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 32 of 356
Found at i:10902329 original size:56 final size:56
Alignment explanation
Indices: 10902259--10902366 Score: 216
Period size: 56 Copynumber: 1.9 Consensus size: 56
10902249 ATGGGATGGT
10902259 GTTTCACAAGTTGGACAAAGTGAGAATAGAAAGGAAGACAATTTGATCCTTTTCGC
1 GTTTCACAAGTTGGACAAAGTGAGAATAGAAAGGAAGACAATTTGATCCTTTTCGC
10902315 GTTTCACAAGTTGGACAAAGTGAGAATAGAAAGGAAGACAATTTGATCCTTT
1 GTTTCACAAGTTGGACAAAGTGAGAATAGAAAGGAAGACAATTTGATCCTTT
10902367 CTAACTTATC
Statistics
Matches: 52, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
56 52 1.00
ACGTcount: A:0.37, C:0.13, G:0.23, T:0.27
Consensus pattern (56 bp):
GTTTCACAAGTTGGACAAAGTGAGAATAGAAAGGAAGACAATTTGATCCTTTTCGC
Found at i:10905411 original size:35 final size:35
Alignment explanation
Indices: 10905365--10905432 Score: 136
Period size: 35 Copynumber: 1.9 Consensus size: 35
10905355 TGTACTAAGT
10905365 GGTTGTCTAAATTAAATTTATTTAATTAAAAATAA
1 GGTTGTCTAAATTAAATTTATTTAATTAAAAATAA
10905400 GGTTGTCTAAATTAAATTTATTTAATTAAAAAT
1 GGTTGTCTAAATTAAATTTATTTAATTAAAAAT
10905433 TTATTTTCAT
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
35 33 1.00
ACGTcount: A:0.44, C:0.03, G:0.09, T:0.44
Consensus pattern (35 bp):
GGTTGTCTAAATTAAATTTATTTAATTAAAAATAA
Found at i:10911082 original size:14 final size:14
Alignment explanation
Indices: 10911063--10911089 Score: 54
Period size: 14 Copynumber: 1.9 Consensus size: 14
10911053 AATTGCTCTA
10911063 TTATGTCCAAATAT
1 TTATGTCCAAATAT
10911077 TTATGTCCAAATA
1 TTATGTCCAAATA
10911090 CACCCTCAAT
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:0.37, C:0.15, G:0.07, T:0.41
Consensus pattern (14 bp):
TTATGTCCAAATAT
Found at i:10911224 original size:14 final size:14
Alignment explanation
Indices: 10911205--10911232 Score: 56
Period size: 14 Copynumber: 2.0 Consensus size: 14
10911195 AATATTATAA
10911205 AAATTATTTAGTTC
1 AAATTATTTAGTTC
10911219 AAATTATTTAGTTC
1 AAATTATTTAGTTC
10911233 TATAAAAGAA
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:0.36, C:0.07, G:0.07, T:0.50
Consensus pattern (14 bp):
AAATTATTTAGTTC
Found at i:10912677 original size:23 final size:23
Alignment explanation
Indices: 10912651--10912695 Score: 56
Period size: 23 Copynumber: 2.0 Consensus size: 23
10912641 ATGTTTTTTT
10912651 ATTTA-AAAATAAATTAATTTTAA
1 ATTTATAAAATAAA-TAATTTTAA
* *
10912674 ATTTATATAATTAATAATTTTA
1 ATTTATAAAATAAATAATTTTA
10912696 CTACATTATA
Statistics
Matches: 19, Mismatches: 2, Indels: 2
0.83 0.09 0.09
Matches are distributed among these distances:
23 13 0.68
24 6 0.32
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (23 bp):
ATTTATAAAATAAATAATTTTAA
Found at i:10918658 original size:53 final size:53
Alignment explanation
Indices: 10918577--10918727 Score: 205
Period size: 53 Copynumber: 2.8 Consensus size: 53
10918567 CTTACACGGT
* * *
10918577 TCACATATCATACCGAAGTCATATCCCAGAC-ATGGTCTTATACGGAATCACATTA
1 TCACAT-T-ATACCGATGCCATAGCCCAG-CTATGGTCTTATACGGAATCACATTA
*
10918632 TCACATTATACCGATGCCATAGCCCAGCTATGGTCTTATACGGAGTCACATTA
1 TCACATTATACCGATGCCATAGCCCAGCTATGGTCTTATACGGAATCACATTA
* * *
10918685 TCACATTGTACCGATGCCATAGCACAGCTATGGTCTTAAACGG
1 TCACATTATACCGATGCCATAGCCCAGCTATGGTCTTATACGG
10918728 GCGCACTTAT
Statistics
Matches: 88, Mismatches: 7, Indels: 4
0.89 0.07 0.04
Matches are distributed among these distances:
52 1 0.01
53 80 0.91
54 1 0.01
55 6 0.07
ACGTcount: A:0.30, C:0.26, G:0.17, T:0.27
Consensus pattern (53 bp):
TCACATTATACCGATGCCATAGCCCAGCTATGGTCTTATACGGAATCACATTA
Found at i:10925319 original size:16 final size:17
Alignment explanation
Indices: 10925283--10925319 Score: 51
Period size: 16 Copynumber: 2.3 Consensus size: 17
10925273 AATTTTATTT
*
10925283 TAATTATAAATTTTAAA
1 TAATAATAAATTTTAAA
10925300 -AATAATAAA-TTTAAA
1 TAATAATAAATTTTAAA
10925315 TAATA
1 TAATA
10925320 TTCTTCAAAA
Statistics
Matches: 18, Mismatches: 1, Indels: 3
0.82 0.05 0.14
Matches are distributed among these distances:
15 6 0.33
16 12 0.67
ACGTcount: A:0.59, C:0.00, G:0.00, T:0.41
Consensus pattern (17 bp):
TAATAATAAATTTTAAA
Found at i:10928613 original size:46 final size:46
Alignment explanation
Indices: 10928546--10928712 Score: 171
Period size: 46 Copynumber: 3.6 Consensus size: 46
10928536 TGTAACCCGA
*
10928546 CCATAAGTGAACTCAGACTCAACTCAACGAGCTCGGGCGTTCGCAT
1 CCATAAGTGAACTCGGACTCAACTCAACGAGCTCGGGCGTTCGCAT
* * *
10928592 CCATAAGTGAACTCGGGCTCAACTCAATGAGCTCGGATGCCTAGTT-ACAT
1 CCATAAGTGAACTCGGACTCAACTCAACGAGCTCGG--G-C--GTTCGCAT
* * * ** *
10928642 -C-TCA-TGAACTTGGACTCAACTCAACGAGTTCGAACATTCGCAT
1 CCATAAGTGAACTCGGACTCAACTCAACGAGCTCGGGCGTTCGCAT
10928685 CCATAAGTGAACTCGGACTCAACTCAAC
1 CCATAAGTGAACTCGGACTCAACTCAAC
10928713 AAGTTCGGAT
Statistics
Matches: 97, Mismatches: 15, Indels: 18
0.75 0.12 0.14
Matches are distributed among these distances:
42 2 0.02
43 3 0.03
44 2 0.02
45 2 0.02
46 53 0.55
47 24 0.25
48 3 0.03
49 2 0.02
50 3 0.03
51 3 0.03
ACGTcount: A:0.30, C:0.29, G:0.19, T:0.22
Consensus pattern (46 bp):
CCATAAGTGAACTCGGACTCAACTCAACGAGCTCGGGCGTTCGCAT
Found at i:10931154 original size:22 final size:21
Alignment explanation
Indices: 10931088--10931157 Score: 86
Period size: 23 Copynumber: 3.2 Consensus size: 21
10931078 TCATCCTAAA
*
10931088 CCAAGCCTAAACCAACCTAGC
1 CCAATCCTAAACCAACCTAGC
10931109 CCAATACCCTAAACCAACCTAGC
1 CCAAT--CCTAAACCAACCTAGC
* *
10931132 CCAATCCTAAAACTACCTGAGC
1 CCAATCCTAAACCAACCT-AGC
10931154 CCAA
1 CCAA
10931158 ATTTTAAAAC
Statistics
Matches: 43, Mismatches: 3, Indels: 5
0.84 0.06 0.10
Matches are distributed among these distances:
21 15 0.35
22 7 0.16
23 21 0.49
ACGTcount: A:0.39, C:0.41, G:0.07, T:0.13
Consensus pattern (21 bp):
CCAATCCTAAACCAACCTAGC
Found at i:10933755 original size:106 final size:106
Alignment explanation
Indices: 10933619--10933819 Score: 375
Period size: 106 Copynumber: 1.9 Consensus size: 106
10933609 AAAATTTTTC
10933619 TAAATAAGGCAATATTTCGCGTTTGGAAAATCGAGAAAACGTGCCCTAACGTGCTGGGTTTCGAT
1 TAAATAAGGCAATATTTCGCGTTTGGAAAATCGAGAAAACGTGCCCTAACGTGCTGGGTTTCGAT
*
10933684 TTCTCGTTCGACCAAATAGCCAAATATCCTTTTTAAACTTT
66 TTCTCGTTCGACCAAACAGCCAAATATCCTTTTTAAACTTT
*
10933725 TAAATAAGGCAATATTTCGCGTTTGGAAAATCGAGGAAACGTGCCCTAACGTGCTGGGTTTCGAT
1 TAAATAAGGCAATATTTCGCGTTTGGAAAATCGAGAAAACGTGCCCTAACGTGCTGGGTTTCGAT
*
10933790 TTCTCGTTCGACTAAACAGCCAAATATCCT
66 TTCTCGTTCGACCAAACAGCCAAATATCCT
10933820 CTTAAAGCTT
Statistics
Matches: 92, Mismatches: 3, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
106 92 1.00
ACGTcount: A:0.30, C:0.20, G:0.19, T:0.30
Consensus pattern (106 bp):
TAAATAAGGCAATATTTCGCGTTTGGAAAATCGAGAAAACGTGCCCTAACGTGCTGGGTTTCGAT
TTCTCGTTCGACCAAACAGCCAAATATCCTTTTTAAACTTT
Found at i:10945764 original size:3 final size:3
Alignment explanation
Indices: 10945756--10945801 Score: 92
Period size: 3 Copynumber: 15.3 Consensus size: 3
10945746 CAAAGCGATA
10945756 AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG A
1 AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG A
10945802 GTAAAAGGGC
Statistics
Matches: 43, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 43 1.00
ACGTcount: A:0.67, C:0.00, G:0.33, T:0.00
Consensus pattern (3 bp):
AAG
Found at i:10951627 original size:20 final size:20
Alignment explanation
Indices: 10951594--10951682 Score: 90
Period size: 20 Copynumber: 4.4 Consensus size: 20
10951584 CGTGTTTGCT
* * *
10951594 TTTCATTTAGCTCACATGAG
1 TTTCAGTTAACTCATATGAG
* *
10951614 CTTCAGTTAACTCATATTAG
1 TTTCAGTTAACTCATATGAG
*
10951634 TTTCAGTTAAC-CCTAATGAG
1 TTTCAGTTAACTCAT-ATGAG
*
10951654 TTTCAGTTCAACTCTTATGAG
1 TTTCAGTT-AACTCATATGAG
10951675 TTTCAGTT
1 TTTCAGTT
10951683 TAACCCTACT
Statistics
Matches: 57, Mismatches: 9, Indels: 5
0.80 0.13 0.07
Matches are distributed among these distances:
19 2 0.04
20 37 0.65
21 16 0.28
22 2 0.04
ACGTcount: A:0.26, C:0.19, G:0.13, T:0.42
Consensus pattern (20 bp):
TTTCAGTTAACTCATATGAG
Found at i:10951675 original size:21 final size:20
Alignment explanation
Indices: 10951609--10951682 Score: 94
Period size: 20 Copynumber: 3.6 Consensus size: 20
10951599 TTTAGCTCAC
* *
10951609 ATGAGCTTCAGTTAACTCAT
1 ATGAGTTTCAGTTAACTCTT
* * *
10951629 ATTAGTTTCAGTTAACCCTA
1 ATGAGTTTCAGTTAACTCTT
10951649 ATGAGTTTCAGTTCAACTCTT
1 ATGAGTTTCAGTT-AACTCTT
10951670 ATGAGTTTCAGTT
1 ATGAGTTTCAGTT
10951683 TAACCCTACT
Statistics
Matches: 45, Mismatches: 8, Indels: 1
0.83 0.15 0.02
Matches are distributed among these distances:
20 27 0.60
21 18 0.40
ACGTcount: A:0.27, C:0.18, G:0.15, T:0.41
Consensus pattern (20 bp):
ATGAGTTTCAGTTAACTCTT
Found at i:10951716 original size:42 final size:41
Alignment explanation
Indices: 10951609--10951690 Score: 121
Period size: 41 Copynumber: 2.0 Consensus size: 41
10951599 TTTAGCTCAC
* * *
10951609 ATGAGCTTCAGTT-AACTCATATTAGTTTCAGTTAACCCTA
1 ATGAGTTTCAGTTCAACTCTTATGAGTTTCAGTTAACCCTA
10951649 ATGAGTTTCAGTTCAACTCTTATGAGTTTCAGTTTAACCCTA
1 ATGAGTTTCAGTTCAACTCTTATGAGTTTCAG-TTAACCCTA
10951691 CTGGGTTTTT
Statistics
Matches: 37, Mismatches: 3, Indels: 2
0.88 0.07 0.05
Matches are distributed among these distances:
40 12 0.32
41 16 0.43
42 9 0.24
ACGTcount: A:0.28, C:0.20, G:0.13, T:0.39
Consensus pattern (41 bp):
ATGAGTTTCAGTTCAACTCTTATGAGTTTCAGTTAACCCTA
Found at i:10954718 original size:46 final size:46
Alignment explanation
Indices: 10954647--10954874 Score: 287
Period size: 46 Copynumber: 5.0 Consensus size: 46
10954637 GCTTTCTGAA
* * * *
10954647 ATGAAATGTGTAATACCATGGTTGAAAGATACCATAGCAACATGAT
1 ATGAAATGAGTAAGACCATGGTTGAAAGATACCATGGCAACATGAC
* * * *
10954693 ATGAAATGTGTAAGACCATGATTGAAAGATATCATGGCAACGTGAC
1 ATGAAATGAGTAAGACCATGGTTGAAAGATACCATGGCAACATGAC
** *
10954739 ATGAAATGAACAAGACCATGGTTGAAAAATACCATGGCAACATGAC
1 ATGAAATGAGTAAGACCATGGTTGAAAGATACCATGGCAACATGAC
** *
10954785 GGGAAATGAATAAGACCATGGTTGAAAGATACCATGGCAACATGAC
1 ATGAAATGAGTAAGACCATGGTTGAAAGATACCATGGCAACATGAC
* * *
10954831 AGGAAATGAGTAAGACCATGGTTGGAAA-ATACTATGGCATCATG
1 ATGAAATGAGTAAGACCATGGTT-GAAAGATACCATGGCAACATG
10954875 TCAAAGATAA
Statistics
Matches: 160, Mismatches: 21, Indels: 2
0.87 0.11 0.01
Matches are distributed among these distances:
46 156 0.98
47 4 0.03
ACGTcount: A:0.41, C:0.14, G:0.23, T:0.21
Consensus pattern (46 bp):
ATGAAATGAGTAAGACCATGGTTGAAAGATACCATGGCAACATGAC
Found at i:10957097 original size:42 final size:42
Alignment explanation
Indices: 10957049--10957130 Score: 128
Period size: 42 Copynumber: 2.0 Consensus size: 42
10957039 TCATTTTCTC
** *
10957049 GATGCCATAGTTCAACTATGGTCTTACACATCTTCACATAAT
1 GATGCCATAGACCAACTATGGTCTTACACATATTCACATAAT
*
10957091 GATGCCATAGACCAGCTATGGTCTTACACATATTCACATA
1 GATGCCATAGACCAACTATGGTCTTACACATATTCACATA
10957131 TCAATACCAT
Statistics
Matches: 36, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
42 36 1.00
ACGTcount: A:0.32, C:0.24, G:0.13, T:0.30
Consensus pattern (42 bp):
GATGCCATAGACCAACTATGGTCTTACACATATTCACATAAT
Found at i:10957141 original size:42 final size:42
Alignment explanation
Indices: 10957064--10957175 Score: 136
Period size: 42 Copynumber: 2.7 Consensus size: 42
10957054 CATAGTTCAA
* * *
10957064 CTATGGTCTTACACATCTTCACATAAT-GATGCCATAGACCAG
1 CTATGGTCTTACACATATTCACAT-ATCAATACCATAGACCAG
*
10957106 CTATGGTCTTACACATATTCACATATCAATACCATAGCCCAG
1 CTATGGTCTTACACATATTCACATATCAATACCATAGACCAG
* * * *
10957148 CTGTGGTTTTACACGTAATCACATATCA
1 CTATGGTCTTACACATATTCACATATCA
10957176 CATATCGATG
Statistics
Matches: 61, Mismatches: 8, Indels: 2
0.86 0.11 0.03
Matches are distributed among these distances:
41 2 0.03
42 59 0.97
ACGTcount: A:0.31, C:0.26, G:0.12, T:0.30
Consensus pattern (42 bp):
CTATGGTCTTACACATATTCACATATCAATACCATAGACCAG
Found at i:10957342 original size:53 final size:51
Alignment explanation
Indices: 10957213--10957374 Score: 170
Period size: 53 Copynumber: 3.1 Consensus size: 51
10957203 TCTTACACGA
* * * *
10957213 ATCACATATCTCACTGATGCCATATCCCAGATATGGTCTTATGCAGTAGCATAT
1 ATCACAT-TCTC-C-GATGCCATATCCCAGATATGGTCTTATACGGAAGCACAT
*
10957267 ATCACA----CCGATGCTATATCCCAGATATGGTCTTATACGGAAGCACAT
1 ATCACATTCTCCGATGCCATATCCCAGATATGGTCTTATACGGAAGCACAT
* * *
10957314 AATCACATCTCTCCGATGCCATAGCCCAGCTATGGTCTTATACGGAAATCACAT
1 -ATCACAT-TCTCCGATGCCATATCCCAGATATGGTCTTATACGG-AAGCACAT
10957368 ATCACAT
1 ATCACAT
10957375 GTTGCCATGG
Statistics
Matches: 92, Mismatches: 9, Indels: 15
0.79 0.08 0.13
Matches are distributed among these distances:
47 34 0.37
48 7 0.08
49 1 0.01
53 37 0.40
54 13 0.14
ACGTcount: A:0.31, C:0.27, G:0.15, T:0.28
Consensus pattern (51 bp):
ATCACATTCTCCGATGCCATATCCCAGATATGGTCTTATACGGAAGCACAT
Found at i:10968724 original size:39 final size:40
Alignment explanation
Indices: 10968520--10968742 Score: 245
Period size: 40 Copynumber: 5.6 Consensus size: 40
10968510 TTGAATGCTG
* * * * * *
10968520 TCCGGGCTAAGTCCCGAAGGC-TTTGTGCTAAGTGAATATA
1 TCCGGGTTAAGTCCCGAAGGCATTCGTGC-GAGTTACTAAA
** * * *
10968560 TCCGGACTAAGAT-CCGAAGGCCTTTGTGCGAGATACTAAA
1 TCCGGGTTAAG-TCCCGAAGGCATTCGTGCGAGTTACTAAA
*
10968600 TCCGGGTTAAGTCCCGAAGGCATTCGTGCGAGTTATTAAA
1 TCCGGGTTAAGTCCCGAAGGCATTCGTGCGAGTTACTAAA
*
10968640 TCCGGGTTAAGTCCCGAAGGCATTCGTGCGAGTTATTAAA
1 TCCGGGTTAAGTCCCGAAGGCATTCGTGCGAGTTACTAAA
* *
10968680 TCCGGGTTATGTCCCGAAGGCATT-GTGTGAGTTACTAAA
1 TCCGGGTTAAGTCCCGAAGGCATTCGTGCGAGTTACTAAA
* * *
10968719 ACCGGGCTATGTCCCGAAGGCATT
1 TCCGGGTTAAGTCCCGAAGGCATT
10968743 TGAACGAGGA
Statistics
Matches: 163, Mismatches: 17, Indels: 7
0.87 0.09 0.04
Matches are distributed among these distances:
39 36 0.22
40 119 0.73
41 8 0.05
ACGTcount: A:0.25, C:0.21, G:0.27, T:0.26
Consensus pattern (40 bp):
TCCGGGTTAAGTCCCGAAGGCATTCGTGCGAGTTACTAAA
Found at i:10968762 original size:79 final size:80
Alignment explanation
Indices: 10968594--10968777 Score: 221
Period size: 79 Copynumber: 2.3 Consensus size: 80
10968584 TGTGCGAGAT
* * *
10968594 ACTAAATCCGGGTTAAGTCCCGAAGGCATTCGTGCGAGTTATTAAATCCGGGTTAAGTCCCGAAG
1 ACTAAATCCGGGTTAAGTCCCGAAGGCATTCGTGCGAGTTACTAAAACCGGGCTAAGTCCCGAAG
** *
10968659 GCATTCGTGCGAGTT
66 GCATTCGAACGAGTG
* * * *
10968674 ATTAAATCCGGGTTATGTCCCGAAGGCATT-GTGTGAGTTACTAAAACCGGGCTATGTCCCGAAG
1 ACTAAATCCGGGTTAAGTCCCGAAGGCATTCGTGCGAGTTACTAAAACCGGGCTAAGTCCCGAAG
*
10968738 GCATTTGAACGAG-G
66 GCATTCGAACGAGTG
* *
10968752 AGCTATATCC-GGTTAAATCCCGAAGG
1 A-CTAAATCCGGGTTAAGTCCCGAAGG
10968778 TACGTGATTT
Statistics
Matches: 88, Mismatches: 15, Indels: 4
0.82 0.14 0.04
Matches are distributed among these distances:
78 15 0.17
79 45 0.51
80 28 0.32
ACGTcount: A:0.27, C:0.21, G:0.27, T:0.26
Consensus pattern (80 bp):
ACTAAATCCGGGTTAAGTCCCGAAGGCATTCGTGCGAGTTACTAAAACCGGGCTAAGTCCCGAAG
GCATTCGAACGAGTG
Found at i:10976195 original size:39 final size:40
Alignment explanation
Indices: 10975991--10976213 Score: 236
Period size: 40 Copynumber: 5.6 Consensus size: 40
10975981 TTGAATGCTG
* * * * * *
10975991 TCCGGGCTAAGTCCCGAAGGC-TTTGTGCTAAGTGAATATA
1 TCCGGGTTAAGTCCCGAAGGCATTCGTGC-GAGTTACTAAA
** * * *
10976031 TCCGGACTAAGAT-CCGAAGGCCTTTGTGCGAGATACTAAA
1 TCCGGGTTAAG-TCCCGAAGGCATTCGTGCGAGTTACTAAA
* *
10976071 TCCGAGTTAAGTCCCGAAGGCATTCGTGCGAGTTATTAAA
1 TCCGGGTTAAGTCCCGAAGGCATTCGTGCGAGTTACTAAA
*
10976111 TCCGGGTTAAGTCCCGAAGGCATTCGTGCGAGTTATTAAA
1 TCCGGGTTAAGTCCCGAAGGCATTCGTGCGAGTTACTAAA
* *
10976151 TCCGGGTTATGTCCCGAAGGCATT-GTGTGAGTTACTAAA
1 TCCGGGTTAAGTCCCGAAGGCATTCGTGCGAGTTACTAAA
* * *
10976190 ACCGGGCTATGTCCCGAAGGCATT
1 TCCGGGTTAAGTCCCGAAGGCATT
10976214 TGAACGAGGA
Statistics
Matches: 161, Mismatches: 19, Indels: 7
0.86 0.10 0.04
Matches are distributed among these distances:
39 36 0.22
40 117 0.73
41 8 0.05
ACGTcount: A:0.26, C:0.21, G:0.27, T:0.26
Consensus pattern (40 bp):
TCCGGGTTAAGTCCCGAAGGCATTCGTGCGAGTTACTAAA
Found at i:10976233 original size:79 final size:80
Alignment explanation
Indices: 10976065--10976248 Score: 212
Period size: 79 Copynumber: 2.3 Consensus size: 80
10976055 TGTGCGAGAT
* * * *
10976065 ACTAAATCCGAGTTAAGTCCCGAAGGCATTCGTGCGAGTTATTAAATCCGGGTTAAGTCCCGAAG
1 ACTAAATCCGGGTTAAGTCCCGAAGGCATTCGTGCGAGTTACTAAAACCGGGCTAAGTCCCGAAG
** *
10976130 GCATTCGTGCGAGTT
66 GCATTCGAACGAGTG
* * * *
10976145 ATTAAATCCGGGTTATGTCCCGAAGGCATT-GTGTGAGTTACTAAAACCGGGCTATGTCCCGAAG
1 ACTAAATCCGGGTTAAGTCCCGAAGGCATTCGTGCGAGTTACTAAAACCGGGCTAAGTCCCGAAG
*
10976209 GCATTTGAACGAG-G
66 GCATTCGAACGAGTG
* *
10976223 AGCTATATCC-GGTTAAATCCCGAAGG
1 A-CTAAATCCGGGTTAAGTCCCGAAGG
10976249 TACGTGATTT
Statistics
Matches: 87, Mismatches: 16, Indels: 4
0.81 0.15 0.04
Matches are distributed among these distances:
78 15 0.17
79 45 0.52
80 27 0.31
ACGTcount: A:0.27, C:0.21, G:0.27, T:0.26
Consensus pattern (80 bp):
ACTAAATCCGGGTTAAGTCCCGAAGGCATTCGTGCGAGTTACTAAAACCGGGCTAAGTCCCGAAG
GCATTCGAACGAGTG
Found at i:10981373 original size:19 final size:18
Alignment explanation
Indices: 10981349--10981385 Score: 56
Period size: 18 Copynumber: 2.0 Consensus size: 18
10981339 TATTATTTAT
10981349 CATTTTTATACTTTTTAAA
1 CATTTTTA-ACTTTTTAAA
*
10981368 CATTTTTAAGTTTTTAAA
1 CATTTTTAACTTTTTAAA
10981386 ATAATTTATT
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
18 9 0.53
19 8 0.47
ACGTcount: A:0.32, C:0.08, G:0.03, T:0.57
Consensus pattern (18 bp):
CATTTTTAACTTTTTAAA
Found at i:10995282 original size:126 final size:127
Alignment explanation
Indices: 10995017--10995328 Score: 380
Period size: 126 Copynumber: 2.5 Consensus size: 127
10995007 TGAAACTTCA
* * * *
10995017 AAAGGATATTCTGTATTTTAGTCGGATGGAAAATTGAAGCCCAGCACGATTGGGCACGACTCCCC
1 AAAGGATATTCCGTATTTTAGCCGAATGGAAAATTGAAGCCCAGCACGATTGGGCACAACTCCCC
** * *
10995082 AAACTCCCCAAGTACGAAATATAGTCTCATTTTAATTTTTAAAAAAACATGACGAAATTTTC
66 AAACTCCCCAAACACGAAATATAGCCTCATTTTAATTTTTAAAAAAACATGACAAAATTTTC
*
10995144 AAAGGATATTCCGTATTTTAGCCGAATGGAAAATTGAAGCCCAGCACGATTGGGCACAAC-CTCC
1 AAAGGATATTCCGTATTTTAGCCGAATGGAAAATTGAAGCCCAGCACGATTGGGCACAACTCCCC
* * * *
10995208 TAAC-CTTCCAAACACGAAATATTGCCTCGTTTTAA-TTTTAAAAAAA-ATTGGACAAAATTTTC
66 AAACTC-CCCAAACACGAAATATAGCCTCATTTTAATTTTTAAAAAAACA-T-GACAAAATTTTC
* *** * * * *
10995270 AAAGGATATTCCGTATTTTAGCTGAACAAAAAATCGAAACCTAACACGATTGGGCACAA
1 AAAGGATATTCCGTATTTTAGCCGAATGGAAAATTGAAGCCCAGCACGATTGGGCACAA
10995329 TTTGTCGAAC
Statistics
Matches: 161, Mismatches: 21, Indels: 7
0.85 0.11 0.04
Matches are distributed among these distances:
124 1 0.01
125 13 0.08
126 91 0.57
127 56 0.35
ACGTcount: A:0.37, C:0.20, G:0.16, T:0.27
Consensus pattern (127 bp):
AAAGGATATTCCGTATTTTAGCCGAATGGAAAATTGAAGCCCAGCACGATTGGGCACAACTCCCC
AAACTCCCCAAACACGAAATATAGCCTCATTTTAATTTTTAAAAAAACATGACAAAATTTTC
Found at i:10998090 original size:16 final size:18
Alignment explanation
Indices: 10998059--10998092 Score: 54
Period size: 18 Copynumber: 2.0 Consensus size: 18
10998049 AATTTTAAAA
10998059 TTATATATCAACTTTGAT
1 TTATATATCAACTTTGAT
10998077 TTATATAT-AA-TTTGAT
1 TTATATATCAACTTTGAT
10998093 ATATGAACTT
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
16 6 0.38
17 2 0.12
18 8 0.50
ACGTcount: A:0.35, C:0.06, G:0.06, T:0.53
Consensus pattern (18 bp):
TTATATATCAACTTTGAT
Found at i:11002876 original size:3 final size:3
Alignment explanation
Indices: 11002870--11002910 Score: 82
Period size: 3 Copynumber: 13.7 Consensus size: 3
11002860 AATTATTATT
11002870 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TA
11002911 CCAAAAGCCT
Statistics
Matches: 38, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 38 1.00
ACGTcount: A:0.66, C:0.00, G:0.00, T:0.34
Consensus pattern (3 bp):
TAA
Found at i:11003406 original size:27 final size:29
Alignment explanation
Indices: 11003376--11003429 Score: 76
Period size: 28 Copynumber: 1.9 Consensus size: 29
11003366 TGTGAAAATT
11003376 AAATT-AAATTAATAT-TAAAATTGCACA
1 AAATTAAAATTAATATATAAAATTGCACA
* *
11003403 AAATTAAAATTTATATATAATATTGCA
1 AAATTAAAATTAATATATAAAATTGCA
11003430 TATCGAACCA
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
27 5 0.22
28 9 0.39
29 9 0.39
ACGTcount: A:0.54, C:0.06, G:0.04, T:0.37
Consensus pattern (29 bp):
AAATTAAAATTAATATATAAAATTGCACA
Found at i:11005559 original size:24 final size:24
Alignment explanation
Indices: 11005526--11005579 Score: 81
Period size: 24 Copynumber: 2.2 Consensus size: 24
11005516 TCCTTCTCCA
* * *
11005526 GCACCCGAGCCTTCCAGTCCCTTT
1 GCACCTGAGCCTTCCAGTCCATCT
11005550 GCACCTGAGCCTTCCAGTCCATCT
1 GCACCTGAGCCTTCCAGTCCATCT
11005574 GCACCT
1 GCACCT
11005580 CACCCCACTG
Statistics
Matches: 27, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
24 27 1.00
ACGTcount: A:0.15, C:0.44, G:0.17, T:0.24
Consensus pattern (24 bp):
GCACCTGAGCCTTCCAGTCCATCT
Found at i:11007998 original size:16 final size:16
Alignment explanation
Indices: 11007977--11008008 Score: 64
Period size: 16 Copynumber: 2.0 Consensus size: 16
11007967 CATGCAGTAA
11007977 ATAAACTGTCATCACT
1 ATAAACTGTCATCACT
11007993 ATAAACTGTCATCACT
1 ATAAACTGTCATCACT
11008009 TTCTTTCTTT
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 16 1.00
ACGTcount: A:0.38, C:0.25, G:0.06, T:0.31
Consensus pattern (16 bp):
ATAAACTGTCATCACT
Found at i:11016783 original size:16 final size:18
Alignment explanation
Indices: 11016761--11016800 Score: 57
Period size: 16 Copynumber: 2.3 Consensus size: 18
11016751 CATACAATAC
*
11016761 TATCAAATTCAATT-CAA
1 TATCAAAATCAATTACAA
11016778 -ATCAAAATCAATTACAA
1 TATCAAAATCAATTACAA
11016795 TATCAA
1 TATCAA
11016801 GCATATTTTA
Statistics
Matches: 20, Mismatches: 1, Indels: 3
0.83 0.04 0.12
Matches are distributed among these distances:
16 12 0.60
17 3 0.15
18 5 0.25
ACGTcount: A:0.53, C:0.17, G:0.00, T:0.30
Consensus pattern (18 bp):
TATCAAAATCAATTACAA
Found at i:11020497 original size:25 final size:25
Alignment explanation
Indices: 11020468--11020543 Score: 116
Period size: 25 Copynumber: 3.0 Consensus size: 25
11020458 TGCTATACAA
* * *
11020468 AGAGCACAAATATGCTAATAATCGG
1 AGAGCACTAACATGCTAATAATCAG
*
11020493 AGAGCACTAACATGCTAAAAATCAG
1 AGAGCACTAACATGCTAATAATCAG
11020518 AGAGCACTAACATGCTAATAATCAG
1 AGAGCACTAACATGCTAATAATCAG
11020543 A
1 A
11020544 TAACGCGCTA
Statistics
Matches: 46, Mismatches: 5, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
25 46 1.00
ACGTcount: A:0.46, C:0.18, G:0.17, T:0.18
Consensus pattern (25 bp):
AGAGCACTAACATGCTAATAATCAG
Found at i:11021139 original size:40 final size:40
Alignment explanation
Indices: 11021084--11021165 Score: 164
Period size: 40 Copynumber: 2.0 Consensus size: 40
11021074 GCTTTATTAC
11021084 CAGTATTTTCTTATAAACTTTTATAATTTTCCAATTTAAT
1 CAGTATTTTCTTATAAACTTTTATAATTTTCCAATTTAAT
11021124 CAGTATTTTCTTATAAACTTTTATAATTTTCCAATTTAAT
1 CAGTATTTTCTTATAAACTTTTATAATTTTCCAATTTAAT
11021164 CA
1 CA
11021166 CATTTTTTCA
Statistics
Matches: 42, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
40 42 1.00
ACGTcount: A:0.33, C:0.13, G:0.02, T:0.51
Consensus pattern (40 bp):
CAGTATTTTCTTATAAACTTTTATAATTTTCCAATTTAAT
Found at i:11026016 original size:21 final size:21
Alignment explanation
Indices: 11025990--11026098 Score: 137
Period size: 21 Copynumber: 5.2 Consensus size: 21
11025980 GAAGCTCGTA
11025990 AGCTGAACAGAAGCTCATAAG
1 AGCTGAACAGAAGCTCATAAG
* * *
11026011 AGCTGAACAAAAACTCTTAAG
1 AGCTGAACAGAAGCTCATAAG
** *
11026032 ATTTGAACAGAAGCTCATAAA
1 AGCTGAACAGAAGCTCATAAG
*
11026053 AGCTGAACAGAAACTCATAAG
1 AGCTGAACAGAAGCTCATAAG
* *
11026074 AGTTGAACAGAAGCTCCTAAG
1 AGCTGAACAGAAGCTCATAAG
11026095 AGCT
1 AGCT
11026099 AAATAAAAAC
Statistics
Matches: 71, Mismatches: 17, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
21 71 1.00
ACGTcount: A:0.44, C:0.18, G:0.19, T:0.18
Consensus pattern (21 bp):
AGCTGAACAGAAGCTCATAAG
Found at i:11026057 original size:42 final size:42
Alignment explanation
Indices: 11025993--11026115 Score: 183
Period size: 42 Copynumber: 2.9 Consensus size: 42
11025983 GCTCGTAAGC
* *
11025993 TGAACAGAAGCTCATAAGAGCTGAACAAAAACTCTTAAGATT
1 TGAACAGAAGCTCATAAGAGCTGAACAAAAACTCATAAGAGT
* *
11026035 TGAACAGAAGCTCATAAAAGCTGAACAGAAACTCATAAGAGT
1 TGAACAGAAGCTCATAAGAGCTGAACAAAAACTCATAAGAGT
* * *
11026077 TGAACAGAAGCTCCTAAGAGCTAAATAAAAACTCATAAG
1 TGAACAGAAGCTCATAAGAGCTGAACAAAAACTCATAAG
11026116 TAGGGGTGTG
Statistics
Matches: 72, Mismatches: 9, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
42 72 1.00
ACGTcount: A:0.47, C:0.17, G:0.17, T:0.19
Consensus pattern (42 bp):
TGAACAGAAGCTCATAAGAGCTGAACAAAAACTCATAAGAGT
Found at i:11026112 original size:63 final size:63
Alignment explanation
Indices: 11025989--11026114 Score: 153
Period size: 63 Copynumber: 2.0 Consensus size: 63
11025979 TGAAGCTCGT
* * ** * * *
11025989 AAGCTGAACAGAAGCTCATAAGAGCTGAACAAAAACTCTTAAGATTTGAACAGAAGCTCATAA
1 AAGCTGAACAGAAACTCATAAGAGCTGAACAAAAACTCCTAAGAGCTAAACAAAAACTCATAA
* * * *
11026052 AAGCTGAACAGAAACTCATAAGAGTTGAACAGAAGCTCCTAAGAGCTAAATAAAAACTCATAA
1 AAGCTGAACAGAAACTCATAAGAGCTGAACAAAAACTCCTAAGAGCTAAACAAAAACTCATAA
11026115 GTAGGGGTGT
Statistics
Matches: 52, Mismatches: 11, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
63 52 1.00
ACGTcount: A:0.48, C:0.17, G:0.17, T:0.18
Consensus pattern (63 bp):
AAGCTGAACAGAAACTCATAAGAGCTGAACAAAAACTCCTAAGAGCTAAACAAAAACTCATAA
Found at i:11026115 original size:21 final size:21
Alignment explanation
Indices: 11025990--11026115 Score: 135
Period size: 21 Copynumber: 6.0 Consensus size: 21
11025980 GAAGCTCGTA
*
11025990 AGCTGAACAGAAGCTCATAAG
1 AGCTGAACAGAAACTCATAAG
* *
11026011 AGCTGAACAAAAACTCTTAAG
1 AGCTGAACAGAAACTCATAAG
** * *
11026032 ATTTGAACAGAAGCTCATAAA
1 AGCTGAACAGAAACTCATAAG
11026053 AGCTGAACAGAAACTCATAAG
1 AGCTGAACAGAAACTCATAAG
* * *
11026074 AGTTGAACAGAAGCTCCTAAG
1 AGCTGAACAGAAACTCATAAG
* * *
11026095 AGCTAAATAAAAACTCATAAG
1 AGCTGAACAGAAACTCATAAG
11026116 TAGGGGTGTG
Statistics
Matches: 83, Mismatches: 22, Indels: 0
0.79 0.21 0.00
Matches are distributed among these distances:
21 83 1.00
ACGTcount: A:0.47, C:0.17, G:0.17, T:0.18
Consensus pattern (21 bp):
AGCTGAACAGAAACTCATAAG
Found at i:11026492 original size:18 final size:18
Alignment explanation
Indices: 11026469--11026518 Score: 55
Period size: 18 Copynumber: 2.8 Consensus size: 18
11026459 TTTATACAAA
*
11026469 TAATTCGGTTAATTCGGG
1 TAATTCGGTTAATTCAGG
* **
11026487 TAATTCAGAAAATTCAGG
1 TAATTCGGTTAATTCAGG
*
11026505 TAATTCGTTTAATT
1 TAATTCGGTTAATT
11026519 TTATACTATT
Statistics
Matches: 24, Mismatches: 8, Indels: 0
0.75 0.25 0.00
Matches are distributed among these distances:
18 24 1.00
ACGTcount: A:0.32, C:0.10, G:0.18, T:0.40
Consensus pattern (18 bp):
TAATTCGGTTAATTCAGG
Found at i:11026728 original size:21 final size:21
Alignment explanation
Indices: 11026704--11026803 Score: 87
Period size: 21 Copynumber: 4.8 Consensus size: 21
11026694 AAAAGCTTGC
11026704 AAGAGCTAAACAGAAACTCAT
1 AAGAGCTAAACAGAAACTCAT
* * * *
11026725 AAGAGTTGAATAGAAGCTCAAT
1 AAGAGCTAAACAGAAACTC-AT
*
11026747 AA-AGCTGAAC-GAAAACTCAT
1 AAGAGCTAAACAG-AAACTCAT
* * *
11026767 ATGAGTTAAACAGAAACTCGT
1 AAGAGCTAAACAGAAACTCAT
*
11026788 AAGAGCTAAATAGAAA
1 AAGAGCTAAACAGAAA
11026804 GTAAAACATG
Statistics
Matches: 61, Mismatches: 14, Indels: 8
0.73 0.17 0.10
Matches are distributed among these distances:
20 4 0.07
21 52 0.85
22 5 0.08
ACGTcount: A:0.50, C:0.14, G:0.18, T:0.18
Consensus pattern (21 bp):
AAGAGCTAAACAGAAACTCAT
Found at i:11028620 original size:21 final size:21
Alignment explanation
Indices: 11028591--11028630 Score: 62
Period size: 21 Copynumber: 1.9 Consensus size: 21
11028581 TCATATGTAA
11028591 CATCATATGGCAATACCTCAG
1 CATCATATGGCAATACCTCAG
* *
11028612 CATCGTATGGCAATTCCTC
1 CATCATATGGCAATACCTC
11028631 CATACTCAAC
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
21 17 1.00
ACGTcount: A:0.28, C:0.30, G:0.15, T:0.28
Consensus pattern (21 bp):
CATCATATGGCAATACCTCAG
Found at i:11033507 original size:53 final size:53
Alignment explanation
Indices: 11033426--11033576 Score: 214
Period size: 53 Copynumber: 2.8 Consensus size: 53
11033416 CTTACACGGT
* *
11033426 TCACATATCATACCGAAGCCATATCCCAGAC-ATGGTCTTATACGGAATCACATTA
1 TCACAT-T-ATACCGATGCCATAGCCCAG-CTATGGTCTTATACGGAATCACATTA
*
11033481 TCACATTATACCGATGCCATAGCCCAGCTATGGTCTTATACGGAGTCACATTA
1 TCACATTATACCGATGCCATAGCCCAGCTATGGTCTTATACGGAATCACATTA
** *
11033534 TCACATTGCACCGATGCCATAGCCCAGCTATGGTCTTAAACGG
1 TCACATTATACCGATGCCATAGCCCAGCTATGGTCTTATACGG
11033577 GCACACTTAT
Statistics
Matches: 89, Mismatches: 6, Indels: 4
0.90 0.06 0.04
Matches are distributed among these distances:
52 1 0.01
53 81 0.91
54 1 0.01
55 6 0.07
ACGTcount: A:0.30, C:0.28, G:0.17, T:0.26
Consensus pattern (53 bp):
TCACATTATACCGATGCCATAGCCCAGCTATGGTCTTATACGGAATCACATTA
Found at i:11035097 original size:13 final size:13
Alignment explanation
Indices: 11035079--11035115 Score: 56
Period size: 13 Copynumber: 2.8 Consensus size: 13
11035069 AGATAATTAG
11035079 CAAATCATACATA
1 CAAATCATACATA
11035092 CAAATCATACATA
1 CAAATCATACATA
*
11035105 TAAATTCATAC
1 CAAA-TCATAC
11035116 CAAACTATCA
Statistics
Matches: 22, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
13 16 0.73
14 6 0.27
ACGTcount: A:0.51, C:0.22, G:0.00, T:0.27
Consensus pattern (13 bp):
CAAATCATACATA
Found at i:11036396 original size:17 final size:16
Alignment explanation
Indices: 11036374--11036411 Score: 51
Period size: 17 Copynumber: 2.3 Consensus size: 16
11036364 CCCTAATTTC
11036374 TCTTTT-TTCTTTTCTTT
1 TCTTTTCTTC-TTTC-TT
11036391 TCTTTTCTTCTTTCTT
1 TCTTTTCTTCTTTCTT
11036407 TCTTT
1 TCTTT
11036412 CTATTTCGTT
Statistics
Matches: 20, Mismatches: 0, Indels: 3
0.87 0.00 0.13
Matches are distributed among these distances:
16 7 0.35
17 10 0.50
18 3 0.15
ACGTcount: A:0.00, C:0.21, G:0.00, T:0.79
Consensus pattern (16 bp):
TCTTTTCTTCTTTCTT
Found at i:11036477 original size:16 final size:16
Alignment explanation
Indices: 11036456--11036486 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
11036446 TTTCTTTTGT
*
11036456 TTCTTTATTTTATTTA
1 TTCTTTATTTCATTTA
11036472 TTCTTTATTTCATTT
1 TTCTTTATTTCATTT
11036487 TATTTACTTA
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
16 14 1.00
ACGTcount: A:0.16, C:0.10, G:0.00, T:0.74
Consensus pattern (16 bp):
TTCTTTATTTCATTTA
Found at i:11036633 original size:3 final size:3
Alignment explanation
Indices: 11036612--11036649 Score: 53
Period size: 3 Copynumber: 13.0 Consensus size: 3
11036602 CTATCTCAAT
11036612 TAA TAGA TAA -AA T-A TAA TAA TAA TAA TAA TAA TAA TAA
1 TAA TA-A TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
11036650 GTAAATATCT
Statistics
Matches: 32, Mismatches: 0, Indels: 6
0.84 0.00 0.16
Matches are distributed among these distances:
2 4 0.12
3 25 0.78
4 3 0.09
ACGTcount: A:0.66, C:0.00, G:0.03, T:0.32
Consensus pattern (3 bp):
TAA
Found at i:11036798 original size:44 final size:44
Alignment explanation
Indices: 11036749--11036833 Score: 170
Period size: 44 Copynumber: 1.9 Consensus size: 44
11036739 CTTACACATG
11036749 TCACTAATTTGGTTTAAATACTAATTTAGTCCCTTGTCATTATA
1 TCACTAATTTGGTTTAAATACTAATTTAGTCCCTTGTCATTATA
11036793 TCACTAATTTGGTTTAAATACTAATTTAGTCCCTTGTCATT
1 TCACTAATTTGGTTTAAATACTAATTTAGTCCCTTGTCATT
11036834 TTTTTCTATT
Statistics
Matches: 41, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
44 41 1.00
ACGTcount: A:0.28, C:0.16, G:0.09, T:0.46
Consensus pattern (44 bp):
TCACTAATTTGGTTTAAATACTAATTTAGTCCCTTGTCATTATA
Found at i:11039419 original size:30 final size:30
Alignment explanation
Indices: 11039383--11039474 Score: 107
Period size: 30 Copynumber: 3.1 Consensus size: 30
11039373 ATAATCTACA
* *
11039383 AAAATTAGATCAAATCAAAATTTCATGTAT
1 AAAATTACATCAAATCAAAATTTCATATAT
*
11039413 AAAATTACATAAAATCAAAATTT-ATATAT
1 AAAATTACATCAAATCAAAATTTCATATAT
* *
11039442 AAAATTATATCTTAAATCATAA-TTCATATAT
1 AAAATTACATC--AAATCAAAATTTCATATAT
11039473 AA
1 AA
11039475 TTTTCGTATT
Statistics
Matches: 53, Mismatches: 6, Indels: 5
0.83 0.09 0.08
Matches are distributed among these distances:
29 14 0.26
30 23 0.43
31 16 0.30
ACGTcount: A:0.53, C:0.09, G:0.02, T:0.36
Consensus pattern (30 bp):
AAAATTACATCAAATCAAAATTTCATATAT
Found at i:11039471 original size:31 final size:29
Alignment explanation
Indices: 11039383--11039474 Score: 94
Period size: 31 Copynumber: 3.1 Consensus size: 29
11039373 ATAATCTACA
* * *
11039383 AAAATTAGATCAAATCAAAATTTCATGTAT
1 AAAATTACATAAAATCAAAA-TTCATATAT
*
11039413 AAAATTACATAAAATCAAAATTTATATAT
1 AAAATTACATAAAATCAAAATTCATATAT
* * *
11039442 AAAATTATATCTTAAATCATAATTCATATAT
1 AAAATTACA--TAAAATCAAAATTCATATAT
11039473 AA
1 AA
11039475 TTTTCGTATT
Statistics
Matches: 52, Mismatches: 8, Indels: 3
0.83 0.13 0.05
Matches are distributed among these distances:
29 15 0.29
30 18 0.35
31 19 0.37
ACGTcount: A:0.53, C:0.09, G:0.02, T:0.36
Consensus pattern (29 bp):
AAAATTACATAAAATCAAAATTCATATAT
Found at i:11040441 original size:16 final size:17
Alignment explanation
Indices: 11040405--11040443 Score: 55
Period size: 16 Copynumber: 2.4 Consensus size: 17
11040395 AATTTTATTT
*
11040405 TAATAATAAGTTTTAAA
1 TAATATTAAGTTTTAAA
11040422 -AATATTAA-TTTTAAA
1 TAATATTAAGTTTTAAA
11040437 TAATATT
1 TAATATT
11040444 TTCACATATT
Statistics
Matches: 20, Mismatches: 1, Indels: 3
0.83 0.04 0.12
Matches are distributed among these distances:
15 7 0.35
16 13 0.65
ACGTcount: A:0.51, C:0.00, G:0.03, T:0.46
Consensus pattern (17 bp):
TAATATTAAGTTTTAAA
Found at i:11041112 original size:26 final size:27
Alignment explanation
Indices: 11041078--11041134 Score: 80
Period size: 26 Copynumber: 2.1 Consensus size: 27
11041068 CTCTATTTGG
* * *
11041078 TTTTCGAAAGTAATTTTTATTTTC-AT
1 TTTTAGAAAATAATTTTAATTTTCTAT
11041104 TTTTAGAAAATAATTTTAATTTTCTAT
1 TTTTAGAAAATAATTTTAATTTTCTAT
11041131 TTTT
1 TTTT
11041135 TTAAAAATTA
Statistics
Matches: 27, Mismatches: 3, Indels: 1
0.87 0.10 0.03
Matches are distributed among these distances:
26 21 0.78
27 6 0.22
ACGTcount: A:0.30, C:0.05, G:0.05, T:0.60
Consensus pattern (27 bp):
TTTTAGAAAATAATTTTAATTTTCTAT
Found at i:11041489 original size:22 final size:23
Alignment explanation
Indices: 11041446--11041499 Score: 56
Period size: 23 Copynumber: 2.3 Consensus size: 23
11041436 TTTTGAGCAA
* *
11041446 TTTAATTTTTTATTTTATATTCT
1 TTTAACTTTTTATTTTACATTCT
*
11041469 TTTAACTTTTT-TTTTCCATTCT
1 TTTAACTTTTTATTTTACATTCT
*
11041491 CTTATACTT
1 TTTA-ACTT
11041500 CTCCCTGTAT
Statistics
Matches: 26, Mismatches: 4, Indels: 2
0.81 0.12 0.06
Matches are distributed among these distances:
22 12 0.46
23 14 0.54
ACGTcount: A:0.19, C:0.13, G:0.00, T:0.69
Consensus pattern (23 bp):
TTTAACTTTTTATTTTACATTCT
Found at i:11042180 original size:14 final size:16
Alignment explanation
Indices: 11042140--11042181 Score: 52
Period size: 14 Copynumber: 2.6 Consensus size: 16
11042130 CATACAAGTG
11042140 TTAAATAAGTATTTGTTA
1 TTAAAT-AG-ATTTGTTA
11042158 TTAAATAGATTT-TTA
1 TTAAATAGATTTGTTA
11042173 TT-AATAGAT
1 TTAAATAGAT
11042182 ATCTTTATTG
Statistics
Matches: 24, Mismatches: 0, Indels: 4
0.86 0.00 0.14
Matches are distributed among these distances:
14 7 0.29
15 5 0.21
16 4 0.17
17 2 0.08
18 6 0.25
ACGTcount: A:0.40, C:0.00, G:0.10, T:0.50
Consensus pattern (16 bp):
TTAAATAGATTTGTTA
Found at i:11043420 original size:12 final size:12
Alignment explanation
Indices: 11043405--11043429 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
11043395 TACTGCTATT
11043405 GTTACTGTTACC
1 GTTACTGTTACC
11043417 GTTACTGTTACC
1 GTTACTGTTACC
11043429 G
1 G
11043430 ATACGGTGTA
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:0.16, C:0.24, G:0.20, T:0.40
Consensus pattern (12 bp):
GTTACTGTTACC
Found at i:11043564 original size:18 final size:18
Alignment explanation
Indices: 11043541--11043708 Score: 183
Period size: 18 Copynumber: 9.3 Consensus size: 18
11043531 AAAATAAAGG
* *
11043541 TACTGAATAACTGACTGC
1 TACTGAATAAATGACTGT
11043559 TACTGAATAAATGACTGT
1 TACTGAATAAATGACTGT
* * * *
11043577 TATTGAATAACTGATTAT
1 TACTGAATAAATGACTGT
* *
11043595 TATTGAATAATTGACTGT
1 TACTGAATAAATGACTGT
* *
11043613 GACTGAATAAATGATTGT
1 TACTGAATAAATGACTGT
* * *
11043631 TACTGAATAACTGATTTT
1 TACTGAATAAATGACTGT
*
11043649 TACTGAATAATTGACTGT
1 TACTGAATAAATGACTGT
*
11043667 GACTGAATAAATGACTGT
1 TACTGAATAAATGACTGT
* *
11043685 TACTGAATAAATGATTAT
1 TACTGAATAAATGACTGT
11043703 TACTGA
1 TACTGA
11043709 GTAACTGATT
Statistics
Matches: 126, Mismatches: 24, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
18 126 1.00
ACGTcount: A:0.37, C:0.10, G:0.16, T:0.37
Consensus pattern (18 bp):
TACTGAATAAATGACTGT
Found at i:11043610 original size:54 final size:54
Alignment explanation
Indices: 11043541--11043708 Score: 266
Period size: 54 Copynumber: 3.1 Consensus size: 54
11043531 AAAATAAAGG
* *
11043541 TACTGAATAACTGACTGCT-ACTGAATAAATGACTGTTATTGAATAACTGATTAT
1 TACTGAATAATTGACTG-TGACTGAATAAATGACTGTTACTGAATAACTGATTAT
* * *
11043595 TATTGAATAATTGACTGTGACTGAATAAATGATTGTTACTGAATAACTGATTTT
1 TACTGAATAATTGACTGTGACTGAATAAATGACTGTTACTGAATAACTGATTAT
*
11043649 TACTGAATAATTGACTGTGACTGAATAAATGACTGTTACTGAATAAATGATTAT
1 TACTGAATAATTGACTGTGACTGAATAAATGACTGTTACTGAATAACTGATTAT
11043703 TACTGA
1 TACTGA
11043709 GTAACTGATT
Statistics
Matches: 104, Mismatches: 9, Indels: 2
0.90 0.08 0.02
Matches are distributed among these distances:
53 1 0.01
54 103 0.99
ACGTcount: A:0.37, C:0.10, G:0.16, T:0.37
Consensus pattern (54 bp):
TACTGAATAATTGACTGTGACTGAATAAATGACTGTTACTGAATAACTGATTAT
Found at i:11043724 original size:18 final size:18
Alignment explanation
Indices: 11043559--11043726 Score: 88
Period size: 18 Copynumber: 9.3 Consensus size: 18
11043549 AACTGACTGC
* **
11043559 TACTGAATAAATGACTGT
1 TACTGAATAAATGATTAA
* * *
11043577 TATTGAATAACTGATTAT
1 TACTGAATAAATGATTAA
* * * *
11043595 TATTGAATAATTGACT-G
1 TACTGAATAAATGATTAA
**
11043612 TGACTGAATAAATGATTGT
1 T-ACTGAATAAATGATTAA
* **
11043631 TACTGAATAACTGATTTT
1 TACTGAATAAATGATTAA
* * *
11043649 TACTGAATAATTGACT-G
1 TACTGAATAAATGATTAA
* **
11043666 TGACTGAATAAATGACTGT
1 T-ACTGAATAAATGATTAA
*
11043685 TACTGAATAAATGATTAT
1 TACTGAATAAATGATTAA
* *
11043703 TACTGAGTAACTGATTAA
1 TACTGAATAAATGATTAA
11043721 TACTGA
1 TACTGA
11043727 TGACTGACCG
Statistics
Matches: 123, Mismatches: 23, Indels: 8
0.80 0.15 0.05
Matches are distributed among these distances:
17 2 0.02
18 119 0.97
19 2 0.02
ACGTcount: A:0.38, C:0.09, G:0.16, T:0.38
Consensus pattern (18 bp):
TACTGAATAAATGATTAA
Found at i:11045189 original size:31 final size:29
Alignment explanation
Indices: 11045151--11045226 Score: 98
Period size: 29 Copynumber: 2.6 Consensus size: 29
11045141 TAATGGCTCG
* *
11045151 GTGACTAAAATGTTACATCACGTTAACATAA
1 GTGACTAAAATGTAACATCAC--AAACATAA
**
11045182 GTGACTAAAATGTAACATTTCAAACATAA
1 GTGACTAAAATGTAACATCACAAACATAA
11045211 GTGACTAAAATGTAAC
1 GTGACTAAAATGTAAC
11045227 TGAGGTAAAT
Statistics
Matches: 41, Mismatches: 4, Indels: 2
0.87 0.09 0.04
Matches are distributed among these distances:
29 23 0.56
31 18 0.44
ACGTcount: A:0.45, C:0.14, G:0.13, T:0.28
Consensus pattern (29 bp):
GTGACTAAAATGTAACATCACAAACATAA
Found at i:11046113 original size:17 final size:17
Alignment explanation
Indices: 11046093--11046129 Score: 58
Period size: 17 Copynumber: 2.2 Consensus size: 17
11046083 GTTAAAACTG
11046093 TTTTTA-TCTCAAAAGTA
1 TTTTTATTC-CAAAAGTA
11046110 TTTTTATTCCAAAAGTA
1 TTTTTATTCCAAAAGTA
11046127 TTT
1 TTT
11046130 CTTAAAAATA
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
17 17 0.89
18 2 0.11
ACGTcount: A:0.32, C:0.11, G:0.05, T:0.51
Consensus pattern (17 bp):
TTTTTATTCCAAAAGTA
Found at i:11047606 original size:11 final size:12
Alignment explanation
Indices: 11047576--11047609 Score: 61
Period size: 12 Copynumber: 2.9 Consensus size: 12
11047566 CGGCCCGCCC
11047576 ATATTAATTTTT
1 ATATTAATTTTT
11047588 ATATTAATTTTT
1 ATATTAATTTTT
11047600 ATA-TAATTTT
1 ATATTAATTTT
11047610 AAAATATATA
Statistics
Matches: 22, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
11 7 0.32
12 15 0.68
ACGTcount: A:0.35, C:0.00, G:0.00, T:0.65
Consensus pattern (12 bp):
ATATTAATTTTT
Found at i:11047766 original size:30 final size:30
Alignment explanation
Indices: 11047732--11047794 Score: 101
Period size: 30 Copynumber: 2.1 Consensus size: 30
11047722 ACTTAACAAG
*
11047732 CAAATGT-TTCTAAAATAATAACAAAATTAA
1 CAAATGTGTT-TAAAATAATAAAAAAATTAA
11047762 CAAATGTGTTTAAAATAATAAAAAAATTAA
1 CAAATGTGTTTAAAATAATAAAAAAATTAA
11047792 CAA
1 CAA
11047795 TAAAATAAAT
Statistics
Matches: 31, Mismatches: 1, Indels: 2
0.91 0.03 0.06
Matches are distributed among these distances:
30 29 0.94
31 2 0.06
ACGTcount: A:0.59, C:0.08, G:0.05, T:0.29
Consensus pattern (30 bp):
CAAATGTGTTTAAAATAATAAAAAAATTAA
Found at i:11047849 original size:22 final size:22
Alignment explanation
Indices: 11047824--11047866 Score: 68
Period size: 22 Copynumber: 2.0 Consensus size: 22
11047814 TATCCAAACA
11047824 ATAACAACAAAATAGTAGCAAC
1 ATAACAACAAAATAGTAGCAAC
* *
11047846 ATAATAATAAAATAGTAGCAA
1 ATAACAACAAAATAGTAGCAA
11047867 AATAGGGAGA
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
22 19 1.00
ACGTcount: A:0.60, C:0.12, G:0.09, T:0.19
Consensus pattern (22 bp):
ATAACAACAAAATAGTAGCAAC
Found at i:11051990 original size:37 final size:36
Alignment explanation
Indices: 11051909--11051990 Score: 103
Period size: 37 Copynumber: 2.2 Consensus size: 36
11051899 TATTTACATT
* *
11051909 AAATAATAAAATATTTTAAAATTATATTATGATTAA
1 AAATAATTAAATATTTTAAAATCATATTATGATTAA
*
11051945 ATAATAATTAAATATTATTAAGATCATATCTAT-ATTAA
1 A-AATAATTAAATATT-TTAAAATCATAT-TATGATTAA
11051983 AAATAATT
1 AAATAATT
11051991 TTATTTAAAA
Statistics
Matches: 40, Mismatches: 3, Indels: 5
0.83 0.06 0.10
Matches are distributed among these distances:
36 1 0.03
37 20 0.50
38 16 0.40
39 3 0.08
ACGTcount: A:0.54, C:0.02, G:0.02, T:0.41
Consensus pattern (36 bp):
AAATAATTAAATATTTTAAAATCATATTATGATTAA
Found at i:11055690 original size:35 final size:35
Alignment explanation
Indices: 11055644--11055713 Score: 122
Period size: 35 Copynumber: 2.0 Consensus size: 35
11055634 CCTTATACTT
*
11055644 AGATTTGTGCTATTTAGTACCTACGAGAAGCCTAA
1 AGATTTGTGCTATTTAGTACCCACGAGAAGCCTAA
*
11055679 AGATTTGTGCTATTTAGTACCCATGAGAAGCCTAA
1 AGATTTGTGCTATTTAGTACCCACGAGAAGCCTAA
11055714 CCCTTGCCAT
Statistics
Matches: 33, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
35 33 1.00
ACGTcount: A:0.31, C:0.17, G:0.20, T:0.31
Consensus pattern (35 bp):
AGATTTGTGCTATTTAGTACCCACGAGAAGCCTAA
Found at i:11057204 original size:35 final size:35
Alignment explanation
Indices: 11057158--11057228 Score: 142
Period size: 35 Copynumber: 2.0 Consensus size: 35
11057148 ATAGTATGAA
11057158 TGATTAAGTATGTAAAGTAAATTGAATGCGATGGT
1 TGATTAAGTATGTAAAGTAAATTGAATGCGATGGT
11057193 TGATTAAGTATGTAAAGTAAATTGAATGCGATGGT
1 TGATTAAGTATGTAAAGTAAATTGAATGCGATGGT
11057228 T
1 T
11057229 ATGTTTGATA
Statistics
Matches: 36, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
35 36 1.00
ACGTcount: A:0.37, C:0.03, G:0.25, T:0.35
Consensus pattern (35 bp):
TGATTAAGTATGTAAAGTAAATTGAATGCGATGGT
Found at i:11061883 original size:24 final size:26
Alignment explanation
Indices: 11061856--11061903 Score: 66
Period size: 24 Copynumber: 1.9 Consensus size: 26
11061846 TATGAATACG
11061856 TACAT-ATAATATA-ATAT-TAAAATA
1 TACATAAT-ATATACATATATAAAATA
11061880 TACATAATATATACATATATAAAA
1 TACATAATATATACATATATAAAA
11061904 CATGTATTAA
Statistics
Matches: 21, Mismatches: 0, Indels: 4
0.84 0.00 0.16
Matches are distributed among these distances:
24 10 0.48
25 6 0.29
26 5 0.24
ACGTcount: A:0.58, C:0.06, G:0.00, T:0.35
Consensus pattern (26 bp):
TACATAATATATACATATATAAAATA
Found at i:11061990 original size:18 final size:18
Alignment explanation
Indices: 11061956--11061990 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
11061946 GTACATGAAA
*
11061956 TAATAAAAAACATATAAC
1 TAATAAAAAACAAATAAC
*
11061974 TAATAAAAAATAAATAA
1 TAATAAAAAACAAATAA
11061991 GGGAAATATA
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:0.71, C:0.06, G:0.00, T:0.23
Consensus pattern (18 bp):
TAATAAAAAACAAATAAC
Found at i:11062355 original size:3 final size:3
Alignment explanation
Indices: 11062347--11062377 Score: 62
Period size: 3 Copynumber: 10.3 Consensus size: 3
11062337 ACATTAGAAG
11062347 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA T
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA T
11062378 TAAAGTAGAG
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 28 1.00
ACGTcount: A:0.65, C:0.00, G:0.00, T:0.35
Consensus pattern (3 bp):
TAA
Found at i:11062938 original size:17 final size:17
Alignment explanation
Indices: 11062916--11062948 Score: 57
Period size: 17 Copynumber: 1.9 Consensus size: 17
11062906 AAAGTTGCCT
*
11062916 CTTTTTCTTTATTTTTA
1 CTTTTTATTTATTTTTA
11062933 CTTTTTATTTATTTTT
1 CTTTTTATTTATTTTT
11062949 TTATATGTTT
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
17 15 1.00
ACGTcount: A:0.12, C:0.09, G:0.00, T:0.79
Consensus pattern (17 bp):
CTTTTTATTTATTTTTA
Found at i:11063964 original size:25 final size:27
Alignment explanation
Indices: 11063929--11063982 Score: 76
Period size: 25 Copynumber: 2.1 Consensus size: 27
11063919 TTAGAATAAA
* *
11063929 AAAACAGAAATTAAAAA-C-CAAAAAT
1 AAAACAAAAATAAAAAACCTCAAAAAT
11063954 AAAACAAAAATAAAAAACCTCAAAAAT
1 AAAACAAAAATAAAAAACCTCAAAAAT
11063981 AA
1 AA
11063983 TAAAAGTCCA
Statistics
Matches: 25, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
25 15 0.60
26 1 0.04
27 9 0.36
ACGTcount: A:0.74, C:0.13, G:0.02, T:0.11
Consensus pattern (27 bp):
AAAACAAAAATAAAAAACCTCAAAAAT
Found at i:11064444 original size:21 final size:21
Alignment explanation
Indices: 11064420--11064459 Score: 55
Period size: 21 Copynumber: 1.9 Consensus size: 21
11064410 TCCGTCTTCA
*
11064420 ATATAT-TTTTTTTCTTTTTGC
1 ATATATCTTGTTTT-TTTTTGC
11064441 ATATATCTTGTTTTTTTTT
1 ATATATCTTGTTTTTTTTT
11064460 AGTTTTTTTA
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
21 11 0.65
22 6 0.35
ACGTcount: A:0.15, C:0.07, G:0.05, T:0.72
Consensus pattern (21 bp):
ATATATCTTGTTTTTTTTTGC
Found at i:11069427 original size:16 final size:16
Alignment explanation
Indices: 11069393--11069427 Score: 61
Period size: 16 Copynumber: 2.2 Consensus size: 16
11069383 AAATTTTTCC
*
11069393 AAATTTTTTTATTTTA
1 AAATTTTTTTATTTAA
11069409 AAATTTTTTTATTTAA
1 AAATTTTTTTATTTAA
11069425 AAA
1 AAA
11069428 AAAACTCAAT
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
16 18 1.00
ACGTcount: A:0.40, C:0.00, G:0.00, T:0.60
Consensus pattern (16 bp):
AAATTTTTTTATTTAA
Found at i:11069826 original size:28 final size:29
Alignment explanation
Indices: 11069794--11069855 Score: 108
Period size: 29 Copynumber: 2.2 Consensus size: 29
11069784 ATTTTACGTT
*
11069794 GAATAATATAATCC-TCCCAAACACACCA
1 GAATAATATAATCCATCCAAAACACACCA
11069822 GAATAATATAATCCATCCAAAACACACCA
1 GAATAATATAATCCATCCAAAACACACCA
11069851 GAATA
1 GAATA
11069856 GCACAGAGTG
Statistics
Matches: 32, Mismatches: 1, Indels: 1
0.94 0.03 0.03
Matches are distributed among these distances:
28 14 0.44
29 18 0.56
ACGTcount: A:0.50, C:0.27, G:0.05, T:0.18
Consensus pattern (29 bp):
GAATAATATAATCCATCCAAAACACACCA
Found at i:11069919 original size:13 final size:14
Alignment explanation
Indices: 11069896--11069925 Score: 53
Period size: 13 Copynumber: 2.2 Consensus size: 14
11069886 AGATATAAAC
11069896 ATCAGCATCTCCAA
1 ATCAGCATCTCCAA
11069910 ATCA-CATCTCCAA
1 ATCAGCATCTCCAA
11069923 ATC
1 ATC
11069926 CCTTCTCAAA
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
13 12 0.75
14 4 0.25
ACGTcount: A:0.37, C:0.37, G:0.03, T:0.23
Consensus pattern (14 bp):
ATCAGCATCTCCAA
Found at i:11070621 original size:26 final size:26
Alignment explanation
Indices: 11070585--11070694 Score: 193
Period size: 26 Copynumber: 4.2 Consensus size: 26
11070575 TGATACAAAT
11070585 TGATAATAGGTTAGGTAAATGTTCCA
1 TGATAATAGGTTAGGTAAATGTTCCA
11070611 TGATAATAGGTTAGGTAAATGTTCCA
1 TGATAATAGGTTAGGTAAATGTTCCA
*
11070637 TGATAATAGGTTAGGTAAATGTTTCA
1 TGATAATAGGTTAGGTAAATGTTCCA
* *
11070663 TGATAATGGGTTAGGTAAATGTTTCA
1 TGATAATAGGTTAGGTAAATGTTCCA
11070689 TGATAA
1 TGATAA
11070695 GAATTTCATG
Statistics
Matches: 82, Mismatches: 2, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
26 82 1.00
ACGTcount: A:0.35, C:0.05, G:0.24, T:0.36
Consensus pattern (26 bp):
TGATAATAGGTTAGGTAAATGTTCCA
Found at i:11076365 original size:26 final size:26
Alignment explanation
Indices: 11076329--11076436 Score: 171
Period size: 26 Copynumber: 4.2 Consensus size: 26
11076319 ATACAAATTA
11076329 ATAATAGGTTAGGTAAATGTTCCATG
1 ATAATAGGTTAGGTAAATGTTCCATG
11076355 ATAATAGGTTAGGTAAATGTTCCATG
1 ATAATAGGTTAGGTAAATGTTCCATG
* * *
11076381 ATAATGGGTTAGGTAAATGTTTCACG
1 ATAATAGGTTAGGTAAATGTTCCATG
* *
11076407 ATAATGGGTTAGGTAAATGTTTCATG
1 ATAATAGGTTAGGTAAATGTTCCATG
11076433 ATAA
1 ATAA
11076437 GAATTTTATG
Statistics
Matches: 78, Mismatches: 4, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
26 78 1.00
ACGTcount: A:0.34, C:0.06, G:0.24, T:0.35
Consensus pattern (26 bp):
ATAATAGGTTAGGTAAATGTTCCATG
Found at i:11080214 original size:46 final size:46
Alignment explanation
Indices: 11080164--11080339 Score: 187
Period size: 46 Copynumber: 3.8 Consensus size: 46
11080154 TGGTTGAGCA
*
11080164 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCAAATG
1 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCAAACG
* * * * *
11080210 TCCGAACTTGTTGAGTTGAGTCCGAGTTC-GTGA--GATGTAACTAGGCA
1 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCAA--A--CG
* * *
11080257 TCCGAACTCGTTGAGTTGAGTCTGAGTTCACTCATGGATGCGAACG
1 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCAAACG
* * *
11080303 CCCGAGCTCGTTGAGTTGAGTCCGAGTTCGCTTATGG
1 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGG
11080340 GCGGGTTACA
Statistics
Matches: 105, Mismatches: 18, Indels: 14
0.77 0.13 0.10
Matches are distributed among these distances:
43 6 0.06
45 3 0.03
46 61 0.58
47 27 0.26
48 3 0.03
50 5 0.05
ACGTcount: A:0.21, C:0.20, G:0.29, T:0.30
Consensus pattern (46 bp):
TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCAAACG
Found at i:11080320 original size:93 final size:93
Alignment explanation
Indices: 11080161--11080332 Score: 281
Period size: 93 Copynumber: 1.8 Consensus size: 93
11080151 GGATGGTTGA
* * * *
11080161 GCATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCAAATGTCCGAACTTGTTGAGT
1 GCATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTCATGGATGCAAACGCCCGAACTCGTTGAGT
11080226 TGAGTCCGAGTTCGTGAGATGTAACTAG
66 TGAGTCCGAGTTCGTGAGATGTAACTAG
* * *
11080254 GCATCCGAACTCGTTGAGTTGAGTCTGAGTTCACTCATGGATGCGAACGCCCGAGCTCGTTGAGT
1 GCATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTCATGGATGCAAACGCCCGAACTCGTTGAGT
11080319 TGAGTCCGAGTTCG
66 TGAGTCCGAGTTCG
11080333 CTTATGGGCG
Statistics
Matches: 72, Mismatches: 7, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
93 72 1.00
ACGTcount: A:0.22, C:0.21, G:0.29, T:0.28
Consensus pattern (93 bp):
GCATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTCATGGATGCAAACGCCCGAACTCGTTGAGT
TGAGTCCGAGTTCGTGAGATGTAACTAG
Found at i:11083061 original size:23 final size:24
Alignment explanation
Indices: 11083035--11083080 Score: 60
Period size: 24 Copynumber: 2.0 Consensus size: 24
11083025 TATCATTCAT
11083035 TTCATTATAT-CA-ATATTTTATGC
1 TTCA-TATATCCATATATTTTATGC
*
11083058 TTCATATTTCCATATATTTTATG
1 TTCATATATCCATATATTTTATG
11083081 TATATTTATT
Statistics
Matches: 20, Mismatches: 1, Indels: 3
0.83 0.04 0.12
Matches are distributed among these distances:
22 4 0.20
23 6 0.30
24 10 0.50
ACGTcount: A:0.28, C:0.13, G:0.04, T:0.54
Consensus pattern (24 bp):
TTCATATATCCATATATTTTATGC
Found at i:11083400 original size:46 final size:46
Alignment explanation
Indices: 11083335--11083461 Score: 175
Period size: 46 Copynumber: 2.8 Consensus size: 46
11083325 TTATCTTTGA
* * * *
11083335 CATGATGCCATAGTGTCTTTCAACTATGGTCTTACTCATTTTC-TGT
1 CATGTTGCCATGGTATCTTTCAACCATGGTCTTACTC-TTTTCATGT
*
11083381 CATGTTGCCATGGTATCTTTCAACCATGGTCTTATTCTTTTCATGT
1 CATGTTGCCATGGTATCTTTCAACCATGGTCTTACTCTTTTCATGT
* *
11083427 CACGTTGCCATGATATCTTTCAACCATGGTCTTAC
1 CATGTTGCCATGGTATCTTTCAACCATGGTCTTAC
11083462 ACACAGGTTG
Statistics
Matches: 72, Mismatches: 8, Indels: 2
0.88 0.10 0.02
Matches are distributed among these distances:
45 5 0.07
46 67 0.93
ACGTcount: A:0.20, C:0.24, G:0.15, T:0.42
Consensus pattern (46 bp):
CATGTTGCCATGGTATCTTTCAACCATGGTCTTACTCTTTTCATGT
Found at i:11083482 original size:38 final size:38
Alignment explanation
Indices: 11083430--11083502 Score: 137
Period size: 38 Copynumber: 1.9 Consensus size: 38
11083420 TTCATGTCAC
11083430 GTTGCCATGATATCTTTCAACCATGGTCTTACACACAG
1 GTTGCCATGATATCTTTCAACCATGGTCTTACACACAG
*
11083468 GTTGCCATGGTATCTTTCAACCATGGTCTTACACA
1 GTTGCCATGATATCTTTCAACCATGGTCTTACACA
11083503 TTTCATATCA
Statistics
Matches: 34, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
38 34 1.00
ACGTcount: A:0.25, C:0.26, G:0.16, T:0.33
Consensus pattern (38 bp):
GTTGCCATGATATCTTTCAACCATGGTCTTACACACAG
Found at i:11086376 original size:3 final size:3
Alignment explanation
Indices: 11086368--11086446 Score: 65
Period size: 3 Copynumber: 26.7 Consensus size: 3
11086358 TTACTTTATT
**
11086368 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA T-A TAA -AA CCA TAA TAA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
** * *
11086414 TGGT TAA TAA TTA TAA TAA TTA T-A TATA TAA TA
1 T-AA TAA TAA TAA TAA TAA TAA TAA TA-A TAA TA
11086447 TTTATATATA
Statistics
Matches: 61, Mismatches: 10, Indels: 10
0.75 0.12 0.12
Matches are distributed among these distances:
2 6 0.10
3 51 0.84
4 4 0.07
ACGTcount: A:0.58, C:0.03, G:0.03, T:0.37
Consensus pattern (3 bp):
TAA
Found at i:11086451 original size:15 final size:15
Alignment explanation
Indices: 11086425--11086456 Score: 55
Period size: 15 Copynumber: 2.1 Consensus size: 15
11086415 GGTTAATAAT
11086425 TATAATAATTATATA
1 TATAATAATTATATA
*
11086440 TATAATATTTATATA
1 TATAATAATTATATA
11086455 TA
1 TA
11086457 ACTTAAATAA
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 16 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (15 bp):
TATAATAATTATATA
Found at i:11087314 original size:22 final size:22
Alignment explanation
Indices: 11087289--11087377 Score: 72
Period size: 22 Copynumber: 3.9 Consensus size: 22
11087279 ACGCTAATAA
11087289 ACAGAGAGCACTAAAGTGCTAT
1 ACAGAGAGCACTAAAGTGCTAT
* *
11087311 ACAGAGAGCAC-AAATGTGCCAA
1 ACAGAGAGCACTAAA-GTGCTAT
* * *
11087333 ACAAAGAGTACTAACGTGCTAAT
1 ACAGAGAGCACTAAAGTGCT-AT
* *
11087356 AATCGGAGAGCACTAACGTGCT
1 -A-CAGAGAGCACTAAAGTGCT
11087378 TGAGAAAAAT
Statistics
Matches: 52, Mismatches: 10, Indels: 7
0.75 0.14 0.10
Matches are distributed among these distances:
21 3 0.06
22 29 0.56
23 3 0.06
24 1 0.02
25 16 0.31
ACGTcount: A:0.40, C:0.20, G:0.22, T:0.17
Consensus pattern (22 bp):
ACAGAGAGCACTAAAGTGCTAT
Found at i:11087408 original size:4 final size:5
Alignment explanation
Indices: 11087383--11087415 Score: 50
Period size: 5 Copynumber: 6.6 Consensus size: 5
11087373 GTGCTTGAGA
11087383 AAAAT AAAAT AAAAT AAAAT -AAAT AAAAAT AAA
1 AAAAT AAAAT AAAAT AAAAT AAAAT -AAAAT AAA
11087416 GAACACACAA
Statistics
Matches: 26, Mismatches: 0, Indels: 4
0.87 0.00 0.13
Matches are distributed among these distances:
4 4 0.15
5 18 0.69
6 4 0.15
ACGTcount: A:0.82, C:0.00, G:0.00, T:0.18
Consensus pattern (5 bp):
AAAAT
Found at i:11099345 original size:46 final size:46
Alignment explanation
Indices: 11099262--11099497 Score: 246
Period size: 46 Copynumber: 5.2 Consensus size: 46
11099252 TCCCATCCAC
* * * * * * *
11099262 GGTCTTATTTATCTT-TGACATGATGCCATAGTGTCTTTCAACTAT
1 GGTCTTACTTATTTTCTGTCATGTTGCCATGGTATCTTTCAACCAT
*
11099307 GGTCTTACTTATTTTCTGTCAGGTTGCCATGGTATCTTTCAACCAT
1 GGTCTTACTTATTTTCTGTCATGTTGCCATGGTATCTTTCAACCAT
** * *
11099353 GGTCTTA-TTCA-TCCCCGTCATGTTGCCATGGTATCTTTCCACCAT
1 GGTCTTACTT-ATTTTCTGTCATGTTGCCATGGTATCTTTCAACCAT
* **
11099398 GGTCTTA-TTCTTTTCATGTCACATTGCCATGGTATCTTTCAACCAT
1 GGTCTTACTTATTTTC-TGTCATGTTGCCATGGTATCTTTCAACCAT
** * * *
11099444 GGTCTTACACATTTTATATCCTGTTGCCATGGTATCTTTCAACCAT
1 GGTCTTACTTATTTTCTGTCATGTTGCCATGGTATCTTTCAACCAT
11099490 GGTCTTAC
1 GGTCTTAC
11099498 ACATTTCATT
Statistics
Matches: 158, Mismatches: 28, Indels: 9
0.81 0.14 0.05
Matches are distributed among these distances:
45 55 0.35
46 99 0.63
47 4 0.03
ACGTcount: A:0.19, C:0.24, G:0.15, T:0.42
Consensus pattern (46 bp):
GGTCTTACTTATTTTCTGTCATGTTGCCATGGTATCTTTCAACCAT
Found at i:11099418 original size:91 final size:92
Alignment explanation
Indices: 11099280--11099497 Score: 269
Period size: 91 Copynumber: 2.4 Consensus size: 92
11099270 TTATCTTTGA
* * * * **
11099280 CATGATGCCATAGTGTCTTTCAACTATGGTCTTACTTATTTTCTGTCAGGTTGCCATGGTATCTT
1 CATGTTGCCATGGTATCTTTCAACCATGGTCTTACTTATTTTCTGTCACATTGCCATGGTATCTT
** * *
11099345 TCAACCATGGTCTTATTCA-TCCCCGT
66 TCAACCATGGTCTTACACATTCCACAT
* *
11099371 CATGTTGCCATGGTATCTTTCCACCATGGTCTTA-TTCTTTTCATGTCACATTGCCATGGTATCT
1 CATGTTGCCATGGTATCTTTCAACCATGGTCTTACTTATTTTC-TGTCACATTGCCATGGTATCT
** *
11099435 TTCAACCATGGTCTTACACATTTTATAT
65 TTCAACCATGGTCTTACACATTCCACAT
*
11099463 CCTGTTGCCATGGTATCTTTCAACCATGGTCTTAC
1 CATGTTGCCATGGTATCTTTCAACCATGGTCTTAC
11099498 ACATTTCATT
Statistics
Matches: 107, Mismatches: 17, Indels: 4
0.84 0.13 0.03
Matches are distributed among these distances:
90 7 0.07
91 66 0.62
92 34 0.32
ACGTcount: A:0.19, C:0.25, G:0.15, T:0.41
Consensus pattern (92 bp):
CATGTTGCCATGGTATCTTTCAACCATGGTCTTACTTATTTTCTGTCACATTGCCATGGTATCTT
TCAACCATGGTCTTACACATTCCACAT
Found at i:11101364 original size:16 final size:15
Alignment explanation
Indices: 11101339--11101369 Score: 53
Period size: 16 Copynumber: 2.0 Consensus size: 15
11101329 CTTTTATACT
11101339 AAATAAATAATAATA
1 AAATAAATAATAATA
11101354 AAATAAAATAATAATA
1 AAAT-AAATAATAATA
11101370 CTAAAACATC
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
15 4 0.27
16 11 0.73
ACGTcount: A:0.74, C:0.00, G:0.00, T:0.26
Consensus pattern (15 bp):
AAATAAATAATAATA
Found at i:11115720 original size:24 final size:24
Alignment explanation
Indices: 11115688--11115736 Score: 98
Period size: 24 Copynumber: 2.0 Consensus size: 24
11115678 TAGATAAAAA
11115688 AACAAGTCAAATGGTAGTCCACAT
1 AACAAGTCAAATGGTAGTCCACAT
11115712 AACAAGTCAAATGGTAGTCCACAT
1 AACAAGTCAAATGGTAGTCCACAT
11115736 A
1 A
11115737 CGGTAATCAA
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
24 25 1.00
ACGTcount: A:0.43, C:0.20, G:0.16, T:0.20
Consensus pattern (24 bp):
AACAAGTCAAATGGTAGTCCACAT
Found at i:11123268 original size:27 final size:27
Alignment explanation
Indices: 11123237--11123288 Score: 86
Period size: 27 Copynumber: 1.9 Consensus size: 27
11123227 CCAATGAACT
* *
11123237 GGGGAATCAGCACTTAGCAACCCCTCG
1 GGGGAATCAGCACATAACAACCCCTCG
11123264 GGGGAATCAGCACATAACAACCCCT
1 GGGGAATCAGCACATAACAACCCCT
11123289 TTTCACATTT
Statistics
Matches: 23, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
27 23 1.00
ACGTcount: A:0.31, C:0.33, G:0.23, T:0.13
Consensus pattern (27 bp):
GGGGAATCAGCACATAACAACCCCTCG
Found at i:11123347 original size:104 final size:103
Alignment explanation
Indices: 11123101--11123365 Score: 399
Period size: 103 Copynumber: 2.6 Consensus size: 103
11123091 AACCGTTATT
* * * *
11123101 GGTGGATCTCGCACTTAGCACCACCACTTAATCGGGGAATCAGCACTTAGCAACCCCTTGGGGGA
1 GGTGGATATCGCACTTAGCACCACCAATGAATCGGGGAATCAGCACTTAGCAACCCCTCGGGGGA
* * *
11123166 ATCAGCACATAGCAACCCCCTTTTTATTTCAGAGATAC
66 ATCAGCACATAACAACCCCCTTTTCATTTCAAAGATAC
11123204 GGTGGATATCGCACTTAGCACCACCAATGAA-CTGGGGAATCAGCACTTAGCAACCCCTCGGGGG
1 GGTGGATATCGCACTTAGCACCACCAATGAATC-GGGGAATCAGCACTTAGCAACCCCTCGGGGG
11123268 AATCAGCACATAACAA-CCCCTTTTCACATTTCAAAGATAC
65 AATCAGCACATAACAACCCCCTTTT--CATTTCAAAGATAC
* **
11123308 GGTGGATATCGCACATAGCACCACCAATGAATCGGGGAATCAGCACACAGCAACCCCT
1 GGTGGATATCGCACTTAGCACCACCAATGAATCGGGGAATCAGCACTTAGCAACCCCT
11123366 TTATGTACAA
Statistics
Matches: 148, Mismatches: 10, Indels: 7
0.90 0.06 0.04
Matches are distributed among these distances:
102 9 0.06
103 73 0.49
104 65 0.44
105 1 0.01
ACGTcount: A:0.30, C:0.29, G:0.20, T:0.20
Consensus pattern (103 bp):
GGTGGATATCGCACTTAGCACCACCAATGAATCGGGGAATCAGCACTTAGCAACCCCTCGGGGGA
ATCAGCACATAACAACCCCCTTTTCATTTCAAAGATAC
Found at i:11123727 original size:30 final size:29
Alignment explanation
Indices: 11123693--11123757 Score: 76
Period size: 30 Copynumber: 2.2 Consensus size: 29
11123683 TAATCCACCA
11123693 CCCAACTTTTTGAAAAATTACAATTTTGCC
1 CCCAAC-TTTTGAAAAATTACAATTTTGCC
* * * *
11123723 CCCAAACTTTTGCATAATTACACTTTTGTC
1 CCC-AACTTTTGAAAAATTACAATTTTGCC
11123753 CCCAA
1 CCCAA
11123758 GCTCGGAAAT
Statistics
Matches: 30, Mismatches: 4, Indels: 3
0.81 0.11 0.08
Matches are distributed among these distances:
29 2 0.07
30 25 0.83
31 3 0.10
ACGTcount: A:0.31, C:0.28, G:0.06, T:0.35
Consensus pattern (29 bp):
CCCAACTTTTGAAAAATTACAATTTTGCC
Found at i:11123731 original size:31 final size:30
Alignment explanation
Indices: 11123700--11123757 Score: 80
Period size: 30 Copynumber: 1.9 Consensus size: 30
11123690 CCACCCAACT
11123700 TTTTGAAAAATTACAATTTTGCCCCCAAAC
1 TTTTGAAAAATTACAATTTTGCCCCCAAAC
* * * *
11123730 TTTTGCATAATTACACTTTTGTCCCCAA
1 TTTTGAAAAATTACAATTTTGCCCCCAA
11123758 GCTCGGAAAT
Statistics
Matches: 24, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
30 24 1.00
ACGTcount: A:0.31, C:0.24, G:0.07, T:0.38
Consensus pattern (30 bp):
TTTTGAAAAATTACAATTTTGCCCCCAAAC
Found at i:11132853 original size:18 final size:18
Alignment explanation
Indices: 11132832--11132910 Score: 76
Period size: 18 Copynumber: 4.6 Consensus size: 18
11132822 GAAAGTTTTT
* *
11132832 TTTTTTAAAATACGAGAA
1 TTTTTGAAAACACGAGAA
11132850 TTTTTGAAAACACGAGAA
1 TTTTTGAAAACACGAGAA
*
11132868 --TTTGTAAACACGA-ATA
1 TTTTTGAAAACACGAGA-A
* *
11132884 TTTTAG-AAACACGAAAA
1 TTTTTGAAAACACGAGAA
11132901 TTTTTGAAAA
1 TTTTTGAAAA
11132911 AAAAAACGAA
Statistics
Matches: 51, Mismatches: 5, Indels: 10
0.77 0.08 0.15
Matches are distributed among these distances:
15 1 0.02
16 13 0.25
17 14 0.27
18 23 0.45
ACGTcount: A:0.46, C:0.09, G:0.13, T:0.33
Consensus pattern (18 bp):
TTTTTGAAAACACGAGAA
Found at i:11132871 original size:16 final size:16
Alignment explanation
Indices: 11132838--11132903 Score: 53
Period size: 16 Copynumber: 3.9 Consensus size: 16
11132828 TTTTTTTTTT
*
11132838 AAAATACGAGAATTTTTG
1 AAAACACGAGAA--TTTG
11132856 AAAACACGAGAATTTG
1 AAAACACGAGAATTTG
* *
11132872 TAAACACGA-ATATTTT
1 AAAACACGAGA-ATTTG
*
11132888 AGAAACACGAAAATTT
1 A-AAACACGAGAATTT
11132904 TTGAAAAAAA
Statistics
Matches: 41, Mismatches: 4, Indels: 7
0.79 0.08 0.13
Matches are distributed among these distances:
15 1 0.02
16 16 0.39
17 12 0.29
18 12 0.29
ACGTcount: A:0.48, C:0.11, G:0.14, T:0.27
Consensus pattern (16 bp):
AAAACACGAGAATTTG
Found at i:11132982 original size:18 final size:16
Alignment explanation
Indices: 11132961--11133013 Score: 54
Period size: 18 Copynumber: 3.1 Consensus size: 16
11132951 AACACGGGAA
11132961 TTTTTAAAACAAGACATT
1 TTTTTAAAACAA-A-ATT
*
11132979 TTTTTGAAACAAAATTT
1 TTTTTAAAACAAAA-TT
11132996 TTTCTTAAAA-AAAATT
1 TTT-TTAAAACAAAATT
11133012 TT
1 TT
11133014 AAATACGAGA
Statistics
Matches: 31, Mismatches: 2, Indels: 6
0.79 0.05 0.15
Matches are distributed among these distances:
16 5 0.16
17 10 0.32
18 16 0.52
ACGTcount: A:0.43, C:0.08, G:0.04, T:0.45
Consensus pattern (16 bp):
TTTTTAAAACAAAATT
Found at i:11133058 original size:18 final size:17
Alignment explanation
Indices: 11132833--11133280 Score: 140
Period size: 17 Copynumber: 25.1 Consensus size: 17
11132823 AAAGTTTTTT
* *
11132833 TTTTTAAAATACGAGAA
1 TTTTTAAAACACGAAAA
*
11132850 TTTTTGAAAACACGAGAA
1 TTTTT-AAAACACGAAAA
* *
11132868 TTTGT-AAACACGAATA
1 TTTTTAAAACACGAAAA
11132884 -TTTTAGAAACACGAAAA
1 TTTTTA-AAACACGAAAA
* *
11132901 TTTTTGAAAAAAAAAACGAAAT
1 TTTTT-----AAAACACGAAAA
**
11132923 TTTCTTAAAACACGACATTTT
1 TTT-TTAAAACACGA-A--AA
* **
11132944 TTTTTGAAACACGGGAA
1 TTTTTAAAACACGAAAA
* **
11132961 TTTTTAAAACAAGACATT
1 TTTTTAAAACACGA-AAA
* *
11132979 TTTTTGAAACA--AAATT
1 TTTTTAAAACACGAAA-A
*
11132995 TTTTCTTAAA-A--AAAA
1 TTTT-TAAAACACGAAAA
* *
11133010 -TTTT-AAATACGAGAA
1 TTTTTAAAACACGAAAA
11133025 TTTTTAAAACACGAAAA
1 TTTTTAAAACACGAAAA
11133042 TTTTTAAAACACGGAAATA
1 TTTTTAAAACAC-GAAA-A
* * *
11133061 TTTTTTTTTTAAACAGGAAATTTT
1 ----TTTTTAAAACACGAAA---A
*
11133085 TTTTTGAAAACAAGAAAA
1 TTTTT-AAAACACGAAAA
* * *
11133103 TTTTTGAAACACTAGAA
1 TTTTTAAAACACGAAAA
* *
11133120 TTTTGAAAACACGAAGA
1 TTTTTAAAACACGAAAA
* * *
11133137 TTTTTGAAACATGAGAA
1 TTTTTAAAACACGAAAA
**
11133154 TTTTTAAAAGCACGAGGA
1 TTTTTAAAA-CACGAAAA
* * *
11133172 TTATTGAAAGCACGAAGA
1 TT-TTTAAAACACGAAAA
* * *
11133190 TTTATAAAAAACGACAA
1 TTTTTAAAACACGAAAA
* *
11133207 TTTTTGAAATACGAGAAA
1 TTTTTAAAACACGA-AAA
* *
11133225 TTTTTTAAACGCGAAAA
1 TTTTTAAAACACGAAAA
*
11133242 TTTTTTTCAAACACGAAAA
1 --TTTTTAAAACACGAAAA
* *
11133261 CTTTTGAAAACGCGAAAA
1 -TTTTTAAAACACGAAAA
11133279 TT
1 TT
11133281 CGAAAATTTC
Statistics
Matches: 323, Mismatches: 73, Indels: 70
0.69 0.16 0.15
Matches are distributed among these distances:
12 3 0.01
13 2 0.01
14 3 0.01
15 7 0.02
16 23 0.07
17 116 0.36
18 90 0.28
19 22 0.07
20 14 0.04
21 13 0.04
22 16 0.05
23 13 0.04
24 1 0.00
ACGTcount: A:0.45, C:0.10, G:0.12, T:0.33
Consensus pattern (17 bp):
TTTTTAAAACACGAAAA
Found at i:11133079 original size:22 final size:22
Alignment explanation
Indices: 11133042--11133107 Score: 82
Period size: 21 Copynumber: 3.0 Consensus size: 22
11133032 AACACGAAAA
11133042 TTTTTAAAACACGGAAATATTTT
1 TTTTTAAAACA-GGAAATATTTT
*
11133065 TTTTTTAAACAGGAAAT-TTTT
1 TTTTTAAAACAGGAAATATTTT
* *
11133086 TTTTGAAAACAAGAAA-ATTTT
1 TTTTTAAAACAGGAAATATTTT
11133107 T
1 T
11133108 GAAACACTAG
Statistics
Matches: 38, Mismatches: 4, Indels: 4
0.83 0.09 0.09
Matches are distributed among these distances:
21 22 0.58
22 6 0.16
23 10 0.26
ACGTcount: A:0.39, C:0.06, G:0.09, T:0.45
Consensus pattern (22 bp):
TTTTTAAAACAGGAAATATTTT
Found at i:11133247 original size:19 final size:19
Alignment explanation
Indices: 11133225--11133280 Score: 62
Period size: 18 Copynumber: 3.1 Consensus size: 19
11133215 ATACGAGAAA
11133225 TTTTTT-AAACGCGAAAAT
1 TTTTTTAAAACGCGAAAAT
* *
11133243 TTTTTTCAAACACGAAAA-
1 TTTTTTAAAACGCGAAAAT
* *
11133261 CTTTTGAAAACGCGAAAAT
1 TTTTTTAAAACGCGAAAAT
11133280 T
1 T
11133281 CGAAAATTTC
Statistics
Matches: 30, Mismatches: 6, Indels: 3
0.77 0.15 0.08
Matches are distributed among these distances:
18 20 0.67
19 10 0.33
ACGTcount: A:0.41, C:0.14, G:0.11, T:0.34
Consensus pattern (19 bp):
TTTTTTAAAACGCGAAAAT
Found at i:11133324 original size:18 final size:17
Alignment explanation
Indices: 11133275--11133325 Score: 57
Period size: 18 Copynumber: 2.9 Consensus size: 17
11133265 TGAAAACGCG
11133275 AAAATTCGAAAATTTCT
1 AAAATTCGAAAATTTCT
* * *
11133292 AAAATACGAGTAATTTTT
1 AAAATTCGA-AAATTTCT
11133310 AAAGATTCGAAAATTT
1 AAA-ATTCGAAAATTT
11133326 GAAACAAGAA
Statistics
Matches: 27, Mismatches: 5, Indels: 3
0.77 0.14 0.09
Matches are distributed among these distances:
17 8 0.30
18 14 0.52
19 5 0.19
ACGTcount: A:0.47, C:0.08, G:0.10, T:0.35
Consensus pattern (17 bp):
AAAATTCGAAAATTTCT
Found at i:11133839 original size:7 final size:7
Alignment explanation
Indices: 11133822--11133877 Score: 78
Period size: 7 Copynumber: 7.9 Consensus size: 7
11133812 TGAACCCCCT
11133822 TTTTCTTC
1 TTTT-TTC
11133830 TTTTTTC
1 TTTTTTC
11133837 TTTTTTC
1 TTTTTTC
11133844 TTTTTTC
1 TTTTTTC
*
11133851 CTTTTTC
1 TTTTTTC
11133858 -TTTTTC
1 TTTTTTC
11133864 TTTTTTC
1 TTTTTTC
11133871 TTCTTTT
1 TT-TTTT
11133878 TCTTCCTTTT
Statistics
Matches: 45, Mismatches: 1, Indels: 4
0.90 0.02 0.08
Matches are distributed among these distances:
6 6 0.13
7 31 0.69
8 8 0.18
ACGTcount: A:0.00, C:0.18, G:0.00, T:0.82
Consensus pattern (7 bp):
TTTTTTC
Found at i:11133886 original size:20 final size:19
Alignment explanation
Indices: 11133820--11133894 Score: 70
Period size: 20 Copynumber: 4.1 Consensus size: 19
11133810 ATTGAACCCC
11133820 CTTTTTCTTCTTTTTTC-T
1 CTTTTTCTTCTTTTTTCTT
*
11133838 -TTTTTC-T-TTTTTCCTT
1 CTTTTTCTTCTTTTTTCTT
*
11133854 -TTTCTTTTTCTTTTTTCTT
1 CTTT-TTCTTCTTTTTTCTT
*
11133873 CTTTTTCTTCCTTTTTTTTT
1 CTTTTTCTT-CTTTTTTCTT
11133893 CT
1 CT
11133895 GCTGGGCTGC
Statistics
Matches: 46, Mismatches: 5, Indels: 10
0.75 0.08 0.16
Matches are distributed among these distances:
15 6 0.13
16 5 0.11
17 8 0.17
18 1 0.02
19 12 0.26
20 14 0.30
ACGTcount: A:0.00, C:0.20, G:0.00, T:0.80
Consensus pattern (19 bp):
CTTTTTCTTCTTTTTTCTT
Found at i:11134041 original size:12 final size:12
Alignment explanation
Indices: 11134024--11134049 Score: 52
Period size: 12 Copynumber: 2.2 Consensus size: 12
11134014 CTTTCCCTTC
11134024 TTTTTTTTTGCT
1 TTTTTTTTTGCT
11134036 TTTTTTTTTGCT
1 TTTTTTTTTGCT
11134048 TT
1 TT
11134050 GATTTTTTTT
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:0.00, C:0.08, G:0.08, T:0.85
Consensus pattern (12 bp):
TTTTTTTTTGCT
Found at i:11134189 original size:3 final size:3
Alignment explanation
Indices: 11134183--11134228 Score: 58
Period size: 3 Copynumber: 15.0 Consensus size: 3
11134173 TTTTCTTTCT
*
11134183 TTC TTC TTC CTC TT- TTC TTC TTCC TTC TTC TTCC TTC TTC TTC TTC
1 TTC TTC TTC TTC TTC TTC TTC TT-C TTC TTC TT-C TTC TTC TTC TTC
11134229 AAAGTCTAGC
Statistics
Matches: 38, Mismatches: 2, Indels: 6
0.83 0.04 0.13
Matches are distributed among these distances:
2 2 0.05
3 30 0.79
4 6 0.16
ACGTcount: A:0.00, C:0.37, G:0.00, T:0.63
Consensus pattern (3 bp):
TTC
Found at i:11134212 original size:10 final size:10
Alignment explanation
Indices: 11134197--11134225 Score: 58
Period size: 10 Copynumber: 2.9 Consensus size: 10
11134187 TCTTCCTCTT
11134197 TTCTTCTTCC
1 TTCTTCTTCC
11134207 TTCTTCTTCC
1 TTCTTCTTCC
11134217 TTCTTCTTC
1 TTCTTCTTC
11134226 TTCAAAGTCT
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 19 1.00
ACGTcount: A:0.00, C:0.38, G:0.00, T:0.62
Consensus pattern (10 bp):
TTCTTCTTCC
Found at i:11134213 original size:13 final size:13
Alignment explanation
Indices: 11134183--11134228 Score: 62
Period size: 13 Copynumber: 3.7 Consensus size: 13
11134173 TTTTCTTTCT
11134183 TTCTTCTTCC-TC
1 TTCTTCTTCCTTC
11134195 TT-TTCTT-CTTCC
1 TTCTTCTTCCTT-C
11134207 TTCTTCTTCCTTC
1 TTCTTCTTCCTTC
11134220 TTCTTCTTC
1 TTCTTCTTC
11134229 AAAGTCTAGC
Statistics
Matches: 30, Mismatches: 0, Indels: 7
0.81 0.00 0.19
Matches are distributed among these distances:
10 1 0.03
11 6 0.20
12 5 0.17
13 15 0.50
14 3 0.10
ACGTcount: A:0.00, C:0.37, G:0.00, T:0.63
Consensus pattern (13 bp):
TTCTTCTTCCTTC
Found at i:11134319 original size:10 final size:10
Alignment explanation
Indices: 11134284--11134333 Score: 59
Period size: 10 Copynumber: 5.2 Consensus size: 10
11134274 ACGCCGGTAC
11134284 TCTT-TCTTT
1 TCTTCTCTTT
* *
11134293 TCTTCTCCTC
1 TCTTCTCTTT
11134303 T-TTCTCTTT
1 TCTTCTCTTT
11134312 TCTTCTCTTT
1 TCTTCTCTTT
*
11134322 TCTTCTTTTT
1 TCTTCTCTTT
11134332 TC
1 TC
11134334 CTTCGAAAAA
Statistics
Matches: 34, Mismatches: 5, Indels: 3
0.81 0.12 0.07
Matches are distributed among these distances:
9 11 0.32
10 23 0.68
ACGTcount: A:0.00, C:0.30, G:0.00, T:0.70
Consensus pattern (10 bp):
TCTTCTCTTT
Found at i:11134331 original size:19 final size:19
Alignment explanation
Indices: 11134288--11134330 Score: 63
Period size: 19 Copynumber: 2.3 Consensus size: 19
11134278 CGGTACTCTT
11134288 TCTTTTCTTCTCCTCTTTC
1 TCTTTTCTTCTCCTCTTTC
11134307 TCTTTTCTTCT-CT-TTTC
1 TCTTTTCTTCTCCTCTTTC
11134324 TTCTTTT
1 -TCTTTT
11134331 TTCCTTCGAA
Statistics
Matches: 23, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
17 4 0.17
18 8 0.35
19 11 0.48
ACGTcount: A:0.00, C:0.30, G:0.00, T:0.70
Consensus pattern (19 bp):
TCTTTTCTTCTCCTCTTTC
Found at i:11134611 original size:29 final size:29
Alignment explanation
Indices: 11134578--11134694 Score: 94
Period size: 30 Copynumber: 3.9 Consensus size: 29
11134568 TGTAATTTTT
*
11134578 AGAAAATTTAGGATTAAAATGAAATTTAA
1 AGAAAATTTAGGGTTAAAATGAAATTTAA
* * *
11134607 TGAAAGTTTAGGGGTCT-AAGTGAAATTTAA
1 AGAAAATTTA-GGGT-TAAAATGAAATTTAA
* *
11134637 AGAAAGTTTAAGGGTCAAAATGAAATTT-A
1 AGAAAATTT-AGGGTTAAAATGAAATTTAA
* * *
11134666 GGAAAAGTTTAGGTGTCAAAATGTAATTT
1 AGAAAA-TTTAGG-GTTAAAATGAAATTT
11134695 TTATTTTTTA
Statistics
Matches: 72, Mismatches: 10, Indels: 11
0.77 0.11 0.12
Matches are distributed among these distances:
29 16 0.22
30 54 0.75
31 2 0.03
ACGTcount: A:0.44, C:0.03, G:0.21, T:0.32
Consensus pattern (29 bp):
AGAAAATTTAGGGTTAAAATGAAATTTAA
Found at i:11134633 original size:30 final size:30
Alignment explanation
Indices: 11134593--11134694 Score: 125
Period size: 30 Copynumber: 3.4 Consensus size: 30
11134583 ATTTAGGATT
*
11134593 AAAATGAAATTTAATGAAAGTTTAGGGGTC
1 AAAATGAAATTTAAAGAAAGTTTAGGGGTC
* * *
11134623 TAAGTGAAATTTAAAGAAAGTTTAAGGGTC
1 AAAATGAAATTTAAAGAAAGTTTAGGGGTC
* *
11134653 AAAATGAAATTT-AGGAAAAGTTTAGGTGTC
1 AAAATGAAATTTAAAG-AAAGTTTAGGGGTC
*
11134683 AAAATGTAATTT
1 AAAATGAAATTT
11134695 TTATTTTTTA
Statistics
Matches: 61, Mismatches: 10, Indels: 2
0.84 0.14 0.03
Matches are distributed among these distances:
29 2 0.03
30 59 0.97
ACGTcount: A:0.44, C:0.03, G:0.22, T:0.31
Consensus pattern (30 bp):
AAAATGAAATTTAAAGAAAGTTTAGGGGTC
Found at i:11134694 original size:60 final size:59
Alignment explanation
Indices: 11134565--11134694 Score: 145
Period size: 60 Copynumber: 2.2 Consensus size: 59
11134555 TTCTGGGGCT
** * * *
11134565 AAATGTAATTTTTAGAAAATTTAGGATTAAAATGAAATTTAATGAAAGTTTAGGGGTCT
1 AAATGTAATTTAAAGAAAATTTAGGATCAAAATGAAATTTAAGGAAAGTTTAGGGGTCA
* * * * *
11134624 AAGTGAAATTTAAAGAAAGTTTAAGGGTCAAAATGAAATTT-AGGAAAAGTTTAGGTGTCA
1 AAATGTAATTTAAAGAAAATTT-AGGATCAAAATGAAATTTAAGG-AAAGTTTAGGGGTCA
11134684 AAATGTAATTT
1 AAATGTAATTT
11134695 TTATTTTTTA
Statistics
Matches: 57, Mismatches: 12, Indels: 3
0.79 0.17 0.04
Matches are distributed among these distances:
59 19 0.33
60 38 0.67
ACGTcount: A:0.44, C:0.02, G:0.20, T:0.34
Consensus pattern (59 bp):
AAATGTAATTTAAAGAAAATTTAGGATCAAAATGAAATTTAAGGAAAGTTTAGGGGTCA
Found at i:11134710 original size:15 final size:16
Alignment explanation
Indices: 11134690--11134726 Score: 58
Period size: 15 Copynumber: 2.4 Consensus size: 16
11134680 GTCAAAATGT
11134690 AATTTTTATTTTTT-A
1 AATTTTTATTTTTTGA
*
11134705 AATTTTTTTTTTTTGA
1 AATTTTTATTTTTTGA
11134721 AATTTT
1 AATTTT
11134727 GAAAATTAAA
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
15 13 0.65
16 7 0.35
ACGTcount: A:0.24, C:0.00, G:0.03, T:0.73
Consensus pattern (16 bp):
AATTTTTATTTTTTGA
Found at i:11134717 original size:16 final size:16
Alignment explanation
Indices: 11134692--11134726 Score: 52
Period size: 16 Copynumber: 2.2 Consensus size: 16
11134682 CAAAATGTAA
*
11134692 TTTTTATTTTTTAAAT
1 TTTTTATTTTTGAAAT
*
11134708 TTTTTTTTTTTGAAAT
1 TTTTTATTTTTGAAAT
11134724 TTT
1 TTT
11134727 GAAAATTAAA
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
16 17 1.00
ACGTcount: A:0.20, C:0.00, G:0.03, T:0.77
Consensus pattern (16 bp):
TTTTTATTTTTGAAAT
Found at i:11135051 original size:55 final size:53
Alignment explanation
Indices: 11134967--11135267 Score: 429
Period size: 50 Copynumber: 5.7 Consensus size: 53
11134957 CACGTGAGCC
* *
11134967 AAGGCTCAACTCACTTCTCGCAATATGAGTTGATTTTTGAAAACAGAATTTGCAA
1 AAGGCTCAACTCACCTCTCGCAATATGAGTTGATTTTTGAAAA-AGAA-TTGAAA
*
11135022 AAGGCTCAACTCACCTCTCGCAATATGAGTTGATTTTTG--AAA-AATAGAAA
1 AAGGCTCAACTCACCTCTCGCAATATGAGTTGATTTTTGAAAAAGAATTGAAA
*
11135072 AAGGCTCAACTCACCTCTCGCAATATGAGTTGATTTTTGAAAACAGAATTTGCAA
1 AAGGCTCAACTCACCTCTCGCAATATGAGTTGATTTTTGAAAA-AGAA-TTGAAA
*
11135127 AAGGCTCAACTCACCTCTCGCAATATGAGTTGATTTTTG--AAA-AATAGAAA
1 AAGGCTCAACTCACCTCTCGCAATATGAGTTGATTTTTGAAAAAGAATTGAAA
*
11135177 AAGGCTCAACTCACCTCTCGCAATATGAGTTGGTTTTTGAAAATAGAAATT--AA
1 AAGGCTCAACTCACCTCTCGCAATATGAGTTGATTTTTGAAAA-AG-AATTGAAA
*
11135230 AAGGCTCAACTCACCTCTTGCAATATGAGTTGATTTTT
1 AAGGCTCAACTCACCTCTCGCAATATGAGTTGATTTTT
11135268 TTTTTTGAAA
Statistics
Matches: 225, Mismatches: 11, Indels: 22
0.87 0.04 0.09
Matches are distributed among these distances:
50 85 0.38
51 4 0.02
52 6 0.03
53 44 0.20
54 2 0.01
55 84 0.37
ACGTcount: A:0.35, C:0.19, G:0.16, T:0.30
Consensus pattern (53 bp):
AAGGCTCAACTCACCTCTCGCAATATGAGTTGATTTTTGAAAAAGAATTGAAA
Found at i:11135149 original size:105 final size:105
Alignment explanation
Indices: 11134967--11135267 Score: 543
Period size: 105 Copynumber: 2.9 Consensus size: 105
11134957 CACGTGAGCC
*
11134967 AAGGCTCAACTCACTTCTCGCAATATGAGTTGATTTTTGAAAACAGAATTTGCAAAAGGCTCAAC
1 AAGGCTCAACTCACCTCTCGCAATATGAGTTGATTTTTGAAAACAGAATTTGCAAAAGGCTCAAC
11135032 TCACCTCTCGCAATATGAGTTGATTTTTGAAAAATAGAAA
66 TCACCTCTCGCAATATGAGTTGATTTTTGAAAAATAGAAA
11135072 AAGGCTCAACTCACCTCTCGCAATATGAGTTGATTTTTGAAAACAGAATTTGCAAAAGGCTCAAC
1 AAGGCTCAACTCACCTCTCGCAATATGAGTTGATTTTTGAAAACAGAATTTGCAAAAGGCTCAAC
11135137 TCACCTCTCGCAATATGAGTTGATTTTTGAAAAATAGAAA
66 TCACCTCTCGCAATATGAGTTGATTTTTGAAAAATAGAAA
* * *
11135177 AAGGCTCAACTCACCTCTCGCAATATGAGTTGGTTTTTGAAAATAGAAATT--AAAAGGCTCAAC
1 AAGGCTCAACTCACCTCTCGCAATATGAGTTGATTTTTGAAAACAGAATTTGCAAAAGGCTCAAC
*
11135240 TCACCTCTTGCAATATGAGTTGATTTTT
66 TCACCTCTCGCAATATGAGTTGATTTTT
11135268 TTTTTTGAAA
Statistics
Matches: 191, Mismatches: 5, Indels: 2
0.96 0.03 0.01
Matches are distributed among these distances:
103 39 0.20
105 152 0.80
ACGTcount: A:0.35, C:0.19, G:0.16, T:0.30
Consensus pattern (105 bp):
AAGGCTCAACTCACCTCTCGCAATATGAGTTGATTTTTGAAAACAGAATTTGCAAAAGGCTCAAC
TCACCTCTCGCAATATGAGTTGATTTTTGAAAAATAGAAA
Found at i:11135307 original size:13 final size:14
Alignment explanation
Indices: 11135279--11135311 Score: 59
Period size: 13 Copynumber: 2.4 Consensus size: 14
11135269 TTTTTGAAAC
11135279 ACAGAAATTAAAAA
1 ACAGAAATTAAAAA
11135293 ACAGAAATT-AAAA
1 ACAGAAATTAAAAA
11135306 ACAGAA
1 ACAGAA
11135312 TTTGAAAAGA
Statistics
Matches: 19, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
13 10 0.53
14 9 0.47
ACGTcount: A:0.70, C:0.09, G:0.09, T:0.12
Consensus pattern (14 bp):
ACAGAAATTAAAAA
Found at i:11135319 original size:14 final size:14
Alignment explanation
Indices: 11135272--11135319 Score: 62
Period size: 14 Copynumber: 3.5 Consensus size: 14
11135262 ATTTTTTTTT
*
11135272 TTGAAACACAGAAA
1 TTGAAAAACAGAAA
*
11135286 TTAAAAAACAGAAA
1 TTGAAAAACAGAAA
*
11135300 TT-AAAAACAGAAT
1 TTGAAAAACAGAAA
11135313 TTGAAAA
1 TTGAAAA
11135320 GACCTCAGCG
Statistics
Matches: 30, Mismatches: 3, Indels: 2
0.86 0.09 0.06
Matches are distributed among these distances:
13 12 0.40
14 18 0.60
ACGTcount: A:0.62, C:0.08, G:0.10, T:0.19
Consensus pattern (14 bp):
TTGAAAAACAGAAA
Found at i:11135903 original size:71 final size:72
Alignment explanation
Indices: 11135395--11137137 Score: 2260
Period size: 72 Copynumber: 24.1 Consensus size: 72
11135385 ATTAGTAAAG
* * * *
11135395 CAGAAATTGAAAATACCTCAGCGTGCCTTGAGGCTCAACTCATCTCTCGCAATATGAGTT-AAGT
1 CAGAAATTGAAATTACCTCAACGTGTCTTGAGGCTCAACTCATTTCTCGCAATATGAGTTGAA-T
11135459 TTTGAAAA
65 TTTGAAAA
* *
11135467 GCAGAAATTGAAAATACCTCAATGTGTCTTGAGGCTCAACTCATTTCTCGCAATATGAGTTGAAT
1 -CAGAAATTGAAATTACCTCAACGTGTCTTGAGGCTCAACTCATTTCTCGCAATATGAGTTGAAT
11135532 TTTGAAAA
65 TTTGAAAA
11135540 CAGAAATTGAAATTACCTCAACGTGTCTTGAGGCTCAACTCATTTCTCGCAATATGAGTTGAATT
1 CAGAAATTGAAATTACCTCAACGTGTCTTGAGGCTCAACTCATTTCTCGCAATATGAGTTGAATT
*
11135605 TTGAGAAG
66 TTGA-AAA
*
11135613 CAGAAATTGAAAATACCTCAACGTGTCTTGAGGCTCAACTCATTTCTCGCAATATGAGTTGAATT
1 CAGAAATTGAAATTACCTCAACGTGTCTTGAGGCTCAACTCATTTCTCGCAATATGAGTTGAATT
11135678 TTGAAAA
66 TTGAAAA
11135685 CAGAAATTGAAATTACCTCAACGTGTCTTGAGGCTCAACTCATTTCTCGCAATATGAGTTGAATT
1 CAGAAATTGAAATTACCTCAACGTGTCTTGAGGCTCAACTCATTTCTCGCAATATGAGTTGAATT
11135750 TTGAAAA
66 TTGAAAA
11135757 CAGAAATTGAAATTACCTCAACGTGTCTTGAGGCTCAACTCATTTCTCGCAATATGAGTTGAATT
1 CAGAAATTGAAATTACCTCAACGTGTCTTGAGGCTCAACTCATTTCTCGCAATATGAGTTGAATT
11135822 TTG-AAA
66 TTGAAAA
11135828 CAGAAATTGAAA-TACCTCAACGTGTCTTGAGGCTCAACTCATTTCTCGCAATATGAGTTGAATT
1 CAGAAATTGAAATTACCTCAACGTGTCTTGAGGCTCAACTCATTTCTCGCAATATGAGTTGAATT
11135892 TTGAAAA
66 TTGAAAA
11135899 CAGAAATTGAAATTACCTCAACGTGTCTTGAGGCTCAACTCATTTCTCGCAATATGAGTTGAATT
1 CAGAAATTGAAATTACCTCAACGTGTCTTGAGGCTCAACTCATTTCTCGCAATATGAGTTGAATT
11135964 TTGAAAA
66 TTGAAAA
11135971 CAGAAATTGAAA-TACCTCAACGTGTCTTGAGGCTCAACTCATTTCTCGCAATATGAGTTGAATT
1 CAGAAATTGAAATTACCTCAACGTGTCTTGAGGCTCAACTCATTTCTCGCAATATGAGTTGAATT
*
11136035 TTGAAAG
66 TTGAAAA
*
11136042 CAGAAATTGAAAATACCTC-ACGTGTC-TGAGGCTCAACTCATTTCTCGCAATATGAGTTGAATT
1 CAGAAATTGAAATTACCTCAACGTGTCTTGAGGCTCAACTCATTTCTCGCAATATGAGTTGAATT
11136105 TTG-AAA
66 TTGAAAA
*
11136111 CAGAAATTGAAAATACCTCAACGTGTCTTGAGGCTCAACTCATTTCTCGCAATATGAGTTGAATT
1 CAGAAATTGAAATTACCTCAACGTGTCTTGAGGCTCAACTCATTTCTCGCAATATGAGTTGAATT
11136176 TTGAAAA
66 TTGAAAA
*
11136183 CAGAAATTGAAATTACCTCAACGTGTCTTGAGGCTCAAC-CATTTC-CGCAATATGA-TTGAA-A
1 CAGAAATTGAAATTACCTCAACGTGTCTTGAGGCTCAACTCATTTCTCGCAATATGAGTTGAATT
***
11136244 AAAAAAA
66 TTGAAAA
* * *** ** **** ** * * * *
11136251 AAAAAAAAAAAAAAAAAAAAAATTGAAAATACCTCACGTGTCTTGAGGCTCAACTCATTTCTCGC
1 CAGAAATTGAAATTACCTCAACGTG----T-CTTGA-G-G-C-TCA---AC---TCATTTCTCGC
11136316 AATATGAGTTGAATTTTGAAAA
51 AATATGAGTTGAATTTTGAAAA
11136338 CAGAAATTGAAATTACCTCAACGTGTCTTGAGGCTCAACTCATTTCTCGCAATATGAGTTGAATT
1 CAGAAATTGAAATTACCTCAACGTGTCTTGAGGCTCAACTCATTTCTCGCAATATGAGTTGAATT
11136403 TTGAAAA
66 TTGAAAA
11136410 CAGAAATTGAAATTACCTCAACGTGTCTTGAGGCTCAACTCATTTCTCGCAATATGAGTTG-ATT
1 CAGAAATTGAAATTACCTCAACGTGTCTTGAGGCTCAACTCATTTCTCGCAATATGAGTTGAATT
11136474 TTGAAAA
66 TTGAAAA
11136481 GCAGAAATTGAAA-TACCTCAACGTGTCTTGAGGCTCAACTCATTTCTCGCAATATGAGTTGAAT
1 -CAGAAATTGAAATTACCTCAACGTGTCTTGAGGCTCAACTCATTTCTCGCAATATGAGTTGAAT
11136545 TTTG-AAA
65 TTTGAAAA
11136552 CAGAAATTGAAA-TACCTC-ACGTGTC-TGAGGCTCAACTCATTTCTCGCAATATGAGTTGAATT
1 CAGAAATTGAAATTACCTCAACGTGTCTTGAGGCTCAACTCATTTCTCGCAATATGAGTTGAATT
11136614 TTGAAAA
66 TTGAAAA
11136621 CAGAAATTGAAATTACCTCAACGTGTCTTGAGGCTCAACTCATTTCTCGCAATATGAGTTGAATT
1 CAGAAATTGAAATTACCTCAACGTGTCTTGAGGCTCAACTCATTTCTCGCAATATGAGTTGAATT
11136686 TTG-AAA
66 TTGAAAA
** ** *** * *** * *
11136692 CATGAATATTGAAA--A-CAGAAATTGAAAAT-A-CCTCAACGTGTC-TTGAGGCTCAACTCATT
1 CA-GAA-ATTGAAATTACCTCAACGTG-TCTTGAGGCTCAAC---TCATT-TCTCGCAA-T-ATG
** * **
11136751 TCTCGCAATATGAGTTGAATT
57 AGTTG-AAT-T---TTGAAAA
** **
11136772 TTGAAAACAGAAATTGAAATTACCTCAACGTGTCTTGAGGCTCAACTCATTTCTCGCAATATGAG
1 CAG-AAATTG-AA-----ATTACCTCAACGTGTCTTGAGGCTCAACTCATTTCTCGCAATATGAG
11136837 TTGAATTTTGAAAA
59 TTGAATTTTGAAAA
11136851 CAGAAATTGAAATTACCTCAACGTGTCTTGAGGCTCAACTCATTTCTCGCAATATGAGTTGAATT
1 CAGAAATTGAAATTACCTCAACGTGTCTTGAGGCTCAACTCATTTCTCGCAATATGAGTTGAATT
11136916 TTGAAAA
66 TTGAAAA
* *
11136923 GCAGAAATTGAAA-TA-CTCAGCGTGTCCTGAGGCTCAACTCATTTCTCGCAATAT-AGTTG-AT
1 -CAGAAATTGAAATTACCTCAACGTGTCTTGAGGCTCAACTCATTTCTCGCAATATGAGTTGAAT
11136984 TTTG-AAA
65 TTTGAAAA
* *
11136991 -A-AAATT-AAATTA-CTCAGCGTGTC-TGAGGCTCAACTCATTTCTCGCAATATGAGTTGATTT
1 CAGAAATTGAAATTACCTCAACGTGTCTTGAGGCTCAACTCATTTCTCGCAATATGAGTTGAATT
*
11137051 TTTAACAA
66 TTGAA-AA
* * * ** * *
11137059 CAGAAATTAAAATTACCTCAGCGTGTCCTGAGGCTCAACTCACCTCTAGCAATATGAATTG-ATT
1 CAGAAATTGAAATTACCTCAACGTGTCTTGAGGCTCAACTCATTTCTCGCAATATGAGTTGAATT
11137123 TTGAAAA
66 TTGAAAA
*
11137130 CATAAATT
1 CAGAAATT
11137138 AAAAGGCTTA
Statistics
Matches: 1488, Mismatches: 110, Indels: 146
0.85 0.06 0.08
Matches are distributed among these distances:
64 30 0.02
65 23 0.02
66 5 0.00
67 1 0.00
68 61 0.04
69 61 0.04
70 152 0.10
71 282 0.19
72 568 0.38
73 187 0.13
74 7 0.00
75 5 0.00
76 2 0.00
77 4 0.00
78 6 0.00
79 13 0.01
80 7 0.00
81 1 0.00
82 4 0.00
83 4 0.00
84 10 0.01
85 12 0.01
86 11 0.01
87 20 0.01
88 6 0.00
89 6 0.00
ACGTcount: A:0.35, C:0.18, G:0.17, T:0.31
Consensus pattern (72 bp):
CAGAAATTGAAATTACCTCAACGTGTCTTGAGGCTCAACTCATTTCTCGCAATATGAGTTGAATT
TTGAAAA
Found at i:11136247 original size:1 final size:1
Alignment explanation
Indices: 11136241--11136272 Score: 64
Period size: 1 Copynumber: 32.0 Consensus size: 1
11136231 AATATGATTG
11136241 AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA
1 AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA
11136273 TTGAAAATAC
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
1 31 1.00
ACGTcount: A:1.00, C:0.00, G:0.00, T:0.00
Consensus pattern (1 bp):
A
Found at i:11136717 original size:13 final size:15
Alignment explanation
Indices: 11136680--11136719 Score: 50
Period size: 14 Copynumber: 2.9 Consensus size: 15
11136670 CAATATGAGT
*
11136680 TGAATTTTG-AAACA
1 TGAATATTGAAAACA
11136694 TGAATATTGAAAACA
1 TGAATATTGAAAACA
11136709 -GAA-ATTGAAAA
1 TGAATATTGAAAA
11136720 TACCTCAACG
Statistics
Matches: 24, Mismatches: 1, Indels: 3
0.86 0.04 0.11
Matches are distributed among these distances:
13 8 0.33
14 11 0.46
15 5 0.21
ACGTcount: A:0.53, C:0.05, G:0.15, T:0.28
Consensus pattern (15 bp):
TGAATATTGAAAACA
Found at i:11136753 original size:86 final size:87
Alignment explanation
Indices: 11136608--11136790 Score: 327
Period size: 86 Copynumber: 2.1 Consensus size: 87
11136598 CAATATGAGT
* *
11136608 TGAATTTTGAAAACAGAAATTGAAATTACCTCAACGTGTCTTGAGGCTCAACTCATTTCTCGCAA
1 TGAATATTGAAAACAGAAATTGAAAATACCTCAACGTGTCTTGAGGCTCAACTCATTTCTCGCAA
11136673 TATGAGTTGAATTTTG-AAACA
66 TATGAGTTGAATTTTGAAAACA
11136694 TGAATATTGAAAACAGAAATTGAAAATACCTCAACGTGTCTTGAGGCTCAACTCATTTCTCGCAA
1 TGAATATTGAAAACAGAAATTGAAAATACCTCAACGTGTCTTGAGGCTCAACTCATTTCTCGCAA
11136759 TATGAGTTGAATTTTGAAAACA
66 TATGAGTTGAATTTTGAAAACA
11136781 -GAA-ATTGAAA
1 TGAATATTGAAA
11136791 TTACCTCAAC
Statistics
Matches: 94, Mismatches: 2, Indels: 3
0.95 0.02 0.03
Matches are distributed among these distances:
85 7 0.07
86 82 0.87
87 5 0.05
ACGTcount: A:0.38, C:0.15, G:0.16, T:0.31
Consensus pattern (87 bp):
TGAATATTGAAAACAGAAATTGAAAATACCTCAACGTGTCTTGAGGCTCAACTCATTTCTCGCAA
TATGAGTTGAATTTTGAAAACA
Found at i:11136835 original size:441 final size:442
Alignment explanation
Indices: 11135303--11137138 Score: 2858
Period size: 441 Copynumber: 4.2 Consensus size: 442
11135293 ACAGAAATTA
* ** * * * ** *
11135303 AAAACAGAATTTGAAAAGACCTCAGCGTGTGGCCTGAGACTCAACTCACCTCTTGCAATATGAGT
1 AAAACAGAAATTGAAATTACCTCAACGTGT--CTTGAGGCTCAACTCATTTCTCGCAATATGA-T
* * *
11135368 TGATTTGAAAAAGTAGAATTAGTAAAGCAGAAATTGAAAATACCTCAGCGTGCCTTGAGGCTCAA
63 TGATTTGAAAAA-T-GAATTAG-AAAACAGAAATTGAAAATACCTCAACGTGTCTTGAGGCTCAA
* * *
11135433 CTCATCTCTCGCAATATGAGTT-AAGTTTTGAAAAGCAGAAATTGAAAATACCTCAATGTGTCTT
125 CTCATTTCTCGCAATATGAGTTGAA-TTTTGAAAA-CAGAAATTGAAATTACCTCAACGTGTCTT
11135497 GAGGCTCAACTCATTTCTCGCAATATGAGTTGAATTTTGAAAACAGAAATTGAAATTACCTCAAC
188 GAGGCTCAACTCATTTCTCGCAATATGAGTTGAATTTTGAAAACAGAAATTGAAATTACCTCAAC
*
11135562 GTGTCTTGAGGCTCAACTCATTTCTCGCAATATGAGTTGAATTTTGAGAAGCAGAAATTGAAAAT
253 GTGTCTTGAGGCTCAACTCATTTCTCGCAATATGAGTTGAATTTTGAAAAGCAGAAATTGAAAAT
11135627 ACCTCAACGTGTCTTGAGGCTCAACTCATTTCTCGCAATATGAGTTGAATTTTGAAAACAGAAAT
318 ACCTCAACGTGTCTTGAGGCTCAACTCATTTCTCGCAATATGAGTTGAATTTTG-AAACAGAAAT
11135692 TGAAATTACCTCAACGTGTCTTGAGGCTCAACTCATTTCTCGCAATATGAGTTGAATTTTG
382 TGAAATTACCTCAACGTGTCTTGAGGCTCAACTCATTTCTCGCAATATGAGTTGAATTTTG
11135753 AAAACAGAAATTGAAATTACCTCAACGTGTCTTGAGGCTCAACTCATTTCTCGCAATATGA--G-
1 AAAACAGAAATTGAAATTACCTCAACGTGTCTTGAGGCTCAACTCATTTCTCGCAATATGATTGA
*
11135815 -TTG---AAT---TTTG-AAACAGAAATTG-AAATACCTCAACGTGTCTTGAGGCTCAACTCATT
66 TTTGAAAAATGAATTAGAAAACAGAAATTGAAAATACCTCAACGTGTCTTGAGGCTCAACTCATT
11135871 TCTCGCAATATGAGTTGAATTTTGAAAACAGAAATTGAAATTACCTCAACGTGTCTTGAGGCTCA
131 TCTCGCAATATGAGTTGAATTTTGAAAACAGAAATTGAAATTACCTCAACGTGTCTTGAGGCTCA
11135936 ACTCATTTCTCGCAATATGAGTTGAATTTTGAAAACAGAAATTGAAA-TACCTCAACGTGTCTTG
196 ACTCATTTCTCGCAATATGAGTTGAATTTTGAAAACAGAAATTGAAATTACCTCAACGTGTCTTG
11136000 AGGCTCAACTCATTTCTCGCAATATGAGTTGAATTTTG-AAAGCAGAAATTGAAAATACCTC-AC
261 AGGCTCAACTCATTTCTCGCAATATGAGTTGAATTTTGAAAAGCAGAAATTGAAAATACCTCAAC
*
11136063 GTGTC-TGAGGCTCAACTCATTTCTCGCAATATGAGTTGAATTTTGAAACAGAAATTGAAAATAC
326 GTGTCTTGAGGCTCAACTCATTTCTCGCAATATGAGTTGAATTTTGAAACAGAAATTGAAATTAC
11136127 CTCAACGTGTCTTGAGGCTCAACTCATTTCTCGCAATATGAGTTGAATTTTG
391 CTCAACGTGTCTTGAGGCTCAACTCATTTCTCGCAATATGAGTTGAATTTTG
11136179 AAAACAGAAATTGAAATTACCTCAACGTGTCTTGAGGCTCAAC-CATTTC-CGCAATATGATTGA
1 AAAACAGAAATTGAAATTACCTCAACGTGTCTTGAGGCTCAACTCATTTCTCGCAATATGATTG-
**** ** ** * * *
11136242 AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAATTGAAAATACCTC-ACGTGTCTTGAGGCTCAACT
65 ---ATTTGAAAAATGAATTAGAAAACAGAAATTGAAAATACCTCAACGTGTCTTGAGGCTCAACT
11136306 CATTTCTCGCAATATGAGTTGAATTTTGAAAACAGAAATTGAAATTACCTCAACGTGTCTTGAGG
127 CATTTCTCGCAATATGAGTTGAATTTTGAAAACAGAAATTGAAATTACCTCAACGTGTCTTGAGG
11136371 CTCAACTCATTTCTCGCAATATGAGTTGAATTTTGAAAACAGAAATTGAAATTACCTCAACGTGT
192 CTCAACTCATTTCTCGCAATATGAGTTGAATTTTGAAAACAGAAATTGAAATTACCTCAACGTGT
11136436 CTTGAGGCTCAACTCATTTCTCGCAATATGAGTTG-ATTTTGAAAAGCAGAAATTG-AAATACCT
257 CTTGAGGCTCAACTCATTTCTCGCAATATGAGTTGAATTTTGAAAAGCAGAAATTGAAAATACCT
11136499 CAACGTGTCTTGAGGCTCAACTCATTTCTCGCAATATGAGTTGAATTTTGAAACAGAAATTGAAA
322 CAACGTGTCTTGAGGCTCAACTCATTTCTCGCAATATGAGTTGAATTTTGAAACAGAAATTGAAA
11136564 -TACCTC-ACGTGTC-TGAGGCTCAACTCATTTCTCGCAATATGAGTTGAATTTTG
387 TTACCTCAACGTGTCTTGAGGCTCAACTCATTTCTCGCAATATGAGTTGAATTTTG
11136617 AAAACAGAAATTGAAATTACCTCAACGTGTCTTGAGGCTCAACTCATTTCTCGCAATATGAGTTG
1 AAAACAGAAATTGAAATTACCTCAACGTGTCTTGAGGCTCAACTCATTTCTCGCAATATGA-TTG
* *
11136682 AATTTTGAAACATGAATATTGAAAACAGAAATTGAAAATACCTCAACGTGTCTTGAGGCTCAACT
65 -A-TTTGAAAAATGAAT-TAGAAAACAGAAATTGAAAATACCTCAACGTGTCTTGAGGCTCAACT
11136747 CATTTCTCGCAATATGAGTTGAATTTTGAAAACAGAAATTGAAATTACCTCAACGTGTCTTGAGG
127 CATTTCTCGCAATATGAGTTGAATTTTGAAAACAGAAATTGAAATTACCTCAACGTGTCTTGAGG
11136812 CTCAACTCATTTCTCGCAATATGAGTTGAATTTTGAAAACAGAAATTGAAATTACCTCAACGTGT
192 CTCAACTCATTTCTCGCAATATGAGTTGAATTTTGAAAACAGAAATTGAAATTACCTCAACGTGT
11136877 CTTGAGGCTCAACTCATTTCTCGCAATATGAGTTGAATTTTGAAAAGCAGAAATTG-AAATA-CT
257 CTTGAGGCTCAACTCATTTCTCGCAATATGAGTTGAATTTTGAAAAGCAGAAATTGAAAATACCT
* *
11136940 CAGCGTGTCCTGAGGCTCAACTCATTTCTCGCAATAT-AGTTG-ATTTTGAAA-A-AAATT-AAA
322 CAACGTGTCTTGAGGCTCAACTCATTTCTCGCAATATGAGTTGAATTTTGAAACAGAAATTGAAA
* * *
11137000 TTA-CTCAGCGTGTC-TGAGGCTCAACTCATTTCTCGCAATATGAGTTGATTTTTT
387 TTACCTCAACGTGTCTTGAGGCTCAACTCATTTCTCGCAATATGAGTTGAATTTTG
* * * ** *
11137054 AACAACAGAAATTAAAATTACCTCAGCGTGTCCTGAGGCTCAACTCACCTCTAGCAATATGAATT
1 AA-AACAGAAATTGAAATTACCTCAACGTGTCTTGAGGCTCAACTCATTTCTCGCAATATG-ATT
*
11137119 GATTTTGAAAACATAAATTA
64 GA-TTTGAAAA-ATGAATTA
11137139 AAAGGCTTAA
Statistics
Matches: 1298, Mismatches: 55, Indels: 79
0.91 0.04 0.06
Matches are distributed among these distances:
424 10 0.01
425 6 0.00
426 114 0.09
427 40 0.03
428 7 0.01
429 22 0.02
430 55 0.04
431 82 0.06
432 56 0.04
433 13 0.01
435 5 0.00
436 6 0.00
437 63 0.05
438 146 0.11
439 191 0.15
440 121 0.09
441 280 0.22
442 25 0.02
443 3 0.00
445 1 0.00
448 26 0.02
450 26 0.02
ACGTcount: A:0.35, C:0.18, G:0.17, T:0.30
Consensus pattern (442 bp):
AAAACAGAAATTGAAATTACCTCAACGTGTCTTGAGGCTCAACTCATTTCTCGCAATATGATTGA
TTTGAAAAATGAATTAGAAAACAGAAATTGAAAATACCTCAACGTGTCTTGAGGCTCAACTCATT
TCTCGCAATATGAGTTGAATTTTGAAAACAGAAATTGAAATTACCTCAACGTGTCTTGAGGCTCA
ACTCATTTCTCGCAATATGAGTTGAATTTTGAAAACAGAAATTGAAATTACCTCAACGTGTCTTG
AGGCTCAACTCATTTCTCGCAATATGAGTTGAATTTTGAAAAGCAGAAATTGAAAATACCTCAAC
GTGTCTTGAGGCTCAACTCATTTCTCGCAATATGAGTTGAATTTTGAAACAGAAATTGAAATTAC
CTCAACGTGTCTTGAGGCTCAACTCATTTCTCGCAATATGAGTTGAATTTTG
Done.