Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NW_019168026.1 Durio zibethinus cultivar Musang King isolate D1 unplaced genomic scaffold, Duzib1.0 scaffold_28, 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: 15507587
ACGTcount: A:0.35, C:0.15, G:0.15, T:0.35
Warning! 97000 characters in sequence are not A, C, G, or T
File 67 of 91
Found at i:11153850 original size:13 final size:13
Alignment explanation
Indices: 11153834--11153875 Score: 57
Period size: 13 Copynumber: 3.2 Consensus size: 13
11153824 TTTATTTTGT
*
11153834 TTTTTTTTTAAAA
1 TTTTTTTCTAAAA
**
11153847 TTTTTTTCTCTAA
1 TTTTTTTCTAAAA
11153860 TTTTTTTCTAAAA
1 TTTTTTTCTAAAA
11153873 TTT
1 TTT
11153876 AATCATGCAA
Statistics
Matches: 24, Mismatches: 5, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
13 24 1.00
ACGTcount: A:0.24, C:0.07, G:0.00, T:0.69
Consensus pattern (13 bp):
TTTTTTTCTAAAA
Found at i:11153910 original size:9 final size:9
Alignment explanation
Indices: 11153896--11153927 Score: 55
Period size: 9 Copynumber: 3.4 Consensus size: 9
11153886 AAATACTTTA
11153896 AAAATAAAT
1 AAAATAAAT
11153905 AAAATAAAT
1 AAAATAAAT
11153914 AAAATAAAAT
1 AAAAT-AAAT
11153924 AAAA
1 AAAA
11153928 ATACCAAAAT
Statistics
Matches: 22, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
9 14 0.64
10 8 0.36
ACGTcount: A:0.81, C:0.00, G:0.00, T:0.19
Consensus pattern (9 bp):
AAAATAAAT
Found at i:11153911 original size:5 final size:5
Alignment explanation
Indices: 11153896--11153927 Score: 50
Period size: 5 Copynumber: 6.8 Consensus size: 5
11153886 AAATACTTTA
11153896 AAAAT -AAAT AAAAT -AAAT AAAAT AAAAT AAAA
1 AAAAT AAAAT AAAAT AAAAT AAAAT AAAAT AAAA
11153928 ATACCAAAAT
Statistics
Matches: 25, Mismatches: 0, Indels: 4
0.86 0.00 0.14
Matches are distributed among these distances:
4 8 0.32
5 17 0.68
ACGTcount: A:0.81, C:0.00, G:0.00, T:0.19
Consensus pattern (5 bp):
AAAAT
Found at i:11157777 original size:17 final size:18
Alignment explanation
Indices: 11157755--11157789 Score: 63
Period size: 18 Copynumber: 2.0 Consensus size: 18
11157745 GATGAGTGCA
11157755 TTCCATT-TTATATTTTT
1 TTCCATTCTTATATTTTT
11157772 TTCCATTCTTATATTTTT
1 TTCCATTCTTATATTTTT
11157790 GTATATCATT
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
17 7 0.41
18 10 0.59
ACGTcount: A:0.17, C:0.14, G:0.00, T:0.69
Consensus pattern (18 bp):
TTCCATTCTTATATTTTT
Found at i:11161476 original size:34 final size:34
Alignment explanation
Indices: 11161423--11161543 Score: 120
Period size: 34 Copynumber: 3.6 Consensus size: 34
11161413 GTTCAATTTC
* *
11161423 AGTCATTTCA-TTTTCAACTTGCAGCTCAATCCT
1 AGTCACTTCATTTTTCAACTTACAGCTCAATCCT
* *
11161456 AGTCACTTCATTTTTCAACTTACGGCTCAATTCT
1 AGTCACTTCATTTTTCAACTTACAGCTCAATCCT
* * * * * * *
11161490 GGTTACTTCATTTTTCAACTTATAGTTTAGTCAT
1 AGTCACTTCATTTTTCAACTTACAGCTCAATCCT
*
11161524 AGTCATTTCATTTTT-AACTT
1 AGTCACTTCATTTTTCAACTT
11161544 TTGGTTTAGT
Statistics
Matches: 71, Mismatches: 16, Indels: 2
0.80 0.18 0.02
Matches are distributed among these distances:
33 14 0.20
34 57 0.80
ACGTcount: A:0.24, C:0.21, G:0.09, T:0.45
Consensus pattern (34 bp):
AGTCACTTCATTTTTCAACTTACAGCTCAATCCT
Found at i:11161486 original size:67 final size:67
Alignment explanation
Indices: 11161354--11161487 Score: 169
Period size: 67 Copynumber: 2.0 Consensus size: 67
11161344 CGATTCACTC
* * ** ** * * *
11161354 TCAGTCATTTCATTTTCAACTTGCAACTTAGTCCCAGTCACTTTGTTTTTTGATTTATGGTTCAA
1 TCAGTCATTTCATTTTCAACTTGCAACTCAATCCCAGTCACTTCATTTTTCAACTTACGGCTCAA
11161419 TT
66 TT
* *
11161421 TCAGTCATTTCATTTTCAACTTGCAGCTCAATCCTAGTCACTTCATTTTTCAACTTACGGCTCAA
1 TCAGTCATTTCATTTTCAACTTGCAACTCAATCCCAGTCACTTCATTTTTCAACTTACGGCTCAA
11161486 TT
66 TT
11161488 CTGGTTACTT
Statistics
Matches: 56, Mismatches: 11, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
67 56 1.00
ACGTcount: A:0.22, C:0.23, G:0.10, T:0.44
Consensus pattern (67 bp):
TCAGTCATTTCATTTTCAACTTGCAACTCAATCCCAGTCACTTCATTTTTCAACTTACGGCTCAA
TT
Found at i:11161551 original size:33 final size:33
Alignment explanation
Indices: 11161496--11161638 Score: 146
Period size: 33 Copynumber: 4.3 Consensus size: 33
11161486 TTCTGGTTAC
* * *
11161496 TTCATTTTTCAACTTATAGTTTAGTCATAGTCAT
1 TTCATTTTT-AACTTATGGTTTAGTCTTGGTCAT
* * *
11161530 TTCATTTTTAACTTTTGGTTTAGTCTTGTTCAC
1 TTCATTTTTAACTTATGGTTTAGTCTTGGTCAT
* * *
11161563 TTCATTTTTTTACTTGT-GTTTAAATCTTGGTCAT
1 TTCA-TTTTTAACTTATGGTTT-AGTCTTGGTCAT
*
11161597 TTCATTTTTAACTTATGGCTTAGTCTTGGTCACT
1 TTCATTTTTAACTTATGGTTTAGTCTTGGTCA-T
11161631 TT-ATTTTT
1 TTCATTTTT
11161639 TGACTTGCGG
Statistics
Matches: 90, Mismatches: 15, Indels: 9
0.79 0.13 0.08
Matches are distributed among these distances:
33 52 0.58
34 38 0.42
ACGTcount: A:0.19, C:0.14, G:0.11, T:0.56
Consensus pattern (33 bp):
TTCATTTTTAACTTATGGTTTAGTCTTGGTCAT
Found at i:11161664 original size:67 final size:67
Alignment explanation
Indices: 11161526--11161671 Score: 168
Period size: 67 Copynumber: 2.2 Consensus size: 67
11161516 TTAGTCATAG
* * * * * * *
11161526 TCATTTCATTTTTAACTTTTGGTTTAGTCTTGTTCACTTCATTTTTTTACTTGTGTTTAAATCTT
1 TCATTTCATTTTTAACTTATGGCTTAGTCTTGGTCACTTCATTTTTTGACTTGGGTTCAAATCTC
**
11161591 GG
66 AA
* *
11161593 TCATTTCATTTTTAACTTATGGCTTAGTCTTGGTCACTTTATTTTTTGACTTGCGGTTCAATTC-
1 TCATTTCATTTTTAACTTATGGCTTAGTCTTGGTCACTTCATTTTTTGACTTG-GGTTCAAATCT
11161657 CAA
65 CAA
*
11161660 TCATTTTATTTT
1 TCATTTCATTTT
11161672 AGACTTAGGG
Statistics
Matches: 66, Mismatches: 12, Indels: 2
0.82 0.15 0.03
Matches are distributed among these distances:
67 59 0.89
68 7 0.11
ACGTcount: A:0.18, C:0.15, G:0.12, T:0.55
Consensus pattern (67 bp):
TCATTTCATTTTTAACTTATGGCTTAGTCTTGGTCACTTCATTTTTTGACTTGGGTTCAAATCTC
AA
Found at i:11161664 original size:134 final size:134
Alignment explanation
Indices: 11161559--11161805 Score: 293
Period size: 134 Copynumber: 1.8 Consensus size: 134
11161549 TTAGTCTTGT
* * * ** *
11161559 TCACTTCATTTTTTTACTTGTG-T-TTAAATCTTGGTCATTTCATTTTTAACTTATGGCTTAGTC
1 TCACTTCATTTTTTGA-TT-TGCTATTAAATCTTGATCATTTCATTTTTAACTGATAACTCAGTC
* ** *
11161622 TTGGTCACTTTATTTTTTGACTTGCGGTTCAATTCCAATCATTTTA-TTTTAGACTTAGGGTTTA
64 TTGATCACTTTA-TTTTTGACTTGCGACTCAATTCCAATCATTTCATTTTTAGACTTAGGGTTTA
11161686 ATCCCAC
128 ATCCCAC
* * *
11161693 TCACTTCATTTTTTGATTTGCTATTCAATCTTGATCATTTCATTTTTGACTGGTAACTCAGTCTT
1 TCACTTCATTTTTTGATTTGCTATTAAATCTTGATCATTTCATTTTTAACTGATAACTCAGTCTT
* * * *
11161758 GATCATTTTATTTTTGACTTGCGACTCAATTTCGATTATTTCATTTTT
66 GATCACTTTATTTTTGACTTGCGACTCAATTCCAATCATTTCATTTTT
11161806 GATTTGCAGC
Statistics
Matches: 93, Mismatches: 17, Indels: 6
0.80 0.15 0.05
Matches are distributed among these distances:
132 2 0.02
133 30 0.32
134 61 0.66
ACGTcount: A:0.20, C:0.17, G:0.12, T:0.51
Consensus pattern (134 bp):
TCACTTCATTTTTTGATTTGCTATTAAATCTTGATCATTTCATTTTTAACTGATAACTCAGTCTT
GATCACTTTATTTTTGACTTGCGACTCAATTCCAATCATTTCATTTTTAGACTTAGGGTTTAATC
CCAC
Found at i:11161737 original size:34 final size:32
Alignment explanation
Indices: 11161697--11161871 Score: 138
Period size: 33 Copynumber: 5.2 Consensus size: 32
11161687 TCCCACTCAC
* *
11161697 TTCATTTTTTGATTTGCTATTCAATCTTGATCAT
1 TTCA-TTTTTGACTTGC-ACTCAATCTTGATCAT
* * *
11161731 TTCATTTTTGACTGGTAACTCAGTCTTGATCAT
1 TTCATTTTTGACTTG-CACTCAATCTTGATCAT
* *
11161764 TTTATTTTTGACTTGCGACTCAAT-TTCGATTAT
1 TTCATTTTTGACTTGC-ACTCAATCTT-GATCAT
* * *
11161797 TTCATTTTTGATTTGCAGCTCAATCTCGGTCAT
1 TTCATTTTTGACTTGCA-CTCAATCTTGATCAT
* * *
11161830 GTT-ATTTTTGGACTTGCAGTTCAGTCTCGATCAT
1 -TTCATTTTT-GACTTGCA-CTCAATCTTGATCAT
11161864 TTCATTTT
1 TTCATTTT
11161872 GAATTGTGGT
Statistics
Matches: 114, Mismatches: 19, Indels: 16
0.77 0.13 0.11
Matches are distributed among these distances:
32 3 0.03
33 79 0.69
34 32 0.28
ACGTcount: A:0.19, C:0.17, G:0.14, T:0.50
Consensus pattern (32 bp):
TTCATTTTTGACTTGCACTCAATCTTGATCAT
Found at i:11161771 original size:67 final size:66
Alignment explanation
Indices: 11161700--11161871 Score: 168
Period size: 66 Copynumber: 2.6 Consensus size: 66
11161690 CACTCACTTC
* * * * *
11161700 ATTTTTTGATTTGCTATTCAATCTTGATCATTTCATTTTTGACTGGTAACTCAGTCTTGATCATT
1 ATTTTTTGACTTGC-ATTCAATCTTGATCATTTCATTTTTGACTGGCAACTCAATCTCGATCATG
11161765 TT
65 TT
* * * * * *
11161767 A-TTTTTGACTTGCGACTCAAT-TTCGATTATTTCATTTTTGATTTGCAGCTCAATCTCGGTCAT
1 ATTTTTTGACTTGC-ATTCAATCTT-GATCATTTCATTTTTGACTGGCAACTCAATCTCGATCAT
11161830 GTT
64 GTT
* * *
11161833 ATTTTTGGACTTGCAGTTCAGTCTCGATCATTTCATTTT
1 ATTTTTTGACTTGCA-TTCAATCTTGATCATTTCATTTT
11161872 GAATTGTGGT
Statistics
Matches: 84, Mismatches: 17, Indels: 8
0.77 0.16 0.07
Matches are distributed among these distances:
65 2 0.02
66 52 0.62
67 29 0.35
68 1 0.01
ACGTcount: A:0.20, C:0.17, G:0.14, T:0.49
Consensus pattern (66 bp):
ATTTTTTGACTTGCATTCAATCTTGATCATTTCATTTTTGACTGGCAACTCAATCTCGATCATGT
T
Found at i:11161872 original size:33 final size:33
Alignment explanation
Indices: 11161717--11161871 Score: 152
Period size: 33 Copynumber: 4.7 Consensus size: 33
11161707 GATTTGCTAT
* * * *
11161717 TCAATCTTGATCATTTCATTTTTGACTGGTAAC
1 TCAATCTCGATCATTTCATTTTTGACTTGCAGC
* * *
11161750 TCAGTCTTGATCATTTTATTTTTGACTTGC-GAC
1 TCAATCTCGATCATTTCATTTTTGACTTGCAG-C
* * *
11161783 TCAATTTCGATTATTTCATTTTTGATTTGCAGC
1 TCAATCTCGATCATTTCATTTTTGACTTGCAGC
* *
11161816 TCAATCTCGGTCATGTT-ATTTTTGGACTTGCAGT
1 TCAATCTCGATCAT-TTCATTTTT-GACTTGCAGC
*
11161850 TCAGTCTCGATCATTTCATTTT
1 TCAATCTCGATCATTTCATTTT
11161872 GAATTGTGGT
Statistics
Matches: 99, Mismatches: 18, Indels: 9
0.79 0.14 0.07
Matches are distributed among these distances:
33 71 0.72
34 28 0.28
ACGTcount: A:0.20, C:0.18, G:0.14, T:0.48
Consensus pattern (33 bp):
TCAATCTCGATCATTTCATTTTTGACTTGCAGC
Found at i:11164203 original size:140 final size:145
Alignment explanation
Indices: 11163985--11164312 Score: 364
Period size: 144 Copynumber: 2.3 Consensus size: 145
11163975 TGAAAAAAAC
* * * * *
11163985 TTTTCCTTAGAATAAATTTTTGACAACATTTA-AGAAAAAGTTGAAATATAAAATTTTCTTCAAT
1 TTTTGCTTAGAATAAATTTTT-A-AATATTCAGA-AAAAAGTTAAAATATAAAATTTTCTTAAAT
* * **** * ** * *
11164049 TCTTTGAAAATAAAAATAAAATAAAGT-GAATAAAATTTTTTGTTT-TTGAAATATGCT-AGGGA
63 TCTTTGAAAATAAAAATAAAATAAAATAAAATAAAATAAAATCTTTCTCAAAAAATGCTAAGGAA
**
11164111 AAATTTTGAAATATCAAT
128 AAAAATTGAAATATCAAT
* * *
11164129 TTCTT-CTTAGTATAAATTTTTAAATATTCAGAAAAAAGTTAAAATAT-CAA-TTTCTTAAATTG
1 TT-TTGCTTAGAATAAATTTTTAAATATTCAGAAAAAAGTTAAAATATAAAATTTTCTTAAATTC
11164191 TTTGAAAATAAAAATAAAATAAAATAAAATAAAATAAAATCTTTGCTCAAAAAATGCTAAGGAAA
65 TTTGAAAATAAAAATAAAATAAAATAAAATAAAATAAAATCTTT-CTCAAAAAATGCTAAGGAAA
11164256 AAAATTGAAATATCAAT
129 AAAATTGAAATATCAAT
*
11164273 TTTTGCTTAGAATTAATTTTTAAATATTCAGAAAAAAGTT
1 TTTTGCTTAGAATAAATTTTTAAATATTCAGAAAAAAGTT
11164313 TATTGTTGAT
Statistics
Matches: 155, Mismatches: 22, Indels: 14
0.81 0.12 0.07
Matches are distributed among these distances:
140 34 0.22
141 14 0.09
142 20 0.13
143 13 0.08
144 72 0.46
145 2 0.01
ACGTcount: A:0.48, C:0.06, G:0.09, T:0.37
Consensus pattern (145 bp):
TTTTGCTTAGAATAAATTTTTAAATATTCAGAAAAAAGTTAAAATATAAAATTTTCTTAAATTCT
TTGAAAATAAAAATAAAATAAAATAAAATAAAATAAAATCTTTCTCAAAAAATGCTAAGGAAAAA
AATTGAAATATCAAT
Found at i:11164209 original size:5 final size:5
Alignment explanation
Indices: 11164195--11164230 Score: 63
Period size: 5 Copynumber: 7.0 Consensus size: 5
11164185 AAATTGTTTG
11164195 AAAAT AAAAAT AAAAT AAAAT AAAAT AAAAT AAAAT
1 AAAAT -AAAAT AAAAT AAAAT AAAAT AAAAT AAAAT
11164231 CTTTGCTCAA
Statistics
Matches: 30, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
5 25 0.83
6 5 0.17
ACGTcount: A:0.81, C:0.00, G:0.00, T:0.19
Consensus pattern (5 bp):
AAAAT
Found at i:11164619 original size:15 final size:16
Alignment explanation
Indices: 11164582--11164621 Score: 50
Period size: 15 Copynumber: 2.7 Consensus size: 16
11164572 TAATATTTAG
11164582 AAAATT-TTTTAATAT
1 AAAATTATTTTAATAT
*
11164597 CAAA-TATTTTAATA-
1 AAAATTATTTTAATAT
11164611 AAAATTATTTT
1 AAAATTATTTT
11164622 TAGATCTAAT
Statistics
Matches: 21, Mismatches: 2, Indels: 4
0.78 0.07 0.15
Matches are distributed among these distances:
14 4 0.19
15 17 0.81
ACGTcount: A:0.47, C:0.03, G:0.00, T:0.50
Consensus pattern (16 bp):
AAAATTATTTTAATAT
Found at i:11166420 original size:19 final size:19
Alignment explanation
Indices: 11166385--11166445 Score: 53
Period size: 19 Copynumber: 3.4 Consensus size: 19
11166375 TTTTTATTTT
*
11166385 AAAAT-AATTACATAAAATA
1 AAAATAAATTA-ACAAAATA
11166404 AAAATAAATTAACAAAA-A
1 AAAATAAATTAACAAAATA
11166422 AAAA-AAA--AACAACAAT-
1 AAAATAAATTAACAA-AATA
11166438 AAAATAAA
1 AAAATAAA
11166446 GTAAAATCAA
Statistics
Matches: 37, Mismatches: 1, Indels: 10
0.77 0.02 0.21
Matches are distributed among these distances:
15 5 0.14
16 6 0.16
17 6 0.16
18 5 0.14
19 10 0.27
20 5 0.14
ACGTcount: A:0.77, C:0.07, G:0.00, T:0.16
Consensus pattern (19 bp):
AAAATAAATTAACAAAATA
Found at i:11166427 original size:20 final size:19
Alignment explanation
Indices: 11166385--11166427 Score: 52
Period size: 20 Copynumber: 2.2 Consensus size: 19
11166375 TTTTTATTTT
*
11166385 AAAATAATTACATAAAATA
1 AAAATAATTACATAAAAAA
11166404 AAAATAAATTAACA-AAAAAA
1 AAAAT-AATT-ACATAAAAAA
11166424 AAAA
1 AAAA
11166428 AAACAACAAT
Statistics
Matches: 21, Mismatches: 1, Indels: 3
0.84 0.04 0.12
Matches are distributed among these distances:
19 5 0.24
20 13 0.62
21 3 0.14
ACGTcount: A:0.77, C:0.05, G:0.00, T:0.19
Consensus pattern (19 bp):
AAAATAATTACATAAAAAA
Found at i:11167062 original size:2 final size:2
Alignment explanation
Indices: 11167055--11167102 Score: 69
Period size: 2 Copynumber: 24.0 Consensus size: 2
11167045 GAGTGGTAGG
* * *
11167055 AT AT AT AT AT AA AT AA AT AA AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
11167097 AT AT AT
1 AT AT AT
11167103 TTCAATTACT
Statistics
Matches: 40, Mismatches: 6, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
2 40 1.00
ACGTcount: A:0.56, C:0.00, G:0.00, T:0.44
Consensus pattern (2 bp):
AT
Found at i:11170839 original size:19 final size:19
Alignment explanation
Indices: 11170811--11170860 Score: 79
Period size: 19 Copynumber: 2.8 Consensus size: 19
11170801 ATTAATAAGG
11170811 TTAA-ATTATTAAAAGCTT
1 TTAATATTATTAAAAGCTT
11170829 TTAATATTATTAAAAGCTT
1 TTAATATTATTAAAAGCTT
11170848 TTAAT-TT-TTAAAA
1 TTAATATTATTAAAA
11170861 ATTGTTAGTC
Statistics
Matches: 31, Mismatches: 0, Indels: 3
0.91 0.00 0.09
Matches are distributed among these distances:
17 6 0.19
18 6 0.19
19 19 0.61
ACGTcount: A:0.44, C:0.04, G:0.04, T:0.48
Consensus pattern (19 bp):
TTAATATTATTAAAAGCTT
Found at i:11171662 original size:16 final size:16
Alignment explanation
Indices: 11171641--11171672 Score: 64
Period size: 16 Copynumber: 2.0 Consensus size: 16
11171631 GCAATTGATT
11171641 CGAAATAAACTCGAAC
1 CGAAATAAACTCGAAC
11171657 CGAAATAAACTCGAAC
1 CGAAATAAACTCGAAC
11171673 AATATTTTCG
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 16 1.00
ACGTcount: A:0.50, C:0.25, G:0.12, T:0.12
Consensus pattern (16 bp):
CGAAATAAACTCGAAC
Found at i:11177094 original size:24 final size:23
Alignment explanation
Indices: 11177049--11177094 Score: 58
Period size: 24 Copynumber: 2.0 Consensus size: 23
11177039 ATGTGATATA
*
11177049 GCTTCTATGGATGCTTGCCATTT
1 GCTTCTATGGATGCTTGACATTT
11177072 GCTTCT-TGGATGACCTTGACATT
1 GCTTCTATGGATG--CTTGACATT
11177095 ATGATAGAAT
Statistics
Matches: 20, Mismatches: 1, Indels: 3
0.83 0.04 0.12
Matches are distributed among these distances:
22 6 0.30
23 6 0.30
24 8 0.40
ACGTcount: A:0.15, C:0.22, G:0.22, T:0.41
Consensus pattern (23 bp):
GCTTCTATGGATGCTTGACATTT
Found at i:11177617 original size:9 final size:9
Alignment explanation
Indices: 11177603--11177639 Score: 56
Period size: 9 Copynumber: 4.0 Consensus size: 9
11177593 ACTCTATCAA
11177603 TTTTATTAT
1 TTTTATTAT
11177612 TTTTATTTAT
1 TTTTA-TTAT
*
11177622 TTTTTTTAT
1 TTTTATTAT
11177631 TTTTATTAT
1 TTTTATTAT
11177640 CATATATATA
Statistics
Matches: 25, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
9 17 0.68
10 8 0.32
ACGTcount: A:0.19, C:0.00, G:0.00, T:0.81
Consensus pattern (9 bp):
TTTTATTAT
Found at i:11177622 original size:13 final size:13
Alignment explanation
Indices: 11177604--11177637 Score: 52
Period size: 13 Copynumber: 2.7 Consensus size: 13
11177594 CTCTATCAAT
11177604 TTTATTATTTTTA
1 TTTATTATTTTTA
*
11177617 TTTATTTTTTTTA
1 TTTATTATTTTTA
11177630 TTT-TTATT
1 TTTATTATT
11177638 ATCATATATA
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
12 4 0.21
13 15 0.79
ACGTcount: A:0.18, C:0.00, G:0.00, T:0.82
Consensus pattern (13 bp):
TTTATTATTTTTA
Found at i:11179042 original size:13 final size:13
Alignment explanation
Indices: 11179026--11179070 Score: 63
Period size: 13 Copynumber: 3.4 Consensus size: 13
11179016 AAATATTTTT
11179026 AAAATAAAAATAA
1 AAAATAAAAATAA
11179039 AAAATAAAAATAA
1 AAAATAAAAATAA
* *
11179052 ACAATGAAAAATGA
1 AAAAT-AAAAATAA
11179066 AAAAT
1 AAAAT
11179071 TTTGTTTTTT
Statistics
Matches: 28, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
13 17 0.61
14 11 0.39
ACGTcount: A:0.78, C:0.02, G:0.04, T:0.16
Consensus pattern (13 bp):
AAAATAAAAATAA
Found at i:11179043 original size:7 final size:6
Alignment explanation
Indices: 11179026--11179070 Score: 54
Period size: 7 Copynumber: 6.8 Consensus size: 6
11179016 AAATATTTTT
11179026 AAAATA AAAATAA AAAATA AAAATA AACAATGA AAAATGA AAAAT
1 AAAATA AAAAT-A AAAATA AAAATA AA-AAT-A AAAAT-A AAAAT
11179071 TTTGTTTTTT
Statistics
Matches: 36, Mismatches: 0, Indels: 5
0.88 0.00 0.12
Matches are distributed among these distances:
6 14 0.39
7 19 0.53
8 3 0.08
ACGTcount: A:0.78, C:0.02, G:0.04, T:0.16
Consensus pattern (6 bp):
AAAATA
Found at i:11179314 original size:53 final size:52
Alignment explanation
Indices: 11179220--11179329 Score: 127
Period size: 53 Copynumber: 2.1 Consensus size: 52
11179210 AAAAATGTAT
* *
11179220 TAAAATTTGAAAATGTTAGGAAAAAGTAGAAATATCAAATTTTCCTT-AAAA
1 TAAAATTTGAAAATATTAGCAAAAAGTAGAAATATCAAATTTTCCTTGAAAA
* *
11179271 TAAAATTTTGAAAATATTCAGCAAAAAGTTA-AAATTTTC-AATTTTTCTTGAAAA
1 TAAAA-TTTGAAAATATT-AGCAAAAAG-TAGAAA-TATCAAATTTTCCTTGAAAA
11179325 TAAAA
1 TAAAA
11179330 ATTATTATTT
Statistics
Matches: 50, Mismatches: 4, Indels: 7
0.82 0.07 0.11
Matches are distributed among these distances:
51 5 0.10
52 11 0.22
53 20 0.40
54 14 0.28
ACGTcount: A:0.50, C:0.06, G:0.09, T:0.35
Consensus pattern (52 bp):
TAAAATTTGAAAATATTAGCAAAAAGTAGAAATATCAAATTTTCCTTGAAAA
Found at i:11187285 original size:14 final size:14
Alignment explanation
Indices: 11187268--11187317 Score: 55
Period size: 14 Copynumber: 3.4 Consensus size: 14
11187258 ATGAAAACCA
11187268 AAAAAGGAAAAAAG
1 AAAAAGGAAAAAAG
11187282 AAAAAGGAAAAAAAAAG
1 AAAAAGG---AAAAAAG
* *
11187299 AGAAAGGAAAGAAG
1 AAAAAGGAAAAAAG
11187313 AAAAA
1 AAAAA
11187318 AAAGAAAAAA
Statistics
Matches: 30, Mismatches: 3, Indels: 6
0.77 0.08 0.15
Matches are distributed among these distances:
14 17 0.57
17 13 0.43
ACGTcount: A:0.78, C:0.00, G:0.22, T:0.00
Consensus pattern (14 bp):
AAAAAGGAAAAAAG
Found at i:11187297 original size:17 final size:17
Alignment explanation
Indices: 11187275--11187328 Score: 67
Period size: 17 Copynumber: 3.2 Consensus size: 17
11187265 CCAAAAAAGG
11187275 AAAAAAGAAAAAGGAAA
1 AAAAAAGAAAAAGGAAA
*
11187292 AAAAAAGAGAAAGGAAA
1 AAAAAAGAAAAAGGAAA
*
11187309 GAAGAAA-AAAAA-GAAA
1 -AAAAAAGAAAAAGGAAA
11187325 AAAA
1 AAAA
11187329 TGATAATAAA
Statistics
Matches: 32, Mismatches: 4, Indels: 4
0.80 0.10 0.10
Matches are distributed among these distances:
15 3 0.09
16 4 0.12
17 20 0.62
18 5 0.16
ACGTcount: A:0.81, C:0.00, G:0.19, T:0.00
Consensus pattern (17 bp):
AAAAAAGAAAAAGGAAA
Found at i:11187308 original size:24 final size:24
Alignment explanation
Indices: 11187267--11187327 Score: 72
Period size: 24 Copynumber: 2.6 Consensus size: 24
11187257 CATGAAAACC
*
11187267 AAAAAAGGAAAAAAGAAA-AAGGAA
1 AAAAAAAGAAAAAAGAAAGAA-GAA
* *
11187291 AAAAAAAGAGAAAGGAAAGAAG-A
1 AAAAAAAGAAAAAAGAAAGAAGAA
11187314 AAAAAAAGAAAAAA
1 AAAAAAAGAAAAAA
11187328 ATGATAATAA
Statistics
Matches: 31, Mismatches: 5, Indels: 3
0.79 0.13 0.08
Matches are distributed among these distances:
23 13 0.42
24 16 0.52
25 2 0.06
ACGTcount: A:0.80, C:0.00, G:0.20, T:0.00
Consensus pattern (24 bp):
AAAAAAAGAAAAAAGAAAGAAGAA
Found at i:11187326 original size:31 final size:31
Alignment explanation
Indices: 11187270--11187328 Score: 84
Period size: 31 Copynumber: 1.9 Consensus size: 31
11187260 GAAAACCAAA
*
11187270 AAAGGAAAAAAGAAAAAGGAAAAAAAAAGAG
1 AAAGGAAAAAAGAAAAAGAAAAAAAAAAGAG
*
11187301 AAAGGAAAGAAGAAAAA-AAAGAAAAAAA
1 AAAGGAAAAAAGAAAAAGAAA-AAAAAAA
11187329 TGATAATAAA
Statistics
Matches: 25, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
30 2 0.08
31 23 0.92
ACGTcount: A:0.80, C:0.00, G:0.20, T:0.00
Consensus pattern (31 bp):
AAAGGAAAAAAGAAAAAGAAAAAAAAAAGAG
Found at i:11187358 original size:15 final size:16
Alignment explanation
Indices: 11187318--11187365 Score: 53
Period size: 15 Copynumber: 2.9 Consensus size: 16
11187308 AGAAGAAAAA
*
11187318 AAAGAAAAAAATGATAAT
1 AAAGATAAAAAT-A-AAT
*
11187336 AAAGATAATAATAAAT
1 AAAGATAAAAATAAAT
11187352 AAA-ATAAAAATAAA
1 AAAGATAAAAATAAA
11187366 AATAAATAAA
Statistics
Matches: 27, Mismatches: 3, Indels: 3
0.82 0.09 0.09
Matches are distributed among these distances:
15 10 0.37
16 6 0.22
17 1 0.04
18 10 0.37
ACGTcount: A:0.75, C:0.00, G:0.06, T:0.19
Consensus pattern (16 bp):
AAAGATAAAAATAAAT
Found at i:11187358 original size:21 final size:21
Alignment explanation
Indices: 11187333--11187376 Score: 70
Period size: 21 Copynumber: 2.1 Consensus size: 21
11187323 AAAAAATGAT
* *
11187333 AATAAAGATAATAATAAATAA
1 AATAAAAATAAAAATAAATAA
11187354 AATAAAAATAAAAATAAATAA
1 AATAAAAATAAAAATAAATAA
11187375 AA
1 AA
11187377 GTTTAAGAGT
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
21 21 1.00
ACGTcount: A:0.77, C:0.00, G:0.02, T:0.20
Consensus pattern (21 bp):
AATAAAAATAAAAATAAATAA
Found at i:11192258 original size:17 final size:17
Alignment explanation
Indices: 11192225--11192257 Score: 59
Period size: 17 Copynumber: 2.0 Consensus size: 17
11192215 GATACTTCGC
11192225 TTAAAAAAAAGAGAAAA
1 TTAAAAAAAAGAGAAAA
11192242 TTAAAAAAAAG-GAAAA
1 TTAAAAAAAAGAGAAAA
11192258 AAAAGCATCT
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
16 5 0.31
17 11 0.69
ACGTcount: A:0.76, C:0.00, G:0.12, T:0.12
Consensus pattern (17 bp):
TTAAAAAAAAGAGAAAA
Found at i:11195221 original size:9 final size:9
Alignment explanation
Indices: 11195207--11195245 Score: 51
Period size: 9 Copynumber: 4.3 Consensus size: 9
11195197 ATAGTAATAG
11195207 TAACAACAA
1 TAACAACAA
11195216 TAACAACAA
1 TAACAACAA
*
11195225 CAACAACAA
1 TAACAACAA
* *
11195234 CAACAATAA
1 TAACAACAA
11195243 TAA
1 TAA
11195246 TAATAATAAT
Statistics
Matches: 27, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
9 27 1.00
ACGTcount: A:0.67, C:0.23, G:0.00, T:0.10
Consensus pattern (9 bp):
TAACAACAA
Found at i:11195223 original size:3 final size:3
Alignment explanation
Indices: 11195208--11195239 Score: 55
Period size: 3 Copynumber: 10.7 Consensus size: 3
11195198 TAGTAATAGT
*
11195208 AAC AAC AAT AAC AAC AAC AAC AAC AAC AAC AA
1 AAC AAC AAC AAC AAC AAC AAC AAC AAC AAC AA
11195240 TAATAATAAT
Statistics
Matches: 27, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
3 27 1.00
ACGTcount: A:0.69, C:0.28, G:0.00, T:0.03
Consensus pattern (3 bp):
AAC
Found at i:11200102 original size:39 final size:38
Alignment explanation
Indices: 11200059--11200199 Score: 117
Period size: 40 Copynumber: 3.6 Consensus size: 38
11200049 AATTTTTTGT
* *
11200059 AAATTTTAGAATGTTTTAGAATCTTGAAAATTTTTTCAT
1 AAATTTTAGAAT-TTTTAGAATTTTGAAAATTTTTTCAA
* * *
11200098 AAATTTAAAGAAATTTTCAGAATTTTTTAAAA-TTTTTCAA
1 AAATTT-TAG-AATTTTTAGAA-TTTTGAAAATTTTTTCAA
* ** *
11200138 AAAGTGTTAGAATTTTTTTAATTTTGAAAATTTTTTAAAA
1 AAA-TTTTAGAATTTTTAGAATTTTGAAAATTTTTT-CAA
*
11200178 AAATTTTAG-A-TTTTAGATTTTT
1 AAATTTTAGAATTTTTAGAATTTT
11200200 TGGTTTTGTT
Statistics
Matches: 80, Mismatches: 16, Indels: 14
0.73 0.15 0.13
Matches are distributed among these distances:
37 9 0.11
38 9 0.11
39 24 0.30
40 26 0.32
41 12 0.15
ACGTcount: A:0.39, C:0.03, G:0.09, T:0.50
Consensus pattern (38 bp):
AAATTTTAGAATTTTTAGAATTTTGAAAATTTTTTCAA
Found at i:11200345 original size:9 final size:9
Alignment explanation
Indices: 11200333--11200380 Score: 69
Period size: 9 Copynumber: 5.1 Consensus size: 9
11200323 ATTTTTTTAT
11200333 TTTTTAAAA
1 TTTTTAAAA
*
11200342 TTTTCAAAA
1 TTTTTAAAA
11200351 TTTTTAAAAAA
1 TTTTT--AAAA
11200362 TTTTTAAAA
1 TTTTTAAAA
11200371 TTTTTAAAA
1 TTTTTAAAA
11200380 T
1 T
11200381 ATTTCATATT
Statistics
Matches: 35, Mismatches: 2, Indels: 4
0.85 0.05 0.10
Matches are distributed among these distances:
9 26 0.74
11 9 0.26
ACGTcount: A:0.46, C:0.02, G:0.00, T:0.52
Consensus pattern (9 bp):
TTTTTAAAA
Found at i:11200361 original size:20 final size:20
Alignment explanation
Indices: 11200338--11200384 Score: 76
Period size: 20 Copynumber: 2.4 Consensus size: 20
11200328 TTTATTTTTT
11200338 AAAATTTTCAAAATTTTTAA
1 AAAATTTTCAAAATTTTTAA
*
11200358 AAAATTTTTAAAATTTTTAA
1 AAAATTTTCAAAATTTTTAA
*
11200378 AATATTT
1 AAAATTT
11200385 CATATTTTTT
Statistics
Matches: 25, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
20 25 1.00
ACGTcount: A:0.49, C:0.02, G:0.00, T:0.49
Consensus pattern (20 bp):
AAAATTTTCAAAATTTTTAA
Found at i:11200363 original size:11 final size:11
Alignment explanation
Indices: 11200347--11200384 Score: 53
Period size: 11 Copynumber: 3.6 Consensus size: 11
11200337 TAAAATTTTC
11200347 AAAATTTTTAA
1 AAAATTTTTAA
11200358 AAAATTTTT--
1 AAAATTTTTAA
11200367 AAAATTTTTAA
1 AAAATTTTTAA
*
11200378 AATATTT
1 AAAATTT
11200385 CATATTTTTT
Statistics
Matches: 24, Mismatches: 1, Indels: 4
0.83 0.03 0.14
Matches are distributed among these distances:
9 9 0.38
11 15 0.62
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (11 bp):
AAAATTTTTAA
Found at i:11203144 original size:6 final size:6
Alignment explanation
Indices: 11203135--11203184 Score: 61
Period size: 6 Copynumber: 8.8 Consensus size: 6
11203125 TATATCTTGA
* *
11203135 TTTTGT TTTTGT TTTTG- TTTTG- TTTTG- TTTTGT TTTTTT TTTTTT
1 TTTTGT TTTTGT TTTTGT TTTTGT TTTTGT TTTTGT TTTTGT TTTTGT
11203180 TTTTG
1 TTTTG
11203185 AGACTTTGTT
Statistics
Matches: 41, Mismatches: 2, Indels: 2
0.91 0.04 0.04
Matches are distributed among these distances:
5 15 0.37
6 26 0.63
ACGTcount: A:0.00, C:0.00, G:0.14, T:0.86
Consensus pattern (6 bp):
TTTTGT
Found at i:11203149 original size:5 final size:5
Alignment explanation
Indices: 11203135--11203184 Score: 59
Period size: 5 Copynumber: 10.0 Consensus size: 5
11203125 TATATCTTGA
*
11203135 TTTTG TTTTTG TTTTTG TTTTG TTTTG TTTTG TTTT- TTTT- TTTTT TTTTG
1 TTTTG -TTTTG -TTTTG TTTTG TTTTG TTTTG TTTTG TTTTG TTTTG TTTTG
11203185 AGACTTTGTT
Statistics
Matches: 42, Mismatches: 1, Indels: 3
0.91 0.02 0.07
Matches are distributed among these distances:
4 8 0.19
5 23 0.55
6 11 0.26
ACGTcount: A:0.00, C:0.00, G:0.14, T:0.86
Consensus pattern (5 bp):
TTTTG
Found at i:11204340 original size:13 final size:12
Alignment explanation
Indices: 11204305--11204343 Score: 51
Period size: 12 Copynumber: 3.2 Consensus size: 12
11204295 TAAATATAAC
*
11204305 AAAAAATATCTT
1 AAAAAATATATT
11204317 AAAAAATATATT
1 AAAAAATATATT
*
11204329 AAAATATAATATT
1 AAAAAAT-ATATT
11204342 AA
1 AA
11204344 TTGACCATCT
Statistics
Matches: 24, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
12 17 0.71
13 7 0.29
ACGTcount: A:0.64, C:0.03, G:0.00, T:0.33
Consensus pattern (12 bp):
AAAAAATATATT
Found at i:11205744 original size:14 final size:14
Alignment explanation
Indices: 11205727--11205753 Score: 54
Period size: 14 Copynumber: 1.9 Consensus size: 14
11205717 GTGTATTTAT
11205727 TGAGATTTATTTTG
1 TGAGATTTATTTTG
11205741 TGAGATTTATTTT
1 TGAGATTTATTTT
11205754 ATTTTTTAAT
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:0.22, C:0.00, G:0.19, T:0.59
Consensus pattern (14 bp):
TGAGATTTATTTTG
Found at i:11208744 original size:10 final size:10
Alignment explanation
Indices: 11208729--11208775 Score: 51
Period size: 10 Copynumber: 4.5 Consensus size: 10
11208719 ACTGTATGTG
11208729 AATTTTATTT
1 AATTTTATTT
11208739 AATTTTATGTT
1 AATTTTAT-TT
11208750 AGA-TTTATTT
1 A-ATTTTATTT
*
11208760 AATTATATTCT
1 AATTTTATT-T
11208771 AATTT
1 AATTT
11208776 GTTAGTTATA
Statistics
Matches: 31, Mismatches: 2, Indels: 7
0.77 0.05 0.17
Matches are distributed among these distances:
9 1 0.03
10 16 0.52
11 13 0.42
12 1 0.03
ACGTcount: A:0.32, C:0.02, G:0.04, T:0.62
Consensus pattern (10 bp):
AATTTTATTT
Found at i:11208747 original size:21 final size:21
Alignment explanation
Indices: 11208723--11208763 Score: 57
Period size: 21 Copynumber: 2.0 Consensus size: 21
11208713 AAGTTTACTG
11208723 TATGTGA-ATTTTATTTAATTT
1 TATGTGAGA-TTTATTTAATTT
*
11208744 TATGTTAGATTTATTTAATT
1 TATGTGAGATTTATTTAATT
11208764 ATATTCTAAT
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
21 17 0.94
22 1 0.06
ACGTcount: A:0.29, C:0.00, G:0.10, T:0.61
Consensus pattern (21 bp):
TATGTGAGATTTATTTAATTT
Found at i:11210805 original size:30 final size:31
Alignment explanation
Indices: 11210753--11210812 Score: 104
Period size: 30 Copynumber: 2.0 Consensus size: 31
11210743 GTTATCTTAT
11210753 CATAGATACGTAGTATTTTTTATGCTGATGG
1 CATAGATACGTAGTATTTTTTATGCTGATGG
*
11210784 CATAGATACGTTGTA-TTTTTATGCTGATG
1 CATAGATACGTAGTATTTTTTATGCTGATG
11210813 TGATATGCTG
Statistics
Matches: 28, Mismatches: 1, Indels: 1
0.93 0.03 0.03
Matches are distributed among these distances:
30 14 0.50
31 14 0.50
ACGTcount: A:0.25, C:0.10, G:0.22, T:0.43
Consensus pattern (31 bp):
CATAGATACGTAGTATTTTTTATGCTGATGG
Found at i:11211487 original size:15 final size:16
Alignment explanation
Indices: 11211462--11211502 Score: 57
Period size: 16 Copynumber: 2.6 Consensus size: 16
11211452 ATTAATTTAT
11211462 ATAATTATTTT-TAAAG
1 ATAA-TATTTTATAAAG
*
11211478 ATAATATTTTATAAAT
1 ATAATATTTTATAAAG
11211494 ATAATATTT
1 ATAATATTT
11211503 AAATCTCAAT
Statistics
Matches: 23, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
15 6 0.26
16 17 0.74
ACGTcount: A:0.46, C:0.00, G:0.02, T:0.51
Consensus pattern (16 bp):
ATAATATTTTATAAAG
Found at i:11212025 original size:19 final size:19
Alignment explanation
Indices: 11212001--11212039 Score: 62
Period size: 19 Copynumber: 2.1 Consensus size: 19
11211991 CTTCATGAAC
11212001 AAAGACTTAT-ATATAAGCA
1 AAAGACTTATAAT-TAAGCA
11212020 AAAGACTTATAATTAAGCA
1 AAAGACTTATAATTAAGCA
11212039 A
1 A
11212040 CACCACAATA
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
19 17 0.89
20 2 0.11
ACGTcount: A:0.54, C:0.10, G:0.10, T:0.26
Consensus pattern (19 bp):
AAAGACTTATAATTAAGCA
Found at i:11213095 original size:41 final size:41
Alignment explanation
Indices: 11213038--11213140 Score: 179
Period size: 41 Copynumber: 2.5 Consensus size: 41
11213028 ATACGTTTTT
*
11213038 ATGCTGATCTCATAGATACGTTGTATTCTTATGCTGATCCC
1 ATGCTGATCTCATAGATACGTTGTATTCTTATGCCGATCCC
* *
11213079 ATGCTGATCTCATAGATACGTTTTATTCTTATGCCGATCTC
1 ATGCTGATCTCATAGATACGTTGTATTCTTATGCCGATCCC
11213120 ATGCTGATCTCATAGATACGT
1 ATGCTGATCTCATAGATACGT
11213141 ACATTGCCTA
Statistics
Matches: 59, Mismatches: 3, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
41 59 1.00
ACGTcount: A:0.23, C:0.21, G:0.17, T:0.39
Consensus pattern (41 bp):
ATGCTGATCTCATAGATACGTTGTATTCTTATGCCGATCCC
Found at i:11214139 original size:12 final size:13
Alignment explanation
Indices: 11214111--11214147 Score: 51
Period size: 12 Copynumber: 3.0 Consensus size: 13
11214101 CACAATTATT
11214111 TTTA-TTATTTGA
1 TTTATTTATTTGA
*
11214123 CTTATTTATTT-A
1 TTTATTTATTTGA
11214135 TTTATTTATTTGA
1 TTTATTTATTTGA
11214148 AGTCCATATA
Statistics
Matches: 21, Mismatches: 2, Indels: 3
0.81 0.08 0.12
Matches are distributed among these distances:
12 14 0.67
13 7 0.33
ACGTcount: A:0.24, C:0.03, G:0.05, T:0.68
Consensus pattern (13 bp):
TTTATTTATTTGA
Found at i:11214573 original size:8 final size:9
Alignment explanation
Indices: 11214555--11214590 Score: 63
Period size: 9 Copynumber: 4.0 Consensus size: 9
11214545 GGAAAGAATA
11214555 TTAATTTTT
1 TTAATTTTT
11214564 TTAATTTTT
1 TTAATTTTT
11214573 TTAATTTTT
1 TTAATTTTT
*
11214582 TCAATTTTT
1 TTAATTTTT
11214591 GAGTGTTAAT
Statistics
Matches: 26, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
9 26 1.00
ACGTcount: A:0.22, C:0.03, G:0.00, T:0.75
Consensus pattern (9 bp):
TTAATTTTT
Found at i:11216840 original size:30 final size:30
Alignment explanation
Indices: 11216804--11216875 Score: 117
Period size: 30 Copynumber: 2.4 Consensus size: 30
11216794 AGTTAGCGTA
*
11216804 TCATAGATACGTTGTATTTTTATGCCGATC
1 TCATAGATACGTTGTATTCTTATGCCGATC
*
11216834 TCATAGATACGTTGTATTCTTATGCTGATC
1 TCATAGATACGTTGTATTCTTATGCCGATC
*
11216864 TCATAAATACGT
1 TCATAGATACGT
11216876 ACATTGCCCA
Statistics
Matches: 39, Mismatches: 3, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
30 39 1.00
ACGTcount: A:0.26, C:0.17, G:0.15, T:0.42
Consensus pattern (30 bp):
TCATAGATACGTTGTATTCTTATGCCGATC
Found at i:11219321 original size:53 final size:54
Alignment explanation
Indices: 11219220--11219326 Score: 198
Period size: 53 Copynumber: 2.0 Consensus size: 54
11219210 ATCTAAGTGG
11219220 TAATCATAAGTCTTCTCAAATTTTTTTTTATTACTGATTCTAAATGAATATATT
1 TAATCATAAGTCTTCTCAAATTTTTTTTTATTACTGATTCTAAATGAATATATT
*
11219274 TAATCATAAGTCTTCTCAAA-TTTTTTTTATTATTGATTCTAAATGAATATATT
1 TAATCATAAGTCTTCTCAAATTTTTTTTTATTACTGATTCTAAATGAATATATT
11219327 ATTTTAAAAT
Statistics
Matches: 52, Mismatches: 1, Indels: 1
0.96 0.02 0.02
Matches are distributed among these distances:
53 32 0.62
54 20 0.38
ACGTcount: A:0.34, C:0.10, G:0.06, T:0.50
Consensus pattern (54 bp):
TAATCATAAGTCTTCTCAAATTTTTTTTTATTACTGATTCTAAATGAATATATT
Found at i:11225526 original size:20 final size:21
Alignment explanation
Indices: 11225488--11225527 Score: 55
Period size: 21 Copynumber: 2.0 Consensus size: 21
11225478 TTTCTTTCTT
**
11225488 TTTTTTTTTACTTTTTTTCCC
1 TTTTTTTTTACTTGGTTTCCC
11225509 TTTTTTTTT-CTTGGTTTCC
1 TTTTTTTTTACTTGGTTTCC
11225528 AACACCACAT
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
20 8 0.47
21 9 0.53
ACGTcount: A:0.03, C:0.17, G:0.05, T:0.75
Consensus pattern (21 bp):
TTTTTTTTTACTTGGTTTCCC
Found at i:11226306 original size:18 final size:18
Alignment explanation
Indices: 11226285--11226382 Score: 60
Period size: 19 Copynumber: 5.3 Consensus size: 18
11226275 AAAAAATCCA
11226285 AAAAAATTTC-AAAAAAT
1 AAAAAATTTCAAAAAAAT
* *
11226302 TAAAAATTTTAAAAAAAT
1 AAAAAATTTCAAAAAAAT
*
11226320 --AAAATTTTAATAAAAAT
1 AAAAAATTTCAA-AAAAAT
** *
11226337 AAAATTTTTTAAAATTAAAT
1 AAAAAATTTCAAAA--AAAT
11226357 -AAAAATATTCACAAAAAATT
1 AAAAAAT-TTCA-AAAAAA-T
11226377 AAAAAA
1 AAAAAA
11226383 GTTGAATATA
Statistics
Matches: 64, Mismatches: 7, Indels: 16
0.74 0.08 0.18
Matches are distributed among these distances:
16 10 0.16
17 14 0.22
18 9 0.14
19 15 0.23
20 8 0.12
21 8 0.12
ACGTcount: A:0.66, C:0.03, G:0.00, T:0.31
Consensus pattern (18 bp):
AAAAAATTTCAAAAAAAT
Found at i:11226308 original size:17 final size:17
Alignment explanation
Indices: 11226286--11226381 Score: 86
Period size: 17 Copynumber: 5.3 Consensus size: 17
11226276 AAAAATCCAA
* *
11226286 AAAAATTTCAAAAAATT
1 AAAAATTTTAAAAAAAT
11226303 AAAAATTTTAAAAAAAT
1 AAAAATTTTAAAAAAAT
11226320 -AAAATTTTAATAAAAAT
1 AAAAATTTTAA-AAAAAT
*
11226337 AAAATTTTTTAAAATTAAAT
1 AAAA-ATTTTAAAA--AAAT
*
11226357 AAAAATATTCACAAAAAATT
1 AAAAAT-TTTA-AAAAAA-T
11226377 AAAAA
1 AAAAA
11226382 AGTTGAATAT
Statistics
Matches: 66, Mismatches: 5, Indels: 13
0.79 0.06 0.15
Matches are distributed among these distances:
16 10 0.15
17 21 0.32
18 5 0.08
19 10 0.15
20 17 0.26
21 3 0.05
ACGTcount: A:0.66, C:0.03, G:0.00, T:0.31
Consensus pattern (17 bp):
AAAAATTTTAAAAAAAT
Found at i:11226315 original size:16 final size:16
Alignment explanation
Indices: 11226286--11226355 Score: 52
Period size: 16 Copynumber: 4.2 Consensus size: 16
11226276 AAAAATCCAA
*
11226286 AAAAATTTCAAAAAATT
1 AAAAATTT-TAAAAATT
*
11226303 AAAAATTTTAAAAA-A
1 AAAAATTTTAAAAATT
*
11226318 ATAAAATTTTAATAAAAAT
1 A-AAAATTTT-A-AAAATT
* *
11226337 AAAATTTTTTAAAATT
1 AAAAATTTTAAAAATT
11226353 AAA
1 AAA
11226356 TAAAAATATT
Statistics
Matches: 43, Mismatches: 6, Indels: 9
0.74 0.10 0.16
Matches are distributed among these distances:
15 1 0.02
16 21 0.49
17 9 0.21
18 11 0.26
19 1 0.02
ACGTcount: A:0.64, C:0.01, G:0.00, T:0.34
Consensus pattern (16 bp):
AAAAATTTTAAAAATT
Found at i:11226446 original size:20 final size:19
Alignment explanation
Indices: 11226295--11226443 Score: 76
Period size: 19 Copynumber: 7.7 Consensus size: 19
11226285 AAAAAATTTC
11226295 AAAAAATTAAAAATTTT-A
1 AAAAAATTAAAAATTTTAA
11226313 AAAAAA-T-AAAATTTTAA
1 AAAAAATTAAAAATTTTAA
* *
11226330 TAAAAA-TAAAATTTTTTAA
1 AAAAAATTAAAA-ATTTTAA
* * *
11226349 AATTAAA-TAAAAATATTCAC
1 AA-AAAATTAAAAAT-TTTAA
* *
11226369 AAAAAATTAAAAAAGTTGAATAT
1 AAAAAATT-AAAAA-TT--TTAA
* **
11226392 AAAAAATCTAAAATTTTTTG
1 AAAAAAT-TAAAAATTTTAA
*
11226412 AAACAATCT-AAAATTTTAA
1 AAAAAAT-TAAAAATTTTAA
11226431 AAAAAATTAAAAA
1 AAAAAATTAAAAA
11226444 ATTAAAATTT
Statistics
Matches: 99, Mismatches: 20, Indels: 23
0.70 0.14 0.16
Matches are distributed among these distances:
16 8 0.08
17 8 0.08
18 10 0.10
19 28 0.28
20 23 0.23
21 6 0.06
22 3 0.03
23 12 0.12
24 1 0.01
ACGTcount: A:0.63, C:0.03, G:0.02, T:0.32
Consensus pattern (19 bp):
AAAAAATTAAAAATTTTAA
Found at i:11226631 original size:18 final size:19
Alignment explanation
Indices: 11226585--11226631 Score: 53
Period size: 19 Copynumber: 2.5 Consensus size: 19
11226575 AATTTTTTTA
11226585 TTTAGTTTTTTAAAAATGT
1 TTTAGTTTTTTAAAAATGT
* *
11226604 TTTA-TATTTTTTAAACT-T
1 TTTAGT-TTTTTAAAAATGT
11226622 TTTAGTTTTT
1 TTTAGTTTTT
11226632 AGAAAATTTA
Statistics
Matches: 24, Mismatches: 2, Indels: 5
0.77 0.06 0.16
Matches are distributed among these distances:
18 10 0.42
19 14 0.58
ACGTcount: A:0.26, C:0.02, G:0.06, T:0.66
Consensus pattern (19 bp):
TTTAGTTTTTTAAAAATGT
Found at i:11226891 original size:17 final size:17
Alignment explanation
Indices: 11226841--11226891 Score: 61
Period size: 18 Copynumber: 3.0 Consensus size: 17
11226831 TTTTTAGATT
11226841 TTTTTAT-ATTTT-AAA
1 TTTTTATAATTTTAAAA
*
11226856 TCTTTCATAATTTTTAAAA
1 T-TTTTATAA-TTTTAAAA
11226875 TTTTTATAATTTTAAAA
1 TTTTTATAATTTTAAAA
11226892 AATATTTTAT
Statistics
Matches: 30, Mismatches: 2, Indels: 6
0.79 0.05 0.16
Matches are distributed among these distances:
15 1 0.03
16 5 0.17
17 9 0.30
18 11 0.37
19 4 0.13
ACGTcount: A:0.37, C:0.04, G:0.00, T:0.59
Consensus pattern (17 bp):
TTTTTATAATTTTAAAA
Found at i:11226892 original size:18 final size:18
Alignment explanation
Indices: 11226842--11226907 Score: 57
Period size: 19 Copynumber: 3.7 Consensus size: 18
11226832 TTTTAGATTT
*
11226842 TTTTATATTTT--AAATC
1 TTTTATATTTTAAAAATA
* *
11226858 TTTCATAATTTTTAAAAT-
1 TTTTAT-ATTTTAAAAATA
11226876 TTTTATAATTTTAAAAAATA
1 TTTTAT-ATTTT-AAAAATA
11226896 TTTTATATTTTA
1 TTTTATATTTTA
11226908 TATTTTGTCA
Statistics
Matches: 42, Mismatches: 3, Indels: 8
0.79 0.06 0.15
Matches are distributed among these distances:
16 5 0.12
17 5 0.12
18 12 0.29
19 14 0.33
20 6 0.14
ACGTcount: A:0.38, C:0.03, G:0.00, T:0.59
Consensus pattern (18 bp):
TTTTATATTTTAAAAATA
Found at i:11226893 original size:19 final size:20
Alignment explanation
Indices: 11226862--11226907 Score: 62
Period size: 19 Copynumber: 2.5 Consensus size: 20
11226852 TAAATCTTTC
*
11226862 ATAATTTT-TAAAAT-TTTT
1 ATAATTTTAAAAAATATTTT
11226880 ATAATTTTAAAAAATATTTT
1 ATAATTTTAAAAAATATTTT
11226900 AT-ATTTTA
1 ATAATTTTA
11226908 TATTTTGTCA
Statistics
Matches: 25, Mismatches: 1, Indels: 3
0.86 0.03 0.10
Matches are distributed among these distances:
18 8 0.32
19 11 0.44
20 6 0.24
ACGTcount: A:0.43, C:0.00, G:0.00, T:0.57
Consensus pattern (20 bp):
ATAATTTTAAAAAATATTTT
Found at i:11226952 original size:45 final size:44
Alignment explanation
Indices: 11226873--11226958 Score: 120
Period size: 45 Copynumber: 1.9 Consensus size: 44
11226863 TAATTTTTAA
*
11226873 AATTTTTATAATTTTAAAAAATATTTTATATTTTATATTTTGTC
1 AATTTTTATAATTTTAAAAAATATTTAATATTTTATATTTTGTC
* *
11226917 AATTTATTATAATTTTTAAAAATATTTAACT-TTTTATTTTTT
1 AATTT-TTATAATTTTAAAAAATATTTAA-TATTTTATATTTT
11226959 AAAAATATTT
Statistics
Matches: 37, Mismatches: 3, Indels: 3
0.86 0.07 0.07
Matches are distributed among these distances:
44 5 0.14
45 31 0.84
46 1 0.03
ACGTcount: A:0.36, C:0.02, G:0.01, T:0.60
Consensus pattern (44 bp):
AATTTTTATAATTTTAAAAAATATTTAATATTTTATATTTTGTC
Found at i:11229414 original size:80 final size:83
Alignment explanation
Indices: 11229251--11229507 Score: 376
Period size: 80 Copynumber: 3.0 Consensus size: 83
11229241 AAAACATATA
11229251 TTTTCATAAGGATACCTTTGCCTAGTTCATGAAATTGCGCTGAATTTAAACATTGAAAGCTGTCA
1 TTTTCATAAGGATACCTTTGCC----TCATGAAATTGCGCTGAATTT-AACATTGAAAGCTGTCA
*
11229316 GTTCAGTGTACCGGAGACGGCTT
61 GTTCACTGTACCGGAGACGGCTT
11229339 TTTTCATAAGGATACCTTTG-C-C-TGAAATTGCGCTGAATTTAACATTGAAAGCTGTCAGTTCA
1 TTTTCATAAGGATACCTTTGCCTCATGAAATTGCGCTGAATTTAACATTGAAAGCTGTCAGTTCA
11229401 CTGTACCGGAGACGGCTT
66 CTGTACCGGAGACGGCTT
* * *
11229419 TTTTCATAAGGATACCTTTGCCTAGTTCATGAAATTGTGCTGAATTTAACATTTAGAGCTGTCAG
1 TTTTCATAAGGATACCTTTGCC----TCATGAAATTGCGCTGAATTTAACATTGAAAGCTGTCAG
11229484 TTCACTGTACCGGAGACGGCTT
62 TTCACTGTACCGGAGACGGCTT
11229506 TT
1 TT
11229508 CTTATTAAGG
Statistics
Matches: 158, Mismatches: 4, Indels: 15
0.89 0.02 0.08
Matches are distributed among these distances:
80 59 0.37
81 19 0.12
82 1 0.01
86 1 0.01
87 58 0.37
88 20 0.13
ACGTcount: A:0.26, C:0.19, G:0.21, T:0.34
Consensus pattern (83 bp):
TTTTCATAAGGATACCTTTGCCTCATGAAATTGCGCTGAATTTAACATTGAAAGCTGTCAGTTCA
CTGTACCGGAGACGGCTT
Found at i:11230513 original size:27 final size:27
Alignment explanation
Indices: 11230482--11230537 Score: 112
Period size: 27 Copynumber: 2.1 Consensus size: 27
11230472 CTTAGTAATT
11230482 AATTATATTTGTAATAGTTACTATGTA
1 AATTATATTTGTAATAGTTACTATGTA
11230509 AATTATATTTGTAATAGTTACTATGTA
1 AATTATATTTGTAATAGTTACTATGTA
11230536 AA
1 AA
11230538 AGAATTTCGT
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
27 29 1.00
ACGTcount: A:0.39, C:0.04, G:0.11, T:0.46
Consensus pattern (27 bp):
AATTATATTTGTAATAGTTACTATGTA
Found at i:11232042 original size:2 final size:2
Alignment explanation
Indices: 11232035--11232062 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
11232025 TTTTTCAGCA
11232035 AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT
11232063 CGATGCAACG
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:11232571 original size:17 final size:17
Alignment explanation
Indices: 11232535--11232569 Score: 54
Period size: 17 Copynumber: 2.1 Consensus size: 17
11232525 TTGTCGATTT
11232535 AATAAAAATATTTATAA
1 AATAAAAATATTTATAA
*
11232552 AATATAAATATTT-TAA
1 AATAAAAATATTTATAA
11232568 AA
1 AA
11232570 ATTCAAACTT
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
16 5 0.29
17 12 0.71
ACGTcount: A:0.63, C:0.00, G:0.00, T:0.37
Consensus pattern (17 bp):
AATAAAAATATTTATAA
Found at i:11232773 original size:27 final size:28
Alignment explanation
Indices: 11232718--11232778 Score: 81
Period size: 27 Copynumber: 2.2 Consensus size: 28
11232708 CATTTTATTA
* **
11232718 AAATTATATTTTATATTTTAATAGTTAT
1 AAATAATATTTTATATTTTAATAAATAT
11232746 AAATAATA-TTTATATTTTAATAAATAT
1 AAATAATATTTTATATTTTAATAAATAT
11232773 -AATAAT
1 AAATAAT
11232779 TAATGACTAA
Statistics
Matches: 30, Mismatches: 3, Indels: 2
0.86 0.09 0.06
Matches are distributed among these distances:
26 6 0.20
27 17 0.57
28 7 0.23
ACGTcount: A:0.48, C:0.00, G:0.02, T:0.51
Consensus pattern (28 bp):
AAATAATATTTTATATTTTAATAAATAT
Found at i:11232825 original size:21 final size:20
Alignment explanation
Indices: 11232800--11232847 Score: 69
Period size: 21 Copynumber: 2.4 Consensus size: 20
11232790 AAATAATTAT
11232800 TAATAATATTTATTAAAATA
1 TAATAATATTTATTAAAATA
* *
11232820 TAAATATTATTTATTAATATA
1 T-AATAATATTTATTAAAATA
11232841 TAATAAT
1 TAATAAT
11232848 TAATCTTTAT
Statistics
Matches: 24, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
20 6 0.25
21 18 0.75
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (20 bp):
TAATAATATTTATTAAAATA
Found at i:11232896 original size:29 final size:29
Alignment explanation
Indices: 11232859--11232933 Score: 71
Period size: 29 Copynumber: 2.5 Consensus size: 29
11232849 AATCTTTATG
*
11232859 TAATAAAAAAGAAATATCTATATAT-AAAA
1 TAAT-AAAAAGAAATATATATATATGAAAA
* * *
11232888 TTAATAAAAATATATATATTTATATGAAAA
1 -TAATAAAAAGAAATATATATATATGAAAA
11232918 TAAGTAAAAAGGAAAT
1 TAA-TAAAAA-GAAAT
11232934 TAAAATCATT
Statistics
Matches: 36, Mismatches: 6, Indels: 5
0.77 0.13 0.11
Matches are distributed among these distances:
29 19 0.53
30 14 0.39
31 3 0.08
ACGTcount: A:0.61, C:0.01, G:0.07, T:0.31
Consensus pattern (29 bp):
TAATAAAAAGAAATATATATATATGAAAA
Found at i:11233447 original size:17 final size:17
Alignment explanation
Indices: 11233421--11233460 Score: 53
Period size: 17 Copynumber: 2.4 Consensus size: 17
11233411 TCATAATGGT
* *
11233421 TTAAAGTAATTTAATTA
1 TTAAATTAATCTAATTA
11233438 TTAAATTAATCTAATTA
1 TTAAATTAATCTAATTA
*
11233455 TAAAAT
1 TTAAAT
11233461 CAGATCAATT
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
17 20 1.00
ACGTcount: A:0.50, C:0.03, G:0.03, T:0.45
Consensus pattern (17 bp):
TTAAATTAATCTAATTA
Found at i:11235580 original size:33 final size:33
Alignment explanation
Indices: 11235539--11235750 Score: 178
Period size: 33 Copynumber: 6.4 Consensus size: 33
11235529 GTCAAAACTC
*
11235539 AAATGACCTAGACTAAACCGAAGTCTAAAAATG
1 AAATGACCTAGACTAAATCGAAGTCTAAAAATG
* * * *
11235572 AAACGACCTATACTAAATCAAAGTCTTAAAATG
1 AAATGACCTAGACTAAATCGAAGTCTAAAAATG
* * * * * *
11235605 AAATGACTTAGACTGAATTGAAGTTTGAAAGTG
1 AAATGACCTAGACTAAATCGAAGTCTAAAAATG
* * * * * *
11235638 AAATGACCCGGACTACTAAAT-TAGAGTCTGAAAGTT
1 AAATGA-CC-TA-GACTAAATCGA-AGTCTAAAAATG
* *
11235674 AAATGACCTAGACTGAAAT-GAAGTGTAAAAATT
1 AAATGACCTAGACT-AAATCGAAGTCTAAAAATG
*
11235707 AAATGACCTAGACTAAATCGAAGTCCAAAAATG
1 AAATGACCTAGACTAAATCGAAGTCTAAAAATG
11235740 AAATGA-CTAGA
1 AAATGACCTAGA
11235751 TTGAACCAAA
Statistics
Matches: 143, Mismatches: 30, Indels: 13
0.77 0.16 0.07
Matches are distributed among these distances:
32 9 0.06
33 101 0.71
34 7 0.05
35 4 0.03
36 22 0.15
ACGTcount: A:0.46, C:0.14, G:0.17, T:0.23
Consensus pattern (33 bp):
AAATGACCTAGACTAAATCGAAGTCTAAAAATG
Found at i:11235711 original size:69 final size:67
Alignment explanation
Indices: 11235539--11235755 Score: 190
Period size: 69 Copynumber: 3.3 Consensus size: 67
11235529 GTCAAAACTC
* * * *
11235539 AAATGACCTAGACT-AAACCGAAGTCTAAAAATGAAACGA-CCTATACTAAATCAAAGTCTTAAA
1 AAATGACCTAGACTGAAA-TGAAGTCTAAAAATGAAATGACCCGATACTAAATCAAAGTCTGAAA
11235602 ATG
65 ATG
* * * * * * *
11235605 AAATGACTTAGACTGAATTGAAGTTTGAAAGTGAAATGACCCGGACTACTAAATTAGAGTCTGAA
1 AAATGACCTAGACTGAAATGAAGTCTAAAAATGAAATGACCC-GA-TACTAAATCAAAGTCTGAA
* *
11235670 AGTT
64 AATG
* * * * * **
11235674 AAATGACCTAGACTGAAATGAAGTGTAAAAATTAAATGA-CCTAGACTAAATCGAAGTCCAAAAA
1 AAATGACCTAGACTGAAATGAAGTCTAAAAATGAAATGACCCGATACTAAATCAAAGTCTGAAAA
11235738 TG
66 TG
*
11235740 AAATGA-CTAGATTGAA
1 AAATGACCTAGACTGAA
11235756 CCAAAGCGTA
Statistics
Matches: 118, Mismatches: 29, Indels: 9
0.76 0.19 0.06
Matches are distributed among these distances:
65 9 0.08
66 50 0.42
67 5 0.04
68 3 0.03
69 51 0.43
ACGTcount: A:0.46, C:0.14, G:0.17, T:0.24
Consensus pattern (67 bp):
AAATGACCTAGACTGAAATGAAGTCTAAAAATGAAATGACCCGATACTAAATCAAAGTCTGAAAA
TG
Found at i:11235842 original size:32 final size:31
Alignment explanation
Indices: 11235733--11235853 Score: 120
Period size: 33 Copynumber: 3.8 Consensus size: 31
11235723 ATCGAAGTCC
*
11235733 AAAAATGAAATGAC-TAGATTGAACCAAAGCGT
1 AAAAATGAAATGACTTGGATTGAACCAAA--GT
* *
11235765 AAAGATGAAATGACTTGGATTGAACTAAAGTTT
1 AAAAATGAAATGACTTGGATTGAACCAAAG--T
**
11235798 AAAAATTCAATGACTTGGATTGAACCAAAGT
1 AAAAATGAAATGACTTGGATTGAACCAAAGT
*
11235829 AAAAAACGAAATGA-TTGAGATTGAA
1 -AAAAATGAAATGACTTG-GATTGAA
11235854 TTGCAAGTTG
Statistics
Matches: 74, Mismatches: 10, Indels: 10
0.79 0.11 0.11
Matches are distributed among these distances:
31 5 0.07
32 30 0.41
33 39 0.53
ACGTcount: A:0.48, C:0.09, G:0.19, T:0.24
Consensus pattern (31 bp):
AAAAATGAAATGACTTGGATTGAACCAAAGT
Found at i:11235868 original size:66 final size:64
Alignment explanation
Indices: 11235741--11235869 Score: 145
Period size: 65 Copynumber: 2.0 Consensus size: 64
11235731 CCAAAAATGA
* * *
11235741 AATGACTAGATTGAACCAAAGCGTAAAGATGAAATGACTTGGATTGAACTAAAGTTTAAAAATTC
1 AATGACTAGATTGAACCAAA-CGTAAAAACGAAATGACTTGGATTGAACTAAAGTTGAAAAATTC
* * *
11235806 AATGACTTGGATTGAACCAAA-GTAAAAAACGAAATGA-TTGAGATTGAATTGCAAGTTGAAAAA
1 AATGAC-TAGATTGAACCAAACGT-AAAAACGAAATGACTTG-GATTGAACT-AAAGTTGAAAAA
11235869 T
62 T
11235870 AAAATAATTA
Statistics
Matches: 54, Mismatches: 6, Indels: 7
0.81 0.09 0.10
Matches are distributed among these distances:
64 5 0.09
65 25 0.46
66 24 0.44
ACGTcount: A:0.46, C:0.09, G:0.19, T:0.26
Consensus pattern (64 bp):
AATGACTAGATTGAACCAAACGTAAAAACGAAATGACTTGGATTGAACTAAAGTTGAAAAATTC
Found at i:11235942 original size:53 final size:53
Alignment explanation
Indices: 11235858--11235959 Score: 132
Period size: 53 Copynumber: 1.9 Consensus size: 53
11235848 ATTGAATTGC
* * * *
11235858 AAGTTGAAAAATAAAATAATTAAGACTAAACTGCAAGTCGAAAAATGAACCAT
1 AAGTTGAAAAATAAAATAACTAAGACAAAACTACAAGTCAAAAAATGAACCAT
* * * *
11235911 AAGTTGAAAAATGAAATGACTAGGACAAAACTACAAGTTAAAAAATGAA
1 AAGTTGAAAAATAAAATAACTAAGACAAAACTACAAGTCAAAAAATGAA
11235960 ATGATCAGGA
Statistics
Matches: 41, Mismatches: 8, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
53 41 1.00
ACGTcount: A:0.56, C:0.10, G:0.15, T:0.20
Consensus pattern (53 bp):
AAGTTGAAAAATAAAATAACTAAGACAAAACTACAAGTCAAAAAATGAACCAT
Found at i:11235955 original size:34 final size:34
Alignment explanation
Indices: 11235911--11236016 Score: 103
Period size: 34 Copynumber: 3.1 Consensus size: 34
11235901 AATGAACCAT
*
11235911 AAGTTGAAAAATGAAATGACTAGGACAAAACTAC
1 AAGTTAAAAAATGAAATGACTAGGACAAAACTAC
11235945 AAGTTAAAAAATGAAATGA-TCAGGA-ATAAA-TCAC
1 AAGTTAAAAAATGAAATGACT-AGGACA-AAACT-AC
* * * *
11235979 AAATCAAAAAATTAAATGACT-GAGACTAAACTAC
1 AAGTTAAAAAATGAAATGACTAG-GACAAAACTAC
11236013 AAGT
1 AAGT
11236017 AGAAAATCAG
Statistics
Matches: 59, Mismatches: 6, Indels: 14
0.75 0.08 0.18
Matches are distributed among these distances:
33 4 0.07
34 53 0.90
35 2 0.03
ACGTcount: A:0.55, C:0.11, G:0.14, T:0.20
Consensus pattern (34 bp):
AAGTTAAAAAATGAAATGACTAGGACAAAACTAC
Found at i:11237502 original size:18 final size:18
Alignment explanation
Indices: 11237481--11237520 Score: 62
Period size: 18 Copynumber: 2.2 Consensus size: 18
11237471 TTTTTATATA
11237481 TTTTTTTCTTTTGTTGCT
1 TTTTTTTCTTTTGTTGCT
* *
11237499 TTTTTTTGTTTTGTTTCT
1 TTTTTTTCTTTTGTTGCT
11237517 TTTT
1 TTTT
11237521 ATGTTGTTGA
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
18 20 1.00
ACGTcount: A:0.00, C:0.07, G:0.10, T:0.82
Consensus pattern (18 bp):
TTTTTTTCTTTTGTTGCT
Found at i:11246861 original size:19 final size:19
Alignment explanation
Indices: 11246829--11246876 Score: 62
Period size: 19 Copynumber: 2.6 Consensus size: 19
11246819 ATAATGCCCT
11246829 TCATTTTTTA-AAAAAAAA
1 TCATTTTTTATAAAAAAAA
* *
11246847 TTATTTTTTATAAAAGAAA
1 TCATTTTTTATAAAAAAAA
*
11246866 TCATTATTTAT
1 TCATTTTTTAT
11246877 GAATATTGTA
Statistics
Matches: 25, Mismatches: 4, Indels: 1
0.83 0.13 0.03
Matches are distributed among these distances:
18 9 0.36
19 16 0.64
ACGTcount: A:0.46, C:0.04, G:0.02, T:0.48
Consensus pattern (19 bp):
TCATTTTTTATAAAAAAAA
Found at i:11254006 original size:63 final size:63
Alignment explanation
Indices: 11253888--11254441 Score: 401
Period size: 63 Copynumber: 8.7 Consensus size: 63
11253878 TTTAAAACGT
* * * *
11253888 AGTAATTGATAATTATAATTTTTT-CAAATAATCAATTACTGCATTGCTTTGTTTTATAAAGC
1 AGTAATTGATAATTGTAATTTTTTACAAACAATCAATTACTACGTTGCTTTGTTTTATAAAGC
* * ** * *
11253950 AGTAATTGATAATTGTAAATTTTTACAAACAATTAATTACTATTTTTCTTT-ATTT-TAAAGC
1 AGTAATTGATAATTGTAATTTTTTACAAACAATCAATTACTACGTTGCTTTGTTTTATAAAGC
* * * * * * *
11254011 ATAATAATTAATTATTATAATTGTTTTAAAAACAATCAATTACTGCATTGCTTTGTTTTATAAAG
1 --AGTAATTGATAATTGTAATT-TTTTACAAACAATCAATTACTACGTTGCTTTGTTTTATAAAG
11254076 C
63 C
* * * * ***
11254077 AATAATTGATCATTGTAATTGTTTTA-AAACAATCAATGACTGA-GTTACTTTGTTTTATAACTT
1 AGTAATTGATAATTGTAATT-TTTTACAAACAATCAATTACT-ACGTTGCTTTGTTTTATAAAGC
* ** * * *
11254140 AGTAATTGATAATTGTAA-TTTTAATCAAATGATCAATTATTGCATTGCTTTGTTTTATAACA-C
1 AGTAATTGATAATTGTAATTTTTTA-CAAACAATCAATTACTACGTTGCTTTGTTTTATAA-AGC
* * * * *
11254203 AGTAATTGATCATTGTAATTTTTTTCAAACAACCAATTATTGCGTTGCTTTGTTTTATAACA-C
1 AGTAATTGATAATTGTAATTTTTTACAAACAATCAATTACTACGTTGCTTTGTTTTATAA-AGC
* * * * ***
11254266 AGTAATTGATCATTGTAATTGTTTTA-AAATAATCAATTACTACGTTACTTTATTTTATAACTT
1 AGTAATTGATAATTGTAATT-TTTTACAAACAATCAATTACTACGTTGCTTTGTTTTATAAAGC
* * * * * * * * * * *
11254329 AGTAATTAATAATTTTAA-TTTTAATCAAATAATCAATTATTATGTTTCTTTATTTCATAATGT
1 AGTAATTGATAATTGTAATTTTTTA-CAAACAATCAATTACTACGTTGCTTTGTTTTATAAAGC
* *
11254392 AGTAATTAATTAATCATTGTAATTTTTTTA-AAACAATTAATTACTACGTT
1 AGTAATTGA-T-A--ATTGTAA-TTTTTTACAAACAATCAATTACTACGTT
11254442 ACTAGTCTTT
Statistics
Matches: 395, Mismatches: 75, Indels: 39
0.78 0.15 0.08
Matches are distributed among these distances:
61 14 0.04
62 27 0.07
63 260 0.66
64 57 0.14
65 4 0.01
66 6 0.02
67 22 0.06
69 5 0.01
ACGTcount: A:0.36, C:0.09, G:0.08, T:0.46
Consensus pattern (63 bp):
AGTAATTGATAATTGTAATTTTTTACAAACAATCAATTACTACGTTGCTTTGTTTTATAAAGC
Found at i:11254052 original size:32 final size:32
Alignment explanation
Indices: 11254016--11254113 Score: 87
Period size: 32 Copynumber: 3.1 Consensus size: 32
11254006 AAAGCATAAT
*
11254016 AATTAATTATTATAATTGTTTTAAAAACAATC
1 AATTAATCATTATAATTGTTTTAAAAACAATC
* * *
11254048 AATTACTGCATTGCT--TTGTTTTATAAAGCAAT-
1 AATTAAT-CATT-ATAATTGTTTTA-AAAACAATC
* *
11254080 AATTGATCATTGTAATTGTTTT-AAAACAATC
1 AATTAATCATTATAATTGTTTTAAAAACAATC
11254111 AAT
1 AAT
11254114 GACTGAGTTA
Statistics
Matches: 52, Mismatches: 8, Indels: 13
0.71 0.11 0.18
Matches are distributed among these distances:
30 8 0.15
31 7 0.13
32 26 0.50
33 10 0.19
34 1 0.02
ACGTcount: A:0.40, C:0.09, G:0.08, T:0.43
Consensus pattern (32 bp):
AATTAATCATTATAATTGTTTTAAAAACAATC
Found at i:11254133 original size:31 final size:30
Alignment explanation
Indices: 11254031--11254133 Score: 77
Period size: 32 Copynumber: 3.3 Consensus size: 30
11254021 ATTATTATAA
* *
11254031 TTGTTTTAAAAACAATCAATTACTGCATTGCT
1 TTGTTTT-AAAACAATCAATGACTG-ATTACT
* *
11254063 TTGTTTTATAAAGCAAT-AATTGA-TCATTGTA-A
1 TTGTTTTA-AAA-CAATCAA-TGACTGA-T-TACT
11254095 TTGTTTTAAAACAATCAATGACTGAGTTACT
1 TTGTTTTAAAACAATCAATGACTGA-TTACT
11254126 TTGTTTTA
1 TTGTTTTA
11254134 TAACTTAGTA
Statistics
Matches: 56, Mismatches: 7, Indels: 17
0.70 0.09 0.21
Matches are distributed among these distances:
30 9 0.16
31 18 0.32
32 22 0.39
33 7 0.12
ACGTcount: A:0.34, C:0.11, G:0.12, T:0.44
Consensus pattern (30 bp):
TTGTTTTAAAACAATCAATGACTGATTACT
Found at i:11254217 original size:31 final size:31
Alignment explanation
Indices: 11254182--11254280 Score: 89
Period size: 31 Copynumber: 3.2 Consensus size: 31
11254172 TCAATTATTG
11254182 CATTGCTTTGTTTTATAACACAGTAATTGAT
1 CATTGCTTTGTTTTATAACACAGTAATTGAT
* **
11254213 CATTG-TAATTTTTTTCA-AACA-ACCAATT-ATT
1 CATTGCT--TTGTTTT-ATAACACAGTAATTGA-T
*
11254244 GCGTTGCTTTGTTTTATAACACAGTAATTGAT
1 -CATTGCTTTGTTTTATAACACAGTAATTGAT
11254276 CATTG
1 CATTG
11254281 TAATTGTTTT
Statistics
Matches: 51, Mismatches: 8, Indels: 18
0.66 0.10 0.23
Matches are distributed among these distances:
30 3 0.06
31 25 0.49
32 20 0.39
33 3 0.06
ACGTcount: A:0.29, C:0.14, G:0.12, T:0.44
Consensus pattern (31 bp):
CATTGCTTTGTTTTATAACACAGTAATTGAT
Found at i:11254288 original size:32 final size:32
Alignment explanation
Indices: 11254189--11254291 Score: 99
Period size: 32 Copynumber: 3.2 Consensus size: 32
11254179 TTGCATTGCT
11254189 TTGTTTTATAACACAGTAATTGATCATTGTAA
1 TTGTTTTATAACACAGTAATTGATCATTGTAA
* ** *
11254221 TTTTTTTCA-AACA-ACCAATT-ATTGCGTTGCT--
1 TTGTTTT-ATAACACAGTAATTGA-T-CATTG-TAA
11254252 TTGTTTTATAACACAGTAATTGATCATTGTAA
1 TTGTTTTATAACACAGTAATTGATCATTGTAA
11254284 TTGTTTTA
1 TTGTTTTA
11254292 AAATAATCAA
Statistics
Matches: 54, Mismatches: 8, Indels: 18
0.68 0.10 0.22
Matches are distributed among these distances:
30 3 0.06
31 20 0.37
32 28 0.52
33 3 0.06
ACGTcount: A:0.30, C:0.12, G:0.12, T:0.47
Consensus pattern (32 bp):
TTGTTTTATAACACAGTAATTGATCATTGTAA
Found at i:11254289 original size:189 final size:190
Alignment explanation
Indices: 11253888--11254424 Score: 575
Period size: 189 Copynumber: 2.8 Consensus size: 190
11253878 TTTAAAACGT
* * * * ***
11253888 AGTAATTGATAATTATAATT-TTTTCAAATAATCAATTACTGCA-TTGCTTTGTTTTATAAAGCA
1 AGTAATTGATCATTGTAATTGTTTTAAAATAATCAATTACTG-AGTTACTTTGTTTTATAACTTA
* * * * ** * *
11253951 GTAATTGATAATTGTAAATTTTTA-CAAACAATTAATTACTATTTTTCTTTATTTTAAAGCATAA
65 GTAATTGATAATTGT-AATTTTAATCAAATAATCAATTATTACATTGCTTTATTTTAAAGCACAA
* *
11254015 TAATTAATTATTATAATTGTTTTAAAAACAATCAATTACTGCATTGCTTTGTTTTATAAAGC
129 TAATTAATCATTATAATTGTTTTAAAAACAACCAATTACTGCATTGCTTTGTTTTATAAAGC
* * *
11254077 AATAATTGATCATTGTAATTGTTTTAAAACAATCAATGACTGAGTTACTTTGTTTTATAACTTAG
1 AGTAATTGATCATTGTAATTGTTTTAAAATAATCAATTACTGAGTTACTTTGTTTTATAACTTAG
* * * *
11254142 TAATTGATAATTGTAATTTTAATCAAATGATCAATTATTGCATTGCTTTGTTTTATAA-CACAGT
66 TAATTGATAATTGTAATTTTAATCAAATAATCAATTATTACATTGCTTTATTTTA-AAGCACAAT
* * ** * *
11254206 AATTGATCATTGTAATT-TTTTTCAAACAACCAATTATTGCGTTGCTTTGTTTTATAACA-C
130 AATTAATCATTATAATTGTTTTAAAAACAACCAATTACTGCATTGCTTTGTTTTATAA-AGC
*
11254266 AGTAATTGATCATTGTAATTGTTTTAAAATAATCAATTACT-ACGTTACTTTATTTTATAACTTA
1 AGTAATTGATCATTGTAATTGTTTTAAAATAATCAATTACTGA-GTTACTTTGTTTTATAACTTA
* * ** * * * *
11254330 GTAATTAATAATTTTAATTTTAATCAAATAATCAATTATTATGTTTCTTTATTTCATAATGTAGT
65 GTAATTGATAATTGTAATTTTAATCAAATAATCAATTATTACATTGCTTTATTT--TAAAGCA-C
* *
11254395 AATTAATTAATCATTGTAATTTTTTTAAAA
127 AA-TAATTAATCATTATAATTGTTTTAAAA
11254425 CAATTAATTA
Statistics
Matches: 287, Mismatches: 49, Indels: 19
0.81 0.14 0.05
Matches are distributed among these distances:
188 1 0.00
189 165 0.57
190 92 0.32
191 5 0.02
192 1 0.00
193 17 0.06
194 6 0.02
ACGTcount: A:0.36, C:0.09, G:0.09, T:0.46
Consensus pattern (190 bp):
AGTAATTGATCATTGTAATTGTTTTAAAATAATCAATTACTGAGTTACTTTGTTTTATAACTTAG
TAATTGATAATTGTAATTTTAATCAAATAATCAATTATTACATTGCTTTATTTTAAAGCACAATA
ATTAATCATTATAATTGTTTTAAAAACAACCAATTACTGCATTGCTTTGTTTTATAAAGC
Found at i:11254326 original size:126 final size:126
Alignment explanation
Indices: 11253887--11254436 Score: 507
Period size: 126 Copynumber: 4.3 Consensus size: 126
11253877 CTTTAAAACG
* *
11253887 TAGTAATTGATAATTATAATTTTTTCAAATAATCAATTACTGCATTGCTTTGTTTTATAAAGCAG
1 TAGTAATTGATAATTGTAATTTTTTAAAATAATCAATTACTGCATTGCTTTGTTTTATAAAGCAG
* * * *
11253952 TAATTGATAATTGTAAATTTTTACAAACAATTAATTACTATTTTTCTTTATTTTA-AAGCA
66 TAATTGATAATTGTAATTTTTTTCAAACAATCAATTACTATGTTTCTTTATTTTATAAGCA
* * * * *
11254012 TAATAATTAATTATTATAATTGTTTTAAAAACAATCAATTACTGCATTGCTTTGTTTTATAAAGC
1 TAGTAATTGATAATTGTAATT-TTTT-AAAATAATCAATTACTGCATTGCTTTGTTTTATAAAGC
* * * * * * * *
11254077 AATAATTGATCATTGTAATTGTTTTAAAACAATCAATGACTGA-GTTACTTTGTTTTATAA-CT
64 AGTAATTGATAATTGTAATTTTTTTCAAACAATCAATTACT-ATGTTTCTTTATTTTATAAGCA
* * * *
11254139 TAGTAATTGATAATTGTAATTTTAATCAAATGATCAATTATTGCATTGCTTTGTTTTATAACA-C
1 TAGTAATTGATAATTGTAATTTT-TTAAAATAATCAATTACTGCATTGCTTTGTTTTATAA-AGC
* * * ** * *
11254203 AGTAATTGATCATTGTAATTTTTTTCAAACAACCAATTATTGCGTTGCTTTGTTTTATAA-CA
64 AGTAATTGATAATTGTAATTTTTTTCAAACAATCAATTACTATGTTTCTTTATTTTATAAGCA
* * * * * * ***
11254265 CAGTAATTGATCATTGTAATTGTTTTAAAATAATCAATTACTACGTTACTTTATTTTATAACTTA
1 TAGTAATTGATAATTGTAATT-TTTTAAAATAATCAATTACTGCATTGCTTTGTTTTATAAAGCA
* * ** * * * *
11254330 GTAATTAATAATTTTAATTTTAATCAAATAATCAATTATTATGTTTCTTTATTTCATAATGTA
65 GTAATTGATAATTGTAATTTTTTTCAAACAATCAATTACTATGTTTCTTTATTTTATAA-GCA
* * * * *
11254393 GTAATTAATTAATCATTGTAATTTTTTTAAAACAATTAATTACT
1 -T-AGTAATTGATAATTGTAA-TTTTTTAAAATAATCAATTACT
11254437 ACGTTACTAG
Statistics
Matches: 346, Mismatches: 65, Indels: 23
0.80 0.15 0.05
Matches are distributed among these distances:
125 18 0.05
126 186 0.54
127 102 0.29
128 4 0.01
130 34 0.10
131 2 0.01
ACGTcount: A:0.36, C:0.09, G:0.08, T:0.46
Consensus pattern (126 bp):
TAGTAATTGATAATTGTAATTTTTTAAAATAATCAATTACTGCATTGCTTTGTTTTATAAAGCAG
TAATTGATAATTGTAATTTTTTTCAAACAATCAATTACTATGTTTCTTTATTTTATAAGCA
Found at i:11255366 original size:28 final size:29
Alignment explanation
Indices: 11255310--11255366 Score: 89
Period size: 28 Copynumber: 2.0 Consensus size: 29
11255300 ACCAACAAAG
* *
11255310 ATATACACGAATAAACATGACTAATATAA
1 ATATACACGAATAAACATGACCAAAATAA
11255339 ATATACACGAAT-AACATGACCAAAATAA
1 ATATACACGAATAAACATGACCAAAATAA
11255367 TAAACAACTA
Statistics
Matches: 26, Mismatches: 2, Indels: 1
0.90 0.07 0.03
Matches are distributed among these distances:
28 14 0.54
29 12 0.46
ACGTcount: A:0.56, C:0.16, G:0.07, T:0.21
Consensus pattern (29 bp):
ATATACACGAATAAACATGACCAAAATAA
Found at i:11256304 original size:61 final size:61
Alignment explanation
Indices: 11256133--11256304 Score: 159
Period size: 61 Copynumber: 2.8 Consensus size: 61
11256123 TATGATGGGT
* * * * ** **
11256133 ATTATAGTAATTTTTATCAATTATGATAGGAAG-ACATTTTCGTAATTATGATATTAGTGGT
1 ATTATAGTAATTTTAACCAATTATGGTAGGAAGAACATTTT-ATAATTATGATATTAAAGAC
* * * * ** *
11256194 ATTATACTAATTTTACCCAATTATGGTTGAAAGAGTATTTTTATTATTATGATA-TAAAGAC
1 ATTATAGTAATTTTAACCAATTATGGTAGGAAGAACA-TTTTATAATTATGATATTAAAGAC
*
11256255 ATTATAGTAATTTTAACCAATTATGGTAGGAGGAACATTTCTATAATTAT
1 ATTATAGTAATTTTAACCAATTATGGTAGGAAGAACATTT-TATAATTAT
11256305 AATAATTTTA
Statistics
Matches: 85, Mismatches: 23, Indels: 6
0.75 0.20 0.05
Matches are distributed among these distances:
60 3 0.04
61 67 0.79
62 11 0.13
63 4 0.05
ACGTcount: A:0.37, C:0.07, G:0.14, T:0.42
Consensus pattern (61 bp):
ATTATAGTAATTTTAACCAATTATGGTAGGAAGAACATTTTATAATTATGATATTAAAGAC
Found at i:11260813 original size:27 final size:27
Alignment explanation
Indices: 11260764--11260822 Score: 75
Period size: 27 Copynumber: 2.1 Consensus size: 27
11260754 AAAAAGAATT
11260764 AAAAAAAAGGAAAAAATGCAGCATAGGA
1 AAAAAAAAGGAAAAAAT-CAGCATAGGA
* *
11260792 AAAAAAAAGAGGAAAAAT-AGCATATGA
1 AAAAAAAAG-GAAAAAATCAGCATAGGA
11260819 AAAA
1 AAAA
11260823 TTAGAAAGAG
Statistics
Matches: 28, Mismatches: 2, Indels: 3
0.85 0.06 0.09
Matches are distributed among these distances:
27 12 0.43
28 9 0.32
29 7 0.25
ACGTcount: A:0.68, C:0.05, G:0.19, T:0.08
Consensus pattern (27 bp):
AAAAAAAAGGAAAAAATCAGCATAGGA
Found at i:11263110 original size:29 final size:29
Alignment explanation
Indices: 11263052--11263110 Score: 91
Period size: 29 Copynumber: 2.0 Consensus size: 29
11263042 AGAGAATTCA
* *
11263052 AGCTAAATATCTTATCAATTTTTGTTTTT
1 AGCTAAATATCTTATCAATTTTTATCTTT
*
11263081 AGCTAAATATCTTGTCAATTTTTATCTTT
1 AGCTAAATATCTTATCAATTTTTATCTTT
11263110 A
1 A
11263111 TTGATTGGAT
Statistics
Matches: 27, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
29 27 1.00
ACGTcount: A:0.29, C:0.12, G:0.07, T:0.53
Consensus pattern (29 bp):
AGCTAAATATCTTATCAATTTTTATCTTT
Found at i:11264564 original size:15 final size:15
Alignment explanation
Indices: 11264544--11264576 Score: 66
Period size: 15 Copynumber: 2.2 Consensus size: 15
11264534 TGAGAAAGAG
11264544 ATTTTAAAATTTTAA
1 ATTTTAAAATTTTAA
11264559 ATTTTAAAATTTTAA
1 ATTTTAAAATTTTAA
11264574 ATT
1 ATT
11264577 CAAAATTATT
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 18 1.00
ACGTcount: A:0.45, C:0.00, G:0.00, T:0.55
Consensus pattern (15 bp):
ATTTTAAAATTTTAA
Found at i:11264576 original size:7 final size:8
Alignment explanation
Indices: 11264544--11264574 Score: 55
Period size: 8 Copynumber: 4.0 Consensus size: 8
11264534 TGAGAAAGAG
11264544 ATTTTAAA
1 ATTTTAAA
11264552 ATTTT-AA
1 ATTTTAAA
11264559 ATTTTAAA
1 ATTTTAAA
11264567 ATTTTAAA
1 ATTTTAAA
11264575 TTCAAAATTA
Statistics
Matches: 22, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
7 7 0.32
8 15 0.68
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (8 bp):
ATTTTAAA
Found at i:11269658 original size:1 final size:1
Alignment explanation
Indices: 11269652--11269679 Score: 56
Period size: 1 Copynumber: 28.0 Consensus size: 1
11269642 TCCTAAGGTG
11269652 TTTTTTTTTTTTTTTTTTTTTTTTTTTT
1 TTTTTTTTTTTTTTTTTTTTTTTTTTTT
11269680 GAGTTGAGCA
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
1 27 1.00
ACGTcount: A:0.00, C:0.00, G:0.00, T:1.00
Consensus pattern (1 bp):
T
Found at i:11271283 original size:15 final size:15
Alignment explanation
Indices: 11271234--11271284 Score: 50
Period size: 15 Copynumber: 3.3 Consensus size: 15
11271224 TTGTAAGTTT
*
11271234 TTTTCTTTTTATTTTA
1 TTTT-TTTTTACTTTA
*
11271250 TTTTTTGTTT-CTCTA
1 TTTTTT-TTTACTTTA
*
11271265 TTTTTTTTTACTTTG
1 TTTTTTTTTACTTTA
11271280 TTTTT
1 TTTTT
11271285 ATTCTCCTAT
Statistics
Matches: 29, Mismatches: 4, Indels: 5
0.76 0.11 0.13
Matches are distributed among these distances:
14 3 0.10
15 19 0.66
16 7 0.24
ACGTcount: A:0.08, C:0.08, G:0.04, T:0.80
Consensus pattern (15 bp):
TTTTTTTTTACTTTA
Found at i:11272474 original size:20 final size:20
Alignment explanation
Indices: 11272449--11272492 Score: 61
Period size: 20 Copynumber: 2.2 Consensus size: 20
11272439 GCATAAAAAG
**
11272449 AAAATTTAAAAAAATGATAA
1 AAAATTTAAAAAAACCATAA
*
11272469 AAAATTTAAAGAAACCATAA
1 AAAATTTAAAAAAACCATAA
11272489 AAAA
1 AAAA
11272493 AGAAACTAAA
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
20 21 1.00
ACGTcount: A:0.70, C:0.05, G:0.05, T:0.20
Consensus pattern (20 bp):
AAAATTTAAAAAAACCATAA
Found at i:11272542 original size:16 final size:16
Alignment explanation
Indices: 11272513--11272557 Score: 54
Period size: 16 Copynumber: 2.8 Consensus size: 16
11272503 ATATTTTTTT
**
11272513 AAATTTTAAAAATTATG
1 AAATTTT-AAAATTAAA
11272530 AAATTTTAAAATTAAA
1 AAATTTTAAAATTAAA
*
11272546 AAATTTCAAAAT
1 AAATTTTAAAAT
11272558 CTTTAATAAA
Statistics
Matches: 25, Mismatches: 3, Indels: 1
0.86 0.10 0.03
Matches are distributed among these distances:
16 18 0.72
17 7 0.28
ACGTcount: A:0.58, C:0.02, G:0.02, T:0.38
Consensus pattern (16 bp):
AAATTTTAAAATTAAA
Found at i:11272625 original size:20 final size:20
Alignment explanation
Indices: 11272583--11272629 Score: 60
Period size: 19 Copynumber: 2.4 Consensus size: 20
11272573 AAAAGATTCA
*
11272583 AAAAATATGAAAATTTTTTT
1 AAAAATATGAAAATTTTTAT
*
11272603 AAAAA-ATGAAAGTTTTTAAT
1 AAAAATATGAAAATTTTT-AT
11272623 AAAAATA
1 AAAAATA
11272630 AACTTCTTAA
Statistics
Matches: 23, Mismatches: 2, Indels: 3
0.82 0.07 0.11
Matches are distributed among these distances:
19 11 0.48
20 11 0.48
21 1 0.04
ACGTcount: A:0.57, C:0.00, G:0.06, T:0.36
Consensus pattern (20 bp):
AAAAATATGAAAATTTTTAT
Found at i:11272688 original size:24 final size:23
Alignment explanation
Indices: 11272661--11272714 Score: 56
Period size: 24 Copynumber: 2.3 Consensus size: 23
11272651 AAAGATTCAC
11272661 AAAAACT-TAAAAAATTTCAAAATA
1 AAAAACTCT-AAAAATTTCAAAA-A
* * *
11272685 AAAAAATCTAAAAGTTTGAAAAA
1 AAAAACTCTAAAAATTTCAAAAA
11272708 AAAAACT
1 AAAAACT
11272715 ATGAAATTTT
Statistics
Matches: 25, Mismatches: 4, Indels: 3
0.78 0.12 0.09
Matches are distributed among these distances:
23 7 0.28
24 17 0.68
25 1 0.04
ACGTcount: A:0.67, C:0.07, G:0.04, T:0.22
Consensus pattern (23 bp):
AAAAACTCTAAAAATTTCAAAAA
Found at i:11272954 original size:21 final size:19
Alignment explanation
Indices: 11272928--11272992 Score: 76
Period size: 20 Copynumber: 3.3 Consensus size: 19
11272918 TTTCAAAAAA
11272928 TTTAAAAATTTTCAGAATTTT
1 TTTAAAAATTTT-AG-ATTTT
* *
11272949 TTTAAAACTTTAAGATTTT
1 TTTAAAAATTTTAGATTTT
*
11272968 TTCAAAAAATTTTAGATTTT
1 TT-TAAAAATTTTAGATTTT
11272988 TTTAA
1 TTTAA
11272993 TTTTATAAAA
Statistics
Matches: 37, Mismatches: 6, Indels: 4
0.79 0.13 0.09
Matches are distributed among these distances:
19 9 0.24
20 18 0.49
21 10 0.27
ACGTcount: A:0.38, C:0.05, G:0.05, T:0.52
Consensus pattern (19 bp):
TTTAAAAATTTTAGATTTT
Found at i:11273074 original size:17 final size:16
Alignment explanation
Indices: 11273054--11273105 Score: 54
Period size: 17 Copynumber: 3.2 Consensus size: 16
11273044 TTTTTTTAAA
11273054 TTTAAGAAAATTTTATT
1 TTTAA-AAAATTTTATT
*
11273071 TTTATTAAAATTTTCATT
1 TTTA-AAAAATTTT-ATT
11273089 TTT-AAAAATTTT-TT
1 TTTAAAAAATTTTATT
11273103 TTT
1 TTT
11273106 TGCATTGTTA
Statistics
Matches: 31, Mismatches: 2, Indels: 7
0.77 0.05 0.17
Matches are distributed among these distances:
14 5 0.16
16 8 0.26
17 12 0.39
18 6 0.19
ACGTcount: A:0.35, C:0.02, G:0.02, T:0.62
Consensus pattern (16 bp):
TTTAAAAAATTTTATT
Found at i:11273098 original size:16 final size:16
Alignment explanation
Indices: 11273060--11273105 Score: 60
Period size: 16 Copynumber: 2.9 Consensus size: 16
11273050 TAAATTTAAG
11273060 AAAATTTTATTTTTATT
1 AAAATTTTATTTTTA-T
11273077 AAAATTTTCATTTTTA-
1 AAAATTTT-ATTTTTAT
11273093 AAAATTTT-TTTTT
1 AAAATTTTATTTTT
11273106 TGCATTGTTA
Statistics
Matches: 28, Mismatches: 0, Indels: 5
0.85 0.00 0.15
Matches are distributed among these distances:
14 5 0.18
16 8 0.29
17 8 0.29
18 7 0.25
ACGTcount: A:0.35, C:0.02, G:0.00, T:0.63
Consensus pattern (16 bp):
AAAATTTTATTTTTAT
Found at i:11273228 original size:28 final size:27
Alignment explanation
Indices: 11273167--11273239 Score: 101
Period size: 27 Copynumber: 2.7 Consensus size: 27
11273157 TTAATTTGTA
*
11273167 TAATTTTTAAAAAATTTTGGAATCTTT
1 TAATTTTTAAAAAATTTTGAAATCTTT
* *
11273194 TAATTTTAAAAAAATTTTGAAATTTTT
1 TAATTTTTAAAAAATTTTGAAATCTTT
*
11273221 TAATTTTTTAGAAAATTTT
1 TAA-TTTTTAAAAAATTTT
11273240 TTCTAATACT
Statistics
Matches: 40, Mismatches: 5, Indels: 1
0.87 0.11 0.02
Matches are distributed among these distances:
27 27 0.68
28 13 0.32
ACGTcount: A:0.40, C:0.01, G:0.05, T:0.53
Consensus pattern (27 bp):
TAATTTTTAAAAAATTTTGAAATCTTT
Found at i:11277226 original size:21 final size:20
Alignment explanation
Indices: 11277187--11277235 Score: 62
Period size: 21 Copynumber: 2.4 Consensus size: 20
11277177 TTTGTATAAA
* *
11277187 TGTTGCAAAAAATTATATTT
1 TGTTGCAAAAAAATATATTG
*
11277207 TTTTGCAAAATAAATATATTG
1 TGTTGCAAAA-AAATATATTG
11277228 TGTTGCAA
1 TGTTGCAA
11277236 TAGACTAGTA
Statistics
Matches: 24, Mismatches: 4, Indels: 1
0.83 0.14 0.03
Matches are distributed among these distances:
20 9 0.38
21 15 0.62
ACGTcount: A:0.39, C:0.06, G:0.12, T:0.43
Consensus pattern (20 bp):
TGTTGCAAAAAAATATATTG
Found at i:11279105 original size:61 final size:61
Alignment explanation
Indices: 11278980--11279110 Score: 158
Period size: 61 Copynumber: 2.1 Consensus size: 61
11278970 ATTTTAGAAA
* * *
11278980 TTTTATTTTTAAGAAAAATTAATACTTTCAACTTTTCCCTAAAAATATATTTTTTAAGCCT
1 TTTTATTTTCAAGAAAAATTAATACTTTCAACTTTTCCCTAAAAATATATTTTTGAAACCT
* * * **
11279041 TTTTATTTTCAAGAGAAATTGATACTTTCAACTTTCTCCCCT-AAAA-ATGTTTTTGAAATTT
1 TTTTATTTTCAAGAAAAATTAATACTTTCAACTTT-T-CCCTAAAAATATATTTTTGAAACCT
11279102 TTTTATTTT
1 TTTTATTTT
11279111 AGAAACTTTA
Statistics
Matches: 60, Mismatches: 8, Indels: 4
0.83 0.11 0.06
Matches are distributed among these distances:
61 51 0.85
62 5 0.08
63 4 0.07
ACGTcount: A:0.32, C:0.13, G:0.05, T:0.50
Consensus pattern (61 bp):
TTTTATTTTCAAGAAAAATTAATACTTTCAACTTTTCCCTAAAAATATATTTTTGAAACCT
Found at i:11279181 original size:136 final size:132
Alignment explanation
Indices: 11278861--11279185 Score: 345
Period size: 136 Copynumber: 2.4 Consensus size: 132
11278851 TTTGTACGAA
* * * ***
11278861 AAAAATTGATACTTTCAACTTTTCCTTAAAATA-TTTATTTTGAAATTTTAAGCTCAAGGAAAAT
1 AAAAATTGATACTTTCAATTTTTCCTAAAAATATTTTTTTTTGAAATTTTATTTTCAAGGAAAAT
* * *
11278925 TGATACTTTCAACTTTTTCTTAAAATGCTTTTCTTGATAAATTTTATTTTAGAAATTTTATTTTT
66 TGATACTTTCAACTTTTCCTAAAAATGC-TTTCTTGATAAATTTTATTTTAGAAACTTTATTTTT
11278990 AAG
130 AAG
* * ** ***
11278993 AAAAATTAATACTTTCAACTTTTCCCTAAAAATATATTTTTTAAGCCTTTTTATTTTCAA-GAGA
1 AAAAATTGATACTTTCAA-TTTTTCCTAAAAATAT-TTTTTTTTGAAATTTTATTTTCAAGGA-A
*
11279057 AATTGATACTTTCAACTTTCTCCCCTAAAAATG-TTT-TTGA-AATTTTTTTATTTTAGAAACTT
63 AATTGATACTTTCAACTTT-T--CCTAAAAATGCTTTCTTGATAA--ATTTTATTTTAGAAACTT
11279119 TATTTTTAAG
123 TATTTTTAAG
* *
11279129 GAAAATTGATACTTTCAATTTTTTCCTAAAAATATTTTTTTTTTGGAATTTTATTTT
1 AAAAATTGATACTTTCAA-TTTTTCCTAAAAATA-TTTTTTTTTGAAATTTTATTTT
11279186 AGAAATTTCA
Statistics
Matches: 157, Mismatches: 26, Indels: 16
0.79 0.13 0.08
Matches are distributed among these distances:
132 17 0.11
133 12 0.08
134 4 0.03
135 39 0.25
136 76 0.48
137 1 0.01
138 8 0.05
ACGTcount: A:0.34, C:0.11, G:0.07, T:0.49
Consensus pattern (132 bp):
AAAAATTGATACTTTCAATTTTTCCTAAAAATATTTTTTTTTGAAATTTTATTTTCAAGGAAAAT
TGATACTTTCAACTTTTCCTAAAAATGCTTTCTTGATAAATTTTATTTTAGAAACTTTATTTTTA
AG
Found at i:11279238 original size:15 final size:15
Alignment explanation
Indices: 11279204--11279242 Score: 53
Period size: 15 Copynumber: 2.6 Consensus size: 15
11279194 CAACAAAAAG
11279204 AAAAA-TAAAATAAA
1 AAAAATTAAAATAAA
*
11279218 ACAAAATTAAAATTAA
1 A-AAAATTAAAATAAA
11279234 AAAAATTAA
1 AAAAATTAA
11279243 GGAATACCTA
Statistics
Matches: 22, Mismatches: 1, Indels: 3
0.85 0.04 0.12
Matches are distributed among these distances:
14 1 0.05
15 12 0.55
16 9 0.41
ACGTcount: A:0.77, C:0.03, G:0.00, T:0.21
Consensus pattern (15 bp):
AAAAATTAAAATAAA
Found at i:11280128 original size:19 final size:18
Alignment explanation
Indices: 11280101--11280141 Score: 52
Period size: 18 Copynumber: 2.4 Consensus size: 18
11280091 AGATAAACCC
11280101 AAAAAATA-AT-AATA-A
1 AAAAAATAGATAAATATA
*
11280116 TAAAAATAGATAAATATA
1 AAAAAATAGATAAATATA
11280134 AAAAAATA
1 AAAAAATA
11280142 CATTAATAGA
Statistics
Matches: 21, Mismatches: 2, Indels: 3
0.81 0.08 0.12
Matches are distributed among these distances:
15 7 0.33
16 2 0.10
17 4 0.19
18 8 0.38
ACGTcount: A:0.76, C:0.00, G:0.02, T:0.22
Consensus pattern (18 bp):
AAAAAATAGATAAATATA
Found at i:11280171 original size:25 final size:24
Alignment explanation
Indices: 11280120--11280205 Score: 118
Period size: 25 Copynumber: 3.4 Consensus size: 24
11280110 TAATAATAAA
11280120 AATAGATAAATATAAAAAAATACATT
1 AATAGATAAATATAAAAAAAT--ATT
11280146 AATAGATAAATAGTAAAAAAATATT
1 AATAGATAAATA-TAAAAAAATATT
* *
11280171 AATAGATAAATAATAAATATATATT
1 AATAGATAAAT-ATAAAAAAATATT
11280196 AATAGATAAA
1 AATAGATAAA
11280206 AAATACAAAA
Statistics
Matches: 56, Mismatches: 2, Indels: 5
0.89 0.03 0.08
Matches are distributed among these distances:
25 34 0.61
26 13 0.23
27 9 0.16
ACGTcount: A:0.64, C:0.01, G:0.06, T:0.29
Consensus pattern (24 bp):
AATAGATAAATATAAAAAAATATT
Found at i:11280210 original size:25 final size:25
Alignment explanation
Indices: 11280101--11280215 Score: 106
Period size: 25 Copynumber: 4.5 Consensus size: 25
11280091 AGATAAACCC
* **
11280101 AAAAAATAATAATAATAAAAATAGAT
1 AAAAAATAAAAAT-ATATTAATAGAT
*
11280127 AAATATAA-AAAAATACATTAATAGAT
1 AAA-A-AATAAAAATATATTAATAGAT
* * *
11280153 AAATAGTAAAAAAATATTAATAGAT
1 AAAAAATAAAAATATATTAATAGAT
* *
11280178 AAATAATAAATATATATTAATAGAT
1 AAAAAATAAAAATATATTAATAGAT
11280203 AAAAAATACAAAA
1 AAAAAATA-AAAA
11280216 AAATGGGTCA
Statistics
Matches: 72, Mismatches: 13, Indels: 8
0.77 0.14 0.09
Matches are distributed among these distances:
24 1 0.01
25 45 0.62
26 18 0.25
27 6 0.08
28 2 0.03
ACGTcount: A:0.68, C:0.02, G:0.04, T:0.26
Consensus pattern (25 bp):
AAAAAATAAAAATATATTAATAGAT
Found at i:11280216 original size:50 final size:51
Alignment explanation
Indices: 11280101--11280217 Score: 137
Period size: 51 Copynumber: 2.3 Consensus size: 51
11280091 AGATAAACCC
* **
11280101 AAAAAATAATAATAATAAAAATAGATAAATATAAAAAAATACATTAATAGAT
1 AAAAAATAA-AAAAATATTAATAGATAAATATAAAAAAATACATTAATAGAT
* * * * *
11280153 AAATAGTAAAAAAATATTAATAGATAAATA-ATAAATATATATTAATAGAT
1 AAAAAATAAAAAAATATTAATAGATAAATATAAAAAAATACATTAATAGAT
11280203 AAAAAATACAAAAAA
1 AAAAAATA-AAAAAA
11280218 ATGGGTCATC
Statistics
Matches: 54, Mismatches: 10, Indels: 3
0.81 0.15 0.04
Matches are distributed among these distances:
50 23 0.43
51 24 0.44
52 7 0.13
ACGTcount: A:0.68, C:0.02, G:0.04, T:0.26
Consensus pattern (51 bp):
AAAAAATAAAAAAATATTAATAGATAAATATAAAAAAATACATTAATAGAT
Found at i:11280387 original size:18 final size:16
Alignment explanation
Indices: 11280364--11280409 Score: 58
Period size: 16 Copynumber: 2.8 Consensus size: 16
11280354 CAACTCGACA
11280364 CTTTTTTCTTTTTCTGTT-
1 CTTTTTT-TTTTT-T-TTG
11280382 CTTTTTTTTTTTTTTG
1 CTTTTTTTTTTTTTTG
11280398 CTTTTTTTTTTT
1 CTTTTTTTTTTT
11280410 GGTTAAAATT
Statistics
Matches: 27, Mismatches: 0, Indels: 4
0.87 0.00 0.13
Matches are distributed among these distances:
15 2 0.07
16 13 0.48
17 5 0.19
18 7 0.26
ACGTcount: A:0.00, C:0.11, G:0.04, T:0.85
Consensus pattern (16 bp):
CTTTTTTTTTTTTTTG
Found at i:11280389 original size:19 final size:18
Alignment explanation
Indices: 11280365--11280409 Score: 56
Period size: 18 Copynumber: 2.5 Consensus size: 18
11280355 AACTCGACAC
*
11280365 TTTTTTCTTTTTCTG-TT
1 TTTTTTTTTTTTCTGCTT
*
11280382 CTTTTTTTTTTTTTTGCTT
1 -TTTTTTTTTTTTCTGCTT
11280401 TTTTTTTTT
1 TTTTTTTTT
11280410 GGTTAAAATT
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
18 22 0.92
19 2 0.08
ACGTcount: A:0.00, C:0.09, G:0.04, T:0.87
Consensus pattern (18 bp):
TTTTTTTTTTTTCTGCTT
Found at i:11280402 original size:13 final size:13
Alignment explanation
Indices: 11280386--11280410 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
11280376 TCTGTTCTTT
11280386 TTTTTTTTTTTGC
1 TTTTTTTTTTTGC
11280399 TTTTTTTTTTTG
1 TTTTTTTTTTTG
11280411 GTTAAAATTT
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.00, C:0.04, G:0.08, T:0.88
Consensus pattern (13 bp):
TTTTTTTTTTTGC
Found at i:11280673 original size:16 final size:19
Alignment explanation
Indices: 11280652--11280700 Score: 59
Period size: 16 Copynumber: 2.7 Consensus size: 19
11280642 TTTTATGTAT
11280652 TGTATTATTTATT-AT-TA
1 TGTATTATTTATTAATATA
*
11280669 T-TATTATGTATTAATATA
1 TGTATTATTTATTAATATA
11280687 TGTATATATTTATT
1 TGTAT-TATTTATT
11280701 TATTTATTTT
Statistics
Matches: 26, Mismatches: 2, Indels: 5
0.79 0.06 0.15
Matches are distributed among these distances:
16 10 0.38
17 3 0.12
18 3 0.12
19 3 0.12
20 7 0.27
ACGTcount: A:0.33, C:0.00, G:0.06, T:0.61
Consensus pattern (19 bp):
TGTATTATTTATTAATATA
Found at i:11281930 original size:60 final size:58
Alignment explanation
Indices: 11281846--11282558 Score: 799
Period size: 59 Copynumber: 11.9 Consensus size: 58
11281836 TAAAAATAAA
* *
11281846 AAATTCCAAAAAAATATATTTTTAGGGAAAAGTTGAAAGTATCAATTTTCCTCAGAAAT
1 AAATTTCAAAAAAAAATATTTTTAGGGAAAAGTTGAAAGTATCAATTTTCCT-AGAAAT
* **
11281905 AAATTTCAAAAAAAAAATATTTTTAGGGAAAAGTTGAAAATATTTATTTTCCTCAGAAAT
1 AAATTTC-AAAAAAAAATATTTTTAGGGAAAAGTTGAAAGTATCAATTTTCCT-AGAAAT
11281965 AAATTTCAAAAAAAAATATTTTTAGGGAAAAGTTGAAAGTATCAATTTTCCTTA-AGAAT
1 AAATTTCAAAAAAAAATATTTTTAGGGAAAAGTTGAAAGTATCAATTTTCC-TAGA-AAT
* * *
11282024 AAATTTC--CAAAAAATATTTTTGGGGAAAAGTTGAAAGTATCAATTTTTCTTAAAAGAAAAAT
1 AAATTTCAAAAAAAAATATTTTTAGGGAAAAGTTGAAAGTATCAA-TTTTCCT---AG--AAAT
* *
11282086 AAATTTCCAAAAAAAAATATTTTTGGGGAAAAGTTGAAAGTATCAATTTTCCTTGAAAAT
1 AAATTT-CAAAAAAAAATATTTTTAGGGAAAAGTTGAAAGTATCAATTTTCCTAG-AAAT
**
11282146 CAAAATTTC---AAAAAATATTTTTAGGGAAAAGTTGAAAGTATTTATTTTCCTCAGAAAT
1 --AAATTTCAAAAAAAAATATTTTTAGGGAAAAGTTGAAAGTATCAATTTTCCT-AGAAAT
11282204 AAATTTCAAAAAAAAATATTTTTAGGGAAAAGTTGAAAGTATCAATTTTCCTTA-AGAAT
1 AAATTTCAAAAAAAAATATTTTTAGGGAAAAGTTGAAAGTATCAATTTTCC-TAGA-AAT
* *
11282263 AAATTTC--CAAAAAATATTTTT-GGAAAAAAGTTGAAAGTATCAATTTTCCTTAAAAGAAAAAT
1 AAATTTCAAAAAAAAATATTTTTAGG-GAAAAGTTGAAAGTATCAATTTTCC-T---AG--AAAT
* *
11282325 AAATTTCCAAAAAAAAATATTTTTGGGGAAAAGTTGAAAGTATCAATTTTCCTTGAAAAT
1 AAATTT-CAAAAAAAAATATTTTTAGGGAAAAGTTGAAAGTATCAATTTTCCTAG-AAAT
11282385 CAAAATTTC-AAAAAAAATATTTTT-GAGGAAAAGTTGAAAGTATCAATTTTCCTTAGAAAT
1 --AAATTTCAAAAAAAAATATTTTTAG-GGAAAAGTTGAAAGTATCAATTTTCC-TAGAAAT
** *
11282445 AAATTTTCAAAAAAAGGT-TTTTT-GAGGAAAAGTTGAAAGTATCAATTTTCCTTGAAAAT
1 AAA-TTTCAAAAAAAAATATTTTTAG-GGAAAAGTTGAAAGTATCAATTTTCCTAG-AAAT
* *
11282504 CGAAATTTC-CAAAAAAATATTTTTGGGGAAAAGTTGAAAGTATCAATTTTTCCTA
1 --AAATTTCAAAAAAAAATATTTTTAGGGAAAAGTTGAAAGTATCAA-TTTTCCTA
11282559 CAAAAAAAAA
Statistics
Matches: 577, Mismatches: 33, Indels: 86
0.83 0.05 0.12
Matches are distributed among these distances:
56 9 0.02
57 74 0.13
58 55 0.10
59 157 0.27
60 150 0.26
61 17 0.03
62 30 0.05
63 4 0.01
64 7 0.01
65 72 0.12
66 2 0.00
ACGTcount: A:0.46, C:0.08, G:0.12, T:0.34
Consensus pattern (58 bp):
AAATTTCAAAAAAAAATATTTTTAGGGAAAAGTTGAAAGTATCAATTTTCCTAGAAAT
Found at i:11282248 original size:239 final size:240
Alignment explanation
Indices: 11281825--11282569 Score: 1146
Period size: 239 Copynumber: 3.1 Consensus size: 240
11281815 TATTATTTTA
* * * * *
11281825 TTTTCTTTAAATAAAAATAAAAAATTCCAAAAAAATATATTTTTAGGGAAAAGTTGAAAGTATCA
1 TTTTCTTAAAAGAAAAAT--AAATTTCCAAAAAAAAATATTTTTGGGGAAAAGTTGAAAGTATCA
* *
11281890 ATTTTCC-TCAGAAAT--AAATTTCAAAAAAAAAATATTTTTAGGGAAAAGTTGAAAATATTTAT
64 ATTTTCCTTGA-AAATCAAAATTTC---AAAAAAATATTTTTAGGGAAAAGTTGAAAGTATTTAT
11281952 TTTCCTCAGAAATAAATTTCAAAAAAAAATATTTTTAGGGAAAAGTTGAAAGTATCAATTTTCCT
125 TTTCCTCAGAAATAAATTTCAAAAAAAAATATTTTTAGGGAAAAGTTGAAAGTATCAATTTTCCT
11282017 TAAGAATAAATTTCCAAAAAATATTTTTGGGGAAAAGTTGAAAGTATCAAT
190 TAAGAATAAATTTCCAAAAAATATTTTTGGGGAAAAGTTGAAAGTATCAAT
11282068 TTTTCTTAAAAGAAAAATAAATTTCCAAAAAAAAATATTTTTGGGGAAAAGTTGAAAGTATCAAT
1 TTTTCTTAAAAGAAAAATAAATTTCCAAAAAAAAATATTTTTGGGGAAAAGTTGAAAGTATCAAT
11282133 TTTCCTTGAAAATCAAAATTTC-AAAAAATATTTTTAGGGAAAAGTTGAAAGTATTTATTTTCCT
66 TTTCCTTGAAAATCAAAATTTCAAAAAAATATTTTTAGGGAAAAGTTGAAAGTATTTATTTTCCT
11282197 CAGAAATAAATTTCAAAAAAAAATATTTTTAGGGAAAAGTTGAAAGTATCAATTTTCCTTAAGAA
131 CAGAAATAAATTTCAAAAAAAAATATTTTTAGGGAAAAGTTGAAAGTATCAATTTTCCTTAAGAA
**
11282262 TAAATTTCCAAAAAATATTTTTGGAAAAAAGTTGAAAGTATCAAT
196 TAAATTTCCAAAAAATATTTTTGGGGAAAAGTTGAAAGTATCAAT
*
11282307 TTTCCTTAAAAGAAAAATAAATTTCCAAAAAAAAATATTTTTGGGGAAAAGTTGAAAGTATCAAT
1 TTTTCTTAAAAGAAAAATAAATTTCCAAAAAAAAATATTTTTGGGGAAAAGTTGAAAGTATCAAT
**
11282372 TTTCCTTGAAAATCAAAATTTCAAAAAAAATATTTTT-GAGGAAAAGTTGAAAGTATCAATTTTC
66 TTTCCTTGAAAATCAAAATTTC-AAAAAAATATTTTTAG-GGAAAAGTTGAAAGTATTTATTTTC
* **
11282436 CTTAGAAATAAATTTTCAAAAAAAGGT-TTTTT-GAGGAAAAGTTGAAAGTATCAATTTTCCTTG
129 CTCAGAAATAAA-TTTCAAAAAAAAATATTTTTAG-GGAAAAGTTGAAAGTATCAATTTTCCTT-
11282499 AA-AATCGAAATTTCCAAAAAAATATTTTTGGGGAAAAGTTGAAAGTATCAAT
191 AAGAAT--AAATTTCC-AAAAAATATTTTTGGGGAAAAGTTGAAAGTATCAAT
* *
11282551 TTTTCCTACAAAAAAAAAT
1 TTTTCTTA-AAAGAAAAAT
11282570 CATTCTTTCC
Statistics
Matches: 469, Mismatches: 20, Indels: 24
0.91 0.04 0.05
Matches are distributed among these distances:
239 235 0.50
240 2 0.00
241 136 0.29
242 16 0.03
243 31 0.07
244 40 0.09
245 9 0.02
ACGTcount: A:0.46, C:0.08, G:0.12, T:0.34
Consensus pattern (240 bp):
TTTTCTTAAAAGAAAAATAAATTTCCAAAAAAAAATATTTTTGGGGAAAAGTTGAAAGTATCAAT
TTTCCTTGAAAATCAAAATTTCAAAAAAATATTTTTAGGGAAAAGTTGAAAGTATTTATTTTCCT
CAGAAATAAATTTCAAAAAAAAATATTTTTAGGGAAAAGTTGAAAGTATCAATTTTCCTTAAGAA
TAAATTTCCAAAAAATATTTTTGGGGAAAAGTTGAAAGTATCAAT
Found at i:11290946 original size:36 final size:38
Alignment explanation
Indices: 11290896--11290967 Score: 121
Period size: 37 Copynumber: 1.9 Consensus size: 38
11290886 CTATGCTTGA
*
11290896 AAAAAATGACAAAAATGGAAAAATG-AAAATGAAAATG
1 AAAAAATGACAAAAATGAAAAAATGAAAAATGAAAATG
11290933 AAAAAATGA-AAAAATGAAAAAATGAAAAATGAAAA
1 AAAAAATGACAAAAATGAAAAAATGAAAAATGAAAA
11290968 AAATGAAATG
Statistics
Matches: 33, Mismatches: 1, Indels: 2
0.92 0.03 0.06
Matches are distributed among these distances:
36 14 0.42
37 19 0.58
ACGTcount: A:0.72, C:0.01, G:0.14, T:0.12
Consensus pattern (38 bp):
AAAAAATGACAAAAATGAAAAAATGAAAAATGAAAATG
Found at i:11290969 original size:8 final size:8
Alignment explanation
Indices: 11290896--11290986 Score: 102
Period size: 8 Copynumber: 11.8 Consensus size: 8
11290886 CTATGCTTGA
11290896 AAAAAATG
1 AAAAAATG
11290904 ACAAAAATG
1 A-AAAAATG
*
11290913 GAAAAATG
1 AAAAAATG
11290921 --AAAATG
1 AAAAAATG
11290927 --AAAATG
1 AAAAAATG
11290933 AAAAAATG
1 AAAAAATG
11290941 AAAAAATG
1 AAAAAATG
11290949 AAAAAATG
1 AAAAAATG
11290957 -AAAAATG
1 AAAAAATG
11290964 AAAAAAATG
1 -AAAAAATG
**
11290973 AAATGATG
1 AAAAAATG
11290981 AAAAAA
1 AAAAAA
11290987 GGTGAACAAG
Statistics
Matches: 73, Mismatches: 5, Indels: 10
0.83 0.06 0.11
Matches are distributed among these distances:
6 12 0.16
7 7 0.10
8 40 0.55
9 14 0.19
ACGTcount: A:0.71, C:0.01, G:0.14, T:0.13
Consensus pattern (8 bp):
AAAAAATG
Found at i:11292138 original size:43 final size:41
Alignment explanation
Indices: 11292012--11292666 Score: 830
Period size: 42 Copynumber: 16.0 Consensus size: 41
11292002 GTCTAGGAGT
*
11292012 ATTTACTTTTTCAAAGTTCGTTGCCTCTGTTTAGAGGAGCA
1 ATTTACTTTTCCAAAGTTCGTTGCCTCTGTTTAGAGGAGCA
11292053 ATTTACTTTTCCCAAAGTTCGTTGCCTCTGTTTAGAGGAGCA
1 ATTTACTTTT-CCAAAGTTCGTTGCCTCTGTTTAGAGGAGCA
*
11292095 ATTTACTTTTCCCAAAG-TCGTGGTACCTCTGTTTAGAGGAGCA
1 ATTTACTTTT-CCAAAGTTCGT--TGCCTCTGTTTAGAGGAGCA
*
11292138 ATTTACTTTTCCCAAAG-TCGTGGTACCTCTGTTTAGAGGAGCA
1 ATTTACTTTT-CCAAAGTTCGT--TGCCTCTGTTTAGAGGAGCA
* * * *
11292181 ATTCACTTTTCAAAAG-TCATGGTACCTCTGTTTAGAGGAGCA
1 ATTTACTTTTCCAAAGTTC--GTTGCCTCTGTTTAGAGGAGCA
* *
11292223 ATTTACTTTTCC-AAGTTCGTTACCTCTGTTTAAAGGAGCA
1 ATTTACTTTTCCAAAGTTCGTTGCCTCTGTTTAGAGGAGCA
*
11292263 ATTTACTTTTTTCAAAGTTCGTTGCCTCTGTTTAGAGGAGCA
1 ATTTAC-TTTTCCAAAGTTCGTTGCCTCTGTTTAGAGGAGCA
11292305 ATTTACTTTT-CAAAGTTCGTTGCCTCTGTTTAGAGGAGCA
1 ATTTACTTTTCCAAAGTTCGTTGCCTCTGTTTAGAGGAGCA
11292345 ATTTAC-TTTCCAAAG-TCGTGGTGCCTCTGTTTAGAGGAGCA
1 ATTTACTTTTCCAAAGTTCGT--TGCCTCTGTTTAGAGGAGCA
*
11292386 ATTTAC-TTT-C-AAGTTCGTTGCCTCTATTTAGAGGAGCA
1 ATTTACTTTTCCAAAGTTCGTTGCCTCTGTTTAGAGGAGCA
11292424 ATTTACTTTT-CAAAG-TCGTGGTGCCTCTGTTTAGAGGAGCA
1 ATTTACTTTTCCAAAGTTCGT--TGCCTCTGTTTAGAGGAGCA
11292465 ATTTAC-TTT-C-AAGTTCGTTGCCTCTGTTTAGAGGAGCA
1 ATTTACTTTTCCAAAGTTCGTTGCCTCTGTTTAGAGGAGCA
*
11292503 ATTTAC-TTTCC-AAGTTCGTTGCCTCTATTTAGAGGAGCA
1 ATTTACTTTTCCAAAGTTCGTTGCCTCTGTTTAGAGGAGCA
*
11292542 ATTTA-TTTTTCAAAGTTTCGTTGCCTCTGTTTAGAGGAGCA
1 ATTTACTTTTCCAAAG-TTCGTTGCCTCTGTTTAGAGGAGCA
* *
11292583 ATTTAC-TTTCCAAAAG-TCATGGTACCTCTGTTTAGAGGAGCA
1 ATTTACTTTTCC-AAAGTTC--GTTGCCTCTGTTTAGAGGAGCA
*
11292625 ATTTACGTTTCTCAAAG-TCGTTGAGCCTCTGTTTAGAGGAGC
1 ATTTACTTTTC-CAAAGTTCGTT--GCCTCTGTTTAGAGGAGC
11292667 TTTGGTAAAA
Statistics
Matches: 563, Mismatches: 22, Indels: 56
0.88 0.03 0.09
Matches are distributed among these distances:
38 54 0.10
39 58 0.10
40 88 0.16
41 115 0.20
42 148 0.26
43 98 0.17
44 2 0.00
ACGTcount: A:0.23, C:0.19, G:0.20, T:0.38
Consensus pattern (41 bp):
ATTTACTTTTCCAAAGTTCGTTGCCTCTGTTTAGAGGAGCA
Found at i:11292425 original size:79 final size:82
Alignment explanation
Indices: 11292012--11292666 Score: 894
Period size: 79 Copynumber: 8.0 Consensus size: 82
11292002 GTCTAGGAGT
*
11292012 ATTTACTTTTTCAAAGTTCGT--TGCCTCTGTTTAGAGGAGCAATTTACTTTTCCCAAAGTTCGT
1 ATTTACTTTTCCAAAG-TCGTGGTGCCTCTGTTTAGAGGAGCAATTTACTTTT--CAAAGTTCGT
11292075 TGCCTCTGTTTAGAGGAGCA
63 TGCCTCTGTTTAGAGGAGCA
*
11292095 ATTTACTTTTCCCAAAGTCGTGGTACCTCTGTTTAGAGGAGCAATTTACTTTTCCCAAAG-TCGT
1 ATTTACTTTT-CCAAAGTCGTGGTGCCTCTGTTTAGAGGAGCAATTTACTTTT--CAAAGTTCGT
*
11292159 GGTACCTCTGTTTAGAGGAGCA
63 --TGCCTCTGTTTAGAGGAGCA
* * * * * *
11292181 ATTCACTTTTCAAAAGTCATGGTACCTCTGTTTAGAGGAGCAATTTACTTTTCCAAGTTCGTTAC
1 ATTTACTTTTCCAAAGTCGTGGTGCCTCTGTTTAGAGGAGCAATTTACTTTTCAAAGTTCGTTGC
*
11292246 CTCTGTTTAAAGGAGCA
66 CTCTGTTTAGAGGAGCA
*
11292263 ATTTACTTTTTTCAAAGTTCGT--TGCCTCTGTTTAGAGGAGCAATTTACTTTTCAAAGTTCGTT
1 ATTTAC-TTTTCCAAAG-TCGTGGTGCCTCTGTTTAGAGGAGCAATTTACTTTTCAAAGTTCGTT
11292326 GCCTCTGTTTAGAGGAGCA
64 GCCTCTGTTTAGAGGAGCA
11292345 ATTTAC-TTTCCAAAGTCGTGGTGCCTCTGTTTAGAGGAGCAATTTAC-TTTC-AAGTTCGTTGC
1 ATTTACTTTTCCAAAGTCGTGGTGCCTCTGTTTAGAGGAGCAATTTACTTTTCAAAGTTCGTTGC
*
11292407 CTCTATTTAGAGGAGCA
66 CTCTGTTTAGAGGAGCA
11292424 ATTTACTTTT-CAAAGTCGTGGTGCCTCTGTTTAGAGGAGCAATTTAC-TTTC-AAGTTCGTTGC
1 ATTTACTTTTCCAAAGTCGTGGTGCCTCTGTTTAGAGGAGCAATTTACTTTTCAAAGTTCGTTGC
11292486 CTCTGTTTAGAGGAGCA
66 CTCTGTTTAGAGGAGCA
* *
11292503 ATTTAC-TTTCC-AAGTTCGT--TGCCTCTATTTAGAGGAGCAATTTATTTTTCAAAGTTTCGTT
1 ATTTACTTTTCCAAAG-TCGTGGTGCCTCTGTTTAGAGGAGCAATTTACTTTTCAAAG-TTCGTT
11292564 GCCTCTGTTTAGAGGAGCA
64 GCCTCTGTTTAGAGGAGCA
* *
11292583 ATTTAC-TTTCCAAAAGTCATGGTACCTCTGTTTAGAGGAGCAATTTACGTTTCTCAAAG-TCGT
1 ATTTACTTTTCC-AAAGTCGTGGTGCCTCTGTTTAGAGGAGCAATTTAC-TTT-TCAAAGTTCGT
11292646 TGAGCCTCTGTTTAGAGGAGC
63 T--GCCTCTGTTTAGAGGAGC
11292667 TTTGGTAAAA
Statistics
Matches: 523, Mismatches: 25, Indels: 46
0.88 0.04 0.08
Matches are distributed among these distances:
77 24 0.05
78 10 0.02
79 119 0.23
80 51 0.10
81 29 0.06
82 89 0.17
83 54 0.10
84 19 0.04
85 100 0.19
86 28 0.05
ACGTcount: A:0.23, C:0.19, G:0.20, T:0.38
Consensus pattern (82 bp):
ATTTACTTTTCCAAAGTCGTGGTGCCTCTGTTTAGAGGAGCAATTTACTTTTCAAAGTTCGTTGC
CTCTGTTTAGAGGAGCA
Done.