Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold8
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: 6381039
ACGTcount: A:0.34, C:0.16, G:0.16, T:0.34
Warning! 22487 characters in sequence are not A, C, G, or T
File 24 of 33
Found at i:4011437 original size:30 final size:30
Alignment explanation
Indices: 4011403--4011463 Score: 122
Period size: 30 Copynumber: 2.0 Consensus size: 30
4011393 TTTTTAAATA
4011403 ATAAAACTTCGAAATAGAGCAACAATACTT
1 ATAAAACTTCGAAATAGAGCAACAATACTT
4011433 ATAAAACTTCGAAATAGAGCAACAATACTT
1 ATAAAACTTCGAAATAGAGCAACAATACTT
4011463 A
1 A
4011464 AGTAGAAATA
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
30 31 1.00
ACGTcount: A:0.51, C:0.16, G:0.10, T:0.23
Consensus pattern (30 bp):
ATAAAACTTCGAAATAGAGCAACAATACTT
Found at i:4011875 original size:17 final size:17
Alignment explanation
Indices: 4011837--4011877 Score: 50
Period size: 17 Copynumber: 2.5 Consensus size: 17
4011827 TAAATAAAAT
*
4011837 TAATTACAATTTATTAG
1 TAATTACAATTAATTAG
4011854 T-ATTACTAATTAATTA-
1 TAATTAC-AATTAATTAG
4011870 TAATTACA
1 TAATTACA
4011878 GTTTTGCATA
Statistics
Matches: 21, Mismatches: 1, Indels: 5
0.78 0.04 0.19
Matches are distributed among these distances:
16 7 0.33
17 14 0.67
ACGTcount: A:0.44, C:0.07, G:0.02, T:0.46
Consensus pattern (17 bp):
TAATTACAATTAATTAG
Found at i:4016885 original size:47 final size:42
Alignment explanation
Indices: 4016790--4016869 Score: 101
Period size: 41 Copynumber: 1.9 Consensus size: 42
4016780 AAATATAATA
* *
4016790 AATATAATATGTTTAATATATATATCATATTTATATTTAAAT
1 AATATAAAATATTTAATATATATATCATATTTATATTTAAAT
* *
4016832 --TTTAAAATATTTAATAATTTATATCATATTTATATTTA
1 AATATAAAATATTTAAT-ATATATATCATATTTATATTTA
4016870 TAAAACTAAT
Statistics
Matches: 33, Mismatches: 4, Indels: 3
0.82 0.10 0.08
Matches are distributed among these distances:
40 12 0.36
41 21 0.64
ACGTcount: A:0.44, C:0.03, G:0.01, T:0.53
Consensus pattern (42 bp):
AATATAAAATATTTAATATATATATCATATTTATATTTAAAT
Found at i:4017097 original size:1 final size:1
Alignment explanation
Indices: 4017093--4017118 Score: 52
Period size: 1 Copynumber: 26.0 Consensus size: 1
4017083 TAAAAAAAGC
4017093 AAAAAAAAAAAAAAAAAAAAAAAAAA
1 AAAAAAAAAAAAAAAAAAAAAAAAAA
4017119 GAAGATGTTT
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
1 25 1.00
ACGTcount: A:1.00, C:0.00, G:0.00, T:0.00
Consensus pattern (1 bp):
A
Found at i:4017316 original size:17 final size:16
Alignment explanation
Indices: 4017283--4017339 Score: 53
Period size: 17 Copynumber: 3.4 Consensus size: 16
4017273 ATTAAATACG
4017283 ATAT-ATATAAAATTAAA
1 ATATAATAT-AAA-TAAA
*
4017300 ATATAATATTATATAAA
1 ATATAATA-TAAATAAA
*
4017317 AAATAATATAAATAAA
1 ATATAATATAAATAAA
4017333 ATTATAA
1 A-TATAA
4017340 ACTATAAATT
Statistics
Matches: 33, Mismatches: 4, Indels: 6
0.77 0.09 0.14
Matches are distributed among these distances:
16 8 0.24
17 19 0.58
18 5 0.15
19 1 0.03
ACGTcount: A:0.65, C:0.00, G:0.00, T:0.35
Consensus pattern (16 bp):
ATATAATATAAATAAA
Found at i:4017330 original size:23 final size:25
Alignment explanation
Indices: 4017284--4017330 Score: 62
Period size: 24 Copynumber: 2.0 Consensus size: 25
4017274 TTAAATACGA
*
4017284 TATATATAAAATTAAAATATAATAT
1 TATATATAAAAATAAAATATAATAT
*
4017309 TATATA-AAAAATAATATA-AATA
1 TATATATAAAAATAAAATATAATA
4017331 AAATTATAAA
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
23 4 0.20
24 10 0.50
25 6 0.30
ACGTcount: A:0.64, C:0.00, G:0.00, T:0.36
Consensus pattern (25 bp):
TATATATAAAAATAAAATATAATAT
Found at i:4017400 original size:30 final size:30
Alignment explanation
Indices: 4017352--4017417 Score: 80
Period size: 29 Copynumber: 2.2 Consensus size: 30
4017342 TATAAATTTA
* *
4017352 TTAAAATTTATTTAAAATAAATTATAATATT
1 TTAAATTTTATATAAAATAAA-TATAATATT
*
4017383 TTAAATTTTATAT-AAATATATATAATATT
1 TTAAATTTTATATAAAATAAATATAATATT
*
4017412 TGAAAT
1 TTAAAT
4017418 ATAATTACAA
Statistics
Matches: 31, Mismatches: 4, Indels: 2
0.84 0.11 0.05
Matches are distributed among these distances:
29 14 0.45
30 6 0.19
31 11 0.35
ACGTcount: A:0.50, C:0.00, G:0.02, T:0.48
Consensus pattern (30 bp):
TTAAATTTTATATAAAATAAATATAATATT
Found at i:4017429 original size:29 final size:29
Alignment explanation
Indices: 4017374--4017437 Score: 78
Period size: 29 Copynumber: 2.2 Consensus size: 29
4017364 TAAAATAAAT
* * *
4017374 TATAATATTTTAAATTTTATATAAATATA
1 TATAATATTTGAAATATAATATAAATATA
4017403 TATAATATTTGAAATATAAT-TACAATATA
1 TATAATATTTGAAATATAATATA-AATATA
4017432 TA-AATA
1 TATAATA
4017438 AAAAATAAAT
Statistics
Matches: 31, Mismatches: 3, Indels: 3
0.84 0.08 0.08
Matches are distributed among these distances:
28 6 0.19
29 25 0.81
ACGTcount: A:0.52, C:0.02, G:0.02, T:0.45
Consensus pattern (29 bp):
TATAATATTTGAAATATAATATAAATATA
Found at i:4017965 original size:12 final size:12
Alignment explanation
Indices: 4017941--4017973 Score: 50
Period size: 12 Copynumber: 2.8 Consensus size: 12
4017931 TTGAAAGTAG
*
4017941 TAAT-TAAATTA
1 TAATATAAAATA
4017952 TAATATAAAATA
1 TAATATAAAATA
4017964 TAATATAAAA
1 TAATATAAAA
4017974 GAGTTTGATT
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
11 4 0.20
12 16 0.80
ACGTcount: A:0.64, C:0.00, G:0.00, T:0.36
Consensus pattern (12 bp):
TAATATAAAATA
Found at i:4024590 original size:133 final size:131
Alignment explanation
Indices: 4024354--4024617 Score: 501
Period size: 133 Copynumber: 2.0 Consensus size: 131
4024344 TCCTTTGCAA
4024354 CAGATAAAAGAAACCATTGCCATTTGCCAGTAGATAATTCCTTTTTTTTTCTTCTTTTCTTCCAA
1 CAGATAAAAGAAACCATTGCCATTTGCCAGTAGATAATTCCTTTTTTTTTCTTCTTTTCTTCCAA
4024419 CAAAGATCATAAATTACGGGGAGAAAAGAAAAAAGGAAAGAAGGAGCAAAATGCAGTGAGATTGT
66 CAAAGATCATAAATTACGGGGAGAAAAGAAAAAAGGAAAGAAGGAGCAAAATGCAGTGAGATTGT
4024484 G
131 G
*
4024485 CAGATAAAAGAAACCATTGCCATTTGCCAGTAGATAATTCCTTTTTTTTTTTCTTCTTTTTTTCC
1 CAGATAAAAGAAACCATTGCCATTTGCCAGTAGATAATTCC--TTTTTTTTTCTTCTTTTCTTCC
4024550 AACAAAGATCATAAATTACGGGGAGAAAAGAAAAAAGGAAAGAAGGAGCAAAATGCAGTGAGATT
64 AACAAAGATCATAAATTACGGGGAGAAAAGAAAAAAGGAAAGAAGGAGCAAAATGCAGTGAGATT
4024615 GTG
129 GTG
4024618 TGTAGCCTTT
Statistics
Matches: 130, Mismatches: 1, Indels: 2
0.98 0.01 0.02
Matches are distributed among these distances:
131 41 0.32
133 89 0.68
ACGTcount: A:0.39, C:0.14, G:0.19, T:0.28
Consensus pattern (131 bp):
CAGATAAAAGAAACCATTGCCATTTGCCAGTAGATAATTCCTTTTTTTTTCTTCTTTTCTTCCAA
CAAAGATCATAAATTACGGGGAGAAAAGAAAAAAGGAAAGAAGGAGCAAAATGCAGTGAGATTGT
G
Found at i:4027781 original size:18 final size:18
Alignment explanation
Indices: 4027754--4027798 Score: 56
Period size: 18 Copynumber: 2.6 Consensus size: 18
4027744 TAATTATATG
*
4027754 ATATTCAAAAATAAAATT
1 ATATTTAAAAATAAAATT
* *
4027772 ATATTTAAAATTTAAATT
1 ATATTTAAAAATAAAATT
4027790 -TATTTAAAA
1 ATATTTAAAA
4027799 GTAACGTGGT
Statistics
Matches: 24, Mismatches: 3, Indels: 1
0.86 0.11 0.04
Matches are distributed among these distances:
17 9 0.38
18 15 0.62
ACGTcount: A:0.56, C:0.02, G:0.00, T:0.42
Consensus pattern (18 bp):
ATATTTAAAAATAAAATT
Found at i:4027935 original size:16 final size:16
Alignment explanation
Indices: 4027914--4027952 Score: 60
Period size: 16 Copynumber: 2.4 Consensus size: 16
4027904 ATTTAAATTT
4027914 AAATATAAATATATAA
1 AAATATAAATATATAA
*
4027930 AAATATTAATATATAA
1 AAATATAAATATATAA
4027946 ATAATAT
1 A-AATAT
4027953 TTTAATATTT
Statistics
Matches: 21, Mismatches: 1, Indels: 1
0.91 0.04 0.04
Matches are distributed among these distances:
16 16 0.76
17 5 0.24
ACGTcount: A:0.64, C:0.00, G:0.00, T:0.36
Consensus pattern (16 bp):
AAATATAAATATATAA
Found at i:4029926 original size:39 final size:38
Alignment explanation
Indices: 4029852--4029924 Score: 105
Period size: 38 Copynumber: 1.9 Consensus size: 38
4029842 TTTAAATTTT
4029852 ATAATATAAATTTTTAAATTTATATTTTAAAAAAATAA
1 ATAATATAAATTTTTAAATTTATATTTTAAAAAAATAA
*
4029890 ATAAT-TATAATTTTTTAA-TTATATTTGTAAAAAAA
1 ATAATATA-AATTTTTAAATTTATATTT-TAAAAAAA
4029925 ATTATTATTA
Statistics
Matches: 32, Mismatches: 1, Indels: 4
0.86 0.03 0.11
Matches are distributed among these distances:
37 10 0.31
38 22 0.69
ACGTcount: A:0.52, C:0.00, G:0.01, T:0.47
Consensus pattern (38 bp):
ATAATATAAATTTTTAAATTTATATTTTAAAAAAATAA
Found at i:4031728 original size:10 final size:10
Alignment explanation
Indices: 4031715--4031830 Score: 56
Period size: 10 Copynumber: 12.2 Consensus size: 10
4031705 TTTAAAATAT
4031715 TATATATTTA
1 TATATATTTA
*
4031725 TATAAATTT-
1 TATATATTTA
4031734 TA-ATATATTA
1 TATATAT-TTA
4031744 -ATA-ATTTA
1 TATATATTTA
*
4031752 TAT-TATATA
1 TATATATTTA
4031761 TCA-AT-TTTA
1 T-ATATATTTA
4031770 -ATATATTT-
1 TATATATTTA
4031778 TATATTATATTA
1 TATA-TAT-TTA
*
4031790 TAT-T-TTTT
1 TATATATTTA
*
4031798 TATATCTTTA
1 TATATATTTA
* *
4031808 CATATATATA
1 TATATATTTA
4031818 TATATATCTTA
1 TATATAT-TTA
4031829 TA
1 TA
4031831 CTTTAATAAT
Statistics
Matches: 79, Mismatches: 11, Indels: 31
0.65 0.09 0.26
Matches are distributed among these distances:
7 1 0.01
8 13 0.16
9 25 0.32
10 31 0.39
11 6 0.08
12 3 0.04
ACGTcount: A:0.40, C:0.03, G:0.00, T:0.57
Consensus pattern (10 bp):
TATATATTTA
Found at i:4031735 original size:27 final size:28
Alignment explanation
Indices: 4031694--4031754 Score: 81
Period size: 27 Copynumber: 2.2 Consensus size: 28
4031684 ATTATTTTTA
*
4031694 TTATAAAAATATTTAAAATATT-ATATAT
1 TTATATAAATATTTAAAATATTAATA-AT
*
4031722 TTATATAAAT-TTTAATATATTAATAAT
1 TTATATAAATATTTAAAATATTAATAAT
4031749 TTATAT
1 TTATAT
4031755 TATATATCAA
Statistics
Matches: 30, Mismatches: 2, Indels: 3
0.86 0.06 0.09
Matches are distributed among these distances:
27 18 0.60
28 12 0.40
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (28 bp):
TTATATAAATATTTAAAATATTAATAAT
Found at i:4031739 original size:34 final size:34
Alignment explanation
Indices: 4031717--4031792 Score: 104
Period size: 34 Copynumber: 2.3 Consensus size: 34
4031707 TAAAATATTA
4031717 TATATT-TATATAAATTTTAATATATTAATAATT
1 TATATTATATATAAATTTTAATATATTAATAATT
* *
4031750 TATATTATATATCAATTTTAATATATT--TTATAT
1 TATATTATATATAAATTTTAATATATTAATAAT-T
4031783 TATATTATAT
1 TATATTATAT
4031793 TTTTTTATAT
Statistics
Matches: 39, Mismatches: 2, Indels: 4
0.87 0.04 0.09
Matches are distributed among these distances:
32 3 0.08
33 17 0.44
34 19 0.49
ACGTcount: A:0.42, C:0.01, G:0.00, T:0.57
Consensus pattern (34 bp):
TATATTATATATAAATTTTAATATATTAATAATT
Found at i:4031747 original size:18 final size:17
Alignment explanation
Indices: 4031729--4031776 Score: 55
Period size: 17 Copynumber: 2.8 Consensus size: 17
4031719 TATTTATATA
4031729 AATTTTAATATATTAAT
1 AATTTTAATATATTAAT
*
4031746 AATTTATATTATA-T-AT
1 AATTT-TAATATATTAAT
4031762 CAATTTTAATATATT
1 -AATTTTAATATATT
4031777 TTATATTATA
Statistics
Matches: 26, Mismatches: 2, Indels: 6
0.76 0.06 0.18
Matches are distributed among these distances:
16 8 0.31
17 12 0.46
18 6 0.23
ACGTcount: A:0.44, C:0.02, G:0.00, T:0.54
Consensus pattern (17 bp):
AATTTTAATATATTAAT
Found at i:4031766 original size:17 final size:16
Alignment explanation
Indices: 4031717--4031792 Score: 50
Period size: 17 Copynumber: 4.6 Consensus size: 16
4031707 TAAAATATTA
4031717 TATATT-TATATAAATT
1 TATATTATATAT-AATT
*
4031733 T-TAATATATTAATAATT
1 TATATTATA-T-ATAATT
4031750 TATATTATATATCAATT
1 TATATTATATAT-AATT
* * *
4031767 T-TAATATATTTTATAT
1 TATATTATATATAAT-T
4031783 TATATTATAT
1 TATATTATAT
4031793 TTTTTTATAT
Statistics
Matches: 47, Mismatches: 6, Indels: 13
0.71 0.09 0.20
Matches are distributed among these distances:
15 5 0.11
16 15 0.32
17 19 0.40
18 8 0.17
ACGTcount: A:0.42, C:0.01, G:0.00, T:0.57
Consensus pattern (16 bp):
TATATTATATATAATT
Found at i:4031796 original size:28 final size:28
Alignment explanation
Indices: 4031741--4031822 Score: 73
Period size: 28 Copynumber: 2.9 Consensus size: 28
4031731 TTTTAATATA
*
4031741 TTAATA-A-TTTATATTATA-TATCAATT
1 TTAATATATTTTATATTATATTAT-ATTT
4031767 TTAATATATTTTATATTATATTATATTT
1 TTAATATATTTTATATTATATTATATTT
* *
4031795 TT-TTATATCTTTACATATATATATATAT
1 TTAATATAT-TTTATAT-TATAT-TATAT
4031823 ATCTTATACT
Statistics
Matches: 47, Mismatches: 3, Indels: 8
0.81 0.05 0.14
Matches are distributed among these distances:
26 6 0.13
27 6 0.13
28 22 0.47
29 8 0.17
30 5 0.11
ACGTcount: A:0.38, C:0.04, G:0.00, T:0.59
Consensus pattern (28 bp):
TTAATATATTTTATATTATATTATATTT
Found at i:4032113 original size:27 final size:29
Alignment explanation
Indices: 4032075--4032144 Score: 69
Period size: 27 Copynumber: 2.6 Consensus size: 29
4032065 CGCAATCGAG
* *
4032075 TATT-TTAATAAAATTAT-TCTCT-AATGT
1 TATTATTATTAAAATTATATCACTAAAT-T
*
4032102 TATTA-TATT-AAATAATATCACTAAATT
1 TATTATTATTAAAATTATATCACTAAATT
4032129 TATTATTATTAAAATT
1 TATTATTATTAAAATT
4032145 TTATTTTATT
Statistics
Matches: 34, Mismatches: 4, Indels: 8
0.74 0.09 0.17
Matches are distributed among these distances:
26 6 0.18
27 17 0.50
28 7 0.21
29 4 0.12
ACGTcount: A:0.43, C:0.06, G:0.01, T:0.50
Consensus pattern (29 bp):
TATTATTATTAAAATTATATCACTAAATT
Found at i:4032309 original size:16 final size:15
Alignment explanation
Indices: 4032279--4032323 Score: 58
Period size: 15 Copynumber: 3.1 Consensus size: 15
4032269 AGTCAGTTCA
4032279 TTTTAAAAATAATTT
1 TTTTAAAAATAATTT
*
4032294 TTTTAAACAGTAA-TT
1 TTTTAAA-AATAATTT
4032309 TTTTAAAAAT-ATTT
1 TTTTAAAAATAATTT
4032323 T
1 T
4032324 AATTAATGTT
Statistics
Matches: 26, Mismatches: 2, Indels: 5
0.79 0.06 0.15
Matches are distributed among these distances:
13 1 0.04
14 5 0.19
15 16 0.62
16 4 0.15
ACGTcount: A:0.42, C:0.02, G:0.02, T:0.53
Consensus pattern (15 bp):
TTTTAAAAATAATTT
Found at i:4033228 original size:29 final size:29
Alignment explanation
Indices: 4033164--4033238 Score: 82
Period size: 29 Copynumber: 2.6 Consensus size: 29
4033154 TTATAAAATT
* * *
4033164 TTATGTAATTTAAA-TTTATTTAATTTGA
1 TTATGTATTTTAAATTTTATTCAATTTAA
4033192 TTATTGTATTTTAAATTTTATTC-ATATTAA
1 TTA-TGTATTTTAAATTTTATTCAAT-TTAA
*
4033222 TTATGTATATTAAATTT
1 TTATGTATTTTAAATTT
4033239 AAATAAATTA
Statistics
Matches: 40, Mismatches: 4, Indels: 5
0.82 0.08 0.10
Matches are distributed among these distances:
28 3 0.08
29 25 0.62
30 12 0.30
ACGTcount: A:0.35, C:0.01, G:0.05, T:0.59
Consensus pattern (29 bp):
TTATGTATTTTAAATTTTATTCAATTTAA
Found at i:4035650 original size:21 final size:23
Alignment explanation
Indices: 4035598--4035651 Score: 76
Period size: 24 Copynumber: 2.4 Consensus size: 23
4035588 TTTTAAGTTG
*
4035598 ATATTATGTAAAATTAATAAATTT
1 ATATTATGTAAAATTAATAAA-TC
4035622 ATATTATGTAAAATTAATAAA-C
1 ATATTATGTAAAATTAATAAATC
4035644 A-ATTATGT
1 ATATTATGT
4035652 TGTTGGATAT
Statistics
Matches: 29, Mismatches: 1, Indels: 3
0.88 0.03 0.09
Matches are distributed among these distances:
21 7 0.24
22 1 0.03
24 21 0.72
ACGTcount: A:0.50, C:0.02, G:0.06, T:0.43
Consensus pattern (23 bp):
ATATTATGTAAAATTAATAAATC
Found at i:4037020 original size:2 final size:2
Alignment explanation
Indices: 4037008--4037045 Score: 67
Period size: 2 Copynumber: 19.0 Consensus size: 2
4036998 TTGATTTTGC
*
4037008 TA TA CA 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 TA TA
4037046 GTATTATACA
Statistics
Matches: 34, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
2 34 1.00
ACGTcount: A:0.50, C:0.03, G:0.00, T:0.47
Consensus pattern (2 bp):
TA
Found at i:4037928 original size:23 final size:23
Alignment explanation
Indices: 4037878--4037929 Score: 72
Period size: 22 Copynumber: 2.3 Consensus size: 23
4037868 ATATTATTAA
4037878 AATATTATTTTTATATTAATATTT
1 AATA-TATTTTTATATTAATATTT
4037902 -ATATATTTTTATAATTAA-ATTT
1 AATATATTTTTAT-ATTAATATTT
4037924 AATATA
1 AATATA
4037930 AATATTTTTA
Statistics
Matches: 26, Mismatches: 0, Indels: 5
0.84 0.00 0.16
Matches are distributed among these distances:
22 13 0.50
23 13 0.50
ACGTcount: A:0.42, C:0.00, G:0.00, T:0.58
Consensus pattern (23 bp):
AATATATTTTTATATTAATATTT
Found at i:4043831 original size:51 final size:51
Alignment explanation
Indices: 4043740--4043842 Score: 136
Period size: 51 Copynumber: 2.0 Consensus size: 51
4043730 ATAACCAAAA
* *
4043740 AAAGAGATTCGAATTGGGATCAGGAATTAACAAAAACCTAACGGAGGTTAG
1 AAAGAAATTCGAATTGGGATCAGGAATTAACAAAAACCTAACGCAGGTTAG
** **
4043791 AAAGAAATTCGAATTGGGATCAGGCTTTAA-AAAGCCCCTAACGCAGGTTAG
1 AAAGAAATTCGAATTGGGATCAGGAATTAACAAA-AACCTAACGCAGGTTAG
4043842 A
1 A
4043843 TAAAATTAGA
Statistics
Matches: 45, Mismatches: 6, Indels: 2
0.85 0.11 0.04
Matches are distributed among these distances:
50 3 0.07
51 42 0.93
ACGTcount: A:0.41, C:0.15, G:0.24, T:0.20
Consensus pattern (51 bp):
AAAGAAATTCGAATTGGGATCAGGAATTAACAAAAACCTAACGCAGGTTAG
Found at i:4044354 original size:2 final size:2
Alignment explanation
Indices: 4044347--4044391 Score: 72
Period size: 2 Copynumber: 22.5 Consensus size: 2
4044337 GGTTTTGTTA
* *
4044347 TC TC TC TC TC TC TC TC TC TC TC TC CC TC TC CC 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 TC
4044389 TC T
1 TC T
4044392 TCAACGCTCG
Statistics
Matches: 39, Mismatches: 4, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
2 39 1.00
ACGTcount: A:0.00, C:0.53, G:0.00, T:0.47
Consensus pattern (2 bp):
TC
Found at i:4044772 original size:33 final size:33
Alignment explanation
Indices: 4044735--4044807 Score: 94
Period size: 33 Copynumber: 2.2 Consensus size: 33
4044725 TTTTTATAAA
* * * *
4044735 TTTAAATAATTTAATTTAATTTAATTT-ATTATT
1 TTTAAATAA-TAAATTAAATTAAATTTAAATATT
4044768 TTTAAATAATAAATTAAATTAAATTTAAATATT
1 TTTAAATAATAAATTAAATTAAATTTAAATATT
4044801 TTTAAAT
1 TTTAAAT
4044808 TACAATATAA
Statistics
Matches: 35, Mismatches: 4, Indels: 2
0.85 0.10 0.05
Matches are distributed among these distances:
32 14 0.40
33 21 0.60
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (33 bp):
TTTAAATAATAAATTAAATTAAATTTAAATATT
Found at i:4048017 original size:2 final size:2
Alignment explanation
Indices: 4048010--4048051 Score: 84
Period size: 2 Copynumber: 21.0 Consensus size: 2
4048000 TAAACAATGC
4048010 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
4048052 TTCAACTATT
Statistics
Matches: 40, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 40 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:4057204 original size:6 final size:6
Alignment explanation
Indices: 4057189--4057220 Score: 50
Period size: 6 Copynumber: 5.7 Consensus size: 6
4057179 TATAGCAATG
4057189 TTTT-A TTTTAA TTTTAA TTTTAA TTTT-A TTTT
1 TTTTAA TTTTAA TTTTAA TTTTAA TTTTAA TTTT
4057221 CCTTGAAAAC
Statistics
Matches: 26, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
5 9 0.35
6 17 0.65
ACGTcount: A:0.25, C:0.00, G:0.00, T:0.75
Consensus pattern (6 bp):
TTTTAA
Found at i:4058240 original size:24 final size:25
Alignment explanation
Indices: 4058207--4058253 Score: 78
Period size: 24 Copynumber: 1.9 Consensus size: 25
4058197 AAAGGGAATC
*
4058207 AATGATTTTATAATTAATTATATCA
1 AATGATTTTATAATTAAATATATCA
4058232 AATGA-TTTATAATTAAATATAT
1 AATGATTTTATAATTAAATATAT
4058254 AATTAAGATG
Statistics
Matches: 21, Mismatches: 1, Indels: 1
0.91 0.04 0.04
Matches are distributed among these distances:
24 16 0.76
25 5 0.24
ACGTcount: A:0.47, C:0.02, G:0.04, T:0.47
Consensus pattern (25 bp):
AATGATTTTATAATTAAATATATCA
Found at i:4058703 original size:21 final size:23
Alignment explanation
Indices: 4058653--4058705 Score: 65
Period size: 21 Copynumber: 2.4 Consensus size: 23
4058643 AACGTGGCTG
*
4058653 TTATCTATTTTATTGTTCTAAAT
1 TTATATATTTTATTGTTCTAAAT
* *
4058676 TTTTATATTTT-TTGTT-TATAT
1 TTATATATTTTATTGTTCTAAAT
4058697 TTATATATT
1 TTATATATT
4058706 AAATATAATT
Statistics
Matches: 26, Mismatches: 4, Indels: 2
0.81 0.12 0.06
Matches are distributed among these distances:
21 12 0.46
22 5 0.19
23 9 0.35
ACGTcount: A:0.25, C:0.04, G:0.04, T:0.68
Consensus pattern (23 bp):
TTATATATTTTATTGTTCTAAAT
Found at i:4059645 original size:24 final size:23
Alignment explanation
Indices: 4059622--4059680 Score: 66
Period size: 23 Copynumber: 2.6 Consensus size: 23
4059612 TTCGTATAAT
*
4059622 TATTTTTAAAATTTAAATTTTAA
1 TATTTTTAAAATTTAAATATTAA
** *
4059645 TAAATTTAAAATGTTTAATATTAA
1 TATTTTTAAAAT-TTAAATATTAA
4059669 T-TTTTTAAAATT
1 TATTTTTAAAATT
4059681 ATGACTTTTA
Statistics
Matches: 29, Mismatches: 6, Indels: 3
0.76 0.16 0.08
Matches are distributed among these distances:
22 1 0.03
23 18 0.62
24 10 0.34
ACGTcount: A:0.44, C:0.00, G:0.02, T:0.54
Consensus pattern (23 bp):
TATTTTTAAAATTTAAATATTAA
Found at i:4059651 original size:16 final size:18
Alignment explanation
Indices: 4059630--4059664 Score: 56
Period size: 18 Copynumber: 2.1 Consensus size: 18
4059620 ATTATTTTTA
4059630 AAATTT-AAAT-TTTAAT
1 AAATTTAAAATGTTTAAT
4059646 AAATTTAAAATGTTTAAT
1 AAATTTAAAATGTTTAAT
4059664 A
1 A
4059665 TTAATTTTTT
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
16 6 0.35
17 4 0.24
18 7 0.41
ACGTcount: A:0.51, C:0.00, G:0.03, T:0.46
Consensus pattern (18 bp):
AAATTTAAAATGTTTAAT
Found at i:4062133 original size:18 final size:18
Alignment explanation
Indices: 4062080--4062133 Score: 56
Period size: 18 Copynumber: 3.0 Consensus size: 18
4062070 AATATTTAAA
4062080 ATTTATTAA-TTAATTATT
1 ATTT-TTAATTTAATTATT
* ** *
4062098 ATATTTAATAAAAATATT
1 ATTTTTAATTTAATTATT
4062116 ATTTTTAATTTAATTATT
1 ATTTTTAATTTAATTATT
4062134 TTAAAAATCA
Statistics
Matches: 27, Mismatches: 8, Indels: 2
0.73 0.22 0.05
Matches are distributed among these distances:
17 4 0.15
18 23 0.85
ACGTcount: A:0.43, C:0.00, G:0.00, T:0.57
Consensus pattern (18 bp):
ATTTTTAATTTAATTATT
Found at i:4063425 original size:21 final size:21
Alignment explanation
Indices: 4063388--4063430 Score: 52
Period size: 21 Copynumber: 2.0 Consensus size: 21
4063378 ATTATTATAG
*
4063388 ATAATATAATAATATTATCTT
1 ATAATATAATAATATTAGCTT
*
4063409 ATAA-ATAATATTAATTAGCTT
1 ATAATATAATAAT-ATTAGCTT
4063430 A
1 A
4063431 GAAGTGTCCC
Statistics
Matches: 19, Mismatches: 2, Indels: 2
0.83 0.09 0.09
Matches are distributed among these distances:
20 7 0.37
21 12 0.63
ACGTcount: A:0.49, C:0.05, G:0.02, T:0.44
Consensus pattern (21 bp):
ATAATATAATAATATTAGCTT
Found at i:4063915 original size:17 final size:16
Alignment explanation
Indices: 4063876--4063907 Score: 64
Period size: 16 Copynumber: 2.0 Consensus size: 16
4063866 AGAGAGAAGA
4063876 GTAATAAATATATTTT
1 GTAATAAATATATTTT
4063892 GTAATAAATATATTTT
1 GTAATAAATATATTTT
4063908 TATTATAATT
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 16 1.00
ACGTcount: A:0.44, C:0.00, G:0.06, T:0.50
Consensus pattern (16 bp):
GTAATAAATATATTTT
Found at i:4063941 original size:16 final size:17
Alignment explanation
Indices: 4063920--4063958 Score: 55
Period size: 17 Copynumber: 2.4 Consensus size: 17
4063910 TTATAATTAA
4063920 TTATATTTA-A-AATATT
1 TTATATTTATATAA-ATT
4063936 TTATATTTATATAAATT
1 TTATATTTATATAAATT
4063953 TTATAT
1 TTATAT
4063959 GTATTTTATA
Statistics
Matches: 21, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
16 9 0.43
17 10 0.48
18 2 0.10
ACGTcount: A:0.41, C:0.00, G:0.00, T:0.59
Consensus pattern (17 bp):
TTATATTTATATAAATT
Found at i:4063957 original size:11 final size:11
Alignment explanation
Indices: 4063941--4063977 Score: 56
Period size: 11 Copynumber: 3.4 Consensus size: 11
4063931 ATATTTTATA
4063941 TTTATATAAAT
1 TTTATATAAAT
**
4063952 TTTATATGTAT
1 TTTATATAAAT
4063963 TTTATATAAAT
1 TTTATATAAAT
4063974 TTTA
1 TTTA
4063978 AATATTTATA
Statistics
Matches: 22, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
11 22 1.00
ACGTcount: A:0.38, C:0.00, G:0.03, T:0.59
Consensus pattern (11 bp):
TTTATATAAAT
Found at i:4064955 original size:2 final size:2
Alignment explanation
Indices: 4064948--4064976 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
4064938 GGAATACTTT
4064948 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
4064977 GAAATTAATA
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:4065258 original size:2 final size:2
Alignment explanation
Indices: 4065251--4065282 Score: 55
Period size: 2 Copynumber: 16.0 Consensus size: 2
4065241 TGTTAGGTGC
*
4065251 AT AT AT AT AT AT AT AT AT AT AT AC AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
4065283 GCTTTGCTAG
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:0.03, G:0.00, T:0.47
Consensus pattern (2 bp):
AT
Found at i:4067517 original size:14 final size:14
Alignment explanation
Indices: 4067494--4067527 Score: 52
Period size: 14 Copynumber: 2.5 Consensus size: 14
4067484 TACTCAAAAA
4067494 ATTT-AATCTAAAC
1 ATTTAAATCTAAAC
4067507 ATTTAAATCTAAAC
1 ATTTAAATCTAAAC
*
4067521 AGTTAAA
1 ATTTAAA
4067528 AATTTTAATC
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
13 4 0.21
14 15 0.79
ACGTcount: A:0.50, C:0.12, G:0.03, T:0.35
Consensus pattern (14 bp):
ATTTAAATCTAAAC
Found at i:4069013 original size:21 final size:21
Alignment explanation
Indices: 4068989--4069035 Score: 78
Period size: 21 Copynumber: 2.3 Consensus size: 21
4068979 GACAGCAGCT
*
4068989 GATAGGACAATCATCAGATCA
1 GATAGGAAAATCATCAGATCA
4069010 GATAGGAAAATCATCAGATCA
1 GATAGGAAAATCATCAGATCA
4069031 -ATAGG
1 GATAGG
4069036 GCACCACAAT
Statistics
Matches: 25, Mismatches: 1, Indels: 1
0.93 0.04 0.04
Matches are distributed among these distances:
20 5 0.20
21 20 0.80
ACGTcount: A:0.45, C:0.15, G:0.21, T:0.19
Consensus pattern (21 bp):
GATAGGAAAATCATCAGATCA
Found at i:4072238 original size:53 final size:53
Alignment explanation
Indices: 4072175--4072283 Score: 209
Period size: 53 Copynumber: 2.1 Consensus size: 53
4072165 AAATTAAAGA
4072175 TAAAAGTGTGAAGATTTAACTTGAAGATAAGAGTTTAGTATTTATCATATTTG
1 TAAAAGTGTGAAGATTTAACTTGAAGATAAGAGTTTAGTATTTATCATATTTG
*
4072228 TAAAAGTGTGAAGATTTAACTTGAAGCTAAGAGTTTAGTATTTATCATATTTG
1 TAAAAGTGTGAAGATTTAACTTGAAGATAAGAGTTTAGTATTTATCATATTTG
4072281 TAA
1 TAA
4072284 CATTTAATAA
Statistics
Matches: 55, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
53 55 1.00
ACGTcount: A:0.38, C:0.05, G:0.18, T:0.39
Consensus pattern (53 bp):
TAAAAGTGTGAAGATTTAACTTGAAGATAAGAGTTTAGTATTTATCATATTTG
Found at i:4073156 original size:21 final size:21
Alignment explanation
Indices: 4073132--4073171 Score: 71
Period size: 21 Copynumber: 1.9 Consensus size: 21
4073122 AAAAAAAGTT
4073132 AGGAATAAAATTTATAACTAA
1 AGGAATAAAATTTATAACTAA
*
4073153 AGGAATAGAATTTATAACT
1 AGGAATAAAATTTATAACT
4073172 CTAATTATAA
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
21 18 1.00
ACGTcount: A:0.53, C:0.05, G:0.12, T:0.30
Consensus pattern (21 bp):
AGGAATAAAATTTATAACTAA
Found at i:4074548 original size:17 final size:17
Alignment explanation
Indices: 4074526--4074577 Score: 61
Period size: 17 Copynumber: 3.1 Consensus size: 17
4074516 ATTTAAATTG
*
4074526 ATTAATGTTAAAATTAA
1 ATTAATTTTAAAATTAA
**
4074543 ATTAATTTTAATTTTAA
1 ATTAATTTTAAAATTAA
4074560 ATT-ATTTTAAAAGTTAA
1 ATTAATTTTAAAA-TTAA
4074577 A
1 A
4074578 ATTTTTAAAT
Statistics
Matches: 29, Mismatches: 5, Indels: 2
0.81 0.14 0.06
Matches are distributed among these distances:
16 7 0.24
17 22 0.76
ACGTcount: A:0.48, C:0.00, G:0.04, T:0.48
Consensus pattern (17 bp):
ATTAATTTTAAAATTAA
Found at i:4076767 original size:24 final size:23
Alignment explanation
Indices: 4076734--4076780 Score: 67
Period size: 23 Copynumber: 2.0 Consensus size: 23
4076724 ACAGTAGTTA
4076734 AAAAAATTATTAAATGATTAAATT
1 AAAAAATTATT-AATGATTAAATT
* *
4076758 AAAAATTTATTAATGATTTAATT
1 AAAAAATTATTAATGATTAAATT
4076781 TGATATATAC
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
23 11 0.52
24 10 0.48
ACGTcount: A:0.53, C:0.00, G:0.04, T:0.43
Consensus pattern (23 bp):
AAAAAATTATTAATGATTAAATT
Found at i:4076829 original size:20 final size:21
Alignment explanation
Indices: 4076799--4076839 Score: 66
Period size: 20 Copynumber: 2.0 Consensus size: 21
4076789 ACATTAAAAT
4076799 TAAAGATTAATTAAATTAGTA
1 TAAAGATTAATTAAATTAGTA
*
4076820 TAAA-ATTAATTTAATTAGTA
1 TAAAGATTAATTAAATTAGTA
4076840 AACATATAAA
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
20 15 0.79
21 4 0.21
ACGTcount: A:0.51, C:0.00, G:0.07, T:0.41
Consensus pattern (21 bp):
TAAAGATTAATTAAATTAGTA
Found at i:4077948 original size:6 final size:6
Alignment explanation
Indices: 4077939--4077966 Score: 56
Period size: 6 Copynumber: 4.7 Consensus size: 6
4077929 TGGCGTTGGT
4077939 TTTGAG TTTGAG TTTGAG TTTGAG TTTG
1 TTTGAG TTTGAG TTTGAG TTTGAG TTTG
4077967 TTGTTTGGGG
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 22 1.00
ACGTcount: A:0.14, C:0.00, G:0.32, T:0.54
Consensus pattern (6 bp):
TTTGAG
Found at i:4080833 original size:22 final size:22
Alignment explanation
Indices: 4080773--4080833 Score: 63
Period size: 22 Copynumber: 2.7 Consensus size: 22
4080763 TTTAATCATG
4080773 AATT-TAATTAAAATTATTTTTAT
1 AATTATAATT-AAA-TATTTTTAT
* *
4080796 -ATTAATATTTATATATTTTTAT
1 AATT-ATAATTAAATATTTTTAT
4080818 AATTATAATTAAATAT
1 AATTATAATTAAATAT
4080834 AAAAATATTA
Statistics
Matches: 31, Mismatches: 4, Indels: 7
0.74 0.10 0.17
Matches are distributed among these distances:
22 22 0.71
23 5 0.16
24 4 0.13
ACGTcount: A:0.44, C:0.00, G:0.00, T:0.56
Consensus pattern (22 bp):
AATTATAATTAAATATTTTTAT
Found at i:4080892 original size:41 final size:41
Alignment explanation
Indices: 4080836--4080913 Score: 106
Period size: 41 Copynumber: 1.9 Consensus size: 41
4080826 TTAAATATAA
* *
4080836 AAATATTATTTAATTATATAA-ATAATGATTTAAACTAAATC
1 AAATATTATTTAATTATAAAATATAAT-ATCTAAACTAAATC
4080877 AAAT-TTATTTAAATTATAAAATATAATATCTAAACTA
1 AAATATTATTT-AATTATAAAATATAATATCTAAACTA
4080914 GATCTGTCAA
Statistics
Matches: 33, Mismatches: 2, Indels: 4
0.85 0.05 0.10
Matches are distributed among these distances:
40 6 0.18
41 22 0.67
42 5 0.15
ACGTcount: A:0.53, C:0.05, G:0.01, T:0.41
Consensus pattern (41 bp):
AAATATTATTTAATTATAAAATATAATATCTAAACTAAATC
Found at i:4088982 original size:2 final size:2
Alignment explanation
Indices: 4088975--4089019 Score: 90
Period size: 2 Copynumber: 22.5 Consensus size: 2
4088965 GCATTGCATT
4088975 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
4089017 AG A
1 AG A
4089020 CCTTTTGAAA
Statistics
Matches: 43, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 43 1.00
ACGTcount: A:0.51, C:0.00, G:0.49, T:0.00
Consensus pattern (2 bp):
AG
Found at i:4090449 original size:6 final size:6
Alignment explanation
Indices: 4090438--4090463 Score: 52
Period size: 6 Copynumber: 4.3 Consensus size: 6
4090428 TTATTAAACA
4090438 TGGAAG TGGAAG TGGAAG TGGAAG TG
1 TGGAAG TGGAAG TGGAAG TGGAAG TG
4090464 AGTGACCCTT
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 20 1.00
ACGTcount: A:0.31, C:0.00, G:0.50, T:0.19
Consensus pattern (6 bp):
TGGAAG
Found at i:4093606 original size:170 final size:172
Alignment explanation
Indices: 4093307--4093636 Score: 538
Period size: 170 Copynumber: 1.9 Consensus size: 172
4093297 GTGTCCAGCT
*
4093307 TTTTACAGGCTCAACTTTATACTTCCACTCAATGTCGCACCATTATTCACTTTCATTGTCGATTC
1 TTTTACAGGCTCAACTTTATACTTCCACTCAATGTCGCACCATTATTCACTTTCACTGTCGATTC
* *
4093372 ATAAGAATTGAAACCAGCATTGCCATTAACAATGAAATAGCTAAAAAAACTATTTCACTTGGGTC
66 ATAAGAATTGAAACCAGCACTGCCATTAACAATGAAATAGCTAAAAAAACCATTTCACTTGGGTC
*
4093437 AATGGATTGCAATTTCTACTTAATCTAGTTTACAGTCTAGCC
131 AATAGATTGCAATTTCTACTTAATCTAGTTTACAGTCTAGCC
* * * * *
4093479 TTTTACAGGCTTAACTTTATTCTTCCACTCAATGTCGCACTATTA-T-GCTTTCACTGTCTATTC
1 TTTTACAGGCTCAACTTTATACTTCCACTCAATGTCGCACCATTATTCACTTTCACTGTCGATTC
* *
4093542 ATAAGAATTGAAACCAGCACTGCCATTAACAATGAAATAGCTACAAAAACCATTTCAGTTGGGTC
66 ATAAGAATTGAAACCAGCACTGCCATTAACAATGAAATAGCTAAAAAAACCATTTCACTTGGGTC
*
4093607 AATAGATTGCAATTTCTTCTTAATCTAGTT
131 AATAGATTGCAATTTCTACTTAATCTAGTT
4093637 CACATATTGA
Statistics
Matches: 146, Mismatches: 12, Indels: 2
0.91 0.08 0.01
Matches are distributed among these distances:
170 103 0.71
171 1 0.01
172 42 0.29
ACGTcount: A:0.32, C:0.21, G:0.12, T:0.35
Consensus pattern (172 bp):
TTTTACAGGCTCAACTTTATACTTCCACTCAATGTCGCACCATTATTCACTTTCACTGTCGATTC
ATAAGAATTGAAACCAGCACTGCCATTAACAATGAAATAGCTAAAAAAACCATTTCACTTGGGTC
AATAGATTGCAATTTCTACTTAATCTAGTTTACAGTCTAGCC
Found at i:4096216 original size:24 final size:26
Alignment explanation
Indices: 4096189--4096240 Score: 81
Period size: 25 Copynumber: 2.1 Consensus size: 26
4096179 TTAAAACTTT
4096189 ATTTATAT-ATTTTTTTAT-AATTAA
1 ATTTATATAATTTTTTTATGAATTAA
*
4096213 ATTTATATAATTTTTTTATGATTTAA
1 ATTTATATAATTTTTTTATGAATTAA
4096239 AT
1 AT
4096241 AATGATTCAG
Statistics
Matches: 25, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
24 8 0.32
25 10 0.40
26 7 0.28
ACGTcount: A:0.37, C:0.00, G:0.02, T:0.62
Consensus pattern (26 bp):
ATTTATATAATTTTTTTATGAATTAA
Found at i:4105296 original size:16 final size:17
Alignment explanation
Indices: 4105275--4105308 Score: 52
Period size: 16 Copynumber: 2.1 Consensus size: 17
4105265 AAAAAATTAA
4105275 ATATATTC-TATTAAAT
1 ATATATTCGTATTAAAT
*
4105291 ATATATTCGTATTTAAT
1 ATATATTCGTATTAAAT
4105308 A
1 A
4105309 CTATCACTTA
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:0.41, C:0.06, G:0.03, T:0.50
Consensus pattern (17 bp):
ATATATTCGTATTAAAT
Found at i:4115072 original size:9 final size:9
Alignment explanation
Indices: 4115060--4115094 Score: 52
Period size: 9 Copynumber: 3.8 Consensus size: 9
4115050 TAAAAATATC
4115060 ATATTAATT
1 ATATTAATT
4115069 ATATTAATT
1 ATATTAATT
*
4115078 TTATTTAATT
1 ATA-TTAATT
4115088 ATATTAA
1 ATATTAA
4115095 ATTTTTTATT
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
9 15 0.65
10 8 0.35
ACGTcount: A:0.43, C:0.00, G:0.00, T:0.57
Consensus pattern (9 bp):
ATATTAATT
Found at i:4115087 original size:19 final size:18
Alignment explanation
Indices: 4115063--4115111 Score: 66
Period size: 19 Copynumber: 2.8 Consensus size: 18
4115053 AAATATCATA
*
4115063 TTAATTATATTAATTTTAT
1 TTAATTATATTAAATTT-T
4115082 TTAATTATATTAAATTTT
1 TTAATTATATTAAATTTT
4115100 TT-ATT-TATTAAA
1 TTAATTATATTAAA
4115112 CAGTATCTTA
Statistics
Matches: 29, Mismatches: 1, Indels: 3
0.88 0.03 0.09
Matches are distributed among these distances:
16 7 0.24
17 3 0.10
18 3 0.10
19 16 0.55
ACGTcount: A:0.39, C:0.00, G:0.00, T:0.61
Consensus pattern (18 bp):
TTAATTATATTAAATTTT
Found at i:4115768 original size:21 final size:21
Alignment explanation
Indices: 4115744--4115786 Score: 86
Period size: 21 Copynumber: 2.0 Consensus size: 21
4115734 AGCGATAAAC
4115744 TATTTCAACTCTCATGTCCGA
1 TATTTCAACTCTCATGTCCGA
4115765 TATTTCAACTCTCATGTCCGA
1 TATTTCAACTCTCATGTCCGA
4115786 T
1 T
4115787 GCATACCTGG
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 22 1.00
ACGTcount: A:0.23, C:0.28, G:0.09, T:0.40
Consensus pattern (21 bp):
TATTTCAACTCTCATGTCCGA
Found at i:4124669 original size:22 final size:22
Alignment explanation
Indices: 4124644--4124688 Score: 63
Period size: 22 Copynumber: 2.0 Consensus size: 22
4124634 AATATAAATT
*
4124644 TATTTTTTAAATATTTAAAAAA
1 TATTTATTAAATATTTAAAAAA
* *
4124666 TATTTATTAAATTTTTTAAAAA
1 TATTTATTAAATATTTAAAAAA
4124688 T
1 T
4124689 TTAACAAAAA
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
22 20 1.00
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (22 bp):
TATTTATTAAATATTTAAAAAA
Found at i:4125467 original size:18 final size:18
Alignment explanation
Indices: 4125429--4125467 Score: 53
Period size: 18 Copynumber: 2.2 Consensus size: 18
4125419 AACTTAATAG
*
4125429 TAATTAAAAATAATTTTA
1 TAATTAAAAATAATTTAA
4125447 TAATTAAAAAT-ATTTGAA
1 TAATTAAAAATAATTT-AA
4125465 TAA
1 TAA
4125468 AAAATAAAAA
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
17 4 0.21
18 15 0.79
ACGTcount: A:0.56, C:0.00, G:0.03, T:0.41
Consensus pattern (18 bp):
TAATTAAAAATAATTTAA
Found at i:4126355 original size:17 final size:18
Alignment explanation
Indices: 4126335--4126390 Score: 55
Period size: 18 Copynumber: 3.1 Consensus size: 18
4126325 TTTTAATATT
4126335 ATTTAATAATAAAAT-AA
1 ATTTAATAATAAAATAAA
4126352 ATTT-ATAAATAAAATTAAA
1 ATTTAAT-AATAAAA-TAAA
*
4126371 ATTAAATAA-AAAATTAAA
1 ATTTAATAATAAAA-TAAA
4126389 AT
1 AT
4126391 AATTTTAAAT
Statistics
Matches: 34, Mismatches: 1, Indels: 7
0.81 0.02 0.17
Matches are distributed among these distances:
16 2 0.06
17 11 0.32
18 12 0.35
19 7 0.21
20 2 0.06
ACGTcount: A:0.66, C:0.00, G:0.00, T:0.34
Consensus pattern (18 bp):
ATTTAATAATAAAATAAA
Found at i:4130381 original size:2 final size:2
Alignment explanation
Indices: 4130374--4130408 Score: 70
Period size: 2 Copynumber: 17.5 Consensus size: 2
4130364 GGTAATTAGG
4130374 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
4130409 ATGGAATGGT
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 33 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:4138738 original size:28 final size:29
Alignment explanation
Indices: 4138687--4138742 Score: 78
Period size: 28 Copynumber: 2.0 Consensus size: 29
4138677 ATTTAAATTG
* *
4138687 ATTTTATTTGATATTTCATAATAAAATAA
1 ATTTTATTTGAAATTTAATAATAAAATAA
*
4138716 ATTTTATTT-AAATTTAATTATAAAATA
1 ATTTTATTTGAAATTTAATAATAAAATA
4138743 TATAAATATT
Statistics
Matches: 24, Mismatches: 3, Indels: 1
0.86 0.11 0.04
Matches are distributed among these distances:
28 15 0.62
29 9 0.38
ACGTcount: A:0.46, C:0.02, G:0.02, T:0.50
Consensus pattern (29 bp):
ATTTTATTTGAAATTTAATAATAAAATAA
Found at i:4138755 original size:32 final size:32
Alignment explanation
Indices: 4138712--4138775 Score: 85
Period size: 32 Copynumber: 2.0 Consensus size: 32
4138702 TCATAATAAA
* *
4138712 ATAAATTTTATT-TAAATTTAATTATAAAATAT
1 ATAAATATTATTAT-AATTTAATTAAAAAATAT
*
4138744 ATAAATATTATTATAATTTATTTAAAAAATAT
1 ATAAATATTATTATAATTTAATTAAAAAATAT
4138776 TAATTTATAA
Statistics
Matches: 28, Mismatches: 3, Indels: 2
0.85 0.09 0.06
Matches are distributed among these distances:
32 27 0.96
33 1 0.04
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (32 bp):
ATAAATATTATTATAATTTAATTAAAAAATAT
Found at i:4138769 original size:21 final size:21
Alignment explanation
Indices: 4138718--4138769 Score: 61
Period size: 21 Copynumber: 2.5 Consensus size: 21
4138708 TAAAATAAAT
4138718 TTTATTTAAATTTAATTATAA
1 TTTATTTAAATTTAATTATAA
** *
4138739 AATATATAAATATT-ATTATAA
1 TTTATTTAAAT-TTAATTATAA
4138760 TTTATTTAAA
1 TTTATTTAAA
4138770 AAATATTAAT
Statistics
Matches: 24, Mismatches: 6, Indels: 2
0.75 0.19 0.06
Matches are distributed among these distances:
21 22 0.92
22 2 0.08
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (21 bp):
TTTATTTAAATTTAATTATAA
Found at i:4147964 original size:24 final size:25
Alignment explanation
Indices: 4147937--4147986 Score: 75
Period size: 24 Copynumber: 2.0 Consensus size: 25
4147927 ATATTTTTAA
* *
4147937 TAAATTTATTTAGAATAT-AAATAT
1 TAAATTTATTAACAATATAAAATAT
4147961 TAAATTTATTAACAATATAAAATAT
1 TAAATTTATTAACAATATAAAATAT
4147986 T
1 T
4147987 TATATTTAAT
Statistics
Matches: 23, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
24 16 0.70
25 7 0.30
ACGTcount: A:0.52, C:0.02, G:0.02, T:0.44
Consensus pattern (25 bp):
TAAATTTATTAACAATATAAAATAT
Found at i:4150047 original size:534 final size:523
Alignment explanation
Indices: 4148895--4150222 Score: 1360
Period size: 545 Copynumber: 2.5 Consensus size: 523
4148885 TCTAAATTAG
*
4148895 TTTTATAAAATTAATTAGAGTATAAAGCTATATTCTTTACCATTGGTAGAAAACTT-CTATTTAT
1 TTTTATAAAATTAATTAGAGTATAAAGCTATATTCTTTACCATTCGTAG-AAA-TTCCTATTTAT
** * *
4148959 AATACCTAGTAAATAAATTTAAGTTT-ATATTTTTTTAAGATACGAAAGGAAAATTAAAATTGTA
64 -ATAATTAGTAAATAAATTTAA-TTTAATATTTTTTTAAGATATGAAA-GAAAATTAAAATTCTA
* *
4149023 TTTGTTTACTTGTGTATATATATAAAAGATAAGTCAATTAAAAGTATAAAAAGAAACATATATAA
126 TTTGTTTACATGTGTATATATAT-ATAG-TAAGTCAATTAAAAGTATAAAAAGAAACAT-TATAA
*
4149088 TTAATTATATGAAATATTTTAATTTTAAATTAAATCAAATCAAATCAAAATAATTAAATATACGA
188 TTAATTATATAAAAT-TTTTAATTTTAAA-T---T-AAATCAAATCAAAATAATTAAATATACGA
* *
4149153 CACATAATGAATTTTTCTACATTAGACAATTACCTTTTTCTAAAAGAGTTTTATCTTTTATATAT
247 CACATAATAAATTTTTCTACATGAGACAATTACCTTTTTCTAAAAGAGTTTTATCTTTTATATAT
* * *
4149218 TTATTATATAAGGTTTTGTCTATATTTTTACTTATCAAAATTATTATAAATTACTATTTACTATT
312 TTATTATATAAGGATTTGTCTATATTTTTACTTATCAAAATTATCATAAATTACTATTTACTATC
* * *
4149283 TGAATTTAATTATTTTTAAAATTAAATACAATTTGTAAAAAACCCTTTAATTTAATATTTTTTTT
377 TGAACTTAATTATTTTTAAAATTAAATACAACTTGTAAAAAACCCTTTAATTTAATATTTTTGTT
* * *
4149348 GAGATATGAAAATAAAAATAAAATTTTATTTATTTACACACACACACATATATATATAAGATATG
442 GAGACATGAAAAGAAAAATAAAATTTTATTTATTT------A-ACACATATATATATAAGAAATG
* *
4149413 CTAATTGAAAGTATAAAAAAAAATTAA
500 CTAATTAAAAGTAT---AAAAAATGAA
* * **
4149440 TTTTATAAAATTAATTAGAGTACAAAGCTATATTCTTTACCATACGTAGAAAACCTCTATTTATA
1 TTTTATAAAATTAATTAGAGTATAAAGCTATATTCTTTACCATTCGTAGAAATTC-CTATTTATA
* *
4149505 TCAATTAGTAAATAAATTTAATTTAATATTTTTTTAAGATATGAAAGAAATTTTAAAATTTTATT
65 T-AATTAGTAAATAAATTTAATTTAATATTTTTTTAAGATATGAAAGAAA-ATTAAAATTCTATT
* *
4149570 TGTTTACGTGTGTGTATATATATAGTAAGTCAATTAAAAGTAT-AAAAGAAACATTCATAATTAA
128 TGTTTACATGTGTATATATATATAGTAAGTCAATTAAAAGTATAAAAAGAAACATT-ATAATTAA
* * * * * *
4149634 TTACATAAAAATTTTTAATTTTAAATTAAATCAAGTCAAAATAATTAAATTTGCTACATATAATA
192 TTATAT-AAAATTTTTAATTTTAAATTAAATCAAATCAAAATAATTAAATATACGACACATAATA
* * * *
4149699 AATTTTTTCT-CATCGA-ACAATTACCTTTTTTGTAAAAG-GTTTTGTTTTTTATATGTTTATTA
256 AA-TTTTTCTACAT-GAGACAATTACC-TTTTTCTAAAAGAGTTTTATCTTTTATATATTTATTA
* * * ** *
4149761 TATAA-GATTT-T-TATATTTTTATTTATTAAAATTATCGT-GGTTACTATTTATTATCTGAACT
318 TATAAGGATTTGTCTATATTTTTACTTATCAAAATTATCATAAATTACTATTTACTATCTGAACT
* * * *
4149822 TAATTTATTTTTAAAATTATATACCACTTGTAGAAAACCTAGTTTAGTAAATAAATTTAAGTAAA
383 TAA-TTATTTTTAAAATTAAATACAACTTGTAAAAAACC----CT--T---T-AATTTAA-T--A
* *
4149887 TATCTTTGTT-AGACATGGAAAGAAAAATAAAATTTTATTTATTT-ACATATATATATATAAGGT
434 T-T-TTTGTTGAGACATGAAAAGAAAAATAAAATTTTATTTATTTAACACATATATATATAA-G-
4149950 AAAT-C-AATTAAAAGTAT-AAAAA-GAA
495 AAATGCTAATTAAAAGTATAAAAAATGAA
* * ** * *
4149975 -TTTATAAAATTAATTAAAGTATAAAACTGCATTATTTTACCATTTGTAGAAATTCCTATTTATA
1 TTTTATAAAATTAATTAGAGTATAAAGCTATATT-CTTTACCATTCGTAGAAATTCCTATTTATA
* * **
4150039 GTAATTAGTAAATAAATTTTAATTTAATATTTTTGTAAGATATGGAAAGAAAAATAAAATTCGGT
65 -TAATTAGTAAATAAA-TTTAATTTAATATTTTTTTAAGATAT-GAAAGAAAATTAAAATTCTAT
* * * * * *
4150104 TTGTTTATATATATATATATATATATAAGGTAAGTCAATTAAAAGTATAAAAAGAAATAAATATC
127 TTG-TT-TACATGTGTATATATATAT-A-GTAAGTCAATTAAAAGTATAAAAAGAAA-CATTATA
* * *
4150169 ATTAATTATAT-GAATATTTTAATCTTAAATTAAATCAAATTAAAATAATTAAAT
187 ATTAATTATATAAAAT-TTTTAATTTTAAATTAAATCAAATCAAAATAATTAAAT
4150223 GTGTAATAGA
Statistics
Matches: 666, Mismatches: 78, Indels: 84
0.80 0.09 0.10
Matches are distributed among these distances:
533 21 0.03
534 105 0.16
535 56 0.08
536 19 0.03
537 86 0.13
538 25 0.04
539 54 0.08
540 47 0.07
541 6 0.01
542 40 0.06
543 23 0.03
544 22 0.03
545 123 0.18
547 2 0.00
548 32 0.05
549 5 0.01
ACGTcount: A:0.44, C:0.07, G:0.08, T:0.42
Consensus pattern (523 bp):
TTTTATAAAATTAATTAGAGTATAAAGCTATATTCTTTACCATTCGTAGAAATTCCTATTTATAT
AATTAGTAAATAAATTTAATTTAATATTTTTTTAAGATATGAAAGAAAATTAAAATTCTATTTGT
TTACATGTGTATATATATATAGTAAGTCAATTAAAAGTATAAAAAGAAACATTATAATTAATTAT
ATAAAATTTTTAATTTTAAATTAAATCAAATCAAAATAATTAAATATACGACACATAATAAATTT
TTCTACATGAGACAATTACCTTTTTCTAAAAGAGTTTTATCTTTTATATATTTATTATATAAGGA
TTTGTCTATATTTTTACTTATCAAAATTATCATAAATTACTATTTACTATCTGAACTTAATTATT
TTTAAAATTAAATACAACTTGTAAAAAACCCTTTAATTTAATATTTTTGTTGAGACATGAAAAGA
AAAATAAAATTTTATTTATTTAACACATATATATATAAGAAATGCTAATTAAAAGTATAAAAAAT
GAA
Found at i:4150697 original size:22 final size:24
Alignment explanation
Indices: 4150664--4150711 Score: 66
Period size: 23 Copynumber: 2.1 Consensus size: 24
4150654 AGATTTTGAC
4150664 TTTTATATA-TTT-ATTATATAAAA
1 TTTTATATATTTTAATTAT-TAAAA
4150687 TTTT-TATATTTTAATTATTAAAA
1 TTTTATATATTTTAATTATTAAAA
4150710 TT
1 TT
4150712 AATATTGATT
Statistics
Matches: 23, Mismatches: 0, Indels: 4
0.85 0.00 0.15
Matches are distributed among these distances:
22 4 0.17
23 14 0.61
24 5 0.22
ACGTcount: A:0.40, C:0.00, G:0.00, T:0.60
Consensus pattern (24 bp):
TTTTATATATTTTAATTATTAAAA
Found at i:4150699 original size:23 final size:24
Alignment explanation
Indices: 4150664--4150711 Score: 73
Period size: 24 Copynumber: 2.0 Consensus size: 24
4150654 AGATTTTGAC
4150664 TTTTATATATTT-ATTATATAAAAT
1 TTTTATATATTTAATTAT-TAAAAT
4150688 TTTTATAT-TTTAATTATTAAAAT
1 TTTTATATATTTAATTATTAAAAT
4150711 T
1 T
4150712 AATATTGATT
Statistics
Matches: 23, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
23 10 0.43
24 13 0.57
ACGTcount: A:0.40, C:0.00, G:0.00, T:0.60
Consensus pattern (24 bp):
TTTTATATATTTAATTATTAAAAT
Found at i:4160488 original size:18 final size:19
Alignment explanation
Indices: 4160458--4160507 Score: 57
Period size: 18 Copynumber: 2.7 Consensus size: 19
4160448 TTATTTAATT
*
4160458 ATAAAATATATAAATATTA
1 ATAAAATAAATAAATATTA
* * *
4160477 ATATAA-AAATAATTTTTA
1 ATAAAATAAATAAATATTA
4160495 ATAAAATAAATAA
1 ATAAAATAAATAA
4160508 TAAATTTAAA
Statistics
Matches: 25, Mismatches: 5, Indels: 2
0.78 0.16 0.06
Matches are distributed among these distances:
18 14 0.56
19 11 0.44
ACGTcount: A:0.64, C:0.00, G:0.00, T:0.36
Consensus pattern (19 bp):
ATAAAATAAATAAATATTA
Found at i:4160515 original size:21 final size:20
Alignment explanation
Indices: 4160450--4160516 Score: 57
Period size: 22 Copynumber: 3.3 Consensus size: 20
4160440 TATATTTTTT
* *
4160450 ATTTAATTATAAAATATATAA
1 ATTTAATAAAAAAATA-ATAA
*
4160471 ATATTAATATAAAAATAAT--
1 AT-TTAATAAAAAAATAATAA
*
4160490 TTTTAATAAAATAAATAATAA
1 ATTTAATAAAA-AAATAATAA
4160511 ATTTAA
1 ATTTAA
4160517 ATTTACATTT
Statistics
Matches: 36, Mismatches: 6, Indels: 8
0.72 0.12 0.16
Matches are distributed among these distances:
18 8 0.22
19 8 0.22
21 9 0.25
22 11 0.31
ACGTcount: A:0.60, C:0.00, G:0.00, T:0.40
Consensus pattern (20 bp):
ATTTAATAAAAAAATAATAA
Found at i:4165300 original size:16 final size:17
Alignment explanation
Indices: 4165272--4165309 Score: 69
Period size: 16 Copynumber: 2.3 Consensus size: 17
4165262 TTTATTCTCA
4165272 AGTGCTCAAAATAGATC
1 AGTGCTCAAAATAGATC
4165289 AGTGCT-AAAATAGATC
1 AGTGCTCAAAATAGATC
4165305 AGTGC
1 AGTGC
4165310 ATCATAGTCT
Statistics
Matches: 21, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
16 15 0.71
17 6 0.29
ACGTcount: A:0.39, C:0.16, G:0.21, T:0.24
Consensus pattern (17 bp):
AGTGCTCAAAATAGATC
Found at i:4169697 original size:10 final size:10
Alignment explanation
Indices: 4169682--4169736 Score: 51
Period size: 10 Copynumber: 5.6 Consensus size: 10
4169672 AAAATAATAA
4169682 TTATTTAATT
1 TTATTTAATT
*
4169692 TTATTTTA-T
1 TTATTTAATT
*
4169701 TAATATTAATT
1 TTAT-TTAATT
**
4169712 TTAAATAATT
1 TTATTTAATT
4169722 TT-TTTAATT
1 TTATTTAATT
4169731 TTATTT
1 TTATTT
4169737 TAAGTATCAA
Statistics
Matches: 34, Mismatches: 8, Indels: 6
0.71 0.17 0.12
Matches are distributed among these distances:
9 11 0.32
10 20 0.59
11 3 0.09
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (10 bp):
TTATTTAATT
Found at i:4171208 original size:30 final size:30
Alignment explanation
Indices: 4171167--4171227 Score: 95
Period size: 30 Copynumber: 2.0 Consensus size: 30
4171157 ATTATAATTA
* *
4171167 TTTTAACATAGATTTTTATTTTAATTTATT
1 TTTTAACATAGATTTTTATTTCAACTTATT
*
4171197 TTTTAATATAGATTTTTATTTCAACTTATT
1 TTTTAACATAGATTTTTATTTCAACTTATT
4171227 T
1 T
4171228 CATACTTAAT
Statistics
Matches: 28, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
30 28 1.00
ACGTcount: A:0.30, C:0.05, G:0.03, T:0.62
Consensus pattern (30 bp):
TTTTAACATAGATTTTTATTTCAACTTATT
Found at i:4176222 original size:34 final size:34
Alignment explanation
Indices: 4176179--4176247 Score: 138
Period size: 34 Copynumber: 2.0 Consensus size: 34
4176169 AGATTTGCAC
4176179 TTCCTCCAAGAGGCTATTTATATATAATAATGAT
1 TTCCTCCAAGAGGCTATTTATATATAATAATGAT
4176213 TTCCTCCAAGAGGCTATTTATATATAATAATGAT
1 TTCCTCCAAGAGGCTATTTATATATAATAATGAT
4176247 T
1 T
4176248 GATCATATTA
Statistics
Matches: 35, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
34 35 1.00
ACGTcount: A:0.35, C:0.14, G:0.12, T:0.39
Consensus pattern (34 bp):
TTCCTCCAAGAGGCTATTTATATATAATAATGAT
Found at i:4183584 original size:18 final size:19
Alignment explanation
Indices: 4183561--4183597 Score: 58
Period size: 19 Copynumber: 2.0 Consensus size: 19
4183551 GATCTGCAAC
*
4183561 AAACCAATG-AAATGAAAA
1 AAACCAAAGAAAATGAAAA
4183579 AAACCAAAGAAAATGAAAA
1 AAACCAAAGAAAATGAAAA
4183598 TGCAAAAAAA
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
18 8 0.47
19 9 0.53
ACGTcount: A:0.70, C:0.11, G:0.11, T:0.08
Consensus pattern (19 bp):
AAACCAAAGAAAATGAAAA
Found at i:4183615 original size:24 final size:23
Alignment explanation
Indices: 4183566--4183616 Score: 57
Period size: 25 Copynumber: 2.1 Consensus size: 23
4183556 GCAACAAACC
*
4183566 AATGAAATGAAAAAAACCAAAGAA
1 AATGAAATGAAAAAAA-CAAAAAA
*
4183590 AATGAAAATGCAAAAAAAAAAAAAA
1 AATG-AAATG-AAAAAAACAAAAAA
4183615 AA
1 AA
4183617 AAGAACACCC
Statistics
Matches: 23, Mismatches: 2, Indels: 3
0.82 0.07 0.11
Matches are distributed among these distances:
24 4 0.17
25 12 0.52
26 7 0.30
ACGTcount: A:0.76, C:0.06, G:0.10, T:0.08
Consensus pattern (23 bp):
AATGAAATGAAAAAAACAAAAAA
Found at i:4185870 original size:28 final size:29
Alignment explanation
Indices: 4185809--4185864 Score: 78
Period size: 28 Copynumber: 2.0 Consensus size: 29
4185799 ATTTAAATTA
* * *
4185809 TTAATTAATAAAAATATTTTTATTTTAAG
1 TTAATTAATAAAAATATATTAATATTAAG
4185838 TTAATT-ATAAAAATATATTAATATTAA
1 TTAATTAATAAAAATATATTAATATTAA
4185865 TATAATAATA
Statistics
Matches: 24, Mismatches: 3, Indels: 1
0.86 0.11 0.04
Matches are distributed among these distances:
28 18 0.75
29 6 0.25
ACGTcount: A:0.50, C:0.00, G:0.02, T:0.48
Consensus pattern (29 bp):
TTAATTAATAAAAATATATTAATATTAAG
Found at i:4186660 original size:21 final size:23
Alignment explanation
Indices: 4186636--4186683 Score: 64
Period size: 23 Copynumber: 2.2 Consensus size: 23
4186626 TTTTAATATT
* *
4186636 TATATCTAAT-AA-ATATTTTAA
1 TATATATAATAAACATATTTAAA
4186657 TATATATAATAAACATATTTAAA
1 TATATATAATAAACATATTTAAA
4186680 TATA
1 TATA
4186684 CATTTAATAA
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
21 9 0.39
22 2 0.09
23 12 0.52
ACGTcount: A:0.52, C:0.04, G:0.00, T:0.44
Consensus pattern (23 bp):
TATATATAATAAACATATTTAAA
Found at i:4194427 original size:2 final size:2
Alignment explanation
Indices: 4194412--4194482 Score: 90
Period size: 2 Copynumber: 35.5 Consensus size: 2
4194402 CCCTCATAGA
* * * *
4194412 TC TC TC TA TG TC TC TC TC TC AT- TC AC TC AC 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 TC
4194454 TC TC TC TC TC TC TC TC TC TC TC TC TC TC T
1 TC TC TC TC TC TC TC TC TC TC TC TC TC TC T
4194483 TTGTCTGCCA
Statistics
Matches: 60, Mismatches: 7, Indels: 4
0.85 0.10 0.06
Matches are distributed among these distances:
1 1 0.02
2 58 0.97
3 1 0.02
ACGTcount: A:0.06, C:0.45, G:0.01, T:0.48
Consensus pattern (2 bp):
TC
Found at i:4199133 original size:53 final size:52
Alignment explanation
Indices: 4199076--4199177 Score: 152
Period size: 53 Copynumber: 1.9 Consensus size: 52
4199066 TGCTTTGAAC
4199076 CAAGA-GACGATTTGAGCCAAAAAGCAATCAAACAGTGGCTGTTTTGGCATTGT
1 CAAGACGA-GATTTGAGCCAAAAAGCAATCAAACAGTGGCTG-TTTGGCATTGT
* * *
4199129 CAAGACTAGGTTTGAGCTAAAAAGCAATCAAACAGTGGCTGTTTGGCAT
1 CAAGACGAGATTTGAGCCAAAAAGCAATCAAACAGTGGCTGTTTGGCAT
4199178 CATCAAAACT
Statistics
Matches: 45, Mismatches: 3, Indels: 3
0.88 0.06 0.06
Matches are distributed among these distances:
52 8 0.18
53 36 0.80
54 1 0.02
ACGTcount: A:0.34, C:0.17, G:0.25, T:0.25
Consensus pattern (52 bp):
CAAGACGAGATTTGAGCCAAAAAGCAATCAAACAGTGGCTGTTTGGCATTGT
Found at i:4199532 original size:21 final size:21
Alignment explanation
Indices: 4199506--4199545 Score: 62
Period size: 21 Copynumber: 1.9 Consensus size: 21
4199496 TAATTATAAT
4199506 TATAAAATTTATAAATATTAA
1 TATAAAATTTATAAATATTAA
* *
4199527 TATAAAATTTTTTAATATT
1 TATAAAATTTATAAATATT
4199546 TTATGTAATA
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
21 17 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (21 bp):
TATAAAATTTATAAATATTAA
Found at i:4203517 original size:20 final size:21
Alignment explanation
Indices: 4203486--4203547 Score: 67
Period size: 20 Copynumber: 3.0 Consensus size: 21
4203476 TATATAATTA
4203486 AATTACTTTTATATATTTTTAT
1 AATT-CTTTTATATATTTTTAT
4203508 AATT-TTTTATAT-TTATTT-T
1 AATTCTTTTATATATT-TTTAT
*
4203527 AATTCTATTATTATATTTTTA
1 AATTCTTTTA-TATATTTTTA
4203548 ATATCTATTC
Statistics
Matches: 34, Mismatches: 1, Indels: 10
0.76 0.02 0.22
Matches are distributed among these distances:
19 7 0.21
20 15 0.44
21 6 0.18
22 6 0.18
ACGTcount: A:0.31, C:0.03, G:0.00, T:0.66
Consensus pattern (21 bp):
AATTCTTTTATATATTTTTAT
Found at i:4204526 original size:19 final size:20
Alignment explanation
Indices: 4204498--4204536 Score: 62
Period size: 19 Copynumber: 2.0 Consensus size: 20
4204488 TATTAGAAAA
*
4204498 TGCGTTTATT-TATTACATT
1 TGCGTCTATTGTATTACATT
4204517 TGCGTCTATTGTATTACATT
1 TGCGTCTATTGTATTACATT
4204537 AAATATATAG
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
19 9 0.50
20 9 0.50
ACGTcount: A:0.21, C:0.13, G:0.13, T:0.54
Consensus pattern (20 bp):
TGCGTCTATTGTATTACATT
Found at i:4205277 original size:16 final size:16
Alignment explanation
Indices: 4205256--4205303 Score: 62
Period size: 16 Copynumber: 3.0 Consensus size: 16
4205246 ATTTAAATAA
4205256 TTATATTATTATTATT
1 TTATATTATTATTATT
4205272 TTATATTATT-TTAATT
1 TTATATTATTATT-ATT
* *
4205288 TAATATTTTTATTATT
1 TTATATTATTATTATT
4205304 AAATTTACAT
Statistics
Matches: 28, Mismatches: 2, Indels: 4
0.82 0.06 0.12
Matches are distributed among these distances:
15 2 0.07
16 24 0.86
17 2 0.07
ACGTcount: A:0.31, C:0.00, G:0.00, T:0.69
Consensus pattern (16 bp):
TTATATTATTATTATT
Found at i:4207366 original size:1 final size:1
Alignment explanation
Indices: 4207360--4207385 Score: 52
Period size: 1 Copynumber: 26.0 Consensus size: 1
4207350 AGTACCCTCT
4207360 CCCCCCCCCCCCCCCCCCCCCCCCCC
1 CCCCCCCCCCCCCCCCCCCCCCCCCC
4207386 ACAAAAAAAA
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
1 25 1.00
ACGTcount: A:0.00, C:1.00, G:0.00, T:0.00
Consensus pattern (1 bp):
C
Found at i:4212249 original size:9 final size:9
Alignment explanation
Indices: 4212237--4212261 Score: 50
Period size: 9 Copynumber: 2.8 Consensus size: 9
4212227 AATAAAAAAA
4212237 ATAAATACT
1 ATAAATACT
4212246 ATAAATACT
1 ATAAATACT
4212255 ATAAATA
1 ATAAATA
4212262 AATAAATATT
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
9 16 1.00
ACGTcount: A:0.60, C:0.08, G:0.00, T:0.32
Consensus pattern (9 bp):
ATAAATACT
Found at i:4212298 original size:18 final size:19
Alignment explanation
Indices: 4212284--4212321 Score: 53
Period size: 18 Copynumber: 2.1 Consensus size: 19
4212274 TAAAAAATTA
4212284 AAATATAATA-TAAAATAAT
1 AAAT-TAATATTAAAATAAT
4212303 AAATTAATATTAAAA-AAT
1 AAATTAATATTAAAATAAT
4212321 A
1 A
4212322 GCATAGATGT
Statistics
Matches: 18, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
18 9 0.50
19 9 0.50
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.32
Consensus pattern (19 bp):
AAATTAATATTAAAATAAT
Found at i:4218371 original size:12 final size:12
Alignment explanation
Indices: 4218356--4218390 Score: 54
Period size: 12 Copynumber: 3.0 Consensus size: 12
4218346 GAAAAGAGGG
4218356 AAAAAAA-AAAA
1 AAAAAAAGAAAA
4218367 AAAAAAAGAAAA
1 AAAAAAAGAAAA
*
4218379 AGAAAAAGAAAA
1 AAAAAAAGAAAA
4218391 CAGCATACCT
Statistics
Matches: 22, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
11 7 0.32
12 15 0.68
ACGTcount: A:0.91, C:0.00, G:0.09, T:0.00
Consensus pattern (12 bp):
AAAAAAAGAAAA
Found at i:4222181 original size:28 final size:29
Alignment explanation
Indices: 4222059--4222218 Score: 85
Period size: 31 Copynumber: 5.3 Consensus size: 29
4222049 TTGTATTTGT
* * *
4222059 ATTTTTTTATATTTATAAATTTATATAAA
1 ATTTTTATATAATTATTAATTTATATAAA
* * * * *
4222088 ATTTTATCTATTAATAATTTATTT-TTTATAT
1 ATTTT-TATA-TAATTATTAATTTATATA-AA
* ** * *
4222119 ATTTTTAAATATATTCGTATATTTATATTAT
1 ATTTTTATATA-ATTATTA-ATTTATATAAA
*
4222150 ATTTATTATA-AATT-TTAGTTTATATAAA
1 ATTT-TTATATAATTATTAATTTATATAAA
4222178 ATTTTTTATATTAATTATTAATTT-TATATAA
1 A-TTTTTATA-TAATTATTAATTTATATA-AA
4222209 ATTTTTATAT
1 ATTTTTATAT
4222219 GTTTATTTAT
Statistics
Matches: 98, Mismatches: 21, Indels: 24
0.69 0.15 0.17
Matches are distributed among these distances:
28 14 0.14
29 13 0.13
30 30 0.31
31 35 0.36
32 6 0.06
ACGTcount: A:0.38, C:0.01, G:0.01, T:0.60
Consensus pattern (29 bp):
ATTTTTATATAATTATTAATTTATATAAA
Found at i:4222208 original size:32 final size:33
Alignment explanation
Indices: 4222168--4222237 Score: 90
Period size: 33 Copynumber: 2.2 Consensus size: 33
4222158 TAAATTTTAG
4222168 TTTATATAAAATTTTT-TAT-ATTAATTATTAAT
1 TTTATAT-AAATTTTTATATGATTAATTATTAAT
* *
4222200 TTTATATAAATTTTTATATGTTTATTTATTAAT
1 TTTATATAAATTTTTATATGATTAATTATTAAT
*
4222233 ATTAT
1 TTTAT
4222238 TTTTTACGTT
Statistics
Matches: 33, Mismatches: 3, Indels: 3
0.85 0.08 0.08
Matches are distributed among these distances:
31 8 0.24
32 10 0.30
33 15 0.45
ACGTcount: A:0.37, C:0.00, G:0.01, T:0.61
Consensus pattern (33 bp):
TTTATATAAATTTTTATATGATTAATTATTAAT
Found at i:4222268 original size:9 final size:10
Alignment explanation
Indices: 4222254--4222319 Score: 55
Period size: 10 Copynumber: 6.5 Consensus size: 10
4222244 CGTTATATTA
4222254 TATTTTA-AT
1 TATTTTATAT
4222263 TATTTTATAT
1 TATTTTATAT
4222273 TATTTTTATAT
1 TA-TTTTATAT
4222284 TATATTTAGT-T
1 TAT-TTTA-TAT
* *
4222295 TATCTTAGAT
1 TATTTTATAT
*
4222305 TTTTTTATAT
1 TATTTTATAT
*
4222315 AATTT
1 TATTT
4222320 ATTATAATTA
Statistics
Matches: 45, Mismatches: 7, Indels: 9
0.74 0.11 0.15
Matches are distributed among these distances:
9 7 0.16
10 19 0.42
11 18 0.40
12 1 0.02
ACGTcount: A:0.29, C:0.02, G:0.03, T:0.67
Consensus pattern (10 bp):
TATTTTATAT
Found at i:4222296 original size:16 final size:15
Alignment explanation
Indices: 4222138--4222360 Score: 83
Period size: 16 Copynumber: 14.9 Consensus size: 15
4222128 TATATTCGTA
4222138 TATTTATATTATATT
1 TATTTATATTATATT
*
4222153 TA-TTATA-AAT-TT
1 TATTTATATTATATT
* *
4222165 TAGTTTATATAAAATT
1 TA-TTTATATTATATT
4222181 T-TTTATATTAATTATT
1 TATTTATATT-A-TATT
* *
4222197 AATTT-TA-TATAAAT
1 TATTTATATTAT-ATT
*
4222211 T-TTTATATGTTTATT
1 TATTTATAT-TATATT
* *
4222226 TATTAATATTATTTTT
1 TATTTATATTA-TATT
*
4222242 TACGTTATATTATATTT
1 TA-TTTATATTATA-TT
* *
4222259 TAATTATTTTATATT
1 TATTTATATTATATT
*
4222274 ATTTTTATATTATATT
1 -TATTTATATTATATT
* *
4222290 TAGTTTATCTTAGATT
1 TA-TTTATATTATATT
*
4222306 TTTTTATA-TA-ATT
1 TATTTATATTATATT
*
4222319 TA-TTATAAT-TATT
1 TATTTATATTATATT
* * *
4222332 AATTTTAAATTTAAATT
1 TA-TTTATA-TTATATT
4222349 TATTTAT-TTATA
1 TATTTATATTATA
4222361 ATGATCTAAA
Statistics
Matches: 152, Mismatches: 33, Indels: 47
0.66 0.14 0.20
Matches are distributed among these distances:
12 9 0.06
13 15 0.10
14 28 0.18
15 22 0.14
16 60 0.39
17 18 0.12
ACGTcount: A:0.35, C:0.01, G:0.02, T:0.62
Consensus pattern (15 bp):
TATTTATATTATATT
Found at i:4222571 original size:2 final size:2
Alignment explanation
Indices: 4222566--4222591 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
4222556 TGAAGAAGGG
4222566 GA GA GA GA GA GA GA GA GA GA GA GA GA
1 GA GA GA GA GA GA GA GA GA GA GA GA GA
4222592 ATTCCAAAGT
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:0.50, C:0.00, G:0.50, T:0.00
Consensus pattern (2 bp):
GA
Found at i:4223795 original size:32 final size:31
Alignment explanation
Indices: 4223759--4223830 Score: 74
Period size: 32 Copynumber: 2.3 Consensus size: 31
4223749 ATAATGAATT
* *
4223759 ATTAAATTTAATATTAATAAA-TAAATCATCAA
1 ATTAAATTTAAT-TAAATAAATTAAAT-ATAAA
* *
4223791 ATTAATATATAATTAAATAAATTTAATATAAA
1 ATTAA-ATTTAATTAAATAAATTAAATATAAA
4223823 ATTAAATT
1 ATTAAATT
4223831 AAACTCGGAC
Statistics
Matches: 33, Mismatches: 5, Indels: 5
0.77 0.12 0.12
Matches are distributed among these distances:
31 2 0.06
32 21 0.64
33 10 0.30
ACGTcount: A:0.57, C:0.03, G:0.00, T:0.40
Consensus pattern (31 bp):
ATTAAATTTAATTAAATAAATTAAATATAAA
Found at i:4228759 original size:40 final size:37
Alignment explanation
Indices: 4228699--4228775 Score: 93
Period size: 39 Copynumber: 2.0 Consensus size: 37
4228689 AATAATATTT
* *
4228699 AAAAAATATATAATTAATAAATTATTTTTTAATTCAATA
1 AAAAAATATATAAATAATAAAATA-TTTTTAATT-AATA
4228738 AAAATAATATATTAAAT-ATAAAATATTTTTAATTAATA
1 AAAA-AATATA-TAAATAATAAAATATTTTTAATTAATA
4228776 TTTATAAGTA
Statistics
Matches: 34, Mismatches: 2, Indels: 5
0.83 0.05 0.12
Matches are distributed among these distances:
38 4 0.12
39 13 0.38
40 13 0.38
41 4 0.12
ACGTcount: A:0.56, C:0.01, G:0.00, T:0.43
Consensus pattern (37 bp):
AAAAAATATATAAATAATAAAATATTTTTAATTAATA
Found at i:4229620 original size:12 final size:12
Alignment explanation
Indices: 4229603--4229628 Score: 52
Period size: 12 Copynumber: 2.2 Consensus size: 12
4229593 TAAACAAATA
4229603 ATATATACATAT
1 ATATATACATAT
4229615 ATATATACATAT
1 ATATATACATAT
4229627 AT
1 AT
4229629 TGTACCTAAT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 14 1.00
ACGTcount: A:0.50, C:0.08, G:0.00, T:0.42
Consensus pattern (12 bp):
ATATATACATAT
Found at i:4238830 original size:2 final size:2
Alignment explanation
Indices: 4238825--4238852 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
4238815 TCTCTCTCTC
4238825 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
4238853 AAGAAGGAAT
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:4239350 original size:2 final size:2
Alignment explanation
Indices: 4239343--4239381 Score: 60
Period size: 2 Copynumber: 19.5 Consensus size: 2
4239333 ATGAACAAGC
* *
4239343 AT AT AT AT AT AT AT AT AT AT AT AT GT AT GT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
4239382 ATCAGTGAGT
Statistics
Matches: 33, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
2 33 1.00
ACGTcount: A:0.46, C:0.00, G:0.05, T:0.49
Consensus pattern (2 bp):
AT
Found at i:4241180 original size:2 final size:2
Alignment explanation
Indices: 4241173--4241202 Score: 60
Period size: 2 Copynumber: 15.0 Consensus size: 2
4241163 AAAGCAAAGA
4241173 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
4241203 GGGGGGGGGT
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:0.50, T:0.00
Consensus pattern (2 bp):
AG
Found at i:4241469 original size:26 final size:25
Alignment explanation
Indices: 4241411--4241462 Score: 68
Period size: 26 Copynumber: 2.0 Consensus size: 25
4241401 AATTTTTGTT
* *
4241411 AAAAATGTATTATTTTTTAATATTTA
1 AAAAATAT-TTATTTTTTAAAATTTA
4241437 AAAAATATTTATTTTTTAAAAATTTA
1 AAAAATATTTATTTTTT-AAAATTTA
4241463 TTAAATAATA
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
25 9 0.39
26 14 0.61
ACGTcount: A:0.46, C:0.00, G:0.02, T:0.52
Consensus pattern (25 bp):
AAAAATATTTATTTTTTAAAATTTA
Found at i:4242111 original size:2 final size:2
Alignment explanation
Indices: 4242104--4242130 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
4242094 AGGGGATAAT
4242104 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 T
4242131 CCATAACATG
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 25 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:4242857 original size:2 final size:2
Alignment explanation
Indices: 4242850--4242891 Score: 84
Period size: 2 Copynumber: 21.0 Consensus size: 2
4242840 CAACTATGTA
4242850 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
4242892 CTTTTCAGCG
Statistics
Matches: 40, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 40 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:4252001 original size:18 final size:18
Alignment explanation
Indices: 4251980--4252014 Score: 70
Period size: 18 Copynumber: 1.9 Consensus size: 18
4251970 TTTGATAAAA
4251980 ATTTAATAAAAATTTTAT
1 ATTTAATAAAAATTTTAT
4251998 ATTTAATAAAAATTTTA
1 ATTTAATAAAAATTTTA
4252015 AAATTCTATA
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 17 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (18 bp):
ATTTAATAAAAATTTTAT
Found at i:4252025 original size:19 final size:18
Alignment explanation
Indices: 4251978--4252016 Score: 69
Period size: 18 Copynumber: 2.2 Consensus size: 18
4251968 TATTTGATAA
4251978 AAATTTAATAAAAATTTT
1 AAATTTAATAAAAATTTT
*
4251996 ATATTTAATAAAAATTTT
1 AAATTTAATAAAAATTTT
4252014 AAA
1 AAA
4252017 ATTCTATAAT
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
18 19 1.00
ACGTcount: A:0.56, C:0.00, G:0.00, T:0.44
Consensus pattern (18 bp):
AAATTTAATAAAAATTTT
Found at i:4252028 original size:29 final size:30
Alignment explanation
Indices: 4251961--4252030 Score: 85
Period size: 29 Copynumber: 2.4 Consensus size: 30
4251951 TTAATAAATT
*
4251961 TTTATAATATTTGATAAAAATTTAATAAAAA
1 TTTATAATATTTAATAAAAATTT-ATAAAAA
4251992 TTT-T-ATATTTAATAAAAATTT-T-AAAA
1 TTTATAATATTTAATAAAAATTTATAAAAA
4252018 TTCTATAATATTT
1 TT-TATAATATTT
4252031 GATTACAGAA
Statistics
Matches: 35, Mismatches: 1, Indels: 8
0.80 0.02 0.18
Matches are distributed among these distances:
26 6 0.17
27 2 0.06
28 1 0.03
29 22 0.63
30 1 0.03
31 3 0.09
ACGTcount: A:0.49, C:0.01, G:0.01, T:0.49
Consensus pattern (30 bp):
TTTATAATATTTAATAAAAATTTATAAAAA
Found at i:4252392 original size:2 final size:2
Alignment explanation
Indices: 4252385--4252422 Score: 76
Period size: 2 Copynumber: 19.0 Consensus size: 2
4252375 TTGATGATAC
4252385 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
4252423 TTTAAGAGAA
Statistics
Matches: 36, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 36 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:4254117 original size:2 final size:2
Alignment explanation
Indices: 4254110--4254136 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
4254100 GTTTATAACC
4254110 AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT A
4254137 GAGGAAAATT
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 25 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:4258153 original size:20 final size:20
Alignment explanation
Indices: 4258116--4258154 Score: 51
Period size: 20 Copynumber: 1.9 Consensus size: 20
4258106 AAAAATTTAA
*
4258116 ACTAAGTAAATTAAAAAATT
1 ACTAAGTAAAATAAAAAATT
* *
4258136 ACTAATTAAAATACAAAAT
1 ACTAAGTAAAATAAAAAAT
4258155 CAATATCAAC
Statistics
Matches: 16, Mismatches: 3, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
20 16 1.00
ACGTcount: A:0.62, C:0.08, G:0.03, T:0.28
Consensus pattern (20 bp):
ACTAAGTAAAATAAAAAATT
Found at i:4259459 original size:2 final size:2
Alignment explanation
Indices: 4259454--4259483 Score: 51
Period size: 2 Copynumber: 15.0 Consensus size: 2
4259444 TTTCTTTCTG
*
4259454 AT AT AT AT AT AT GT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
4259484 TATCTTTTGA
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.47, C:0.00, G:0.03, T:0.50
Consensus pattern (2 bp):
AT
Found at i:4263100 original size:18 final size:17
Alignment explanation
Indices: 4263075--4263121 Score: 60
Period size: 17 Copynumber: 2.6 Consensus size: 17
4263065 TAAATTATCA
4263075 TATATTTTACTTTTA-AT
1 TATATTTTA-TTTTACAT
4263092 TATTATTTTTATTTTACAT
1 TA-TA-TTTTATTTTACAT
4263111 TATATTTTATT
1 TATATTTTATT
4263122 AGTGTGTCAT
Statistics
Matches: 27, Mismatches: 0, Indels: 6
0.82 0.00 0.18
Matches are distributed among these distances:
17 9 0.33
18 9 0.33
19 9 0.33
ACGTcount: A:0.28, C:0.04, G:0.00, T:0.68
Consensus pattern (17 bp):
TATATTTTATTTTACAT
Found at i:4263112 original size:19 final size:18
Alignment explanation
Indices: 4263074--4263118 Score: 56
Period size: 18 Copynumber: 2.4 Consensus size: 18
4263064 TTAAATTATC
4263074 ATATATTTTACTTTTAATT
1 ATAT-TTTTACTTTTAATT
4263093 ATTATTTTTA-TTTTACATT
1 A-TATTTTTACTTTTA-ATT
4263112 ATATTTT
1 ATATTTT
4263119 ATTAGTGTGT
Statistics
Matches: 24, Mismatches: 0, Indels: 5
0.83 0.00 0.17
Matches are distributed among these distances:
18 11 0.46
19 10 0.42
20 3 0.12
ACGTcount: A:0.29, C:0.04, G:0.00, T:0.67
Consensus pattern (18 bp):
ATATTTTTACTTTTAATT
Found at i:4268651 original size:2 final size:2
Alignment explanation
Indices: 4268644--4268690 Score: 94
Period size: 2 Copynumber: 23.5 Consensus size: 2
4268634 CACTTTTAAA
4268644 TC 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 TC
4268686 TC TC T
1 TC TC T
4268691 ATCTATATTT
Statistics
Matches: 45, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 45 1.00
ACGTcount: A:0.00, C:0.49, G:0.00, T:0.51
Consensus pattern (2 bp):
TC
Found at i:4270381 original size:3 final size:3
Alignment explanation
Indices: 4270373--4270413 Score: 82
Period size: 3 Copynumber: 13.7 Consensus size: 3
4270363 GCTTTTTTAT
4270373 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TT
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TT
4270414 TTGACCCTTG
Statistics
Matches: 38, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 38 1.00
ACGTcount: A:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (3 bp):
TTA
Found at i:4271512 original size:2 final size:2
Alignment explanation
Indices: 4271505--4271531 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
4271495 TTGATTCGTG
4271505 AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT A
4271532 GATCCAAAAA
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 25 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:4279912 original size:19 final size:19
Alignment explanation
Indices: 4279862--4279918 Score: 55
Period size: 19 Copynumber: 2.9 Consensus size: 19
4279852 AATATTTAAA
* *
4279862 AATTTATTA-AATTTTAATT
1 AATTTATTATAA-ATTAATC
4279881 AATTTAATT-TAAATTAATC
1 AATTT-ATTATAAATTAATC
4279900 AATTTATTATAAAATTAAT
1 AATTTATTAT-AAATTAAT
4279919 TTTTTTTAGT
Statistics
Matches: 32, Mismatches: 2, Indels: 7
0.78 0.05 0.17
Matches are distributed among these distances:
18 3 0.09
19 16 0.50
20 13 0.41
ACGTcount: A:0.47, C:0.02, G:0.00, T:0.51
Consensus pattern (19 bp):
AATTTATTATAAATTAATC
Found at i:4280034 original size:48 final size:47
Alignment explanation
Indices: 4279964--4280055 Score: 148
Period size: 48 Copynumber: 1.9 Consensus size: 47
4279954 ATTAAGTATT
* *
4279964 AAATCATTTAACTAACACTGATATTTTGCCTTTTCTTTTTACATTAG
1 AAATCATTTAACTAACACTGATATTTTGCCTATTCATTTTACATTAG
*
4280011 AAATCATTTTAACTAACAGTGATATTTTGCCTATTCATTTTACAT
1 AAATCA-TTTAACTAACACTGATATTTTGCCTATTCATTTTACAT
4280056 AGAGGTGAGA
Statistics
Matches: 41, Mismatches: 3, Indels: 1
0.91 0.07 0.02
Matches are distributed among these distances:
47 6 0.15
48 35 0.85
ACGTcount: A:0.32, C:0.16, G:0.07, T:0.46
Consensus pattern (47 bp):
AAATCATTTAACTAACACTGATATTTTGCCTATTCATTTTACATTAG
Found at i:4290475 original size:24 final size:25
Alignment explanation
Indices: 4290433--4290480 Score: 64
Period size: 24 Copynumber: 2.0 Consensus size: 25
4290423 TATTAATTCG
4290433 TAATACTAAATTAATTAAA-AATAC
1 TAATACTAAATTAATTAAATAATAC
*
4290457 TAATATTAAATTAGA-TAAATAATA
1 TAATACTAAATTA-ATTAAATAATA
4290481 TGTTAATATC
Statistics
Matches: 21, Mismatches: 1, Indels: 3
0.84 0.04 0.12
Matches are distributed among these distances:
24 16 0.76
25 5 0.24
ACGTcount: A:0.58, C:0.04, G:0.02, T:0.35
Consensus pattern (25 bp):
TAATACTAAATTAATTAAATAATAC
Found at i:4303327 original size:29 final size:30
Alignment explanation
Indices: 4303280--4303336 Score: 71
Period size: 29 Copynumber: 1.9 Consensus size: 30
4303270 ATTATTATTT
* *
4303280 ATTTATAAAATTTAAATTATTAATATAATA
1 ATTTATAAAATTTAAATTAATAAAATAATA
* *
4303310 ATTT-TAATATTTTAATTAATAAAATAA
1 ATTTATAAAATTTAAATTAATAAAATAA
4303337 ACAACCAAAT
Statistics
Matches: 23, Mismatches: 4, Indels: 1
0.82 0.14 0.04
Matches are distributed among these distances:
29 19 0.83
30 4 0.17
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (30 bp):
ATTTATAAAATTTAAATTAATAAAATAATA
Done.