Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: At_chr12
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: 101062743
ACGTcount: A:0.31, C:0.17, G:0.17, T:0.31
Warning! 4026412 characters in sequence are not A, C, G, or T
File 79 of 297
Found at i:28220931 original size:24 final size:24
Alignment explanation
Indices: 28220695--28220931 Score: 149
Period size: 24 Copynumber: 10.0 Consensus size: 24
28220685 AAAATTATTT
*
28220695 TTTTCTTT-TTT-TTCCTTCCTTCCC
1 TTTTCTTTCTTTCTT-CTT-CTTTCC
* *
28220719 TTTT-TTTTTTCTCTTCTCCTTTCC
1 TTTTCTTTCTT-TCTTCTTCTTTCC
* *
28220743 TTTT-TTT-TTCTCTTCTCCTTTCT
1 TTTTCTTTCTT-TCTTCTTCTTTCC
* * *
28220766 TTTTCTTTCCTTCTTTTTCTTTCTT
1 TTTTCTTTCTTTCTTCTTCTTTC-C
* *
28220791 TTTTCTTCTTTTTCTTCTCCTTTCC
1 TTTTCTT-TCTTTCTTCTTCTTTCC
* * *
28220816 TTTTCTTTCCTTCTTTTTCTTTCA
1 TTTTCTTTCTTTCTTCTTCTTTCC
28220840 TTTT-TCTTC-TTCTTCTTCTTCTCC
1 TTTTCT-TTCTTTCTTCTTCTT-TCC
*
28220864 TTTCCTTTCCTTTC--C-T-TTT-C
1 TTTTCTTT-CTTTCTTCTTCTTTCC
* *
28220884 TTCTT-TTTCTTTCCTCTCCTTTCC
1 TT-TTCTTTCTTTCTTCTTCTTTCC
28220908 TTTTCTTTCTTTCTTCTTCTTTCC
1 TTTTCTTTCTTTCTTCTTCTTTCC
28220932 CTCTCTTCTC
Statistics
Matches: 171, Mismatches: 23, Indels: 38
0.74 0.10 0.16
Matches are distributed among these distances:
19 5 0.03
20 6 0.04
21 3 0.02
22 2 0.01
23 39 0.23
24 78 0.46
25 21 0.12
26 17 0.10
ACGTcount: A:0.00, C:0.30, G:0.00, T:0.69
Consensus pattern (24 bp):
TTTTCTTTCTTTCTTCTTCTTTCC
Found at i:28225256 original size:12 final size:12
Alignment explanation
Indices: 28225239--28225263 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
28225229 GGTGTTCATT
28225239 CGGTTAACCGAC
1 CGGTTAACCGAC
28225251 CGGTTAACCGAC
1 CGGTTAACCGAC
28225263 C
1 C
28225264 CGAAATTACT
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:0.24, C:0.36, G:0.24, T:0.16
Consensus pattern (12 bp):
CGGTTAACCGAC
Found at i:28225436 original size:9 final size:9
Alignment explanation
Indices: 28225423--28225465 Score: 59
Period size: 9 Copynumber: 4.8 Consensus size: 9
28225413 TTTGGTTAAA
*
28225423 AATTACCCA
1 AATTACCCG
28225432 AATTACCCG
1 AATTACCCG
*
28225441 AATTAACCG
1 AATTACCCG
*
28225450 AATTAACCG
1 AATTACCCG
28225459 AATTACC
1 AATTACC
28225466 GAAAAATACC
Statistics
Matches: 31, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
9 31 1.00
ACGTcount: A:0.42, C:0.28, G:0.07, T:0.23
Consensus pattern (9 bp):
AATTACCCG
Found at i:28225599 original size:21 final size:21
Alignment explanation
Indices: 28225569--28225608 Score: 55
Period size: 21 Copynumber: 1.9 Consensus size: 21
28225559 GACTCCACTG
*
28225569 TTGAGGAAGGAACAA-AATGGC
1 TTGAGCAAGG-ACAAGAATGGC
28225590 TTGAGCAAGGACAAGAATG
1 TTGAGCAAGGACAAGAATG
28225609 ATGAAGCAAA
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
20 4 0.24
21 13 0.76
ACGTcount: A:0.42, C:0.10, G:0.33, T:0.15
Consensus pattern (21 bp):
TTGAGCAAGGACAAGAATGGC
Found at i:28227098 original size:20 final size:20
Alignment explanation
Indices: 28227073--28227112 Score: 62
Period size: 20 Copynumber: 2.0 Consensus size: 20
28227063 CGTAAAATGA
*
28227073 TTTCTGGAAAATGTTTTACT
1 TTTCTGGAAAATGATTTACT
*
28227093 TTTCTGTAAAATGATTTACT
1 TTTCTGGAAAATGATTTACT
28227113 GGAAAATATT
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
20 18 1.00
ACGTcount: A:0.28, C:0.10, G:0.12, T:0.50
Consensus pattern (20 bp):
TTTCTGGAAAATGATTTACT
Found at i:28227102 original size:34 final size:35
Alignment explanation
Indices: 28227058--28227124 Score: 109
Period size: 34 Copynumber: 1.9 Consensus size: 35
28227048 CAGTAAAATA
*
28227058 TTTTCCGTAAAATGATTT-CTGGAAAATGTTTTAC
1 TTTTCCGTAAAATGATTTACTGGAAAATATTTTAC
*
28227092 TTTTCTGTAAAATGATTTACTGGAAAATATTTT
1 TTTTCCGTAAAATGATTTACTGGAAAATATTTT
28227125 CTGGTGTTTG
Statistics
Matches: 30, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
34 17 0.57
35 13 0.43
ACGTcount: A:0.31, C:0.09, G:0.13, T:0.46
Consensus pattern (35 bp):
TTTTCCGTAAAATGATTTACTGGAAAATATTTTAC
Found at i:28227128 original size:14 final size:15
Alignment explanation
Indices: 28227052--28227128 Score: 52
Period size: 14 Copynumber: 5.0 Consensus size: 15
28227042 GATTGCCAGT
* *
28227052 AAAAT-ATTTTCCGT
1 AAAATGATTTTCTGG
28227066 AAAATGA-TTTCTGG
1 AAAATGATTTTCTGG
*
28227080 AAAATGTTTTACTTTTCTGT
1 AAAATG----A-TTTTCTGG
*
28227100 AAAATGATTTACTGG
1 AAAATGATTTTCTGG
28227115 AAAAT-ATTTTCTGG
1 AAAATGATTTTCTGG
28227129 TGTTTGATTG
Statistics
Matches: 50, Mismatches: 6, Indels: 14
0.71 0.09 0.20
Matches are distributed among these distances:
14 24 0.48
15 12 0.24
16 1 0.02
18 1 0.02
20 12 0.24
ACGTcount: A:0.34, C:0.09, G:0.14, T:0.43
Consensus pattern (15 bp):
AAAATGATTTTCTGG
Found at i:28228607 original size:41 final size:41
Alignment explanation
Indices: 28228560--28228697 Score: 136
Period size: 41 Copynumber: 3.3 Consensus size: 41
28228550 GGTATAACAA
*
28228560 CAATAGCGGTGTTTTTCCCATAAATGCCACAAAAGGTAAAG
1 CAATAGCGGCGTTTTTCCCATAAATGCCACAAAAGGTAAAG
* * * * * *
28228601 CAATAGCAGCATTTTT-GCATAAACGCTGA-AAAAGGTTAAAAA
1 CAATAGCGGCGTTTTTCCCATAAATGC-CACAAAAGG-T-AAAG
* * * *
28228643 CGATAGCGGCGTTTTTCTCACAAATGCCACTAAAGGTAAAG
1 CAATAGCGGCGTTTTTCCCATAAATGCCACAAAAGGTAAAG
28228684 CAATAGCGGCGTTT
1 CAATAGCGGCGTTT
28228698 CGCCTATAAA
Statistics
Matches: 75, Mismatches: 17, Indels: 10
0.74 0.17 0.10
Matches are distributed among these distances:
40 14 0.19
41 31 0.41
42 18 0.24
43 12 0.16
ACGTcount: A:0.36, C:0.19, G:0.20, T:0.25
Consensus pattern (41 bp):
CAATAGCGGCGTTTTTCCCATAAATGCCACAAAAGGTAAAG
Found at i:28228851 original size:26 final size:25
Alignment explanation
Indices: 28228787--28228842 Score: 94
Period size: 25 Copynumber: 2.2 Consensus size: 25
28228777 CTTAAAATCG
* *
28228787 TTTTCCCTAAATCCTTAACTTAGTT
1 TTTTCCCCAAATCCCTAACTTAGTT
28228812 TTTTCCCCAAATCCCTAACTTAGTT
1 TTTTCCCCAAATCCCTAACTTAGTT
28228837 TTTTCC
1 TTTTCC
28228843 TTCCCATCCG
Statistics
Matches: 29, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
25 29 1.00
ACGTcount: A:0.21, C:0.29, G:0.04, T:0.46
Consensus pattern (25 bp):
TTTTCCCCAAATCCCTAACTTAGTT
Found at i:28236039 original size:25 final size:24
Alignment explanation
Indices: 28236003--28236055 Score: 72
Period size: 25 Copynumber: 2.2 Consensus size: 24
28235993 ACATACTGCA
28236003 GCTCTTTATGAG-TGTCCTGATATAG
1 GCTCTTTATGAGCT-TCCTGATAT-G
*
28236028 GCTCTTTGTGAGCTTCCTGATATG
1 GCTCTTTATGAGCTTCCTGATATG
28236052 GCTC
1 GCTC
28236056 ACTTGAACTT
Statistics
Matches: 26, Mismatches: 1, Indels: 3
0.87 0.03 0.10
Matches are distributed among these distances:
24 5 0.19
25 20 0.77
26 1 0.04
ACGTcount: A:0.15, C:0.21, G:0.25, T:0.40
Consensus pattern (24 bp):
GCTCTTTATGAGCTTCCTGATATG
Found at i:28236197 original size:25 final size:25
Alignment explanation
Indices: 28236169--28236223 Score: 58
Period size: 25 Copynumber: 2.2 Consensus size: 25
28236159 TCCTATTATT
* *
28236169 GCTCGGATAAGC-TTCATGTTATATG
1 GCTCGCATAAGCATTC-TGTTATATA
* *
28236194 GCTCACATGAGCATTCTGTTATATA
1 GCTCGCATAAGCATTCTGTTATATA
28236219 GCTCG
1 GCTCG
28236224 AGAGAGTGCT
Statistics
Matches: 24, Mismatches: 5, Indels: 2
0.77 0.16 0.06
Matches are distributed among these distances:
25 21 0.88
26 3 0.12
ACGTcount: A:0.24, C:0.20, G:0.22, T:0.35
Consensus pattern (25 bp):
GCTCGCATAAGCATTCTGTTATATA
Found at i:28242583 original size:25 final size:25
Alignment explanation
Indices: 28242555--28242741 Score: 132
Period size: 25 Copynumber: 7.5 Consensus size: 25
28242545 AATTATCTAG
* * *
28242555 AAAGCTTTTATGGCTAATCTTATGA
1 AAAGCCTTTGTGGCTATTCTTATGA
* * *
28242580 AAAGACTTTGTGGCGTATTGTT-TGG
1 AAAGCCTTTGTGGC-TATTCTTATGA
* * *
28242605 AAAGTCTTTGTAGTG-TATTC-TCTGG
1 AAAGCCTTTGT-G-GCTATTCTTATGA
* * *
28242630 AAAGCCTTTGTGACTAATCTTATGG
1 AAAGCCTTTGTGGCTATTCTTATGA
*
28242655 AAAGCCTTTGTGGCGTATTGTCTA-G-
1 AAAGCCTTTGTGGC-TATTCT-TATGA
*
28242680 AAAGCTTTTGTGGCTATTCTTATGA
1 AAAGCCTTTGTGGCTATTCTTATGA
* *
28242705 AAAGCCTTTGTGGCTAATCTTACGA
1 AAAGCCTTTGTGGCTATTCTTATGA
* *
28242730 AAAACCCTTGTG
1 AAAGCCTTTGTG
28242742 TCATATTGTA
Statistics
Matches: 130, Mismatches: 22, Indels: 20
0.76 0.13 0.12
Matches are distributed among these distances:
23 2 0.02
24 12 0.09
25 102 0.78
26 11 0.08
27 3 0.02
ACGTcount: A:0.25, C:0.14, G:0.22, T:0.38
Consensus pattern (25 bp):
AAAGCCTTTGTGGCTATTCTTATGA
Found at i:28242683 original size:75 final size:75
Alignment explanation
Indices: 28242554--28242732 Score: 220
Period size: 75 Copynumber: 2.4 Consensus size: 75
28242544 GAATTATCTA
* * * *
28242554 GAAAGCTTTTATGGCTAATCTTATGAAAAGACTTTGTGGCGTATTGTTTGGAAAG-TCTTTGTAG
1 GAAAGCCTTTGTGGCTAATCTTATGAAAAGACTTTGTGGCGTATTGTCTAGAAAGCT-TTTGT-G
*
28242618 TG-TATTC-TCTG
64 -GCTATTCTTATG
* * *
28242629 GAAAGCCTTTGTGACTAATCTTATGGAAAGCCTTTGTGGCGTATTGTCTAGAAAGCTTTTGTGGC
1 GAAAGCCTTTGTGGCTAATCTTATGAAAAGACTTTGTGGCGTATTGTCTAGAAAGCTTTTGTGGC
28242694 TATTCTTATG
66 TATTCTTATG
* *
28242704 AAAAGCCTTTGTGGCTAATCTTACGAAAA
1 GAAAGCCTTTGTGGCTAATCTTATGAAAA
28242733 ACCCTTGTGT
Statistics
Matches: 89, Mismatches: 12, Indels: 6
0.83 0.11 0.06
Matches are distributed among these distances:
73 1 0.01
74 6 0.07
75 81 0.91
76 1 0.01
ACGTcount: A:0.26, C:0.13, G:0.23, T:0.38
Consensus pattern (75 bp):
GAAAGCCTTTGTGGCTAATCTTATGAAAAGACTTTGTGGCGTATTGTCTAGAAAGCTTTTGTGGC
TATTCTTATG
Found at i:28242716 original size:50 final size:50
Alignment explanation
Indices: 28242580--28242718 Score: 163
Period size: 50 Copynumber: 2.8 Consensus size: 50
28242570 AATCTTATGA
* * * * * *
28242580 AAAGACTTTGTGGCGTATTGTT-TGGAAAGTCTTTGTAGTGTATTCTCTGG
1 AAAGCCTTTGTGGC-TATTCTTATGGAAAGCCTTTGTGGCGTATTCTCTAG
* * *
28242630 AAAGCCTTTGTGACTAATCTTATGGAAAGCCTTTGTGGCGTATTGTCTAG
1 AAAGCCTTTGTGGCTATTCTTATGGAAAGCCTTTGTGGCGTATTCTCTAG
* *
28242680 AAAGCTTTTGTGGCTATTCTTATGAAAAGCCTTTGTGGC
1 AAAGCCTTTGTGGCTATTCTTATGGAAAGCCTTTGTGGC
28242719 TAATCTTACG
Statistics
Matches: 75, Mismatches: 13, Indels: 2
0.83 0.14 0.02
Matches are distributed among these distances:
49 5 0.07
50 70 0.93
ACGTcount: A:0.22, C:0.14, G:0.25, T:0.39
Consensus pattern (50 bp):
AAAGCCTTTGTGGCTATTCTTATGGAAAGCCTTTGTGGCGTATTCTCTAG
Found at i:28242758 original size:75 final size:75
Alignment explanation
Indices: 28242555--28242758 Score: 218
Period size: 75 Copynumber: 2.7 Consensus size: 75
28242545 AATTATCTAG
* * *
28242555 AAAGCTTTTATGGCTAATCTTATGAAAAGA-CTTTGTGGCGTATTGTTTGGAAAGTCTTTGTAGT
1 AAAGCCTTTGTGGCTAATCTTATGAAAA-ACCTTTGTGGCGTATTGTATGGAAAGTCTTTGTAGT
* *
28242619 GTATTCTCTGG
65 GTATTCTATGA
* * * * *
28242630 AAAGCCTTTGTGACTAATCTTATGGAAAGCCTTTGTGGCGTATTGTCTAGAAAG-CTTT-T-GTG
1 AAAGCCTTTGTGGCTAATCTTATGAAAAACCTTTGTGGCGTATTGTATGGAAAGTCTTTGTAGT-
28242692 GCTATTCTTATGA
65 G-TATTC-TATGA
* * * *
28242705 AAAGCCTTTGTGGCTAATCTTACGAAAAACCCTTGTGTCATATTGTATGGAAAG
1 AAAGCCTTTGTGGCTAATCTTATGAAAAACCTTTGTGGCGTATTGTATGGAAAG
28242759 ACTGTATGAT
Statistics
Matches: 107, Mismatches: 18, Indels: 8
0.80 0.14 0.06
Matches are distributed among these distances:
72 2 0.02
73 2 0.02
74 9 0.08
75 94 0.88
ACGTcount: A:0.26, C:0.14, G:0.23, T:0.38
Consensus pattern (75 bp):
AAAGCCTTTGTGGCTAATCTTATGAAAAACCTTTGTGGCGTATTGTATGGAAAGTCTTTGTAGTG
TATTCTATGA
Found at i:28243040 original size:70 final size:70
Alignment explanation
Indices: 28242927--28243065 Score: 251
Period size: 70 Copynumber: 2.0 Consensus size: 70
28242917 CTCGAAACAC
* * *
28242927 AATTTCAAACAACTTCATTATTTCAACCAAATACAATTATATGTTCAGACGCAATTTATCTATCC
1 AATTTCAAAAAACTTCAATATTTCAACCAAATACAATTATATGTTCAGACACAATTTATCTATCC
28242992 ACAAT
66 ACAAT
28242997 AATTTCAAAAAACTTCAATATTTCAACCAAATACAATTATATGTTCAGACACAATTTATCTATCC
1 AATTTCAAAAAACTTCAATATTTCAACCAAATACAATTATATGTTCAGACACAATTTATCTATCC
28243062 ACAA
66 ACAA
28243066 CATTCTAATT
Statistics
Matches: 66, Mismatches: 3, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
70 66 1.00
ACGTcount: A:0.42, C:0.21, G:0.04, T:0.33
Consensus pattern (70 bp):
AATTTCAAAAAACTTCAATATTTCAACCAAATACAATTATATGTTCAGACACAATTTATCTATCC
ACAAT
Found at i:28244242 original size:50 final size:50
Alignment explanation
Indices: 28244183--28244470 Score: 283
Period size: 51 Copynumber: 5.7 Consensus size: 50
28244173 TTTTATCATT
* * * * *
28244183 CGATACACGTAGTAGCCTTCATATAGCACTACACACATGATCAAGTTTTA
1 CGATTCACGTAGTAGCCTTCACATAGTACTACACACGTGACCAAGTTTTA
* * * *
28244233 CGATTCACGTAGTAGCCTTCACATAATACTACATATGTGATCAAGTTTTA
1 CGATTCACGTAGTAGCCTTCACATAGTACTACACACGTGACCAAGTTTTA
* *
28244283 CGGTTCACGTAGTAGCCTTCACATAGTACTACATACGTGACCAAAGCTTTT-
1 CGATTCACGTAGTAGCCTTCACATAGTACTACACACGTGACC-AAG-TTTTA
* * * * * ***
28244334 CGGTACACATAGTAGCCTTCACTTAGTACTACACATGTGACCATCATTTA
1 CGATTCACGTAGTAGCCTTCACATAGTACTACACACGTGACCAAGTTTTA
* *
28244384 CCGATTCACGTAGTAGCCTTCACACAGTACTACACACGTGACCAAAGCTTCT-
1 -CGATTCACGTAGTAGCCTTCACATAGTACTACACACGTGACC-AAG-TTTTA
* * * * *
28244436 CGGTACACATTGTAGCCTTCACACAGTACTACACA
1 CGATTCACGTAGTAGCCTTCACATAGTACTACACA
28244471 AGTGTTCATC
Statistics
Matches: 199, Mismatches: 33, Indels: 11
0.82 0.14 0.05
Matches are distributed among these distances:
49 3 0.02
50 82 0.41
51 107 0.54
52 5 0.03
53 2 0.01
ACGTcount: A:0.31, C:0.26, G:0.15, T:0.28
Consensus pattern (50 bp):
CGATTCACGTAGTAGCCTTCACATAGTACTACACACGTGACCAAGTTTTA
Found at i:28244423 original size:102 final size:101
Alignment explanation
Indices: 28244183--28244470 Score: 355
Period size: 102 Copynumber: 2.9 Consensus size: 101
28244173 TTTTATCATT
* * * * * * * *
28244183 CGATACACGTAGTAGCCTTCATATAGCACTACACACATGATC-AAG-TTTTACGATTCACGTAGT
1 CGATTCACGTAGTAGCCTTCACATAGTACTACACACGTGACCAAAGCTTTT-CGGTACACATAGT
* * * **
28244246 AGCCTTCACATAATACTACATATGTGATCAAGTTTTA
65 AGCCTTCACATAGTACTACACATGTGACCAACATTTA
* *
28244283 CGGTTCACGTAGTAGCCTTCACATAGTACTACATACGTGACCAAAGCTTTTCGGTACACATAGTA
1 CGATTCACGTAGTAGCCTTCACATAGTACTACACACGTGACCAAAGCTTTTCGGTACACATAGTA
* *
28244348 GCCTTCACTTAGTACTACACATGTGACCATCATTTA
66 GCCTTCACATAGTACTACACATGTGACCAACATTTA
* * *
28244384 CCGATTCACGTAGTAGCCTTCACACAGTACTACACACGTGACCAAAGCTTCTCGGTACACATTGT
1 -CGATTCACGTAGTAGCCTTCACATAGTACTACACACGTGACCAAAGCTTTTCGGTACACATAGT
*
28244449 AGCCTTCACACAGTACTACACA
65 AGCCTTCACATAGTACTACACA
28244471 AGTGTTCATC
Statistics
Matches: 161, Mismatches: 24, Indels: 4
0.85 0.13 0.02
Matches are distributed among these distances:
100 35 0.22
101 43 0.27
102 83 0.52
ACGTcount: A:0.31, C:0.26, G:0.15, T:0.28
Consensus pattern (101 bp):
CGATTCACGTAGTAGCCTTCACATAGTACTACACACGTGACCAAAGCTTTTCGGTACACATAGTA
GCCTTCACATAGTACTACACATGTGACCAACATTTA
Found at i:28247644 original size:27 final size:27
Alignment explanation
Indices: 28247613--28247669 Score: 105
Period size: 27 Copynumber: 2.1 Consensus size: 27
28247603 GTAAATTATA
28247613 AACTCTTTCCCTGACTCAGGTTATACC
1 AACTCTTTCCCTGACTCAGGTTATACC
*
28247640 AACTCTTTCCCTGACTCAGGTTGTACC
1 AACTCTTTCCCTGACTCAGGTTATACC
28247667 AAC
1 AAC
28247670 ACTGGCACCT
Statistics
Matches: 29, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
27 29 1.00
ACGTcount: A:0.23, C:0.33, G:0.12, T:0.32
Consensus pattern (27 bp):
AACTCTTTCCCTGACTCAGGTTATACC
Found at i:28251323 original size:43 final size:43
Alignment explanation
Indices: 28251200--28251323 Score: 153
Period size: 42 Copynumber: 2.9 Consensus size: 43
28251190 GCGCAGGAAA
* * *
28251200 AAACGCCGCTAAAGATCAT-AACCTTTAGTGGCGCTTTTACCAC
1 AAACGCCGCTAAAGAACATGAA-CTTTAGCGGCGCTTTTCCCAC
* * *
28251243 AAACGCCGCTAAAG-CCATGACCTTTAGCGGCGTTTTTCCCAC
1 AAACGCCGCTAAAGAACATGAACTTTAGCGGCGCTTTTCCCAC
* *
28251285 AAACGCCGCTAAAGAACATGAACTTTAACGGTGCTTTTC
1 AAACGCCGCTAAAGAACATGAACTTTAGCGGCGCTTTTC
28251324 GCTGCTAAAG
Statistics
Matches: 69, Mismatches: 10, Indels: 4
0.83 0.12 0.05
Matches are distributed among these distances:
42 35 0.51
43 34 0.49
ACGTcount: A:0.29, C:0.28, G:0.18, T:0.25
Consensus pattern (43 bp):
AAACGCCGCTAAAGAACATGAACTTTAGCGGCGCTTTTCCCAC
Found at i:28251450 original size:43 final size:42
Alignment explanation
Indices: 28251377--28251463 Score: 120
Period size: 43 Copynumber: 2.0 Consensus size: 42
28251367 TTTAAAAACT
* * * *
28251377 ATGACCTTTAGCGGCGCTTTCCCACTAACGCCGCTAAAGACC
1 ATGACCTTTAACGACACTTTCCCACAAACGCCGCTAAAGACC
*
28251419 ATGACCTTTAACGACACTTTTCCCACAAACGCCGTTAAAGACC
1 ATGACCTTTAACGACAC-TTTCCCACAAACGCCGCTAAAGACC
28251462 AT
1 AT
28251464 AATCTTTAGC
Statistics
Matches: 39, Mismatches: 5, Indels: 1
0.87 0.11 0.02
Matches are distributed among these distances:
42 14 0.36
43 25 0.64
ACGTcount: A:0.29, C:0.33, G:0.15, T:0.23
Consensus pattern (42 bp):
ATGACCTTTAACGACACTTTCCCACAAACGCCGCTAAAGACC
Found at i:28251557 original size:20 final size:20
Alignment explanation
Indices: 28251532--28251578 Score: 53
Period size: 20 Copynumber: 2.4 Consensus size: 20
28251522 TGAAAAAATA
28251532 TATTTTAATCGA-ATAATA-TT
1 TATTTTAAT-GATA-AATATTT
*
28251552 TATTTTTATGATAAATATTT
1 TATTTTAATGATAAATATTT
28251572 TATTTTA
1 TATTTTA
28251579 TTTTTTAAAT
Statistics
Matches: 23, Mismatches: 2, Indels: 4
0.79 0.07 0.14
Matches are distributed among these distances:
19 6 0.26
20 17 0.74
ACGTcount: A:0.36, C:0.02, G:0.04, T:0.57
Consensus pattern (20 bp):
TATTTTAATGATAAATATTT
Found at i:28256103 original size:13 final size:14
Alignment explanation
Indices: 28256082--28256115 Score: 52
Period size: 13 Copynumber: 2.5 Consensus size: 14
28256072 ACTGATTAAT
28256082 CTAAACCCTAA-CC
1 CTAAACCCTAAGCC
*
28256095 CTAAGCCCTAAGCC
1 CTAAACCCTAAGCC
28256109 CTAAACC
1 CTAAACC
28256116 TTATTTAATA
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
13 10 0.56
14 8 0.44
ACGTcount: A:0.35, C:0.44, G:0.06, T:0.15
Consensus pattern (14 bp):
CTAAACCCTAAGCC
Found at i:28256189 original size:21 final size:21
Alignment explanation
Indices: 28256178--28256219 Score: 57
Period size: 21 Copynumber: 2.0 Consensus size: 21
28256168 CTCTTAATCT
*
28256178 CTAACCTCTAACTCATAACCC
1 CTAACCCCTAACTCATAACCC
* *
28256199 CTAACCCCTAAATCACAACCC
1 CTAACCCCTAACTCATAACCC
28256220 TTAAACTAGA
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
21 18 1.00
ACGTcount: A:0.36, C:0.45, G:0.00, T:0.19
Consensus pattern (21 bp):
CTAACCCCTAACTCATAACCC
Found at i:28256521 original size:54 final size:56
Alignment explanation
Indices: 28256454--28256564 Score: 138
Period size: 56 Copynumber: 2.0 Consensus size: 56
28256444 ACCCAAAAAA
* *
28256454 TTTTAAAATTATTT-TAAATAAT-AGTATTT-TAATTTTTCCATTTTTAACAAATAT
1 TTTTAAAATTATTTCTAAAT-ATCAGTATTTCAAATTTATCCATTTTTAACAAATAT
* * * *
28256508 TTTTCAAATTATTTCTAAGTTTCATTATTTCAAATTTATCCATTTTTAACAAATAT
1 TTTTAAAATTATTTCTAAATATCAGTATTTCAAATTTATCCATTTTTAACAAATAT
28256564 T
1 T
28256565 CAATTAAAAA
Statistics
Matches: 48, Mismatches: 6, Indels: 4
0.83 0.10 0.07
Matches are distributed among these distances:
54 14 0.29
55 10 0.21
56 24 0.50
ACGTcount: A:0.36, C:0.09, G:0.02, T:0.53
Consensus pattern (56 bp):
TTTTAAAATTATTTCTAAATATCAGTATTTCAAATTTATCCATTTTTAACAAATAT
Found at i:28256755 original size:41 final size:41
Alignment explanation
Indices: 28256647--28256871 Score: 342
Period size: 41 Copynumber: 5.5 Consensus size: 41
28256637 ACGCTTCCCT
* *
28256647 AAAAACGCCGCTAAAGCCCCAAGCATTAGCGGCGCTTCTCC
1 AAAAACGCCGCTAAAGCCCTAAGCATTAGCGGCGCTTCTTC
* *
28256688 AAAAAACGCCGCTAAATCCCTAAGCATTAGCGGCACTTCTTC
1 -AAAAACGCCGCTAAAGCCCTAAGCATTAGCGGCGCTTCTTC
* * *
28256730 AAAAACGCTGCTAAAGCCCTGAGCATTAGTGGCGCTTCTTC
1 AAAAACGCCGCTAAAGCCCTAAGCATTAGCGGCGCTTCTTC
* *
28256771 AAAAACGTCGCTAAATCCCTAAGCATTAGCGGCGCTTCTTC
1 AAAAACGCCGCTAAAGCCCTAAGCATTAGCGGCGCTTCTTC
* *
28256812 AAAAACGCTGCTAAAGCCCTAAGCATTAGCGGCGCTTCTTA
1 AAAAACGCCGCTAAAGCCCTAAGCATTAGCGGCGCTTCTTC
28256853 AAAAACGCCGCTAAAGCCC
1 AAAAACGCCGCTAAAGCCC
28256872 CGAAAGTTCA
Statistics
Matches: 164, Mismatches: 19, Indels: 1
0.89 0.10 0.01
Matches are distributed among these distances:
41 127 0.77
42 37 0.23
ACGTcount: A:0.31, C:0.31, G:0.18, T:0.20
Consensus pattern (41 bp):
AAAAACGCCGCTAAAGCCCTAAGCATTAGCGGCGCTTCTTC
Found at i:28257188 original size:51 final size:51
Alignment explanation
Indices: 28257064--28257341 Score: 300
Period size: 51 Copynumber: 5.5 Consensus size: 51
28257054 TTGGTGTAGT
* * * *
28257064 GTAGCCTTCACATAGTACTACATACGTGATC-AAG-TTTTACGGTTCACGTA
1 GTAGCCTTCACATAGTACTACACATGTGACCAAAGCTTTT-CGGTACACGTA
* *
28257114 GTAGCCTTCACATAGTACTACACATGTGACCAAAGCTTTTCAGTACACATA
1 GTAGCCTTCACATAGTACTACACATGTGACCAAAGCTTTTCGGTACACGTA
* * * * *
28257165 GTAGCCTTCACTTAGTACTACACATGTGACC--ATCATTTACCGATTCACGTA
1 GTAGCCTTCACATAGTACTACACATGTGACCAAAGC-TTT-TCGGTACACGTA
* * * *
28257216 GTAACCTTCACACAGTACTACACATGTGACCAAAGCTTTTCGGTACACATT
1 GTAGCCTTCACATAGTACTACACATGTGACCAAAGCTTTTCGGTACACGTA
* *
28257267 GTAGCCTTCA-ATTAGTACTACACATGTGACCATTA--TTTATCGATACACGTA
1 GTAGCCTTCACA-TAGTACTACACATGTGACCA-AAGCTTT-TCGGTACACGTA
28257318 GTAGCCTTCACATAGTACTACACA
1 GTAGCCTTCACATAGTACTACACA
28257342 CGTGTTCATC
Statistics
Matches: 190, Mismatches: 28, Indels: 19
0.80 0.12 0.08
Matches are distributed among these distances:
49 2 0.01
50 35 0.18
51 142 0.75
52 9 0.05
53 2 0.01
ACGTcount: A:0.31, C:0.25, G:0.14, T:0.30
Consensus pattern (51 bp):
GTAGCCTTCACATAGTACTACACATGTGACCAAAGCTTTTCGGTACACGTA
Found at i:28257240 original size:102 final size:101
Alignment explanation
Indices: 28257064--28257341 Score: 403
Period size: 102 Copynumber: 2.7 Consensus size: 101
28257054 TTGGTGTAGT
* * * * *** *
28257064 GTAGCCTTCACATAGTACTACATACGTGATCAAGTTTTACGGTTCACGTAGTAGCCTTCACATAG
1 GTAGCCTTCACTTAGTACTACACATGTGACCATCATTTACGATTCACGTAGTAGCCTTCACATAG
28257129 TACTACACATGTGACCAAAGCTTTTCAGTACACATA
66 TACTACACATGTGACCAAAGCTTTTCAGTACACATA
* *
28257165 GTAGCCTTCACTTAGTACTACACATGTGACCATCATTTACCGATTCACGTAGTAACCTTCACACA
1 GTAGCCTTCACTTAGTACTACACATGTGACCATCATTTA-CGATTCACGTAGTAGCCTTCACATA
* *
28257230 GTACTACACATGTGACCAAAGCTTTTCGGTACACATT
65 GTACTACACATGTGACCAAAGCTTTTCAGTACACATA
* * *
28257267 GTAGCCTTCAATTAGTACTACACATGTGACCATTATTTATCGATACACGTAGTAGCCTTCACATA
1 GTAGCCTTCACTTAGTACTACACATGTGACCATCATTTA-CGATTCACGTAGTAGCCTTCACATA
28257332 GTACTACACA
65 GTACTACACA
28257342 CGTGTTCATC
Statistics
Matches: 158, Mismatches: 18, Indels: 1
0.89 0.10 0.01
Matches are distributed among these distances:
101 32 0.20
102 126 0.80
ACGTcount: A:0.31, C:0.25, G:0.14, T:0.30
Consensus pattern (101 bp):
GTAGCCTTCACTTAGTACTACACATGTGACCATCATTTACGATTCACGTAGTAGCCTTCACATAG
TACTACACATGTGACCAAAGCTTTTCAGTACACATA
Found at i:28260183 original size:19 final size:19
Alignment explanation
Indices: 28260161--28260224 Score: 67
Period size: 19 Copynumber: 3.2 Consensus size: 19
28260151 AAATTACAAA
28260161 AAAATTCAAAATAAATTTT
1 AAAATTCAAAATAAATTTT
*
28260180 AAAATTCAAAAT-AATTATA
1 AAAATTCAAAATAAATT-TT
*
28260199 AAAATTCCAAAACTTATATTTT
1 AAAATT-CAAAA--TAAATTTT
28260221 AAAA
1 AAAA
28260225 AAAAAATTAT
Statistics
Matches: 37, Mismatches: 3, Indels: 7
0.79 0.06 0.15
Matches are distributed among these distances:
18 4 0.11
19 19 0.51
20 5 0.14
22 6 0.16
23 3 0.08
ACGTcount: A:0.58, C:0.08, G:0.00, T:0.34
Consensus pattern (19 bp):
AAAATTCAAAATAAATTTT
Found at i:28260216 original size:18 final size:19
Alignment explanation
Indices: 28260160--28260210 Score: 68
Period size: 19 Copynumber: 2.6 Consensus size: 19
28260150 AAAATTACAA
28260160 AAAAATTCAAAATAAATT-T
1 AAAAATTCAAAAT-AATTAT
*
28260179 TAAAATTCAAAATAATTAT
1 AAAAATTCAAAATAATTAT
28260198 AAAAATTCCAAAA
1 AAAAATT-CAAAA
28260211 CTTATATTTT
Statistics
Matches: 28, Mismatches: 2, Indels: 3
0.85 0.06 0.09
Matches are distributed among these distances:
18 4 0.14
19 19 0.68
20 5 0.18
ACGTcount: A:0.63, C:0.08, G:0.00, T:0.29
Consensus pattern (19 bp):
AAAAATTCAAAATAATTAT
Found at i:28262259 original size:21 final size:20
Alignment explanation
Indices: 28262218--28262262 Score: 54
Period size: 20 Copynumber: 2.2 Consensus size: 20
28262208 TTCCCTCTTT
* *
28262218 TTTTTATTTTTATTTTAAAA
1 TTTTTAATTTTATTATAAAA
*
28262238 TTTTTAATTTTATATATCAAA
1 TTTTTAATTTTAT-TATAAAA
28262259 TTTT
1 TTTT
28262263 AAAATTTAAT
Statistics
Matches: 21, Mismatches: 3, Indels: 1
0.84 0.12 0.04
Matches are distributed among these distances:
20 12 0.57
21 9 0.43
ACGTcount: A:0.31, C:0.02, G:0.00, T:0.67
Consensus pattern (20 bp):
TTTTTAATTTTATTATAAAA
Found at i:28266857 original size:43 final size:43
Alignment explanation
Indices: 28266817--28267100 Score: 361
Period size: 43 Copynumber: 6.6 Consensus size: 43
28266807 AATAAACACT
* * * * * *
28266817 GCTATAGAACATGATCTTTAGCAGTGCTTCTCCCACAAACACC
1 GCTATAGACCATGACCTTTAGCGGCGCTTTTCCCACAAACGCC
** * *
28266860 GCTATAGATTATGATCTTTAGCGGCACTTTTCCCACAAACGCC
1 GCTATAGACCATGACCTTTAGCGGCGCTTTTCCCACAAACGCC
*
28266903 GCTATAGACCATGATCTTTAGCGGCGCTTTTCCCACAAACGCC
1 GCTATAGACCATGACCTTTAGCGGCGCTTTTCCCACAAACGCC
* * * *
28266946 GTTATAGGCCATGACCTTTAGCGGCACTTTTCCCACAAATGCC
1 GCTATAGACCATGACCTTTAGCGGCGCTTTTCCCACAAACGCC
* * *
28266989 GCTATAGGCCATGACCTTTAGCGGCGCTTCTCCCACAAACGTC
1 GCTATAGACCATGACCTTTAGCGGCGCTTTTCCCACAAACGCC
* *
28267032 GCTATAGGCCATGACCTTTAGCGGCGGTTTTCCCACAAACGCC
1 GCTATAGACCATGACCTTTAGCGGCGCTTTTCCCACAAACGCC
* * *
28267075 GCTATAGGCCATAACTTTTAGCGGCG
1 GCTATAGACCATGACCTTTAGCGGCG
28267101 TTTGGTATAA
Statistics
Matches: 216, Mismatches: 25, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
43 216 1.00
ACGTcount: A:0.24, C:0.31, G:0.19, T:0.26
Consensus pattern (43 bp):
GCTATAGACCATGACCTTTAGCGGCGCTTTTCCCACAAACGCC
Found at i:28267273 original size:26 final size:26
Alignment explanation
Indices: 28267209--28267265 Score: 80
Period size: 26 Copynumber: 2.2 Consensus size: 26
28267199 AAACTAACCG
*
28267209 AATAATATATAATATAAAATTAAACG
1 AATAATATATAATATAAAATTAAACA
*
28267235 AATAATATATAATAT-AAATATAAATA
1 AATAATATATAATATAAAAT-TAAACA
28267261 AATAA
1 AATAA
28267266 GATGTAATTT
Statistics
Matches: 28, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
25 4 0.14
26 24 0.86
ACGTcount: A:0.65, C:0.02, G:0.02, T:0.32
Consensus pattern (26 bp):
AATAATATATAATATAAAATTAAACA
Found at i:28267508 original size:21 final size:21
Alignment explanation
Indices: 28267482--28267530 Score: 71
Period size: 21 Copynumber: 2.3 Consensus size: 21
28267472 GTAGCTTGAA
*
28267482 CCTCTGCTTCTCTCACTGCAG
1 CCTCTGCTTCCCTCACTGCAG
* *
28267503 CCTCTGCTTCCCTCGCTGCCG
1 CCTCTGCTTCCCTCACTGCAG
28267524 CCTCTGC
1 CCTCTGC
28267531 CTTGGAGTTC
Statistics
Matches: 25, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
21 25 1.00
ACGTcount: A:0.04, C:0.49, G:0.16, T:0.31
Consensus pattern (21 bp):
CCTCTGCTTCCCTCACTGCAG
Found at i:28273060 original size:9 final size:9
Alignment explanation
Indices: 28273046--28273295 Score: 135
Period size: 9 Copynumber: 27.2 Consensus size: 9
28273036 AGTTTATATA
28273046 TAAGTTATG
1 TAAGTTATG
*
28273055 TAAGTTATA
1 TAAGTTATG
28273064 T-A-TTATG
1 TAAGTTATG
*
28273071 TATGTTATG
1 TAAGTTATG
*
28273080 TAAGTTGTATA
1 TAAG-T-TATG
*
28273091 TAATGTAAT-
1 TAA-GTTATG
28273100 TAAGTTATG
1 TAAGTTATG
28273109 TAAG-T-TG
1 TAAGTTATG
28273116 TAAGTTATG
1 TAAGTTATG
28273125 TAAGTTATG
1 TAAGTTATG
*
28273134 TCTAATATTAATG
1 --TAA-GTT-ATG
28273147 TAAGTTATG
1 TAAGTTATG
28273156 T-A-TTATG
1 TAAGTTATG
*
28273163 TAAGTTATT
1 TAAGTTATG
28273172 TAAGTTATG
1 TAAGTTATG
*
28273181 TAAGTTGTG
1 TAAGTTATG
28273190 T-A-TTATG
1 TAAGTTATG
*
28273197 TGAGTTATG
1 TAAGTTATG
* *
28273206 CAATTTATG
1 TAAGTTATG
* * *
28273215 TAGGCTATA
1 TAAGTTATG
28273224 T-A-TTATG
1 TAAGTTATG
28273231 TAAGTTATG
1 TAAGTTATG
* *
28273240 CAAGTTTATATA
1 TAAG--T-TATG
*
28273252 TAAGTTTCTATA
1 TAAG--T-TATG
28273264 TAAGTTATG
1 TAAGTTATG
28273273 TAAGTTATTATG
1 TAAG---TTATG
28273285 TAAGTTATG
1 TAAGTTATG
28273294 TA
1 TA
28273296 TTACGTAAGT
Statistics
Matches: 188, Mismatches: 29, Indels: 48
0.71 0.11 0.18
Matches are distributed among these distances:
7 26 0.14
8 12 0.06
9 98 0.52
10 6 0.03
11 14 0.07
12 29 0.15
13 3 0.02
ACGTcount: A:0.33, C:0.02, G:0.18, T:0.47
Consensus pattern (9 bp):
TAAGTTATG
Found at i:28273069 original size:16 final size:16
Alignment explanation
Indices: 28273050--28273238 Score: 78
Period size: 16 Copynumber: 11.8 Consensus size: 16
28273040 TATATATAAG
28273050 TTATGTAAGTTATATA
1 TTATGTAAGTTATATA
* *
28273066 TTATGTATGTTATGTA
1 TTATGTAAGTTATATA
*
28273082 --A-GT-TG-TATATA
1 TTATGTAAGTTATATA
*
28273093 --ATGTAA-TTA-A-G
1 TTATGTAAGTTATATA
*
28273104 TTATGTAAGTTGTA-A
1 TTATGTAAGTTATATA
28273119 GTTATGTAAGTTATGTCTAATA
1 -TTATGTAAGTTA----TA-TA
*
28273141 TTAATGTAAGTTATGTA
1 TT-ATGTAAGTTATATA
*
28273158 TTATGTAAGTTATTTAA
1 TTATGTAAGTTATAT-A
* *
28273175 GTTATGTAAGTTGTGTA
1 -TTATGTAAGTTATATA
*
28273192 TTATGTGAGTTATGCA-A
1 TTATGTAAGTTAT--ATA
* *
28273209 TTTATGTAGGCTATATA
1 -TTATGTAAGTTATATA
28273226 TTATGTAAGTTAT
1 TTATGTAAGTTAT
28273239 GCAAGTTTAT
Statistics
Matches: 132, Mismatches: 20, Indels: 42
0.68 0.10 0.22
Matches are distributed among these distances:
11 6 0.05
12 5 0.04
13 10 0.08
14 3 0.02
15 1 0.01
16 60 0.45
17 8 0.06
18 24 0.18
20 2 0.02
21 2 0.02
22 11 0.08
ACGTcount: A:0.32, C:0.02, G:0.19, T:0.48
Consensus pattern (16 bp):
TTATGTAAGTTATATA
Found at i:28273096 original size:25 final size:25
Alignment explanation
Indices: 28273018--28273205 Score: 128
Period size: 25 Copynumber: 7.6 Consensus size: 25
28273008 TATATTTATG
* *
28273018 TATTAAGTAAATTATGTAAGTT-TA
1 TATTATGTAAGTTATGTAAGTTGTA
*
28273042 TA-TA--TAAGTTATGTAAGTTATA
1 TATTATGTAAGTTATGTAAGTTGTA
*
28273064 TATTATGTATGTTATGTAAGTTGTA
1 TATTATGTAAGTTATGTAAGTTGTA
*
28273089 TATAATGTAATTAAGTTATGTAAGTTGTA
1 TATTATG----TAAGTTATGTAAGTTGTA
* *
28273118 -AGTTATGTAAGTTATGT---CT-AA
1 TA-TTATGTAAGTTATGTAAGTTGTA
*
28273139 TATTAATGTAAGTTATGT-ATTATGTA
1 TATT-ATGTAAGTTATGTAAGT-TGTA
* *
28273165 -AGTTATTTAAGTTATGTAAGTTGTG
1 TA-TTATGTAAGTTATGTAAGTTGTA
*
28273190 TATTATGTGAGTTATG
1 TATTATGTAAGTTATG
28273206 CAATTTATGT
Statistics
Matches: 131, Mismatches: 15, Indels: 35
0.72 0.08 0.19
Matches are distributed among these distances:
21 17 0.13
22 19 0.15
23 4 0.03
24 2 0.02
25 61 0.47
26 6 0.05
28 1 0.01
29 21 0.16
ACGTcount: A:0.34, C:0.01, G:0.18, T:0.47
Consensus pattern (25 bp):
TATTATGTAAGTTATGTAAGTTGTA
Found at i:28273192 original size:34 final size:34
Alignment explanation
Indices: 28273099--28273321 Score: 134
Period size: 34 Copynumber: 6.3 Consensus size: 34
28273089 TATAATGTAA
28273099 TTAAGTTATGTAAG-T-TGTAAGTTATGTAAGTTAT
1 TTAAGTTATGTAAGTTATGT-A-TTATGTAAGTTAT
*
28273133 GTCTAATATTAATGTAAGTTATGTATTATGTAAGTTAT
1 -T-TAA-GTT-ATGTAAGTTATGTATTATGTAAGTTAT
* *
28273171 TTAAGTTATGTAAGTTGTGTATTATGTGAGTTAT
1 TTAAGTTATGTAAGTTATGTATTATGTAAGTTAT
** * * * *
28273205 GCAATTTATGTAGGCTATATATTATGTAAGTTAT
1 TTAAGTTATGTAAGTTATGTATTATGTAAGTTAT
** * *
28273239 GCAAGTTTATATATAAGTT-TCTA-TA--TAAGTTAT
1 TTAAG--T-TATGTAAGTTATGTATTATGTAAGTTAT
* *
28273272 GTAAGTTATTATGTAAGTTATGTATTACGTAAGTTTAT
1 TTAAG---TTATGTAAGTTATGTATTATGTAAG-TTAT
28273310 ATATAAGTTATG
1 -T-TAAGTTATG
28273322 ATATGATTGA
Statistics
Matches: 150, Mismatches: 22, Indels: 30
0.74 0.11 0.15
Matches are distributed among these distances:
33 21 0.14
34 60 0.40
35 7 0.05
36 10 0.07
37 19 0.13
38 24 0.16
39 2 0.01
40 7 0.05
ACGTcount: A:0.33, C:0.03, G:0.18, T:0.47
Consensus pattern (34 bp):
TTAAGTTATGTAAGTTATGTATTATGTAAGTTAT
Found at i:28273276 original size:21 final size:21
Alignment explanation
Indices: 28273252--28273295 Score: 63
Period size: 21 Copynumber: 2.1 Consensus size: 21
28273242 AGTTTATATA
28273252 TAAGTT-TCTATATAAGTTATG
1 TAAGTTAT-TATATAAGTTATG
*
28273273 TAAGTTATTATGTAAGTTATG
1 TAAGTTATTATATAAGTTATG
28273294 TA
1 TA
28273296 TTACGTAAGT
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
21 20 0.95
22 1 0.05
ACGTcount: A:0.34, C:0.02, G:0.16, T:0.48
Consensus pattern (21 bp):
TAAGTTATTATATAAGTTATG
Found at i:28273278 original size:33 final size:32
Alignment explanation
Indices: 28273226--28273318 Score: 88
Period size: 33 Copynumber: 3.0 Consensus size: 32
28273216 AGGCTATATA
* *
28273226 TTATGTAAGTTATGCAAGTTTATATATAAGTT
1 TTATATAAGTTATGTAAGTTTATATATAAGTT
*
28273258 TCTATATAAGTTATGTAAG-TTATTATGTAAG--
1 T-TATATAAGTTATGTAAGTTTA-TATATAAGTT
* *
28273289 TTATGT-A-TTACGTAAGTTTATATATAAGTT
1 TTATATAAGTTATGTAAGTTTATATATAAGTT
28273319 ATGATATGAT
Statistics
Matches: 50, Mismatches: 6, Indels: 12
0.74 0.09 0.18
Matches are distributed among these distances:
28 15 0.30
29 4 0.08
30 4 0.08
31 1 0.02
32 4 0.08
33 22 0.44
ACGTcount: A:0.34, C:0.03, G:0.15, T:0.47
Consensus pattern (32 bp):
TTATATAAGTTATGTAAGTTTATATATAAGTT
Found at i:28273283 original size:12 final size:12
Alignment explanation
Indices: 28273268--28273292 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
28273258 TCTATATAAG
28273268 TTATGTAAGTTA
1 TTATGTAAGTTA
28273280 TTATGTAAGTTA
1 TTATGTAAGTTA
28273292 T
1 T
28273293 GTATTACGTA
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:0.32, C:0.00, G:0.16, T:0.52
Consensus pattern (12 bp):
TTATGTAAGTTA
Found at i:28273472 original size:24 final size:24
Alignment explanation
Indices: 28273445--28273552 Score: 66
Period size: 24 Copynumber: 4.6 Consensus size: 24
28273435 AACATTTTCA
28273445 ATTATTTTTAAAATTATAAAATTT
1 ATTATTTTTAAAATTATAAAATTT
* **
28273469 ATTA--TTGAAAA-TAT-AGGTTT
1 ATTATTTTTAAAATTATAAAATTT
* * * *
28273489 -TAATATTTAAAA-AATAACATTT
1 ATTATTTTTAAAATTATAAAATTT
28273511 ACAATTATTTTTAAAATTATAAAATTT
1 ---ATTATTTTTAAAATTATAAAATTT
**
28273538 ATTATTAATAAAATT
1 ATTATTTTTAAAATT
28273553 GGTTTTAATA
Statistics
Matches: 62, Mismatches: 14, Indels: 16
0.67 0.15 0.17
Matches are distributed among these distances:
19 2 0.03
20 4 0.06
21 11 0.18
22 10 0.16
24 17 0.27
26 10 0.16
27 8 0.13
ACGTcount: A:0.48, C:0.02, G:0.03, T:0.47
Consensus pattern (24 bp):
ATTATTTTTAAAATTATAAAATTT
Found at i:28273492 original size:69 final size:69
Alignment explanation
Indices: 28273402--28273678 Score: 468
Period size: 69 Copynumber: 4.0 Consensus size: 69
28273392 TGGGGTGATA
* * * * *
28273402 TATTAAAAATATAGGTGTTAATCTTTAGAAAATAACATTTTCAATTATTTTTAAAATTATAAAAT
1 TATTGAAAATATAGGTTTTAATATTTAAAAAATAACATTTACAATTATTTTTAAAATTATAAAAT
28273467 TTAT
66 TTAT
28273471 TATTGAAAATATAGGTTTTAATATTTAAAAAATAACATTTACAATTATTTTTAAAATTATAAAAT
1 TATTGAAAATATAGGTTTTAATATTTAAAAAATAACATTTACAATTATTTTTAAAATTATAAAAT
28273536 TTAT
66 TTAT
* *
28273540 TATT-AATAAAATTGGTTTTAATATTTAAAAAATAACATTTACAATTATTTTTAAAATTATAAAA
1 TATTGAA-AATATAGGTTTTAATATTTAAAAAATAACATTTACAATTATTTTTAAAATTATAAAA
28273604 TTTAT
65 TTTAT
28273609 TATTGAAAATATAGGTTTTAATATTTAAAAAATAACATTTACAATTATTTTTAAAATTATAAAA-
1 TATTGAAAATATAGGTTTTAATATTTAAAAAATAACATTTACAATTATTTTTAAAATTATAAAAT
28273673 TTAT
66 TTAT
28273677 TA
1 TA
28273679 ATATATGTTA
Statistics
Matches: 197, Mismatches: 9, Indels: 5
0.93 0.04 0.02
Matches are distributed among these distances:
68 8 0.04
69 187 0.95
70 2 0.01
ACGTcount: A:0.47, C:0.03, G:0.04, T:0.45
Consensus pattern (69 bp):
TATTGAAAATATAGGTTTTAATATTTAAAAAATAACATTTACAATTATTTTTAAAATTATAAAAT
TTAT
Found at i:28273511 original size:21 final size:21
Alignment explanation
Indices: 28273487--28273649 Score: 67
Period size: 21 Copynumber: 7.2 Consensus size: 21
28273477 AAATATAGGT
28273487 TTTAATATTTAAAAAATAACA
1 TTTAATATTTAAAAAATAACA
* *
28273508 TTTACAATTATTTTTAAAATTATAAAA
1 TTT--AA-TA--TTTAAAA-AATAACA
* ****
28273535 TTTATTA-TTAATAAAATTGGT
1 TTTAATATTTAA-AAAATAACA
28273556 TTTAATATTTAAAAAATAACA
1 TTTAATATTTAAAAAATAACA
* *
28273577 TTTACAATTATTTTTAAAATTATAAAA
1 TTT--AA-TA--TTTAAAA-AATAACA
* * * ***
28273604 TTTATTATTGAAAATATAGGT
1 TTTAATATTTAAAAAATAACA
28273625 TTTAATATTTAAAAAATAACA
1 TTTAATATTTAAAAAATAACA
28273646 TTTA
1 TTTA
28273650 CAATTATTTT
Statistics
Matches: 102, Mismatches: 26, Indels: 28
0.65 0.17 0.18
Matches are distributed among these distances:
21 46 0.45
22 12 0.12
23 4 0.04
24 8 0.08
25 2 0.02
26 14 0.14
27 16 0.16
ACGTcount: A:0.48, C:0.03, G:0.03, T:0.45
Consensus pattern (21 bp):
TTTAATATTTAAAAAATAACA
Found at i:28274724 original size:11 final size:11
Alignment explanation
Indices: 28274710--28274734 Score: 50
Period size: 11 Copynumber: 2.3 Consensus size: 11
28274700 AGTCAAAATT
28274710 CAACAGAAACC
1 CAACAGAAACC
28274721 CAACAGAAACC
1 CAACAGAAACC
28274732 CAA
1 CAA
28274735 ATAACAAAAT
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:0.56, C:0.36, G:0.08, T:0.00
Consensus pattern (11 bp):
CAACAGAAACC
Found at i:28274757 original size:14 final size:14
Alignment explanation
Indices: 28274734--28274763 Score: 51
Period size: 14 Copynumber: 2.1 Consensus size: 14
28274724 CAGAAACCCA
*
28274734 AATAACAAAATCTG
1 AATAAAAAAATCTG
28274748 AATAAAAAAATCTG
1 AATAAAAAAATCTG
28274762 AA
1 AA
28274764 ATATTCCACA
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:0.63, C:0.10, G:0.07, T:0.20
Consensus pattern (14 bp):
AATAAAAAAATCTG
Found at i:28275437 original size:147 final size:148
Alignment explanation
Indices: 28275281--28276058 Score: 542
Period size: 147 Copynumber: 5.3 Consensus size: 148
28275271 AGACAGTCTT
* * *
28275281 AATTT-TGGCGTTTTGGCATAAAACGCCACTCATAACATTGAAAAACGACGACGTTTTCCTTGAC
1 AATTTCTGGCGTTTTGGCATAAAACGCCACTCATAACATGGAAAAACGACGACGTATTCCATGAC
* * *
28275345 TAAACTAACAAATTTGCGGCGTTTCTACATAAGCGCCACTAAA-TAACCCCAGAAATGATGTCGT
66 TAAACTAACAAATTTGCGGCGTTTATACATAAGCGCCACTAAACTAACCGCAGAAACGATGTCGT
*
28275409 TT-CCAAACACTTACGACA
131 TTCCCAAACAATTA-GACA
* * * *
28275427 AATTTCTGGCGTTTTGGTATAAAACGCCACT-ACTAAC-TAGTAAAACAACGACGTATTCC-TGA
1 AATTTCTGGCGTTTTGGCATAAAACGCCACTCA-TAACATGGAAAAACGACGACGTATTCCATGA
* * ** * * ** * * * *
28275489 CTAAATTTACCCATTTGCGGTGTTTATACACAAGCGCCAC-AAACTAAAAGTAGAAACGCTATCT
65 CTAAACTAACAAATTTGCGGCGTTTATACATAAGCGCCACTAAACTAACCGCAGAAACGATGTCG
** ** * *
28275553 TTTAACAGCCAGTTAGTCA
130 TTTCCCAAACAATTAGACA
* * * * * * * * *
28275572 AAATTGTGGCGTTTAGGCATAAAATGCCAATCACAACATGGAAAAATGACGACATTTTCCATGAC
1 AATTTCTGGCGTTTTGGCATAAAACGCCACTCATAACATGGAAAAACGACGACGTATTCCATGAC
* * * * * * *** *
28275637 TAAACGAAGAACTTTGCGGCGTTTACACGTAAGCGCCACTAAATTAACCATGGAAACGAAGTCGT
66 TAAACTAACAAATTTGCGGCGTTTATACATAAGCGCCACTAAACTAACCGCAGAAACGATGTCGT
28275702 TTCCCAAACAATTAGGACA
131 TTCCCAAACAATTA-GACA
* * * *
28275721 ACA-TTCTGGCATTTTGGTATAAAACGCCACTAAGAACATGGAAAAACGACGACGTATT-CATGA
1 A-ATTTCTGGCGTTTTGGCATAAAACGCCACTCATAACATGGAAAAACGACGACGTATTCCATGA
** * ** *
28275784 CTAAA-TGAACCCATTCGCGGCGTTTATA-ATCTTGCGCCACTAAA-TAACCGCAGAAACGACGT
65 CTAAACT-AACAAATTTGCGGCGTTTATACAT-AAGCGCCACTAAACTAACCGCAGAAACGATGT
* * *
28275846 CATTTCCCACACAATTATG-TA
128 CGTTTCCCAAACAATTA-GACA
* * * * * * * * * ****
28275867 AATATTCTGGCGTTTTGGCATAAAACGCCACTAAGAATATAGTAATACGATGTCGTTTTTTGGGA
1 AAT-TTCTGGCGTTTTGGCATAAAACGCCACTCATAACATGGAAAAACGACGACGTATTCCATGA
* * *** * * * * *
28275932 TTAAATTAACCCGTTTGTGGCGTTTATACGTATGCGCCACTAAA-TAACCG-TGAAACGCTGTCG
65 CTAAACTAACAAATTTGCGGCGTTTATACATAAGCGCCACTAAACTAACCGCAGAAACGATGTCG
** *
28275995 TTTCCCCGATAATTAGGACA
130 TTTCCCAAACAATTA-GACA
* * * * *
28276015 ATTTTGTGGCGTTTTTGCATAAAACGCCACTAAGAACATGGAAA
1 AATTTCTGGCGTTTTGGCATAAAACGCCACTCATAACATGGAAA
28276059 TTTTGAAAAA
Statistics
Matches: 488, Mismatches: 126, Indels: 35
0.75 0.19 0.05
Matches are distributed among these distances:
144 3 0.01
145 83 0.17
146 50 0.10
147 195 0.40
148 106 0.22
149 50 0.10
150 1 0.00
ACGTcount: A:0.34, C:0.22, G:0.17, T:0.27
Consensus pattern (148 bp):
AATTTCTGGCGTTTTGGCATAAAACGCCACTCATAACATGGAAAAACGACGACGTATTCCATGAC
TAAACTAACAAATTTGCGGCGTTTATACATAAGCGCCACTAAACTAACCGCAGAAACGATGTCGT
TTCCCAAACAATTAGACA
Found at i:28275771 original size:292 final size:294
Alignment explanation
Indices: 28275281--28275811 Score: 705
Period size: 292 Copynumber: 1.8 Consensus size: 294
28275271 AGACAGTCTT
* * * * * * *
28275281 AATTTTGGCGTTTTGGCATAAAACGCCACTCATAACATTGAAAAACGACGACGTTTTCCTTGACT
1 AATTGTGGCGTTTAGGCATAAAACGCCAATCACAACATGGAAAAACGACGACATTTTCCATGACT
* * * *
28275346 AAACTAACAAATTTGCGGCGTTTCTACATAAGCGCCACTAAATAACCCCAGAAATGATGTCGTTT
66 AAACGAACAAATTTGCGGCGTTTCTACATAAGCGCCACTAAATAACCACAGAAACGAAGTCGTTT
* * **
28275411 CCAAACACTTACGACAAATTTCTGGCGTTTTGGTATAAAACGCCACTACTAACTAGT-AAAACA-
131 CCAAACAATTACGACAAATTTCTGGCATTTTGGTATAAAACGCCACTAAGAACTAGTAAAAACAC
* ** * *
28275474 ACGACGTATTCCTGACTAAATTTACCCATTTGCGGTGTTTATACACAAGCGCCACAAACTAAAAG
196 ACGACGTATTCATGACTAAATGAACCCATTCGCGGCGTTTATACACAAGCGCCACAAACTAAAAG
28275539 TAGAAACGCTATCTTTTAACAGCCAGTTAGTCAA
261 TAGAAACGCTATCTTTTAACAGCCAGTTAGTCAA
* *
28275573 AATTGTGGCGTTTAGGCATAAAATGCCAATCACAACATGGAAAAATGACGACATTTTCCATGACT
1 AATTGTGGCGTTTAGGCATAAAACGCCAATCACAACATGGAAAAACGACGACATTTTCCATGACT
* * * **
28275638 AAACGAAGAACTTTGCGGCGTTTAC-ACGTAAGCGCCACTAAATTAACCATGGAAACGAAGTCGT
66 AAACGAACAAATTTGCGGCGTTT-CTACATAAGCGCCACTAAA-TAACCACAGAAACGAAGTCGT
* *
28275702 TTCCCAAACAATTAGGACAACA-TTCTGGCATTTTGGTATAAAACGCCACTAAGAAC-ATGGAAA
129 TT-CCAAACAATTACGACAA-ATTTCTGGCATTTTGGTATAAAACGCCACTAAGAACTA-GTAAA
*
28275765 AAC-GACGACGTATTCATGACTAAATGAACCCATTCGCGGCGTTTATA
191 AACACACGACGTATTCATGACTAAATGAACCCATTCGCGGCGTTTATA
28275812 ATCTTGCGCC
Statistics
Matches: 203, Mismatches: 29, Indels: 11
0.84 0.12 0.05
Matches are distributed among these distances:
292 92 0.45
293 20 0.10
294 47 0.23
295 44 0.22
ACGTcount: A:0.35, C:0.22, G:0.17, T:0.26
Consensus pattern (294 bp):
AATTGTGGCGTTTAGGCATAAAACGCCAATCACAACATGGAAAAACGACGACATTTTCCATGACT
AAACGAACAAATTTGCGGCGTTTCTACATAAGCGCCACTAAATAACCACAGAAACGAAGTCGTTT
CCAAACAATTACGACAAATTTCTGGCATTTTGGTATAAAACGCCACTAAGAACTAGTAAAAACAC
ACGACGTATTCATGACTAAATGAACCCATTCGCGGCGTTTATACACAAGCGCCACAAACTAAAAG
TAGAAACGCTATCTTTTAACAGCCAGTTAGTCAA
Found at i:28276396 original size:21 final size:21
Alignment explanation
Indices: 28276372--28276419 Score: 53
Period size: 21 Copynumber: 2.3 Consensus size: 21
28276362 CCTTAAACCC
*
28276372 TAAATCATAAACTATAAACTG
1 TAAACCATAAACTATAAACTG
* *
28276393 TAAACCCTAAACTGTAAACAT-
1 TAAACCATAAACTATAAAC-TG
28276414 TAAACC
1 TAAACC
28276420 CGTAAACCAC
Statistics
Matches: 23, Mismatches: 3, Indels: 2
0.82 0.11 0.07
Matches are distributed among these distances:
21 22 0.96
22 1 0.04
ACGTcount: A:0.50, C:0.21, G:0.04, T:0.25
Consensus pattern (21 bp):
TAAACCATAAACTATAAACTG
Found at i:28276420 original size:21 final size:22
Alignment explanation
Indices: 28276379--28276426 Score: 64
Period size: 21 Copynumber: 2.2 Consensus size: 22
28276369 CCCTAAATCA
28276379 TAAACTATAAACTGTAAACCC-
1 TAAACTATAAACTGTAAACCCG
*
28276400 TAAACTGTAAACAT-TAAACCCG
1 TAAACTATAAAC-TGTAAACCCG
28276422 TAAAC
1 TAAAC
28276427 CACAAACACC
Statistics
Matches: 24, Mismatches: 1, Indels: 3
0.86 0.04 0.11
Matches are distributed among these distances:
21 18 0.75
22 6 0.25
ACGTcount: A:0.48, C:0.23, G:0.06, T:0.23
Consensus pattern (22 bp):
TAAACTATAAACTGTAAACCCG
Found at i:28276447 original size:21 final size:20
Alignment explanation
Indices: 28276423--28276465 Score: 52
Period size: 21 Copynumber: 2.1 Consensus size: 20
28276413 TTAAACCCGT
28276423 AAACCACAAACA-CCAACCACC
1 AAACCACAAA-ATCCAACC-CC
*
28276444 AAACCTCAAAATCCAACCCC
1 AAACCACAAAATCCAACCCC
28276464 AA
1 AA
28276466 TATACCATAA
Statistics
Matches: 20, Mismatches: 1, Indels: 3
0.83 0.04 0.12
Matches are distributed among these distances:
20 5 0.25
21 15 0.75
ACGTcount: A:0.51, C:0.44, G:0.00, T:0.05
Consensus pattern (20 bp):
AAACCACAAAATCCAACCCC
Found at i:28277102 original size:73 final size:73
Alignment explanation
Indices: 28276972--28277134 Score: 249
Period size: 73 Copynumber: 2.2 Consensus size: 73
28276962 TTTTACGAAA
* * *
28276972 AAGCGCCGCTAATGCCACTACATCTCAAATCAAAACGATGTGTTTTGATTAT-CTTTTTGCGGCG
1 AAGCGCCGCTAATGCCACTACATCTCAAATCAAAACGATGCGTTTGGATTATATTTTTTGCGGCG
*
28277036 CTTTTACAG
66 -TTTAACAG
28277045 AAGCGCCGCTAATGCCACTACATCTCAAATCAAAACGATGCGTTTGGATT-TAATTTTTTGCGGC
1 AAGCGCCGCTAATGCCACTACATCTCAAATCAAAACGATGCGTTTGGATTAT-ATTTTTTGCGGC
28277109 GTTTAACAG
65 GTTTAACAG
*
28277118 AAGGGCCGCTAATGCCA
1 AAGCGCCGCTAATGCCA
28277135 ATCTTTTGTA
Statistics
Matches: 83, Mismatches: 5, Indels: 4
0.90 0.05 0.04
Matches are distributed among these distances:
72 1 0.01
73 71 0.86
74 11 0.13
ACGTcount: A:0.28, C:0.23, G:0.20, T:0.29
Consensus pattern (73 bp):
AAGCGCCGCTAATGCCACTACATCTCAAATCAAAACGATGCGTTTGGATTATATTTTTTGCGGCG
TTTAACAG
Found at i:28277375 original size:40 final size:41
Alignment explanation
Indices: 28277305--28277386 Score: 105
Period size: 40 Copynumber: 2.0 Consensus size: 41
28277295 ATGCATATTA
** *
28277305 TTAGCGGCGTTTTATTAGAATTGCCGCTAATGCTC-ATTTT
1 TTAGCGGCGTTTTATTAGAAGCGCCACTAATGCTCGATTTT
*
28277345 TTAGCGGCGTTTTCTCT-GAAGCGCCACTAATGCTCGATTTT
1 TTAGCGGCGTTTTAT-TAGAAGCGCCACTAATGCTCGATTTT
28277386 T
1 T
28277387 ACCGGTGTTT
Statistics
Matches: 36, Mismatches: 4, Indels: 3
0.84 0.09 0.07
Matches are distributed among these distances:
40 29 0.81
41 7 0.19
ACGTcount: A:0.18, C:0.21, G:0.21, T:0.40
Consensus pattern (41 bp):
TTAGCGGCGTTTTATTAGAAGCGCCACTAATGCTCGATTTT
Found at i:28280128 original size:22 final size:23
Alignment explanation
Indices: 28280096--28280171 Score: 88
Period size: 22 Copynumber: 3.4 Consensus size: 23
28280086 AACTAATCCT
28280096 CTCTCAAATTTCCTCTCAATTTC
1 CTCTCAAATTTCCTCTCAATTTC
* *
28280119 CTCT-AAATTTTCTCTCAATTTG
1 CTCTCAAATTTCCTCTCAATTTC
28280141 CTCTCAAA-TTCCT-TCCAAATTT-
1 CTCTCAAATTTCCTCT-C-AATTTC
28280163 CTCTCAAAT
1 CTCTCAAAT
28280172 CCATATTTAA
Statistics
Matches: 46, Mismatches: 3, Indels: 8
0.81 0.05 0.14
Matches are distributed among these distances:
21 1 0.02
22 33 0.72
23 12 0.26
ACGTcount: A:0.25, C:0.30, G:0.01, T:0.43
Consensus pattern (23 bp):
CTCTCAAATTTCCTCTCAATTTC
Found at i:28280145 original size:33 final size:33
Alignment explanation
Indices: 28280095--28280169 Score: 98
Period size: 33 Copynumber: 2.2 Consensus size: 33
28280085 AAACTAATCC
* *
28280095 TCTCTCAAATTTCCTCTCAATTTCC-TCTAAATTT
1 TCTCTC-AATTTCCTCTCAAATTCCTTCCAAA-TT
*
28280129 TCTCTCAATTTGCTCTCAAATTCCTTCCAAATT
1 TCTCTCAATTTCCTCTCAAATTCCTTCCAAATT
28280162 TCTCTCAA
1 TCTCTCAA
28280170 ATCCATATTT
Statistics
Matches: 37, Mismatches: 3, Indels: 3
0.86 0.07 0.07
Matches are distributed among these distances:
33 26 0.70
34 11 0.30
ACGTcount: A:0.24, C:0.31, G:0.01, T:0.44
Consensus pattern (33 bp):
TCTCTCAATTTCCTCTCAAATTCCTTCCAAATT
Found at i:28280170 original size:11 final size:11
Alignment explanation
Indices: 28280095--28280171 Score: 72
Period size: 11 Copynumber: 6.9 Consensus size: 11
28280085 AAACTAATCC
28280095 TCTCTCAAATT
1 TCTCTCAAATT
28280106 TCCTCTC-AATT
1 T-CTCTCAAATT
28280117 TC-CTCTAAATTT
1 TCTCTC-AAA-TT
28280129 TCTCTC-AATT
1 TCTCTCAAATT
28280139 TGCTCTCAAATT
1 T-CTCTCAAATT
*
28280151 CCT-TCCAAATT
1 TCTCT-CAAATT
28280162 TCTCTCAAAT
1 TCTCTCAAAT
28280172 CCATATTTAA
Statistics
Matches: 55, Mismatches: 2, Indels: 18
0.73 0.03 0.24
Matches are distributed among these distances:
9 3 0.05
10 5 0.09
11 30 0.55
12 14 0.25
13 3 0.05
ACGTcount: A:0.25, C:0.30, G:0.01, T:0.44
Consensus pattern (11 bp):
TCTCTCAAATT
Found at i:28281420 original size:7 final size:7
Alignment explanation
Indices: 28281408--28281440 Score: 66
Period size: 7 Copynumber: 4.7 Consensus size: 7
28281398 TAGTCGATTG
28281408 GTATTTA
1 GTATTTA
28281415 GTATTTA
1 GTATTTA
28281422 GTATTTA
1 GTATTTA
28281429 GTATTTA
1 GTATTTA
28281436 GTATT
1 GTATT
28281441 ATGTATATAA
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 26 1.00
ACGTcount: A:0.27, C:0.00, G:0.15, T:0.58
Consensus pattern (7 bp):
GTATTTA
Found at i:28286000 original size:125 final size:126
Alignment explanation
Indices: 28285756--28286122 Score: 546
Period size: 125 Copynumber: 2.9 Consensus size: 126
28285746 AACATGCTAT
*
28285756 TGTAGCAAAAGCGCGTCCACGTGGGCGCGATTTCACAAATTCTTCTCATAAAGCATCCTGGTAGA
1 TGTAGCAAAAGCGCGTCCACGTGGGCGCGATTTCACAAATTCTTCTCATAAAGCATCCTGCTAGA
*
28285821 AGC-TATTTTATACTATTTGCTCAGAAACGTCAACTCAAAATTATTTCTTCCAGGACCAAC
66 AGCGTATTTTATACTATTTGCTCAGAAACGTCAACTCAAAATAATTTCTTCCAGGACCAAC
* * * *
28285881 TGTAGCAAAAGTGCGTCCACGAGGGCTCGATTTCACAAATTCTTCTCA-AATAGCATCCTGCTTG
1 TGTAGCAAAAGCGCGTCCACGTGGGCGCGATTTCACAAATTCTTCTCATAA-AGCATCCTGCTAG
* * * * *
28285945 AAGCGTTTTTTATACTATTTGCTTAGAAACGTCAACTCGAAATAATTT-TTTCAGGACCTAC
65 AAGCGTATTTTATACTATTTGCTCAGAAACGTCAACTCAAAATAATTTCTTCCAGGACCAAC
* * * *
28286006 TGTAGCAAAAGCGCGACCATGTGGGCGCGATTTAACAAATTCTTCTCATAAAGCATCCTGCTAAA
1 TGTAGCAAAAGCGCGTCCACGTGGGCGCGATTTCACAAATTCTTCTCATAAAGCATCCTGCTAGA
28286071 AGCG-ATTTTATACTATTTGCTCAGAAACGTCAACTCAAAATTAA-TTCTTCCA
66 AGCGTATTTTATACTATTTGCTCAGAAACGTCAACTCAAAA-TAATTTCTTCCA
28286123 AGACTTAAAA
Statistics
Matches: 214, Mismatches: 23, Indels: 10
0.87 0.09 0.04
Matches are distributed among these distances:
124 37 0.17
125 136 0.64
126 41 0.19
ACGTcount: A:0.31, C:0.23, G:0.16, T:0.30
Consensus pattern (126 bp):
TGTAGCAAAAGCGCGTCCACGTGGGCGCGATTTCACAAATTCTTCTCATAAAGCATCCTGCTAGA
AGCGTATTTTATACTATTTGCTCAGAAACGTCAACTCAAAATAATTTCTTCCAGGACCAAC
Found at i:28298535 original size:34 final size:34
Alignment explanation
Indices: 28298463--28298545 Score: 94
Period size: 34 Copynumber: 2.4 Consensus size: 34
28298453 TGCTATCTAC
** * * *
28298463 TTGTGTGGGATGGATATGCTTATGTGCAATTTGG
1 TTGTGTGGGATGGATACACTGATGTGCAATCTGA
*
28298497 TTGTGTGGGATGGATACACTGATGTGCAGTCTGA
1 TTGTGTGGGATGGATACACTGATGTGCAATCTGA
* *
28298531 TTGTGTTGGAGGGAT
1 TTGTGTGGGATGGAT
28298546 GTGCTATGGT
Statistics
Matches: 41, Mismatches: 8, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
34 41 1.00
ACGTcount: A:0.18, C:0.07, G:0.37, T:0.37
Consensus pattern (34 bp):
TTGTGTGGGATGGATACACTGATGTGCAATCTGA
Found at i:28299821 original size:9 final size:9
Alignment explanation
Indices: 28299809--28299921 Score: 138
Period size: 9 Copynumber: 12.4 Consensus size: 9
28299799 AAAATAAAAA
*
28299809 AATTCAGGT
1 AATTCGGGT
28299818 AATTCGGGT
1 AATTCGGGT
*
28299827 ATTTTTC-GGT
1 A--ATTCGGGT
*
28299837 AATTCGGTT
1 AATTCGGGT
*
28299846 AATTCGGTT
1 AATTCGGGT
* *
28299855 AATTCAGTT
1 AATTCGGGT
*
28299864 AATTCGAGT
1 AATTCGGGT
28299873 AATTCGGGT
1 AATTCGGGT
28299882 AATTCGGGT
1 AATTCGGGT
28299891 AATTCGGGT
1 AATTCGGGT
28299900 AATTCGGGT
1 AATTCGGGT
28299909 AATTCGGGT
1 AATTCGGGT
28299918 AATT
1 AATT
28299922 TTTAACCAAA
Statistics
Matches: 92, Mismatches: 9, Indels: 6
0.86 0.08 0.06
Matches are distributed among these distances:
8 3 0.03
9 82 0.89
10 4 0.04
11 3 0.03
ACGTcount: A:0.25, C:0.11, G:0.26, T:0.39
Consensus pattern (9 bp):
AATTCGGGT
Found at i:28304147 original size:27 final size:27
Alignment explanation
Indices: 28304097--28304165 Score: 84
Period size: 27 Copynumber: 2.6 Consensus size: 27
28304087 GCAGACATTT
*
28304097 TTGTGTTTACTGTCCCAACGAACTATC
1 TTGTGTTTACTGTCCCAACAAACTATC
* ** *
28304124 TTGTGTTTATTGTCCCGGCAAACTATT
1 TTGTGTTTACTGTCCCAACAAACTATC
*
28304151 TTGTTTTTACTGTCC
1 TTGTGTTTACTGTCC
28304166 TAGTGAACTC
Statistics
Matches: 35, Mismatches: 7, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
27 35 1.00
ACGTcount: A:0.17, C:0.22, G:0.16, T:0.45
Consensus pattern (27 bp):
TTGTGTTTACTGTCCCAACAAACTATC
Found at i:28309964 original size:28 final size:28
Alignment explanation
Indices: 28309932--28309988 Score: 114
Period size: 28 Copynumber: 2.0 Consensus size: 28
28309922 TCTTAATTAG
28309932 ATGTATTTACCTATTTAGATTTCTTTTT
1 ATGTATTTACCTATTTAGATTTCTTTTT
28309960 ATGTATTTACCTATTTAGATTTCTTTTT
1 ATGTATTTACCTATTTAGATTTCTTTTT
28309988 A
1 A
28309989 CTTTTAAATT
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
28 29 1.00
ACGTcount: A:0.23, C:0.11, G:0.07, T:0.60
Consensus pattern (28 bp):
ATGTATTTACCTATTTAGATTTCTTTTT
Found at i:28315693 original size:14 final size:14
Alignment explanation
Indices: 28315676--28315708 Score: 57
Period size: 14 Copynumber: 2.4 Consensus size: 14
28315666 ATAATAACAA
28315676 AATAGTAGCAATAT
1 AATAGTAGCAATAT
*
28315690 AATAATAGCAATAT
1 AATAGTAGCAATAT
28315704 AATAG
1 AATAG
28315709 CGAAATGATG
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
14 17 1.00
ACGTcount: A:0.55, C:0.06, G:0.12, T:0.27
Consensus pattern (14 bp):
AATAGTAGCAATAT
Found at i:28330571 original size:24 final size:22
Alignment explanation
Indices: 28330526--28330604 Score: 77
Period size: 22 Copynumber: 3.5 Consensus size: 22
28330516 AATGTACAAT
*
28330526 GGTTTGCATATATCATATATAG
1 GGTTTGCATATAACATATATAG
28330548 GGTTTGCATATAACACATATATAG
1 GGTTTGCATAT-A-ACATATATAG
** ** *
28330572 AATTCACATGTAACATATATAG
1 GGTTTGCATATAACATATATAG
*
28330594 GGTTCGCATAT
1 GGTTTGCATAT
28330605 TTGAATCTAG
Statistics
Matches: 45, Mismatches: 10, Indels: 4
0.76 0.17 0.07
Matches are distributed among these distances:
22 28 0.62
23 2 0.04
24 15 0.33
ACGTcount: A:0.35, C:0.13, G:0.16, T:0.35
Consensus pattern (22 bp):
GGTTTGCATATAACATATATAG
Found at i:28330636 original size:20 final size:21
Alignment explanation
Indices: 28330591--28330638 Score: 71
Period size: 21 Copynumber: 2.3 Consensus size: 21
28330581 GTAACATATA
*
28330591 TAGGGTTCGCATATTTGAATC
1 TAGGGTTCGCATATTTGAACC
*
28330612 TAGGGTTCGCATGTTT-AACC
1 TAGGGTTCGCATATTTGAACC
28330632 TAGGGTT
1 TAGGGTT
28330639 TGAATGAAAC
Statistics
Matches: 25, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
20 10 0.40
21 15 0.60
ACGTcount: A:0.21, C:0.15, G:0.27, T:0.38
Consensus pattern (21 bp):
TAGGGTTCGCATATTTGAACC
Found at i:28340195 original size:13 final size:13
Alignment explanation
Indices: 28340177--28340201 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
28340167 GCCGCTTCAG
28340177 TTTACCCTCCCCT
1 TTTACCCTCCCCT
28340190 TTTACCCTCCCC
1 TTTACCCTCCCC
28340202 ATTCACGCTT
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:0.08, C:0.56, G:0.00, T:0.36
Consensus pattern (13 bp):
TTTACCCTCCCCT
Found at i:28340738 original size:15 final size:16
Alignment explanation
Indices: 28340718--28340747 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
28340708 TATTCTACTA
28340718 TTTC-TTTTTTCTTTG
1 TTTCTTTTTTTCTTTG
28340733 TTTCTTTTTTTCTTT
1 TTTCTTTTTTTCTTT
28340748 TTTAGAATCT
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 4 0.29
16 10 0.71
ACGTcount: A:0.00, C:0.13, G:0.03, T:0.83
Consensus pattern (16 bp):
TTTCTTTTTTTCTTTG
Found at i:28345398 original size:11 final size:11
Alignment explanation
Indices: 28345379--28345408 Score: 51
Period size: 11 Copynumber: 2.7 Consensus size: 11
28345369 ATACATGATG
28345379 GCAACCGAGGA
1 GCAACCGAGGA
*
28345390 GCAATCGAGGA
1 GCAACCGAGGA
28345401 GCAACCGA
1 GCAACCGA
28345409 TTGCAATTAA
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
11 17 1.00
ACGTcount: A:0.37, C:0.27, G:0.33, T:0.03
Consensus pattern (11 bp):
GCAACCGAGGA
Found at i:28347144 original size:41 final size:40
Alignment explanation
Indices: 28347081--28347245 Score: 172
Period size: 41 Copynumber: 4.0 Consensus size: 40
28347071 GTGATTGAAT
* * * *
28347081 ATAATACAGACGTTACGTCTAGCAGGCTTAATGCCGGTGA
1 ATAATTCAGACTTTAAGTCTAGCAGGCTAAATGCCGGTGA
28347121 AGTAATTCAGACTTTAAGTCTAGCAGGCTAAATGCCGGTG-
1 A-TAATTCAGACTTTAAGTCTAGCAGGCTAAATGCCGGTGA
* * *
28347161 ATACATTTCAGACTATATGTCTAGCAGGCTAAGTGCCGGTGTA
1 ATA-A-TTCAGACTTTAAGTCTAGCAGGCTAAATGCCGGTG-A
* * * *
28347204 CTGAA-TCAGGCTTTAAGCCTAGCAGGCAAAATGCCGGTGA
1 AT-AATTCAGACTTTAAGTCTAGCAGGCTAAATGCCGGTGA
28347244 AT
1 AT
28347246 CTGTTTAAAT
Statistics
Matches: 104, Mismatches: 15, Indels: 12
0.79 0.11 0.09
Matches are distributed among these distances:
39 2 0.02
40 5 0.05
41 94 0.90
43 2 0.02
44 1 0.01
ACGTcount: A:0.30, C:0.19, G:0.25, T:0.26
Consensus pattern (40 bp):
ATAATTCAGACTTTAAGTCTAGCAGGCTAAATGCCGGTGA
Found at i:28354695 original size:41 final size:41
Alignment explanation
Indices: 28354638--28355490 Score: 1672
Period size: 41 Copynumber: 20.8 Consensus size: 41
28354628 GAATGTAATA
* *
28354638 CAGACTTTAAGTCTAGCAGGCTTAATGCCGGTGATACATTT
1 CAGACTATATGTCTAGCAGGCTTAATGCCGGTGATACATTT
28354679 CAGACTATATGTCTAGCAGGCTTAATGCCGGTGATACATTT
1 CAGACTATATGTCTAGCAGGCTTAATGCCGGTGATACATTT
28354720 CAGACTATATGTCTAGCAGGCTTAATGCCGGTGATACATTT
1 CAGACTATATGTCTAGCAGGCTTAATGCCGGTGATACATTT
28354761 CAGACTATATGTCTAGCAGGCTTAATGCCGGTGATACATTT
1 CAGACTATATGTCTAGCAGGCTTAATGCCGGTGATACATTT
28354802 CAGACTATATGTCTAGCAGGCTTAATGCCGGTGATACATTT
1 CAGACTATATGTCTAGCAGGCTTAATGCCGGTGATACATTT
28354843 CAGACTATATGTCTAGCAGGCTTAATGCCGGTGATACATTT
1 CAGACTATATGTCTAGCAGGCTTAATGCCGGTGATACATTT
28354884 CAGACTATATGTCTAGCAGGCTTAATGCCGGTGATACATTT
1 CAGACTATATGTCTAGCAGGCTTAATGCCGGTGATACATTT
28354925 CAGACTATATGTCTAGCAGGCTTAATGCCGGTGATACATTT
1 CAGACTATATGTCTAGCAGGCTTAATGCCGGTGATACATTT
28354966 CAGACTATATGTCTAGCAGGCTTAATGCCGGTGATACATTT
1 CAGACTATATGTCTAGCAGGCTTAATGCCGGTGATACATTT
28355007 CAGACTATATGTCTAGCAGGCTTAATGCCGGTGATACATTT
1 CAGACTATATGTCTAGCAGGCTTAATGCCGGTGATACATTT
28355048 CAGACTATATGTCTAGCAGGCTTAATGCCGGTGATACATTT
1 CAGACTATATGTCTAGCAGGCTTAATGCCGGTGATACATTT
28355089 CAGACTATATGTCTAGCAGGCTTAATGCCGGTGATACATTT
1 CAGACTATATGTCTAGCAGGCTTAATGCCGGTGATACATTT
28355130 CAGACTATATGTCTAGCAGGCTTAATGCCGGTGATACATTT
1 CAGACTATATGTCTAGCAGGCTTAATGCCGGTGATACATTT
28355171 CAGACTATATGTCTAGCAGGCTTAATGCCGGTGATACATTT
1 CAGACTATATGTCTAGCAGGCTTAATGCCGGTGATACATTT
28355212 CAGACTATATGTCTAGCAGGCTTAATGCCGGTGATACATTT
1 CAGACTATATGTCTAGCAGGCTTAATGCCGGTGATACATTT
28355253 CAGACTATATGTCTAGCAGGCTTAATGCCGGTGATACATTT
1 CAGACTATATGTCTAGCAGGCTTAATGCCGGTGATACATTT
28355294 CAGACTATATGTCTAGCAGGCTTAATGCCGGTGATACATTT
1 CAGACTATATGTCTAGCAGGCTTAATGCCGGTGATACATTT
28355335 CAGACTATATGTCTAGCAGGCTTAATGCCGGTGATACATTT
1 CAGACTATATGTCTAGCAGGCTTAATGCCGGTGATACATTT
28355376 CAGACTATATGTCTAGCAGGCTTAATGCCGGTGATACATTT
1 CAGACTATATGTCTAGCAGGCTTAATGCCGGTGATACATTT
28355417 CAGACTATATGTCTAGCAGGCTTAATGCCGGTGATACATTT
1 CAGACTATATGTCTAGCAGGCTTAATGCCGGTGATACATTT
28355458 CAGACTATATGTCTAGCAGGC-TAAGTGCCGGTG
1 CAGACTATATGTCTAGCAGGCTTAA-TGCCGGTG
28355491 TATTGAATCA
Statistics
Matches: 809, Mismatches: 2, Indels: 2
1.00 0.00 0.00
Matches are distributed among these distances:
40 3 0.00
41 806 1.00
ACGTcount: A:0.27, C:0.20, G:0.22, T:0.31
Consensus pattern (41 bp):
CAGACTATATGTCTAGCAGGCTTAATGCCGGTGATACATTT
Found at i:28356534 original size:92 final size:92
Alignment explanation
Indices: 28356392--28356575 Score: 359
Period size: 92 Copynumber: 2.0 Consensus size: 92
28356382 ATATATGTTC
28356392 ATGAATTGGACTTGCATTTGGAATTAGATATTAAAGTTATGTTTATGTGAGCTTGGTTTCGTAAT
1 ATGAATTGGACTTGCATTTGGAATTAGATATTAAAGTTATGTTTATGTGAGCTTGGTTTCGTAAT
*
28356457 GCCTCGTAACCCTGATTCGGCGACGGA
66 GCCTCGTAACCCTGATTCGGCAACGGA
28356484 ATGAATTGGACTTGCATTTGGAATTAGATATTAAAGTTATGTTTATGTGAGCTTGGTTTCGTAAT
1 ATGAATTGGACTTGCATTTGGAATTAGATATTAAAGTTATGTTTATGTGAGCTTGGTTTCGTAAT
28356549 GCCTCGTAACCCTGATTCGGCAACGGA
66 GCCTCGTAACCCTGATTCGGCAACGGA
28356576 GACGGGTTAG
Statistics
Matches: 91, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
92 91 1.00
ACGTcount: A:0.26, C:0.14, G:0.24, T:0.36
Consensus pattern (92 bp):
ATGAATTGGACTTGCATTTGGAATTAGATATTAAAGTTATGTTTATGTGAGCTTGGTTTCGTAAT
GCCTCGTAACCCTGATTCGGCAACGGA
Found at i:28359224 original size:41 final size:41
Alignment explanation
Indices: 28359167--28359580 Score: 812
Period size: 41 Copynumber: 10.1 Consensus size: 41
28359157 TTATCAAAAN
28359167 GGTGATACATTTCAGACTATATGTCTAGCAGGCTTAATGCC
1 GGTGATACATTTCAGACTATATGTCTAGCAGGCTTAATGCC
28359208 GGTGATACATTTCAGACTATATGTCTAGCAGGCTTAATGCC
1 GGTGATACATTTCAGACTATATGTCTAGCAGGCTTAATGCC
28359249 GGTGATACATTTCAGACTATATGTCTAGCAGGCTTAATGCC
1 GGTGATACATTTCAGACTATATGTCTAGCAGGCTTAATGCC
28359290 GGTGATACATTTCAGACTATATGTCTAGCAGGCTTAATGCC
1 GGTGATACATTTCAGACTATATGTCTAGCAGGCTTAATGCC
28359331 GGTGATACATTTCAGACTATATGTCTAGCAGGCTTAATGCC
1 GGTGATACATTTCAGACTATATGTCTAGCAGGCTTAATGCC
28359372 GGTGATACATTTCAGACTATATGTCTAGCAGGCTTAATGCC
1 GGTGATACATTTCAGACTATATGTCTAGCAGGCTTAATGCC
28359413 GGTGATACATTTCAGACTATATGTCTAGCAGGCTTAATGCC
1 GGTGATACATTTCAGACTATATGTCTAGCAGGCTTAATGCC
28359454 GGTGATACATTTCAGACTATATGTCTAGCAGGCTTAATGCC
1 GGTGATACATTTCAGACTATATGTCTAGCAGGCTTAATGCC
28359495 GGTGATACATTTCAGACTATATGTCTAGCAGGCTTAATGCC
1 GGTGATACATTTCAGACTATATGTCTAGCAGGCTTAATGCC
28359536 GGTGATACATTTCAGACTATATGTCTAGCAGGC-TAAGTGCC
1 GGTGATACATTTCAGACTATATGTCTAGCAGGCTTAA-TGCC
28359577 GGTG
1 GGTG
28359581 TACTGAATCA
Statistics
Matches: 372, Mismatches: 0, Indels: 2
0.99 0.00 0.01
Matches are distributed among these distances:
40 3 0.01
41 369 0.99
ACGTcount: A:0.27, C:0.19, G:0.23, T:0.31
Consensus pattern (41 bp):
GGTGATACATTTCAGACTATATGTCTAGCAGGCTTAATGCC
Found at i:28363833 original size:15 final size:16
Alignment explanation
Indices: 28363800--28363833 Score: 52
Period size: 17 Copynumber: 2.1 Consensus size: 16
28363790 TATCTCGTTC
28363800 AAAAATAATGCACTATA
1 AAAAATAATGCAC-ATA
28363817 AAAAATAATGCAC-TA
1 AAAAATAATGCACATA
28363832 AA
1 AA
28363834 CCTATTTGAA
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
15 4 0.24
17 13 0.76
ACGTcount: A:0.62, C:0.12, G:0.06, T:0.21
Consensus pattern (16 bp):
AAAAATAATGCACATA
Found at i:28368550 original size:6 final size:6
Alignment explanation
Indices: 28368541--28368567 Score: 54
Period size: 6 Copynumber: 4.5 Consensus size: 6
28368531 GGTTATTGAT
28368541 TAAATA TAAATA TAAATA TAAATA TAA
1 TAAATA TAAATA TAAATA TAAATA TAA
28368568 TATTTTTATA
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 21 1.00
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (6 bp):
TAAATA
Found at i:28372997 original size:24 final size:24
Alignment explanation
Indices: 28372969--28373021 Score: 79
Period size: 24 Copynumber: 2.2 Consensus size: 24
28372959 AAGGCAATTA
* *
28372969 AAGGAAGCTATAAGAGAATGAGGC
1 AAGGAAGCAATAAGAGAATAAGGC
*
28372993 AAGGAAGCAATAAGAGAATAAGGT
1 AAGGAAGCAATAAGAGAATAAGGC
28373017 AAGGA
1 AAGGA
28373022 GAGAGATAGA
Statistics
Matches: 26, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
24 26 1.00
ACGTcount: A:0.51, C:0.06, G:0.32, T:0.11
Consensus pattern (24 bp):
AAGGAAGCAATAAGAGAATAAGGC
Found at i:28374157 original size:14 final size:16
Alignment explanation
Indices: 28374127--28374162 Score: 51
Period size: 16 Copynumber: 2.4 Consensus size: 16
28374117 AATAAAGAGA
28374127 AATAAAAAGAGTAAAG
1 AATAAAAAGAGTAAAG
28374143 AATAAAAA-A-TAAAG
1 AATAAAAAGAGTAAAG
28374157 AA-AAAA
1 AATAAAA
28374163 TGAGAGAAAA
Statistics
Matches: 20, Mismatches: 0, Indels: 3
0.87 0.00 0.13
Matches are distributed among these distances:
13 4 0.20
14 7 0.35
15 1 0.05
16 8 0.40
ACGTcount: A:0.78, C:0.00, G:0.11, T:0.11
Consensus pattern (16 bp):
AATAAAAAGAGTAAAG
Found at i:28374873 original size:96 final size:96
Alignment explanation
Indices: 28374759--28374948 Score: 326
Period size: 96 Copynumber: 2.0 Consensus size: 96
28374749 TGATGCATGG
* *
28374759 ACATGTACACATCCACTTCATTTGGACGACAAGACCGTGAAAAATTGGGTCATAAGGATGTTAAT
1 ACATGTACACATCAACTTCATTTGGACGACAAGACCGTGAAAAACTGGGTCATAAGGATGTTAAT
*
28374824 TTGACCCAGTAAAAGATGTGATAAAAGATGT
66 TTGACCCAATAAAAGATGTGATAAAAGATGT
* *
28374855 ACATGTACACATCAACTTCATTTGGATGACAAGACCGTGTAAAACTGGGTCATAAGGATGTTAAT
1 ACATGTACACATCAACTTCATTTGGACGACAAGACCGTGAAAAACTGGGTCATAAGGATGTTAAT
*
28374920 TTGACCTAATAAAAGATGTGATAAAAGAT
66 TTGACCCAATAAAAGATGTGATAAAAGAT
28374949 AAACATGTTT
Statistics
Matches: 88, Mismatches: 6, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
96 88 1.00
ACGTcount: A:0.38, C:0.15, G:0.20, T:0.27
Consensus pattern (96 bp):
ACATGTACACATCAACTTCATTTGGACGACAAGACCGTGAAAAACTGGGTCATAAGGATGTTAAT
TTGACCCAATAAAAGATGTGATAAAAGATGT
Found at i:28379524 original size:31 final size:31
Alignment explanation
Indices: 28379459--28379540 Score: 83
Period size: 31 Copynumber: 2.6 Consensus size: 31
28379449 ATGTAAAAAA
* ** * *
28379459 AAAAGAATGAAAGAACAAAGGTAAGTTTGTTC
1 AAAAGAAT-AAAAAACAAAGAAAAATTTGCTC
28379491 AAAAGAATAAAAAACAAAGAAAAATTTGCTC
1 AAAAGAATAAAAAACAAAGAAAAATTTGCTC
** *
28379522 AAAAGTCTAAAAAATAAAG
1 AAAAGAATAAAAAACAAAG
28379541 GTTGAGCATG
Statistics
Matches: 42, Mismatches: 8, Indels: 1
0.82 0.16 0.02
Matches are distributed among these distances:
31 34 0.81
32 8 0.19
ACGTcount: A:0.60, C:0.07, G:0.15, T:0.18
Consensus pattern (31 bp):
AAAAGAATAAAAAACAAAGAAAAATTTGCTC
Found at i:28381117 original size:39 final size:39
Alignment explanation
Indices: 28381022--28381102 Score: 130
Period size: 39 Copynumber: 2.1 Consensus size: 39
28381012 CGCGTACCTA
*
28381022 GAAAAAAATTAAAA-AAAATAGAATTAAAAGTTTTGATCT
1 GAAAAAAA-TAAAATAAAACAGAATTAAAAGTTTTGATCT
28381061 GAAAAAAATAAAATAAAACAGAATTAAAAGTTTTGAT-T
1 GAAAAAAATAAAATAAAACAGAATTAAAAGTTTTGATCT
28381099 GAAA
1 GAAA
28381103 TTTCAAAAAT
Statistics
Matches: 40, Mismatches: 1, Indels: 3
0.91 0.02 0.07
Matches are distributed among these distances:
38 10 0.25
39 30 0.75
ACGTcount: A:0.60, C:0.02, G:0.11, T:0.26
Consensus pattern (39 bp):
GAAAAAAATAAAATAAAACAGAATTAAAAGTTTTGATCT
Found at i:28381853 original size:10 final size:10
Alignment explanation
Indices: 28381826--28381873 Score: 71
Period size: 10 Copynumber: 4.8 Consensus size: 10
28381816 TTAAATTCTA
*
28381826 AAAGATAAAT
1 AAAGATAATT
28381836 ACAA-ATAATT
1 A-AAGATAATT
28381846 AAAGATAATT
1 AAAGATAATT
28381856 AAAGATAATT
1 AAAGATAATT
28381866 AAAGATAA
1 AAAGATAA
28381874 ATGAAAATAA
Statistics
Matches: 35, Mismatches: 1, Indels: 4
0.88 0.03 0.10
Matches are distributed among these distances:
9 2 0.06
10 31 0.89
11 2 0.06
ACGTcount: A:0.65, C:0.02, G:0.08, T:0.25
Consensus pattern (10 bp):
AAAGATAATT
Found at i:28381883 original size:20 final size:19
Alignment explanation
Indices: 28381826--28381883 Score: 80
Period size: 20 Copynumber: 2.9 Consensus size: 19
28381816 TTAAATTCTA
28381826 AAAGATAAATACAAATAATT
1 AAAGATAAATA-AAATAATT
*
28381846 AAAGATAATTAAAGATAATT
1 AAAGATAAATAAA-ATAATT
28381866 AAAGATAAATGAAAATAA
1 AAAGATAAAT-AAAATAA
28381884 ATCCTAAAAT
Statistics
Matches: 34, Mismatches: 2, Indels: 4
0.85 0.05 0.10
Matches are distributed among these distances:
19 2 0.06
20 29 0.85
21 3 0.09
ACGTcount: A:0.66, C:0.02, G:0.09, T:0.24
Consensus pattern (19 bp):
AAAGATAAATAAAATAATT
Found at i:28382706 original size:99 final size:99
Alignment explanation
Indices: 28382530--28382721 Score: 289
Period size: 99 Copynumber: 1.9 Consensus size: 99
28382520 TTAATTTATT
**
28382530 ATTTATTTATTTTTGCTTAAGAATATATTGAACCTTTTGACGCGAAGAGAGATGACAACCAAGCA
1 ATTTATTTATTTTTGCTTAAGAATATATCAAACCTTTTGACGCGAAGAGAGATGACAACCAAGCA
28382595 CCCCAACTCGGTTACTCAGCCCAACATACTCCTA
66 CCCCAACTCGGTTACTCAGCCCAACATACTCCTA
* * * *
28382629 ATTTATTATATTTTT-CTTAAGAATATATCAAACCTTTTGACGCGAAGAGATATGATAGCTAAGC
1 ATTTATT-TATTTTTGCTTAAGAATATATCAAACCTTTTGACGCGAAGAGAGATGACAACCAAGC
*
28382693 ACCTC-ACTCCGGTTACTCAGCCCAACATA
65 ACCCCAACT-CGGTTACTCAGCCCAACATA
28382722 TTCTTAAGTA
Statistics
Matches: 84, Mismatches: 7, Indels: 4
0.88 0.07 0.04
Matches are distributed among these distances:
98 3 0.04
99 74 0.88
100 7 0.08
ACGTcount: A:0.33, C:0.23, G:0.14, T:0.31
Consensus pattern (99 bp):
ATTTATTTATTTTTGCTTAAGAATATATCAAACCTTTTGACGCGAAGAGAGATGACAACCAAGCA
CCCCAACTCGGTTACTCAGCCCAACATACTCCTA
Found at i:28383725 original size:20 final size:20
Alignment explanation
Indices: 28383700--28383760 Score: 70
Period size: 23 Copynumber: 3.0 Consensus size: 20
28383690 ATATCCAAAC
*
28383700 AAAATAAATTAATAAATAAT
1 AAAATAAAATAATAAATAAT
*
28383720 AAAATAAAGTAATAAAATAAAAT
1 AAAATAAAATAAT-AAAT--AAT
28383743 AAAATAAAATAA-AAATAA
1 AAAATAAAATAATAAATAA
28383761 AAATTTGGTT
Statistics
Matches: 36, Mismatches: 2, Indels: 7
0.80 0.04 0.16
Matches are distributed among these distances:
19 2 0.06
20 12 0.33
21 8 0.22
23 14 0.39
ACGTcount: A:0.75, C:0.00, G:0.02, T:0.23
Consensus pattern (20 bp):
AAAATAAAATAATAAATAAT
Found at i:28383727 original size:5 final size:5
Alignment explanation
Indices: 28383717--28383762 Score: 60
Period size: 5 Copynumber: 9.4 Consensus size: 5
28383707 ATTAATAAAT
*
28383717 AATAA AATAA AGT-- AATAA AATAA AATAA AATAA AATAAA AATAA AA
1 AATAA AATAA AATAA AATAA AATAA AATAA AATAA AAT-AA AATAA AA
28383763 ATTTGGTTGC
Statistics
Matches: 36, Mismatches: 2, Indels: 6
0.82 0.05 0.14
Matches are distributed among these distances:
3 2 0.06
5 29 0.81
6 5 0.14
ACGTcount: A:0.78, C:0.00, G:0.02, T:0.20
Consensus pattern (5 bp):
AATAA
Found at i:28386149 original size:49 final size:50
Alignment explanation
Indices: 28386075--28386301 Score: 251
Period size: 49 Copynumber: 4.6 Consensus size: 50
28386065 TGAGGTCACG
*
28386075 TGTGTAGTACTAAGTGCAGGGTACTACGTGTACCGGATAATT-GGTCGCA
1 TGTGTAGTACTAAGTGCAGGCTACTACGTGTACCGGATAATTAGGTCGCA
* * * * * * * *
28386124 TGTGTAGTACTAAGTGTAGGCTACTATGCGTACCCGATAACTTCGATCACG
1 TGTGTAGTACTAAGTGCAGGCTACTACGTGTACCGGATAA-TTAGGTCGCA
* * ** * *
28386175 TGTGTAGTACTAAGTGCAGGCTACTACGTGTATCAGATGGTTAGGTCTCG
1 TGTGTAGTACTAAGTGCAGGCTACTACGTGTACCGGATAATTAGGTCGCA
* * * *
28386225 TGTGTAGTACTAAGTACAAGCTACTACGTGTACCGGATAACT-GGTCGTA
1 TGTGTAGTACTAAGTGCAGGCTACTACGTGTACCGGATAATTAGGTCGCA
*
28386274 TGTGTAGTACTAAGCGCAGGCTACTACG
1 TGTGTAGTACTAAGTGCAGGCTACTACG
28386302 CATACCAGAT
Statistics
Matches: 145, Mismatches: 31, Indels: 4
0.81 0.17 0.02
Matches are distributed among these distances:
49 64 0.44
50 44 0.30
51 37 0.26
ACGTcount: A:0.25, C:0.19, G:0.27, T:0.29
Consensus pattern (50 bp):
TGTGTAGTACTAAGTGCAGGCTACTACGTGTACCGGATAATTAGGTCGCA
Found at i:28389126 original size:15 final size:15
Alignment explanation
Indices: 28389097--28389141 Score: 63
Period size: 15 Copynumber: 2.9 Consensus size: 15
28389087 AATGCTGTAA
28389097 ATGGTATTTCCTTATC
1 ATGG-ATTTCCTTATC
*
28389113 ATGGATTTCTTTATC
1 ATGGATTTCCTTATC
*
28389128 TTGGATTTCCTTAT
1 ATGGATTTCCTTAT
28389142 TCTGGGCTTG
Statistics
Matches: 26, Mismatches: 3, Indels: 1
0.87 0.10 0.03
Matches are distributed among these distances:
15 22 0.85
16 4 0.15
ACGTcount: A:0.18, C:0.16, G:0.13, T:0.53
Consensus pattern (15 bp):
ATGGATTTCCTTATC
Found at i:28393225 original size:49 final size:50
Alignment explanation
Indices: 28393143--28393387 Score: 309
Period size: 49 Copynumber: 5.0 Consensus size: 50
28393133 ATCTATTGTG
* *
28393143 AGGTCACGTGTGTAGTACTAAGTGCAGGGTACTACGTGTACCAGATAATT
1 AGGTCACATGTGTAGTACTAAGTGCAGGCTACTACGTGTACCAGATAATT
* * *
28393193 -GGTCGCATGTGTAGTACTAAGTGCAGGCTACTATGTGTACCCGATAACTT
1 AGGTCACATGTGTAGTACTAAGTGCAGGCTACTACGTGTACCAGATAA-TT
* * * **
28393243 CGATCACGTGTGTAGTACTAAGTGCAGGCTACTACGTGT--CAGATGGTT
1 AGGTCACATGTGTAGTACTAAGTGCAGGCTACTACGTGTACCAGATAATT
* * *
28393291 AGGTCACATGTGTAGTACTAAGTCCAGGCTACTTCGTGTACCGGATAATT
1 AGGTCACATGTGTAGTACTAAGTGCAGGCTACTACGTGTACCAGATAATT
* * *
28393341 -GGTCGCATGTGTAGTACTAAGTGCAGGCTACTATGCGTACCAGATAA
1 AGGTCACATGTGTAGTACTAAGTGCAGGCTACTACGTGTACCAGATAA
28393388 CTTTGGCTAC
Statistics
Matches: 165, Mismatches: 26, Indels: 9
0.82 0.13 0.05
Matches are distributed among these distances:
48 36 0.22
49 87 0.53
50 8 0.05
51 34 0.21
ACGTcount: A:0.26, C:0.19, G:0.27, T:0.29
Consensus pattern (50 bp):
AGGTCACATGTGTAGTACTAAGTGCAGGCTACTACGTGTACCAGATAATT
Found at i:28393338 original size:99 final size:97
Alignment explanation
Indices: 28393146--28393387 Score: 317
Period size: 99 Copynumber: 2.5 Consensus size: 97
28393136 TATTGTGAGG
* *
28393146 TCACGTGTGTAGTACTAAGTGCAGGGTACTACGTGTACCAGATAATTGGTCGCATGTGTAGTACT
1 TCACGTGTGTAGTACTAAGTGCAGGCTACTACGTGTA-CAGATAATTGGTCACATGTGTAGTACT
*
28393211 AAGTGCAGGCTACTATGTGTACCCGATAACTTCGA
65 AAGTCCAGGCTACTATGTGTACCCGATAA-TT-GA
**
28393246 TCACGTGTGTAGTACTAAGTGCAGGCTACTACGTGT-CAGATGGTTAGGTCACATGTGTAGTACT
1 TCACGTGTGTAGTACTAAGTGCAGGCTACTACGTGTACAGATAATT-GGTCACATGTGTAGTACT
* *
28393310 AAGTCCAGGCTACT-TCGTGTACCGGATAATTGG
65 AAGTCCAGGCTACTAT-GTGTACCCGATAATTGA
* * * *
28393343 TCGCATGTGTAGTACTAAGTGCAGGCTACTATGCGTACCAGATAA
1 TCACGTGTGTAGTACTAAGTGCAGGCTACTACGTGTA-CAGATAA
28393388 CTTTGGCTAC
Statistics
Matches: 125, Mismatches: 13, Indels: 9
0.85 0.09 0.06
Matches are distributed among these distances:
97 33 0.26
98 10 0.08
99 47 0.38
100 35 0.28
ACGTcount: A:0.26, C:0.19, G:0.26, T:0.29
Consensus pattern (97 bp):
TCACGTGTGTAGTACTAAGTGCAGGCTACTACGTGTACAGATAATTGGTCACATGTGTAGTACTA
AGTCCAGGCTACTATGTGTACCCGATAATTGA
Found at i:28395295 original size:37 final size:39
Alignment explanation
Indices: 28395254--28395327 Score: 107
Period size: 39 Copynumber: 1.9 Consensus size: 39
28395244 TGCGTACCTA
*
28395254 GAAAAAAAT-AAA-AAAACAGTATTAAAAATTTTGATCT
1 GAAAAAAATAAAATAAAACAGAATTAAAAATTTTGATCT
* *
28395291 GAAAAAAATAAAATAAAATAGAATTAAAAGTTTTGAT
1 GAAAAAAATAAAATAAAACAGAATTAAAAATTTTGAT
28395328 TGGAATTTCA
Statistics
Matches: 32, Mismatches: 3, Indels: 2
0.86 0.08 0.05
Matches are distributed among these distances:
37 9 0.28
38 3 0.09
39 20 0.62
ACGTcount: A:0.61, C:0.03, G:0.09, T:0.27
Consensus pattern (39 bp):
GAAAAAAATAAAATAAAACAGAATTAAAAATTTTGATCT
Found at i:28404696 original size:288 final size:288
Alignment explanation
Indices: 28404174--28404729 Score: 810
Period size: 288 Copynumber: 1.9 Consensus size: 288
28404164 TGGGATCCAA
*
28404174 GGGTCAATAACTAAACTACTCCGATCCAACAGTGCTGAGCTGTTTAGGGGTGTTACTGGGGTCGC
1 GGGTCAATAACTAAACTACTCCGATCCAACAGTGCTGAGCTGTTTAGGGGTGTTACTAGGGTCGC
*
28404239 CCCGATTGTGGCCGAATATTGGTTGGAGGTCACAGAGAGAATTATGAATGATATCGACTACACTC
66 CCCGATTGTGGCCGAATATTGGTTGGAGGCCACAGAGAGAATTATGAATGATATCGACTACACTC
* * ** * * **
28404304 CTGAGCAGAAATTAAAGGGTGCAGTGTCGCTGCTGTGTGATGAAGCTTACTTGTGGTGGCTGACA
131 CTAAGAAGAAATTAAAAAGTGCAATGTCGCTGCTGTGCGATGAAGCTTACCAGTGGTGGCTGACA
* * * *
28404369 ATTGAGGAGGGTACTCAGCCTGATTAGGTCATTTGGGAATATTTTAAG-AATGTCTTCCAGAGCA
196 ATTGAGGAGGGTACTAAGCCTGATTAGATCACTTGGGAATATTTT-AGTAACGTCTTCCAGAGCA
28404433 AGTATATGGGGGGTGTTACTGGGAGCCGT
260 AGTATATGGGGGGTGTTACTGGGAGCCGT
* * * *
28404462 GGGTCGATAACTAAA-TAACTTCGGTCCAACGGTGCTGAGCTGTTTAGGGGTGTTACTAGGGTCG
1 GGGTCAATAACTAAACT-ACTCCGATCCAACAGTGCTGAGCTGTTTAGGGGTGTTACTAGGGTCG
* * * **
28404526 CCTCGATTGTGGCTGAATATTGGTTGGAGGCCACAGAGAGGATTATGAATGATATCGACTGTACT
65 CCCCGATTGTGGCCGAATATTGGTTGGAGGCCACAGAGAGAATTATGAATGATATCGACTACACT
** * *
28404591 TTTAAGAAGAAATTAAAAAGTGCAATGTCGTTGCTTTGCGATGAAGCTTACCAGTGGTGGCTGAC
130 CCTAAGAAGAAATTAAAAAGTGCAATGTCGCTGCTGTGCGATGAAGCTTACCAGTGGTGGCTGAC
* * *
28404656 CATTGAGGAGGGTATTAAGCTTGATTAGATCACTTGGGAATATTTTAGTAACGTCTTCCAGAGCA
195 AATTGAGGAGGGTACTAAGCCTGATTAGATCACTTGGGAATATTTTAGTAACGTCTTCCAGAGCA
28404721 AGTATATGG
260 AGTATATGG
28404730 AGTGGAGGCT
Statistics
Matches: 236, Mismatches: 30, Indels: 4
0.87 0.11 0.01
Matches are distributed among these distances:
287 3 0.01
288 233 0.99
ACGTcount: A:0.26, C:0.16, G:0.29, T:0.29
Consensus pattern (288 bp):
GGGTCAATAACTAAACTACTCCGATCCAACAGTGCTGAGCTGTTTAGGGGTGTTACTAGGGTCGC
CCCGATTGTGGCCGAATATTGGTTGGAGGCCACAGAGAGAATTATGAATGATATCGACTACACTC
CTAAGAAGAAATTAAAAAGTGCAATGTCGCTGCTGTGCGATGAAGCTTACCAGTGGTGGCTGACA
ATTGAGGAGGGTACTAAGCCTGATTAGATCACTTGGGAATATTTTAGTAACGTCTTCCAGAGCAA
GTATATGGGGGGTGTTACTGGGAGCCGT
Found at i:28411894 original size:46 final size:46
Alignment explanation
Indices: 28411832--28412059 Score: 289
Period size: 46 Copynumber: 5.0 Consensus size: 46
28411822 GCTCTCTGAT
* * *
28411832 ATGAAATGTATAAGACCATGGTTGAAAGATACCATGGCAACCTGAT
1 ATGAAATGAATAAGACCATGGTTGAAAGATACCATGGCAACATGAC
28411878 ATGAAATGAATAAGACCATGGTTGAAAGATACCATGGCAACATGAC
1 ATGAAATGAATAAGACCATGGTTGAAAGATACCATGGCAACATGAC
** *
28411924 GGGAAATGAATAAGACCATGGTTGAAAGATACCATGGCAGA-GTGAC
1 ATGAAATGAATAAGACCATGGTTGAAAGATACCATGGCA-ACATGAC
* ** *
28411970 ACGAAATGTGTAAGACCATGGTTGAAAAATACCATGGCAACATGAC
1 ATGAAATGAATAAGACCATGGTTGAAAGATACCATGGCAACATGAC
* * * * *
28412016 A-GAAAGTGAGTAAGACCATAGTTGAAAGACACTATGGCATCATG
1 ATGAAA-TGAATAAGACCATGGTTGAAAGATACCATGGCAACATG
28412060 TCAAAGATAA
Statistics
Matches: 161, Mismatches: 18, Indels: 6
0.87 0.10 0.03
Matches are distributed among these distances:
45 5 0.03
46 155 0.96
47 1 0.01
ACGTcount: A:0.41, C:0.15, G:0.24, T:0.20
Consensus pattern (46 bp):
ATGAAATGAATAAGACCATGGTTGAAAGATACCATGGCAACATGAC
Found at i:28412360 original size:16 final size:17
Alignment explanation
Indices: 28412339--28412371 Score: 59
Period size: 17 Copynumber: 2.0 Consensus size: 17
28412329 ATGATGGTGC
28412339 ATGAAAT-ATTGATATA
1 ATGAAATGATTGATATA
28412355 ATGAAATGATTGATATA
1 ATGAAATGATTGATATA
28412372 TACTTATGAA
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
16 7 0.44
17 9 0.56
ACGTcount: A:0.48, C:0.00, G:0.15, T:0.36
Consensus pattern (17 bp):
ATGAAATGATTGATATA
Found at i:28413511 original size:20 final size:20
Alignment explanation
Indices: 28413486--28413534 Score: 62
Period size: 20 Copynumber: 2.5 Consensus size: 20
28413476 GCGTGTGTCT
*
28413486 CCTCCACATAATCGTGTAGG
1 CCTCCACATAAGCGTGTAGG
**
28413506 CCTCCACATGGGCGTGTAGG
1 CCTCCACATAAGCGTGTAGG
*
28413526 CCTCGACAT
1 CCTCCACAT
28413535 GGCCTAGACA
Statistics
Matches: 25, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
20 25 1.00
ACGTcount: A:0.20, C:0.33, G:0.24, T:0.22
Consensus pattern (20 bp):
CCTCCACATAAGCGTGTAGG
Found at i:28413535 original size:20 final size:20
Alignment explanation
Indices: 28413498--28413536 Score: 69
Period size: 20 Copynumber: 1.9 Consensus size: 20
28413488 TCCACATAAT
28413498 CGTGTAGGCCTCCACATGGG
1 CGTGTAGGCCTCCACATGGG
*
28413518 CGTGTAGGCCTCGACATGG
1 CGTGTAGGCCTCCACATGG
28413537 CCTAGACACT
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
20 18 1.00
ACGTcount: A:0.15, C:0.28, G:0.36, T:0.21
Consensus pattern (20 bp):
CGTGTAGGCCTCCACATGGG
Found at i:28418181 original size:19 final size:20
Alignment explanation
Indices: 28418157--28418194 Score: 53
Period size: 19 Copynumber: 1.9 Consensus size: 20
28418147 GGTACCACCA
28418157 AAACAT-ATATCA-CATCTTT
1 AAACATCAT-TCATCATCTTT
28418176 AAACATCATTCATCATCTT
1 AAACATCATTCATCATCTT
28418195 ACCACCTTAT
Statistics
Matches: 17, Mismatches: 0, Indels: 3
0.85 0.00 0.15
Matches are distributed among these distances:
19 9 0.53
20 8 0.47
ACGTcount: A:0.39, C:0.24, G:0.00, T:0.37
Consensus pattern (20 bp):
AAACATCATTCATCATCTTT
Found at i:28418485 original size:46 final size:46
Alignment explanation
Indices: 28418418--28419326 Score: 1673
Period size: 46 Copynumber: 19.7 Consensus size: 46
28418408 AACCCGCCCC
* * *
28418418 TAAGTGAACTCGGACTCAACTCAACGAGATCGGGCGTTCGCATCCA
1 TAAGTGAACTCGGACTCAACTCAACGAGTTCGGACATTCGCATCCA
* * *
28418464 TAAGTGAACTCAGACTCAACTCAACGAGTTCGGATGCCTAGTT-ACAT--T
1 TAAGTGAACTCGGACTCAACTCAACGAGTTCGGA---C-A-TTCGCATCCA
* *
28418512 TCA-CGAACTCGGACTCAACTCAACGAGTTCGGACATTCGCATCCA
1 TAAGTGAACTCGGACTCAACTCAACGAGTTCGGACATTCGCATCCA
28418557 TAAGTGAACTCGGACTCAACTCAACGAGTTCGGACATTCGCATCCA
1 TAAGTGAACTCGGACTCAACTCAACGAGTTCGGACATTCGCATCCA
28418603 TAAGTGAACTCGGACTCAACTCAACGAGTTCGGACATTCGCATCCA
1 TAAGTGAACTCGGACTCAACTCAACGAGTTCGGACATTCGCATCCA
28418649 TAAGTGAACTCGGACTCAACTCAACGAGTTCGGACATTCGCATCCA
1 TAAGTGAACTCGGACTCAACTCAACGAGTTCGGACATTCGCATCCA
28418695 TAAGTGAACTCGGACTCAACTCAACGAGTTCGGACATTCGCATCCA
1 TAAGTGAACTCGGACTCAACTCAACGAGTTCGGACATTCGCATCCA
28418741 TAAGTGAACTCGGACTCAACTCAACGAGTTCGGACATTCGCATCCA
1 TAAGTGAACTCGGACTCAACTCAACGAGTTCGGACATTCGCATCCA
28418787 TAAGTGAACTCGGACTCAACTCAACGAGTTCGGACATTCGCATCCA
1 TAAGTGAACTCGGACTCAACTCAACGAGTTCGGACATTCGCATCCA
28418833 TAAGTGAACTCGGACTCAACTCAACGAGTTCGGACATTCGCATCCA
1 TAAGTGAACTCGGACTCAACTCAACGAGTTCGGACATTCGCATCCA
28418879 TAAGTGAACTCGGACTCAACTCAACGAGTTCGGACATTCGCATCCA
1 TAAGTGAACTCGGACTCAACTCAACGAGTTCGGACATTCGCATCCA
28418925 TAAGTGAACTCGGACTCAACTCAACGAGTTCGGACATTCGCATCCA
1 TAAGTGAACTCGGACTCAACTCAACGAGTTCGGACATTCGCATCCA
28418971 TAAGTGAACTCGGACTCAACTCAACGAGTTCGGACATTCGCATCCA
1 TAAGTGAACTCGGACTCAACTCAACGAGTTCGGACATTCGCATCCA
28419017 TAAGTGAACTCGGACTCAACTCAACGAGTTCGGACATTCGCATCCA
1 TAAGTGAACTCGGACTCAACTCAACGAGTTCGGACATTCGCATCCA
28419063 TAAGTGAACTCGGACTCAACTCAACGAGTTCGGACATTCGCATCCA
1 TAAGTGAACTCGGACTCAACTCAACGAGTTCGGACATTCGCATCCA
28419109 TAAGTGAACTCGGACTCAACTCAACGAGTTCGGACATTCGCATCCA
1 TAAGTGAACTCGGACTCAACTCAACGAGTTCGGACATTCGCATCCA
28419155 TAAGTGAACTCGGACTCAACTCAACGAGTTCGGACATTCGCATCCA
1 TAAGTGAACTCGGACTCAACTCAACGAGTTCGGACATTCGCATCCA
28419201 TAAGTGAACTCGGACTCAACTCAACGAGTTCGGACATTCGCATCCA
1 TAAGTGAACTCGGACTCAACTCAACGAGTTCGGACATTCGCATCCA
28419247 TAAGTGAACTCGGACTCAACTCAACGAGTTCGGACATTCGCATCCA
1 TAAGTGAACTCGGACTCAACTCAACGAGTTCGGACATTCGCATCCA
28419293 TAAGTGAACTCGGACTCAACTCAACGAGTTCGGA
1 TAAGTGAACTCGGACTCAACTCAACGAGTTCGGA
28419327 TGCTCAACCA
Statistics
Matches: 841, Mismatches: 13, Indels: 18
0.96 0.01 0.02
Matches are distributed among these distances:
42 2 0.00
43 4 0.00
44 1 0.00
45 2 0.00
46 796 0.95
47 28 0.03
48 2 0.00
49 1 0.00
50 3 0.00
51 2 0.00
ACGTcount: A:0.30, C:0.28, G:0.20, T:0.22
Consensus pattern (46 bp):
TAAGTGAACTCGGACTCAACTCAACGAGTTCGGACATTCGCATCCA
Found at i:28426495 original size:19 final size:20
Alignment explanation
Indices: 28426471--28426508 Score: 53
Period size: 19 Copynumber: 1.9 Consensus size: 20
28426461 GGTACCACCA
28426471 AAACAT-ATATCA-CATCTTT
1 AAACATCAT-TCATCATCTTT
28426490 AAACATCATTCATCATCTT
1 AAACATCATTCATCATCTT
28426509 ACCACCTTAT
Statistics
Matches: 17, Mismatches: 0, Indels: 3
0.85 0.00 0.15
Matches are distributed among these distances:
19 9 0.53
20 8 0.47
ACGTcount: A:0.39, C:0.24, G:0.00, T:0.37
Consensus pattern (20 bp):
AAACATCATTCATCATCTTT
Found at i:28426888 original size:19 final size:20
Alignment explanation
Indices: 28426864--28426901 Score: 53
Period size: 19 Copynumber: 1.9 Consensus size: 20
28426854 GGTACCACCA
28426864 AAACAT-ATATCA-CATCTTT
1 AAACATCAT-TCATCATCTTT
28426883 AAACATCATTCATCATCTT
1 AAACATCATTCATCATCTT
28426902 ACCACCTTAT
Statistics
Matches: 17, Mismatches: 0, Indels: 3
0.85 0.00 0.15
Matches are distributed among these distances:
19 9 0.53
20 8 0.47
ACGTcount: A:0.39, C:0.24, G:0.00, T:0.37
Consensus pattern (20 bp):
AAACATCATTCATCATCTTT
Found at i:28443105 original size:4 final size:4
Alignment explanation
Indices: 28443096--28443120 Score: 50
Period size: 4 Copynumber: 6.2 Consensus size: 4
28443086 ATTAAAGTAA
28443096 AAAT AAAT AAAT AAAT AAAT AAAT A
1 AAAT AAAT AAAT AAAT AAAT AAAT A
28443121 CTCAAAAATT
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 21 1.00
ACGTcount: A:0.76, C:0.00, G:0.00, T:0.24
Consensus pattern (4 bp):
AAAT
Found at i:28449696 original size:10 final size:10
Alignment explanation
Indices: 28449681--28449705 Score: 50
Period size: 10 Copynumber: 2.5 Consensus size: 10
28449671 ATTAATGTAG
28449681 TATTTATGAA
1 TATTTATGAA
28449691 TATTTATGAA
1 TATTTATGAA
28449701 TATTT
1 TATTT
28449706 GTATGAAATA
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 15 1.00
ACGTcount: A:0.36, C:0.00, G:0.08, T:0.56
Consensus pattern (10 bp):
TATTTATGAA
Found at i:28453640 original size:21 final size:21
Alignment explanation
Indices: 28453616--28453656 Score: 55
Period size: 21 Copynumber: 2.0 Consensus size: 21
28453606 ATATTTTTAG
28453616 AATTTTAATATAATTACTAAT
1 AATTTTAATATAATTACTAAT
** *
28453637 AATTTTTTTATAATTTCTAA
1 AATTTTAATATAATTACTAA
28453657 ACTTTTTATA
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:0.41, C:0.05, G:0.00, T:0.54
Consensus pattern (21 bp):
AATTTTAATATAATTACTAAT
Found at i:28472630 original size:17 final size:17
Alignment explanation
Indices: 28472608--28472644 Score: 56
Period size: 17 Copynumber: 2.2 Consensus size: 17
28472598 TCATTGTCAC
*
28472608 AAAGTTATTCATATTAA
1 AAAGTTATTAATATTAA
*
28472625 AAAGTTATTAATTTTAA
1 AAAGTTATTAATATTAA
28472642 AAA
1 AAA
28472645 CGTCATTTAT
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
17 18 1.00
ACGTcount: A:0.51, C:0.03, G:0.05, T:0.41
Consensus pattern (17 bp):
AAAGTTATTAATATTAA
Found at i:28481708 original size:9 final size:8
Alignment explanation
Indices: 28481690--28481738 Score: 57
Period size: 9 Copynumber: 6.0 Consensus size: 8
28481680 GTTAATTTAG
28481690 GTTTAATA
1 GTTTAATA
28481698 GTTTAAATA
1 GTTT-AATA
28481707 GTTT--TA
1 GTTTAATA
28481713 GGTTTAATA
1 -GTTTAATA
28481722 GTTTAATTA
1 GTTTAA-TA
28481731 GTTTAATA
1 GTTTAATA
28481739 AATATATTAA
Statistics
Matches: 36, Mismatches: 0, Indels: 10
0.78 0.00 0.22
Matches are distributed among these distances:
6 2 0.06
7 4 0.11
8 12 0.33
9 18 0.50
ACGTcount: A:0.35, C:0.00, G:0.14, T:0.51
Consensus pattern (8 bp):
GTTTAATA
Found at i:28481717 original size:24 final size:24
Alignment explanation
Indices: 28481685--28481734 Score: 91
Period size: 24 Copynumber: 2.1 Consensus size: 24
28481675 ATAAGGTTAA
28481685 TTTAGGTTTAATAGTTTAAATAGT
1 TTTAGGTTTAATAGTTTAAATAGT
*
28481709 TTTAGGTTTAATAGTTTAATTAGT
1 TTTAGGTTTAATAGTTTAAATAGT
28481733 TT
1 TT
28481735 AATAAATATA
Statistics
Matches: 25, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
24 25 1.00
ACGTcount: A:0.30, C:0.00, G:0.16, T:0.54
Consensus pattern (24 bp):
TTTAGGTTTAATAGTTTAAATAGT
Found at i:28486264 original size:47 final size:47
Alignment explanation
Indices: 28486195--28486415 Score: 234
Period size: 47 Copynumber: 4.7 Consensus size: 47
28486185 AAGGTACCGG
*
28486195 TGCCATGTCCCAGACACGGTCTTACACTAGCTCATATCTCATGTCGA
1 TGCCATGTCCCAGACATGGTCTTACACTAGCTCATATCTCATGTCGA
* * *
28486242 TGCCATGTCCCAGACATGGTCTTACACTAGTTCCTATCTCACGTCGA
1 TGCCATGTCCCAGACATGGTCTTACACTAGCTCATATCTCATGTCGA
* *
28486289 TGCCATGTCCCAGACATGGTCTTACACT-GACT-ATCATCTCGTAGACGA
1 TGCCATGTCCCAGACATGGTCTTACACTAG-CTCAT-ATCTCAT-GTCGA
* * *** *
28486337 TG-CATGTCCCAAACAT-GTCTTACACTAGCACCCGTCTCGATGCCGA
1 TGCCATGTCCCAGACATGGTCTTACACTAGCTCATATCTC-ATGTCGA
* * * *
28486383 TTCTATGTCCCAGACAGGGCCTTACACTAGCTC
1 TGCCATGTCCCAGACATGGTCTTACACTAGCTC
28486416 TCATAATGTG
Statistics
Matches: 144, Mismatches: 22, Indels: 15
0.80 0.12 0.08
Matches are distributed among these distances:
46 22 0.15
47 103 0.72
48 19 0.13
ACGTcount: A:0.23, C:0.32, G:0.18, T:0.27
Consensus pattern (47 bp):
TGCCATGTCCCAGACATGGTCTTACACTAGCTCATATCTCATGTCGA
Found at i:28497856 original size:12 final size:12
Alignment explanation
Indices: 28497836--28497869 Score: 52
Period size: 12 Copynumber: 2.8 Consensus size: 12
28497826 CTGGAGTTTT
28497836 ATATTATTTAGAA
1 ATATTATTTA-AA
28497849 AT-TTATTTAAA
1 ATATTATTTAAA
28497860 ATATTATTTA
1 ATATTATTTA
28497870 TTTATTGAGT
Statistics
Matches: 20, Mismatches: 0, Indels: 3
0.87 0.00 0.13
Matches are distributed among these distances:
11 4 0.20
12 14 0.70
13 2 0.10
ACGTcount: A:0.44, C:0.00, G:0.03, T:0.53
Consensus pattern (12 bp):
ATATTATTTAAA
Found at i:28501461 original size:13 final size:13
Alignment explanation
Indices: 28501424--28501464 Score: 57
Period size: 13 Copynumber: 3.2 Consensus size: 13
28501414 TTTTATTTAC
*
28501424 CTTTTACTTTTTA
1 CTTTTACTTTTTT
28501437 CTTTT-CTCTTTTT
1 CTTTTACT-TTTTT
28501450 CTTTTACTTTTTT
1 CTTTTACTTTTTT
28501463 CT
1 CT
28501465 GAAATAATTA
Statistics
Matches: 25, Mismatches: 1, Indels: 4
0.83 0.03 0.13
Matches are distributed among these distances:
12 2 0.08
13 21 0.84
14 2 0.08
ACGTcount: A:0.07, C:0.20, G:0.00, T:0.73
Consensus pattern (13 bp):
CTTTTACTTTTTT
Found at i:28501794 original size:20 final size:20
Alignment explanation
Indices: 28501771--28501813 Score: 61
Period size: 20 Copynumber: 2.1 Consensus size: 20
28501761 GGATACTTCT
*
28501771 AATTAA-TTTAATTTTCTAAA
1 AATTAATTTTAAATTT-TAAA
28501791 AATTAATTTTAAATTTTAAA
1 AATTAATTTTAAATTTTAAA
28501811 AAT
1 AAT
28501814 AGAATATGGT
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
20 13 0.62
21 8 0.38
ACGTcount: A:0.49, C:0.02, G:0.00, T:0.49
Consensus pattern (20 bp):
AATTAATTTTAAATTTTAAA
Found at i:28501812 original size:21 final size:20
Alignment explanation
Indices: 28501771--28501812 Score: 50
Period size: 21 Copynumber: 2.0 Consensus size: 20
28501761 GGATACTTCT
*
28501771 AATTAATTTAATTTTCTAAA
1 AATTAATTTAATTTTCAAAA
28501791 AATTAATTTTAAATTTT-AAAA
1 AATTAA-TTT-AATTTTCAAAA
28501812 A
1 A
28501813 TAGAATATGG
Statistics
Matches: 19, Mismatches: 1, Indels: 3
0.83 0.04 0.13
Matches are distributed among these distances:
20 6 0.32
21 7 0.37
22 6 0.32
ACGTcount: A:0.50, C:0.02, G:0.00, T:0.48
Consensus pattern (20 bp):
AATTAATTTAATTTTCAAAA
Found at i:28504025 original size:41 final size:40
Alignment explanation
Indices: 28503967--28504060 Score: 116
Period size: 40 Copynumber: 2.3 Consensus size: 40
28503957 TCAAATACAT
* *
28503967 CCTTTTCATTTGTTATCCTTTATGTAGAACATCATTTTCAA
1 CCTTTTCATTTGATATCCTTTATGCA-AACATCATTTTCAA
* * * *
28504008 CCTTTTCATTTGATATCCTTTTTGCATATATCCTTTTCAA
1 CCTTTTCATTTGATATCCTTTATGCAAACATCATTTTCAA
*
28504048 CCTTTTCGTTTGA
1 CCTTTTCATTTGA
28504061 ACTATTACAA
Statistics
Matches: 46, Mismatches: 7, Indels: 1
0.85 0.13 0.02
Matches are distributed among these distances:
40 23 0.50
41 23 0.50
ACGTcount: A:0.20, C:0.21, G:0.07, T:0.51
Consensus pattern (40 bp):
CCTTTTCATTTGATATCCTTTATGCAAACATCATTTTCAA
Found at i:28512095 original size:28 final size:29
Alignment explanation
Indices: 28512055--28512109 Score: 85
Period size: 28 Copynumber: 1.9 Consensus size: 29
28512045 CACAGGGGAT
28512055 GACACGGGCGTGT-CTAAGCCGTGTGAGG
1 GACACGGGCGTGTGCTAAGCCGTGTGAGG
**
28512083 GACACGGGCGTGTGCTTGGCCGTGTGA
1 GACACGGGCGTGTGCTAAGCCGTGTGA
28512110 AAATCCCTAT
Statistics
Matches: 24, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
28 13 0.54
29 11 0.46
ACGTcount: A:0.15, C:0.22, G:0.44, T:0.20
Consensus pattern (29 bp):
GACACGGGCGTGTGCTAAGCCGTGTGAGG
Found at i:28516757 original size:44 final size:43
Alignment explanation
Indices: 28516707--28516831 Score: 137
Period size: 43 Copynumber: 2.9 Consensus size: 43
28516697 TTCGAGCCTC
*
28516707 GGCCTAGCAAGCTTTAA-ACTGGTGA-ATAATATTATCGGGCTTCG
1 GGCCTAGCAAGCTATAATACTGGTGAGAT-A-A-TATCGGGCTTCG
* *
28516751 GGCCTAGCAGGCTATAATGCTGGTGAGATAATATCGGGCTTCG
1 GGCCTAGCAAGCTATAATACTGGTGAGATAATATCGGGCTTCG
* * * * *
28516794 GGCCTAGCAGGCTATAATGCCGGTGAAATGATATCGGG
1 GGCCTAGCAAGCTATAATACTGGTGAGATAATATCGGG
28516832 TTTCAAGCCT
Statistics
Matches: 73, Mismatches: 6, Indels: 5
0.87 0.07 0.06
Matches are distributed among these distances:
43 47 0.64
44 16 0.22
45 8 0.11
46 2 0.03
ACGTcount: A:0.26, C:0.18, G:0.30, T:0.26
Consensus pattern (43 bp):
GGCCTAGCAAGCTATAATACTGGTGAGATAATATCGGGCTTCG
Found at i:28516790 original size:43 final size:43
Alignment explanation
Indices: 28516734--28516831 Score: 160
Period size: 43 Copynumber: 2.3 Consensus size: 43
28516724 ACTGGTGAAT
* *
28516734 AATATTATCGGGCTTCGGGCCTAGCAGGCTATAATGCTGGTGA
1 AATAATATCGGGCTTCGGGCCTAGCAGGCTATAATGCCGGTGA
*
28516777 GATAATATCGGGCTTCGGGCCTAGCAGGCTATAATGCCGGTGA
1 AATAATATCGGGCTTCGGGCCTAGCAGGCTATAATGCCGGTGA
*
28516820 AATGATATCGGG
1 AATAATATCGGG
28516832 TTTCAAGCCT
Statistics
Matches: 50, Mismatches: 5, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
43 50 1.00
ACGTcount: A:0.24, C:0.18, G:0.32, T:0.26
Consensus pattern (43 bp):
AATAATATCGGGCTTCGGGCCTAGCAGGCTATAATGCCGGTGA
Found at i:28516842 original size:43 final size:43
Alignment explanation
Indices: 28516734--28516842 Score: 137
Period size: 43 Copynumber: 2.5 Consensus size: 43
28516724 ACTGGTGAAT
* ** *
28516734 AATATTATCGGGCTTCGGGCCTAGCAGGCTATAATGCTGGTGA
1 AATAATATCGGGCTTCAAGCCTAGCAGGCTATAATGCCGGTGA
* **
28516777 GATAATATCGGGCTTCGGGCCTAGCAGGCTATAATGCCGGTGA
1 AATAATATCGGGCTTCAAGCCTAGCAGGCTATAATGCCGGTGA
* *
28516820 AATGATATCGGGTTTCAAGCCTA
1 AATAATATCGGGCTTCAAGCCTA
28516843 ATAGGCGAAA
Statistics
Matches: 58, Mismatches: 8, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
43 58 1.00
ACGTcount: A:0.25, C:0.19, G:0.29, T:0.27
Consensus pattern (43 bp):
AATAATATCGGGCTTCAAGCCTAGCAGGCTATAATGCCGGTGA
Found at i:28521315 original size:14 final size:15
Alignment explanation
Indices: 28521296--28521325 Score: 53
Period size: 15 Copynumber: 2.1 Consensus size: 15
28521286 GGTTATTATA
28521296 TGTG-AAGTATCATG
1 TGTGAAAGTATCATG
28521310 TGTGAAAGTATCATG
1 TGTGAAAGTATCATG
28521325 T
1 T
28521326 CTAAATTTTG
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
14 4 0.27
15 11 0.73
ACGTcount: A:0.30, C:0.07, G:0.27, T:0.37
Consensus pattern (15 bp):
TGTGAAAGTATCATG
Found at i:28521615 original size:63 final size:63
Alignment explanation
Indices: 28521537--28521663 Score: 245
Period size: 63 Copynumber: 2.0 Consensus size: 63
28521527 AATATAATTA
*
28521537 TTAAATGTTTTATAATAAACATAAGGAATTAATAAAAGAAAAGAAAGCCATACATCCTTGCCT
1 TTAAATGTTTTATAATAAAAATAAGGAATTAATAAAAGAAAAGAAAGCCATACATCCTTGCCT
28521600 TTAAATGTTTTATAATAAAAATAAGGAATTAATAAAAGAAAAGAAAGCCATACATCCTTGCCT
1 TTAAATGTTTTATAATAAAAATAAGGAATTAATAAAAGAAAAGAAAGCCATACATCCTTGCCT
28521663 T
1 T
28521664 GTTCTTGCCG
Statistics
Matches: 63, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
63 63 1.00
ACGTcount: A:0.48, C:0.12, G:0.11, T:0.29
Consensus pattern (63 bp):
TTAAATGTTTTATAATAAAAATAAGGAATTAATAAAAGAAAAGAAAGCCATACATCCTTGCCT
Found at i:28523140 original size:43 final size:43
Alignment explanation
Indices: 28523088--28523202 Score: 149
Period size: 43 Copynumber: 2.7 Consensus size: 43
28523078 GCTGGTGAAT
* *
28523088 AATATTATCGGGCTTCGGGCCTAGTAGGCAATAATACCGGTGA
1 AATAATATCGGGCTTCAGGCCTAGTAGGCAATAATACCGGTGA
* * * * *
28523131 GATAATATCGGGCTCCAGGCCTAGCAGGCTATAATGCCGGTGA
1 AATAATATCGGGCTTCAGGCCTAGTAGGCAATAATACCGGTGA
* *
28523174 AATGATATCGGGCTTCAAGCCTAGTAGGC
1 AATAATATCGGGCTTCAGGCCTAGTAGGC
28523203 GAAATGCCAG
Statistics
Matches: 60, Mismatches: 12, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
43 60 1.00
ACGTcount: A:0.27, C:0.21, G:0.29, T:0.23
Consensus pattern (43 bp):
AATAATATCGGGCTTCAGGCCTAGTAGGCAATAATACCGGTGA
Found at i:28524106 original size:67 final size:66
Alignment explanation
Indices: 28524023--28524156 Score: 198
Period size: 67 Copynumber: 2.0 Consensus size: 66
28524013 GACTTCGGGG
* *
28524023 TCCCCTGTTCTATTTTTAGAAAATCATTATAATTTGTA-AAAGAGCGGTCATAAGATAAAATTTA
1 TCCCCTGTTCTATTTTTAGAAAATCATTATAAATTGTACAAA-AACGGTCATAAGATAAAATTTA
28524087 TNA
65 T-A
* * *
28524090 TCCCCTGTTCTGTTTTTAGAAAATCATTATAAATTGTACAAAAATGGTTATAAGATAAAATTTAT
1 TCCCCTGTTCTATTTTTAGAAAATCATTATAAATTGTACAAAAACGGTCATAAGATAAAATTTAT
28524155 A
66 A
28524156 T
1 T
28524157 GCTTATACTC
Statistics
Matches: 61, Mismatches: 5, Indels: 3
0.88 0.07 0.04
Matches are distributed among these distances:
66 2 0.03
67 56 0.92
68 3 0.05
ACGTcount: A:0.38, C:0.11, G:0.11, T:0.39
Consensus pattern (66 bp):
TCCCCTGTTCTATTTTTAGAAAATCATTATAAATTGTACAAAAACGGTCATAAGATAAAATTTAT
A
Found at i:28526845 original size:21 final size:21
Alignment explanation
Indices: 28526820--28526870 Score: 75
Period size: 21 Copynumber: 2.4 Consensus size: 21
28526810 GACATCATCG
28526820 TCGCAGCCACCAGTGCCACCA
1 TCGCAGCCACCAGTGCCACCA
* * *
28526841 TCGCAGCTACCAGTGTCGCCA
1 TCGCAGCCACCAGTGCCACCA
28526862 TCGCAGCCA
1 TCGCAGCCA
28526871 TTAGCACTAC
Statistics
Matches: 26, Mismatches: 4, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
21 26 1.00
ACGTcount: A:0.22, C:0.43, G:0.22, T:0.14
Consensus pattern (21 bp):
TCGCAGCCACCAGTGCCACCA
Found at i:28527171 original size:23 final size:24
Alignment explanation
Indices: 28527143--28527199 Score: 64
Period size: 23 Copynumber: 2.5 Consensus size: 24
28527133 CCAAAAATAT
28527143 CAAATTAATTTCAATT-GATTTTC
1 CAAATTAATTTCAATTAGATTTTC
* * * *
28527166 CAAATT-GTCTGACTTAGATTTTC
1 CAAATTAATTTCAATTAGATTTTC
28527189 CAAATTAATTT
1 CAAATTAATTT
28527200 TTCAAGAAAA
Statistics
Matches: 26, Mismatches: 6, Indels: 3
0.74 0.17 0.09
Matches are distributed among these distances:
22 5 0.19
23 19 0.73
24 2 0.08
ACGTcount: A:0.33, C:0.14, G:0.07, T:0.46
Consensus pattern (24 bp):
CAAATTAATTTCAATTAGATTTTC
Done.