Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Gbar_D04
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: 52479919
ACGTcount: A:0.33, C:0.16, G:0.17, T:0.33
Warning! 336953 characters in sequence are not A, C, G, or T
File 95 of 173
Found at i:29754099 original size:13 final size:13
Alignment explanation
Indices: 29754081--29754106 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
29754071 ATATAATCTG
29754081 ATTGGGTCAGCTT
1 ATTGGGTCAGCTT
29754094 ATTGGGTCAGCTT
1 ATTGGGTCAGCTT
29754107 TGGGCTGCAA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.15, C:0.15, G:0.31, T:0.38
Consensus pattern (13 bp):
ATTGGGTCAGCTT
Found at i:29761161 original size:27 final size:28
Alignment explanation
Indices: 29761108--29761161 Score: 76
Period size: 27 Copynumber: 2.0 Consensus size: 28
29761098 AAAATAATTA
*
29761108 AAATTCAATATTTTAATAATTTAAGTGC
1 AAATTCAATATTTTAATAATTCAAGTGC
29761136 AAATT-AATTATTTT-ATAATTCAAGTG
1 AAATTCAA-TATTTTAATAATTCAAGTG
29761162 TGAATTTCGA
Statistics
Matches: 24, Mismatches: 1, Indels: 3
0.86 0.04 0.11
Matches are distributed among these distances:
27 13 0.54
28 11 0.46
ACGTcount: A:0.43, C:0.06, G:0.07, T:0.44
Consensus pattern (28 bp):
AAATTCAATATTTTAATAATTCAAGTGC
Found at i:29767030 original size:51 final size:52
Alignment explanation
Indices: 29766954--29767098 Score: 174
Period size: 50 Copynumber: 2.8 Consensus size: 52
29766944 TATAAACACG
* *
29766954 TGTGTAGTACTAAGTGCAGGCTACTACGTGTATCGATTGATAATG-G-TCACA
1 TGTGTAGTACTATGTGAAGGCTACTACGTGTATCGA-TGATAATGTGATCACA
* * * *
29767005 TGTGTAGTACTATGTGTAGGCTACTACGTGAACCGA--A-AAGTGTGATCACG
1 TGTGTAGTACTATGTGAAGGCTACTACGTGTATCGATGATAA-TGTGATCACA
29767055 TGTGTAGTACTATGTGAAGGCTACTACGTGTATCGAATGATAAT
1 TGTGTAGTACTATGTGAAGGCTACTACGTGTATCG-ATGATAAT
29767099 AATTACACGG
Statistics
Matches: 79, Mismatches: 8, Indels: 12
0.80 0.08 0.12
Matches are distributed among these distances:
47 2 0.03
48 3 0.04
49 1 0.01
50 36 0.46
51 33 0.42
53 2 0.03
54 2 0.03
ACGTcount: A:0.28, C:0.14, G:0.26, T:0.31
Consensus pattern (52 bp):
TGTGTAGTACTATGTGAAGGCTACTACGTGTATCGATGATAATGTGATCACA
Found at i:29767067 original size:50 final size:49
Alignment explanation
Indices: 29766950--29767084 Score: 157
Period size: 51 Copynumber: 2.7 Consensus size: 49
29766940 TGCCTATAAA
* * * *
29766950 CACGTGTGTAGTACTAAGTGCAGGCTACTACGTGTATCGATTGATAATGGT
1 CACGTGTGTAGTACTATGTGAAGGCTACTACGTGAACCGA-T-ATAATGGT
* *
29767001 CACATGTGTAGTACTATGTGTAGGCTACTACGTGAACCGA-A-AAGTGTGAT
1 CACGTGTGTAGTACTATGTGAAGGCTACTACGTGAACCGATATAA-TG-G-T
29767051 CACGTGTGTAGTACTATGTGAAGGCTACTACGTG
1 CACGTGTGTAGTACTATGTGAAGGCTACTACGTG
29767085 TATCGAATGA
Statistics
Matches: 74, Mismatches: 7, Indels: 7
0.84 0.08 0.08
Matches are distributed among these distances:
47 2 0.03
48 3 0.04
49 1 0.01
50 33 0.45
51 35 0.47
ACGTcount: A:0.27, C:0.16, G:0.27, T:0.30
Consensus pattern (49 bp):
CACGTGTGTAGTACTATGTGAAGGCTACTACGTGAACCGATATAATGGT
Found at i:29771312 original size:22 final size:23
Alignment explanation
Indices: 29771286--29771328 Score: 70
Period size: 22 Copynumber: 1.9 Consensus size: 23
29771276 GAAAATAGTC
29771286 AAAATTAATAAAAATT-AACAAT
1 AAAATTAATAAAAATTCAACAAT
*
29771308 AAAATTAATTAAAATTCAACA
1 AAAATTAATAAAAATTCAACA
29771329 TGTTCATATT
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
22 15 0.79
23 4 0.21
ACGTcount: A:0.65, C:0.07, G:0.00, T:0.28
Consensus pattern (23 bp):
AAAATTAATAAAAATTCAACAAT
Found at i:29781681 original size:8 final size:9
Alignment explanation
Indices: 29781663--29781735 Score: 51
Period size: 10 Copynumber: 7.4 Consensus size: 9
29781653 AAAGTATTTT
29781663 AAAATTAAA
1 AAAATTAAA
29781672 AAAATTAAAA
1 AAAATT-AAA
29781682 AAAGTATTTAAA
1 AAA--A-TTAAA
29781694 AAAATTTTAAAA
1 AAAA--TT-AAA
*
29781706 AAAATT--T
1 AAAATTAAA
29781713 AAAATTAAA
1 AAAATTAAA
29781722 AAAATTTAAA
1 AAAA-TTAAA
29781732 AAAA
1 AAAA
29781736 GTATTTTAAA
Statistics
Matches: 53, Mismatches: 2, Indels: 17
0.74 0.03 0.24
Matches are distributed among these distances:
7 6 0.11
9 10 0.19
10 18 0.34
11 3 0.06
12 14 0.26
13 2 0.04
ACGTcount: A:0.71, C:0.00, G:0.01, T:0.27
Consensus pattern (9 bp):
AAAATTAAA
Found at i:29781684 original size:12 final size:12
Alignment explanation
Indices: 29781669--29781716 Score: 55
Period size: 12 Copynumber: 4.2 Consensus size: 12
29781659 TTTTAAAATT
29781669 AAAAAA-ATTAA
1 AAAAAATATTAA
* *
29781680 AAAAAGTATTTA
1 AAAAAATATTAA
*
29781692 AAAAAATTTTAA
1 AAAAAATATTAA
29781704 AAAAAAT-TTAA
1 AAAAAATATTAA
29781715 AA
1 AA
29781717 TTAAAAAAAT
Statistics
Matches: 31, Mismatches: 5, Indels: 2
0.82 0.13 0.05
Matches are distributed among these distances:
11 11 0.35
12 20 0.65
ACGTcount: A:0.71, C:0.00, G:0.02, T:0.27
Consensus pattern (12 bp):
AAAAAATATTAA
Found at i:29781684 original size:29 final size:31
Alignment explanation
Indices: 29781624--29781695 Score: 103
Period size: 29 Copynumber: 2.3 Consensus size: 31
29781614 ACCAAAAATT
29781624 TATTTTAAAAATTAAAATAAAAATTAAAAAAAG
1 TATTTT-AAAATT-AAATAAAAATTAAAAAAAG
29781657 TATTTTAAAATT-AA-AAAAATTAAAAAAAG
1 TATTTTAAAATTAAATAAAAATTAAAAAAAG
*
29781686 TATTTAAAAA
1 TATTTTAAAA
29781696 AATTTTAAAA
Statistics
Matches: 38, Mismatches: 1, Indels: 4
0.88 0.02 0.09
Matches are distributed among these distances:
29 24 0.63
30 2 0.05
32 6 0.16
33 6 0.16
ACGTcount: A:0.65, C:0.00, G:0.03, T:0.32
Consensus pattern (31 bp):
TATTTTAAAATTAAATAAAAATTAAAAAAAG
Found at i:29781734 original size:29 final size:29
Alignment explanation
Indices: 29781689--29781755 Score: 84
Period size: 29 Copynumber: 2.3 Consensus size: 29
29781679 AAAAAAGTAT
*
29781689 TTAAAAAAATTTTAAAAA-AAATTTAAAA
1 TTAAAAAAATTTAAAAAAGAAATTTAAAA
* *
29781717 TTAAAAAAATTTAAAAAAAGTATTTTAAAA
1 TTAAAAAAATTT-AAAAAAGAAATTTAAAA
29781747 -TAAAAAAAT
1 TTAAAAAAAT
29781756 AAAAATATTT
Statistics
Matches: 34, Mismatches: 3, Indels: 3
0.85 0.08 0.08
Matches are distributed among these distances:
28 12 0.35
29 14 0.41
30 8 0.24
ACGTcount: A:0.67, C:0.00, G:0.01, T:0.31
Consensus pattern (29 bp):
TTAAAAAAATTTAAAAAAGAAATTTAAAA
Found at i:29781735 original size:11 final size:11
Alignment explanation
Indices: 29781669--29781716 Score: 62
Period size: 11 Copynumber: 4.3 Consensus size: 11
29781659 TTTTAAAATT
29781669 AAAAAAA-TTA
1 AAAAAAATTTA
29781679 AAAAAAGTATTTA
1 AAAAAA--ATTTA
*
29781692 AAAAAATTTTA
1 AAAAAAATTTA
29781703 AAAAAAATTTA
1 AAAAAAATTTA
29781714 AAA
1 AAA
29781717 TTAAAAAAAT
Statistics
Matches: 33, Mismatches: 2, Indels: 5
0.82 0.05 0.12
Matches are distributed among these distances:
10 6 0.18
11 17 0.52
12 1 0.03
13 9 0.27
ACGTcount: A:0.71, C:0.00, G:0.02, T:0.27
Consensus pattern (11 bp):
AAAAAAATTTA
Found at i:29781760 original size:51 final size:48
Alignment explanation
Indices: 29781642--29781761 Score: 134
Period size: 50 Copynumber: 2.4 Consensus size: 48
29781632 AAATTAAAAT
* *
29781642 AAAAATTAAAAAAAGTATTTTAAAATTAAAAAAATTAAAAAAAGTATTTA
1 AAAAAATAAAAAAA--AATTTAAAATTAAAAAAATTAAAAAAAGTATTTA
*
29781692 AAAAAATTTTAAAAAAAATTTAAAATTAAAAAAATTTAAAAAAAGTATTTTA
1 AAAAAA--TAAAAAAAAATTTAAAATTAAAAAAA-TTAAAAAAAGTA-TTTA
29781744 AAATAAA-AAAATAAAAAT
1 AAA-AAATAAAA-AAAAAT
29781762 ATTTATTATT
Statistics
Matches: 60, Mismatches: 4, Indels: 11
0.80 0.05 0.15
Matches are distributed among these distances:
50 25 0.42
51 18 0.30
52 14 0.23
53 3 0.05
ACGTcount: A:0.68, C:0.00, G:0.03, T:0.29
Consensus pattern (48 bp):
AAAAAATAAAAAAAAATTTAAAATTAAAAAAATTAAAAAAAGTATTTA
Found at i:29784746 original size:7 final size:7
Alignment explanation
Indices: 29784734--29784760 Score: 54
Period size: 7 Copynumber: 3.9 Consensus size: 7
29784724 ATGTTAAAAA
29784734 AAAGAAC
1 AAAGAAC
29784741 AAAGAAC
1 AAAGAAC
29784748 AAAGAAC
1 AAAGAAC
29784755 AAAGAA
1 AAAGAA
29784761 AAGTTTGTTC
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 20 1.00
ACGTcount: A:0.74, C:0.11, G:0.15, T:0.00
Consensus pattern (7 bp):
AAAGAAC
Found at i:29788727 original size:43 final size:44
Alignment explanation
Indices: 29788661--29788745 Score: 136
Period size: 43 Copynumber: 2.0 Consensus size: 44
29788651 CATGGCCTGG
*
29788661 TACAAGGGCATGTGGCTTAGCCGTGTGACCCAACTTC-AAAAGT
1 TACAAGGGCACGTGGCTTAGCCGTGTGACCCAACTTCGAAAAGT
* *
29788704 TACATGGGCACGTGGCTTGGCCGTGTGACCCAACTTCGAAAA
1 TACAAGGGCACGTGGCTTAGCCGTGTGACCCAACTTCGAAAA
29788746 TTGCATTGGC
Statistics
Matches: 38, Mismatches: 3, Indels: 1
0.90 0.07 0.02
Matches are distributed among these distances:
43 34 0.89
44 4 0.11
ACGTcount: A:0.26, C:0.25, G:0.27, T:0.22
Consensus pattern (44 bp):
TACAAGGGCACGTGGCTTAGCCGTGTGACCCAACTTCGAAAAGT
Found at i:29793206 original size:51 final size:50
Alignment explanation
Indices: 29793077--29793210 Score: 171
Period size: 50 Copynumber: 2.7 Consensus size: 50
29793067 AAAGTGATGG
* * * *
29793077 TCACGTGTGTAGTACTATGTGCAGGCTACTACGTGTACCAGAATGATAGG
1 TCACATGTGTAGTACTATGTGCAGGCTACTATGCGTACCAGAATGATAGA
* * *
29793127 TCGCATGTGTAGTACTATGTGCAGGCTACTATGCGTACCA-AATAGCTTCGA
1 TCACATGTGTAGTACTATGTGCAGGCTACTATGCGTACCAGAAT-G-ATAGA
*
29793178 TCACATGTGTAGTACTATGTGTAGGCTACTATG
1 TCACATGTGTAGTACTATGTGCAGGCTACTATG
29793211 TGAACCGATG
Statistics
Matches: 73, Mismatches: 9, Indels: 3
0.86 0.11 0.04
Matches are distributed among these distances:
49 3 0.04
50 37 0.51
51 33 0.45
ACGTcount: A:0.25, C:0.19, G:0.25, T:0.31
Consensus pattern (50 bp):
TCACATGTGTAGTACTATGTGCAGGCTACTATGCGTACCAGAATGATAGA
Found at i:29795631 original size:25 final size:25
Alignment explanation
Indices: 29795602--29795652 Score: 102
Period size: 25 Copynumber: 2.0 Consensus size: 25
29795592 TTGAGCTGTA
29795602 TCCTCAGCATGAAGAAAATAGTATC
1 TCCTCAGCATGAAGAAAATAGTATC
29795627 TCCTCAGCATGAAGAAAATAGTATC
1 TCCTCAGCATGAAGAAAATAGTATC
29795652 T
1 T
29795653 TGATATGTTA
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
25 26 1.00
ACGTcount: A:0.39, C:0.20, G:0.16, T:0.25
Consensus pattern (25 bp):
TCCTCAGCATGAAGAAAATAGTATC
Found at i:29799225 original size:101 final size:102
Alignment explanation
Indices: 29799102--29799294 Score: 273
Period size: 101 Copynumber: 1.9 Consensus size: 102
29799092 AAAGTGATGG
* * * *
29799102 TCACGTGTGTAGTACTATGTGCAGGCTACTACGTGTACCAGA-A-TGATAGGTCGCATGTGTAGT
1 TCACGTGTGTAGTACTATGTGCAGGCTAATACATGTACCAGATAGTGAT-GGTCACATCTGTAGT
* * *
29799165 ACTCTGTGCAGGCTACTATGTGTACCGGATAGCTTTGA
65 ACTATATGCAGGCTACTATGTGAACCGGATAGCTTTGA
* *
29799203 TCACGTGTGTAGTACTATGTGCAGGCTAATACATGTATCGGATAGTGATGGTCACATCTGTAGTA
1 TCACGTGTGTAGTACTATGTGCAGGCTAATACATGTACCAGATAGTGATGGTCACATCTGTAGTA
*
29799268 TTATATGCAGGCTACTATGTGAACCGG
66 CTATATGCAGGCTACTATGTGAACCGG
29799295 TGTCATTAAT
Statistics
Matches: 80, Mismatches: 10, Indels: 3
0.86 0.11 0.03
Matches are distributed among these distances:
101 38 0.47
102 38 0.47
103 4 0.05
ACGTcount: A:0.24, C:0.18, G:0.27, T:0.31
Consensus pattern (102 bp):
TCACGTGTGTAGTACTATGTGCAGGCTAATACATGTACCAGATAGTGATGGTCACATCTGTAGTA
CTATATGCAGGCTACTATGTGAACCGGATAGCTTTGA
Found at i:29799229 original size:51 final size:50
Alignment explanation
Indices: 29799099--29799294 Score: 196
Period size: 51 Copynumber: 3.9 Consensus size: 50
29799089 GTGAAAGTGA
* * *
29799099 TGGTCACGTGTGTAGTACTATGTGCAGGCTACTACGTGTACCAGA-ATGAT
1 TGGTCACATGTGTAGTACTATGTGCAGGCTACTACGTGTACCGGATA-GTT
* * * *
29799149 AGGTCGCATGTGTAGTACTCTGTGCAGGCTACTATGTGTACCGGATAGCTT
1 TGGTCACATGTGTAGTACTATGTGCAGGCTACTACGTGTACCGGATAG-TT
* * * * * *
29799200 TGATCACGTGTGTAGTACTATGTGCAGGCTAATACATGTATCGGATAGTGA
1 TGGTCACATGTGTAGTACTATGTGCAGGCTACTACGTGTACCGGATAGT-T
* * * * *
29799251 TGGTCACATCTGTAGTATTATATGCAGGCTACTATGTGAACCGG
1 TGGTCACATGTGTAGTACTATGTGCAGGCTACTACGTGTACCGG
29799295 TGTCATTAAT
Statistics
Matches: 116, Mismatches: 27, Indels: 5
0.78 0.18 0.03
Matches are distributed among these distances:
50 41 0.35
51 75 0.65
ACGTcount: A:0.24, C:0.17, G:0.28, T:0.31
Consensus pattern (50 bp):
TGGTCACATGTGTAGTACTATGTGCAGGCTACTACGTGTACCGGATAGTT
Found at i:29805517 original size:42 final size:42
Alignment explanation
Indices: 29805450--29805537 Score: 122
Period size: 42 Copynumber: 2.1 Consensus size: 42
29805440 CTTAACACAC
* * *
29805450 GGCCTGACACATGGGCATGTAAGGCAATTTCGAGAGTTACAT
1 GGCCCGACACATGGGCATGTAAGGCAATTTCAAGAGTTAAAT
** *
29805492 GGCCCGACACATGGGTGTGTGAGGCAATTTCAAGAGTTAAAT
1 GGCCCGACACATGGGCATGTAAGGCAATTTCAAGAGTTAAAT
29805534 GGCC
1 GGCC
29805538 TAGCACACAG
Statistics
Matches: 40, Mismatches: 6, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
42 40 1.00
ACGTcount: A:0.27, C:0.19, G:0.31, T:0.23
Consensus pattern (42 bp):
GGCCCGACACATGGGCATGTAAGGCAATTTCAAGAGTTAAAT
Found at i:29811743 original size:7 final size:8
Alignment explanation
Indices: 29811726--29811757 Score: 57
Period size: 8 Copynumber: 4.1 Consensus size: 8
29811716 AGTGAGATGC
29811726 ATTGAAAA
1 ATTGAAAA
29811734 ATTG-AAA
1 ATTGAAAA
29811741 ATTGAAAA
1 ATTGAAAA
29811749 ATTGAAAA
1 ATTGAAAA
29811757 A
1 A
29811758 AAATTCATGA
Statistics
Matches: 23, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
7 7 0.30
8 16 0.70
ACGTcount: A:0.62, C:0.00, G:0.12, T:0.25
Consensus pattern (8 bp):
ATTGAAAA
Found at i:29811746 original size:15 final size:15
Alignment explanation
Indices: 29811726--29811756 Score: 62
Period size: 15 Copynumber: 2.1 Consensus size: 15
29811716 AGTGAGATGC
29811726 ATTGAAAAATTGAAA
1 ATTGAAAAATTGAAA
29811741 ATTGAAAAATTGAAA
1 ATTGAAAAATTGAAA
29811756 A
1 A
29811757 AAAATTCATG
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 16 1.00
ACGTcount: A:0.61, C:0.00, G:0.13, T:0.26
Consensus pattern (15 bp):
ATTGAAAAATTGAAA
Found at i:29811784 original size:26 final size:26
Alignment explanation
Indices: 29811704--29811840 Score: 151
Period size: 26 Copynumber: 5.4 Consensus size: 26
29811694 TGAGACAGCA
29811704 AAAAAATTCATGAGTGAGATGCATTG
1 AAAAAATTCATGAGTGAGATGCATTG
* ** * **
29811730 -AAAAATTGAAAATTGA-A-AAATTG
1 AAAAAATTCATGAGTGAGATGCATTG
29811753 AAAAAAAATTCATGAGTGAGATGCATTG
1 --AAAAAATTCATGAGTGAGATGCATTG
29811781 AAAAAATTCATGAGTGAGATGCATTG
1 AAAAAATTCATGAGTGAGATGCATTG
*
29811807 -AAAAATTCATGAGTGAGATGCA--A
1 AAAAAATTCATGAGTGAGATGCATTG
29811830 AAAAAATTCAT
1 AAAAAATTCAT
29811841 TATGTTCTCG
Statistics
Matches: 92, Mismatches: 13, Indels: 14
0.77 0.11 0.12
Matches are distributed among these distances:
23 4 0.04
24 11 0.12
25 34 0.37
26 38 0.41
27 1 0.01
28 4 0.04
ACGTcount: A:0.49, C:0.07, G:0.19, T:0.26
Consensus pattern (26 bp):
AAAAAATTCATGAGTGAGATGCATTG
Found at i:29811811 original size:51 final size:50
Alignment explanation
Indices: 29811704--29811840 Score: 147
Period size: 51 Copynumber: 2.7 Consensus size: 50
29811694 TGAGACAGCA
* * *
29811704 AAAAAATTCATGAGTGAGATGCATTG-AAAAATTGAAAATTGAAAAATTG
1 AAAAAATTCATGAGTGAGATGCATTGAAAAAATTCATAAGTGAAAAATTG
* **
29811753 AAAAAAAATTCATGAGTGAGATGCATTGAAAAAATTCATGAGTGAGATGCATTG
1 --AAAAAATTCATGAGTGAGATGCATTGAAAAAATTCATAAGTGA-A-AAATTG
*
29811807 -AAAAATTCATGAGTGAGATGCA--AAAAAAATTCAT
1 AAAAAATTCATGAGTGAGATGCATTGAAAAAATTCAT
29811841 TATGTTCTCG
Statistics
Matches: 76, Mismatches: 7, Indels: 8
0.84 0.08 0.09
Matches are distributed among these distances:
49 11 0.14
51 48 0.63
52 12 0.16
53 1 0.01
54 4 0.05
ACGTcount: A:0.49, C:0.07, G:0.19, T:0.26
Consensus pattern (50 bp):
AAAAAATTCATGAGTGAGATGCATTGAAAAAATTCATAAGTGAAAAATTG
Found at i:29821656 original size:29 final size:29
Alignment explanation
Indices: 29821623--29821685 Score: 99
Period size: 29 Copynumber: 2.2 Consensus size: 29
29821613 TGCACTGTGA
* * *
29821623 TACTTAGTCTGACATTGAACTATGCTTTC
1 TACTTAGGCTAACATTAAACTATGCTTTC
29821652 TACTTAGGCTAACATTAAACTATGCTTTC
1 TACTTAGGCTAACATTAAACTATGCTTTC
29821681 TACTT
1 TACTT
29821686 GTGGAACAAT
Statistics
Matches: 31, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
29 31 1.00
ACGTcount: A:0.27, C:0.21, G:0.11, T:0.41
Consensus pattern (29 bp):
TACTTAGGCTAACATTAAACTATGCTTTC
Found at i:29843575 original size:23 final size:23
Alignment explanation
Indices: 29843549--29843593 Score: 72
Period size: 23 Copynumber: 2.0 Consensus size: 23
29843539 GTTCAAAATT
*
29843549 TTAAAATAAACAATATATATGAG
1 TTAAAACAAACAATATATATGAG
*
29843572 TTAAAACAAATAATATATATGA
1 TTAAAACAAACAATATATATGA
29843594 ATGTACAATT
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
23 20 1.00
ACGTcount: A:0.58, C:0.04, G:0.07, T:0.31
Consensus pattern (23 bp):
TTAAAACAAACAATATATATGAG
Found at i:29843682 original size:24 final size:24
Alignment explanation
Indices: 29843642--29843893 Score: 163
Period size: 24 Copynumber: 10.8 Consensus size: 24
29843632 TGAATTGGAT
* *
29843642 AATTTACAATAACTAATATATAATA
1 AATTTAAAATAA-TAATATATGATA
* *
29843667 AATTTGAAATAATAATACAT-ATAA
1 AATTTAAAATAATAATATATGAT-A
*
29843691 AATTT-AAA-AAT--TTTGATGAT-
1 AATTTAAAATAATAATAT-ATGATA
*
29843711 AATTCTAAAATAATCATACT-TGATA
1 AATT-TAAAATAATAATA-TATGATA
** * *
29843736 AATCCAAAATAATAGTATATAATA
1 AATTTAAAATAATAATATATGATA
*
29843760 AATTT-AAA-AATATTA-ATGATA
1 AATTTAAAATAATAATATATGATA
* *
29843781 AATTTGAAATAGAT-ATACATGATA
1 AATTTAAAATA-ATAATATATGATA
** **
29843805 AATTTAAAATAATGTTA-ACAATA
1 AATTTAAAATAATAATATATGATA
29843828 AATTTAAAATAATAATAT-TGATA
1 AATTTAAAATAATAATATATGATA
* *
29843851 AA-TTACAAATAATAAAACATGATA
1 AATTTA-AAATAATAATATATGATA
*
29843875 AATCTAAAATAATAATATA
1 AATTTAAAATAATAATATA
29843894 CAATACACTT
Statistics
Matches: 178, Mismatches: 29, Indels: 41
0.72 0.12 0.17
Matches are distributed among these distances:
20 5 0.03
21 13 0.07
22 20 0.11
23 51 0.29
24 72 0.40
25 16 0.09
26 1 0.01
ACGTcount: A:0.56, C:0.05, G:0.05, T:0.35
Consensus pattern (24 bp):
AATTTAAAATAATAATATATGATA
Found at i:29843737 original size:69 final size:69
Alignment explanation
Indices: 29843664--29843891 Score: 207
Period size: 69 Copynumber: 3.3 Consensus size: 69
29843654 CTAATATATA
* * *
29843664 ATAAATTTGAAATAATAATACAT-ATAAAATTTAAAAATTTTGATGAT-AATTCTAAAATA-ATC
1 ATAAATTTAAAATAATAATACATAAT-AAATTTAAAAATATTAATGATAAATT-TAAAATAGAT-
*
29843726 ATACTTG
63 ATACATG
** * * *
29843733 ATAAATCCAAAATAATAGTATATAATAAATTTAAAAATATTAATGATAAATTTGAAATAGATATA
1 ATAAATTTAAAATAATAATACATAATAAATTTAAAAATATTAATGATAAATTTAAAATAGATATA
29843798 CATG
66 CATG
** * * *
29843802 ATAAATTTAAAATAATGTTA-ACAATAAATTTAAAATAATAATATTGATAAA-TTACAAATA-AT
1 ATAAATTTAAAATAATAATACATAATAAATTT-AAA-AATATTAATGATAAATTTA-AAATAGAT
*
29843864 AAAACATG
63 -ATACATG
*
29843872 ATAAATCTAAAATAATAATA
1 ATAAATTTAAAATAATAATA
29843892 TACAATACAC
Statistics
Matches: 131, Mismatches: 21, Indels: 13
0.79 0.13 0.08
Matches are distributed among these distances:
68 10 0.08
69 72 0.55
70 49 0.37
ACGTcount: A:0.56, C:0.05, G:0.05, T:0.34
Consensus pattern (69 bp):
ATAAATTTAAAATAATAATACATAATAAATTTAAAAATATTAATGATAAATTTAAAATAGATATA
CATG
Found at i:29843876 original size:47 final size:48
Alignment explanation
Indices: 29843642--29843892 Score: 131
Period size: 45 Copynumber: 5.4 Consensus size: 48
29843632 TGAATTGGAT
* * * *
29843642 AATTTACAATAACTAATATATAATAAATTTGAAATAAT-AATACAT-ATAA
1 AATTTAAAATAA-TAATAT-TGATAAATTTAAAATAATGAAAACATGAT-A
* * *
29843691 AATTT-AAA-AAT--T-TTGATGATAATTCTAAAATAAT-CATACTTGATA
1 AATTTAAAATAATAATATTGAT-A-AATT-TAAAATAATGAAAACATGATA
** * * **
29843736 AATCCAAAATAATAGTATATAATAAATTT-AAA-AAT-ATTA-ATGATA
1 AATTTAAAATAATAATAT-TGATAAATTTAAAATAATGAAAACATGATA
* * **
29843781 AATTTGAAATAGAT-ATACATGATAAATTTAAAATAATGTTAACA--ATA
1 AATTTAAAATA-ATAATA-TTGATAAATTTAAAATAATGAAAACATGATA
29843828 AATTTAAAATAATAATATTGATAAA-TTACAAATAAT-AAAACATGATA
1 AATTTAAAATAATAATATTGATAAATTTA-AAATAATGAAAACATGATA
*
29843875 AATCTAAAATAATAATAT
1 AATTTAAAATAATAATAT
29843893 ACAATACACT
Statistics
Matches: 158, Mismatches: 24, Indels: 42
0.71 0.11 0.19
Matches are distributed among these distances:
42 3 0.02
43 2 0.01
44 5 0.03
45 48 0.30
46 32 0.20
47 47 0.30
48 5 0.03
49 11 0.07
50 2 0.01
51 3 0.02
ACGTcount: A:0.55, C:0.05, G:0.05, T:0.35
Consensus pattern (48 bp):
AATTTAAAATAATAATATTGATAAATTTAAAATAATGAAAACATGATA
Found at i:29843910 original size:70 final size:69
Alignment explanation
Indices: 29843731--29843898 Score: 187
Period size: 70 Copynumber: 2.4 Consensus size: 69
29843721 TAATCATACT
* * * * * **
29843731 TGATAAATCCAAAATAATAGTATATAATAAATTTAAAAATATTAATGATAAATTTGAAATAGATA
1 TGATAAATCTAAAATAATAATATACAATAAATTTAATAATAATAATGATAAATTACAAATAGATA
*
29843796 TACA
66 AACA
* ** *
29843800 TGATAAATTTAAAATAATGTTA-ACAATAAATTTAAAATAATAATATTGATAAATTACAAATA-A
1 TGATAAATCTAAAATAATAATATACAATAAATTT--AATAATAATAATGATAAATTACAAATAGA
29843863 TAAAACA
64 T-AAACA
29843870 TGATAAATCTAAAATAATAATATACAATA
1 TGATAAATCTAAAATAATAATATACAATA
29843899 CACTTAGATA
Statistics
Matches: 81, Mismatches: 14, Indels: 6
0.80 0.14 0.06
Matches are distributed among these distances:
68 10 0.12
69 20 0.25
70 45 0.56
71 6 0.07
ACGTcount: A:0.57, C:0.05, G:0.05, T:0.33
Consensus pattern (69 bp):
TGATAAATCTAAAATAATAATATACAATAAATTTAATAATAATAATGATAAATTACAAATAGATA
AACA
Found at i:29844754 original size:23 final size:22
Alignment explanation
Indices: 29844727--29844771 Score: 63
Period size: 22 Copynumber: 2.0 Consensus size: 22
29844717 AATTTAAATC
29844727 TCTAAGATTACAAAATCTTATCT
1 TCTAAGATTAC-AAATCTTATCT
* *
29844750 TCTAAGATTGCATATCTTATCT
1 TCTAAGATTACAAATCTTATCT
29844772 AAGATTGCAT
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
22 10 0.50
23 10 0.50
ACGTcount: A:0.33, C:0.18, G:0.07, T:0.42
Consensus pattern (22 bp):
TCTAAGATTACAAATCTTATCT
Found at i:29844774 original size:19 final size:19
Alignment explanation
Indices: 29844750--29844804 Score: 101
Period size: 19 Copynumber: 2.9 Consensus size: 19
29844740 AATCTTATCT
*
29844750 TCTAAGATTGCATATCTTA
1 TCTAAGATTGCATATCCTA
29844769 TCTAAGATTGCATATCCTA
1 TCTAAGATTGCATATCCTA
29844788 TCTAAGATTGCATATCC
1 TCTAAGATTGCATATCC
29844805 GTTTTCAAGT
Statistics
Matches: 35, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
19 35 1.00
ACGTcount: A:0.31, C:0.20, G:0.11, T:0.38
Consensus pattern (19 bp):
TCTAAGATTGCATATCCTA
Found at i:29845212 original size:51 final size:50
Alignment explanation
Indices: 29845122--29845248 Score: 130
Period size: 51 Copynumber: 2.5 Consensus size: 50
29845112 CAATGAGATG
* * *
29845122 AGATTCGTTGCCTTCAACTTTAATCTGCTCTGCTACAACGCCAGGGAAATA
1 AGATTCGCTGCCTTCAGCTTTAATCTGCTCT-CTACAACGCCAAGGAAATA
* * *
29845173 AGATTCGCTGCCTTCAGCTTTAATCTG-TTTCATTGCAACGCCAAGGAGATA
1 AGATTCGCTGCCTTCAGCTTTAATCTGCTCTC--TACAACGCCAAGGAAATA
* * **
29845224 GGATTTGCTGTATTCAGCTTTAATC
1 AGATTCGCTGCCTTCAGCTTTAATC
29845249 CACTCCACTT
Statistics
Matches: 64, Mismatches: 10, Indels: 4
0.82 0.13 0.05
Matches are distributed among these distances:
49 1 0.02
50 2 0.03
51 61 0.95
ACGTcount: A:0.25, C:0.23, G:0.19, T:0.33
Consensus pattern (50 bp):
AGATTCGCTGCCTTCAGCTTTAATCTGCTCTCTACAACGCCAAGGAAATA
Found at i:29845262 original size:21 final size:21
Alignment explanation
Indices: 29845236--29845278 Score: 68
Period size: 21 Copynumber: 2.0 Consensus size: 21
29845226 ATTTGCTGTA
*
29845236 TTCAGCTTTAATCCACTCCAC
1 TTCAGCTTTAACCCACTCCAC
*
29845257 TTCAGCTTTAACCCATTCCAC
1 TTCAGCTTTAACCCACTCCAC
29845278 T
1 T
29845279 GCAACACTAG
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
21 20 1.00
ACGTcount: A:0.23, C:0.37, G:0.05, T:0.35
Consensus pattern (21 bp):
TTCAGCTTTAACCCACTCCAC
Found at i:29845365 original size:123 final size:123
Alignment explanation
Indices: 29845164--29845386 Score: 284
Period size: 123 Copynumber: 1.8 Consensus size: 123
29845154 CTACAACGCC
* * * * * *
29845164 AGGGAAATAAGATTCGCTGCCTTCAGCTTTAATCTGTTTCATTGCAACGCCAAGGAGATAGGATT
1 AGGGAAACAAGATTCGCTACCTTCAGCTTTAATCTGTTCCACTACAACGCCAAAGAGATAGGATT
* * ** *
29845229 TGCTGTATTCAGCTTTAATCCACTCCACTTCAGCTTTAACCCATTCCACTGCAACACT
66 CGCTGCACACAGCTTTAATCCACTCCACCTCAGCTTTAACCCATTCCACTGCAACACT
* * * * *
29845287 AGGGAAACAAGATTCGCTACCTTTATCTTTAATTTGTTCCACTATAATGCCAAAGAGATAGGATT
1 AGGGAAACAAGATTCGCTACCTTCAGCTTTAATCTGTTCCACTACAACGCCAAAGAGATAGGATT
* *
29845352 CGCTGCCCACAGCTTTAATCCGCTCCACCTCAGCT
66 CGCTGCACACAGCTTTAATCCACTCCACCTCAGCT
29845387 ATTCCAAGTC
Statistics
Matches: 82, Mismatches: 18, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
123 82 1.00
ACGTcount: A:0.27, C:0.26, G:0.16, T:0.30
Consensus pattern (123 bp):
AGGGAAACAAGATTCGCTACCTTCAGCTTTAATCTGTTCCACTACAACGCCAAAGAGATAGGATT
CGCTGCACACAGCTTTAATCCACTCCACCTCAGCTTTAACCCATTCCACTGCAACACT
Found at i:29845648 original size:46 final size:46
Alignment explanation
Indices: 29845528--29845760 Score: 286
Period size: 46 Copynumber: 5.0 Consensus size: 46
29845518 ATTCACTGCT
* * * * *
29845528 ATCTACTATGACGCCAGGGAAATAAAATTCGCTGCCCTCAGCTTCA
1 ATCTACTACGACGCCATGGAAATGAGATTCGCTGCCCTCAGCTTTA
* * * * **
29845574 ATTTATTCTACTGCAATGCCAAGGAAATGAGATTCACAACCCTCAGCTTTA
1 ATCTA--CTAC-G--ACGCCATGGAAATGAGATTCGCTGCCCTCAGCTTTA
*
29845625 ATCTACTACGACGTCATGGAAATGAGATTCGCTGCCCTCAGCTTTA
1 ATCTACTACGACGCCATGGAAATGAGATTCGCTGCCCTCAGCTTTA
*
29845671 ATCTACTACGACGCCATGGAAATGAGACTCGCTGCCCTCAGCTTTA
1 ATCTACTACGACGCCATGGAAATGAGATTCGCTGCCCTCAGCTTTA
* *
29845717 ATCTACTATGACGCCATGGAAATGAGATTCGCTGCCCACAGCTT
1 ATCTACTACGACGCCATGGAAATGAGATTCGCTGCCCTCAGCTT
29845761 CAATTTATTC
Statistics
Matches: 160, Mismatches: 22, Indels: 10
0.83 0.11 0.05
Matches are distributed among these distances:
46 119 0.74
48 4 0.03
49 5 0.03
51 32 0.20
ACGTcount: A:0.29, C:0.27, G:0.18, T:0.26
Consensus pattern (46 bp):
ATCTACTACGACGCCATGGAAATGAGATTCGCTGCCCTCAGCTTTA
Found at i:29845720 original size:92 final size:95
Alignment explanation
Indices: 29845528--29845792 Score: 311
Period size: 92 Copynumber: 2.8 Consensus size: 95
29845518 ATTCACTGCT
* * * * *
29845528 ATCTACTATGACGCCAGGGAAATAAAATTCGCTGCCCTCAGCTTCAATTTATTCTACTGCAATGC
1 ATCTACTATGACGCCATGGAAATGAGATTCGCTGCCCTCAGCTTCAATCTA-TCTACTG-AACGC
*
29845593 CAAGGAAATGAGATTCACAACCCTCAGCTTTA
64 CAAGGAAATGAGACTCACAACCCTCAGCTTTA
* * *
29845625 ATCTACTACGACGTCATGGAAATGAGATTCGCTGCCCTCAGCTTTAATCTA-CTAC-G-ACGCCA
1 ATCTACTATGACGCCATGGAAATGAGATTCGCTGCCCTCAGCTTCAATCTATCTACTGAACGCCA
* * **
29845687 TGGAAATGAGACTCGCTGCCCTCAGCTTTA
66 AGGAAATGAGACTCACAACCCTCAGCTTTA
* * * * *
29845717 ATCTACTATGACGCCATGGAAATGAGATTCGCTGCCCACAGCTTCAATTTATTCCACTACAATGC
1 ATCTACTATGACGCCATGGAAATGAGATTCGCTGCCCTCAGCTTCAATCTA-TCTACT-GAACGC
29845782 CAAGGAAATGA
64 CAAGGAAATGA
29845793 TATTGGTGTC
Statistics
Matches: 141, Mismatches: 22, Indels: 10
0.82 0.13 0.06
Matches are distributed among these distances:
92 76 0.54
94 4 0.03
95 4 0.03
97 57 0.40
ACGTcount: A:0.30, C:0.26, G:0.17, T:0.26
Consensus pattern (95 bp):
ATCTACTATGACGCCATGGAAATGAGATTCGCTGCCCTCAGCTTCAATCTATCTACTGAACGCCA
AGGAAATGAGACTCACAACCCTCAGCTTTA
Found at i:29846603 original size:12 final size:12
Alignment explanation
Indices: 29846586--29846610 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
29846576 TGACAACAAA
29846586 ATCTGAAGGGAT
1 ATCTGAAGGGAT
29846598 ATCTGAAGGGAT
1 ATCTGAAGGGAT
29846610 A
1 A
29846611 GTCTCAATTT
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:0.08, G:0.32, T:0.24
Consensus pattern (12 bp):
ATCTGAAGGGAT
Found at i:29848135 original size:16 final size:17
Alignment explanation
Indices: 29848110--29848147 Score: 60
Period size: 16 Copynumber: 2.3 Consensus size: 17
29848100 TGGCCTCTCC
*
29848110 TTTTCCTTTTCTTTT-T
1 TTTTCATTTTCTTTTCT
29848126 TTTTCATTTTCTTTTCT
1 TTTTCATTTTCTTTTCT
29848143 TTTTC
1 TTTTC
29848148 CATCATTTTC
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
16 14 0.70
17 6 0.30
ACGTcount: A:0.03, C:0.18, G:0.00, T:0.79
Consensus pattern (17 bp):
TTTTCATTTTCTTTTCT
Found at i:29848146 original size:11 final size:11
Alignment explanation
Indices: 29848109--29848147 Score: 53
Period size: 11 Copynumber: 3.6 Consensus size: 11
29848099 TTGGCCTCTC
*
29848109 CTTTTCCTTTT
1 CTTTTTCTTTT
29848120 CTTTTT-TTTT
1 CTTTTTCTTTT
*
29848130 CATTTTCTTTT
1 CTTTTTCTTTT
29848141 CTTTTTC
1 CTTTTTC
29848148 CATCATTTTC
Statistics
Matches: 24, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
10 9 0.38
11 15 0.62
ACGTcount: A:0.03, C:0.21, G:0.00, T:0.77
Consensus pattern (11 bp):
CTTTTTCTTTT
Found at i:29848153 original size:21 final size:21
Alignment explanation
Indices: 29848110--29848163 Score: 63
Period size: 21 Copynumber: 2.5 Consensus size: 21
29848100 TGGCCTCTCC
***
29848110 TTTTCCTTTTCTTTTTTTTTCA
1 TTTT-CTTTTCTTTTTCCATCA
29848132 TTTTCTTTTCTTTTTCCATCA
1 TTTTCTTTTCTTTTTCCATCA
29848153 TTTTCATTTTC
1 TTTTC-TTTTC
29848164 ATATTTTTGA
Statistics
Matches: 28, Mismatches: 3, Indels: 2
0.85 0.09 0.06
Matches are distributed among these distances:
21 19 0.68
22 9 0.32
ACGTcount: A:0.07, C:0.20, G:0.00, T:0.72
Consensus pattern (21 bp):
TTTTCTTTTCTTTTTCCATCA
Found at i:29850323 original size:19 final size:19
Alignment explanation
Indices: 29850278--29850325 Score: 53
Period size: 19 Copynumber: 2.5 Consensus size: 19
29850268 TTAATGGATT
* *
29850278 TTAATGCATATGAAGTAAT
1 TTAATGCAAATGAAGTAAA
*
29850297 TTAGTGCAAATGAA-TGAAA
1 TTAATGCAAATGAAGT-AAA
29850316 TTAATGCAAA
1 TTAATGCAAA
29850326 AAGAAACGTT
Statistics
Matches: 24, Mismatches: 4, Indels: 2
0.80 0.13 0.07
Matches are distributed among these distances:
18 1 0.04
19 23 0.96
ACGTcount: A:0.46, C:0.06, G:0.17, T:0.31
Consensus pattern (19 bp):
TTAATGCAAATGAAGTAAA
Found at i:29850782 original size:16 final size:16
Alignment explanation
Indices: 29850757--29850791 Score: 52
Period size: 16 Copynumber: 2.2 Consensus size: 16
29850747 TTCTATGATG
*
29850757 AAATGCCATGCAGTCA
1 AAATGCCATGCAGCCA
*
29850773 AAATGTCATGCAGCCA
1 AAATGCCATGCAGCCA
29850789 AAA
1 AAA
29850792 CAAAACATAA
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:0.23, G:0.17, T:0.17
Consensus pattern (16 bp):
AAATGCCATGCAGCCA
Found at i:29852293 original size:23 final size:23
Alignment explanation
Indices: 29852267--29852320 Score: 63
Period size: 23 Copynumber: 2.3 Consensus size: 23
29852257 GTTCAAAATT
*
29852267 TTAAAATAAACAATATATATGAG
1 TTAAAATAAACAATATATATGAA
* * *
29852290 TTAAAACAAATAATTTATATGAA
1 TTAAAATAAACAATATATATGAA
29852313 TGTAAAAT
1 T-TAAAAT
29852321 TTAATACAAA
Statistics
Matches: 25, Mismatches: 5, Indels: 1
0.81 0.16 0.03
Matches are distributed among these distances:
23 20 0.80
24 5 0.20
ACGTcount: A:0.56, C:0.04, G:0.07, T:0.33
Consensus pattern (23 bp):
TTAAAATAAACAATATATATGAA
Found at i:29852400 original size:24 final size:24
Alignment explanation
Indices: 29852360--29852608 Score: 139
Period size: 24 Copynumber: 10.7 Consensus size: 24
29852350 TGAATTGGAT
* *
29852360 AATTTACAATAACTAATATATAATA
1 AATTTAAAATAA-TAATATATGATA
* *
29852385 AATTTGAAATAATAATACAT-ATAA
1 AATTTAAAATAATAATATATGAT-A
*
29852409 AATTT-AAA-AAT--TTTGATGAT-
1 AATTTAAAATAATAATAT-ATGATA
*
29852429 AATTCTAAAATAATCATACT-TGATA
1 AATT-TAAAATAATAATA-TATGATA
** * *
29852454 AATCCAAAATAATAGTATATAATA
1 AATTTAAAATAATAATATATGATA
* *
29852478 AATTT-AAA-AATATTA-ATTATA
1 AATTTAAAATAATAATATATGATA
* *
29852499 AATTTGAAATAGAT-ATACATGATA
1 AATTTAAAATA-ATAATATATGATA
** **
29852523 AATTTAAAATAATGTTA-AAAATA
1 AATTTAAAATAATAATATATGATA
29852546 AATTTAAAATAATAATAT-TGATA
1 AATTTAAAATAATAATATATGATA
* * *
29852569 AATTACAAAAT-ATAAAACATGATA
1 AATT-TAAAATAATAATATATGATA
*
29852593 AATCTAAAATAATAAT
1 AATTTAAAATAATAAT
29852609 GTACAATACA
Statistics
Matches: 173, Mismatches: 31, Indels: 41
0.71 0.13 0.17
Matches are distributed among these distances:
20 5 0.03
21 13 0.08
22 17 0.10
23 53 0.31
24 70 0.40
25 14 0.08
26 1 0.01
ACGTcount: A:0.56, C:0.05, G:0.04, T:0.35
Consensus pattern (24 bp):
AATTTAAAATAATAATATATGATA
Found at i:29852455 original size:69 final size:69
Alignment explanation
Indices: 29852382--29852608 Score: 194
Period size: 69 Copynumber: 3.3 Consensus size: 69
29852372 CTAATATATA
* * *
29852382 ATAAATTTGAAATAATAATACAT-ATAAAATTTAAAAATTTTGATGAT-AATTCTAAAATA-ATC
1 ATAAATTTAAAATAATAATACATAAT-AAATTTAAAAATATTAATGATAAATT-TAAAATAGAT-
*
29852444 ATACTTG
63 ATACATG
** * * * *
29852451 ATAAATCCAAAATAATAGTATATAATAAATTTAAAAATATTAATTATAAATTTGAAATAGATATA
1 ATAAATTTAAAATAATAATACATAATAAATTTAAAAATATTAATGATAAATTTAAAATAGATATA
29852516 CATG
66 CATG
** * * * * *
29852520 ATAAATTTAAAATAATGTTA-AAAATAAATTTAAAATAATAATATTGATAAATTACAAAATATA-
1 ATAAATTTAAAATAATAATACATAATAAATTT-AAA-AATATTAATGATAAATT-TAAAATAGAT
*
29852583 AAACATG
63 ATACATG
*
29852590 ATAAATCTAAAATAATAAT
1 ATAAATTTAAAATAATAAT
29852609 GTACAATACA
Statistics
Matches: 127, Mismatches: 25, Indels: 11
0.78 0.15 0.07
Matches are distributed among these distances:
68 10 0.08
69 67 0.53
70 44 0.35
71 6 0.05
ACGTcount: A:0.56, C:0.04, G:0.05, T:0.35
Consensus pattern (69 bp):
ATAAATTTAAAATAATAATACATAATAAATTTAAAAATATTAATGATAAATTTAAAATAGATATA
CATG
Found at i:29852556 original size:47 final size:44
Alignment explanation
Indices: 29852459--29852608 Score: 124
Period size: 47 Copynumber: 3.2 Consensus size: 44
29852449 TGATAAATCC
* * **
29852459 AAAATAATAGTATATAATAAATTTAAAAATATTAATTATAAATTT
1 AAAATAATAATA-ATGATAAATTTAAAAATATTAAAAATAAATTT
* *
29852504 GAAATAGAT-ATACATGATAAATTTAAAATAATGTTAAAAATAAATTT
1 AAAATA-ATAATA-ATGATAAATTT-AAA-AATATTAAAAATAAATTT
* * *
29852551 AAAATAATAATATTGATAAA-TTACAAAATATAAAACATGATAAATCT
1 AAAATAATAATAATGATAAATTTA-AAAATATTAAA-A--ATAAATTT
29852598 AAAATAATAAT
1 AAAATAATAAT
29852609 GTACAATACA
Statistics
Matches: 85, Mismatches: 12, Indels: 14
0.77 0.11 0.13
Matches are distributed among these distances:
44 8 0.09
45 22 0.26
46 14 0.16
47 41 0.48
ACGTcount: A:0.59, C:0.03, G:0.05, T:0.34
Consensus pattern (44 bp):
AAAATAATAATAATGATAAATTTAAAAATATTAAAAATAAATTT
Found at i:29853522 original size:19 final size:19
Alignment explanation
Indices: 29853470--29853516 Score: 78
Period size: 18 Copynumber: 2.5 Consensus size: 19
29853460 AATCTTATCT
*
29853470 TCTAAGATTGCATATCTTA
1 TCTAAGATTGCATATCCTA
29853489 TC-AAGATTGCATATCCTA
1 TCTAAGATTGCATATCCTA
29853507 TCTAAGATTG
1 TCTAAGATTG
29853517 TTTATCATTT
Statistics
Matches: 26, Mismatches: 1, Indels: 2
0.90 0.03 0.07
Matches are distributed among these distances:
18 17 0.65
19 9 0.35
ACGTcount: A:0.32, C:0.17, G:0.13, T:0.38
Consensus pattern (19 bp):
TCTAAGATTGCATATCCTA
Found at i:29863929 original size:272 final size:272
Alignment explanation
Indices: 29863443--29863995 Score: 1072
Period size: 272 Copynumber: 2.0 Consensus size: 272
29863433 ATAGTAGGGG
*
29863443 TTAAATTATAAAATCTCAAGATTTTGAGGAGAGAGAGAGAGACTATTTTGCAAATTGTGCAAATT
1 TTAAATTATAAAATCTCAAGATTTTGAAGAGAGAGAGAGAGACTATTTTGCAAATTGTGCAAATT
*
29863508 GAGATTTAAGATTGAATTGAAAATAAAAATATAGAAAATATGATTCCTAGGGATTGAATTGTAAA
66 GAGATTTAAGATTGAACTGAAAATAAAAATATAGAAAATATGATTCCTAGGGATTGAATTGTAAA
*
29863573 ATGTGTAAATTTTGGACTTCAACGACTAAATCATAAAAACTGCAAAACTAGAATTTTCGGGAATA
131 ATGTGTAAATTTTGGACTTCAACGACTAAATCATAAAAACTGCAAAACTAGAATTTTAGGGAATA
29863638 TTTTTTAAATTCTGTAATATTGAAAAATAGGGGTTGTTTAATGAATTTGCAAAAATATAGGAGTG
196 TTTTTTAAATTCTGTAATATTGAAAAATAGGGGTTGTTTAATGAATTTGCAAAAATATAGGAGTG
29863703 AAAATGAGCAAA
261 AAAATGAGCAAA
29863715 TTAAATTATAAAATCTCAAGATTTTGAAGAGAGAGAGAGAGACTATTTTGCAAATTGTGCAAATT
1 TTAAATTATAAAATCTCAAGATTTTGAAGAGAGAGAGAGAGACTATTTTGCAAATTGTGCAAATT
29863780 GAGATTTAAGATTGAACTGAAAATAAAAATATAGAAAATATGATTCCTAGGGATTGAATTGTAAA
66 GAGATTTAAGATTGAACTGAAAATAAAAATATAGAAAATATGATTCCTAGGGATTGAATTGTAAA
29863845 ATGTGTAAATTTTGGACTTCAACGACTAAATCATAAAAACTGCAAAACTAGAATTTTAGGGAATA
131 ATGTGTAAATTTTGGACTTCAACGACTAAATCATAAAAACTGCAAAACTAGAATTTTAGGGAATA
29863910 TTTTTTAAATTCTGTAATATTGAAAAATAGGGGTTGTTTAATGAATTTGCAAAAATATAGGAGTG
196 TTTTTTAAATTCTGTAATATTGAAAAATAGGGGTTGTTTAATGAATTTGCAAAAATATAGGAGTG
29863975 AAAATGAGCAAA
261 AAAATGAGCAAA
29863987 TT-AATTATA
1 TTAAATTATA
29863996 TAAGTGTTTA
Statistics
Matches: 278, Mismatches: 3, Indels: 1
0.99 0.01 0.00
Matches are distributed among these distances:
271 7 0.03
272 271 0.97
ACGTcount: A:0.43, C:0.07, G:0.18, T:0.32
Consensus pattern (272 bp):
TTAAATTATAAAATCTCAAGATTTTGAAGAGAGAGAGAGAGACTATTTTGCAAATTGTGCAAATT
GAGATTTAAGATTGAACTGAAAATAAAAATATAGAAAATATGATTCCTAGGGATTGAATTGTAAA
ATGTGTAAATTTTGGACTTCAACGACTAAATCATAAAAACTGCAAAACTAGAATTTTAGGGAATA
TTTTTTAAATTCTGTAATATTGAAAAATAGGGGTTGTTTAATGAATTTGCAAAAATATAGGAGTG
AAAATGAGCAAA
Found at i:29865787 original size:20 final size:19
Alignment explanation
Indices: 29865746--29865788 Score: 50
Period size: 20 Copynumber: 2.2 Consensus size: 19
29865736 GCTTTTATGC
*
29865746 GCCAGTATGCGCTTCGTTT
1 GCCAGTATGCGCTTCGTAT
* *
29865765 GCCAGGTATGCGTTTTGTAT
1 GCCA-GTATGCGCTTCGTAT
29865785 GCCA
1 GCCA
29865789 AGATGCACTT
Statistics
Matches: 20, Mismatches: 3, Indels: 1
0.83 0.12 0.04
Matches are distributed among these distances:
19 4 0.20
20 16 0.80
ACGTcount: A:0.14, C:0.23, G:0.28, T:0.35
Consensus pattern (19 bp):
GCCAGTATGCGCTTCGTAT
Found at i:29866999 original size:29 final size:29
Alignment explanation
Indices: 29866957--29867012 Score: 94
Period size: 29 Copynumber: 1.9 Consensus size: 29
29866947 AATGGCCTCT
29866957 TAGGGAGTGGCCTTGTTCCCAGAAGGCCC
1 TAGGGAGTGGCCTTGTTCCCAGAAGGCCC
**
29866986 TAGGGAGTGGCCTTGTTCTTAGAAGGC
1 TAGGGAGTGGCCTTGTTCCCAGAAGGC
29867013 TCGTGCCCCT
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:0.18, C:0.21, G:0.36, T:0.25
Consensus pattern (29 bp):
TAGGGAGTGGCCTTGTTCCCAGAAGGCCC
Found at i:29872484 original size:12 final size:12
Alignment explanation
Indices: 29872467--29872498 Score: 55
Period size: 12 Copynumber: 2.7 Consensus size: 12
29872457 AGTCTTAAAA
29872467 ACTCGGCCTCAT
1 ACTCGGCCTCAT
*
29872479 ACTCGGCCTTAT
1 ACTCGGCCTCAT
29872491 ACTCGGCC
1 ACTCGGCC
29872499 ACTGATCAAT
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
12 19 1.00
ACGTcount: A:0.16, C:0.41, G:0.19, T:0.25
Consensus pattern (12 bp):
ACTCGGCCTCAT
Found at i:29876156 original size:41 final size:41
Alignment explanation
Indices: 29876107--29876297 Score: 303
Period size: 41 Copynumber: 4.6 Consensus size: 41
29876097 GACTTTACGT
*
29876107 CTAGCAGGCTAAGTGCCGGTGATCTAAATCAGGCTATAAGC
1 CTAGCAGGCTAAGTGCCGGTGATCTGAATCAGGCTATAAGC
*
29876148 CTAACAGGCTAAGTGCCGGTGATCTGAATCAGGCTATAAGC
1 CTAGCAGGCTAAGTGCCGGTGATCTGAATCAGGCTATAAGC
29876189 CTAGCAGGCTAAGTGCCGGTGATCTGAATCAGGCTATAAGC
1 CTAGCAGGCTAAGTGCCGGTGATCTGAATCAGGCTATAAGC
* *
29876230 CTAGCAGGCTAAGTGCCGGTGAACTGAATTAGGCTATAAGC
1 CTAGCAGGCTAAGTGCCGGTGATCTGAATCAGGCTATAAGC
* *
29876271 TTAGCAGG-TGAAGTGCCAGTGAATCTG
1 CTAGCAGGCT-AAGTGCCGGTG-ATCTG
29876298 TTTAAATTAA
Statistics
Matches: 140, Mismatches: 8, Indels: 3
0.93 0.05 0.02
Matches are distributed among these distances:
40 1 0.01
41 135 0.96
42 4 0.03
ACGTcount: A:0.28, C:0.20, G:0.29, T:0.23
Consensus pattern (41 bp):
CTAGCAGGCTAAGTGCCGGTGATCTGAATCAGGCTATAAGC
Found at i:29884562 original size:28 final size:28
Alignment explanation
Indices: 29884531--29884587 Score: 80
Period size: 28 Copynumber: 2.0 Consensus size: 28
29884521 TCGATGAACA
* *
29884531 TTCCACATAAGATAGT-TTGTGGCAGACT
1 TTCCACATAAGACAATCTT-TGGCAGACT
29884559 TTCCACATAAGACAATCTTTGGCAGACT
1 TTCCACATAAGACAATCTTTGGCAGACT
29884587 T
1 T
29884588 CCTTTTTACT
Statistics
Matches: 26, Mismatches: 2, Indels: 2
0.87 0.07 0.07
Matches are distributed among these distances:
28 24 0.92
29 2 0.08
ACGTcount: A:0.30, C:0.21, G:0.18, T:0.32
Consensus pattern (28 bp):
TTCCACATAAGACAATCTTTGGCAGACT
Found at i:29887281 original size:35 final size:35
Alignment explanation
Indices: 29887222--29887347 Score: 112
Period size: 35 Copynumber: 3.6 Consensus size: 35
29887212 GTGCATCAAA
* *
29887222 AATCCAACC-AAACACACTAGATGCTCCAAAGAG-T
1 AATCCATCCGAAACACACCA-ATGCTCCAAAGAGCT
**
29887256 CAATCCATCCGAAACACACCAATGCTCGGAAGAGCT
1 -AATCCATCCGAAACACACCAATGCTCCAAAGAGCT
* * ***
29887292 AATCCCTCCGGAACACACCAATGCTTGTAAGAGCT
1 AATCCATCCGAAACACACCAATGCTCCAAAGAGCT
* * *
29887327 AATCCAACCAAAACATACCAA
1 AATCCATCCGAAACACACCAA
29887348 AATAGAGACT
Statistics
Matches: 76, Mismatches: 13, Indels: 4
0.82 0.14 0.04
Matches are distributed among these distances:
35 66 0.87
36 10 0.13
ACGTcount: A:0.40, C:0.32, G:0.13, T:0.15
Consensus pattern (35 bp):
AATCCATCCGAAACACACCAATGCTCCAAAGAGCT
Found at i:29887961 original size:31 final size:31
Alignment explanation
Indices: 29887923--29887984 Score: 124
Period size: 31 Copynumber: 2.0 Consensus size: 31
29887913 AAAAAGTCCT
29887923 TAATGAATGTTAAATTCACTATCAAACCCTA
1 TAATGAATGTTAAATTCACTATCAAACCCTA
29887954 TAATGAATGTTAAATTCACTATCAAACCCTA
1 TAATGAATGTTAAATTCACTATCAAACCCTA
29887985 ATATTTTGAC
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
31 31 1.00
ACGTcount: A:0.42, C:0.19, G:0.06, T:0.32
Consensus pattern (31 bp):
TAATGAATGTTAAATTCACTATCAAACCCTA
Found at i:29889346 original size:18 final size:18
Alignment explanation
Indices: 29889320--29889354 Score: 61
Period size: 18 Copynumber: 1.9 Consensus size: 18
29889310 TATCGATACC
29889320 TATCAATACCAAAAATGT
1 TATCAATACCAAAAATGT
*
29889338 TATCGATACCAAAAATG
1 TATCAATACCAAAAATG
29889355 CATTTTGGCT
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
18 16 1.00
ACGTcount: A:0.49, C:0.17, G:0.09, T:0.26
Consensus pattern (18 bp):
TATCAATACCAAAAATGT
Found at i:29890920 original size:19 final size:19
Alignment explanation
Indices: 29890896--29890935 Score: 53
Period size: 19 Copynumber: 2.1 Consensus size: 19
29890886 CATATATTAT
* *
29890896 TTTATTTTTTAATATATTC
1 TTTATTTATCAATATATTC
*
29890915 TTTATTTATCAATATTTTC
1 TTTATTTATCAATATATTC
29890934 TT
1 TT
29890936 GTAAACTATA
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
19 18 1.00
ACGTcount: A:0.25, C:0.07, G:0.00, T:0.68
Consensus pattern (19 bp):
TTTATTTATCAATATATTC
Found at i:29891216 original size:3 final size:3
Alignment explanation
Indices: 29891201--29891257 Score: 50
Period size: 3 Copynumber: 20.3 Consensus size: 3
29891191 AATAATTAGT
* *
29891201 TAA TAA TAG TAA TAA TAA TAA TAA TTA -AA T-A TAA T-A TAA T-A TAA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
* *
29891245 TAG TAT TAA TAA T
1 TAA TAA TAA TAA T
29891258 TAAGGCATTA
Statistics
Matches: 43, Mismatches: 7, Indels: 8
0.74 0.12 0.14
Matches are distributed among these distances:
2 7 0.16
3 36 0.84
ACGTcount: A:0.58, C:0.00, G:0.04, T:0.39
Consensus pattern (3 bp):
TAA
Found at i:29892533 original size:34 final size:34
Alignment explanation
Indices: 29892490--29892567 Score: 111
Period size: 34 Copynumber: 2.3 Consensus size: 34
29892480 GTTATTTATA
* *
29892490 TATAATATATATTTACGTTCATGGGTGTTATATC
1 TATAATATATATTTACGTGCATGGATGTTATATC
** *
29892524 TATAATATATATTTGGGTGCATGGATGTTATATG
1 TATAATATATATTTACGTGCATGGATGTTATATC
29892558 TATAATATAT
1 TATAATATAT
29892568 TTGACTGGGT
Statistics
Matches: 39, Mismatches: 5, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
34 39 1.00
ACGTcount: A:0.32, C:0.05, G:0.17, T:0.46
Consensus pattern (34 bp):
TATAATATATATTTACGTGCATGGATGTTATATC
Found at i:29899632 original size:50 final size:51
Alignment explanation
Indices: 29899556--29899728 Score: 224
Period size: 50 Copynumber: 3.3 Consensus size: 51
29899546 GGTGCCCATG
** *
29899556 CATGGTCTTACGGGGGACCTCC-CATCTCGGTGCCAACGCCATGTCCCAGA
1 CATGGTCTTACATGGGACCTCCTCATCTCGGTGCCAATGCCATGTCCCAGA
29899606 CATGGTCTTACATGGGACC-CCTCATCTCGGTGCCAATGCCATGTCCCAGA
1 CATGGTCTTACATGGGACCTCCTCATCTCGGTGCCAATGCCATGTCCCAGA
* * * *
29899656 CATGGTCTTACATTGGACCTCTCATAATCTCAATGATGCCAATGTCATGTCCCAGA
1 CATGGTCTTACATGGGACCTC-C-TCATCTC---GGTGCCAATGCCATGTCCCAGA
29899712 CATGGTCTTACATGGGA
1 CATGGTCTTACATGGGA
29899729 TCTCATCCTC
Statistics
Matches: 108, Mismatches: 8, Indels: 8
0.87 0.06 0.06
Matches are distributed among these distances:
49 2 0.02
50 62 0.57
51 1 0.01
52 1 0.01
53 6 0.06
56 36 0.33
ACGTcount: A:0.22, C:0.31, G:0.22, T:0.25
Consensus pattern (51 bp):
CATGGTCTTACATGGGACCTCCTCATCTCGGTGCCAATGCCATGTCCCAGA
Found at i:29902990 original size:43 final size:43
Alignment explanation
Indices: 29902929--29903014 Score: 163
Period size: 43 Copynumber: 2.0 Consensus size: 43
29902919 TCGAGTTTGG
29902929 GACGTCATAATTTCACTTATATTATTTCCAACACATATAATTT
1 GACGTCATAATTTCACTTATATTATTTCCAACACATATAATTT
*
29902972 GACGTCATAATTTCACTTATATTATTTCCACCACATATAATTT
1 GACGTCATAATTTCACTTATATTATTTCCAACACATATAATTT
29903015 TTAAGTCTTT
Statistics
Matches: 42, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
43 42 1.00
ACGTcount: A:0.34, C:0.20, G:0.05, T:0.42
Consensus pattern (43 bp):
GACGTCATAATTTCACTTATATTATTTCCAACACATATAATTT
Found at i:29903076 original size:41 final size:41
Alignment explanation
Indices: 29903030--29903111 Score: 164
Period size: 41 Copynumber: 2.0 Consensus size: 41
29903020 TCTTTCAATT
29903030 TAGTCCTTGTTTCTATAAAAATTTATATTTTTCATAGTTTC
1 TAGTCCTTGTTTCTATAAAAATTTATATTTTTCATAGTTTC
29903071 TAGTCCTTGTTTCTATAAAAATTTATATTTTTCATAGTTTC
1 TAGTCCTTGTTTCTATAAAAATTTATATTTTTCATAGTTTC
29903112 ACTTATTCAA
Statistics
Matches: 41, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
41 41 1.00
ACGTcount: A:0.27, C:0.12, G:0.07, T:0.54
Consensus pattern (41 bp):
TAGTCCTTGTTTCTATAAAAATTTATATTTTTCATAGTTTC
Found at i:29905268 original size:40 final size:40
Alignment explanation
Indices: 29905224--29905303 Score: 160
Period size: 40 Copynumber: 2.0 Consensus size: 40
29905214 CCAGAGAGAA
29905224 AGAAAACCTTTGTCTTTCAAAAAGAAAAATCTATTTGCCT
1 AGAAAACCTTTGTCTTTCAAAAAGAAAAATCTATTTGCCT
29905264 AGAAAACCTTTGTCTTTCAAAAAGAAAAATCTATTTGCCT
1 AGAAAACCTTTGTCTTTCAAAAAGAAAAATCTATTTGCCT
29905304 TTGAATTTCT
Statistics
Matches: 40, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
40 40 1.00
ACGTcount: A:0.40, C:0.17, G:0.10, T:0.33
Consensus pattern (40 bp):
AGAAAACCTTTGTCTTTCAAAAAGAAAAATCTATTTGCCT
Found at i:29905492 original size:14 final size:14
Alignment explanation
Indices: 29905473--29905499 Score: 54
Period size: 14 Copynumber: 1.9 Consensus size: 14
29905463 GTGGAAGCGC
29905473 GCGACGAGTGCGGA
1 GCGACGAGTGCGGA
29905487 GCGACGAGTGCGG
1 GCGACGAGTGCGG
29905500 CGTGTGGGCG
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:0.19, C:0.22, G:0.52, T:0.07
Consensus pattern (14 bp):
GCGACGAGTGCGGA
Found at i:29912885 original size:15 final size:15
Alignment explanation
Indices: 29912840--29912889 Score: 64
Period size: 15 Copynumber: 3.2 Consensus size: 15
29912830 GAGTCCTTAA
29912840 AAAAAATTTAAAATTT
1 AAAAAATTT-AAATTT
*
29912856 ATAATAATTTAAATTT
1 A-AAAAATTTAAATTT
*
29912872 AAAAAATCTAAATTT
1 AAAAAATTTAAATTT
29912887 AAA
1 AAA
29912890 CTCAAGATAA
Statistics
Matches: 30, Mismatches: 3, Indels: 3
0.83 0.08 0.08
Matches are distributed among these distances:
15 15 0.50
16 8 0.27
17 7 0.23
ACGTcount: A:0.60, C:0.02, G:0.00, T:0.38
Consensus pattern (15 bp):
AAAAAATTTAAATTT
Found at i:29916734 original size:14 final size:13
Alignment explanation
Indices: 29916691--29916730 Score: 53
Period size: 14 Copynumber: 2.9 Consensus size: 13
29916681 GAGAAAAAAA
*
29916691 AAGAGAGAAAGGAG
1 AAGA-AGAAAGAAG
29916705 AAGAAGAGAAGAAG
1 AAGAAGA-AAGAAG
29916719 AAGAAGAAAGAA
1 AAGAAGAAAGAA
29916731 AGAAAAAAGG
Statistics
Matches: 24, Mismatches: 1, Indels: 3
0.86 0.04 0.11
Matches are distributed among these distances:
13 8 0.33
14 16 0.67
ACGTcount: A:0.65, C:0.00, G:0.35, T:0.00
Consensus pattern (13 bp):
AAGAAGAAAGAAG
Found at i:29916819 original size:12 final size:12
Alignment explanation
Indices: 29916802--29916827 Score: 52
Period size: 12 Copynumber: 2.2 Consensus size: 12
29916792 TTTGTGAATT
29916802 TTTTAGAAGATA
1 TTTTAGAAGATA
29916814 TTTTAGAAGATA
1 TTTTAGAAGATA
29916826 TT
1 TT
29916828 GTGAATTTTT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 14 1.00
ACGTcount: A:0.38, C:0.00, G:0.15, T:0.46
Consensus pattern (12 bp):
TTTTAGAAGATA
Found at i:29916919 original size:22 final size:22
Alignment explanation
Indices: 29916894--29916960 Score: 77
Period size: 22 Copynumber: 3.2 Consensus size: 22
29916884 TGGATTAGAA
*
29916894 TTTTGTATGAATATTCTATTTT
1 TTTTGTATGAATATTCTAATTT
*
29916916 TTTTGTATGAATATTGTAA--T
1 TTTTGTATGAATATTCTAATTT
* *
29916936 TTTT-TATGAATATTGTAATTA
1 TTTTGTATGAATATTCTAATTT
29916957 TTTT
1 TTTT
29916961 ATAATTAAAT
Statistics
Matches: 40, Mismatches: 3, Indels: 5
0.83 0.06 0.10
Matches are distributed among these distances:
19 14 0.35
20 5 0.12
21 4 0.10
22 17 0.43
ACGTcount: A:0.27, C:0.01, G:0.10, T:0.61
Consensus pattern (22 bp):
TTTTGTATGAATATTCTAATTT
Found at i:29917039 original size:101 final size:101
Alignment explanation
Indices: 29916875--29917061 Score: 304
Period size: 101 Copynumber: 1.9 Consensus size: 101
29916865 CTATTTAGTG
* * *
29916875 TTTATAGTTTGGATTAGAATTTTGTATGAATATTCTATTTTTTTTGTATGAATATTGTAATTTTT
1 TTTATAGTTTGGATTAGAATTTTGTATGAATATTCTATATTTTTTGTATGAATATCGTAATTTTG
29916940 TATGAATATTGTAATTATTTTATAATTAAATTTGTA
66 TATGAATATTGTAATTATTTTATAATTAAATTTGTA
* *
29916976 TTTATAGTTTTGGATTAGTATTTTGTATGAATATTGTA-ATTTTTTGTATGAATATCGTAATTTT
1 TTTATAG-TTTGGATTAGAATTTTGTATGAATATTCTATATTTTTTGTATGAATATCGTAATTTT
*
29917040 GTATGAATATTGTAATTTTTTT
65 GTATGAATATTGTAATTATTTT
29917062 GTATGAATAT
Statistics
Matches: 79, Mismatches: 6, Indels: 2
0.91 0.07 0.02
Matches are distributed among these distances:
101 51 0.65
102 28 0.35
ACGTcount: A:0.29, C:0.01, G:0.13, T:0.57
Consensus pattern (101 bp):
TTTATAGTTTGGATTAGAATTTTGTATGAATATTCTATATTTTTTGTATGAATATCGTAATTTTG
TATGAATATTGTAATTATTTTATAATTAAATTTGTA
Found at i:29917077 original size:41 final size:41
Alignment explanation
Indices: 29916995--29917132 Score: 161
Period size: 49 Copynumber: 3.2 Consensus size: 41
29916985 TTGGATTAGT
*
29916995 ATTTTGTATGAATATTGTAA-TTTTTTGTATGAATATCGTA
1 ATTTTGTATGAATATTGTAATTTTTTTGTATGAATATTGTA
29917035 ATTTTGTATGAATATTGTAATTTTTTTGTATGAATATTGTAATATTATA
1 ATTTTGTATGAATATTGTAATTTTTTTGTATGAATATTG--------TA
* * *
29917084 ATTTTATATGAATATTGCAATATTTTTGTATGAATATTGTA
1 ATTTTGTATGAATATTGTAATTTTTTTGTATGAATATTGTA
29917125 ATTTTGTA
1 ATTTTGTA
29917133 ATTTTGTATG
Statistics
Matches: 84, Mismatches: 5, Indels: 17
0.79 0.05 0.16
Matches are distributed among these distances:
40 20 0.24
41 26 0.31
49 38 0.45
ACGTcount: A:0.32, C:0.01, G:0.13, T:0.54
Consensus pattern (41 bp):
ATTTTGTATGAATATTGTAATTTTTTTGTATGAATATTGTA
Found at i:29917086 original size:49 final size:49
Alignment explanation
Indices: 29917033--29917154 Score: 199
Period size: 49 Copynumber: 2.5 Consensus size: 49
29917023 ATGAATATCG
*
29917033 TAATTTTGTATGAATATTGTAATTTTTTTGTATGAATATTGTAATATTA
1 TAATTTTGTATGAATATTGTAATATTTTTGTATGAATATTGTAATATTA
* * * *
29917082 TAATTTTATATGAATATTGCAATATTTTTGTATGAATATTGTAATTTTG
1 TAATTTTGTATGAATATTGTAATATTTTTGTATGAATATTGTAATATTA
29917131 TAATTTTGTATGAATATTGTAATA
1 TAATTTTGTATGAATATTGTAATA
29917155 CTGTTGAGGA
Statistics
Matches: 66, Mismatches: 7, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
49 66 1.00
ACGTcount: A:0.34, C:0.01, G:0.12, T:0.53
Consensus pattern (49 bp):
TAATTTTGTATGAATATTGTAATATTTTTGTATGAATATTGTAATATTA
Found at i:29917096 original size:27 final size:27
Alignment explanation
Indices: 29917033--29917154 Score: 138
Period size: 27 Copynumber: 4.9 Consensus size: 27
29917023 ATGAATATCG
29917033 TAATTTTGTATGAATATTGT-A-ATT-
1 TAATTTTGTATGAATATTGTAATATTA
29917057 T--TTTTGTATGAATATTGTAATATTA
1 TAATTTTGTATGAATATTGTAATATTA
* *
29917082 TAATTTTATATGAATATTG-CA-A-TA
1 TAATTTTGTATGAATATTGTAATATTA
* *
29917106 T--TTTTGTATGAATATTGTAATTTTG
1 TAATTTTGTATGAATATTGTAATATTA
29917131 TAATTTTGTATGAATATTGTAATA
1 TAATTTTGTATGAATATTGTAATA
29917155 CTGTTGAGGA
Statistics
Matches: 81, Mismatches: 7, Indels: 17
0.77 0.07 0.16
Matches are distributed among these distances:
22 32 0.40
23 2 0.02
24 7 0.09
25 4 0.05
26 1 0.01
27 35 0.43
ACGTcount: A:0.34, C:0.01, G:0.12, T:0.53
Consensus pattern (27 bp):
TAATTTTGTATGAATATTGTAATATTA
Found at i:29917152 original size:19 final size:19
Alignment explanation
Indices: 29916892--29917132 Score: 137
Period size: 19 Copynumber: 12.5 Consensus size: 19
29916882 TTTGGATTAG
*
29916892 AATTTTGTATGAATATTCT
1 AATTTTGTATGAATATTGT
*
29916911 ATTTTTTTTGTATGAATATTGT
1 A---ATTTTGTATGAATATTGT
*
29916933 AATTTTTTATGAATATTGT
1 AATTTTGTATGAATATTGT
*
29916952 AATTATTTTAT-AATTAAATTTGT
1 AATT-TTGTATGAA-T--A-TTGT
* * *
29916975 -ATTTATAGTTTTGGAT-TAGT
1 AATTT-T-G-TATGAATATTGT
29916995 -ATTTTGTATGAATATTGT
1 AATTTTGTATGAATATTGT
*
29917013 AATTTTTTGTATGAATATCGT
1 AA--TTTTGTATGAATATTGT
29917034 AATTTTGTATGAATATTGT
1 AATTTTGTATGAATATTGT
*
29917053 AATTTT-TTTG--TA-TG-
1 AATTTTGTATGAATATTGT
* *
29917067 AATATTG--T-AATATTAT
1 AATTTTGTATGAATATTGT
*
29917083 AATTTTATATGAATATTGCAAT
1 AATTTTGTATGAATATTG---T
*
29917105 ATTTTTGTATGAATATTGT
1 AATTTTGTATGAATATTGT
29917124 AATTTTGTA
1 AATTTTGTA
29917133 ATTTTGTATG
Statistics
Matches: 173, Mismatches: 22, Indels: 54
0.69 0.09 0.22
Matches are distributed among these distances:
13 1 0.01
14 7 0.04
15 3 0.02
16 7 0.04
17 5 0.03
18 8 0.05
19 62 0.36
20 14 0.08
21 19 0.11
22 39 0.23
23 4 0.02
24 3 0.02
25 1 0.01
ACGTcount: A:0.31, C:0.01, G:0.12, T:0.55
Consensus pattern (19 bp):
AATTTTGTATGAATATTGT
Found at i:29920429 original size:27 final size:27
Alignment explanation
Indices: 29920381--29920460 Score: 81
Period size: 27 Copynumber: 3.0 Consensus size: 27
29920371 ATCAGACCAT
*
29920381 TGGCGCCTCTCA-ATATGACACCAATAA
1 TGGCGCCTCTCAGATA-GGCACCAATAA
* ** *
29920408 TGGCGCCTCCCAGATAGGCACCACCAT
1 TGGCGCCTCTCAGATAGGCACCAATAA
* *
29920435 TGGCGCCTCTGAGATAGGCGCCAATA
1 TGGCGCCTCTCAGATAGGCACCAATA
29920461 CTATGTATTA
Statistics
Matches: 42, Mismatches: 10, Indels: 2
0.78 0.19 0.04
Matches are distributed among these distances:
27 39 0.93
28 3 0.07
ACGTcount: A:0.26, C:0.33, G:0.23, T:0.19
Consensus pattern (27 bp):
TGGCGCCTCTCAGATAGGCACCAATAA
Found at i:29924768 original size:13 final size:13
Alignment explanation
Indices: 29924750--29924823 Score: 78
Period size: 13 Copynumber: 5.7 Consensus size: 13
29924740 CTCAAATTTT
29924750 TCAAAAGCACTTC
1 TCAAAAGCACTTC
* *
29924763 TCAAAAGTAATTC
1 TCAAAAGCACTTC
*
29924776 TCAAAAGCACTTT
1 TCAAAAGCACTTC
*
29924789 TCCACAA-CACTTC
1 T-CAAAAGCACTTC
* *
29924802 TCAAAAGTACTTT
1 TCAAAAGCACTTC
29924815 TCAAAAGCA
1 TCAAAAGCA
29924824 ATGAAGAACT
Statistics
Matches: 48, Mismatches: 11, Indels: 4
0.76 0.17 0.06
Matches are distributed among these distances:
12 4 0.08
13 40 0.83
14 4 0.08
ACGTcount: A:0.41, C:0.26, G:0.07, T:0.27
Consensus pattern (13 bp):
TCAAAAGCACTTC
Found at i:29927440 original size:63 final size:63
Alignment explanation
Indices: 29927361--29927536 Score: 192
Period size: 63 Copynumber: 2.8 Consensus size: 63
29927351 CACACATCCA
** * ** *
29927361 TGTCTCTAGCTTGTGTGACTTTAATTCCAAAACAATGAGTTATATGGCTTGGACACACGCCCG
1 TGTCTCTAGCCCGTGTGACTTTAATTCCAAAACAATGAGTTACACAGCCTGGACACACGCCCG
* * * * **
29927424 TGTCTTTGGCCCGTGTGA-TTCTAATTCCAAAACAGTGAGTTACACAGCCTGGACACTCGTTCG
1 TGTCTCTAGCCCGTGTGACTT-TAATTCCAAAACAATGAGTTACACAGCCTGGACACACGCCCG
* * * *
29927487 TGTCTCTAGCTCGTGTGACTCTAATTCCAAAATAATGAGTTACACGGCCT
1 TGTCTCTAGCCCGTGTGACTTTAATTCCAAAACAATGAGTTACACAGCCT
29927537 TGCGCACGGT
Statistics
Matches: 92, Mismatches: 19, Indels: 4
0.80 0.17 0.03
Matches are distributed among these distances:
62 2 0.02
63 89 0.97
64 1 0.01
ACGTcount: A:0.24, C:0.24, G:0.20, T:0.31
Consensus pattern (63 bp):
TGTCTCTAGCCCGTGTGACTTTAATTCCAAAACAATGAGTTACACAGCCTGGACACACGCCCG
Found at i:29928064 original size:21 final size:21
Alignment explanation
Indices: 29928040--29928079 Score: 62
Period size: 21 Copynumber: 1.9 Consensus size: 21
29928030 AGAGTTATCA
29928040 AAAAGAAAAAGAAAAAGAACC
1 AAAAGAAAAAGAAAAAGAACC
* *
29928061 AAAAGAAGAAGAAGAAGAA
1 AAAAGAAAAAGAAAAAGAA
29928080 GAAGAACAGA
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
21 17 1.00
ACGTcount: A:0.75, C:0.05, G:0.20, T:0.00
Consensus pattern (21 bp):
AAAAGAAAAAGAAAAAGAACC
Found at i:29930263 original size:29 final size:30
Alignment explanation
Indices: 29930231--29930290 Score: 77
Period size: 30 Copynumber: 2.0 Consensus size: 30
29930221 CTTATTTCCT
*
29930231 TAAAT-AATTTTAAAACCGGCCTAAAAGCC
1 TAAATAAATTTCAAAACCGGCCTAAAAGCC
** *
29930260 TAAATAAATTTCAAAATGGGCCTATAAGCC
1 TAAATAAATTTCAAAACCGGCCTAAAAGCC
29930290 T
1 T
29930291 TATTTAGCCT
Statistics
Matches: 26, Mismatches: 4, Indels: 1
0.84 0.13 0.03
Matches are distributed among these distances:
29 5 0.19
30 21 0.81
ACGTcount: A:0.43, C:0.18, G:0.12, T:0.27
Consensus pattern (30 bp):
TAAATAAATTTCAAAACCGGCCTAAAAGCC
Found at i:29932371 original size:27 final size:28
Alignment explanation
Indices: 29932336--29932392 Score: 98
Period size: 27 Copynumber: 2.1 Consensus size: 28
29932326 TAAAAAAAAG
29932336 TATGATATAAATGATAAATAATTTGTGA
1 TATGATATAAATGATAAATAATTTGTGA
*
29932364 TATG-TATAAATGATAGATAATTTGTGA
1 TATGATATAAATGATAAATAATTTGTGA
29932391 TA
1 TA
29932393 CAAAATGACG
Statistics
Matches: 28, Mismatches: 1, Indels: 1
0.93 0.03 0.03
Matches are distributed among these distances:
27 24 0.86
28 4 0.14
ACGTcount: A:0.44, C:0.00, G:0.16, T:0.40
Consensus pattern (28 bp):
TATGATATAAATGATAAATAATTTGTGA
Found at i:29945307 original size:29 final size:29
Alignment explanation
Indices: 29945265--29945322 Score: 98
Period size: 29 Copynumber: 2.0 Consensus size: 29
29945255 CACAAAGTTA
29945265 TTCCACTACAGTATCGTGGCTTAGATCTC
1 TTCCACTACAGTATCGTGGCTTAGATCTC
* *
29945294 TTCCACTATAGTATCGTGGTTTAGATCTC
1 TTCCACTACAGTATCGTGGCTTAGATCTC
29945323 CTTAATAAGA
Statistics
Matches: 27, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
29 27 1.00
ACGTcount: A:0.21, C:0.24, G:0.17, T:0.38
Consensus pattern (29 bp):
TTCCACTACAGTATCGTGGCTTAGATCTC
Found at i:29954774 original size:15 final size:15
Alignment explanation
Indices: 29954754--29954793 Score: 80
Period size: 15 Copynumber: 2.7 Consensus size: 15
29954744 TTTTAAGCAT
29954754 TGCATTATGTATATG
1 TGCATTATGTATATG
29954769 TGCATTATGTATATG
1 TGCATTATGTATATG
29954784 TGCATTATGT
1 TGCATTATGT
29954794 TGATCTGATA
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 25 1.00
ACGTcount: A:0.25, C:0.07, G:0.20, T:0.47
Consensus pattern (15 bp):
TGCATTATGTATATG
Found at i:29961718 original size:5 final size:5
Alignment explanation
Indices: 29961708--29961734 Score: 54
Period size: 5 Copynumber: 5.4 Consensus size: 5
29961698 TAAGAAAGGG
29961708 AAAAT AAAAT AAAAT AAAAT AAAAT AA
1 AAAAT AAAAT AAAAT AAAAT AAAAT AA
29961735 CATATAATCC
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 22 1.00
ACGTcount: A:0.81, C:0.00, G:0.00, T:0.19
Consensus pattern (5 bp):
AAAAT
Found at i:29963557 original size:38 final size:37
Alignment explanation
Indices: 29963497--29963657 Score: 139
Period size: 38 Copynumber: 4.3 Consensus size: 37
29963487 TGGTCAATAC
* * * *
29963497 AATC-GACAATTATACGTATGCCCAATACTTGTCGCT-
1 AATCTGACAAATATATGTGTGCCCAATACTGGTCG-TG
* *
29963533 ATATCTGACAAATATATGTGTGCCCAACACTGGTTAGTG
1 A-ATCTGACAAATATATGTGTGCCCAATACTGG-TCGTG
*
29963572 AATCTGACAAATATATGTGTGCCCAGTACTGGTCGGTG
1 AATCTGACAAATATATGTGTGCCCAATACTGGTC-GTG
* * * * *
29963610 AATTTAATAAATATATGTGTGACC-ATCACTAGTCAGTG
1 AATCTGACAAATATATGTGTGCCCAAT-ACTGGTC-GTG
29963648 AATCTGACAA
1 AATCTGACAA
29963658 TACTCAAAAT
Statistics
Matches: 100, Mismatches: 19, Indels: 10
0.78 0.15 0.08
Matches are distributed among these distances:
36 1 0.01
37 5 0.05
38 91 0.91
39 3 0.03
ACGTcount: A:0.32, C:0.19, G:0.19, T:0.30
Consensus pattern (37 bp):
AATCTGACAAATATATGTGTGCCCAATACTGGTCGTG
Found at i:29963595 original size:76 final size:76
Alignment explanation
Indices: 29963497--29963657 Score: 182
Period size: 76 Copynumber: 2.1 Consensus size: 76
29963487 TGGTCAATAC
* * * *
29963497 AATC-GACAATTATACGTATGCCCAATACTTGTCGCT-ATATCTGACAAATATATGTGTGCCCAA
1 AATCTGACAAATATACGTATGCCCAATACTGGTCGCTGA-ATCTAACAAATATATGTGTGACCAA
* *
29963560 CACTGGTTAGTG
65 CACTAGTCAGTG
* * * * * * *
29963572 AATCTGACAAATATATGTGTGCCCAGTACTGGTCGGTGAATTTAATAAATATATGTGTGACCATC
1 AATCTGACAAATATACGTATGCCCAATACTGGTCGCTGAATCTAACAAATATATGTGTGACCAAC
29963637 ACTAGTCAGTG
66 ACTAGTCAGTG
29963648 AATCTGACAA
1 AATCTGACAA
29963658 TACTCAAAAT
Statistics
Matches: 71, Mismatches: 13, Indels: 3
0.82 0.15 0.03
Matches are distributed among these distances:
75 4 0.06
76 66 0.93
77 1 0.01
ACGTcount: A:0.32, C:0.19, G:0.19, T:0.30
Consensus pattern (76 bp):
AATCTGACAAATATACGTATGCCCAATACTGGTCGCTGAATCTAACAAATATATGTGTGACCAAC
ACTAGTCAGTG
Found at i:29965658 original size:40 final size:40
Alignment explanation
Indices: 29965607--29965792 Score: 234
Period size: 40 Copynumber: 4.7 Consensus size: 40
29965597 AAGTGACCAT
* *
29965607 ATCCGGACTAAGAT-CCGAAGGCATTTGTGCGAGATACTAA
1 ATCCGGGCTAAG-TCCCGAAGGCATTTGTGCGAGTTACTAA
* * * *
29965647 TTCCGGGCTAAG-CTCGAAGGCATTGGTGCAAGTTACTAA
1 ATCCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTAA
* *
29965686 ATCTGGGTTAAGTCCCGAAGGCATTTGTGCGAGTTACTAA
1 ATCCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTAA
* *
29965726 ATCCGGGTTAAGTCCCGAAGGCATTTGTCCGAGTTACTATA
1 ATCCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTA-A
*
29965767 A-CCGGGCTATGTCCCGAAGGCATTTG
1 ATCCGGGCTAAGTCCCGAAGGCATTTG
29965793 AACGAGTAGC
Statistics
Matches: 127, Mismatches: 16, Indels: 6
0.85 0.11 0.04
Matches are distributed among these distances:
39 31 0.24
40 94 0.74
41 2 0.02
ACGTcount: A:0.26, C:0.21, G:0.27, T:0.26
Consensus pattern (40 bp):
ATCCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTAA
Found at i:29965789 original size:80 final size:79
Alignment explanation
Indices: 29965607--29965792 Score: 232
Period size: 79 Copynumber: 2.3 Consensus size: 79
29965597 AAGTGACCAT
* * *
29965607 ATCCGGACTAAGAT-CCGAAGGCATTTGTGCGAGATACTAATTCCGGGCTAAGCTCGAAGGCATT
1 ATCCGGGCTAAG-TCCCGAAGGCATTTGTGCGAGATACTAAATCCGGGCTAAGCCCGAAGGCATT
*
29965671 GGTGCAAGTTACTAA
65 GGTCCAAGTTACTAA
* * * *
29965686 ATCTGGGTTAAGTCCCGAAGGCATTTGTGCGAGTTACTAAATCCGGGTTAAGTCCCGAAGGCATT
1 ATCCGGGCTAAGTCCCGAAGGCATTTGTGCGAGATACTAAATCCGGGCTAAG-CCCGAAGGCATT
* *
29965751 TGTCCGAGTTACTATA
65 GGTCCAAGTTACTA-A
*
29965767 A-CCGGGCTATGTCCCGAAGGCATTTG
1 ATCCGGGCTAAGTCCCGAAGGCATTTG
29965793 AACGAGTAGC
Statistics
Matches: 91, Mismatches: 13, Indels: 5
0.83 0.12 0.05
Matches are distributed among these distances:
78 1 0.01
79 44 0.48
80 44 0.48
81 2 0.02
ACGTcount: A:0.26, C:0.21, G:0.27, T:0.26
Consensus pattern (79 bp):
ATCCGGGCTAAGTCCCGAAGGCATTTGTGCGAGATACTAAATCCGGGCTAAGCCCGAAGGCATTG
GTCCAAGTTACTAA
Found at i:29965799 original size:80 final size:78
Alignment explanation
Indices: 29965607--29965815 Score: 226
Period size: 80 Copynumber: 2.6 Consensus size: 78
29965597 AAGTGACCAT
* * * *
29965607 ATCCGGACTAAGAT-CCGAAGGCATTTGTGCGAGATACTAATTCCGGGCTAAGCTCGAAGGCATT
1 ATCCGGGCTAAG-TCCCGAAGGCATTTGTGCGAG-TACTAAATCCGGGTTAAGCCCGAAGGCATT
*
29965671 GGTGCAAGTTACTAA
64 GGTCCAAGTTACTAA
* *
29965686 ATCTGGGTTAAGTCCCGAAGGCATTTGTGCGAGTTACTAAATCCGGGTTAAGTCCCGAAGGCATT
1 ATCCGGGCTAAGTCCCGAAGGCATTTGTGCGAG-TACTAAATCCGGGTTAAG-CCCGAAGGCATT
* *
29965751 TGTCCGAGTTACTATA
64 GGTCCAAGTTACTA-A
* ** *
29965767 A-CCGGGCTATGTCCCGAAGGCATTTGAACGAGTAGCTATATCC-GGTTAA
1 ATCCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTA-CTAAATCCGGGTTAA
29965816 ATTTCGAAGG
Statistics
Matches: 110, Mismatches: 16, Indels: 8
0.82 0.12 0.06
Matches are distributed among these distances:
78 1 0.01
79 52 0.47
80 55 0.50
81 2 0.02
ACGTcount: A:0.27, C:0.21, G:0.26, T:0.26
Consensus pattern (78 bp):
ATCCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTACTAAATCCGGGTTAAGCCCGAAGGCATTGG
TCCAAGTTACTAA
Found at i:29971313 original size:56 final size:56
Alignment explanation
Indices: 29971227--29971346 Score: 231
Period size: 56 Copynumber: 2.1 Consensus size: 56
29971217 ACAAGGGATG
29971227 ATGGGCAAAACATGTCATGAAACATGTTGTGTTAATGGAAAAATAAAATAAGAAGC
1 ATGGGCAAAACATGTCATGAAACATGTTGTGTTAATGGAAAAATAAAATAAGAAGC
*
29971283 ATGGGCAAAACATGTCATGAAACATGTTGTGTTAATGGAAGAATAAAATAAGAAGC
1 ATGGGCAAAACATGTCATGAAACATGTTGTGTTAATGGAAAAATAAAATAAGAAGC
29971339 ATGGGCAA
1 ATGGGCAA
29971347 TAAACTAATA
Statistics
Matches: 63, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
56 63 1.00
ACGTcount: A:0.45, C:0.09, G:0.23, T:0.23
Consensus pattern (56 bp):
ATGGGCAAAACATGTCATGAAACATGTTGTGTTAATGGAAAAATAAAATAAGAAGC
Found at i:29972706 original size:40 final size:40
Alignment explanation
Indices: 29972475--29972699 Score: 260
Period size: 40 Copynumber: 5.7 Consensus size: 40
29972465 TCGAATGATG
* * * *
29972475 TCCGGGCTAAGTCCCGAAGGC-TTTGTGCTAAGTGACCATA
1 TCCGGGCTAAGTCCCGAAGGCATTTGTGC-GAGTTACTAAA
* * * *
29972515 TTCGGACTAAGAT-CCGAAGGCATTTGTGCGAGATACTAAT
1 TCCGGGCTAAG-TCCCGAAGGCATTTGTGCGAGTTACTAAA
* *
29972555 TCCGGGCTAAG-CTCGAAGGCATTGGTGCGAGTTACTAAA
1 TCCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTAAA
* *
29972594 TTCGGGTTAAGTCCCGAAGGCATTTGTGCGAGTTACTAAA
1 TCCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTAAA
* *
29972634 TCCCGGTTAAGTCCCGAAGGCATTTGTGCGAGTTACTATAA
1 TCCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTA-AA
*
29972675 -CCGGGCTATGTCCCGAAGGCATTTG
1 TCCGGGCTAAGTCCCGAAGGCATTTG
29972700 AACGAGTAGC
Statistics
Matches: 157, Mismatches: 23, Indels: 10
0.83 0.12 0.05
Matches are distributed among these distances:
39 32 0.20
40 115 0.73
41 10 0.06
ACGTcount: A:0.24, C:0.21, G:0.28, T:0.27
Consensus pattern (40 bp):
TCCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTAAA
Found at i:29972706 original size:80 final size:79
Alignment explanation
Indices: 29972528--29972732 Score: 236
Period size: 80 Copynumber: 2.6 Consensus size: 79
29972518 GGACTAAGAT
* * * *
29972528 CCGAAGGCATTTGTGCGAGATACTAATTCCGGGCTAAG-CTCGAAGGCATTGGTGCGAGTTACTA
1 CCGAAGGCATTTGTGCGAG-TACTAAATCCCGGTTAAGTCCCGAAGGCATTGGTGCGAGTTACTA
* *
29972592 AATTCGGGTTAAGTC
65 AATCCGGGCTAAGTC
*
29972607 CCGAAGGCATTTGTGCGAGTTACTAAATCCCGGTTAAGTCCCGAAGGCATTTGTGCGAGTTACTA
1 CCGAAGGCATTTGTGCGAG-TACTAAATCCCGGTTAAGTCCCGAAGGCATTGGTGCGAGTTACTA
*
29972672 TAA-CCGGGCTATGTC
65 -AATCCGGGCTAAGTC
** * * *
29972687 CCGAAGGCATTTGAACGAGTAGCTATAT-CCGGTTAAATTCCGAAGG
1 CCGAAGGCATTTGTGCGAGTA-CTAAATCCCGGTTAAGTCCCGAAGG
29972733 TACGTGATTT
Statistics
Matches: 109, Mismatches: 14, Indels: 6
0.84 0.11 0.05
Matches are distributed among these distances:
79 52 0.48
80 55 0.50
81 2 0.02
ACGTcount: A:0.26, C:0.20, G:0.27, T:0.26
Consensus pattern (79 bp):
CCGAAGGCATTTGTGCGAGTACTAAATCCCGGTTAAGTCCCGAAGGCATTGGTGCGAGTTACTAA
ATCCGGGCTAAGTC
Found at i:29979935 original size:5 final size:5
Alignment explanation
Indices: 29979925--29979970 Score: 51
Period size: 5 Copynumber: 9.4 Consensus size: 5
29979915 AATAAAAAAT
* *
29979925 TTAAA TTAAA TTAAA TTATAA --AAA TCAAA TTTAA TTAAA TTAAA TT
1 TTAAA TTAAA TTAAA TTA-AA TTAAA TTAAA TTAAA TTAAA TTAAA TT
29979971 TTTTCTATAT
Statistics
Matches: 35, Mismatches: 3, Indels: 6
0.80 0.07 0.14
Matches are distributed among these distances:
3 2 0.06
4 1 0.03
5 30 0.86
6 2 0.06
ACGTcount: A:0.57, C:0.02, G:0.00, T:0.41
Consensus pattern (5 bp):
TTAAA
Found at i:29982600 original size:37 final size:37
Alignment explanation
Indices: 29982550--29982626 Score: 118
Period size: 37 Copynumber: 2.1 Consensus size: 37
29982540 AATATTATGA
* * *
29982550 TTACAAAGTTTAAACATAATAGTGTATCCATTTAATT
1 TTACAAAGTTTAAACATAATACTATATCAATTTAATT
*
29982587 TTACAAAGTTTAAACATCATACTATATCAATTTAATT
1 TTACAAAGTTTAAACATAATACTATATCAATTTAATT
29982624 TTA
1 TTA
29982627 AAAAATGATA
Statistics
Matches: 36, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
37 36 1.00
ACGTcount: A:0.42, C:0.12, G:0.05, T:0.42
Consensus pattern (37 bp):
TTACAAAGTTTAAACATAATACTATATCAATTTAATT
Found at i:29987340 original size:30 final size:30
Alignment explanation
Indices: 29987300--29987454 Score: 197
Period size: 30 Copynumber: 5.2 Consensus size: 30
29987290 ATTCCAACCT
* *
29987300 TTTTCATGGCTCGAGAGTCGAAGCTATCCC
1 TTTTCGTGGCTCGATAGTCGAAGCTATCCC
* *
29987330 TTTTCGTGGCTCGATAGTCAAAGCTATCCA
1 TTTTCGTGGCTCGATAGTCGAAGCTATCCC
* *
29987360 TTTTCATAGCTCGATAG-CTGAAGCTATCCC
1 TTTTCGTGGCTCGATAGTC-GAAGCTATCCC
*
29987390 TTTTCGTGGCTCGATAGTCAAAGCTATCCC
1 TTTTCGTGGCTCGATAGTCGAAGCTATCCC
* *
29987420 TTTTCGTAGCTCGATA-CCTGAAGCTATCCC
1 TTTTCGTGGCTCGATAGTC-GAAGCTATCCC
29987450 TTTTC
1 TTTTC
29987455 ATTATTTAAT
Statistics
Matches: 108, Mismatches: 14, Indels: 6
0.84 0.11 0.05
Matches are distributed among these distances:
29 2 0.02
30 105 0.97
31 1 0.01
ACGTcount: A:0.21, C:0.26, G:0.19, T:0.34
Consensus pattern (30 bp):
TTTTCGTGGCTCGATAGTCGAAGCTATCCC
Found at i:29987372 original size:60 final size:60
Alignment explanation
Indices: 29987300--29987454 Score: 249
Period size: 60 Copynumber: 2.6 Consensus size: 60
29987290 ATTCCAACCT
* *
29987300 TTTTCATGGCTCGAGAG-TCGAAGCTATCCCTTTTCGTGGCTCGATAGTCAAAGCTATCCA
1 TTTTCATAGCTCGATAGCT-GAAGCTATCCCTTTTCGTGGCTCGATAGTCAAAGCTATCCA
*
29987360 TTTTCATAGCTCGATAGCTGAAGCTATCCCTTTTCGTGGCTCGATAGTCAAAGCTATCCC
1 TTTTCATAGCTCGATAGCTGAAGCTATCCCTTTTCGTGGCTCGATAGTCAAAGCTATCCA
* *
29987420 TTTTCGTAGCTCGATACCTGAAGCTATCCCTTTTC
1 TTTTCATAGCTCGATAGCTGAAGCTATCCCTTTTC
29987455 ATTATTTAAT
Statistics
Matches: 89, Mismatches: 5, Indels: 2
0.93 0.05 0.02
Matches are distributed among these distances:
60 88 0.99
61 1 0.01
ACGTcount: A:0.21, C:0.26, G:0.19, T:0.34
Consensus pattern (60 bp):
TTTTCATAGCTCGATAGCTGAAGCTATCCCTTTTCGTGGCTCGATAGTCAAAGCTATCCA
Found at i:29987479 original size:30 final size:30
Alignment explanation
Indices: 29987445--29987642 Score: 170
Period size: 30 Copynumber: 6.7 Consensus size: 30
29987435 ACCTGAAGCT
*
29987445 ATCCCTTTTCATTATTTAATGGTCGTCACC
1 ATCCCTTTTCATTATTTGATGGTCGTCACC
* * *
29987475 ATCCCTTTTCATT-GTTGATGATCATCACC
1 ATCCCTTTTCATTATTTGATGGTCGTCACC
* * * * *
29987504 ATCCCTTTTCATAATTTGATAGCCG-AAGCT
1 ATCCCTTTTCATTATTTGATGGTCGTCA-CC
* * * * * *
29987534 ATCCCTTTTCATAATTCGATAGCCG-AAGCT
1 ATCCCTTTTCATTATTTGATGGTCGTCA-CC
* *
29987564 ATCCCTTTTCATTGTTCGATGGTCGTCACC
1 ATCCCTTTTCATTATTTGATGGTCGTCACC
* *
29987594 ATCCTTTTTCATTGTTT-ATGGTCGTCACC
1 ATCCCTTTTCATTATTTGATGGTCGTCACC
*
29987623 GTCCCTTTTCATTATTTGAT
1 ATCCCTTTTCATTATTTGAT
29987643 AGCCGAGGCT
Statistics
Matches: 140, Mismatches: 24, Indels: 8
0.81 0.14 0.05
Matches are distributed among these distances:
29 51 0.36
30 88 0.63
31 1 0.01
ACGTcount: A:0.20, C:0.26, G:0.13, T:0.42
Consensus pattern (30 bp):
ATCCCTTTTCATTATTTGATGGTCGTCACC
Found at i:29987511 original size:29 final size:30
Alignment explanation
Indices: 29987445--29987515 Score: 99
Period size: 29 Copynumber: 2.4 Consensus size: 30
29987435 ACCTGAAGCT
* * *
29987445 ATCCCTTTTCATTATTTAATGGTCGTCACC
1 ATCCCTTTTCATTAGTTAATGATCATCACC
*
29987475 ATCCCTTTTCATT-GTTGATGATCATCACC
1 ATCCCTTTTCATTAGTTAATGATCATCACC
29987504 ATCCCTTTTCAT
1 ATCCCTTTTCAT
29987516 AATTTGATAG
Statistics
Matches: 37, Mismatches: 4, Indels: 1
0.88 0.10 0.02
Matches are distributed among these distances:
29 24 0.65
30 13 0.35
ACGTcount: A:0.20, C:0.28, G:0.08, T:0.44
Consensus pattern (30 bp):
ATCCCTTTTCATTAGTTAATGATCATCACC
Found at i:29987538 original size:89 final size:90
Alignment explanation
Indices: 29987439--29987605 Score: 221
Period size: 89 Copynumber: 1.9 Consensus size: 90
29987429 CTCGATACCT
* * * * *
29987439 GAAGCTATCCCTTTTCATTATTTAATGGTCGTCA-CCATCCCTTTTCATTGTT-GATGATCATCA
1 GAAGCTATCCCTTTTCATAATTCAATAGCCG-AAGCCATCCCTTTTCATTGTTCGATGATCATCA
29987502 CCATCCCTTTTCATAATTTGATAGCC
65 CCATCCCTTTTCATAATTTGATAGCC
* * * *
29987528 GAAGCTATCCCTTTTCATAATTCGATAGCCGAAGCTATCCCTTTTCATTGTTCGATGGTCGTCAC
1 GAAGCTATCCCTTTTCATAATTCAATAGCCGAAGCCATCCCTTTTCATTGTTCGATGATCATCAC
*
29987593 CATCCTTTTTCAT
66 CATCCCTTTTCAT
29987606 TGTTTATGGT
Statistics
Matches: 66, Mismatches: 10, Indels: 3
0.84 0.13 0.04
Matches are distributed among these distances:
88 1 0.02
89 43 0.65
90 22 0.33
ACGTcount: A:0.22, C:0.26, G:0.13, T:0.40
Consensus pattern (90 bp):
GAAGCTATCCCTTTTCATAATTCAATAGCCGAAGCCATCCCTTTTCATTGTTCGATGATCATCAC
CATCCCTTTTCATAATTTGATAGCC
Found at i:29987553 original size:119 final size:119
Alignment explanation
Indices: 29987410--29987708 Score: 429
Period size: 119 Copynumber: 2.5 Consensus size: 119
29987400 TCGATAGTCA
* ** *
29987410 AAGCTATCCCTTTTCGTAGCTCGATA-CCTGAAGCTATCCCTTTTCATTATTTAATGGTCGTCAC
1 AAGCTATCCCTTTTCATAATTCGATAGCC-GAAGCTATCCCTTTTCATTATTCAATGGTCGTCAC
29987474 CATCCCTTTTCATTGTTGATGATCATCACCATCCCTTTTCATAATTTGATAGCCG
65 CATCCCTTTTCATTGTTGATGATCATCACCATCCCTTTTCATAATTTGATAGCCG
* *
29987529 AAGCTATCCCTTTTCATAATTCGATAGCCGAAGCTATCCCTTTTCATTGTTCGATGGTCGTCACC
1 AAGCTATCCCTTTTCATAATTCGATAGCCGAAGCTATCCCTTTTCATTATTCAATGGTCGTCACC
* * * * * *
29987594 ATCCTTTTTCATTGTTTATGGTCGTCACCGTCCCTTTTCATTATTTGATAGCCG
66 ATCCCTTTTCATTGTTGATGATCATCACCATCCCTTTTCATAATTTGATAGCCG
* * * * *
29987648 AGGCTATCCCTTTTCATAATTTGATAGCCGAAGCTATCCATTTTCATTAGTCAATGATCGT
1 AAGCTATCCCTTTTCATAATTCGATAGCCGAAGCTATCCCTTTTCATTATTCAATGGTCGT
29987709 TGATAAACCA
Statistics
Matches: 160, Mismatches: 19, Indels: 2
0.88 0.10 0.01
Matches are distributed among these distances:
119 158 0.99
120 2 0.01
ACGTcount: A:0.21, C:0.25, G:0.14, T:0.39
Consensus pattern (119 bp):
AAGCTATCCCTTTTCATAATTCGATAGCCGAAGCTATCCCTTTTCATTATTCAATGGTCGTCACC
ATCCCTTTTCATTGTTGATGATCATCACCATCCCTTTTCATAATTTGATAGCCG
Found at i:29987575 original size:60 final size:60
Alignment explanation
Indices: 29987300--29987696 Score: 232
Period size: 60 Copynumber: 6.7 Consensus size: 60
29987290 ATTCCAACCT
* * * * * *** * *
29987300 TTTTCATGGCTCGAGAGTCGAAGCTATCCCTTTTCGTGGCTCGATAGTCAAAGCTATCCA
1 TTTTCATAGTTCGATAGCCGAAGCTATCCCTTTTCATTATTCGATAGTCGAAGCTATCCC
* * * *** *
29987360 TTTTCATAGCTCGATAGCTGAAGCTATCCCTTTTCGTGGCTCGATAGTCAAAGCTATCCC
1 TTTTCATAGTTCGATAGCCGAAGCTATCCCTTTTCATTATTCGATAGTCGAAGCTATCCC
* * ** * * *
29987420 TTTTCGTAGCTCGATA-CCTGAAGCTATCCCTTTTCATTATTTAATGGTCGTCA-CCATCCC
1 TTTTCATAGTTCGATAGCC-GAAGCTATCCCTTTTCATTATTCGATAGTCG-AAGCTATCCC
* * *** * * * *
29987480 TTTTCATTGTT-GATGATCATCA-CCATCCCTTTTCATAATTTGATAGCCGAAGCTATCCC
1 TTTTCATAGTTCGAT-AGCCGAAGCTATCCCTTTTCATTATTCGATAGTCGAAGCTATCCC
* * * * * *
29987539 TTTTCATAATTCGATAGCCGAAGCTATCCCTTTTCATTGTTCGATGGTCGTCA-CCATCCT
1 TTTTCATAGTTCGATAGCCGAAGCTATCCCTTTTCATTATTCGATAGTCG-AAGCTATCCC
* * * * * ** * * *
29987599 TTTTCATTGTT-TATGGTCGTCA-CCGTCCCTTTTCATTATTTGATAGCCGAGGCTATCCC
1 TTTTCATAGTTCGATAGCCG-AAGCTATCCCTTTTCATTATTCGATAGTCGAAGCTATCCC
* * *
29987658 TTTTCATAATTTGATAGCCGAAGCTATCCATTTTCATTA
1 TTTTCATAGTTCGATAGCCGAAGCTATCCCTTTTCATTA
29987697 GTCAATGATC
Statistics
Matches: 255, Mismatches: 70, Indels: 24
0.73 0.20 0.07
Matches are distributed among these distances:
58 1 0.00
59 85 0.33
60 166 0.65
61 3 0.01
ACGTcount: A:0.21, C:0.25, G:0.16, T:0.38
Consensus pattern (60 bp):
TTTTCATAGTTCGATAGCCGAAGCTATCCCTTTTCATTATTCGATAGTCGAAGCTATCCC
Found at i:29987658 original size:30 final size:30
Alignment explanation
Indices: 29987624--29987696 Score: 119
Period size: 30 Copynumber: 2.4 Consensus size: 30
29987614 GTCGTCACCG
*
29987624 TCCCTTTTCATTATTTGATAGCCGAGGCTA
1 TCCCTTTTCATTATTTGATAGCCGAAGCTA
*
29987654 TCCCTTTTCATAATTTGATAGCCGAAGCTA
1 TCCCTTTTCATTATTTGATAGCCGAAGCTA
*
29987684 TCCATTTTCATTA
1 TCCCTTTTCATTA
29987697 GTCAATGATC
Statistics
Matches: 39, Mismatches: 4, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
30 39 1.00
ACGTcount: A:0.23, C:0.23, G:0.12, T:0.41
Consensus pattern (30 bp):
TCCCTTTTCATTATTTGATAGCCGAAGCTA
Found at i:29989177 original size:16 final size:16
Alignment explanation
Indices: 29989156--29989223 Score: 57
Period size: 14 Copynumber: 4.9 Consensus size: 16
29989146 TATATTGTAA
29989156 TAATAGTTATATATAT
1 TAATAGTTATATATAT
*
29989172 TAATAG-T-T-T-TAG
1 TAATAGTTATATATAT
29989184 TAATAG-T-TATATAT
1 TAATAGTTATATATAT
29989198 T-ATA-TTATAT-TAT
1 TAATAGTTATATATAT
29989211 TAATA-TTATATAT
1 TAATAGTTATATAT
29989224 TATATTATTT
Statistics
Matches: 44, Mismatches: 2, Indels: 13
0.75 0.03 0.22
Matches are distributed among these distances:
12 10 0.23
13 10 0.23
14 16 0.36
15 2 0.05
16 6 0.14
ACGTcount: A:0.41, C:0.00, G:0.06, T:0.53
Consensus pattern (16 bp):
TAATAGTTATATATAT
Found at i:29989219 original size:26 final size:27
Alignment explanation
Indices: 29989156--29989236 Score: 94
Period size: 26 Copynumber: 3.0 Consensus size: 27
29989146 TATATTGTAA
* * *
29989156 TAATAGTTATATA-TATTAATAGTTTTAG
1 TAATAGTTATATATTA-TATTA-TATTAT
29989184 TAATAGTTATATATTATATTATATTAT
1 TAATAGTTATATATTATATTATATTAT
*
29989211 TAATA-TTATATATTATATTATTTTAT
1 TAATAGTTATATATTATATTATATTAT
29989237 GTTTTAGTAG
Statistics
Matches: 48, Mismatches: 4, Indels: 4
0.86 0.07 0.07
Matches are distributed among these distances:
26 20 0.42
27 9 0.19
28 17 0.35
29 2 0.04
ACGTcount: A:0.40, C:0.00, G:0.05, T:0.56
Consensus pattern (27 bp):
TAATAGTTATATATTATATTATATTAT
Found at i:29999124 original size:14 final size:14
Alignment explanation
Indices: 29999102--29999140 Score: 62
Period size: 14 Copynumber: 2.8 Consensus size: 14
29999092 CCAAAAAAGT
29999102 AAGTCATTTTCTAGA
1 AAGTCATTTTCT-GA
29999117 AA-TCATTTTCTGA
1 AAGTCATTTTCTGA
29999130 AAGTCATTTTC
1 AAGTCATTTTC
29999141 AGTAAAACAA
Statistics
Matches: 23, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
13 4 0.17
14 17 0.74
15 2 0.09
ACGTcount: A:0.31, C:0.15, G:0.10, T:0.44
Consensus pattern (14 bp):
AAGTCATTTTCTGA
Found at i:30002541 original size:11 final size:11
Alignment explanation
Indices: 30002515--30002549 Score: 54
Period size: 11 Copynumber: 3.3 Consensus size: 11
30002505 TTGATGATTT
30002515 TTTATTTTT-A
1 TTTATTTTTCA
*
30002525 TATATTTTTCA
1 TTTATTTTTCA
30002536 TTTATTTTTCA
1 TTTATTTTTCA
30002547 TTT
1 TTT
30002550 TCATTGAATA
Statistics
Matches: 22, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
10 8 0.36
11 14 0.64
ACGTcount: A:0.20, C:0.06, G:0.00, T:0.74
Consensus pattern (11 bp):
TTTATTTTTCA
Found at i:30006679 original size:21 final size:21
Alignment explanation
Indices: 30006654--30006732 Score: 104
Period size: 21 Copynumber: 3.8 Consensus size: 21
30006644 GCTTCTCTAG
*
30006654 CTGCTTCTCTTGCTGCGGCCT
1 CTGCTTCTCTCGCTGCGGCCT
*
30006675 TTGCTTCTCTCGCTGCGGCCT
1 CTGCTTCTCTCGCTGCGGCCT
* **
30006696 CTGCTTCTCTCGTTGTAGCCT
1 CTGCTTCTCTCGCTGCGGCCT
*
30006717 CTGCTTCCCTCGCTGC
1 CTGCTTCTCTCGCTGC
30006733 CGCATCTACT
Statistics
Matches: 49, Mismatches: 9, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
21 49 1.00
ACGTcount: A:0.01, C:0.39, G:0.22, T:0.38
Consensus pattern (21 bp):
CTGCTTCTCTCGCTGCGGCCT
Found at i:30011204 original size:8 final size:7
Alignment explanation
Indices: 30011189--30011323 Score: 51
Period size: 7 Copynumber: 18.4 Consensus size: 7
30011179 CTTGACACCT
30011189 TAAACCC
1 TAAACCC
30011196 TAAATCCC
1 TAAA-CCC
*
30011204 T-AACCAG
1 TAAACC-C
*
30011211 TAACCCC
1 TAAACCC
30011218 TAAATCTCC
1 TAAA-C-CC
**
30011227 TAGCCCC
1 TAAACCC
*
30011234 TAAATTCC
1 TAAA-CCC
*
30011242 TAACCCC
1 TAAACCC
*
30011249 TAACCCC
1 TAAACCC
30011256 TAAATCCC
1 TAAA-CCC
30011264 T-AACCC
1 TAAACCC
*
30011270 TTAACCCC
1 -TAAACCC
*
30011278 TAAATCTC
1 TAAA-CCC
*
30011286 TAATCCC
1 TAAACCC
*
30011293 TAACCCC
1 TAAACCC
*
30011300 TAAACCT
1 TAAACCC
*
30011307 TATATCCC
1 TA-AACCC
30011315 -AAACCC
1 TAAACCC
30011321 TAA
1 TAA
30011324 TAGAGTACAT
Statistics
Matches: 93, Mismatches: 23, Indels: 24
0.66 0.16 0.17
Matches are distributed among these distances:
6 9 0.10
7 50 0.54
8 30 0.32
9 4 0.04
ACGTcount: A:0.34, C:0.41, G:0.01, T:0.23
Consensus pattern (7 bp):
TAAACCC
Found at i:30011219 original size:22 final size:21
Alignment explanation
Indices: 30011193--30011303 Score: 115
Period size: 22 Copynumber: 5.3 Consensus size: 21
30011183 ACACCTTAAA
*
30011193 CCCTAAATCCCTAACCAGTAAC
1 CCCTAAATCCCTAACC-CTAAC
*
30011215 CCCTAAAT--CT---CCTAGC
1 CCCTAAATCCCTAACCCTAAC
*
30011231 CCCTAAATTCCTAACCCCTAAC
1 CCCTAAATCCCTAA-CCCTAAC
30011253 CCCTAAATCCCTAACCCTTAAC
1 CCCTAAATCCCTAACCC-TAAC
*
30011275 CCCTAAATCTCTAATCCCTAAC
1 CCCTAAATCCCTAA-CCCTAAC
30011297 CCCTAAA
1 CCCTAAA
30011304 CCTTATATCC
Statistics
Matches: 76, Mismatches: 5, Indels: 16
0.78 0.05 0.16
Matches are distributed among these distances:
16 11 0.14
17 1 0.01
18 2 0.03
20 2 0.03
21 3 0.04
22 54 0.71
23 3 0.04
ACGTcount: A:0.32, C:0.43, G:0.02, T:0.23
Consensus pattern (21 bp):
CCCTAAATCCCTAACCCTAAC
Found at i:30011235 original size:38 final size:37
Alignment explanation
Indices: 30011193--30011265 Score: 110
Period size: 38 Copynumber: 1.9 Consensus size: 37
30011183 ACACCTTAAA
*
30011193 CCCTAAATCCCTAACCAGTAACCCCTAAATCTCCTAGC
1 CCCTAAATCCCTAACCACTAACCCCTAAATC-CCTAGC
* *
30011231 CCCTAAATTCCTAACCCCTAACCCCTAAATCCCTA
1 CCCTAAATCCCTAACCACTAACCCCTAAATCCCTA
30011266 ACCCTTAACC
Statistics
Matches: 32, Mismatches: 3, Indels: 1
0.89 0.08 0.03
Matches are distributed among these distances:
37 4 0.12
38 28 0.88
ACGTcount: A:0.32, C:0.44, G:0.03, T:0.22
Consensus pattern (37 bp):
CCCTAAATCCCTAACCACTAACCCCTAAATCCCTAGC
Found at i:30011248 original size:15 final size:16
Alignment explanation
Indices: 30011211--30011295 Score: 67
Period size: 15 Copynumber: 5.6 Consensus size: 16
30011201 CCCTAACCAG
30011211 TAACCCCTAAATCTCC
1 TAACCCCTAAATCTCC
*
30011227 TAGCCCCTAAAT-TCC
1 TAACCCCTAAATCTCC
*
30011242 TAACCCCT-AA-CCCC
1 TAACCCCTAAATCTCC
*
30011256 TAAATCCCT-AA-C-CC
1 T-AACCCCTAAATCTCC
30011270 TTAACCCCTAAATCT-C
1 -TAACCCCTAAATCTCC
*
30011286 TAATCCCTAA
1 TAACCCCTAA
30011296 CCCCTAAACC
Statistics
Matches: 57, Mismatches: 6, Indels: 13
0.75 0.08 0.17
Matches are distributed among these distances:
14 13 0.23
15 31 0.54
16 13 0.23
ACGTcount: A:0.32, C:0.42, G:0.01, T:0.25
Consensus pattern (16 bp):
TAACCCCTAAATCTCC
Found at i:30011250 original size:7 final size:7
Alignment explanation
Indices: 30011240--30011302 Score: 63
Period size: 7 Copynumber: 8.7 Consensus size: 7
30011230 CCCCTAAATT
30011240 CCTAACC
1 CCTAACC
30011247 CCTAACC
1 CCTAACC
*
30011254 CCTAAATC
1 CCT-AACC
30011262 CCTAACC
1 CCTAACC
*
30011269 CTTAACC
1 CCTAACC
*
30011276 CCTAAATC
1 CCT-AACC
* *
30011284 TCTAATC
1 CCTAACC
30011291 CCTAACC
1 CCTAACC
30011298 CCTAA
1 CCTAA
30011303 ACCTTATATC
Statistics
Matches: 46, Mismatches: 8, Indels: 4
0.79 0.14 0.07
Matches are distributed among these distances:
7 35 0.76
8 11 0.24
ACGTcount: A:0.32, C:0.46, G:0.00, T:0.22
Consensus pattern (7 bp):
CCTAACC
Found at i:30011275 original size:29 final size:29
Alignment explanation
Indices: 30011189--30011298 Score: 82
Period size: 29 Copynumber: 3.7 Consensus size: 29
30011179 CTTGACACCT
**
30011189 TAAA-CCCTAAATCCCTAACCAGTAACCCC
1 TAAACCCCT-AATCCCTAACCCTTAACCCC
* ** *
30011218 TAAATCTCCTAGCCCCTAAATTCC-TAACCCC
1 TAAA-CCCCTAATCCCT-AA-CCCTTAACCCC
30011249 T-AACCCCTAAATCCCTAACCCTTAACCCC
1 TAAACCCCT-AATCCCTAACCCTTAACCCC
* *
30011278 TAAATCTCTAATCCCTAACCC
1 TAAACCCCTAATCCCTAACCC
30011299 CTAAACCTTA
Statistics
Matches: 63, Mismatches: 11, Indels: 14
0.72 0.12 0.16
Matches are distributed among these distances:
28 2 0.03
29 30 0.48
30 17 0.27
31 13 0.21
32 1 0.02
ACGTcount: A:0.33, C:0.43, G:0.02, T:0.23
Consensus pattern (29 bp):
TAAACCCCTAATCCCTAACCCTTAACCCC
Found at i:30011313 original size:22 final size:21
Alignment explanation
Indices: 30011220--30011320 Score: 80
Period size: 22 Copynumber: 4.6 Consensus size: 21
30011210 GTAACCCCTA
*
30011220 AATCTCCTAGCCCCTAAATTCC-T
1 AATC-CCTAACCCCTAAA--CCTT
* *
30011243 AACCCCTAACCCCTAAATCCCT
1 AATCCCTAACCCCTAAA-CCTT
*
30011265 AA-CCCTTAACCCCTAAATCTCT
1 AATCCC-TAACCCCTAAACCT-T
30011287 AATCCCTAACCCCTAAACCTT
1 AATCCCTAACCCCTAAACCTT
*
30011308 ATATCCCAAACCC
1 A-ATCCCTAACCC
30011321 TAATAGAGTA
Statistics
Matches: 67, Mismatches: 6, Indels: 11
0.80 0.07 0.13
Matches are distributed among these distances:
21 9 0.13
22 52 0.78
23 6 0.09
ACGTcount: A:0.32, C:0.44, G:0.01, T:0.24
Consensus pattern (21 bp):
AATCCCTAACCCCTAAACCTT
Found at i:30013248 original size:41 final size:41
Alignment explanation
Indices: 30013186--30013383 Score: 206
Period size: 41 Copynumber: 4.8 Consensus size: 41
30013176 TTTTGTTACT
** *
30013186 ATTAGCGGCGCTTC-GGCAAAAACGCCGCTAAAGGCTAGAGA
1 ATTAGCGGCGC-TCAGATAAAAACGCCGCTAAAGGCCAGAGA
* * **
30013227 ATTAGTGGCGCTCAGATAAAAATGCCGCTAAATATCC-GA-A
1 ATTAGCGGCGCTCAGATAAAAACGCCGCTAAA-GGCCAGAGA
*
30013267 CATTAGCGGCGCTTAGATAAAAACGCCGCTAAAGGCCAGAGA
1 -ATTAGCGGCGCTCAGATAAAAACGCCGCTAAAGGCCAGAGA
* * ** *
30013309 ATTAGCGGCGCTCGGATACAAACGCCGCTAAATATCCA-AGC
1 ATTAGCGGCGCTCAGATAAAAACGCCGCTAAA-GGCCAGAGA
*
30013350 ATTAGCGGCGCTTAGATAAAAACGCCGCTAAAGG
1 ATTAGCGGCGCTCAGATAAAAACGCCGCTAAAGG
30013384 TTTAAAAATC
Statistics
Matches: 128, Mismatches: 23, Indels: 13
0.78 0.14 0.08
Matches are distributed among these distances:
40 5 0.04
41 118 0.92
42 5 0.04
ACGTcount: A:0.34, C:0.24, G:0.25, T:0.17
Consensus pattern (41 bp):
ATTAGCGGCGCTCAGATAAAAACGCCGCTAAAGGCCAGAGA
Found at i:30013336 original size:82 final size:82
Alignment explanation
Indices: 30013186--30013383 Score: 308
Period size: 82 Copynumber: 2.4 Consensus size: 82
30013176 TTTTGTTACT
* ** * * *
30013186 ATTAGCGGCGCTTCGGCAAAAACGCCGCTAAAGGCTAGAGAATTAGTGGCGCTCAGATAAAAATG
1 ATTAGCGGCGCTTAGATAAAAACGCCGCTAAAGGCCAGAGAATTAGCGGCGCTCAGATAAAAACG
30013251 CCGCTAAATATCCGAA-C
66 CCGCTAAATATCC-AAGC
* *
30013268 ATTAGCGGCGCTTAGATAAAAACGCCGCTAAAGGCCAGAGAATTAGCGGCGCTCGGATACAAACG
1 ATTAGCGGCGCTTAGATAAAAACGCCGCTAAAGGCCAGAGAATTAGCGGCGCTCAGATAAAAACG
30013333 CCGCTAAATATCCAAGC
66 CCGCTAAATATCCAAGC
30013350 ATTAGCGGCGCTTAGATAAAAACGCCGCTAAAGG
1 ATTAGCGGCGCTTAGATAAAAACGCCGCTAAAGG
30013384 TTTAAAAATC
Statistics
Matches: 107, Mismatches: 8, Indels: 2
0.91 0.07 0.02
Matches are distributed among these distances:
81 2 0.02
82 105 0.98
ACGTcount: A:0.34, C:0.24, G:0.25, T:0.17
Consensus pattern (82 bp):
ATTAGCGGCGCTTAGATAAAAACGCCGCTAAAGGCCAGAGAATTAGCGGCGCTCAGATAAAAACG
CCGCTAAATATCCAAGC
Found at i:30015054 original size:32 final size:32
Alignment explanation
Indices: 30014984--30015063 Score: 81
Period size: 32 Copynumber: 2.5 Consensus size: 32
30014974 ACTTCACACC
* * *
30014984 CCCGTGTGGTTTCATATGGCCTGAATATCTAG
1 CCCGTGTGGTTTCACATGGCCTAAATATATAG
* *
30015016 CTCGTGTGGTTTCACA-GGTCCTAAATATATGG
1 CCCGTGTGGTTTCACATGG-CCTAAATATATAG
* *
30015048 CCCGTGTTGTTCCACA
1 CCCGTGTGGTTTCACA
30015064 CGACCATGTG
Statistics
Matches: 39, Mismatches: 8, Indels: 2
0.80 0.16 0.04
Matches are distributed among these distances:
31 2 0.05
32 37 0.95
ACGTcount: A:0.19, C:0.24, G:0.24, T:0.34
Consensus pattern (32 bp):
CCCGTGTGGTTTCACATGGCCTAAATATATAG
Found at i:30015319 original size:17 final size:17
Alignment explanation
Indices: 30015278--30015319 Score: 57
Period size: 17 Copynumber: 2.5 Consensus size: 17
30015268 AGTGAGTTAC
30015278 ACGGCCATGTGGCATCG
1 ACGGCCATGTGGCATCG
* *
30015295 ACGACCATGTGGCGTCG
1 ACGGCCATGTGGCATCG
*
30015312 ATGGCCAT
1 ACGGCCAT
30015320 ATTTTCCAGC
Statistics
Matches: 21, Mismatches: 4, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
17 21 1.00
ACGTcount: A:0.19, C:0.29, G:0.33, T:0.19
Consensus pattern (17 bp):
ACGGCCATGTGGCATCG
Found at i:30028213 original size:26 final size:26
Alignment explanation
Indices: 30028184--30028270 Score: 97
Period size: 26 Copynumber: 3.4 Consensus size: 26
30028174 GCGCTGATGC
30028184 TTATTTAGCAGGCCTTGAGTTGGTGT
1 TTATTTAGCAGGCCTTGAGTTGGTGT
* *** *
30028210 TTATTTAGAAGGCCTTGAGTCAATGG
1 TTATTTAGCAGGCCTTGAGTTGGTGT
*
30028236 TTATTTAGCAGGCTTTGA-TCTGGTGT
1 TTATTTAGCAGGCCTTGAGT-TGGTGT
30028262 TT-TTTAGCA
1 TTATTTAGCA
30028271 TGTTTTGATC
Statistics
Matches: 49, Mismatches: 11, Indels: 3
0.78 0.17 0.05
Matches are distributed among these distances:
25 8 0.16
26 41 0.84
ACGTcount: A:0.20, C:0.11, G:0.26, T:0.43
Consensus pattern (26 bp):
TTATTTAGCAGGCCTTGAGTTGGTGT
Found at i:30029510 original size:21 final size:21
Alignment explanation
Indices: 30029486--30029527 Score: 59
Period size: 21 Copynumber: 2.0 Consensus size: 21
30029476 TTTAGATATG
30029486 AAATG-CTTTTGGTCATTAGCT
1 AAATGCCTTTT-GTCATTAGCT
*
30029507 AAATGCCTTTTGTGATTAGCT
1 AAATGCCTTTTGTCATTAGCT
30029528 TGATATATGG
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
21 14 0.74
22 5 0.26
ACGTcount: A:0.24, C:0.14, G:0.19, T:0.43
Consensus pattern (21 bp):
AAATGCCTTTTGTCATTAGCT
Found at i:30033090 original size:38 final size:38
Alignment explanation
Indices: 30033039--30033113 Score: 123
Period size: 38 Copynumber: 2.0 Consensus size: 38
30033029 GTTGAATTTG
*
30033039 CTAAGTTTGATTTGTTTCGAAAATGATTTCAGTGATAA
1 CTAAGTCTGATTTGTTTCGAAAATGATTTCAGTGATAA
* *
30033077 CTAAGTCTGATTTGTTTCGAAAATTATTTTAGTGATA
1 CTAAGTCTGATTTGTTTCGAAAATGATTTCAGTGATA
30033114 TCTATATAGA
Statistics
Matches: 34, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
38 34 1.00
ACGTcount: A:0.31, C:0.08, G:0.17, T:0.44
Consensus pattern (38 bp):
CTAAGTCTGATTTGTTTCGAAAATGATTTCAGTGATAA
Found at i:30036036 original size:26 final size:26
Alignment explanation
Indices: 30036007--30036260 Score: 163
Period size: 26 Copynumber: 9.8 Consensus size: 26
30035997 AATAGCAGGG
*
30036007 CTTGAGTCGGTGTTTATTTAGCAAGC
1 CTTGAGCCGGTGTTTATTTAGCAAGC
* * * *
30036033 CTTG-GACCTGTGTTTCTTTAGTAGGC
1 CTTGAG-CCGGTGTTTATTTAGCAAGC
* * *
30036059 CTTGAGACGGTGTTTATTTAGTAGGC
1 CTTGAGCCGGTGTTTATTTAGCAAGC
* * * * *
30036085 CTTGGGCTGATGTTTCTTGAGCAAGC
1 CTTGAGCCGGTGTTTATTTAGCAAGC
* * *
30036111 CTTGAGCCGATGTTTATTTAACAGGC
1 CTTGAGCCGGTGTTTATTTAGCAAGC
* * * * *
30036137 TTTGGGCAGGTGTTTCTTTAGCAAGT
1 CTTGAGCCGGTGTTTATTTAGCAAGC
* * *
30036163 TTTGAGCCAGTGTTTATTTAGCACGC
1 CTTGAGCCGGTGTTTATTTAGCAAGC
** *
30036189 CTTGAGCTAGTGGTTATTTAGCAA-C
1 CTTGAGCCGGTGTTTATTTAGCAAGC
* * * *
30036214 TTTGAGCTGGTTTTTATTTAG-ATGGC
1 CTTGAGCCGGTGTTTATTTAGCA-AGC
* **
30036240 TTTGAGCCGGTGAATATTTAG
1 CTTGAGCCGGTGTTTATTTAG
30036261 TAGGTACTAT
Statistics
Matches: 175, Mismatches: 49, Indels: 8
0.75 0.21 0.03
Matches are distributed among these distances:
24 1 0.01
25 19 0.11
26 154 0.88
27 1 0.01
ACGTcount: A:0.19, C:0.15, G:0.27, T:0.39
Consensus pattern (26 bp):
CTTGAGCCGGTGTTTATTTAGCAAGC
Found at i:30036087 original size:52 final size:51
Alignment explanation
Indices: 30036007--30036234 Score: 183
Period size: 52 Copynumber: 4.4 Consensus size: 51
30035997 AATAGCAGGG
* * * *
30036007 CTTGAGTCGGTGTTTATTTAGCAAGCCTTGGACCTGTGTTTCTTTAGTAGGC
1 CTTGAGACGGTGTTTATTTAGCAGGCCTTGG-CCTGTGTTTCTTTAGCAAGC
* * *
30036059 CTTGAGACGGTGTTTATTTAGTAGGCCTTGGGCTGATGTTTCTTGAGCAAGC
1 CTTGAGACGGTGTTTATTTAGCAGGCCTTGGCCTG-TGTTTCTTTAGCAAGC
* * * * ** *
30036111 CTTGAGCCGATGTTTATTTAACAGGCTTTGGGCAGGTGTTTCTTTAGCAAGT
1 CTTGAGACGGTGTTTATTTAGCAGGCCTT-GGCCTGTGTTTCTTTAGCAAGC
* * * * * *
30036163 TTTGAGCCAGTGTTTATTTAGCACGCCTTGAG-CTAGTGGTTATTTAGCAA-C
1 CTTGAGACGGTGTTTATTTAGCAGGCCTTG-GCCT-GTGTTTCTTTAGCAAGC
* *
30036214 TTTGAG-CTGGTTTTTATTTAG
1 CTTGAGAC-GGTGTTTATTTAG
30036235 ATGGCTTTGA
Statistics
Matches: 141, Mismatches: 30, Indels: 11
0.77 0.16 0.06
Matches are distributed among these distances:
50 1 0.01
51 21 0.15
52 116 0.82
53 3 0.02
ACGTcount: A:0.18, C:0.15, G:0.27, T:0.40
Consensus pattern (51 bp):
CTTGAGACGGTGTTTATTTAGCAGGCCTTGGCCTGTGTTTCTTTAGCAAGC
Done.