Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: chr5
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: 39371879
ACGTcount: A:0.31, C:0.16, G:0.16, T:0.31
Warning! 2227820 characters in sequence are not A, C, G, or T
File 46 of 103
Found at i:17257334 original size:17 final size:17
Alignment explanation
Indices: 17257312--17257347 Score: 63
Period size: 17 Copynumber: 2.1 Consensus size: 17
17257302 AAATATGAAT
17257312 TTATAAAATAAATGGAA
1 TTATAAAATAAATGGAA
*
17257329 TTATAAAATAAATTGAA
1 TTATAAAATAAATGGAA
17257346 TT
1 TT
17257348 TTTTATAAAT
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
17 18 1.00
ACGTcount: A:0.56, C:0.00, G:0.08, T:0.36
Consensus pattern (17 bp):
TTATAAAATAAATGGAA
Found at i:17258808 original size:24 final size:25
Alignment explanation
Indices: 17258780--17258828 Score: 73
Period size: 24 Copynumber: 2.0 Consensus size: 25
17258770 CTTTTTCCAT
17258780 TTTCTTTTCCTTCCTT-TCTTTTCA
1 TTTCTTTTCCTTCCTTATCTTTTCA
*
17258804 TTTCTTTTCTTTCCTTACTCTTTTC
1 TTTCTTTTCCTTCCTTA-TCTTTTC
17258829 TTCTCCTAAC
Statistics
Matches: 22, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
24 15 0.68
26 7 0.32
ACGTcount: A:0.04, C:0.29, G:0.00, T:0.67
Consensus pattern (25 bp):
TTTCTTTTCCTTCCTTATCTTTTCA
Found at i:17258810 original size:14 final size:15
Alignment explanation
Indices: 17258774--17258815 Score: 50
Period size: 14 Copynumber: 2.8 Consensus size: 15
17258764 ATCAAGCTTT
*
17258774 TTCCATTTTCTTTTCC
1 TTCC-TTTTCTTTTCA
17258790 TTCC-TTTCTTTTCA
1 TTCCTTTTCTTTTCA
*
17258804 TTTCTTTTCTTT
1 TTCCTTTTCTTT
17258816 CCTTACTCTT
Statistics
Matches: 23, Mismatches: 2, Indels: 3
0.82 0.07 0.11
Matches are distributed among these distances:
14 12 0.52
15 7 0.30
16 4 0.17
ACGTcount: A:0.05, C:0.26, G:0.00, T:0.69
Consensus pattern (15 bp):
TTCCTTTTCTTTTCA
Found at i:17259431 original size:53 final size:54
Alignment explanation
Indices: 17259349--17259452 Score: 147
Period size: 53 Copynumber: 1.9 Consensus size: 54
17259339 TGATGACAGG
* *
17259349 TGATTCCAGCTATGTGCAATGTGAGAGTGCACATGAGTTGATGACTTGTGGGTGA
1 TGATTCCAGC-ATGTGCAATGTGAGAGTGCACATGAGCTGATGACTGGTGGGTGA
** *
17259404 TGATTCCAGC-TGTGCGGTGTGGGAGTGCACATGAGCTGATGACTGGTGG
1 TGATTCCAGCATGTGCAATGTGAGAGTGCACATGAGCTGATGACTGGTGG
17259453 TTGTATACAT
Statistics
Matches: 44, Mismatches: 5, Indels: 2
0.86 0.10 0.04
Matches are distributed among these distances:
53 34 0.77
55 10 0.23
ACGTcount: A:0.20, C:0.14, G:0.37, T:0.29
Consensus pattern (54 bp):
TGATTCCAGCATGTGCAATGTGAGAGTGCACATGAGCTGATGACTGGTGGGTGA
Found at i:17262635 original size:17 final size:17
Alignment explanation
Indices: 17262613--17262646 Score: 52
Period size: 17 Copynumber: 2.0 Consensus size: 17
17262603 GTTCTTGATA
17262613 AAATAA-AACTCCTTATT
1 AAATAATAACT-CTTATT
17262630 AAATAATAACTCTTATT
1 AAATAATAACTCTTATT
17262647 TTATTCTTAT
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
17 12 0.75
18 4 0.25
ACGTcount: A:0.47, C:0.15, G:0.00, T:0.38
Consensus pattern (17 bp):
AAATAATAACTCTTATT
Found at i:17262852 original size:28 final size:28
Alignment explanation
Indices: 17262821--17262961 Score: 183
Period size: 29 Copynumber: 4.9 Consensus size: 28
17262811 AAATATTTTA
* *
17262821 TCTTGTCTAAATTGAGACAAATATGTTT
1 TCTTGTCTAAATTAAGACAAACATGTTT
* * *
17262849 TCTTGACTAAATTAAGACAAAAAATATTT
1 TCTTGTCTAAATTAAGAC-AAACATGTTT
* *
17262878 TCTTGTCTTAAATTAAGGCAAACATATTT
1 TCTTGTC-TAAATTAAGACAAACATGTTT
*
17262907 TCTTGTCTAAATTAAGACCGAACATGTTT
1 TCTTGTCTAAATTAAGA-CAAACATGTTT
17262936 TCTTGTCTAAATTAAGACAAACATGT
1 TCTTGTCTAAATTAAGACAAACATGT
17262962 CAAAGCTGCC
Statistics
Matches: 99, Mismatches: 11, Indels: 6
0.85 0.09 0.05
Matches are distributed among these distances:
28 33 0.33
29 56 0.57
30 10 0.10
ACGTcount: A:0.37, C:0.13, G:0.11, T:0.38
Consensus pattern (28 bp):
TCTTGTCTAAATTAAGACAAACATGTTT
Found at i:17262904 original size:29 final size:28
Alignment explanation
Indices: 17262788--17262959 Score: 182
Period size: 29 Copynumber: 5.9 Consensus size: 28
17262778 TTAAGACAAC
* *
17262788 TCTTGTCTGTAATTAAGACAAAAAAATATTTT
1 TCTTGTCT-AAATTAAGAC--AAACATA-TTT
* * *
17262820 ATCTTGTCTAAATTGAGACAAATATGTTT
1 -TCTTGTCTAAATTAAGACAAACATATTT
* *
17262849 TCTTGACTAAATTAAGACAAAAAATATTT
1 TCTTGTCTAAATTAAGAC-AAACATATTT
*
17262878 TCTTGTCTTAAATTAAGGCAAACATATTT
1 TCTTGTC-TAAATTAAGACAAACATATTT
* *
17262907 TCTTGTCTAAATTAAGACCGAACATGTTT
1 TCTTGTCTAAATTAAGA-CAAACATATTT
17262936 TCTTGTCTAAATTAAGACAAACAT
1 TCTTGTCTAAATTAAGACAAACAT
17262960 GTCAAAGCTG
Statistics
Matches: 121, Mismatches: 15, Indels: 11
0.82 0.10 0.07
Matches are distributed among these distances:
28 31 0.26
29 59 0.49
30 15 0.12
32 8 0.07
33 8 0.07
ACGTcount: A:0.38, C:0.13, G:0.10, T:0.38
Consensus pattern (28 bp):
TCTTGTCTAAATTAAGACAAACATATTT
Found at i:17262908 original size:58 final size:57
Alignment explanation
Indices: 17262798--17262959 Score: 207
Period size: 58 Copynumber: 2.8 Consensus size: 57
17262788 TCTTGTCTGT
* * *
17262798 AATTAAGACAAAAAAATATTTTATCTTGTCTAAATTGAGACAAATATGTTTTCTTGACTA
1 AATTAAGAC-AAAAAATA-TTT-TCTTGTCTAAATTAAGACAAACATATTTTCTTGACTA
* *
17262858 AATTAAGACAAAAAATATTTTCTTGTCTTAAATTAAGGCAAACATATTTTCTTGTCTA
1 AATTAAGACAAAAAATATTTTCTTGTC-TAAATTAAGACAAACATATTTTCTTGACTA
** * *
17262916 AATTAAGACCGAACATGTTTTCTTGTCTAAATTAAGACAAACAT
1 AATTAAGACAAAAAATATTTTCTTGTCTAAATTAAGACAAACAT
17262960 GTCAAAGCTG
Statistics
Matches: 91, Mismatches: 10, Indels: 5
0.86 0.09 0.05
Matches are distributed among these distances:
57 23 0.25
58 51 0.56
59 8 0.09
60 9 0.10
ACGTcount: A:0.41, C:0.12, G:0.10, T:0.37
Consensus pattern (57 bp):
AATTAAGACAAAAAATATTTTCTTGTCTAAATTAAGACAAACATATTTTCTTGACTA
Found at i:17282596 original size:4 final size:4
Alignment explanation
Indices: 17282587--17282641 Score: 110
Period size: 4 Copynumber: 13.8 Consensus size: 4
17282577 TATGTGTCAG
17282587 TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA
1 TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA
17282635 TGTA TGT
1 TGTA TGT
17282642 GTGTGTGTGT
Statistics
Matches: 51, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 51 1.00
ACGTcount: A:0.24, C:0.00, G:0.25, T:0.51
Consensus pattern (4 bp):
TGTA
Found at i:17282646 original size:2 final size:2
Alignment explanation
Indices: 17282639--17282675 Score: 74
Period size: 2 Copynumber: 18.5 Consensus size: 2
17282629 TATGTATGTA
17282639 TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG T
1 TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG T
17282676 AAGGAGGGGA
Statistics
Matches: 35, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 35 1.00
ACGTcount: A:0.00, C:0.00, G:0.49, T:0.51
Consensus pattern (2 bp):
TG
Found at i:17293034 original size:19 final size:19
Alignment explanation
Indices: 17293010--17293047 Score: 67
Period size: 19 Copynumber: 2.0 Consensus size: 19
17293000 CTACCAAACC
*
17293010 CTCAAATTATACTCCAATA
1 CTCAAATCATACTCCAATA
17293029 CTCAAATCATACTCCAATA
1 CTCAAATCATACTCCAATA
17293048 AGTTAAATGG
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
19 18 1.00
ACGTcount: A:0.42, C:0.29, G:0.00, T:0.29
Consensus pattern (19 bp):
CTCAAATCATACTCCAATA
Found at i:17296088 original size:74 final size:74
Alignment explanation
Indices: 17295967--17296116 Score: 228
Period size: 74 Copynumber: 2.0 Consensus size: 74
17295957 AAGTAAAGTA
* * *
17295967 GATTGCGAGACAAAGAAGGCTTAATCGACTAAGAAGTATGGTAAGCCAGCTAAAAGCTCACTATT
1 GATTGCGAGACAAAGAAGACTTAATCGACTAAGAAGTATGGTAAGCCAACTAAAAGCACACTATT
17296032 AGAGAATTT
66 AGAGAATTT
* * * *
17296041 GATTGTGAGACAGAGAAGACTTAATCGACTAAGAAGTATGGTTAGCCAACTAAAAGCACACTGTT
1 GATTGCGAGACAAAGAAGACTTAATCGACTAAGAAGTATGGTAAGCCAACTAAAAGCACACTATT
*
17296106 TGAGAATTT
66 AGAGAATTT
17296115 GA
1 GA
17296117 ATTTAAATGT
Statistics
Matches: 68, Mismatches: 8, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
74 68 1.00
ACGTcount: A:0.39, C:0.14, G:0.23, T:0.24
Consensus pattern (74 bp):
GATTGCGAGACAAAGAAGACTTAATCGACTAAGAAGTATGGTAAGCCAACTAAAAGCACACTATT
AGAGAATTT
Found at i:17301267 original size:21 final size:21
Alignment explanation
Indices: 17301242--17301285 Score: 88
Period size: 21 Copynumber: 2.1 Consensus size: 21
17301232 AGTTTCTCTT
17301242 CTCTTCTGGTTTGGCTGACCA
1 CTCTTCTGGTTTGGCTGACCA
17301263 CTCTTCTGGTTTGGCTGACCA
1 CTCTTCTGGTTTGGCTGACCA
17301284 CT
1 CT
17301286 ATGGGAGAAA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 23 1.00
ACGTcount: A:0.09, C:0.30, G:0.23, T:0.39
Consensus pattern (21 bp):
CTCTTCTGGTTTGGCTGACCA
Found at i:17306537 original size:109 final size:108
Alignment explanation
Indices: 17306416--17306632 Score: 425
Period size: 109 Copynumber: 2.0 Consensus size: 108
17306406 CCTTAATTAA
17306416 AGGAAATTTTTTAATGATAAAAGACTTGCCTTTATTTGTTTTTACTTCCATAATTCTTGAAATCA
1 AGGAAATTTTTTAATGATAAAAGACTTGCCTTTATTTGTTTTTACTTCCATAATTCTTGAAATCA
17306481 AATTCCTTAATTTATGGTGTCTACAAATAAATTTTCTAACATC
66 AATTCCTTAATTTATGGTGTCTACAAATAAATTTTCTAACATC
17306524 NAGGAAATTTTTTAATGATAAAAGACTTGCCTTTATTTGTTTTTACTTCCATAATTCTTGAAATC
1 -AGGAAATTTTTTAATGATAAAAGACTTGCCTTTATTTGTTTTTACTTCCATAATTCTTGAAATC
17306589 AAATTCCTTAATTTATGGTGTCTACAAATAAATTTTCTAACATC
65 AAATTCCTTAATTTATGGTGTCTACAAATAAATTTTCTAACATC
17306633 TTTGAATTAA
Statistics
Matches: 108, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
109 108 1.00
ACGTcount: A:0.33, C:0.14, G:0.09, T:0.43
Consensus pattern (108 bp):
AGGAAATTTTTTAATGATAAAAGACTTGCCTTTATTTGTTTTTACTTCCATAATTCTTGAAATCA
AATTCCTTAATTTATGGTGTCTACAAATAAATTTTCTAACATC
Found at i:17310514 original size:43 final size:42
Alignment explanation
Indices: 17310349--17310520 Score: 238
Period size: 42 Copynumber: 4.1 Consensus size: 42
17310339 TGTGATAATT
*
17310349 ATGACCCAGCTATGTGCGTGTGGGAGTGCACATGAGCTGATG
1 ATGACCCAACTATGTGCGTGTGGGAGTGCACATGAGCTGATG
* * * *
17310391 ATGACCTAGCTATGTGCGTGTGGGAGTGCACATAAGTTGATG
1 ATGACCCAACTATGTGCGTGTGGGAGTGCACATGAGCTGATG
*
17310433 ATGACCCAACTATATGCG-GTGTGGAGTGCACATGAGCTGATG
1 ATGACCCAACTATGTGCGTGTG-GGAGTGCACATGAGCTGATG
* * *
17310475 ATAACCCAACTATGTGTGAGTGGGGAGTGCACATGAGCTGATG
1 ATGACCCAACTATGTGCGTGT-GGGAGTGCACATGAGCTGATG
17310518 ATG
1 ATG
17310521 GTGGGATGGT
Statistics
Matches: 115, Mismatches: 12, Indels: 5
0.87 0.09 0.04
Matches are distributed among these distances:
41 3 0.03
42 87 0.76
43 24 0.21
44 1 0.01
ACGTcount: A:0.25, C:0.17, G:0.33, T:0.25
Consensus pattern (42 bp):
ATGACCCAACTATGTGCGTGTGGGAGTGCACATGAGCTGATG
Found at i:17310553 original size:2 final size:2
Alignment explanation
Indices: 17310546--17310572 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
17310536 TGATGATGTG
17310546 TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA T
17310573 GTGTGTGTGT
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 25 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:17310577 original size:2 final size:2
Alignment explanation
Indices: 17310572--17310596 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
17310562 TATATATATA
17310572 TG TG TG TG TG TG TG TG TG TG TG TG T
1 TG TG TG TG TG TG TG TG TG TG TG TG T
17310597 TATAGAAAGT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.00, C:0.00, G:0.48, T:0.52
Consensus pattern (2 bp):
TG
Found at i:17316730 original size:21 final size:21
Alignment explanation
Indices: 17316682--17316723 Score: 75
Period size: 21 Copynumber: 2.0 Consensus size: 21
17316672 CTAACAATTG
*
17316682 ACTAACGGCTGAACCTACATT
1 ACTAACGGCAGAACCTACATT
17316703 ACTAACGGCAGAACCTACATT
1 ACTAACGGCAGAACCTACATT
17316724 TGCAACGAAA
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
21 20 1.00
ACGTcount: A:0.36, C:0.29, G:0.14, T:0.21
Consensus pattern (21 bp):
ACTAACGGCAGAACCTACATT
Found at i:17317870 original size:35 final size:36
Alignment explanation
Indices: 17317823--17317893 Score: 92
Period size: 35 Copynumber: 2.0 Consensus size: 36
17317813 ACAATGTTTC
*
17317823 TTCACAAGAGCAAATGGAACCC-T-CAACAGCTTTTT
1 TTCACAAGAGCAAACGGAACCCTTACAA-AGCTTTTT
* *
17317858 TTCATAAGAGCAAGCGGAACCCTTACAAAGCTTTTT
1 TTCACAAGAGCAAACGGAACCCTTACAAAGCTTTTT
17317894 CACGAGAGCA
Statistics
Matches: 31, Mismatches: 3, Indels: 3
0.84 0.08 0.08
Matches are distributed among these distances:
35 19 0.61
36 9 0.29
37 3 0.10
ACGTcount: A:0.34, C:0.24, G:0.15, T:0.27
Consensus pattern (36 bp):
TTCACAAGAGCAAACGGAACCCTTACAAAGCTTTTT
Found at i:17329839 original size:6 final size:6
Alignment explanation
Indices: 17329818--17329859 Score: 59
Period size: 6 Copynumber: 6.8 Consensus size: 6
17329808 GCCTTCCTAC
17329818 CTTTTCT CTCTTTT CTTTTT CTTTTT C-TTTT CTTTTT CTTTT
1 CTTTT-T CT-TTTT CTTTTT CTTTTT CTTTTT CTTTTT CTTTT
17329860 CTTCCTCTCA
Statistics
Matches: 33, Mismatches: 0, Indels: 5
0.87 0.00 0.13
Matches are distributed among these distances:
5 5 0.15
6 20 0.61
7 5 0.15
8 3 0.09
ACGTcount: A:0.00, C:0.21, G:0.00, T:0.79
Consensus pattern (6 bp):
CTTTTT
Found at i:17329842 original size:11 final size:11
Alignment explanation
Indices: 17329828--17329862 Score: 61
Period size: 11 Copynumber: 3.1 Consensus size: 11
17329818 CTTTTCTCTC
17329828 TTTTCTTTTTCT
1 TTTTC-TTTTCT
17329840 TTTTCTTTTCT
1 TTTTCTTTTCT
17329851 TTTTCTTTTCT
1 TTTTCTTTTCT
17329862 T
1 T
17329863 CCTCTCAGTT
Statistics
Matches: 23, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
11 18 0.78
12 5 0.22
ACGTcount: A:0.00, C:0.17, G:0.00, T:0.83
Consensus pattern (11 bp):
TTTTCTTTTCT
Found at i:17329848 original size:17 final size:17
Alignment explanation
Indices: 17329826--17329859 Score: 68
Period size: 17 Copynumber: 2.0 Consensus size: 17
17329816 ACCTTTTCTC
17329826 TCTTTTCTTTTTCTTTT
1 TCTTTTCTTTTTCTTTT
17329843 TCTTTTCTTTTTCTTTT
1 TCTTTTCTTTTTCTTTT
17329860 CTTCCTCTCA
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 17 1.00
ACGTcount: A:0.00, C:0.18, G:0.00, T:0.82
Consensus pattern (17 bp):
TCTTTTCTTTTTCTTTT
Found at i:17339801 original size:7 final size:7
Alignment explanation
Indices: 17339791--17339822 Score: 64
Period size: 7 Copynumber: 4.6 Consensus size: 7
17339781 AATTAACAAT
17339791 TTCAACA
1 TTCAACA
17339798 TTCAACA
1 TTCAACA
17339805 TTCAACA
1 TTCAACA
17339812 TTCAACA
1 TTCAACA
17339819 TTCA
1 TTCA
17339823 TTGCAATCAC
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 25 1.00
ACGTcount: A:0.41, C:0.28, G:0.00, T:0.31
Consensus pattern (7 bp):
TTCAACA
Found at i:17340037 original size:33 final size:33
Alignment explanation
Indices: 17340000--17340065 Score: 132
Period size: 33 Copynumber: 2.0 Consensus size: 33
17339990 AAATTTTTGA
17340000 AATAAAATAATATTAAAATATTAATATTTTATT
1 AATAAAATAATATTAAAATATTAATATTTTATT
17340033 AATAAAATAATATTAAAATATTAATATTTTATT
1 AATAAAATAATATTAAAATATTAATATTTTATT
17340066 CAGTGTCAAA
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
33 33 1.00
ACGTcount: A:0.55, C:0.00, G:0.00, T:0.45
Consensus pattern (33 bp):
AATAAAATAATATTAAAATATTAATATTTTATT
Found at i:17344594 original size:35 final size:35
Alignment explanation
Indices: 17344512--17344716 Score: 204
Period size: 35 Copynumber: 5.9 Consensus size: 35
17344502 TTAAAGGAGT
* **
17344512 AAAGAGAGAGGCTTTGTGCTGTAAATTTTG-GAAAGAA
1 AAAGAGAGA-G-TTT-TGCTGCAAATTTTGAGAGGGAA
* * *
17344549 ATAGAAAGAGTTGTGCTGCAAATTTTGAGAGGGAA
1 AAAGAGAGAGTTTTGCTGCAAATTTTGAGAGGGAA
* *
17344584 ATAGAGAGAGTTTTGCTGCAAATTTTGAGAGGAAA
1 AAAGAGAGAGTTTTGCTGCAAATTTTGAGAGGGAA
* *
17344619 AAAGAGAGAGTTTTGTTGCAAATTTTGAGAGGAAAA
1 AAAGAGAGAGTTTTGCTGCAAATTTTGAGAGG-GAA
* * *
17344655 AAAAAGAGAG-TTTGCTGCAACTTTTGA-AAGG-A
1 AAAGAGAGAGTTTTGCTGCAAATTTTGAGAGGGAA
* *
17344687 GAAGAAAGAGTTTTGCTGCAAA-TTTGAGAG
1 AAAGAGAGAGTTTTGCTGCAAATTTTGAGAG
17344717 AGCAAACAAG
Statistics
Matches: 143, Mismatches: 21, Indels: 12
0.81 0.12 0.07
Matches are distributed among these distances:
32 13 0.09
33 11 0.08
34 15 0.10
35 84 0.59
36 13 0.09
37 7 0.05
ACGTcount: A:0.39, C:0.06, G:0.29, T:0.27
Consensus pattern (35 bp):
AAAGAGAGAGTTTTGCTGCAAATTTTGAGAGGGAA
Found at i:17345983 original size:28 final size:28
Alignment explanation
Indices: 17345951--17346005 Score: 76
Period size: 28 Copynumber: 2.0 Consensus size: 28
17345941 TTCGGAGTAA
*
17345951 AAGGGCAAAAT-AGTAATTTTTTCACCCT
1 AAGGGC-AAATCAGTAAATTTTTCACCCT
*
17345979 AAGGGCAAATCGGTAAATTTTTCACCC
1 AAGGGCAAATCAGTAAATTTTTCACCC
17346006 CAGCACTTGT
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
27 4 0.17
28 20 0.83
ACGTcount: A:0.35, C:0.20, G:0.16, T:0.29
Consensus pattern (28 bp):
AAGGGCAAATCAGTAAATTTTTCACCCT
Found at i:17347302 original size:42 final size:42
Alignment explanation
Indices: 17347237--17347317 Score: 144
Period size: 42 Copynumber: 1.9 Consensus size: 42
17347227 GTTGATTTGA
17347237 ACCCGGCTATGTGCGAGTAGGAGTGCACATAAGCCGTTGCTG
1 ACCCGGCTATGTGCGAGTAGGAGTGCACATAAGCCGTTGCTG
* *
17347279 ACCCGGCTATGTGTGAGTGGGAGTGCACATAAGCCGTTG
1 ACCCGGCTATGTGCGAGTAGGAGTGCACATAAGCCGTTG
17347318 TTGCCTCCAT
Statistics
Matches: 37, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
42 37 1.00
ACGTcount: A:0.21, C:0.22, G:0.35, T:0.22
Consensus pattern (42 bp):
ACCCGGCTATGTGCGAGTAGGAGTGCACATAAGCCGTTGCTG
Found at i:17347613 original size:26 final size:26
Alignment explanation
Indices: 17347552--17347613 Score: 97
Period size: 26 Copynumber: 2.4 Consensus size: 26
17347542 TTGCATATGA
*
17347552 GATGATGATAATGGGATGATGTGCAT
1 GATGATGATGATGGGATGATGTGCAT
*
17347578 GATGATGATGATGGGATGGTGTGCAT
1 GATGATGATGATGGGATGATGTGCAT
*
17347604 GTTGATGATG
1 GATGATGATG
17347614 GGTATATGGT
Statistics
Matches: 33, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
26 33 1.00
ACGTcount: A:0.26, C:0.03, G:0.39, T:0.32
Consensus pattern (26 bp):
GATGATGATGATGGGATGATGTGCAT
Found at i:17348729 original size:42 final size:42
Alignment explanation
Indices: 17348670--17348780 Score: 179
Period size: 42 Copynumber: 2.6 Consensus size: 42
17348660 TGTTGGTGTG
* *
17348670 GACCCGGCTATGTGCGAGTAGGAGTGTGCATAAGCCGATGAT
1 GACCCGACTATGTGCGAGTAGGAGTGCGCATAAGCCGATGAT
*
17348712 GACCCGACTATGCGCGAGTAGGAGTGCGCATAAGCCGATGAT
1 GACCCGACTATGTGCGAGTAGGAGTGCGCATAAGCCGATGAT
17348754 GACCC-AGCTATGTGCGAGTAGGAGTGC
1 GACCCGA-CTATGTGCGAGTAGGAGTGC
17348781 ACATGAGCTA
Statistics
Matches: 64, Mismatches: 4, Indels: 2
0.91 0.06 0.03
Matches are distributed among these distances:
41 1 0.02
42 63 0.98
ACGTcount: A:0.24, C:0.22, G:0.35, T:0.19
Consensus pattern (42 bp):
GACCCGACTATGTGCGAGTAGGAGTGCGCATAAGCCGATGAT
Found at i:17349787 original size:55 final size:55
Alignment explanation
Indices: 17349703--17349892 Score: 277
Period size: 55 Copynumber: 3.6 Consensus size: 55
17349693 GGCTGTGACA
17349703 CATCAGCTCATGTGCACTCCCACACCGCACATAGTTGGAATCATCATCCACCAGT
1 CATCAGCTCATGTGCACTCCCACACCGCACATAGTTGGAATCATCATCCACCAGT
*
17349758 CATCAGCTCATGTGCACTCCCACACCGCACATAGCTGGAATCATCATCCACC-GAT
1 CATCAGCTCATGTGCACTCCCACACCGCACATAGTTGGAATCATCATCCACCAG-T
* *
17349813 CATCAGCTTATGTGCACTCCCACACCGCACATAGTTGGAATCA-C--CCATCA-T
1 CATCAGCTCATGTGCACTCCCACACCGCACATAGTTGGAATCATCATCCACCAGT
* *
17349864 CACCAG--CATGTGCACTCCCATACCGCACA
1 CATCAGCTCATGTGCACTCCCACACCGCACA
17349893 CGCGCGGTTA
Statistics
Matches: 126, Mismatches: 7, Indels: 10
0.88 0.05 0.07
Matches are distributed among these distances:
49 21 0.17
51 6 0.05
52 4 0.03
54 2 0.02
55 93 0.74
ACGTcount: A:0.27, C:0.38, G:0.14, T:0.21
Consensus pattern (55 bp):
CATCAGCTCATGTGCACTCCCACACCGCACATAGTTGGAATCATCATCCACCAGT
Found at i:17355687 original size:28 final size:30
Alignment explanation
Indices: 17355633--17355692 Score: 79
Period size: 28 Copynumber: 2.1 Consensus size: 30
17355623 TTTTTTAAAT
*
17355633 TTACACTTTTACCCCTATAAAAGTGAAAAA
1 TTACACTTTTACCCCTATAAAACTGAAAAA
* *
17355663 TTACATTTTTGCCCC-A-AAAACTGAAAAA
1 TTACACTTTTACCCCTATAAAACTGAAAAA
17355691 TT
1 TT
17355693 GTCCATAGAC
Statistics
Matches: 27, Mismatches: 3, Indels: 2
0.84 0.09 0.06
Matches are distributed among these distances:
28 13 0.48
29 1 0.04
30 13 0.48
ACGTcount: A:0.42, C:0.20, G:0.07, T:0.32
Consensus pattern (30 bp):
TTACACTTTTACCCCTATAAAACTGAAAAA
Found at i:17361752 original size:28 final size:28
Alignment explanation
Indices: 17361693--17361752 Score: 68
Period size: 28 Copynumber: 2.1 Consensus size: 28
17361683 TGGGTGGTGC
* * *
17361693 AAAATTACAATTTTGCCCTTAAGGTGGC
1 AAAATGACAATTTTGCCCTTAAGGTCGA
*
17361721 AAAATGACTATTTTGCCCTT-AGGCTCGA
1 AAAATGACAATTTTGCCCTTAAGG-TCGA
17361749 AAAA
1 AAAA
17361753 ATGCCGAAAT
Statistics
Matches: 27, Mismatches: 4, Indels: 2
0.82 0.12 0.06
Matches are distributed among these distances:
27 3 0.11
28 24 0.89
ACGTcount: A:0.35, C:0.18, G:0.17, T:0.30
Consensus pattern (28 bp):
AAAATGACAATTTTGCCCTTAAGGTCGA
Found at i:17363181 original size:34 final size:34
Alignment explanation
Indices: 17363138--17363293 Score: 127
Period size: 34 Copynumber: 4.6 Consensus size: 34
17363128 AATGCTTTTT
* *
17363138 AAAGCTCAAGCATAACCTTTACAATGCC-ATTTC
1 AAAGATCAAGCACAACCTTTACAATGCCTATTTC
* * * *
17363171 ACAAGATCAAGGACAAACTTTATAATGCCTTTTTC
1 A-AAGATCAAGCACAACCTTTACAATGCCTATTTC
* * * * *
17363206 AAGGATCAAGCACAACCTTCACAATGCTTTTTTT
1 AAAGATCAAGCACAACCTTTACAATGCCTATTTC
* * * * *
17363240 TAAGAATTAA-CACAGCCTTCACAATGCCTTTTTC
1 AAAG-ATCAAGCACAACCTTTACAATGCCTATTTC
*
17363274 AAGGATCAAGCACAACCTTT
1 AAAGATCAAGCACAACCTTT
17363294 TTTCTCTTAC
Statistics
Matches: 95, Mismatches: 24, Indels: 7
0.75 0.19 0.06
Matches are distributed among these distances:
33 5 0.05
34 81 0.85
35 9 0.09
ACGTcount: A:0.35, C:0.24, G:0.11, T:0.29
Consensus pattern (34 bp):
AAAGATCAAGCACAACCTTTACAATGCCTATTTC
Found at i:17370066 original size:67 final size:67
Alignment explanation
Indices: 17369958--17370086 Score: 204
Period size: 67 Copynumber: 1.9 Consensus size: 67
17369948 GATGTAGCTG
* * * *
17369958 AATCAAAGAATTTAAGCTTAGACAAGGATGCTCTGTTTTGAGAGTTTGTTTTAGAATGAGAATGT
1 AATCAAAGAATTTAAGCTTAAACAAGGATGCTCTATTTTGAGAGCTTATTTTAGAATGAGAATGT
17370023 TA
66 TA
* *
17370025 AATCAAAGAATTTATGCTTAAACAAGGATGCTCTATTTTGAGAGCTTATTTTAGAGTGAGAA
1 AATCAAAGAATTTAAGCTTAAACAAGGATGCTCTATTTTGAGAGCTTATTTTAGAATGAGAA
17370087 AGGAATAAAC
Statistics
Matches: 56, Mismatches: 6, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
67 56 1.00
ACGTcount: A:0.36, C:0.09, G:0.21, T:0.35
Consensus pattern (67 bp):
AATCAAAGAATTTAAGCTTAAACAAGGATGCTCTATTTTGAGAGCTTATTTTAGAATGAGAATGT
TA
Found at i:17372159 original size:26 final size:26
Alignment explanation
Indices: 17372129--17372181 Score: 106
Period size: 26 Copynumber: 2.0 Consensus size: 26
17372119 ATGTTAATCT
17372129 CTAGATAGAAAGTGATTTTATGAATG
1 CTAGATAGAAAGTGATTTTATGAATG
17372155 CTAGATAGAAAGTGATTTTATGAATG
1 CTAGATAGAAAGTGATTTTATGAATG
17372181 C
1 C
17372182 AGTTAAATGG
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
26 27 1.00
ACGTcount: A:0.38, C:0.06, G:0.23, T:0.34
Consensus pattern (26 bp):
CTAGATAGAAAGTGATTTTATGAATG
Found at i:17374342 original size:2 final size:2
Alignment explanation
Indices: 17374337--17374373 Score: 74
Period size: 2 Copynumber: 18.5 Consensus size: 2
17374327 TTATAGTGTG
17374337 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
17374374 CTAAAGAGAA
Statistics
Matches: 35, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 35 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:17374550 original size:35 final size:34
Alignment explanation
Indices: 17374480--17374553 Score: 87
Period size: 35 Copynumber: 2.1 Consensus size: 34
17374470 TGTAATGTTG
* * *
17374480 TTTAAGTTGTTGTTTAGATATTTATTTTTAGTTA
1 TTTAAGTTGATATTTAGATATTTATTTTGAGTTA
*
17374514 TTTAAGTTGATATTTGAGATATTTGTTGTTGA-TTA
1 TTTAAGTTGATATTT-AGATATTTATT-TTGAGTTA
17374549 TTTAA
1 TTTAA
17374554 ATTTAAATTT
Statistics
Matches: 34, Mismatches: 4, Indels: 3
0.83 0.10 0.07
Matches are distributed among these distances:
34 13 0.38
35 18 0.53
36 3 0.09
ACGTcount: A:0.26, C:0.00, G:0.16, T:0.58
Consensus pattern (34 bp):
TTTAAGTTGATATTTAGATATTTATTTTGAGTTA
Found at i:17381472 original size:93 final size:90
Alignment explanation
Indices: 17381294--17381472 Score: 232
Period size: 93 Copynumber: 2.0 Consensus size: 90
17381284 CCAATTCTGT
* * * *
17381294 AACAATTCTATCGATACATGCAATTTTATCAATACCTTTGGTAATGCATTGATACATTCCACACA
1 AACAATTCTATCGATACATGCAAATCTATCAATACCCTTGGTAATGCATCGATACATTCCACACA
* *
17381359 GAGTGCCTTTTATAGTATTCTAGAA
66 GAGTGCCTCTTATAGCATTCTAGAA
* * * *
17381384 AACAATTTTATCGATACATGCAAGGAATCTATCGATACCCTTGGTAATGTATCGATATATTCCAC
1 AACAATTCTATCGATACATGC-A--AATCTATCAATACCCTTGGTAATGCATCGATACATTCCAC
*
17381449 ACAGAGTGCCTCTTGTAGCATTCT
63 ACAGAGTGCCTCTTATAGCATTCT
17381473 GTTGAAAATG
Statistics
Matches: 75, Mismatches: 11, Indels: 3
0.84 0.12 0.03
Matches are distributed among these distances:
90 20 0.27
91 1 0.01
93 54 0.72
ACGTcount: A:0.32, C:0.20, G:0.14, T:0.34
Consensus pattern (90 bp):
AACAATTCTATCGATACATGCAAATCTATCAATACCCTTGGTAATGCATCGATACATTCCACACA
GAGTGCCTCTTATAGCATTCTAGAA
Found at i:17385830 original size:2 final size:2
Alignment explanation
Indices: 17385823--17385848 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
17385813 AACGTTTTAC
17385823 AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT
17385849 TCTGCACAAA
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 24 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:17387116 original size:12 final size:14
Alignment explanation
Indices: 17387085--17387114 Score: 53
Period size: 13 Copynumber: 2.2 Consensus size: 14
17387075 GCTTTCCTTC
17387085 CTTTCTCTCTTTTT
1 CTTTCTCTCTTTTT
17387099 CTTTCTCT-TTTTT
1 CTTTCTCTCTTTTT
17387112 CTT
1 CTT
17387115 CTTCTCGGGT
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
13 8 0.50
14 8 0.50
ACGTcount: A:0.00, C:0.27, G:0.00, T:0.73
Consensus pattern (14 bp):
CTTTCTCTCTTTTT
Found at i:17388047 original size:504 final size:503
Alignment explanation
Indices: 17387355--17388375 Score: 1751
Period size: 504 Copynumber: 2.0 Consensus size: 503
17387345 TGGTCAATTA
* * * * *
17387355 TCTATCCTTACTTGCTTTCCCATTCGCCACCTTCACTATCCCTTTCTTTCTTCCTTTATCATTTA
1 TCTAT-CTTTCTTACTTTCCCATCCACCACCTTCACTATCCCTCTCTTTCTTCCTTTATCATTTA
*
17387420 TTTCATGCACCACCTTATTCATCCGATCACATTTCATGCACAAGCTTCACTTTATATTTTATTTT
65 TTTCATGCACCACCTTATTCATCCGATCACATTTCATGCACAAGCTTCACTTTATATTTTATTTG
*
17387485 GTCATTTATTAAACCATTCAAGTCTCATGCATCCATATTTTTCTTTCCTCATTTGGCCACCTAAT
130 GTCATTTATTAAACCATTCAAGTCTCATGCATCCATATTTTCCTTTCCTCATTTGGCCACCTAAT
17387550 GCACCAATCTCTTTACATGCAAATAGATTTAGGCCTATCCTTTCTTTTACTTCACATGGTGGGGG
195 GCACCAATCTCTTTACATGCAAATAGATTTAGGCCTATCCTTTCTTTTACTTCACATGGTGGGGG
*
17387615 TCCCACATGTTCCCCACTAATTTCCTCCTTTTTACATGCTAGTATTTACATGTAATAGTGATTTA
260 TCCCACATGTTCCCCACTAACTTCCTCCTTTTTACATGCTAGTATTTACATGTAATAGTGATTTA
* * *
17387680 CATGCACATTTCATTATCTCATATAATTTAACTTTCCTTGGTTAGTTAA-TTTTCTATTTAGCTT
325 CATACACATTTCATTATCCCATATAATCTAAC-TTCCTTGGTTAGTTAATTTTTC-ATTTAGCTT
**
17387744 CAAATATTGTAATTGCACATAAGTCCTCGACTTTTCCTTATTTACCATTCGACCCTCTTTACTTT
388 CAAATATTGTAATTGCACATAAGTCCTCGACTTTTCCTTATTTACCATTCGACCCTCCATACTTT
17387809 TCATCCTTTGCAATTA-AGTCTTTCAATCATTTCTTTGATTCCAAATTTCCT
453 TCATCCTTTGCAATTAGA-TCTTTCAATCATTTCTTTGATTCCAAATTTCCT
*
17387860 TCTATCTTTCTTACTTTCCCATCCACCACCTTCACTATCCCATCT-TTTCTTCCTTTATTATTTA
1 TCTATCTTTCTTACTTTCCCATCCACCACCTTCACTATCCC-TCTCTTTCTTCCTTTATCATTTA
* * *
17387924 TTTCATGCACCACCTTATTCTTCTGATCGCATTTCATGCACAAGCTTCACTTTATATTTTATTTG
65 TTTCATGCACCACCTTATTCATCCGATCACATTTCATGCACAAGCTTCACTTTATATTTTATTTG
* *
17387989 GTCATTTATTAAACCATTCAAGTCTCATGCATCTATATTTTCCTTTTCTCATTTGGCCACCTAAT
130 GTCATTTATTAAACCATTCAAGTCTCATGCATCCATATTTTCCTTTCCTCATTTGGCCACCTAAT
*
17388054 GCACCAATCTCTTTACATGCAAATAGATTTAGGCCTATCCTTTCTTTTACTTTACATGGTGGGGG
195 GCACCAATCTCTTTACATGCAAATAGATTTAGGCCTATCCTTTCTTTTACTTCACATGGTGGGGG
* * * * *
17388119 TCCCATATGTTCCCCATTAACTTCTTCCTTTTTACATGTTATTATTTACATGTAATAGTGATTTA
260 TCCCACATGTTCCCCACTAACTTCCTCCTTTTTACATGCTAGTATTTACATGTAATAGTGATTTA
17388184 CATACACATTTCATTATCCCATATAATCTAACTTCCTTGGTTAGTTAATTTTTCATTTAGCTTCA
325 CATACACATTTCATTATCCCATATAATCTAACTTCCTTGGTTAGTTAATTTTTCATTTAGCTTCA
17388249 AATATTGTAATTGCACATAAGTCCTCGACTTTTCCTTATTTACCATTCGACCCTCCATACTTTTC
390 AATATTGTAATTGCACATAAGTCCTCGACTTTTCCTTATTTACCATTCGACCCTCCATACTTTTC
17388314 ATCCTTTGCAATTAGATCTTTCAATCATTTCTTTGATTCCAAATTTCCT
455 ATCCTTTGCAATTAGATCTTTCAATCATTTCTTTGATTCCAAATTTCCT
17388363 TCTATCTTTCTTA
1 TCTATCTTTCTTA
17388376 TTTTACACTT
Statistics
Matches: 488, Mismatches: 25, Indels: 8
0.94 0.05 0.02
Matches are distributed among these distances:
503 150 0.31
504 331 0.68
505 7 0.01
ACGTcount: A:0.23, C:0.25, G:0.08, T:0.44
Consensus pattern (503 bp):
TCTATCTTTCTTACTTTCCCATCCACCACCTTCACTATCCCTCTCTTTCTTCCTTTATCATTTAT
TTCATGCACCACCTTATTCATCCGATCACATTTCATGCACAAGCTTCACTTTATATTTTATTTGG
TCATTTATTAAACCATTCAAGTCTCATGCATCCATATTTTCCTTTCCTCATTTGGCCACCTAATG
CACCAATCTCTTTACATGCAAATAGATTTAGGCCTATCCTTTCTTTTACTTCACATGGTGGGGGT
CCCACATGTTCCCCACTAACTTCCTCCTTTTTACATGCTAGTATTTACATGTAATAGTGATTTAC
ATACACATTTCATTATCCCATATAATCTAACTTCCTTGGTTAGTTAATTTTTCATTTAGCTTCAA
ATATTGTAATTGCACATAAGTCCTCGACTTTTCCTTATTTACCATTCGACCCTCCATACTTTTCA
TCCTTTGCAATTAGATCTTTCAATCATTTCTTTGATTCCAAATTTCCT
Found at i:17389579 original size:21 final size:21
Alignment explanation
Indices: 17389555--17389676 Score: 70
Period size: 21 Copynumber: 5.5 Consensus size: 21
17389545 AGATAGGATA
17389555 TAAATTTAAATTTAATTTATC
1 TAAATTTAAATTTAATTTATC
*
17389576 TAAATTAAAATAAGAATT-ATTTATAC
1 TAAATT----TAA-ATTTAATTTAT-C
* * *
17389602 ATTATATTTAAATTTAATTTGTT
1 --TAAATTTAAATTTAATTTATC
*
17389625 TAAATTTAAA-TAAATATTAAT-
1 TAAATTTAAATTTAAT-TT-ATC
* *
17389646 TACATTTAAATTTAATTTATT
1 TAAATTTAAATTTAATTTATC
17389667 TAAATTTAAA
1 TAAATTTAAA
17389677 AATAATATCC
Statistics
Matches: 77, Mismatches: 11, Indels: 26
0.68 0.10 0.23
Matches are distributed among these distances:
20 6 0.08
21 37 0.48
22 5 0.06
23 3 0.04
24 8 0.10
25 9 0.12
26 4 0.05
28 5 0.06
ACGTcount: A:0.47, C:0.02, G:0.02, T:0.49
Consensus pattern (21 bp):
TAAATTTAAATTTAATTTATC
Found at i:17389612 original size:49 final size:42
Alignment explanation
Indices: 17389565--17389677 Score: 118
Period size: 42 Copynumber: 2.5 Consensus size: 42
17389555 TAAATTTAAA
* *
17389565 TTTAATTTATCTAAATTAAAATAAGAATTATTTATACATTATATTTAAA
1 TTTAATTTATTTAAATTAAAAT-A-AA-TA--T-TA-ATTACATTTAAA
* *
17389614 TTTAATTTGTTTAAATTTAAATAAATATTAATTACATTTAAA
1 TTTAATTTATTTAAATTAAAATAAATATTAATTACATTTAAA
17389656 TTTAATTTATTTAAATTTAAAA
1 TTTAATTTATTTAAA-TTAAAA
17389678 ATAATATCCT
Statistics
Matches: 57, Mismatches: 6, Indels: 8
0.80 0.08 0.11
Matches are distributed among these distances:
42 25 0.44
43 7 0.12
44 1 0.02
46 2 0.04
47 2 0.04
48 1 0.02
49 19 0.33
ACGTcount: A:0.46, C:0.03, G:0.02, T:0.50
Consensus pattern (42 bp):
TTTAATTTATTTAAATTAAAATAAATATTAATTACATTTAAA
Found at i:17389682 original size:21 final size:21
Alignment explanation
Indices: 17389607--17389682 Score: 82
Period size: 21 Copynumber: 3.6 Consensus size: 21
17389597 TATACATTAT
* *
17389607 ATTTAAATTTAATTTGTTTAA
1 ATTTAAATATAATTTATTTAA
* *
17389628 ATTTAAATA-AATATTAATTAC
1 ATTTAAATATAAT-TTATTTAA
*
17389649 ATTTAAATTTAATTTATTTAA
1 ATTTAAATATAATTTATTTAA
*
17389670 ATTTAAAAATAAT
1 ATTTAAATATAAT
17389683 ATCCTATCTC
Statistics
Matches: 44, Mismatches: 9, Indels: 4
0.77 0.16 0.07
Matches are distributed among these distances:
20 3 0.07
21 38 0.86
22 3 0.07
ACGTcount: A:0.47, C:0.01, G:0.01, T:0.50
Consensus pattern (21 bp):
ATTTAAATATAATTTATTTAA
Found at i:17399807 original size:6 final size:6
Alignment explanation
Indices: 17399796--17399826 Score: 62
Period size: 6 Copynumber: 5.2 Consensus size: 6
17399786 TCCAGAACAA
17399796 AATCAG AATCAG AATCAG AATCAG AATCAG A
1 AATCAG AATCAG AATCAG AATCAG AATCAG A
17399827 TGTTGTTTCT
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 25 1.00
ACGTcount: A:0.52, C:0.16, G:0.16, T:0.16
Consensus pattern (6 bp):
AATCAG
Found at i:17400451 original size:15 final size:15
Alignment explanation
Indices: 17400431--17400463 Score: 66
Period size: 15 Copynumber: 2.2 Consensus size: 15
17400421 AGTATCTAGA
17400431 TATTATTAGTATTAT
1 TATTATTAGTATTAT
17400446 TATTATTAGTATTAT
1 TATTATTAGTATTAT
17400461 TAT
1 TAT
17400464 ATCGCTTCCT
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 18 1.00
ACGTcount: A:0.33, C:0.00, G:0.06, T:0.61
Consensus pattern (15 bp):
TATTATTAGTATTAT
Found at i:17401318 original size:18 final size:18
Alignment explanation
Indices: 17401277--17401320 Score: 61
Period size: 18 Copynumber: 2.4 Consensus size: 18
17401267 AATTAATATG
*
17401277 AAAAATGTATATTTTATT
1 AAAAATATATATTTTATT
**
17401295 TTAAATATATATTTTATT
1 AAAAATATATATTTTATT
17401313 AAAAATAT
1 AAAAATAT
17401321 GTTGAGAGTT
Statistics
Matches: 21, Mismatches: 5, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
18 21 1.00
ACGTcount: A:0.48, C:0.00, G:0.02, T:0.50
Consensus pattern (18 bp):
AAAAATATATATTTTATT
Found at i:17402192 original size:1 final size:1
Alignment explanation
Indices: 17402186--17402213 Score: 56
Period size: 1 Copynumber: 28.0 Consensus size: 1
17402176 ATTTAAAATT
17402186 AAAAAAAAAAAAAAAAAAAAAAAAAAAA
1 AAAAAAAAAAAAAAAAAAAAAAAAAAAA
17402214 GTTTAAAGTT
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
1 27 1.00
ACGTcount: A:1.00, C:0.00, G:0.00, T:0.00
Consensus pattern (1 bp):
A
Found at i:17406389 original size:22 final size:22
Alignment explanation
Indices: 17406351--17406406 Score: 60
Period size: 22 Copynumber: 2.5 Consensus size: 22
17406341 TTTTTATTTA
** *
17406351 AAATATATTAAGAATTTTTAA-
1 AAATATATTAATCATTTATAAG
*
17406372 AAATTTTATTAATCATTTATAAG
1 AAA-TATATTAATCATTTATAAG
17406395 AAATATATTAAT
1 AAATATATTAAT
17406407 AAAATTAAAT
Statistics
Matches: 28, Mismatches: 5, Indels: 3
0.78 0.14 0.08
Matches are distributed among these distances:
21 3 0.11
22 22 0.79
23 3 0.11
ACGTcount: A:0.50, C:0.02, G:0.04, T:0.45
Consensus pattern (22 bp):
AAATATATTAATCATTTATAAG
Found at i:17409803 original size:72 final size:71
Alignment explanation
Indices: 17409686--17409835 Score: 203
Period size: 72 Copynumber: 2.1 Consensus size: 71
17409676 CCCAAAAGCT
* * * *
17409686 CCCAAATCTTTCTTCCTCTCTCCCTACTACCGGCGTCACACAACCAAGCCCCAAAGCTCTCCCTT
1 CCCAAATCTTTCTTCCTCTCTCCCTACTACCGACGCCACAAAACCAAGCCCAAAAGCTCTCCC-T
*
17409751 TTCGATG
65 TTCGACG
* * *
17409758 CCCAAATCTTTC-TCCTTCTCTCCCTTCTATCGATGCCACAAAACCAAGCCCAAAAGCTCTCCCT
1 CCCAAATCTTTCTTCC-TCTCTCCCTACTACCGACGCCACAAAACCAAGCCCAAAAGCTCTCCCT
17409822 TTCGACG
65 TTCGACG
17409829 CCCAAAT
1 CCCAAAT
17409836 ATTTTTCTCT
Statistics
Matches: 69, Mismatches: 8, Indels: 3
0.86 0.10 0.04
Matches are distributed among these distances:
71 17 0.25
72 52 0.75
ACGTcount: A:0.23, C:0.42, G:0.09, T:0.26
Consensus pattern (71 bp):
CCCAAATCTTTCTTCCTCTCTCCCTACTACCGACGCCACAAAACCAAGCCCAAAAGCTCTCCCTT
TCGACG
Found at i:17413596 original size:9 final size:9
Alignment explanation
Indices: 17413584--17413621 Score: 51
Period size: 9 Copynumber: 4.2 Consensus size: 9
17413574 TAAATTTTGG
17413584 TTTAATTTA
1 TTTAATTTA
17413593 TTTAA-TTA
1 TTTAATTTA
*
17413601 ATTAATTTTA
1 TTTAA-TTTA
17413611 TTTAATTTA
1 TTTAATTTA
17413620 TT
1 TT
17413622 AAAAAGGGTG
Statistics
Matches: 25, Mismatches: 2, Indels: 4
0.81 0.06 0.13
Matches are distributed among these distances:
8 7 0.28
9 11 0.44
10 7 0.28
ACGTcount: A:0.34, C:0.00, G:0.00, T:0.66
Consensus pattern (9 bp):
TTTAATTTA
Found at i:17413612 original size:18 final size:17
Alignment explanation
Indices: 17413585--17413623 Score: 60
Period size: 18 Copynumber: 2.2 Consensus size: 17
17413575 AAATTTTGGT
17413585 TTAATTTATTTAATTAA
1 TTAATTTATTTAATTAA
*
17413602 TTAATTTTATTTAATTTA
1 TTAA-TTTATTTAATTAA
17413620 TTAA
1 TTAA
17413624 AAAGGGTGTC
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
17 4 0.20
18 16 0.80
ACGTcount: A:0.38, C:0.00, G:0.00, T:0.62
Consensus pattern (17 bp):
TTAATTTATTTAATTAA
Found at i:17414947 original size:3 final size:3
Alignment explanation
Indices: 17414939--17414964 Score: 52
Period size: 3 Copynumber: 8.7 Consensus size: 3
17414929 TGTCTTTTAC
17414939 TAT TAT TAT TAT TAT TAT TAT TAT TA
1 TAT TAT TAT TAT TAT TAT TAT TAT TA
17414965 CATCTTTGAG
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 23 1.00
ACGTcount: A:0.35, C:0.00, G:0.00, T:0.65
Consensus pattern (3 bp):
TAT
Found at i:17415903 original size:28 final size:28
Alignment explanation
Indices: 17415871--17415930 Score: 86
Period size: 28 Copynumber: 2.1 Consensus size: 28
17415861 GAAAATTACT
*
17415871 AACAGAA-TTCAGTAGGAAATGCTTTTCC
1 AACAGAATTTC-GTAGGAAATGCTTCTCC
*
17415899 AACAGAATTTCGTTGGAAATGCTTCTCC
1 AACAGAATTTCGTAGGAAATGCTTCTCC
17415927 AACA
1 AACA
17415931 AAAAAGTCCG
Statistics
Matches: 29, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
28 26 0.90
29 3 0.10
ACGTcount: A:0.35, C:0.20, G:0.17, T:0.28
Consensus pattern (28 bp):
AACAGAATTTCGTAGGAAATGCTTCTCC
Found at i:17416050 original size:15 final size:16
Alignment explanation
Indices: 17416025--17416059 Score: 54
Period size: 15 Copynumber: 2.2 Consensus size: 16
17416015 TTCCGTTGGA
*
17416025 AATTGATTTCCTACGG
1 AATTGATTTCCAACGG
17416041 AATT-ATTTCCAACGG
1 AATTGATTTCCAACGG
17416056 AATT
1 AATT
17416060 TTTTGTGGGC
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
15 14 0.78
16 4 0.22
ACGTcount: A:0.31, C:0.17, G:0.14, T:0.37
Consensus pattern (16 bp):
AATTGATTTCCAACGG
Found at i:17419010 original size:23 final size:23
Alignment explanation
Indices: 17418984--17419046 Score: 99
Period size: 23 Copynumber: 2.7 Consensus size: 23
17418974 AGGAAGAAGA
*
17418984 AGAAGAAGCTGCTGGAAAATGGG
1 AGAAGAAGTTGCTGGAAAATGGG
*
17419007 AGAAAAAGTTGCTGGAAAATGGG
1 AGAAGAAGTTGCTGGAAAATGGG
*
17419030 AGAAGAAGTTGTTGGAA
1 AGAAGAAGTTGCTGGAA
17419047 GAAAGAAATA
Statistics
Matches: 36, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
23 36 1.00
ACGTcount: A:0.41, C:0.05, G:0.37, T:0.17
Consensus pattern (23 bp):
AGAAGAAGTTGCTGGAAAATGGG
Found at i:17419607 original size:35 final size:36
Alignment explanation
Indices: 17419520--17419612 Score: 100
Period size: 36 Copynumber: 2.6 Consensus size: 36
17419510 CCTCACAACA
* *
17419520 ACTTTTTCATGAGATTAAGCGATAACTCCCATAACG
1 ACTTTTTCACGAGATCAAGCGATAACTCCCATAACG
* * * * *
17419556 ACTTTTTAACGGGATCAAGTGATAACTCTCACT-ATG
1 ACTTTTTCACGAGATCAAGCGATAACTCCCA-TAACG
17419592 -CTTTTTCACGAGATCAAGCGA
1 ACTTTTTCACGAGATCAAGCGA
17419613 AACCCATGGT
Statistics
Matches: 46, Mismatches: 10, Indels: 3
0.78 0.17 0.05
Matches are distributed among these distances:
35 18 0.39
36 27 0.59
37 1 0.02
ACGTcount: A:0.31, C:0.22, G:0.16, T:0.31
Consensus pattern (36 bp):
ACTTTTTCACGAGATCAAGCGATAACTCCCATAACG
Found at i:17419811 original size:13 final size:13
Alignment explanation
Indices: 17419793--17419817 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
17419783 GTAGCATTGG
17419793 ATATAAAGATAGA
1 ATATAAAGATAGA
17419806 ATATAAAGATAG
1 ATATAAAGATAG
17419818 GAGTGAAAGC
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.60, C:0.00, G:0.16, T:0.24
Consensus pattern (13 bp):
ATATAAAGATAGA
Found at i:17423525 original size:68 final size:68
Alignment explanation
Indices: 17423364--17423663 Score: 285
Period size: 68 Copynumber: 4.5 Consensus size: 68
17423354 GCATGTTGGT
* * * * * * *
17423364 ATGATGAATGTCATAAGATTATGTATATGATGTGA-ATTCCATATACCATATGAGATGATCAAGT
1 ATGATTAATGCCATGAGAATATGTATATGATGT-ATATTCCATATACTACATGAGATGATTAAGT
17423428 ATGC
65 ATGC
* * * * * * * * * * *
17423432 ATAATGT-ATACTA-CAGGATGGTGTATATGATGTAAATTCCATATA-TCATATGAGGTGGTTTA
1 ATGAT-TAATGCCATGAGAAT-ATGTATATGATGTATATTCCATATACT-ACATGAGATGATTAA
*
17423494 GTATTC
63 GTATGC
17423500 ATGATTAATGCCATGAGAATATGTATACT-ATGTATATTCCATATACTACATGAGATGATTAAGT
1 ATGATTAATGCCATGAGAATATGTATA-TGATGTATATTCCATATACTACATGAGATGATTAAGT
17423564 ATGC
65 ATGC
*
17423568 ATGATTAATGCCATGAGAATATGTATATGATGTATATTCCATATACTACATGAGATGATTGAGCT
1 ATGATTAATGCCATGAGAATATGTATATGATGTATATTCCATATACTACATGAGATGATTAAG-T
17423633 A-GC
65 ATGC
* *
17423636 AT-A--AATGCCAAGAGATTATGTATATGAT
1 ATGATTAATGCCATGAGAATATGTATATGAT
17423664 ATAAATTCTA
Statistics
Matches: 192, Mismatches: 30, Indels: 23
0.78 0.12 0.09
Matches are distributed among these distances:
65 23 0.12
67 7 0.04
68 154 0.80
69 8 0.04
ACGTcount: A:0.36, C:0.10, G:0.19, T:0.35
Consensus pattern (68 bp):
ATGATTAATGCCATGAGAATATGTATATGATGTATATTCCATATACTACATGAGATGATTAAGTA
TGC
Found at i:17423882 original size:31 final size:31
Alignment explanation
Indices: 17423817--17423895 Score: 88
Period size: 31 Copynumber: 2.6 Consensus size: 31
17423807 ATCATAAAAT
* **
17423817 GCCCAAGGTGCAATGGGGATATATGTTACCA
1 GCCCAAGGTGTAATGGGGATATACATTACCA
* * *
17423848 GCCCAAGGTGTAATGGGGATGTACATTGCTA
1 GCCCAAGGTGTAATGGGGATATACATTACCA
*
17423879 GCCCAAGGT-TGATGGGG
1 GCCCAAGGTGTAATGGGG
17423896 GTCAAACCAT
Statistics
Matches: 41, Mismatches: 7, Indels: 1
0.84 0.14 0.02
Matches are distributed among these distances:
30 7 0.17
31 34 0.83
ACGTcount: A:0.25, C:0.18, G:0.34, T:0.23
Consensus pattern (31 bp):
GCCCAAGGTGTAATGGGGATATACATTACCA
Found at i:17425126 original size:14 final size:14
Alignment explanation
Indices: 17425107--17425147 Score: 52
Period size: 12 Copynumber: 3.1 Consensus size: 14
17425097 AAAGGAAGGC
17425107 AAAGAGAAAGAAGA
1 AAAGAGAAAGAAGA
17425121 AAAGAGAAAG--GA
1 AAAGAGAAAGAAGA
*
17425133 AAGGAGAAA-AAGA
1 AAAGAGAAAGAAGA
17425146 AA
1 AA
17425148 GAGGGGTCGG
Statistics
Matches: 24, Mismatches: 1, Indels: 5
0.80 0.03 0.17
Matches are distributed among these distances:
12 10 0.42
13 4 0.17
14 10 0.42
ACGTcount: A:0.71, C:0.00, G:0.29, T:0.00
Consensus pattern (14 bp):
AAAGAGAAAGAAGA
Found at i:17425143 original size:20 final size:20
Alignment explanation
Indices: 17425107--17425150 Score: 65
Period size: 19 Copynumber: 2.3 Consensus size: 20
17425097 AAAGGAAGGC
17425107 AAAGAGAAAGAAGAAAAGAG
1 AAAGAGAAAGAAGAAAAGAG
*
17425127 AAAG-GAAAGGAGAAAA-AG
1 AAAGAGAAAGAAGAAAAGAG
17425145 AAAGAG
1 AAAGAG
17425151 GGGTCGGCCT
Statistics
Matches: 22, Mismatches: 1, Indels: 3
0.85 0.04 0.12
Matches are distributed among these distances:
18 6 0.27
19 12 0.55
20 4 0.18
ACGTcount: A:0.68, C:0.00, G:0.32, T:0.00
Consensus pattern (20 bp):
AAAGAGAAAGAAGAAAAGAG
Found at i:17427762 original size:2 final size:2
Alignment explanation
Indices: 17427755--17427788 Score: 68
Period size: 2 Copynumber: 17.0 Consensus size: 2
17427745 ACCATGTATG
17427755 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
17427789 CTAATCATCA
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 32 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:17427907 original size:2 final size:2
Alignment explanation
Indices: 17427900--17427932 Score: 66
Period size: 2 Copynumber: 16.5 Consensus size: 2
17427890 NNNNNNNNTG
17427900 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
17427933 CAATCATCAT
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 31 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:17428020 original size:42 final size:42
Alignment explanation
Indices: 17427973--17428056 Score: 132
Period size: 42 Copynumber: 2.0 Consensus size: 42
17427963 CAGCTCATTT
*
17427973 GCATCGGCTTATGTGCACTCCCACTCGCACATAACCGGGTCA
1 GCATCGGCTTATGTACACTCCCACTCGCACATAACCGGGTCA
* * *
17428015 GCATCGGCTTATGTACATTCCTACTCGCACATAGCCGGGTCA
1 GCATCGGCTTATGTACACTCCCACTCGCACATAACCGGGTCA
17428057 ATATCATTAC
Statistics
Matches: 38, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
42 38 1.00
ACGTcount: A:0.21, C:0.33, G:0.21, T:0.24
Consensus pattern (42 bp):
GCATCGGCTTATGTACACTCCCACTCGCACATAACCGGGTCA
Found at i:17429302 original size:25 final size:25
Alignment explanation
Indices: 17429268--17429327 Score: 95
Period size: 25 Copynumber: 2.4 Consensus size: 25
17429258 GGTTTGTGAA
17429268 ATATACGTGGCAAGGCCAC-AGGTTG
1 ATATACGTGGCAAGGCCACGA-GTTG
*
17429293 ATATACGTGGCTAGGCCACGAGTTG
1 ATATACGTGGCAAGGCCACGAGTTG
17429318 ATATACGTGG
1 ATATACGTGG
17429328 TTGCGACCAC
Statistics
Matches: 33, Mismatches: 1, Indels: 2
0.92 0.03 0.06
Matches are distributed among these distances:
25 32 0.97
26 1 0.03
ACGTcount: A:0.27, C:0.18, G:0.32, T:0.23
Consensus pattern (25 bp):
ATATACGTGGCAAGGCCACGAGTTG
Found at i:17430281 original size:36 final size:35
Alignment explanation
Indices: 17430235--17430380 Score: 202
Period size: 36 Copynumber: 4.1 Consensus size: 35
17430225 TCAACTTAGC
* *
17430235 TCATGTGCACTCCCACACCGCACATAGCTAATATCC
1 TCATGTGCACTCCCACACCGCACATGGC-AATATCA
*
17430271 TCATGTGCACTCCCACACCGCACATGGAAAATATCA
1 TCATGTGCACTCCCACACCGCACATGG-CAATATCA
**
17430307 TCATGTGCACTCCCACACTTCACATGGCATATATCA
1 TCATGTGCACTCCCACACCGCACATGGCA-ATATCA
*
17430343 TCATGTGCACTCCCACACCGCACATGGCATATGTCA
1 TCATGTGCACTCCCACACCGCACATGGCA-ATATCA
17430379 TC
1 TC
17430381 GGCGTGTGTT
Statistics
Matches: 99, Mismatches: 9, Indels: 4
0.88 0.08 0.04
Matches are distributed among these distances:
35 1 0.01
36 98 0.99
ACGTcount: A:0.28, C:0.36, G:0.13, T:0.23
Consensus pattern (35 bp):
TCATGTGCACTCCCACACCGCACATGGCAATATCA
Found at i:17442195 original size:27 final size:26
Alignment explanation
Indices: 17442165--17442224 Score: 66
Period size: 27 Copynumber: 2.3 Consensus size: 26
17442155 ATTTTCTAGT
* * *
17442165 TTTCCTTTGTTTTTTCTCTTTTCTTCC
1 TTTCCTTTCTATTTTCTCTCTTCTT-C
* *
17442192 TTTCCTCTCTATTTTCTCTCTTGTTC
1 TTTCCTTTCTATTTTCTCTCTTCTTC
17442218 TTTCCTT
1 TTTCCTT
17442225 ATGGCCGGCC
Statistics
Matches: 27, Mismatches: 6, Indels: 1
0.79 0.18 0.03
Matches are distributed among these distances:
26 7 0.26
27 20 0.74
ACGTcount: A:0.02, C:0.28, G:0.03, T:0.67
Consensus pattern (26 bp):
TTTCCTTTCTATTTTCTCTCTTCTTC
Found at i:17453598 original size:18 final size:19
Alignment explanation
Indices: 17453575--17453615 Score: 57
Period size: 19 Copynumber: 2.2 Consensus size: 19
17453565 CAAATGGAAA
*
17453575 ATTTTA-TAATTAAATAAT
1 ATTTTATTAATAAAATAAT
*
17453593 ATTTTATTAATAAAATATT
1 ATTTTATTAATAAAATAAT
17453612 ATTT
1 ATTT
17453616 AAATAATATT
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
18 6 0.30
19 14 0.70
ACGTcount: A:0.46, C:0.00, G:0.00, T:0.54
Consensus pattern (19 bp):
ATTTTATTAATAAAATAAT
Found at i:17453622 original size:19 final size:19
Alignment explanation
Indices: 17453580--17453623 Score: 52
Period size: 19 Copynumber: 2.3 Consensus size: 19
17453570 GGAAAATTTT
* *
17453580 ATAATTAAATAATATTTTA
1 ATAATAAAATAATATTTAA
* *
17453599 TTAATAAAATATTATTTAA
1 ATAATAAAATAATATTTAA
17453618 ATAATA
1 ATAATA
17453624 TTGAGATATT
Statistics
Matches: 20, Mismatches: 5, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
19 20 1.00
ACGTcount: A:0.55, C:0.00, G:0.00, T:0.45
Consensus pattern (19 bp):
ATAATAAAATAATATTTAA
Found at i:17453623 original size:14 final size:15
Alignment explanation
Indices: 17453578--17453625 Score: 53
Period size: 16 Copynumber: 3.1 Consensus size: 15
17453568 ATGGAAAATT
17453578 TTATAATTAAATAATA
1 TTAT-ATTAAATAATA
* *
17453594 TTTTATTAATAAAATA
1 TTATATTAA-ATAATA
17453610 TTAT-TTAAATAATA
1 TTATATTAAATAATA
17453624 TT
1 TT
17453626 GAGATATTTC
Statistics
Matches: 27, Mismatches: 4, Indels: 4
0.77 0.11 0.11
Matches are distributed among these distances:
14 7 0.26
15 9 0.33
16 11 0.41
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (15 bp):
TTATATTAAATAATA
Found at i:17455925 original size:29 final size:29
Alignment explanation
Indices: 17455883--17455952 Score: 131
Period size: 29 Copynumber: 2.4 Consensus size: 29
17455873 AGGCTGTTAG
17455883 ACGTGGCTAGGCTATGGTCTGTGATATAT
1 ACGTGGCTAGGCTATGGTCTGTGATATAT
17455912 ACGTGGCTAGGCTATGGTCTGTGATATAT
1 ACGTGGCTAGGCTATGGTCTGTGATATAT
*
17455941 ACGTGGCAAGGC
1 ACGTGGCTAGGC
17455953 CACGAGTTGA
Statistics
Matches: 40, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
29 40 1.00
ACGTcount: A:0.21, C:0.16, G:0.33, T:0.30
Consensus pattern (29 bp):
ACGTGGCTAGGCTATGGTCTGTGATATAT
Found at i:17455969 original size:25 final size:25
Alignment explanation
Indices: 17455937--17455996 Score: 102
Period size: 25 Copynumber: 2.4 Consensus size: 25
17455927 GGTCTGTGAT
17455937 ATATACGTGGCAAGGCCACGAGTTG
1 ATATACGTGGCAAGGCCACGAGTTG
* *
17455962 ATATACGTGGCTAGGGCACGAGTTG
1 ATATACGTGGCAAGGCCACGAGTTG
17455987 ATATACGTGG
1 ATATACGTGG
17455997 TTGCAACCAC
Statistics
Matches: 33, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
25 33 1.00
ACGTcount: A:0.27, C:0.17, G:0.33, T:0.23
Consensus pattern (25 bp):
ATATACGTGGCAAGGCCACGAGTTG
Found at i:17458215 original size:25 final size:25
Alignment explanation
Indices: 17458184--17458258 Score: 125
Period size: 25 Copynumber: 3.0 Consensus size: 25
17458174 CATTTCTTCA
*
17458184 TATTGGGCCATGCCCATTCTTTTCT
1 TATTGGGCTATGCCCATTCTTTTCT
17458209 TATTGGGCTATGCCCATTCTTTTCT
1 TATTGGGCTATGCCCATTCTTTTCT
*
17458234 TATTGGGCTATGCCCACT-TTTTCT
1 TATTGGGCTATGCCCATTCTTTTCT
17458258 T
1 T
17458259 CTTTTTTTTT
Statistics
Matches: 48, Mismatches: 2, Indels: 1
0.94 0.04 0.02
Matches are distributed among these distances:
24 7 0.15
25 41 0.85
ACGTcount: A:0.12, C:0.25, G:0.16, T:0.47
Consensus pattern (25 bp):
TATTGGGCTATGCCCATTCTTTTCT
Found at i:17458270 original size:10 final size:10
Alignment explanation
Indices: 17458251--17458311 Score: 52
Period size: 10 Copynumber: 6.0 Consensus size: 10
17458241 CTATGCCCAC
17458251 TTTTTCTTCT
1 TTTTTCTTCT
*
17458261 TTTTTTTTCT
1 TTTTTCTTCT
*
17458271 TTCTTTCTTCC
1 TT-TTTCTTCT
* *
17458282 TTTCTCGT-T
1 TTTTTCTTCT
*
17458291 TCTTTCTCTCT
1 TTTTTCT-TCT
17458302 TTTTTCTTCT
1 TTTTTCTTCT
17458312 CCTCTCTCCC
Statistics
Matches: 38, Mismatches: 10, Indels: 6
0.70 0.19 0.11
Matches are distributed among these distances:
9 4 0.11
10 19 0.50
11 15 0.39
ACGTcount: A:0.00, C:0.25, G:0.02, T:0.74
Consensus pattern (10 bp):
TTTTTCTTCT
Found at i:17465384 original size:29 final size:28
Alignment explanation
Indices: 17465342--17465505 Score: 184
Period size: 28 Copynumber: 5.6 Consensus size: 28
17465332 TGACAGCTTT
17465342 AACATGTTTGTCTTAATTTAGACAAGAA
1 AACATGTTTGTCTTAATTTAGACAAGAA
*
17465370 AACATGTTTGGTCTTAATTTAGACAACAA
1 AACATGTTT-GTCTTAATTTAGACAAGAA
*
17465399 AATATGTTTGTCTTAATTTAGGACAAGAAA
1 AACATGTTTGTCTTAATTTA-GACAAG-AA
* * * *
17465429 AATATTTTTTTTCTTAATCTAGACAAGAA
1 AACA-TGTTTGTCTTAATTTAGACAAGAA
* *
17465458 AACATATTTGTCTCAATTTAGACAAGATAA
1 AACATGTTTGTCTTAATTTAGACAAG--AA
* *
17465488 AATATTTTTGTCTTAATT
1 AACATGTTTGTCTTAATT
17465506 ACAAACAAGA
Statistics
Matches: 116, Mismatches: 14, Indels: 10
0.83 0.10 0.07
Matches are distributed among these distances:
28 38 0.33
29 36 0.31
30 29 0.25
31 13 0.11
ACGTcount: A:0.38, C:0.10, G:0.12, T:0.40
Consensus pattern (28 bp):
AACATGTTTGTCTTAATTTAGACAAGAA
Found at i:17465468 original size:59 final size:58
Alignment explanation
Indices: 17465342--17465504 Score: 213
Period size: 59 Copynumber: 2.8 Consensus size: 58
17465332 TGACAGCTTT
* * * *
17465342 AACATGTTTGTCTTAATTTAGACAAG-AAAACATGTTTGGTCTTAATTTAGACAACAA
1 AACATGTTTGTCTTAATTTAGACAAGAAAAATATTTTTTGTCTTAATCTAGACAACAA
* * *
17465399 AATATGTTTGTCTTAATTTAGGACAAGAAAAATATTTTTTTTCTTAATCTAGACAAGAA
1 AACATGTTTGTCTTAATTTA-GACAAGAAAAATATTTTTTGTCTTAATCTAGACAACAA
* *
17465458 AACATATTTGTCTCAATTTAGACAAGATAAAATA-TTTTTGTCTTAAT
1 AACATGTTTGTCTTAATTTAGACAAGA-AAAATATTTTTTGTCTTAAT
17465505 TACAAACAAG
Statistics
Matches: 92, Mismatches: 11, Indels: 5
0.85 0.10 0.05
Matches are distributed among these distances:
57 19 0.21
58 25 0.27
59 48 0.52
ACGTcount: A:0.39, C:0.10, G:0.12, T:0.39
Consensus pattern (58 bp):
AACATGTTTGTCTTAATTTAGACAAGAAAAATATTTTTTGTCTTAATCTAGACAACAA
Found at i:17466646 original size:40 final size:40
Alignment explanation
Indices: 17466602--17466679 Score: 129
Period size: 40 Copynumber: 1.9 Consensus size: 40
17466592 TAGGGATCTC
* * *
17466602 ATAACTGCATCCTATTATAGTTCCCTTTCAAGGCAAATCA
1 ATAACTGCAACCCATTACAGTTCCCTTTCAAGGCAAATCA
17466642 ATAACTGCAACCCATTACAGTTCCCTTTCAAGGCAAAT
1 ATAACTGCAACCCATTACAGTTCCCTTTCAAGGCAAAT
17466680 TAATCTCATG
Statistics
Matches: 35, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
40 35 1.00
ACGTcount: A:0.33, C:0.27, G:0.10, T:0.29
Consensus pattern (40 bp):
ATAACTGCAACCCATTACAGTTCCCTTTCAAGGCAAATCA
Found at i:17469128 original size:13 final size:13
Alignment explanation
Indices: 17469110--17469134 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
17469100 AGAGAAATTG
17469110 TGATTTTATAAAA
1 TGATTTTATAAAA
17469123 TGATTTTATAAA
1 TGATTTTATAAA
17469135 TTTTCTGAAA
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.44, C:0.00, G:0.08, T:0.48
Consensus pattern (13 bp):
TGATTTTATAAAA
Found at i:17473031 original size:10 final size:10
Alignment explanation
Indices: 17473003--17473041 Score: 51
Period size: 10 Copynumber: 3.8 Consensus size: 10
17472993 CCTCACCAAA
17473003 CATCAAATAT
1 CATCAAATAT
*
17473013 CACCAAAATAT
1 CATC-AAATAT
*
17473024 CATGAAATAT
1 CATCAAATAT
17473034 CATCAAAT
1 CATCAAAT
17473042 TCAGCCACAA
Statistics
Matches: 24, Mismatches: 4, Indels: 2
0.80 0.13 0.07
Matches are distributed among these distances:
10 16 0.67
11 8 0.33
ACGTcount: A:0.51, C:0.21, G:0.03, T:0.26
Consensus pattern (10 bp):
CATCAAATAT
Found at i:17481542 original size:20 final size:21
Alignment explanation
Indices: 17481497--17481543 Score: 60
Period size: 20 Copynumber: 2.3 Consensus size: 21
17481487 AGATGTCTAA
*
17481497 AATAATTATTTGAAATGAAAT
1 AATAATTATTTGAAATAAAAT
* *
17481518 TATAATTGTTTG-AATAAAAT
1 AATAATTATTTGAAATAAAAT
17481538 AATAAT
1 AATAAT
17481544 ATTCAATAAA
Statistics
Matches: 22, Mismatches: 4, Indels: 1
0.81 0.15 0.04
Matches are distributed among these distances:
20 12 0.55
21 10 0.45
ACGTcount: A:0.51, C:0.00, G:0.09, T:0.40
Consensus pattern (21 bp):
AATAATTATTTGAAATAAAAT
Found at i:17482518 original size:13 final size:13
Alignment explanation
Indices: 17482500--17482524 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
17482490 TTTCTAAAAA
17482500 TTTATAAAATCAT
1 TTTATAAAATCAT
17482513 TTTATAAAATCA
1 TTTATAAAATCA
17482525 CATTTATTCA
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.48, C:0.08, G:0.00, T:0.44
Consensus pattern (13 bp):
TTTATAAAATCAT
Found at i:17484283 original size:21 final size:20
Alignment explanation
Indices: 17484257--17484313 Score: 60
Period size: 21 Copynumber: 2.8 Consensus size: 20
17484247 CAAACACTTT
17484257 TCTTTTATTTTTTATTTTTTA
1 TCTTTT-TTTTTTATTTTTTA
* * *
17484278 TCTTTTTCTTCTTCTTTTTTC
1 TCTTTTT-TTTTTATTTTTTA
*
17484299 TCTTTTTCTTTTATT
1 TCTTTTTTTTTTATT
17484314 CACAATTTAA
Statistics
Matches: 29, Mismatches: 6, Indels: 3
0.76 0.16 0.08
Matches are distributed among these distances:
20 6 0.21
21 23 0.79
ACGTcount: A:0.07, C:0.14, G:0.00, T:0.79
Consensus pattern (20 bp):
TCTTTTTTTTTTATTTTTTA
Found at i:17494899 original size:29 final size:27
Alignment explanation
Indices: 17494811--17494901 Score: 83
Period size: 29 Copynumber: 3.1 Consensus size: 27
17494801 CTTTAACATG
*
17494811 TTTGTCTTAATTTAAGACAAGAAAAATA
1 TTTGTCTAAATTT-AGACAAGAAAAATA
* * *
17494839 TTTTTTGTCTATATCTAGACAAGAATACATA
1 ---TTTGTCTAAATTTAGACAAGAA-AAATA
17494870 TTTGTCTCAAATTTAGACAAGATAAAATA
1 TTTGTCT-AAATTTAGACAAGA-AAAATA
17494899 TTT
1 TTT
17494902 TTTGTCTTAA
Statistics
Matches: 50, Mismatches: 7, Indels: 8
0.77 0.11 0.12
Matches are distributed among these distances:
28 7 0.14
29 19 0.38
30 10 0.20
31 14 0.28
ACGTcount: A:0.41, C:0.10, G:0.10, T:0.40
Consensus pattern (27 bp):
TTTGTCTAAATTTAGACAAGAAAAATA
Found at i:17499629 original size:35 final size:35
Alignment explanation
Indices: 17499584--17499655 Score: 126
Period size: 35 Copynumber: 2.1 Consensus size: 35
17499574 GGAATGCGTG
*
17499584 TGATGATATTGAAATGTTCGTGTAGGGAGTACACA
1 TGATGATATTGAAATGTGCGTGTAGGGAGTACACA
*
17499619 TGATGATATTGAAATGTGCGTGTAGGGAGTGCACA
1 TGATGATATTGAAATGTGCGTGTAGGGAGTACACA
17499654 TG
1 TG
17499656 TGTTTGGTTT
Statistics
Matches: 35, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
35 35 1.00
ACGTcount: A:0.29, C:0.08, G:0.32, T:0.31
Consensus pattern (35 bp):
TGATGATATTGAAATGTGCGTGTAGGGAGTACACA
Found at i:17500819 original size:20 final size:21
Alignment explanation
Indices: 17500794--17500848 Score: 69
Period size: 20 Copynumber: 2.7 Consensus size: 21
17500784 CGTGATGAAC
17500794 ATCTATAGATAGATGA-CCAG
1 ATCTATAGATAGATGAGCCAG
**
17500814 ATCTATCCATAGAT-AGCCAG
1 ATCTATAGATAGATGAGCCAG
*
17500834 ATCTATTGATAGATG
1 ATCTATAGATAGATG
17500849 GCTCTCATCT
Statistics
Matches: 29, Mismatches: 4, Indels: 3
0.81 0.11 0.08
Matches are distributed among these distances:
19 1 0.03
20 28 0.97
ACGTcount: A:0.36, C:0.16, G:0.18, T:0.29
Consensus pattern (21 bp):
ATCTATAGATAGATGAGCCAG
Found at i:17506862 original size:19 final size:18
Alignment explanation
Indices: 17506819--17506862 Score: 61
Period size: 19 Copynumber: 2.3 Consensus size: 18
17506809 AAGAAGAAAG
17506819 AAAAGAAGCTGCTGAAGA
1 AAAAGAAGCTGCTGAAGA
*
17506837 ATGAAGAAGCTGCTGGAAGA
1 A-AAAGAAGCTGCT-GAAGA
17506857 AAAAGA
1 AAAAGA
17506863 TATTTATAGC
Statistics
Matches: 22, Mismatches: 2, Indels: 3
0.81 0.07 0.11
Matches are distributed among these distances:
18 1 0.05
19 15 0.68
20 6 0.27
ACGTcount: A:0.50, C:0.09, G:0.30, T:0.11
Consensus pattern (18 bp):
AAAAGAAGCTGCTGAAGA
Found at i:17515470 original size:20 final size:20
Alignment explanation
Indices: 17515432--17515470 Score: 51
Period size: 20 Copynumber: 1.9 Consensus size: 20
17515422 GGGGGAGTAT
*
17515432 AATGGGTACACGAACTAAAG
1 AATGGGTACAAGAACTAAAG
* *
17515452 AATGGGTGCAAGAATTAAA
1 AATGGGTACAAGAACTAAA
17515471 AAAAAACTGT
Statistics
Matches: 16, Mismatches: 3, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
20 16 1.00
ACGTcount: A:0.46, C:0.10, G:0.26, T:0.18
Consensus pattern (20 bp):
AATGGGTACAAGAACTAAAG
Found at i:17516120 original size:16 final size:17
Alignment explanation
Indices: 17516092--17516123 Score: 57
Period size: 16 Copynumber: 1.9 Consensus size: 17
17516082 AAATATGCAC
17516092 ATACTTAGGGGGAGCAT
1 ATACTTAGGGGGAGCAT
17516109 ATACTT-GGGGGAGCA
1 ATACTTAGGGGGAGCA
17516124 ATCCTCATTT
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
16 9 0.60
17 6 0.40
ACGTcount: A:0.28, C:0.12, G:0.38, T:0.22
Consensus pattern (17 bp):
ATACTTAGGGGGAGCAT
Found at i:17521050 original size:18 final size:19
Alignment explanation
Indices: 17521015--17521058 Score: 63
Period size: 18 Copynumber: 2.4 Consensus size: 19
17521005 TATATTTATT
17521015 TTATTTTATTAATAAAATA
1 TTATTTTATTAATAAAATA
*
17521034 TTATTTTATT-CTAAAATA
1 TTATTTTATTAATAAAATA
*
17521052 TTCTTTT
1 TTATTTT
17521059 CACACGTCAC
Statistics
Matches: 23, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
18 13 0.57
19 10 0.43
ACGTcount: A:0.36, C:0.05, G:0.00, T:0.59
Consensus pattern (19 bp):
TTATTTTATTAATAAAATA
Found at i:17522921 original size:39 final size:38
Alignment explanation
Indices: 17522876--17522976 Score: 159
Period size: 37 Copynumber: 2.7 Consensus size: 38
17522866 CCCCAGCTCA
*
17522876 TGTGCATCCCCCCACATCGTGCACATAGCTGGAGTCATG
1 TGTGCATCCCCCCACATCGTGCACA-AGCTAGAGTCATG
*
17522915 TGTGCATCCCCCCACATCATGCAC-AGCTAGAGTCATG
1 TGTGCATCCCCCCACATCGTGCACAAGCTAGAGTCATG
*
17522952 TGTGCATCCCCCCACATAGTGCACA
1 TGTGCATCCCCCCACATCGTGCACA
17522977 CAGGCAATAT
Statistics
Matches: 57, Mismatches: 4, Indels: 3
0.89 0.06 0.05
Matches are distributed among these distances:
37 34 0.60
39 23 0.40
ACGTcount: A:0.23, C:0.36, G:0.20, T:0.22
Consensus pattern (38 bp):
TGTGCATCCCCCCACATCGTGCACAAGCTAGAGTCATG
Found at i:17528513 original size:18 final size:18
Alignment explanation
Indices: 17528481--17528515 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
17528471 ATAAAAATAT
*
17528481 ATATTTTTTGCTATTAAA
1 ATATTTTTTACTATTAAA
*
17528499 ATATTTTTTATTATTAA
1 ATATTTTTTACTATTAA
17528516 TAAAAAAAAG
Statistics
Matches: 15, Mismatches: 2, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
18 15 1.00
ACGTcount: A:0.34, C:0.03, G:0.03, T:0.60
Consensus pattern (18 bp):
ATATTTTTTACTATTAAA
Found at i:17546908 original size:13 final size:13
Alignment explanation
Indices: 17546890--17546914 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
17546880 ATTTTCAAAA
17546890 ATTTTATAAAATT
1 ATTTTATAAAATT
17546903 ATTTTATAAAAT
1 ATTTTATAAAAT
17546915 CTCATTTTCC
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (13 bp):
ATTTTATAAAATT
Found at i:17548101 original size:29 final size:28
Alignment explanation
Indices: 17548068--17548131 Score: 74
Period size: 28 Copynumber: 2.2 Consensus size: 28
17548058 GTAAATTTTT
* * *
17548068 AAAAATTACACTTTTGCCCCCATAAAGTG
1 AAAAATTAC-CTTTTGACCCCAAAAACTG
* *
17548097 AAAAATTACGTTTTTACCCCAAAAACTG
1 AAAAATTACCTTTTGACCCCAAAAACTG
17548125 AAAAATT
1 AAAAATT
17548132 GCCCATAGAC
Statistics
Matches: 30, Mismatches: 5, Indels: 1
0.83 0.14 0.03
Matches are distributed among these distances:
28 21 0.70
29 9 0.30
ACGTcount: A:0.44, C:0.20, G:0.08, T:0.28
Consensus pattern (28 bp):
AAAAATTACCTTTTGACCCCAAAAACTG
Found at i:17554549 original size:2 final size:2
Alignment explanation
Indices: 17554542--17554568 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
17554532 AGACAATGCT
17554542 TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA T
17554569 TTGCTTTTAC
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 25 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:17555342 original size:2 final size:2
Alignment explanation
Indices: 17555335--17555372 Score: 62
Period size: 2 Copynumber: 20.0 Consensus size: 2
17555325 AAGCTAAGGA
17555335 AT AT AT AT A- AT AT AT AT AT AT AT AT AT AT AT AT A- AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
17555373 CATTGTTGTT
Statistics
Matches: 34, Mismatches: 0, Indels: 4
0.89 0.00 0.11
Matches are distributed among these distances:
1 2 0.06
2 32 0.94
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (2 bp):
AT
Found at i:17558514 original size:39 final size:39
Alignment explanation
Indices: 17558458--17558532 Score: 89
Period size: 39 Copynumber: 1.9 Consensus size: 39
17558448 TTCTCCTGAA
**
17558458 GGTGTTCTAAATACTACTTGCAATGGTTCTTCTTCTAGG
1 GGTGTTCTAAATACTACTCACAATGGTTCTTCTTCTAGG
* **
17558497 GGTGTTC-AGAATTCTACTCACAATTTTTCTTCTTCT
1 GGTGTTCTA-AATACTACTCACAATGGTTCTTCTTCT
17558533 CTTAGAGGTA
Statistics
Matches: 30, Mismatches: 5, Indels: 2
0.81 0.14 0.05
Matches are distributed among these distances:
38 1 0.03
39 29 0.97
ACGTcount: A:0.20, C:0.20, G:0.16, T:0.44
Consensus pattern (39 bp):
GGTGTTCTAAATACTACTCACAATGGTTCTTCTTCTAGG
Found at i:17559960 original size:21 final size:22
Alignment explanation
Indices: 17559927--17559971 Score: 67
Period size: 21 Copynumber: 2.1 Consensus size: 22
17559917 AATTCACCAC
17559927 ATTGACGTTAAATCTCTATA-TA
1 ATTGACGTTAAATC-CTATACTA
17559949 ATTGAC-TTAAATCCTATACTA
1 ATTGACGTTAAATCCTATACTA
17559970 AT
1 AT
17559972 GCATGGTATG
Statistics
Matches: 22, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
20 5 0.23
21 11 0.50
22 6 0.27
ACGTcount: A:0.38, C:0.16, G:0.07, T:0.40
Consensus pattern (22 bp):
ATTGACGTTAAATCCTATACTA
Found at i:17560627 original size:26 final size:26
Alignment explanation
Indices: 17560598--17560656 Score: 66
Period size: 26 Copynumber: 2.3 Consensus size: 26
17560588 ATTTTCTAGT
* *
17560598 TTTCCTTTGT-TTTTCTCTTTTCTTCC
1 TTTCCTTTCTATTTTCTCTCTTCTT-C
* *
17560624 TTTCCTCTCTATTTTCTCTCTTGTTC
1 TTTCCTTTCTATTTTCTCTCTTCTTC
17560650 TTTCCTT
1 TTTCCTT
17560657 ATGGCCGGCC
Statistics
Matches: 27, Mismatches: 5, Indels: 2
0.79 0.15 0.06
Matches are distributed among these distances:
26 15 0.56
27 12 0.44
ACGTcount: A:0.02, C:0.29, G:0.03, T:0.66
Consensus pattern (26 bp):
TTTCCTTTCTATTTTCTCTCTTCTTC
Found at i:17560798 original size:21 final size:22
Alignment explanation
Indices: 17560757--17560798 Score: 59
Period size: 22 Copynumber: 2.0 Consensus size: 22
17560747 CCCATTGGCC
*
17560757 TGTTTTTAAAATTTCATCCATT
1 TGTTTTCAAAATTTCATCCATT
*
17560779 TGTTTTCAAATTTTCA-CCAT
1 TGTTTTCAAAATTTCATCCAT
17560799 ACACTTGTCC
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
21 4 0.22
22 14 0.78
ACGTcount: A:0.26, C:0.17, G:0.05, T:0.52
Consensus pattern (22 bp):
TGTTTTCAAAATTTCATCCATT
Found at i:17560934 original size:28 final size:30
Alignment explanation
Indices: 17560876--17560935 Score: 79
Period size: 28 Copynumber: 2.1 Consensus size: 30
17560866 TTTTTGAAAT
* *
17560876 TTACACTTTTGCCCTCATAAAAGTGAAAAA
1 TTACACTTTTGCCCTCAAAAAACTGAAAAA
*
17560906 TTACATTTTTG-CC-CAAAAAACTGAAAAA
1 TTACACTTTTGCCCTCAAAAAACTGAAAAA
17560934 TT
1 TT
17560936 GCCCATAGAC
Statistics
Matches: 27, Mismatches: 3, Indels: 2
0.84 0.09 0.06
Matches are distributed among these distances:
28 15 0.56
29 2 0.07
30 10 0.37
ACGTcount: A:0.42, C:0.18, G:0.08, T:0.32
Consensus pattern (30 bp):
TTACACTTTTGCCCTCAAAAAACTGAAAAA
Found at i:17563451 original size:27 final size:27
Alignment explanation
Indices: 17563388--17563465 Score: 77
Period size: 27 Copynumber: 2.9 Consensus size: 27
17563378 CCCCTGGCGC
* *
17563388 TTCTGTGCATGGAACACCCTTGGGCAT
1 TTCTATGCTTGGAACACCCTTGGGCAT
* *
17563415 TTCCACGCTTGGAAC-CTCCTTGGGCAT
1 TTCTATGCTTGGAACAC-CCTTGGGCAT
** *
17563442 TTCTATGCTTATAACACCCCTGGG
1 TTCTATGCTTGGAACACCCTTGGG
17563466 TACTTCGTGC
Statistics
Matches: 40, Mismatches: 9, Indels: 4
0.75 0.17 0.08
Matches are distributed among these distances:
26 1 0.03
27 38 0.95
28 1 0.03
ACGTcount: A:0.18, C:0.29, G:0.22, T:0.31
Consensus pattern (27 bp):
TTCTATGCTTGGAACACCCTTGGGCAT
Found at i:17564672 original size:107 final size:109
Alignment explanation
Indices: 17564519--17564799 Score: 284
Period size: 107 Copynumber: 2.6 Consensus size: 109
17564509 TGCTTGTTCT
* * *
17564519 TGGGTGTTTTTGTGCTTGTAACACTCCTTGGGTGCTTCTATGCTTGGAACACCCTT-GGCCGCTT
1 TGGGTGTTTATGTGCTTGGAACACTCCTTAGGTGCTTCTATGCTTGGAACACCCTTAGG-CGCTT
* * *
17564583 CTGCGCTTGGAACGCCCCTGAGC-GTTTCCACGCTTGGAGCACCCC
65 CTGCGCTAGGAACGCCCCTGAGCACTTT-CACGCTTGGAACACCCC
* * * *
17564628 TGGGTGTTTATGTGCTTGGAATAC-CC-TAGGTGCTTCTATGCTTGGAACGCTCTTAGGCGCTTT
1 TGGGTGTTTATGTGCTTGGAACACTCCTTAGGTGCTTCTATGCTTGGAACACCCTTAGGCGCTTC
* * *
17564691 TGCGCTAGGAACGCCTCTGGGCACTTTCACGCTTGGAACACCCT
66 TGCGCTAGGAACGCCCCTGAGCACTTTCACGCTTGGAACACCCC
* * * * * * ** * * * *
17564735 TGAGCGCTTCTATGCTTGGAACAC-CCTTGGGCACTTTTGTGCTTGAAAGACCCTTAGGCGCTTC
1 TGGGTGTTTATGTGCTTGGAACACTCCTTAGGTGCTTCTATGCTTGGAACACCCTTAGGCGCTTC
17564799 T
66 T
17564800 ATGCCTGGAA
Statistics
Matches: 140, Mismatches: 29, Indels: 7
0.80 0.16 0.04
Matches are distributed among these distances:
107 84 0.60
108 35 0.25
109 21 0.15
ACGTcount: A:0.15, C:0.27, G:0.26, T:0.32
Consensus pattern (109 bp):
TGGGTGTTTATGTGCTTGGAACACTCCTTAGGTGCTTCTATGCTTGGAACACCCTTAGGCGCTTC
TGCGCTAGGAACGCCCCTGAGCACTTTCACGCTTGGAACACCCC
Found at i:17564868 original size:25 final size:25
Alignment explanation
Indices: 17564830--17564930 Score: 94
Period size: 25 Copynumber: 4.0 Consensus size: 25
17564820 TGCTTCTGCG
* * *
17564830 CTTAGAATAGCCTAGGGGCTTCCAT
1 CTTAGAACACCCTAGGGACTTCCAT
* * *
17564855 CTTAGAACACCCTAGGCACTTCTAA
1 CTTAGAACACCCTAGGGACTTCCAT
* *
17564880 CTTGGAACACCCTTGGGCACTTCCAT
1 CTTAGAACACCCTAGGG-ACTTCCAT
* *
17564906 GCTTGGAACACCCTAGGCACTTCCA
1 -CTTAGAACACCCTAGGGACTTCCA
17564931 GTTTGTAACA
Statistics
Matches: 61, Mismatches: 13, Indels: 3
0.79 0.17 0.04
Matches are distributed among these distances:
25 33 0.54
26 13 0.21
27 15 0.25
ACGTcount: A:0.25, C:0.32, G:0.19, T:0.25
Consensus pattern (25 bp):
CTTAGAACACCCTAGGGACTTCCAT
Found at i:17564924 original size:26 final size:26
Alignment explanation
Indices: 17564552--17565047 Score: 241
Period size: 27 Copynumber: 18.8 Consensus size: 26
17564542 CTCCTTGGGT
*
17564552 GCTTCTATGCTTGGAACACCCTTGGCC
1 GCTTCTATGCTTGGAACACCCTAGG-C
** *
17564579 GCTTCTGCGCTTGGAACGCCCCT-GAGC
1 GCTTCTATGCTTGGAAC-ACCCTAG-GC
* * * * * *
17564606 GTTTCCACGCTTGGAGCACCCCTGGGT
1 GCTTCTATGCTTGGAACA-CCCTAGGC
* * * * *
17564633 GTTTATGTGCTTGGAATACCCTAGGT
1 GCTTCTATGCTTGGAACACCCTAGGC
* *
17564659 GCTTCTATGCTTGGAACGCTCTTAGGC
1 GCTTCTATGCTTGGAACAC-CCTAGGC
* ** * * *
17564686 GCTTTTGCGCTAGGAACGCCTCTGGGC
1 GCTTCTATGCTTGGAACACC-CTAGGC
* * *
17564713 ACTT-TCACGCTTGGAACACCCTTGAGC
1 GCTTCT-ATGCTTGGAACACCCTAG-GC
*
17564740 GCTTCTATGCTTGGAACACCCTTGGGC
1 GCTTCTATGCTTGGAACACCC-TAGGC
* * * * *
17564767 ACTTTTGTGCTTGAAAGACCCTTAGGC
1 GCTTCTATGCTTGGAACACCC-TAGGC
* * *
17564794 GCTTCTATGCCTGGAAGACCCTTAGGT
1 GCTTCTATGCTTGGAACACCC-TAGGC
** * * * *
17564821 GCTTCTGCGCTTAGAATAGCCTAGGG
1 GCTTCTATGCTTGGAACACCCTAGGC
* *
17564847 GCTTCCAT-CTTAGAACACCCTAGGC
1 GCTTCTATGCTTGGAACACCCTAGGC
* * *
17564872 ACTTCTA-ACTTGGAACACCCTTGGGC
1 GCTTCTATGCTTGGAACACCC-TAGGC
* *
17564898 ACTTCCATGCTTGGAACACCCTAGGC
1 GCTTCTATGCTTGGAACACCCTAGGC
* * * *
17564924 ACTTCCA-GTTTGTAACACCCCTAGGC
1 GCTTCTATGCTTGGAACA-CCCTAGGC
* * * *
17564950 TCTTCTA-GCTTGAAACACTTCTGGGC
1 GCTTCTATGCTTGGAACAC-CCTAGGC
* * *
17564976 GTTTCCATGCTTGGAACACCCTAAGC
1 GCTTCTATGCTTGGAACACCCTAGGC
* *
17565002 GCTTCCA-GCTTGGAACATCCTAGGC
1 GCTTCTATGCTTGGAACACCCTAGGC
* * *
17565027 TCTTTTATACTTGGAACACCC
1 GCTTCTATGCTTGGAACACCC
17565048 CTAATGTAAT
Statistics
Matches: 360, Mismatches: 92, Indels: 35
0.74 0.19 0.07
Matches are distributed among these distances:
25 59 0.16
26 107 0.30
27 185 0.51
28 9 0.03
ACGTcount: A:0.19, C:0.30, G:0.23, T:0.29
Consensus pattern (26 bp):
GCTTCTATGCTTGGAACACCCTAGGC
Found at i:17564975 original size:78 final size:77
Alignment explanation
Indices: 17564848--17565047 Score: 231
Period size: 78 Copynumber: 2.6 Consensus size: 77
17564838 AGCCTAGGGG
* * * *
17564848 CTTCCATCTTAGAACACCCTAGGCACTTCTAACTTGGAACACCCTTGGGCACTTCCATGCTTGGA
1 CTTCCAGCTTGGAACACCCTAGGCTCTTCTAACTTGAAACACCCTTGGGCACTTCCATGCTTGGA
*
17564913 ACACCCTAGGCA
66 ACACCCTAAGCA
* * * * **
17564925 CTTCCAGTTTGTAACACCCCTAGGCTCTTCTAGCTTGAAACA-CTTCTGGGCGTTTCCATGCTTG
1 CTTCCAGCTTGGAACA-CCCTAGGCTCTTCTAACTTGAAACACCCT-TGGGCACTTCCATGCTTG
*
17564989 GAACACCCTAAGCG
64 GAACACCCTAAGCA
* * *
17565003 CTTCCAGCTTGGAACATCCTAGGCTCTTTTATACTTGGAACACCC
1 CTTCCAGCTTGGAACACCCTAGGCTCTTCTA-ACTTGAAACACCC
17565048 CTAATGTAAT
Statistics
Matches: 100, Mismatches: 19, Indels: 6
0.80 0.15 0.05
Matches are distributed among these distances:
77 27 0.27
78 72 0.72
79 1 0.01
ACGTcount: A:0.23, C:0.32, G:0.17, T:0.28
Consensus pattern (77 bp):
CTTCCAGCTTGGAACACCCTAGGCTCTTCTAACTTGAAACACCCTTGGGCACTTCCATGCTTGGA
ACACCCTAAGCA
Found at i:17565051 original size:52 final size:52
Alignment explanation
Indices: 17564847--17565051 Score: 166
Period size: 52 Copynumber: 4.0 Consensus size: 52
17564837 TAGCCTAGGG
* * * * **
17564847 GCTTCCATCTTAGAACACCCTAGGCACTTCTA-ACTTGGAACACCCTTGGGC
1 GCTTCCAGCTTGGAACACCCTAGGCACTTCCATACTTGGAACACCCCTAAGC
* * *
17564898 ACTTCCATGCTTGGAACACCCTAGGCACTTCCAGT--TTGTAACACCCCTAGGC
1 GCTTCCA-GCTTGGAACACCCTAGGCACTTCCA-TACTTGGAACACCCCTAAGC
* * * * * ** *
17564950 TCTTCTAGCTTGAAACACTTCTGGGCGTTTCCATGCTTGGAACA-CCCTAAGC
1 GCTTCCAGCTTGGAACAC-CCTAGGCACTTCCATACTTGGAACACCCCTAAGC
* * **
17565002 GCTTCCAGCTTGGAACATCCTAGGCTCTTTTATACTTGGAACACCCCTAA
1 GCTTCCAGCTTGGAACACCCTAGGCACTTCCATACTTGGAACACCCCTAA
17565052 TGTAATTTTC
Statistics
Matches: 120, Mismatches: 27, Indels: 13
0.75 0.17 0.08
Matches are distributed among these distances:
51 35 0.29
52 78 0.65
53 7 0.06
ACGTcount: A:0.23, C:0.32, G:0.18, T:0.28
Consensus pattern (52 bp):
GCTTCCAGCTTGGAACACCCTAGGCACTTCCATACTTGGAACACCCCTAAGC
Found at i:17569700 original size:2 final size:2
Alignment explanation
Indices: 17569607--17569685 Score: 103
Period size: 2 Copynumber: 41.0 Consensus size: 2
17569597 AATTTAGTAC
* *
17569607 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA NTC TA T- TA -A TT
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA -TA TA TA TA TA TA
17569648 TA -A T- TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
17569686 ATTTGAGATA
Statistics
Matches: 68, Mismatches: 4, Indels: 10
0.83 0.05 0.12
Matches are distributed among these distances:
1 4 0.06
2 63 0.93
3 1 0.01
ACGTcount: A:0.47, C:0.01, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:17574408 original size:25 final size:25
Alignment explanation
Indices: 17574374--17574432 Score: 73
Period size: 25 Copynumber: 2.4 Consensus size: 25
17574364 GGTCTGTGAT
* * *
17574374 TATACATGGCAAAGCCACGGGTTGT
1 TATACGTGGCAAAGCCACGAGTTGA
* *
17574399 TATTCGTGGCAAGGCCACGAGTTGA
1 TATACGTGGCAAAGCCACGAGTTGA
17574424 TATACGTGG
1 TATACGTGG
17574433 TTGAGACCAA
Statistics
Matches: 28, Mismatches: 6, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
25 28 1.00
ACGTcount: A:0.25, C:0.19, G:0.31, T:0.25
Consensus pattern (25 bp):
TATACGTGGCAAAGCCACGAGTTGA
Found at i:17585262 original size:38 final size:40
Alignment explanation
Indices: 17585176--17585278 Score: 165
Period size: 38 Copynumber: 2.6 Consensus size: 40
17585166 ACTCGGCTCA
*
17585176 TGTACATCCCCCCACATCGTGCACATAGCCGGTGCCATCG
1 TGTACATCCCCCCACATCGTGCACATAGCCAGTGCCATCG
* *
17585216 TGTGCATCCCCCCACATCGTGCACA-A-TCAGTGCCATCG
1 TGTACATCCCCCCACATCGTGCACATAGCCAGTGCCATCG
17585254 TGTACATCCCCCCACATCGTGCACA
1 TGTACATCCCCCCACATCGTGCACA
17585279 CGAGCACTAT
Statistics
Matches: 59, Mismatches: 4, Indels: 2
0.91 0.06 0.03
Matches are distributed among these distances:
38 34 0.58
39 1 0.02
40 24 0.41
ACGTcount: A:0.21, C:0.41, G:0.17, T:0.20
Consensus pattern (40 bp):
TGTACATCCCCCCACATCGTGCACATAGCCAGTGCCATCG
Found at i:17585271 original size:19 final size:19
Alignment explanation
Indices: 17585211--17585274 Score: 58
Period size: 19 Copynumber: 3.4 Consensus size: 19
17585201 TAGCCGGTGC
*
17585211 CATCGTGTGCATCCCCCCA
1 CATCGTGTACATCCCCCCA
* ****
17585230 CATCGTGCACAATCAGTGC-
1 CATCGTGTAC-ATCCCCCCA
17585249 CATCGTGTACATCCCCCCA
1 CATCGTGTACATCCCCCCA
17585268 CATCGTG
1 CATCGTG
17585275 CACACGAGCA
Statistics
Matches: 32, Mismatches: 11, Indels: 4
0.68 0.23 0.09
Matches are distributed among these distances:
18 4 0.12
19 24 0.75
20 4 0.12
ACGTcount: A:0.20, C:0.41, G:0.17, T:0.22
Consensus pattern (19 bp):
CATCGTGTACATCCCCCCA
Found at i:17590002 original size:2 final size:2
Alignment explanation
Indices: 17589995--17590033 Score: 78
Period size: 2 Copynumber: 19.5 Consensus size: 2
17589985 ATAATAATGA
17589995 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
17590034 CTATGTCATA
Statistics
Matches: 37, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 37 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:17592131 original size:40 final size:38
Alignment explanation
Indices: 17592036--17592137 Score: 123
Period size: 38 Copynumber: 2.6 Consensus size: 38
17592026 AAAGTGCCCG
* * *
17592036 TGTGCACGATGTGGGGGGATGTACACGATGGCACTAAT
1 TGTGCACGATGTGGGGGGATGCACACGATGACACGAAT
* * **
17592074 TGTGCACGATGTAGGGGGATGCACACGATGACTCCGGCT
1 TGTGCACGATGTGGGGGGATGCACACGATGAC-ACGAAT
17592113 ATGTGCACGATGTGGGGGGATGCAC
1 -TGTGCACGATGTGGGGGGATGCAC
17592138 GTGAGCTGGA
Statistics
Matches: 54, Mismatches: 8, Indels: 2
0.84 0.12 0.03
Matches are distributed among these distances:
38 29 0.54
39 2 0.04
40 23 0.43
ACGTcount: A:0.22, C:0.19, G:0.38, T:0.22
Consensus pattern (38 bp):
TGTGCACGATGTGGGGGGATGCACACGATGACACGAAT
Found at i:17593598 original size:22 final size:22
Alignment explanation
Indices: 17593573--17593622 Score: 57
Period size: 22 Copynumber: 2.2 Consensus size: 22
17593563 AAAGTTGTAA
* *
17593573 ATGAAAGCTTA-AAAATTAGAGT
1 ATGAAAACTTAGAAAA-TAAAGT
17593595 ATGAAAACTTATGAAAATAAAGT
1 ATGAAAACTTA-GAAAATAAAGT
17593618 ATGAA
1 ATGAA
17593623 GCTAGAAAAG
Statistics
Matches: 24, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
22 10 0.42
23 10 0.42
24 4 0.17
ACGTcount: A:0.54, C:0.04, G:0.16, T:0.26
Consensus pattern (22 bp):
ATGAAAACTTAGAAAATAAAGT
Found at i:17593854 original size:31 final size:31
Alignment explanation
Indices: 17593775--17593961 Score: 157
Period size: 31 Copynumber: 6.1 Consensus size: 31
17593765 ACTTTCAACA
* * *
17593775 CACTACCTTTT-CTTATGGAGGCATAACCTTG
1 CACTACCTTTTAC-AATGGAGGTATAACCTTT
** * *
17593806 CTTTACC-TTTACTATGGAGGTATAATCTTT
1 CACTACCTTTTACAATGGAGGTATAACCTTT
* * *
17593836 CTCTACCTTTTACAATGGAGGTACAACCTTA
1 CACTACCTTTTACAATGGAGGTATAACCTTT
* * *
17593867 CAGTACCTTTTACAAAT-GAGGTACAACCTAAT
1 CACTACCTTTTAC-AATGGAGGTATAACCT-TT
* * *
17593899 -ACTAGCTTTTACAATTGAGGTATAACCTTA
1 CACTACCTTTTACAATGGAGGTATAACCTTT
* *
17593929 CACTACCTTTTACAATGGAAGTATAACTTTT
1 CACTACCTTTTACAATGGAGGTATAACCTTT
17593960 CA
1 CA
17593962 ACGATGGATT
Statistics
Matches: 126, Mismatches: 24, Indels: 12
0.78 0.15 0.07
Matches are distributed among these distances:
30 27 0.21
31 96 0.76
32 3 0.02
ACGTcount: A:0.30, C:0.21, G:0.13, T:0.36
Consensus pattern (31 bp):
CACTACCTTTTACAATGGAGGTATAACCTTT
Found at i:17598739 original size:19 final size:19
Alignment explanation
Indices: 17598712--17598766 Score: 74
Period size: 20 Copynumber: 2.8 Consensus size: 19
17598702 GAACTAGTCC
*
17598712 AAATAGAAATTTTAAGATG
1 AAATTGAAATTTTAAGATG
*
17598731 AAATTGAAAATTTTCAGATG
1 AAATTG-AAATTTTAAGATG
17598751 AAATTGAGAATTTTAA
1 AAATTGA-AATTTTAA
17598767 AAGCCCAGAA
Statistics
Matches: 31, Mismatches: 3, Indels: 3
0.84 0.08 0.08
Matches are distributed among these distances:
19 6 0.19
20 25 0.81
ACGTcount: A:0.49, C:0.02, G:0.15, T:0.35
Consensus pattern (19 bp):
AAATTGAAATTTTAAGATG
Found at i:17598743 original size:20 final size:20
Alignment explanation
Indices: 17598718--17598766 Score: 80
Period size: 20 Copynumber: 2.5 Consensus size: 20
17598708 GTCCAAATAG
17598718 AAATTTTAAGATGAAATTGA
1 AAATTTTAAGATGAAATTGA
*
17598738 AAATTTTCAGATGAAATTGA
1 AAATTTTAAGATGAAATTGA
*
17598758 GAATTTTAA
1 AAATTTTAA
17598767 AAGCCCAGAA
Statistics
Matches: 26, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
20 26 1.00
ACGTcount: A:0.47, C:0.02, G:0.14, T:0.37
Consensus pattern (20 bp):
AAATTTTAAGATGAAATTGA
Found at i:17611716 original size:20 final size:20
Alignment explanation
Indices: 17611680--17611717 Score: 58
Period size: 20 Copynumber: 1.9 Consensus size: 20
17611670 ATGTCAATTT
* *
17611680 TATTTAAAAACTTATTTAAA
1 TATTTAAAAAATAATTTAAA
17611700 TATTTAAAAAATAATTTA
1 TATTTAAAAAATAATTTA
17611718 TTGAATTATT
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 16 1.00
ACGTcount: A:0.53, C:0.03, G:0.00, T:0.45
Consensus pattern (20 bp):
TATTTAAAAAATAATTTAAA
Found at i:17615715 original size:2 final size:2
Alignment explanation
Indices: 17615708--17615769 Score: 99
Period size: 2 Copynumber: 31.5 Consensus size: 2
17615698 TAATTCANTA
*
17615708 TC TC TC TC TC TC TC TC TC TC T- TC TC TC TC TC TC AC TC TC TC
1 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC
*
17615749 TC AC TC TC TC TC TC TC TC TC T
1 TC TC TC TC TC TC TC TC TC TC T
17615770 AAAATGTCCA
Statistics
Matches: 55, Mismatches: 4, Indels: 2
0.90 0.07 0.03
Matches are distributed among these distances:
1 1 0.02
2 54 0.98
ACGTcount: A:0.03, C:0.48, G:0.00, T:0.48
Consensus pattern (2 bp):
TC
Found at i:17616004 original size:20 final size:20
Alignment explanation
Indices: 17615979--17616021 Score: 68
Period size: 20 Copynumber: 2.1 Consensus size: 20
17615969 AAGAAGAAGA
*
17615979 AGAAGAAGCTGGTGAAAGTT
1 AGAAGAAGCTGCTGAAAGTT
*
17615999 AGAAGAAGCTGCTGGAAGTT
1 AGAAGAAGCTGCTGAAAGTT
17616019 AGA
1 AGA
17616022 TATTTATGCT
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
20 21 1.00
ACGTcount: A:0.40, C:0.07, G:0.35, T:0.19
Consensus pattern (20 bp):
AGAAGAAGCTGCTGAAAGTT
Done.