Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: At_chr2
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: 61750188
ACGTcount: A:0.32, C:0.17, G:0.17, T:0.32
Warning! 1877335 characters in sequence are not A, C, G, or T
File 162 of 186
Found at i:53850611 original size:12 final size:12
Alignment explanation
Indices: 53850594--53850630 Score: 74
Period size: 12 Copynumber: 3.1 Consensus size: 12
53850584 TCAGATAGTT
53850594 ACACGGGTGGGG
1 ACACGGGTGGGG
53850606 ACACGGGTGGGG
1 ACACGGGTGGGG
53850618 ACACGGGTGGGG
1 ACACGGGTGGGG
53850630 A
1 A
53850631 GACGACCATG
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 25 1.00
ACGTcount: A:0.19, C:0.16, G:0.57, T:0.08
Consensus pattern (12 bp):
ACACGGGTGGGG
Found at i:53857742 original size:25 final size:25
Alignment explanation
Indices: 53857709--53857756 Score: 78
Period size: 25 Copynumber: 1.9 Consensus size: 25
53857699 TTATAATATG
* *
53857709 AAAATGACCATTTTGCCCCTAGGTA
1 AAAATGACCATTATACCCCTAGGTA
53857734 AAAATGACCATTATACCCCTAGG
1 AAAATGACCATTATACCCCTAGG
53857757 GTTTATACAT
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
25 21 1.00
ACGTcount: A:0.35, C:0.25, G:0.15, T:0.25
Consensus pattern (25 bp):
AAAATGACCATTATACCCCTAGGTA
Found at i:53857859 original size:20 final size:20
Alignment explanation
Indices: 53857793--53857859 Score: 98
Period size: 20 Copynumber: 3.4 Consensus size: 20
53857783 ATTTTGATAA
* *
53857793 ACATGGTATGTAAGATATGC
1 ACATGATATGTATGATATGC
*
53857813 ACATGACATGTATGATATGC
1 ACATGATATGTATGATATGC
*
53857833 ACATGATATGTATGACATGC
1 ACATGATATGTATGATATGC
53857853 ACATGAT
1 ACATGAT
53857860 GTATTTATGA
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:0.36, C:0.13, G:0.21, T:0.30
Consensus pattern (20 bp):
ACATGATATGTATGATATGC
Found at i:53857999 original size:23 final size:24
Alignment explanation
Indices: 53857908--53858027 Score: 154
Period size: 24 Copynumber: 5.0 Consensus size: 24
53857898 GGAGGAAGTG
*
53857908 CAAAAGGGCTTATGCCTCAGTTAT
1 CAAAAGGGCTTATGCCCCAGTTAT
53857932 CAAAAGGGCTTATGCCCCAGTTAT
1 CAAAAGGGCTTATGCCCCAGTTAT
*
53857956 CAAAAGGGCTTACGCCCCAGTTAT
1 CAAAAGGGCTTATGCCCCAGTTAT
* *
53857980 TAAAAGGGCTT-TGCCCCAGTTGT
1 CAAAAGGGCTTATGCCCCAGTTAT
* *
53858003 TAAAAGAGGC-TAGGCCTCCAGTTAT
1 CAAAAG-GGCTTATGCC-CCAGTTAT
53858028 ATGAAAAAGC
Statistics
Matches: 86, Mismatches: 7, Indels: 5
0.88 0.07 0.05
Matches are distributed among these distances:
23 17 0.20
24 62 0.72
25 7 0.08
ACGTcount: A:0.28, C:0.23, G:0.23, T:0.26
Consensus pattern (24 bp):
CAAAAGGGCTTATGCCCCAGTTAT
Found at i:53858257 original size:31 final size:31
Alignment explanation
Indices: 53858221--53858281 Score: 95
Period size: 31 Copynumber: 2.0 Consensus size: 31
53858211 CGTTTACAGT
*
53858221 AAAGGCTTCGGCCTAGTAATATGAAATATGG
1 AAAGGCTTCGACCTAGTAATATGAAATATGG
**
53858252 AAAGGCTTCGACCTAGTGTTATGAAATATG
1 AAAGGCTTCGACCTAGTAATATGAAATATG
53858282 AAATGTGAAA
Statistics
Matches: 27, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
31 27 1.00
ACGTcount: A:0.34, C:0.13, G:0.25, T:0.28
Consensus pattern (31 bp):
AAAGGCTTCGACCTAGTAATATGAAATATGG
Found at i:53865841 original size:25 final size:25
Alignment explanation
Indices: 53865805--53865852 Score: 69
Period size: 25 Copynumber: 1.9 Consensus size: 25
53865795 TTATAATATG
* *
53865805 AAAATGACCATTTTTCCCCTAGGTA
1 AAAATGACCATTATACCCCTAGGTA
*
53865830 AAAATGAGCATTATACCCCTAGG
1 AAAATGACCATTATACCCCTAGG
53865853 GTTTATACAT
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
25 20 1.00
ACGTcount: A:0.35, C:0.23, G:0.15, T:0.27
Consensus pattern (25 bp):
AAAATGACCATTATACCCCTAGGTA
Found at i:53865955 original size:20 final size:20
Alignment explanation
Indices: 53865889--53865955 Score: 98
Period size: 20 Copynumber: 3.4 Consensus size: 20
53865879 ATTTTGATAA
*
53865889 ACATGGTATGTATGATATGC
1 ACATGATATGTATGATATGC
*
53865909 ACATGACATGTATGATATGC
1 ACATGATATGTATGATATGC
* *
53865929 AAATGATATGTATGACATGC
1 ACATGATATGTATGATATGC
53865949 ACATGAT
1 ACATGAT
53865956 GTATTTATGA
Statistics
Matches: 41, Mismatches: 6, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
20 41 1.00
ACGTcount: A:0.36, C:0.12, G:0.21, T:0.31
Consensus pattern (20 bp):
ACATGATATGTATGATATGC
Found at i:53866085 original size:24 final size:24
Alignment explanation
Indices: 53866005--53866085 Score: 110
Period size: 24 Copynumber: 3.4 Consensus size: 24
53865995 GAGGAAGTGC
* *
53866005 AAAATGGCTTATGCCCCAGTTATC
1 AAAAGGGCTTATGCCCCAGTTATT
*
53866029 AAAAGGGCTTACGCCCCAGTTATT
1 AAAAGGGCTTATGCCCCAGTTATT
*
53866053 AAAAGGGCTT-TGCCCCAGTTGTT
1 AAAAGGGCTTATGCCCCAGTTATT
53866076 AAAAGAGGCT
1 AAAAG-GGCT
53866086 AGTCCTCTAG
Statistics
Matches: 51, Mismatches: 5, Indels: 2
0.88 0.09 0.03
Matches are distributed among these distances:
23 16 0.31
24 35 0.69
ACGTcount: A:0.30, C:0.22, G:0.22, T:0.26
Consensus pattern (24 bp):
AAAAGGGCTTATGCCCCAGTTATT
Found at i:53866331 original size:31 final size:31
Alignment explanation
Indices: 53866293--53866353 Score: 86
Period size: 31 Copynumber: 2.0 Consensus size: 31
53866283 CATTTACAGT
*
53866293 AAAGGCTTCGGCCCAGTAATATGAAATATGG
1 AAAGGCTTCGACCCAGTAATATGAAATATGG
* **
53866324 AAAGGCTTCGACCTAGTGTTATGAAATATG
1 AAAGGCTTCGACCCAGTAATATGAAATATG
53866354 AAATGTGAAA
Statistics
Matches: 26, Mismatches: 4, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
31 26 1.00
ACGTcount: A:0.34, C:0.15, G:0.25, T:0.26
Consensus pattern (31 bp):
AAAGGCTTCGACCCAGTAATATGAAATATGG
Found at i:53867510 original size:82 final size:82
Alignment explanation
Indices: 53867368--53867535 Score: 318
Period size: 82 Copynumber: 2.0 Consensus size: 82
53867358 TGTTTTGTAT
*
53867368 TCTTTATTCTTCTGAGATGTTTTCTTATTTAGTTATGAACTAAAACCCCTAAATACCTAAGGGGA
1 TCTTAATTCTTCTGAGATGTTTTCTTATTTAGTTATGAACTAAAACCCCTAAATACCTAAGGGGA
*
53867433 ATGAAACCTAAGACGAA
66 ATGAAACCTAAGACAAA
53867450 TCTTAATTCTTCTGAGATGTTTTCTTATTTAGTTATGAACTAAAACCCCTAAATACCTAAGGGGA
1 TCTTAATTCTTCTGAGATGTTTTCTTATTTAGTTATGAACTAAAACCCCTAAATACCTAAGGGGA
53867515 ATGAAACCTAAGACAAA
66 ATGAAACCTAAGACAAA
53867532 TCTT
1 TCTT
53867536 GTTATTATTT
Statistics
Matches: 84, Mismatches: 2, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
82 84 1.00
ACGTcount: A:0.35, C:0.17, G:0.14, T:0.35
Consensus pattern (82 bp):
TCTTAATTCTTCTGAGATGTTTTCTTATTTAGTTATGAACTAAAACCCCTAAATACCTAAGGGGA
ATGAAACCTAAGACAAA
Found at i:53886537 original size:45 final size:45
Alignment explanation
Indices: 53886471--53886696 Score: 210
Period size: 45 Copynumber: 5.1 Consensus size: 45
53886461 ATAGGATTCT
** *
53886471 GATATATGTGTTTTCTTGTAAGACCATGTCTGGGACATTGGCATC
1 GATATATGTGTTTTCGAGTAAGACCACGTCTGGGACATTGGCATC
* * * *
53886516 GATATATTTGTTTTTGAGTAAGACCACGTCTAGGACGTTGGCATC
1 GATATATGTGTTTTCGAGTAAGACCACGTCTGGGACATTGGCATC
* * * *
53886561 GATATATGCGTTTTCGAGTAAGACCACATCTGGGACGTTGGCTTC
1 GATATATGTGTTTTCGAGTAAGACCACGTCTGGGACATTGGCATC
* * * * * *
53886606 TATATATGTGGTTACGTGTAAGACCATGTCTGGGACATCGGCATC
1 GATATATGTGTTTTCGAGTAAGACCACGTCTGGGACATTGGCATC
* * * * *
53886651 G-TAT-T-TG-ATTCGTGTAAGACC-CTATCTGGGACAGTGGCATT
1 GATATATGTGTTTTCGAGTAAGACCAC-GTCTGGGACATTGGCATC
53886692 GATAT
1 GATAT
53886697 GAGATAGCAT
Statistics
Matches: 148, Mismatches: 31, Indels: 7
0.80 0.17 0.04
Matches are distributed among these distances:
41 27 0.18
42 5 0.03
43 1 0.01
44 3 0.02
45 112 0.76
ACGTcount: A:0.23, C:0.17, G:0.26, T:0.34
Consensus pattern (45 bp):
GATATATGTGTTTTCGAGTAAGACCACGTCTGGGACATTGGCATC
Found at i:53887959 original size:12 final size:12
Alignment explanation
Indices: 53887942--53887969 Score: 56
Period size: 12 Copynumber: 2.3 Consensus size: 12
53887932 TGTGGTTTAT
53887942 TTTGACATAAAA
1 TTTGACATAAAA
53887954 TTTGACATAAAA
1 TTTGACATAAAA
53887966 TTTG
1 TTTG
53887970 TCTTATAAGC
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 16 1.00
ACGTcount: A:0.43, C:0.07, G:0.11, T:0.39
Consensus pattern (12 bp):
TTTGACATAAAA
Found at i:53890052 original size:45 final size:44
Alignment explanation
Indices: 53889927--53890052 Score: 137
Period size: 44 Copynumber: 2.8 Consensus size: 44
53889917 ATGCCTAAAC
* * * * * *
53889927 TGAGTAAGACCATGTTGAAAGTTGTTATGGCATAAGGGCAACAA
1 TGAGTAAGACCATGCTGAAAGATGTTATGGCATCATGACAAAAA
* *
53889971 TGAGTAAGA-CATAGCTAAAAGATGTTATGACATCATGACAAAAA
1 TGAGTAAGACCAT-GCTGAAAGATGTTATGGCATCATGACAAAAA
* *
53890015 TGAGTAAGACCATGGCTGAAAGACGTTGTGGCATCATG
1 TGAGTAAGACCAT-GCTGAAAGATGTTATGGCATCATG
53890053 GTAAATAGGA
Statistics
Matches: 67, Mismatches: 13, Indels: 3
0.81 0.16 0.04
Matches are distributed among these distances:
43 3 0.04
44 41 0.61
45 23 0.34
ACGTcount: A:0.38, C:0.13, G:0.25, T:0.24
Consensus pattern (44 bp):
TGAGTAAGACCATGCTGAAAGATGTTATGGCATCATGACAAAAA
Found at i:53890304 original size:56 final size:57
Alignment explanation
Indices: 53890235--53890346 Score: 190
Period size: 56 Copynumber: 2.0 Consensus size: 57
53890225 ATGCTGTGAC
*
53890235 AACAAGATATGATTTGACAGTAAAACGAGTAAGACCATAGCTAAAAGATG-TATGGA
1 AACAAGAGATGATTTGACAGTAAAACGAGTAAGACCATAGCTAAAAGATGTTATGGA
* *
53890291 AACAAGAGATGATTTGACAGTAAAACGAGTAGGACCATAGCTGAAAGATGTTATGG
1 AACAAGAGATGATTTGACAGTAAAACGAGTAAGACCATAGCTAAAAGATGTTATGG
53890347 TAGTGTAGAG
Statistics
Matches: 52, Mismatches: 3, Indels: 1
0.93 0.05 0.02
Matches are distributed among these distances:
56 47 0.90
57 5 0.10
ACGTcount: A:0.44, C:0.11, G:0.24, T:0.21
Consensus pattern (57 bp):
AACAAGAGATGATTTGACAGTAAAACGAGTAAGACCATAGCTAAAAGATGTTATGGA
Found at i:53897611 original size:23 final size:23
Alignment explanation
Indices: 53897577--53897620 Score: 63
Period size: 22 Copynumber: 1.9 Consensus size: 23
53897567 TAACTAAAAA
53897577 GAAAACCTAAATCTAAAAAGAACT
1 GAAAACCTAAAT-TAAAAAGAACT
*
53897601 GAAAA-CTAAATTACAAAGAA
1 GAAAACCTAAATTAAAAAGAA
53897621 AATTATAAAT
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
22 8 0.42
23 6 0.32
24 5 0.26
ACGTcount: A:0.61, C:0.14, G:0.09, T:0.16
Consensus pattern (23 bp):
GAAAACCTAAATTAAAAAGAACT
Found at i:53901062 original size:34 final size:34
Alignment explanation
Indices: 53901024--53901089 Score: 114
Period size: 34 Copynumber: 1.9 Consensus size: 34
53901014 CCAATGTCAT
*
53901024 GACATCCTTACCTCGTGTCGTGATACTAATGTGA
1 GACATCCTTACCTCATGTCGTGATACTAATGTGA
*
53901058 GACATCCTTTCCTCATGTCGTGATACTAATGT
1 GACATCCTTACCTCATGTCGTGATACTAATGT
53901090 AAGGCCTACA
Statistics
Matches: 30, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
34 30 1.00
ACGTcount: A:0.23, C:0.24, G:0.18, T:0.35
Consensus pattern (34 bp):
GACATCCTTACCTCATGTCGTGATACTAATGTGA
Found at i:53902861 original size:20 final size:20
Alignment explanation
Indices: 53902808--53902861 Score: 56
Period size: 20 Copynumber: 2.6 Consensus size: 20
53902798 AACTTTTAGT
53902808 TATTTTTATTTTTGGACTGTA
1 TATTTTT-TTTTTGGACTGTA
* **
53902829 TAATTTTAGTTTGGA-TGATA
1 TATTTTTTTTTTGGACTG-TA
53902849 TATTTTTTTTTTG
1 TATTTTTTTTTTG
53902862 TCTTATTTAG
Statistics
Matches: 26, Mismatches: 6, Indels: 3
0.74 0.17 0.09
Matches are distributed among these distances:
19 2 0.08
20 18 0.69
21 6 0.23
ACGTcount: A:0.20, C:0.02, G:0.15, T:0.63
Consensus pattern (20 bp):
TATTTTTTTTTTGGACTGTA
Found at i:53903812 original size:13 final size:13
Alignment explanation
Indices: 53903794--53903830 Score: 51
Period size: 13 Copynumber: 2.9 Consensus size: 13
53903784 GCAAAGTGAG
53903794 TAGAAAATAAAAA
1 TAGAAAATAAAAA
53903807 TAG-AAATCAAAAA
1 TAGAAAAT-AAAAA
53903820 TAGAAAA-AAAA
1 TAGAAAATAAAA
53903831 CAAAGAAAAA
Statistics
Matches: 22, Mismatches: 0, Indels: 5
0.81 0.00 0.19
Matches are distributed among these distances:
12 8 0.36
13 11 0.50
14 3 0.14
ACGTcount: A:0.76, C:0.03, G:0.08, T:0.14
Consensus pattern (13 bp):
TAGAAAATAAAAA
Found at i:53904910 original size:46 final size:46
Alignment explanation
Indices: 53904829--53905018 Score: 200
Period size: 46 Copynumber: 4.0 Consensus size: 46
53904819 GATACTAGGG
* *
53904829 TTATGTGAGCTAGTGTAAGACCATGTTTGGAACATGGCATCAGCAT
1 TTATATGAGCTAGTGTAAGACCATGTCTGGAACATGGCATCAGCAT
* * *
53904875 TTATATGAGCTAGTGTAAGACCATGTCTGGGACATGGCATCGGCCT
1 TTATATGAGCTAGTGTAAGACCATGTCTGGAACATGGCATCAGCAT
* *
53904921 TTATATGTAGGCTAGTGTAAGACCATGTTTGGAACATGGCATCGGCACCGAT
1 TTATATG-A-GCTAGTGTAAGACCATGTCTGGAACATGGCAT---CAGC-AT
* * * * * * *
53904973 ATATAAGAGCCAATGTAAGATCATGTCTGGGACATGGCATCGGCAT
1 TTATATGAGCTAGTGTAAGACCATGTCTGGAACATGGCATCAGCAT
53905019 CTTACCCTTT
Statistics
Matches: 119, Mismatches: 19, Indels: 12
0.79 0.13 0.08
Matches are distributed among these distances:
46 50 0.42
47 3 0.03
48 30 0.25
50 27 0.23
51 3 0.03
52 6 0.05
ACGTcount: A:0.28, C:0.17, G:0.27, T:0.28
Consensus pattern (46 bp):
TTATATGAGCTAGTGTAAGACCATGTCTGGAACATGGCATCAGCAT
Found at i:53917185 original size:43 final size:43
Alignment explanation
Indices: 53917137--53917222 Score: 118
Period size: 43 Copynumber: 2.0 Consensus size: 43
53917127 CTTATCTACT
* * * *
53917137 ACGACCTACACGGCATCTTTCTTCTTCGGGGTCAATGGCATTC
1 ACGACCCACACGACATCTTTCTTCTTCGGAGTCAATGGAATTC
* *
53917180 ACGACCCATACGACATCTTTCTTCTTTGGAGTCAATGGAATTC
1 ACGACCCACACGACATCTTTCTTCTTCGGAGTCAATGGAATTC
53917223 CTGTCACAAA
Statistics
Matches: 37, Mismatches: 6, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
43 37 1.00
ACGTcount: A:0.22, C:0.28, G:0.19, T:0.31
Consensus pattern (43 bp):
ACGACCCACACGACATCTTTCTTCTTCGGAGTCAATGGAATTC
Found at i:53923454 original size:48 final size:48
Alignment explanation
Indices: 53923383--53923479 Score: 185
Period size: 48 Copynumber: 2.0 Consensus size: 48
53923373 GAGCACTTAC
*
53923383 TAATGAGCTTGAAAAGCTTGGAAACCCTACCTATGGTGGCTTAGGAAT
1 TAATGAGCTTGAAAAGCTTGGAAACCCTACCTATAGTGGCTTAGGAAT
53923431 TAATGAGCTTGAAAAGCTTGGAAACCCTACCTATAGTGGCTTAGGAAT
1 TAATGAGCTTGAAAAGCTTGGAAACCCTACCTATAGTGGCTTAGGAAT
53923479 T
1 T
53923480 TCGGCTGGAC
Statistics
Matches: 48, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
48 48 1.00
ACGTcount: A:0.32, C:0.16, G:0.24, T:0.28
Consensus pattern (48 bp):
TAATGAGCTTGAAAAGCTTGGAAACCCTACCTATAGTGGCTTAGGAAT
Found at i:53925687 original size:28 final size:28
Alignment explanation
Indices: 53925632--53925747 Score: 155
Period size: 28 Copynumber: 4.2 Consensus size: 28
53925622 AGCATGGATG
* *
53925632 CCAG-AACAGAT-ATTGTGACAGAGTCA
1 CCAGAAACAGATAATTGTGGCAGAGCCA
* *
53925658 CCAGATACAGATAATTGTGGCAGGGCCA
1 CCAGAAACAGATAATTGTGGCAGAGCCA
*
53925686 CCAGAAACAGATATTTGTGGCAGAGCCA
1 CCAGAAACAGATAATTGTGGCAGAGCCA
* *
53925714 CCAAAAACAGATATTTGTGGCAGAGCCA
1 CCAGAAACAGATAATTGTGGCAGAGCCA
53925742 CCAGAA
1 CCAGAA
53925748 CGCTTCCTCT
Statistics
Matches: 79, Mismatches: 9, Indels: 2
0.88 0.10 0.02
Matches are distributed among these distances:
26 4 0.05
27 6 0.08
28 69 0.87
ACGTcount: A:0.37, C:0.22, G:0.24, T:0.17
Consensus pattern (28 bp):
CCAGAAACAGATAATTGTGGCAGAGCCA
Found at i:53927025 original size:18 final size:19
Alignment explanation
Indices: 53926979--53927028 Score: 59
Period size: 18 Copynumber: 2.7 Consensus size: 19
53926969 GCTATAGAGG
*
53926979 AAAAGAAGTAGA-AGAGAA
1 AAAAGAAGAAGAGAGAGAA
* *
53926997 AATAGATGAAGAGAG-GAA
1 AAAAGAAGAAGAGAGAGAA
53927015 AAAAGAAGAAGAGA
1 AAAAGAAGAAGAGA
53927029 AAAGAATTGT
Statistics
Matches: 26, Mismatches: 5, Indels: 2
0.79 0.15 0.06
Matches are distributed among these distances:
18 24 0.92
19 2 0.08
ACGTcount: A:0.64, C:0.00, G:0.30, T:0.06
Consensus pattern (19 bp):
AAAAGAAGAAGAGAGAGAA
Found at i:53927030 original size:15 final size:16
Alignment explanation
Indices: 53926978--53927034 Score: 55
Period size: 15 Copynumber: 3.5 Consensus size: 16
53926968 GGCTATAGAG
*
53926978 GAAAAGAAGTAGAAGA
1 GAAAAGAAGAAGAAGA
*
53926994 GAAAATAGATGAAG-AGA
1 G-AAA-AGAAGAAGAAGA
53927011 GGAAAA-AAGAAGAAGA
1 -GAAAAGAAGAAGAAGA
53927027 GAAAAGAA
1 GAAAAGAA
53927035 TTGTCAGAAA
Statistics
Matches: 33, Mismatches: 3, Indels: 10
0.72 0.07 0.22
Matches are distributed among these distances:
15 10 0.30
16 7 0.21
17 9 0.27
18 7 0.21
ACGTcount: A:0.65, C:0.00, G:0.30, T:0.05
Consensus pattern (16 bp):
GAAAAGAAGAAGAAGA
Found at i:53929196 original size:19 final size:19
Alignment explanation
Indices: 53929172--53929209 Score: 51
Period size: 19 Copynumber: 1.9 Consensus size: 19
53929162 GCTATGAATC
53929172 CCTAAT-CTCCTTATTTGAG
1 CCTAATACTCCTT-TTTGAG
53929191 CCTAATAACTCCTTTTTGA
1 CCTAAT-ACTCCTTTTTGA
53929210 TGAACCAAGG
Statistics
Matches: 17, Mismatches: 0, Indels: 3
0.85 0.00 0.15
Matches are distributed among these distances:
19 6 0.35
20 5 0.29
21 6 0.35
ACGTcount: A:0.24, C:0.26, G:0.08, T:0.42
Consensus pattern (19 bp):
CCTAATACTCCTTTTTGAG
Found at i:53931767 original size:27 final size:27
Alignment explanation
Indices: 53931715--53931767 Score: 72
Period size: 27 Copynumber: 2.0 Consensus size: 27
53931705 CTACTCCATA
* *
53931715 TCATTCTTCTCTCTTTCTTCCTCATCT
1 TCATTCTCCTCTCTTTCTTCCCCATCT
53931742 TCATTCTCCTCATCTTTC-TCCCCATC
1 TCATTCTCCTC-TCTTTCTTCCCCATC
53931768 ATCCTCGGAC
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
27 17 0.74
28 6 0.26
ACGTcount: A:0.09, C:0.42, G:0.00, T:0.49
Consensus pattern (27 bp):
TCATTCTCCTCTCTTTCTTCCCCATCT
Found at i:53936005 original size:20 final size:20
Alignment explanation
Indices: 53935980--53936046 Score: 75
Period size: 20 Copynumber: 3.4 Consensus size: 20
53935970 CTTATACGGA
53935980 ATTGCACTTCGATGCCTCTT
1 ATTGCACTTCGATGCCTCTT
*
53936000 ATTGCACATTTG-TGCCTCTT
1 ATTGCAC-TTCGATGCCTCTT
* *
53936020 TTTGCACTTC-AGTGCCTCTA
1 ATTGCACTTCGA-TGCCTCTT
53936040 ATTGCAC
1 ATTGCAC
53936047 ATTTGTGCTT
Statistics
Matches: 39, Mismatches: 5, Indels: 6
0.78 0.10 0.12
Matches are distributed among these distances:
19 2 0.05
20 34 0.87
21 3 0.08
ACGTcount: A:0.16, C:0.28, G:0.15, T:0.40
Consensus pattern (20 bp):
ATTGCACTTCGATGCCTCTT
Found at i:53936054 original size:20 final size:19
Alignment explanation
Indices: 53935979--53936054 Score: 71
Period size: 20 Copynumber: 3.8 Consensus size: 19
53935969 GCTTATACGG
*
53935979 AATTGCACTTCGATGCCTCT
1 AATTGCACTTTG-TGCCTCT
*
53935999 TATTGCACATTTGTGCCTCT
1 AATTGCAC-TTTGTGCCTCT
** *
53936019 TTTTGCACTTCAGTGCCTCT
1 AATTGCACTT-TGTGCCTCT
53936039 AATTGCACATTTGTGC
1 AATTGCAC-TTTGTGC
53936055 TTTTTTTTTC
Statistics
Matches: 46, Mismatches: 7, Indels: 6
0.78 0.12 0.10
Matches are distributed among these distances:
19 2 0.04
20 39 0.85
21 5 0.11
ACGTcount: A:0.17, C:0.26, G:0.16, T:0.41
Consensus pattern (19 bp):
AATTGCACTTTGTGCCTCT
Found at i:53939301 original size:27 final size:27
Alignment explanation
Indices: 53939270--53939447 Score: 196
Period size: 27 Copynumber: 6.6 Consensus size: 27
53939260 TAAATTGTAC
53939270 AGCACTAAGTGTGCGATTTGACTATGT
1 AGCACTAAGTGTGCGATTTGACTATGT
* * ** *
53939297 TGCACTAAGTGTCCGAAATGAATATG-
1 AGCACTAAGTGTGCGATTTGACTATGT
* * *
53939323 ATGCACTAAGTGTGCGAATTGACCATGC
1 A-GCACTAAGTGTGCGATTTGACTATGT
*
53939351 GGCACTAAGTGTGCGAGTTTGACTATGT
1 AGCACTAAGTGTGCGA-TTTGACTATGT
* *
53939379 AGCACTAAGTGTGCGATTTGATTACGT
1 AGCACTAAGTGTGCGATTTGACTATGT
* * *
53939406 AGCACTAAGTGTGCGAGTTGATTATAT
1 AGCACTAAGTGTGCGATTTGACTATGT
*
53939433 AGCACTGAGTGTGCG
1 AGCACTAAGTGTGCG
53939448 GACTCAATAT
Statistics
Matches: 127, Mismatches: 21, Indels: 6
0.82 0.14 0.04
Matches are distributed among these distances:
27 104 0.82
28 23 0.18
ACGTcount: A:0.27, C:0.16, G:0.28, T:0.30
Consensus pattern (27 bp):
AGCACTAAGTGTGCGATTTGACTATGT
Found at i:53939384 original size:82 final size:81
Alignment explanation
Indices: 53939271--53939426 Score: 224
Period size: 82 Copynumber: 1.9 Consensus size: 81
53939261 AAATTGTACA
* *
53939271 GCACTAAGTGTGCGATTTGACTATGTTGCACTAAGTGTCCGAAATGAATATG-ATGCACTAAGTG
1 GCACTAAGTGTGCGATTTGACTATGTAGCACTAAGTGTCCGAAATGAATACGTA-GCACTAAGTG
53939335 TGCGAATTGACCATGCG
65 TGCGAATTGACCATGCG
* ** *
53939352 GCACTAAGTGTGCGAGTTTGACTATGTAGCACTAAGTGTGCGATTTGATTACGTAGCACTAAGTG
1 GCACTAAGTGTGCGA-TTTGACTATGTAGCACTAAGTGTCCGAAATGAATACGTAGCACTAAGTG
*
53939417 TGCGAGTTGA
65 TGCGAATTGA
53939427 TTATATAGCA
Statistics
Matches: 66, Mismatches: 7, Indels: 3
0.87 0.09 0.04
Matches are distributed among these distances:
81 15 0.23
82 50 0.76
83 1 0.02
ACGTcount: A:0.27, C:0.16, G:0.28, T:0.29
Consensus pattern (81 bp):
GCACTAAGTGTGCGATTTGACTATGTAGCACTAAGTGTCCGAAATGAATACGTAGCACTAAGTGT
GCGAATTGACCATGCG
Found at i:53939438 original size:82 final size:81
Alignment explanation
Indices: 53939267--53939447 Score: 220
Period size: 82 Copynumber: 2.2 Consensus size: 81
53939257 GATTAAATTG
* *
53939267 TACAGCACTAAGTGTGCGATTTGACTATGTTGCACTAAGTGTCCGAAATGAATATGATGCACTAA
1 TACAGCACTAAGTGTGCGATTTGACTATGTAGCACTAAGTGTCCGAAATGAATACGATGCACTAA
53939332 GTGTGCGAATTGACCA
66 GTGTGCGAATTGACCA
* * * ** *
53939348 TGCGGCACTAAGTGTGCGAGTTTGACTATGTAGCACTAAGTGTGCGATTTGATTACG-TAGCACT
1 TACAGCACTAAGTGTGCGA-TTTGACTATGTAGCACTAAGTGTCCGAAATGAATACGAT-GCACT
* **
53939412 AAGTGTGCGAGTTGATTA
64 AAGTGTGCGAATTGACCA
* *
53939430 TATAGCACTGAGTGTGCG
1 TACAGCACTAAGTGTGCG
53939448 GACTCAATAT
Statistics
Matches: 83, Mismatches: 15, Indels: 3
0.82 0.15 0.03
Matches are distributed among these distances:
81 18 0.22
82 65 0.78
ACGTcount: A:0.27, C:0.16, G:0.27, T:0.30
Consensus pattern (81 bp):
TACAGCACTAAGTGTGCGATTTGACTATGTAGCACTAAGTGTCCGAAATGAATACGATGCACTAA
GTGTGCGAATTGACCA
Found at i:53948776 original size:27 final size:27
Alignment explanation
Indices: 53948745--53948922 Score: 187
Period size: 27 Copynumber: 6.6 Consensus size: 27
53948735 TAAATTGTAC
53948745 AGCACTAAGTGTGCGATTTGACTATGT
1 AGCACTAAGTGTGCGATTTGACTATGT
* ** *
53948772 TGCACTAAGTGTGCGAAATGAATATG-
1 AGCACTAAGTGTGCGATTTGACTATGT
* * *
53948798 ATGCACTAAGTGTGCGAATTGACCATGC
1 A-GCACTAAGTGTGCGATTTGACTATGT
*
53948826 GGCACTAAGTGTGCGAGTTTGACTATGT
1 AGCACTAAGTGTGCGA-TTTGACTATGT
* *
53948854 AGCACTAAGTGTGCGATTTGATTACGT
1 AGCACTAAGTGTGCGATTTGACTATGT
* * * * *
53948881 AGCACTAAGTGTGCTAGTTGATTGTAT
1 AGCACTAAGTGTGCGATTTGACTATGT
*
53948908 AGCACTGAGTGTGCG
1 AGCACTAAGTGTGCG
53948923 GACTCAATAT
Statistics
Matches: 126, Mismatches: 22, Indels: 6
0.82 0.14 0.04
Matches are distributed among these distances:
27 103 0.82
28 23 0.18
ACGTcount: A:0.26, C:0.15, G:0.28, T:0.30
Consensus pattern (27 bp):
AGCACTAAGTGTGCGATTTGACTATGT
Found at i:53948913 original size:82 final size:81
Alignment explanation
Indices: 53948738--53948922 Score: 219
Period size: 82 Copynumber: 2.3 Consensus size: 81
53948728 GCGGGATTAA
* *
53948738 ATTGTACAGCACTAAGTGTGCGATTTGACTATGTTGCACTAAGTGTGCGAAATGAATATGATGCA
1 ATTGTACAGCACTAAGTGTGCGATTTGACTATGTAGCACTAAGTGTGCGAAATGAATACGATGCA
53948803 CTAAGTGTGCGAATTG
66 CTAAGTGTGCGAATTG
*** * * ** *
53948819 ACCATGCGGCACTAAGTGTGCGAGTTTGACTATGTAGCACTAAGTGTGCGATTTGATTACG-TAG
1 ATTGTACAGCACTAAGTGTGCGA-TTTGACTATGTAGCACTAAGTGTGCGAAATGAATACGAT-G
* *
53948883 CACTAAGTGTGCTAGTTG
64 CACTAAGTGTGCGAATTG
* *
53948901 ATTGTATAGCACTGAGTGTGCG
1 ATTGTACAGCACTAAGTGTGCG
53948923 GACTCAATAT
Statistics
Matches: 83, Mismatches: 19, Indels: 3
0.79 0.18 0.03
Matches are distributed among these distances:
81 19 0.23
82 64 0.77
ACGTcount: A:0.26, C:0.15, G:0.28, T:0.31
Consensus pattern (81 bp):
ATTGTACAGCACTAAGTGTGCGATTTGACTATGTAGCACTAAGTGTGCGAAATGAATACGATGCA
CTAAGTGTGCGAATTG
Found at i:53964842 original size:5 final size:5
Alignment explanation
Indices: 53964832--53964860 Score: 58
Period size: 5 Copynumber: 5.8 Consensus size: 5
53964822 AATTCTTACA
53964832 TGATT TGATT TGATT TGATT TGATT TGAT
1 TGATT TGATT TGATT TGATT TGATT TGAT
53964861 AAGGCATATC
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 24 1.00
ACGTcount: A:0.21, C:0.00, G:0.21, T:0.59
Consensus pattern (5 bp):
TGATT
Found at i:53971681 original size:5 final size:5
Alignment explanation
Indices: 53971671--53971699 Score: 58
Period size: 5 Copynumber: 5.8 Consensus size: 5
53971661 AATTCTTACA
53971671 TGATT TGATT TGATT TGATT TGATT TGAT
1 TGATT TGATT TGATT TGATT TGATT TGAT
53971700 AAGGCATATC
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 24 1.00
ACGTcount: A:0.21, C:0.00, G:0.21, T:0.59
Consensus pattern (5 bp):
TGATT
Found at i:53974845 original size:31 final size:31
Alignment explanation
Indices: 53974810--53974879 Score: 86
Period size: 31 Copynumber: 2.3 Consensus size: 31
53974800 CTTGTCACTT
* * *
53974810 GTAGCCGAAGCTATCACTATTCACTGATCAG
1 GTAGCCGAAGCTACCACTATTCACTAATCAA
* * *
53974841 GTAGCCGGAGCTACCATTTTTCACTAATCAA
1 GTAGCCGAAGCTACCACTATTCACTAATCAA
53974872 GTAGCCGA
1 GTAGCCGA
53974880 TGATCAGGTA
Statistics
Matches: 32, Mismatches: 7, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
31 32 1.00
ACGTcount: A:0.29, C:0.26, G:0.20, T:0.26
Consensus pattern (31 bp):
GTAGCCGAAGCTACCACTATTCACTAATCAA
Found at i:53974901 original size:46 final size:46
Alignment explanation
Indices: 53974834--53974925 Score: 130
Period size: 46 Copynumber: 2.0 Consensus size: 46
53974824 CACTATTCAC
** *
53974834 TGATCAGGTAGCCGGAGCTACCATTTTTCACTAATCAAGTAGCCGA
1 TGATCAGGTAGCCAAAGCTACCACTTTTCACTAATCAAGTAGCCGA
* * *
53974880 TGATCAGGTAGCCAAAGCTACCACTTTTCATTGATCAGGTAGCCGA
1 TGATCAGGTAGCCAAAGCTACCACTTTTCACTAATCAAGTAGCCGA
53974926 AGCTACCACT
Statistics
Matches: 40, Mismatches: 6, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
46 40 1.00
ACGTcount: A:0.28, C:0.24, G:0.22, T:0.26
Consensus pattern (46 bp):
TGATCAGGTAGCCAAAGCTACCACTTTTCACTAATCAAGTAGCCGA
Found at i:53974918 original size:31 final size:31
Alignment explanation
Indices: 53974880--53974938 Score: 109
Period size: 31 Copynumber: 1.9 Consensus size: 31
53974870 AAGTAGCCGA
53974880 TGATCAGGTAGCCAAAGCTACCACTTTTCAT
1 TGATCAGGTAGCCAAAGCTACCACTTTTCAT
*
53974911 TGATCAGGTAGCCGAAGCTACCACTTTT
1 TGATCAGGTAGCCAAAGCTACCACTTTT
53974939 TACTTGCCAT
Statistics
Matches: 27, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
31 27 1.00
ACGTcount: A:0.27, C:0.25, G:0.19, T:0.29
Consensus pattern (31 bp):
TGATCAGGTAGCCAAAGCTACCACTTTTCAT
Found at i:53975011 original size:50 final size:50
Alignment explanation
Indices: 53974918--53975044 Score: 173
Period size: 50 Copynumber: 2.5 Consensus size: 50
53974908 CATTGATCAG
* * * * *
53974918 GTAGCCGAAGCTACCACTTTTTACTTGCCATTTCTCCTTGATCAGATAAGT
1 GTAGCCGAAGCTATCACTTATCACTT-TCATTTCTCATTGATCAGATAAGT
** *
53974969 GTAGTTGAAGCTATCACTTATCACTTTCATTTGTCATTGATCAGATAAGT
1 GTAGCCGAAGCTATCACTTATCACTTTCATTTCTCATTGATCAGATAAGT
53975019 GTAGCCGAAGCTATCACTTATCACTT
1 GTAGCCGAAGCTATCACTTATCACTT
53975045 GTTGCCATGG
Statistics
Matches: 66, Mismatches: 10, Indels: 1
0.86 0.13 0.01
Matches are distributed among these distances:
50 45 0.68
51 21 0.32
ACGTcount: A:0.26, C:0.22, G:0.16, T:0.36
Consensus pattern (50 bp):
GTAGCCGAAGCTATCACTTATCACTTTCATTTCTCATTGATCAGATAAGT
Found at i:53975065 original size:11 final size:11
Alignment explanation
Indices: 53975049--53975078 Score: 60
Period size: 11 Copynumber: 2.7 Consensus size: 11
53975039 TCACTTGTTG
53975049 CCATGGTCCAA
1 CCATGGTCCAA
53975060 CCATGGTCCAA
1 CCATGGTCCAA
53975071 CCATGGTC
1 CCATGGTC
53975079 TTTTCCTTCA
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 19 1.00
ACGTcount: A:0.23, C:0.37, G:0.20, T:0.20
Consensus pattern (11 bp):
CCATGGTCCAA
Found at i:53982353 original size:22 final size:22
Alignment explanation
Indices: 53982303--53982362 Score: 61
Period size: 22 Copynumber: 2.8 Consensus size: 22
53982293 ATTTTTTAAA
53982303 TTTTTTTCTTGCTATTTTTTTC
1 TTTTTTTCTTGCTATTTTTTTC
* * * *
53982325 ATGTTTTGTTGCTATTTTCTT-
1 TTTTTTTCTTGCTATTTTTTTC
*
53982346 TTTTTTT-TTACTATTTT
1 TTTTTTTCTTGCTATTTT
53982363 GCTACCATTT
Statistics
Matches: 31, Mismatches: 7, Indels: 2
0.77 0.17 0.05
Matches are distributed among these distances:
20 9 0.29
21 5 0.16
22 17 0.55
ACGTcount: A:0.08, C:0.10, G:0.07, T:0.75
Consensus pattern (22 bp):
TTTTTTTCTTGCTATTTTTTTC
Found at i:53983912 original size:124 final size:124
Alignment explanation
Indices: 53983692--53984007 Score: 510
Period size: 124 Copynumber: 2.5 Consensus size: 124
53983682 GATAAAATCA
**
53983692 AAGCAGGATGCTTTATCAGAAGAATTTCTGAAGCCGCGCTCA-CGTGGACGCGCTTTTGCTACAG
1 AAGCAGGATGCTTTATCAGAAGAATTTCTGAAATCGCGC-CATCGTGGACGCGCTTTTGCTACAG
53983756 TAGGTCCTGGAAAAATAATTTCGAGTTGACGTTTCTGAGCAAATAGTATAAAAAA-ACTTC
65 TAGGTCCTGGAAAAATAATTTCGAGTTGACGTTTCTGAGCAAATAGTATAAAAAACA-TTC
* * *
53983816 AAGCAGGATGCTTTATTAGAAGAATTTCTAAAATCGCGCCATCGTGGATGCGCTTTTGCTACAGT
1 AAGCAGGATGCTTTATCAGAAGAATTTCTGAAATCGCGCCATCGTGGACGCGCTTTTGCTACAGT
*
53983881 AGGTCCTGGAAAAATAATTTCGAGTTGACGTTTCTGAGTAAATAGTATAAAAAACGATTC
66 AGGTCCTGGAAAAATAATTTCGAGTTGACGTTTCTGAGCAAATAGTATAAAAAAC-ATTC
* * *
53983941 AAGTAGGATGCTTTATCAGAAGAATTTCTGAAATCGCGCCCTCGTGGACACGCTTTTGCTACAGT
1 AAGCAGGATGCTTTATCAGAAGAATTTCTGAAATCGCGCCATCGTGGACGCGCTTTTGCTACAGT
53984006 AG
66 AG
53984008 CATGTTTGGG
Statistics
Matches: 177, Mismatches: 12, Indels: 5
0.91 0.06 0.03
Matches are distributed among these distances:
123 2 0.01
124 110 0.62
125 64 0.36
126 1 0.01
ACGTcount: A:0.31, C:0.18, G:0.22, T:0.29
Consensus pattern (124 bp):
AAGCAGGATGCTTTATCAGAAGAATTTCTGAAATCGCGCCATCGTGGACGCGCTTTTGCTACAGT
AGGTCCTGGAAAAATAATTTCGAGTTGACGTTTCTGAGCAAATAGTATAAAAAACATTC
Found at i:53985282 original size:5 final size:6
Alignment explanation
Indices: 53985248--53985312 Score: 51
Period size: 5 Copynumber: 12.3 Consensus size: 6
53985238 CTTAATCATT
53985248 TTAATA TTAA-A TTAATA -T-ATA TT-ATA TTAAT- TTAATA TTAA-A
1 TTAATA TTAATA TTAATA TTAATA TTAATA TTAATA TTAATA TTAATA
53985290 TCT--TA TTAA-A TTAATA -TAATA TT
1 T-TAATA TTAATA TTAATA TTAATA TT
53985313 TATCTACAAG
Statistics
Matches: 49, Mismatches: 0, Indels: 20
0.71 0.00 0.29
Matches are distributed among these distances:
4 4 0.08
5 31 0.63
6 14 0.29
ACGTcount: A:0.48, C:0.02, G:0.00, T:0.51
Consensus pattern (6 bp):
TTAATA
Found at i:53985287 original size:26 final size:26
Alignment explanation
Indices: 53985248--53985312 Score: 71
Period size: 26 Copynumber: 2.5 Consensus size: 26
53985238 CTTAATCATT
*
53985248 TTAATATTAA-ATTAATAT-ATATTATA
1 TTAAT-TTAATATTAA-ATCATATTAAA
*
53985274 TTAATTTAATATTAAATCTTATTAAA
1 TTAATTTAATATTAAATCATATTAAA
*
53985300 TTAATATAATATT
1 TTAATTTAATATT
53985313 TATCTACAAG
Statistics
Matches: 34, Mismatches: 3, Indels: 4
0.83 0.07 0.10
Matches are distributed among these distances:
25 6 0.18
26 28 0.82
ACGTcount: A:0.48, C:0.02, G:0.00, T:0.51
Consensus pattern (26 bp):
TTAATTTAATATTAAATCATATTAAA
Found at i:53985389 original size:25 final size:25
Alignment explanation
Indices: 53985335--53985389 Score: 60
Period size: 25 Copynumber: 2.2 Consensus size: 25
53985325 AAACATTAAA
*
53985335 TTTAATTTAATATTAAGATAATCAC
1 TTTAATTTAATATTAAGAAAATCAC
*
53985360 TTTAATATTAA-ATTAATAAAAT-AC
1 TTTAAT-TTAATATTAAGAAAATCAC
53985384 TATTAA
1 T-TTAA
53985390 GATAAGTATT
Statistics
Matches: 26, Mismatches: 2, Indels: 4
0.81 0.06 0.12
Matches are distributed among these distances:
24 3 0.12
25 19 0.73
26 4 0.15
ACGTcount: A:0.49, C:0.05, G:0.02, T:0.44
Consensus pattern (25 bp):
TTTAATTTAATATTAAGAAAATCAC
Found at i:53997651 original size:26 final size:26
Alignment explanation
Indices: 53997622--53997673 Score: 70
Period size: 26 Copynumber: 2.0 Consensus size: 26
53997612 CTTGCTCGAC
*
53997622 CTTCACTGGGTCTAGGTT-AGAATTTT
1 CTTCACTCGGTCTAGGTTCA-AATTTT
*
53997648 CTTCCCTCGGTCTAGGTTCAAATTTT
1 CTTCACTCGGTCTAGGTTCAAATTTT
53997674 GTATTTCTTG
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
26 22 0.96
27 1 0.04
ACGTcount: A:0.17, C:0.21, G:0.19, T:0.42
Consensus pattern (26 bp):
CTTCACTCGGTCTAGGTTCAAATTTT
Found at i:53999691 original size:19 final size:18
Alignment explanation
Indices: 53999649--53999691 Score: 52
Period size: 18 Copynumber: 2.3 Consensus size: 18
53999639 ATGCAAGTAG
*
53999649 TTTGGTTTGTAATGTGGA
1 TTTGGTTTGTAATGTGAA
53999667 TTTGGTTTGATAAT-TGAA
1 TTTGGTTTG-TAATGTGAA
53999685 TTGTGGT
1 TT-TGGT
53999692 GTCAATGAGG
Statistics
Matches: 22, Mismatches: 1, Indels: 3
0.85 0.04 0.12
Matches are distributed among these distances:
18 14 0.64
19 8 0.36
ACGTcount: A:0.19, C:0.00, G:0.30, T:0.51
Consensus pattern (18 bp):
TTTGGTTTGTAATGTGAA
Found at i:54000609 original size:21 final size:21
Alignment explanation
Indices: 54000585--54000626 Score: 84
Period size: 21 Copynumber: 2.0 Consensus size: 21
54000575 AGCGCCATAG
54000585 GTACCCGTTATTAGAGTTAGA
1 GTACCCGTTATTAGAGTTAGA
54000606 GTACCCGTTATTAGAGTTAGA
1 GTACCCGTTATTAGAGTTAGA
54000627 AGTTTTAAGC
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 21 1.00
ACGTcount: A:0.29, C:0.14, G:0.24, T:0.33
Consensus pattern (21 bp):
GTACCCGTTATTAGAGTTAGA
Found at i:54003435 original size:20 final size:20
Alignment explanation
Indices: 54003377--54003441 Score: 77
Period size: 20 Copynumber: 3.4 Consensus size: 20
54003367 TTCAATTATG
54003377 ATTAAACTTAATCACTTTAAT
1 ATTAAA-TTAATCACTTTAAT
54003398 ATTAAATTAAT-A---TAAT
1 ATTAAATTAATCACTTTAAT
54003414 ATTAAGA-TAATCACTTTAAT
1 ATTAA-ATTAATCACTTTAAT
54003434 ATTAAATT
1 ATTAAATT
54003442 CACAAAATAC
Statistics
Matches: 38, Mismatches: 0, Indels: 13
0.75 0.00 0.25
Matches are distributed among these distances:
16 13 0.34
17 2 0.05
19 2 0.05
20 15 0.39
21 6 0.16
ACGTcount: A:0.48, C:0.08, G:0.02, T:0.43
Consensus pattern (20 bp):
ATTAAATTAATCACTTTAAT
Found at i:54007660 original size:15 final size:15
Alignment explanation
Indices: 54007637--54007678 Score: 66
Period size: 15 Copynumber: 2.8 Consensus size: 15
54007627 TCATTTACGT
* *
54007637 AAATATTGAAATTTC
1 AAATTTTGAAAATTC
54007652 AAATTTTGAAAATTC
1 AAATTTTGAAAATTC
54007667 AAATTTTGAAAA
1 AAATTTTGAAAA
54007679 GTATAGGGAC
Statistics
Matches: 25, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
15 25 1.00
ACGTcount: A:0.50, C:0.05, G:0.07, T:0.38
Consensus pattern (15 bp):
AAATTTTGAAAATTC
Found at i:54010708 original size:23 final size:23
Alignment explanation
Indices: 54010676--54010731 Score: 76
Period size: 23 Copynumber: 2.4 Consensus size: 23
54010666 TATGGAACAG
*
54010676 AACAGAACACTGTCGAAGTGGAT
1 AACAGAACACTGTCAAAGTGGAT
* *
54010699 AACAGGACACTGTTAAAGTGGAT
1 AACAGAACACTGTCAAAGTGGAT
*
54010722 AATAGAACAC
1 AACAGAACAC
54010732 CGCAGAAGCG
Statistics
Matches: 28, Mismatches: 5, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
23 28 1.00
ACGTcount: A:0.43, C:0.16, G:0.23, T:0.18
Consensus pattern (23 bp):
AACAGAACACTGTCAAAGTGGAT
Found at i:54014543 original size:15 final size:15
Alignment explanation
Indices: 54014520--54014549 Score: 51
Period size: 15 Copynumber: 2.0 Consensus size: 15
54014510 AACATATGTA
*
54014520 CATTGTTTCACATAT
1 CATTATTTCACATAT
54014535 CATTATTTCACATAT
1 CATTATTTCACATAT
54014550 TTCTCATCAC
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.30, C:0.20, G:0.03, T:0.47
Consensus pattern (15 bp):
CATTATTTCACATAT
Found at i:54015812 original size:18 final size:20
Alignment explanation
Indices: 54015776--54015814 Score: 64
Period size: 18 Copynumber: 2.0 Consensus size: 20
54015766 TTTGGCATCA
54015776 ATTTTAGAAAATGTATTGAT
1 ATTTTAGAAAATGTATTGAT
54015796 ATTTT-GAAAAT-TATTGAT
1 ATTTTAGAAAATGTATTGAT
54015814 A
1 A
54015815 CTCGATACTT
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
18 8 0.42
19 6 0.32
20 5 0.26
ACGTcount: A:0.41, C:0.00, G:0.13, T:0.46
Consensus pattern (20 bp):
ATTTTAGAAAATGTATTGAT
Found at i:54015979 original size:23 final size:22
Alignment explanation
Indices: 54015936--54015979 Score: 52
Period size: 22 Copynumber: 2.0 Consensus size: 22
54015926 ATTTTGTTCA
*
54015936 ATTTTAACTTTTATTTAAAAAC
1 ATTTTAACTTTTATATAAAAAC
* *
54015958 ATTTTAATTTGTTATATCAAAA
1 ATTTTAACTT-TTATATAAAAA
54015980 TAAATTATCA
Statistics
Matches: 18, Mismatches: 3, Indels: 1
0.82 0.14 0.05
Matches are distributed among these distances:
22 9 0.50
23 9 0.50
ACGTcount: A:0.41, C:0.07, G:0.02, T:0.50
Consensus pattern (22 bp):
ATTTTAACTTTTATATAAAAAC
Found at i:54020388 original size:17 final size:18
Alignment explanation
Indices: 54020361--54020418 Score: 59
Period size: 17 Copynumber: 3.3 Consensus size: 18
54020351 AAAAATATAT
*
54020361 ATTTTTTATTTTTTAATA
1 ATTTTTAATTTTTTAATA
**
54020379 A-TTTTAATTTTAAAATA
1 ATTTTTAATTTTTTAATA
54020396 ATTTTTATATTTTTT--TA
1 ATTTTTA-ATTTTTTAATA
54020413 ATTTTT
1 ATTTTT
54020419 TGAATTTAAA
Statistics
Matches: 33, Mismatches: 5, Indels: 5
0.77 0.12 0.12
Matches are distributed among these distances:
17 22 0.67
18 6 0.18
19 5 0.15
ACGTcount: A:0.31, C:0.00, G:0.00, T:0.69
Consensus pattern (18 bp):
ATTTTTAATTTTTTAATA
Found at i:54025004 original size:16 final size:16
Alignment explanation
Indices: 54024979--54025037 Score: 66
Period size: 16 Copynumber: 3.6 Consensus size: 16
54024969 AGTCGTTCTC
54024979 TTTATAATAATTATTT
1 TTTATAATAATTATTT
*
54024995 TTTATGATAA-TATTT
1 TTTATAATAATTATTT
54025010 TATTATAATAATTAAGTTT
1 T-TTATAATAATT-A-TTT
*
54025029 GTTATAATA
1 TTTATAATA
54025038 TTGGGCTTTA
Statistics
Matches: 36, Mismatches: 3, Indels: 6
0.80 0.07 0.13
Matches are distributed among these distances:
15 6 0.17
16 17 0.47
17 1 0.03
18 9 0.25
19 3 0.08
ACGTcount: A:0.39, C:0.00, G:0.05, T:0.56
Consensus pattern (16 bp):
TTTATAATAATTATTT
Found at i:54039270 original size:9 final size:9
Alignment explanation
Indices: 54039256--54039282 Score: 54
Period size: 9 Copynumber: 3.0 Consensus size: 9
54039246 TATTCCCTGT
54039256 AAAATAATA
1 AAAATAATA
54039265 AAAATAATA
1 AAAATAATA
54039274 AAAATAATA
1 AAAATAATA
54039283 GTAAAGGGGA
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
9 18 1.00
ACGTcount: A:0.78, C:0.00, G:0.00, T:0.22
Consensus pattern (9 bp):
AAAATAATA
Found at i:54040375 original size:20 final size:18
Alignment explanation
Indices: 54040350--54040386 Score: 56
Period size: 20 Copynumber: 1.9 Consensus size: 18
54040340 ATTGCTAAGT
54040350 TGTAAAATGAGTTGTAAATG
1 TGTAAAAT-AGTTG-AAATG
54040370 TGTAAAATAGTTGAAAT
1 TGTAAAATAGTTGAAAT
54040387 TATGAGTTGC
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
18 4 0.24
19 5 0.29
20 8 0.47
ACGTcount: A:0.43, C:0.00, G:0.22, T:0.35
Consensus pattern (18 bp):
TGTAAAATAGTTGAAATG
Found at i:54043382 original size:46 final size:46
Alignment explanation
Indices: 54043280--54043532 Score: 160
Period size: 46 Copynumber: 5.5 Consensus size: 46
54043270 ATTTGTGTGC
* * * * *
54043280 CAGTGTAAGACCATGTATGGGACATGGCATC-GGCATTGAGACGAG-GG
1 CAGTGTAAGA-CATGTCTGGGACAT-GCATCAGCCA-CGAGATGAGAGT
54043327 CTAGTGTAAGACATGTCTGGGACATGCATCAGCCAC-AGTATGAGAGT
1 C-AGTGTAAGACATGTCTGGGACATGCATCAGCCACGAG-ATGAGAGT
* * * ** *
54043374 CAGTGTAAGACATGTCTAGGACATGCATCGGCCTCGAGATGTTAGC
1 CAGTGTAAGACATGTCTGGGACATGCATCAGCCACGAGATGAGAGT
* * * ** * * * *
54043420 CAATGTCAGACATGTCCGGGACATGTGTCGGCTACGAGATGTG-CT
1 CAGTGTAAGACATGTCTGGGACATGCATCAGCCACGAGATGAGAGT
* * * * *
54043465 -AGTGTAAGATATGTCTGGGACATGCGTCAG-CACG-GTTACATGTGT
1 CAGTGTAAGACATGTCTGGGACATGCATCAGCCACGAGAT-GA-GAGT
*
54043510 CAGTGTAAGACCTGTCTGGGACA
1 CAGTGTAAGACATGTCTGGGACA
54043533 CGGCATCGAC
Statistics
Matches: 162, Mismatches: 35, Indels: 19
0.75 0.16 0.09
Matches are distributed among these distances:
42 2 0.01
43 3 0.02
44 25 0.15
45 3 0.02
46 99 0.61
47 21 0.13
48 9 0.06
ACGTcount: A:0.26, C:0.19, G:0.31, T:0.24
Consensus pattern (46 bp):
CAGTGTAAGACATGTCTGGGACATGCATCAGCCACGAGATGAGAGT
Found at i:54046330 original size:20 final size:18
Alignment explanation
Indices: 54046305--54046341 Score: 56
Period size: 20 Copynumber: 1.9 Consensus size: 18
54046295 ATTGCTAAGT
54046305 TGTAAAATGAGTTGTAAATG
1 TGTAAAAT-AGTTG-AAATG
54046325 TGTAAAATAGTTGAAAT
1 TGTAAAATAGTTGAAAT
54046342 TATGAGTTGC
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
18 4 0.24
19 5 0.29
20 8 0.47
ACGTcount: A:0.43, C:0.00, G:0.22, T:0.35
Consensus pattern (18 bp):
TGTAAAATAGTTGAAATG
Found at i:54049753 original size:20 final size:20
Alignment explanation
Indices: 54049728--54049768 Score: 64
Period size: 20 Copynumber: 2.0 Consensus size: 20
54049718 TAAATTCTAA
* *
54049728 AAAGATAAATACATTTAATT
1 AAAGATAAATAAATATAATT
54049748 AAAGATAAATAAATATAATT
1 AAAGATAAATAAATATAATT
54049768 A
1 A
54049769 GAATCAAATC
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
20 19 1.00
ACGTcount: A:0.61, C:0.02, G:0.05, T:0.32
Consensus pattern (20 bp):
AAAGATAAATAAATATAATT
Found at i:54051569 original size:30 final size:30
Alignment explanation
Indices: 54051535--54051594 Score: 102
Period size: 30 Copynumber: 2.0 Consensus size: 30
54051525 TACTTTATTA
54051535 TTAATTTTGTTATTATTTTAAAGGCATTTG
1 TTAATTTTGTTATTATTTTAAAGGCATTTG
* *
54051565 TTAATTTTGTTATTATTTTAGAGGTATTTG
1 TTAATTTTGTTATTATTTTAAAGGCATTTG
54051595 CTTGTTAAGT
Statistics
Matches: 28, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
30 28 1.00
ACGTcount: A:0.25, C:0.02, G:0.15, T:0.58
Consensus pattern (30 bp):
TTAATTTTGTTATTATTTTAAAGGCATTTG
Found at i:54054587 original size:46 final size:48
Alignment explanation
Indices: 54054515--54054634 Score: 145
Period size: 48 Copynumber: 2.5 Consensus size: 48
54054505 GACAAGACAG
* * *
54054515 GACAGAAATGAGCCATGTAAGTCCATATCA-GT-TATATGGCTTTGGA
1 GACAGAAATGAGTCATGTAAGTCCATATCATATATATATGGCATTGGA
* * *
54054561 GACAGTAATGAGTCATGTAAGCCCATATTATATATATATGGCATTGGA
1 GACAGAAATGAGTCATGTAAGTCCATATCATATATATATGGCATTGGA
* * *
54054609 GACAGGAATAATTCATGTAAGTCCAT
1 GACAGAAATGAGTCATGTAAGTCCAT
54054635 GTCGAAGACA
Statistics
Matches: 62, Mismatches: 10, Indels: 2
0.84 0.14 0.03
Matches are distributed among these distances:
46 26 0.42
47 1 0.02
48 35 0.56
ACGTcount: A:0.35, C:0.14, G:0.22, T:0.29
Consensus pattern (48 bp):
GACAGAAATGAGTCATGTAAGTCCATATCATATATATATGGCATTGGA
Found at i:54057800 original size:57 final size:57
Alignment explanation
Indices: 54057722--54057832 Score: 213
Period size: 57 Copynumber: 1.9 Consensus size: 57
54057712 AGAAAAATTT
54057722 ATTTTATTATTATTTTGAGGTTCATGATATGATTGCATGATTGTGTGAAAATTTTAA
1 ATTTTATTATTATTTTGAGGTTCATGATATGATTGCATGATTGTGTGAAAATTTTAA
*
54057779 ATTTTATTATTATTTTTAGGTTCATGATATGATTGCATGATTGTGTGAAAATTT
1 ATTTTATTATTATTTTGAGGTTCATGATATGATTGCATGATTGTGTGAAAATTT
54057833 CGTGATGAAA
Statistics
Matches: 53, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
57 53 1.00
ACGTcount: A:0.29, C:0.04, G:0.17, T:0.50
Consensus pattern (57 bp):
ATTTTATTATTATTTTGAGGTTCATGATATGATTGCATGATTGTGTGAAAATTTTAA
Found at i:54058985 original size:46 final size:48
Alignment explanation
Indices: 54058913--54059032 Score: 147
Period size: 48 Copynumber: 2.5 Consensus size: 48
54058903 GACAAGACAG
* * * *
54058913 GACAGAAATGAGCCATGTAAGTCCATATCA-GT-TATATGGCTTTGGA
1 GACAGGAATGAACCATGTAAGTCCATATCATATATATATGGCATTGGA
* *
54058959 GACAGGAATGAACCATGTAAGCCCATATTATATATATATGGCATTGGA
1 GACAGGAATGAACCATGTAAGTCCATATCATATATATATGGCATTGGA
*
54059007 GACAGGAAT-AATTCATGTAAGTCCAT
1 GACAGGAATGAA-CCATGTAAGTCCAT
54059033 GTCGAAGACA
Statistics
Matches: 63, Mismatches: 8, Indels: 4
0.84 0.11 0.05
Matches are distributed among these distances:
46 26 0.41
47 3 0.05
48 34 0.54
ACGTcount: A:0.36, C:0.15, G:0.22, T:0.28
Consensus pattern (48 bp):
GACAGGAATGAACCATGTAAGTCCATATCATATATATATGGCATTGGA
Found at i:54059360 original size:36 final size:36
Alignment explanation
Indices: 54059308--54059379 Score: 135
Period size: 36 Copynumber: 2.0 Consensus size: 36
54059298 AATTTATTTG
*
54059308 CTTGTAAGCTTTCTAAGCCTAGTGCTTACTCTCTTT
1 CTTGTAAGCTTACTAAGCCTAGTGCTTACTCTCTTT
54059344 CTTGTAAGCTTACTAAGCCTAGTGCTTACTCTCTTT
1 CTTGTAAGCTTACTAAGCCTAGTGCTTACTCTCTTT
54059380 ATTTTCTTTT
Statistics
Matches: 35, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
36 35 1.00
ACGTcount: A:0.18, C:0.25, G:0.14, T:0.43
Consensus pattern (36 bp):
CTTGTAAGCTTACTAAGCCTAGTGCTTACTCTCTTT
Found at i:54061806 original size:46 final size:46
Alignment explanation
Indices: 54061756--54062621 Score: 1587
Period size: 46 Copynumber: 18.8 Consensus size: 46
54061746 TGGTTGAGCA
54061756 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAATG
1 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAATG
* * *
54061802 TCCGAACTCGTTGAGTTGAGTCCGAGTTC-GTGA--GATG-TAACTAGG
1 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAA-T--G
54061847 CATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAATG
1 --TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAATG
54061895 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAATG
1 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAATG
54061941 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAATG
1 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAATG
54061987 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAATG
1 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAATG
54062033 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAATG
1 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAATG
54062079 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAATG
1 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAATG
54062125 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAATG
1 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAATG
54062171 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAATG
1 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAATG
54062217 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAATG
1 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAATG
54062263 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAATG
1 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAATG
54062309 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAATG
1 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAATG
54062355 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAATG
1 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAATG
54062401 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAATG
1 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAATG
54062447 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAATG
1 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAATG
54062493 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAATG
1 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAATG
* *
54062539 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATACGAACG
1 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAATG
* * *
54062585 CCCGAGCTCGTTGAGTTGAGTCCGAGTTCGCTTATGG
1 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGG
54062622 GCGGGTTACA
Statistics
Matches: 800, Mismatches: 11, Indels: 18
0.97 0.01 0.02
Matches are distributed among these distances:
42 2 0.00
43 5 0.01
45 3 0.00
46 751 0.94
47 29 0.04
48 3 0.00
50 5 0.01
51 2 0.00
ACGTcount: A:0.22, C:0.20, G:0.28, T:0.30
Consensus pattern (46 bp):
TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAATG
Found at i:54067704 original size:13 final size:12
Alignment explanation
Indices: 54067683--54067717 Score: 52
Period size: 12 Copynumber: 2.8 Consensus size: 12
54067673 CCTTTTGGGC
54067683 CTTTGTTTTTTT
1 CTTTGTTTTTTT
54067695 CTTTGTTTTTTT
1 CTTTGTTTTTTT
*
54067707 ATTCTGTTTTT
1 CTT-TGTTTTT
54067718 GATTTTCAAC
Statistics
Matches: 21, Mismatches: 1, Indels: 1
0.91 0.04 0.04
Matches are distributed among these distances:
12 14 0.67
13 7 0.33
ACGTcount: A:0.03, C:0.09, G:0.09, T:0.80
Consensus pattern (12 bp):
CTTTGTTTTTTT
Found at i:54068271 original size:29 final size:30
Alignment explanation
Indices: 54068224--54068288 Score: 114
Period size: 29 Copynumber: 2.2 Consensus size: 30
54068214 GGAGATAAAG
54068224 CAAGAGTTAGCACAAACAAAAGACAGAAAT
1 CAAGAGTTAGCACAAACAAAAGACAGAAAT
*
54068254 CAAG-GTTAGCACAAACAAAAGAGAGAAAT
1 CAAGAGTTAGCACAAACAAAAGACAGAAAT
54068283 CAAGAG
1 CAAGAG
54068289 ATAGAAAGTT
Statistics
Matches: 33, Mismatches: 1, Indels: 2
0.92 0.03 0.06
Matches are distributed among these distances:
29 28 0.85
30 5 0.15
ACGTcount: A:0.55, C:0.15, G:0.20, T:0.09
Consensus pattern (30 bp):
CAAGAGTTAGCACAAACAAAAGACAGAAAT
Found at i:54069218 original size:57 final size:58
Alignment explanation
Indices: 54069156--54069283 Score: 136
Period size: 57 Copynumber: 2.2 Consensus size: 58
54069146 TACAAGTTCA
* * * *
54069156 GGCTAAATCCTTTTTATGACATATGCTCTAAAGAGCTTGAT-CT-GGATTACCTGTCCG
1 GGCTAAATCCTTTTCATAACATATGCTCGAAAGAGCTT-ATACTAGGATTACCCGTCCG
* * * * *
54069213 GGCTAAAT-CTAATTCATAACATATGCTCGAGAGGGCTTATATTAGGATTACCCGTCTG
1 GGCTAAATCCT-TTTCATAACATATGCTCGAAAGAGCTTATACTAGGATTACCCGTCCG
54069271 GGCTAAATCCTTT
1 GGCTAAATCCTTT
54069284 CTATAATAAG
Statistics
Matches: 57, Mismatches: 10, Indels: 7
0.77 0.14 0.09
Matches are distributed among these distances:
56 4 0.07
57 30 0.53
58 21 0.37
59 2 0.04
ACGTcount: A:0.27, C:0.20, G:0.20, T:0.34
Consensus pattern (58 bp):
GGCTAAATCCTTTTCATAACATATGCTCGAAAGAGCTTATACTAGGATTACCCGTCCG
Found at i:54076164 original size:22 final size:21
Alignment explanation
Indices: 54076139--54076179 Score: 64
Period size: 21 Copynumber: 1.9 Consensus size: 21
54076129 GAAGGAATAG
54076139 TTATATAAAATTTTAAATTAAT
1 TTAT-TAAAATTTTAAATTAAT
*
54076161 TTATTTAAATTTTAAATTA
1 TTATTAAAATTTTAAATTA
54076180 GTAATTGTTG
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
21 14 0.78
22 4 0.22
ACGTcount: A:0.46, C:0.00, G:0.00, T:0.54
Consensus pattern (21 bp):
TTATTAAAATTTTAAATTAAT
Found at i:54085365 original size:16 final size:15
Alignment explanation
Indices: 54085340--54085387 Score: 51
Period size: 16 Copynumber: 3.1 Consensus size: 15
54085330 TTATATTATT
*
54085340 ATAATAATAAAATAA
1 ATAATAATAAAAGAA
54085355 ATAAGTAATAAAAGAA
1 ATAA-TAATAAAAGAA
* *
54085371 ATAGAAAAAAAAAGAA
1 ATA-ATAATAAAAGAA
54085387 A
1 A
54085388 AGAAAGCCAA
Statistics
Matches: 28, Mismatches: 3, Indels: 3
0.82 0.09 0.09
Matches are distributed among these distances:
15 4 0.14
16 23 0.82
17 1 0.04
ACGTcount: A:0.75, C:0.00, G:0.08, T:0.17
Consensus pattern (15 bp):
ATAATAATAAAAGAA
Found at i:54085388 original size:10 final size:10
Alignment explanation
Indices: 54085373--54085427 Score: 51
Period size: 10 Copynumber: 5.6 Consensus size: 10
54085363 TAAAAGAAAT
*
54085373 AGAAAAAAAA
1 AGAAAAAGAA
54085383 AG-AAAAGAA
1 AGAAAAAGAA
* *
54085392 AGCCAAAACAA
1 AG-AAAAAGAA
*
54085403 A-AAACAGAA
1 AGAAAAAGAA
54085412 AGAAAAAGAA
1 AGAAAAAGAA
54085422 AGAAAA
1 AGAAAA
54085428 GGGGGAAAGA
Statistics
Matches: 36, Mismatches: 6, Indels: 6
0.75 0.12 0.12
Matches are distributed among these distances:
9 14 0.39
10 15 0.42
11 7 0.19
ACGTcount: A:0.78, C:0.07, G:0.15, T:0.00
Consensus pattern (10 bp):
AGAAAAAGAA
Found at i:54089641 original size:44 final size:44
Alignment explanation
Indices: 54089593--54089819 Score: 156
Period size: 44 Copynumber: 5.2 Consensus size: 44
54089583 GTATATTCAG
*
54089593 TCTACTCCAATGCCATTTCAGGGAGAAGAGATTTGTAGCCTCGA
1 TCTACTCCAATGCCATTTCAGGGAGAAGAGATTTGTAGCTTCGA
* * ** * * * *
54089637 TCTACTCTACTGGAACTTCAAGGAGATACGA-A-TTGTGGCTTTGA
1 TCTACTCCAATGCCATTTCAGGGAGA-A-GAGATTTGTAGCTTCGA
* ** *
54089681 GCCGCTCCAAT-ACATTTCAGGGAGAAGAGATTTGTAGCTTCGA
1 TCTACTCCAATGCCATTTCAGGGAGAAGAGATTTGTAGCTTCGA
* * * ** * * * ** *
54089724 TCTTCTTCACTGGAACTTCAAGGAGATACA-AACTGTGGCTTCGA
1 TCTACTCCAATGCCATTTCAGGGAGA-AGAGATTTGTAGCTTCGA
* **
54089768 GCCGCTCCAATGCCATTTCAGGGAGAAGAGATTTGTAGCTTCGA
1 TCTACTCCAATGCCATTTCAGGGAGAAGAGATTTGTAGCTTCGA
54089812 TCTACTCC
1 TCTACTCC
54089820 GCTGAAACTT
Statistics
Matches: 127, Mismatches: 49, Indels: 14
0.67 0.26 0.07
Matches are distributed among these distances:
41 2 0.02
42 2 0.02
43 28 0.22
44 89 0.70
45 4 0.03
46 2 0.02
ACGTcount: A:0.26, C:0.22, G:0.23, T:0.28
Consensus pattern (44 bp):
TCTACTCCAATGCCATTTCAGGGAGAAGAGATTTGTAGCTTCGA
Found at i:54089706 original size:87 final size:88
Alignment explanation
Indices: 54089597--54089847 Score: 380
Period size: 87 Copynumber: 2.9 Consensus size: 88
54089587 ATTCAGTCTA
*
54089597 CTCCAATGCCATTTCAGGGAGAAGAGATTTGTAGCCTCGATCTACTCTACTGGAACTTCAAGGAG
1 CTCCAATGCCATTTCAGGGAGAAGAGATTTGTAGCTTCGATCTACTCTACTGGAACTTCAAGGAG
*
54089662 ATACGAATTGTGGCTTTGAGCCG
66 ATACGAATTGTGGCTTCGAGCCG
* *
54089685 CTCCAAT-ACATTTCAGGGAGAAGAGATTTGTAGCTTCGATCTTCT-TCACTGGAACTTCAAGGA
1 CTCCAATGCCATTTCAGGGAGAAGAGATTTGTAGCTTCGATCTACTCT-ACTGGAACTTCAAGGA
* *
54089748 GATACAAACTGTGGCTTCGAGCCG
65 GATACGAATTGTGGCTTCGAGCCG
** * *
54089772 CTCCAATGCCATTTCAGGGAGAAGAGATTTGTAGCTTCGATCTACTCCGCTGAAACTTCAATGAG
1 CTCCAATGCCATTTCAGGGAGAAGAGATTTGTAGCTTCGATCTACTCTACTGGAACTTCAAGGAG
*
54089837 ATAAGAATTGT
66 ATACGAATTGT
54089848 TGATTTCAAC
Statistics
Matches: 145, Mismatches: 15, Indels: 6
0.87 0.09 0.04
Matches are distributed among these distances:
86 1 0.01
87 79 0.54
88 65 0.45
ACGTcount: A:0.28, C:0.21, G:0.23, T:0.28
Consensus pattern (88 bp):
CTCCAATGCCATTTCAGGGAGAAGAGATTTGTAGCTTCGATCTACTCTACTGGAACTTCAAGGAG
ATACGAATTGTGGCTTCGAGCCG
Found at i:54090257 original size:64 final size:64
Alignment explanation
Indices: 54090178--54090304 Score: 209
Period size: 64 Copynumber: 2.0 Consensus size: 64
54090168 CATGTATCTG
* *
54090178 TGCTTATGCCAAATAATTAAGATGTTATGATCGAAATGAATCAAATGCTCCTAACCAGATGTGA
1 TGCTTATGCCAAATAATTAAGATGATATGATCGAAATGAATCAAATACTCCTAACCAGATGTGA
* * *
54090242 TGCTTATGTCAAATAATTAGGATGATATGATCGAAATGAATCAAATACTCCTAACTAGATGTG
1 TGCTTATGCCAAATAATTAAGATGATATGATCGAAATGAATCAAATACTCCTAACCAGATGTG
54090305 TTATGAATGA
Statistics
Matches: 58, Mismatches: 5, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
64 58 1.00
ACGTcount: A:0.38, C:0.14, G:0.17, T:0.31
Consensus pattern (64 bp):
TGCTTATGCCAAATAATTAAGATGATATGATCGAAATGAATCAAATACTCCTAACCAGATGTGA
Found at i:54094964 original size:19 final size:20
Alignment explanation
Indices: 54094940--54094986 Score: 71
Period size: 19 Copynumber: 2.5 Consensus size: 20
54094930 TGTGAAAATC
54094940 CAATGCAAATG-ATGCAATG
1 CAATGCAAATGCATGCAATG
*
54094959 CAATGCAAATGCATGGAATG
1 CAATGCAAATGCATGCAATG
54094979 -AATGCAAA
1 CAATGCAAA
54094987 AGAAAGAAAG
Statistics
Matches: 26, Mismatches: 1, Indels: 2
0.90 0.03 0.07
Matches are distributed among these distances:
19 19 0.73
20 7 0.27
ACGTcount: A:0.45, C:0.15, G:0.21, T:0.19
Consensus pattern (20 bp):
CAATGCAAATGCATGCAATG
Found at i:54099341 original size:110 final size:110
Alignment explanation
Indices: 54099148--54099506 Score: 718
Period size: 110 Copynumber: 3.3 Consensus size: 110
54099138 ACTAAACTAG
54099148 AAGAGGAAAAACGGAACCAATAATACAAACAATGATAACTGAACTACAATTTCTCAATATTCTTC
1 AAGAGGAAAAACGGAACCAATAATACAAACAATGATAACTGAACTACAATTTCTCAATATTCTTC
54099213 AAGGTAATTCTTATAACAATGATAATTGAAAAAAATTCGAAAGAA
66 AAGGTAATTCTTATAACAATGATAATTGAAAAAAATTCGAAAGAA
54099258 AAGAGGAAAAACGGAACCAATAATACAAACAATGATAACTGAACTACAATTTCTCAATATTCTTC
1 AAGAGGAAAAACGGAACCAATAATACAAACAATGATAACTGAACTACAATTTCTCAATATTCTTC
54099323 AAGGTAATTCTTATAACAATGATAATTGAAAAAAATTCGAAAGAA
66 AAGGTAATTCTTATAACAATGATAATTGAAAAAAATTCGAAAGAA
54099368 AAGAGGAAAAACGGAACCAATAATACAAACAATGATAACTGAACTACAATTTCTCAATATTCTTC
1 AAGAGGAAAAACGGAACCAATAATACAAACAATGATAACTGAACTACAATTTCTCAATATTCTTC
54099433 AAGGTAATTCTTATAACAATGATAATTGAAAAAAATTCGAAAGAA
66 AAGGTAATTCTTATAACAATGATAATTGAAAAAAATTCGAAAGAA
54099478 AAGAGGAAAAACGGAACCAATAATACAAA
1 AAGAGGAAAAACGGAACCAATAATACAAA
54099507 TAATAGTGGA
Statistics
Matches: 249, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
110 249 1.00
ACGTcount: A:0.51, C:0.14, G:0.12, T:0.23
Consensus pattern (110 bp):
AAGAGGAAAAACGGAACCAATAATACAAACAATGATAACTGAACTACAATTTCTCAATATTCTTC
AAGGTAATTCTTATAACAATGATAATTGAAAAAAATTCGAAAGAA
Found at i:54103319 original size:60 final size:60
Alignment explanation
Indices: 54103202--54103322 Score: 215
Period size: 60 Copynumber: 2.0 Consensus size: 60
54103192 CATTCTGTAT
*
54103202 GTTGGATTCATCTTCATGTTTAAATTATCCAAATTAAATGCTAATTATACTATTATGACC
1 GTTGGATTCATCTTCATGTTTAAATTATCCAAATTAAATGCTAATTATACTAGTATGACC
* *
54103262 GTTGGATTCATCTTCATGTTTAAATTATCCAAATTAAATGCTAATTATATTGGTATGACC
1 GTTGGATTCATCTTCATGTTTAAATTATCCAAATTAAATGCTAATTATACTAGTATGACC
54103322 G
1 G
54103323 ATCTTTTGTT
Statistics
Matches: 58, Mismatches: 3, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
60 58 1.00
ACGTcount: A:0.32, C:0.14, G:0.12, T:0.41
Consensus pattern (60 bp):
GTTGGATTCATCTTCATGTTTAAATTATCCAAATTAAATGCTAATTATACTAGTATGACC
Found at i:54104016 original size:19 final size:19
Alignment explanation
Indices: 54103992--54104030 Score: 69
Period size: 19 Copynumber: 2.1 Consensus size: 19
54103982 CATATGACCC
54103992 TCCAAAAACATGAAAAGGT
1 TCCAAAAACATGAAAAGGT
*
54104011 TCCAAATACATGAAAAGGT
1 TCCAAAAACATGAAAAGGT
54104030 T
1 T
54104031 ATGTTAACTC
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
19 19 1.00
ACGTcount: A:0.49, C:0.15, G:0.15, T:0.21
Consensus pattern (19 bp):
TCCAAAAACATGAAAAGGT
Found at i:54106782 original size:13 final size:13
Alignment explanation
Indices: 54106766--54106807 Score: 57
Period size: 13 Copynumber: 3.2 Consensus size: 13
54106756 GTGTGAAAAT
54106766 TGAAATTTTAATG
1 TGAAATTTTAATG
*
54106779 TGAAAATTTAATG
1 TGAAATTTTAATG
* *
54106792 TGTAATATTAATG
1 TGAAATTTTAATG
54106805 TGA
1 TGA
54106808 TTTAATTGTT
Statistics
Matches: 24, Mismatches: 5, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
13 24 1.00
ACGTcount: A:0.40, C:0.00, G:0.17, T:0.43
Consensus pattern (13 bp):
TGAAATTTTAATG
Found at i:54111575 original size:42 final size:42
Alignment explanation
Indices: 54111509--54111611 Score: 109
Period size: 42 Copynumber: 2.5 Consensus size: 42
54111499 ACCGAGGTTA
* * *
54111509 TGTGTAAGACCATATGTGAAATATGACATC-ATTATGAGATTT
1 TGTGTAAGACCATATCTGGAATATGACATCGA-TATGAAATTT
* * **
54111551 TGTGTAAAACCATATCTGGGATATGGTATCGATATGAAATTT
1 TGTGTAAGACCATATCTGGAATATGACATCGATATGAAATTT
* *
54111593 CGTGTAAGACCATAGCTGG
1 TGTGTAAGACCATATCTGG
54111612 TCTATTGGCA
Statistics
Matches: 50, Mismatches: 10, Indels: 2
0.81 0.16 0.03
Matches are distributed among these distances:
42 49 0.98
43 1 0.02
ACGTcount: A:0.33, C:0.12, G:0.22, T:0.33
Consensus pattern (42 bp):
TGTGTAAGACCATATCTGGAATATGACATCGATATGAAATTT
Found at i:54122400 original size:27 final size:28
Alignment explanation
Indices: 54122316--54122440 Score: 173
Period size: 27 Copynumber: 4.5 Consensus size: 28
54122306 CATGAGATTG
* * * *
54122316 GCACTAAGTGTGCGGGTTTAAATTGTACA
1 GCACTAAGTGTGCGAGTTT-GATTATATA
54122345 GCACTAAGTGTGCGAGTTTGATTATATA
1 GCACTAAGTGTGCGAGTTTGATTATATA
54122373 GCACTAAGTGTGCGAG-TTGATTATATA
1 GCACTAAGTGTGCGAGTTTGATTATATA
*
54122400 GCACTGAGTGTGCGAG-TTGATTATATA
1 GCACTAAGTGTGCGAGTTTGATTATATA
*
54122427 GCACTGAGTGTGCG
1 GCACTAAGTGTGCG
54122441 GACTTAATAT
Statistics
Matches: 91, Mismatches: 5, Indels: 2
0.93 0.05 0.02
Matches are distributed among these distances:
27 51 0.56
28 22 0.24
29 18 0.20
ACGTcount: A:0.26, C:0.13, G:0.29, T:0.32
Consensus pattern (28 bp):
GCACTAAGTGTGCGAGTTTGATTATATA
Found at i:54122452 original size:54 final size:55
Alignment explanation
Indices: 54122344--54122453 Score: 161
Period size: 54 Copynumber: 2.0 Consensus size: 55
54122334 TAAATTGTAC
* *
54122344 AGCACTAAGTGTGCGAGTTTGATTATATAGCACTAAGTGTGCGAGTTGATTATAT
1 AGCACTAAGTGTGCGAGTTTGATTATATAGCACTAAGTGTGCGACTTGAATATAT
* *
54122399 AGCACTGAGTGTGCGAG-TTGATTATATAGCACTGAGTGTGCGGACTT-AATATAT
1 AGCACTAAGTGTGCGAGTTTGATTATATAGCACTAAGTGTGC-GACTTGAATATAT
54122453 A
1 A
54122454 TTTTTGAATC
Statistics
Matches: 50, Mismatches: 4, Indels: 3
0.88 0.07 0.05
Matches are distributed among these distances:
54 30 0.60
55 20 0.40
ACGTcount: A:0.29, C:0.12, G:0.26, T:0.33
Consensus pattern (55 bp):
AGCACTAAGTGTGCGAGTTTGATTATATAGCACTAAGTGTGCGACTTGAATATAT
Found at i:54143554 original size:47 final size:47
Alignment explanation
Indices: 54143435--54143657 Score: 195
Period size: 47 Copynumber: 4.7 Consensus size: 47
54143425 ATAAGTTTCT
* * * * *
54143435 GATGCCATGTCCCAGACATGGTCTTACACTAGCTCTCGTATATACG-TGCT
1 GATG-CATGTCCCAGACAT-GTCTTACACTGGCACTCAT-TAT-CGAGGCC
** *
54143485 GATGCATGT-CCAGACACATCTTACACTGGCTA-TCATTGTCGAGGCC
1 GATGCATGTCCCAGACATGTCTTACACTGGC-ACTCATTATCGAGGCC
* * * * * *
54143531 AATGCATGTCCCATATATGTCTTACACTGGCACTCA-TCTCTACGCC
1 GATGCATGTCCCAGACATGTCTTACACTGGCACTCATTATCGAGGCC
* *
54143577 GATGCCATGTCCCAGACATGGTCTTACACTGGCACTCATAAT-GTGGCC
1 GATG-CATGTCCCAGACAT-GTCTTACACTGGCACTCATTATCGAGGCC
*
54143625 GATGCATGTCCCAGACATGTCTTACACTAGCAC
1 GATGCATGTCCCAGACATGTCTTACACTGGCAC
54143658 ACAAGAAATT
Statistics
Matches: 141, Mismatches: 25, Indels: 18
0.77 0.14 0.10
Matches are distributed among these distances:
45 2 0.01
46 37 0.26
47 60 0.43
48 32 0.23
49 6 0.04
50 4 0.03
ACGTcount: A:0.24, C:0.30, G:0.19, T:0.27
Consensus pattern (47 bp):
GATGCATGTCCCAGACATGTCTTACACTGGCACTCATTATCGAGGCC
Found at i:54144394 original size:12 final size:12
Alignment explanation
Indices: 54144377--54144401 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
54144367 CAAAAATGTA
54144377 AAAATCATCAAG
1 AAAATCATCAAG
54144389 AAAATCATCAAG
1 AAAATCATCAAG
54144401 A
1 A
54144402 TCACTTGCAT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.60, C:0.16, G:0.08, T:0.16
Consensus pattern (12 bp):
AAAATCATCAAG
Found at i:54147052 original size:19 final size:20
Alignment explanation
Indices: 54147030--54147074 Score: 58
Period size: 19 Copynumber: 2.3 Consensus size: 20
54147020 AAAAAATAGG
*
54147030 AAATAGTAATATAG-TAA-AA
1 AAATAATAATAT-GTTAATAA
54147049 AAATAATAATATGTTAATAA
1 AAATAATAATATGTTAATAA
54147069 AAATAA
1 AAATAA
54147075 CAGTAGTAGT
Statistics
Matches: 23, Mismatches: 1, Indels: 3
0.85 0.04 0.11
Matches are distributed among these distances:
18 1 0.04
19 14 0.61
20 8 0.35
ACGTcount: A:0.64, C:0.00, G:0.07, T:0.29
Consensus pattern (20 bp):
AAATAATAATATGTTAATAA
Found at i:54147059 original size:25 final size:24
Alignment explanation
Indices: 54147006--54147053 Score: 69
Period size: 25 Copynumber: 1.9 Consensus size: 24
54146996 TGTTAATATC
54147006 AATAATAATATATAAAAAAATAGGA
1 AATAATAATATATAAAAAAATA-GA
*
54147031 AATAGTAATATAGTAAAAAAATA
1 AATAATAATATA-TAAAAAAATA
54147054 ATAATATGTT
Statistics
Matches: 21, Mismatches: 1, Indels: 1
0.91 0.04 0.04
Matches are distributed among these distances:
25 11 0.52
26 10 0.48
ACGTcount: A:0.67, C:0.00, G:0.08, T:0.25
Consensus pattern (24 bp):
AATAATAATATATAAAAAAATAGA
Found at i:54147137 original size:3 final size:3
Alignment explanation
Indices: 54147104--54147321 Score: 81
Period size: 3 Copynumber: 72.7 Consensus size: 3
54147094 AAAGTTATAG
* * * * * *
54147104 TAA TAA AAA TAA AAA TAA CAA TAA TAG TAA TAA TGA TAG TAA TAA TAA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
* * * * * * *
54147152 TGA TAA T-A TAA CAA TAA CAG TAA TATA TAA AAA GGAA TAA TAA TAG
1 TAA TAA TAA TAA TAA TAA TAA TAA TA-A TAA TAA -TAA TAA TAA TAA
* * * * * * *
54147198 T-A TAG TAA AAA TAA TAA TAA T-G TAT TAA TAG GAA TGA TAA TAA TAA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
* * * *
54147244 -AA TGAGA TTA TAA TAA TAA TAT TAA TAA AAA TAA -ACA TAA -AA GAAA
1 TAA T-A-A TAA TAA TAA TAA TAA TAA TAA TAA TAA TA-A TAA TAA -TAA
* * *
54147290 TAG TAA TAA TAG TAA TAC T-A TAAA TAA TAA TA
1 TAA TAA TAA TAA TAA TAA TAA T-AA TAA TAA TA
54147322 TATGTATGGA
Statistics
Matches: 150, Mismatches: 51, Indels: 28
0.66 0.22 0.12
Matches are distributed among these distances:
2 10 0.07
3 127 0.85
4 11 0.07
5 2 0.01
ACGTcount: A:0.61, C:0.02, G:0.08, T:0.29
Consensus pattern (3 bp):
TAA
Found at i:54147201 original size:23 final size:23
Alignment explanation
Indices: 54147175--54147239 Score: 66
Period size: 23 Copynumber: 3.0 Consensus size: 23
54147165 ATAACAGTAA
54147175 TATATAAAAAGGAATAATAATAG
1 TATATAAAAAGGAATAATAATAG
*
54147198 TATAGTAAAAA-TAATAATAAT-G
1 TATA-TAAAAAGGAATAATAATAG
* *
54147220 TAT-T-AATAGGAATGATAATA
1 TATATAAAAAGGAATAATAATA
54147240 ATAAAATGAG
Statistics
Matches: 35, Mismatches: 4, Indels: 8
0.74 0.09 0.17
Matches are distributed among these distances:
19 3 0.09
20 9 0.26
22 4 0.11
23 13 0.37
24 6 0.17
ACGTcount: A:0.57, C:0.00, G:0.12, T:0.31
Consensus pattern (23 bp):
TATATAAAAAGGAATAATAATAG
Found at i:54147226 original size:14 final size:15
Alignment explanation
Indices: 54147209--54147271 Score: 60
Period size: 14 Copynumber: 4.4 Consensus size: 15
54147199 ATAGTAAAAA
54147209 TAATAATAATG-TAT
1 TAATAATAATGATAT
** *
54147223 TAATAGGAATGATAA
1 TAATAATAATGATAT
*
54147238 TAATAA-AATGAGAT
1 TAATAATAATGATAT
*
54147252 T-ATAATAATAATAT
1 TAATAATAATGATAT
54147266 TAATAA
1 TAATAA
54147272 AAATAAACAT
Statistics
Matches: 38, Mismatches: 8, Indels: 5
0.75 0.16 0.10
Matches are distributed among these distances:
13 4 0.11
14 23 0.61
15 11 0.29
ACGTcount: A:0.56, C:0.00, G:0.10, T:0.35
Consensus pattern (15 bp):
TAATAATAATGATAT
Found at i:54147401 original size:16 final size:16
Alignment explanation
Indices: 54147367--54147413 Score: 60
Period size: 16 Copynumber: 2.9 Consensus size: 16
54147357 GAAAAGAAAA
*
54147367 ATATGTATATACATAAAT
1 ATATATATATA-AT-AAT
54147385 ATATATATATAATAAT
1 ATATATATATAATAAT
54147401 ATATATA-ATAATA
1 ATATATATATAATA
54147414 GAAATAGTAA
Statistics
Matches: 28, Mismatches: 1, Indels: 3
0.88 0.03 0.09
Matches are distributed among these distances:
15 6 0.21
16 10 0.36
17 2 0.07
18 10 0.36
ACGTcount: A:0.55, C:0.02, G:0.02, T:0.40
Consensus pattern (16 bp):
ATATATATATAATAAT
Found at i:54147409 original size:12 final size:12
Alignment explanation
Indices: 54147382--54147413 Score: 55
Period size: 12 Copynumber: 2.6 Consensus size: 12
54147372 TATATACATA
54147382 AATATATATATAT
1 AATA-ATATATAT
54147395 AATAATATATAT
1 AATAATATATAT
54147407 AATAATA
1 AATAATA
54147414 GAAATAGTAA
Statistics
Matches: 19, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
12 15 0.79
13 4 0.21
ACGTcount: A:0.59, C:0.00, G:0.00, T:0.41
Consensus pattern (12 bp):
AATAATATATAT
Found at i:54147419 original size:18 final size:17
Alignment explanation
Indices: 54147364--54147430 Score: 54
Period size: 16 Copynumber: 4.0 Consensus size: 17
54147354 AAAGAAAAGA
*
54147364 AAAATATGTAT-ATACAT
1 AAAATATATATAATA-AT
54147381 -AAATATATAT-AT-AT
1 AAAATATATATAATAAT
54147395 AATAATATATATAATAAT
1 AA-AATATATATAATAAT
54147413 AGAAATAGTA-ATAATAAT
1 A-AAATA-TATATAATAAT
54147431 GGCATTAGAA
Statistics
Matches: 43, Mismatches: 1, Indels: 11
0.78 0.02 0.20
Matches are distributed among these distances:
14 2 0.05
15 1 0.02
16 20 0.47
17 2 0.05
18 15 0.35
19 3 0.07
ACGTcount: A:0.58, C:0.01, G:0.04, T:0.36
Consensus pattern (17 bp):
AAAATATATATAATAAT
Found at i:54147473 original size:3 final size:3
Alignment explanation
Indices: 54147465--54147499 Score: 52
Period size: 3 Copynumber: 11.7 Consensus size: 3
54147455 GTACAAGTAC
* *
54147465 AAT AAT AAT AAT AAT AAT AAT AAG AGT AAT AAT AA
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AA
54147500 CATTTTAGAT
Statistics
Matches: 28, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
3 28 1.00
ACGTcount: A:0.66, C:0.00, G:0.06, T:0.29
Consensus pattern (3 bp):
AAT
Found at i:54149003 original size:44 final size:45
Alignment explanation
Indices: 54148908--54149006 Score: 112
Period size: 45 Copynumber: 2.2 Consensus size: 45
54148898 TCTGCTCCGT
* ** * * *
54148908 TGCAACTTCAAGGAGATGAGGTTTGCTATCTTCAGTCTGCTCCAC
1 TGCAACTTCAAGGAGATAAGACTTGCTAACTTCACTCTGCCCCAC
*
54148953 TACAACTTCAAGGAGATAAGACTTG-TAACTTCAACT-TGCCCCAC
1 TGCAACTTCAAGGAGATAAGACTTGCTAACTTC-ACTCTGCCCCAC
54148997 TGCAACTTCA
1 TGCAACTTCA
54149007 GGGGGTAAGG
Statistics
Matches: 45, Mismatches: 8, Indels: 3
0.80 0.14 0.05
Matches are distributed among these distances:
44 22 0.49
45 23 0.51
ACGTcount: A:0.28, C:0.26, G:0.17, T:0.28
Consensus pattern (45 bp):
TGCAACTTCAAGGAGATAAGACTTGCTAACTTCACTCTGCCCCAC
Found at i:54149134 original size:86 final size:86
Alignment explanation
Indices: 54149035--54149199 Score: 267
Period size: 86 Copynumber: 1.9 Consensus size: 86
54149025 TTCCAGCCTT
**
54149035 TTACCCTACTGCTTAGGGGGTTAAGACTCACTGTCTTTGATCTCCTCCACTACTACTTAGGGAGA
1 TTACCCTACTGCTTAGGGGGTTAAGACTCACCATCTTTGATCTCCTCCACTACTACTTAGGGAGA
*
54149100 TAAGATCTATAATTTGGCATG
66 CAAGATCTATAATTTGGCATG
* * *
54149121 TTACCCTACTGCTTAGGGGGTTAAGGCTCACCATCTTTGATCTGCTCCACTACTGCTTAGGGAGA
1 TTACCCTACTGCTTAGGGGGTTAAGACTCACCATCTTTGATCTCCTCCACTACTACTTAGGGAGA
*
54149186 CAAGATCTGTAATT
66 CAAGATCTATAATT
54149200 CGGCCACTAC
Statistics
Matches: 72, Mismatches: 7, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
86 72 1.00
ACGTcount: A:0.24, C:0.23, G:0.21, T:0.33
Consensus pattern (86 bp):
TTACCCTACTGCTTAGGGGGTTAAGACTCACCATCTTTGATCTCCTCCACTACTACTTAGGGAGA
CAAGATCTATAATTTGGCATG
Found at i:54149176 original size:44 final size:44
Alignment explanation
Indices: 54149040--54149182 Score: 125
Period size: 44 Copynumber: 3.3 Consensus size: 44
54149030 GCCTTTTACC
* * *
54149040 CTACTGCTTAGGGGGTTAAGACTCACTGTCTTTGATCTCCTCCA
1 CTACTGCTTAGGGGGTTAAGGCTCACTATCTTTGATCTGCTCCA
* * * * * * *
54149084 CTACTACTTAGGGAGATAA-GAT--CTATAATTTG-GCATGTTACC-
1 CTACTGCTTAGGGGGTTAAGGCTCACTAT-CTTTGATC-TGCT-CCA
*
54149126 CTACTGCTTAGGGGGTTAAGGCTCACCATCTTTGATCTGCTCCA
1 CTACTGCTTAGGGGGTTAAGGCTCACTATCTTTGATCTGCTCCA
54149170 CTACTGCTTAGGG
1 CTACTGCTTAGGG
54149183 AGACAAGATC
Statistics
Matches: 73, Mismatches: 18, Indels: 16
0.68 0.17 0.15
Matches are distributed among these distances:
41 4 0.05
42 22 0.30
43 7 0.10
44 36 0.49
45 4 0.05
ACGTcount: A:0.22, C:0.24, G:0.22, T:0.33
Consensus pattern (44 bp):
CTACTGCTTAGGGGGTTAAGGCTCACTATCTTTGATCTGCTCCA
Found at i:54149214 original size:36 final size:36
Alignment explanation
Indices: 54149167--54149240 Score: 139
Period size: 36 Copynumber: 2.1 Consensus size: 36
54149157 TTGATCTGCT
54149167 CCACTACTGCTTAGGGAGACAAGATCTGTAATTCGG
1 CCACTACTGCTTAGGGAGACAAGATCTGTAATTCGG
*
54149203 CCACTACTGCTTAGGGAGACAAGGTCTGTAATTCGG
1 CCACTACTGCTTAGGGAGACAAGATCTGTAATTCGG
54149239 CC
1 CC
54149241 TATTACCCTA
Statistics
Matches: 37, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
36 37 1.00
ACGTcount: A:0.26, C:0.24, G:0.26, T:0.24
Consensus pattern (36 bp):
CCACTACTGCTTAGGGAGACAAGATCTGTAATTCGG
Found at i:54149247 original size:122 final size:122
Alignment explanation
Indices: 54149081--54149326 Score: 420
Period size: 122 Copynumber: 2.0 Consensus size: 122
54149071 TTGATCTCCT
* * *
54149081 CCACTACTACTTAGGGAGATAAGATCTATAATTTGGCATGTTACCCTACTGCTTAGGGGGTTAAG
1 CCACTACTACTTAGGGAGACAAGATCTATAATTCGGCATATTACCCTACTGCTTAGGGGGTTAAG
54149146 GCTCACCATCTTTGATCTGCTCCACTACTGCTTAGGGAGACAAGATCTGTAATTCGG
66 GCTCACCATCTTTGATCTGCTCCACTACTGCTTAGGGAGACAAGATCTGTAATTCGG
* * * * *
54149203 CCACTACTGCTTAGGGAGACAAGGTCTGTAATTCGGCCTATTACCCTACTGCTTAGGGTGTTAAG
1 CCACTACTACTTAGGGAGACAAGATCTATAATTCGGCATATTACCCTACTGCTTAGGGGGTTAAG
54149268 GCTCACCATCTTTGATCTGCTCCACTACTGCTTAGGGAGACAAGATCTGTAATTCGG
66 GCTCACCATCTTTGATCTGCTCCACTACTGCTTAGGGAGACAAGATCTGTAATTCGG
54149325 CC
1 CC
54149327 TGTTACCCTA
Statistics
Matches: 116, Mismatches: 8, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
122 116 1.00
ACGTcount: A:0.24, C:0.24, G:0.22, T:0.30
Consensus pattern (122 bp):
CCACTACTACTTAGGGAGACAAGATCTATAATTCGGCATATTACCCTACTGCTTAGGGGGTTAAG
GCTCACCATCTTTGATCTGCTCCACTACTGCTTAGGGAGACAAGATCTGTAATTCGG
Found at i:54149393 original size:208 final size:208
Alignment explanation
Indices: 54149030--54149408 Score: 632
Period size: 208 Copynumber: 1.8 Consensus size: 208
54149020 GTAATTTCCA
* **
54149030 GCCTTTTACCCTACTGCTTAGGGGGTTAAGACTCACTGTCTTTGATCTCCTCCACTACTACTTAG
1 GCCTATTACCCTACTGCTTAGGGGGTTAAGACTCACCATCTTTGATCTCCTCCACTACTACTTAG
* * *
54149095 GGAGATAAGATCTATAATTTGGCATGTTACCCTACTGCTTAGGGGGTTAAGGCTCACCATCTTTG
66 GGAGACAAGATCTATAATTCGGCATGTTACCCTACTGCTTAGGGGGTTAAGGCTCACCATCTTCG
54149160 ATCTGCTCCACTACTGCTTAGGGAGACAAGATCTGTAATTCGGCCACTACTGCTTAGGGAGACAA
131 ATCTGCTCCACTACTGCTTAGGGAGACAAGATCTGTAATTCGGCCACTACTGCTTAGGGAGACAA
54149225 GGTCTGTAATTCG
196 GGTCTGTAATTCG
* * * *
54149238 GCCTATTACCCTACTGCTTAGGGTGTTAAGGCTCACCATCTTTGATCTGCTCCACTACTGCTTAG
1 GCCTATTACCCTACTGCTTAGGGGGTTAAGACTCACCATCTTTGATCTCCTCCACTACTACTTAG
* * *
54149303 GGAGACAAGATCTGTAATTCGGCCTGTTACCCTACTGCTTAGGGGGTTAAGGCTCACCGTCTTCG
66 GGAGACAAGATCTATAATTCGGCATGTTACCCTACTGCTTAGGGGGTTAAGGCTCACCATCTTCG
*
54149368 ATCTGCTCCACTATTGCTTAGGGAGACAAGATCTGTAATTC
131 ATCTGCTCCACTACTGCTTAGGGAGACAAGATCTGTAATTC
54149409 TCCAGCCTGT
Statistics
Matches: 157, Mismatches: 14, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
208 157 1.00
ACGTcount: A:0.22, C:0.25, G:0.22, T:0.31
Consensus pattern (208 bp):
GCCTATTACCCTACTGCTTAGGGGGTTAAGACTCACCATCTTTGATCTCCTCCACTACTACTTAG
GGAGACAAGATCTATAATTCGGCATGTTACCCTACTGCTTAGGGGGTTAAGGCTCACCATCTTCG
ATCTGCTCCACTACTGCTTAGGGAGACAAGATCTGTAATTCGGCCACTACTGCTTAGGGAGACAA
GGTCTGTAATTCG
Found at i:54149469 original size:44 final size:44
Alignment explanation
Indices: 54149415--54149567 Score: 139
Period size: 44 Copynumber: 3.5 Consensus size: 44
54149405 ATTCTCCAGC
*
54149415 CTGTTACCCTACTACTTAGGGGGTTAAGGCCCATCATCTTAGAT
1 CTGTTACCCTACTGCTTAGGGGGTTAAGGCCCATCATCTTAGAT
* * * ** ** ** * * *
54149459 CTGTTCCCCTACTGCTGAGGGAGACAAGATCTGTAATTCTCCAGCT
1 CTGTTACCCTACTGCTTAGGGGGTTAAGGCCCATCA-TCT-TAGAT
*
54149505 -TGTTACCCTACTGCTTAGGGGGTTAAGGCTCATCATCTTAGAT
1 CTGTTACCCTACTGCTTAGGGGGTTAAGGCCCATCATCTTAGAT
*
54149548 CTGTT-CCCCACTGCTTAGGG
1 CTGTTACCCTACTGCTTAGGG
54149568 AGACAAGATT
Statistics
Matches: 79, Mismatches: 27, Indels: 7
0.70 0.24 0.06
Matches are distributed among these distances:
43 17 0.22
44 32 0.41
45 27 0.34
46 3 0.04
ACGTcount: A:0.20, C:0.26, G:0.22, T:0.31
Consensus pattern (44 bp):
CTGTTACCCTACTGCTTAGGGGGTTAAGGCCCATCATCTTAGAT
Found at i:54149480 original size:89 final size:89
Alignment explanation
Indices: 54149203--54149622 Score: 575
Period size: 89 Copynumber: 4.8 Consensus size: 89
54149193 TGTAATTCGG
* * * *
54149203 CCACTACTGCTTAGGGAGACAAGGTCTGTAA-T-T-CGGCCTATTACCCTACTGCTTAGGGTGTT
1 CCACTACTGCTTAGGGAGACAAGATCTGTAATTCTCCAGCCTGTTACCCTACTGCTTAGGGGGTT
*
54149265 AAGGCTCACCATCTTTGATCTGCT
66 AAGGCTCACCATCTTAGATCTGCT
*
54149289 CCACTACTGCTTAGGGAGACAAGATCTGTAA-T-T-CGGCCTGTTACCCTACTGCTTAGGGGGTT
1 CCACTACTGCTTAGGGAGACAAGATCTGTAATTCTCCAGCCTGTTACCCTACTGCTTAGGGGGTT
* *
54149351 AAGGCTCACCGTCTTCGATCTGCT
66 AAGGCTCACCATCTTAGATCTGCT
* *
54149375 CCACTATTGCTTAGGGAGACAAGATCTGTAATTCTCCAGCCTGTTACCCTACTACTTAGGGGGTT
1 CCACTACTGCTTAGGGAGACAAGATCTGTAATTCTCCAGCCTGTTACCCTACTGCTTAGGGGGTT
* * *
54149440 AAGGCCCATCATCTTAGATCTGTT
66 AAGGCTCACCATCTTAGATCTGCT
* * *
54149464 CCCCTACTGCTGAGGGAGACAAGATCTGTAATTCTCCAGCTTGTTACCCTACTGCTTAGGGGGTT
1 CCACTACTGCTTAGGGAGACAAGATCTGTAATTCTCCAGCCTGTTACCCTACTGCTTAGGGGGTT
* *
54149529 AAGGCTCATCATCTTAGATCTGTT
66 AAGGCTCACCATCTTAGATCTGCT
* * * * * *
54149553 CC-CCACTGCTTAGGGAGACAAGATTTGTATTTCTCCAGCCTGTTACCCTACTACTTTGGAGGTT
1 CCACTACTGCTTAGGGAGACAAGATCTGTAATTCTCCAGCCTGTTACCCTACTGCTTAGGGGGTT
54149617 AAGGCT
66 AAGGCT
54149623 TACAAATTCA
Statistics
Matches: 304, Mismatches: 27, Indels: 4
0.91 0.08 0.01
Matches are distributed among these distances:
86 111 0.37
87 1 0.00
88 61 0.20
89 131 0.43
ACGTcount: A:0.21, C:0.25, G:0.22, T:0.31
Consensus pattern (89 bp):
CCACTACTGCTTAGGGAGACAAGATCTGTAATTCTCCAGCCTGTTACCCTACTGCTTAGGGGGTT
AAGGCTCACCATCTTAGATCTGCT
Found at i:54157649 original size:9 final size:9
Alignment explanation
Indices: 54157635--54157673 Score: 60
Period size: 9 Copynumber: 4.3 Consensus size: 9
54157625 TGTTGATGCC
54157635 TGAATGCAA
1 TGAATGCAA
54157644 TGAATGCAA
1 TGAATGCAA
*
54157653 TAAATGCAA
1 TGAATGCAA
*
54157662 TGAATACAA
1 TGAATGCAA
54157671 TGA
1 TGA
54157674 CTGTAAAAAA
Statistics
Matches: 27, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
9 27 1.00
ACGTcount: A:0.49, C:0.10, G:0.18, T:0.23
Consensus pattern (9 bp):
TGAATGCAA
Found at i:54157684 original size:27 final size:27
Alignment explanation
Indices: 54157635--54157686 Score: 68
Period size: 27 Copynumber: 1.9 Consensus size: 27
54157625 TGTTGATGCC
* *
54157635 TGAATGCAATGAATGCAATAAATGCAA
1 TGAATACAATGAATGCAAAAAATGCAA
* *
54157662 TGAATACAATGACTGTAAAAAATGC
1 TGAATACAATGAATGCAAAAAATGC
54157687 GTCGATTCTA
Statistics
Matches: 21, Mismatches: 4, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
27 21 1.00
ACGTcount: A:0.48, C:0.12, G:0.17, T:0.23
Consensus pattern (27 bp):
TGAATACAATGAATGCAAAAAATGCAA
Found at i:54161451 original size:3 final size:3
Alignment explanation
Indices: 54161431--54161696 Score: 63
Period size: 3 Copynumber: 88.7 Consensus size: 3
54161421 GATGTAAGAG
* * * **
54161431 AAT AAT AAA AGAT CAAT AAT AAT TAT AAT AGT ATAT GTT AAT -AT CAAT
1 AAT AAT AAT A-AT -AAT AAT AAT AAT AAT AAT A-AT AAT AAT AAT -AAT
* *
54161479 AAT AAT ATAT AA- AA- AAT AGGA- AAT AGT AAT -AT AGT AA- AAT AAT
1 AAT AAT A-AT AAT AAT AAT A--AT AAT AAT AAT AAT AAT AAT AAT AAT
** * * *
54161522 AAT AAT -AT GTT AAT AAA AAT AAC AAT AAT AGT AAT AAT AA- AA- AAGT
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AA-T
* * * * * * *
54161568 TAT AGT AGAT AAT -AT AAC AAT AAC AGT AAT ATAT AAA AAGG AAT AAT
1 AAT AAT A-AT AAT AAT AAT AAT AAT AAT AAT A-AT AAT AA-T AAT AAT
* * * * * * *
54161615 AAT AGT -AT AGT AAA AAT AAT AAT -GT ATT AAT AAG AAT GAT AAT AAT
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
* * *
54161661 AA- AAT GAGAT TAT AAT AAT AAT ATT AAT AAA AAT AA
1 AAT AAT -A-AT AAT AAT AAT AAT AAT AAT AAT AAT AA
54161697 ACATAAAAGA
Statistics
Matches: 184, Mismatches: 55, Indels: 48
0.64 0.19 0.17
Matches are distributed among these distances:
2 23 0.12
3 138 0.75
4 19 0.10
5 4 0.02
ACGTcount: A:0.59, C:0.02, G:0.08, T:0.30
Consensus pattern (3 bp):
AAT
Found at i:54161635 original size:23 final size:22
Alignment explanation
Indices: 54161448--54161637 Score: 81
Period size: 23 Copynumber: 8.4 Consensus size: 22
54161438 AAAGATCAAT
* *
54161448 AATAATTATAATAGTATATGTTAA
1 AATAATAATAATAGTATA--TAAA
*
54161472 TATCAATAATAATA-TATA-AAA
1 AAT-AATAATAATAGTATATAAA
**
54161493 AAT-AGGA-AATAGTAATATAGTAA
1 AATAATAATAATAGT-ATATA--AA
54161516 AATAATAATAATATGT-TAATAAA
1 AATAATAATAATA-GTAT-ATAAA
*
54161539 AATAACAATAATAGTAATAATAAA
1 AATAATAATAATAGT-AT-ATAAA
* * * *
54161563 AA-AGTTATAGTAGATAATATAAC
1 AATAATAATAATAG-T-ATATAAA
* *
54161586 AATAACAGTAATA-TATA-AAA
1 AATAATAATAATAGTATATAAA
**
54161606 AGGAATAATAATAGTATAGTAAA
1 AATAATAATAATAGTATA-TAAA
54161629 AATAATAAT
1 AATAATAAT
54161638 GTATTAATAA
Statistics
Matches: 123, Mismatches: 26, Indels: 35
0.67 0.14 0.19
Matches are distributed among these distances:
18 4 0.03
19 3 0.02
20 14 0.11
21 12 0.10
22 3 0.02
23 42 0.34
24 27 0.22
25 16 0.13
26 2 0.02
ACGTcount: A:0.59, C:0.02, G:0.08, T:0.31
Consensus pattern (22 bp):
AATAATAATAATAGTATATAAA
Found at i:54170264 original size:17 final size:17
Alignment explanation
Indices: 54170242--54170276 Score: 61
Period size: 17 Copynumber: 2.1 Consensus size: 17
54170232 ATGTTTTTTG
*
54170242 TCATTCTAAGATGGAGT
1 TCATTCTAAGATAGAGT
54170259 TCATTCTAAGATAGAGT
1 TCATTCTAAGATAGAGT
54170276 T
1 T
54170277 AGGATTTGAA
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:0.31, C:0.11, G:0.20, T:0.37
Consensus pattern (17 bp):
TCATTCTAAGATAGAGT
Found at i:54171141 original size:45 final size:45
Alignment explanation
Indices: 54171090--54171175 Score: 172
Period size: 45 Copynumber: 1.9 Consensus size: 45
54171080 AGAAGTTTCG
54171090 TGGAATTTGCTGAGGAATTTAAGTCAGTCATAGGGTTTACCTTCA
1 TGGAATTTGCTGAGGAATTTAAGTCAGTCATAGGGTTTACCTTCA
54171135 TGGAATTTGCTGAGGAATTTAAGTCAGTCATAGGGTTTACC
1 TGGAATTTGCTGAGGAATTTAAGTCAGTCATAGGGTTTACC
54171176 ATGGATGGTA
Statistics
Matches: 41, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
45 41 1.00
ACGTcount: A:0.27, C:0.13, G:0.26, T:0.35
Consensus pattern (45 bp):
TGGAATTTGCTGAGGAATTTAAGTCAGTCATAGGGTTTACCTTCA
Found at i:54177228 original size:38 final size:38
Alignment explanation
Indices: 54177177--54177327 Score: 187
Period size: 38 Copynumber: 4.0 Consensus size: 38
54177167 AATAAGTCTA
* * * * *
54177177 AATAACACCAGCACTAAGCCTGCTAAGTACTAAGCCAG
1 AATAACACTAGCACTAAGCCTACTAGGCACTAAGCCTG
* *
54177215 AATAACACTAGCACTAAGCTTACTAGGCACAAAGCCTG
1 AATAACACTAGCACTAAGCCTACTAGGCACTAAGCCTG
*
54177253 AATAACAC-CGACACTAAGCCTACTAGGCACTAAGCCTG
1 AATAACACTAG-CACTAAGCCTACTAGGCACTAAGCCTG
* * *
54177291 AATAACACTGGCATTAAGCCTGCTAGGCACTAAGCCT
1 AATAACACTAGCACTAAGCCTACTAGGCACTAAGCCT
54177328 ACTAGGCACA
Statistics
Matches: 98, Mismatches: 13, Indels: 4
0.85 0.11 0.03
Matches are distributed among these distances:
37 1 0.01
38 96 0.98
39 1 0.01
ACGTcount: A:0.37, C:0.28, G:0.17, T:0.18
Consensus pattern (38 bp):
AATAACACTAGCACTAAGCCTACTAGGCACTAAGCCTG
Found at i:54177285 original size:16 final size:16
Alignment explanation
Indices: 54177264--54177343 Score: 70
Period size: 16 Copynumber: 4.6 Consensus size: 16
54177254 ATAACACCGA
54177264 CACTAAGCCTACTAGG
1 CACTAAGCCTACTAGG
*
54177280 CACTAAGCCTGAATAACACTGG
1 CACTAAGCCT-ACT---A--GG
* *
54177302 CATTAAGCCTGCTAGG
1 CACTAAGCCTACTAGG
54177318 CACTAAGCCTACTAGG
1 CACTAAGCCTACTAGG
*
54177334 CACAAAGCCT
1 CACTAAGCCT
54177344 GAGTAACATC
Statistics
Matches: 51, Mismatches: 7, Indels: 12
0.73 0.10 0.17
Matches are distributed among these distances:
16 35 0.69
17 2 0.04
18 1 0.02
20 1 0.02
21 1 0.02
22 11 0.22
ACGTcount: A:0.33, C:0.30, G:0.19, T:0.19
Consensus pattern (16 bp):
CACTAAGCCTACTAGG
Found at i:54177322 original size:54 final size:54
Alignment explanation
Indices: 54177264--54177381 Score: 184
Period size: 54 Copynumber: 2.2 Consensus size: 54
54177254 ATAACACCGA
* *
54177264 CACTAAGCCTACTAGGCACTAAGCCTGAATAACA-CTGGCATTAAGCCTGCTAGG
1 CACTAAGCCTACTAGGCACAAAGCCTGAATAACATC-GGCACTAAGCCTGCTAGG
* *
54177318 CACTAAGCCTACTAGGCACAAAGCCTGAGTAACATCGGTACTAAGCCTGCTAGG
1 CACTAAGCCTACTAGGCACAAAGCCTGAATAACATCGGCACTAAGCCTGCTAGG
54177372 CACTAAGCCT
1 CACTAAGCCT
54177382 GAATAACACT
Statistics
Matches: 59, Mismatches: 4, Indels: 2
0.91 0.06 0.03
Matches are distributed among these distances:
54 58 0.98
55 1 0.02
ACGTcount: A:0.31, C:0.29, G:0.20, T:0.19
Consensus pattern (54 bp):
CACTAAGCCTACTAGGCACAAAGCCTGAATAACATCGGCACTAAGCCTGCTAGG
Found at i:54177323 original size:92 final size:92
Alignment explanation
Indices: 54177225--54177419 Score: 309
Period size: 92 Copynumber: 2.1 Consensus size: 92
54177215 AATAACACTA
*
54177225 GCACTAAGCTTACTAGGCACAAAGCCTGAATAACACCGACACTAAGCCTACTAGGCACTAAGCCT
1 GCACTAAGCCTACTAGGCACAAAGCCTGAATAACACCGACACTAAGCCTACTAGGCACTAAGCCT
* *
54177290 GAATAACACTGGCATTAAGCCTGCTAG
66 GAATAACACTGACACTAAGCCTGCTAG
* * ** *
54177317 GCACTAAGCCTACTAGGCACAAAGCCTGAGTAACATCGGTACTAAGCCTGCTAGGCACTAAGCCT
1 GCACTAAGCCTACTAGGCACAAAGCCTGAATAACACCGACACTAAGCCTACTAGGCACTAAGCCT
54177382 GAATAACACTGACACTAAGCCTGCTAG
66 GAATAACACTGACACTAAGCCTGCTAG
*
54177409 GCACAAAGCCT
1 GCACTAAGCCT
54177420 GAATAATAGT
Statistics
Matches: 94, Mismatches: 9, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
92 94 1.00
ACGTcount: A:0.34, C:0.29, G:0.19, T:0.18
Consensus pattern (92 bp):
GCACTAAGCCTACTAGGCACAAAGCCTGAATAACACCGACACTAAGCCTACTAGGCACTAAGCCT
GAATAACACTGACACTAAGCCTGCTAG
Found at i:54177361 original size:38 final size:38
Alignment explanation
Indices: 54177318--54177425 Score: 155
Period size: 38 Copynumber: 2.8 Consensus size: 38
54177308 GCCTGCTAGG
* * *
54177318 CACTAAGCCTACTAGGCACAAAGCCTGAGTAACA-TCGG
1 CACTAAGCCTGCTAGGCACAAAGCCTGAATAACACT-GA
* *
54177356 TACTAAGCCTGCTAGGCACTAAGCCTGAATAACACTGA
1 CACTAAGCCTGCTAGGCACAAAGCCTGAATAACACTGA
54177394 CACTAAGCCTGCTAGGCACAAAGCCTGAATAA
1 CACTAAGCCTGCTAGGCACAAAGCCTGAATAA
54177426 TAGTACGATT
Statistics
Matches: 62, Mismatches: 7, Indels: 2
0.87 0.10 0.03
Matches are distributed among these distances:
38 61 0.98
39 1 0.02
ACGTcount: A:0.35, C:0.28, G:0.19, T:0.18
Consensus pattern (38 bp):
CACTAAGCCTGCTAGGCACAAAGCCTGAATAACACTGA
Found at i:54182554 original size:12 final size:12
Alignment explanation
Indices: 54182537--54182569 Score: 52
Period size: 11 Copynumber: 2.9 Consensus size: 12
54182527 CGGCCCACCC
54182537 ATATTAATTTTT
1 ATATTAATTTTT
54182549 ATATT-ATTTTT
1 ATATTAATTTTT
54182560 ATA-TAATTTT
1 ATATTAATTTT
54182570 AAAATATATA
Statistics
Matches: 20, Mismatches: 0, Indels: 3
0.87 0.00 0.13
Matches are distributed among these distances:
10 1 0.05
11 14 0.70
12 5 0.25
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (12 bp):
ATATTAATTTTT
Found at i:54182805 original size:14 final size:14
Alignment explanation
Indices: 54182788--54182814 Score: 54
Period size: 14 Copynumber: 1.9 Consensus size: 14
54182778 CAAACAATAA
54182788 CAACATAATAGTAG
1 CAACATAATAGTAG
54182802 CAACATAATAGTA
1 CAACATAATAGTA
54182815 AAATAGTAGT
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:0.52, C:0.15, G:0.11, T:0.22
Consensus pattern (14 bp):
CAACATAATAGTAG
Found at i:54192806 original size:14 final size:13
Alignment explanation
Indices: 54192774--54192799 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
54192764 TCTAAGTAAA
54192774 AAAAATTCTTTTC
1 AAAAATTCTTTTC
54192787 AAAAATTCTTTTC
1 AAAAATTCTTTTC
54192800 TCTAAATAGT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.38, C:0.15, G:0.00, T:0.46
Consensus pattern (13 bp):
AAAAATTCTTTTC
Found at i:54204910 original size:19 final size:19
Alignment explanation
Indices: 54204888--54204925 Score: 58
Period size: 19 Copynumber: 2.0 Consensus size: 19
54204878 TAAAAAGCCT
*
54204888 ATAAAATTTAAAAAAATAA
1 ATAAAAATTAAAAAAATAA
*
54204907 ATAAAAATTAAAAATATAA
1 ATAAAAATTAAAAAAATAA
54204926 GTAATAAAAA
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
19 17 1.00
ACGTcount: A:0.74, C:0.00, G:0.00, T:0.26
Consensus pattern (19 bp):
ATAAAAATTAAAAAAATAA
Found at i:54205146 original size:25 final size:25
Alignment explanation
Indices: 54205098--54205147 Score: 66
Period size: 25 Copynumber: 2.0 Consensus size: 25
54205088 TTTTAATTAA
*
54205098 TTTATATATTTTATTTTTTAAAAAT
1 TTTATATATTTTATTATTTAAAAAT
*
54205123 TTTATATATTTT-TTAATTTCAAAAT
1 TTTATATATTTTATT-ATTTAAAAAT
54205148 AATAATATAA
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
24 2 0.09
25 20 0.91
ACGTcount: A:0.36, C:0.02, G:0.00, T:0.62
Consensus pattern (25 bp):
TTTATATATTTTATTATTTAAAAAT
Found at i:54206823 original size:16 final size:17
Alignment explanation
Indices: 54206802--54206835 Score: 52
Period size: 18 Copynumber: 2.0 Consensus size: 17
54206792 TTTATTGATG
54206802 GATTTG-GTATTAATTT
1 GATTTGAGTATTAATTT
54206818 GATTTGTAGTATTAATTT
1 GATTTG-AGTATTAATTT
54206836 AATAATACAC
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
16 6 0.38
18 10 0.62
ACGTcount: A:0.26, C:0.00, G:0.18, T:0.56
Consensus pattern (17 bp):
GATTTGAGTATTAATTT
Done.