Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold158
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: 1811518
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 8 of 13
Found at i:1016788 original size:21 final size:21
Alignment explanation
Indices: 1016755--1016821 Score: 57
Period size: 21 Copynumber: 3.1 Consensus size: 21
1016745 TATAAAAAAT
1016755 AAAATA-AATTATTAATATATA
1 AAAATATAA-TATTAATATATA
*
1016776 AAAATATAATATTTAA-ATAAA
1 AAAATATAATA-TTAATATATA
* *
1016797 AAAATTATAAATATAAATACATA
1 AAAA-TAT-AATATTAATATATA
1016820 AA
1 AA
1016822 TTTTTTCTTT
Statistics
Matches: 37, Mismatches: 4, Indels: 8
0.76 0.08 0.16
Matches are distributed among these distances:
21 16 0.43
22 12 0.32
23 9 0.24
ACGTcount: A:0.66, C:0.01, G:0.00, T:0.33
Consensus pattern (21 bp):
AAAATATAATATTAATATATA
Found at i:1016822 original size:21 final size:20
Alignment explanation
Indices: 1016720--1016823 Score: 54
Period size: 21 Copynumber: 5.0 Consensus size: 20
1016710 ATCTCTCATA
*
1016720 TATAAA-ATAAATTATAAA-
1 TATAAATATAAATAATAAAT
* *
1016738 TAAAATATATAAAAAATAAA-
1 TATAA-ATATAAATAATAAAT
* *
1016758 -ATAAATTATTAATATATAAAAA
1 TATAAA-TATAAATA-AT-AAAT
* *
1016780 TATAATATTTAAATAAAAAAAT
1 TATAA-ATATAAAT-AATAAAT
1016802 TATAAATATAAATACATAAAT
1 TATAAATATAAATA-ATAAAT
1016823 T
1 T
1016824 TTTTCTTTTT
Statistics
Matches: 64, Mismatches: 12, Indels: 17
0.69 0.13 0.18
Matches are distributed among these distances:
18 5 0.08
19 10 0.16
20 13 0.20
21 16 0.25
22 8 0.12
23 10 0.16
24 2 0.03
ACGTcount: A:0.65, C:0.01, G:0.00, T:0.34
Consensus pattern (20 bp):
TATAAATATAAATAATAAAT
Found at i:1016861 original size:30 final size:31
Alignment explanation
Indices: 1016825--1016897 Score: 123
Period size: 29 Copynumber: 2.4 Consensus size: 31
1016815 ACATAAATTT
1016825 TTTCTTTTTTTTTTCTTTTTTTC-TTCTTTC
1 TTTCTTTTTTTTTTCTTTTTTTCTTTCTTTC
1016855 TTTC-TTTTTTTTTCTTTTTTTCTTTCTTTC
1 TTTCTTTTTTTTTTCTTTTTTTCTTTCTTTC
*
1016885 TTTCTTTCTTTTT
1 TTTCTTTTTTTTT
1016898 CACGTAAAGG
Statistics
Matches: 40, Mismatches: 1, Indels: 3
0.91 0.02 0.07
Matches are distributed among these distances:
29 18 0.45
30 15 0.38
31 7 0.17
ACGTcount: A:0.00, C:0.16, G:0.00, T:0.84
Consensus pattern (31 bp):
TTTCTTTTTTTTTTCTTTTTTTCTTTCTTTC
Found at i:1016880 original size:4 final size:4
Alignment explanation
Indices: 1016825--1016895 Score: 87
Period size: 4 Copynumber: 18.8 Consensus size: 4
1016815 ACATAAATTT
* *
1016825 TTTC TTT- TTTT TTTC TTTT TTTC -TTC TTTC TTTC TTT- TTT- TTTC
1 TTTC TTTC TTTC TTTC TTTC TTTC TTTC TTTC TTTC TTTC TTTC TTTC
*
1016869 TTTT TTTC TTTC TTTC TTTC TTTC TTT
1 TTTC TTTC TTTC TTTC TTTC TTTC TTT
1016896 TTCACGTAAA
Statistics
Matches: 59, Mismatches: 5, Indels: 6
0.84 0.07 0.09
Matches are distributed among these distances:
3 12 0.20
4 47 0.80
ACGTcount: A:0.00, C:0.17, G:0.00, T:0.83
Consensus pattern (4 bp):
TTTC
Found at i:1016898 original size:30 final size:29
Alignment explanation
Indices: 1016825--1016898 Score: 121
Period size: 30 Copynumber: 2.5 Consensus size: 29
1016815 ACATAAATTT
1016825 TTTCTTTTTTTTTTCTTTTTTTCTTCTTTC
1 TTTC-TTTTTTTTTCTTTTTTTCTTCTTTC
1016855 TTTCTTTTTTTTTCTTTTTTTCTTTCTTTC
1 TTTCTTTTTTTTTCTTTTTTTC-TTCTTTC
*
1016885 TTTCTTTCTTTTTC
1 TTTCTTTTTTTTTC
1016899 ACGTAAAGGT
Statistics
Matches: 42, Mismatches: 1, Indels: 2
0.93 0.02 0.04
Matches are distributed among these distances:
29 18 0.43
30 24 0.57
ACGTcount: A:0.00, C:0.18, G:0.00, T:0.82
Consensus pattern (29 bp):
TTTCTTTTTTTTTCTTTTTTTCTTCTTTC
Found at i:1017074 original size:15 final size:16
Alignment explanation
Indices: 1017038--1017077 Score: 55
Period size: 15 Copynumber: 2.5 Consensus size: 16
1017028 TTTAATATTT
*
1017038 ATAAAATTTTTAATTAA
1 ATAAAA-TTATAATTAA
1017055 ATAAAATTATAATT-A
1 ATAAAATTATAATTAA
1017070 ATAAAATT
1 ATAAAATT
1017078 TATTTAAAAA
Statistics
Matches: 22, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
15 9 0.41
16 7 0.32
17 6 0.27
ACGTcount: A:0.57, C:0.00, G:0.00, T:0.42
Consensus pattern (16 bp):
ATAAAATTATAATTAA
Found at i:1017080 original size:16 final size:17
Alignment explanation
Indices: 1017038--1017080 Score: 63
Period size: 16 Copynumber: 2.6 Consensus size: 17
1017028 TTTAATATTT
*
1017038 ATAAAATTTTTAATTAA
1 ATAAAATTTATAATTAA
1017055 ATAAAA-TTATAATT-A
1 ATAAAATTTATAATTAA
1017070 ATAAAATTTAT
1 ATAAAATTTAT
1017081 TTAAAAATAA
Statistics
Matches: 24, Mismatches: 1, Indels: 3
0.86 0.04 0.11
Matches are distributed among these distances:
15 7 0.29
16 11 0.46
17 6 0.25
ACGTcount: A:0.56, C:0.00, G:0.00, T:0.44
Consensus pattern (17 bp):
ATAAAATTTATAATTAA
Found at i:1017114 original size:19 final size:19
Alignment explanation
Indices: 1017090--1017143 Score: 62
Period size: 19 Copynumber: 3.1 Consensus size: 19
1017080 TTTAAAAATA
1017090 ATATAAATATATTATTAAT
1 ATATAAATATATTATTAAT
* *
1017109 ATATAAATTTTTTATTAA-
1 ATATAAATATATTATTAAT
1017127 AT-TAAA-ATATT-TTAAT
1 ATATAAATATATTATTAAT
1017143 A
1 A
1017144 AATTATGTAA
Statistics
Matches: 30, Mismatches: 4, Indels: 5
0.77 0.10 0.13
Matches are distributed among these distances:
15 4 0.13
16 4 0.13
17 4 0.13
18 2 0.07
19 16 0.53
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (19 bp):
ATATAAATATATTATTAAT
Found at i:1017135 original size:37 final size:35
Alignment explanation
Indices: 1017037--1017136 Score: 91
Period size: 32 Copynumber: 2.8 Consensus size: 35
1017027 CTTTAATATT
*
1017037 TATAAAATTTTTAATTAAA-TAAAAT-TATAATTA
1 TATAAAATTTTTTATTAAATTAAAATATATAATTA
* *
1017070 -ATAAAATTTATTTA-AAAATAATATAAATATATTATTAA
1 TATAAAATTT-TTTATTAAAT--TA-AAATATATAATT-A
1017108 TATATAAATTTTTTATTAAATTAAAATAT
1 TATA-AAATTTTTTATTAAATTAAAATAT
1017137 TTTAATAAAT
Statistics
Matches: 53, Mismatches: 4, Indels: 16
0.73 0.05 0.22
Matches are distributed among these distances:
32 12 0.23
33 3 0.06
35 2 0.04
36 4 0.08
37 12 0.23
38 3 0.06
39 7 0.13
40 10 0.19
ACGTcount: A:0.54, C:0.00, G:0.00, T:0.46
Consensus pattern (35 bp):
TATAAAATTTTTTATTAAATTAAAATATATAATTA
Found at i:1017139 original size:18 final size:19
Alignment explanation
Indices: 1017091--1017149 Score: 68
Period size: 18 Copynumber: 3.2 Consensus size: 19
1017081 TTAAAAATAA
*
1017091 TATAAATATATTATT-AAT
1 TATAAATATTTTATTAAAT
*
1017109 ATATAAATTTTTTATTAAAT
1 -TATAAATATTTTATTAAAT
*
1017129 TA-AAATATTTTAATAAAT
1 TATAAATATTTTATTAAAT
1017147 TAT
1 TAT
1017150 GTAAAATAAG
Statistics
Matches: 34, Mismatches: 4, Indels: 4
0.81 0.10 0.10
Matches are distributed among these distances:
18 16 0.47
19 15 0.44
20 3 0.09
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (19 bp):
TATAAATATTTTATTAAAT
Found at i:1018429 original size:12 final size:12
Alignment explanation
Indices: 1018412--1018483 Score: 67
Period size: 12 Copynumber: 6.1 Consensus size: 12
1018402 AATATATAAA
1018412 TATTTTTTTCTT
1 TATTTTTTTCTT
*
1018424 TATTTTCTT-TT
1 TATTTTTTTCTT
*
1018435 TCTTTTTTTCTCT
1 TATTTTTTTCT-T
*
1018448 TTTTTTTTTCTT
1 TATTTTTTTCTT
*
1018460 T-TTTCTTTCTT
1 TATTTTTTTCTT
* *
1018471 TCTTTCTTTCTT
1 TATTTTTTTCTT
1018483 T
1 T
1018484 TTTGGCTGAA
Statistics
Matches: 52, Mismatches: 5, Indels: 6
0.83 0.08 0.10
Matches are distributed among these distances:
11 19 0.37
12 22 0.42
13 11 0.21
ACGTcount: A:0.03, C:0.15, G:0.00, T:0.82
Consensus pattern (12 bp):
TATTTTTTTCTT
Found at i:1018440 original size:11 final size:10
Alignment explanation
Indices: 1018415--1018486 Score: 72
Period size: 11 Copynumber: 6.6 Consensus size: 10
1018405 ATATAAATAT
*
1018415 TTTTTTCTTTA
1 TTTTTT-TTTC
1018426 TTTTCTTTTTC
1 TTTT-TTTTTC
*
1018437 TTTTTTTCTC
1 TTTTTTTTTC
1018447 TTTTTTTTTTC
1 -TTTTTTTTTC
1018458 TTTTTTCTTTC
1 TTTTTT-TTTC
1018469 TTTCTTTCTTTC
1 TTT-TTT-TTTC
1018481 TTTTTT
1 TTTTTT
1018487 GGCTGAACAC
Statistics
Matches: 54, Mismatches: 3, Indels: 8
0.83 0.05 0.12
Matches are distributed among these distances:
10 11 0.20
11 30 0.56
12 13 0.24
ACGTcount: A:0.01, C:0.15, G:0.00, T:0.83
Consensus pattern (10 bp):
TTTTTTTTTC
Found at i:1018444 original size:8 final size:8
Alignment explanation
Indices: 1018414--1018486 Score: 68
Period size: 8 Copynumber: 9.8 Consensus size: 8
1018404 TATATAAATA
1018414 TTTTTTTC
1 TTTTTTTC
1018422 TTTATTTTC
1 TTT-TTTTC
1018431 --TTTTTC
1 TTTTTTTC
1018437 TTTTTTTC
1 TTTTTTTC
*
1018445 --TCTTT-
1 TTTTTTTC
1018450 TTTTTTTC
1 TTTTTTTC
1018458 -TTTTTTC
1 TTTTTTTC
*
1018465 TTTCTTTC
1 TTTTTTTC
*
1018473 TTTCTTTC
1 TTTTTTTC
1018481 TTTTTT
1 TTTTTT
1018487 GGCTGAACAC
Statistics
Matches: 54, Mismatches: 4, Indels: 14
0.75 0.06 0.19
Matches are distributed among these distances:
6 9 0.17
7 12 0.22
8 28 0.52
9 5 0.09
ACGTcount: A:0.01, C:0.15, G:0.00, T:0.84
Consensus pattern (8 bp):
TTTTTTTC
Found at i:1018458 original size:36 final size:35
Alignment explanation
Indices: 1018414--1018486 Score: 96
Period size: 36 Copynumber: 2.1 Consensus size: 35
1018404 TATATAAATA
*
1018414 TTTTTTTCTTTATTT-TCTT-TTTCTTTTTTTCTCTTT
1 TTTTTTTCTTT-TTTCT-TTCTTTCTTTCTTTCT-TTT
1018450 TTTTTTTCTTTTTTCTTTCTTTCTTTCTTTCTTTT
1 TTTTTTTCTTTTTTCTTTCTTTCTTTCTTTCTTTT
1018485 TT
1 TT
1018487 GGCTGAACAC
Statistics
Matches: 34, Mismatches: 1, Indels: 5
0.85 0.03 0.12
Matches are distributed among these distances:
35 10 0.29
36 24 0.71
ACGTcount: A:0.01, C:0.15, G:0.00, T:0.84
Consensus pattern (35 bp):
TTTTTTTCTTTTTTCTTTCTTTCTTTCTTTCTTTT
Found at i:1018484 original size:28 final size:27
Alignment explanation
Indices: 1018418--1018484 Score: 82
Period size: 28 Copynumber: 2.4 Consensus size: 27
1018408 TAAATATTTT
*
1018418 TTTCTTTATTTTCTTTTTCTTTTTTTC
1 TTTCTTTATTTTCTTTTTCTTTCTTTC
*
1018445 TCTT-TTTTTTTTCTTTTTTCTTTCTTTC
1 T-TTCTTTATTTTC-TTTTTCTTTCTTTC
*
1018473 TTTCTTTCTTTT
1 TTTCTTTATTTT
1018485 TTGGCTGAAC
Statistics
Matches: 34, Mismatches: 3, Indels: 5
0.81 0.07 0.12
Matches are distributed among these distances:
27 11 0.32
28 23 0.68
ACGTcount: A:0.01, C:0.16, G:0.00, T:0.82
Consensus pattern (27 bp):
TTTCTTTATTTTCTTTTTCTTTCTTTC
Found at i:1020796 original size:14 final size:14
Alignment explanation
Indices: 1020777--1020805 Score: 58
Period size: 14 Copynumber: 2.1 Consensus size: 14
1020767 TCTGGGTAAG
1020777 AAATAAATTCAGAA
1 AAATAAATTCAGAA
1020791 AAATAAATTCAGAA
1 AAATAAATTCAGAA
1020805 A
1 A
1020806 GCACATTAGG
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 15 1.00
ACGTcount: A:0.66, C:0.07, G:0.07, T:0.21
Consensus pattern (14 bp):
AAATAAATTCAGAA
Found at i:1024897 original size:63 final size:64
Alignment explanation
Indices: 1024682--1024896 Score: 179
Period size: 64 Copynumber: 3.5 Consensus size: 64
1024672 CTCGACCTAC
* * *
1024682 TTCTCGAAAAGTAGATTTGACTTGAAA-AAAAAG--CTCAGAGTTTA-TTCT----T-GACCCAT
1 TTCTC-AAAAGTAGATTTGACTTAAAAGAAAAAGACCTAAGAGTTTACTTCTAGACTCAACCCAT
* * * *
1024738 TTCTCAAATGTAGATTTGACTTAAAAGAAAAAGACTTAAGAGTTTACTTCTAGGCTCGACCCAT
1 TTCTCAAAAGTAGATTTGACTTAAAAGAAAAAGACCTAAGAGTTTACTTCTAGACTCAACCCAT
* *
1024802 TTCTTAAAAAGTA-ATTTGAC-TAAATAGAAAAAGACCT-AGAG-TT-CGTTCTTAGACTCAACT
1 TTC-TCAAAAGTAGATTTGACTTAAA-AGAAAAAGACCTAAGAGTTTAC-TTC-TAGACTCAACC
*
1024862 TAT
62 CAT
*
1024865 TTCTCAGAAAGTAGATTCGACTTAAAAGAAAA
1 TTCTCA-AAAGTAGATTTGACTTAAAAGAAAA
1024897 GGATTTAGAG
Statistics
Matches: 130, Mismatches: 13, Indels: 24
0.78 0.08 0.14
Matches are distributed among these distances:
55 19 0.15
56 11 0.08
58 9 0.07
59 4 0.03
61 1 0.01
62 7 0.05
63 28 0.22
64 40 0.31
65 11 0.08
ACGTcount: A:0.39, C:0.15, G:0.15, T:0.31
Consensus pattern (64 bp):
TTCTCAAAAGTAGATTTGACTTAAAAGAAAAAGACCTAAGAGTTTACTTCTAGACTCAACCCAT
Found at i:1024927 original size:64 final size:63
Alignment explanation
Indices: 1024736--1024955 Score: 189
Period size: 64 Copynumber: 3.5 Consensus size: 63
1024726 TTCTTGACCC
* * * * **
1024736 ATTTCTCA-AATGTAGATTTGACTTAAAAGAAAAAGACTTAAGAGTTTACTTCTAGGCTCGACCC
1 ATTTCTCAGAAAGTAGATTTGACTTAAAAGAAAAAGA-TTTAGAGTTT-GTTCTAGGCTAGACTT
* * ** * *
1024800 ATTTCTTAAAAAGTA-ATTTGAC-TAAATAGAAAAAGACCTAGAGTTCGTTCTTAGACTCA-ACT
1 ATTTCTCAGAAAGTAGATTTGACTTAAA-AGAAAAAGATTTAGAGTTTGTTC-TAGGCT-AGACT
1024862 T
63 T
* *
1024863 ATTTCTCAGAAAGTAGATTCGACTTAAAAGAAAAGGATTTAGAGTTTGTATCTAGGCTAGACTT
1 ATTTCTCAGAAAGTAGATTTGACTTAAAAGAAAAAGATTTAGAGTTTGT-TCTAGGCTAGACTT
* **
1024927 ACTTCTC-GAAAAGTAGATAGGACTTAAAA
1 ATTTCTCAG-AAAGTAGATTTGACTTAAAA
1024956 CAAGGATCAC
Statistics
Matches: 125, Mismatches: 22, Indels: 18
0.76 0.13 0.11
Matches are distributed among these distances:
62 3 0.02
63 32 0.26
64 79 0.63
65 11 0.09
ACGTcount: A:0.38, C:0.14, G:0.16, T:0.31
Consensus pattern (63 bp):
ATTTCTCAGAAAGTAGATTTGACTTAAAAGAAAAAGATTTAGAGTTTGTTCTAGGCTAGACTT
Found at i:1027329 original size:20 final size:20
Alignment explanation
Indices: 1027306--1027344 Score: 60
Period size: 20 Copynumber: 1.9 Consensus size: 20
1027296 ACATTCTATT
*
1027306 ACAACTTGTGAAATTCCGTC
1 ACAACTTATGAAATTCCGTC
*
1027326 ACAACTTATGACATTCCGT
1 ACAACTTATGAAATTCCGT
1027345 TATAATTTTC
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.31, C:0.26, G:0.13, T:0.31
Consensus pattern (20 bp):
ACAACTTATGAAATTCCGTC
Found at i:1031591 original size:17 final size:17
Alignment explanation
Indices: 1031550--1031599 Score: 61
Period size: 17 Copynumber: 3.1 Consensus size: 17
1031540 ATACACTAAT
1031550 ATATCAAAATTTATATA
1 ATATCAAAATTTATATA
*
1031567 ATAT--AAA-TTATTATC
1 ATATCAAAATTTA-TATA
1031582 ATATCAAAATTTATATA
1 ATATCAAAATTTATATA
1031599 A
1 A
1031600 ATATATAGCA
Statistics
Matches: 27, Mismatches: 2, Indels: 8
0.73 0.05 0.22
Matches are distributed among these distances:
14 3 0.11
15 10 0.37
17 11 0.41
18 3 0.11
ACGTcount: A:0.52, C:0.06, G:0.00, T:0.42
Consensus pattern (17 bp):
ATATCAAAATTTATATA
Found at i:1031595 original size:15 final size:14
Alignment explanation
Indices: 1031548--1031598 Score: 50
Period size: 15 Copynumber: 3.4 Consensus size: 14
1031538 GAATACACTA
1031548 ATATATCAAAATTT
1 ATATATCAAAATTT
1031562 ATATAAT-ATAAATTATT
1 ATAT-ATCA-AAA-T-TT
1031579 ATCATATCAAAATTT
1 AT-ATATCAAAATTT
1031594 ATATA
1 ATATA
1031599 AATATATAGC
Statistics
Matches: 31, Mismatches: 0, Indels: 12
0.72 0.00 0.28
Matches are distributed among these distances:
14 8 0.26
15 9 0.29
16 2 0.06
17 9 0.29
18 3 0.10
ACGTcount: A:0.51, C:0.06, G:0.00, T:0.43
Consensus pattern (14 bp):
ATATATCAAAATTT
Found at i:1047572 original size:13 final size:12
Alignment explanation
Indices: 1047527--1047579 Score: 54
Period size: 12 Copynumber: 4.4 Consensus size: 12
1047517 TTAAAAAAAA
1047527 TTTAAGAAAATT
1 TTTAAGAAAATT
* ***
1047539 TTTAATTATTCTT
1 TTTAA-GAAAATT
1047552 TTTAA-AAAATT
1 TTTAAGAAAATT
1047563 TTTAAGAAAATT
1 TTTAAGAAAATT
1047575 TTTAA
1 TTTAA
1047580 TTATTATTTT
Statistics
Matches: 32, Mismatches: 7, Indels: 4
0.74 0.16 0.09
Matches are distributed among these distances:
11 8 0.25
12 16 0.50
13 8 0.25
ACGTcount: A:0.43, C:0.02, G:0.04, T:0.51
Consensus pattern (12 bp):
TTTAAGAAAATT
Found at i:1047590 original size:36 final size:36
Alignment explanation
Indices: 1047489--1047599 Score: 170
Period size: 36 Copynumber: 3.1 Consensus size: 36
1047479 ATTATTAATT
1047489 TTTTTAAGAAAATTATTTAATTATTA-TTTTAAAAAA
1 TTTTTAAGAAAATT-TTTAATTATTATTTTTAAAAAA
** *
1047525 AATTTAAGAAAATTTTTAATTATTCTTTTTAAAAAA
1 TTTTTAAGAAAATTTTTAATTATTATTTTTAAAAAA
*
1047561 TTTTTAAGAAAATTTTTAATTATTATTTTTAAGAAA
1 TTTTTAAGAAAATTTTTAATTATTATTTTTAAAAAA
1047597 TTT
1 TTT
1047600 ATTTATATTA
Statistics
Matches: 67, Mismatches: 7, Indels: 2
0.88 0.09 0.03
Matches are distributed among these distances:
35 10 0.15
36 57 0.85
ACGTcount: A:0.44, C:0.01, G:0.04, T:0.51
Consensus pattern (36 bp):
TTTTTAAGAAAATTTTTAATTATTATTTTTAAAAAA
Found at i:1047616 original size:15 final size:15
Alignment explanation
Indices: 1047598--1047649 Score: 61
Period size: 15 Copynumber: 3.3 Consensus size: 15
1047588 TTTAAGAAAT
1047598 TTATTTATATTAAAA
1 TTATTTATATTAAAA
1047613 TTATTTA-ATTCCAAAAA
1 TTATTTATATT---AAAA
*
1047630 TCATTTATATTAAAA
1 TTATTTATATTAAAA
1047645 TTATT
1 TTATT
1047650 AAATAATTCA
Statistics
Matches: 31, Mismatches: 2, Indels: 8
0.76 0.05 0.20
Matches are distributed among these distances:
14 3 0.10
15 15 0.48
17 10 0.32
18 3 0.10
ACGTcount: A:0.44, C:0.06, G:0.00, T:0.50
Consensus pattern (15 bp):
TTATTTATATTAAAA
Found at i:1047779 original size:21 final size:21
Alignment explanation
Indices: 1047754--1047802 Score: 55
Period size: 21 Copynumber: 2.3 Consensus size: 21
1047744 AATTTAATTT
1047754 TTAA-TTAAATAATAATTCAAA
1 TTAATTTAAATAA-AATTCAAA
* *
1047775 TTAATTTAATTAAAATTTAAA
1 TTAATTTAAATAAAATTCAAA
*
1047796 TTTATTT
1 TTAATTT
1047803 CATGCAAAAT
Statistics
Matches: 24, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
21 17 0.71
22 7 0.29
ACGTcount: A:0.49, C:0.02, G:0.00, T:0.49
Consensus pattern (21 bp):
TTAATTTAAATAAAATTCAAA
Found at i:1048333 original size:18 final size:17
Alignment explanation
Indices: 1048300--1048333 Score: 50
Period size: 17 Copynumber: 1.9 Consensus size: 17
1048290 ATGTGTGCTG
*
1048300 CAAAGTATTTTTGTGAT
1 CAAAGTATTTTAGTGAT
1048317 CAAAGTATTTATAGTGA
1 CAAAGTATTT-TAGTGA
1048334 CAATGATACC
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 10 0.67
18 5 0.33
ACGTcount: A:0.35, C:0.06, G:0.18, T:0.41
Consensus pattern (17 bp):
CAAAGTATTTTAGTGAT
Found at i:1054139 original size:5 final size:5
Alignment explanation
Indices: 1054129--1054165 Score: 74
Period size: 5 Copynumber: 7.4 Consensus size: 5
1054119 GCCAAAATGC
1054129 TTATT TTATT TTATT TTATT TTATT TTATT TTATT TT
1 TTATT TTATT TTATT TTATT TTATT TTATT TTATT TT
1054166 TATTGCTTAG
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 32 1.00
ACGTcount: A:0.19, C:0.00, G:0.00, T:0.81
Consensus pattern (5 bp):
TTATT
Found at i:1057120 original size:60 final size:58
Alignment explanation
Indices: 1056908--1057246 Score: 252
Period size: 59 Copynumber: 5.8 Consensus size: 58
1056898 ACATAGTAGG
** * * * * *
1056908 GACCATTTAAAAATTTTCATACATTTTAAACTTATTTAGATTATTTTTCATAATCTAGA
1 GACCATTTAGCAATTTTTATGCATTTTAAAGTCATTTAGGTTATTTTTCATAATCTA-A
** * * * *
1056967 GAAAATTTAGCAATTTCTATGCATTTTAAAATCATGTAGGTCA-TTTT-ATAATCTAA
1 GACCATTTAGCAATTTTTATGCATTTTAAAGTCATTTAGGTTATTTTTCATAATCTAA
* * * * **
1057023 AACCATTTAACAATTTTCACGCATTTTAGGGTCATTTAGGTTATTTTTCATAATCTCAA
1 GACCATTTAGCAATTTTTATGCATTTTAAAGTCATTTAGGTTATTTTTCATAATCT-AA
* * * *
1057082 GACCTTTTAGTAATTTTTAATGCATTTTAAGGTTATTTAGGTTATTTTTCATAATCTAA
1 GACCATTTAGCAATTTTT-ATGCATTTTAAAGTCATTTAGGTTATTTTTCATAATCTAA
* ** * ** * * * *
1057141 GGATCATTTAATAATTTTCATATACTTTAAAGTCATTTAGGTTGCTTCTT-ATAATCTAG
1 -GACCATTTAGCAATTTTTATGCATTTTAAAGTCATTTAGGTT-ATTTTTCATAATCTAA
* * * * * *
1057200 GAACCATTTTGTAATTTTTATGTAATTTAGAGTAATTTAGGTTATTT
1 G-ACCATTTAGCAATTTTTATGCATTTTAAAGTCATTTAGGTTATTT
1057247 ACAACAATCT
Statistics
Matches: 219, Mismatches: 54, Indels: 15
0.76 0.19 0.05
Matches are distributed among these distances:
56 32 0.15
57 12 0.05
58 14 0.06
59 108 0.49
60 53 0.24
ACGTcount: A:0.32, C:0.11, G:0.11, T:0.46
Consensus pattern (58 bp):
GACCATTTAGCAATTTTTATGCATTTTAAAGTCATTTAGGTTATTTTTCATAATCTAA
Found at i:1057150 original size:30 final size:30
Alignment explanation
Indices: 1057054--1057150 Score: 83
Period size: 29 Copynumber: 3.2 Consensus size: 30
1057044 CATTTTAGGG
1057054 TCATTTAGGTTATTTTTCATAATCTCAA-GA
1 TCATTTAGGTTATTTTTCATAATCT-AAGGA
* * * * * *
1057084 CCTTTTA-GTAATTTTTAATGCATTTTAAGG-
1 TCATTTAGGTTATTTTTCAT--AATCTAAGGA
*
1057114 TTATTTAGGTTATTTTTCATAATCTAAGGA
1 TCATTTAGGTTATTTTTCATAATCTAAGGA
1057144 TCATTTA
1 TCATTTA
1057151 ATAATTTTCA
Statistics
Matches: 48, Mismatches: 14, Indels: 10
0.67 0.19 0.14
Matches are distributed among these distances:
29 17 0.35
30 17 0.35
31 14 0.29
ACGTcount: A:0.29, C:0.10, G:0.11, T:0.49
Consensus pattern (30 bp):
TCATTTAGGTTATTTTTCATAATCTAAGGA
Found at i:1057375 original size:48 final size:49
Alignment explanation
Indices: 1057322--1057431 Score: 161
Period size: 49 Copynumber: 2.3 Consensus size: 49
1057312 CTTTTCATCA
1057322 AAATTAACTAAAAT-AAGTCTTTTAGGATTAGTTTTCTACCTACCATTC
1 AAATTAACTAAAATCAAGTCTTTTAGGATTAGTTTTCTACCTACCATTC
* * * *
1057370 AAATTAACTAAAATCAAGTCTTTTAGGTTTAGTTTTGTACTTACCATTG
1 AAATTAACTAAAATCAAGTCTTTTAGGATTAGTTTTCTACCTACCATTC
*
1057419 AAA-TGACTAAAAT
1 AAATTAACTAAAAT
1057432 TGAGTTTTTT
Statistics
Matches: 56, Mismatches: 5, Indels: 2
0.89 0.08 0.03
Matches are distributed among these distances:
48 23 0.41
49 33 0.59
ACGTcount: A:0.37, C:0.14, G:0.10, T:0.39
Consensus pattern (49 bp):
AAATTAACTAAAATCAAGTCTTTTAGGATTAGTTTTCTACCTACCATTC
Found at i:1060269 original size:21 final size:21
Alignment explanation
Indices: 1060243--1060300 Score: 55
Period size: 21 Copynumber: 2.7 Consensus size: 21
1060233 GAAACTATTA
**
1060243 CTTTTT-CTTTCTCTTTTTTTT
1 CTTTTTCCTTTCT-TTTTTGCT
1060264 CTTTTTTCCTTTCTTTTTTGCT
1 C-TTTTTCCTTTCTTTTTTGCT
* *
1060286 CTTTTTTCGTTCTTT
1 CTTTTTCCTTTCTTT
1060301 AGTTTTTCTC
Statistics
Matches: 31, Mismatches: 4, Indels: 4
0.79 0.10 0.10
Matches are distributed among these distances:
21 13 0.42
22 12 0.39
23 6 0.19
ACGTcount: A:0.00, C:0.21, G:0.03, T:0.76
Consensus pattern (21 bp):
CTTTTTCCTTTCTTTTTTGCT
Found at i:1060271 original size:22 final size:21
Alignment explanation
Indices: 1060244--1060300 Score: 69
Period size: 22 Copynumber: 2.6 Consensus size: 21
1060234 AAACTATTAC
**
1060244 TTTTTCTTTCTCTTTTTTTTCT
1 TTTTTCTTTCT-TTTTTGCTCT
1060266 TTTTTCCTTTCTTTTTTGCTCT
1 TTTTT-CTTTCTTTTTTGCTCT
*
1060288 TTTTTCGTTCTTT
1 TTTTTCTTTCTTT
1060301 AGTTTTTCTC
Statistics
Matches: 31, Mismatches: 3, Indels: 3
0.84 0.08 0.08
Matches are distributed among these distances:
21 7 0.23
22 18 0.58
23 6 0.19
ACGTcount: A:0.00, C:0.19, G:0.04, T:0.77
Consensus pattern (21 bp):
TTTTTCTTTCTTTTTTGCTCT
Found at i:1060299 original size:11 final size:11
Alignment explanation
Indices: 1060244--1060300 Score: 57
Period size: 12 Copynumber: 5.2 Consensus size: 11
1060234 AAACTATTAC
1060244 TTTTTCTTTCT
1 TTTTTCTTTCT
1060255 CTTTTT-TTTCT
1 -TTTTTCTTTCT
1060266 TTTTTCCTTTCT
1 TTTTT-CTTTCT
1060278 TTTTTGC--TCT
1 TTTTT-CTTTCT
*
1060288 TTTTTCGTTCT
1 TTTTTCTTTCT
1060299 TT
1 TT
1060301 AGTTTTTCTC
Statistics
Matches: 40, Mismatches: 1, Indels: 9
0.80 0.02 0.18
Matches are distributed among these distances:
9 1 0.03
10 13 0.32
11 10 0.25
12 16 0.40
ACGTcount: A:0.00, C:0.19, G:0.04, T:0.77
Consensus pattern (11 bp):
TTTTTCTTTCT
Found at i:1062234 original size:842 final size:827
Alignment explanation
Indices: 1060640--1062289 Score: 2315
Period size: 842 Copynumber: 2.0 Consensus size: 827
1060630 AAATAGAAAA
*
1060640 AAAAAAAAACAACCAAACTATATGCTATTTAATTCCCATGCATAATTTGAATATTAAACTTATTT
1 AAAAAAAAACAACCAAACTAGATGCTATTTAATTCCCATGCATAATTTGAATATTAAACTTATTT
* *
1060705 ATCTTAAGCTTATTTAAGTTTTAATAACCTAATTTATGTAGTAGTTTTTATGCTTATATTTCAAT
66 ATCTTAAGCATATTTAAGTTTTAATAACCTAATTTATGTAGTAGTTTTTATGCTTATATTTAAAT
* *
1060770 TTAAAAATATTTGTGAAGAACCTCTTGTATTAAAGTGATCTAAAGCTATTAAAAAAGTAGAATGT
131 GTAAAAATATTTGTGAAGAACCTCTTGTATTAAAGTGATATAAAGCTATTAAAAAAGTAGAATGT
* *
1060835 ATGAAACTTGGAGAAAAAGCTCGTTTTTAGTGAAAATGTTCATGCAATACCAATACATTGGTGTT
196 ATGAAACTTGGAGAAAAAGCTCGTTTGTAGTG-AAATGTTCATGCAATACCAATACATTAGTGTT
** *
1060900 TTCTATCGGTACAAGTGCTTCTTAGAACCAAAAAATCTCAAAAAAATCGATATTTTGTCAATAAA
260 TTCTATCAATACAAGTGCTTCTTAGAACCAAAAAATCTCAAAAAAATCGATATTTTCTCAATAAA
* * * * *
1060965 AAGCACGTTGTATCGATAACACATGGCTTTATATCGATATACATACATGTGCAAGCTTGGATCAA
325 AAGCACATTGTATCGATAAAACATGACCTTATAACGATATACATACATGTGCAAGCTTGGATCAA
* *
1061030 TCAAAATTTGATGATATATCAATACATTAATGAAATATATCAATATATTTTCGTATAATATCTTT
390 TCAAAATTTGATGATATATCAATACATTAATAAAATATATCAATATATTTACGTATAATATCTTT
* *
1061095 TCACATTCCAAAGGTTTTCAATTGTTCGATTTGGTCCTTAAACATTTTAAATATTCTTTTCTCCC
455 TCACATTCCAAAGGTTTTCAATTATTCGATTTGGTCCTTAAACATTTCAAATATTCTTTTCTCCC
* * * *
1061160 TTTTTCCTAGTGATACAGTGTCTTACAACCTTTCTTTTTATTTTATTTTTTGTTAGGCTTCTAAT
520 TTTTTCCTAGTGACACAGTGTCTTACAACCTTTCTTTTTATTATATCTTTTATTAGGCTTCTAAT
* * * *
1061225 TAATTCTCGGGACATTGTATCAATATAAAGTACATTGTAACGATACAATAGACCTTGTATCGATA
585 TAATTCTCGGGACATTGTATCAAAACAAAGCACATTGTAACAATACAATAGACCTTGTATCGATA
* *
1061290 CAACATGGCCTTATCTCTTGGATCGATCAAAACTAGATAATGTATCGATAAATTAAAAATATGCT
650 CAACATGGCCCTATCTCTTGGATCAATCAAAACTAGATAATGTATCGATAAATTAAAAATATGCT
* ** * *
1061355 TCGTTACCTTTTTGTGAATTTTTTGAAAATAACATC-TTTTCATATTTCAAAGATTTCTAATTAT
715 TCATTACCTTTTCATGAATTTTTTGAAAATAACATCTTTTTCA-ATTCCAAAGATTTCCAATTAT
1061419 TCGATTTGATCCCTAAACATTTGAAACCTAACTAGACTCAAAATAGTTT
779 TCGATTTGATCCCTAAACATTTGAAACCTAACTAGACTCAAAATAGTTT
* * **
1061468 AAAAAAAAACAACCAAACTAGATGCTATTTAGTTCCCATGCATGATTTGTGTATTAAACTTATTT
1 AAAAAAAAACAACCAAACTAGATGCTATTTAATTCCCATGCATAATTTGAATATTAAACTTATTT
* *
1061533 ATGTTAAGCATATTTAAGTTTTAATAGCCTAATTTATGTAGATAGTTTTTATGCTTATATTTAAA
66 ATCTTAAGCATATTTAAGTTTTAATAACCTAATTTATGTAG-TAGTTTTTATGCTTATATTTAAA
* * * *
1061598 TGTAAAAATGTTTGTGAAGAACCTCTTGTATTGAAGTGATATAAAGTTATTAAAAAGGTAGAATG
130 TGTAAAAATATTTGTGAAGAACCTCTTGTATTAAAGTGATATAAAGCTATTAAAAAAGTAGAATG
* * * *
1061663 TTTGAAAACTTGGAGAAAAAGCTCGTTTGTAGTG-AATTTTCATGCAATATCGATACATTAGTGT
195 TATG-AAACTTGGAGAAAAAGCTCGTTTGTAGTGAAATGTTCATGCAATACCAATACATTAGTGT
* * * * *
1061727 TTTGTATCAATACACGTGCTTTTTAGAACTAAAAAATCTCAAAAAAATTGATATTTTACT-AATA
259 TTTCTATCAATACAAGTGCTTCTTAGAACCAAAAAATCTCAAAAAAATCGATATTTT-CTCAATA
* * *
1061791 CAAAGCACATTGTATCGATAAAACATGACCTTATAACGATATACATGCATGTGCCAAGCTTTGAT
323 AAAAGCACATTGTATCGATAAAACATGACCTTATAACGATATACATACATGTG-CAAGCTTGGAT
* *
1061856 TAATCAAAATTTGATGATATATCAATACATTAATAAAATATTTCAATATATCTTCACGAATTTCA
387 CAATCAAAATTTGATGATATATCAATACATTAATAAAATATATCAATATAT-TT-ACG----T-A
* * * *
1061921 TGAAAATGATATTTTTTCACGTTCCAAAGGTTTTTAATTATTTGATTTGGTCCTTAAACATTTCA
445 T----A--ATATCTTTTCACATTCCAAAGGTTTTCAATTATTCGATTTGGTCCTTAAACATTTCA
* * *
1061986 AACCT-TTCTTTT-TCCCTTTTTCCTTGTGACATAGTGTCTTGCAACCTTTCTTTTTATTATATC
504 AA--TATTCTTTTCTCCCTTTTTCCTAGTGACACAGTGTCTTACAACCTTTCTTTTTATTATATC
* * * *
1062049 TTTTATT-GAGCTTCTAATTGATTCTTGGGATATTGTATCAAAACAGAGCACATTGTAACAATAC
567 TTTTATTAG-GCTTCTAATTAATTCTCGGGACATTGTATCAAAACAAAGCACATTGTAACAATAC
* * * * * * * *
1062113 AATGGGCTTTGTATTGATGCAACATGGCCCTATCTCTTGTATCAATCAAAACTTGATAATGTATT
631 AATAGACCTTGTATCGATACAACATGGCCCTATCTCTTGGATCAATCAAAACTAGATAATGTATC
*
1062178 GATAAATTAAAAATATGCATT-ATTACCTTTTCATGAATTTTTTGAAAATAACATCTTTTTGAAT
696 GATAAATTAAAAATATGC-TTCATTACCTTTTCATGAATTTTTTGAAAATAACATCTTTTTCAAT
* * *
1062242 TCCAAAGGTTTCCAATTGTTCGATTTGGTCCCTAAACATTTGAAACCT
760 TCCAAAGATTTCCAATTATTCGATTTGATCCCTAAACATTTGAAACCT
1062290 TTTCTTTTTC
Statistics
Matches: 719, Mismatches: 81, Indels: 30
0.87 0.10 0.04
Matches are distributed among these distances:
828 224 0.31
829 143 0.20
830 30 0.04
831 2 0.00
835 1 0.00
836 2 0.00
840 1 0.00
841 1 0.00
842 300 0.42
843 14 0.02
844 1 0.00
ACGTcount: A:0.35, C:0.14, G:0.12, T:0.39
Consensus pattern (827 bp):
AAAAAAAAACAACCAAACTAGATGCTATTTAATTCCCATGCATAATTTGAATATTAAACTTATTT
ATCTTAAGCATATTTAAGTTTTAATAACCTAATTTATGTAGTAGTTTTTATGCTTATATTTAAAT
GTAAAAATATTTGTGAAGAACCTCTTGTATTAAAGTGATATAAAGCTATTAAAAAAGTAGAATGT
ATGAAACTTGGAGAAAAAGCTCGTTTGTAGTGAAATGTTCATGCAATACCAATACATTAGTGTTT
TCTATCAATACAAGTGCTTCTTAGAACCAAAAAATCTCAAAAAAATCGATATTTTCTCAATAAAA
AGCACATTGTATCGATAAAACATGACCTTATAACGATATACATACATGTGCAAGCTTGGATCAAT
CAAAATTTGATGATATATCAATACATTAATAAAATATATCAATATATTTACGTATAATATCTTTT
CACATTCCAAAGGTTTTCAATTATTCGATTTGGTCCTTAAACATTTCAAATATTCTTTTCTCCCT
TTTTCCTAGTGACACAGTGTCTTACAACCTTTCTTTTTATTATATCTTTTATTAGGCTTCTAATT
AATTCTCGGGACATTGTATCAAAACAAAGCACATTGTAACAATACAATAGACCTTGTATCGATAC
AACATGGCCCTATCTCTTGGATCAATCAAAACTAGATAATGTATCGATAAATTAAAAATATGCTT
CATTACCTTTTCATGAATTTTTTGAAAATAACATCTTTTTCAATTCCAAAGATTTCCAATTATTC
GATTTGATCCCTAAACATTTGAAACCTAACTAGACTCAAAATAGTTT
Found at i:1062600 original size:5 final size:5
Alignment explanation
Indices: 1062590--1062619 Score: 60
Period size: 5 Copynumber: 6.0 Consensus size: 5
1062580 GGAAAAAGTT
1062590 ATAAA ATAAA ATAAA ATAAA ATAAA ATAAA
1 ATAAA ATAAA ATAAA ATAAA ATAAA ATAAA
1062620 TTAATAAAGA
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 25 1.00
ACGTcount: A:0.80, C:0.00, G:0.00, T:0.20
Consensus pattern (5 bp):
ATAAA
Found at i:1067516 original size:12 final size:12
Alignment explanation
Indices: 1067501--1067537 Score: 56
Period size: 12 Copynumber: 3.0 Consensus size: 12
1067491 TAATTTTTAT
1067501 AAAAATTATAAA
1 AAAAATTATAAA
*
1067513 AAAAATTTTTAAA
1 AAAAA-TTATAAA
1067526 AAAAATTATAAA
1 AAAAATTATAAA
1067538 TATAATAAAA
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
12 11 0.50
13 11 0.50
ACGTcount: A:0.70, C:0.00, G:0.00, T:0.30
Consensus pattern (12 bp):
AAAAATTATAAA
Found at i:1069823 original size:21 final size:20
Alignment explanation
Indices: 1069788--1069827 Score: 55
Period size: 21 Copynumber: 1.9 Consensus size: 20
1069778 ATTAAATGTG
1069788 TAATTTATTTATAAATATTTT
1 TAATTTATTTATAAA-ATTTT
1069809 TAATTTATATT-TAAAATTT
1 TAATTTAT-TTATAAAATTT
1069828 ATTTTTATAT
Statistics
Matches: 18, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
20 4 0.22
21 12 0.67
22 2 0.11
ACGTcount: A:0.40, C:0.00, G:0.00, T:0.60
Consensus pattern (20 bp):
TAATTTATTTATAAAATTTT
Found at i:1075316 original size:3 final size:3
Alignment explanation
Indices: 1075310--1075335 Score: 52
Period size: 3 Copynumber: 8.7 Consensus size: 3
1075300 TGAGAAGAAG
1075310 ATT ATT ATT ATT ATT ATT ATT ATT AT
1 ATT ATT ATT ATT ATT ATT ATT ATT AT
1075336 CACTAATTTG
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 23 1.00
ACGTcount: A:0.35, C:0.00, G:0.00, T:0.65
Consensus pattern (3 bp):
ATT
Found at i:1076381 original size:2 final size:2
Alignment explanation
Indices: 1076337--1076369 Score: 66
Period size: 2 Copynumber: 16.5 Consensus size: 2
1076327 ACTTGTTTCC
1076337 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1076370 GATGCATATA
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 31 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:1078539 original size:2 final size:2
Alignment explanation
Indices: 1078532--1078566 Score: 70
Period size: 2 Copynumber: 17.5 Consensus size: 2
1078522 TCTTTTTGTC
1078532 CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT C
1 CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT C
1078567 ATCTTTCACT
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:0.00, C:0.51, G:0.00, T:0.49
Consensus pattern (2 bp):
CT
Found at i:1086081 original size:8 final size:8
Alignment explanation
Indices: 1086068--1086100 Score: 50
Period size: 8 Copynumber: 4.2 Consensus size: 8
1086058 AAGCTACTGC
1086068 TTTTTTT-
1 TTTTTTTG
1086075 TTTTTTTG
1 TTTTTTTG
1086083 TTTTTTTG
1 TTTTTTTG
*
1086091 TTTTTATG
1 TTTTTTTG
1086099 TT
1 TT
1086101 GAATGCGCTG
Statistics
Matches: 24, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
7 7 0.29
8 17 0.71
ACGTcount: A:0.03, C:0.00, G:0.09, T:0.88
Consensus pattern (8 bp):
TTTTTTTG
Found at i:1089976 original size:4 final size:4
Alignment explanation
Indices: 1089967--1089997 Score: 55
Period size: 4 Copynumber: 8.0 Consensus size: 4
1089957 GGGAAAAAGC
1089967 AAAT AAAT AAAT AAAT AAAT AAAT AAA- AAAT
1 AAAT AAAT AAAT AAAT AAAT AAAT AAAT AAAT
1089998 TGGACATGGT
Statistics
Matches: 26, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
3 3 0.12
4 23 0.88
ACGTcount: A:0.77, C:0.00, G:0.00, T:0.23
Consensus pattern (4 bp):
AAAT
Found at i:1090338 original size:16 final size:15
Alignment explanation
Indices: 1090317--1090346 Score: 51
Period size: 15 Copynumber: 1.9 Consensus size: 15
1090307 ATATGGGATT
1090317 GGTTTAAATGGGTTTG
1 GGTTT-AATGGGTTTG
1090333 GGTTTAATGGGTTT
1 GGTTTAATGGGTTT
1090347 TTGATTGGAT
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 9 0.64
16 5 0.36
ACGTcount: A:0.17, C:0.00, G:0.37, T:0.47
Consensus pattern (15 bp):
GGTTTAATGGGTTTG
Found at i:1094616 original size:2 final size:2
Alignment explanation
Indices: 1094611--1094642 Score: 64
Period size: 2 Copynumber: 16.0 Consensus size: 2
1094601 ATATATATAT
1094611 AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC
1 AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC
1094643 GTATGTATAT
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 30 1.00
ACGTcount: A:0.50, C:0.50, G:0.00, T:0.00
Consensus pattern (2 bp):
AC
Found at i:1099615 original size:2 final size:2
Alignment explanation
Indices: 1099602--1099639 Score: 58
Period size: 2 Copynumber: 19.0 Consensus size: 2
1099592 AAACTACTTT
* *
1099602 TC TC TC TT TC TC TC TC TC TC TC TC TC TC TG TC TC TC TC
1 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC
1099640 ACACACACAC
Statistics
Matches: 32, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
2 32 1.00
ACGTcount: A:0.00, C:0.45, G:0.03, T:0.53
Consensus pattern (2 bp):
TC
Found at i:1102399 original size:2 final size:2
Alignment explanation
Indices: 1102392--1102428 Score: 74
Period size: 2 Copynumber: 18.5 Consensus size: 2
1102382 GTATATTCAC
1102392 AT 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 AT A
1102429 GAGAGAGAGA
Statistics
Matches: 35, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 35 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:1102433 original size:2 final size:2
Alignment explanation
Indices: 1102428--1102462 Score: 70
Period size: 2 Copynumber: 17.5 Consensus size: 2
1102418 ATATATATAT
1102428 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG A
1 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG A
1102463 TTACTTGAAT
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:0.49, T:0.00
Consensus pattern (2 bp):
AG
Found at i:1116605 original size:30 final size:30
Alignment explanation
Indices: 1116571--1116628 Score: 91
Period size: 30 Copynumber: 1.9 Consensus size: 30
1116561 TATACTTTGA
1116571 TTGTACC-AATATAAACCCTTAACCTTTAAT
1 TTGTACCTAA-ATAAACCCTTAACCTTTAAT
*
1116601 TTGTACCTAAATAAGCCCTTAACCTTTA
1 TTGTACCTAAATAAACCCTTAACCTTTA
1116629 TTTTATTTAT
Statistics
Matches: 26, Mismatches: 1, Indels: 2
0.90 0.03 0.07
Matches are distributed among these distances:
30 24 0.92
31 2 0.08
ACGTcount: A:0.34, C:0.24, G:0.05, T:0.36
Consensus pattern (30 bp):
TTGTACCTAAATAAACCCTTAACCTTTAAT
Found at i:1120447 original size:54 final size:54
Alignment explanation
Indices: 1120383--1120511 Score: 222
Period size: 54 Copynumber: 2.4 Consensus size: 54
1120373 CTTAGCTTGG
*
1120383 TTTTGAGACTCAGAATGTGGCAGATTTTGGTTTTTGTTATGTACTTGGGACTGA
1 TTTTGAGACTCAGAATGTGGCAGATTTTGGTTATTGTTATGTACTTGGGACTGA
*
1120437 TTTTGAGACTCAGAATGTGGCAGATTTTGGTTATTGTTATGTATTTGGGACTGA
1 TTTTGAGACTCAGAATGTGGCAGATTTTGGTTATTGTTATGTACTTGGGACTGA
*
1120491 TTTTGAGACTCAAAACTGTGG
1 TTTTGAGACTCAGAA-TGTGG
1120512 TAAACTATGG
Statistics
Matches: 71, Mismatches: 3, Indels: 1
0.95 0.04 0.01
Matches are distributed among these distances:
54 66 0.93
55 5 0.07
ACGTcount: A:0.22, C:0.09, G:0.27, T:0.41
Consensus pattern (54 bp):
TTTTGAGACTCAGAATGTGGCAGATTTTGGTTATTGTTATGTACTTGGGACTGA
Found at i:1124764 original size:19 final size:20
Alignment explanation
Indices: 1124735--1124775 Score: 57
Period size: 19 Copynumber: 2.1 Consensus size: 20
1124725 ATATTAATTT
* *
1124735 AATTAAAAAAATTACATAAA
1 AATTAAAAAAATAAAATAAA
1124755 AATT-AAAAAATAAAATAAA
1 AATTAAAAAAATAAAATAAA
1124774 AA
1 AA
1124776 AATATTATTA
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
19 15 0.79
20 4 0.21
ACGTcount: A:0.76, C:0.02, G:0.00, T:0.22
Consensus pattern (20 bp):
AATTAAAAAAATAAAATAAA
Found at i:1126318 original size:34 final size:34
Alignment explanation
Indices: 1126280--1126347 Score: 100
Period size: 34 Copynumber: 2.0 Consensus size: 34
1126270 CACCCAGGTT
* *
1126280 TGGTCGCCAAGCTTGGCGACCATGTTCGCTCCTC
1 TGGTCGCCAAGCATGGCGACCATGTTCGCCCCTC
* *
1126314 TGGTCTCCAAGCATGGCGATCATGTTCGCCCCTC
1 TGGTCGCCAAGCATGGCGACCATGTTCGCCCCTC
1126348 GAGCATAGCT
Statistics
Matches: 30, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
34 30 1.00
ACGTcount: A:0.13, C:0.35, G:0.25, T:0.26
Consensus pattern (34 bp):
TGGTCGCCAAGCATGGCGACCATGTTCGCCCCTC
Found at i:1131288 original size:25 final size:25
Alignment explanation
Indices: 1131254--1131303 Score: 91
Period size: 25 Copynumber: 2.0 Consensus size: 25
1131244 TTATAGAGGT
1131254 TTAGTCCAAACACGACACCTACGTC
1 TTAGTCCAAACACGACACCTACGTC
*
1131279 TTAGTCCAAACATGACACCTACGTC
1 TTAGTCCAAACACGACACCTACGTC
1131304 CTCTTTCCTC
Statistics
Matches: 24, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
25 24 1.00
ACGTcount: A:0.32, C:0.34, G:0.12, T:0.22
Consensus pattern (25 bp):
TTAGTCCAAACACGACACCTACGTC
Found at i:1131991 original size:13 final size:13
Alignment explanation
Indices: 1131973--1131997 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
1131963 TATTTTAGTG
1131973 TGTATCGATACAA
1 TGTATCGATACAA
1131986 TGTATCGATACA
1 TGTATCGATACA
1131998 TTTGGGTGTG
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:0.36, C:0.16, G:0.16, T:0.32
Consensus pattern (13 bp):
TGTATCGATACAA
Found at i:1131994 original size:33 final size:33
Alignment explanation
Indices: 1131952--1132016 Score: 94
Period size: 33 Copynumber: 2.0 Consensus size: 33
1131942 TGCCAGTTTC
* * *
1131952 ATGTGTCGATATATTTTAGTGTGTATCGATACA
1 ATGTATCGATACATTTGAGTGTGTATCGATACA
*
1131985 ATGTATCGATACATTTGGGTGTGTATCGATAC
1 ATGTATCGATACATTTGAGTGTGTATCGATAC
1132017 TTTCAAGGGT
Statistics
Matches: 28, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
33 28 1.00
ACGTcount: A:0.26, C:0.11, G:0.23, T:0.40
Consensus pattern (33 bp):
ATGTATCGATACATTTGAGTGTGTATCGATACA
Found at i:1132799 original size:13 final size:13
Alignment explanation
Indices: 1132781--1132869 Score: 70
Period size: 13 Copynumber: 5.9 Consensus size: 13
1132771 CATAAAGTGT
1132781 TGTATCGATACAA
1 TGTATCGATACAA
1132794 TGTATCGATACATAA
1 TGTATCGATAC--AA
1132809 GTGTTGTATCGATACAA
1 ----TGTATCGATACAA
1132826 TGTATCGATACATAA
1 TGTATCGATAC--AA
1132841 GTGTTGTATCGATACAA
1 ----TGTATCGATACAA
1132858 TGTATCGATACA
1 TGTATCGATACA
1132870 TAAGTTTTGT
Statistics
Matches: 64, Mismatches: 0, Indels: 24
0.73 0.00 0.27
Matches are distributed among these distances:
13 34 0.53
15 4 0.06
17 4 0.06
19 22 0.34
ACGTcount: A:0.35, C:0.13, G:0.18, T:0.34
Consensus pattern (13 bp):
TGTATCGATACAA
Found at i:1132816 original size:32 final size:32
Alignment explanation
Indices: 1132761--1132890 Score: 242
Period size: 32 Copynumber: 4.0 Consensus size: 32
1132751 TTCAACGATT
1132761 TGTATCGATACATAAAGTGTTGTATCGATACAA
1 TGTATCGATACAT-AAGTGTTGTATCGATACAA
1132794 TGTATCGATACATAAGTGTTGTATCGATACAA
1 TGTATCGATACATAAGTGTTGTATCGATACAA
1132826 TGTATCGATACATAAGTGTTGTATCGATACAA
1 TGTATCGATACATAAGTGTTGTATCGATACAA
*
1132858 TGTATCGATACATAAGTTTTGTATCGATACAA
1 TGTATCGATACATAAGTGTTGTATCGATACAA
1132890 T
1 T
1132891 TTAAGCTACT
Statistics
Matches: 96, Mismatches: 1, Indels: 1
0.98 0.01 0.01
Matches are distributed among these distances:
32 83 0.86
33 13 0.14
ACGTcount: A:0.35, C:0.12, G:0.18, T:0.35
Consensus pattern (32 bp):
TGTATCGATACATAAGTGTTGTATCGATACAA
Found at i:1132818 original size:19 final size:18
Alignment explanation
Indices: 1132759--1132888 Score: 110
Period size: 19 Copynumber: 7.8 Consensus size: 18
1132749 ATTTCAACGA
1132759 TTTGTATCGATACATAAAG
1 TTTGTATCGATACAT-AAG
1132778 TGTTGTATCGATAC--AA-
1 T-TTGTATCGATACATAAG
1132794 --TGTATCGATACATAAG
1 TTTGTATCGATACATAAG
1132810 TGTTGTATCGATAC--AA-
1 T-TTGTATCGATACATAAG
1132826 --TGTATCGATACATAAG
1 TTTGTATCGATACATAAG
1132842 TGTTGTATCGATAC--AA-
1 T-TTGTATCGATACATAAG
1132858 --TGTATCGATACATAAG
1 TTTGTATCGATACATAAG
1132874 TTTTGTATCGATACA
1 -TTTGTATCGATACA
1132889 ATTTAAGCTA
Statistics
Matches: 92, Mismatches: 0, Indels: 38
0.71 0.00 0.29
Matches are distributed among these distances:
13 33 0.36
15 6 0.07
17 6 0.07
19 35 0.38
20 12 0.13
ACGTcount: A:0.34, C:0.12, G:0.18, T:0.36
Consensus pattern (18 bp):
TTTGTATCGATACATAAG
Found at i:1132949 original size:13 final size:13
Alignment explanation
Indices: 1132931--1132955 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
1132921 ATTACTCAAA
1132931 TGTATCGATACAT
1 TGTATCGATACAT
1132944 TGTATCGATACA
1 TGTATCGATACA
1132956 CTGATCTTTG
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:0.32, C:0.16, G:0.16, T:0.36
Consensus pattern (13 bp):
TGTATCGATACAT
Found at i:1133020 original size:52 final size:52
Alignment explanation
Indices: 1132964--1133088 Score: 232
Period size: 52 Copynumber: 2.4 Consensus size: 52
1132954 CACTGATCTT
*
1132964 TGTATCGATACATGCAGGCAAATTTGCCCAGATGTATCGATACATTATAAAA
1 TGTATCGATACATGCAGGCAAATTTGCCCAGATGTATCGATACACTATAAAA
*
1133016 TGTATCGATACATGCAGGCAAATTTGCCCAGATGTATCGATACACTATTAAA
1 TGTATCGATACATGCAGGCAAATTTGCCCAGATGTATCGATACACTATAAAA
1133068 TGTATCGATACATGCAGGCAA
1 TGTATCGATACATGCAGGCAA
1133089 CTTTTCATAT
Statistics
Matches: 71, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
52 71 1.00
ACGTcount: A:0.35, C:0.18, G:0.18, T:0.28
Consensus pattern (52 bp):
TGTATCGATACATGCAGGCAAATTTGCCCAGATGTATCGATACACTATAAAA
Found at i:1138367 original size:20 final size:20
Alignment explanation
Indices: 1138342--1138379 Score: 58
Period size: 20 Copynumber: 1.9 Consensus size: 20
1138332 GAGTTTTCCA
1138342 AATGTATCAATACATTGTTT
1 AATGTATCAATACATTGTTT
**
1138362 AATGTATTGATACATTGT
1 AATGTATCAATACATTGT
1138380 GAGAAATTCT
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 16 1.00
ACGTcount: A:0.34, C:0.08, G:0.13, T:0.45
Consensus pattern (20 bp):
AATGTATCAATACATTGTTT
Found at i:1141401 original size:20 final size:20
Alignment explanation
Indices: 1141376--1141416 Score: 82
Period size: 20 Copynumber: 2.0 Consensus size: 20
1141366 ATTTTCCCAG
1141376 ATGTATCGATACACTATTCA
1 ATGTATCGATACACTATTCA
1141396 ATGTATCGATACACTATTCA
1 ATGTATCGATACACTATTCA
1141416 A
1 A
1141417 GGTTCTTCCT
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:0.37, C:0.20, G:0.10, T:0.34
Consensus pattern (20 bp):
ATGTATCGATACACTATTCA
Found at i:1141517 original size:52 final size:52
Alignment explanation
Indices: 1141431--1141539 Score: 173
Period size: 52 Copynumber: 2.1 Consensus size: 52
1141421 CTTCCTAGAT
* **
1141431 AATTTGCCCAGATGTATCGATACACTATTCAATGTATCGATACATGCAGGAA
1 AATTTGCCCAGACGTATCGATACACTATAAAATGTATCGATACATGCAGGAA
* *
1141483 AATTTGCCCAGACGTATCGATACATTATAAAATGTATCGATACATGCAGGCA
1 AATTTGCCCAGACGTATCGATACACTATAAAATGTATCGATACATGCAGGAA
1141535 AATTT
1 AATTT
1141540 TCATATTTCG
Statistics
Matches: 52, Mismatches: 5, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
52 52 1.00
ACGTcount: A:0.36, C:0.18, G:0.17, T:0.29
Consensus pattern (52 bp):
AATTTGCCCAGACGTATCGATACACTATAAAATGTATCGATACATGCAGGAA
Found at i:1145647 original size:10 final size:10
Alignment explanation
Indices: 1145632--1145658 Score: 54
Period size: 10 Copynumber: 2.7 Consensus size: 10
1145622 TGCTAACTAA
1145632 GTTTTTGTTT
1 GTTTTTGTTT
1145642 GTTTTTGTTT
1 GTTTTTGTTT
1145652 GTTTTTG
1 GTTTTTG
1145659 CTTGATACAT
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 17 1.00
ACGTcount: A:0.00, C:0.00, G:0.22, T:0.78
Consensus pattern (10 bp):
GTTTTTGTTT
Found at i:1155353 original size:1 final size:1
Alignment explanation
Indices: 1155347--1155459 Score: 73
Period size: 1 Copynumber: 113.0 Consensus size: 1
1155337 GGCGTCCTCC
** ** ** ** *
1155347 AAAAAAAAAAAAAAAAACGAAAAAAATGAAAAACCAAAAAAAAAAAAACCAAAAAAAAAAAAACA
1 AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA
** * * * * * *
1155412 AAAGGAAAAAAAAACAAAAACAATAAAAAAACAAACAAAAACAAAAAA
1 AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA
1155460 GGGGGTCCGG
Statistics
Matches: 86, Mismatches: 26, Indels: 0
0.77 0.23 0.00
Matches are distributed among these distances:
1 86 1.00
ACGTcount: A:0.85, C:0.10, G:0.04, T:0.02
Consensus pattern (1 bp):
A
Found at i:1155371 original size:15 final size:14
Alignment explanation
Indices: 1155347--1155459 Score: 113
Period size: 14 Copynumber: 7.8 Consensus size: 14
1155337 GGCGTCCTCC
1155347 AAAA-AAAAAAAAA
1 AAAACAAAAAAAAA
1155360 AAAACGAAAAAAATGAA
1 AAAAC-AAAAAAA--AA
*
1155377 AAACCAAAAAAAAA
1 AAAACAAAAAAAAA
1155391 AAAACCAAAAAAAAA
1 AAAA-CAAAAAAAAA
1155406 AAAACAAAAGGAAAAA
1 AAAACAAAA--AAAAA
* *
1155422 AAAACAAAAACAAT
1 AAAACAAAAAAAAA
* *
1155436 AAAA-AAACAAACA
1 AAAACAAAAAAAAA
1155449 AAAACAAAAAA
1 AAAACAAAAAA
1155460 GGGGGTCCGG
Statistics
Matches: 83, Mismatches: 9, Indels: 15
0.78 0.08 0.14
Matches are distributed among these distances:
13 13 0.16
14 22 0.27
15 21 0.25
16 21 0.25
17 6 0.07
ACGTcount: A:0.85, C:0.10, G:0.04, T:0.02
Consensus pattern (14 bp):
AAAACAAAAAAAAA
Found at i:1155406 original size:51 final size:51
Alignment explanation
Indices: 1155347--1155459 Score: 140
Period size: 51 Copynumber: 2.2 Consensus size: 51
1155337 GGCGTCCTCC
* *
1155347 AAAAAAAAAAAAAAAAACGAAAAAAATGA-AAAACCAA-AAAAAAAAAAACCA
1 AAAAAAAAAAAAAAAAACGAAAAAAA-AACAAAAACAATAAAAAAAAAAA-CA
* * *
1155398 AAAAAAAAAAAACAAAAGGAAAAAAAAACAAAAACAATAAAAAAACAAACA
1 AAAAAAAAAAAAAAAAACGAAAAAAAAACAAAAACAATAAAAAAAAAAACA
*
1155449 AAAACAAAAAA
1 AAAAAAAAAAA
1155460 GGGGGTCCGG
Statistics
Matches: 54, Mismatches: 6, Indels: 4
0.84 0.09 0.06
Matches are distributed among these distances:
50 1 0.02
51 43 0.80
52 10 0.19
ACGTcount: A:0.85, C:0.10, G:0.04, T:0.02
Consensus pattern (51 bp):
AAAAAAAAAAAAAAAAACGAAAAAAAAACAAAAACAATAAAAAAAAAAACA
Found at i:1155407 original size:37 final size:34
Alignment explanation
Indices: 1155345--1155459 Score: 99
Period size: 35 Copynumber: 3.2 Consensus size: 34
1155335 ACGGCGTCCT
**
1155345 CCAAAAAAAAAAAAA-AAAACGAAAAAAATGAAAAA
1 CCAAAAAAAAAAAAACAAAA--AAAAAAAAAAAAAA
*
1155380 CCAAAAAAAAAAAAACCAAAAAAAAAAAAACAAAAG
1 CCAAAAAAAAAAAAA-CAAAAAAAAAAAAA-AAAAA
** *
1155416 GAAAAAAAAACAAAAACAATAAAAAAACAAACAAAAA
1 CCAAAAAAAA-AAAAACAA-AAAAAAA-AAAAAAAAA
1155453 -CAAAAAA
1 CCAAAAAA
1155460 GGGGGTCCGG
Statistics
Matches: 66, Mismatches: 8, Indels: 11
0.78 0.09 0.13
Matches are distributed among these distances:
35 22 0.33
36 21 0.32
37 20 0.30
38 3 0.05
ACGTcount: A:0.83, C:0.11, G:0.03, T:0.02
Consensus pattern (34 bp):
CCAAAAAAAAAAAAACAAAAAAAAAAAAAAAAAA
Found at i:1156935 original size:30 final size:29
Alignment explanation
Indices: 1156899--1157484 Score: 518
Period size: 30 Copynumber: 20.1 Consensus size: 29
1156889 TTTATCACCC
*
1156899 TTCAAAAGCCCACAAGTCAGTGGCATATTT
1 TTCAAAAGCCCACAAGTCAGTGGCA-ACTT
*
1156929 TTCAAAAGCCCACAAGTCAGTGGCAACCT
1 TTCAAAAGCCCACAAGTCAGTGGCAACTT
*
1156958 TT-AAAAGCCCACAAGTCAGTGGCAAC-C
1 TTCAAAAGCCCACAAGTCAGTGGCAACTT
* *
1156985 TTC-AAAGCCCACAAATCAGTGGCACCCTTT
1 TTCAAAAGCCCACAAGTCAGTGGCA-AC-TT
* * *
1157015 TTC-GAAGCCCACAAGTCGGTGGCATCTT
1 TTCAAAAGCCCACAAGTCAGTGGCAACTT
* * * * *
1157043 TTCCAAAGTCCACAACTCCGTGGCACTCTTT
1 TTCAAAAGCCCACAAGTCAGTGGCA-AC-TT
** * * *
1157074 TTCTTTTGTAAGCTCACAACTCTA-TAGC-ACTCT
1 TTC----AAAAGCCCACAAGTC-AGTGGCAACT-T
** * *
1157107 TT--TTAGCCCACAAGTTAGTGGCACCCTT
1 TTCAAAAGCCCACAAGTCAGTGGCA-ACTT
*
1157135 TTCAAAAGCCCACAAGTCAGTGGCATATTT
1 TTCAAAAGCCCACAAGTCAGTGGCA-ACTT
*
1157165 TTCAAAAGCCCACAAGTCAGTGGCAACCT
1 TTCAAAAGCCCACAAGTCAGTGGCAACTT
* * *
1157194 TT-AAAAGCCCACAAGTTAGTGGCACCCTG
1 TTCAAAAGCCCACAAGTCAGTGGCA-ACTT
*
1157223 TTCAAAAGCCCACAAGTCAGTGGCATATTT
1 TTCAAAAGCCCACAAGTCAGTGGCA-ACTT
*
1157253 TTCAAAAGCCCACAAGTCAGTGGCAACCT
1 TTCAAAAGCCCACAAGTCAGTGGCAACTT
* *
1157282 TT-AAAAGCCCACAAGTCGGTGGCAAC-C
1 TTCAAAAGCCCACAAGTCAGTGGCAACTT
* * *
1157309 TTC-AAAGCCCACAAGTTAGTGGCACCCTG
1 TTCAAAAGCCCACAAGTCAGTGGCA-ACTT
*
1157338 TTCAAAAGCCCACAAGTCAGTGGCATATTT
1 TTCAAAAGCCCACAAGTCAGTGGCA-ACTT
*
1157368 TTCAAAAGCCCACAAGTCAGTGGCAACCT
1 TTCAAAAGCCCACAAGTCAGTGGCAACTT
*
1157397 TT-AAAAGCCCACAAGTCAGTGGCAAC-C
1 TTCAAAAGCCCACAAGTCAGTGGCAACTT
* *
1157424 TTC-AAAGCCCACAAATCAGTGGCACCCTT
1 TTCAAAAGCCCACAAGTCAGTGGCA-ACTT
** * *
1157453 TTCCGAAGCCCACAAGTCGGTGGCACCTT
1 TTCAAAAGCCCACAAGTCAGTGGCAACTT
1157482 TTC
1 TTC
1157485 CATCTTTAAG
Statistics
Matches: 462, Mismatches: 66, Indels: 57
0.79 0.11 0.10
Matches are distributed among these distances:
26 1 0.00
27 78 0.17
28 103 0.22
29 52 0.11
30 204 0.44
31 5 0.01
32 1 0.00
33 4 0.01
35 14 0.03
ACGTcount: A:0.30, C:0.29, G:0.17, T:0.23
Consensus pattern (29 bp):
TTCAAAAGCCCACAAGTCAGTGGCAACTT
Found at i:1157356 original size:115 final size:115
Alignment explanation
Indices: 1157111--1157477 Score: 581
Period size: 115 Copynumber: 3.2 Consensus size: 115
1157101 CACTCTTTTT
* *** **
1157111 AGCCCACAAGTTAGTGGCACCCTTTTCAAAAGCCCACAAGTCAGTGGCATATTTTTCAAAAGCCC
1 AGCCCACAAGTCAGTGGCATATTTTTCAAAAGCCCACAAGTCAGTGGCA-ACCTTT-AAAAGCCC
*
1157176 ACAAGTCAGTGGCAACCTTTAAAAGCCCACAAGTTAGTGGCACCCTGTTCAAA
64 ACAAGTCAGTGGCAACC-TTCAAAGCCCACAAGTTAGTGGCACCCTGTTCAAA
1157229 AGCCCACAAGTCAGTGGCATATTTTTCAAAAGCCCACAAGTCAGTGGCAACCTTTAAAAGCCCAC
1 AGCCCACAAGTCAGTGGCATATTTTTCAAAAGCCCACAAGTCAGTGGCAACCTTTAAAAGCCCAC
*
1157294 AAGTCGGTGGCAACCTTCAAAGCCCACAAGTTAGTGGCACCCTGTTCAAA
66 AAGTCAGTGGCAACCTTCAAAGCCCACAAGTTAGTGGCACCCTGTTCAAA
1157344 AGCCCACAAGTCAGTGGCATATTTTTCAAAAGCCCACAAGTCAGTGGCAACCTTTAAAAGCCCAC
1 AGCCCACAAGTCAGTGGCATATTTTTCAAAAGCCCACAAGTCAGTGGCAACCTTTAAAAGCCCAC
* * * **
1157409 AAGTCAGTGGCAACCTTCAAAGCCCACAAATCAGTGGCACCCTTTTCCGA
66 AAGTCAGTGGCAACCTTCAAAGCCCACAAGTTAGTGGCACCCTGTTCAAA
*
1157459 AGCCCACAAGTCGGTGGCA
1 AGCCCACAAGTCAGTGGCA
1157478 CCTTTTCCAT
Statistics
Matches: 234, Mismatches: 15, Indels: 3
0.93 0.06 0.01
Matches are distributed among these distances:
115 161 0.69
116 24 0.10
117 4 0.02
118 45 0.19
ACGTcount: A:0.32, C:0.29, G:0.19, T:0.20
Consensus pattern (115 bp):
AGCCCACAAGTCAGTGGCATATTTTTCAAAAGCCCACAAGTCAGTGGCAACCTTTAAAAGCCCAC
AAGTCAGTGGCAACCTTCAAAGCCCACAAGTTAGTGGCACCCTGTTCAAA
Found at i:1157530 original size:52 final size:52
Alignment explanation
Indices: 1157473--1157681 Score: 204
Period size: 52 Copynumber: 4.2 Consensus size: 52
1157463 CACAAGTCGG
*
1157473 TGGCACCTTTTCCATCTTTAAGTCCAATGTAGCTGACCTTGAATCAGCACAT
1 TGGCACCTTTTCCATCTTTAAGTCCAATGTAGCTGGCCTTGAATCAGCACAT
* *
1157525 TGGCA-------C--CTTTAAGTCCAATATAGCTGGCCTTGAATCAGCATAT
1 TGGCACCTTTTCCATCTTTAAGTCCAATGTAGCTGGCCTTGAATCAGCACAT
*
1157568 TGGCACCTTTTCCATCTTTAAGTTCAATGTAGCTGGCCTTGAATCAGCACAT
1 TGGCACCTTTTCCATCTTTAAGTCCAATGTAGCTGGCCTTGAATCAGCACAT
* * * * * * * * * *
1157620 TGACATCCTTTTTC-TCATTAAGCCCAATATCGTTGGCCGTGAATCAACATAT
1 TGGCA-CCTTTTCCATCTTTAAGTCCAATGTAGCTGGCCTTGAATCAGCACAT
*
1157672 TGGCATCTTT
1 TGGCACCTTT
1157682 ATCACTTTTC
Statistics
Matches: 128, Mismatches: 19, Indels: 21
0.76 0.11 0.12
Matches are distributed among these distances:
43 39 0.30
45 1 0.01
50 1 0.01
51 4 0.03
52 76 0.59
53 7 0.05
ACGTcount: A:0.25, C:0.25, G:0.16, T:0.34
Consensus pattern (52 bp):
TGGCACCTTTTCCATCTTTAAGTCCAATGTAGCTGGCCTTGAATCAGCACAT
Found at i:1157549 original size:43 final size:43
Alignment explanation
Indices: 1157488--1157577 Score: 153
Period size: 43 Copynumber: 2.1 Consensus size: 43
1157478 CCTTTTCCAT
*
1157488 CTTTAAGTCCAATGTAGCTGACCTTGAATCAGCACATTGGCAC
1 CTTTAAGTCCAATATAGCTGACCTTGAATCAGCACATTGGCAC
* *
1157531 CTTTAAGTCCAATATAGCTGGCCTTGAATCAGCATATTGGCAC
1 CTTTAAGTCCAATATAGCTGACCTTGAATCAGCACATTGGCAC
1157574 CTTT
1 CTTT
1157578 TCCATCTTTA
Statistics
Matches: 44, Mismatches: 3, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
43 44 1.00
ACGTcount: A:0.27, C:0.24, G:0.18, T:0.31
Consensus pattern (43 bp):
CTTTAAGTCCAATATAGCTGACCTTGAATCAGCACATTGGCAC
Found at i:1158590 original size:20 final size:20
Alignment explanation
Indices: 1158546--1158603 Score: 73
Period size: 20 Copynumber: 3.0 Consensus size: 20
1158536 ATTTCAACGA
***
1158546 TTTGTATCGATACATAAAGT
1 TTTGTATCGATACATATTTT
*
1158566 GTTGTATCGATACATATTTT
1 TTTGTATCGATACATATTTT
1158586 TTTGTATCGATACA-ATTT
1 TTTGTATCGATACATATTT
1158604 AAGCTACTGC
Statistics
Matches: 33, Mismatches: 5, Indels: 1
0.85 0.13 0.03
Matches are distributed among these distances:
19 4 0.12
20 29 0.88
ACGTcount: A:0.29, C:0.10, G:0.14, T:0.47
Consensus pattern (20 bp):
TTTGTATCGATACATATTTT
Found at i:1158660 original size:13 final size:13
Alignment explanation
Indices: 1158642--1158666 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
1158632 ATCACTTAAA
1158642 TGTATCGATACAT
1 TGTATCGATACAT
1158655 TGTATCGATACA
1 TGTATCGATACA
1158667 CTGATCTTTG
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:0.32, C:0.16, G:0.16, T:0.36
Consensus pattern (13 bp):
TGTATCGATACAT
Found at i:1158731 original size:52 final size:52
Alignment explanation
Indices: 1158675--1159011 Score: 584
Period size: 52 Copynumber: 6.5 Consensus size: 52
1158665 CACTGATCTT
*
1158675 TGTATCGATACATGCAGGCAAATTTGCCCAGATGTATCGATACATTATAAAA
1 TGTATCGATACATGCAGGCAAATTTGCCCAGATGTATCGATACACTATAAAA
1158727 TGTATCGATACATGCAGGCAAATTTGCCCAGATGTATCGATACACTATAAAA
1 TGTATCGATACATGCAGGCAAATTTGCCCAGATGTATCGATACACTATAAAA
**
1158779 TGTATCGATACATGCAGGCAAATTTGCCCAGATGTATCGATACACTATTCAA
1 TGTATCGATACATGCAGGCAAATTTGCCCAGATGTATCGATACACTATAAAA
* * *
1158831 TGTATCGATACATGCAGGAAAATTTGCCCAGACGTATCGATACATTATAAAA
1 TGTATCGATACATGCAGGCAAATTTGCCCAGATGTATCGATACACTATAAAA
*
1158883 TGTATCGATACATGCAGGCAAATTTGCCCAGATGTATCGATACATTATAAAA
1 TGTATCGATACATGCAGGCAAATTTGCCCAGATGTATCGATACACTATAAAA
* **
1158935 TGTATCGATACATGCAGGCAAATTTGCCCAGATGTATCGATTCACTATTCAA
1 TGTATCGATACATGCAGGCAAATTTGCCCAGATGTATCGATACACTATAAAA
1158987 TGTATCGATACATGCAGGCAAATTT
1 TGTATCGATACATGCAGGCAAATTT
1159012 TCATATTTCG
Statistics
Matches: 271, Mismatches: 14, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
52 271 1.00
ACGTcount: A:0.35, C:0.19, G:0.18, T:0.29
Consensus pattern (52 bp):
TGTATCGATACATGCAGGCAAATTTGCCCAGATGTATCGATACACTATAAAA
Found at i:1158842 original size:156 final size:156
Alignment explanation
Indices: 1158655--1159011 Score: 644
Period size: 156 Copynumber: 2.3 Consensus size: 156
1158645 ATCGATACAT
** *
1158655 TGTATCGATACACTGA-TCTTTGTATCGATACATGCAGGCAAATTTGCCCAGATGTATCGATACA
1 TGTATCGATACACT-ATTCAATGTATCGATACATGCAGGCAAATTTGCCCAGACGTATCGATACA
1158719 TTATAAAATGTATCGATACATGCAGGCAAATTTGCCCAGATGTATCGATACACTATAAAATGTAT
65 TTATAAAATGTATCGATACATGCAGGCAAATTTGCCCAGATGTATCGATACACTATAAAATGTAT
1158784 CGATACATGCAGGCAAATTTGCCCAGA
130 CGATACATGCAGGCAAATTTGCCCAGA
*
1158811 TGTATCGATACACTATTCAATGTATCGATACATGCAGGAAAATTTGCCCAGACGTATCGATACAT
1 TGTATCGATACACTATTCAATGTATCGATACATGCAGGCAAATTTGCCCAGACGTATCGATACAT
*
1158876 TATAAAATGTATCGATACATGCAGGCAAATTTGCCCAGATGTATCGATACATTATAAAATGTATC
66 TATAAAATGTATCGATACATGCAGGCAAATTTGCCCAGATGTATCGATACACTATAAAATGTATC
1158941 GATACATGCAGGCAAATTTGCCCAGA
131 GATACATGCAGGCAAATTTGCCCAGA
*
1158967 TGTATCGATTCACTATTCAATGTATCGATACATGCAGGCAAATTT
1 TGTATCGATACACTATTCAATGTATCGATACATGCAGGCAAATTT
1159012 TCATATTTCG
Statistics
Matches: 193, Mismatches: 7, Indels: 2
0.96 0.03 0.01
Matches are distributed among these distances:
155 1 0.01
156 192 0.99
ACGTcount: A:0.34, C:0.19, G:0.17, T:0.29
Consensus pattern (156 bp):
TGTATCGATACACTATTCAATGTATCGATACATGCAGGCAAATTTGCCCAGACGTATCGATACAT
TATAAAATGTATCGATACATGCAGGCAAATTTGCCCAGATGTATCGATACACTATAAAATGTATC
GATACATGCAGGCAAATTTGCCCAGA
Found at i:1165346 original size:20 final size:19
Alignment explanation
Indices: 1165304--1165353 Score: 66
Period size: 20 Copynumber: 2.6 Consensus size: 19
1165294 TATTTTAGTG
*
1165304 TGTA-CGATACAATGAACA
1 TGTATCGATACAAAGAACA
*
1165322 TGTATCGATACAAAGCAATA
1 TGTATCGATACAAAG-AACA
1165342 TGTATCGATACA
1 TGTATCGATACA
1165354 TCTGGATGTG
Statistics
Matches: 28, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
18 4 0.14
19 9 0.32
20 15 0.54
ACGTcount: A:0.42, C:0.16, G:0.16, T:0.26
Consensus pattern (19 bp):
TGTATCGATACAAAGAACA
Found at i:1170830 original size:13 final size:13
Alignment explanation
Indices: 1170812--1170839 Score: 56
Period size: 13 Copynumber: 2.2 Consensus size: 13
1170802 ATACAAAGAT
1170812 CAATGTATCGATA
1 CAATGTATCGATA
1170825 CAATGTATCGATA
1 CAATGTATCGATA
1170838 CA
1 CA
1170840 TTGAATGATG
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 15 1.00
ACGTcount: A:0.39, C:0.18, G:0.14, T:0.29
Consensus pattern (13 bp):
CAATGTATCGATA
Found at i:1170906 original size:18 final size:19
Alignment explanation
Indices: 1170883--1170921 Score: 62
Period size: 19 Copynumber: 2.1 Consensus size: 19
1170873 AGCTTTGTAG
1170883 CAATACAT-TGTATCGATA
1 CAATACATATGTATCGATA
*
1170901 CAATACTTATGTATCGATA
1 CAATACATATGTATCGATA
1170920 CA
1 CA
1170922 TTGTATCAAT
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
18 7 0.37
19 12 0.63
ACGTcount: A:0.38, C:0.18, G:0.10, T:0.33
Consensus pattern (19 bp):
CAATACATATGTATCGATA
Found at i:1170915 original size:19 final size:19
Alignment explanation
Indices: 1170891--1170975 Score: 74
Period size: 19 Copynumber: 4.7 Consensus size: 19
1170881 AGCAATACAT
1170891 TGTATCGATACAATACTTA
1 TGTATCGATACAATACTTA
1170910 TGTATCGATAC---A--T-
1 TGTATCGATACAATACTTA
* *
1170923 TGTATCAATACAACACTTA
1 TGTATCGATACAATACTTA
* *
1170942 TGTATCGATACATTTACTGTT
1 TGTATCGATACA-ATACT-TA
1170963 TGTATCGATACAA
1 TGTATCGATACAA
1170976 ATTGTTGAAA
Statistics
Matches: 52, Mismatches: 6, Indels: 15
0.71 0.08 0.21
Matches are distributed among these distances:
13 10 0.19
14 1 0.02
16 2 0.04
18 1 0.02
19 22 0.42
20 3 0.06
21 13 0.25
ACGTcount: A:0.34, C:0.16, G:0.12, T:0.38
Consensus pattern (19 bp):
TGTATCGATACAATACTTA
Found at i:1170926 original size:32 final size:32
Alignment explanation
Indices: 1170814--1170955 Score: 130
Period size: 32 Copynumber: 4.5 Consensus size: 32
1170804 ACAAAGATCA
* * * *
1170814 ATGTATCGATACAATGTATCGATACATTGAATG
1 ATGTATCGATACATTGTATCGATACAAT-ACTT
* * *
1170847 ATGTATCGATACATT-TCATTG--GCAGTAGCTT
1 ATGTATCGATACATTGT-ATCGATACAATA-CTT
* *
1170878 -TGTAGCAATACATTGTATCGATACAATACTT
1 ATGTATCGATACATTGTATCGATACAATACTT
* *
1170909 ATGTATCGATACATTGTATCAATACAACACTT
1 ATGTATCGATACATTGTATCGATACAATACTT
1170941 ATGTATCGATACATT
1 ATGTATCGATACATT
1170956 TACTGTTTGT
Statistics
Matches: 88, Mismatches: 15, Indels: 13
0.76 0.13 0.11
Matches are distributed among these distances:
30 16 0.18
31 8 0.09
32 47 0.53
33 17 0.19
ACGTcount: A:0.34, C:0.15, G:0.15, T:0.36
Consensus pattern (32 bp):
ATGTATCGATACATTGTATCGATACAATACTT
Found at i:1171037 original size:21 final size:21
Alignment explanation
Indices: 1171011--1171066 Score: 112
Period size: 21 Copynumber: 2.7 Consensus size: 21
1171001 GTTGGGACCT
1171011 TGTATCGATACATTCTAGAAA
1 TGTATCGATACATTCTAGAAA
1171032 TGTATCGATACATTCTAGAAA
1 TGTATCGATACATTCTAGAAA
1171053 TGTATCGATACATT
1 TGTATCGATACATT
1171067 TGGATAAAAA
Statistics
Matches: 35, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 35 1.00
ACGTcount: A:0.36, C:0.14, G:0.14, T:0.36
Consensus pattern (21 bp):
TGTATCGATACATTCTAGAAA
Found at i:1171891 original size:52 final size:52
Alignment explanation
Indices: 1171819--1172010 Score: 273
Period size: 52 Copynumber: 3.8 Consensus size: 52
1171809 ATGATTCAAT
* **
1171819 GAAGGTGCCAATGTGCTGATTCAAGGCCAGCGACATTGGTTTTAAAGATGAC
1 GAAGGTGCCAATATGCTGATTCAAGGCCAGCGACATTGGACTTAAAGATGAC
* * * *
1171871 GAAGGCGCCAATATGCTGATTCAAGGCCAGCGATATTGGACTTAAA-CT--T
1 GAAGGTGCCAATATGCTGATTCAAGGCCAGCGACATTGGACTTAAAGATGAC
*
1171920 GAAGGTGCCAATGTGCTGATTCAAGGCCAGCGACATTGGACTTAAAGATGAC
1 GAAGGTGCCAATATGCTGATTCAAGGCCAGCGACATTGGACTTAAAGATGAC
* *
1171972 GAAGGTACCAATATGCTGATTCAAGGCCAGCGATATTGG
1 GAAGGTGCCAATATGCTGATTCAAGGCCAGCGACATTGG
1172011 GCTTGTGCCA
Statistics
Matches: 122, Mismatches: 15, Indels: 6
0.85 0.10 0.04
Matches are distributed among these distances:
49 43 0.35
50 1 0.01
51 1 0.01
52 77 0.63
ACGTcount: A:0.30, C:0.19, G:0.28, T:0.23
Consensus pattern (52 bp):
GAAGGTGCCAATATGCTGATTCAAGGCCAGCGACATTGGACTTAAAGATGAC
Found at i:1172033 original size:39 final size:39
Alignment explanation
Indices: 1171979--1172396 Score: 235
Period size: 39 Copynumber: 9.8 Consensus size: 39
1171969 GACGAAGGTA
*
1171979 CCAATATGCTGATTCAAGGCCAGCGATATTGGGCTTGTG
1 CCAATGTGCTGATTCAAGGCCAGCGATATTGGGCTTGTG
* * *
1172018 CCAATGTGCTGATTCATGGCCAACGATA-TGGTCTTAAAGACAAGGTG
1 CCAATGTGCTGATTCAAGGCCAGCGATATTGGGCTT---------GTG
* *
1172065 CCAATATGCTGATTCAAGGCCAGCGATATTGGGCTTATG
1 CCAATGTGCTGATTCAAGGCCAGCGATATTGGGCTTGTG
* * *
1172104 CCAATGTGCTGATTCAAGGCTAGCGACATTGGTCTTAGAGACAAGGTG
1 CCAATGTGCTGATTCAAGGCCAGCGATATTGGGCTT---------GTG
* * *
1172152 TCAATATGCTGATTCAAGGCCAGCGATATTGGGCTTATG
1 CCAATGTGCTGATTCAAGGCCAGCGATATTGGGCTTGTG
* * * ** *
1172191 CAAATGTGCTGATTCAAGGCTAGCGACATTGGTTTTAGAG
1 CCAATGTGCTGATTCAAGGCCAGCGATATTGGGCTT-GTG
* * *
1172231 ACAAGGTGTTAATATGCTAATTCAAGGCCAGCGATATTGGGCTTATG
1 CCAA--TG------TGCTGATTCAAGGCCAGCGATATTGGGCTTGTG
* * **
1172278 CCAATGTGCTGATTCAAGGCCAACGACATTGGTTTTAGAGACAAGGTG
1 CCAATGTGCTGATTCAAGGCCAGCGATATT-G-----G-G-C-TTGTG
* * * *
1172326 TCAATATGCTGATTCAAGGCTAGCGATATTGGGCTTATG
1 CCAATGTGCTGATTCAAGGCCAGCGATATTGGGCTTGTG
*
1172365 CCAATGTGCTGATTCAAGGCCAGCGACATTGG
1 CCAATGTGCTGATTCAAGGCCAGCGATATTGG
1172397 TCTTAAAGAT
Statistics
Matches: 285, Mismatches: 57, Indels: 74
0.69 0.14 0.18
Matches are distributed among these distances:
38 6 0.02
39 141 0.49
40 5 0.02
41 1 0.00
42 3 0.01
45 3 0.01
46 1 0.00
47 34 0.12
48 91 0.32
ACGTcount: A:0.27, C:0.18, G:0.27, T:0.28
Consensus pattern (39 bp):
CCAATGTGCTGATTCAAGGCCAGCGATATTGGGCTTGTG
Found at i:1172183 original size:48 final size:48
Alignment explanation
Indices: 1172102--1172501 Score: 296
Period size: 48 Copynumber: 8.8 Consensus size: 48
1172092 ATTGGGCTTA
*
1172102 TGCCAATGTGCTGATTCAAGGCTAGCGACATTGGTCTTAGAGACAAGG
1 TGCCAATGTGCTGATTCAAGGCCAGCGACATTGGTCTTAGAGACAAGG
* * * *
1172150 TGTCAATATGCTGATTCAAGGCCAGCGATATTGGGCTT-------A--
1 TGCCAATGTGCTGATTCAAGGCCAGCGACATTGGTCTTAGAGACAAGG
* * *
1172189 TGCAAATGTGCTGATTCAAGGCTAGCGACATTGGTTTTAGAGACAAGG
1 TGCCAATGTGCTGATTCAAGGCCAGCGACATTGGTCTTAGAGACAAGG
** * * * *
1172237 TGTTAATATGCTAATTCAAGGCCAGCGATATTGGGCTT-------A--
1 TGCCAATGTGCTGATTCAAGGCCAGCGACATTGGTCTTAGAGACAAGG
* *
1172276 TGCCAATGTGCTGATTCAAGGCCAACGACATTGGTTTTAGAGACAAGG
1 TGCCAATGTGCTGATTCAAGGCCAGCGACATTGGTCTTAGAGACAAGG
* * * * *
1172324 TGTCAATATGCTGATTCAAGGCTAGCGATATTGGGCTT-------A--
1 TGCCAATGTGCTGATTCAAGGCCAGCGACATTGGTCTTAGAGACAAGG
**
1172363 TGCCAATGTGCTGATTCAAGGCCAGCGACATTGGTCTTAAAGATGGTTAAGG
1 TGCCAATGTGCTGATTCAAGGCCAGCGACATTGGTCTT--AGA--GACAAGG
* * * * *
1172415 TGCCAATGTGTTAAGTCAAGGCCAGCGACATTGGTCTTAAAAACAAGG
1 TGCCAATGTGCTGATTCAAGGCCAGCGACATTGGTCTTAGAGACAAGG
* * *
1172463 TGCCAATATGCTGATTCAAGGCCAGCGATATTGGACTTA
1 TGCCAATGTGCTGATTCAAGGCCAGCGACATTGGTCTTA
1172502 AAGGTGCCAC
Statistics
Matches: 268, Mismatches: 53, Indels: 62
0.70 0.14 0.16
Matches are distributed among these distances:
39 94 0.35
41 3 0.01
46 2 0.01
48 131 0.49
50 3 0.01
52 35 0.13
ACGTcount: A:0.28, C:0.17, G:0.27, T:0.28
Consensus pattern (48 bp):
TGCCAATGTGCTGATTCAAGGCCAGCGACATTGGTCTTAGAGACAAGG
Found at i:1172186 original size:87 final size:87
Alignment explanation
Indices: 1171925--1172401 Score: 749
Period size: 87 Copynumber: 5.4 Consensus size: 87
1171915 AACTTGAAGG
* **
1171925 TGCCAATGTGCTGATTCAAGGCCAGCGACATTGGACTTAAAGATGACGAAGGTACCAATATGCTG
1 TGCCAATGTGCTGATTCAAGGCCAGCGACATTGGTCTT--AGA-GAC-AAGGTGTCAATATGCTG
*
1171990 ATTCAAGGCCAGCGATATTGGGCTTG
62 ATTCAAGGCCAGCGATATTGGGCTTA
* * * * *
1172016 TGCCAATGTGCTGATTCATGGCCAACGATA-TGGTCTTAAAGACAAGGTGCCAATATGCTGATTC
1 TGCCAATGTGCTGATTCAAGGCCAGCGACATTGGTCTTAGAGACAAGGTGTCAATATGCTGATTC
1172080 AAGGCCAGCGATATTGGGCTTA
66 AAGGCCAGCGATATTGGGCTTA
*
1172102 TGCCAATGTGCTGATTCAAGGCTAGCGACATTGGTCTTAGAGACAAGGTGTCAATATGCTGATTC
1 TGCCAATGTGCTGATTCAAGGCCAGCGACATTGGTCTTAGAGACAAGGTGTCAATATGCTGATTC
1172167 AAGGCCAGCGATATTGGGCTTA
66 AAGGCCAGCGATATTGGGCTTA
* * * * *
1172189 TGCAAATGTGCTGATTCAAGGCTAGCGACATTGGTTTTAGAGACAAGGTGTTAATATGCTAATTC
1 TGCCAATGTGCTGATTCAAGGCCAGCGACATTGGTCTTAGAGACAAGGTGTCAATATGCTGATTC
1172254 AAGGCCAGCGATATTGGGCTTA
66 AAGGCCAGCGATATTGGGCTTA
* *
1172276 TGCCAATGTGCTGATTCAAGGCCAACGACATTGGTTTTAGAGACAAGGTGTCAATATGCTGATTC
1 TGCCAATGTGCTGATTCAAGGCCAGCGACATTGGTCTTAGAGACAAGGTGTCAATATGCTGATTC
*
1172341 AAGGCTAGCGATATTGGGCTTA
66 AAGGCCAGCGATATTGGGCTTA
1172363 TGCCAATGTGCTGATTCAAGGCCAGCGACATTGGTCTTA
1 TGCCAATGTGCTGATTCAAGGCCAGCGACATTGGTCTTA
1172402 AAGATGGTTA
Statistics
Matches: 360, Mismatches: 25, Indels: 6
0.92 0.06 0.02
Matches are distributed among these distances:
86 67 0.19
87 258 0.72
88 2 0.01
90 6 0.02
91 27 0.08
ACGTcount: A:0.27, C:0.18, G:0.27, T:0.27
Consensus pattern (87 bp):
TGCCAATGTGCTGATTCAAGGCCAGCGACATTGGTCTTAGAGACAAGGTGTCAATATGCTGATTC
AAGGCCAGCGATATTGGGCTTA
Found at i:1172604 original size:61 final size:60
Alignment explanation
Indices: 1172501--1172651 Score: 216
Period size: 61 Copynumber: 2.5 Consensus size: 60
1172491 TATTGGACTT
* **
1172501 AAAGG-TGCCACGGAGTTGTGGACTTAAAAGGGTGCCTTAGAGTTGTGGACTTAAAAGGAA
1 AAAGGTTGCCACAGAGTTGTGGACTTAAAAGGGTGCCACAGAGTTGTGGACTTAAAAGG-A
* *
1172561 AAAGAG-TGCCATAGAGTTGTGGGCTTAAAAGGGTGCCACAGAGTTGTGGACTTAAAAGGA
1 AAAG-GTTGCCACAGAGTTGTGGACTTAAAAGGGTGCCACAGAGTTGTGGACTTAAAAGGA
*
1172621 AAAGGTTTCCACAGAGTTGTGGACTTAAAAG
1 AAAGGTTGCCACAGAGTTGTGGACTTAAAAG
1172652 AAAAAAGATG
Statistics
Matches: 81, Mismatches: 8, Indels: 4
0.87 0.09 0.04
Matches are distributed among these distances:
59 1 0.01
60 31 0.38
61 49 0.60
ACGTcount: A:0.33, C:0.12, G:0.32, T:0.23
Consensus pattern (60 bp):
AAAGGTTGCCACAGAGTTGTGGACTTAAAAGGGTGCCACAGAGTTGTGGACTTAAAAGGA
Found at i:1172633 original size:33 final size:32
Alignment explanation
Indices: 1172501--1173082 Score: 276
Period size: 27 Copynumber: 18.8 Consensus size: 32
1172491 TATTGGACTT
*
1172501 AAAGGTGCCACGGAGTTGTGGACTTAAAA-G-
1 AAAGGTGCCACAGAGTTGTGGACTTAAAAGGA
**
1172531 ---GGTGCCTTAGAGTTGTGGACTTAAAAGGAA
1 AAAGGTGCCACAGAGTTGTGGACTTAAAAGG-A
* *
1172561 AAAGAGTGCCATAGAGTTGTGGGCTTAAAA-G-
1 AAAG-GTGCCACAGAGTTGTGGACTTAAAAGGA
1172592 ---GGTGCCACAGAGTTGTGGACTTAAAAGGA
1 AAAGGTGCCACAGAGTTGTGGACTTAAAAGGA
* *
1172621 AAAGGTTTCCACAGAGTTGTGGACTTAAAAGAAA
1 AAAGG-TGCCACAGAGTTGTGGACTTAAAAG-GA
* ** * *
1172655 AAAGATGCCATGGAGTTGTAGACTTCAAA-G-
1 AAAGGTGCCACAGAGTTGTGGACTTAAAAGGA
1172685 ---GGTGCCAC-GAAGTTGTGGACTTAAAAGGA
1 AAAGGTGCCACAG-AGTTGTGGACTTAAAAGGA
** *
1172714 ACAAGGCACCACGGAGTTGTGGACTTAAAA-G-
1 A-AAGGTGCCACAGAGTTGTGGACTTAAAAGGA
* *
1172745 ---GGTACCACGGAGTTGTGGACTTAAAAGGGA
1 AAAGGTGCCACAGAGTTGTGGACTTAAAA-GGA
* * * *
1172775 TAAGGGGCCACGGAGTTGTGGACTTTGAAAAGAA
1 AAAGGTGCCACAGAGTTGTGGAC-TT-AAAAGGA
* * *
1172809 AAAGGTGCCATAGAGTCGTGGACTTAGAA--A
1 AAAGGTGCCACAGAGTTGTGGACTTAAAAGGA
* * * * **
1172839 AGAGATGCCACTGAGTCGTGGACTTGGAA-GA
1 AAAGGTGCCACAGAGTTGTGGACTTAAAAGGA
* * * *
1172870 AAAGGATGCCACTGAGTCGTGGGCTTAGAA-GA
1 AAAGG-TGCCACAGAGTTGTGGACTTAAAAGGA
* * * *
1172902 AAAGATGCCACTGAGTTATGGACTT---TGGA
1 AAAGGTGCCACAGAGTTGTGGACTTAAAAGGA
* ** * ** *
1172931 AAGAGATGCCATTGAGTCGTGGACTTGGAAGAA
1 AA-AGGTGCCACAGAGTTGTGGACTTAAAAGGA
* * * *
1172964 AAAGATGCCACTGAGTCGTGGACTTAGAA-GA
1 AAAGGTGCCACAGAGTTGTGGACTTAAAAGGA
* * * *
1172995 AAAGATGCCACTGAGTCGTGGACTT---TGGA
1 AAAGGTGCCACAGAGTTGTGGACTTAAAAGGA
* * * *
1173024 AAGAGATGCCACTGAGTTGTGTACTTGAAA-GA
1 AA-AGGTGCCACAGAGTTGTGGACTTAAAAGGA
** *
1173056 AAAGGATGCCATTGAGTCGTGGACTTA
1 AAAGG-TGCCACAGAGTTGTGGACTTA
1173083 GAAAAGAGAT
Statistics
Matches: 446, Mismatches: 63, Indels: 84
0.75 0.11 0.14
Matches are distributed among these distances:
26 1 0.00
27 91 0.20
28 4 0.01
29 9 0.02
30 66 0.15
31 49 0.11
32 80 0.18
33 91 0.20
34 51 0.11
35 4 0.01
ACGTcount: A:0.33, C:0.14, G:0.31, T:0.22
Consensus pattern (32 bp):
AAAGGTGCCACAGAGTTGTGGACTTAAAAGGA
Found at i:1172699 original size:93 final size:94
Alignment explanation
Indices: 1172539--1172744 Score: 301
Period size: 93 Copynumber: 2.2 Consensus size: 94
1172529 AGGGTGCCTT
* * *
1172539 AGAGTTGTGGACTTAAAAGGAAAAAGAGTGCCATAGAGTTGTGGGCTTAAAAGGGTGCCACAGAG
1 AGAGTTGTGGACTTAAAAGAAAAAAGAGTGCCATAGAGTTGTAGACTTAAAAGGGTGCCACAGAG
**
1172604 TTGTGGACTTAAAAGGAA-AAGGTTTCCAC
66 TTGTGGACTTAAAAGGAACAAGG-CACCAC
* *
1172633 AGAGTTGTGGACTTAAAAGAAAAAAGA-TGCCATGGAGTTGTAGACTTCAAAGGGTGCCAC-GAA
1 AGAGTTGTGGACTTAAAAGAAAAAAGAGTGCCATAGAGTTGTAGACTTAAAAGGGTGCCACAG-A
1172696 GTTGTGGACTTAAAAGGAACAAGGCACCAC
65 GTTGTGGACTTAAAAGGAACAAGGCACCAC
*
1172726 GGAGTTGTGGACTTAAAAG
1 AGAGTTGTGGACTTAAAAG
1172745 GGTACCACGG
Statistics
Matches: 102, Mismatches: 8, Indels: 5
0.89 0.07 0.04
Matches are distributed among these distances:
92 1 0.01
93 71 0.70
94 30 0.29
ACGTcount: A:0.36, C:0.13, G:0.30, T:0.21
Consensus pattern (94 bp):
AGAGTTGTGGACTTAAAAGAAAAAAGAGTGCCATAGAGTTGTAGACTTAAAAGGGTGCCACAGAG
TTGTGGACTTAAAAGGAACAAGGCACCAC
Found at i:1172772 original size:60 final size:60
Alignment explanation
Indices: 1172620--1172799 Score: 216
Period size: 60 Copynumber: 3.0 Consensus size: 60
1172610 ACTTAAAAGG
* * * * ** * *
1172620 AAAAGGTTTCCACAGAGTTGTGGACTTAAAAGAAAAAAGATGCCATGGAGTTGTAGACTT
1 AAAAGGGTACCACGGAGTTGTGGACTTAAAAGGAAAAAGGCGCCACGGAGTTGTGGACTT
* * * * *
1172680 CAAAGGGTGCCACGAAGTTGTGGACTTAAAAGGAACAAGGCACCACGGAGTTGTGGACTT
1 AAAAGGGTACCACGGAGTTGTGGACTTAAAAGGAAAAAGGCGCCACGGAGTTGTGGACTT
* * *
1172740 AAAAGGGTACCACGGAGTTGTGGACTTAAAAGGGATAAGGGGCCACGGAGTTGTGGACTT
1 AAAAGGGTACCACGGAGTTGTGGACTTAAAAGGAAAAAGGCGCCACGGAGTTGTGGACTT
1172800 TGAAAAGAAA
Statistics
Matches: 101, Mismatches: 19, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
60 101 1.00
ACGTcount: A:0.33, C:0.14, G:0.31, T:0.21
Consensus pattern (60 bp):
AAAAGGGTACCACGGAGTTGTGGACTTAAAAGGAAAAAGGCGCCACGGAGTTGTGGACTT
Found at i:1172883 original size:32 final size:32
Alignment explanation
Indices: 1172781--1173081 Score: 304
Period size: 32 Copynumber: 9.6 Consensus size: 32
1172771 GGGATAAGGG
* * *
1172781 GCCACGGAGTTGTGGACTTTGAAAAGAAAAAGG-T
1 GCCACTGAGTCGTGGAC-TTG-GAAG-AAAAGGAT
1172815 GCCA-TAGAGTCGTGGACTT---AGAAAAGAGAT
1 GCCACT-GAGTCGTGGACTTGGAAGAAAAG-GAT
1172845 GCCACTGAGTCGTGGACTTGGAAGAAAAGGAT
1 GCCACTGAGTCGTGGACTTGGAAGAAAAGGAT
* *
1172877 GCCACTGAGTCGTGGGCTTAGAAGAAAA-GAT
1 GCCACTGAGTCGTGGACTTGGAAGAAAAGGAT
** *
1172908 GCCACTGAGTTATGGACTTTG--G-AAAGAGAT
1 GCCACTGAGTCGTGGACTTGGAAGAAAAG-GAT
* *
1172938 GCCATTGAGTCGTGGACTTGGAAGAAAAAGAT
1 GCCACTGAGTCGTGGACTTGGAAGAAAAGGAT
*
1172970 GCCACTGAGTCGTGGACTTAGAAGAAAA-GAT
1 GCCACTGAGTCGTGGACTTGGAAGAAAAGGAT
*
1173001 GCCACTGAGTCGTGGACTTTG--G-AAAGAGAT
1 GCCACTGAGTCGTGGACTTGGAAGAAAAG-GAT
* * *
1173031 GCCACTGAGTTGTGTACTTGAAAGAAAAGGAT
1 GCCACTGAGTCGTGGACTTGGAAGAAAAGGAT
*
1173063 GCCATTGAGTCGTGGACTT
1 GCCACTGAGTCGTGGACTT
1173082 AGAAAAGAGA
Statistics
Matches: 227, Mismatches: 23, Indels: 36
0.79 0.08 0.13
Matches are distributed among these distances:
28 11 0.05
29 5 0.02
30 58 0.26
31 44 0.19
32 79 0.35
33 16 0.07
34 14 0.06
ACGTcount: A:0.32, C:0.15, G:0.31, T:0.22
Consensus pattern (32 bp):
GCCACTGAGTCGTGGACTTGGAAGAAAAGGAT
Found at i:1172925 original size:93 final size:93
Alignment explanation
Indices: 1172781--1173085 Score: 423
Period size: 93 Copynumber: 3.2 Consensus size: 93
1172771 GGGATAAGGG
* * * * * * *
1172781 GCCACGGAGTTGTGGACTTTGAAAAGAAAAAGGTGCCA-TAGAGTCGTGGACTTAGAAAAGAGAT
1 GCCACTGAGTCGTGGAC-TT-AGAAG-AAAAGATGCCACT-GAGTCATGGACTTTGGAAAGAGAT
1172845 GCCACTGAGTCGTGGACTTGGAAGAAAAGGAT
62 GCCACTGAGTCGTGGACTTGGAAGAAAAGGAT
* *
1172877 GCCACTGAGTCGTGGGCTTAGAAGAAAAGATGCCACTGAGTTATGGACTTTGGAAAGAGATGCCA
1 GCCACTGAGTCGTGGACTTAGAAGAAAAGATGCCACTGAGTCATGGACTTTGGAAAGAGATGCCA
* *
1172942 TTGAGTCGTGGACTTGGAAGAAAAAGAT
66 CTGAGTCGTGGACTTGGAAGAAAAGGAT
*
1172970 GCCACTGAGTCGTGGACTTAGAAGAAAAGATGCCACTGAGTCGTGGACTTTGGAAAGAGATGCCA
1 GCCACTGAGTCGTGGACTTAGAAGAAAAGATGCCACTGAGTCATGGACTTTGGAAAGAGATGCCA
* * *
1173035 CTGAGTTGTGTACTTGAAAGAAAAGGAT
66 CTGAGTCGTGGACTTGGAAGAAAAGGAT
*
1173063 GCCATTGAGTCGTGGACTTAGAA
1 GCCACTGAGTCGTGGACTTAGAA
1173086 AAGAGATTTG
Statistics
Matches: 188, Mismatches: 20, Indels: 5
0.88 0.09 0.02
Matches are distributed among these distances:
93 167 0.89
94 5 0.03
95 2 0.01
96 14 0.07
ACGTcount: A:0.32, C:0.14, G:0.31, T:0.22
Consensus pattern (93 bp):
GCCACTGAGTCGTGGACTTAGAAGAAAAGATGCCACTGAGTCATGGACTTTGGAAAGAGATGCCA
CTGAGTCGTGGACTTGGAAGAAAAGGAT
Found at i:1174303 original size:22 final size:20
Alignment explanation
Indices: 1174264--1174324 Score: 50
Period size: 22 Copynumber: 2.8 Consensus size: 20
1174254 TGTTGTTCCC
*
1174264 TTTTTGATTTTGCCTTTGCACTT
1 TTTTTG-TTTTGTCTTTG--CTT
* *
1174287 TTTTTGTTTTGTTTTTGTTT
1 TTTTTGTTTTGTCTTTGCTT
1174307 TTTTTGTGTTTGTACTTT
1 TTTTTGT-TTTGT-CTTT
1174325 TGAGGGAACT
Statistics
Matches: 32, Mismatches: 4, Indels: 5
0.78 0.10 0.12
Matches are distributed among these distances:
20 9 0.28
21 5 0.16
22 12 0.38
23 6 0.19
ACGTcount: A:0.05, C:0.08, G:0.15, T:0.72
Consensus pattern (20 bp):
TTTTTGTTTTGTCTTTGCTT
Found at i:1181259 original size:13 final size:13
Alignment explanation
Indices: 1181241--1181268 Score: 56
Period size: 13 Copynumber: 2.2 Consensus size: 13
1181231 ATACAAAGAT
1181241 CAATGTATCGATA
1 CAATGTATCGATA
1181254 CAATGTATCGATA
1 CAATGTATCGATA
1181267 CA
1 CA
1181269 TTGAATAATG
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 15 1.00
ACGTcount: A:0.39, C:0.18, G:0.14, T:0.29
Consensus pattern (13 bp):
CAATGTATCGATA
Found at i:1181265 original size:33 final size:33
Alignment explanation
Indices: 1181223--1181288 Score: 98
Period size: 33 Copynumber: 2.0 Consensus size: 33
1181213 AAATTCCCAG
1181223 ATGTATCGATACAAAG-ATCAATGTATCGATACA
1 ATGTATCGATACAAAGAAT-AATGTATCGATACA
**
1181256 ATGTATCGATACATTGAATAATGTATCGATACA
1 ATGTATCGATACAAAGAATAATGTATCGATACA
1181289 TTTCCTTGGC
Statistics
Matches: 30, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
33 28 0.93
34 2 0.07
ACGTcount: A:0.41, C:0.14, G:0.15, T:0.30
Consensus pattern (33 bp):
ATGTATCGATACAAAGAATAATGTATCGATACA
Found at i:1181344 original size:19 final size:19
Alignment explanation
Indices: 1181320--1181382 Score: 66
Period size: 19 Copynumber: 3.6 Consensus size: 19
1181310 AGCGATACAT
1181320 TGTATCGATACAACACTTA
1 TGTATCGATACAACACTTA
1181339 TGTATCGAT---ACA--T-
1 TGTATCGATACAACACTTA
*
1181352 TGTATCAATACAACACTTA
1 TGTATCGATACAACACTTA
*
1181371 TGTATCTATACA
1 TGTATCGATACA
1181383 TTTACTGTTT
Statistics
Matches: 36, Mismatches: 2, Indels: 12
0.72 0.04 0.24
Matches are distributed among these distances:
13 8 0.22
14 1 0.03
16 6 0.17
18 1 0.03
19 20 0.56
ACGTcount: A:0.37, C:0.19, G:0.10, T:0.35
Consensus pattern (19 bp):
TGTATCGATACAACACTTA
Found at i:1181353 original size:32 final size:32
Alignment explanation
Indices: 1181307--1181384 Score: 129
Period size: 32 Copynumber: 2.4 Consensus size: 32
1181297 GCAGTAGCTT
* *
1181307 TGTAGCGATACATTGTATCGATACAACACTTA
1 TGTATCGATACATTGTATCAATACAACACTTA
1181339 TGTATCGATACATTGTATCAATACAACACTTA
1 TGTATCGATACATTGTATCAATACAACACTTA
*
1181371 TGTATCTATACATT
1 TGTATCGATACATT
1181385 TACTGTTTGT
Statistics
Matches: 43, Mismatches: 3, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
32 43 1.00
ACGTcount: A:0.35, C:0.18, G:0.12, T:0.36
Consensus pattern (32 bp):
TGTATCGATACATTGTATCAATACAACACTTA
Found at i:1184299 original size:99 final size:99
Alignment explanation
Indices: 1184188--1184367 Score: 324
Period size: 99 Copynumber: 1.8 Consensus size: 99
1184178 ATTTTTTAAA
* *
1184188 AAATTTTTAGATCAACTTTTGACTAATTCAAATAAAGTTAGAGTTAGCATAATTTTGATAGTTAG
1 AAATTTTCAGATCAACTTTTGACTAATTCAAATAAAGTTAGAGTTAGCATAATTTTAATAGTTAG
1184253 TAATCAATCAATCTTTGTGCTTTGTTTTTTTTTT
66 TAATCAATCAATCTTTGTGCTTTGTTTTTTTTTT
*
1184287 AAATTTTCAGATCAACTTTTGATTAATTCAAATAAAGTTAGAGTTAGCATAATTTTAATAGTTAG
1 AAATTTTCAGATCAACTTTTGACTAATTCAAATAAAGTTAGAGTTAGCATAATTTTAATAGTTAG
*
1184352 TAATCGATCAATCTTT
66 TAATCAATCAATCTTT
1184368 ATGGGATGAT
Statistics
Matches: 77, Mismatches: 4, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
99 77 1.00
ACGTcount: A:0.34, C:0.09, G:0.12, T:0.44
Consensus pattern (99 bp):
AAATTTTCAGATCAACTTTTGACTAATTCAAATAAAGTTAGAGTTAGCATAATTTTAATAGTTAG
TAATCAATCAATCTTTGTGCTTTGTTTTTTTTTT
Found at i:1192597 original size:31 final size:31
Alignment explanation
Indices: 1192544--1192630 Score: 102
Period size: 31 Copynumber: 2.8 Consensus size: 31
1192534 AACTTCGATG
* * **
1192544 CCACCAACTCATGTAGGTTTTGACTCGGGTA
1 CCACCAACTCATGTGGGCTTTGACAAGGGTA
* ** *
1192575 CCGCCAACTTGTGTGGGCTTTGACAAGGGTG
1 CCACCAACTCATGTGGGCTTTGACAAGGGTA
1192606 CCACCAACTCATGTGGGCTTTGACA
1 CCACCAACTCATGTGGGCTTTGACA
1192631 TTCTAAGGCT
Statistics
Matches: 45, Mismatches: 11, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
31 45 1.00
ACGTcount: A:0.21, C:0.26, G:0.26, T:0.26
Consensus pattern (31 bp):
CCACCAACTCATGTGGGCTTTGACAAGGGTA
Found at i:1192701 original size:149 final size:149
Alignment explanation
Indices: 1192332--1192922 Score: 693
Period size: 149 Copynumber: 4.0 Consensus size: 149
1192322 GGTTTTTGTT
* * * *
1192332 TTCTAAGGCTTGACCTCTTTAGACAGGTGCCAGCTAATGTGGACTTGACTTGAACTTAGGTGCCA
1 TTCTAAGGCTTAACCTCCTTAGACAGGTGCCAACTAATGTGGACTTGACTCGAACTTAGGTGCCA
* * * * * *
1192397 CCAACTCGTATAAGTTTTGACTCGAGTGCCACCAACTTGTGCGGGCTTTTATCTAGAGTTCCACC
66 CCAACTCGTGTAGGCTTTGACTCGAGTGCCACCAACTTGTGCGGGCTTTGA-CTAGGGTGCCACC
* *
1192462 ATCTCGTGTGAGCTTTGACA
130 AACTCGTGTGGGCTTTGACA
* * * * * *
1192482 TTCTAAGGTTTAACCTCTTTAGATAGGTGCCAACTAATGTGGACTTAACTCGAACTTCGATGCCA
1 TTCTAAGGCTTAACCTCCTTAGACAGGTGCCAACTAATGTGGACTTGACTCGAACTTAGGTGCCA
* * * * * * *
1192547 CCAACTCATGTAGGTTTTGACTCGGGTACCGCCAACTTGTGTGGGCTTTGACAAGGGTGCCACCA
66 CCAACTCGTGTAGGCTTTGACTCGAGTGCCACCAACTTGTGCGGGCTTTGACTAGGGTGCCACCA
*
1192612 ACTCATGTGGGCTTTGACA
131 ACTCGTGTGGGCTTTGACA
* * * *
1192631 TTCTAAGGC-TAACCTCCTTAAATAGGTGTCAACTAATGTGGACTTTGACTTGAACTTAGGTGCC
1 TTCTAAGGCTTAACCTCCTTAGACAGGTGCCAACTAATGTGGAC-TTGACTCGAACTTAGGTGCC
* * * * *
1192695 ACCAACTTGTGTGGGCTTTGACTCGGGTGCCACTAACTTGTGCGGCCTTTGACTAGGGTGCCACC
65 ACCAACTCGTGTAGGCTTTGACTCGAGTGCCACCAACTTGTGCGGGCTTTGACTAGGGTGCCACC
* *
1192760 AACTCGTGTGTGCTTTGTCA
130 AACTCGTGTGGGCTTTGACA
* * **
1192780 TTCTAAGGCTTAACCTCCTTAGACAGGTGCCAACT--TATGGACTTGACTCAAACTTAGGTGATA
1 TTCTAAGGCTTAACCTCCTTAGACAGGTGCCAACTAATGTGGACTTGACTCGAACTTAGGTGCCA
* * ** * ** *
1192843 CCAACTCGTGTGGGCTTTGACTCAAGTGCTGCCAACTTCTGTAGGCTTTGACTATGGTGCCACCA
66 CCAACTCGTGTAGGCTTTGACTCGAGTGCCACCAACTTGTGCGGGCTTTGACTAGGGTGCCACCA
*
1192908 ATTCGTGTGGGCTTT
131 ACTCGTGTGGGCTTT
1192923 AGAGAAGGGT
Statistics
Matches: 375, Mismatches: 64, Indels: 7
0.84 0.14 0.02
Matches are distributed among these distances:
147 84 0.22
148 37 0.10
149 132 0.35
150 122 0.33
ACGTcount: A:0.22, C:0.24, G:0.24, T:0.31
Consensus pattern (149 bp):
TTCTAAGGCTTAACCTCCTTAGACAGGTGCCAACTAATGTGGACTTGACTCGAACTTAGGTGCCA
CCAACTCGTGTAGGCTTTGACTCGAGTGCCACCAACTTGTGCGGGCTTTGACTAGGGTGCCACCA
ACTCGTGTGGGCTTTGACA
Found at i:1192725 original size:31 final size:31
Alignment explanation
Indices: 1192689--1192776 Score: 122
Period size: 31 Copynumber: 2.8 Consensus size: 31
1192679 CTTGAACTTA
*
1192689 GGTGCCACCAACTTGTGTGGGCTTTGACTCG
1 GGTGCCACCAACTTGTGTGGGCTTTGACTAG
* * *
1192720 GGTGCCACTAACTTGTGCGGCCTTTGACTAG
1 GGTGCCACCAACTTGTGTGGGCTTTGACTAG
* *
1192751 GGTGCCACCAACTCGTGTGTGCTTTG
1 GGTGCCACCAACTTGTGTGGGCTTTG
1192777 TCATTCTAAG
Statistics
Matches: 48, Mismatches: 9, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
31 48 1.00
ACGTcount: A:0.14, C:0.26, G:0.31, T:0.30
Consensus pattern (31 bp):
GGTGCCACCAACTTGTGTGGGCTTTGACTAG
Found at i:1192879 original size:31 final size:31
Alignment explanation
Indices: 1192842--1192922 Score: 85
Period size: 31 Copynumber: 2.6 Consensus size: 31
1192832 CTTAGGTGAT
*
1192842 ACCAACTCGTGTGGGCTTTGACTCA-AGTGCT
1 ACCAACTCGTGTGGGCTTTGACT-ATAGTGCC
* * *
1192873 GCCAACTTC-TGTAGGCTTTGACTATGGTGCC
1 ACCAAC-TCGTGTGGGCTTTGACTATAGTGCC
*
1192904 ACCAATTCGTGTGGGCTTT
1 ACCAACTCGTGTGGGCTTT
1192923 AGAGAAGGGT
Statistics
Matches: 40, Mismatches: 7, Indels: 6
0.75 0.13 0.11
Matches are distributed among these distances:
30 3 0.08
31 35 0.88
32 2 0.05
ACGTcount: A:0.17, C:0.25, G:0.26, T:0.32
Consensus pattern (31 bp):
ACCAACTCGTGTGGGCTTTGACTATAGTGCC
Found at i:1193118 original size:42 final size:41
Alignment explanation
Indices: 1193055--1193263 Score: 177
Period size: 42 Copynumber: 4.9 Consensus size: 41
1193045 AAAATGAGTA
* *
1193055 CGTCCTGCT-TTTCAAGGACAAAGGAAAAAGGAGAATAAAATG
1 CGTCCTGCTCTTTGAA-GACAAAGGAAAAAGGA-AATAAAGTG
* * * ** *
1193097 CGTCATTCTCTTTGAATACAAAGGAAAAAAAAGAATGAAGTG
1 CGTCCTGCTCTTTGAAGACAAAGGAAAAAGGA-AATAAAGTG
* *
1193139 CGTCCTGCTCTTTGAAGACAAAGGGAAAAGAAGGAAATGAGGTG
1 CGTCCTGCTCTTTGAAGACAAA-GG-AAA-AAGGAAATAAAGTG
** *
1193183 CGTCCTGCTCTTTGACTACAAAAGAGAAAAGGAAATAAAGTG
1 CGTCCTGCTCTTTGAAGACAAAGGA-AAAAGGAAATAAAGTG
* * *
1193225 CGTTCTACTCTTTGAGGACAAAGGGAAAAGAAGGAAATA
1 CGTCCTGCTCTTTGAAGACAAA-GG-AAA-AAGGAAATA
1193264 CGTCCAGTTT
Statistics
Matches: 135, Mismatches: 24, Indels: 14
0.78 0.14 0.08
Matches are distributed among these distances:
42 78 0.58
43 13 0.10
44 41 0.30
45 3 0.02
ACGTcount: A:0.41, C:0.14, G:0.24, T:0.21
Consensus pattern (41 bp):
CGTCCTGCTCTTTGAAGACAAAGGAAAAAGGAAATAAAGTG
Found at i:1193435 original size:32 final size:32
Alignment explanation
Indices: 1193373--1193752 Score: 206
Period size: 32 Copynumber: 12.1 Consensus size: 32
1193363 TATGGACATA
**
1193373 AAAAGAAAAAGGGTGCCATAGAGTTGTGGACTTT
1 AAAA-AAAAA-GGTGCCACGGAGTTGTGGACTTT
* * *
1193407 GAAGAAAAAA-GTGCCACGAAGTTATGGACTTT
1 -AAAAAAAAAGGTGCCACGGAGTTGTGGACTTT
* *
1193439 AAAAAGAAAAGGTGACACGGAGTTGTGGAGTTT
1 AAAAA-AAAAGGTGCCACGGAGTTGTGGACTTT
*
1193472 -AAAAAAAAGGTACCACGGAGTTGTGGACTTT
1 AAAAAAAAAGGTGCCACGGAGTTGTGGACTTT
* * *
1193503 AAAAGAAAAA-GTGCCATGCAGTTATGGACTTT
1 AAAA-AAAAAGGTGCCACGGAGTTGTGGACTTT
* * * **
1193535 -----AAAGGGTGCAACGAAAAAATGTGGACTTT
1 AAAAAAAAAGGTGCCACG--GAGTTGTGGACTTT
* * * * *
1193564 AAAAGAAGAAGGTGTCACAGAGTTCTAGACTTT
1 AAAA-AAAAAGGTGCCACGGAGTTGTGGACTTT
* * *
1193597 AAAAGAAAAAGGTGCCATGGAGTTATGGACTAT
1 AAAA-AAAAAGGTGCCACGGAGTTGTGGACTTT
* *
1193630 -AAAAAAAA--TGCCACAGAGTTTTGGAC-TT
1 AAAAAAAAAGGTGCCACGGAGTTGTGGACTTT
* *
1193658 ----AAAAGGGTGCTA-GGAAGTTGTGGACTTTT
1 AAAAAAAAAGGTGCCACGG-AGTTGTGGAC-TTT
* * * *
1193687 GAAGAAAAA-GTACCACAGAGTTGTGGACTTT
1 AAAAAAAAAGGTGCCACGGAGTTGTGGACTTT
* *
1193718 AAAAGAAAAA-GTGCCACAGAGTTGTAGAC-TT
1 AAAA-AAAAAGGTGCCACGGAGTTGTGGACTTT
1193749 AAAA
1 AAAA
1193753 GGGTGTCACA
Statistics
Matches: 264, Mismatches: 57, Indels: 52
0.71 0.15 0.14
Matches are distributed among these distances:
25 4 0.02
26 4 0.02
27 19 0.07
28 1 0.00
29 27 0.10
31 44 0.17
32 86 0.33
33 63 0.24
34 5 0.02
35 11 0.04
ACGTcount: A:0.40, C:0.11, G:0.26, T:0.23
Consensus pattern (32 bp):
AAAAAAAAAGGTGCCACGGAGTTGTGGACTTT
Found at i:1193607 original size:94 final size:93
Alignment explanation
Indices: 1193462--1193632 Score: 245
Period size: 94 Copynumber: 1.8 Consensus size: 93
1193452 GACACGGAGT
* * * *
1193462 TGTGGAGTTTAAAAAAAAGGTACCACGGAGTTGTGGACTTTAAAAGAAAAA-GTGCCATGCAGTT
1 TGTGGACTTTAAAAAAAAGGTACCACAGAGTTCTAGACTTTAAAAGAAAAAGGTGCCATGCAGTT
*
1193526 ATGGACTTTAAAGGGTGCAACGAAAAAA
66 ATGGACTATAAAGGGTGCAACGAAAAAA
** *
1193554 TGTGGACTTTAAAAGAAGAAGGTGTCACAGAGTTCTAGACTTTAAAAGAAAAAGGTGCCATGGAG
1 TGTGGACTTTAAAA-AA-AAGGTACCACAGAGTTCTAGACTTTAAAAGAAAAAGGTGCCATGCAG
1193619 TTATGGACTATAAA
64 TTATGGACTATAAA
1193633 AAAAATGCCA
Statistics
Matches: 68, Mismatches: 8, Indels: 3
0.86 0.10 0.04
Matches are distributed among these distances:
92 13 0.19
93 2 0.03
94 30 0.44
95 23 0.34
ACGTcount: A:0.40, C:0.11, G:0.26, T:0.24
Consensus pattern (93 bp):
TGTGGACTTTAAAAAAAAGGTACCACAGAGTTCTAGACTTTAAAAGAAAAAGGTGCCATGCAGTT
ATGGACTATAAAGGGTGCAACGAAAAAA
Found at i:1193778 original size:91 final size:89
Alignment explanation
Indices: 1193574--1193784 Score: 223
Period size: 91 Copynumber: 2.4 Consensus size: 89
1193564 AAAAGAAGAA
* ** * **
1193574 GGTGTCACAGAGTTCTAGACTTTAAAAGAAAAAGGTGCCATGGAGTTATGGACTATAAAAAAAAT
1 GGTGTCACAGAGTTATAGACTTTTGAAGAAAAAGGTACCACAGAGTTATGGACTATAAAAAAAAT
* *
1193639 GCCACAGAGTTTTGGACTTAAAAG
66 GCCACAGAGTTGTAGACTTAAAAG
* * * * *
1193663 GGTG-CTA-GGAAGTTGTGGACTTTTGAAGAAAAA-GTACCACAGAGTTGTGGACTTTAAAAGAA
1 GGTGTC-ACAG-AGTTATAGACTTTTGAAGAAAAAGGTACCACAGAGTTATGGACTAT-AAA-AA
1193725 AAAGTGCCACAGAGTTGTAGACTTAAAAG
62 AAA-TGCCACAGAGTTGTAGACTTAAAAG
*
1193754 GGTGTCACAGAGTTATAGATTTTTGAA-AAAA
1 GGTGTCACAGAGTTATAGACTTTTGAAGAAAA
1193785 GTTTGGAGGA
Statistics
Matches: 99, Mismatches: 16, Indels: 13
0.77 0.12 0.10
Matches are distributed among these distances:
88 19 0.19
89 27 0.27
90 9 0.09
91 42 0.42
92 2 0.02
ACGTcount: A:0.38, C:0.11, G:0.25, T:0.26
Consensus pattern (89 bp):
GGTGTCACAGAGTTATAGACTTTTGAAGAAAAAGGTACCACAGAGTTATGGACTATAAAAAAAAT
GCCACAGAGTTGTAGACTTAAAAG
Found at i:1194972 original size:7 final size:7
Alignment explanation
Indices: 1194962--1195003 Score: 50
Period size: 7 Copynumber: 6.1 Consensus size: 7
1194952 GCTTTTGCAC
1194962 TTTTTTA
1 TTTTTTA
1194969 TTTTTT-
1 TTTTTTA
*
1194975 TATTTTA
1 TTTTTTA
*
1194982 TTTTTCA
1 TTTTTTA
*
1194989 TTTTTCA
1 TTTTTTA
1194996 TTTTTTA
1 TTTTTTA
1195003 T
1 T
1195004 GCTTTTGCTC
Statistics
Matches: 30, Mismatches: 4, Indels: 2
0.83 0.11 0.06
Matches are distributed among these distances:
6 5 0.17
7 25 0.83
ACGTcount: A:0.14, C:0.05, G:0.00, T:0.81
Consensus pattern (7 bp):
TTTTTTA
Found at i:1194986 original size:35 final size:35
Alignment explanation
Indices: 1194932--1195003 Score: 94
Period size: 35 Copynumber: 2.1 Consensus size: 35
1194922 TTGTTTTTCG
*
1194932 ATTTTTGTTATTTTCTTTTTGC-TTTTGCACTTTTTT
1 ATTTTTGTTATTTTATTTTT-CATTTTGCA-TTTTTT
*
1194968 ATTTTT-TTATTTTATTTTTCATTTTTCATTTTTT
1 ATTTTTGTTATTTTATTTTTCATTTTGCATTTTTT
1195002 AT
1 AT
1195004 GCTTTTGCTC
Statistics
Matches: 33, Mismatches: 2, Indels: 4
0.85 0.05 0.10
Matches are distributed among these distances:
34 9 0.27
35 18 0.55
36 6 0.18
ACGTcount: A:0.12, C:0.08, G:0.04, T:0.75
Consensus pattern (35 bp):
ATTTTTGTTATTTTATTTTTCATTTTGCATTTTTT
Found at i:1199862 original size:2 final size:2
Alignment explanation
Indices: 1199855--1199891 Score: 74
Period size: 2 Copynumber: 18.5 Consensus size: 2
1199845 AAAGGCATTG
1199855 TA TA 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 TA TA T
1199892 TCTAAAAAAC
Statistics
Matches: 35, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 35 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:1202852 original size:79 final size:80
Alignment explanation
Indices: 1202769--1203200 Score: 266
Period size: 79 Copynumber: 5.5 Consensus size: 80
1202759 AAAAGTGATG
* * *
1202769 AGGTTGAAGTATCCCCGATGGTGAAAAATCAATATTTTAAAAATAAAAATAAGGGTTGGAGTATC
1 AGGTTGAAGTATCCCCGA-GATGAAAAATTAATATTTTAAAAATAAAAATAGGGGTTGGAGTATC
1202834 CTCTT-GAAAATAAC-
65 CTCTTCGAAAATAACA
** * * *
1202848 AGGTTTAGAA-TATCCTTGAGATGAAAATTTTAACATTTTGAAAAA-GAAAAT-GGGGTTGGAGT
1 AGG-TT-GAAGTATCCCCGAGATGAAAA-ATTAATATTTT-AAAAATAAAAATAGGGGTTGGAGT
*
1202910 AT-CTCTTCAAAAATAACA
62 ATCCTCTTCGAAAATAACA
* * * *
1202928 AGGTTGGAGTATCTCCGCGATGAAAAATTTAATATTTTGAAAATAAAAA-ACGGGGTTGGAGTAT
1 AGGTTGAAGTATCCCCGAGATGAAAAA-TTAATATTTTAAAAATAAAAATA-GGGGTTGGAGTAT
* * *
1202992 CC-CTTCGAAATTGA-T
64 CCTCTTCGAAAATAACA
* * * * * * ** *
1203007 GGGATAGGAGTATCCTCAAGATGAAAATTTTAATATTTTTGAAATAAAAAT-GAGGTTGGAGTAT
1 AGG-TTGAAGTATCCCCGAGATGAAAA-ATTAATATTTTAAAAATAAAAATAGGGGTTGGAGTAT
* * **
1203071 CC-CATT-GGAAATCATG
64 CCTC-TTCGAAAATAACA
* * * ** * ** *
1203087 GGGCTGGAGTATCTTCGAGATGAAAAATTGATATTTTGGAAGTAAAAATA-GGGTTGGAGTATCC
1 AGGTTGAAGTATCCCCGAGATGAAAAATTAATATTTTAAAAATAAAAATAGGGGTTGGAGTATCC
*
1203151 -CTTCAAAAATAAC-
66 TCTTCGAAAATAACA
* * * *
1203164 GGGATTGGAGTATCCCTGAGATG-AAAATCAATATTTT
1 AGG-TTGAAGTATCCCCGAGATGAAAAATTAATATTTT
1203201 TGGAAGGAAA
Statistics
Matches: 278, Mismatches: 55, Indels: 42
0.74 0.15 0.11
Matches are distributed among these distances:
77 17 0.06
78 64 0.23
79 99 0.36
80 89 0.32
81 9 0.03
ACGTcount: A:0.38, C:0.10, G:0.22, T:0.30
Consensus pattern (80 bp):
AGGTTGAAGTATCCCCGAGATGAAAAATTAATATTTTAAAAATAAAAATAGGGGTTGGAGTATCC
TCTTCGAAAATAACA
Found at i:1202910 original size:159 final size:158
Alignment explanation
Indices: 1202734--1203191 Score: 469
Period size: 159 Copynumber: 2.9 Consensus size: 158
1202724 TTTTGGAAGT
* * * * * * *
1202734 GAAAATGGGGTTTGAGTATCGCTTCAAAAGTGATGAGGTTGAAGTATCCCCGATGGTGAAAAATC
1 GAAAATGGGGTTGGAGTATCCCTTCAAAA-TAATGAGGTTGGAGTATCTCCGA-GATGAAAAATT
* * *
1202799 AATATTTTAAAAATAAAAATAAGGGTTGGAGTATCCTCTT-GAAAATAACAGGTTTAGAATATCC
64 AATATTTTGAAAATAAAAATAAGGGTTGGAGTATCC-CTTCGAAAATAACAGGATTAGAGTATCC
1202863 TTGAGATGAAAATTTTAACA-TTTTGAAAAA
128 TTGAGATGAAAATTTTAACATTTTTGAAAAA
* ** *
1202893 GAAAATGGGGTTGGAGTATCTCTTCAAAAATAACAAGGTTGGAGTATCTCCGCGATGAAAAATTT
1 GAAAATGGGGTTGGAGTATCCCTTC-AAAATAATGAGGTTGGAGTATCTCCGAGATGAAAAA-TT
* * * **
1202958 AATATTTTGAAAATAAAAA-ACGGGGTTGGAGTATCCCTTCGAAATTGATGGGA-TAGGAGTATC
64 AATATTTTGAAAATAAAAATA-AGGGTTGGAGTATCCCTTCGAAAATAACAGGATTA-GAGTATC
** * *
1203021 CTCAAGATGAAAATTTTAATATTTTTGAAATA
127 CTTGAGATGAAAATTTTAACATTTTTGAAAAA
* ** * * * * *
1203053 -AAAATGAGGTTGGAGTATCCCATTGGAAATCATGGGGCTGGAGTATCTTCGAGATGAAAAATTG
1 GAAAATGGGGTTGGAGTATCCC-TTCAAAATAATGAGGTTGGAGTATCTCCGAGATGAAAAATTA
* * * * * *
1203117 ATATTTTGGAAGTAAAAAT-AGGGTTGGAGTATCCCTTCAAAAATAACGGGATTGGAGTATCCCT
65 ATATTTTGAAAATAAAAATAAGGGTTGGAGTATCCCTTCGAAAATAACAGGATTAGAGTATCCTT
1203181 GAGATGAAAAT
130 GAGATGAAAAT
1203192 CAATATTTTT
Statistics
Matches: 245, Mismatches: 45, Indels: 20
0.79 0.15 0.06
Matches are distributed among these distances:
157 45 0.18
158 33 0.13
159 152 0.62
160 15 0.06
ACGTcount: A:0.38, C:0.10, G:0.23, T:0.29
Consensus pattern (158 bp):
GAAAATGGGGTTGGAGTATCCCTTCAAAATAATGAGGTTGGAGTATCTCCGAGATGAAAAATTAA
TATTTTGAAAATAAAAATAAGGGTTGGAGTATCCCTTCGAAAATAACAGGATTAGAGTATCCTTG
AGATGAAAATTTTAACATTTTTGAAAAA
Found at i:1205637 original size:21 final size:21
Alignment explanation
Indices: 1205611--1205665 Score: 67
Period size: 20 Copynumber: 2.7 Consensus size: 21
1205601 AGAGTGGTTT
1205611 TGTATCGATACATTTCAAGCA
1 TGTATCGATACATTTCAAGCA
* ***
1205632 TGTATCGATACA-ATCACTTA
1 TGTATCGATACATTTCAAGCA
1205652 TGTATCGATACATT
1 TGTATCGATACATT
1205666 ACCTATTATA
Statistics
Matches: 28, Mismatches: 5, Indels: 2
0.80 0.14 0.06
Matches are distributed among these distances:
20 16 0.57
21 12 0.43
ACGTcount: A:0.33, C:0.18, G:0.13, T:0.36
Consensus pattern (21 bp):
TGTATCGATACATTTCAAGCA
Found at i:1206412 original size:20 final size:21
Alignment explanation
Indices: 1206387--1206439 Score: 83
Period size: 20 Copynumber: 2.6 Consensus size: 21
1206377 CATTTTTGGC
1206387 ATGTATCGATACATTCACT-T
1 ATGTATCGATACATTCACTGT
*
1206407 ATGTATCGATACATTTACTGT
1 ATGTATCGATACATTCACTGT
1206428 -TGTATCGATACA
1 ATGTATCGATACA
1206440 AATTGTAAAA
Statistics
Matches: 31, Mismatches: 1, Indels: 2
0.91 0.03 0.06
Matches are distributed among these distances:
20 30 0.97
21 1 0.03
ACGTcount: A:0.30, C:0.17, G:0.13, T:0.40
Consensus pattern (21 bp):
ATGTATCGATACATTCACTGT
Found at i:1209735 original size:13 final size:13
Alignment explanation
Indices: 1209717--1209741 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
1209707 CAAAGATCAG
1209717 TGTATCGATACAA
1 TGTATCGATACAA
1209730 TGTATCGATACA
1 TGTATCGATACA
1209742 TTTTTTGGCA
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:0.36, C:0.16, G:0.16, T:0.32
Consensus pattern (13 bp):
TGTATCGATACAA
Found at i:1209787 original size:19 final size:18
Alignment explanation
Indices: 1209763--1209860 Score: 90
Period size: 19 Copynumber: 5.8 Consensus size: 18
1209753 TAGCTTACAT
1209763 TGTATCGATACAAAACTTA
1 TGTATCGATAC-AAACTTA
1209782 TGTATCGATAC--A--T-
1 TGTATCGATACAAACTTA
1209795 TGTATCGATACAACACTTA
1 TGTATCGATACAA-ACTTA
1209814 TGTATCGATAC--A--T-
1 TGTATCGATACAAACTTA
1209827 TGTATCGATACAACACTTTA
1 TGTATCGATACAA-AC-TTA
1209847 TGTATCGATACAAA
1 TGTATCGATACAAA
1209861 TCATTGAAAT
Statistics
Matches: 66, Mismatches: 0, Indels: 26
0.72 0.00 0.28
Matches are distributed among these distances:
13 22 0.33
14 2 0.03
16 4 0.06
18 1 0.02
19 24 0.36
20 13 0.20
ACGTcount: A:0.37, C:0.17, G:0.12, T:0.34
Consensus pattern (18 bp):
TGTATCGATACAAACTTA
Found at i:1209799 original size:32 final size:32
Alignment explanation
Indices: 1209758--1209858 Score: 184
Period size: 32 Copynumber: 3.1 Consensus size: 32
1209748 GGCAGTAGCT
*
1209758 TACATTGTATCGATACAAAACTTATGTATCGA
1 TACATTGTATCGATACAACACTTATGTATCGA
1209790 TACATTGTATCGATACAACACTTATGTATCGA
1 TACATTGTATCGATACAACACTTATGTATCGA
1209822 TACATTGTATCGATACAACACTTTATGTATCGA
1 TACATTGTATCGATACAACAC-TTATGTATCGA
1209855 TACA
1 TACA
1209859 AATCATTGAA
Statistics
Matches: 67, Mismatches: 1, Indels: 1
0.97 0.01 0.01
Matches are distributed among these distances:
32 52 0.78
33 15 0.22
ACGTcount: A:0.36, C:0.18, G:0.12, T:0.35
Consensus pattern (32 bp):
TACATTGTATCGATACAACACTTATGTATCGA
Found at i:1209800 original size:13 final size:13
Alignment explanation
Indices: 1209782--1209838 Score: 60
Period size: 13 Copynumber: 3.9 Consensus size: 13
1209772 ACAAAACTTA
1209782 TGTATCGATACAT
1 TGTATCGATACAT
1209795 TGTATCGATACAACACTT
1 TGTATCGAT---ACA--T
1209813 ATGTATCGATACAT
1 -TGTATCGATACAT
1209827 TGTATCGATACA
1 TGTATCGATACA
1209839 ACACTTTATG
Statistics
Matches: 38, Mismatches: 0, Indels: 12
0.76 0.00 0.24
Matches are distributed among these distances:
13 21 0.55
14 1 0.03
16 6 0.16
18 1 0.03
19 9 0.24
ACGTcount: A:0.33, C:0.18, G:0.14, T:0.35
Consensus pattern (13 bp):
TGTATCGATACAT
Found at i:1210622 original size:52 final size:52
Alignment explanation
Indices: 1210486--1210906 Score: 180
Period size: 52 Copynumber: 7.8 Consensus size: 52
1210476 GATAAAAGGA
* * * * *
1210486 CCAATATGTTGATTCATGGCCAACGATATTGGATTTAAAGATGAGAAAAAGGATG
1 CCAATATGCTGATTCAAGGCCAACAACATTGGACTTAAAGATGAG-AAAA--ATG
* * * ** * * * *
1210541 TCAATGTGCTGATTCATGGTTAGCGACATTAGACTTGAAGATGAGAAAAATG
1 CCAATATGCTGATTCAAGGCCAACAACATTGGACTTAAAGATGAGAAAAATG
* ** **
1210593 CCAATGTGCTGATTCAAGGCCAACAACATTGGGTTTTAAAGATGATG-AAGGTG
1 CCAATATGCTGATTCAAGGCCAACAACATT-GGACTTAAAGATGA-GAAAAATG
*
1210646 CCAATATGCTGATTCAAGGCCAACAATATTGGACTTAAAGATGAAGATGAGAAAAGTG
1 CCAATATGCTGATTCAAGGCCAACAACATTGGACTTAAAGAT---GA-GA-AAAA-TG
** * * * * *
1210704 ATAAAGATGCCAATATGTTGATTCACGGCCAACGATATTGGGCTTAAAGATGAGAAAAAGGATG
1 --CCA-A------TATGCTGATTCAAGGCCAACAACATTGGACTTAAAGATGAG-AAAA--ATG
* * * * * * *
1210768 TCAATGTGCTGATTCAAAGCCAGCTACATTGAACTTAAAGATG-GAAAAGGTG
1 CCAATATGCTGATTCAAGGCCAACAACATTGGACTTAAAGATGAGAAAA-ATG
* * * *
1210820 CCAATATGCTGATTCAAAGCCAGCTATATTGGACTT-AA-A-G-G-----TG
1 CCAATATGCTGATTCAAGGCCAACAACATTGGACTTAAAGATGAGAAAAATG
* * *
1210863 CCAATGTGCTGATTCAAGGCCAGCTACATTGGACTTAAAGATGA
1 CCAATATGCTGATTCAAGGCCAACAACATTGGACTTAAAGATGA
1210907 TGAGCATGAA
Statistics
Matches: 289, Mismatches: 53, Indels: 56
0.73 0.13 0.14
Matches are distributed among these distances:
43 35 0.12
44 2 0.01
45 1 0.00
46 1 0.00
49 2 0.01
50 1 0.00
51 2 0.01
52 72 0.25
53 46 0.16
54 6 0.02
55 69 0.24
57 2 0.01
58 2 0.01
60 1 0.00
61 2 0.01
62 1 0.00
63 4 0.01
64 5 0.02
65 1 0.00
67 34 0.12
ACGTcount: A:0.36, C:0.14, G:0.24, T:0.26
Consensus pattern (52 bp):
CCAATATGCTGATTCAAGGCCAACAACATTGGACTTAAAGATGAGAAAAATG
Found at i:1210752 original size:67 final size:68
Alignment explanation
Indices: 1210630--1210756 Score: 193
Period size: 67 Copynumber: 1.9 Consensus size: 68
1210620 ATTGGGTTTT
* *
1210630 AAAGATGATGAAGGTGCCAATATGCTGATTCAAGGCCAACAATATTGGACTTAAAGATGAAGATG
1 AAAGATGATAAAGATGCCAATATGCTGATTCAAGGCCAACAATATTGGACTTAAAGATGAAGATG
1210695 AGA
66 AGA
* * * *
1210698 AAAG-TGATAAAGATGCCAATATGTTGATTCACGGCCAACGATATTGGGCTTAAAGATGA
1 AAAGATGATAAAGATGCCAATATGCTGATTCAAGGCCAACAATATTGGACTTAAAGATGA
1210757 GAAAAAGGAT
Statistics
Matches: 53, Mismatches: 6, Indels: 1
0.88 0.10 0.02
Matches are distributed among these distances:
67 49 0.92
68 4 0.08
ACGTcount: A:0.39, C:0.13, G:0.24, T:0.24
Consensus pattern (68 bp):
AAAGATGATAAAGATGCCAATATGCTGATTCAAGGCCAACAATATTGGACTTAAAGATGAAGATG
AGA
Found at i:1210810 original size:55 final size:52
Alignment explanation
Indices: 1210746--1210905 Score: 167
Period size: 43 Copynumber: 3.2 Consensus size: 52
1210736 CGATATTGGG
* *
1210746 CTTAAAGATGAGAAAAAGGATGTCAATGTGCTGATTCAAAGCCAGCTACATTGAA
1 CTTAAAGATG-G-AAAAGG-TGCCAATATGCTGATTCAAAGCCAGCTACATTGAA
* *
1210801 CTTAAAGATGGAAAAGGTGCCAATATGCTGATTCAAAGCCAGCTATATTGGA
1 CTTAAAGATGGAAAAGGTGCCAATATGCTGATTCAAAGCCAGCTACATTGAA
* * *
1210853 C-T-----T---AAAGGTGCCAATGTGCTGATTCAAGGCCAGCTACATTGGA
1 CTTAAAGATGGAAAAGGTGCCAATATGCTGATTCAAAGCCAGCTACATTGAA
1210896 CTTAAAGATG
1 CTTAAAGATG
1210906 ATGAGCATGA
Statistics
Matches: 91, Mismatches: 7, Indels: 19
0.78 0.06 0.16
Matches are distributed among these distances:
43 38 0.42
44 1 0.01
46 1 0.01
49 1 0.01
51 1 0.01
52 32 0.35
53 6 0.07
54 1 0.01
55 10 0.11
ACGTcount: A:0.36, C:0.16, G:0.23, T:0.25
Consensus pattern (52 bp):
CTTAAAGATGGAAAAGGTGCCAATATGCTGATTCAAAGCCAGCTACATTGAA
Found at i:1210824 original size:227 final size:224
Alignment explanation
Indices: 1210428--1211575 Score: 1390
Period size: 227 Copynumber: 5.1 Consensus size: 224
1210418 CCACTGTGCA
* * * * * * *
1210428 GATTCAAGGCCTGCCACACTGGACTTAAAGATGATGAGGATAAAGAGTGATAAAAGGACCAATAT
1 GATTCAAGGCCAGCAATATTGGACTTAAAGATGAAGATGAGAAA-AGTGATAAAAGGACCAATAT
* * *
1210493 GTTGATTCATGGCCAACGATATTGGATTTAAAGATGAGAAAAAGGATGTCAATGTGCTGATTCAT
65 GTTGATTCACGGCCAACGATATTGGGTTTAAAGATGAGAAAAAGGATGTCAATGTGCTGATTCAA
*
1210558 GGTTAGCGACATTAGACTTGAAGATGAGAAAAATGCCAATGTGCTGATTCAAGGCCAACAACATT
130 GGTCAGCGACATTAGACTTGAAGATGAGAAAAATGCCAATGTGCTGATTCAAGGCCAACAACATT
*
1210623 GGGTTTTAAAGATGATGAAGGTGCCAATATGCT
195 -GG--TTAAAGATGATAAAGGTGCCAATATGCT
* *
1210656 GATTCAAGGCCAACAATATTGGACTTAAAGATGAAGATGAGAAAAGTGATAAAGATG-CCAATAT
1 GATTCAAGGCCAGCAATATTGGACTTAAAGATGAAGATGAGAAAAGTGATAAA-AGGACCAATAT
*
1210720 GTTGATTCACGGCCAACGATATTGGGCTTAAAGATGAGAAAAAGGATGTCAATGTGCTGATTCAA
65 GTTGATTCACGGCCAACGATATTGGGTTTAAAGATGAGAAAAAGGATGTCAATGTGCTGATTCAA
* * * * * * * * * *
1210785 AGCCAGCTACATT-GAACTTAAAGATG-GAAAAGGTGCCAATATGCTGATTCAAAGCCAGCTATA
130 GGTCAGCGACATTAG-ACTTGAAGATGAGAAAA-ATGCCAATGTGCTGATTCAAGGCCAACAACA
* *
1210848 TTGG----A-CT--TAAAGGTGCCAATGTGCT
193 TTGGTTAAAGATGATAAAGGTGCCAATATGCT
* * * *
1210873 GATTCAAGGCCAGCTACATTGGACTTAAAGATGATGA-GCATGAAGAGTGATAAAAGGACCAATA
1 GATTCAAGGCCAGCAATATTGGACTTAAAGATGAAGATG-A-GAAAAGTGATAAAAGGACCAATA
* *
1210937 TGTTGATTCACGGCCAACGATATTGGGTTTACAGATGACAAAAAGGATGTCAATGTGCTGATTCA
64 TGTTGATTCACGGCCAACGATATTGGGTTTAAAGATGAGAAAAAGGATGTCAATGTGCTGATTCA
* *
1211002 CGGTCAACGACATTAGACTTGAAGATGAGAAAAATGCCAATGTGCTGATTCAAGGCCAACAACAT
129 AGGTCAGCGACATTAGACTTGAAGATGAGAAAAATGCCAATGTGCTGATTCAAGGCCAACAACAT
*
1211067 TGGGTTTTAAAGATGATGAAGGTGCCAATATGCT
194 T-GG--TTAAAGATGATAAAGGTGCCAATATGCT
* *
1211101 GATTCAAGGCCAGCAATATTGGACTTAAAGATGAAGGTGAGAAAAGTGATAAAGATG-CCAATAT
1 GATTCAAGGCCAGCAATATTGGACTTAAAGATGAAGATGAGAAAAGTGATAAA-AGGACCAATAT
* *
1211165 GTTGATTCACGGCCAACAATATTGGGCTTAAAGATGAGAAAAAGGATGTCAATGTGCTGATTCAA
65 GTTGATTCACGGCCAACGATATTGGGTTTAAAGATGAGAAAAAGGATGTCAATGTGCTGATTCAA
* * * * * * * *
1211230 GGCCAGCTACATT-GAACTTAAAGATG-GAAAAGGTGCCAATATGCTGATTCAAGGCCAGCTATA
130 GGTCAGCGACATTAG-ACTTGAAGATGAGAAAA-ATGCCAATGTGCTGATTCAAGGCCAACAACA
* * *
1211293 TTGG----A-CT--TAAAGGTGCCACTGTG-T
193 TTGGTTAAAGATGATAAAGGTGCCAATATGCT
*
1211317 AGATTCAAGGCCAG-ATACATTGGACTTAAAGATGATGAGGATG-GAAAAGTGATAAAAGGACCA
1 -GATTCAAGGCCAGCA-ATATTGGACTTAAAGATGA--A-GATGAGAAAAGTGATAAAAGGACCA
* *
1211380 ATATGTTGATTCACGGCCAACGATATTGGGTTTAAAGATGAAAAAAAGGATGTAAATGTGCTGAT
61 ATATGTTGATTCACGGCCAACGATATTGGGTTTAAAGATGAGAAAAAGGATGTCAATGTGCTGAT
*
1211445 TCACGGTCAGCGACATTAGACTTGAAGATGAGAAAAATGCCAATGTGCTGATTCAAGGCCAACAA
126 TCAAGGTCAGCGACATTAGACTTGAAGATGAGAAAAATGCCAATGTGCTGATTCAAGGCCAACAA
* **
1211510 CATTGGACTTAAAGATGACAAAGACGCCAATATGCT
191 CATTGG--TTAAAGATGATAAAGGTGCCAATATGCT
* *
1211546 GATTCAGGGCCAGCGATATTGGACTTAAAG
1 GATTCAAGGCCAGCAATATTGGACTTAAAG
1211576 GTATCAATGT
Statistics
Matches: 779, Mismatches: 100, Indels: 82
0.81 0.10 0.09
Matches are distributed among these distances:
216 3 0.00
217 96 0.12
218 128 0.16
219 142 0.18
220 11 0.01
225 2 0.00
226 18 0.02
227 250 0.32
228 127 0.16
229 2 0.00
ACGTcount: A:0.36, C:0.15, G:0.25, T:0.24
Consensus pattern (224 bp):
GATTCAAGGCCAGCAATATTGGACTTAAAGATGAAGATGAGAAAAGTGATAAAAGGACCAATATG
TTGATTCACGGCCAACGATATTGGGTTTAAAGATGAGAAAAAGGATGTCAATGTGCTGATTCAAG
GTCAGCGACATTAGACTTGAAGATGAGAAAAATGCCAATGTGCTGATTCAAGGCCAACAACATTG
GTTAAAGATGATAAAGGTGCCAATATGCT
Done.