Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: A11
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: 114316535
ACGTcount: A:0.31, C:0.16, G:0.16, T:0.31
Warning! 4920000 characters in sequence are not A, C, G, or T
File 27 of 356
Found at i:9187038 original size:21 final size:22
Alignment explanation
Indices: 9187012--9187053 Score: 68
Period size: 21 Copynumber: 2.0 Consensus size: 22
9187002 TGACCTTTCC
*
9187012 AAGGTATGGG-TAGGTATGGGA
1 AAGGTATGGGCAAGGTATGGGA
9187033 AAGGTATGGGCAAGGTATGGG
1 AAGGTATGGGCAAGGTATGGG
9187054 GTATATTCTA
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
21 10 0.53
22 9 0.47
ACGTcount: A:0.29, C:0.02, G:0.48, T:0.21
Consensus pattern (22 bp):
AAGGTATGGGCAAGGTATGGGA
Found at i:9187039 original size:11 final size:10
Alignment explanation
Indices: 9187012--9187053 Score: 57
Period size: 11 Copynumber: 4.0 Consensus size: 10
9187002 TGACCTTTCC
9187012 AAGGTATGGG
1 AAGGTATGGG
*
9187022 TAGGTATGGG
1 AAGGTATGGG
9187032 AAAGGTATGGG
1 -AAGGTATGGG
9187043 CAAGGTATGGG
1 -AAGGTATGGG
9187054 GTATATTCTA
Statistics
Matches: 28, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
10 9 0.32
11 19 0.68
ACGTcount: A:0.29, C:0.02, G:0.48, T:0.21
Consensus pattern (10 bp):
AAGGTATGGG
Found at i:9195643 original size:14 final size:14
Alignment explanation
Indices: 9195624--9195651 Score: 56
Period size: 14 Copynumber: 2.0 Consensus size: 14
9195614 ATGGAATATG
9195624 ATGGCTCTAATCTA
1 ATGGCTCTAATCTA
9195638 ATGGCTCTAATCTA
1 ATGGCTCTAATCTA
9195652 GGGAAGGAAA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 14 1.00
ACGTcount: A:0.29, C:0.21, G:0.14, T:0.36
Consensus pattern (14 bp):
ATGGCTCTAATCTA
Found at i:9197710 original size:14 final size:14
Alignment explanation
Indices: 9197691--9197720 Score: 60
Period size: 14 Copynumber: 2.1 Consensus size: 14
9197681 TTTTTGCCTT
9197691 AGCCAACTGAATAG
1 AGCCAACTGAATAG
9197705 AGCCAACTGAATAG
1 AGCCAACTGAATAG
9197719 AG
1 AG
9197721 GTATGAACGT
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 16 1.00
ACGTcount: A:0.43, C:0.20, G:0.23, T:0.13
Consensus pattern (14 bp):
AGCCAACTGAATAG
Found at i:9209175 original size:22 final size:21
Alignment explanation
Indices: 9209137--9209188 Score: 59
Period size: 22 Copynumber: 2.3 Consensus size: 21
9209127 AAAAAAACTG
*
9209137 TTATTTTTTTCACTATTTTAT
1 TTATTTTTCTCACTATTTTAT
*
9209158 TTATATTTTCTCATTATTTTACT
1 TTAT-TTTTCTCACTATTTTA-T
9209181 GTTATTTT
1 -TTATTTT
9209189 ATTATTATGT
Statistics
Matches: 26, Mismatches: 2, Indels: 4
0.81 0.06 0.12
Matches are distributed among these distances:
21 4 0.15
22 14 0.54
23 4 0.15
24 4 0.15
ACGTcount: A:0.19, C:0.10, G:0.02, T:0.69
Consensus pattern (21 bp):
TTATTTTTCTCACTATTTTAT
Found at i:9209195 original size:22 final size:22
Alignment explanation
Indices: 9209133--9209196 Score: 58
Period size: 22 Copynumber: 2.9 Consensus size: 22
9209123 GTAAAAAAAA
* *
9209133 ACTGTTATTTTTTTCACTATTTT
1 ACTGTTATTTTATT-ATTATTTT
* * *
9209156 A-TTTATATTTTCTCATTATTTT
1 ACTGT-TATTTTATTATTATTTT
9209178 ACTGTTATTTTATTATTAT
1 ACTGTTATTTTATTATTAT
9209197 GTTGCTACCA
Statistics
Matches: 32, Mismatches: 7, Indels: 5
0.73 0.16 0.11
Matches are distributed among these distances:
22 22 0.69
23 10 0.31
ACGTcount: A:0.22, C:0.09, G:0.03, T:0.66
Consensus pattern (22 bp):
ACTGTTATTTTATTATTATTTT
Found at i:9212533 original size:14 final size:14
Alignment explanation
Indices: 9212511--9212540 Score: 51
Period size: 14 Copynumber: 2.1 Consensus size: 14
9212501 TTAAAGTATG
9212511 TTCTCTTTTTTCTT
1 TTCTCTTTTTTCTT
*
9212525 TTCTTTTTTTTCTT
1 TTCTCTTTTTTCTT
9212539 TT
1 TT
9212541 ATCCCTTTGT
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
14 15 1.00
ACGTcount: A:0.00, C:0.17, G:0.00, T:0.83
Consensus pattern (14 bp):
TTCTCTTTTTTCTT
Found at i:9214599 original size:137 final size:138
Alignment explanation
Indices: 9214351--9214620 Score: 472
Period size: 137 Copynumber: 2.0 Consensus size: 138
9214341 AAAATGATGG
* *
9214351 ATAAATCATGGGATTTGATAAATATTTAGAGAATTGTACGGTGATTGAGGCTAAACTTTAAGACA
1 ATAAATCATGAGATTTGATAAATATTTAGAGAATTGTACGGTGATTGACGCTAAACTTTAAGACA
*
9214416 TCATTGACAGTTTAAAATTTATTATAGATAGAATATTTGAAAAGATCTTAATCGAAATTGATATT
66 TCATTGACAGTTTAAAATTTATTATAGATAGAATATTTAAAAAGATCTTAATCGAAATTGATATT
9214481 GATTTTTC
131 GATTTTTC
*
9214489 ATAAATCATGAGATTTGATAAATATTTAGAGAATTGTACTGTGATTGACGCTAAA-TTTAAGACA
1 ATAAATCATGAGATTTGATAAATATTTAGAGAATTGTACGGTGATTGACGCTAAACTTTAAGACA
*
9214553 TCA-TGAACAGTTTAAAGTTTATTATAGATAGAATATTTAAAAAGATCTTAATCGAAATTGATAT
66 TCATTG-ACAGTTTAAAATTTATTATAGATAGAATATTTAAAAAGATCTTAATCGAAATTGATAT
9214617 TGAT
130 TGAT
9214621 ATTGATATTT
Statistics
Matches: 126, Mismatches: 5, Indels: 3
0.94 0.04 0.02
Matches are distributed among these distances:
136 2 0.02
137 72 0.57
138 52 0.41
ACGTcount: A:0.40, C:0.07, G:0.16, T:0.37
Consensus pattern (138 bp):
ATAAATCATGAGATTTGATAAATATTTAGAGAATTGTACGGTGATTGACGCTAAACTTTAAGACA
TCATTGACAGTTTAAAATTTATTATAGATAGAATATTTAAAAAGATCTTAATCGAAATTGATATT
GATTTTTC
Found at i:9217433 original size:28 final size:25
Alignment explanation
Indices: 9217401--9217463 Score: 63
Period size: 27 Copynumber: 2.3 Consensus size: 25
9217391 AGAGTATTTG
*
9217401 AAATTTATGATATTTATCTTATTTAAAA
1 AAATTTATGATA-TAATCTTA--TAAAA
*
9217429 AAATTAATTTGATATAATCTTATAAAA
1 AAATT--TATGATATAATCTTATAAAA
9217456 AAATTTAT
1 AAATTTAT
9217464 CAAAGAGAAA
Statistics
Matches: 30, Mismatches: 3, Indels: 7
0.75 0.08 0.17
Matches are distributed among these distances:
25 2 0.07
27 10 0.33
28 5 0.17
29 7 0.23
30 6 0.20
ACGTcount: A:0.48, C:0.03, G:0.03, T:0.46
Consensus pattern (25 bp):
AAATTTATGATATAATCTTATAAAA
Found at i:9218862 original size:19 final size:20
Alignment explanation
Indices: 9218840--9218877 Score: 53
Period size: 20 Copynumber: 1.9 Consensus size: 20
9218830 ATAAATAAGT
9218840 ATTT-TCAA-ATTACAAATTA
1 ATTTATCAATATTA-AAATTA
9218859 ATTTATCAATATTAAAATT
1 ATTTATCAATATTAAAATT
9218878 TTAAAACAAA
Statistics
Matches: 17, Mismatches: 0, Indels: 3
0.85 0.00 0.15
Matches are distributed among these distances:
19 4 0.24
20 9 0.53
21 4 0.24
ACGTcount: A:0.47, C:0.08, G:0.00, T:0.45
Consensus pattern (20 bp):
ATTTATCAATATTAAAATTA
Found at i:9224090 original size:17 final size:16
Alignment explanation
Indices: 9224040--9224084 Score: 65
Period size: 17 Copynumber: 2.8 Consensus size: 16
9224030 TTTAATTTTT
9224040 TAAAAATTATAAATATA
1 TAAAAATTATAAATA-A
9224057 TAAAATATTA-AAATAA
1 TAAAA-ATTATAAATAA
9224073 TAAAAATTATAA
1 TAAAAATTATAA
9224085 TTTAATTTCA
Statistics
Matches: 26, Mismatches: 0, Indels: 5
0.84 0.00 0.16
Matches are distributed among these distances:
15 4 0.15
16 8 0.31
17 10 0.38
18 4 0.15
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (16 bp):
TAAAAATTATAAATAA
Found at i:9231597 original size:13 final size:14
Alignment explanation
Indices: 9231560--9231587 Score: 56
Period size: 14 Copynumber: 2.0 Consensus size: 14
9231550 GTTCTTCGTC
9231560 CAAATATTTAATTA
1 CAAATATTTAATTA
9231574 CAAATATTTAATTA
1 CAAATATTTAATTA
9231588 TTATATTTAA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 14 1.00
ACGTcount: A:0.50, C:0.07, G:0.00, T:0.43
Consensus pattern (14 bp):
CAAATATTTAATTA
Found at i:9231611 original size:19 final size:19
Alignment explanation
Indices: 9231589--9231626 Score: 51
Period size: 19 Copynumber: 2.0 Consensus size: 19
9231579 ATTTAATTAT
9231589 TATATT-TAAATATAATTTA
1 TATATTCTAAATA-AATTTA
*
9231608 TATATTCTAATTAAATTTA
1 TATATTCTAAATAAATTTA
9231627 ATAAATAATT
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
19 12 0.71
20 5 0.29
ACGTcount: A:0.45, C:0.03, G:0.00, T:0.53
Consensus pattern (19 bp):
TATATTCTAAATAAATTTA
Found at i:9231882 original size:26 final size:26
Alignment explanation
Indices: 9231853--9231918 Score: 69
Period size: 26 Copynumber: 2.5 Consensus size: 26
9231843 ATCATTCAAA
* * **
9231853 TTTTCAAAAGTATTTCTTAAAATTAC
1 TTTTCAAAAGCATTTCTCAAAAGCAC
* *
9231879 TTTTCCACAGCATTTCTCAAAAGCAC
1 TTTTCAAAAGCATTTCTCAAAAGCAC
*
9231905 TTTTCAAAGGCATT
1 TTTTCAAAAGCATT
9231919 GCTAAACTAG
Statistics
Matches: 31, Mismatches: 9, Indels: 0
0.77 0.22 0.00
Matches are distributed among these distances:
26 31 1.00
ACGTcount: A:0.33, C:0.20, G:0.08, T:0.39
Consensus pattern (26 bp):
TTTTCAAAAGCATTTCTCAAAAGCAC
Found at i:9234824 original size:45 final size:45
Alignment explanation
Indices: 9234749--9234860 Score: 170
Period size: 45 Copynumber: 2.5 Consensus size: 45
9234739 AATCAATAAT
* * *
9234749 GGTAGCAGTAACAGTAACAGAATTCAACACACAAAGTGTCGAATC
1 GGTAACAGTAACGGTAACAGTATTCAACACACAAAGTGTCGAATC
* *
9234794 TGTAACAGTAACGGTAACAGTATTCGACACACAAAGTGTCGAATC
1 GGTAACAGTAACGGTAACAGTATTCAACACACAAAGTGTCGAATC
*
9234839 GGTGACAGTAACGGTAACAGTA
1 GGTAACAGTAACGGTAACAGTA
9234861 ACAATAGTCG
Statistics
Matches: 60, Mismatches: 7, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
45 60 1.00
ACGTcount: A:0.39, C:0.19, G:0.22, T:0.20
Consensus pattern (45 bp):
GGTAACAGTAACGGTAACAGTATTCAACACACAAAGTGTCGAATC
Found at i:9235979 original size:23 final size:24
Alignment explanation
Indices: 9235952--9235999 Score: 64
Period size: 24 Copynumber: 2.0 Consensus size: 24
9235942 AGTTTATTGT
9235952 ATTATTA-TATTAACTT-AATAATA
1 ATTATTATTATT-ACTTAAATAATA
*
9235975 ATTATTATTATTTCTTAAATAATA
1 ATTATTATTATTACTTAAATAATA
9235999 A
1 A
9236000 GTAAATAAAT
Statistics
Matches: 22, Mismatches: 1, Indels: 3
0.85 0.04 0.12
Matches are distributed among these distances:
23 10 0.45
24 12 0.55
ACGTcount: A:0.46, C:0.04, G:0.00, T:0.50
Consensus pattern (24 bp):
ATTATTATTATTACTTAAATAATA
Found at i:9236351 original size:9 final size:9
Alignment explanation
Indices: 9236337--9236361 Score: 50
Period size: 9 Copynumber: 2.8 Consensus size: 9
9236327 AATTTATAAT
9236337 ATAATAACA
1 ATAATAACA
9236346 ATAATAACA
1 ATAATAACA
9236355 ATAATAA
1 ATAATAA
9236362 TATATTTTAT
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
9 16 1.00
ACGTcount: A:0.68, C:0.08, G:0.00, T:0.24
Consensus pattern (9 bp):
ATAATAACA
Found at i:9241913 original size:52 final size:53
Alignment explanation
Indices: 9241804--9241963 Score: 173
Period size: 52 Copynumber: 3.1 Consensus size: 53
9241794 TGACGGAAAA
* * * * *
9241804 GATGTGA-TACATGATTCCGTATAAGACCATAGCCGAGCTACGGCATCGGTAC
1 GATGTGATTACGTGATCCCGTATAAGACCATAGCCGGGCTATGGCATCGGTAT
* * *
9241856 CATGTGATT-CGT-ATCCCCGTATAAGACCATAGCTGGGCTATGGCATCGGTGT
1 GATGTGATTACGTGAT-CCCGTATAAGACCATAGCCGGGCTATGGCATCGGTAT
* * * **
9241908 GATGTGATTATGTGATTCCGTATAAGACCATATCCGGAATATGGCATCGGTAT
1 GATGTGATTACGTGATCCCGTATAAGACCATAGCCGGGCTATGGCATCGGTAT
9241961 GAT
1 GAT
9241964 ATGTGGTCCG
Statistics
Matches: 88, Mismatches: 16, Indels: 7
0.79 0.14 0.06
Matches are distributed among these distances:
51 2 0.02
52 47 0.53
53 37 0.42
54 2 0.02
ACGTcount: A:0.26, C:0.20, G:0.26, T:0.28
Consensus pattern (53 bp):
GATGTGATTACGTGATCCCGTATAAGACCATAGCCGGGCTATGGCATCGGTAT
Found at i:9242291 original size:19 final size:19
Alignment explanation
Indices: 9242267--9242312 Score: 92
Period size: 19 Copynumber: 2.4 Consensus size: 19
9242257 TATGCCTAAG
9242267 AGCTTACTAAGCTTCAATA
1 AGCTTACTAAGCTTCAATA
9242286 AGCTTACTAAGCTTCAATA
1 AGCTTACTAAGCTTCAATA
9242305 AGCTTACT
1 AGCTTACT
9242313 TGTGTGTGTT
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 27 1.00
ACGTcount: A:0.35, C:0.22, G:0.11, T:0.33
Consensus pattern (19 bp):
AGCTTACTAAGCTTCAATA
Found at i:9242296 original size:9 final size:9
Alignment explanation
Indices: 9242267--9242312 Score: 56
Period size: 10 Copynumber: 4.9 Consensus size: 9
9242257 TATGCCTAAG
9242267 AGCTTACTA
1 AGCTTACTA
*
9242276 AGCTTCAATA
1 AGCTT-ACTA
9242286 AGCTTACTA
1 AGCTTACTA
*
9242295 AGCTTCAATA
1 AGCTT-ACTA
9242305 AGCTTACT
1 AGCTTACT
9242313 TGTGTGTGTT
Statistics
Matches: 31, Mismatches: 4, Indels: 4
0.79 0.10 0.10
Matches are distributed among these distances:
9 15 0.48
10 16 0.52
ACGTcount: A:0.35, C:0.22, G:0.11, T:0.33
Consensus pattern (9 bp):
AGCTTACTA
Found at i:9245673 original size:50 final size:50
Alignment explanation
Indices: 9245598--9245774 Score: 248
Period size: 50 Copynumber: 3.5 Consensus size: 50
9245588 CCATGGCAAC
9245598 AAGTGATAAGTGATAGCTTCGGCTACACTTATCTGATCAAGGACAAATGA
1 AAGTGATAAGTGATAGCTTCGGCTACACTTATCTGATCAAGGACAAATGA
* * *
9245648 AAGTGATAAGTAATAGCTTCGGCTACATTTATCTGATCAAGGACAAGTGA
1 AAGTGATAAGTGATAGCTTCGGCTACACTTATCTGATCAAGGACAAATGA
* * *
9245698 AAGTGATAAGTGATAGCTTCAGCTACACTTATCTGATCAATGATAAAT-A
1 AAGTGATAAGTGATAGCTTCGGCTACACTTATCTGATCAAGGACAAATGA
* * *
9245747 ATACGTGAAAAGTGGTAGCTTCAGCTAC
1 A-A-GTGATAAGTGATAGCTTCGGCTAC
9245775 CTAATCAGTG
Statistics
Matches: 114, Mismatches: 11, Indels: 3
0.89 0.09 0.02
Matches are distributed among these distances:
49 2 0.02
50 90 0.79
51 22 0.19
ACGTcount: A:0.36, C:0.15, G:0.21, T:0.28
Consensus pattern (50 bp):
AAGTGATAAGTGATAGCTTCGGCTACACTTATCTGATCAAGGACAAATGA
Found at i:9245789 original size:31 final size:31
Alignment explanation
Indices: 9245751--9245835 Score: 134
Period size: 31 Copynumber: 2.7 Consensus size: 31
9245741 TAAATAATAC
*
9245751 GTGAAAAGTGGTAGCTTCAGCTACCTAATCA
1 GTGAAAAGTGGTAGCTTCGGCTACCTAATCA
* *
9245782 GTGAAAAGTGGTAGCTCCGGCTACCTGATCA
1 GTGAAAAGTGGTAGCTTCGGCTACCTAATCA
*
9245813 GTGAATAGTGGTAGCTTCGGCTA
1 GTGAAAAGTGGTAGCTTCGGCTA
9245836 TAAGTGACAA
Statistics
Matches: 49, Mismatches: 5, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
31 49 1.00
ACGTcount: A:0.27, C:0.19, G:0.28, T:0.26
Consensus pattern (31 bp):
GTGAAAAGTGGTAGCTTCGGCTACCTAATCA
Found at i:9246006 original size:49 final size:48
Alignment explanation
Indices: 9245936--9246068 Score: 188
Period size: 49 Copynumber: 2.9 Consensus size: 48
9245926 GCATCAGTGA
* *
9245936 GATATGTGATTCGTGTAAGACCATAGCTGGGCTATGACATCAATATGT
1 GATATGTGATTCGTGTAAGACCATAGCTGGGCTATGGCATCAATATAT
*
9245984 GATATGTGATTACGTGTAAGACCATAGCTGGGCTATGGCATCGATATAT
1 GATATGTGATT-CGTGTAAGACCATAGCTGGGCTATGGCATCAATATAT
9246033 GA-A--T-A-T-GTGTAAGACCATAGCTGGGCTATGGCATCA
1 GATATGTGATTCGTGTAAGACCATAGCTGGGCTATGGCATCA
9246069 TTATCTGAAG
Statistics
Matches: 80, Mismatches: 4, Indels: 8
0.87 0.04 0.09
Matches are distributed among these distances:
42 29 0.36
44 1 0.01
45 1 0.01
46 1 0.01
48 12 0.15
49 36 0.45
ACGTcount: A:0.29, C:0.15, G:0.26, T:0.29
Consensus pattern (48 bp):
GATATGTGATTCGTGTAAGACCATAGCTGGGCTATGGCATCAATATAT
Found at i:9246043 original size:42 final size:43
Alignment explanation
Indices: 9245948--9246111 Score: 172
Period size: 42 Copynumber: 3.7 Consensus size: 43
9245938 TATGTGATTC
* * *
9245948 GTGTAAGACCATAGCTGGGCTATGACATCAATATGTGATATG-TGATT
1 GTGTAAGACCATAGCTGGGCTATGGCATC--GAT-T-ATATGAAGA-T
*
9245995 ACGTGTAAGACCATAGCTGGGCTATGGCATCGA-TATATGAATAT
1 --GTGTAAGACCATAGCTGGGCTATGGCATCGATTATATGAAGAT
*
9246039 GTGTAAGACCATAGCTGGGCTATGGCATC-ATTATCTGAAGAT
1 GTGTAAGACCATAGCTGGGCTATGGCATCGATTATATGAAGAT
* **
9246081 GTGTAAGACCATAGTTGAACTATGGCATCGA
1 GTGTAAGACCATAGCTGGGCTATGGCATCGA
9246112 GAAAACGAAG
Statistics
Matches: 103, Mismatches: 9, Indels: 12
0.83 0.07 0.10
Matches are distributed among these distances:
41 1 0.01
42 64 0.62
43 1 0.01
44 6 0.06
45 2 0.02
47 1 0.01
49 28 0.27
ACGTcount: A:0.30, C:0.15, G:0.26, T:0.29
Consensus pattern (43 bp):
GTGTAAGACCATAGCTGGGCTATGGCATCGATTATATGAAGAT
Found at i:9250404 original size:18 final size:18
Alignment explanation
Indices: 9250381--9250425 Score: 81
Period size: 18 Copynumber: 2.5 Consensus size: 18
9250371 TATAACTCCC
*
9250381 ATATTTTCTGTCTCTATA
1 ATATTTCCTGTCTCTATA
9250399 ATATTTCCTGTCTCTATA
1 ATATTTCCTGTCTCTATA
9250417 ATATTTCCT
1 ATATTTCCT
9250426 ATTACTTTCT
Statistics
Matches: 26, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
18 26 1.00
ACGTcount: A:0.22, C:0.20, G:0.04, T:0.53
Consensus pattern (18 bp):
ATATTTCCTGTCTCTATA
Found at i:9252148 original size:11 final size:11
Alignment explanation
Indices: 9252132--9252156 Score: 50
Period size: 11 Copynumber: 2.3 Consensus size: 11
9252122 ATATCTAGAA
9252132 TTCTCTTCATT
1 TTCTCTTCATT
9252143 TTCTCTTCATT
1 TTCTCTTCATT
9252154 TTC
1 TTC
9252157 ATCAGTTGAA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 14 1.00
ACGTcount: A:0.08, C:0.28, G:0.00, T:0.64
Consensus pattern (11 bp):
TTCTCTTCATT
Found at i:9256971 original size:13 final size:13
Alignment explanation
Indices: 9256953--9256977 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
9256943 GTTGGAAGGT
9256953 TTTTTCTTTTTTC
1 TTTTTCTTTTTTC
9256966 TTTTTCTTTTTT
1 TTTTTCTTTTTT
9256978 AACTTTACTC
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:0.00, C:0.12, G:0.00, T:0.88
Consensus pattern (13 bp):
TTTTTCTTTTTTC
Found at i:9260518 original size:18 final size:18
Alignment explanation
Indices: 9260495--9260530 Score: 54
Period size: 18 Copynumber: 2.0 Consensus size: 18
9260485 AAAATTAGAT
9260495 GATTTGAATAAAAATATA
1 GATTTGAATAAAAATATA
**
9260513 GATTTGTGTAAAAATATA
1 GATTTGAATAAAAATATA
9260531 ATATTTTTTT
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
18 16 1.00
ACGTcount: A:0.50, C:0.00, G:0.14, T:0.36
Consensus pattern (18 bp):
GATTTGAATAAAAATATA
Found at i:9263503 original size:13 final size:13
Alignment explanation
Indices: 9263485--9263509 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
9263475 TTTTTTTATA
9263485 TTTTTAATTAATG
1 TTTTTAATTAATG
9263498 TTTTTAATTAAT
1 TTTTTAATTAAT
9263510 AAATATATTG
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:0.04, T:0.64
Consensus pattern (13 bp):
TTTTTAATTAATG
Found at i:9263541 original size:16 final size:15
Alignment explanation
Indices: 9263520--9263568 Score: 53
Period size: 16 Copynumber: 3.1 Consensus size: 15
9263510 AAATATATTG
9263520 TTTTTAATTATTAAAA
1 TTTTTAATTA-TAAAA
**
9263536 TTTTTAATTAATAACT
1 TTTTTAATT-ATAAAA
*
9263552 TTTTTATTTATAAAA
1 TTTTTAATTATAAAA
9263567 TT
1 TT
9263569 AAATAATAAA
Statistics
Matches: 27, Mismatches: 5, Indels: 3
0.77 0.14 0.09
Matches are distributed among these distances:
15 6 0.22
16 20 0.74
17 1 0.04
ACGTcount: A:0.39, C:0.02, G:0.00, T:0.59
Consensus pattern (15 bp):
TTTTTAATTATAAAA
Found at i:9263829 original size:12 final size:13
Alignment explanation
Indices: 9263801--9263829 Score: 51
Period size: 13 Copynumber: 2.3 Consensus size: 13
9263791 ATATGTAAAA
9263801 TATTTCAAATAAT
1 TATTTCAAATAAT
9263814 TATTTCAAAT-AT
1 TATTTCAAATAAT
9263826 TATT
1 TATT
9263830 ATGTTTATTT
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
12 6 0.38
13 10 0.62
ACGTcount: A:0.41, C:0.07, G:0.00, T:0.52
Consensus pattern (13 bp):
TATTTCAAATAAT
Found at i:9275508 original size:40 final size:40
Alignment explanation
Indices: 9275453--9275532 Score: 160
Period size: 40 Copynumber: 2.0 Consensus size: 40
9275443 TTTTAAAATC
9275453 AGAGATTCTCCAGGACTATTGAAACACAATCCAGTTCTTT
1 AGAGATTCTCCAGGACTATTGAAACACAATCCAGTTCTTT
9275493 AGAGATTCTCCAGGACTATTGAAACACAATCCAGTTCTTT
1 AGAGATTCTCCAGGACTATTGAAACACAATCCAGTTCTTT
9275533 CCCCAGATGG
Statistics
Matches: 40, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
40 40 1.00
ACGTcount: A:0.33, C:0.23, G:0.15, T:0.30
Consensus pattern (40 bp):
AGAGATTCTCCAGGACTATTGAAACACAATCCAGTTCTTT
Found at i:9280230 original size:63 final size:63
Alignment explanation
Indices: 9280131--9280255 Score: 232
Period size: 63 Copynumber: 2.0 Consensus size: 63
9280121 CAGTCTGAGG
9280131 TGTTAAGTACTTCTAGTTCTATGAGAAAGGTCATGTCCCTCGAGCCAGCGGAGCATAAATCTA
1 TGTTAAGTACTTCTAGTTCTATGAGAAAGGTCATGTCCCTCGAGCCAGCGGAGCATAAATCTA
* *
9280194 TGTTAAGTACTTCTAGTTCTATGAGAAAGGTCATGTCTCTTGAGCCAGCGGAGCATAAATCT
1 TGTTAAGTACTTCTAGTTCTATGAGAAAGGTCATGTCCCTCGAGCCAGCGGAGCATAAATCT
9280256 GACATTCTTA
Statistics
Matches: 60, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
63 60 1.00
ACGTcount: A:0.28, C:0.19, G:0.22, T:0.30
Consensus pattern (63 bp):
TGTTAAGTACTTCTAGTTCTATGAGAAAGGTCATGTCCCTCGAGCCAGCGGAGCATAAATCTA
Found at i:9290495 original size:52 final size:48
Alignment explanation
Indices: 9290454--9290607 Score: 145
Period size: 47 Copynumber: 3.2 Consensus size: 48
9290444 CTTCGGAGAA
* *
9290454 ATGTGATATGTGCTTCCGTATGAGACCATATCCGGGATATGGCATCGG
1 ATGTGATATGTGCTTCCGTATAAGACCATATACGGGATATGGCATCGG
* * * *
9290502 -TGTGATATGTGCTACTGTATAAGACCATATATGGGATATGGCATC-A
1 ATGTGATATGTGCTTCCGTATAAGACCATATACGGGATATGGCATCGG
* * * ** * *
9290548 ATGTGATATATG-ATCCGTGTAAGACCAT-GGCTGGGCTATGGCCTCGG
1 ATGTGATATGTGCTTCCGTATAAGACCATATAC-GGGATATGGCATCGG
9290595 TATGTGATATGTG
1 -ATGTGATATGTG
9290608 ACTATGTGCC
Statistics
Matches: 84, Mismatches: 18, Indels: 8
0.76 0.16 0.07
Matches are distributed among these distances:
46 23 0.27
47 50 0.60
48 11 0.13
ACGTcount: A:0.25, C:0.16, G:0.29, T:0.31
Consensus pattern (48 bp):
ATGTGATATGTGCTTCCGTATAAGACCATATACGGGATATGGCATCGG
Found at i:9290527 original size:47 final size:47
Alignment explanation
Indices: 9290453--9290575 Score: 149
Period size: 47 Copynumber: 2.6 Consensus size: 47
9290443 GCTTCGGAGA
* * *
9290453 AATGTGATATGTGCTTCCGTATGAGACCATATCCGGGATATGGCATC
1 AATGTGATATGTGCTACCGTATAAGACCATATACGGGATATGGCATC
** * *
9290500 GGTGTGATATGTGCTACTGTATAAGACCATATATGGGATATGGCATC
1 AATGTGATATGTGCTACCGTATAAGACCATATACGGGATATGGCATC
* * *
9290547 AATGTGATATATGAT-CCGTGTAAGACCAT
1 AATGTGATATGTGCTACCGTATAAGACCAT
9290576 GGCTGGGCTA
Statistics
Matches: 63, Mismatches: 13, Indels: 1
0.82 0.17 0.01
Matches are distributed among these distances:
46 12 0.19
47 51 0.81
ACGTcount: A:0.28, C:0.15, G:0.25, T:0.31
Consensus pattern (47 bp):
AATGTGATATGTGCTACCGTATAAGACCATATACGGGATATGGCATC
Found at i:9293948 original size:78 final size:77
Alignment explanation
Indices: 9293815--9294044 Score: 370
Period size: 78 Copynumber: 2.9 Consensus size: 77
9293805 GAGTCACATC
* * *
9293815 TCATGTAACTATAGTGATTCAGGATTACCTTTTCAGGTCAAATCCTATCCACCTTAGGTTACCAT
1 TCATGTAACTGTAGTGAATCAGGATTA-CTTTTCAGGTCAAATCCTATCCACCTTAAGTTACCAT
*
9293880 AATGAATCATATA
65 AGTGAATCATATA
*
9293893 TCATGTAACTGTAGTGAATCAGGATTATCTTTTCAGGTCAAATCCTATCCTCCTTAAGTTACCAT
1 TCATGTAACTGTAGTGAATCAGGATTA-CTTTTCAGGTCAAATCCTATCCACCTTAAGTTACCAT
9293958 AGTGAATCATATA
65 AGTGAATCATATA
* *
9293971 TCATGTAACTGTAGCGAATCAAGATTACTTTTTCAGGTCAAATCCTATCCACCTTAAGTTACCAT
1 TCATGTAACTGTAGTGAATCAGGATTAC-TTTTCAGGTCAAATCCTATCCACCTTAAGTTACCAT
9294036 AGTGAATCA
65 AGTGAATCA
9294045 GGAATAAATC
Statistics
Matches: 142, Mismatches: 9, Indels: 2
0.93 0.06 0.01
Matches are distributed among these distances:
77 1 0.01
78 141 0.99
ACGTcount: A:0.32, C:0.20, G:0.13, T:0.34
Consensus pattern (77 bp):
TCATGTAACTGTAGTGAATCAGGATTACTTTTCAGGTCAAATCCTATCCACCTTAAGTTACCATA
GTGAATCATATA
Found at i:9294057 original size:40 final size:40
Alignment explanation
Indices: 9294009--9294146 Score: 177
Period size: 40 Copynumber: 3.5 Consensus size: 40
9293999 TTTTTCAGGT
*
9294009 CAAATCCTATCCACCTTAAGTTACCATAGTGAATCAGGAA
1 CAAATCCTATCCACTTTAAGTTACCATAGTGAATCAGGAA
* * * *
9294049 TAAATCCTATTCACTTTAAATTACCATAGTGAATTAGGAA
1 CAAATCCTATCCACTTTAAGTTACCATAGTGAATCAGGAA
* * * **
9294089 CAAATTCTATCCACTTTGAGGTATTATAGTGAATCAGGAA
1 CAAATCCTATCCACTTTAAGTTACCATAGTGAATCAGGAA
*
9294129 CGAATCCTATCCACTTTA
1 CAAATCCTATCCACTTTA
9294147 TATTCTCGAG
Statistics
Matches: 81, Mismatches: 17, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
40 81 1.00
ACGTcount: A:0.36, C:0.20, G:0.12, T:0.31
Consensus pattern (40 bp):
CAAATCCTATCCACTTTAAGTTACCATAGTGAATCAGGAA
Found at i:9296586 original size:31 final size:30
Alignment explanation
Indices: 9296551--9296620 Score: 79
Period size: 31 Copynumber: 2.3 Consensus size: 30
9296541 ATACACAAAT
9296551 AATTTTATGTGTATGACTGAATCAAAATCAA
1 AATTTTATGTGTATGACTGAA-CAAAATCAA
* * * * *
9296582 AATTTTATATTTATGATTGCACCAAATCAA
1 AATTTTATGTGTATGACTGAACAAAATCAA
9296612 AA-TTTATGT
1 AATTTTATGT
9296621 ATCAAATTAT
Statistics
Matches: 33, Mismatches: 6, Indels: 2
0.80 0.15 0.05
Matches are distributed among these distances:
29 6 0.18
30 10 0.30
31 17 0.52
ACGTcount: A:0.40, C:0.10, G:0.10, T:0.40
Consensus pattern (30 bp):
AATTTTATGTGTATGACTGAACAAAATCAA
Found at i:9297420 original size:3 final size:3
Alignment explanation
Indices: 9297412--9297440 Score: 58
Period size: 3 Copynumber: 9.7 Consensus size: 3
9297402 GAAAGGAGCA
9297412 AAT AAT AAT AAT AAT AAT AAT AAT AAT AA
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AA
9297441 GGCAAAAACA
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 26 1.00
ACGTcount: A:0.69, C:0.00, G:0.00, T:0.31
Consensus pattern (3 bp):
AAT
Found at i:9298839 original size:30 final size:30
Alignment explanation
Indices: 9298803--9298865 Score: 99
Period size: 30 Copynumber: 2.1 Consensus size: 30
9298793 ACTTAACAAG
9298803 CAAATGCCTCAAAAATAATAAAAAAATTAA
1 CAAATGCCTCAAAAATAATAAAAAAATTAA
** *
9298833 CAAATGCCTTTAAAATAATAACAAAATTAA
1 CAAATGCCTCAAAAATAATAAAAAAATTAA
9298863 CAA
1 CAA
9298866 TAAAATAAGT
Statistics
Matches: 30, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
30 30 1.00
ACGTcount: A:0.60, C:0.14, G:0.03, T:0.22
Consensus pattern (30 bp):
CAAATGCCTCAAAAATAATAAAAAAATTAA
Found at i:9299817 original size:46 final size:46
Alignment explanation
Indices: 9299746--9299840 Score: 156
Period size: 46 Copynumber: 2.1 Consensus size: 46
9299736 TACGAAACTG
* *
9299746 TATTTTTTTCATGAATCTAAGTCGAAGTTTGTTAAAATGGATATAT
1 TATTTTTCTCATGAATCTAAGTCGAAGTTTATTAAAATGGATATAT
9299792 TATTTTTCTCATGAATCTGAA-TCGAAGTTTATTAAAATGGATATAT
1 TATTTTTCTCATGAATCT-AAGTCGAAGTTTATTAAAATGGATATAT
9299838 TAT
1 TAT
9299841 CAAAATAAAA
Statistics
Matches: 46, Mismatches: 2, Indels: 2
0.92 0.04 0.04
Matches are distributed among these distances:
46 44 0.96
47 2 0.04
ACGTcount: A:0.34, C:0.07, G:0.14, T:0.45
Consensus pattern (46 bp):
TATTTTTCTCATGAATCTAAGTCGAAGTTTATTAAAATGGATATAT
Found at i:9300940 original size:21 final size:21
Alignment explanation
Indices: 9300914--9300954 Score: 55
Period size: 21 Copynumber: 2.0 Consensus size: 21
9300904 ATAAATGTTA
* * *
9300914 AAAATCTTAAATTTTAAACTT
1 AAAATCCTAAACTTAAAACTT
9300935 AAAATCCTAAACTTAAAACT
1 AAAATCCTAAACTTAAAACT
9300955 CAAGATGTTA
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:0.51, C:0.15, G:0.00, T:0.34
Consensus pattern (21 bp):
AAAATCCTAAACTTAAAACTT
Found at i:9301951 original size:18 final size:18
Alignment explanation
Indices: 9301930--9301972 Score: 52
Period size: 18 Copynumber: 2.4 Consensus size: 18
9301920 CATTTATAAA
*
9301930 TTTATAAATTTTTA-ATTT
1 TTTATAAATTTATATA-TT
*
9301948 TTTATATATTTATATATT
1 TTTATAAATTTATATATT
9301966 TTTATAA
1 TTTATAA
9301973 TAAGTGGATA
Statistics
Matches: 21, Mismatches: 3, Indels: 2
0.81 0.12 0.08
Matches are distributed among these distances:
18 20 0.95
19 1 0.05
ACGTcount: A:0.35, C:0.00, G:0.00, T:0.65
Consensus pattern (18 bp):
TTTATAAATTTATATATT
Found at i:9308169 original size:8 final size:8
Alignment explanation
Indices: 9308158--9308182 Score: 50
Period size: 8 Copynumber: 3.1 Consensus size: 8
9308148 CTTTTCATAT
9308158 TTTTGAAA
1 TTTTGAAA
9308166 TTTTGAAA
1 TTTTGAAA
9308174 TTTTGAAA
1 TTTTGAAA
9308182 T
1 T
9308183 ATTCTTATTT
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
8 17 1.00
ACGTcount: A:0.36, C:0.00, G:0.12, T:0.52
Consensus pattern (8 bp):
TTTTGAAA
Found at i:9308597 original size:16 final size:16
Alignment explanation
Indices: 9308573--9308626 Score: 90
Period size: 16 Copynumber: 3.4 Consensus size: 16
9308563 TTTGGTTCGC
*
9308573 TGTATTGGATTAGAGG
1 TGTAATGGATTAGAGG
9308589 TGTAATGGATTAGAGG
1 TGTAATGGATTAGAGG
*
9308605 TGTATTGGATTAGAGG
1 TGTAATGGATTAGAGG
9308621 TGTAAT
1 TGTAAT
9308627 AGCAAATCAA
Statistics
Matches: 35, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
16 35 1.00
ACGTcount: A:0.28, C:0.00, G:0.35, T:0.37
Consensus pattern (16 bp):
TGTAATGGATTAGAGG
Found at i:9308877 original size:16 final size:16
Alignment explanation
Indices: 9308840--9308881 Score: 52
Period size: 15 Copynumber: 2.7 Consensus size: 16
9308830 TTAATCATAT
*
9308840 TTAAACATA-ATTATTA
1 TTAAA-ATATATTATAA
9308856 TT-AAATATATTATAA
1 TTAAAATATATTATAA
9308871 TTAAAATATAT
1 TTAAAATATAT
9308882 AATTTAATAA
Statistics
Matches: 23, Mismatches: 1, Indels: 4
0.82 0.04 0.14
Matches are distributed among these distances:
14 3 0.13
15 10 0.43
16 10 0.43
ACGTcount: A:0.52, C:0.02, G:0.00, T:0.45
Consensus pattern (16 bp):
TTAAAATATATTATAA
Found at i:9308888 original size:14 final size:15
Alignment explanation
Indices: 9308849--9308890 Score: 52
Period size: 15 Copynumber: 2.9 Consensus size: 15
9308839 TTTAAACATA
*
9308849 ATTATTATTAAATAT
1 ATTATAATTAAATAT
9308864 ATTATAATTAAA-AT
1 ATTATAATTAAATAT
*
9308878 A-TATAATTTAATA
1 ATTATAATTAAATA
9308891 AAATTCTTAA
Statistics
Matches: 24, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
13 9 0.38
14 4 0.17
15 11 0.46
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (15 bp):
ATTATAATTAAATAT
Found at i:9308987 original size:15 final size:15
Alignment explanation
Indices: 9308959--9309017 Score: 61
Period size: 15 Copynumber: 4.0 Consensus size: 15
9308949 ATAAAATATA
9308959 AATTAACATA-ATTAT
1 AATTAA-ATATATTAT
*
9308974 TATTAAATATATTAT
1 AATTAAATATATTAT
9308989 AATTAAA-ATA-TAT
1 AATTAAATATATTAT
*
9309002 AATTTAATAATATTAT
1 AATTAAAT-ATATTAT
9309018 TAATAATCAA
Statistics
Matches: 37, Mismatches: 3, Indels: 7
0.79 0.06 0.15
Matches are distributed among these distances:
13 9 0.24
14 6 0.16
15 19 0.51
16 3 0.08
ACGTcount: A:0.53, C:0.02, G:0.00, T:0.46
Consensus pattern (15 bp):
AATTAAATATATTAT
Found at i:9308988 original size:120 final size:120
Alignment explanation
Indices: 9308843--9309324 Score: 734
Period size: 120 Copynumber: 4.0 Consensus size: 120
9308833 ATCATATTTA
* *
9308843 AACATAATTATTATTAAATAT-ATTATAATTAAAATATATAATTTAATAAAATTCTTAATAATCA
1 AACATAATTATTATTAAATATAATT-TAATAAAAATATATAATTTAATAAAATTCTTAATAATAA
* * *
9308907 ATATTCTTATATGAATTTACTCAAATCATAATATATGATACTATAAAATATAAATT
65 ATATTCTTATATGAATTTAATAAAATCATAATATATAATACTATAAAATATAAATT
* * * *
9308963 AACATAATTATTATTAAATAT-ATTATAATTAAAATATATAATTTAATAATATTATTAATAATCA
1 AACATAATTATTATTAAATATAATT-TAATAAAAATATATAATTTAATAAAATTCTTAATAATAA
* * * *
9309027 ATATTCTTATATGAATTTACTCAAATCATAATATATGATACTATAAAATATAATTT
65 ATATTCTTATATGAATTTAATAAAATCATAATATATAATACTATAAAATATAAATT
*
9309083 AACATAATTATTATTAAATATAATTTAATAAAAATATATAATTTAATAAAATTCTTAATATTAAA
1 AACATAATTATTATTAAATATAATTTAATAAAAATATATAATTTAATAAAATTCTTAATAATAAA
* * *
9309148 TATTCTTATATGAATTCAATAAAATCATAATATATAATACTATATAATATAATTT
66 TATTCTTATATGAATTTAATAAAATCATAATATATAATACTATAAAATATAAATT
* * *
9309203 AAAATAATTATTATTAAATATAATTTAATAAAAATATATAATTTAATAAAATTTTTAATATTAAA
1 AACATAATTATTATTAAATATAATTTAATAAAAATATATAATTTAATAAAATTCTTAATAATAAA
* *
9309268 TATTCTTATATGAATTTAATAAAATCATAATATATAATACTATATAATATAGATT
66 TATTCTTATATGAATTTAATAAAATCATAATATATAATACTATAAAATATAAATT
9309323 AA
1 AA
9309325 TAATGTAGAT
Statistics
Matches: 343, Mismatches: 18, Indels: 2
0.94 0.05 0.01
Matches are distributed among these distances:
120 340 0.99
121 3 0.01
ACGTcount: A:0.51, C:0.05, G:0.01, T:0.43
Consensus pattern (120 bp):
AACATAATTATTATTAAATATAATTTAATAAAAATATATAATTTAATAAAATTCTTAATAATAAA
TATTCTTATATGAATTTAATAAAATCATAATATATAATACTATAAAATATAAATT
Found at i:9309018 original size:44 final size:43
Alignment explanation
Indices: 9308936--9309020 Score: 104
Period size: 43 Copynumber: 2.0 Consensus size: 43
9308926 CTCAAATCAT
* *
9308936 AATATATGATACTATAAAATATAAATTAACATAATTATTATTA
1 AATATATGATAATATAAAATATAAATTAAAATAATTATTATTA
* *
9308979 AATATATTATAAT-TAAAATATATAATT-TAATAA-TATTATTA
1 AATATATGATAATATAAAATATA-AATTAAAATAATTATTATTA
9309020 A
1 A
9309021 TAATCAATAT
Statistics
Matches: 37, Mismatches: 4, Indels: 4
0.82 0.09 0.09
Matches are distributed among these distances:
41 9 0.24
42 13 0.35
43 15 0.41
ACGTcount: A:0.54, C:0.02, G:0.01, T:0.42
Consensus pattern (43 bp):
AATATATGATAATATAAAATATAAATTAAAATAATTATTATTA
Found at i:9319262 original size:89 final size:89
Alignment explanation
Indices: 9319111--9319286 Score: 334
Period size: 89 Copynumber: 2.0 Consensus size: 89
9319101 ATGAAATTTT
*
9319111 TGTATATAATTGCATTAAATCGGTGTTCCATATCATGTTGCAAATTCAATTAAAGTTAGTGAAAT
1 TGTATACAATTGCATTAAATCGGTGTTCCATATCATGTTGCAAATTCAATTAAAGTTAGTGAAAT
9319176 GTTGGGATTTATCCCTTGAATTCA
66 GTTGGGATTTATCCCTTGAATTCA
*
9319200 TGTATACAATTGCATTAAATCGGTGTTCCATATCATGTTGCAAATTCAATTAAAGTTTGTGAAAT
1 TGTATACAATTGCATTAAATCGGTGTTCCATATCATGTTGCAAATTCAATTAAAGTTAGTGAAAT
9319265 GTTGGGATTTATCCCTTGAATT
66 GTTGGGATTTATCCCTTGAATT
9319287 GATATTCATG
Statistics
Matches: 85, Mismatches: 2, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
89 85 1.00
ACGTcount: A:0.31, C:0.12, G:0.17, T:0.40
Consensus pattern (89 bp):
TGTATACAATTGCATTAAATCGGTGTTCCATATCATGTTGCAAATTCAATTAAAGTTAGTGAAAT
GTTGGGATTTATCCCTTGAATTCA
Found at i:9346856 original size:30 final size:30
Alignment explanation
Indices: 9346820--9346882 Score: 126
Period size: 30 Copynumber: 2.1 Consensus size: 30
9346810 TCACCTGCTA
9346820 CAAAATTTAGAATATTGATATTGTATTCAC
1 CAAAATTTAGAATATTGATATTGTATTCAC
9346850 CAAAATTTAGAATATTGATATTGTATTCAC
1 CAAAATTTAGAATATTGATATTGTATTCAC
9346880 CAA
1 CAA
9346883 TTATAGGAGC
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
30 33 1.00
ACGTcount: A:0.41, C:0.11, G:0.10, T:0.38
Consensus pattern (30 bp):
CAAAATTTAGAATATTGATATTGTATTCAC
Found at i:9347094 original size:27 final size:27
Alignment explanation
Indices: 9347040--9347094 Score: 67
Period size: 27 Copynumber: 2.0 Consensus size: 27
9347030 TGGGCCCCAC
**
9347040 CACAACCATTTGCGCCTCTGAGGTAGG
1 CACAACCATTTGCGCCTCTGAGAAAGG
*
9347067 CACAATCATTTGCGCCT-TAGAGAAAGG
1 CACAACCATTTGCGCCTCT-GAGAAAGG
9347094 C
1 C
9347095 TCGATTAGTC
Statistics
Matches: 24, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
26 1 0.04
27 23 0.96
ACGTcount: A:0.27, C:0.27, G:0.24, T:0.22
Consensus pattern (27 bp):
CACAACCATTTGCGCCTCTGAGAAAGG
Found at i:9351788 original size:23 final size:23
Alignment explanation
Indices: 9351760--9351806 Score: 94
Period size: 23 Copynumber: 2.0 Consensus size: 23
9351750 ACTCTAACAT
9351760 CCCTATCTCTATTTACTTTATTC
1 CCCTATCTCTATTTACTTTATTC
9351783 CCCTATCTCTATTTACTTTATTC
1 CCCTATCTCTATTTACTTTATTC
9351806 C
1 C
9351807 TTCTAAAGCC
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
23 24 1.00
ACGTcount: A:0.17, C:0.32, G:0.00, T:0.51
Consensus pattern (23 bp):
CCCTATCTCTATTTACTTTATTC
Found at i:9354094 original size:34 final size:34
Alignment explanation
Indices: 9354056--9354122 Score: 98
Period size: 34 Copynumber: 2.0 Consensus size: 34
9354046 ATTGCCATTT
* * *
9354056 AACCCATACTCCTCACAGCTCACCATCAACCAGC
1 AACCCATAATCCTAACAACTCACCATCAACCAGC
*
9354090 AACCCATAATCCTAACAACTCACTATCAACCAG
1 AACCCATAATCCTAACAACTCACCATCAACCAG
9354123 TAAGCCCCCT
Statistics
Matches: 29, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
34 29 1.00
ACGTcount: A:0.37, C:0.42, G:0.04, T:0.16
Consensus pattern (34 bp):
AACCCATAATCCTAACAACTCACCATCAACCAGC
Found at i:9355090 original size:14 final size:15
Alignment explanation
Indices: 9355049--9355090 Score: 50
Period size: 14 Copynumber: 2.8 Consensus size: 15
9355039 TTAAGTTTTT
9355049 ATATTTTAATTTCGAA
1 ATATTTTAATTTC-AA
* *
9355065 ACATTTTTATTT-AA
1 ATATTTTAATTTCAA
9355079 ATATTTTAATTT
1 ATATTTTAATTT
9355091 TTCAATCTAA
Statistics
Matches: 22, Mismatches: 4, Indels: 2
0.79 0.14 0.07
Matches are distributed among these distances:
14 12 0.55
16 10 0.45
ACGTcount: A:0.36, C:0.05, G:0.02, T:0.57
Consensus pattern (15 bp):
ATATTTTAATTTCAA
Found at i:9369394 original size:15 final size:17
Alignment explanation
Indices: 9369363--9369396 Score: 54
Period size: 15 Copynumber: 2.1 Consensus size: 17
9369353 ATTAAGTAAA
9369363 AATAATATAATATTTAT
1 AATAATATAATATTTAT
9369380 AATAA-ATAA-ATTTAT
1 AATAATATAATATTTAT
9369395 AA
1 AA
9369397 ATAAGATTTT
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
15 8 0.47
16 4 0.24
17 5 0.29
ACGTcount: A:0.59, C:0.00, G:0.00, T:0.41
Consensus pattern (17 bp):
AATAATATAATATTTAT
Found at i:9369396 original size:12 final size:14
Alignment explanation
Indices: 9369381--9369412 Score: 50
Period size: 14 Copynumber: 2.4 Consensus size: 14
9369371 AATATTTATA
9369381 ATAAATAA-A-TTT
1 ATAAATAAGATTTT
9369393 ATAAATAAGATTTT
1 ATAAATAAGATTTT
9369407 ATAAAT
1 ATAAAT
9369413 TGTCTAATAA
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
12 8 0.44
13 1 0.06
14 9 0.50
ACGTcount: A:0.56, C:0.00, G:0.03, T:0.41
Consensus pattern (14 bp):
ATAAATAAGATTTT
Found at i:9370986 original size:107 final size:109
Alignment explanation
Indices: 9370847--9371055 Score: 332
Period size: 111 Copynumber: 1.9 Consensus size: 109
9370837 ATAAATATAT
* *
9370847 AATATTAGATTTTGAAAACTTGATATTAAAATAAAATTTAT-A-AAAATTAGCAATTGAATTAAA
1 AATAATAGATTTTGAAAACTTGATATTAAAATAAAATTTATAAGAAAATTAACAATTGAATTAAA
9370910 ATAGGTAGAATGATAAAGATACATATAAATAAATCCTCCAAATG
66 ATAGGTAGAATGATAAAGATACATATAAATAAATCCTCCAAATG
* *
9370954 AATAATAGATTTTGTAAACTTGATATTGAAATAAAATTTATAAAAGAAAATTAACAATTGAATTA
1 AATAATAGATTTTGAAAACTTGATATTAAAATAAAATTTAT--AAGAAAATTAACAATTGAATTA
* *
9371019 AATTAGGTAGAATGATAAAGATGCATATAAATAAATC
64 AAATAGGTAGAATGATAAAGATACATATAAATAAATC
9371056 TTCATTTGTC
Statistics
Matches: 92, Mismatches: 6, Indels: 4
0.90 0.06 0.04
Matches are distributed among these distances:
107 38 0.41
110 1 0.01
111 53 0.58
ACGTcount: A:0.52, C:0.05, G:0.11, T:0.32
Consensus pattern (109 bp):
AATAATAGATTTTGAAAACTTGATATTAAAATAAAATTTATAAGAAAATTAACAATTGAATTAAA
ATAGGTAGAATGATAAAGATACATATAAATAAATCCTCCAAATG
Found at i:9374412 original size:21 final size:21
Alignment explanation
Indices: 9374392--9374430 Score: 53
Period size: 20 Copynumber: 1.9 Consensus size: 21
9374382 AACATTTAAT
9374392 TAATTTTTAATT-AATTATAA
1 TAATTTTTAATTAAATTATAA
* *
9374412 TATTTTTTATTTAAATTAT
1 TAATTTTTAATTAAATTAT
9374431 TAAATATAAT
Statistics
Matches: 16, Mismatches: 2, Indels: 1
0.84 0.11 0.05
Matches are distributed among these distances:
20 10 0.62
21 6 0.38
ACGTcount: A:0.38, C:0.00, G:0.00, T:0.62
Consensus pattern (21 bp):
TAATTTTTAATTAAATTATAA
Found at i:9382213 original size:16 final size:16
Alignment explanation
Indices: 9382192--9382222 Score: 62
Period size: 16 Copynumber: 1.9 Consensus size: 16
9382182 AGGCACTGTC
9382192 AAAACACAAAAAAAAT
1 AAAACACAAAAAAAAT
9382208 AAAACACAAAAAAAA
1 AAAACACAAAAAAAA
9382223 AATCCCCCAG
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:0.84, C:0.13, G:0.00, T:0.03
Consensus pattern (16 bp):
AAAACACAAAAAAAAT
Found at i:9386593 original size:23 final size:21
Alignment explanation
Indices: 9386567--9386619 Score: 63
Period size: 23 Copynumber: 2.4 Consensus size: 21
9386557 TTAATTTTTT
9386567 AAATCTAAAAATTAAAAATACTA
1 AAATCTAAAAA-TAAAAATAC-A
*
9386590 AAATCCTAAAAATAGAAATACA
1 AAAT-CTAAAAATAAAAATACA
9386612 AAAT-TAAA
1 AAATCTAAA
9386620 TTTGAAAATT
Statistics
Matches: 28, Mismatches: 1, Indels: 5
0.82 0.03 0.15
Matches are distributed among these distances:
20 4 0.14
22 5 0.18
23 12 0.43
24 7 0.25
ACGTcount: A:0.66, C:0.09, G:0.02, T:0.23
Consensus pattern (21 bp):
AAATCTAAAAATAAAAATACA
Found at i:9395004 original size:16 final size:18
Alignment explanation
Indices: 9394971--9395006 Score: 56
Period size: 18 Copynumber: 2.0 Consensus size: 18
9394961 AAAAATCACA
9394971 TTTTTACATTTAATATAT
1 TTTTTACATTTAATATAT
9394989 TTTTTA-ATTTCAATATAT
1 TTTTTACATTT-AATATAT
9395007 ATAGTGACAA
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
17 4 0.24
18 13 0.76
ACGTcount: A:0.33, C:0.06, G:0.00, T:0.61
Consensus pattern (18 bp):
TTTTTACATTTAATATAT
Found at i:9398146 original size:21 final size:21
Alignment explanation
Indices: 9398120--9398160 Score: 64
Period size: 21 Copynumber: 2.0 Consensus size: 21
9398110 AGACGAGCAA
* *
9398120 TACTCCACAGCAGGTGGAGTG
1 TACTCCAAAACAGGTGGAGTG
9398141 TACTCCAAAACAGGTGGAGT
1 TACTCCAAAACAGGTGGAGT
9398161 TTGAGCAGAT
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
21 18 1.00
ACGTcount: A:0.29, C:0.22, G:0.29, T:0.20
Consensus pattern (21 bp):
TACTCCAAAACAGGTGGAGTG
Found at i:9401802 original size:23 final size:23
Alignment explanation
Indices: 9401759--9401802 Score: 54
Period size: 23 Copynumber: 1.9 Consensus size: 23
9401749 AATATTATAT
* *
9401759 ATATTAAATGAATAAATTAAAAA
1 ATATTAAATCAATAAAATAAAAA
9401782 ATATTAAATC-ATAAAAATAAA
1 ATATTAAATCAAT-AAAATAAA
9401803 TGTGAATATT
Statistics
Matches: 18, Mismatches: 2, Indels: 2
0.82 0.09 0.09
Matches are distributed among these distances:
22 2 0.11
23 16 0.89
ACGTcount: A:0.66, C:0.02, G:0.02, T:0.30
Consensus pattern (23 bp):
ATATTAAATCAATAAAATAAAAA
Found at i:9402184 original size:17 final size:17
Alignment explanation
Indices: 9402162--9402198 Score: 67
Period size: 16 Copynumber: 2.2 Consensus size: 17
9402152 ATAAGAGCAT
9402162 AATAAAATATTTAAAAA
1 AATAAAATATTTAAAAA
9402179 AAT-AAATATTTAAAAA
1 AATAAAATATTTAAAAA
9402195 AATA
1 AATA
9402199 TATAGAAAAT
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
16 16 0.84
17 3 0.16
ACGTcount: A:0.70, C:0.00, G:0.00, T:0.30
Consensus pattern (17 bp):
AATAAAATATTTAAAAA
Found at i:9403804 original size:21 final size:21
Alignment explanation
Indices: 9403776--9403826 Score: 93
Period size: 21 Copynumber: 2.4 Consensus size: 21
9403766 CTTAAACCCC
9403776 AAGGTTTAGGGTTTGAGATTT
1 AAGGTTTAGGGTTTGAGATTT
*
9403797 ATGGTTTAGGGTTTGAGATTT
1 AAGGTTTAGGGTTTGAGATTT
9403818 AAGGTTTAG
1 AAGGTTTAG
9403827 ATTTAAGGTT
Statistics
Matches: 28, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
21 28 1.00
ACGTcount: A:0.24, C:0.00, G:0.33, T:0.43
Consensus pattern (21 bp):
AAGGTTTAGGGTTTGAGATTT
Found at i:9403825 original size:7 final size:7
Alignment explanation
Indices: 9403776--9403840 Score: 51
Period size: 7 Copynumber: 9.4 Consensus size: 7
9403766 CTTAAACCCC
9403776 AAGGTTT
1 AAGGTTT
*
9403783 AGGGTTT
1 AAGGTTT
* *
9403790 GAGATTT
1 AAGGTTT
*
9403797 ATGGTTT
1 AAGGTTT
*
9403804 AGGGTTT
1 AAGGTTT
* *
9403811 GAGATTT
1 AAGGTTT
9403818 AAGGTTT
1 AAGGTTT
*
9403825 -AGATTT
1 AAGGTTT
9403831 AAGGTTT
1 AAGGTTT
9403838 AAG
1 AAG
9403841 TATTCAAAGT
Statistics
Matches: 42, Mismatches: 15, Indels: 2
0.71 0.25 0.03
Matches are distributed among these distances:
6 5 0.12
7 37 0.88
ACGTcount: A:0.26, C:0.00, G:0.31, T:0.43
Consensus pattern (7 bp):
AAGGTTT
Found at i:9403830 original size:13 final size:13
Alignment explanation
Indices: 9403801--9403838 Score: 58
Period size: 13 Copynumber: 2.8 Consensus size: 13
9403791 AGATTTATGG
*
9403801 TTTAGGGTTTGAGA
1 TTTAAGGTTT-AGA
9403815 TTTAAGGTTTAGA
1 TTTAAGGTTTAGA
9403828 TTTAAGGTTTA
1 TTTAAGGTTTA
9403839 AGTATTCAAA
Statistics
Matches: 23, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
13 14 0.61
14 9 0.39
ACGTcount: A:0.26, C:0.00, G:0.26, T:0.47
Consensus pattern (13 bp):
TTTAAGGTTTAGA
Found at i:9403904 original size:21 final size:21
Alignment explanation
Indices: 9403878--9403922 Score: 72
Period size: 21 Copynumber: 2.1 Consensus size: 21
9403868 GGTTCAAGGG
9403878 TTCAAGATTACGAGTTTAGGA
1 TTCAAGATTACGAGTTTAGGA
* *
9403899 TTCAAGTTTACGATTTTAGGA
1 TTCAAGATTACGAGTTTAGGA
9403920 TTC
1 TTC
9403923 TATATTTTGG
Statistics
Matches: 22, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
21 22 1.00
ACGTcount: A:0.29, C:0.11, G:0.20, T:0.40
Consensus pattern (21 bp):
TTCAAGATTACGAGTTTAGGA
Found at i:9414637 original size:37 final size:38
Alignment explanation
Indices: 9414596--9414668 Score: 112
Period size: 37 Copynumber: 1.9 Consensus size: 38
9414586 TCCCCACTAT
* * *
9414596 TTTAAATTCAAAGCTATTACTATAAT-TTTTTTTTTGC
1 TTTAAAATAAAAGCTATTACTATAATATTTATTTTTGC
9414633 TTTAAAATAAAAGCTATTACTATAATATTTATTTTT
1 TTTAAAATAAAAGCTATTACTATAATATTTATTTTT
9414669 AGTAATCTTT
Statistics
Matches: 32, Mismatches: 3, Indels: 1
0.89 0.08 0.03
Matches are distributed among these distances:
37 24 0.75
38 8 0.25
ACGTcount: A:0.36, C:0.08, G:0.04, T:0.52
Consensus pattern (38 bp):
TTTAAAATAAAAGCTATTACTATAATATTTATTTTTGC
Found at i:9416640 original size:22 final size:21
Alignment explanation
Indices: 9416586--9416641 Score: 69
Period size: 22 Copynumber: 2.6 Consensus size: 21
9416576 TTACGGTTGG
9416586 TTTTGTTGTTATTTGCTATCA
1 TTTTGTTGTTATTTGCTATCA
* *
9416607 TTTTATTATTATATTGCTA-CTA
1 TTTTGTTGTTAT-TTGCTATC-A
9416629 TTTTGTTGTTATT
1 TTTTGTTGTTATT
9416642 GTTTTGATAT
Statistics
Matches: 29, Mismatches: 4, Indels: 4
0.78 0.11 0.11
Matches are distributed among these distances:
21 12 0.41
22 17 0.59
ACGTcount: A:0.18, C:0.07, G:0.11, T:0.64
Consensus pattern (21 bp):
TTTTGTTGTTATTTGCTATCA
Found at i:9420454 original size:19 final size:19
Alignment explanation
Indices: 9420432--9420472 Score: 55
Period size: 19 Copynumber: 2.1 Consensus size: 19
9420422 GACTAAATTG
9420432 AAAATATGTAAAATTCATGA
1 AAAAT-TGTAAAATTCATGA
* *
9420452 AAAATTGTAAATTTTATGA
1 AAAATTGTAAAATTCATGA
9420471 AA
1 AA
9420473 TATACGGACT
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
19 14 0.74
20 5 0.26
ACGTcount: A:0.54, C:0.02, G:0.10, T:0.34
Consensus pattern (19 bp):
AAAATTGTAAAATTCATGA
Found at i:9421152 original size:65 final size:65
Alignment explanation
Indices: 9421015--9421201 Score: 218
Period size: 65 Copynumber: 2.9 Consensus size: 65
9421005 GCGAACATCC
* * * *
9421015 TGATCGGTAGTGATCCTGCATGTGTTGCGGACTAC---CGCAACTCTTTGTGAGCATCCTGTTAT
1 TGATCGGTTGTGATCCTGCATATATTGCGGAC-ACAAACGCAACTCTTTGTGAGCATCCTATTAT
9421077 A
65 A
* * * * * * *
9421078 TGATCGGTTGTGATCTTGCATGTATTGTGGACACAAACGTAGCTCTTTGTGAGCGTCCTATTTTA
1 TGATCGGTTGTGATCCTGCATATATTGCGGACACAAACGCAACTCTTTGTGAGCATCCTATTATA
* * *
9421143 TGATTGGTTGTGATCCTGTATATATTGCGGACACAAACGCAACTCTTTGTGAGTATCCT
1 TGATCGGTTGTGATCCTGCATATATTGCGGACACAAACGCAACTCTTTGTGAGCATCCT
9421202 GATATGGCTC
Statistics
Matches: 103, Mismatches: 18, Indels: 4
0.82 0.14 0.03
Matches are distributed among these distances:
62 2 0.02
63 28 0.27
65 73 0.71
ACGTcount: A:0.21, C:0.19, G:0.24, T:0.36
Consensus pattern (65 bp):
TGATCGGTTGTGATCCTGCATATATTGCGGACACAAACGCAACTCTTTGTGAGCATCCTATTATA
Found at i:9421993 original size:20 final size:20
Alignment explanation
Indices: 9421965--9422003 Score: 60
Period size: 20 Copynumber: 1.9 Consensus size: 20
9421955 GTATGGCAAA
9421965 AATAAAATACATGTGTAATT
1 AATAAAATACATGTGTAATT
* *
9421985 AATATAATACATTTGTAAT
1 AATAAAATACATGTGTAAT
9422004 ACATGTATGT
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.49, C:0.05, G:0.08, T:0.38
Consensus pattern (20 bp):
AATAAAATACATGTGTAATT
Found at i:9426266 original size:19 final size:19
Alignment explanation
Indices: 9426239--9426283 Score: 56
Period size: 19 Copynumber: 2.4 Consensus size: 19
9426229 TTTGATCAAA
* *
9426239 ATAATAACA-TAATTTTTT
1 ATAAAAACACTAATTTTAT
9426257 CATAAAAACACTAATTTTAT
1 -ATAAAAACACTAATTTTAT
9426277 ATAAAAA
1 ATAAAAA
9426284 AATTTATTAC
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
19 15 0.65
20 8 0.35
ACGTcount: A:0.53, C:0.09, G:0.00, T:0.38
Consensus pattern (19 bp):
ATAAAAACACTAATTTTAT
Found at i:9432006 original size:16 final size:16
Alignment explanation
Indices: 9431973--9432006 Score: 50
Period size: 16 Copynumber: 2.1 Consensus size: 16
9431963 GGAGATTGTT
* *
9431973 AACATTAATGGGAGAC
1 AACATTAATGGCAAAC
9431989 AACATTAATGGCAAAC
1 AACATTAATGGCAAAC
9432005 AA
1 AA
9432007 TACAAAGTGG
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
16 16 1.00
ACGTcount: A:0.50, C:0.15, G:0.18, T:0.18
Consensus pattern (16 bp):
AACATTAATGGCAAAC
Found at i:9440192 original size:24 final size:25
Alignment explanation
Indices: 9440142--9440193 Score: 61
Period size: 24 Copynumber: 2.1 Consensus size: 25
9440132 ATAAATTTTG
* *
9440142 AATTATGCAAATTGATAGTTATTTA
1 AATTATGCAAATTAATAGTTATGTA
**
9440167 AATTATGCAAA-TAATTTTTATGTA
1 AATTATGCAAATTAATAGTTATGTA
9440191 AAT
1 AAT
9440194 CATTTATATA
Statistics
Matches: 23, Mismatches: 4, Indels: 1
0.82 0.14 0.04
Matches are distributed among these distances:
24 12 0.52
25 11 0.48
ACGTcount: A:0.42, C:0.04, G:0.10, T:0.44
Consensus pattern (25 bp):
AATTATGCAAATTAATAGTTATGTA
Found at i:9445348 original size:14 final size:14
Alignment explanation
Indices: 9445329--9445364 Score: 56
Period size: 13 Copynumber: 2.6 Consensus size: 14
9445319 GTGTGAGTTC
9445329 AAAAAAGGAAAAAA
1 AAAAAAGGAAAAAA
9445343 AAAAAA-GAAAAAA
1 AAAAAAGGAAAAAA
9445356 AAAAGAAGG
1 AAAA-AAGG
9445365 TTGCAATCTC
Statistics
Matches: 20, Mismatches: 0, Indels: 3
0.87 0.00 0.13
Matches are distributed among these distances:
13 11 0.55
14 8 0.40
15 1 0.05
ACGTcount: A:0.83, C:0.00, G:0.17, T:0.00
Consensus pattern (14 bp):
AAAAAAGGAAAAAA
Found at i:9450998 original size:23 final size:23
Alignment explanation
Indices: 9450971--9451018 Score: 60
Period size: 23 Copynumber: 2.1 Consensus size: 23
9450961 TTTTTATAAA
*
9450971 TTTATTCTAGTTAGTTAGTTAAT
1 TTTATTCTAATTAGTTAGTTAAT
* * *
9450994 TTTATTTTAATTATTTATTTAAT
1 TTTATTCTAATTAGTTAGTTAAT
9451017 TT
1 TT
9451019 GAATTAACAG
Statistics
Matches: 21, Mismatches: 4, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
23 21 1.00
ACGTcount: A:0.27, C:0.02, G:0.06, T:0.65
Consensus pattern (23 bp):
TTTATTCTAATTAGTTAGTTAAT
Found at i:9459809 original size:35 final size:36
Alignment explanation
Indices: 9459765--9459835 Score: 108
Period size: 36 Copynumber: 2.0 Consensus size: 36
9459755 GCATCCCACA
* *
9459765 AAGACTCAA-TTACTGGATTCTTTAACTTCCCAAGT
1 AAGACTCAATTTACCGGATTCTTTAAATTCCCAAGT
*
9459800 AAGACTCAATTTACCGGGTTCTTTAAATTCCCAAGT
1 AAGACTCAATTTACCGGATTCTTTAAATTCCCAAGT
9459836 TTTTTTTTAC
Statistics
Matches: 32, Mismatches: 3, Indels: 1
0.89 0.08 0.03
Matches are distributed among these distances:
35 9 0.28
36 23 0.72
ACGTcount: A:0.31, C:0.23, G:0.13, T:0.34
Consensus pattern (36 bp):
AAGACTCAATTTACCGGATTCTTTAAATTCCCAAGT
Found at i:9467305 original size:12 final size:12
Alignment explanation
Indices: 9467288--9467313 Score: 52
Period size: 12 Copynumber: 2.2 Consensus size: 12
9467278 ATATGAAGAA
9467288 TTTTCTTCATCT
1 TTTTCTTCATCT
9467300 TTTTCTTCATCT
1 TTTTCTTCATCT
9467312 TT
1 TT
9467314 CCATGCTACT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 14 1.00
ACGTcount: A:0.08, C:0.23, G:0.00, T:0.69
Consensus pattern (12 bp):
TTTTCTTCATCT
Found at i:9467812 original size:2 final size:2
Alignment explanation
Indices: 9467805--9467833 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
9467795 TAATTAAGTA
9467805 AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
9467834 GTGTGAAACA
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 27 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:9467950 original size:18 final size:20
Alignment explanation
Indices: 9467927--9467966 Score: 57
Period size: 20 Copynumber: 2.0 Consensus size: 20
9467917 TATTAGATAA
9467927 GTGAAA-TTATGGAAA-AAT
1 GTGAAATTTATGGAAACAAT
9467945 GTGAAATTTTATGGAAACAAT
1 GTGAAA-TTTATGGAAACAAT
9467966 G
1 G
9467967 ACTAAATTGA
Statistics
Matches: 19, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
18 6 0.32
20 9 0.47
21 4 0.21
ACGTcount: A:0.45, C:0.03, G:0.23, T:0.30
Consensus pattern (20 bp):
GTGAAATTTATGGAAACAAT
Found at i:9469851 original size:47 final size:47
Alignment explanation
Indices: 9469787--9469897 Score: 145
Period size: 47 Copynumber: 2.4 Consensus size: 47
9469777 GACATTGAGT
*
9469787 CGATG-AGACACTATGTGT-CGACTACTGTTAAAGTTCCGGATTTGTTC
1 CGATGAAG-CACTATGTGTACGA-TAATGTTAAAGTTCCGGATTTGTTC
* * * *
9469834 CGATGAAGTACTTTGTGTACTATAATGTTAAAGTTCTGGATTTGTTC
1 CGATGAAGCACTATGTGTACGATAATGTTAAAGTTCCGGATTTGTTC
9469881 CGATGAAGCACTATGTG
1 CGATGAAGCACTATGTG
9469898 CTTATCCCGG
Statistics
Matches: 55, Mismatches: 7, Indels: 4
0.83 0.11 0.06
Matches are distributed among these distances:
47 51 0.93
48 4 0.07
ACGTcount: A:0.25, C:0.15, G:0.23, T:0.36
Consensus pattern (47 bp):
CGATGAAGCACTATGTGTACGATAATGTTAAAGTTCCGGATTTGTTC
Found at i:9472988 original size:25 final size:25
Alignment explanation
Indices: 9472951--9473016 Score: 87
Period size: 25 Copynumber: 2.6 Consensus size: 25
9472941 TGTAAACAGG
* *
9472951 AAGCTCCTTCGAGCTGAATAACGGA
1 AAGCTCATGCGAGCTGAATAACGGA
* * *
9472976 AAGCTCATGCGAGCTGAATTAGGGG
1 AAGCTCATGCGAGCTGAATAACGGA
9473001 AAGCTCATGCGAGCTG
1 AAGCTCATGCGAGCTG
9473017 TGGTGTGTCC
Statistics
Matches: 36, Mismatches: 5, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
25 36 1.00
ACGTcount: A:0.29, C:0.21, G:0.30, T:0.20
Consensus pattern (25 bp):
AAGCTCATGCGAGCTGAATAACGGA
Found at i:9474837 original size:22 final size:22
Alignment explanation
Indices: 9474809--9474870 Score: 88
Period size: 22 Copynumber: 2.8 Consensus size: 22
9474799 TTTCCTATTA
9474809 TTAGCACATTAGTGCTCTTCGT
1 TTAGCACATTAGTGCTCTTCGT
* *
9474831 TTAGCACATTTGTGCTCTTTGT
1 TTAGCACATTAGTGCTCTTCGT
* *
9474853 ATAGCACTTTAGTGCTCT
1 TTAGCACATTAGTGCTCT
9474871 CTGATTAATA
Statistics
Matches: 35, Mismatches: 5, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
22 35 1.00
ACGTcount: A:0.18, C:0.21, G:0.18, T:0.44
Consensus pattern (22 bp):
TTAGCACATTAGTGCTCTTCGT
Found at i:9493691 original size:18 final size:19
Alignment explanation
Indices: 9493650--9493690 Score: 82
Period size: 19 Copynumber: 2.2 Consensus size: 19
9493640 AAACAATGGT
9493650 AAAATTTCAAATGTAAAAA
1 AAAATTTCAAATGTAAAAA
9493669 AAAATTTCAAATGTAAAAA
1 AAAATTTCAAATGTAAAAA
9493688 AAA
1 AAA
9493691 TATATATATA
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 22 1.00
ACGTcount: A:0.66, C:0.05, G:0.05, T:0.24
Consensus pattern (19 bp):
AAAATTTCAAATGTAAAAA
Found at i:9501598 original size:22 final size:22
Alignment explanation
Indices: 9501570--9501613 Score: 88
Period size: 22 Copynumber: 2.0 Consensus size: 22
9501560 TAAAAACCTG
9501570 ATTTGAGGATTTTATGTGCAGT
1 ATTTGAGGATTTTATGTGCAGT
9501592 ATTTGAGGATTTTATGTGCAGT
1 ATTTGAGGATTTTATGTGCAGT
9501614 CTTATTTCCA
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 22 1.00
ACGTcount: A:0.23, C:0.05, G:0.27, T:0.45
Consensus pattern (22 bp):
ATTTGAGGATTTTATGTGCAGT
Found at i:9505621 original size:165 final size:165
Alignment explanation
Indices: 9505433--9505764 Score: 664
Period size: 165 Copynumber: 2.0 Consensus size: 165
9505423 TGTTTAGCGT
9505433 TATTCCTCAATGAAAAAGGGAATAACCGAAGGCGAATGACATCATCAGAAACACCATTGATTTTA
1 TATTCCTCAATGAAAAAGGGAATAACCGAAGGCGAATGACATCATCAGAAACACCATTGATTTTA
9505498 AAAGTATTACAAAACTCTAAAAAATTCGTCAGGTGATTGTTTGGATCCTCATCCTGCAAACCATC
66 AAAGTATTACAAAACTCTAAAAAATTCGTCAGGTGATTGTTTGGATCCTCATCCTGCAAACCATC
9505563 AAACTGAACAAACTGTTGTATCATTTGAATTATGC
131 AAACTGAACAAACTGTTGTATCATTTGAATTATGC
9505598 TATTCCTCAATGAAAAAGGGAATAACCGAAGGCGAATGACATCATCAGAAACACCATTGATTTTA
1 TATTCCTCAATGAAAAAGGGAATAACCGAAGGCGAATGACATCATCAGAAACACCATTGATTTTA
9505663 AAAGTATTACAAAACTCTAAAAAATTCGTCAGGTGATTGTTTGGATCCTCATCCTGCAAACCATC
66 AAAGTATTACAAAACTCTAAAAAATTCGTCAGGTGATTGTTTGGATCCTCATCCTGCAAACCATC
9505728 AAACTGAACAAACTGTTGTATCATTTGAATTATGC
131 AAACTGAACAAACTGTTGTATCATTTGAATTATGC
9505763 TA
1 TA
9505765 AGTTTCAGTT
Statistics
Matches: 167, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
165 167 1.00
ACGTcount: A:0.38, C:0.19, G:0.15, T:0.28
Consensus pattern (165 bp):
TATTCCTCAATGAAAAAGGGAATAACCGAAGGCGAATGACATCATCAGAAACACCATTGATTTTA
AAAGTATTACAAAACTCTAAAAAATTCGTCAGGTGATTGTTTGGATCCTCATCCTGCAAACCATC
AAACTGAACAAACTGTTGTATCATTTGAATTATGC
Found at i:9517311 original size:19 final size:19
Alignment explanation
Indices: 9517278--9517328 Score: 86
Period size: 19 Copynumber: 2.7 Consensus size: 19
9517268 TCGAAACTGG
*
9517278 TCGGTT-AATCGAATTTTT
1 TCGGTTCAACCGAATTTTT
9517296 TCGGTTCAACCGAATTTTT
1 TCGGTTCAACCGAATTTTT
9517315 TCGGTTCAACCGAA
1 TCGGTTCAACCGAA
9517329 AAAATTAATA
Statistics
Matches: 31, Mismatches: 1, Indels: 1
0.94 0.03 0.03
Matches are distributed among these distances:
18 6 0.19
19 25 0.81
ACGTcount: A:0.24, C:0.20, G:0.18, T:0.39
Consensus pattern (19 bp):
TCGGTTCAACCGAATTTTT
Found at i:9517526 original size:7 final size:6
Alignment explanation
Indices: 9517485--9517525 Score: 55
Period size: 6 Copynumber: 6.5 Consensus size: 6
9517475 ATAACTTAAT
*
9517485 AAATAA AAATAA AAATCTAA AACTAA AAATAA AAATAA AAA
1 AAATAA AAATAA AAA--TAA AAATAA AAATAA AAATAA AAA
9517526 AACATAATTT
Statistics
Matches: 31, Mismatches: 2, Indels: 4
0.84 0.05 0.11
Matches are distributed among these distances:
6 26 0.84
8 5 0.16
ACGTcount: A:0.78, C:0.05, G:0.00, T:0.17
Consensus pattern (6 bp):
AAATAA
Found at i:9517526 original size:20 final size:20
Alignment explanation
Indices: 9517488--9517526 Score: 60
Period size: 20 Copynumber: 1.9 Consensus size: 20
9517478 ACTTAATAAA
**
9517488 TAAAAATAAAAATCTAAAAC
1 TAAAAATAAAAATAAAAAAC
9517508 TAAAAATAAAAATAAAAAA
1 TAAAAATAAAAATAAAAAA
9517527 ACATAATTTT
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.77, C:0.05, G:0.00, T:0.18
Consensus pattern (20 bp):
TAAAAATAAAAATAAAAAAC
Found at i:9517559 original size:9 final size:9
Alignment explanation
Indices: 9517545--9517602 Score: 80
Period size: 9 Copynumber: 6.4 Consensus size: 9
9517535 TTATATAAAC
9517545 AATTCGGTT
1 AATTCGGTT
9517554 AATTCGGTT
1 AATTCGGTT
* *
9517563 AATTTGGGT
1 AATTCGGTT
*
9517572 AATTCGGGT
1 AATTCGGTT
*
9517581 AATTCAGTT
1 AATTCGGTT
9517590 AATTCGGTT
1 AATTCGGTT
9517599 AATT
1 AATT
9517603 TTATACTTAT
Statistics
Matches: 43, Mismatches: 6, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
9 43 1.00
ACGTcount: A:0.26, C:0.09, G:0.22, T:0.43
Consensus pattern (9 bp):
AATTCGGTT
Found at i:9518265 original size:3 final size:3
Alignment explanation
Indices: 9518243--9518426 Score: 167
Period size: 3 Copynumber: 61.3 Consensus size: 3
9518233 TAATTTAATA
* * * * *
9518243 TAT TAT TGT TAT TAC CAT TAT TAT TAT T-T TAC TAT TAT TATT TAC
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TA-T TAT
* * *
9518288 TAT GAT TAT TAT TAC TAT TAT TAT TAT TAT TAT TAT TAT TAT T-T TAC
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
* * * * *
9518335 TAT TATT TAT TAT TAC CAT TAT TAT TAC TGT TAA TAT TAT T-T TAT
1 TAT TA-T TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
* * * *
9518380 TAC TAT TAC TCT TCTT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
1 TAT TAT TAT TAT T-AT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
9518426 T
1 T
9518427 GTCATTTGTA
Statistics
Matches: 142, Mismatches: 33, Indels: 12
0.76 0.18 0.06
Matches are distributed among these distances:
2 6 0.04
3 128 0.90
4 8 0.06
ACGTcount: A:0.30, C:0.07, G:0.02, T:0.61
Consensus pattern (3 bp):
TAT
Found at i:9518281 original size:60 final size:60
Alignment explanation
Indices: 9518217--9518346 Score: 147
Period size: 60 Copynumber: 2.1 Consensus size: 60
9518207 TTTCACTGTT
*
9518217 TTATTATTAAAT-TAACTAATTTAATA-TATTATTGTTATTACCATTATTATTATTTTACTA
1 TTATTATTAAATATAA-TAA-TTAATACTATTATTATTATTACCATTATTATTATTTTACTA
* * * * * **
9518277 TTATTATTTACTATGATTATTATTACTATTATTATTATTATTATTATTATTATTTTACTA
1 TTATTATTAAATATAATAATTAATACTATTATTATTATTACCATTATTATTATTTTACTA
9518337 TTATTTATTA
1 TTA-TTATTA
9518347 TTACCATTAT
Statistics
Matches: 58, Mismatches: 9, Indels: 5
0.81 0.12 0.07
Matches are distributed among these distances:
59 5 0.09
60 46 0.79
61 7 0.12
ACGTcount: A:0.34, C:0.05, G:0.02, T:0.59
Consensus pattern (60 bp):
TTATTATTAAATATAATAATTAATACTATTATTATTATTACCATTATTATTATTTTACTA
Found at i:9518356 original size:60 final size:59
Alignment explanation
Indices: 9518243--9518426 Score: 212
Period size: 60 Copynumber: 3.1 Consensus size: 59
9518233 TAATTTAATA
* ** * *
9518243 TATTATTGTTATTACCATTATTATTATTTTACTATTATTATTTACTATGATTATTATTAC
1 TATTATTATTATTATTATTATTATTATTTTACTATTATTA-TTATTATCATTATTATTAC
*
9518303 TATTATTATTATTATTATTATTATTATTTTACTATTATTTATTATTACCATTATTATTAC
1 TATTATTATTATTATTATTATTATTATTTTACTATTA-TTATTATTATCATTATTATTAC
* * * * * *
9518363 TGTTAATATTATT-TTATTACTATTACTCTT-CT-TTATTATTATTATTATTATTATTAT
1 TATTATTATTATTATTATTATTATTA-TTTTACTATTATTATTATTATCATTATTATTAC
9518420 TATTATT
1 TATTATT
9518427 GTCATTTGTA
Statistics
Matches: 107, Mismatches: 15, Indels: 7
0.83 0.12 0.05
Matches are distributed among these distances:
57 24 0.22
58 3 0.03
59 13 0.12
60 64 0.60
61 3 0.03
ACGTcount: A:0.30, C:0.07, G:0.02, T:0.61
Consensus pattern (59 bp):
TATTATTATTATTATTATTATTATTATTTTACTATTATTATTATTATCATTATTATTAC
Found at i:9526470 original size:6 final size:6
Alignment explanation
Indices: 9526461--9526745 Score: 561
Period size: 6 Copynumber: 47.5 Consensus size: 6
9526451 AAAAAGAGGA
*
9526461 AGAAGG AGAAGG AGAAAG AGAAGG AGAAGG AGAAGG AGAAGG AGAAGG
1 AGAAGG AGAAGG AGAAGG AGAAGG AGAAGG AGAAGG AGAAGG AGAAGG
9526509 AGAAGG AGAAGG AGAAGG AGAAGG AGAAGG AGAAGG AGAAGG AGAAGG
1 AGAAGG AGAAGG AGAAGG AGAAGG AGAAGG AGAAGG AGAAGG AGAAGG
9526557 AGAAGG AGAAGG AGAAGG AGAAGG AGAAGG AGAAGG AGAAGG AGAAGG
1 AGAAGG AGAAGG AGAAGG AGAAGG AGAAGG AGAAGG AGAAGG AGAAGG
9526605 AGAAGG AGAAGG AGAAGG AGAAGG AGAAGG AGAAGG AGAAGG AGAAGG
1 AGAAGG AGAAGG AGAAGG AGAAGG AGAAGG AGAAGG AGAAGG AGAAGG
9526653 AGAAGG AGAAGG AGAAGG AGAAGG AGAAGG AGAAGG AGAAGG AGAAGG
1 AGAAGG AGAAGG AGAAGG AGAAGG AGAAGG AGAAGG AGAAGG AGAAGG
9526701 AGAAGG AGAAGG AGAAGG AGAAGG AGAAGG AGAAGG AGAAGG AGA
1 AGAAGG AGAAGG AGAAGG AGAAGG AGAAGG AGAAGG AGAAGG AGA
9526746 GGCCAAGGTG
Statistics
Matches: 277, Mismatches: 2, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
6 277 1.00
ACGTcount: A:0.51, C:0.00, G:0.49, T:0.00
Consensus pattern (6 bp):
AGAAGG
Found at i:9527712 original size:44 final size:44
Alignment explanation
Indices: 9527561--9528227 Score: 372
Period size: 44 Copynumber: 14.9 Consensus size: 44
9527551 GAAGATTGGT
* * * ** *
9527561 AAATTCACAAGTCTTATCTCCCTGAAGTTGCAGCGGAGCAGACTA
1 AAATT-ACAAATCTTATCTCTCTGAAGTTGCAGTGGAGCAGGTTG
*** * * * * *
9527606 AAGATGGTAAATCTTATCTCTCTAAAATTGTAGTGGAGCAGATTA
1 AA-ATTACAAATCTTATCTCTCTGAAGTTGCAGTGGAGCAGGTTG
*** * * *
9527651 AAACCGCAAACCCTATCTCTCTGAAGTTGCAGTAGAGCAGGTTG
1 AAATTACAAATCTTATCTCTCTGAAGTTGCAGTGGAGCAGGTTG
* * * * *
9527695 AAGTTACAAGTCTTATCTCCCTGAAGTTACAGTGGAACAGGTTG
1 AAATTACAAATCTTATCTCTCTGAAGTTGCAGTGGAGCAGGTTG
* * * ***
9527739 AAATTACAAGTCTTATCTCCCTGCAGTTGCAGTGGAGCAAACTG
1 AAATTACAAATCTTATCTCTCTGAAGTTGCAGTGGAGCAGGTTG
* * * * *
9527783 AAGA-TAGCGAATCTTATTTCCCTGAAGTTGCTGTGGAAC-GGATTGAAG
1 AA-ATTA-CAAATCTTATCTCTCTGAAGTTGCAGTGGAGCAGG-TT---G
* * * *
9527831 CTATAATTACAAATCTTATCCCTCTGAAGTTGCAGTAGAGCA-GATC
1 --A-AATTACAAATCTTATCTCTCTGAAGTTGCAGTGGAGCAGGTTG
* * * *
9527877 AAA--ATAAACCTTATCTCTCTGAAGCTGCAGTGGAGCAGGTTA
1 AAATTACAAATCTTATCTCTCTGAAGTTGCAGTGGAGCAGGTTG
* * * *
9527919 AAATTACAAACCTTATCTC-CTTAAAGTTGTAGTGGAGTAGGTTG
1 AAATTACAAATCTTATCTCTC-TGAAGTTGCAGTGGAGCAGGTTG
* * **
9527963 AAATTACAAGTCTTATCTCCCTGAAGTTGCAGTGGAGCAGACTG
1 AAATTACAAATCTTATCTCTCTGAAGTTGCAGTGGAGCAGGTTG
* * * *
9528007 AAGA-TAGCAAATCTTATTTCCCTGAAGTTGCTGTGGAAC-GGATTGAAG
1 AA-ATTA-CAAATCTTATCTCTCTGAAGTTGCAGTGGAGCAGG-TT---G
* * * *
9528055 CTATAATTACAAATCTTATCCCTCTGAAGTTGCAGTAGAGCA-GATC
1 --A-AATTACAAATCTTATCTCTCTGAAGTTGCAGTGGAGCAGGTTG
* *
9528101 AAA--ATAAACCTTATCTCTCTGAAGTTGCAGTGGAGCAGGTT-
1 AAATTACAAATCTTATCTCTCTGAAGTTGCAGTGGAGCAGGTTG
* * * ***
9528142 AATATTACAAACCTTATCTC-CTTAAAGTTGTAGTGGAGCATACTG
1 AA-ATTACAAATCTTATCTCTC-TGAAGTTGCAGTGGAGCAGGTTG
* * *
9528187 AAGA-TAGCTAATCCTATCTCTCTGAAGTTGCAGTAGAGCAG
1 AA-ATTA-CAAATCTTATCTCTCTGAAGTTGCAGTGGAGCAG
9528228 ATTAAAACAA
Statistics
Matches: 476, Mismatches: 110, Indels: 72
0.72 0.17 0.11
Matches are distributed among these distances:
41 61 0.13
42 8 0.02
43 6 0.01
44 210 0.44
45 121 0.25
46 3 0.01
48 2 0.00
49 2 0.00
50 57 0.12
51 6 0.01
ACGTcount: A:0.31, C:0.19, G:0.21, T:0.29
Consensus pattern (44 bp):
AAATTACAAATCTTATCTCTCTGAAGTTGCAGTGGAGCAGGTTG
Found at i:9528054 original size:224 final size:224
Alignment explanation
Indices: 9527658--9528181 Score: 895
Period size: 224 Copynumber: 2.3 Consensus size: 224
9527648 TTAAAACCGC
* * * * ** * *
9527658 AAACCCTATCTCTCTGAAGTTGCAGTAGAGCAGGTTGAAGTTACAAGTCTTATCTCCCTGAAGTT
1 AAACCTTATCTCTCTGAAGTTGCAGTGGAGCAGGTTAAAATTACAAACCTTATCTCCTTAAAGTT
** * *
9527723 ACAGTGGAACAGGTTGAAATTACAAGTCTTATCTCCCTGCAGTTGCAGTGGAGCAAACTGAAGAT
66 GTAGTGGAGCAGGTTGAAATTACAAGTCTTATCTCCCTGAAGTTGCAGTGGAGCAAACTGAAGAT
*
9527788 AGCGAATCTTATTTCCCTGAAGTTGCTGTGGAACGGATTGAAGCTATAATTACAAATCTTATCCC
131 AGCAAATCTTATTTCCCTGAAGTTGCTGTGGAACGGATTGAAGCTATAATTACAAATCTTATCCC
9527853 TCTGAAGTTGCAGTAGAGCAGATCAAAAT
196 TCTGAAGTTGCAGTAGAGCAGATCAAAAT
*
9527882 AAACCTTATCTCTCTGAAGCTGCAGTGGAGCAGGTTAAAATTACAAACCTTATCTCCTTAAAGTT
1 AAACCTTATCTCTCTGAAGTTGCAGTGGAGCAGGTTAAAATTACAAACCTTATCTCCTTAAAGTT
* *
9527947 GTAGTGGAGTAGGTTGAAATTACAAGTCTTATCTCCCTGAAGTTGCAGTGGAGCAGACTGAAGAT
66 GTAGTGGAGCAGGTTGAAATTACAAGTCTTATCTCCCTGAAGTTGCAGTGGAGCAAACTGAAGAT
9528012 AGCAAATCTTATTTCCCTGAAGTTGCTGTGGAACGGATTGAAGCTATAATTACAAATCTTATCCC
131 AGCAAATCTTATTTCCCTGAAGTTGCTGTGGAACGGATTGAAGCTATAATTACAAATCTTATCCC
9528077 TCTGAAGTTGCAGTAGAGCAGATCAAAAT
196 TCTGAAGTTGCAGTAGAGCAGATCAAAAT
*
9528106 AAACCTTATCTCTCTGAAGTTGCAGTGGAGCAGGTTAATATTACAAACCTTATCTCCTTAAAGTT
1 AAACCTTATCTCTCTGAAGTTGCAGTGGAGCAGGTTAAAATTACAAACCTTATCTCCTTAAAGTT
9528171 GTAGTGGAGCA
66 GTAGTGGAGCA
9528182 TACTGAAGAT
Statistics
Matches: 281, Mismatches: 19, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
224 281 1.00
ACGTcount: A:0.31, C:0.19, G:0.21, T:0.29
Consensus pattern (224 bp):
AAACCTTATCTCTCTGAAGTTGCAGTGGAGCAGGTTAAAATTACAAACCTTATCTCCTTAAAGTT
GTAGTGGAGCAGGTTGAAATTACAAGTCTTATCTCCCTGAAGTTGCAGTGGAGCAAACTGAAGAT
AGCAAATCTTATTTCCCTGAAGTTGCTGTGGAACGGATTGAAGCTATAATTACAAATCTTATCCC
TCTGAAGTTGCAGTAGAGCAGATCAAAAT
Found at i:9528112 original size:180 final size:182
Alignment explanation
Indices: 9527886--9528217 Score: 447
Period size: 180 Copynumber: 1.8 Consensus size: 182
9527876 CAAAATAAAC
* * * * *
9527886 CTTATCTCTCTGAAGCTGCAGTGGAGCAGGTTAAAATTACAAACCTTATCTC-CTTAAAGTTGTA
1 CTTATCCCTCTGAAGCTGCAGTAGAGCAGATCAAAATTA-AAACCTTATCTCTC-TAAAGTTGCA
* ** *
9527950 GTGGAGTAGGTTGAA-ATTACAAGTCTTATCTCCCTGAAGTTGCAGTGGAGCAGACTGAAGATAG
64 GTGGAGCAGGTT-AATATTACAAACCTTATCTCCCTAAAGTTGCAGTGGAGCAGACTGAAGATAG
* *
9528014 CAAATCTTATTTCCCTGAAGTTGCTGTGGAACGGATTGAAGCTATAATTACAAAT
128 CAAATCCTATCTCCCTGAAGTTGCTGTGGAACGGATTGAAGCTATAATTACAAAT
* *
9528069 CTTATCCCTCTGAAGTTGCAGTAGAGCAGATCAAAA-T-AAACCTTATCTCTCTGAAGTTGCAGT
1 CTTATCCCTCTGAAGCTGCAGTAGAGCAGATCAAAATTAAAACCTTATCTCTCTAAAGTTGCAGT
* * * *
9528132 GGAGCAGGTTAATATTACAAACCTTATCTCCTTAAAGTTGTAGTGGAGCATACTGAAGATAGCTA
66 GGAGCAGGTTAATATTACAAACCTTATCTCCCTAAAGTTGCAGTGGAGCAGACTGAAGATAGCAA
*
9528197 ATCCTATCTCTCTGAAGTTGC
131 ATCCTATCTCCCTGAAGTTGC
9528218 AGTAGAGCAG
Statistics
Matches: 129, Mismatches: 18, Indels: 7
0.84 0.12 0.05
Matches are distributed among these distances:
179 2 0.02
180 94 0.73
181 1 0.01
182 1 0.01
183 31 0.24
ACGTcount: A:0.30, C:0.18, G:0.20, T:0.31
Consensus pattern (182 bp):
CTTATCCCTCTGAAGCTGCAGTAGAGCAGATCAAAATTAAAACCTTATCTCTCTAAAGTTGCAGT
GGAGCAGGTTAATATTACAAACCTTATCTCCCTAAAGTTGCAGTGGAGCAGACTGAAGATAGCAA
ATCCTATCTCCCTGAAGTTGCTGTGGAACGGATTGAAGCTATAATTACAAAT
Found at i:9528258 original size:224 final size:224
Alignment explanation
Indices: 9527658--9528261 Score: 775
Period size: 224 Copynumber: 2.7 Consensus size: 224
9527648 TTAAAACCGC
* * * * * ** * *
9527658 AAACCCTATCTCTCTGAAGTTGCAGTAGAGCAGGTTGAAGTTACAAGTCTTATCTCCCTGAAGTT
1 AAACCTTATCTCTCTGAAGCTGCAGTGGAGCAGGTTAAAATTACAAACCTTATCTCCTTAAAGTT
** * ** * * * * * *
9527723 ACAGTGGAACAGGTTGAAATTACAAGTCTTATCTCCCTGCAGTTGCAGTGGAGCAAACTGAAGAT
66 GTAGTGGAGCAGACTGAAATTACAAGTCCTATCTCCCTGAAGTTGCAGTAGAGCAGACTGAAAAC
* * * *
9527788 AGCGAATCTTATTTCCCTGAAGTTGCTGTGGAACGGATTGAAGCTATAATTACAAATCTTATCCC
131 AACAAATCCTATTACCCTGAAGTTGCTGTGGAACGGATTGAAGCTATAATTACAAATCTTATCCC
9527853 TCTGAAGTTGCAGTAGAGCAGATCAAAAT
196 TCTGAAGTTGCAGTAGAGCAGATCAAAAT
9527882 AAACCTTATCTCTCTGAAGCTGCAGTGGAGCAGGTTAAAATTACAAACCTTATCTCCTTAAAGTT
1 AAACCTTATCTCTCTGAAGCTGCAGTGGAGCAGGTTAAAATTACAAACCTTATCTCCTTAAAGTT
* ** * * * *
9527947 GTAGTGGAGTAGGTTGAAATTACAAGTCTTATCTCCCTGAAGTTGCAGTGGAGCAGACTGAAGAT
66 GTAGTGGAGCAGACTGAAATTACAAGTCCTATCTCCCTGAAGTTGCAGTAGAGCAGACTGAAAAC
* * *
9528012 AGCAAATCTTATTTCCCTGAAGTTGCTGTGGAACGGATTGAAGCTATAATTACAAATCTTATCCC
131 AACAAATCCTATTACCCTGAAGTTGCTGTGGAACGGATTGAAGCTATAATTACAAATCTTATCCC
9528077 TCTGAAGTTGCAGTAGAGCAGATCAAAAT
196 TCTGAAGTTGCAGTAGAGCAGATCAAAAT
* *
9528106 AAACCTTATCTCTCTGAAGTTGCAGTGGAGCAGGTTAATATTACAAACCTTATCTCCTTAAAGTT
1 AAACCTTATCTCTCTGAAGCTGCAGTGGAGCAGGTTAAAATTACAAACCTTATCTCCTTAAAGTT
* * *
9528171 GTAGTGGAGCATACTGAAGA-TAGCTAA-TCCTATCTCTCTGAAGTTGCAGTAGAGCAGA-TTAA
66 GTAGTGGAGCAGACTGAA-ATTA-C-AAGTCCTATCTCCCTGAAGTTGCAGTAGAGCAGACTGAA
* *
9528233 AACAACGAGTCCTA-TACCTCTGAAGTTGC
128 AACAACAAATCCTATTACC-CTGAAGTTGC
9528262 AGTAGGTCGG
Statistics
Matches: 343, Mismatches: 33, Indels: 8
0.89 0.09 0.02
Matches are distributed among these distances:
223 3 0.01
224 308 0.90
225 30 0.09
226 2 0.01
ACGTcount: A:0.31, C:0.19, G:0.21, T:0.29
Consensus pattern (224 bp):
AAACCTTATCTCTCTGAAGCTGCAGTGGAGCAGGTTAAAATTACAAACCTTATCTCCTTAAAGTT
GTAGTGGAGCAGACTGAAATTACAAGTCCTATCTCCCTGAAGTTGCAGTAGAGCAGACTGAAAAC
AACAAATCCTATTACCCTGAAGTTGCTGTGGAACGGATTGAAGCTATAATTACAAATCTTATCCC
TCTGAAGTTGCAGTAGAGCAGATCAAAAT
Found at i:9529851 original size:3 final size:3
Alignment explanation
Indices: 9529830--9529995 Score: 152
Period size: 3 Copynumber: 54.3 Consensus size: 3
9529820 TAATTTAATA
* * * *
9529830 TAT TAT TGT TAT TAC TAT TAT TATT TAT TAT CAT TAT TAT TAC TAT
1 TAT TAT TAT TAT TAT TAT TAT TA-T TAT TAT TAT TAT TAT TAT TAT
* * * * * *
9529876 TAT TAT TAT TTT TAC TAT TATT TAT TAT TAC CAT TAT TAT TAC TGT
1 TAT TAT TAT TAT TAT TAT TA-T TAT TAT TAT TAT TAT TAT TAT TAT
* * * * * * *
9529922 TAA TAT TAT TTT TAT TAC TAT TAA TGT TCTT TGT TAT TAT TAT TAT
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT T-AT TAT TAT TAT TAT TAT
9529968 TAT TAT TAT TAT TAT TAT TAT TAT TAT T
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT T
9529996 GTCATTTGTA
Statistics
Matches: 128, Mismatches: 32, Indels: 6
0.77 0.19 0.04
Matches are distributed among these distances:
3 120 0.94
4 8 0.06
ACGTcount: A:0.30, C:0.05, G:0.02, T:0.63
Consensus pattern (3 bp):
TAT
Found at i:9530041 original size:4 final size:4
Alignment explanation
Indices: 9530017--9530072 Score: 51
Period size: 4 Copynumber: 14.0 Consensus size: 4
9530007 TTTGTTATAT
* * * *
9530017 TTTA TTTT TTTA TTTA CTTA TTTA TTTG CTTA TTTCA TTT- TTTA TTTA
1 TTTA TTTA TTTA TTTA TTTA TTTA TTTA TTTA TTT-A TTTA TTTA TTTA
*
9530065 TTTG TTTA
1 TTTA TTTA
9530073 AACTTTTTAA
Statistics
Matches: 40, Mismatches: 10, Indels: 4
0.74 0.19 0.07
Matches are distributed among these distances:
3 3 0.08
4 33 0.82
5 4 0.10
ACGTcount: A:0.18, C:0.05, G:0.04, T:0.73
Consensus pattern (4 bp):
TTTA
Found at i:9532247 original size:38 final size:37
Alignment explanation
Indices: 9532203--9532298 Score: 101
Period size: 38 Copynumber: 2.6 Consensus size: 37
9532193 TAATTATGTA
*
9532203 AATATATATAATTTAATTATTAATTACTCTTTTATTT
1 AATATATATAATTTAATTATTAATTACTATTTTATTT
* * *
9532240 AAGTATATAGATATTT-ATTATTTATTATTATTTTA-TT
1 AA-TATATATA-ATTTAATTATTAATTACTATTTTATTT
9532277 AA-AT-TATAATTTATATTATTAA
1 AATATATATAATTTA-ATTATTAA
9532299 ATTATGATTA
Statistics
Matches: 49, Mismatches: 6, Indels: 10
0.75 0.09 0.15
Matches are distributed among these distances:
33 4 0.08
34 3 0.06
35 9 0.18
37 6 0.12
38 23 0.47
39 4 0.08
ACGTcount: A:0.40, C:0.02, G:0.02, T:0.56
Consensus pattern (37 bp):
AATATATATAATTTAATTATTAATTACTATTTTATTT
Found at i:9532267 original size:3 final size:3
Alignment explanation
Indices: 9532254--9532320 Score: 52
Period size: 3 Copynumber: 23.0 Consensus size: 3
9532244 ATATAGATAT
* *
9532254 TTA TTA TTTA TTA TTA TT- TTA TTA -AA TTA TAA TT- TATA TTA TTA
1 TTA TTA -TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA T-TA TTA TTA
* *
9532298 -AA TTA TGA TTA TTA TTA TTA TTA
1 TTA TTA TTA TTA TTA TTA TTA TTA
9532321 AAAATAAATT
Statistics
Matches: 50, Mismatches: 8, Indels: 12
0.71 0.11 0.17
Matches are distributed among these distances:
2 5 0.10
3 41 0.82
4 4 0.08
ACGTcount: A:0.37, C:0.00, G:0.01, T:0.61
Consensus pattern (3 bp):
TTA
Found at i:9532282 original size:23 final size:22
Alignment explanation
Indices: 9532256--9532322 Score: 75
Period size: 20 Copynumber: 3.0 Consensus size: 22
9532246 ATAGATATTT
9532256 ATTATTTATTATTATTTTATTAA
1 ATTA-TTATTATTATTTTATTAA
* *
9532279 ATTA-TAAT-TTATATTATTAA
1 ATTATTATTATTATTTTATTAA
*
9532299 ATTATGATTATTATTATTATTAA
1 ATTATTATTATTATT-TTATTAA
9532322 A
1 A
9532323 AATAAATTAA
Statistics
Matches: 36, Mismatches: 5, Indels: 6
0.77 0.11 0.13
Matches are distributed among these distances:
20 15 0.42
21 5 0.14
22 4 0.11
23 12 0.33
ACGTcount: A:0.40, C:0.00, G:0.01, T:0.58
Consensus pattern (22 bp):
ATTATTATTATTATTTTATTAA
Found at i:9532302 original size:25 final size:26
Alignment explanation
Indices: 9532254--9532320 Score: 66
Period size: 26 Copynumber: 2.6 Consensus size: 26
9532244 ATATAGATAT
* **
9532254 TTATTATTTATTATTATTTTATTAAA
1 TTATAATTTATTATTATTAAATTAAA
*
9532280 TTATAATTTA-TATTATTAAATTATGA
1 TTATAATTTATTATTATTAAATTA-AA
*
9532306 TTATTA-TTATTATTA
1 TTATAATTTATTATTA
9532321 AAAATAAATT
Statistics
Matches: 34, Mismatches: 5, Indels: 4
0.79 0.12 0.09
Matches are distributed among these distances:
25 14 0.41
26 20 0.59
ACGTcount: A:0.37, C:0.00, G:0.01, T:0.61
Consensus pattern (26 bp):
TTATAATTTATTATTATTAAATTAAA
Found at i:9532629 original size:13 final size:14
Alignment explanation
Indices: 9532611--9532648 Score: 51
Period size: 13 Copynumber: 2.8 Consensus size: 14
9532601 TTATGAAATT
9532611 AATAAAATAAAAG-
1 AATAAAATAAAAGA
* *
9532624 AATAAAAGAAATGA
1 AATAAAATAAAAGA
9532638 AATAAAATAAA
1 AATAAAATAAA
9532649 GTAAAGAAGA
Statistics
Matches: 21, Mismatches: 3, Indels: 1
0.84 0.12 0.04
Matches are distributed among these distances:
13 11 0.52
14 10 0.48
ACGTcount: A:0.76, C:0.00, G:0.08, T:0.16
Consensus pattern (14 bp):
AATAAAATAAAAGA
Found at i:9533797 original size:43 final size:44
Alignment explanation
Indices: 9533687--9533806 Score: 161
Period size: 45 Copynumber: 2.7 Consensus size: 44
9533677 ACTGATCAGG
* * * * *
9533687 CACTTATGTGCCGACTACTGTTACTGTTACTGTTACCGATTCGA
1 CACTTGTGTGTCGAATACTGTTACTGTTACTGTTACAGATTCAA
*
9533731 CACTTTGTGTGTCGAATACTGTTACCGTTACTGTTACAGATTCAA
1 CAC-TTGTGTGTCGAATACTGTTACTGTTACTGTTACAGATTCAA
*
9533776 CAC-TGTGTGTTGAATACTGTTACTGTTACTG
1 CACTTGTGTGTCGAATACTGTTACTGTTACTG
9533807 CTACTGCTAC
Statistics
Matches: 67, Mismatches: 8, Indels: 3
0.86 0.10 0.04
Matches are distributed among these distances:
43 26 0.39
44 3 0.04
45 38 0.57
ACGTcount: A:0.22, C:0.21, G:0.19, T:0.38
Consensus pattern (44 bp):
CACTTGTGTGTCGAATACTGTTACTGTTACTGTTACAGATTCAA
Found at i:9533821 original size:18 final size:18
Alignment explanation
Indices: 9533790--9533824 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
9533780 GTGTGTTGAA
* *
9533790 TACTGTTACTGTTACTGC
1 TACTGCTACCGTTACTGC
9533808 TACTGCTACCGTTACTG
1 TACTGCTACCGTTACTG
9533825 ATTACTGATT
Statistics
Matches: 15, Mismatches: 2, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
18 15 1.00
ACGTcount: A:0.17, C:0.26, G:0.17, T:0.40
Consensus pattern (18 bp):
TACTGCTACCGTTACTGC
Found at i:9539865 original size:38 final size:37
Alignment explanation
Indices: 9539821--9539931 Score: 97
Period size: 38 Copynumber: 3.0 Consensus size: 37
9539811 TAATTATGTA
9539821 AATATATATAATTTAATTATTAATTACTT-TTTTATTT
1 AATATATATAATTTAATTATTAATTA-TTATTTTATTT
* * *
9539858 AAGTATATAGATATTT-ATTATTTATTATTATTCTA-TT
1 AA-TATATATA-ATTTAATTATTAATTATTATTTTATTT
*
9539895 AA-AT-TATAATTTATATTATTAAATTATGATTATTATT
1 AATATATATAATTTA-ATTATT-AATTATTATT-TTATT
9539932 ATTAAAAATA
Statistics
Matches: 59, Mismatches: 7, Indels: 15
0.73 0.09 0.19
Matches are distributed among these distances:
33 4 0.07
34 3 0.05
35 8 0.14
36 8 0.14
37 10 0.17
38 22 0.37
39 4 0.07
ACGTcount: A:0.39, C:0.02, G:0.03, T:0.57
Consensus pattern (37 bp):
AATATATATAATTTAATTATTAATTATTATTTTATTT
Found at i:9539914 original size:20 final size:20
Alignment explanation
Indices: 9539881--9539937 Score: 71
Period size: 20 Copynumber: 2.8 Consensus size: 20
9539871 TTTATTATTT
9539881 ATTATTATTCTATTAAATTATA
1 ATTATTA-T-TATTAAATTATA
*
9539903 ATT-TATATTATTAAATTATG
1 ATTAT-TATTATTAAATTATA
9539923 ATTATTATTATTAAA
1 ATTATTATTATTAAA
9539938 AATAAATTAA
Statistics
Matches: 32, Mismatches: 1, Indels: 6
0.82 0.03 0.15
Matches are distributed among these distances:
20 24 0.75
21 3 0.09
22 5 0.16
ACGTcount: A:0.42, C:0.02, G:0.02, T:0.54
Consensus pattern (20 bp):
ATTATTATTATTAAATTATA
Found at i:9539920 original size:25 final size:26
Alignment explanation
Indices: 9539872--9539920 Score: 64
Period size: 25 Copynumber: 1.9 Consensus size: 26
9539862 ATATAGATAT
* **
9539872 TTATTATTTATTATTATTCTATTAAA
1 TTATAATTTATTATTATTAAATTAAA
9539898 TTATAATTTA-TATTATTAAATTA
1 TTATAATTTATTATTATTAAATTA
9539921 TGATTATTAT
Statistics
Matches: 20, Mismatches: 3, Indels: 1
0.83 0.12 0.04
Matches are distributed among these distances:
25 11 0.55
26 9 0.45
ACGTcount: A:0.39, C:0.02, G:0.00, T:0.59
Consensus pattern (26 bp):
TTATAATTTATTATTATTAAATTAAA
Found at i:9541394 original size:43 final size:44
Alignment explanation
Indices: 9541284--9541403 Score: 161
Period size: 45 Copynumber: 2.7 Consensus size: 44
9541274 ACTGATCAGG
* * * * *
9541284 CACTTATGTGCCGACTACTGTTACTGTTACTGTTACCGATTCGA
1 CACTTGTGTGTCGAATACTGTTACTGTTACTGTTACAGATTCAA
*
9541328 CACTTTGTGTGTCGAATACTGTTACCGTTACTGTTACAGATTCAA
1 CAC-TTGTGTGTCGAATACTGTTACTGTTACTGTTACAGATTCAA
*
9541373 CAC-TGTGTGTTGAATACTGTTACTGTTACTG
1 CACTTGTGTGTCGAATACTGTTACTGTTACTG
9541404 CTACTGCTAC
Statistics
Matches: 67, Mismatches: 8, Indels: 3
0.86 0.10 0.04
Matches are distributed among these distances:
43 26 0.39
44 3 0.04
45 38 0.57
ACGTcount: A:0.22, C:0.21, G:0.19, T:0.38
Consensus pattern (44 bp):
CACTTGTGTGTCGAATACTGTTACTGTTACTGTTACAGATTCAA
Found at i:9541418 original size:18 final size:18
Alignment explanation
Indices: 9541387--9541421 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
9541377 GTGTGTTGAA
* *
9541387 TACTGTTACTGTTACTGC
1 TACTGCTACCGTTACTGC
9541405 TACTGCTACCGTTACTG
1 TACTGCTACCGTTACTG
9541422 ATTACTGATT
Statistics
Matches: 15, Mismatches: 2, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
18 15 1.00
ACGTcount: A:0.17, C:0.26, G:0.17, T:0.40
Consensus pattern (18 bp):
TACTGCTACCGTTACTGC
Found at i:9565774 original size:12 final size:12
Alignment explanation
Indices: 9565757--9565781 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
9565747 GAAAGAAATT
9565757 CGCTTCCACTTC
1 CGCTTCCACTTC
9565769 CGCTTCCACTTC
1 CGCTTCCACTTC
9565781 C
1 C
9565782 ATTTTTTCCA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.08, C:0.52, G:0.08, T:0.32
Consensus pattern (12 bp):
CGCTTCCACTTC
Found at i:9567606 original size:3 final size:3
Alignment explanation
Indices: 9567598--9567631 Score: 68
Period size: 3 Copynumber: 11.3 Consensus size: 3
9567588 AAATAATGTA
9567598 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT A
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT A
9567632 TCCTATTGCC
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 31 1.00
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.32
Consensus pattern (3 bp):
AAT
Found at i:9575566 original size:18 final size:18
Alignment explanation
Indices: 9575540--9575595 Score: 63
Period size: 15 Copynumber: 3.5 Consensus size: 18
9575530 GATTATTAGA
9575540 ATTTT-ATTAAATTATAT
1 ATTTTAATTAAATTATAT
9575557 ATTTTAATTAAA--ATAT
1 ATTTTAATTAAATTATAT
9575573 A-TTTAA-T-AATTAT-T
1 ATTTTAATTAAATTATAT
9575587 ATTTTAATT
1 ATTTTAATT
9575596 TATATTTTAC
Statistics
Matches: 34, Mismatches: 0, Indels: 11
0.76 0.00 0.24
Matches are distributed among these distances:
13 2 0.06
14 3 0.09
15 12 0.35
16 6 0.18
17 5 0.15
18 6 0.18
ACGTcount: A:0.43, C:0.00, G:0.00, T:0.57
Consensus pattern (18 bp):
ATTTTAATTAAATTATAT
Found at i:9575638 original size:119 final size:119
Alignment explanation
Indices: 9575421--9575714 Score: 493
Period size: 119 Copynumber: 2.5 Consensus size: 119
9575411 AATTATTTTA
* *
9575421 AATTTTATTAAATCATATATTTTAATTAAAATATATTTAAT-ATTAATTATTTCAATTATATTTT
1 AATTTTATTAAATTATATATTTTAATTAAAATATATTTAATAATT-ATTATTTTAATTATATTTT
* * *
9575485 ATAGTATCATATATTATGATTTTAGTAAATTCATATAAGAATATTGATTATT-AG
65 ACAGTATCATATATTATGATTTGAGTAAATTCATATAAGAATATTAATTATTAAG
9575539 AATTTTATTAAATTATATATTTTAATTAAAATATATTTAATAATTATTATTTTAATTTATATTTT
1 AATTTTATTAAATTATATATTTTAATTAAAATATATTTAATAATTATTATTTTAA-TTATATTTT
9575604 ACAGTATCATATATTATGATTTGAGTAAATTCATATAAGAATATTAATTATTAAG
65 ACAGTATCATATATTATGATTTGAGTAAATTCATATAAGAATATTAATTATTAAG
*
9575659 AATTTTATTAAATTATATATTTTAATTAAAATATATTTAATAATAATTATGTTTAA
1 AATTTTATTAAATTATATATTTTAATTAAAATATATTTAATAATTATTAT-TTTAA
9575715 ATATGAGTAA
Statistics
Matches: 166, Mismatches: 6, Indels: 5
0.94 0.03 0.03
Matches are distributed among these distances:
118 49 0.30
119 61 0.37
120 51 0.31
121 5 0.03
ACGTcount: A:0.43, C:0.02, G:0.04, T:0.50
Consensus pattern (119 bp):
AATTTTATTAAATTATATATTTTAATTAAAATATATTTAATAATTATTATTTTAATTATATTTTA
CAGTATCATATATTATGATTTGAGTAAATTCATATAAGAATATTAATTATTAAG
Done.