Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NW_019168492.1 Durio zibethinus cultivar Musang King isolate D1 unplaced genomic scaffold, Duzib1.0 scaffold_9, whole genome shotgun sequence
Parameters: 2 7 7 80 10 50 1000
Pmatch=0.80,Pindel=0.10
tuple sizes 0,4,5,7
tuple distances 0, 29, 159, 1000
Length: 25814696
ACGTcount: A:0.35, C:0.15, G:0.15, T:0.35
Warning! 122000 characters in sequence are not A, C, G, or T
File 12 of 126
Found at i:2871738 original size:35 final size:35
Alignment explanation
Indices: 2871686--2871766 Score: 101
Period size: 35 Copynumber: 2.3 Consensus size: 35
2871676 TAGAACAGTT
* *
2871686 AAATAAAAAAAATAGATATATTA-TAGGATAAATAA
1 AAATAAAAAAAACAGATATATAATTA-GATAAATAA
* *
2871721 TAATAAAAATAACAGATATATAATTAGATAAATAA
1 AAATAAAAAAAACAGATATATAATTAGATAAATAA
*
2871756 AAATACAAAAA
1 AAATAAAAAAA
2871767 TAAATAAAAT
Statistics
Matches: 38, Mismatches: 7, Indels: 2
0.81 0.15 0.04
Matches are distributed among these distances:
35 36 0.95
36 2 0.05
ACGTcount: A:0.67, C:0.02, G:0.06, T:0.25
Consensus pattern (35 bp):
AAATAAAAAAAACAGATATATAATTAGATAAATAA
Found at i:2871776 original size:78 final size:72
Alignment explanation
Indices: 2871686--2871827 Score: 167
Period size: 78 Copynumber: 1.9 Consensus size: 72
2871676 TAGAACAGTT
* * *
2871686 AAATAAAAAAAATAGATATATTATAGGATAAATAATAATAAAAATAACAGATATATAATTAGATA
1 AAATAAAAAAAATAGAAAAATTATA--AT-AATAATAATAAAAA-AA-A-ATATATAACTAGATA
2871751 AATAAAAATACAA
60 AATAAAAATACAA
* * * *
2871764 AAATAAATAAAATATAAAAATTATAATAATAATAATAATAAAAAATATATAACTATATAAATAA
1 AAATAAAAAAAATAGAAAAATTATAATAATAATAATAAAAAAAAATATATAACTAGATAAATAA
2871828 TATACATATA
Statistics
Matches: 57, Mismatches: 7, Indels: 6
0.81 0.10 0.09
Matches are distributed among these distances:
72 18 0.32
73 1 0.02
74 2 0.04
75 13 0.23
76 2 0.04
78 21 0.37
ACGTcount: A:0.67, C:0.02, G:0.04, T:0.27
Consensus pattern (72 bp):
AAATAAAAAAAATAGAAAAATTATAATAATAATAATAAAAAAAAATATATAACTAGATAAATAAA
AATACAA
Found at i:2871777 original size:17 final size:18
Alignment explanation
Indices: 2871748--2871784 Score: 58
Period size: 17 Copynumber: 2.1 Consensus size: 18
2871738 ATATAATTAG
2871748 ATAAATAAAAATACAAAA
1 ATAAATAAAAATACAAAA
*
2871766 ATAAAT-AAAATATAAAA
1 ATAAATAAAAATACAAAA
2871783 AT
1 AT
2871785 TATAATAATA
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
17 12 0.67
18 6 0.33
ACGTcount: A:0.76, C:0.03, G:0.00, T:0.22
Consensus pattern (18 bp):
ATAAATAAAAATACAAAA
Found at i:2871781 original size:25 final size:25
Alignment explanation
Indices: 2871716--2871810 Score: 70
Period size: 25 Copynumber: 3.6 Consensus size: 25
2871706 TTATAGGATA
*
2871716 AATAATAATAAAAATAACAGATATATAATT
1 AATAAT-ATAAAAAT-ACA-A-AAATAA-T
2871746 AGATAA-ATAAAAATACAAAAATAAAT
1 A-ATAATATAAAAATACAAAAAT-AAT
* *
2871772 AA-AATATAAAAATTATAATAATAAT
1 AATAATATAAAAA-TACAAAAATAAT
2871797 AATAATA-AAAAATA
1 AATAATATAAAAATA
2871811 TATAACTATA
Statistics
Matches: 57, Mismatches: 3, Indels: 16
0.75 0.04 0.21
Matches are distributed among these distances:
24 4 0.07
25 18 0.32
26 16 0.28
27 3 0.05
28 3 0.05
29 8 0.14
30 1 0.02
31 4 0.07
ACGTcount: A:0.69, C:0.02, G:0.02, T:0.26
Consensus pattern (25 bp):
AATAATATAAAAATACAAAAATAAT
Found at i:2871814 original size:26 final size:29
Alignment explanation
Indices: 2871766--2871829 Score: 84
Period size: 25 Copynumber: 2.3 Consensus size: 29
2871756 AAATACAAAA
2871766 ATAAATAA-AATATAAAAATTATAA-TA-
1 ATAAATAATAATATAAAAATTATAACTAT
2871792 AT-AATAATAATA-AAAAATATATAACTAT
1 ATAAATAATAATATAAAAAT-TATAACTAT
2871820 ATAAATAATA
1 ATAAATAATA
2871830 TACATATAAA
Statistics
Matches: 33, Mismatches: 0, Indels: 7
0.82 0.00 0.17
Matches are distributed among these distances:
25 11 0.33
26 11 0.33
27 2 0.06
28 2 0.06
29 7 0.21
ACGTcount: A:0.67, C:0.02, G:0.00, T:0.31
Consensus pattern (29 bp):
ATAAATAATAATATAAAAATTATAACTAT
Found at i:2871815 original size:23 final size:23
Alignment explanation
Indices: 2871717--2871829 Score: 70
Period size: 26 Copynumber: 4.7 Consensus size: 23
2871707 TATAGGATAA
* * *
2871717 ATAATAATAAAAATAACAGATAT
1 ATAATAATAATAATAAAAAATAT
* *
2871740 ATAATTAGATAAATAAAAATACAAAAAT
1 ATAA-TA-AT-AATAATAA-A-AAATAT
*
2871768 A-AATAA-AAT-ATAAAAATTAT
1 ATAATAATAATAATAAAAAATAT
2871788 AATAATAATAATAATAAAAAATAT
1 -ATAATAATAATAATAAAAAATAT
2871812 ATAACTATATAAATAATA
1 ATAA-TA-AT-AATAATA
2871830 TACATATAAA
Statistics
Matches: 69, Mismatches: 9, Indels: 21
0.70 0.09 0.21
Matches are distributed among these distances:
20 4 0.06
21 2 0.03
22 8 0.12
23 14 0.20
24 14 0.20
25 5 0.07
26 15 0.22
27 2 0.03
28 5 0.07
ACGTcount: A:0.67, C:0.03, G:0.02, T:0.28
Consensus pattern (23 bp):
ATAATAATAATAATAAAAAATAT
Found at i:2871827 original size:35 final size:35
Alignment explanation
Indices: 2871713--2871829 Score: 112
Period size: 35 Copynumber: 3.3 Consensus size: 35
2871703 ATATTATAGG
* * * *
2871713 ATAAATAATAATAAAAATAACAGATATATAATTAG
1 ATAAATAATAATAAAAATAAAAAATATATAAATAT
* *
2871748 ATAAATAAAAATACAAAAATAAATAAA-ATATAAAAAT
1 ATAAATAATAAT--AAAAATAAA-AAATATATAAATAT
* *
2871785 -TATAATAATAATAATAATAAAAAATATATAACTAT
1 ATA-AATAATAATAAAAATAAAAAATATATAAATAT
2871820 ATAAATAATA
1 ATAAATAATA
2871830 TACATATAAA
Statistics
Matches: 66, Mismatches: 10, Indels: 12
0.75 0.11 0.14
Matches are distributed among these distances:
34 3 0.05
35 34 0.52
36 4 0.06
37 23 0.35
38 2 0.03
ACGTcount: A:0.68, C:0.03, G:0.02, T:0.28
Consensus pattern (35 bp):
ATAAATAATAATAAAAATAAAAAATATATAAATAT
Found at i:2872112 original size:1 final size:1
Alignment explanation
Indices: 2872106--2872230 Score: 97
Period size: 1 Copynumber: 125.0 Consensus size: 1
2872096 AACATTGTCA
* * * * * * ** * * * *
2872106 TTTTTTTTGTTTTTTTGTGTTTTTTGTGTTTTTTTGTTTTTTTGGTTTTGTTTTTTGTGTTTTGT
1 TTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTT
* * * * *
2872171 TTTTTTTTTTTTTTTTGTTTTTTTTTTTTTTGTTTTTTTGTTTTGTTTTATTTTTTTTTT
1 TTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTT
2872231 ACCAAAGCTC
Statistics
Matches: 92, Mismatches: 32, Indels: 0
0.74 0.26 0.00
Matches are distributed among these distances:
1 92 1.00
ACGTcount: A:0.01, C:0.00, G:0.13, T:0.86
Consensus pattern (1 bp):
T
Found at i:2872120 original size:9 final size:9
Alignment explanation
Indices: 2872106--2872228 Score: 123
Period size: 8 Copynumber: 13.9 Consensus size: 9
2872096 AACATTGTCA
2872106 TTTTTTTTG
1 TTTTTTTTG
2872115 -TTTTTTTG
1 TTTTTTTTG
*
2872123 TGTTTTTTG
1 TTTTTTTTG
2872132 TGTTTTTTTG
1 T-TTTTTTTG
*
2872142 TTTTTTTGG
1 TTTTTTTTG
2872151 TTTTGTTTT-
1 TTTT-TTTTG
*
2872160 TTGTGTTTTG
1 TT-TTTTTTG
2872170 TTTTTTTT-
1 TTTTTTTTG
2872178 TTTTTTTT-
1 TTTTTTTTG
*
2872186 TGTTTTTT-
1 TTTTTTTTG
2872194 TTTTTTTTG
1 TTTTTTTTG
2872203 -TTTTTTTG
1 TTTTTTTTG
*
2872211 TTTTGTTTTA
1 TTTT-TTTTG
2872221 TTTTTTTT
1 TTTTTTTT
2872229 TTACCAAAGC
Statistics
Matches: 97, Mismatches: 9, Indels: 16
0.80 0.07 0.13
Matches are distributed among these distances:
8 38 0.39
9 37 0.38
10 22 0.23
ACGTcount: A:0.01, C:0.00, G:0.13, T:0.86
Consensus pattern (9 bp):
TTTTTTTTG
Found at i:2872225 original size:46 final size:44
Alignment explanation
Indices: 2872107--2872230 Score: 135
Period size: 46 Copynumber: 2.8 Consensus size: 44
2872097 ACATTGTCAT
* * *
2872107 TTTTTTTGTTTTT-TTGTGTTTTTTGTGTTTTTTTGTTTTTTTGG
1 TTTTTTTTTTTTTGTTTTGTTTTTT-TTTTTTTTTGTTTTTTTGG
* * *
2872151 TTTTGTTTTTTGTGTTTTGTTTTTTTTTTTTTTTTTGTTTTTTT-T
1 TTTTTTTTTTTTTGTTTTG--TTTTTTTTTTTTTTTGTTTTTTTGG
*
2872196 TTTTTTGTTTTTTTGTTTTGTTTTATTTTTTTTTT
1 TTTTTT-TTTTTTTGTTTTGTTTTTTTTTTTTTTT
2872231 ACCAAAGCTC
Statistics
Matches: 67, Mismatches: 9, Indels: 8
0.80 0.11 0.10
Matches are distributed among these distances:
44 24 0.36
45 9 0.13
46 28 0.42
47 6 0.09
ACGTcount: A:0.01, C:0.00, G:0.13, T:0.86
Consensus pattern (44 bp):
TTTTTTTTTTTTTGTTTTGTTTTTTTTTTTTTTTGTTTTTTTGG
Found at i:2872227 original size:8 final size:8
Alignment explanation
Indices: 2872107--2872214 Score: 127
Period size: 8 Copynumber: 13.5 Consensus size: 8
2872097 ACATTGTCAT
2872107 TTTTTTTG
1 TTTTTTTG
2872115 TTTTTTTGTG
1 -TTTTTT-TG
2872125 TTTTTTGTG
1 TTTTTT-TG
2872134 TTTTTTTG
1 TTTTTTTG
2872142 TTTTTTTG
1 TTTTTTTG
*
2872150 --GTTTTG
1 TTTTTTTG
2872156 TTTTTTGTG
1 TTTTTT-TG
2872165 TTTTGTTT-
1 TTTT-TTTG
2872173 TTTTTTT-
1 TTTTTTTG
2872180 TTTTTTTG
1 TTTTTTTG
2872188 TTTTTTT-
1 TTTTTTTG
2872195 TTTTTTTG
1 TTTTTTTG
2872203 TTTTTTTG
1 TTTTTTTG
2872211 TTTT
1 TTTT
2872215 GTTTTATTTT
Statistics
Matches: 90, Mismatches: 2, Indels: 15
0.84 0.02 0.14
Matches are distributed among these distances:
6 5 0.06
7 17 0.19
8 36 0.40
9 28 0.31
10 4 0.04
ACGTcount: A:0.00, C:0.00, G:0.14, T:0.86
Consensus pattern (8 bp):
TTTTTTTG
Found at i:2872331 original size:41 final size:42
Alignment explanation
Indices: 2872237--2872660 Score: 623
Period size: 41 Copynumber: 10.1 Consensus size: 42
2872227 TTTTACCAAA
* * *
2872237 GCTCTTCTAAACAGAGGCTCAACGACTTTGAGAAACA-TAAATT
1 GCTCCTCTAAACAGAGGCACCACGACTTTG-GAAA-AGTAAATT
*
2872280 GCTCCTCTAAACAGAGGGACCACGAC-TTGGAAAAGTAAATT
1 GCTCCTCTAAACAGAGGCACCACGACTTTGGAAAAGTAAATT
* *
2872321 GCTCCTCTAAACAGAGGGACCACGACTTTGTATTGGAAAGTAAATT
1 GCTCCTCTAAACAGAGGCACCACGACTTTG----GAAAAGTAAATT
* *
2872367 GCTCCTCTAAACAGAGGCACCGCGACTTT-GAAAAATAAATT
1 GCTCCTCTAAACAGAGGCACCACGACTTTGGAAAAGTAAATT
2872408 GCTCCTCTAAACAGAGGCACCACGACTTT-GAAAAGTAAATT
1 GCTCCTCTAAACAGAGGCACCACGACTTTGGAAAAGTAAATT
2872449 GCTCCTCTAAACAGAGGCACCACGACTTT-GAAAAGTAAATT
1 GCTCCTCTAAACAGAGGCACCACGACTTTGGAAAAGTAAATT
2872490 GCTCCTCTAAACAGAGG--CCACGACTTTGGAAAA-TAAATT
1 GCTCCTCTAAACAGAGGCACCACGACTTTGGAAAAGTAAATT
*
2872529 GCTCCTCTAAACAGAGGCACCACGACTTTGAAAAAGTAAATT
1 GCTCCTCTAAACAGAGGCACCACGACTTTGGAAAAGTAAATT
2872571 GCTCCTCTAAACAGAGGCACCACGACTTTGGAAAAGTAAATT
1 GCTCCTCTAAACAGAGGCACCACGACTTTGGAAAAGTAAATT
*
2872613 GCTCCTCTAAATAGAGGCACCACGACTTTGGGAAAA-TAAATT
1 GCTCCTCTAAACAGAGGCACCACGACTTT-GGAAAAGTAAATT
*
2872655 ACTCCT
1 GCTCCT
2872661 TGACAATCAT
Statistics
Matches: 355, Mismatches: 15, Indels: 23
0.90 0.04 0.06
Matches are distributed among these distances:
39 33 0.09
40 6 0.02
41 158 0.45
42 92 0.26
43 28 0.08
46 38 0.11
ACGTcount: A:0.36, C:0.23, G:0.18, T:0.23
Consensus pattern (42 bp):
GCTCCTCTAAACAGAGGCACCACGACTTTGGAAAAGTAAATT
Found at i:2872472 original size:128 final size:124
Alignment explanation
Indices: 2872237--2872660 Score: 640
Period size: 128 Copynumber: 3.4 Consensus size: 124
2872227 TTTTACCAAA
* * * *
2872237 GCTCTTCTAAACAGAGGCTCAACGACTTTGAGAAACATAAATTGCTCCTCTAAACAGAGGGACCA
1 GCTCCTCTAAACAGAGGCACCACGACTTTGA-AAA-ATAAATTGCTCCTCTAAACAGAGGCACCA
* *
2872302 CGACTTGGAAAAGTAAATTGCTCCTCTAAACAGAGGGACCACGACTTTGTATTGGAAAGTAAATT
64 CGACTTTGAAAAGTAAATTGCTCCTCTAAACAGAGGCACCACGACTTTG-A---GAAAGTAAATT
*
2872367 GCTCCTCTAAACAGAGGCACCGCGACTTTGAAAAATAAATTGCTCCTCTAAACAGAGGCACCACG
1 GCTCCTCTAAACAGAGGCACCACGACTTTGAAAAATAAATTGCTCCTCTAAACAGAGGCACCACG
2872432 ACTTTGAAAAGTAAATTGCTCCTCTAAACAGAGGCACCACGACTTTGA-AAAGTAAATT
66 ACTTTGAAAAGTAAATTGCTCCTCTAAACAGAGGCACCACGACTTTGAGAAAGTAAATT
*
2872490 GCTCCTCTAAACAGAGG--CCACGACTTTGGAAAATAAATTGCTCCTCTAAACAGAGGCACCACG
1 GCTCCTCTAAACAGAGGCACCACGACTTTGAAAAATAAATTGCTCCTCTAAACAGAGGCACCACG
2872553 ACTTTGAAAAAGTAAATTGCTCCTCTAAACAGAGGCACCACGACTTTG-GAAAAGTAAATT
66 ACTTTG-AAAAGTAAATTGCTCCTCTAAACAGAGGCACCACGACTTTGAG-AAAGTAAATT
* * *
2872613 GCTCCTCTAAATAGAGGCACCACGACTTTGGGAAAATAAATTACTCCT
1 GCTCCTCTAAACAGAGGCACCACGACTTT-GAAAAATAAATTGCTCCT
2872661 TGACAATCAT
Statistics
Matches: 277, Mismatches: 11, Indels: 16
0.91 0.04 0.05
Matches are distributed among these distances:
121 50 0.18
122 41 0.15
123 53 0.19
125 10 0.04
126 17 0.06
127 1 0.00
128 75 0.27
129 3 0.01
130 27 0.10
ACGTcount: A:0.36, C:0.23, G:0.18, T:0.23
Consensus pattern (124 bp):
GCTCCTCTAAACAGAGGCACCACGACTTTGAAAAATAAATTGCTCCTCTAAACAGAGGCACCACG
ACTTTGAAAAGTAAATTGCTCCTCTAAACAGAGGCACCACGACTTTGAGAAAGTAAATT
Found at i:2873886 original size:26 final size:25
Alignment explanation
Indices: 2873868--2873915 Score: 73
Period size: 25 Copynumber: 2.0 Consensus size: 25
2873858 CTTTTTTTCA
2873868 TTTTC-TCAT-TTTTTTTCTTTTTT
1 TTTTCATCATCTTTTTTTCTTTTTT
*
2873891 TTTTCATCATCTTTTTTTCATTTTT
1 TTTTCATCATCTTTTTTTCTTTTTT
2873916 CATCCATTGT
Statistics
Matches: 22, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
23 5 0.23
24 4 0.18
25 13 0.59
ACGTcount: A:0.08, C:0.15, G:0.00, T:0.77
Consensus pattern (25 bp):
TTTTCATCATCTTTTTTTCTTTTTT
Found at i:2873916 original size:21 final size:21
Alignment explanation
Indices: 2873857--2873919 Score: 65
Period size: 21 Copynumber: 3.0 Consensus size: 21
2873847 AATTTGAATC
*
2873857 TCTTTTTTTCATTTTCTCAT-T
1 TCTTTTTTTCATTTT-TCATCA
* **
2873878 TTTTTTCTTTTTTTTTTCATCA
1 TCTTTT-TTTCATTTTTCATCA
2873900 TCTTTTTTTCATTTTTCATC
1 TCTTTTTTTCATTTTTCATC
2873920 CATTGTTGAT
Statistics
Matches: 33, Mismatches: 7, Indels: 4
0.75 0.16 0.09
Matches are distributed among these distances:
21 21 0.64
22 12 0.36
ACGTcount: A:0.10, C:0.17, G:0.00, T:0.73
Consensus pattern (21 bp):
TCTTTTTTTCATTTTTCATCA
Found at i:2874805 original size:24 final size:23
Alignment explanation
Indices: 2874750--2874805 Score: 58
Period size: 24 Copynumber: 2.3 Consensus size: 23
2874740 AAGCGAAGTC
*
2874750 ACATTGCAAAAAGAAATCCAACAA
1 ACATT-CAAAAAAAAATCCAACAA
* * *
2874774 TCACTCAAAAAAAAATCCTAAGAA
1 ACATTCAAAAAAAAATCC-AACAA
2874798 ACATTCAA
1 ACATTCAA
2874806 CCAGCCTTAT
Statistics
Matches: 25, Mismatches: 6, Indels: 2
0.76 0.18 0.06
Matches are distributed among these distances:
23 12 0.48
24 13 0.52
ACGTcount: A:0.57, C:0.21, G:0.05, T:0.16
Consensus pattern (23 bp):
ACATTCAAAAAAAAATCCAACAA
Found at i:2878022 original size:62 final size:60
Alignment explanation
Indices: 2877781--2878113 Score: 447
Period size: 61 Copynumber: 5.7 Consensus size: 60
2877771 TGTGCAGGGG
2877781 AAATTGATACTTTCAACTTTT-CTC-AAAAA-A--TTTTTTG-AAATTTATTTTTAAGGA
1 AAATTGATACTTTCAACTTTTCCTCAAAAAATATTTTTTTTGAAAATTTATTTTTAAGGA
*
2877835 AAATTGATACTTTCAACTTTTCCT-AAAAAATCTTTTTTTTGAAAATTTATTTTTAAGGA
1 AAATTGATACTTTCAACTTTTCCTCAAAAAATATTTTTTTTGAAAATTTATTTTTAAGGA
* * *
2877894 AAATTGATACTTTCAGCTTTTCC-CCAAAAATA--TTTTTTGAAAATTTATTTCTAAGGA
1 AAATTGATACTTTCAACTTTTCCTCAAAAAATATTTTTTTTGAAAATTTATTTTTAAGGA
* **
2877951 AAATTGATACTTTCAACTTTTCCTCAAAAATATATTTTTTTTGAAACTTTGATTTCCAAGGA
1 AAATTGATACTTTCAACTTTTCCTCAAAAA-ATATTTTTTTTGAAAATTT-ATTTTTAAGGA
* * *
2878013 AAATTGATACTTTCAACTTTTCCT-AAAAAATCTTTTTTTTTCAAAAATTTATTTTTAAGAA
1 AAATTGATACTTTCAACTTTTCCTCAAAAAAT-ATTTTTTTT-GAAAATTTATTTTTAAGGA
*
2878074 AAATTGATACTTTCAACTTTTCC-CCAAAAATATTTTTTTT
1 AAATTGATACTTTCAACTTTTCCTCAAAAAATATTTTTTTT
2878114 TTTGGAATTT
Statistics
Matches: 247, Mismatches: 17, Indels: 24
0.86 0.06 0.08
Matches are distributed among these distances:
54 21 0.09
55 7 0.03
57 46 0.19
58 12 0.05
59 48 0.19
60 10 0.04
61 63 0.26
62 40 0.16
ACGTcount: A:0.35, C:0.13, G:0.06, T:0.46
Consensus pattern (60 bp):
AAATTGATACTTTCAACTTTTCCTCAAAAAATATTTTTTTTGAAAATTTATTTTTAAGGA
Found at i:2878173 original size:6 final size:6
Alignment explanation
Indices: 2878141--2878220 Score: 56
Period size: 6 Copynumber: 12.7 Consensus size: 6
2878131 TTATTTAAAG
* * *
2878141 AAAATA GAATAATA AAAAGA TAAATA AAAATA AAAATA AAGAA-A AGTAGAACA
1 AAAATA -AA-AATA AAAATA AAAATA AAAATA AAAATA AA-AATA A--A-AATA
*
2878194 AAAATA AAAAT- AAAATA AAGATA AAAA
1 AAAATA AAAATA AAAATA AAAATA AAAA
2878221 GAATATTAAA
Statistics
Matches: 60, Mismatches: 7, Indels: 13
0.75 0.09 0.16
Matches are distributed among these distances:
5 5 0.08
6 38 0.63
7 7 0.12
8 8 0.13
9 2 0.03
ACGTcount: A:0.76, C:0.01, G:0.07, T:0.15
Consensus pattern (6 bp):
AAAATA
Found at i:2878185 original size:27 final size:26
Alignment explanation
Indices: 2878148--2878218 Score: 90
Period size: 27 Copynumber: 2.6 Consensus size: 26
2878138 AAGAAAATAG
*
2878148 AATAATAAAAAGATAAATAAAAATAAA
1 AATAA-AAAAAGATAAACAAAAATAAA
2878175 AATAAAGAAAAG-TAGAACAAAAATAAA
1 AATAAA-AAAAGATA-AACAAAAATAAA
2878202 AATAAAATAAAGATAAA
1 AATAAAA-AAAGATAAA
2878219 AAGAATATTA
Statistics
Matches: 39, Mismatches: 1, Indels: 8
0.81 0.02 0.17
Matches are distributed among these distances:
26 4 0.10
27 33 0.85
28 2 0.05
ACGTcount: A:0.76, C:0.01, G:0.07, T:0.15
Consensus pattern (26 bp):
AATAAAAAAAGATAAACAAAAATAAA
Found at i:2878219 original size:11 final size:11
Alignment explanation
Indices: 2878156--2878219 Score: 53
Period size: 11 Copynumber: 5.9 Consensus size: 11
2878146 AGAATAATAA
2878156 AAAGAT-AAAT
1 AAAGATAAAAT
*
2878166 AAAAATAAAAAT
1 AAAGAT-AAAAT
*
2878178 AAAGA-AAAGT
1 AAAGATAAAAT
*
2878188 AGAACA-AAAAT
1 A-AAGATAAAAT
*
2878199 AAAAATAAAAT
1 AAAGATAAAAT
2878210 AAAGATAAAA
1 AAAGATAAAA
2878220 AGAATATTAA
Statistics
Matches: 43, Mismatches: 7, Indels: 7
0.75 0.12 0.12
Matches are distributed among these distances:
10 13 0.30
11 22 0.51
12 8 0.19
ACGTcount: A:0.77, C:0.02, G:0.08, T:0.14
Consensus pattern (11 bp):
AAAGATAAAAT
Found at i:2878737 original size:30 final size:31
Alignment explanation
Indices: 2878701--2878760 Score: 86
Period size: 31 Copynumber: 2.0 Consensus size: 31
2878691 GGGTTGGTCG
* * *
2878701 CCGAAAACTTC-AAGTTGGCCGGAATTTTCA
1 CCGAAAAATTCAAACTTCGCCGGAATTTTCA
2878731 CCGAAAAATTCAAACTTCGCCGGAATTTTC
1 CCGAAAAATTCAAACTTCGCCGGAATTTTC
2878761 GTCGGAATCT
Statistics
Matches: 26, Mismatches: 3, Indels: 1
0.87 0.10 0.03
Matches are distributed among these distances:
30 10 0.38
31 16 0.62
ACGTcount: A:0.32, C:0.25, G:0.17, T:0.27
Consensus pattern (31 bp):
CCGAAAAATTCAAACTTCGCCGGAATTTTCA
Found at i:2879198 original size:35 final size:35
Alignment explanation
Indices: 2879159--2879225 Score: 100
Period size: 35 Copynumber: 1.9 Consensus size: 35
2879149 AGATAAATCG
*
2879159 AAAAAAAAACAGATATATTA-TAGGATAAATAATAA
1 AAAAAAAAACAGATATATAATTA-GATAAATAATAA
*
2879194 AAAAAATAACAGATATATAATTAGATAAATAA
1 AAAAAAAAACAGATATATAATTAGATAAATAA
2879226 AAATACAAAA
Statistics
Matches: 29, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
35 27 0.93
36 2 0.07
ACGTcount: A:0.66, C:0.03, G:0.07, T:0.24
Consensus pattern (35 bp):
AAAAAAAAACAGATATATAATTAGATAAATAATAA
Found at i:2879225 original size:32 final size:31
Alignment explanation
Indices: 2879119--2879228 Score: 89
Period size: 32 Copynumber: 3.4 Consensus size: 31
2879109 TAAAAATCAA
* * *
2879119 ATAAATATAAAAAATAATAGATA-ATTAAACAG
1 ATAAATAAAAAAAATAACAGATATA-T-AATAG
* *
2879151 ATAAATCGAAAAAAA-AACAGATATATTATAGG
1 ATAAAT-AAAAAAAATAACAGATATATAATA-G
2879183 ATAAATAATAAAAAAAATAACAGATATATAATTAG
1 AT--A-AATAAAAAAAATAACAGATATATAA-TAG
2879218 ATAAATAAAAA
1 ATAAATAAAAA
2879229 TACAAAAATA
Statistics
Matches: 63, Mismatches: 7, Indels: 16
0.73 0.08 0.19
Matches are distributed among these distances:
31 2 0.03
32 25 0.40
33 8 0.13
34 8 0.13
35 18 0.29
36 2 0.03
ACGTcount: A:0.65, C:0.04, G:0.07, T:0.24
Consensus pattern (31 bp):
ATAAATAAAAAAAATAACAGATATATAATAG
Found at i:2879241 original size:18 final size:18
Alignment explanation
Indices: 2879218--2879268 Score: 77
Period size: 18 Copynumber: 2.8 Consensus size: 18
2879208 ATATAATTAG
*
2879218 ATAAATAAAAATACAAAA
1 ATAAATAAAAATAAAAAA
2879236 ATAAATAAAAATAAAAAAA
1 ATAAATAAAAAT-AAAAAA
2879255 ATAAA-AAAAATAAA
1 ATAAATAAAAATAAA
2879269 TATATAACTA
Statistics
Matches: 31, Mismatches: 1, Indels: 3
0.89 0.03 0.09
Matches are distributed among these distances:
17 3 0.10
18 18 0.58
19 10 0.32
ACGTcount: A:0.82, C:0.02, G:0.00, T:0.16
Consensus pattern (18 bp):
ATAAATAAAAATAAAAAA
Found at i:2879245 original size:9 final size:9
Alignment explanation
Indices: 2879218--2879270 Score: 54
Period size: 9 Copynumber: 5.8 Consensus size: 9
2879208 ATATAATTAG
2879218 ATAAATAAAA
1 ATAAAT-AAA
*
2879228 ATACA-AAA
1 ATAAATAAA
2879236 ATAAATAAAA
1 ATAAAT-AAA
*
2879246 ATAAAAAAA
1 ATAAATAAA
*
2879255 ATAAAAAAA
1 ATAAATAAA
2879264 ATAAATA
1 ATAAATA
2879271 TATAACTATA
Statistics
Matches: 37, Mismatches: 4, Indels: 5
0.80 0.09 0.11
Matches are distributed among these distances:
8 7 0.19
9 18 0.49
10 12 0.32
ACGTcount: A:0.81, C:0.02, G:0.00, T:0.17
Consensus pattern (9 bp):
ATAAATAAA
Found at i:2879260 original size:24 final size:24
Alignment explanation
Indices: 2879220--2879268 Score: 64
Period size: 24 Copynumber: 2.0 Consensus size: 24
2879210 ATAATTAGAT
* *
2879220 AAATAAAAATACAAAAATAAATAA
1 AAATAAAAATAAAAAAAAAAATAA
2879244 AAATAAAAA-AAATAAAAAAAATAA
1 AAATAAAAATAAA-AAAAAAAATAA
2879268 A
1 A
2879269 TATATAACTA
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
23 2 0.09
24 20 0.91
ACGTcount: A:0.84, C:0.02, G:0.00, T:0.14
Consensus pattern (24 bp):
AAATAAAAATAAAAAAAAAAATAA
Found at i:2879298 original size:15 final size:16
Alignment explanation
Indices: 2879264--2879300 Score: 51
Period size: 15 Copynumber: 2.4 Consensus size: 16
2879254 AATAAAAAAA
2879264 ATAAATATATAACTAT
1 ATAAATATATAACTAT
2879280 ATAAATA-ATATAC-AT
1 ATAAATATATA-ACTAT
2879295 ATAAAT
1 ATAAAT
2879301 CTATTCTAAA
Statistics
Matches: 20, Mismatches: 0, Indels: 3
0.87 0.00 0.13
Matches are distributed among these distances:
15 11 0.55
16 9 0.45
ACGTcount: A:0.59, C:0.05, G:0.00, T:0.35
Consensus pattern (16 bp):
ATAAATATATAACTAT
Found at i:2879538 original size:22 final size:22
Alignment explanation
Indices: 2879498--2879570 Score: 76
Period size: 22 Copynumber: 3.3 Consensus size: 22
2879488 TAGTCAAAGC
* **
2879498 ATAATAACTTAATAATAAATCA
1 ATAATAACGTAATTGTAAATCA
*
2879520 ATTATAACGTAATTGTAAATGCA
1 ATAATAACGTAATTGTAAAT-CA
* *
2879543 A-AATAACGTAGTTGTAAATTA
1 ATAATAACGTAATTGTAAATCA
2879564 ATAATAA
1 ATAATAA
2879571 TTTCATAAAA
Statistics
Matches: 42, Mismatches: 7, Indels: 4
0.79 0.13 0.08
Matches are distributed among these distances:
21 2 0.05
22 37 0.88
23 3 0.07
ACGTcount: A:0.52, C:0.07, G:0.08, T:0.33
Consensus pattern (22 bp):
ATAATAACGTAATTGTAAATCA
Found at i:2879839 original size:22 final size:22
Alignment explanation
Indices: 2879814--2879900 Score: 75
Period size: 22 Copynumber: 4.0 Consensus size: 22
2879804 AACAGTATAG
*
2879814 TAGTAAATCGCTAATAATTTAA
1 TAGTAAATCACTAATAATTTAA
* * * * *
2879836 TAGTGAATTATTGATAATTTAG
1 TAGTAAATCACTAATAATTTAA
* **
2879858 TATTAAATCACTAATAACGTAA
1 TAGTAAATCACTAATAATTTAA
* *
2879880 TAGTAAATCATTGATAATTTA
1 TAGTAAATCACTAATAATTTA
2879901 TTTATAAATT
Statistics
Matches: 46, Mismatches: 19, Indels: 0
0.71 0.29 0.00
Matches are distributed among these distances:
22 46 1.00
ACGTcount: A:0.44, C:0.07, G:0.10, T:0.39
Consensus pattern (22 bp):
TAGTAAATCACTAATAATTTAA
Found at i:2879909 original size:44 final size:44
Alignment explanation
Indices: 2879811--2879900 Score: 126
Period size: 44 Copynumber: 2.0 Consensus size: 44
2879801 TATAACAGTA
* * ** * *
2879811 TAGTAGTAAATCGCTAATAATTTAATAGTGAATTATTGATAATT
1 TAGTATTAAATCACTAATAACGTAATAGTAAATCATTGATAATT
2879855 TAGTATTAAATCACTAATAACGTAATAGTAAATCATTGATAATT
1 TAGTATTAAATCACTAATAACGTAATAGTAAATCATTGATAATT
2879899 TA
1 TA
2879901 TTTATAAATT
Statistics
Matches: 40, Mismatches: 6, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
44 40 1.00
ACGTcount: A:0.43, C:0.07, G:0.11, T:0.39
Consensus pattern (44 bp):
TAGTATTAAATCACTAATAACGTAATAGTAAATCATTGATAATT
Found at i:2879956 original size:22 final size:22
Alignment explanation
Indices: 2879931--2880070 Score: 129
Period size: 22 Copynumber: 6.4 Consensus size: 22
2879921 AGTTATAAAT
* * *
2879931 TAGTTAATTATTAATAATTTTA
1 TAGTAAATTATCAATAACTTTA
*
2879953 TAGTAAATCATCAATAACTTTA
1 TAGTAAATTATCAATAACTTTA
** *
2879975 TAGTAAATTAGAAATAACATTA
1 TAGTAAATTATCAATAACTTTA
* * *
2879997 TAATAAATTATTAATAACTTAA
1 TAGTAAATTATCAATAACTTTA
*
2880019 TAGTAAATTATCAATAACTTAA
1 TAGTAAATTATCAATAACTTTA
* * **
2880041 TAATAAATCATTTATAAC-TTA
1 TAGTAAATTATCAATAACTTTA
2880062 GTAGTAAAT
1 -TAGTAAAT
2880071 CATTTTATAA
Statistics
Matches: 96, Mismatches: 21, Indels: 2
0.81 0.18 0.02
Matches are distributed among these distances:
21 2 0.02
22 94 0.98
ACGTcount: A:0.49, C:0.06, G:0.05, T:0.40
Consensus pattern (22 bp):
TAGTAAATTATCAATAACTTTA
Found at i:2879991 original size:44 final size:44
Alignment explanation
Indices: 2879943--2880070 Score: 150
Period size: 44 Copynumber: 2.9 Consensus size: 44
2879933 GTTAATTATT
* * *
2879943 AATAATTTTATAGTAAATCATCAATAACTTTATAGTAAATTAGA
1 AATAACTTTATAATAAATCATTAATAACTTTATAGTAAATTAGA
* * * **
2879987 AATAACATTATAATAAATTATTAATAACTTAATAGTAAATTATC
1 AATAACTTTATAATAAATCATTAATAACTTTATAGTAAATTAGA
* *
2880031 AATAACTTAATAATAAATCATTTATAAC-TTAGTAGTAAAT
1 AATAACTTTATAATAAATCATTAATAACTTTA-TAGTAAAT
2880071 CATTTTATAA
Statistics
Matches: 70, Mismatches: 13, Indels: 2
0.82 0.15 0.02
Matches are distributed among these distances:
43 2 0.03
44 68 0.97
ACGTcount: A:0.50, C:0.07, G:0.05, T:0.38
Consensus pattern (44 bp):
AATAACTTTATAATAAATCATTAATAACTTTATAGTAAATTAGA
Found at i:2880011 original size:11 final size:11
Alignment explanation
Indices: 2879978--2880048 Score: 58
Period size: 11 Copynumber: 6.5 Consensus size: 11
2879968 AACTTTATAG
2879978 TAAATTAGA-AA
1 TAAATTA-ATAA
2879989 TAACATT-ATAA
1 TAA-ATTAATAA
*
2880000 TAAATTATTAA
1 TAAATTAATAA
* *
2880011 TAACTTAATAG
1 TAAATTAATAA
2880022 TAAATT-ATCAA
1 TAAATTAAT-AA
*
2880033 TAACTTAATAA
1 TAAATTAATAA
2880044 TAAAT
1 TAAAT
2880049 CATTTATAAC
Statistics
Matches: 47, Mismatches: 8, Indels: 10
0.72 0.12 0.15
Matches are distributed among these distances:
10 6 0.13
11 36 0.77
12 5 0.11
ACGTcount: A:0.55, C:0.06, G:0.03, T:0.37
Consensus pattern (11 bp):
TAAATTAATAA
Found at i:2880058 original size:66 final size:66
Alignment explanation
Indices: 2879936--2880084 Score: 165
Period size: 66 Copynumber: 2.2 Consensus size: 66
2879926 TAAATTAGTT
* * * * *
2879936 AATTATTAATAATTTTATAGTAAATCATCAATAACTTTATAGTAAATTAGAAATAACATTA-TAA
1 AATTATTAATAACTTAATAGTAAATCATCAATAACTTAATAATAAATCAGAAATAAC-TTAGTAA
2880000 TA
65 TA
* *** *
2880002 AATTATTAATAACTTAATAGTAAATTATCAATAACTTAATAATAAATCATTTATAACTTAGTAGT
1 AATTATTAATAACTTAATAGTAAATCATCAATAACTTAATAATAAATCAGAAATAACTTAGTAAT
2880067 A
66 A
* *
2880068 AATCATTTTATAACTTA
1 AATTA-TTAATAACTTA
2880085 GTGATAAATC
Statistics
Matches: 69, Mismatches: 12, Indels: 3
0.82 0.14 0.04
Matches are distributed among these distances:
65 3 0.04
66 56 0.81
67 10 0.14
ACGTcount: A:0.48, C:0.07, G:0.04, T:0.40
Consensus pattern (66 bp):
AATTATTAATAACTTAATAGTAAATCATCAATAACTTAATAATAAATCAGAAATAACTTAGTAAT
A
Found at i:2880071 original size:22 final size:22
Alignment explanation
Indices: 2879931--2880115 Score: 128
Period size: 22 Copynumber: 8.4 Consensus size: 22
2879921 AGTTATAAAT
* * *
2879931 TAGTTAATTATTAATAATTTTA-
1 TAGTAAATCATTAATAA-CTTAG
*
2879953 TAGTAAATCATCAATAACTTTA-
1 TAGTAAATCATTAATAAC-TTAG
* **
2879975 TAGTAAATTAGAAATAACATTA-
1 TAGTAAATCATTAATAAC-TTAG
* * *
2879997 TAATAAATTATTAATAACTTAA
1 TAGTAAATCATTAATAACTTAG
* * *
2880019 TAGTAAATTATCAATAACTTAA
1 TAGTAAATCATTAATAACTTAG
* *
2880041 TAATAAATCATTTATAACTTAG
1 TAGTAAATCATTAATAACTTAG
*
2880063 TAGTAAATCATTTTATAACTTAG
1 TAGTAAATCA-TTAATAACTTAG
* *
2880086 T-GATAAATCA-TGATAATTTAG
1 TAG-TAAATCATTAATAACTTAG
2880107 TAGTAAATC
1 TAGTAAATC
2880116 GATGATAAAG
Statistics
Matches: 137, Mismatches: 21, Indels: 11
0.81 0.12 0.07
Matches are distributed among these distances:
21 19 0.14
22 98 0.72
23 20 0.15
ACGTcount: A:0.46, C:0.07, G:0.06, T:0.40
Consensus pattern (22 bp):
TAGTAAATCATTAATAACTTAG
Found at i:2880106 original size:21 final size:22
Alignment explanation
Indices: 2880010--2880134 Score: 80
Period size: 22 Copynumber: 5.7 Consensus size: 22
2880000 TAAATTATTA
* * *
2880010 ATAACTTAATAGTAAAT-TATCA
1 ATAACTTAGTAGTAAATCGAT-G
* * *
2880032 ATAACTTAATAATAAATC-ATTT
1 ATAACTTAGTAGTAAATCGA-TG
*
2880054 ATAACTTAGTAGTAAATC-ATTTT
1 ATAACTTAGTAGTAAATCGA--TG
2880077 ATAACTTAGT-GATAAATC-ATG
1 ATAACTTAGTAG-TAAATCGATG
*
2880098 ATAATTTAGTAGTAAATCGATG
1 ATAACTTAGTAGTAAATCGATG
**
2880120 ATAAAGTAGTAGTAA
1 ATAACTTAGTAGTAA
2880135 GTGAGTTGTA
Statistics
Matches: 89, Mismatches: 8, Indels: 12
0.82 0.07 0.11
Matches are distributed among these distances:
21 16 0.18
22 52 0.58
23 21 0.24
ACGTcount: A:0.46, C:0.07, G:0.10, T:0.37
Consensus pattern (22 bp):
ATAACTTAGTAGTAAATCGATG
Found at i:2880405 original size:22 final size:22
Alignment explanation
Indices: 2880375--2880426 Score: 61
Period size: 22 Copynumber: 2.4 Consensus size: 22
2880365 TATATCATAA
* *
2880375 ATAACTTAGTAATAATTCAA-TG
1 ATAATTTAGTAATAAAT-AATTG
*
2880397 ATAATTTAGTAGTAAATAATTG
1 ATAATTTAGTAATAAATAATTG
2880419 ATAATTTA
1 ATAATTTA
2880427 ATAGCTAACT
Statistics
Matches: 26, Mismatches: 3, Indels: 2
0.84 0.10 0.06
Matches are distributed among these distances:
21 2 0.08
22 24 0.92
ACGTcount: A:0.46, C:0.04, G:0.10, T:0.40
Consensus pattern (22 bp):
ATAATTTAGTAATAAATAATTG
Found at i:2880602 original size:22 final size:22
Alignment explanation
Indices: 2880576--2880717 Score: 151
Period size: 22 Copynumber: 6.5 Consensus size: 22
2880566 GATAATTTTG
* *
2880576 TAGTAAATCATTGATAACTTCA
1 TAGTAAATCATTAATAACTTAA
* * *
2880598 CAGTAAATTAGTT-ATAACTTTA
1 TAGTAAATCA-TTAATAACTTAA
* * *
2880620 TAATAAATTATTAATAACTTAG
1 TAGTAAATCATTAATAACTTAA
* *
2880642 TACTAAATCATCAATAACTTAA
1 TAGTAAATCATTAATAACTTAA
*
2880664 TAGTAAATCATTCATAACTTAA
1 TAGTAAATCATTAATAACTTAA
*
2880686 TAGTAAATCATTAATAATTTAA
1 TAGTAAATCATTAATAACTTAA
*
2880708 TAATAAATCA
1 TAGTAAATCA
2880718 CTGATAATAT
Statistics
Matches: 101, Mismatches: 17, Indels: 4
0.83 0.14 0.03
Matches are distributed among these distances:
21 2 0.02
22 97 0.96
23 2 0.02
ACGTcount: A:0.47, C:0.11, G:0.05, T:0.37
Consensus pattern (22 bp):
TAGTAAATCATTAATAACTTAA
Found at i:2880649 original size:66 final size:66
Alignment explanation
Indices: 2880579--2880724 Score: 168
Period size: 66 Copynumber: 2.2 Consensus size: 66
2880569 AATTTTGTAG
* * * * *
2880579 TAAATCATTGATAACTTCACAGTAAATTAGTT-ATAACTTTATAATAAATTATTAATAACTTAGT
1 TAAATCATTGATAACTTAACAGTAAATCA-TTCATAACTTAATAATAAATCATTAATAACTTAAT
*
2880643 AC
65 AA
** * * *
2880645 TAAATCATCAATAACTTAATAGTAAATCATTCATAACTTAATAGTAAATCATTAATAATTTAATA
1 TAAATCATTGATAACTTAACAGTAAATCATTCATAACTTAATAATAAATCATTAATAACTTAATA
2880710 A
66 A
*
2880711 TAAATCACTGATAA
1 TAAATCATTGATAA
2880725 TATAGTAATA
Statistics
Matches: 65, Mismatches: 14, Indels: 2
0.80 0.17 0.02
Matches are distributed among these distances:
65 2 0.03
66 63 0.97
ACGTcount: A:0.47, C:0.11, G:0.05, T:0.37
Consensus pattern (66 bp):
TAAATCATTGATAACTTAACAGTAAATCATTCATAACTTAATAATAAATCATTAATAACTTAATA
A
Found at i:2880724 original size:22 final size:22
Alignment explanation
Indices: 2880579--2880748 Score: 137
Period size: 22 Copynumber: 7.7 Consensus size: 22
2880569 AATTTTGTAG
* * * *
2880579 TAAATCATTGATAACTTCACAG
1 TAAATCATTAATAACTTAATAA
* *
2880601 TAAATTAGTT-ATAACTTTATAA
1 TAAATCA-TTAATAACTTAATAA
* * *
2880623 TAAATTATTAATAACTTAGTAC
1 TAAATCATTAATAACTTAATAA
* *
2880645 TAAATCATCAATAACTTAATAG
1 TAAATCATTAATAACTTAATAA
* *
2880667 TAAATCATTCATAACTTAATAG
1 TAAATCATTAATAACTTAATAA
*
2880689 TAAATCATTAATAATTTAATAA
1 TAAATCATTAATAACTTAATAA
* * *
2880711 TAAATCACTGATAA-TATAGTAA
1 TAAATCATTAATAACT-TAATAA
* *
2880733 TAAATTAGTAATAACT
1 TAAATCATTAATAACT
2880749 CAATTGTCAA
Statistics
Matches: 122, Mismatches: 22, Indels: 7
0.81 0.15 0.05
Matches are distributed among these distances:
21 3 0.02
22 116 0.95
23 3 0.02
ACGTcount: A:0.48, C:0.10, G:0.05, T:0.37
Consensus pattern (22 bp):
TAAATCATTAATAACTTAATAA
Found at i:2880747 original size:66 final size:66
Alignment explanation
Indices: 2880601--2880768 Score: 151
Period size: 66 Copynumber: 2.5 Consensus size: 66
2880591 AACTTCACAG
* * * * * *
2880601 TAAATTAGTTATAACTTTATAATAAATTATTAATAACTTAGTACTAAATCATCAATAACTTAATA
1 TAAATTAGTAATAACTTAATAGTAAATCATTAATAACTTAATAATAAATCATCAATAACTTAATA
*
2880666 G
66 A
* * * * * *
2880667 TAAATCATTCATAACTTAATAGTAAATCATTAATAATTTAATAATAAATCA-CTGATAA-TATAG
1 TAAATTAGTAATAACTTAATAGTAAATCATTAATAACTTAATAATAAATCATC-AATAACT-TAA
2880730 TAA
64 TAA
* * * *
2880733 TAAATTAGTAATAACTCAATTGTCAATCAATAATAA
1 TAAATTAGTAATAACTTAATAGTAAATCATTAATAA
2880769 GTTTTTTTAT
Statistics
Matches: 81, Mismatches: 19, Indels: 4
0.78 0.18 0.04
Matches are distributed among these distances:
65 2 0.02
66 79 0.98
ACGTcount: A:0.49, C:0.10, G:0.05, T:0.37
Consensus pattern (66 bp):
TAAATTAGTAATAACTTAATAGTAAATCATTAATAACTTAATAATAAATCATCAATAACTTAATA
A
Found at i:2882594 original size:2 final size:2
Alignment explanation
Indices: 2882589--2882629 Score: 73
Period size: 2 Copynumber: 20.5 Consensus size: 2
2882579 GAAAAAACTA
*
2882589 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AC AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
2882630 AGAATGAAGA
Statistics
Matches: 37, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
2 37 1.00
ACGTcount: A:0.51, C:0.02, G:0.00, T:0.46
Consensus pattern (2 bp):
AT
Found at i:2889090 original size:18 final size:18
Alignment explanation
Indices: 2889069--2889115 Score: 53
Period size: 18 Copynumber: 2.6 Consensus size: 18
2889059 AGTAAGGATG
2889069 AGAGAGAGAGATTGA-GAA
1 AGAGAGAGAGA-TGAGGAA
*
2889087 AGAGAGTGAG-TGAGTGAA
1 AGAGAGAGAGATGAG-GAA
2889105 AGAGAGAGAGA
1 AGAGAGAGAGA
2889116 AAGGGCTTTT
Statistics
Matches: 24, Mismatches: 2, Indels: 5
0.77 0.06 0.16
Matches are distributed among these distances:
16 3 0.12
18 21 0.88
ACGTcount: A:0.47, C:0.00, G:0.43, T:0.11
Consensus pattern (18 bp):
AGAGAGAGAGATGAGGAA
Found at i:2894530 original size:89 final size:89
Alignment explanation
Indices: 2894379--2894548 Score: 277
Period size: 89 Copynumber: 1.9 Consensus size: 89
2894369 GGGGAGAGTA
* *
2894379 AAAATGAAGATTCTGTCTTTGACATCTAAATAGAAATGCCACCTATGATGTCTACCTTAAATTCA
1 AAAATGAAGATTCTGTCTTTGACATCTAAATAGAAATGCCACATATGATGTCTACCCTAAATTCA
2894444 GAGATACTTGCAAACCTTAGAATG
66 GAGATACTTGCAAACCTTAGAATG
* * * * *
2894468 AAAATGAAGATTTTGTCTTTGACATCTAGATAGAAATGCTACATGTGATGTCTACCCTAAATTTA
1 AAAATGAAGATTCTGTCTTTGACATCTAAATAGAAATGCCACATATGATGTCTACCCTAAATTCA
2894533 GAGATACTTGCAAACC
66 GAGATACTTGCAAACC
2894549 CTACTTCAGA
Statistics
Matches: 74, Mismatches: 7, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
89 74 1.00
ACGTcount: A:0.36, C:0.17, G:0.15, T:0.31
Consensus pattern (89 bp):
AAAATGAAGATTCTGTCTTTGACATCTAAATAGAAATGCCACATATGATGTCTACCCTAAATTCA
GAGATACTTGCAAACCTTAGAATG
Found at i:2900747 original size:12 final size:11
Alignment explanation
Indices: 2900710--2900749 Score: 55
Period size: 12 Copynumber: 3.5 Consensus size: 11
2900700 GAGATTAAAA
2900710 GTTTTTGTTTT
1 GTTTTTGTTTT
2900721 G-TTTTGTTTT
1 GTTTTTGTTTT
2900731 CGTTTTTGTTTGT
1 -GTTTTTGTTT-T
2900744 GTTTTT
1 GTTTTT
2900750 TTATTACACT
Statistics
Matches: 26, Mismatches: 0, Indels: 5
0.84 0.00 0.16
Matches are distributed among these distances:
10 9 0.35
11 2 0.08
12 14 0.54
13 1 0.04
ACGTcount: A:0.00, C:0.03, G:0.20, T:0.78
Consensus pattern (11 bp):
GTTTTTGTTTT
Found at i:2902549 original size:21 final size:21
Alignment explanation
Indices: 2902525--2902568 Score: 52
Period size: 21 Copynumber: 2.1 Consensus size: 21
2902515 AAATATTAAT
*
2902525 AATAAAATTTAAAATAACAAA
1 AATAAAATTTAAAAAAACAAA
** *
2902546 AATAATTTTTAAAAAAATAAA
1 AATAAAATTTAAAAAAACAAA
2902567 AA
1 AA
2902569 AATTTCACCT
Statistics
Matches: 19, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
21 19 1.00
ACGTcount: A:0.70, C:0.02, G:0.00, T:0.27
Consensus pattern (21 bp):
AATAAAATTTAAAAAAACAAA
Found at i:2902572 original size:20 final size:21
Alignment explanation
Indices: 2902532--2902573 Score: 59
Period size: 21 Copynumber: 2.0 Consensus size: 21
2902522 AATAATAAAA
*
2902532 TTTAAAATAACAAAAATAATT
1 TTTAAAAAAACAAAAATAATT
*
2902553 TTTAAAAAAATAAAAA-AATT
1 TTTAAAAAAACAAAAATAATT
2902573 T
1 T
2902574 CACCTGAATC
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
20 5 0.26
21 14 0.74
ACGTcount: A:0.64, C:0.02, G:0.00, T:0.33
Consensus pattern (21 bp):
TTTAAAAAAACAAAAATAATT
Found at i:2903864 original size:2 final size:2
Alignment explanation
Indices: 2903857--2903883 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
2903847 TAATAGTTTG
2903857 AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT A
2903884 CTTTACTTCA
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 25 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:2904364 original size:2 final size:2
Alignment explanation
Indices: 2904351--2904380 Score: 51
Period size: 2 Copynumber: 15.0 Consensus size: 2
2904341 TAACTAATGG
*
2904351 AT AT AT AC 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
2904381 CAAAATATTA
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.50, C:0.03, G:0.00, T:0.47
Consensus pattern (2 bp):
AT
Found at i:2904765 original size:2 final size:2
Alignment explanation
Indices: 2904760--2904789 Score: 60
Period size: 2 Copynumber: 15.0 Consensus size: 2
2904750 TGTGTGTGTC
2904760 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
2904790 AGTTACTGAT
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):
TA
Found at i:2904960 original size:2 final size:2
Alignment explanation
Indices: 2904955--2904992 Score: 67
Period size: 2 Copynumber: 19.0 Consensus size: 2
2904945 TTTACACACA
*
2904955 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AG AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
2904993 TCAAAATATC
Statistics
Matches: 34, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
2 34 1.00
ACGTcount: A:0.50, C:0.00, G:0.03, T:0.47
Consensus pattern (2 bp):
AT
Found at i:2914365 original size:4 final size:4
Alignment explanation
Indices: 2914356--2914382 Score: 54
Period size: 4 Copynumber: 6.8 Consensus size: 4
2914346 AGGATTAGGT
2914356 TTAA TTAA TTAA TTAA TTAA TTAA TTA
1 TTAA TTAA TTAA TTAA TTAA TTAA TTA
2914383 TTATGTTATT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 23 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (4 bp):
TTAA
Found at i:2915141 original size:21 final size:22
Alignment explanation
Indices: 2915109--2915175 Score: 75
Period size: 22 Copynumber: 3.0 Consensus size: 22
2915099 GCCAAGCCAT
*
2915109 TTTATTTATTTTTTGTATTTCTT
1 TTTA-TTATTTTTTGTATTTCTG
2915132 TTTA-TATTTTTTTGTATTT-TG
1 TTTATTA-TTTTTTGTATTTCTG
*
2915153 TTTATTGTTTTTTAGTATTTCTG
1 TTTATTATTTTTT-GTATTTCTG
2915176 CATGATTAAA
Statistics
Matches: 38, Mismatches: 2, Indels: 8
0.79 0.04 0.17
Matches are distributed among these distances:
21 13 0.34
22 19 0.50
23 6 0.16
ACGTcount: A:0.13, C:0.03, G:0.09, T:0.75
Consensus pattern (22 bp):
TTTATTATTTTTTGTATTTCTG
Found at i:2915150 original size:31 final size:31
Alignment explanation
Indices: 2915107--2915172 Score: 75
Period size: 31 Copynumber: 2.1 Consensus size: 31
2915097 CAGCCAAGCC
2915107 ATTTTATTTATTTT-TTGTATT-TCTTTTTA-T
1 ATTTTATTTATTTTGTT-TATTGT-TTTTTAGT
*
2915137 ATTTTTTTGTATTTTGTTTATTGTTTTTTAGT
1 ATTTTATT-TATTTTGTTTATTGTTTTTTAGT
2915169 ATTT
1 ATTT
2915173 CTGCATGATT
Statistics
Matches: 31, Mismatches: 1, Indels: 6
0.82 0.03 0.16
Matches are distributed among these distances:
30 7 0.23
31 16 0.52
32 8 0.26
ACGTcount: A:0.15, C:0.02, G:0.08, T:0.76
Consensus pattern (31 bp):
ATTTTATTTATTTTGTTTATTGTTTTTTAGT
Found at i:2915563 original size:171 final size:170
Alignment explanation
Indices: 2915239--2915561 Score: 388
Period size: 171 Copynumber: 1.9 Consensus size: 170
2915229 GAATAAATAT
* * * * * * *
2915239 TAATTATCTAATGATGTGATTTATAGAAATTTTAAATTATAAATTTTTATAAAATTTTTAGGTGA
1 TAATTATCCAATGATGAGATTCATAGAAAATTTAAATGATAAATTTTTATAAAATCTCTAGGTGA
* * * *
2915304 GAAATTTTATTTAAATTTATTCCAAATGAGGGAATAATTTAGATGAAGTTTCAATAAAAGTAATT
66 GAAATTTTATTTAAATTTATCCCAAATGAGGGAAGAATTTAAATGAAGTTTCAATAAAAGAAATT
* *
2915369 GTATTCTTTTTCAAATAAAAAATTAGGTTGAAAATATTTGA
131 GTATTATTTAT-AAATAAAAAATTAGGTTGAAAATATTTGA
*
2915410 TAATTATCCAATGATGAGATTCATAGAAAATTTAAATGGTAAATTTTT-TAAGAAATCTCTAGGT
1 TAATTATCCAATGATGAGATTCATAGAAAATTTAAATGATAAATTTTTAT-A-AAATCTCTAGGT
*
2915474 GAGAAA-TTTCTTTAAATTTATCCCAAATG-GTGGAAGAATTTAAATG-AGATTTCAATAAAA-A
64 GAGAAATTTTATTTAAATTTATCCCAAATGAG-GGAAGAATTTAAATGAAG-TTTCAATAAAAGA
2915535 AATTATCGTATTATCTTATAAA-AAAAA
127 AA-T-T-GTATTAT-TTATAAATAAAAA
2915562 TTTCTAAATA
Statistics
Matches: 129, Mismatches: 15, Indels: 15
0.81 0.09 0.09
Matches are distributed among these distances:
170 6 0.05
171 89 0.69
172 22 0.17
173 9 0.07
174 3 0.02
ACGTcount: A:0.43, C:0.06, G:0.12, T:0.39
Consensus pattern (170 bp):
TAATTATCCAATGATGAGATTCATAGAAAATTTAAATGATAAATTTTTATAAAATCTCTAGGTGA
GAAATTTTATTTAAATTTATCCCAAATGAGGGAAGAATTTAAATGAAGTTTCAATAAAAGAAATT
GTATTATTTATAAATAAAAAATTAGGTTGAAAATATTTGA
Found at i:2925557 original size:18 final size:18
Alignment explanation
Indices: 2925527--2925573 Score: 64
Period size: 18 Copynumber: 2.8 Consensus size: 18
2925517 CTACACTTGA
2925527 AAAAAAATG--AAAAAA-
1 AAAAAAATGAAAAAAAAT
*
2925542 ACAAAAATGAAAAAAAAT
1 AAAAAAATGAAAAAAAAT
2925560 AAAAAAATGAAAAA
1 AAAAAAATGAAAAA
2925574 TAGGGTTTAT
Statistics
Matches: 27, Mismatches: 2, Indels: 3
0.84 0.06 0.09
Matches are distributed among these distances:
15 8 0.30
17 6 0.22
18 13 0.48
ACGTcount: A:0.83, C:0.02, G:0.06, T:0.09
Consensus pattern (18 bp):
AAAAAAATGAAAAAAAAT
Found at i:2925563 original size:15 final size:14
Alignment explanation
Indices: 2925526--2925563 Score: 58
Period size: 15 Copynumber: 2.6 Consensus size: 14
2925516 ACTACACTTG
2925526 AAAAAAAATGAAAA
1 AAAAAAAATGAAAA
2925540 AAACAAAAATGAAAA
1 AAA-AAAAATGAAAA
2925555 AAAATAAAA
1 AAAA-AAAA
2925564 AAATGAAAAA
Statistics
Matches: 22, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
14 4 0.18
15 18 0.82
ACGTcount: A:0.84, C:0.03, G:0.05, T:0.08
Consensus pattern (14 bp):
AAAAAAAATGAAAA
Found at i:2925572 original size:15 final size:15
Alignment explanation
Indices: 2925527--2925575 Score: 55
Period size: 15 Copynumber: 3.1 Consensus size: 15
2925517 CTACACTTGA
2925527 AAAAAAATGAAAAA-
1 AAAAAAATGAAAAAT
2925541 AACAAAAATGAAAAAAAAT
1 AA-AAAAATG---AAAAAT
2925560 AAAAAAATGAAAAAT
1 AAAAAAATGAAAAAT
2925575 A
1 A
2925576 GGGTTTATCT
Statistics
Matches: 30, Mismatches: 0, Indels: 9
0.77 0.00 0.23
Matches are distributed among these distances:
14 2 0.07
15 14 0.47
18 12 0.40
19 2 0.07
ACGTcount: A:0.82, C:0.02, G:0.06, T:0.10
Consensus pattern (15 bp):
AAAAAAATGAAAAAT
Found at i:2926570 original size:43 final size:44
Alignment explanation
Indices: 2926523--2926766 Score: 264
Period size: 44 Copynumber: 5.6 Consensus size: 44
2926513 AAATTATGGT
* *
2926523 GCCT-TGATTAGAGGAGCCTTGTTTATTTTTTCAAATTCGTTGA
1 GCCTCTGATTAGAGGAGCTTTGTTTATTTTTTCAAAGTCGTTGA
* * * *
2926566 GCCTTTGATT-GATGAGCTTTGTTTATTTTTTCAAAGTTGTTAA
1 GCCTCTGATTAGAGGAGCTTTGTTTATTTTTTCAAAGTCGTTGA
* * *
2926609 GCCTCTGATTAGAGGAGCCTTATTTATTTTTTCAAAGTCGTTAA
1 GCCTCTGATTAGAGGAGCTTTGTTTATTTTTTCAAAGTCGTTGA
* * * *
2926653 ACCTCTTATTAGAGGAGCTTTGTTTATTTTTCCAAAGTCATTGA
1 GCCTCTGATTAGAGGAGCTTTGTTTATTTTTTCAAAGTCGTTGA
* *
2926697 --CTCTGATTAGAGGAGCTTTATTTATTTTTT-AGAAGTCATTGA
1 GCCTCTGATTAGAGGAGCTTTGTTTATTTTTTCA-AAGTCGTTGA
* * * * *
2926739 GCCTTTGTTTAGATGAGTTTTATTTATT
1 GCCTCTGATTAGAGGAGCTTTGTTTATT
2926767 CTCTAAAAAT
Statistics
Matches: 172, Mismatches: 24, Indels: 9
0.84 0.12 0.04
Matches are distributed among these distances:
41 1 0.01
42 37 0.22
43 41 0.24
44 93 0.54
ACGTcount: A:0.23, C:0.12, G:0.18, T:0.46
Consensus pattern (44 bp):
GCCTCTGATTAGAGGAGCTTTGTTTATTTTTTCAAAGTCGTTGA
Found at i:2926683 original size:87 final size:86
Alignment explanation
Indices: 2926522--2926726 Score: 265
Period size: 87 Copynumber: 2.4 Consensus size: 86
2926512 AAAATTATGG
* * * * *
2926522 TGCCT-TGATTAGAGGAGCCTTGTTTATTTTTTCAAATTCGTTGAGCCTTTGATTGATGAGCTTT
1 TGCCTCTGATTAGAGGAGCCTTATTTATTTTTTCAAAGTCGTTAAACCTTTGATTGAGGAGCTTT
**
2926586 GTTTATTTTTT-CAAAGTTGT
66 GTTTATTTTTTCCAAAGTCAT
2926606 TAAGCCTCTGATTAGAGGAGCCTTATTTATTTTTTCAAAGTCGTTAAACCTCTT-ATTAGAGGAG
1 T--GCCTCTGATTAGAGGAGCCTTATTTATTTTTTCAAAGTCGTTAAACCT-TTGATT-GAGGAG
2926670 CTTTGTTTA-TTTTTCCAAAGTCAT
62 CTTTGTTTATTTTTTCCAAAGTCAT
* *
2926694 TGACTCTGATTAGAGGAGCTTTATTTATTTTTT
1 TGCCTCTGATTAGAGGAGCCTTATTTATTTTTT
2926727 AGAAGTCATT
Statistics
Matches: 106, Mismatches: 9, Indels: 10
0.85 0.07 0.08
Matches are distributed among these distances:
84 1 0.01
86 34 0.32
87 47 0.44
88 24 0.23
ACGTcount: A:0.22, C:0.13, G:0.18, T:0.46
Consensus pattern (86 bp):
TGCCTCTGATTAGAGGAGCCTTATTTATTTTTTCAAAGTCGTTAAACCTTTGATTGAGGAGCTTT
GTTTATTTTTTCCAAAGTCAT
Found at i:2926751 original size:86 final size:87
Alignment explanation
Indices: 2926527--2926766 Score: 299
Period size: 86 Copynumber: 2.8 Consensus size: 87
2926517 TATGGTGCCT
* *
2926527 TGATTAGAGGAGCCTTGTTTATTTTTTCAAATTCGTTGAGCCTTTGATT-GATGAGCTTTGTTTA
1 TGATTAGAGGAGCCTTATTTATTTTTTCAAAGTCGTTGAGCCTTTGATTAGATGAGCTTTGTTTA
* ** *
2926591 TTTTTTCAAAGTTGTTAAGCCTC
66 TTTTTCCAAAGTCATT-AGACTC
* * *
2926614 TGATTAGAGGAGCCTTATTTATTTTTTCAAAGTCGTTAAACCTCTT-ATTAGAGGAGCTTTGTTT
1 TGATTAGAGGAGCCTTATTTATTTTTTCAAAGTCGTTGAGCCT-TTGATTAGATGAGCTTTGTTT
2926678 ATTTTTCCAAAGTCATT-GACTC
65 ATTTTTCCAAAGTCATTAGACTC
* * * * *
2926700 TGATTAGAGGAGCTTTATTTATTTTTT-AGAAGTCATTGAGCCTTTGTTTAGATGAGTTTTATTT
1 TGATTAGAGGAGCCTTATTTATTTTTTCA-AAGTCGTTGAGCCTTTGATTAGATGAGCTTTGTTT
2926764 ATT
65 ATT
2926767 CTCTAAAAAT
Statistics
Matches: 132, Mismatches: 17, Indels: 9
0.84 0.11 0.06
Matches are distributed among these distances:
85 3 0.02
86 58 0.44
87 42 0.32
88 29 0.22
ACGTcount: A:0.23, C:0.12, G:0.18, T:0.47
Consensus pattern (87 bp):
TGATTAGAGGAGCCTTATTTATTTTTTCAAAGTCGTTGAGCCTTTGATTAGATGAGCTTTGTTTA
TTTTTCCAAAGTCATTAGACTC
Found at i:2927037 original size:4 final size:4
Alignment explanation
Indices: 2927030--2927077 Score: 53
Period size: 4 Copynumber: 11.5 Consensus size: 4
2927020 AATTAATTAA
*
2927030 TTAT TTAT TTAT TTA- TTAT GTTAT TTAT TATAA TTATT TTAT TTAT TT
1 TTAT TTAT TTAT TTAT TTAT -TTAT TTAT T-TAT TTA-T TTAT TTAT TT
2927078 TATAGATTTA
Statistics
Matches: 38, Mismatches: 2, Indels: 8
0.79 0.04 0.17
Matches are distributed among these distances:
3 3 0.08
4 25 0.66
5 10 0.26
ACGTcount: A:0.27, C:0.00, G:0.02, T:0.71
Consensus pattern (4 bp):
TTAT
Found at i:2927075 original size:9 final size:9
Alignment explanation
Indices: 2927033--2927080 Score: 55
Period size: 9 Copynumber: 5.6 Consensus size: 9
2927023 TAATTAATTA
2927033 TTTATTTA-
1 TTTATTTAT
2927041 TTTA-TTAT
1 TTTATTTAT
*
2927049 GTTATTTAT
1 TTTATTTAT
* *
2927058 TATAATTAT
1 TTTATTTAT
2927067 TTTATTTAT
1 TTTATTTAT
2927076 TTTAT
1 TTTAT
2927081 AGATTTATCT
Statistics
Matches: 32, Mismatches: 6, Indels: 3
0.78 0.15 0.07
Matches are distributed among these distances:
7 3 0.09
8 7 0.22
9 22 0.69
ACGTcount: A:0.27, C:0.00, G:0.02, T:0.71
Consensus pattern (9 bp):
TTTATTTAT
Found at i:2927660 original size:51 final size:51
Alignment explanation
Indices: 2927605--2927703 Score: 128
Period size: 51 Copynumber: 1.9 Consensus size: 51
2927595 TGATAATTCC
* * *
2927605 AGAATTCGGTGAAAGATTGAACCGA-TGCACTTGAATCCTAGAGAGAGAAAG
1 AGAATTCGATGAAAGATTCAA-CGAGTGCACTCGAATCCTAGAGAGAGAAAG
* * *
2927656 AGAATTCGATGAAGGATTCAACTAGTGCTCTCGAATCCTAGAGAGAGA
1 AGAATTCGATGAAAGATTCAACGAGTGCACTCGAATCCTAGAGAGAGA
2927704 GGGAGAAAAA
Statistics
Matches: 41, Mismatches: 6, Indels: 2
0.84 0.12 0.04
Matches are distributed among these distances:
50 2 0.05
51 39 0.95
ACGTcount: A:0.37, C:0.15, G:0.26, T:0.21
Consensus pattern (51 bp):
AGAATTCGATGAAAGATTCAACGAGTGCACTCGAATCCTAGAGAGAGAAAG
Found at i:2928146 original size:26 final size:26
Alignment explanation
Indices: 2928092--2928146 Score: 60
Period size: 26 Copynumber: 2.1 Consensus size: 26
2928082 AATAATGGGA
* *
2928092 TTTATAGAAATTTCAAATGATAAATT
1 TTTATAGAAATTTCAAATGAGAAAAT
2928118 TTTATA-AAA-TTCATAAGTGAGAAAAT
1 TTTATAGAAATTTCA-AA-TGAGAAAAT
2928144 TTT
1 TTT
2928147 GTCTAAATTT
Statistics
Matches: 25, Mismatches: 2, Indels: 4
0.81 0.06 0.13
Matches are distributed among these distances:
24 4 0.16
25 5 0.20
26 16 0.64
ACGTcount: A:0.45, C:0.04, G:0.09, T:0.42
Consensus pattern (26 bp):
TTTATAGAAATTTCAAATGAGAAAAT
Found at i:2929831 original size:59 final size:59
Alignment explanation
Indices: 2929683--2929831 Score: 219
Period size: 59 Copynumber: 2.5 Consensus size: 59
2929673 TTTGTTATAA
* * *
2929683 ATTTGTTGAAATATGTTTGGGTTTTAGTTACCAATGCATTGAGTTTTTGTTAGTTATTT
1 ATTTGTTGAAATTTGTTTGGGTTTTGGTTATCAATGCATTGAGTTTTTGTTAGTTATTT
* ** *
2929742 ATTTGTTGAAATTTATTTGGGTTTTGGTTATCAATTTATTGAGTTTTTGTTGGTT-TTAT
1 ATTTGTTGAAATTTGTTTGGGTTTTGGTTATCAATGCATTGAGTTTTTGTTAGTTATT-T
2929801 ATTTGTTGAAATTTGTTTGGGTTTTGGTTAT
1 ATTTGTTGAAATTTGTTTGGGTTTTGGTTAT
2929832 ATTTTTGTTG
Statistics
Matches: 81, Mismatches: 8, Indels: 2
0.89 0.09 0.02
Matches are distributed among these distances:
58 2 0.02
59 79 0.98
ACGTcount: A:0.19, C:0.03, G:0.21, T:0.56
Consensus pattern (59 bp):
ATTTGTTGAAATTTGTTTGGGTTTTGGTTATCAATGCATTGAGTTTTTGTTAGTTATTT
Found at i:2938462 original size:21 final size:21
Alignment explanation
Indices: 2938446--2938491 Score: 78
Period size: 19 Copynumber: 2.3 Consensus size: 21
2938436 TTATATCCTT
2938446 TAGCCATATAGATATATATGG
1 TAGCCATATAGATATATATGG
2938467 TAGCCATATAG--ATATATGG
1 TAGCCATATAGATATATATGG
2938486 TAGCCA
1 TAGCCA
2938492 AATTGCTTAT
Statistics
Matches: 25, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
19 14 0.56
21 11 0.44
ACGTcount: A:0.37, C:0.13, G:0.20, T:0.30
Consensus pattern (21 bp):
TAGCCATATAGATATATATGG
Found at i:2942343 original size:2 final size:2
Alignment explanation
Indices: 2942336--2942364 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
2942326 TAATATTTTG
2942336 AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
2942365 GTAGGGATCT
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 27 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:2946993 original size:30 final size:30
Alignment explanation
Indices: 2946953--2947024 Score: 94
Period size: 30 Copynumber: 2.4 Consensus size: 30
2946943 ATGAAAGATT
* * *
2946953 AATT-AAAGTTAAGTGTTTATTTAGT-TATA
1 AATTAAAAGTTAAGAGTGTATTCA-TATATA
2946982 AATTAAAAGTTAAGAGTGTATTCATATATA
1 AATTAAAAGTTAAGAGTGTATTCATATATA
2947012 AATTAAAAGTTAA
1 AATTAAAAGTTAA
2947025 AAACTTATTT
Statistics
Matches: 38, Mismatches: 3, Indels: 3
0.86 0.07 0.07
Matches are distributed among these distances:
29 5 0.13
30 33 0.87
ACGTcount: A:0.46, C:0.01, G:0.12, T:0.40
Consensus pattern (30 bp):
AATTAAAAGTTAAGAGTGTATTCATATATA
Found at i:2948629 original size:6 final size:6
Alignment explanation
Indices: 2948618--2948652 Score: 61
Period size: 6 Copynumber: 5.8 Consensus size: 6
2948608 TTTCTAATTG
*
2948618 TAGATA TAGATA TAGATA TAGATA TAGATA AAGAT
1 TAGATA TAGATA TAGATA TAGATA TAGATA TAGAT
2948653 TTTGACTTTT
Statistics
Matches: 28, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
6 28 1.00
ACGTcount: A:0.51, C:0.00, G:0.17, T:0.31
Consensus pattern (6 bp):
TAGATA
Found at i:2951847 original size:43 final size:44
Alignment explanation
Indices: 2951666--2951865 Score: 128
Period size: 43 Copynumber: 4.7 Consensus size: 44
2951656 GCTAATTTGT
* * * * **
2951666 AAGGCCTTGAAACTTTGGAAAATCTAACATGCTCTCCCTTATTA
1 AAGGCTTTGAAACTTTGAAAAATCTAAAATGCTCTCCCTCAACA
* * * * * * *
2951710 GAGGCTTCG-AACTTTGGAAATTTTAAAATGCTC-CTCTC-A-T
1 AAGGCTTTGAAACTTTGAAAAATCTAAAATGCTCTCCCTCAACA
* * * * * *
2951750 AAGTGATTTTAAAATTTTGAAAAATCTAAAAAGC-CTCCAT-TACA
1 AAG-G-CTTTGAAACTTTGAAAAATCTAAAATGCTCTCCCTCAACA
*
2951794 ATAGGTTTTGAAACTTTGAAAAATCTAAAATGCTC-CCCTCAACA
1 A-AGGCTTTGAAACTTTGAAAAATCTAAAATGCTCTCCCTCAACA
*
2951838 AAGGCTTTGAAACTTTAAAAAAT-TAAAA
1 AAGGCTTTGAAACTTTGAAAAATCTAAAA
2951866 AATTCTTCTC
Statistics
Matches: 118, Mismatches: 29, Indels: 20
0.71 0.17 0.12
Matches are distributed among these distances:
40 2 0.02
41 1 0.01
42 11 0.09
43 89 0.75
44 13 0.11
45 2 0.02
ACGTcount: A:0.39, C:0.17, G:0.12, T:0.32
Consensus pattern (44 bp):
AAGGCTTTGAAACTTTGAAAAATCTAAAATGCTCTCCCTCAACA
Found at i:2951914 original size:41 final size:40
Alignment explanation
Indices: 2951847--2951983 Score: 125
Period size: 41 Copynumber: 3.3 Consensus size: 40
2951837 AAAGGCTTTG
* *
2951847 AAACTTTAAAAAATTAAAAAATTCTTCTCACTAGAGGCTTC-
1 AAACTTT-AAAAATT-AAAAACTCTTCTCACTAGAGGCTACA
* * * *
2951888 AAATTTTGGAAAATTAAAAAGCTCTTCTTA-TCAAAGGCTACA
1 AAACTTT-AAAAATTAAAAA-CTCTTCTCACT-AGAGGCTACA
* * *
2951930 AAACTTTAAAAATTAAAGAACTCCTCTCACTAGAGGCTGCG
1 AAACTTTAAAAATTAAA-AACTCTTCTCACTAGAGGCTACA
2951971 AAACTTTAAAAAT
1 AAACTTTAAAAAT
2951984 CAAAGGACCG
Statistics
Matches: 77, Mismatches: 14, Indels: 10
0.76 0.14 0.10
Matches are distributed among these distances:
40 6 0.08
41 62 0.81
42 9 0.12
ACGTcount: A:0.44, C:0.17, G:0.10, T:0.29
Consensus pattern (40 bp):
AAACTTTAAAAATTAAAAACTCTTCTCACTAGAGGCTACA
Found at i:2951999 original size:82 final size:82
Alignment explanation
Indices: 2951847--2952029 Score: 190
Period size: 82 Copynumber: 2.2 Consensus size: 82
2951837 AAAGGCTTTG
* * * * * * * *
2951847 AAACTTTAAAAAATTAAAAAATTCTTCTCACTAGAGGCTTCAAATTTTGGAAAATTAAAAAGCTC
1 AAACTTT-AAAAATTAAAAAACTCCTCTCACTAGAGGCTGCAAACTTTGAAAAATCAAAAACCGC
*
2951912 TTCTTATCAAAGGCTACA
65 TTCTTACCAAAGGCTACA
* *
2951930 AAACTTTAAAAATTAAAGAACTCCTCTCACTAGAGGCTGCGAAACTTT-AAAAATCAAAGGACCG
1 AAACTTTAAAAATTAAAAAACTCCTCTCACTAGAGGCTGC-AAACTTTGAAAAATCAAA-AACCG
* **
2951994 C-TCTTACCAGAGGCTATG
64 CTTCTTACCAAAGGCTACA
2952012 AAACATTTAAAAATTAAA
1 AAAC-TTTAAAAATTAAA
2952030 TAGTACCCAG
Statistics
Matches: 83, Mismatches: 14, Indels: 6
0.81 0.14 0.06
Matches are distributed among these distances:
82 54 0.65
83 29 0.35
ACGTcount: A:0.44, C:0.17, G:0.11, T:0.27
Consensus pattern (82 bp):
AAACTTTAAAAATTAAAAAACTCCTCTCACTAGAGGCTGCAAACTTTGAAAAATCAAAAACCGCT
TCTTACCAAAGGCTACA
Found at i:2952006 original size:41 final size:41
Alignment explanation
Indices: 2951922--2952025 Score: 120
Period size: 41 Copynumber: 2.5 Consensus size: 41
2951912 TTCTTATCAA
* * *
2951922 AGGCTACAAAACTTTAAAAATTAAAGAACTCCTCTCACTAG
1 AGGCTACGAAACTTTAAAAATCAAAGAACTCCTCTCACCAG
* * *
2951963 AGGCTGCGAAACTTTAAAAATCAAAGGAC-CGCTCTTACCAG
1 AGGCTACGAAACTTTAAAAATCAAAGAACTC-CTCTCACCAG
*
2952004 AGGCTATGAAACATTTAAAAAT
1 AGGCTACGAAAC-TTTAAAAAT
2952026 TAAATAGTAC
Statistics
Matches: 53, Mismatches: 8, Indels: 3
0.83 0.12 0.05
Matches are distributed among these distances:
40 1 0.02
41 43 0.81
42 9 0.17
ACGTcount: A:0.42, C:0.20, G:0.14, T:0.23
Consensus pattern (41 bp):
AGGCTACGAAACTTTAAAAATCAAAGAACTCCTCTCACCAG
Found at i:2952107 original size:22 final size:22
Alignment explanation
Indices: 2952064--2952225 Score: 92
Period size: 22 Copynumber: 7.6 Consensus size: 22
2952054 ATGCCCGAAA
2952064 GTCTTATAAATCATG----AAG
1 GTCTTATAAATCATGACCTAAG
* *
2952082 GTCTTTTAGATCATGACCTAAG
1 GTCTTATAAATCATGACCTAAG
*
2952104 GTCTTATAAATCAT-ACCTAAAA
1 GTCTTATAAATCATGACCT-AAG
*
2952126 GTCTTATAAATCATG-CCAAAAG
1 GTCTTATAAATCATGACC-TAAG
* * * *
2952148 GTCTTTTAGATCATGTA-C-GAT
1 GTCTTATAAATCATG-ACCTAAG
** * *
2952169 GTCTTATAAATTTTG-CCAAAA
1 GTCTTATAAATCATGACCTAAG
* *
2952190 ATCTTATAAATCATG-TCTAAAG
1 GTCTTATAAATCATGACCT-AAG
2952212 GTCTTATAAATCAT
1 GTCTTATAAATCAT
2952226 TCTAATTTTT
Statistics
Matches: 108, Mismatches: 24, Indels: 20
0.71 0.16 0.13
Matches are distributed among these distances:
18 13 0.12
20 1 0.01
21 30 0.28
22 63 0.58
23 1 0.01
ACGTcount: A:0.36, C:0.15, G:0.12, T:0.36
Consensus pattern (22 bp):
GTCTTATAAATCATGACCTAAG
Found at i:2952212 original size:64 final size:64
Alignment explanation
Indices: 2952065--2952225 Score: 170
Period size: 64 Copynumber: 2.5 Consensus size: 64
2952055 TGCCCGAAAG
*
2952065 TCTTATAAATCATG--AAGGTCTTTTAGATCATGACCTAAGGTCTTATAAATCATACCTAAAAG
1 TCTTATAAATCATGCAAAGGTCTTTTAGATCATGACCTAAGGTCTTATAAATCATACCTAAAAA
* * ** *
2952127 TCTTATAAATCATGCCAAAAGGTCTTTTAGATCATGTA-C-GATGTCTTATAAATTTTGCC-AAA
1 TCTTATAAATCATG-C-AAAGGTCTTTTAGATCATG-ACCTAAGGTCTTATAAATCATACCTAAA
2952189 AA
63 AA
* *
2952191 TCTTATAAATCATGTCTAAAGGTCTTATAAATCAT
1 TCTTATAAATCATG-C-AAAGGTCTTTTAGATCAT
2952226 TCTAATTTTT
Statistics
Matches: 84, Mismatches: 10, Indels: 8
0.82 0.10 0.08
Matches are distributed among these distances:
62 14 0.17
64 35 0.42
65 15 0.18
66 19 0.23
67 1 0.01
ACGTcount: A:0.37, C:0.16, G:0.12, T:0.36
Consensus pattern (64 bp):
TCTTATAAATCATGCAAAGGTCTTTTAGATCATGACCTAAGGTCTTATAAATCATACCTAAAAA
Found at i:2953748 original size:22 final size:20
Alignment explanation
Indices: 2953719--2953758 Score: 53
Period size: 21 Copynumber: 1.9 Consensus size: 20
2953709 CACCCTAGAG
2953719 CTTCATTTAATCTTTTTTTCT
1 CTTCATTT-ATCTTTTTTTCT
*
2953740 CTTCTATTTTTCTTTTTTT
1 CTTC-ATTTATCTTTTTTT
2953759 TTTAATATTC
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
21 13 0.76
22 4 0.24
ACGTcount: A:0.10, C:0.17, G:0.00, T:0.72
Consensus pattern (20 bp):
CTTCATTTATCTTTTTTTCT
Found at i:2955834 original size:280 final size:278
Alignment explanation
Indices: 2955229--2955913 Score: 796
Period size: 280 Copynumber: 2.4 Consensus size: 278
2955219 ATCTTCACAA
* *
2955229 CATAATGAAAACAAGAATTCATATTT-AAAACTTATGTACCAAAACTAAAAA-ACAAAAATTGCC
1 CATAATGAAAACAAGAA-TC-TATTTCAAAAC-TATGTA-CAAAACTAAAAAGGCAAAGATTGCC
* * *
2955292 CTAAACAAATGAAATAATGCA-AAAAAAAATGTTTACATAGATAAAAAATGTATATGCAAATAAA
62 CCAAACAAATGAAATAATGTACAAAAAAAATGTTTACGTAGATAAAAAATGTATATGCAAATAAA
* * * *
2955356 TGTATGCAATACATAGAAAAATAAAAACTTATATTCAAAACTATGTACAAAACTATAAAAGGTAA
127 TATATGCAATACATAGAAAAACAAAAACTTATATTCAAAACTATGTACAAAACTAGAAAAGGCAA
* * * *
2955421 TGATTCTTCCAAACAAATGAAATAATGTACATACATAGATGCTTACATAGATAAAAAAAAATTGC
192 AGATTCTTCCAAACAAATGAAATAATATACATACAAAAATGCTTACATAGAT--AAAAAAATTGC
*
2955486 AGATGCAAATACATGTATGCAATG
255 AGATGCAAATACATGTATACAATG
* *
2955510 CATAATGAAAACAAGAATTTGTATTCAAAA-TATGTACAAAACTAAAAAGGCAAAGATTGCCTCC
1 CATAATGAAAACAAGAATCTAT-TTCAAAACTATGTACAAAACTAAAAAGGCAAAGATTGCC-CC
** * * *
2955574 AAATGAATGAAATAATGTACACAAAAAGATGTTTACGTGGATAACAAAATGTATATGCAAATACA
64 AAACAAATGAAATAATGTACA-AAAAAAATGTTTACGTAGATAA-AAAATGTATATGCAAATAAA
* * * * *
2955639 TATATGCAATGCATAATAAAAACAAGAATTTGTATTCAAAACTATAG-ACAAAACT-GAAAAGGC
127 TATATGCAATACAT-AGAAAAACAAAAACTTATATTCAAAACTAT-GTACAAAACTAGAAAAGGC
* ** *
2955702 AAAGATTGCTTTCAAACAAATGAAATAATATACATACAAAAATTTTTACATGGAT-AAAAAA-TG
190 AAAGATT-CTTCCAAACAAATGAAATAATATACATACAAAAATGCTTACATAGATAAAAAAATTG
* *
2955765 TATATGCAAATACATGTATACAATG
254 CAGATGCAAATACATGTATACAATG
* *
2955790 CATAGT-AAAACAAGAACTCTATTTCAAAACTATTTACAAAACTAAAAAGGCAAAGATTGCCCCC
1 CATAATGAAAACAAGAA-TCTATTTCAAAACTATGTACAAAACTAAAAAGGCAAAGATTG-CCCC
* * * * * *
2955854 AAACAAATGAAATAACGTACATATAAAAATATTTGCGTTGAT-AAAAATGTGTATGCAAAT
64 AAACAAATGAAATAATGTACA-AAAAAAATGTTTACGTAGATAAAAAATGTATATGCAAAT
2955914 GTATGCAAAT
Statistics
Matches: 345, Mismatches: 46, Indels: 29
0.82 0.11 0.07
Matches are distributed among these distances:
278 28 0.08
279 36 0.10
280 115 0.33
281 30 0.09
282 19 0.06
283 43 0.12
284 73 0.21
285 1 0.00
ACGTcount: A:0.51, C:0.13, G:0.11, T:0.25
Consensus pattern (278 bp):
CATAATGAAAACAAGAATCTATTTCAAAACTATGTACAAAACTAAAAAGGCAAAGATTGCCCCAA
ACAAATGAAATAATGTACAAAAAAAATGTTTACGTAGATAAAAAATGTATATGCAAATAAATATA
TGCAATACATAGAAAAACAAAAACTTATATTCAAAACTATGTACAAAACTAGAAAAGGCAAAGAT
TCTTCCAAACAAATGAAATAATATACATACAAAAATGCTTACATAGATAAAAAAATTGCAGATGC
AAATACATGTATACAATG
Found at i:2955843 original size:139 final size:140
Alignment explanation
Indices: 2955229--2955913 Score: 723
Period size: 139 Copynumber: 4.9 Consensus size: 140
2955219 ATCTTCACAA
* * * *
2955229 CATAATGAAAACAAGAAT-TCATATTTAAAACTTATGTACCAAAACTAAAAA-ACAAAAATTGCC
1 CATAATAAAAACAAGAATCT-ATATTCAAAAC-TATGTA-CAAAACTAAAAAGGCAAAGATTGCC
* * *
2955292 -CTAAACAAATGAAATAATG--CAAAAAAAAATGTTTACATAGATAAAAAATGTATATGCAAATA
63 TCCAAACAAATGAAATAATGTACATACAAAAATGTTTACATAGATAAAAAATGTATATGCAAATA
* *
2955354 AATGTATGCAATA
128 CATGTATGCAATG
* * * * * *
2955367 CAT-AGAAAAATAA-AAACTTATATTCAAAACTATGTACAAAACTATAAAAGGTAATGATT-CTT
1 CATAATAAAAACAAGAATC-TATATTCAAAACTATGTACAAAACTA-AAAAGGCAAAGATTGCCT
* * * * *
2955429 CCAAACAAATGAAATAATGTACATACATAGATGCTTACATAGATAAAAAAAAATTGCAGATGCAA
64 CCAAACAAATGAAATAATGTACATACAAAAATGTTTACATAGAT---AAAAAA-TGTATATGCAA
2955494 ATACATGTATGCAATG
125 ATACATGTATGCAATG
* * *
2955510 CATAATGAAAACAAGAATTTGTATTCAAAA-TATGTACAAAACTAAAAAGGCAAAGATTGCCTCC
1 CATAATAAAAACAAGAATCTATATTCAAAACTATGTACAAAACTAAAAAGGCAAAGATTGCCTCC
** * * *
2955574 AAATGAATGAAATAATGTACACA-AAAAGATGTTTACGTGGATAACAAAATGTATATGCAAATAC
66 AAACAAATGAAATAATGTACATACAAAA-ATGTTTACATAGATAA-AAAATGTATATGCAAATAC
*
2955638 ATATATGCAATG
129 ATGTATGCAATG
* * * * *
2955650 CATAATAAAAACAAGAATTTGTATTCAAAACTATAG-ACAAAACTGAAAAGGCAAAGATTGCTTT
1 CATAATAAAAACAAGAATCTATATTCAAAACTAT-GTACAAAACTAAAAAGGCAAAGATTGCCTC
* * *
2955714 CAAACAAATGAAATAATATACATACAAAAATTTTTACATGGATAAAAAATGTATATGCAAATACA
65 CAAACAAATGAAATAATGTACATACAAAAATGTTTACATAGATAAAAAATGTATATGCAAATACA
*
2955779 TGTATACAATG
130 TGTATGCAATG
* * *
2955790 CATAGT-AAAACAAGAACTCTAT-TTCAAAACTATTTACAAAACTAAAAAGGCAAAGATTGCCCC
1 CATAATAAAAACAAGAA-TCTATATTCAAAACTATGTACAAAACTAAAAAGGCAAAGATTGCCTC
* * * * * * *
2955853 CAAACAAATGAAATAACGTACATATAAAAATATTTGCGTTGAT-AAAAATGTGTATGCAAAT
65 CAAACAAATGAAATAATGTACATACAAAAATGTTTACATAGATAAAAAATGTATATGCAAAT
2955914 GTATGCAAAT
Statistics
Matches: 458, Mismatches: 68, Indels: 42
0.81 0.12 0.07
Matches are distributed among these distances:
135 8 0.02
136 13 0.03
137 40 0.09
138 21 0.05
139 99 0.22
140 92 0.20
141 66 0.14
142 25 0.05
143 75 0.16
144 17 0.04
145 2 0.00
ACGTcount: A:0.51, C:0.13, G:0.11, T:0.25
Consensus pattern (140 bp):
CATAATAAAAACAAGAATCTATATTCAAAACTATGTACAAAACTAAAAAGGCAAAGATTGCCTCC
AAACAAATGAAATAATGTACATACAAAAATGTTTACATAGATAAAAAATGTATATGCAAATACAT
GTATGCAATG
Found at i:2956658 original size:44 final size:44
Alignment explanation
Indices: 2956603--2956725 Score: 147
Period size: 44 Copynumber: 2.8 Consensus size: 44
2956593 ATGCCAATCC
* * * * *
2956603 AAATAATCAAATAAATTAGTGCACATGAAGAATCAAAATCTATA
1 AAATAAACAAATAAATTAGTGCACATGAAAAATCAAAAGCCACA
* * * *
2956647 AAATAAACAAATAAATTAGTACATATAAAAAATCATAAGCCACA
1 AAATAAACAAATAAATTAGTGCACATGAAAAATCAAAAGCCACA
* *
2956691 AAATAAACAAATAAGTTAGTGCACATGAGAAATCA
1 AAATAAACAAATAAATTAGTGCACATGAAAAATCA
2956726 TAAATAATTA
Statistics
Matches: 65, Mismatches: 14, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
44 65 1.00
ACGTcount: A:0.57, C:0.12, G:0.09, T:0.22
Consensus pattern (44 bp):
AAATAAACAAATAAATTAGTGCACATGAAAAATCAAAAGCCACA
Found at i:2957286 original size:4 final size:4
Alignment explanation
Indices: 2957245--2957327 Score: 71
Period size: 4 Copynumber: 20.8 Consensus size: 4
2957235 TTACATCAAT
* * * *
2957245 TAAA TCAA TAAA TCAA TAGA TAAA -AAA AAAA TCAAAA TAAA TAAA TAAA
1 TAAA TAAA TAAA TAAA TAAA TAAA TAAA TAAA T--AAA TAAA TAAA TAAA
* * *
2957294 T-AA TGAA TAAA TAAA TATA GAAA TAAA TAAA TAA
1 TAAA TAAA TAAA TAAA TAAA TAAA TAAA TAAA TAA
2957328 GTTAAAAAAA
Statistics
Matches: 63, Mismatches: 12, Indels: 8
0.76 0.14 0.10
Matches are distributed among these distances:
3 6 0.10
4 53 0.84
6 4 0.06
ACGTcount: A:0.70, C:0.04, G:0.04, T:0.23
Consensus pattern (4 bp):
TAAA
Found at i:2961189 original size:33 final size:31
Alignment explanation
Indices: 2961131--2961207 Score: 75
Period size: 36 Copynumber: 2.4 Consensus size: 31
2961121 CTTCTTCTGA
**
2961131 TTCTGCTTCTTCTCATTGTTTTTGTT-TGTC
1 TTCTGCTTCTTCTCATTGTCATTGTTCTGTC
2961161 TTCTGCTTCTTCTCCATATTGTCATTGTTGCCTGTC
1 TTCTGCTTCTTCT-C--ATTGTCATTGTT--CTGTC
*
2961197 TTCTGTTTCTT
1 TTCTGCTTCTT
2961208 TTGCGTCCTG
Statistics
Matches: 38, Mismatches: 3, Indels: 6
0.81 0.06 0.13
Matches are distributed among these distances:
30 13 0.34
31 1 0.03
33 10 0.26
36 14 0.37
ACGTcount: A:0.05, C:0.23, G:0.13, T:0.58
Consensus pattern (31 bp):
TTCTGCTTCTTCTCATTGTCATTGTTCTGTC
Found at i:2961604 original size:2 final size:2
Alignment explanation
Indices: 2961597--2961623 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
2961587 CCGCCTCTTA
2961597 AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT A
2961624 GAGAGAGAGA
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 25 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:2963901 original size:225 final size:226
Alignment explanation
Indices: 2963510--2963958 Score: 837
Period size: 225 Copynumber: 2.0 Consensus size: 226
2963500 ACATTGAATG
2963510 TTGGATTGAAATTAAATTGGAGAGCTTTTATTTTTAATAAAATTTTACATTTTAAGAGGAAAACA
1 TTGGATTGAAATTAAATTGGAGAGCTTTTATTTTTAATAAAATTTTACATTTTAAGAGGAAAACA
* *
2963575 AAATATCAATAGACAAAATGTGATCAATTGATTAATTTAATTTAATATATCAAATTAAATTTTGA
66 AAATATCAATAGAAAAAATGTGATAAATTGATTAATTTAATTTAATATATCAAATTAAATTTTGA
2963640 AAAAAAAAACTAAAAAAATTATTAAAAATTTAAAAATG-TTTTTTTTTCAAAAAAATTTTAACAT
131 AAAAAAAAACTAAAAAAATTATTAAAAATTTAAAAATGTTTTTTTTTTCAAAAAAATTTTAACAT
* *
2963704 AAAAATAGATTTTTAACTTTTATATTAAAGT
196 AAAAATAAATTTTTAAATTTTATATTAAAGT
* *
2963735 TTGGATTGAAATTAAATTGGAGGGCTTTTATTTTTAATAAAATTTTACATTTTCAGAGGAAAACA
1 TTGGATTGAAATTAAATTGGAGAGCTTTTATTTTTAATAAAATTTTACATTTTAAGAGGAAAACA
2963800 AAATATCAATAGAAAAAATGTGATAAATTGATTAATTTAATTTAATATATCAAATTAAATTTTGA
66 AAATATCAATAGAAAAAATGTGATAAATTGATTAATTTAATTTAATATATCAAATTAAATTTTGA
2963865 AAAAAAAAACTAAAAAAATTATTAAAAATTTAAAAATGTTTTTTTTTTCAAAAAAATTTTAACAT
131 AAAAAAAAACTAAAAAAATTATTAAAAATTTAAAAATGTTTTTTTTTTCAAAAAAATTTTAACAT
2963930 AAAAATAAATTTTTAAATTTTATATTAAA
196 AAAAATAAATTTTTAAATTTTATATTAAA
2963959 AATCTATTTT
Statistics
Matches: 217, Mismatches: 6, Indels: 1
0.97 0.03 0.00
Matches are distributed among these distances:
225 164 0.76
226 53 0.24
ACGTcount: A:0.49, C:0.04, G:0.08, T:0.39
Consensus pattern (226 bp):
TTGGATTGAAATTAAATTGGAGAGCTTTTATTTTTAATAAAATTTTACATTTTAAGAGGAAAACA
AAATATCAATAGAAAAAATGTGATAAATTGATTAATTTAATTTAATATATCAAATTAAATTTTGA
AAAAAAAAACTAAAAAAATTATTAAAAATTTAAAAATGTTTTTTTTTTCAAAAAAATTTTAACAT
AAAAATAAATTTTTAAATTTTATATTAAAGT
Found at i:2966006 original size:15 final size:15
Alignment explanation
Indices: 2965986--2966015 Score: 60
Period size: 15 Copynumber: 2.0 Consensus size: 15
2965976 GACGAGGAAA
2965986 GCATAATGTTTGAGG
1 GCATAATGTTTGAGG
2966001 GCATAATGTTTGAGG
1 GCATAATGTTTGAGG
2966016 ACACCGTTGT
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.27, C:0.07, G:0.33, T:0.33
Consensus pattern (15 bp):
GCATAATGTTTGAGG
Found at i:2969414 original size:4 final size:4
Alignment explanation
Indices: 2969407--2969466 Score: 58
Period size: 4 Copynumber: 16.0 Consensus size: 4
2969397 TAGGCATGTC
* *
2969407 TATT TATT TATT TATT TATT TATT T-TAT TA-T TA-T TA-T TATA TCTT
1 TATT TATT TATT TATT TATT TATT TAT-T TATT TATT TATT TATT TATT
2969452 TATT TATT T-TT TATT
1 TATT TATT TATT TATT
2969467 ATTATTTTTA
Statistics
Matches: 48, Mismatches: 4, Indels: 8
0.80 0.07 0.13
Matches are distributed among these distances:
3 13 0.27
4 35 0.73
ACGTcount: A:0.25, C:0.02, G:0.00, T:0.73
Consensus pattern (4 bp):
TATT
Found at i:2969446 original size:25 final size:25
Alignment explanation
Indices: 2969414--2969473 Score: 84
Period size: 29 Copynumber: 2.2 Consensus size: 25
2969404 GTCTATTTAT
2969414 TTATTTATTTATTTATTTTATTATTA
1 TTATTTATTTATTTATTTT-TTATTA
2969440 TTATTATATCTTTATTTATTTTTTATTA
1 TTATT-TA--TTTATTTATTTTTTATTA
2969468 TTATTT
1 TTATTT
2969474 TTATGACTAT
Statistics
Matches: 31, Mismatches: 0, Indels: 5
0.86 0.00 0.14
Matches are distributed among these distances:
26 5 0.16
27 3 0.10
28 11 0.35
29 12 0.39
ACGTcount: A:0.25, C:0.02, G:0.00, T:0.73
Consensus pattern (25 bp):
TTATTTATTTATTTATTTTTTATTA
Found at i:2969474 original size:11 final size:11
Alignment explanation
Indices: 2969426--2969474 Score: 52
Period size: 11 Copynumber: 4.6 Consensus size: 11
2969416 ATTTATTTAT
2969426 TTATTTTATTA
1 TTATTTTATTA
2969437 TTA--TTATTA
1 TTATTTTATTA
2969446 -TATCTTTATTTA
1 TTAT-TTTA-TTA
2969458 TT-TTTTATTA
1 TTATTTTATTA
2969468 TTATTTT
1 TTATTTT
2969475 TATGACTATT
Statistics
Matches: 32, Mismatches: 0, Indels: 12
0.73 0.00 0.27
Matches are distributed among these distances:
8 2 0.06
9 6 0.19
10 5 0.16
11 14 0.44
12 4 0.12
13 1 0.03
ACGTcount: A:0.24, C:0.02, G:0.00, T:0.73
Consensus pattern (11 bp):
TTATTTTATTA
Found at i:2973818 original size:36 final size:33
Alignment explanation
Indices: 2973755--2973839 Score: 100
Period size: 33 Copynumber: 2.5 Consensus size: 33
2973745 TTCTTTTTGG
*
2973755 CTGTCTTCTGCTTCTGCATCTTCTCATTGTTGTTGC
1 CTGTCTTCTGCTTCTTCATCTTCTCA---TTGTTGC
* *
2973791 TTGTCTTCTGCTTCTTC-TCGTTGTCATTGTTGC
1 CTGTCTTCTGCTTCTTCATC-TTCTCATTGTTGC
2973824 CTGTCTTCTGCTTCTT
1 CTGTCTTCTGCTTCTT
2973840 TTGCTTCCTG
Statistics
Matches: 44, Mismatches: 4, Indels: 5
0.83 0.08 0.09
Matches are distributed among these distances:
33 22 0.50
35 2 0.05
36 20 0.45
ACGTcount: A:0.04, C:0.27, G:0.16, T:0.53
Consensus pattern (33 bp):
CTGTCTTCTGCTTCTTCATCTTCTCATTGTTGC
Found at i:2976645 original size:9 final size:9
Alignment explanation
Indices: 2976631--2976681 Score: 57
Period size: 9 Copynumber: 5.7 Consensus size: 9
2976621 ATACGAATAA
2976631 ATATTTAAC
1 ATATTTAAC
2976640 ATATTTAAC
1 ATATTTAAC
** *
2976649 ACGTGTAAC
1 ATATTTAAC
2976658 ATATTTAAC
1 ATATTTAAC
* *
2976667 ACATTTAAT
1 ATATTTAAC
2976676 ATATTT
1 ATATTT
2976682 TTATATTTAT
Statistics
Matches: 33, Mismatches: 9, Indels: 0
0.79 0.21 0.00
Matches are distributed among these distances:
9 33 1.00
ACGTcount: A:0.41, C:0.12, G:0.04, T:0.43
Consensus pattern (9 bp):
ATATTTAAC
Found at i:2976679 original size:18 final size:18
Alignment explanation
Indices: 2976633--2976681 Score: 71
Period size: 18 Copynumber: 2.7 Consensus size: 18
2976623 ACGAATAAAT
2976633 ATTTAACATATTTAACAC
1 ATTTAACATATTTAACAC
* *
2976651 GTGTAACATATTTAACAC
1 ATTTAACATATTTAACAC
*
2976669 ATTTAATATATTT
1 ATTTAACATATTT
2976682 TTATATTTAT
Statistics
Matches: 26, Mismatches: 5, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
18 26 1.00
ACGTcount: A:0.41, C:0.12, G:0.04, T:0.43
Consensus pattern (18 bp):
ATTTAACATATTTAACAC
Found at i:2977043 original size:28 final size:27
Alignment explanation
Indices: 2976991--2977043 Score: 70
Period size: 27 Copynumber: 1.9 Consensus size: 27
2976981 TGAGTATTAA
* * *
2976991 TTTTTTATTTTTTTAATATGTAAGTAC
1 TTTTTTATATTATTAATATGCAAGTAC
2977018 TTTTTTATATTATTAATATGCCAAGT
1 TTTTTTATATTATTAATATG-CAAGT
2977044 TTATTAAGTT
Statistics
Matches: 22, Mismatches: 3, Indels: 1
0.85 0.12 0.04
Matches are distributed among these distances:
27 18 0.82
28 4 0.18
ACGTcount: A:0.28, C:0.06, G:0.08, T:0.58
Consensus pattern (27 bp):
TTTTTTATATTATTAATATGCAAGTAC
Found at i:2978175 original size:6 final size:6
Alignment explanation
Indices: 2978163--2978195 Score: 50
Period size: 6 Copynumber: 5.7 Consensus size: 6
2978153 TTTATAGTAA
*
2978163 TAATAT AAATA- TAATAT TAATAT TAATAT TAAT
1 TAATAT TAATAT TAATAT TAATAT TAATAT TAAT
2978196 CCTATACGTT
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
5 4 0.17
6 20 0.83
ACGTcount: A:0.55, C:0.00, G:0.00, T:0.45
Consensus pattern (6 bp):
TAATAT
Found at i:2978191 original size:12 final size:11
Alignment explanation
Indices: 2978162--2978195 Score: 50
Period size: 11 Copynumber: 3.0 Consensus size: 11
2978152 TTTTATAGTA
*
2978162 ATAATATAAAT
1 ATAATATTAAT
2978173 ATAATATTAAT
1 ATAATATTAAT
2978184 ATTAATATTAAT
1 A-TAATATTAAT
2978196 CCTATACGTT
Statistics
Matches: 21, Mismatches: 1, Indels: 1
0.91 0.04 0.04
Matches are distributed among these distances:
11 11 0.52
12 10 0.48
ACGTcount: A:0.56, C:0.00, G:0.00, T:0.44
Consensus pattern (11 bp):
ATAATATTAAT
Found at i:2996071 original size:2 final size:2
Alignment explanation
Indices: 2996021--2996054 Score: 50
Period size: 2 Copynumber: 17.0 Consensus size: 2
2996011 ATGCTAAAGC
* *
2996021 AT AT AA AT AA AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
2996055 TCATCACACA
Statistics
Matches: 28, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
2 28 1.00
ACGTcount: A:0.56, C:0.00, G:0.00, T:0.44
Consensus pattern (2 bp):
AT
Found at i:3000073 original size:42 final size:42
Alignment explanation
Indices: 3000014--3000115 Score: 152
Period size: 42 Copynumber: 2.4 Consensus size: 42
3000004 GTTGCAAGAG
* * *
3000014 AATGGATCGATCTATTTTGATAGAGGATCAAC-CTATTTTCAT
1 AATGGATCAATCCATTTTGATAGAGGATCAACTC-ATTTTCAA
*
3000056 AATGGATCAATCCATTTTGATAGAGGATCAATTCATTTTCAA
1 AATGGATCAATCCATTTTGATAGAGGATCAACTCATTTTCAA
3000098 AATGGATCAATCCATTTT
1 AATGGATCAATCCATTTT
3000116 ATAAGGGATT
Statistics
Matches: 55, Mismatches: 4, Indels: 2
0.90 0.07 0.03
Matches are distributed among these distances:
42 54 0.98
43 1 0.02
ACGTcount: A:0.33, C:0.15, G:0.15, T:0.37
Consensus pattern (42 bp):
AATGGATCAATCCATTTTGATAGAGGATCAACTCATTTTCAA
Found at i:3000092 original size:21 final size:21
Alignment explanation
Indices: 3000017--3000115 Score: 96
Period size: 21 Copynumber: 4.7 Consensus size: 21
3000007 GCAAGAGAAT
* *
3000017 GGATCGATCTATTTTGATAGA
1 GGATCAATCCATTTTGATAGA
*
3000038 GGATCAA-CCTATTTTCATA-A
1 GGATCAATCC-ATTTTGATAGA
3000058 TGGATCAATCCATTTTGATAGA
1 -GGATCAATCCATTTTGATAGA
* * *
3000080 GGATCAATTCATTTTCA-AAA
1 GGATCAATCCATTTTGATAGA
3000100 TGGATCAATCCATTTT
1 -GGATCAATCCATTTT
3000116 ATAAGGGATT
Statistics
Matches: 65, Mismatches: 8, Indels: 10
0.78 0.10 0.12
Matches are distributed among these distances:
20 4 0.06
21 58 0.89
22 3 0.05
ACGTcount: A:0.32, C:0.15, G:0.15, T:0.37
Consensus pattern (21 bp):
GGATCAATCCATTTTGATAGA
Found at i:3003467 original size:21 final size:21
Alignment explanation
Indices: 3003443--3003483 Score: 64
Period size: 21 Copynumber: 2.0 Consensus size: 21
3003433 GAGAGAAAGA
* *
3003443 GGTAGTTATGCGAGAAAATTT
1 GGTAGTTAGGCAAGAAAATTT
3003464 GGTAGTTAGGCAAGAAAATT
1 GGTAGTTAGGCAAGAAAATT
3003484 GTCAACTCAA
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
21 18 1.00
ACGTcount: A:0.37, C:0.05, G:0.29, T:0.29
Consensus pattern (21 bp):
GGTAGTTAGGCAAGAAAATTT
Found at i:3003750 original size:84 final size:84
Alignment explanation
Indices: 3003606--3003766 Score: 268
Period size: 84 Copynumber: 1.9 Consensus size: 84
3003596 AACATGTGAA
* * * *
3003606 AACCCCTCGCCAAGACTTAGAGGGGCGTAGCAATAATCTCCATGAGAGAGTAGTTCAATATACAG
1 AACCCCTCGCCAAGACTTAGAGGAGCGTAGCAATAATCTCAAAGAGAGAGTAGTTCAATATACAA
3003671 TATATAGATATAGACTTTT
66 TATATAGATATAGACTTTT
* *
3003690 AACCCCTCGCCAAGACTTAGAGGAGCGTAGCAATAATCTCAAAGGGAGAGTAGTTTAATATACAA
1 AACCCCTCGCCAAGACTTAGAGGAGCGTAGCAATAATCTCAAAGAGAGAGTAGTTCAATATACAA
3003755 TATATAGATATA
66 TATATAGATATA
3003767 ATATAGATAT
Statistics
Matches: 71, Mismatches: 6, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
84 71 1.00
ACGTcount: A:0.37, C:0.18, G:0.20, T:0.25
Consensus pattern (84 bp):
AACCCCTCGCCAAGACTTAGAGGAGCGTAGCAATAATCTCAAAGAGAGAGTAGTTCAATATACAA
TATATAGATATAGACTTTT
Found at i:3005404 original size:105 final size:103
Alignment explanation
Indices: 3005291--3005499 Score: 305
Period size: 105 Copynumber: 2.0 Consensus size: 103
3005281 AAGCCCACCT
* *
3005291 TACAATTTTGCCATTAATGTCATATTTGTCATTTTTAAAAATACAAATAAAAAATATTTTTATAT
1 TACAATTTTGCCATTAATATCATATTTGTCATTCTTAAAAATACAAATAAAAAATA-TTTTATAT
*
3005356 ATATT-TA-TATTATATAATATATTTAAAAATGTATTATAAA
65 AT-TTATATTA-TATATAATATATTTAAAAATCTATTA-AAA
* * **
3005396 TACAATTTTGCCATTAATATTATATTTTTCATTCTTGCAAATACAAATAAAAAATATTTTATATA
1 TACAATTTTGCCATTAATATCATATTTGTCATTCTTAAAAATACAAATAAAAAATATTTTATATA
3005461 TTTATATTATATATAATATATTTAAAAATCTATTAAAA
66 TTTATATTATATATAATATATTTAAAAATCTATTAAAA
3005499 T
1 T
3005500 GTTAATTAAT
Statistics
Matches: 95, Mismatches: 7, Indels: 6
0.88 0.06 0.06
Matches are distributed among these distances:
103 6 0.06
104 37 0.39
105 52 0.55
ACGTcount: A:0.44, C:0.07, G:0.03, T:0.46
Consensus pattern (103 bp):
TACAATTTTGCCATTAATATCATATTTGTCATTCTTAAAAATACAAATAAAAAATATTTTATATA
TTTATATTATATATAATATATTTAAAAATCTATTAAAA
Found at i:3013114 original size:23 final size:23
Alignment explanation
Indices: 3013075--3013124 Score: 57
Period size: 23 Copynumber: 2.2 Consensus size: 23
3013065 AAATTAATAA
* * *
3013075 TTATATAAAAAATTTTTATTTTT
1 TTATATAAAAAAATTTTAATTAT
3013098 TTAT-TAAATAAAATTTTAATTAT
1 TTATATAAA-AAAATTTTAATTAT
3013121 TTAT
1 TTAT
3013125 GTTCAAATTT
Statistics
Matches: 23, Mismatches: 3, Indels: 2
0.82 0.11 0.07
Matches are distributed among these distances:
22 4 0.17
23 19 0.83
ACGTcount: A:0.42, C:0.00, G:0.00, T:0.58
Consensus pattern (23 bp):
TTATATAAAAAAATTTTAATTAT
Found at i:3017919 original size:2 final size:2
Alignment explanation
Indices: 3017907--3017940 Score: 59
Period size: 2 Copynumber: 17.0 Consensus size: 2
3017897 CTCCACATGC
*
3017907 AT AT AT GT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
3017941 GTGCGTGTTT
Statistics
Matches: 30, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
2 30 1.00
ACGTcount: A:0.47, C:0.00, G:0.03, T:0.50
Consensus pattern (2 bp):
AT
Found at i:3029702 original size:16 final size:17
Alignment explanation
Indices: 3029671--3029704 Score: 52
Period size: 18 Copynumber: 2.0 Consensus size: 17
3029661 TATCTATAAC
3029671 TTTTTTTATATCTTAAAA
1 TTTTTTTATA-CTTAAAA
3029689 TTTTTTTATA-TTAAAA
1 TTTTTTTATACTTAAAA
3029705 AGTAAGAAAT
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
16 6 0.38
18 10 0.62
ACGTcount: A:0.35, C:0.03, G:0.00, T:0.62
Consensus pattern (17 bp):
TTTTTTTATACTTAAAA
Found at i:3030590 original size:17 final size:17
Alignment explanation
Indices: 3030568--3030601 Score: 50
Period size: 17 Copynumber: 2.0 Consensus size: 17
3030558 ATCGAGCAAC
3030568 TTAATCTAACAATTTAT
1 TTAATCTAACAATTTAT
* *
3030585 TTAATCTGATAATTTAT
1 TTAATCTAACAATTTAT
3030602 GTATTTATAT
Statistics
Matches: 15, Mismatches: 2, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
17 15 1.00
ACGTcount: A:0.38, C:0.09, G:0.03, T:0.50
Consensus pattern (17 bp):
TTAATCTAACAATTTAT
Found at i:3032853 original size:14 final size:14
Alignment explanation
Indices: 3032834--3032863 Score: 51
Period size: 14 Copynumber: 2.1 Consensus size: 14
3032824 ATACCATAAA
*
3032834 ATTTGGGATATATT
1 ATTTGGGATACATT
3032848 ATTTGGGATACATT
1 ATTTGGGATACATT
3032862 AT
1 AT
3032864 GTGAAACGCA
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
14 15 1.00
ACGTcount: A:0.30, C:0.03, G:0.20, T:0.47
Consensus pattern (14 bp):
ATTTGGGATACATT
Found at i:3037482 original size:27 final size:27
Alignment explanation
Indices: 3037452--3037507 Score: 85
Period size: 27 Copynumber: 2.1 Consensus size: 27
3037442 AAACTCTTTT
* * *
3037452 AAATTTATTTTTTATTTATAAAATTTA
1 AAATTAATTTTTTATTTAAAAAAATTA
3037479 AAATTAATTTTTTATTTAAAAAAATTA
1 AAATTAATTTTTTATTTAAAAAAATTA
3037506 AA
1 AA
3037508 CTCTTTATCA
Statistics
Matches: 26, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
27 26 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (27 bp):
AAATTAATTTTTTATTTAAAAAAATTA
Found at i:3042227 original size:20 final size:21
Alignment explanation
Indices: 3042202--3042249 Score: 80
Period size: 21 Copynumber: 2.3 Consensus size: 21
3042192 TTAATTCAAT
*
3042202 CTGAAAAGTTTC-ATTTTTTC
1 CTGAAAAGTTTCAATTTTTCC
3042222 CTGAAAAGTTTCAATTTTTCC
1 CTGAAAAGTTTCAATTTTTCC
3042243 CTGAAAA
1 CTGAAAA
3042250 AGTTGCAACT
Statistics
Matches: 26, Mismatches: 1, Indels: 1
0.93 0.04 0.04
Matches are distributed among these distances:
20 12 0.46
21 14 0.54
ACGTcount: A:0.31, C:0.17, G:0.10, T:0.42
Consensus pattern (21 bp):
CTGAAAAGTTTCAATTTTTCC
Found at i:3042927 original size:12 final size:12
Alignment explanation
Indices: 3042892--3042930 Score: 53
Period size: 12 Copynumber: 3.2 Consensus size: 12
3042882 TTTTTAATAA
3042892 TAATAAATAAA-T
1 TAATAAA-AAATT
*
3042904 AAATAAAAAATT
1 TAATAAAAAATT
3042916 TAATAAAAAATT
1 TAATAAAAAATT
3042928 TAA
1 TAA
3042931 ATTGATAGAT
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
11 3 0.12
12 21 0.88
ACGTcount: A:0.69, C:0.00, G:0.00, T:0.31
Consensus pattern (12 bp):
TAATAAAAAATT
Found at i:3052824 original size:30 final size:30
Alignment explanation
Indices: 3052788--3052849 Score: 124
Period size: 30 Copynumber: 2.1 Consensus size: 30
3052778 AAAACAGCCT
3052788 TAAATTAACTTTGTTTCTTTCATTATCATA
1 TAAATTAACTTTGTTTCTTTCATTATCATA
3052818 TAAATTAACTTTGTTTCTTTCATTATCATA
1 TAAATTAACTTTGTTTCTTTCATTATCATA
3052848 TA
1 TA
3052850 GCTTGAAGAC
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
30 32 1.00
ACGTcount: A:0.31, C:0.13, G:0.03, T:0.53
Consensus pattern (30 bp):
TAAATTAACTTTGTTTCTTTCATTATCATA
Found at i:3057402 original size:32 final size:31
Alignment explanation
Indices: 3057366--3057451 Score: 84
Period size: 31 Copynumber: 2.7 Consensus size: 31
3057356 CATGAAATCT
3057366 AAATACATAAAAGATAAATTGCAAGAAAATTA
1 AAATACATAAAA-ATAAATTGCAAGAAAATTA
* * * *
3057398 AAATATATGAAAATTAAATTG-AATAAATTTA
1 AAATACAT-AAAAATAAATTGCAAGAAAATTA
* *
3057429 AAATGTCCTAAAAATAAATTGCA
1 AAAT-ACATAAAAATAAATTGCA
3057452 TTAAAAATAA
Statistics
Matches: 43, Mismatches: 8, Indels: 6
0.75 0.14 0.11
Matches are distributed among these distances:
31 23 0.53
32 16 0.37
33 4 0.09
ACGTcount: A:0.58, C:0.06, G:0.08, T:0.28
Consensus pattern (31 bp):
AAATACATAAAAATAAATTGCAAGAAAATTA
Found at i:3057532 original size:17 final size:18
Alignment explanation
Indices: 3057487--3057532 Score: 51
Period size: 16 Copynumber: 2.6 Consensus size: 18
3057477 TAAATAACAT
*
3057487 AAAATTTAATTTGCTTAAA
1 AAAATTTAAATTGC-TAAA
*
3057506 AAAA-TAAAATTGC-AAA
1 AAAATTTAAATTGCTAAA
3057522 AAAATTTAAAT
1 AAAATTTAAAT
3057533 GATTACATAA
Statistics
Matches: 23, Mismatches: 3, Indels: 4
0.77 0.10 0.13
Matches are distributed among these distances:
16 7 0.30
17 5 0.22
18 7 0.30
19 4 0.17
ACGTcount: A:0.59, C:0.04, G:0.04, T:0.33
Consensus pattern (18 bp):
AAAATTTAAATTGCTAAA
Found at i:3058105 original size:3 final size:3
Alignment explanation
Indices: 3058097--3058127 Score: 62
Period size: 3 Copynumber: 10.3 Consensus size: 3
3058087 ATTGATGTTC
3058097 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA T
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA T
3058128 GGTGTTTTTT
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 28 1.00
ACGTcount: A:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (3 bp):
TTA
Found at i:3059241 original size:4 final size:4
Alignment explanation
Indices: 3059234--3059297 Score: 74
Period size: 4 Copynumber: 16.0 Consensus size: 4
3059224 TCTATCTATC
* * *
3059234 TATA TATA TATA TATA TATA TATA TATA TAGA TATA GATA TAGA TATA
1 TATA TATA TATA TATA TATA TATA TATA TATA TATA TATA TATA TATA
* * *
3059282 GATA GATA GATA TATA
1 TATA TATA TATA TATA
3059298 ATGGGCCCTA
Statistics
Matches: 52, Mismatches: 8, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
4 52 1.00
ACGTcount: A:0.50, C:0.00, G:0.09, T:0.41
Consensus pattern (4 bp):
TATA
Found at i:3059245 original size:6 final size:6
Alignment explanation
Indices: 3059234--3059297 Score: 74
Period size: 6 Copynumber: 10.7 Consensus size: 6
3059224 TCTATCTATC
* * *
3059234 TATATA TATATA TATATA TATATA TATATA GATATA GATATA GATATA
1 TATATA TATATA TATATA TATATA TATATA TATATA TATATA TATATA
* * *
3059282 GATAGA TAGATA TATA
1 TATATA TATATA TATA
3059298 ATGGGCCCTA
Statistics
Matches: 52, Mismatches: 6, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
6 52 1.00
ACGTcount: A:0.50, C:0.00, G:0.09, T:0.41
Consensus pattern (6 bp):
TATATA
Found at i:3061540 original size:2 final size:2
Alignment explanation
Indices: 3061533--3061560 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
3061523 GTATAAGAAC
3061533 GA GA GA GA GA GA GA GA GA GA GA GA GA GA
1 GA GA GA GA GA GA GA GA GA GA GA GA GA GA
3061561 AACAAACCTT
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:0.50, T:0.00
Consensus pattern (2 bp):
GA
Found at i:3067332 original size:28 final size:28
Alignment explanation
Indices: 3067298--3067378 Score: 103
Period size: 27 Copynumber: 2.9 Consensus size: 28
3067288 ACAAAATCAT
* *
3067298 CACTTGTAAGATTTCAACCAATCTTTTG
1 CACTTGTAAGATTTCAAACAATCATTTG
*
3067326 CCCTTGTGAA-A-TTCAAACAATCATTTG
1 CACTTGT-AAGATTTCAAACAATCATTTG
*
3067353 CACTTGTAAGATTTTAAACAATCATT
1 CACTTGTAAGATTTCAAACAATCATT
3067379 CTTAACCAAA
Statistics
Matches: 45, Mismatches: 5, Indels: 6
0.80 0.09 0.11
Matches are distributed among these distances:
26 2 0.04
27 21 0.47
28 20 0.44
29 2 0.04
ACGTcount: A:0.33, C:0.20, G:0.10, T:0.37
Consensus pattern (28 bp):
CACTTGTAAGATTTCAAACAATCATTTG
Found at i:3070028 original size:138 final size:139
Alignment explanation
Indices: 3069823--3070104 Score: 503
Period size: 138 Copynumber: 2.0 Consensus size: 139
3069813 TTTTTTCCTT
3069823 TATTAATATCTATCCAAACATAGCGCTAAAAAAAGAAAAGAATGGCTGAAATTAAGAATTTAATT
1 TATTAATATCTATCCAAACATAGCGCTAAAAAAAGAAAAGAATGGCTGAAATTAAGAATTTAATT
*
3069888 ATGCATTTGAAGATTTGGAGGTAAAACTTATTTTTTAAACTGTTTAATTTTCGTCTTTATAAGAA
66 ATGCATTTGAAGATTTGGAGGTAAAACTTACTTTTTAAACTGTTTAATTTTCGTCTTTATAAGAA
*
3069953 AAACTCAAA
131 AAACCCAAA
* * *
3069962 TATTAATATCTATCCAAACATAGCGCTAAAAAAA-AAGAGAATGGTTGAAATTAAGGATTTAATT
1 TATTAATATCTATCCAAACATAGCGCTAAAAAAAGAAAAGAATGGCTGAAATTAAGAATTTAATT
*
3070026 ATGCATTTGAAGATTTGGAGGTAAAACTTACTTTTTAAACTGTTTAATTTTCGTCTTTATGAGAA
66 ATGCATTTGAAGATTTGGAGGTAAAACTTACTTTTTAAACTGTTTAATTTTCGTCTTTATAAGAA
3070091 AAACCCAAA
131 AAACCCAAA
3070100 TATTA
1 TATTA
3070105 GATTAAAATT
Statistics
Matches: 137, Mismatches: 6, Indels: 1
0.95 0.04 0.01
Matches are distributed among these distances:
138 103 0.75
139 34 0.25
ACGTcount: A:0.41, C:0.10, G:0.13, T:0.35
Consensus pattern (139 bp):
TATTAATATCTATCCAAACATAGCGCTAAAAAAAGAAAAGAATGGCTGAAATTAAGAATTTAATT
ATGCATTTGAAGATTTGGAGGTAAAACTTACTTTTTAAACTGTTTAATTTTCGTCTTTATAAGAA
AAACCCAAA
Found at i:3071387 original size:11 final size:11
Alignment explanation
Indices: 3071359--3071389 Score: 53
Period size: 11 Copynumber: 2.8 Consensus size: 11
3071349 TGAAATATGG
*
3071359 TTTGATATTAT
1 TTTGATTTTAT
3071370 TTTGATTTTAT
1 TTTGATTTTAT
3071381 TTTGATTTT
1 TTTGATTTT
3071390 CGAATATGAT
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
11 19 1.00
ACGTcount: A:0.19, C:0.00, G:0.10, T:0.71
Consensus pattern (11 bp):
TTTGATTTTAT
Found at i:3073234 original size:50 final size:50
Alignment explanation
Indices: 3073158--3073257 Score: 191
Period size: 50 Copynumber: 2.0 Consensus size: 50
3073148 GCACCCTTTG
3073158 TCGTCAGCACCGTGTGAGGTACTTTATGTTAGCAAGAAGAAAGAAGTTTC
1 TCGTCAGCACCGTGTGAGGTACTTTATGTTAGCAAGAAGAAAGAAGTTTC
*
3073208 TCGTCAGCACCGTGTGAGGTATTTTATGTTAGCAAGAAGAAAGAAGTTTC
1 TCGTCAGCACCGTGTGAGGTACTTTATGTTAGCAAGAAGAAAGAAGTTTC
3073258 ATAGGAATCT
Statistics
Matches: 49, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
50 49 1.00
ACGTcount: A:0.30, C:0.15, G:0.26, T:0.29
Consensus pattern (50 bp):
TCGTCAGCACCGTGTGAGGTACTTTATGTTAGCAAGAAGAAAGAAGTTTC
Found at i:3084350 original size:19 final size:16
Alignment explanation
Indices: 3084311--3084343 Score: 66
Period size: 16 Copynumber: 2.1 Consensus size: 16
3084301 AACGATTTGA
3084311 ATGATAATGATGATTT
1 ATGATAATGATGATTT
3084327 ATGATAATGATGATTT
1 ATGATAATGATGATTT
3084343 A
1 A
3084344 CGATGATTTT
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 17 1.00
ACGTcount: A:0.39, C:0.00, G:0.18, T:0.42
Consensus pattern (16 bp):
ATGATAATGATGATTT
Done.