Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: chr7
Parameters: 2 7 7 80 10 50 1000
Pmatch=0.80,Pindel=0.10
tuple sizes 0,4,5,7
tuple distances 0, 29, 159, 1000
Length: 21614486
ACGTcount: A:0.31, C:0.16, G:0.16, T:0.31
Warning! 1093914 characters in sequence are not A, C, G, or T
File 54 of 54
Found at i:21375190 original size:14 final size:15
Alignment explanation
Indices: 21375166--21375194 Score: 51
Period size: 14 Copynumber: 2.0 Consensus size: 15
21375156 TTTTGGAGGA
21375166 ATATCCAAGGAAATG
1 ATATCCAAGGAAATG
21375181 ATAT-CAAGGAAATG
1 ATATCCAAGGAAATG
21375195 TAATCTATAG
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
14 10 0.71
15 4 0.29
ACGTcount: A:0.48, C:0.10, G:0.21, T:0.21
Consensus pattern (15 bp):
ATATCCAAGGAAATG
Found at i:21385601 original size:73 final size:73
Alignment explanation
Indices: 21385482--21385628 Score: 276
Period size: 73 Copynumber: 2.0 Consensus size: 73
21385472 CTGTTCTGTT
*
21385482 TGGGCATGGTTTCTTGATGATGGCGTGGGTGACTTTATGGTGTATGGTTTTGCTAGAGAATAGAA
1 TGGGCATGGTTTCTTGATGATGGCGTGGGTGACTTTATGGTATATGGTTTTGCTAGAGAATAGAA
21385547 AGATTGTC
66 AGATTGTC
*
21385555 TGGGCATGGTTTCTTGATGATGGCGTGGGTGACTTTATGGTATATGGTTTTGCTAGAGAATATAA
1 TGGGCATGGTTTCTTGATGATGGCGTGGGTGACTTTATGGTATATGGTTTTGCTAGAGAATAGAA
21385620 AGATTGTC
66 AGATTGTC
21385628 T
1 T
21385629 TTCTATGTGT
Statistics
Matches: 72, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
73 72 1.00
ACGTcount: A:0.21, C:0.08, G:0.33, T:0.38
Consensus pattern (73 bp):
TGGGCATGGTTTCTTGATGATGGCGTGGGTGACTTTATGGTATATGGTTTTGCTAGAGAATAGAA
AGATTGTC
Found at i:21392046 original size:123 final size:122
Alignment explanation
Indices: 21391827--21392116 Score: 400
Period size: 123 Copynumber: 2.4 Consensus size: 122
21391817 TAATAAATAG
** * * * *
21391827 ATTAGTCTATTAATATTTAATAACTTTAAGCCATCGGTTAAAGTCTCTTTTCTTTATTGTTACAT
1 ATTAGTCTATTAATATTTAATAACTTTAA-ATATCTGTTAAAGTCTATTTTCTTTACTATTACAT
*
21391892 TTTTATTTAACTTTGGAGTATATCCTTCTTAATTATGATAATAAATAGAACACCAACT
65 TTTTATTTAACTCTGGAGTATATCCTTCTTAATTATGATAATAAATAGAACACCAACT
**
21391950 ATTAGTCTATTAATATTTAATAACTTTAAATAGTCTGTTAAAGTCTATTTTCTTTACTATTATTT
1 ATTAGTCTATTAATATTTAATAACTTTAAATA-TCTGTTAAAGTCTATTTTCTTTACTATTACAT
* * * * * *
21392015 TTTTATTTAACTCTGTAGTTTATCTTTCTTAATTATGATAATAAATAGAATAGCGACT
65 TTTTATTTAACTCTGGAGTATATCCTTCTTAATTATGATAATAAATAGAACACCAACT
* *
21392073 ATTAGTCTATTAATATTTAATAACATTAAATAATCTATTAAAGT
1 ATTAGTCTATTAATATTTAATAACTTTAAAT-ATCTGTTAAAGT
21392117 TTCTATAATA
Statistics
Matches: 148, Mismatches: 17, Indels: 4
0.88 0.10 0.02
Matches are distributed among these distances:
122 1 0.01
123 146 0.99
124 1 0.01
ACGTcount: A:0.34, C:0.11, G:0.08, T:0.47
Consensus pattern (122 bp):
ATTAGTCTATTAATATTTAATAACTTTAAATATCTGTTAAAGTCTATTTTCTTTACTATTACATT
TTTATTTAACTCTGGAGTATATCCTTCTTAATTATGATAATAAATAGAACACCAACT
Found at i:21393328 original size:40 final size:41
Alignment explanation
Indices: 21393252--21393333 Score: 132
Period size: 40 Copynumber: 2.0 Consensus size: 41
21393242 TTCTAAATCT
*
21393252 AAATTTTGAAATTATTTTTCTTTTCCTTTTTTCCTTAGCTC
1 AAATTTTGAAATTATTATTCTTTTCCTTTTTTCCTTAGCTC
21393293 AAATTTTGAAATTA-TATTC-TTTCCTTTTTTCCCTTAGCTC
1 AAATTTTGAAATTATTATTCTTTTCCTTTTTT-CCTTAGCTC
21393333 A
1 A
21393334 TAAAGCTATG
Statistics
Matches: 39, Mismatches: 1, Indels: 3
0.91 0.02 0.07
Matches are distributed among these distances:
39 11 0.28
40 14 0.36
41 14 0.36
ACGTcount: A:0.22, C:0.18, G:0.05, T:0.55
Consensus pattern (41 bp):
AAATTTTGAAATTATTATTCTTTTCCTTTTTTCCTTAGCTC
Found at i:21395581 original size:19 final size:19
Alignment explanation
Indices: 21395546--21395612 Score: 68
Period size: 19 Copynumber: 3.5 Consensus size: 19
21395536 CAGCAGGGAG
21395546 AGAAAGAAAAATG-AAAGAA
1 AGAAA-AAAAATGCAAAGAA
*
21395565 AGAAATAACAA-GCAAAGAA
1 AGAAA-AAAAATGCAAAGAA
*
21395584 ACAAAAAAAATGCAAA-AA
1 AGAAAAAAAATGCAAAGAA
21395602 AGAAAAGAAAA
1 AGAAAA-AAAA
21395613 GAGAAAAAGG
Statistics
Matches: 40, Mismatches: 5, Indels: 6
0.78 0.10 0.12
Matches are distributed among these distances:
18 12 0.30
19 28 0.70
ACGTcount: A:0.75, C:0.06, G:0.15, T:0.04
Consensus pattern (19 bp):
AGAAAAAAAATGCAAAGAA
Found at i:21395717 original size:55 final size:54
Alignment explanation
Indices: 21395574--21395729 Score: 146
Period size: 55 Copynumber: 2.9 Consensus size: 54
21395564 AAGAAATAAC
* * * *
21395574 AAGCAAA-GAAACAAAAAAAATGCAAAAAAG--A-AAAGAAAAGAG-AAAAAGG
1 AAGCAAAGGAAAGAAAAAAAATGGAAAAAAGAAAGAAACAAAAGAGAAAAAAAG
* * *
21395623 AAGCACAGGAAAGAATGAAAAACAT-GAAAACA-AAGGAAACAAAAGAGAAAAAAAG
1 AAGCAAAGGAAAGAA--AAAAA-ATGGAAAAAAGAAAGAAACAAAAGAGAAAAAAAG
*
21395678 ATGCAAAGGAAAGAAAAAAAATGGAAAAAAGGAAAGAAACGAAAAGAGAAAA
1 AAGCAAAGGAAAGAAAAAAAATGGAAAAAA-GAAAGAAAC-AAAAGAGAAAA
21395730 GAAGGATTTA
Statistics
Matches: 84, Mismatches: 11, Indels: 17
0.75 0.10 0.15
Matches are distributed among these distances:
49 6 0.07
50 6 0.07
52 12 0.14
53 13 0.15
54 10 0.12
55 26 0.31
56 11 0.13
ACGTcount: A:0.70, C:0.06, G:0.21, T:0.03
Consensus pattern (54 bp):
AAGCAAAGGAAAGAAAAAAAATGGAAAAAAGAAAGAAACAAAAGAGAAAAAAAG
Found at i:21397615 original size:20 final size:20
Alignment explanation
Indices: 21397590--21397630 Score: 73
Period size: 20 Copynumber: 2.0 Consensus size: 20
21397580 TTGACGTTTT
*
21397590 AGAGTGGGCGAGCCAGCTTG
1 AGAGTGGGCAAGCCAGCTTG
21397610 AGAGTGGGCAAGCCAGCTTG
1 AGAGTGGGCAAGCCAGCTTG
21397630 A
1 A
21397631 TGATGGACGA
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
20 20 1.00
ACGTcount: A:0.24, C:0.20, G:0.41, T:0.15
Consensus pattern (20 bp):
AGAGTGGGCAAGCCAGCTTG
Found at i:21410346 original size:46 final size:45
Alignment explanation
Indices: 21410290--21410382 Score: 168
Period size: 46 Copynumber: 2.0 Consensus size: 45
21410280 TTCTTTGAAT
21410290 TTTCACCTAGGTTTTCTTGTTTTTCCCTTTGTTCTCCCTTTGTTC
1 TTTCACCTAGGTTTTCTTGTTTTTCCCTTTGTTCTCCCTTTGTTC
*
21410335 TTNTCACCTAGGTTTTCTTGTTTTTCCCTTTGTTCTTCCTTTGTTC
1 TT-TCACCTAGGTTTTCTTGTTTTTCCCTTTGTTCTCCCTTTGTTC
21410381 TT
1 TT
21410383 GTTGCTGGTT
Statistics
Matches: 46, Mismatches: 1, Indels: 1
0.96 0.02 0.02
Matches are distributed among these distances:
45 2 0.04
46 44 0.96
ACGTcount: A:0.04, C:0.25, G:0.11, T:0.59
Consensus pattern (45 bp):
TTTCACCTAGGTTTTCTTGTTTTTCCCTTTGTTCTCCCTTTGTTC
Found at i:21413365 original size:2 final size:2
Alignment explanation
Indices: 21413316--21413347 Score: 64
Period size: 2 Copynumber: 16.0 Consensus size: 2
21413306 ACAAGCAAGA
21413316 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG
1 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG
21413348 CTTCGGGAAC
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 30 1.00
ACGTcount: A:0.50, C:0.00, G:0.50, T:0.00
Consensus pattern (2 bp):
AG
Found at i:21419006 original size:42 final size:42
Alignment explanation
Indices: 21418890--21419014 Score: 151
Period size: 42 Copynumber: 3.0 Consensus size: 42
21418880 TGTTGATGTG
* * * *
21418890 GACCCGGCTATGTGCAAGTTGGAGTGCACATAAGCCATTGCT
1 GACCCGGCTATGTGCGAGTGGGAGTGCACATAAGTCGTTGCT
** *
21418932 GACCCGATTATGTGCGAATGGGAGTGCACATAAGTCGTTGCT
1 GACCCGGCTATGTGCGAGTGGGAGTGCACATAAGTCGTTGCT
* * **
21418974 GACTCGGCTATGTGTGAGTGGGAGTGTGCATAAGTCGTTGC
1 GACCCGGCTATGTGCGAGTGGGAGTGCACATAAGTCGTTGC
21419015 ATATGAGATA
Statistics
Matches: 69, Mismatches: 14, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
42 69 1.00
ACGTcount: A:0.22, C:0.19, G:0.33, T:0.26
Consensus pattern (42 bp):
GACCCGGCTATGTGCGAGTGGGAGTGCACATAAGTCGTTGCT
Found at i:21423490 original size:34 final size:35
Alignment explanation
Indices: 21423447--21423555 Score: 98
Period size: 36 Copynumber: 3.0 Consensus size: 35
21423437 GGCATATATA
21423447 ATTAGTATGTGCACTCACACAGCACACCACTATCAC
1 ATTA-TATGTGCACTCACACAGCACACCACTATCAC
* *
21423483 ATT-TATGTGCACTCCCACACCGCACATGGCA-TAT-ATC
1 ATTATATGTGCACT--CACACAGCACA--CCACTATCA-C
* *
21423520 ATTAGTGTGTGCACTCCCACAGCACACCACTATCAC
1 ATTA-TATGTGCACTCACACAGCACACCACTATCAC
21423556 CGCCATGTGC
Statistics
Matches: 58, Mismatches: 6, Indels: 18
0.71 0.07 0.22
Matches are distributed among these distances:
34 10 0.17
35 2 0.03
36 18 0.31
37 17 0.29
38 2 0.03
39 9 0.16
ACGTcount: A:0.29, C:0.34, G:0.13, T:0.24
Consensus pattern (35 bp):
ATTATATGTGCACTCACACAGCACACCACTATCAC
Found at i:21423509 original size:73 final size:73
Alignment explanation
Indices: 21423408--21423583 Score: 255
Period size: 73 Copynumber: 2.4 Consensus size: 73
21423398 CCCATCTCAC
*
21423408 CAGCTCATGTGCACTCCTAC-CTCGCACATGGCATATATAATTAGTATGTGCACTCACACAGCAC
1 CAGC-CATGTGCACTCCCACAC-CGCACATGGCATATATAATTAGTATGTGCACTCACACAGCAC
21423472 ACCACTATCA
64 ACCACTATCA
*** * * *
21423482 CATTTATGTGCACTCCCACACCGCACATGGCATATATCATTAGTGTGTGCACTCCCACAGCACAC
1 CAGCCATGTGCACTCCCACACCGCACATGGCATATATAATTAGTATGTGCACTCACACAGCACAC
21423547 CACTATCA
66 CACTATCA
*
21423555 CCGCCATGTGCACTCCCACACCGCACATG
1 CAGCCATGTGCACTCCCACACCGCACATG
21423584 CACGGTTACA
Statistics
Matches: 90, Mismatches: 11, Indels: 3
0.87 0.11 0.03
Matches are distributed among these distances:
73 87 0.97
74 3 0.03
ACGTcount: A:0.27, C:0.36, G:0.14, T:0.23
Consensus pattern (73 bp):
CAGCCATGTGCACTCCCACACCGCACATGGCATATATAATTAGTATGTGCACTCACACAGCACAC
CACTATCA
Found at i:21423531 original size:39 final size:39
Alignment explanation
Indices: 21423414--21423540 Score: 126
Period size: 39 Copynumber: 3.4 Consensus size: 39
21423404 TCACCAGCTC
* *
21423414 ATGTGCACTCCTAC-CTCGCACATGGCATATATAATTAGT
1 ATGTGCACTCCCACAC-CGCACATGGCATATATCATTAGT
* *
21423453 ATGTGCACT--CACACAGCACA--CCACTATCA-CATT--T
1 ATGTGCACTCCCACACCGCACATGGCA-TAT-ATCATTAGT
21423487 ATGTGCACTCCCACACCGCACATGGCATATATCATTAGT
1 ATGTGCACTCCCACACCGCACATGGCATATATCATTAGT
*
21423526 GTGTGCACTCCCACA
1 ATGTGCACTCCCACA
21423541 GCACACCACT
Statistics
Matches: 71, Mismatches: 7, Indels: 20
0.72 0.07 0.20
Matches are distributed among these distances:
34 10 0.14
35 2 0.03
36 17 0.24
37 15 0.21
38 3 0.04
39 24 0.34
ACGTcount: A:0.28, C:0.31, G:0.14, T:0.26
Consensus pattern (39 bp):
ATGTGCACTCCCACACCGCACATGGCATATATCATTAGT
Found at i:21427895 original size:15 final size:15
Alignment explanation
Indices: 21427875--21427920 Score: 58
Period size: 15 Copynumber: 3.1 Consensus size: 15
21427865 TTCTTAGAAC
21427875 AACTTTAAAACCAAA
1 AACTTTAAAACCAAA
*
21427890 AACTTTAAAATTC-AA
1 AACTTTAAAA-CCAAA
*
21427905 AGCTTTAAAACCAAA
1 AACTTTAAAACCAAA
21427920 A
1 A
21427921 TCTCTTATCT
Statistics
Matches: 26, Mismatches: 3, Indels: 4
0.79 0.09 0.12
Matches are distributed among these distances:
14 1 0.04
15 24 0.92
16 1 0.04
ACGTcount: A:0.57, C:0.17, G:0.02, T:0.24
Consensus pattern (15 bp):
AACTTTAAAACCAAA
Found at i:21446250 original size:18 final size:18
Alignment explanation
Indices: 21446227--21446265 Score: 51
Period size: 18 Copynumber: 2.2 Consensus size: 18
21446217 GAATCTGACC
*
21446227 CTATTAAATATATAGAAG
1 CTATTAAAGATATAGAAG
* *
21446245 CTATTAACGATATAGATG
1 CTATTAAAGATATAGAAG
21446263 CTA
1 CTA
21446266 AGGAATGGCA
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
18 18 1.00
ACGTcount: A:0.44, C:0.10, G:0.13, T:0.33
Consensus pattern (18 bp):
CTATTAAAGATATAGAAG
Found at i:21455806 original size:2 final size:2
Alignment explanation
Indices: 21455801--21455863 Score: 69
Period size: 2 Copynumber: 31.0 Consensus size: 2
21455791 ACATATTTAC
21455801 AT AT AT AT AT AT AT ACT -T AT AT ACT AT AT AT -T ACT AT AT AT
1 AT AT AT AT AT AT AT A-T AT AT AT A-T AT AT AT AT A-T AT AT AT
21455842 AT ACT AT -T AT AT AT AT AT AT AT
1 AT A-T AT AT AT AT AT AT AT AT AT
21455864 TGATAGTTAT
Statistics
Matches: 54, Mismatches: 0, Indels: 14
0.79 0.00 0.21
Matches are distributed among these distances:
1 3 0.06
2 44 0.81
3 7 0.13
ACGTcount: A:0.44, C:0.06, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:21455821 original size:12 final size:11
Alignment explanation
Indices: 21455802--21455863 Score: 78
Period size: 10 Copynumber: 5.8 Consensus size: 11
21455792 CATATTTACA
21455802 TATATATATA-
1 TATATATATAC
21455812 TATACTTATATAC
1 TATA--TATATAC
21455825 TATATAT-TAC
1 TATATATATAC
21455835 TATATATATAC
1 TATATATATAC
21455846 TAT-TATATA-
1 TATATATATAC
21455855 TATATATAT
1 TATATATAT
21455864 TGATAGTTAT
Statistics
Matches: 47, Mismatches: 0, Indels: 10
0.82 0.00 0.18
Matches are distributed among these distances:
9 3 0.06
10 25 0.53
11 9 0.19
12 6 0.13
13 4 0.09
ACGTcount: A:0.44, C:0.06, G:0.00, T:0.50
Consensus pattern (11 bp):
TATATATATAC
Found at i:21466364 original size:35 final size:36
Alignment explanation
Indices: 21466316--21466383 Score: 120
Period size: 35 Copynumber: 1.9 Consensus size: 36
21466306 AAGATTCTTG
21466316 CTTTTTAATGGGATCAAGCGATAACCCTTACACCGA
1 CTTTTTAATGGGATCAAGCGATAACCCTTACACCGA
*
21466352 CTTTTT-ATGGGATCAAGTGATAACCCTTACAC
1 CTTTTTAATGGGATCAAGCGATAACCCTTACAC
21466384 AATCCACAAA
Statistics
Matches: 31, Mismatches: 1, Indels: 1
0.94 0.03 0.03
Matches are distributed among these distances:
35 25 0.81
36 6 0.19
ACGTcount: A:0.29, C:0.24, G:0.16, T:0.31
Consensus pattern (36 bp):
CTTTTTAATGGGATCAAGCGATAACCCTTACACCGA
Found at i:21467167 original size:21 final size:21
Alignment explanation
Indices: 21467120--21467168 Score: 64
Period size: 21 Copynumber: 2.3 Consensus size: 21
21467110 GCCGTTGGAT
*
21467120 CAACTCTAGTTTCTCTAAGGC
1 CAACTCTAGCTTCTCTAAGGC
*
21467141 CGACTCTAGCTTCTCT-AGGAC
1 CAACTCTAGCTTCTCTAAGG-C
21467162 CAACTCT
1 CAACTCT
21467169 TGACATGTGT
Statistics
Matches: 24, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
20 3 0.12
21 21 0.88
ACGTcount: A:0.22, C:0.33, G:0.14, T:0.31
Consensus pattern (21 bp):
CAACTCTAGCTTCTCTAAGGC
Found at i:21468543 original size:30 final size:29
Alignment explanation
Indices: 21468509--21468619 Score: 107
Period size: 30 Copynumber: 3.7 Consensus size: 29
21468499 ACTAAGTTAT
* *
21468509 TACACACCATACCTAAAATTCTTAAGTTGC
1 TACACGCCATACCTAAAA-TCATAAGTTGC
* *
21468539 TACACGCTA-AGCCTAAAAATCCTAAGTTGC
1 TACACGCCATA-CCT-AAAATCATAAGTTGC
* *
21468569 TACACGCCATGCATCAAAATCATAAGTTGC
1 TACACGCCATACCT-AAAATCATAAGTTGC
*
21468599 TACACGCCATGCCTAACAATC
1 TACACGCCATACCTAA-AATC
21468620 TACATTTTTA
Statistics
Matches: 68, Mismatches: 9, Indels: 8
0.80 0.11 0.09
Matches are distributed among these distances:
29 3 0.04
30 61 0.90
31 4 0.06
ACGTcount: A:0.36, C:0.29, G:0.11, T:0.24
Consensus pattern (29 bp):
TACACGCCATACCTAAAATCATAAGTTGC
Found at i:21468573 original size:60 final size:60
Alignment explanation
Indices: 21468500--21468619 Score: 143
Period size: 60 Copynumber: 2.0 Consensus size: 60
21468490 TGCCTAATAA
* * * *
21468500 CTAAGTTATTACACACCATACCT-AAAATTCTTAAGTTGCTACACGCTAAGCCTAAAAATC
1 CTAAGTTACTACACACCATACATCAAAA-TCATAAGTTGCTACACGCCAAGCCTAAAAATC
* * * * *
21468560 CTAAGTTGCTACACGCCATGCATCAAAATCATAAGTTGCTACACGCCATGCCTAACAATC
1 CTAAGTTACTACACACCATACATCAAAATCATAAGTTGCTACACGCCAAGCCTAAAAATC
21468620 TACATTTTTA
Statistics
Matches: 50, Mismatches: 9, Indels: 2
0.82 0.15 0.03
Matches are distributed among these distances:
60 46 0.92
61 4 0.08
ACGTcount: A:0.36, C:0.28, G:0.11, T:0.26
Consensus pattern (60 bp):
CTAAGTTACTACACACCATACATCAAAATCATAAGTTGCTACACGCCAAGCCTAAAAATC
Found at i:21469956 original size:10 final size:11
Alignment explanation
Indices: 21469938--21469967 Score: 53
Period size: 10 Copynumber: 2.8 Consensus size: 11
21469928 CTCCTACAAA
21469938 AACATAAAAAT
1 AACATAAAAAT
21469949 AA-ATAAAAAT
1 AACATAAAAAT
21469959 AACATAAAA
1 AACATAAAA
21469968 CTAATATTAT
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
10 10 0.56
11 8 0.44
ACGTcount: A:0.77, C:0.07, G:0.00, T:0.17
Consensus pattern (11 bp):
AACATAAAAAT
Found at i:21469981 original size:20 final size:19
Alignment explanation
Indices: 21469958--21470004 Score: 51
Period size: 20 Copynumber: 2.4 Consensus size: 19
21469948 TAAATAAAAA
21469958 TAACATAAAACT-AATATTAT
1 TAACATAAAA-TAAATATT-T
*
21469978 TAACTTAAAATAAATATTT
1 TAACATAAAATAAATATTT
*
21469997 AAACATAA
1 TAACATAA
21470005 TTTAAACTAA
Statistics
Matches: 23, Mismatches: 3, Indels: 3
0.79 0.10 0.10
Matches are distributed among these distances:
19 8 0.35
20 15 0.65
ACGTcount: A:0.57, C:0.09, G:0.00, T:0.34
Consensus pattern (19 bp):
TAACATAAAATAAATATTT
Found at i:21482262 original size:19 final size:19
Alignment explanation
Indices: 21482240--21482277 Score: 67
Period size: 19 Copynumber: 2.0 Consensus size: 19
21482230 ACTTCTAAAT
*
21482240 CTCAAATCATACTCTAATA
1 CTCAAATCATACTCCAATA
21482259 CTCAAATCATACTCCAATA
1 CTCAAATCATACTCCAATA
21482278 AGTCAAATGG
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
19 18 1.00
ACGTcount: A:0.42, C:0.29, G:0.00, T:0.29
Consensus pattern (19 bp):
CTCAAATCATACTCCAATA
Found at i:21485455 original size:27 final size:27
Alignment explanation
Indices: 21485425--21485583 Score: 147
Period size: 27 Copynumber: 5.7 Consensus size: 27
21485415 AACAATTAAA
* * *
21485425 ATGGCATGTAGCAAAATTTTTTTGAAT
1 ATGGCGTGTAACAAAATTTTTTTGAAC
* * *
21485452 ATGGTGTGCAACAATAATTTTTTTTTTAAC
1 ATGGCGTGTAACAA-AA--TTTTTTTGAAC
* * *
21485482 ATGACGTGTAGCAATAATTTTTTTCAAC
1 ATGGCGTGTAACAA-AATTTTTTTGAAC
* *
21485510 ATGGCGTGTAACAACATTTTTTTGAAT
1 ATGGCGTGTAACAAAATTTTTTTGAAC
* * *
21485537 ATGACGTGTAACAACATTTTTTTAAAC
1 ATGGCGTGTAACAAAATTTTTTTGAAC
*
21485564 ATGGCGTGTAGCAAAATTTT
1 ATGGCGTGTAACAAAATTTT
21485584 AGAACATGTG
Statistics
Matches: 107, Mismatches: 22, Indels: 6
0.79 0.16 0.04
Matches are distributed among these distances:
27 61 0.57
28 24 0.22
30 22 0.21
ACGTcount: A:0.32, C:0.11, G:0.16, T:0.40
Consensus pattern (27 bp):
ATGGCGTGTAACAAAATTTTTTTGAAC
Found at i:21485530 original size:85 final size:81
Alignment explanation
Indices: 21485425--21485583 Score: 201
Period size: 85 Copynumber: 1.9 Consensus size: 81
21485415 AACAATTAAA
* ** *
21485425 ATGGCATGTAGCAAAATTTTTTTGAATATGGTGTGCAACAATAATTTTTTTTTTAACATGACGTG
1 ATGGCATGTAACAAAATTTTTTTGAATATGACGTGCAACAA-AA--TTTTTTTAAACATGACGTG
21485490 TAGCAATAATTTTTTTCAAC
63 TAGCAA-AATTTTTTTCAAC
* * * * *
21485510 ATGGCGTGTAACAACATTTTTTTGAATATGACGTGTAACAACATTTTTTTAAACATGGCGTGTAG
1 ATGGCATGTAACAAAATTTTTTTGAATATGACGTGCAACAAAATTTTTTTAAACATGACGTGTAG
21485575 CAAAATTTT
66 CAAAATTTT
21485584 AGAACATGTG
Statistics
Matches: 65, Mismatches: 9, Indels: 4
0.83 0.12 0.05
Matches are distributed among these distances:
81 6 0.09
82 23 0.35
84 1 0.02
85 35 0.54
ACGTcount: A:0.32, C:0.11, G:0.16, T:0.40
Consensus pattern (81 bp):
ATGGCATGTAACAAAATTTTTTTGAATATGACGTGCAACAAAATTTTTTTAAACATGACGTGTAG
CAAAATTTTTTTCAAC
Found at i:21496901 original size:2 final size:2
Alignment explanation
Indices: 21496884--21496917 Score: 50
Period size: 2 Copynumber: 17.0 Consensus size: 2
21496874 TGACTGAAGC
* *
21496884 AT AT AC AT AC AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
21496918 CCATATTCAT
Statistics
Matches: 28, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
2 28 1.00
ACGTcount: A:0.50, C:0.06, G:0.00, T:0.44
Consensus pattern (2 bp):
AT
Found at i:21499738 original size:28 final size:28
Alignment explanation
Indices: 21499698--21499751 Score: 90
Period size: 28 Copynumber: 1.9 Consensus size: 28
21499688 CTATAAAAAA
*
21499698 TTTTCAAACGAAATTTCGTTAAAAATCC
1 TTTTCAAAAGAAATTTCGTTAAAAATCC
*
21499726 TTTTCAAAAGAAATTTCGTTGAAAAT
1 TTTTCAAAAGAAATTTCGTTAAAAAT
21499752 TTTCAACAAA
Statistics
Matches: 24, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
28 24 1.00
ACGTcount: A:0.41, C:0.13, G:0.09, T:0.37
Consensus pattern (28 bp):
TTTTCAAAAGAAATTTCGTTAAAAATCC
Found at i:21502421 original size:12 final size:12
Alignment explanation
Indices: 21502404--21502437 Score: 59
Period size: 12 Copynumber: 2.8 Consensus size: 12
21502394 TCTTAACAGA
21502404 ATTATTATTAAC
1 ATTATTATTAAC
21502416 ATTATTATTAAC
1 ATTATTATTAAC
*
21502428 ACTATTATTA
1 ATTATTATTA
21502438 TTTCTAGAAT
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
12 21 1.00
ACGTcount: A:0.41, C:0.09, G:0.00, T:0.50
Consensus pattern (12 bp):
ATTATTATTAAC
Found at i:21506011 original size:22 final size:22
Alignment explanation
Indices: 21505985--21506043 Score: 75
Period size: 22 Copynumber: 2.7 Consensus size: 22
21505975 ACCCGAGAGT
21505985 TTCTCGTTGCAGCGAGAATGCA
1 TTCTCGTTGCAGCGAGAATGCA
*
21506007 TTCTCGTTGTC-GAGAGAATGCA
1 TTCTCGTTG-CAGCGAGAATGCA
* *
21506029 TTTTCGCTGCAGCGA
1 TTCTCGTTGCAGCGA
21506044 AAATCTAGGC
Statistics
Matches: 31, Mismatches: 4, Indels: 4
0.79 0.10 0.10
Matches are distributed among these distances:
21 1 0.03
22 29 0.94
23 1 0.03
ACGTcount: A:0.20, C:0.22, G:0.27, T:0.31
Consensus pattern (22 bp):
TTCTCGTTGCAGCGAGAATGCA
Found at i:21506454 original size:35 final size:36
Alignment explanation
Indices: 21506371--21506454 Score: 89
Period size: 36 Copynumber: 2.4 Consensus size: 36
21506361 TCTCATCAGC
* ** *
21506371 TCATGTACACTCCCACACCGCACATAGTTAGAATCA
1 TCATGTGCACTCCCACACCGCACATAGGCACAATCA
* * * *
21506407 TCTTGTGGACTCCCATACCGCACA-AGGCACTATCA
1 TCATGTGCACTCCCACACCGCACATAGGCACAATCA
21506442 TCATGTGCACTCC
1 TCATGTGCACTCC
21506455 ACATCTCACA
Statistics
Matches: 38, Mismatches: 10, Indels: 1
0.78 0.20 0.02
Matches are distributed among these distances:
35 18 0.47
36 20 0.53
ACGTcount: A:0.27, C:0.35, G:0.14, T:0.24
Consensus pattern (36 bp):
TCATGTGCACTCCCACACCGCACATAGGCACAATCA
Found at i:21506521 original size:34 final size:34
Alignment explanation
Indices: 21506483--21506609 Score: 114
Period size: 34 Copynumber: 3.6 Consensus size: 34
21506473 ATCATCAGTG
*
21506483 TGTGCACTCACACATCACACCACTATCACCGTCA
1 TGTGCACTCACACACCACACCACTATCACCGTCA
* * * *
21506517 TGTGCACTCCCACACCGCA-CATGGCATAAATCATCAGT-G
1 TGTGCACTCACACACCACACCA---C-T--ATCA-CCGTCA
*
21506556 TGTGCACTCACACAGCACACCACTATCACCGTCA
1 TGTGCACTCACACACCACACCACTATCACCGTCA
*
21506590 TGTGCACTCCCACACCACAC
1 TGTGCACTCACACACCACAC
21506610 ATGTCACGCC
Statistics
Matches: 72, Mismatches: 12, Indels: 18
0.71 0.12 0.18
Matches are distributed among these distances:
33 5 0.07
34 38 0.53
36 2 0.03
37 2 0.03
39 20 0.28
40 5 0.07
ACGTcount: A:0.28, C:0.40, G:0.13, T:0.19
Consensus pattern (34 bp):
TGTGCACTCACACACCACACCACTATCACCGTCA
Found at i:21506550 original size:73 final size:73
Alignment explanation
Indices: 21506442--21506612 Score: 281
Period size: 73 Copynumber: 2.4 Consensus size: 73
21506432 GGCACTATCA
* * * *
21506442 TCATGTGCACT-CCACATCTCACATGACATATATCATCAGTGTGTGCACTCACACATCACACCAC
1 TCATGTGCACTCCCACACCACACATGACATAAATCATCAGTGTGTGCACTCACACAGCACACCAC
21506506 TATCACCG
66 TATCACCG
* *
21506514 TCATGTGCACTCCCACACCGCACATGGCATAAATCATCAGTGTGTGCACTCACACAGCACACCAC
1 TCATGTGCACTCCCACACCACACATGACATAAATCATCAGTGTGTGCACTCACACAGCACACCAC
21506579 TATCACCG
66 TATCACCG
21506587 TCATGTGCACTCCCACACCACACATG
1 TCATGTGCACTCCCACACCACACATG
21506613 TCACGCCCTT
Statistics
Matches: 92, Mismatches: 6, Indels: 1
0.93 0.06 0.01
Matches are distributed among these distances:
72 11 0.12
73 81 0.88
ACGTcount: A:0.29, C:0.37, G:0.13, T:0.22
Consensus pattern (73 bp):
TCATGTGCACTCCCACACCACACATGACATAAATCATCAGTGTGTGCACTCACACAGCACACCAC
TATCACCG
Found at i:21513162 original size:42 final size:42
Alignment explanation
Indices: 21513115--21513197 Score: 139
Period size: 42 Copynumber: 2.0 Consensus size: 42
21513105 TGTTGATGTG
21513115 GACCCGGCTATGTGCGAGTGGGAGTGCACATAAGCCGTTGCT
1 GACCCGGCTATGTGCGAGTGGGAGTGCACATAAGCCGTTGCT
* **
21513157 GACCCGGCTATGTGGGAGTGGGAGTGCGTATAAGCCGTTGC
1 GACCCGGCTATGTGCGAGTGGGAGTGCACATAAGCCGTTGC
21513198 ATATGAGATG
Statistics
Matches: 38, Mismatches: 3, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
42 38 1.00
ACGTcount: A:0.18, C:0.22, G:0.39, T:0.22
Consensus pattern (42 bp):
GACCCGGCTATGTGCGAGTGGGAGTGCACATAAGCCGTTGCT
Found at i:21523040 original size:16 final size:15
Alignment explanation
Indices: 21523019--21523048 Score: 51
Period size: 16 Copynumber: 1.9 Consensus size: 15
21523009 AGAAATAGAA
21523019 AAATTTAAAGAGAAGT
1 AAATTTAAAG-GAAGT
21523035 AAATTTAAAGGAAG
1 AAATTTAAAGGAAG
21523049 ATAGTTTACT
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:0.57, C:0.00, G:0.20, T:0.23
Consensus pattern (15 bp):
AAATTTAAAGGAAGT
Found at i:21535957 original size:41 final size:41
Alignment explanation
Indices: 21535875--21535960 Score: 111
Period size: 41 Copynumber: 2.1 Consensus size: 41
21535865 TAAGGCCTAA
*
21535875 TGCTGCATGTGAGTGTGCTTGCGTACTGACCGGCAGACTTG
1 TGCTGCATGTGAGTGTGCTTGCGTACTGACCGGAAGACTTG
* * * *
21535916 TGCTGCATGTGTGTGTGCTTGCTTA-TCGACTGGAAGCCTTG
1 TGCTGCATGTGAGTGTGCTTGCGTACT-GACCGGAAGACTTG
21535957 TGCT
1 TGCT
21535961 ACGTGTGCTT
Statistics
Matches: 39, Mismatches: 5, Indels: 2
0.85 0.11 0.04
Matches are distributed among these distances:
40 1 0.03
41 38 0.97
ACGTcount: A:0.13, C:0.21, G:0.33, T:0.34
Consensus pattern (41 bp):
TGCTGCATGTGAGTGTGCTTGCGTACTGACCGGAAGACTTG
Found at i:21536965 original size:16 final size:18
Alignment explanation
Indices: 21536932--21536967 Score: 58
Period size: 16 Copynumber: 2.1 Consensus size: 18
21536922 AATATAACCT
21536932 AAAATATTAAACAAAATA
1 AAAATATTAAACAAAATA
21536950 AAAATA-TAAA-AAAATA
1 AAAATATTAAACAAAATA
21536966 AA
1 AA
21536968 TAATTGAAGG
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
16 8 0.44
17 4 0.22
18 6 0.33
ACGTcount: A:0.78, C:0.03, G:0.00, T:0.19
Consensus pattern (18 bp):
AAAATATTAAACAAAATA
Found at i:21537559 original size:31 final size:31
Alignment explanation
Indices: 21537484--21537566 Score: 98
Period size: 31 Copynumber: 2.7 Consensus size: 31
21537474 TATTTTTCAA
21537484 ATATTTTT-TTCAATTTAGTCCCTTAATATC
1 ATATTTTTGTTCAATTTAGTCCCTTAATATC
* * * *
21537514 TTAATTTAGTTCAATTTAGTCCCTGTACTAT-
1 ATATTTTTGTTCAATTTAGTCCCT-TAATATC
*
21537545 ATATTTTTGCTCAATTTAGTCC
1 ATATTTTTGTTCAATTTAGTCC
21537567 TTATGATGTA
Statistics
Matches: 43, Mismatches: 8, Indels: 3
0.80 0.15 0.06
Matches are distributed among these distances:
30 5 0.12
31 33 0.77
32 5 0.12
ACGTcount: A:0.25, C:0.17, G:0.07, T:0.51
Consensus pattern (31 bp):
ATATTTTTGTTCAATTTAGTCCCTTAATATC
Found at i:21548621 original size:18 final size:18
Alignment explanation
Indices: 21548598--21548634 Score: 56
Period size: 18 Copynumber: 2.1 Consensus size: 18
21548588 CTTAGCTATT
*
21548598 TTAGCTCCCTCAATTCTC
1 TTAGCTCCCTCAACTCTC
*
21548616 TTAGCTCTCTCAACTCTC
1 TTAGCTCCCTCAACTCTC
21548634 T
1 T
21548635 CAACTAAATT
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
18 17 1.00
ACGTcount: A:0.16, C:0.38, G:0.05, T:0.41
Consensus pattern (18 bp):
TTAGCTCCCTCAACTCTC
Found at i:21549180 original size:26 final size:26
Alignment explanation
Indices: 21549146--21549222 Score: 84
Period size: 26 Copynumber: 3.0 Consensus size: 26
21549136 TGTAATAGTT
* * *
21549146 TTTTGAACATGGCGTGTAAGAAAATA
1 TTTTCAACATGGCATGTAACAAAATA
* *
21549172 TTTTCAACATGGCATGTAACAACATG
1 TTTTCAACATGGCATGTAACAAAATA
*
21549198 TTTTCAACA-GGACATGTAGCAAAAT
1 TTTTCAACATGG-CATGTAACAAAAT
21549223 TTTAGAACAC
Statistics
Matches: 43, Mismatches: 7, Indels: 2
0.83 0.13 0.04
Matches are distributed among these distances:
25 2 0.05
26 41 0.95
ACGTcount: A:0.38, C:0.14, G:0.18, T:0.30
Consensus pattern (26 bp):
TTTTCAACATGGCATGTAACAAAATA
Found at i:21550610 original size:28 final size:27
Alignment explanation
Indices: 21550579--21550632 Score: 90
Period size: 28 Copynumber: 2.0 Consensus size: 27
21550569 TTTTGGAGCA
*
21550579 TAGGGGCAAAATGGTAATTTTGCCACCC
1 TAGGGGCAAAATAGTAATTTT-CCACCC
21550607 TAGGGGCAAAATAGTAATTTTCCACC
1 TAGGGGCAAAATAGTAATTTTCCACC
21550633 ACCAGGACAT
Statistics
Matches: 25, Mismatches: 1, Indels: 1
0.93 0.04 0.04
Matches are distributed among these distances:
27 5 0.20
28 20 0.80
ACGTcount: A:0.31, C:0.20, G:0.22, T:0.26
Consensus pattern (27 bp):
TAGGGGCAAAATAGTAATTTTCCACCC
Found at i:21553162 original size:21 final size:22
Alignment explanation
Indices: 21553124--21553167 Score: 70
Period size: 22 Copynumber: 2.0 Consensus size: 22
21553114 TTTGATTGAC
21553124 ATCAGAGCTTTTGATTTTAAAG
1 ATCAGAGCTTTTGATTTTAAAG
* *
21553146 ATCAGAGTTTTTGTTTTTAAAG
1 ATCAGAGCTTTTGATTTTAAAG
21553168 TGGTTTTAAA
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
22 20 1.00
ACGTcount: A:0.30, C:0.07, G:0.18, T:0.45
Consensus pattern (22 bp):
ATCAGAGCTTTTGATTTTAAAG
Found at i:21561833 original size:63 final size:63
Alignment explanation
Indices: 21561724--21561895 Score: 263
Period size: 63 Copynumber: 2.7 Consensus size: 63
21561714 GGTACCATTG
*
21561724 TGTGATAACTGTAACCGTGCATGTGCAGAGTGGGCAGTGCACATGCCGGGTGAATGACAATGT
1 TGTGATAATTGTAACCGTGCATGTGCAGAGTGGGCAGTGCACATGCCGGGTGAATGACAATGT
* * * *
21561787 TGTGATAATTGTAACCGTGCATGTGCAGAGTGGGCAATGCATATGCCGGTTGAATGATAATGT
1 TGTGATAATTGTAACCGTGCATGTGCAGAGTGGGCAGTGCACATGCCGGGTGAATGACAATGT
* * * *
21561850 CGTGATAATTATAACCATGCATGTGCAAAGTGGGCAGTGCACATGC
1 TGTGATAATTGTAACCGTGCATGTGCAGAGTGGGCAGTGCACATGC
21561896 TGGTAATGAT
Statistics
Matches: 98, Mismatches: 11, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
63 98 1.00
ACGTcount: A:0.27, C:0.16, G:0.30, T:0.26
Consensus pattern (63 bp):
TGTGATAATTGTAACCGTGCATGTGCAGAGTGGGCAGTGCACATGCCGGGTGAATGACAATGT
Found at i:21563427 original size:17 final size:19
Alignment explanation
Indices: 21563386--21563427 Score: 52
Period size: 20 Copynumber: 2.2 Consensus size: 19
21563376 ATTTATATAT
21563386 ATGAATATATGTTGTGCATTG
1 ATGAATATATGTTGTG-A-TG
21563407 ATGAATA-ATGTTGTG-TG
1 ATGAATATATGTTGTGATG
21563424 ATGA
1 ATGA
21563428 TGTTGAAGTG
Statistics
Matches: 21, Mismatches: 0, Indels: 4
0.84 0.00 0.16
Matches are distributed among these distances:
17 6 0.29
20 8 0.38
21 7 0.33
ACGTcount: A:0.31, C:0.02, G:0.26, T:0.40
Consensus pattern (19 bp):
ATGAATATATGTTGTGATG
Found at i:21563462 original size:37 final size:37
Alignment explanation
Indices: 21563422--21563576 Score: 197
Period size: 37 Copynumber: 4.2 Consensus size: 37
21563412 TAATGTTGTG
**
21563422 TGATGATGTTGAAGTGTGCGAATAGGGAGTGCACATG
1 TGATGATGTTGAAGTGTGCGAATAGGGAGTGCACACA
* *
21563459 TGATGATGTTGAAGTGTGCGAGTAGGGAGTGCAAACA
1 TGATGATGTTGAAGTGTGCGAATAGGGAGTGCACACA
* *
21563496 TGATGATGTTGAATTATGCGAGA-AGGGAGTGCACACA
1 TGATGATGTTGAAGTGTGCGA-ATAGGGAGTGCACACA
* * * *
21563533 TGATGATG-TGAAGTGTGTGAGTGGGGAGTACACACA
1 TGATGATGTTGAAGTGTGCGAATAGGGAGTGCACACA
21563569 TGATGATG
1 TGATGATG
21563577 ATATTGTATT
Statistics
Matches: 102, Mismatches: 14, Indels: 5
0.84 0.12 0.04
Matches are distributed among these distances:
36 29 0.28
37 73 0.72
ACGTcount: A:0.29, C:0.08, G:0.37, T:0.26
Consensus pattern (37 bp):
TGATGATGTTGAAGTGTGCGAATAGGGAGTGCACACA
Found at i:21563631 original size:2 final size:2
Alignment explanation
Indices: 21563619--21563658 Score: 53
Period size: 2 Copynumber: 20.0 Consensus size: 2
21563609 ATGCATGATG
* * *
21563619 AT AT AT GT AT AT AC AA AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
21563659 GTTATAGAAA
Statistics
Matches: 33, Mismatches: 5, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
2 33 1.00
ACGTcount: A:0.50, C:0.03, G:0.03, T:0.45
Consensus pattern (2 bp):
AT
Found at i:21569839 original size:20 final size:20
Alignment explanation
Indices: 21569802--21569841 Score: 53
Period size: 20 Copynumber: 2.0 Consensus size: 20
21569792 CTATAAATAT
*
21569802 CTCATTTCTCCAGTAGCTTC
1 CTCATTTCTCCAGCAGCTTC
* *
21569822 CTCATTTTTTCAGCAGCTTC
1 CTCATTTCTCCAGCAGCTTC
21569842 TTCTTCCTTT
Statistics
Matches: 17, Mismatches: 3, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.15, C:0.33, G:0.10, T:0.42
Consensus pattern (20 bp):
CTCATTTCTCCAGCAGCTTC
Found at i:21570683 original size:17 final size:19
Alignment explanation
Indices: 21570642--21570683 Score: 52
Period size: 20 Copynumber: 2.2 Consensus size: 19
21570632 ATGTATATCT
21570642 ATGAATATATGTTGTGCATTG
1 ATGAATATATGTTGTG-A-TG
21570663 ATGAATA-ATGTTGTG-TG
1 ATGAATATATGTTGTGATG
21570680 ATGA
1 ATGA
21570684 TGTTGAAGTG
Statistics
Matches: 21, Mismatches: 0, Indels: 4
0.84 0.00 0.16
Matches are distributed among these distances:
17 6 0.29
20 8 0.38
21 7 0.33
ACGTcount: A:0.31, C:0.02, G:0.26, T:0.40
Consensus pattern (19 bp):
ATGAATATATGTTGTGATG
Found at i:21570720 original size:37 final size:37
Alignment explanation
Indices: 21570678--21570869 Score: 248
Period size: 37 Copynumber: 5.2 Consensus size: 37
21570668 TAATGTTGTG
21570678 TGATGATGTTGAAGTGTGCGAGTAAGGAGTGCACACA
1 TGATGATGTTGAAGTGTGCGAGTAAGGAGTGCACACA
*
21570715 TGATGATGTTGAAGTGTGCGGGT-AGAGAGTGCACACA
1 TGATGATGTTGAAGTGTGCGAGTAAG-GAGTGCACACA
* * *
21570752 TGATGATG-TGAAGAGTGCAAGTAGGGAGTGCACACA
1 TGATGATGTTGAAGTGTGCGAGTAAGGAGTGCACACA
* * *
21570788 TGATGATGTT-AGAGTGTGTGAGT-AGATAGTTCACACA
1 TGATGATGTTGA-AGTGTGCGAGTAAG-GAGTGCACACA
**
21570825 TGATGATGTTGAAGTGTGCGAGTAAGGAGTTTACACA
1 TGATGATGTTGAAGTGTGCGAGTAAGGAGTGCACACA
21570862 TGATGATG
1 TGATGATG
21570870 ATATTGCATT
Statistics
Matches: 134, Mismatches: 14, Indels: 14
0.83 0.09 0.09
Matches are distributed among these distances:
36 34 0.25
37 97 0.72
38 3 0.02
ACGTcount: A:0.30, C:0.09, G:0.34, T:0.27
Consensus pattern (37 bp):
TGATGATGTTGAAGTGTGCGAGTAAGGAGTGCACACA
Found at i:21570780 original size:73 final size:74
Alignment explanation
Indices: 21570678--21570869 Score: 280
Period size: 73 Copynumber: 2.6 Consensus size: 74
21570668 TAATGTTGTG
*
21570678 TGATGATGTTGAAGTGTGCGAGTAAGGAGTGCACACATGATGATGTT-GAAGTGTGCGGGTAGAG
1 TGATGATGTTGAAGTGTGCGAGTAAGGAGTGCACACATGATGATGTTAG-AGTGTGCGAGTAGAG
21570742 AGTGCACACA
65 AGTGCACACA
* * * * *
21570752 TGATGATG-TGAAGAGTGCAAGTAGGGAGTGCACACATGATGATGTTAGAGTGTGTGAGTAGATA
1 TGATGATGTTGAAGTGTGCGAGTAAGGAGTGCACACATGATGATGTTAGAGTGTGCGAGTAGAGA
*
21570816 GTTCACACA
66 GTGCACACA
**
21570825 TGATGATGTTGAAGTGTGCGAGTAAGGAGTTTACACATGATGATG
1 TGATGATGTTGAAGTGTGCGAGTAAGGAGTGCACACATGATGATG
21570870 ATATTGCATT
Statistics
Matches: 104, Mismatches: 12, Indels: 4
0.87 0.10 0.03
Matches are distributed among these distances:
73 64 0.62
74 40 0.38
ACGTcount: A:0.30, C:0.09, G:0.34, T:0.27
Consensus pattern (74 bp):
TGATGATGTTGAAGTGTGCGAGTAAGGAGTGCACACATGATGATGTTAGAGTGTGCGAGTAGAGA
GTGCACACA
Found at i:21570933 original size:2 final size:2
Alignment explanation
Indices: 21570928--21570955 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
21570918 GTATATACAA
21570928 AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT
21570956 GTTATAGAAA
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:21574691 original size:26 final size:26
Alignment explanation
Indices: 21574661--21574710 Score: 84
Period size: 26 Copynumber: 1.9 Consensus size: 26
21574651 TGTGTGATGC
21574661 GGTTGGTTGTCCTT-AAAACACTATAT
1 GGTTGGTTGT-CTTGAAAACACTATAT
21574687 GGTTGGTTGTCTTGAAAACACTAT
1 GGTTGGTTGTCTTGAAAACACTAT
21574711 GTTCATTTTT
Statistics
Matches: 23, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
25 3 0.13
26 20 0.87
ACGTcount: A:0.26, C:0.14, G:0.22, T:0.38
Consensus pattern (26 bp):
GGTTGGTTGTCTTGAAAACACTATAT
Found at i:21576593 original size:149 final size:149
Alignment explanation
Indices: 21576351--21576707 Score: 405
Period size: 149 Copynumber: 2.4 Consensus size: 149
21576341 TCCAATTGTT
**
21576351 AGATGTCGTTGACATCTTGTCGTGACACACATGAGTCATTGCAGTATTATAGGGTGACATGCCAT
1 AGATGTCGTTGACATCTTGTCGTGACACACATGAGTCATTGCAGTATTATAGGGTGACACACCAT
** * * * ** *
21576416 GCTTTAGTTTTACTTATGTCGTTGACATCTTGTCACGACACACTGAGTTGTTGTAATATT-GTAG
66 GCTCAAATTTCACCTATGTCGTCAACATCTTGTCACGACACACTGAGTTATTGTAATATTAG-AG
21576480 GGTGACACGCCACACT-CCAA
130 GGTGACACGCCAC-CTACCAA
* * * * *
21576500 AGATGTCGTCGACATCTTGTCATGACACACATGAGTCGTTGCAGTACTATAGGGTGACACACCTT
1 AGATGTCGTTGACATCTTGTCGTGACACACATGAGTCATTGCAGTATTATAGGGTGACACACCAT
* *** * * *
21576565 GCTCAAATTTCACCTATGTTGTCAACATCTTGTTGTGACACATTGAGTTATTTTAGTATTAGAGG
66 GCTCAAATTTCACCTATGTCGTCAACATCTTGTCACGACACACTGAGTTATTGTAATATTAGAGG
* *
21576630 GTGACATGCCACGTACCAA
131 GTGACACGCCACCTACCAA
* * * * * *
21576649 AGATGTCTTTGACATCATGTCGTGACAC-GATGAGTCATTGTAATATTATAGAGTGACAC
1 AGATGTCGTTGACATCTTGTCGTGACACACATGAGTCATTGCAGTATTATAGGGTGACAC
21576708 GTCACGTTCC
Statistics
Matches: 172, Mismatches: 34, Indels: 5
0.82 0.16 0.02
Matches are distributed among these distances:
148 26 0.15
149 145 0.84
150 1 0.01
ACGTcount: A:0.27, C:0.20, G:0.22, T:0.32
Consensus pattern (149 bp):
AGATGTCGTTGACATCTTGTCGTGACACACATGAGTCATTGCAGTATTATAGGGTGACACACCAT
GCTCAAATTTCACCTATGTCGTCAACATCTTGTCACGACACACTGAGTTATTGTAATATTAGAGG
GTGACACGCCACCTACCAA
Found at i:21576683 original size:71 final size:71
Alignment explanation
Indices: 21576589--21576756 Score: 203
Period size: 71 Copynumber: 2.4 Consensus size: 71
21576579 TATGTTGTCA
* * * * * *
21576589 ACATCTTGTTGTGACAC-ATTGAGTTATTTTAGTATTAGAGGGTGACATGCCACGTACCAAAGAT
1 ACATCTTGTCGTGACACGA-TGAGTTATTGTAATATTAGAGAGTGACACGCCACGTACCAAAAAT
*
21576653 GTCTTTG
65 GTCGTTG
* * * * *
21576660 ACATCATGTCGTGACACGATGAGTCATTGTAATATTATAGAGTGACACGTCACGTTCCAAAAATG
1 ACATCTTGTCGTGACACGATGAGTTATTGTAATATTAGAGAGTGACACGCCACGTACCAAAAATG
21576725 TCGTTG
66 TCGTTG
21576731 ACATCTTGTCGTGACACGTATGAGTT
1 ACATCTTGTCGTGACACG-ATGAGTT
21576757 GCTCCAATTT
Statistics
Matches: 81, Mismatches: 14, Indels: 3
0.83 0.14 0.03
Matches are distributed among these distances:
71 74 0.91
72 7 0.09
ACGTcount: A:0.28, C:0.17, G:0.22, T:0.33
Consensus pattern (71 bp):
ACATCTTGTCGTGACACGATGAGTTATTGTAATATTAGAGAGTGACACGCCACGTACCAAAAATG
TCGTTG
Found at i:21576849 original size:24 final size:24
Alignment explanation
Indices: 21576822--21576878 Score: 96
Period size: 24 Copynumber: 2.4 Consensus size: 24
21576812 GTATTATAGG
*
21576822 GTGACACGCCATGCTCATGTTATT
1 GTGACACGCCATGCTCATCTTATT
*
21576846 GTGACACACCATGCTCATCTTATT
1 GTGACACGCCATGCTCATCTTATT
21576870 GTGACACGC
1 GTGACACGC
21576879 ATGAGTCATT
Statistics
Matches: 30, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
24 30 1.00
ACGTcount: A:0.23, C:0.28, G:0.19, T:0.30
Consensus pattern (24 bp):
GTGACACGCCATGCTCATCTTATT
Found at i:21585103 original size:26 final size:26
Alignment explanation
Indices: 21585074--21585132 Score: 66
Period size: 26 Copynumber: 2.3 Consensus size: 26
21585064 ATTTTCTAGT
* *
21585074 TTTCCTTTGT-TTTTCTCTTTTCTTCC
1 TTTCCTTTCTATTTTCTCTCTTCTT-C
* *
21585100 TTTCCTCTCTATTTTCTCTCTTGTTC
1 TTTCCTTTCTATTTTCTCTCTTCTTC
21585126 TTTCCTT
1 TTTCCTT
21585133 ATGGCCGGCC
Statistics
Matches: 27, Mismatches: 5, Indels: 2
0.79 0.15 0.06
Matches are distributed among these distances:
26 15 0.56
27 12 0.44
ACGTcount: A:0.02, C:0.29, G:0.03, T:0.66
Consensus pattern (26 bp):
TTTCCTTTCTATTTTCTCTCTTCTTC
Found at i:21591647 original size:16 final size:15
Alignment explanation
Indices: 21591622--21591670 Score: 62
Period size: 16 Copynumber: 3.1 Consensus size: 15
21591612 ACTTAATTAG
21591622 TTTATTTATATTTTT
1 TTTATTTATATTTTT
*
21591637 CTTTGTTTATATCTTTT
1 -TTTATTTATAT-TTTT
21591654 TTTATTTCATATTTTT
1 TTTATTT-ATATTTTT
21591670 T
1 T
21591671 ACTCTATTTT
Statistics
Matches: 29, Mismatches: 2, Indels: 4
0.83 0.06 0.11
Matches are distributed among these distances:
16 21 0.72
17 8 0.28
ACGTcount: A:0.16, C:0.06, G:0.02, T:0.76
Consensus pattern (15 bp):
TTTATTTATATTTTT
Found at i:21602724 original size:2 final size:2
Alignment explanation
Indices: 21602717--21602759 Score: 50
Period size: 2 Copynumber: 21.0 Consensus size: 2
21602707 TTTCAAACCC
* * *
21602717 TA TA TA TA TA TA TA TA TA TA TA TCA TA CA TA AA CA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA T-A TA TA TA TA TA TA TA TA TA
21602760 ACCACCGGAC
Statistics
Matches: 35, Mismatches: 5, Indels: 2
0.83 0.12 0.05
Matches are distributed among these distances:
2 33 0.94
3 2 0.06
ACGTcount: A:0.51, C:0.07, G:0.00, T:0.42
Consensus pattern (2 bp):
TA
Found at i:21602834 original size:42 final size:41
Alignment explanation
Indices: 21602788--21602910 Score: 156
Period size: 42 Copynumber: 2.9 Consensus size: 41
21602778 AACTCTGTCT
* * * *
21602788 CAGCTTATGTGCATTACCACACCGCACATAGCCGGGTCAGCA
1 CAGCTCATGTGCACT-CCACACCGCACATGGCTGGGTCAGCA
* *
21602830 CAGCTCATGTGCACTCATACACCGCACATGGCTGGGTCAGCC
1 CAGCTCATGTGCACTC-CACACCGCACATGGCTGGGTCAGCA
*
21602872 CAACTCATGTGCACTCCTACACCGCACATGGCTGGGTCA
1 CAGCTCATGTGCACTCC-ACACCGCACATGGCTGGGTCA
21602911 TAATTATCAC
Statistics
Matches: 71, Mismatches: 8, Indels: 4
0.86 0.10 0.05
Matches are distributed among these distances:
41 1 0.01
42 70 0.99
ACGTcount: A:0.24, C:0.35, G:0.22, T:0.20
Consensus pattern (41 bp):
CAGCTCATGTGCACTCCACACCGCACATGGCTGGGTCAGCA
Found at i:21614364 original size:33 final size:33
Alignment explanation
Indices: 21614327--21614392 Score: 105
Period size: 33 Copynumber: 2.0 Consensus size: 33
21614317 CAGTGGTACT
*
21614327 AAGGTTGACCTCGGCCGTGGCAGCAGCGGCACC
1 AAGGTTGACCTCGGCCGTGGCAACAGCGGCACC
* *
21614360 AAGGTTGATCTCGGCCGTGGCAACAGCTGCACC
1 AAGGTTGACCTCGGCCGTGGCAACAGCGGCACC
21614393 GGGCAGCAAA
Statistics
Matches: 30, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
33 30 1.00
ACGTcount: A:0.20, C:0.32, G:0.33, T:0.15
Consensus pattern (33 bp):
AAGGTTGACCTCGGCCGTGGCAACAGCGGCACC
Done.