Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Chr11
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: 47972186
ACGTcount: A:0.32, C:0.16, G:0.16, T:0.32
Warning! 2603476 characters in sequence are not A, C, G, or T
File 34 of 145
Found at i:12240886 original size:42 final size:41
Alignment explanation
Indices: 12240752--12240887 Score: 130
Period size: 42 Copynumber: 3.2 Consensus size: 41
12240742 TTTCATGAGC
* * * *
12240752 TTCAGTTAACTCATATGAGTTTCCGTTTAACCCTAATGGGT
1 TTCATTTAGCTCATATGAGCTTCCGTTTAACCCTTATGGGT
* * * *
12240793 TTCAGTTCAGCTCCTTTGAGCTTCAGTTTAACTCC-TATGGGTT
1 TTCA-TTTAGCTCATATGAGCTTCCGTTTAAC-CCTTATGGG-T
* * *
12240836 TTCGTTTAGCTCATATGAGCTTCCGTTCAACCCTTATAGGT
1 TTCATTTAGCTCATATGAGCTTCCGTTTAACCCTTATGGGT
12240877 TTCCATTTAGC
1 TT-CATTTAGC
12240888 ATTTGTGTGC
Statistics
Matches: 74, Mismatches: 16, Indels: 9
0.75 0.16 0.09
Matches are distributed among these distances:
41 9 0.12
42 59 0.80
43 6 0.08
ACGTcount: A:0.20, C:0.23, G:0.17, T:0.40
Consensus pattern (41 bp):
TTCATTTAGCTCATATGAGCTTCCGTTTAACCCTTATGGGT
Found at i:12246577 original size:17 final size:17
Alignment explanation
Indices: 12246555--12246588 Score: 68
Period size: 17 Copynumber: 2.0 Consensus size: 17
12246545 TTAAATTAAT
12246555 TTAAATAAAATTTTCAA
1 TTAAATAAAATTTTCAA
12246572 TTAAATAAAATTTTCAA
1 TTAAATAAAATTTTCAA
12246589 CCCAATTCTA
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 17 1.00
ACGTcount: A:0.53, C:0.06, G:0.00, T:0.41
Consensus pattern (17 bp):
TTAAATAAAATTTTCAA
Found at i:12246724 original size:13 final size:13
Alignment explanation
Indices: 12246708--12246734 Score: 54
Period size: 13 Copynumber: 2.1 Consensus size: 13
12246698 TCAATGTGTT
12246708 TTATTATAGTACC
1 TTATTATAGTACC
12246721 TTATTATAGTACC
1 TTATTATAGTACC
12246734 T
1 T
12246735 AGTGTTAACA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 14 1.00
ACGTcount: A:0.30, C:0.15, G:0.07, T:0.48
Consensus pattern (13 bp):
TTATTATAGTACC
Found at i:12247008 original size:11 final size:12
Alignment explanation
Indices: 12246978--12247019 Score: 50
Period size: 11 Copynumber: 3.5 Consensus size: 12
12246968 AGAGTTTTTC
*
12246978 ATTTGAAATAAT
1 ATTTTAAATAAT
*
12246990 AATTTTAATTAAT
1 -ATTTTAAATAAT
12247003 -TTTTAAATAAT
1 ATTTTAAATAAT
12247014 ATTTTA
1 ATTTTA
12247020 TTATTATCCA
Statistics
Matches: 25, Mismatches: 3, Indels: 3
0.81 0.10 0.10
Matches are distributed among these distances:
11 10 0.40
12 5 0.20
13 10 0.40
ACGTcount: A:0.45, C:0.00, G:0.02, T:0.52
Consensus pattern (12 bp):
ATTTTAAATAAT
Found at i:12247631 original size:3 final size:3
Alignment explanation
Indices: 12247623--12247653 Score: 62
Period size: 3 Copynumber: 10.3 Consensus size: 3
12247613 TTCAAACTAG
12247623 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA T
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA T
12247654 AAATATTCCT
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:12262607 original size:31 final size:31
Alignment explanation
Indices: 12262580--12262650 Score: 115
Period size: 31 Copynumber: 2.3 Consensus size: 31
12262570 GATGGTAAGT
12262580 CATCGTTGTCGGACAATTCGGGGTGGTAAAC
1 CATCGTTGTCGGACAATTCGGGGTGGTAAAC
* *
12262611 CATCGTTGTTGGGCAATTCGGGGTGGTAAAC
1 CATCGTTGTCGGACAATTCGGGGTGGTAAAC
*
12262642 CATCATTGT
1 CATCGTTGT
12262651 TAGGCAATCT
Statistics
Matches: 37, Mismatches: 3, Indels: 0
0.93 0.08 0.00
Matches are distributed among these distances:
31 37 1.00
ACGTcount: A:0.21, C:0.18, G:0.31, T:0.30
Consensus pattern (31 bp):
CATCGTTGTCGGACAATTCGGGGTGGTAAAC
Found at i:12262651 original size:31 final size:31
Alignment explanation
Indices: 12262593--12262658 Score: 114
Period size: 31 Copynumber: 2.1 Consensus size: 31
12262583 CGTTGTCGGA
* *
12262593 CAATTCGGGGTGGTAAACCATCGTTGTTGGG
1 CAATTCGGGGTGGTAAACCATCATTGTTAGG
12262624 CAATTCGGGGTGGTAAACCATCATTGTTAGG
1 CAATTCGGGGTGGTAAACCATCATTGTTAGG
12262655 CAAT
1 CAAT
12262659 CTGAAGTGGT
Statistics
Matches: 33, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
31 33 1.00
ACGTcount: A:0.24, C:0.17, G:0.30, T:0.29
Consensus pattern (31 bp):
CAATTCGGGGTGGTAAACCATCATTGTTAGG
Found at i:12262668 original size:31 final size:31
Alignment explanation
Indices: 12262593--12262668 Score: 82
Period size: 31 Copynumber: 2.5 Consensus size: 31
12262583 CGTTGTCGGA
** * *
12262593 CAATTCGGGGTGGTAAACCATCGTTGTTGGG
1 CAATTCGAAGTGGTAAACCATCATTGTTAGG
**
12262624 CAATTCGGGGTGGTAAACCATCATTGTTAGG
1 CAATTCGAAGTGGTAAACCATCATTGTTAGG
12262655 CAA-TCTGAAGTGGT
1 CAATTC-GAAGTGGT
12262669 GAGTCATCAT
Statistics
Matches: 40, Mismatches: 4, Indels: 2
0.87 0.09 0.04
Matches are distributed among these distances:
30 2 0.05
31 38 0.95
ACGTcount: A:0.24, C:0.16, G:0.32, T:0.29
Consensus pattern (31 bp):
CAATTCGAAGTGGTAAACCATCATTGTTAGG
Found at i:12264803 original size:33 final size:33
Alignment explanation
Indices: 12264766--12264830 Score: 80
Period size: 33 Copynumber: 2.0 Consensus size: 33
12264756 ATTTAAAATA
*
12264766 TATATT-ATATATTATGTTTACTTA-AATAATAAG
1 TATATTGATATATTAT-ATTA-TTATAATAATAAG
*
12264799 TATATTGTTATATTATATTATTATAATAATAA
1 TATATTGATATATTATATTATTATAATAATAA
12264831 TAAACCAAGA
Statistics
Matches: 28, Mismatches: 2, Indels: 4
0.82 0.06 0.12
Matches are distributed among these distances:
32 3 0.11
33 17 0.61
34 8 0.29
ACGTcount: A:0.43, C:0.02, G:0.05, T:0.51
Consensus pattern (33 bp):
TATATTGATATATTATATTATTATAATAATAAG
Found at i:12271685 original size:36 final size:36
Alignment explanation
Indices: 12271638--12271711 Score: 148
Period size: 36 Copynumber: 2.1 Consensus size: 36
12271628 TGGTAACCAT
12271638 TACATCTTCCTTAATGAAAAGTCAATTACTATAAAA
1 TACATCTTCCTTAATGAAAAGTCAATTACTATAAAA
12271674 TACATCTTCCTTAATGAAAAGTCAATTACTATAAAA
1 TACATCTTCCTTAATGAAAAGTCAATTACTATAAAA
12271710 TA
1 TA
12271712 GTAATCAAGT
Statistics
Matches: 38, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
36 38 1.00
ACGTcount: A:0.45, C:0.16, G:0.05, T:0.34
Consensus pattern (36 bp):
TACATCTTCCTTAATGAAAAGTCAATTACTATAAAA
Found at i:12273129 original size:22 final size:22
Alignment explanation
Indices: 12273104--12273146 Score: 52
Period size: 22 Copynumber: 2.0 Consensus size: 22
12273094 TATTCAAACA
12273104 ATAACAACAAAAT-AGTAGCAAT
1 ATAACAACAAAATGA-TAGCAAT
* *
12273126 ATAATAACGAAATGATAGCAA
1 ATAACAACAAAATGATAGCAA
12273147 AACAATAAAA
Statistics
Matches: 18, Mismatches: 2, Indels: 2
0.82 0.09 0.09
Matches are distributed among these distances:
22 17 0.94
23 1 0.06
ACGTcount: A:0.58, C:0.12, G:0.12, T:0.19
Consensus pattern (22 bp):
ATAACAACAAAATGATAGCAAT
Found at i:12286737 original size:21 final size:22
Alignment explanation
Indices: 12286703--12286756 Score: 58
Period size: 21 Copynumber: 2.5 Consensus size: 22
12286693 ATATGTGGAT
*
12286703 TATAAAAATA-ACATAAAATAA
1 TATATAAATATACATAAAATAA
***
12286724 TATAT-AATATACATATTTTAA
1 TATATAAATATACATAAAATAA
12286745 TATATAAATATA
1 TATATAAATATA
12286757 TATATATATA
Statistics
Matches: 27, Mismatches: 4, Indels: 3
0.79 0.12 0.09
Matches are distributed among these distances:
20 4 0.15
21 17 0.63
22 6 0.22
ACGTcount: A:0.59, C:0.04, G:0.00, T:0.37
Consensus pattern (22 bp):
TATATAAATATACATAAAATAA
Found at i:12286950 original size:21 final size:21
Alignment explanation
Indices: 12286918--12286958 Score: 50
Period size: 21 Copynumber: 2.0 Consensus size: 21
12286908 AATAAAAACC
12286918 TAACAATAATAACAAA-AATAT
1 TAACAATAATAA-AAATAATAT
12286939 TAACGAAT-ATAAAAATAATA
1 TAAC-AATAATAAAAATAATA
12286959 ATAGTAAAGA
Statistics
Matches: 18, Mismatches: 0, Indels: 4
0.82 0.00 0.18
Matches are distributed among these distances:
20 3 0.17
21 12 0.67
22 3 0.17
ACGTcount: A:0.66, C:0.07, G:0.02, T:0.24
Consensus pattern (21 bp):
TAACAATAATAAAAATAATAT
Found at i:12286960 original size:3 final size:3
Alignment explanation
Indices: 12286947--12287001 Score: 67
Period size: 3 Copynumber: 18.3 Consensus size: 3
12286937 ATTAACGAAT
* * *
12286947 ATA AAA ATA ATA ATA GTA A-A GACA ATA ATA ATA ATA ATA ATA ATA
1 ATA ATA ATA ATA ATA ATA ATA -ATA ATA ATA ATA ATA ATA ATA ATA
12286992 ATA ATA ATA A
1 ATA ATA ATA A
12287002 AATTGCCCAG
Statistics
Matches: 45, Mismatches: 5, Indels: 4
0.83 0.09 0.07
Matches are distributed among these distances:
2 1 0.02
3 43 0.96
4 1 0.02
ACGTcount: A:0.67, C:0.02, G:0.04, T:0.27
Consensus pattern (3 bp):
ATA
Found at i:12288715 original size:46 final size:45
Alignment explanation
Indices: 12288589--12288798 Score: 179
Period size: 44 Copynumber: 4.8 Consensus size: 45
12288579 AGATAAGATC
* * *
12288589 CTTCAATCCGCTCCACTGTAATCTCAGGGAAATAGGAT-TACTAT
1 CTTCGATCTGCTCCACTGTAATCTCAGGGAAATAAGATCTACTAT
* * * *
12288633 CTTTGATCTACTCCGCTGTAATCTCAGGGAGATAAGATCTGCACT-T
1 CTTCGATCTGCTCCACTGTAATCTCAGGGAAATAAGATCT--ACTAT
*
12288679 CTTCGGTCTGCTCCACTGTAATCTCAGGGAAATAAGATC--C--T
1 CTTCGATCTGCTCCACTGTAATCTCAGGGAAATAAGATCTACTAT
* ** *
12288720 -TT-AATCCACTCCACTGTAATCTCA-GGAAGATAGGAT-TACTAT
1 CTTCGATCTGCTCCACTGTAATCTCAGGGAA-ATAAGATCTACTAT
* * * *
12288762 CTTTGGTCTGCTCCGCTGTAATCTCAGGGAGATAAGA
1 CTTCGATCTGCTCCACTGTAATCTCAGGGAAATAAGA
12288799 CTTGACACGA
Statistics
Matches: 131, Mismatches: 24, Indels: 22
0.74 0.14 0.12
Matches are distributed among these distances:
38 4 0.03
39 24 0.18
40 3 0.02
41 1 0.01
42 2 0.02
43 2 0.02
44 53 0.40
45 4 0.03
46 35 0.27
47 3 0.02
ACGTcount: A:0.27, C:0.24, G:0.19, T:0.30
Consensus pattern (45 bp):
CTTCGATCTGCTCCACTGTAATCTCAGGGAAATAAGATCTACTAT
Found at i:12288726 original size:129 final size:124
Alignment explanation
Indices: 12288515--12288924 Score: 479
Period size: 129 Copynumber: 3.3 Consensus size: 124
12288505 AATTCTTCGG
* * * * * * * **
12288515 TCTGTTCCACTGTAACCTCAGGGAAATATGACCTGACGCGATCTACTCTGCTGTAACTTCAGAGA
1 TCTGCTCCGCTGTAATCTCAGGGAGATAAGATCTGACACGATCTACTCCACTGTAACTTCAGAGA
* *
12288580 GATAAGATCCTTCAATCCGCTCCACTGTAATCTCAGGGAAATAGGATTACTATCTTTGA
66 AATAAGATCCTTTAATCCGCTCCACTGTAATCTCAGGGAAATAGGATTACTATCTTTGA
* * * *
12288639 TCTACTCCGCTGTAATCTCAGGGAGATAAGATCTGCACTTCTTCGGTCTGCTCCACTGTAA-TCT
1 TCTGCTCCGCTGTAATCTCAGGGAGATAAGATCTG-A---C-ACGATCTACTCCACTGTAACT-T
* *
12288703 CAGGGAAATAAGATCCTTTAATCCACTCCACTGTAATCTCA-GGAAGATAGGATTACTATCTTTG
60 CAGAGAAATAAGATCCTTTAATCCGCTCCACTGTAATCTCAGGGAA-ATAGGATTACTATCTTTG
*
12288767 G
124 A
**
12288768 TCTGCTCCGCTGTAATCTCAGGGAGATAAGA-CTTGACACGATCTACTCTGCTGTAACTTCAGAG
1 TCTGCTCCGCTGTAATCTCAGGGAGATAAGATC-TGACACGATCTACTCCACTGTAACTTCAGAG
* * * * *
12288832 AGATAAGATCCTTTAATCCGCTCCACTGTAA-CTTCAGGGAGATAGGA-TAGTGTCTTCGA
65 AAATAAGATCCTTTAATCCGCTCCACTGTAATC-TCAGGGAAATAGGATTACTATCTTTGA
12288891 TCTGCTCCGCTGTAATCTCAGGGAGATAAGATCT
1 TCTGCTCCGCTGTAATCTCAGGGAGATAAGATCT
12288925 CTGGCTTCAA
Statistics
Matches: 243, Mismatches: 31, Indels: 25
0.81 0.10 0.08
Matches are distributed among these distances:
123 41 0.17
124 86 0.35
125 6 0.02
128 8 0.03
129 102 0.42
ACGTcount: A:0.27, C:0.24, G:0.20, T:0.30
Consensus pattern (124 bp):
TCTGCTCCGCTGTAATCTCAGGGAGATAAGATCTGACACGATCTACTCCACTGTAACTTCAGAGA
AATAAGATCCTTTAATCCGCTCCACTGTAATCTCAGGGAAATAGGATTACTATCTTTGA
Found at i:12300342 original size:19 final size:18
Alignment explanation
Indices: 12300314--12300349 Score: 54
Period size: 19 Copynumber: 1.9 Consensus size: 18
12300304 AAGATACCAA
*
12300314 AATTTAAACCACCACAAC
1 AATTTAAACCACAACAAC
12300332 AATTATAAACCACAACAA
1 AATT-TAAACCACAACAA
12300350 TGACAATTAT
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
18 4 0.25
19 12 0.75
ACGTcount: A:0.56, C:0.28, G:0.00, T:0.17
Consensus pattern (18 bp):
AATTTAAACCACAACAAC
Found at i:12301714 original size:21 final size:21
Alignment explanation
Indices: 12301681--12301722 Score: 52
Period size: 21 Copynumber: 2.0 Consensus size: 21
12301671 AAATAAAAAC
12301681 TTAACAATAATAACAAA-AATA
1 TTAACAATAATAA-AAATAATA
12301702 TTAACGAAT-ATAAAAATAATA
1 TTAAC-AATAATAAAAATAATA
12301723 ATAGTAAAGA
Statistics
Matches: 19, Mismatches: 0, Indels: 4
0.83 0.00 0.17
Matches are distributed among these distances:
20 3 0.16
21 13 0.68
22 3 0.16
ACGTcount: A:0.64, C:0.07, G:0.02, T:0.26
Consensus pattern (21 bp):
TTAACAATAATAAAAATAATA
Found at i:12301724 original size:3 final size:3
Alignment explanation
Indices: 12301711--12301765 Score: 67
Period size: 3 Copynumber: 18.3 Consensus size: 3
12301701 ATTAACGAAT
* * *
12301711 ATA AAA ATA ATA ATA GTA A-A GACA ATA ATA ATA ATA ATA ATA ATA
1 ATA ATA ATA ATA ATA ATA ATA -ATA ATA ATA ATA ATA ATA ATA ATA
12301756 ATA ATA ATA A
1 ATA ATA ATA A
12301766 AATTGCCCAG
Statistics
Matches: 45, Mismatches: 5, Indels: 4
0.83 0.09 0.07
Matches are distributed among these distances:
2 1 0.02
3 43 0.96
4 1 0.02
ACGTcount: A:0.67, C:0.02, G:0.04, T:0.27
Consensus pattern (3 bp):
ATA
Found at i:12304212 original size:11 final size:11
Alignment explanation
Indices: 12304181--12304263 Score: 57
Period size: 11 Copynumber: 7.7 Consensus size: 11
12304171 GCCCGGCCCA
*
12304181 AAATTTTTTTA
1 AAATTTTTTTT
**
12304192 AAATACTTTTT
1 AAATTTTTTTT
12304203 AAATTTTTTTT
1 AAATTTTTTTT
*
12304214 -AA---TTTTA
1 AAATTTTTTTT
*
12304221 AAATTTTTTTA
1 AAATTTTTTTT
*
12304232 AAATACTTTTTT
1 AAAT-TTTTTTT
12304244 AAATTTTTATTT
1 AAATTTTT-TTT
*
12304256 TAATTTTT
1 AAATTTTT
12304264 AAAATAATTT
Statistics
Matches: 56, Mismatches: 10, Indels: 11
0.73 0.13 0.14
Matches are distributed among these distances:
7 4 0.07
8 2 0.04
10 2 0.04
11 29 0.52
12 19 0.34
ACGTcount: A:0.34, C:0.02, G:0.00, T:0.64
Consensus pattern (11 bp):
AAATTTTTTTT
Found at i:12304217 original size:10 final size:10
Alignment explanation
Indices: 12304181--12304251 Score: 56
Period size: 10 Copynumber: 6.8 Consensus size: 10
12304171 GCCCGGCCCA
12304181 AAATTTTTTT
1 AAATTTTTTT
*
12304191 AAAATACTTTTT
1 -AAAT-TTTTTT
12304203 AAATTTTTTT
1 AAATTTTTTT
* *
12304213 TAA--TTTTA
1 AAATTTTTTT
12304221 AAATTTTTTT
1 AAATTTTTTT
12304231 AAAATACTTTTTT
1 -AAAT--TTTTTT
12304244 AAATTTTT
1 AAATTTTT
12304252 ATTTTAATTT
Statistics
Matches: 48, Mismatches: 6, Indels: 13
0.72 0.09 0.19
Matches are distributed among these distances:
8 6 0.12
10 15 0.31
11 12 0.25
12 9 0.19
13 6 0.12
ACGTcount: A:0.35, C:0.03, G:0.00, T:0.62
Consensus pattern (10 bp):
AAATTTTTTT
Found at i:12304221 original size:17 final size:17
Alignment explanation
Indices: 12304199--12304232 Score: 59
Period size: 17 Copynumber: 2.0 Consensus size: 17
12304189 TTAAAATACT
*
12304199 TTTTAAATTTTTTTTAA
1 TTTTAAAATTTTTTTAA
12304216 TTTTAAAATTTTTTTAA
1 TTTTAAAATTTTTTTAA
12304233 AATACTTTTT
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
17 16 1.00
ACGTcount: A:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (17 bp):
TTTTAAAATTTTTTTAA
Found at i:12304227 original size:40 final size:44
Alignment explanation
Indices: 12304180--12304268 Score: 150
Period size: 40 Copynumber: 2.1 Consensus size: 44
12304170 GGCCCGGCCC
12304180 AAAATTTTTTTAAAATAC-TTTTTAAA-TTTT-TTTTAA-TTTT
1 AAAATTTTTTTAAAATACTTTTTTAAATTTTTATTTTAATTTTT
12304220 AAAATTTTTTTAAAATACTTTTTTAAATTTTTATTTTAATTTTT
1 AAAATTTTTTTAAAATACTTTTTTAAATTTTTATTTTAATTTTT
12304264 AAAAT
1 AAAAT
12304269 AATTTTTTGG
Statistics
Matches: 45, Mismatches: 0, Indels: 4
0.92 0.00 0.08
Matches are distributed among these distances:
40 18 0.40
41 8 0.18
42 4 0.09
43 6 0.13
44 9 0.20
ACGTcount: A:0.37, C:0.02, G:0.00, T:0.61
Consensus pattern (44 bp):
AAAATTTTTTTAAAATACTTTTTTAAATTTTTATTTTAATTTTT
Found at i:12310216 original size:7 final size:7
Alignment explanation
Indices: 12310206--12310232 Score: 54
Period size: 7 Copynumber: 3.9 Consensus size: 7
12310196 GGAAATAAGA
12310206 AAAAAAT
1 AAAAAAT
12310213 AAAAAAT
1 AAAAAAT
12310220 AAAAAAT
1 AAAAAAT
12310227 AAAAAA
1 AAAAAA
12310233 AAGGATAAAG
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 20 1.00
ACGTcount: A:0.89, C:0.00, G:0.00, T:0.11
Consensus pattern (7 bp):
AAAAAAT
Found at i:12316211 original size:40 final size:40
Alignment explanation
Indices: 12316045--12316225 Score: 105
Period size: 40 Copynumber: 4.4 Consensus size: 40
12316035 ATAGTCCTCC
*
12316045 AACTTTTTTTTTATATAATTAATTTATATGTTCTAATTTT
1 AACTTTTTTTATATATAATTAATTTATATGTTCTAATTTT
* * * ** * *
12316085 AACTATTTTTAAATATATTTAGGTTACATAGTTTTAATATTT
1 AACTTTTTTTATATATAATTAATTTATAT-GTTCTAAT-TTT
* ** * * * * * **
12316127 ACAAGATTTCATAATATTTATTTTATTTA-AT-TTTTAAAAATT
1 --AA-CTTTTTTTATATATAATTAATTTATATGTTCT-AATTTT
*
12316169 AACTTTTTTTTTATATAATTAATTTATATGTTCTAATTTT
1 AACTTTTTTTATATATAATTAATTTATATGTTCTAATTTT
* *
12316209 AACTATTTTTAAATATA
1 AACTTTTTTTATATATA
12316226 TTTAGGTTAC
Statistics
Matches: 99, Mismatches: 34, Indels: 16
0.66 0.23 0.11
Matches are distributed among these distances:
39 16 0.16
40 44 0.44
41 10 0.10
42 9 0.09
43 2 0.02
44 4 0.04
45 14 0.14
ACGTcount: A:0.35, C:0.05, G:0.03, T:0.56
Consensus pattern (40 bp):
AACTTTTTTTATATATAATTAATTTATATGTTCTAATTTT
Found at i:12316265 original size:124 final size:125
Alignment explanation
Indices: 12316045--12316295 Score: 495
Period size: 124 Copynumber: 2.0 Consensus size: 125
12316035 ATAGTCCTCC
12316045 AACTTTTTTTTTATATAATTAATTTATATGTTCTAATTTTAACTATTTTTAAATATATTTAGGTT
1 AACTTTTTTTTTATATAATTAATTTATATGTTCTAATTTTAACTATTTTTAAATATATTTAGGTT
12316110 ACATAGTTTTAATATTTACAAGATTTCATAATATTTATTTTATTTAATT-TTTAAAAATT
66 ACATAGTTTTAATATTTACAAGATTTCATAATATTTATTTTATTTAATTATTTAAAAATT
12316169 AACTTTTTTTTTATATAATTAATTTATATGTTCTAATTTTAACTATTTTTAAATATATTTAGGTT
1 AACTTTTTTTTTATATAATTAATTTATATGTTCTAATTTTAACTATTTTTAAATATATTTAGGTT
12316234 ACATAGTTTTAATATTTACAAGATTTCATAATATTTATTTTATTTAATTATTTAAAAATT
66 ACATAGTTTTAATATTTACAAGATTTCATAATATTTATTTTATTTAATTATTTAAAAATT
12316294 AA
1 AA
12316296 TATAATATAA
Statistics
Matches: 126, Mismatches: 0, Indels: 1
0.99 0.00 0.01
Matches are distributed among these distances:
124 114 0.90
125 12 0.10
ACGTcount: A:0.36, C:0.05, G:0.04, T:0.55
Consensus pattern (125 bp):
AACTTTTTTTTTATATAATTAATTTATATGTTCTAATTTTAACTATTTTTAAATATATTTAGGTT
ACATAGTTTTAATATTTACAAGATTTCATAATATTTATTTTATTTAATTATTTAAAAATT
Found at i:12316312 original size:16 final size:17
Alignment explanation
Indices: 12316286--12316319 Score: 52
Period size: 16 Copynumber: 2.1 Consensus size: 17
12316276 TTTAATTATT
12316286 TAAAAATTAATATAATA
1 TAAAAATTAATATAATA
*
12316303 TAAAAA-TAATTTAATA
1 TAAAAATTAATATAATA
12316319 T
1 T
12316320 TTTCTTCTTC
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
16 10 0.62
17 6 0.38
ACGTcount: A:0.62, C:0.00, G:0.00, T:0.38
Consensus pattern (17 bp):
TAAAAATTAATATAATA
Found at i:12327173 original size:14 final size:16
Alignment explanation
Indices: 12327154--12327188 Score: 54
Period size: 16 Copynumber: 2.2 Consensus size: 16
12327144 TTAATACCAC
12327154 ATTTTTTA-ATATATT
1 ATTTTTTACATATATT
*
12327169 ATTTTTTACTTATATT
1 ATTTTTTACATATATT
12327185 ATTT
1 ATTT
12327189 GTAAATCCGT
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
15 8 0.44
16 10 0.56
ACGTcount: A:0.29, C:0.03, G:0.00, T:0.69
Consensus pattern (16 bp):
ATTTTTTACATATATT
Found at i:12330733 original size:3 final size:3
Alignment explanation
Indices: 12330725--12330764 Score: 80
Period size: 3 Copynumber: 13.3 Consensus size: 3
12330715 GTGTATCAGT
12330725 TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC T
1 TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC T
12330765 CTCTAGAGAA
Statistics
Matches: 37, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 37 1.00
ACGTcount: A:0.00, C:0.33, G:0.00, T:0.68
Consensus pattern (3 bp):
TTC
Found at i:12340130 original size:45 final size:45
Alignment explanation
Indices: 12340046--12340131 Score: 127
Period size: 45 Copynumber: 1.9 Consensus size: 45
12340036 GCTATTTGCC
* *
12340046 AAAATGAGTAAGACTATAGCTGAAAGATGCTATGACATCATGATA
1 AAAATGAGTAAGACCATAGCTGAAAGATACTATGACATCATGATA
* * *
12340091 AAAATGAGTAAGACCATGGCTGAAAGATATTATGGCATCAT
1 AAAATGAGTAAGACCATAGCTGAAAGATACTATGACATCAT
12340132 ATGAAATCAT
Statistics
Matches: 36, Mismatches: 5, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
45 36 1.00
ACGTcount: A:0.43, C:0.12, G:0.21, T:0.24
Consensus pattern (45 bp):
AAAATGAGTAAGACCATAGCTGAAAGATACTATGACATCATGATA
Found at i:12343096 original size:23 final size:23
Alignment explanation
Indices: 12343013--12343146 Score: 179
Period size: 23 Copynumber: 6.0 Consensus size: 23
12343003 ACTTGATCAG
*
12343013 TATATGACACAT-AAGTGCCTGA
1 TATACGACACATAAAGTGCCTGA
* ** *
12343035 -A-ATGACACACGAGGTGCCTGA
1 TATACGACACATAAAGTGCCTGA
*
12343056 AATACGACAC--AAAGTGCCTGA
1 TATACGACACATAAAGTGCCTGA
12343077 TATACGACACATAAAGTGCCTGA
1 TATACGACACATAAAGTGCCTGA
12343100 TATACGACACATAAAGTGCCTGA
1 TATACGACACATAAAGTGCCTGA
12343123 TATACGACACATAAAGTGCCTGA
1 TATACGACACATAAAGTGCCTGA
12343146 T
1 T
12343147 CGGCAGAGCC
Statistics
Matches: 101, Mismatches: 6, Indels: 9
0.87 0.05 0.08
Matches are distributed among these distances:
20 8 0.08
21 28 0.28
22 1 0.01
23 64 0.63
ACGTcount: A:0.38, C:0.22, G:0.19, T:0.21
Consensus pattern (23 bp):
TATACGACACATAAAGTGCCTGA
Found at i:12344559 original size:23 final size:23
Alignment explanation
Indices: 12344528--12344574 Score: 67
Period size: 23 Copynumber: 2.0 Consensus size: 23
12344518 CTTAGTTAAT
*
12344528 AAGTATATATATATATTAATTAC
1 AAGTATATACATATATTAATTAC
* *
12344551 AAGTTTATACATATATTTATTAC
1 AAGTATATACATATATTAATTAC
12344574 A
1 A
12344575 CATGTATTTA
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
23 21 1.00
ACGTcount: A:0.45, C:0.06, G:0.04, T:0.45
Consensus pattern (23 bp):
AAGTATATACATATATTAATTAC
Found at i:12345222 original size:41 final size:41
Alignment explanation
Indices: 12345165--12345360 Score: 288
Period size: 41 Copynumber: 4.8 Consensus size: 41
12345155 AACCTTTCGG
* *
12345165 GGCTTTTAGCAGCGTTTTTGAAAAAGCGCTGCTAATGCTCA
1 GGCTTTTAGCGGCGTTTTTGAAAAAGCGCCGCTAATGCTCA
12345206 GGCTTTTAGCGGCGTTTTTGAAAAAGCGCCGCTAATGCTCA
1 GGCTTTTAGCGGCGTTTTTGAAAAAGCGCCGCTAATGCTCA
* *
12345247 GGCTTTTAGCGGCGTTTTTGAAAAAGCGCCACTAATGCTCTG
1 GGCTTTTAGCGGCGTTTTTGAAAAAGCGCCGCTAATGCTC-A
** * *
12345289 GGC-TTTAGCGGCGTTTTCCAAGAAGCGCCGCTAATGCTTAA
1 GGCTTTTAGCGGCGTTTTTGAAAAAGCGCCGCTAATGC-TCA
12345330 GGC-TTTAGCGGCGTTTTTGAAAAAGCGCCGC
1 GGCTTTTAGCGGCGTTTTTGAAAAAGCGCCGC
12345361 AAAAACATTT
Statistics
Matches: 140, Mismatches: 13, Indels: 4
0.89 0.08 0.03
Matches are distributed among these distances:
41 136 0.97
42 4 0.03
ACGTcount: A:0.22, C:0.22, G:0.27, T:0.29
Consensus pattern (41 bp):
GGCTTTTAGCGGCGTTTTTGAAAAAGCGCCGCTAATGCTCA
Found at i:12345830 original size:20 final size:21
Alignment explanation
Indices: 12345809--12345852 Score: 56
Period size: 20 Copynumber: 2.2 Consensus size: 21
12345799 TGATTTAGGG
12345809 GTTAGGGGTTAGGGATTT-GG
1 GTTAGGGGTTAGGGATTTAGG
* *
12345829 GTTAGTGTTTAGGG-TTTAGG
1 GTTAGGGGTTAGGGATTTAGG
12345849 GTTA
1 GTTA
12345853 ATTAGTGTTT
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
19 3 0.14
20 18 0.86
ACGTcount: A:0.16, C:0.00, G:0.43, T:0.41
Consensus pattern (21 bp):
GTTAGGGGTTAGGGATTTAGG
Found at i:12345850 original size:7 final size:7
Alignment explanation
Indices: 12345802--12345851 Score: 50
Period size: 7 Copynumber: 7.3 Consensus size: 7
12345792 AGGGTTGTGA
12345802 TTTAGGG
1 TTTAGGG
*
12345809 GTTAGGG
1 TTTAGGG
*
12345816 GTTAGGG
1 TTTAGGG
12345823 ATTT-GGG
1 -TTTAGGG
*
12345830 -TTAGTG
1 TTTAGGG
12345836 TTTAGGG
1 TTTAGGG
12345843 TTTAGGG
1 TTTAGGG
12345850 TT
1 TT
12345852 AATTAGTGTT
Statistics
Matches: 36, Mismatches: 4, Indels: 6
0.78 0.09 0.13
Matches are distributed among these distances:
5 2 0.06
6 2 0.06
7 30 0.83
8 2 0.06
ACGTcount: A:0.14, C:0.00, G:0.44, T:0.42
Consensus pattern (7 bp):
TTTAGGG
Found at i:12345915 original size:7 final size:7
Alignment explanation
Indices: 12345905--12345972 Score: 55
Period size: 7 Copynumber: 9.7 Consensus size: 7
12345895 TAGTAGTTAT
12345905 GGGTTTG
1 GGGTTTG
*
12345912 GGGTCTG
1 GGGTTTG
*
12345919 GGGTTTA
1 GGGTTTG
12345926 GGGTTTG
1 GGGTTTG
* *
12345933 AGGTTTA
1 GGGTTTG
**
12345940 GGGTTAA
1 GGGTTTG
*
12345947 GGGTTTA
1 GGGTTTG
*
12345954 GGATTTG
1 GGGTTTG
*
12345961 GGGTTAG
1 GGGTTTG
12345968 GGGTT
1 GGGTT
12345973 AGAGGTTAAG
Statistics
Matches: 48, Mismatches: 13, Indels: 0
0.79 0.21 0.00
Matches are distributed among these distances:
7 48 1.00
ACGTcount: A:0.12, C:0.01, G:0.49, T:0.38
Consensus pattern (7 bp):
GGGTTTG
Found at i:12345929 original size:21 final size:21
Alignment explanation
Indices: 12345905--12345969 Score: 69
Period size: 21 Copynumber: 3.1 Consensus size: 21
12345895 TAGTAGTTAT
*
12345905 GGGTTTGGGGTCTGGGGTTTA
1 GGGTTTGGGGTTTGGGGTTTA
* * *
12345926 GGGTTTGAGGTTTAGGGTTAA
1 GGGTTTGGGGTTTGGGGTTTA
* *
12345947 GGGTTTAGGATTTGGGG-TTA
1 GGGTTTGGGGTTTGGGGTTTA
12345967 GGG
1 GGG
12345970 GTTAGAGGTT
Statistics
Matches: 35, Mismatches: 9, Indels: 1
0.78 0.20 0.02
Matches are distributed among these distances:
20 5 0.14
21 30 0.86
ACGTcount: A:0.12, C:0.02, G:0.49, T:0.37
Consensus pattern (21 bp):
GGGTTTGGGGTTTGGGGTTTA
Found at i:12352884 original size:42 final size:43
Alignment explanation
Indices: 12352719--12352900 Score: 303
Period size: 43 Copynumber: 4.3 Consensus size: 43
12352709 ATGGCACTTT
* * *
12352719 TAGCGGCGTTTGTGGGAGAAGCGTCGCTAAAGGTCTTGATCTA
1 TAGCGGCGTTTGTGGGAAAAGCGCCGCTAAAGGTCCTGATCTA
12352762 TAGCGGCGTTTGTGGGAAAAGCGCCGCTAAAGGTCCTGATCTA
1 TAGCGGCGTTTGTGGGAAAAGCGCCGCTAAAGGTCCTGATCTA
* *
12352805 TAGCGGTGTTTGTGGGAAAAGCGCCGCTAAAGATCCTGATCTA
1 TAGCGGCGTTTGTGGGAAAAGCGCCGCTAAAGGTCCTGATCTA
*
12352848 TAGCGGCGTTTGTGGG-AAAGCGCCGCTAAAGGTCCTGATCTT
1 TAGCGGCGTTTGTGGGAAAAGCGCCGCTAAAGGTCCTGATCTA
12352890 TAGCGGCGTTT
1 TAGCGGCGTTT
12352901 ATTTCTAAAA
Statistics
Matches: 131, Mismatches: 8, Indels: 1
0.94 0.06 0.01
Matches are distributed among these distances:
42 35 0.27
43 96 0.73
ACGTcount: A:0.21, C:0.19, G:0.33, T:0.26
Consensus pattern (43 bp):
TAGCGGCGTTTGTGGGAAAAGCGCCGCTAAAGGTCCTGATCTA
Found at i:12352916 original size:86 final size:86
Alignment explanation
Indices: 12352719--12352922 Score: 275
Period size: 86 Copynumber: 2.4 Consensus size: 86
12352709 ATGGCACTTT
* * * * * *
12352719 TAGCGGCGTTTGTGGGAGAAGCGTCGCTAAAGGTCTTGATCTATAGCGGCGTTTGTGGGAAAAGC
1 TAGCGGCGTTTGTGCGAAAAACGCCGCTAAAGATCCTGATCTATAGCGGCGTTTGTGGGAAAAGC
12352784 GCCGCTAAAGGTCCTGATCTA
66 GCCGCTAAAGGTCCTGATCTA
* * *
12352805 TAGCGGTGTTTGTGGGAAAAGCGCCGCTAAAGATCCTGATCTATAGCGGCGTTTGTGGG-AAAGC
1 TAGCGGCGTTTGTGCGAAAAACGCCGCTAAAGATCCTGATCTATAGCGGCGTTTGTGGGAAAAGC
*
12352869 GCCGCTAAAGGTCCTGATCTT
66 GCCGCTAAAGGTCCTGATCTA
* * *
12352890 TAGCGGCGTTTATTTCTAAAAACGCCGCTAAAG
1 TAGCGGCGTTT-GTGCGAAAAACGCCGCTAAAG
12352923 TTAGCGGCAC
Statistics
Matches: 105, Mismatches: 12, Indels: 2
0.88 0.10 0.02
Matches are distributed among these distances:
85 35 0.33
86 70 0.67
ACGTcount: A:0.24, C:0.20, G:0.31, T:0.26
Consensus pattern (86 bp):
TAGCGGCGTTTGTGCGAAAAACGCCGCTAAAGATCCTGATCTATAGCGGCGTTTGTGGGAAAAGC
GCCGCTAAAGGTCCTGATCTA
Found at i:12353271 original size:44 final size:44
Alignment explanation
Indices: 12353185--12353271 Score: 99
Period size: 45 Copynumber: 2.0 Consensus size: 44
12353175 CATTCCTGAA
* *
12353185 AAAAATAAAAAAAGTAACAGAATTAAATGTTTGGATCTGAAAACG
1 AAAAATAAAAAAAG-AACAGAATTAAATGATTGAATCTGAAAACG
12353230 AAAAATAAAATAAA-AACAGAATTAAGAAT-ATTGAATC-GAAAA
1 AAAAATAAAA-AAAGAACAGAATT-A-AATGATTGAATCTGAAAA
12353272 TTAGAGAAAT
Statistics
Matches: 37, Mismatches: 2, Indels: 7
0.80 0.04 0.15
Matches are distributed among these distances:
44 14 0.38
45 17 0.46
46 6 0.16
ACGTcount: A:0.61, C:0.06, G:0.13, T:0.21
Consensus pattern (44 bp):
AAAAATAAAAAAAGAACAGAATTAAATGATTGAATCTGAAAACG
Found at i:12354994 original size:21 final size:21
Alignment explanation
Indices: 12354969--12355011 Score: 59
Period size: 21 Copynumber: 2.0 Consensus size: 21
12354959 CAACGATAGA
*
12354969 AGGAACAACAGCAGCGACATG
1 AGGAACAACAGCAACGACATG
* *
12354990 AGGAACACCCGCAACGACATG
1 AGGAACAACAGCAACGACATG
12355011 A
1 A
12355012 TCACTGGCGG
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
21 19 1.00
ACGTcount: A:0.42, C:0.28, G:0.26, T:0.05
Consensus pattern (21 bp):
AGGAACAACAGCAACGACATG
Found at i:12359742 original size:59 final size:60
Alignment explanation
Indices: 12359617--12359752 Score: 154
Period size: 59 Copynumber: 2.3 Consensus size: 60
12359607 TACGTTAGCC
* * * *
12359617 AGTT-GGTGACCAAAAAAGACAAAATTAAATAGTTAGATGACTATTTTGTAACTTTTCGT
1 AGTTAGGTGACCAAAAAAGACAAAATTAAATAGTTAGATGACCATTTAGTAACTTTCCAT
* *
12359676 AGTTAGGTGACCAAAAAAG--AAATTTATTAATAGTTAGGTGACCA-TTAGTAACTTTCCAT
1 AGTTAGGTGACCAAAAAAGACAAAATTA--AATAGTTAGATGACCATTTAGTAACTTTCCAT
* *
12359735 ATTTAGGTGACAAAAAAA
1 AGTTAGGTGACCAAAAAA
12359753 ATCATAGTTG
Statistics
Matches: 66, Mismatches: 8, Indels: 6
0.82 0.10 0.08
Matches are distributed among these distances:
58 6 0.09
59 32 0.48
60 28 0.42
ACGTcount: A:0.41, C:0.10, G:0.17, T:0.32
Consensus pattern (60 bp):
AGTTAGGTGACCAAAAAAGACAAAATTAAATAGTTAGATGACCATTTAGTAACTTTCCAT
Found at i:12371189 original size:433 final size:433
Alignment explanation
Indices: 12370366--12371223 Score: 1308
Period size: 433 Copynumber: 2.0 Consensus size: 433
12370356 AAAACGAATT
12370366 AGATAATAGTGTCTGGTCACCTGTTAGGGTTGAACCTACACAACAAATAGCCTGGCCAGGGCTTA
1 AGATAATAGTGTCTGGTCACCTGTTAGGGTTGAACCTACACAACAAATAGCCTGGCCAGGGCTTA
* * * *
12370431 ATAAACCTATATTGTCGAGTCCGCAACACATGCTGGAGCTCGGAACATGCAGGCAATAACCCGTA
66 ATAAACCTATATTCTCGAGTCCACAACACATGCTGAAGCTCAGAACATGCAGGCAATAACCCGTA
*
12370496 ACCTGGTATACGGAACTTTTACTAATTTCATCAGGATTTATTTCACATTATAACATAATTCCAAT
131 ACCTGGTATACGGAACTTTTACTAATTTCATCAGGATTTATCTCACATTATAACATAATTCCAAT
*
12370561 CACCAACAATCACCATTACCAAATCAAATATAATACATCAACATAAATAATTTAAATTATATTGT
196 CACCAACAATCACCATTACCAAATCAAATATAATACATCAACATAAATAATTTAAATTATACTGT
* * * * *
12370626 ATGAGCTTACCTGAAAAAACTGTAGTAGTTTAGCTAATAGGGACTAGTCGACAATTTTTCCTTTT
261 ATGAACTGACCTGAAAAAACCGTAGCAGTTTAACTAATAGGGACTAGTCGACAATTTTTCCTTTT
* * * ** * *
12370691 CCTCGTACGTCATTTGATTGTTAAAATTCTTAATCTGAATCATAATTTTTCTCTATTAGCTAATC
326 CCTCGTACGTCATCTAATTATTAAAATTCTTAATCTGAATCATAATTCGTCTCAATTAACTAATC
12370756 CAATTATCATTTAACAACATATAGAAATCATACTACACAAATC
391 CAATTATCATTTAACAACATATAGAAATCATACTACACAAATC
* * *
12370799 AGATAATAGTGTCTGGTCATCC-GTTAGGGTTGAACCTACACAGCAAATAGCTTGGTCAGGGCTT
1 AGATAATAGTGTCTGGTCA-CCTGTTAGGGTTGAACCTACACAACAAATAGCCTGGCCAGGGCTT
* * * * *
12370863 AATAAACTTGTATTCTTGAGTCCACAACACATGCTGAAGCTCAGAACTTGCTGGCAATAACCCGT
65 AATAAACCTATATTCTCGAGTCCACAACACATGCTGAAGCTCAGAACATGCAGGCAATAACCCGT
* * * *
12370928 AACCTTGTATA-TGAGACTTTTACTAATTTCATCGGGATTTATCTCACATTATAACATAATTCTA
130 AACCTGGTATACGGA-ACTTTTACTAATTTCATCAGGATTTATCTCACATTATAACATAATTCCA
* * * *
12370992 ATCACCAACAATCATCATTACCAAATCAAATATAATACATTAGCATAAGTAATTTAAATTATACT
194 ATCACCAACAATCACCATTACCAAATCAAATATAATACATCAACATAAATAATTTAAATTATACT
* * *
12371057 GTATGAACTGACCTGACAAAACCGTAGCGGTTTAACTAATAGTGACTAGTCGACAATTTTTCCTT
259 GTATGAACTGACCTGAAAAAACCGTAGCAGTTTAACTAATAGGGACTAGTCGACAATTTTTCCTT
* * *
12371122 TTCCTCTTACGTCCTCTAATTATTAAAATTCTTGATCT-AAGTCATAATTCGTCTCAATTAACTA
324 TTCCTCGTACGTCATCTAATTATTAAAATTCTTAATCTGAA-TCATAATTCGTCTCAATTAACTA
12371186 ATCCAATTATCATTTAACAACATATAGAAATCATACTA
388 ATCCAATTATCATTTAACAACATATAGAAATCATACTA
12371224 TATCTCAATT
Statistics
Matches: 382, Mismatches: 40, Indels: 6
0.89 0.09 0.01
Matches are distributed among these distances:
432 4 0.01
433 376 0.98
434 2 0.01
ACGTcount: A:0.35, C:0.20, G:0.13, T:0.32
Consensus pattern (433 bp):
AGATAATAGTGTCTGGTCACCTGTTAGGGTTGAACCTACACAACAAATAGCCTGGCCAGGGCTTA
ATAAACCTATATTCTCGAGTCCACAACACATGCTGAAGCTCAGAACATGCAGGCAATAACCCGTA
ACCTGGTATACGGAACTTTTACTAATTTCATCAGGATTTATCTCACATTATAACATAATTCCAAT
CACCAACAATCACCATTACCAAATCAAATATAATACATCAACATAAATAATTTAAATTATACTGT
ATGAACTGACCTGAAAAAACCGTAGCAGTTTAACTAATAGGGACTAGTCGACAATTTTTCCTTTT
CCTCGTACGTCATCTAATTATTAAAATTCTTAATCTGAATCATAATTCGTCTCAATTAACTAATC
CAATTATCATTTAACAACATATAGAAATCATACTACACAAATC
Found at i:12375645 original size:21 final size:21
Alignment explanation
Indices: 12375597--12375651 Score: 58
Period size: 21 Copynumber: 2.6 Consensus size: 21
12375587 AAAATCATTT
* *
12375597 TATTTTAGAGTTTAATGTTTAG
1 TATTTAAG-GTTTAATGTCTAG
12375619 TATTTAAGGTTTAATGTCTA-
1 TATTTAAGGTTTAATGTCTAG
*
12375639 TAGTTTATGGTTT
1 TA-TTTAAGGTTT
12375652 TAGGGTTTAT
Statistics
Matches: 29, Mismatches: 3, Indels: 3
0.83 0.09 0.09
Matches are distributed among these distances:
20 2 0.07
21 20 0.69
22 7 0.24
ACGTcount: A:0.25, C:0.02, G:0.18, T:0.55
Consensus pattern (21 bp):
TATTTAAGGTTTAATGTCTAG
Found at i:12375767 original size:22 final size:22
Alignment explanation
Indices: 12375754--12375859 Score: 76
Period size: 22 Copynumber: 4.8 Consensus size: 22
12375744 AGTGTTTAGA
12375754 GGTTA-GGAGCTTAGGGTTTAAG
1 GGTTATGG-GCTTAGGGTTTAAG
* *
12375776 GGTTATGGGCTTAGGATCT-AG
1 GGTTATGGGCTTAGGGTTTAAG
*
12375797 GGTTA-GTGGCTTAGGATTT-AG
1 GGTTATG-GGCTTAGGGTTTAAG
* ** *
12375818 GGTTTAAGGATTTATGGTTTAAG
1 GG-TTATGGGCTTAGGGTTTAAG
*
12375841 GGTTTATGGGGTTAGGGTT
1 GG-TTATGGGCTTAGGGTT
12375860 ATGGCCTTAG
Statistics
Matches: 68, Mismatches: 11, Indels: 9
0.77 0.12 0.10
Matches are distributed among these distances:
20 1 0.01
21 22 0.32
22 25 0.37
23 20 0.29
ACGTcount: A:0.20, C:0.04, G:0.39, T:0.38
Consensus pattern (22 bp):
GGTTATGGGCTTAGGGTTTAAG
Found at i:12375823 original size:7 final size:7
Alignment explanation
Indices: 12375726--12376073 Score: 136
Period size: 7 Copynumber: 48.7 Consensus size: 7
12375716 ACAATTTGTA
*
12375726 GTTTATG
1 GTTTAGG
*
12375733 GTTTAGT
1 GTTTAGG
*
12375740 GTTTAGT
1 GTTTAGG
12375747 GTTTAGAG
1 GTTTAG-G
12375755 G-TTAGG
1 GTTTAGG
*
12375761 AGCTTAGG
1 -GTTTAGG
12375769 GTTTAAGG
1 GTTT-AGG
12375777 G-TTATGG
1 GTTTA-GG
*
12375784 GCTTAGG
1 GTTTAGG
* *
12375791 ATCTAGG
1 GTTTAGG
12375798 G-TTAGTG
1 GTTTAG-G
*
12375805 GCTTAGG
1 GTTTAGG
*
12375812 ATTTAGG
1 GTTTAGG
12375819 GTTTAAGG
1 GTTT-AGG
* *
12375827 ATTTATG
1 GTTTAGG
12375834 GTTTAAGG
1 GTTT-AGG
12375842 GTTTATGG
1 GTTTA-GG
*
12375850 GGTTAGG
1 GTTTAGG
12375857 G-TTATGG
1 GTTTA-GG
**
12375864 CCTTAGG
1 GTTTAGG
12375871 GTTTAGG
1 GTTTAGG
* *
12375878 GGTTATTG
1 GTTTA-GG
*
12375886 GCTTAGG
1 GTTTAGG
12375893 GTTTAGG
1 GTTTAGG
*
12375900 GTGTA-G
1 GTTTAGG
*
12375906 GTTTATG
1 GTTTAGG
**
12375913 GTTTAAA
1 GTTTAGG
*
12375920 GTTTAAG
1 GTTTAGG
* *
12375927 TTTTATG
1 GTTTAGG
* *
12375934 ATTTAGT
1 GTTTAGG
* *
12375941 GTTAAGA
1 GTTTAGG
*
12375948 GTTTAGT
1 GTTTAGG
*
12375955 GTTTATG
1 GTTTAGG
*
12375962 GTTTAAG
1 GTTTAGG
*
12375969 GTGTA-G
1 GTTTAGG
*
12375975 GTTTATG
1 GTTTAGG
*
12375982 GTTTAGT
1 GTTTAGG
12375989 GTTTAGG
1 GTTTAGG
12375996 GTTTAGG
1 GTTTAGG
*
12376003 GTTTAAGA
1 GTTT-AGG
* *
12376011 GCTTAGA
1 GTTTAGG
*
12376018 TTTTAGGG
1 GTTTA-GG
12376026 GTTATA-G
1 GTT-TAGG
*
12376033 GCTTAGG
1 GTTTAGG
12376040 GTTTATGG
1 GTTTA-GG
12376048 G-TTAGGG
1 GTTTA-GG
* *
12376055 GCTTATG
1 GTTTAGG
12376062 GTTTAGG
1 GTTTAGG
12376069 GTTTA
1 GTTTA
12376074 AATTTTATAT
Statistics
Matches: 259, Mismatches: 60, Indels: 44
0.71 0.17 0.12
Matches are distributed among these distances:
6 20 0.08
7 180 0.69
8 57 0.22
9 2 0.01
ACGTcount: A:0.20, C:0.03, G:0.35, T:0.43
Consensus pattern (7 bp):
GTTTAGG
Found at i:12375827 original size:15 final size:15
Alignment explanation
Indices: 12375809--12375846 Score: 58
Period size: 15 Copynumber: 2.5 Consensus size: 15
12375799 TTAGTGGCTT
12375809 AGGATTTAGGGTTTA
1 AGGATTTAGGGTTTA
*
12375824 AGGATTTATGGTTTA
1 AGGATTTAGGGTTTA
*
12375839 AGGGTTTA
1 AGGATTTA
12375847 TGGGGTTAGG
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
15 21 1.00
ACGTcount: A:0.26, C:0.00, G:0.32, T:0.42
Consensus pattern (15 bp):
AGGATTTAGGGTTTA
Found at i:12375882 original size:22 final size:22
Alignment explanation
Indices: 12375855--12375900 Score: 76
Period size: 22 Copynumber: 2.1 Consensus size: 22
12375845 TATGGGGTTA
12375855 GGGTTA-TGGCCTTAGGGTTTAG
1 GGGTTATTGG-CTTAGGGTTTAG
12375877 GGGTTATTGGCTTAGGGTTTAG
1 GGGTTATTGGCTTAGGGTTTAG
12375899 GG
1 GG
12375901 TGTAGGTTTA
Statistics
Matches: 23, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
22 20 0.87
23 3 0.13
ACGTcount: A:0.13, C:0.07, G:0.43, T:0.37
Consensus pattern (22 bp):
GGGTTATTGGCTTAGGGTTTAG
Found at i:12375980 original size:20 final size:22
Alignment explanation
Indices: 12375955--12376009 Score: 71
Period size: 20 Copynumber: 2.6 Consensus size: 22
12375945 AGAGTTTAGT
12375955 GTTTATGGTTTAAG-GTGTA-G
1 GTTTATGGTTTAAGTGTGTAGG
*
12375975 GTTTATGGTTT-AGTGTTTAGG
1 GTTTATGGTTTAAGTGTGTAGG
*
12375996 GTTTAGGGTTTAAG
1 GTTTATGGTTTAAG
12376010 AGCTTAGATT
Statistics
Matches: 30, Mismatches: 2, Indels: 4
0.83 0.06 0.11
Matches are distributed among these distances:
19 2 0.07
20 15 0.50
21 11 0.37
22 2 0.07
ACGTcount: A:0.18, C:0.00, G:0.35, T:0.47
Consensus pattern (22 bp):
GTTTATGGTTTAAGTGTGTAGG
Found at i:12376022 original size:22 final size:22
Alignment explanation
Indices: 12376002--12376074 Score: 53
Period size: 22 Copynumber: 3.3 Consensus size: 22
12375992 TAGGGTTTAG
*
12376002 GGTTTAAGAGCTTAGATTTTAG
1 GGTTTAAGAGCTTAGAGTTTAG
* *
12376024 GGGTTATAG-GCTTAGGGTTTATG
1 GGTTTA-AGAGCTTAGAGTTTA-G
* *
12376047 GG-TTAGGGGCTTATG-GTTTAG
1 GGTTTAAGAGCTTA-GAGTTTAG
12376068 GGTTTAA
1 GGTTTAA
12376075 ATTTTATATT
Statistics
Matches: 41, Mismatches: 5, Indels: 10
0.73 0.09 0.18
Matches are distributed among these distances:
21 4 0.10
22 31 0.76
23 6 0.15
ACGTcount: A:0.21, C:0.04, G:0.36, T:0.40
Consensus pattern (22 bp):
GGTTTAAGAGCTTAGAGTTTAG
Found at i:12376371 original size:115 final size:115
Alignment explanation
Indices: 12376248--12376722 Score: 691
Period size: 115 Copynumber: 4.1 Consensus size: 115
12376238 AGCATAACGG
* *
12376248 TGTCGTTTTATCTGCATTTTTAGTGGCGTTTTTACTAAAATGCCGCAAAAGGATATGTGTTAGTG
1 TGTCGTTTTATCTGCATTTTTAGTGGCGTTTTTACTAAAACGCCGCAAAAGGATATGTGCTAGTG
* *
12376313 GCGTTTTTACGAAAAACGCCGCAATCATGTTTTAAGTGTTTGCTAGACAT
66 GCGTTTTTACGAAAAACGCCGCAATTATGTTTTAAGTGTTTGCTAAACAT
* **
12376363 TGTCGTTTTATCTGCGTTTTTAGTGGCGTTTTTACTAAAACGCTACAAAAGGATATGTGCTAGTG
1 TGTCGTTTTATCTGCATTTTTAGTGGCGTTTTTACTAAAACGCCGCAAAAGGATATGTGCTAGTG
* * * * *
12376428 GCATTTTTCCGGAAAACGCTGCAATTATGTTTTAAGTGTTTGCTAAACGT
66 GCGTTTTTACGAAAAACGCCGCAATTATGTTTTAAGTGTTTGCTAAACAT
* * *
12376478 TGTAGTTTTATCTG-AGTTTTTAGTGGCGTTTTTACTAAAATGCCGCAAAAGGATATGTGTTAGT
1 TGTCGTTTTATCTGCA-TTTTTAGTGGCGTTTTTACTAAAACGCCGCAAAAGGATATGTGCTAGT
* * * *
12376542 GGCGATTTTACGAAAAACGCCACAATTATGTTTTAAGTGTTTGCCAGACAT
65 GGCGTTTTTACGAAAAACGCCGCAATTATGTTTTAAGTGTTTGCTAAACAT
* * *
12376593 TGTCGTTTTATATACGTTTTTAGTGGCGTTTTTACTAAAACGCCGCAAAAGGATATGTGCTAGTG
1 TGTCGTTTTATCTGCATTTTTAGTGGCGTTTTTACTAAAACGCCGCAAAAGGATATGTGCTAGTG
* * *
12376658 GTGTTTTTACGGAAAACGCCGCAATTATGTTTTAAGTGTTTGCTAAACGT
66 GCGTTTTTACGAAAAACGCCGCAATTATGTTTTAAGTGTTTGCTAAACAT
*
12376708 TGTAGTTTTTATCTG
1 TGTCG-TTTTATCTG
12376723 TGATTTTAGC
Statistics
Matches: 314, Mismatches: 43, Indels: 5
0.87 0.12 0.01
Matches are distributed among these distances:
115 307 0.98
116 7 0.02
ACGTcount: A:0.25, C:0.14, G:0.22, T:0.39
Consensus pattern (115 bp):
TGTCGTTTTATCTGCATTTTTAGTGGCGTTTTTACTAAAACGCCGCAAAAGGATATGTGCTAGTG
GCGTTTTTACGAAAAACGCCGCAATTATGTTTTAAGTGTTTGCTAAACAT
Found at i:12376655 original size:230 final size:230
Alignment explanation
Indices: 12376243--12376731 Score: 809
Period size: 230 Copynumber: 2.1 Consensus size: 230
12376233 AAGATAGCAT
* *
12376243 AACGGTGTCGTTTTATCTGCA-TTTTTAGTGGCGTTTTTACTAAAATGCCGCAAAAGGATATGTG
1 AACGTTGTAGTTTTATCTG-AGTTTTTAGTGGCGTTTTTACTAAAATGCCGCAAAAGGATATGTG
* * *
12376307 TTAGTGGCGTTTTTACGAAAAACGCCGCAATCATGTTTTAAGTGTTTGCTAGACATTGTCGTTTT
65 TTAGTGGCGATTTTACGAAAAACGCCACAATCATGTTTTAAGTGTTTGCCAGACATTGTCGTTTT
* * * *
12376372 ATCTGCGTTTTTAGTGGCGTTTTTACTAAAACGCTACAAAAGGATATGTGCTAGTGGCATTTTTC
130 ATATACGTTTTTAGTGGCGTTTTTACTAAAACGCCACAAAAGGATATGTGCTAGTGGCATTTTTA
*
12376437 CGGAAAACGCTGCAATTATGTTTTAAGTGTTTGCTA
195 CGGAAAACGCCGCAATTATGTTTTAAGTGTTTGCTA
12376473 AACGTTGTAGTTTTATCTGAGTTTTTAGTGGCGTTTTTACTAAAATGCCGCAAAAGGATATGTGT
1 AACGTTGTAGTTTTATCTGAGTTTTTAGTGGCGTTTTTACTAAAATGCCGCAAAAGGATATGTGT
*
12376538 TAGTGGCGATTTTACGAAAAACGCCACAATTATGTTTTAAGTGTTTGCCAGACATTGTCGTTTTA
66 TAGTGGCGATTTTACGAAAAACGCCACAATCATGTTTTAAGTGTTTGCCAGACATTGTCGTTTTA
* **
12376603 TATACGTTTTTAGTGGCGTTTTTACTAAAACGCCGCAAAAGGATATGTGCTAGTGGTGTTTTTAC
131 TATACGTTTTTAGTGGCGTTTTTACTAAAACGCCACAAAAGGATATGTGCTAGTGGCATTTTTAC
12376668 GGAAAACGCCGCAATTATGTTTTAAGTGTTTGCTA
196 GGAAAACGCCGCAATTATGTTTTAAGTGTTTGCTA
* *
12376703 AACGTTGTAGTTTTTATCTGTGATTTTAG
1 AACGTTGTAG-TTTTATCTGAGTTTTTAG
12376732 CTGCGTTAGC
Statistics
Matches: 241, Mismatches: 16, Indels: 3
0.93 0.06 0.01
Matches are distributed among these distances:
229 1 0.00
230 224 0.93
231 16 0.07
ACGTcount: A:0.25, C:0.14, G:0.22, T:0.39
Consensus pattern (230 bp):
AACGTTGTAGTTTTATCTGAGTTTTTAGTGGCGTTTTTACTAAAATGCCGCAAAAGGATATGTGT
TAGTGGCGATTTTACGAAAAACGCCACAATCATGTTTTAAGTGTTTGCCAGACATTGTCGTTTTA
TATACGTTTTTAGTGGCGTTTTTACTAAAACGCCACAAAAGGATATGTGCTAGTGGCATTTTTAC
GGAAAACGCCGCAATTATGTTTTAAGTGTTTGCTA
Found at i:12376863 original size:23 final size:23
Alignment explanation
Indices: 12376835--12376956 Score: 108
Period size: 23 Copynumber: 5.3 Consensus size: 23
12376825 CCCCACTCAG
*
12376835 ATTTCCCCAATTTCATTTCCCTA
1 ATTTCCCCAATTTCATTTCCCCA
*
12376858 ATTT-CCC-ATTTCCTATTCCCCAA
1 ATTTCCCCAATTTCAT-TTCCCC-A
* ** *
12376881 ATTTCTCCGGTTTAATTTCCCCA
1 ATTTCCCCAATTTCATTTCCCCA
12376904 ATTT-CCCAA-TTCATTTTCCCCCA
1 ATTTCCCCAATTTCA-TTT-CCCCA
* *
12376927 ATTTCCCCGATTTCATTTCTCCA
1 ATTTCCCCAATTTCATTTCCCCA
12376950 ATTTCCC
1 ATTTCCC
12376957 AACTGACCTG
Statistics
Matches: 79, Mismatches: 12, Indels: 16
0.74 0.11 0.15
Matches are distributed among these distances:
21 9 0.11
22 13 0.16
23 34 0.43
24 15 0.19
25 8 0.10
ACGTcount: A:0.20, C:0.36, G:0.02, T:0.42
Consensus pattern (23 bp):
ATTTCCCCAATTTCATTTCCCCA
Found at i:12376899 original size:46 final size:45
Alignment explanation
Indices: 12376835--12376958 Score: 140
Period size: 46 Copynumber: 2.7 Consensus size: 45
12376825 CCCCACTCAG
* * * *
12376835 ATTTCCCCAATTTCATTTCCCTAATTTCCCATTTCCTATTCCCCAA
1 ATTTCCCCGATTTAATTTCCC-AATTTCCCAATTCATATTCCCCAA
* * * *
12376881 ATTTCTCCGGTTTAATTTCCCCAATTTCCCAATTCATTTTCCCCCA
1 ATTTCCCCGATTTAATTT-CCCAATTTCCCAATTCATATTCCCCAA
*
12376927 ATTTCCCCGATTTCATTTCTCCAATTTCCCAA
1 ATTTCCCCGATTTAATTTC-CCAATTTCCCAA
12376959 CTGACCTGTC
Statistics
Matches: 65, Mismatches: 11, Indels: 4
0.81 0.14 0.05
Matches are distributed among these distances:
45 1 0.02
46 61 0.94
47 3 0.05
ACGTcount: A:0.21, C:0.35, G:0.02, T:0.41
Consensus pattern (45 bp):
ATTTCCCCGATTTAATTTCCCAATTTCCCAATTCATATTCCCCAA
Found at i:12377060 original size:13 final size:13
Alignment explanation
Indices: 12377042--12377066 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
12377032 CGCCCGCTTC
12377042 CTCTATTCACGGA
1 CTCTATTCACGGA
12377055 CTCTATTCACGG
1 CTCTATTCACGG
12377067 TCAGTTTCGC
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:0.20, C:0.32, G:0.16, T:0.32
Consensus pattern (13 bp):
CTCTATTCACGGA
Found at i:12377129 original size:13 final size:12
Alignment explanation
Indices: 12377096--12377129 Score: 59
Period size: 12 Copynumber: 2.8 Consensus size: 12
12377086 GGTCAAATTC
12377096 TTTTGTTGGCAT
1 TTTTGTTGGCAT
12377108 TTTTGTTGGCAT
1 TTTTGTTGGCAT
12377120 TTTTGCTTGG
1 TTTTG-TTGG
12377130 GCTGTTTGTT
Statistics
Matches: 21, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
12 17 0.81
13 4 0.19
ACGTcount: A:0.06, C:0.09, G:0.26, T:0.59
Consensus pattern (12 bp):
TTTTGTTGGCAT
Found at i:12379189 original size:34 final size:34
Alignment explanation
Indices: 12379128--12379192 Score: 85
Period size: 34 Copynumber: 1.9 Consensus size: 34
12379118 TACTAATAAC
* * *
12379128 TTTTTAAATTTTAAACATAATTCTTTATTTTATA
1 TTTTTAAATATTAAACACAATTATTTATTTTATA
* *
12379162 TTTTTAAATATTATATACAATTATTTATTTT
1 TTTTTAAATATTAAACACAATTATTTATTTT
12379193 TAAATATTAT
Statistics
Matches: 26, Mismatches: 5, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
34 26 1.00
ACGTcount: A:0.35, C:0.05, G:0.00, T:0.60
Consensus pattern (34 bp):
TTTTTAAATATTAAACACAATTATTTATTTTATA
Found at i:12379212 original size:29 final size:26
Alignment explanation
Indices: 12379154--12379221 Score: 82
Period size: 27 Copynumber: 2.5 Consensus size: 26
12379144 ATAATTCTTT
*
12379154 ATTTTATATTTTTAAATATTATATACA
1 ATTTT-TATTTTTAAATATTATATAAA
12379181 ATTATTTATTTTTAAATATTATACATAAA
1 ATT-TTTATTTTTAAATATTAT--ATAAA
*
12379210 ATTTTAATTTTT
1 ATTTTTATTTTT
12379222 TTACATAATT
Statistics
Matches: 36, Mismatches: 2, Indels: 5
0.84 0.05 0.12
Matches are distributed among these distances:
27 19 0.53
28 10 0.28
29 7 0.19
ACGTcount: A:0.40, C:0.03, G:0.00, T:0.57
Consensus pattern (26 bp):
ATTTTTATTTTTAAATATTATATAAA
Found at i:12379433 original size:9 final size:9
Alignment explanation
Indices: 12379316--12379478 Score: 94
Period size: 9 Copynumber: 18.7 Consensus size: 9
12379306 ACTAATTTCC
*
12379316 ACATAACAT
1 ACATAACTT
* *
12379325 GCATAACTC
1 ACATAACTT
*
12379334 ACATAACAT
1 ACATAACTT
12379343 ACATAACTT
1 ACATAACTT
12379352 A-ATAAC-T
1 ACATAACTT
12379359 -C--AACTT
1 ACATAACTT
12379365 ACATAACTT
1 ACATAACTT
12379374 ACATAA--T
1 ACATAACTT
* *
12379381 ACACAAATAT
1 ACATAACT-T
*
12379391 ATATAA--T
1 ACATAACTT
12379398 ATCATAACTT
1 A-CATAACTT
*
12379408 ACATAACTC
1 ACATAACTT
*
12379417 ACACAACTT
1 ACATAACTT
12379426 ACATAACTT
1 ACATAACTT
12379435 A-ATAACTT
1 ACATAACTT
* * *
12379443 ATGTATATCAT
1 A--CATAACTT
12379454 ATCATAACTT
1 A-CATAACTT
12379464 ACATAACTT
1 ACATAACTT
*
12379473 GCATAA
1 ACATAA
12379479 TACATAAATA
Statistics
Matches: 118, Mismatches: 22, Indels: 28
0.70 0.13 0.17
Matches are distributed among these distances:
5 3 0.03
6 1 0.01
7 10 0.08
8 17 0.14
9 68 0.58
10 13 0.11
11 6 0.05
ACGTcount: A:0.47, C:0.21, G:0.02, T:0.31
Consensus pattern (9 bp):
ACATAACTT
Found at i:12379434 original size:61 final size:56
Alignment explanation
Indices: 12379359--12379471 Score: 145
Period size: 56 Copynumber: 1.9 Consensus size: 56
12379349 CTTAATAACT
12379359 CAACTTACATAACTTACATAATACACAAATATATATAATATCATAACTTACATAACTCACA
1 CAACTTACATAAC-T---TAATA-ACAAATATATATAATATCATAACTTACATAACTCACA
** * *
12379420 CAACTTACATAACTTAATAACTTATGTATATCATATCATAACTTACATAACT
1 CAACTTACATAACTTAATAACAAATATATATAATATCATAACTTACATAACT
12379472 TGCATAATAC
Statistics
Matches: 48, Mismatches: 4, Indels: 5
0.84 0.07 0.09
Matches are distributed among these distances:
56 29 0.60
57 5 0.10
60 1 0.02
61 13 0.27
ACGTcount: A:0.46, C:0.20, G:0.01, T:0.33
Consensus pattern (56 bp):
CAACTTACATAACTTAATAACAAATATATATAATATCATAACTTACATAACTCACA
Found at i:12379466 original size:38 final size:39
Alignment explanation
Indices: 12379421--12379528 Score: 119
Period size: 43 Copynumber: 2.7 Consensus size: 39
12379411 TAACTCACAC
*
12379421 AACTTACATAACTTAATA-ACTTATGTATATCATATCAT
1 AACTTACATAACTTAATATACTTATATATATCATATCAT
* *
12379459 AACTTACATAACTTGCATAATACATAAATATATATCATATCAT
1 AACTTACATAACTT-AAT-ATAC-T-TATATATATCATATCAT
* *
12379502 AAGTTACATAATTTAATTATACTTATA
1 AACTTACATAACTTAA-TATACTTATA
12379529 AATAACCATG
Statistics
Matches: 57, Mismatches: 7, Indels: 10
0.77 0.09 0.14
Matches are distributed among these distances:
38 14 0.25
39 2 0.04
40 4 0.07
41 3 0.05
42 6 0.11
43 28 0.49
ACGTcount: A:0.44, C:0.14, G:0.03, T:0.39
Consensus pattern (39 bp):
AACTTACATAACTTAATATACTTATATATATCATATCAT
Found at i:12385024 original size:21 final size:21
Alignment explanation
Indices: 12384998--12385044 Score: 76
Period size: 21 Copynumber: 2.2 Consensus size: 21
12384988 CTAGAACTTA
*
12384998 AAGCAGAGGCAGTAACGAGGG
1 AAGCAGAGGCAGCAACGAGGG
*
12385019 AAGCAGAGGCAGCAGCGAGGG
1 AAGCAGAGGCAGCAACGAGGG
12385040 AAGCA
1 AAGCA
12385045 AAGCAAAGCA
Statistics
Matches: 24, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
21 24 1.00
ACGTcount: A:0.38, C:0.17, G:0.43, T:0.02
Consensus pattern (21 bp):
AAGCAGAGGCAGCAACGAGGG
Found at i:12385551 original size:42 final size:43
Alignment explanation
Indices: 12385375--12385567 Score: 237
Period size: 43 Copynumber: 4.5 Consensus size: 43
12385365 ACATGACCTT
* * *
12385375 ATCATGTTCTTTAGCGGCATTTG-TGATAAAAACGCCACTAAAG
1 ATCATGTTCTTTAGCGGCATTTGCT-ACAAAAGCGCCGCTAAAG
* * * * * *
12385418 ATTATGTTCTTTAGCAGCGTTTACTAGAAAAGCGCAGCTAAAG
1 ATCATGTTCTTTAGCGGCATTTGCTACAAAAGCGCCGCTAAAG
* *
12385461 GTCCTGTTCTTTAGCGGCATTTGCTACAAAAGCGCCGCTAAAG
1 ATCATGTTCTTTAGCGGCATTTGCTACAAAAGCGCCGCTAAAG
12385504 ATCATGTTCTTTAGCGGCATTTGCTA-AAAAGCGCCGCTAAAG
1 ATCATGTTCTTTAGCGGCATTTGCTACAAAAGCGCCGCTAAAG
* **
12385546 GTCATGACCTTTAGCGGCATTT
1 ATCATGTTCTTTAGCGGCATTT
12385568 TTGTAAAAAA
Statistics
Matches: 128, Mismatches: 21, Indels: 3
0.84 0.14 0.02
Matches are distributed among these distances:
42 35 0.27
43 92 0.72
44 1 0.01
ACGTcount: A:0.28, C:0.21, G:0.21, T:0.30
Consensus pattern (43 bp):
ATCATGTTCTTTAGCGGCATTTGCTACAAAAGCGCCGCTAAAG
Found at i:12386996 original size:23 final size:23
Alignment explanation
Indices: 12386966--12387013 Score: 96
Period size: 23 Copynumber: 2.1 Consensus size: 23
12386956 AGAATACCAA
12386966 AAGAAAGTTGATTAACTTTTATT
1 AAGAAAGTTGATTAACTTTTATT
12386989 AAGAAAGTTGATTAACTTTTATT
1 AAGAAAGTTGATTAACTTTTATT
12387012 AA
1 AA
12387014 ATCAACCCTA
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
23 25 1.00
ACGTcount: A:0.42, C:0.04, G:0.12, T:0.42
Consensus pattern (23 bp):
AAGAAAGTTGATTAACTTTTATT
Found at i:12387194 original size:2 final size:2
Alignment explanation
Indices: 12387187--12387212 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
12387177 CATTTTAAAC
12387187 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
12387213 NNNNNNNNNN
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 24 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:12393807 original size:1 final size:1
Alignment explanation
Indices: 12393801--12393831 Score: 62
Period size: 1 Copynumber: 31.0 Consensus size: 1
12393791 TCCTCTTCCC
12393801 TTTTTTTTTTTTTTTTTTTTTTTTTTTTTTT
1 TTTTTTTTTTTTTTTTTTTTTTTTTTTTTTT
12393832 ACATTTGAAC
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
1 30 1.00
ACGTcount: A:0.00, C:0.00, G:0.00, T:1.00
Consensus pattern (1 bp):
T
Found at i:12397235 original size:22 final size:22
Alignment explanation
Indices: 12397210--12397262 Score: 58
Period size: 22 Copynumber: 2.4 Consensus size: 22
12397200 ATTAAATTGT
12397210 AAATTTTATAATAGTAA-AAA-TA
1 AAATTTTATAA-AG-AATAAATTA
12397232 AAATTTT-TAAAGAATTAAATTA
1 AAATTTTATAAAGAA-TAAATTA
12397254 AAATTTTAT
1 AAATTTTAT
12397263 TATTTTAAGG
Statistics
Matches: 27, Mismatches: 0, Indels: 7
0.79 0.00 0.21
Matches are distributed among these distances:
19 2 0.07
20 2 0.07
21 6 0.22
22 16 0.59
23 1 0.04
ACGTcount: A:0.55, C:0.00, G:0.04, T:0.42
Consensus pattern (22 bp):
AAATTTTATAAAGAATAAATTA
Found at i:12397269 original size:29 final size:30
Alignment explanation
Indices: 12397236--12397293 Score: 73
Period size: 29 Copynumber: 2.0 Consensus size: 30
12397226 AAAATAAAAT
**
12397236 TTTTAAAGAATTAAAT-TAAAATTTTATTA
1 TTTTAAAGAAAAAAATGTAAAATTTTATTA
* *
12397265 TTTTAAGGAAAAAAATGTATAATTTTATT
1 TTTTAAAGAAAAAAATGTAAAATTTTATT
12397294 TTTACTAATT
Statistics
Matches: 24, Mismatches: 4, Indels: 1
0.83 0.14 0.03
Matches are distributed among these distances:
29 13 0.54
30 11 0.46
ACGTcount: A:0.47, C:0.00, G:0.07, T:0.47
Consensus pattern (30 bp):
TTTTAAAGAAAAAAATGTAAAATTTTATTA
Found at i:12402987 original size:20 final size:20
Alignment explanation
Indices: 12402964--12403003 Score: 53
Period size: 20 Copynumber: 2.0 Consensus size: 20
12402954 TTCAATTGAA
* *
12402964 TATTCTAATTTTATTTTATT
1 TATTCTAATGTTATATTATT
*
12402984 TATTTTAATGTTATATTATT
1 TATTCTAATGTTATATTATT
12403004 CTATGGAAAA
Statistics
Matches: 17, Mismatches: 3, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.28, C:0.03, G:0.03, T:0.68
Consensus pattern (20 bp):
TATTCTAATGTTATATTATT
Found at i:12412835 original size:38 final size:38
Alignment explanation
Indices: 12412793--12412865 Score: 130
Period size: 38 Copynumber: 1.9 Consensus size: 38
12412783 CCCTACTGAT
12412793 TACATGTTAAGCATGTCT-ACTGCTAGTGTTGAATTAAA
1 TACATGTTAAGCATGT-TGACTGCTAGTGTTGAATTAAA
12412831 TACATGTTAAGCATGTTGACTGCTAGTGTTGAATT
1 TACATGTTAAGCATGTTGACTGCTAGTGTTGAATT
12412866 GTTCTATTAC
Statistics
Matches: 34, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
37 1 0.03
38 33 0.97
ACGTcount: A:0.29, C:0.12, G:0.21, T:0.38
Consensus pattern (38 bp):
TACATGTTAAGCATGTTGACTGCTAGTGTTGAATTAAA
Found at i:12415376 original size:2 final size:2
Alignment explanation
Indices: 12415369--12415422 Score: 90
Period size: 2 Copynumber: 26.5 Consensus size: 2
12415359 TAAAGAGACT
*
12415369 TA TA TA TA TA GA CTA 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 TA TA TA TA TA TA
12415412 TA TA TA TA TA T
1 TA TA TA TA TA T
12415423 CAACTTATCA
Statistics
Matches: 49, Mismatches: 2, Indels: 2
0.92 0.04 0.04
Matches are distributed among these distances:
2 48 0.98
3 1 0.02
ACGTcount: A:0.48, C:0.02, G:0.02, T:0.48
Consensus pattern (2 bp):
TA
Found at i:12419488 original size:2 final size:2
Alignment explanation
Indices: 12419481--12419511 Score: 62
Period size: 2 Copynumber: 15.5 Consensus size: 2
12419471 CATAAAACTC
12419481 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG A
1 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG A
12419512 TGAGGATGAG
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 29 1.00
ACGTcount: A:0.52, C:0.00, G:0.48, T:0.00
Consensus pattern (2 bp):
AG
Found at i:12425426 original size:13 final size:13
Alignment explanation
Indices: 12425402--12425440 Score: 62
Period size: 12 Copynumber: 3.0 Consensus size: 13
12425392 CTCTCTCAAC
12425402 AAAAATTACAAAAA
1 AAAAATT-CAAAAA
12425416 AAAAATTC-AAAA
1 AAAAATTCAAAAA
12425428 AAAAATTCAAAAA
1 AAAAATTCAAAAA
12425441 TTCAAAAAAA
Statistics
Matches: 24, Mismatches: 0, Indels: 3
0.89 0.00 0.11
Matches are distributed among these distances:
12 12 0.50
13 5 0.21
14 7 0.29
ACGTcount: A:0.77, C:0.08, G:0.00, T:0.15
Consensus pattern (13 bp):
AAAAATTCAAAAA
Found at i:12433959 original size:20 final size:20
Alignment explanation
Indices: 12433936--12433993 Score: 80
Period size: 20 Copynumber: 2.9 Consensus size: 20
12433926 TATATGTACG
*
12433936 TATATATATATTATACTTTC
1 TATATATATATTATAATTTC
* *
12433956 TATACATATTTTATAATTTC
1 TATATATATATTATAATTTC
12433976 TATATATATATATATAAT
1 TATATATATAT-TATAAT
12433994 CATTATCTTT
Statistics
Matches: 32, Mismatches: 5, Indels: 1
0.84 0.13 0.03
Matches are distributed among these distances:
20 26 0.81
21 6 0.19
ACGTcount: A:0.40, C:0.07, G:0.00, T:0.53
Consensus pattern (20 bp):
TATATATATATTATAATTTC
Found at i:12434053 original size:54 final size:51
Alignment explanation
Indices: 12433923--12434087 Score: 153
Period size: 52 Copynumber: 3.2 Consensus size: 51
12433913 TTTACCCTAA
* *
12433923 ATATATATGTACGTATATATATATTATACTTTCTATACATATTTTATAATTT
1 ATATATATGTACGTATATAT-TATTATACTTTATATACATATTTTATAACTT
* * *
12433975 CTATATATATA--TATATAATCATTAT-CTTTATGAT-CTATATATTTATTAACTT
1 ATATATATGTACGTATAT-ATTATTATACTTTAT-ATAC-ATAT-TTTA-TAACTT
* *
12434027 ATATATATGTACGTATATATGTATTATACTTTCTATCCATATTTTATAA-TT
1 ATATATATGTACGTATATAT-TATTATACTTTATATACATATTTTATAACTT
*
12434078 -TCTATATGTA
1 ATATATATGTA
12434088 TATTTTTCTT
Statistics
Matches: 93, Mismatches: 10, Indels: 22
0.74 0.08 0.18
Matches are distributed among these distances:
49 6 0.06
50 25 0.27
51 8 0.09
52 26 0.28
53 6 0.06
54 16 0.17
55 6 0.06
ACGTcount: A:0.35, C:0.09, G:0.04, T:0.52
Consensus pattern (51 bp):
ATATATATGTACGTATATATTATTATACTTTATATACATATTTTATAACTT
Found at i:12455824 original size:63 final size:60
Alignment explanation
Indices: 12455722--12455837 Score: 135
Period size: 63 Copynumber: 1.9 Consensus size: 60
12455712 TCTTTTTTAA
**
12455722 AAAGTTTTAGAAAATTTTAATTAGAACTCTCCATTTTTTTTAGAAAAATTTCATTTTCCGTC
1 AAAGTTTTAGAAAATTTTAATTAGAACTCTCCA-AGTTTTTA-AAAAATTTCATTTTCCGTC
* * * *
12455784 AAAGTTTTAAGATAATTTTAATTAG-GCTCTTTCAAGTTTTTAAAAATTTTCATT
1 AAAGTTTT-AGAAAATTTTAATTAGAACTC-TCCAAGTTTTTAAAAAATTTCATT
12455838 ATACCTTCTA
Statistics
Matches: 46, Mismatches: 6, Indels: 5
0.81 0.11 0.09
Matches are distributed among these distances:
61 11 0.24
62 17 0.37
63 18 0.39
ACGTcount: A:0.34, C:0.10, G:0.09, T:0.47
Consensus pattern (60 bp):
AAAGTTTTAGAAAATTTTAATTAGAACTCTCCAAGTTTTTAAAAAATTTCATTTTCCGTC
Found at i:12459589 original size:23 final size:23
Alignment explanation
Indices: 12459559--12459612 Score: 101
Period size: 23 Copynumber: 2.4 Consensus size: 23
12459549 AGAACAAACA
12459559 GAACAAAAGTAGTTAAGGACTTG
1 GAACAAAAGTAGTTAAGGACTTG
12459582 GAACAAAAGTAGTTAAGGACTTG
1 GAACAAAAGTAGTTAAGGACTTG
12459605 GAA-AAAAG
1 GAACAAAAG
12459613 GAAAAAAAAT
Statistics
Matches: 31, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
22 5 0.16
23 26 0.84
ACGTcount: A:0.48, C:0.07, G:0.26, T:0.19
Consensus pattern (23 bp):
GAACAAAAGTAGTTAAGGACTTG
Found at i:12460866 original size:142 final size:142
Alignment explanation
Indices: 12460372--12461074 Score: 1044
Period size: 142 Copynumber: 5.0 Consensus size: 142
12460362 TCTTTATGGG
** * * * *
12460372 AATTCACCAATTCCTTCCCTACGTAAGCATTGGTTTCAAGTTCATTTCATTTAGAACCGACCACA
1 AATTCACTGATTCCTTCCCTACGTAAGCATCGGTTTCAAGTTCATTTCACTTAGAACCGACAATA
** * * * * * *
12460437 TAGTTTAAGGACTGTCTTAAGTAATGGTTACAGTAAACCAC-TGTTAGCAAGTTATGTCCAAATG
66 TAGTTCGAGGACCGTCTTAAGTAACGGTTACAATAAGCC-CTTGTTTGCAAGTTATGTCCAAGTG
12460501 TGGCCTAGATTTC
130 TGGCCTAGATTTC
* *
12460514 AATTCACTGATTCCTTCCCTACGTAAGCATC-GTTTCAAGTTCATTTCATTTAGAAGCGACAATA
1 AATTCACTGATTCCTTCCCTACGTAAGCATCGGTTTCAAGTTCATTTCACTTAGAACCGACAATA
** * ** *
12460578 TAGTTCGAGGACTATCTTAAGTAACAGTTACAATAAAACCTTGTTTGCAAGTTATATCCAAGTGT
66 TAGTTCGAGGACCGTCTTAAGTAACGGTTACAATAAGCCCTTGTTTGCAAGTTATGTCCAAGTGT
12460643 GGCCTAG-----
131 GGCCTAGATTTC
12460650 -ATTCACTGATTCCTTCCCTACGTAAGCATCGGTTTCAAGTTCATTTCACTTAGAACCGACAATA
1 AATTCACTGATTCCTTCCCTACGTAAGCATCGGTTTCAAGTTCATTTCACTTAGAACCGACAATA
* * *
12460714 TAGTTCGAGGACCATCTTAAGTAATGGTTACATTAAGCCCTTGTTTGCAAGTTATGTCCAAGTGT
66 TAGTTCGAGGACCGTCTTAAGTAACGGTTACAATAAGCCCTTGTTTGCAAGTTATGTCCAAGTGT
12460779 GGCCTAGATTTC
131 GGCCTAGATTTC
*
12460791 AATTCACTGATTCCTTCCCTACGTAAGCATCGGTTTCAAGCTCATTTCACTTAGAACCGACAATA
1 AATTCACTGATTCCTTCCCTACGTAAGCATCGGTTTCAAGTTCATTTCACTTAGAACCGACAATA
* *
12460856 TAGTTAGAGGACCGTCTTAAGTAACGGTTACAGTAAGCCCTTGTTTGCAAGTTATGTCCAAGTGT
66 TAGTTCGAGGACCGTCTTAAGTAACGGTTACAATAAGCCCTTGTTTGCAAGTTATGTCCAAGTGT
12460921 GGCCTAGATTTC
131 GGCCTAGATTTC
* *
12460933 AATTCACTGATTCCTTCCCTACGTAAGCATCGGTTTCAAGTTCATTTCACTTAGAACGGATAATA
1 AATTCACTGATTCCTTCCCTACGTAAGCATCGGTTTCAAGTTCATTTCACTTAGAACCGACAATA
* * *
12460998 TAGTTCGAGGACCGTCTTAAGTAACGGTTACAATAAGCCCTTGTTTGCAAGTAATGCCCAAATGT
66 TAGTTCGAGGACCGTCTTAAGTAACGGTTACAATAAGCCCTTGTTTGCAAGTTATGTCCAAGTGT
12461063 GGCCTAGATTTC
131 GGCCTAGATTTC
12461075 CTCACTTAAT
Statistics
Matches: 515, Mismatches: 38, Indels: 16
0.91 0.07 0.03
Matches are distributed among these distances:
135 30 0.06
136 96 0.19
140 1 0.00
141 90 0.17
142 298 0.58
ACGTcount: A:0.28, C:0.21, G:0.17, T:0.33
Consensus pattern (142 bp):
AATTCACTGATTCCTTCCCTACGTAAGCATCGGTTTCAAGTTCATTTCACTTAGAACCGACAATA
TAGTTCGAGGACCGTCTTAAGTAACGGTTACAATAAGCCCTTGTTTGCAAGTTATGTCCAAGTGT
GGCCTAGATTTC
Found at i:12467682 original size:17 final size:17
Alignment explanation
Indices: 12467660--12467693 Score: 52
Period size: 17 Copynumber: 2.0 Consensus size: 17
12467650 AAAATTGAAA
12467660 TATATAATATT-TAAATT
1 TATATAA-ATTATAAATT
12467677 TATATAAATTATAAATT
1 TATATAAATTATAAATT
12467694 ATAAAACATC
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
16 3 0.19
17 13 0.81
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (17 bp):
TATATAAATTATAAATT
Found at i:12477523 original size:69 final size:69
Alignment explanation
Indices: 12477433--12478079 Score: 592
Period size: 69 Copynumber: 9.4 Consensus size: 69
12477423 ATTATCGTCA
* * *
12477433 GTAAAAACAAGGTTCGCAGGCGAAGAGCCGTAGCCTCTAAAATAGTTAGCGAGAGCAAAGTTCCC
1 GTAAAAACAAGGTTCGCAGGCGAAGAGCCGCAGCCTCTAAAACAGTTAGCGAGAGCAAAGCTCCC
*
12477498 AGCG
66 AGCT
* * * * * *
12477502 GTAAAAATAAGGTTTGTAGGCGAAGAGCCGCAACCTCTAAAACAGTTAGCAAGAGCAAAGCTCTC
1 GTAAAAACAAGGTTCGCAGGCGAAGAGCCGCAGCCTCTAAAACAGTTAGCGAGAGCAAAGCTCCC
*
12477567 AACT
66 AGCT
** ** * *
12477571 GTGCAAACAAGGTTCATAGGCGAAGAGCCGCAGCTTCTAAAACAGTTAGCGAGAGTAAAGCTCCC
1 GTAAAAACAAGGTTCGCAGGCGAAGAGCCGCAGCCTCTAAAACAGTTAGCGAGAGCAAAGCTCCC
*
12477636 AACT
66 AGCT
* * * * * * *
12477640 GTAAAAACAAAGTTTGTAGGCAAAGAGTCACAGCCTCTAAAATAGTTAGCGAGAGCAAAGCTCCC
1 GTAAAAACAAGGTTCGCAGGCGAAGAGCCGCAGCCTCTAAAACAGTTAGCGAGAGCAAAGCTCCC
*
12477705 AGGT
66 AGCT
** * ** * * * * * * * * *
12477709 GTGGAAATAAAATTCACAAGCGAAAAGTCGCAGCCTCTAAAACAGTTAGCTAAAGCTAAGTTTCC
1 GTAAAAACAAGGTTCGCAGGCGAAGAGCCGCAGCCTCTAAAACAGTTAGCGAGAGCAAAGCTCCC
12477774 AGCT
66 AGCT
* * * * * *
12477778 GTAAAAACAAGGTTCGCAGGTGAAGAGTCGAAGTCTCTAAAACATTTAGCGAGAGTAAAGCTCCC
1 GTAAAAACAAGGTTCGCAGGCGAAGAGCCGCAGCCTCTAAAACAGTTAGCGAGAGCAAAGCTCCC
*
12477843 AGTT
66 AGCT
* * * * * * ** *
12477847 GTGAAAATAAGGTTTGCAGGTGAAGAGCTGCAACCTCTAAATTAGTTAGCGAGAGCGAAGCTCCC
1 GTAAAAACAAGGTTCGCAGGCGAAGAGCCGCAGCCTCTAAAACAGTTAGCGAGAGCAAAGCTCCC
*
12477912 AGTT
66 AGCT
* * * * * * * * *
12477916 GTAAAAATAAGGTTTGTAGGCAAAGAGCCGTAGACTTTAAAACAGTTAGCGATAGCAAAACTCCC
1 GTAAAAACAAGGTTCGCAGGCGAAGAGCCGCAGCCTCTAAAACAGTTAGCGAGAGCAAAGCTCCC
**
12477981 AATT
66 AGCT
* * * * *
12477985 GTAAAAACAAAGTTCGCAGGCGAAGAGCCACGGCTTCTAAAATAGTTAGCGAGAGCAAAGCTCCC
1 GTAAAAACAAGGTTCGCAGGCGAAGAGCCGCAGCCTCTAAAACAGTTAGCGAGAGCAAAGCTCCC
*
12478050 AGTT
66 AGCT
* * **
12478054 ATAAAAACAAAGTTTACAGGCGAAGA
1 GTAAAAACAAGGTTCGCAGGCGAAGA
12478080 ATTTTATAAC
Statistics
Matches: 461, Mismatches: 117, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
69 461 1.00
ACGTcount: A:0.38, C:0.19, G:0.23, T:0.20
Consensus pattern (69 bp):
GTAAAAACAAGGTTCGCAGGCGAAGAGCCGCAGCCTCTAAAACAGTTAGCGAGAGCAAAGCTCCC
AGCT
Found at i:12477788 original size:207 final size:206
Alignment explanation
Indices: 12477433--12478079 Score: 669
Period size: 207 Copynumber: 3.1 Consensus size: 206
12477423 ATTATCGTCA
* * * * * *
12477433 GTAAAAACAAGGTTCGCAGGCGAAGAGCCG-TAGCCTCTAAAATAGTTAGCGAGAGCAAAGTTCC
1 GTAAAAACAAAGTTTGCAGGCAAAGAGCTGCAAGCCTCTAAAATAGTTAGCGAGAGCAAAGCTCC
* *
12477497 CAGCG-GTAAAAATAAGGTTTGTAGGCGAAGAGCCGCAACCTCTAAAACAGTTAGCAAGAGCAAA
66 CAG-GTGTAAAAATAAGGTTTGTAGGCGAAAAGCCGCAGCCTCTAAAACAGTTAGCAA-AGCAAA
* ** **
12477561 GCTCTCAACTGTGCAAACAAGGTTCATAGGCGAAGAGCCGCAGCTTCTAAAACAGTTAGCGAGAG
129 GTTC-CAACTGTAAAAACAAGGTTCGCAGGCGAAGAGCCGCAGCTTCTAAAACAGTTAGCGAGAG
**
12477626 TAAAGCTCCCAACT
193 TAAAGCTCCCAGTT
*
12477640 GTAAAAACAAAGTTTGTAGGCAAAGAG-T-CACAGCCTCTAAAATAGTTAGCGAGAGCAAAGCTC
1 GTAAAAACAAAGTTTGCAGGCAAAGAGCTGCA-AGCCTCTAAAATAGTTAGCGAGAGCAAAGCTC
** ** *** * * *
12477703 CCAGGTGTGGAAATAAAATTCACAAGCGAAAAGTCGCAGCCTCTAAAACAGTTAGCTAAAGCTAA
65 CCAGGTGTAAAAATAAGGTTTGTAGGCGAAAAGCCGCAGCCTCTAAAACAGTTAGC-AAAGCAAA
* * * * *
12477768 GTTTCCAGCTGTAAAAACAAGGTTCGCAGGTGAAGAGTCGAAG-TCTCTAAAACATTTAGCGAGA
129 G-TTCCAACTGTAAAAACAAGGTTCGCAGGCGAAGAGCCGCAGCT-TCTAAAACAGTTAGCGAGA
12477832 GTAAAGCTCCCAGTT
192 GTAAAGCTCCCAGTT
* * * ** * *
12477847 GTGAAAATAAGGTTTGCAGGTGAAGAGCTGCAA-CCTCTAAATTAGTTAGCGAGAGCGAAGCTCC
1 GTAAAAACAAAGTTTGCAGGCAAAGAGCTGCAAGCCTCTAAAATAGTTAGCGAGAGCAAAGCTCC
* * * * *
12477911 CAGTTGTAAAAATAAGGTTTGTAGGC-AAAGAGCCGTAGACTTTAAAACAGTTAGCGATAGCAAA
66 CAGGTGTAAAAATAAGGTTTGTAGGCGAAA-AGCCGCAGCCTCTAAAACAGTTAGC-AAAGC-AA
* * * * * * *
12477975 ACTCCCAATTGTAAAAACAAAGTTCGCAGGCGAAGAGCCACGGCTTCTAAAATAGTTAGCGAGAG
128 AGTTCCAACTGTAAAAACAAGGTTCGCAGGCGAAGAGCCGCAGCTTCTAAAACAGTTAGCGAGAG
*
12478040 CAAAGCTCCCAGTT
193 TAAAGCTCCCAGTT
* * *
12478054 ATAAAAACAAAGTTTACAGGCGAAGA
1 GTAAAAACAAAGTTTGCAGGCAAAGA
12478080 ATTTTATAAC
Statistics
Matches: 355, Mismatches: 74, Indels: 22
0.79 0.16 0.05
Matches are distributed among these distances:
206 5 0.01
207 339 0.95
208 9 0.03
209 2 0.01
ACGTcount: A:0.38, C:0.19, G:0.23, T:0.20
Consensus pattern (206 bp):
GTAAAAACAAAGTTTGCAGGCAAAGAGCTGCAAGCCTCTAAAATAGTTAGCGAGAGCAAAGCTCC
CAGGTGTAAAAATAAGGTTTGTAGGCGAAAAGCCGCAGCCTCTAAAACAGTTAGCAAAGCAAAGT
TCCAACTGTAAAAACAAGGTTCGCAGGCGAAGAGCCGCAGCTTCTAAAACAGTTAGCGAGAGTAA
AGCTCCCAGTT
Found at i:12492328 original size:135 final size:136
Alignment explanation
Indices: 12492160--12492409 Score: 382
Period size: 135 Copynumber: 1.8 Consensus size: 136
12492150 TTAGAAAATG
* *
12492160 ACATACATTGATTATTTTTTATCAGTAAAAATGGATGAAATTTT-AACAAAATGGACTAGTTTGC
1 ACATACATTGACTATTTTTTATCAGTAAAAATGGATG-AATTTTGAACAAAAT-AACTAGTTTGC
*
12492224 TCTTTGATCAAACGTATAAGGACTAAAATGCCCA-TTTTTTT-AGTAGAATGGACAACATGTATC
64 TCTTTGATCAAACGTATAAGAACTAAAATGCCCATTTTTTTTGAGTAGAATGGACAACATGTATC
12492287 TCATGCTA
129 TCATGCTA
12492295 ACATACATTGACTATTTTTTA-CTAGTAAAAATGGATGAATTTTGAACAAAATAACTAGTTTGCT
1 ACATACATTGACTATTTTTTATC-AGTAAAAATGGATGAATTTTGAACAAAATAACTAGTTTGCT
* ** *
12492359 CTTTGATCTAACGTATAAGAACTAAGCTGTCCATTTTTTTTGAGTAGAATG
65 CTTTGATCAAACGTATAAGAACTAAAATGCCCATTTTTTTTGAGTAGAATG
12492410 AATTAAATGC
Statistics
Matches: 104, Mismatches: 7, Indels: 7
0.88 0.06 0.06
Matches are distributed among these distances:
134 46 0.44
135 49 0.47
136 9 0.09
ACGTcount: A:0.36, C:0.13, G:0.15, T:0.37
Consensus pattern (136 bp):
ACATACATTGACTATTTTTTATCAGTAAAAATGGATGAATTTTGAACAAAATAACTAGTTTGCTC
TTTGATCAAACGTATAAGAACTAAAATGCCCATTTTTTTTGAGTAGAATGGACAACATGTATCTC
ATGCTA
Found at i:12496855 original size:67 final size:67
Alignment explanation
Indices: 12496747--12496877 Score: 228
Period size: 67 Copynumber: 2.0 Consensus size: 67
12496737 TTCTGGAAAA
*
12496747 AATTGAAGAGTCAAACATTACAACTGAATTTGAATGTGTTTTACTTTTGATAGTCCTCAAAGTTA
1 AATTGAAGAGTCAAACATTACAACTGAATTTGAATGTGTTTTACATTTGATAGTCCTCAAAGTTA
12496812 AC
66 AC
*
12496814 AATTG-AGAAGTCAAACATTACAACTGGATTTGAATGTGTTTTACATTTGATAGTCCTCAAAGTT
1 AATTGAAG-AGTCAAACATTACAACTGAATTTGAATGTGTTTTACATTTGATAGTCCTCAAAGTT
12496878 TTCCAACCAT
Statistics
Matches: 61, Mismatches: 2, Indels: 2
0.94 0.03 0.03
Matches are distributed among these distances:
66 2 0.03
67 59 0.97
ACGTcount: A:0.35, C:0.13, G:0.16, T:0.36
Consensus pattern (67 bp):
AATTGAAGAGTCAAACATTACAACTGAATTTGAATGTGTTTTACATTTGATAGTCCTCAAAGTTA
AC
Found at i:12497386 original size:6 final size:6
Alignment explanation
Indices: 12497375--12497425 Score: 84
Period size: 6 Copynumber: 8.5 Consensus size: 6
12497365 CACAAATCTT
* *
12497375 CCCTTC CCCTTC CCCTTC CCCTTC CCCTTC CCTTTC CTCTTC CCCTTC
1 CCCTTC CCCTTC CCCTTC CCCTTC CCCTTC CCCTTC CCCTTC CCCTTC
12497423 CCC
1 CCC
12497426 CATCCTTGAT
Statistics
Matches: 41, Mismatches: 4, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
6 41 1.00
ACGTcount: A:0.00, C:0.65, G:0.00, T:0.35
Consensus pattern (6 bp):
CCCTTC
Found at i:12499908 original size:14 final size:15
Alignment explanation
Indices: 12499886--12499962 Score: 52
Period size: 14 Copynumber: 5.0 Consensus size: 15
12499876 CATCAAAACA
12499886 CCAGAAAAT-ATTTT
1 CCAGAAAATCATTTT
*
12499900 CCAGTAAATCATTTT
1 CCAGAAAATCATTTT
*
12499915 ACAGAAAAGTAAAACATTTT
1 CCAGAAAA-T----CATTTT
12499935 CCAG-AAATCATTTT
1 CCAGAAAATCATTTT
* *
12499949 ACGGAAAAT-ATTTT
1 CCAGAAAATCATTTT
12499963 ACTGGCAAAC
Statistics
Matches: 50, Mismatches: 6, Indels: 14
0.71 0.09 0.20
Matches are distributed among these distances:
14 21 0.42
15 15 0.30
16 1 0.02
18 1 0.02
19 3 0.06
20 9 0.18
ACGTcount: A:0.43, C:0.14, G:0.09, T:0.34
Consensus pattern (15 bp):
CCAGAAAATCATTTT
Found at i:12499927 original size:20 final size:20
Alignment explanation
Indices: 12499902--12499941 Score: 62
Period size: 20 Copynumber: 2.0 Consensus size: 20
12499892 AATATTTTCC
*
12499902 AGTAAATCATTTTACAGAAA
1 AGTAAAACATTTTACAGAAA
*
12499922 AGTAAAACATTTTCCAGAAA
1 AGTAAAACATTTTACAGAAA
12499942 TCATTTTACG
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
20 18 1.00
ACGTcount: A:0.50, C:0.12, G:0.10, T:0.28
Consensus pattern (20 bp):
AGTAAAACATTTTACAGAAA
Found at i:12499947 original size:34 final size:35
Alignment explanation
Indices: 12499890--12499956 Score: 109
Period size: 34 Copynumber: 1.9 Consensus size: 35
12499880 AAAACACCAG
*
12499890 AAAATATTTTCCAGTAAATCATTTTACAGAAAAGT
1 AAAACATTTTCCAGTAAATCATTTTACAGAAAAGT
*
12499925 AAAACATTTTCCAG-AAATCATTTTACGGAAAA
1 AAAACATTTTCCAGTAAATCATTTTACAGAAAA
12499957 TATTTTACTG
Statistics
Matches: 30, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
34 17 0.57
35 13 0.43
ACGTcount: A:0.46, C:0.13, G:0.09, T:0.31
Consensus pattern (35 bp):
AAAACATTTTCCAGTAAATCATTTTACAGAAAAGT
Found at i:12504754 original size:18 final size:18
Alignment explanation
Indices: 12504709--12504754 Score: 56
Period size: 18 Copynumber: 2.6 Consensus size: 18
12504699 AAGCCACCTG
*
12504709 CTTTTTAGAGTGAACACT
1 CTTTTTAGTGTGAACACT
** *
12504727 CTTTCAAGTGTGAAGACT
1 CTTTTTAGTGTGAACACT
12504745 CTTTTTAGTG
1 CTTTTTAGTG
12504755 GCCACTAGAG
Statistics
Matches: 22, Mismatches: 6, Indels: 0
0.79 0.21 0.00
Matches are distributed among these distances:
18 22 1.00
ACGTcount: A:0.24, C:0.15, G:0.20, T:0.41
Consensus pattern (18 bp):
CTTTTTAGTGTGAACACT
Found at i:12508734 original size:51 final size:51
Alignment explanation
Indices: 12508679--12508844 Score: 289
Period size: 51 Copynumber: 3.3 Consensus size: 51
12508669 GGGATCACAT
* *
12508679 TTATCACTTGTCACTTGTC-CTTGATCAGATAAATGTACCTAAAGCTACCAC
1 TTATCACTTGTCACTTGTCAC-TGATCAGATAAGTGTAGCTAAAGCTACCAC
12508730 TTATCACTTGTCACTTGTCACTGATCAGATAAGTGTAGCTAAAGCTACCAC
1 TTATCACTTGTCACTTGTCACTGATCAGATAAGTGTAGCTAAAGCTACCAC
*
12508781 TTATCACTTGTCACTTGTCACTGATCAGATAAGTGTAGCTAAAGCTACCAT
1 TTATCACTTGTCACTTGTCACTGATCAGATAAGTGTAGCTAAAGCTACCAC
12508832 TTATCACTTGTCA
1 TTATCACTTGTCA
12508845 TTGATTAAAA
Statistics
Matches: 111, Mismatches: 3, Indels: 2
0.96 0.03 0.02
Matches are distributed among these distances:
51 110 0.99
52 1 0.01
ACGTcount: A:0.29, C:0.23, G:0.14, T:0.34
Consensus pattern (51 bp):
TTATCACTTGTCACTTGTCACTGATCAGATAAGTGTAGCTAAAGCTACCAC
Found at i:12510451 original size:23 final size:23
Alignment explanation
Indices: 12510431--12510523 Score: 125
Period size: 23 Copynumber: 4.0 Consensus size: 23
12510421 GCCACACTAT
12510431 TATCTAGCCGAAGCTACCACTGA
1 TATCTAGCCGAAGCTACCACTGA
12510454 TA-CGTAGCCGAAGCTACCACTGA
1 TATC-TAGCCGAAGCTACCACTGA
* * *
12510477 TATGTAGCCGTAGCTACCACTAA
1 TATCTAGCCGAAGCTACCACTGA
* *
12510500 AATGTAGCCGAAGCTACCACTGA
1 TATCTAGCCGAAGCTACCACTGA
12510523 T
1 T
12510524 CAATAACACT
Statistics
Matches: 61, Mismatches: 7, Indels: 4
0.85 0.10 0.06
Matches are distributed among these distances:
22 1 0.02
23 60 0.98
ACGTcount: A:0.31, C:0.28, G:0.19, T:0.22
Consensus pattern (23 bp):
TATCTAGCCGAAGCTACCACTGA
Found at i:12510507 original size:46 final size:46
Alignment explanation
Indices: 12510435--12510523 Score: 142
Period size: 46 Copynumber: 1.9 Consensus size: 46
12510425 CACTATTATC
* *
12510435 TAGCCGAAGCTACCACTGATACGTAGCCGAAGCTACCACTGATATG
1 TAGCCGAAGCTACCACTAAAACGTAGCCGAAGCTACCACTGATATG
* *
12510481 TAGCCGTAGCTACCACTAAAATGTAGCCGAAGCTACCACTGAT
1 TAGCCGAAGCTACCACTAAAACGTAGCCGAAGCTACCACTGAT
12510524 CAATAACACT
Statistics
Matches: 39, Mismatches: 4, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
46 39 1.00
ACGTcount: A:0.31, C:0.28, G:0.20, T:0.20
Consensus pattern (46 bp):
TAGCCGAAGCTACCACTAAAACGTAGCCGAAGCTACCACTGATATG
Found at i:12517218 original size:2 final size:2
Alignment explanation
Indices: 12517211--12517266 Score: 87
Period size: 2 Copynumber: 28.5 Consensus size: 2
12517201 GAGAAATTAT
12517211 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC
1 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC
* *
12517253 T- TC TA TT TC TC TC T
1 TC TC TC TC TC TC TC T
12517267 TCTGTTTATT
Statistics
Matches: 50, Mismatches: 3, Indels: 2
0.91 0.05 0.04
Matches are distributed among these distances:
1 1 0.02
2 49 0.98
ACGTcount: A:0.02, C:0.45, G:0.00, T:0.54
Consensus pattern (2 bp):
TC
Found at i:12519694 original size:6 final size:6
Alignment explanation
Indices: 12519685--12519779 Score: 88
Period size: 6 Copynumber: 16.3 Consensus size: 6
12519675 TTATTTTTAA
* * * * *
12519685 TATTGC TATTAC TATTAT TATTAT TATTAT TATTAC TATT-- T-TTAT
1 TATTAC TATTAC TATTAC TATTAC TATTAC TATTAC TATTAC TATTAC
* * * *
12519730 TATTAC TATTAC TTTTAT TATTAC TATTAC TATTAC TTTTAT TATTAC
1 TATTAC TATTAC TATTAC TATTAC TATTAC TATTAC TATTAC TATTAC
12519778 TA
1 TA
12519780 ATATTTTTAT
Statistics
Matches: 74, Mismatches: 12, Indels: 6
0.80 0.13 0.07
Matches are distributed among these distances:
3 2 0.03
4 1 0.01
5 1 0.01
6 70 0.95
ACGTcount: A:0.29, C:0.09, G:0.01, T:0.60
Consensus pattern (6 bp):
TATTAC
Found at i:12519712 original size:18 final size:18
Alignment explanation
Indices: 12519675--12519784 Score: 102
Period size: 18 Copynumber: 6.3 Consensus size: 18
12519665 ATTTTTATTT
* * *
12519675 TTATTTTTAATATTGCTA
1 TTATTATTACTATTACTA
* * *
12519693 TTACTATTATTATTATTA
1 TTATTATTACTATTACTA
12519711 TTATTATTACTATT--T-
1 TTATTATTACTATTACTA
*
12519726 TTATTATTACTATTACTT
1 TTATTATTACTATTACTA
12519744 TTATTATTACTATTACTA
1 TTATTATTACTATTACTA
*
12519762 TTACTT-TTATTATTACTA
1 TTA-TTATTACTATTACTA
*
12519780 ATATT
1 TTATT
12519785 TTTATTTTTA
Statistics
Matches: 78, Mismatches: 10, Indels: 9
0.80 0.10 0.09
Matches are distributed among these distances:
15 14 0.18
16 1 0.01
17 3 0.04
18 58 0.74
19 2 0.03
ACGTcount: A:0.30, C:0.08, G:0.01, T:0.61
Consensus pattern (18 bp):
TTATTATTACTATTACTA
Found at i:12519777 original size:24 final size:24
Alignment explanation
Indices: 12519673--12519779 Score: 123
Period size: 24 Copynumber: 4.6 Consensus size: 24
12519663 TCATTTTTAT
* * *
12519673 TTTTATTTTTAATATTGCTATTAC
1 TTTTATTATTACTATTACTATTAC
* * *
12519697 TATTATTATTATTATTATTATTAC
1 TTTTATTATTACTATTACTATTAC
12519721 TATTT-TTA-T--TATTACTATTAC
1 T-TTTATTATTACTATTACTATTAC
12519742 TTTTATTATTACTATTACTATTAC
1 TTTTATTATTACTATTACTATTAC
12519766 TTTTATTATTACTA
1 TTTTATTATTACTA
12519780 ATATTTTTAT
Statistics
Matches: 71, Mismatches: 7, Indels: 10
0.81 0.08 0.11
Matches are distributed among these distances:
20 3 0.04
21 15 0.21
22 1 0.01
23 1 0.01
24 49 0.69
25 2 0.03
ACGTcount: A:0.29, C:0.08, G:0.01, T:0.62
Consensus pattern (24 bp):
TTTTATTATTACTATTACTATTAC
Found at i:12519793 original size:24 final size:24
Alignment explanation
Indices: 12519690--12519796 Score: 105
Period size: 24 Copynumber: 4.6 Consensus size: 24
12519680 TTTAATATTG
* * *
12519690 CTATTACTATTATTATTATTATTA
1 CTATTACTTTTATTATTACTAATA
*
12519714 TTATTACTATTT-TTATTA-T--TA
1 CTATTACT-TTTATTATTACTAATA
*
12519735 CTATTACTTTTATTATTACTATTA
1 CTATTACTTTTATTATTACTAATA
12519759 CTATTACTTTTATTATTACTAATA
1 CTATTACTTTTATTATTACTAATA
* * *
12519783 TTTTTATTTTTATT
1 CTATTACTTTTATT
12519797 TTTAAACTGT
Statistics
Matches: 71, Mismatches: 7, Indels: 10
0.81 0.08 0.11
Matches are distributed among these distances:
20 3 0.04
21 15 0.21
22 1 0.01
23 1 0.01
24 49 0.69
25 2 0.03
ACGTcount: A:0.29, C:0.08, G:0.00, T:0.63
Consensus pattern (24 bp):
CTATTACTTTTATTATTACTAATA
Found at i:12519800 original size:12 final size:12
Alignment explanation
Indices: 12519691--12519796 Score: 90
Period size: 12 Copynumber: 8.8 Consensus size: 12
12519681 TTAATATTGC
*
12519691 TATTACTATTAT
1 TATTATTATTAT
12519703 TATTATTATTAT
1 TATTATTATTAT
* *
12519715 TATTACTATTTT
1 TATTATTATTAT
*
12519727 TATTATTACTAT
1 TATTATTATTAT
12519739 TACTT-TTATTAT
1 TA-TTATTATTAT
* *
12519751 TACTATTACTAT
1 TATTATTATTAT
12519763 TACTT-TTATTAT
1 TA-TTATTATTAT
* * *
12519775 TACTAATATTTT
1 TATTATTATTAT
*
12519787 TATTTTTATT
1 TATTATTATT
12519797 TTTAAACTGT
Statistics
Matches: 73, Mismatches: 17, Indels: 8
0.74 0.17 0.08
Matches are distributed among these distances:
11 2 0.03
12 68 0.93
13 3 0.04
ACGTcount: A:0.29, C:0.08, G:0.00, T:0.63
Consensus pattern (12 bp):
TATTATTATTAT
Found at i:12519931 original size:21 final size:21
Alignment explanation
Indices: 12519894--12519950 Score: 71
Period size: 21 Copynumber: 2.7 Consensus size: 21
12519884 TACTTACTCG
* *
12519894 TATTTTTA-ATTAGTTTGTTT
1 TATTTTTATTTTATTTTGTTT
12519914 TATTTTTATTTTATTTTGTTT
1 TATTTTTATTTTATTTTGTTT
*
12519935 TGTTTTTATTCTTATT
1 TATTTTTATT-TTATT
12519951 ATTCCTTTTT
Statistics
Matches: 32, Mismatches: 3, Indels: 2
0.86 0.08 0.05
Matches are distributed among these distances:
20 8 0.25
21 19 0.59
22 5 0.16
ACGTcount: A:0.16, C:0.02, G:0.07, T:0.75
Consensus pattern (21 bp):
TATTTTTATTTTATTTTGTTT
Found at i:12521919 original size:3 final size:3
Alignment explanation
Indices: 12521911--12521935 Score: 50
Period size: 3 Copynumber: 8.3 Consensus size: 3
12521901 TAAATTTTAT
12521911 TAA TAA TAA TAA TAA TAA TAA TAA T
1 TAA TAA TAA TAA TAA TAA TAA TAA T
12521936 TCAACTTAAA
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 22 1.00
ACGTcount: A:0.64, C:0.00, G:0.00, T:0.36
Consensus pattern (3 bp):
TAA
Found at i:12527092 original size:3 final size:3
Alignment explanation
Indices: 12527084--12527120 Score: 74
Period size: 3 Copynumber: 12.3 Consensus size: 3
12527074 AGGAGAAGTC
12527084 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA T
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA T
12527121 TAGTATCTTT
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 34 1.00
ACGTcount: A:0.65, C:0.00, G:0.00, T:0.35
Consensus pattern (3 bp):
TAA
Found at i:12540315 original size:29 final size:29
Alignment explanation
Indices: 12540282--12540342 Score: 97
Period size: 29 Copynumber: 2.1 Consensus size: 29
12540272 TAATTGCACA
*
12540282 ATTACACTAATTATTACAACAT-TCGTAAT
1 ATTACACAAATTATTACAA-ATCTCGTAAT
12540311 ATTACACAAATTATTACAAATCTCGTAAT
1 ATTACACAAATTATTACAAATCTCGTAAT
12540340 ATT
1 ATT
12540343 TTGTGTAACA
Statistics
Matches: 30, Mismatches: 1, Indels: 2
0.91 0.03 0.06
Matches are distributed among these distances:
28 2 0.07
29 28 0.93
ACGTcount: A:0.43, C:0.16, G:0.03, T:0.38
Consensus pattern (29 bp):
ATTACACAAATTATTACAAATCTCGTAAT
Found at i:12542734 original size:2 final size:2
Alignment explanation
Indices: 12542727--12542755 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
12542717 AATGTTGCTT
12542727 TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
12542756 GTGAGTAAAN
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:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:12546199 original size:4 final size:4
Alignment explanation
Indices: 12546190--12546224 Score: 61
Period size: 4 Copynumber: 8.8 Consensus size: 4
12546180 ATATATTGCC
*
12546190 TTTG TTTG TTTG TTTG TTTG TTTG TTTG TATG TTT
1 TTTG TTTG TTTG TTTG TTTG TTTG TTTG TTTG TTT
12546225 AAGAAATTTG
Statistics
Matches: 29, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
4 29 1.00
ACGTcount: A:0.03, C:0.00, G:0.23, T:0.74
Consensus pattern (4 bp):
TTTG
Found at i:12546672 original size:26 final size:26
Alignment explanation
Indices: 12546651--12546707 Score: 82
Period size: 26 Copynumber: 2.2 Consensus size: 26
12546641 CCAAAAATTT
12546651 ATTTTAAAAAT-AAAAATAAAAAATA
1 ATTTTAAAAATAAAAAATAAAAAATA
*
12546676 ATTTTAAAATTAAAAAATAAAAAA-A
1 ATTTTAAAAATAAAAAATAAAAAATA
12546701 ATATTTA
1 AT-TTTA
12546708 TTATATTCGG
Statistics
Matches: 29, Mismatches: 1, Indels: 3
0.88 0.03 0.09
Matches are distributed among these distances:
25 13 0.45
26 16 0.55
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.32
Consensus pattern (26 bp):
ATTTTAAAAATAAAAAATAAAAAATA
Found at i:12547849 original size:17 final size:17
Alignment explanation
Indices: 12547826--12547864 Score: 53
Period size: 17 Copynumber: 2.3 Consensus size: 17
12547816 TATGAATATG
12547826 AAAATATT-ATATAAAT
1 AAAATATTAATATAAAT
*
12547842 ACAAATATTAATATTAAT
1 A-AAATATTAATATAAAT
12547860 AAAAT
1 AAAAT
12547865 GACTAAATTG
Statistics
Matches: 20, Mismatches: 1, Indels: 3
0.83 0.04 0.12
Matches are distributed among these distances:
16 1 0.05
17 11 0.55
18 8 0.40
ACGTcount: A:0.62, C:0.03, G:0.00, T:0.36
Consensus pattern (17 bp):
AAAATATTAATATAAAT
Found at i:12551856 original size:18 final size:18
Alignment explanation
Indices: 12551833--12551872 Score: 80
Period size: 18 Copynumber: 2.2 Consensus size: 18
12551823 TATTTAATCT
12551833 TGAGTGTATTATTTTCTG
1 TGAGTGTATTATTTTCTG
12551851 TGAGTGTATTATTTTCTG
1 TGAGTGTATTATTTTCTG
12551869 TGAG
1 TGAG
12551873 AGACAAATGG
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 22 1.00
ACGTcount: A:0.17, C:0.05, G:0.25, T:0.53
Consensus pattern (18 bp):
TGAGTGTATTATTTTCTG
Found at i:12558220 original size:22 final size:22
Alignment explanation
Indices: 12558195--12558260 Score: 60
Period size: 22 Copynumber: 3.0 Consensus size: 22
12558185 TATGTAAACA
*
12558195 ATAATAATAAAATAGTAGTAAT
1 ATAATAAAAAAATAGTAGTAAT
*** * * *
12558217 ATAATAGGGAAATAATAGCAAA
1 ATAATAAAAAAATAGTAGTAAT
*
12558239 ACAATAAAAAAATAGTAGTAAT
1 ATAATAAAAAAATAGTAGTAAT
12558261 TTTTTTTTAT
Statistics
Matches: 31, Mismatches: 13, Indels: 0
0.70 0.30 0.00
Matches are distributed among these distances:
22 31 1.00
ACGTcount: A:0.61, C:0.03, G:0.12, T:0.24
Consensus pattern (22 bp):
ATAATAAAAAAATAGTAGTAAT
Found at i:12559824 original size:16 final size:18
Alignment explanation
Indices: 12559797--12559832 Score: 58
Period size: 17 Copynumber: 2.1 Consensus size: 18
12559787 TCAAAATCGG
12559797 ATTGAGAAAATT-ATTTA
1 ATTGAGAAAATTAATTTA
12559814 ATTGA-AAAATTAATTTA
1 ATTGAGAAAATTAATTTA
12559831 AT
1 AT
12559833 AAATAATGTC
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
16 6 0.33
17 12 0.67
ACGTcount: A:0.50, C:0.00, G:0.08, T:0.42
Consensus pattern (18 bp):
ATTGAGAAAATTAATTTA
Found at i:12559909 original size:45 final size:45
Alignment explanation
Indices: 12559837--12559929 Score: 141
Period size: 45 Copynumber: 2.1 Consensus size: 45
12559827 TTTAATAAAT
* * * *
12559837 AATGTCTATTTTGATAAATAGAGAAACATGCACTGGGTTAGATTG
1 AATGTCTATTTTGAGAAAAAGAAAAACATGCACTAGGTTAGATTG
*
12559882 AATGTCTATTTTGAGAAAAAGAAAAACATGCACTAGGTTATATTG
1 AATGTCTATTTTGAGAAAAAGAAAAACATGCACTAGGTTAGATTG
12559927 AAT
1 AAT
12559930 TATAAAGTGT
Statistics
Matches: 43, Mismatches: 5, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
45 43 1.00
ACGTcount: A:0.40, C:0.09, G:0.19, T:0.32
Consensus pattern (45 bp):
AATGTCTATTTTGAGAAAAAGAAAAACATGCACTAGGTTAGATTG
Found at i:12562480 original size:21 final size:21
Alignment explanation
Indices: 12562454--12562517 Score: 92
Period size: 21 Copynumber: 3.0 Consensus size: 21
12562444 ATTGGGTGAA
*
12562454 TCAGCTCTTATGAGCTTTTGT
1 TCAGCTCTTATGAGCTTCTGT
*
12562475 TCAGCTCTTACGAGCTTCTGT
1 TCAGCTCTTATGAGCTTCTGT
* *
12562496 TCAACTCTTATAAGCTTCTGT
1 TCAGCTCTTATGAGCTTCTGT
12562517 T
1 T
12562518 GGCATATTCT
Statistics
Matches: 38, Mismatches: 5, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
21 38 1.00
ACGTcount: A:0.17, C:0.23, G:0.16, T:0.44
Consensus pattern (21 bp):
TCAGCTCTTATGAGCTTCTGT
Found at i:12566693 original size:77 final size:77
Alignment explanation
Indices: 12566565--12566714 Score: 239
Period size: 77 Copynumber: 1.9 Consensus size: 77
12566555 CATTCCCTAA
* * *
12566565 TTCCAACAAGGATTGTGTCTGGTTTAGTTGAAATTAGAGTCAAGTACAAATGTACCATGATATTA
1 TTCCAACAAGGATTGAGTCAGGTTTAGTTGAAATTAGAGTCAAGTACAAATGTACAATGATATTA
12566630 ACTAAAAGATAG
66 ACTAAAAGATAG
* *
12566642 TTCCAACAAGGATTGAGTCAGGTTT-GATTGAAATTAGAGTTAAGTAGAAATGTACAATGATATT
1 TTCCAACAAGGATTGAGTCAGGTTTAG-TTGAAATTAGAGTCAAGTACAAATGTACAATGATATT
12566706 AACTAAAAG
65 AACTAAAAG
12566715 GGTAGGGTTG
Statistics
Matches: 67, Mismatches: 5, Indels: 2
0.91 0.07 0.03
Matches are distributed among these distances:
76 1 0.01
77 66 0.99
ACGTcount: A:0.39, C:0.10, G:0.20, T:0.31
Consensus pattern (77 bp):
TTCCAACAAGGATTGAGTCAGGTTTAGTTGAAATTAGAGTCAAGTACAAATGTACAATGATATTA
ACTAAAAGATAG
Found at i:12567961 original size:27 final size:28
Alignment explanation
Indices: 12567924--12567976 Score: 90
Period size: 27 Copynumber: 1.9 Consensus size: 28
12567914 ACTGAATGTA
12567924 AAGGGAGTTGCTAAGTGCTGATTCCCTC
1 AAGGGAGTTGCTAAGTGCTGATTCCCTC
*
12567952 AAGGG-GTTGCTAAGTTCTGATTCCC
1 AAGGGAGTTGCTAAGTGCTGATTCCC
12567977 CGAATTATTG
Statistics
Matches: 24, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
27 19 0.79
28 5 0.21
ACGTcount: A:0.21, C:0.21, G:0.28, T:0.30
Consensus pattern (28 bp):
AAGGGAGTTGCTAAGTGCTGATTCCCTC
Found at i:12567998 original size:33 final size:33
Alignment explanation
Indices: 12567956--12568152 Score: 142
Period size: 33 Copynumber: 5.4 Consensus size: 33
12567946 TCCCTCAAGG
*
12567956 GGTTGCTAAGTTCTGATTCCCCGAATTATTGGT
1 GGTTGCTAAGTGCTGATTCCCCGAATTATTGGT
*
12567989 GGTTGCTAAGTGCTGATTCCACCGTAACTTGAATGTGAATGG
1 GGTTGCTAAGTGCTGATTCC-CCG-AA-TT--AT-TG---GT
* *
12568031 GGTTGCTAAGTGCTGATTCCCCGAATCATTAGT
1 GGTTGCTAAGTGCTGATTCCCCGAATTATTGGT
* *
12568064 GGTTGCTAAGTGCTGATTCCACCGTATCTTGAATGTGAAAGG
1 GGTTGCTAAGTGCTGATTCC-CCG-A-ATT--AT-TG---GT
* * *
12568106 GGTTGCTAGGTGCTGATTCCCTGAATCATTGGT
1 GGTTGCTAAGTGCTGATTCCCCGAATTATTGGT
*
12568139 GGTTGATAAGTGCT
1 GGTTGCTAAGTGCT
12568153 AGAAAGGTGT
Statistics
Matches: 130, Mismatches: 16, Indels: 36
0.71 0.09 0.20
Matches are distributed among these distances:
33 53 0.41
34 6 0.05
35 3 0.02
36 6 0.05
37 4 0.03
38 4 0.03
39 5 0.04
40 3 0.02
41 5 0.04
42 41 0.32
ACGTcount: A:0.21, C:0.17, G:0.28, T:0.34
Consensus pattern (33 bp):
GGTTGCTAAGTGCTGATTCCCCGAATTATTGGT
Found at i:12568048 original size:42 final size:41
Alignment explanation
Indices: 12567989--12568125 Score: 164
Period size: 42 Copynumber: 3.5 Consensus size: 41
12567979 AATTATTGGT
12567989 GGTTGCTAAGTGCTGATTCCACCGTAACTTGAATGTGAATGG
1 GGTTGCTAAGTGCTGATTCCACCGTAACTTGAATGTGAA-GG
* *
12568031 GGTTGCTAAGTGCTGATTCC-CCG-AA--T-CAT-T--AGT
1 GGTTGCTAAGTGCTGATTCCACCGTAACTTGAATGTGAAGG
*
12568064 GGTTGCTAAGTGCTGATTCCACCGTATCTTGAATGTGAAAGG
1 GGTTGCTAAGTGCTGATTCCACCGTAACTTGAATGTG-AAGG
*
12568106 GGTTGCTAGGTGCTGATTCC
1 GGTTGCTAAGTGCTGATTCC
12568126 CTGAATCATT
Statistics
Matches: 80, Mismatches: 6, Indels: 18
0.77 0.06 0.17
Matches are distributed among these distances:
33 21 0.26
34 4 0.05
35 1 0.01
36 1 0.01
37 3 0.04
38 3 0.04
39 1 0.01
40 2 0.03
41 3 0.04
42 41 0.51
ACGTcount: A:0.21, C:0.18, G:0.28, T:0.32
Consensus pattern (41 bp):
GGTTGCTAAGTGCTGATTCCACCGTAACTTGAATGTGAAGG
Found at i:12568077 original size:75 final size:75
Alignment explanation
Indices: 12567952--12568152 Score: 330
Period size: 75 Copynumber: 2.7 Consensus size: 75
12567942 TGATTCCCTC
* *
12567952 AAGGGGTTGCTAAGTTCTGATTCCCCGAATTATTGGTGGTTGCTAAGTGCTGATTCCACCGTAAC
1 AAGGGGTTGCTAAGTGCTGATTCCCCGAATCATTGGTGGTTGCTAAGTGCTGATTCCACCGTAAC
12568017 TTGAATGTGA
66 TTGAATGTGA
* * *
12568027 ATGGGGTTGCTAAGTGCTGATTCCCCGAATCATTAGTGGTTGCTAAGTGCTGATTCCACCGTATC
1 AAGGGGTTGCTAAGTGCTGATTCCCCGAATCATTGGTGGTTGCTAAGTGCTGATTCCACCGTAAC
12568092 TTGAATGTGA
66 TTGAATGTGA
* * *
12568102 AAGGGGTTGCTAGGTGCTGATTCCCTGAATCATTGGTGGTTGATAAGTGCT
1 AAGGGGTTGCTAAGTGCTGATTCCCCGAATCATTGGTGGTTGCTAAGTGCT
12568153 AGAAAGGTGT
Statistics
Matches: 116, Mismatches: 10, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
75 116 1.00
ACGTcount: A:0.21, C:0.17, G:0.28, T:0.33
Consensus pattern (75 bp):
AAGGGGTTGCTAAGTGCTGATTCCCCGAATCATTGGTGGTTGCTAAGTGCTGATTCCACCGTAAC
TTGAATGTGA
Found at i:12572932 original size:138 final size:138
Alignment explanation
Indices: 12572684--12573101 Score: 773
Period size: 138 Copynumber: 3.0 Consensus size: 138
12572674 AAAACATAAA
*
12572684 AACCACTTAAATCTGGTTTCATTATCATATAAGCATTTGAAGCTCTTTTCTAAAAGACATACAAG
1 AACCACTTAAATCTGGTTTCATTGTCATATAAGCATTTGAAGCTCTTTTCTAAAAGACATACAAG
12572749 GCTTATCCAAGAAAGAATAGTGAGTCTGGATTAAGAATTTTATCACATAGGATGAAGTTCACCAA
66 GCTTATCCAAGAAAGAATAGTGAGTCTGGATTAAGAATTTTATCACATAGGATGAAGTTCACCAA
*
12572814 GAGATCGT
131 GAGATCAT
12572822 AACCACTTAAATCTGGTTTCATTGTCATATAAGCATTTGAAGCTCTTTTCTAAAAGACATACAAG
1 AACCACTTAAATCTGGTTTCATTGTCATATAAGCATTTGAAGCTCTTTTCTAAAAGACATACAAG
*
12572887 GCTTATCCAAGAAAGAATAGTGAGTCTGGATTAAGAATTTTATCACATAGGATGAAGTTCACCTA
66 GCTTATCCAAGAAAGAATAGTGAGTCTGGATTAAGAATTTTATCACATAGGATGAAGTTCACCAA
12572952 GAGATCAT
131 GAGATCAT
*
12572960 AACCACTTAAATCTGGTTTCTTTGTCATATAAGCATTTGAAGCTCTTTTCTAAAAGACATACAAG
1 AACCACTTAAATCTGGTTTCATTGTCATATAAGCATTTGAAGCTCTTTTCTAAAAGACATACAAG
12573025 GCTTATCCAAGAAAGAATGAGTGAGAGTCTGGATTAAGAATTTTATCACATAGGATGAAGTTCAC
66 GCTTATCCAAGAAAGAAT-AGT--GAGTCTGGATTAAGAATTTTATCACATAGGATGAAGTTCAC
12573090 CAAGAGATCAT
128 CAAGAGATCAT
12573101 A
1 A
12573102 TGGTTTTTAA
Statistics
Matches: 272, Mismatches: 5, Indels: 3
0.97 0.02 0.01
Matches are distributed among these distances:
138 217 0.80
139 3 0.01
141 52 0.19
ACGTcount: A:0.37, C:0.16, G:0.17, T:0.31
Consensus pattern (138 bp):
AACCACTTAAATCTGGTTTCATTGTCATATAAGCATTTGAAGCTCTTTTCTAAAAGACATACAAG
GCTTATCCAAGAAAGAATAGTGAGTCTGGATTAAGAATTTTATCACATAGGATGAAGTTCACCAA
GAGATCAT
Found at i:12583247 original size:30 final size:29
Alignment explanation
Indices: 12583208--12583268 Score: 72
Period size: 29 Copynumber: 2.1 Consensus size: 29
12583198 TTGAATTTTG
12583208 AAATGTAAAAAGTA-AATGAACCAAATTTCTA
1 AAATGT-AAAAGTACAATG-ACCAAA-TTCTA
*
12583239 AAAT-TAAAAGTACAATGACTAAATTCTA
1 AAATGTAAAAGTACAATGACCAAATTCTA
12583267 AA
1 AA
12583269 TATTCGAAAA
Statistics
Matches: 28, Mismatches: 1, Indels: 5
0.82 0.03 0.15
Matches are distributed among these distances:
28 7 0.25
29 12 0.43
30 5 0.18
31 4 0.14
ACGTcount: A:0.56, C:0.10, G:0.08, T:0.26
Consensus pattern (29 bp):
AAATGTAAAAGTACAATGACCAAATTCTA
Found at i:12587600 original size:3 final size:3
Alignment explanation
Indices: 12587592--12587671 Score: 79
Period size: 3 Copynumber: 25.7 Consensus size: 3
12587582 CTTAGTCCCT
* * *
12587592 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTTA GTTCA TTG TTT TTA TTG
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA -TTA -TT-A TTA TTA TTA TTA
* * *
12587640 CTA TTA TTA TTA ATG TTA TTA TTA TTA TTA TT
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TT
12587672 GTTTCTACAT
Statistics
Matches: 63, Mismatches: 12, Indels: 4
0.80 0.15 0.05
Matches are distributed among these distances:
3 55 0.87
4 7 0.11
5 1 0.02
ACGTcount: A:0.28, C:0.03, G:0.05, T:0.65
Consensus pattern (3 bp):
TTA
Found at i:12593891 original size:12 final size:11
Alignment explanation
Indices: 12593870--12593899 Score: 51
Period size: 12 Copynumber: 2.6 Consensus size: 11
12593860 GTTCAGATTC
12593870 AAAAAAAAACA
1 AAAAAAAAACA
12593881 AAAACAAAAACA
1 AAAA-AAAAACA
12593893 AAAAAAA
1 AAAAAAA
12593900 TCGAAAAACT
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
11 7 0.39
12 11 0.61
ACGTcount: A:0.90, C:0.10, G:0.00, T:0.00
Consensus pattern (11 bp):
AAAAAAAAACA
Found at i:12594767 original size:10 final size:10
Alignment explanation
Indices: 12594752--12594790 Score: 60
Period size: 10 Copynumber: 3.9 Consensus size: 10
12594742 ACTTTGAGTC
* *
12594752 AAAAAAAGAT
1 AAAAAATGAG
12594762 AAAAAATGAG
1 AAAAAATGAG
12594772 AAAAAATGAG
1 AAAAAATGAG
12594782 AAAAAATGA
1 AAAAAATGA
12594791 AAATGGAAAA
Statistics
Matches: 27, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
10 27 1.00
ACGTcount: A:0.74, C:0.00, G:0.15, T:0.10
Consensus pattern (10 bp):
AAAAAATGAG
Done.