Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Chr12 ID=Chr12-JGI_221_v2.0
Parameters: 2 7 7 80 10 50 1000
Pmatch=0.80,Pindel=0.10
tuple sizes 0,4,5,7
tuple distances 0, 29, 159, 1000
Length: 35429946
ACGTcount: A:0.33, C:0.16, G:0.16, T:0.33
Warning! 509281 characters in sequence are not A, C, G, or T
File 38 of 120
Found at i:10310892 original size:45 final size:45
Alignment explanation
Indices: 10310818--10310935 Score: 182
Period size: 45 Copynumber: 2.6 Consensus size: 45
10310808 GCTATAAACA
* *
10310818 AAAAATGAGTAAGACCCTAGCTGAAAGATGTTATGGCATCATGAT
1 AAAAGTGAGTAAGACCATAGCTGAAAGATGTTATGGCATCATGAT
* * *
10310863 AAAAGTGAGAAAGACCATAGTTGAAAGATGTTATTGCATCATGAT
1 AAAAGTGAGTAAGACCATAGCTGAAAGATGTTATGGCATCATGAT
*
10310908 AAAAGTGAGTAAGACCATAGCTAAAAGA
1 AAAAGTGAGTAAGACCATAGCTGAAAGA
10310936 CGCTATGATA
Statistics
Matches: 65, Mismatches: 8, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
45 65 1.00
ACGTcount: A:0.44, C:0.11, G:0.22, T:0.23
Consensus pattern (45 bp):
AAAAGTGAGTAAGACCATAGCTGAAAGATGTTATGGCATCATGAT
Found at i:10311131 original size:27 final size:27
Alignment explanation
Indices: 10311087--10311148 Score: 81
Period size: 27 Copynumber: 2.3 Consensus size: 27
10311077 ACGACATCAT
*
10311087 AGGTAGTCCACTAGGACACTAAATACG
1 AGGTAGTCCACGAGGACACTAAATACG
*
10311114 AGGTAGTCCACCGA-GACACTAAGTACG
1 AGGTAGTCCA-CGAGGACACTAAATACG
*
10311141 TGGTAGTC
1 AGGTAGTC
10311149 AGCTGGGACT
Statistics
Matches: 31, Mismatches: 3, Indels: 2
0.86 0.08 0.06
Matches are distributed among these distances:
27 29 0.94
28 2 0.06
ACGTcount: A:0.32, C:0.23, G:0.26, T:0.19
Consensus pattern (27 bp):
AGGTAGTCCACGAGGACACTAAATACG
Found at i:10317107 original size:101 final size:101
Alignment explanation
Indices: 10316932--10317116 Score: 334
Period size: 101 Copynumber: 1.8 Consensus size: 101
10316922 GTAACTATTC
* *
10316932 AGACGTAAGACCATGGTTGGACCATGGCAGTGTATATATGTAAGACCATAGCTGCGCTATGACAT
1 AGACGTAAGACCATGGTTGGACCATGGCAATGTATACATGTAAGACCATAGCTGCGCTATGACAT
10316997 TCTGATGATAAGACCATAACTAGGTTATGGCACTAT
66 TCTGATGATAAGACCATAACTAGGTTATGGCACTAT
* *
10317033 AGACGTAAGACCATGGTTGGACCATGGCAATGTATACATGTAAGACCATAGTTGGGCTATGACAT
1 AGACGTAAGACCATGGTTGGACCATGGCAATGTATACATGTAAGACCATAGCTGCGCTATGACAT
10317098 TCTGATGATAAGACCATAA
66 TCTGATGATAAGACCATAA
10317117 TTGGGCTATA
Statistics
Matches: 80, Mismatches: 4, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
101 80 1.00
ACGTcount: A:0.33, C:0.17, G:0.24, T:0.26
Consensus pattern (101 bp):
AGACGTAAGACCATGGTTGGACCATGGCAATGTATACATGTAAGACCATAGCTGCGCTATGACAT
TCTGATGATAAGACCATAACTAGGTTATGGCACTAT
Found at i:10317161 original size:101 final size:100
Alignment explanation
Indices: 10316955--10317263 Score: 257
Period size: 101 Copynumber: 3.1 Consensus size: 100
10316945 TGGTTGGACC
* * * * *
10316955 ATGGCAGTGTATATATGTAAGACCATAGCTGCGCTATGACATTCTGATGATAAGACCATAACTAG
1 ATGGCAATGTATACATGTAAGACCATAGTTGGGCTATGACATTCTGATGATAAGACCATAACTGG
* * * * * *** ***
10317020 GTTATGGCACTATAGACG-TAAGACCATGGTTGGACC
66 GCTATAG-ATTCT-GATGATAAGACCATAACTGGGTT
*
10317056 ATGGCAATGTATACATGTAAGACCATAGTTGGGCTATGACATTCTGATGATAAGACCATAATTGG
1 ATGGCAATGTATACATGTAAGACCATAGTTGGGCTATGACATTCTGATGATAAGACCATAACTGG
10317121 GCTATAAGATTCTGATGATAAGACCATAACTGGGTT
66 GCTAT-AGATTCTGATGATAAGACCATAACTGGGTT
* * * * * * * * * * *
10317157 ATGGC-A-CTATAGACGTAAGACCATGGTTGGACCATGGCTGTGTATACATG-TAAGACCATAGC
1 ATGGCAATGTATACATGTAAGACCATAGTTGGGCTATGAC-AT-TCT-GATGATAAGACCATAAC
* *
10317219 TGGGCTATGATATTCTGATGATAAGACCATAACAGGGTT
63 TGGGCTAT-AGATTCTGATGATAAGACCATAACTGGGTT
10317258 ATGGCA
1 ATGGCA
10317264 CTATGAACGT
Statistics
Matches: 170, Mismatches: 32, Indels: 11
0.80 0.15 0.05
Matches are distributed among these distances:
99 25 0.15
100 5 0.03
101 136 0.80
102 4 0.02
ACGTcount: A:0.32, C:0.16, G:0.24, T:0.28
Consensus pattern (100 bp):
ATGGCAATGTATACATGTAAGACCATAGTTGGGCTATGACATTCTGATGATAAGACCATAACTGG
GCTATAGATTCTGATGATAAGACCATAACTGGGTT
Found at i:10317212 original size:134 final size:134
Alignment explanation
Indices: 10316972--10317251 Score: 470
Period size: 134 Copynumber: 2.1 Consensus size: 134
10316962 TGTATATATG
* *
10316972 TAAGACCATAGCTGCGCTATGACATTCTGATGATAAGACCATAACTAGGTTATGGCACTATAGAC
1 TAAGACCATAACTGCGCTATAACATTCTGATGATAAGACCATAACTAGGTTATGGCACTATAGAC
*
10317037 GTAAGACCATGGTTGGACCATGGCAATGTATACATGTAAGACCATAGTTGGGCTATGACATTCTG
66 GTAAGACCATGGTTGGACCATGGCAATGTATACATGTAAGACCATAGCTGGGCTATGACATTCTG
10317102 ATGA
131 ATGA
* * * *
10317106 TAAGACCATAATTGGGCTATAAGATTCTGATGATAAGACCATAACTGGGTTATGGCACTATAGAC
1 TAAGACCATAACTGCGCTATAACATTCTGATGATAAGACCATAACTAGGTTATGGCACTATAGAC
** *
10317171 GTAAGACCATGGTTGGACCATGGCTGTGTATACATGTAAGACCATAGCTGGGCTATGATATTCTG
66 GTAAGACCATGGTTGGACCATGGCAATGTATACATGTAAGACCATAGCTGGGCTATGACATTCTG
10317236 ATGA
131 ATGA
10317240 TAAGACCATAAC
1 TAAGACCATAAC
10317252 AGGGTTATGG
Statistics
Matches: 135, Mismatches: 11, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
134 135 1.00
ACGTcount: A:0.33, C:0.17, G:0.23, T:0.27
Consensus pattern (134 bp):
TAAGACCATAACTGCGCTATAACATTCTGATGATAAGACCATAACTAGGTTATGGCACTATAGAC
GTAAGACCATGGTTGGACCATGGCAATGTATACATGTAAGACCATAGCTGGGCTATGACATTCTG
ATGA
Found at i:10317249 original size:33 final size:33
Alignment explanation
Indices: 10316972--10317249 Score: 141
Period size: 33 Copynumber: 8.3 Consensus size: 33
10316962 TGTATATATG
* *
10316972 TAAGACCATAGCTGCGCTATGACATTCTGATGA
1 TAAGACCATAGTTGGGCTATGACATTCTGATGA
** * * * * * *
10317005 TAAGACCATAACTAGGTTATGGCACTATAGACG-
1 TAAGACCATAGTTGGGCTATGACATTCT-GATGA
* * * * * *
10317038 TAAGACCATGGTTGGACCATGGCAATGTATACATG-
1 TAAGACCATAGTTGGGCTATGAC-AT-TCT-GATGA
10317073 TAAGACCATAGTTGGGCTATGACATTCTGATGA
1 TAAGACCATAGTTGGGCTATGACATTCTGATGA
* * *
10317106 TAAGACCATAATTGGGCTATAAGATTCTGATGA
1 TAAGACCATAGTTGGGCTATGACATTCTGATGA
** * * * * *
10317139 TAAGACCATAACTGGGTTATGGCACTATAGACG-
1 TAAGACCATAGTTGGGCTATGACATTCT-GATGA
* * * * * * *
10317172 TAAGACCATGGTTGGACCATGGCTGTGTATACATG-
1 TAAGACCATAGTTGGGCTATGAC-AT-TCT-GATGA
* *
10317207 TAAGACCATAGCTGGGCTATGATATTCTGATGA
1 TAAGACCATAGTTGGGCTATGACATTCTGATGA
10317240 TAAGACCATA
1 TAAGACCATA
10317250 ACAGGGTTAT
Statistics
Matches: 183, Mismatches: 54, Indels: 16
0.72 0.21 0.06
Matches are distributed among these distances:
32 6 0.03
33 119 0.65
34 10 0.05
35 48 0.26
ACGTcount: A:0.32, C:0.17, G:0.23, T:0.27
Consensus pattern (33 bp):
TAAGACCATAGTTGGGCTATGACATTCTGATGA
Found at i:10317277 original size:134 final size:134
Alignment explanation
Indices: 10317003--10317281 Score: 418
Period size: 134 Copynumber: 2.1 Consensus size: 134
10316993 ACATTCTGAT
10317003 GATAAGACCATAACTAGGTTATGGCACTATAGACGTAAGACCATGGTTGGACCATGGCAATGTAT
1 GATAAGACCATAACTAGGTTATGGCACTATAGACGTAAGACCATGGTTGGACCATGGCAATGTAT
* ** * *
10317068 ACATGTAAGACCATAGTTGGGCTATGACATTCTGATGATAAGACCATAATTGGGCTATAAGATTC
66 ACATGTAAGACCATAGCTGGGCTATGACATTCTGATGATAAGACCATAACAGGGCTATAAGACTA
*
10317133 TGAT
131 TGAC
* **
10317137 GATAAGACCATAACTGGGTTATGGCACTATAGACGTAAGACCATGGTTGGACCATGGCTGTGTAT
1 GATAAGACCATAACTAGGTTATGGCACTATAGACGTAAGACCATGGTTGGACCATGGCAATGTAT
* * *
10317202 ACATGTAAGACCATAGCTGGGCTATGATATTCTGATGATAAGACCATAACAGGGTTAT-GGCACT
66 ACATGTAAGACCATAGCTGGGCTATGACATTCTGATGATAAGACCATAACAGGGCTATAAG-ACT
10317266 ATGAAC
130 ATG-AC
10317272 G-TAAGACCAT
1 GATAAGACCAT
10317282 GGCAAGGCCA
Statistics
Matches: 131, Mismatches: 12, Indels: 4
0.89 0.08 0.03
Matches are distributed among these distances:
133 1 0.01
134 128 0.98
135 2 0.02
ACGTcount: A:0.33, C:0.16, G:0.24, T:0.27
Consensus pattern (134 bp):
GATAAGACCATAACTAGGTTATGGCACTATAGACGTAAGACCATGGTTGGACCATGGCAATGTAT
ACATGTAAGACCATAGCTGGGCTATGACATTCTGATGATAAGACCATAACAGGGCTATAAGACTA
TGAC
Found at i:10317293 original size:101 final size:99
Alignment explanation
Indices: 10317105--10317316 Score: 284
Period size: 101 Copynumber: 2.1 Consensus size: 99
10317095 CATTCTGATG
** *
10317105 ATAAGACCATAATTGGGCTATAAGATTCTGATGATAAGACCATAACTGGGTTATGGCACTATAGA
1 ATAAGACCATAGCTGGGCTATAAGATTCTGATGATAAGACCATAACAGGGTTATGGCACTATAGA
** **
10317170 CGTAAGACCATGGTTGGACCATGGCTGTGTATACAT
66 CGTAAGACCATGGAAGGACCATGGCAATG--TACAT
* * *
10317206 GTAAGACCATAGCTGGGCTATGATATTCTGATGATAAGACCATAACAGGGTTATGGCACTAT-GA
1 ATAAGACCATAGCTGGGCTATAAGATTCTGATGATAAGACCATAACAGGGTTATGGCACTATAG-
10317270 ACGTAAGACCATGGCAAGG-CCATGGCAATGTACAT
65 ACGTAAGACCATGG-AAGGACCATGGCAATGTACAT
10317305 ATAAGACCATAG
1 ATAAGACCATAG
10317317 TTGAACTATG
Statistics
Matches: 98, Mismatches: 11, Indels: 6
0.85 0.10 0.05
Matches are distributed among these distances:
99 16 0.16
100 1 0.01
101 79 0.81
102 2 0.02
ACGTcount: A:0.34, C:0.17, G:0.24, T:0.25
Consensus pattern (99 bp):
ATAAGACCATAGCTGGGCTATAAGATTCTGATGATAAGACCATAACAGGGTTATGGCACTATAGA
CGTAAGACCATGGAAGGACCATGGCAATGTACAT
Found at i:10317310 original size:134 final size:134
Alignment explanation
Indices: 10317003--10317329 Score: 343
Period size: 134 Copynumber: 2.4 Consensus size: 134
10316993 ACATTCTGAT
* ** * * *
10317003 GATAAGACCATAACTAGGTTATGGCACTATAGACGTAAGACCATGGTTGGACCATGGCAATGTAT
1 GATAAGACCATAACAAGGCCATGGCAATATACACATAAGACCATGGTTGGACCATGGCAATGTAT
* ** * *
10317068 ACATGTAAGACCATAGTTGGGCTATGACATTCTGATGATAAGACCATAATTGGGCTATAAGATTC
66 ACATGTAAGACCATAGCTGGGCTATGACATTCTGATGATAAGACCATAACAGGGCTATAAGACTA
*
10317133 TGAT
131 TGAC
** ** * * * **
10317137 GATAAGACCATAACTGGGTTATGGCACTATAGACGTAAGACCATGGTTGGACCATGGCTGTGTAT
1 GATAAGACCATAACAAGGCCATGGCAATATACACATAAGACCATGGTTGGACCATGGCAATGTAT
* * *
10317202 ACATGTAAGACCATAGCTGGGCTATGATATTCTGATGATAAGACCATAACAGGGTTAT-GGCACT
66 ACATGTAAGACCATAGCTGGGCTATGACATTCTGATGATAAGACCATAACAGGGCTATAAG-ACT
10317266 ATGAAC
130 ATG-AC
** * * * * *
10317272 G-TAAGACCATGGCAAGGCCATGGCAATGTACATATAAGACCATAGTTGAACTATGGCA
1 GATAAGACCATAACAAGGCCATGGCAATATACACATAAGACCATGGTTGGACCATGGCA
10317330 CAATATGAAA
Statistics
Matches: 164, Mismatches: 27, Indels: 4
0.84 0.14 0.02
Matches are distributed among these distances:
133 1 0.01
134 161 0.98
135 2 0.01
ACGTcount: A:0.33, C:0.17, G:0.24, T:0.26
Consensus pattern (134 bp):
GATAAGACCATAACAAGGCCATGGCAATATACACATAAGACCATGGTTGGACCATGGCAATGTAT
ACATGTAAGACCATAGCTGGGCTATGACATTCTGATGATAAGACCATAACAGGGCTATAAGACTA
TGAC
Found at i:10320553 original size:18 final size:17
Alignment explanation
Indices: 10320530--10320705 Score: 89
Period size: 19 Copynumber: 10.0 Consensus size: 17
10320520 GAAGGAGAGG
10320530 GGAAG-AAGAAGAAAGAAA
1 GGAAGAAAGAA-AAAG-AA
10320548 GGAAGAAAGAAAAAGAA
1 GGAAGAAAGAAAAAGAA
* *
10320565 GG-A-AAAGGAAAGGAGA
1 GGAAGAAAGAAAAAGA-A
10320581 GGAAAGAAAGAAAAAGAA
1 GG-AAGAAAGAAAAAGAA
* * *
10320599 GGAAAGAAAAGGAAAGGGA
1 GG-AAG-AAAGAAAAAGAA
*
10320618 GGAAAGAAAGAAAAATAA
1 GG-AAGAAAGAAAAAGAA
*
10320636 GGAAAGAAAAGGAAAGGAGAA
1 GG-AAG-AAA-GAAA-AAGAA
10320657 GAGAA-AAA-AAAAAGAA
1 G-GAAGAAAGAAAAAGAA
**
10320673 -GAAG-AAGAAGAGGGAA
1 GGAAGAAAGAA-AAAGAA
10320689 GGAAGGAAA-AAAAAGAA
1 GGAA-GAAAGAAAAAGAA
10320706 AATAAAGTAA
Statistics
Matches: 124, Mismatches: 18, Indels: 33
0.71 0.10 0.19
Matches are distributed among these distances:
14 5 0.04
15 11 0.09
16 12 0.10
17 14 0.11
18 34 0.27
19 37 0.30
20 4 0.03
21 6 0.05
22 1 0.01
ACGTcount: A:0.66, C:0.00, G:0.33, T:0.01
Consensus pattern (17 bp):
GGAAGAAAGAAAAAGAA
Found at i:10320563 original size:10 final size:10
Alignment explanation
Indices: 10320532--10320603 Score: 54
Period size: 10 Copynumber: 6.6 Consensus size: 10
10320522 AGGAGAGGGG
*
10320532 AAGAAGAAGA
1 AAGAAAAAGA
10320542 AAGAAAGGAAGA
1 AAGAAA--AAGA
10320554 AAGAAAAAGA
1 AAGAAAAAGA
* *
10320564 AGGAAAAGGA
1 AAGAAAAAGA
10320574 AAGGAGAGGAAAGA
1 AA-GA-A--AAAGA
10320588 AAGAAAAAGA
1 AAGAAAAAGA
*
10320598 AGGAAA
1 AAGAAA
10320604 GAAAAGGAAA
Statistics
Matches: 50, Mismatches: 6, Indels: 12
0.74 0.09 0.18
Matches are distributed among these distances:
10 28 0.56
11 2 0.04
12 12 0.24
13 2 0.04
14 6 0.12
ACGTcount: A:0.68, C:0.00, G:0.32, T:0.00
Consensus pattern (10 bp):
AAGAAAAAGA
Found at i:10320563 original size:22 final size:23
Alignment explanation
Indices: 10320532--10320632 Score: 73
Period size: 24 Copynumber: 4.3 Consensus size: 23
10320522 AGGAGAGGGG
*
10320532 AAGAAGAAGAAAG-AAAGGAAGA
1 AAGAAAAAGAAAGAAAAGGAAGA
*
10320554 AAGAAAAAGAAGGAAAAGGAA-A
1 AAGAAAAAGAAAGAAAAGGAAGA
* * *
10320576 GGAGAGGAAAGAAAGAAAAAGAAGGA
1 -AAGA-AAAAGAAAGAAAAGGAA-GA
* **
10320602 AAGAAAAGGAAAG-GGAGGAAAGA
1 AAGAAAAAGAAAGAAAAGG-AAGA
10320625 AAGAAAAA
1 AAGAAAAA
10320633 TAAGGAAAGA
Statistics
Matches: 60, Mismatches: 13, Indels: 11
0.71 0.15 0.13
Matches are distributed among these distances:
22 12 0.20
23 21 0.35
24 23 0.38
25 3 0.05
26 1 0.02
ACGTcount: A:0.67, C:0.00, G:0.33, T:0.00
Consensus pattern (23 bp):
AAGAAAAAGAAAGAAAAGGAAGA
Found at i:10320578 original size:5 final size:5
Alignment explanation
Indices: 10320563--10320653 Score: 59
Period size: 5 Copynumber: 19.0 Consensus size: 5
10320553 AAAGAAAAAG
* * * *
10320563 AAGGAA AAGGA AAGGA GAGGA AA-GA AAGAA AAAG- AAGGA AAGAA AAGGA
1 AAGG-A AAGGA AAGGA AAGGA AAGGA AAGGA AAGGA AAGGA AAGGA AAGGA
* * *
10320612 AAGG- GAGGA AA-GA AA-GA AA-AA TAAGGA AAGAA AAGGA AAGGA
1 AAGGA AAGGA AAGGA AAGGA AAGGA -AAGGA AAGGA AAGGA AAGGA
10320654 GAAGAGAAAA
Statistics
Matches: 66, Mismatches: 14, Indels: 11
0.73 0.15 0.12
Matches are distributed among these distances:
4 19 0.29
5 42 0.64
6 5 0.08
ACGTcount: A:0.65, C:0.00, G:0.34, T:0.01
Consensus pattern (5 bp):
AAGGA
Found at i:10320590 original size:28 final size:28
Alignment explanation
Indices: 10320535--10320644 Score: 86
Period size: 27 Copynumber: 3.9 Consensus size: 28
10320525 AGAGGGGAAG
10320535 AAGAA-GAAAG-AAAGG-AAGAAAGAAA
1 AAGAAGGAAAGAAAAGGAAAGAAAGAAA
10320560 AAGAAGGAAAAGGAAAGGAGAGGAAAGAAAGAAA
1 AAGAAGG-AAA-G-AA--A-AGGAAAGAAAGAAA
** *
10320594 AAGAAGGAAAGAAAAGGAAAGGGAG-GA
1 AAGAAGGAAAGAAAAGGAAAGAAAGAAA
*
10320621 AAGAAAGAAA-AATAAGGAAAGAAA
1 AAGAAGGAAAGAA-AAGGAAAGAAA
10320645 AGGAAAGGAG
Statistics
Matches: 69, Mismatches: 6, Indels: 18
0.74 0.06 0.19
Matches are distributed among these distances:
25 5 0.07
26 3 0.04
27 22 0.32
28 10 0.14
29 1 0.01
30 1 0.01
31 2 0.03
32 2 0.03
33 6 0.09
34 17 0.25
ACGTcount: A:0.67, C:0.00, G:0.32, T:0.01
Consensus pattern (28 bp):
AAGAAGGAAAGAAAAGGAAAGAAAGAAA
Found at i:10320608 original size:38 final size:38
Alignment explanation
Indices: 10320550--10320707 Score: 179
Period size: 37 Copynumber: 4.3 Consensus size: 38
10320540 GAAAGAAAGG
10320550 AAGAAAGAAAAAGAA-G---GAAAAGGAAAGGAGAGGA
1 AAGAAAGAAAAAGAAGGAAAGAAAAGGAAAGGAGAGGA
10320584 AAGAAAGAAAAAGAAGGAAAGAAAAGGAAAGG-GAGGA
1 AAGAAAGAAAAAGAAGGAAAGAAAAGGAAAGGAGAGGA
* *
10320621 AAGAAAGAAAAATAAGGAAAGAAAAGGAAAGGAGAAGA
1 AAGAAAGAAAAAGAAGGAAAGAAAAGGAAAGGAGAGGA
* * *
10320659 GAA-AAA-AAAAAGAAGAAGAAGAAGAGGGAAGGA-AGGAA
1 -AAGAAAGAAAAAGAAGGA-AAGAAAAGGAAAGGAGAGG-A
*
10320697 AAAAAAGAAAA
1 AAGAAAGAAAA
10320708 TAAAGTAATT
Statistics
Matches: 107, Mismatches: 7, Indels: 15
0.83 0.05 0.12
Matches are distributed among these distances:
34 15 0.14
35 1 0.01
37 49 0.46
38 36 0.34
39 6 0.06
ACGTcount: A:0.68, C:0.00, G:0.32, T:0.01
Consensus pattern (38 bp):
AAGAAAGAAAAAGAAGGAAAGAAAAGGAAAGGAGAGGA
Found at i:10320610 original size:10 final size:10
Alignment explanation
Indices: 10320552--10320651 Score: 79
Period size: 10 Copynumber: 10.5 Consensus size: 10
10320542 AAGAAAGGAA
*
10320552 GAAAGAAAAA
1 GAAAGAAAAG
*
10320562 GAAGGAAAAG
1 GAAAGAAAAG
* *
10320572 GAAAGGAGAG
1 GAAAGAAAAG
10320582 GAAAG-AAA-
1 GAAAGAAAAG
10320590 GAAA-AAGAAG
1 GAAAGAA-AAG
10320600 GAAAGAAAAG
1 GAAAGAAAAG
**
10320610 GAAAG-GGAG
1 GAAAGAAAAG
10320619 GAAAG-AAA-
1 GAAAGAAAAG
10320627 GAAA-AATAAG
1 GAAAGAA-AAG
10320637 GAAAGAAAAG
1 GAAAGAAAAG
10320647 GAAAG
1 GAAAG
10320652 GAGAAGAGAA
Statistics
Matches: 72, Mismatches: 10, Indels: 16
0.73 0.10 0.16
Matches are distributed among these distances:
8 10 0.14
9 14 0.19
10 44 0.61
11 4 0.06
ACGTcount: A:0.66, C:0.00, G:0.33, T:0.01
Consensus pattern (10 bp):
GAAAGAAAAG
Found at i:10320655 original size:75 final size:74
Alignment explanation
Indices: 10320544--10320712 Score: 189
Period size: 75 Copynumber: 2.2 Consensus size: 74
10320534 GAAGAAGAAA
* * * *
10320544 GAAAGGAAGAAAGAAAAAGAAGGAAAAGGAAAGGAGAGGA-AAGAAAGAAAAAGAAGGA-AAGAA
1 GAAAGAAAGAAA-AAAAAGAAAGAAAAGGAAAGGAGAAGAGAA-AAA-AAAAAGAAGAAGAAGAA
*
10320607 AAGGAAAGGGAG
63 AAGGAAAGGAAG
* *
10320619 GAAAGAAAGAAAAATAAGGAAAGAAAAGGAAAGGAGAAGAGAAAAAAAAAAGAAGAAGAAGAAGA
1 GAAAGAAAGAAAAA-AAAGAAAGAAAAGGAAAGGAGAAGAGAAAAAAAAAAGAAGAAGAAGAAAA
*
10320684 GGGAAGGAAG
65 GGAAAGGAAG
* *
10320694 GAAAAAAAAGAAAATAAAG
1 G-AAAGAAAGAAAAAAAAG
10320713 TAATTTTTAT
Statistics
Matches: 79, Mismatches: 11, Indels: 8
0.81 0.11 0.08
Matches are distributed among these distances:
74 12 0.15
75 54 0.68
76 13 0.16
ACGTcount: A:0.67, C:0.00, G:0.32, T:0.01
Consensus pattern (74 bp):
GAAAGAAAGAAAAAAAAGAAAGAAAAGGAAAGGAGAAGAGAAAAAAAAAAGAAGAAGAAGAAAAG
GAAAGGAAG
Found at i:10321413 original size:18 final size:17
Alignment explanation
Indices: 10321390--10321436 Score: 60
Period size: 17 Copynumber: 2.7 Consensus size: 17
10321380 AAAAAATATA
10321390 TAATATTTTGATATTTTT-
1 TAATATTTT-AT-TTTTTG
10321408 TAATATTTTATTTTTTG
1 TAATATTTTATTTTTTG
*
10321425 TAATGTTTTATT
1 TAATATTTTATT
10321437 ATGGGTTTTA
Statistics
Matches: 27, Mismatches: 1, Indels: 3
0.87 0.03 0.10
Matches are distributed among these distances:
16 5 0.19
17 13 0.48
18 9 0.33
ACGTcount: A:0.26, C:0.00, G:0.06, T:0.68
Consensus pattern (17 bp):
TAATATTTTATTTTTTG
Found at i:10321463 original size:13 final size:13
Alignment explanation
Indices: 10321445--10321470 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
10321435 TTATGGGTTT
10321445 TATAAAAAAATAA
1 TATAAAAAAATAA
10321458 TATAAAAAAATAA
1 TATAAAAAAATAA
10321471 AAAATTACCA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.77, C:0.00, G:0.00, T:0.23
Consensus pattern (13 bp):
TATAAAAAAATAA
Found at i:10321565 original size:16 final size:16
Alignment explanation
Indices: 10321544--10321575 Score: 55
Period size: 16 Copynumber: 2.0 Consensus size: 16
10321534 CAAAATATAT
*
10321544 CAAAAAAAGTAAAAAA
1 CAAAAAAAATAAAAAA
10321560 CAAAAAAAATAAAAAA
1 CAAAAAAAATAAAAAA
10321576 AACAGAAAAA
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 15 1.00
ACGTcount: A:0.84, C:0.06, G:0.03, T:0.06
Consensus pattern (16 bp):
CAAAAAAAATAAAAAA
Found at i:10321577 original size:9 final size:9
Alignment explanation
Indices: 10321554--10321589 Score: 54
Period size: 9 Copynumber: 3.9 Consensus size: 9
10321544 CAAAAAAAGT
10321554 AAAAAACAA
1 AAAAAACAA
*
10321563 AAAAAATAA
1 AAAAAACAA
10321572 AAAAAACAGA
1 AAAAAACA-A
10321582 AAAAAACA
1 AAAAAACA
10321590 CACTAAATTA
Statistics
Matches: 24, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
9 15 0.62
10 9 0.38
ACGTcount: A:0.86, C:0.08, G:0.03, T:0.03
Consensus pattern (9 bp):
AAAAAACAA
Found at i:10327452 original size:27 final size:27
Alignment explanation
Indices: 10327422--10327500 Score: 95
Period size: 27 Copynumber: 2.9 Consensus size: 27
10327412 GGCAGGGCTA
*
10327422 GTGCCGCCAACCTGGTTCCCTCCACTG
1 GTGCCGCCAACCTGCTTCCCTCCACTG
****
10327449 GTGCCGCCAACCTGCTTCCCTTGTTTG
1 GTGCCGCCAACCTGCTTCCCTCCACTG
* *
10327476 GTGCCGCCAACCTACTTCTCTCCAC
1 GTGCCGCCAACCTGCTTCCCTCCAC
10327501 CCAGGGAGTT
Statistics
Matches: 41, Mismatches: 11, Indels: 0
0.79 0.21 0.00
Matches are distributed among these distances:
27 41 1.00
ACGTcount: A:0.11, C:0.43, G:0.19, T:0.27
Consensus pattern (27 bp):
GTGCCGCCAACCTGCTTCCCTCCACTG
Found at i:10327548 original size:16 final size:16
Alignment explanation
Indices: 10327526--10327563 Score: 51
Period size: 16 Copynumber: 2.4 Consensus size: 16
10327516 ATCAGTTCAG
*
10327526 GTTTTTTTT-CTTTCT
1 GTTTTTTTTGTTTTCT
*
10327541 GTTTTTTTTGTTTTTT
1 GTTTTTTTTGTTTTCT
10327557 GTTTTTT
1 GTTTTTT
10327564 ATATATTTTG
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
15 9 0.45
16 11 0.55
ACGTcount: A:0.00, C:0.05, G:0.11, T:0.84
Consensus pattern (16 bp):
GTTTTTTTTGTTTTCT
Found at i:10327620 original size:27 final size:26
Alignment explanation
Indices: 10327562--10327620 Score: 91
Period size: 27 Copynumber: 2.2 Consensus size: 26
10327552 TTTTTGTTTT
*
10327562 TTATATATTTTGGTAAATAAAAAAAT
1 TTATATATTTTGGTAAATAAAAAAAG
10327588 TATATATATTTTGGTAAATAAAAAAAAG
1 T-TATATATTTTGGTAAAT-AAAAAAAG
10327616 TTATA
1 TTATA
10327621 ACATTTTAGT
Statistics
Matches: 30, Mismatches: 1, Indels: 3
0.88 0.03 0.09
Matches are distributed among these distances:
26 1 0.03
27 21 0.70
28 8 0.27
ACGTcount: A:0.51, C:0.00, G:0.08, T:0.41
Consensus pattern (26 bp):
TTATATATTTTGGTAAATAAAAAAAG
Found at i:10327626 original size:28 final size:27
Alignment explanation
Indices: 10327563--10327632 Score: 88
Period size: 27 Copynumber: 2.6 Consensus size: 27
10327553 TTTTGTTTTT
*
10327563 TATATATTTTGGTAAATAAAAAAATTA
1 TATACATTTTGGTAAATAAAAAAATTA
*
10327590 TATATATTTTGGTAAATAAAAAAAAGTTA
1 TATACATTTTGGTAAAT-AAAAAAA-TTA
*
10327619 TA-ACATTTTAGTAA
1 TATACATTTTGGTAA
10327633 TTTTTATTTT
Statistics
Matches: 39, Mismatches: 2, Indels: 3
0.89 0.05 0.07
Matches are distributed among these distances:
27 17 0.44
28 17 0.44
29 5 0.13
ACGTcount: A:0.50, C:0.01, G:0.09, T:0.40
Consensus pattern (27 bp):
TATACATTTTGGTAAATAAAAAAATTA
Found at i:10337296 original size:14 final size:14
Alignment explanation
Indices: 10337274--10337307 Score: 50
Period size: 14 Copynumber: 2.4 Consensus size: 14
10337264 TGTTAACATC
* *
10337274 ATTATAATTAACTA
1 ATTAAAATTAAATA
10337288 ATTAAAATTAAATA
1 ATTAAAATTAAATA
10337302 ATTAAA
1 ATTAAA
10337308 TAATATTTTC
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
14 18 1.00
ACGTcount: A:0.59, C:0.03, G:0.00, T:0.38
Consensus pattern (14 bp):
ATTAAAATTAAATA
Found at i:10337747 original size:29 final size:30
Alignment explanation
Indices: 10337688--10337747 Score: 95
Period size: 29 Copynumber: 2.0 Consensus size: 30
10337678 GGGGGTGGGA
**
10337688 TGGGAGGAGAGTAAAAGTTTTGGGGGGAAG
1 TGGGAGGAGAGTAAAAGTTTTGGGGAAAAG
10337718 TGGGAGG-GAGTAAAAGTTTTGGGGAAAAG
1 TGGGAGGAGAGTAAAAGTTTTGGGGAAAAG
10337747 T
1 T
10337748 AAAGAGGTTT
Statistics
Matches: 28, Mismatches: 2, Indels: 1
0.90 0.06 0.03
Matches are distributed among these distances:
29 21 0.75
30 7 0.25
ACGTcount: A:0.32, C:0.00, G:0.47, T:0.22
Consensus pattern (30 bp):
TGGGAGGAGAGTAAAAGTTTTGGGGAAAAG
Found at i:10341750 original size:15 final size:15
Alignment explanation
Indices: 10341730--10341760 Score: 62
Period size: 15 Copynumber: 2.1 Consensus size: 15
10341720 ACATCTATCG
10341730 AAATAGATGAATTAC
1 AAATAGATGAATTAC
10341745 AAATAGATGAATTAC
1 AAATAGATGAATTAC
10341760 A
1 A
10341761 TGCAACATCC
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 16 1.00
ACGTcount: A:0.55, C:0.06, G:0.13, T:0.26
Consensus pattern (15 bp):
AAATAGATGAATTAC
Found at i:10345311 original size:16 final size:16
Alignment explanation
Indices: 10345290--10345330 Score: 55
Period size: 16 Copynumber: 2.6 Consensus size: 16
10345280 AAACATCTTA
*
10345290 AAAATAAATGGTATAT
1 AAAATAAATAGTATAT
*
10345306 AAAATAGATAGTATAT
1 AAAATAAATAGTATAT
*
10345322 AAAAAAAAT
1 AAAATAAAT
10345331 TGCAATTGAT
Statistics
Matches: 21, Mismatches: 4, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
16 21 1.00
ACGTcount: A:0.63, C:0.00, G:0.10, T:0.27
Consensus pattern (16 bp):
AAAATAAATAGTATAT
Found at i:10348991 original size:138 final size:140
Alignment explanation
Indices: 10348809--10349095 Score: 519
Period size: 138 Copynumber: 2.1 Consensus size: 140
10348799 AAGCCATTGG
10348809 ATTCTC-AAAAATCCAACAATATTATGAAAACATACTGGTTCAAACACTATATAGACCCAAAAGA
1 ATTCTCTAAAAATCCAACAATATTATGAAAACATACTGGTTCAAACACTATATAGACCCAAAAGA
10348873 TCCAAATTTTATTACCCATTCAACAACCCAAATATTAAAAATTCTTTGACC-AAAGGATTGGG-T
66 TCCAAATTTTATTACCCATTCAACAACCCAAATATTAAAAATTCTTTGACCAAAAGGATTGGGAT
10348936 GAAAACCCAA
131 GAAAACCCAA
*
10348946 ATTCTCTAAAACA-CCAGCAATATTATGAAAACATACTGGTTCAAACACTATATAGACCCAAAAG
1 ATTCTCTAAAA-ATCCAACAATATTATGAAAACATACTGGTTCAAACACTATATAGACCCAAAAG
*
10349010 ATCCAAATTTTATTACCCATTCAACAGCCCAAATATTAAAAATTCTTTGACCAAAAGGATTGGGA
65 ATCCAAATTTTATTACCCATTCAACAACCCAAATATTAAAAATTCTTTGACCAAAAGGATTGGGA
10349075 TGAAAACCCAA
130 TGAAAACCCAA
10349086 ATTCTCTAAA
1 ATTCTCTAAA
10349096 GAAATTTCTA
Statistics
Matches: 144, Mismatches: 2, Indels: 5
0.95 0.01 0.03
Matches are distributed among these distances:
137 6 0.04
138 105 0.73
139 12 0.08
140 21 0.15
ACGTcount: A:0.44, C:0.21, G:0.09, T:0.26
Consensus pattern (140 bp):
ATTCTCTAAAAATCCAACAATATTATGAAAACATACTGGTTCAAACACTATATAGACCCAAAAGA
TCCAAATTTTATTACCCATTCAACAACCCAAATATTAAAAATTCTTTGACCAAAAGGATTGGGAT
GAAAACCCAA
Found at i:10350430 original size:22 final size:22
Alignment explanation
Indices: 10350402--10350446 Score: 65
Period size: 22 Copynumber: 2.0 Consensus size: 22
10350392 CGTTTGATTC
*
10350402 TATTAAATAAATCAT-TAAAAAA
1 TATTAAAAAAAT-ATCTAAAAAA
10350424 TATTAAAAAAATATCTAAAAAA
1 TATTAAAAAAATATCTAAAAAA
10350446 T
1 T
10350447 TGGTTCAACT
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
21 2 0.10
22 19 0.90
ACGTcount: A:0.64, C:0.04, G:0.00, T:0.31
Consensus pattern (22 bp):
TATTAAAAAAATATCTAAAAAA
Found at i:10350446 original size:11 final size:10
Alignment explanation
Indices: 10350402--10350446 Score: 54
Period size: 11 Copynumber: 4.1 Consensus size: 10
10350392 CGTTTGATTC
10350402 TATTAAATAAA
1 TATTAAA-AAA
10350413 TCATTAAAAAA
1 T-ATTAAAAAA
10350424 TATTAAAAAAA
1 TATT-AAAAAA
10350435 TATCTAAAAAA
1 TAT-TAAAAAA
10350446 T
1 T
10350447 TGGTTCAACT
Statistics
Matches: 31, Mismatches: 0, Indels: 6
0.84 0.00 0.16
Matches are distributed among these distances:
10 3 0.10
11 21 0.68
12 7 0.23
ACGTcount: A:0.64, C:0.04, G:0.00, T:0.31
Consensus pattern (10 bp):
TATTAAAAAA
Found at i:10350972 original size:22 final size:22
Alignment explanation
Indices: 10350926--10350973 Score: 62
Period size: 22 Copynumber: 2.2 Consensus size: 22
10350916 TTTGTTAATT
*
10350926 TAAATTTAATGATAAAAACATA
1 TAAATTTAATGATAAAAACAAA
*
10350948 TAAATATTAAT-ATAAAAATAAA
1 TAAAT-TTAATGATAAAAACAAA
10350970 TAAA
1 TAAA
10350974 AATTTCTGAA
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
22 18 0.78
23 5 0.22
ACGTcount: A:0.65, C:0.02, G:0.02, T:0.31
Consensus pattern (22 bp):
TAAATTTAATGATAAAAACAAA
Found at i:10353243 original size:36 final size:36
Alignment explanation
Indices: 10353192--10353272 Score: 126
Period size: 36 Copynumber: 2.2 Consensus size: 36
10353182 AAATGTGATA
* *
10353192 TTAATATATTTTATATTTATTTAAGTTTTGTTCGGT
1 TTAAAATATTTTATATTTATTTAAGTTTTATTCGGT
*
10353228 TTAAAATATTTTATATTTGTTTAAGTTTTATTCGGT
1 TTAAAATATTTTATATTTATTTAAGTTTTATTCGGT
*
10353264 CTAAAATAT
1 TTAAAATAT
10353273 GAGTTTAAAA
Statistics
Matches: 41, Mismatches: 4, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
36 41 1.00
ACGTcount: A:0.30, C:0.04, G:0.10, T:0.57
Consensus pattern (36 bp):
TTAAAATATTTTATATTTATTTAAGTTTTATTCGGT
Found at i:10353379 original size:26 final size:27
Alignment explanation
Indices: 10353341--10353414 Score: 80
Period size: 27 Copynumber: 2.8 Consensus size: 27
10353331 TTACTTCCCC
*
10353341 ATATTATTTTTTATTTTTAAAATATTT
1 ATATTATTTTTAATTTTTAAAATATTT
* * *
10353368 ATATTATATTTAATATTT-AAATTTTT
1 ATATTATTTTTAATTTTTAAAATATTT
*
10353394 ATA-TATTTTTCATTTATTAAA
1 ATATTATTTTTAATTT-TTAAA
10353415 TTTATATAAA
Statistics
Matches: 38, Mismatches: 7, Indels: 4
0.78 0.14 0.08
Matches are distributed among these distances:
25 9 0.24
26 12 0.32
27 17 0.45
ACGTcount: A:0.36, C:0.01, G:0.00, T:0.62
Consensus pattern (27 bp):
ATATTATTTTTAATTTTTAAAATATTT
Found at i:10353415 original size:26 final size:26
Alignment explanation
Indices: 10353341--10353422 Score: 85
Period size: 26 Copynumber: 3.1 Consensus size: 26
10353331 TTACTTCCCC
* *
10353341 ATATTATTTTTTATTTTTAAAATATTT
1 ATATTATTTTTAATTTTT-AAATTTTT
* *
10353368 ATATTATATTTAATATTTAAATTTTT
1 ATATTATTTTTAATTTTTAAATTTTT
* *
10353394 ATA-TATTTTTCATTTATTAAATTTAT
1 ATATTATTTTTAATTT-TTAAATTTTT
10353420 ATA
1 ATA
10353423 AATACGGAAC
Statistics
Matches: 46, Mismatches: 8, Indels: 3
0.81 0.14 0.05
Matches are distributed among these distances:
25 9 0.20
26 22 0.48
27 15 0.33
ACGTcount: A:0.37, C:0.01, G:0.00, T:0.62
Consensus pattern (26 bp):
ATATTATTTTTAATTTTTAAATTTTT
Found at i:10361729 original size:2 final size:2
Alignment explanation
Indices: 10361722--10361755 Score: 68
Period size: 2 Copynumber: 17.0 Consensus size: 2
10361712 TTGAACATGC
10361722 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
10361756 CTTTTCTTAA
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 32 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:10362783 original size:2 final size:2
Alignment explanation
Indices: 10362776--10362811 Score: 72
Period size: 2 Copynumber: 18.0 Consensus size: 2
10362766 TAAAACTCTT
10362776 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
10362812 AACATCAACT
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 34 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:10364019 original size:15 final size:14
Alignment explanation
Indices: 10363998--10364033 Score: 54
Period size: 15 Copynumber: 2.5 Consensus size: 14
10363988 ATAATCCTTA
*
10363998 ATAATTATCTTAAT
1 ATAATTATCCTAAT
10364012 ATTAATTATCCTAAT
1 A-TAATTATCCTAAT
10364027 ATAATTA
1 ATAATTA
10364034 AAATAGAGTT
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
14 7 0.35
15 13 0.65
ACGTcount: A:0.44, C:0.08, G:0.00, T:0.47
Consensus pattern (14 bp):
ATAATTATCCTAAT
Found at i:10364901 original size:30 final size:30
Alignment explanation
Indices: 10364867--10364929 Score: 99
Period size: 30 Copynumber: 2.1 Consensus size: 30
10364857 ACTTATTTTA
10364867 TTGTTAATTTTGTTATTATTTTAAAGACAT
1 TTGTTAATTTTGTTATTATTTTAAAGACAT
* * *
10364897 TTGTTAATTTTGTTATTCTTTTAGAGGCAT
1 TTGTTAATTTTGTTATTATTTTAAAGACAT
10364927 TTG
1 TTG
10364930 CTTGTTAAGT
Statistics
Matches: 30, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
30 30 1.00
ACGTcount: A:0.24, C:0.05, G:0.14, T:0.57
Consensus pattern (30 bp):
TTGTTAATTTTGTTATTATTTTAAAGACAT
Found at i:10366285 original size:2 final size:2
Alignment explanation
Indices: 10366280--10366319 Score: 62
Period size: 2 Copynumber: 20.0 Consensus size: 2
10366270 AAAAATTAAA
* *
10366280 AT AT AT GT AT AT AT 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
10366320 GTATTTACAA
Statistics
Matches: 34, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
2 34 1.00
ACGTcount: A:0.50, C:0.00, G:0.03, T:0.47
Consensus pattern (2 bp):
AT
Found at i:10366624 original size:3 final size:3
Alignment explanation
Indices: 10366616--10366661 Score: 83
Period size: 3 Copynumber: 15.3 Consensus size: 3
10366606 AAAAACAATT
*
10366616 ATA ATA ATA ATA ATA ACA ATA ATA ATA ATA ATA ATA ATA ATA ATA A
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA A
10366662 AATTGCTAAA
Statistics
Matches: 41, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
3 41 1.00
ACGTcount: A:0.67, C:0.02, G:0.00, T:0.30
Consensus pattern (3 bp):
ATA
Found at i:10368220 original size:44 final size:43
Alignment explanation
Indices: 10368161--10368698 Score: 202
Period size: 44 Copynumber: 12.5 Consensus size: 43
10368151 CTATTCTGCC
* * * *
10368161 GTAACCTCAGAGAGATAAGATCCTTTATTTTAATCCGCTCCACT
1 GTAACTTCAGGGAGATAAGAT-CTTTACTTTAATCTGCTCCACT
* * * ** *
10368205 GTAACTTCAGGGAGATAGGATAGTGT-CTTCGATCTGCTCCGCT
1 GTAACTTCAGGGAGATAAGAT-CTTTACTTTAATCTGCTCCACT
** *
10368248 GTAA-TCTCAGGGAGATAAGATCTCTGGCTTCAATCTGCTCCACT
1 GTAACT-TCAGGGAGATAAGATCT-TTACTTTAATCTGCTCCACT
* * ** * ** *
10368292 GTAACCTCAAGGAGATAAGATCTGAAATTCTCCGGTCTACTCCACT
1 GTAACTTCAGGGAGATAAGATCTTTACTT-T--AATCTGCTCCACT
* * * * * * * *
10368338 GTAACCTCAGGGAAATAAGA-CCTGA-TGTGATCTTCTCTACT
1 GTAACTTCAGGGAGATAAGATCTTTACTTTAATCTGCTCCACT
* * *
10368379 GTAACTTCAGAGAGATAAGATC----CTTTAATCCGCTCCATT
1 GTAACTTCAGGGAGATAAGATCTTTACTTTAATCTGCTCCACT
* * * * *
10368418 GTAA-TCTCAAGGAGATAGGAT-TACTATCTTTGATCTGCTCCGCT
1 GTAACT-TCAGGGAGATAAGATCT-TTA-CTTTAATCTGCTCCACT
* *
10368462 GTAA-TCTCAGGGAGATAAGATCTTTGGCTTTAACCTGCTCCACT
1 GTAACT-TCAGGGAGATAAGATCTTT-ACTTTAATCTGCTCCACT
* *** *
10368506 GTAACCTCAGGGAGATAAGATCTGAAATT-CTTCGGTCTACTCCACT
1 GTAACTTCAGGGAGATAAGATCT----TTACTTTAATCTGCTCCACT
* * * * * * * * *
10368552 GTAACCTCAGGGAAATTAGA-CCTGA-TGTGATCTACTCTACT
1 GTAACTTCAGGGAGATAAGATCTTTACTTTAATCTGCTCCACT
* * *
10368593 GTAACTTCAGAGAGATAAGATC----CTTTAATCCGCTCCATT
1 GTAACTTCAGGGAGATAAGATCTTTACTTTAATCTGCTCCACT
* * *
10368632 GTAA-TCTCAAGGAGAT-AGAAT-TACTATCTTTGATCTGCTCCACT
1 GTAACT-TCAGGGAGATAAG-ATCT-TTA-CTTTAATCTGCTCCACT
10368676 GTAA-TCTCAGGGAGATAAGATCT
1 GTAACT-TCAGGGAGATAAGATCT
10368699 GCAATTCTTC
Statistics
Matches: 369, Mismatches: 89, Indels: 71
0.70 0.17 0.13
Matches are distributed among these distances:
38 4 0.01
39 50 0.14
41 56 0.15
42 4 0.01
43 33 0.09
44 155 0.42
45 7 0.02
46 58 0.16
48 2 0.01
ACGTcount: A:0.28, C:0.22, G:0.19, T:0.30
Consensus pattern (43 bp):
GTAACTTCAGGGAGATAAGATCTTTACTTTAATCTGCTCCACT
Found at i:10368522 original size:214 final size:214
Alignment explanation
Indices: 10368108--10368698 Score: 909
Period size: 214 Copynumber: 2.7 Consensus size: 214
10368098 TTAGGTTTAA
** * * * * *
10368108 GTCTACTCCACTGTAATATCAGGGAGATAAGACCTGATGCGATCTAT-TCTGCCGTAACCTCAGA
1 GTCTACTCCACTGTAACCTCAGGGAAATAAGACCTGATGTGATCT-TCTCTACTGTAACTTCAGA
* * * * *
10368172 GAGATAAGATCCTTTATTTTAATCCGCTCCACTGTAA-CTTCAGGGAGATAGGA-TAGTGTCTTC
65 GAGATAAGATCC-----TTTAATCCGCTCCATTGTAATC-TCAAGGAGATAGGATTACTATCTTT
*
10368235 GATCTGCTCCGCTGTAATCTCAGGGAGATAAGATCTCTGGCTTCAATCTGCTCCACTGTAACCTC
124 GATCTGCTCCGCTGTAATCTCAGGGAGATAAGATCTCTGGCTTCAACCTGCTCCACTGTAACCTC
10368300 AAGGAGATAAGATCTGAAATTCTCCG
189 AAGGAGATAAGATCTGAAATTCTCCG
10368326 GTCTACTCCACTGTAACCTCAGGGAAATAAGACCTGATGTGATCTTCTCTACTGTAACTTCAGAG
1 GTCTACTCCACTGTAACCTCAGGGAAATAAGACCTGATGTGATCTTCTCTACTGTAACTTCAGAG
10368391 AGATAAGATCCTTTAATCCGCTCCATTGTAATCTCAAGGAGATAGGATTACTATCTTTGATCTGC
66 AGATAAGATCCTTTAATCCGCTCCATTGTAATCTCAAGGAGATAGGATTACTATCTTTGATCTGC
* * *
10368456 TCCGCTGTAATCTCAGGGAGATAAGATCTTTGGCTTTAACCTGCTCCACTGTAACCTCAGGGAGA
131 TCCGCTGTAATCTCAGGGAGATAAGATCTCTGGCTTCAACCTGCTCCACTGTAACCTCAAGGAGA
*
10368521 TAAGATCTGAAATTCTTCG
196 TAAGATCTGAAATTCTCCG
* *
10368540 GTCTACTCCACTGTAACCTCAGGGAAATTAGACCTGATGTGATCTACTCTACTGTAACTTCAGAG
1 GTCTACTCCACTGTAACCTCAGGGAAATAAGACCTGATGTGATCTTCTCTACTGTAACTTCAGAG
*
10368605 AGATAAGATCCTTTAATCCGCTCCATTGTAATCTCAAGGAGATAGAATTACTATCTTTGATCTGC
66 AGATAAGATCCTTTAATCCGCTCCATTGTAATCTCAAGGAGATAGGATTACTATCTTTGATCTGC
*
10368670 TCCACTGTAATCTCAGGGAGATAAGATCT
131 TCCGCTGTAATCTCAGGGAGATAAGATCT
10368699 GCAATTCTTC
Statistics
Matches: 349, Mismatches: 21, Indels: 10
0.92 0.06 0.03
Matches are distributed among these distances:
213 32 0.09
214 249 0.71
217 1 0.00
218 67 0.19
ACGTcount: A:0.28, C:0.23, G:0.19, T:0.30
Consensus pattern (214 bp):
GTCTACTCCACTGTAACCTCAGGGAAATAAGACCTGATGTGATCTTCTCTACTGTAACTTCAGAG
AGATAAGATCCTTTAATCCGCTCCATTGTAATCTCAAGGAGATAGGATTACTATCTTTGATCTGC
TCCGCTGTAATCTCAGGGAGATAAGATCTCTGGCTTCAACCTGCTCCACTGTAACCTCAAGGAGA
TAAGATCTGAAATTCTCCG
Found at i:10369926 original size:5 final size:5
Alignment explanation
Indices: 10369913--10369951 Score: 53
Period size: 5 Copynumber: 7.8 Consensus size: 5
10369903 GCCTCTCCCT
*
10369913 TTTTT TTTTG TTTTTG TTTTG TTTTG TTTTG TTTT- TTTT
1 TTTTG TTTTG -TTTTG TTTTG TTTTG TTTTG TTTTG TTTT
10369952 TTTGGACCTT
Statistics
Matches: 32, Mismatches: 1, Indels: 3
0.89 0.03 0.08
Matches are distributed among these distances:
4 4 0.12
5 23 0.72
6 5 0.16
ACGTcount: A:0.00, C:0.00, G:0.13, T:0.87
Consensus pattern (5 bp):
TTTTG
Found at i:10369937 original size:21 final size:21
Alignment explanation
Indices: 10369913--10369953 Score: 64
Period size: 21 Copynumber: 2.0 Consensus size: 21
10369903 GCCTCTCCCT
*
10369913 TTTTTTTTTGTTTTTGTTTTG
1 TTTTGTTTTGTTTTTGTTTTG
*
10369934 TTTTGTTTTGTTTTTTTTTT
1 TTTTGTTTTGTTTTTGTTTT
10369954 TGGACCTTCA
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
21 18 1.00
ACGTcount: A:0.00, C:0.00, G:0.12, T:0.88
Consensus pattern (21 bp):
TTTTGTTTTGTTTTTGTTTTG
Found at i:10369952 original size:10 final size:10
Alignment explanation
Indices: 10369913--10369952 Score: 62
Period size: 10 Copynumber: 3.9 Consensus size: 10
10369903 GCCTCTCCCT
10369913 TTTTTTTTTG
1 TTTTTTTTTG
10369923 TTTTTGTTTTG
1 TTTTT-TTTTG
*
10369934 TTTTGTTTTG
1 TTTTTTTTTG
10369944 TTTTTTTTT
1 TTTTTTTTT
10369953 TTGGACCTTC
Statistics
Matches: 27, Mismatches: 2, Indels: 2
0.87 0.06 0.06
Matches are distributed among these distances:
10 18 0.67
11 9 0.33
ACGTcount: A:0.00, C:0.00, G:0.12, T:0.88
Consensus pattern (10 bp):
TTTTTTTTTG
Found at i:10381033 original size:2 final size:2
Alignment explanation
Indices: 10381028--10381063 Score: 63
Period size: 2 Copynumber: 18.0 Consensus size: 2
10381018 AAAAATTAAA
*
10381028 AT AT AT GT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
10381064 GTATTTACAA
Statistics
Matches: 32, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
2 32 1.00
ACGTcount: A:0.47, C:0.00, G:0.03, T:0.50
Consensus pattern (2 bp):
AT
Found at i:10384308 original size:9 final size:9
Alignment explanation
Indices: 10384294--10384348 Score: 101
Period size: 9 Copynumber: 6.1 Consensus size: 9
10384284 TATAGTTTAA
10384294 TATTCGAAT
1 TATTCGAAT
10384303 TATTCGAAT
1 TATTCGAAT
10384312 TATTCGAAT
1 TATTCGAAT
10384321 TATTCGAAT
1 TATTCGAAT
*
10384330 TATTCGAGT
1 TATTCGAAT
10384339 TATTCGAAT
1 TATTCGAAT
10384348 T
1 T
10384349 CGAAAACTCA
Statistics
Matches: 44, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
9 44 1.00
ACGTcount: A:0.31, C:0.11, G:0.13, T:0.45
Consensus pattern (9 bp):
TATTCGAAT
Found at i:10385664 original size:26 final size:26
Alignment explanation
Indices: 10385628--10385696 Score: 79
Period size: 25 Copynumber: 2.7 Consensus size: 26
10385618 ACCATTATCG
* *
10385628 GGTTACTAACACTAGCTTTGGATT-TA
1 GGTTGCTAACACTAGCTTTGG-TTCAA
10385654 GGTTGCTAACACTAGC-TTGGTTCAA
1 GGTTGCTAACACTAGCTTTGGTTCAA
* *
10385679 TGCTGCTAACACTAGCTT
1 GGTTGCTAACACTAGCTT
10385697 CAGAGAATCC
Statistics
Matches: 37, Mismatches: 4, Indels: 4
0.82 0.09 0.09
Matches are distributed among these distances:
24 2 0.05
25 19 0.51
26 16 0.43
ACGTcount: A:0.25, C:0.20, G:0.20, T:0.35
Consensus pattern (26 bp):
GGTTGCTAACACTAGCTTTGGTTCAA
Found at i:10386777 original size:10 final size:10
Alignment explanation
Indices: 10386762--10386791 Score: 51
Period size: 10 Copynumber: 3.0 Consensus size: 10
10386752 ACTTAGATTA
10386762 AATTATAATT
1 AATTATAATT
10386772 AATTATAATT
1 AATTATAATT
*
10386782 AACTATAATT
1 AATTATAATT
10386792 GACTAACGTT
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
10 19 1.00
ACGTcount: A:0.50, C:0.03, G:0.00, T:0.47
Consensus pattern (10 bp):
AATTATAATT
Found at i:10388145 original size:51 final size:51
Alignment explanation
Indices: 10388046--10388151 Score: 117
Period size: 51 Copynumber: 2.1 Consensus size: 51
10388036 ATGTATTTTT
* **
10388046 TTAATTTTTTAGAATTAGGATCAAATTGAGAACATTTGTAAATTTTGAGAG
1 TTAATTTTTTAGAATTAGGATCAAATTGAGAACATATGTAAAAATTGAGAG
* * * *
10388097 TTAATTTTTTTA-AATTATGATTAAATTGA-AATAGTATGTAAAAATTGAGGG
1 TTAA-TTTTTTAGAATTAGGATCAAATTGAGAACA-TATGTAAAAATTGAGAG
10388148 TTAA
1 TTAA
10388152 ATTTATTATT
Statistics
Matches: 46, Mismatches: 7, Indels: 4
0.81 0.12 0.07
Matches are distributed among these distances:
50 3 0.07
51 36 0.78
52 7 0.15
ACGTcount: A:0.40, C:0.02, G:0.16, T:0.42
Consensus pattern (51 bp):
TTAATTTTTTAGAATTAGGATCAAATTGAGAACATATGTAAAAATTGAGAG
Found at i:10396942 original size:34 final size:32
Alignment explanation
Indices: 10396889--10396992 Score: 111
Period size: 34 Copynumber: 3.1 Consensus size: 32
10396879 CTTTTATATA
*
10396889 TTTTATGTTTTATAAATATATACATATACATTT
1 TTTTATGTTGTA-AAATATATACATATACATTT
* *
10396922 CTTTTATGTTGTAAATATATAGACTTATACATTTT
1 -TTTTATGTTGTAAA-ATATATACATATACA-TTT
* *
10396957 TTTCTATTTTGT-AAATATATACATATGCATTT
1 TTT-TATGTTGTAAAATATATACATATACATTT
10396989 TTTT
1 TTTT
10396993 CCTTTATTTT
Statistics
Matches: 60, Mismatches: 7, Indels: 9
0.79 0.09 0.12
Matches are distributed among these distances:
31 1 0.02
32 6 0.10
33 14 0.23
34 29 0.48
35 10 0.17
ACGTcount: A:0.32, C:0.08, G:0.06, T:0.55
Consensus pattern (32 bp):
TTTTATGTTGTAAAATATATACATATACATTT
Found at i:10398992 original size:19 final size:20
Alignment explanation
Indices: 10398955--10398994 Score: 55
Period size: 19 Copynumber: 2.0 Consensus size: 20
10398945 TCTTTAGGCA
* *
10398955 TTCATTATATGCATTTGCAT
1 TTCATTACATGCATATGCAT
10398975 TTCATTACAT-CATATGCAT
1 TTCATTACATGCATATGCAT
10398994 T
1 T
10398995 AGACACCTCT
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
19 9 0.50
20 9 0.50
ACGTcount: A:0.28, C:0.17, G:0.07, T:0.47
Consensus pattern (20 bp):
TTCATTACATGCATATGCAT
Found at i:10401880 original size:7 final size:7
Alignment explanation
Indices: 10401855--10401896 Score: 52
Period size: 7 Copynumber: 6.0 Consensus size: 7
10401845 AGTGATGTGA
10401855 AAAAATG
1 AAAAATG
10401862 AAAAGATG
1 AAAA-ATG
10401870 -AAAATG
1 AAAAATG
10401876 AAAAATG
1 AAAAATG
10401883 AAAAA-G
1 AAAAATG
10401889 TAAAAATG
1 -AAAAATG
10401897 GATAGGCTAA
Statistics
Matches: 31, Mismatches: 0, Indels: 7
0.82 0.00 0.18
Matches are distributed among these distances:
6 4 0.13
7 23 0.74
8 4 0.13
ACGTcount: A:0.69, C:0.00, G:0.17, T:0.14
Consensus pattern (7 bp):
AAAAATG
Found at i:10401894 original size:21 final size:21
Alignment explanation
Indices: 10401855--10401896 Score: 59
Period size: 21 Copynumber: 2.0 Consensus size: 21
10401845 AGTGATGTGA
*
10401855 AAAAATGAAAAGATGAAAATG
1 AAAAATGAAAAGATAAAAATG
10401876 AAAAATGAAAA-AGTAAAAATG
1 AAAAATGAAAAGA-TAAAAATG
10401897 GATAGGCTAA
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
20 1 0.05
21 18 0.95
ACGTcount: A:0.69, C:0.00, G:0.17, T:0.14
Consensus pattern (21 bp):
AAAAATGAAAAGATAAAAATG
Found at i:10403839 original size:264 final size:263
Alignment explanation
Indices: 10403222--10403865 Score: 952
Period size: 264 Copynumber: 2.4 Consensus size: 263
10403212 TACACAGCGA
* * * *
10403222 AGCAGATCGAAGATGGCGGATTTTACCT-CCTCGTAGTTACAGTGGAGTACATTGAAGCCAATGA
1 AGCAGATCGAAGATGGCGGATTTTACCTCCCT-GAAGTTGCAGTGGAGTACATTGAAGCCAGTAA
* * *
10403286 TTCTAAT-TCCCTGGACAGCAGCGGAATAGATTGAAGATTTTAGATCTTGTCTCCCTAAGCAGTA
65 TTCT-ATCTCCCTGGACAGCAGTGGAATAGA-TCAAGATTTCAGATCTTGTCTCCCTAAGCAGTA
* *
10403350 GTGGAGCAGATCAAAGACGGCAGATTTTACCTCCCTGTGGTTACAGTGGAGTACATTGAAGCCAG
128 GTGGAGCAGATCAAAGACGGCAGATTTTACCTCCCTGTGGTTACAATGGAGCACATTGAAGCCAG
10403415 TAATTCTATCTCCCTGGGCAACAATGGAATAGATTGAAGATTACAGATCTTGCCTCCCTAAGCAG
193 TAATTCTATCTCCCTGGGCAACAATGGAATAGATTGAAGATTACAGATCTTGCCTCCCTAAGCAG
10403480 TAGTGG
258 TAGTGG
* * *
10403486 AGCAGATTGAAGATGCCGGATTTTACCTCCCTGAGGTTGCAGTGGAGTACATTGAAGCCAG-AAT
1 AGCAGATCGAAGATGGCGGATTTTACCTCCCTGAAGTTGCAGTGGAGTACATTGAAGCCAGTAA-
*
10403550 TTCTATCTCCCTGGGCAGCAGTGGAATAGATCACAGATTTCAGATCTTGTCTCCCTAAGCAGTAG
65 TTCTATCTCCCTGGACAGCAGTGGAATAGATCA-AGATTTCAGATCTTGTCTCCCTAAGCAGTAG
* * *
10403615 TGGAGCAGATCAGAGATGGCGGATTTTACCTCCCTGTGGTTACAATGGAGCACATTGAAGCCAGT
129 TGGAGCAGATCAAAGACGGCAGATTTTACCTCCCTGTGGTTACAATGGAGCACATTGAAGCCAGT
*
10403680 AATTCTATCTCCCTGGGCAACAGTGGAATAGATTGAAGATTACAGATCTTGCCTCCCTAAGCAGT
194 AATTCTATCTCCCTGGGCAACAATGGAATAGATTGAAGATTACAGATCTTGCCTCCCTAAGCAGT
10403745 AGTGG
259 AGTGG
* * * *
10403750 AGTAGATCAAAGATGGCGGATTTTACCTCCCTGAAGTTGCAGTGGAGTATATTAAAGCCAGTAAT
1 AGCAGATCGAAGATGGCGGATTTTACCTCCCTGAAGTTGCAGTGGAGTACATTGAAGCCAGTAAT
* * * * * ***
10403815 TCTATCTCCCCGGTCGGTAGTGGAATCGATCGAAGAAAGCAGATCTTGTCT
66 TCTATCTCCCTGGACAGCAGTGGAATAGATC-AAGATTTCAGATCTTGTCT
10403866 TCCCATACTG
Statistics
Matches: 342, Mismatches: 32, Indels: 12
0.89 0.08 0.03
Matches are distributed among these distances:
263 5 0.01
264 331 0.97
265 6 0.02
ACGTcount: A:0.28, C:0.20, G:0.25, T:0.27
Consensus pattern (263 bp):
AGCAGATCGAAGATGGCGGATTTTACCTCCCTGAAGTTGCAGTGGAGTACATTGAAGCCAGTAAT
TCTATCTCCCTGGACAGCAGTGGAATAGATCAAGATTTCAGATCTTGTCTCCCTAAGCAGTAGTG
GAGCAGATCAAAGACGGCAGATTTTACCTCCCTGTGGTTACAATGGAGCACATTGAAGCCAGTAA
TTCTATCTCCCTGGGCAACAATGGAATAGATTGAAGATTACAGATCTTGCCTCCCTAAGCAGTAG
TGG
Found at i:10403850 original size:132 final size:132
Alignment explanation
Indices: 10403222--10403824 Score: 863
Period size: 132 Copynumber: 4.6 Consensus size: 132
10403212 TACACAGCGA
* * * *
10403222 AGCAGATCGAAGATGGCGGATTTTACCT-CCTCGTAGTTACAGTGGAGTACATTGAAGCCAATGA
1 AGCAGATCAAAGATGGCGGATTTTACCTCCCT-GTGGTTACAGTGGAGTACATTGAAGCCAGTAA
* * ** *
10403286 TTCTAAT-TCCCTGGACAGCAGCGGAATAGATTGAAGATTTTAGATCTTGTCTCCCTAAGCAGTA
65 TTCT-ATCTCCCTGGGCAGCAGTGGAATAGATTGAAGATTACAGATCTTGCCTCCCTAAGCAGTA
10403350 GTGG
129 GTGG
* *
10403354 AGCAGATCAAAGACGGCAGATTTTACCTCCCTGTGGTTACAGTGGAGTACATTGAAGCCAGTAAT
1 AGCAGATCAAAGATGGCGGATTTTACCTCCCTGTGGTTACAGTGGAGTACATTGAAGCCAGTAAT
* *
10403419 TCTATCTCCCTGGGCAACAATGGAATAGATTGAAGATTACAGATCTTGCCTCCCTAAGCAGTAGT
66 TCTATCTCCCTGGGCAGCAGTGGAATAGATTGAAGATTACAGATCTTGCCTCCCTAAGCAGTAGT
10403484 GG
131 GG
** * * *
10403486 AGCAGATTGAAGATGCCGGATTTTACCTCCCTGAGGTTGCAGTGGAGTACATTGAAGCCAG-AAT
1 AGCAGATCAAAGATGGCGGATTTTACCTCCCTGTGGTTACAGTGGAGTACATTGAAGCCAGTAA-
* * *
10403550 TTCTATCTCCCTGGGCAGCAGTGGAATAGA-TCACAGATTTCAGATCTTGTCTCCCTAAGCAGTA
65 TTCTATCTCCCTGGGCAGCAGTGGAATAGATTGA-AGATTACAGATCTTGCCTCCCTAAGCAGTA
10403614 GTGG
129 GTGG
* * *
10403618 AGCAGATCAGAGATGGCGGATTTTACCTCCCTGTGGTTACAATGGAGCACATTGAAGCCAGTAAT
1 AGCAGATCAAAGATGGCGGATTTTACCTCCCTGTGGTTACAGTGGAGTACATTGAAGCCAGTAAT
*
10403683 TCTATCTCCCTGGGCAACAGTGGAATAGATTGAAGATTACAGATCTTGCCTCCCTAAGCAGTAGT
66 TCTATCTCCCTGGGCAGCAGTGGAATAGATTGAAGATTACAGATCTTGCCTCCCTAAGCAGTAGT
10403748 GG
131 GG
* ** * * *
10403750 AGTAGATCAAAGATGGCGGATTTTACCTCCCTGAAGTTGCAGTGGAGTATATTAAAGCCAGTAAT
1 AGCAGATCAAAGATGGCGGATTTTACCTCCCTGTGGTTACAGTGGAGTACATTGAAGCCAGTAAT
10403815 TCTATCTCCC
66 TCTATCTCCC
10403825 CGGTCGGTAG
Statistics
Matches: 419, Mismatches: 46, Indels: 12
0.88 0.10 0.03
Matches are distributed among these distances:
131 6 0.01
132 406 0.97
133 7 0.02
ACGTcount: A:0.28, C:0.21, G:0.24, T:0.27
Consensus pattern (132 bp):
AGCAGATCAAAGATGGCGGATTTTACCTCCCTGTGGTTACAGTGGAGTACATTGAAGCCAGTAAT
TCTATCTCCCTGGGCAGCAGTGGAATAGATTGAAGATTACAGATCTTGCCTCCCTAAGCAGTAGT
GG
Found at i:10403954 original size:264 final size:264
Alignment explanation
Indices: 10403222--10403955 Score: 698
Period size: 264 Copynumber: 2.8 Consensus size: 264
10403212 TACACAGCGA
* * * * *
10403222 AGCAGATCGAAGATGGCGGATTTTACCT-CCTCGTAGTTACAGTGGAGTACATTGAAGCC--AAT
1 AGCAGATCAAAGATGCCGGATTTTACCTCCCT-GAAGTTGCAGTGGAGTACATTAAAGCCAGAAT
* * * * ****
10403284 GATTCTAAT-TCCCTGGACAGCAGCGGAATAGATTGA-AGATTTTAGATCTTGTCTCCCTAAGCA
65 --TTCT-ATCTCCCCGGGCAGCAGTGGAATAGA-TCACAGAAAGCAGATCTTGTCTCCCTAAGCA
* * * * ** * * ***
10403347 GTAGTGGAGCAGATCAAAGACGGCAGATTTTACCTCCCTGTGGTTACAGTGGAGTACATTGAAGC
126 GTAGTGAAGCAGATCAAAGATGACAGATCTTACCTCCCTGAAGTTACAATGGAGCACACAAAAGC
* ** *
10403412 CAGTAATTCTATCTCCCTGGGCAACAATGGAATAGATTGAAGATTACAGATCTTGCCTCCCTAAG
191 AACCAATCCTATCTCCCTGGGCAACAATGGAATAGATTGAAGATTACAGATCTTGCCTCCCTAAG
10403477 CAGTAGTGG
256 CAGTAGTGG
** * *
10403486 AGCAGATTGAAGATGCCGGATTTTACCTCCCTGAGGTTGCAGTGGAGTACATTGAAGCCAGAATT
1 AGCAGATCAAAGATGCCGGATTTTACCTCCCTGAAGTTGCAGTGGAGTACATTAAAGCCAGAATT
* ***
10403551 TCTATCTCCCTGGGCAGCAGTGGAATAGATCACAGATTTCAGATCTTGTCTCCCTAAGCAGTAGT
66 TCTATCTCCCCGGGCAGCAGTGGAATAGATCACAGAAAGCAGATCTTGTCTCCCTAAGCAGTAGT
* * * * * ** *** * **
10403616 GGAGCAGATCAGAGATGGCGGATTTTACCTCCCTGTGGTTACAATGGAGCACATTGAAGCCAGTA
131 GAAGCAGATCAAAGATGACAGATCTTACCTCCCTGAAGTTACAATGGAGCACACAAAAGCAACCA
* *
10403681 ATTCTATCTCCCTGGGCAACAGTGGAATAGATTGAAGATTACAGATCTTGCCTCCCTAAGCAGTA
196 ATCCTATCTCCCTGGGCAACAATGGAATAGATTGAAGATTACAGATCTTGCCTCCCTAAGCAGTA
10403746 GTGG
261 GTGG
* * *
10403750 AGTAGATCAAAGATGGCGGATTTTACCTCCCTGAAGTTGCAGTGGAGTATATTAAAGCCAGTAA-
1 AGCAGATCAAAGATGCCGGATTTTACCTCCCTGAAGTTGCAGTGGAGTACATTAAAGCCAG-AAT
* * * * *
10403814 TTCTATCTCCCCGGTCGGTAGTGGAATCGATCGA-AGAAAGCAGATCTTGTCTTCCC-ATA-CTG
65 TTCTATCTCCCCGGGCAGCAGTGGAATAGATC-ACAGAAAGCAGATCTTGTC-TCCCTA-AGC-A
* * * * * *
10403876 GTGGTGAAGTAGATCAAAGAT-ACA-AGTCTTATCTCCCTGAAGTTGCAGTGGAGCAGACAAAAG
126 GTAGTGAAGCAGATCAAAGATGACAGA-TCTTACCTCCCTGAAGTTACAATGGAGCACACAAAAG
*
10403939 TAACCAATCCTATCTCC
190 CAACCAATCCTATCTCC
10403956 TTGAAGTTGC
Statistics
Matches: 407, Mismatches: 52, Indels: 22
0.85 0.11 0.05
Matches are distributed among these distances:
263 5 0.01
264 371 0.91
265 28 0.07
266 3 0.01
ACGTcount: A:0.28, C:0.21, G:0.24, T:0.27
Consensus pattern (264 bp):
AGCAGATCAAAGATGCCGGATTTTACCTCCCTGAAGTTGCAGTGGAGTACATTAAAGCCAGAATT
TCTATCTCCCCGGGCAGCAGTGGAATAGATCACAGAAAGCAGATCTTGTCTCCCTAAGCAGTAGT
GAAGCAGATCAAAGATGACAGATCTTACCTCCCTGAAGTTACAATGGAGCACACAAAAGCAACCA
ATCCTATCTCCCTGGGCAACAATGGAATAGATTGAAGATTACAGATCTTGCCTCCCTAAGCAGTA
GTGG
Found at i:10403954 original size:396 final size:396
Alignment explanation
Indices: 10403222--10403955 Score: 890
Period size: 396 Copynumber: 1.9 Consensus size: 396
10403212 TACACAGCGA
* * *
10403222 AGCAGATCGAAGATGGCGGATTTTACCTCCTCGTAGTTACAGTGGAGTACATTGAAGCCAATGAT
1 AGCAGATCGAAGATGGCGGATTTTACCTCCTCGTAGTTACAATGGAGCACATTGAAGCCAATAAT
* ** *
10403287 TCTAATTCCCTGGACAGCAGCGGAATAGATTGAAGATTTTAGATCTTGTCTCCCTAAGCAGTAGT
66 TCTAATTCCCTGGACAACAGCGGAATAGATTGAAGATTACAGATCTTGCCTCCCTAAGCAGTAGT
** *
10403352 GGAGCAGATCAAAGACGGCAGATTTTACCTCCCTGTGGTTACAGTGGAGTACATTGAAGCCAGTA
131 GGAGCAGATCAAAGACGGCAGATTTTACCTCCCTGAAGTTACAGTGGAGTACATTAAAGCCAGTA
* * *
10403417 ATTCTATCTCCCTGGGCAACAATGGAATAGATTGAAGATTACAGATCTTGCCTCCCTAAGCAGTA
196 ATTCTATCTCCCCGGGCAACAATGGAATAGATCGAAGATAACAGATCTTGCCTCCCTAAGCAGTA
* ** * ** * * * *** * *
10403482 GTGGAGCAGATTGAAGATGCCGGATTTTACCTCCCTGAGGTTGCAGTGGAGTACATTGAAGCCAG
261 GTGAAGCAGATCAAAGATACAAGATCTTACCTCCCTGAAGTTGCAGTGGAGCACACAAAAGCAAC
*
10403547 AATTTCTATCTCCCTGGGCAGCAGTGGAATAGATCACAGATTTCAGATCTTGTCTCCCTAAGCAG
326 AATTCCTATCTCCCTGGGCAGCAGTGGAATAGATCACAGATTTCAGATCTTGTCTCCCTAAGCAG
10403612 TAGTGG
391 TAGTGG
* *
10403618 AGCAGATC-AGAGATGGCGGATTTTACCTCC-CTGTGGTTACAATGGAGCACATTGAAGCCAGTA
1 AGCAGATCGA-AGATGGCGGATTTTACCTCCTC-GTAGTTACAATGGAGCACATTGAAGCCAATA
* *
10403681 ATTCT-ATCTCCCTGGGCAACAGTGGAATAGATTGAAGATTACAGATCTTGCCTCCCTAAGCAGT
64 ATTCTAAT-TCCCTGGACAACAGCGGAATAGATTGAAGATTACAGATCTTGCCTCCCTAAGCAGT
* * * * *
10403745 AGTGGAGTAGATCAAAGATGGCGGATTTTACCTCCCTGAAGTTGCAGTGGAGTATATTAAAGCCA
128 AGTGGAGCAGATCAAAGACGGCAGATTTTACCTCCCTGAAGTTACAGTGGAGTACATTAAAGCCA
* *** * * *
10403810 GTAATTCTATCTCCCCGGTCGGTAGTGGAATCGATCGAAGA-AAGCAGATCTTGTCTTCCC-ATA
193 GTAATTCTATCTCCCCGGGCAACAATGGAATAGATCGAAGATAA-CAGATCTTG-CCTCCCTA-A
* * * * *
10403873 -CTGGTGGTGAAGTAGATCAAAGATACAAG-TCTTATCTCCCTGAAGTTGCAGTGGAGCAGACAA
255 GC-AGTAGTGAAGCAGATCAAAGATACAAGATCTTACCTCCCTGAAGTTGCAGTGGAGCACACAA
*
10403936 AAGTAACCAA-TCCTATCTCC
319 AAGCAA-CAATTCCTATCTCC
10403956 TTGAAGTTGC
Statistics
Matches: 280, Mismatches: 50, Indels: 16
0.81 0.14 0.05
Matches are distributed among these distances:
395 5 0.02
396 249 0.89
397 26 0.09
ACGTcount: A:0.28, C:0.21, G:0.24, T:0.27
Consensus pattern (396 bp):
AGCAGATCGAAGATGGCGGATTTTACCTCCTCGTAGTTACAATGGAGCACATTGAAGCCAATAAT
TCTAATTCCCTGGACAACAGCGGAATAGATTGAAGATTACAGATCTTGCCTCCCTAAGCAGTAGT
GGAGCAGATCAAAGACGGCAGATTTTACCTCCCTGAAGTTACAGTGGAGTACATTAAAGCCAGTA
ATTCTATCTCCCCGGGCAACAATGGAATAGATCGAAGATAACAGATCTTGCCTCCCTAAGCAGTA
GTGAAGCAGATCAAAGATACAAGATCTTACCTCCCTGAAGTTGCAGTGGAGCACACAAAAGCAAC
AATTCCTATCTCCCTGGGCAGCAGTGGAATAGATCACAGATTTCAGATCTTGTCTCCCTAAGCAG
TAGTGG
Found at i:10405591 original size:34 final size:32
Alignment explanation
Indices: 10405538--10405642 Score: 104
Period size: 34 Copynumber: 3.1 Consensus size: 32
10405528 CTTTTATATA
*
10405538 TTTTATGTTTTATAAATATATACATATACATTT
1 TTTTATGTTGTA-AAATATATACATATACATTT
* *
10405571 CTTTTATGTTGTAAATATATAGACTTATACATTTTT
1 -TTTTATGTTGTAAA-ATATATACATATACA--TTT
* *
10405607 TTTCTATTTTGT-AAATATATACATATGCATTT
1 TTT-TATGTTGTAAAATATATACATATACATTT
10405639 TTTT
1 TTTT
10405643 CCTTTATTTT
Statistics
Matches: 60, Mismatches: 7, Indels: 11
0.77 0.09 0.14
Matches are distributed among these distances:
31 1 0.02
32 6 0.10
33 2 0.03
34 36 0.60
35 5 0.08
36 10 0.17
ACGTcount: A:0.31, C:0.08, G:0.06, T:0.55
Consensus pattern (32 bp):
TTTTATGTTGTAAAATATATACATATACATTT
Found at i:10405626 original size:36 final size:33
Alignment explanation
Indices: 10405545--10405642 Score: 103
Period size: 32 Copynumber: 3.0 Consensus size: 33
10405535 ATATTTTATG
*
10405545 TTTTATAAATATAT-ACATATACATTTCTTTTA
1 TTTTGTAAATATATAACATATACATTTCTTTTA
* * *
10405577 TGTTGTAAATATATAGACTTATACATTTTTTTTCTA
1 TTTTGTAAATATATA-ACATATACA-TTTCTTT-TA
*
10405613 TTTTGTAAATATAT-ACATATGCATTT-TTTT
1 TTTTGTAAATATATAACATATACATTTCTTTT
10405643 CCTTTATTTT
Statistics
Matches: 55, Mismatches: 7, Indels: 9
0.77 0.10 0.13
Matches are distributed among these distances:
31 1 0.02
32 15 0.27
33 3 0.05
34 15 0.27
35 6 0.11
36 15 0.27
ACGTcount: A:0.33, C:0.08, G:0.05, T:0.54
Consensus pattern (33 bp):
TTTTGTAAATATATAACATATACATTTCTTTTA
Found at i:10405651 original size:36 final size:35
Alignment explanation
Indices: 10405545--10405652 Score: 107
Period size: 36 Copynumber: 3.1 Consensus size: 35
10405535 ATATTTTATG
* *
10405545 TTTTATAAATATATACATATACA--TTTCT-TTTA
1 TTTTGTAAATATATACATATACATTTTTTTCTTTA
* * *
10405577 TGTTGTAAATATATAGACTTATACATTTTTTT-TCTA
1 TTTTGTAAATATAT--ACATATACATTTTTTTCTTTA
*
10405613 TTTTGTAAATATATACATATGCATTTTTTTCCTTTA
1 TTTTGTAAATATATACATATACATTTTTTT-CTTTA
10405649 TTTT
1 TTTT
10405653 ATTTTGAATA
Statistics
Matches: 61, Mismatches: 9, Indels: 8
0.78 0.12 0.10
Matches are distributed among these distances:
32 12 0.20
34 22 0.36
36 27 0.44
ACGTcount: A:0.31, C:0.09, G:0.05, T:0.56
Consensus pattern (35 bp):
TTTTGTAAATATATACATATACATTTTTTTCTTTA
Found at i:10408726 original size:17 final size:18
Alignment explanation
Indices: 10408706--10408755 Score: 50
Period size: 17 Copynumber: 2.9 Consensus size: 18
10408696 TAAAAAAAAG
10408706 AAAATATAT-TAAAAATT
1 AAAATATATATAAAAATT
* * *
10408723 AAAA-AAATCTCAAAATT
1 AAAATATATATAAAAATT
*
10408740 AAAATGTATATAAAAA
1 AAAATATATATAAAAA
10408756 ATACACCAAT
Statistics
Matches: 25, Mismatches: 6, Indels: 3
0.74 0.18 0.09
Matches are distributed among these distances:
16 3 0.12
17 15 0.60
18 7 0.28
ACGTcount: A:0.66, C:0.04, G:0.02, T:0.28
Consensus pattern (18 bp):
AAAATATATATAAAAATT
Found at i:10411042 original size:2 final size:2
Alignment explanation
Indices: 10411037--10411103 Score: 61
Period size: 2 Copynumber: 35.5 Consensus size: 2
10411027 TTTCTATACC
* * *
10411037 AT AT AT AT AC AT AT AT AT AT -T AT AT AC AT AT -T CT -T A- AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
* *
10411075 TT CT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
10411104 CACGTAATTC
Statistics
Matches: 54, Mismatches: 7, Indels: 8
0.78 0.10 0.12
Matches are distributed among these distances:
1 4 0.07
2 50 0.93
ACGTcount: A:0.45, C:0.06, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:10411176 original size:14 final size:16
Alignment explanation
Indices: 10411141--10411179 Score: 60
Period size: 16 Copynumber: 2.4 Consensus size: 16
10411131 CTTTAATTTA
10411141 TATATATACATACTTT
1 TATATATACATACTTT
**
10411157 TATATATACATGTTTT
1 TATATATACATACTTT
10411173 TATATAT
1 TATATAT
10411180 TTCCATTATT
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
16 21 1.00
ACGTcount: A:0.36, C:0.08, G:0.03, T:0.54
Consensus pattern (16 bp):
TATATATACATACTTT
Found at i:10415691 original size:20 final size:20
Alignment explanation
Indices: 10415668--10415733 Score: 55
Period size: 20 Copynumber: 3.2 Consensus size: 20
10415658 TTTTTTTTAA
10415668 TTTTTGTAATATTTTTAATT
1 TTTTTGTAATATTTTTAATT
*
10415688 TTTTAGATATATATTTTTATAATT
1 TTTTTG-TA-ATA-TTTT-TAATT
* *
10415712 TCTTT-T-ATATTTTCAATT
1 TTTTTGTAATATTTTTAATT
10415730 TTTT
1 TTTT
10415734 ATATTTTCTT
Statistics
Matches: 37, Mismatches: 5, Indels: 10
0.71 0.10 0.19
Matches are distributed among these distances:
18 7 0.19
19 4 0.11
20 8 0.22
21 2 0.05
22 4 0.11
23 4 0.11
24 8 0.22
ACGTcount: A:0.26, C:0.03, G:0.03, T:0.68
Consensus pattern (20 bp):
TTTTTGTAATATTTTTAATT
Found at i:10434801 original size:21 final size:21
Alignment explanation
Indices: 10434775--10434827 Score: 70
Period size: 21 Copynumber: 2.5 Consensus size: 21
10434765 CATTGTTTCT
* * *
10434775 AATCTCGCTGCTACAGTATCC
1 AATCTCACCGCTACAGTAACC
*
10434796 AATCTCACCGCTACAGTAACT
1 AATCTCACCGCTACAGTAACC
10434817 AATCTCACCGC
1 AATCTCACCGC
10434828 CACCGCTATT
Statistics
Matches: 28, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
21 28 1.00
ACGTcount: A:0.28, C:0.36, G:0.11, T:0.25
Consensus pattern (21 bp):
AATCTCACCGCTACAGTAACC
Found at i:10440307 original size:3 final size:3
Alignment explanation
Indices: 10440299--10440333 Score: 70
Period size: 3 Copynumber: 11.7 Consensus size: 3
10440289 TACATGATGT
10440299 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TT
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TT
10440334 TGCAGCTTAT
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 32 1.00
ACGTcount: A:0.31, C:0.00, G:0.00, T:0.69
Consensus pattern (3 bp):
TTA
Found at i:10447785 original size:31 final size:32
Alignment explanation
Indices: 10447740--10447802 Score: 119
Period size: 31 Copynumber: 2.0 Consensus size: 32
10447730 AGATAATTTT
10447740 AAAGAGTTTTTATTAGGATTCAATTACTCTTG
1 AAAGAGTTTTTATTAGGATTCAATTACTCTTG
10447772 AAAGAG-TTTTATTAGGATTCAATTACTCTTG
1 AAAGAGTTTTTATTAGGATTCAATTACTCTTG
10447803 TAATTTGCCT
Statistics
Matches: 31, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
31 25 0.81
32 6 0.19
ACGTcount: A:0.32, C:0.10, G:0.16, T:0.43
Consensus pattern (32 bp):
AAAGAGTTTTTATTAGGATTCAATTACTCTTG
Found at i:10448698 original size:12 final size:12
Alignment explanation
Indices: 10448681--10448713 Score: 66
Period size: 12 Copynumber: 2.8 Consensus size: 12
10448671 TCTTCCTCAT
10448681 TTGTTCTCTGTA
1 TTGTTCTCTGTA
10448693 TTGTTCTCTGTA
1 TTGTTCTCTGTA
10448705 TTGTTCTCT
1 TTGTTCTCT
10448714 TCTTTTGCTA
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 21 1.00
ACGTcount: A:0.06, C:0.18, G:0.15, T:0.61
Consensus pattern (12 bp):
TTGTTCTCTGTA
Found at i:10449823 original size:25 final size:25
Alignment explanation
Indices: 10449748--10449826 Score: 71
Period size: 23 Copynumber: 3.4 Consensus size: 25
10449738 GACGCTGGCT
*
10449748 CCCTCTGCTGCTACACTGCTCTCTG
1 CCCTCTGTTGCTACACTGCTCTCTG
** *
10449773 --CTCT-TTGCTA-TTTGCTGGT-T-
1 CCCTCTGTTGCTACACTGCT-CTCTG
10449793 CCCTCTGTTGCTACACTGCTCTCTG
1 CCCTCTGTTGCTACACTGCTCTCTG
10449818 CCCTCTGTT
1 CCCTCTGTT
10449827 TTGTTCTGCC
Statistics
Matches: 40, Mismatches: 7, Indels: 14
0.66 0.11 0.23
Matches are distributed among these distances:
21 5 0.12
22 10 0.25
23 11 0.28
24 5 0.12
25 9 0.22
ACGTcount: A:0.06, C:0.37, G:0.16, T:0.41
Consensus pattern (25 bp):
CCCTCTGTTGCTACACTGCTCTCTG
Found at i:10450895 original size:13 final size:13
Alignment explanation
Indices: 10450877--10450929 Score: 56
Period size: 13 Copynumber: 4.2 Consensus size: 13
10450867 ATTTTTGTTC
10450877 ATGTATATAGTTA
1 ATGTATATAGTTA
10450890 ATGTATATAGTTAA
1 ATGTATATAGTT-A
* * *
10450904 AT-T-TTTTGTTC
1 ATGTATATAGTTA
10450915 ATGTATATAGTTA
1 ATGTATATAGTTA
10450928 AT
1 AT
10450930 TTTTTAATCA
Statistics
Matches: 31, Mismatches: 6, Indels: 6
0.72 0.14 0.14
Matches are distributed among these distances:
11 2 0.06
12 6 0.19
13 20 0.65
14 3 0.10
ACGTcount: A:0.34, C:0.02, G:0.13, T:0.51
Consensus pattern (13 bp):
ATGTATATAGTTA
Found at i:10450924 original size:25 final size:25
Alignment explanation
Indices: 10450890--10451014 Score: 119
Period size: 24 Copynumber: 4.9 Consensus size: 25
10450880 TATATAGTTA
*
10450890 ATGTATATAGTTAAATTTTTTGTTC
1 ATGTATATAGTTAAATTTTTTATTC
*
10450915 ATGTATATAGTT-AATTTTTTAATC
1 ATGTATATAGTTAAATTTTTTATTC
* *
10450939 ATGTATATAGTTAGATTTTTTATAC
1 ATGTATATAGTTAAATTTTTTATTC
* * * * *
10450964 -TGTTTTTTGTTAATATTGTTTTTTGTTT
1 ATGTATATAGTTAA-A---TTTTTTATTC
10450992 ATGTATATAGTTAAATTTTTTAT
1 ATGTATATAGTTAAATTTTTTAT
10451015 ACACATGTAA
Statistics
Matches: 78, Mismatches: 16, Indels: 12
0.74 0.15 0.11
Matches are distributed among these distances:
24 31 0.40
25 29 0.37
28 8 0.10
29 10 0.13
ACGTcount: A:0.27, C:0.02, G:0.11, T:0.59
Consensus pattern (25 bp):
ATGTATATAGTTAAATTTTTTATTC
Found at i:10452316 original size:72 final size:72
Alignment explanation
Indices: 10452198--10452361 Score: 224
Period size: 72 Copynumber: 2.3 Consensus size: 72
10452188 CAAAATATGT
* * * * *
10452198 TTTTATCAATAGTTATTTATGTTTAGTTTTTAGATATTGAACTTATGTTCTACTTATTTATGT-G
1 TTTTATTAATAGTTGTTTATGTTTAGTCTTTAGATATTGAACTTATGTTCCACTTATTT-TGTAC
10452262 T-AATCTAG
65 TAAAT-TAG
* * *
10452270 TTTTATTAATAGTTGTTTATGTTTGGTCTTTAGATATTGAATTTATGTTCCACTTATTTTTTACT
1 TTTTATTAATAGTTGTTTATGTTTAGTCTTTAGATATTGAACTTATGTTCCACTTATTTTGTACT
10452335 AAATTAG
66 AAATTAG
10452342 TTTTATTAATAGTTGTTTAT
1 TTTTATTAATAGTTGTTTAT
10452362 ATGTGATTTT
Statistics
Matches: 82, Mismatches: 8, Indels: 4
0.87 0.09 0.04
Matches are distributed among these distances:
71 2 0.02
72 77 0.94
73 3 0.04
ACGTcount: A:0.26, C:0.06, G:0.12, T:0.56
Consensus pattern (72 bp):
TTTTATTAATAGTTGTTTATGTTTAGTCTTTAGATATTGAACTTATGTTCCACTTATTTTGTACT
AAATTAG
Found at i:10455332 original size:9 final size:9
Alignment explanation
Indices: 10455315--10455351 Score: 56
Period size: 9 Copynumber: 4.1 Consensus size: 9
10455305 TGAGTTTTCG
10455315 AATTCGAAT
1 AATTCGAAT
*
10455324 AACTCGAAT
1 AATTCGAAT
*
10455333 AATTTGAAT
1 AATTCGAAT
10455342 AATTCGAAT
1 AATTCGAAT
10455351 A
1 A
10455352 TGAAACTATA
Statistics
Matches: 24, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
9 24 1.00
ACGTcount: A:0.46, C:0.11, G:0.11, T:0.32
Consensus pattern (9 bp):
AATTCGAAT
Found at i:10457662 original size:28 final size:27
Alignment explanation
Indices: 10457611--10457668 Score: 82
Period size: 28 Copynumber: 2.1 Consensus size: 27
10457601 ACCTAACTTC
*
10457611 AAATGTAAAAACCTTATGGTTTCATTA
1 AAATGTAAAAACCTTATGATTTCATTA
10457638 AAATGTAAAAA-CTTCAATGATTTCATTA
1 AAATGTAAAAACCTT--ATGATTTCATTA
10457666 AAA
1 AAA
10457669 CATAGCAACT
Statistics
Matches: 28, Mismatches: 1, Indels: 3
0.88 0.03 0.09
Matches are distributed among these distances:
26 3 0.11
27 11 0.39
28 14 0.50
ACGTcount: A:0.47, C:0.10, G:0.09, T:0.34
Consensus pattern (27 bp):
AAATGTAAAAACCTTATGATTTCATTA
Found at i:10458021 original size:15 final size:16
Alignment explanation
Indices: 10457977--10458018 Score: 50
Period size: 16 Copynumber: 2.6 Consensus size: 16
10457967 TGTGTAAAAA
10457977 AAACAT-AAATATAAAT
1 AAACATGAAA-ATAAAT
*
10457993 AAACATGAAAATAATT
1 AAACATGAAAATAAAT
*
10458009 AAAGATGAAA
1 AAACATGAAA
10458019 TAAGAATAAA
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
16 20 0.87
17 3 0.13
ACGTcount: A:0.67, C:0.05, G:0.07, T:0.21
Consensus pattern (16 bp):
AAACATGAAAATAAAT
Found at i:10458434 original size:11 final size:11
Alignment explanation
Indices: 10458418--10458446 Score: 58
Period size: 11 Copynumber: 2.6 Consensus size: 11
10458408 ATTCATTCTT
10458418 TCATTTTAACC
1 TCATTTTAACC
10458429 TCATTTTAACC
1 TCATTTTAACC
10458440 TCATTTT
1 TCATTTT
10458447 TTTCAAAAAA
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 18 1.00
ACGTcount: A:0.24, C:0.24, G:0.00, T:0.52
Consensus pattern (11 bp):
TCATTTTAACC
Found at i:10462171 original size:57 final size:59
Alignment explanation
Indices: 10462059--10462206 Score: 167
Period size: 57 Copynumber: 2.5 Consensus size: 59
10462049 AATTGACGGT
* *
10462059 AAAAAGGATCTAGCCCAGACGGGTGATCCTATCCTGATATAGCCCTCCCAAAGAATATTTGCG
1 AAAAA-GATCTAGCCCGGACGGGTGATCC-AT-CTGATATAGCCCTCCCAAAGAATATGTG-G
*
10462122 AAAAAGATCTAGCCCGGACGGGTGAT-C-T-TGATATAGCCCTCCCGAAGAATATGTGG
1 AAAAAGATCTAGCCCGGACGGGTGATCCATCTGATATAGCCCTCCCAAAGAATATGTGG
* * * *
10462178 AAAATGGATTTAGCTCGGACGGGTAATCC
1 AAAA-AGATCTAGCCCGGACGGGTGATCC
10462207 GAATTAGGGT
Statistics
Matches: 76, Mismatches: 7, Indels: 9
0.83 0.08 0.10
Matches are distributed among these distances:
56 5 0.07
57 43 0.57
58 1 0.01
59 1 0.01
61 1 0.01
62 20 0.26
63 5 0.07
ACGTcount: A:0.31, C:0.22, G:0.24, T:0.22
Consensus pattern (59 bp):
AAAAAGATCTAGCCCGGACGGGTGATCCATCTGATATAGCCCTCCCAAAGAATATGTGG
Found at i:10466100 original size:12 final size:12
Alignment explanation
Indices: 10466066--10466178 Score: 55
Period size: 12 Copynumber: 9.8 Consensus size: 12
10466056 ATTCCAAAAA
*
10466066 TAATA-TTATTT
1 TAATATTTAATT
10466077 TAATATTTTAATAT
1 TAATA-TTTAAT-T
10466091 TAA-ATTTAATT
1 TAATATTTAATT
10466102 TAATATTT-ATCT
1 TAATATTTAAT-T
*
10466114 TAATA-GT-ATT
1 TAATATTTAATT
10466124 T--TA-TTAATT
1 TAATATTTAATT
* *
10466133 TAATATTAAAGT
1 TAATATTTAATT
* *
10466145 GATTATCTTAATAT
1 TAATAT-TTAAT-T
10466159 TAA-ATTTAATT
1 TAATATTTAATT
*
10466170 TAATGTTTA
1 TAATATTTA
10466179 TCTTCTAGAT
Statistics
Matches: 78, Mismatches: 12, Indels: 23
0.69 0.11 0.20
Matches are distributed among these distances:
8 3 0.04
9 4 0.05
10 2 0.03
11 20 0.26
12 33 0.42
13 10 0.13
14 6 0.08
ACGTcount: A:0.40, C:0.02, G:0.04, T:0.55
Consensus pattern (12 bp):
TAATATTTAATT
Found at i:10466141 original size:11 final size:11
Alignment explanation
Indices: 10466066--10466141 Score: 52
Period size: 11 Copynumber: 6.8 Consensus size: 11
10466056 ATTCCAAAAA
*
10466066 TAATATTATTT
1 TAATATTAATT
10466077 TAATATTTTAATAT
1 TAATA--TTAAT-T
10466091 TAA-ATTTAATT
1 TAATA-TTAATT
*
10466102 TAATATTTATCT
1 TAATATTAAT-T
*
10466114 TAATAGT-ATT
1 TAATATTAATT
10466124 T--TATTAATT
1 TAATATTAATT
10466133 TAATATTAA
1 TAATATTAA
10466142 AGTGATTATC
Statistics
Matches: 53, Mismatches: 4, Indels: 16
0.73 0.05 0.22
Matches are distributed among these distances:
8 3 0.06
9 4 0.08
10 2 0.04
11 21 0.40
12 14 0.26
13 5 0.09
14 4 0.08
ACGTcount: A:0.41, C:0.01, G:0.01, T:0.57
Consensus pattern (11 bp):
TAATATTAATT
Found at i:10466161 original size:68 final size:72
Alignment explanation
Indices: 10466084--10466221 Score: 203
Period size: 68 Copynumber: 2.0 Consensus size: 72
10466074 TTTTAATATT
** *
10466084 TTAATATTAAATTTAATTTAATATTTATC-T-TA-AT-AGTATTTTATTAATTTAATATTAAAGT
1 TTAATATTAAATTTAATTTAATATTTATCTTCTAGATAAACATTCTATTAATTTAATATTAAAGT
10466145 GATTATC
66 GATTATC
* *
10466152 TTAATATTAAATTTAATTTAATGTTTATCTTCTAGATAAACATTCTATTAATTTAATTTTAAAGT
1 TTAATATTAAATTTAATTTAATATTTATCTTCTAGATAAACATTCTATTAATTTAATATTAAAGT
10466217 GATTA
66 GATTA
10466222 AGTTTAATTA
Statistics
Matches: 61, Mismatches: 5, Indels: 4
0.87 0.07 0.06
Matches are distributed among these distances:
68 28 0.46
69 1 0.02
70 2 0.03
71 2 0.03
72 28 0.46
ACGTcount: A:0.39, C:0.04, G:0.05, T:0.51
Consensus pattern (72 bp):
TTAATATTAAATTTAATTTAATATTTATCTTCTAGATAAACATTCTATTAATTTAATATTAAAGT
GATTATC
Found at i:10471052 original size:13 final size:13
Alignment explanation
Indices: 10471034--10471058 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
10471024 CTGCATAACT
10471034 AAAAAGGTAATCC
1 AAAAAGGTAATCC
10471047 AAAAAGGTAATC
1 AAAAAGGTAATC
10471059 TAATTTTTTT
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:0.56, C:0.12, G:0.16, T:0.16
Consensus pattern (13 bp):
AAAAAGGTAATCC
Found at i:10473443 original size:19 final size:19
Alignment explanation
Indices: 10473419--10473456 Score: 76
Period size: 19 Copynumber: 2.0 Consensus size: 19
10473409 GATGTTTGTG
10473419 ATATGGAAAATACACAAAA
1 ATATGGAAAATACACAAAA
10473438 ATATGGAAAATACACAAAA
1 ATATGGAAAATACACAAAA
10473457 GAATCATATT
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 19 1.00
ACGTcount: A:0.63, C:0.11, G:0.11, T:0.16
Consensus pattern (19 bp):
ATATGGAAAATACACAAAA
Found at i:10476318 original size:42 final size:41
Alignment explanation
Indices: 10476264--10476387 Score: 133
Period size: 42 Copynumber: 3.0 Consensus size: 41
10476254 ACATACATTC
* *
10476264 TCCTA-TCTCTATGGGTCACACCACAACACCACCTACCAATAT
1 TCCTACTC-CTATGGATCCCACCACAACACCACC-ACCAATAT
* * * *
10476306 TCCTACTCCTATGGACCCCATCACAACACCACCCAACAATCT
1 TCCTACTCCTATGGATCCCACCACAACACCA-CCACCAATAT
* *
10476348 TCCCACTCTTATGGATCCCACCACAACACCATCCACCAAT
1 TCCTACTCCTATGGATCCCACCACAACACCA-CCACCAAT
10476388 TTCACGTCTC
Statistics
Matches: 68, Mismatches: 12, Indels: 4
0.81 0.14 0.05
Matches are distributed among these distances:
42 64 0.94
43 4 0.06
ACGTcount: A:0.31, C:0.43, G:0.06, T:0.21
Consensus pattern (41 bp):
TCCTACTCCTATGGATCCCACCACAACACCACCACCAATAT
Found at i:10480269 original size:91 final size:91
Alignment explanation
Indices: 10480163--10480331 Score: 329
Period size: 91 Copynumber: 1.9 Consensus size: 91
10480153 CTTCTCTTGT
10480163 TTGTTTCCTAAATATGCAGTTCACAACTATGTGTAGGTCTTTTTCAGGAAGACAATACACTCCTT
1 TTGTTTCCTAAATATGCAGTTCACAACTATGTGTAGGTCTTTTTCAGGAAGACAATACACTCCTT
10480228 GTGACCCTTGAGATCCGTGACCGAGC
66 GTGACCCTTGAGATCCGTGACCGAGC
*
10480254 TTGTTTCCTAAATATGCAGTTCACAACTATGTGTAGGTCTTTTTCAGGAAGACTATACACTCCTT
1 TTGTTTCCTAAATATGCAGTTCACAACTATGTGTAGGTCTTTTTCAGGAAGACAATACACTCCTT
10480319 GTGACCCTTGAGA
66 GTGACCCTTGAGA
10480332 GATGAAATTG
Statistics
Matches: 77, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
91 77 1.00
ACGTcount: A:0.25, C:0.22, G:0.19, T:0.34
Consensus pattern (91 bp):
TTGTTTCCTAAATATGCAGTTCACAACTATGTGTAGGTCTTTTTCAGGAAGACAATACACTCCTT
GTGACCCTTGAGATCCGTGACCGAGC
Found at i:10484864 original size:18 final size:18
Alignment explanation
Indices: 10484823--10484865 Score: 52
Period size: 18 Copynumber: 2.4 Consensus size: 18
10484813 AATTTTTTAA
10484823 AAAAAATTTAAAAAAACT
1 AAAAAATTTAAAAAAACT
**
10484841 TTAAAATTTAAAAAATA-T
1 AAAAAATTTAAAAAA-ACT
10484859 AAAAAAT
1 AAAAAAT
10484866 ATTTTTATTA
Statistics
Matches: 20, Mismatches: 4, Indels: 2
0.77 0.15 0.08
Matches are distributed among these distances:
18 19 0.95
19 1 0.05
ACGTcount: A:0.70, C:0.02, G:0.00, T:0.28
Consensus pattern (18 bp):
AAAAAATTTAAAAAAACT
Found at i:10487120 original size:17 final size:17
Alignment explanation
Indices: 10487098--10487141 Score: 63
Period size: 17 Copynumber: 2.5 Consensus size: 17
10487088 TAACCGAATT
10487098 TTTTTATTTATTGTT-TA
1 TTTTTATTTATT-TTATA
10487115 TTTTTATTTATTTTATA
1 TTTTTATTTATTTTATA
10487132 TTTTATATTT
1 TTTT-TATTT
10487142 TATGTTCTTT
Statistics
Matches: 25, Mismatches: 0, Indels: 3
0.89 0.00 0.11
Matches are distributed among these distances:
16 2 0.08
17 18 0.72
18 5 0.20
ACGTcount: A:0.20, C:0.00, G:0.02, T:0.77
Consensus pattern (17 bp):
TTTTTATTTATTTTATA
Found at i:10494312 original size:5 final size:5
Alignment explanation
Indices: 10494302--10494333 Score: 55
Period size: 5 Copynumber: 6.2 Consensus size: 5
10494292 AAGAATGGTT
10494302 AATTA AATTA AATTA AATTA AATTA ATATTA A
1 AATTA AATTA AATTA AATTA AATTA A-ATTA A
10494334 TCTAAGTATA
Statistics
Matches: 26, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
5 21 0.81
6 5 0.19
ACGTcount: A:0.59, C:0.00, G:0.00, T:0.41
Consensus pattern (5 bp):
AATTA
Found at i:10495018 original size:2 final size:2
Alignment explanation
Indices: 10495011--10495057 Score: 94
Period size: 2 Copynumber: 23.5 Consensus size: 2
10495001 TTTATGATTT
10495011 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
10495053 TA TA T
1 TA TA T
10495058 TTACATGTTG
Statistics
Matches: 45, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 45 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:10496543 original size:30 final size:30
Alignment explanation
Indices: 10496497--10496559 Score: 90
Period size: 30 Copynumber: 2.1 Consensus size: 30
10496487 GGTTAAGATA
* * *
10496497 GTGCCACACACGGTCGCACCACATGATCGT
1 GTGCCACACACAGTCGCACCACACGACCGT
*
10496527 GTGCTACACACAGTCGCACCACACGACCGT
1 GTGCCACACACAGTCGCACCACACGACCGT
10496557 GTG
1 GTG
10496560 GACTATTTAA
Statistics
Matches: 29, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
30 29 1.00
ACGTcount: A:0.24, C:0.37, G:0.24, T:0.16
Consensus pattern (30 bp):
GTGCCACACACAGTCGCACCACACGACCGT
Found at i:10497097 original size:14 final size:15
Alignment explanation
Indices: 10497078--10497115 Score: 53
Period size: 14 Copynumber: 2.7 Consensus size: 15
10497068 TGTTTCATTG
10497078 AAAATGACTTT-TGA
1 AAAATGACTTTCTGA
*
10497092 AAAATGA-TTTCTGG
1 AAAATGACTTTCTGA
10497106 AAAATGACTT
1 AAAATGACTT
10497116 ACTCTCCTGG
Statistics
Matches: 21, Mismatches: 1, Indels: 3
0.84 0.04 0.12
Matches are distributed among these distances:
13 3 0.14
14 16 0.76
15 2 0.10
ACGTcount: A:0.42, C:0.08, G:0.16, T:0.34
Consensus pattern (15 bp):
AAAATGACTTTCTGA
Found at i:10497810 original size:26 final size:26
Alignment explanation
Indices: 10497791--10497840 Score: 77
Period size: 26 Copynumber: 2.0 Consensus size: 26
10497781 ATAAATAATT
10497791 AAATAT-ATA-TTTAATAATAATAAA
1 AAATATAATATTTTAATAATAATAAA
*
10497815 AAATATAATATTTTAATAATTATAAA
1 AAATATAATATTTTAATAATAATAAA
10497841 TATTTTTAAA
Statistics
Matches: 23, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
24 6 0.26
25 3 0.13
26 14 0.61
ACGTcount: A:0.60, C:0.00, G:0.00, T:0.40
Consensus pattern (26 bp):
AAATATAATATTTTAATAATAATAAA
Found at i:10497814 original size:29 final size:27
Alignment explanation
Indices: 10497781--10497842 Score: 72
Period size: 26 Copynumber: 2.3 Consensus size: 27
10497771 ATGACTAAAT
*
10497781 ATAAATAATTAAATATATATTTAATAATA
1 ATAAATAAATAAA-ATAT-TTTAATAATA
* *
10497810 ATAAA-AAATATAATATTTTAATAATT
1 ATAAATAAATAAAATATTTTAATAATA
10497836 ATAAATA
1 ATAAATA
10497843 TTTTTAAAAA
Statistics
Matches: 29, Mismatches: 3, Indels: 4
0.81 0.08 0.11
Matches are distributed among these distances:
26 14 0.48
27 5 0.17
28 5 0.17
29 5 0.17
ACGTcount: A:0.60, C:0.00, G:0.00, T:0.40
Consensus pattern (27 bp):
ATAAATAAATAAAATATTTTAATAATA
Found at i:10497841 original size:23 final size:23
Alignment explanation
Indices: 10497784--10497843 Score: 68
Period size: 23 Copynumber: 2.5 Consensus size: 23
10497774 ACTAAATATA
10497784 AATAATTAAATATATATTTAATAAT
1 AATAA-TAAATATATATTT-ATAAT
*
10497809 AATAAAAAATATAATATTT-TAAT
1 AATAATAAATAT-ATATTTATAAT
*
10497832 AATTATAAATAT
1 AATAATAAATAT
10497844 TTTTAAAAAT
Statistics
Matches: 31, Mismatches: 3, Indels: 4
0.82 0.08 0.11
Matches are distributed among these distances:
23 14 0.45
24 6 0.19
25 11 0.35
ACGTcount: A:0.58, C:0.00, G:0.00, T:0.42
Consensus pattern (23 bp):
AATAATAAATATATATTTATAAT
Found at i:10503064 original size:1 final size:1
Alignment explanation
Indices: 10503058--10503082 Score: 50
Period size: 1 Copynumber: 25.0 Consensus size: 1
10503048 CTTCTTCTTC
10503058 TTTTTTTTTTTTTTTTTTTTTTTTT
1 TTTTTTTTTTTTTTTTTTTTTTTTT
10503083 ATCTCAGGAA
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
1 24 1.00
ACGTcount: A:0.00, C:0.00, G:0.00, T:1.00
Consensus pattern (1 bp):
T
Found at i:10503779 original size:19 final size:18
Alignment explanation
Indices: 10503757--10503823 Score: 66
Period size: 18 Copynumber: 3.6 Consensus size: 18
10503747 ATAATTTAAT
10503757 AATTATAAAATATTAAAAA
1 AATTATAAAAT-TTAAAAA
*
10503776 AATT-TAAAATTCAAATAA
1 AATTATAAAATTTAAA-AA
10503794 AATTATAAAAATTTTATAAAA
1 AATTAT-AAAA-TTTA-AAAA
10503815 AATTA-AAAA
1 AATTATAAAA
10503824 GTCAATATGA
Statistics
Matches: 41, Mismatches: 2, Indels: 10
0.77 0.04 0.19
Matches are distributed among these distances:
17 4 0.10
18 12 0.29
19 9 0.22
20 4 0.10
21 10 0.24
22 2 0.05
ACGTcount: A:0.66, C:0.01, G:0.00, T:0.33
Consensus pattern (18 bp):
AATTATAAAATTTAAAAA
Found at i:10509753 original size:17 final size:17
Alignment explanation
Indices: 10509727--10509793 Score: 62
Period size: 17 Copynumber: 3.8 Consensus size: 17
10509717 ACCTGAATTG
10509727 AATCACTACATAATTAA
1 AATCACTACATAATTAA
* **
10509744 AATCATTACATAAGTCTTTG
1 AATCACTACATAA---TTAA
10509764 AATCACTACATAATTAA
1 AATCACTACATAATTAA
* *
10509781 AAACATTACATAA
1 AATCACTACATAA
10509794 GTCTTGAAAT
Statistics
Matches: 39, Mismatches: 8, Indels: 6
0.74 0.15 0.11
Matches are distributed among these distances:
17 25 0.64
20 14 0.36
ACGTcount: A:0.49, C:0.16, G:0.03, T:0.31
Consensus pattern (17 bp):
AATCACTACATAATTAA
Found at i:10509770 original size:37 final size:37
Alignment explanation
Indices: 10509724--10509798 Score: 141
Period size: 37 Copynumber: 2.0 Consensus size: 37
10509714 ATTACCTGAA
*
10509724 TTGAATCACTACATAATTAAAATCATTACATAAGTCT
1 TTGAATCACTACATAATTAAAAACATTACATAAGTCT
10509761 TTGAATCACTACATAATTAAAAACATTACATAAGTCT
1 TTGAATCACTACATAATTAAAAACATTACATAAGTCT
10509798 T
1 T
10509799 GAAATTAACA
Statistics
Matches: 37, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
37 37 1.00
ACGTcount: A:0.44, C:0.16, G:0.05, T:0.35
Consensus pattern (37 bp):
TTGAATCACTACATAATTAAAAACATTACATAAGTCT
Found at i:10509812 original size:37 final size:37
Alignment explanation
Indices: 10509724--10509815 Score: 125
Period size: 37 Copynumber: 2.5 Consensus size: 37
10509714 ATTACCTGAA
* *
10509724 TTGAATCACTACATAATTAAAATCATTACATAAGTCT
1 TTGAATAACTACATAATTAAAAACATTACATAAGTCT
*
10509761 TTGAATCACTACATAATTAAAAACATTACATAAGTC-
1 TTGAATAACTACATAATTAAAAACATTACATAAGTCT
10509797 TTGAAATTAAC-ACATAATT
1 TTG-AA-TAACTACATAATT
10509816 GAAATGTAAG
Statistics
Matches: 51, Mismatches: 2, Indels: 4
0.89 0.04 0.07
Matches are distributed among these distances:
36 3 0.06
37 45 0.88
38 3 0.06
ACGTcount: A:0.46, C:0.15, G:0.05, T:0.34
Consensus pattern (37 bp):
TTGAATAACTACATAATTAAAAACATTACATAAGTCT
Found at i:10513907 original size:38 final size:39
Alignment explanation
Indices: 10513865--10513981 Score: 209
Period size: 39 Copynumber: 3.0 Consensus size: 39
10513855 GTTAGAGACT
10513865 TAGACTTTAGTTTTAGTTTTATTGGGTT-GGTAATTGGG
1 TAGACTTTAGTTTTAGTTTTATTGGGTTGGGTAATTGGG
*
10513903 TAGACTTTAGTTTTAGTTTTATTGGGTTGGGTAATTAGG
1 TAGACTTTAGTTTTAGTTTTATTGGGTTGGGTAATTGGG
*
10513942 TAGATTTTAGTTTTAGTTTTATTGGGTTGGGTAATTGGG
1 TAGACTTTAGTTTTAGTTTTATTGGGTTGGGTAATTGGG
10513981 T
1 T
10513982 TGGGTTGGAT
Statistics
Matches: 75, Mismatches: 3, Indels: 1
0.95 0.04 0.01
Matches are distributed among these distances:
38 28 0.37
39 47 0.63
ACGTcount: A:0.19, C:0.02, G:0.29, T:0.50
Consensus pattern (39 bp):
TAGACTTTAGTTTTAGTTTTATTGGGTTGGGTAATTGGG
Found at i:10513980 original size:13 final size:13
Alignment explanation
Indices: 10513962--10513986 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
10513952 TTTTAGTTTT
10513962 ATTGGGTTGGGTA
1 ATTGGGTTGGGTA
10513975 ATTGGGTTGGGT
1 ATTGGGTTGGGT
10513987 TGGATAATTT
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:0.12, C:0.00, G:0.48, T:0.40
Consensus pattern (13 bp):
ATTGGGTTGGGTA
Found at i:10520820 original size:13 final size:13
Alignment explanation
Indices: 10520802--10520827 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
10520792 TTTATTGAAA
10520802 GTAAAAAAATACG
1 GTAAAAAAATACG
10520815 GTAAAAAAATACG
1 GTAAAAAAATACG
10520828 AACAAAGGGC
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.62, C:0.08, G:0.15, T:0.15
Consensus pattern (13 bp):
GTAAAAAAATACG
Found at i:10521082 original size:152 final size:152
Alignment explanation
Indices: 10520799--10521294 Score: 658
Period size: 155 Copynumber: 3.2 Consensus size: 152
10520789 TTTTTTATTG
* * *
10520799 AAAGTAAAAAAATACGGTAAAAAAATACGAACAAAGGGCCGAAATAAGGGGTTTTT-TTAAATTT
1 AAAGTAATAAAATCCGG-AAAAAAATACGAACAAAGGGCCGAAATAAGGGGTTTTTAATAAATTT
10520863 ATTTAAAAAACACACTAAATGAATACATTTCAAACATAATGTACTAAAATAATGTAAAATTAA-A
65 ATTTAAAAAACACACTAAATGAATACATTTCAAACATAATGTACTAAAATAATGTAAAA-TAATA
*
10520927 AAATTAGAAAATAGCATATTTTTT
129 AAATTAGAAAATAGTATATTTTTT
*
10520951 AAAGTAATAAAATCCGGAAAAAAATACGAACAAAGGGCCGAAATAAGGGGTTTTTACTAAATTTA
1 AAAGTAATAAAATCCGGAAAAAAATACGAACAAAGGGCCGAAATAAGGGGTTTTTAATAAATTTA
* * *
10521016 TTTAAAAAATACAGTAAATTAATACATTTCAAACATAATGTACTAAAATAATGTAAAATAATAAA
66 TTTAAAAAACACACTAAATGAATACATTTCAAACATAATGTACTAAAATAATGTAAAATAATAAA
*
10521081 A-TACGAAAATAATATATTTTTATT
131 ATTA-GAAAATAGTATA-TTTT-TT
* ** * * * ***
10521105 AAAAATAATAAAATTTGGAAAAAAATACGAATAAAGGGTCGAAATAA-GGGTTTTTAAAAAAAAA
1 -AAAGTAATAAAATCCGGAAAAAAATACGAACAAAGGGCCGAAATAAGGGGTTTTTAATAAATTT
* * * *
10521169 ATTTTAAAACACACACTAAATGAATACATTTCAAACATAATGTACTGAAATAATATAAAATAATG
65 A-TTTAAAAAACACACTAAATGAATACATTTCAAACATAATGTACTAAAATAATGTAAAATAATA
*
10521234 AAATTAGAAAATAGTATTTTTTTTT
129 AAATTAGAAAATAGTA-TATTTTTT
*
10521259 AAAGTAATAAAATCCGAGGAAAAAATTACGAACAAA
1 AAAGTAATAAAATCC--GGAAAAAAATACGAACAAA
10521295 TAGCTGAAAT
Statistics
Matches: 301, Mismatches: 32, Indels: 19
0.86 0.09 0.05
Matches are distributed among these distances:
151 43 0.14
152 92 0.31
153 16 0.05
154 17 0.06
155 130 0.43
156 3 0.01
ACGTcount: A:0.53, C:0.08, G:0.11, T:0.28
Consensus pattern (152 bp):
AAAGTAATAAAATCCGGAAAAAAATACGAACAAAGGGCCGAAATAAGGGGTTTTTAATAAATTTA
TTTAAAAAACACACTAAATGAATACATTTCAAACATAATGTACTAAAATAATGTAAAATAATAAA
ATTAGAAAATAGTATATTTTTT
Found at i:10545606 original size:16 final size:16
Alignment explanation
Indices: 10545585--10545628 Score: 56
Period size: 14 Copynumber: 2.9 Consensus size: 16
10545575 TTGGTTGAAA
*
10545585 AAATTATTTAATTGAG
1 AAATTAATTAATTGAG
10545601 AAATTAATTAATT--G
1 AAATTAATTAATTGAG
*
10545615 AATTTAATTAATTG
1 AAATTAATTAATTG
10545629 TTTAAGTGAT
Statistics
Matches: 25, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
14 13 0.52
16 12 0.48
ACGTcount: A:0.45, C:0.00, G:0.09, T:0.45
Consensus pattern (16 bp):
AAATTAATTAATTGAG
Found at i:10551671 original size:13 final size:13
Alignment explanation
Indices: 10551653--10551679 Score: 54
Period size: 13 Copynumber: 2.1 Consensus size: 13
10551643 AAAGTATTTT
10551653 AGAAATTGAATTG
1 AGAAATTGAATTG
10551666 AGAAATTGAATTG
1 AGAAATTGAATTG
10551679 A
1 A
10551680 TTATTATTGT
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:0.48, C:0.00, G:0.22, T:0.30
Consensus pattern (13 bp):
AGAAATTGAATTG
Found at i:10552393 original size:16 final size:16
Alignment explanation
Indices: 10552356--10552395 Score: 62
Period size: 16 Copynumber: 2.5 Consensus size: 16
10552346 TTGATAAAAT
* *
10552356 TAAAACTAATTGTTAT
1 TAAAATTAATTGTTAG
10552372 TAAAATTAATTGTTAG
1 TAAAATTAATTGTTAG
10552388 TAAAATTA
1 TAAAATTA
10552396 TCAAATTATT
Statistics
Matches: 22, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
16 22 1.00
ACGTcount: A:0.47, C:0.03, G:0.07, T:0.42
Consensus pattern (16 bp):
TAAAATTAATTGTTAG
Found at i:10552489 original size:75 final size:74
Alignment explanation
Indices: 10552390--10552529 Score: 244
Period size: 75 Copynumber: 1.9 Consensus size: 74
10552380 ATTGTTAGTA
* *
10552390 AAATTATCAAATTATTAATTGTTAATTGTATTAATTGTTGTAATAAAATCTAACATTTGATTAGT
1 AAATTATCAAATTATTAATTGTTAATTATATTAATTGTTGTAACAAAATCTAACATTTGATTAGT
10552455 AAAATCATC
66 AAAATCATC
*
10552464 AAATTATTAAATGTATTAATTGTTAATTATATTAATTGTTGTAACAAAATCTAACATTTGATTAG
1 AAATTATCAAAT-TATTAATTGTTAATTATATTAATTGTTGTAACAAAATCTAACATTTGATTAG
10552529 T
65 T
10552530 TTACATTTTT
Statistics
Matches: 62, Mismatches: 3, Indels: 1
0.94 0.05 0.02
Matches are distributed among these distances:
74 11 0.18
75 51 0.82
ACGTcount: A:0.41, C:0.06, G:0.09, T:0.44
Consensus pattern (74 bp):
AAATTATCAAATTATTAATTGTTAATTATATTAATTGTTGTAACAAAATCTAACATTTGATTAGT
AAAATCATC
Found at i:10552781 original size:20 final size:19
Alignment explanation
Indices: 10552740--10552805 Score: 96
Period size: 19 Copynumber: 3.4 Consensus size: 19
10552730 TCTGTCGGGG
*
10552740 AAATGAAATTGAAAACTAA
1 AAATAAAATTGAAAACTAA
10552759 AAATAAAATTGAAAACATAA
1 AAATAAAATTGAAAAC-TAA
*
10552779 AAATAAAATTGAAAACTTA
1 AAATAAAATTGAAAACTAA
*
10552798 AACTAAAA
1 AAATAAAA
10552806 ACTTAACCAT
Statistics
Matches: 43, Mismatches: 3, Indels: 2
0.90 0.06 0.04
Matches are distributed among these distances:
19 24 0.56
20 19 0.44
ACGTcount: A:0.67, C:0.06, G:0.06, T:0.21
Consensus pattern (19 bp):
AAATAAAATTGAAAACTAA
Found at i:10552806 original size:20 final size:19
Alignment explanation
Indices: 10552745--10552806 Score: 63
Period size: 20 Copynumber: 3.2 Consensus size: 19
10552735 CGGGGAAATG
*
10552745 AAATTGAAAAC-TAAAAATA
1 AAATTGAAAACTTAAATA-A
* *
10552764 AAATTGAAAACATAAAAATA
1 AAATTGAAAACTTAAATA-A
10552784 AAATTGAAAACTTAAACTAA
1 AAATTGAAAACTTAAA-TAA
10552804 AAA
1 AAA
10552807 CTTAACCATA
Statistics
Matches: 39, Mismatches: 2, Indels: 3
0.89 0.05 0.07
Matches are distributed among these distances:
19 11 0.28
20 27 0.69
21 1 0.03
ACGTcount: A:0.68, C:0.06, G:0.05, T:0.21
Consensus pattern (19 bp):
AAATTGAAAACTTAAATAA
Found at i:10552825 original size:2 final size:2
Alignment explanation
Indices: 10552818--10552843 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
10552808 TTAACCATAA
10552818 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
10552844 TAGAAAAGAA
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:10553013 original size:16 final size:16
Alignment explanation
Indices: 10552992--10553024 Score: 66
Period size: 16 Copynumber: 2.1 Consensus size: 16
10552982 TTTTTTTTTT
10552992 AAACATAAAAAACTTA
1 AAACATAAAAAACTTA
10553008 AAACATAAAAAACTTA
1 AAACATAAAAAACTTA
10553024 A
1 A
10553025 TATATATTTA
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 17 1.00
ACGTcount: A:0.70, C:0.12, G:0.00, T:0.18
Consensus pattern (16 bp):
AAACATAAAAAACTTA
Found at i:10555489 original size:22 final size:22
Alignment explanation
Indices: 10555459--10555502 Score: 70
Period size: 22 Copynumber: 2.0 Consensus size: 22
10555449 AATCCTATCC
*
10555459 ATTACTTTAAATCCCGTTTTTT
1 ATTACTTTAAATCCCATTTTTT
*
10555481 ATTATTTTAAATCCCATTTTTT
1 ATTACTTTAAATCCCATTTTTT
10555503 CTTTAATTAC
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
22 20 1.00
ACGTcount: A:0.25, C:0.16, G:0.02, T:0.57
Consensus pattern (22 bp):
ATTACTTTAAATCCCATTTTTT
Found at i:10555757 original size:19 final size:19
Alignment explanation
Indices: 10555718--10555753 Score: 65
Period size: 19 Copynumber: 1.9 Consensus size: 19
10555708 AATTATTAGG
10555718 TTTTTTTAATTAAAATAAT
1 TTTTTTTAATTAAAATAAT
10555737 TTTTTTTAA-TAAAATAA
1 TTTTTTTAATTAAAATAA
10555754 ATTTATTCCT
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
18 8 0.47
19 9 0.53
ACGTcount: A:0.44, C:0.00, G:0.00, T:0.56
Consensus pattern (19 bp):
TTTTTTTAATTAAAATAAT
Found at i:10555815 original size:74 final size:74
Alignment explanation
Indices: 10555603--10555852 Score: 377
Period size: 74 Copynumber: 3.4 Consensus size: 74
10555593 TTTTTAAAGA
* *
10555603 AAAATCAATTTATTCCTTTAAATTGATTTATCATTTAATTATTTC-ATTTTTAATTAAAATCAAA
1 AAAATCAATTTATTCCTTTAAATTGATTTATCATTTAATTATTACGTTTTTTAATTAAAAT-AAA
10555667 ----TTTAA-
65 TTTTTTTAAT
* *
10555672 AAAATCAATTTATTCCTTTAAATTGATTTATCATTTAATTATTAGGTTTTTTTAATTAAAATAAT
1 AAAATCAATTTATTCCTTTAAATTGATTTATCATTTAATTATTACG-TTTTTTAATTAAAATAAA
10555737 TTTTTTTAAT
65 TTTTTTTAAT
*
10555747 AAAATAAATTTATTCCTTTAAATTGATTTATCATTTAATTATTACGTTTTTTAATTAAAATAAAT
1 AAAATCAATTTATTCCTTTAAATTGATTTATCATTTAATTATTACGTTTTTTAATTAAAATAAAT
*
10555812 TTTTTAAAT
66 TTTTTTAAT
*
10555821 AAAATCAATTTATTTCTTTAAATTGATTTATC
1 AAAATCAATTTATTCCTTTAAATTGATTTATC
10555853 TTGTAAAACT
Statistics
Matches: 164, Mismatches: 10, Indels: 9
0.90 0.05 0.05
Matches are distributed among these distances:
69 43 0.26
70 2 0.01
71 14 0.09
74 61 0.37
75 44 0.27
ACGTcount: A:0.39, C:0.07, G:0.03, T:0.52
Consensus pattern (74 bp):
AAAATCAATTTATTCCTTTAAATTGATTTATCATTTAATTATTACGTTTTTTAATTAAAATAAAT
TTTTTTAAT
Found at i:10555816 original size:18 final size:18
Alignment explanation
Indices: 10555793--10555831 Score: 60
Period size: 18 Copynumber: 2.2 Consensus size: 18
10555783 AATTATTACG
*
10555793 TTTTTTAATTAAAATAAA
1 TTTTTTAAATAAAATAAA
*
10555811 TTTTTTAAATAAAATCAA
1 TTTTTTAAATAAAATAAA
10555829 TTT
1 TTT
10555832 ATTTCTTTAA
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
18 19 1.00
ACGTcount: A:0.46, C:0.03, G:0.00, T:0.51
Consensus pattern (18 bp):
TTTTTTAAATAAAATAAA
Found at i:10555881 original size:144 final size:141
Alignment explanation
Indices: 10555603--10555871 Score: 330
Period size: 144 Copynumber: 1.9 Consensus size: 141
10555593 TTTTTAAAGA
* *
10555603 AAAATCAATTTATTCCTTTAAATTGATTTATCATTTAATTATTTCATTTTTAATTAAAATCAAAT
1 AAAATAAATTTATTCCTTTAAATTGATTTATCATTTAATTATTACATTTTTAATTAAAATCAAAT
* * *** *
10555668 TTAAAAAATCAATTTATTCCTTTAAATTGATTTATCATTTAATTATTAGGTTTTTTTAATTAAAA
66 TTAAAAAATCAATTTATTCCTTTAAATTGATTTATCATTTAATAACTA-GTAAATTGAATT--AA
10555733 TAATTTTTTTTAAT
128 TAATTTTTTTTAAT
*
10555747 AAAATAAATTTATTCCTTTAAATTGATTTATCATTTAATTATTACGTTTTTTAATTAAAAT-AAA
1 AAAATAAATTTATTCCTTTAAATTGATTTATCATTTAATTATTAC-ATTTTTAATTAAAATCAAA
*
10555811 TTTTTTAAATAAAATCAATTTATTTCTTTAAATTGATTTATC-TTGTAA-AACT-GTAAATTGA
65 ---TTT-AA-AAAATCAATTTATTCCTTTAAATTGATTTATCATT-TAATAACTAGTAAATTGA
10555872 TATTTTAATT
Statistics
Matches: 108, Mismatches: 10, Indels: 12
0.83 0.08 0.09
Matches are distributed among these distances:
144 46 0.43
145 14 0.13
146 5 0.05
147 3 0.03
148 6 0.06
149 34 0.31
ACGTcount: A:0.39, C:0.07, G:0.04, T:0.51
Consensus pattern (141 bp):
AAAATAAATTTATTCCTTTAAATTGATTTATCATTTAATTATTACATTTTTAATTAAAATCAAAT
TTAAAAAATCAATTTATTCCTTTAAATTGATTTATCATTTAATAACTAGTAAATTGAATTAATAA
TTTTTTTTAAT
Found at i:10558843 original size:18 final size:19
Alignment explanation
Indices: 10558808--10558845 Score: 51
Period size: 18 Copynumber: 2.1 Consensus size: 19
10558798 GAATAGAAAT
*
10558808 AAATCATTTGATTATAGAA
1 AAATCATTTGAATATAGAA
*
10558827 AAATCA-TTGAATGTAGAA
1 AAATCATTTGAATATAGAA
10558845 A
1 A
10558846 TATTAAATAT
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
18 11 0.65
19 6 0.35
ACGTcount: A:0.50, C:0.05, G:0.13, T:0.32
Consensus pattern (19 bp):
AAATCATTTGAATATAGAA
Found at i:10559879 original size:49 final size:48
Alignment explanation
Indices: 10559762--10559880 Score: 116
Period size: 49 Copynumber: 2.4 Consensus size: 48
10559752 GATATTAAAT
* **
10559762 GCCATCATTGTCGGGCTATCTGGGATGGCAGGATAAGTAAATTGTGAAA
1 GCCATCATTGTCGGGCTATCCGGGATGGCA-GATAAGTAAATAATGAAA
* *** *
10559811 ACCATCATTGTCAAACTATCCGGGATGGTA-A-AATGTAAGAATAATGAAA
1 GCCATCATTGTCGGGCTATCCGGGATGGCAGATAA-GT-A-AATAATGAAA
10559860 GCCATCATTGTCGGGCTATCC
1 GCCATCATTGTCGGGCTATCC
10559881 CAAATAATAG
Statistics
Matches: 55, Mismatches: 12, Indels: 6
0.75 0.16 0.08
Matches are distributed among these distances:
46 2 0.04
47 3 0.05
48 1 0.02
49 49 0.89
ACGTcount: A:0.32, C:0.18, G:0.24, T:0.26
Consensus pattern (48 bp):
GCCATCATTGTCGGGCTATCCGGGATGGCAGATAAGTAAATAATGAAA
Done.