Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: scaffold1983.1
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: 321518
ACGTcount: A:0.31, C:0.16, G:0.15, T:0.31
Warning! 17836 characters in sequence are not A, C, G, or T
File 1 of 2
Found at i:106 original size:19 final size:19
Alignment explanation
Indices: 79--116 Score: 67
Period size: 19 Copynumber: 2.0 Consensus size: 19
69 TTGAGATTGC
*
79 CAACTTATTTGCCTGAAAT
1 CAACCTATTTGCCTGAAAT
98 CAACCTATTTGCCTGAAAT
1 CAACCTATTTGCCTGAAAT
117 TATTCATTTC
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
19 18 1.00
ACGTcount: A:0.32, C:0.24, G:0.11, T:0.34
Consensus pattern (19 bp):
CAACCTATTTGCCTGAAAT
Found at i:210 original size:6 final size:7
Alignment explanation
Indices: 192--217 Score: 52
Period size: 7 Copynumber: 3.7 Consensus size: 7
182 CACTCCCTTT
192 TAAAAAA
1 TAAAAAA
199 TAAAAAA
1 TAAAAAA
206 TAAAAAA
1 TAAAAAA
213 TAAAA
1 TAAAA
218 TTTCAAAGCG
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 19 1.00
ACGTcount: A:0.85, C:0.00, G:0.00, T:0.15
Consensus pattern (7 bp):
TAAAAAA
Found at i:3562 original size:9 final size:9
Alignment explanation
Indices: 3548--3605 Score: 61
Period size: 9 Copynumber: 6.7 Consensus size: 9
3538 GTGAGTAAAG
3548 GAGAAGAAA
1 GAGAAGAAA
3557 GAGAAG---
1 GAGAAGAAA
3563 GAGAAGAAA
1 GAGAAGAAA
3572 GAGAAGAGAA
1 GAGAAGA-AA
3582 GAGAAG-AA
1 GAGAAGAAA
*
3590 GAAGAAGAAG
1 G-AGAAGAAA
3600 GAGAAG
1 GAGAAG
3606 GAGAGGGCAT
Statistics
Matches: 42, Mismatches: 1, Indels: 12
0.76 0.02 0.22
Matches are distributed among these distances:
6 6 0.14
8 3 0.07
9 23 0.55
10 10 0.24
ACGTcount: A:0.60, C:0.00, G:0.40, T:0.00
Consensus pattern (9 bp):
GAGAAGAAA
Found at i:3565 original size:15 final size:15
Alignment explanation
Indices: 3545--3609 Score: 89
Period size: 15 Copynumber: 4.5 Consensus size: 15
3535 CCAGTGAGTA
3545 AAGGAGAAGAAAGAG
1 AAGGAGAAGAAAGAG
3560 AAGGAGAAGAAAGAG
1 AAGGAGAAGAAAGAG
*
3575 AA-GAGAAGAGA-AG
1 AAGGAGAAGAAAGAG
* *
3588 AAGAAGAAGAAGGAG
1 AAGGAGAAGAAAGAG
3603 AAGGAGA
1 AAGGAGA
3610 GGGCATGAGG
Statistics
Matches: 43, Mismatches: 5, Indels: 4
0.83 0.10 0.08
Matches are distributed among these distances:
13 4 0.09
14 14 0.33
15 25 0.58
ACGTcount: A:0.60, C:0.00, G:0.40, T:0.00
Consensus pattern (15 bp):
AAGGAGAAGAAAGAG
Found at i:3570 original size:3 final size:3
Alignment explanation
Indices: 3549--3605 Score: 50
Period size: 3 Copynumber: 19.7 Consensus size: 3
3539 TGAGTAAAGG
*
3549 AGA AGA A-A GAGA AGG AGA AGA A-A GAGA AG- AGA AG- AGA AGA AGA
1 AGA AGA AGA -AGA AGA AGA AGA AGA -AGA AGA AGA AGA AGA AGA AGA
*
3592 AGA AGA AGG AGA AG
1 AGA AGA AGA AGA AG
3606 GAGAGGGCAT
Statistics
Matches: 44, Mismatches: 4, Indels: 12
0.73 0.07 0.20
Matches are distributed among these distances:
2 6 0.14
3 36 0.82
4 2 0.05
ACGTcount: A:0.61, C:0.00, G:0.39, T:0.00
Consensus pattern (3 bp):
AGA
Found at i:3583 original size:25 final size:24
Alignment explanation
Indices: 3548--3595 Score: 78
Period size: 25 Copynumber: 2.0 Consensus size: 24
3538 GTGAGTAAAG
*
3548 GAGAAGAAAGAGAAGGAGAAGAAA
1 GAGAAGAAAGAGAAGAAGAAGAAA
3572 GAGAAGAGAAGAGAAGAAGAAGAA
1 GAGAAGA-AAGAGAAGAAGAAGAA
3596 GAAGGAGAAG
Statistics
Matches: 22, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
24 7 0.32
25 15 0.68
ACGTcount: A:0.62, C:0.00, G:0.38, T:0.00
Consensus pattern (24 bp):
GAGAAGAAAGAGAAGAAGAAGAAA
Found at i:3585 original size:19 final size:19
Alignment explanation
Indices: 3551--3605 Score: 71
Period size: 19 Copynumber: 2.9 Consensus size: 19
3541 AGTAAAGGAG
3551 AAGAAAGAGAAGGAGAAGA
1 AAGAAAGAGAAGGAGAAGA
3570 AAGAGAAGAGAA-GAGAAG-
1 AAGA-AAGAGAAGGAGAAGA
3588 AAG-AAGAAGAAGGAGAAG
1 AAGAAAG-AGAAGGAGAAG
3606 GAGAGGGCAT
Statistics
Matches: 33, Mismatches: 0, Indels: 7
0.82 0.00 0.17
Matches are distributed among these distances:
16 3 0.09
17 4 0.12
18 9 0.27
19 10 0.30
20 7 0.21
ACGTcount: A:0.62, C:0.00, G:0.38, T:0.00
Consensus pattern (19 bp):
AAGAAAGAGAAGGAGAAGA
Found at i:3609 original size:6 final size:5
Alignment explanation
Indices: 3548--3605 Score: 66
Period size: 5 Copynumber: 11.2 Consensus size: 5
3538 GTGAGTAAAG
3548 GAGAA GA-AA GAGAA GGAGAA GA-AA GAGAA GAGAA GAGAA GAAGAA GAAGAA
1 GAGAA GAGAA GAGAA -GAGAA GAGAA GAGAA GAGAA GAGAA G-AGAA G-AGAA
3599 GGAGAA G
1 -GAGAA G
3606 GAGAGGGCAT
Statistics
Matches: 48, Mismatches: 0, Indels: 10
0.83 0.00 0.17
Matches are distributed among these distances:
4 8 0.17
5 20 0.42
6 19 0.40
7 1 0.02
ACGTcount: A:0.60, C:0.00, G:0.40, T:0.00
Consensus pattern (5 bp):
GAGAA
Found at i:5403 original size:14 final size:14
Alignment explanation
Indices: 5384--5417 Score: 68
Period size: 14 Copynumber: 2.4 Consensus size: 14
5374 GACATTTTTT
5384 TTCTAATGATACTA
1 TTCTAATGATACTA
5398 TTCTAATGATACTA
1 TTCTAATGATACTA
5412 TTCTAA
1 TTCTAA
5418 CGTGTAATTT
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 20 1.00
ACGTcount: A:0.35, C:0.15, G:0.06, T:0.44
Consensus pattern (14 bp):
TTCTAATGATACTA
Found at i:6618 original size:62 final size:62
Alignment explanation
Indices: 6552--6910 Score: 314
Period size: 62 Copynumber: 5.6 Consensus size: 62
6542 AGATTAATTG
* *
6552 CAACATTAAAACTTGGAACAAACTTTATAATATAAATTTTGTTATATAAATTAAATACATTA
1 CAACATTAAAAATTGGAACAAACTTTGTAATATAAATTTTGTTATATAAATTAAATACATTA
*
6614 CAACATTAAAAATTGGAACAAACTTTGTAATATAAATTTTGTTATATAAATTACATAAGCTCAAT
1 CAACATTAAAAATTGGAACAAACTTTGTAATATAAATTTTGTTATATAAATTAAAT-A---C-AT
*
6679 TC
61 TA
* * * * * * * * ** *** * **
6681 CTAC-TTAATCGTGACGATT-G-TCCAACATGGTGATTTCGATGCGGGTATTTACTCCGATT--A
1 CAACATTAA-----A-AATTGGAACAAACTTTGTAATATAAAT-TTTGT-TATA-T-AAATTAAA
* *
6741 TGATATAA
56 T-ACATTA
* *
6749 CAACATTAAAAATTGGAACAAACTTTGTAATATAAATTTTGTTATATAAATTAAATATATAA
1 CAACATTAAAAATTGGAACAAACTTTGTAATATAAATTTTGTTATATAAATTAAATACATTA
6811 CAACATTAAAAATTGGAACAAACTTTGTAATATAAATTTTGTTATATAAATTAAATACATTA
1 CAACATTAAAAATTGGAACAAACTTTGTAATATAAATTTTGTTATATAAATTAAATACATTA
*
6873 CAACAATAAAAATTGGAACAAACTTTGTAATATAAATT
1 CAACATTAAAAATTGGAACAAACTTTGTAATATAAATT
6911 AGGTACATTG
Statistics
Matches: 234, Mismatches: 43, Indels: 40
0.74 0.14 0.13
Matches are distributed among these distances:
61 3 0.01
62 157 0.67
63 9 0.04
64 4 0.02
65 12 0.05
66 5 0.02
67 6 0.03
68 5 0.02
69 4 0.02
70 12 0.05
71 4 0.02
72 9 0.04
73 1 0.00
74 3 0.01
ACGTcount: A:0.44, C:0.11, G:0.09, T:0.36
Consensus pattern (62 bp):
CAACATTAAAAATTGGAACAAACTTTGTAATATAAATTTTGTTATATAAATTAAATACATTA
Found at i:9317 original size:68 final size:65
Alignment explanation
Indices: 9157--9310 Score: 175
Period size: 64 Copynumber: 2.3 Consensus size: 65
9147 CTAACCAGTT
* * * *
9157 TATCTCGTAGCTCTCTTGTCTACATGGTGTCCTTCACCTAGAACCACGCATGCGACCTAGCTACA
1 TATCTCGTAGCTCTCTTGTCTACATGGTG--CTACACATAGAACCACCCATGCAACCTAGCTACA
9222 TA
64 TA
* * * *
9224 TATCCCGTAGCTCTCTTATCTACATGGTG-TACACATAGCATCACCCATGCAACCTAGCTACATC
1 TATCTCGTAGCTCTCTTGTCTACATGGTGCTACACATAGAACCACCCATGCAACCTAGCTACAT-
9288 A
65 A
9289 TAATGTCTCGTAGCTCTCTTGT
1 T-A--TCTCGTAGCTCTCTTGT
9311 ACACATGATG
Statistics
Matches: 73, Mismatches: 10, Indels: 7
0.81 0.11 0.08
Matches are distributed among these distances:
64 28 0.38
65 2 0.03
66 1 0.01
67 27 0.37
68 15 0.21
ACGTcount: A:0.23, C:0.31, G:0.15, T:0.31
Consensus pattern (65 bp):
TATCTCGTAGCTCTCTTGTCTACATGGTGCTACACATAGAACCACCCATGCAACCTAGCTACATA
Found at i:9855 original size:30 final size:30
Alignment explanation
Indices: 9821--9881 Score: 77
Period size: 30 Copynumber: 2.0 Consensus size: 30
9811 CCTTAAACTC
9821 AAACTTTGGAAAAATTACAATTTTGCCCCT
1 AAACTTTGGAAAAATTACAATTTTGCCCCT
* * * * *
9851 AAACTTTTGCATATTTACACTTTTGCCCCT
1 AAACTTTGGAAAAATTACAATTTTGCCCCT
9881 A
1 A
9882 GGCTCGGGAA
Statistics
Matches: 26, Mismatches: 5, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
30 26 1.00
ACGTcount: A:0.31, C:0.23, G:0.08, T:0.38
Consensus pattern (30 bp):
AAACTTTGGAAAAATTACAATTTTGCCCCT
Found at i:12698 original size:23 final size:25
Alignment explanation
Indices: 12672--12718 Score: 62
Period size: 25 Copynumber: 2.0 Consensus size: 25
12662 TATCATTCAT
*
12672 TTCATTATAT-CA-ATATTTTATGC
1 TTCATCATATCCATATATTTTATGC
*
12695 TTCATCATTTCCATATATTTTATG
1 TTCATCATATCCATATATTTTATG
12719 TATATTTATT
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
23 8 0.40
24 2 0.10
25 10 0.50
ACGTcount: A:0.28, C:0.15, G:0.04, T:0.53
Consensus pattern (25 bp):
TTCATCATATCCATATATTTTATGC
Found at i:13039 original size:46 final size:46
Alignment explanation
Indices: 12979--13244 Score: 343
Period size: 46 Copynumber: 6.0 Consensus size: 46
12969 TTTGACGTGA
* * * * * *
12979 TGCCATAGTGTCTTTCAACTATGGTCTTACTCATTTTC-TGTCATGT
1 TGCCATGGTATCTTTCAACCATGGTCTTACACA-TTTCATATCAGGT
** * * *
13025 TGCCATGGTATCTTTCAACCATGGTCTTATTCTTTTCATGTCACGT
1 TGCCATGGTATCTTTCAACCATGGTCTTACACATTTCATATCAGGT
*
13071 TGCCATGGTATCTTTCAACCATGGTCTTACACATCTCATATCAGGT
1 TGCCATGGTATCTTTCAACCATGGTCTTACACATTTCATATCAGGT
13117 TGCCATGGTATCTTTCAACCATGGTCTTACACATTTCATATCAGGT
1 TGCCATGGTATCTTTCAACCATGGTCTTACACATTTCATATCAGGT
*
13163 TGCCGTGGTATCTTTCAACCATGGTCTT--ACA---C--A-CAGGT
1 TGCCATGGTATCTTTCAACCATGGTCTTACACATTTCATATCAGGT
13201 TGCCATGGTATCTTTCAACCATGGTCTTACACATTTCATATCAG
1 TGCCATGGTATCTTTCAACCATGGTCTTACACATTTCATATCAG
13245 AGAGCACACT
Statistics
Matches: 196, Mismatches: 15, Indels: 18
0.86 0.07 0.08
Matches are distributed among these distances:
38 32 0.16
39 1 0.01
40 3 0.02
41 1 0.01
43 1 0.01
44 3 0.02
45 5 0.03
46 150 0.77
ACGTcount: A:0.21, C:0.24, G:0.16, T:0.38
Consensus pattern (46 bp):
TGCCATGGTATCTTTCAACCATGGTCTTACACATTTCATATCAGGT
Found at i:13210 original size:38 final size:38
Alignment explanation
Indices: 13158--13233 Score: 143
Period size: 38 Copynumber: 2.0 Consensus size: 38
13148 CATTTCATAT
*
13158 CAGGTTGCCGTGGTATCTTTCAACCATGGTCTTACACA
1 CAGGTTGCCATGGTATCTTTCAACCATGGTCTTACACA
13196 CAGGTTGCCATGGTATCTTTCAACCATGGTCTTACACA
1 CAGGTTGCCATGGTATCTTTCAACCATGGTCTTACACA
13234 TTTCATATCA
Statistics
Matches: 37, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
38 37 1.00
ACGTcount: A:0.22, C:0.26, G:0.20, T:0.32
Consensus pattern (38 bp):
CAGGTTGCCATGGTATCTTTCAACCATGGTCTTACACA
Found at i:17679 original size:19 final size:19
Alignment explanation
Indices: 17647--17712 Score: 60
Period size: 19 Copynumber: 3.5 Consensus size: 19
17637 ACCCAAATAA
**
17647 GTTGCTATGCTGTTATTTT
1 GTTGCTATTTTGTTATTTT
*
17666 GTTGCTATTTTGTTGTTTT
1 GTTGCTATTTTGTTATTTT
* * * *
17685 GCTACCATTTTGTTATTAT
1 GTTGCTATTTTGTTATTTT
*
17704 ATTGCTATT
1 GTTGCTATT
17713 ATTTTGTTGT
Statistics
Matches: 35, Mismatches: 12, Indels: 0
0.74 0.26 0.00
Matches are distributed among these distances:
19 35 1.00
ACGTcount: A:0.14, C:0.11, G:0.17, T:0.59
Consensus pattern (19 bp):
GTTGCTATTTTGTTATTTT
Found at i:39470 original size:98 final size:98
Alignment explanation
Indices: 39367--39545 Score: 243
Period size: 98 Copynumber: 1.8 Consensus size: 98
39357 ATGATACAAT
* * * *
39367 TTGAAAAGGTTAGGTATACTTTGTGTATAC-CATATGAAAAGGAAATGTATACTTTGTGTATACC
1 TTGAAAAGGTTAGGTACACTTTGTGTATACAAAT-TGAAAAGGAAATGTACACTTCGTGTATACC
39431 ACTTGAAAAGGAAATGTACACTATATGTGTACAC
65 ACTTGAAAAGGAAATGTACACTATATGTGTACAC
* * * ** *
39465 TTGAAAAGGTTATGTGCACTTTGTGTGTACAAATTGAAAAGGGTATGTACACTTCGTGTGTACCA
1 TTGAAAAGGTTAGGTACACTTTGTGTATACAAATTGAAAAGGAAATGTACACTTCGTGTATACCA
*
39530 CTTGAAAAGGGAATGT
66 CTTGAAAAGGAAATGT
39546 GCACCTCGGG
Statistics
Matches: 69, Mismatches: 11, Indels: 2
0.84 0.13 0.02
Matches are distributed among these distances:
98 67 0.97
99 2 0.03
ACGTcount: A:0.34, C:0.11, G:0.22, T:0.32
Consensus pattern (98 bp):
TTGAAAAGGTTAGGTACACTTTGTGTATACAAATTGAAAAGGAAATGTACACTTCGTGTATACCA
CTTGAAAAGGAAATGTACACTATATGTGTACAC
Found at i:39486 original size:65 final size:66
Alignment explanation
Indices: 39401--39575 Score: 176
Period size: 65 Copynumber: 2.7 Consensus size: 66
39391 GTATACCATA
* ** * *
39401 TGAAAAGGAAATGTATACTTTGTGTATACCACTTGAAAAGGAAATGTACACTAT-ATGTGTA-CA
1 TGAAAAGGGAATGTGCACTTTGTGTATACAAATTGAAAAGGAAATGTACACT-TCATGTGTACCA
39464 CT
65 CT
** * ** *
39466 TGAAAAGGTTATGTGCACTTTGTGTGTACAAATTGAAAAGGGTATGTACACTTCGTGTGTACCAC
1 TGAAAAGGGAATGTGCACTTTGTGTATACAAATTGAAAAGGAAATGTACACTTCATGTGTACCAC
39531 T
66 T
* * * *
39532 TGAAAAGGGAATGTGCACCTCGGGTGTAC-AATTAGAAAAGGAAA
1 TGAAAAGGGAATGTGCACTTTGTGTATACAAATT-GAAAAGGAAA
39576 GGTCCATCAG
Statistics
Matches: 90, Mismatches: 17, Indels: 5
0.80 0.15 0.04
Matches are distributed among these distances:
64 1 0.01
65 53 0.59
66 36 0.40
ACGTcount: A:0.35, C:0.13, G:0.23, T:0.29
Consensus pattern (66 bp):
TGAAAAGGGAATGTGCACTTTGTGTATACAAATTGAAAAGGAAATGTACACTTCATGTGTACCAC
T
Found at i:39540 original size:33 final size:33
Alignment explanation
Indices: 39384--39545 Score: 175
Period size: 33 Copynumber: 4.9 Consensus size: 33
39374 GGTTAGGTAT
* *
39384 ACTTTGTGTATACCA-TATGAAAAGGAAATGTAT
1 ACTTTGTGTGTACCACT-TGAAAAGGAAATGTAC
*
39417 ACTTTGTGTATACCACTTGAAAAGGAAATGTAC
1 ACTTTGTGTGTACCACTTGAAAAGGAAATGTAC
* * ** *
39450 ACTATATGTGTA-CACTTGAAAAGGTTATGTGC
1 ACTTTGTGTGTACCACTTGAAAAGGAAATGTAC
* * **
39482 ACTTTGTGTGTACAAATTGAAAAGGGTATGTAC
1 ACTTTGTGTGTACCACTTGAAAAGGAAATGTAC
* *
39515 ACTTCGTGTGTACCACTTGAAAAGGGAATGT
1 ACTTTGTGTGTACCACTTGAAAAGGAAATGT
39546 GCACCTCGGG
Statistics
Matches: 110, Mismatches: 17, Indels: 4
0.84 0.13 0.03
Matches are distributed among these distances:
32 27 0.25
33 82 0.75
34 1 0.01
ACGTcount: A:0.34, C:0.12, G:0.22, T:0.32
Consensus pattern (33 bp):
ACTTTGTGTGTACCACTTGAAAAGGAAATGTAC
Found at i:39559 original size:33 final size:33
Alignment explanation
Indices: 39417--39560 Score: 139
Period size: 33 Copynumber: 4.4 Consensus size: 33
39407 GGAAATGTAT
* * ** *
39417 ACTTTGTGTATACCACTTGAAAAGGAAATGTAC
1 ACTTCGTGTGTACCACTTGAAAAGGGTATGTGC
* *
39450 ACTAT-ATGTGTA-CACTTGAAAAGGTTATGTGC
1 ACT-TCGTGTGTACCACTTGAAAAGGGTATGTGC
* * * *
39482 ACTTTGTGTGTACAAATTGAAAAGGGTATGTAC
1 ACTTCGTGTGTACCACTTGAAAAGGGTATGTGC
*
39515 ACTTCGTGTGTACCACTTGAAAAGGGAATGTGC
1 ACTTCGTGTGTACCACTTGAAAAGGGTATGTGC
* *
39548 ACCTCGGGTGTAC
1 ACTTCGTGTGTAC
39561 AATTAGAAAA
Statistics
Matches: 91, Mismatches: 17, Indels: 6
0.80 0.15 0.05
Matches are distributed among these distances:
31 1 0.01
32 26 0.29
33 63 0.69
34 1 0.01
ACGTcount: A:0.31, C:0.15, G:0.24, T:0.31
Consensus pattern (33 bp):
ACTTCGTGTGTACCACTTGAAAAGGGTATGTGC
Found at i:39559 original size:66 final size:64
Alignment explanation
Indices: 39433--39575 Score: 171
Period size: 66 Copynumber: 2.2 Consensus size: 64
39423 TGTATACCAC
** * * *
39433 TTGAAAAGGAAATGTACACTATATGTGTACACTTGAAAAGGTTATGTGCACTTTGTGTGTACAAA
1 TTGAAAAGGAAATGTACACTATATGTGTACACTTGAAAAGGGAATGTGCACCTCGGGTGTAC-AA
** *
39498 TTGAAAAGGGTATGTACACT-TCGTGTGTACCACTTGAAAAGGGAATGTGCACCTCGGGTGTACA
1 TTGAAAAGGAAATGTACACTAT-ATGTGTA-CACTTGAAAAGGGAATGTGCACCTCGGGTGTACA
39562 A
64 A
39563 TTAGAAAAGGAAA
1 TT-GAAAAGGAAA
39576 GGTCCATCAG
Statistics
Matches: 65, Mismatches: 10, Indels: 5
0.81 0.12 0.06
Matches are distributed among these distances:
64 1 0.02
65 28 0.43
66 36 0.55
ACGTcount: A:0.35, C:0.13, G:0.24, T:0.28
Consensus pattern (64 bp):
TTGAAAAGGAAATGTACACTATATGTGTACACTTGAAAAGGGAATGTGCACCTCGGGTGTACAA
Found at i:39559 original size:98 final size:98
Alignment explanation
Indices: 39361--39572 Score: 230
Period size: 98 Copynumber: 2.1 Consensus size: 98
39351 ACCCAAATGA
* * * *
39361 TACAATTTGAAAAGGTTAGGTATACTTTGTGTATACCATATGAAAAGGAAATGTATACTTTGTGT
1 TACAA-TTGAAAAGGTTAGGTACACTTTGTGTATACAATATGAAAAGGAAATGTACACTTCGTGT
* *
39426 ATACCACTTGAAAAGGAAATGTACACTATATGTG
65 ATACCACTTGAAAAGGAAATGTACACTACAGGTG
* * * * **
39460 TACACTTGAAAAGGTTATGTGCACTTTGTGTGTACAA-ATTGAAAAGGGTATGTACACTTCGTGT
1 TACAATTGAAAAGGTTAGGTACACTTTGTGTATACAATA-TGAAAAGGAAATGTACACTTCGTGT
* * * *
39524 GTACCACTTGAAAAGGGAATGTGCACCT-CGGGTG
65 ATACCACTTGAAAAGGAAATGTACA-CTACAGGTG
39558 TACAATTAGAAAAGG
1 TACAATT-GAAAAGG
39573 AAAGGTCCAT
Statistics
Matches: 93, Mismatches: 17, Indels: 6
0.80 0.15 0.05
Matches are distributed among these distances:
97 1 0.01
98 79 0.85
99 13 0.14
ACGTcount: A:0.34, C:0.12, G:0.23, T:0.31
Consensus pattern (98 bp):
TACAATTGAAAAGGTTAGGTACACTTTGTGTATACAATATGAAAAGGAAATGTACACTTCGTGTA
TACCACTTGAAAAGGAAATGTACACTACAGGTG
Found at i:39570 original size:33 final size:32
Alignment explanation
Indices: 39456--39572 Score: 135
Period size: 33 Copynumber: 3.6 Consensus size: 32
39446 GTACACTATA
* * *
39456 TGTGTACACTTGAAAAGGTTATGTGCACTTTG
1 TGTGTACAATTGAAAAGGGTATGTGCACTTCG
*
39488 TGTGTACAAATTGAAAAGGGTATGTACACTTCG
1 TGTGTAC-AATTGAAAAGGGTATGTGCACTTCG
* * *
39521 TGTGTACCACTTGAAAAGGGAATGTGCACCTCG
1 TGTGTA-CAATTGAAAAGGGTATGTGCACTTCG
*
39554 GGTGTACAATTAGAAAAGG
1 TGTGTACAATT-GAAAAGG
39573 AAAGGTCCAT
Statistics
Matches: 72, Mismatches: 10, Indels: 5
0.83 0.11 0.06
Matches are distributed among these distances:
32 11 0.15
33 60 0.83
34 1 0.01
ACGTcount: A:0.31, C:0.14, G:0.26, T:0.29
Consensus pattern (32 bp):
TGTGTACAATTGAAAAGGGTATGTGCACTTCG
Found at i:45864 original size:26 final size:26
Alignment explanation
Indices: 45835--45945 Score: 74
Period size: 26 Copynumber: 4.4 Consensus size: 26
45825 GGTATATAAA
*
45835 AAATAGATAATACATATAAAAATTTG
1 AAATAGATAATACATAAAAAAATTTG
* *
45861 AAATTGATAATATATAAAAAAA-TT-
1 AAATAGATAATACATAAAAAAATTTG
* *
45885 -AA-AG-TAAATA-ATAAAACAATTTA
1 AAATAGAT-AATACATAAAAAAATTTG
* *
45908 AAAT-GAATAATACATAAAACAAGTTTA
1 AAATAG-ATAATACATAAAA-AAATTTG
*
45935 AAATAAATAAT
1 AAATAGATAAT
45946 GTATAAAAGC
Statistics
Matches: 67, Mismatches: 8, Indels: 19
0.71 0.09 0.20
Matches are distributed among these distances:
21 9 0.13
22 7 0.10
23 2 0.03
24 3 0.04
25 6 0.09
26 26 0.39
27 14 0.21
ACGTcount: A:0.62, C:0.04, G:0.05, T:0.29
Consensus pattern (26 bp):
AAATAGATAATACATAAAAAAATTTG
Found at i:45900 original size:21 final size:22
Alignment explanation
Indices: 45869--45945 Score: 66
Period size: 22 Copynumber: 3.3 Consensus size: 22
45859 TGAAATTGAT
*
45869 AATATATAAAA-AAATTAAAGTA
1 AATA-ATAAAACAAATTAAAATA
*
45891 AATAATAAAACAATTTAAAATGAA
1 AATAATAAAACAAATTAAAAT--A
*
45915 TAATACATAAAACAAGTTTAAAATA
1 -AATA-ATAAAACAA-ATTAAAATA
45940 AATAAT
1 AATAAT
45946 GTATAAAAGC
Statistics
Matches: 47, Mismatches: 2, Indels: 11
0.78 0.03 0.18
Matches are distributed among these distances:
21 6 0.13
22 12 0.26
23 2 0.04
24 5 0.11
25 5 0.11
26 9 0.19
27 8 0.17
ACGTcount: A:0.65, C:0.04, G:0.04, T:0.27
Consensus pattern (22 bp):
AATAATAAAACAAATTAAAATA
Found at i:45938 original size:27 final size:25
Alignment explanation
Indices: 45891--45965 Score: 87
Period size: 27 Copynumber: 2.8 Consensus size: 25
45881 AATTAAAGTA
*
45891 AATAATAAAACAATTTAAAATGAAT
1 AATAATAAAACAATTTAAAATAAAT
45916 AATACATAAAACAAGTTTAAAATAAAT
1 AATA-ATAAAACAA-TTTAAAATAAAT
* *
45943 AATGTATAAAAGCATTTTAAAAT
1 AAT-AATAAAA-CAATTTAAAAT
45966 CTATATTACA
Statistics
Matches: 43, Mismatches: 3, Indels: 6
0.83 0.06 0.12
Matches are distributed among these distances:
25 4 0.09
26 9 0.21
27 28 0.65
28 2 0.05
ACGTcount: A:0.60, C:0.05, G:0.05, T:0.29
Consensus pattern (25 bp):
AATAATAAAACAATTTAAAATAAAT
Found at i:46445 original size:23 final size:25
Alignment explanation
Indices: 46413--46459 Score: 62
Period size: 23 Copynumber: 2.0 Consensus size: 25
46403 GATGTAAAAT
*
46413 AAATAACATA-AAA-AAAATGTTTG
1 AAATAACATATAAATAAAACGTTTG
*
46436 AAATAGCATATAAATAAAACGTTT
1 AAATAACATATAAATAAAACGTTT
46460 TTTTTAAAAG
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
23 9 0.45
24 3 0.15
25 8 0.40
ACGTcount: A:0.57, C:0.06, G:0.09, T:0.28
Consensus pattern (25 bp):
AAATAACATATAAATAAAACGTTTG
Found at i:47777 original size:72 final size:72
Alignment explanation
Indices: 47670--47816 Score: 285
Period size: 72 Copynumber: 2.0 Consensus size: 72
47660 TTTTATTTCG
47670 AATCTGCCCCAAAACTTCACTTTAAGTTCAATTTAGTCCCCATTTTGTTATTTTTGATATTTTAA
1 AATCTGCCCCAAAACTTCACTTTAAGTTCAATTTAGTCCCCATTTTGTTATTTTTGATATTTTAA
47735 TTAAATT
66 TTAAATT
*
47742 AATCTGCCCCAAAACTTCACTTTAAGTTCATTTTAGTCCCCATTTTGTTATTTTTGATATTTTAA
1 AATCTGCCCCAAAACTTCACTTTAAGTTCAATTTAGTCCCCATTTTGTTATTTTTGATATTTTAA
47807 TTAAATT
66 TTAAATT
47814 AAT
1 AAT
47817 TATTTTAATA
Statistics
Matches: 74, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
72 74 1.00
ACGTcount: A:0.29, C:0.18, G:0.07, T:0.46
Consensus pattern (72 bp):
AATCTGCCCCAAAACTTCACTTTAAGTTCAATTTAGTCCCCATTTTGTTATTTTTGATATTTTAA
TTAAATT
Found at i:47833 original size:13 final size:13
Alignment explanation
Indices: 47810--47860 Score: 52
Period size: 13 Copynumber: 3.9 Consensus size: 13
47800 ATTTTAATTA
47810 AATTAATTATT-TT
1 AATT-ATTATTATT
47823 AATATATTATTATT
1 AAT-TATTATTATT
*
47837 TATTATTATTA-T
1 AATTATTATTATT
*
47849 CATTATTATTAT
1 AATTATTATTAT
47861 ACTAGTATTT
Statistics
Matches: 33, Mismatches: 2, Indels: 6
0.80 0.05 0.15
Matches are distributed among these distances:
12 11 0.33
13 17 0.52
14 5 0.15
ACGTcount: A:0.37, C:0.02, G:0.00, T:0.61
Consensus pattern (13 bp):
AATTATTATTATT
Found at i:47835 original size:3 final size:3
Alignment explanation
Indices: 47815--47860 Score: 51
Period size: 3 Copynumber: 15.7 Consensus size: 3
47805 AATTAAATTA
* *
47815 ATT ATT -TT AAT A-T ATT ATT ATTT ATT ATT ATT ATC ATT ATT ATT
1 ATT ATT ATT ATT ATT ATT ATT A-TT ATT ATT ATT ATT ATT ATT ATT
47859 AT
1 AT
47861 ACTAGTATTT
Statistics
Matches: 37, Mismatches: 3, Indels: 6
0.80 0.07 0.13
Matches are distributed among these distances:
2 4 0.11
3 30 0.81
4 3 0.08
ACGTcount: A:0.35, C:0.02, G:0.00, T:0.63
Consensus pattern (3 bp):
ATT
Found at i:48006 original size:16 final size:17
Alignment explanation
Indices: 47985--48049 Score: 55
Period size: 16 Copynumber: 3.9 Consensus size: 17
47975 TCACCATTGC
47985 TATTATGTT-TTATCAT
1 TATTATGTTATTATCAT
* *
48001 TATTAT-TTTTTATTAT
1 TATTATGTTATTATCAT
* * *
48017 TATCAATGTTCTTATTAT
1 TAT-TATGTTATTATCAT
48035 TATTAT-TTATTATCA
1 TATTATGTTATTATCA
48050 ATAATTTTAT
Statistics
Matches: 40, Mismatches: 6, Indels: 6
0.77 0.12 0.12
Matches are distributed among these distances:
15 2 0.05
16 22 0.55
17 4 0.10
18 12 0.30
ACGTcount: A:0.28, C:0.06, G:0.03, T:0.63
Consensus pattern (17 bp):
TATTATGTTATTATCAT
Found at i:48007 original size:3 final size:3
Alignment explanation
Indices: 47994--48210 Score: 77
Period size: 3 Copynumber: 71.0 Consensus size: 3
47984 CTATTATGTT
* * * * *
47994 TTA TCA TTA TTA TT- TT- TTA TTA TTA TCA ATG TTC TTA TTA TTA TTA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
* * * * * *
48040 TTTA TTA TCAA TAA TT- TTA TTA TTG TTA CTA TTA TTA TTA TCAA CCTA
1 -TTA TTA T-TA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA T-TA -TTA
* * * * *
48088 TTA TTA TTC TTG TTA GTA -TA TTA TTG TT- TCCTA TTT TTA -TA TTA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA T--TA TTA TTA TTA TTA
* * ** * * *
48132 TTT TTG TTA TTA ACA TATA TTA TTA TTA TTAA TGTA GTG TTA TTC TTA
1 TTA TTA TTA TTA TTA T-TA TTA TTA TTA TT-A T-TA TTA TTA TTA TTA
* *
48180 TTA TTT TCTA TTA TTA CTA TTA TTA TTA TTA
1 TTA TTA T-TA TTA TTA TTA TTA TTA TTA TTA
48211 CACTATTAAA
Statistics
Matches: 156, Mismatches: 43, Indels: 30
0.68 0.19 0.13
Matches are distributed among these distances:
2 11 0.07
3 128 0.82
4 15 0.10
5 2 0.01
ACGTcount: A:0.29, C:0.07, G:0.04, T:0.60
Consensus pattern (3 bp):
TTA
Found at i:48033 original size:28 final size:28
Alignment explanation
Indices: 48000--48077 Score: 79
Period size: 28 Copynumber: 2.7 Consensus size: 28
47990 TGTTTTATCA
*
48000 TTATTATTTTTTATTATTATCAAT-GTT
1 TTATTATTTTTTATTATTATCAATAATT
*
48027 CTTATTA-TTATTATTTATTATCAATAATT
1 -TTATTATTTTTTA-TTATTATCAATAATT
*
48056 TTATTATTGTTACTATTATTAT
1 TTATTATT-TT-TTATTATTAT
48078 TATCAACCTA
Statistics
Matches: 41, Mismatches: 4, Indels: 8
0.77 0.08 0.15
Matches are distributed among these distances:
27 5 0.12
28 23 0.56
29 3 0.07
30 8 0.20
31 2 0.05
ACGTcount: A:0.29, C:0.05, G:0.03, T:0.63
Consensus pattern (28 bp):
TTATTATTTTTTATTATTATCAATAATT
Found at i:48063 original size:31 final size:32
Alignment explanation
Indices: 47992--48083 Score: 89
Period size: 31 Copynumber: 2.9 Consensus size: 32
47982 TGCTATTATG
* * *
47992 TTTTATCATTATTATTTTTTATTAT-TATCAA
1 TTTTATTATTATTATTATTTATTATCAATCAA
* *
48023 TGTTCTTATTATTATTATTTATTATCAAT-AA
1 TTTTATTATTATTATTATTTATTATCAATCAA
* *
48054 TTTTATTATTGTTACTATTATTATTATCAA
1 TTTTATTATTATTATTA-T-TTATTATCAA
48084 CCTATTATTA
Statistics
Matches: 49, Mismatches: 9, Indels: 4
0.79 0.15 0.06
Matches are distributed among these distances:
31 36 0.73
32 3 0.06
33 10 0.20
ACGTcount: A:0.30, C:0.07, G:0.02, T:0.61
Consensus pattern (32 bp):
TTTTATTATTATTATTATTTATTATCAATCAA
Found at i:48405 original size:17 final size:17
Alignment explanation
Indices: 48373--48405 Score: 50
Period size: 17 Copynumber: 1.9 Consensus size: 17
48363 ATGCGTTTAT
48373 TTTACTTTATTTTATCA
1 TTTACTTTATTTTATCA
48390 TTTA-TTTATTTATATC
1 TTTACTTTATTT-TATC
48406 CTTTTTATAA
Statistics
Matches: 15, Mismatches: 0, Indels: 2
0.88 0.00 0.12
Matches are distributed among these distances:
16 7 0.47
17 8 0.53
ACGTcount: A:0.24, C:0.09, G:0.00, T:0.67
Consensus pattern (17 bp):
TTTACTTTATTTTATCA
Found at i:48441 original size:3 final size:3
Alignment explanation
Indices: 48433--48523 Score: 103
Period size: 3 Copynumber: 29.7 Consensus size: 3
48423 ACTTTAGATT
* * *
48433 TTA TTA TTA -TA TTA TTA TTT TTC TTGA TCTT TTCA TTA TTA TTA TTA
1 TTA TTA TTA TTA TTA TTA TTA TTA TT-A T-TA TT-A TTA TTA TTA TTA
* *
48480 TTA TTA TTA TTA TTA TTA TTA TTA TTG TTA TTA TTT TTA TTA TT
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TT
48524 GTTGTTGTTC
Statistics
Matches: 75, Mismatches: 9, Indels: 8
0.82 0.10 0.09
Matches are distributed among these distances:
2 2 0.03
3 68 0.91
4 4 0.05
5 1 0.01
ACGTcount: A:0.26, C:0.03, G:0.02, T:0.68
Consensus pattern (3 bp):
TTA
Found at i:49872 original size:36 final size:36
Alignment explanation
Indices: 49789--49872 Score: 82
Period size: 36 Copynumber: 2.4 Consensus size: 36
49779 TTTTTAATAT
* *
49789 TTTTAAAATGTT-AAATTAATAAAAATAAAATTACA
1 TTTTAAAATTTTAAAAATAATAAAAATAAAATTACA
** * * *
49824 TTTTAATTTTTTAAAAATAATAAAATTTTAATTTA-A
1 TTTTAAAATTTTAAAAATAATAAAA-ATAAAATTACA
49860 TTTTAAAATTTTA
1 TTTTAAAATTTTA
49873 TATTTATTAC
Statistics
Matches: 38, Mismatches: 9, Indels: 3
0.76 0.18 0.06
Matches are distributed among these distances:
35 9 0.24
36 23 0.61
37 6 0.16
ACGTcount: A:0.50, C:0.01, G:0.01, T:0.48
Consensus pattern (36 bp):
TTTTAAAATTTTAAAAATAATAAAAATAAAATTACA
Found at i:49878 original size:25 final size:26
Alignment explanation
Indices: 49850--49907 Score: 61
Period size: 26 Copynumber: 2.3 Consensus size: 26
49840 ATAATAAAAT
*
49850 TTTAATTTA-ATT-TTAAAATTTTATA
1 TTTAATTTACATTATAAAAATTTTA-A
49875 TTT-A-TTACTATTATAAAAATTTTAA
1 TTTAATTTAC-ATTATAAAAATTTTAA
49900 TTTAATTT
1 TTTAATTT
49908 TCATCTCCTA
Statistics
Matches: 27, Mismatches: 1, Indels: 8
0.75 0.03 0.22
Matches are distributed among these distances:
23 3 0.11
24 1 0.04
25 10 0.37
26 11 0.41
27 2 0.07
ACGTcount: A:0.40, C:0.02, G:0.00, T:0.59
Consensus pattern (26 bp):
TTTAATTTACATTATAAAAATTTTAA
Found at i:52619 original size:20 final size:20
Alignment explanation
Indices: 52594--52662 Score: 84
Period size: 20 Copynumber: 3.4 Consensus size: 20
52584 CAAGACACCA
***
52594 AAATATCATAGGGCATAATG
1 AAATATCATAGCTTATAATG
*
52614 AAATATCAATATCTTATAATG
1 AAATATC-ATAGCTTATAATG
*
52635 AAATATCATAGTTTATAATG
1 AAATATCATAGCTTATAATG
52655 AAATATCA
1 AAATATCA
52663 ATATCTCATA
Statistics
Matches: 42, Mismatches: 6, Indels: 2
0.84 0.12 0.04
Matches are distributed among these distances:
20 26 0.62
21 16 0.38
ACGTcount: A:0.48, C:0.09, G:0.10, T:0.33
Consensus pattern (20 bp):
AAATATCATAGCTTATAATG
Found at i:52634 original size:21 final size:21
Alignment explanation
Indices: 52608--52673 Score: 100
Period size: 21 Copynumber: 3.2 Consensus size: 21
52598 ATCATAGGGC
52608 ATAATGAAATATCAATATCTT
1 ATAATGAAATATCAATATCTT
52629 ATAATGAAATATC-ATAGT-TT
1 ATAATGAAATATCAATA-TCTT
*
52649 ATAATGAAATATCAATATCTC
1 ATAATGAAATATCAATATCTT
52670 ATAA
1 ATAA
52674 AATCATTTCC
Statistics
Matches: 41, Mismatches: 1, Indels: 6
0.85 0.02 0.12
Matches are distributed among these distances:
20 19 0.46
21 22 0.54
ACGTcount: A:0.48, C:0.09, G:0.06, T:0.36
Consensus pattern (21 bp):
ATAATGAAATATCAATATCTT
Found at i:52639 original size:41 final size:41
Alignment explanation
Indices: 52594--52673 Score: 124
Period size: 41 Copynumber: 2.0 Consensus size: 41
52584 CAAGACACCA
*
52594 AAATATCATAGGGCATAATGAAATATCAATATCTTATAATG
1 AAATATCATAGGGCATAATGAAATATCAATATCTCATAATG
***
52635 AAATATCATAGTTTATAATGAAATATCAATATCTCATAA
1 AAATATCATAGGGCATAATGAAATATCAATATCTCATAA
52674 AATCATTTCC
Statistics
Matches: 35, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
41 35 1.00
ACGTcount: A:0.47, C:0.10, G:0.09, T:0.34
Consensus pattern (41 bp):
AAATATCATAGGGCATAATGAAATATCAATATCTCATAATG
Found at i:54214 original size:18 final size:19
Alignment explanation
Indices: 54183--54219 Score: 58
Period size: 18 Copynumber: 2.0 Consensus size: 19
54173 CCTAGCCTTT
54183 GCCACCACTAACTCCACTA
1 GCCACCACTAACTCCACTA
*
54202 GCCA-CACTTACTCCACTA
1 GCCACCACTAACTCCACTA
54220 CCTACTCCAC
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
18 13 0.76
19 4 0.24
ACGTcount: A:0.30, C:0.46, G:0.05, T:0.19
Consensus pattern (19 bp):
GCCACCACTAACTCCACTA
Found at i:54776 original size:24 final size:23
Alignment explanation
Indices: 54728--54779 Score: 61
Period size: 24 Copynumber: 2.2 Consensus size: 23
54718 CTCTTTTTGT
*
54728 TATTATTATATTTCTTAATATTA
1 TATTATTATATTTCTTAATAATA
*
54751 TATTATATATATATTCTT-TTAATA
1 TATTAT-TATAT-TTCTTAATAATA
54775 TATTA
1 TATTA
54780 GGTATATTCT
Statistics
Matches: 25, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
23 6 0.24
24 14 0.56
25 5 0.20
ACGTcount: A:0.37, C:0.04, G:0.00, T:0.60
Consensus pattern (23 bp):
TATTATTATATTTCTTAATAATA
Found at i:54835 original size:27 final size:26
Alignment explanation
Indices: 54795--54946 Score: 95
Period size: 25 Copynumber: 6.0 Consensus size: 26
54785 ATTCTAAATT
*
54795 CTATATTACGTATATATATATT-ATA
1 CTATATTATGTATATATATATTAATA
* *
54820 CTATTTTATGTATATATCT-TTAATA
1 CTATATTATGTATATATATATTAATA
* *
54845 CTATATTATTTATATATATATTTTTACATG
1 CTATATTATGTATATATATA---TTA-ATA
* *
54875 TTATCTTATGTATATAT-T-TTAAT-
1 CTATATTATGTATATATATATTAATA
* * * *
54898 -TATATTATGTATGTAT-TTTTTACA
1 CTATATTATGTATATATATATTAATA
* *
54922 CTATATTATGTACATAT-TTTTAATA
1 CTATATTATGTATATATATATTAATA
54947 TTATCACGTA
Statistics
Matches: 100, Mismatches: 18, Indels: 18
0.74 0.13 0.13
Matches are distributed among these distances:
22 15 0.15
23 3 0.03
24 4 0.04
25 58 0.58
29 4 0.04
30 16 0.16
ACGTcount: A:0.34, C:0.07, G:0.05, T:0.55
Consensus pattern (26 bp):
CTATATTATGTATATATATATTAATA
Found at i:54962 original size:23 final size:23
Alignment explanation
Indices: 54936--54984 Score: 64
Period size: 23 Copynumber: 2.1 Consensus size: 23
54926 ATTATGTACA
*
54936 TATTTTTAATAT-TATCACGTATT
1 TATTTTTAATATATAT-ACATATT
*
54959 TATTTTTTATATATATACATATT
1 TATTTTTAATATATATACATATT
54982 TAT
1 TAT
54985 GTAGTATTAT
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
23 20 0.87
24 3 0.13
ACGTcount: A:0.33, C:0.06, G:0.02, T:0.59
Consensus pattern (23 bp):
TATTTTTAATATATATACATATT
Found at i:55121 original size:16 final size:15
Alignment explanation
Indices: 55102--55136 Score: 52
Period size: 16 Copynumber: 2.3 Consensus size: 15
55092 TTATTATTAT
55102 TATTCTAATATTTTGA
1 TATTCTAATATTTT-A
*
55118 TATTTTAATATTTTA
1 TATTCTAATATTTTA
55133 TATT
1 TATT
55137 ATTCACATCA
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
15 5 0.28
16 13 0.72
ACGTcount: A:0.31, C:0.03, G:0.03, T:0.63
Consensus pattern (15 bp):
TATTCTAATATTTTA
Found at i:67075 original size:73 final size:74
Alignment explanation
Indices: 66927--67332 Score: 491
Period size: 73 Copynumber: 5.5 Consensus size: 74
66917 CTACGGTTCA
* * * * * *
66927 AAAAAATCAGCGCATATTGCGAGAGGTGAGTTGAGCCTTGACTGACATGTTGAGGTATTTTCAAT
1 AAAAAATCAACTCATATTGCAAGAGGTGAGTTGAGCC-TCA-AGACACGTTGAGGTATTTTCAAT
* *
66992 TTTTGCCTTTC
64 TTCTGTCTTTC
* *
67003 -AAAAATCAACTCATACTGCAAGAAGTGAGTTGAGCCTCAAGACACGTTGAGGTATTTTCAATTT
1 AAAAAATCAACTCATATTGCAAGAGGTGAGTTGAGCCTCAAGACACGTTGAGGTATTTTCAATTT
67067 CTGTCTTTC
66 CTGTCTTTC
* * * *
67076 AAAAAAATTCAACTCATACTGCAAGAAGCGAGTTGAGCCTTAAGACACGTTGAGGTATTTTCAAT
1 -AAAAAA-TCAACTCATATTGCAAGAGGTGAGTTGAGCCTCAAGACACGTTGAGGTATTTTCAAT
67141 TTCTGTCTTTC
64 TTCTGTCTTTC
** *
67152 AAAAAATCAACTCATATTGCAAGAGGTGAGTTGAGCCTCAAGACACACTGAGGTAATTTCAA-TT
1 AAAAAATCAACTCATATTGCAAGAGGTGAGTTGAGCCTCAAGACACGTTGAGGTATTTTCAATTT
67216 -TGTCTTTC
66 CTGTCTTTC
** * * *
67224 AAAATAATCAACTCATATTGTGAGAGGTGAGTTGAGCCTCAGGACACGCTGAGGTAATTTT-GAT
1 AAAA-AATCAACTCATATTGCAAGAGGTGAGTTGAGCCTCAAGACACGTTGAGGT-ATTTTCAAT
*
67288 CTCTGT-TTTC
64 TTCTGTCTTTC
* *
67298 -AAAAATCAACTCATATTGCGAGAGGTGAGTGGAGC
1 AAAAAATCAACTCATATTGCAAGAGGTGAGTTGAGC
67333 TTCGGATCAC
Statistics
Matches: 295, Mismatches: 28, Indels: 18
0.87 0.08 0.05
Matches are distributed among these distances:
72 42 0.14
73 82 0.28
74 60 0.20
75 45 0.15
76 66 0.22
ACGTcount: A:0.31, C:0.17, G:0.21, T:0.31
Consensus pattern (74 bp):
AAAAAATCAACTCATATTGCAAGAGGTGAGTTGAGCCTCAAGACACGTTGAGGTATTTTCAATTT
CTGTCTTTC
Found at i:67471 original size:87 final size:86
Alignment explanation
Indices: 67292--67519 Score: 214
Period size: 87 Copynumber: 2.6 Consensus size: 86
67282 TTTGATCTCT
* * * *
67292 GTTTTCAAAAATCAACTCATATTGCGAGAGGTGAGTGGAGCTTCGGATCACATGTCGAGGTATTT
1 GTTTT-AAAAATCAACTCATATTGCGAAAAGTGAGTTGAGCTTCGGATCACATGTCGAGCTATTT
*
67357 TCAAAATCTGTTTTACAAATTTT
65 TCAAAATCTGTTTTA-AAATTTA
* * *
67380 GTTTTAAAAATCAACTCATTTTGCGAAAAGTGAGTTGAGCCTT-GGCTCACGTG-CTGAGCTATT
1 GTTTTAAAAATCAACTCATATTGCGAAAAGTGAGTTGAG-CTTCGGATCACATGTC-GAGCTATT
** *
67443 TTCAATTTCTGTTTT-TAATGTCTA
64 TTCAAAATCTGTTTTAAAAT-T-TA
* * *
67467 GTTTTAAAGAGTCAATTCATATTGCGAGAAA-TGAGTTAAGC-TCAGGATCACAT
1 GTTTTAAA-AATCAACTCATATTGCGA-AAAGTGAGTTGAGCTTC-GGATCACAT
67520 ACCGAGTAAA
Statistics
Matches: 115, Mismatches: 17, Indels: 16
0.78 0.11 0.11
Matches are distributed among these distances:
85 3 0.03
86 3 0.03
87 68 0.59
88 38 0.33
89 3 0.03
ACGTcount: A:0.29, C:0.15, G:0.20, T:0.36
Consensus pattern (86 bp):
GTTTTAAAAATCAACTCATATTGCGAAAAGTGAGTTGAGCTTCGGATCACATGTCGAGCTATTTT
CAAAATCTGTTTTAAAATTTA
Found at i:68173 original size:18 final size:18
Alignment explanation
Indices: 68150--68205 Score: 61
Period size: 18 Copynumber: 3.4 Consensus size: 18
68140 CCACTACCAA
68150 CTCCACTAGCCACACTTG
1 CTCCACTAGCCACACTTG
*
68168 CTCCACCA-CCA-A----
1 CTCCACTAGCCACACTTG
68180 CTCCACTAGCCACACTTG
1 CTCCACTAGCCACACTTG
68198 CTCCACTA
1 CTCCACTA
68206 CCTACTCCAC
Statistics
Matches: 30, Mismatches: 2, Indels: 12
0.68 0.05 0.27
Matches are distributed among these distances:
12 7 0.23
13 3 0.10
14 1 0.03
16 1 0.03
17 3 0.10
18 15 0.50
ACGTcount: A:0.25, C:0.48, G:0.07, T:0.20
Consensus pattern (18 bp):
CTCCACTAGCCACACTTG
Found at i:68179 original size:30 final size:30
Alignment explanation
Indices: 68140--68225 Score: 154
Period size: 30 Copynumber: 2.9 Consensus size: 30
68130 CTAGCCTTTG
68140 CCACTACCAACTCCACTAGCCACACTTGCT
1 CCACTACCAACTCCACTAGCCACACTTGCT
*
68170 CCACCACCAACTCCACTAGCCACACTTGCT
1 CCACTACCAACTCCACTAGCCACACTTGCT
*
68200 CCACTACCTACTCCACTAGCCACACT
1 CCACTACCAACTCCACTAGCCACACT
68226 CTACCACCCC
Statistics
Matches: 53, Mismatches: 3, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
30 53 1.00
ACGTcount: A:0.27, C:0.49, G:0.06, T:0.19
Consensus pattern (30 bp):
CCACTACCAACTCCACTAGCCACACTTGCT
Found at i:68759 original size:23 final size:23
Alignment explanation
Indices: 68722--68851 Score: 86
Period size: 25 Copynumber: 5.5 Consensus size: 23
68712 CTTTTTTTTT
*
68722 TATTAT-TATATTTCTTAATATTA
1 TATTATATATA-TTCTTAATACTA
* *
68745 TATTATATATATTCTT-TTAATA
1 TATTATATATATTCTTAATACTA
** * *
68767 TATTAGGTATATTCTAAATTCTA
1 TATTATATATATTCTTAATACTA
*
68790 TATTACGTATATATATATT-ATACTA
1 TATTA--TATATAT-TCTTAATACTA
* *
68815 TTTTATGTATATATCTTTAATACTA
1 TATTATATATAT-TC-TTAATACTA
*
68840 TATTATTTATAT
1 TATTATATATAT
68852 ATATATTTTT
Statistics
Matches: 82, Mismatches: 18, Indels: 12
0.73 0.16 0.11
Matches are distributed among these distances:
22 17 0.21
23 27 0.33
24 6 0.07
25 30 0.37
26 2 0.02
ACGTcount: A:0.35, C:0.06, G:0.03, T:0.55
Consensus pattern (23 bp):
TATTATATATATTCTTAATACTA
Found at i:68827 original size:27 final size:26
Alignment explanation
Indices: 68787--68938 Score: 95
Period size: 25 Copynumber: 6.0 Consensus size: 26
68777 ATTCTAAATT
*
68787 CTATATTACGTATATATATATT-ATA
1 CTATATTATGTATATATATATTAATA
* *
68812 CTATTTTATGTATATATCT-TTAATA
1 CTATATTATGTATATATATATTAATA
* *
68837 CTATATTATTTATATATATATTTTTTAATG
1 CTATATTATGTATATATATA----TTAATA
* *
68867 TTATCTTATGTATATAT-T-TTAAT-
1 CTATATTATGTATATATATATTAATA
* * * *
68890 -TATATTATGTATGTAT-TTTTTACA
1 CTATATTATGTATATATATATTAATA
* *
68914 CTATATTATGTACATAT-TTTTAATA
1 CTATATTATGTATATATATATTAATA
68939 TTATCACGTA
Statistics
Matches: 100, Mismatches: 18, Indels: 18
0.74 0.13 0.13
Matches are distributed among these distances:
22 15 0.15
23 3 0.03
24 7 0.07
25 55 0.55
29 1 0.01
30 19 0.19
ACGTcount: A:0.34, C:0.06, G:0.05, T:0.56
Consensus pattern (26 bp):
CTATATTATGTATATATATATTAATA
Found at i:68880 original size:26 final size:23
Alignment explanation
Indices: 68841--68959 Score: 84
Period size: 24 Copynumber: 5.0 Consensus size: 23
68831 TTAATACTAT
*
68841 ATTATTTATATATATATTTTTTA
1 ATTATTTATGTATATATTTTTTA
68864 ATGTTATCTTATGTATATA--TTTTA
1 A--TTAT-TTATGTATATATTTTTTA
*
68888 ATTATATTATGTATGTATTTTTTA
1 ATTAT-TTATGTATATATTTTTTA
* *
68912 CACTATATTATGTACATA-TTTTTA
1 -ATTAT-TTATGTATATATTTTTTA
* *
68936 A-TATTATCACGTATTTATTTTTTA
1 ATTATT-T-ATGTATATATTTTTTA
68960 TATATGTACA
Statistics
Matches: 78, Mismatches: 9, Indels: 17
0.75 0.09 0.16
Matches are distributed among these distances:
21 1 0.01
22 18 0.23
23 8 0.10
24 23 0.29
25 18 0.23
26 10 0.13
ACGTcount: A:0.31, C:0.05, G:0.05, T:0.59
Consensus pattern (23 bp):
ATTATTTATGTATATATTTTTTA
Found at i:68886 original size:24 final size:22
Alignment explanation
Indices: 68853--68974 Score: 72
Period size: 24 Copynumber: 5.4 Consensus size: 22
68843 TATTTATATA
* *
68853 TATATTTTTTAATGTTATCTTATG
1 TATATATTTTAA--TTATATTATG
68877 TATATATTTTAATTATATTATG
1 TATATATTTTAATTATATTATG
* *
68899 TATGTATTTTTTACACTATATTATG
1 TA--TATATTTTA-ATTATATTATG
* * *
68924 TACATATTTTTAA-TATTATCACG
1 TATATA-TTTTAATTA-TATTATG
*
68947 TATTTATTTT--TTATA-TATG
1 TATATATTTTAATTATATTATG
*
68966 TACATATTT
1 TATATATTT
68975 ATGTAGTATT
Statistics
Matches: 78, Mismatches: 14, Indels: 17
0.72 0.13 0.16
Matches are distributed among these distances:
19 9 0.12
20 2 0.03
21 2 0.03
22 17 0.22
23 12 0.15
24 24 0.31
25 12 0.15
ACGTcount: A:0.30, C:0.06, G:0.06, T:0.58
Consensus pattern (22 bp):
TATATATTTTAATTATATTATG
Found at i:68941 original size:20 final size:20
Alignment explanation
Indices: 68916--68974 Score: 57
Period size: 23 Copynumber: 2.9 Consensus size: 20
68906 TTTTTACACT
68916 ATATTATGTACATATTTTTA
1 ATATTATGTACATATTTTTA
** *
68936 ATATTATCACGTATTTATTTTTT
1 ATATTAT---GTACATATTTTTA
68959 ATA-TATGTACATATTT
1 ATATTATGTACATATTT
68975 ATGTAGTATT
Statistics
Matches: 31, Mismatches: 5, Indels: 7
0.72 0.12 0.16
Matches are distributed among these distances:
19 8 0.26
20 7 0.23
22 3 0.10
23 13 0.42
ACGTcount: A:0.32, C:0.07, G:0.05, T:0.56
Consensus pattern (20 bp):
ATATTATGTACATATTTTTA
Found at i:69113 original size:16 final size:15
Alignment explanation
Indices: 69089--69123 Score: 52
Period size: 16 Copynumber: 2.3 Consensus size: 15
69079 TAATTATTAT
69089 TATTCTAATATTTTGA
1 TATTCTAATATTTT-A
*
69105 TATTTTAATATTTTA
1 TATTCTAATATTTTA
69120 TATT
1 TATT
69124 ATTCACATCA
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
15 5 0.28
16 13 0.72
ACGTcount: A:0.31, C:0.03, G:0.03, T:0.63
Consensus pattern (15 bp):
TATTCTAATATTTTA
Found at i:71718 original size:28 final size:26
Alignment explanation
Indices: 71686--71747 Score: 88
Period size: 28 Copynumber: 2.3 Consensus size: 26
71676 TGTAAGAATT
71686 TAAAATAAATAATATATACATAAAAATG
1 TAAAATAAATAATATATA-A-AAAAATG
* *
71714 TAAAATAAATAATATATAAAATAATT
1 TAAAATAAATAATATATAAAAAAATG
71740 TAAAATAA
1 TAAAATAA
71748 TATGTAATAA
Statistics
Matches: 32, Mismatches: 2, Indels: 2
0.89 0.06 0.06
Matches are distributed among these distances:
26 13 0.41
27 1 0.03
28 18 0.56
ACGTcount: A:0.66, C:0.02, G:0.02, T:0.31
Consensus pattern (26 bp):
TAAAATAAATAATATATAAAAAAATG
Found at i:77992 original size:19 final size:19
Alignment explanation
Indices: 77968--78004 Score: 56
Period size: 19 Copynumber: 1.9 Consensus size: 19
77958 GTTATAAATT
*
77968 TAATTATGTTAAATTATAA
1 TAATTATATTAAATTATAA
*
77987 TAATTATATTATATTATA
1 TAATTATATTAAATTATA
78005 TTATGAAATA
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
19 16 1.00
ACGTcount: A:0.46, C:0.00, G:0.03, T:0.51
Consensus pattern (19 bp):
TAATTATATTAAATTATAA
Found at i:78439 original size:12 final size:12
Alignment explanation
Indices: 78422--78450 Score: 51
Period size: 12 Copynumber: 2.5 Consensus size: 12
78412 AGATATTTAT
78422 TATATTATATTA
1 TATATTATATTA
78434 TATATTATATTA
1 TATATTATATTA
78446 T-TATT
1 TATATT
78451 GTTGTTGTTG
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
11 4 0.24
12 13 0.76
ACGTcount: A:0.38, C:0.00, G:0.00, T:0.62
Consensus pattern (12 bp):
TATATTATATTA
Found at i:78455 original size:3 final size:3
Alignment explanation
Indices: 78449--78495 Score: 94
Period size: 3 Copynumber: 15.7 Consensus size: 3
78439 TATATTATTA
78449 TTG TTG TTG TTG TTG TTG TTG TTG TTG TTG TTG TTG TTG TTG TTG TT
1 TTG TTG TTG TTG TTG TTG TTG TTG TTG TTG TTG TTG TTG TTG TTG TT
78496 AACTAATACA
Statistics
Matches: 44, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 44 1.00
ACGTcount: A:0.00, C:0.00, G:0.32, T:0.68
Consensus pattern (3 bp):
TTG
Found at i:79432 original size:69 final size:75
Alignment explanation
Indices: 79340--79514 Score: 184
Period size: 77 Copynumber: 2.3 Consensus size: 75
79330 ACGTGAACAA
* * *
79340 ATTGGAAATTAAAAGTGATTTGAATT-AAGT-AATTG-ATT-T-ATG-AATTATGTGAATATTTG
1 ATTGGAAACT-AAAGTGATTTGAATTGAA-TAAATTGAATTATGAAGAAAATATGTGAATATTTG
79399 AAA-GTATATTG
64 AAATGTATATTG
*
79410 ATTGGAAACTAAAGTGATTTGAATTGAATCAAATTGAATTGAATGAAGAAAATATGTGAGTATTT
1 ATTGGAAACTAAAGTGATTTGAATTGAAT-AAATTGAATT--ATGAAGAAAATATGTGAATATTT
79475 GAAATGTATATTG
63 GAAATGTATATTG
* *
79488 ATTGAAAAGTAATTAGTGATTTGAATT
1 ATTGGAAACTAA--AGTGATTTGAATT
79515 TGATTGGAAA
Statistics
Matches: 87, Mismatches: 6, Indels: 14
0.81 0.06 0.13
Matches are distributed among these distances:
69 16 0.18
70 11 0.13
71 5 0.06
72 3 0.03
75 1 0.01
76 2 0.02
77 18 0.21
78 18 0.21
80 13 0.15
ACGTcount: A:0.41, C:0.01, G:0.19, T:0.38
Consensus pattern (75 bp):
ATTGGAAACTAAAGTGATTTGAATTGAATAAATTGAATTATGAAGAAAATATGTGAATATTTGAA
ATGTATATTG
Found at i:79867 original size:21 final size:21
Alignment explanation
Indices: 79841--79926 Score: 111
Period size: 21 Copynumber: 4.1 Consensus size: 21
79831 AGCTTTGCTG
79841 ATCAGGCA-CTATATGTGTCGT
1 ATCAGGCACCT-TATGTGTCGT
*
79862 ATCAGGCACCTCATGTGTCGT
1 ATCAGGCACCTTATGTGTCGT
* *
79883 ATCAGGCACCTTGTGTATCGT
1 ATCAGGCACCTTATGTGTCGT
* *
79904 TTCAGGCACTTTATGTGTCGT
1 ATCAGGCACCTTATGTGTCGT
79925 AT
1 AT
79927 ACTGTTTCTG
Statistics
Matches: 55, Mismatches: 9, Indels: 2
0.83 0.14 0.03
Matches are distributed among these distances:
21 53 0.96
22 2 0.04
ACGTcount: A:0.20, C:0.22, G:0.23, T:0.35
Consensus pattern (21 bp):
ATCAGGCACCTTATGTGTCGT
Found at i:82286 original size:32 final size:32
Alignment explanation
Indices: 82247--82310 Score: 119
Period size: 32 Copynumber: 2.0 Consensus size: 32
82237 AAATATATTA
82247 AAAACATAAAACAATGGTAATCTTCAACCATT
1 AAAACATAAAACAATGGTAATCTTCAACCATT
*
82279 AAAACATAAAACAATGGTCATCTTCAACCATT
1 AAAACATAAAACAATGGTAATCTTCAACCATT
82311 CTTTCCTCTC
Statistics
Matches: 31, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
32 31 1.00
ACGTcount: A:0.48, C:0.20, G:0.06, T:0.25
Consensus pattern (32 bp):
AAAACATAAAACAATGGTAATCTTCAACCATT
Found at i:85323 original size:27 final size:26
Alignment explanation
Indices: 85283--85336 Score: 65
Period size: 27 Copynumber: 2.0 Consensus size: 26
85273 TCTATATGAT
85283 TTTTTAAAGATT-AAGTTAAAATTTTA
1 TTTTTAAAGATTAAAG-TAAAATTTTA
* *
85309 TTTTTAGAGAGTTAAAGTATAATTTTA
1 TTTTTAAAGA-TTAAAGTAAAATTTTA
85336 T
1 T
85337 CATTATTAAT
Statistics
Matches: 24, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
26 9 0.38
27 12 0.50
28 3 0.12
ACGTcount: A:0.39, C:0.00, G:0.11, T:0.50
Consensus pattern (26 bp):
TTTTTAAAGATTAAAGTAAAATTTTA
Found at i:87984 original size:7 final size:7
Alignment explanation
Indices: 87972--88016 Score: 65
Period size: 7 Copynumber: 6.6 Consensus size: 7
87962 AGCAACTCAA
87972 TTTTTCT
1 TTTTTCT
87979 TTTTTCT
1 TTTTTCT
87986 TTTTTCT
1 TTTTTCT
87993 TTTTTC-
1 TTTTTCT
*
87999 TTTTCCT
1 TTTTTCT
*
88006 TCTTTCT
1 TTTTTCT
88013 TTTT
1 TTTT
88017 CTCTCTTCTC
Statistics
Matches: 33, Mismatches: 4, Indels: 2
0.85 0.10 0.05
Matches are distributed among these distances:
6 5 0.15
7 28 0.85
ACGTcount: A:0.00, C:0.18, G:0.00, T:0.82
Consensus pattern (7 bp):
TTTTTCT
Found at i:87995 original size:13 final size:13
Alignment explanation
Indices: 87972--88018 Score: 67
Period size: 13 Copynumber: 3.5 Consensus size: 13
87962 AGCAACTCAA
87972 TTTTTCTTTTTTC
1 TTTTTCTTTTTTC
87985 TTTTTTCTTTTTTC
1 -TTTTTCTTTTTTC
* *
87999 TTTTCCTTCTTTC
1 TTTTTCTTTTTTC
88012 TTTTTCT
1 TTTTTCT
88019 CTCTTCTCCC
Statistics
Matches: 30, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
13 17 0.57
14 13 0.43
ACGTcount: A:0.00, C:0.19, G:0.00, T:0.81
Consensus pattern (13 bp):
TTTTTCTTTTTTC
Found at i:88002 original size:20 final size:21
Alignment explanation
Indices: 87972--88016 Score: 65
Period size: 20 Copynumber: 2.2 Consensus size: 21
87962 AGCAACTCAA
* *
87972 TTTTTCTTTTTTCTTTTTTCT
1 TTTTTCTTTTTCCTTCTTTCT
87993 TTTTTC-TTTTCCTTCTTTCT
1 TTTTTCTTTTTCCTTCTTTCT
88013 TTTT
1 TTTT
88017 CTCTCTTCTC
Statistics
Matches: 22, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
20 16 0.73
21 6 0.27
ACGTcount: A:0.00, C:0.18, G:0.00, T:0.82
Consensus pattern (21 bp):
TTTTTCTTTTTCCTTCTTTCT
Found at i:97142 original size:21 final size:21
Alignment explanation
Indices: 97100--97142 Score: 50
Period size: 21 Copynumber: 2.0 Consensus size: 21
97090 TTTTCTGAAT
* ***
97100 ATTTTTATTAATTATTTTTAA
1 ATTTTTATGAATTATACGTAA
97121 ATTTTTATGAATTATACGTAA
1 ATTTTTATGAATTATACGTAA
97142 A
1 A
97143 CTATCACGCG
Statistics
Matches: 18, Mismatches: 4, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
21 18 1.00
ACGTcount: A:0.37, C:0.02, G:0.05, T:0.56
Consensus pattern (21 bp):
ATTTTTATGAATTATACGTAA
Found at i:100423 original size:21 final size:21
Alignment explanation
Indices: 100399--100440 Score: 57
Period size: 21 Copynumber: 2.0 Consensus size: 21
100389 TTCTGATTTG
*
100399 TTAAAATTTCTTGAGATTTTT
1 TTAAAATTTCTTGACATTTTT
* *
100420 TTAAATTTTTTTGACATTTTT
1 TTAAAATTTCTTGACATTTTT
100441 GTATTTTTGC
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
21 18 1.00
ACGTcount: A:0.26, C:0.05, G:0.07, T:0.62
Consensus pattern (21 bp):
TTAAAATTTCTTGACATTTTT
Found at i:100514 original size:15 final size:14
Alignment explanation
Indices: 100484--100525 Score: 50
Period size: 14 Copynumber: 2.9 Consensus size: 14
100474 AATTTCTGAG
100484 AATTTTTTATTTTA
1 AATTTTTTATTTTA
100498 AATTTTTT-TTTGATA
1 AATTTTTTATTT--TA
*
100513 AATTTTCTATTTT
1 AATTTTTTATTTT
100526 TTTAATTTTC
Statistics
Matches: 24, Mismatches: 1, Indels: 6
0.77 0.03 0.19
Matches are distributed among these distances:
13 3 0.12
14 9 0.38
15 9 0.38
16 3 0.12
ACGTcount: A:0.26, C:0.02, G:0.02, T:0.69
Consensus pattern (14 bp):
AATTTTTTATTTTA
Found at i:101012 original size:22 final size:21
Alignment explanation
Indices: 100965--101012 Score: 60
Period size: 21 Copynumber: 2.2 Consensus size: 21
100955 AGAAAAAATT
* * *
100965 ATTAAAGGTGTTTTTTTTATA
1 ATTAAAAGTGTTTTTTTAAGA
100986 ATTAAAAGTGTTTTTTTAAGA
1 ATTAAAAGTGTTTTTTTAAGA
101007 AGTTAA
1 A-TTAA
101013 TGAAAGGTTG
Statistics
Matches: 23, Mismatches: 3, Indels: 1
0.85 0.11 0.04
Matches are distributed among these distances:
21 19 0.83
22 4 0.17
ACGTcount: A:0.35, C:0.00, G:0.15, T:0.50
Consensus pattern (21 bp):
ATTAAAAGTGTTTTTTTAAGA
Found at i:102488 original size:30 final size:31
Alignment explanation
Indices: 102464--102522 Score: 84
Period size: 30 Copynumber: 1.9 Consensus size: 31
102454 GTAAATACTT
* * *
102464 AAAATTTGAGGGATTAA-AGTGTAAATATAA
1 AAAATTTAAAGGACTAATAGTGTAAATATAA
102494 AAAATTTAAAGGACTAATAGTGTAAATAT
1 AAAATTTAAAGGACTAATAGTGTAAATAT
102523 TTTAAGGGTG
Statistics
Matches: 25, Mismatches: 3, Indels: 1
0.86 0.10 0.03
Matches are distributed among these distances:
30 14 0.56
31 11 0.44
ACGTcount: A:0.51, C:0.02, G:0.17, T:0.31
Consensus pattern (31 bp):
AAAATTTAAAGGACTAATAGTGTAAATATAA
Found at i:108525 original size:46 final size:46
Alignment explanation
Indices: 108472--108562 Score: 173
Period size: 46 Copynumber: 2.0 Consensus size: 46
108462 GAGTATTGCC
108472 TTCATTTTAGAGGATTTTTAGAAGACCTGAATGGAATCTCGAAGGG
1 TTCATTTTAGAGGATTTTTAGAAGACCTGAATGGAATCTCGAAGGG
*
108518 TTCATTTTAGAGGATTTTTAGAAGACCTGAATGGAATCTTGAAGG
1 TTCATTTTAGAGGATTTTTAGAAGACCTGAATGGAATCTCGAAGG
108563 AATATTTGAT
Statistics
Matches: 44, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
46 44 1.00
ACGTcount: A:0.31, C:0.10, G:0.25, T:0.34
Consensus pattern (46 bp):
TTCATTTTAGAGGATTTTTAGAAGACCTGAATGGAATCTCGAAGGG
Found at i:110720 original size:44 final size:42
Alignment explanation
Indices: 110668--110925 Score: 223
Period size: 44 Copynumber: 5.9 Consensus size: 42
110658 TGTTATTTTC
*
110668 GATCTGCTCTCTGCCAATACAGAAATGCCAAATCTGTCATATTT
1 GATCTGCTCTCTGCCAATACA-AAACGCCAAATCTG-CATATTT
* * *
110712 GATTTGCTCTCTGCCAATACCAAGACGCCAAATCTAC-TATCTT
1 GATCTGCTCTCTGCCAATA-CAAAACGCCAAATCTGCATAT-TT
* * * * *
110755 CGATCTGCTCTCTGTCAATATAGAGACGCCAAATTTGCTATCTTT
1 -GATCTGCTCTCTGCCAATACA-AAACGCCAAATCTGC-ATATTT
* * *
110800 GATTTGCTCTCTGCCAATACAAAGACGCCAAATATGCTATCTTT
1 GATCTGCTCTCTGCCAATACAAA-ACGCCAAATCTGC-ATATTT
* * *
110844 GATCTGCTCTCCGCCAATACAGAGATGCCAAATCTGC-TACCTTT
1 GATCTGCTCTCTGCCAATACA-AAACGCCAAATCTGCATA--TTT
* * *
110888 GATCTGCTCTCTGTCAACACAAAGATGCCAAATCTGCA
1 GATCTGCTCTCTGCCAATACAAA-ACGCCAAATCTGCA
110926 GGATTCGCCA
Statistics
Matches: 177, Mismatches: 25, Indels: 23
0.79 0.11 0.10
Matches are distributed among these distances:
42 4 0.02
43 6 0.03
44 160 0.90
45 5 0.03
46 2 0.01
ACGTcount: A:0.28, C:0.28, G:0.14, T:0.30
Consensus pattern (42 bp):
GATCTGCTCTCTGCCAATACAAAACGCCAAATCTGCATATTT
Found at i:110763 original size:88 final size:87
Alignment explanation
Indices: 110665--110922 Score: 338
Period size: 88 Copynumber: 2.9 Consensus size: 87
110655 ATCTGTTATT
*
110665 TTCGATCTGCTCTCTGCCAATACAGAAATGCCAAATCTGTCATATTTGATTTGCTCTCTGCCAAT
1 TTCGATCTGCTCTCTGCCAATACAGAGATGCCAAATCTG-CATATTTGATTTGCTCTCTGCCAAT
*
110730 ACCAAGACGCCAAATCTACTATC
65 ACAAAGACGCCAAATCTACTATC
* * * * *
110753 TTCGATCTGCTCTCTGTCAATATAGAGACGCCAAATTTGCTATCTTTGATTTGCTCTCTGCCAAT
1 TTCGATCTGCTCTCTGCCAATACAGAGATGCCAAATCTGC-ATATTTGATTTGCTCTCTGCCAAT
* *
110818 ACAAAGACGCCAAATATGCTATC
65 ACAAAGACGCCAAATCTACTATC
* * * *
110841 TTTGATCTGCTCTCCGCCAATACAGAGATGCCAAATCTGC-TACCTTTGATCTGCTCTCTGTCAA
1 TTCGATCTGCTCTCTGCCAATACAGAGATGCCAAATCTGCATA--TTTGATTTGCTCTCTGCCAA
* *
110905 CACAAAGATGCCAAATCT
64 TACAAAGACGCCAAATCT
110923 GCAGGATTCG
Statistics
Matches: 146, Mismatches: 21, Indels: 6
0.84 0.12 0.03
Matches are distributed among these distances:
86 1 0.01
87 1 0.01
88 144 0.99
ACGTcount: A:0.28, C:0.28, G:0.14, T:0.31
Consensus pattern (87 bp):
TTCGATCTGCTCTCTGCCAATACAGAGATGCCAAATCTGCATATTTGATTTGCTCTCTGCCAATA
CAAAGACGCCAAATCTACTATC
Found at i:110918 original size:132 final size:132
Alignment explanation
Indices: 110672--110920 Score: 333
Period size: 132 Copynumber: 1.9 Consensus size: 132
110662 ATTTTCGATC
* * * *
110672 TGCTCTCTGCCAATACAGAAATGCCAAATCTGTCATATTTGATTTGCTCTCTGCCAATACCAAGA
1 TGCTCTCTGCCAATACAGAAACGCCAAATATGTCATATTTGATCTGCTCTCCGCCAATACCAAGA
* * * *
110737 CGCCAAATCTACTATCTTCGATCTGCTCTCTGTCAATATAGAGACGCCAAATTTGCTATCTTTGA
66 CGCCAAATCTACTACCTTCGATCTGCTCTCTGTCAACACAAAGACGCCAAATTTGCTATCTTTGA
110802 TT
131 TT
*
110804 TGCTCTCTGCCAATACA-AAGACGCCAAATATG-CTATCTTTGATCTGCTCTCCGCCAATA-CAG
1 TGCTCTCTGCCAATACAGAA-ACGCCAAATATGTC-ATATTTGATCTGCTCTCCGCCAATACCA-
* * * *
110866 AGATGCCAAATCTGCTACCTTTGATCTGCTCTCTGTCAACACAAAGATGCCAAAT
63 AGACGCCAAATCTACTACCTTCGATCTGCTCTCTGTCAACACAAAGACGCCAAAT
110921 CTGCAGGATT
Statistics
Matches: 101, Mismatches: 13, Indels: 6
0.84 0.11 0.05
Matches are distributed among these distances:
131 5 0.05
132 96 0.95
ACGTcount: A:0.28, C:0.27, G:0.14, T:0.31
Consensus pattern (132 bp):
TGCTCTCTGCCAATACAGAAACGCCAAATATGTCATATTTGATCTGCTCTCCGCCAATACCAAGA
CGCCAAATCTACTACCTTCGATCTGCTCTCTGTCAACACAAAGACGCCAAATTTGCTATCTTTGA
TT
Found at i:123202 original size:132 final size:132
Alignment explanation
Indices: 123066--123310 Score: 384
Period size: 132 Copynumber: 1.9 Consensus size: 132
123056 TGGAATCTCA
* * * *
123066 AAGGGATGTTTGATTATTTTGAGCAAACGAGAAATTGCAACCCAACACGTTAGGGCACGATTCCG
1 AAGGGATATTCGATTATTTCGAGCAAACGAGAAATTGCAACCCAACACGTTAAGGCACGATTCCG
*
123131 CGAATTGCCAAATATCAAA-CTTTGCCTTCGTTTTAAAGAATTTTTAAAAGGCATGAGTGAAAGT
66 CGAATTGCCAAATATCAAATC-TCGCCTTCGTTTTAAAGAATTTTTAAAAGGCATGAGTGAAAGT
123195 TTG
130 TTG
* *
123198 AAGGGATATTCGATTATTTCGAGCAAACGTGAAATTGCAACCCAACACGTTAAGGCACTATTCCG
1 AAGGGATATTCGATTATTTCGAGCAAACGAGAAATTGCAACCCAACACGTTAAGGCACGATTCCG
** *
123263 CGAATTGCCAAATATCAAATCTCGTTTTCGTTTTTAAGAATTTTTAAA
66 CGAATTGCCAAATATCAAATCTCGCCTTCGTTTTAAAGAATTTTTAAA
123311 TGAATACTTA
Statistics
Matches: 102, Mismatches: 10, Indels: 2
0.89 0.09 0.02
Matches are distributed among these distances:
132 101 0.99
133 1 0.01
ACGTcount: A:0.33, C:0.17, G:0.19, T:0.31
Consensus pattern (132 bp):
AAGGGATATTCGATTATTTCGAGCAAACGAGAAATTGCAACCCAACACGTTAAGGCACGATTCCG
CGAATTGCCAAATATCAAATCTCGCCTTCGTTTTAAAGAATTTTTAAAAGGCATGAGTGAAAGTT
TG
Found at i:126134 original size:44 final size:44
Alignment explanation
Indices: 126081--127128 Score: 1884
Period size: 44 Copynumber: 23.8 Consensus size: 44
126071 ATTATTTTCA
* *
126081 ATCTGCTCTCTGCCAATACAGAGATGCCAAATCTG-TCATCTTCG
1 ATCTGCTCTCTGTCAACACAGAGATGCCAAATCTGCT-ATCTTCG
* * * * *
126125 ATTTGCTCTCCGCCAATACCA-AGACGCCAAATCTGCTATCTTCG
1 ATCTGCTCTCTGTCAACA-CAGAGATGCCAAATCTGCTATCTTCG
* * * *
126169 ATCTGCTCTCTGCCAATACAGAGACGCCAAATCTGCTATCTTTG
1 ATCTGCTCTCTGTCAACACAGAGATGCCAAATCTGCTATCTTCG
* * * * *
126213 ATCTACTTTCTGCCAATACAGAGACGCCAAATCTGCTATCTTCG
1 ATCTGCTCTCTGTCAACACAGAGATGCCAAATCTGCTATCTTCG
* * * *
126257 ATCTGCTTTCTGCCAATACAGAGACGCCAAATCTGCTATCTTCG
1 ATCTGCTCTCTGTCAACACAGAGATGCCAAATCTGCTATCTTCG
126301 ATCTGCTCTCTGTCAACACAGAGATGCCAAATCTGCTATCTTCG
1 ATCTGCTCTCTGTCAACACAGAGATGCCAAATCTGCTATCTTCG
126345 ATCTGCTCTCTGTCAACACAGAGATGCCAAATCTGCTATCTTCG
1 ATCTGCTCTCTGTCAACACAGAGATGCCAAATCTGCTATCTTCG
126389 ATCTGCTCTCTGTCAACACAGAGATGCCAAATCTGCTATCTTCG
1 ATCTGCTCTCTGTCAACACAGAGATGCCAAATCTGCTATCTTCG
126433 ATCTGCTCTCTGTCAACACAGAGATGCCAAATCTGCTATCTTCG
1 ATCTGCTCTCTGTCAACACAGAGATGCCAAATCTGCTATCTTCG
126477 ATCTGCTCTCTGTCAACACAGAGATGCCAAATCTGCTATCTTCG
1 ATCTGCTCTCTGTCAACACAGAGATGCCAAATCTGCTATCTTCG
126521 ATCTGCTCTCTGTCAACACAGAGATGCCAAATCTGCTATCTTCG
1 ATCTGCTCTCTGTCAACACAGAGATGCCAAATCTGCTATCTTCG
126565 ATCTGCTCTCTGTCAACACAGAGATGCCAAATCTGCTATCTTCG
1 ATCTGCTCTCTGTCAACACAGAGATGCCAAATCTGCTATCTTCG
126609 ATCTGCTCTCTGTCAACACAGAGATGCCAAATCTGCTATCTTCG
1 ATCTGCTCTCTGTCAACACAGAGATGCCAAATCTGCTATCTTCG
126653 ATCTGCTCTCTGTCAACACAGAGATGCCAAATCTGCTATCTTCG
1 ATCTGCTCTCTGTCAACACAGAGATGCCAAATCTGCTATCTTCG
126697 ATCTGCTCTCTGTCAACACAGAGATGCCAAATCTGCTATCTTCG
1 ATCTGCTCTCTGTCAACACAGAGATGCCAAATCTGCTATCTTCG
126741 ATCTGCTCTCTGTCAACACAGAGATGCCAAATCTGCTATCTTCG
1 ATCTGCTCTCTGTCAACACAGAGATGCCAAATCTGCTATCTTCG
126785 ATCTGCTCTCTGTCAACACAGAGATGCCAAATCTGCTATCTTCG
1 ATCTGCTCTCTGTCAACACAGAGATGCCAAATCTGCTATCTTCG
126829 ATCTGCTCTCTGTCAACACAGAGATGCCAAATCTGCTATCTTCG
1 ATCTGCTCTCTGTCAACACAGAGATGCCAAATCTGCTATCTTCG
126873 ATCTGCTCTCTGTCAACACAGAGATGCCAAATCTGCTATCTTCG
1 ATCTGCTCTCTGTCAACACAGAGATGCCAAATCTGCTATCTTCG
126917 ATCTGCTCTCTGTCAACACAGAGATGCCAAATCTGCTATCTTCG
1 ATCTGCTCTCTGTCAACACAGAGATGCCAAATCTGCTATCTTCG
126961 ATCTGCTCTCTGTCAACACAGAGATGCCAAATCTGCTATCTTCG
1 ATCTGCTCTCTGTCAACACAGAGATGCCAAATCTGCTATCTTCG
127005 ATCTGCTCTCTGTCAACACAGAGATGCCAAATCTGCTATCTTCG
1 ATCTGCTCTCTGTCAACACAGAGATGCCAAATCTGCTATCTTCG
127049 ATCTGCTCTCTGTCAACACAGAGATGCCAAATCTGCTATCTTCG
1 ATCTGCTCTCTGTCAACACAGAGATGCCAAATCTGCTATCTTCG
127093 ATCTGCTCTCTGTCAACACAGAGATGCCAAATCTGC
1 ATCTGCTCTCTGTCAACACAGAGATGCCAAATCTGC
127129 AGGATTCGCC
Statistics
Matches: 987, Mismatches: 14, Indels: 6
0.98 0.01 0.01
Matches are distributed among these distances:
43 2 0.00
44 982 0.99
45 3 0.00
ACGTcount: A:0.25, C:0.30, G:0.16, T:0.29
Consensus pattern (44 bp):
ATCTGCTCTCTGTCAACACAGAGATGCCAAATCTGCTATCTTCG
Found at i:130666 original size:23 final size:23
Alignment explanation
Indices: 130640--130732 Score: 80
Period size: 23 Copynumber: 3.8 Consensus size: 23
130630 GATGGATTAT
130640 ATTATTCTGGTGTGTTTGGGAGG
1 ATTATTCTGGTGTGTTTGGGAGG
*
130663 ATTATATGATACTGGTGTGTTTTGGAGG
1 A-T-TAT--T-CTGGTGTGTTTGGGAGG
* *
130691 ATTATACTGGTGTGTTTTGGTAGG
1 ATTATTCTGGTGTG-TTTGGGAGG
* *
130715 A-CATTTTGGTGTGTTTGG
1 ATTATTCTGGTGTGTTTGG
130733 ATGGAATCCG
Statistics
Matches: 57, Mismatches: 7, Indels: 13
0.74 0.09 0.17
Matches are distributed among these distances:
22 5 0.09
23 18 0.32
24 9 0.16
25 3 0.05
26 3 0.05
27 2 0.04
28 17 0.30
ACGTcount: A:0.16, C:0.04, G:0.34, T:0.45
Consensus pattern (23 bp):
ATTATTCTGGTGTGTTTGGGAGG
Found at i:130666 original size:28 final size:28
Alignment explanation
Indices: 130613--130696 Score: 123
Period size: 28 Copynumber: 3.0 Consensus size: 28
130603 CACTTTGTGC
*
130613 TATTCTGGTGTATTTTGGATGGATTATAT
1 TATTCTGGTGTGTTTTGGA-GGATTATAT
*
130642 TATTCTGGTGTGTTTGGGAGGATTATAT
1 TATTCTGGTGTGTTTTGGAGGATTATAT
* *
130670 GATACTGGTGTGTTTTGGAGGATTATA
1 TATTCTGGTGTGTTTTGGAGGATTATA
130697 CTGGTGTGTT
Statistics
Matches: 50, Mismatches: 5, Indels: 1
0.89 0.09 0.02
Matches are distributed among these distances:
28 33 0.66
29 17 0.34
ACGTcount: A:0.20, C:0.04, G:0.30, T:0.46
Consensus pattern (28 bp):
TATTCTGGTGTGTTTTGGAGGATTATAT
Found at i:130970 original size:21 final size:21
Alignment explanation
Indices: 130913--130973 Score: 59
Period size: 21 Copynumber: 2.8 Consensus size: 21
130903 AGGCACTTTA
*
130913 TATGTCGTATTTCAGGCACCTTG
1 TATGTCG--TTTCAGGCACCTCG
***
130936 TATGTCGCAACAGGCACCTCG
1 TATGTCGTTTCAGGCACCTCG
*
130957 TGTGTCGTTTCAGGCAC
1 TATGTCGTTTCAGGCAC
130974 TTATGTGTCG
Statistics
Matches: 30, Mismatches: 8, Indels: 2
0.75 0.20 0.05
Matches are distributed among these distances:
21 23 0.77
23 7 0.23
ACGTcount: A:0.18, C:0.26, G:0.25, T:0.31
Consensus pattern (21 bp):
TATGTCGTTTCAGGCACCTCG
Found at i:145800 original size:45 final size:45
Alignment explanation
Indices: 145751--145840 Score: 171
Period size: 45 Copynumber: 2.0 Consensus size: 45
145741 GTTGATTGTC
145751 AAAAAACTTCTTGTTTCGACGTCTGAAAATTTATAATTTGAAAAT
1 AAAAAACTTCTTGTTTCGACGTCTGAAAATTTATAATTTGAAAAT
*
145796 AAAAATCTTCTTGTTTCGACGTCTGAAAATTTATAATTTGAAAAT
1 AAAAAACTTCTTGTTTCGACGTCTGAAAATTTATAATTTGAAAAT
145841 CACAAAAGGA
Statistics
Matches: 44, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
45 44 1.00
ACGTcount: A:0.39, C:0.11, G:0.11, T:0.39
Consensus pattern (45 bp):
AAAAAACTTCTTGTTTCGACGTCTGAAAATTTATAATTTGAAAAT
Found at i:146297 original size:131 final size:133
Alignment explanation
Indices: 145969--146435 Score: 365
Period size: 131 Copynumber: 3.5 Consensus size: 133
145959 TTCCGAAGAG
* * * * * * **
145969 ATATTCGATTGTTTTGAACAAACAAGAGATTGCAACCCAGCACGATAGGGCACGATT-CTTGAAT
1 ATATTCGATTATTTTGAGCAAACGAGAAATTGCAACCCAACACGTTAGGGCACGATTCCGCGAAT
* * ** ** ** * * ***
146033 T-TCTAAAC-ATCGAACATAACCTTTGTTTTAAAGGGTTTTCTTAAAAAACATGAGTGAAAACCT
66 TGTC-AAACTACCAAACATTGCCTTCATTTTAAA-GAATTT-TTAAAAGACATGAATGAAAGTTT
*
146096 AAAGGA
128 GAAGGA
** * * ** * * * *
146102 ATATTCGATCGTTTTGAACAAACGAAAAATCACAGCCCAACACGATAGGGCATGATTCC-TGAAT
1 ATATTCGATTATTTTGAGCAAACGAGAAATTGCAACCCAACACGTTAGGGCACGATTCCGCGAAT
* * * * * * *
146166 TGTCAAAC-ACCGAGCATTGCCTTCATTTTAGAGGATTTTTAGAAGACCTGAATGGAA-TCTTGA
66 TGTCAAACTACCAAACATTGCCTTCATTTTAAAGAATTTTTAAAAGACATGAATGAAAGT-TTGA
146229 AGGA
130 AGGA
*
146233 ATATTTGATTATTTTGAGCAAACGAGAAATTGCAACCCAACACGTTA-GGCACGATTCCGCGAAT
1 ATATTCGATTATTTTGAGCAAACGAGAAATTGCAACCCAACACGTTAGGGCACGATTCCGCGAAT
* * * * * *
146297 T-TCCAACTATCAAACTTTGCCTTCGTTTTAAAGAATTTTTAAAAGGCATGAGTGAAAGTTTGAA
66 TGTCAAACTACCAAACATTGCCTTCATTTTAAAGAATTTTTAAAAGACATGAATGAAAGTTTGAA
*
146361 GGG
131 GGA
* * * * *
146364 ATATTCGATTATTTCGAGCAAACGCGAAATTGCAACCCAACACGTTAGGGCACTATTCTGCTAAT
1 ATATTCGATTATTTTGAGCAAACGAGAAATTGCAACCCAACACGTTAGGGCACGATTCCGCGAAT
*
146429 TGCCAAA
66 TGTCAAA
146436 TATCAAATCT
Statistics
Matches: 268, Mismatches: 58, Indels: 16
0.78 0.17 0.05
Matches are distributed among these distances:
130 15 0.06
131 151 0.56
132 21 0.08
133 78 0.29
134 3 0.01
ACGTcount: A:0.35, C:0.18, G:0.18, T:0.28
Consensus pattern (133 bp):
ATATTCGATTATTTTGAGCAAACGAGAAATTGCAACCCAACACGTTAGGGCACGATTCCGCGAAT
TGTCAAACTACCAAACATTGCCTTCATTTTAAAGAATTTTTAAAAGACATGAATGAAAGTTTGAA
GGA
Found at i:146991 original size:17 final size:18
Alignment explanation
Indices: 146957--146996 Score: 55
Period size: 17 Copynumber: 2.3 Consensus size: 18
146947 AGAAGTTAAT
* *
146957 AAAATATATGATGGTACA
1 AAAAAATATGATGATACA
146975 AAAAAATAT-ATGATACA
1 AAAAAATATGATGATACA
146992 AAAAA
1 AAAAA
146997 TACATGACAA
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
17 12 0.60
18 8 0.40
ACGTcount: A:0.62, C:0.05, G:0.10, T:0.23
Consensus pattern (18 bp):
AAAAAATATGATGATACA
Found at i:149379 original size:44 final size:42
Alignment explanation
Indices: 149327--149584 Score: 223
Period size: 44 Copynumber: 5.9 Consensus size: 42
149317 TGTTATTTTC
*
149327 GATCTGCTCTCTGCCAATACAGAAATGCCAAATCTGTCATATTT
1 GATCTGCTCTCTGCCAATACA-AAACGCCAAATCTG-CATATTT
* * *
149371 GATTTGCTCTCTGCCAATACCAAGACGCCAAATCTAC-TATCTT
1 GATCTGCTCTCTGCCAATA-CAAAACGCCAAATCTGCATAT-TT
* * * * *
149414 CGATCTGCTCTCTGTCAATATAGAGACGCCAAATTTGCTATCTTT
1 -GATCTGCTCTCTGCCAATACA-AAACGCCAAATCTGC-ATATTT
* * *
149459 GATTTGCTCTCTGCCAATACAAAGACGCCAAATATGCTATCTTT
1 GATCTGCTCTCTGCCAATACAAA-ACGCCAAATCTGC-ATATTT
* * *
149503 GATCTGCTCTCCGCCAATACAGAGATGCCAAATCTGC-TACCTTT
1 GATCTGCTCTCTGCCAATACA-AAACGCCAAATCTGCATA--TTT
* * *
149547 GATCTGCTCTCTGTCAACACAAAGATGCCAAATCTGCA
1 GATCTGCTCTCTGCCAATACAAA-ACGCCAAATCTGCA
149585 GGATTCGCCA
Statistics
Matches: 177, Mismatches: 25, Indels: 23
0.79 0.11 0.10
Matches are distributed among these distances:
42 4 0.02
43 6 0.03
44 160 0.90
45 5 0.03
46 2 0.01
ACGTcount: A:0.28, C:0.28, G:0.14, T:0.30
Consensus pattern (42 bp):
GATCTGCTCTCTGCCAATACAAAACGCCAAATCTGCATATTT
Found at i:149422 original size:88 final size:87
Alignment explanation
Indices: 149324--149581 Score: 338
Period size: 88 Copynumber: 2.9 Consensus size: 87
149314 ATCTGTTATT
*
149324 TTCGATCTGCTCTCTGCCAATACAGAAATGCCAAATCTGTCATATTTGATTTGCTCTCTGCCAAT
1 TTCGATCTGCTCTCTGCCAATACAGAGATGCCAAATCTG-CATATTTGATTTGCTCTCTGCCAAT
*
149389 ACCAAGACGCCAAATCTACTATC
65 ACAAAGACGCCAAATCTACTATC
* * * * *
149412 TTCGATCTGCTCTCTGTCAATATAGAGACGCCAAATTTGCTATCTTTGATTTGCTCTCTGCCAAT
1 TTCGATCTGCTCTCTGCCAATACAGAGATGCCAAATCTGC-ATATTTGATTTGCTCTCTGCCAAT
* *
149477 ACAAAGACGCCAAATATGCTATC
65 ACAAAGACGCCAAATCTACTATC
* * * *
149500 TTTGATCTGCTCTCCGCCAATACAGAGATGCCAAATCTGC-TACCTTTGATCTGCTCTCTGTCAA
1 TTCGATCTGCTCTCTGCCAATACAGAGATGCCAAATCTGCATA--TTTGATTTGCTCTCTGCCAA
* *
149564 CACAAAGATGCCAAATCT
64 TACAAAGACGCCAAATCT
149582 GCAGGATTCG
Statistics
Matches: 146, Mismatches: 21, Indels: 6
0.84 0.12 0.03
Matches are distributed among these distances:
86 1 0.01
87 1 0.01
88 144 0.99
ACGTcount: A:0.28, C:0.28, G:0.14, T:0.31
Consensus pattern (87 bp):
TTCGATCTGCTCTCTGCCAATACAGAGATGCCAAATCTGCATATTTGATTTGCTCTCTGCCAATA
CAAAGACGCCAAATCTACTATC
Found at i:149577 original size:132 final size:132
Alignment explanation
Indices: 149331--149579 Score: 333
Period size: 132 Copynumber: 1.9 Consensus size: 132
149321 ATTTTCGATC
* * * *
149331 TGCTCTCTGCCAATACAGAAATGCCAAATCTGTCATATTTGATTTGCTCTCTGCCAATACCAAGA
1 TGCTCTCTGCCAATACAGAAACGCCAAATATGTCATATTTGATCTGCTCTCCGCCAATACCAAGA
* * * *
149396 CGCCAAATCTACTATCTTCGATCTGCTCTCTGTCAATATAGAGACGCCAAATTTGCTATCTTTGA
66 CGCCAAATCTACTACCTTCGATCTGCTCTCTGTCAACACAAAGACGCCAAATTTGCTATCTTTGA
149461 TT
131 TT
*
149463 TGCTCTCTGCCAATACA-AAGACGCCAAATATG-CTATCTTTGATCTGCTCTCCGCCAATA-CAG
1 TGCTCTCTGCCAATACAGAA-ACGCCAAATATGTC-ATATTTGATCTGCTCTCCGCCAATACCA-
* * * *
149525 AGATGCCAAATCTGCTACCTTTGATCTGCTCTCTGTCAACACAAAGATGCCAAAT
63 AGACGCCAAATCTACTACCTTCGATCTGCTCTCTGTCAACACAAAGACGCCAAAT
149580 CTGCAGGATT
Statistics
Matches: 101, Mismatches: 13, Indels: 6
0.84 0.11 0.05
Matches are distributed among these distances:
131 5 0.05
132 96 0.95
ACGTcount: A:0.28, C:0.27, G:0.14, T:0.31
Consensus pattern (132 bp):
TGCTCTCTGCCAATACAGAAACGCCAAATATGTCATATTTGATCTGCTCTCCGCCAATACCAAGA
CGCCAAATCTACTACCTTCGATCTGCTCTCTGTCAACACAAAGACGCCAAATTTGCTATCTTTGA
TT
Found at i:160387 original size:42 final size:42
Alignment explanation
Indices: 160327--160411 Score: 152
Period size: 42 Copynumber: 2.0 Consensus size: 42
160317 GCACGAACGA
* *
160327 CCGCATTATCCTCGACTTTACTAAGAAATTCATTCTCCATGT
1 CCGCATTATCCTCAACTTTAATAAGAAATTCATTCTCCATGT
160369 CCGCATTATCCTCAACTTTAATAAGAAATTCATTCTCCATGT
1 CCGCATTATCCTCAACTTTAATAAGAAATTCATTCTCCATGT
160411 C
1 C
160412 AAACTTTCTA
Statistics
Matches: 41, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
42 41 1.00
ACGTcount: A:0.28, C:0.28, G:0.08, T:0.35
Consensus pattern (42 bp):
CCGCATTATCCTCAACTTTAATAAGAAATTCATTCTCCATGT
Found at i:161922 original size:132 final size:132
Alignment explanation
Indices: 161786--162030 Score: 384
Period size: 132 Copynumber: 1.9 Consensus size: 132
161776 TGGAATCTCA
* * * *
161786 AAGGGATGTTTGATTATTTTGAGCAAACGAGAAATTGCAACCCAACACGTTAGGGCACGATTCCG
1 AAGGGATATTCGATTATTTCGAGCAAACGAGAAATTGCAACCCAACACGTTAAGGCACGATTCCG
*
161851 CGAATTGCCAAATATCAAA-CTTTGCCTTCGTTTTAAAGAATTTTTAAAAGGCATGAGTGAAAGT
66 CGAATTGCCAAATATCAAATC-TCGCCTTCGTTTTAAAGAATTTTTAAAAGGCATGAGTGAAAGT
161915 TTG
130 TTG
* *
161918 AAGGGATATTCGATTATTTCGAGCAAACGTGAAATTGCAACCCAACACGTTAAGGCACTATTCCG
1 AAGGGATATTCGATTATTTCGAGCAAACGAGAAATTGCAACCCAACACGTTAAGGCACGATTCCG
** *
161983 CGAATTGCCAAATATCAAATCTCGTTTTCGTTTTTAAGAATTTTTAAA
66 CGAATTGCCAAATATCAAATCTCGCCTTCGTTTTAAAGAATTTTTAAA
162031 TGAATACTTA
Statistics
Matches: 102, Mismatches: 10, Indels: 2
0.89 0.09 0.02
Matches are distributed among these distances:
132 101 0.99
133 1 0.01
ACGTcount: A:0.33, C:0.17, G:0.19, T:0.31
Consensus pattern (132 bp):
AAGGGATATTCGATTATTTCGAGCAAACGAGAAATTGCAACCCAACACGTTAAGGCACGATTCCG
CGAATTGCCAAATATCAAATCTCGCCTTCGTTTTAAAGAATTTTTAAAAGGCATGAGTGAAAGTT
TG
Found at i:162464 original size:58 final size:57
Alignment explanation
Indices: 162375--162489 Score: 212
Period size: 58 Copynumber: 2.0 Consensus size: 57
162365 TCCAAAATAA
*
162375 AATGATAAAAAAACTATGGTATAAGACAAATTTACAATAATGATGGACACAATATAT
1 AATGATAAAAAAACTATGGTATAAGACAAATTCACAATAATGATGGACACAATATAT
162432 AATGATAAAAAAGACTATGGTATAAGACAAATTCACAATAATGATGGACACAATATAT
1 AATGATAAAAAA-ACTATGGTATAAGACAAATTCACAATAATGATGGACACAATATAT
162490 GCTTTGACGA
Statistics
Matches: 56, Mismatches: 1, Indels: 1
0.97 0.02 0.02
Matches are distributed among these distances:
57 12 0.21
58 44 0.79
ACGTcount: A:0.52, C:0.10, G:0.13, T:0.25
Consensus pattern (57 bp):
AATGATAAAAAAACTATGGTATAAGACAAATTCACAATAATGATGGACACAATATAT
Found at i:163865 original size:149 final size:149
Alignment explanation
Indices: 163595--163882 Score: 576
Period size: 149 Copynumber: 1.9 Consensus size: 149
163585 TGATCTGTGT
163595 CAATGTATAGGGACTAGAACTGGGAATAAACCAAGTTCTAAAATGCTGAGTAGAGGCATGGACCA
1 CAATGTATAGGGACTAGAACTGGGAATAAACCAAGTTCTAAAATGCTGAGTAGAGGCATGGACCA
163660 AAGCACAAACACGCGCAAATTGCAGAGGTAATTTTTTAAAAAAAGGAAATACAAATATGGGCTGA
66 AAGCACAAACACGCGCAAATTGCAGAGGTAATTTTTTAAAAAAAGGAAATACAAATATGGGCTGA
163725 TTAAAATGCAGTGCAAAAG
131 TTAAAATGCAGTGCAAAAG
163744 CAATGTATAGGGACTAGAACTGGGAATAAACCAAGTTCTAAAATGCTGAGTAGAGGCATGGACCA
1 CAATGTATAGGGACTAGAACTGGGAATAAACCAAGTTCTAAAATGCTGAGTAGAGGCATGGACCA
163809 AAGCACAAACACGCGCAAATTGCAGAGGTAATTTTTTAAAAAAAGGAAATACAAATATGGGCTGA
66 AAGCACAAACACGCGCAAATTGCAGAGGTAATTTTTTAAAAAAAGGAAATACAAATATGGGCTGA
163874 TTAAAATGC
131 TTAAAATGC
163883 GGCCCAAAAA
Statistics
Matches: 139, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
149 139 1.00
ACGTcount: A:0.43, C:0.14, G:0.23, T:0.20
Consensus pattern (149 bp):
CAATGTATAGGGACTAGAACTGGGAATAAACCAAGTTCTAAAATGCTGAGTAGAGGCATGGACCA
AAGCACAAACACGCGCAAATTGCAGAGGTAATTTTTTAAAAAAAGGAAATACAAATATGGGCTGA
TTAAAATGCAGTGCAAAAG
Found at i:164350 original size:183 final size:183
Alignment explanation
Indices: 164034--164406 Score: 658
Period size: 183 Copynumber: 2.0 Consensus size: 183
164024 CCCTTCTTAA
*
164034 AACA-CAGCCTATCCCTAAAATAAAAGCTGCTAACTCCCCTTGTTAGGGTTTCGTTCGACAAGTG
1 AACAGCAGACTATCCCTAAAATAAAAGCTGCTAACTCCCCTTGTTAGGGTTTCGTTCGACAAGTG
*
164098 GCCGTCCAACCACCATTTATTTGGTGATCGACAGTTCTCAGGCCAGATCCGGCCTTTTTTAGCCA
66 GCCGTCCAACCACCATTTATTTGGTGATCGACAGTTCTCAGGCCAGATCCAGCCTTTTTTAGCCA
* *
164163 CAAACTTTCCTTTAAACTTCGATCTCGATGAAGTGAAAGGGAATCAATGACCT
131 CAAACTTCCCTTTAAACTTCGATCTCGATGAAGTGAAAGGGAATCAACGACCT
* * *
164216 AACAGCAGACTATCCCTAAAATAAAAGCTGCTAACTCTCCTTGTTAGGGTTTTGTTCGGCAAGTG
1 AACAGCAGACTATCCCTAAAATAAAAGCTGCTAACTCCCCTTGTTAGGGTTTCGTTCGACAAGTG
164281 GCCGTCCAACCACCATTTATTTGGTGATCGACAGTTCTCAGGCCAGATCCAGCCTTTTTTAGCCA
66 GCCGTCCAACCACCATTTATTTGGTGATCGACAGTTCTCAGGCCAGATCCAGCCTTTTTTAGCCA
* *
164346 CAAACTTCCCTTTAAACTTTGATCTCGATGAAGTGAAAGGGAATCAACGGCCT
131 CAAACTTCCCTTTAAACTTCGATCTCGATGAAGTGAAAGGGAATCAACGACCT
164399 AACAGCAG
1 AACAGCAG
164407 GGTAAGTCCT
Statistics
Matches: 181, Mismatches: 9, Indels: 1
0.95 0.05 0.01
Matches are distributed among these distances:
182 4 0.02
183 177 0.98
ACGTcount: A:0.28, C:0.26, G:0.19, T:0.28
Consensus pattern (183 bp):
AACAGCAGACTATCCCTAAAATAAAAGCTGCTAACTCCCCTTGTTAGGGTTTCGTTCGACAAGTG
GCCGTCCAACCACCATTTATTTGGTGATCGACAGTTCTCAGGCCAGATCCAGCCTTTTTTAGCCA
CAAACTTCCCTTTAAACTTCGATCTCGATGAAGTGAAAGGGAATCAACGACCT
Found at i:164907 original size:38 final size:39
Alignment explanation
Indices: 164864--164938 Score: 125
Period size: 38 Copynumber: 1.9 Consensus size: 39
164854 GTACGGTACT
*
164864 GGGGGCTCGGCTACGGTGCAAA-GAAGGGGGTGACCTTG
1 GGGGGCTCGGCTACGGCGCAAAGGAAGGGGGTGACCTTG
*
164902 GGGGGCTCGGCTACGGCGCAAAGGAGGGGGGTGACCT
1 GGGGGCTCGGCTACGGCGCAAAGGAAGGGGGTGACCT
164939 AGGGTTGTTA
Statistics
Matches: 34, Mismatches: 2, Indels: 1
0.92 0.05 0.03
Matches are distributed among these distances:
38 21 0.62
39 13 0.38
ACGTcount: A:0.17, C:0.20, G:0.49, T:0.13
Consensus pattern (39 bp):
GGGGGCTCGGCTACGGCGCAAAGGAAGGGGGTGACCTTG
Found at i:165229 original size:5 final size:5
Alignment explanation
Indices: 165219--165293 Score: 50
Period size: 5 Copynumber: 14.8 Consensus size: 5
165209 AATTTCTCCT
* *
165219 TTTTC TTTTC TTTTC TTCTT- TCTTTC -TTTC TATTTC GTTTC TTCTC
1 TTTTC TTTTC TTTTC TT-TTC T-TTTC TTTTC T-TTTC TTTTC TTTTC
*
165265 TGTTTC TTTTTC TTGT- TTTTC -TTTC TTTT
1 T-TTTC -TTTTC TTTTC TTTTC TTTTC TTTT
165294 ATTTATTCTT
Statistics
Matches: 55, Mismatches: 6, Indels: 18
0.70 0.08 0.23
Matches are distributed among these distances:
4 11 0.20
5 29 0.53
6 14 0.25
7 1 0.02
ACGTcount: A:0.01, C:0.20, G:0.04, T:0.75
Consensus pattern (5 bp):
TTTTC
Found at i:165237 original size:22 final size:22
Alignment explanation
Indices: 165212--165274 Score: 56
Period size: 26 Copynumber: 2.7 Consensus size: 22
165202 AAACCCTAAT
*
165212 TTCTCCTTTTTCTTTTCTTTTC
1 TTCTCCTTTTTCTTTTCGTTTC
*
165234 TTCTTTCTTTCTTTCTATTTCGTTTC
1 TTC--TCCTT-TTTCT-TTTCGTTTC
*
165260 TTCT-CTGTTTCTTTT
1 TTCTCCTTTTTCTTTT
165275 TCTTGTTTTT
Statistics
Matches: 33, Mismatches: 4, Indels: 9
0.72 0.09 0.20
Matches are distributed among these distances:
21 3 0.09
22 8 0.24
23 1 0.03
24 5 0.15
25 5 0.15
26 11 0.33
ACGTcount: A:0.02, C:0.24, G:0.03, T:0.71
Consensus pattern (22 bp):
TTCTCCTTTTTCTTTTCGTTTC
Found at i:165240 original size:26 final size:26
Alignment explanation
Indices: 165220--165292 Score: 75
Period size: 26 Copynumber: 3.0 Consensus size: 26
165210 ATTTCTCCTT
*
165220 TTTCT-TTTCTTTTCTTCTTTCTTTC
1 TTTCTATTTCGTTTCTTCTTTCTTTC
* *
165245 TTTCTATTTCGTTTCTTCTCTGTTTC
1 TTTCTATTTCGTTTCTTCTTTCTTTC
165271 TTT-T-TCTT-GTTT-TTCTTTCTTT
1 TTTCTAT-TTCGTTTCTTCTTTCTTT
165293 TATTTATTCT
Statistics
Matches: 41, Mismatches: 5, Indels: 6
0.79 0.10 0.12
Matches are distributed among these distances:
23 8 0.20
24 5 0.12
25 8 0.20
26 20 0.49
ACGTcount: A:0.01, C:0.21, G:0.04, T:0.74
Consensus pattern (26 bp):
TTTCTATTTCGTTTCTTCTTTCTTTC
Found at i:165469 original size:3 final size:3
Alignment explanation
Indices: 165461--165503 Score: 86
Period size: 3 Copynumber: 14.3 Consensus size: 3
165451 TTGATAAAAT
165461 ATA ATA ATA ATA ATA 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 A
165504 GTAAATATCT
Statistics
Matches: 40, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 40 1.00
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (3 bp):
ATA
Found at i:171085 original size:16 final size:16
Alignment explanation
Indices: 171063--171131 Score: 120
Period size: 16 Copynumber: 4.2 Consensus size: 16
171053 TTTGGTTCGC
171063 TGTATTGGATTAGAGG
1 TGTATTGGATTAGAGG
*
171079 CGTATTGGATTAGAGG
1 TGTATTGGATTAGAGG
171095 TGTATTGGGATTAGAGG
1 TGTATT-GGATTAGAGG
171112 TGTATTGGATTAGAGG
1 TGTATTGGATTAGAGG
171128 TGTA
1 TGTA
171132 ATAGCTAATC
Statistics
Matches: 50, Mismatches: 2, Indels: 2
0.93 0.04 0.04
Matches are distributed among these distances:
16 34 0.68
17 16 0.32
ACGTcount: A:0.25, C:0.01, G:0.38, T:0.36
Consensus pattern (16 bp):
TGTATTGGATTAGAGG
Found at i:171109 original size:33 final size:32
Alignment explanation
Indices: 171063--171131 Score: 120
Period size: 33 Copynumber: 2.1 Consensus size: 32
171053 TTTGGTTCGC
171063 TGTATTGGATTAGAGGCGTATTGGATTAGAGG
1 TGTATTGGATTAGAGGCGTATTGGATTAGAGG
*
171095 TGTATTGGGATTAGAGGTGTATTGGATTAGAGG
1 TGTATT-GGATTAGAGGCGTATTGGATTAGAGG
171128 TGTA
1 TGTA
171132 ATAGCTAATC
Statistics
Matches: 35, Mismatches: 1, Indels: 1
0.95 0.03 0.03
Matches are distributed among these distances:
32 6 0.17
33 29 0.83
ACGTcount: A:0.25, C:0.01, G:0.38, T:0.36
Consensus pattern (32 bp):
TGTATTGGATTAGAGGCGTATTGGATTAGAGG
Found at i:171196 original size:44 final size:45
Alignment explanation
Indices: 171112--171202 Score: 121
Period size: 45 Copynumber: 2.0 Consensus size: 45
171102 GGATTAGAGG
* * *
171112 TGTATTGGATTAGAGGTGTAATAGCTAATCCACTGTTTGGTTGAA
1 TGTAATGGAATAGAGGCGTAATAGCTAATCCACTGTTTGGTTGAA
***
171157 TGTAATGGAATAGAGGCGTAATAG-TAATCTTGTGTTTGGTTGAA
1 TGTAATGGAATAGAGGCGTAATAGCTAATCCACTGTTTGGTTGAA
171201 TG
1 TG
171203 GAATAGAGGT
Statistics
Matches: 40, Mismatches: 6, Indels: 1
0.85 0.13 0.02
Matches are distributed among these distances:
44 19 0.47
45 21 0.52
ACGTcount: A:0.27, C:0.07, G:0.29, T:0.37
Consensus pattern (45 bp):
TGTAATGGAATAGAGGCGTAATAGCTAATCCACTGTTTGGTTGAA
Found at i:177465 original size:47 final size:46
Alignment explanation
Indices: 177362--177501 Score: 136
Period size: 47 Copynumber: 2.9 Consensus size: 46
177352 TTTTACTAAA
* * * ** * *
177362 ATGCCATAGCTCAGCTATGGTCTTACATCTTATACACATATCACACCG
1 ATGCCATATCCCAGATATGGTCTTACA-CAAAT-CACTTATCACTCCG
177410 ATGCCATATCCCAGATATGGTCTTACACAAATGCACTTATCACTCCG
1 ATGCCATATCCCAGATATGGTCTTACACAAAT-CACTTATCACTCCG
* * * *
177457 ATGCCATATCCCATATATGATTTTACACGGAAATCACTTGTCACT
1 ATGCCATATCCCAGATATGGTCTTACAC--AAATCACTTATCACT
177502 TGTAGCCGAA
Statistics
Matches: 78, Mismatches: 12, Indels: 4
0.83 0.13 0.04
Matches are distributed among these distances:
47 40 0.51
48 34 0.44
49 4 0.05
ACGTcount: A:0.30, C:0.28, G:0.12, T:0.30
Consensus pattern (46 bp):
ATGCCATATCCCAGATATGGTCTTACACAAATCACTTATCACTCCG
Found at i:177538 original size:31 final size:31
Alignment explanation
Indices: 177503--177589 Score: 138
Period size: 31 Copynumber: 2.8 Consensus size: 31
177493 CTTGTCACTT
* *
177503 GTAGCCGAAGCTACCACTATTCACTGATCAG
1 GTAGCTGAAGCTACCACTTTTCACTGATCAG
177534 GTAGCTGAAGCTACCACTTTTCACTGATCAG
1 GTAGCTGAAGCTACCACTTTTCACTGATCAG
* *
177565 GTAACTGAAACTACCACTTTTCACT
1 GTAGCTGAAGCTACCACTTTTCACT
177590 TGTCATTAGT
Statistics
Matches: 52, Mismatches: 4, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
31 52 1.00
ACGTcount: A:0.29, C:0.28, G:0.16, T:0.28
Consensus pattern (31 bp):
GTAGCTGAAGCTACCACTTTTCACTGATCAG
Found at i:177669 original size:50 final size:50
Alignment explanation
Indices: 177609--177741 Score: 239
Period size: 50 Copynumber: 2.7 Consensus size: 50
177599 TCCTTAATCG
177609 GATAAGTGTAGCCGAAGCTATCACTTATCACTTTCACTTGTTCTTGATCA
1 GATAAGTGTAGCCGAAGCTATCACTTATCACTTTCACTTGTTCTTGATCA
* *
177659 GATAAGTGTAGCCGAAGCTATCATTTATCTCTTTCACTTGTTCTTGATCA
1 GATAAGTGTAGCCGAAGCTATCACTTATCACTTTCACTTGTTCTTGATCA
*
177709 GATAAGTGTAGTCGAAGCTATCACTTATCACTT
1 GATAAGTGTAGCCGAAGCTATCACTTATCACTT
177742 GTTGCCATGG
Statistics
Matches: 78, Mismatches: 5, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
50 78 1.00
ACGTcount: A:0.26, C:0.20, G:0.17, T:0.37
Consensus pattern (50 bp):
GATAAGTGTAGCCGAAGCTATCACTTATCACTTTCACTTGTTCTTGATCA
Found at i:181626 original size:13 final size:13
Alignment explanation
Indices: 181608--181632 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
181598 GTTGTCATTT
181608 TACTATTATGTTC
1 TACTATTATGTTC
181621 TACTATTATGTT
1 TACTATTATGTT
181633 GTTATTATTA
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:0.24, C:0.12, G:0.08, T:0.56
Consensus pattern (13 bp):
TACTATTATGTTC
Found at i:194081 original size:18 final size:19
Alignment explanation
Indices: 194057--194129 Score: 94
Period size: 20 Copynumber: 3.7 Consensus size: 19
194047 ATTGCACATT
194057 AAAAAATATATAAAAATAG
1 AAAAAATATATAAAAATAG
194076 AAAAATATATATAAAAATTCAG
1 AAAAA-ATATATAAAAA-T-AG
* *
194098 AATAAATATA-AAATATAG
1 AAAAAATATATAAAAATAG
194116 AAAAAATATATAAA
1 AAAAAATATATAAA
194130 TTTATAGAAT
Statistics
Matches: 47, Mismatches: 3, Indels: 8
0.81 0.05 0.14
Matches are distributed among these distances:
18 11 0.23
19 9 0.19
20 15 0.32
21 6 0.13
22 6 0.13
ACGTcount: A:0.70, C:0.01, G:0.04, T:0.25
Consensus pattern (19 bp):
AAAAAATATATAAAAATAG
Found at i:194139 original size:39 final size:41
Alignment explanation
Indices: 194064--194151 Score: 112
Period size: 39 Copynumber: 2.2 Consensus size: 41
194054 ATTAAAAAAT
194064 ATATAAAA-ATAGAAAAATATATATAAAAATTCAGAATA-A
1 ATATAAAATATAGAAAAATATATATAAAAATTCAGAATATA
* *
194103 ATATAAAATATAGAAAAA-ATATAT-AAATTTATAGAATATA
1 ATATAAAATATAGAAAAATATATATAAAAATT-CAGAATATA
*
194143 AGATAAAAT
1 ATATAAAAT
194152 TTACAAAAGA
Statistics
Matches: 43, Mismatches: 3, Indels: 5
0.84 0.06 0.10
Matches are distributed among these distances:
38 5 0.12
39 20 0.47
40 18 0.42
ACGTcount: A:0.65, C:0.01, G:0.06, T:0.28
Consensus pattern (41 bp):
ATATAAAATATAGAAAAATATATATAAAAATTCAGAATATA
Found at i:195590 original size:7 final size:7
Alignment explanation
Indices: 195574--195607 Score: 59
Period size: 7 Copynumber: 4.9 Consensus size: 7
195564 CCAGTCCATC
*
195574 GGCCTTA
1 GGCCTCA
195581 GGCCTCA
1 GGCCTCA
195588 GGCCTCA
1 GGCCTCA
195595 GGCCTCA
1 GGCCTCA
195602 GGCCTC
1 GGCCTC
195608 TTAGCTAAGC
Statistics
Matches: 26, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
7 26 1.00
ACGTcount: A:0.12, C:0.41, G:0.29, T:0.18
Consensus pattern (7 bp):
GGCCTCA
Found at i:196868 original size:20 final size:23
Alignment explanation
Indices: 196820--196870 Score: 63
Period size: 20 Copynumber: 2.3 Consensus size: 23
196810 GATTGGATTA
196820 ATTTATAATTTATTATATTAAATT
1 ATTTA-AATTTATTATATTAAATT
*
196844 ATTTAAATTTA-TAT-TTAAGTT
1 ATTTAAATTTATTATATTAAATT
196865 -TTTAAA
1 ATTTAAA
196871 ATATTTTTTG
Statistics
Matches: 26, Mismatches: 1, Indels: 4
0.84 0.03 0.13
Matches are distributed among these distances:
20 6 0.23
21 6 0.23
22 3 0.12
23 6 0.23
24 5 0.19
ACGTcount: A:0.41, C:0.00, G:0.02, T:0.57
Consensus pattern (23 bp):
ATTTAAATTTATTATATTAAATT
Found at i:207159 original size:22 final size:22
Alignment explanation
Indices: 207116--207170 Score: 58
Period size: 22 Copynumber: 2.4 Consensus size: 22
207106 TTTAAAAGAT
207116 TAAAAAAATTATTACTTTTTAAAA
1 TAAAAAAA-TATTA-TTTTTAAAA
**
207140 TAAAAAAATATT-TTTATTAATT
1 TAAAAAAATATTATTT-TTAAAA
207162 TAAAAAAAT
1 TAAAAAAAT
207171 TAAGTGAAAA
Statistics
Matches: 28, Mismatches: 2, Indels: 4
0.82 0.06 0.12
Matches are distributed among these distances:
21 3 0.11
22 13 0.46
23 4 0.14
24 8 0.29
ACGTcount: A:0.56, C:0.02, G:0.00, T:0.42
Consensus pattern (22 bp):
TAAAAAAATATTATTTTTAAAA
Found at i:210329 original size:50 final size:50
Alignment explanation
Indices: 210239--210334 Score: 138
Period size: 50 Copynumber: 1.9 Consensus size: 50
210229 CACCTTCCTT
*
210239 TTTAATTCAATATCATCCATTCCCATGAAGACGCGAGCATCAATCAGTCA
1 TTTAATTCAATATCATCCATTCCCATGAAGACGAGAGCATCAATCAGTCA
* * * * *
210289 TTTAATTCAATGTCATCCGTTCCCATGAAGATGAGGGCATCGATCA
1 TTTAATTCAATATCATCCATTCCCATGAAGACGAGAGCATCAATCA
210335 AAGTTAAAAA
Statistics
Matches: 40, Mismatches: 6, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
50 40 1.00
ACGTcount: A:0.31, C:0.24, G:0.16, T:0.29
Consensus pattern (50 bp):
TTTAATTCAATATCATCCATTCCCATGAAGACGAGAGCATCAATCAGTCA
Found at i:213418 original size:22 final size:22
Alignment explanation
Indices: 213390--213434 Score: 72
Period size: 22 Copynumber: 2.0 Consensus size: 22
213380 ACTGACATTG
213390 TAGGAATATTCTGTAAATATTT
1 TAGGAATATTCTGTAAATATTT
* *
213412 TAGGAATATTTTGTAGATATTT
1 TAGGAATATTCTGTAAATATTT
213434 T
1 T
213435 TTTTATTAAA
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
22 21 1.00
ACGTcount: A:0.33, C:0.02, G:0.16, T:0.49
Consensus pattern (22 bp):
TAGGAATATTCTGTAAATATTT
Found at i:216258 original size:22 final size:22
Alignment explanation
Indices: 216230--216274 Score: 72
Period size: 22 Copynumber: 2.0 Consensus size: 22
216220 AGGGGGAGTG
216230 TAGGAATATTCTGTAAATATTT
1 TAGGAATATTCTGTAAATATTT
* *
216252 TAGGAATATTTTGTAGATATTT
1 TAGGAATATTCTGTAAATATTT
216274 T
1 T
216275 TTTTATTAAA
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
22 21 1.00
ACGTcount: A:0.33, C:0.02, G:0.16, T:0.49
Consensus pattern (22 bp):
TAGGAATATTCTGTAAATATTT
Found at i:218813 original size:34 final size:34
Alignment explanation
Indices: 218775--218843 Score: 120
Period size: 34 Copynumber: 2.0 Consensus size: 34
218765 ATAACAAAGA
218775 AAAAACTATCAAGGGAATTAAGGTTAAATAATGT
1 AAAAACTATCAAGGGAATTAAGGTTAAATAATGT
* *
218809 AAAAATTATCAAGGGAATTAAGGTTAGATAATGT
1 AAAAACTATCAAGGGAATTAAGGTTAAATAATGT
218843 A
1 A
218844 CAGAAACATA
Statistics
Matches: 33, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
34 33 1.00
ACGTcount: A:0.49, C:0.04, G:0.19, T:0.28
Consensus pattern (34 bp):
AAAAACTATCAAGGGAATTAAGGTTAAATAATGT
Found at i:229506 original size:13 final size:13
Alignment explanation
Indices: 229484--229519 Score: 56
Period size: 13 Copynumber: 2.8 Consensus size: 13
229474 CTACATGATC
229484 AATT-TTATAATA
1 AATTATTATAATA
229496 AATTATTATAATA
1 AATTATTATAATA
*
229509 AATCATTATAA
1 AATTATTATAA
229520 AATAGAAATA
Statistics
Matches: 22, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
12 4 0.18
13 18 0.82
ACGTcount: A:0.53, C:0.03, G:0.00, T:0.44
Consensus pattern (13 bp):
AATTATTATAATA
Found at i:237314 original size:56 final size:55
Alignment explanation
Indices: 237228--237376 Score: 221
Period size: 56 Copynumber: 2.7 Consensus size: 55
237218 GTTACGCAGG
237228 AATCAAATTGCTAAAAGATAATATGCCATAATAATATC-CTATAATATCCTATTAGA
1 AATCAAATTGCTAAAAGATAATAT-CCATAATAATATCTC-ATAATATCCTATTAGA
* *
237284 AATCAAATTGCTAATAA-ATAATATCTCATAACAATATCTCATAATATCCTATTAGG
1 AATCAAATTGCTAA-AAGATAATATC-CATAATAATATCTCATAATATCCTATTAGA
237340 AATCAAATTGCTAAAAGATAATATCCCATAATAATAT
1 AATCAAATTGCTAAAAGATAATAT-CCATAATAATAT
237377 TCTAACACCC
Statistics
Matches: 85, Mismatches: 3, Indels: 10
0.87 0.03 0.10
Matches are distributed among these distances:
55 3 0.04
56 78 0.92
57 4 0.05
ACGTcount: A:0.47, C:0.15, G:0.06, T:0.32
Consensus pattern (55 bp):
AATCAAATTGCTAAAAGATAATATCCATAATAATATCTCATAATATCCTATTAGA
Found at i:237321 original size:13 final size:13
Alignment explanation
Indices: 237303--237327 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
237293 GCTAATAAAT
237303 AATATCTCATAAC
1 AATATCTCATAAC
237316 AATATCTCATAA
1 AATATCTCATAA
237328 TATCCTATTA
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:0.48, C:0.20, G:0.00, T:0.32
Consensus pattern (13 bp):
AATATCTCATAAC
Found at i:244416 original size:14 final size:15
Alignment explanation
Indices: 244397--244425 Score: 51
Period size: 14 Copynumber: 2.0 Consensus size: 15
244387 TAAAAAAGGC
244397 AAGATTAAAT-GAAA
1 AAGATTAAATCGAAA
244411 AAGATTAAATCGAAA
1 AAGATTAAATCGAAA
244426 CCATAATAAA
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
14 10 0.71
15 4 0.29
ACGTcount: A:0.62, C:0.03, G:0.14, T:0.21
Consensus pattern (15 bp):
AAGATTAAATCGAAA
Found at i:246185 original size:93 final size:93
Alignment explanation
Indices: 246079--246247 Score: 225
Period size: 93 Copynumber: 1.8 Consensus size: 93
246069 CAACCCACTG
* * *
246079 CAACTTCATGGGTATAG-GAATTGTAGCTTCAACTTGCTCCACTGCAA-TTTCAGGAAGATAAGA
1 CAACTTCAAGGGTATAGAG-ATTGTAGCTTCAACTTACTCCACTGCAACTTCCAGG-AGATAAGA
*
246142 TTCGCTATTGTAGCTTCATTCAACCCCTTA
64 TTCGCTATGGTAGCTTCATTCAACCCCTTA
* * * * *
246172 CAACTTCAAGGGTATAGAGTTTGTAGCTTTATCTTACTCCACTGTAACTTCCAGGATATAAGATT
1 CAACTTCAAGGGTATAGAGATTGTAGCTTCAACTTACTCCACTGCAACTTCCAGGAGATAAGATT
246237 CGCTATGGTAG
66 CGCTATGGTAG
246248 ATGTAACACC
Statistics
Matches: 65, Mismatches: 9, Indels: 4
0.83 0.12 0.05
Matches are distributed among these distances:
93 58 0.89
94 7 0.11
ACGTcount: A:0.28, C:0.21, G:0.18, T:0.33
Consensus pattern (93 bp):
CAACTTCAAGGGTATAGAGATTGTAGCTTCAACTTACTCCACTGCAACTTCCAGGAGATAAGATT
CGCTATGGTAGCTTCATTCAACCCCTTA
Found at i:247618 original size:47 final size:47
Alignment explanation
Indices: 247555--248084 Score: 875
Period size: 47 Copynumber: 11.3 Consensus size: 47
247545 CCCTTCGGGA
* * * * * *
247555 CTTATCACATTTATACACTTTCACATCCATCACATTGGCCATTCGGC
1 CTTATCTCATATATACACTTTCACATTCATCACATCGGCCATTAGGT
* * *
247602 CTTATCACATATATACACCTTCACATCCATCACATCGGCCATTAGGT
1 CTTATCTCATATATACACTTTCACATTCATCACATCGGCCATTAGGT
247649 CTTATCTCATATATACACTTTCACATTCATCACATCGGCCATTAGGT
1 CTTATCTCATATATACACTTTCACATTCATCACATCGGCCATTAGGT
247696 CTTATCTCATATATACACTTTCACATTCATCACATCGGCCATTAGGT
1 CTTATCTCATATATACACTTTCACATTCATCACATCGGCCATTAGGT
247743 CTTATCTCATATATACACTTTCACATTCATCACATCGGCCATTAGGT
1 CTTATCTCATATATACACTTTCACATTCATCACATCGGCCATTAGGT
247790 CTTATCTCATATATACACTTTCACATTCATCACATCGGCCATTAGGT
1 CTTATCTCATATATACACTTTCACATTCATCACATCGGCCATTAGGT
247837 CTTATCTCATATATACACTTTCACATTCATCACATCGGCCATTAGGT
1 CTTATCTCATATATACACTTTCACATTCATCACATCGGCCATTAGGT
*
247884 CTTATCTCATATATACACTTTCACATTCATCACATTGGCCATTAGG-
1 CTTATCTCATATATACACTTTCACATTCATCACATCGGCCATTAGGT
*
247930 CTTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGT
1 C-TTATCTCATATATACACTTTCACATTCATCACATCGGCCATTAGGT
*
247978 CTTATCTCATATATACACTTTCACATTCATCACATTGGCCATTAGG-
1 CTTATCTCATATATACACTTTCACATTCATCACATCGGCCATTAGGT
* * * *
248024 CTTTATCACATATATACACTTTCACATTCATCACATTGGCCATTCGGC
1 C-TTATCTCATATATACACTTTCACATTCATCACATCGGCCATTAGGT
*
248072 CTTATCACATATA
1 CTTATCTCATATA
248085 CATATCTTGT
Statistics
Matches: 464, Mismatches: 15, Indels: 8
0.95 0.03 0.02
Matches are distributed among these distances:
46 2 0.00
47 460 0.99
48 2 0.00
ACGTcount: A:0.28, C:0.28, G:0.08, T:0.35
Consensus pattern (47 bp):
CTTATCTCATATATACACTTTCACATTCATCACATCGGCCATTAGGT
Found at i:250607 original size:44 final size:44
Alignment explanation
Indices: 250552--250657 Score: 151
Period size: 44 Copynumber: 2.4 Consensus size: 44
250542 TCAATCCGAC
* *
250552 CCACTGTAACTTCAGGGGTATAGGATTTGTAGCTTCAATC-TGAT
1 CCACTGTAACTTCAGGGATATAGGAATTGTAGCTTC-ATCTTGAT
* * *
250596 TCACTGCAACTTCAGGGATATAGGAATTGTAGCTTCATCTTGCT
1 CCACTGTAACTTCAGGGATATAGGAATTGTAGCTTCATCTTGAT
250640 CCACTGTAACTTCAGGGA
1 CCACTGTAACTTCAGGGA
250658 GATAAGATTC
Statistics
Matches: 54, Mismatches: 7, Indels: 2
0.86 0.11 0.03
Matches are distributed among these distances:
43 3 0.06
44 51 0.94
ACGTcount: A:0.25, C:0.21, G:0.22, T:0.32
Consensus pattern (44 bp):
CCACTGTAACTTCAGGGATATAGGAATTGTAGCTTCATCTTGAT
Done.