Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Chr09 ID=Chr09-JGI_221_v2.0
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: 70713020
ACGTcount: A:0.33, C:0.16, G:0.16, T:0.33
Warning! 1142373 characters in sequence are not A, C, G, or T
File 222 of 226
Found at i:69402512 original size:9 final size:9
Alignment explanation
Indices: 69402458--69402515 Score: 71
Period size: 9 Copynumber: 6.4 Consensus size: 9
69402448 GTAGTGATTC
*
69402458 AATTTGGTT
1 AATTCGGTT
*
69402467 AATTCGGGT
1 AATTCGGTT
69402476 AATTCGGTT
1 AATTCGGTT
*
69402485 AATTCGGGT
1 AATTCGGTT
*
69402494 AATTTGGTT
1 AATTCGGTT
*
69402503 AATTCAGTT
1 AATTCGGTT
69402512 AATT
1 AATT
69402516 TTTAACCAAA
Statistics
Matches: 41, Mismatches: 8, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
9 41 1.00
ACGTcount: A:0.26, C:0.07, G:0.22, T:0.45
Consensus pattern (9 bp):
AATTCGGTT
Found at i:69402516 original size:18 final size:18
Alignment explanation
Indices: 69402458--69402507 Score: 91
Period size: 18 Copynumber: 2.8 Consensus size: 18
69402448 GTAGTGATTC
69402458 AATTTGGTTAATTCGGGT
1 AATTTGGTTAATTCGGGT
*
69402476 AATTCGGTTAATTCGGGT
1 AATTTGGTTAATTCGGGT
69402494 AATTTGGTTAATTC
1 AATTTGGTTAATTC
69402508 AGTTAATTTT
Statistics
Matches: 30, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
18 30 1.00
ACGTcount: A:0.24, C:0.08, G:0.24, T:0.44
Consensus pattern (18 bp):
AATTTGGTTAATTCGGGT
Found at i:69402944 original size:16 final size:16
Alignment explanation
Indices: 69402905--69402944 Score: 53
Period size: 16 Copynumber: 2.5 Consensus size: 16
69402895 ATCTATATTT
*
69402905 TATTTTTAATCAAATA
1 TATTTTTTATCAAATA
* *
69402921 TACTTTTTATTAAATA
1 TATTTTTTATCAAATA
69402937 TATTTTTT
1 TATTTTTT
69402945 TTTGAACTTT
Statistics
Matches: 20, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
16 20 1.00
ACGTcount: A:0.35, C:0.05, G:0.00, T:0.60
Consensus pattern (16 bp):
TATTTTTTATCAAATA
Found at i:69414544 original size:18 final size:18
Alignment explanation
Indices: 69414521--69414556 Score: 54
Period size: 18 Copynumber: 2.0 Consensus size: 18
69414511 CTGATGGTAG
69414521 GCTAATTTATCAAAAAAA
1 GCTAATTTATCAAAAAAA
* *
69414539 GCTAATTTTTTAAAAAAA
1 GCTAATTTATCAAAAAAA
69414557 TTATCGAAAT
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
18 16 1.00
ACGTcount: A:0.53, C:0.08, G:0.06, T:0.33
Consensus pattern (18 bp):
GCTAATTTATCAAAAAAA
Found at i:69414838 original size:24 final size:22
Alignment explanation
Indices: 69414807--69414923 Score: 89
Period size: 22 Copynumber: 5.2 Consensus size: 22
69414797 ATTTTCACAA
69414807 AAAAATTCAATATCAATATCC-TTC
1 AAAAATTC--TATCAAT-TCCGTTC
*
69414831 AAAAATTCTCTCAATTCCGTTC
1 AAAAATTCTATCAATTCCGTTC
* *
69414853 AAAAATTCTCTCAAATTCCTTTC
1 AAAAATTCTATC-AATTCCGTTC
*
69414876 -AAAATTCTCTCAAATTCC-TTC
1 AAAAATTCTATC-AATTCCGTTC
* * *
69414897 TAAAATCCTCTCAATTTCC-TTC
1 AAAAATTCTATCAA-TTCCGTTC
69414919 AAAAA
1 AAAAA
69414924 ATCTCCAAAT
Statistics
Matches: 85, Mismatches: 4, Indels: 10
0.86 0.04 0.10
Matches are distributed among these distances:
21 8 0.09
22 60 0.71
23 9 0.11
24 8 0.09
ACGTcount: A:0.38, C:0.26, G:0.01, T:0.36
Consensus pattern (22 bp):
AAAAATTCTATCAATTCCGTTC
Found at i:69414853 original size:22 final size:21
Alignment explanation
Indices: 69414819--69414928 Score: 132
Period size: 22 Copynumber: 5.0 Consensus size: 21
69414809 AAATTCAATA
69414819 TCAATATCCTTCAAAAATTCTC
1 TCAAT-TCCTTCAAAAATTCTC
69414841 TCAATTCCGTTCAAAAATTCTC
1 TCAATTCC-TTCAAAAATTCTC
69414863 TCAAATTCCTTTC-AAAATTCTC
1 TC-AATTCC-TTCAAAAATTCTC
* *
69414885 TCAAATTCCTTCTAAAATCCTC
1 TC-AATTCCTTCAAAAATTCTC
*
69414907 TCAATTTCCTTCAAAAAATCTC
1 TCAA-TTCCTTCAAAAATTCTC
69414929 CAAATCCATA
Statistics
Matches: 79, Mismatches: 5, Indels: 8
0.86 0.05 0.09
Matches are distributed among these distances:
21 8 0.10
22 62 0.78
23 9 0.11
ACGTcount: A:0.34, C:0.28, G:0.01, T:0.37
Consensus pattern (21 bp):
TCAATTCCTTCAAAAATTCTC
Found at i:69414988 original size:27 final size:27
Alignment explanation
Indices: 69414958--69415018 Score: 72
Period size: 28 Copynumber: 2.2 Consensus size: 27
69414948 TTTTTTCATT
69414958 AAATTTCATTA-TTTTAAGAA-AATTTTA
1 AAATTT-ATTATTTTTAA-AATAATTTTA
*
69414985 AAATTTTTTATTTTTTAAAATAATTTTA
1 AAATTTATTA-TTTTTAAAATAATTTTA
69415013 AAATTT
1 AAATTT
69415019 TTAATATTTT
Statistics
Matches: 30, Mismatches: 1, Indels: 5
0.83 0.03 0.14
Matches are distributed among these distances:
26 3 0.10
27 8 0.27
28 19 0.63
ACGTcount: A:0.43, C:0.02, G:0.02, T:0.54
Consensus pattern (27 bp):
AAATTTATTATTTTTAAAATAATTTTA
Found at i:69415028 original size:28 final size:28
Alignment explanation
Indices: 69414967--69415028 Score: 90
Period size: 28 Copynumber: 2.2 Consensus size: 28
69414957 TAAATTTCAT
*
69414967 TATTTTAAGAAAATTTTAAAATTTTTTA
1 TATTTTAAGAAAATTTTAAAATTTTTAA
*
69414995 TTTTTTAA-AATAATTTTAAAATTTTTAA
1 TATTTTAAGAA-AATTTTAAAATTTTTAA
69415023 TATTTT
1 TATTTT
69415029 CAACAATGGC
Statistics
Matches: 30, Mismatches: 3, Indels: 2
0.86 0.09 0.06
Matches are distributed among these distances:
27 2 0.07
28 28 0.93
ACGTcount: A:0.40, C:0.00, G:0.02, T:0.58
Consensus pattern (28 bp):
TATTTTAAGAAAATTTTAAAATTTTTAA
Found at i:69415174 original size:24 final size:23
Alignment explanation
Indices: 69415118--69415174 Score: 62
Period size: 24 Copynumber: 2.3 Consensus size: 23
69415108 TAAATTTTAA
69415118 ATTTTATTTAAGATATTTTAATTT
1 ATTTT-TTTAAGATATTTTAATTT
69415142 ATGTATTTTT-AGATATTTATTAATTT
1 AT-T-TTTTTAAGATA-TT-TTAATTT
69415168 ATTTTTT
1 ATTTTTT
69415175 CTTATAAAAG
Statistics
Matches: 29, Mismatches: 0, Indels: 8
0.78 0.00 0.22
Matches are distributed among these distances:
24 11 0.38
25 7 0.24
26 11 0.38
ACGTcount: A:0.30, C:0.00, G:0.05, T:0.65
Consensus pattern (23 bp):
ATTTTTTTAAGATATTTTAATTT
Found at i:69419085 original size:23 final size:23
Alignment explanation
Indices: 69419059--69419112 Score: 81
Period size: 23 Copynumber: 2.3 Consensus size: 23
69419049 AATGGAACAA
* *
69419059 TAAACAAGCTTTGAATGATTTAT
1 TAAACAAGCTTTAAATGATCTAT
*
69419082 TAAACGAGCTTTAAATGATCTAT
1 TAAACAAGCTTTAAATGATCTAT
69419105 TAAACAAG
1 TAAACAAG
69419113 TTTCAGATGA
Statistics
Matches: 27, Mismatches: 4, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
23 27 1.00
ACGTcount: A:0.43, C:0.11, G:0.13, T:0.33
Consensus pattern (23 bp):
TAAACAAGCTTTAAATGATCTAT
Found at i:69423740 original size:24 final size:23
Alignment explanation
Indices: 69423713--69423758 Score: 65
Period size: 23 Copynumber: 2.0 Consensus size: 23
69423703 TCAAATCTTA
* *
69423713 AAACAAAATCAAAGGAAAAGAAAC
1 AAACAAAA-AAAAAGAAAAGAAAC
69423737 AAACAAAAAAAAAGAAAAGAAA
1 AAACAAAAAAAAAGAAAAGAAA
69423759 AACAGGAGGA
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
23 12 0.60
24 8 0.40
ACGTcount: A:0.78, C:0.09, G:0.11, T:0.02
Consensus pattern (23 bp):
AAACAAAAAAAAAGAAAAGAAAC
Found at i:69425875 original size:14 final size:15
Alignment explanation
Indices: 69425844--69425881 Score: 60
Period size: 14 Copynumber: 2.6 Consensus size: 15
69425834 CATTCAACAT
69425844 GAAAAGAAAAAGAAA
1 GAAAAGAAAAAGAAA
*
69425859 GAAAAGAAATA-AAA
1 GAAAAGAAAAAGAAA
69425873 GAAAAGAAA
1 GAAAAGAAA
69425882 GTTATGAAGC
Statistics
Matches: 22, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
14 12 0.55
15 10 0.45
ACGTcount: A:0.79, C:0.00, G:0.18, T:0.03
Consensus pattern (15 bp):
GAAAAGAAAAAGAAA
Found at i:69426096 original size:19 final size:19
Alignment explanation
Indices: 69426070--69426115 Score: 51
Period size: 19 Copynumber: 2.5 Consensus size: 19
69426060 CAGTAATTCT
69426070 TCAA-CATTTAACTAA-TA
1 TCAATCATTTAACTAATTA
* *
69426087 TCATATCATTTCAGTAATTA
1 TCA-ATCATTTAACTAATTA
69426107 TCAATCATT
1 TCAATCATT
69426116 CATGATTGAA
Statistics
Matches: 24, Mismatches: 2, Indels: 4
0.80 0.07 0.13
Matches are distributed among these distances:
17 3 0.12
18 1 0.04
19 15 0.62
20 5 0.21
ACGTcount: A:0.39, C:0.17, G:0.02, T:0.41
Consensus pattern (19 bp):
TCAATCATTTAACTAATTA
Found at i:69427804 original size:2 final size:2
Alignment explanation
Indices: 69427797--69427837 Score: 82
Period size: 2 Copynumber: 20.5 Consensus size: 2
69427787 ACTCATTCTT
69427797 TA TA 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 TA TA T
69427838 TTCTAAATTT
Statistics
Matches: 39, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 39 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:69432667 original size:19 final size:19
Alignment explanation
Indices: 69432634--69432686 Score: 56
Period size: 19 Copynumber: 2.8 Consensus size: 19
69432624 TTCAGAACAA
69432634 TAATTCATCAA-CATTTAAC
1 TAATT-ATCAATCATTTAAC
* *
69432653 TAA-TATCACATCATTTCAG
1 TAATTATCA-ATCATTTAAC
69432672 TAATTATCAATCATT
1 TAATTATCAATCATT
69432687 CATAATTGAA
Statistics
Matches: 29, Mismatches: 2, Indels: 6
0.78 0.05 0.16
Matches are distributed among these distances:
17 4 0.14
18 2 0.07
19 18 0.62
20 5 0.17
ACGTcount: A:0.40, C:0.19, G:0.02, T:0.40
Consensus pattern (19 bp):
TAATTATCAATCATTTAAC
Found at i:69434194 original size:21 final size:21
Alignment explanation
Indices: 69434147--69434195 Score: 53
Period size: 21 Copynumber: 2.3 Consensus size: 21
69434137 TTGTCTCTTT
* **
69434147 AATTTCCTCACTTTTTCTACC
1 AATTTCTTCACTTTCACTACC
* *
69434168 ATTTTCTTCACTTTCACTTCC
1 AATTTCTTCACTTTCACTACC
69434189 AATTTCT
1 AATTTCT
69434196 CTCTTCCAAG
Statistics
Matches: 22, Mismatches: 6, Indels: 0
0.79 0.21 0.00
Matches are distributed among these distances:
21 22 1.00
ACGTcount: A:0.18, C:0.31, G:0.00, T:0.51
Consensus pattern (21 bp):
AATTTCTTCACTTTCACTACC
Found at i:69435076 original size:2 final size:2
Alignment explanation
Indices: 69435071--69435100 Score: 60
Period size: 2 Copynumber: 15.0 Consensus size: 2
69435061 TCTCACCCTC
69435071 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
69435101 TTAAAAATCA
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 28 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:69437621 original size:17 final size:18
Alignment explanation
Indices: 69437592--69437853 Score: 108
Period size: 18 Copynumber: 14.1 Consensus size: 18
69437582 ACACAATAAT
69437592 AATTTTTGAAAACACGAA
1 AATTTTTGAAAACACGAA
*
69437610 GATTTTTG-AAACACGAA
1 AATTTTTGAAAACACGAA
69437627 AATTTTTTGAAAACACGGAA
1 AA-TTTTTGAAAACAC-GAA
** * *
69437647 TTTTTTTGAAAACAAGGA
1 AATTTTTGAAAACACGAA
* * *
69437665 AATTTTCG-ATACATGAGA
1 AATTTTTGAAAACACGA-A
*
69437683 ATTTTTTG---ACACGAA
1 AATTTTTGAAAACACGAA
* *
69437698 AAATTTTGAAAATACGAA
1 AATTTTTGAAAACACGAA
* *
69437716 AA-TTTCGAAAACATG-A
1 AATTTTTGAAAACACGAA
* * * *
69437732 ATTTTTTTAAAATACGATT
1 AATTTTTGAAAACACGA-A
** *
69437751 TTTTTTTAAAAACACGAGA
1 AATTTTTGAAAACACGA-A
* *
69437770 ATTTTTTTTGAAAACCCGAAA
1 A--ATTTTTGAAAACACG-AA
69437791 ACATGAAAATTTTGAAAACACGAA
1 A-AT-----TTTTGAAAACACGAA
69437815 AATTTTTTG-AAACACGAGA
1 AA-TTTTTGAAAACACGA-A
* *
69437834 ATTTTTTGAAAATACGAA
1 AATTTTTGAAAACACGAA
69437852 AA
1 AA
69437854 CACGAAAATT
Statistics
Matches: 182, Mismatches: 41, Indels: 42
0.69 0.15 0.16
Matches are distributed among these distances:
15 7 0.04
16 7 0.04
17 34 0.19
18 51 0.28
19 46 0.25
20 4 0.02
21 15 0.08
22 1 0.01
23 1 0.01
24 4 0.02
25 12 0.07
ACGTcount: A:0.44, C:0.10, G:0.13, T:0.33
Consensus pattern (18 bp):
AATTTTTGAAAACACGAA
Found at i:69437639 original size:36 final size:38
Alignment explanation
Indices: 69437576--69437661 Score: 108
Period size: 36 Copynumber: 2.3 Consensus size: 38
69437566 ACACGAGAAC
69437576 TTTGAAACACAATAATAATTTTTGAAAACAC-GAAGATT
1 TTTGAAACACAATAAT-ATTTTTGAAAACACGGAAGATT
**
69437614 TTTGAAACACGAA-AAT-TTTTTGAAAACACGGAATTTT
1 TTTGAAACAC-AATAATATTTTTGAAAACACGGAAGATT
69437651 TTTGAAA-ACAA
1 TTTGAAACACAA
69437662 GGAAATTTTC
Statistics
Matches: 44, Mismatches: 2, Indels: 7
0.83 0.04 0.13
Matches are distributed among these distances:
35 2 0.05
36 15 0.34
37 12 0.27
38 13 0.30
39 2 0.05
ACGTcount: A:0.45, C:0.10, G:0.12, T:0.33
Consensus pattern (38 bp):
TTTGAAACACAATAATATTTTTGAAAACACGGAAGATT
Found at i:69437836 original size:64 final size:65
Alignment explanation
Indices: 69437753--69437904 Score: 179
Period size: 64 Copynumber: 2.4 Consensus size: 65
69437743 ATACGATTTT
* * *
69437753 TTTTTAAAAACACGAGAATTTTTTTTGAAAACCCGAAAACATGAAAA-TTTTGAAAACACGAAAA
1 TTTTTGAAAACACGAGAATTTTTTTTGAAAACACGAAAACACGAAAATTTTTGAAAACACGAAAA
* ** **
69437817 TTTTTTG-AAACACGAGAA--TTTTTTGAAAATACGAAAACACGAAAATTTTTTTTAAACACGGG
1 -TTTTTGAAAACACGAGAATTTTTTTTGAAAACACGAAAACACGAAAA-TTTTTGAAAACACGAA
69437879 AA
64 AA
69437881 TTTTTGAAAACACGA-AATTTTTTT
1 TTTTTGAAAACACGAGAATTTTTTT
69437905 ATTCACGAGA
Statistics
Matches: 74, Mismatches: 8, Indels: 10
0.80 0.09 0.11
Matches are distributed among these distances:
62 24 0.32
63 8 0.11
64 32 0.43
65 10 0.14
ACGTcount: A:0.43, C:0.11, G:0.12, T:0.34
Consensus pattern (65 bp):
TTTTTGAAAACACGAGAATTTTTTTTGAAAACACGAAAACACGAAAATTTTTGAAAACACGAAAA
Found at i:69437850 original size:19 final size:19
Alignment explanation
Indices: 69437594--69437853 Score: 141
Period size: 19 Copynumber: 13.9 Consensus size: 19
69437584 ACAATAATAA
*
69437594 TTTTTGAAAACACGAAGA-
1 TTTTTGAAAACACGAAAAT
69437612 TTTTTG-AAACACGAAAAT
1 TTTTTGAAAACACGAAAAT
* *
69437630 TTTTTGAAAACACGGAATT
1 TTTTTGAAAACACGAAAAT
* *
69437649 TTTTTGAAAACAAGGAAA-
1 TTTTTGAAAACACGAAAAT
* * * *
69437667 TTTTCG-ATACATGAGAAT
1 TTTTTGAAAACACGAAAAT
69437685 TTTTTG---ACACGAAAA-
1 TTTTTGAAAACACGAAAAT
* *
69437700 ATTTTGAAAATACGAAAA-
1 TTTTTGAAAACACGAAAAT
* *
69437718 -TTTCGAAAACATG--AAT
1 TTTTTGAAAACACGAAAAT
* * ***
69437734 TTTTTTAAAATACGATTTT
1 TTTTTGAAAACACGAAAAT
* *
69437753 TTTTTAAAAACACGAGAATTT
1 TTTTTGAAAACACGA-AA-AT
*
69437774 TTTTTGAAAACCCGAAAACAT
1 TTTTTGAAAACACG-AAA-AT
*
69437795 GAAAATTTTGAAAACACGAAAAT
1 ----TTTTTGAAAACACGAAAAT
*
69437818 TTTTTG-AAACACGAGAAT
1 TTTTTGAAAACACGAAAAT
*
69437836 TTTTTGAAAATACGAAAA
1 TTTTTGAAAACACGAAAA
69437854 CACGAAAATT
Statistics
Matches: 186, Mismatches: 38, Indels: 35
0.72 0.15 0.14
Matches are distributed among these distances:
15 7 0.04
16 7 0.04
17 36 0.19
18 47 0.25
19 54 0.29
21 17 0.09
22 1 0.01
23 2 0.01
24 3 0.02
25 12 0.06
ACGTcount: A:0.44, C:0.10, G:0.13, T:0.33
Consensus pattern (19 bp):
TTTTTGAAAACACGAAAAT
Found at i:69437854 original size:45 final size:45
Alignment explanation
Indices: 69437804--69437897 Score: 145
Period size: 45 Copynumber: 2.1 Consensus size: 45
69437794 TGAAAATTTT
*
69437804 GAAAACACGAAAA-TTTTTTGAAACACGAGAATTTTTTGAAAATAC
1 GAAAACACGAAAATTTTTTTGAAACACGAGAA-TTTTTGAAAACAC
* *
69437849 GAAAACACGAAAATTTTTTTTAAACACGGGAATTTTTGAAAACAC
1 GAAAACACGAAAATTTTTTTGAAACACGAGAATTTTTGAAAACAC
69437894 GAAA
1 GAAA
69437898 TTTTTTTATT
Statistics
Matches: 45, Mismatches: 3, Indels: 2
0.90 0.06 0.04
Matches are distributed among these distances:
45 29 0.64
46 16 0.36
ACGTcount: A:0.47, C:0.12, G:0.14, T:0.28
Consensus pattern (45 bp):
GAAAACACGAAAATTTTTTTGAAACACGAGAATTTTTGAAAACAC
Found at i:69437875 original size:19 final size:18
Alignment explanation
Indices: 69437850--69437905 Score: 60
Period size: 18 Copynumber: 3.1 Consensus size: 18
69437840 TGAAAATACG
69437850 AAAACACGAAAATTTTTTT
1 AAAACACG-AAATTTTTTT
* * *
69437869 TAAACACGGGAA-TTTTTG
1 AAAACAC-GAAATTTTTTT
69437887 AAAACACGAAATTTTTTT
1 AAAACACGAAATTTTTTT
69437905 A
1 A
69437906 TTCACGAGAA
Statistics
Matches: 29, Mismatches: 6, Indels: 5
0.73 0.15 0.12
Matches are distributed among these distances:
17 3 0.10
18 17 0.59
19 8 0.28
20 1 0.03
ACGTcount: A:0.43, C:0.11, G:0.11, T:0.36
Consensus pattern (18 bp):
AAAACACGAAATTTTTTT
Found at i:69437917 original size:35 final size:35
Alignment explanation
Indices: 69437849--69437940 Score: 116
Period size: 35 Copynumber: 2.6 Consensus size: 35
69437839 TTGAAAATAC
*
69437849 GAAAACACGAAAATTTTTTTTAAACACGGGAATTTTT
1 GAAAACACG-AAA-TTTTTTTAAACACGAGAATTTTT
**
69437886 GAAAACACGAAATTTTTTTATTCACGAGAATTTTT
1 GAAAACACGAAATTTTTTTAAACACGAGAATTTTT
*
69437921 G-AAACACG-GATTTTTTTAAA
1 GAAAACACGAAATTTTTTTAAA
69437941 GAAAGAAACA
Statistics
Matches: 49, Mismatches: 6, Indels: 4
0.83 0.10 0.07
Matches are distributed among these distances:
33 9 0.18
34 7 0.14
35 21 0.43
36 3 0.06
37 9 0.18
ACGTcount: A:0.39, C:0.11, G:0.13, T:0.37
Consensus pattern (35 bp):
GAAAACACGAAATTTTTTTAAACACGAGAATTTTT
Found at i:69437928 original size:17 final size:17
Alignment explanation
Indices: 69437864--69437928 Score: 60
Period size: 17 Copynumber: 3.8 Consensus size: 17
69437854 CACGAAAATT
* *
69437864 TTTTTTAAACACGGGAA
1 TTTTTGAAACACGAGAA
69437881 TTTTTGAAAACACGA-AA
1 TTTTTG-AAACACGAGAA
* **
69437898 TTTTTTTATTCACGAGAA
1 -TTTTTGAAACACGAGAA
69437916 TTTTTGAAACACG
1 TTTTTGAAACACG
69437929 GATTTTTTTA
Statistics
Matches: 37, Mismatches: 8, Indels: 6
0.73 0.16 0.12
Matches are distributed among these distances:
17 23 0.62
18 14 0.38
ACGTcount: A:0.35, C:0.12, G:0.14, T:0.38
Consensus pattern (17 bp):
TTTTTGAAACACGAGAA
Found at i:69438032 original size:18 final size:17
Alignment explanation
Indices: 69437991--69438039 Score: 64
Period size: 17 Copynumber: 2.8 Consensus size: 17
69437981 TATTATTATT
69437991 ATTTTGAAACACGAGAA
1 ATTTTGAAACACGAGAA
*
69438008 ATTTTGAAGACATGA-AA
1 ATTTTGAA-ACACGAGAA
69438025 ATTTTTGAAACACGA
1 A-TTTTGAAACACGA
69438040 TTTTTTTCTT
Statistics
Matches: 28, Mismatches: 2, Indels: 4
0.82 0.06 0.12
Matches are distributed among these distances:
17 16 0.57
18 12 0.43
ACGTcount: A:0.45, C:0.10, G:0.16, T:0.29
Consensus pattern (17 bp):
ATTTTGAAACACGAGAA
Found at i:69438490 original size:27 final size:27
Alignment explanation
Indices: 69438450--69438523 Score: 121
Period size: 27 Copynumber: 2.7 Consensus size: 27
69438440 TGCCAAATTT
69438450 GGGCCTGGGTGCTGGGCTGCCGCTGGAAC
1 GGGCCT-GG-GCTGGGCTGCCGCTGGAAC
69438479 GGGCCTGGGCTGGGCTGCCGCTGGAAC
1 GGGCCTGGGCTGGGCTGCCGCTGGAAC
*
69438506 GGGCCTGGGCTGGCCTGC
1 GGGCCTGGGCTGGGCTGC
69438524 TGCAGATTTT
Statistics
Matches: 44, Mismatches: 1, Indels: 2
0.94 0.02 0.04
Matches are distributed among these distances:
27 36 0.82
28 2 0.05
29 6 0.14
ACGTcount: A:0.05, C:0.30, G:0.49, T:0.16
Consensus pattern (27 bp):
GGGCCTGGGCTGGGCTGCCGCTGGAAC
Found at i:69438625 original size:10 final size:10
Alignment explanation
Indices: 69438593--69438653 Score: 52
Period size: 10 Copynumber: 5.9 Consensus size: 10
69438583 GGGCTGCTAC
*
69438593 TTTTGTTCTT
1 TTTTTTTCTT
69438603 TTTTATTGT-TT
1 TTTT-TT-TCTT
69438614 TTTTTTTCTT
1 TTTTTTTCTT
*
69438624 TTTCTTTCTT
1 TTTTTTTCTT
* *
69438634 TTTCTCTCTT
1 TTTTTTTCTT
69438644 TTTTCTTTCT
1 TTTT-TTTCT
69438654 CCTTTCTTCT
Statistics
Matches: 42, Mismatches: 5, Indels: 7
0.78 0.09 0.13
Matches are distributed among these distances:
9 1 0.02
10 29 0.69
11 11 0.26
12 1 0.02
ACGTcount: A:0.02, C:0.15, G:0.03, T:0.80
Consensus pattern (10 bp):
TTTTTTTCTT
Found at i:69438635 original size:21 final size:21
Alignment explanation
Indices: 69438593--69438653 Score: 54
Period size: 21 Copynumber: 2.9 Consensus size: 21
69438583 GGGCTGCTAC
* *
69438593 TTTTGTTCTTTTT-TATTGTTT
1 TTTTTTTCTTTTTCT-TTCTTT
69438614 TTTTTTTCTTTTTCTTTC-TT
1 TTTTTTTCTTTTTCTTTCTTT
* *
69438634 TTTCTCTCTTTTTTCTTTCT
1 TTTTTTTC-TTTTTCTTTCT
69438654 CCTTTCTTCT
Statistics
Matches: 33, Mismatches: 4, Indels: 5
0.79 0.10 0.12
Matches are distributed among these distances:
20 8 0.24
21 24 0.73
22 1 0.03
ACGTcount: A:0.02, C:0.15, G:0.03, T:0.80
Consensus pattern (21 bp):
TTTTTTTCTTTTTCTTTCTTT
Found at i:69438664 original size:21 final size:21
Alignment explanation
Indices: 69438622--69438664 Score: 61
Period size: 21 Copynumber: 2.0 Consensus size: 21
69438612 TTTTTTTTTC
*
69438622 TTTTTCTTTCTTTTTCTCTCT
1 TTTTTCTTTCTCTTTCTCTCT
69438643 TTTTTCTTTCTCCTTTCT-TCT
1 TTTTTCTTTCT-CTTTCTCTCT
69438664 T
1 T
69438665 CTTCTTCCCT
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
21 15 0.75
22 5 0.25
ACGTcount: A:0.00, C:0.26, G:0.00, T:0.74
Consensus pattern (21 bp):
TTTTTCTTTCTCTTTCTCTCT
Found at i:69438664 original size:31 final size:31
Alignment explanation
Indices: 69438611--69438669 Score: 75
Period size: 31 Copynumber: 1.9 Consensus size: 31
69438601 TTTTTTATTG
* * *
69438611 TTTTTTTTTTCTTTTTCTTTCTTTTTCTCTC
1 TTTTTTCTTTCTCTTTCTTTCTTCTTCTCTC
69438642 TTTTTTCTTTCTCCTTTC-TTCTTCTTCT
1 TTTTTTCTTTCT-CTTTCTTTCTTCTTCT
69438670 TCCCTTTACT
Statistics
Matches: 24, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
31 20 0.83
32 4 0.17
ACGTcount: A:0.00, C:0.24, G:0.00, T:0.76
Consensus pattern (31 bp):
TTTTTTCTTTCTCTTTCTTTCTTCTTCTCTC
Found at i:69439480 original size:29 final size:29
Alignment explanation
Indices: 69439365--69439509 Score: 129
Period size: 30 Copynumber: 4.9 Consensus size: 29
69439355 TTCTGGGGCA
* *
69439365 AAAGTGTAATTTTAGGAAAA-TATAGGGCT
1 AAAGTGTAATTTTA-GAAAAGTTTAGGGTT
* *
69439394 AAAGGGTAATTTCTAG-AAACTTTAGGGGTT
1 AAAGTGTAATTT-TAGAAAAGTTTA-GGGTT
*
69439424 AAAGTGAAATTTT-GAGAAAGTTTAAGGGTT
1 AAAGTGTAATTTTAGA-AAAGTTT-AGGGTT
69439454 GAAA-TGTAATTTTAGAAAAGTTTAGGGTT
1 -AAAGTGTAATTTTAGAAAAGTTTAGGGTT
* *
69439483 AAAATGTAAATTTT-GAAAAGTATAGGG
1 AAAGTGT-AATTTTAGAAAAGTTTAGGG
69439510 GTCAAAATGC
Statistics
Matches: 98, Mismatches: 8, Indels: 20
0.78 0.06 0.16
Matches are distributed among these distances:
28 7 0.07
29 37 0.38
30 48 0.49
31 6 0.06
ACGTcount: A:0.40, C:0.02, G:0.25, T:0.33
Consensus pattern (29 bp):
AAAGTGTAATTTTAGAAAAGTTTAGGGTT
Found at i:69439518 original size:59 final size:59
Alignment explanation
Indices: 69439399--69439525 Score: 150
Period size: 59 Copynumber: 2.1 Consensus size: 59
69439389 GGGCTAAAGG
* * **
69439399 GTAATTTCTAGAAACTTTAGGGGTTAAAGTGAAATTTTGAGAAAGTTTAAGGGTTGAAAT
1 GTAATTT-TAGAAACTTTAGGGGTTAAAATGAAATTTTGAGAAAGTATAAGGGTCAAAAT
* *
69439459 GTAATTTTAGAAAAGTTTA-GGGTTAAAATGTAAATTTTGA-AAAGTATAGGGGTCAAAAT
1 GTAATTTTAG-AAACTTTAGGGGTTAAAATG-AAATTTTGAGAAAGTATAAGGGTCAAAAT
*
69439518 GCAATTTT
1 GTAATTTT
69439526 TTTAATTTTT
Statistics
Matches: 58, Mismatches: 7, Indels: 5
0.83 0.10 0.07
Matches are distributed among these distances:
59 35 0.60
60 23 0.40
ACGTcount: A:0.39, C:0.03, G:0.23, T:0.35
Consensus pattern (59 bp):
GTAATTTTAGAAACTTTAGGGGTTAAAATGAAATTTTGAGAAAGTATAAGGGTCAAAAT
Found at i:69439523 original size:29 final size:29
Alignment explanation
Indices: 69439414--69439525 Score: 127
Period size: 30 Copynumber: 3.8 Consensus size: 29
69439404 TTCTAGAAAC
*
69439414 TTTAGGGGTTAAAGTGAAATTTTGAGAAAG
1 TTTAGGGGTTAAAATGAAATTTTGA-AAAG
* * *
69439444 TTTAAGGGTTGAAATGTAATTTTAGAAAAG
1 TTTAGGGGTTAAAATGAAATTTT-GAAAAG
69439474 TTTA-GGGTTAAAATGTAAATTTTGAAAAG
1 TTTAGGGGTTAAAATG-AAATTTTGAAAAG
* * *
69439503 TATAGGGGTCAAAATGCAATTTT
1 TTTAGGGGTTAAAATGAAATTTT
69439526 TTTAATTTTT
Statistics
Matches: 70, Mismatches: 9, Indels: 7
0.81 0.10 0.08
Matches are distributed among these distances:
29 25 0.36
30 43 0.61
31 2 0.03
ACGTcount: A:0.38, C:0.02, G:0.24, T:0.36
Consensus pattern (29 bp):
TTTAGGGGTTAAAATGAAATTTTGAAAAG
Found at i:69439903 original size:3 final size:3
Alignment explanation
Indices: 69439895--69439930 Score: 72
Period size: 3 Copynumber: 12.0 Consensus size: 3
69439885 GATCAAGAAC
69439895 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
69439931 GAAAAGATAA
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 33 1.00
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (3 bp):
AAT
Found at i:69440884 original size:22 final size:23
Alignment explanation
Indices: 69440829--69440886 Score: 68
Period size: 22 Copynumber: 2.7 Consensus size: 23
69440819 AAAGGGTATC
*
69440829 TACAAATTAA-ATC-TCTAAGAT
1 TACAAAATAATATCTTCTAAGAT
*
69440850 TACAAAATCATATCTTCTAAGAT
1 TACAAAATAATATCTTCTAAGAT
*
69440873 TAC-ATATAATATCT
1 TACAAAATAATATCT
69440887 AAGATTGTAT
Statistics
Matches: 31, Mismatches: 4, Indels: 3
0.82 0.11 0.08
Matches are distributed among these distances:
21 8 0.26
22 12 0.39
23 11 0.35
ACGTcount: A:0.45, C:0.16, G:0.03, T:0.36
Consensus pattern (23 bp):
TACAAAATAATATCTTCTAAGAT
Found at i:69440898 original size:19 final size:19
Alignment explanation
Indices: 69440865--69440919 Score: 65
Period size: 21 Copynumber: 2.8 Consensus size: 19
69440855 AATCATATCT
*
69440865 TCTAAGATTACATATAATA
1 TCTAAGATTGCATATAATA
* *
69440884 TCTAAGATTGTATATGTCATA
1 TCTAAGATTGCATA--TAATA
69440905 TCTAAGATTGCATAT
1 TCTAAGATTGCATAT
69440920 CCTTGAAGAT
Statistics
Matches: 30, Mismatches: 4, Indels: 4
0.79 0.11 0.11
Matches are distributed among these distances:
19 13 0.43
21 17 0.57
ACGTcount: A:0.38, C:0.11, G:0.11, T:0.40
Consensus pattern (19 bp):
TCTAAGATTGCATATAATA
Found at i:69441495 original size:44 final size:45
Alignment explanation
Indices: 69441405--69441561 Score: 137
Period size: 44 Copynumber: 3.5 Consensus size: 45
69441395 GATCTGTTCT
* * * *
69441405 ACTGCAACTTCAGAGAGATAAGATCTGTG-GTT-TTAATTC-GCTCC
1 ACTGCAACTTCAGGGAGATAAGA-CT-TGCTTTCTTCAGTCTGCTCC
* ** *
69441449 ACTGTAACTTCAGGGAGATGGGA-TTGGTTTCTTCAGTCTG-TCCC
1 ACTGCAACTTCAGGGAGATAAGACTTGCTTTCTTCAGTCTGCT-CC
*
69441493 ACTGCAACTTCAAGGG-GATAAGACTTGCTTTCTTGAGTCTGCTCC
1 ACTGCAACTTC-AGGGAGATAAGACTTGCTTTCTTCAGTCTGCTCC
* *
69441538 GCTGCAACCTCAGGGAGATAAGAC
1 ACTGCAACTTCAGGGAGATAAGAC
69441562 CTGATGTGAT
Statistics
Matches: 91, Mismatches: 14, Indels: 15
0.76 0.12 0.12
Matches are distributed among these distances:
41 2 0.02
42 3 0.03
43 6 0.07
44 41 0.45
45 38 0.42
46 1 0.01
ACGTcount: A:0.24, C:0.22, G:0.24, T:0.29
Consensus pattern (45 bp):
ACTGCAACTTCAGGGAGATAAGACTTGCTTTCTTCAGTCTGCTCC
Found at i:69441543 original size:45 final size:45
Alignment explanation
Indices: 69441447--69441561 Score: 119
Period size: 45 Copynumber: 2.6 Consensus size: 45
69441437 TTAATTCGCT
* * ** *
69441447 CCACTGTAACTTCAGGGAGATGGGA-TTGGTTTCTTCAGTCTGTC
1 CCACTGCAACCTCAGGGAGATAAGACTTGCTTTCTTCAGTCTGTC
* *
69441491 CCACTGCAACTTCAAGGG-GATAAGACTTGCTTTCTTGAGTCTG-C
1 CCACTGCAACCTC-AGGGAGATAAGACTTGCTTTCTTCAGTCTGTC
*
69441535 TCCGCTGCAACCTCAGGGAGATAAGAC
1 -CCACTGCAACCTCAGGGAGATAAGAC
69441562 CTGATGTGAT
Statistics
Matches: 60, Mismatches: 7, Indels: 7
0.81 0.09 0.09
Matches are distributed among these distances:
44 22 0.37
45 38 0.63
ACGTcount: A:0.23, C:0.24, G:0.25, T:0.28
Consensus pattern (45 bp):
CCACTGCAACCTCAGGGAGATAAGACTTGCTTTCTTCAGTCTGTC
Found at i:69442050 original size:87 final size:87
Alignment explanation
Indices: 69441948--69442120 Score: 267
Period size: 87 Copynumber: 2.0 Consensus size: 87
69441938 CCAGAGAGGT
* * * *
69441948 AAGGCTGGTGTCTTCGATTTGCTCCACTACTGTTTAGCGAGATAAGATCTGTAATTTTCAACCTA
1 AAGGCTGGGGTCTTCGATCTGCTCCACTACTGCTTAGCGAGATAAGATCTGTAATCTTCAACCTA
69442013 CTCCACTGCTG-CTCAGGGAGAC
66 CTCCACTGCTGAC-CAGGGAGAC
* *
69442035 AAGGCTGGGGTCTTCGATCTGCTCCACTACTGCTTAGGGAGATAAGATCTGTAATCTTCAACTTA
1 AAGGCTGGGGTCTTCGATCTGCTCCACTACTGCTTAGCGAGATAAGATCTGTAATCTTCAACCTA
*
69442100 TTCCACTGCTGACCAGGGAGA
66 CTCCACTGCTGACCAGGGAGA
69442121 TAGAATTCAC
Statistics
Matches: 78, Mismatches: 7, Indels: 2
0.90 0.08 0.02
Matches are distributed among these distances:
87 77 0.99
88 1 0.01
ACGTcount: A:0.24, C:0.24, G:0.23, T:0.29
Consensus pattern (87 bp):
AAGGCTGGGGTCTTCGATCTGCTCCACTACTGCTTAGCGAGATAAGATCTGTAATCTTCAACCTA
CTCCACTGCTGACCAGGGAGAC
Found at i:69442118 original size:44 final size:44
Alignment explanation
Indices: 69441986--69442342 Score: 164
Period size: 44 Copynumber: 8.1 Consensus size: 44
69441976 ACTGTTTAGC
* *
69441986 GAGATAAGATCTGTAATTTTCAACCTACTCCACTGCTG-CTCAGG
1 GAGATAAGATCTGTAATCTTCAACCTATTCCACTGCTGAC-CAGG
* * *** * * ** * *
69442030 GAGACAAG-GCTGGGGTCTTCGATCTGCTCCACTACTG-CTTAGG
1 GAGATAAGATCTGTAATCTTCAACCTATTCCACTGCTGAC-CAGG
*
69442073 GAGATAAGATCTGTAATCTTCAACTTATTCCACTGCTGACCAGG
1 GAGATAAGATCTGTAATCTTCAACCTATTCCACTGCTGACCAGG
**
69442117 GAGAT-AGAAT-TCACAATCTTCAACCTATTCCACTGCTGACCAGG
1 GAGATAAG-ATCT-GTAATCTTCAACCTATTCCACTGCTGACCAGG
* * * *
69442161 GAGATAGGA-CT-TACAATCTTCGATCTACTTCGC-C-GTCAGTA-CAGG
1 GAGATAAGATCTGT--AATCTTCAACCTA-TTC-CACTG-CTG-ACCAGG
* ** * * *
69442206 AAGGCAAGATCTATTATTTTCAACCTATTCCACTGCTG-CTCAGG
1 GAGATAAGATCTGTAATCTTCAACCTATTCCACTGCTGAC-CAGG
* * *** ** ** * * *
69442250 GAGACAAGGT-TGGGGTCTTCAATTTGCTCCACTACTG-CTTAAG
1 GAGATAAGATCTGTAATCTTCAACCTATTCCACTGCTGAC-CAGG
*
69442293 GAGATAAGATCTGTAATCTTCAACCCATTCCACTGCTGACCAGG
1 GAGATAAGATCTGTAATCTTCAACCTATTCCACTGCTGACCAGG
69442337 GAGATA
1 GAGATA
69442343 GGACTTACAA
Statistics
Matches: 225, Mismatches: 68, Indels: 40
0.68 0.20 0.12
Matches are distributed among these distances:
43 65 0.29
44 127 0.56
45 28 0.12
46 4 0.02
47 1 0.00
ACGTcount: A:0.27, C:0.24, G:0.21, T:0.28
Consensus pattern (44 bp):
GAGATAAGATCTGTAATCTTCAACCTATTCCACTGCTGACCAGG
Found at i:69442240 original size:89 final size:88
Alignment explanation
Indices: 69442135--69442407 Score: 272
Period size: 89 Copynumber: 3.1 Consensus size: 88
69442125 ATTCACAATC
* *
69442135 TTCAACCTATTCCACTGCTGACCAGGGAGATAGGACTTACAATCTTCGATCTACTTCGCCGTCAG
1 TTCAACCTATTCCACTGCTGACCAGGGAGATAGGACTTACAATCTTCGATTTGCTTCGCCGTCAG
*
69442200 TACAGGAAGGCAAGATCTATTATT
66 TA-AGGAAGGCAAGATCTGTTATT
* **** *
69442224 TTCAACCTATTCCACTGCTG-CTCAGGGAGACAAGG--TTGGGGTCTTCAATTTGC-TC-CAC-T
1 TTCAACCTATTCCACTGCTGAC-CAGGGAGA-TAGGACTTACAATCTTCGATTTGCTTCGC-CGT
* ** * *
69442283 ACTGCTTAAGG-AGATAAGATCTGTAATC
63 -CAG--TAAGGAAGGCAAGATCTGTTATT
*
69442311 TTCAACCCATTCCACTGCTGACCAGGGAGATAGGACTTACAATCTTCGATTTGCTTCGCCGTCAG
1 TTCAACCTATTCCACTGCTGACCAGGGAGATAGGACTTACAATCTTCGATTTGCTTCGCCGTCAG
* *
69442376 TATAGGAAGGGAAGATTTGTTATT
66 TA-AGGAAGGCAAGATCTGTTATT
69442400 TTCAACCT
1 TTCAACCT
69442408 GCTCCGCTAC
Statistics
Matches: 142, Mismatches: 28, Indels: 28
0.72 0.14 0.14
Matches are distributed among these distances:
86 5 0.04
87 46 0.32
88 32 0.23
89 54 0.38
90 5 0.04
ACGTcount: A:0.26, C:0.23, G:0.21, T:0.30
Consensus pattern (88 bp):
TTCAACCTATTCCACTGCTGACCAGGGAGATAGGACTTACAATCTTCGATTTGCTTCGCCGTCAG
TAAGGAAGGCAAGATCTGTTATT
Found at i:69443698 original size:13 final size:13
Alignment explanation
Indices: 69443673--69443718 Score: 51
Period size: 13 Copynumber: 3.6 Consensus size: 13
69443663 TTTTCTTTGG
69443673 TTTATTATT-ATTT
1 TTTATT-TTGATTT
69443686 TTTATTTTGA-TT
1 TTTATTTTGATTT
*
69443698 TTGATTTTGATTT
1 TTTATTTTGATTT
*
69443711 TTTCTTTT
1 TTTATTTT
69443719 TTTTGCTTTT
Statistics
Matches: 28, Mismatches: 3, Indels: 4
0.80 0.09 0.11
Matches are distributed among these distances:
12 13 0.46
13 15 0.54
ACGTcount: A:0.15, C:0.02, G:0.07, T:0.76
Consensus pattern (13 bp):
TTTATTTTGATTT
Found at i:69443711 original size:23 final size:22
Alignment explanation
Indices: 69443685--69443738 Score: 63
Period size: 23 Copynumber: 2.4 Consensus size: 22
69443675 TATTATTATT
69443685 TTTTATTTTGATTTTGATTTTGA
1 TTTT-TTTTGATTTTGATTTTGA
** *
69443708 TTTTTTCTTTTTTTTGCTTTTGA
1 TTTTTT-TTGATTTTGATTTTGA
69443731 TTTTTTTT
1 TTTTTTTT
69443739 TGTGAATTGG
Statistics
Matches: 27, Mismatches: 3, Indels: 3
0.82 0.09 0.09
Matches are distributed among these distances:
22 4 0.15
23 23 0.85
ACGTcount: A:0.09, C:0.04, G:0.09, T:0.78
Consensus pattern (22 bp):
TTTTTTTTGATTTTGATTTTGA
Found at i:69449856 original size:23 final size:23
Alignment explanation
Indices: 69449830--69449891 Score: 74
Period size: 23 Copynumber: 2.7 Consensus size: 23
69449820 AATGGAACAA
* *
69449830 TAAACAAGCTTTGAATGAT-TCAT
1 TAAACAAGCTTTAAATAATCT-AT
69449853 TAAACAAGCTTTAAATAATCTAT
1 TAAACAAGCTTTAAATAATCTAT
69449876 TAAACAAG-TTTCAAAT
1 TAAACAAGCTTT-AAAT
69449892 GAACATAAAC
Statistics
Matches: 35, Mismatches: 2, Indels: 4
0.85 0.05 0.10
Matches are distributed among these distances:
22 3 0.09
23 31 0.89
24 1 0.03
ACGTcount: A:0.45, C:0.13, G:0.08, T:0.34
Consensus pattern (23 bp):
TAAACAAGCTTTAAATAATCTAT
Found at i:69450617 original size:16 final size:17
Alignment explanation
Indices: 69450575--69450620 Score: 58
Period size: 16 Copynumber: 2.6 Consensus size: 17
69450565 AAGCTTGAGT
*
69450575 TTAGCATTTTAATCTGGG
1 TTAGC-TTTTTATCTGGG
69450593 TTGAGCTTTTTATC-GGG
1 TT-AGCTTTTTATCTGGG
69450610 TTAGCTTTTTA
1 TTAGCTTTTTA
69450621 GCTCGAAAAT
Statistics
Matches: 26, Mismatches: 1, Indels: 4
0.84 0.03 0.13
Matches are distributed among these distances:
16 9 0.35
17 5 0.19
18 9 0.35
19 3 0.12
ACGTcount: A:0.17, C:0.11, G:0.22, T:0.50
Consensus pattern (17 bp):
TTAGCTTTTTATCTGGG
Found at i:69450619 original size:17 final size:17
Alignment explanation
Indices: 69450575--69450618 Score: 54
Period size: 18 Copynumber: 2.5 Consensus size: 17
69450565 AAGCTTGAGT
69450575 TTAGCATTTTAATCTGGG
1 TTAGC-TTTTAATCTGGG
*
69450593 TTGAGCTTTTTATC-GGG
1 TT-AGCTTTTAATCTGGG
69450610 TTAGCTTTT
1 TTAGCTTTT
69450619 TAGCTCGAAA
Statistics
Matches: 24, Mismatches: 1, Indels: 4
0.83 0.03 0.14
Matches are distributed among these distances:
16 7 0.29
17 5 0.21
18 9 0.38
19 3 0.12
ACGTcount: A:0.16, C:0.11, G:0.23, T:0.50
Consensus pattern (17 bp):
TTAGCTTTTAATCTGGG
Found at i:69453540 original size:38 final size:37
Alignment explanation
Indices: 69453488--69453569 Score: 89
Period size: 37 Copynumber: 2.2 Consensus size: 37
69453478 TGTGGAATTA
*
69453488 AATTGAATATTGATTTGAGAA-TGGAAAAG-TGAATTTTG
1 AATTGAATATTGA-TTGA-AAGTGAAAAAGATGAA-TTTG
*
69453526 GATTGAAT-TGTGATTGAAAGTGAAAAAGATGAATTTG
1 AATTGAATAT-TGATTGAAAGTGAAAAAGATGAATTTG
69453563 AATTGAA
1 AATTGAA
69453570 ATCTGAATTT
Statistics
Matches: 38, Mismatches: 3, Indels: 7
0.79 0.06 0.15
Matches are distributed among these distances:
36 2 0.05
37 22 0.58
38 14 0.37
ACGTcount: A:0.41, C:0.00, G:0.24, T:0.34
Consensus pattern (37 bp):
AATTGAATATTGATTGAAAGTGAAAAAGATGAATTTG
Found at i:69466797 original size:3 final size:3
Alignment explanation
Indices: 69466789--69466817 Score: 58
Period size: 3 Copynumber: 9.7 Consensus size: 3
69466779 TATTTAAATA
69466789 AAT AAT AAT AAT AAT AAT AAT AAT AAT AA
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AA
69466818 ACAGAAAAGC
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 26 1.00
ACGTcount: A:0.69, C:0.00, G:0.00, T:0.31
Consensus pattern (3 bp):
AAT
Found at i:69467212 original size:31 final size:31
Alignment explanation
Indices: 69467176--69467251 Score: 100
Period size: 31 Copynumber: 2.5 Consensus size: 31
69467166 TTACAAAATT
* *
69467176 GTTATTAAATTATTTGAAAGTTTTTATTCAA
1 GTTATTAAACTATTCGAAAGTTTTTATTCAA
*
69467207 GTTATTAAACTATTCGAAAGTTTTTATTTAA
1 GTTATTAAACTATTCGAAAGTTTTTATTCAA
*
69467238 ATTACTT-AACTATT
1 GTTA-TTAAACTATT
69467252 AAGTTTTTTT
Statistics
Matches: 40, Mismatches: 4, Indels: 2
0.87 0.09 0.04
Matches are distributed among these distances:
31 38 0.95
32 2 0.05
ACGTcount: A:0.36, C:0.07, G:0.08, T:0.50
Consensus pattern (31 bp):
GTTATTAAACTATTCGAAAGTTTTTATTCAA
Found at i:69467256 original size:28 final size:29
Alignment explanation
Indices: 69467177--69467268 Score: 89
Period size: 31 Copynumber: 3.1 Consensus size: 29
69467167 TACAAAATTG
* * *
69467177 TTATTAAATTATTTGAAAGTTTTTATTCAAG
1 TTATTAAACTA-TT-AAAGTTTTTATTTAAA
69467208 TTATTAAACTATTCGAAAGTTTTTATTTAAA
1 TTATTAAACTATT--AAAGTTTTTATTTAAA
*
69467239 TTACTT-AACTATT-AAGTTTTTTTTTAAA
1 TTA-TTAAACTATTAAAGTTTTTATTTAAA
69467267 TT
1 TT
69467269 CGGTTAGCGA
Statistics
Matches: 55, Mismatches: 4, Indels: 7
0.83 0.06 0.11
Matches are distributed among these distances:
28 16 0.29
30 2 0.04
31 35 0.64
32 2 0.04
ACGTcount: A:0.35, C:0.05, G:0.07, T:0.53
Consensus pattern (29 bp):
TTATTAAACTATTAAAGTTTTTATTTAAA
Found at i:69469197 original size:23 final size:22
Alignment explanation
Indices: 69469167--69469228 Score: 79
Period size: 23 Copynumber: 2.7 Consensus size: 22
69469157 TTGTTTAAGT
*
69469167 TAAACGAACATGTTCGTGAATGC
1 TAAACGAACATGTTCGTGAAT-A
*
69469190 TAAACGAACATGTTCATGAATA
1 TAAACGAACATGTTCGTGAATA
*
69469212 TATAATGAACATGTTCG
1 TA-AACGAACATGTTCG
69469229 CAAACAATAT
Statistics
Matches: 34, Mismatches: 4, Indels: 2
0.85 0.10 0.05
Matches are distributed among these distances:
22 2 0.06
23 32 0.94
ACGTcount: A:0.39, C:0.15, G:0.18, T:0.29
Consensus pattern (22 bp):
TAAACGAACATGTTCGTGAATA
Found at i:69475907 original size:86 final size:86
Alignment explanation
Indices: 69475762--69475932 Score: 306
Period size: 86 Copynumber: 2.0 Consensus size: 86
69475752 TGGTTAAGCC
* * *
69475762 TATGAGCATCAAATATATGACCAATGTTTTTTACGAGACCTTGGCATTTGTGAGTGTTGAAGTTT
1 TATGAGCATCAAATATATAACCAATGTTTTTTACAAGACCTTGGCATCTGTGAGTGTTGAAGTTT
69475827 AACCCGTGCACATATTCTTAA
66 AACCCGTGCACATATTCTTAA
*
69475848 TATGAGCATCAAATATATAATCAATGTTTTTTACAAGACCTTGGCATCTGTGAGTGTTGAAGTTT
1 TATGAGCATCAAATATATAACCAATGTTTTTTACAAGACCTTGGCATCTGTGAGTGTTGAAGTTT
69475913 AACCCGTGCACATATTCTTA
66 AACCCGTGCACATATTCTTA
69475933 GTGTTCTCAA
Statistics
Matches: 81, Mismatches: 4, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
86 81 1.00
ACGTcount: A:0.30, C:0.16, G:0.18, T:0.36
Consensus pattern (86 bp):
TATGAGCATCAAATATATAACCAATGTTTTTTACAAGACCTTGGCATCTGTGAGTGTTGAAGTTT
AACCCGTGCACATATTCTTAA
Found at i:69477810 original size:2 final size:2
Alignment explanation
Indices: 69477803--69477834 Score: 55
Period size: 2 Copynumber: 16.0 Consensus size: 2
69477793 GACTTAGTTT
*
69477803 TA TA TA TA TA TA TG TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
69477835 AGAAAATAAG
Statistics
Matches: 28, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
2 28 1.00
ACGTcount: A:0.47, C:0.00, G:0.03, T:0.50
Consensus pattern (2 bp):
TA
Found at i:69481670 original size:22 final size:22
Alignment explanation
Indices: 69481638--69481679 Score: 57
Period size: 22 Copynumber: 1.9 Consensus size: 22
69481628 AACCAAAATC
*
69481638 TATTTTTATTTAATATATAATT
1 TATTTTAATTTAATATATAATT
**
69481660 TATTTTAATTTTTTATATAA
1 TATTTTAATTTAATATATAA
69481680 AATAAATATT
Statistics
Matches: 17, Mismatches: 3, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
22 17 1.00
ACGTcount: A:0.36, C:0.00, G:0.00, T:0.64
Consensus pattern (22 bp):
TATTTTAATTTAATATATAATT
Found at i:69485552 original size:31 final size:32
Alignment explanation
Indices: 69485517--69485577 Score: 79
Period size: 33 Copynumber: 1.9 Consensus size: 32
69485507 TTGGTACATG
*
69485517 TACTTTCATAA-AATATCCAATGTGATACTTA
1 TACTTTCAAAAGAATATCCAATGTGATACTTA
* *
69485548 TACTTTGAAAATGAATGTCCAATGTGATAC
1 TACTTTCAAAA-GAATATCCAATGTGATAC
69485578 ATGAACTATC
Statistics
Matches: 25, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
31 9 0.36
33 16 0.64
ACGTcount: A:0.38, C:0.15, G:0.11, T:0.36
Consensus pattern (32 bp):
TACTTTCAAAAGAATATCCAATGTGATACTTA
Found at i:69488477 original size:22 final size:22
Alignment explanation
Indices: 69488413--69488479 Score: 107
Period size: 22 Copynumber: 3.0 Consensus size: 22
69488403 AAAATGTGCC
**
69488413 TAACGTACTAAGCTCTCATGGC
1 TAACGTACTAAGCTCTCATGTT
69488435 TAACGTACTAAGCTCTCATGTT
1 TAACGTACTAAGCTCTCATGTT
*
69488457 TCACGTACTAAGCTCTCATGTT
1 TAACGTACTAAGCTCTCATGTT
69488479 T
1 T
69488480 GAACAATAAA
Statistics
Matches: 42, Mismatches: 3, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
22 42 1.00
ACGTcount: A:0.25, C:0.25, G:0.15, T:0.34
Consensus pattern (22 bp):
TAACGTACTAAGCTCTCATGTT
Found at i:69497897 original size:30 final size:31
Alignment explanation
Indices: 69497849--69497911 Score: 101
Period size: 30 Copynumber: 2.1 Consensus size: 31
69497839 CTCCCCAACT
*
69497849 TACTTATAAATGATTCAAACTCAAAATGACC
1 TACTTATAAATGACTCAAACTCAAAATGACC
*
69497880 TACTTA-AAATGACTCAAACTCGAAATGACC
1 TACTTATAAATGACTCAAACTCAAAATGACC
69497910 TA
1 TA
69497912 TCTTGCATAC
Statistics
Matches: 30, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
30 24 0.80
31 6 0.20
ACGTcount: A:0.44, C:0.21, G:0.08, T:0.27
Consensus pattern (31 bp):
TACTTATAAATGACTCAAACTCAAAATGACC
Found at i:69497908 original size:16 final size:16
Alignment explanation
Indices: 69497856--69497908 Score: 56
Period size: 16 Copynumber: 3.4 Consensus size: 16
69497846 ACTTACTTAT
*
69497856 AAATGATTCAAACTCA
1 AAATGACTCAAACTCA
* *
69497872 AAATGAC-C-TACTTA
1 AAATGACTCAAACTCA
*
69497886 AAATGACTCAAACTCG
1 AAATGACTCAAACTCA
69497902 AAATGAC
1 AAATGAC
69497909 CTATCTTGCA
Statistics
Matches: 29, Mismatches: 6, Indels: 4
0.74 0.15 0.10
Matches are distributed among these distances:
14 11 0.38
15 2 0.07
16 16 0.55
ACGTcount: A:0.47, C:0.21, G:0.09, T:0.23
Consensus pattern (16 bp):
AAATGACTCAAACTCA
Found at i:69497983 original size:16 final size:16
Alignment explanation
Indices: 69497962--69497996 Score: 52
Period size: 16 Copynumber: 2.2 Consensus size: 16
69497952 GAAATACATT
*
69497962 AAACTTGGAATGATTC
1 AAACTTGGAATGACTC
*
69497978 AAACTTGTAATGACTC
1 AAACTTGGAATGACTC
69497994 AAA
1 AAA
69497997 GAATTTAAAC
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
16 17 1.00
ACGTcount: A:0.43, C:0.14, G:0.14, T:0.29
Consensus pattern (16 bp):
AAACTTGGAATGACTC
Found at i:69499019 original size:4 final size:4
Alignment explanation
Indices: 69499010--69499048 Score: 51
Period size: 4 Copynumber: 9.0 Consensus size: 4
69499000 GTAGTTTTGC
69499010 TTAT TTAT TTAT TTAT TTAT TTAT GGTTAT TTCAT TTAT
1 TTAT TTAT TTAT TTAT TTAT TTAT --TTAT TT-AT TTAT
69499049 AAAGCTAAAA
Statistics
Matches: 32, Mismatches: 0, Indels: 6
0.84 0.00 0.16
Matches are distributed among these distances:
4 24 0.75
5 4 0.12
6 4 0.12
ACGTcount: A:0.23, C:0.03, G:0.05, T:0.69
Consensus pattern (4 bp):
TTAT
Found at i:69511288 original size:12 final size:12
Alignment explanation
Indices: 69511271--69511295 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
69511261 TTAAGGGTTT
69511271 ACTGAGCTCATA
1 ACTGAGCTCATA
69511283 ACTGAGCTCATA
1 ACTGAGCTCATA
69511295 A
1 A
69511296 ATGGTAATTA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.36, C:0.24, G:0.16, T:0.24
Consensus pattern (12 bp):
ACTGAGCTCATA
Found at i:69512081 original size:16 final size:16
Alignment explanation
Indices: 69512060--69512091 Score: 64
Period size: 16 Copynumber: 2.0 Consensus size: 16
69512050 ATTTTCGTAC
69512060 CATTTTACTAAAAAAT
1 CATTTTACTAAAAAAT
69512076 CATTTTACTAAAAAAT
1 CATTTTACTAAAAAAT
69512092 AACTTATATT
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 16 1.00
ACGTcount: A:0.50, C:0.12, G:0.00, T:0.38
Consensus pattern (16 bp):
CATTTTACTAAAAAAT
Found at i:69514547 original size:22 final size:22
Alignment explanation
Indices: 69514517--69514580 Score: 67
Period size: 22 Copynumber: 2.9 Consensus size: 22
69514507 TAGTACCGAC
*
69514517 GCTTGTAGTTTAGGAAACTTGG
1 GCTTATAGTTTAGGAAACTTGG
* *
69514539 GCTTATAGTTTAGGAATCTCAGG
1 GCTTATAGTTTAGGAAACT-TGG
* *
69514562 G-TCATAGTTTAGGTAACTT
1 GCTTATAGTTTAGGAAACTT
69514581 TAAGTAATAA
Statistics
Matches: 34, Mismatches: 7, Indels: 3
0.77 0.16 0.07
Matches are distributed among these distances:
22 31 0.91
23 3 0.09
ACGTcount: A:0.25, C:0.11, G:0.27, T:0.38
Consensus pattern (22 bp):
GCTTATAGTTTAGGAAACTTGG
Found at i:69514608 original size:104 final size:102
Alignment explanation
Indices: 69514421--69514616 Score: 311
Period size: 104 Copynumber: 1.9 Consensus size: 102
69514411 AACATTTTGA
69514421 AGTTTGGAACTTGGGCTCATAGTTTAGGAATCCCAGGGTCATAGTTTAGGAAACTCTAAGCAATA
1 AGTTTGGAACTTGGGCTCATAGTTTAGGAATCCCAGGGTCATAGTTTAGGAAACTCTAAGCAATA
*
69514486 AGTTGAATCCAAACTATGCACTAGTACCGACGCTTGT
66 AGTTAAATCCAAACTATGCACTAGTACCGACGCTTGT
* * * * *
69514523 AGTTTAGGAAACTTGGGCTTATAGTTTAGGAATCTCAGGGTCATAGTTTAGGTAACTTTAAGTAA
1 AGTTT-GG-AACTTGGGCTCATAGTTTAGGAATCCCAGGGTCATAGTTTAGGAAACTCTAAGCAA
*
69514588 TAAGTTAAATCCAAATTATGCACTAGTAC
64 TAAGTTAAATCCAAACTATGCACTAGTAC
69514617 TGAGGCTCCA
Statistics
Matches: 85, Mismatches: 7, Indels: 2
0.90 0.07 0.02
Matches are distributed among these distances:
102 5 0.06
103 2 0.02
104 78 0.92
ACGTcount: A:0.32, C:0.15, G:0.21, T:0.31
Consensus pattern (102 bp):
AGTTTGGAACTTGGGCTCATAGTTTAGGAATCCCAGGGTCATAGTTTAGGAAACTCTAAGCAATA
AGTTAAATCCAAACTATGCACTAGTACCGACGCTTGT
Found at i:69516149 original size:63 final size:63
Alignment explanation
Indices: 69516072--69516201 Score: 251
Period size: 63 Copynumber: 2.1 Consensus size: 63
69516062 AGTTTACCTG
69516072 CAGCCCCGTCTCACTATCCATCATCCTATCAAGGTTCCGAGACTCCTTACAATCCTCCACAGT
1 CAGCCCCGTCTCACTATCCATCATCCTATCAAGGTTCCGAGACTCCTTACAATCCTCCACAGT
*
69516135 CAGCCCCGTCTCACTATCCATCATCCTATCAAGGTTCCGAGACTCCTTACAATCCTCCCCAGT
1 CAGCCCCGTCTCACTATCCATCATCCTATCAAGGTTCCGAGACTCCTTACAATCCTCCACAGT
69516198 CAGC
1 CAGC
69516202 TCCTCCGACA
Statistics
Matches: 66, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
63 66 1.00
ACGTcount: A:0.23, C:0.41, G:0.12, T:0.25
Consensus pattern (63 bp):
CAGCCCCGTCTCACTATCCATCATCCTATCAAGGTTCCGAGACTCCTTACAATCCTCCACAGT
Found at i:69518108 original size:4 final size:4
Alignment explanation
Indices: 69518099--69518149 Score: 102
Period size: 4 Copynumber: 12.8 Consensus size: 4
69518089 GTAGAAGAAG
69518099 ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC
1 ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC
69518147 ATA
1 ATA
69518150 TGAAGTGATA
Statistics
Matches: 47, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 47 1.00
ACGTcount: A:0.51, C:0.24, G:0.00, T:0.25
Consensus pattern (4 bp):
ATAC
Found at i:69518425 original size:29 final size:30
Alignment explanation
Indices: 69518387--69518445 Score: 84
Period size: 29 Copynumber: 2.0 Consensus size: 30
69518377 CTTTGTTTTG
69518387 TTAATGCACTTCAATGCCACTCTGTTCTGA
1 TTAATGCACTTCAATGCCACTCTGTTCTGA
* * *
69518417 TTAA-GCACTTCAGTGCTATTCTGTTCTGA
1 TTAATGCACTTCAATGCCACTCTGTTCTGA
69518446 CATTGCACTC
Statistics
Matches: 26, Mismatches: 3, Indels: 1
0.87 0.10 0.03
Matches are distributed among these distances:
29 22 0.85
30 4 0.15
ACGTcount: A:0.22, C:0.24, G:0.15, T:0.39
Consensus pattern (30 bp):
TTAATGCACTTCAATGCCACTCTGTTCTGA
Found at i:69518453 original size:29 final size:27
Alignment explanation
Indices: 69518391--69518454 Score: 65
Period size: 29 Copynumber: 2.2 Consensus size: 27
69518381 GTTTTGTTAA
69518391 TGCACTTCAATGCCACTCTGTTCTGAT
1 TGCACTTCAATGCCACTCTGTTCTGAT
* * *
69518418 TAAGCACTTCAGTGCTATTCTGTTCTGACAT
1 T--GCACTTCAATGCCACTCTGTTCTG--AT
69518449 TGCACT
1 TGCACT
69518455 CCGATATTAT
Statistics
Matches: 30, Mismatches: 3, Indels: 6
0.77 0.08 0.15
Matches are distributed among these distances:
27 1 0.03
29 26 0.87
31 3 0.10
ACGTcount: A:0.20, C:0.27, G:0.16, T:0.38
Consensus pattern (27 bp):
TGCACTTCAATGCCACTCTGTTCTGAT
Found at i:69521438 original size:33 final size:33
Alignment explanation
Indices: 69521401--69521466 Score: 87
Period size: 33 Copynumber: 2.0 Consensus size: 33
69521391 CAACATTCTC
69521401 GTAAATAATTCTTAACTCAACCTATTTTAGTAA
1 GTAAATAATTCTTAACTCAACCTATTTTAGTAA
* * * * *
69521434 GTAAATAATTTTTATCTTAATCTATTTTCGTAA
1 GTAAATAATTCTTAACTCAACCTATTTTAGTAA
69521467 ATATATTTTT
Statistics
Matches: 28, Mismatches: 5, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
33 28 1.00
ACGTcount: A:0.36, C:0.12, G:0.06, T:0.45
Consensus pattern (33 bp):
GTAAATAATTCTTAACTCAACCTATTTTAGTAA
Found at i:69522254 original size:18 final size:20
Alignment explanation
Indices: 69522211--69522254 Score: 51
Period size: 18 Copynumber: 2.4 Consensus size: 20
69522201 ATATCATACT
*
69522211 TAATTTTTTGTATTTGTTAA
1 TAATTTTTTATATTTGTTAA
69522231 -AA-TTTTTATA-TT-TTAA
1 TAATTTTTTATATTTGTTAA
69522247 TAATTTTT
1 TAATTTTT
69522255 CGGTGTTGTT
Statistics
Matches: 21, Mismatches: 1, Indels: 6
0.75 0.04 0.21
Matches are distributed among these distances:
16 4 0.19
17 4 0.19
18 11 0.52
19 2 0.10
ACGTcount: A:0.30, C:0.00, G:0.05, T:0.66
Consensus pattern (20 bp):
TAATTTTTTATATTTGTTAA
Found at i:69527487 original size:162 final size:159
Alignment explanation
Indices: 69527186--69527699 Score: 641
Period size: 161 Copynumber: 3.2 Consensus size: 159
69527176 TTTTTGTGCT
* *
69527186 ATGGTTGTTTACTCTGAA-TTGGAATGAACCTTATC-TTTTTGGTTAGGAGATCGGTGTTCCTCG
1 ATGGTTGTTTACTCTGAACTT-GAATGAACCTTATCGATTTT-GATAGGAGATC-GTGTT-CTCG
* * * *
69527249 G-AACCGATATT-CTCGGATTTTCATCGTGATTTAGTATAGCTTGGTTTTTCATCTTGAGACTAA
62 GAAACCAATATTCCT-GGATTTTCATCGTGATTTATTATAGCTTGGTTTATCATCTAGAGACTAA
69527312 GGAAGTTCACTTTTGTTTGATTGTCATCTCCTCCC
126 GGAAGTTCACTTTTGTTTGATTGTCATCTCCT-CC
69527347 ATGGTTGTTTACTCTGAACTTGAATGAACCTTATCGATTTTGATAGGAGATCAGTGTTTCTCGGA
1 ATGGTTGTTTACTCTGAACTTGAATGAACCTTATCGATTTTGATAGGAGATC-GTG-TTCTCGGA
*
69527412 AACCAATATTCCTGGATTTTCATCGTGATTTCTTATAGCTTGGTTTATCATCTAGAGACTAAGGA
64 AACCAATATTCCTGGATTTTCATCGTGATTTATTATAGCTTGGTTTATCATCTAGAGACTAAGGA
* * *
69527477 AGTCCACTTTTGTTTGATTGTGATCTCCTGC
129 AGTTCACTTTTGTTTGATTGTCATCTCCTCC
* * * *
69527508 ATGGTTGTTTACTCTGAACTTGAATGAACCTTATCGATTTGGATTGGTGATC-----CTCAGAAA
1 ATGGTTGTTTACTCTGAACTTGAATGAACCTTATCGATTTTGATAGGAGATCGTGTTCTCGGAAA
** * * * * * *
69527568 CCAATATTCCCAGATTTTCATCTTGAGTTAGTACAAAGCTTGGTTTATCATCTAGAGACCAGGGA
66 CCAATATTCCTGGATTTTCATCGTGATTTA-T-TATAGCTTGGTTTATCATCTAGAGACTAAGGA
*
69527633 AGTTCACTTTTGTTTGATTGTCGTCTCCTGCC
129 AGTTCACTTTTGTTTGATTGTCATCTCCT-CC
* *
69527665 ATGGTTGTTTACACTGAACTTGAATAAACCTTATC
1 ATGGTTGTTTACTCTGAACTTGAATGAACCTTATC
69527700 ATCTAGAAAC
Statistics
Matches: 315, Mismatches: 30, Indels: 20
0.86 0.08 0.05
Matches are distributed among these distances:
154 32 0.10
155 1 0.00
156 54 0.17
157 34 0.11
161 100 0.32
162 92 0.29
163 2 0.01
ACGTcount: A:0.23, C:0.18, G:0.20, T:0.39
Consensus pattern (159 bp):
ATGGTTGTTTACTCTGAACTTGAATGAACCTTATCGATTTTGATAGGAGATCGTGTTCTCGGAAA
CCAATATTCCTGGATTTTCATCGTGATTTATTATAGCTTGGTTTATCATCTAGAGACTAAGGAAG
TTCACTTTTGTTTGATTGTCATCTCCTCC
Found at i:69527815 original size:139 final size:139
Alignment explanation
Indices: 69527563--69527834 Score: 393
Period size: 139 Copynumber: 1.9 Consensus size: 139
69527553 GGTGATCCTC
*
69527563 AGAAACCAATATTCCCAGATTTTCATCTTGAGTTAGTACAAAGCTTGGTTTATCATCTAGAGACC
1 AGAAACCAATATTCCCAGATTTTCATCGTGAGTTAGTA-AAAGCTTGGTTTATCATCTAGAGACC
* *
69527628 AGGGAAGTTCACTTTTGTTTGATTGTCGTCTCCTGCCATGGTTGTTTACACTGAACTTGAATAAA
65 AGGGAAGTTCACTTTTGTTTGATTGTCATCTCCTGCCATGGTTGTTTACACTAAAC-TGAATAAA
69527693 CCTTATCATCT
129 CCTTATCATCT
** * * * * * *
69527704 AGAAACCGGTATTCCCGGATTTTTATCGTGATTTAGT-ATAGCTTGGTTTGTCATCTAGAGACTA
1 AGAAACCAATATTCCCAGATTTTCATCGTGAGTTAGTAAAAGCTTGGTTTATCATCTAGAGACCA
* * *
69527768 GGGAAGTTCACTTTTGTTTGATTGTCATCTCCTGCCATGTTTGTTTACTCTAAACTGAATGAACC
66 GGGAAGTTCACTTTTGTTTGATTGTCATCTCCTGCCATGGTTGTTTACACTAAACTGAATAAACC
69527833 TT
131 TT
69527835 TCAATTTGGA
Statistics
Matches: 117, Mismatches: 14, Indels: 3
0.87 0.10 0.02
Matches are distributed among these distances:
138 11 0.09
139 75 0.64
141 31 0.26
ACGTcount: A:0.25, C:0.19, G:0.18, T:0.38
Consensus pattern (139 bp):
AGAAACCAATATTCCCAGATTTTCATCGTGAGTTAGTAAAAGCTTGGTTTATCATCTAGAGACCA
GGGAAGTTCACTTTTGTTTGATTGTCATCTCCTGCCATGGTTGTTTACACTAAACTGAATAAACC
TTATCATCT
Found at i:69528095 original size:155 final size:156
Alignment explanation
Indices: 69527713--69528281 Score: 702
Period size: 155 Copynumber: 3.6 Consensus size: 156
69527703 TAGAAACCGG
*
69527713 TATTCCCGGATTTTTATCGTGATTTAGTATAGCTTGGTTTGTCATCTAGAGACTAGGGAAGTTCA
1 TATTCCCGGATTTTCATCGTGATTTAGTATAGCTTGGTTTGTCATCTAGAGACTAGGGAAGTTCA
* * *
69527778 CTTTTGTTTGATTGTCATCTCCTGCCA-TGTTTGTTTACTCTAAAC-TGAATGAACCTT-TCAAT
66 CTTTTGTTTGATTATCATCTCCTGCCATTG-TTGTATACTCTAAACTTGAATGAACCTTATCAGT
*
69527840 TTGGATAGGAGATCAGTGATCCTTGGAAACAGA
130 TTGGATAGGAGATCGGTGAT-CTT-----CAGA
* * * * * * *
69527873 TAGT-CCTGATTTCTCGTCGTGATTTAGTGTAGCTTCGTTTGGCAACTAGAGACTA-GGAAGTTC
1 TATTCCCGGATTT-TCATCGTGATTTAGTATAGCTTGGTTTGTCATCTAGAGACTAGGGAAGTTC
* * * *
69527936 ACTTTTGTTTGATTGTCGTCTCCTGCCATTGTTGTGTACTCTGAACTTGAATGAACCTTATCAGT
65 ACTTTTGTTTGATTATCATCTCCTGCCATTGTTGTATACTCTAAACTTGAATGAACCTTATCAGT
*
69528001 TTGGATAGGAGAACGGTGATCTTCAGA
130 TTGGATAGGAGATCGGTGATCTTCAGA
* * *
69528028 TATTCCTGGATTTTCATCGTGATTTAGTATAGTTTGGTTTGTCATCTAGAGACTTGGGAAGTT-A
1 TATTCCCGGATTTTCATCGTGATTTAGTATAGCTTGGTTTGTCATCTAGAGACTAGGGAAGTTCA
* * * *
69528092 CTTTTGTTTGATTATCATCTCCTGCCATGGTTTTATACTCTCAACTTGAATGAACCTTAT-TGAT
66 CTTTTGTTTGATTATCATCTCCTGCCATTGTTGTATACTCTAAACTTGAATGAACCTTATCAG-T
* *
69528156 TTGGATAGGAGATTGGTGATCCTCGGAAACCGA
130 TTGGATAGGAGATCGGTGATCTTC----A--GA
* *
69528189 TATTCCCGGATTTTCATCATGATTTAGTATAGCTTGGTTTGTTATCTAGAGACTAGGGAAGTTCA
1 TATTCCCGGATTTTCATCGTGATTTAGTATAGCTTGGTTTGTCATCTAGAGACTAGGGAAGTTCA
69528254 CTTTTGTTTGATTATCATCTCCTGCCAT
66 CTTTTGTTTGATTATCATCTCCTGCCAT
69528282 GATACCCTAT
Statistics
Matches: 356, Mismatches: 39, Indels: 26
0.85 0.09 0.06
Matches are distributed among these distances:
154 1 0.00
155 119 0.33
156 13 0.04
159 56 0.16
160 56 0.16
161 82 0.23
162 29 0.08
ACGTcount: A:0.23, C:0.17, G:0.21, T:0.40
Consensus pattern (156 bp):
TATTCCCGGATTTTCATCGTGATTTAGTATAGCTTGGTTTGTCATCTAGAGACTAGGGAAGTTCA
CTTTTGTTTGATTATCATCTCCTGCCATTGTTGTATACTCTAAACTTGAATGAACCTTATCAGTT
TGGATAGGAGATCGGTGATCTTCAGA
Found at i:69529882 original size:62 final size:63
Alignment explanation
Indices: 69529800--69529930 Score: 173
Period size: 62 Copynumber: 2.1 Consensus size: 63
69529790 TGATGTTAAA
* *
69529800 TATAAAAAATTCAAAGAATTTA-ACTTTCAATATTTACAAAATTTGTCATTTTAGTT-TAAATTT
1 TATAAAAAATTCAAAGAATTTAGACCTT-AATATTTACAAAATTTGTCAATTTAGTTCT-AATTT
*
69529863 TATAAAAAA-TCAATA-AATTTAGCCCTTAATATTTACAAAATTTGTCAATTTAGTTCTAATTT
1 TATAAAAAATTCAA-AGAATTTAGACCTTAATATTTACAAAATTTGTCAATTTAGTTCTAATTT
69529925 TA-AAAA
1 TATAAAA
69529931 TTAAAGAAAA
Statistics
Matches: 62, Mismatches: 3, Indels: 8
0.85 0.04 0.11
Matches are distributed among these distances:
61 4 0.06
62 44 0.71
63 14 0.23
ACGTcount: A:0.44, C:0.09, G:0.05, T:0.42
Consensus pattern (63 bp):
TATAAAAAATTCAAAGAATTTAGACCTTAATATTTACAAAATTTGTCAATTTAGTTCTAATTT
Found at i:69537359 original size:22 final size:22
Alignment explanation
Indices: 69537334--69537388 Score: 110
Period size: 22 Copynumber: 2.5 Consensus size: 22
69537324 CTAAAAGAAA
69537334 AAACATCCAATTTAAGGACTAT
1 AAACATCCAATTTAAGGACTAT
69537356 AAACATCCAATTTAAGGACTAT
1 AAACATCCAATTTAAGGACTAT
69537378 AAACATCCAAT
1 AAACATCCAAT
69537389 GTAAAAGAAA
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 33 1.00
ACGTcount: A:0.47, C:0.20, G:0.07, T:0.25
Consensus pattern (22 bp):
AAACATCCAATTTAAGGACTAT
Found at i:69541450 original size:89 final size:87
Alignment explanation
Indices: 69541313--69541538 Score: 247
Period size: 89 Copynumber: 2.6 Consensus size: 87
69541303 ATTTAAGTCC
* * * * * * * *
69541313 TTTTTTTTCTACTCAATTGAGCACTTAAACTTTTAAAATGTATCAAAAATATCTT-TACACTTCT
1 TTTTTTTTCCACTCAATTGGGTACTTGAACTTTCATAATGCATCAAAAA-ACCTTATACACTTCT
69541377 TCAAAAAAAGCAATTAAACCCCTA
65 TCAAAAAAA-CAATTAAACCCCTA
* **** *
69541401 TTTTTTTTTCCACTCAATTGGGTACTTGAACTTTCATAATGCATAAAAAAACCTTAATTTTTTTT
1 -TTTTTTTTCCACTCAATTGGGTACTTGAACTTTCATAATGCATCAAAAAACCTT-ATACACTTC
* * *
69541466 TTCAAAGAAACAATTAAGCCTCTA
64 TTCAAAAAAACAATTAAACCCCTA
*
69541490 TTTTTTTCCCACTCAATTGGGTACTTGAACTTTCATAATGCATCAAAAA
1 TTTTTTTTCCACTCAATTGGGTACTTGAACTTTCATAATGCATCAAAAA
69541539 GGCCTTAATT
Statistics
Matches: 116, Mismatches: 19, Indels: 5
0.83 0.14 0.04
Matches are distributed among these distances:
88 51 0.44
89 53 0.46
90 12 0.10
ACGTcount: A:0.35, C:0.19, G:0.07, T:0.39
Consensus pattern (87 bp):
TTTTTTTTCCACTCAATTGGGTACTTGAACTTTCATAATGCATCAAAAAACCTTATACACTTCTT
CAAAAAAACAATTAAACCCCTA
Found at i:69541513 original size:88 final size:88
Alignment explanation
Indices: 69541380--69541573 Score: 295
Period size: 88 Copynumber: 2.2 Consensus size: 88
69541370 CACTTCTTCA
* *
69541380 AAAAAAGCAATTAAACCCCTATTTTTTTTTCCACTCAATTGGGTACTTGAACTTTCATAATGCAT
1 AAAAAAGCAATTAAGCCCCTATTTTTTTTCCCACTCAATTGGGTACTTGAACTTTCATAATGCAT
69541445 -AAAAAAACCTTAATTTTTTTTTTC
66 CAAAAAAACCTTAA--TTTTTTTTC
*
69541469 AAAGAAA-CAATTAAGCCTCTA-TTTTTTTCCCACTCAATTGGGTACTTGAACTTTCATAATGCA
1 AAA-AAAGCAATTAAGCCCCTATTTTTTTTCCCACTCAATTGGGTACTTGAACTTTCATAATGCA
**
69541532 TCAAAAAGGCCTTAATTTTTTTTC
65 TCAAAAAAACCTTAATTTTTTTTC
69541556 AAAAAAGCAATTAAGCCC
1 AAAAAAGCAATTAAGCCC
69541574 TACTCTTATT
Statistics
Matches: 96, Mismatches: 6, Indels: 8
0.87 0.05 0.07
Matches are distributed among these distances:
86 3 0.03
87 22 0.23
88 42 0.44
89 26 0.27
90 3 0.03
ACGTcount: A:0.36, C:0.19, G:0.09, T:0.37
Consensus pattern (88 bp):
AAAAAAGCAATTAAGCCCCTATTTTTTTTCCCACTCAATTGGGTACTTGAACTTTCATAATGCAT
CAAAAAAACCTTAATTTTTTTTC
Found at i:69541646 original size:19 final size:20
Alignment explanation
Indices: 69541602--69541646 Score: 65
Period size: 20 Copynumber: 2.3 Consensus size: 20
69541592 GAAAAAAATC
69541602 ATAAAAATAATAAATTTTAG
1 ATAAAAATAATAAATTTTAG
* *
69541622 AAAAAAATATTAAATTTTA-
1 ATAAAAATAATAAATTTTAG
69541641 ATAAAA
1 ATAAAA
69541647 TTTAAAAACT
Statistics
Matches: 22, Mismatches: 3, Indels: 1
0.85 0.12 0.04
Matches are distributed among these distances:
19 5 0.23
20 17 0.77
ACGTcount: A:0.64, C:0.00, G:0.02, T:0.33
Consensus pattern (20 bp):
ATAAAAATAATAAATTTTAG
Found at i:69541706 original size:27 final size:28
Alignment explanation
Indices: 69541676--69541731 Score: 71
Period size: 28 Copynumber: 2.0 Consensus size: 28
69541666 TTTGAATTTT
*
69541676 TTTTAGAAAAAT-AGT-CAAAAAATAAAA
1 TTTTAGAAAAATCA-TAAAAAAAATAAAA
*
69541703 TTTTATAAAAATCATAAAAAAAATAAAA
1 TTTTAGAAAAATCATAAAAAAAATAAAA
69541731 T
1 T
69541732 CCATCAAAAG
Statistics
Matches: 25, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
27 12 0.48
28 13 0.52
ACGTcount: A:0.64, C:0.04, G:0.04, T:0.29
Consensus pattern (28 bp):
TTTTAGAAAAATCATAAAAAAAATAAAA
Found at i:69541966 original size:90 final size:92
Alignment explanation
Indices: 69541853--69542026 Score: 298
Period size: 92 Copynumber: 1.9 Consensus size: 92
69541843 AAAACAGATA
* *
69541853 AAAGTAGGGGCTTAATTGCTTTTTTT-AAAA-GTTTGAGGGTCTTTTTGATGCATTTTGAAAGTT
1 AAAGTAGGGGCCTAATTGCTTTTTTTGAAAATGTTTGAGGGCCTTTTTGATGCATTTTGAAAGTT
*
69541916 CAAGTACCCAATTGAGTGCCAAAAAAT
66 CAAGTACCCAAATGAGTGCCAAAAAAT
*
69541943 AAAGTAGGGGCCTAATTGCTTTTTTTGAAAATGTTTGAGGGCCTTTTTGATGTATTTTGAAAGTT
1 AAAGTAGGGGCCTAATTGCTTTTTTTGAAAATGTTTGAGGGCCTTTTTGATGCATTTTGAAAGTT
69542008 CAAGTACCCAAATGAGTGC
66 CAAGTACCCAAATGAGTGC
69542027 TTAAAAAGAA
Statistics
Matches: 78, Mismatches: 4, Indels: 2
0.93 0.05 0.02
Matches are distributed among these distances:
90 25 0.32
91 4 0.05
92 49 0.63
ACGTcount: A:0.29, C:0.11, G:0.22, T:0.37
Consensus pattern (92 bp):
AAAGTAGGGGCCTAATTGCTTTTTTTGAAAATGTTTGAGGGCCTTTTTGATGCATTTTGAAAGTT
CAAGTACCCAAATGAGTGCCAAAAAAT
Found at i:69542393 original size:27 final size:30
Alignment explanation
Indices: 69542363--69542434 Score: 78
Period size: 27 Copynumber: 2.4 Consensus size: 30
69542353 CTCAATTGGG
69542363 TATTTAAATTTTTAATATT-T-GATTTT-T
1 TATTTAAATTTTTAATATTATAGATTTTAT
* *
69542390 TATTAAAATTTAATAATATTATAGATTTTAT
1 TATTTAAATTT-TTAATATTATAGATTTTAT
*
69542421 TGATTTTAATTTTT
1 T-ATTTAAATTTTT
69542435 TTCTAATTTG
Statistics
Matches: 35, Mismatches: 5, Indels: 6
0.76 0.11 0.13
Matches are distributed among these distances:
27 10 0.29
28 7 0.20
29 1 0.03
30 6 0.17
31 3 0.09
32 8 0.23
ACGTcount: A:0.35, C:0.00, G:0.04, T:0.61
Consensus pattern (30 bp):
TATTTAAATTTTTAATATTATAGATTTTAT
Found at i:69542820 original size:2 final size:2
Alignment explanation
Indices: 69542815--69542842 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
69542805 CCTAGGGACC
69542815 AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT
69542843 TCCAGTCTGG
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:69544049 original size:10 final size:10
Alignment explanation
Indices: 69544029--69544145 Score: 68
Period size: 9 Copynumber: 12.2 Consensus size: 10
69544019 TTCTTATGAC
*
69544029 TATAAAATTT
1 TATAAATTTT
69544039 TAT-AATTTT
1 TATAAATTTT
* *
69544048 T-TATATTTC
1 TATAAATTTT
*
69544057 TATATA-TTT
1 TATAAATTTT
69544066 TA-AAATTTT
1 TATAAATTTT
69544075 TA-AAATTTT
1 TATAAATTTT
*
69544084 TATAAAATTT
1 TATAAATTTT
* *
69544094 CA-CAATTTT
1 TATAAATTTT
*
69544103 TATAAAATTT
1 TATAAATTTT
* *
69544113 CA-CAATTTT
1 TATAAATTTT
*
69544122 TATATATTTTT
1 TATA-AATTTT
69544133 TAATAAATTTT
1 T-ATAAATTTT
69544144 TA
1 TA
69544146 AGATTTGAAT
Statistics
Matches: 80, Mismatches: 19, Indels: 16
0.70 0.17 0.14
Matches are distributed among these distances:
8 3 0.04
9 41 0.51
10 21 0.26
11 12 0.15
12 3 0.04
ACGTcount: A:0.39, C:0.04, G:0.00, T:0.56
Consensus pattern (10 bp):
TATAAATTTT
Found at i:69544060 original size:28 final size:28
Alignment explanation
Indices: 69543991--69544103 Score: 86
Period size: 27 Copynumber: 4.1 Consensus size: 28
69543981 TTTTACAAAA
* * *
69543991 TTTATATTTCTTTACATTTTGTATAATTT
1 TTTATATTTCTATAAAATTT-TATAATTT
* **
69544020 TCT-TATGACTATAAAATTTTATAATTT
1 TTTATATTTCTATAAAATTTTATAATTT
* *
69544047 TTTATATTTCTAT-ATATTTTAAAATTT
1 TTTATATTTCTATAAAATTTTATAATTT
* * * * *
69544074 TTAAAATTTTTATAAAATTTCACAATTT
1 TTTATATTTCTATAAAATTTTATAATTT
69544102 TT
1 TT
69544104 ATAAAATTTC
Statistics
Matches: 65, Mismatches: 17, Indels: 5
0.75 0.20 0.06
Matches are distributed among these distances:
27 32 0.49
28 31 0.48
29 2 0.03
ACGTcount: A:0.34, C:0.06, G:0.02, T:0.58
Consensus pattern (28 bp):
TTTATATTTCTATAAAATTTTATAATTT
Found at i:69544065 original size:27 final size:27
Alignment explanation
Indices: 69543991--69544134 Score: 76
Period size: 28 Copynumber: 5.1 Consensus size: 27
69543981 TTTTACAAAA
* *
69543991 TTTATATTTCTTTACATTTTGTATAATTT
1 TTTATATTTCTATA-AATTT-TATAATTT
* **
69544020 TCT-TATGACTATAAAATTTTATAATTT
1 TTTATATTTCTAT-AAATTTTATAATTT
* *
69544047 TTTATATTTCTATATATTTTAAAATTT
1 TTTATATTTCTATAAATTTTATAATTT
* * * * *
69544074 TTAAAATTTTTATAAAATTTCACAATTT
1 TTTATATTTCTAT-AAATTTTATAATTT
* * *
69544102 TTATAAAATTTC-ACAATTTTTATATATTT
1 TT-T-ATATTTCTATAAATTTTATA-ATTT
69544131 TTTA
1 TTTA
69544135 ATAAATTTTT
Statistics
Matches: 87, Mismatches: 22, Indels: 14
0.71 0.18 0.11
Matches are distributed among these distances:
27 33 0.38
28 38 0.44
29 10 0.11
30 6 0.07
ACGTcount: A:0.35, C:0.06, G:0.01, T:0.58
Consensus pattern (27 bp):
TTTATATTTCTATAAATTTTATAATTT
Found at i:69544073 original size:18 final size:17
Alignment explanation
Indices: 69544031--69544123 Score: 53
Period size: 19 Copynumber: 5.1 Consensus size: 17
69544021 CTTATGACTA
69544031 TAAAATTTTATAATTTT
1 TAAAATTTTATAATTTT
* *
69544048 TTATATTTCTAT-ATATTT
1 TAAAATTT-TATAAT-TTT
*
69544066 TAAAATTTTTAAAATTTTT
1 TAAAA-TTTTATAA-TTTT
* *
69544085 ATAAAATTTCACAATTTTT
1 -TAAAATTTTATAA-TTTT
* *
69544104 ATAAAATTTCACAATTTT
1 -TAAAATTTTATAATTTT
69544122 TA
1 TA
69544124 TATATTTTTT
Statistics
Matches: 63, Mismatches: 7, Indels: 12
0.77 0.09 0.15
Matches are distributed among these distances:
17 10 0.16
18 15 0.24
19 32 0.51
20 6 0.10
ACGTcount: A:0.40, C:0.05, G:0.00, T:0.55
Consensus pattern (17 bp):
TAAAATTTTATAATTTT
Found at i:69544102 original size:19 final size:19
Alignment explanation
Indices: 69544078--69544125 Score: 96
Period size: 19 Copynumber: 2.5 Consensus size: 19
69544068 AAATTTTTAA
69544078 AATTTTTATAAAATTTCAC
1 AATTTTTATAAAATTTCAC
69544097 AATTTTTATAAAATTTCAC
1 AATTTTTATAAAATTTCAC
69544116 AATTTTTATA
1 AATTTTTATA
69544126 TATTTTTTAA
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 29 1.00
ACGTcount: A:0.42, C:0.08, G:0.00, T:0.50
Consensus pattern (19 bp):
AATTTTTATAAAATTTCAC
Found at i:69544380 original size:89 final size:89
Alignment explanation
Indices: 69544209--69544431 Score: 232
Period size: 89 Copynumber: 2.5 Consensus size: 89
69544199 AATTTTTAAT
* * * * * **
69544209 AAAAGTAGGGACTTAATTGGTTTTTTTTATTAAGTTTGAGGGTGTTTTTGATGCATTTTGAAAGT
1 AAAAGCAGGGGCTTAATTGCTTTTTTTGA-AAAGTTTGAGGGCCTTTTTGATGCATTTTGAAAGT
* *
69544274 TTAAGTACCCAATTGAG-TGCAAAA
65 TCAAGTACCCAAATGAGTTGCAAAA
* *
69544298 AAAAGGAGGGGCTTAATTGCTTTTTTTGAAAATGTTTGAGGGCCTTTTTGATGTATTTTGAAAGT
1 AAAAGCAGGGGCTTAATTGCTTTTTTTGAAAA-GTTTGAGGGCCTTTTTGATGCATTTTGAAAGT
* * **
69544363 TCAAGTTCTCAAATGAGTTTTAAAA
65 TCAAGTACCCAAATGAGTTGCAAAA
* * *
69544388 AAAAGAACAGGGGTTTAGTTGCTATTTTTGAAAAAGTTTGAGGG
1 AAAAG--CAGGGGCTTAATTGCTTTTTTTG-AAAAGTTTGAGGG
69544432 TTTTTTGCAC
Statistics
Matches: 111, Mismatches: 18, Indels: 7
0.82 0.13 0.05
Matches are distributed among these distances:
88 2 0.02
89 67 0.60
90 10 0.09
92 28 0.25
93 4 0.04
ACGTcount: A:0.31, C:0.07, G:0.24, T:0.39
Consensus pattern (89 bp):
AAAAGCAGGGGCTTAATTGCTTTTTTTGAAAAGTTTGAGGGCCTTTTTGATGCATTTTGAAAGTT
CAAGTACCCAAATGAGTTGCAAAA
Found at i:69545692 original size:33 final size:33
Alignment explanation
Indices: 69545655--69545726 Score: 94
Period size: 33 Copynumber: 2.2 Consensus size: 33
69545645 CTTGGAAAGC
69545655 GAAAAAAAAAACAAA-AAAAAGAAGGAAAA-AAAA
1 GAAAAAAAAAACAAATAAAAA-AA-GAAAATAAAA
* *
69545688 GAAAAAAAGAAGAAATAAAAAAAGAAAATAAAA
1 GAAAAAAAAAACAAATAAAAAAAGAAAATAAAA
69545721 GAAAAA
1 GAAAAA
69545727 TAATACTCCT
Statistics
Matches: 35, Mismatches: 2, Indels: 4
0.85 0.05 0.10
Matches are distributed among these distances:
32 5 0.14
33 25 0.71
34 5 0.14
ACGTcount: A:0.83, C:0.01, G:0.12, T:0.03
Consensus pattern (33 bp):
GAAAAAAAAAACAAATAAAAAAAGAAAATAAAA
Found at i:69545727 original size:24 final size:23
Alignment explanation
Indices: 69545659--69545729 Score: 83
Period size: 21 Copynumber: 3.1 Consensus size: 23
69545649 GAAAGCGAAA
* **
69545659 AAAAAAACAAAAAAAAGAAGGA-
1 AAAAAAAGAAAAAAAAGAAAAAT
69545681 AAAAAAAG-AAAAAAAGAAGAAAT
1 AAAAAAAGAAAAAAAAGAA-AAAT
69545704 AAAAAAAGAAAATAAAAGAAAAAT
1 AAAAAAAGAAAA-AAAAGAAAAAT
69545728 AA
1 AA
69545730 TACTCCTCTG
Statistics
Matches: 42, Mismatches: 3, Indels: 6
0.82 0.06 0.12
Matches are distributed among these distances:
21 10 0.24
22 8 0.19
23 8 0.19
24 9 0.21
25 7 0.17
ACGTcount: A:0.83, C:0.01, G:0.11, T:0.04
Consensus pattern (23 bp):
AAAAAAAGAAAAAAAAGAAAAAT
Found at i:69545729 original size:11 final size:11
Alignment explanation
Indices: 69545655--69545726 Score: 76
Period size: 11 Copynumber: 6.5 Consensus size: 11
69545645 CTTGGAAAGC
69545655 GAAAAAAAAAA
1 GAAAAAAAAAA
*
69545666 CAAAAAAAAGAA
1 GAAAAAAAA-AA
*
69545678 G-GAAAAAAAA
1 GAAAAAAAAAA
*
69545688 GAAAAAAAGAA
1 GAAAAAAAAAA
69545699 GAAATAAAAAAA
1 GAAA-AAAAAAA
*
69545711 G-AAAATAAAA
1 GAAAAAAAAAA
69545721 GAAAAA
1 GAAAAA
69545727 TAATACTCCT
Statistics
Matches: 50, Mismatches: 7, Indels: 8
0.77 0.11 0.12
Matches are distributed among these distances:
10 10 0.20
11 31 0.62
12 9 0.18
ACGTcount: A:0.83, C:0.01, G:0.12, T:0.03
Consensus pattern (11 bp):
GAAAAAAAAAA
Found at i:69556094 original size:87 final size:87
Alignment explanation
Indices: 69555904--69556095 Score: 289
Period size: 88 Copynumber: 2.2 Consensus size: 87
69555894 CACTTCTTCA
* *
69555904 AAAAAAGCAATTAAACCCCTTTTTTTTCCCGCTCAATTGGGTACTTGAACTTTCATAATGCATAA
1 AAAAAAGCAATTAAGCCCCTTTTTTTTCCCACTCAATTGGGTACTTGAACTTTCATAATGCATAA
69555969 AAAAAACCTTAAAATTTTTTTC
66 AAAAAACCTTAAAATTTTTTTC
*
69555991 AAAGAAA-CAATTAAGCCTCTATTTTTTTCCCACTCAATTGGGTACTTGAACTTTCATAATGCAT
1 AAA-AAAGCAATTAAGCCCCT-TTTTTTTCCCACTCAATTGGGTACTTGAACTTTCATAATGCAT
* ** *
69556055 CAAAAAGGCCTT-AATTTTTTTTC
64 AAAAAAAACCTTAAAATTTTTTTC
69556078 AAAAAAGCAATTAAGCCC
1 AAAAAAGCAATTAAGCCC
69556096 TACTCTTATT
Statistics
Matches: 94, Mismatches: 8, Indels: 6
0.87 0.07 0.06
Matches are distributed among these distances:
86 3 0.03
87 37 0.39
88 54 0.57
ACGTcount: A:0.36, C:0.20, G:0.09, T:0.34
Consensus pattern (87 bp):
AAAAAAGCAATTAAGCCCCTTTTTTTTCCCACTCAATTGGGTACTTGAACTTTCATAATGCATAA
AAAAAACCTTAAAATTTTTTTC
Found at i:69556168 original size:19 final size:20
Alignment explanation
Indices: 69556124--69556168 Score: 65
Period size: 20 Copynumber: 2.3 Consensus size: 20
69556114 GAAAAAAATC
69556124 ATAAAAATAATAAATTTTAG
1 ATAAAAATAATAAATTTTAG
* *
69556144 AAAAAAATATTAAATTTTA-
1 ATAAAAATAATAAATTTTAG
69556163 ATAAAA
1 ATAAAA
69556169 TTTAAAAACT
Statistics
Matches: 22, Mismatches: 3, Indels: 1
0.85 0.12 0.04
Matches are distributed among these distances:
19 5 0.23
20 17 0.77
ACGTcount: A:0.64, C:0.00, G:0.02, T:0.33
Consensus pattern (20 bp):
ATAAAAATAATAAATTTTAG
Found at i:69556573 original size:11 final size:9
Alignment explanation
Indices: 69556533--69556582 Score: 73
Period size: 9 Copynumber: 5.3 Consensus size: 9
69556523 ATTTTAAATT
69556533 TTTTTAAAA
1 TTTTTAAAA
69556542 TTTTTAAAA
1 TTTTTAAAA
69556551 TTTTTAAAA
1 TTTTTAAAA
69556560 TTTTTAATAAA
1 TTTTT-A-AAA
*
69556571 TTTTTAATA
1 TTTTTAAAA
69556580 TTT
1 TTT
69556583 GATTTTTTAT
Statistics
Matches: 38, Mismatches: 1, Indels: 4
0.88 0.02 0.09
Matches are distributed among these distances:
9 28 0.74
10 2 0.05
11 8 0.21
ACGTcount: A:0.40, C:0.00, G:0.00, T:0.60
Consensus pattern (9 bp):
TTTTTAAAA
Found at i:69556582 original size:9 final size:9
Alignment explanation
Indices: 69556496--69556582 Score: 63
Period size: 9 Copynumber: 9.4 Consensus size: 9
69556486 ACTGTATAAA
69556496 ATTTTATAAT
1 ATTTT-TAAT
69556506 -TTTTT-AT
1 ATTTTTAAT
*
69556513 A-TTTCAAT
1 ATTTTTAAT
69556521 ATATTTTAAAT
1 AT-TTTT-AAT
* *
69556532 TTTTTTAAA
1 ATTTTTAAT
*
69556541 ATTTTTAAA
1 ATTTTTAAT
*
69556550 ATTTTTAAA
1 ATTTTTAAT
69556559 ATTTTTAAT
1 ATTTTTAAT
69556568 AAATTTTTAAT
1 --ATTTTTAAT
69556579 ATTT
1 ATTT
69556583 GATTTTTTAT
Statistics
Matches: 64, Mismatches: 6, Indels: 15
0.75 0.07 0.18
Matches are distributed among these distances:
7 5 0.08
8 4 0.06
9 35 0.55
10 7 0.11
11 13 0.20
ACGTcount: A:0.38, C:0.01, G:0.00, T:0.61
Consensus pattern (9 bp):
ATTTTTAAT
Found at i:69556832 original size:92 final size:92
Alignment explanation
Indices: 69556650--69556825 Score: 273
Period size: 92 Copynumber: 1.9 Consensus size: 92
69556640 ATTTTTAATA
* ** *
69556650 AAAGTAGGGGCTTAATTGCTTTTTTTTTTAAAGTTTGAGGGTCTTTTTGATGCATTTTGAAAGTT
1 AAAGTAGGGGCCTAATTGCTTTTTTTTGAAAAGTTTGAGGGCCTTTTTGATGCATTTTGAAAGTT
* *
69556715 TAAGTACCCAATTGAGTGCCAAAAAAT
66 CAAGTACCCAAATGAGTGCCAAAAAAT
*
69556742 AAAGTAGGGGCCTAATTGC-TTTTTTTGAAAATGTTTGAGGGCCTTTTTGATGTATTTTGAAAGT
1 AAAGTAGGGGCCTAATTGCTTTTTTTTGAAAA-GTTTGAGGGCCTTTTTGATGCATTTTGAAAGT
69556806 TCAAGTACCCAAATGAGTGC
65 TCAAGTACCCAAATGAGTGC
69556826 ATAAAAAGAA
Statistics
Matches: 76, Mismatches: 7, Indels: 2
0.89 0.08 0.02
Matches are distributed among these distances:
91 10 0.13
92 66 0.87
ACGTcount: A:0.28, C:0.11, G:0.22, T:0.39
Consensus pattern (92 bp):
AAAGTAGGGGCCTAATTGCTTTTTTTTGAAAAGTTTGAGGGCCTTTTTGATGCATTTTGAAAGTT
CAAGTACCCAAATGAGTGCCAAAAAAT
Found at i:69556857 original size:92 final size:92
Alignment explanation
Indices: 69556650--69556867 Score: 257
Period size: 92 Copynumber: 2.4 Consensus size: 92
69556640 ATTTTTAATA
* ** *
69556650 AAAGTAGGGGCTTAATTGCTTTTTTTTTTAAAGTTTGAGGGTCTTTTTGATGCATTTTGAAAGTT
1 AAAGCAGGGGCTTAATTGCTTTTTTTTGAAAAGTTTGAGGGCCTTTTTGATGCATTTTGAAAGTT
* *
69556715 TAAGTACCCAATTGAGTGCCAAAAAAT
66 CAAGTACCCAAATGAGTGCCAAAAAAT
* * *
69556742 AAAGTAGGGGCCTAATTGC-TTTTTTTGAAAATGTTTGAGGGCCTTTTTGATGTATTTTGAAAGT
1 AAAGCAGGGGCTTAATTGCTTTTTTTTGAAAA-GTTTGAGGGCCTTTTTGATGCATTTTGAAAGT
69556806 TCAAGTACCCAAATGAGTG-CATAAAAA-
65 TCAAGTACCCAAATGAGTGCCA-AAAAAT
* * * *
69556833 GAA-CAGGGGTTTAGTTGC-TATTTTTGAAAAAGTTT
1 AAAGCAGGGGCTTAATTGCTTTTTTTTG-AAAAGTTT
69556868 TTACCCTTAA
Statistics
Matches: 110, Mismatches: 13, Indels: 8
0.84 0.10 0.06
Matches are distributed among these distances:
90 22 0.20
91 18 0.16
92 70 0.64
ACGTcount: A:0.30, C:0.10, G:0.22, T:0.38
Consensus pattern (92 bp):
AAAGCAGGGGCTTAATTGCTTTTTTTTGAAAAGTTTGAGGGCCTTTTTGATGCATTTTGAAAGTT
CAAGTACCCAAATGAGTGCCAAAAAAT
Found at i:69558576 original size:29 final size:29
Alignment explanation
Indices: 69558534--69558589 Score: 94
Period size: 29 Copynumber: 1.9 Consensus size: 29
69558524 TTTTTTCATC
69558534 TGATAAACAATGTAAGTTTAAGGGTTATT
1 TGATAAACAATGTAAGTTTAAGGGTTATT
* *
69558563 TGATAAATAATGTAGGTTTAAGGGTTA
1 TGATAAACAATGTAAGTTTAAGGGTTA
69558590 AAAAAGATGA
Statistics
Matches: 25, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
29 25 1.00
ACGTcount: A:0.38, C:0.02, G:0.23, T:0.38
Consensus pattern (29 bp):
TGATAAACAATGTAAGTTTAAGGGTTATT
Found at i:69561552 original size:72 final size:71
Alignment explanation
Indices: 69561464--69561684 Score: 318
Period size: 72 Copynumber: 3.1 Consensus size: 71
69561454 TCAGGACCGG
* * * * * * *
69561464 TTCCAAAATCACTGGGGAATCTCTTGCAACTCACTCATTTAGACTTATCCGG-GAACCAGTTGAG
1 TTCCAAGATCATTGGGGAACCTCTTGCAACTCACTTATTTAGGCTTGT--GGAGAACCAATTGAG
69561528 TGGACAAA
64 TGGACAAA
*
69561536 TTCCAAGATCATTGGGGAACCTCTTGCAACTCACTTATTTAGGCTTGTGGCAAAACCAATTGAGT
1 TTCCAAGATCATTGGGGAACCTCTTGCAACTCACTTATTTAGGCTTGTGG-AGAACCAATTGAGT
69561601 GGACAAA
65 GGACAAA
*
69561608 TTCCAAGATCATTGGGGAACCTCTTGCAACTCACTTATTTAGGCTTGTGGCAGAACCAATTGAAT
1 TTCCAAGATCATTGGGGAACCTCTTGCAACTCACTTATTTAGGCTTGTGG-AGAACCAATTGAGT
69561673 GGACAAA
65 GGACAAA
69561680 TTCCA
1 TTCCA
69561685 TTGTCAATTC
Statistics
Matches: 137, Mismatches: 10, Indels: 4
0.91 0.07 0.03
Matches are distributed among these distances:
70 2 0.01
72 135 0.99
ACGTcount: A:0.30, C:0.22, G:0.20, T:0.28
Consensus pattern (71 bp):
TTCCAAGATCATTGGGGAACCTCTTGCAACTCACTTATTTAGGCTTGTGGAGAACCAATTGAGTG
GACAAA
Found at i:69566310 original size:25 final size:25
Alignment explanation
Indices: 69566278--69566343 Score: 100
Period size: 24 Copynumber: 2.7 Consensus size: 25
69566268 TTTTAGATTT
69566278 ATTATGTATTATTACTTTAAAATTC
1 ATTATGTATTATTACTTTAAAATTC
*
69566303 ATTATGTATTATTA-TTTAAAATTT
1 ATTATGTATTATTACTTTAAAATTC
69566327 ATTATGT-TTCATTACTT
1 ATTATGTATT-ATTACTT
69566344 AAATTTATCA
Statistics
Matches: 38, Mismatches: 1, Indels: 4
0.88 0.02 0.09
Matches are distributed among these distances:
23 2 0.05
24 20 0.53
25 16 0.42
ACGTcount: A:0.33, C:0.06, G:0.05, T:0.56
Consensus pattern (25 bp):
ATTATGTATTATTACTTTAAAATTC
Found at i:69566488 original size:16 final size:15
Alignment explanation
Indices: 69566467--69566537 Score: 52
Period size: 16 Copynumber: 4.3 Consensus size: 15
69566457 GTATTAAAGA
69566467 TTTATATGAAAATATT
1 TTTATAT-AAAATATT
*
69566483 TTTATATAATACTATT
1 TTTATATAA-AATATT
* *
69566499 TTATATATATACATATAA
1 TT-TATATA-AAATAT-T
*
69566517 TTTATATTAAATTATT
1 TTTATA-TAAAATATT
69566533 TTTAT
1 TTTAT
69566538 TCTATATATA
Statistics
Matches: 43, Mismatches: 7, Indels: 10
0.72 0.12 0.17
Matches are distributed among these distances:
15 2 0.05
16 19 0.44
17 17 0.40
18 5 0.12
ACGTcount: A:0.41, C:0.03, G:0.01, T:0.55
Consensus pattern (15 bp):
TTTATATAAAATATT
Found at i:69566509 original size:19 final size:19
Alignment explanation
Indices: 69566483--69566523 Score: 54
Period size: 15 Copynumber: 2.4 Consensus size: 19
69566473 TGAAAATATT
69566483 TTTATATA-ATAC-TAT--
1 TTTATATATATACATATAA
69566498 TTTATATATATACATATAA
1 TTTATATATATACATATAA
69566517 TTTATAT
1 TTTATAT
69566524 TAAATTATTT
Statistics
Matches: 22, Mismatches: 0, Indels: 4
0.85 0.00 0.15
Matches are distributed among these distances:
15 8 0.36
16 4 0.18
17 3 0.14
19 7 0.32
ACGTcount: A:0.41, C:0.05, G:0.00, T:0.54
Consensus pattern (19 bp):
TTTATATATATACATATAA
Found at i:69567491 original size:3 final size:3
Alignment explanation
Indices: 69567483--69567508 Score: 52
Period size: 3 Copynumber: 8.7 Consensus size: 3
69567473 AAGTGGTGCT
69567483 AAC AAC AAC AAC AAC AAC AAC AAC AA
1 AAC AAC AAC AAC AAC AAC AAC AAC AA
69567509 TAATAATAAT
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:0.69, C:0.31, G:0.00, T:0.00
Consensus pattern (3 bp):
AAC
Found at i:69568957 original size:21 final size:20
Alignment explanation
Indices: 69568923--69568961 Score: 51
Period size: 21 Copynumber: 1.9 Consensus size: 20
69568913 GTTAAAAATG
69568923 ATTTTTTAAAAAAATATTTTT
1 ATTTTTTAAAAAAA-ATTTTT
**
69568944 ATTTTTTATTAAAAATTT
1 ATTTTTTAAAAAAAATTT
69568962 AGAATTAGAA
Statistics
Matches: 16, Mismatches: 2, Indels: 1
0.84 0.11 0.05
Matches are distributed among these distances:
20 4 0.25
21 12 0.75
ACGTcount: A:0.41, C:0.00, G:0.00, T:0.59
Consensus pattern (20 bp):
ATTTTTTAAAAAAAATTTTT
Found at i:69572678 original size:55 final size:55
Alignment explanation
Indices: 69572602--69572706 Score: 129
Period size: 55 Copynumber: 1.9 Consensus size: 55
69572592 TTAACATTAA
* * * * * *
69572602 GTACCATAATAAAACATATATTGATAGTTGATGTACCACATTAGACATTCAACAT
1 GTACCATAATAAAACACATATTAATAATTGAGGTACCACATCAAACATTCAACAT
* * *
69572657 GTACTATAATAGAACACATATTAATAATTTAGGTACCACATCAAACATTC
1 GTACCATAATAAAACACATATTAATAATTGAGGTACCACATCAAACATTC
69572707 TATGAAAGCA
Statistics
Matches: 41, Mismatches: 9, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
55 41 1.00
ACGTcount: A:0.43, C:0.17, G:0.10, T:0.30
Consensus pattern (55 bp):
GTACCATAATAAAACACATATTAATAATTGAGGTACCACATCAAACATTCAACAT
Found at i:69578402 original size:26 final size:26
Alignment explanation
Indices: 69578348--69578405 Score: 66
Period size: 26 Copynumber: 2.2 Consensus size: 26
69578338 TTATATATAT
*
69578348 TTTTTAAATTTTTATGTATTATAAGA
1 TTTTTAAATTTTTATATATTATAAGA
*
69578374 TTTTTAAATTTAATTATAT-TTTTAA-A
1 TTTTTAAATTT--TTATATATTATAAGA
69578400 TTTTTA
1 TTTTTA
69578406 GAATCATGAC
Statistics
Matches: 28, Mismatches: 2, Indels: 4
0.82 0.06 0.12
Matches are distributed among these distances:
26 18 0.64
27 5 0.18
28 5 0.18
ACGTcount: A:0.34, C:0.00, G:0.03, T:0.62
Consensus pattern (26 bp):
TTTTTAAATTTTTATATATTATAAGA
Found at i:69586738 original size:11 final size:11
Alignment explanation
Indices: 69586724--69586748 Score: 50
Period size: 11 Copynumber: 2.3 Consensus size: 11
69586714 CTTTTTAGGT
69586724 GAAAAAAAAAA
1 GAAAAAAAAAA
69586735 GAAAAAAAAAA
1 GAAAAAAAAAA
69586746 GAA
1 GAA
69586749 TAAGAAGATT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 14 1.00
ACGTcount: A:0.88, C:0.00, G:0.12, T:0.00
Consensus pattern (11 bp):
GAAAAAAAAAA
Found at i:69588359 original size:17 final size:17
Alignment explanation
Indices: 69588337--69588373 Score: 74
Period size: 17 Copynumber: 2.2 Consensus size: 17
69588327 ACCTAGAGTT
69588337 CTAAGAGAATGTCAGTA
1 CTAAGAGAATGTCAGTA
69588354 CTAAGAGAATGTCAGTA
1 CTAAGAGAATGTCAGTA
69588371 CTA
1 CTA
69588374 GGGACAGAGA
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 20 1.00
ACGTcount: A:0.41, C:0.14, G:0.22, T:0.24
Consensus pattern (17 bp):
CTAAGAGAATGTCAGTA
Found at i:69589515 original size:67 final size:67
Alignment explanation
Indices: 69589407--69589541 Score: 243
Period size: 67 Copynumber: 2.0 Consensus size: 67
69589397 TTTCCAATTC
*
69589407 AGAGAGCACACTCCCGCGAACCTCATTTCTTACAGCGGGATTACCAGTCCAGGCTAAATCCCCTG
1 AGAGAGCACACTCCCGCAAACCTCATTTCTTACAGCGGGATTACCAGTCCAGGCTAAATCCCCTG
69589472 CA
66 CA
* *
69589474 AGAGAGCACACTCCCGCAAACCTCATTTCTTACTGCGGGATTACCAGTCCAGGCTAAATCCCTTG
1 AGAGAGCACACTCCCGCAAACCTCATTTCTTACAGCGGGATTACCAGTCCAGGCTAAATCCCCTG
69589539 CA
66 CA
69589541 A
1 A
69589542 CGACAATTAC
Statistics
Matches: 65, Mismatches: 3, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
67 65 1.00
ACGTcount: A:0.27, C:0.33, G:0.19, T:0.21
Consensus pattern (67 bp):
AGAGAGCACACTCCCGCAAACCTCATTTCTTACAGCGGGATTACCAGTCCAGGCTAAATCCCCTG
CA
Found at i:69589697 original size:57 final size:60
Alignment explanation
Indices: 69589615--69589753 Score: 180
Period size: 57 Copynumber: 2.3 Consensus size: 60
69589605 TGGATTACTC
* *
69589615 GTCCGGGCTAAATCCATTTTCCACATATTCTTCAGG-AGGCCTATATC-A-A-GATCACCT
1 GTCCGGGCTAGATCCTTTTTCCACATATTCTTC-GGAAGGCCTATATCGATAGGATCACCT
*
69589672 GTCCGGGCTAGAT-CTTTTTCACACATATTCTTCGGAAGGGCTATATCAGGATAGGATCACCT
1 GTCCGGGCTAGATCCTTTTTC-CACATATTCTTCGGAAGGCCTATATC--GATAGGATCACCT
69589734 GTCCGGGCTAGATCCTTTTT
1 GTCCGGGCTAGATCCTTTTT
69589754 ACCGTCAATT
Statistics
Matches: 71, Mismatches: 3, Indels: 10
0.85 0.04 0.12
Matches are distributed among these distances:
56 8 0.11
57 34 0.48
60 1 0.01
61 1 0.01
62 21 0.30
63 6 0.08
ACGTcount: A:0.23, C:0.25, G:0.20, T:0.32
Consensus pattern (60 bp):
GTCCGGGCTAGATCCTTTTTCCACATATTCTTCGGAAGGCCTATATCGATAGGATCACCT
Found at i:69593405 original size:12 final size:12
Alignment explanation
Indices: 69593388--69593417 Score: 51
Period size: 12 Copynumber: 2.5 Consensus size: 12
69593378 TTTGTTTCTT
*
69593388 TTATTATATTTA
1 TTATTATATCTA
69593400 TTATTATATCTA
1 TTATTATATCTA
69593412 TTATTA
1 TTATTA
69593418 CGATCTATTT
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
12 17 1.00
ACGTcount: A:0.33, C:0.03, G:0.00, T:0.63
Consensus pattern (12 bp):
TTATTATATCTA
Found at i:69594031 original size:131 final size:131
Alignment explanation
Indices: 69593797--69594063 Score: 437
Period size: 131 Copynumber: 2.0 Consensus size: 131
69593787 GAAAATTTCG
* * *
69593797 AAAAATAAAGGTAATATTTCATATTTAGAAATTCGAAAAGTTGTGCCCTAACTTACTGGTTTTCG
1 AAAAATAAAGGCAATATTCCATATTTAAAAATTCGAAAAGTTGTGCCCTAACTTACTGGTTTTCG
69593862 ATTTTTCTCGCGTTAAACCTAAATAACCGAATATCCTTTTAAAACTAAAATAAATGTGTTTTAAA
66 ATTTTTCTCGCGTTAAACCTAAATAACCGAATATCCTTTTAAAACTAAAATAAATGTGTTTTAAA
69593927 T
131 T
* * *
69593928 AAAAATAAAGGCAATATTCCATATTTAAAAATTTGAGAAGTTGTGCCTTAACTTACTGGGTTTT-
1 AAAAATAAAGGCAATATTCCATATTTAAAAATTCGAAAAGTTGTGCCCTAACTTACT-GGTTTTC
* * *
69593992 GATTTTTCTGGCGTTGAACCTAAATAACTGAATATCCTTTTAAAACTAAAATAAATGTGTTTTAA
65 GATTTTTCTCGCGTTAAACCTAAATAACCGAATATCCTTTTAAAACTAAAATAAATGTGTTTTAA
69594057 AT
130 AT
69594059 AAAAA
1 AAAAA
69594064 CAAATGCGAG
Statistics
Matches: 126, Mismatches: 9, Indels: 2
0.92 0.07 0.01
Matches are distributed among these distances:
131 120 0.95
132 6 0.05
ACGTcount: A:0.39, C:0.12, G:0.12, T:0.36
Consensus pattern (131 bp):
AAAAATAAAGGCAATATTCCATATTTAAAAATTCGAAAAGTTGTGCCCTAACTTACTGGTTTTCG
ATTTTTCTCGCGTTAAACCTAAATAACCGAATATCCTTTTAAAACTAAAATAAATGTGTTTTAAA
T
Found at i:69596456 original size:35 final size:35
Alignment explanation
Indices: 69596410--69596479 Score: 140
Period size: 35 Copynumber: 2.0 Consensus size: 35
69596400 AAAATCTTAA
69596410 ATACTCAAATGGCATGCAAATTTATTATTAATTGT
1 ATACTCAAATGGCATGCAAATTTATTATTAATTGT
69596445 ATACTCAAATGGCATGCAAATTTATTATTAATTGT
1 ATACTCAAATGGCATGCAAATTTATTATTAATTGT
69596480 GAATTTAGTC
Statistics
Matches: 35, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
35 35 1.00
ACGTcount: A:0.37, C:0.11, G:0.11, T:0.40
Consensus pattern (35 bp):
ATACTCAAATGGCATGCAAATTTATTATTAATTGT
Found at i:69597181 original size:14 final size:14
Alignment explanation
Indices: 69597162--69597188 Score: 54
Period size: 14 Copynumber: 1.9 Consensus size: 14
69597152 TATAATTATC
69597162 AAATATTAAATAAT
1 AAATATTAAATAAT
69597176 AAATATTAAATAA
1 AAATATTAAATAA
69597189 AATAATTATA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 13 1.00
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (14 bp):
AAATATTAAATAAT
Found at i:69598220 original size:20 final size:20
Alignment explanation
Indices: 69598183--69598221 Score: 51
Period size: 20 Copynumber: 1.9 Consensus size: 20
69598173 AAGTTTAAAA
* **
69598183 TATTTTAAAATTTCTTTTTT
1 TATTTTAAAAATAATTTTTT
69598203 TATTTTAAAAATAATTTTT
1 TATTTTAAAAATAATTTTT
69598222 CGATATTTAT
Statistics
Matches: 16, Mismatches: 3, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
20 16 1.00
ACGTcount: A:0.33, C:0.03, G:0.00, T:0.64
Consensus pattern (20 bp):
TATTTTAAAAATAATTTTTT
Found at i:69602835 original size:3 final size:3
Alignment explanation
Indices: 69602827--69602872 Score: 65
Period size: 3 Copynumber: 15.3 Consensus size: 3
69602817 TTTAATTTCG
* * *
69602827 TAT TAT TAT TAT TAT TAT TAT CAT AAT TAT TAT TAT TAC TAT TAT T
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT T
69602873 TGCTCATTTG
Statistics
Matches: 38, Mismatches: 5, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
3 38 1.00
ACGTcount: A:0.35, C:0.04, G:0.00, T:0.61
Consensus pattern (3 bp):
TAT
Found at i:69603275 original size:35 final size:36
Alignment explanation
Indices: 69603215--69603284 Score: 99
Period size: 35 Copynumber: 1.9 Consensus size: 36
69603205 AAATAGTTTA
*
69603215 TTTTTATATTTTATAATTCACACATA-TACATATGT
1 TTTTTATACTTTATAATTCACACATACTACATATGT
69603250 TTTTTATACTTTATAATTCTA-ACATACGTACATAT
1 TTTTTATACTTTATAATTC-ACACATAC-TACATAT
69603285 ATATATATAT
Statistics
Matches: 31, Mismatches: 1, Indels: 4
0.86 0.03 0.11
Matches are distributed among these distances:
35 23 0.74
36 1 0.03
37 7 0.23
ACGTcount: A:0.34, C:0.13, G:0.03, T:0.50
Consensus pattern (36 bp):
TTTTTATACTTTATAATTCACACATACTACATATGT
Found at i:69603836 original size:12 final size:12
Alignment explanation
Indices: 69603819--69603843 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
69603809 AATTATACAC
69603819 TAACGTATTGGG
1 TAACGTATTGGG
69603831 TAACGTATTGGG
1 TAACGTATTGGG
69603843 T
1 T
69603844 TGCAATTCTT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.24, C:0.08, G:0.32, T:0.36
Consensus pattern (12 bp):
TAACGTATTGGG
Found at i:69604151 original size:18 final size:17
Alignment explanation
Indices: 69604128--69604161 Score: 59
Period size: 18 Copynumber: 1.9 Consensus size: 17
69604118 GGTGCTAATC
69604128 CTTTTATATTTACATAAA
1 CTTTTATATTTA-ATAAA
69604146 CTTTTATATTTAATAA
1 CTTTTATATTTAATAA
69604162 TTTTAAAATA
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
17 4 0.25
18 12 0.75
ACGTcount: A:0.38, C:0.09, G:0.00, T:0.53
Consensus pattern (17 bp):
CTTTTATATTTAATAAA
Done.