Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: chr10
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: 21822658
ACGTcount: A:0.31, C:0.16, G:0.16, T:0.32
Warning! 1067834 characters in sequence are not A, C, G, or T
File 48 of 59
Found at i:17334812 original size:29 final size:28
Alignment explanation
Indices: 17334770--17334824 Score: 83
Period size: 29 Copynumber: 1.9 Consensus size: 28
17334760 AAAACGTAAT
17334770 AGAAAAGAGGTGTACAAGAATAGGTACA
1 AGAAAAGAGGTGTACAAGAATAGGTACA
* *
17334798 AGAAAAGAAGTTGTACGAGAATAGGTA
1 AGAAAAG-AGGTGTACAAGAATAGGTA
17334825 TGCTAGAACA
Statistics
Matches: 24, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
28 7 0.29
29 17 0.71
ACGTcount: A:0.49, C:0.05, G:0.29, T:0.16
Consensus pattern (28 bp):
AGAAAAGAGGTGTACAAGAATAGGTACA
Found at i:17335120 original size:35 final size:35
Alignment explanation
Indices: 17335049--17335175 Score: 128
Period size: 35 Copynumber: 3.6 Consensus size: 35
17335039 GTAGTGCTCT
* * * *
17335049 ACTTATTCTTGTTATTCTATGTTAAGTAGTATTTC
1 ACTTATTCTAGTTATTCTATGTGAAGTAGCACTTC
* * *
17335084 ACTTATTTTAGTTGTTCTATGTGAAGTAGCGCTTC
1 ACTTATTCTAGTTATTCTATGTGAAGTAGCACTTC
* * **
17335119 ACTTGTTCTAATTATTCTGCGTGAAGTAGCACTTC
1 ACTTATTCTAGTTATTCTATGTGAAGTAGCACTTC
* * *
17335154 ACTTGTTCTAGTTGTTATATGT
1 ACTTATTCTAGTTATTCTATGT
17335176 CAATATTATG
Statistics
Matches: 73, Mismatches: 19, Indels: 0
0.79 0.21 0.00
Matches are distributed among these distances:
35 73 1.00
ACGTcount: A:0.21, C:0.14, G:0.17, T:0.48
Consensus pattern (35 bp):
ACTTATTCTAGTTATTCTATGTGAAGTAGCACTTC
Found at i:17336044 original size:2 final size:2
Alignment explanation
Indices: 17336037--17336103 Score: 89
Period size: 2 Copynumber: 33.5 Consensus size: 2
17336027 TAGAAAGGTA
* * *
17336037 AT AT AT AT AC AT AT AT AT AT AT AT AT AT AT GT AT AT AC AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
* *
17336079 AT GT AT AT AT GT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT A
17336104 ACCTAGTAAT
Statistics
Matches: 55, Mismatches: 10, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
2 55 1.00
ACGTcount: A:0.46, C:0.03, G:0.04, T:0.46
Consensus pattern (2 bp):
AT
Found at i:17336129 original size:27 final size:27
Alignment explanation
Indices: 17336099--17336153 Score: 92
Period size: 27 Copynumber: 2.0 Consensus size: 27
17336089 GTATATATAT
*
17336099 ATATAACCTAGTAATATTTATAATAAA
1 ATATAACCTAGTAATATTTAAAATAAA
*
17336126 ATATAATCTAGTAATATTTAAAATAAA
1 ATATAACCTAGTAATATTTAAAATAAA
17336153 A
1 A
17336154 AATTACAAAA
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
27 26 1.00
ACGTcount: A:0.55, C:0.05, G:0.04, T:0.36
Consensus pattern (27 bp):
ATATAACCTAGTAATATTTAAAATAAA
Found at i:17339004 original size:16 final size:16
Alignment explanation
Indices: 17338983--17339013 Score: 62
Period size: 16 Copynumber: 1.9 Consensus size: 16
17338973 GTAGCTATTA
17338983 ACCCCAATGAAAGGCT
1 ACCCCAATGAAAGGCT
17338999 ACCCCAATGAAAGGC
1 ACCCCAATGAAAGGC
17339014 CTACATCCAT
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 15 1.00
ACGTcount: A:0.39, C:0.32, G:0.19, T:0.10
Consensus pattern (16 bp):
ACCCCAATGAAAGGCT
Found at i:17342117 original size:55 final size:56
Alignment explanation
Indices: 17342058--17342199 Score: 178
Period size: 55 Copynumber: 2.5 Consensus size: 56
17342048 AAAAACCATG
* *
17342058 AATGTCCATTCCCTGAAGTGAATGTGACAAACGAGATACTAAT-AAAAAAATTATA
1 AATGTCCATTCCCTGAAGTGAATGTGACAAACGAGATACGAATAAAAAAAAATATA
** * * *
17342113 AATGTTTATTCCCTGAAGTAAATGTGACAAATGAGCTACGAATAAAAAAAAATATA
1 AATGTCCATTCCCTGAAGTGAATGTGACAAACGAGATACGAATAAAAAAAAATATA
* *
17342169 AATCCGTCCATTCCTTAAAGTGAATGTGACA
1 AAT--GTCCATTCCCTGAAGTGAATGTGACA
17342200 TCATTTAATA
Statistics
Matches: 72, Mismatches: 12, Indels: 3
0.83 0.14 0.03
Matches are distributed among these distances:
55 37 0.51
56 14 0.19
58 21 0.29
ACGTcount: A:0.44, C:0.15, G:0.15, T:0.27
Consensus pattern (56 bp):
AATGTCCATTCCCTGAAGTGAATGTGACAAACGAGATACGAATAAAAAAAAATATA
Found at i:17344810 original size:26 final size:26
Alignment explanation
Indices: 17344781--17344882 Score: 75
Period size: 26 Copynumber: 4.0 Consensus size: 26
17344771 TTTAATTATT
17344781 ATTTTACCACTAGAAGTGGATGGATA
1 ATTTTACCACTAGAAGTGGATGGATA
* ** * *
17344807 ATTTTATCATCTA-AA-TTTAAGAATA
1 ATTTTACCA-CTAGAAGTGGATGGATA
* ** *
17344832 ATTTTACCATTAGAAGTGGACAGAGA
1 ATTTTACCACTAGAAGTGGATGGATA
*
17344858 ATTTTACCA-TCAAAAGTGGATGGAT
1 ATTTTACCACT-AGAAGTGGATGGAT
17344883 GCCTTAACTC
Statistics
Matches: 55, Mismatches: 17, Indels: 8
0.69 0.21 0.10
Matches are distributed among these distances:
24 2 0.04
25 17 0.31
26 33 0.60
27 3 0.05
ACGTcount: A:0.38, C:0.11, G:0.18, T:0.33
Consensus pattern (26 bp):
ATTTTACCACTAGAAGTGGATGGATA
Found at i:17344942 original size:18 final size:18
Alignment explanation
Indices: 17344902--17344960 Score: 64
Period size: 18 Copynumber: 3.3 Consensus size: 18
17344892 CACTAAAAAA
17344902 TGGATAACCCACCAGAAG
1 TGGATAACCCACCAGAAG
* * * *
17344920 AGGATAACCCATCATATG
1 TGGATAACCCACCAGAAG
* *
17344938 TGGATAACCTACCAAAAG
1 TGGATAACCCACCAGAAG
17344956 TGGAT
1 TGGAT
17344961 GTATACTTGT
Statistics
Matches: 32, Mismatches: 9, Indels: 0
0.78 0.22 0.00
Matches are distributed among these distances:
18 32 1.00
ACGTcount: A:0.39, C:0.22, G:0.20, T:0.19
Consensus pattern (18 bp):
TGGATAACCCACCAGAAG
Found at i:17344989 original size:28 final size:28
Alignment explanation
Indices: 17344942--17345017 Score: 86
Period size: 28 Copynumber: 2.7 Consensus size: 28
17344932 CATATGTGGA
* *
17344942 TAACCTACCAAAAGTGGATGTATACTTG
1 TAACCTACCAAAAGTAGATGAATACTTG
17344970 TAACCTACCACAAA-TAGATGAATACTT-
1 TAACCTACCA-AAAGTAGATGAATACTTG
17344997 TCAACAC-ACCAAAAGTAGATG
1 T-AAC-CTACCAAAAGTAGATG
17345018 GATGGATAAC
Statistics
Matches: 42, Mismatches: 2, Indels: 8
0.81 0.04 0.15
Matches are distributed among these distances:
27 4 0.10
28 34 0.81
29 4 0.10
ACGTcount: A:0.42, C:0.21, G:0.13, T:0.24
Consensus pattern (28 bp):
TAACCTACCAAAAGTAGATGAATACTTG
Found at i:17348764 original size:57 final size:57
Alignment explanation
Indices: 17348703--17348814 Score: 206
Period size: 57 Copynumber: 2.0 Consensus size: 57
17348693 ACTAAGAAGG
*
17348703 AAATTCCAACAACGTTATATGAGGATAATACTGCTTGCATAATATAGTTAAAGGAGA
1 AAATTCCAACAACGTTATATGAGGATAATACTGCTTGCATAACATAGTTAAAGGAGA
*
17348760 AAATTCCAACAACGTTATATGAGGATAATACTGCTTGCATAGCATAGTTAAAGGA
1 AAATTCCAACAACGTTATATGAGGATAATACTGCTTGCATAACATAGTTAAAGGA
17348815 AGGATATTTA
Statistics
Matches: 53, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
57 53 1.00
ACGTcount: A:0.41, C:0.13, G:0.18, T:0.28
Consensus pattern (57 bp):
AAATTCCAACAACGTTATATGAGGATAATACTGCTTGCATAACATAGTTAAAGGAGA
Found at i:17356108 original size:61 final size:62
Alignment explanation
Indices: 17356036--17356156 Score: 208
Period size: 62 Copynumber: 2.0 Consensus size: 62
17356026 CCTCACTTTC
17356036 TTTTAAGGCTTAGATAGAA-CTCTAAACAATACCTTTTGAAGGCTAAGGTATAACCTCCCTA
1 TTTTAAGGCTTAGATAGAACCTCTAAACAATACCTTTTGAAGGCTAAGGTATAACCTCCCTA
***
17356097 TTTTAAGGCTTAGATAGAACCTCTAATTTATACCTTTTGAAGGCTAAGGTATAACCTCCC
1 TTTTAAGGCTTAGATAGAACCTCTAAACAATACCTTTTGAAGGCTAAGGTATAACCTCCC
17356157 ATTCTCTCAA
Statistics
Matches: 56, Mismatches: 3, Indels: 1
0.93 0.05 0.02
Matches are distributed among these distances:
61 19 0.34
62 37 0.66
ACGTcount: A:0.32, C:0.20, G:0.15, T:0.33
Consensus pattern (62 bp):
TTTTAAGGCTTAGATAGAACCTCTAAACAATACCTTTTGAAGGCTAAGGTATAACCTCCCTA
Found at i:17356769 original size:19 final size:18
Alignment explanation
Indices: 17356731--17356769 Score: 51
Period size: 19 Copynumber: 2.1 Consensus size: 18
17356721 CCCTTTTTTT
*
17356731 TAATTAAAACAACTTTAA
1 TAATTAAAACAACTTAAA
*
17356749 TAATTCAAAACACCTTAAA
1 TAATT-AAAACAACTTAAA
17356768 TA
1 TA
17356770 CTTGATAAAA
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
18 5 0.28
19 13 0.72
ACGTcount: A:0.54, C:0.15, G:0.00, T:0.31
Consensus pattern (18 bp):
TAATTAAAACAACTTAAA
Found at i:17359975 original size:2 final size:2
Alignment explanation
Indices: 17359968--17359994 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
17359958 GGAATCTAGC
17359968 AG AG AG AG AG AG AG AG AG AG AG AG AG A
1 AG AG AG AG AG AG AG AG AG AG AG AG AG A
17359995 AAACTTGCAT
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 25 1.00
ACGTcount: A:0.52, C:0.00, G:0.48, T:0.00
Consensus pattern (2 bp):
AG
Found at i:17362615 original size:2 final size:2
Alignment explanation
Indices: 17362591--17362670 Score: 85
Period size: 2 Copynumber: 40.5 Consensus size: 2
17362581 CAACTTTGCC
*
17362591 AT AT AT A- AT A- AT AGT AT AA AT AT AT AT AT AT AT AT A- AT AT
1 AT AT AT AT AT AT AT A-T AT AT AT AT AT AT AT AT AT AT AT AT AT
* * *
17362631 AA AA AA ANT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT A-T AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
17362671 AAACAAAGGA
Statistics
Matches: 69, Mismatches: 4, Indels: 10
0.83 0.05 0.12
Matches are distributed among these distances:
1 3 0.04
2 63 0.91
3 3 0.04
ACGTcount: A:0.56, C:0.00, G:0.01, T:0.41
Consensus pattern (2 bp):
AT
Found at i:17377341 original size:36 final size:36
Alignment explanation
Indices: 17377283--17377355 Score: 94
Period size: 36 Copynumber: 2.0 Consensus size: 36
17377273 AGAGCTCATA
* *
17377283 ACGATAATAACTATATGTGGTGT-AGGAGTGCATATG
1 ACGATAATAACTATATGCGGTGTGA-GAGTGCACATG
* *
17377319 ACGATAATAGCTATGTGCGGTGTGAGAGTGCACATG
1 ACGATAATAACTATATGCGGTGTGAGAGTGCACATG
17377355 A
1 A
17377356 GCTGAGATGA
Statistics
Matches: 32, Mismatches: 4, Indels: 2
0.84 0.11 0.05
Matches are distributed among these distances:
36 31 0.97
37 1 0.03
ACGTcount: A:0.32, C:0.11, G:0.30, T:0.27
Consensus pattern (36 bp):
ACGATAATAACTATATGCGGTGTGAGAGTGCACATG
Found at i:17383495 original size:30 final size:29
Alignment explanation
Indices: 17383422--17383500 Score: 97
Period size: 30 Copynumber: 2.7 Consensus size: 29
17383412 AAAAAAAAAT
*
17383422 TTAAATAAATTTTTAT-ATTTTAATTACA
1 TTAAATAAATTTTTATAATTTTAATTAAA
* * *
17383450 TTCAATTAAACTTTTATAATTTTATTTAAA
1 TT-AAATAAATTTTTATAATTTTAATTAAA
17383480 TCTAAATAAATTTTTATAATT
1 T-TAAATAAATTTTTATAATT
17383501 AACAACCAAT
Statistics
Matches: 42, Mismatches: 6, Indels: 4
0.81 0.12 0.08
Matches are distributed among these distances:
28 2 0.05
29 12 0.29
30 27 0.64
31 1 0.02
ACGTcount: A:0.42, C:0.05, G:0.00, T:0.53
Consensus pattern (29 bp):
TTAAATAAATTTTTATAATTTTAATTAAA
Found at i:17384600 original size:6 final size:6
Alignment explanation
Indices: 17384586--17384641 Score: 58
Period size: 6 Copynumber: 9.3 Consensus size: 6
17384576 TACTCATCAA
* * * * * *
17384586 ATATGT ATATAT ATATGT ATATAC ATATGT ATATAT ACATAT ATATGT
1 ATATAT ATATAT ATATAT ATATAT ATATAT ATATAT ATATAT ATATAT
17384634 ATATAT AT
1 ATATAT AT
17384642 TCTGGTTTGG
Statistics
Matches: 39, Mismatches: 11, Indels: 0
0.78 0.22 0.00
Matches are distributed among these distances:
6 39 1.00
ACGTcount: A:0.43, C:0.04, G:0.07, T:0.46
Consensus pattern (6 bp):
ATATAT
Found at i:17384606 original size:8 final size:8
Alignment explanation
Indices: 17384586--17384641 Score: 58
Period size: 8 Copynumber: 7.0 Consensus size: 8
17384576 TACTCATCAA
*
17384586 ATATGTAT
1 ATATATAT
17384594 ATATATAT
1 ATATATAT
* *
17384602 GTATATAC
1 ATATATAT
*
17384610 ATATGTAT
1 ATATATAT
*
17384618 ATATACAT
1 ATATATAT
*
17384626 ATATATGT
1 ATATATAT
17384634 ATATATAT
1 ATATATAT
17384642 TCTGGTTTGG
Statistics
Matches: 37, Mismatches: 11, Indels: 0
0.77 0.23 0.00
Matches are distributed among these distances:
8 37 1.00
ACGTcount: A:0.43, C:0.04, G:0.07, T:0.46
Consensus pattern (8 bp):
ATATATAT
Found at i:17384606 original size:10 final size:10
Alignment explanation
Indices: 17384593--17384641 Score: 57
Period size: 10 Copynumber: 4.9 Consensus size: 10
17384583 CAAATATGTA
17384593 TATATATATG
1 TATATATATG
17384603 TATATACATATG
1 TATAT--ATATG
17384615 TATATATA--
1 TATATATATG
*
17384623 CATATATATG
1 TATATATATG
17384633 TATATATAT
1 TATATATAT
17384642 TCTGGTTTGG
Statistics
Matches: 33, Mismatches: 2, Indels: 8
0.77 0.05 0.19
Matches are distributed among these distances:
8 7 0.21
10 16 0.48
12 10 0.30
ACGTcount: A:0.43, C:0.04, G:0.06, T:0.47
Consensus pattern (10 bp):
TATATATATG
Found at i:17384641 original size:12 final size:12
Alignment explanation
Indices: 17384586--17384637 Score: 68
Period size: 12 Copynumber: 4.3 Consensus size: 12
17384576 TACTCATCAA
17384586 ATATGTATATAT
1 ATATGTATATAT
*
17384598 ATATGTATATAC
1 ATATGTATATAT
17384610 ATATGTATATAT
1 ATATGTATATAT
* * *
17384622 ACATATATATGT
1 ATATGTATATAT
17384634 ATAT
1 ATAT
17384638 ATATTCTGGT
Statistics
Matches: 34, Mismatches: 6, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
12 34 1.00
ACGTcount: A:0.42, C:0.04, G:0.08, T:0.46
Consensus pattern (12 bp):
ATATGTATATAT
Found at i:17389502 original size:24 final size:24
Alignment explanation
Indices: 17389451--17389504 Score: 65
Period size: 24 Copynumber: 2.2 Consensus size: 24
17389441 TTTGATTAAT
* *
17389451 AAATATTAATTTATTTATAATTAT
1 AAATATTAATTTATTTATAAATAA
*
17389475 AAATATTTATTTAATTTA-AAATAA
1 AAATATTAATTT-ATTTATAAATAA
17389499 AAATAT
1 AAATAT
17389505 AAAAATTAAT
Statistics
Matches: 26, Mismatches: 3, Indels: 2
0.84 0.10 0.06
Matches are distributed among these distances:
24 21 0.81
25 5 0.19
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (24 bp):
AAATATTAATTTATTTATAAATAA
Found at i:17390420 original size:28 final size:28
Alignment explanation
Indices: 17390386--17390571 Score: 264
Period size: 28 Copynumber: 6.6 Consensus size: 28
17390376 TTTTATCATT
17390386 CAGAAGTGGATGGATAATTTCAACCCAC
1 CAGAAGTGGATGGATAATTTCAACCCAC
*
17390414 CAGAAGTGGATGGATAATTTCAATCCAC
1 CAGAAGTGGATGGATAATTTCAACCCAC
*
17390442 CAGAAGTTGATGGATAATTTCAACCCAC
1 CAGAAGTGGATGGATAATTTCAACCCAC
*
17390470 CAGAAGTTGATGGATAATTTCAACCCAC
1 CAGAAGTGGATGGATAATTTCAACCCAC
* * *
17390498 CAGATGTGGATGGATAATTTTAATCCAC
1 CAGAAGTGGATGGATAATTTCAACCCAC
* * * *
17390526 CAGATGTGGATGAATACTTTTAACCCAC
1 CAGAAGTGGATGGATAATTTCAACCCAC
* *
17390554 TAGAAGTGGATGAATAAT
1 CAGAAGTGGATGGATAAT
17390572 GAAAATACAA
Statistics
Matches: 145, Mismatches: 13, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
28 145 1.00
ACGTcount: A:0.35, C:0.18, G:0.20, T:0.26
Consensus pattern (28 bp):
CAGAAGTGGATGGATAATTTCAACCCAC
Found at i:17394941 original size:12 final size:12
Alignment explanation
Indices: 17394921--17394959 Score: 51
Period size: 12 Copynumber: 3.2 Consensus size: 12
17394911 GATTTATTTC
* *
17394921 ATAACAAATATA
1 ATAAAAAATAAA
*
17394933 ATAAAAAATACA
1 ATAAAAAATAAA
17394945 ATAAAAAATAAA
1 ATAAAAAATAAA
17394957 ATA
1 ATA
17394960 TTATTTAAAA
Statistics
Matches: 24, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
12 24 1.00
ACGTcount: A:0.74, C:0.05, G:0.00, T:0.21
Consensus pattern (12 bp):
ATAAAAAATAAA
Found at i:17409981 original size:2 final size:2
Alignment explanation
Indices: 17409974--17410017 Score: 81
Period size: 2 Copynumber: 22.5 Consensus size: 2
17409964 GTTGTTCTAC
17409974 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT -T
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
17410015 AT A
1 AT A
17410018 NNNNNNNNNN
Statistics
Matches: 41, Mismatches: 0, Indels: 2
0.95 0.00 0.05
Matches are distributed among these distances:
1 1 0.02
2 40 0.98
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:17410862 original size:2 final size:2
Alignment explanation
Indices: 17410855--17410911 Score: 105
Period size: 2 Copynumber: 28.0 Consensus size: 2
17410845 CTTGCAAGAT
17410855 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
17410897 TA TA TA TA TA GTA TA
1 TA TA TA TA TA -TA TA
17410912 AAATAATTGT
Statistics
Matches: 54, Mismatches: 0, Indels: 2
0.96 0.00 0.04
Matches are distributed among these distances:
2 52 0.96
3 2 0.04
ACGTcount: A:0.49, C:0.00, G:0.02, T:0.49
Consensus pattern (2 bp):
TA
Found at i:17417996 original size:29 final size:28
Alignment explanation
Indices: 17417945--17417999 Score: 83
Period size: 29 Copynumber: 1.9 Consensus size: 28
17417935 TCAAGTACAC
* *
17417945 ATGTTGAAAAAAAATGTTGTTACATACT
1 ATGTTGAAAAAAAAAGTTATTACATACT
17417973 ATGTTGAAAAAAAAAAGTTATTACATA
1 ATGTTG-AAAAAAAAAGTTATTACATA
17418000 TTATATTTAA
Statistics
Matches: 24, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
28 6 0.25
29 18 0.75
ACGTcount: A:0.49, C:0.05, G:0.13, T:0.33
Consensus pattern (28 bp):
ATGTTGAAAAAAAAAGTTATTACATACT
Found at i:17421377 original size:24 final size:24
Alignment explanation
Indices: 17421319--17421370 Score: 74
Period size: 23 Copynumber: 2.3 Consensus size: 24
17421309 ATTATTTTAA
*
17421319 TTAATTTA-AT-AATTTAATATAT
1 TTAATTTATATAAAATTAATATAT
17421341 TTAATTTATATAAAATTAATA-AT
1 TTAATTTATATAAAATTAATATAT
17421364 TTAATTT
1 TTAATTT
17421371 CTAATAATAT
Statistics
Matches: 27, Mismatches: 1, Indels: 3
0.87 0.03 0.10
Matches are distributed among these distances:
22 8 0.30
23 11 0.41
24 8 0.30
ACGTcount: A:0.46, C:0.00, G:0.00, T:0.54
Consensus pattern (24 bp):
TTAATTTATATAAAATTAATATAT
Found at i:17421382 original size:24 final size:25
Alignment explanation
Indices: 17421325--17421382 Score: 77
Period size: 24 Copynumber: 2.4 Consensus size: 25
17421315 TTAATTAATT
17421325 TAATAAT-TTAATATATTTAATTTA
1 TAATAATATTAATATATTTAATTTA
* *
17421349 T-ATAAAATTAATA-ATTTAATTTC
1 TAATAATATTAATATATTTAATTTA
17421372 TAATAATATTA
1 TAATAATATTA
17421383 CTTATTTTAT
Statistics
Matches: 29, Mismatches: 3, Indels: 4
0.81 0.08 0.11
Matches are distributed among these distances:
23 14 0.48
24 15 0.52
ACGTcount: A:0.48, C:0.02, G:0.00, T:0.50
Consensus pattern (25 bp):
TAATAATATTAATATATTTAATTTA
Found at i:17421389 original size:24 final size:24
Alignment explanation
Indices: 17421307--17421389 Score: 71
Period size: 24 Copynumber: 3.4 Consensus size: 24
17421297 ACCAAAAAAA
*
17421307 TAATTATTTTAATTAATTTAATAAT-T
1 TAATTA-TTTAATT--TATAATAATAT
*
17421333 TAATATATTTAATTTAT-ATAAAAT
1 TAAT-TATTTAATTTATAATAATAT
* *
17421357 TAATAATTTAATTTCTAATAATAT
1 TAATTATTTAATTTATAATAATAT
*
17421381 TACTTATTT
1 TAATTATTT
17421390 TATATATTTT
Statistics
Matches: 47, Mismatches: 7, Indels: 8
0.76 0.11 0.13
Matches are distributed among these distances:
23 14 0.30
24 20 0.43
26 11 0.23
27 2 0.04
ACGTcount: A:0.43, C:0.02, G:0.00, T:0.54
Consensus pattern (24 bp):
TAATTATTTAATTTATAATAATAT
Found at i:17427915 original size:4 final size:4
Alignment explanation
Indices: 17427906--17427956 Score: 68
Period size: 4 Copynumber: 13.0 Consensus size: 4
17427896 CCACTAATCG
* * *
17427906 AATA AATA AATT TATA AA-A AATA AAAA AATA AATA AATA AATA AATA
1 AATA AATA AATA AATA AATA AATA AATA AATA AATA AATA AATA AATA
17427953 AATA
1 AATA
17427957 TATATATATA
Statistics
Matches: 40, Mismatches: 6, Indels: 2
0.83 0.12 0.04
Matches are distributed among these distances:
3 3 0.08
4 37 0.93
ACGTcount: A:0.75, C:0.00, G:0.00, T:0.25
Consensus pattern (4 bp):
AATA
Found at i:17430362 original size:59 final size:59
Alignment explanation
Indices: 17430281--17430810 Score: 808
Period size: 59 Copynumber: 9.0 Consensus size: 59
17430271 AATTCGATTA
* * * *
17430281 AAATTCCTAGACTTCATCTAGGCTCGACCTATCTCACAACAGGTTCAATTTAAAAATTC
1 AAATTCCTAAACTTAATTTAGGCTCGACCTATCTCACAACAGGTTCGATTTAAAAATTC
*
17430340 AAATTTCTAAACTTAATTTAGGCTCGACCTATCTCACAACAGGTTCGATTTAAAAATTC
1 AAATTCCTAAACTTAATTTAGGCTCGACCTATCTCACAACAGGTTCGATTTAAAAATTC
* * * *
17430399 AAATTTCTAAACTTAATTTAGGCTCGATCTATCTCACAACAGGTTTGATTTAAAAACTC
1 AAATTCCTAAACTTAATTTAGGCTCGACCTATCTCACAACAGGTTCGATTTAAAAATTC
* *
17430458 AAATTCCTAAACTTAATTTAGGCTCGACCTATCTTACAACAGGTTCGATTTAAAAACTC
1 AAATTCCTAAACTTAATTTAGGCTCGACCTATCTCACAACAGGTTCGATTTAAAAATTC
* * *
17430517 AAATTCCTAAACTTAATTTAGGCTCGACCCATCTCATAACACGTTCGATTTAAAAATTC
1 AAATTCCTAAACTTAATTTAGGCTCGACCTATCTCACAACAGGTTCGATTTAAAAATTC
*
17430576 AAATTCCTAAACTTAATTTAGGCTCGACCTATCTCACAACAGGTTCGATTTAAAAATTA
1 AAATTCCTAAACTTAATTTAGGCTCGACCTATCTCACAACAGGTTCGATTTAAAAATTC
* * * * *
17430635 AAATTCTTAGACTTAATCTAGGCTCGACCTATCTCACAACAGGTTTGATTTAAAAATTG
1 AAATTCCTAAACTTAATTTAGGCTCGACCTATCTCACAACAGGTTCGATTTAAAAATTC
* * * *
17430694 AAATTCCTAAACTTAATCTAGGCTCGACCTATCTCATAATAGGTTCGATTTAAAAATTG
1 AAATTCCTAAACTTAATTTAGGCTCGACCTATCTCACAACAGGTTCGATTTAAAAATTC
* * *
17430753 AAATTCTTAGACTTAAATCTAGGCTCGACCTATCTCACAACAGGTTCGATTTAAAAAT
1 AAATTCCTAAACTT-AATTTAGGCTCGACCTATCTCACAACAGGTTCGATTTAAAAAT
17430811 CTAATGCCAA
Statistics
Matches: 435, Mismatches: 35, Indels: 1
0.92 0.07 0.00
Matches are distributed among these distances:
59 394 0.91
60 41 0.09
ACGTcount: A:0.35, C:0.21, G:0.11, T:0.33
Consensus pattern (59 bp):
AAATTCCTAAACTTAATTTAGGCTCGACCTATCTCACAACAGGTTCGATTTAAAAATTC
Found at i:17440441 original size:28 final size:28
Alignment explanation
Indices: 17440401--17440455 Score: 67
Period size: 28 Copynumber: 2.0 Consensus size: 28
17440391 ATATTACAAA
*
17440401 CAAATAAATTACA-CTAAACATAAATAAG
1 CAAATAAACTACATC-AAACATAAATAAG
* *
17440429 CAAATACACTACATCAAATATAAATAA
1 CAAATAAACTACATCAAACATAAATAA
17440456 AATTTTAATC
Statistics
Matches: 23, Mismatches: 3, Indels: 2
0.82 0.11 0.07
Matches are distributed among these distances:
28 22 0.96
29 1 0.04
ACGTcount: A:0.60, C:0.16, G:0.02, T:0.22
Consensus pattern (28 bp):
CAAATAAACTACATCAAACATAAATAAG
Found at i:17444364 original size:14 final size:15
Alignment explanation
Indices: 17444344--17444380 Score: 51
Period size: 14 Copynumber: 2.6 Consensus size: 15
17444334 GGGGGTTAGG
17444344 CGATTGCCT-ATTGC
1 CGATTGCCTGATTGC
*
17444358 TGATTG-CTGATTGC
1 CGATTGCCTGATTGC
17444372 CGATTGCCT
1 CGATTGCCT
17444381 CTAAGCTTAG
Statistics
Matches: 19, Mismatches: 2, Indels: 3
0.79 0.08 0.12
Matches are distributed among these distances:
13 2 0.11
14 15 0.79
15 2 0.11
ACGTcount: A:0.14, C:0.24, G:0.24, T:0.38
Consensus pattern (15 bp):
CGATTGCCTGATTGC
Found at i:17447362 original size:15 final size:15
Alignment explanation
Indices: 17447342--17447384 Score: 52
Period size: 15 Copynumber: 2.9 Consensus size: 15
17447332 TTTCTATTTT
17447342 TATTTTATATTATTA
1 TATTTTATATTATTA
* *
17447357 TATTTTTTATTGTTA
1 TATTTTATATTATTA
*
17447372 TTTTTTAT-TTATT
1 TATTTTATATTATT
17447385 TTTTGATCTT
Statistics
Matches: 23, Mismatches: 5, Indels: 1
0.79 0.17 0.03
Matches are distributed among these distances:
14 4 0.17
15 19 0.83
ACGTcount: A:0.23, C:0.00, G:0.02, T:0.74
Consensus pattern (15 bp):
TATTTTATATTATTA
Found at i:17447379 original size:22 final size:23
Alignment explanation
Indices: 17447338--17447402 Score: 61
Period size: 22 Copynumber: 3.0 Consensus size: 23
17447328 NNTATTTCTA
*
17447338 TTTTTATT-TTATATTATTATAT
1 TTTTTATTGTTATATTTTTATAT
17447360 TTTTTATTGTTAT-TTTTTAT-T
1 TTTTTATTGTTATATTTTTATAT
*
17447381 TATTTT-TTG--ATCTTTTTATAT
1 T-TTTTATTGTTATATTTTTATAT
17447402 T
1 T
17447403 CTAAGTTTCT
Statistics
Matches: 38, Mismatches: 1, Indels: 9
0.79 0.02 0.19
Matches are distributed among these distances:
19 2 0.05
20 7 0.18
21 7 0.18
22 18 0.47
23 4 0.11
ACGTcount: A:0.20, C:0.02, G:0.03, T:0.75
Consensus pattern (23 bp):
TTTTTATTGTTATATTTTTATAT
Found at i:17447559 original size:10 final size:9
Alignment explanation
Indices: 17447533--17447581 Score: 53
Period size: 9 Copynumber: 4.9 Consensus size: 9
17447523 ATTTTTATTT
17447533 TATTTATTTA
1 TATTT-TTTA
17447543 TTATTTTCTTA
1 -TATTTT-TTA
17447554 TATTTTTTA
1 TATTTTTTA
17447563 TATTTTTTA
1 TATTTTTTA
17447572 CTATTATTTT
1 -TATT-TTTT
17447582 TTTGTAGTAA
Statistics
Matches: 35, Mismatches: 0, Indels: 6
0.85 0.00 0.15
Matches are distributed among these distances:
9 12 0.34
10 11 0.31
11 12 0.34
ACGTcount: A:0.22, C:0.04, G:0.00, T:0.73
Consensus pattern (9 bp):
TATTTTTTA
Found at i:17447566 original size:19 final size:20
Alignment explanation
Indices: 17447533--17447581 Score: 57
Period size: 19 Copynumber: 2.4 Consensus size: 20
17447523 ATTTTTATTT
17447533 TATTTATTTATTATTTTCTTA-
1 TATTT-TTTATTATTTT-TTAC
17447554 TATTTTTTA-TATTTTTTAC
1 TATTTTTTATTATTTTTTAC
17447573 TATTATTTT
1 TATT-TTTT
17447582 TTTGTAGTAA
Statistics
Matches: 26, Mismatches: 0, Indels: 5
0.84 0.00 0.16
Matches are distributed among these distances:
18 3 0.12
19 10 0.38
20 8 0.31
21 5 0.19
ACGTcount: A:0.22, C:0.04, G:0.00, T:0.73
Consensus pattern (20 bp):
TATTTTTTATTATTTTTTAC
Found at i:17447748 original size:19 final size:19
Alignment explanation
Indices: 17447724--17447761 Score: 76
Period size: 19 Copynumber: 2.0 Consensus size: 19
17447714 GTCCCAACCG
17447724 ATAATCCCATTATTGGTAT
1 ATAATCCCATTATTGGTAT
17447743 ATAATCCCATTATTGGTAT
1 ATAATCCCATTATTGGTAT
17447762 TAAATTAAAC
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 19 1.00
ACGTcount: A:0.32, C:0.16, G:0.11, T:0.42
Consensus pattern (19 bp):
ATAATCCCATTATTGGTAT
Found at i:17449024 original size:14 final size:14
Alignment explanation
Indices: 17449005--17449031 Score: 54
Period size: 14 Copynumber: 1.9 Consensus size: 14
17448995 TCTGTAATGA
17449005 TTTTTTGGTTTTTC
1 TTTTTTGGTTTTTC
17449019 TTTTTTGGTTTTT
1 TTTTTTGGTTTTT
17449032 TTGGTTTTTT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 13 1.00
ACGTcount: A:0.00, C:0.04, G:0.15, T:0.81
Consensus pattern (14 bp):
TTTTTTGGTTTTTC
Found at i:17449048 original size:23 final size:23
Alignment explanation
Indices: 17449005--17449048 Score: 54
Period size: 23 Copynumber: 1.9 Consensus size: 23
17448995 TCTGTAATGA
**
17449005 TTTTTTGGTTTTTCTTTTTTGGT
1 TTTTTTGGTTTTTCTGATTTGGT
17449028 TTTTTTGGTTTTT-TGGATTTG
1 TTTTTTGGTTTTTCT-GATTTG
17449049 ATTGCCGATT
Statistics
Matches: 18, Mismatches: 2, Indels: 2
0.82 0.09 0.09
Matches are distributed among these distances:
22 1 0.06
23 17 0.94
ACGTcount: A:0.02, C:0.02, G:0.20, T:0.75
Consensus pattern (23 bp):
TTTTTTGGTTTTTCTGATTTGGT
Found at i:17449176 original size:22 final size:22
Alignment explanation
Indices: 17449152--17449193 Score: 68
Period size: 21 Copynumber: 2.0 Consensus size: 22
17449142 TAAAACAATT
*
17449152 TTTTTTTGTTTTG-AATCTCCG
1 TTTTCTTGTTTTGAAATCTCCG
17449173 TTTTCTTGTTTTGAAATCTCC
1 TTTTCTTGTTTTGAAATCTCC
17449194 CTTCTCCAGA
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
21 12 0.63
22 7 0.37
ACGTcount: A:0.12, C:0.17, G:0.12, T:0.60
Consensus pattern (22 bp):
TTTTCTTGTTTTGAAATCTCCG
Found at i:17449427 original size:14 final size:14
Alignment explanation
Indices: 17449408--17449434 Score: 54
Period size: 14 Copynumber: 1.9 Consensus size: 14
17449398 TTAGAATATG
17449408 TTTTATTTTTATTT
1 TTTTATTTTTATTT
17449422 TTTTATTTTTATT
1 TTTTATTTTTATT
17449435 AGATTTATTT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 13 1.00
ACGTcount: A:0.15, C:0.00, G:0.00, T:0.85
Consensus pattern (14 bp):
TTTTATTTTTATTT
Found at i:17451710 original size:18 final size:18
Alignment explanation
Indices: 17451687--17451721 Score: 61
Period size: 18 Copynumber: 1.9 Consensus size: 18
17451677 GGTCTGGGTT
17451687 TGGAAAAAAGAAAAAATA
1 TGGAAAAAAGAAAAAATA
*
17451705 TGGAAAAGAGAAAAAAT
1 TGGAAAAAAGAAAAAAT
17451722 CTAGAAAATG
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
18 16 1.00
ACGTcount: A:0.69, C:0.00, G:0.20, T:0.11
Consensus pattern (18 bp):
TGGAAAAAAGAAAAAATA
Found at i:17451734 original size:17 final size:17
Alignment explanation
Indices: 17451691--17451739 Score: 62
Period size: 18 Copynumber: 2.8 Consensus size: 17
17451681 TGGGTTTGGA
* *
17451691 AAAAAGAAAAAATATGG
1 AAAAAGAAAAAATCTAG
17451708 AAAAGAGAAAAAATCTAG
1 AAAA-AGAAAAAATCTAG
*
17451726 AAAATGAAAAAATC
1 AAAAAGAAAAAATC
17451740 CTGTGTTTGG
Statistics
Matches: 28, Mismatches: 3, Indels: 2
0.85 0.09 0.06
Matches are distributed among these distances:
17 13 0.46
18 15 0.54
ACGTcount: A:0.69, C:0.04, G:0.14, T:0.12
Consensus pattern (17 bp):
AAAAAGAAAAAATCTAG
Found at i:17460031 original size:2 final size:2
Alignment explanation
Indices: 17460026--17460055 Score: 60
Period size: 2 Copynumber: 15.0 Consensus size: 2
17460016 GCGCACGTGC
17460026 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
17460056 GATGATTTTG
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 28 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:17461466 original size:2 final size:2
Alignment explanation
Indices: 17461451--17461483 Score: 50
Period size: 2 Copynumber: 16.5 Consensus size: 2
17461441 GTAAATTACA
17461451 AT AT AT AGT A- AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT A-T AT AT AT AT AT AT AT AT AT AT AT AT A
17461484 GTGGAAAAAA
Statistics
Matches: 29, Mismatches: 0, Indels: 4
0.88 0.00 0.12
Matches are distributed among these distances:
1 1 0.03
2 26 0.90
3 2 0.07
ACGTcount: A:0.52, C:0.00, G:0.03, T:0.45
Consensus pattern (2 bp):
AT
Found at i:17463528 original size:25 final size:25
Alignment explanation
Indices: 17463484--17463544 Score: 70
Period size: 25 Copynumber: 2.4 Consensus size: 25
17463474 GATTCTTCTA
*
17463484 GAGAGAAGAACATTGATGAAATAAT
1 GAGAGAAGAACATTGATGAAATAAC
* *
17463509 GAGAGAAGAGCATT-AGTGAAGTAAC
1 GAGAGAAGAACATTGA-TGAAATAAC
*
17463534 GGGAGAAGAAC
1 GAGAGAAGAAC
17463545 TTTAATGCAG
Statistics
Matches: 30, Mismatches: 5, Indels: 2
0.81 0.14 0.05
Matches are distributed among these distances:
24 1 0.03
25 29 0.97
ACGTcount: A:0.48, C:0.07, G:0.31, T:0.15
Consensus pattern (25 bp):
GAGAGAAGAACATTGATGAAATAAC
Found at i:17467959 original size:53 final size:54
Alignment explanation
Indices: 17467893--17468015 Score: 130
Period size: 53 Copynumber: 2.3 Consensus size: 54
17467883 CTCTAAGATT
* * **
17467893 TTTCTTTTTTCTTTCTCCT-TCTTCTTCTTCTCTT-TTT-TTTCCCTCTTTCTCCC
1 TTTCCTTTCTCTTTCTCCTGTCGACTTCTTCT-TTCTTTCTTTCCCTCTTTCT-CC
**
17467946 TTTCCTTTCTCTTTC-CCTGTCGACTTCTTCTTTCTTTCTTTCTTTCTTTCTCC
1 TTTCCTTTCTCTTTCTCCTGTCGACTTCTTCTTTCTTTCTTTCCCTCTTTCTCC
17467999 -TTCTCTTTCTCTTTCTC
1 TTTC-CTTTCTCTTTCTC
17468016 TCCTTTCTCC
Statistics
Matches: 59, Mismatches: 6, Indels: 9
0.80 0.08 0.12
Matches are distributed among these distances:
52 8 0.14
53 39 0.66
54 12 0.20
ACGTcount: A:0.01, C:0.34, G:0.02, T:0.63
Consensus pattern (54 bp):
TTTCCTTTCTCTTTCTCCTGTCGACTTCTTCTTTCTTTCTTTCCCTCTTTCTCC
Found at i:17468085 original size:16 final size:15
Alignment explanation
Indices: 17468043--17468088 Score: 51
Period size: 16 Copynumber: 3.0 Consensus size: 15
17468033 AGTCGCACCA
17468043 TTCTTC-TCTTCTCTC
1 TTCTTCTTC-TCTCTC
17468058 TTCTTCTTCTCTCTC
1 TTCTTCTTCTCTCTC
17468073 ATTCCTT-TTCTCTCTC
1 -TT-CTTCTTCTCTCTC
17468089 CCAACCGATG
Statistics
Matches: 28, Mismatches: 0, Indels: 5
0.85 0.00 0.15
Matches are distributed among these distances:
15 12 0.43
16 13 0.46
17 3 0.11
ACGTcount: A:0.02, C:0.39, G:0.00, T:0.59
Consensus pattern (15 bp):
TTCTTCTTCTCTCTC
Found at i:17468531 original size:7 final size:7
Alignment explanation
Indices: 17468519--17468559 Score: 57
Period size: 7 Copynumber: 5.9 Consensus size: 7
17468509 TCTCTGTCTT
17468519 TTTTTTA
1 TTTTTTA
17468526 TTTTTTA
1 TTTTTTA
*
17468533 -ATTTTA
1 TTTTTTA
17468539 TTTTTTA
1 TTTTTTA
17468546 TTTTTTA
1 TTTTTTA
17468553 TTATTTT
1 TT-TTTT
17468560 TATATTATTA
Statistics
Matches: 30, Mismatches: 2, Indels: 3
0.86 0.06 0.09
Matches are distributed among these distances:
6 5 0.17
7 21 0.70
8 4 0.13
ACGTcount: A:0.17, C:0.00, G:0.00, T:0.83
Consensus pattern (7 bp):
TTTTTTA
Found at i:17468550 original size:13 final size:13
Alignment explanation
Indices: 17468520--17468550 Score: 53
Period size: 13 Copynumber: 2.4 Consensus size: 13
17468510 CTCTGTCTTT
17468520 TTTTTATTTTTTA
1 TTTTTATTTTTTA
*
17468533 ATTTTATTTTTTA
1 TTTTTATTTTTTA
17468546 TTTTT
1 TTTTT
17468551 TATTATTTTT
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
13 16 1.00
ACGTcount: A:0.16, C:0.00, G:0.00, T:0.84
Consensus pattern (13 bp):
TTTTTATTTTTTA
Found at i:17468565 original size:8 final size:8
Alignment explanation
Indices: 17468518--17468571 Score: 51
Period size: 7 Copynumber: 7.0 Consensus size: 8
17468508 CTCTCTGTCT
*
17468518 TTTTTTTA
1 TTTTTATA
17468526 TTTTT-TA
1 TTTTTATA
*
17468533 ATTTTAT-
1 TTTTTATA
17468540 TTTTTAT-
1 TTTTTATA
17468547 TTTTTATTA
1 TTTTTA-TA
17468556 TTTTTATA
1 TTTTTATA
*
17468564 TTATTATA
1 TTTTTATA
17468572 AAAAATGGTG
Statistics
Matches: 40, Mismatches: 3, Indels: 6
0.82 0.06 0.12
Matches are distributed among these distances:
7 18 0.45
8 16 0.40
9 6 0.15
ACGTcount: A:0.22, C:0.00, G:0.00, T:0.78
Consensus pattern (8 bp):
TTTTTATA
Found at i:17468801 original size:24 final size:24
Alignment explanation
Indices: 17468762--17468823 Score: 65
Period size: 24 Copynumber: 2.6 Consensus size: 24
17468752 AATGATAAAG
*
17468762 ATTTAAAACTAAATATTAA-AAAAA
1 ATTTAAAAATAAATA-TAAGAAAAA
* *
17468786 ATTTAAAAATACATATAAGATAAA
1 ATTTAAAAATAAATATAAGAAAAA
*
17468810 A-TTAAAAATCAATA
1 ATTTAAAAATAAATA
17468824 ATTTTTTCGA
Statistics
Matches: 32, Mismatches: 5, Indels: 3
0.80 0.12 0.08
Matches are distributed among these distances:
23 14 0.44
24 18 0.56
ACGTcount: A:0.65, C:0.05, G:0.02, T:0.29
Consensus pattern (24 bp):
ATTTAAAAATAAATATAAGAAAAA
Found at i:17471560 original size:356 final size:349
Alignment explanation
Indices: 17470948--17471592 Score: 868
Period size: 356 Copynumber: 1.8 Consensus size: 349
17470938 GAAGACATAT
* * * ** *
17470948 ATATTGCATGTATTTTTACAATATTGAGAAACCGACCAAGCAGGGAGGATCGAGAAACTAGGCTC
1 ATATTGCAGGTATTTTTACAATATTGAGAAACCAACCAAGCAGAGAGGAAAGAGAAACTAGACTC
* * * *
17471013 ATAATCCAACACAAACCCAAAGACCTTGAAAGCCAACCAAAACTTGATTGACATATTCGGTTCTC
66 ACAATCCAACACAAACCCAAAGACCTTGAAAACCAACCAAAACCTGATTGACATATTCGGTCCTC
* * *
17471078 TAATGTTTGTCATAGGACTAGGGTTGAGCGAAGCAAAAGGGGATAAAAATGAGATTGATAGGCCA
131 TAATGTTTGTCATAGGACTAGGGTTGAGCAAAACAAAAGGGGAAAAAAATGAGATTGATAGGCCA
*
17471143 TCGGCAAGCACCCCATATATTTCTATTTCAAGGCAATTCTATTAGGGTTCAGGGGTGATGAGAGA
196 TCGGCAAGCACCCCA-ATATTTCTATTTCAAGGCAATTCTATAAGGGTTCAGGGGTGATGAGAGA
17471208 GAAATAAGGCAAACATGTATATGTATAAGCTAATGACTTTGCTGGATTATGAGTCCAGTTCCCCC
260 GAAATAAGGCAAACATGTAT-T-TATAAGCTAATGACTTTGCTGGATTATGAGTCCAGTTCCCCC
17471273 TTCATTTGCTCCCACTCAATCGAAGAC
323 TTCATTTGCTCCCACTCAATCGAAGAC
*
17471300 ATATTGCAGGTATTTTTCACAATTATATTGTGAAACCAACCAAGCAGAGAGGAAAGAGAAACTAG
1 ATATTGCAGGTATTTTT-AC-A--ATATTGAGAAACCAACCAAGCAGAGAGGAAAGAGAAACTAG
* * **
17471365 ACTCACAATCCAACA-AAAGCACTAGAGATGTTGAAAACCAACCAAAACCTGATTGACATATT-G
62 ACTCACAATCCAACACAAA-C-CCAAAGACCTTGAAAACCAACCAAAACCTGATTGACATATTCG
* *
17471428 GATCCTCT-ATGTTTGTCATATAGGGCTAGGGTTGGGCAAAACAAAA-GGGAAAAAAATTGAGAT
125 G-TCCTCTAATGTTTGTC--ATAGGACTAGGGTTGAGCAAAACAAAAGGGGAAAAAAA-TGAGAT
** * * * *
17471491 TGATAGGCTTTTGGCAAGCACCCC-ATATTTCTATTTCAAGGGAATTCTATAAGGGTTTAGGGTT
186 TGATAGGCCATCGGCAAGCACCCCAATATTTCTATTTCAAGGCAATTCTATAAGGGTTCAGGGGT
** *
17471555 GATGAGAGAGCCATGAGGCAAACATGTATTTATAAGCT
251 GATGAGAGAGAAATAAGGCAAACATGTATTTATAAGCT
17471593 GCCAAGTCTA
Statistics
Matches: 253, Mismatches: 30, Indels: 18
0.84 0.10 0.06
Matches are distributed among these distances:
352 16 0.06
353 2 0.01
354 9 0.04
355 4 0.02
356 123 0.49
357 49 0.19
358 50 0.20
ACGTcount: A:0.35, C:0.18, G:0.21, T:0.26
Consensus pattern (349 bp):
ATATTGCAGGTATTTTTACAATATTGAGAAACCAACCAAGCAGAGAGGAAAGAGAAACTAGACTC
ACAATCCAACACAAACCCAAAGACCTTGAAAACCAACCAAAACCTGATTGACATATTCGGTCCTC
TAATGTTTGTCATAGGACTAGGGTTGAGCAAAACAAAAGGGGAAAAAAATGAGATTGATAGGCCA
TCGGCAAGCACCCCAATATTTCTATTTCAAGGCAATTCTATAAGGGTTCAGGGGTGATGAGAGAG
AAATAAGGCAAACATGTATTTATAAGCTAATGACTTTGCTGGATTATGAGTCCAGTTCCCCCTTC
ATTTGCTCCCACTCAATCGAAGAC
Found at i:17479345 original size:23 final size:23
Alignment explanation
Indices: 17479319--17479364 Score: 74
Period size: 23 Copynumber: 2.0 Consensus size: 23
17479309 TAGAATAACA
*
17479319 ATTCCTAATTCTATTAGGATAAG
1 ATTCCTAATTATATTAGGATAAG
*
17479342 ATTCTTAATTATATTAGGATAAG
1 ATTCCTAATTATATTAGGATAAG
17479365 GTTATTGTAT
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
23 21 1.00
ACGTcount: A:0.37, C:0.09, G:0.13, T:0.41
Consensus pattern (23 bp):
ATTCCTAATTATATTAGGATAAG
Found at i:17482708 original size:23 final size:23
Alignment explanation
Indices: 17482682--17482730 Score: 89
Period size: 23 Copynumber: 2.1 Consensus size: 23
17482672 TAGAATAACA
*
17482682 ATTCCTAATTCTATTAGGATAAG
1 ATTCCTAATTATATTAGGATAAG
17482705 ATTCCTAATTATATTAGGATAAG
1 ATTCCTAATTATATTAGGATAAG
17482728 ATT
1 ATT
17482731 ATTGTATTTG
Statistics
Matches: 25, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
23 25 1.00
ACGTcount: A:0.37, C:0.10, G:0.12, T:0.41
Consensus pattern (23 bp):
ATTCCTAATTATATTAGGATAAG
Found at i:17485301 original size:10 final size:10
Alignment explanation
Indices: 17485286--17485326 Score: 55
Period size: 10 Copynumber: 4.1 Consensus size: 10
17485276 TTGCAACATG
*
17485286 ATATGTGTAT
1 ATATGTATAT
17485296 ATATGTATAT
1 ATATGTATAT
*
17485306 ATATATATAT
1 ATATGTATAT
*
17485316 ATATATATAT
1 ATATGTATAT
17485326 A
1 A
17485327 GATAGATAGA
Statistics
Matches: 29, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
10 29 1.00
ACGTcount: A:0.44, C:0.00, G:0.07, T:0.49
Consensus pattern (10 bp):
ATATGTATAT
Found at i:17485306 original size:2 final size:2
Alignment explanation
Indices: 17485293--17485326 Score: 59
Period size: 2 Copynumber: 17.0 Consensus size: 2
17485283 ATGATATGTG
*
17485293 TA TA TA TG TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
17485327 GATAGATAGA
Statistics
Matches: 30, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
2 30 1.00
ACGTcount: A:0.47, C:0.00, G:0.03, T:0.50
Consensus pattern (2 bp):
TA
Found at i:17493376 original size:2 final size:2
Alignment explanation
Indices: 17493371--17493396 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
17493361 ATATAGTGGT
17493371 TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA
17493397 AATACACATT
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 24 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:17496820 original size:151 final size:151
Alignment explanation
Indices: 17496546--17496844 Score: 535
Period size: 151 Copynumber: 2.0 Consensus size: 151
17496536 CAGGTGCAAC
* *
17496546 TTATGTCCATAGTTTGTATTTATACTTTTATATTCTTAATTTCAGAAAGAAAAAATACTTGATAG
1 TTATGTCCATAGTTTGTATTTATACTTCTATATTCTTAATTTCAAAAAGAAAAAATACTTGATAG
*
17496611 GTTAAACTAGTTTTCCTATGTATTTAAGATGCTTGACTTTGAAATTATGAACGTTTCAAACAAGT
66 GTTAAACTAGTTTTCCTATGTATTTAAGAAGCTTGACTTTGAAATTATGAACGTTTCAAACAAGT
17496676 TTTATATATTAGTACATAACT
131 TTTATATATTAGTACATAACT
* * * *
17496697 TTATGTCCATGGTTTGTATTTATACTTCTATATTCTTAATTTCAAAAAGGAAAAATATTTGGTAG
1 TTATGTCCATAGTTTGTATTTATACTTCTATATTCTTAATTTCAAAAAGAAAAAATACTTGATAG
17496762 GTTAAACTAGTTTTCCTATGTATTTAAGAAGCTTGACTTTGAAATTATGAACGTTTCAAACAAGT
66 GTTAAACTAGTTTTCCTATGTATTTAAGAAGCTTGACTTTGAAATTATGAACGTTTCAAACAAGT
17496827 TTTATATATTAGTACATA
131 TTTATATATTAGTACATA
17496845 GTGGGATGTA
Statistics
Matches: 141, Mismatches: 7, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
151 141 1.00
ACGTcount: A:0.34, C:0.10, G:0.13, T:0.43
Consensus pattern (151 bp):
TTATGTCCATAGTTTGTATTTATACTTCTATATTCTTAATTTCAAAAAGAAAAAATACTTGATAG
GTTAAACTAGTTTTCCTATGTATTTAAGAAGCTTGACTTTGAAATTATGAACGTTTCAAACAAGT
TTTATATATTAGTACATAACT
Found at i:17498731 original size:17 final size:17
Alignment explanation
Indices: 17498709--17498744 Score: 54
Period size: 17 Copynumber: 2.1 Consensus size: 17
17498699 AACAAACTTT
17498709 ACTTTAACTATGACACC
1 ACTTTAACTATGACACC
* *
17498726 ACTTTAATTATGATACC
1 ACTTTAACTATGACACC
17498743 AC
1 AC
17498745 CCAAAAAAAT
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
17 17 1.00
ACGTcount: A:0.36, C:0.25, G:0.06, T:0.33
Consensus pattern (17 bp):
ACTTTAACTATGACACC
Found at i:17504653 original size:29 final size:30
Alignment explanation
Indices: 17504597--17504654 Score: 82
Period size: 30 Copynumber: 2.0 Consensus size: 30
17504587 GTGGAGTAAA
* *
17504597 TTTTCCAAAATTACACTTTTTGCCCCAAAC
1 TTTTCAAAAATTACACTTTTTACCCCAAAC
*
17504627 TTTTCAAAAATTACA-TTTTTACTCCAAA
1 TTTTCAAAAATTACACTTTTTACCCCAAA
17504655 AATTAAAAAT
Statistics
Matches: 25, Mismatches: 3, Indels: 1
0.86 0.10 0.03
Matches are distributed among these distances:
29 11 0.44
30 14 0.56
ACGTcount: A:0.34, C:0.24, G:0.02, T:0.40
Consensus pattern (30 bp):
TTTTCAAAAATTACACTTTTTACCCCAAAC
Found at i:17505679 original size:21 final size:20
Alignment explanation
Indices: 17505654--17505703 Score: 55
Period size: 21 Copynumber: 2.4 Consensus size: 20
17505644 GATTTCTCTG
*
17505654 AAGATCCTCAAACTGCATCT
1 AAGATCCTCAAACTACATCT
* *
17505674 AGAGATTCTCAAGCTACATCT
1 A-AGATCCTCAAACTACATCT
17505695 AAGGATCCT
1 AA-GATCCT
17505704 TAAGATACAA
Statistics
Matches: 24, Mismatches: 4, Indels: 3
0.77 0.13 0.10
Matches are distributed among these distances:
20 2 0.08
21 22 0.92
ACGTcount: A:0.34, C:0.26, G:0.14, T:0.26
Consensus pattern (20 bp):
AAGATCCTCAAACTACATCT
Found at i:17511407 original size:15 final size:15
Alignment explanation
Indices: 17511396--17511481 Score: 77
Period size: 15 Copynumber: 5.7 Consensus size: 15
17511386 ACATTACTGG
*
17511396 CTAAGGTGTTACTAT
1 CTAAGGAGTTACTAT
*
17511411 CTAAGGCAG-TACTAG
1 CTAAGG-AGTTACTAT
*
17511426 CTAAGGTGTTACTAT
1 CTAAGGAGTTACTAT
**
17511441 CTAAGGCAG-TACTGC
1 CTAAGG-AGTTACTAT
*
17511456 CTAAGGAGTTACTGT
1 CTAAGGAGTTACTAT
*
17511471 CTAAGGCGTTA
1 CTAAGGAGTTA
17511482 TTACCCACAG
Statistics
Matches: 58, Mismatches: 9, Indels: 8
0.77 0.12 0.11
Matches are distributed among these distances:
14 3 0.05
15 53 0.91
16 2 0.03
ACGTcount: A:0.28, C:0.17, G:0.24, T:0.30
Consensus pattern (15 bp):
CTAAGGAGTTACTAT
Found at i:17511408 original size:30 final size:30
Alignment explanation
Indices: 17511372--17511477 Score: 140
Period size: 30 Copynumber: 3.5 Consensus size: 30
17511362 GATAGTAACA
* ** *
17511372 TGTTACTACCTAAAACATTACTGGCTAAGG
1 TGTTACTATCTAAGGCAGTACTGGCTAAGG
*
17511402 TGTTACTATCTAAGGCAGTACTAGCTAAGG
1 TGTTACTATCTAAGGCAGTACTGGCTAAGG
*
17511432 TGTTACTATCTAAGGCAGTACTGCCTAAGG
1 TGTTACTATCTAAGGCAGTACTGGCTAAGG
* *
17511462 AGTTACTGTCTAAGGC
1 TGTTACTATCTAAGGC
17511478 GTTATTACCC
Statistics
Matches: 67, Mismatches: 9, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
30 67 1.00
ACGTcount: A:0.29, C:0.19, G:0.22, T:0.30
Consensus pattern (30 bp):
TGTTACTATCTAAGGCAGTACTGGCTAAGG
Found at i:17511733 original size:35 final size:35
Alignment explanation
Indices: 17511681--17511781 Score: 123
Period size: 35 Copynumber: 2.9 Consensus size: 35
17511671 AACTGCCATT
*
17511681 ACAAGTGAAG-TACTATTTCACGTAGAATAATTAGA
1 ACAAGTGAAGCTA-TATTTCACGTAGAATAACTAGA
* *
17511716 ACAAGAGAAGCTATATTTCACGTAAAATAACTAGA
1 ACAAGTGAAGCTATATTTCACGTAGAATAACTAGA
* * * *
17511751 ACAAGTGAAGCAATACTTCATGTGGAATAAC
1 ACAAGTGAAGCTATATTTCACGTAGAATAAC
17511782 CACTTCATAC
Statistics
Matches: 56, Mismatches: 9, Indels: 2
0.84 0.13 0.03
Matches are distributed among these distances:
35 54 0.96
36 2 0.04
ACGTcount: A:0.45, C:0.14, G:0.17, T:0.25
Consensus pattern (35 bp):
ACAAGTGAAGCTATATTTCACGTAGAATAACTAGA
Found at i:17513508 original size:24 final size:24
Alignment explanation
Indices: 17513458--17513513 Score: 67
Period size: 24 Copynumber: 2.3 Consensus size: 24
17513448 CCATTACCGA
* * **
17513458 GTTTGTTTTTAACTCTTACAATGT
1 GTTTGGTTCTAACTCTTACAACAT
*
17513482 GTTTGGTTCTAACTTTTACAACAT
1 GTTTGGTTCTAACTCTTACAACAT
17513506 GTTTGGTT
1 GTTTGGTT
17513514 AGGGGGGAAT
Statistics
Matches: 27, Mismatches: 5, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
24 27 1.00
ACGTcount: A:0.20, C:0.12, G:0.16, T:0.52
Consensus pattern (24 bp):
GTTTGGTTCTAACTCTTACAACAT
Found at i:17523988 original size:22 final size:22
Alignment explanation
Indices: 17523945--17523988 Score: 61
Period size: 22 Copynumber: 2.0 Consensus size: 22
17523935 TTTAAAACAA
* *
17523945 CTTTAAAACTAAAAACTTTGAT
1 CTTTAAAACCAAAAACTCTGAT
*
17523967 CTTTAAAACCAAAAGCTCTGAT
1 CTTTAAAACCAAAAACTCTGAT
17523989 ACCAATCGAA
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
22 19 1.00
ACGTcount: A:0.43, C:0.18, G:0.07, T:0.32
Consensus pattern (22 bp):
CTTTAAAACCAAAAACTCTGAT
Found at i:17527821 original size:18 final size:18
Alignment explanation
Indices: 17527793--17527849 Score: 78
Period size: 18 Copynumber: 3.2 Consensus size: 18
17527783 ACACGATTAA
* *
17527793 TAACACATTTAACATGAT
1 TAACACGTTTAACACGAT
*
17527811 TAACATGTTTAACACGAT
1 TAACACGTTTAACACGAT
*
17527829 TAACACGTTTACCACGAT
1 TAACACGTTTAACACGAT
17527847 TAA
1 TAA
17527850 ATAAAAATAT
Statistics
Matches: 34, Mismatches: 5, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
18 34 1.00
ACGTcount: A:0.40, C:0.19, G:0.09, T:0.32
Consensus pattern (18 bp):
TAACACGTTTAACACGAT
Found at i:17527834 original size:9 final size:9
Alignment explanation
Indices: 17527801--17527849 Score: 53
Period size: 9 Copynumber: 5.4 Consensus size: 9
17527791 AATAACACAT
*
17527801 TTAACATGA
1 TTAACACGA
* *
17527810 TTAACATGT
1 TTAACACGA
17527819 TTAACACGA
1 TTAACACGA
*
17527828 TTAACACGT
1 TTAACACGA
*
17527837 TTACCACGA
1 TTAACACGA
17527846 TTAA
1 TTAA
17527850 ATAAAAATAT
Statistics
Matches: 33, Mismatches: 7, Indels: 0
0.82 0.17 0.00
Matches are distributed among these distances:
9 33 1.00
ACGTcount: A:0.39, C:0.18, G:0.10, T:0.33
Consensus pattern (9 bp):
TTAACACGA
Found at i:17528120 original size:18 final size:18
Alignment explanation
Indices: 17528099--17528144 Score: 74
Period size: 18 Copynumber: 2.6 Consensus size: 18
17528089 TGTCACGTAT
* *
17528099 ACACGTTTAAACACGATA
1 ACACGATTAAACACAATA
17528117 ACACGATTAAACACAATA
1 ACACGATTAAACACAATA
17528135 ACACGATTAA
1 ACACGATTAA
17528145 GTAAACGTGT
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
18 26 1.00
ACGTcount: A:0.50, C:0.22, G:0.09, T:0.20
Consensus pattern (18 bp):
ACACGATTAAACACAATA
Found at i:17528225 original size:41 final size:41
Alignment explanation
Indices: 17528180--17528287 Score: 146
Period size: 41 Copynumber: 2.6 Consensus size: 41
17528170 ACGTGTTTGT
* *
17528180 CGTGTCTGACACG-TTAAGACAAGAAAATTTTTGTATCTTAA
1 CGTGTCAGACACGATT-AGACAAGAAAATTTTCGTATCTTAA
* *
17528221 CGTGTCAGACACGATTAGACACGAAAATTTTCGTTTCTTAA
1 CGTGTCAGACACGATTAGACAAGAAAATTTTCGTATCTTAA
* *
17528262 CGTGTCAGACATGATTAGACACGAAA
1 CGTGTCAGACACGATTAGACAAGAAA
17528288 CACGTTAAAA
Statistics
Matches: 61, Mismatches: 5, Indels: 2
0.90 0.07 0.03
Matches are distributed among these distances:
41 59 0.97
42 2 0.03
ACGTcount: A:0.34, C:0.18, G:0.19, T:0.30
Consensus pattern (41 bp):
CGTGTCAGACACGATTAGACAAGAAAATTTTCGTATCTTAA
Found at i:17529812 original size:32 final size:33
Alignment explanation
Indices: 17529750--17529814 Score: 96
Period size: 33 Copynumber: 2.0 Consensus size: 33
17529740 TTAATATTAC
17529750 ATCATCATCAATTATGATATATTAGCATGTCAT
1 ATCATCATCAATTATGATATATTAGCATGTCAT
* * *
17529783 ATCATCGTCAGTTATGAT-TTTTAGCATGTCAT
1 ATCATCATCAATTATGATATATTAGCATGTCAT
17529815 GTTAGCGTTA
Statistics
Matches: 29, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
32 13 0.45
33 16 0.55
ACGTcount: A:0.31, C:0.15, G:0.12, T:0.42
Consensus pattern (33 bp):
ATCATCATCAATTATGATATATTAGCATGTCAT
Found at i:17529910 original size:30 final size:30
Alignment explanation
Indices: 17529874--17529947 Score: 94
Period size: 30 Copynumber: 2.5 Consensus size: 30
17529864 TATTAGCCAT
*
17529874 AAGGGCTTATTTGACTCAAAATAAAAGTAC
1 AAGGGCTTATTTGACTCAAAACAAAAGTAC
* ** *
17529904 ATGGGCTTATTTGGTTCAAAACAAAAGTAT
1 AAGGGCTTATTTGACTCAAAACAAAAGTAC
*
17529934 AAGGGCTTAGTTGA
1 AAGGGCTTATTTGA
17529948 AAGCAATAAA
Statistics
Matches: 36, Mismatches: 8, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
30 36 1.00
ACGTcount: A:0.38, C:0.11, G:0.22, T:0.30
Consensus pattern (30 bp):
AAGGGCTTATTTGACTCAAAACAAAAGTAC
Found at i:17530351 original size:24 final size:22
Alignment explanation
Indices: 17530295--17530373 Score: 81
Period size: 24 Copynumber: 3.4 Consensus size: 22
17530285 ATAATATTAT
17530295 AATTAAAATAAA-AAACATTA-A
1 AATTAAAATAAATAAA-ATTAGA
17530316 AATTAAATATAATATAAGAATTAGA
1 AATTAAA-ATAA-ATAA-AATTAGA
*
17530341 AATTAAAATAAAATAAAAATGAGA
1 AATTAAAAT-AAAT-AAAATTAGA
17530365 AATTAAAAT
1 AATTAAAAT
17530374 TTATATAATA
Statistics
Matches: 50, Mismatches: 1, Indels: 11
0.81 0.02 0.18
Matches are distributed among these distances:
21 7 0.14
22 4 0.08
23 1 0.02
24 25 0.50
25 13 0.26
ACGTcount: A:0.67, C:0.01, G:0.05, T:0.27
Consensus pattern (22 bp):
AATTAAAATAAATAAAATTAGA
Found at i:17530432 original size:30 final size:30
Alignment explanation
Indices: 17530362--17530433 Score: 99
Period size: 30 Copynumber: 2.4 Consensus size: 30
17530352 AATAAAAATG
*
17530362 AGAAATTAAAATTTATATAATATTAGTAAA
1 AGAAAATAAAATTTATATAATATTAGTAAA
* *
17530392 AGAAATTAAAATTTATATAATATTAGTANA
1 AGAAAATAAAATTTATATAATATTAGTAAA
**
17530422 TTAAAATAAAAT
1 AGAAAATAAAAT
17530434 AAAATATAAG
Statistics
Matches: 38, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
30 38 1.00
ACGTcount: A:0.57, C:0.00, G:0.06, T:0.36
Consensus pattern (30 bp):
AGAAAATAAAATTTATATAATATTAGTAAA
Found at i:17530452 original size:50 final size:50
Alignment explanation
Indices: 17530391--17530491 Score: 150
Period size: 50 Copynumber: 2.0 Consensus size: 50
17530381 ATATTAGTAA
* **
17530391 AAGAAATTAAAATTTATATAATATTA-GTANATTAAAATAAAATAAAATAT
1 AAGAAATTAAAATTTATATAATA-TAGGTAAAAGAAAATAAAATAAAATAT
*
17530441 AAGAAATTAAAATTTATATAATATAGGTAAAAGAAATTAAAATAAAATAT
1 AAGAAATTAAAATTTATATAATATAGGTAAAAGAAAATAAAATAAAATAT
17530491 A
1 A
17530492 TAATATAAAA
Statistics
Matches: 46, Mismatches: 4, Indels: 2
0.88 0.08 0.04
Matches are distributed among these distances:
49 2 0.04
50 44 0.96
ACGTcount: A:0.61, C:0.00, G:0.06, T:0.32
Consensus pattern (50 bp):
AAGAAATTAAAATTTATATAATATAGGTAAAAGAAAATAAAATAAAATAT
Found at i:17530501 original size:14 final size:14
Alignment explanation
Indices: 17530481--17530552 Score: 58
Period size: 14 Copynumber: 5.1 Consensus size: 14
17530471 AAGAAATTAA
17530481 AATAAAATATATAAT
1 AATAAAA-ATATAAT
*
17530496 -ATAAAAA-ATTAT
1 AATAAAAATATAAT
* * *
17530508 ATTAAAAAAATAAG
1 AATAAAAATATAAT
*
17530522 AATAGAAAATATGAT
1 AATA-AAAATATAAT
*
17530537 AATAAAAATAAAAT
1 AATAAAAATATAAT
17530551 AA
1 AA
17530553 AATATATGAC
Statistics
Matches: 44, Mismatches: 10, Indels: 7
0.72 0.16 0.11
Matches are distributed among these distances:
12 4 0.09
13 7 0.16
14 22 0.50
15 11 0.25
ACGTcount: A:0.69, C:0.00, G:0.04, T:0.26
Consensus pattern (14 bp):
AATAAAAATATAAT
Found at i:17530519 original size:80 final size:80
Alignment explanation
Indices: 17530315--17530506 Score: 232
Period size: 80 Copynumber: 2.4 Consensus size: 80
17530305 AAAAACATTA
* * *
17530315 AAATT-AAATATAATATAAGAATT-AGAAATTAAAATAAAATAAAA-ATGAGAAATTAAAATTTA
1 AAATTAAAATAT-ATATAA-TATTAAAAAATTAAAATAAAATAAAATATAAGAAATTAAAATTTA
17530377 TATAATATTAGTAAAAG
64 TATAATATTAGTAAAAG
* ** *
17530394 AAATTAAAATTTATATAATATTAGTANATTAAAATAAAATAAAATATAAGAAATTAAAATTTATA
1 AAATTAAAATATATATAATATTAAAAAATTAAAATAAAATAAAATATAAGAAATTAAAATTTATA
17530459 TAATA-TAGGTAAAAG
66 TAATATTA-GTAAAAG
17530474 AAATTAAAATAAAATATATAATA-TAAAAAATTA
1 AAATTAAAAT---ATATATAATATTAAAAAATTA
17530507 TATTAAAAAA
Statistics
Matches: 96, Mismatches: 10, Indels: 11
0.82 0.09 0.09
Matches are distributed among these distances:
78 3 0.03
79 31 0.32
80 46 0.48
82 7 0.07
83 9 0.09
ACGTcount: A:0.62, C:0.00, G:0.06, T:0.32
Consensus pattern (80 bp):
AAATTAAAATATATATAATATTAAAAAATTAAAATAAAATAAAATATAAGAAATTAAAATTTATA
TAATATTAGTAAAAG
Found at i:17530525 original size:29 final size:30
Alignment explanation
Indices: 17530484--17530544 Score: 70
Period size: 29 Copynumber: 2.1 Consensus size: 30
17530474 AAATTAAAAT
* * * *
17530484 AAAATATATAATATAAAAAATTATATTAAA
1 AAAATATAGAATAGAAAAAATGATAATAAA
*
17530514 AAAATA-AGAATAGAAAATATGATAATAAA
1 AAAATATAGAATAGAAAAAATGATAATAAA
17530543 AA
1 AA
17530545 TAAAATAAAA
Statistics
Matches: 26, Mismatches: 5, Indels: 1
0.81 0.16 0.03
Matches are distributed among these distances:
29 20 0.77
30 6 0.23
ACGTcount: A:0.69, C:0.00, G:0.05, T:0.26
Consensus pattern (30 bp):
AAAATATAGAATAGAAAAAATGATAATAAA
Found at i:17530568 original size:26 final size:27
Alignment explanation
Indices: 17530513--17530572 Score: 79
Period size: 26 Copynumber: 2.3 Consensus size: 27
17530503 ATTATATTAA
*
17530513 AAAAATAAGAATAGAAAATATGATAAT
1 AAAAATAAGAATAGAAAATATGACAAT
*
17530540 AAAAATAA-AATA-AAATATATGACATT
1 AAAAATAAGAATAGAAA-ATATGACAAT
17530566 AAAAATA
1 AAAAATA
17530573 TATTTAAGAG
Statistics
Matches: 30, Mismatches: 2, Indels: 3
0.86 0.06 0.09
Matches are distributed among these distances:
25 3 0.10
26 19 0.63
27 8 0.27
ACGTcount: A:0.68, C:0.02, G:0.07, T:0.23
Consensus pattern (27 bp):
AAAAATAAGAATAGAAAATATGACAAT
Found at i:17540099 original size:15 final size:15
Alignment explanation
Indices: 17540079--17540110 Score: 64
Period size: 15 Copynumber: 2.1 Consensus size: 15
17540069 CTGACTCTAT
17540079 TCTTTAACTAACTAC
1 TCTTTAACTAACTAC
17540094 TCTTTAACTAACTAC
1 TCTTTAACTAACTAC
17540109 TC
1 TC
17540111 CCTGCTTATG
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 17 1.00
ACGTcount: A:0.31, C:0.28, G:0.00, T:0.41
Consensus pattern (15 bp):
TCTTTAACTAACTAC
Found at i:17541524 original size:16 final size:15
Alignment explanation
Indices: 17541487--17541525 Score: 53
Period size: 14 Copynumber: 2.6 Consensus size: 15
17541477 TTGTTAAATT
*
17541487 TATTTTTATAAGTTC
1 TATTTTTATAAGTTA
17541502 T-TTTTTATAAGTTA
1 TATTTTTATAAGTTA
17541516 TAATTTTTAT
1 T-ATTTTTAT
17541526 TAAAATTATC
Statistics
Matches: 21, Mismatches: 1, Indels: 3
0.84 0.04 0.12
Matches are distributed among these distances:
14 13 0.62
15 1 0.05
16 7 0.33
ACGTcount: A:0.28, C:0.03, G:0.05, T:0.64
Consensus pattern (15 bp):
TATTTTTATAAGTTA
Found at i:17547120 original size:35 final size:32
Alignment explanation
Indices: 17547081--17547276 Score: 164
Period size: 35 Copynumber: 5.8 Consensus size: 32
17547071 ATTGATCCCG
17547081 TGAAAAACCACTGTTGTAGGTTGTGGTTGAGCCTT
1 TGAAAAACCACT-TTG--GGTTGTGGTTGAGCCTT
* * *
17547116 TGAAAAACCACTTTGGGTTTTGGTTAAG-CTCG
1 TGAAAAACCACTTTGGGTTGTGGTTGAGCCT-T
* * *
17547148 TGAAAAATCA-TTGTGAAAGGTTGTCGTTGAGCTTT
1 TGAAAAACCACTT-TG---GGTTGTGGTTGAGCCTT
* **
17547183 TGAAAAACCACTTTGGGTTTTGGTTGAGCCCG
1 TGAAAAACCACTTTGGGTTGTGGTTGAGCCTT
*
17547215 TGAAAAACCA-TTGTGAAAGGTTGTCGTTGAGCCTT
1 TGAAAAACCACTT-TG---GGTTGTGGTTGAGCCTT
*
17547250 TGAAAAACCACTTTGGGTTTTGGTTGA
1 TGAAAAACCACTTTGGGTTGTGGTTGA
17547277 TCCCGGTAAA
Statistics
Matches: 128, Mismatches: 21, Indels: 27
0.73 0.12 0.15
Matches are distributed among these distances:
31 6 0.05
32 56 0.44
34 3 0.02
35 58 0.45
36 5 0.04
ACGTcount: A:0.26, C:0.14, G:0.27, T:0.34
Consensus pattern (32 bp):
TGAAAAACCACTTTGGGTTGTGGTTGAGCCTT
Found at i:17547136 original size:67 final size:67
Alignment explanation
Indices: 17547061--17547303 Score: 355
Period size: 67 Copynumber: 3.6 Consensus size: 67
17547051 AAGTTAGTTG
* * * * *
17547061 TTGGGTTTTGATTGATCCCGTGAAAAACCACTGTTG-TAGGTTGTGGTTGAGCCTTTGAAAAACC
1 TTGGGTTTTGGTTGAGCCCGTGAAAAACCATTG-TGAAAGGTTGTCGTTGAGCCTTTGAAAAACC
17547125 ACT
65 ACT
* * * *
17547128 TTGGGTTTTGGTTAAGCTCGTGAAAAATCATTGTGAAAGGTTGTCGTTGAGCTTTTGAAAAACCA
1 TTGGGTTTTGGTTGAGCCCGTGAAAAACCATTGTGAAAGGTTGTCGTTGAGCCTTTGAAAAACCA
17547193 CT
66 CT
17547195 TTGGGTTTTGGTTGAGCCCGTGAAAAACCATTGTGAAAGGTTGTCGTTGAGCCTTTGAAAAACCA
1 TTGGGTTTTGGTTGAGCCCGTGAAAAACCATTGTGAAAGGTTGTCGTTGAGCCTTTGAAAAACCA
17547260 CT
66 CT
* *
17547262 TTGGGTTTTGGTTGATCCCG-GTAAAAACTATTGTGAAAGGTT
1 TTGGGTTTTGGTTGAGCCCGTG-AAAAACCATTGTGAAAGGTT
17547304 TTGGCTAAGC
Statistics
Matches: 159, Mismatches: 15, Indels: 4
0.89 0.08 0.02
Matches are distributed among these distances:
66 3 0.02
67 156 0.98
ACGTcount: A:0.25, C:0.14, G:0.26, T:0.35
Consensus pattern (67 bp):
TTGGGTTTTGGTTGAGCCCGTGAAAAACCATTGTGAAAGGTTGTCGTTGAGCCTTTGAAAAACCA
CT
Found at i:17547288 original size:32 final size:31
Alignment explanation
Indices: 17547061--17547289 Score: 122
Period size: 35 Copynumber: 6.9 Consensus size: 31
17547051 AAGTTAGTTG
*
17547061 TTGGGTTTTGATTGATCCCGTGAAAAACCACT
1 TTGGGTTTTGGTTGA-CCCGTGAAAAACCACT
* **
17547093 GTTGTAGGTTGTGGTTGAGCCTTTGAAAAACCACT
1 -TTG--GGTTTTGGTTGA-CCCGTGAAAAACCACT
* * *
17547128 TTGGGTTTTGGTTAAGCTCGTGAAAAATCA-T
1 TTGGGTTTTGGTTGA-CCCGTGAAAAACCACT
* * ***
17547159 TGTGAAAGGTTGTCGTTGAGCTTTTGAAAAACCACT
1 T-TG---GGTTTTGGTTGA-CCCGTGAAAAACCACT
17547195 TTGGGTTTTGGTTGAGCCCGTGAAAAACCA-T
1 TTGGGTTTTGGTTGA-CCCGTGAAAAACCACT
* * **
17547226 TGTGAAAGGTTGTCGTTGAGCCTTTGAAAAACCACT
1 T-TG---GGTTTTGGTTGA-CCCGTGAAAAACCACT
17547262 TTGGGTTTTGGTTGATCCCG-GTAAAAAC
1 TTGGGTTTTGGTTGA-CCCGTG-AAAAAC
17547290 TATTGTGAAA
Statistics
Matches: 152, Mismatches: 31, Indels: 27
0.72 0.15 0.13
Matches are distributed among these distances:
31 5 0.03
32 65 0.43
33 3 0.02
34 3 0.02
35 72 0.47
36 4 0.03
ACGTcount: A:0.25, C:0.15, G:0.26, T:0.34
Consensus pattern (31 bp):
TTGGGTTTTGGTTGACCCGTGAAAAACCACT
Found at i:17556299 original size:31 final size:31
Alignment explanation
Indices: 17556256--17556318 Score: 108
Period size: 31 Copynumber: 2.0 Consensus size: 31
17556246 AACGCAACTT
17556256 AGATTTAAGACACTTTTAAATAAAGGTTTTC
1 AGATTTAAGACACTTTTAAATAAAGGTTTTC
* *
17556287 AGATTTAGGACACTTTTAAATAGAGGTTTTC
1 AGATTTAAGACACTTTTAAATAAAGGTTTTC
17556318 A
1 A
17556319 TTACCTGATG
Statistics
Matches: 30, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
31 30 1.00
ACGTcount: A:0.37, C:0.10, G:0.16, T:0.38
Consensus pattern (31 bp):
AGATTTAAGACACTTTTAAATAAAGGTTTTC
Found at i:17564091 original size:2 final size:2
Alignment explanation
Indices: 17564084--17564108 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
17564074 GTAAAAATTA
17564084 AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT A
17564109 GGTGCCCTCA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:17569527 original size:27 final size:27
Alignment explanation
Indices: 17569450--17569531 Score: 76
Period size: 27 Copynumber: 2.9 Consensus size: 27
17569440 AGTCAATATC
17569450 ATTGATTAATTTAACAAATTTAAGAAAAAA
1 ATTGATTAATTTAACAAATTT---AAAAAA
* * *
17569480 ATATGATTAAAAATT-AGAAATTTAAAAAG
1 AT-TGATT--AATTTAACAAATTTAAAAAA
17569509 ATTGATTAATTTAACAAATTTAA
1 ATTGATTAATTTAACAAATTTAA
17569532 GATAAATTTT
Statistics
Matches: 43, Mismatches: 5, Indels: 11
0.73 0.08 0.19
Matches are distributed among these distances:
26 4 0.09
27 9 0.21
28 5 0.12
29 7 0.16
30 2 0.05
31 5 0.12
32 7 0.16
33 4 0.09
ACGTcount: A:0.55, C:0.02, G:0.07, T:0.35
Consensus pattern (27 bp):
ATTGATTAATTTAACAAATTTAAAAAA
Found at i:17570814 original size:21 final size:21
Alignment explanation
Indices: 17570782--17570821 Score: 64
Period size: 20 Copynumber: 1.9 Consensus size: 21
17570772 TTATTATACC
17570782 TTTATAAGTTTTTACGTCAATT
1 TTTATAAG-TTTTACGTCAATT
17570804 TTTAT-AGTTTTACGTCAA
1 TTTATAAGTTTTACGTCAA
17570822 GGCTTATCTA
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
20 11 0.61
21 2 0.11
22 5 0.28
ACGTcount: A:0.28, C:0.10, G:0.10, T:0.53
Consensus pattern (21 bp):
TTTATAAGTTTTACGTCAATT
Found at i:17570966 original size:252 final size:251
Alignment explanation
Indices: 17570472--17572036 Score: 1771
Period size: 252 Copynumber: 6.2 Consensus size: 251
17570462 TATTATTATC
* * * *
17570472 ACTTGTTACGTTAACTCTCAAACATTTACATTAAGATTTTAAATTT-GCTTATTCTACTTTTATA
1 ACTTGTTACGTTAACTCTCACACATTTACGTTAAGATTTAAAATTTAG-TTATTCTACCTTTATA
* ** * * * ** * *
17570536 AGATTTTATATCAATTTTTA-TGACTTTACGTCAACCCTTTTCAATA-CTAACTTTT-AACTATA
65 AGTTTTTACGTCAATTCTTACAG-TTTTACGTCAAGGCTTATCTATATC-AA-TTTTGAACTATA
* * * ** * * * *
17570598 ATTATCTTTATCTTTATTATTCTTTATTTAAAAATAAAAATTTAAATATTGTTACATACTTTTAG
127 ATTATTTTTATCCTTATTATTCTTTATTTAAAAATTAAAATTTGTATATCGTTAAACACTTTTAA
* * * * * * * *
17570663 CCCAATAATAAAAATATAAATGTTTGTTTTTTTATTAAAATTAGA-TTTTTTTACTTAATTA
192 CTCGAGAATATAAATTTAAAT-ATTG-TTTTTCACTAAAATTAGATTTTTTTTACTTAATTA
* * * *
17570724 ACTTATTACGTTAACTTTAACACATTTACGTTAAGATTTAAAATTTAGTTATTATACCTTTATAA
1 ACTTGTTACGTTAACTCTCACACATTTACGTTAAGATTTAAAATTTAGTTATTCTACCTTTATAA
* * *
17570789 GTTTTTACGTCAATTTTTATAGTTTTACGTCAAGGCTTATCTATATTAATTTTGAACTATAATTA
66 GTTTTTACGTCAATTCTTACAGTTTTACGTCAAGGCTTATCTATATCAATTTTGAACTATAATTA
* * *
17570854 TTTTTATCATTATTATTCTTCATTTAAAAATTAAAATTTGTATATCGTTAAACACTTTTAACTGG
131 TTTTTATCCTTATTATTCTTTATTTAAAAATTAAAATTTGTATATCGTTAAACACTTTTAACTCG
* * *
17570919 AGAATATAAGTTTAAATATTAGGTTTTCACTGAAATTAGATTTTTTTTACTTAATTA
196 AGAATATAAATTTAAATATT-GTTTTTCACTAAAATTAGATTTTTTTTACTTAATTA
* * *
17570976 ACTTATTACGTTAACTCTCACACTTTTACATTAAGATTTAAAATTTAGTTATT-TCACCTTTATA
1 ACTTGTTACGTTAACTCTCACACATTTACGTTAAGATTTAAAATTTAGTTATTCT-ACCTTTATA
* * *
17571040 AGTTTTTACGTCAATTATTACAGTTTTACGTCCAGGCTTATCTATGTCAATTTTGAACTATAATT
65 AGTTTTTACGTCAATTCTTACAGTTTTACGTCAAGGCTTATCTATATCAATTTTGAACTATAATT
* * *
17571105 ATTTTTATCCTTATTATTCTTCATTTAAAAATTAAAATTTGTATATCGTTAAATACTTTT-AGTC
130 ATTTTTATCCTTATTATTCTTTATTTAAAAATTAAAATTTGTATATCGTTAAACACTTTTAACT-
17571169 CGAGAAT-TAAATTTAAATATT-TTTTTCACTAAAATTAGA-TTTTTTTACTTAATTA
194 CGAGAATATAAATTTAAATATTGTTTTTCACTAAAATTAGATTTTTTTTACTTAATTA
* * * *
17571224 ACTTGTTGCGCTAACTCTCACACTTTTGCGTTAAGATTTAAAATTTAGTTATTCTACCTTTATAA
1 ACTTGTTACGTTAACTCTCACACATTTACGTTAAGATTTAAAATTTAGTTATTCTACCTTTATAA
* * * * * *
17571289 GTTTTTATGTCAATTGTTACAGTTTTACGTAAAGGTTTATC--TGTCAATTTTGAGCTATAATTA
66 GTTTTTACGTCAATTCTTACAGTTTTACGTCAAGGCTTATCTATATCAATTTTGAACTATAATTA
* * * * *
17571352 TTTTTAACCTTATTATTCTTTATTTTAAAATTTAAATTTGTATATCGTTATATACTTTTAA-TCC
131 TTTTTATCCTTATTATTCTTTATTTAAAAATTAAAATTTGTATATCGTTAAACACTTTTAACT-C
* * *
17571416 GAGAATATAAATTTAAAT-TTTTTTTTTACTAAAATTAGATTTTTTTCACTTAATTA
195 GAGAATATAAATTTAAATATTGTTTTTCACTAAAATTAGATTTTTTTTACTTAATTA
* * * ** * *
17571472 ACTTGTTACGTTAACACTCACACGTTTACGTTAAGATTTAAACTTTAACTACTCCACCTTTATAA
1 ACTTGTTACGTTAACTCTCACACATTTACGTTAAGATTTAAAATTTAGTTATTCTACCTTTATAA
* *
17571537 GTTTTTACATCAATTCTTACAATTTTACGTCAAGGCATT-TCTATATCAATTTTGAACTATAATT
66 GTTTTTACGTCAATTCTTACAGTTTTACGTCAAGGC-TTATCTATATCAATTTTGAACTATAATT
* * *
17571601 ATTTTTATCTTTATTATTCTTTATTTAAAAATTAAAATTTGTATATTGTTAAACA-TTTT-AGTC
130 ATTTTTATCCTTATTATTCTTTATTTAAAAATTAAAATTTGTATATCGTTAAACACTTTTAACTC
* * * * * *
17571664 TAAGAGTATAAATTTAAATGTTTGTTTTTTAGTAAAATTAGATTTTTTTTTACTTAATTG
195 -GAGAATATAAATTTAAAT-ATTGTTTTTCACTAAAATTAGA-TTTTTTTTACTTAATTA
* * * * * *
17571724 ATTTATTACATTAATTCTAACACATTTACGTTAAGATTTAAAATTTAGTTATTCCACCTTTATAA
1 ACTTGTTACGTTAACTCTCACACATTTACGTTAAGATTTAAAATTTAGTTATTCTACCTTTATAA
* * * * * * * * * *
17571789 GTTTGTGCGTCAATTCTTACAATTTTACATCAAAGTTTTTCTATGTCAATTTTGAGCTATATTTA
66 GTTTTTACGTCAATTCTTACAGTTTTACGTCAAGGCTTATCTATATCAATTTTGAACTATAATTA
* * * * *
17571854 TTTTTATCCTTATTATTCTTTATTTAAAAATTAAAATTTTTGTATCGTTAAACACTTTTAGCCCT
131 TTTTTATCCTTATTATTCTTTATTTAAAAATTAAAATTTGTATATCGTTAAACACTTTTAACTCG
* * * *
17571919 ACAATATAAATTTAAATATTTATTTTTCATTAAAATTAGATTTTTTTT-CTTAATTG
196 AGAATATAAATTTAAATA-TTGTTTTTCACTAAAATTAGATTTTTTTTACTTAATTA
* * * * * * * *
17571975 ACTTGCTATGTTAACTCTCATATATTTACGATAAAATTTTAAATTTAGTTATTCTACTTTTA
1 ACTTGTTACGTTAACTCTCACACATTTACGTTAAGATTTAAAATTTAGTTATTCTACCTTTA
17572037 CGAGATTTAT
Statistics
Matches: 1135, Mismatches: 153, Indels: 51
0.85 0.11 0.04
Matches are distributed among these distances:
246 86 0.08
247 29 0.03
248 214 0.19
249 40 0.04
250 67 0.06
251 113 0.10
252 546 0.48
253 39 0.03
254 1 0.00
ACGTcount: A:0.33, C:0.12, G:0.07, T:0.48
Consensus pattern (251 bp):
ACTTGTTACGTTAACTCTCACACATTTACGTTAAGATTTAAAATTTAGTTATTCTACCTTTATAA
GTTTTTACGTCAATTCTTACAGTTTTACGTCAAGGCTTATCTATATCAATTTTGAACTATAATTA
TTTTTATCCTTATTATTCTTTATTTAAAAATTAAAATTTGTATATCGTTAAACACTTTTAACTCG
AGAATATAAATTTAAATATTGTTTTTCACTAAAATTAGATTTTTTTTACTTAATTA
Found at i:17573471 original size:76 final size:77
Alignment explanation
Indices: 17573324--17573504 Score: 184
Period size: 76 Copynumber: 2.3 Consensus size: 77
17573314 ATCATACATT
* * **
17573324 AAGGTATAATAATGTCAATATGTAAATACCATCAAGGTCCATATGAAAGGTTGACATATGGCATT
1 AAGGTATAATAATGT-AATATGTAAATACCATCAAGGTCCATATGAAAGGTAGACATATGACAAA
17573389 CCTATTATATATA
65 CCTATTATATATA
* * * * * *
17573402 AAGGTATAATGATGT-TTATGTAAATACCATCAAGGTCCATGTGATAGGTAGGCATGTGACAAAC
1 AAGGTATAATAATGTAATATGTAAATACCATCAAGGTCCATATGAAAGGTAGACATATGACAAAC
* * * *
17573466 TTATTACACATG
66 CTATTATATATA
* * *
17573478 AAGGTGTAATAGTGCCAATATGTAAAT
1 AAGGTATAATAATG-TAATATGTAAAT
17573505 TTAACATCTT
Statistics
Matches: 82, Mismatches: 19, Indels: 4
0.78 0.18 0.04
Matches are distributed among these distances:
76 59 0.72
78 23 0.28
ACGTcount: A:0.38, C:0.12, G:0.19, T:0.31
Consensus pattern (77 bp):
AAGGTATAATAATGTAATATGTAAATACCATCAAGGTCCATATGAAAGGTAGACATATGACAAAC
CTATTATATATA
Found at i:17575327 original size:16 final size:15
Alignment explanation
Indices: 17575306--17575340 Score: 52
Period size: 16 Copynumber: 2.3 Consensus size: 15
17575296 TACTTAAATA
17575306 TTATCAAAAAGTATAT
1 TTATCAAAAAGTA-AT
*
17575322 TTATCAAAATGTAAT
1 TTATCAAAAAGTAAT
17575337 TTAT
1 TTAT
17575341 ATATTAATAT
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
15 6 0.33
16 12 0.67
ACGTcount: A:0.46, C:0.06, G:0.06, T:0.43
Consensus pattern (15 bp):
TTATCAAAAAGTAAT
Found at i:17576406 original size:13 final size:13
Alignment explanation
Indices: 17576371--17576413 Score: 50
Period size: 14 Copynumber: 3.2 Consensus size: 13
17576361 AAAAGTTAAA
*
17576371 AATTTTTAAAATT
1 AATTATTAAAATT
*
17576384 AATATATTAAACTT
1 AAT-TATTAAAATT
17576398 AATTATTAATAATT
1 AATTATTAA-AATT
17576412 AA
1 AA
17576414 AAGATTTAAA
Statistics
Matches: 25, Mismatches: 3, Indels: 3
0.81 0.10 0.10
Matches are distributed among these distances:
13 9 0.36
14 16 0.64
ACGTcount: A:0.51, C:0.02, G:0.00, T:0.47
Consensus pattern (13 bp):
AATTATTAAAATT
Found at i:17576939 original size:16 final size:15
Alignment explanation
Indices: 17576915--17576948 Score: 50
Period size: 16 Copynumber: 2.2 Consensus size: 15
17576905 TTAATTTTTT
*
17576915 AATTTTTAAAAATTAA
1 AATTATTAAAAA-TAA
17576931 AATTATTAAAAATAA
1 AATTATTAAAAATAA
17576946 AAT
1 AAT
17576949 CCACATAATA
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
15 6 0.35
16 11 0.65
ACGTcount: A:0.62, C:0.00, G:0.00, T:0.38
Consensus pattern (15 bp):
AATTATTAAAAATAA
Found at i:17581922 original size:17 final size:17
Alignment explanation
Indices: 17581889--17581923 Score: 52
Period size: 17 Copynumber: 2.1 Consensus size: 17
17581879 CAAGGCACAA
**
17581889 GGCAGTGGAGGCGGACG
1 GGCAGTGGAGGAAGACG
17581906 GGCAGTGGAGGAAGACG
1 GGCAGTGGAGGAAGACG
17581923 G
1 G
17581924 CTGCAGGACG
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
17 16 1.00
ACGTcount: A:0.23, C:0.14, G:0.57, T:0.06
Consensus pattern (17 bp):
GGCAGTGGAGGAAGACG
Found at i:17583266 original size:14 final size:16
Alignment explanation
Indices: 17583247--17583279 Score: 52
Period size: 14 Copynumber: 2.2 Consensus size: 16
17583237 AAAAAAATTC
17583247 ATTTTATT-T-TAATA
1 ATTTTATTATCTAATA
17583261 ATTTTATTATCTAATA
1 ATTTTATTATCTAATA
17583277 ATT
1 ATT
17583280 ATGTAACTTA
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
14 8 0.47
15 1 0.06
16 8 0.47
ACGTcount: A:0.36, C:0.03, G:0.00, T:0.61
Consensus pattern (16 bp):
ATTTTATTATCTAATA
Found at i:17584097 original size:20 final size:20
Alignment explanation
Indices: 17584072--17584117 Score: 67
Period size: 20 Copynumber: 2.3 Consensus size: 20
17584062 TTTTGACCCC
17584072 ATTTGACTTATT-AGAGTATA
1 ATTTGACTTATTGA-AGTATA
*
17584092 ATTTGACTTATTGAAGTATG
1 ATTTGACTTATTGAAGTATA
17584112 ATTTGA
1 ATTTGA
17584118 GGTTTAGAAG
Statistics
Matches: 24, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
20 23 0.96
21 1 0.04
ACGTcount: A:0.33, C:0.04, G:0.17, T:0.46
Consensus pattern (20 bp):
ATTTGACTTATTGAAGTATA
Found at i:17587005 original size:27 final size:27
Alignment explanation
Indices: 17586921--17587197 Score: 132
Period size: 28 Copynumber: 10.1 Consensus size: 27
17586911 TGATAAAAAA
* * *
17586921 TCATATTGAAAATATAATTATTATACG
1 TCATATTGAAAATTTAATTGTTACACG
* * * * **
17586948 TCATGTT-AAAATTTAGTTATTATATA
1 TCATATTGAAAATTTAATTGTTACACG
17586974 TCATATTGAAAATTTAATTGTTACACG
1 TCATATTGAAAATTTAATTGTTACACG
* *
17587001 CCATATTGAAAAATGTT-ATTGTTATACG
1 TCATATTG-AAAAT-TTAATTGTTACACG
* *
17587029 TCATATT-AAAGATTTAGTTGTTACATG
1 TCATATTGAAA-ATTTAATTGTTACACG
* * * *
17587056 -CTATGTTAAAAATTGTAGTTGTTACACA
1 TC-ATATTGAAAATT-TAATTGTTACACG
* * * * *
17587084 TAATGTTGAAGATTTAGTTGTTACACA
1 TCATATTGAAAATTTAATTGTTACACG
* * * *
17587111 TCATGTTGAAAAATGTAATTATTACACA
1 TCATATTG-AAAATTTAATTGTTACACG
* * * **
17587139 TCATGTT-AAAGGTTTAATTGTTATATA
1 TCATATTGAAA-ATTTAATTGTTACACG
* * * *
17587166 CCATGTTGAAAAATTTAATTATTATACG
1 TCATATTG-AAAATTTAATTGTTACACG
17587194 TCAT
1 TCAT
17587198 GATGAAGAAG
Statistics
Matches: 198, Mismatches: 39, Indels: 25
0.76 0.15 0.10
Matches are distributed among these distances:
26 30 0.15
27 81 0.41
28 82 0.41
29 5 0.03
ACGTcount: A:0.37, C:0.09, G:0.12, T:0.42
Consensus pattern (27 bp):
TCATATTGAAAATTTAATTGTTACACG
Found at i:17587198 original size:28 final size:28
Alignment explanation
Indices: 17586920--17587203 Score: 158
Period size: 27 Copynumber: 10.4 Consensus size: 28
17586910 ATGATAAAAA
* * * *
17586920 ATCATATTG-AAAATATAATTATTATAC
1 ATCATGTTGAAAAATTTAATTGTTACAC
* * * * *
17586947 GTCATGTT--AAAATTTAGTTATTATAT
1 ATCATGTTGAAAAATTTAATTGTTACAC
*
17586973 ATCATATTG-AAAATTTAATTGTTACAC
1 ATCATGTTGAAAAATTTAATTGTTACAC
** * *
17587000 GCCATATTGAAAAATGTT-ATTGTTATAC
1 ATCATGTTGAAAAAT-TTAATTGTTACAC
* * * *
17587028 GTCATATT-AAAGATTTAGTTGTT--AC
1 ATCATGTTGAAAAATTTAATTGTTACAC
*
17587053 ATGCTATGTT-AAAAATTGTAGTTGTTACAC
1 AT-C-ATGTTGAAAAATT-TAATTGTTACAC
* * *
17587083 ATAATGTTG-AAGATTTAGTTGTTACAC
1 ATCATGTTGAAAAATTTAATTGTTACAC
* *
17587110 ATCATGTTGAAAAATGTAATTATTACAC
1 ATCATGTTGAAAAATTTAATTGTTACAC
** * *
17587138 ATCATGTT-AAAGGTTTAATTGTTATAT
1 ATCATGTTGAAAAATTTAATTGTTACAC
* * *
17587165 ACCATGTTGAAAAATTTAATTATTATAC
1 ATCATGTTGAAAAATTTAATTGTTACAC
* *
17587193 GTCATGATGAA
1 ATCATGTTGAA
17587204 GAAGTTGTTA
Statistics
Matches: 204, Mismatches: 41, Indels: 23
0.76 0.15 0.09
Matches are distributed among these distances:
25 3 0.01
26 24 0.12
27 87 0.43
28 84 0.41
29 2 0.01
30 4 0.02
ACGTcount: A:0.38, C:0.08, G:0.13, T:0.41
Consensus pattern (28 bp):
ATCATGTTGAAAAATTTAATTGTTACAC
Found at i:17587198 original size:55 final size:55
Alignment explanation
Indices: 17586955--17587198 Score: 215
Period size: 55 Copynumber: 4.4 Consensus size: 55
17586945 ACGTCATGTT
* * * * *
17586955 AAAATTTAGTTATTATATATCATATTGAAA-ATTTAATTGTTACACGCCATATTGA
1 AAAATTTAATTATTATACATCATGTT-AAAGATTTAATTGTTACACACCATGTTGA
* * * * ** *
17587010 AAAATGTT-ATTGTTATACGTCATATTAAAGATTTAGTTGTTACATGCTATGTT-A
1 AAAAT-TTAATTATTATACATCATGTTAAAGATTTAATTGTTACACACCATGTTGA
* * * * * * *
17587064 AAAATTGTAGTTGTTACACATAATGTTGAAGATTTAGTTGTTACACATCATGTTGA
1 AAAATT-TAATTATTATACATCATGTTAAAGATTTAATTGTTACACACCATGTTGA
* * * * *
17587120 AAAATGTAATTATTACACATCATGTTAAAGGTTTAATTGTTATATACCATGTTGA
1 AAAATTTAATTATTATACATCATGTTAAAGATTTAATTGTTACACACCATGTTGA
*
17587175 AAAATTTAATTATTATACGTCATG
1 AAAATTTAATTATTATACATCATG
17587199 ATGAAGAAGT
Statistics
Matches: 153, Mismatches: 31, Indels: 10
0.79 0.16 0.05
Matches are distributed among these distances:
53 1 0.01
54 10 0.07
55 134 0.88
56 8 0.05
ACGTcount: A:0.37, C:0.09, G:0.13, T:0.41
Consensus pattern (55 bp):
AAAATTTAATTATTATACATCATGTTAAAGATTTAATTGTTACACACCATGTTGA
Found at i:17587204 original size:110 final size:109
Alignment explanation
Indices: 17586949--17587220 Score: 284
Period size: 110 Copynumber: 2.5 Consensus size: 109
17586939 TATTATACGT
* * * **
17586949 CATGTT-AAAATTTAGTTATTATATATCAT-ATTGAAAATTTAATTGTTACACGCCATATTGAAA
1 CATGTTAAAAATTTAGTTATTATACATCATGA-TGAAGATTTAGTTGTTACACATCATATTGAAA
* * * * * *
17587012 AATGTTATTGTTATACGTCATATTAAAGATTTAGTTGTTACATGC
65 AATGTAATTATTACACATCATATTAAAGATTTAATTGTTACATAC
* * * * * *
17587057 TATGTTAAAAATTGTAGTTGTTACACATAATGTTGAAGATTTAGTTGTTACACATCATGTTGAAA
1 CATGTTAAAAATT-TAGTTATTATACATCATGATGAAGATTTAGTTGTTACACATCATATTGAAA
* * *
17587122 AATGTAATTATTACACATCATGTTAAAGGTTTAATTGTTATATAC
65 AATGTAATTATTACACATCATATTAAAGATTTAATTGTTACATAC
* *
17587167 CATGTTGAAAAATTTAATTATTATACGTCATGATGAAGA---AGTTGTTACACATCA
1 CATGTT-AAAAATTTAGTTATTATACATCATGATGAAGATTTAGTTGTTACACATCA
17587221 CGTCATAATT
Statistics
Matches: 133, Mismatches: 27, Indels: 9
0.79 0.16 0.05
Matches are distributed among these distances:
107 15 0.11
108 5 0.04
109 6 0.05
110 100 0.75
111 7 0.05
ACGTcount: A:0.37, C:0.09, G:0.14, T:0.40
Consensus pattern (109 bp):
CATGTTAAAAATTTAGTTATTATACATCATGATGAAGATTTAGTTGTTACACATCATATTGAAAA
ATGTAATTATTACACATCATATTAAAGATTTAATTGTTACATAC
Found at i:17592267 original size:2 final size:2
Alignment explanation
Indices: 17592260--17592316 Score: 96
Period size: 2 Copynumber: 28.5 Consensus size: 2
17592250 TATTCCCTAT
* *
17592260 TA TA TA TA AA GA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
17592302 TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA T
17592317 CTACATGTGA
Statistics
Matches: 52, Mismatches: 3, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
2 52 1.00
ACGTcount: A:0.51, C:0.00, G:0.02, T:0.47
Consensus pattern (2 bp):
TA
Found at i:17593068 original size:12 final size:14
Alignment explanation
Indices: 17593041--17593082 Score: 52
Period size: 13 Copynumber: 3.1 Consensus size: 14
17593031 CTTTTATAAA
*
17593041 ATTTAAAAAAATTT
1 ATTTAAAATAATTT
17593055 A-TTAAAATAA-TT
1 ATTTAAAATAATTT
*
17593067 ATTTAAAATTATTT
1 ATTTAAAATAATTT
17593081 AT
1 AT
17593083 ATAAGGTTAA
Statistics
Matches: 24, Mismatches: 2, Indels: 4
0.80 0.07 0.13
Matches are distributed among these distances:
12 3 0.12
13 16 0.67
14 5 0.21
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (14 bp):
ATTTAAAATAATTT
Found at i:17593170 original size:18 final size:18
Alignment explanation
Indices: 17593143--17593177 Score: 61
Period size: 18 Copynumber: 1.9 Consensus size: 18
17593133 TGTTACGTAT
*
17593143 ACACGTTTAAACACGATA
1 ACACGATTAAACACGATA
17593161 ACACGATTAAACACGAT
1 ACACGATTAAACACGAT
17593178 TAAATAAACG
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
18 16 1.00
ACGTcount: A:0.46, C:0.23, G:0.11, T:0.20
Consensus pattern (18 bp):
ACACGATTAAACACGATA
Found at i:17593173 original size:10 final size:10
Alignment explanation
Indices: 17593143--17593181 Score: 55
Period size: 10 Copynumber: 4.1 Consensus size: 10
17593133 TGTTACGTAT
*
17593143 ACACGTTTAA
1 ACACGATTAA
17593153 ACACGA-T-A
1 ACACGATTAA
17593161 ACACGATTAA
1 ACACGATTAA
17593171 ACACGATTAA
1 ACACGATTAA
17593181 A
1 A
17593182 TAAACGTGTT
Statistics
Matches: 26, Mismatches: 1, Indels: 4
0.84 0.03 0.13
Matches are distributed among these distances:
8 7 0.27
9 2 0.08
10 17 0.65
ACGTcount: A:0.49, C:0.21, G:0.10, T:0.21
Consensus pattern (10 bp):
ACACGATTAA
Found at i:17595136 original size:1 final size:1
Alignment explanation
Indices: 17595126--17595251 Score: 243
Period size: 1 Copynumber: 126.0 Consensus size: 1
17595116 AAACAAAACC
*
17595126 AAAAAGAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA
1 AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA
17595191 AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA
1 AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA
17595252 CCTTGCAGAG
Statistics
Matches: 123, Mismatches: 2, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
1 123 1.00
ACGTcount: A:0.99, C:0.00, G:0.01, T:0.00
Consensus pattern (1 bp):
A
Found at i:17600777 original size:12 final size:11
Alignment explanation
Indices: 17600732--17600784 Score: 56
Period size: 10 Copynumber: 4.8 Consensus size: 11
17600722 AAAAGGTGAG
17600732 AGAAGAAAAAGAA
1 AGAAG-AAAA-AA
*
17600745 AGGAGAAAAAA
1 AGAAGAAAAAA
*
17600756 A-AAGAAAAAG
1 AGAAGAAAAAA
17600766 AG-AGAAAAAA
1 AGAAGAAAAAA
17600776 AGAAGAAAA
1 AGAAGAAAA
17600785 GAAACAAAAG
Statistics
Matches: 34, Mismatches: 4, Indels: 6
0.77 0.09 0.14
Matches are distributed among these distances:
10 17 0.50
11 9 0.26
12 4 0.12
13 4 0.12
ACGTcount: A:0.77, C:0.00, G:0.23, T:0.00
Consensus pattern (11 bp):
AGAAGAAAAAA
Found at i:17600779 original size:8 final size:8
Alignment explanation
Indices: 17600752--17600794 Score: 50
Period size: 8 Copynumber: 5.0 Consensus size: 8
17600742 GAAAGGAGAA
17600752 AAAAAAAG
1 AAAAAAAG
17600760 AAAAAGAGAG
1 AAAAA-A-AG
17600770 AAAAAAAG
1 AAAAAAAG
*
17600778 AAGAAAAG
1 AAAAAAAG
17600786 AAACAAAAG
1 AAA-AAAAG
17600795 TAAGAAATAA
Statistics
Matches: 30, Mismatches: 2, Indels: 5
0.81 0.05 0.14
Matches are distributed among these distances:
8 16 0.53
9 7 0.23
10 7 0.23
ACGTcount: A:0.79, C:0.02, G:0.19, T:0.00
Consensus pattern (8 bp):
AAAAAAAG
Found at i:17600786 original size:20 final size:20
Alignment explanation
Indices: 17600743--17600784 Score: 68
Period size: 20 Copynumber: 2.1 Consensus size: 20
17600733 GAAGAAAAAG
17600743 AAAG-GAGAAAAAAAAAGAA
1 AAAGAGAGAAAAAAAAAGAA
17600762 AAAGAGAGAAAAAAAGAAGAA
1 AAAGAGAGAAAAAAA-AAGAA
17600783 AA
1 AA
17600785 GAAACAAAAG
Statistics
Matches: 21, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
19 4 0.19
20 10 0.48
21 7 0.33
ACGTcount: A:0.79, C:0.00, G:0.21, T:0.00
Consensus pattern (20 bp):
AAAGAGAGAAAAAAAAAGAA
Found at i:17600793 original size:18 final size:17
Alignment explanation
Indices: 17600730--17600794 Score: 62
Period size: 18 Copynumber: 3.8 Consensus size: 17
17600720 GGAAAAGGTG
*
17600730 AGAGAAGAAAAAG-AAA
1 AGAGAAAAAAAAGAAAA
*
17600746 GGAGAAAAAAAAAGAAAA
1 AGAG-AAAAAAAAGAAAA
17600764 AGAGAGAAAAAAAGAAGAA
1 AGAGA-AAAAAAAGAA-AA
*
17600783 A-AGAAACAAAAG
1 AGAGAAAAAAAAG
17600795 TAAGAAATAA
Statistics
Matches: 41, Mismatches: 4, Indels: 7
0.79 0.08 0.13
Matches are distributed among these distances:
16 3 0.07
17 16 0.39
18 19 0.46
19 3 0.07
ACGTcount: A:0.75, C:0.02, G:0.23, T:0.00
Consensus pattern (17 bp):
AGAGAAAAAAAAGAAAA
Found at i:17600793 original size:20 final size:20
Alignment explanation
Indices: 17600750--17600793 Score: 54
Period size: 20 Copynumber: 2.2 Consensus size: 20
17600740 AAGAAAGGAG
* *
17600750 AAAAAAAAAGAAAAAGAGAG
1 AAAAAAAAAGAAAAAGAAAC
17600770 AAAAAAAGAAG-AAAAGAAAC
1 AAAAAAA-AAGAAAAAGAAAC
17600790 AAAA
1 AAAA
17600794 GTAAGAAATA
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
20 18 0.86
21 3 0.14
ACGTcount: A:0.82, C:0.02, G:0.16, T:0.00
Consensus pattern (20 bp):
AAAAAAAAAGAAAAAGAAAC
Found at i:17600799 original size:18 final size:16
Alignment explanation
Indices: 17600752--17600801 Score: 55
Period size: 18 Copynumber: 2.9 Consensus size: 16
17600742 GAAAGGAGAA
*
17600752 AAAAAAAGAAAAAGAGAG
1 AAAAAAAGAAGAA-A-AG
17600770 AAAAAAAGAAGAAAAG
1 AAAAAAAGAAGAAAAG
17600786 AAACAAAAGTAAGAAA
1 AAA-AAAAG-AAGAAA
17600802 TAATTAGAAG
Statistics
Matches: 29, Mismatches: 1, Indels: 4
0.85 0.03 0.12
Matches are distributed among these distances:
16 5 0.17
17 6 0.21
18 18 0.62
ACGTcount: A:0.78, C:0.02, G:0.18, T:0.02
Consensus pattern (16 bp):
AAAAAAAGAAGAAAAG
Found at i:17601034 original size:25 final size:25
Alignment explanation
Indices: 17601000--17601047 Score: 78
Period size: 25 Copynumber: 1.9 Consensus size: 25
17600990 GTTTACCACT
17601000 TCAGCATTGACGTGGTAGTGCCATA
1 TCAGCATTGACGTGGTAGTGCCATA
* *
17601025 TCAGCATTGATGTGTTAGTGCCA
1 TCAGCATTGACGTGGTAGTGCCA
17601048 CGTTAACAAC
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
25 21 1.00
ACGTcount: A:0.23, C:0.19, G:0.27, T:0.31
Consensus pattern (25 bp):
TCAGCATTGACGTGGTAGTGCCATA
Found at i:17604088 original size:23 final size:23
Alignment explanation
Indices: 17604039--17604089 Score: 59
Period size: 23 Copynumber: 2.2 Consensus size: 23
17604029 TAACGTAATG
*
17604039 CCTAACAAACCAGTCTGGCAATG
1 CCTAACAAACCAGTCTGGCAATA
* *
17604062 CCTAACAAACTATTCAT-GCAATA
1 CCTAACAAACCAGTC-TGGCAATA
17604085 CCTAA
1 CCTAA
17604090 AAATTAGTCC
Statistics
Matches: 24, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
23 23 0.96
24 1 0.04
ACGTcount: A:0.39, C:0.29, G:0.10, T:0.22
Consensus pattern (23 bp):
CCTAACAAACCAGTCTGGCAATA
Found at i:17604190 original size:22 final size:22
Alignment explanation
Indices: 17604165--17604221 Score: 60
Period size: 22 Copynumber: 2.6 Consensus size: 22
17604155 AAATCAATCT
* *
17604165 CGTAATTCCTACAACCTAGTCA
1 CGTAATACCTAAAACCTAGTCA
* *
17604187 CGTAATACCTAAAAGCTAGTCT
1 CGTAATACCTAAAACCTAGTCA
* *
17604209 CGCAATGCCTAAA
1 CGTAATACCTAAA
17604222 CACTAATCTT
Statistics
Matches: 29, Mismatches: 6, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
22 29 1.00
ACGTcount: A:0.35, C:0.28, G:0.12, T:0.25
Consensus pattern (22 bp):
CGTAATACCTAAAACCTAGTCA
Found at i:17604258 original size:22 final size:21
Alignment explanation
Indices: 17604180--17604267 Score: 86
Period size: 22 Copynumber: 4.0 Consensus size: 21
17604170 TTCCTACAAC
* *
17604180 CTAGTCACGTAATACCTAAAA
1 CTAGTCACGCAATGCCTAAAA
*
17604201 GCTAGTCTCGCAATGCCTAAACA
1 -CTAGTCACGCAATGCCTAAA-A
* **
17604224 CTAATCTTGCAATGCCTACAAA
1 CTAGTCACGCAATGCCTA-AAA
*
17604246 CTAGTCACACAATGCCTAAAA
1 CTAGTCACGCAATGCCTAAAA
17604267 C
1 C
17604268 CCTTCTTTCT
Statistics
Matches: 55, Mismatches: 9, Indels: 5
0.80 0.13 0.07
Matches are distributed among these distances:
21 4 0.07
22 48 0.87
23 3 0.05
ACGTcount: A:0.38, C:0.28, G:0.11, T:0.23
Consensus pattern (21 bp):
CTAGTCACGCAATGCCTAAAA
Found at i:17605262 original size:22 final size:22
Alignment explanation
Indices: 17605230--17605284 Score: 83
Period size: 23 Copynumber: 2.4 Consensus size: 22
17605220 GTTTGAAAAC
17605230 AAGGATAAAAATTCATAAGTTTT
1 AAGG-TAAAAATTCATAAGTTTT
*
17605253 AAGGTTAAAAATTCATAATTTTT
1 AAGG-TAAAAATTCATAAGTTTT
17605276 AAGGTAAAA
1 AAGGTAAAA
17605285 TGGTAAAAAG
Statistics
Matches: 30, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
22 5 0.17
23 25 0.83
ACGTcount: A:0.49, C:0.04, G:0.13, T:0.35
Consensus pattern (22 bp):
AAGGTAAAAATTCATAAGTTTT
Found at i:17605633 original size:21 final size:22
Alignment explanation
Indices: 17605590--17605633 Score: 63
Period size: 22 Copynumber: 2.0 Consensus size: 22
17605580 TATAAGCATT
**
17605590 AAAAATAACCTTTTTGTTCTAA
1 AAAAATAACCTTTTTGTAATAA
17605612 AAAAATAACCTTTTTG-AATAA
1 AAAAATAACCTTTTTGTAATAA
17605633 A
1 A
17605634 GATAACAAAA
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
21 4 0.20
22 16 0.80
ACGTcount: A:0.48, C:0.11, G:0.05, T:0.36
Consensus pattern (22 bp):
AAAAATAACCTTTTTGTAATAA
Found at i:17607034 original size:24 final size:24
Alignment explanation
Indices: 17606986--17607034 Score: 64
Period size: 24 Copynumber: 2.0 Consensus size: 24
17606976 ACAAAAAAGC
*
17606986 ACCAAAAGAAATAAAGAAAACAAA
1 ACCAAAAGAAATAAAAAAAACAAA
*
17607010 ACCAAATA-AAATAAAAAAAAGAAA
1 ACCAAA-AGAAATAAAAAAAACAAA
17607034 A
1 A
17607035 GAGCAGTGAA
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
24 21 0.95
25 1 0.05
ACGTcount: A:0.78, C:0.10, G:0.06, T:0.06
Consensus pattern (24 bp):
ACCAAAAGAAATAAAAAAAACAAA
Done.