Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold36
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: 4808052
ACGTcount: A:0.34, C:0.16, G:0.16, T:0.34
Warning! 18886 characters in sequence are not A, C, G, or T
File 10 of 28
Found at i:1575062 original size:78 final size:79
Alignment explanation
Indices: 1574852--1575098 Score: 336
Period size: 78 Copynumber: 3.2 Consensus size: 79
1574842 CTTCATCTCA
* * *
1574852 GGGATACTCCAACCCCGGTTTTATTTCCAAAACATCAATTTTTCATAATCGGGGATACTCCAATC
1 GGGATACTCCAACCTCGATTTTATTTCCAAAACACCAATTTTTCATAATCGGGGATACTCCAATC
*
1574917 CCGTTATTTCCGAG
66 CCGTTATTTTCGAG
* * * * * * *
1574931 GGGATAATCCAACTTCGATTTTATTCCCAAAACACCAGTTTTTCA-CATTGGGGATACTCCAACC
1 GGGATACTCCAACCTCGATTTTATTTCCAAAACACCAATTTTTCATAATCGGGGATACTCCAATC
*
1574995 CCGTCATTTTCGAG
66 CCGTTATTTTCGAG
*
1575009 GGGAT-CTCCAACCTCGATTTTATTTCCAAAATACCAATTTTTCATAATCGGGGATACTCCAATC
1 GGGATACTCCAACCTCGATTTTATTTCCAAAACACCAATTTTTCATAATCGGGGATACTCCAATC
***
1575073 CCGTTATTTTATCG
66 CCGTTATTTTCGAG
1575087 GGGATACTCCAA
1 GGGATACTCCAA
1575099 TCCCGTTATT
Statistics
Matches: 142, Mismatches: 24, Indels: 4
0.84 0.14 0.02
Matches are distributed among these distances:
77 34 0.24
78 64 0.45
79 44 0.31
ACGTcount: A:0.27, C:0.26, G:0.15, T:0.32
Consensus pattern (79 bp):
GGGATACTCCAACCTCGATTTTATTTCCAAAACACCAATTTTTCATAATCGGGGATACTCCAATC
CCGTTATTTTCGAG
Found at i:1575087 original size:28 final size:28
Alignment explanation
Indices: 1575055--1575131 Score: 118
Period size: 28 Copynumber: 2.8 Consensus size: 28
1575045 ATTTTTCATA
1575055 ATCGGGGATACTCCAATCCCGTTATTTT
1 ATCGGGGATACTCCAATCCCGTTATTTT
1575083 ATCGGGGATACTCCAATCCCGTTATTTT
1 ATCGGGGATACTCCAATCCCGTTATTTT
*** *
1575111 CGAGGGGATACTCCAACCCCG
1 ATCGGGGATACTCCAATCCCG
1575132 GCTTTATTTT
Statistics
Matches: 45, Mismatches: 4, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
28 45 1.00
ACGTcount: A:0.22, C:0.29, G:0.21, T:0.29
Consensus pattern (28 bp):
ATCGGGGATACTCCAATCCCGTTATTTT
Found at i:1575179 original size:51 final size:51
Alignment explanation
Indices: 1575113--1575233 Score: 172
Period size: 51 Copynumber: 2.4 Consensus size: 51
1575103 GTTATTTTCG
* *
1575113 AGGGGATACTCCAACCCCGGCTTTATTTTTAAAAT-ATTGATTTCTCACAAT
1 AGGGGATACTCCAACCCCGGCCTTATTTCT-AAATCATTGATTTCTCACAAT
* *
1575164 AGGGGATACTTCAACCCCGGCCTTATTTCTAAATCATTGATTTTTCACAAT
1 AGGGGATACTCCAACCCCGGCCTTATTTCTAAATCATTGATTTCTCACAAT
* *
1575215 CGGGGATAATCCAACCCCG
1 AGGGGATACTCCAACCCCG
1575234 TTATTTTCGA
Statistics
Matches: 62, Mismatches: 7, Indels: 2
0.87 0.10 0.03
Matches are distributed among these distances:
50 4 0.06
51 58 0.94
ACGTcount: A:0.28, C:0.25, G:0.16, T:0.31
Consensus pattern (51 bp):
AGGGGATACTCCAACCCCGGCCTTATTTCTAAATCATTGATTTCTCACAAT
Found at i:1575300 original size:79 final size:79
Alignment explanation
Indices: 1575202--1575390 Score: 245
Period size: 79 Copynumber: 2.4 Consensus size: 79
1575192 CTAAATCATT
* *
1575202 GATTTTTCACAATCGGGGATAATCCAACCCCGTTATTTTCGAAGGGATACTCCAACCCT-GATTT
1 GATTTTTCATAATCGGGGATACTCCAACCCCGTTATTTTCGAAGGGATACTCCAACCCTAG-TTT
* * *
1575266 TATTTTCAAAATACC
65 TATTTCCAAAACACA
* * * * * *
1575281 GATTTTTTATAATCAGGGATACTCCATCCCTGTTATTTTCGAGGGGATACTTCAACCCTAGTTTT
1 GATTTTTCATAATCGGGGATACTCCAACCCCGTTATTTTCGAAGGGATACTCCAACCCTAGTTTT
*
1575346 ATTTCCAGAACACA
66 ATTTCCAAAACACA
*
1575360 GATTTTTCATAATCGGGGATACTCCAGCCCC
1 GATTTTTCATAATCGGGGATACTCCAACCCC
1575391 ATTGTTATCT
Statistics
Matches: 93, Mismatches: 16, Indels: 2
0.84 0.14 0.02
Matches are distributed among these distances:
79 92 0.99
80 1 0.01
ACGTcount: A:0.27, C:0.24, G:0.15, T:0.34
Consensus pattern (79 bp):
GATTTTTCATAATCGGGGATACTCCAACCCCGTTATTTTCGAAGGGATACTCCAACCCTAGTTTT
ATTTCCAAAACACA
Found at i:1582047 original size:15 final size:15
Alignment explanation
Indices: 1582027--1582061 Score: 52
Period size: 15 Copynumber: 2.3 Consensus size: 15
1582017 CTAGAATATT
*
1582027 AATAATAAAAATTAA
1 AATAATAAAAATAAA
*
1582042 AATAATTAAAATAAA
1 AATAATAAAAATAAA
1582057 AATAA
1 AATAA
1582062 ATAATTTATT
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
15 18 1.00
ACGTcount: A:0.74, C:0.00, G:0.00, T:0.26
Consensus pattern (15 bp):
AATAATAAAAATAAA
Found at i:1582067 original size:19 final size:22
Alignment explanation
Indices: 1582024--1582067 Score: 67
Period size: 19 Copynumber: 2.1 Consensus size: 22
1582014 ATTCTAGAAT
1582024 ATTAATAATAAAAATTAAAATA
1 ATTAATAATAAAAATTAAAATA
1582046 ATTAA-AATAAAAA-T-AAATA
1 ATTAATAATAAAAATTAAAATA
1582065 ATT
1 ATT
1582068 TATTAAAAAT
Statistics
Matches: 22, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
19 8 0.36
20 1 0.05
21 8 0.36
22 5 0.23
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.32
Consensus pattern (22 bp):
ATTAATAATAAAAATTAAAATA
Found at i:1582097 original size:20 final size:18
Alignment explanation
Indices: 1582053--1582161 Score: 78
Period size: 18 Copynumber: 5.7 Consensus size: 18
1582043 ATAATTAAAA
*
1582053 TAAAAATAAATAATTTAT
1 TAAAAATATATAATTTAT
1582071 TAAAAATATATAATATGTAT
1 TAAAAATATATAAT-T-TAT
*
1582091 TAGAAATATATTAAAATTTA-
1 TA-AAA-ATA-TATAATTTAT
* *
1582111 TATAGATATAT-ATTTAT
1 TAAAAATATATAATTTAT
*
1582128 TAAATAATATTATAATATTAA
1 TAAA-AATA-TATAAT-TTAT
*
1582149 AAAAAATATATAA
1 TAAAAATATATAA
1582162 ATACAATAAA
Statistics
Matches: 72, Mismatches: 9, Indels: 19
0.72 0.09 0.19
Matches are distributed among these distances:
16 5 0.07
17 5 0.07
18 19 0.26
19 10 0.14
20 13 0.18
21 11 0.15
22 4 0.06
23 5 0.07
ACGTcount: A:0.57, C:0.00, G:0.03, T:0.40
Consensus pattern (18 bp):
TAAAAATATATAATTTAT
Found at i:1582101 original size:22 final size:21
Alignment explanation
Indices: 1582068--1582124 Score: 62
Period size: 20 Copynumber: 2.7 Consensus size: 21
1582058 ATAAATAATT
* *
1582068 TATTAAAAATATA-TAATATG
1 TATTAGAAATATATTAAAATG
*
1582088 TATTAGAAATATATTAAAATT
1 TATTAGAAATATATTAAAATG
*
1582109 TATATAGATATATATT
1 TAT-TAGAAATATATT
1582125 TATTAAATAA
Statistics
Matches: 31, Mismatches: 4, Indels: 2
0.84 0.11 0.05
Matches are distributed among these distances:
20 12 0.39
21 8 0.26
22 11 0.35
ACGTcount: A:0.51, C:0.00, G:0.05, T:0.44
Consensus pattern (21 bp):
TATTAGAAATATATTAAAATG
Found at i:1582104 original size:54 final size:57
Alignment explanation
Indices: 1582037--1582145 Score: 138
Period size: 54 Copynumber: 2.0 Consensus size: 57
1582027 AATAATAAAA
1582037 ATTAAAATAATTAAAATAAAAATA-A-ATA-ATTTATTAAA-AATA-TATAATATGT
1 ATTAAAATAATTAAAATAAAAATAGATATATATTTATTAAATAATATTATAATATGT
** *
1582089 ATTAGAAATATATTAAAATTTATATAGATATATATTTATTAAATAATATTATAATAT
1 ATTA-AAATA-ATTAAAATAAAAATAGATATATATTTATTAAATAATATTATAATAT
1582146 TAAAAAAAAT
Statistics
Matches: 47, Mismatches: 3, Indels: 7
0.82 0.05 0.12
Matches are distributed among these distances:
52 4 0.09
53 5 0.11
54 12 0.26
55 1 0.02
56 3 0.06
57 10 0.21
58 4 0.09
59 8 0.17
ACGTcount: A:0.56, C:0.00, G:0.03, T:0.41
Consensus pattern (57 bp):
ATTAAAATAATTAAAATAAAAATAGATATATATTTATTAAATAATATTATAATATGT
Found at i:1583056 original size:10 final size:10
Alignment explanation
Indices: 1583031--1583081 Score: 50
Period size: 10 Copynumber: 5.1 Consensus size: 10
1583021 TAAAAATATT
1583031 TATATTTAATA
1 TATATTTAA-A
1583042 TATATTTAAA
1 TATATTTAAA
*
1583052 TATATATAAA
1 TATATTTAAA
* *
1583062 AAAATTTAAA
1 TATATTTAAA
*
1583072 AATA-TTAAA
1 TATATTTAAA
1583081 T
1 T
1583082 GTATATTTAT
Statistics
Matches: 34, Mismatches: 6, Indels: 2
0.81 0.14 0.05
Matches are distributed among these distances:
9 5 0.15
10 20 0.59
11 9 0.26
ACGTcount: A:0.57, C:0.00, G:0.00, T:0.43
Consensus pattern (10 bp):
TATATTTAAA
Found at i:1583407 original size:16 final size:17
Alignment explanation
Indices: 1583388--1583451 Score: 64
Period size: 16 Copynumber: 3.9 Consensus size: 17
1583378 AAATTTGAAA
1583388 TAATT-TAAAATAAATT
1 TAATTATAAAATAAATT
*
1583404 TAATTAATAAAA-AATTTT
1 TAATT-ATAAAATAA-ATT
1583422 TAATT-TAAAAT-AATT
1 TAATTATAAAATAAATT
*
1583437 TAATTAAAAAATAAA
1 TAATTATAAAATAAA
1583452 AAAAATGACT
Statistics
Matches: 39, Mismatches: 3, Indels: 11
0.74 0.06 0.21
Matches are distributed among these distances:
15 7 0.18
16 16 0.41
17 4 0.10
18 12 0.31
ACGTcount: A:0.59, C:0.00, G:0.00, T:0.41
Consensus pattern (17 bp):
TAATTATAAAATAAATT
Found at i:1584698 original size:2 final size:2
Alignment explanation
Indices: 1584691--1584733 Score: 86
Period size: 2 Copynumber: 21.5 Consensus size: 2
1584681 AATTAACAGC
1584691 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
1584733 A
1 A
1584734 CTGAACAAAA
Statistics
Matches: 41, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 41 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:1584867 original size:2 final size:2
Alignment explanation
Indices: 1584862--1584893 Score: 55
Period size: 2 Copynumber: 16.0 Consensus size: 2
1584852 ATATAGTACA
*
1584862 AT AT AT AT TT 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
1584894 TCAATAACAG
Statistics
Matches: 28, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
2 28 1.00
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (2 bp):
AT
Found at i:1590834 original size:19 final size:17
Alignment explanation
Indices: 1590810--1590876 Score: 55
Period size: 19 Copynumber: 3.6 Consensus size: 17
1590800 TCTATAATTA
1590810 TTAATTAAATTAATATCAT
1 TTAATTAAA-TAATAT-AT
*
1590829 TTAATT-TATAATATTAAT
1 TTAATTAAATAATA-T-AT
1590847 TTAATTAAATAATTTATAT
1 TTAATTAAATAA--TATAT
1590866 TTAATTTAAAT
1 TTAA-TTAAAT
1590877 TTTTAAAAAA
Statistics
Matches: 40, Mismatches: 3, Indels: 9
0.77 0.06 0.17
Matches are distributed among these distances:
17 5 0.12
18 10 0.25
19 16 0.40
20 7 0.17
21 2 0.05
ACGTcount: A:0.46, C:0.01, G:0.00, T:0.52
Consensus pattern (17 bp):
TTAATTAAATAATATAT
Found at i:1590868 original size:32 final size:33
Alignment explanation
Indices: 1590787--1590868 Score: 98
Period size: 32 Copynumber: 2.5 Consensus size: 33
1590777 TAAAATAATT
* *
1590787 TTAATTTAATTT-ATCTATAATTATTAATTAAA
1 TTAATATAATTTAATTTATAATTATTAATTAAA
* *
1590819 TTAATATCATTTAATTTATAA-TATTAATTTAA
1 TTAATATAATTTAATTTATAATTATTAATTAAA
1590851 TTAA-ATAATTTATATTTA
1 TTAATATAATTTA-ATTTA
1590869 ATTTAAATTT
Statistics
Matches: 43, Mismatches: 5, Indels: 4
0.83 0.10 0.08
Matches are distributed among these distances:
31 7 0.16
32 29 0.67
33 7 0.16
ACGTcount: A:0.44, C:0.02, G:0.00, T:0.54
Consensus pattern (33 bp):
TTAATATAATTTAATTTATAATTATTAATTAAA
Found at i:1590881 original size:19 final size:18
Alignment explanation
Indices: 1590827--1590882 Score: 53
Period size: 18 Copynumber: 3.1 Consensus size: 18
1590817 AATTAATATC
*
1590827 ATTTAATTTATAA-TATTA
1 ATTTAATTTA-AATTTTTA
*
1590845 ATTTAA-TTAAATAATTTA
1 ATTTAATTTAAAT-TTTTA
1590863 TATTTAATTTAAATTTTTA
1 -ATTTAATTTAAATTTTTA
1590882 A
1 A
1590883 AAAATAAAAT
Statistics
Matches: 31, Mismatches: 3, Indels: 8
0.74 0.07 0.19
Matches are distributed among these distances:
16 2 0.06
17 3 0.10
18 10 0.32
19 10 0.32
20 6 0.19
ACGTcount: A:0.45, C:0.00, G:0.00, T:0.55
Consensus pattern (18 bp):
ATTTAATTTAAATTTTTA
Found at i:1591323 original size:21 final size:20
Alignment explanation
Indices: 1591299--1591356 Score: 57
Period size: 21 Copynumber: 2.9 Consensus size: 20
1591289 AATATTAAAA
1591299 TATTATTTTTATTTTTATAT
1 TATTATTTTTATTTTTATAT
* * *
1591319 CTATTAATTATATTTATA-AT
1 -TATTATTTTTATTTTTATAT
1591339 TATT-TTATTTATTTTTAT
1 TATTATT-TTTATTTTTAT
1591357 TAATTAAATT
Statistics
Matches: 29, Mismatches: 6, Indels: 5
0.73 0.15 0.12
Matches are distributed among these distances:
18 1 0.03
19 12 0.41
20 2 0.07
21 14 0.48
ACGTcount: A:0.29, C:0.02, G:0.00, T:0.69
Consensus pattern (20 bp):
TATTATTTTTATTTTTATAT
Found at i:1592170 original size:22 final size:22
Alignment explanation
Indices: 1592129--1592170 Score: 59
Period size: 22 Copynumber: 1.9 Consensus size: 22
1592119 AATTATGATT
*
1592129 ATAAATTATTTTATTTTAAAGA
1 ATAAATTATTTTATTATAAAGA
1592151 ATAAATTTATTTT-TTATAAA
1 ATAAA-TTATTTTATTATAAA
1592171 AATTTATTTT
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
22 11 0.61
23 7 0.39
ACGTcount: A:0.45, C:0.00, G:0.02, T:0.52
Consensus pattern (22 bp):
ATAAATTATTTTATTATAAAGA
Found at i:1592188 original size:16 final size:17
Alignment explanation
Indices: 1592153--1592189 Score: 65
Period size: 17 Copynumber: 2.2 Consensus size: 17
1592143 TTTAAAGAAT
1592153 AAATTTATTTTTTATAA
1 AAATTTATTTTTTATAA
*
1592170 AAATTTATTTTTTACAA
1 AAATTTATTTTTTATAA
1592187 AAA
1 AAA
1592190 ATTGAGATTT
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
17 19 1.00
ACGTcount: A:0.46, C:0.03, G:0.00, T:0.51
Consensus pattern (17 bp):
AAATTTATTTTTTATAA
Found at i:1593176 original size:17 final size:18
Alignment explanation
Indices: 1593154--1593188 Score: 54
Period size: 17 Copynumber: 2.0 Consensus size: 18
1593144 AAAATTTTTA
1593154 TTTCTATT-TTTAAAAAT
1 TTTCTATTGTTTAAAAAT
*
1593171 TTTCTATTGTTTTAAAAT
1 TTTCTATTGTTTAAAAAT
1593189 AAATTTAAAA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
17 8 0.50
18 8 0.50
ACGTcount: A:0.31, C:0.06, G:0.03, T:0.60
Consensus pattern (18 bp):
TTTCTATTGTTTAAAAAT
Found at i:1597000 original size:32 final size:32
Alignment explanation
Indices: 1596952--1597042 Score: 128
Period size: 32 Copynumber: 2.8 Consensus size: 32
1596942 TAAAATATAA
*
1596952 TATTGATATATAAAAATTTATATAAATTAAAG
1 TATTAATATATAAAAATTTATATAAATTAAAG
* * * *
1596984 TATTAATATATTAAAATTTATATAAAATATAT
1 TATTAATATATAAAAATTTATATAAATTAAAG
*
1597016 TATTAATATATCAAAATTTATATAAAT
1 TATTAATATATAAAAATTTATATAAAT
1597043 ATATGATAAT
Statistics
Matches: 52, Mismatches: 7, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
32 52 1.00
ACGTcount: A:0.53, C:0.01, G:0.02, T:0.44
Consensus pattern (32 bp):
TATTAATATATAAAAATTTATATAAATTAAAG
Found at i:1597043 original size:20 final size:20
Alignment explanation
Indices: 1596988--1597046 Score: 59
Period size: 21 Copynumber: 2.9 Consensus size: 20
1596978 TTAAAGTATT
1596988 AATATATTA-AAATTTATATAA
1 AATATATTATAAA--TATATAA
*
1597009 AATATATTATTAATATATCAA
1 AATATATTATAAATATAT-AA
*
1597030 AATTTA-TATAAATATAT
1 AATATATTATAAATATAT
1597047 GATAATAATA
Statistics
Matches: 33, Mismatches: 3, Indels: 5
0.80 0.07 0.12
Matches are distributed among these distances:
20 15 0.45
21 16 0.48
22 2 0.06
ACGTcount: A:0.54, C:0.02, G:0.00, T:0.44
Consensus pattern (20 bp):
AATATATTATAAATATATAA
Found at i:1597681 original size:2 final size:2
Alignment explanation
Indices: 1597674--1597723 Score: 82
Period size: 2 Copynumber: 25.0 Consensus size: 2
1597664 TCTAACAGGC
**
1597674 AT AT AT AT AT AT AT AT AT GC 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
1597716 AT AT AT AT
1 AT AT AT AT
1597724 TCCCATTAGA
Statistics
Matches: 44, Mismatches: 4, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
2 44 1.00
ACGTcount: A:0.48, C:0.02, G:0.02, T:0.48
Consensus pattern (2 bp):
AT
Found at i:1599364 original size:24 final size:24
Alignment explanation
Indices: 1599332--1599378 Score: 60
Period size: 24 Copynumber: 2.0 Consensus size: 24
1599322 AATTAAAAAA
*
1599332 ATTATTTATATAAAT-AATACAAAT
1 ATTACTTAT-TAAATAAATACAAAT
*
1599356 ATTACTTATTTAATAAATACAAA
1 ATTACTTATTAAATAAATACAAA
1599379 ATAAGAGAAA
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
23 4 0.20
24 16 0.80
ACGTcount: A:0.53, C:0.06, G:0.00, T:0.40
Consensus pattern (24 bp):
ATTACTTATTAAATAAATACAAAT
Found at i:1599572 original size:31 final size:30
Alignment explanation
Indices: 1599522--1599593 Score: 92
Period size: 30 Copynumber: 2.3 Consensus size: 30
1599512 TATTATTTTA
* *
1599522 TTTTTAAA-AAATAATTAATTAATTTAAAAT
1 TTTTTAAATAAATAAATAATT-ATTAAAAAT
1599552 TTTTTAAATAAATAAATAATTATTAAAAAT
1 TTTTTAAATAAATAAATAATTATTAAAAAT
1599582 TATTTATAAATA
1 T-TTT-TAAATA
1599594 CTCCTTAATT
Statistics
Matches: 37, Mismatches: 2, Indels: 4
0.86 0.05 0.09
Matches are distributed among these distances:
30 17 0.46
31 14 0.38
32 6 0.16
ACGTcount: A:0.54, C:0.00, G:0.00, T:0.46
Consensus pattern (30 bp):
TTTTTAAATAAATAAATAATTATTAAAAAT
Found at i:1599671 original size:2 final size:2
Alignment explanation
Indices: 1599664--1599688 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
1599654 AGACAGAAAC
1599664 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 T
1599689 GAATAAAACT
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:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:1600909 original size:20 final size:20
Alignment explanation
Indices: 1600881--1600955 Score: 87
Period size: 20 Copynumber: 3.8 Consensus size: 20
1600871 TCATACCCTG
1600881 ATGTATCGATACATTTTTCA
1 ATGTATCGATACATTTTTCA
* * * *
1600901 ATATATCGATACATGTATGA
1 ATGTATCGATACATTTTTCA
* * *
1600921 ATGTATCGATATATTCTACA
1 ATGTATCGATACATTTTTCA
1600941 ATGTATCGATACATT
1 ATGTATCGATACATT
1600956 ATGTCTTTTT
Statistics
Matches: 43, Mismatches: 12, Indels: 0
0.78 0.22 0.00
Matches are distributed among these distances:
20 43 1.00
ACGTcount: A:0.35, C:0.13, G:0.12, T:0.40
Consensus pattern (20 bp):
ATGTATCGATACATTTTTCA
Found at i:1600948 original size:40 final size:39
Alignment explanation
Indices: 1600881--1600958 Score: 111
Period size: 40 Copynumber: 2.0 Consensus size: 39
1600871 TCATACCCTG
* *
1600881 ATGTATCGATACATTTTTCAATATATCGATACATGTATGA
1 ATGTATCGATACATTCTACAATATATCGATACAT-TATGA
* *
1600921 ATGTATCGATATATTCTACAATGTATCGATACATTATG
1 ATGTATCGATACATTCTACAATATATCGATACATTATG
1600959 TCTTTTTACC
Statistics
Matches: 34, Mismatches: 4, Indels: 1
0.87 0.10 0.03
Matches are distributed among these distances:
39 4 0.12
40 30 0.88
ACGTcount: A:0.35, C:0.13, G:0.13, T:0.40
Consensus pattern (39 bp):
ATGTATCGATACATTCTACAATATATCGATACATTATGA
Found at i:1601894 original size:23 final size:23
Alignment explanation
Indices: 1601867--1601919 Score: 106
Period size: 23 Copynumber: 2.3 Consensus size: 23
1601857 AGCCTTTGAC
1601867 CATGCATTTTTTTTATTATGTTT
1 CATGCATTTTTTTTATTATGTTT
1601890 CATGCATTTTTTTTATTATGTTT
1 CATGCATTTTTTTTATTATGTTT
1601913 CATGCAT
1 CATGCAT
1601920 ATTTAACATG
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
23 30 1.00
ACGTcount: A:0.19, C:0.11, G:0.09, T:0.60
Consensus pattern (23 bp):
CATGCATTTTTTTTATTATGTTT
Found at i:1601924 original size:20 final size:21
Alignment explanation
Indices: 1601878--1601924 Score: 60
Period size: 23 Copynumber: 2.2 Consensus size: 21
1601868 ATGCATTTTT
*
1601878 TTTATTATGTTTCATGCATTTTT
1 TTTATTATGTTTCATGCA--TTA
1601901 TTTATTATGTTTCATGCA-TA
1 TTTATTATGTTTCATGCATTA
1601921 TTTA
1 TTTA
1601925 ACATGTCCAG
Statistics
Matches: 23, Mismatches: 1, Indels: 3
0.85 0.04 0.11
Matches are distributed among these distances:
20 5 0.22
23 18 0.78
ACGTcount: A:0.21, C:0.09, G:0.09, T:0.62
Consensus pattern (21 bp):
TTTATTATGTTTCATGCATTA
Found at i:1605249 original size:4 final size:4
Alignment explanation
Indices: 1605242--1605268 Score: 54
Period size: 4 Copynumber: 6.8 Consensus size: 4
1605232 GATGTTCATT
1605242 TTTA TTTA TTTA TTTA TTTA TTTA TTT
1 TTTA TTTA TTTA TTTA TTTA TTTA TTT
1605269 TGCTATTCAT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 23 1.00
ACGTcount: A:0.22, C:0.00, G:0.00, T:0.78
Consensus pattern (4 bp):
TTTA
Found at i:1615012 original size:8 final size:8
Alignment explanation
Indices: 1614997--1615043 Score: 60
Period size: 8 Copynumber: 5.8 Consensus size: 8
1614987 GTTACACCCA
*
1614997 AAAAAAAA
1 AAAAAAAC
1615005 AAACAAAAC
1 AAA-AAAAC
1615014 AAAAAAAC
1 AAAAAAAC
1615022 AAAAAAA-
1 AAAAAAAC
1615029 AAAAAAAGC
1 AAAAAAA-C
1615038 AAAAAA
1 AAAAAA
1615044 TAGAAGGGTC
Statistics
Matches: 35, Mismatches: 1, Indels: 5
0.85 0.02 0.12
Matches are distributed among these distances:
7 7 0.20
8 15 0.43
9 13 0.37
ACGTcount: A:0.89, C:0.09, G:0.02, T:0.00
Consensus pattern (8 bp):
AAAAAAAC
Found at i:1615017 original size:13 final size:13
Alignment explanation
Indices: 1614995--1615043 Score: 66
Period size: 13 Copynumber: 3.9 Consensus size: 13
1614985 CCGTTACACC
*
1614995 CAAAAAAAAAAAA
1 CAAAACAAAAAAA
1615008 CAAAACAAAAAAA
1 CAAAACAAAAAAA
1615021 CAAAA-AAAAAAA
1 CAAAACAAAAAAA
*
1615033 -AAAGCAAAAAA
1 CAAAACAAAAAA
1615044 TAGAAGGGTC
Statistics
Matches: 33, Mismatches: 2, Indels: 3
0.87 0.05 0.08
Matches are distributed among these distances:
11 3 0.09
12 13 0.39
13 17 0.52
ACGTcount: A:0.88, C:0.10, G:0.02, T:0.00
Consensus pattern (13 bp):
CAAAACAAAAAAA
Found at i:1615029 original size:23 final size:24
Alignment explanation
Indices: 1614997--1615043 Score: 76
Period size: 25 Copynumber: 1.9 Consensus size: 24
1614987 GTTACACCCA
*
1614997 AAAAAAAAAAACAAAACAAAAAAAC
1 AAAAAAAAAAA-AAAGCAAAAAAAC
1615022 AAAAAAAAAAAAAAGCAAAAAA
1 AAAAAAAAAAAAAAGCAAAAAA
1615044 TAGAAGGGTC
Statistics
Matches: 21, Mismatches: 1, Indels: 1
0.91 0.04 0.04
Matches are distributed among these distances:
24 10 0.48
25 11 0.52
ACGTcount: A:0.89, C:0.09, G:0.02, T:0.00
Consensus pattern (24 bp):
AAAAAAAAAAAAAAGCAAAAAAAC
Found at i:1615043 original size:1 final size:1
Alignment explanation
Indices: 1614996--1615035 Score: 53
Period size: 1 Copynumber: 40.0 Consensus size: 1
1614986 CGTTACACCC
* * *
1614996 AAAAAAAAAAAACAAAACAAAAAAACAAAAAAAAAAAAAA
1 AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA
1615036 GCAAAAAATA
Statistics
Matches: 33, Mismatches: 6, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
1 33 1.00
ACGTcount: A:0.93, C:0.07, G:0.00, T:0.00
Consensus pattern (1 bp):
A
Found at i:1616367 original size:29 final size:29
Alignment explanation
Indices: 1616267--1617606 Score: 1938
Period size: 28 Copynumber: 46.9 Consensus size: 29
1616257 AATGTTCATC
1616267 CCTTTCAAAGCCCACAAGTCAGTGGCAC-
1 CCTTTCAAAGCCCACAAGTCAGTGGCACT
1616295 CCTTTCAAAGCCCACAAGTCAGTGGCAC-
1 CCTTTCAAAGCCCACAAGTCAGTGGCACT
*
1616323 CTTTTCAAAGCCCACAAGTCAGTGGCACT
1 CCTTTCAAAGCCCACAAGTCAGTGGCACT
*
1616352 CCTTTCAAAGCCCACAAGTTAGTGGCAC-
1 CCTTTCAAAGCCCACAAGTCAGTGGCACT
*
1616380 CCTTTCAAAGCCCACAAGTCAGTGGCACC
1 CCTTTCAAAGCCCACAAGTCAGTGGCACT
*
1616409 CCTTTCAAAGCCCACAAGTCAGTGGCACC
1 CCTTTCAAAGCCCACAAGTCAGTGGCACT
1616438 CCTTTCAAAGCCCACAAGTCAGTGGCACT
1 CCTTTCAAAGCCCACAAGTCAGTGGCACT
*
1616467 -CTTTCAAAGCCCACAAGTCAGTGGCATT
1 CCTTTCAAAGCCCACAAGTCAGTGGCACT
*
1616495 CCTTTCAAAGCCCACAAGTCAGTGGCATT
1 CCTTTCAAAGCCCACAAGTCAGTGGCACT
1616524 CCTTTCAAAGCCCACAAGTCAGTGGCACT
1 CCTTTCAAAGCCCACAAGTCAGTGGCACT
* * * *
1616553 CTTTTTAAAGCCCATAAATCAGTGGCACT
1 CCTTTCAAAGCCCACAAGTCAGTGGCACT
* *
1616582 CTTTTCAAAGCCCACAAGTTAGTGGCAC-
1 CCTTTCAAAGCCCACAAGTCAGTGGCACT
1616610 CCTTTCAAAGCCCACAAGTCAGTGGCACT
1 CCTTTCAAAGCCCACAAGTCAGTGGCACT
* *
1616639 CCTTTCAAAGCCCATAAATCAGTGGCACT
1 CCTTTCAAAGCCCACAAGTCAGTGGCACT
* *
1616668 CTTTTCAAAGCCCACAAGTTAGTGGCAC-
1 CCTTTCAAAGCCCACAAGTCAGTGGCACT
1616696 CCTTTCAAAGCCCACAAGTCAGTGGCACT
1 CCTTTCAAAGCCCACAAGTCAGTGGCACT
* *
1616725 CCTTTCAAAGTCCACAAGTTAGTGGCACT
1 CCTTTCAAAGCCCACAAGTCAGTGGCACT
* * *
1616754 CTTTTCAAAGCCCACAAATCGGTGGCACT
1 CCTTTCAAAGCCCACAAGTCAGTGGCACT
* *
1616783 CTTTTTAAAGCCCACAAGTCAGTGGCAC-
1 CCTTTCAAAGCCCACAAGTCAGTGGCACT
*
1616811 CCTTTCAAAGCCCACAAGTTAGTGGCAC-
1 CCTTTCAAAGCCCACAAGTCAGTGGCACT
*
1616839 CCTTTCAGAGCCCACAAGTCAGTGGCAC-
1 CCTTTCAAAGCCCACAAGTCAGTGGCACT
*
1616867 CCTTTCGAAGCCCACAAGTCAGTGGCAC-
1 CCTTTCAAAGCCCACAAGTCAGTGGCACT
* * * *
1616895 CATTGCGAAGCCCACAATTCAGTGGCAC-
1 CCTTTCAAAGCCCACAAGTCAGTGGCACT
1616923 CCTTTCAAAGCCCACAAGTCAGTGGCACT
1 CCTTTCAAAGCCCACAAGTCAGTGGCACT
*
1616952 CCTTTCAAAGCCCACAAGTTAGTGGCACT
1 CCTTTCAAAGCCCACAAGTCAGTGGCACT
1616981 CCTTTCAAAGCCCACAAGTCAGTGGCACT
1 CCTTTCAAAGCCCACAAGTCAGTGGCACT
*
1617010 CCTTTCAAAGCTCACAAGTCAGTGGCAC-
1 CCTTTCAAAGCCCACAAGTCAGTGGCACT
*
1617038 CCTTTCAAAGCCCACAACTCAGTGGCAC-
1 CCTTTCAAAGCCCACAAGTCAGTGGCACT
* *
1617066 CCTTTCAGAGCCCACAAGTTAGTGGCAC-
1 CCTTTCAAAGCCCACAAGTCAGTGGCACT
1617094 CCTTTCAAAGCCCACAAGTCAGTGGCACT
1 CCTTTCAAAGCCCACAAGTCAGTGGCACT
1617123 CCTTTCAAAGCCCACAAGTCAGTGGCACT
1 CCTTTCAAAGCCCACAAGTCAGTGGCACT
* *
1617152 CTTTTCAAAGCCCACAAATCAGTGGCACT
1 CCTTTCAAAGCCCACAAGTCAGTGGCACT
** * *
1617181 ATTTTCAAAGACCACAAGTCAATGGCAC-
1 CCTTTCAAAGCCCACAAGTCAGTGGCACT
1617209 CCTTTCAAAGCCCACAAGTCAGTGGCACT
1 CCTTTCAAAGCCCACAAGTCAGTGGCACT
1617238 CCTTTCAAAGCCCACAAGTCAGTGGCACT
1 CCTTTCAAAGCCCACAAGTCAGTGGCACT
* * *
1617267 CTTTTCAAAGCCCACAAATCAGTGGCGCT
1 CCTTTCAAAGCCCACAAGTCAGTGGCACT
*
1617296 CTTTTCAAAGCCCACAAGTCAGTGGCAC-
1 CCTTTCAAAGCCCACAAGTCAGTGGCACT
*
1617324 CCTTTCAAAGCCCACAAGTTAGTGGCAC-
1 CCTTTCAAAGCCCACAAGTCAGTGGCACT
*
1617352 CCTTTCAGAGCCCACAAGTCAGTGGCAC-
1 CCTTTCAAAGCCCACAAGTCAGTGGCACT
* *
1617380 CCTTTCGAGGCCCACAAGTCAGTGGCAC-
1 CCTTTCAAAGCCCACAAGTCAGTGGCACT
* * * *
1617408 CATTGCGAAGCCCACAATTCAGTGGCACT
1 CCTTTCAAAGCCCACAAGTCAGTGGCACT
1617437 -CTTTCAAAGCCCACAAGTCAGTGGCAC-
1 CCTTTCAAAGCCCACAAGTCAGTGGCACT
*
1617464 CCTTTTAAAGCCCACAAGTCAGTGGCACT
1 CCTTTCAAAGCCCACAAGTCAGTGGCACT
1617493 -CTTTCAAAGCCCACAAGTCAGTGGCA-T
1 CCTTTCAAAGCCCACAAGTCAGTGGCACT
* *
1617520 CCTTTCAAAGCCCACGAGTTAGTGGCA-T
1 CCTTTCAAAGCCCACAAGTCAGTGGCACT
*
1617548 TCTTTCAAAGCCCACGCAAGTCAGTGGCAC-
1 CCTTTCAAAGCCCA--CAAGTCAGTGGCACT
* *
1617578 CCTTTTAAAGCCCATGCAAGTCAATGGCA
1 CCTTTCAAAGCCCA--CAAGTCAGTGGCA
1617607 ACCCTTTTCA
Statistics
Matches: 1197, Mismatches: 100, Indels: 28
0.90 0.08 0.02
Matches are distributed among these distances:
27 1 0.00
28 601 0.50
29 559 0.47
30 36 0.03
ACGTcount: A:0.28, C:0.32, G:0.18, T:0.22
Consensus pattern (29 bp):
CCTTTCAAAGCCCACAAGTCAGTGGCACT
Found at i:1616455 original size:86 final size:85
Alignment explanation
Indices: 1616266--1617618 Score: 1865
Period size: 86 Copynumber: 15.8 Consensus size: 85
1616256 GAATGTTCAT
*
1616266 CCCTTTCAAAGCCCACAAGTCAGTGGCACCCTTTCAAAGCCCACAAGTCAGTGGCA-CCTTTTCA
1 CCCTTTCAAAGCCCACAAGTCAGTGGCACCCTTTCAAAGCCCACAAGTCAGTGGCACCCCTTTCA
1616330 AAGCCCACAAGTCAGTGGCA
66 AAGCCCACAAGTCAGTGGCA
*
1616350 CTCCTTTCAAAGCCCACAAGTTAGTGGCACCCTTTCAAAGCCCACAAGTCAGTGGCACCCCTTTC
1 C-CCTTTCAAAGCCCACAAGTCAGTGGCACCCTTTCAAAGCCCACAAGTCAGTGGCACCCCTTTC
1616415 AAAGCCCACAAGTCAGTGGCA
65 AAAGCCCACAAGTCAGTGGCA
* **
1616436 CCCCTTTCAAAGCCCACAAGTCAGTGGCACTCTTTCAAAGCCCACAAGTCAGTGGCATTCCTTTC
1 -CCCTTTCAAAGCCCACAAGTCAGTGGCACCCTTTCAAAGCCCACAAGTCAGTGGCACCCCTTTC
1616501 AAAGCCCACAAGTCAGTGGCA
65 AAAGCCCACAAGTCAGTGGCA
* * * * * * *
1616522 TTCCTTTCAAAGCCCACAAGTCAGTGGCACTCTTTTTAAAGCCCATAAATCAGTGGCACTCTTTT
1 -CCCTTTCAAAGCCCACAAGTCAGTGGCAC-CCTTTCAAAGCCCACAAGTCAGTGGCACCCCTTT
*
1616587 CAAAGCCCACAAGTTAGTGGCA
64 CAAAGCCCACAAGTCAGTGGCA
* * * *
1616609 CCCTTTCAAAGCCCACAAGTCAGTGGCACTCCTTTCAAAGCCCATAAATCAGTGGCACTCTTTTC
1 CCCTTTCAAAGCCCACAAGTCAGTGGCAC-CCTTTCAAAGCCCACAAGTCAGTGGCACCCCTTTC
*
1616674 AAAGCCCACAAGTTAGTGGCA
65 AAAGCCCACAAGTCAGTGGCA
* * * *
1616695 CCCTTTCAAAGCCCACAAGTCAGTGGCACTCCTTTCAAAGTCCACAAGTTAGTGGCACTCTTTTC
1 CCCTTTCAAAGCCCACAAGTCAGTGGCAC-CCTTTCAAAGCCCACAAGTCAGTGGCACCCCTTTC
* *
1616760 AAAGCCCACAAATCGGTGGCA
65 AAAGCCCACAAGTCAGTGGCA
* * *
1616781 CTCTTTTTAAAGCCCACAAGTCAGTGGCACCCTTTCAAAGCCCACAAGTTAGTGGCA-CCCTTTC
1 C-CCTTTCAAAGCCCACAAGTCAGTGGCACCCTTTCAAAGCCCACAAGTCAGTGGCACCCCTTTC
*
1616845 AGAGCCCACAAGTCAGTGGCA
65 AAAGCCCACAAGTCAGTGGCA
* * * * *
1616866 CCCTTTCGAAGCCCACAAGTCAGTGGCACCATTGCGAAGCCCACAATTCAGTGGCA-CCCTTTCA
1 CCCTTTCAAAGCCCACAAGTCAGTGGCACCCTTTCAAAGCCCACAAGTCAGTGGCACCCCTTTCA
1616930 AAGCCCACAAGTCAGTGGCA
66 AAGCCCACAAGTCAGTGGCA
* *
1616950 CTCCTTTCAAAGCCCACAAGTTAGTGGCACTCCTTTCAAAGCCCACAAGTCAGTGGCACTCCTTT
1 C-CCTTTCAAAGCCCACAAGTCAGTGGCAC-CCTTTCAAAGCCCACAAGTCAGTGGCACCCCTTT
*
1617015 CAAAGCTCACAAGTCAGTGGCA
64 CAAAGCCCACAAGTCAGTGGCA
* * *
1617037 CCCTTTCAAAGCCCACAACTCAGTGGCACCCTTTCAGAGCCCACAAGTTAGTGGCA-CCCTTTCA
1 CCCTTTCAAAGCCCACAAGTCAGTGGCACCCTTTCAAAGCCCACAAGTCAGTGGCACCCCTTTCA
1617101 AAGCCCACAAGTCAGTGGCA
66 AAGCCCACAAGTCAGTGGCA
* * ***
1617121 CTCCTTTCAAAGCCCACAAGTCAGTGGCACTCTTTTCAAAGCCCACAAATCAGTGGCACTATTTT
1 C-CCTTTCAAAGCCCACAAGTCAGTGGCAC-CCTTTCAAAGCCCACAAGTCAGTGGCACCCCTTT
* *
1617186 CAAAGACCACAAGTCAATGGCA
64 CAAAGCCCACAAGTCAGTGGCA
* *
1617208 CCCTTTCAAAGCCCACAAGTCAGTGGCACTCCTTTCAAAGCCCACAAGTCAGTGGCACTCTTTTC
1 CCCTTTCAAAGCCCACAAGTCAGTGGCAC-CCTTTCAAAGCCCACAAGTCAGTGGCACCCCTTTC
* *
1617273 AAAGCCCACAAATCAGTGGCG
65 AAAGCCCACAAGTCAGTGGCA
* *
1617294 CTCTTTTCAAAGCCCACAAGTCAGTGGCACCCTTTCAAAGCCCACAAGTTAGTGGCA-CCCTTTC
1 C-CCTTTCAAAGCCCACAAGTCAGTGGCACCCTTTCAAAGCCCACAAGTCAGTGGCACCCCTTTC
*
1617358 AGAGCCCACAAGTCAGTGGCA
65 AAAGCCCACAAGTCAGTGGCA
* * * * * * *
1617379 CCCTTTCGAGGCCCACAAGTCAGTGGCACCATTGCGAAGCCCACAATTCAGTGGCA-CTCTTTCA
1 CCCTTTCAAAGCCCACAAGTCAGTGGCACCCTTTCAAAGCCCACAAGTCAGTGGCACCCCTTTCA
1617443 AAGCCCACAAGTCAGTGGCA
66 AAGCCCACAAGTCAGTGGCA
* * *
1617463 CCCTTTTAAAGCCCACAAGTCAGTGGCACTCTTTCAAAGCCCACAAGTCAGTGGCA-TCCTTTCA
1 CCCTTTCAAAGCCCACAAGTCAGTGGCACCCTTTCAAAGCCCACAAGTCAGTGGCACCCCTTTCA
* *
1617527 AAGCCCACGAGTTAGTGGCA
66 AAGCCCACAAGTCAGTGGCA
** * * *
1617547 TTCTTTCAAAGCCCACGCAAGTCAGTGGCACCCTTTTAAAGCCCATGCAAGTCAATGGCAACCCT
1 CCCTTTCAAAGCCCA--CAAGTCAGTGGCACCCTTTCAAAGCCCA--CAAGTCAGTGGC-ACCCC
1617612 TTTCAAA
61 TTTCAAA
1617619 TCACCACTGT
Statistics
Matches: 1140, Mismatches: 111, Indels: 30
0.89 0.09 0.02
Matches are distributed among these distances:
84 260 0.23
85 180 0.16
86 527 0.46
87 153 0.13
88 11 0.01
89 1 0.00
90 8 0.01
ACGTcount: A:0.28, C:0.32, G:0.18, T:0.22
Consensus pattern (85 bp):
CCCTTTCAAAGCCCACAAGTCAGTGGCACCCTTTCAAAGCCCACAAGTCAGTGGCACCCCTTTCA
AAGCCCACAAGTCAGTGGCA
Found at i:1618160 original size:20 final size:20
Alignment explanation
Indices: 1618132--1618206 Score: 87
Period size: 20 Copynumber: 3.8 Consensus size: 20
1618122 TCATACCCTG
1618132 ATGTATCGATACATTTTTCA
1 ATGTATCGATACATTTTTCA
* * * *
1618152 ATATATCGATACATGTATGA
1 ATGTATCGATACATTTTTCA
* * *
1618172 ATGTATCGATATATTCTACA
1 ATGTATCGATACATTTTTCA
1618192 ATGTATCGATACATT
1 ATGTATCGATACATT
1618207 ATGTCTTTTT
Statistics
Matches: 43, Mismatches: 12, Indels: 0
0.78 0.22 0.00
Matches are distributed among these distances:
20 43 1.00
ACGTcount: A:0.35, C:0.13, G:0.12, T:0.40
Consensus pattern (20 bp):
ATGTATCGATACATTTTTCA
Found at i:1618199 original size:40 final size:39
Alignment explanation
Indices: 1618132--1618209 Score: 111
Period size: 40 Copynumber: 2.0 Consensus size: 39
1618122 TCATACCCTG
* *
1618132 ATGTATCGATACATTTTTCAATATATCGATACATGTATGA
1 ATGTATCGATACATTCTACAATATATCGATACAT-TATGA
* *
1618172 ATGTATCGATATATTCTACAATGTATCGATACATTATG
1 ATGTATCGATACATTCTACAATATATCGATACATTATG
1618210 TCTTTTTACC
Statistics
Matches: 34, Mismatches: 4, Indels: 1
0.87 0.10 0.03
Matches are distributed among these distances:
39 4 0.12
40 30 0.88
ACGTcount: A:0.35, C:0.13, G:0.13, T:0.40
Consensus pattern (39 bp):
ATGTATCGATACATTCTACAATATATCGATACATTATGA
Found at i:1619145 original size:23 final size:23
Alignment explanation
Indices: 1619118--1619170 Score: 106
Period size: 23 Copynumber: 2.3 Consensus size: 23
1619108 AGCCTTTGAC
1619118 CATGCATTTTTTTTATTATGTTT
1 CATGCATTTTTTTTATTATGTTT
1619141 CATGCATTTTTTTTATTATGTTT
1 CATGCATTTTTTTTATTATGTTT
1619164 CATGCAT
1 CATGCAT
1619171 ATTTAACATG
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
23 30 1.00
ACGTcount: A:0.19, C:0.11, G:0.09, T:0.60
Consensus pattern (23 bp):
CATGCATTTTTTTTATTATGTTT
Found at i:1619175 original size:20 final size:21
Alignment explanation
Indices: 1619129--1619175 Score: 60
Period size: 23 Copynumber: 2.2 Consensus size: 21
1619119 ATGCATTTTT
*
1619129 TTTATTATGTTTCATGCATTTTT
1 TTTATTATGTTTCATGCA--TTA
1619152 TTTATTATGTTTCATGCA-TA
1 TTTATTATGTTTCATGCATTA
1619172 TTTA
1 TTTA
1619176 ACATGTCCAG
Statistics
Matches: 23, Mismatches: 1, Indels: 3
0.85 0.04 0.11
Matches are distributed among these distances:
20 5 0.22
23 18 0.78
ACGTcount: A:0.21, C:0.09, G:0.09, T:0.62
Consensus pattern (21 bp):
TTTATTATGTTTCATGCATTA
Found at i:1621524 original size:25 final size:22
Alignment explanation
Indices: 1621491--1621562 Score: 58
Period size: 25 Copynumber: 3.1 Consensus size: 22
1621481 ATGATTATAT
1621491 AATAT-AAATACAATAAATAAAA
1 AATATAAAATACAAT-AATAAAA
* *
1621513 AATAATTAAAATATAAT-ATAAAT
1 AAT-A-TAAAATACAATAATAAAA
1621536 AATATAAATATACAACTATATAAAA
1 AATATAAA-ATACAA-TA-ATAAAA
1621561 AA
1 AA
1621563 AATATATAAT
Statistics
Matches: 39, Mismatches: 4, Indels: 11
0.72 0.07 0.20
Matches are distributed among these distances:
21 4 0.10
22 9 0.23
23 10 0.26
24 1 0.03
25 15 0.38
ACGTcount: A:0.68, C:0.04, G:0.00, T:0.28
Consensus pattern (22 bp):
AATATAAAATACAATAATAAAA
Found at i:1621525 original size:20 final size:21
Alignment explanation
Indices: 1621494--1621547 Score: 53
Period size: 20 Copynumber: 2.7 Consensus size: 21
1621484 ATTATATAAT
*
1621494 ATAA-ATACAATA-AATAAAAA
1 ATAATATAAAATATAAT-AAAA
*
1621514 ATAAT-TAAAATATAATATAA
1 ATAATATAAAATATAATAAAA
1621534 ATAATAT-AAATATA
1 ATAATATAAAATATA
1621548 CAACTATATA
Statistics
Matches: 29, Mismatches: 2, Indels: 6
0.78 0.05 0.16
Matches are distributed among these distances:
20 25 0.86
21 4 0.14
ACGTcount: A:0.69, C:0.02, G:0.00, T:0.30
Consensus pattern (21 bp):
ATAATATAAAATATAATAAAA
Found at i:1621537 original size:9 final size:9
Alignment explanation
Indices: 1621489--1621545 Score: 57
Period size: 9 Copynumber: 6.3 Consensus size: 9
1621479 ATATGATTAT
1621489 ATAATATAA
1 ATAATATAA
1621498 ATACA-ATAA
1 ATA-ATATAA
1621507 ATAA-A-AA
1 ATAATATAA
*
1621514 ATAATTAAAA
1 ATAA-TATAA
1621524 TATAATATAA
1 -ATAATATAA
1621534 ATAATATAA
1 ATAATATAA
1621543 ATA
1 ATA
1621546 TACAACTATA
Statistics
Matches: 42, Mismatches: 1, Indels: 10
0.79 0.02 0.19
Matches are distributed among these distances:
7 6 0.14
8 2 0.05
9 23 0.55
10 7 0.17
11 4 0.10
ACGTcount: A:0.68, C:0.02, G:0.00, T:0.30
Consensus pattern (9 bp):
ATAATATAA
Found at i:1621979 original size:19 final size:19
Alignment explanation
Indices: 1621928--1621979 Score: 54
Period size: 19 Copynumber: 2.8 Consensus size: 19
1621918 ATATAATTTT
*
1621928 ATTTAATT-TAAATTAAAA
1 ATTTAATTATAAATAAAAA
* *
1621946 TTTTATTTA-ATAATAAAAA
1 ATTTAATTATA-AATAAAAA
1621965 ATTTAATTATAAATA
1 ATTTAATTATAAATA
1621980 TATATAATTA
Statistics
Matches: 26, Mismatches: 5, Indels: 5
0.72 0.14 0.14
Matches are distributed among these distances:
18 7 0.27
19 18 0.69
20 1 0.04
ACGTcount: A:0.54, C:0.00, G:0.00, T:0.46
Consensus pattern (19 bp):
ATTTAATTATAAATAAAAA
Found at i:1622015 original size:11 final size:11
Alignment explanation
Indices: 1621996--1622034 Score: 51
Period size: 11 Copynumber: 3.5 Consensus size: 11
1621986 ATTATTAATA
*
1621996 TAAAAATATTT
1 TAAATATATTT
1622007 TAAATATATTT
1 TAAATATATTT
*
1622018 TAAATAATAATT
1 TAAAT-ATATTT
1622030 TAAAT
1 TAAAT
1622035 TTTTAAATTA
Statistics
Matches: 25, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
11 15 0.60
12 10 0.40
ACGTcount: A:0.54, C:0.00, G:0.00, T:0.46
Consensus pattern (11 bp):
TAAATATATTT
Found at i:1622620 original size:24 final size:24
Alignment explanation
Indices: 1622575--1622621 Score: 60
Period size: 24 Copynumber: 2.0 Consensus size: 24
1622565 TTATTACAAT
*
1622575 TTAAAATTTATAGAGATTAAAATA
1 TTAAAATTTATAGAGATAAAAATA
*
1622599 TTAAAATTTAATAG-TATAAAAAT
1 TTAAAATTT-ATAGAGATAAAAAT
1622622 TAAAATAATT
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
24 16 0.80
25 4 0.20
ACGTcount: A:0.55, C:0.00, G:0.06, T:0.38
Consensus pattern (24 bp):
TTAAAATTTATAGAGATAAAAATA
Found at i:1623075 original size:21 final size:21
Alignment explanation
Indices: 1623049--1623094 Score: 67
Period size: 21 Copynumber: 2.2 Consensus size: 21
1623039 GATAAAATTT
*
1623049 AAAATTTTCATCAGA-ATAATA
1 AAAATTTT-ATAAGATATAATA
1623070 AAAATTTTATAAGATATAATA
1 AAAATTTTATAAGATATAATA
1623091 AAAA
1 AAAA
1623095 ATCTTAAAAA
Statistics
Matches: 23, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
20 5 0.22
21 18 0.78
ACGTcount: A:0.59, C:0.04, G:0.04, T:0.33
Consensus pattern (21 bp):
AAAATTTTATAAGATATAATA
Found at i:1624398 original size:19 final size:19
Alignment explanation
Indices: 1624358--1624397 Score: 64
Period size: 19 Copynumber: 2.2 Consensus size: 19
1624348 TGACGTAAGT
*
1624358 AAATATTGAATTATAATTA
1 AAATATTGAATTATAATAA
1624377 AAATATTGAATTAT-ATAA
1 AAATATTGAATTATAATAA
1624395 AAA
1 AAA
1624398 AAATTTAGAT
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
18 6 0.30
19 14 0.70
ACGTcount: A:0.57, C:0.00, G:0.05, T:0.38
Consensus pattern (19 bp):
AAATATTGAATTATAATAA
Found at i:1624683 original size:75 final size:75
Alignment explanation
Indices: 1624599--1624746 Score: 260
Period size: 75 Copynumber: 2.0 Consensus size: 75
1624589 ATTTTCACTC
* *
1624599 TAGCTCCGGTATAAAAAATAATTATTTATAATATAAATGAATTAAATTTTTATACCCATCTTAAT
1 TAGCTCCGGTATAAAAAATAATTATCTATAATATAAATGAATTAAAATTTTATACCCATCTTAAT
1624664 TTGTCTTATA
66 TTGTCTTATA
**
1624674 TAGCTCCGGTATAAAAAATAATTATCTATAATATAAATGAATTAAAATTTTATATTCATCTTAAT
1 TAGCTCCGGTATAAAAAATAATTATCTATAATATAAATGAATTAAAATTTTATACCCATCTTAAT
1624739 TTGTCTTA
66 TTGTCTTA
1624747 CATATAATAT
Statistics
Matches: 69, Mismatches: 4, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
75 69 1.00
ACGTcount: A:0.41, C:0.10, G:0.07, T:0.43
Consensus pattern (75 bp):
TAGCTCCGGTATAAAAAATAATTATCTATAATATAAATGAATTAAAATTTTATACCCATCTTAAT
TTGTCTTATA
Found at i:1625073 original size:24 final size:26
Alignment explanation
Indices: 1625041--1625103 Score: 76
Period size: 27 Copynumber: 2.4 Consensus size: 26
1625031 TTGATAAATT
* *
1625041 TAAATATAATATAAT-T-ATATGATA
1 TAAAAATAATAAAATATGATATGATA
1625065 TAAAAATAATTAAAATATGATATGATA
1 TAAAAATAA-TAAAATATGATATGATA
1625092 TGAAAAATAATA
1 T-AAAAATAATA
1625104 CGAATGTGAT
Statistics
Matches: 33, Mismatches: 2, Indels: 5
0.82 0.05 0.12
Matches are distributed among these distances:
24 8 0.24
25 5 0.15
26 1 0.03
27 11 0.33
28 8 0.24
ACGTcount: A:0.59, C:0.00, G:0.06, T:0.35
Consensus pattern (26 bp):
TAAAAATAATAAAATATGATATGATA
Found at i:1625383 original size:27 final size:28
Alignment explanation
Indices: 1625325--1625385 Score: 72
Period size: 27 Copynumber: 2.2 Consensus size: 28
1625315 CAACATGAAC
* *
1625325 ATATAACATGAAAAATAATTAAAACTTG
1 ATATAACATGAAAAATAATTAAAACATA
*
1625353 ATATGACAT-AAAAATAA-TATAAACATA
1 ATATAACATGAAAAATAATTA-AAACATA
1625380 ATATAA
1 ATATAA
1625386 ATATATAAAT
Statistics
Matches: 28, Mismatches: 4, Indels: 3
0.80 0.11 0.09
Matches are distributed among these distances:
26 2 0.07
27 18 0.64
28 8 0.29
ACGTcount: A:0.61, C:0.07, G:0.05, T:0.28
Consensus pattern (28 bp):
ATATAACATGAAAAATAATTAAAACATA
Found at i:1629877 original size:14 final size:15
Alignment explanation
Indices: 1629853--1629882 Score: 60
Period size: 15 Copynumber: 2.0 Consensus size: 15
1629843 AAAGCTTCTC
1629853 TTTTCCTTTTTTTTT
1 TTTTCCTTTTTTTTT
1629868 TTTTCCTTTTTTTTT
1 TTTTCCTTTTTTTTT
1629883 ATTATTTGCT
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.00, C:0.13, G:0.00, T:0.87
Consensus pattern (15 bp):
TTTTCCTTTTTTTTT
Found at i:1629895 original size:18 final size:16
Alignment explanation
Indices: 1629853--1629882 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
1629843 AAAGCTTCTC
1629853 TTTTCC-TTTTTTTTT
1 TTTTCCTTTTTTTTTT
1629868 TTTTCCTTTTTTTTT
1 TTTTCCTTTTTTTTT
1629883 ATTATTTGCT
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 6 0.43
16 8 0.57
ACGTcount: A:0.00, C:0.13, G:0.00, T:0.87
Consensus pattern (16 bp):
TTTTCCTTTTTTTTTT
Found at i:1632591 original size:2 final size:2
Alignment explanation
Indices: 1632586--1632614 Score: 51
Period size: 2 Copynumber: 15.0 Consensus size: 2
1632576 TTGAATATGA
1632586 AT AT AT AT AT AT AT AT AT AT AT AT A- AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1632615 CTTTCCTTAG
Statistics
Matches: 26, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
1 1 0.04
2 25 0.96
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:1632907 original size:16 final size:15
Alignment explanation
Indices: 1632886--1632919 Score: 50
Period size: 16 Copynumber: 2.2 Consensus size: 15
1632876 TATGACCGTA
1632886 AATAAATAGTATATAT
1 AATAAATAGTAT-TAT
*
1632902 AATAAATATTATTAT
1 AATAAATAGTATTAT
1632917 AAT
1 AAT
1632920 CATTTAGTCA
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
15 6 0.35
16 11 0.65
ACGTcount: A:0.56, C:0.00, G:0.03, T:0.41
Consensus pattern (15 bp):
AATAAATAGTATTAT
Found at i:1634216 original size:21 final size:21
Alignment explanation
Indices: 1634192--1634253 Score: 52
Period size: 21 Copynumber: 2.8 Consensus size: 21
1634182 TTTTTTTAAA
*
1634192 TAATAAATAAATATTTTCATT
1 TAATAAATAAATATTTTCAAT
** * *
1634213 TAATATTTATATATTTTTAAT
1 TAATAAATAAATATTTTCAAT
1634234 TAATTTAAATAAAATATTTT
1 TAA--TAAAT-AAATATTTT
1634254 TACTAATCAA
Statistics
Matches: 30, Mismatches: 8, Indels: 3
0.73 0.20 0.07
Matches are distributed among these distances:
21 19 0.63
23 3 0.10
24 8 0.27
ACGTcount: A:0.45, C:0.02, G:0.00, T:0.53
Consensus pattern (21 bp):
TAATAAATAAATATTTTCAAT
Found at i:1635843 original size:50 final size:50
Alignment explanation
Indices: 1635768--1635937 Score: 252
Period size: 50 Copynumber: 3.4 Consensus size: 50
1635758 AGTTGTTGTC
* * * * *
1635768 ATTGTTGACTATCCTTCACCAACCTTTGACAATAGAGAGAGGTGGTCGTA
1 ATTGTTGACGATTCTTCACCAACCTTTGACAATAGAGAGAGGTGGCCATT
**
1635818 ATTGTTGACGATTCTTCATAAACCTTTGACAATAGAGAGAGGTGGCCATT
1 ATTGTTGACGATTCTTCACCAACCTTTGACAATAGAGAGAGGTGGCCATT
*
1635868 ATTGTTGACGATTCTTCACCAACCTTTGACAA-ATGTGAGAGGTGGCCATT
1 ATTGTTGACGATTCTTCACCAACCTTTGACAATA-GAGAGAGGTGGCCATT
1635918 ATTGTTGACGATTCTTCACC
1 ATTGTTGACGATTCTTCACC
1635938 GATTCTTCAC
Statistics
Matches: 109, Mismatches: 10, Indels: 2
0.90 0.08 0.02
Matches are distributed among these distances:
49 1 0.01
50 108 0.99
ACGTcount: A:0.27, C:0.19, G:0.21, T:0.32
Consensus pattern (50 bp):
ATTGTTGACGATTCTTCACCAACCTTTGACAATAGAGAGAGGTGGCCATT
Found at i:1635971 original size:61 final size:61
Alignment explanation
Indices: 1635876--1636026 Score: 293
Period size: 61 Copynumber: 2.5 Consensus size: 61
1635866 TTATTGTTGA
1635876 CGATTCTTCACCAACCTTTGACAAATGTGAGAGGTGGCCATTATTGTTGACGATTCTTCAC
1 CGATTCTTCACCAACCTTTGACAAATGTGAGAGGTGGCCATTATTGTTGACGATTCTTCAC
1635937 CGATTCTTCACCAACCTTTGACAAATGTGAGAGGTGGCCATTATTGTTGACGATTCTTCAC
1 CGATTCTTCACCAACCTTTGACAAATGTGAGAGGTGGCCATTATTGTTGACGATTCTTCAC
*
1635998 CGATTCTTCACCAACTTTTGACAAATGTG
1 CGATTCTTCACCAACCTTTGACAAATGTG
1636027 GCCATAATTG
Statistics
Matches: 89, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
61 89 1.00
ACGTcount: A:0.25, C:0.23, G:0.19, T:0.33
Consensus pattern (61 bp):
CGATTCTTCACCAACCTTTGACAAATGTGAGAGGTGGCCATTATTGTTGACGATTCTTCAC
Found at i:1640509 original size:50 final size:50
Alignment explanation
Indices: 1640434--1640665 Score: 376
Period size: 50 Copynumber: 4.6 Consensus size: 50
1640424 AGTTGTTGCC
* * * * *
1640434 ATTGTTGACTATCCTTCACCAACCTTTGACAATAGAGAGAGGTGGTCGTA
1 ATTGTTGACGATTCTTCACCAACCTTTGACAATAGAGAGAGGTGGCCATT
**
1640484 ATTGTTGACGATTCTTCATAAACCTTTGACAATAGAGAGAGGTGGCCATT
1 ATTGTTGACGATTCTTCACCAACCTTTGACAATAGAGAGAGGTGGCCATT
*
1640534 ATTGTTGACGATTCTTCACCAACCTTTGACAA-ATGTGAGAGGTGGCCATT
1 ATTGTTGACGATTCTTCACCAACCTTTGACAATA-GAGAGAGGTGGCCATT
1640584 ATTGTTGACGATTCTTCACCAACCTTTGACAATAGAGAGAGGTGGCCATT
1 ATTGTTGACGATTCTTCACCAACCTTTGACAATAGAGAGAGGTGGCCATT
1640634 ATTGTTGACGATTCTTCACCAACCTTTGACAA
1 ATTGTTGACGATTCTTCACCAACCTTTGACAA
1640666 ATGTGGCCAT
Statistics
Matches: 169, Mismatches: 11, Indels: 4
0.92 0.06 0.02
Matches are distributed among these distances:
49 1 0.01
50 167 0.99
51 1 0.01
ACGTcount: A:0.28, C:0.20, G:0.21, T:0.31
Consensus pattern (50 bp):
ATTGTTGACGATTCTTCACCAACCTTTGACAATAGAGAGAGGTGGCCATT
Found at i:1643099 original size:13 final size:13
Alignment explanation
Indices: 1643062--1643099 Score: 51
Period size: 13 Copynumber: 2.9 Consensus size: 13
1643052 CTTGAGGTTA
*
1643062 TATTTAATCTTTT
1 TATTTAATATTTT
1643075 TATTTTAA-ATTTT
1 TA-TTTAATATTTT
1643088 TATTTAATATTT
1 TATTTAATATTT
1643100 AAGTGTATGA
Statistics
Matches: 22, Mismatches: 1, Indels: 4
0.81 0.04 0.15
Matches are distributed among these distances:
12 5 0.23
13 12 0.55
14 5 0.23
ACGTcount: A:0.29, C:0.03, G:0.00, T:0.68
Consensus pattern (13 bp):
TATTTAATATTTT
Found at i:1643375 original size:22 final size:24
Alignment explanation
Indices: 1643341--1643404 Score: 78
Period size: 25 Copynumber: 2.7 Consensus size: 24
1643331 AATATCTTTG
*
1643341 TTAAGTGTATTAGGT-A-AACATA
1 TTAAGTGTGTTAGGTGACAACATA
* *
1643363 TTAGGTGTGTTAGGTGAGCAATATA
1 TTAAGTGTGTTAGGTGA-CAACATA
1643388 TTAAGTGTGTTAGGTGA
1 TTAAGTGTGTTAGGTGA
1643405 TGTGTATGGT
Statistics
Matches: 35, Mismatches: 4, Indels: 3
0.83 0.10 0.07
Matches are distributed among these distances:
22 13 0.37
23 1 0.03
25 21 0.60
ACGTcount: A:0.31, C:0.03, G:0.28, T:0.38
Consensus pattern (24 bp):
TTAAGTGTGTTAGGTGACAACATA
Found at i:1648071 original size:22 final size:22
Alignment explanation
Indices: 1648043--1648132 Score: 90
Period size: 22 Copynumber: 4.0 Consensus size: 22
1648033 TATCTTTATT
*
1648043 AAGTGTGTTAGGTAAACATATA
1 AAGTGTGTTAAGTAAACATATA
* *
1648065 AAGTGTGTTAGGTAAGCAATATA
1 AAGTGTGTTAAGTAAAC-ATATA
* * *
1648088 TTAAGTGTATTAAATAAACATATT
1 --AAGTGTGTTAAGTAAACATATA
*
1648112 AAGTGTGTTAAGTAAATATAT
1 AAGTGTGTTAAGTAAACATAT
1648133 CTTATATAAA
Statistics
Matches: 56, Mismatches: 9, Indels: 6
0.79 0.13 0.08
Matches are distributed among these distances:
22 34 0.61
23 5 0.09
24 4 0.07
25 13 0.23
ACGTcount: A:0.42, C:0.03, G:0.19, T:0.36
Consensus pattern (22 bp):
AAGTGTGTTAAGTAAACATATA
Found at i:1649535 original size:20 final size:19
Alignment explanation
Indices: 1649489--1649537 Score: 55
Period size: 20 Copynumber: 2.5 Consensus size: 19
1649479 ATTCTTAAAC
*
1649489 ATTATATAATTTAATTCAA
1 ATTATATAATATAATTCAA
1649508 ATTAATATAATATAATGT-AA
1 ATT-ATATAATATAAT-TCAA
1649528 ATCTATATAA
1 AT-TATATAA
1649538 GCTATTGGAG
Statistics
Matches: 26, Mismatches: 1, Indels: 5
0.81 0.03 0.16
Matches are distributed among these distances:
19 3 0.12
20 21 0.81
21 2 0.08
ACGTcount: A:0.51, C:0.04, G:0.02, T:0.43
Consensus pattern (19 bp):
ATTATATAATATAATTCAA
Found at i:1649720 original size:14 final size:14
Alignment explanation
Indices: 1649703--1649751 Score: 73
Period size: 14 Copynumber: 3.5 Consensus size: 14
1649693 TGTAAAGTTA
1649703 ATATTTTAATTTAT
1 ATATTTTAATTTAT
1649717 ATATTATTAATTTA-
1 ATATT-TTAATTTAT
*
1649731 ATATTTTAATTTTT
1 ATATTTTAATTTAT
1649745 ATATTTT
1 ATATTTT
1649752 TAAAATTATA
Statistics
Matches: 32, Mismatches: 1, Indels: 4
0.86 0.03 0.11
Matches are distributed among these distances:
13 7 0.22
14 17 0.53
15 8 0.25
ACGTcount: A:0.35, C:0.00, G:0.00, T:0.65
Consensus pattern (14 bp):
ATATTTTAATTTAT
Found at i:1649732 original size:28 final size:28
Alignment explanation
Indices: 1649700--1649754 Score: 92
Period size: 28 Copynumber: 2.0 Consensus size: 28
1649690 TATTGTAAAG
1649700 TTAATATTTTAATTTATATATTATTAAT
1 TTAATATTTTAATTTATATATTATTAAT
* *
1649728 TTAATATTTTAATTTTTATATTTTTAA
1 TTAATATTTTAATTTATATATTATTAA
1649755 AATTATAATC
Statistics
Matches: 25, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
28 25 1.00
ACGTcount: A:0.36, C:0.00, G:0.00, T:0.64
Consensus pattern (28 bp):
TTAATATTTTAATTTATATATTATTAAT
Found at i:1651694 original size:23 final size:23
Alignment explanation
Indices: 1651654--1651697 Score: 63
Period size: 23 Copynumber: 1.9 Consensus size: 23
1651644 TGAAAATAAT
*
1651654 AATTATTATTCATTATATTTTAA
1 AATTATTATTCATAATATTTTAA
1651677 AATTATTATT-ATAAATATTTT
1 AATTATTATTCAT-AATATTTT
1651698 TATTATTAAT
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
22 2 0.11
23 17 0.89
ACGTcount: A:0.41, C:0.02, G:0.00, T:0.57
Consensus pattern (23 bp):
AATTATTATTCATAATATTTTAA
Found at i:1651702 original size:15 final size:15
Alignment explanation
Indices: 1651669--1651719 Score: 50
Period size: 15 Copynumber: 3.3 Consensus size: 15
1651659 TTATTCATTA
* *
1651669 TATTTTAAA-ATTAT
1 TATTATAAATATTTT
1651683 TATTATAAATATTTT
1 TATTATAAATATTTT
*
1651698 TATTATTAATAATATTT
1 TATTATAAAT-AT-TTT
1651715 TATTA
1 TATTA
1651720 AGATTAATTT
Statistics
Matches: 31, Mismatches: 3, Indels: 3
0.84 0.08 0.08
Matches are distributed among these distances:
14 8 0.26
15 13 0.42
16 2 0.06
17 8 0.26
ACGTcount: A:0.41, C:0.00, G:0.00, T:0.59
Consensus pattern (15 bp):
TATTATAAATATTTT
Found at i:1651702 original size:18 final size:17
Alignment explanation
Indices: 1651679--1651719 Score: 57
Period size: 18 Copynumber: 2.4 Consensus size: 17
1651669 TATTTTAAAA
1651679 TTATTATT-ATAAATATTT
1 TTATTATTAAT-AATA-TT
1651697 TTATTATTAATAATATT
1 TTATTATTAATAATATT
1651714 TTATTA
1 TTATTA
1651720 AGATTAATTT
Statistics
Matches: 22, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
17 8 0.36
18 12 0.55
19 2 0.09
ACGTcount: A:0.39, C:0.00, G:0.00, T:0.61
Consensus pattern (17 bp):
TTATTATTAATAATATT
Found at i:1653785 original size:21 final size:20
Alignment explanation
Indices: 1653761--1653809 Score: 55
Period size: 21 Copynumber: 2.4 Consensus size: 20
1653751 CATTTAGTTC
1653761 AAAACAAATAATTAAAATATT-
1 AAAACAAATAA-T-AAATATTA
* *
1653782 AAAATAAATAATAATTATTA
1 AAAACAAATAATAAATATTA
1653802 AAAACAAA
1 AAAACAAA
1653810 ATTTTGATTT
Statistics
Matches: 24, Mismatches: 3, Indels: 3
0.80 0.10 0.10
Matches are distributed among these distances:
19 6 0.25
20 8 0.33
21 10 0.42
ACGTcount: A:0.69, C:0.04, G:0.00, T:0.27
Consensus pattern (20 bp):
AAAACAAATAATAAATATTA
Found at i:1653864 original size:22 final size:23
Alignment explanation
Indices: 1653824--1653881 Score: 59
Period size: 22 Copynumber: 2.6 Consensus size: 23
1653814 TGATTTAATA
* *
1653824 AAATAATTTATAATA-TAAAAT-T
1 AAAT-ATTTATAAAATTTAAATCT
1653846 AAATATTTA-AAAATTTAAATCT
1 AAATATTTATAAAATTTAAATCT
*
1653868 CAATATTTATAAAA
1 AAATATTTATAAAA
1653882 AATAAAAAAT
Statistics
Matches: 30, Mismatches: 3, Indels: 5
0.79 0.08 0.13
Matches are distributed among these distances:
20 3 0.10
21 10 0.33
22 13 0.43
23 4 0.13
ACGTcount: A:0.57, C:0.03, G:0.00, T:0.40
Consensus pattern (23 bp):
AAATATTTATAAAATTTAAATCT
Found at i:1654226 original size:21 final size:21
Alignment explanation
Indices: 1654200--1654240 Score: 64
Period size: 21 Copynumber: 2.0 Consensus size: 21
1654190 GAAAAAAAAA
1654200 AAAAAAAAAAAAGCTTTTTTT
1 AAAAAAAAAAAAGCTTTTTTT
**
1654221 AAAAAAAAAAATTCTTTTTT
1 AAAAAAAAAAAAGCTTTTTT
1654241 GTTAAAAGAA
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
21 18 1.00
ACGTcount: A:0.56, C:0.05, G:0.02, T:0.37
Consensus pattern (21 bp):
AAAAAAAAAAAAGCTTTTTTT
Found at i:1654490 original size:21 final size:22
Alignment explanation
Indices: 1654454--1654499 Score: 58
Period size: 21 Copynumber: 2.1 Consensus size: 22
1654444 TAAATGTATT
1654454 TTTAAAAATAATAATTAATAAA
1 TTTAAAAATAATAATTAATAAA
* **
1654476 TTTAAAATTAA-AATTTTTAAA
1 TTTAAAAATAATAATTAATAAA
1654497 TTT
1 TTT
1654500 TTAAATTTTA
Statistics
Matches: 21, Mismatches: 3, Indels: 1
0.84 0.12 0.04
Matches are distributed among these distances:
21 11 0.52
22 10 0.48
ACGTcount: A:0.54, C:0.00, G:0.00, T:0.46
Consensus pattern (22 bp):
TTTAAAAATAATAATTAATAAA
Found at i:1655818 original size:17 final size:17
Alignment explanation
Indices: 1655787--1655867 Score: 58
Period size: 16 Copynumber: 4.6 Consensus size: 17
1655777 TAAAATTTGA
1655787 TATATAATATAAAAAATAT
1 TATA-AATAT-AAAAATAT
*
1655806 TATAAATATAAAAAAAT
1 TATAAATATAAAAATAT
*
1655823 TATTAATATATCAAAAT-T
1 TA-TAA-ATATAAAAATAT
* * *
1655841 TTTATATAT-ATAATAT
1 TATAAATATAAAAATAT
*
1655857 TTTAAATATAA
1 TATAAATATAA
1655868 TTATTATAAA
Statistics
Matches: 51, Mismatches: 7, Indels: 10
0.75 0.10 0.15
Matches are distributed among these distances:
15 4 0.08
16 13 0.25
17 12 0.24
18 10 0.20
19 12 0.24
ACGTcount: A:0.57, C:0.01, G:0.00, T:0.42
Consensus pattern (17 bp):
TATAAATATAAAAATAT
Found at i:1655838 original size:20 final size:18
Alignment explanation
Indices: 1655787--1655832 Score: 67
Period size: 17 Copynumber: 2.6 Consensus size: 18
1655777 TAAAATTTGA
1655787 TATATAATATAAAAAATAT
1 TATA-AATATAAAAAATAT
1655806 TATAAATATAAAAAA-AT
1 TATAAATATAAAAAATAT
*
1655823 TATTAATATA
1 TATAAATATA
1655833 TCAAAATTTT
Statistics
Matches: 26, Mismatches: 1, Indels: 2
0.90 0.03 0.07
Matches are distributed among these distances:
17 11 0.42
18 11 0.42
19 4 0.15
ACGTcount: A:0.63, C:0.00, G:0.00, T:0.37
Consensus pattern (18 bp):
TATAAATATAAAAAATAT
Found at i:1655886 original size:21 final size:21
Alignment explanation
Indices: 1655861--1655914 Score: 56
Period size: 21 Copynumber: 2.6 Consensus size: 21
1655851 TAATATTTTA
1655861 AATATAATTATTATAAAAAAT
1 AATATAATTATTATAAAAAAT
* * * *
1655882 AATATAAATATAATATAAATT
1 AATATAATTATTATAAAAAAT
*
1655903 ATTA-AATTATTA
1 AATATAATTATTA
1655915 AATGTAATAA
Statistics
Matches: 26, Mismatches: 7, Indels: 1
0.76 0.21 0.03
Matches are distributed among these distances:
20 6 0.23
21 20 0.77
ACGTcount: A:0.59, C:0.00, G:0.00, T:0.41
Consensus pattern (21 bp):
AATATAATTATTATAAAAAAT
Found at i:1655911 original size:41 final size:40
Alignment explanation
Indices: 1655794--1655914 Score: 117
Period size: 41 Copynumber: 3.0 Consensus size: 40
1655784 TGATATATAA
*
1655794 TATAAAAAATATTATAAATATAA-AAAAATTATTAA-TA-
1 TATAAAAAATATTATAAATATAATATAAATTATTAATTAT
* * * *
1655831 TATCAAAATTTTTATATATATAATATTTTAAA-TA-TAATTAT
1 TATAAAAAATATTATAAATATAATA---TAAATTATTAATTAT
*
1655872 TATAAAAAATAATATAAATATAATATAAATTATTAAATTAT
1 TATAAAAAATATTATAAATATAATATAAATTATT-AATTAT
1655913 TA
1 TA
1655915 AATGTAATAA
Statistics
Matches: 65, Mismatches: 10, Indels: 14
0.73 0.11 0.16
Matches are distributed among these distances:
37 19 0.29
38 5 0.08
39 5 0.08
40 5 0.08
41 31 0.48
ACGTcount: A:0.57, C:0.01, G:0.00, T:0.42
Consensus pattern (40 bp):
TATAAAAAATATTATAAATATAATATAAATTATTAATTAT
Found at i:1657818 original size:12 final size:12
Alignment explanation
Indices: 1657801--1657869 Score: 50
Period size: 12 Copynumber: 5.4 Consensus size: 12
1657791 TTTCAATTTT
1657801 AAATTAAAAATA
1 AAATTAAAAATA
**
1657813 AAATTATCCAA-A
1 AAATTA-AAAATA
*
1657825 AAATAAAATAAATA
1 AAAT-TAA-AAATA
1657839 AGTAATTAAAAATA
1 A--AATTAAAAATA
*
1657853 AAATTAAAATTA
1 AAATTAAAAATA
1657865 AAATT
1 AAATT
1657870 TTAAAGTACG
Statistics
Matches: 44, Mismatches: 7, Indels: 12
0.70 0.11 0.19
Matches are distributed among these distances:
12 26 0.59
13 5 0.11
14 8 0.18
15 2 0.05
16 3 0.07
ACGTcount: A:0.68, C:0.03, G:0.01, T:0.28
Consensus pattern (12 bp):
AAATTAAAAATA
Found at i:1659874 original size:21 final size:21
Alignment explanation
Indices: 1659848--1659892 Score: 90
Period size: 21 Copynumber: 2.1 Consensus size: 21
1659838 AACTCACCTC
1659848 TCACCTTCAATTTCAAACACA
1 TCACCTTCAATTTCAAACACA
1659869 TCACCTTCAATTTCAAACACA
1 TCACCTTCAATTTCAAACACA
1659890 TCA
1 TCA
1659893 AAGGACTCCT
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 24 1.00
ACGTcount: A:0.38, C:0.33, G:0.00, T:0.29
Consensus pattern (21 bp):
TCACCTTCAATTTCAAACACA
Found at i:1666817 original size:12 final size:12
Alignment explanation
Indices: 1666802--1666826 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
1666792 AATAAAAATT
1666802 AAAAAAAAAAAG
1 AAAAAAAAAAAG
1666814 AAAAAAAAAAAG
1 AAAAAAAAAAAG
1666826 A
1 A
1666827 GAAAGGGAAA
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:0.92, C:0.00, G:0.08, T:0.00
Consensus pattern (12 bp):
AAAAAAAAAAAG
Found at i:1667302 original size:27 final size:26
Alignment explanation
Indices: 1667272--1667332 Score: 63
Period size: 27 Copynumber: 2.3 Consensus size: 26
1667262 TTATTTTTAA
* *
1667272 AATTTAATAAA-ATTAATATTTATATAT
1 AATTTAATAAACAATAATAATTA-A-AT
*
1667299 AATTT-TTAAACAATAATAATTAAAT
1 AATTTAATAAACAATAATAATTAAAT
1667324 AATTTAATA
1 AATTTAATA
1667333 CATGTGGTCA
Statistics
Matches: 28, Mismatches: 4, Indels: 5
0.76 0.11 0.14
Matches are distributed among these distances:
25 7 0.25
26 7 0.25
27 14 0.50
ACGTcount: A:0.54, C:0.02, G:0.00, T:0.44
Consensus pattern (26 bp):
AATTTAATAAACAATAATAATTAAAT
Found at i:1668020 original size:10 final size:10
Alignment explanation
Indices: 1668005--1668030 Score: 52
Period size: 10 Copynumber: 2.6 Consensus size: 10
1667995 CTATATTGTA
1668005 TTAATTATTT
1 TTAATTATTT
1668015 TTAATTATTT
1 TTAATTATTT
1668025 TTAATT
1 TTAATT
1668031 CACCATATAA
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 16 1.00
ACGTcount: A:0.31, C:0.00, G:0.00, T:0.69
Consensus pattern (10 bp):
TTAATTATTT
Found at i:1668807 original size:21 final size:22
Alignment explanation
Indices: 1668750--1668798 Score: 66
Period size: 22 Copynumber: 2.3 Consensus size: 22
1668740 TTAATAAAGA
* *
1668750 TTTAATTTA-ATTT-AAAATTT
1 TTTAAATTATATTTAAAAAGTT
1668770 TTTAAATTATATTTAAAAAGTT
1 TTTAAATTATATTTAAAAAGTT
1668792 TTTAAAT
1 TTTAAAT
1668799 ATTATTAAAC
Statistics
Matches: 25, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
20 8 0.32
21 4 0.16
22 13 0.52
ACGTcount: A:0.43, C:0.00, G:0.02, T:0.55
Consensus pattern (22 bp):
TTTAAATTATATTTAAAAAGTT
Found at i:1668826 original size:14 final size:16
Alignment explanation
Indices: 1668794--1668835 Score: 52
Period size: 14 Copynumber: 2.8 Consensus size: 16
1668784 AAAAAGTTTT
*
1668794 TAAATATTATTAAACA
1 TAAATATTATTAAAAA
1668810 TAAATA-TA-TAAAAA
1 TAAATATTATTAAAAA
*
1668824 TAAATAATATTA
1 TAAATATTATTA
1668836 CATCATTATT
Statistics
Matches: 23, Mismatches: 1, Indels: 4
0.82 0.04 0.14
Matches are distributed among these distances:
14 11 0.48
15 4 0.17
16 8 0.35
ACGTcount: A:0.62, C:0.02, G:0.00, T:0.36
Consensus pattern (16 bp):
TAAATATTATTAAAAA
Found at i:1670245 original size:20 final size:21
Alignment explanation
Indices: 1670220--1670260 Score: 57
Period size: 21 Copynumber: 2.0 Consensus size: 21
1670210 TAAATTTTAT
1670220 ATTAAAAAT-TATATTATTAA
1 ATTAAAAATATATATTATTAA
* *
1670240 ATTAAATATATATTTTATTAA
1 ATTAAAAATATATATTATTAA
1670261 TTATTTATCA
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
20 8 0.44
21 10 0.56
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (21 bp):
ATTAAAAATATATATTATTAA
Found at i:1670925 original size:28 final size:28
Alignment explanation
Indices: 1670846--1670925 Score: 65
Period size: 28 Copynumber: 2.8 Consensus size: 28
1670836 TATAATTTTT
* *
1670846 AAATTAATTTTTTATTTAATTTCTTAAAA
1 AAATTAATTATTTATATAA-TTCTTAAAA
* *
1670875 ATAATTGATTTTATTTA-AAAATT-TTAAAA
1 A-AATT-A-ATTATTTATATAATTCTTAAAA
1670904 AAATTAATTCATTTATATAATT
1 AAATTAATT-ATTTATATAATT
1670926 ATTTTTAAAA
Statistics
Matches: 40, Mismatches: 6, Indels: 11
0.70 0.11 0.19
Matches are distributed among these distances:
26 2 0.05
27 6 0.15
28 9 0.22
29 8 0.20
30 6 0.15
31 3 0.08
32 6 0.15
ACGTcount: A:0.45, C:0.03, G:0.01, T:0.51
Consensus pattern (28 bp):
AAATTAATTATTTATATAATTCTTAAAA
Found at i:1670964 original size:13 final size:15
Alignment explanation
Indices: 1670936--1670979 Score: 56
Period size: 15 Copynumber: 2.9 Consensus size: 15
1670926 ATTTTTAAAA
1670936 TAATATTTAATAAATT
1 TAATATTT-ATAAATT
1670952 TAA-ATTT-TAAATTT
1 TAATATTTATAAA-TT
1670966 TAATATTTATAAAT
1 TAATATTTATAAAT
1670980 ATTTTTATTC
Statistics
Matches: 25, Mismatches: 0, Indels: 7
0.78 0.00 0.22
Matches are distributed among these distances:
13 4 0.16
14 5 0.20
15 9 0.36
16 7 0.28
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (15 bp):
TAATATTTATAAATT
Found at i:1671056 original size:32 final size:31
Alignment explanation
Indices: 1670998--1671062 Score: 78
Period size: 32 Copynumber: 2.1 Consensus size: 31
1670988 TCTTTAAATT
*
1670998 ATAATTTTTTAATATTAAATTAAAAATATATA
1 ATAATATTTTAATATTAAATTAAAAAT-TATA
* *
1671030 ATAATATTTTAAT-TTTACTTATAAAATTATA
1 ATAATATTTTAATATTAAATTA-AAAATTATA
1671061 AT
1 AT
1671063 TAAATTAATA
Statistics
Matches: 29, Mismatches: 3, Indels: 3
0.83 0.09 0.09
Matches are distributed among these distances:
31 12 0.41
32 17 0.59
ACGTcount: A:0.49, C:0.02, G:0.00, T:0.49
Consensus pattern (31 bp):
ATAATATTTTAATATTAAATTAAAAATTATA
Found at i:1671113 original size:17 final size:17
Alignment explanation
Indices: 1671086--1671126 Score: 50
Period size: 17 Copynumber: 2.5 Consensus size: 17
1671076 ATATAAATTT
1671086 AAAAA-ATAAAA-ATAAC
1 AAAAACATAAAATA-AAC
*
1671102 ATAAACATAAAATAAAC
1 AAAAACATAAAATAAAC
1671119 AAAAACAT
1 AAAAACAT
1671127 TTAAATTTTG
Statistics
Matches: 21, Mismatches: 2, Indels: 3
0.81 0.08 0.12
Matches are distributed among these distances:
16 4 0.19
17 16 0.76
18 1 0.05
ACGTcount: A:0.76, C:0.10, G:0.00, T:0.15
Consensus pattern (17 bp):
AAAAACATAAAATAAAC
Found at i:1671259 original size:21 final size:21
Alignment explanation
Indices: 1671233--1671272 Score: 55
Period size: 21 Copynumber: 1.9 Consensus size: 21
1671223 AAAAATTTAA
1671233 AATAAATATAA-ATAATTTTTT
1 AATAAA-ATAATATAATTTTTT
*
1671254 AATAAAATAATATTATTTT
1 AATAAAATAATATAATTTT
1671273 ATTTTACATT
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
20 4 0.24
21 13 0.76
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (21 bp):
AATAAAATAATATAATTTTTT
Found at i:1671391 original size:37 final size:36
Alignment explanation
Indices: 1671320--1671391 Score: 85
Period size: 37 Copynumber: 2.0 Consensus size: 36
1671310 AGTAAATTTT
* *
1671320 ATATTTTTAATAATTTATAATAAAAAAGATTAAATA
1 ATATTTTTAAAAATTTATAATAAAAAAGAATAAATA
1671356 ATATTTTTAAAAATATTGA-AATAAAAATA-AATAAAT
1 ATATTTTTAAAAAT-TT-ATAATAAAAA-AGAATAAAT
1671392 TTTTTAAAAA
Statistics
Matches: 31, Mismatches: 2, Indels: 5
0.82 0.05 0.13
Matches are distributed among these distances:
36 13 0.42
37 16 0.52
38 2 0.06
ACGTcount: A:0.58, C:0.00, G:0.03, T:0.39
Consensus pattern (36 bp):
ATATTTTTAAAAATTTATAATAAAAAAGAATAAATA
Found at i:1671401 original size:20 final size:19
Alignment explanation
Indices: 1671378--1671437 Score: 57
Period size: 20 Copynumber: 2.9 Consensus size: 19
1671368 ATATTGAAAT
*
1671378 AAAAATAAATAAATTTTTTAA
1 AAAAATAAATAAA--TATTAA
*
1671399 AAAATTAAATTAAATATTAA
1 AAAAATAAA-TAAATATTAA
*
1671419 AAAAATATAATAATTATTA
1 AAAAATA-AATAAATATTA
1671438 TTTTATTTGT
Statistics
Matches: 33, Mismatches: 4, Indels: 5
0.79 0.10 0.12
Matches are distributed among these distances:
20 19 0.58
21 10 0.30
22 4 0.12
ACGTcount: A:0.63, C:0.00, G:0.00, T:0.37
Consensus pattern (19 bp):
AAAAATAAATAAATATTAA
Found at i:1671421 original size:21 final size:20
Alignment explanation
Indices: 1671366--1671437 Score: 56
Period size: 21 Copynumber: 3.4 Consensus size: 20
1671356 ATATTTTTAA
*
1671366 AAATATTGAAATAAAAATAAAT
1 AAATATT-AAA-AAAATTAAAT
* *
1671388 AAATTTTTTAAAAAATTAAATT
1 AAA-TATTAAAAAAATTAAA-T
1671410 AAATATTAAAAAAA-TATAAT
1 AAATATTAAAAAAATTA-AAT
*
1671430 AATTATTA
1 AAATATTA
1671438 TTTTATTTGT
Statistics
Matches: 41, Mismatches: 6, Indels: 8
0.75 0.11 0.15
Matches are distributed among these distances:
20 10 0.24
21 19 0.46
22 9 0.22
23 3 0.07
ACGTcount: A:0.62, C:0.00, G:0.01, T:0.36
Consensus pattern (20 bp):
AAATATTAAAAAAATTAAAT
Found at i:1671422 original size:22 final size:20
Alignment explanation
Indices: 1671366--1671437 Score: 56
Period size: 20 Copynumber: 3.4 Consensus size: 20
1671356 ATATTTTTAA
1671366 AAATATTGAAATAAAAATAAAT
1 AAATATT-AAA-AAAAATAAAT
* * *
1671388 AAATTTTTTAAAAAATTAAATT
1 AAA-TATTAAAAAAAATAAA-T
1671410 AAATATT-AAAAAAATATAAT
1 AAATATTAAAAAAAATA-AAT
*
1671430 AATTATTA
1 AAATATTA
1671438 TTTTATTTGT
Statistics
Matches: 40, Mismatches: 6, Indels: 9
0.73 0.11 0.16
Matches are distributed among these distances:
20 15 0.38
21 13 0.32
22 9 0.22
23 3 0.08
ACGTcount: A:0.62, C:0.00, G:0.01, T:0.36
Consensus pattern (20 bp):
AAATATTAAAAAAAATAAAT
Found at i:1671481 original size:18 final size:20
Alignment explanation
Indices: 1671452--1671488 Score: 60
Period size: 19 Copynumber: 1.9 Consensus size: 20
1671442 ATTTGTTAAA
1671452 TTTATAAATATTA-TAATTT
1 TTTATAAATATTATTAATTT
1671471 TTTAT-AATATTATTAATT
1 TTTATAAATATTATTAATT
1671489 GAGTTGATGG
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
18 7 0.41
19 10 0.59
ACGTcount: A:0.41, C:0.00, G:0.00, T:0.59
Consensus pattern (20 bp):
TTTATAAATATTATTAATTT
Found at i:1677100 original size:16 final size:15
Alignment explanation
Indices: 1677079--1677109 Score: 53
Period size: 15 Copynumber: 2.0 Consensus size: 15
1677069 ATATTAATTC
1677079 AATTAAAAAAATAAAA
1 AATT-AAAAAATAAAA
1677095 AATTAAAAAATAAAA
1 AATTAAAAAATAAAA
1677110 CTATATTAAC
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
15 11 0.73
16 4 0.27
ACGTcount: A:0.81, C:0.00, G:0.00, T:0.19
Consensus pattern (15 bp):
AATTAAAAAATAAAA
Found at i:1678911 original size:21 final size:22
Alignment explanation
Indices: 1678887--1678934 Score: 64
Period size: 21 Copynumber: 2.2 Consensus size: 22
1678877 GTAATGATTG
1678887 AAAAAAATA-ATATTTTT-TAAT
1 AAAAAAATATA-ATTTTTATAAT
1678908 AAAAAAATATAATTTTTATAAT
1 AAAAAAATATAATTTTTATAAT
*
1678930 CAAAA
1 AAAAA
1678935 GTTGTCATAT
Statistics
Matches: 24, Mismatches: 1, Indels: 3
0.86 0.04 0.11
Matches are distributed among these distances:
21 15 0.62
22 9 0.38
ACGTcount: A:0.60, C:0.02, G:0.00, T:0.38
Consensus pattern (22 bp):
AAAAAAATATAATTTTTATAAT
Found at i:1678923 original size:20 final size:21
Alignment explanation
Indices: 1678887--1678925 Score: 62
Period size: 20 Copynumber: 1.9 Consensus size: 21
1678877 GTAATGATTG
*
1678887 AAAAAAATAATATTTTTTAAT
1 AAAAAAATAATAATTTTTAAT
1678908 AAAAAAAT-ATAATTTTTA
1 AAAAAAATAATAATTTTTA
1678926 TAATCAAAAG
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
20 9 0.53
21 8 0.47
ACGTcount: A:0.59, C:0.00, G:0.00, T:0.41
Consensus pattern (21 bp):
AAAAAAATAATAATTTTTAAT
Found at i:1683512 original size:2 final size:2
Alignment explanation
Indices: 1683507--1683539 Score: 66
Period size: 2 Copynumber: 16.5 Consensus size: 2
1683497 TTATTTTTAA
1683507 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1683540 CACACACACG
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 31 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:1689293 original size:25 final size:22
Alignment explanation
Indices: 1689236--1689284 Score: 98
Period size: 22 Copynumber: 2.2 Consensus size: 22
1689226 TGGACATGTT
1689236 AAAAATGCATGAAACATAATAA
1 AAAAATGCATGAAACATAATAA
1689258 AAAAATGCATGAAACATAATAA
1 AAAAATGCATGAAACATAATAA
1689280 AAAAA
1 AAAAA
1689285 AGATGCATGG
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 27 1.00
ACGTcount: A:0.67, C:0.08, G:0.08, T:0.16
Consensus pattern (22 bp):
AAAAATGCATGAAACATAATAA
Found at i:1690252 original size:20 final size:20
Alignment explanation
Indices: 1690205--1690279 Score: 80
Period size: 20 Copynumber: 3.8 Consensus size: 20
1690195 AAAAAGACAT
*
1690205 AATGTATCGATACATT-GTA
1 AATGTATCGATACATTCATA
*
1690224 GAATATATCGATACATTCATA
1 -AATGTATCGATACATTCATA
* * * *
1690245 CATGTATCGATATATTGAAA
1 AATGTATCGATACATTCATA
1690265 AATGTATCGATACAT
1 AATGTATCGATACAT
1690280 CAGGGTATGA
Statistics
Matches: 45, Mismatches: 9, Indels: 2
0.80 0.16 0.04
Matches are distributed among these distances:
20 43 0.96
21 2 0.04
ACGTcount: A:0.40, C:0.12, G:0.13, T:0.35
Consensus pattern (20 bp):
AATGTATCGATACATTCATA
Found at i:1690273 original size:40 final size:39
Alignment explanation
Indices: 1690202--1690279 Score: 111
Period size: 40 Copynumber: 2.0 Consensus size: 39
1690192 GTAAAAAAGA
* *
1690202 CATAATGTATCGATACATTGTAGAATATATCGATACATT
1 CATAATGTATCGATACATTGAAAAATATATCGATACATT
* *
1690241 CATACATGTATCGATATATTGAAAAATGTATCGATACAT
1 CATA-ATGTATCGATACATTGAAAAATATATCGATACAT
1690280 CAGGGTATGA
Statistics
Matches: 34, Mismatches: 4, Indels: 1
0.87 0.10 0.03
Matches are distributed among these distances:
39 4 0.12
40 30 0.88
ACGTcount: A:0.40, C:0.13, G:0.13, T:0.35
Consensus pattern (39 bp):
CATAATGTATCGATACATTGAAAAATATATCGATACATT
Found at i:1690883 original size:28 final size:28
Alignment explanation
Indices: 1690806--1692581 Score: 964
Period size: 28 Copynumber: 61.6 Consensus size: 28
1690796 TGAAAAGGGT
* * * *
1690806 TGCCATTGACTTGCATGGGATTTAAAAGGG
1 TGCCACTGACTTG--TGGGCTTTGAAAGAG
*
1690836 TGCCACTGACTTGCGTGGGCTTTGAAAGAA
1 TGCCACTGACTT--GTGGGCTTTGAAAGAG
* *
1690866 TGCCACTAACTCGTGGGCTTTGAAAG-G
1 TGCCACTGACTTGTGGGCTTTGAAAGAG
1690893 ATGCCACTGACTTGTGGGCTTTGAAAGAG
1 -TGCCACTGACTTGTGGGCTTTGAAAGAG
1690922 TGCCACTGACTTGTGGGCTTTGAAA-AGG
1 TGCCACTGACTTGTGGGCTTTGAAAGA-G
* * *
1690950 TACCACTGACTTGCGTGAGCTTTAAAAGGAG
1 TGCCACTGACTT--GTGGGCTTTGAAA-GAG
* *
1690981 TGCCACTGACTTGTGTGGGCTTTAAAAGGG
1 TGCCACTGAC-T-TGTGGGCTTTGAAAGAG
*
1691011 TGCCACTGACTTGTGGGCTTTAAAAGAG
1 TGCCACTGACTTGTGGGCTTTGAAAGAG
* *
1691039 TGCCACTGAATTGTGGGC-TTCACAATG-G
1 TGCCACTGACTTGTGGGCTTTGA-AA-GAG
* *
1691067 TGCCACTGACTTGTGGGCTTCGAAAGGG
1 TGCCACTGACTTGTGGGCTTTGAAAGAG
* *
1691095 TGCCACTGACTTGTGGGCTCTGAAAGGG
1 TGCCACTGACTTGTGGGCTTTGAAAGAG
* *
1691123 TGCCACTAACTTGTGGGCTTTGAAAGGG
1 TGCCACTGACTTGTGGGCTTTGAAAGAG
1691151 TGCCACTGACTTGTGGGCTTTGAAAAGAG
1 TGCCACTGACTTGTGGGCTTTG-AAAGAG
* *
1691180 TGCCACTGATTTGTGGGCTTTGAAAAGAA
1 TGCCACTGACTTGTGGGCTTTG-AAAGAG
*
1691209 TGCCACTAACTTGTGGGCTTTGAAAGGAG
1 TGCCACTGACTTGTGGGCTTTGAAA-GAG
*
1691238 TGCCACTGACTTGTGGGCTTTGAAAGGG
1 TGCCACTGACTTGTGGGCTTTGAAAGAG
*
1691266 TGCCACTAACTTGTGGGCTTTGAAAAGAG
1 TGCCACTGACTTGTGGGCTTTG-AAAGAG
*
1691295 TGCCACTGATTTGTGGGCTTTGAAAAGAG
1 TGCCACTGACTTGTGGGCTTTG-AAAGAG
1691324 TGCCACTGACTTGTGGGCTTTGAAAGGAG
1 TGCCACTGACTTGTGGGCTTTGAAA-GAG
*
1691353 TGCCACTGACTTGTGGGCTTTGAAAGGG
1 TGCCACTGACTTGTGGGCTTTGAAAGAG
* *
1691381 TGCCACTGAGTTGTGGGCTTTGAAAGGG
1 TGCCACTGACTTGTGGGCTTTGAAAGAG
*
1691409 TGCCACTAACTTGTGGGCTTTGAAAAGAG
1 TGCCACTGACTTGTGGGCTTTG-AAAGAG
* *
1691438 TGCCACTGATTTGTGGGCTTTGAAATGGG
1 TGCCACTGACTTGTGGGCTTTGAAA-GAG
* *
1691467 TTGCCACTGACTTGTGTGGGCTTTGGAATGGG
1 -TGCCACTGAC-T-TGTGGGCTTT-GAAAGAG
* *
1691499 TTGCCACTGACTTGTGTGGGCTTTGGAATGGG
1 -TGCCACTGAC-T-TGTGGGCTTT-GAAAGAG
* *
1691531 TTGCCACCGACTTGTGTGGGCTTTGAAATGGG
1 -TGCCACTGAC-T-TGTGGGCTTTGAAA-GAG
* * *
1691563 TTGCCACCGACTTGTGTGGGCTTTGGAATGGG
1 -TGCCACTGAC-T-TGTGGGCTTT-GAAAGAG
* * *
1691595 TTGCCACCGACTTGTGTGGGCTTTGGAATGGG
1 -TGCCACTGAC-T-TGTGGGCTTT-GAAAGAG
* * *
1691627 TTGCCACCGACTTGTGTGGGCTTTGGAATGGG
1 -TGCCACTGAC-T-TGTGGGCTTT-GAAAGAG
* * *
1691659 TTGCCACCGACTTGTGTGGGCTTTGGAATGGG
1 -TGCCACTGAC-T-TGTGGGCTTT-GAAAGAG
* * *
1691691 TTGCCACCGACTTGTGTGGGCTTTGGAATGGG
1 -TGCCACTGAC-T-TGTGGGCTTT-GAAAGAG
* * *
1691723 TTGCCACCGACTTGTGTGGGCTTTGGAATGGG
1 -TGCCACTGAC-T-TGTGGGCTTT-GAAAGAG
* *
1691755 TTGCCACCGACTTGTGTGGGCTTTGAAATGGG
1 -TGCCACTGAC-T-TGTGGGCTTTGAAA-GAG
* *
1691787 TTGCCACCGACTTGTGTGGGCTTTGAAATGGG
1 -TGCCACTGAC-T-TGTGGGCTTTGAAA-GAG
* *
1691819 TTGCCACCGACTTGTGTGGGCTTTGAAATGGG
1 -TGCCACTGAC-T-TGTGGGCTTTGAAA-GAG
* *
1691851 TTGCCACTGACTTGTGTGGGCTTTGAATTGGG
1 -TGCCACTGAC-T-TGTGGGCTTTGAA-AGAG
* * * *
1691883 TGCCACGGAGTTGT-GGATTT-AAAAAG
1 TGCCACTGACTTGTGGGCTTTGAAAGAG
* * * * *
1691909 ATGCCACGGAGTTGTGGAC-TTAAAAGGG
1 -TGCCACTGACTTGTGGGCTTTGAAAGAG
* * * * *
1691937 TGCCACAGAGTTGTGGTC-TTAAAAGGG
1 TGCCACTGACTTGTGGGCTTTGAAAGAG
* * * * *
1691964 ATGCCACGGAGTTGTGGAC-TTAAAAGGG
1 -TGCCACTGACTTGTGGGCTTTGAAAGAG
* * * * *
1691992 TGCCACGGAGTTGTGGAC-TTAAAAGGG
1 TGCCACTGACTTGTGGGCTTTGAAAGAG
* * * * *
1692019 TGCCACGGAGTTGTGGAC-TTAAAAGGG
1 TGCCACTGACTTGTGGGCTTTGAAAGAG
* * * * * *
1692046 TACCACGGAGTTGTGGAC-TTAAAAGGG
1 TGCCACTGACTTGTGGGCTTTGAAAGAG
* * * * *
1692073 TGCCACGGAGTTATGGAC-TTAAAAGAG
1 TGCCACTGACTTGTGGGCTTTGAAAGAG
* * * **
1692100 TGCCACGGAGTTGTGGACTTAAAAAG-G
1 TGCCACTGACTTGTGGGCTTTGAAAGAG
* * * * *
1692127 TGCTAC-GAAGTTGTGGAC-TTAAAAGGG
1 TGCCACTG-ACTTGTGGGCTTTGAAAGAG
* * * * *
1692154 TGCCACAGAGTTGTGGAC-TTAAAAGGG
1 TGCCACTGACTTGTGGGCTTTGAAAGAG
* * * * *
1692181 TGCCACGGAGTTATGGAC-TTAAAAGAG
1 TGCCACTGACTTGTGGGCTTTGAAAGAG
* * * * *
1692208 ATGCCACGGAGTTGTGGAC-TTAAAAGGG
1 -TGCCACTGACTTGTGGGCTTTGAAAGAG
* * * * *
1692236 ATGCCACGGAGTTGTGGAC-TTAAAAGGG
1 -TGCCACTGACTTGTGGGCTTTGAAAGAG
* * * * *
1692264 TGCCACGGAGTTGTGGAC-TTAAAAGGG
1 TGCCACTGACTTGTGGGCTTTGAAAGAG
* *
1692291 TGCCA-TGGAGTTGTGGAC-TT-AAAGAGGG
1 TGCCACT-GACTTGTGGGCTTTGAAAGA--G
* * * *
1692319 TGCCACGGAGTTGTGGACTTTAAAAGAG
1 TGCCACTGACTTGTGGGCTTTGAAAGAG
* * * * * * *
1692347 CGCTACGGAGTTGTGGAC-TTAAAAGGG
1 TGCCACTGACTTGTGGGCTTTGAAAGAG
* * *
1692374 TGCCACGGAGTTGTGGACTTTGAAAG-G
1 TGCCACTGACTTGTGGGCTTTGAAAGAG
* * * * *
1692401 TGCCACAGAGTTGTGGAC-TTAAAAGGG
1 TGCCACTGACTTGTGGGCTTTGAAAGAG
* * * * *
1692428 TGCTACGGAGTTGTGGACTTTAAAAGAG
1 TGCCACTGACTTGTGGGCTTTGAAAGAG
* * * *
1692456 TGCCACGGAGTTGTGGACTTTG-AAGGG
1 TGCCACTGACTTGTGGGCTTTGAAAGAG
* * * *
1692483 TGCCACGGAGTTGTGGAC-TTAAAAGAG
1 TGCCACTGACTTGTGGGCTTTGAAAGAG
* * * *
1692510 TGCCACAGAGTTGTGGACTTTAAAAGAG
1 TGCCACTGACTTGTGGGCTTTGAAAGAG
* * * *
1692538 TGCCACGGAGTTGTGGACTTTAAAAGAG
1 TGCCACTGACTTGTGGGCTTTGAAAGAG
* *
1692566 TGCCACGGAGTTGTGG
1 TGCCACTGACTTGTGG
1692582 ATTTAAAAGG
Statistics
Matches: 1592, Mismatches: 105, Indels: 100
0.89 0.06 0.06
Matches are distributed among these distances:
26 20 0.01
27 381 0.24
28 500 0.31
29 196 0.12
30 70 0.04
31 37 0.02
32 381 0.24
33 7 0.00
ACGTcount: A:0.22, C:0.16, G:0.34, T:0.27
Consensus pattern (28 bp):
TGCCACTGACTTGTGGGCTTTGAAAGAG
Found at i:1691490 original size:32 final size:30
Alignment explanation
Indices: 1690794--1691888 Score: 1078
Period size: 32 Copynumber: 36.6 Consensus size: 30
1690784 ACAGTGGTGA
* * *
1690794 TTTGAAAAGGGTTGCCATTGAC-TTGCATGGGA
1 TTTGAAATGGG-TGCCACTGACTTTG--TGGGC
* *
1690826 TTT-AAAAGGGTGCCACTGACTTGCGTGGGC
1 TTTGAAATGGGTGCCACTGACTT-TGTGGGC
** * *
1690856 TTTGAAA-GAATGCCACTAAC-TCGTGGGC
1 TTTGAAATGGGTGCCACTGACTTTGTGGGC
*
1690884 TTTGAAA-GGATGCCACTGAC-TTGTGGGC
1 TTTGAAATGGGTGCCACTGACTTTGTGGGC
*
1690912 TTTGAAA-GAGTGCCACTGAC-TTGTGGGC
1 TTTGAAATGGGTGCCACTGACTTTGTGGGC
* * * *
1690940 TTTGAAA-AGGTACCACTGACTTGCGTGAGC
1 TTTGAAATGGGTGCCACTGACTT-TGTGGGC
*
1690970 TTT-AAAAGGAGTGCCACTGACTTGTGTGGGC
1 TTTGAAATGG-GTGCCACTGACTT-TGTGGGC
*
1691001 TTT-AAAAGGGTGCCACTGAC-TTGTGGGC
1 TTTGAAATGGGTGCCACTGACTTTGTGGGC
* * *
1691029 TTT-AAAAGAGTGCCACTGA-ATTGTGGGC
1 TTTGAAATGGGTGCCACTGACTTTGTGGGC
*
1691057 -TTCACAAT-GGTGCCACTGAC-TTGTGGGC
1 TTTGA-AATGGGTGCCACTGACTTTGTGGGC
*
1691085 TTCGAAA-GGGTGCCACTGAC-TTGTGGGC
1 TTTGAAATGGGTGCCACTGACTTTGTGGGC
* *
1691113 TCTGAAA-GGGTGCCACTAAC-TTGTGGGC
1 TTTGAAATGGGTGCCACTGACTTTGTGGGC
1691141 TTTGAAA-GGGTGCCACTGAC-TTGTGGGC
1 TTTGAAATGGGTGCCACTGACTTTGTGGGC
* *
1691169 TTTGAAAAGAGTGCCACTGA-TTTGTGGGC
1 TTTGAAATGGGTGCCACTGACTTTGTGGGC
* ** *
1691198 TTTGAAAAGAATGCCACTAAC-TTGTGGGC
1 TTTGAAATGGGTGCCACTGACTTTGTGGGC
1691227 TTTGAAA-GGAGTGCCACTGAC-TTGTGGGC
1 TTTGAAATGG-GTGCCACTGACTTTGTGGGC
*
1691256 TTTGAAA-GGGTGCCACTAAC-TTGTGGGC
1 TTTGAAATGGGTGCCACTGACTTTGTGGGC
* *
1691284 TTTGAAAAGAGTGCCACTGA-TTTGTGGGC
1 TTTGAAATGGGTGCCACTGACTTTGTGGGC
* *
1691313 TTTGAAAAGAGTGCCACTGAC-TTGTGGGC
1 TTTGAAATGGGTGCCACTGACTTTGTGGGC
1691342 TTTGAAA-GGAGTGCCACTGAC-TTGTGGGC
1 TTTGAAATGG-GTGCCACTGACTTTGTGGGC
*
1691371 TTTGAAA-GGGTGCCACTGA-GTTGTGGGC
1 TTTGAAATGGGTGCCACTGACTTTGTGGGC
*
1691399 TTTGAAA-GGGTGCCACTAAC-TTGTGGGC
1 TTTGAAATGGGTGCCACTGACTTTGTGGGC
* *
1691427 TTTGAAAAGAGTGCCACTGA-TTTGTGGGC
1 TTTGAAATGGGTGCCACTGACTTTGTGGGC
1691456 TTTGAAATGGGTTGCCACTGACTTGTGTGGGC
1 TTTGAAATGGG-TGCCACTGACTT-TGTGGGC
*
1691488 TTTGGAATGGGTTGCCACTGACTTGTGTGGGC
1 TTTGAAATGGG-TGCCACTGACTT-TGTGGGC
* *
1691520 TTTGGAATGGGTTGCCACCGACTTGTGTGGGC
1 TTTGAAATGGG-TGCCACTGACTT-TGTGGGC
*
1691552 TTTGAAATGGGTTGCCACCGACTTGTGTGGGC
1 TTTGAAATGGG-TGCCACTGACTT-TGTGGGC
* *
1691584 TTTGGAATGGGTTGCCACCGACTTGTGTGGGC
1 TTTGAAATGGG-TGCCACTGACTT-TGTGGGC
* *
1691616 TTTGGAATGGGTTGCCACCGACTTGTGTGGGC
1 TTTGAAATGGG-TGCCACTGACTT-TGTGGGC
* *
1691648 TTTGGAATGGGTTGCCACCGACTTGTGTGGGC
1 TTTGAAATGGG-TGCCACTGACTT-TGTGGGC
* *
1691680 TTTGGAATGGGTTGCCACCGACTTGTGTGGGC
1 TTTGAAATGGG-TGCCACTGACTT-TGTGGGC
* *
1691712 TTTGGAATGGGTTGCCACCGACTTGTGTGGGC
1 TTTGAAATGGG-TGCCACTGACTT-TGTGGGC
* *
1691744 TTTGGAATGGGTTGCCACCGACTTGTGTGGGC
1 TTTGAAATGGG-TGCCACTGACTT-TGTGGGC
*
1691776 TTTGAAATGGGTTGCCACCGACTTGTGTGGGC
1 TTTGAAATGGG-TGCCACTGACTT-TGTGGGC
*
1691808 TTTGAAATGGGTTGCCACCGACTTGTGTGGGC
1 TTTGAAATGGG-TGCCACTGACTT-TGTGGGC
1691840 TTTGAAATGGGTTGCCACTGACTTGTGTGGGC
1 TTTGAAATGGG-TGCCACTGACTT-TGTGGGC
*
1691872 TTTGAATTGGGTGCCAC
1 TTTGAAATGGGTGCCAC
1691889 GGAGTTGTGG
Statistics
Matches: 983, Mismatches: 52, Indels: 57
0.90 0.05 0.05
Matches are distributed among these distances:
27 2 0.00
28 285 0.29
29 196 0.20
30 55 0.06
31 46 0.05
32 399 0.41
ACGTcount: A:0.19, C:0.18, G:0.33, T:0.30
Consensus pattern (30 bp):
TTTGAAATGGGTGCCACTGACTTTGTGGGC
Found at i:1691921 original size:27 final size:27
Alignment explanation
Indices: 1691880--1692617 Score: 1100
Period size: 27 Copynumber: 27.0 Consensus size: 27
1691870 GCTTTGAATT
*
1691880 GGGTGCCACGGAGTTGTGGATTTAAAA
1 GGGTGCCACGGAGTTGTGGACTTAAAA
* *
1691907 AGATGCCACGGAGTTGTGGACTTAAAA
1 GGGTGCCACGGAGTTGTGGACTTAAAA
* *
1691934 GGGTGCCACAGAGTTGTGGTCTTAAAA
1 GGGTGCCACGGAGTTGTGGACTTAAAA
1691961 GGGATGCCACGGAGTTGTGGACTTAAAA
1 GGG-TGCCACGGAGTTGTGGACTTAAAA
1691989 GGGTGCCACGGAGTTGTGGACTTAAAA
1 GGGTGCCACGGAGTTGTGGACTTAAAA
1692016 GGGTGCCACGGAGTTGTGGACTTAAAA
1 GGGTGCCACGGAGTTGTGGACTTAAAA
*
1692043 GGGTACCACGGAGTTGTGGACTTAAAA
1 GGGTGCCACGGAGTTGTGGACTTAAAA
*
1692070 GGGTGCCACGGAGTTATGGACTTAAAA
1 GGGTGCCACGGAGTTGTGGACTTAAAA
*
1692097 GAGTGCCACGGAGTTGTGGACTTAAAA
1 GGGTGCCACGGAGTTGTGGACTTAAAA
* * *
1692124 AGGTGCTACGAAGTTGTGGACTTAAAA
1 GGGTGCCACGGAGTTGTGGACTTAAAA
*
1692151 GGGTGCCACAGAGTTGTGGACTTAAAA
1 GGGTGCCACGGAGTTGTGGACTTAAAA
*
1692178 GGGTGCCACGGAGTTATGGACTTAAAA
1 GGGTGCCACGGAGTTGTGGACTTAAAA
*
1692205 GAGATGCCACGGAGTTGTGGACTTAAAA
1 G-GGTGCCACGGAGTTGTGGACTTAAAA
1692233 GGGATGCCACGGAGTTGTGGACTTAAAA
1 GGG-TGCCACGGAGTTGTGGACTTAAAA
1692261 GGGTGCCACGGAGTTGTGGACTTAAAA
1 GGGTGCCACGGAGTTGTGGACTTAAAA
*
1692288 GGGTGCCATGGAGTTGTGGACTTAAAGA
1 GGGTGCCACGGAGTTGTGGACTTAAA-A
1692316 GGGTGCCACGGAGTTGTGGACTTTAAAA
1 GGGTGCCACGGAGTTGTGGAC-TTAAAA
* * *
1692344 GAGCGCTACGGAGTTGTGGACTTAAAA
1 GGGTGCCACGGAGTTGTGGACTTAAAA
*
1692371 GGGTGCCACGGAGTTGTGGACTTTGAAA
1 GGGTGCCACGGAGTTGTGGAC-TTAAAA
*
1692399 -GGTGCCACAGAGTTGTGGACTTAAAA
1 GGGTGCCACGGAGTTGTGGACTTAAAA
*
1692425 GGGTGCTACGGAGTTGTGGACTTTAAAA
1 GGGTGCCACGGAGTTGTGGAC-TTAAAA
* **
1692453 GAGTGCCACGGAGTTGTGGACTTTGAA
1 GGGTGCCACGGAGTTGTGGACTTAAAA
1692480 GGGTGCCACGGAGTTGTGGACTTAAAA
1 GGGTGCCACGGAGTTGTGGACTTAAAA
* *
1692507 GAGTGCCACAGAGTTGTGGACTTTAAAA
1 GGGTGCCACGGAGTTGTGGAC-TTAAAA
*
1692535 GAGTGCCACGGAGTTGTGGACTTTAAAA
1 GGGTGCCACGGAGTTGTGGAC-TTAAAA
* *
1692563 GAGTGCCACGGAGTTGTGGATTTAAAA
1 GGGTGCCACGGAGTTGTGGACTTAAAA
* *
1692590 GGATGCCACGGAGATGTGGACTTCAAAA
1 GGGTGCCACGGAGTTGTGGACTT-AAAA
1692618 AGAAATGCCA
Statistics
Matches: 646, Mismatches: 55, Indels: 19
0.90 0.08 0.03
Matches are distributed among these distances:
26 5 0.01
27 432 0.67
28 204 0.32
29 5 0.01
ACGTcount: A:0.28, C:0.14, G:0.34, T:0.23
Consensus pattern (27 bp):
GGGTGCCACGGAGTTGTGGACTTAAAA
Found at i:1692020 original size:82 final size:81
Alignment explanation
Indices: 1691880--1692617 Score: 1100
Period size: 82 Copynumber: 9.0 Consensus size: 81
1691870 GCTTTGAATT
* * * *
1691880 GGGTGCCACGGAGTTGTGGATTTAAAAAGATGCCACGGAGTTGTGGACTTAAAAGGGTGCCACAG
1 GGGTGCCACGGAGTTGTGGACTTAAAAGGGTGCCACGGAGTTGTGGACTTAAAAGGGTGCCACGG
*
1691945 AGTTGTGGTCTTAAAA
66 AGTTGTGGACTTAAAA
1691961 GGGATGCCACGGAGTTGTGGACTTAAAAGGGTGCCACGGAGTTGTGGACTTAAAAGGGTGCCACG
1 GGG-TGCCACGGAGTTGTGGACTTAAAAGGGTGCCACGGAGTTGTGGACTTAAAAGGGTGCCACG
1692026 GAGTTGTGGACTTAAAA
65 GAGTTGTGGACTTAAAA
* * *
1692043 GGGTACCACGGAGTTGTGGACTTAAAAGGGTGCCACGGAGTTATGGACTTAAAAGAGTGCCACGG
1 GGGTGCCACGGAGTTGTGGACTTAAAAGGGTGCCACGGAGTTGTGGACTTAAAAGGGTGCCACGG
1692108 AGTTGTGGACTTAAAA
66 AGTTGTGGACTTAAAA
* * * *
1692124 AGGTGCTACGAAGTTGTGGACTTAAAAGGGTGCCACAGAGTTGTGGACTTAAAAGGGTGCCACGG
1 GGGTGCCACGGAGTTGTGGACTTAAAAGGGTGCCACGGAGTTGTGGACTTAAAAGGGTGCCACGG
*
1692189 AGTTATGGACTTAAAA
66 AGTTGTGGACTTAAAA
*
1692205 GAGATGCCACGGAGTTGTGGACTTAAAAGGGATGCCACGGAGTTGTGGACTTAAAAGGGTGCCAC
1 G-GGTGCCACGGAGTTGTGGACTTAAAAGGG-TGCCACGGAGTTGTGGACTTAAAAGGGTGCCAC
1692270 GGAGTTGTGGACTTAAAA
64 GGAGTTGTGGACTTAAAA
* * * *
1692288 GGGTGCCATGGAGTTGTGGACTTAAAGAGGGTGCCACGGAGTTGTGGACTTTAAAAGAGCGCTAC
1 GGGTGCCACGGAGTTGTGGACTTAAA-AGGGTGCCACGGAGTTGTGGAC-TTAAAAGGGTGCCAC
1692353 GGAGTTGTGGACTTAAAA
64 GGAGTTGTGGACTTAAAA
* * *
1692371 GGGTGCCACGGAGTTGTGGACTTTGAAA-GGTGCCACAGAGTTGTGGACTTAAAAGGGTGCTACG
1 GGGTGCCACGGAGTTGTGGAC-TTAAAAGGGTGCCACGGAGTTGTGGACTTAAAAGGGTGCCACG
1692435 GAGTTGTGGACTTTAAAA
65 GAGTTGTGGAC-TTAAAA
* ** * *
1692453 GAGTGCCACGGAGTTGTGGACTTTGAAGGGTGCCACGGAGTTGTGGACTTAAAAGAGTGCCACAG
1 GGGTGCCACGGAGTTGTGGACTTAAAAGGGTGCCACGGAGTTGTGGACTTAAAAGGGTGCCACGG
1692518 AGTTGTGGACTTTAAAA
66 AGTTGTGGAC-TTAAAA
* * * *
1692535 GAGTGCCACGGAGTTGTGGACTTTAAAAGAGTGCCACGGAGTTGTGGATTTAAAAGGATGCCACG
1 GGGTGCCACGGAGTTGTGGAC-TTAAAAGGGTGCCACGGAGTTGTGGACTTAAAAGGGTGCCACG
*
1692600 GAGATGTGGACTTCAAAA
65 GAGTTGTGGACTT-AAAA
1692618 AGAAATGCCA
Statistics
Matches: 600, Mismatches: 47, Indels: 18
0.90 0.07 0.03
Matches are distributed among these distances:
81 180 0.30
82 261 0.44
83 155 0.26
84 4 0.01
ACGTcount: A:0.28, C:0.14, G:0.34, T:0.23
Consensus pattern (81 bp):
GGGTGCCACGGAGTTGTGGACTTAAAAGGGTGCCACGGAGTTGTGGACTTAAAAGGGTGCCACGG
AGTTGTGGACTTAAAA
Found at i:1700182 original size:25 final size:22
Alignment explanation
Indices: 1700125--1700173 Score: 98
Period size: 22 Copynumber: 2.2 Consensus size: 22
1700115 TGGACATGTT
1700125 AAAAATGCATGAAACATAATAA
1 AAAAATGCATGAAACATAATAA
1700147 AAAAATGCATGAAACATAATAA
1 AAAAATGCATGAAACATAATAA
1700169 AAAAA
1 AAAAA
1700174 AGATGCATGG
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 27 1.00
ACGTcount: A:0.67, C:0.08, G:0.08, T:0.16
Consensus pattern (22 bp):
AAAAATGCATGAAACATAATAA
Found at i:1701141 original size:20 final size:20
Alignment explanation
Indices: 1701094--1701168 Score: 80
Period size: 20 Copynumber: 3.8 Consensus size: 20
1701084 AAAAAGACAT
*
1701094 AATGTATCGATACATT-GTA
1 AATGTATCGATACATTCATA
*
1701113 GAATATATCGATACATTCATA
1 -AATGTATCGATACATTCATA
* * * *
1701134 CATGTATCGATATATTGAAA
1 AATGTATCGATACATTCATA
1701154 AATGTATCGATACAT
1 AATGTATCGATACAT
1701169 CAGGGTATGA
Statistics
Matches: 45, Mismatches: 9, Indels: 2
0.80 0.16 0.04
Matches are distributed among these distances:
20 43 0.96
21 2 0.04
ACGTcount: A:0.40, C:0.12, G:0.13, T:0.35
Consensus pattern (20 bp):
AATGTATCGATACATTCATA
Found at i:1701162 original size:40 final size:39
Alignment explanation
Indices: 1701091--1701168 Score: 111
Period size: 40 Copynumber: 2.0 Consensus size: 39
1701081 GTAAAAAAGA
* *
1701091 CATAATGTATCGATACATTGTAGAATATATCGATACATT
1 CATAATGTATCGATACATTGAAAAATATATCGATACATT
* *
1701130 CATACATGTATCGATATATTGAAAAATGTATCGATACAT
1 CATA-ATGTATCGATACATTGAAAAATATATCGATACAT
1701169 CAGGGTATGA
Statistics
Matches: 34, Mismatches: 4, Indels: 1
0.87 0.10 0.03
Matches are distributed among these distances:
39 4 0.12
40 30 0.88
ACGTcount: A:0.40, C:0.13, G:0.13, T:0.35
Consensus pattern (39 bp):
CATAATGTATCGATACATTGAAAAATATATCGATACATT
Found at i:1701772 original size:28 final size:28
Alignment explanation
Indices: 1701695--1703470 Score: 964
Period size: 28 Copynumber: 61.6 Consensus size: 28
1701685 TGAAAAGGGT
* * * *
1701695 TGCCATTGACTTGCATGGGATTTAAAAGGG
1 TGCCACTGACTTG--TGGGCTTTGAAAGAG
*
1701725 TGCCACTGACTTGCGTGGGCTTTGAAAGAA
1 TGCCACTGACTT--GTGGGCTTTGAAAGAG
* *
1701755 TGCCACTAACTCGTGGGCTTTGAAAG-G
1 TGCCACTGACTTGTGGGCTTTGAAAGAG
1701782 ATGCCACTGACTTGTGGGCTTTGAAAGAG
1 -TGCCACTGACTTGTGGGCTTTGAAAGAG
1701811 TGCCACTGACTTGTGGGCTTTGAAA-AGG
1 TGCCACTGACTTGTGGGCTTTGAAAGA-G
* * *
1701839 TACCACTGACTTGCGTGAGCTTTAAAAGGAG
1 TGCCACTGACTT--GTGGGCTTTGAAA-GAG
* *
1701870 TGCCACTGACTTGTGTGGGCTTTAAAAGGG
1 TGCCACTGAC-T-TGTGGGCTTTGAAAGAG
*
1701900 TGCCACTGACTTGTGGGCTTTAAAAGAG
1 TGCCACTGACTTGTGGGCTTTGAAAGAG
* *
1701928 TGCCACTGAATTGTGGGC-TTCACAATG-G
1 TGCCACTGACTTGTGGGCTTTGA-AA-GAG
* *
1701956 TGCCACTGACTTGTGGGCTTCGAAAGGG
1 TGCCACTGACTTGTGGGCTTTGAAAGAG
* *
1701984 TGCCACTGACTTGTGGGCTCTGAAAGGG
1 TGCCACTGACTTGTGGGCTTTGAAAGAG
* *
1702012 TGCCACTAACTTGTGGGCTTTGAAAGGG
1 TGCCACTGACTTGTGGGCTTTGAAAGAG
1702040 TGCCACTGACTTGTGGGCTTTGAAAAGAG
1 TGCCACTGACTTGTGGGCTTTG-AAAGAG
* *
1702069 TGCCACTGATTTGTGGGCTTTGAAAAGAA
1 TGCCACTGACTTGTGGGCTTTG-AAAGAG
*
1702098 TGCCACTAACTTGTGGGCTTTGAAAGGAG
1 TGCCACTGACTTGTGGGCTTTGAAA-GAG
*
1702127 TGCCACTGACTTGTGGGCTTTGAAAGGG
1 TGCCACTGACTTGTGGGCTTTGAAAGAG
*
1702155 TGCCACTAACTTGTGGGCTTTGAAAAGAG
1 TGCCACTGACTTGTGGGCTTTG-AAAGAG
*
1702184 TGCCACTGATTTGTGGGCTTTGAAAAGAG
1 TGCCACTGACTTGTGGGCTTTG-AAAGAG
1702213 TGCCACTGACTTGTGGGCTTTGAAAGGAG
1 TGCCACTGACTTGTGGGCTTTGAAA-GAG
*
1702242 TGCCACTGACTTGTGGGCTTTGAAAGGG
1 TGCCACTGACTTGTGGGCTTTGAAAGAG
* *
1702270 TGCCACTGAGTTGTGGGCTTTGAAAGGG
1 TGCCACTGACTTGTGGGCTTTGAAAGAG
*
1702298 TGCCACTAACTTGTGGGCTTTGAAAAGAG
1 TGCCACTGACTTGTGGGCTTTG-AAAGAG
* *
1702327 TGCCACTGATTTGTGGGCTTTGAAATGGG
1 TGCCACTGACTTGTGGGCTTTGAAA-GAG
* *
1702356 TTGCCACTGACTTGTGTGGGCTTTGGAATGGG
1 -TGCCACTGAC-T-TGTGGGCTTT-GAAAGAG
* *
1702388 TTGCCACTGACTTGTGTGGGCTTTGGAATGGG
1 -TGCCACTGAC-T-TGTGGGCTTT-GAAAGAG
* *
1702420 TTGCCACCGACTTGTGTGGGCTTTGAAATGGG
1 -TGCCACTGAC-T-TGTGGGCTTTGAAA-GAG
* * *
1702452 TTGCCACCGACTTGTGTGGGCTTTGGAATGGG
1 -TGCCACTGAC-T-TGTGGGCTTT-GAAAGAG
* * *
1702484 TTGCCACCGACTTGTGTGGGCTTTGGAATGGG
1 -TGCCACTGAC-T-TGTGGGCTTT-GAAAGAG
* * *
1702516 TTGCCACCGACTTGTGTGGGCTTTGGAATGGG
1 -TGCCACTGAC-T-TGTGGGCTTT-GAAAGAG
* * *
1702548 TTGCCACCGACTTGTGTGGGCTTTGGAATGGG
1 -TGCCACTGAC-T-TGTGGGCTTT-GAAAGAG
* * *
1702580 TTGCCACCGACTTGTGTGGGCTTTGGAATGGG
1 -TGCCACTGAC-T-TGTGGGCTTT-GAAAGAG
* * *
1702612 TTGCCACCGACTTGTGTGGGCTTTGGAATGGG
1 -TGCCACTGAC-T-TGTGGGCTTT-GAAAGAG
* *
1702644 TTGCCACCGACTTGTGTGGGCTTTGAAATGGG
1 -TGCCACTGAC-T-TGTGGGCTTTGAAA-GAG
* *
1702676 TTGCCACCGACTTGTGTGGGCTTTGAAATGGG
1 -TGCCACTGAC-T-TGTGGGCTTTGAAA-GAG
* *
1702708 TTGCCACCGACTTGTGTGGGCTTTGAAATGGG
1 -TGCCACTGAC-T-TGTGGGCTTTGAAA-GAG
* *
1702740 TTGCCACTGACTTGTGTGGGCTTTGAATTGGG
1 -TGCCACTGAC-T-TGTGGGCTTTGAA-AGAG
* * * *
1702772 TGCCACGGAGTTGT-GGATTT-AAAAAG
1 TGCCACTGACTTGTGGGCTTTGAAAGAG
* * * * *
1702798 ATGCCACGGAGTTGTGGAC-TTAAAAGGG
1 -TGCCACTGACTTGTGGGCTTTGAAAGAG
* * * * *
1702826 TGCCACAGAGTTGTGGTC-TTAAAAGGG
1 TGCCACTGACTTGTGGGCTTTGAAAGAG
* * * * *
1702853 ATGCCACGGAGTTGTGGAC-TTAAAAGGG
1 -TGCCACTGACTTGTGGGCTTTGAAAGAG
* * * * *
1702881 TGCCACGGAGTTGTGGAC-TTAAAAGGG
1 TGCCACTGACTTGTGGGCTTTGAAAGAG
* * * * *
1702908 TGCCACGGAGTTGTGGAC-TTAAAAGGG
1 TGCCACTGACTTGTGGGCTTTGAAAGAG
* * * * * *
1702935 TACCACGGAGTTGTGGAC-TTAAAAGGG
1 TGCCACTGACTTGTGGGCTTTGAAAGAG
* * * * *
1702962 TGCCACGGAGTTATGGAC-TTAAAAGAG
1 TGCCACTGACTTGTGGGCTTTGAAAGAG
* * * **
1702989 TGCCACGGAGTTGTGGACTTAAAAAG-G
1 TGCCACTGACTTGTGGGCTTTGAAAGAG
* * * * *
1703016 TGCTAC-GAAGTTGTGGAC-TTAAAAGGG
1 TGCCACTG-ACTTGTGGGCTTTGAAAGAG
* * * * *
1703043 TGCCACAGAGTTGTGGAC-TTAAAAGGG
1 TGCCACTGACTTGTGGGCTTTGAAAGAG
* * * * *
1703070 TGCCACGGAGTTATGGAC-TTAAAAGAG
1 TGCCACTGACTTGTGGGCTTTGAAAGAG
* * * * *
1703097 ATGCCACGGAGTTGTGGAC-TTAAAAGGG
1 -TGCCACTGACTTGTGGGCTTTGAAAGAG
* * * * *
1703125 ATGCCACGGAGTTGTGGAC-TTAAAAGGG
1 -TGCCACTGACTTGTGGGCTTTGAAAGAG
* * * * *
1703153 TGCCACGGAGTTGTGGAC-TTAAAAGGG
1 TGCCACTGACTTGTGGGCTTTGAAAGAG
* *
1703180 TGCCA-TGGAGTTGTGGAC-TT-AAAGAGGG
1 TGCCACT-GACTTGTGGGCTTTGAAAGA--G
* * * *
1703208 TGCCACGGAGTTGTGGACTTTAAAAGAG
1 TGCCACTGACTTGTGGGCTTTGAAAGAG
* * * * * * *
1703236 CGCTACGGAGTTGTGGAC-TTAAAAGGG
1 TGCCACTGACTTGTGGGCTTTGAAAGAG
* * *
1703263 TGCCACGGAGTTGTGGACTTTGAAAG-G
1 TGCCACTGACTTGTGGGCTTTGAAAGAG
* * * * *
1703290 TGCCACAGAGTTGTGGAC-TTAAAAGGG
1 TGCCACTGACTTGTGGGCTTTGAAAGAG
* * * * *
1703317 TGCTACGGAGTTGTGGACTTTAAAAGAG
1 TGCCACTGACTTGTGGGCTTTGAAAGAG
* * * *
1703345 TGCCACGGAGTTGTGGACTTTG-AAGGG
1 TGCCACTGACTTGTGGGCTTTGAAAGAG
* * * *
1703372 TGCCACGGAGTTGTGGAC-TTAAAAGAG
1 TGCCACTGACTTGTGGGCTTTGAAAGAG
* * * *
1703399 TGCCACAGAGTTGTGGACTTTAAAAGAG
1 TGCCACTGACTTGTGGGCTTTGAAAGAG
* * * *
1703427 TGCCACGGAGTTGTGGACTTTAAAAGAG
1 TGCCACTGACTTGTGGGCTTTGAAAGAG
* *
1703455 TGCCACGGAGTTGTGG
1 TGCCACTGACTTGTGG
1703471 ATTTAAAAGG
Statistics
Matches: 1592, Mismatches: 105, Indels: 100
0.89 0.06 0.06
Matches are distributed among these distances:
26 20 0.01
27 381 0.24
28 500 0.31
29 196 0.12
30 70 0.04
31 37 0.02
32 381 0.24
33 7 0.00
ACGTcount: A:0.22, C:0.16, G:0.34, T:0.27
Consensus pattern (28 bp):
TGCCACTGACTTGTGGGCTTTGAAAGAG
Found at i:1702379 original size:32 final size:30
Alignment explanation
Indices: 1701683--1702777 Score: 1078
Period size: 32 Copynumber: 36.6 Consensus size: 30
1701673 ACAGTGGTGA
* * *
1701683 TTTGAAAAGGGTTGCCATTGAC-TTGCATGGGA
1 TTTGAAATGGG-TGCCACTGACTTTG--TGGGC
* *
1701715 TTT-AAAAGGGTGCCACTGACTTGCGTGGGC
1 TTTGAAATGGGTGCCACTGACTT-TGTGGGC
** * *
1701745 TTTGAAA-GAATGCCACTAAC-TCGTGGGC
1 TTTGAAATGGGTGCCACTGACTTTGTGGGC
*
1701773 TTTGAAA-GGATGCCACTGAC-TTGTGGGC
1 TTTGAAATGGGTGCCACTGACTTTGTGGGC
*
1701801 TTTGAAA-GAGTGCCACTGAC-TTGTGGGC
1 TTTGAAATGGGTGCCACTGACTTTGTGGGC
* * * *
1701829 TTTGAAA-AGGTACCACTGACTTGCGTGAGC
1 TTTGAAATGGGTGCCACTGACTT-TGTGGGC
*
1701859 TTT-AAAAGGAGTGCCACTGACTTGTGTGGGC
1 TTTGAAATGG-GTGCCACTGACTT-TGTGGGC
*
1701890 TTT-AAAAGGGTGCCACTGAC-TTGTGGGC
1 TTTGAAATGGGTGCCACTGACTTTGTGGGC
* * *
1701918 TTT-AAAAGAGTGCCACTGA-ATTGTGGGC
1 TTTGAAATGGGTGCCACTGACTTTGTGGGC
*
1701946 -TTCACAAT-GGTGCCACTGAC-TTGTGGGC
1 TTTGA-AATGGGTGCCACTGACTTTGTGGGC
*
1701974 TTCGAAA-GGGTGCCACTGAC-TTGTGGGC
1 TTTGAAATGGGTGCCACTGACTTTGTGGGC
* *
1702002 TCTGAAA-GGGTGCCACTAAC-TTGTGGGC
1 TTTGAAATGGGTGCCACTGACTTTGTGGGC
1702030 TTTGAAA-GGGTGCCACTGAC-TTGTGGGC
1 TTTGAAATGGGTGCCACTGACTTTGTGGGC
* *
1702058 TTTGAAAAGAGTGCCACTGA-TTTGTGGGC
1 TTTGAAATGGGTGCCACTGACTTTGTGGGC
* ** *
1702087 TTTGAAAAGAATGCCACTAAC-TTGTGGGC
1 TTTGAAATGGGTGCCACTGACTTTGTGGGC
1702116 TTTGAAA-GGAGTGCCACTGAC-TTGTGGGC
1 TTTGAAATGG-GTGCCACTGACTTTGTGGGC
*
1702145 TTTGAAA-GGGTGCCACTAAC-TTGTGGGC
1 TTTGAAATGGGTGCCACTGACTTTGTGGGC
* *
1702173 TTTGAAAAGAGTGCCACTGA-TTTGTGGGC
1 TTTGAAATGGGTGCCACTGACTTTGTGGGC
* *
1702202 TTTGAAAAGAGTGCCACTGAC-TTGTGGGC
1 TTTGAAATGGGTGCCACTGACTTTGTGGGC
1702231 TTTGAAA-GGAGTGCCACTGAC-TTGTGGGC
1 TTTGAAATGG-GTGCCACTGACTTTGTGGGC
*
1702260 TTTGAAA-GGGTGCCACTGA-GTTGTGGGC
1 TTTGAAATGGGTGCCACTGACTTTGTGGGC
*
1702288 TTTGAAA-GGGTGCCACTAAC-TTGTGGGC
1 TTTGAAATGGGTGCCACTGACTTTGTGGGC
* *
1702316 TTTGAAAAGAGTGCCACTGA-TTTGTGGGC
1 TTTGAAATGGGTGCCACTGACTTTGTGGGC
1702345 TTTGAAATGGGTTGCCACTGACTTGTGTGGGC
1 TTTGAAATGGG-TGCCACTGACTT-TGTGGGC
*
1702377 TTTGGAATGGGTTGCCACTGACTTGTGTGGGC
1 TTTGAAATGGG-TGCCACTGACTT-TGTGGGC
* *
1702409 TTTGGAATGGGTTGCCACCGACTTGTGTGGGC
1 TTTGAAATGGG-TGCCACTGACTT-TGTGGGC
*
1702441 TTTGAAATGGGTTGCCACCGACTTGTGTGGGC
1 TTTGAAATGGG-TGCCACTGACTT-TGTGGGC
* *
1702473 TTTGGAATGGGTTGCCACCGACTTGTGTGGGC
1 TTTGAAATGGG-TGCCACTGACTT-TGTGGGC
* *
1702505 TTTGGAATGGGTTGCCACCGACTTGTGTGGGC
1 TTTGAAATGGG-TGCCACTGACTT-TGTGGGC
* *
1702537 TTTGGAATGGGTTGCCACCGACTTGTGTGGGC
1 TTTGAAATGGG-TGCCACTGACTT-TGTGGGC
* *
1702569 TTTGGAATGGGTTGCCACCGACTTGTGTGGGC
1 TTTGAAATGGG-TGCCACTGACTT-TGTGGGC
* *
1702601 TTTGGAATGGGTTGCCACCGACTTGTGTGGGC
1 TTTGAAATGGG-TGCCACTGACTT-TGTGGGC
* *
1702633 TTTGGAATGGGTTGCCACCGACTTGTGTGGGC
1 TTTGAAATGGG-TGCCACTGACTT-TGTGGGC
*
1702665 TTTGAAATGGGTTGCCACCGACTTGTGTGGGC
1 TTTGAAATGGG-TGCCACTGACTT-TGTGGGC
*
1702697 TTTGAAATGGGTTGCCACCGACTTGTGTGGGC
1 TTTGAAATGGG-TGCCACTGACTT-TGTGGGC
1702729 TTTGAAATGGGTTGCCACTGACTTGTGTGGGC
1 TTTGAAATGGG-TGCCACTGACTT-TGTGGGC
*
1702761 TTTGAATTGGGTGCCAC
1 TTTGAAATGGGTGCCAC
1702778 GGAGTTGTGG
Statistics
Matches: 983, Mismatches: 52, Indels: 57
0.90 0.05 0.05
Matches are distributed among these distances:
27 2 0.00
28 285 0.29
29 196 0.20
30 55 0.06
31 46 0.05
32 399 0.41
ACGTcount: A:0.19, C:0.18, G:0.33, T:0.30
Consensus pattern (30 bp):
TTTGAAATGGGTGCCACTGACTTTGTGGGC
Found at i:1702810 original size:27 final size:27
Alignment explanation
Indices: 1702769--1703506 Score: 1100
Period size: 27 Copynumber: 27.0 Consensus size: 27
1702759 GCTTTGAATT
*
1702769 GGGTGCCACGGAGTTGTGGATTTAAAA
1 GGGTGCCACGGAGTTGTGGACTTAAAA
* *
1702796 AGATGCCACGGAGTTGTGGACTTAAAA
1 GGGTGCCACGGAGTTGTGGACTTAAAA
* *
1702823 GGGTGCCACAGAGTTGTGGTCTTAAAA
1 GGGTGCCACGGAGTTGTGGACTTAAAA
1702850 GGGATGCCACGGAGTTGTGGACTTAAAA
1 GGG-TGCCACGGAGTTGTGGACTTAAAA
1702878 GGGTGCCACGGAGTTGTGGACTTAAAA
1 GGGTGCCACGGAGTTGTGGACTTAAAA
1702905 GGGTGCCACGGAGTTGTGGACTTAAAA
1 GGGTGCCACGGAGTTGTGGACTTAAAA
*
1702932 GGGTACCACGGAGTTGTGGACTTAAAA
1 GGGTGCCACGGAGTTGTGGACTTAAAA
*
1702959 GGGTGCCACGGAGTTATGGACTTAAAA
1 GGGTGCCACGGAGTTGTGGACTTAAAA
*
1702986 GAGTGCCACGGAGTTGTGGACTTAAAA
1 GGGTGCCACGGAGTTGTGGACTTAAAA
* * *
1703013 AGGTGCTACGAAGTTGTGGACTTAAAA
1 GGGTGCCACGGAGTTGTGGACTTAAAA
*
1703040 GGGTGCCACAGAGTTGTGGACTTAAAA
1 GGGTGCCACGGAGTTGTGGACTTAAAA
*
1703067 GGGTGCCACGGAGTTATGGACTTAAAA
1 GGGTGCCACGGAGTTGTGGACTTAAAA
*
1703094 GAGATGCCACGGAGTTGTGGACTTAAAA
1 G-GGTGCCACGGAGTTGTGGACTTAAAA
1703122 GGGATGCCACGGAGTTGTGGACTTAAAA
1 GGG-TGCCACGGAGTTGTGGACTTAAAA
1703150 GGGTGCCACGGAGTTGTGGACTTAAAA
1 GGGTGCCACGGAGTTGTGGACTTAAAA
*
1703177 GGGTGCCATGGAGTTGTGGACTTAAAGA
1 GGGTGCCACGGAGTTGTGGACTTAAA-A
1703205 GGGTGCCACGGAGTTGTGGACTTTAAAA
1 GGGTGCCACGGAGTTGTGGAC-TTAAAA
* * *
1703233 GAGCGCTACGGAGTTGTGGACTTAAAA
1 GGGTGCCACGGAGTTGTGGACTTAAAA
*
1703260 GGGTGCCACGGAGTTGTGGACTTTGAAA
1 GGGTGCCACGGAGTTGTGGAC-TTAAAA
*
1703288 -GGTGCCACAGAGTTGTGGACTTAAAA
1 GGGTGCCACGGAGTTGTGGACTTAAAA
*
1703314 GGGTGCTACGGAGTTGTGGACTTTAAAA
1 GGGTGCCACGGAGTTGTGGAC-TTAAAA
* **
1703342 GAGTGCCACGGAGTTGTGGACTTTGAA
1 GGGTGCCACGGAGTTGTGGACTTAAAA
1703369 GGGTGCCACGGAGTTGTGGACTTAAAA
1 GGGTGCCACGGAGTTGTGGACTTAAAA
* *
1703396 GAGTGCCACAGAGTTGTGGACTTTAAAA
1 GGGTGCCACGGAGTTGTGGAC-TTAAAA
*
1703424 GAGTGCCACGGAGTTGTGGACTTTAAAA
1 GGGTGCCACGGAGTTGTGGAC-TTAAAA
* *
1703452 GAGTGCCACGGAGTTGTGGATTTAAAA
1 GGGTGCCACGGAGTTGTGGACTTAAAA
* *
1703479 GGATGCCACGGAGATGTGGACTTCAAAA
1 GGGTGCCACGGAGTTGTGGACTT-AAAA
1703507 AGAAATGCCA
Statistics
Matches: 646, Mismatches: 55, Indels: 19
0.90 0.08 0.03
Matches are distributed among these distances:
26 5 0.01
27 432 0.67
28 204 0.32
29 5 0.01
ACGTcount: A:0.28, C:0.14, G:0.34, T:0.23
Consensus pattern (27 bp):
GGGTGCCACGGAGTTGTGGACTTAAAA
Found at i:1702909 original size:82 final size:81
Alignment explanation
Indices: 1702769--1703506 Score: 1100
Period size: 82 Copynumber: 9.0 Consensus size: 81
1702759 GCTTTGAATT
* * * *
1702769 GGGTGCCACGGAGTTGTGGATTTAAAAAGATGCCACGGAGTTGTGGACTTAAAAGGGTGCCACAG
1 GGGTGCCACGGAGTTGTGGACTTAAAAGGGTGCCACGGAGTTGTGGACTTAAAAGGGTGCCACGG
*
1702834 AGTTGTGGTCTTAAAA
66 AGTTGTGGACTTAAAA
1702850 GGGATGCCACGGAGTTGTGGACTTAAAAGGGTGCCACGGAGTTGTGGACTTAAAAGGGTGCCACG
1 GGG-TGCCACGGAGTTGTGGACTTAAAAGGGTGCCACGGAGTTGTGGACTTAAAAGGGTGCCACG
1702915 GAGTTGTGGACTTAAAA
65 GAGTTGTGGACTTAAAA
* * *
1702932 GGGTACCACGGAGTTGTGGACTTAAAAGGGTGCCACGGAGTTATGGACTTAAAAGAGTGCCACGG
1 GGGTGCCACGGAGTTGTGGACTTAAAAGGGTGCCACGGAGTTGTGGACTTAAAAGGGTGCCACGG
1702997 AGTTGTGGACTTAAAA
66 AGTTGTGGACTTAAAA
* * * *
1703013 AGGTGCTACGAAGTTGTGGACTTAAAAGGGTGCCACAGAGTTGTGGACTTAAAAGGGTGCCACGG
1 GGGTGCCACGGAGTTGTGGACTTAAAAGGGTGCCACGGAGTTGTGGACTTAAAAGGGTGCCACGG
*
1703078 AGTTATGGACTTAAAA
66 AGTTGTGGACTTAAAA
*
1703094 GAGATGCCACGGAGTTGTGGACTTAAAAGGGATGCCACGGAGTTGTGGACTTAAAAGGGTGCCAC
1 G-GGTGCCACGGAGTTGTGGACTTAAAAGGG-TGCCACGGAGTTGTGGACTTAAAAGGGTGCCAC
1703159 GGAGTTGTGGACTTAAAA
64 GGAGTTGTGGACTTAAAA
* * * *
1703177 GGGTGCCATGGAGTTGTGGACTTAAAGAGGGTGCCACGGAGTTGTGGACTTTAAAAGAGCGCTAC
1 GGGTGCCACGGAGTTGTGGACTTAAA-AGGGTGCCACGGAGTTGTGGAC-TTAAAAGGGTGCCAC
1703242 GGAGTTGTGGACTTAAAA
64 GGAGTTGTGGACTTAAAA
* * *
1703260 GGGTGCCACGGAGTTGTGGACTTTGAAA-GGTGCCACAGAGTTGTGGACTTAAAAGGGTGCTACG
1 GGGTGCCACGGAGTTGTGGAC-TTAAAAGGGTGCCACGGAGTTGTGGACTTAAAAGGGTGCCACG
1703324 GAGTTGTGGACTTTAAAA
65 GAGTTGTGGAC-TTAAAA
* ** * *
1703342 GAGTGCCACGGAGTTGTGGACTTTGAAGGGTGCCACGGAGTTGTGGACTTAAAAGAGTGCCACAG
1 GGGTGCCACGGAGTTGTGGACTTAAAAGGGTGCCACGGAGTTGTGGACTTAAAAGGGTGCCACGG
1703407 AGTTGTGGACTTTAAAA
66 AGTTGTGGAC-TTAAAA
* * * *
1703424 GAGTGCCACGGAGTTGTGGACTTTAAAAGAGTGCCACGGAGTTGTGGATTTAAAAGGATGCCACG
1 GGGTGCCACGGAGTTGTGGAC-TTAAAAGGGTGCCACGGAGTTGTGGACTTAAAAGGGTGCCACG
*
1703489 GAGATGTGGACTTCAAAA
65 GAGTTGTGGACTT-AAAA
1703507 AGAAATGCCA
Statistics
Matches: 600, Mismatches: 47, Indels: 18
0.90 0.07 0.03
Matches are distributed among these distances:
81 180 0.30
82 261 0.44
83 155 0.26
84 4 0.01
ACGTcount: A:0.28, C:0.14, G:0.34, T:0.23
Consensus pattern (81 bp):
GGGTGCCACGGAGTTGTGGACTTAAAAGGGTGCCACGGAGTTGTGGACTTAAAAGGGTGCCACGG
AGTTGTGGACTTAAAA
Found at i:1711071 original size:25 final size:22
Alignment explanation
Indices: 1711014--1711062 Score: 98
Period size: 22 Copynumber: 2.2 Consensus size: 22
1711004 TGGACATGTT
1711014 AAAAATGCATGAAACATAATAA
1 AAAAATGCATGAAACATAATAA
1711036 AAAAATGCATGAAACATAATAA
1 AAAAATGCATGAAACATAATAA
1711058 AAAAA
1 AAAAA
1711063 AGATGCATGG
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 27 1.00
ACGTcount: A:0.67, C:0.08, G:0.08, T:0.16
Consensus pattern (22 bp):
AAAAATGCATGAAACATAATAA
Found at i:1712030 original size:20 final size:20
Alignment explanation
Indices: 1711983--1712057 Score: 80
Period size: 20 Copynumber: 3.8 Consensus size: 20
1711973 AAAAAGACAT
*
1711983 AATGTATCGATACATT-GTA
1 AATGTATCGATACATTCATA
*
1712002 GAATATATCGATACATTCATA
1 -AATGTATCGATACATTCATA
* * * *
1712023 CATGTATCGATATATTGAAA
1 AATGTATCGATACATTCATA
1712043 AATGTATCGATACAT
1 AATGTATCGATACAT
1712058 CAGGGTATGA
Statistics
Matches: 45, Mismatches: 9, Indels: 2
0.80 0.16 0.04
Matches are distributed among these distances:
20 43 0.96
21 2 0.04
ACGTcount: A:0.40, C:0.12, G:0.13, T:0.35
Consensus pattern (20 bp):
AATGTATCGATACATTCATA
Found at i:1712051 original size:40 final size:39
Alignment explanation
Indices: 1711980--1712057 Score: 111
Period size: 40 Copynumber: 2.0 Consensus size: 39
1711970 GTAAAAAAGA
* *
1711980 CATAATGTATCGATACATTGTAGAATATATCGATACATT
1 CATAATGTATCGATACATTGAAAAATATATCGATACATT
* *
1712019 CATACATGTATCGATATATTGAAAAATGTATCGATACAT
1 CATA-ATGTATCGATACATTGAAAAATATATCGATACAT
1712058 CAGGGTATGA
Statistics
Matches: 34, Mismatches: 4, Indels: 1
0.87 0.10 0.03
Matches are distributed among these distances:
39 4 0.12
40 30 0.88
ACGTcount: A:0.40, C:0.13, G:0.13, T:0.35
Consensus pattern (39 bp):
CATAATGTATCGATACATTGAAAAATATATCGATACATT
Found at i:1715746 original size:97 final size:97
Alignment explanation
Indices: 1715568--1715810 Score: 315
Period size: 97 Copynumber: 2.5 Consensus size: 97
1715558 TTTTTGATTG
* * * * * ** *
1715568 AAAAACGGGATTGGAGTATCTCTTCGGAGAAATGGGGTTGGAGTATCCCTGATGATGATAATTTA
1 AAAAGCGGGGTTGGAGTATCCCCTCGGAGGAATGGGGTTGGAGTATCCCCAATGATGACAATTTA
1715633 AGTAAGAATAAAATTTAAACTTTAATGCGTTT
66 AGTAAGAATAAAATTTAAACTTTAATGCGTTT
* * *
1715665 AAAAGCGGGGTTGGAGTATCCCCTCGGAGGAATGGGGTTGAAGTGTCCCCAATGATGGCAATTTA
1 AAAAGCGGGGTTGGAGTATCCCCTCGGAGGAATGGGGTTGGAGTATCCCCAATGATGACAATTTA
* * * *
1715730 AGTGAGAATAAGATTTAAACTTTGATGTGTTT
66 AGTAAGAATAAAATTTAAACTTTAATGCGTTT
* * * *
1715762 AAAAGCGAGGTTAGAGTATCCCCTCAGAGGAATAGGGTTGGAGTATCCC
1 AAAAGCGGGGTTGGAGTATCCCCTCGGAGGAATGGGGTTGGAGTATCCC
1715811 GATAAATAAA
Statistics
Matches: 125, Mismatches: 21, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
97 125 1.00
ACGTcount: A:0.32, C:0.12, G:0.28, T:0.28
Consensus pattern (97 bp):
AAAAGCGGGGTTGGAGTATCCCCTCGGAGGAATGGGGTTGGAGTATCCCCAATGATGACAATTTA
AGTAAGAATAAAATTTAAACTTTAATGCGTTT
Found at i:1718027 original size:20 final size:19
Alignment explanation
Indices: 1718000--1718076 Score: 100
Period size: 20 Copynumber: 3.9 Consensus size: 19
1717990 AAAACAAGAC
*
1718000 AAAATGTATTGATACATTG
1 AAAATGTATCGATACATTG
*
1718019 AAGAATGTATCGATACATTC
1 AA-AATGTATCGATACATTG
*
1718039 ATACATGTATCGATACATTG
1 A-AAATGTATCGATACATTG
1718059 AAAAATGTATCGATACAT
1 -AAAATGTATCGATACAT
1718077 CTGGGTAAAA
Statistics
Matches: 50, Mismatches: 5, Indels: 5
0.83 0.08 0.08
Matches are distributed among these distances:
19 2 0.04
20 46 0.92
21 2 0.04
ACGTcount: A:0.42, C:0.12, G:0.14, T:0.32
Consensus pattern (19 bp):
AAAATGTATCGATACATTG
Found at i:1718844 original size:17 final size:17
Alignment explanation
Indices: 1718822--1718854 Score: 66
Period size: 17 Copynumber: 1.9 Consensus size: 17
1718812 TCAAATCTAG
1718822 CAAAGAACCAACCACTA
1 CAAAGAACCAACCACTA
1718839 CAAAGAACCAACCACT
1 CAAAGAACCAACCACT
1718855 GCACCACAAT
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 16 1.00
ACGTcount: A:0.52, C:0.36, G:0.06, T:0.06
Consensus pattern (17 bp):
CAAAGAACCAACCACTA
Found at i:1721504 original size:17 final size:18
Alignment explanation
Indices: 1721461--1721513 Score: 56
Period size: 18 Copynumber: 2.9 Consensus size: 18
1721451 TTTATAATTA
1721461 ATATATA-TATAAATATTT
1 ATATATATTAT-AATATTT
1721479 ATATCATATTATAAT-TTT
1 ATAT-ATATTATAATATTT
* *
1721497 TTATATATTTTAATATT
1 ATATATATTATAATATT
1721514 AATTTTAATC
Statistics
Matches: 30, Mismatches: 2, Indels: 6
0.79 0.05 0.16
Matches are distributed among these distances:
17 9 0.30
18 12 0.40
19 6 0.20
20 3 0.10
ACGTcount: A:0.42, C:0.02, G:0.00, T:0.57
Consensus pattern (18 bp):
ATATATATTATAATATTT
Done.