Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Chr7
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: 55462051
ACGTcount: A:0.32, C:0.16, G:0.16, T:0.32
Warning! 2780933 characters in sequence are not A, C, G, or T
File 92 of 163
Found at i:29574560 original size:21 final size:21
Alignment explanation
Indices: 29574526--29574565 Score: 62
Period size: 21 Copynumber: 1.9 Consensus size: 21
29574516 CCATTCATCA
* *
29574526 ACATCTCATCTCACATATCTT
1 ACATCACATATCACATATCTT
29574547 ACATCACATATCACATATC
1 ACATCACATATCACATATC
29574566 GCATATCGAT
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
21 17 1.00
ACGTcount: A:0.35, C:0.33, G:0.00, T:0.33
Consensus pattern (21 bp):
ACATCACATATCACATATCTT
Found at i:29581325 original size:22 final size:21
Alignment explanation
Indices: 29581300--29581340 Score: 55
Period size: 22 Copynumber: 1.9 Consensus size: 21
29581290 AGGTAATGTG
*
29581300 TAAATATTAAGTACTAAATTTT
1 TAAAAATTAAG-ACTAAATTTT
*
29581322 TAAAAATTAAGATTAAATT
1 TAAAAATTAAGACTAAATT
29581341 GACACAATAT
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
21 7 0.41
22 10 0.59
ACGTcount: A:0.51, C:0.02, G:0.05, T:0.41
Consensus pattern (21 bp):
TAAAAATTAAGACTAAATTTT
Found at i:29582494 original size:18 final size:18
Alignment explanation
Indices: 29582473--29582521 Score: 71
Period size: 18 Copynumber: 2.7 Consensus size: 18
29582463 AAATTAACCA
29582473 AATTAACCGAATTACCCG
1 AATTAACCGAATTACCCG
* *
29582491 AATTAACTGAATTACCTG
1 AATTAACCGAATTACCCG
*
29582509 AATTACCCGAATT
1 AATTAACCGAATT
29582522 GAATCACTAC
Statistics
Matches: 27, Mismatches: 4, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
18 27 1.00
ACGTcount: A:0.39, C:0.22, G:0.10, T:0.29
Consensus pattern (18 bp):
AATTAACCGAATTACCCG
Found at i:29582502 original size:9 final size:9
Alignment explanation
Indices: 29582464--29582521 Score: 64
Period size: 9 Copynumber: 6.4 Consensus size: 9
29582454 TTTGGTTAAA
*
29582464 AATTAACCA
1 AATTAACCG
29582473 AATTAACCG
1 AATTAACCG
*
29582482 AATTACCCG
1 AATTAACCG
*
29582491 AATTAACTG
1 AATTAACCG
29582500 AATT-ACCTG
1 AATTAACC-G
*
29582509 AATTACCCG
1 AATTAACCG
29582518 AATT
1 AATT
29582522 GAATCACTAC
Statistics
Matches: 41, Mismatches: 6, Indels: 4
0.80 0.12 0.08
Matches are distributed among these distances:
8 2 0.05
9 37 0.90
10 2 0.05
ACGTcount: A:0.41, C:0.22, G:0.09, T:0.28
Consensus pattern (9 bp):
AATTAACCG
Found at i:29582503 original size:27 final size:27
Alignment explanation
Indices: 29582464--29582521 Score: 82
Period size: 27 Copynumber: 2.1 Consensus size: 27
29582454 TTTGGTTAAA
29582464 AATTAACCAAATTAACC-GAATTACCCG
1 AATTAACCAAATT-ACCTGAATTACCCG
**
29582491 AATTAACTGAATTACCTGAATTACCCG
1 AATTAACCAAATTACCTGAATTACCCG
29582518 AATT
1 AATT
29582522 GAATCACTAC
Statistics
Matches: 28, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
26 3 0.11
27 25 0.89
ACGTcount: A:0.41, C:0.22, G:0.09, T:0.28
Consensus pattern (27 bp):
AATTAACCAAATTACCTGAATTACCCG
Found at i:29582551 original size:17 final size:17
Alignment explanation
Indices: 29582529--29582591 Score: 54
Period size: 17 Copynumber: 3.5 Consensus size: 17
29582519 ATTGAATCAC
29582529 TACATAATTAAAAATAT
1 TACATAATTAAAAATAT
*** *
29582546 TACATAAGTCTTTGAATCAC
1 TACATAA-T-TAAAAAT-AT
*
29582566 TACATAATTAAAAACAT
1 TACATAATTAAAAATAT
29582583 TACATAATT
1 TACATAATT
29582592 CTTGAAATTA
Statistics
Matches: 34, Mismatches: 9, Indels: 6
0.69 0.18 0.12
Matches are distributed among these distances:
17 17 0.50
18 4 0.12
19 5 0.15
20 8 0.24
ACGTcount: A:0.49, C:0.13, G:0.03, T:0.35
Consensus pattern (17 bp):
TACATAATTAAAAATAT
Found at i:29582566 original size:37 final size:37
Alignment explanation
Indices: 29582520--29582594 Score: 132
Period size: 37 Copynumber: 2.0 Consensus size: 37
29582510 ATTACCCGAA
*
29582520 TTGAATCACTACATAATTAAAAATATTACATAAGTCT
1 TTGAATCACTACATAATTAAAAACATTACATAAGTCT
*
29582557 TTGAATCACTACATAATTAAAAACATTACATAATTCT
1 TTGAATCACTACATAATTAAAAACATTACATAAGTCT
29582594 T
1 T
29582595 GAAATTAACA
Statistics
Matches: 36, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
37 36 1.00
ACGTcount: A:0.45, C:0.15, G:0.04, T:0.36
Consensus pattern (37 bp):
TTGAATCACTACATAATTAAAAACATTACATAAGTCT
Found at i:29582764 original size:37 final size:39
Alignment explanation
Indices: 29582723--29582814 Score: 152
Period size: 39 Copynumber: 2.4 Consensus size: 39
29582713 ACTTAAGAGT
*
29582723 TAGACTTTAGTTTTATTTTTATT-GGTT-GATAATTGGG
1 TAGACTTTAGTTTTAGTTTTATTGGGTTGGATAATTGGG
*
29582760 TAGACTTTAGTTTTAGTTTTATTGGGTTGGGTAATTGGG
1 TAGACTTTAGTTTTAGTTTTATTGGGTTGGATAATTGGG
29582799 TAGACTTTAGTTTTAG
1 TAGACTTTAGTTTTAG
29582815 GGTCAGTTCT
Statistics
Matches: 51, Mismatches: 2, Indels: 2
0.93 0.04 0.04
Matches are distributed among these distances:
37 22 0.43
38 4 0.08
39 25 0.49
ACGTcount: A:0.21, C:0.03, G:0.25, T:0.51
Consensus pattern (39 bp):
TAGACTTTAGTTTTAGTTTTATTGGGTTGGATAATTGGG
Found at i:29582894 original size:13 final size:13
Alignment explanation
Indices: 29582829--29582905 Score: 75
Period size: 13 Copynumber: 5.9 Consensus size: 13
29582819 AGTTCTTCAT
*
29582829 TGCTTTTGAAAAA
1 TGCTTTTGAAAAG
*
29582842 TACTTTTGAAAAG
1 TGCTTTTGAAAAG
* * *
29582855 TACTATAGAAAAG
1 TGCTTTTGAAAAG
*
29582868 TGATTTT-AAGAAG
1 TGCTTTTGAA-AAG
29582881 TGCTTTTGAAAAG
1 TGCTTTTGAAAAG
*
29582894 TGCTGTTGAAAA
1 TGCTTTTGAAAA
29582906 TTTTGAGTGT
Statistics
Matches: 52, Mismatches: 10, Indels: 4
0.79 0.15 0.06
Matches are distributed among these distances:
12 2 0.04
13 48 0.92
14 2 0.04
ACGTcount: A:0.39, C:0.06, G:0.19, T:0.35
Consensus pattern (13 bp):
TGCTTTTGAAAAG
Found at i:29585303 original size:18 final size:18
Alignment explanation
Indices: 29585282--29585347 Score: 105
Period size: 18 Copynumber: 3.7 Consensus size: 18
29585272 TCCATCAATT
* *
29585282 TGAACATCATCTGAGATG
1 TGAACATCATTTGAAATG
29585300 TGAACATCATTTGAAATG
1 TGAACATCATTTGAAATG
*
29585318 TGAACATCATTTAAAATG
1 TGAACATCATTTGAAATG
29585336 TGAACATCATTT
1 TGAACATCATTT
29585348 CTCATATTTT
Statistics
Matches: 45, Mismatches: 3, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
18 45 1.00
ACGTcount: A:0.38, C:0.14, G:0.15, T:0.33
Consensus pattern (18 bp):
TGAACATCATTTGAAATG
Found at i:29588584 original size:17 final size:17
Alignment explanation
Indices: 29588539--29588585 Score: 58
Period size: 20 Copynumber: 2.6 Consensus size: 17
29588529 AGAGGAACAA
*
29588539 AGAACAAGCACCAGCAG
1 AGAACCAGCACCAGCAG
29588556 AGGAACACCAGCACCAGCAG
1 A-G-A-ACCAGCACCAGCAG
29588576 AGAACCAGCA
1 AGAACCAGCA
29588586 GAGAACAAAA
Statistics
Matches: 26, Mismatches: 1, Indels: 6
0.79 0.03 0.18
Matches are distributed among these distances:
17 8 0.31
18 2 0.08
19 2 0.08
20 14 0.54
ACGTcount: A:0.45, C:0.32, G:0.23, T:0.00
Consensus pattern (17 bp):
AGAACCAGCACCAGCAG
Found at i:29588966 original size:12 final size:13
Alignment explanation
Indices: 29588949--29588980 Score: 57
Period size: 13 Copynumber: 2.5 Consensus size: 13
29588939 AATAATTGGG
29588949 TTGGGTT-GGTAA
1 TTGGGTTGGGTAA
29588961 TTGGGTTGGGTAA
1 TTGGGTTGGGTAA
29588974 TTGGGTT
1 TTGGGTT
29588981 TGGTTGGATA
Statistics
Matches: 19, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
12 7 0.37
13 12 0.63
ACGTcount: A:0.12, C:0.00, G:0.44, T:0.44
Consensus pattern (13 bp):
TTGGGTTGGGTAA
Found at i:29605159 original size:107 final size:106
Alignment explanation
Indices: 29604982--29605176 Score: 275
Period size: 107 Copynumber: 1.8 Consensus size: 106
29604972 GATTTAAGAG
* * * * * * *
29604982 GATATTTGGCTATTTGGTCAAACGAGAAGTCGAAACCCAGCACGTTAGGGCATGTTTTCTCAAAT
1 GATATTTGACTATTTGGTCAAACGAAAAATCGAAACCCAACACATTAGGGCACGTTTCCTCAAAT
29605047 TTCCAAACGCAAAATATTGCCTTACTTTGAAATTTTAAAAA
66 TTCCAAACGCAAAATATTGCCTTACTTTGAAATTTTAAAAA
* *
29605088 GATATTTGACTATTTGGTCTAAA-GAAAAAATCGAAACCCAACATATTAGGGCACGTTTCCTCGA
1 GATATTTGACTATTTGGTC-AAACG-AAAAATCGAAACCCAACACATTAGGGCACGTTTCCTCAA
*
29605152 ATTTCCAAATGCAAAATATTGCCTT
64 ATTTCCAAACGCAAAATATTGCCTT
29605177 TATTATTTTT
Statistics
Matches: 77, Mismatches: 10, Indels: 3
0.86 0.11 0.03
Matches are distributed among these distances:
106 19 0.25
107 58 0.75
ACGTcount: A:0.35, C:0.18, G:0.16, T:0.31
Consensus pattern (106 bp):
GATATTTGACTATTTGGTCAAACGAAAAATCGAAACCCAACACATTAGGGCACGTTTCCTCAAAT
TTCCAAACGCAAAATATTGCCTTACTTTGAAATTTTAAAAA
Found at i:29605402 original size:73 final size:73
Alignment explanation
Indices: 29605318--29605455 Score: 240
Period size: 73 Copynumber: 1.9 Consensus size: 73
29605308 TCTTGGGTTT
* *
29605318 AAAAAAGGGATCATGCCCAGTAAGTTAGGACACAATCTTTTCTTAATTCCCGAGATCGTTTAAAA
1 AAAAAAGGGATCATGCCCAGTAAGTTAGGACACAATCTCTTCTTAATTCCCGAGATAGTTTAAAA
29605383 TTTTGAGG
66 TTTTGAGG
* *
29605391 AAAAAAGGGATCATGCCCGGTAAGTTAGGACACGATCTCTTCTTAATTCCCGAGATAGTTTAAAA
1 AAAAAAGGGATCATGCCCAGTAAGTTAGGACACAATCTCTTCTTAATTCCCGAGATAGTTTAAAA
29605456 CTTGAATTTG
Statistics
Matches: 61, Mismatches: 4, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
73 61 1.00
ACGTcount: A:0.35, C:0.17, G:0.20, T:0.28
Consensus pattern (73 bp):
AAAAAAGGGATCATGCCCAGTAAGTTAGGACACAATCTCTTCTTAATTCCCGAGATAGTTTAAAA
TTTTGAGG
Found at i:29605894 original size:47 final size:47
Alignment explanation
Indices: 29605802--29605893 Score: 127
Period size: 45 Copynumber: 2.0 Consensus size: 47
29605792 GAAAATGAAT
*
29605802 AAAATTATAGAAATATAAAAAGATATATATGAATATATATGTATATA
1 AAAATTATAGAAATATAAAAAGATATATATGAATATATATATATATA
* *
29605849 AAAATTATA-AAATATAAAAA-ATATATGT-AAGTATGTATATATATA
1 AAAATTATAGAAATATAAAAAGATATATATGAA-TATATATATATATA
29605894 TTCGTGTGAA
Statistics
Matches: 41, Mismatches: 3, Indels: 4
0.85 0.06 0.08
Matches are distributed among these distances:
44 2 0.05
45 19 0.46
46 11 0.27
47 9 0.22
ACGTcount: A:0.58, C:0.00, G:0.08, T:0.35
Consensus pattern (47 bp):
AAAATTATAGAAATATAAAAAGATATATATGAATATATATATATATA
Found at i:29606705 original size:6 final size:6
Alignment explanation
Indices: 29606694--29606721 Score: 56
Period size: 6 Copynumber: 4.7 Consensus size: 6
29606684 CGAAATAAAT
29606694 AAATAG AAATAG AAATAG AAATAG AAAT
1 AAATAG AAATAG AAATAG AAATAG AAAT
29606722 GCAAAAAATC
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 22 1.00
ACGTcount: A:0.68, C:0.00, G:0.14, T:0.18
Consensus pattern (6 bp):
AAATAG
Found at i:29607663 original size:44 final size:45
Alignment explanation
Indices: 29607581--29607713 Score: 139
Period size: 44 Copynumber: 3.0 Consensus size: 45
29607571 TTCAGTCTGT
* ** * *
29607581 TCCACTGCAATTTCAGGGAGATAAGACTCGTA-ATTTCAACCTGC
1 TCCACTGCAACTTCAGGGAGATAAGGTTTGTATACTTCAACCTGC
* *
29607625 TCCACTGCAACTTCAAGGAGATAAGGTTTGTATA-TTCAATCTGC
1 TCCACTGCAACTTCAGGGAGATAAGGTTTGTATACTTCAACCTGC
* * *
29607669 -CCTACTGCAACTTTAGGGGGATAACGTTTGT-TACTTCAACCTGC
1 TCC-ACTGCAACTTCAGGGAGATAAGGTTTGTATACTTCAACCTGC
29607713 T
1 T
29607714 TTGCTGCGAC
Statistics
Matches: 74, Mismatches: 11, Indels: 7
0.80 0.12 0.08
Matches are distributed among these distances:
43 4 0.05
44 69 0.93
45 1 0.01
ACGTcount: A:0.27, C:0.23, G:0.19, T:0.31
Consensus pattern (45 bp):
TCCACTGCAACTTCAGGGAGATAAGGTTTGTATACTTCAACCTGC
Found at i:29608012 original size:46 final size:44
Alignment explanation
Indices: 29607536--29608014 Score: 199
Period size: 45 Copynumber: 10.5 Consensus size: 44
29607526 TTTCATCCGT
* * * * *
29607536 TCCACTGTAACTTTAGAGAAATAAGACTTGCTATCTTCAGTCTGT
1 TCCACTGCAACTTCAG-GAGATAAGACTTGTTATCTTCAGTCTGC
* * * **
29607581 TCCACTGCAATTTCAGGGAGATAAGACTCGTAAT-TTCAACCTGC
1 TCCACTGCAACTTCA-GGAGATAAGACTTGTTATCTTCAGTCTGC
** * *
29607625 TCCACTGCAACTTCAAGGAGATAAGGTTTG-TATATTCAATCTGC
1 TCCACTGCAACTTC-AGGAGATAAGACTTGTTATCTTCAGTCTGC
* * * *
29607669 -CCTACTGCAACTTTAGGGGGATAACG-TTTGTTA-CTTCAACCTGCTTTGC
1 TCC-ACTGCAACTTCA-GGAGATAA-GACTTGTTATCTTC-A---G-TCTGC
* * * * *
29607718 TGCGAC-GTAACTTCA-GAGGTAAGATTTGTTATCTTCAGTCTAC
1 T-CCACTGCAACTTCAGGAGATAAGACTTGTTATCTTCAGTCTGC
* * ** * *
29607761 TCCATTGCAACTTCAAGGAGATAAGACTCGTTATGGT-AGATTTAATTC
1 TCCACTGCAACTTC-AGGAGATAAGACTTGTTATCTTCAG---T-CTGC
* * * * * *
29607809 GACCTACTGCAACTT-TGGAGGTATAAGAATAG-TAGCTTCAATCTGC
1 -TCC-ACTGCAACTTCAGGA-G-ATAAGACTTGTTATCTTCAGTCTGC
* * * ** *
29607855 TTCACTGTAACTTCAGGGAGATAGGA-TTGGTTATCTTCAACCTAC
1 TCCACTGCAACTTCA-GGAGATAAGACTT-GTTATCTTCAGTCTGC
* *
29607900 TCCACTACAACTTCAGGAAGATAAGATTTGTTATCTTCAGTCTGC
1 TCCACTGCAACTTCAGG-AGATAAGACTTGTTATCTTCAGTCTGC
* *
29607945 TCCACTGCAACTTCAGGGAGATAAGACTTGTTATGGTGTGA-TCTGC
1 TCCACTGCAACTTCA-GGAGATAAGACTTGTTAT-CT-TCAGTCTGC
* *
29607991 TCTACTTCAACTTCAGAGAGATAA
1 TCCACTGCAACTTCAG-GAGATAA
29608015 TATCTGTAGC
Statistics
Matches: 325, Mismatches: 71, Indels: 75
0.69 0.15 0.16
Matches are distributed among these distances:
42 2 0.01
43 17 0.05
44 85 0.26
45 120 0.37
46 37 0.11
47 17 0.05
48 9 0.03
49 17 0.05
50 20 0.06
51 1 0.00
ACGTcount: A:0.28, C:0.21, G:0.19, T:0.32
Consensus pattern (44 bp):
TCCACTGCAACTTCAGGAGATAAGACTTGTTATCTTCAGTCTGC
Found at i:29608200 original size:44 final size:43
Alignment explanation
Indices: 29608148--29608747 Score: 286
Period size: 44 Copynumber: 13.9 Consensus size: 43
29608138 TCTGTTCTAT
* * *
29608148 TGCAACTTCAGAGAGATAAGATCCATCATTTTAATCTGCTTCAC
1 TGCAACTTCAGAGAGATAAGAT-CGTGATTTTAATCTGCTCCAC
* * *
29608192 TGCAACTTCAG-GAAGATAGGATTG-GTTTCTTTAATCTGCTCCAC
1 TGCAACTTCAGAG-AGATAAGATCGTG-AT-TTTAATCTGCTCCAC
* * *** * *
29608236 TGCAACTTTAGGGAGATAAGAT--TAGA-TGCGATTTGCTCTAC
1 TGCAACTTCAGAGAGATAAGATCGT-GATTTTAATCTGCTCCAC
* *
29608277 TGCAACTTCAGAGAGATAAGATCTGTGGTTTTAATCCGCTCCAC
1 TGCAACTTCAGAGAGATAAGATC-GTGATTTTAATCTGCTCCAC
* * * * * ** *
29608321 TACAACTTCAGTGAGATAGGATTG-GCTTCTTCTGTTTGCTCCAC
1 TGCAACTTCAGAGAGATAAGATCGTGATT-TT-AATCTGCTCCAC
* * *
29608365 TGCAACTTCAGGGAGATAAGA-C-TGGA--TGAGATCTGCTCTAC
1 TGCAACTTCAGAGAGATAAGATCGT-GATTTTA-ATCTGCTCCAC
* *
29608406 TGCAACTTCAGAGAGATAAGATTTGTGATTTTAATCCGCTCCAC
1 TGCAACTTCAGAGAGATAAGA-TCGTGATTTTAATCTGCTCCAC
* * * * **
29608450 TGCAACTTCAGGGAGATAGGATTG-GCTTCTTCTGTCTGCTCCAC
1 TGCAACTTCAGAGAGATAAGATCGTGATT-TT-AATCTGCTCCAC
* * * *** **
29608494 TGTAACTTTAGGGAGATAAGA-C-TGGA-TGCGATCTGCTTTAC
1 TGCAACTTCAGAGAGATAAGATCGT-GATTTTAATCTGCTCCAC
* *
29608535 TGCAACTTCAGAGAGATAAGATCTGTGGTTTTAATCCGCTCCAC
1 TGCAACTTCAGAGAGATAAGATC-GTGATTTTAATCTGCTCCAC
* * * * * **
29608579 TGCAACTTTAGGGAGATAGGATTG-GCTTCTTCTGTCTGCTCCAC
1 TGCAACTTCAGAGAGATAAGATCGTGATT-TT-AATCTGCTCCAC
* * *** * *
29608623 TGCAACTTTAGGGAGATAAGA-C-TGGA-TGCGATATGCTCTAC
1 TGCAACTTCAGAGAGATAAGATCGT-GATTTTAATCTGCTCCAC
* * *
29608664 TGCAACTTCAGAAAGAT-AGCATCTGTGGTTTTAATCCGCTCCAC
1 TGCAACTTCAGAGAGATAAG-ATC-GTGATTTTAATCTGCTCCAC
* * *
29608708 TGCAACTTCAGGGAGATAGGACTGGTG-TTTTAAATCTGCT
1 TGCAACTTCAGAGAGATAAGA-TCGTGATTTT-AATCTGCT
29608748 TCCCTACTAC
Statistics
Matches: 410, Mismatches: 106, Indels: 80
0.69 0.18 0.13
Matches are distributed among these distances:
40 2 0.00
41 108 0.26
42 11 0.03
43 24 0.06
44 260 0.63
45 5 0.01
ACGTcount: A:0.26, C:0.20, G:0.22, T:0.31
Consensus pattern (43 bp):
TGCAACTTCAGAGAGATAAGATCGTGATTTTAATCTGCTCCAC
Found at i:29608318 original size:85 final size:85
Alignment explanation
Indices: 29608221--29608603 Score: 339
Period size: 85 Copynumber: 4.5 Consensus size: 85
29608211 GATTGGTTTC
* *
29608221 TTTAATCTGCTCCACTGCAACTTTAGGGAGATAAGATTAGATGCGATTTGCTCTACTGCAACTTC
1 TTTAATCTGCTCCACTGCAACTTTAGGGAGATAAGATTGGATGCGATTTGCTCCACTGCAACTTC
29608286 AGAGAGATAAGATCTGTGGT
66 AGAGAGATAAGATCTGTGGT
* * * * * * *
29608306 TTTAATCCGCTCCACTACAACTTCAGTGAGATAGGATTGGCTTCTTCTG-TTTGCTCCACTGCAA
1 TTTAATCTGCTCCACTGCAACTTTAGGGAGATAAGATTGG---ATGC-GATTTGCTCCACTGCAA
*
29608370 CTTCAGGGAGATAAGA-C--TGG-
62 CTTCAGAGAGATAAGATCTGTGGT
* * * * * *** **
29608390 ATGAGATCTGCTCTACTGCAACTTCAGAGAGATAAGATTTGTGATTTTAATCCGCTCCACTGCAA
1 TTTA-ATCTGCTCCACTGCAACTTTAGGGAGATAAGA-TTG-GA-TGCGATTTGCTCCACTGCAA
* * *
29608455 CTTCAGGGAGATAGGAT-TG-GCT
62 CTTCAGAGAGATAAGATCTGTGGT
** * * * **
29608477 TCTTCTGTCTGCTCCACTGTAACTTTAGGGAGATAAGACTGGATGCGATCTGCTTTACTGCAACT
1 T-TT-AATCTGCTCCACTGCAACTTTAGGGAGATAAGATTGGATGCGATTTGCTCCACTGCAACT
29608542 TCAGAGAGATAAGATCTGTGGT
64 TCAGAGAGATAAGATCTGTGGT
* *
29608564 TTTAATCCGCTCCACTGCAACTTTAGGGAGATAGGATTGG
1 TTTAATCTGCTCCACTGCAACTTTAGGGAGATAAGATTGG
29608604 CTTCTTCTGT
Statistics
Matches: 233, Mismatches: 48, Indels: 34
0.74 0.15 0.11
Matches are distributed among these distances:
84 2 0.01
85 154 0.66
86 10 0.04
87 7 0.03
88 59 0.25
89 1 0.00
ACGTcount: A:0.26, C:0.20, G:0.23, T:0.31
Consensus pattern (85 bp):
TTTAATCTGCTCCACTGCAACTTTAGGGAGATAAGATTGGATGCGATTTGCTCCACTGCAACTTC
AGAGAGATAAGATCTGTGGT
Found at i:29608671 original size:85 final size:84
Alignment explanation
Indices: 29608314--29608732 Score: 285
Period size: 85 Copynumber: 4.9 Consensus size: 84
29608304 GTTTTAATCC
* * * *
29608314 GCTCCACTACAACTTCAGTGAGATAGGATTGGCTTCTTCTGTTTGCTCCACTGCAACTTCAGGGA
1 GCTCCACTGCAACTTCAGAGAGATAGGATTGGCTT-TTCAGTCTGCTCCACTGCAACTTCAGGGA
* *
29608379 GATAAGACTGGATGAGATCT
65 GATAAGACTGGATGCGATAT
* * * * *
29608399 GCTCTACTGCAACTTCAGAGAGATAAGATTTGTGATTTT-AATCCGCTCCACTGCAACTTCAGGG
1 GCTCCACTGCAACTTCAGAGAGATAGGA-TTG-GCTTTTCAGTCTGCTCCACTGCAACTTCAGGG
* * * * *
29608463 AGATAGGATTGGCTTCTTCTG-TCT
64 AGATAAGACTGG---ATGC-GATAT
* * * * * * * ** *
29608487 GCTCCACTGTAACTTTAGGGAGATAAGACTGG--ATGC-GATCTGCTTTACTGCAACTTCAGAGA
1 GCTCCACTGCAACTTCAGAGAGATAGGATTGGCTTTTCAG-TCTGCTCCACTGCAACTTCAGGGA
* ***
29608549 GATAAGATCTGTGGTTTTA-AT
65 GATAAGA-CTG-GATGCGATAT
* * * *
29608570 CCGCTCCACTGCAACTTTAGGGAGATAGGATTGGCTTCTTCTGTCTGCTCCACTGCAACTTTAGG
1 --GCTCCACTGCAACTTCAGAGAGATAGGATTGGCTT-TTCAGTCTGCTCCACTGCAACTTCAGG
29608635 GAGATAAGACTGGATGCGATAT
63 GAGATAAGACTGGATGCGATAT
* * * * * *
29608657 GCTCTACTGCAACTTCAGAAAGATAGCATCTGTGGTTTT-AATCCGCTCCACTGCAACTTCAGGG
1 GCTCCACTGCAACTTCAGAGAGATAGGAT-TG-GCTTTTCAGTCTGCTCCACTGCAACTTCAGGG
*
29608721 AGATAGGACTGG
64 AGATAAGACTGG
29608733 TGTTTTAAAT
Statistics
Matches: 258, Mismatches: 56, Indels: 40
0.73 0.16 0.11
Matches are distributed among these distances:
83 1 0.00
84 3 0.01
85 166 0.64
86 15 0.06
87 14 0.05
88 57 0.22
89 2 0.01
ACGTcount: A:0.25, C:0.21, G:0.24, T:0.30
Consensus pattern (84 bp):
GCTCCACTGCAACTTCAGAGAGATAGGATTGGCTTTTCAGTCTGCTCCACTGCAACTTCAGGGAG
ATAAGACTGGATGCGATAT
Found at i:29608772 original size:129 final size:129
Alignment explanation
Indices: 29608131--29608728 Score: 930
Period size: 129 Copynumber: 4.6 Consensus size: 129
29608121 AATAAAGTCT
* * ** ** * *
29608131 GATGCGATCTGTTCTATTGCAACTTCAGAGAGATAAGATCCATCATTTTAATCTGCTTCACTGCA
1 GATGCGATCTGCTCTACTGCAACTTCAGAGAGATAAGATCTGTGGTTTTAATCCGCTCCACTGCA
* * * * *
29608196 ACTTCAGGAAGATAGGATTGGTTTCTT-TAATCTGCTCCACTGCAACTTTAGGGAGATAAGATTA
66 ACTTCAGGGAGATAGGATTGGCTTCTTCT-GTCTGCTCCACTGCAACTTTAGGGAGATAAGACTG
* *
29608260 GATGCGATTTGCTCTACTGCAACTTCAGAGAGATAAGATCTGTGGTTTTAATCCGCTCCACTACA
1 GATGCGATCTGCTCTACTGCAACTTCAGAGAGATAAGATCTGTGGTTTTAATCCGCTCCACTGCA
* * *
29608325 ACTTCAGTGAGATAGGATTGGCTTCTTCTGTTTGCTCCACTGCAACTTCAGGGAGATAAGACTG
66 ACTTCAGGGAGATAGGATTGGCTTCTTCTGTCTGCTCCACTGCAACTTTAGGGAGATAAGACTG
* * *
29608389 GATGAGATCTGCTCTACTGCAACTTCAGAGAGATAAGATTTGTGATTTTAATCCGCTCCACTGCA
1 GATGCGATCTGCTCTACTGCAACTTCAGAGAGATAAGATCTGTGGTTTTAATCCGCTCCACTGCA
*
29608454 ACTTCAGGGAGATAGGATTGGCTTCTTCTGTCTGCTCCACTGTAACTTTAGGGAGATAAGACTG
66 ACTTCAGGGAGATAGGATTGGCTTCTTCTGTCTGCTCCACTGCAACTTTAGGGAGATAAGACTG
*
29608518 GATGCGATCTGCTTTACTGCAACTTCAGAGAGATAAGATCTGTGGTTTTAATCCGCTCCACTGCA
1 GATGCGATCTGCTCTACTGCAACTTCAGAGAGATAAGATCTGTGGTTTTAATCCGCTCCACTGCA
*
29608583 ACTTTAGGGAGATAGGATTGGCTTCTTCTGTCTGCTCCACTGCAACTTTAGGGAGATAAGACTG
66 ACTTCAGGGAGATAGGATTGGCTTCTTCTGTCTGCTCCACTGCAACTTTAGGGAGATAAGACTG
* *
29608647 GATGCGATATGCTCTACTGCAACTTCAGAAAGAT-AGCATCTGTGGTTTTAATCCGCTCCACTGC
1 GATGCGATCTGCTCTACTGCAACTTCAGAGAGATAAG-ATCTGTGGTTTTAATCCGCTCCACTGC
29608711 AACTTCAGGGAGATAGGA
65 AACTTCAGGGAGATAGGA
29608729 CTGGTGTTTT
Statistics
Matches: 430, Mismatches: 37, Indels: 4
0.91 0.08 0.01
Matches are distributed among these distances:
128 2 0.00
129 427 0.99
130 1 0.00
ACGTcount: A:0.26, C:0.21, G:0.22, T:0.31
Consensus pattern (129 bp):
GATGCGATCTGCTCTACTGCAACTTCAGAGAGATAAGATCTGTGGTTTTAATCCGCTCCACTGCA
ACTTCAGGGAGATAGGATTGGCTTCTTCTGTCTGCTCCACTGCAACTTTAGGGAGATAAGACTG
Found at i:29609155 original size:24 final size:23
Alignment explanation
Indices: 29609123--29609179 Score: 71
Period size: 22 Copynumber: 2.5 Consensus size: 23
29609113 CAGATTGCCC
29609123 CCACTGTAATCTTCAAGGTCCAAT
1 CCACTGTAAT-TTCAAGGTCCAAT
* * *
29609147 CCACTGTAA-TTCTATGTTCAAT
1 CCACTGTAATTTCAAGGTCCAAT
29609169 CCACTGTAATT
1 CCACTGTAATT
29609180 CTTGGACATA
Statistics
Matches: 29, Mismatches: 3, Indels: 3
0.83 0.09 0.09
Matches are distributed among these distances:
22 19 0.66
23 1 0.03
24 9 0.31
ACGTcount: A:0.28, C:0.26, G:0.11, T:0.35
Consensus pattern (23 bp):
CCACTGTAATTTCAAGGTCCAAT
Found at i:29610138 original size:20 final size:21
Alignment explanation
Indices: 29610113--29610151 Score: 71
Period size: 20 Copynumber: 1.9 Consensus size: 21
29610103 TTGGCCTCTC
29610113 TTTCTTCTT-TTTCTTTTTGT
1 TTTCTTCTTATTTCTTTTTGT
29610133 TTTCTTCTTATTTCTTTTT
1 TTTCTTCTTATTTCTTTTT
29610152 TCTCTTTTTT
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
20 9 0.50
21 9 0.50
ACGTcount: A:0.03, C:0.15, G:0.03, T:0.79
Consensus pattern (21 bp):
TTTCTTCTTATTTCTTTTTGT
Found at i:29614061 original size:107 final size:106
Alignment explanation
Indices: 29613853--29614047 Score: 293
Period size: 107 Copynumber: 1.8 Consensus size: 106
29613843 GATTTAAGAG
* * * * * *
29613853 GATATTTGGCTATTTGGTCAAACAAGAAGTCGAAACCCAGCACGTTAGGGCACGTTTTCTCGAAT
1 GATATTTGACTATTTGGTCAAACAAAAAATCGAAACCCAGCACATTAGGGCACGTTTCCTCGAAC
29613918 TTCCAAACTCAAAATATTGTCTTACTTTGAAATTTTAAAAA
66 TTCCAAACTCAAAATATTGTCTTACTTTGAAATTTTAAAAA
*
29613959 GATATTTGACTATTTGGTCGAACGAAAAAATCGAAACCCAGCACATTAGGGCACGTTTCCTCGAA
1 GATATTTGACTATTTGGTCAAAC-AAAAAATCGAAACCCAGCACATTAGGGCACGTTTCCTCGAA
*
29614024 CTTCC-AAGTGCAAAATATTGTCTT
65 CTTCCAAACT-CAAAATATTGTCTT
29614048 TATTATTTTT
Statistics
Matches: 79, Mismatches: 8, Indels: 3
0.88 0.09 0.03
Matches are distributed among these distances:
106 24 0.30
107 55 0.70
ACGTcount: A:0.33, C:0.19, G:0.17, T:0.30
Consensus pattern (106 bp):
GATATTTGACTATTTGGTCAAACAAAAAATCGAAACCCAGCACATTAGGGCACGTTTCCTCGAAC
TTCCAAACTCAAAATATTGTCTTACTTTGAAATTTTAAAAA
Found at i:29614341 original size:73 final size:73
Alignment explanation
Indices: 29614187--29614341 Score: 222
Period size: 73 Copynumber: 2.1 Consensus size: 73
29614177 CTATCTCAGG
* *
29614187 TTTGGAAAGGGATCATGCCCAGTAAGTTAGGACACGATCTTTTCTTAATTCCCGAGATCGTTTAA
1 TTTGAAAAGGGATCATGCCCAGTAAGTTAGGACACGATCTCTTCTTAATTCCCGAGATCGTTTAA
*
29614252 AAATTTGA
66 AAACTTGA
**** *
29614260 GGAAAAAAGGGATCATGCCCAGTAAGTTAGGACATGATCTCTTCTTAATTCCCGAGATCGTTT-A
1 TTTGAAAAGGGATCATGCCCAGTAAGTTAGGACACGATCTCTTCTTAATTCCCGAGATCGTTTAA
29614324 AAACTTGAA
66 AAACTTG-A
29614333 TTTGAAAAG
1 TTTGAAAAG
29614342 ATTCGTGTAT
Statistics
Matches: 69, Mismatches: 12, Indels: 2
0.83 0.14 0.02
Matches are distributed among these distances:
72 7 0.10
73 62 0.90
ACGTcount: A:0.33, C:0.16, G:0.21, T:0.30
Consensus pattern (73 bp):
TTTGAAAAGGGATCATGCCCAGTAAGTTAGGACACGATCTCTTCTTAATTCCCGAGATCGTTTAA
AAACTTGA
Found at i:29614759 original size:10 final size:10
Alignment explanation
Indices: 29614680--29614769 Score: 50
Period size: 10 Copynumber: 9.6 Consensus size: 10
29614670 AAAATGAATA
*
29614680 AAAT-TATAG
1 AAATATATAT
*
29614689 AAATATA-AA
1 AAATATATAT
29614698 AAGATATATAT
1 AA-ATATATAT
*
29614709 GAATATATAT
1 AAATATATAT
* *
29614719 --GTATATAA
1 AAATATATAT
29614727 AAAT-TATA-
1 AAATATATAT
*
29614735 AAATATA-AA
1 AAATATATAT
29614744 AAATATATAT
1 AAATATATAT
*
29614754 AAATATGTAT
1 AAATATATAT
*
29614764 ATATAT
1 AAATAT
29614770 TCGTGAGAAA
Statistics
Matches: 64, Mismatches: 9, Indels: 15
0.73 0.10 0.17
Matches are distributed among these distances:
8 11 0.17
9 20 0.31
10 31 0.48
11 2 0.03
ACGTcount: A:0.59, C:0.00, G:0.06, T:0.36
Consensus pattern (10 bp):
AAATATATAT
Found at i:29617602 original size:20 final size:20
Alignment explanation
Indices: 29617577--29617616 Score: 62
Period size: 20 Copynumber: 2.0 Consensus size: 20
29617567 AATATTTTCC
*
29617577 AGTAAATCATTTTACAGAAA
1 AGTAAAACATTTTACAGAAA
*
29617597 AGTAAAACATTTTTCAGAAA
1 AGTAAAACATTTTACAGAAA
29617617 TCATTTTACG
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
20 18 1.00
ACGTcount: A:0.50, C:0.10, G:0.10, T:0.30
Consensus pattern (20 bp):
AGTAAAACATTTTACAGAAA
Found at i:29617618 original size:34 final size:35
Alignment explanation
Indices: 29617565--29617631 Score: 100
Period size: 34 Copynumber: 1.9 Consensus size: 35
29617555 CAAACACCAA
*
29617565 AAAATATTTTCCAGTAAATCATTTTACAGAAAAGT
1 AAAACATTTTCCAGTAAATCATTTTACAGAAAAGT
* *
29617600 AAAACATTTTTCAG-AAATCATTTTACGGAAAA
1 AAAACATTTTCCAGTAAATCATTTTACAGAAAA
29617632 TATTTTACTG
Statistics
Matches: 29, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
34 17 0.59
35 12 0.41
ACGTcount: A:0.46, C:0.12, G:0.09, T:0.33
Consensus pattern (35 bp):
AAAACATTTTCCAGTAAATCATTTTACAGAAAAGT
Found at i:29619054 original size:28 final size:27
Alignment explanation
Indices: 29618999--29619054 Score: 67
Period size: 28 Copynumber: 2.0 Consensus size: 27
29618989 CAGAAACTCT
* * * *
29618999 TTTATTATTATTTGTTTTAAATTTTTA
1 TTTATTATTATTTATTGTAAACTATTA
29619026 TTTATTTATTATTTATTGTAAACTATTA
1 TTTA-TTATTATTTATTGTAAACTATTA
29619054 T
1 T
29619055 ATATATATAT
Statistics
Matches: 24, Mismatches: 4, Indels: 1
0.83 0.14 0.03
Matches are distributed among these distances:
27 4 0.17
28 20 0.83
ACGTcount: A:0.29, C:0.02, G:0.04, T:0.66
Consensus pattern (27 bp):
TTTATTATTATTTATTGTAAACTATTA
Found at i:29639365 original size:26 final size:27
Alignment explanation
Indices: 29639336--29639397 Score: 72
Period size: 26 Copynumber: 2.3 Consensus size: 27
29639326 ATTATACAAT
* *
29639336 TATGAAAATATATAAACAATTA-AAAA
1 TATGAAAAAAAATAAACAATTAGAAAA
*
29639362 TATGAAAAAAAATATACAATTATGAAAA
1 TATGAAAAAAAATAAACAATTA-GAAAA
*
29639390 TATCAAAA
1 TATGAAAA
29639398 CATTTTCAAT
Statistics
Matches: 30, Mismatches: 4, Indels: 2
0.83 0.11 0.06
Matches are distributed among these distances:
26 19 0.63
28 11 0.37
ACGTcount: A:0.65, C:0.05, G:0.05, T:0.26
Consensus pattern (27 bp):
TATGAAAAAAAATAAACAATTAGAAAA
Found at i:29640495 original size:16 final size:15
Alignment explanation
Indices: 29640434--29640483 Score: 50
Period size: 15 Copynumber: 3.3 Consensus size: 15
29640424 TTTCCTTTTG
*
29640434 TTATTATTATTAT-T
1 TTATTGTTATTATAT
*
29640448 TTATT-TTCATTTTTAT
1 TTATTGTT-A-TTATAT
29640464 TTATTGTTATTATAT
1 TTATTGTTATTATAT
29640479 TTATT
1 TTATT
29640484 TGTTTTACTA
Statistics
Matches: 30, Mismatches: 2, Indels: 7
0.77 0.05 0.18
Matches are distributed among these distances:
13 2 0.07
14 6 0.20
15 13 0.43
16 7 0.23
17 2 0.07
ACGTcount: A:0.24, C:0.02, G:0.02, T:0.72
Consensus pattern (15 bp):
TTATTGTTATTATAT
Found at i:29640619 original size:22 final size:22
Alignment explanation
Indices: 29640594--29640635 Score: 68
Period size: 22 Copynumber: 1.9 Consensus size: 22
29640584 TTAATTGTCA
29640594 TTTTTATTATTT-TTATTCTTGT
1 TTTTTATTATTTATT-TTCTTGT
29640616 TTTTTATTATTTATTTTCTT
1 TTTTTATTATTTATTTTCTT
29640636 TAGTTTTTCC
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
22 17 0.89
23 2 0.11
ACGTcount: A:0.14, C:0.05, G:0.02, T:0.79
Consensus pattern (22 bp):
TTTTTATTATTTATTTTCTTGT
Found at i:29642075 original size:18 final size:17
Alignment explanation
Indices: 29642052--29642093 Score: 52
Period size: 15 Copynumber: 2.5 Consensus size: 17
29642042 GGACCTCTCC
29642052 GAGTGGTTCACTCATTTT
1 GAGTGGTTCACT-ATTTT
29642070 GAGTGG--CACTATTTT
1 GAGTGGTTCACTATTTT
*
29642085 GAGCGGTTC
1 GAGTGGTTC
29642094 GACAGTATTG
Statistics
Matches: 21, Mismatches: 1, Indels: 5
0.78 0.04 0.19
Matches are distributed among these distances:
15 10 0.48
16 4 0.19
17 1 0.05
18 6 0.29
ACGTcount: A:0.17, C:0.17, G:0.29, T:0.38
Consensus pattern (17 bp):
GAGTGGTTCACTATTTT
Found at i:29642246 original size:21 final size:22
Alignment explanation
Indices: 29642222--29642262 Score: 57
Period size: 21 Copynumber: 1.9 Consensus size: 22
29642212 TTTTTTTTCA
* *
29642222 GTTTTATTTTTGTTT-TTAGTT
1 GTTTCATTTTTATTTCTTAGTT
29642243 GTTTCATTTTTATTTCTTAG
1 GTTTCATTTTTATTTCTTAG
29642263 ACTTCTTTAG
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
21 13 0.76
22 4 0.24
ACGTcount: A:0.12, C:0.05, G:0.12, T:0.71
Consensus pattern (22 bp):
GTTTCATTTTTATTTCTTAGTT
Found at i:29658524 original size:51 final size:51
Alignment explanation
Indices: 29658446--29658620 Score: 247
Period size: 51 Copynumber: 3.6 Consensus size: 51
29658436 TTTGAGTATT
* * *
29658446 TCTGATCAGTGTCAAGTGACAAGTGATAAGTAGTAGCTTTAGCTACACTTA
1 TCTGATCAGTGACAAGTGACAAATGATAAGTGGTAGCTTTAGCTACACTTA
29658497 TCTGATCAGTGACAAGTGACAAATGATAAGTGGTAGCTTTAGCTACACTTA
1 TCTGATCAGTGACAAGTGACAAATGATAAGTGGTAGCTTTAGCTACACTTA
29658548 TCTGATCAGTGACAAGTG----AT-A-AA-TGGTAGCTTTAGCTACACTTA
1 TCTGATCAGTGACAAGTGACAAATGATAAGTGGTAGCTTTAGCTACACTTA
* * *
29658592 TCTGATTAGGGACAAGTGACAAGTGATAA
1 TCTGATCAGTGACAAGTGACAAATGATAA
29658621 ATGTGATCCG
Statistics
Matches: 112, Mismatches: 6, Indels: 13
0.85 0.05 0.10
Matches are distributed among these distances:
44 37 0.33
45 2 0.02
46 1 0.01
47 2 0.02
48 1 0.01
49 1 0.01
50 2 0.02
51 66 0.59
ACGTcount: A:0.33, C:0.15, G:0.22, T:0.30
Consensus pattern (51 bp):
TCTGATCAGTGACAAGTGACAAATGATAAGTGGTAGCTTTAGCTACACTTA
Found at i:29658561 original size:44 final size:44
Alignment explanation
Indices: 29658511--29658616 Score: 167
Period size: 44 Copynumber: 2.4 Consensus size: 44
29658501 ATCAGTGACA
*
29658511 AGTGACAAATGATAAGTGGTAGCTTTAGCTACACTTATCTGATC
1 AGTGACAAGTGATAAGTGGTAGCTTTAGCTACACTTATCTGATC
* *
29658555 AGTGACAAGTGATAAATGGTAGCTTTAGCTACACTTATCTGATT
1 AGTGACAAGTGATAAGTGGTAGCTTTAGCTACACTTATCTGATC
* *
29658599 AGGGACAAGTGACAAGTG
1 AGTGACAAGTGATAAGTG
29658617 ATAAATGTGA
Statistics
Matches: 56, Mismatches: 6, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
44 56 1.00
ACGTcount: A:0.33, C:0.14, G:0.24, T:0.29
Consensus pattern (44 bp):
AGTGACAAGTGATAAGTGGTAGCTTTAGCTACACTTATCTGATC
Found at i:29662765 original size:17 final size:18
Alignment explanation
Indices: 29662743--29662784 Score: 59
Period size: 18 Copynumber: 2.4 Consensus size: 18
29662733 GCAAATACAT
* *
29662743 AATAAAAG-AAATCATCA
1 AATAAAAGTAAATAAACA
29662760 AATAAAAGTAAATAAACA
1 AATAAAAGTAAATAAACA
29662778 AATAAAA
1 AATAAAA
29662785 ATTAAAGCAC
Statistics
Matches: 22, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
17 8 0.36
18 14 0.64
ACGTcount: A:0.71, C:0.07, G:0.05, T:0.17
Consensus pattern (18 bp):
AATAAAAGTAAATAAACA
Found at i:29662942 original size:3 final size:3
Alignment explanation
Indices: 29662934--29662984 Score: 102
Period size: 3 Copynumber: 17.0 Consensus size: 3
29662924 AATAAATAGG
29662934 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
29662982 TAA
1 TAA
29662985 AGATACTACA
Statistics
Matches: 48, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 48 1.00
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (3 bp):
TAA
Found at i:29665140 original size:31 final size:29
Alignment explanation
Indices: 29665102--29665178 Score: 91
Period size: 29 Copynumber: 2.6 Consensus size: 29
29665092 TTAACGGCTC
* *
29665102 AGTGACTAAAATGTTACATCATGATAACATA
1 AGTGACTAAAATGTAACAT-ATCA-AACATA
* *
29665133 AGTGACTAAAACGTAACATTTCAAACATA
1 AGTGACTAAAATGTAACATATCAAACATA
*
29665162 AATGACTAAAATGTAAC
1 AGTGACTAAAATGTAAC
29665179 CTGAACCAAA
Statistics
Matches: 40, Mismatches: 6, Indels: 2
0.83 0.12 0.04
Matches are distributed among these distances:
29 21 0.52
30 2 0.05
31 17 0.43
ACGTcount: A:0.48, C:0.14, G:0.12, T:0.26
Consensus pattern (29 bp):
AGTGACTAAAATGTAACATATCAAACATA
Found at i:29665546 original size:20 final size:22
Alignment explanation
Indices: 29665503--29665546 Score: 56
Period size: 21 Copynumber: 2.1 Consensus size: 22
29665493 ACGAAGATAT
* *
29665503 ATTAGATTACTTTTTTTTTACA
1 ATTAAATTACTTTTTTATTACA
29665525 ATTAAATTA-TTTTTTATT-CA
1 ATTAAATTACTTTTTTATTACA
29665545 AT
1 AT
29665547 AATACTACAA
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
20 4 0.20
21 8 0.40
22 8 0.40
ACGTcount: A:0.32, C:0.07, G:0.02, T:0.59
Consensus pattern (22 bp):
ATTAAATTACTTTTTTATTACA
Found at i:29666100 original size:24 final size:24
Alignment explanation
Indices: 29666056--29666102 Score: 60
Period size: 24 Copynumber: 2.0 Consensus size: 24
29666046 AAATTCACAT
* *
29666056 TTTATATATAATTATATTAAATTA
1 TTTAAATATAATTATAATAAATTA
29666080 TTTAAATATAATT-TAAATAAATT
1 TTTAAATATAATTAT-AATAAATT
29666103 TATTATTTTA
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
23 1 0.05
24 19 0.95
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (24 bp):
TTTAAATATAATTATAATAAATTA
Found at i:29666112 original size:53 final size:50
Alignment explanation
Indices: 29666003--29666113 Score: 127
Period size: 49 Copynumber: 2.2 Consensus size: 50
29665993 TATGTACCAT
*
29666003 TTATTTTATAAATAATTTATATTAATTATTTAAAATATATATAAAATTCA
1 TTATTTTATAAATAATTTATATTAATTATTTAAAATATATAAAAAATTCA
* * * *
29666053 -CATTTTATATATAA-TTATATTAAATTATTTAAATATAATTTAAATAAATTTA
1 TTATTTTATAAATAATTTATATT-AATTATTTAAA-AT-ATATAAA-AAATTCA
29666105 TTATTTTAT
1 TTATTTTAT
29666114 TTTCTAACAT
Statistics
Matches: 50, Mismatches: 6, Indels: 7
0.79 0.10 0.11
Matches are distributed among these distances:
48 7 0.14
49 23 0.46
50 2 0.04
51 5 0.10
52 6 0.12
53 7 0.14
ACGTcount: A:0.46, C:0.02, G:0.00, T:0.52
Consensus pattern (50 bp):
TTATTTTATAAATAATTTATATTAATTATTTAAAATATATAAAAAATTCA
Found at i:29666636 original size:15 final size:15
Alignment explanation
Indices: 29666611--29666645 Score: 54
Period size: 15 Copynumber: 2.4 Consensus size: 15
29666601 GACTCTATTT
*
29666611 TAATT-ATATTAGGA
1 TAATTAATATTAAGA
29666625 TAATTAATATTAAGA
1 TAATTAATATTAAGA
29666640 TAATTA
1 TAATTA
29666646 TTAAGGATTA
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
14 5 0.26
15 14 0.74
ACGTcount: A:0.49, C:0.00, G:0.09, T:0.43
Consensus pattern (15 bp):
TAATTAATATTAAGA
Found at i:29670576 original size:12 final size:11
Alignment explanation
Indices: 29670556--29670626 Score: 81
Period size: 12 Copynumber: 6.3 Consensus size: 11
29670546 GCAGCCCAAT
29670556 TTTTATTTTTA
1 TTTTATTTTTA
29670567 TTTTATTTTTA
1 TTTTATTTTTA
*
29670578 TTTTTTTCTTTA
1 TTTTATT-TTTA
*
29670590 CTTTATTTATTA
1 TTTTATTT-TTA
*
29670602 CTTTA-TTTTA
1 TTTTATTTTTA
29670612 TTTTATTATTTA
1 TTTTATT-TTTA
29670624 TTT
1 TTT
29670627 GGATATTAAT
Statistics
Matches: 52, Mismatches: 4, Indels: 7
0.83 0.06 0.11
Matches are distributed among these distances:
10 7 0.13
11 21 0.40
12 24 0.46
ACGTcount: A:0.18, C:0.04, G:0.00, T:0.77
Consensus pattern (11 bp):
TTTTATTTTTA
Found at i:29670576 original size:17 final size:18
Alignment explanation
Indices: 29670554--29670626 Score: 71
Period size: 17 Copynumber: 3.9 Consensus size: 18
29670544 AGGCAGCCCA
29670554 ATTTTTATT-TTTATTTT
1 ATTTTTATTATTTATTTT
*
29670571 ATTTTTATT-TTTTTCTTT
1 ATTTTTATTATTTAT-TTT
29670589 ACTTTATTTATTACTTTATTTT
1 A--TT-TTTATTA-TTTATTTT
29670611 A-TTTTATTATTTATTT
1 ATTTTTATTATTTATTT
29670627 GGATATTAAT
Statistics
Matches: 48, Mismatches: 2, Indels: 12
0.77 0.03 0.19
Matches are distributed among these distances:
17 20 0.42
18 11 0.23
19 1 0.02
20 2 0.04
21 6 0.12
22 4 0.08
23 4 0.08
ACGTcount: A:0.19, C:0.04, G:0.00, T:0.77
Consensus pattern (18 bp):
ATTTTTATTATTTATTTT
Found at i:29672266 original size:15 final size:15
Alignment explanation
Indices: 29672241--29672275 Score: 54
Period size: 15 Copynumber: 2.4 Consensus size: 15
29672231 GACTCTATTT
*
29672241 TAATT-ATATTAGGA
1 TAATTAATATTAAGA
29672255 TAATTAATATTAAGA
1 TAATTAATATTAAGA
29672270 TAATTA
1 TAATTA
29672276 TTAAGGATTA
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
14 5 0.26
15 14 0.74
ACGTcount: A:0.49, C:0.00, G:0.09, T:0.43
Consensus pattern (15 bp):
TAATTAATATTAAGA
Found at i:29672276 original size:29 final size:29
Alignment explanation
Indices: 29672241--29672299 Score: 75
Period size: 29 Copynumber: 2.0 Consensus size: 29
29672231 GACTCTATTT
*
29672241 TAATTATATTAGGA-TAATTAATATTAAGA
1 TAATTAT-TAAGGATTAATTAATATTAAGA
* *
29672270 TAATTATTAAGGATTATTTAATTTTAAGA
1 TAATTATTAAGGATTAATTAATATTAAGA
29672299 T
1 T
29672300 TTAATTTTAT
Statistics
Matches: 26, Mismatches: 3, Indels: 2
0.84 0.10 0.06
Matches are distributed among these distances:
28 5 0.19
29 21 0.81
ACGTcount: A:0.44, C:0.00, G:0.10, T:0.46
Consensus pattern (29 bp):
TAATTATTAAGGATTAATTAATATTAAGA
Found at i:29673745 original size:27 final size:29
Alignment explanation
Indices: 29673715--29673780 Score: 75
Period size: 27 Copynumber: 2.4 Consensus size: 29
29673705 CTAAAAACCC
* *
29673715 AAAATTCAAAATTACTA-TAAAAAAA-CT
1 AAAATACAAAATCACTATTAAAAAAATCT
*
29673742 AAAA-ACCAAATCACTATTAAAAAAATCT
1 AAAATACAAAATCACTATTAAAAAAATCT
*
29673770 AAAATAAAAAA
1 AAAATACAAAA
29673781 ATTAACAAAC
Statistics
Matches: 31, Mismatches: 5, Indels: 4
0.77 0.12 0.10
Matches are distributed among these distances:
26 9 0.29
27 12 0.39
28 6 0.19
29 4 0.13
ACGTcount: A:0.67, C:0.12, G:0.00, T:0.21
Consensus pattern (29 bp):
AAAATACAAAATCACTATTAAAAAAATCT
Found at i:29675433 original size:2 final size:2
Alignment explanation
Indices: 29675419--29675456 Score: 60
Period size: 2 Copynumber: 19.0 Consensus size: 2
29675409 TTGCATCATG
29675419 GA GA GA GCA -A GA GA GA GA GA GA GA GA GA GA GA GA GA GA
1 GA GA GA G-A GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA
29675457 ATACAAAAAA
Statistics
Matches: 34, Mismatches: 0, Indels: 4
0.89 0.00 0.11
Matches are distributed among these distances:
1 1 0.03
2 32 0.94
3 1 0.03
ACGTcount: A:0.50, C:0.03, G:0.47, T:0.00
Consensus pattern (2 bp):
GA
Found at i:29676131 original size:26 final size:25
Alignment explanation
Indices: 29676089--29676139 Score: 68
Period size: 26 Copynumber: 2.0 Consensus size: 25
29676079 GGCCATGGGA
*
29676089 TTGTCTGTATGTGGGAGTTGGGATT
1 TTGTCTGTATGTGGGAGTGGGGATT
29676114 TTGTCATGTAATGT-GGAGTGGGGATT
1 TTGTC-TGT-ATGTGGGAGTGGGGATT
29676140 ATAAGCCATT
Statistics
Matches: 23, Mismatches: 1, Indels: 3
0.85 0.04 0.11
Matches are distributed among these distances:
25 5 0.22
26 14 0.61
27 4 0.17
ACGTcount: A:0.16, C:0.04, G:0.39, T:0.41
Consensus pattern (25 bp):
TTGTCTGTATGTGGGAGTGGGGATT
Found at i:29685490 original size:3 final size:3
Alignment explanation
Indices: 29685478--29685517 Score: 73
Period size: 3 Copynumber: 13.7 Consensus size: 3
29685468 ATAACGTATT
29685478 ATA A-A ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA AT
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA AT
29685518 GCAAAAAACA
Statistics
Matches: 36, Mismatches: 0, Indels: 2
0.95 0.00 0.05
Matches are distributed among these distances:
2 2 0.06
3 34 0.94
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.33
Consensus pattern (3 bp):
ATA
Found at i:29685553 original size:36 final size:37
Alignment explanation
Indices: 29685501--29685570 Score: 115
Period size: 36 Copynumber: 1.9 Consensus size: 37
29685491 AATAATAATA
29685501 ATAATAATAATAATAATGCAAAAAACACAAGAATGTT
1 ATAATAATAATAATAATGCAAAAAACACAAGAATGTT
* *
29685538 ATAA-AATAATAATAATGCAAAGAACATAAGAAT
1 ATAATAATAATAATAATGCAAAAAACACAAGAAT
29685571 AATATATCAG
Statistics
Matches: 31, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
36 27 0.87
37 4 0.13
ACGTcount: A:0.61, C:0.07, G:0.09, T:0.23
Consensus pattern (37 bp):
ATAATAATAATAATAATGCAAAAAACACAAGAATGTT
Found at i:29685585 original size:36 final size:36
Alignment explanation
Indices: 29685492--29685577 Score: 111
Period size: 36 Copynumber: 2.4 Consensus size: 36
29685482 AATAATAATA
*
29685492 ATAATAATAATA-ATAATAATAATAATGCAAAAAAC
1 ATAAGAATAATATATAATAATAATAATGCAAAAAAC
* ** * *
29685527 ACAAGAATGTTATAAAATAATAATAATGCAAAGAAC
1 ATAAGAATAATATATAATAATAATAATGCAAAAAAC
29685563 ATAAGAATAATATAT
1 ATAAGAATAATATAT
29685578 CAGAATAAAA
Statistics
Matches: 40, Mismatches: 10, Indels: 1
0.78 0.20 0.02
Matches are distributed among these distances:
35 8 0.20
36 32 0.80
ACGTcount: A:0.62, C:0.06, G:0.07, T:0.26
Consensus pattern (36 bp):
ATAAGAATAATATATAATAATAATAATGCAAAAAAC
Found at i:29695189 original size:18 final size:18
Alignment explanation
Indices: 29695166--29695202 Score: 56
Period size: 18 Copynumber: 2.1 Consensus size: 18
29695156 TATATTTTCG
* *
29695166 TATTCGATTTATTTGAAT
1 TATTCGAGTTATTCGAAT
29695184 TATTCGAGTTATTCGAAT
1 TATTCGAGTTATTCGAAT
29695202 T
1 T
29695203 CAAATACCAA
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
18 17 1.00
ACGTcount: A:0.27, C:0.08, G:0.14, T:0.51
Consensus pattern (18 bp):
TATTCGAGTTATTCGAAT
Found at i:29695937 original size:23 final size:23
Alignment explanation
Indices: 29695911--29695955 Score: 63
Period size: 23 Copynumber: 2.0 Consensus size: 23
29695901 AAAGAAGTCT
29695911 TACAAATAAAAATAAAAATAAAG
1 TACAAATAAAAATAAAAATAAAG
* * *
29695934 TACAACTGAAAATAATAATAAA
1 TACAAATAAAAATAAAAATAAA
29695956 TAAAGCAAAT
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
23 19 1.00
ACGTcount: A:0.69, C:0.07, G:0.04, T:0.20
Consensus pattern (23 bp):
TACAAATAAAAATAAAAATAAAG
Found at i:29696643 original size:21 final size:19
Alignment explanation
Indices: 29696619--29696660 Score: 57
Period size: 21 Copynumber: 2.1 Consensus size: 19
29696609 TAAAAGTCAA
29696619 AATAATAAAAATTAATATAAT
1 AATAATAAAAA-T-ATATAAT
*
29696640 AATAATAAAGATATATAAT
1 AATAATAAAAATATATAAT
29696659 AA
1 AA
29696661 ATAAAAGGAA
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
19 9 0.45
20 1 0.05
21 10 0.50
ACGTcount: A:0.67, C:0.00, G:0.02, T:0.31
Consensus pattern (19 bp):
AATAATAAAAATATATAAT
Found at i:29696663 original size:17 final size:17
Alignment explanation
Indices: 29696633--29696665 Score: 50
Period size: 17 Copynumber: 1.9 Consensus size: 17
29696623 ATAAAAATTA
29696633 ATATAATAATAATAAAG
1 ATATAATAATAATAAAG
29696650 ATAT-ATAATAAATAAA
1 ATATAATAAT-AATAAA
29696666 AGGAACAAAA
Statistics
Matches: 15, Mismatches: 0, Indels: 2
0.88 0.00 0.12
Matches are distributed among these distances:
16 5 0.33
17 10 0.67
ACGTcount: A:0.67, C:0.00, G:0.03, T:0.30
Consensus pattern (17 bp):
ATATAATAATAATAAAG
Found at i:29699285 original size:19 final size:20
Alignment explanation
Indices: 29699260--29699308 Score: 66
Period size: 19 Copynumber: 2.5 Consensus size: 20
29699250 ACAAACGAAA
*
29699260 AAAATAAAAATGTAAAA-ATT
1 AAAATAAAAAT-AAAAATATT
29699280 -AAATAAAAATAAAAATATT
1 AAAATAAAAATAAAAATATT
29699299 AAAATAAAAA
1 AAAATAAAAA
29699309 ATGGATAAAT
Statistics
Matches: 26, Mismatches: 1, Indels: 4
0.84 0.03 0.13
Matches are distributed among these distances:
18 4 0.15
19 13 0.50
20 9 0.35
ACGTcount: A:0.76, C:0.00, G:0.02, T:0.22
Consensus pattern (20 bp):
AAAATAAAAATAAAAATATT
Found at i:29704823 original size:79 final size:79
Alignment explanation
Indices: 29704690--29704850 Score: 295
Period size: 79 Copynumber: 2.0 Consensus size: 79
29704680 GCTTTCATCG
29704690 AACTAATGATAGTAGAACTTCTGATTTTAGACTGAATAGTGACGGGGTTCTGTGTTTTAGGAGTT
1 AACTAATGATAGTAGAACTTCTGATTTTAGACTGAATAGTGACGGGGTTCTGTGTTTTAGGAGTT
*
29704755 AGATCTGTATGCTT
66 AGATCTGTATGCCT
*
29704769 AACTAATGATAGTAGAACTTCTGATTTTAGACTGAATAGTGACGGGGTTTTGTGTTTTAGGAGTT
1 AACTAATGATAGTAGAACTTCTGATTTTAGACTGAATAGTGACGGGGTTCTGTGTTTTAGGAGTT
*
29704834 GGATCTGTATGCCT
66 AGATCTGTATGCCT
29704848 AAC
1 AAC
29704851 GATGTTGTGT
Statistics
Matches: 79, Mismatches: 3, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
79 79 1.00
ACGTcount: A:0.27, C:0.11, G:0.25, T:0.37
Consensus pattern (79 bp):
AACTAATGATAGTAGAACTTCTGATTTTAGACTGAATAGTGACGGGGTTCTGTGTTTTAGGAGTT
AGATCTGTATGCCT
Found at i:29706463 original size:19 final size:21
Alignment explanation
Indices: 29706417--29706464 Score: 55
Period size: 22 Copynumber: 2.3 Consensus size: 21
29706407 AAAAAAAATG
*
29706417 TTTCTTTCTTCTCCTTTCTTAC
1 TTTC-TTCTTCTCCCTTCTTAC
29706439 TGTTCTTCTTCTCCCTTC-T-C
1 T-TTCTTCTTCTCCCTTCTTAC
29706459 TTTCTT
1 TTTCTT
29706465 TCCTCTTTTT
Statistics
Matches: 24, Mismatches: 1, Indels: 5
0.80 0.03 0.17
Matches are distributed among these distances:
19 5 0.21
20 2 0.08
21 1 0.04
22 13 0.54
23 3 0.12
ACGTcount: A:0.02, C:0.33, G:0.02, T:0.62
Consensus pattern (21 bp):
TTTCTTCTTCTCCCTTCTTAC
Found at i:29707402 original size:5 final size:5
Alignment explanation
Indices: 29707392--29707422 Score: 62
Period size: 5 Copynumber: 6.2 Consensus size: 5
29707382 TGAGCATTCG
29707392 ATCGA ATCGA ATCGA ATCGA ATCGA ATCGA A
1 ATCGA ATCGA ATCGA ATCGA ATCGA ATCGA A
29707423 AATTTTCGAG
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 26 1.00
ACGTcount: A:0.42, C:0.19, G:0.19, T:0.19
Consensus pattern (5 bp):
ATCGA
Found at i:29708264 original size:9 final size:9
Alignment explanation
Indices: 29708250--29708286 Score: 65
Period size: 9 Copynumber: 4.1 Consensus size: 9
29708240 TATAGTTTGA
29708250 TATTCGAAT
1 TATTCGAAT
29708259 TATTCGAAT
1 TATTCGAAT
*
29708268 TATTCGAGT
1 TATTCGAAT
29708277 TATTCGAAT
1 TATTCGAAT
29708286 T
1 T
29708287 CGAAAACTCA
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
9 26 1.00
ACGTcount: A:0.30, C:0.11, G:0.14, T:0.46
Consensus pattern (9 bp):
TATTCGAAT
Found at i:29708658 original size:20 final size:20
Alignment explanation
Indices: 29708635--29708689 Score: 62
Period size: 18 Copynumber: 2.8 Consensus size: 20
29708625 TTTTATAAAA
29708635 AAATATTTTATTTTTTATTT
1 AAATATTTTATTTTTTATTT
29708655 -AA-ATTTTATTTTTAATATTT
1 AAATATTTTATTTTT--TATTT
*
29708675 AAAT-TTATATTTTTT
1 AAATATTTTATTTTTT
29708690 TATCAAACTA
Statistics
Matches: 30, Mismatches: 1, Indels: 9
0.75 0.03 0.22
Matches are distributed among these distances:
18 11 0.37
19 3 0.10
20 5 0.17
21 11 0.37
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (20 bp):
AAATATTTTATTTTTTATTT
Found at i:29708867 original size:20 final size:20
Alignment explanation
Indices: 29708828--29708867 Score: 53
Period size: 20 Copynumber: 2.0 Consensus size: 20
29708818 TAGAATTATT
* **
29708828 AAAATTATTAAAAAGGTATA
1 AAAATTATAAAAAAAATATA
29708848 AAAATTATAAAAAAAATATA
1 AAAATTATAAAAAAAATATA
29708868 TTTTTAATAA
Statistics
Matches: 17, Mismatches: 3, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.68, C:0.00, G:0.05, T:0.28
Consensus pattern (20 bp):
AAAATTATAAAAAAAATATA
Found at i:29715394 original size:21 final size:21
Alignment explanation
Indices: 29715364--29715404 Score: 55
Period size: 21 Copynumber: 2.0 Consensus size: 21
29715354 TTTTCCAAAG
* *
29715364 ATGTGTATTGGATTGAATTGA
1 ATGTGAATTGGATTAAATTGA
*
29715385 ATGTGAATTGTATTAAATTG
1 ATGTGAATTGGATTAAATTG
29715405 TGTTAAATTT
Statistics
Matches: 17, Mismatches: 3, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
21 17 1.00
ACGTcount: A:0.32, C:0.00, G:0.24, T:0.44
Consensus pattern (21 bp):
ATGTGAATTGGATTAAATTGA
Found at i:29715789 original size:25 final size:25
Alignment explanation
Indices: 29715761--29715873 Score: 99
Period size: 24 Copynumber: 4.6 Consensus size: 25
29715751 CCGTTATATA
*
29715761 GATCTCACGAGCTTCCCAATTAATG
1 GATCTCATGAGCTTCCCAATTAATG
* * *
29715786 GATCTCTTAAGCTTCCC-ATTTATG
1 GATCTCATGAGCTTCCCAATTAATG
*
29715810 GCTCGT-ATGAGCTTCCCAATTAATG
1 GATC-TCATGAGCTTCCCAATTAATG
* * *
29715835 GATCTCTTAAGCTTCCC-ATTTATG
1 GATCTCATGAGCTTCCCAATTAATG
*
29715859 GCTCGT-ATGAGCTTC
1 GATC-TCATGAGCTTC
29715874 TCGATAATTG
Statistics
Matches: 69, Mismatches: 15, Indels: 9
0.74 0.16 0.10
Matches are distributed among these distances:
24 35 0.51
25 34 0.49
ACGTcount: A:0.22, C:0.26, G:0.17, T:0.35
Consensus pattern (25 bp):
GATCTCATGAGCTTCCCAATTAATG
Found at i:29715890 original size:49 final size:49
Alignment explanation
Indices: 29715769--29715873 Score: 210
Period size: 49 Copynumber: 2.1 Consensus size: 49
29715759 TAGATCTCAC
29715769 GAGCTTCCCAATTAATGGATCTCTTAAGCTTCCCATTTATGGCTCGTAT
1 GAGCTTCCCAATTAATGGATCTCTTAAGCTTCCCATTTATGGCTCGTAT
29715818 GAGCTTCCCAATTAATGGATCTCTTAAGCTTCCCATTTATGGCTCGTAT
1 GAGCTTCCCAATTAATGGATCTCTTAAGCTTCCCATTTATGGCTCGTAT
29715867 GAGCTTC
1 GAGCTTC
29715874 TCGATAATTG
Statistics
Matches: 56, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
49 56 1.00
ACGTcount: A:0.22, C:0.25, G:0.17, T:0.36
Consensus pattern (49 bp):
GAGCTTCCCAATTAATGGATCTCTTAAGCTTCCCATTTATGGCTCGTAT
Found at i:29715897 original size:49 final size:49
Alignment explanation
Indices: 29715769--29715900 Score: 194
Period size: 49 Copynumber: 2.7 Consensus size: 49
29715759 TAGATCTCAC
*
29715769 GAGCTTCCCAATTAATGGATCTCTTAAGCTTCCCATTTATGGCTCGTAT
1 GAGCTTCCCAATTAATGGATCTCTGAAGCTTCCCATTTATGGCTCGTAT
*
29715818 GAGCTTCCCAATTAATGGATCTCTTAAGCTTCCCATTTATGGCTCGTAT
1 GAGCTTCCCAATTAATGGATCTCTGAAGCTTCCCATTTATGGCTCGTAT
* * * *
29715867 GAGCTTCTCGA-TAATTGGCTCTCTGGAGCTTCCC
1 GAGCTTCCCAATTAA-TGGATCTCTGAAGCTTCCC
29715901 GATAAAAGAC
Statistics
Matches: 77, Mismatches: 5, Indels: 2
0.92 0.06 0.02
Matches are distributed among these distances:
48 3 0.04
49 74 0.96
ACGTcount: A:0.20, C:0.26, G:0.18, T:0.36
Consensus pattern (49 bp):
GAGCTTCCCAATTAATGGATCTCTGAAGCTTCCCATTTATGGCTCGTAT
Found at i:29715913 original size:25 final size:25
Alignment explanation
Indices: 29715769--29715956 Score: 96
Period size: 25 Copynumber: 7.5 Consensus size: 25
29715759 TAGATCTCAC
* * * *
29715769 GAGCTTCCCAATTAATGGATCTCTT
1 GAGCTTCCCGATAAATGGCTCTCTG
* ** *
29715794 AAGCTTCCC-ATTTATGGCTCGTAT-
1 GAGCTTCCCGATAAATGGCTC-TCTG
* * * *
29715818 GAGCTTCCCAATTAATGGATCTCTT
1 GAGCTTCCCGATAAATGGCTCTCTG
* ** *
29715843 AAGCTTCCC-ATTTATGGCTCGTAT-
1 GAGCTTCCCGATAAATGGCTC-TCTG
* *
29715867 GAGCTTCTCGATAATTGGCTCTCTG
1 GAGCTTCCCGATAAATGGCTCTCTG
* * *
29715892 GAGCTTCCCGATAAAAGACTCTCTCAT
1 GAGCTTCCCGATAAATGGCTCTCT--G
* *
29715919 GAGCTTCCGGATTAATGGCTCTCTG
1 GAGCTTCCCGATAAATGGCTCTCTG
*
29715944 GAGCTACCCGATA
1 GAGCTTCCCGATA
29715957 TTAGCTCACA
Statistics
Matches: 124, Mismatches: 31, Indels: 16
0.73 0.18 0.09
Matches are distributed among these distances:
24 37 0.30
25 67 0.54
27 20 0.16
ACGTcount: A:0.22, C:0.26, G:0.19, T:0.33
Consensus pattern (25 bp):
GAGCTTCCCGATAAATGGCTCTCTG
Found at i:29716046 original size:25 final size:25
Alignment explanation
Indices: 29715960--29716046 Score: 74
Period size: 25 Copynumber: 3.5 Consensus size: 25
29715950 CCCGATATTA
* *
29715960 GCTCACATGATCTTCTCG-TTACATG
1 GCTCACATGAGC-TCTCGTTTATATG
*
29715985 GCTCACATGAGCT-TCCTGTTATATG
1 GCTCACATGAGCTCTCGT-TTATATG
*
29716010 GCTCGA-AAGAGCTACTCGTTTATAT-
1 GCTC-ACATGAGCT-CTCGTTTATATG
29716035 GCTCACATGAGC
1 GCTCACATGAGC
29716047 ATTCCTGAAT
Statistics
Matches: 50, Mismatches: 6, Indels: 12
0.74 0.09 0.18
Matches are distributed among these distances:
23 2 0.04
24 2 0.04
25 36 0.72
26 7 0.14
27 3 0.06
ACGTcount: A:0.23, C:0.25, G:0.20, T:0.32
Consensus pattern (25 bp):
GCTCACATGAGCTCTCGTTTATATG
Found at i:29723592 original size:25 final size:25
Alignment explanation
Indices: 29723555--29723611 Score: 69
Period size: 25 Copynumber: 2.3 Consensus size: 25
29723545 CTTCTCGAAT
**
29723555 ATGGCTCTTATGAGCTTCCCGTTAC
1 ATGGCTCACATGAGCTTCCCGTTAC
* * *
29723580 ATGGCTCACATGAGCTTTCTGTTAT
1 ATGGCTCACATGAGCTTCCCGTTAC
29723605 ATGGCTC
1 ATGGCTC
29723612 GAAAGAGCTA
Statistics
Matches: 27, Mismatches: 5, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
25 27 1.00
ACGTcount: A:0.18, C:0.25, G:0.21, T:0.37
Consensus pattern (25 bp):
ATGGCTCACATGAGCTTCCCGTTAC
Found at i:29736941 original size:35 final size:33
Alignment explanation
Indices: 29736887--29736951 Score: 94
Period size: 35 Copynumber: 1.9 Consensus size: 33
29736877 TCTAATACAT
*
29736887 ATTTCATTTCATGTCATTTGCTATTTCAATAGC
1 ATTTCATTTCATGTCATTTGCCATTTCAATAGC
*
29736920 ATTTCATCTTCAATTTCATTTGCCATTTCAAT
1 ATTTCAT-TTC-ATGTCATTTGCCATTTCAAT
29736952 TTCCATAATA
Statistics
Matches: 28, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
33 7 0.25
34 3 0.11
35 18 0.64
ACGTcount: A:0.25, C:0.20, G:0.06, T:0.49
Consensus pattern (33 bp):
ATTTCATTTCATGTCATTTGCCATTTCAATAGC
Found at i:29752908 original size:25 final size:23
Alignment explanation
Indices: 29752848--29752901 Score: 83
Period size: 23 Copynumber: 2.3 Consensus size: 23
29752838 ATGAATAAAG
29752848 ATGAACAGGAAATATTCTTTGGC
1 ATGAACAGGAAATATTCTTTGGC
*
29752871 ATGAATAGGAAATATT-TTCTGGC
1 ATGAACAGGAAATATTCTT-TGGC
29752894 ATGAACAG
1 ATGAACAG
29752902 TAGAAATCTC
Statistics
Matches: 28, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
22 2 0.07
23 26 0.93
ACGTcount: A:0.37, C:0.11, G:0.22, T:0.30
Consensus pattern (23 bp):
ATGAACAGGAAATATTCTTTGGC
Found at i:29752981 original size:23 final size:23
Alignment explanation
Indices: 29752848--29752981 Score: 80
Period size: 23 Copynumber: 5.9 Consensus size: 23
29752838 ATGAATAAAG
** *
29752848 ATGAACAGGAAATATTCTTTGGC
1 ATGAACAATAAATATTCTCTGGC
* ** *
29752871 ATGAATAGGAAATATTTTCTGGC
1 ATGAACAATAAATATTCTCTGGC
* *
29752894 ATGAACAGTAGAA-A-TCTCT--A
1 ATGAACAATA-AATATTCTCTGGC
* *
29752914 ATAGAAACAAT-AAGATTCTCTTGC
1 AT-G-AACAATAAATATTCTCTGGC
*
29752938 ATGAACAGTAAATATTCTCTGGC
1 ATGAACAATAAATATTCTCTGGC
* *
29752961 ATGAATAATGAATATTCTCTG
1 ATGAACAATAAATATTCTCTG
29752982 TAGTTTTTAT
Statistics
Matches: 88, Mismatches: 15, Indels: 16
0.74 0.13 0.13
Matches are distributed among these distances:
20 4 0.05
21 2 0.02
22 19 0.22
23 59 0.67
24 4 0.05
ACGTcount: A:0.38, C:0.13, G:0.17, T:0.31
Consensus pattern (23 bp):
ATGAACAATAAATATTCTCTGGC
Found at i:29765237 original size:5 final size:5
Alignment explanation
Indices: 29765227--29765260 Score: 68
Period size: 5 Copynumber: 6.8 Consensus size: 5
29765217 GAAAATTTTT
29765227 GATTC GATTC GATTC GATTC GATTC GATTC GATT
1 GATTC GATTC GATTC GATTC GATTC GATTC GATT
29765261 GAATGCTCAC
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 29 1.00
ACGTcount: A:0.21, C:0.18, G:0.21, T:0.41
Consensus pattern (5 bp):
GATTC
Found at i:29766259 original size:114 final size:115
Alignment explanation
Indices: 29766130--29766358 Score: 451
Period size: 114 Copynumber: 2.0 Consensus size: 115
29766120 TTAGGTTGAA
29766130 GTTTAATTATTTATGAATTTAATTTAAGTGTAAATTATTTTTCTATAAATTCTATATAAAAATAA
1 GTTTAATTATTTATGAATTTAATTTAAGTGTAAATTATTTTTCTATAAATTCTATATAAAAATAA
29766195 AATACTATTATGATATATATATATATTTTACATTTTAAG-AGAAAATCTT
66 AATACTATTATGATATATATATATATTTTACATTTTAAGTAGAAAATCTT
29766244 GTTTAATTATTTATGAATTTAATTTAAGTGTAAATTATTTTTCTATAAATTCTATATAAAAATAA
1 GTTTAATTATTTATGAATTTAATTTAAGTGTAAATTATTTTTCTATAAATTCTATATAAAAATAA
29766309 AATACTATTATGATATATATATATATTTTACATTTTAAGTAGAAAATCTT
66 AATACTATTATGATATATATATATATTTTACATTTTAAGTAGAAAATCTT
29766359 TATAGTGAAC
Statistics
Matches: 114, Mismatches: 0, Indels: 1
0.99 0.00 0.01
Matches are distributed among these distances:
114 104 0.91
115 10 0.09
ACGTcount: A:0.42, C:0.04, G:0.06, T:0.48
Consensus pattern (115 bp):
GTTTAATTATTTATGAATTTAATTTAAGTGTAAATTATTTTTCTATAAATTCTATATAAAAATAA
AATACTATTATGATATATATATATATTTTACATTTTAAGTAGAAAATCTT
Found at i:29771848 original size:15 final size:15
Alignment explanation
Indices: 29771823--29771867 Score: 83
Period size: 15 Copynumber: 3.1 Consensus size: 15
29771813 GTTGGCTTGA
29771823 GGTTA-GGTTTCCAT
1 GGTTAGGGTTTCCAT
29771837 GGTTAGGGTTTCCAT
1 GGTTAGGGTTTCCAT
29771852 GGTTAGGGTTTCCAT
1 GGTTAGGGTTTCCAT
29771867 G
1 G
29771868 CTTTTAATTT
Statistics
Matches: 30, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
14 5 0.17
15 25 0.83
ACGTcount: A:0.13, C:0.13, G:0.33, T:0.40
Consensus pattern (15 bp):
GGTTAGGGTTTCCAT
Found at i:29772935 original size:4 final size:4
Alignment explanation
Indices: 29772926--29772968 Score: 86
Period size: 4 Copynumber: 10.8 Consensus size: 4
29772916 TTTGAAAAGT
29772926 TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGT
1 TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGT
29772969 GCTCTCTGTG
Statistics
Matches: 39, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 39 1.00
ACGTcount: A:0.23, C:0.00, G:0.26, T:0.51
Consensus pattern (4 bp):
TGTA
Found at i:29773602 original size:25 final size:26
Alignment explanation
Indices: 29773574--29773681 Score: 89
Period size: 25 Copynumber: 4.3 Consensus size: 26
29773564 TGGCAAATTG
*
29773574 TTTGGGAAA-TCTTTGTGGTGAGTCA
1 TTTGGGAAAGCCTTTGTGGTGAGTCA
* * **
29773599 TTT-GTAAAGCCTTTGTGGTGAATTG
1 TTTGGGAAAGCCTTTGTGGTGAGTCA
* * **
29773624 TTTGGGAAA-TCTTAGTGGCAAGTCA
1 TTTGGGAAAGCCTTTGTGGTGAGTCA
*
29773649 TTT-GGAAAGCCTTTGTGGGGAGTCA
1 TTTGGGAAAGCCTTTGTGGTGAGTCA
*
29773674 TCTGGGAA
1 TTTGGGAA
29773682 GTTTGTAAGG
Statistics
Matches: 61, Mismatches: 18, Indels: 7
0.71 0.21 0.08
Matches are distributed among these distances:
24 9 0.15
25 44 0.72
26 8 0.13
ACGTcount: A:0.22, C:0.10, G:0.31, T:0.36
Consensus pattern (26 bp):
TTTGGGAAAGCCTTTGTGGTGAGTCA
Found at i:29773660 original size:50 final size:50
Alignment explanation
Indices: 29773505--29773666 Score: 198
Period size: 50 Copynumber: 3.2 Consensus size: 50
29773495 AAACCAAACC
* ** * * *
29773505 AAGCCTTTGTAGTGAATTGTTTGGGAAGCCTTTGTGACGAGTCATCTGGG
1 AAGCCTTTGTGGTGAATTGTTTGGGAAATCTTTGTGGCGAGTCATTTGGA
* * ** * *
29773555 AAGCCCTTATGGCAAATTGTTTGGGAAATCTTTGTGGTGAGTCATTTGTA
1 AAGCCTTTGTGGTGAATTGTTTGGGAAATCTTTGTGGCGAGTCATTTGGA
* *
29773605 AAGCCTTTGTGGTGAATTGTTTGGGAAATCTTAGTGGCAAGTCATTTGGA
1 AAGCCTTTGTGGTGAATTGTTTGGGAAATCTTTGTGGCGAGTCATTTGGA
29773655 AAGCCTTTGTGG
1 AAGCCTTTGTGG
29773667 GGAGTCATCT
Statistics
Matches: 92, Mismatches: 20, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
50 92 1.00
ACGTcount: A:0.22, C:0.12, G:0.30, T:0.36
Consensus pattern (50 bp):
AAGCCTTTGTGGTGAATTGTTTGGGAAATCTTTGTGGCGAGTCATTTGGA
Found at i:29773680 original size:50 final size:50
Alignment explanation
Indices: 29773576--29773681 Score: 131
Period size: 50 Copynumber: 2.1 Consensus size: 50
29773566 GCAAATTGTT
* ** * * ** *
29773576 TGGGAAATCTTTGTGGTGAGTCATTTGTAAAGCCTTTGTGGTGAATTGTT
1 TGGGAAATCTTAGTGGCAAGTCATTTGGAAAGCCTTTGTGGGGAATCATC
*
29773626 TGGGAAATCTTAGTGGCAAGTCATTTGGAAAGCCTTTGTGGGGAGTCATC
1 TGGGAAATCTTAGTGGCAAGTCATTTGGAAAGCCTTTGTGGGGAATCATC
29773676 TGGGAA
1 TGGGAA
29773682 GTTTGTAAGG
Statistics
Matches: 47, Mismatches: 9, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
50 47 1.00
ACGTcount: A:0.23, C:0.10, G:0.32, T:0.35
Consensus pattern (50 bp):
TGGGAAATCTTAGTGGCAAGTCATTTGGAAAGCCTTTGTGGGGAATCATC
Found at i:29775413 original size:39 final size:39
Alignment explanation
Indices: 29775254--29775430 Score: 183
Period size: 39 Copynumber: 4.5 Consensus size: 39
29775244 ATTCACTTTT
** * * * **
29775254 AAGCATATATCATATTACACATATAATCACATAAAATTT
1 AAGCATATATCGCAATACTCATATAATCACATAACATCC
* * * *
29775293 AAGTATATATCACAATACTCATATAATTACATAACTTCC
1 AAGCATATATCGCAATACTCATATAATCACATAACATCC
* * * * * *
29775332 AAGCACATATCGCAATAATGATATAATAACATAGCATTC
1 AAGCATATATCGCAATACTCATATAATCACATAACATCC
29775371 AAGCATATATCGCAATACTCATATAATCACATAACATCC
1 AAGCATATATCGCAATACTCATATAATCACATAACATCC
* *
29775410 AAGCATATGTTGCAATACTCA
1 AAGCATATATCGCAATACTCA
29775431 AAAACATGTT
Statistics
Matches: 112, Mismatches: 26, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
39 112 1.00
ACGTcount: A:0.45, C:0.20, G:0.06, T:0.29
Consensus pattern (39 bp):
AAGCATATATCGCAATACTCATATAATCACATAACATCC
Found at i:29776150 original size:26 final size:28
Alignment explanation
Indices: 29776121--29776186 Score: 84
Period size: 28 Copynumber: 2.4 Consensus size: 28
29776111 AATAAACACC
* *
29776121 AAAAATTTATTTT-AAA-AATAAAATAA
1 AAAAATATATTTTAAAATAAAAAAATAA
29776147 AAAAA-AGTATTTTAAAATAAAAAAATAA
1 AAAAATA-TATTTTAAAATAAAAAAATAA
29776175 AAAAATATATTT
1 AAAAATATATTT
29776187 ATTATATATT
Statistics
Matches: 34, Mismatches: 2, Indels: 6
0.81 0.05 0.14
Matches are distributed among these distances:
26 11 0.32
27 3 0.09
28 19 0.56
29 1 0.03
ACGTcount: A:0.67, C:0.00, G:0.02, T:0.32
Consensus pattern (28 bp):
AAAAATATATTTTAAAATAAAAAAATAA
Found at i:29783752 original size:25 final size:25
Alignment explanation
Indices: 29783678--29783755 Score: 88
Period size: 25 Copynumber: 3.1 Consensus size: 25
29783668 GTCATTAGGG
* *
29783678 TTACCGATTCTCAACTCGTATGAGC
1 TTACCGATTCTCAGCTCATATGAGC
*
29783703 TTACCGATT-TGCAGCTCTTGA-GAGC
1 TTACCGATTCT-CAGCTCAT-ATGAGC
*
29783728 TTACCGATTCTTAGCTCATATGAGC
1 TTACCGATTCTCAGCTCATATGAGC
29783753 TTA
1 TTA
29783756 TAGATTTACA
Statistics
Matches: 45, Mismatches: 4, Indels: 8
0.79 0.07 0.14
Matches are distributed among these distances:
24 2 0.04
25 41 0.91
26 2 0.04
ACGTcount: A:0.23, C:0.24, G:0.18, T:0.35
Consensus pattern (25 bp):
TTACCGATTCTCAGCTCATATGAGC
Found at i:29793094 original size:19 final size:19
Alignment explanation
Indices: 29793070--29793106 Score: 74
Period size: 19 Copynumber: 1.9 Consensus size: 19
29793060 TAGGTCAAAG
29793070 TGTAATAGTTAATTTAATA
1 TGTAATAGTTAATTTAATA
29793089 TGTAATAGTTAATTTAAT
1 TGTAATAGTTAATTTAAT
29793107 TTGATGTGTA
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 18 1.00
ACGTcount: A:0.41, C:0.00, G:0.11, T:0.49
Consensus pattern (19 bp):
TGTAATAGTTAATTTAATA
Found at i:29795388 original size:22 final size:22
Alignment explanation
Indices: 29795358--29795401 Score: 70
Period size: 22 Copynumber: 2.0 Consensus size: 22
29795348 GAAAGTTTCA
* *
29795358 CCTTTGAAGAAAGTATTTTGGT
1 CCTTGGAAGAAAGTACTTTGGT
29795380 CCTTGGAAGAAAGTACTTTGGT
1 CCTTGGAAGAAAGTACTTTGGT
29795402 TTGACAGAAA
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:0.27, C:0.11, G:0.25, T:0.36
Consensus pattern (22 bp):
CCTTGGAAGAAAGTACTTTGGT
Found at i:29798799 original size:13 final size:13
Alignment explanation
Indices: 29798783--29798807 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
29798773 TTAAAATAAA
29798783 ATTTTAATATTTT
1 ATTTTAATATTTT
29798796 ATTTTAATATTT
1 ATTTTAATATTT
29798808 AAAATAAAAC
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:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (13 bp):
ATTTTAATATTTT
Found at i:29814503 original size:21 final size:23
Alignment explanation
Indices: 29814455--29814504 Score: 70
Period size: 21 Copynumber: 2.3 Consensus size: 23
29814445 ATTAAAAATA
29814455 GTTTAATTAAAGAATAAATTAAG
1 GTTTAATTAAAGAATAAATTAAG
*
29814478 G-TTAATT-AAGATTAAA-TAAG
1 GTTTAATTAAAGAATAAATTAAG
29814498 GTTTAAT
1 GTTTAAT
29814505 ATTAGTATAT
Statistics
Matches: 25, Mismatches: 1, Indels: 4
0.83 0.03 0.13
Matches are distributed among these distances:
20 5 0.20
21 13 0.52
22 6 0.24
23 1 0.04
ACGTcount: A:0.48, C:0.00, G:0.14, T:0.38
Consensus pattern (23 bp):
GTTTAATTAAAGAATAAATTAAG
Found at i:29815926 original size:20 final size:20
Alignment explanation
Indices: 29815886--29815927 Score: 59
Period size: 20 Copynumber: 2.1 Consensus size: 20
29815876 ATTTAAATTT
*
29815886 TTTTTGAAAATTATTTAGAA
1 TTTTTGAAAATAATTTAGAA
29815906 TTTTTGAAAATCAATTT-GAA
1 TTTTTGAAAAT-AATTTAGAA
29815926 TT
1 TT
29815928 ATTTTTGCAT
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
20 16 0.80
21 4 0.20
ACGTcount: A:0.38, C:0.02, G:0.10, T:0.50
Consensus pattern (20 bp):
TTTTTGAAAATAATTTAGAA
Found at i:29816560 original size:290 final size:286
Alignment explanation
Indices: 29816018--29816567 Score: 746
Period size: 290 Copynumber: 1.9 Consensus size: 286
29816008 CTGTTATTCG
**
29816018 AATTATTCAAGTTAATCGAATTACAAAATTTAACTTGACTCAAACTCAAAACTTGAATTACTTAT
1 AATTATTCAAGTTAATCGAATTACAAAATTTAACTTGACTCAAACTCAAAACTCAAATTACTTAT
* * *
29816083 CCGAGTTTACTCAAATAACTCAATTGGATGAACTTAAAATTCGATTTTTTTTCACTTTTTTTAAT
66 CCGAGTTTACTCAAATAACTCAATTGGATGAACTCAAAATTCGATTTTTTTTCAATTTTTTGAAT
*
29816148 CGAATTGAGTTTTTCTCACCCTAGTTGGCATGCCATAGGGTCAAGATATTGATTAGAAATCATCA
131 CGAATTGAGTTTTTCTCACCCTAGTTGGCATGCCATAGGGTCAAGATATTGATTAGAAACCATCA
** * ** * ** *
29816213 TTTCTCAGGAATTCCGGGTGGTAGATTGTGCATATAAAGTCATCGTTGTTGTAACACCCCATACA
196 TTTCTCAGGAACCCCAGGTAATAGATTGTACATATAAAGTCATCGTTACTATAACACCCCATACA
29816278 TGACTCGGTTGCCAATCCGTTATTTA
261 TGACTCGGTTGCCAATCCGTTATTTA
* * * * ** *
29816304 AATTA-TCGAGTTATTCGAATTACAAATTTTAACTCT-ACTCGAGTTCGAAACTCAAATTACTTA
1 AATTATTCAAGTTAATCGAATTACAAAATTTAACT-TGACTCAAACTCAAAACTCAAATTACTTA
** * *
29816367 TCCGAGTTTACTCAAATAACTTTATTGGATGAACTCAAATTTTGATTTTTTTTTTCCAATTTTTT
65 TCCGAGTTTACTCAAATAACTCAATTGGATGAACTCAAAATTCGA--TTTTTTTT-CAATTTTTT
* *
29816432 CGAATCGAATTGAGTTTTTCTCACCCCTATTTGGCATGCCATATGGTCAAGATATTGATTAGAAA
127 -GAATCGAATTGAGTTTTTCTCA-CCCTAGTTGGCATGCCATAGGGTCAAGATATTGATTAGAAA
**
29816497 CCATCATTT-TTGGGCAACCCCAGGTAATAGATTGTACATATAAAGTCATCGTTACTATAACACC
190 CCATCATTTCTCAGG-AACCCCAGGTAATAGATTGTACATATAAAGTCATCGTTACTATAACACC
29816561 CCATACA
254 CCATACA
29816568 CGACCCGATT
Statistics
Matches: 227, Mismatches: 30, Indels: 10
0.85 0.11 0.04
Matches are distributed among these distances:
285 87 0.38
286 6 0.03
287 8 0.04
288 8 0.04
289 24 0.11
290 94 0.41
ACGTcount: A:0.31, C:0.18, G:0.14, T:0.37
Consensus pattern (286 bp):
AATTATTCAAGTTAATCGAATTACAAAATTTAACTTGACTCAAACTCAAAACTCAAATTACTTAT
CCGAGTTTACTCAAATAACTCAATTGGATGAACTCAAAATTCGATTTTTTTTCAATTTTTTGAAT
CGAATTGAGTTTTTCTCACCCTAGTTGGCATGCCATAGGGTCAAGATATTGATTAGAAACCATCA
TTTCTCAGGAACCCCAGGTAATAGATTGTACATATAAAGTCATCGTTACTATAACACCCCATACA
TGACTCGGTTGCCAATCCGTTATTTA
Found at i:29817637 original size:14 final size:14
Alignment explanation
Indices: 29817593--29817640 Score: 53
Period size: 14 Copynumber: 3.4 Consensus size: 14
29817583 TAGTTATTTG
29817593 TTTATTTTATTGTTTA
1 TTTATTTT-TTG-TTA
*
29817609 TTTA-TTTTAGTTA
1 TTTATTTTTTGTTA
*
29817622 TTTATTTTTTGATA
1 TTTATTTTTTGTTA
29817636 TTTAT
1 TTTAT
29817641 CTCTTTTATG
Statistics
Matches: 28, Mismatches: 3, Indels: 4
0.80 0.09 0.11
Matches are distributed among these distances:
13 7 0.25
14 14 0.50
15 3 0.11
16 4 0.14
ACGTcount: A:0.21, C:0.00, G:0.06, T:0.73
Consensus pattern (14 bp):
TTTATTTTTTGTTA
Found at i:29818694 original size:6 final size:6
Alignment explanation
Indices: 29818674--29818706 Score: 50
Period size: 6 Copynumber: 5.5 Consensus size: 6
29818664 GGGACTGCTG
29818674 AAAA-A AAAAGAA AAAAGA AAAAGA AAAAGA AAA
1 AAAAGA AAAAG-A AAAAGA AAAAGA AAAAGA AAA
29818707 GAATAATAGG
Statistics
Matches: 26, Mismatches: 0, Indels: 3
0.90 0.00 0.10
Matches are distributed among these distances:
5 4 0.15
6 16 0.62
7 6 0.23
ACGTcount: A:0.88, C:0.00, G:0.12, T:0.00
Consensus pattern (6 bp):
AAAAGA
Found at i:29820939 original size:44 final size:43
Alignment explanation
Indices: 29820875--29820957 Score: 114
Period size: 44 Copynumber: 1.9 Consensus size: 43
29820865 AAAATTTTTA
*
29820875 TTTAATCTTTTAAAAAATATAAACTCTTA-AAATGATATTACAT
1 TTTAATCTTATAAAAAATATAAACTCTTATAAAT-ATATTACAT
**
29820918 TTTAATTCTTATAAAAAATATAATTTCTTATAAATATATT
1 TTTAA-TCTTATAAAAAATATAAACTCTTATAAATATATT
29820958 CAAATAAAAA
Statistics
Matches: 35, Mismatches: 3, Indels: 3
0.85 0.07 0.07
Matches are distributed among these distances:
43 5 0.14
44 26 0.74
45 4 0.11
ACGTcount: A:0.46, C:0.07, G:0.01, T:0.46
Consensus pattern (43 bp):
TTTAATCTTATAAAAAATATAAACTCTTATAAATATATTACAT
Found at i:29821487 original size:20 final size:19
Alignment explanation
Indices: 29821462--29821501 Score: 53
Period size: 19 Copynumber: 2.1 Consensus size: 19
29821452 TATTAATTTC
29821462 ATTAATAATATAATTGTAAA
1 ATTAATAATA-AATTGTAAA
* *
29821482 ATTAATACTAAATTTTAAA
1 ATTAATAATAAATTGTAAA
29821501 A
1 A
29821502 ACATGAATCA
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:0.55, C:0.03, G:0.03, T:0.40
Consensus pattern (19 bp):
ATTAATAATAAATTGTAAA
Found at i:29826793 original size:27 final size:27
Alignment explanation
Indices: 29826756--29826811 Score: 69
Period size: 27 Copynumber: 2.1 Consensus size: 27
29826746 TGATACATTC
*
29826756 ATATAACTAAAATAAAAATT-AAATTAT
1 ATATAAATAAAATAAAAATTGAAA-TAT
* *
29826783 ATATAAATAAATTAATAATTGAAATAT
1 ATATAAATAAAATAAAAATTGAAATAT
29826810 AT
1 AT
29826812 TTGAATAAGA
Statistics
Matches: 25, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
27 22 0.88
28 3 0.12
ACGTcount: A:0.61, C:0.02, G:0.02, T:0.36
Consensus pattern (27 bp):
ATATAAATAAAATAAAAATTGAAATAT
Found at i:29828446 original size:20 final size:19
Alignment explanation
Indices: 29828396--29828446 Score: 61
Period size: 17 Copynumber: 2.7 Consensus size: 19
29828386 AATAGTTCTG
*
29828396 TCTCTTGATGAACATTTGTA
1 TCTCTTG-TGAACAATTGTA
29828416 TCT-TT-TGAACAATTGTA
1 TCTCTTGTGAACAATTGTA
29828433 TCTCTTGGTGAACA
1 TCTCTT-GTGAACA
29828447 GATTTATTGC
Statistics
Matches: 27, Mismatches: 1, Indels: 6
0.79 0.03 0.18
Matches are distributed among these distances:
17 14 0.52
18 2 0.07
19 2 0.07
20 9 0.33
ACGTcount: A:0.25, C:0.16, G:0.16, T:0.43
Consensus pattern (19 bp):
TCTCTTGTGAACAATTGTA
Found at i:29831922 original size:42 final size:41
Alignment explanation
Indices: 29831789--29831930 Score: 164
Period size: 42 Copynumber: 3.4 Consensus size: 41
29831779 CTCGGTGGAT
* * *
29831789 TCAGCACTTAGCAACCACC-TTAAATTCAGTGATACGGGGAA
1 TCAGCACTTAGCAACCACCTTTAAA-TCAATAATATGGGGAA
* *
29831830 TCAGCACATAACAACC-CCTTTCACAATCAA-AGATATGGTGGAA
1 TCAGCACTTAGCAACCACCTTT-A-AATCAATA-ATATGG-GGAA
29831873 TCAGCACTTAGCAACCACCTTTAAAGTCAATAATATGGGGAA
1 TCAGCACTTAGCAACCACCTTTAAA-TCAATAATATGGGGAA
29831915 TCAGCACTTAGCAACC
1 TCAGCACTTAGCAACC
29831931 CCTCGGGGAA
Statistics
Matches: 86, Mismatches: 7, Indels: 15
0.80 0.06 0.14
Matches are distributed among these distances:
40 2 0.02
41 16 0.19
42 31 0.36
43 31 0.36
44 6 0.07
ACGTcount: A:0.37, C:0.25, G:0.16, T:0.22
Consensus pattern (41 bp):
TCAGCACTTAGCAACCACCTTTAAATCAATAATATGGGGAA
Found at i:29831947 original size:26 final size:26
Alignment explanation
Indices: 29831909--29831959 Score: 84
Period size: 26 Copynumber: 2.0 Consensus size: 26
29831899 TCAATAATAT
29831909 GGGGAATCAGCACTTAGCAACCCCTC
1 GGGGAATCAGCACTTAGCAACCCCTC
* *
29831935 GGGGAATCTGCACTTAGCGACCCCT
1 GGGGAATCAGCACTTAGCAACCCCT
29831960 TTTTATTCAA
Statistics
Matches: 23, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
26 23 1.00
ACGTcount: A:0.24, C:0.33, G:0.25, T:0.18
Consensus pattern (26 bp):
GGGGAATCAGCACTTAGCAACCCCTC
Found at i:29839463 original size:42 final size:42
Alignment explanation
Indices: 29839330--29839469 Score: 144
Period size: 42 Copynumber: 3.3 Consensus size: 42
29839320 CTCGGTGGAT
* * *
29839330 TCAGCACTTAGCAACCACC-TTAAATTCAGTGATACGGGGAA
1 TCAGCACTTAGCAACCACCTTTAAAATCAATAATACGGGGAA
*
29839371 TCAGCACATT-GCAACC-CCTTTCACAATCAA-AGATACGGTGGAA
1 TCAGCAC-TTAGCAACCACCTTT-AAAATCAATA-ATACGG-GGAA
* * * *
29839414 TCAGCACTTAGCAACCACCTTTAGAGTCAATAATTCAGGGAA
1 TCAGCACTTAGCAACCACCTTTAAAATCAATAATACGGGGAA
29839456 TCAGCACTTAGCAA
1 TCAGCACTTAGCAA
29839470 ACCCTCAAGG
Statistics
Matches: 83, Mismatches: 8, Indels: 15
0.78 0.08 0.14
Matches are distributed among these distances:
40 2 0.02
41 15 0.18
42 33 0.40
43 27 0.33
44 6 0.07
ACGTcount: A:0.35, C:0.26, G:0.17, T:0.22
Consensus pattern (42 bp):
TCAGCACTTAGCAACCACCTTTAAAATCAATAATACGGGGAA
Found at i:29844092 original size:20 final size:20
Alignment explanation
Indices: 29844067--29844104 Score: 58
Period size: 20 Copynumber: 1.9 Consensus size: 20
29844057 CAAATTAAAC
*
29844067 AATAGTTCTGTCTTTTGATG
1 AATAGTTCTATCTTTTGATG
*
29844087 AATAGTTGTATCTTTTGA
1 AATAGTTCTATCTTTTGA
29844105 ACAATTGTAT
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 16 1.00
ACGTcount: A:0.24, C:0.08, G:0.18, T:0.50
Consensus pattern (20 bp):
AATAGTTCTATCTTTTGATG
Found at i:29849360 original size:77 final size:76
Alignment explanation
Indices: 29849222--29850062 Score: 793
Period size: 77 Copynumber: 10.9 Consensus size: 76
29849212 AGTTCGCTTT
* * * * *
29849222 ATTTAATATCGCGACTGTTATTTTTAAGGTTTGCTCGAATTAAGATCGTGACCTTCGGTATTCTA
1 ATTTAAGATTGCGACTGTCATTTTTAAGGTTCGCTCGATTTAAGATCGTGACCTTC-GTATTCTA
* **
29849287 ACAATTTGCTCG
65 ACAGTTCACTCG
* * * * * * * *
29849299 ATTGAAGATTGCGACTTTTATTTTTATGGTTCACTTGATTTAATATCATGACCTTCAGTATTCTA
1 ATTTAAGATTGCGACTGTCATTTTTAAGGTTCGCTCGATTTAAGATCGTGACCTTC-GTATTCTA
** *
29849364 ACAGTTTGCTCA
65 ACAGTTCACTCG
* ** *
29849376 ATTTAAGATTGCGACTGTCATTTTTAAGGTTCGCTAGATTTAAGATCGCAATCTTCGATATTCTA
1 ATTTAAGATTGCGACTGTCATTTTTAAGGTTCGCTCGATTTAAGATCGTGACCTTCG-TATTCTA
29849441 ACAGTTCACTCG
65 ACAGTTCACTCG
** * * ** * **
29849453 ATTTAAGACCGTGACTGTTATTTTTAAGGTTCTTTTGATTTAAGATCCAGACCTTCGATATTCTA
1 ATTTAAGATTGCGACTGTCATTTTTAAGGTTCGCTCGATTTAAGATCGTGACCTTCG-TATTCTA
29849518 ACAGTTCACTCG
65 ACAGTTCACTCG
* * * *
29849530 ATTTAAGATTGCGACTGTCATTTTTACGGTTCACTCGATTTAAGATTGCGACCTTCGGTATTCTA
1 ATTTAAGATTGCGACTGTCATTTTTAAGGTTCGCTCGATTTAAGATCGTGACCTTC-GTATTCTA
*
29849595 ATAGTTCACTCG
65 ACAGTTCACTCG
* * * * *
29849607 ATTTAAGATCGCGACTGTCATTTTTATGGTTTGCTCAATTTAATATCGTGACCTTCAGTATTCTA
1 ATTTAAGATTGCGACTGTCATTTTTAAGGTTCGCTCGATTTAAGATCGTGACCTTC-GTATTCTA
**
29849672 ACAGTTTGCTCG
65 ACAGTTCACTCG
* * *** * * * * * * *
29849684 ATTGAATATCAAGACTGTTATTTTTACGGTTTGCTCGTTTTGAGATCGAGACTTTCGGTATTCTA
1 ATTTAAGATTGCGACTGTCATTTTTAAGGTTCGCTCGATTTAAGATCGTGACCTTC-GTATTCTA
*
29849749 ATAGTTCACTCG
65 ACAGTTCACTCG
* *** * * * *
29849761 ATTTAATATAATGACTTTCATTTTTACGGTTCGCTCGATTTAAGATCGTGACTTTTTGTATTCTA
1 ATTTAAGATTGCGACTGTCATTTTTAAGGTTCGCTCGATTTAAGATCGTGAC-CTTCGTATTCTA
29849826 ACAGTTCACTCG
65 ACAGTTCACTCG
* *** * * * *
29849838 ATTTAATATAATGACTTTCATTTTTACGGTTCGCTCGATTTAAGATCGTGACTTTTTGTATTCTA
1 ATTTAAGATTGCGACTGTCATTTTTAAGGTTCGCTCGATTTAAGATCGTGAC-CTTCGTATTCTA
29849903 ACAGTTCACTCG
65 ACAGTTCACTCG
* *** * * * *
29849915 ATTTAATATAATGACTTTCATTTTTACGGTTCGCTCGATTTAAGATCGTGACTTTTTGTATTCTA
1 ATTTAAGATTGCGACTGTCATTTTTAAGGTTCGCTCGATTTAAGATCGTGAC-CTTCGTATTCTA
29849980 ACAGTTCACTCG
65 ACAGTTCACTCG
* * * *
29849992 ATTTAAGATTGTGTCTGTCATTTTTAAGGATT-GCTCGATTTAAGATTGAGACCTTCGATATTCT
1 ATTTAAGATTGCGACTGTCATTTTTAAGG-TTCGCTCGATTTAAGATCGTGACCTTCG-TATTCT
*
29850056 AATAGTT
64 AACAGTT
29850063 TGACCTTGGT
Statistics
Matches: 658, Mismatches: 101, Indels: 10
0.86 0.13 0.01
Matches are distributed among these distances:
76 4 0.01
77 648 0.98
78 6 0.01
ACGTcount: A:0.25, C:0.17, G:0.16, T:0.42
Consensus pattern (76 bp):
ATTTAAGATTGCGACTGTCATTTTTAAGGTTCGCTCGATTTAAGATCGTGACCTTCGTATTCTAA
CAGTTCACTCG
Found at i:29849418 original size:37 final size:37
Alignment explanation
Indices: 29849376--29849637 Score: 181
Period size: 40 Copynumber: 6.8 Consensus size: 37
29849366 AGTTTGCTCA
* *
29849376 ATTTAAGATTGCGACTGTCATTTTTAAGGTTCGCTAG
1 ATTTAAGATTGCGACTGTCATTTTTAAGGTTCACTCG
* * * *
29849413 ATTTAAGATCGCAATCT-TCGATATTCTAACAGTTCACTCG
1 ATTTAAGATTGCGA-CTGTC-AT-TTTTAA-GGTTCACTCG
** * * ** *
29849453 ATTTAAGACCGTGACTGTTATTTTTAAGGTTCTTTTG
1 ATTTAAGATTGCGACTGTCATTTTTAAGGTTCACTCG
* * *
29849490 ATTTAAGA-TCCAGACCT-TCGATATTCTAACAGTTCACTCG
1 ATTTAAGATTGC-GA-CTGTC-AT-TTTTAA-GGTTCACTCG
*
29849530 ATTTAAGATTGCGACTGTCATTTTTACGGTTCACTCG
1 ATTTAAGATTGCGACTGTCATTTTTAAGGTTCACTCG
* * *
29849567 ATTTAAGATTGCGACCT-TCGGTATTCTAATAGTTCACTCG
1 ATTTAAGATTGCGA-CTGTC-AT-TTTTAA-GGTTCACTCG
* *
29849607 ATTTAAGATCGCGACTGTCATTTTTATGGTT
1 ATTTAAGATTGCGACTGTCATTTTTAAGGTT
29849638 TGCTCAATTT
Statistics
Matches: 171, Mismatches: 37, Indels: 34
0.71 0.15 0.14
Matches are distributed among these distances:
37 59 0.35
38 24 0.14
39 25 0.15
40 61 0.36
41 2 0.01
ACGTcount: A:0.25, C:0.18, G:0.17, T:0.40
Consensus pattern (37 bp):
ATTTAAGATTGCGACTGTCATTTTTAAGGTTCACTCG
Found at i:29849671 original size:231 final size:230
Alignment explanation
Indices: 29849222--29850062 Score: 898
Period size: 231 Copynumber: 3.6 Consensus size: 230
29849212 AGTTCGCTTT
** * *
29849222 ATTTAATATCGCGACTGTTATTTTTAAGGTTTGCTCGAATTAAGATCGTGACCTTCGGTATTCTA
1 ATTTAATATCATGACTGTTATTTTTAAGGTTTGCTCGATTTAAGATCGAGACCTTCGGTATTCTA
* ** * * * * * * *
29849287 ACAATTTGCTCGATTGAAGATTGCGACTTTTATTTTTATGGTTCACTTGATTTAATATCATGACC
66 ACAGTTCACTCGATTTAAGATTGCGACTGTCATTTTTACGGTTCACTCGATTTAAGATCGTGACC
* ** * *
29849352 TTCAGTATTCTAACAGTTTGCTCAATTTAAGATTGCGACTGTCATTTTTAAGGTTCGCT-AGATT
131 TTCGGTATTCTAACAGTTCACTCGATTTAAGATAGCGACTGTCATTTTTAAGGTTCGCTCA-ATT
** *
29849416 TAAGATCGCAATCTTCGATATTCTAACAGTTCACTCG
195 TAAGATCGTGACCTTCG-TATTCTAACAGTTCACTCG
* * * * * * *
29849453 ATTTAAGACCGTGACTGTTATTTTTAAGGTTCT-TTTGATTTAAGATCCAGACCTTCGATATTCT
1 ATTTAATATCATGACTGTTATTTTTAAGGTT-TGCTCGATTTAAGATCGAGACCTTCGGTATTCT
* *
29849517 AACAGTTCACTCGATTTAAGATTGCGACTGTCATTTTTACGGTTCACTCGATTTAAGATTGCGAC
65 AACAGTTCACTCGATTTAAGATTGCGACTGTCATTTTTACGGTTCACTCGATTTAAGATCGTGAC
* * * *
29849582 CTTCGGTATTCTAATAGTTCACTCGATTTAAGATCGCGACTGTCATTTTTATGGTTTGCTCAATT
130 CTTCGGTATTCTAACAGTTCACTCGATTTAAGATAGCGACTGTCATTTTTAAGGTTCGCTCAATT
* **
29849647 TAATATCGTGACCTTCAGTATTCTAACAGTTTGCTCG
195 TAAGATCGTGACCTTC-GTATTCTAACAGTTCACTCG
* * * * * *
29849684 ATTGAATATCAAGACTGTTATTTTTACGGTTTGCTCGTTTTGAGATCGAGACTTTCGGTATTCTA
1 ATTTAATATCATGACTGTTATTTTTAAGGTTTGCTCGATTTAAGATCGAGACCTTCGGTATTCTA
* * *** * * *
29849749 ATAGTTCACTCGATTTAATATAATGACTTTCATTTTTACGGTTCGCTCGATTTAAGATCGTGACT
66 ACAGTTCACTCGATTTAAGATTGCGACTGTCATTTTTACGGTTCACTCGATTTAAGATCGTGACC
** * ** * * *
29849814 TTTTGTATTCTAACAGTTCACTCGATTTAATATAATGACTTTCATTTTTACGGTTCGCTCGATTT
131 TTCGGTATTCTAACAGTTCACTCGATTTAAGATAGCGACTGTCATTTTTAAGGTTCGCTCAATTT
* *
29849879 AAGATCGTGACTTTTTGTATTCTAACAGTTCACTCG
196 AAGATCGTGAC-CTTCGTATTCTAACAGTTCACTCG
* * * * * **
29849915 ATTTAATATAATGACT-TTCATTTTTACGGTTCGCTCGATTTAAGATCGTGACTTTTTGTATTCT
1 ATTTAATATCATGACTGTT-ATTTTTAAGGTTTGCTCGATTTAAGATCGAGACCTTCGGTATTCT
* * * * * *
29849979 AACAGTTCACTCGATTTAAGATTGTGTCTGTCATTTTTAAGGATT-GCTCGATTTAAGATTGAGA
65 AACAGTTCACTCGATTTAAGATTGCGACTGTCATTTTTACGG-TTCACTCGATTTAAGATCGTGA
* *
29850043 CCTTCGATATTCTAATAGTT
129 CCTTCGGTATTCTAACAGTT
29850063 TGACCTTGGT
Statistics
Matches: 506, Mismatches: 97, Indels: 14
0.82 0.16 0.02
Matches are distributed among these distances:
230 3 0.01
231 496 0.98
232 7 0.01
ACGTcount: A:0.25, C:0.17, G:0.16, T:0.42
Consensus pattern (230 bp):
ATTTAATATCATGACTGTTATTTTTAAGGTTTGCTCGATTTAAGATCGAGACCTTCGGTATTCTA
ACAGTTCACTCGATTTAAGATTGCGACTGTCATTTTTACGGTTCACTCGATTTAAGATCGTGACC
TTCGGTATTCTAACAGTTCACTCGATTTAAGATAGCGACTGTCATTTTTAAGGTTCGCTCAATTT
AAGATCGTGACCTTCGTATTCTAACAGTTCACTCG
Found at i:29849800 original size:37 final size:37
Alignment explanation
Indices: 29849752--29849957 Score: 209
Period size: 37 Copynumber: 5.4 Consensus size: 37
29849742 TATTCTAATA
29849752 GTTCACTCGATTTAATATAATGACTTTCATTTTTACG
1 GTTCACTCGATTTAATATAATGACTTTCATTTTTACG
* * ** * *
29849789 GTTCGCTCGATTTAAGATCGTGACTTT-TTGTATTCTAACA
1 GTTCACTCGATTTAATATAATGACTTTCAT-T-TT-T-ACG
29849829 GTTCACTCGATTTAATATAATGACTTTCATTTTTACG
1 GTTCACTCGATTTAATATAATGACTTTCATTTTTACG
* * ** * *
29849866 GTTCGCTCGATTTAAGATCGTGACTTT-TTGTATTCTAACA
1 GTTCACTCGATTTAATATAATGACTTTCAT-T-TT-T-ACG
29849906 GTTCACTCGATTTAATATAATGACTTTCATTTTTACG
1 GTTCACTCGATTTAATATAATGACTTTCATTTTTACG
*
29849943 GTTCGCTCGATTTAA
1 GTTCACTCGATTTAA
29849958 GATCGTGACT
Statistics
Matches: 134, Mismatches: 25, Indels: 20
0.75 0.14 0.11
Matches are distributed among these distances:
36 2 0.01
37 66 0.49
38 6 0.04
39 6 0.04
40 52 0.39
41 2 0.01
ACGTcount: A:0.25, C:0.17, G:0.14, T:0.44
Consensus pattern (37 bp):
GTTCACTCGATTTAATATAATGACTTTCATTTTTACG
Found at i:29850081 original size:22 final size:23
Alignment explanation
Indices: 29850041--29850085 Score: 65
Period size: 22 Copynumber: 2.0 Consensus size: 23
29850031 TTAAGATTGA
*
29850041 GACCTTCGATATTCTAATAGTTT
1 GACCTTCGATATTCGAATAGTTT
*
29850064 GACCTT-GGTATTCGAATAGTTT
1 GACCTTCGATATTCGAATAGTTT
29850086 ATTCGATTTA
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
22 14 0.70
23 6 0.30
ACGTcount: A:0.24, C:0.16, G:0.18, T:0.42
Consensus pattern (23 bp):
GACCTTCGATATTCGAATAGTTT
Found at i:29850210 original size:37 final size:36
Alignment explanation
Indices: 29850168--29850292 Score: 97
Period size: 37 Copynumber: 3.3 Consensus size: 36
29850158 AATTTCCTCG
* *
29850168 ATTTAATATCACAACTGTTATTTTTAAGGTTCGCTCA
1 ATTTAAGATCACAACTGTTATTTCTAA-GTTCGCTCA
* * *
29850205 ATTTAAGATCTCAACAGTTGATATTCTAACAGTTCGCTCG
1 ATTTAAGATCACAACTGTT-AT-TTCT-A-AGTTCGCTCA
*** * *
29850245 ATTTAAGATCATGTCTGTCATTTCTACAGTTCACTCA
1 ATTTAAGATCACAACTGTTATTTCTA-AGTTCGCTCA
*
29850282 ATTTAATATCA
1 ATTTAAGATCA
29850293 TGACTTTCAT
Statistics
Matches: 70, Mismatches: 14, Indels: 8
0.76 0.15 0.09
Matches are distributed among these distances:
37 36 0.51
38 6 0.09
39 5 0.07
40 22 0.31
41 1 0.01
ACGTcount: A:0.30, C:0.18, G:0.11, T:0.40
Consensus pattern (36 bp):
ATTTAAGATCACAACTGTTATTTCTAAGTTCGCTCA
Found at i:29850230 original size:77 final size:77
Alignment explanation
Indices: 29850088--29850255 Score: 189
Period size: 77 Copynumber: 2.2 Consensus size: 77
29850078 AATAGTTTAT
** * * * * * *
29850088 TCGATTTAAGATCGTAACTATCATTTTTACGGTTCGCTCAATTTAAGATAGTGACCTTTAGTATT
1 TCGATTTAAGATCACAACTGTTATTTTTAAGGTTCGCTCAATTTAAGATACTAACCTTGAGTATT
*
29850153 CTAACAATTTC-C
66 CTAAC-AGTTCGC
* *
29850165 TCGATTTAATATCACAACTGTTATTTTTAAGGTTCGCTCAATTTAAGAT-CTCAACAGTTGA-TA
1 TCGATTTAAGATCACAACTGTTATTTTTAAGGTTCGCTCAATTTAAGATACT-AAC-CTTGAGTA
29850228 TTCTAACAGTTCGC
64 TTCTAACAGTTCGC
29850242 TCGATTTAAGATCA
1 TCGATTTAAGATCA
29850256 TGTCTGTCAT
Statistics
Matches: 76, Mismatches: 12, Indels: 6
0.81 0.13 0.06
Matches are distributed among these distances:
76 5 0.07
77 68 0.89
78 3 0.04
ACGTcount: A:0.30, C:0.18, G:0.13, T:0.39
Consensus pattern (77 bp):
TCGATTTAAGATCACAACTGTTATTTTTAAGGTTCGCTCAATTTAAGATACTAACCTTGAGTATT
CTAACAGTTCGC
Found at i:29850293 original size:37 final size:37
Alignment explanation
Indices: 29850228--29850324 Score: 124
Period size: 37 Copynumber: 2.6 Consensus size: 37
29850218 ACAGTTGATA
* * *
29850228 TTCTAACAGTTCGCTCGATTTAAGATCATGTCTGTCAT
1 TTCT-ACAGTTCACTCAATTTAAGATCATGACTGTCAT
* *
29850266 TTCTACAGTTCACTCAATTTAATATCATGACTTTCAT
1 TTCTACAGTTCACTCAATTTAAGATCATGACTGTCAT
*
29850303 TTTTACAGTTCACT-AATTTAAG
1 TTCTACAGTTCACTCAATTTAAG
29850325 GTCGCGACCT
Statistics
Matches: 52, Mismatches: 7, Indels: 2
0.85 0.11 0.03
Matches are distributed among these distances:
36 7 0.13
37 41 0.79
38 4 0.08
ACGTcount: A:0.28, C:0.20, G:0.10, T:0.42
Consensus pattern (37 bp):
TTCTACAGTTCACTCAATTTAAGATCATGACTGTCAT
Found at i:29850341 original size:37 final size:37
Alignment explanation
Indices: 29850233--29850351 Score: 98
Period size: 37 Copynumber: 3.2 Consensus size: 37
29850223 TGATATTCTA
* * * * *
29850233 ACAGTTCGCTCGATTTAAGATCATGTCTGT-CATTTCT
1 ACAGTTCACTCAATTTAAGATCACGACT-TCCATTTTT
* * *
29850270 ACAGTTCACTCAATTTAATATCATGACTTTCATTTTT
1 ACAGTTCACTCAATTTAAGATCACGACTTCCATTTTT
* *
29850307 ACAGTTCACT-AATTTAAGGTCGCGACCTTCCATTTTCT
1 ACAGTTCACTCAATTTAAGATCACGA-CTTCCATTTT-T
29850345 AACAGTT
1 -ACAGTT
29850352 TGCTTTGTTT
Statistics
Matches: 68, Mismatches: 10, Indels: 6
0.81 0.12 0.07
Matches are distributed among these distances:
36 12 0.18
37 49 0.72
38 1 0.01
39 6 0.09
ACGTcount: A:0.26, C:0.22, G:0.12, T:0.40
Consensus pattern (37 bp):
ACAGTTCACTCAATTTAAGATCACGACTTCCATTTTT
Found at i:29856715 original size:32 final size:32
Alignment explanation
Indices: 29856671--29856919 Score: 164
Period size: 32 Copynumber: 7.8 Consensus size: 32
29856661 AATGTGATTG
* *
29856671 GCACAAAGCCATCAGTAGCAATGATATGATCG
1 GCACAAAGCCATCAGTAACAATGATATGATCA
* ** * *
29856703 GTACACAA-CCATCAGTAACGGTAACATGATCA
1 GCACA-AAGCCATCAGTAACAATGATATGATCA
* * * * *
29856735 GCATAAAGCCATCAGTAGCAGTGGTTTGATCA
1 GCACAAAGCCATCAGTAACAATGATATGATCA
* * *
29856767 GCACACAGCCATCAGTAACAATGAAATGGTCA
1 GCACAAAGCCATCAGTAACAATGATATGATCA
* * * * *
29856799 GTACACAA-CCATCGGTAACGATAATATGATCG
1 GCACA-AAGCCATCAGTAACAATGATATGATCA
* * * *
29856831 GTACAAAGCCATCAATAACGAT-ACTATGATCG
1 GCACAAAGCCATCAGTAACAATGA-TATGATCA
*** *
29856863 GCACAAAGCCATCAGTAATGGT-ACTATGATCG
1 GCACAAAGCCATCAGTAACAATGA-TATGATCA
* *
29856895 GAACAAAGCCATCAGTAACAGTGAT
1 GCACAAAGCCATCAGTAACAATGAT
29856920 TGTGGTAGAG
Statistics
Matches: 171, Mismatches: 40, Indels: 12
0.77 0.18 0.05
Matches are distributed among these distances:
31 5 0.03
32 162 0.95
33 4 0.02
ACGTcount: A:0.38, C:0.22, G:0.20, T:0.20
Consensus pattern (32 bp):
GCACAAAGCCATCAGTAACAATGATATGATCA
Found at i:29856839 original size:96 final size:96
Alignment explanation
Indices: 29856671--29856880 Score: 251
Period size: 96 Copynumber: 2.2 Consensus size: 96
29856661 AATGTGATTG
* * * *
29856671 GCACAAAGCCATCAGTAGCAATGATATGATCGGTACACAACCATCAGTAACGGTAACATGATCAG
1 GCACAAAGCCATCAGTAACAATGAAATGATCAGTACACAACCATCAGTAACGATAACATGATCAG
*
29856736 CATAAAGCCATCAGTAGCAGTGGTTTGATCA
66 CACAAAGCCATCAGTAGCAGTGGTTTGATCA
* * * * *
29856767 GCACACAGCCATCAGTAACAATGAAATGGTCAGTACACAACCATCGGTAACGATAATATGATCGG
1 GCACAAAGCCATCAGTAACAATGAAATGATCAGTACACAACCATCAGTAACGATAACATGATCAG
* * * ** * *
29856832 TACAAAGCCATCAATAAC-GATACTATGATCG
66 CACAAAGCCATCAGTAGCAG-TGGTTTGATCA
29856863 GCACAAAGCCATCAGTAA
1 GCACAAAGCCATCAGTAA
29856881 TGGTACTATG
Statistics
Matches: 95, Mismatches: 18, Indels: 2
0.83 0.16 0.02
Matches are distributed among these distances:
95 1 0.01
96 94 0.99
ACGTcount: A:0.39, C:0.23, G:0.19, T:0.20
Consensus pattern (96 bp):
GCACAAAGCCATCAGTAACAATGAAATGATCAGTACACAACCATCAGTAACGATAACATGATCAG
CACAAAGCCATCAGTAGCAGTGGTTTGATCA
Found at i:29866105 original size:24 final size:25
Alignment explanation
Indices: 29866067--29866116 Score: 75
Period size: 24 Copynumber: 2.0 Consensus size: 25
29866057 AATCTTTTAG
* *
29866067 AAACTAAATATAACTAAGTTAAATA
1 AAACTAAATAGAACTAAGTAAAATA
29866092 AAACT-AATAGAACTAAGTAAAATA
1 AAACTAAATAGAACTAAGTAAAATA
29866116 A
1 A
29866117 CAAAACCAGT
Statistics
Matches: 23, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
24 18 0.78
25 5 0.22
ACGTcount: A:0.62, C:0.08, G:0.06, T:0.24
Consensus pattern (25 bp):
AAACTAAATAGAACTAAGTAAAATA
Found at i:29866835 original size:41 final size:41
Alignment explanation
Indices: 29866773--29866866 Score: 179
Period size: 41 Copynumber: 2.3 Consensus size: 41
29866763 TACAAGTGTC
29866773 AATCGAATTTTAATCCAACCAATCCAACCCTTTTAGAATTAG
1 AATC-AATTTTAATCCAACCAATCCAACCCTTTTAGAATTAG
29866815 AATCAATTTTAATCCAACCAATCCAACCCTTTTAGAATTAG
1 AATCAATTTTAATCCAACCAATCCAACCCTTTTAGAATTAG
29866856 AATCAATTTTA
1 AATCAATTTTA
29866867 GAAGTATGCG
Statistics
Matches: 52, Mismatches: 0, Indels: 1
0.98 0.00 0.02
Matches are distributed among these distances:
41 48 0.92
42 4 0.08
ACGTcount: A:0.39, C:0.22, G:0.05, T:0.33
Consensus pattern (41 bp):
AATCAATTTTAATCCAACCAATCCAACCCTTTTAGAATTAG
Found at i:29879607 original size:20 final size:21
Alignment explanation
Indices: 29879582--29879622 Score: 59
Period size: 20 Copynumber: 2.0 Consensus size: 21
29879572 GAGTTTTATT
29879582 TATTTTATGTA-CTAA-TTAGA
1 TATTTTA-GTATCTAAGTTAGA
29879602 TATTTTAGTATCTAAGTTAGA
1 TATTTTAGTATCTAAGTTAGA
29879623 ACTGATCTAG
Statistics
Matches: 19, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
19 3 0.16
20 11 0.58
21 5 0.26
ACGTcount: A:0.34, C:0.05, G:0.12, T:0.49
Consensus pattern (21 bp):
TATTTTAGTATCTAAGTTAGA
Found at i:29886080 original size:14 final size:14
Alignment explanation
Indices: 29886056--29886091 Score: 56
Period size: 14 Copynumber: 2.6 Consensus size: 14
29886046 AATTGAATAT
29886056 AATTA-GGTTACAC
1 AATTAGGGTTACAC
29886069 AATTAGGGTTACAC
1 AATTAGGGTTACAC
*
29886083 AATTTGGGT
1 AATTAGGGT
29886092 CGGGTCAACC
Statistics
Matches: 21, Mismatches: 1, Indels: 1
0.91 0.04 0.04
Matches are distributed among these distances:
13 5 0.24
14 16 0.76
ACGTcount: A:0.33, C:0.11, G:0.22, T:0.33
Consensus pattern (14 bp):
AATTAGGGTTACAC
Found at i:29893596 original size:7 final size:6
Alignment explanation
Indices: 29893551--29893618 Score: 65
Period size: 6 Copynumber: 12.0 Consensus size: 6
29893541 GACCCCTTTT
* *
29893551 ATTAAA A-T-AA A-TAAA ACTAAC ATTAAA ATTAAA ATTAAA GATT-AA
1 ATTAAA ATTAAA ATTAAA ATTAAA ATTAAA ATTAAA ATTAAA -ATTAAA
*
29893596 ATTGAA ATT-AA ATTAAA ATTAAA
1 ATTAAA ATTAAA ATTAAA ATTAAA
29893619 GACAAAGATA
Statistics
Matches: 54, Mismatches: 3, Indels: 10
0.81 0.04 0.15
Matches are distributed among these distances:
4 4 0.07
5 12 0.22
6 35 0.65
7 3 0.06
ACGTcount: A:0.63, C:0.03, G:0.03, T:0.31
Consensus pattern (6 bp):
ATTAAA
Found at i:29893607 original size:11 final size:11
Alignment explanation
Indices: 29893551--29893618 Score: 77
Period size: 12 Copynumber: 6.1 Consensus size: 11
29893541 GACCCCTTTT
29893551 ATTAAAA-TAA
1 ATTAAAATTAA
*
29893561 A-TAAAACTAA
1 ATTAAAATTAA
29893571 CATTAAAATTAAA
1 -ATTAAAATT-AA
29893584 ATTAAAGATTAA
1 ATTAAA-ATTAA
*
29893596 ATTGAAATTAA
1 ATTAAAATTAA
29893607 ATTAAAATTAA
1 ATTAAAATTAA
29893618 A
1 A
29893619 GACAAAGATA
Statistics
Matches: 50, Mismatches: 3, Indels: 9
0.81 0.05 0.15
Matches are distributed among these distances:
9 5 0.10
10 4 0.08
11 17 0.34
12 19 0.38
13 5 0.10
ACGTcount: A:0.63, C:0.03, G:0.03, T:0.31
Consensus pattern (11 bp):
ATTAAAATTAA
Found at i:29903021 original size:45 final size:45
Alignment explanation
Indices: 29902972--29903150 Score: 202
Period size: 45 Copynumber: 4.0 Consensus size: 45
29902962 ATTCACACTG
* * *
29902972 TATTATCAACTTTTATTTGCATCGAA-TAGTGGTTTATCCACTCCA
1 TATTATCAACTTTTATCTACATC-AAGTAGTGGTTTATCCACACCA
* * *
29903017 TATTAGCAACTTTTATCTACACCAAGTAGCGGTTTATCCACACCA
1 TATTATCAACTTTTATCTACATCAAGTAGTGGTTTATCCACACCA
* * *
29903062 TATT-TGTAACTTTTATCTACATCAAGTAGTGGTTTATCCACATCG
1 TATTAT-CAACTTTTATCTACATCAAGTAGTGGTTTATCCACACCA
* * *
29903107 TATTAGT-AGCTTTTATCTACATCAATTAGTGGTCTATCCACACC
1 TATTA-TCAACTTTTATCTACATCAAGTAGTGGTTTATCCACACC
29903151 GTACTAGCAA
Statistics
Matches: 114, Mismatches: 16, Indels: 8
0.83 0.12 0.06
Matches are distributed among these distances:
44 2 0.02
45 111 0.97
47 1 0.01
ACGTcount: A:0.28, C:0.22, G:0.12, T:0.39
Consensus pattern (45 bp):
TATTATCAACTTTTATCTACATCAAGTAGTGGTTTATCCACACCA
Found at i:29903099 original size:21 final size:21
Alignment explanation
Indices: 29903073--29903144 Score: 72
Period size: 21 Copynumber: 3.3 Consensus size: 21
29903063 ATTTGTAACT
*
29903073 TTTATCTACATCAAGTAGTGG
1 TTTATCTACATCAATTAGTGG
* * *
29903094 TTTATCCACATCGTATTAGTAGCT
1 TTTATCTACATC-AATTAGT-G-G
29903118 TTTATCTACATCAATTAGTGG
1 TTTATCTACATCAATTAGTGG
*
29903139 TCTATC
1 TTTATC
29903145 CACACCGTAC
Statistics
Matches: 40, Mismatches: 8, Indels: 6
0.74 0.15 0.11
Matches are distributed among these distances:
21 16 0.40
22 6 0.15
23 7 0.17
24 11 0.28
ACGTcount: A:0.26, C:0.18, G:0.14, T:0.42
Consensus pattern (21 bp):
TTTATCTACATCAATTAGTGG
Done.