Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold189
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: 2243555
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
Warning! 25 characters in sequence are not A, C, G, or T
File 5 of 9
Found at i:986064 original size:11 final size:11
Alignment explanation
Indices: 986037--986070 Score: 50
Period size: 11 Copynumber: 3.0 Consensus size: 11
986027 TATAATACTT
986037 AATAATATTAAA
1 AATAATA-TAAA
*
986049 TATAATATAAA
1 AATAATATAAA
986060 AATAATATAAA
1 AATAATATAAA
986071 TATTTTAAAA
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
11 14 0.70
12 6 0.30
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.32
Consensus pattern (11 bp):
AATAATATAAA
Found at i:991156 original size:17 final size:17
Alignment explanation
Indices: 991129--991170 Score: 52
Period size: 17 Copynumber: 2.5 Consensus size: 17
991119 TGTTAGATTC
991129 TTATA-TATTTTTGTAT-
1 TTATATTATTTTT-TATA
991145 TTATATTATTTTTTATA
1 TTATATTATTTTTTATA
*
991162 TTTTATTAT
1 TTATATTAT
991171 ATGTTAACTA
Statistics
Matches: 23, Mismatches: 1, Indels: 3
0.85 0.04 0.11
Matches are distributed among these distances:
16 8 0.35
17 15 0.65
ACGTcount: A:0.26, C:0.00, G:0.02, T:0.71
Consensus pattern (17 bp):
TTATATTATTTTTTATA
Found at i:991163 original size:18 final size:17
Alignment explanation
Indices: 991136--991170 Score: 52
Period size: 18 Copynumber: 2.0 Consensus size: 17
991126 TTCTTATATA
*
991136 TTTTTGTATTTATATTAT
1 TTTTTATATTT-TATTAT
991154 TTTTTATATTTTATTAT
1 TTTTTATATTTTATTAT
991171 ATGTTAACTA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
17 6 0.38
18 10 0.62
ACGTcount: A:0.23, C:0.00, G:0.03, T:0.74
Consensus pattern (17 bp):
TTTTTATATTTTATTAT
Found at i:991942 original size:2 final size:2
Alignment explanation
Indices: 991935--991974 Score: 80
Period size: 2 Copynumber: 20.0 Consensus size: 2
991925 CACAGCCAAA
991935 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC
1 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC
991975 CTTCCAGAAT
Statistics
Matches: 38, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 38 1.00
ACGTcount: A:0.00, C:0.50, G:0.00, T:0.50
Consensus pattern (2 bp):
TC
Found at i:995940 original size:9 final size:9
Alignment explanation
Indices: 995921--995952 Score: 57
Period size: 9 Copynumber: 3.7 Consensus size: 9
995911 ACATCTCATC
995921 TCATC-TCA
1 TCATCTTCA
995929 TCATCTTCA
1 TCATCTTCA
995938 TCATCTTCA
1 TCATCTTCA
995947 TCATCT
1 TCATCT
995953 ACGCAGAATG
Statistics
Matches: 23, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
8 5 0.22
9 18 0.78
ACGTcount: A:0.22, C:0.34, G:0.00, T:0.44
Consensus pattern (9 bp):
TCATCTTCA
Found at i:997645 original size:2 final size:2
Alignment explanation
Indices: 997638--997677 Score: 80
Period size: 2 Copynumber: 20.0 Consensus size: 2
997628 ATTTAAGATC
997638 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
997678 GTGTGTGTGT
Statistics
Matches: 38, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 38 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:998139 original size:12 final size:12
Alignment explanation
Indices: 998122--998157 Score: 54
Period size: 12 Copynumber: 3.0 Consensus size: 12
998112 CAATTAATAT
998122 TAATAATATTAA
1 TAATAATATTAA
*
998134 TAATAATATTGA
1 TAATAATATTAA
*
998146 TATTAATATTAA
1 TAATAATATTAA
998158 ACCCTTTCCC
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
12 21 1.00
ACGTcount: A:0.53, C:0.00, G:0.03, T:0.44
Consensus pattern (12 bp):
TAATAATATTAA
Found at i:998390 original size:3 final size:3
Alignment explanation
Indices: 998382--998418 Score: 56
Period size: 3 Copynumber: 12.3 Consensus size: 3
998372 TGTTAGTATT
* *
998382 TAG TAG TAG TAG TGG TGG TAG TAG TAG TAG TAG TAG T
1 TAG TAG TAG TAG TAG TAG TAG TAG TAG TAG TAG TAG T
998419 TAACTTAGTG
Statistics
Matches: 32, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
3 32 1.00
ACGTcount: A:0.27, C:0.00, G:0.38, T:0.35
Consensus pattern (3 bp):
TAG
Found at i:1004476 original size:2 final size:2
Alignment explanation
Indices: 1004469--1004511 Score: 86
Period size: 2 Copynumber: 21.5 Consensus size: 2
1004459 TGAAAAGAAA
1004469 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG
1 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG
1004511 A
1 A
1004512 ATGTAATTTT
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:0.49, T:0.00
Consensus pattern (2 bp):
AG
Found at i:1007896 original size:8 final size:8
Alignment explanation
Indices: 1007885--1007909 Score: 50
Period size: 8 Copynumber: 3.1 Consensus size: 8
1007875 CAAATTCAAA
1007885 AATATTTT
1 AATATTTT
1007893 AATATTTT
1 AATATTTT
1007901 AATATTTT
1 AATATTTT
1007909 A
1 A
1007910 CTGATAAAAT
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
8 17 1.00
ACGTcount: A:0.40, C:0.00, G:0.00, T:0.60
Consensus pattern (8 bp):
AATATTTT
Found at i:1013375 original size:15 final size:14
Alignment explanation
Indices: 1013342--1013391 Score: 57
Period size: 13 Copynumber: 3.4 Consensus size: 14
1013332 TTATTTTTTA
1013342 AAATATTTATATTT
1 AAATATTTATATTT
*
1013356 -AATATTTGTATTT
1 AAATATTTATATTT
1013369 AATATATTTTTATATTT
1 AA-ATA--TTTATATTT
1013386 AAATAT
1 AAATAT
1013392 AAAAAATATA
Statistics
Matches: 30, Mismatches: 2, Indels: 8
0.75 0.05 0.20
Matches are distributed among these distances:
13 12 0.40
14 2 0.07
15 3 0.10
16 3 0.10
17 10 0.33
ACGTcount: A:0.40, C:0.00, G:0.02, T:0.58
Consensus pattern (14 bp):
AAATATTTATATTT
Found at i:1015419 original size:25 final size:26
Alignment explanation
Indices: 1015385--1015435 Score: 70
Period size: 27 Copynumber: 2.0 Consensus size: 26
1015375 AATTTTAAAA
1015385 TTTTTTATTT-ATTTAAATA-ATTAT
1 TTTTTTATTTAATTTAAATATATTAT
1015409 TTTTTATATTTACATTTAAATATATTA
1 TTTTT-TATTTA-ATTTAAATATATTA
1015436 AATATAAATA
Statistics
Matches: 23, Mismatches: 0, Indels: 4
0.85 0.00 0.15
Matches are distributed among these distances:
24 5 0.22
25 5 0.22
27 9 0.39
28 4 0.17
ACGTcount: A:0.35, C:0.02, G:0.00, T:0.63
Consensus pattern (26 bp):
TTTTTTATTTAATTTAAATATATTAT
Found at i:1017456 original size:26 final size:26
Alignment explanation
Indices: 1017399--1017448 Score: 75
Period size: 26 Copynumber: 1.9 Consensus size: 26
1017389 TGATTAAAAT
1017399 TAAATTTAATAATATTTTTAATTAAA
1 TAAATTTAATAATATTTTTAATTAAA
*
1017425 TAAATTTGAATTATA-TTTTAATTA
1 TAAATTT-AATAATATTTTTAATTA
1017449 TTTTAATTAA
Statistics
Matches: 22, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
26 16 0.73
27 6 0.27
ACGTcount: A:0.46, C:0.00, G:0.02, T:0.52
Consensus pattern (26 bp):
TAAATTTAATAATATTTTTAATTAAA
Found at i:1017492 original size:32 final size:34
Alignment explanation
Indices: 1017449--1017512 Score: 96
Period size: 34 Copynumber: 1.9 Consensus size: 34
1017439 ATTTTAATTA
*
1017449 TTTTAATTAA-TTTTTTA-TAATTAAAAAATATT
1 TTTTAAATAATTTTTTTATTAATTAAAAAATATT
*
1017481 TTTTAAATAATTTTTTTATTAATTTAAAAATA
1 TTTTAAATAATTTTTTTATTAATTAAAAAATA
1017513 AAATATTTAT
Statistics
Matches: 28, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
32 9 0.32
33 7 0.25
34 12 0.43
ACGTcount: A:0.44, C:0.00, G:0.00, T:0.56
Consensus pattern (34 bp):
TTTTAAATAATTTTTTTATTAATTAAAAAATATT
Found at i:1017551 original size:27 final size:27
Alignment explanation
Indices: 1017484--1017582 Score: 69
Period size: 31 Copynumber: 3.5 Consensus size: 27
1017474 AAATATTTTT
* *
1017484 TAAATAATTTTTTTATTAATTTAAAAA
1 TAAATAATTTTATAATTAATTTAAAAA
**
1017511 TAAAATATTTATTTTATAATTTTTTTAAAAA
1 T-AAATA---ATTTTATAATTAATTTAAAAA
1017542 TAAATAA-TTT-TAATTAAATTTAAATAA
1 TAAATAATTTTATAATT-AATTTAAA-AA
1017569 TTATAAT-ATTTTAT
1 -TA-AATAATTTTAT
1017583 TTGTGACTAA
Statistics
Matches: 56, Mismatches: 6, Indels: 17
0.71 0.08 0.22
Matches are distributed among these distances:
25 5 0.09
26 9 0.16
27 4 0.07
28 8 0.14
29 6 0.11
30 6 0.11
31 18 0.32
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (27 bp):
TAAATAATTTTATAATTAATTTAAAAA
Found at i:1017937 original size:5 final size:5
Alignment explanation
Indices: 1017927--1017954 Score: 56
Period size: 5 Copynumber: 5.6 Consensus size: 5
1017917 ATTAATTATA
1017927 TAATT TAATT TAATT TAATT TAATT TAA
1 TAATT TAATT TAATT TAATT TAATT TAA
1017955 ATTTGATATT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 23 1.00
ACGTcount: A:0.43, C:0.00, G:0.00, T:0.57
Consensus pattern (5 bp):
TAATT
Found at i:1018062 original size:18 final size:19
Alignment explanation
Indices: 1018029--1018077 Score: 57
Period size: 18 Copynumber: 2.6 Consensus size: 19
1018019 TCATATTTTT
*
1018029 TTAAAA-AAAAATTTATTA
1 TTAAAATAAAAATTTATAA
1018047 TTAAAATAAAAA-TTATAA
1 TTAAAATAAAAATTTATAA
*
1018065 ATAAAATTAAAAA
1 TTAAAA-TAAAAA
1018078 ATAAATTAAG
Statistics
Matches: 27, Mismatches: 2, Indels: 3
0.84 0.06 0.09
Matches are distributed among these distances:
18 16 0.59
19 11 0.41
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (19 bp):
TTAAAATAAAAATTTATAA
Found at i:1018066 original size:13 final size:12
Alignment explanation
Indices: 1018046--1018086 Score: 50
Period size: 12 Copynumber: 3.4 Consensus size: 12
1018036 AAAATTTATT
1018046 ATTAAAATAAAA
1 ATTAAAATAAAA
1018058 ATTATAAAT-AAA
1 ATTA-AAATAAAA
1018070 ATTAAAA-AATAA
1 ATTAAAATAA-AA
1018082 ATTAA
1 ATTAA
1018087 GTTACATGTG
Statistics
Matches: 26, Mismatches: 0, Indels: 6
0.81 0.00 0.19
Matches are distributed among these distances:
11 4 0.15
12 18 0.69
13 4 0.15
ACGTcount: A:0.71, C:0.00, G:0.00, T:0.29
Consensus pattern (12 bp):
ATTAAAATAAAA
Found at i:1020767 original size:3 final size:3
Alignment explanation
Indices: 1020761--1020797 Score: 56
Period size: 3 Copynumber: 12.3 Consensus size: 3
1020751 GCAAGAGAAG
* *
1020761 AAC AAC ATC AAC AAC AAC AAC AAC AAC AAC AGC AAC A
1 AAC AAC AAC AAC AAC AAC AAC AAC AAC AAC AAC AAC A
1020798 GCAGCTGCTA
Statistics
Matches: 30, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
3 30 1.00
ACGTcount: A:0.62, C:0.32, G:0.03, T:0.03
Consensus pattern (3 bp):
AAC
Found at i:1023972 original size:31 final size:30
Alignment explanation
Indices: 1023908--1023989 Score: 78
Period size: 31 Copynumber: 2.6 Consensus size: 30
1023898 AAAGAAGAAT
*
1023908 ATAAATATTAAATTAGT-AACTTTAATATTAA
1 ATAAATATTAAATTA-TAAAATTTAATA-TAA
1023939 ATAAATATTAAATATATAAATATTTAATA-AA
1 ATAAATATTAAAT-TATAAA-ATTTAATATAA
*
1023970 ATATATTTATTAAATTATAA
1 ATA-A-ATATTAAATTATAA
1023990 TTAAAATTTA
Statistics
Matches: 44, Mismatches: 2, Indels: 9
0.80 0.04 0.16
Matches are distributed among these distances:
31 19 0.43
32 10 0.23
33 15 0.34
ACGTcount: A:0.55, C:0.01, G:0.01, T:0.43
Consensus pattern (30 bp):
ATAAATATTAAATTATAAAATTTAATATAA
Found at i:1029127 original size:52 final size:52
Alignment explanation
Indices: 1029070--1029168 Score: 162
Period size: 52 Copynumber: 1.9 Consensus size: 52
1029060 TCAACCAACA
* * *
1029070 AAAATCTGCCTTTCAATACATATATCTTATGGATTATAATCTCGCTTTTAGC
1 AAAATCTGCCTTTCAATACAAAAATCTTATGGATTAGAATCTCGCTTTTAGC
*
1029122 AAAATCTGCTTTTCAATACAAAAATCTTATGGATTAGAATCTCGCTT
1 AAAATCTGCCTTTCAATACAAAAATCTTATGGATTAGAATCTCGCTT
1029169 AAAGTCTTTT
Statistics
Matches: 43, Mismatches: 4, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
52 43 1.00
ACGTcount: A:0.33, C:0.18, G:0.10, T:0.38
Consensus pattern (52 bp):
AAAATCTGCCTTTCAATACAAAAATCTTATGGATTAGAATCTCGCTTTTAGC
Found at i:1030821 original size:23 final size:23
Alignment explanation
Indices: 1030766--1030821 Score: 57
Period size: 21 Copynumber: 2.5 Consensus size: 23
1030756 TTGATCCAAA
*
1030766 ATAATT-TAAATATATTATAAAAT
1 ATAATTATAAA-ATATTATAAAAC
1030789 ATAA-TA-AAAATA-TATAAACAC
1 ATAATTATAAAATATTATAAA-AC
1030810 ATAATTATAAAA
1 ATAATTATAAAA
1030822 CATAAAAATA
Statistics
Matches: 28, Mismatches: 1, Indels: 8
0.76 0.03 0.22
Matches are distributed among these distances:
20 6 0.21
21 8 0.29
22 6 0.21
23 8 0.29
ACGTcount: A:0.62, C:0.04, G:0.00, T:0.34
Consensus pattern (23 bp):
ATAATTATAAAATATTATAAAAC
Found at i:1031055 original size:25 final size:25
Alignment explanation
Indices: 1031026--1031085 Score: 68
Period size: 25 Copynumber: 2.4 Consensus size: 25
1031016 CTTAAAAAGG
* *
1031026 AAAGAAAGAAAGAACCAAAGAAAAA
1 AAAGAAAAAAAAAACCAAAGAAAAA
**
1031051 AAAGAAAAAAAAAATGAAAG-AAAA
1 AAAGAAAAAAAAAACCAAAGAAAAA
*
1031075 AGAGAAAAAAA
1 AAAGAAAAAAA
1031086 TTATGGCTTC
Statistics
Matches: 30, Mismatches: 5, Indels: 1
0.83 0.14 0.03
Matches are distributed among these distances:
24 14 0.47
25 16 0.53
ACGTcount: A:0.80, C:0.03, G:0.15, T:0.02
Consensus pattern (25 bp):
AAAGAAAAAAAAAACCAAAGAAAAA
Found at i:1031061 original size:12 final size:12
Alignment explanation
Indices: 1031046--1031085 Score: 53
Period size: 12 Copynumber: 3.3 Consensus size: 12
1031036 AGAACCAAAG
1031046 AAAAAAAAGAAA
1 AAAAAAAAGAAA
*
1031058 AAAAAAATGAAA
1 AAAAAAAAGAAA
* *
1031070 GAAAAAGAGAAA
1 AAAAAAAAGAAA
1031082 AAAA
1 AAAA
1031086 TTATGGCTTC
Statistics
Matches: 23, Mismatches: 5, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
12 23 1.00
ACGTcount: A:0.85, C:0.00, G:0.12, T:0.03
Consensus pattern (12 bp):
AAAAAAAAGAAA
Found at i:1031077 original size:22 final size:21
Alignment explanation
Indices: 1031045--1031085 Score: 64
Period size: 22 Copynumber: 1.9 Consensus size: 21
1031035 AAGAACCAAA
1031045 GAAAAAAAAGAAAAAAAAAAT
1 GAAAAAAAAGAAAAAAAAAAT
*
1031066 GAAAGAAAAAGAGAAAAAAA
1 GAAA-AAAAAGAAAAAAAAA
1031086 TTATGGCTTC
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
21 4 0.22
22 14 0.78
ACGTcount: A:0.83, C:0.00, G:0.15, T:0.02
Consensus pattern (21 bp):
GAAAAAAAAGAAAAAAAAAAT
Found at i:1031086 original size:21 final size:21
Alignment explanation
Indices: 1031019--1031086 Score: 61
Period size: 21 Copynumber: 3.3 Consensus size: 21
1031009 TTTTCAGCTT
*
1031019 AAAAAGGAAAGAAAGAA-AGAA
1 AAAAATGAAAGAAA-AAGAGAA
** *
1031040 CCAAA-GAAA-AAAAAGAAAAA
1 AAAAATGAAAGAAAAAG-AGAA
1031060 AAAAATGAAAGAAAAAGAGAA
1 AAAAATGAAAGAAAAAGAGAA
1031081 AAAAAT
1 AAAAAT
1031087 TATGGCTTCA
Statistics
Matches: 37, Mismatches: 6, Indels: 8
0.73 0.12 0.16
Matches are distributed among these distances:
18 2 0.05
19 3 0.08
20 10 0.27
21 16 0.43
22 6 0.16
ACGTcount: A:0.78, C:0.03, G:0.16, T:0.03
Consensus pattern (21 bp):
AAAAATGAAAGAAAAAGAGAA
Found at i:1031129 original size:21 final size:23
Alignment explanation
Indices: 1031103--1031155 Score: 76
Period size: 22 Copynumber: 2.4 Consensus size: 23
1031093 TTCATATTTT
1031103 TATTATTTTTTATAT-TTAA-AA
1 TATTATTTTTTATATATTAATAA
1031124 TATTATATTTTTATATATTAATAA
1 TATTAT-TTTTTATATATTAATAA
1031148 T-TTATTTT
1 TATTATTTT
1031156 ATTTTATGTA
Statistics
Matches: 29, Mismatches: 0, Indels: 5
0.85 0.00 0.15
Matches are distributed among these distances:
21 6 0.21
22 12 0.41
23 8 0.28
24 3 0.10
ACGTcount: A:0.36, C:0.00, G:0.00, T:0.64
Consensus pattern (23 bp):
TATTATTTTTTATATATTAATAA
Found at i:1031941 original size:136 final size:137
Alignment explanation
Indices: 1031785--1032070 Score: 436
Period size: 136 Copynumber: 2.1 Consensus size: 137
1031775 AATAAATTTT
* * *
1031785 TATAAATTTTTACACATTAATTATTTATTTATCTATATTTTGACATATTTGTGTATTCGTA-TCA
1 TATAAA-TTTTACACATTAATTATTTATTTATCTATATTTTGACATATTTATATACTCGTACT-A
* * *
1031849 TGTTTATATTATTTTTCATGTTGTGTTTTAA-TTTTT-TATATATGTTGAGTTTGTATTATATCT
64 TGTTTATATTATTTTTCATGTTATGTTTTAATTTTTTATATATATATTGAGTTTGAATTATATCT
*
1031912 TAATTCATGG
129 CAATTCAT-G
*
1031922 TATAAATTTTACACGTTAATTATTTATTTATCTATATTTTGACATATTTATATACTCGTACTATG
1 TATAAATTTTACACATTAATTATTTATTTATCTATATTTTGACATATTTATATACTCGTACTATG
1031987 TTTATATTATTTTTCATGTTATGTTTTAATTTTTTATATATATATTGAGTTTGAATTATATCTCA
66 TTTATATTATTTTTCATGTTATGTTTTAATTTTTTATATATATATTGAGTTTGAATTATATCTCA
1032052 ATTCATG
131 ATTCATG
*
1032059 T-TATATTTTACA
1 TATAAATTTTACA
1032071 TAGTTAATCA
Statistics
Matches: 137, Mismatches: 9, Indels: 7
0.90 0.06 0.05
Matches are distributed among these distances:
136 91 0.66
137 14 0.10
138 32 0.23
ACGTcount: A:0.28, C:0.07, G:0.08, T:0.56
Consensus pattern (137 bp):
TATAAATTTTACACATTAATTATTTATTTATCTATATTTTGACATATTTATATACTCGTACTATG
TTTATATTATTTTTCATGTTATGTTTTAATTTTTTATATATATATTGAGTTTGAATTATATCTCA
ATTCATG
Found at i:1032117 original size:136 final size:133
Alignment explanation
Indices: 1031831--1032124 Score: 326
Period size: 136 Copynumber: 2.2 Consensus size: 133
1031821 ATTTTGACAT
* * *
1031831 ATTTGTGTATTCGTATCATGTTTATATTATTTTTCATGTTGTGTTTTAATTTTTTATATATGTTG
1 ATTTGTATATTCGTAT-ATGTTTATATTATTTTTCATGTTATGTTTTAATTTTTTATATATATTG
* * * * *
1031896 AGTTTGTATTATATCTTAATTCATGGTATAAATTTTACACGTTAATTATTTATTTATCTATATTT
65 AGTTTGAATTATATCTCAATTCATGGTATAAATTTTACAAGTTAATCATTGATTTA--TATATTT
** * *
1031961 TGACAT
128 AAAAAA
* *
1031967 ATTTATATACTCGTACTATGTTTATATTATTTTTCATGTTATGTTTTAATTTTTTATATATATAT
1 ATTTGTATATTCGTA-TATGTTTATATTATTTTTCATGTTATGTTTTAA-TTTTT-TATATATAT
*
1032032 TGAGTTTGAATTATATCTCAATTCAT-GT-TATATTTTACATAGTTAATCACTGTGATTTA-AT-
63 TGAGTTTGAATTATATCTCAATTCATGGTATAAATTTTACA-AGTTAATCA-T-TGATTTATATA
1032093 TTGTAAAAAA
125 TT-TAAAAAA
1032103 ATTTGTATATTCGTATTATGTT
1 ATTTGTATATTCGTA-TATGTT
1032125 AATGGCTTGT
Statistics
Matches: 133, Mismatches: 18, Indels: 14
0.81 0.11 0.08
Matches are distributed among these distances:
135 2 0.02
136 77 0.58
137 15 0.11
138 33 0.25
139 6 0.05
ACGTcount: A:0.28, C:0.07, G:0.10, T:0.55
Consensus pattern (133 bp):
ATTTGTATATTCGTATATGTTTATATTATTTTTCATGTTATGTTTTAATTTTTTATATATATTGA
GTTTGAATTATATCTCAATTCATGGTATAAATTTTACAAGTTAATCATTGATTTATATATTTAAA
AAA
Found at i:1032778 original size:35 final size:35
Alignment explanation
Indices: 1032700--1032779 Score: 92
Period size: 35 Copynumber: 2.3 Consensus size: 35
1032690 ATGTTTATAT
* *
1032700 TATTTT-TATGTTATATTATATTTTAATTATTTTT
1 TATTTTATATGTTATATTATATTTTAATTATCTTA
* *
1032734 TAATATTATAT-TTATATTATATTTTCATTTATCTTA
1 T-ATTTTATATGTTATATTATATTTT-AATTATCTTA
1032770 TATTTTATAT
1 TATTTTATAT
1032780 AAATTTTTTA
Statistics
Matches: 38, Mismatches: 5, Indels: 5
0.79 0.10 0.10
Matches are distributed among these distances:
34 1 0.03
35 26 0.68
36 11 0.29
ACGTcount: A:0.30, C:0.03, G:0.01, T:0.66
Consensus pattern (35 bp):
TATTTTATATGTTATATTATATTTTAATTATCTTA
Found at i:1032839 original size:27 final size:27
Alignment explanation
Indices: 1032800--1032858 Score: 66
Period size: 27 Copynumber: 2.1 Consensus size: 27
1032790 TATGATTAAA
*
1032800 TTTAAAATTTAAAATTATTTATTAAATAT
1 TTTAAAA-TTAAAATTATTAATTAAA-AT
* *
1032829 TTTAAAA-TAAATTTATTAATTATAAT
1 TTTAAAATTAAAATTATTAATTAAAAT
1032855 TTTA
1 TTTA
1032859 TTTAATTAAA
Statistics
Matches: 27, Mismatches: 3, Indels: 3
0.82 0.09 0.09
Matches are distributed among these distances:
26 6 0.22
27 14 0.52
29 7 0.26
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (27 bp):
TTTAAAATTAAAATTATTAATTAAAAT
Found at i:1032858 original size:15 final size:16
Alignment explanation
Indices: 1032834--1032876 Score: 52
Period size: 15 Copynumber: 2.7 Consensus size: 16
1032824 AATATTTTAA
*
1032834 AATAAATTTATTAATT
1 AATAATTTTATTAATT
1032850 -ATAATTTTATTTAATT
1 AATAATTTTA-TTAATT
*
1032866 AAAAATTTTAT
1 AATAATTTTAT
1032877 AAATATTAAA
Statistics
Matches: 23, Mismatches: 2, Indels: 4
0.79 0.07 0.14
Matches are distributed among these distances:
15 8 0.35
16 7 0.30
17 8 0.35
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (16 bp):
AATAATTTTATTAATT
Found at i:1032863 original size:16 final size:17
Alignment explanation
Indices: 1032834--1032876 Score: 54
Period size: 17 Copynumber: 2.6 Consensus size: 17
1032824 AATATTTTAA
*
1032834 AATAAATTTA-TTAATT
1 AATAATTTTATTTAATT
1032850 -ATAATTTTATTTAATT
1 AATAATTTTATTTAATT
*
1032866 AAAAATTTTAT
1 AATAATTTTAT
1032877 AAATATTAAA
Statistics
Matches: 23, Mismatches: 2, Indels: 3
0.82 0.07 0.11
Matches are distributed among these distances:
15 8 0.35
16 6 0.26
17 9 0.39
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (17 bp):
AATAATTTTATTTAATT
Found at i:1039307 original size:20 final size:20
Alignment explanation
Indices: 1039282--1039321 Score: 80
Period size: 20 Copynumber: 2.0 Consensus size: 20
1039272 TTTGATATAA
1039282 TTTATTAATTAATAAAAAAT
1 TTTATTAATTAATAAAAAAT
1039302 TTTATTAATTAATAAAAAAT
1 TTTATTAATTAATAAAAAAT
1039322 AAAATTATTT
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 20 1.00
ACGTcount: A:0.55, C:0.00, G:0.00, T:0.45
Consensus pattern (20 bp):
TTTATTAATTAATAAAAAAT
Found at i:1039328 original size:20 final size:20
Alignment explanation
Indices: 1039285--1039328 Score: 61
Period size: 20 Copynumber: 2.2 Consensus size: 20
1039275 GATATAATTT
***
1039285 ATTAATTAATAAAAAATTTT
1 ATTAATTAATAAAAAATAAA
1039305 ATTAATTAATAAAAAATAAA
1 ATTAATTAATAAAAAATAAA
1039325 ATTA
1 ATTA
1039329 TTTTTTTAAA
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
20 21 1.00
ACGTcount: A:0.61, C:0.00, G:0.00, T:0.39
Consensus pattern (20 bp):
ATTAATTAATAAAAAATAAA
Found at i:1039431 original size:24 final size:22
Alignment explanation
Indices: 1039379--1039455 Score: 68
Period size: 22 Copynumber: 3.4 Consensus size: 22
1039369 GATATTTATA
1039379 AATTT-AATATAATTTTAGTTG
1 AATTTAAATATAATTTTAGTTG
1039400 AATCTTTAAATATAAATTTTAGATTG
1 AA--TTTAAATAT-AATTTTAG-TTG
* * *
1039426 AATTT-AATTTAATTTGAATTG
1 AATTTAAATATAATTTTAGTTG
1039447 AAATTTAAA
1 -AATTTAAA
1039456 AAAATAAATA
Statistics
Matches: 46, Mismatches: 3, Indels: 12
0.75 0.05 0.20
Matches are distributed among these distances:
21 5 0.11
22 11 0.24
23 9 0.20
24 8 0.17
25 8 0.17
26 5 0.11
ACGTcount: A:0.43, C:0.01, G:0.08, T:0.48
Consensus pattern (22 bp):
AATTTAAATATAATTTTAGTTG
Found at i:1040448 original size:37 final size:37
Alignment explanation
Indices: 1040407--1040477 Score: 124
Period size: 37 Copynumber: 1.9 Consensus size: 37
1040397 TAGATTGGCG
*
1040407 CTGCCACCCAAATTCTAACAATCATAGTGGATTGTCA
1 CTGCCACCCAAATACTAACAATCATAGTGGATTGTCA
*
1040444 CTGCCACCCAAATACTGACAATCATAGTGGATTG
1 CTGCCACCCAAATACTAACAATCATAGTGGATTG
1040478 GCCAAGCCAT
Statistics
Matches: 32, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
37 32 1.00
ACGTcount: A:0.32, C:0.27, G:0.15, T:0.25
Consensus pattern (37 bp):
CTGCCACCCAAATACTAACAATCATAGTGGATTGTCA
Found at i:1045194 original size:37 final size:37
Alignment explanation
Indices: 1045144--1045237 Score: 118
Period size: 37 Copynumber: 2.5 Consensus size: 37
1045134 TTTTCGTAGT
* * *
1045144 TTGGCGCTACCACCCAAATTCTAACAATTATAGTGGA
1 TTGGCACTACCACCCAAATACTAACAATCATAGTGGA
* *
1045181 TTGGCACTGCCACCCAAATACTGACAATCATAGTGGA
1 TTGGCACTACCACCCAAATACTAACAATCATAGTGGA
*
1045218 TTGGCTA-AACCACCCAAATA
1 TTGGC-ACTACCACCCAAATA
1045238 TTACTTATCG
Statistics
Matches: 49, Mismatches: 7, Indels: 2
0.84 0.12 0.03
Matches are distributed among these distances:
37 48 0.98
38 1 0.02
ACGTcount: A:0.34, C:0.27, G:0.16, T:0.23
Consensus pattern (37 bp):
TTGGCACTACCACCCAAATACTAACAATCATAGTGGA
Found at i:1047439 original size:13 final size:14
Alignment explanation
Indices: 1047415--1047444 Score: 53
Period size: 13 Copynumber: 2.2 Consensus size: 14
1047405 ATGATTGTAA
1047415 AAATCAAAAATCAT
1 AAATCAAAAATCAT
1047429 AAATC-AAAATCAT
1 AAATCAAAAATCAT
1047442 AAA
1 AAA
1047445 ACTATTAAAC
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
13 11 0.69
14 5 0.31
ACGTcount: A:0.67, C:0.13, G:0.00, T:0.20
Consensus pattern (14 bp):
AAATCAAAAATCAT
Found at i:1048700 original size:16 final size:16
Alignment explanation
Indices: 1048676--1048707 Score: 55
Period size: 16 Copynumber: 2.0 Consensus size: 16
1048666 TATAAAAGTA
*
1048676 ATTTGCATATTTTTAT
1 ATTTACATATTTTTAT
1048692 ATTTACATATTTTTAT
1 ATTTACATATTTTTAT
1048708 TATCTCATAA
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 15 1.00
ACGTcount: A:0.28, C:0.06, G:0.03, T:0.62
Consensus pattern (16 bp):
ATTTACATATTTTTAT
Found at i:1051766 original size:17 final size:15
Alignment explanation
Indices: 1051744--1051782 Score: 51
Period size: 15 Copynumber: 2.5 Consensus size: 15
1051734 CATTAATACA
1051744 TATATATATATATAAAG
1 TATATATA-ATAT-AAG
*
1051761 TATATATAATATTAG
1 TATATATAATATAAG
1051776 TATATAT
1 TATATAT
1051783 GCTTTTAACG
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
15 9 0.43
16 4 0.19
17 8 0.38
ACGTcount: A:0.49, C:0.00, G:0.05, T:0.46
Consensus pattern (15 bp):
TATATATAATATAAG
Found at i:1055226 original size:14 final size:14
Alignment explanation
Indices: 1055209--1055239 Score: 53
Period size: 14 Copynumber: 2.2 Consensus size: 14
1055199 TTAAAATAAT
1055209 ATTTATAAAAATTA
1 ATTTATAAAAATTA
*
1055223 ATTTATAATAATTA
1 ATTTATAAAAATTA
1055237 ATT
1 ATT
1055240 AATTACTATT
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
14 16 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (14 bp):
ATTTATAAAAATTA
Found at i:1055461 original size:22 final size:21
Alignment explanation
Indices: 1055417--1055465 Score: 64
Period size: 22 Copynumber: 2.3 Consensus size: 21
1055407 ATTTAATTAC
*
1055417 TATTTATAAATATAATTTTTA
1 TATTTATAAATATAATTTATA
1055438 TAATTTATAAATA-AATTATATA
1 T-ATTTATAAATATAATT-TATA
1055460 TATTTA
1 TATTTA
1055466 AATAATAATA
Statistics
Matches: 25, Mismatches: 1, Indels: 4
0.83 0.03 0.13
Matches are distributed among these distances:
21 10 0.40
22 15 0.60
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (21 bp):
TATTTATAAATATAATTTATA
Found at i:1055472 original size:22 final size:21
Alignment explanation
Indices: 1055423--1055473 Score: 52
Period size: 20 Copynumber: 2.5 Consensus size: 21
1055413 TTACTATTTA
* *
1055423 TAAAT-ATAATTTTTATAATT
1 TAAATAATAAATTATATAATT
*
1055443 TATA-AATAAATTATATATATT
1 TAAATAATAAATTATATA-ATT
1055464 TAAATAATAA
1 TAAATAATAA
1055474 TAATAATTAA
Statistics
Matches: 24, Mismatches: 4, Indels: 4
0.75 0.12 0.12
Matches are distributed among these distances:
20 13 0.54
21 6 0.25
22 5 0.21
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (21 bp):
TAAATAATAAATTATATAATT
Found at i:1056450 original size:20 final size:22
Alignment explanation
Indices: 1056395--1056450 Score: 64
Period size: 20 Copynumber: 2.6 Consensus size: 22
1056385 ATTTAATTTC
1056395 ATAAATAAAATTAATTAAAAAAT
1 ATAAATAAAATT-ATTAAAAAAT
**
1056418 ATAAA-AATTTTATT-AAAAAT
1 ATAAATAAAATTATTAAAAAAT
1056438 A-AAATAAAATTAT
1 ATAAATAAAATTAT
1056451 ATATGATAAT
Statistics
Matches: 28, Mismatches: 4, Indels: 5
0.76 0.11 0.14
Matches are distributed among these distances:
19 3 0.11
20 13 0.46
21 3 0.11
22 4 0.14
23 5 0.18
ACGTcount: A:0.66, C:0.00, G:0.00, T:0.34
Consensus pattern (22 bp):
ATAAATAAAATTATTAAAAAAT
Found at i:1062392 original size:21 final size:20
Alignment explanation
Indices: 1062359--1062465 Score: 103
Period size: 21 Copynumber: 5.2 Consensus size: 20
1062349 GAGTTGCATC
*
1062359 TTTTATATGATTTTGTTAATA
1 TTTTATATAATTTTG-TAATA
*
1062380 TTTGATATAATTTTGATAAT-
1 TTTTATATAATTTTG-TAATA
1062400 TTTTATATAATTTTGATAATA
1 TTTTATATAATTTTG-TAATA
*
1062421 TTTTAGATAATTTTAGTAAT-
1 TTTTATATAATTTT-GTAATA
* *
1062441 TATTTAAATAATGTTGTAAT-
1 T-TTTATATAATTTTGTAATA
1062461 TTTTA
1 TTTTA
1062466 ATAGTTCTTG
Statistics
Matches: 76, Mismatches: 7, Indels: 8
0.84 0.08 0.09
Matches are distributed among these distances:
19 4 0.05
20 26 0.34
21 45 0.59
22 1 0.01
ACGTcount: A:0.35, C:0.00, G:0.08, T:0.57
Consensus pattern (20 bp):
TTTTATATAATTTTGTAATA
Found at i:1062394 original size:11 final size:11
Alignment explanation
Indices: 1062359--1062434 Score: 58
Period size: 11 Copynumber: 7.4 Consensus size: 11
1062349 GAGTTGCATC
*
1062359 TTTT-ATATGA
1 TTTTGATATAA
1062369 TTTTG-T-TAA
1 TTTTGATATAA
1062378 TATTTGATATAA
1 T-TTTGATATAA
1062390 TTTTG--ATAA
1 TTTTGATATAA
*
1062399 TTTTTATATAA
1 TTTTGATATAA
1062410 TTTTGATA-ATA
1 TTTTGATATA-A
*
1062421 TTTT-AGATAA
1 TTTTGATATAA
1062431 TTTT
1 TTTT
1062435 AGTAATTATT
Statistics
Matches: 54, Mismatches: 4, Indels: 16
0.73 0.05 0.22
Matches are distributed among these distances:
9 11 0.20
10 17 0.31
11 22 0.41
12 4 0.07
ACGTcount: A:0.33, C:0.00, G:0.08, T:0.59
Consensus pattern (11 bp):
TTTTGATATAA
Found at i:1062400 original size:9 final size:10
Alignment explanation
Indices: 1062386--1062441 Score: 55
Period size: 10 Copynumber: 5.6 Consensus size: 10
1062376 AATATTTGAT
1062386 ATAATTTT-G
1 ATAATTTTAG
*
1062395 ATAATTTTTAT
1 ATAA-TTTTAG
1062406 ATAATTTT-G
1 ATAATTTTAG
1062415 ATAATATTTTAG
1 AT-A-ATTTTAG
1062427 ATAATTTTAG
1 ATAATTTTAG
1062437 -TAATT
1 ATAATT
1062442 ATTTAAATAA
Statistics
Matches: 40, Mismatches: 2, Indels: 10
0.77 0.04 0.19
Matches are distributed among these distances:
9 11 0.28
10 16 0.40
11 10 0.25
12 3 0.08
ACGTcount: A:0.38, C:0.00, G:0.07, T:0.55
Consensus pattern (10 bp):
ATAATTTTAG
Found at i:1062441 original size:41 final size:40
Alignment explanation
Indices: 1062359--1062465 Score: 119
Period size: 41 Copynumber: 2.6 Consensus size: 40
1062349 GAGTTGCATC
* * *
1062359 TTTTATATGATTTTGTTAATATTTGATATAATTTTGATAAT
1 TTTTATATAATTTTG-TAATATTTTAGATAATTTTGATAAT
1062400 TTTTATATAATTTTGATAATATTTTAGATAATTTT-AGTAAT
1 TTTTATATAATTTTG-TAATATTTTAGATAATTTTGA-TAAT
* *
1062441 TATTTAAATAATGTTGTAAT-TTTTA
1 T-TTTATATAATTTTGTAATATTTTA
1062466 ATAGTTCTTG
Statistics
Matches: 58, Mismatches: 6, Indels: 5
0.84 0.09 0.07
Matches are distributed among these distances:
40 6 0.10
41 40 0.69
42 12 0.21
ACGTcount: A:0.35, C:0.00, G:0.08, T:0.57
Consensus pattern (40 bp):
TTTTATATAATTTTGTAATATTTTAGATAATTTTGATAAT
Found at i:1067023 original size:24 final size:25
Alignment explanation
Indices: 1066996--1067042 Score: 69
Period size: 24 Copynumber: 1.9 Consensus size: 25
1066986 ATTATAAATA
1066996 TTAATATTAATATAAA-AATAATTT
1 TTAATATTAATATAAATAATAATTT
* *
1067020 TTAATATTATTTTAAATAATAAT
1 TTAATATTAATATAAATAATAAT
1067043 ATATATTTTT
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
24 14 0.70
25 6 0.30
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (25 bp):
TTAATATTAATATAAATAATAATTT
Found at i:1070210 original size:21 final size:20
Alignment explanation
Indices: 1070161--1070235 Score: 62
Period size: 21 Copynumber: 3.6 Consensus size: 20
1070151 AACATATTAT
1070161 TAATATAT-AAATTTATAAA
1 TAATATATAAAATTTATAAA
**
1070180 TAATATTATAAAATTTATTGA
1 TAATA-TATAAAATTTATAAA
* * *
1070201 TGAATATATATATATATATAGA
1 T-AATATATA-AAATTTATAAA
*
1070223 TAATATATTAAAT
1 TAATATATAAAAT
1070236 ATAAATTTAT
Statistics
Matches: 45, Mismatches: 7, Indels: 7
0.76 0.12 0.12
Matches are distributed among these distances:
19 5 0.11
20 6 0.13
21 21 0.47
22 13 0.29
ACGTcount: A:0.52, C:0.00, G:0.04, T:0.44
Consensus pattern (20 bp):
TAATATATAAAATTTATAAA
Found at i:1070486 original size:23 final size:21
Alignment explanation
Indices: 1070459--1070514 Score: 60
Period size: 20 Copynumber: 2.6 Consensus size: 21
1070449 TATTAACATA
1070459 TTAATATTAATTATAATAAATAT
1 TTAATATTAATT-TAA-AAATAT
*
1070482 TTAATA-TAAATTAAAAATAT
1 TTAATATTAATTTAAAAATAT
*
1070502 TAAATATTTAATT
1 TTAATA-TTAATT
1070515 CTGATAACAT
Statistics
Matches: 28, Mismatches: 3, Indels: 5
0.78 0.08 0.14
Matches are distributed among these distances:
20 11 0.39
21 3 0.11
22 8 0.29
23 6 0.21
ACGTcount: A:0.54, C:0.00, G:0.00, T:0.46
Consensus pattern (21 bp):
TTAATATTAATTTAAAAATAT
Found at i:1081808 original size:2 final size:2
Alignment explanation
Indices: 1081801--1081834 Score: 68
Period size: 2 Copynumber: 17.0 Consensus size: 2
1081791 AAAACGCTAT
1081801 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1081835 GAGAGAGAGA
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 32 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:1081839 original size:2 final size:2
Alignment explanation
Indices: 1081834--1081873 Score: 80
Period size: 2 Copynumber: 20.0 Consensus size: 2
1081824 ATATATATAT
1081834 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG
1 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG
1081874 GATTGTGCAT
Statistics
Matches: 38, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 38 1.00
ACGTcount: A:0.50, C:0.00, G:0.50, T:0.00
Consensus pattern (2 bp):
AG
Found at i:1084269 original size:4 final size:4
Alignment explanation
Indices: 1084262--1084300 Score: 60
Period size: 4 Copynumber: 9.8 Consensus size: 4
1084252 AGCCTGCCAG
* *
1084262 CCAT CCAT TCAT CTAT CCAT CCAT CCAT CCAT CCAT CCA
1 CCAT CCAT CCAT CCAT CCAT CCAT CCAT CCAT CCAT CCA
1084301 GGGTTTGTTA
Statistics
Matches: 31, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
4 31 1.00
ACGTcount: A:0.26, C:0.46, G:0.00, T:0.28
Consensus pattern (4 bp):
CCAT
Found at i:1084345 original size:15 final size:17
Alignment explanation
Indices: 1084327--1084358 Score: 50
Period size: 15 Copynumber: 2.0 Consensus size: 17
1084317 CTTTATTTAT
1084327 ATATTAT-AT-ATGTGA
1 ATATTATGATCATGTGA
1084342 ATATTATGATCATGTGA
1 ATATTATGATCATGTGA
1084359 TGTAATGTCG
Statistics
Matches: 15, Mismatches: 0, Indels: 2
0.88 0.00 0.12
Matches are distributed among these distances:
15 7 0.47
16 2 0.13
17 6 0.40
ACGTcount: A:0.38, C:0.03, G:0.16, T:0.44
Consensus pattern (17 bp):
ATATTATGATCATGTGA
Found at i:1085054 original size:2 final size:2
Alignment explanation
Indices: 1085049--1085077 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
1085039 CATAAAAAAC
1085049 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 A
1085078 ATCACAGCTA
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 27 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:1085989 original size:13 final size:13
Alignment explanation
Indices: 1085965--1085998 Score: 52
Period size: 13 Copynumber: 2.7 Consensus size: 13
1085955 GGAACTGAAG
1085965 AAAGAA-AGAACA
1 AAAGAAGAGAACA
*
1085977 AGAGAAGAGAACA
1 AAAGAAGAGAACA
1085990 AAAGAAGAG
1 AAAGAAGAG
1085999 CTTAAGACCG
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
12 5 0.26
13 14 0.74
ACGTcount: A:0.68, C:0.06, G:0.26, T:0.00
Consensus pattern (13 bp):
AAAGAAGAGAACA
Found at i:1087638 original size:21 final size:20
Alignment explanation
Indices: 1087607--1087653 Score: 58
Period size: 21 Copynumber: 2.2 Consensus size: 20
1087597 TAAAATATAA
1087607 AAAATTATTTTATATTAATATT
1 AAAA-TATTTTATATTAA-ATT
*
1087629 AAAATATTTTATTTTAAATT
1 AAAATATTTTATATTAAATT
*
1087649 TAAAT
1 AAAAT
1087654 GATAATTCAA
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
20 7 0.30
21 12 0.52
22 4 0.17
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (20 bp):
AAAATATTTTATATTAAATT
Found at i:1088318 original size:5 final size:5
Alignment explanation
Indices: 1088277--1088326 Score: 54
Period size: 5 Copynumber: 10.8 Consensus size: 5
1088267 AAATAATAAA
* *
1088277 TATAT TA-AA TATCT TATAT TA-AT TATAT T-TA- TATAT TATAT TATAT
1 TATAT TATAT TATAT TATAT TATAT TATAT TATAT TATAT TATAT TATAT
1088323 TATA
1 TATA
1088327 ATTAAAAATT
Statistics
Matches: 37, Mismatches: 4, Indels: 8
0.76 0.08 0.16
Matches are distributed among these distances:
3 1 0.03
4 11 0.30
5 25 0.68
ACGTcount: A:0.42, C:0.02, G:0.00, T:0.56
Consensus pattern (5 bp):
TATAT
Found at i:1088868 original size:6 final size:6
Alignment explanation
Indices: 1088857--1088885 Score: 58
Period size: 6 Copynumber: 4.8 Consensus size: 6
1088847 TTCCCCCCCA
1088857 TCTCTT TCTCTT TCTCTT TCTCTT TCTCT
1 TCTCTT TCTCTT TCTCTT TCTCTT TCTCT
1088886 GGGGGAAGGA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 23 1.00
ACGTcount: A:0.00, C:0.34, G:0.00, T:0.66
Consensus pattern (6 bp):
TCTCTT
Found at i:1093180 original size:2 final size:2
Alignment explanation
Indices: 1093173--1093205 Score: 57
Period size: 2 Copynumber: 16.5 Consensus size: 2
1093163 GTAGTGACCT
*
1093173 TA TA TA TA TA TA TA TA TA TA TA TA TA CA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1093206 TAATACTCCA
Statistics
Matches: 29, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
2 29 1.00
ACGTcount: A:0.48, C:0.03, G:0.00, T:0.48
Consensus pattern (2 bp):
TA
Found at i:1096547 original size:2 final size:2
Alignment explanation
Indices: 1096540--1096569 Score: 60
Period size: 2 Copynumber: 15.0 Consensus size: 2
1096530 ATACATACAG
1096540 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
1096570 TCCGCCGCCT
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 28 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:1096734 original size:14 final size:15
Alignment explanation
Indices: 1096712--1096748 Score: 58
Period size: 14 Copynumber: 2.5 Consensus size: 15
1096702 ATAATATCTA
*
1096712 ATAAATTTAATATTT
1 ATAATTTTAATATTT
1096727 AT-ATTTTAATATTT
1 ATAATTTTAATATTT
1096741 ATAATTTT
1 ATAATTTT
1096749 TTATTATTTT
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
14 13 0.65
15 7 0.35
ACGTcount: A:0.41, C:0.00, G:0.00, T:0.59
Consensus pattern (15 bp):
ATAATTTTAATATTT
Found at i:1097438 original size:16 final size:17
Alignment explanation
Indices: 1097417--1097450 Score: 52
Period size: 16 Copynumber: 2.1 Consensus size: 17
1097407 TTTAAATTTT
1097417 TATATAATT-TTTTATA
1 TATATAATTATTTTATA
*
1097433 TATATATTTATTTTATA
1 TATATAATTATTTTATA
1097450 T
1 T
1097451 TCGTATTAAA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
16 8 0.50
17 8 0.50
ACGTcount: A:0.35, C:0.00, G:0.00, T:0.65
Consensus pattern (17 bp):
TATATAATTATTTTATA
Found at i:1106711 original size:14 final size:14
Alignment explanation
Indices: 1106692--1106758 Score: 50
Period size: 14 Copynumber: 4.9 Consensus size: 14
1106682 TAATCAAATC
1106692 AATTAATTTTTATT
1 AATTAATTTTTATT
*
1106706 AATTAA-TTTAATTT
1 AATTAATTTTTA-TT
* *
1106720 AATCAATTTTT-TA
1 AATTAATTTTTATT
* *
1106733 AATTTA-TTTAATT
1 AATTAATTTTTATT
1106746 AATTTAATTTTTA
1 AA-TTAATTTTTA
1106759 AAATTTTAAT
Statistics
Matches: 38, Mismatches: 10, Indels: 9
0.67 0.18 0.16
Matches are distributed among these distances:
12 3 0.08
13 12 0.32
14 16 0.42
15 7 0.18
ACGTcount: A:0.39, C:0.01, G:0.00, T:0.60
Consensus pattern (14 bp):
AATTAATTTTTATT
Found at i:1106727 original size:18 final size:18
Alignment explanation
Indices: 1106706--1106755 Score: 57
Period size: 18 Copynumber: 2.8 Consensus size: 18
1106696 AATTTTTATT
1106706 AATTAATTTAATTTAATC
1 AATTAATTTAATTTAATC
* * *
1106724 AATT-TTTTAAATTTATTT
1 AATTAATTT-AATTTAATC
1106742 AATTAATTTAATTT
1 AATTAATTTAATTT
1106756 TTAAAATTTT
Statistics
Matches: 26, Mismatches: 4, Indels: 4
0.76 0.12 0.12
Matches are distributed among these distances:
17 3 0.12
18 20 0.77
19 3 0.12
ACGTcount: A:0.40, C:0.02, G:0.00, T:0.58
Consensus pattern (18 bp):
AATTAATTTAATTTAATC
Found at i:1112695 original size:2 final size:2
Alignment explanation
Indices: 1112688--1112716 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
1112678 TCTTAATTGC
1112688 TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1112717 CCCTTCCCTC
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 27 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:1116309 original size:20 final size:20
Alignment explanation
Indices: 1116262--1116312 Score: 59
Period size: 20 Copynumber: 2.5 Consensus size: 20
1116252 TTAAATAATT
1116262 ATTTTTAAAAATTATAATTAA
1 ATTTTT-AAAATTATAATTAA
**
1116283 ACATTTAAAATT-TAATTTAA
1 ATTTTTAAAATTATAA-TTAA
1116303 ATTTTTAAAA
1 ATTTTTAAAA
1116313 AAAAAATTGC
Statistics
Matches: 25, Mismatches: 4, Indels: 3
0.78 0.12 0.09
Matches are distributed among these distances:
19 3 0.12
20 18 0.72
21 4 0.16
ACGTcount: A:0.51, C:0.02, G:0.00, T:0.47
Consensus pattern (20 bp):
ATTTTTAAAATTATAATTAA
Found at i:1117924 original size:158 final size:158
Alignment explanation
Indices: 1117671--1117983 Score: 563
Period size: 158 Copynumber: 2.0 Consensus size: 158
1117661 AGAAAAGATA
* *
1117671 ATAAAAAGAAGCCAATGTGCCGTGCATGATCCATGATGCATATGGCAATGATTCCCAGAAGACCA
1 ATAAAAAGAAGCCAATGTGCCGTGCATGATCCATAATGCACATGGCAATGATTCCCAGAAGACCA
* * *
1117736 ACCAAATCTAAGGGAAGCTCACCTTAACATGACATGGCGAAACCCAGATTTCTTACATGAAAATA
66 ACCAAATCTAAGCGAAGCTCACCTTAACATGACATGGCGAAAACCAGATTTCTGACATGAAAATA
1117801 AACATCATAATAAATTACTATTTTCTTT
131 AACATCATAATAAATTACTATTTTCTTT
*
1117829 ATAAAAAGAAGCCATTGTGCCGTGCATGATCCATAATGCACATGGCAATGATTCCCAGAAGACCA
1 ATAAAAAGAAGCCAATGTGCCGTGCATGATCCATAATGCACATGGCAATGATTCCCAGAAGACCA
*
1117894 ACCAAATCTAAGCGAGGCTCACCTTAACATGACATGGCGAAAACCAGATTTCTGACATGAAAATA
66 ACCAAATCTAAGCGAAGCTCACCTTAACATGACATGGCGAAAACCAGATTTCTGACATGAAAATA
1117959 AACATCATAATAAATTACTATTTTC
131 AACATCATAATAAATTACTATTTTC
1117984 AGCAAGAAGT
Statistics
Matches: 148, Mismatches: 7, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
158 148 1.00
ACGTcount: A:0.39, C:0.21, G:0.15, T:0.24
Consensus pattern (158 bp):
ATAAAAAGAAGCCAATGTGCCGTGCATGATCCATAATGCACATGGCAATGATTCCCAGAAGACCA
ACCAAATCTAAGCGAAGCTCACCTTAACATGACATGGCGAAAACCAGATTTCTGACATGAAAATA
AACATCATAATAAATTACTATTTTCTTT
Found at i:1124282 original size:14 final size:14
Alignment explanation
Indices: 1124265--1124291 Score: 54
Period size: 14 Copynumber: 1.9 Consensus size: 14
1124255 TGAGTTATTA
1124265 TTTTTTTTTCTTTC
1 TTTTTTTTTCTTTC
1124279 TTTTTTTTTCTTT
1 TTTTTTTTTCTTT
1124292 TGGTGCTGCA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 13 1.00
ACGTcount: A:0.00, C:0.11, G:0.00, T:0.89
Consensus pattern (14 bp):
TTTTTTTTTCTTTC
Found at i:1127567 original size:11 final size:10
Alignment explanation
Indices: 1127551--1127708 Score: 84
Period size: 11 Copynumber: 15.6 Consensus size: 10
1127541 ATTTATAACG
1127551 TTAAAATCATA
1 TTAAAAT-ATA
1127562 TTAAAA-ATTA
1 TTAAAATA-TA
1127572 TTAAAATTATA
1 TTAAAA-TATA
*
1127583 TT-AAATATTT
1 TTAAAATA-TA
1127593 TTAAAA-ATA
1 TTAAAATATA
**
1127602 TATAATTTATTA
1 T-TAAAATA-TA
1127614 TTAAAATTATA
1 TTAAAA-TATA
1127625 TTAAAA-A-A
1 TTAAAATATA
1127633 TTAAAGATTATA
1 TTAAA-A-TATA
1127645 TTAAAGAT-TA
1 TTAAA-ATATA
*
1127655 -TAAATTAT-
1 TTAAAATATA
1127663 TATAAAAT-TA
1 T-TAAAATATA
*
1127673 TTAAATTATA
1 TTAAAATATA
*
1127683 -TAAAATTTA
1 TTAAAATATA
1127692 TTAAAATTATA
1 TTAAAA-TATA
1127703 TTAAAA
1 TTAAAA
1127709 GTTTAAATAA
Statistics
Matches: 115, Mismatches: 12, Indels: 40
0.69 0.07 0.24
Matches are distributed among these distances:
8 7 0.06
9 25 0.22
10 33 0.29
11 36 0.31
12 14 0.12
ACGTcount: A:0.54, C:0.01, G:0.01, T:0.44
Consensus pattern (10 bp):
TTAAAATATA
Found at i:1127577 original size:21 final size:21
Alignment explanation
Indices: 1127551--1127708 Score: 154
Period size: 21 Copynumber: 7.8 Consensus size: 21
1127541 ATTTATAACG
*
1127551 TTAAAATCATATTAAAAATTA
1 TTAAAATTATATTAAAAATTA
* *
1127572 TTAAAATTATATTAAATATTT
1 TTAAAATTATATTAAAAATTA
* **
1127593 TTAAAAATATA-TAATTTATTA
1 TTAAAATTATATTAA-AAATTA
1127614 TTAAAATTATATTAAAAA--A
1 TTAAAATTATATTAAAAATTA
*
1127633 TTAAAGATTATATTAAAGATTA
1 TTAAA-ATTATATTAAAAATTA
1127655 -T-AAA-T-TATTATAAAATTA
1 TTAAAATTATATTA-AAAATTA
*
1127673 TT-AAATTATA-TAAAATTTA
1 TTAAAATTATATTAAAAATTA
1127692 TTAAAATTATATTAAAA
1 TTAAAATTATATTAAAA
1127709 GTTTAAATAA
Statistics
Matches: 114, Mismatches: 12, Indels: 22
0.77 0.08 0.15
Matches are distributed among these distances:
17 5 0.04
18 7 0.06
19 19 0.17
20 28 0.25
21 51 0.45
22 4 0.04
ACGTcount: A:0.54, C:0.01, G:0.01, T:0.44
Consensus pattern (21 bp):
TTAAAATTATATTAAAAATTA
Found at i:1127644 original size:20 final size:19
Alignment explanation
Indices: 1127613--1127708 Score: 83
Period size: 20 Copynumber: 4.9 Consensus size: 19
1127603 ATAATTTATT
1127613 ATTAAAATTATATTAAAAA
1 ATTAAAATTATATTAAAAA
*
1127632 ATTAAAGATTATATT-AAAG
1 ATTAAA-ATTATATTAAAAA
*
1127651 ATTATAAA-T-TATTATAAA
1 ATTA-AAATTATATTAAAAA
*
1127669 ATTATTAAATTATA-TAAAATTT
1 ATTA--AAATTATATTAAAA--A
1127691 ATTAAAATTATATTAAAA
1 ATTAAAATTATATTAAAA
1127709 GTTTAAATAA
Statistics
Matches: 63, Mismatches: 5, Indels: 16
0.75 0.06 0.19
Matches are distributed among these distances:
17 4 0.06
18 7 0.11
19 18 0.29
20 23 0.37
21 7 0.11
22 4 0.06
ACGTcount: A:0.56, C:0.00, G:0.02, T:0.42
Consensus pattern (19 bp):
ATTAAAATTATATTAAAAA
Found at i:1130620 original size:29 final size:30
Alignment explanation
Indices: 1130570--1130630 Score: 72
Period size: 29 Copynumber: 2.1 Consensus size: 30
1130560 TTTATATTAA
**
1130570 ATTTAAATTATATTTATTA-TTTATTAAAT
1 ATTTAAATTATATAAATTATTTTATTAAAT
*
1130599 ATTTAAATTA-ATAAATTAATTTTTTTAAAT
1 ATTTAAATTATATAAATT-ATTTTATTAAAT
1130629 AT
1 AT
1130631 AATTAAATAT
Statistics
Matches: 27, Mismatches: 3, Indels: 3
0.82 0.09 0.09
Matches are distributed among these distances:
28 5 0.19
29 11 0.41
30 11 0.41
ACGTcount: A:0.44, C:0.00, G:0.00, T:0.56
Consensus pattern (30 bp):
ATTTAAATTATATAAATTATTTTATTAAAT
Found at i:1130674 original size:26 final size:26
Alignment explanation
Indices: 1130620--1130671 Score: 68
Period size: 26 Copynumber: 2.0 Consensus size: 26
1130610 TAAATTAATT
*
1130620 TTTTTAAATATAATTAAATATTAAAA
1 TTTTTAAATATAATTAAATAATAAAA
* *
1130646 TTTTTAAATTTATTATAAATAATAAA
1 TTTTTAAATATAAT-TAAATAATAAA
1130672 TTTAATATTT
Statistics
Matches: 22, Mismatches: 3, Indels: 1
0.85 0.12 0.04
Matches are distributed among these distances:
26 12 0.55
27 10 0.45
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (26 bp):
TTTTTAAATATAATTAAATAATAAAA
Found at i:1131414 original size:59 final size:60
Alignment explanation
Indices: 1131288--1131448 Score: 180
Period size: 59 Copynumber: 2.6 Consensus size: 60
1131278 GTCCTGCATG
* * * **
1131288 CCTATTTAAATTTTAGTCTTATTCTTACCATAAAAAGTTTTTTTAAATTTTATTAATTATTCTTA
1 CCTACTTAGATTTTACTCTTATTCTTACCA-AAAAAG-GGTTTT---TTTTATTAATTATTCTTA
* *
1131353 CCTACTTAGATTTTACTCTTGTTCTTACTAAAAAAGGGTTTTTTTTATT-ATTATTCTTA
1 CCTACTTAGATTTTACTCTTATTCTTACCAAAAAAGGGTTTTTTTTATTAATTATTCTTA
** *
1131412 CCTGTTTAGATTTTAGTCTTATTCTTACCAAAAAAGG
1 CCTACTTAGATTTTACTCTTATTCTTACCAAAAAAGG
1131449 TAATGACTAT
Statistics
Matches: 84, Mismatches: 12, Indels: 6
0.82 0.12 0.06
Matches are distributed among these distances:
59 42 0.50
60 7 0.08
63 4 0.05
64 6 0.07
65 25 0.30
ACGTcount: A:0.29, C:0.13, G:0.07, T:0.50
Consensus pattern (60 bp):
CCTACTTAGATTTTACTCTTATTCTTACCAAAAAAGGGTTTTTTTTATTAATTATTCTTA
Found at i:1131484 original size:2 final size:2
Alignment explanation
Indices: 1131477--1131512 Score: 63
Period size: 2 Copynumber: 17.5 Consensus size: 2
1131467 AATTACTAGT
1131477 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TCA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T-A TA T
1131513 TTCTAAAAAA
Statistics
Matches: 33, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
2 31 0.94
3 2 0.06
ACGTcount: A:0.47, C:0.03, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:1131791 original size:21 final size:19
Alignment explanation
Indices: 1131745--1131794 Score: 57
Period size: 18 Copynumber: 2.5 Consensus size: 19
1131735 GAATTTATAA
1131745 TATTATATTTTTATCATATT
1 TATTATA-TTTTATCATATT
*
1131765 TA-TATATTTTATTATATT
1 TATTATATTTTATCATATT
1131783 ATAATTATATTT
1 -T-ATTATATTT
1131795 AAGATATTTT
Statistics
Matches: 26, Mismatches: 1, Indels: 5
0.81 0.03 0.16
Matches are distributed among these distances:
18 11 0.42
19 5 0.19
20 3 0.12
21 7 0.27
ACGTcount: A:0.34, C:0.02, G:0.00, T:0.64
Consensus pattern (19 bp):
TATTATATTTTATCATATT
Found at i:1131792 original size:29 final size:30
Alignment explanation
Indices: 1131745--1131813 Score: 81
Period size: 29 Copynumber: 2.4 Consensus size: 30
1131735 GAATTTATAA
* * *
1131745 TATTATATTTTTATCATATTT-ATATATTT
1 TATTATATTATAATCATATTTAAGATATTT
*
1131774 TATTATATTATAATTATATTTAAGATATTT
1 TATTATATTATAATCATATTTAAGATATTT
1131804 TA-TAT-TTATA
1 TATTATATTATA
1131814 TAAATTTTGA
Statistics
Matches: 35, Mismatches: 4, Indels: 3
0.83 0.10 0.07
Matches are distributed among these distances:
28 5 0.14
29 21 0.60
30 9 0.26
ACGTcount: A:0.36, C:0.01, G:0.01, T:0.61
Consensus pattern (30 bp):
TATTATATTATAATCATATTTAAGATATTT
Found at i:1131793 original size:45 final size:46
Alignment explanation
Indices: 1131744--1131853 Score: 102
Period size: 47 Copynumber: 2.3 Consensus size: 46
1131734 AGAATTTATA
*
1131744 ATATTATATTTTTATCATATT-TATATATTTT-ATTATATT-ATAA-TT
1 ATATTATATTTTTAT-AT-TTATATAAATTTTGA-TATATTAATAATTT
*
1131789 ATATTTAAGATATTTTATATTTATATAAATTTTGATATATTAATAATTTT
1 ATA-TT-ATAT-TTTTATATTTATATAAATTTTGATATATTAATAA-TTT
*
1131839 ATATTATATATTTAT
1 ATATTATATTTTTAT
1131854 TTATATCATA
Statistics
Matches: 53, Mismatches: 4, Indels: 14
0.75 0.06 0.20
Matches are distributed among these distances:
45 3 0.06
46 4 0.08
47 25 0.47
48 14 0.26
49 2 0.04
50 5 0.09
ACGTcount: A:0.38, C:0.01, G:0.02, T:0.59
Consensus pattern (46 bp):
ATATTATATTTTTATATTTATATAAATTTTGATATATTAATAATTT
Found at i:1131806 original size:16 final size:15
Alignment explanation
Indices: 1131787--1131843 Score: 60
Period size: 16 Copynumber: 3.5 Consensus size: 15
1131777 TATATTATAA
*
1131787 TTATATTTAAGATATT
1 TTATATTTAATA-ATT
1131803 TTATATTTATATAAATT
1 TTATATTTA-AT-AATT
1131820 TTGATATATTAATAATT
1 TT-ATAT-TTAATAATT
1131837 TTATATT
1 TTATATT
1131844 ATATATTTAT
Statistics
Matches: 36, Mismatches: 1, Indels: 9
0.78 0.02 0.20
Matches are distributed among these distances:
15 1 0.03
16 13 0.36
17 12 0.33
18 7 0.19
19 3 0.08
ACGTcount: A:0.39, C:0.00, G:0.04, T:0.58
Consensus pattern (15 bp):
TTATATTTAATAATT
Found at i:1148865 original size:14 final size:13
Alignment explanation
Indices: 1148832--1148870 Score: 51
Period size: 14 Copynumber: 2.8 Consensus size: 13
1148822 AGAAAAACTA
1148832 TTTAAATAATTTTT
1 TTTAAA-AATTTTT
1148846 TCTTAAAAATTATTT
1 T-TTAAAAATT-TTT
1148861 TTTAAAAATT
1 TTTAAAAATT
1148871 GACTCAAAAA
Statistics
Matches: 23, Mismatches: 0, Indels: 4
0.85 0.00 0.15
Matches are distributed among these distances:
14 14 0.61
15 9 0.39
ACGTcount: A:0.41, C:0.03, G:0.00, T:0.56
Consensus pattern (13 bp):
TTTAAAAATTTTT
Found at i:1150464 original size:18 final size:18
Alignment explanation
Indices: 1150437--1150480 Score: 54
Period size: 18 Copynumber: 2.4 Consensus size: 18
1150427 ATCATATAGG
1150437 TAAAATAAA-TATTATATTT
1 TAAAA-AAATTATTAT-TTT
*
1150456 TAAAAAAATTATTCTTTT
1 TAAAAAAATTATTATTTT
1150474 TAAAAAA
1 TAAAAAA
1150481 TATGAAGTTA
Statistics
Matches: 23, Mismatches: 1, Indels: 3
0.85 0.04 0.11
Matches are distributed among these distances:
18 13 0.57
19 10 0.43
ACGTcount: A:0.55, C:0.02, G:0.00, T:0.43
Consensus pattern (18 bp):
TAAAAAAATTATTATTTT
Found at i:1153279 original size:10 final size:10
Alignment explanation
Indices: 1153258--1153322 Score: 62
Period size: 11 Copynumber: 6.3 Consensus size: 10
1153248 TTTATGTTTT
1153258 TTTTATATATA
1 TTTTA-ATATA
1153269 TTTTAATATA
1 TTTTAATATA
1153279 TATTTAAGTATA
1 T-TTTAA-TATA
* *
1153291 TATAAATATA
1 TTTTAATATA
1153301 TTTTTAA-ATA
1 -TTTTAATATA
1153311 TTTT-ATATA
1 TTTTAATATA
1153320 TTT
1 TTT
1153323 AAAAAATTAT
Statistics
Matches: 46, Mismatches: 4, Indels: 10
0.77 0.07 0.17
Matches are distributed among these distances:
8 1 0.02
9 10 0.22
10 13 0.28
11 17 0.37
12 5 0.11
ACGTcount: A:0.40, C:0.00, G:0.02, T:0.58
Consensus pattern (10 bp):
TTTTAATATA
Found at i:1156945 original size:16 final size:17
Alignment explanation
Indices: 1156911--1156946 Score: 56
Period size: 16 Copynumber: 2.2 Consensus size: 17
1156901 TTCAAGTGAG
*
1156911 TATTTAAAGTAAATTTT
1 TATTTAAAGTAAATATT
1156928 TATTTAAA-TAAATATT
1 TATTTAAAGTAAATATT
1156944 TAT
1 TAT
1156947 ATTATGATTA
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
16 10 0.56
17 8 0.44
ACGTcount: A:0.44, C:0.00, G:0.03, T:0.53
Consensus pattern (17 bp):
TATTTAAAGTAAATATT
Found at i:1161110 original size:2 final size:2
Alignment explanation
Indices: 1161103--1161135 Score: 57
Period size: 2 Copynumber: 16.5 Consensus size: 2
1161093 GGTGATAATG
*
1161103 CT CT CT CT TT CT CT CT CT CT CT CT CT CT CT CT C
1 CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT C
1161136 AAATTCAATG
Statistics
Matches: 29, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
2 29 1.00
ACGTcount: A:0.00, C:0.48, G:0.00, T:0.52
Consensus pattern (2 bp):
CT
Found at i:1162569 original size:30 final size:30
Alignment explanation
Indices: 1162530--1162591 Score: 83
Period size: 30 Copynumber: 2.1 Consensus size: 30
1162520 TTACATTTTA
1162530 AATTAATTTATT-TATATAATTAATTA-AAT
1 AATTAATTTATTAT-TATAATTAATTATAAT
*
1162559 AATTAGATTTATTATTATTATTAATTATAAT
1 AATTA-ATTTATTATTATAATTAATTATAAT
1162590 AA
1 AA
1162592 ATATTTAAAA
Statistics
Matches: 29, Mismatches: 1, Indels: 4
0.85 0.03 0.12
Matches are distributed among these distances:
29 5 0.17
30 18 0.62
31 6 0.21
ACGTcount: A:0.47, C:0.00, G:0.02, T:0.52
Consensus pattern (30 bp):
AATTAATTTATTATTATAATTAATTATAAT
Found at i:1170287 original size:15 final size:15
Alignment explanation
Indices: 1170267--1170306 Score: 55
Period size: 15 Copynumber: 2.7 Consensus size: 15
1170257 TATTATGTGA
*
1170267 AATTAGGTTTAGCG-T
1 AATTA-GTTTAGAGAT
1170282 AATTAGTTTAGAGAT
1 AATTAGTTTAGAGAT
1170297 AATTAGTTTA
1 AATTAGTTTA
1170307 AGGCCTATAA
Statistics
Matches: 23, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
14 7 0.30
15 16 0.70
ACGTcount: A:0.35, C:0.03, G:0.20, T:0.42
Consensus pattern (15 bp):
AATTAGTTTAGAGAT
Found at i:1175210 original size:16 final size:15
Alignment explanation
Indices: 1175189--1175230 Score: 66
Period size: 15 Copynumber: 2.7 Consensus size: 15
1175179 TGATCTTGTC
1175189 CATCCACCACCCTGTG
1 CATCCACCACCC-GTG
*
1175205 CATCCACAACCCGTG
1 CATCCACCACCCGTG
1175220 CATCCACCACC
1 CATCCACCACC
1175231 TGTTTACCCA
Statistics
Matches: 24, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
15 13 0.54
16 11 0.46
ACGTcount: A:0.24, C:0.52, G:0.10, T:0.14
Consensus pattern (15 bp):
CATCCACCACCCGTG
Found at i:1175222 original size:15 final size:16
Alignment explanation
Indices: 1175189--1175226 Score: 60
Period size: 16 Copynumber: 2.4 Consensus size: 16
1175179 TGATCTTGTC
*
1175189 CATCCACCACCCTGTG
1 CATCCACAACCCTGTG
1175205 CATCCACAACCC-GTG
1 CATCCACAACCCTGTG
1175220 CATCCAC
1 CATCCAC
1175227 CACCTGTTTA
Statistics
Matches: 21, Mismatches: 1, Indels: 1
0.91 0.04 0.04
Matches are distributed among these distances:
15 10 0.48
16 11 0.52
ACGTcount: A:0.24, C:0.50, G:0.11, T:0.16
Consensus pattern (16 bp):
CATCCACAACCCTGTG
Found at i:1175378 original size:27 final size:27
Alignment explanation
Indices: 1175324--1175380 Score: 78
Period size: 27 Copynumber: 2.1 Consensus size: 27
1175314 CACAATTTTC
* ** *
1175324 CCTACTCAATCTCCATACCCGTCGTAT
1 CCTACTCAACCTCCATACCCAACATAT
1175351 CCTACTCAACCTCCATACCCAACATAT
1 CCTACTCAACCTCCATACCCAACATAT
1175378 CCT
1 CCT
1175381 GCTACGACCC
Statistics
Matches: 26, Mismatches: 4, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
27 26 1.00
ACGTcount: A:0.26, C:0.44, G:0.04, T:0.26
Consensus pattern (27 bp):
CCTACTCAACCTCCATACCCAACATAT
Found at i:1175742 original size:75 final size:75
Alignment explanation
Indices: 1175653--1175804 Score: 204
Period size: 75 Copynumber: 2.0 Consensus size: 75
1175643 TTGTTGATTA
*
1175653 TAGTTGTTGATAGTAGC-AATGTAAAATATG-TAGAAACATTTGTTGA-TGAT-AGTTATCATGC
1 TAGTTGTTGATAGTA-CTAATGTAAAATATGCT-GAAACATTTGTTGATTG-TGA-ATATCATGC
1175714 AGATTATCTCAGAT
62 AGATTATCTCAGAT
* *
1175728 TAGTTGTTGATAGTACTACTGTGAAATATGCTGAAACATTTGTTGATTGTGAATATCATGCAGAT
1 TAGTTGTTGATAGTACTAATGTAAAATATGCTGAAACATTTGTTGATTGTGAATATCATGCAGAT
*
1175793 TATCTCGGAT
66 TATCTCAGAT
1175803 TA
1 TA
1175805 TCGTTTCATC
Statistics
Matches: 69, Mismatches: 4, Indels: 8
0.85 0.05 0.10
Matches are distributed among these distances:
74 1 0.01
75 64 0.93
76 4 0.06
ACGTcount: A:0.32, C:0.09, G:0.20, T:0.38
Consensus pattern (75 bp):
TAGTTGTTGATAGTACTAATGTAAAATATGCTGAAACATTTGTTGATTGTGAATATCATGCAGAT
TATCTCAGAT
Found at i:1181300 original size:5 final size:5
Alignment explanation
Indices: 1181253--1181281 Score: 58
Period size: 5 Copynumber: 5.8 Consensus size: 5
1181243 TAAAAATTAA
1181253 AATAT AATAT AATAT AATAT AATAT AATA
1 AATAT AATAT AATAT AATAT AATAT AATA
1181282 ATTAACATGC
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 24 1.00
ACGTcount: A:0.62, C:0.00, G:0.00, T:0.38
Consensus pattern (5 bp):
AATAT
Found at i:1183700 original size:3 final size:3
Alignment explanation
Indices: 1183692--1183717 Score: 52
Period size: 3 Copynumber: 8.7 Consensus size: 3
1183682 GATTTCTTTT
1183692 TTA TTA TTA TTA TTA TTA TTA TTA TT
1 TTA TTA TTA TTA TTA TTA TTA TTA TT
1183718 GTCAATTATG
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 23 1.00
ACGTcount: A:0.31, C:0.00, G:0.00, T:0.69
Consensus pattern (3 bp):
TTA
Found at i:1184509 original size:15 final size:15
Alignment explanation
Indices: 1184491--1184537 Score: 67
Period size: 15 Copynumber: 3.0 Consensus size: 15
1184481 TAAAAATAGG
1184491 AAATATTAATAATAA
1 AAATATTAATAATAA
*
1184506 AAATATTAATATTAAAA
1 AAATATTAATA--ATAA
1184523 AAATATTAATAATAA
1 AAATATTAATAATAA
1184538 TTAATAAAAA
Statistics
Matches: 28, Mismatches: 2, Indels: 4
0.82 0.06 0.12
Matches are distributed among these distances:
15 14 0.50
17 14 0.50
ACGTcount: A:0.66, C:0.00, G:0.00, T:0.34
Consensus pattern (15 bp):
AAATATTAATAATAA
Found at i:1184526 original size:17 final size:15
Alignment explanation
Indices: 1184491--1184534 Score: 61
Period size: 17 Copynumber: 2.8 Consensus size: 15
1184481 TAAAAATAGG
*
1184491 AAATATTAATAATAA
1 AAATATTAATAAAAA
1184506 AAATATTAATATTAAAA
1 AAATATTAATA--AAAA
1184523 AAATATTAATAA
1 AAATATTAATAA
1184535 TAATTAATAA
Statistics
Matches: 26, Mismatches: 1, Indels: 4
0.84 0.03 0.13
Matches are distributed among these distances:
15 12 0.46
17 14 0.54
ACGTcount: A:0.66, C:0.00, G:0.00, T:0.34
Consensus pattern (15 bp):
AAATATTAATAAAAA
Found at i:1184568 original size:34 final size:34
Alignment explanation
Indices: 1184481--1184587 Score: 108
Period size: 34 Copynumber: 3.0 Consensus size: 34
1184471 AGATACCATA
* * *
1184481 TAAAAATAGGAAATATTAA-TAATAAAAATATTAATAT
1 TAAAAAAAGAAAATAATAATTAATAAAAA-A-T-A-AT
* *
1184518 TAAAAAAATATTAATAATAATTAATAAAAAATAAT
1 TAAAAAAAGA-AAATAATAATTAATAAAAAATAAT
*
1184553 TAAAAAAAGAAAATAATAATTAATAAAAAAAAAT
1 TAAAAAAAGAAAATAATAATTAATAAAAAATAAT
1184587 T
1 T
1184588 GACTAAATTC
Statistics
Matches: 60, Mismatches: 8, Indels: 7
0.80 0.11 0.09
Matches are distributed among these distances:
34 23 0.38
35 11 0.18
36 1 0.02
37 8 0.13
38 8 0.13
39 9 0.15
ACGTcount: A:0.68, C:0.00, G:0.03, T:0.29
Consensus pattern (34 bp):
TAAAAAAAGAAAATAATAATTAATAAAAAATAAT
Found at i:1184801 original size:27 final size:25
Alignment explanation
Indices: 1184742--1184808 Score: 84
Period size: 25 Copynumber: 2.7 Consensus size: 25
1184732 ATTTATTATA
* *
1184742 TATTCTATTATTATATTCTATATTC
1 TATTATATTAATATATTCTATATTC
1184767 TATTATATTAATATATTCTATTAATTC
1 TATTATATTAATATATTCTA-T-ATTC
1184794 TATTATA-T-ATATATT
1 TATTATATTAATATATT
1184809 AATATATATA
Statistics
Matches: 38, Mismatches: 2, Indels: 4
0.86 0.05 0.09
Matches are distributed among these distances:
25 25 0.66
26 2 0.05
27 11 0.29
ACGTcount: A:0.34, C:0.07, G:0.00, T:0.58
Consensus pattern (25 bp):
TATTATATTAATATATTCTATATTC
Found at i:1185810 original size:2 final size:2
Alignment explanation
Indices: 1185803--1185827 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
1185793 CAACTTTTTC
1185803 AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT A
1185828 ATTTAACAGA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:1188784 original size:21 final size:21
Alignment explanation
Indices: 1188760--1188799 Score: 53
Period size: 21 Copynumber: 1.9 Consensus size: 21
1188750 CCAAATAACG
*
1188760 AAAAATTAAAGAAGAAAAATC
1 AAAAACTAAAGAAGAAAAATC
* *
1188781 AAAAACTAAATAATAAAAA
1 AAAAACTAAAGAAGAAAAA
1188800 AATAAAAAAA
Statistics
Matches: 16, Mismatches: 3, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
21 16 1.00
ACGTcount: A:0.75, C:0.05, G:0.05, T:0.15
Consensus pattern (21 bp):
AAAAACTAAAGAAGAAAAATC
Found at i:1189340 original size:20 final size:20
Alignment explanation
Indices: 1189303--1189339 Score: 60
Period size: 18 Copynumber: 1.9 Consensus size: 20
1189293 ATATATTTAA
1189303 TTTAAAATTAAAATTATATT
1 TTTAAAATTAAAATTATATT
1189323 TTTAAAA-T-AAATTATAT
1 TTTAAAATTAAAATTATAT
1189340 AAAATATTAA
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
18 9 0.53
19 1 0.06
20 7 0.41
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (20 bp):
TTTAAAATTAAAATTATATT
Found at i:1189352 original size:17 final size:17
Alignment explanation
Indices: 1189330--1189387 Score: 61
Period size: 17 Copynumber: 3.5 Consensus size: 17
1189320 ATTTTTAAAA
*
1189330 TAAATTATATAAAATAT
1 TAAATTATATTAAATAT
1189347 TAAATTA-ATTAAATA-
1 TAAATTATATTAAATAT
1189362 TAAATATAATATTAAA-AT
1 TAAAT-T-ATATTAAATAT
1189380 T-AATTATA
1 TAAATTATA
1189388 ATATAATATA
Statistics
Matches: 36, Mismatches: 1, Indels: 10
0.77 0.02 0.21
Matches are distributed among these distances:
15 8 0.22
16 9 0.25
17 12 0.33
18 7 0.19
ACGTcount: A:0.59, C:0.00, G:0.00, T:0.41
Consensus pattern (17 bp):
TAAATTATATTAAATAT
Found at i:1189366 original size:22 final size:20
Alignment explanation
Indices: 1189327--1189376 Score: 55
Period size: 21 Copynumber: 2.4 Consensus size: 20
1189317 TATATTTTTA
* *
1189327 AAATAAATTATATAAAATATT
1 AAATTAATTAAATAAAATA-T
1189348 AAATTAATTAAATATAAATAT
1 AAATTAATTAAATA-AAATAT
1189369 AATATTAA
1 AA-ATTAA
1189377 AATTAATTAT
Statistics
Matches: 25, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
21 15 0.60
22 10 0.40
ACGTcount: A:0.62, C:0.00, G:0.00, T:0.38
Consensus pattern (20 bp):
AAATTAATTAAATAAAATAT
Found at i:1189377 original size:18 final size:18
Alignment explanation
Indices: 1189300--1189391 Score: 56
Period size: 18 Copynumber: 5.3 Consensus size: 18
1189290 TTAATATATT
1189300 TAAT-TTAAAATTAAAATTA
1 TAATATTAAAATT-AAA-TA
* *
1189319 TATTTTTAAAA-TAAAT-
1 TAATATTAAAATTAAATA
*
1189335 T-ATATAAAATATTAAAT-
1 TAATATTAAA-ATTAAATA
1189352 T-A-ATT-AAATATAAATA
1 TAATATTAAAAT-TAAATA
*
1189368 TAATATTAAAATTAATTA
1 TAATATTAAAATTAAATA
1189386 TAATAT
1 TAATAT
1189392 AATATAATAT
Statistics
Matches: 59, Mismatches: 6, Indels: 17
0.72 0.07 0.21
Matches are distributed among these distances:
14 2 0.03
15 12 0.20
16 5 0.08
17 9 0.15
18 17 0.29
19 8 0.14
20 6 0.10
ACGTcount: A:0.57, C:0.00, G:0.00, T:0.43
Consensus pattern (18 bp):
TAATATTAAAATTAAATA
Found at i:1189383 original size:12 final size:13
Alignment explanation
Indices: 1189309--1189413 Score: 55
Period size: 13 Copynumber: 8.2 Consensus size: 13
1189299 TTAATTTAAA
*
1189309 ATTAAAATTATATT
1 ATTAAAA-TATAAT
*
1189323 TTTAAAATA-AATT
1 ATTAAAATATAA-T
1189336 ATATAAAATATTAA-
1 AT-TAAAATA-TAAT
*
1189350 ATT-AATTA-AAT
1 ATTAAAATATAAT
1189361 A-T-AAATATAAT
1 ATTAAAATATAAT
1189372 ATTAAAAT-TAATT
1 ATTAAAATATAA-T
*
1189385 ATAATATAATATAAT
1 AT--TAAAATATAAT
1189400 ATTAAAAT-TAAT
1 ATTAAAATATAAT
1189412 AT
1 AT
1189414 ATTTAAATTT
Statistics
Matches: 72, Mismatches: 7, Indels: 26
0.69 0.07 0.25
Matches are distributed among these distances:
10 7 0.10
11 5 0.07
12 15 0.21
13 17 0.24
14 15 0.21
15 8 0.11
16 5 0.07
ACGTcount: A:0.57, C:0.00, G:0.00, T:0.43
Consensus pattern (13 bp):
ATTAAAATATAAT
Found at i:1189384 original size:28 final size:28
Alignment explanation
Indices: 1189342--1189411 Score: 117
Period size: 28 Copynumber: 2.5 Consensus size: 28
1189332 AATTATATAA
1189342 AATATT-AAATTAATTA-AATATAAATAT
1 AATATTAAAATTAATTATAATAT-AATAT
1189369 AATATTAAAATTAATTATAATATAATAT
1 AATATTAAAATTAATTATAATATAATAT
1189397 AATATTAAAATTAAT
1 AATATTAAAATTAAT
1189412 ATATTTAAAT
Statistics
Matches: 41, Mismatches: 0, Indels: 3
0.93 0.00 0.07
Matches are distributed among these distances:
27 6 0.15
28 30 0.73
29 5 0.12
ACGTcount: A:0.59, C:0.00, G:0.00, T:0.41
Consensus pattern (28 bp):
AATATTAAAATTAATTATAATATAATAT
Found at i:1189410 original size:34 final size:31
Alignment explanation
Indices: 1189289--1189410 Score: 97
Period size: 34 Copynumber: 3.8 Consensus size: 31
1189279 TAGATGAATT
* *
1189289 TTTAATATATTTAATTTAAAATTAAAATTATA
1 TTTAATATATATAATATAAAATTAAAATTA-A
* * * *
1189321 TTTTTAAAATAAATTATATAAAATATTAAATTAA
1 --TTTAATATATATAATATAAAAT-TAAAATTAA
*
1189355 -TTAA-ATATA-AATATAATATTAAAATTAA
1 TTTAATATATATAATATAAAATTAAAATTAA
1189383 TTATAATATAATATAATATTAAAATTAA
1 TT-TAATAT-ATATAATA-TAAAATTAA
1189411 TATATTTAAA
Statistics
Matches: 70, Mismatches: 11, Indels: 14
0.74 0.12 0.15
Matches are distributed among these distances:
28 8 0.11
29 9 0.13
30 7 0.10
31 6 0.09
32 3 0.04
33 4 0.06
34 26 0.37
35 7 0.10
ACGTcount: A:0.56, C:0.00, G:0.00, T:0.44
Consensus pattern (31 bp):
TTTAATATATATAATATAAAATTAAAATTAA
Found at i:1192041 original size:30 final size:32
Alignment explanation
Indices: 1191976--1192049 Score: 87
Period size: 33 Copynumber: 2.2 Consensus size: 32
1191966 TAAAATAAAA
*
1191976 ATATTTTATTAAATTTAATAATATATATTTAT
1 ATATTTTATTAAATTTAATAATATATATATAT
*
1192008 ATATTTT-TTAATATATTAATAATTTATATTATAT
1 ATATTTTATTAA-AT-TTAATAATATATA-TATAT
*
1192042 AAATTTTA
1 ATATTTTA
1192050 AGATATTTTA
Statistics
Matches: 35, Mismatches: 3, Indels: 5
0.81 0.07 0.12
Matches are distributed among these distances:
31 4 0.11
32 9 0.26
33 12 0.34
34 10 0.29
ACGTcount: A:0.43, C:0.00, G:0.00, T:0.57
Consensus pattern (32 bp):
ATATTTTATTAAATTTAATAATATATATATAT
Found at i:1192042 original size:42 final size:43
Alignment explanation
Indices: 1191987--1192089 Score: 104
Period size: 44 Copynumber: 2.4 Consensus size: 43
1191977 TATTTTATTA
* *
1191987 AATTTA-ATAATATATATTT-ATATATTTT-TTAATATATTAAT
1 AATTTATATTATATATATTTAAGATATTTTATT-ATATATTAAT
* * *
1192028 AATTTATATTATATAAATTTTAAGATATTTTATTATATTTTTAT
1 AATTTATATTATATATA-TTTAAGATATTTTATTATATATTAAT
* *
1192072 TATTAATATTATATATAT
1 AATTTATATTATATATAT
1192090 ATATTTTCAT
Statistics
Matches: 50, Mismatches: 8, Indels: 6
0.78 0.12 0.09
Matches are distributed among these distances:
41 6 0.12
42 8 0.16
43 4 0.08
44 30 0.60
45 2 0.04
ACGTcount: A:0.42, C:0.00, G:0.01, T:0.57
Consensus pattern (43 bp):
AATTTATATTATATATATTTAAGATATTTTATTATATATTAAT
Found at i:1192050 original size:32 final size:33
Alignment explanation
Indices: 1191990--1192056 Score: 91
Period size: 32 Copynumber: 2.1 Consensus size: 33
1191980 TTTATTAAAT
** *
1191990 TTAATAATATATATTTATATATTTTTTAATATA
1 TTAATAATATATATTTATATAAATTTTAAGATA
*
1192023 TTAATAATTTATA-TTATATAAATTTTAAGATA
1 TTAATAATATATATTTATATAAATTTTAAGATA
1192055 TT
1 TT
1192057 TTATTATATT
Statistics
Matches: 30, Mismatches: 4, Indels: 1
0.86 0.11 0.03
Matches are distributed among these distances:
32 18 0.60
33 12 0.40
ACGTcount: A:0.43, C:0.00, G:0.01, T:0.55
Consensus pattern (33 bp):
TTAATAATATATATTTATATAAATTTTAAGATA
Found at i:1193220 original size:2 final size:2
Alignment explanation
Indices: 1193213--1193238 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
1193203 TCCTAGTTGT
1193213 TC TC TC TC TC TC TC TC TC TC TC TC TC
1 TC TC TC TC TC TC TC TC TC TC TC TC TC
1193239 GTTGTTTGTT
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 24 1.00
ACGTcount: A:0.00, C:0.50, G:0.00, T:0.50
Consensus pattern (2 bp):
TC
Found at i:1203615 original size:3 final size:3
Alignment explanation
Indices: 1203607--1203635 Score: 58
Period size: 3 Copynumber: 9.7 Consensus size: 3
1203597 ATTATGAAAA
1203607 AAT AAT AAT AAT AAT AAT AAT AAT AAT AA
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AA
1203636 AGAACAGAAA
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 26 1.00
ACGTcount: A:0.69, C:0.00, G:0.00, T:0.31
Consensus pattern (3 bp):
AAT
Found at i:1204125 original size:11 final size:11
Alignment explanation
Indices: 1204109--1204143 Score: 52
Period size: 11 Copynumber: 3.2 Consensus size: 11
1204099 ATAATTTTAA
*
1204109 AATATAAAAAT
1 AATATAAATAT
1204120 AATATAAATAT
1 AATATAAATAT
*
1204131 AAGATAAATAT
1 AATATAAATAT
1204142 AA
1 AA
1204144 AATATAATTT
Statistics
Matches: 22, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
11 22 1.00
ACGTcount: A:0.69, C:0.00, G:0.03, T:0.29
Consensus pattern (11 bp):
AATATAAATAT
Found at i:1204130 original size:17 final size:19
Alignment explanation
Indices: 1204106--1204150 Score: 60
Period size: 17 Copynumber: 2.5 Consensus size: 19
1204096 TATATAATTT
1204106 TAAAATATAAAAAT-AATA
1 TAAAATATAAAAATAAATA
*
1204124 T-AAATAT-AAGATAAATA
1 TAAAATATAAAAATAAATA
1204141 TAAAATATAA
1 TAAAATATAA
1204151 TTTTATTAAA
Statistics
Matches: 23, Mismatches: 1, Indels: 5
0.79 0.03 0.17
Matches are distributed among these distances:
16 4 0.17
17 11 0.48
18 7 0.30
19 1 0.04
ACGTcount: A:0.69, C:0.00, G:0.02, T:0.29
Consensus pattern (19 bp):
TAAAATATAAAAATAAATA
Found at i:1204215 original size:15 final size:16
Alignment explanation
Indices: 1204190--1204220 Score: 55
Period size: 15 Copynumber: 2.0 Consensus size: 16
1204180 TGACATGAAA
1204190 GTCATATAAATTTGAC
1 GTCATATAAATTTGAC
1204206 GTCA-ATAAATTTGAC
1 GTCATATAAATTTGAC
1204221 AATGATTAAT
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:0.39, C:0.13, G:0.13, T:0.35
Consensus pattern (16 bp):
GTCATATAAATTTGAC
Found at i:1204486 original size:17 final size:16
Alignment explanation
Indices: 1204436--1204486 Score: 50
Period size: 17 Copynumber: 3.1 Consensus size: 16
1204426 ATTATAATAT
*
1204436 TTAAATAATAAATAAAT
1 TTAAA-AATAAATAAAA
*
1204453 TTAAAATTTAAA-AAAA
1 TTAAAA-ATAAATAAAA
1204469 TTAAAAATAAATATAAA
1 TTAAAAATAAATA-AAA
1204486 T
1 T
1204487 AATTATTATT
Statistics
Matches: 28, Mismatches: 3, Indels: 6
0.76 0.08 0.16
Matches are distributed among these distances:
15 4 0.14
16 11 0.39
17 13 0.46
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (16 bp):
TTAAAAATAAATAAAA
Found at i:1205762 original size:13 final size:12
Alignment explanation
Indices: 1205723--1205761 Score: 71
Period size: 12 Copynumber: 3.3 Consensus size: 12
1205713 TTCAACGTTG
1205723 AAAA-GGAAAAA
1 AAAATGGAAAAA
1205734 AAAATGGAAAAA
1 AAAATGGAAAAA
1205746 AAAATGGAAAAA
1 AAAATGGAAAAA
1205758 AAAA
1 AAAA
1205762 ACAAGTAAAA
Statistics
Matches: 27, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
11 4 0.15
12 23 0.85
ACGTcount: A:0.79, C:0.00, G:0.15, T:0.05
Consensus pattern (12 bp):
AAAATGGAAAAA
Found at i:1206071 original size:20 final size:20
Alignment explanation
Indices: 1206020--1206071 Score: 52
Period size: 19 Copynumber: 2.6 Consensus size: 20
1206010 ATTTTGTAAA
* * *
1206020 TTAATATTTAATAAGTATAT
1 TTAATTTTTTATAAATATAT
**
1206040 TT-ATTTGATATAAATATAT
1 TTAATTTTTTATAAATATAT
1206059 TTAATTTTTTATA
1 TTAATTTTTTATA
1206072 TATTTTAAAA
Statistics
Matches: 24, Mismatches: 7, Indels: 2
0.73 0.21 0.06
Matches are distributed among these distances:
19 14 0.58
20 10 0.42
ACGTcount: A:0.40, C:0.00, G:0.04, T:0.56
Consensus pattern (20 bp):
TTAATTTTTTATAAATATAT
Found at i:1207008 original size:2 final size:2
Alignment explanation
Indices: 1207001--1207025 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
1206991 TTGCATCTGA
1207001 AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT A
1207026 CACACACATA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Done.