TGCAATGATA
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 31 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:2898894 original size:15 final size:15
Alignment explanation
Indices: 2898876--2898922 Score: 53
Period size: 15 Copynumber: 3.1 Consensus size: 15
2898866 AATTTAACTA
2898876 AAATTAAATTAATTT
1 AAATTAAATTAATTT
2898891 AAATTAAA--AATTT
1 AAATTAAATTAATTT
2898904 AATATTTAAATCTAATTT
1 AA-A-TTAAAT-TAATTT
2898922 A
1 A
2898923 TTTCGAACCC
Statistics
Matches: 27, Mismatches: 0, Indels: 7
0.79 0.00 0.21
Matches are distributed among these distances:
13 7 0.26
14 1 0.04
15 13 0.48
18 6 0.22
ACGTcount: A:0.53, C:0.02, G:0.00, T:0.45
Consensus pattern (15 bp):
AAATTAAATTAATTT
Found at i:2899194 original size:20 final size:19
Alignment explanation
Indices: 2899158--2899197 Score: 57
Period size: 19 Copynumber: 2.2 Consensus size: 19
2899148 ATTTTTTATT
2899158 TAAATTTAATTATAAAATA
1 TAAATTTAATTATAAAATA
2899177 TAAATATTAA-TATAAAA-A
1 TAAAT-TTAATTATAAAATA
2899195 TAA
1 TAA
2899198 TTTTTTAATT
Statistics
Matches: 20, Mismatches: 0, Indels: 3
0.87 0.00 0.13
Matches are distributed among these distances:
18 4 0.20
19 12 0.60
20 4 0.20
ACGTcount: A:0.62, C:0.00, G:0.00, T:0.38
Consensus pattern (19 bp):
TAAATTTAATTATAAAATA
Found at i:2908120 original size:35 final size:35
Alignment explanation
Indices: 2908072--2908202 Score: 127
Period size: 35 Copynumber: 3.6 Consensus size: 35
2908062 ATGTACATAA
* *
2908072 TCCCCGTTGCACAAGTTAATGTCTACCTCTCAGTC
1 TCCCCGTTTCACAAGTTAATGTCTACCTCTCAATC
*
2908107 TCCCCGTTTCACAAGTTGATGTCTACCTCTCAATC
1 TCCCCGTTTCACAAGTTAATGTCTACCTCTCAATC
* ** * *
2908142 CCACCCCATTCTACAAGGTAATGTCTACCTTTCAATCCC
1 TC-CCCGTTTC-ACAAGTTAATGTCTACCTCTCAAT--C
* * *
2908181 ACCCCATTCCACAAGTTAATGT
1 TCCCCGTTTCACAAGTTAATGT
2908203 ACGACACTTG
Statistics
Matches: 78, Mismatches: 14, Indels: 6
0.80 0.14 0.06
Matches are distributed among these distances:
35 33 0.42
36 6 0.08
37 32 0.41
38 5 0.06
39 2 0.03
ACGTcount: A:0.24, C:0.35, G:0.11, T:0.31
Consensus pattern (35 bp):
TCCCCGTTTCACAAGTTAATGTCTACCTCTCAATC
Found at i:2908167 original size:37 final size:36
Alignment explanation
Indices: 2908081--2908202 Score: 156
Period size: 37 Copynumber: 3.4 Consensus size: 36
2908071 ATCCCCGTTG
* * **
2908081 CACAAGTTAATGTCTACCTCTCAGTCTC-CCCGTTT
1 CACAAGTTAATGTCTACCTCTCAATCCCACCCCATT
*
2908116 CACAAGTTGATGTCTACCTCTCAATCCCACCCCATT
1 CACAAGTTAATGTCTACCTCTCAATCCCACCCCATT
* *
2908152 CTACAAGGTAATGTCTACCTTTCAATCCCACCCCATT
1 C-ACAAGTTAATGTCTACCTCTCAATCCCACCCCATT
2908189 CCACAAGTTAATGT
1 -CACAAGTTAATGT
2908203 ACGACACTTG
Statistics
Matches: 75, Mismatches: 9, Indels: 4
0.85 0.10 0.05
Matches are distributed among these distances:
35 25 0.33
36 6 0.08
37 43 0.57
38 1 0.01
ACGTcount: A:0.25, C:0.34, G:0.10, T:0.30
Consensus pattern (36 bp):
CACAAGTTAATGTCTACCTCTCAATCCCACCCCATT
Found at i:2909503 original size:34 final size:34
Alignment explanation
Indices: 2909465--2909613 Score: 226
Period size: 34 Copynumber: 4.4 Consensus size: 34
2909455 CTTTGTTAAG
* *
2909465 TGTATTTGGTGAGAATGTTAGGTGTGTTAGGTGA
1 TGTATTTGGTGAGAATATTAGGTGTGTTAGGTAA
* *
2909499 TGTATTTGGTGAGAATGTTAGGTGTGTTAGGTGA
1 TGTATTTGGTGAGAATATTAGGTGTGTTAGGTAA
*
2909533 TGTATTTGGTGAGAATATTAGATGTGTTAGGTAA
1 TGTATTTGGTGAGAATATTAGGTGTGTTAGGTAA
*
2909567 TGTATTTGGTGAAAATATTAGGTGTGTTAGGTAA
1 TGTATTTGGTGAGAATATTAGGTGTGTTAGGTAA
* *
2909601 TGTGTTAGGTGAG
1 TGTATTTGGTGAG
2909614 TAAGATATCT
Statistics
Matches: 107, Mismatches: 8, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
34 107 1.00
ACGTcount: A:0.24, C:0.00, G:0.35, T:0.41
Consensus pattern (34 bp):
TGTATTTGGTGAGAATATTAGGTGTGTTAGGTAA
Found at i:2914359 original size:34 final size:34
Alignment explanation
Indices: 2914321--2914469 Score: 217
Period size: 34 Copynumber: 4.4 Consensus size: 34
2914311 CTTTGTTAAG
* * *
2914321 TGTATTCGGTGAGAATGTTAGGTGTGTTAGGTGA
1 TGTATTTGGTGAGAATATTAGGTGTGTTAGGTAA
* *
2914355 TGTATTTGGTGAGAATGTTAGGTGTGTTAGGTGA
1 TGTATTTGGTGAGAATATTAGGTGTGTTAGGTAA
*
2914389 TGTATTTGGTGAGAATATTAGATGTGTTAGGTAA
1 TGTATTTGGTGAGAATATTAGGTGTGTTAGGTAA
*
2914423 TGTATTTGGTGAAAATATTAGGTGTGTTAGGTAA
1 TGTATTTGGTGAGAATATTAGGTGTGTTAGGTAA
* *
2914457 TGTGTTAGGTGAG
1 TGTATTTGGTGAG
2914470 TAAAATACTT
Statistics
Matches: 106, Mismatches: 9, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
34 106 1.00
ACGTcount: A:0.24, C:0.01, G:0.35, T:0.40
Consensus pattern (34 bp):
TGTATTTGGTGAGAATATTAGGTGTGTTAGGTAA
Found at i:2914948 original size:15 final size:15
Alignment explanation
Indices: 2914928--2914957 Score: 51
Period size: 15 Copynumber: 2.0 Consensus size: 15
2914918 AAATAATAAT
2914928 TTAATTAAAATTAAA
1 TTAATTAAAATTAAA
*
2914943 TTAATTTAAATTAAA
1 TTAATTAAAATTAAA
2914958 AATTTAATAT
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.57, C:0.00, G:0.00, T:0.43
Consensus pattern (15 bp):
TTAATTAAAATTAAA
Found at i:2915528 original size:20 final size:19
Alignment explanation
Indices: 2915492--2915531 Score: 57
Period size: 19 Copynumber: 2.2 Consensus size: 19
2915482 ATTTTTTATT
2915492 TAAATTTAATTATAAAATA
1 TAAATTTAATTATAAAATA
2915511 TAAATATTAA-TATAAAA-A
1 TAAAT-TTAATTATAAAATA
2915529 TAA
1 TAA
2915532 TTTTTTAATT
Statistics
Matches: 20, Mismatches: 0, Indels: 3
0.87 0.00 0.13
Matches are distributed among these distances:
18 4 0.20
19 12 0.60
20 4 0.20
ACGTcount: A:0.62, C:0.00, G:0.00, T:0.38
Consensus pattern (19 bp):
TAAATTTAATTATAAAATA
Found at i:2916106 original size:68 final size:68
Alignment explanation
Indices: 2916010--2916175 Score: 172
Period size: 68 Copynumber: 2.4 Consensus size: 68
2916000 TTTATTATTA
* * * * * * * **
2916010 ATTTGATGATTTGTTATTATTAATTAAATAAAAAATTT-AGTAGTATGTTGTTATTAATTAAATA
1 ATTTGATGATTTATCATTGTTGACTAAATAAAAAATTTGA-TAATATATCATTATTAATTAAATA
2916074 GATG
65 GATG
* * *
2916078 ATTTGATGGTTTATCATTGTTGACTAAATAAAAAATTTGATAATTTATCATTGTTAATTAAATAG
1 ATTTGATGATTTATCATTGTTGACTAAATAAAAAATTTGATAATATATCATTATTAATTAAATAG
*
2916143 GTG
66 ATG
* * *
2916146 ATTTGGTGATTTTTCATTGTTGATTAAATA
1 ATTTGATGATTTATCATTGTTGACTAAATA
2916176 GGAGATTTGA
Statistics
Matches: 80, Mismatches: 17, Indels: 2
0.81 0.17 0.02
Matches are distributed among these distances:
68 79 0.99
69 1 0.01
ACGTcount: A:0.36, C:0.02, G:0.14, T:0.47
Consensus pattern (68 bp):
ATTTGATGATTTATCATTGTTGACTAAATAAAAAATTTGATAATATATCATTATTAATTAAATAG
ATG
Found at i:2916204 original size:34 final size:34
Alignment explanation
Indices: 2916066--2916191 Score: 130
Period size: 34 Copynumber: 3.7 Consensus size: 34
2916056 GTTGTTATTA
*
2916066 ATTAAATA-GATGATTTGATGGTTTATCATTGTTG
1 ATTAAATAGGA-GATTTGATAGTTTATCATTGTTG
* ** * * *
2916100 ACTAAATAAAAAATTTGATAATTTATCATTGTTA
1 ATTAAATAGGAGATTTGATAGTTTATCATTGTTG
* * *
2916134 ATTAAATAGGTGATTTGGT-GATTTTTCATTGTTG
1 ATTAAATAGGAGATTTGATAG-TTTATCATTGTTG
2916168 ATTAAATAGGAGATTTGATAGTTT
1 ATTAAATAGGAGATTTGATAGTTT
2916192 GCCATTATTG
Statistics
Matches: 72, Mismatches: 17, Indels: 6
0.76 0.18 0.06
Matches are distributed among these distances:
34 70 0.97
35 2 0.03
ACGTcount: A:0.34, C:0.03, G:0.17, T:0.45
Consensus pattern (34 bp):
ATTAAATAGGAGATTTGATAGTTTATCATTGTTG
Found at i:2917522 original size:16 final size:16
Alignment explanation
Indices: 2917501--2917532 Score: 64
Period size: 16 Copynumber: 2.0 Consensus size: 16
2917491 TGCTTTCTAA
2917501 AACACATACTAAGTTC
1 AACACATACTAAGTTC
2917517 AACACATACTAAGTTC
1 AACACATACTAAGTTC
2917533 TATAATAATT
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 16 1.00
ACGTcount: A:0.44, C:0.25, G:0.06, T:0.25
Consensus pattern (16 bp):
AACACATACTAAGTTC
Found at i:2919026 original size:22 final size:22
Alignment explanation
Indices: 2919001--2919042 Score: 68
Period size: 22 Copynumber: 1.9 Consensus size: 22
2918991 TATTTTTATT
2919001 TAAAT-TTAATTATAAAAATATA
1 TAAATATTAA-TATAAAAATATA
2919023 TAAATATTAATATAAAAATA
1 TAAATATTAATATAAAAATA
2919043 ATTTTTTATT
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
22 15 0.79
23 4 0.21
ACGTcount: A:0.62, C:0.00, G:0.00, T:0.38
Consensus pattern (22 bp):
TAAATATTAATATAAAAATATA
Found at i:2919260 original size:23 final size:23
Alignment explanation
Indices: 2919233--2919297 Score: 80
Period size: 23 Copynumber: 2.8 Consensus size: 23
2919223 GCTTGAATTA
2919233 ATTAATAATAATAAATATTTAAAT
1 ATTAAT-ATAATAAATATTTAAAT
*
2919257 -TTAATTATAA-AAATATATAAAT
1 ATTAA-TATAATAAATATTTAAAT
*
2919279 ATTAATATAATAATTATTT
1 ATTAATATAATAAATATTT
2919298 TTAAAATAGT
Statistics
Matches: 35, Mismatches: 3, Indels: 7
0.78 0.07 0.16
Matches are distributed among these distances:
22 16 0.46
23 18 0.51
24 1 0.03
ACGTcount: A:0.55, C:0.00, G:0.00, T:0.45
Consensus pattern (23 bp):
ATTAATATAATAAATATTTAAAT
Found at i:2921599 original size:25 final size:25
Alignment explanation
Indices: 2921544--2921608 Score: 73
Period size: 24 Copynumber: 2.6 Consensus size: 25
2921534 CAACCCGACC
2921544 ATTTTACTATTATATAATATATATTA
1 ATTTTA-TATTATATAATATATATTA
*
2921570 ATTTTATATTTTAT-ATAT-TATGTA
1 ATTTTATATTATATAATATATAT-TA
*
2921594 ATTTT-TATAATATAA
1 ATTTTATATTATATAA
2921609 AAAATATATA
Statistics
Matches: 34, Mismatches: 3, Indels: 6
0.79 0.07 0.14
Matches are distributed among these distances:
23 9 0.26
24 12 0.35
25 7 0.21
26 6 0.18
ACGTcount: A:0.40, C:0.02, G:0.02, T:0.57
Consensus pattern (25 bp):
ATTTTATATTATATAATATATATTA
Found at i:2922270 original size:17 final size:16
Alignment explanation
Indices: 2922236--2922274 Score: 53
Period size: 16 Copynumber: 2.4 Consensus size: 16
2922226 TATTTTCGAA
*
2922236 TTATTTTGGTTTACAT
1 TTATTTTGGTTTAAAT
2922252 TTATTTTGGTTTTAAAT
1 TTATTTTGG-TTTAAAT
2922269 TT-TTTT
1 TTATTTT
2922275 ATATTGGAGT
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
16 13 0.62
17 8 0.38
ACGTcount: A:0.18, C:0.03, G:0.10, T:0.69
Consensus pattern (16 bp):
TTATTTTGGTTTAAAT
Found at i:2922506 original size:19 final size:17
Alignment explanation
Indices: 2922473--2922524 Score: 54
Period size: 16 Copynumber: 3.1 Consensus size: 17
2922463 TTACCAAAAT
* *
2922473 TAAAATTTTAAAAATAA
1 TAAAATTATATAAATAA
2922490 TAAGTAATTATATAAAT-A
1 TAA--AATTATATAAATAA
2922508 TAAAATTATAT-AATAA
1 TAAAATTATATAAATAA
2922524 T
1 T
2922525 TTTATTTATA
Statistics
Matches: 30, Mismatches: 2, Indels: 7
0.77 0.05 0.18
Matches are distributed among these distances:
15 3 0.10
16 10 0.33
17 3 0.10
18 4 0.13
19 10 0.33
ACGTcount: A:0.60, C:0.00, G:0.02, T:0.38
Consensus pattern (17 bp):
TAAAATTATATAAATAA
Found at i:2923059 original size:18 final size:19
Alignment explanation
Indices: 2923022--2923062 Score: 66
Period size: 19 Copynumber: 2.2 Consensus size: 19
2923012 GAAAATTTGG
*
2923022 ATTTCAAAAATATATTTAA
1 ATTTCAAAAATATATGTAA
2923041 ATTTCAAAAATA-ATGTAA
1 ATTTCAAAAATATATGTAA
2923059 ATTT
1 ATTT
2923063 TGTAGTAAAA
Statistics
Matches: 21, Mismatches: 1, Indels: 1
0.91 0.04 0.04
Matches are distributed among these distances:
18 9 0.43
19 12 0.57
ACGTcount: A:0.51, C:0.05, G:0.02, T:0.41
Consensus pattern (19 bp):
ATTTCAAAAATATATGTAA
Found at i:2924335 original size:17 final size:19
Alignment explanation
Indices: 2924303--2924410 Score: 67
Period size: 19 Copynumber: 5.5 Consensus size: 19
2924293 ACATATCAAA
* *
2924303 ATATATATAAATAAAAATT
1 ATATAAATATATAAAAATT
*
2924322 AT-T-AATATATAAAATTT
1 ATATAAATATATAAAAATT
**
2924339 ATATAAATATATAATATTTT
1 ATATAAATATATAA-AAATT
*
2924359 AAATATAATTATAATAAAATATAT
1 --ATATAAATAT-ATAAAA-AT-T
* * *
2924383 ATATATATATATAAATACT
1 ATATAAATATATAAAAATT
2924402 ATATAAATA
1 ATATAAATA
2924411 CTCAAACTCA
Statistics
Matches: 69, Mismatches: 12, Indels: 16
0.71 0.12 0.16
Matches are distributed among these distances:
17 13 0.19
18 2 0.03
19 20 0.29
20 5 0.07
21 5 0.07
22 18 0.26
23 5 0.07
24 1 0.01
ACGTcount: A:0.57, C:0.01, G:0.00, T:0.42
Consensus pattern (19 bp):
ATATAAATATATAAAAATT
Found at i:2924926 original size:3 final size:3
Alignment explanation
Indices: 2924918--2924964 Score: 94
Period size: 3 Copynumber: 15.7 Consensus size: 3
2924908 TTGATGGGAT
2924918 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TT
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TT
2924965 TTGTCATTTG
Statistics
Matches: 44, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 44 1.00
ACGTcount: A:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (3 bp):
TTA
Found at i:2925041 original size:3 final size:3
Alignment explanation
Indices: 2925033--2925098 Score: 125
Period size: 3 Copynumber: 22.3 Consensus size: 3
2925023 AGGAGTGCAG
2925033 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
2925081 AAT AAT AAT AAT -AT AAT A
1 AAT AAT AAT AAT AAT AAT A
2925099 CTTTTTAATG
Statistics
Matches: 62, Mismatches: 0, Indels: 2
0.97 0.00 0.03
Matches are distributed among these distances:
2 2 0.03
3 60 0.97
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (3 bp):
AAT
Found at i:2927354 original size:34 final size:33
Alignment explanation
Indices: 2927306--2927525 Score: 255
Period size: 34 Copynumber: 6.5 Consensus size: 33
2927296 TGGTAAAAAC
*
2927306 CACCATTTAATCAACAATGGCAACCTACCAAAT
1 CACCATTTAATCAACAATGGTAACCTACCAAAT
* *
2927339 CTACCATTTAGTCAACAATGGTAAGCC-ACAAAAT
1 C-ACCATTTAATCAACAATGGTAA-CCTACCAAAT
* *
2927373 CACCCATTTAATCAATAATGGTAAGCTACCAAAT
1 CA-CCATTTAATCAACAATGGTAACCTACCAAAT
** *
2927407 TTCTCATTTAATCAACAATGGTAAGCTACCAAAT
1 CAC-CATTTAATCAACAATGGTAACCTACCAAAT
* * *
2927441 CTCCCATTTAGTCAACAATGGCAAACC-ACCAAAT
1 C-ACCATTTAATCAACAATGG-TAACCTACCAAAT
*
2927475 CACCCATTTAATCAACAATGGTAAACTACCAAAT
1 CA-CCATTTAATCAACAATGGTAACCTACCAAAT
2927509 CACCATTTAATCAACAA
1 CACCATTTAATCAACAA
2927526 ATCTCCCATT
Statistics
Matches: 159, Mismatches: 19, Indels: 18
0.81 0.10 0.09
Matches are distributed among these distances:
33 22 0.14
34 131 0.82
35 6 0.04
ACGTcount: A:0.41, C:0.26, G:0.08, T:0.25
Consensus pattern (33 bp):
CACCATTTAATCAACAATGGTAACCTACCAAAT
Found at i:2927422 original size:68 final size:67
Alignment explanation
Indices: 2927308--2927525 Score: 285
Period size: 68 Copynumber: 3.2 Consensus size: 67
2927298 GTAAAAACCA
* * * *
2927308 CCATTTAATCAACAATGGCAACCTACCAAATCTACCATTTAGTCAACAATGGTAAGCCACAAAAT
1 CCATTTAATCAACAATGGCAAACTACCAAAT-TACCATTTAATCAACAATGGTAAGCTACCAAAT
2927373 CAC
65 CAC
* * * *
2927376 CCATTTAATCAATAATGGTAAGCTACCAAATTTCTCATTTAATCAACAATGGTAAGCTACCAAAT
1 CCATTTAATCAACAATGGCAAACTACCAAATTAC-CATTTAATCAACAATGGTAAGCTACCAAAT
*
2927441 CTC
65 CAC
* * * *
2927444 CCATTTAGTCAACAATGGCAAACCACCAAATCACCCATTTAATCAACAATGGTAAACTACCAAAT
1 CCATTTAATCAACAATGGCAAACTACCAAATTA-CCATTTAATCAACAATGGTAAGCTACCAAAT
2927509 CA-
65 CAC
2927511 CCATTTAATCAACAA
1 CCATTTAATCAACAA
2927526 ATCTCCCATT
Statistics
Matches: 130, Mismatches: 18, Indels: 5
0.85 0.12 0.03
Matches are distributed among these distances:
67 16 0.12
68 113 0.87
69 1 0.01
ACGTcount: A:0.41, C:0.26, G:0.08, T:0.25
Consensus pattern (67 bp):
CCATTTAATCAACAATGGCAAACTACCAAATTACCATTTAATCAACAATGGTAAGCTACCAAATC
AC
Found at i:2927450 original size:102 final size:101
Alignment explanation
Indices: 2927306--2927525 Score: 341
Period size: 102 Copynumber: 2.2 Consensus size: 101
2927296 TGGTAAAAAC
* *
2927306 CACCATTTAATCAACAATGGCAACCTACCAAATCTACCATTTAGTCAACAATGGTAAGCCACAAA
1 CACCATTTAATCAACAATGGCAACCTACCAAATCTACCATTTAGTCAACAATGGCAAACCACAAA
* *
2927371 ATCACCCATTTAATCAATAATGGTAAGCTACCAAAT
66 ATCACCCATTTAATCAACAATGGTAAACTACCAAAT
** * * * *
2927407 TTCTCATTTAATCAACAATGGTAAGCTACCAAATCTCCCATTTAGTCAACAATGGCAAACCACCA
1 CAC-CATTTAATCAACAATGGCAACCTACCAAATCTACCATTTAGTCAACAATGGCAAACCACAA
2927472 AATCACCCATTTAATCAACAATGGTAAACTACCAAAT
65 AATCACCCATTTAATCAACAATGGTAAACTACCAAAT
2927509 CACCATTTAATCAACAA
1 CACCATTTAATCAACAA
2927526 ATCTCCCATT
Statistics
Matches: 106, Mismatches: 12, Indels: 2
0.88 0.10 0.02
Matches are distributed among these distances:
101 15 0.14
102 91 0.86
ACGTcount: A:0.41, C:0.26, G:0.08, T:0.25
Consensus pattern (101 bp):
CACCATTTAATCAACAATGGCAACCTACCAAATCTACCATTTAGTCAACAATGGCAAACCACAAA
ATCACCCATTTAATCAACAATGGTAAACTACCAAAT
Found at i:2927528 original size:19 final size:20
Alignment explanation
Indices: 2927504--2927541 Score: 60
Period size: 20 Copynumber: 1.9 Consensus size: 20
2927494 GGTAAACTAC
2927504 CAAATC-ACCATTTAATCAA
1 CAAATCTACCATTTAATCAA
*
2927523 CAAATCTCCCATTTAATCA
1 CAAATCTACCATTTAATCA
2927542 CAATGGTAAG
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
19 6 0.35
20 11 0.65
ACGTcount: A:0.42, C:0.29, G:0.00, T:0.29
Consensus pattern (20 bp):
CAAATCTACCATTTAATCAA
Found at i:2931645 original size:34 final size:33
Alignment explanation
Indices: 2931597--2931817 Score: 257
Period size: 34 Copynumber: 6.5 Consensus size: 33
2931587 TGGTAAAAAC
*
2931597 CACCATTTAATCAACAATGGCAACCTACCAAAT
1 CACCATTTAATCAACAATGGTAACCTACCAAAT
* *
2931630 CTACCATTTAGTCAACAATGGTAAGCC-ACAAAAT
1 C-ACCATTTAATCAACAATGGTAA-CCTACCAAAT
* *
2931664 CACCCATTTAATCAATAATGGTAAGCTACCAAAT
1 CA-CCATTTAATCAACAATGGTAACCTACCAAAT
** *
2931698 TTCTCATTTAATCAACAATGGTAAGCTACCAAAT
1 CAC-CATTTAATCAACAATGGTAACCTACCAAAT
* * *
2931732 CTCCCATTTAGTCAACAATGGCAAACC-ACCAAAT
1 C-ACCATTTAATCAACAATGG-TAACCTACCAAAT
*
2931766 CACCCATTTAATCAACAATGGTAAACTACCAAAT
1 CA-CCATTTAATCAACAATGGTAACCTACCAAAT
2931800 CACCATTTAATCAACAAT
1 CACCATTTAATCAACAAT
2931818 TCTCCCACTT
Statistics
Matches: 160, Mismatches: 19, Indels: 18
0.81 0.10 0.09
Matches are distributed among these distances:
33 23 0.14
34 131 0.82
35 6 0.04
ACGTcount: A:0.41, C:0.26, G:0.08, T:0.25
Consensus pattern (33 bp):
CACCATTTAATCAACAATGGTAACCTACCAAAT
Found at i:2931713 original size:68 final size:67
Alignment explanation
Indices: 2931599--2931817 Score: 287
Period size: 68 Copynumber: 3.2 Consensus size: 67
2931589 GTAAAAACCA
* * * *
2931599 CCATTTAATCAACAATGGCAACCTACCAAATCTACCATTTAGTCAACAATGGTAAGCCACAAAAT
1 CCATTTAATCAACAATGGCAAACTACCAAAT-TACCATTTAATCAACAATGGTAAGCTACCAAAT
2931664 CAC
65 CAC
* * * *
2931667 CCATTTAATCAATAATGGTAAGCTACCAAATTTCTCATTTAATCAACAATGGTAAGCTACCAAAT
1 CCATTTAATCAACAATGGCAAACTACCAAATTAC-CATTTAATCAACAATGGTAAGCTACCAAAT
*
2931732 CTC
65 CAC
* * * *
2931735 CCATTTAGTCAACAATGGCAAACCACCAAATCACCCATTTAATCAACAATGGTAAACTACCAAAT
1 CCATTTAATCAACAATGGCAAACTACCAAATTA-CCATTTAATCAACAATGGTAAGCTACCAAAT
2931800 CA-
65 CAC
2931802 CCATTTAATCAACAAT
1 CCATTTAATCAACAAT
2931818 TCTCCCACTT
Statistics
Matches: 131, Mismatches: 18, Indels: 5
0.85 0.12 0.03
Matches are distributed among these distances:
67 17 0.13
68 113 0.86
69 1 0.01
ACGTcount: A:0.41, C:0.26, G:0.08, T:0.25
Consensus pattern (67 bp):
CCATTTAATCAACAATGGCAAACTACCAAATTACCATTTAATCAACAATGGTAAGCTACCAAATC
AC
Found at i:2931741 original size:102 final size:101
Alignment explanation
Indices: 2931597--2931817 Score: 343
Period size: 102 Copynumber: 2.2 Consensus size: 101
2931587 TGGTAAAAAC
* *
2931597 CACCATTTAATCAACAATGGCAACCTACCAAATCTACCATTTAGTCAACAATGGTAAGCCACAAA
1 CACCATTTAATCAACAATGGCAACCTACCAAATCTACCATTTAGTCAACAATGGCAAACCACAAA
* *
2931662 ATCACCCATTTAATCAATAATGGTAAGCTACCAAAT
66 ATCACCCATTTAATCAACAATGGTAAACTACCAAAT
** * * * *
2931698 TTCTCATTTAATCAACAATGGTAAGCTACCAAATCTCCCATTTAGTCAACAATGGCAAACCACCA
1 CAC-CATTTAATCAACAATGGCAACCTACCAAATCTACCATTTAGTCAACAATGGCAAACCACAA
2931763 AATCACCCATTTAATCAACAATGGTAAACTACCAAAT
65 AATCACCCATTTAATCAACAATGGTAAACTACCAAAT
2931800 CACCATTTAATCAACAAT
1 CACCATTTAATCAACAAT
2931818 TCTCCCACTT
Statistics
Matches: 107, Mismatches: 12, Indels: 2
0.88 0.10 0.02
Matches are distributed among these distances:
101 16 0.15
102 91 0.85
ACGTcount: A:0.41, C:0.26, G:0.08, T:0.25
Consensus pattern (101 bp):
CACCATTTAATCAACAATGGCAACCTACCAAATCTACCATTTAGTCAACAATGGCAAACCACAAA
ATCACCCATTTAATCAACAATGGTAAACTACCAAAT
Found at i:2932928 original size:6 final size:6
Alignment explanation
Indices: 2932917--2932941 Score: 50
Period size: 6 Copynumber: 4.2 Consensus size: 6
2932907 GCATATATAC
2932917 TAATAT TAATAT TAATAT TAATAT T
1 TAATAT TAATAT TAATAT TAATAT T
2932942 GAGCTGGTTA
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:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (6 bp):
TAATAT
Found at i:2934818 original size:23 final size:25
Alignment explanation
Indices: 2934787--2934833 Score: 71
Period size: 23 Copynumber: 2.0 Consensus size: 25
2934777 TATACCATAC
*
2934787 ATAAGACTTGCTATAAA-GACAATG
1 ATAAGACTTGCCATAAATGACAATG
2934811 ATAA-ACTTGCCATAAATGACAAT
1 ATAAGACTTGCCATAAATGACAAT
2934834 CTTTTCAAAA
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
23 11 0.52
24 10 0.48
ACGTcount: A:0.47, C:0.15, G:0.13, T:0.26
Consensus pattern (25 bp):
ATAAGACTTGCCATAAATGACAATG
Found at i:2936050 original size:65 final size:65
Alignment explanation
Indices: 2935919--2936040 Score: 151
Period size: 65 Copynumber: 1.9 Consensus size: 65
2935909 AGATTTGAAG
* * *
2935919 AACTTAAATATTAAATTTAATTGATTAAAATCTAAAATAATTCAAATTCAGAATGATACTAATTT
1 AACTTAAATATTAAACTCAATTAATTAAAATCTAAAATAATTCAAATTCAGAATGATACTAATTT
* *
2935984 AACTTAAATTTTAAACTCAATTAATTCAAAAT-TAAAGTGAA-TCAAATTC-GAAATGAT
1 AACTTAAATATTAAACTCAATTAATT-AAAATCTAAAAT-AATTCAAATTCAG-AATGAT
2936041 TTAAATTTAA
Statistics
Matches: 49, Mismatches: 5, Indels: 6
0.82 0.08 0.10
Matches are distributed among these distances:
64 1 0.02
65 41 0.84
66 7 0.14
ACGTcount: A:0.49, C:0.09, G:0.06, T:0.36
Consensus pattern (65 bp):
AACTTAAATATTAAACTCAATTAATTAAAATCTAAAATAATTCAAATTCAGAATGATACTAATTT
Found at i:2936056 original size:17 final size:18
Alignment explanation
Indices: 2936034--2936073 Score: 64
Period size: 19 Copynumber: 2.2 Consensus size: 18
2936024 ATCAAATTCG
2936034 AAATGATTT-AAATTTAA
1 AAATGATTTAAAATTTAA
2936051 AAATGATTTAAAAATTTAA
1 AAATGATTT-AAAATTTAA
2936070 AAAT
1 AAAT
2936074 TAATATAACT
Statistics
Matches: 21, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
17 9 0.43
19 12 0.57
ACGTcount: A:0.57, C:0.00, G:0.05, T:0.38
Consensus pattern (18 bp):
AAATGATTTAAAATTTAA
Found at i:2936166 original size:17 final size:16
Alignment explanation
Indices: 2936146--2936189 Score: 52
Period size: 17 Copynumber: 2.6 Consensus size: 16
2936136 GCTAAAATAA
2936146 AAAAAAAACATTAAAAG
1 AAAAAAAA-ATTAAAAG
*
2936163 AAAAAGGAAATTAAAAG
1 AAAAA-AAAATTAAAAG
2936180 AAACAAAAAA
1 AAA-AAAAAA
2936190 AAACATTAAC
Statistics
Matches: 23, Mismatches: 2, Indels: 4
0.79 0.07 0.14
Matches are distributed among these distances:
17 19 0.83
18 4 0.17
ACGTcount: A:0.77, C:0.05, G:0.09, T:0.09
Consensus pattern (16 bp):
AAAAAAAAATTAAAAG
Found at i:2937953 original size:97 final size:97
Alignment explanation
Indices: 2937793--2937976 Score: 287
Period size: 97 Copynumber: 1.9 Consensus size: 97
2937783 CAAAATTCCC
* * *
2937793 CAGCATTCAAGTGGAATTCAGAAGTAATTCTCCTTCGTAAAGAAAATAGGTAATAATCCCTTGAA
1 CAGCATTAAAGTGGAATTCAGAAGTAATTCTCCTTCATAAAGAAAATACGTAATAATCCCTTGAA
*
2937858 TTTGAGATGGAGCATCCTTCGTCTAAATTTCT
66 TTTCAGATGGAGCATCCTTCGTCTAAATTTCT
* * * * *
2937890 CAGCATTAAAGTGGAATTCAGAAGTAATTCTCCTTTATAAAGAAATTCCTTAATAATCTCTTGAA
1 CAGCATTAAAGTGGAATTCAGAAGTAATTCTCCTTCATAAAGAAAATACGTAATAATCCCTTGAA
2937955 TTTCAGATGGAGCATCCTTCGT
66 TTTCAGATGGAGCATCCTTCGT
2937977 AGAAAATGAT
Statistics
Matches: 78, Mismatches: 9, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
97 78 1.00
ACGTcount: A:0.33, C:0.17, G:0.16, T:0.33
Consensus pattern (97 bp):
CAGCATTAAAGTGGAATTCAGAAGTAATTCTCCTTCATAAAGAAAATACGTAATAATCCCTTGAA
TTTCAGATGGAGCATCCTTCGTCTAAATTTCT
Found at i:2938425 original size:22 final size:22
Alignment explanation
Indices: 2938400--2938441 Score: 68
Period size: 22 Copynumber: 1.9 Consensus size: 22
2938390 TATTTTTATT
2938400 TAAAT-TTAATTATAAAAATATA
1 TAAATATTAA-TATAAAAATATA
2938422 TAAATATTAATATAAAAATA
1 TAAATATTAATATAAAAATA
2938442 ATTTTTATTT
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
22 15 0.79
23 4 0.21
ACGTcount: A:0.62, C:0.00, G:0.00, T:0.38
Consensus pattern (22 bp):
TAAATATTAATATAAAAATATA
Found at i:2938658 original size:23 final size:23
Alignment explanation
Indices: 2938631--2938695 Score: 80
Period size: 23 Copynumber: 2.8 Consensus size: 23
2938621 GCTTGAATTA
2938631 ATTAATAATAATAAATATTTAAAT
1 ATTAAT-ATAATAAATATTTAAAT
*
2938655 -TTAATTATAA-AAATATATAAAT
1 ATTAA-TATAATAAATATTTAAAT
*
2938677 ATTAATATAATAATTATTT
1 ATTAATATAATAAATATTT
2938696 TTAAAATAAT
Statistics
Matches: 35, Mismatches: 3, Indels: 7
0.78 0.07 0.16
Matches are distributed among these distances:
22 16 0.46
23 18 0.51
24 1 0.03
ACGTcount: A:0.55, C:0.00, G:0.00, T:0.45
Consensus pattern (23 bp):
ATTAATATAATAAATATTTAAAT
Found at i:2940513 original size:79 final size:78
Alignment explanation
Indices: 2940346--2940760 Score: 417
Period size: 79 Copynumber: 5.2 Consensus size: 78
2940336 TGAAGATAAC
* * * ** *
2940346 AACGGGATTGGAGTATCCTCGATTATGAAAAATCGATGTTCTGGAAATAAAAATCAGGGTTAGAG
1 AACGGGGTTGGAGTATCC-CGATTATGAAAAATCGATGTTTTAGAAAT-AAAATTGGGGTTGGAG
*
2940411 TATCCCCTCGGAAAT
64 TATCCCCTCGAAAAT
* * *
2940426 AACAGGGTTGGAGTATTCCCGATTAT-AGAAAATCGGTGTTTTAAAAATAAAATTGGGGTTGGAG
1 AACGGGGTTGGAGTA-TCCCGATTATGA-AAAATCGATGTTTTAGAAATAAAATTGGGGTTGGAG
*
2940490 TATCCCCTCAAAAAT
64 TATCCCCTCGAAAAT
* ****
2940505 AACGGGGTTGGAGTATCCTCGATTGTGAAAAATCGATGTTTTAGAAATAAGGCCGGGGTTGGAGT
1 AACGGGGTTGGAGTATCC-CGATTATGAAAAATCGATGTTTTAGAAATAAAATTGGGGTTGGAGT
*
2940570 ATCCCCGCGAAAAT
65 ATCCCCTCGAAAAT
* * * * * *
2940584 AACAGAGTTGGAGTATCCCTGA-TAGTGAAAAATCAATATTTTAGAAATAAAGTCT-GGGTTGGG
1 AACGGGGTTGGAGTATCCC-GATTA-TGAAAAATCGATGTTTTAGAAATAAAAT-TGGGGTTGGA
* *
2940647 GTATCCTCTCGGAAAT
63 GTATCCCCTCGAAAAT
* * * * *
2940663 AACGGGGTTGGAGTATCCCTGATTGTGAGAAATC-AGTGTTTT-GAAAAAAAACCTGGGGTTAGA
1 AACGGGGTTGGAGTATCCC-GATTATGAAAAATCGA-TGTTTTAGAAATAAAA-TTGGGGTTGGA
*
2940726 GTATCTCCTCGAAAAT
63 GTATCCCCTCGAAAAT
2940742 AACGGGGTTGGAGTATCCC
1 AACGGGGTTGGAGTATCCC
2940761 CGATGAAATA
Statistics
Matches: 278, Mismatches: 46, Indels: 23
0.80 0.13 0.07
Matches are distributed among these distances:
78 14 0.05
79 223 0.80
80 38 0.14
81 3 0.01
ACGTcount: A:0.33, C:0.14, G:0.26, T:0.27
Consensus pattern (78 bp):
AACGGGGTTGGAGTATCCCGATTATGAAAAATCGATGTTTTAGAAATAAAATTGGGGTTGGAGTA
TCCCCTCGAAAAT
Found at i:2940643 original size:158 final size:156
Alignment explanation
Indices: 2940346--2940760 Score: 480
Period size: 158 Copynumber: 2.6 Consensus size: 156
2940336 TGAAGATAAC
* * * * *
2940346 AACGGGATTGGAGTATCCTCGATTATGAAAAATCGATGTTCTGGAAATAAAAATCAGGGTTAGAG
1 AACGGGGTTGGAGTATCCTCGATTGTGAAAAATCGATGTT-TTGAAAT-AAAACCGGGGTTAGAG
* ** *
2940411 TATCCCCTCGGAAATAACAGGGTTGGAGTATTCCCGATTATAGAAAATCGGTGTTTTAAAAATAA
64 TATCCCCTCGAAAATAACAGGGTTGGAGTA-TCCCGATTATAGAAAATCAATATTTTAAAAATAA
2940476 AATTGGGGTTGGAGTATCCCCTCAAAAAT
128 AATTGGGGTTGGAGTATCCCCTCAAAAAT
** *
2940505 AACGGGGTTGGAGTATCCTCGATTGTGAAAAATCGATGTTTTAGAAATAAGGCCGGGGTTGGAGT
1 AACGGGGTTGGAGTATCCTCGATTGTGAAAAATCGATGTTTT-GAAATAAAACCGGGGTTAGAGT
* * *
2940570 ATCCCCGCGAAAATAACAGAGTTGGAGTATCCCTGA-TAGT-GAAAAATCAATATTTTAGAAATA
65 ATCCCCTCGAAAATAACAGGGTTGGAGTATCCC-GATTA-TAG-AAAATCAATATTTTAAAAATA
* * * **
2940633 AAGTCT-GGGTTGGGGTATCCTCTCGGAAAT
127 AAAT-TGGGGTTGGAGTATCCCCTCAAAAAT
* *
2940663 AACGGGGTTGGAGTATCC-CTGATTGTGAGAAATC-AGTGTTTTGAAAAAAAACCTGGGGTTAGA
1 AACGGGGTTGGAGTATCCTC-GATTGTGAAAAATCGA-TGTTTTGAAATAAAACC-GGGGTTAGA
* *
2940726 GTATCTCCTCGAAAATAACGGGGTTGGAGTATCCC
63 GTATCCCCTCGAAAATAACAGGGTTGGAGTATCCC
2940761 CGATGAAATA
Statistics
Matches: 219, Mismatches: 29, Indels: 17
0.83 0.11 0.06
Matches are distributed among these distances:
157 17 0.08
158 158 0.72
159 44 0.20
ACGTcount: A:0.33, C:0.14, G:0.26, T:0.27
Consensus pattern (156 bp):
AACGGGGTTGGAGTATCCTCGATTGTGAAAAATCGATGTTTTGAAATAAAACCGGGGTTAGAGTA
TCCCCTCGAAAATAACAGGGTTGGAGTATCCCGATTATAGAAAATCAATATTTTAAAAATAAAAT
TGGGGTTGGAGTATCCCCTCAAAAAT
Found at i:2940769 original size:28 final size:27
Alignment explanation
Indices: 2940717--2940792 Score: 91
Period size: 28 Copynumber: 2.7 Consensus size: 27
2940707 AAAAAAACCT
*
2940717 GGGGTTAGAGTATCTCCTCGA-AAATAAC
1 GGGGTTGGAGTATC-CC-CGATAAATAAC
2940745 GGGGTTGGAGTATCCCCGATGAAATAAC
1 GGGGTTGGAGTATCCCCGAT-AAATAAC
* *
2940773 AGGGTTGAAGTATCCCCGAT
1 GGGGTTGGAGTATCCCCGAT
2940793 TGTGAAAAAT
Statistics
Matches: 43, Mismatches: 3, Indels: 4
0.86 0.06 0.08
Matches are distributed among these distances:
26 3 0.07
27 2 0.05
28 38 0.88
ACGTcount: A:0.29, C:0.18, G:0.29, T:0.24
Consensus pattern (27 bp):
GGGGTTGGAGTATCCCCGATAAATAAC
Found at i:2940984 original size:78 final size:78
Alignment explanation
Indices: 2940822--2941036 Score: 272
Period size: 78 Copynumber: 2.8 Consensus size: 78
2940812 GGAGGAGTTA
* * **
2940822 GAGTATCCCTGATTGTGGAAAATTGATGTTTTAGAAAT-AAA-CTGGGTTGAAGTATCCCCTCGA
1 GAGTATCCCCGATTGTGGAAAATTGATGTTTTAGAAATAAAATCGGGGTTG-AGTATCCCCTAAA
2940885 AAATAACAGGGTTG
65 AAATAACAGGGTTG
*
2940899 GAGTATCCCCGATTGTGAAAAATTGATGTTTTAGAAATAAAATCGGGGTTGAGTATCCCCTAAAA
1 GAGTATCCCCGATTGTGGAAAATTGATGTTTTAGAAATAAAATCGGGGTTGAGTATCCCCTAAAA
*
2940964 AATAACGGGGTTG
66 AATAACAGGGTTG
* * * * * * * *
2940977 GAGTATCCCCAATTATGGAGAATCGCTATTTTGGAAATAAAATTGGGGTTGGAGTATCCC
1 GAGTATCCCCGATTGTGGAAAATTGATGTTTTAGAAATAAAATCGGGGTT-GAGTATCCC
2941037 GGAGATGAAA
Statistics
Matches: 120, Mismatches: 15, Indels: 4
0.86 0.11 0.03
Matches are distributed among these distances:
77 36 0.30
78 68 0.57
79 16 0.13
ACGTcount: A:0.33, C:0.13, G:0.25, T:0.29
Consensus pattern (78 bp):
GAGTATCCCCGATTGTGGAAAATTGATGTTTTAGAAATAAAATCGGGGTTGAGTATCCCCTAAAA
AATAACAGGGTTG
Found at i:2943377 original size:20 final size:20
Alignment explanation
Indices: 2943352--2943475 Score: 122
Period size: 20 Copynumber: 5.8 Consensus size: 20
2943342 TAAAACCCAA
*
2943352 AATGTATTGATACAATGAAC
1 AATGTATCGATACAATGAAC
*
2943372 AATGTATTGATACAATGAAC
1 AATGTATCGATACAATGAAC
* *
2943392 AACGTATCGATACATCAGGGTAAACCC
1 AATGTATCGATACA--A---TGAA--C
2943419 AAAATGTATCGATACAATGAAC
1 --AATGTATCGATACAATGAAC
*
2943441 AATGTATCGATACAATGAAT
1 AATGTATCGATACAATGAAC
2943461 AATGTATCGATACAA
1 AATGTATCGATACAA
2943476 ATTGTGAAAA
Statistics
Matches: 89, Mismatches: 6, Indels: 18
0.79 0.05 0.16
Matches are distributed among these distances:
20 66 0.74
22 2 0.02
24 3 0.03
25 3 0.03
27 2 0.02
29 13 0.15
ACGTcount: A:0.44, C:0.15, G:0.15, T:0.26
Consensus pattern (20 bp):
AATGTATCGATACAATGAAC
Found at i:2943442 original size:69 final size:70
Alignment explanation
Indices: 2943306--2943474 Score: 254
Period size: 69 Copynumber: 2.4 Consensus size: 70
2943296 TGCCTGAATA
*
2943306 TATTGATAC-ATCGAAAAATGTATCGATACATCTAGGTAAAACCCAAAATGTATTGATACAATGA
1 TATTGATACAAT-GAAAAATGTATCGATACATCTAGGTAAAACCCAAAATGTATCGATACAATGA
2943370 ACAATG
65 ACAATG
* *
2943376 TATTGATACAATGAACAACGTATCGATACATC-AGGGT-AAACCCAAAATGTATCGATACAATGA
1 TATTGATACAATGAAAAATGTATCGATACATCTA-GGTAAAACCCAAAATGTATCGATACAATGA
2943439 ACAATG
65 ACAATG
* *
2943445 TATCGATACAATGAATAATGTATCGATACA
1 TATTGATACAATGAAAAATGTATCGATACA
2943475 AATTGTGAAA
Statistics
Matches: 91, Mismatches: 6, Indels: 5
0.89 0.06 0.05
Matches are distributed among these distances:
69 59 0.65
70 30 0.33
71 2 0.02
ACGTcount: A:0.44, C:0.15, G:0.15, T:0.26
Consensus pattern (70 bp):
TATTGATACAATGAAAAATGTATCGATACATCTAGGTAAAACCCAAAATGTATCGATACAATGAA
CAATG
Found at i:2943919 original size:140 final size:141
Alignment explanation
Indices: 2943734--2944030 Score: 411
Period size: 140 Copynumber: 2.1 Consensus size: 141
2943724 GGTGTCTACA
* * * * * *
2943734 GAAATGATTTGATAATATTATATTTTTTTGTAAGTCAAATTAAAAGGCGAAGTTCCAAAAGAAAG
1 GAAATGATTTGATAATATTATATTTTTTTGTAAGTAAAATAAAAAGACAAAATTACAAAAGAAA-
* * *
2943799 A-TAATAGATAATCTTATAAATACATAAACTTGATTCTAATATCTCTCA-TTTGTTTTAGTCTTA
65 ATTAATAAATAATATTATAAATACATAAACTTGACTCTAATATCTCTCATTTTGTTTTAGTCTTA
*
2943862 TCATTTCAATTT
130 TCATTTCAAATT
*
2943874 GAAATGATTTGATAATATTATA-TTTTTTGTAAGTTAAAATAAAAAGATAAAATTACAAAAGAAA
1 GAAATGATTTGATAATATTATATTTTTTTGTAAG-TAAAATAAAAAGACAAAATTACAAAAGAAA
*
2943938 ATTAATAAATAATATTATAAATACATAAATTTGACTCTAATATCTCTCATTTGTTTGTTTTAGTC
65 ATTAATAAATAATATTATAAATACATAAACTTGACTCTAATATCTCTCA--T-TTTGTTTTAGTC
2944003 TTATCATTTCAAATT
127 TTATCATTTCAAATT
*
2944018 GAAATGAATTGAT
1 GAAATGATTTGAT
2944031 TTTATACAAA
Statistics
Matches: 138, Mismatches: 13, Indels: 8
0.87 0.08 0.05
Matches are distributed among these distances:
139 12 0.09
140 88 0.64
144 38 0.28
ACGTcount: A:0.41, C:0.08, G:0.10, T:0.41
Consensus pattern (141 bp):
GAAATGATTTGATAATATTATATTTTTTTGTAAGTAAAATAAAAAGACAAAATTACAAAAGAAAA
TTAATAAATAATATTATAAATACATAAACTTGACTCTAATATCTCTCATTTTGTTTTAGTCTTAT
CATTTCAAATT
Found at i:2944202 original size:15 final size:15
Alignment explanation
Indices: 2944182--2944210 Score: 58
Period size: 15 Copynumber: 1.9 Consensus size: 15
2944172 TTTCATGCAA
2944182 AAACTTCACAAAATC
1 AAACTTCACAAAATC
2944197 AAACTTCACAAAAT
1 AAACTTCACAAAAT
2944211 TTATGACATT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.55, C:0.24, G:0.00, T:0.21
Consensus pattern (15 bp):
AAACTTCACAAAATC
Found at i:2944778 original size:25 final size:25
Alignment explanation
Indices: 2944744--2944791 Score: 87
Period size: 25 Copynumber: 1.9 Consensus size: 25
2944734 GTAATTTACC
*
2944744 TTTATATATATATATATATGTAAAT
1 TTTAAATATATATATATATGTAAAT
2944769 TTTAAATATATATATATATGTAA
1 TTTAAATATATATATATATGTAA
2944792 TATAATTCAT
Statistics
Matches: 22, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
25 22 1.00
ACGTcount: A:0.46, C:0.00, G:0.04, T:0.50
Consensus pattern (25 bp):
TTTAAATATATATATATATGTAAAT
Found at i:2947819 original size:23 final size:21
Alignment explanation
Indices: 2947784--2947845 Score: 61
Period size: 23 Copynumber: 2.8 Consensus size: 21
2947774 AATAGGGAGG
*
2947784 GAAATGAATGAAAAAATAACAAA
1 GAAA-GAAAGAAAAAA-AACAAA
* *
2947807 GAAAGAGAAGAAAAGAAAAGAGA
1 GAAAGA-AAGAAAA-AAAACAAA
2947830 GAAAGAAAGAAAAAAA
1 GAAAGAAAGAAAAAAA
2947846 TTCTTATTTT
Statistics
Matches: 34, Mismatches: 3, Indels: 6
0.79 0.07 0.14
Matches are distributed among these distances:
21 3 0.09
22 9 0.26
23 20 0.59
24 2 0.06
ACGTcount: A:0.73, C:0.02, G:0.21, T:0.05
Consensus pattern (21 bp):
GAAAGAAAGAAAAAAAACAAA
Found at i:2947832 original size:17 final size:17
Alignment explanation
Indices: 2947804--2947842 Score: 51
Period size: 17 Copynumber: 2.2 Consensus size: 17
2947794 AAAAAATAAC
*
2947804 AAAGAAAGAGAAGAAAAGA
1 AAAGAGAGA-AAG-AAAGA
2947823 AAAGAGAGAAAGAAAGA
1 AAAGAGAGAAAGAAAGA
2947840 AAA
1 AAA
2947843 AAATTCTTAT
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
17 8 0.42
18 3 0.16
19 8 0.42
ACGTcount: A:0.74, C:0.00, G:0.26, T:0.00
Consensus pattern (17 bp):
AAAGAGAGAAAGAAAGA
Found at i:2948145 original size:21 final size:22
Alignment explanation
Indices: 2948121--2948161 Score: 57
Period size: 21 Copynumber: 1.9 Consensus size: 22
2948111 TTTTCCAGCC
*
2948121 ATGTCATTTTA-ACTATTTTCT
1 ATGTAATTTTATACTATTTTCT
*
2948142 ATGTAATTTTATATTATTTT
1 ATGTAATTTTATACTATTTT
2948162 TCAGTTCATT
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
21 10 0.59
22 7 0.41
ACGTcount: A:0.27, C:0.07, G:0.05, T:0.61
Consensus pattern (22 bp):
ATGTAATTTTATACTATTTTCT
Found at i:2948740 original size:12 final size:13
Alignment explanation
Indices: 2948727--2948775 Score: 57
Period size: 12 Copynumber: 3.8 Consensus size: 13
2948717 CTGACATATT
2948727 AATTTAAAATTTA
1 AATTTAAAATTTA
*
2948740 AATTT-AATTTTA
1 AATTTAAAATTTA
*
2948752 AATAATAAAATTT-
1 AAT-TTAAAATTTA
2948765 AATTTAAAATT
1 AATTTAAAATT
2948776 ATTTTTTATT
Statistics
Matches: 30, Mismatches: 4, Indels: 5
0.77 0.10 0.13
Matches are distributed among these distances:
12 16 0.53
13 9 0.30
14 5 0.17
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (13 bp):
AATTTAAAATTTA
Found at i:2950364 original size:2 final size:2
Alignment explanation
Indices: 2950357--2950392 Score: 72
Period size: 2 Copynumber: 18.0 Consensus size: 2
2950347 GGCTTGTTTG
2950357 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
2950393 GTACTAATCA
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 34 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:2951555 original size:13 final size:13
Alignment explanation
Indices: 2951519--2951581 Score: 50
Period size: 13 Copynumber: 5.3 Consensus size: 13
2951509 ATATAACATG
2951519 AATAAAATATAAA
1 AATAAAATATAAA
2951532 AAT--AAT-T-AA
1 AATAAAATATAAA
2951541 AATAAAATATAAA
1 AATAAAATATAAA
*
2951554 AA-ATTAATAT--A
1 AATA-AAATATAAA
*
2951565 AATAGAATATAAA
1 AATAAAATATAAA
2951578 AATA
1 AATA
2951582 TTAATATTTA
Statistics
Matches: 40, Mismatches: 2, Indels: 16
0.69 0.03 0.28
Matches are distributed among these distances:
9 5 0.12
10 1 0.03
11 14 0.35
12 3 0.08
13 17 0.43
ACGTcount: A:0.71, C:0.00, G:0.02, T:0.27
Consensus pattern (13 bp):
AATAAAATATAAA
Found at i:2951560 original size:20 final size:22
Alignment explanation
Indices: 2951519--2951585 Score: 84
Period size: 22 Copynumber: 3.0 Consensus size: 22
2951509 ATATAACATG
2951519 AATAAAATATAAAAATAATTAA
1 AATAAAATATAAAAATAATTAA
2951541 AATAAAATATAAAAAATTAA-TATA
1 AATAAAATAT-AAAAA-TAATTA-A
*
2951565 AATAGAATATAAAAAT-ATTAA
1 AATAAAATATAAAAATAATTAA
2951586 TATTTATATA
Statistics
Matches: 40, Mismatches: 1, Indels: 9
0.80 0.02 0.18
Matches are distributed among these distances:
21 2 0.05
22 13 0.32
23 12 0.30
24 13 0.32
ACGTcount: A:0.70, C:0.00, G:0.01, T:0.28
Consensus pattern (22 bp):
AATAAAATATAAAAATAATTAA
Found at i:2951600 original size:24 final size:25
Alignment explanation
Indices: 2951519--2951613 Score: 92
Period size: 24 Copynumber: 4.0 Consensus size: 25
2951509 ATATAACATG
* *
2951519 AATAAAATATAAAAATA--ATTA-A
1 AATAGAATATAAAAATATTAATATA
*
2951541 AATAAAATATAAAAA-ATTAATATA
1 AATAGAATATAAAAATATTAATATA
*
2951565 AATAGAATATAAAAATATTAATATT
1 AATAGAATATAAAAATATTAATATA
* * *
2951590 TATATAA-ATAAAATTATTAATATA
1 AATAGAATATAAAAATATTAATATA
2951614 TAAAAATTTA
Statistics
Matches: 62, Mismatches: 7, Indels: 6
0.83 0.09 0.08
Matches are distributed among these distances:
21 1 0.02
22 15 0.24
23 3 0.05
24 30 0.48
25 13 0.21
ACGTcount: A:0.65, C:0.00, G:0.01, T:0.34
Consensus pattern (25 bp):
AATAGAATATAAAAATATTAATATA
Found at i:2951627 original size:32 final size:31
Alignment explanation
Indices: 2951533--2951631 Score: 112
Period size: 32 Copynumber: 3.2 Consensus size: 31
2951523 AAATATAAAA
* *
2951533 ATAATTAAAATA-AAATATA-AAAAATTAAT
1 ATAAATAAAATATAAATATATAAAAATTTAT
* * * *
2951562 ATAAATAGAATATAAAAATATTAATATTTAT
1 ATAAATAAAATATAAATATATAAAAATTTAT
*
2951593 ATAAATAAAATTATTAATATATAAAAATTTAT
1 ATAAATAAAA-TATAAATATATAAAAATTTAT
2951625 ATAAATA
1 ATAAATA
2951632 TATAAAATTT
Statistics
Matches: 56, Mismatches: 11, Indels: 3
0.80 0.16 0.04
Matches are distributed among these distances:
29 10 0.18
30 6 0.11
31 16 0.29
32 24 0.43
ACGTcount: A:0.63, C:0.00, G:0.01, T:0.36
Consensus pattern (31 bp):
ATAAATAAAATATAAATATATAAAAATTTAT
Found at i:2951634 original size:22 final size:21
Alignment explanation
Indices: 2951520--2951671 Score: 77
Period size: 20 Copynumber: 7.3 Consensus size: 21
2951510 TATAACATGA
* * *
2951520 ATAAAATATAAAAATAATTAAA
1 ATAAAATATATAAA-AATTTAT
*
2951542 ATAAAATATA-AAAAATTAAT
1 ATAAAATATATAAAAATTTAT
*
2951562 ATAAATAGAATATAAAAATATTA-
1 ATAAA-A-TATATAAAAAT-TTAT
** *
2951585 AT-ATTTATATAAATAAAATTAT
1 ATAAAATATAT-AA-AAATTTAT
2951607 -T--AATATATAAAAATTTAT
1 ATAAAATATATAAAAATTTAT
* *
2951625 AT-AAATATATAAAATTTTAA
1 ATAAAATATATAAAAATTTAT
* *
2951645 ATATAAT-TATAAAAAAATTAT
1 ATAAAATATAT-AAAAATTTAT
2951666 ATAAAA
1 ATAAAA
2951672 ATTATATATA
Statistics
Matches: 102, Mismatches: 17, Indels: 23
0.72 0.12 0.16
Matches are distributed among these distances:
18 7 0.07
19 3 0.03
20 40 0.39
21 25 0.25
22 17 0.17
23 8 0.08
24 2 0.02
ACGTcount: A:0.64, C:0.00, G:0.01, T:0.36
Consensus pattern (21 bp):
ATAAAATATATAAAAATTTAT
Found at i:2951665 original size:11 final size:11
Alignment explanation
Indices: 2951635--2951677 Score: 50
Period size: 11 Copynumber: 3.8 Consensus size: 11
2951625 ATAAATATAT
*
2951635 AAAATTTTAAA
1 AAAATTATAAA
*
2951646 TATAATTATAAA
1 -AAAATTATAAA
*
2951658 AAAATTATATA
1 AAAATTATAAA
2951669 AAAATTATA
1 AAAATTATA
2951678 TATATATATA
Statistics
Matches: 27, Mismatches: 4, Indels: 1
0.84 0.12 0.03
Matches are distributed among these distances:
11 18 0.67
12 9 0.33
ACGTcount: A:0.63, C:0.00, G:0.00, T:0.37
Consensus pattern (11 bp):
AAAATTATAAA
Found at i:2952093 original size:12 final size:11
Alignment explanation
Indices: 2952061--2952117 Score: 66
Period size: 12 Copynumber: 5.3 Consensus size: 11
2952051 TGAGACACAT
2952061 ATATAA-TAAA
1 ATATAATTAAA
2952071 A-ATAATTAAA
1 ATATAATTAAA
2952081 ATATAATTTAAA
1 ATATAA-TTAAA
*
2952093 ATATAA-TATA
1 ATATAATTAAA
2952103 ATATAATATAAA
1 ATATAAT-TAAA
2952115 ATA
1 ATA
2952118 ATATATAAAT
Statistics
Matches: 40, Mismatches: 2, Indels: 8
0.80 0.04 0.16
Matches are distributed among these distances:
9 4 0.10
10 15 0.38
11 4 0.10
12 17 0.43
ACGTcount: A:0.65, C:0.00, G:0.00, T:0.35
Consensus pattern (11 bp):
ATATAATTAAA
Found at i:2952102 original size:5 final size:5
Alignment explanation
Indices: 2952061--2952130 Score: 56
Period size: 5 Copynumber: 14.0 Consensus size: 5
2952051 TGAGACACAT
* * *
2952061 ATATA ATA-A AAATA ATTAAA ATATA ATTTAAA ATATA ATATA ATATA
1 ATATA ATATA ATATA A-TATA ATATA A--TATA ATATA ATATA ATATA
*
2952108 ATATA AAATA ATAT- ATA-A ATATA
1 ATATA ATATA ATATA ATATA ATATA
2952131 TAAATTTATT
Statistics
Matches: 51, Mismatches: 8, Indels: 12
0.72 0.11 0.17
Matches are distributed among these distances:
4 9 0.18
5 35 0.69
6 3 0.06
7 4 0.08
ACGTcount: A:0.64, C:0.00, G:0.00, T:0.36
Consensus pattern (5 bp):
ATATA
Found at i:2952168 original size:22 final size:21
Alignment explanation
Indices: 2952066--2952168 Score: 79
Period size: 22 Copynumber: 4.9 Consensus size: 21
2952056 CACATATATA
* *
2952066 ATAAAAATAATTAAAATATAAT
1 ATAAAATTAATTATAAT-TAAT
*
2952088 TTAAAATATAA-TATAATATAAT
1 ATAAAAT-TAATTATAAT-TAAT
*
2952110 ATAAAA-TAATATATAAAT-AT
1 ATAAAATTAAT-TATAATTAAT
* *
2952130 ATAAATTTATTTA-AATTAAT
1 ATAAAATTAATTATAATTAAT
2952150 ATAAAATTAATTATTAATT
1 ATAAAATTAATTA-TAATT
2952169 TATTATAATT
Statistics
Matches: 64, Mismatches: 10, Indels: 14
0.73 0.11 0.16
Matches are distributed among these distances:
19 3 0.05
20 25 0.39
21 4 0.06
22 29 0.45
23 3 0.05
ACGTcount: A:0.59, C:0.00, G:0.00, T:0.41
Consensus pattern (21 bp):
ATAAAATTAATTATAATTAAT
Found at i:2952192 original size:40 final size:39
Alignment explanation
Indices: 2952098--2952193 Score: 106
Period size: 40 Copynumber: 2.4 Consensus size: 39
2952088 TTAAAATATA
2952098 ATATAATATAATATAAAATAATATATAAATATATAAATTT
1 ATATAA-ATAATATAAAATAATATATAAATATATAAATTT
* * *
2952138 ATTTAAATTAATATAAAATTAAT-TATTAATTTATTATAATTT
1 ATATAAA-TAATATAAAA-TAATATATAAATATA-TA-AATTT
2952180 ATATAAAT-ATATAA
1 ATATAAATAATATAA
2952194 TATTTTAAAT
Statistics
Matches: 48, Mismatches: 4, Indels: 8
0.80 0.07 0.13
Matches are distributed among these distances:
39 1 0.02
40 29 0.60
41 7 0.15
42 11 0.23
ACGTcount: A:0.55, C:0.00, G:0.00, T:0.45
Consensus pattern (39 bp):
ATATAAATAATATAAAATAATATATAAATATATAAATTT
Done.