Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: A12
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: 103038859
ACGTcount: A:0.31, C:0.16, G:0.16, T:0.31
Warning! 4950000 characters in sequence are not A, C, G, or T
File 120 of 320
Found at i:39300526 original size:46 final size:49
Alignment explanation
Indices: 39300475--39300613 Score: 175
Period size: 46 Copynumber: 2.9 Consensus size: 49
39300465 ATGGTTGAGC
39300475 ATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAA-T-G
1 ATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAACTAG
* * *
39300522 -TCCGAACTCGTTGAGTTGAGTCCGAGTTC-GTGA--GATG-TAACTAGG
1 ATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAACTA-G
*
39300567 CATCCGAACTTGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAAC
1 -ATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAAC
39300614 GCCCGAGCNN
Statistics
Matches: 76, Mismatches: 7, Indels: 14
0.78 0.07 0.14
Matches are distributed among these distances:
42 2 0.03
43 5 0.07
45 3 0.04
46 29 0.38
47 28 0.37
48 2 0.03
50 4 0.05
51 3 0.04
ACGTcount: A:0.23, C:0.19, G:0.28, T:0.29
Consensus pattern (49 bp):
ATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAACTAG
Found at i:39312840 original size:40 final size:40
Alignment explanation
Indices: 39312740--39312911 Score: 204
Period size: 40 Copynumber: 4.3 Consensus size: 40
39312730 GCTCCTCGTT
* * *
39312740 CAAATGCCTTCGGGACATAGCCCGGTTTTAGTAACTCACA
1 CAAATGCCTTCGGGACATAACCCGGATTTAGTAACTCGCA
**
39312780 C-AATGCCTTCGGGACATAACCCGGATTTAACAACTCGCA
1 CAAATGCCTTCGGGACATAACCCGGATTTAGTAACTCGCA
* * * *
39312819 CGAATGCCTTCGGGACTTAACCCGGAATTAGTATCTCGCA
1 CAAATGCCTTCGGGACATAACCCGGATTTAGTAACTCGCA
* * * *
39312859 CAAAGGCCTTCGGGGCTTAACCCGGAATTT-GTATCTCGCA
1 CAAATGCCTTCGGGACATAACCCGG-ATTTAGTAACTCGCA
39312899 CAAATGCCTTCGG
1 CAAATGCCTTCGG
39312912 ATCTTAGTCC
Statistics
Matches: 115, Mismatches: 15, Indels: 4
0.86 0.11 0.03
Matches are distributed among these distances:
39 34 0.30
40 78 0.68
41 3 0.03
ACGTcount: A:0.26, C:0.28, G:0.22, T:0.24
Consensus pattern (40 bp):
CAAATGCCTTCGGGACATAACCCGGATTTAGTAACTCGCA
Found at i:39312973 original size:41 final size:41
Alignment explanation
Indices: 39312896--39312973 Score: 97
Period size: 40 Copynumber: 1.9 Consensus size: 41
39312886 TTTGTATCTC
* * *
39312896 GCACAAATGCCTTCGGATCTTAGTCCGGATATATTCACTTA
1 GCACAAATGCCTTCGGATCTTAGCCCGGACACATTCACTTA
39312937 GCACAAA-GCCTTCGGGA-CTTAGCCCGGACAGCATTCA
1 GCACAAATGCCTTC-GGATCTTAGCCCGGACA-CATTCA
39312974 ATTAATCATG
Statistics
Matches: 32, Mismatches: 3, Indels: 4
0.82 0.08 0.10
Matches are distributed among these distances:
40 17 0.53
41 15 0.47
ACGTcount: A:0.27, C:0.28, G:0.21, T:0.24
Consensus pattern (41 bp):
GCACAAATGCCTTCGGATCTTAGCCCGGACACATTCACTTA
Found at i:39320973 original size:42 final size:42
Alignment explanation
Indices: 39320921--39321044 Score: 178
Period size: 41 Copynumber: 3.0 Consensus size: 42
39320911 GGAGTAGCTA
* *
39320921 AAAGCCACAGCAGATCTCCTTGAAGTTTCAATGGAATTGATC
1 AAAGCTACAGCAGATCTCCTTGAAGTTTCAGTGGAATTGATC
* *
39320963 AAAGCTACAGCAGATCTCCTTGAAGTTTCAGTGG-ATTAAGC
1 AAAGCTACAGCAGATCTCCTTGAAGTTTCAGTGGAATTGATC
* * *
39321004 GAAGCTACAGTAGATCTTCTTGAAGTTTCAGTGGAATTGAT
1 AAAGCTACAGCAGATCTCCTTGAAGTTTCAGTGGAATTGAT
39321045 TGAAGTCACG
Statistics
Matches: 72, Mismatches: 9, Indels: 2
0.87 0.11 0.02
Matches are distributed among these distances:
41 36 0.50
42 36 0.50
ACGTcount: A:0.31, C:0.18, G:0.22, T:0.29
Consensus pattern (42 bp):
AAAGCTACAGCAGATCTCCTTGAAGTTTCAGTGGAATTGATC
Found at i:39330773 original size:20 final size:21
Alignment explanation
Indices: 39330733--39330773 Score: 57
Period size: 21 Copynumber: 2.0 Consensus size: 21
39330723 GTGTTGATTT
*
39330733 CATTCTTTGGCCCATTTTCTC
1 CATTCTTTGGCCCAGTTTCTC
*
39330754 CATTTTTTGGCCC-GTTTCTC
1 CATTCTTTGGCCCAGTTTCTC
39330774 GTTCCTTCCA
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
20 6 0.33
21 12 0.67
ACGTcount: A:0.07, C:0.32, G:0.12, T:0.49
Consensus pattern (21 bp):
CATTCTTTGGCCCAGTTTCTC
Found at i:39332630 original size:46 final size:46
Alignment explanation
Indices: 39332580--39332752 Score: 167
Period size: 46 Copynumber: 3.7 Consensus size: 46
39332570 TGGTTGAGCA
39332580 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAATG
1 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAATG
* * * * * *
39332626 TCCGAACTCGTTGAGTTGAGCCCAAGTTC-GTGA--AATG-TAACTAGG
1 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAA-T--G
* * *
39332671 CATCCGAACTCATTGAGTTGAGTCTGAGTTCACTTATGGATGCGAACG
1 --TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAATG
*
39332719 -CCTGAGCTCGTTGAGTTGAGTCCGAGTTCACTTA
1 TCC-GAACTCGTTGAGTTGAGTCCGAGTTCACTTA
39332753 GGGGCGGGTT
Statistics
Matches: 99, Mismatches: 18, Indels: 20
0.72 0.13 0.15
Matches are distributed among these distances:
42 2 0.02
43 4 0.04
45 5 0.05
46 55 0.56
47 25 0.25
48 3 0.03
50 3 0.03
51 2 0.02
ACGTcount: A:0.23, C:0.21, G:0.27, T:0.29
Consensus pattern (46 bp):
TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAATG
Found at i:39332714 original size:93 final size:93
Alignment explanation
Indices: 39332577--39332747 Score: 272
Period size: 93 Copynumber: 1.8 Consensus size: 93
39332567 GGATGGTTGA
* *
39332577 GCATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAATGTCC-GAACTCGTTGAG
1 GCATCCGAACTCATTGAGTTGAGTCCGAGTTCACTTATGGATGCGAACG-CCTGAACTCGTTGAG
39332641 TTGAGCCCAAGTTCGTGAAATGTAACTAG
65 TTGAGCCCAAGTTCGTGAAATGTAACTAG
* *
39332670 GCATCCGAACTCATTGAGTTGAGTCTGAGTTCACTTATGGATGCGAACGCCTGAGCTCGTTGAGT
1 GCATCCGAACTCATTGAGTTGAGTCCGAGTTCACTTATGGATGCGAACGCCTGAACTCGTTGAGT
* *
39332735 TGAGTCCGAGTTC
66 TGAGCCCAAGTTC
39332748 ACTTAGGGGC
Statistics
Matches: 71, Mismatches: 6, Indels: 2
0.90 0.08 0.03
Matches are distributed among these distances:
92 2 0.03
93 69 0.97
ACGTcount: A:0.23, C:0.21, G:0.27, T:0.29
Consensus pattern (93 bp):
GCATCCGAACTCATTGAGTTGAGTCCGAGTTCACTTATGGATGCGAACGCCTGAACTCGTTGAGT
TGAGCCCAAGTTCGTGAAATGTAACTAG
Found at i:39340215 original size:46 final size:45
Alignment explanation
Indices: 39340159--39340330 Score: 163
Period size: 46 Copynumber: 3.8 Consensus size: 45
39340149 TGGTTGAGCA
39340159 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAATG
1 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAA-G
* * * * * *
39340205 TCCGAACTCGTTGAGTTGAGCCCAAGTTC-GTAAATGTAACTAG-GCA-
1 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACT-TATG-GA-T-GCGAAG
* *
39340251 TCCAAACTCATTGAGTTGAGTCCGAGTTCACTTATGGATGCGAACG
1 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAA-G
* *
39340297 -CCTGAGCTCGTTGAGTTGAGTCTGAGTTCACTTA
1 TCC-GAACTCGTTGAGTTGAGTCCGAGTTCACTTA
39340331 GGGGCGGGTT
Statistics
Matches: 99, Mismatches: 18, Indels: 18
0.73 0.13 0.13
Matches are distributed among these distances:
43 1 0.01
44 3 0.03
45 4 0.04
46 85 0.86
47 2 0.02
48 3 0.03
49 1 0.01
ACGTcount: A:0.24, C:0.21, G:0.26, T:0.30
Consensus pattern (45 bp):
TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAAG
Found at i:39374321 original size:31 final size:30
Alignment explanation
Indices: 39374285--39374345 Score: 86
Period size: 30 Copynumber: 2.0 Consensus size: 30
39374275 TCCCTAACTC
39374285 AAACTTTAGAAAAATTACAATTTTGCCCCTA
1 AAACTTTA-AAAAATTACAATTTTGCCCCTA
* * *
39374316 AAACTTTATAGAATTACGATTTTGCCCCTA
1 AAACTTTAAAAAATTACAATTTTGCCCCTA
39374346 GGCTCAGAAA
Statistics
Matches: 27, Mismatches: 3, Indels: 1
0.87 0.10 0.03
Matches are distributed among these distances:
30 19 0.70
31 8 0.30
ACGTcount: A:0.38, C:0.20, G:0.08, T:0.34
Consensus pattern (30 bp):
AAACTTTAAAAAATTACAATTTTGCCCCTA
Found at i:39376066 original size:60 final size:60
Alignment explanation
Indices: 39375989--39376111 Score: 219
Period size: 60 Copynumber: 2.0 Consensus size: 60
39375979 ACATAACATT
* *
39375989 TCACGCTCCTACTAGTATAACTAAATCAAGTTATCATCCATCTCTTTACTTCTCAAATAA
1 TCACACTCCTACTAGTATAACTAAATCAAGTTATCATCCATCTCTGTACTTCTCAAATAA
*
39376049 TCACACTCTTACTAGTATAACTAAATCAAGTTATCATCCATCTCTGTACTTCTCAAATAA
1 TCACACTCCTACTAGTATAACTAAATCAAGTTATCATCCATCTCTGTACTTCTCAAATAA
39376109 TCA
1 TCA
39376112 ACTAATTATC
Statistics
Matches: 60, Mismatches: 3, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
60 60 1.00
ACGTcount: A:0.34, C:0.26, G:0.05, T:0.35
Consensus pattern (60 bp):
TCACACTCCTACTAGTATAACTAAATCAAGTTATCATCCATCTCTGTACTTCTCAAATAA
Found at i:39376263 original size:44 final size:44
Alignment explanation
Indices: 39376213--39376301 Score: 169
Period size: 44 Copynumber: 2.0 Consensus size: 44
39376203 AACCAAGCTG
39376213 AATCATAATGGATACTTCAATTGTCAATATCTTCAACTGTTTAT
1 AATCATAATGGATACTTCAATTGTCAATATCTTCAACTGTTTAT
*
39376257 AATCATAATGGATACTTCAATTGTCAATATCTTCAACTTTTTAT
1 AATCATAATGGATACTTCAATTGTCAATATCTTCAACTGTTTAT
39376301 A
1 A
39376302 CTTTATTAGC
Statistics
Matches: 44, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
44 44 1.00
ACGTcount: A:0.35, C:0.16, G:0.08, T:0.42
Consensus pattern (44 bp):
AATCATAATGGATACTTCAATTGTCAATATCTTCAACTGTTTAT
Found at i:39376860 original size:13 final size:13
Alignment explanation
Indices: 39376838--39376870 Score: 50
Period size: 13 Copynumber: 2.6 Consensus size: 13
39376828 AAGGGTTTGT
39376838 TTAT-TAAACTAA
1 TTATCTAAACTAA
39376850 TTATCTAAACTAA
1 TTATCTAAACTAA
*
39376863 TTAACTAA
1 TTATCTAA
39376871 TTTAATTAAA
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
12 4 0.21
13 15 0.79
ACGTcount: A:0.48, C:0.12, G:0.00, T:0.39
Consensus pattern (13 bp):
TTATCTAAACTAA
Found at i:39379789 original size:5 final size:5
Alignment explanation
Indices: 39379779--39379883 Score: 74
Period size: 6 Copynumber: 19.8 Consensus size: 5
39379769 TATGTCTTTC
*
39379779 AAAAT AAAAT AATAA- AATAAT AAAATT GAAAT GAAAAT AAAAAT AAAAAT
1 AAAAT AAAAT AA-AAT AA-AAT AAAA-T AAAAT -AAAAT -AAAAT -AAAAT
*
39379829 AAAAAT AAAAAT AAAAT -AAAT AAAAT AATAA- AAAAT AAAA- AATAT
1 -AAAAT -AAAAT AAAAT AAAAT AAAAT AA-AAT AAAAT AAAAT AAAAT
39379874 AAGAAT AAAA
1 AA-AAT AAAA
39379884 AGATAAAAGG
Statistics
Matches: 86, Mismatches: 5, Indels: 18
0.79 0.05 0.17
Matches are distributed among these distances:
4 9 0.10
5 36 0.42
6 41 0.48
ACGTcount: A:0.77, C:0.00, G:0.03, T:0.20
Consensus pattern (5 bp):
AAAAT
Found at i:39379816 original size:6 final size:6
Alignment explanation
Indices: 39379807--39379884 Score: 79
Period size: 6 Copynumber: 12.5 Consensus size: 6
39379797 AATAAAATTG
*
39379807 AAATGA AAATAA AAATAA AAATAA AAATAA AAAT-A AAATAA ATAA-AA
1 AAATAA AAATAA AAATAA AAATAA AAATAA AAATAA AAATAA A-AATAA
*
39379854 TAATAAA AAATAAA AAATATA AGAATAA AAA
1 AAAT-AA AAAT-AA AAATA-A A-AATAA AAA
39379885 GATAAAAGGA
Statistics
Matches: 63, Mismatches: 3, Indels: 12
0.81 0.04 0.15
Matches are distributed among these distances:
5 7 0.11
6 34 0.54
7 18 0.29
8 4 0.06
ACGTcount: A:0.79, C:0.00, G:0.03, T:0.18
Consensus pattern (6 bp):
AAATAA
Found at i:39379834 original size:24 final size:25
Alignment explanation
Indices: 39379812--39379884 Score: 80
Period size: 23 Copynumber: 2.9 Consensus size: 25
39379802 AATTGAAATG
39379812 AAAATAAAAATAAA-AATAAAAATA
1 AAAATAAAAATAAAGAATAAAAATA
* *
39379836 AAAAT-AAAATAAATAA-AATAATAA
1 AAAATAAAAATAAAGAATAAAAAT-A
39379860 AAAATAAAAAATATAAGAATAAAAA
1 AAAAT-AAAAATA-AAGAATAAAAA
39379885 GATAAAAGGA
Statistics
Matches: 40, Mismatches: 3, Indels: 8
0.78 0.06 0.16
Matches are distributed among these distances:
23 13 0.32
24 13 0.32
26 6 0.15
27 4 0.10
28 4 0.10
ACGTcount: A:0.81, C:0.00, G:0.01, T:0.18
Consensus pattern (25 bp):
AAAATAAAAATAAAGAATAAAAATA
Found at i:39379889 original size:8 final size:7
Alignment explanation
Indices: 39379812--39379891 Score: 78
Period size: 8 Copynumber: 11.3 Consensus size: 7
39379802 AATTGAAATG
39379812 AAAAT-A
1 AAAATAA
39379818 AAAAT-A
1 AAAATAA
39379824 AAAAT-A
1 AAAATAA
39379830 AAAAT-A
1 AAAATAA
39379836 AAAATAAA
1 AAAAT-AA
39379844 ATAAATAA
1 A-AAATAA
39379852 AATAATAA
1 AA-AATAA
39379860 AAAATAA
1 AAAATAA
39379867 AAAATATA
1 AAAATA-A
*
39379875 AGAATAA
1 AAAATAA
39379882 AAAGATAA
1 AAA-ATAA
39379890 AA
1 AA
39379892 GGATTCAATG
Statistics
Matches: 66, Mismatches: 2, Indels: 10
0.85 0.03 0.13
Matches are distributed among these distances:
6 23 0.35
7 15 0.23
8 24 0.36
9 4 0.06
ACGTcount: A:0.80, C:0.00, G:0.03, T:0.17
Consensus pattern (7 bp):
AAAATAA
Found at i:39383428 original size:46 final size:43
Alignment explanation
Indices: 39383285--39383420 Score: 123
Period size: 46 Copynumber: 3.0 Consensus size: 43
39383275 CCAGCCCCTA
*
39383285 AGTGAACTCAGACTCAACTCAACGAGTTCGGATGCCTAGTTA-CATTT
1 AGTGAACTCGGACTCAACTCAACGAGTTCGGATGCC-A---ACCA-TT
* * * *
39383332 CA-CGAACTCGGACTCAACTCAACGAGTTCGGACATTCGCATCCATA
1 -AGTGAACTCGGACTCAACTCAACGAGTTCGG--ATGC-CAACCATT
39383378 AGTGAACTCGGACTCAACTCAACGAGTTCGGATGCTCAACCAT
1 AGTGAACTCGGACTCAACTCAACGAGTTCGGATGC-CAACCAT
39383421 CCTAGTGACA
Statistics
Matches: 74, Mismatches: 9, Indels: 14
0.76 0.09 0.14
Matches are distributed among these distances:
44 9 0.12
45 1 0.01
46 29 0.39
47 29 0.39
48 1 0.01
49 4 0.05
50 1 0.01
ACGTcount: A:0.30, C:0.28, G:0.19, T:0.23
Consensus pattern (43 bp):
AGTGAACTCGGACTCAACTCAACGAGTTCGGATGCCAACCATT
Found at i:39388892 original size:93 final size:93
Alignment explanation
Indices: 39388780--39388950 Score: 299
Period size: 93 Copynumber: 1.8 Consensus size: 93
39388770 GCCCCTAAGT
* *
39388780 GAACTCGGACTCAACTCAACGACCTT-GGGCGTTCGCATCCATAAGTGAACTCGGACTCAACTCA
1 GAACTCGGACTCAACTCAACGA-CTTCGGACATTCGCATCCATAAGTGAACTCGGACTCAACTCA
39388844 ACGAGTTCGGATGCCTAGTTACATTTCAC
65 ACGAGTTCGGATGCCTAGTTACATTTCAC
*
39388873 GAACTCGGACTCAACTCAACGAGTTCGGACATTCGCATCCATAAGTGAACTCGGACTCAACTCAA
1 GAACTCGGACTCAACTCAACGACTTCGGACATTCGCATCCATAAGTGAACTCGGACTCAACTCAA
39388938 CGAGTTCGGATGC
66 CGAGTTCGGATGC
39388951 TCAACCATGC
Statistics
Matches: 74, Mismatches: 3, Indels: 2
0.94 0.04 0.03
Matches are distributed among these distances:
92 2 0.03
93 72 0.97
ACGTcount: A:0.28, C:0.29, G:0.21, T:0.22
Consensus pattern (93 bp):
GAACTCGGACTCAACTCAACGACTTCGGACATTCGCATCCATAAGTGAACTCGGACTCAACTCAA
CGAGTTCGGATGCCTAGTTACATTTCAC
Found at i:39388947 original size:46 final size:46
Alignment explanation
Indices: 39388775--39388947 Score: 194
Period size: 46 Copynumber: 3.7 Consensus size: 46
39388765 AACCCGCCCC
* * *
39388775 TAAGTGAACTCGGACTCAACTCAACGACCTT-GGGCGTTCGCATCCA
1 TAAGTGAACTCGGACTCAACTCAACGA-GTTCGGACATTCGCATCCA
* *
39388821 TAAGTGAACTCGGACTCAACTCAACGAGTTCGGATGCCTAGTT-ACAT--T
1 TAAGTGAACTCGGACTCAACTCAACGAGTTCGGA---C-A-TTCGCATCCA
* *
39388869 TCA-CGAACTCGGACTCAACTCAACGAGTTCGGACATTCGCATCCA
1 TAAGTGAACTCGGACTCAACTCAACGAGTTCGGACATTCGCATCCA
39388914 TAAGTGAACTCGGACTCAACTCAACGAGTTCGGA
1 TAAGTGAACTCGGACTCAACTCAACGAGTTCGGA
39388948 TGCTCAACCA
Statistics
Matches: 106, Mismatches: 11, Indels: 20
0.77 0.08 0.15
Matches are distributed among these distances:
42 2 0.02
43 4 0.04
44 1 0.01
45 4 0.04
46 58 0.55
47 29 0.27
48 2 0.02
49 1 0.01
50 3 0.03
51 2 0.02
ACGTcount: A:0.29, C:0.28, G:0.21, T:0.23
Consensus pattern (46 bp):
TAAGTGAACTCGGACTCAACTCAACGAGTTCGGACATTCGCATCCA
Found at i:39390824 original size:28 final size:28
Alignment explanation
Indices: 39390756--39390906 Score: 205
Period size: 28 Copynumber: 5.4 Consensus size: 28
39390746 GAGATTGGCG
* * * * *
39390756 CTAAGTGTGCGGGTTTAAATTGTACAGGA
1 CTAAGTGTGCGAGTTT-GATTATATAGCA
*
39390785 CTAAGTGTGCGAGTTTGATTATGTAGCA
1 CTAAGTGTGCGAGTTTGATTATATAGCA
* *
39390813 CTAAGTGTGCGAGCTTGATTATGTAGCA
1 CTAAGTGTGCGAGTTTGATTATATAGCA
39390841 CTAAGTGTGCGAGTTTGATTATATAGCA
1 CTAAGTGTGCGAGTTTGATTATATAGCA
39390869 CTAAGTGTGCGAG-TTGATTATATAGCA
1 CTAAGTGTGCGAGTTTGATTATATAGCA
*
39390896 CTGAGTGTGCG
1 CTAAGTGTGCG
39390907 GACTTAATAT
Statistics
Matches: 112, Mismatches: 10, Indels: 2
0.90 0.08 0.02
Matches are distributed among these distances:
27 24 0.21
28 73 0.65
29 15 0.13
ACGTcount: A:0.26, C:0.12, G:0.29, T:0.33
Consensus pattern (28 bp):
CTAAGTGTGCGAGTTTGATTATATAGCA
Found at i:39396047 original size:13 final size:13
Alignment explanation
Indices: 39396025--39396057 Score: 50
Period size: 13 Copynumber: 2.6 Consensus size: 13
39396015 AATGGTTTGT
39396025 TTAT-TAAACTAA
1 TTATCTAAACTAA
39396037 TTATCTAAACTAA
1 TTATCTAAACTAA
*
39396050 TTAACTAA
1 TTATCTAA
39396058 TTTAATTAAA
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
12 4 0.21
13 15 0.79
ACGTcount: A:0.48, C:0.12, G:0.00, T:0.39
Consensus pattern (13 bp):
TTATCTAAACTAA
Found at i:39403986 original size:48 final size:48
Alignment explanation
Indices: 39403927--39404475 Score: 855
Period size: 48 Copynumber: 11.3 Consensus size: 48
39403917 TGTACAAGAT
* *
39403927 AAATATATATGAGATATGTATATGCGGTAAAGCCGAATGGCTAATGTG
1 AAATATGTATGAGATATGTATATGTGGTAAAGCCGAATGGCTAATGTG
* *
39403975 AAATAAGTATGAGATATGTATATGTGGTAAAGCCGAATGGCTACTGTG
1 AAATATGTATGAGATATGTATATGTGGTAAAGCCGAATGGCTAATGTG
* * * *
39404023 AAAAATATATGAGATATGTATATGTGGCAAAGCCGAATGGCTACTGTG
1 AAATATGTATGAGATATGTATATGTGGTAAAGCCGAATGGCTAATGTG
* *
39404071 AAATATATATGAGATATGTATATGTGGTAAAGCCGAATGTCTAATGTG
1 AAATATGTATGAGATATGTATATGTGGTAAAGCCGAATGGCTAATGTG
* *
39404119 AAATATGTATGAGAAATGTATATATGTGGTAAAGCCGAATGGCTACTGTG
1 AAATATGTATGAGATATG--TATATGTGGTAAAGCCGAATGGCTAATGTG
* * *
39404169 AAATATATATGAGAAATGTATATGTGGTAAAGCTGAATGGCTAATGTG
1 AAATATGTATGAGATATGTATATGTGGTAAAGCCGAATGGCTAATGTG
*
39404217 AAATATGTATGAGAAATGTATATATGTGGTAAAGCCGAATGGCTAATGTG
1 AAATATGTATGAGATATG--TATATGTGGTAAAGCCGAATGGCTAATGTG
*
39404267 AAATATGTATGAGATATGTATATGTGGTAAAGCCGAATGGCTACTGTG
1 AAATATGTATGAGATATGTATATGTGGTAAAGCCGAATGGCTAATGTG
*
39404315 AAATATATATGAGATATGTATATGTGGTAAAGCCGAATGGCTAATGTG
1 AAATATGTATGAGATATGTATATGTGGTAAAGCCGAATGGCTAATGTG
*
39404363 AAATATGTATGAGAAATGTATATATGTGGTAAAGCCGAATGGCTAATGTG
1 AAATATGTATGAGATATG--TATATGTGGTAAAGCCGAATGGCTAATGTG
*
39404413 AAATATGTATGAGATATGTATATGTGGTAAAGCCGAATGGCTAGTGTG
1 AAATATGTATGAGATATGTATATGTGGTAAAGCCGAATGGCTAATGTG
*
39404461 AAATATGTAGGAGAT
1 AAATATGTATGAGAT
39404476 GTGTGTATAT
Statistics
Matches: 465, Mismatches: 30, Indels: 12
0.92 0.06 0.02
Matches are distributed among these distances:
48 327 0.70
50 138 0.30
ACGTcount: A:0.37, C:0.07, G:0.26, T:0.30
Consensus pattern (48 bp):
AAATATGTATGAGATATGTATATGTGGTAAAGCCGAATGGCTAATGTG
Found at i:39404201 original size:146 final size:145
Alignment explanation
Indices: 39403927--39404475 Score: 904
Period size: 146 Copynumber: 3.8 Consensus size: 145
39403917 TGTACAAGAT
* * *
39403927 AAATATATATGAGATATG-TATATGCGGTAAAGCCGAATGGCTAATGTGAAATAAGTATGAGATA
1 AAATATATATGAGAAATGATATATGTGGTAAAGCCGAATGGCTAATGTGAAATATGTATGAGATA
* *
39403991 TGTATATGTGGTAAAGCCGAATGGCTACTGTGAAAAATATATGAGATATGTATATGTGGCAAAGC
66 TGTATATGTGGTAAAGCCGAATGGCTACTGTGAAATATATATGAGATATGTATATGTGGTAAAGC
*
39404056 CGAATGGCTACTGTG
131 CGAATGGCTAATGTG
* * *
39404071 AAATATATATGAGATATG-TATATGTGGTAAAGCCGAATGTCTAATGTGAAATATGTATGAGAAA
1 AAATATATATGAGAAATGATATATGTGGTAAAGCCGAATGGCTAATGTGAAATATGTATGAGATA
*
39404135 TGTATATATGTGGTAAAGCCGAATGGCTACTGTGAAATATATATGAGAAATGTATATGTGGTAAA
66 TG--TATATGTGGTAAAGCCGAATGGCTACTGTGAAATATATATGAGATATGTATATGTGGTAAA
*
39404200 GCTGAATGGCTAATGTG
129 GCCGAATGGCTAATGTG
*
39404217 AAATATGTATGAGAAATGTATATATGTGGTAAAGCCGAATGGCTAATGTGAAATATGTATGAGAT
1 AAATATATATGAGAAATG-ATATATGTGGTAAAGCCGAATGGCTAATGTGAAATATGTATGAGAT
39404282 ATGTATATGTGGTAAAGCCGAATGGCTACTGTGAAATATATATGAGATATGTATATGTGGTAAAG
65 ATGTATATGTGGTAAAGCCGAATGGCTACTGTGAAATATATATGAGATATGTATATGTGGTAAAG
39404347 CCGAATGGCTAATGTG
130 CCGAATGGCTAATGTG
*
39404363 AAATATGTATGAGAAATGTATATATGTGGTAAAGCCGAATGGCTAATGTGAAATATGTATGAGAT
1 AAATATATATGAGAAATG-ATATATGTGGTAAAGCCGAATGGCTAATGTGAAATATGTATGAGAT
* * *
39404428 ATGTATATGTGGTAAAGCCGAATGGCTAGTGTGAAATATGTAGGAGAT
65 ATGTATATGTGGTAAAGCCGAATGGCTACTGTGAAATATATATGAGAT
39404476 GTGTGTATAT
Statistics
Matches: 383, Mismatches: 18, Indels: 6
0.94 0.04 0.01
Matches are distributed among these distances:
144 62 0.16
146 275 0.72
148 46 0.12
ACGTcount: A:0.37, C:0.07, G:0.26, T:0.30
Consensus pattern (145 bp):
AAATATATATGAGAAATGATATATGTGGTAAAGCCGAATGGCTAATGTGAAATATGTATGAGATA
TGTATATGTGGTAAAGCCGAATGGCTACTGTGAAATATATATGAGATATGTATATGTGGTAAAGC
CGAATGGCTAATGTG
Found at i:39404485 original size:98 final size:96
Alignment explanation
Indices: 39403927--39404475 Score: 855
Period size: 98 Copynumber: 5.7 Consensus size: 96
39403917 TGTACAAGAT
* *
39403927 AAATATATATGAGATATGTATATGCGGTAAAGCCGAATGGCTAATGTGAAATAAGTATGAGATAT
1 AAATATATATGAGATATGTATATGTGGTAAAGCCGAATGGCTAATGTGAAATATGTATGAGATAT
*
39403992 GTATATGTGGTAAAGCCGAATGGCTACTGTG
66 GTATATGTGGTAAAGCCGAATGGCTAATGTG
* * * *
39404023 AAAAATATATGAGATATGTATATGTGGCAAAGCCGAATGGCTACTGTGAAATATATATGAGATAT
1 AAATATATATGAGATATGTATATGTGGTAAAGCCGAATGGCTAATGTGAAATATGTATGAGATAT
*
39404088 GTATATGTGGTAAAGCCGAATGTCTAATGTG
66 GTATATGTGGTAAAGCCGAATGGCTAATGTG
* * * * *
39404119 AAATATGTATGAGAAATGTATATATGTGGTAAAGCCGAATGGCTACTGTGAAATATATATGAGAA
1 AAATATATATGAGATATG--TATATGTGGTAAAGCCGAATGGCTAATGTGAAATATGTATGAGAT
*
39404184 ATGTATATGTGGTAAAGCTGAATGGCTAATGTG
64 ATGTATATGTGGTAAAGCCGAATGGCTAATGTG
* *
39404217 AAATATGTATGAGAAATGTATATATGTGGTAAAGCCGAATGGCTAATGTGAAATATGTATGAGAT
1 AAATATATATGAGATATG--TATATGTGGTAAAGCCGAATGGCTAATGTGAAATATGTATGAGAT
*
39404282 ATGTATATGTGGTAAAGCCGAATGGCTACTGTG
64 ATGTATATGTGGTAAAGCCGAATGGCTAATGTG
*
39404315 AAATATATATGAGATATGTATATGTGGTAAAGCCGAATGGCTAATGTGAAATATGTATGAGAAAT
1 AAATATATATGAGATATGTATATGTGGTAAAGCCGAATGGCTAATGTGAAATATGTATGAGATAT
39404380 GTATATATGTGGTAAAGCCGAATGGCTAATGTG
66 G--TATATGTGGTAAAGCCGAATGGCTAATGTG
* * *
39404413 AAATATGTATGAGATATGTATATGTGGTAAAGCCGAATGGCTAGTGTGAAATATGTAGGAGAT
1 AAATATATATGAGATATGTATATGTGGTAAAGCCGAATGGCTAATGTGAAATATGTATGAGAT
39404476 GTGTGTATAT
Statistics
Matches: 421, Mismatches: 28, Indels: 6
0.93 0.06 0.01
Matches are distributed among these distances:
96 150 0.36
98 271 0.64
ACGTcount: A:0.37, C:0.07, G:0.26, T:0.30
Consensus pattern (96 bp):
AAATATATATGAGATATGTATATGTGGTAAAGCCGAATGGCTAATGTGAAATATGTATGAGATAT
GTATATGTGGTAAAGCCGAATGGCTAATGTG
Found at i:39411330 original size:40 final size:40
Alignment explanation
Indices: 39411253--39411352 Score: 130
Period size: 40 Copynumber: 2.5 Consensus size: 40
39411243 ACCCAAGTTT
* * *
39411253 CTTCGGAATTTAG-CCGGATATAACCACAAGCACAAATGC
1 CTTCGGGACTTAGCCCGGATAAAACCACAAGCACAAATGC
* * * *
39411292 CTTCGGGTCTTAGCCCGGATAAAATCACTAGCATAAATGC
1 CTTCGGGACTTAGCCCGGATAAAACCACAAGCACAAATGC
39411332 CTTCGGGACTTAGCCCGGATA
1 CTTCGGGACTTAGCCCGGATA
39411353 TCATTCAAAT
Statistics
Matches: 52, Mismatches: 8, Indels: 1
0.85 0.13 0.02
Matches are distributed among these distances:
39 10 0.19
40 42 0.81
ACGTcount: A:0.30, C:0.26, G:0.21, T:0.23
Consensus pattern (40 bp):
CTTCGGGACTTAGCCCGGATAAAACCACAAGCACAAATGC
Found at i:39413677 original size:40 final size:40
Alignment explanation
Indices: 39413604--39413823 Score: 236
Period size: 40 Copynumber: 5.5 Consensus size: 40
39413594 TATTCGAATG
* *
39413604 ATATCCGGGCTAAG-TCCCGAAGGCTTTTATGCTAGTGACT
1 ATATCCGGGCTAAGAT-CCGAAGGCATTTGTGCTAGTGACT
* *
39413644 ATATCCGGACTAAGATCCGTAGGCATTTGTGCTAGTTG-CT
1 ATATCCGGGCTAAGATCCGAAGGCATTTGTGCTAG-TGACT
* *
39413684 ATATCCGGGCTAAGATCTGAAGGCATTTGTGCTAGCGACT
1 ATATCCGGGCTAAGATCCGAAGGCATTTGTGCTAGTGACT
* * *
39413724 ATATCCGGGCTAAG-TCCCGAAGGCATTTATGCCAGTGACC
1 ATATCCGGGCTAAGAT-CCGAAGGCATTTGTGCTAGTGACT
* * * **
39413764 ATATCCGGGCTAAGACCCGAAGGC-CTTGTGCGAGTGGTT
1 ATATCCGGGCTAAGATCCGAAGGCATTTGTGCTAGTGACT
39413803 ATATCC-GGCTAA-ATTCCGAAG
1 ATATCCGGGCTAAGA-TCCGAAG
39413824 ATGCTTGGGT
Statistics
Matches: 153, Mismatches: 21, Indels: 14
0.81 0.11 0.07
Matches are distributed among these distances:
37 1 0.01
38 12 0.08
39 17 0.11
40 120 0.78
41 3 0.02
ACGTcount: A:0.24, C:0.23, G:0.26, T:0.27
Consensus pattern (40 bp):
ATATCCGGGCTAAGATCCGAAGGCATTTGTGCTAGTGACT
Found at i:39414092 original size:22 final size:22
Alignment explanation
Indices: 39414050--39414094 Score: 56
Period size: 22 Copynumber: 2.0 Consensus size: 22
39414040 AAAATGTGCA
* *
39414050 TATATGAAGTTATTCATTTAGC
1 TATATGAAGTTATACACTTAGC
39414072 TATATGAATGTTATAC-CTTAGC
1 TATATGAA-GTTATACACTTAGC
39414094 T
1 T
39414095 GAAACTAATT
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
22 14 0.70
23 6 0.30
ACGTcount: A:0.31, C:0.11, G:0.13, T:0.44
Consensus pattern (22 bp):
TATATGAAGTTATACACTTAGC
Found at i:39430199 original size:53 final size:53
Alignment explanation
Indices: 39430113--39430259 Score: 149
Period size: 53 Copynumber: 2.7 Consensus size: 53
39430103 TTTTCCTTTT
* * * * *
39430113 TGAACTTAC-AATTGCAATGTCTTGACATAGTCTTACGTGGTATCC-CTGCCTTA
1 TGAACTCACTAATTGC-ATGTCTTGGCATGGTCTTACATGGGA-CCTCTGCCTTA
* *
39430166 TGAACTCACTAATTGCATGTCTTGGCATGGTCTTAAATGGGACCTTTGCCTTA
1 TGAACTCACTAATTGCATGTCTTGGCATGGTCTTACATGGGACCTCTGCCTTA
39430219 TAGTAACTCA-TCAA-TGCCATGTCTTGGCATGGTCTTACATG
1 T-G-AACTCACT-AATTG-CATGTCTTGGCATGGTCTTACATG
39430260 ATTTCCTTGC
Statistics
Matches: 80, Mismatches: 8, Indels: 10
0.82 0.08 0.10
Matches are distributed among these distances:
52 2 0.03
53 37 0.46
54 10 0.12
55 31 0.39
ACGTcount: A:0.24, C:0.22, G:0.19, T:0.35
Consensus pattern (53 bp):
TGAACTCACTAATTGCATGTCTTGGCATGGTCTTACATGGGACCTCTGCCTTA
Found at i:39430307 original size:54 final size:55
Alignment explanation
Indices: 39430181--39430321 Score: 178
Period size: 54 Copynumber: 2.6 Consensus size: 55
39430171 TCACTAATTG
* * ** **
39430181 CATGTCTTGGCATGGTCTTAAATGGGA-CCTTTGCCTTATAGTAACTCATCAATGC
1 CATGCCTTGGCATGGTCTTACATGATATCC-TTGCCCGATAGTAACTCATCAATGC
* * *
39430236 CATGTCTTGGCATGGTCTTACATGATTTCCTTGCCCGATAG-AACTTATCAATGC
1 CATGCCTTGGCATGGTCTTACATGATATCCTTGCCCGATAGTAACTCATCAATGC
39430290 CATGCCTTGGCATGGTCTTACATGATATCCTT
1 CATGCCTTGGCATGGTCTTACATGATATCCTT
39430322 ATCTTACCAA
Statistics
Matches: 76, Mismatches: 9, Indels: 3
0.86 0.10 0.03
Matches are distributed among these distances:
54 42 0.55
55 32 0.42
56 2 0.03
ACGTcount: A:0.22, C:0.23, G:0.19, T:0.35
Consensus pattern (55 bp):
CATGCCTTGGCATGGTCTTACATGATATCCTTGCCCGATAGTAACTCATCAATGC
Found at i:39430438 original size:24 final size:24
Alignment explanation
Indices: 39430406--39430453 Score: 96
Period size: 24 Copynumber: 2.0 Consensus size: 24
39430396 ATGGTCGTAC
39430406 ATGGAGTCCTTAATCAATGCCGAT
1 ATGGAGTCCTTAATCAATGCCGAT
39430430 ATGGAGTCCTTAATCAATGCCGAT
1 ATGGAGTCCTTAATCAATGCCGAT
39430454 GCCATGTCTT
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
24 24 1.00
ACGTcount: A:0.29, C:0.21, G:0.21, T:0.29
Consensus pattern (24 bp):
ATGGAGTCCTTAATCAATGCCGAT
Found at i:39431196 original size:31 final size:30
Alignment explanation
Indices: 39431161--39431218 Score: 80
Period size: 30 Copynumber: 1.9 Consensus size: 30
39431151 GTAACTCAAA
*
39431161 CTTTGGCAAAATTGCAATTTTGCCCCTAAAC
1 CTTT-GCAAAATTACAATTTTGCCCCTAAAC
* *
39431192 CTTTGCGAAATTACGATTTTGCCCCTA
1 CTTTGCAAAATTACAATTTTGCCCCTA
39431219 GGCTCGAAAA
Statistics
Matches: 24, Mismatches: 3, Indels: 1
0.86 0.11 0.04
Matches are distributed among these distances:
30 20 0.83
31 4 0.17
ACGTcount: A:0.26, C:0.26, G:0.14, T:0.34
Consensus pattern (30 bp):
CTTTGCAAAATTACAATTTTGCCCCTAAAC
Found at i:39432211 original size:40 final size:40
Alignment explanation
Indices: 39432160--39432245 Score: 154
Period size: 40 Copynumber: 2.1 Consensus size: 40
39432150 GTTCCAATAT
*
39432160 ATAGCCGAAGCTATCTTGAATCGCACACTAAGTGCCATAC
1 ATAGCCAAAGCTATCTTGAATCGCACACTAAGTGCCATAC
*
39432200 ATAGCCAAAGCTATCTTGAATCGCACACTAAGTGCCTTAC
1 ATAGCCAAAGCTATCTTGAATCGCACACTAAGTGCCATAC
39432240 ATAGCC
1 ATAGCC
39432246 CAATTGTGGT
Statistics
Matches: 44, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
40 44 1.00
ACGTcount: A:0.33, C:0.28, G:0.16, T:0.23
Consensus pattern (40 bp):
ATAGCCAAAGCTATCTTGAATCGCACACTAAGTGCCATAC
Found at i:39435138 original size:39 final size:39
Alignment explanation
Indices: 39434877--39435130 Score: 384
Period size: 39 Copynumber: 6.5 Consensus size: 39
39434867 ACAAAGCATG
* * *
39434877 CGGGACTTTAAGCCCGGATATAATACCAGCAC-AAAGCCTG
1 CGGGAC-TT-AGCCCGGATATAACACCAGCACGAATGCCTT
*
39434917 CGGGACTTTAACCCGGATATAACACCAGCACGAATGCCTT
1 CGGGAC-TTAGCCCGGATATAACACCAGCACGAATGCCTT
* *
39434957 CGGGGCTTAGCCCGGATATAACACCAGCACAAATGCCTT
1 CGGGACTTAGCCCGGATATAACACCAGCACGAATGCCTT
39434996 CGGGACTTAGCCCGGATATAACACCAGCACGAATGCCTT
1 CGGGACTTAGCCCGGATATAACACCAGCACGAATGCCTT
**
39435035 CGGGACTTAGCCCAAATATAACACCAGCACGAATGCCTT
1 CGGGACTTAGCCCGGATATAACACCAGCACGAATGCCTT
* *
39435074 CAGGACTTAGCCCGGATATAACACCAACACGAATGCCTT
1 CGGGACTTAGCCCGGATATAACACCAGCACGAATGCCTT
39435113 CGGGACTTAGCCCGGATA
1 CGGGACTTAGCCCGGATA
39435131 GAGCACCATT
Statistics
Matches: 197, Mismatches: 16, Indels: 3
0.91 0.07 0.01
Matches are distributed among these distances:
39 177 0.90
40 20 0.10
ACGTcount: A:0.30, C:0.30, G:0.22, T:0.18
Consensus pattern (39 bp):
CGGGACTTAGCCCGGATATAACACCAGCACGAATGCCTT
Found at i:39435250 original size:28 final size:27
Alignment explanation
Indices: 39435211--39435292 Score: 92
Period size: 28 Copynumber: 2.9 Consensus size: 27
39435201 ATTTAATCAT
*
39435211 TCAATATTTTGCACACTAAGTGTCATTC
1 TCAATA-TTTGCACACTAAGTGCCATTC
* *
39435239 TTAATATCTTGCACATTAAGTGCCATTC
1 TCAATAT-TTGCACACTAAGTGCCATTC
* *
39435267 TCAATATTTCGTACACTAAGTACCAT
1 TCAATATTT-GCACACTAAGTGCCAT
39435293 ATTTGATTGC
Statistics
Matches: 45, Mismatches: 7, Indels: 4
0.80 0.12 0.07
Matches are distributed among these distances:
27 3 0.07
28 42 0.93
ACGTcount: A:0.30, C:0.22, G:0.10, T:0.38
Consensus pattern (27 bp):
TCAATATTTGCACACTAAGTGCCATTC
Found at i:39441484 original size:39 final size:39
Alignment explanation
Indices: 39441417--39441678 Score: 418
Period size: 39 Copynumber: 6.7 Consensus size: 39
39441407 ACAAAGCATG
* * *
39441417 CGGGACTTTAAGCCCGGATATAATACCAGCAC-AAAGCCTG
1 CGGGAC-TT-AGCCCGGATATAACACCAGCACGAATGCCTT
*
39441457 CGGGACTTTAGCCCAGATATAACACCAGCACGAATGCCTT
1 CGGGAC-TTAGCCCGGATATAACACCAGCACGAATGCCTT
*
39441497 CGGGGCTTAGCCCGGATATAACACCAGCACGAATGCCTT
1 CGGGACTTAGCCCGGATATAACACCAGCACGAATGCCTT
* * *
39441536 TGGGACTTAGCCCAGATATAACACCAGCATGAATGCCTT
1 CGGGACTTAGCCCGGATATAACACCAGCACGAATGCCTT
39441575 CGGGACTTAGCCCGGATATAACACCAGCACGAATGCCTT
1 CGGGACTTAGCCCGGATATAACACCAGCACGAATGCCTT
39441614 CGGGACTTAGCCCGGATATAACACCAGCACGAATGCCTT
1 CGGGACTTAGCCCGGATATAACACCAGCACGAATGCCTT
39441653 CGGGACTTAGCCCGGATATAACACCA
1 CGGGACTTAGCCCGGATATAACACCA
39441679 TTATAAAGTC
Statistics
Matches: 208, Mismatches: 13, Indels: 3
0.93 0.06 0.01
Matches are distributed among these distances:
39 188 0.90
40 20 0.10
ACGTcount: A:0.29, C:0.29, G:0.23, T:0.19
Consensus pattern (39 bp):
CGGGACTTAGCCCGGATATAACACCAGCACGAATGCCTT
Found at i:39443753 original size:40 final size:40
Alignment explanation
Indices: 39443683--39443850 Score: 149
Period size: 40 Copynumber: 4.2 Consensus size: 40
39443673 CGGGGTTTAG
** * *
39443683 CCGGATATAACCACTCGCAC-AAGGCCTTCGGGTCTTAAC
1 CCGGATATAGTCACTAGCACAAATGCCTTCGGGTCTTAAC
* * * *
39443722 CCGGATATGGTCACTAGCATAAATGCCTTCGGGACTTAGC
1 CCGGATATAGTCACTAGCACAAATGCCTTCGGGTCTTAAC
* * **
39443762 CCGGATATAGTCGCTAGCACAAATGCCTTCGGATCTTAGT
1 CCGGATATAGTCACTAGCACAAATGCCTTCGGGTCTTAAC
* * ** * * *
39443802 CTGGATGTAGTCGGTTAGCACAAAAGCCTTCGGGACTTAGC
1 CCGGATATAGTC-ACTAGCACAAATGCCTTCGGGTCTTAAC
39443843 CCGGATAT
1 CCGGATAT
39443851 CATTCGAGTA
Statistics
Matches: 104, Mismatches: 23, Indels: 2
0.81 0.18 0.02
Matches are distributed among these distances:
39 15 0.14
40 60 0.58
41 29 0.28
ACGTcount: A:0.25, C:0.26, G:0.24, T:0.24
Consensus pattern (40 bp):
CCGGATATAGTCACTAGCACAAATGCCTTCGGGTCTTAAC
Found at i:39443833 original size:41 final size:39
Alignment explanation
Indices: 39443706--39443850 Score: 155
Period size: 40 Copynumber: 3.6 Consensus size: 39
39443696 CTCGCACAAG
* * * * *
39443706 GCCTTCGGGTCTTAACCCGGATATGGTCACTAGCATAAAT
1 GCCTTC-GGACTTAGCCCGGATATAGTCGCTAGCACAAAT
39443746 GCCTTCGGGACTTAGCCCGGATATAGTCGCTAGCACAAAT
1 GCCTTC-GGACTTAGCCCGGATATAGTCGCTAGCACAAAT
* * * * *
39443786 GCCTTCGGATCTTAGTCTGGATGTAGTCGGTTAGCACAAAA
1 GCCTTCGGA-CTTAGCCCGGATATAGTC-GCTAGCACAAAT
39443827 GCCTTCGGGACTTAGCCCGGATAT
1 GCCTTC-GGACTTAGCCCGGATAT
39443851 CATTCGAGTA
Statistics
Matches: 89, Mismatches: 13, Indels: 5
0.83 0.12 0.05
Matches are distributed among these distances:
39 3 0.03
40 56 0.63
41 27 0.30
42 3 0.03
ACGTcount: A:0.23, C:0.25, G:0.26, T:0.26
Consensus pattern (39 bp):
GCCTTCGGACTTAGCCCGGATATAGTCGCTAGCACAAAT
Found at i:39445080 original size:38 final size:38
Alignment explanation
Indices: 39445037--39445150 Score: 228
Period size: 38 Copynumber: 3.0 Consensus size: 38
39445027 CAAGAACTCC
39445037 TTCCTCCTTCCTTAGAATTTTCGGCCAAAAGAAATGAA
1 TTCCTCCTTCCTTAGAATTTTCGGCCAAAAGAAATGAA
39445075 TTCCTCCTTCCTTAGAATTTTCGGCCAAAAGAAATGAA
1 TTCCTCCTTCCTTAGAATTTTCGGCCAAAAGAAATGAA
39445113 TTCCTCCTTCCTTAGAATTTTCGGCCAAAAGAAATGAA
1 TTCCTCCTTCCTTAGAATTTTCGGCCAAAAGAAATGAA
39445151 AAAGGATGAA
Statistics
Matches: 76, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
38 76 1.00
ACGTcount: A:0.32, C:0.24, G:0.13, T:0.32
Consensus pattern (38 bp):
TTCCTCCTTCCTTAGAATTTTCGGCCAAAAGAAATGAA
Found at i:39447412 original size:24 final size:24
Alignment explanation
Indices: 39447383--39447434 Score: 70
Period size: 24 Copynumber: 2.2 Consensus size: 24
39447373 CCTTTATACC
* *
39447383 CATATACACGTAAA-CACATCCATA
1 CATATACAC-AAAAGCACATACATA
39447407 CATATACACAAAAGCACATACATA
1 CATATACACAAAAGCACATACATA
39447431 CATA
1 CATA
39447435 CCTTTCACGA
Statistics
Matches: 25, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
23 3 0.12
24 22 0.88
ACGTcount: A:0.50, C:0.27, G:0.04, T:0.19
Consensus pattern (24 bp):
CATATACACAAAAGCACATACATA
Found at i:39449418 original size:24 final size:24
Alignment explanation
Indices: 39449389--39449466 Score: 113
Period size: 24 Copynumber: 3.3 Consensus size: 24
39449379 GAGGCCTAGC
*
39449389 CTCTTTTAATAACTAGGGCAAAAG
1 CTCTTTTAATAACTAGGGCATAAG
39449413 CTCTTTTAATAACTAGGGCATAAG
1 CTCTTTTAATAACTAGGGCATAAG
* *
39449437 C-CCTTTAATAACTGGGGCATAAG
1 CTCTTTTAATAACTAGGGCATAAG
*
39449460 CCCTTTT
1 CTCTTTT
39449467 GCACTTCCTC
Statistics
Matches: 49, Mismatches: 4, Indels: 2
0.89 0.07 0.04
Matches are distributed among these distances:
23 21 0.43
24 28 0.57
ACGTcount: A:0.31, C:0.21, G:0.17, T:0.32
Consensus pattern (24 bp):
CTCTTTTAATAACTAGGGCATAAG
Found at i:39449447 original size:23 final size:23
Alignment explanation
Indices: 39449393--39449465 Score: 110
Period size: 23 Copynumber: 3.1 Consensus size: 23
39449383 CCTAGCCTCT
* *
39449393 TTTAATAACTAGGGCAAAAGCTCT
1 TTTAATAACTAGGGCATAAGC-CC
39449417 TTTAATAACTAGGGCATAAGCCC
1 TTTAATAACTAGGGCATAAGCCC
*
39449440 TTTAATAACTGGGGCATAAGCCC
1 TTTAATAACTAGGGCATAAGCCC
39449463 TTT
1 TTT
39449466 TGCACTTCCT
Statistics
Matches: 46, Mismatches: 3, Indels: 1
0.92 0.06 0.02
Matches are distributed among these distances:
23 26 0.57
24 20 0.43
ACGTcount: A:0.33, C:0.19, G:0.18, T:0.30
Consensus pattern (23 bp):
TTTAATAACTAGGGCATAAGCCC
Found at i:39449541 original size:20 final size:20
Alignment explanation
Indices: 39449516--39449582 Score: 107
Period size: 20 Copynumber: 3.4 Consensus size: 20
39449506 TTATGAATAC
39449516 ATCATGTGCATATCATACAT
1 ATCATGTGCATATCATACAT
*
39449536 ATCATGTGCATAGCATACAT
1 ATCATGTGCATATCATACAT
*
39449556 GTCATGTGCATATCATACAT
1 ATCATGTGCATATCATACAT
*
39449576 ACCATGT
1 ATCATGT
39449583 TTACTAAAAT
Statistics
Matches: 42, Mismatches: 5, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 42 1.00
ACGTcount: A:0.33, C:0.21, G:0.13, T:0.33
Consensus pattern (20 bp):
ATCATGTGCATATCATACAT
Found at i:39453408 original size:79 final size:79
Alignment explanation
Indices: 39453297--39453519 Score: 269
Period size: 79 Copynumber: 2.8 Consensus size: 79
39453287 GCTCCTCGTT
* * *
39453297 CAAATGCCTTCGGGACATAGCCCGG-TTATAGTAATTCGCACAAATGCCTTCGGGACTTATCCCG
1 CAAATGCCTTCGGG-CTTAGCCCGGAAT-TAGTAATTCGCACAAATGCCTTCGGGACTTAGCCCG
*
39453361 GATTTAGTAACTCGCA
64 GAATTAGTAACTCGCA
39453377 CAAATGCCTTCGGGCTTAGCCCGGAATTAGT-ATCTCGCACAAATGCCTTCGGG-CTTAGCCCGG
1 CAAATGCCTTCGGGCTTAGCCCGGAATTAGTAAT-TCGCACAAATGCCTTCGGGACTTAGCCCGG
*
39453440 AATTAGTATCTCGCA
65 AATTAGTAACTCGCA
* * * *
39453455 CAAATGCCTTCGGATCTTAGTCCGGATATT-GTCACTTAGCAC-AA-GCCTTCGGGACTTAGCCC
1 CAAATGCCTTCGG-GCTTAGCCCGGA-ATTAGT-AATTCGCACAAATGCCTTCGGGACTTAGCCC
39453517 GGA
63 GGA
39453520 CATCATCCAA
Statistics
Matches: 127, Mismatches: 9, Indels: 15
0.84 0.06 0.10
Matches are distributed among these distances:
78 46 0.36
79 57 0.45
80 23 0.18
81 1 0.01
ACGTcount: A:0.24, C:0.27, G:0.22, T:0.26
Consensus pattern (79 bp):
CAAATGCCTTCGGGCTTAGCCCGGAATTAGTAATTCGCACAAATGCCTTCGGGACTTAGCCCGGA
ATTAGTAACTCGCA
Found at i:39453414 original size:39 final size:40
Alignment explanation
Indices: 39453297--39453519 Score: 266
Period size: 39 Copynumber: 5.7 Consensus size: 40
39453287 GCTCCTCGTT
* *
39453297 CAAATGCCTTCGGGACATAGCCCGG-TTATAGTAAT-TCGCA
1 CAAATGCCTTCGGGACTTAGCCCGGAAT-TAGT-ATCTCGCA
* * *
39453337 CAAATGCCTTCGGGACTTATCCCGGATTTAGTAACTCGCA
1 CAAATGCCTTCGGGACTTAGCCCGGAATTAGTATCTCGCA
39453377 CAAATGCCTTCGGG-CTTAGCCCGGAATTAGTATCTCGCA
1 CAAATGCCTTCGGGACTTAGCCCGGAATTAGTATCTCGCA
39453416 CAAATGCCTTCGGG-CTTAGCCCGGAATTAGTATCTCGCA
1 CAAATGCCTTCGGGACTTAGCCCGGAATTAGTATCTCGCA
* *
39453455 CAAATGCCTTC-GGATCTTAGTCCGGATATT-GTCA-CTTAGCA
1 CAAATGCCTTCGGGA-CTTAGCCCGGA-ATTAGT-ATC-TCGCA
39453496 C-AA-GCCTTCGGGACTTAGCCCGGA
1 CAAATGCCTTCGGGACTTAGCCCGGA
39453520 CATCATCCAA
Statistics
Matches: 166, Mismatches: 9, Indels: 17
0.86 0.05 0.09
Matches are distributed among these distances:
38 2 0.01
39 89 0.54
40 64 0.39
41 11 0.07
ACGTcount: A:0.24, C:0.27, G:0.22, T:0.26
Consensus pattern (40 bp):
CAAATGCCTTCGGGACTTAGCCCGGAATTAGTATCTCGCA
Found at i:39454616 original size:14 final size:14
Alignment explanation
Indices: 39454597--39454623 Score: 54
Period size: 14 Copynumber: 1.9 Consensus size: 14
39454587 AGGATGAGCA
39454597 TTTTTTTTTCTTTG
1 TTTTTTTTTCTTTG
39454611 TTTTTTTTTCTTT
1 TTTTTTTTTCTTT
39454624 CTAGTTTCGG
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 13 1.00
ACGTcount: A:0.00, C:0.07, G:0.04, T:0.89
Consensus pattern (14 bp):
TTTTTTTTTCTTTG
Found at i:39460402 original size:31 final size:31
Alignment explanation
Indices: 39460364--39460427 Score: 110
Period size: 31 Copynumber: 2.1 Consensus size: 31
39460354 CCTTTTCATA
39460364 TTTCATATTTCATAACACTGGGCCGAAGCCT
1 TTTCATATTTCATAACACTGGGCCGAAGCCT
**
39460395 TTTCATATTTCATATTACTGGGCCGAAGCCT
1 TTTCATATTTCATAACACTGGGCCGAAGCCT
39460426 TT
1 TT
39460428 ACTGTAAACG
Statistics
Matches: 31, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
31 31 1.00
ACGTcount: A:0.23, C:0.23, G:0.16, T:0.38
Consensus pattern (31 bp):
TTTCATATTTCATAACACTGGGCCGAAGCCT
Found at i:39460696 original size:23 final size:23
Alignment explanation
Indices: 39460642--39460737 Score: 138
Period size: 23 Copynumber: 4.1 Consensus size: 23
39460632 CCTAGCCTCT
* *
39460642 TTTAATAACCGGGGCAAAAGCCC
1 TTTAATAACTGGGGCATAAGCCC
39460665 TTTTAATAACTGGGGCATAAGCCC
1 -TTTAATAACTGGGGCATAAGCCC
39460689 TTTAATAACTGGGGCATAAGCCC
1 TTTAATAACTGGGGCATAAGCCC
** *
39460712 TTTAATAACTATGGCATAAGCTC
1 TTTAATAACTGGGGCATAAGCCC
39460735 TTT
1 TTT
39460738 TGCACTTCCT
Statistics
Matches: 67, Mismatches: 5, Indels: 1
0.92 0.07 0.01
Matches are distributed among these distances:
23 46 0.69
24 21 0.31
ACGTcount: A:0.31, C:0.21, G:0.19, T:0.29
Consensus pattern (23 bp):
TTTAATAACTGGGGCATAAGCCC
Found at i:39460813 original size:20 final size:20
Alignment explanation
Indices: 39460788--39460854 Score: 107
Period size: 20 Copynumber: 3.4 Consensus size: 20
39460778 TTATGAATAC
39460788 ATCATGTGCATATCATACAT
1 ATCATGTGCATATCATACAT
*
39460808 ATCATGTGCATAGCATACAT
1 ATCATGTGCATATCATACAT
*
39460828 GTCATGTGCATATCATACAT
1 ATCATGTGCATATCATACAT
*
39460848 ACCATGT
1 ATCATGT
39460855 TTACTAAAAT
Statistics
Matches: 42, Mismatches: 5, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 42 1.00
ACGTcount: A:0.33, C:0.21, G:0.13, T:0.33
Consensus pattern (20 bp):
ATCATGTGCATATCATACAT
Found at i:39468028 original size:17 final size:17
Alignment explanation
Indices: 39468006--39468041 Score: 72
Period size: 17 Copynumber: 2.1 Consensus size: 17
39467996 AAATCATATG
39468006 AACTTACAATTTCCCAT
1 AACTTACAATTTCCCAT
39468023 AACTTACAATTTCCCAT
1 AACTTACAATTTCCCAT
39468040 AA
1 AA
39468042 TATCCATAAT
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 19 1.00
ACGTcount: A:0.39, C:0.28, G:0.00, T:0.33
Consensus pattern (17 bp):
AACTTACAATTTCCCAT
Found at i:39468498 original size:30 final size:30
Alignment explanation
Indices: 39468464--39468524 Score: 86
Period size: 30 Copynumber: 2.0 Consensus size: 30
39468454 TCCTTACCTC
39468464 AAACTTTTACAAAATTACAATTTTGCCCCT
1 AAACTTTTACAAAATTACAATTTTGCCCCT
* * * *
39468494 AAACTTTTGCATATTTACACTTTTGCCCCT
1 AAACTTTTACAAAATTACAATTTTGCCCCT
39468524 A
1 A
39468525 GGCTCGGGAA
Statistics
Matches: 27, Mismatches: 4, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
30 27 1.00
ACGTcount: A:0.31, C:0.25, G:0.05, T:0.39
Consensus pattern (30 bp):
AAACTTTTACAAAATTACAATTTTGCCCCT
Found at i:39476856 original size:16 final size:16
Alignment explanation
Indices: 39476835--39476874 Score: 80
Period size: 16 Copynumber: 2.5 Consensus size: 16
39476825 GACTGAAGAT
39476835 TTCTTTATGTTTTGTA
1 TTCTTTATGTTTTGTA
39476851 TTCTTTATGTTTTGTA
1 TTCTTTATGTTTTGTA
39476867 TTCTTTAT
1 TTCTTTAT
39476875 TCTTCTGAGA
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 24 1.00
ACGTcount: A:0.12, C:0.07, G:0.10, T:0.70
Consensus pattern (16 bp):
TTCTTTATGTTTTGTA
Found at i:39484047 original size:31 final size:31
Alignment explanation
Indices: 39484009--39484070 Score: 115
Period size: 31 Copynumber: 2.0 Consensus size: 31
39483999 GAAGATGTTT
39484009 AGAAATATTTATTTATTATTTTCTATTTTTA
1 AGAAATATTTATTTATTATTTTCTATTTTTA
*
39484040 AGAAATATTTATTTATTATTTTCTGTTTTTA
1 AGAAATATTTATTTATTATTTTCTATTTTTA
39484071 CTTATTATTG
Statistics
Matches: 30, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
31 30 1.00
ACGTcount: A:0.31, C:0.03, G:0.05, T:0.61
Consensus pattern (31 bp):
AGAAATATTTATTTATTATTTTCTATTTTTA
Found at i:39487791 original size:40 final size:40
Alignment explanation
Indices: 39487639--39487819 Score: 224
Period size: 40 Copynumber: 4.5 Consensus size: 40
39487629 TATTTGAATG
* * * **
39487639 ATATCCGGGCTAAGTCCCGAAGGCATTTGTGCTAGTAACT
1 ATATCCGAGCTAAGACCCGAAGGCATTTGTGCGAGTTGCT
* * * * *
39487679 ATATCCGGGCCAAGTCCCGAAGGCATTTGTGCTAG-TGATT
1 ATATCCGAGCTAAGACCCGAAGGCATTTGTGCGAGTTG-CT
39487719 ATATCCGAGCTAAGACCCGAAGGCATTTGTGCGAGTTGCT
1 ATATCCGAGCTAAGACCCGAAGGCATTTGTGCGAGTTGCT
*
39487759 ATATCCGAGCTAAGACCCGAAGGCATTTGTGCGAGTTGTT
1 ATATCCGAGCTAAGACCCGAAGGCATTTGTGCGAGTTGCT
39487799 ATATCCG-GCTAA-ATCCCGAAG
1 ATATCCGAGCTAAGA-CCCGAAG
39487820 ATACTTGGGT
Statistics
Matches: 128, Mismatches: 10, Indels: 7
0.88 0.07 0.05
Matches are distributed among these distances:
38 1 0.01
39 12 0.09
40 113 0.88
41 2 0.02
ACGTcount: A:0.25, C:0.23, G:0.26, T:0.26
Consensus pattern (40 bp):
ATATCCGAGCTAAGACCCGAAGGCATTTGTGCGAGTTGCT
Found at i:39499124 original size:23 final size:23
Alignment explanation
Indices: 39499071--39499142 Score: 72
Period size: 23 Copynumber: 3.0 Consensus size: 23
39499061 TGTTTCTCAC
* *
39499071 TTTATATAACTATTATTTTGAAGCTAT
1 TTTATATAA-TATTGTTTT-AA--TAA
*
39499098 TTTATATTATATTGTTTTAATAA
1 TTTATATAATATTGTTTTAATAA
*
39499121 TTTATATAATATTTTTTTAATA
1 TTTATATAATATTGTTTTAATA
39499143 TTTTTGTGTA
Statistics
Matches: 40, Mismatches: 5, Indels: 4
0.82 0.10 0.08
Matches are distributed among these distances:
23 22 0.55
25 2 0.05
26 8 0.20
27 8 0.20
ACGTcount: A:0.35, C:0.03, G:0.04, T:0.58
Consensus pattern (23 bp):
TTTATATAATATTGTTTTAATAA
Found at i:39502180 original size:24 final size:23
Alignment explanation
Indices: 39502137--39502185 Score: 57
Period size: 24 Copynumber: 2.1 Consensus size: 23
39502127 TCTCTTTCTT
39502137 TTGCATTCATCTCATGCATTTGCA
1 TTGCATTCATCTCATGCATTT-CA
39502161 TTGCATTGCAT-TGCAT-CATTTCA
1 TTGCATT-CATCT-CATGCATTTCA
39502184 TT
1 TT
39502186 ATTTGCATTA
Statistics
Matches: 23, Mismatches: 0, Indels: 5
0.82 0.00 0.18
Matches are distributed among these distances:
23 4 0.17
24 13 0.57
25 6 0.26
ACGTcount: A:0.20, C:0.22, G:0.12, T:0.45
Consensus pattern (23 bp):
TTGCATTCATCTCATGCATTTCA
Found at i:39505330 original size:46 final size:44
Alignment explanation
Indices: 39505276--39505451 Score: 176
Period size: 46 Copynumber: 3.8 Consensus size: 44
39505266 TGTTTGGGCA
39505276 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAATG
1 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATG-GAA-G
* * *** * *
39505322 TCCAAACTCATTGAGTTGAGTCCGAGTTCGAGAGATGTAACTAGGCA-
1 TCCGAACTCGTTGAGTTGAGTCCGAGTTC-ACTTATG-GA-T-GGAAG
*
39505369 TCCGAGCTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGTGAACG
1 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATG-GAA-G
*
39505415 -CTCGAGCTCGTTGAGTTGAGTCCGAGTTCACTTATGG
1 TC-CGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGG
39505452 GCGGGTTACA
Statistics
Matches: 107, Mismatches: 15, Indels: 16
0.78 0.11 0.12
Matches are distributed among these distances:
43 1 0.01
44 3 0.03
45 2 0.02
46 66 0.62
47 30 0.28
48 1 0.01
49 3 0.03
50 1 0.01
ACGTcount: A:0.22, C:0.20, G:0.28, T:0.30
Consensus pattern (44 bp):
TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGGAAG
Found at i:39505431 original size:93 final size:93
Alignment explanation
Indices: 39505272--39505443 Score: 274
Period size: 93 Copynumber: 1.8 Consensus size: 93
39505262 AGGATGTTTG
*
39505272 GGCATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAATGTCCAAACTCATTGAG
1 GGCATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAACGTCCAAACTCATTGAG
39505337 TTGAGTCCGAGTTCGAGAGATGTAACTA
66 TTGAGTCCGAGTTCGAGAGATGTAACTA
* * * * *
39505365 GGCATCCGAGCTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGTGAACG-CTCGAGCTCGTTGA
1 GGCATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAACGTC-CAAACTCATTGA
39505429 GTTGAGTCCGAGTTC
65 GTTGAGTCCGAGTTC
39505444 ACTTATGGGC
Statistics
Matches: 72, Mismatches: 6, Indels: 2
0.90 0.08 0.03
Matches are distributed among these distances:
92 1 0.01
93 71 0.99
ACGTcount: A:0.22, C:0.20, G:0.29, T:0.28
Consensus pattern (93 bp):
GGCATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAACGTCCAAACTCATTGAG
TTGAGTCCGAGTTCGAGAGATGTAACTA
Found at i:39509005 original size:28 final size:29
Alignment explanation
Indices: 39508918--39509005 Score: 119
Period size: 28 Copynumber: 3.1 Consensus size: 29
39508908 AAAGCATGAC
*
39508918 TATGTATGTGATTTGGGCCTAATGGGCCA
1 TATGAATGTGATTTGGGCCTAATGGGCCA
*
39508947 TACGAATGTGATTTGGG-CTAATGGGCCA
1 TATGAATGTGATTTGGGCCTAATGGGCCA
*
39508975 TATGAAT-TAGA-TTGGGCCTAGTGGGCCA
1 TATGAATGT-GATTTGGGCCTAATGGGCCA
39509003 TAT
1 TAT
39509006 ACATGTACGT
Statistics
Matches: 53, Mismatches: 4, Indels: 5
0.85 0.06 0.08
Matches are distributed among these distances:
27 6 0.11
28 32 0.60
29 15 0.28
ACGTcount: A:0.24, C:0.14, G:0.31, T:0.32
Consensus pattern (29 bp):
TATGAATGTGATTTGGGCCTAATGGGCCA
Found at i:39510159 original size:17 final size:19
Alignment explanation
Indices: 39510123--39510159 Score: 51
Period size: 18 Copynumber: 2.1 Consensus size: 19
39510113 CATTTTAAGG
39510123 AAGGATTTTCAATGAAAAC
1 AAGGATTTTCAATGAAAAC
*
39510142 AAGG-TTTTCGAT-AAAAC
1 AAGGATTTTCAATGAAAAC
39510159 A
1 A
39510160 CTTCAATGTG
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
17 6 0.35
18 7 0.41
19 4 0.24
ACGTcount: A:0.46, C:0.11, G:0.16, T:0.27
Consensus pattern (19 bp):
AAGGATTTTCAATGAAAAC
Found at i:39516612 original size:17 final size:17
Alignment explanation
Indices: 39516590--39516624 Score: 61
Period size: 17 Copynumber: 2.1 Consensus size: 17
39516580 CAAAGTGGGG
39516590 TAATGGGCCCAATAGGC
1 TAATGGGCCCAATAGGC
*
39516607 TAATGGGCCCAATGGGC
1 TAATGGGCCCAATAGGC
39516624 T
1 T
39516625 GTAGGGCCTA
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
17 17 1.00
ACGTcount: A:0.26, C:0.23, G:0.31, T:0.20
Consensus pattern (17 bp):
TAATGGGCCCAATAGGC
Found at i:39516756 original size:28 final size:29
Alignment explanation
Indices: 39516693--39516780 Score: 99
Period size: 28 Copynumber: 3.1 Consensus size: 29
39516683 AAAGCATGAC
* *
39516693 TATGTATGTGATTTGGGCCTAATGGGCCA
1 TATGAATGTGATGTGGGCCTAATGGGCCA
*
39516722 TACGAATGTGATGTGGGCC-AATGGGCCA
1 TATGAATGTGATGTGGGCCTAATGGGCCA
** * *
39516750 TATGAATAAGAT-TGGGCCTAGTGGGTCA
1 TATGAATGTGATGTGGGCCTAATGGGCCA
39516778 TAT
1 TAT
39516781 ACATGTATGT
Statistics
Matches: 50, Mismatches: 8, Indels: 3
0.82 0.13 0.05
Matches are distributed among these distances:
27 6 0.12
28 28 0.56
29 16 0.32
ACGTcount: A:0.25, C:0.14, G:0.32, T:0.30
Consensus pattern (29 bp):
TATGAATGTGATGTGGGCCTAATGGGCCA
Found at i:39519589 original size:48 final size:48
Alignment explanation
Indices: 39519514--39519696 Score: 209
Period size: 48 Copynumber: 3.9 Consensus size: 48
39519504 TAGGGTTATG
39519514 TGTGATCCCATGTAAGACCATGTCTGGGACATGGC-TCTGGCATCGATA
1 TGTGATCCCATGTAAGACCATGTCTGGGACATGGCAT-TGGCATCGATA
* ** * * *
39519562 TGTAATTTCATATAAGACCATAG-CTGGG-C-T---ATCGGCATCTATA
1 TGTGATCCCATGTAAGACCAT-GTCTGGGACATGGCATTGGCATCGATA
* *
39519605 TGTGATCCCATGTAAGACCATGTCTGGGACTTGGCGTTGGCATCGATA
1 TGTGATCCCATGTAAGACCATGTCTGGGACATGGCATTGGCATCGATA
* *
39519653 TGTGATCCCATGTAAGACCATATCTGGGATATGGCATTGGCATC
1 TGTGATCCCATGTAAGACCATGTCTGGGACATGGCATTGGCATC
39519697 CTACCATGTG
Statistics
Matches: 110, Mismatches: 17, Indels: 16
0.77 0.12 0.11
Matches are distributed among these distances:
42 1 0.01
43 31 0.28
44 2 0.02
45 1 0.01
46 1 0.01
47 1 0.01
48 72 0.65
49 1 0.01
ACGTcount: A:0.25, C:0.21, G:0.25, T:0.30
Consensus pattern (48 bp):
TGTGATCCCATGTAAGACCATGTCTGGGACATGGCATTGGCATCGATA
Found at i:39519669 original size:91 final size:90
Alignment explanation
Indices: 39519514--39519689 Score: 264
Period size: 91 Copynumber: 1.9 Consensus size: 90
39519504 TAGGGTTATG
**
39519514 TGTGATCCCATGTAAGACCATGTCTGGGACATGGCTCTGGCATCGATATGTAATTTCATATAAGA
1 TGTGATCCCATGTAAGACCATGTCTGGGACATGGCTCTGGCATCGATATGTAATCCCATATAAGA
*
39519579 CCATAGCTGGGCTATCGGCATCTATA
66 CCATAGCTGGGATAT-GGCATCTATA
* * *
39519605 TGTGATCCCATGTAAGACCATGTCTGGGACTTGGCGT-TGGCATCGATATGTGATCCCATGTAAG
1 TGTGATCCCATGTAAGACCATGTCTGGGACATGGC-TCTGGCATCGATATGTAATCCCATATAAG
*
39519669 ACCATATCTGGGATATGGCAT
65 ACCATAGCTGGGATATGGCAT
39519690 TGGCATCCTA
Statistics
Matches: 77, Mismatches: 7, Indels: 3
0.89 0.08 0.03
Matches are distributed among these distances:
90 5 0.06
91 71 0.92
92 1 0.01
ACGTcount: A:0.25, C:0.20, G:0.25, T:0.30
Consensus pattern (90 bp):
TGTGATCCCATGTAAGACCATGTCTGGGACATGGCTCTGGCATCGATATGTAATCCCATATAAGA
CCATAGCTGGGATATGGCATCTATA
Found at i:39520501 original size:80 final size:81
Alignment explanation
Indices: 39520373--39520534 Score: 301
Period size: 80 Copynumber: 2.0 Consensus size: 81
39520363 GATGAATTAT
39520373 GGATATGATCATGTATGTTTGATGATGGAAATGTGGTTAAATGGCATAATAACAACTAAGGCATG
1 GGATATGATCATGTATGTTTGATGATGGAAATGTGGTTAAATGGCATAATAACAACTAAGGCATG
39520438 AATGTATGAAAT-GGA
66 AATGTATGAAATAGGA
39520453 GGATATGATCATGTATGTTTGATGATGGAAATGTGAG-TAAATGGCATAATAACAACTAAGGCAT
1 GGATATGATCATGTATGTTTGATGATGGAAATGTG-GTTAAATGGCATAATAACAACTAAGGCAT
39520517 GAATGTATGAAATAGGA
65 GAATGTATGAAATAGGA
39520534 G
1 G
39520535 TAAATTGAGG
Statistics
Matches: 80, Mismatches: 0, Indels: 3
0.96 0.00 0.04
Matches are distributed among these distances:
80 75 0.94
81 5 0.06
ACGTcount: A:0.38, C:0.06, G:0.27, T:0.29
Consensus pattern (81 bp):
GGATATGATCATGTATGTTTGATGATGGAAATGTGGTTAAATGGCATAATAACAACTAAGGCATG
AATGTATGAAATAGGA
Found at i:39525493 original size:46 final size:47
Alignment explanation
Indices: 39525320--39525492 Score: 203
Period size: 46 Copynumber: 3.7 Consensus size: 47
39525310 TTATTTGTGT
* * *
39525320 GCTAGTGTAAGACATGTCTAGGACATGCATC-GACCAC-ATTATGAGA
1 GCTAGTGTAAGACATGTCTGGGACATGCATCAGACCTCGA-GATGAGA
* * * * *
39525366 GCCAGTGTAAGACCATGTCTGGGACATGGCAT-TGACATTGAGACGAGA
1 GCTAGTGTAAGA-CATGTCTGGGACAT-GCATCAGACCTCGAGATGAGA
39525414 GCTAGTGTAAGACATGTCTGGGACATGCATCAG-CCTCGAGATGTA-A
1 GCTAGTGTAAGACATGTCTGGGACATGCATCAGACCTCGAGATG-AGA
39525460 GCTAGTGTAAGACATGTCTGGGACATGCATCAG
1 GCTAGTGTAAGACATGTCTGGGACATGCATCAG
39525493 CTACGAGATG
Statistics
Matches: 109, Mismatches: 12, Indels: 12
0.82 0.09 0.09
Matches are distributed among these distances:
46 56 0.51
47 29 0.27
48 23 0.21
49 1 0.01
ACGTcount: A:0.29, C:0.19, G:0.28, T:0.23
Consensus pattern (47 bp):
GCTAGTGTAAGACATGTCTGGGACATGCATCAGACCTCGAGATGAGA
Found at i:39525500 original size:46 final size:47
Alignment explanation
Indices: 39525320--39525536 Score: 200
Period size: 46 Copynumber: 4.7 Consensus size: 47
39525310 TTATTTGTGT
* * *
39525320 GCTAGTGTAAGACATGTCTAGGACATGCATC-GACCAC-ATTATGAGA
1 GCTAGTGTAAGACATGTCTGGGACATGCATCAGACTACGA-GATGAGA
* * * *
39525366 GCCAGTGTAAGACCATGTCTGGGACATGGCAT-TGAC-ATTGAGACGAGA
1 GCTAGTGTAAGA-CATGTCTGGGACAT-GCATCAGACTA-CGAGATGAGA
*
39525414 GCTAGTGTAAGACATGTCTGGGACATGCATCAGCCT-CGAGATGTA-A
1 GCTAGTGTAAGACATGTCTGGGACATGCATCAGACTACGAGATG-AGA
*
39525460 GCTAGTGTAAGACATGTCTGGGACATGCATCAG-CTACGAGATGTG-
1 GCTAGTGTAAGACATGTCTGGGACATGCATCAGACTACGAGATGAGA
* * *
39525505 TC-AGTGTAAGACCATATTTGGGACATGGCATC
1 GCTAGTGTAAGA-CATGTCTGGGACAT-GCATC
39525537 GGCATTATAC
Statistics
Matches: 145, Mismatches: 14, Indels: 24
0.79 0.08 0.13
Matches are distributed among these distances:
44 9 0.06
45 15 0.10
46 66 0.46
47 31 0.21
48 23 0.16
49 1 0.01
ACGTcount: A:0.29, C:0.19, G:0.28, T:0.24
Consensus pattern (47 bp):
GCTAGTGTAAGACATGTCTGGGACATGCATCAGACTACGAGATGAGA
Found at i:39529177 original size:46 final size:49
Alignment explanation
Indices: 39529020--39529289 Score: 201
Period size: 46 Copynumber: 5.7 Consensus size: 49
39529010 TTATTTGTGT
* * * * *
39529020 GCTAGTGTAAGA-CATGTCTAGGACAT-GCGTCGACCAC-ATTATG-AGA
1 GCTAGTGTAAGACCATGTCTGGGACATGGCATCGGCCTCGA-GATGTAGA
*** * * *
39529066 G-TCAGTGTAAGACCATGTCTGGGACATGGCATTAACATTGAGACG-AGA
1 GCT-AGTGTAAGACCATGTCTGGGACATGGCATCGGCCTCGAGATGTAGA
*
39529114 GCCAGTGTAAGA-CATGTCTGGGACAT-GCATCGGCCTCGAGATGTA-A
1 GCTAGTGTAAGACCATGTCTGGGACATGGCATCGGCCTCGAGATGTAGA
*
39529160 GCTAGTGTAAGA-CATGTCTGGGACAT-GCATCGG-CTATGAGATGT-G-
1 GCTAGTGTAAGACCATGTCTGGGACATGGCATCGGCCT-CGAGATGTAGA
* * *** *
39529205 TC-AGTGTAAGACCATATCTGGGACATGGCATCGGCAAGGATATGTGAGA
1 GCTAGTGTAAGACCATGTCTGGGACATGGCATCGGCCTCGAGATGT-AGA
* **
39529254 GCTAGTGTAAGACCATTTCTGATACATGGCATCGGC
1 GCTAGTGTAAGACCATGTCTGGGACATGGCATCGGC
39529290 ATTATACCCT
Statistics
Matches: 181, Mismatches: 28, Indels: 26
0.77 0.12 0.11
Matches are distributed among these distances:
44 9 0.05
45 17 0.09
46 74 0.41
47 28 0.15
48 21 0.12
49 2 0.01
50 30 0.17
ACGTcount: A:0.28, C:0.19, G:0.29, T:0.24
Consensus pattern (49 bp):
GCTAGTGTAAGACCATGTCTGGGACATGGCATCGGCCTCGAGATGTAGA
Found at i:39539552 original size:37 final size:37
Alignment explanation
Indices: 39539502--39539581 Score: 108
Period size: 37 Copynumber: 2.2 Consensus size: 37
39539492 CTTATTACGA
* *
39539502 AGTCTTACCCGGACATAA-TCTCCACACGAAGTTATCG
1 AGTCTTACCCGGACAAAATTC-CCACACGAAGTCATCG
*
39539539 AGTCTTACCCGGACAAAATTCCCACACGCAGTCATCG
1 AGTCTTACCCGGACAAAATTCCCACACGAAGTCATCG
*
39539576 GGTCTT
1 AGTCTT
39539582 TAGAGCCCGG
Statistics
Matches: 38, Mismatches: 4, Indels: 2
0.86 0.09 0.05
Matches are distributed among these distances:
37 36 0.95
38 2 0.05
ACGTcount: A:0.28, C:0.31, G:0.17, T:0.24
Consensus pattern (37 bp):
AGTCTTACCCGGACAAAATTCCCACACGAAGTCATCG
Found at i:39539771 original size:47 final size:47
Alignment explanation
Indices: 39539700--39540104 Score: 562
Period size: 47 Copynumber: 8.6 Consensus size: 47
39539690 CCCTTCGGGA
** * *
39539700 CTTATCACATTTATACACT-TTCACATTCATCACATCGGCCATTAGGC
1 CTTATCACACATATACA-TGTTCACATTCATCACATTGGCCATTCGGC
* * * *
39539747 CTTATCTCACATACACATGCTCACATTCATCACATTGGCCACTCGGC
1 CTTATCACACATATACATGTTCACATTCATCACATTGGCCATTCGGC
* *
39539794 CTTATCACACATACACATGTTCACTTTCATCACATTGGCCATTCGGC
1 CTTATCACACATATACATGTTCACATTCATCACATTGGCCATTCGGC
*
39539841 CTTATCACACATATACATGTTCACTTTCATCACATTGGCCATTCGGC
1 CTTATCACACATATACATGTTCACATTCATCACATTGGCCATTCGGC
* * *
39539888 CTTATCTCATATATGCATGTTCACATTCATCACATTGGCCATTCGGC
1 CTTATCACACATATACATGTTCACATTCATCACATTGGCCATTCGGC
* * *
39539935 CTTATCTCATATATGCATGTTCACATTCATCACATTGGCCATTCGGC
1 CTTATCACACATATACATGTTCACATTCATCACATTGGCCATTCGGC
* * *
39539982 CCTATTCACACATACACATGTTCACTTTCATCACATTGGCCATTCGGC
1 CTTA-TCACACATATACATGTTCACATTCATCACATTGGCCATTCGGC
*
39540030 CTTATCACACATATACATGTTCACTTTCATCACATTGGCCATTCGGC
1 CTTATCACACATATACATGTTCACATTCATCACATTGGCCATTCGGC
*
39540077 CCTATTCACACATATACACT-TTCACATT
1 CTTA-TCACACATATACA-TGTTCACATT
39540105 TATTCAATTA
Statistics
Matches: 327, Mismatches: 27, Indels: 7
0.91 0.07 0.02
Matches are distributed among these distances:
46 1 0.00
47 264 0.81
48 61 0.19
49 1 0.00
ACGTcount: A:0.26, C:0.31, G:0.10, T:0.33
Consensus pattern (47 bp):
CTTATCACACATATACATGTTCACATTCATCACATTGGCCATTCGGC
Found at i:39544760 original size:40 final size:40
Alignment explanation
Indices: 39544716--39545167 Score: 646
Period size: 40 Copynumber: 11.6 Consensus size: 40
39544706 CCAGCATGAT
* * *
39544716 TGCTCTTCGGGATTTAGCACGGATACATCACTAGCACGAA
1 TGCTCTTCGGGACTTAGCCCGGATATATCACTAGCACGAA
*
39544756 TGCTCTTCGGAACTTAGCCCGGATATATCACTAGCACGAA
1 TGCTCTTCGGGACTTAGCCCGGATATATCACTAGCACGAA
39544796 TGCTCTTCGGGACTTAGCCCGGATATATCACTAGCACGAA
1 TGCTCTTCGGGACTTAGCCCGGATATATCACTAGCACGAA
* *
39544836 TGCTCTTCGGAACTTAGCCCGGATACATCACTAGCACGAA
1 TGCTCTTCGGGACTTAGCCCGGATATATCACTAGCACGAA
39544876 TGCTCTTCGGGACTTAG-CCGG--ATAT-A-T--CACGAA
1 TGCTCTTCGGGACTTAGCCCGGATATATCACTAGCACGAA
39544909 TGCTCTTC-GGACTTAGCCCGGATATATCACTAGCACGAA
1 TGCTCTTCGGGACTTAGCCCGGATATATCACTAGCACGAA
39544948 TGCTCTTCGGGACTTAGCCCGGATATATCACTAGCACGAA
1 TGCTCTTCGGGACTTAGCCCGGATATATCACTAGCACGAA
39544988 TGCTCTTC-GGACTTAGCCCGGATA-ATCACTAGCACGAA
1 TGCTCTTCGGGACTTAGCCCGGATATATCACTAGCACGAA
39545026 TGCTCTTC-GGACTTAGCCCGGATATATCACTAGCACGAA
1 TGCTCTTCGGGACTTAGCCCGGATATATCACTAGCACGAA
* * * *
39545065 TGCTCTTCGGGACTTAGCCCGGATTTAGTAACTCGCACCAA
1 TGCTCTTCGGGACTTAGCCCGGATATA-TCACTAGCACGAA
* *
39545106 TGC-CTTC-GGATCTTAGTCCGGATATGGTCACTTAGCAC-AA
1 TGCTCTTCGGGA-CTTAGCCCGGATAT-ATCAC-TAGCACGAA
*
39545146 AGC-CTTCGGGACTTAGCCCGGA
1 TGCTCTTCGGGACTTAGCCCGGA
39545168 CATCATTCGA
Statistics
Matches: 377, Mismatches: 20, Indels: 30
0.88 0.05 0.07
Matches are distributed among these distances:
32 8 0.02
33 18 0.05
35 5 0.01
36 2 0.01
37 4 0.01
38 38 0.10
39 59 0.16
40 222 0.59
41 21 0.06
ACGTcount: A:0.25, C:0.28, G:0.22, T:0.25
Consensus pattern (40 bp):
TGCTCTTCGGGACTTAGCCCGGATATATCACTAGCACGAA
Found at i:39546894 original size:37 final size:37
Alignment explanation
Indices: 39546844--39546923 Score: 108
Period size: 37 Copynumber: 2.2 Consensus size: 37
39546834 CTTATTACGA
* *
39546844 AGTCTTACCCGGACATAA-TCTCCACACGAAGTTATCG
1 AGTCTTACCCGGACAAAATTC-CCACACGAAGTCATCG
*
39546881 AGTCTTACCCGGACAAAATTCCCACACGCAGTCATCG
1 AGTCTTACCCGGACAAAATTCCCACACGAAGTCATCG
*
39546918 GGTCTT
1 AGTCTT
39546924 TAGAGCCCGG
Statistics
Matches: 38, Mismatches: 4, Indels: 2
0.86 0.09 0.05
Matches are distributed among these distances:
37 36 0.95
38 2 0.05
ACGTcount: A:0.28, C:0.31, G:0.17, T:0.24
Consensus pattern (37 bp):
AGTCTTACCCGGACAAAATTCCCACACGAAGTCATCG
Found at i:39547113 original size:47 final size:47
Alignment explanation
Indices: 39547042--39547446 Score: 562
Period size: 47 Copynumber: 8.6 Consensus size: 47
39547032 CCCTTCGGGA
** * *
39547042 CTTATCACATTTATACACT-TTCACATTCATCACATCGGCCATTAGGC
1 CTTATCACACATATACA-TGTTCACATTCATCACATTGGCCATTCGGC
* * * *
39547089 CTTATCTCACATACACATGCTCACATTCATCACATTGGCCACTCGGC
1 CTTATCACACATATACATGTTCACATTCATCACATTGGCCATTCGGC
* *
39547136 CTTATCACACATACACATGTTCACTTTCATCACATTGGCCATTCGGC
1 CTTATCACACATATACATGTTCACATTCATCACATTGGCCATTCGGC
*
39547183 CTTATCACACATATACATGTTCACTTTCATCACATTGGCCATTCGGC
1 CTTATCACACATATACATGTTCACATTCATCACATTGGCCATTCGGC
* * *
39547230 CTTATCTCATATATGCATGTTCACATTCATCACATTGGCCATTCGGC
1 CTTATCACACATATACATGTTCACATTCATCACATTGGCCATTCGGC
* * *
39547277 CTTATCTCATATATGCATGTTCACATTCATCACATTGGCCATTCGGC
1 CTTATCACACATATACATGTTCACATTCATCACATTGGCCATTCGGC
* * *
39547324 CCTATTCACACATACACATGTTCACTTTCATCACATTGGCCATTCGGC
1 CTTA-TCACACATATACATGTTCACATTCATCACATTGGCCATTCGGC
*
39547372 CTTATCACACATATACATGTTCACTTTCATCACATTGGCCATTCGGC
1 CTTATCACACATATACATGTTCACATTCATCACATTGGCCATTCGGC
*
39547419 CCTATTCACACATATACACT-TTCACATT
1 CTTA-TCACACATATACA-TGTTCACATT
39547447 TATTCAATTA
Statistics
Matches: 327, Mismatches: 27, Indels: 7
0.91 0.07 0.02
Matches are distributed among these distances:
46 1 0.00
47 264 0.81
48 61 0.19
49 1 0.00
ACGTcount: A:0.26, C:0.31, G:0.10, T:0.33
Consensus pattern (47 bp):
CTTATCACACATATACATGTTCACATTCATCACATTGGCCATTCGGC
Found at i:39556555 original size:46 final size:46
Alignment explanation
Indices: 39556503--39556672 Score: 175
Period size: 46 Copynumber: 3.7 Consensus size: 46
39556493 GGCATCCTAA
*
39556503 CTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAATGTCCGAA
1 CTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAATGTCCGAG
* *** * *
39556549 CACGTTGAGTTGAGTCCGAGTTCGAGAGATGTAACTAG-GCAT-T-CGAG
1 CTCGTTGAGTTGAGTCCGAGTTC-ACTTATG-GA-T-GCGAATGTCCGAG
* * * *
39556596 CTCGTTGAGTTGAGTCCAAGTTCACTTATGGATACGAACGCCCGAG
1 CTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAATGTCCGAG
*
39556642 CTCCTTGAGTTGAGTCCGAGTTCACTTATGG
1 CTCGTTGAGTTGAGTCCGAGTTCACTTATGG
39556673 GCGGGTTACA
Statistics
Matches: 98, Mismatches: 19, Indels: 14
0.75 0.15 0.11
Matches are distributed among these distances:
44 3 0.03
45 1 0.01
46 59 0.60
47 28 0.29
48 2 0.02
49 4 0.04
50 1 0.01
ACGTcount: A:0.22, C:0.21, G:0.28, T:0.29
Consensus pattern (46 bp):
CTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAATGTCCGAG
Found at i:39559657 original size:15 final size:15
Alignment explanation
Indices: 39559618--39559697 Score: 83
Period size: 15 Copynumber: 5.4 Consensus size: 15
39559608 GTATCTTGGG
*
39559618 TTTCTTTATCCTGGA
1 TTTCTTTATTCTGGA
*
39559633 TCTCTTTATTCTGGA
1 TTTCTTTATTCTGGA
* *
39559648 TTTCTTTATTTTGGG
1 TTTCTTTATTCTGGA
*
39559663 TTTCTCTA-TCTTGGA
1 TTTCTTTATTC-TGGA
*
39559678 TTTCTTTATTC-GGT
1 TTTCTTTATTCTGGA
39559692 TTTCTT
1 TTTCTT
39559698 ATTATCTTTG
Statistics
Matches: 53, Mismatches: 10, Indels: 5
0.78 0.15 0.07
Matches are distributed among these distances:
14 9 0.17
15 42 0.79
16 2 0.04
ACGTcount: A:0.10, C:0.16, G:0.14, T:0.60
Consensus pattern (15 bp):
TTTCTTTATTCTGGA
Found at i:39559663 original size:45 final size:44
Alignment explanation
Indices: 39559613--39559697 Score: 125
Period size: 45 Copynumber: 1.9 Consensus size: 44
39559603 ATATCGTATC
*
39559613 TTGGGTTTCTTTATCCTGGATCTCTTTATTCTGGATTTCTTTATT
1 TTGGGTTTCTCTATCCTGGATCTCTTTATTC-GGATTTCTTTATT
* * *
39559658 TTGGGTTTCTCTATCTTGGATTTCTTTATTCGGTTTTCTT
1 TTGGGTTTCTCTATCCTGGATCTCTTTATTCGGATTTCTT
39559698 ATTATCTTTG
Statistics
Matches: 36, Mismatches: 4, Indels: 1
0.88 0.10 0.02
Matches are distributed among these distances:
44 8 0.22
45 28 0.78
ACGTcount: A:0.09, C:0.15, G:0.16, T:0.59
Consensus pattern (44 bp):
TTGGGTTTCTCTATCCTGGATCTCTTTATTCGGATTTCTTTATT
Found at i:39559678 original size:30 final size:30
Alignment explanation
Indices: 39559609--39559688 Score: 90
Period size: 30 Copynumber: 2.7 Consensus size: 30
39559599 CATAATATCG
* * *
39559609 TATCTTGGGTTTCTTTATCCTGGATCTCTT
1 TATCTTGGATTTCTTTATTCTGGATCTCTC
* * *
39559639 TAT-TCTGGATTTCTTTATTTTGGGTTTCTC
1 TATCT-TGGATTTCTTTATTCTGGATCTCTC
39559669 TATCTTGGATTTCTTTATTC
1 TATCTTGGATTTCTTTATTC
39559689 GGTTTTCTTA
Statistics
Matches: 41, Mismatches: 7, Indels: 4
0.79 0.13 0.08
Matches are distributed among these distances:
29 1 0.02
30 39 0.95
31 1 0.02
ACGTcount: A:0.11, C:0.16, G:0.15, T:0.57
Consensus pattern (30 bp):
TATCTTGGATTTCTTTATTCTGGATCTCTC
Found at i:39562132 original size:46 final size:45
Alignment explanation
Indices: 39562079--39562254 Score: 194
Period size: 46 Copynumber: 3.8 Consensus size: 45
39562069 TGTTTGGGCA
39562079 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAATG
1 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATG-GAATG
* *** * *
39562125 TCCGAACTCGTTGAGTTGAGTTCGAGTTCGAGAGATGTAACTAGGCAT-
1 TCCGAACTCGTTGAGTTGAGTCCGAGTTC-ACTTATG-GA-T-GGAATG
* *
39562173 T-CGAGCTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGTGAACG
1 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATG-GAATG
* *
39562218 CCCGAGCTCGTTGAGTTGAGTCCGAGTTCACTTATGG
1 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGG
39562255 GCGGGTTACA
Statistics
Matches: 108, Mismatches: 15, Indels: 14
0.79 0.11 0.10
Matches are distributed among these distances:
43 1 0.01
44 3 0.03
45 1 0.01
46 67 0.62
47 29 0.27
48 2 0.02
49 4 0.04
50 1 0.01
ACGTcount: A:0.21, C:0.19, G:0.30, T:0.30
Consensus pattern (45 bp):
TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGGAATG
Found at i:39562234 original size:93 final size:93
Alignment explanation
Indices: 39562075--39562246 Score: 281
Period size: 93 Copynumber: 1.8 Consensus size: 93
39562065 AGAATGTTTG
* *
39562075 GGCATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAATGTCCGAACTCGTTGAG
1 GGCATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAACGCCCGAACTCGTTGAG
*
39562140 TTGAGTTCGAGTTCGAGAGATGTAACTA
66 TTGAGTCCGAGTTCGAGAGATGTAACTA
* * * *
39562168 GGCATTCGAGCTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGTGAACGCCCGAGCTCGTTGAG
1 GGCATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAACGCCCGAACTCGTTGAG
39562233 TTGAGTCCGAGTTC
66 TTGAGTCCGAGTTC
39562247 ACTTATGGGC
Statistics
Matches: 72, Mismatches: 7, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
93 72 1.00
ACGTcount: A:0.21, C:0.20, G:0.30, T:0.29
Consensus pattern (93 bp):
GGCATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAACGCCCGAACTCGTTGAG
TTGAGTCCGAGTTCGAGAGATGTAACTA
Found at i:39564728 original size:22 final size:19
Alignment explanation
Indices: 39564703--39564750 Score: 53
Period size: 18 Copynumber: 2.4 Consensus size: 19
39564693 TATTGTTTCG
39564703 ATTAAATTCTTGTCAAAAAATA
1 ATTAAATT-TT-T-AAAAAATA
*
39564725 ATT-AATTTTTATAAAATA
1 ATTAAATTTTTAAAAAATA
39564743 ATTAAATT
1 ATTAAATT
39564751 ATACTTAAAA
Statistics
Matches: 24, Mismatches: 1, Indels: 5
0.80 0.03 0.17
Matches are distributed among these distances:
18 10 0.42
19 5 0.21
20 2 0.08
21 4 0.17
22 3 0.12
ACGTcount: A:0.50, C:0.04, G:0.02, T:0.44
Consensus pattern (19 bp):
ATTAAATTTTTAAAAAATA
Found at i:39567947 original size:82 final size:81
Alignment explanation
Indices: 39567832--39567987 Score: 215
Period size: 82 Copynumber: 1.9 Consensus size: 81
39567822 AAATTGTACA
* * * *
39567832 GCACTAAGTGTGCGATTTGACTATGTTGCACTAAGTGTGCGAAATGAATATGAT-GCACTAAGTG
1 GCACTAAGTGTGCGAATGGACTATGTGGCACTAAGTGTGCGAAATGAATACG-TGGCACTAAGTG
39567896 TGCGAATTGACCATGCG
65 TGCGAATTGACCATGCG
** *
39567913 GCACTAAGTGTGCGAGATGGACTATGTGGCACTAAGTGTGCGATTTGATTACGTGGCACTAAGTG
1 GCACTAAGTGTGCGA-ATGGACTATGTGGCACTAAGTGTGCGAAATGAATACGTGGCACTAAGTG
*
39567978 TGCGAGTTGA
65 TGCGAATTGA
39567988 TTACATAGCA
Statistics
Matches: 65, Mismatches: 8, Indels: 3
0.86 0.11 0.04
Matches are distributed among these distances:
81 16 0.25
82 49 0.75
ACGTcount: A:0.26, C:0.15, G:0.30, T:0.28
Consensus pattern (81 bp):
GCACTAAGTGTGCGAATGGACTATGTGGCACTAAGTGTGCGAAATGAATACGTGGCACTAAGTGT
GCGAATTGACCATGCG
Found at i:39567971 original size:55 final size:54
Alignment explanation
Indices: 39567832--39567983 Score: 207
Period size: 55 Copynumber: 2.8 Consensus size: 54
39567822 AAATTGTACA
* *
39567832 GCACTAAGTGTGCGATTTGACTATGTTGCACTAAGTGTGCGAAATGAATATGAT
1 GCACTAAGTGTGCGATTTGACTATGTGGCACTAAGTGTGCGAGATGAATATGAT
* * * *
39567886 GCACTAAGTGTGCGAATTGACCATGCGGCACTAAGTGTGCGAGATGGACTATG-T
1 GCACTAAGTGTGCGATTTGACTATGTGGCACTAAGTGTGCGAGAT-GAATATGAT
* *
39567940 GGCACTAAGTGTGCGATTTGATTACGTGGCACTAAGTGTGCGAG
1 -GCACTAAGTGTGCGATTTGACTATGTGGCACTAAGTGTGCGAG
39567984 TTGATTACAT
Statistics
Matches: 85, Mismatches: 11, Indels: 3
0.86 0.11 0.03
Matches are distributed among these distances:
54 41 0.48
55 44 0.52
ACGTcount: A:0.26, C:0.16, G:0.30, T:0.28
Consensus pattern (54 bp):
GCACTAAGTGTGCGATTTGACTATGTGGCACTAAGTGTGCGAGATGAATATGAT
Found at i:39567991 original size:27 final size:27
Alignment explanation
Indices: 39567832--39567987 Score: 188
Period size: 27 Copynumber: 5.7 Consensus size: 27
39567822 AAATTGTACA
* *
39567832 GCACTAAGTGTGCGATTTGACTATGTT
1 GCACTAAGTGTGCGAATTGACTATGTG
* *
39567859 GCACTAAGTGTGCGAAATGAATATGAT-
1 GCACTAAGTGTGCGAATTGACTATG-TG
* *
39567886 GCACTAAGTGTGCGAATTGACCATGCG
1 GCACTAAGTGTGCGAATTGACTATGTG
*
39567913 GCACTAAGTGTGCGAGATGGACTATGTG
1 GCACTAAGTGTGCGA-ATTGACTATGTG
* * *
39567941 GCACTAAGTGTGCGATTTGATTACGTG
1 GCACTAAGTGTGCGAATTGACTATGTG
*
39567968 GCACTAAGTGTGCGAGTTGA
1 GCACTAAGTGTGCGAATTGA
39567988 TTACATAGCA
Statistics
Matches: 111, Mismatches: 15, Indels: 6
0.84 0.11 0.05
Matches are distributed among these distances:
27 86 0.77
28 25 0.23
ACGTcount: A:0.26, C:0.15, G:0.30, T:0.28
Consensus pattern (27 bp):
GCACTAAGTGTGCGAATTGACTATGTG
Found at i:39567998 original size:27 final size:27
Alignment explanation
Indices: 39567832--39568008 Score: 144
Period size: 27 Copynumber: 6.5 Consensus size: 27
39567822 AAATTGTACA
* ** *
39567832 GCACTAAGTGTGCGATTTGACTATGTT
1 GCACTAAGTGTGCGAATTGACTACATG
* * *
39567859 GCACTAAGTGTGCGAAATGAATATGAT-
1 GCACTAAGTGTGCGAATTGACTA-CATG
39567886 GCACTAAGTGTGCGAATTGAC--CATGCG
1 GCACTAAGTGTGCGAATTGACTACAT--G
* **
39567913 GCACTAAGTGTGCGAGATGGACTATGTG
1 GCACTAAGTGTGCGA-ATTGACTACATG
* * *
39567941 GCACTAAGTGTGCGATTTGATTACGTG
1 GCACTAAGTGTGCGAATTGACTACATG
* * *
39567968 GCACTAAGTGTGCGAGTTGATTACATA
1 GCACTAAGTGTGCGAATTGACTACATG
*
39567995 GCACTGAGTGTGCG
1 GCACTAAGTGTGCG
39568009 GGCTCAATAT
Statistics
Matches: 124, Mismatches: 19, Indels: 14
0.79 0.12 0.09
Matches are distributed among these distances:
24 2 0.02
27 99 0.80
28 22 0.18
30 1 0.01
ACGTcount: A:0.26, C:0.16, G:0.30, T:0.28
Consensus pattern (27 bp):
GCACTAAGTGTGCGAATTGACTACATG
Found at i:39567999 original size:82 final size:80
Alignment explanation
Indices: 39567830--39568008 Score: 200
Period size: 82 Copynumber: 2.2 Consensus size: 80
39567820 TTAAATTGTA
* * * *
39567830 CAGCACTAAGTGTGCGATTTGACTATGTTGCACTAAGTGTGCGAAATGAATATGATGCACTAAGT
1 CAGCACTAAGTGTGCGAATGGACTATGTGGCACTAAGTGTGCGAAATGAATACGATGCACTAAGT
*
39567895 GTGCGAATTGACCAT
66 GTGCGAATTGAACAT
* ** *
39567910 GCGGCACTAAGTGTGCGAGATGGACTATGTGGCACTAAGTGTGCGATTTGATTACG-TGGCACTA
1 -CAGCACTAAGTGTGCGA-ATGGACTATGTGGCACTAAGTGTGCGAAATGAATACGAT-GCACTA
*
39567974 AGTGTGCGAGTTGATTACAT
63 AGTGTGCGAATTGA--ACAT
*
39567994 -AGCACTGAGTGTGCG
1 CAGCACTAAGTGTGCG
39568009 GGCTCAATAT
Statistics
Matches: 82, Mismatches: 12, Indels: 7
0.81 0.12 0.07
Matches are distributed among these distances:
81 17 0.21
82 62 0.76
84 3 0.04
ACGTcount: A:0.26, C:0.16, G:0.30, T:0.28
Consensus pattern (80 bp):
CAGCACTAAGTGTGCGAATGGACTATGTGGCACTAAGTGTGCGAAATGAATACGATGCACTAAGT
GTGCGAATTGAACAT
Found at i:39572754 original size:27 final size:27
Alignment explanation
Indices: 39572723--39572899 Score: 149
Period size: 27 Copynumber: 6.5 Consensus size: 27
39572713 ATATTGAGCC
* * * *
39572723 CGCACACTCAGTGCTATGTAATCAACT
1 CGCACACTTAGTGCCACGTAATCAAAT
39572750 CGCACACTTAGTGCCACGTAATCAAAT
1 CGCACACTTAGTGCCACGTAATCAAAT
* * **
39572777 CGCACACTTAGTGCCACATAGTCCATCT
1 CGCACACTTAGTGCCACGTAAT-CAAAT
* * ** *
39572805 CGCACACTTAGTGCCGCATGGTCAATT
1 CGCACACTTAGTGCCACGTAATCAAAT
* * **
39572832 CGCACACTTAGTG-CATCATATTCATTT
1 CGCACACTTAGTGCCA-CGTAATCAAAT
* * *
39572859 CGCACACTTAGTGCAACATAGTCAAAT
1 CGCACACTTAGTGCCACGTAATCAAAT
39572886 CGCACACTTAGTGC
1 CGCACACTTAGTGC
39572900 TGTACAATTT
Statistics
Matches: 127, Mismatches: 20, Indels: 6
0.83 0.13 0.04
Matches are distributed among these distances:
26 1 0.01
27 102 0.80
28 24 0.19
ACGTcount: A:0.28, C:0.30, G:0.16, T:0.26
Consensus pattern (27 bp):
CGCACACTTAGTGCCACGTAATCAAAT
Found at i:39572815 original size:55 final size:55
Alignment explanation
Indices: 39572748--39572899 Score: 209
Period size: 54 Copynumber: 2.8 Consensus size: 55
39572738 ATGTAATCAA
* *
39572748 CTCGCACACTTAGTGCCACGTAATCAAATCGCACACTTAGTGCCA-CATAGTCCAT
1 CTCGCACACTTAGTGCCACATAGTCAAATCGCACACTTAGTGCCATCATA-TCCAT
* * * *
39572803 CTCGCACACTTAGTGCCGCATGGTCAATTCGCACACTTAGTG-CATCATATTCAT
1 CTCGCACACTTAGTGCCACATAGTCAAATCGCACACTTAGTGCCATCATATCCAT
* *
39572857 TTCGCACACTTAGTGCAACATAGTCAAATCGCACACTTAGTGC
1 CTCGCACACTTAGTGCCACATAGTCAAATCGCACACTTAGTGC
39572900 TGTACAATTT
Statistics
Matches: 84, Mismatches: 11, Indels: 4
0.85 0.11 0.04
Matches are distributed among these distances:
54 43 0.51
55 41 0.49
ACGTcount: A:0.28, C:0.30, G:0.16, T:0.26
Consensus pattern (55 bp):
CTCGCACACTTAGTGCCACATAGTCAAATCGCACACTTAGTGCCATCATATCCAT
Found at i:39572862 original size:82 final size:81
Alignment explanation
Indices: 39572744--39572899 Score: 215
Period size: 82 Copynumber: 1.9 Consensus size: 81
39572734 TGCTATGTAA
* * **
39572744 TCAACTCGCACACTTAGTGCCACGTAATCAAATCGCACACTTAGTGCCACATAGTCCATCTCGCA
1 TCAACTCGCACACTTAGTGCCACATAATCAAATCGCACACTTAGTGCAACATAGT-CAAATCGCA
39572809 CACTTAGTGCCGCATGG
65 CACTTAGTGCCGCATGG
* * **
39572826 TCAATTCGCACACTTAGTG-CATCATATTCATTTCGCACACTTAGTGCAACATAGTCAAATCGCA
1 TCAACTCGCACACTTAGTGCCA-CATAATCAAATCGCACACTTAGTGCAACATAGTCAAATCGCA
39572890 CACTTAGTGC
65 CACTTAGTGC
39572900 TGTACAATTT
Statistics
Matches: 65, Mismatches: 8, Indels: 3
0.86 0.11 0.04
Matches are distributed among these distances:
81 19 0.29
82 46 0.71
ACGTcount: A:0.28, C:0.30, G:0.15, T:0.26
Consensus pattern (81 bp):
TCAACTCGCACACTTAGTGCCACATAATCAAATCGCACACTTAGTGCAACATAGTCAAATCGCAC
ACTTAGTGCCGCATGG
Found at i:39588880 original size:27 final size:27
Alignment explanation
Indices: 39588850--39589027 Score: 205
Period size: 27 Copynumber: 6.6 Consensus size: 27
39588840 ATATTGAGTC
* * * *
39588850 CGCACACTCAGTGCTATATAATCAACT
1 CGCACACTTAGTGCTACATAGTCAAAT
* *
39588877 CGCACACTTAGTGCTACGTAATCAAAT
1 CGCACACTTAGTGCTACATAGTCAAAT
39588904 CGCACACTTAGTGCTACATAGTCAAACT
1 CGCACACTTAGTGCTACATAGTCAAA-T
** * *
39588932 CGCACACTTAGTGCCGCATGGTCAATT
1 CGCACACTTAGTGCTACATAGTCAAAT
* **
39588959 CGCACACTTAGTGC-ATCATATTCATTT
1 CGCACACTTAGTGCTA-CATAGTCAAAT
*
39588986 CGCACACTTAGTGCAACATAGTCAAAT
1 CGCACACTTAGTGCTACATAGTCAAAT
39589013 CGCACACTTAGTGCT
1 CGCACACTTAGTGCT
39589028 GTACAATTTA
Statistics
Matches: 130, Mismatches: 18, Indels: 6
0.84 0.12 0.04
Matches are distributed among these distances:
27 106 0.82
28 24 0.18
ACGTcount: A:0.30, C:0.28, G:0.15, T:0.27
Consensus pattern (27 bp):
CGCACACTTAGTGCTACATAGTCAAAT
Found at i:39588989 original size:82 final size:81
Alignment explanation
Indices: 39588871--39589026 Score: 233
Period size: 82 Copynumber: 1.9 Consensus size: 81
39588861 TGCTATATAA
* *
39588871 TCAACTCGCACACTTAGTGCTACGTAATCAAATCGCACACTTAGTGCTACATAGTCAAACTCGCA
1 TCAACTCGCACACTTAGTGCTACATAATCAAATCGCACACTTAGTGCAACATAGTCAAA-TCGCA
39588936 CACTTAGTGCCGCATGG
65 CACTTAGTGCCGCATGG
* * **
39588953 TCAATTCGCACACTTAGTGC-ATCATATTCATTTCGCACACTTAGTGCAACATAGTCAAATCGCA
1 TCAACTCGCACACTTAGTGCTA-CATAATCAAATCGCACACTTAGTGCAACATAGTCAAATCGCA
39589017 CACTTAGTGC
65 CACTTAGTGC
39589027 TGTACAATTT
Statistics
Matches: 67, Mismatches: 6, Indels: 3
0.88 0.08 0.04
Matches are distributed among these distances:
81 16 0.24
82 51 0.76
ACGTcount: A:0.29, C:0.28, G:0.15, T:0.27
Consensus pattern (81 bp):
TCAACTCGCACACTTAGTGCTACATAATCAAATCGCACACTTAGTGCAACATAGTCAAATCGCAC
ACTTAGTGCCGCATGG
Found at i:39589524 original size:12 final size:12
Alignment explanation
Indices: 39589507--39589533 Score: 54
Period size: 12 Copynumber: 2.2 Consensus size: 12
39589497 ATGGCATACT
39589507 TATGTATATATA
1 TATGTATATATA
39589519 TATGTATATATA
1 TATGTATATATA
39589531 TAT
1 TAT
39589534 ACTTCGGAAT
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 15 1.00
ACGTcount: A:0.41, C:0.00, G:0.07, T:0.52
Consensus pattern (12 bp):
TATGTATATATA
Found at i:39596905 original size:27 final size:27
Alignment explanation
Indices: 39596875--39597052 Score: 196
Period size: 27 Copynumber: 6.6 Consensus size: 27
39596865 ATATTGAGTC
* * * *
39596875 CGCACACTCAGTGCTATATAATCAACT
1 CGCACACTTAGTGCTACATAGTCAAAT
* *
39596902 CGCACACTTAGTGCTACGTAATCAAAT
1 CGCACACTTAGTGCTACATAGTCAAAT
*
39596929 CACACACTTAGTGCTACATAGTCAAACT
1 CGCACACTTAGTGCTACATAGTCAAA-T
** * *
39596957 CGCACACTTAGTGCCGCATGGTCAATT
1 CGCACACTTAGTGCTACATAGTCAAAT
* **
39596984 CGCACACTTAGTGC-ATCATATTCATTT
1 CGCACACTTAGTGCTA-CATAGTCAAAT
*
39597011 CGCACACTTAGTGCAACATAGTCAAAT
1 CGCACACTTAGTGCTACATAGTCAAAT
39597038 CGCACACTTAGTGCT
1 CGCACACTTAGTGCT
39597053 GTACAATTTA
Statistics
Matches: 128, Mismatches: 20, Indels: 6
0.83 0.13 0.04
Matches are distributed among these distances:
27 105 0.82
28 23 0.18
ACGTcount: A:0.30, C:0.28, G:0.15, T:0.27
Consensus pattern (27 bp):
CGCACACTTAGTGCTACATAGTCAAAT
Found at i:39597017 original size:82 final size:81
Alignment explanation
Indices: 39596896--39597051 Score: 224
Period size: 82 Copynumber: 1.9 Consensus size: 81
39596886 TGCTATATAA
* *
39596896 TCAACTCGCACACTTAGTGCTACGTAATCAAATCACACACTTAGTGCTACATAGTCAAACTCGCA
1 TCAACTCGCACACTTAGTGCTACATAATCAAATCACACACTTAGTGCAACATAGTCAAA-TCGCA
39596961 CACTTAGTGCCGCATGG
65 CACTTAGTGCCGCATGG
* * ** *
39596978 TCAATTCGCACACTTAGTGC-ATCATATTCATTTCGCACACTTAGTGCAACATAGTCAAATCGCA
1 TCAACTCGCACACTTAGTGCTA-CATAATCAAATCACACACTTAGTGCAACATAGTCAAATCGCA
39597042 CACTTAGTGC
65 CACTTAGTGC
39597052 TGTACAATTT
Statistics
Matches: 66, Mismatches: 7, Indels: 3
0.87 0.09 0.04
Matches are distributed among these distances:
81 16 0.24
82 50 0.76
ACGTcount: A:0.30, C:0.28, G:0.15, T:0.27
Consensus pattern (81 bp):
TCAACTCGCACACTTAGTGCTACATAATCAAATCACACACTTAGTGCAACATAGTCAAATCGCAC
ACTTAGTGCCGCATGG
Found at i:39597431 original size:28 final size:28
Alignment explanation
Indices: 39597391--39597451 Score: 122
Period size: 28 Copynumber: 2.2 Consensus size: 28
39597381 TTAATCAATA
39597391 ATTCACTAGTTTAACCATCTTGTTAAAC
1 ATTCACTAGTTTAACCATCTTGTTAAAC
39597419 ATTCACTAGTTTAACCATCTTGTTAAAC
1 ATTCACTAGTTTAACCATCTTGTTAAAC
39597447 ATTCA
1 ATTCA
39597452 TAATTCAATT
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
28 33 1.00
ACGTcount: A:0.33, C:0.21, G:0.07, T:0.39
Consensus pattern (28 bp):
ATTCACTAGTTTAACCATCTTGTTAAAC
Found at i:39597581 original size:12 final size:12
Alignment explanation
Indices: 39597564--39597590 Score: 54
Period size: 12 Copynumber: 2.2 Consensus size: 12
39597554 ATGGCATACT
39597564 TATGTATATATA
1 TATGTATATATA
39597576 TATGTATATATA
1 TATGTATATATA
39597588 TAT
1 TAT
39597591 ACTTCGGAAT
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 15 1.00
ACGTcount: A:0.41, C:0.00, G:0.07, T:0.52
Consensus pattern (12 bp):
TATGTATATATA
Found at i:39604497 original size:100 final size:100
Alignment explanation
Indices: 39604324--39604527 Score: 390
Period size: 100 Copynumber: 2.0 Consensus size: 100
39604314 CTCTATCCAA
*
39604324 TATTCAGCCACATTAGGGGCAACTCTAGTGACACCCCTAAAGATCTCAGCCCTATTAGACTTAAG
1 TATTCAGACACATTAGGGGCAACTCTAGTGACACCCCTAAAGATCTCAGCCCTATTAGACTTAAG
*
39604389 TCGTTCCGTTACTGACCTGCGGCCCATAGTACCAG
66 TCGTTCCGTTACTGACCTGCAGCCCATAGTACCAG
39604424 TATTCAGACACATTAGGGGCAACTCTAGTGACACCCCTAAAGATCTCAGCCCTATTAGACTTAAG
1 TATTCAGACACATTAGGGGCAACTCTAGTGACACCCCTAAAGATCTCAGCCCTATTAGACTTAAG
39604489 TCGTTCCGTTACTGACCTGCAGCCCATAGTACCAG
66 TCGTTCCGTTACTGACCTGCAGCCCATAGTACCAG
39604524 TATT
1 TATT
39604528 GGGCCTAGCG
Statistics
Matches: 102, Mismatches: 2, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
100 102 1.00
ACGTcount: A:0.27, C:0.29, G:0.18, T:0.26
Consensus pattern (100 bp):
TATTCAGACACATTAGGGGCAACTCTAGTGACACCCCTAAAGATCTCAGCCCTATTAGACTTAAG
TCGTTCCGTTACTGACCTGCAGCCCATAGTACCAG
Found at i:39608218 original size:24 final size:26
Alignment explanation
Indices: 39608181--39608231 Score: 88
Period size: 25 Copynumber: 2.0 Consensus size: 26
39608171 CTGGAGGCCT
39608181 AGCCTCTTTTAAT-AACTGGGGCAAA
1 AGCCTCTTTTAATAAACTGGGGCAAA
39608206 AGCC-CTTTTAATAAACTGGGGCAAA
1 AGCCTCTTTTAATAAACTGGGGCAAA
39608231 A
1 A
39608232 CCATTTTTGG
Statistics
Matches: 25, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
24 8 0.32
25 17 0.68
ACGTcount: A:0.35, C:0.20, G:0.20, T:0.25
Consensus pattern (26 bp):
AGCCTCTTTTAATAAACTGGGGCAAA
Found at i:39608238 original size:24 final size:24
Alignment explanation
Indices: 39608187--39608238 Score: 79
Period size: 24 Copynumber: 2.2 Consensus size: 24
39608177 GCCTAGCCTC
*
39608187 TTTTAATAACTGGGGCAAAAGCCC
1 TTTTAATAACTGGGGCAAAAGCCA
39608211 TTTTAATAAACTGGGGCAAAA-CCA
1 TTTTAAT-AACTGGGGCAAAAGCCA
39608235 TTTT
1 TTTT
39608239 TGGTAAATTG
Statistics
Matches: 26, Mismatches: 1, Indels: 2
0.90 0.03 0.07
Matches are distributed among these distances:
24 13 0.50
25 13 0.50
ACGTcount: A:0.35, C:0.17, G:0.17, T:0.31
Consensus pattern (24 bp):
TTTTAATAACTGGGGCAAAAGCCA
Found at i:39608265 original size:25 final size:25
Alignment explanation
Indices: 39608194--39608253 Score: 68
Period size: 25 Copynumber: 2.4 Consensus size: 25
39608184 CTCTTTTAAT
* **
39608194 AACTGGGGCAAAAGCC-CTTTTAATA
1 AACTGGGGCAAAA-CCATTTTTGGTA
39608219 AACTGGGGCAAAACCATTTTTGGTA
1 AACTGGGGCAAAACCATTTTTGGTA
*
39608244 AATTGGGGCA
1 AACTGGGGCA
39608254 TAGCCCTTTT
Statistics
Matches: 30, Mismatches: 4, Indels: 2
0.83 0.11 0.06
Matches are distributed among these distances:
24 2 0.07
25 28 0.93
ACGTcount: A:0.33, C:0.17, G:0.25, T:0.25
Consensus pattern (25 bp):
AACTGGGGCAAAACCATTTTTGGTA
Found at i:39608334 original size:20 final size:20
Alignment explanation
Indices: 39608311--39608357 Score: 78
Period size: 20 Copynumber: 2.4 Consensus size: 20
39608301 TTATGAATAC
39608311 ATCATGTGCATATCATA-CA
1 ATCATGTGCATATCATATCA
39608330 TATCATGTGCATATCATATCA
1 -ATCATGTGCATATCATATCA
39608351 ATCATGT
1 ATCATGT
39608358 ATATCAAATT
Statistics
Matches: 26, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
20 24 0.92
21 2 0.08
ACGTcount: A:0.34, C:0.19, G:0.11, T:0.36
Consensus pattern (20 bp):
ATCATGTGCATATCATATCA
Found at i:39615643 original size:26 final size:25
Alignment explanation
Indices: 39615601--39615684 Score: 91
Period size: 26 Copynumber: 3.4 Consensus size: 25
39615591 TTGGAGGCCT
*
39615601 AGCCTCTTCTAAT-AACTGGGGCAAA
1 AGCC-CTTTTAATAAACTGGGGCAAA
**
39615626 AGCCCTTTTCGGTAAACTGGGGCAAA
1 AGCCCTTTT-AATAAACTGGGGCAAA
* *
39615652 AGCCCTATTAATAAACTGGGGC-AT
1 AGCCCTTTTAATAAACTGGGGCAAA
39615676 AGCCCTTTT
1 AGCCCTTTT
39615685 TGCACTTCCT
Statistics
Matches: 49, Mismatches: 8, Indels: 5
0.79 0.13 0.08
Matches are distributed among these distances:
24 13 0.27
25 16 0.33
26 20 0.41
ACGTcount: A:0.29, C:0.24, G:0.21, T:0.26
Consensus pattern (25 bp):
AGCCCTTTTAATAAACTGGGGCAAA
Found at i:39615750 original size:5 final size:5
Alignment explanation
Indices: 39615740--39615781 Score: 52
Period size: 5 Copynumber: 8.6 Consensus size: 5
39615730 ACATCATGTG
*
39615740 CATAT CATAT CATAT -ATAT CATGT GCATAT CATAT CA-AT CAT
1 CATAT CATAT CATAT CATAT CATAT -CATAT CATAT CATAT CAT
39615782 GTATATCAAA
Statistics
Matches: 32, Mismatches: 2, Indels: 6
0.80 0.05 0.15
Matches are distributed among these distances:
4 8 0.25
5 20 0.62
6 4 0.12
ACGTcount: A:0.38, C:0.19, G:0.05, T:0.38
Consensus pattern (5 bp):
CATAT
Found at i:39615770 original size:20 final size:20
Alignment explanation
Indices: 39615745--39615783 Score: 62
Period size: 20 Copynumber: 1.9 Consensus size: 20
39615735 ATGTGCATAT
39615745 CATATCATAT-ATATCATGTG
1 CATATCATATCA-ATCATGTG
39615765 CATATCATATCAATCATGT
1 CATATCATATCAATCATGT
39615784 ATATCAAATT
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
20 17 0.94
21 1 0.06
ACGTcount: A:0.36, C:0.18, G:0.08, T:0.38
Consensus pattern (20 bp):
CATATCATATCAATCATGTG
Found at i:39619361 original size:27 final size:27
Alignment explanation
Indices: 39619331--39619454 Score: 151
Period size: 27 Copynumber: 4.6 Consensus size: 27
39619321 TGTAGGGTAG
* *
39619331 AATTACTAAAATACCCTTGGTTTATAA
1 AATTACCAAAATACCCTTGGTTTGTAA
39619358 AATTACCAAAATA-CCTCTGGTTTGTAA
1 AATTACCAAAATACCCT-TGGTTTGTAA
* *
39619385 AATTACCAAAATACCCCTAGTTTGTAA
1 AATTACCAAAATACCCTTGGTTTGTAA
****
39619412 AATTACCAAAATACCCTCAACTTGTAA
1 AATTACCAAAATACCCTTGGTTTGTAA
*
39619439 AATTACCAAAGTACCC
1 AATTACCAAAATACCC
39619455 CCGATTTAAA
Statistics
Matches: 86, Mismatches: 9, Indels: 4
0.87 0.09 0.04
Matches are distributed among these distances:
26 3 0.03
27 81 0.94
28 2 0.02
ACGTcount: A:0.41, C:0.22, G:0.07, T:0.30
Consensus pattern (27 bp):
AATTACCAAAATACCCTTGGTTTGTAA
Found at i:39619413 original size:54 final size:54
Alignment explanation
Indices: 39619331--39619472 Score: 162
Period size: 54 Copynumber: 2.6 Consensus size: 54
39619321 TGTAGGGTAG
* * * ***
39619331 AATTACTAAAATACCCTTGGTTTATAAAATTACCAAAATA-CCTCTGGTTTGTAA
1 AATTACCAAAATACCCCTAGTTTATAAAATTACCAAAATACCCTC-AACTTGTAA
*
39619385 AATTACCAAAATACCCCTAGTTTGTAAAATTACCAAAATACCCTCAACTTGTAA
1 AATTACCAAAATACCCCTAGTTTATAAAATTACCAAAATACCCTCAACTTGTAA
* * *
39619439 AATTACCAAAGTACCCC-CGATTTAAAAAATTACC
1 AATTACCAAAATACCCCTAG-TTTATAAAATTACC
39619473 GTTTTACCCT
Statistics
Matches: 75, Mismatches: 11, Indels: 4
0.83 0.12 0.04
Matches are distributed among these distances:
53 1 0.01
54 70 0.93
55 4 0.05
ACGTcount: A:0.42, C:0.22, G:0.07, T:0.30
Consensus pattern (54 bp):
AATTACCAAAATACCCCTAGTTTATAAAATTACCAAAATACCCTCAACTTGTAA
Found at i:39619467 original size:27 final size:27
Alignment explanation
Indices: 39619331--39619472 Score: 133
Period size: 27 Copynumber: 5.3 Consensus size: 27
39619321 TGTAGGGTAG
* ** * *
39619331 AATTACTAAAATACCCTTGGTTTATAA
1 AATTACCAAAATACCCCCGATTTGTAA
* * *
39619358 AATTACCAAAATACCTCTGGTTTGTAA
1 AATTACCAAAATACCCCCGATTTGTAA
*
39619385 AATTACCAAAATA-CCCCTAGTTTGTAA
1 AATTACCAAAATACCCCCGA-TTTGTAA
* * *
39619412 AATTACCAAAATACCCTCAACTTGTAA
1 AATTACCAAAATACCCCCGATTTGTAA
* **
39619439 AATTACCAAAGTACCCCCGATTTAAAA
1 AATTACCAAAATACCCCCGATTTGTAA
39619466 AATTACC
1 AATTACC
39619473 GTTTTACCCT
Statistics
Matches: 96, Mismatches: 17, Indels: 4
0.82 0.15 0.03
Matches are distributed among these distances:
26 2 0.02
27 90 0.94
28 4 0.04
ACGTcount: A:0.42, C:0.22, G:0.07, T:0.30
Consensus pattern (27 bp):
AATTACCAAAATACCCCCGATTTGTAA
Found at i:39619523 original size:27 final size:27
Alignment explanation
Indices: 39619493--39619632 Score: 165
Period size: 27 Copynumber: 5.2 Consensus size: 27
39619483 TGATTTACAA
* *
39619493 AATTATTGAAATATCCCTGTAGGGTAG
1 AATTATCGAAATACCCCTGTAGGGTAG
*
39619520 AATTA-CTGAAATACCCCTGTACGGTAG
1 AATTATC-GAAATACCCCTGTAGGGTAG
*
39619547 AATTATCGAAATACCCTTGTAGGGTAG
1 AATTATCGAAATACCCCTGTAGGGTAG
* *
39619574 AAATATCGAAATGCCCCTGTAGGGTAG
1 AATTATCGAAATACCCCTGTAGGGTAG
* * * * *
39619601 AATTACCGAGATACCCTTGTTGGGTAA
1 AATTATCGAAATACCCCTGTAGGGTAG
39619628 AATTA
1 AATTA
39619633 CAATTTTGCC
Statistics
Matches: 96, Mismatches: 15, Indels: 4
0.83 0.13 0.03
Matches are distributed among these distances:
27 95 0.99
28 1 0.01
ACGTcount: A:0.34, C:0.16, G:0.21, T:0.29
Consensus pattern (27 bp):
AATTATCGAAATACCCCTGTAGGGTAG
Found at i:39620074 original size:22 final size:22
Alignment explanation
Indices: 39620022--39620086 Score: 87
Period size: 22 Copynumber: 3.0 Consensus size: 22
39620012 GCCAATTATT
*
39620022 CTGATTATGGCTTTGCGCCAAC
1 CTGATTATGGCTTTGTGCCAAC
*
39620044 CT-ACATATGGCTTTGTGCCAAC
1 CTGA-TTATGGCTTTGTGCCAAC
*
39620066 CTGATTATGGCTGTGTGCCAA
1 CTGATTATGGCTTTGTGCCAA
39620087 ACGTATTTGC
Statistics
Matches: 37, Mismatches: 4, Indels: 4
0.82 0.09 0.09
Matches are distributed among these distances:
21 1 0.03
22 35 0.95
23 1 0.03
ACGTcount: A:0.20, C:0.25, G:0.23, T:0.32
Consensus pattern (22 bp):
CTGATTATGGCTTTGTGCCAAC
Found at i:39620313 original size:27 final size:26
Alignment explanation
Indices: 39620286--39620352 Score: 89
Period size: 27 Copynumber: 2.5 Consensus size: 26
39620276 CTATGCTACA
*
39620286 AATATCTGTTCTGGTGGCTCTACCAC
1 AATATCTGTTCTGGTGACTCTACCAC
**
39620312 AATATCTGTATCTGGTGACTCTGTCAC
1 AATATCTGT-TCTGGTGACTCTACCAC
*
39620339 AATATCTATTCTGG
1 AATATCTGTTCTGG
39620353 CAGCCATGCT
Statistics
Matches: 36, Mismatches: 4, Indels: 2
0.86 0.10 0.05
Matches are distributed among these distances:
26 14 0.39
27 22 0.61
ACGTcount: A:0.22, C:0.22, G:0.18, T:0.37
Consensus pattern (26 bp):
AATATCTGTTCTGGTGACTCTACCAC
Found at i:39622055 original size:34 final size:34
Alignment explanation
Indices: 39622002--39622088 Score: 86
Period size: 34 Copynumber: 2.6 Consensus size: 34
39621992 CAGTGTTGAA
* * * * *
39622002 CAGTCTGGGCCTAAACCCA-TATCAGTCGGATTAT
1 CAGTCTGGGCCTTAGCCCATTA-CAGTAGCAATAT
*
39622036 CAGTGTGGGCCTTAGCCCATTACAGTAGCAATAT
1 CAGTCTGGGCCTTAGCCCATTACAGTAGCAATAT
* *
39622070 CAGTTTGAGCCTTAGCCCA
1 CAGTCTGGGCCTTAGCCCA
39622089 ACTCAATACA
Statistics
Matches: 44, Mismatches: 8, Indels: 2
0.81 0.15 0.04
Matches are distributed among these distances:
34 42 0.95
35 2 0.05
ACGTcount: A:0.25, C:0.26, G:0.22, T:0.26
Consensus pattern (34 bp):
CAGTCTGGGCCTTAGCCCATTACAGTAGCAATAT
Found at i:39640871 original size:48 final size:49
Alignment explanation
Indices: 39640787--39640900 Score: 133
Period size: 48 Copynumber: 2.4 Consensus size: 49
39640777 TTTGGATTTG
*** *
39640787 GGCCATGGTATAGGTA-TTTTGGAGATGAGTTACCTTGATTAGGCTACA
1 GGCCATGGTATAGGTACTCCAGGAGATAAGTTACCTTGATTAGGCTACA
* * ***
39640835 GGCCATGGTATAGGTACTCCAGG-GATAAGTTGCCTTGATTTGGCTTTG
1 GGCCATGGTATAGGTACTCCAGGAGATAAGTTACCTTGATTAGGCTACA
39640883 GGCCATGGTATAGGTACT
1 GGCCATGGTATAGGTACT
39640901 TAACGATAGG
Statistics
Matches: 56, Mismatches: 9, Indels: 2
0.84 0.13 0.03
Matches are distributed among these distances:
48 53 0.95
49 3 0.05
ACGTcount: A:0.22, C:0.15, G:0.31, T:0.32
Consensus pattern (49 bp):
GGCCATGGTATAGGTACTCCAGGAGATAAGTTACCTTGATTAGGCTACA
Found at i:39643951 original size:25 final size:25
Alignment explanation
Indices: 39643878--39643957 Score: 106
Period size: 25 Copynumber: 3.2 Consensus size: 25
39643868 TACCTATTTG
* * **
39643878 TAGCTCGTAAGAGCATACTGATTTG
1 TAGCTCATAAGAGCATACCGATTCA
*
39643903 TAGCTCATAAGAGCATATCGATTCA
1 TAGCTCATAAGAGCATACCGATTCA
*
39643928 TAGCTCATAAGAGCATACCAATTCA
1 TAGCTCATAAGAGCATACCGATTCA
39643953 TAGCT
1 TAGCT
39643958 TGTATGAGCA
Statistics
Matches: 48, Mismatches: 7, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
25 48 1.00
ACGTcount: A:0.34, C:0.20, G:0.17, T:0.29
Consensus pattern (25 bp):
TAGCTCATAAGAGCATACCGATTCA
Found at i:39647000 original size:16 final size:16
Alignment explanation
Indices: 39646979--39647010 Score: 64
Period size: 16 Copynumber: 2.0 Consensus size: 16
39646969 TGCCTAAGGG
39646979 CATATTGGTTGTATGT
1 CATATTGGTTGTATGT
39646995 CATATTGGTTGTATGT
1 CATATTGGTTGTATGT
39647011 GATCATACGA
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 16 1.00
ACGTcount: A:0.19, C:0.06, G:0.25, T:0.50
Consensus pattern (16 bp):
CATATTGGTTGTATGT
Found at i:39648059 original size:34 final size:34
Alignment explanation
Indices: 39648016--39648084 Score: 129
Period size: 34 Copynumber: 2.0 Consensus size: 34
39648006 TTACCTGTGA
39648016 TAGTGTGGTATCTCTTGACTTTTAAAAACATGTT
1 TAGTGTGGTATCTCTTGACTTTTAAAAACATGTT
*
39648050 TAGTGTGGTATCTCTTGACTTTTTAAAACATGTT
1 TAGTGTGGTATCTCTTGACTTTTAAAAACATGTT
39648084 T
1 T
39648085 TCATAAAGAA
Statistics
Matches: 34, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
34 34 1.00
ACGTcount: A:0.25, C:0.12, G:0.17, T:0.46
Consensus pattern (34 bp):
TAGTGTGGTATCTCTTGACTTTTAAAAACATGTT
Found at i:39654005 original size:25 final size:25
Alignment explanation
Indices: 39653971--39654052 Score: 92
Period size: 25 Copynumber: 3.3 Consensus size: 25
39653961 TTACCAATTT
* * *
39653971 ATAGCCCGTAAGAGCATACTGATTT
1 ATAGCTCGTAAGAGAATACTGATTC
* **
39653996 ATAGCTCGTAAGAGTATACAAATTC
1 ATAGCTCGTAAGAGAATACTGATTC
* *
39654021 ATAGCTCGTGAGAGAATTCTGATTC
1 ATAGCTCGTAAGAGAATACTGATTC
39654046 ATAGCTC
1 ATAGCTC
39654053 ATATGAACAT
Statistics
Matches: 47, Mismatches: 10, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
25 47 1.00
ACGTcount: A:0.33, C:0.18, G:0.20, T:0.29
Consensus pattern (25 bp):
ATAGCTCGTAAGAGAATACTGATTC
Found at i:39654065 original size:50 final size:50
Alignment explanation
Indices: 39653966--39654065 Score: 110
Period size: 50 Copynumber: 2.0 Consensus size: 50
39653956 TAGTGTTACC
* * * * **
39653966 AATTTATAGCCCGTAAGAGCATACTGATTTATAGCTCGTAAGAGTATACA
1 AATTCATAGCCCGTAAGAGAATACTGATTCATAGCTCATAAGAACATACA
* * * *
39654016 AATTCATAGCTCGTGAGAGAATTCTGATTCATAGCTCATATGAACATACA
1 AATTCATAGCCCGTAAGAGAATACTGATTCATAGCTCATAAGAACATACA
39654066 TGTACATGAA
Statistics
Matches: 40, Mismatches: 10, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
50 40 1.00
ACGTcount: A:0.36, C:0.17, G:0.17, T:0.30
Consensus pattern (50 bp):
AATTCATAGCCCGTAAGAGAATACTGATTCATAGCTCATAAGAACATACA
Found at i:39659517 original size:29 final size:29
Alignment explanation
Indices: 39659482--39659558 Score: 91
Period size: 29 Copynumber: 2.6 Consensus size: 29
39659472 CATGAGATTG
* *
39659482 GCACTAAGTGTGCGGGTTTAAATTGTACA
1 GCACTAAGTGTGCGGGTTTAAAGTGCACA
* * **
39659511 GCACTAAGTGTGTGAGTTTAAAGTGCATG
1 GCACTAAGTGTGCGGGTTTAAAGTGCACA
39659540 GCACTAAGTGTGCGCGGTT
1 GCACTAAGTGTGCG-GGTT
39659559 GATTATTGAG
Statistics
Matches: 39, Mismatches: 8, Indels: 1
0.81 0.17 0.02
Matches are distributed among these distances:
29 36 0.92
30 3 0.08
ACGTcount: A:0.25, C:0.14, G:0.31, T:0.30
Consensus pattern (29 bp):
GCACTAAGTGTGCGGGTTTAAAGTGCACA
Found at i:39659776 original size:174 final size:174
Alignment explanation
Indices: 39659511--39659838 Score: 611
Period size: 174 Copynumber: 1.9 Consensus size: 174
39659501 AAATTGTACA
* *
39659511 GCACTAAGTGTGTGAGTTTAAAGTGCATGGCACTAAGTGTGCGCGGTTGATTATTGAGCACTATG
1 GCACTAAGTGTGTGAGTTTAAAGTACATGGCACTAAGTGTGCGCGGTTGATTATTAAGCACTATG
* *
39659576 TGTGCGAACCCAATATATATTTTCTATAAATTATTTACATTAAGGGTGCGACTTTACCGAGTCGA
66 TGTGCGAACCCAATATATATTTTCTATAAATTATTTACATGAAGGGTGCGACTTTACCGAGTCAA
39659641 TTTTGGACAGCGGAAAAGGTAAGTGTGCGAACTTGAAATGCATG
131 TTTTGGACAGCGGAAAAGGTAAGTGTGCGAACTTGAAATGCATG
39659685 GCACTAAGTGTGTGAGTTTAAAGTACATGGCACTAAGTGTGCGCGGTTGATTATTAAGCACTATG
1 GCACTAAGTGTGTGAGTTTAAAGTACATGGCACTAAGTGTGCGCGGTTGATTATTAAGCACTATG
*
39659750 TGTGCGAACTCAATATATATTTTCTATAAATTATTTACATGAAGGGTGCGACTTTACCGAGTCAA
66 TGTGCGAACCCAATATATATTTTCTATAAATTATTTACATGAAGGGTGCGACTTTACCGAGTCAA
39659815 TTTTGGACAGCGGAAAAGGTAAGT
131 TTTTGGACAGCGGAAAAGGTAAGT
39659839 ACCTTGAGTT
Statistics
Matches: 149, Mismatches: 5, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
174 149 1.00
ACGTcount: A:0.30, C:0.14, G:0.25, T:0.31
Consensus pattern (174 bp):
GCACTAAGTGTGTGAGTTTAAAGTACATGGCACTAAGTGTGCGCGGTTGATTATTAAGCACTATG
TGTGCGAACCCAATATATATTTTCTATAAATTATTTACATGAAGGGTGCGACTTTACCGAGTCAA
TTTTGGACAGCGGAAAAGGTAAGTGTGCGAACTTGAAATGCATG
Found at i:39663249 original size:23 final size:23
Alignment explanation
Indices: 39663219--39663293 Score: 75
Period size: 23 Copynumber: 3.3 Consensus size: 23
39663209 CTGATGAATA
39663219 GTAAGCTCTAATGAGCTGAAACG
1 GTAAGCTCTAATGAGCTGAAACG
* *
39663242 GTAAGCTCT-ATCAAGCTGAAA-A
1 GTAAGCTCTAAT-GAGCTGAAACG
* **
39663264 GTAAGC-CTATTGATATGAAACG
1 GTAAGCTCTAATGAGCTGAAACG
39663286 GTAAGCTC
1 GTAAGCTC
39663294 CAGTGAGTTG
Statistics
Matches: 41, Mismatches: 7, Indels: 8
0.73 0.12 0.14
Matches are distributed among these distances:
21 8 0.20
22 15 0.37
23 18 0.44
ACGTcount: A:0.36, C:0.17, G:0.23, T:0.24
Consensus pattern (23 bp):
GTAAGCTCTAATGAGCTGAAACG
Found at i:39665700 original size:49 final size:51
Alignment explanation
Indices: 39665572--39665704 Score: 171
Period size: 51 Copynumber: 2.6 Consensus size: 51
39665562 TCTATTGTGA
*
39665572 GGTCGCATGTGTAGTACTAAGTGCAGGCTACTATGCATACCCGATAACTTC
1 GGTCGCATGTGTAGTACTAAGTGCAGGCTACTACGCATACCCGATAACTTC
* ** * * ** *
39665623 GATTACGTGTGTAGTACTAAGTGTAGGCTACTACGTGTACCGGATAA-TT-
1 GGTCGCATGTGTAGTACTAAGTGCAGGCTACTACGCATACCCGATAACTTC
39665672 GGTCGCATGTGTAGTACTAAGTGCAGGCTACTA
1 GGTCGCATGTGTAGTACTAAGTGCAGGCTACTA
39665705 TGCGTACCAG
Statistics
Matches: 68, Mismatches: 14, Indels: 2
0.81 0.17 0.02
Matches are distributed among these distances:
49 28 0.41
50 2 0.03
51 38 0.56
ACGTcount: A:0.26, C:0.19, G:0.26, T:0.29
Consensus pattern (51 bp):
GGTCGCATGTGTAGTACTAAGTGCAGGCTACTACGCATACCCGATAACTTC
Found at i:39665712 original size:49 final size:51
Alignment explanation
Indices: 39665572--39665717 Score: 188
Period size: 49 Copynumber: 2.9 Consensus size: 51
39665562 TCTATTGTGA
* *
39665572 GGTCGCATGTGTAGTACTAAGTGCAGGCTACTATGCATACCCGATAACTTC
1 GGTCGCATGTGTAGTACTAAGTGCAGGCTACTATGCGTACCAGATAACTTC
* ** * * * * *
39665623 GATTACGTGTGTAGTACTAAGTGTAGGCTACTACGTGTACCGGATAA-TT-
1 GGTCGCATGTGTAGTACTAAGTGCAGGCTACTATGCGTACCAGATAACTTC
39665672 GGTCGCATGTGTAGTACTAAGTGCAGGCTACTATGCGTACCAGATA
1 GGTCGCATGTGTAGTACTAAGTGCAGGCTACTATGCGTACCAGATA
39665718 GCTTTGGCTA
Statistics
Matches: 78, Mismatches: 17, Indels: 2
0.80 0.18 0.02
Matches are distributed among these distances:
49 38 0.49
50 2 0.03
51 38 0.49
ACGTcount: A:0.26, C:0.19, G:0.26, T:0.29
Consensus pattern (51 bp):
GGTCGCATGTGTAGTACTAAGTGCAGGCTACTATGCGTACCAGATAACTTC
Done.