Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NW_019168470.1 Durio zibethinus cultivar Musang King isolate D1 unplaced genomic scaffold, Duzib1.0 scaffold_7, whole genome shotgun sequence
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: 26282861
ACGTcount: A:0.35, C:0.15, G:0.15, T:0.35
Warning! 74000 characters in sequence are not A, C, G, or T
File 17 of 133
Found at i:4230086 original size:87 final size:86
Alignment explanation
Indices: 4229940--4230113 Score: 330
Period size: 87 Copynumber: 2.0 Consensus size: 86
4229930 TTTCATTAAT
*
4229940 TCCATTTTTTATTACCTTTTATTTTAAATAGTTTATAAATTAAATGAGTATTATTATTAATTCAA
1 TCCATTTTTTAATACCTTTTATTTTAAATAGTTTATAAATTAAATGAGTATTATTATTAATTCAA
4230005 ATATTTTTTATGTAATTATTTC
66 ATA-TTTTTATGTAATTATTTC
4230027 TCCATTTTTTAATACCTTTTATTTTAAATAGTTTATAAATTAAATGAGTATTATTATTAATTCAA
1 TCCATTTTTTAATACCTTTTATTTTAAATAGTTTATAAATTAAATGAGTATTATTATTAATTCAA
4230092 ATATTTTTATGTAATTATTTC
66 ATATTTTTATGTAATTATTTC
4230113 T
1 T
4230114 AATCTATTGT
Statistics
Matches: 86, Mismatches: 1, Indels: 1
0.98 0.01 0.01
Matches are distributed among these distances:
86 19 0.22
87 67 0.78
ACGTcount: A:0.34, C:0.07, G:0.05, T:0.55
Consensus pattern (86 bp):
TCCATTTTTTAATACCTTTTATTTTAAATAGTTTATAAATTAAATGAGTATTATTATTAATTCAA
ATATTTTTATGTAATTATTTC
Found at i:4231212 original size:17 final size:19
Alignment explanation
Indices: 4231169--4231216 Score: 55
Period size: 17 Copynumber: 2.6 Consensus size: 19
4231159 TATGTGAATT
*
4231169 AATTTATATATAATTTAAA
1 AATTTATATATAATTAAAA
* *
4231188 TATGTATATA-AA-TAAAA
1 AATTTATATATAATTAAAA
4231205 AATTTATATATA
1 AATTTATATATA
4231217 TGTAAATTCA
Statistics
Matches: 23, Mismatches: 5, Indels: 3
0.74 0.16 0.10
Matches are distributed among these distances:
17 12 0.52
18 3 0.13
19 8 0.35
ACGTcount: A:0.54, C:0.00, G:0.02, T:0.44
Consensus pattern (19 bp):
AATTTATATATAATTAAAA
Found at i:4234737 original size:37 final size:37
Alignment explanation
Indices: 4234682--4234758 Score: 127
Period size: 37 Copynumber: 2.1 Consensus size: 37
4234672 TATCACTTAC
* *
4234682 AATTCATTTTACGACAATGCTATAATTATTCAATTAT
1 AATTAATTTTACGACAATGCTATAATTATCCAATTAT
*
4234719 AATTAATTTTATGACAATGCTATAATTATCCAATTAT
1 AATTAATTTTACGACAATGCTATAATTATCCAATTAT
4234756 AAT
1 AAT
4234759 AAAAAATTAT
Statistics
Matches: 37, Mismatches: 3, Indels: 0
0.93 0.08 0.00
Matches are distributed among these distances:
37 37 1.00
ACGTcount: A:0.40, C:0.12, G:0.05, T:0.43
Consensus pattern (37 bp):
AATTAATTTTACGACAATGCTATAATTATCCAATTAT
Found at i:4247730 original size:18 final size:18
Alignment explanation
Indices: 4247695--4247811 Score: 82
Period size: 18 Copynumber: 6.5 Consensus size: 18
4247685 ACTTTTGAGC
*
4247695 ATAATATTA-CTT-ATAA
1 ATAATATTATATTAATAA
4247711 ATAATATTATATTAATAA
1 ATAATATTATATTAATAA
** * *
4247729 ATAAATAACATACT-ATTA
1 AT-AATATTATATTAATAA
*
4247747 AT-ATAATATATTAATAAA
1 ATAATATTATATTAAT-AA
*
4247765 ATATTATAATT-TATTCATAA
1 ATA--AT-ATTATATTAATAA
*
4247785 ATAATATTATATTAATAC
1 ATAATATTATATTAATAA
4247803 ATAATATTA
1 ATAATATTA
4247812 CAATATATTA
Statistics
Matches: 79, Mismatches: 12, Indels: 18
0.72 0.11 0.17
Matches are distributed among these distances:
16 17 0.22
17 7 0.09
18 32 0.41
19 8 0.10
20 5 0.06
21 8 0.10
22 2 0.03
ACGTcount: A:0.53, C:0.04, G:0.00, T:0.43
Consensus pattern (18 bp):
ATAATATTATATTAATAA
Found at i:4247745 original size:27 final size:26
Alignment explanation
Indices: 4247707--4247764 Score: 64
Period size: 27 Copynumber: 2.2 Consensus size: 26
4247697 AATATTACTT
4247707 ATAAATAATATT-ATATTAATAAATAA
1 ATAAATAATATTAATA-TAATAAATAA
* * *
4247733 ATAACATACTATTAATATAATATATTA
1 ATAA-ATAATATTAATATAATAAATAA
4247760 ATAAA
1 ATAAA
4247765 ATATTATAAT
Statistics
Matches: 27, Mismatches: 3, Indels: 4
0.79 0.09 0.12
Matches are distributed among these distances:
26 5 0.19
27 19 0.70
28 3 0.11
ACGTcount: A:0.59, C:0.03, G:0.00, T:0.38
Consensus pattern (26 bp):
ATAAATAATATTAATATAATAAATAA
Found at i:4247794 original size:23 final size:21
Alignment explanation
Indices: 4247748--4247826 Score: 83
Period size: 21 Copynumber: 3.8 Consensus size: 21
4247738 ATACTATTAA
4247748 TATAATATATTAATAAAATAT
1 TATAATATATTAATAAAATAT
* *
4247769 TATAATTTATTCAT-AAATA-
1 TATAATATATTAATAAAATAT
*
4247788 -ATATTATATTAATACATAATAT
1 TATAATATATTAATA-A-AATAT
*
4247810 TACAATATATTAATAAA
1 TATAATATATTAATAAA
4247827 GAATATAAAG
Statistics
Matches: 46, Mismatches: 7, Indels: 10
0.73 0.11 0.16
Matches are distributed among these distances:
18 10 0.22
20 6 0.13
21 17 0.37
22 1 0.02
23 12 0.26
ACGTcount: A:0.53, C:0.04, G:0.00, T:0.43
Consensus pattern (21 bp):
TATAATATATTAATAAAATAT
Found at i:4247809 original size:41 final size:39
Alignment explanation
Indices: 4247753--4247832 Score: 106
Period size: 41 Copynumber: 2.0 Consensus size: 39
4247743 ATTAATATAA
* * * *
4247753 TATATTAATAAAATATTATAATTTATTCATAAATAATAT
1 TATATTAATAAAATATTACAATATATTAATAAAGAATAT
4247792 TATATTAATACATAATATTACAATATATTAATAAAGAATAT
1 TATATTAATA-A-AATATTACAATATATTAATAAAGAATAT
4247833 AAAGAATAAT
Statistics
Matches: 35, Mismatches: 4, Indels: 2
0.85 0.10 0.05
Matches are distributed among these distances:
39 10 0.29
40 1 0.03
41 24 0.69
ACGTcount: A:0.53, C:0.04, G:0.01, T:0.42
Consensus pattern (39 bp):
TATATTAATAAAATATTACAATATATTAATAAAGAATAT
Found at i:4247885 original size:19 final size:18
Alignment explanation
Indices: 4247861--4247916 Score: 69
Period size: 19 Copynumber: 3.1 Consensus size: 18
4247851 TTATTTTAAG
4247861 TATTTTTATATTAACATAA
1 TATTTTTATATTAA-ATAA
* *
4247880 TATTTTAATATTAAATAT
1 TATTTTTATATTAAATAA
4247898 TATTTTTAATATT-AATAA
1 TATTTTT-ATATTAAATAA
4247916 T
1 T
4247917 TTAAATAATA
Statistics
Matches: 32, Mismatches: 4, Indels: 3
0.82 0.10 0.08
Matches are distributed among these distances:
18 14 0.44
19 18 0.56
ACGTcount: A:0.43, C:0.02, G:0.00, T:0.55
Consensus pattern (18 bp):
TATTTTTATATTAAATAA
Found at i:4247907 original size:27 final size:27
Alignment explanation
Indices: 4247877--4247974 Score: 85
Period size: 32 Copynumber: 3.5 Consensus size: 27
4247867 TATATTAACA
4247877 TAATATTTTAATATTAAATATTATTTT
1 TAATATTTTAATATTAAATATTATTTT
*
4247904 TAATATTAATAAT-TTAAATAATAAATTATTTT
1 TAATATT-TTAATATT--A-AAT--ATTATTTT
* *
4247936 AATATATTTTAATAAT-AA-ATTATTTT
1 TA-ATATTTTAATATTAAATATTATTTT
4247962 TAATATTTTAATA
1 TAATATTTTAATA
4247975 GTTATATTAA
Statistics
Matches: 58, Mismatches: 5, Indels: 18
0.72 0.06 0.22
Matches are distributed among these distances:
25 11 0.19
26 9 0.16
27 9 0.16
28 4 0.07
29 3 0.05
30 3 0.05
32 13 0.22
33 6 0.10
ACGTcount: A:0.46, C:0.00, G:0.00, T:0.54
Consensus pattern (27 bp):
TAATATTTTAATATTAAATATTATTTT
Found at i:4247948 original size:23 final size:24
Alignment explanation
Indices: 4247921--4247992 Score: 69
Period size: 26 Copynumber: 3.0 Consensus size: 24
4247911 AATAATTTAA
4247921 ATAATAAATTATTTTAATATATTTT
1 ATAATAAATTATTTTAATATA-TTT
*
4247946 AATAATAAATTATTTTTA-ATATTT
1 -ATAATAAATTATTTTAATATATTT
* *
4247970 -TAAT-AGTTATATTAATATTATTT
1 ATAATAAATTATTTTAATA-TATTT
4247993 GAAAAAAATA
Statistics
Matches: 40, Mismatches: 4, Indels: 7
0.78 0.08 0.14
Matches are distributed among these distances:
21 8 0.20
22 5 0.12
23 5 0.12
24 3 0.08
25 3 0.08
26 16 0.40
ACGTcount: A:0.43, C:0.00, G:0.01, T:0.56
Consensus pattern (24 bp):
ATAATAAATTATTTTAATATATTT
Found at i:4247983 original size:26 final size:26
Alignment explanation
Indices: 4247909--4247974 Score: 100
Period size: 26 Copynumber: 2.6 Consensus size: 26
4247899 ATTTTTAATA
*
4247909 TTAATA-ATTTAAATAATAAATTATT
1 TTAATATATTTTAATAATAAATTATT
4247934 TTAATATATTTTAATAATAAATTATT
1 TTAATATATTTTAATAATAAATTATT
*
4247960 TTTA-ATATTTTAATA
1 TTAATATATTTTAATA
4247975 GTTATATTAA
Statistics
Matches: 38, Mismatches: 2, Indels: 2
0.90 0.05 0.05
Matches are distributed among these distances:
25 17 0.45
26 21 0.55
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (26 bp):
TTAATATATTTTAATAATAAATTATT
Found at i:4248079 original size:14 final size:14
Alignment explanation
Indices: 4248060--4248096 Score: 58
Period size: 14 Copynumber: 2.6 Consensus size: 14
4248050 AAAGTATAAA
4248060 TATTTTTTGAAAA-T
1 TATTTTTT-AAAATT
4248074 TATTTTTTAAAATT
1 TATTTTTTAAAATT
4248088 TATTTTTTA
1 TATTTTTTA
4248097 CGAAACAAAT
Statistics
Matches: 22, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
13 4 0.18
14 18 0.82
ACGTcount: A:0.32, C:0.00, G:0.03, T:0.65
Consensus pattern (14 bp):
TATTTTTTAAAATT
Found at i:4251276 original size:19 final size:19
Alignment explanation
Indices: 4251252--4251290 Score: 69
Period size: 19 Copynumber: 2.1 Consensus size: 19
4251242 CTTAAAGAGT
*
4251252 TTAATTTATATTTTCTGCA
1 TTAATTTATATTTCCTGCA
4251271 TTAATTTATATTTCCTGCA
1 TTAATTTATATTTCCTGCA
4251290 T
1 T
4251291 ATACACTCAC
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
19 19 1.00
ACGTcount: A:0.26, C:0.13, G:0.05, T:0.56
Consensus pattern (19 bp):
TTAATTTATATTTCCTGCA
Found at i:4277103 original size:19 final size:20
Alignment explanation
Indices: 4277079--4277116 Score: 60
Period size: 20 Copynumber: 1.9 Consensus size: 20
4277069 CCAACTTTCT
*
4277079 TCTTTT-TTTTTTCTTTTTA
1 TCTTTTCTTTTTGCTTTTTA
4277098 TCTTTTCTTTTTGCTTTTT
1 TCTTTTCTTTTTGCTTTTT
4277117 CTAAATTTTT
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
19 6 0.35
20 11 0.65
ACGTcount: A:0.03, C:0.13, G:0.03, T:0.82
Consensus pattern (20 bp):
TCTTTTCTTTTTGCTTTTTA
Found at i:4277886 original size:15 final size:16
Alignment explanation
Indices: 4277844--4277888 Score: 65
Period size: 16 Copynumber: 2.8 Consensus size: 16
4277834 ATGAACTTTC
4277844 TTTTTCATTTTTATGTT
1 TTTTTCATTTTT-TGTT
*
4277861 TTTAT-ATTTTTTGTT
1 TTTTTCATTTTTTGTT
4277876 TTTTTCATTTTTT
1 TTTTTCATTTTTT
4277889 CCCTTAGCAT
Statistics
Matches: 25, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
15 8 0.32
16 13 0.52
17 4 0.16
ACGTcount: A:0.11, C:0.04, G:0.04, T:0.80
Consensus pattern (16 bp):
TTTTTCATTTTTTGTT
Found at i:4278121 original size:17 final size:17
Alignment explanation
Indices: 4278099--4278134 Score: 63
Period size: 17 Copynumber: 2.1 Consensus size: 17
4278089 AAGGATTGAT
4278099 TTTTTTTTAAATCGAGG
1 TTTTTTTTAAATCGAGG
*
4278116 TTTTTTTTAAATCGTGG
1 TTTTTTTTAAATCGAGG
4278133 TT
1 TT
4278135 GAGTTGAGAC
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
17 18 1.00
ACGTcount: A:0.19, C:0.06, G:0.17, T:0.58
Consensus pattern (17 bp):
TTTTTTTTAAATCGAGG
Found at i:4278379 original size:13 final size:13
Alignment explanation
Indices: 4278361--4278411 Score: 50
Period size: 13 Copynumber: 3.7 Consensus size: 13
4278351 TTTATAAGCT
4278361 TTTTTTTTTAAAA
1 TTTTTTTTTAAAA
4278374 TTTTTTTTTCAATAA
1 TTTTTTTTT-AA-AA
*
4278389 TTTGGTTTTT-AAA
1 TTT-TTTTTTAAAA
4278402 TTTTTATTTT
1 TTTTT-TTTT
4278412 TTAATTAGAT
Statistics
Matches: 32, Mismatches: 2, Indels: 8
0.76 0.05 0.19
Matches are distributed among these distances:
12 1 0.03
13 18 0.56
14 3 0.09
15 5 0.16
16 5 0.16
ACGTcount: A:0.24, C:0.02, G:0.04, T:0.71
Consensus pattern (13 bp):
TTTTTTTTTAAAA
Found at i:4278379 original size:14 final size:14
Alignment explanation
Indices: 4278360--4278415 Score: 58
Period size: 15 Copynumber: 3.9 Consensus size: 14
4278350 CTTTATAAGC
4278360 TTTTTTTTTTAAAA
1 TTTTTTTTTTAAAA
*
4278374 TTTTTTTTTCAATAA
1 TTTTTTTTTTAA-AA
** *
4278389 TTTGGTTTTTAAAT
1 TTTTTTTTTTAAAA
4278403 TTTTATTTTTTAA
1 TTTT-TTTTTTAA
4278416 TTAGATAAAT
Statistics
Matches: 33, Mismatches: 7, Indels: 3
0.77 0.16 0.07
Matches are distributed among these distances:
14 15 0.45
15 18 0.55
ACGTcount: A:0.25, C:0.02, G:0.04, T:0.70
Consensus pattern (14 bp):
TTTTTTTTTTAAAA
Found at i:4279270 original size:13 final size:13
Alignment explanation
Indices: 4279247--4279327 Score: 53
Period size: 13 Copynumber: 6.3 Consensus size: 13
4279237 ATTTATATGA
4279247 ATAATATAAAATTT
1 ATAA-ATAAAATTT
4279261 ATAAATAAAA--T
1 ATAAATAAAATTT
* *
4279272 AT--ATAATATTA
1 ATAAATAAAATTT
* *
4279283 AAAAATAAAATTGA
1 ATAAATAAAATT-T
*
4279297 ATAATATATAATTT
1 ATAA-ATAAAATTT
*
4279311 ATAAATAAAATAT
1 ATAAATAAAATTT
4279324 ATAA
1 ATAA
4279328 TATTAAAAAA
Statistics
Matches: 52, Mismatches: 9, Indels: 13
0.70 0.12 0.18
Matches are distributed among these distances:
9 5 0.10
11 4 0.08
13 24 0.46
14 12 0.23
15 7 0.13
ACGTcount: A:0.63, C:0.00, G:0.01, T:0.36
Consensus pattern (13 bp):
ATAAATAAAATTT
Found at i:4279288 original size:22 final size:22
Alignment explanation
Indices: 4279263--4279343 Score: 92
Period size: 22 Copynumber: 3.4 Consensus size: 22
4279253 TAAAATTTAT
4279263 AAATAAAATATATAATATTAAA
1 AAATAAAATATATAATATTAAA
4279285 AAATAAAAT-TGAATAATATATAATTTA
1 AAATAAAATAT--ATAATAT-TAA---A
4279312 TAAATAAAATATATAATATTAAA
1 -AAATAAAATATATAATATTAAA
4279335 AAATAAAAT
1 AAATAAAAT
4279344 TAACTCATAC
Statistics
Matches: 51, Mismatches: 0, Indels: 16
0.76 0.00 0.24
Matches are distributed among these distances:
21 1 0.02
22 18 0.35
23 8 0.16
24 3 0.06
26 3 0.06
27 8 0.16
28 9 0.18
29 1 0.02
ACGTcount: A:0.65, C:0.00, G:0.01, T:0.33
Consensus pattern (22 bp):
AAATAAAATATATAATATTAAA
Found at i:4279303 original size:50 final size:50
Alignment explanation
Indices: 4279244--4279344 Score: 193
Period size: 50 Copynumber: 2.0 Consensus size: 50
4279234 TACATTTATA
4279244 TGAATAATATAAAATTTATAAATAAAATATATAATATTAAAAAATAAAAT
1 TGAATAATATAAAATTTATAAATAAAATATATAATATTAAAAAATAAAAT
*
4279294 TGAATAATATATAATTTATAAATAAAATATATAATATTAAAAAATAAAAT
1 TGAATAATATAAAATTTATAAATAAAATATATAATATTAAAAAATAAAAT
4279344 T
1 T
4279345 AACTCATACA
Statistics
Matches: 50, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
50 50 1.00
ACGTcount: A:0.62, C:0.00, G:0.02, T:0.36
Consensus pattern (50 bp):
TGAATAATATAAAATTTATAAATAAAATATATAATATTAAAAAATAAAAT
Found at i:4279383 original size:50 final size:50
Alignment explanation
Indices: 4279263--4279380 Score: 150
Period size: 50 Copynumber: 2.3 Consensus size: 50
4279253 TAAAATTTAT
* * * *
4279263 AAATAAAATATATAATATTAAAAAATAAAATTGAATAATATATAATTTAT
1 AAATAAAATATATAATATTAAAAAATAAAATTGAATAACAAATAAATTAA
4279313 AAATAAAATATATAATATTAAAAAATAAAATT-AACTCATACAAATAAATTAA
1 AAATAAAATATATAATATTAAAAAATAAAATTGAA-T-A-ACAAATAAATTAA
4279365 AAATAAAA-ATCATAAT
1 AAATAAAATAT-ATAAT
4279381 TAATATATTT
Statistics
Matches: 60, Mismatches: 4, Indels: 6
0.86 0.06 0.09
Matches are distributed among these distances:
49 2 0.03
50 33 0.55
51 3 0.05
52 22 0.37
ACGTcount: A:0.64, C:0.03, G:0.01, T:0.31
Consensus pattern (50 bp):
AAATAAAATATATAATATTAAAAAATAAAATTGAATAACAAATAAATTAA
Found at i:4279465 original size:19 final size:20
Alignment explanation
Indices: 4279419--4279474 Score: 55
Period size: 19 Copynumber: 2.9 Consensus size: 20
4279409 GATATTATAT
*
4279419 AAATGATATATAATTATAAAT
1 AAAT-ATATATAATTATAAAC
*
4279440 AAA-ATATATAA-TATTAAC
1 AAATATATATAATTATAAAC
*
4279458 AAATATAT-TATTTATAA
1 AAATATATATAATTATAA
4279475 TCGAAGAATT
Statistics
Matches: 29, Mismatches: 4, Indels: 6
0.74 0.10 0.15
Matches are distributed among these distances:
18 10 0.34
19 16 0.55
21 3 0.10
ACGTcount: A:0.57, C:0.02, G:0.02, T:0.39
Consensus pattern (20 bp):
AAATATATATAATTATAAAC
Found at i:4290320 original size:130 final size:131
Alignment explanation
Indices: 4290153--4290411 Score: 322
Period size: 130 Copynumber: 2.0 Consensus size: 131
4290143 TTTCAAACAC
* *
4290153 TGTAATTGAGAAATTTTATCAATTATAAAACCAAATCAATTAAGGCATTTATTTGAACAAAACGT
1 TGTAATTGAGAAATTTTATCAATTAGAAAACCAAATCAATTAAGGCATTTATCTGAACAAAACGT
* * *
4290218 CATAATTGAGA-GCTTTTATCAATTATAAAACCAAATAAAATCAGGTGTTCATCTATTCCAAACG
66 CATAATTGAAAGGCTTTTATCAATTATAAAAACAAATAAAATAAGGTGTTCATCTATTCCAAACG
4290282 T
131 T
* * *** ** * * *
4290283 TGTAATTGATATATTTTATCAATTAGATTTCCAAATCAATTAAGGTTTTTATCTGAGCACAATGT
1 TGTAATTGAGAAATTTTATCAATTAGAAAACCAAATCAATTAAGGCATTTATCTGAACAAAACGT
** * * * *
4290348 TGTAATTGAAAGGTTTTTATCAATTATAAAAACAAATAAATTAAGGTGTTCATTTGTTCCAAAC
66 CATAATTGAAAGGCTTTTATCAATTATAAAAACAAATAAAATAAGGTGTTCATCTATTCCAAAC
4290412 CCTGTAGTTG
Statistics
Matches: 107, Mismatches: 21, Indels: 1
0.83 0.16 0.01
Matches are distributed among these distances:
130 61 0.57
131 46 0.43
ACGTcount: A:0.40, C:0.12, G:0.12, T:0.37
Consensus pattern (131 bp):
TGTAATTGAGAAATTTTATCAATTAGAAAACCAAATCAATTAAGGCATTTATCTGAACAAAACGT
CATAATTGAAAGGCTTTTATCAATTATAAAAACAAATAAAATAAGGTGTTCATCTATTCCAAACG
T
Found at i:4290995 original size:24 final size:24
Alignment explanation
Indices: 4290925--4290977 Score: 70
Period size: 27 Copynumber: 2.1 Consensus size: 24
4290915 ACTATTTAAG
*
4290925 TATTAAAATTAACTTATTATTAAACTA
1 TATTAAAATT-A-TTAATA-TAAACTA
4290952 TATTAAAATTATTAATATAAACTA
1 TATTAAAATTATTAATATAAACTA
4290976 TA
1 TA
4290978 ATTATATTTT
Statistics
Matches: 25, Mismatches: 1, Indels: 3
0.86 0.03 0.10
Matches are distributed among these distances:
24 9 0.36
25 5 0.20
26 1 0.04
27 10 0.40
ACGTcount: A:0.51, C:0.06, G:0.00, T:0.43
Consensus pattern (24 bp):
TATTAAAATTATTAATATAAACTA
Found at i:4291175 original size:29 final size:29
Alignment explanation
Indices: 4291117--4291176 Score: 68
Period size: 29 Copynumber: 2.1 Consensus size: 29
4291107 ATTTTATTAA
* * *
4291117 TATTATAATATTAAAATAGTCATATTTAT
1 TATTAAAATATTAAAATACTCATATCTAT
*
4291146 TATTAAAATATTAAAAATACTTATA-CTAT
1 TATTAAAATATT-AAAATACTCATATCTAT
4291175 TA
1 TA
4291177 ATTTATATTT
Statistics
Matches: 26, Mismatches: 4, Indels: 2
0.81 0.12 0.06
Matches are distributed among these distances:
29 16 0.62
30 10 0.38
ACGTcount: A:0.48, C:0.05, G:0.02, T:0.45
Consensus pattern (29 bp):
TATTAAAATATTAAAATACTCATATCTAT
Found at i:4291349 original size:14 final size:14
Alignment explanation
Indices: 4291330--4291377 Score: 60
Period size: 14 Copynumber: 3.2 Consensus size: 14
4291320 AAAAATATTC
*
4291330 ATATTATGAAAATA
1 ATATTATTAAAATA
4291344 ATATTATTATATTAATA
1 ATATTATTA-A--AATA
4291361 ATATTATTAAAATA
1 ATATTATTAAAATA
4291375 ATA
1 ATA
4291378 AAAATATTAA
Statistics
Matches: 30, Mismatches: 1, Indels: 6
0.81 0.03 0.16
Matches are distributed among these distances:
14 15 0.50
15 1 0.03
16 1 0.03
17 13 0.43
ACGTcount: A:0.54, C:0.00, G:0.02, T:0.44
Consensus pattern (14 bp):
ATATTATTAAAATA
Found at i:4291376 original size:17 final size:17
Alignment explanation
Indices: 4291340--4291388 Score: 62
Period size: 17 Copynumber: 2.9 Consensus size: 17
4291330 ATATTATGAA
* *
4291340 AATAATATTATTATATT
1 AATAATATTATTAAAAT
4291357 AATAATATTATTAAAAT
1 AATAATATTATTAAAAT
* *
4291374 AATAAAAATATTAAA
1 AATAATATTATTAAA
4291389 TATGTTATTA
Statistics
Matches: 28, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
17 28 1.00
ACGTcount: A:0.59, C:0.00, G:0.00, T:0.41
Consensus pattern (17 bp):
AATAATATTATTAAAAT
Found at i:4291581 original size:19 final size:19
Alignment explanation
Indices: 4291543--4291580 Score: 58
Period size: 20 Copynumber: 1.9 Consensus size: 19
4291533 TTTAAATAAA
4291543 ATTAAATAAAAATATTTTT
1 ATTAAATAAAAATATTTTT
*
4291562 ATTAATATAATAATATTTT
1 ATTAA-ATAAAAATATTTT
4291581 AAGTTGGATC
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
19 5 0.29
20 12 0.71
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (19 bp):
ATTAAATAAAAATATTTTT
Found at i:4298769 original size:144 final size:144
Alignment explanation
Indices: 4298435--4298810 Score: 393
Period size: 144 Copynumber: 2.6 Consensus size: 144
4298425 GTGGCTCCAT
* * * *
4298435 TAAGCATAGGCTCAACAATTTTAAAATTCATCATCCTGAAAAAATTTCTCTAAGCAAAGGCTCAA
1 TAAGCAAAGGCTCAACAA-TTTAAAATTCATC-T--TGAAAAAGTTTCTCTTAGTAAAGGCTCAA
* * *
4298500 CAACTTTAAAAATCTCAT-ATGAAAAAAGCTCCTATAAGCAGAGGTTTAGTAACTTTTAAAAAAT
62 CAACTTTAAAAAT-TCATCTTGAAAAAAGCTCCTATAAGCAGAGGCTTAATAACTTTT-AAAAAT
*
4298564 CTATCTTGAAAAAGCTCATC
125 CTATCTTGAAAAAACTCATC
* * * * * * * *
4298584 TCAGCAGAGACTAAAAAAATTTAAAATCTCATCTTGAAAAAGCTCCTCTTAGTAGAGGCTCAACA
1 TAAGCAAAGGCT-CAACAATTTAAAAT-TCATCTTGAAAAAGTTTCTCTTAGTAAAGGCTCAACA
* * * *
4298649 ATTTTAAAAATTCATCTTGGAAAAA-CTCCTCTAAGTAGAGGCTTAATAAC-TTT-AAAATCTCA
64 ACTTTAAAAATTCATCTTGAAAAAAGCTCCTATAAGCAGAGGCTTAATAACTTTTAAAAATCT-A
*
4298711 TCTTGAAAAAACTCCTC
128 TCTTGAAAAAACTCATC
*
4298728 TAAGTAAAGGCTCAACAACTTTAAAAATTCATCTTGAAAAAGTTTCT-TTCAGTAAAGGCTCAAC
1 TAAGCAAAGGCTCAACAA-TTT-AAAATTCATCTTGAAAAAGTTTCTCTT-AGTAAAGGCTCAAC
* *
4298792 AACTTTAAAGATTTATCTT
63 AACTTTAAAAATTCATCTT
4298811 TTCTCGAAAC
Statistics
Matches: 188, Mismatches: 32, Indels: 19
0.79 0.13 0.08
Matches are distributed among these distances:
143 13 0.07
144 73 0.39
145 8 0.04
146 25 0.13
147 42 0.22
149 18 0.10
150 9 0.05
ACGTcount: A:0.41, C:0.18, G:0.11, T:0.30
Consensus pattern (144 bp):
TAAGCAAAGGCTCAACAATTTAAAATTCATCTTGAAAAAGTTTCTCTTAGTAAAGGCTCAACAAC
TTTAAAAATTCATCTTGAAAAAAGCTCCTATAAGCAGAGGCTTAATAACTTTTAAAAATCTATCT
TGAAAAAACTCATC
Found at i:4298810 original size:48 final size:48
Alignment explanation
Indices: 4298442--4298810 Score: 298
Period size: 48 Copynumber: 7.6 Consensus size: 48
4298432 CATTAAGCAT
* ** * *
4298442 AGGCTCAACAA-TTTTAAAATTCATCATCCTGAAAAAATTTCTCTAAGCAA
1 AGGCTCAACAACTTTAAAAATTCATC-T--TGAAAAAGCTCCTCTAAGTAA
* * * *
4298492 AGGCTCAACAACTTTAAAAATCTCAT-ATGAAAAAAGCTCCTATAAGCAG
1 AGGCTCAACAACTTTAAAAAT-TCATCTTG-AAAAAGCTCCTCTAAGTAA
* * ** * * * * *
4298541 AGGTTTAGTAACTTTTAAAAAATCTATCTTGAAAAAGCTCATCTCAGCAG
1 AGGCTCAACAAC-TTTAAAAATTC-ATCTTGAAAAAGCTCCTCTAAGTAA
* * * * * *
4298591 AGACTAAAAAAATTT-AAAATCTCATCTTGAAAAAGCTCCTCTTAGTAG
1 AGGCTCAACAACTTTAAAAAT-TCATCTTGAAAAAGCTCCTCTAAGTAA
* *
4298639 AGGCTCAACAATTTTAAAAATTCATCTTGGAAAAA-CTCCTCTAAGTAG
1 AGGCTCAACAACTTTAAAAATTCATCTT-GAAAAAGCTCCTCTAAGTAA
* * *
4298687 AGGCTTAATAACTTT-AAAATCTCATCTTGAAAAAACTCCTCTAAGTAA
1 AGGCTCAACAACTTTAAAAAT-TCATCTTGAAAAAGCTCCTCTAAGTAA
* * * *
4298735 AGGCTCAACAACTTTAAAAATTCATCTTGAAAAAGTTTCTTTCAGTAA
1 AGGCTCAACAACTTTAAAAATTCATCTTGAAAAAGCTCCTCTAAGTAA
* *
4298783 AGGCTCAACAACTTTAAAGATTTATCTT
1 AGGCTCAACAACTTTAAAAATTCATCTT
4298811 TTCTCGAAAC
Statistics
Matches: 263, Mismatches: 44, Indels: 26
0.79 0.13 0.08
Matches are distributed among these distances:
47 11 0.04
48 150 0.57
49 45 0.17
50 43 0.16
51 10 0.04
52 4 0.02
ACGTcount: A:0.41, C:0.18, G:0.11, T:0.30
Consensus pattern (48 bp):
AGGCTCAACAACTTTAAAAATTCATCTTGAAAAAGCTCCTCTAAGTAA
Found at i:4298810 original size:96 final size:96
Alignment explanation
Indices: 4298442--4298800 Score: 339
Period size: 96 Copynumber: 3.7 Consensus size: 96
4298432 CATTAAGCAT
* *
4298442 AGGCTCAACAA-TTTTAAAATTCATCATCCTGAAAAAATTTCTCTAAGCAAAGGCTCAACAACTT
1 AGGCTCAACAACTTTAAAAATTCATC-T--TGAAAAAGTTTCTCTAAGCAAAGGCTCAACAACTT
* * *
4298506 TAAAAATCTCAT-ATGAAAAAAGCTCCTATAAGCAG
63 T-AAAATCTCATCTTGAAAAAA-CTCCTCTAAGTAG
* * ** * * * * * * * *
4298541 AGGTTTAGTAACTTTTAAAAAATCTATCTTGAAAAAG-CTCATCTCAGCAGAGACTAAAAAAATT
1 AGGCTCAACAAC-TTTAAAAATTC-ATCTTGAAAAAGTTTC-TCTAAGCAAAGGCTCAACAACTT
* *
4298605 TAAAATCTCATCTTGAAAAAGCTCCTCTTAGTAG
63 TAAAATCTCATCTTGAAAAAACTCCTCTAAGTAG
* * * * * * *
4298639 AGGCTCAACAATTTTAAAAATTCATCTTGGAAAAA-CTCCTCTAAGTAGAGGCTTAATAACTTTA
1 AGGCTCAACAACTTTAAAAATTCATCTT-GAAAAAGTTTCTCTAAGCAAAGGCTCAACAACTTTA
*
4298703 AAATCTCATCTTGAAAAAACTCCTCTAAGTAA
65 AAATCTCATCTTGAAAAAACTCCTCTAAGTAG
* * *
4298735 AGGCTCAACAACTTTAAAAATTCATCTTGAAAAAGTTTCTTTCAGTAAAGGCTCAACAACTTTAA
1 AGGCTCAACAACTTTAAAAATTCATCTTGAAAAAGTTTCTCTAAGCAAAGGCTCAACAACTTTAA
4298800 A
66 A
4298801 GATTTATCTT
Statistics
Matches: 208, Mismatches: 44, Indels: 19
0.77 0.16 0.07
Matches are distributed among these distances:
95 6 0.03
96 104 0.50
97 17 0.08
98 29 0.14
99 39 0.19
101 10 0.05
102 3 0.01
ACGTcount: A:0.42, C:0.18, G:0.11, T:0.29
Consensus pattern (96 bp):
AGGCTCAACAACTTTAAAAATTCATCTTGAAAAAGTTTCTCTAAGCAAAGGCTCAACAACTTTAA
AATCTCATCTTGAAAAAACTCCTCTAAGTAG
Found at i:4310847 original size:15 final size:16
Alignment explanation
Indices: 4310812--4310862 Score: 61
Period size: 16 Copynumber: 3.2 Consensus size: 16
4310802 AGTTTTTTTT
4310812 TTTGGATTTGTATTTG
1 TTTGGATTTGTATTTG
4310828 TTTGG-TTTGT-TTTG
1 TTTGGATTTGTATTTG
* *
4310842 TCTTGGATTTTTTTTTG
1 T-TTGGATTTGTATTTG
4310859 TTTG
1 TTTG
4310863 ACAGAAAACT
Statistics
Matches: 31, Mismatches: 1, Indels: 6
0.82 0.03 0.16
Matches are distributed among these distances:
14 5 0.16
15 9 0.29
16 12 0.39
17 5 0.16
ACGTcount: A:0.06, C:0.02, G:0.24, T:0.69
Consensus pattern (16 bp):
TTTGGATTTGTATTTG
Found at i:4311193 original size:14 final size:14
Alignment explanation
Indices: 4311174--4311231 Score: 62
Period size: 14 Copynumber: 4.1 Consensus size: 14
4311164 TGAATCGAAT
*
4311174 AAGGAAAGAAGAAG
1 AAGGAAAGAAAAAG
*
4311188 AAGGAAAAAAAAAG
1 AAGGAAAGAAAAAG
* *
4311202 AAAGAAAGAAAAAA
1 AAGGAAAGAAAAAG
* *
4311216 AAGAAAAAAAAAAG
1 AAGGAAAGAAAAAG
4311230 AA
1 AA
4311232 TATACAAAAT
Statistics
Matches: 35, Mismatches: 9, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
14 35 1.00
ACGTcount: A:0.79, C:0.00, G:0.21, T:0.00
Consensus pattern (14 bp):
AAGGAAAGAAAAAG
Found at i:4311220 original size:9 final size:9
Alignment explanation
Indices: 4311193--4311226 Score: 52
Period size: 9 Copynumber: 3.9 Consensus size: 9
4311183 AGAAGAAGGA
4311193 AAAAAAAAG
1 AAAAAAAAG
*
4311202 -AAAGAAAG
1 AAAAAAAAG
4311210 AAAAAAAAG
1 AAAAAAAAG
4311219 AAAAAAAA
1 AAAAAAAA
4311227 AAGAATATAC
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
8 7 0.32
9 15 0.68
ACGTcount: A:0.88, C:0.00, G:0.12, T:0.00
Consensus pattern (9 bp):
AAAAAAAAG
Found at i:4311223 original size:28 final size:28
Alignment explanation
Indices: 4311177--4311231 Score: 83
Period size: 28 Copynumber: 2.0 Consensus size: 28
4311167 ATCGAATAAG
* * *
4311177 GAAAGAAGAAGAAGGAAAAAAAAAGAAA
1 GAAAGAAAAAAAAGAAAAAAAAAAGAAA
4311205 GAAAGAAAAAAAAGAAAAAAAAAAGAA
1 GAAAGAAAAAAAAGAAAAAAAAAAGAA
4311232 TATACAAAAT
Statistics
Matches: 24, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
28 24 1.00
ACGTcount: A:0.80, C:0.00, G:0.20, T:0.00
Consensus pattern (28 bp):
GAAAGAAAAAAAAGAAAAAAAAAAGAAA
Found at i:4311822 original size:46 final size:46
Alignment explanation
Indices: 4311750--4311839 Score: 126
Period size: 46 Copynumber: 2.0 Consensus size: 46
4311740 GAATGTGAAT
*** *
4311750 TAATTGCATAAATCAAGCATTGAAATTTCTTGCAAAAACTTCAACG
1 TAATTGCATAAATCAAGCACCAAAATTTATTGCAAAAACTTCAACG
* *
4311796 TAATTGTATAAATCAAGCACCAAAATTTATTGCAAAATCTTCAA
1 TAATTGCATAAATCAAGCACCAAAATTTATTGCAAAAACTTCAA
4311840 TGTTTTTTTT
Statistics
Matches: 38, Mismatches: 6, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
46 38 1.00
ACGTcount: A:0.43, C:0.17, G:0.09, T:0.31
Consensus pattern (46 bp):
TAATTGCATAAATCAAGCACCAAAATTTATTGCAAAAACTTCAACG
Found at i:4312358 original size:65 final size:64
Alignment explanation
Indices: 4312188--4312362 Score: 208
Period size: 64 Copynumber: 2.7 Consensus size: 64
4312178 AAGAACTAAC
* * * * *
4312188 ATGATCTGGACTGAGTCGAGATTAAAACAAGTGATTGGGATTGAACTGTAAGTTTGAAAATAAA
1 ATGATATGGACTGAGTCAAGATTAAAACAAGTGATTGGGATTGAATTGCAAGTCTGAAAATAAA
* * * * *
4312252 ATGATTTAGACTGAGTCAGGATTAAAACAAGTGACTAGGATTGAATTGCAAGTCT-AAAAGTAAA
1 ATGATATGGACTGAGTCAAGATTAAAACAAGTGATTGGGATTGAATTGCAAGTCTGAAAA-T-AA
4312316 A
64 A
* * *
4312317 ATGATATGGACTGAGTCAAGATCAAAACGAGTAATTGGGATTGAAT
1 ATGATATGGACTGAGTCAAGATTAAAACAAGTGATTGGGATTGAAT
4312363 CGTAGGTCAA
Statistics
Matches: 92, Mismatches: 17, Indels: 3
0.82 0.15 0.03
Matches are distributed among these distances:
63 4 0.04
64 47 0.51
65 41 0.45
ACGTcount: A:0.41, C:0.09, G:0.24, T:0.27
Consensus pattern (64 bp):
ATGATATGGACTGAGTCAAGATTAAAACAAGTGATTGGGATTGAATTGCAAGTCTGAAAATAAA
Found at i:4312747 original size:86 final size:85
Alignment explanation
Indices: 4312533--4312832 Score: 320
Period size: 86 Copynumber: 3.5 Consensus size: 85
4312523 TTAAATTCAT
* * * ** *
4312533 AAGAATGAAAAATTCACAAGATTTCAAGTTTCGCAGAGGTTTTACATTCACAAAAATTTCAGGTT
1 AAGAATGAAAGATTCACAAGATTTCAAGTTTCACAGAGGTTTTAGATTTGCAAAGATTTCAGGTT
*
4312598 TGCAAGGACTTTTCA-A-TTC
66 CGCAAGGACTTTT-AGATTTC
* * * * *** * *
4312617 -ACAA-GAATGATTCGCAAGATTCCAAGTTTTGTAGAGGTTCTAGATTTGCAAAGATATCAGGTT
1 AAGAATGAAAGATTCACAAGATTTCAAGTTTCACAGAGGTTTTAGATTTGCAAAGATTTCAGGTT
*
4312680 CCCAAGGACTTTTAGATTTGC
66 CGCAAGGACTTTTAGATTT-C
* *
4312701 AAGAATGAAAGATTCGCAAGATTTCAAGTTTCACAAAGGTTTTAGATTTGCAAAGATTTCAGGTT
1 AAGAATGAAAGATTCACAAGATTTCAAGTTTCACAGAGGTTTTAGATTTGCAAAGATTTCAGGTT
* * *
4312766 CGCAAAGACTTTCAGATTCAC
66 CGCAAGGACTTTTAGATT-TC
* * *
4312787 AAGAATGAAAGATTCACAAGATTTTAAGTTTCATAGAGGTTCTAGA
1 AAGAATGAAAGATTCACAAGATTTCAAGTTTCACAGAGGTTTTAGA
4312833 AAAATGATCT
Statistics
Matches: 177, Mismatches: 33, Indels: 10
0.80 0.15 0.05
Matches are distributed among these distances:
81 1 0.01
82 59 0.33
83 5 0.03
84 1 0.01
85 3 0.02
86 108 0.61
ACGTcount: A:0.36, C:0.14, G:0.19, T:0.31
Consensus pattern (85 bp):
AAGAATGAAAGATTCACAAGATTTCAAGTTTCACAGAGGTTTTAGATTTGCAAAGATTTCAGGTT
CGCAAGGACTTTTAGATTTC
Found at i:4312770 original size:17 final size:17
Alignment explanation
Indices: 4312710--4312784 Score: 71
Period size: 17 Copynumber: 4.4 Consensus size: 17
4312700 CAAGAATGAA
4312710 AGATTCGC-AAGATTTC
1 AGATTCGCAAAGATTTC
* * * *
4312726 AAGTTTCACAAAGGTTTT
1 -AGATTCGCAAAGATTTC
*
4312744 AGATTTGCAAAGATTTC
1 AGATTCGCAAAGATTTC
*
4312761 AGGTTCGCAAAGACTTTC
1 AGATTCGCAAAGA-TTTC
4312779 AGATTC
1 AGATTC
4312785 ACAAGAATGA
Statistics
Matches: 44, Mismatches: 12, Indels: 3
0.75 0.20 0.05
Matches are distributed among these distances:
17 29 0.66
18 15 0.34
ACGTcount: A:0.32, C:0.16, G:0.19, T:0.33
Consensus pattern (17 bp):
AGATTCGCAAAGATTTC
Found at i:4312783 original size:35 final size:34
Alignment explanation
Indices: 4312710--4312790 Score: 83
Period size: 34 Copynumber: 2.4 Consensus size: 34
4312700 CAAGAATGAA
* * *
4312710 AGATTCGCAAGATTTCAAGTTTCACAAAGGTTTT
1 AGATTCGCAAGATTTCAAGGTTCACAAAGCTTTC
* *
4312744 AGATTTGCAAAGATTTC-AGGTTCGCAAAGACTTTC
1 AGATTCGC-AAGATTTCAAGGTTCACAAAG-CTTTC
*
4312779 AGATTCACAAGA
1 AGATTCGCAAGA
4312791 ATGAAAGATT
Statistics
Matches: 38, Mismatches: 7, Indels: 4
0.78 0.14 0.08
Matches are distributed among these distances:
34 21 0.55
35 17 0.45
ACGTcount: A:0.35, C:0.16, G:0.19, T:0.31
Consensus pattern (34 bp):
AGATTCGCAAGATTTCAAGGTTCACAAAGCTTTC
Found at i:4313567 original size:16 final size:16
Alignment explanation
Indices: 4313544--4313581 Score: 51
Period size: 16 Copynumber: 2.4 Consensus size: 16
4313534 TAAAATTTCT
*
4313544 AAAA-AATAAAACCAA
1 AAAATAATAAAAACAA
*
4313559 AAAATAATAAAAACTA
1 AAAATAATAAAAACAA
4313575 AAAATAA
1 AAAATAA
4313582 AATGAGCTAA
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
15 4 0.20
16 16 0.80
ACGTcount: A:0.79, C:0.08, G:0.00, T:0.13
Consensus pattern (16 bp):
AAAATAATAAAAACAA
Found at i:4314103 original size:20 final size:19
Alignment explanation
Indices: 4314078--4314140 Score: 72
Period size: 20 Copynumber: 3.2 Consensus size: 19
4314068 CAAAAATTCT
4314078 CTAGAAACTTAAATCAAATC
1 CTAGAAACTTAAATCAAA-C
** *
4314098 CTAGAAACCCAAATCTAAC
1 CTAGAAACTTAAATCAAAC
*
4314117 CCAGAAACTTCAAATCAAAC
1 CTAGAAACTT-AAATCAAAC
4314137 CTAG
1 CTAG
4314141 GATTCTCAAA
Statistics
Matches: 34, Mismatches: 8, Indels: 2
0.77 0.18 0.05
Matches are distributed among these distances:
19 8 0.24
20 26 0.76
ACGTcount: A:0.48, C:0.27, G:0.06, T:0.19
Consensus pattern (19 bp):
CTAGAAACTTAAATCAAAC
Found at i:4314534 original size:18 final size:16
Alignment explanation
Indices: 4314510--4314550 Score: 61
Period size: 15 Copynumber: 2.8 Consensus size: 16
4314500 ACAGAAAGTA
4314510 AATATA-ATAATAA-T
1 AATATATATAATAATT
4314524 AATATATATAATAATT
1 AATATATATAATAATT
4314540 AATATAT-TAAT
1 AATATATATAAT
4314551 TAACATAAAT
Statistics
Matches: 25, Mismatches: 0, Indels: 3
0.89 0.00 0.11
Matches are distributed among these distances:
14 6 0.24
15 11 0.44
16 8 0.32
ACGTcount: A:0.59, C:0.00, G:0.00, T:0.41
Consensus pattern (16 bp):
AATATATATAATAATT
Found at i:4315660 original size:18 final size:17
Alignment explanation
Indices: 4315585--4315660 Score: 57
Period size: 17 Copynumber: 4.4 Consensus size: 17
4315575 CAAGAAAGAA
4315585 AGATTCGT-AAGATTTC
1 AGATTCGTAAAGATTTC
* *
4315601 AAGTTTCGTAAAG-GTTC
1 -AGATTCGTAAAGATTTC
* *
4315618 TATATTCATAAAGATTTC
1 -AGATTCGTAAAGATTTC
* *
4315636 GGGTTCGTAAAGACTTTC
1 AGATTCGTAAAGA-TTTC
4315654 AGATTCG
1 AGATTCG
4315661 CAGGAAAGAA
Statistics
Matches: 43, Mismatches: 13, Indels: 5
0.70 0.21 0.08
Matches are distributed among these distances:
17 28 0.65
18 15 0.35
ACGTcount: A:0.30, C:0.13, G:0.20, T:0.37
Consensus pattern (17 bp):
AGATTCGTAAAGATTTC
Found at i:4315684 original size:17 final size:17
Alignment explanation
Indices: 4315654--4315697 Score: 52
Period size: 17 Copynumber: 2.6 Consensus size: 17
4315644 AAAGACTTTC
* *
4315654 AGATTCGCAGGAAAGAA
1 AGATTCGTAAGAAAGAA
* *
4315671 CGATTCGTAAGAAATAA
1 AGATTCGTAAGAAAGAA
4315688 AGATTCGTAA
1 AGATTCGTAA
4315698 AATTTCAAGT
Statistics
Matches: 22, Mismatches: 5, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
17 22 1.00
ACGTcount: A:0.45, C:0.11, G:0.23, T:0.20
Consensus pattern (17 bp):
AGATTCGTAAGAAAGAA
Found at i:4320861 original size:23 final size:23
Alignment explanation
Indices: 4320835--4320907 Score: 64
Period size: 23 Copynumber: 3.2 Consensus size: 23
4320825 AATAAAACCA
*
4320835 AAAAAATAATAAAAACTAAAAAT
1 AAAAAATAATAAAAAATAAAAAT
*
4320858 --AAAATGAGCTAAAAAAT-AAAAT
1 AAAAAAT-A-ATAAAAAATAAAAAT
4320880 AAAATAA-AATCAAAAAATAAAAAT
1 AAAA-AATAAT-AAAAAATAAAAAT
4320904 AAAA
1 AAAA
4320908 TGAAAAAAAA
Statistics
Matches: 40, Mismatches: 3, Indels: 13
0.71 0.05 0.23
Matches are distributed among these distances:
21 5 0.12
22 7 0.17
23 15 0.38
24 11 0.28
25 2 0.05
ACGTcount: A:0.77, C:0.04, G:0.03, T:0.16
Consensus pattern (23 bp):
AAAAAATAATAAAAAATAAAAAT
Found at i:4320904 original size:19 final size:19
Alignment explanation
Indices: 4320875--4320919 Score: 67
Period size: 19 Copynumber: 2.5 Consensus size: 19
4320865 GCTAAAAAAT
4320875 AAAAT-AAAATAAAATCAA
1 AAAATAAAAATAAAATCAA
*
4320893 AAAATAAAAATAAAATGAA
1 AAAATAAAAATAAAATCAA
4320912 AAAA-AAAA
1 AAAATAAAA
4320920 CCTTACGATC
Statistics
Matches: 25, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
18 9 0.36
19 16 0.64
ACGTcount: A:0.82, C:0.02, G:0.02, T:0.13
Consensus pattern (19 bp):
AAAATAAAAATAAAATCAA
Found at i:4320917 original size:23 final size:23
Alignment explanation
Indices: 4320845--4320919 Score: 82
Period size: 23 Copynumber: 3.3 Consensus size: 23
4320835 AAAAAATAAT
* ***
4320845 AAAAACTAAAAATAAAATGAGCT
1 AAAAAATAAAAATAAAATGAAAA
4320868 AAAAAAT-AAAATAAAAT-AAAA
1 AAAAAATAAAAATAAAATGAAAA
4320889 TCAAAAAATAAAAATAAAATGAAAA
1 --AAAAAATAAAAATAAAATGAAAA
4320914 AAAAAA
1 AAAAAA
4320920 CCTTACGATC
Statistics
Matches: 44, Mismatches: 4, Indels: 8
0.79 0.07 0.14
Matches are distributed among these distances:
21 1 0.02
22 10 0.23
23 19 0.43
24 10 0.23
25 4 0.09
ACGTcount: A:0.77, C:0.04, G:0.04, T:0.15
Consensus pattern (23 bp):
AAAAAATAAAAATAAAATGAAAA
Found at i:4320918 original size:46 final size:47
Alignment explanation
Indices: 4320822--4320919 Score: 119
Period size: 46 Copynumber: 2.1 Consensus size: 47
4320812 AAAATTACTC
* ***
4320822 AAAAATAAAACCAAAAAAATAATAAAAACTAAAAATAAAATGAGCTA
1 AAAAATAAAACCAAAAAAATAATAAAAAATAAAAATAAAATGAAAAA
* *
4320869 AAAAATAAAA-TAAAATAA-AATCAAAAAATAAAAATAAAATGAAAAA
1 AAAAATAAAACCAAAAAAATAAT-AAAAAATAAAAATAAAATGAAAAA
4320915 AAAAA
1 AAAAA
4320920 CCTTACGATC
Statistics
Matches: 44, Mismatches: 6, Indels: 3
0.83 0.11 0.06
Matches are distributed among these distances:
45 3 0.07
46 31 0.70
47 10 0.23
ACGTcount: A:0.78, C:0.05, G:0.03, T:0.14
Consensus pattern (47 bp):
AAAAATAAAACCAAAAAAATAATAAAAAATAAAAATAAAATGAAAAA
Found at i:4321776 original size:5 final size:5
Alignment explanation
Indices: 4321754--4321801 Score: 51
Period size: 5 Copynumber: 9.4 Consensus size: 5
4321744 GAAAGGAAAG
* * * *
4321754 AAAAA AAAAG AAAGT AAAAT AAAAT AAAAT AAATT AAAAT AATAAT AA
1 AAAAT AAAAT AAAAT AAAAT AAAAT AAAAT AAAAT AAAAT AA-AAT AA
4321802 TAATTACAAT
Statistics
Matches: 36, Mismatches: 6, Indels: 1
0.84 0.14 0.02
Matches are distributed among these distances:
5 31 0.86
6 5 0.14
ACGTcount: A:0.77, C:0.00, G:0.04, T:0.19
Consensus pattern (5 bp):
AAAAT
Found at i:4321891 original size:15 final size:14
Alignment explanation
Indices: 4321864--4321895 Score: 55
Period size: 15 Copynumber: 2.2 Consensus size: 14
4321854 TTATAAGAGC
4321864 TATAATAACTATAA
1 TATAATAACTATAA
4321878 TATAATATACTATAA
1 TATAATA-ACTATAA
4321893 TAT
1 TAT
4321896 GGTACCGTAA
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
14 7 0.41
15 10 0.59
ACGTcount: A:0.53, C:0.06, G:0.00, T:0.41
Consensus pattern (14 bp):
TATAATAACTATAA
Found at i:4321954 original size:12 final size:12
Alignment explanation
Indices: 4321903--4321967 Score: 55
Period size: 12 Copynumber: 5.5 Consensus size: 12
4321893 TATGGTACCG
4321903 TAATAATAGT-A
1 TAATAATAGTAA
*
4321914 TAATAATAGTGA
1 TAATAATAGTAA
*
4321926 T-ATACTA-TACTA
1 TAATAATAGTA--A
*
4321938 TAATACTAGTAA
1 TAATAATAGTAA
*
4321950 TAATAATAGAAA
1 TAATAATAGTAA
4321962 TAATAA
1 TAATAA
4321968 ACTTGACTCG
Statistics
Matches: 45, Mismatches: 4, Indels: 9
0.78 0.07 0.16
Matches are distributed among these distances:
10 1 0.02
11 15 0.33
12 21 0.47
13 6 0.13
14 2 0.04
ACGTcount: A:0.54, C:0.05, G:0.08, T:0.34
Consensus pattern (12 bp):
TAATAATAGTAA
Found at i:4326861 original size:4 final size:4
Alignment explanation
Indices: 4326852--4326878 Score: 54
Period size: 4 Copynumber: 6.8 Consensus size: 4
4326842 CATTTTATAG
4326852 AAAT AAAT AAAT AAAT AAAT AAAT AAA
1 AAAT AAAT AAAT AAAT AAAT AAAT AAA
4326879 AATCGTATCA
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:0.78, C:0.00, G:0.00, T:0.22
Consensus pattern (4 bp):
AAAT
Found at i:4327863 original size:46 final size:46
Alignment explanation
Indices: 4327793--4327882 Score: 146
Period size: 46 Copynumber: 2.0 Consensus size: 46
4327783 GAATGTGAAT
* *
4327793 TAATTGCATAAATCAAGCATCAAAATTT-TTAGCAAAATCTTCAACG
1 TAATTGCATAAATCAAGCACCAAAATTTACTA-CAAAATCTTCAACG
4327839 TAATTGCATAAATCAAGCACCAAAATTTACTACAAAATCTTCAA
1 TAATTGCATAAATCAAGCACCAAAATTTACTACAAAATCTTCAA
4327883 TGTTTTTTTT
Statistics
Matches: 41, Mismatches: 2, Indels: 2
0.91 0.04 0.04
Matches are distributed among these distances:
46 39 0.95
47 2 0.05
ACGTcount: A:0.46, C:0.19, G:0.07, T:0.29
Consensus pattern (46 bp):
TAATTGCATAAATCAAGCACCAAAATTTACTACAAAATCTTCAACG
Found at i:4328272 original size:24 final size:24
Alignment explanation
Indices: 4328242--4328302 Score: 79
Period size: 24 Copynumber: 2.5 Consensus size: 24
4328232 AATATCATTC
* *
4328242 AAATATAATATTA-ATTATGCAAT
1 AAATATAATATCATATCATGCAAT
4328265 AACATATAATATCATATCATGCAAT
1 AA-ATATAATATCATATCATGCAAT
*
4328290 AAATATAAAATCA
1 AAATATAATATCA
4328303 CGTAATAATA
Statistics
Matches: 33, Mismatches: 3, Indels: 3
0.85 0.08 0.08
Matches are distributed among these distances:
23 2 0.06
24 20 0.61
25 11 0.33
ACGTcount: A:0.54, C:0.10, G:0.03, T:0.33
Consensus pattern (24 bp):
AAATATAATATCATATCATGCAAT
Found at i:4328416 original size:32 final size:32
Alignment explanation
Indices: 4328344--4328409 Score: 89
Period size: 32 Copynumber: 2.1 Consensus size: 32
4328334 AATAACTATG
* * *
4328344 CAAATAAAGATATTAATAATCATACAATCTCA
1 CAAATAAATAAATTAATAATCATACAATCTAA
*
4328376 CAAATAAATAAATTAATAATCATGCAAT-TAA
1 CAAATAAATAAATTAATAATCATACAATCTAA
4328407 CAA
1 CAA
4328410 TGTAAATCAT
Statistics
Matches: 30, Mismatches: 4, Indels: 1
0.86 0.11 0.03
Matches are distributed among these distances:
31 5 0.17
32 25 0.83
ACGTcount: A:0.56, C:0.14, G:0.03, T:0.27
Consensus pattern (32 bp):
CAAATAAATAAATTAATAATCATACAATCTAA
Found at i:4328433 original size:33 final size:32
Alignment explanation
Indices: 4328390--4328621 Score: 108
Period size: 33 Copynumber: 7.2 Consensus size: 32
4328380 TAAATAAATT
* *
4328390 AATAATCATGCAATTAACA-ATGTAAATCATGCA
1 AATAAACATGCAATTAA-ATATAT-AATCATGCA
*
4328423 AATAAACATGCAATTAAATATATAATCATGTA
1 AATAAACATGCAATTAAATATATAATCATGCA
* * ** *
4328455 AATAAAAAT--ATATATACCATGCA-AATAAAT--A
1 AATAAACATGCA-AT-TA-AATATATAAT-CATGCA
* * * *
4328486 TATAATCATGCAACTAATAATACATAAATCATGCA
1 AATAAACATGCAA-TTA-AATATAT-AATCATGCA
* * * * *
4328521 AATAAACATACAATAAAAAAATATAATTATGCT
1 AATAAACATGCAAT-TAAATATATAATCATGCA
*
4328554 AATAATA-AT--AATAATAATATATAAATCATGCA
1 AATAA-ACATGCAATTA-AATATAT-AATCATGCA
4328586 AA-AAACATGCAATT-AATATATAATCATGCA
1 AATAAACATGCAATTAAATATATAATCATGCA
4328616 AATAAA
1 AATAAA
4328622 TATATTAATA
Statistics
Matches: 152, Mismatches: 27, Indels: 42
0.69 0.12 0.19
Matches are distributed among these distances:
30 15 0.10
31 32 0.21
32 37 0.24
33 45 0.30
34 10 0.07
35 13 0.09
ACGTcount: A:0.56, C:0.11, G:0.05, T:0.28
Consensus pattern (32 bp):
AATAAACATGCAATTAAATATATAATCATGCA
Found at i:4328452 original size:20 final size:20
Alignment explanation
Indices: 4328424--4328526 Score: 80
Period size: 22 Copynumber: 4.8 Consensus size: 20
4328414 AATCATGCAA
*
4328424 ATAAACATGCAATTAAATAT
1 ATAATCATGCAATTAAATAT
* *
4328444 ATAATCATGTAAATAAAAATAT
1 ATAATCATG-CAAT-TAAATAT
* *
4328466 ATATACCATGCAAATAAATAT
1 ATA-ATCATGCAATTAAATAT
* *
4328487 ATAATCATGCAACTAATAATAC
1 ATAATCATGCAA-TTA-AATAT
*
4328509 ATAAATCATGCAAATAAA
1 AT-AATCATGCAATTAAA
4328527 CATACAATAA
Statistics
Matches: 64, Mismatches: 13, Indels: 11
0.73 0.15 0.12
Matches are distributed among these distances:
20 16 0.25
21 15 0.23
22 18 0.28
23 15 0.23
ACGTcount: A:0.55, C:0.12, G:0.05, T:0.28
Consensus pattern (20 bp):
ATAATCATGCAATTAAATAT
Found at i:4328480 original size:23 final size:22
Alignment explanation
Indices: 4328438--4328526 Score: 101
Period size: 23 Copynumber: 4.0 Consensus size: 22
4328428 ACATGCAATT
*
4328438 AAATATATAATCATGTAAATAA
1 AAATATATAATCATGCAAATAA
*
4328460 AAATATATATACCATGCAAAT--
1 AAATATATA-ATCATGCAAATAA
*
4328481 AAATATATAATCATGCAACTAA
1 AAATATATAATCATGCAAATAA
* *
4328503 TAATACATAAATCATGCAAATAA
1 AAATATAT-AATCATGCAAATAA
4328526 A
1 A
4328527 CATACAATAA
Statistics
Matches: 55, Mismatches: 8, Indels: 7
0.79 0.11 0.10
Matches are distributed among these distances:
20 9 0.16
21 9 0.16
22 15 0.27
23 22 0.40
ACGTcount: A:0.56, C:0.11, G:0.04, T:0.28
Consensus pattern (22 bp):
AAATATATAATCATGCAAATAA
Found at i:4328484 original size:43 final size:43
Alignment explanation
Indices: 4328424--4328526 Score: 136
Period size: 43 Copynumber: 2.4 Consensus size: 43
4328414 AATCATGCAA
* * *
4328424 ATAAA-CATGCAATTAAATATATAATCATGTAAATAAAAATAT
1 ATAAACCATGCAAATAAATATATAATCATGCAAATAAAAATAC
* * *
4328466 ATATACCATGCAAATAAATATATAATCATGCAACTAATAATAC
1 ATAAACCATGCAAATAAATATATAATCATGCAAATAAAAATAC
*
4328509 ATAAATCATGCAAATAAA
1 ATAAACCATGCAAATAAA
4328527 CATACAATAA
Statistics
Matches: 52, Mismatches: 8, Indels: 1
0.85 0.13 0.02
Matches are distributed among these distances:
42 4 0.08
43 48 0.92
ACGTcount: A:0.55, C:0.12, G:0.05, T:0.28
Consensus pattern (43 bp):
ATAAACCATGCAAATAAATATATAATCATGCAAATAAAAATAC
Found at i:4328531 original size:23 final size:22
Alignment explanation
Indices: 4328424--4328537 Score: 85
Period size: 23 Copynumber: 5.2 Consensus size: 22
4328414 AATCATGCAA
* *
4328424 ATAAA-CATGC-AATTAAATAT
1 ATAAATCATGCAAATAAAATAC
* *
4328444 AT-AATCATGTAAATAAAAATAT
1 ATAAATCATGCAAAT-AAAATAC
* * *
4328466 ATATACCATGCAAAT-AAATAT
1 ATAAATCATGCAAATAAAATAC
*
4328487 AT-AATCATGCAACTAATAATAC
1 ATAAATCATGCAAATAA-AATAC
4328509 ATAAATCATGCAAATAAACATAC
1 ATAAATCATGCAAATAAA-ATAC
4328532 AATAAA
1 -ATAAA
4328538 AAAATATAAT
Statistics
Matches: 75, Mismatches: 10, Indels: 14
0.76 0.10 0.14
Matches are distributed among these distances:
19 2 0.03
20 15 0.20
21 12 0.16
22 15 0.20
23 26 0.35
24 5 0.07
ACGTcount: A:0.56, C:0.12, G:0.04, T:0.27
Consensus pattern (22 bp):
ATAAATCATGCAAATAAAATAC
Found at i:4328620 original size:62 final size:64
Alignment explanation
Indices: 4328500--4328704 Score: 166
Period size: 71 Copynumber: 3.1 Consensus size: 64
4328490 ATCATGCAAC
* *
4328500 TAATAATACATAAATCATGCAAATAAACATACAATAAAAAAATATAATTATGCTAAT-AATAATA
1 TAATAATACATAAATCATGCAAATAAACATACAAT-AAAAAATATAATCATGCAAATAAAT-ATA
4328564 A
64 A
* * * * *
4328565 TAATAATATATAAATCATGCAAA-AAACATGCAAT-TAATATATAATCATGCAAATAAATATAT
1 TAATAATACATAAATCATGCAAATAAACATACAATAAAAAATATAATCATGCAAATAAATATAA
*** * **
4328627 TAATAATTAAGCAATTAAAT-ATATTAATAATCATGTAATCAAATTAAATATAATCATGCAAATA
1 TAATAA-T-A-C-A-TAAATCATGCAAATAAACATACAAT-AAA--AAATATAATCATGCAAATA
*
4328691 AATATAT
58 AATATAA
4328698 TAATAAT
1 TAATAAT
4328705 TAAGCAATTA
Statistics
Matches: 114, Mismatches: 15, Indels: 17
0.78 0.10 0.12
Matches are distributed among these distances:
62 25 0.22
63 4 0.04
64 11 0.10
65 22 0.19
66 5 0.04
67 14 0.12
69 1 0.01
70 1 0.01
71 31 0.27
ACGTcount: A:0.56, C:0.08, G:0.04, T:0.32
Consensus pattern (64 bp):
TAATAATACATAAATCATGCAAATAAACATACAATAAAAAATATAATCATGCAAATAAATATAA
Found at i:4328631 original size:65 final size:64
Alignment explanation
Indices: 4328500--4328633 Score: 166
Period size: 62 Copynumber: 2.1 Consensus size: 64
4328490 ATCATGCAAC
* *
4328500 TAATAATACATAAATCATGCAAATAAACATACAATAAAAAAATATAATTATGCTAATAATAATAA
1 TAATAATACATAAATCATGCAAATAAACATACAAT-AAAAAATATAATCATGCAAATAATAATAA
* * * * *
4328565 TAATAATATATAAATCATGCAAA-AAACATGCAAT-TAATATATAATCATGCAAATAA-ATATAT
1 TAATAATACATAAATCATGCAAATAAACATACAATAAAAAATATAATCATGCAAATAATA-ATAA
4328627 TAATAAT
1 TAATAAT
4328634 TAAGCAATTA
Statistics
Matches: 61, Mismatches: 7, Indels: 5
0.84 0.10 0.07
Matches are distributed among these distances:
61 1 0.02
62 28 0.46
64 10 0.16
65 22 0.36
ACGTcount: A:0.57, C:0.09, G:0.04, T:0.30
Consensus pattern (64 bp):
TAATAATACATAAATCATGCAAATAAACATACAATAAAAAATATAATCATGCAAATAATAATAA
Found at i:4328632 original size:24 final size:24
Alignment explanation
Indices: 4328605--4328836 Score: 202
Period size: 24 Copynumber: 10.0 Consensus size: 24
4328595 CAATTAATAT
4328605 ATAATCATGCAAATAAATATATTA
1 ATAATCATGCAAATAAATATATTA
* * *
4328629 ATAATTAAGCAATTAAATATATTA
1 ATAATCATGCAAATAAATATATTA
* *
4328653 ATAATCATG-TAATCAAAT-TA-AA
1 ATAATCATGCAAAT-AAATATATTA
4328675 TATAATCATGCAAATAAATATATTA
1 -ATAATCATGCAAATAAATATATTA
* * *
4328700 ATAATTAAGCAATTAAATATATTA
1 ATAATCATGCAAATAAATATATTA
* *
4328724 ATAATCATG-TAATCAAAT-TA-AA
1 ATAATCATGCAAAT-AAATATATTA
*
4328746 TATAATCATACAAATAAATATATTA
1 -ATAATCATGCAAATAAATATATTA
4328771 ATAATCATGC----AAATATATTA
1 ATAATCATGCAAATAAATATATTA
**
4328791 ATAAATCACACAAATAAATATA-T-
1 AT-AATCATGCAAATAAATATATTA
*
4328814 -TAATCATGCAAATAAGTATATTA
1 ATAATCATGCAAATAAATATATTA
4328837 GGTAAATAAA
Statistics
Matches: 164, Mismatches: 27, Indels: 35
0.73 0.12 0.15
Matches are distributed among these distances:
20 12 0.07
21 22 0.13
22 4 0.02
23 33 0.20
24 84 0.51
25 9 0.05
ACGTcount: A:0.54, C:0.08, G:0.04, T:0.34
Consensus pattern (24 bp):
ATAATCATGCAAATAAATATATTA
Found at i:4328678 original size:71 final size:71
Alignment explanation
Indices: 4328596--4328775 Score: 342
Period size: 71 Copynumber: 2.5 Consensus size: 71
4328586 AAAAACATGC
4328596 AATTAATATATAATCATGCAAATAAATATATTAATAATTAAGCAATTAAATATATTAATAATCAT
1 AATTAA-ATATAATCATGCAAATAAATATATTAATAATTAAGCAATTAAATATATTAATAATCAT
4328661 GTAATCA
65 GTAATCA
4328668 AATTAAATATAATCATGCAAATAAATATATTAATAATTAAGCAATTAAATATATTAATAATCATG
1 AATTAAATATAATCATGCAAATAAATATATTAATAATTAAGCAATTAAATATATTAATAATCATG
4328733 TAATCA
66 TAATCA
*
4328739 AATTAAATATAATCATACAAATAAATATATTAATAAT
1 AATTAAATATAATCATGCAAATAAATATATTAATAAT
4328776 CATGCAAATA
Statistics
Matches: 107, Mismatches: 1, Indels: 1
0.98 0.01 0.01
Matches are distributed among these distances:
71 101 0.94
72 6 0.06
ACGTcount: A:0.54, C:0.07, G:0.03, T:0.36
Consensus pattern (71 bp):
AATTAAATATAATCATGCAAATAAATATATTAATAATTAAGCAATTAAATATATTAATAATCATG
TAATCA
Found at i:4328764 original size:47 final size:45
Alignment explanation
Indices: 4328676--4328828 Score: 154
Period size: 47 Copynumber: 3.4 Consensus size: 45
4328666 CAAATTAAAT
* * *
4328676 ATAATCATGCAAATAAATATATTAATAATTA-AGCAATTAAATATATTA
1 ATAATCATGCAAATAAAT-TAAT-A-AATCACA-CAAATAAATATATTA
* *
4328724 ATAATCATG-TAATCAAATTAAATATAATCATACAAATAAATATATTA
1 ATAATCATGCAAAT-AAATT-AATA-AATCACACAAATAAATATATTA
*
4328771 ATAATCATGCAAATATATTAATAAATCACACAAATAAATATA-T-
1 ATAATCATGCAAATAAATTAATAAATCACACAAATAAATATATTA
4328814 -TAATCATGCAAATAA
1 ATAATCATGCAAATAA
4328829 GTATATTAGG
Statistics
Matches: 93, Mismatches: 8, Indels: 14
0.81 0.07 0.12
Matches are distributed among these distances:
42 14 0.15
44 1 0.01
45 18 0.19
46 4 0.04
47 37 0.40
48 19 0.20
ACGTcount: A:0.55, C:0.09, G:0.03, T:0.33
Consensus pattern (45 bp):
ATAATCATGCAAATAAATTAATAAATCACACAAATAAATATATTA
Found at i:4328804 original size:21 final size:20
Alignment explanation
Indices: 4328761--4328806 Score: 65
Period size: 20 Copynumber: 2.2 Consensus size: 20
4328751 TCATACAAAT
**
4328761 AAATATATTAATAATCATGC
1 AAATATATTAATAATCACAC
4328781 AAATATATTAATAAATCACAC
1 AAATATATTAAT-AATCACAC
4328802 AAATA
1 AAATA
4328807 AATATATTAA
Statistics
Matches: 23, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
20 12 0.52
21 11 0.48
ACGTcount: A:0.57, C:0.11, G:0.02, T:0.30
Consensus pattern (20 bp):
AAATATATTAATAATCACAC
Found at i:4328818 original size:21 final size:21
Alignment explanation
Indices: 4328748--4328836 Score: 72
Period size: 21 Copynumber: 4.1 Consensus size: 21
4328738 AAATTAAATA
*
4328748 TAATCATACAAATAAATATAT
1 TAATCACACAAATAAATATAT
* *
4328769 TAATAATCATGCAAATATAT-TAAT
1 TAATCA-CA--CAAATAAATAT-AT
*
4328793 AAATCACACAAATAAATATAT
1 TAATCACACAAATAAATATAT
** *
4328814 TAATCATGCAAATAAGTATAT
1 TAATCACACAAATAAATATAT
4328835 TA
1 TA
4328837 GGTAAATAAA
Statistics
Matches: 53, Mismatches: 10, Indels: 10
0.73 0.14 0.14
Matches are distributed among these distances:
21 34 0.64
22 2 0.04
23 3 0.06
24 14 0.26
ACGTcount: A:0.54, C:0.10, G:0.03, T:0.33
Consensus pattern (21 bp):
TAATCACACAAATAAATATAT
Found at i:4328874 original size:19 final size:17
Alignment explanation
Indices: 4328842--4328876 Score: 52
Period size: 19 Copynumber: 1.9 Consensus size: 17
4328832 TATTAGGTAA
4328842 ATAAATTATCATGCAAG
1 ATAAATTATCATGCAAG
4328859 ATAATATTAGTCATGCAA
1 ATAA-ATTA-TCATGCAA
4328877 ATTCATGCAA
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
17 4 0.25
18 4 0.25
19 8 0.50
ACGTcount: A:0.46, C:0.11, G:0.11, T:0.31
Consensus pattern (17 bp):
ATAAATTATCATGCAAG
Found at i:4329510 original size:15 final size:17
Alignment explanation
Indices: 4329490--4329527 Score: 53
Period size: 17 Copynumber: 2.4 Consensus size: 17
4329480 AAATTAAATC
4329490 AAAATT-AAAC-TAAAA
1 AAAATTAAAACATAAAA
*
4329505 AAAATTAAAACATAAAT
1 AAAATTAAAACATAAAA
4329522 AAAATT
1 AAAATT
4329528 TAGGGCTTAA
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
15 6 0.30
16 4 0.20
17 10 0.50
ACGTcount: A:0.71, C:0.05, G:0.00, T:0.24
Consensus pattern (17 bp):
AAAATTAAAACATAAAA
Found at i:4329525 original size:17 final size:15
Alignment explanation
Indices: 4329484--4329527 Score: 52
Period size: 17 Copynumber: 2.7 Consensus size: 15
4329474 AAACAAAAAT
4329484 TAAATCAAAATTAAAC
1 TAAAT-AAAATTAAAC
*
4329500 TAAAAAAAATTAAAAC
1 TAAATAAAATT-AAAC
4329516 ATAAATAAAATT
1 -TAAATAAAATT
4329528 TAGGGCTTAA
Statistics
Matches: 24, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
15 6 0.25
16 8 0.33
17 10 0.42
ACGTcount: A:0.68, C:0.07, G:0.00, T:0.25
Consensus pattern (15 bp):
TAAATAAAATTAAAC
Found at i:4333283 original size:20 final size:20
Alignment explanation
Indices: 4333261--4333297 Score: 58
Period size: 19 Copynumber: 1.9 Consensus size: 20
4333251 AATGCATAAA
*
4333261 AAAAGGGAA-AACCAAAAGG
1 AAAAGAGAAGAACCAAAAGG
4333280 AAAAGAGAAGAACCAAAA
1 AAAAGAGAAGAACCAAAA
4333298 TTTTTAGCTT
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
19 8 0.50
20 8 0.50
ACGTcount: A:0.68, C:0.11, G:0.22, T:0.00
Consensus pattern (20 bp):
AAAAGAGAAGAACCAAAAGG
Found at i:4333617 original size:7 final size:7
Alignment explanation
Indices: 4333605--4333664 Score: 65
Period size: 7 Copynumber: 9.1 Consensus size: 7
4333595 ATTATTATAT
4333605 TTTTTTC
1 TTTTTTC
4333612 TTTTTT-
1 TTTTTTC
*
4333618 ATTTTTC
1 TTTTTTC
4333625 TTTTTTC
1 TTTTTTC
**
4333632 TCCTTTC
1 TTTTTTC
4333639 -TTTTT-
1 TTTTTTC
4333644 TTTTTTC
1 TTTTTTC
4333651 TTTTTT-
1 TTTTTTC
4333657 TTTTTTC
1 TTTTTTC
4333664 T
1 T
4333665 GTTATGATCG
Statistics
Matches: 43, Mismatches: 6, Indels: 8
0.75 0.11 0.14
Matches are distributed among these distances:
6 19 0.44
7 24 0.56
ACGTcount: A:0.02, C:0.13, G:0.00, T:0.85
Consensus pattern (7 bp):
TTTTTTC
Found at i:4333619 original size:20 final size:19
Alignment explanation
Indices: 4333604--4333662 Score: 75
Period size: 20 Copynumber: 3.1 Consensus size: 19
4333594 TATTATTATA
4333604 TTTTTTTCTTTTTTATTTT
1 TTTTTTTCTTTTTTATTTT
** *
4333623 TCTTTTTTCTCCTTTCTTTT
1 T-TTTTTTCTTTTTTATTTT
4333643 TTTTTTTCTTTTTT-TTTT
1 TTTTTTTCTTTTTTATTTT
4333661 TT
1 TT
4333663 CTGTTATGAT
Statistics
Matches: 34, Mismatches: 5, Indels: 3
0.81 0.12 0.07
Matches are distributed among these distances:
18 6 0.18
19 12 0.35
20 16 0.47
ACGTcount: A:0.02, C:0.12, G:0.00, T:0.86
Consensus pattern (19 bp):
TTTTTTTCTTTTTTATTTT
Found at i:4333624 original size:13 final size:12
Alignment explanation
Indices: 4333604--4333661 Score: 80
Period size: 12 Copynumber: 4.6 Consensus size: 12
4333594 TATTATTATA
4333604 TTTTTTTCTTTT
1 TTTTTTTCTTTT
4333616 TTATTTTTCTTTT
1 TT-TTTTTCTTTT
*
4333629 TTCTCCTTTCTTTT
1 TT-T-TTTTCTTTT
4333643 TTTTTTTCTTTT
1 TTTTTTTCTTTT
4333655 TTTTTTT
1 TTTTTTT
4333662 TCTGTTATGA
Statistics
Matches: 41, Mismatches: 3, Indels: 4
0.85 0.06 0.08
Matches are distributed among these distances:
12 17 0.41
13 14 0.34
14 10 0.24
ACGTcount: A:0.02, C:0.12, G:0.00, T:0.86
Consensus pattern (12 bp):
TTTTTTTCTTTT
Found at i:4334695 original size:15 final size:14
Alignment explanation
Indices: 4334658--4334700 Score: 50
Period size: 15 Copynumber: 2.9 Consensus size: 14
4334648 TTTTTGAATT
4334658 TTTTTAGATTTTTTA
1 TTTTTA-ATTTTTTA
*
4334673 TATATTAATTTTGTTA
1 T-TTTTAATTTT-TTA
4334689 TTTTTAATTTTT
1 TTTTTAATTTTT
4334701 ATTATTAACA
Statistics
Matches: 24, Mismatches: 2, Indels: 5
0.77 0.06 0.16
Matches are distributed among these distances:
14 1 0.04
15 15 0.62
16 8 0.33
ACGTcount: A:0.23, C:0.00, G:0.05, T:0.72
Consensus pattern (14 bp):
TTTTTAATTTTTTA
Found at i:4334702 original size:13 final size:14
Alignment explanation
Indices: 4334665--4334708 Score: 54
Period size: 15 Copynumber: 3.1 Consensus size: 14
4334655 ATTTTTTTAG
4334665 ATTTTTTATATATTA
1 ATTTTTTAT-TATTA
*
4334680 ATTTTGTTATTTTTA
1 ATTTT-TTATTATTA
4334695 A-TTTTTATTATTA
1 ATTTTTTATTATTA
4334708 A
1 A
4334709 CATTTATGCA
Statistics
Matches: 26, Mismatches: 2, Indels: 4
0.81 0.06 0.12
Matches are distributed among these distances:
13 9 0.35
14 3 0.12
15 10 0.38
16 4 0.15
ACGTcount: A:0.30, C:0.00, G:0.02, T:0.68
Consensus pattern (14 bp):
ATTTTTTATTATTA
Found at i:4335994 original size:16 final size:17
Alignment explanation
Indices: 4335965--4336002 Score: 53
Period size: 16 Copynumber: 2.3 Consensus size: 17
4335955 TTTTACTTTT
4335965 TAAAAAAAGCCAAACAAA
1 TAAAAAAA-CCAAACAAA
4335983 TAAAAAAA-CAAACAAA
1 TAAAAAAACCAAACAAA
4335999 -AAAA
1 TAAAA
4336003 TGAAAAAATT
Statistics
Matches: 20, Mismatches: 0, Indels: 3
0.87 0.00 0.13
Matches are distributed among these distances:
15 4 0.20
16 8 0.40
18 8 0.40
ACGTcount: A:0.79, C:0.13, G:0.03, T:0.05
Consensus pattern (17 bp):
TAAAAAAACCAAACAAA
Found at i:4347110 original size:49 final size:48
Alignment explanation
Indices: 4347053--4347217 Score: 210
Period size: 48 Copynumber: 3.4 Consensus size: 48
4347043 TCAAGAACAT
* *
4347053 ATGAGATTTTTAAAGTTATTGAGCCTCTGTTAAGAAAAGCTTTTTGAAG
1 ATGAGATTTTTAAAGTTGTTGAGCCTCTGTT-AGAAAAGCTTTTTCAAG
* * *
4347102 ATGAGATTTTTAAAGTTGTTGAACCTCTACTTAGAAGAGCTTTTTCAAG
1 ATGAGATTTTTAAAGTTGTTGAGCCTCT-GTTAGAAAAGCTTTTTCAAG
* *
4347151 AT-AGATTTTTAAAGTTGTTGAGCCTTTGTTTAGAGAAA-CTTTTTTAAG
1 ATGAGATTTTTAAAGTTGTTGAGCCTCTG-TTAGA-AAAGCTTTTTCAAG
4347199 ATGA-ATTTTTAAAGTTGTT
1 ATGAGATTTTTAAAGTTGTT
4347218 AAGCTTCTAC
Statistics
Matches: 102, Mismatches: 10, Indels: 9
0.84 0.08 0.07
Matches are distributed among these distances:
48 54 0.53
49 46 0.45
50 2 0.02
ACGTcount: A:0.31, C:0.08, G:0.19, T:0.42
Consensus pattern (48 bp):
ATGAGATTTTTAAAGTTGTTGAGCCTCTGTTAGAAAAGCTTTTTCAAG
Found at i:4347170 original size:48 final size:48
Alignment explanation
Indices: 4347056--4347237 Score: 174
Period size: 48 Copynumber: 3.8 Consensus size: 48
4347046 AGAACATATG
* * * * *
4347056 AGATTTTTAAAGTTATTGAGCCTCT-GTTAAGAAAAGCTTTTTGAAGAT
1 AGATTTTTAAAGTTGTTGAACCTCTACTT-AGAAGAGCTTTTTCAAGAT
4347104 GAGATTTTTAAAGTTGTTGAACCTCTACTTAGAAGAGCTTTTTCAAGAT
1 -AGATTTTTAAAGTTGTTGAACCTCTACTTAGAAGAGCTTTTTCAAGAT
* * ** * *
4347153 AGATTTTTAAAGTTGTTGAGCCTTTGTTTAG-AGAAACTTTTTTAAGAT
1 AGATTTTTAAAGTTGTTGAACCTCTACTTAGAAG-AGCTTTTTCAAGAT
* *
4347201 -GAATTTTTAAAGTTGTT-AAGCTTCTACTTAGAGGAGC
1 AG-ATTTTTAAAGTTGTTGAA-CCTCTACTTAGAAGAGC
4347238 CTTTCTAAAT
Statistics
Matches: 110, Mismatches: 18, Indels: 11
0.79 0.13 0.08
Matches are distributed among these distances:
47 4 0.04
48 63 0.57
49 41 0.37
50 2 0.02
ACGTcount: A:0.31, C:0.09, G:0.19, T:0.41
Consensus pattern (48 bp):
AGATTTTTAAAGTTGTTGAACCTCTACTTAGAAGAGCTTTTTCAAGAT
Found at i:4347265 original size:44 final size:42
Alignment explanation
Indices: 4347202--4347424 Score: 222
Period size: 44 Copynumber: 5.3 Consensus size: 42
4347192 TTTTAAGATG
*
4347202 AATTTTT-AAAGTTGTTAAGCTTCTACTTAGAGGAGCCTTTCTA
1 AATTTTTAAAAGTTGTTAAGCCTCTACTTAGAGGAG-CTTT-TA
* *
4347245 AATTTTTAAAAGTTGTTAAGCCTCTGCTTAAAGGAGCTTATTTA
1 AATTTTTAAAAGTTGTTAAGCCTCTACTTAGAGGAGC-T-TTTA
* * *
4347289 AATTTTTAAAAGTTGTTGAGCCTCTACTCAGAGAAGC-TTT-
1 AATTTTTAAAAGTTGTTAAGCCTCTACTTAGAGGAGCTTTTA
* * *
4347329 --TTTTCAAAAGTTGTTATGCCTCTGCTTAGAGGAGCCTATTTA
1 AATTTTTAAAAGTTGTTAAGCCTCTACTTAGAGGAG-CT-TTTA
* * * *
4347371 AATTTTTAAAAGTTGTTGAGCCTTTACTCAGAGAAGCTTTTTA
1 AATTTTTAAAAGTTGTTAAGCCTCTACTTAGAGGAGC-TTTTA
*
4347414 AATTTTCAAAA
1 AATTTTTAAAA
4347425 ATATCATTGA
Statistics
Matches: 148, Mismatches: 22, Indels: 20
0.78 0.12 0.11
Matches are distributed among these distances:
38 28 0.19
39 1 0.01
41 6 0.04
43 23 0.16
44 88 0.59
45 2 0.01
ACGTcount: A:0.30, C:0.13, G:0.16, T:0.40
Consensus pattern (42 bp):
AATTTTTAAAAGTTGTTAAGCCTCTACTTAGAGGAGCTTTTA
Found at i:4347339 original size:38 final size:37
Alignment explanation
Indices: 4347291--4347412 Score: 120
Period size: 38 Copynumber: 3.1 Consensus size: 37
4347281 CTTATTTAAA
4347291 TTTTTAAAAGTTGTTGAGCCTCTACTCAGAGAAGCTT
1 TTTTTAAAAGTTGTTGAGCCTCTACTCAGAGAAGCTT
* * *
4347328 TTTTTCAAAAGTTGTT-ATGCCTCTGCTTAGAGGAGCCTATTT
1 TTTTT-AAAAGTTGTTGA-GCCTCTACTCAGAGAAG-C---TT
*
4347370 AAATTTTTAAAAGTTGTTGAGCCTTTACTCAGAGAAGCTT
1 ---TTTTTAAAAGTTGTTGAGCCTCTACTCAGAGAAGCTT
4347410 TTT
1 TTT
4347413 AAATTTTCAA
Statistics
Matches: 68, Mismatches: 7, Indels: 20
0.72 0.07 0.21
Matches are distributed among these distances:
37 9 0.13
38 24 0.35
39 1 0.01
40 2 0.03
42 2 0.03
43 1 0.01
44 23 0.34
45 6 0.09
ACGTcount: A:0.26, C:0.15, G:0.18, T:0.41
Consensus pattern (37 bp):
TTTTTAAAAGTTGTTGAGCCTCTACTCAGAGAAGCTT
Found at i:4347350 original size:82 final size:81
Alignment explanation
Indices: 4347247--4347412 Score: 287
Period size: 82 Copynumber: 2.0 Consensus size: 81
4347237 CCTTTCTAAA
*
4347247 TTTTTAAAAGTTGTTAAGCCTCTGCTTAAAGGAGCTTATTTAAATTTTTAAAAGTTGTTGAGCCT
1 TTTTTAAAAGTTGTTAAGCCTCTGCTTAAAGGAGCCTATTTAAATTTTTAAAAGTTGTTGAGCCT
4347312 CTACTCAGAGAAGCTT
66 CTACTCAGAGAAGCTT
* *
4347328 TTTTTCAAAAGTTGTTATGCCTCTGCTTAGAGGAGCCTATTTAAATTTTTAAAAGTTGTTGAGCC
1 TTTTT-AAAAGTTGTTAAGCCTCTGCTTAAAGGAGCCTATTTAAATTTTTAAAAGTTGTTGAGCC
*
4347393 TTTACTCAGAGAAGCTT
65 TCTACTCAGAGAAGCTT
4347410 TTT
1 TTT
4347413 AAATTTTCAA
Statistics
Matches: 80, Mismatches: 4, Indels: 1
0.94 0.05 0.01
Matches are distributed among these distances:
81 5 0.06
82 75 0.94
ACGTcount: A:0.28, C:0.14, G:0.17, T:0.41
Consensus pattern (81 bp):
TTTTTAAAAGTTGTTAAGCCTCTGCTTAAAGGAGCCTATTTAAATTTTTAAAAGTTGTTGAGCCT
CTACTCAGAGAAGCTT
Found at i:4347619 original size:22 final size:24
Alignment explanation
Indices: 4347588--4347656 Score: 72
Period size: 26 Copynumber: 2.9 Consensus size: 24
4347578 TGTATTATTA
4347588 TTATTATTATTTTTTTC-TCTTT-T
1 TTATT-TTATTTTTTTCTTCTTTCT
4347611 TTATTTTA-TTTTTTCTTCTTTCT
1 TTATTTTATTTTTTTCTTCTTTCT
* *
4347634 TTCTTTTTTTTTTCTTTCTTCTT
1 TT-ATTTTATTTT-TTTCTTCTT
4347657 CTTATTCTTT
Statistics
Matches: 39, Mismatches: 2, Indels: 7
0.81 0.04 0.15
Matches are distributed among these distances:
21 7 0.18
22 8 0.21
23 8 0.21
24 4 0.10
25 3 0.08
26 9 0.23
ACGTcount: A:0.07, C:0.13, G:0.00, T:0.80
Consensus pattern (24 bp):
TTATTTTATTTTTTTCTTCTTTCT
Found at i:4347627 original size:19 final size:19
Alignment explanation
Indices: 4347599--4347669 Score: 52
Period size: 20 Copynumber: 3.4 Consensus size: 19
4347589 TATTATTATT
4347599 TTTTTCTCTTTTTTATTTTA
1 TTTTT-TCTTTTTTATTTTA
* *
4347619 TTTTTTCTTCTTTCTTTCTTTT
1 TTTTTTCTT-TTT-TAT-TTTA
* *
4347641 TTTTTTCTTTCTTCTTCTTA
1 TTTTTTCTTTTTTATT-TTA
4347661 TTCTTTTCT
1 TT-TTTTCT
4347670 ATTCTAATCG
Statistics
Matches: 41, Mismatches: 5, Indels: 9
0.75 0.09 0.16
Matches are distributed among these distances:
19 5 0.12
20 14 0.34
21 10 0.24
22 12 0.29
ACGTcount: A:0.04, C:0.17, G:0.00, T:0.79
Consensus pattern (19 bp):
TTTTTTCTTTTTTATTTTA
Found at i:4347667 original size:22 final size:21
Alignment explanation
Indices: 4347594--4347667 Score: 73
Period size: 22 Copynumber: 3.5 Consensus size: 21
4347584 ATTATTATTA
*
4347594 TTATTTTTTTCTCTTT-TTTATT
1 TTATTTTTTT-TCTTTCTTT-TC
4347616 TTATTTTTTCTTCTTTC-TTTC
1 TTATTTTTT-TTCTTTCTTTTC
4347637 TT-TTTTTTTTCTTTCTTCTTC
1 TTATTTTTTTTCTTTCTT-TTC
*
4347658 TTATTCTTTT
1 TTATTTTTTT
4347668 CTATTCTAAT
Statistics
Matches: 45, Mismatches: 2, Indels: 10
0.79 0.04 0.18
Matches are distributed among these distances:
19 7 0.16
20 7 0.16
21 8 0.18
22 22 0.49
23 1 0.02
ACGTcount: A:0.05, C:0.15, G:0.00, T:0.80
Consensus pattern (21 bp):
TTATTTTTTTTCTTTCTTTTC
Found at i:4354444 original size:21 final size:21
Alignment explanation
Indices: 4354415--4354471 Score: 71
Period size: 22 Copynumber: 2.7 Consensus size: 21
4354405 CATAATTTTT
*
4354415 AAATAAAAAAATTAAAAT-TA
1 AAATAAAAAAATTAAAATAAA
* *
4354435 AAATTAAAAAATGAAAAATAAA
1 AAATAAAAAAAT-TAAAATAAA
4354457 AAATAAAAAAATTAA
1 AAATAAAAAAATTAA
4354472 GTTGTAATAA
Statistics
Matches: 30, Mismatches: 5, Indels: 3
0.79 0.13 0.08
Matches are distributed among these distances:
20 11 0.37
21 7 0.23
22 12 0.40
ACGTcount: A:0.77, C:0.00, G:0.02, T:0.21
Consensus pattern (21 bp):
AAATAAAAAAATTAAAATAAA
Found at i:4354457 original size:6 final size:7
Alignment explanation
Indices: 4354415--4354466 Score: 52
Period size: 7 Copynumber: 7.4 Consensus size: 7
4354405 CATAATTTTT
4354415 AAATAAA
1 AAATAAA
*
4354422 AAA-ATTA
1 AAATA-AA
*
4354429 AAATTAA
1 AAATAAA
*
4354436 AATTAAA
1 AAATAAA
*
4354443 AAATGAA
1 AAATAAA
4354450 AAATAAA
1 AAATAAA
4354457 AAATAAA
1 AAATAAA
4354464 AAA
1 AAA
4354467 ATTAAGTTGT
Statistics
Matches: 35, Mismatches: 8, Indels: 4
0.74 0.17 0.09
Matches are distributed among these distances:
6 1 0.03
7 34 0.97
ACGTcount: A:0.79, C:0.00, G:0.02, T:0.19
Consensus pattern (7 bp):
AAATAAA
Found at i:4354759 original size:2 final size:2
Alignment explanation
Indices: 4354754--4354798 Score: 56
Period size: 2 Copynumber: 23.0 Consensus size: 2
4354744 ATACACACGC
* * *
4354754 AT AT AT AT AT AT AT AT AT AT GT A- AC AT AT AT AT AT AT TT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
4354795 AT AT
1 AT AT
4354799 GACTGTTCTG
Statistics
Matches: 37, Mismatches: 5, Indels: 2
0.84 0.11 0.05
Matches are distributed among these distances:
1 1 0.03
2 36 0.97
ACGTcount: A:0.47, C:0.02, G:0.02, T:0.49
Consensus pattern (2 bp):
AT
Found at i:4358206 original size:213 final size:210
Alignment explanation
Indices: 4357832--4358213 Score: 439
Period size: 213 Copynumber: 1.8 Consensus size: 210
4357822 AGAAAAATTT
* * * *
4357832 TTTTTATTATATTGAAGATTTTCTATAAATATTTCAATACGCTGGTAATATTAAAAAAAAATCTT
1 TTTTTATTATATTGAAAATTTTCTATAAATACTCCAATACACTGGTAATATTAAAAAAAAATCTT
* * * * ** * * * *
4357897 TTTACCTAGGGATTTCTTAAAGCATTTCTACTCGGAATACTTTTAGAATCCCACATTGGATAAAA
66 ATCACCTAGAGATTTCGTAAAGCATCACTACTCGAAATACTTTTAGAATCCCACATCGAAAAAAA
* * *
4357962 TTTCTTTTCTTTTCATTTTTACTTCTTATATTTTTAATTTATTAATCAATTTTTATTTATTACTT
131 TTCCTTTTCTTTT-ATTTTTAATTCTTATATTATTAATTTATTAATCAATTTTTATTTATTACTT
4358027 AAAGAAAAAAAAAAAA
195 AAAGAAAAAAAAAAAA
* * * *
4358043 TTTTTATTGTATTGAAAAATTATTTTATAAATACTCCAATACACTGGTAGTATTTTAAAAAAAAT
1 TTTTTATTATATTG-AAAATT-TTCTATAAATACTCCAATACACTGGTAATA-TTAAAAAAAAAT
* * * *
4358108 CTTATCACTTAGAGATTTCGT-AGGCATCACTACTCGAAATACTTTT-GAATCTCATCGTCGAAA
63 CTTATCACCTAGAGATTTCGTAAAGCATCACTACTCGAAATACTTTTAGAATCCCA-CATCGAAA
4358171 AAAATTCCTTTTCTTATT-TTTTATCAATT-TTATATTATTAATT
127 AAAATTCCTTTTCTT-TTATTTT-T-AATTCTTATATTATTAATT
4358214 AATATTATAA
Statistics
Matches: 139, Mismatches: 25, Indels: 12
0.79 0.14 0.07
Matches are distributed among these distances:
211 13 0.09
212 16 0.12
213 78 0.56
214 32 0.23
ACGTcount: A:0.35, C:0.12, G:0.08, T:0.45
Consensus pattern (210 bp):
TTTTTATTATATTGAAAATTTTCTATAAATACTCCAATACACTGGTAATATTAAAAAAAAATCTT
ATCACCTAGAGATTTCGTAAAGCATCACTACTCGAAATACTTTTAGAATCCCACATCGAAAAAAA
TTCCTTTTCTTTTATTTTTAATTCTTATATTATTAATTTATTAATCAATTTTTATTTATTACTTA
AAGAAAAAAAAAAAA
Found at i:4358312 original size:20 final size:19
Alignment explanation
Indices: 4358280--4358317 Score: 51
Period size: 20 Copynumber: 1.9 Consensus size: 19
4358270 AAATATTAAT
4358280 AATAATAATTAAAATAAAAA
1 AATAATAATTAAAA-AAAAA
4358300 AATAAT-ATATAAAAAAAA
1 AATAATAAT-TAAAAAAAA
4358318 TCTTTAAAAA
Statistics
Matches: 17, Mismatches: 0, Indels: 3
0.85 0.00 0.15
Matches are distributed among these distances:
19 6 0.35
20 11 0.65
ACGTcount: A:0.76, C:0.00, G:0.00, T:0.24
Consensus pattern (19 bp):
AATAATAATTAAAAAAAAA
Found at i:4358985 original size:18 final size:17
Alignment explanation
Indices: 4358962--4359006 Score: 54
Period size: 18 Copynumber: 2.5 Consensus size: 17
4358952 TAAACCAGAT
*
4358962 AAGAAAAAAGAAGAAGAA
1 AAGAAAAAAGAA-AAAAA
*
4358980 AAGAAAGAAGAAAAAAA
1 AAGAAAAAAGAAAAAAA
4358997 ATAGAAAAAA
1 A-AGAAAAAA
4359007 TAGAAAACAA
Statistics
Matches: 23, Mismatches: 3, Indels: 2
0.82 0.11 0.07
Matches are distributed among these distances:
17 5 0.22
18 18 0.78
ACGTcount: A:0.80, C:0.00, G:0.18, T:0.02
Consensus pattern (17 bp):
AAGAAAAAAGAAAAAAA
Found at i:4359289 original size:51 final size:50
Alignment explanation
Indices: 4359209--4359752 Score: 425
Period size: 51 Copynumber: 10.6 Consensus size: 50
4359199 ATTTAAAAGG
* *
4359209 CTCATCTTAGCAGAGGCTCAACAATTTTAAGAATCTCTCATCTTGGAAAAA
1 CTCATCTCAGCAGAGGCTCAACAACTTTAA-AATCTCTCATCTTGGAAAAA
*
4359260 CTCATCTCAGCTGAGGCTCAACAACTTTAAGAATCTCTCATCTTGGAAAAA
1 CTCATCTCAGCAGAGGCTCAACAACTTTAA-AATCTCTCATCTTGGAAAAA
*
4359311 CTCATCTCAGCTGAGGCTCAACAACTTTAAGAATCTCTCATCTTGGAAAAA
1 CTCATCTCAGCAGAGGCTCAACAACTTTAA-AATCTCTCATCTTGGAAAAA
* ** * *
4359362 CTCATCTCAGCTGAGGCTCAACAACTTTAACTTTAAAAATCTGAT-TTTGAAAAA
1 CTCATCTCAGCAGAGGCTCAACAACTTT-A----AAATCTCTCATCTTGGAAAAA
* ** * *
4359416 GCTCCTCTCAATAGAGGCTCAACAACTTTAACTTTTAAAAAGCTC-CAATCTTGGAAAAG
1 -CTCATCTCAGCAGAGGCT---CAAC---AAC-TTT-AAAATCTCTC-ATCTTGGAAAAA
* * * *
4359475 CTCCTCTCAGCAAAGGCTTAACAACTTTAAAAT-T-TCAT-TTGAAAAAA
1 CTCATCTCAGCAGAGGCTCAACAACTTTAAAATCTCTCATCTTGGAAAAA
* *
4359522 CTCCTTATCAGCAGAGGCTCAACAACTTTAAAAAT-T-TCATCTT-GAAAAA
1 CT-CATCTCAGCAGAGGCTCAACAACTTT-AAAATCTCTCATCTTGGAAAAA
* * *
4359571 GCTCCTTTCAGCAGAGGTTCAACAACTTTAAAATCTCAT-ATCTT-GAAAAGGA
1 -CTCATCTCAGCAGAGGCTCAACAACTTTAAAATCTC-TCATCTTGGAAAA--A
* * * * *
4359623 CTCCTCTCAGCAGAGGTTCAACAACTTTAAAA-ATCTCATCTT-TAAAAGGG
1 CTCATCTCAGCAGAGGCTCAACAACTTTAAAATCTCTCATCTTGGAAAA--A
** * *
4359673 CTCATCTCAATAGAGGCTCAACAACTTTAAAA--TCTCAT-TTCGAAAGAG
1 CTCATCTCAGCAGAGGCTCAACAACTTTAAAATCTCTCATCTTGGAAA-AA
* * *
4359721 CTCTTTTCAACAGAGGCTCAACAACTTTAAAA
1 CTCATCTCAGCAGAGGCTCAACAACTTTAAAA
4359753 AATTTTCATA
Statistics
Matches: 422, Mismatches: 43, Indels: 59
0.81 0.08 0.11
Matches are distributed among these distances:
47 9 0.02
48 61 0.14
49 51 0.12
50 60 0.14
51 162 0.38
52 5 0.01
54 8 0.02
55 24 0.06
56 1 0.00
58 26 0.06
59 7 0.02
61 3 0.01
62 5 0.01
ACGTcount: A:0.36, C:0.23, G:0.12, T:0.28
Consensus pattern (50 bp):
CTCATCTCAGCAGAGGCTCAACAACTTTAAAATCTCTCATCTTGGAAAAA
Found at i:4359442 original size:55 final size:57
Alignment explanation
Indices: 4359350--4359504 Score: 172
Period size: 58 Copynumber: 2.7 Consensus size: 57
4359340 AGAATCTCTC
* * * **
4359350 ATCTTGGAAAAA-CTCATCTCAGCTGAGGCTCAACAACTTTAAC-TTTAAAAA-TCTG
1 ATCTT-GAAAAAGCTCCTCTCAACAGAGGCTCAACAACTTTAACTTTTAAAAACTCCA
* *
4359405 ATTTTGAAAAAGCTCCTCTCAATAGAGGCTCAACAACTTTAACTTTTAAAAAGCTCCA
1 ATCTTGAAAAAGCTCCTCTCAACAGAGGCTCAACAACTTTAACTTTTAAAAA-CTCCA
* * * *
4359463 ATCTTGGAAAAGCTCCTCTCAGCAAAGGCTTAACAACTTTAA
1 ATCTTGAAAAAGCTCCTCTCAACAGAGGCTCAACAACTTTAA
4359505 AATTTCATTT
Statistics
Matches: 83, Mismatches: 13, Indels: 5
0.82 0.13 0.05
Matches are distributed among these distances:
54 6 0.07
55 31 0.37
56 8 0.10
58 38 0.46
ACGTcount: A:0.37, C:0.23, G:0.12, T:0.28
Consensus pattern (57 bp):
ATCTTGAAAAAGCTCCTCTCAACAGAGGCTCAACAACTTTAACTTTTAAAAACTCCA
Found at i:4359534 original size:48 final size:48
Alignment explanation
Indices: 4359463--4359752 Score: 262
Period size: 48 Copynumber: 5.9 Consensus size: 48
4359453 AAAAGCTCCA
* * * *
4359463 ATCTTGGAAAAGCTCCTCTCAGCAAAGGCTT-AACAACTTTAAAATTTC
1 ATCTTGAAAAAACTCCTTTCAGCAGAGG-TTCAACAACTTTAAAATTTC
*
4359511 AT-TTGAAAAAACTCCTTATCAGCAGAGGCTCAACAACTTTAAAAATTTC
1 ATCTTGAAAAAACTCCTT-TCAGCAGAGGTTCAACAACTTT-AAAATTTC
* *
4359560 ATCTTGAAAAAGCTCCTTTCAGCAGAGGTTCAACAACTTTAAAATCTC
1 ATCTTGAAAAAACTCCTTTCAGCAGAGGTTCAACAACTTTAAAATTTC
* * *
4359608 ATATCTTGAAAAGGACTCCTCTCAGCAGAGGTTCAACAACTTTAAAAATCTC
1 --ATCTTGAAAA-AACTCCTTTCAGCAGAGGTTCAACAACTTT-AAAATTTC
* ** * * ** * *
4359660 ATCTTTAAAAGGGCTCATCTCAATAGAGGCTCAACAACTTTAAAATCTC
1 ATCTTGAAAA-AACTCCTTTCAGCAGAGGTTCAACAACTTTAAAATTTC
* * * * *
4359709 AT-TTCGAAAGAGCTCTTTTCAACAGAGGCTCAACAACTTTAAAA
1 ATCTT-GAAAAAACTCCTTTCAGCAGAGGTTCAACAACTTTAAAA
4359753 AATTTTCATA
Statistics
Matches: 210, Mismatches: 23, Indels: 18
0.84 0.09 0.07
Matches are distributed among these distances:
47 13 0.06
48 59 0.28
49 44 0.21
50 59 0.28
51 27 0.13
52 8 0.04
ACGTcount: A:0.37, C:0.22, G:0.12, T:0.28
Consensus pattern (48 bp):
ATCTTGAAAAAACTCCTTTCAGCAGAGGTTCAACAACTTTAAAATTTC
Found at i:4359662 original size:100 final size:98
Alignment explanation
Indices: 4359529--4359753 Score: 283
Period size: 100 Copynumber: 2.3 Consensus size: 98
4359519 AAACTCCTTA
* * * * *
4359529 TCAGCAGAGGCTCAACAACTTTAAAAATTTCATCTTGAAAA-AGCTCCTTTCAGCAGAGGTTCAA
1 TCAGCAGAGGCTCAACAACTTTAAAAATCTCATCTTGAAAAGAGCTCATCTCAACAGAGGCTCAA
*
4359593 CAACTTTAAAATCTCATATCTTGAAA-AGGACTCCTC
66 CAACTTTAAAATCTCAT-T-TCGAAAGA-G-CTCCTC
* * * *
4359629 TCAGCAGAGGTTCAACAACTTTAAAAATCTCATCTTTAAAAGGGCTCATCTCAATAGAGGCTCAA
1 TCAGCAGAGGCTCAACAACTTTAAAAATCTCATCTTGAAAAGAGCTCATCTCAACAGAGGCTCAA
* *
4359694 CAACTTTAAAATCTCATTTCGAAAGAGCTCTTT
66 CAACTTTAAAATCTCATTTCGAAAGAGCTCCTC
*
4359727 TCAACAGAGGCTCAACAACTTTAAAAA
1 TCAGCAGAGGCTCAACAACTTTAAAAA
4359754 ATTTTCATAT
Statistics
Matches: 109, Mismatches: 14, Indels: 6
0.84 0.11 0.05
Matches are distributed among these distances:
98 29 0.27
99 6 0.06
100 40 0.37
101 34 0.31
ACGTcount: A:0.37, C:0.22, G:0.13, T:0.28
Consensus pattern (98 bp):
TCAGCAGAGGCTCAACAACTTTAAAAATCTCATCTTGAAAAGAGCTCATCTCAACAGAGGCTCAA
CAACTTTAAAATCTCATTTCGAAAGAGCTCCTC
Found at i:4367898 original size:15 final size:16
Alignment explanation
Indices: 4367866--4367899 Score: 52
Period size: 15 Copynumber: 2.2 Consensus size: 16
4367856 CATGTGTCAA
*
4367866 AAATTTTATTTTTTTT
1 AAATTTTATTTGTTTT
4367882 AAATTTT-TTTGTTTT
1 AAATTTTATTTGTTTT
4367897 AAA
1 AAA
4367900 AAAAATGGTG
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
15 10 0.59
16 7 0.41
ACGTcount: A:0.29, C:0.00, G:0.03, T:0.68
Consensus pattern (16 bp):
AAATTTTATTTGTTTT
Found at i:4371517 original size:20 final size:17
Alignment explanation
Indices: 4371492--4371533 Score: 57
Period size: 20 Copynumber: 2.3 Consensus size: 17
4371482 TTTAAAAATA
4371492 ATTTTATTAATTGTTTTATT
1 ATTTTATT-ATT-TTTT-TT
4371512 ATTTTATTATTTTTTTT
1 ATTTTATTATTTTTTTT
4371529 ATTTT
1 ATTTT
4371534 GAAGAAAAAT
Statistics
Matches: 22, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
17 7 0.32
18 4 0.18
19 3 0.14
20 8 0.36
ACGTcount: A:0.21, C:0.00, G:0.02, T:0.76
Consensus pattern (17 bp):
ATTTTATTATTTTTTTT
Found at i:4379260 original size:24 final size:23
Alignment explanation
Indices: 4379219--4379268 Score: 55
Period size: 24 Copynumber: 2.1 Consensus size: 23
4379209 ATACTAAGAG
* * * *
4379219 AAAAAATACTAAATAAAATAAATA
1 AAAAAACACCAAAGAAAACAAA-A
4379243 AAAAAACACCAAAGAAAACAAAA
1 AAAAAACACCAAAGAAAACAAAA
4379266 AAA
1 AAA
4379269 TGGCTCAGCT
Statistics
Matches: 22, Mismatches: 4, Indels: 1
0.81 0.15 0.04
Matches are distributed among these distances:
23 4 0.18
24 18 0.82
ACGTcount: A:0.78, C:0.10, G:0.02, T:0.10
Consensus pattern (23 bp):
AAAAAACACCAAAGAAAACAAAA
Found at i:4380060 original size:15 final size:15
Alignment explanation
Indices: 4380037--4380067 Score: 53
Period size: 15 Copynumber: 2.1 Consensus size: 15
4380027 AACCTTCTTC
*
4380037 ATTTTTTATTTTTTT
1 ATTTATTATTTTTTT
4380052 ATTTATTATTTTTTT
1 ATTTATTATTTTTTT
4380067 A
1 A
4380068 ATTTTAATCA
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.19, C:0.00, G:0.00, T:0.81
Consensus pattern (15 bp):
ATTTATTATTTTTTT
Found at i:4380479 original size:41 final size:40
Alignment explanation
Indices: 4380381--4380636 Score: 239
Period size: 42 Copynumber: 6.1 Consensus size: 40
4380371 AGTAATAAAA
*
4380381 CTCCTCTAAATAGAGGCTCAACGACTTTGAGAAACATAAA-TG
1 CTCCTCTAAATAGAGG--CAACGACTTTGA-AAAAATAAATTG
* *** *
4380423 CTCATCTATGCAGAGGTTCAATGACTTTG-AAAAATAAATTG
1 CTCCTCTAAATAGAGG--CAACGACTTTGAAAAAATAAATTG
* *
4380464 CTCCTCTAAATAGAGGCAACACAACTTTGAAAAAATAAATTA
1 CTCCTCTAAATAGAGGC-A-ACGACTTTGAAAAAATAAATTG
* * * *
4380506 CTCCTTTAAATAGAGGTAACAAAAC-TTAAAAAAATAAATTG
1 CTCCTCTAAATAGAGGCAAC--GACTTTGAAAAAATAAATTG
*
4380547 CTCCTCTAAATAGAGGCAACAGTACTTTGAAAAAATAAATTA
1 CTCCTCTAAATAGAGGCAAC-G-ACTTTGAAAAAATAAATTG
*
4380589 CTCCTCTAAATAGAGGCAATAGAACTTTGAAAAAAATAAATTG
1 CTCCTCTAAATAGAGGCAA-CG-ACTTTG-AAAAAATAAATTG
4380632 CTCCT
1 CTCCT
4380637 GGACAATCAT
Statistics
Matches: 178, Mismatches: 26, Indels: 19
0.80 0.12 0.09
Matches are distributed among these distances:
39 1 0.01
40 12 0.07
41 56 0.31
42 92 0.52
43 17 0.10
ACGTcount: A:0.43, C:0.17, G:0.13, T:0.27
Consensus pattern (40 bp):
CTCCTCTAAATAGAGGCAACGACTTTGAAAAAATAAATTG
Found at i:4380510 original size:42 final size:42
Alignment explanation
Indices: 4380446--4380636 Score: 278
Period size: 42 Copynumber: 4.6 Consensus size: 42
4380436 AGGTTCAATG
*
4380446 ACTTTG-AAAAATAAATTGCTCCTCTAAATAGAGGCAACACA
1 ACTTTGAAAAAATAAATTGCTCCTCTAAATAGAGGCAACAGA
* * * *
4380487 ACTTTGAAAAAATAAATTACTCCTTTAAATAGAGGTAACAAA
1 ACTTTGAAAAAATAAATTGCTCCTCTAAATAGAGGCAACAGA
* *
4380529 AC-TTAAAAAAATAAATTGCTCCTCTAAATAGAGGCAACAGT
1 ACTTTGAAAAAATAAATTGCTCCTCTAAATAGAGGCAACAGA
* *
4380570 ACTTTGAAAAAATAAATTACTCCTCTAAATAGAGGCAATAGA
1 ACTTTGAAAAAATAAATTGCTCCTCTAAATAGAGGCAACAGA
4380612 ACTTTGAAAAAAATAAATTGCTCCT
1 ACTTTG-AAAAAATAAATTGCTCCT
4380637 GGACAATCAT
Statistics
Matches: 132, Mismatches: 15, Indels: 4
0.87 0.10 0.03
Matches are distributed among these distances:
41 41 0.31
42 74 0.56
43 17 0.13
ACGTcount: A:0.47, C:0.16, G:0.11, T:0.27
Consensus pattern (42 bp):
ACTTTGAAAAAATAAATTGCTCCTCTAAATAGAGGCAACAGA
Found at i:4380521 original size:83 final size:82
Alignment explanation
Indices: 4380381--4380636 Score: 277
Period size: 83 Copynumber: 3.1 Consensus size: 82
4380371 AGTAATAAAA
* * * * * ***
4380381 CTCCTCTAAATAGAGGC-TCAACGACTTTGAGAAACATAAA-TGCTCATCTATGCAGAGGTTCAA
1 CTCCTCTAAATAGAGGCAAC-ACAACTTTGA-AAAAATAAATTACTCCTCTAAATAGAGG-TCAA
4380444 TGACTTTGAAAAATAAATTG
63 TGACTTTGAAAAATAAATTG
*
4380464 CTCCTCTAAATAGAGGCAACACAACTTTGAAAAAATAAATTACTCCTTTAAATAGAGGTAACAA-
1 CTCCTCTAAATAGAGGCAACACAACTTTGAAAAAATAAATTACTCCTCTAAATAGAGGT--CAAT
* **
4380528 AACTTAAAAAAATAAATTG
64 GACTTTGAAAAATAAATTG
**
4380547 CTCCTCTAAATAGAGGCAACAGTACTTTGAAAAAATAAATTACTCCTCTAAATAGAGG-CAATAG
1 CTCCTCTAAATAGAGGCAACACAACTTTGAAAAAATAAATTACTCCTCTAAATAGAGGTCAAT-G
4380611 AACTTTGAAAAAAATAAATTG
65 -ACTTTG--AAAAATAAATTG
4380632 CTCCT
1 CTCCT
4380637 GGACAATCAT
Statistics
Matches: 146, Mismatches: 18, Indels: 16
0.81 0.10 0.09
Matches are distributed among these distances:
80 3 0.02
82 9 0.06
83 113 0.77
84 4 0.03
85 17 0.12
ACGTcount: A:0.43, C:0.17, G:0.13, T:0.27
Consensus pattern (82 bp):
CTCCTCTAAATAGAGGCAACACAACTTTGAAAAAATAAATTACTCCTCTAAATAGAGGTCAATGA
CTTTGAAAAATAAATTG
Found at i:4380855 original size:16 final size:16
Alignment explanation
Indices: 4380813--4380855 Score: 50
Period size: 16 Copynumber: 2.7 Consensus size: 16
4380803 AATTTGATTG
*
4380813 GCAAAATTTTAGATGT
1 GCAAGATTTTAGATGT
* *
4380829 GCAAGAATTTAGATTT
1 GCAAGATTTTAGATGT
*
4380845 GTAAGATTTTA
1 GCAAGATTTTA
4380856 AAATTTGCAT
Statistics
Matches: 22, Mismatches: 5, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
16 22 1.00
ACGTcount: A:0.37, C:0.05, G:0.19, T:0.40
Consensus pattern (16 bp):
GCAAGATTTTAGATGT
Found at i:4381027 original size:21 final size:22
Alignment explanation
Indices: 4380996--4381050 Score: 58
Period size: 21 Copynumber: 2.5 Consensus size: 22
4380986 GGTTTCACAT
* *
4380996 CTCAAATATTCTCGTTTGA-AA
1 CTCAAAAATTCTCATTTGAGAA
* * *
4381017 TTCAAAGATTCGCATTTGAGAA
1 CTCAAAAATTCTCATTTGAGAA
4381039 CTCAAAAATTCT
1 CTCAAAAATTCT
4381051 TATTAAAAGA
Statistics
Matches: 26, Mismatches: 7, Indels: 1
0.76 0.21 0.03
Matches are distributed among these distances:
21 15 0.58
22 11 0.42
ACGTcount: A:0.36, C:0.18, G:0.11, T:0.35
Consensus pattern (22 bp):
CTCAAAAATTCTCATTTGAGAA
Found at i:4381539 original size:63 final size:63
Alignment explanation
Indices: 4381467--4381588 Score: 172
Period size: 63 Copynumber: 1.9 Consensus size: 63
4381457 TTCGTCTACC
* * * *
4381467 ATCACTAGGTCACTACTCATAGGTGTCTCAGCATTAGCCATTCCAAAACAAATTTCATCATCT
1 ATCACTAGGTCACCACTCATAAGTGTCTCAGCATTAACCATTCCAAAACAAACTTCATCATCT
* * * *
4381530 ATCACTAGGTCACCACTTATAAGTTTTTCAGCCTTAACCATTCCAAAACAAACTTCATC
1 ATCACTAGGTCACCACTCATAAGTGTCTCAGCATTAACCATTCCAAAACAAACTTCATC
4381589 CACTGATCCA
Statistics
Matches: 51, Mismatches: 8, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
63 51 1.00
ACGTcount: A:0.33, C:0.28, G:0.09, T:0.30
Consensus pattern (63 bp):
ATCACTAGGTCACCACTCATAAGTGTCTCAGCATTAACCATTCCAAAACAAACTTCATCATCT
Found at i:4382304 original size:17 final size:17
Alignment explanation
Indices: 4382249--4382297 Score: 73
Period size: 17 Copynumber: 2.9 Consensus size: 17
4382239 TTTGAGTCTT
*
4382249 CATTTTT-TCTTATTTC
1 CATTTTTCTCTTTTTTC
*
4382265 CACTTTTCTCTTTTTTC
1 CATTTTTCTCTTTTTTC
4382282 CATTTTTCTCTTTTTT
1 CATTTTTCTCTTTTTT
4382298 TATTTTTATT
Statistics
Matches: 29, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
16 6 0.21
17 23 0.79
ACGTcount: A:0.08, C:0.22, G:0.00, T:0.69
Consensus pattern (17 bp):
CATTTTTCTCTTTTTTC
Found at i:4382311 original size:13 final size:13
Alignment explanation
Indices: 4382293--4382317 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
4382283 ATTTTTCTCT
4382293 TTTTTTATTTTTA
1 TTTTTTATTTTTA
4382306 TTTTTTATTTTT
1 TTTTTTATTTTT
4382318 TCTTTCTTCA
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.12, C:0.00, G:0.00, T:0.88
Consensus pattern (13 bp):
TTTTTTATTTTTA
Found at i:4382518 original size:20 final size:20
Alignment explanation
Indices: 4382493--4382533 Score: 82
Period size: 20 Copynumber: 2.0 Consensus size: 20
4382483 GAAGGGTCAT
4382493 GAAAGAAATTGATATAATAG
1 GAAAGAAATTGATATAATAG
4382513 GAAAGAAATTGATATAATAG
1 GAAAGAAATTGATATAATAG
4382533 G
1 G
4382534 CTTAAAACAT
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 21 1.00
ACGTcount: A:0.54, C:0.00, G:0.22, T:0.24
Consensus pattern (20 bp):
GAAAGAAATTGATATAATAG
Found at i:4385261 original size:23 final size:23
Alignment explanation
Indices: 4385211--4385262 Score: 70
Period size: 23 Copynumber: 2.3 Consensus size: 23
4385201 AATCATGAGC
* *
4385211 ATGAAAATGATGCATAGAATGAA
1 ATGATAATAATGCATAGAATGAA
4385234 ATGATAATAATGCAT-GAAATGAA
1 ATGATAATAATGCATAG-AATGAA
4385257 ATGATA
1 ATGATA
4385263 TGATAATATG
Statistics
Matches: 26, Mismatches: 2, Indels: 2
0.87 0.07 0.07
Matches are distributed among these distances:
22 1 0.04
23 25 0.96
ACGTcount: A:0.52, C:0.04, G:0.19, T:0.25
Consensus pattern (23 bp):
ATGATAATAATGCATAGAATGAA
Found at i:4385273 original size:23 final size:22
Alignment explanation
Indices: 4385228--4385275 Score: 62
Period size: 23 Copynumber: 2.1 Consensus size: 22
4385218 TGATGCATAG
4385228 AATGAAATGATAATAATGCATGA
1 AATGAAATGATAATAAT-CATGA
4385251 AATGAAATGATATGATAAT-ATGA
1 AATGAAATGATA--ATAATCATGA
4385274 AA
1 AA
4385276 ATGATGCATT
Statistics
Matches: 23, Mismatches: 0, Indels: 4
0.85 0.00 0.15
Matches are distributed among these distances:
23 18 0.78
25 5 0.22
ACGTcount: A:0.54, C:0.02, G:0.17, T:0.27
Consensus pattern (22 bp):
AATGAAATGATAATAATCATGA
Found at i:4387630 original size:22 final size:22
Alignment explanation
Indices: 4387594--4387638 Score: 65
Period size: 22 Copynumber: 2.0 Consensus size: 22
4387584 AAAATTTTTT
4387594 TTTCTGTTTTCTGCTTGCTATG
1 TTTCTGTTTTCTGCTTGCTATG
*
4387616 TTTCTGATTTT-TGCTTTCTATG
1 TTTCTG-TTTTCTGCTTGCTATG
4387638 T
1 T
4387639 GTGTGTTATG
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
22 17 0.81
23 4 0.19
ACGTcount: A:0.07, C:0.16, G:0.16, T:0.62
Consensus pattern (22 bp):
TTTCTGTTTTCTGCTTGCTATG
Found at i:4388540 original size:16 final size:16
Alignment explanation
Indices: 4388519--4388554 Score: 54
Period size: 16 Copynumber: 2.2 Consensus size: 16
4388509 ACTTTAACTT
*
4388519 TTAATTCAATCAAATA
1 TTAATTCAATAAAATA
*
4388535 TTAATTTAATAAAATA
1 TTAATTCAATAAAATA
4388551 TTAA
1 TTAA
4388555 AAATTATTAT
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
16 18 1.00
ACGTcount: A:0.53, C:0.06, G:0.00, T:0.42
Consensus pattern (16 bp):
TTAATTCAATAAAATA
Found at i:4389182 original size:3 final size:3
Alignment explanation
Indices: 4389174--4389207 Score: 68
Period size: 3 Copynumber: 11.3 Consensus size: 3
4389164 TTAAGAAATT
4389174 TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC T
1 TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC T
4389208 GCTGCTGCTG
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 31 1.00
ACGTcount: A:0.00, C:0.32, G:0.00, T:0.68
Consensus pattern (3 bp):
TTC
Found at i:4392318 original size:27 final size:27
Alignment explanation
Indices: 4392263--4392314 Score: 79
Period size: 27 Copynumber: 2.0 Consensus size: 27
4392253 AAAAAATTAA
* *
4392263 TTCATTAATAAAGTGGTATCTATTCAT
1 TTCATTAATAAAATAGTATCTATTCAT
4392290 TTCATTAATAAAATAGTATC-ATTCA
1 TTCATTAATAAAATAGTATCTATTCA
4392315 ATTTATTGAT
Statistics
Matches: 23, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
26 5 0.22
27 18 0.78
ACGTcount: A:0.38, C:0.12, G:0.08, T:0.42
Consensus pattern (27 bp):
TTCATTAATAAAATAGTATCTATTCAT
Found at i:4392541 original size:20 final size:20
Alignment explanation
Indices: 4392516--4392564 Score: 64
Period size: 21 Copynumber: 2.4 Consensus size: 20
4392506 ATTAAATATT
*
4392516 AATATTTTAATAATT-TTAAA
1 AATATTTTAA-AATTAATAAA
4392536 AATATTTTAAAATTAAATAAA
1 AATATTTTAAAATT-AATAAA
4392557 AATATTTT
1 AATATTTT
4392565 TATTAAATAA
Statistics
Matches: 26, Mismatches: 1, Indels: 3
0.87 0.03 0.10
Matches are distributed among these distances:
19 4 0.15
20 10 0.38
21 12 0.46
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (20 bp):
AATATTTTAAAATTAATAAA
Found at i:4392571 original size:19 final size:20
Alignment explanation
Indices: 4392532--4392575 Score: 63
Period size: 21 Copynumber: 2.2 Consensus size: 20
4392522 TTAATAATTT
4392532 TAAAAATATTTTAAAATTAAA
1 TAAAAATATTTT-AAATTAAA
*
4392553 TAAAAATATTTT-TATTAAA
1 TAAAAATATTTTAAATTAAA
4392572 TAAA
1 TAAA
4392576 TATTATCTTT
Statistics
Matches: 22, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
19 10 0.45
21 12 0.55
ACGTcount: A:0.59, C:0.00, G:0.00, T:0.41
Consensus pattern (20 bp):
TAAAAATATTTTAAATTAAA
Found at i:4395196 original size:2 final size:2
Alignment explanation
Indices: 4395183--4395214 Score: 55
Period size: 2 Copynumber: 16.0 Consensus size: 2
4395173 CCCCTTTTAC
*
4395183 AT AT AT AG 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
4395215 CAATATCTCT
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:0.50, C:0.00, G:0.03, T:0.47
Consensus pattern (2 bp):
AT
Found at i:4396842 original size:2 final size:2
Alignment explanation
Indices: 4396835--4396867 Score: 66
Period size: 2 Copynumber: 16.5 Consensus size: 2
4396825 TATATCATTT
4396835 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
4396868 CTTTTGGTGG
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 31 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Done.