Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold65
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: 3097370
ACGTcount: A:0.31, C:0.14, G:0.14, T:0.31
Warning! 315397 characters in sequence are not A, C, G, or T
File 9 of 17
Found at i:1854489 original size:38 final size:37
Alignment explanation
Indices: 1854405--1854490 Score: 102
Period size: 38 Copynumber: 2.3 Consensus size: 37
1854395 ATATAAAATT
*
1854405 AATAAATATAAAATTAATATTAATATAAATATTTTTA
1 AATAAATATAAAATAAATATTAATATAAATATTTTTA
** * *
1854442 AATTTATATAAAATAAATTATTGATAT-AATTTTATTTA
1 AATAAATATAAAATAAA-TATTAATATAAATATT-TTTA
1854480 AATAAATATAA
1 AATAAATATAA
1854491 TATTTTAAAC
Statistics
Matches: 40, Mismatches: 7, Indels: 3
0.80 0.14 0.06
Matches are distributed among these distances:
37 19 0.47
38 21 0.52
ACGTcount: A:0.55, C:0.00, G:0.01, T:0.44
Consensus pattern (37 bp):
AATAAATATAAAATAAATATTAATATAAATATTTTTA
Found at i:1854807 original size:21 final size:23
Alignment explanation
Indices: 1854754--1854807 Score: 58
Period size: 26 Copynumber: 2.3 Consensus size: 23
1854744 CTGACTCTTT
1854754 AATTTATTTTATTTTTAAGCAGAA
1 AATTTATTTTATTTTTAA-CAGAA
*
1854778 ATATGTTATTTTATTTTTTA-A-AA
1 A-AT-TTATTTTATTTTTAACAGAA
1854801 AATTTAT
1 AATTTAT
1854808 ATTTTAATTT
Statistics
Matches: 27, Mismatches: 1, Indels: 7
0.77 0.03 0.20
Matches are distributed among these distances:
21 4 0.15
22 2 0.07
23 3 0.11
24 2 0.07
25 2 0.07
26 14 0.52
ACGTcount: A:0.37, C:0.02, G:0.06, T:0.56
Consensus pattern (23 bp):
AATTTATTTTATTTTTAACAGAA
Found at i:1855223 original size:18 final size:19
Alignment explanation
Indices: 1855188--1855223 Score: 56
Period size: 19 Copynumber: 1.9 Consensus size: 19
1855178 GATTTAGTGA
*
1855188 GTGAGTAATTCGTTTTTTG
1 GTGAGTAATTCATTTTTTG
1855207 GTGAGTAATT-ATTTTTT
1 GTGAGTAATTCATTTTTT
1855224 AATAAAAAAT
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
18 6 0.38
19 10 0.62
ACGTcount: A:0.19, C:0.03, G:0.22, T:0.56
Consensus pattern (19 bp):
GTGAGTAATTCATTTTTTG
Found at i:1855391 original size:17 final size:16
Alignment explanation
Indices: 1855370--1855419 Score: 57
Period size: 17 Copynumber: 3.1 Consensus size: 16
1855360 TATATGTTTA
1855370 TATAATTTTAATATAT
1 TATAATTTTAATATAT
* *
1855386 TAATAATTTT-TTATGT
1 T-ATAATTTTAATATAT
1855402 TATAAATTTTAATATAT
1 TAT-AATTTTAATATAT
1855419 T
1 T
1855420 CATTATTTAT
Statistics
Matches: 27, Mismatches: 4, Indels: 5
0.75 0.11 0.14
Matches are distributed among these distances:
15 2 0.07
16 12 0.44
17 13 0.48
ACGTcount: A:0.40, C:0.00, G:0.02, T:0.58
Consensus pattern (16 bp):
TATAATTTTAATATAT
Found at i:1855711 original size:15 final size:15
Alignment explanation
Indices: 1855691--1855722 Score: 55
Period size: 15 Copynumber: 2.1 Consensus size: 15
1855681 TATTAAAAAT
1855691 TTAAATATATTAATA
1 TTAAATATATTAATA
*
1855706 TTAAATATATTCATA
1 TTAAATATATTAATA
1855721 TT
1 TT
1855723 TATTTTTTTA
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 16 1.00
ACGTcount: A:0.47, C:0.03, G:0.00, T:0.50
Consensus pattern (15 bp):
TTAAATATATTAATA
Found at i:1856166 original size:44 final size:44
Alignment explanation
Indices: 1856103--1856197 Score: 163
Period size: 44 Copynumber: 2.2 Consensus size: 44
1856093 TGAAATTGAA
*
1856103 ATATTCTTGATAAATGCTGACAACTCATATCCTACGCTTTTTGG
1 ATATTCTTGATAAATGCTGACAACTCACATCCTACGCTTTTTGG
*
1856147 ATATTCTTGATAAATGCTGACAACTCACATCCTATGCTTTTTGG
1 ATATTCTTGATAAATGCTGACAACTCACATCCTACGCTTTTTGG
*
1856191 ACATTCT
1 ATATTCT
1856198 CAGCATCTGG
Statistics
Matches: 48, Mismatches: 3, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
44 48 1.00
ACGTcount: A:0.27, C:0.21, G:0.13, T:0.39
Consensus pattern (44 bp):
ATATTCTTGATAAATGCTGACAACTCACATCCTACGCTTTTTGG
Found at i:1865977 original size:30 final size:32
Alignment explanation
Indices: 1865941--1866014 Score: 116
Period size: 32 Copynumber: 2.4 Consensus size: 32
1865931 CTGATATTGA
*
1865941 TCGTAAATTTGATG-A-ATTAGACATAATTAC
1 TCGTAAATTTGATGAATATTAAACATAATTAC
*
1865971 TTGTAAATTTGATGAATATTAAACATAATTAC
1 TCGTAAATTTGATGAATATTAAACATAATTAC
1866003 TCGTAAATTTGA
1 TCGTAAATTTGA
1866015 AAATCATTAA
Statistics
Matches: 39, Mismatches: 3, Indels: 2
0.89 0.07 0.05
Matches are distributed among these distances:
30 13 0.33
31 1 0.03
32 25 0.64
ACGTcount: A:0.41, C:0.08, G:0.12, T:0.39
Consensus pattern (32 bp):
TCGTAAATTTGATGAATATTAAACATAATTAC
Found at i:1866024 original size:32 final size:32
Alignment explanation
Indices: 1865941--1866025 Score: 104
Period size: 32 Copynumber: 2.7 Consensus size: 32
1865931 CTGATATTGA
* *
1865941 TCGTAAATTTGAT-GA-ATTAGACATAATTAC
1 TCGTAAATTTGATAAATATTAAACATAATTAC
* *
1865971 TTGTAAATTTGATGAATATTAAACATAATTAC
1 TCGTAAATTTGATAAATATTAAACATAATTAC
1866003 TCGTAAATTTGA-AAATCATTAAA
1 TCGTAAATTTGATAAAT-ATTAAA
1866026 AAGTGTTAAC
Statistics
Matches: 47, Mismatches: 5, Indels: 4
0.84 0.09 0.07
Matches are distributed among these distances:
30 12 0.26
31 4 0.09
32 31 0.66
ACGTcount: A:0.44, C:0.08, G:0.11, T:0.38
Consensus pattern (32 bp):
TCGTAAATTTGATAAATATTAAACATAATTAC
Found at i:1881056 original size:36 final size:36
Alignment explanation
Indices: 1881007--1881083 Score: 91
Period size: 36 Copynumber: 2.1 Consensus size: 36
1880997 AACCACCTCT
* *
1881007 ATAGGTCTATGCAAAGTCTCCAGAGGAAGTAAATCA
1 ATAGGCCTATGCAAAGACTCCAGAGGAAGTAAATCA
* * * **
1881043 ATAGGCCTGTGCAAAGACTTCTGAGGAAGTACCTCA
1 ATAGGCCTATGCAAAGACTCCAGAGGAAGTAAATCA
1881079 ATAGG
1 ATAGG
1881084 ACCACGTGAA
Statistics
Matches: 34, Mismatches: 7, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
36 34 1.00
ACGTcount: A:0.35, C:0.18, G:0.25, T:0.22
Consensus pattern (36 bp):
ATAGGCCTATGCAAAGACTCCAGAGGAAGTAAATCA
Found at i:1884416 original size:18 final size:17
Alignment explanation
Indices: 1884386--1884419 Score: 50
Period size: 18 Copynumber: 1.9 Consensus size: 17
1884376 AATAATATAT
*
1884386 AAAATAATTAAAAAATA
1 AAAATAATGAAAAAATA
1884403 AAAAGTAATGAAAAAAT
1 AAAA-TAATGAAAAAAT
1884420 TTTGAAAAAA
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 4 0.27
18 11 0.73
ACGTcount: A:0.74, C:0.00, G:0.06, T:0.21
Consensus pattern (17 bp):
AAAATAATGAAAAAATA
Found at i:1884576 original size:24 final size:24
Alignment explanation
Indices: 1884544--1884599 Score: 60
Period size: 24 Copynumber: 2.3 Consensus size: 24
1884534 AATCTTAAAT
* *
1884544 ATTTATAATT-TTTATTATAATTTA
1 ATTTATAATTATTT-TAATAATTAA
*
1884568 ATTTTTAATTATTTTAATAATTAA
1 ATTTATAATTATTTTAATAATTAA
*
1884592 ATTGATAA
1 ATTTATAA
1884600 CATTAATTCA
Statistics
Matches: 26, Mismatches: 5, Indels: 2
0.79 0.15 0.06
Matches are distributed among these distances:
24 23 0.88
25 3 0.12
ACGTcount: A:0.41, C:0.00, G:0.02, T:0.57
Consensus pattern (24 bp):
ATTTATAATTATTTTAATAATTAA
Found at i:1884914 original size:7 final size:7
Alignment explanation
Indices: 1884902--1884926 Score: 50
Period size: 7 Copynumber: 3.6 Consensus size: 7
1884892 TTTAAAACAA
1884902 ATATTTT
1 ATATTTT
1884909 ATATTTT
1 ATATTTT
1884916 ATATTTT
1 ATATTTT
1884923 ATAT
1 ATAT
1884927 ATCATTTCTA
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 18 1.00
ACGTcount: A:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (7 bp):
ATATTTT
Found at i:1885496 original size:15 final size:15
Alignment explanation
Indices: 1885459--1885505 Score: 60
Period size: 15 Copynumber: 3.2 Consensus size: 15
1885449 AAAAATAGTA
1885459 TAATTTTTATATTAT
1 TAATTTTTATATTAT
* *
1885474 TAAATTTAATATT-T
1 TAATTTTTATATTAT
*
1885488 TAATTTTTATATTCT
1 TAATTTTTATATTAT
1885503 TAA
1 TAA
1885506 AATTATAAAA
Statistics
Matches: 27, Mismatches: 4, Indels: 2
0.82 0.12 0.06
Matches are distributed among these distances:
14 12 0.44
15 15 0.56
ACGTcount: A:0.36, C:0.02, G:0.00, T:0.62
Consensus pattern (15 bp):
TAATTTTTATATTAT
Found at i:1885734 original size:30 final size:32
Alignment explanation
Indices: 1885698--1885760 Score: 85
Period size: 30 Copynumber: 2.0 Consensus size: 32
1885688 TTTTCACATC
1885698 AAATAATATATTAATAT-ATT-ATAAATATTT
1 AAATAATATATTAATATCATTAATAAATATTT
* * *
1885728 AAATAATTTTTTAATATCATTAATAAATTTTT
1 AAATAATATATTAATATCATTAATAAATATTT
1885760 A
1 A
1885761 TATTTTTTTA
Statistics
Matches: 28, Mismatches: 3, Indels: 2
0.85 0.09 0.06
Matches are distributed among these distances:
30 15 0.54
31 3 0.11
32 10 0.36
ACGTcount: A:0.49, C:0.02, G:0.00, T:0.49
Consensus pattern (32 bp):
AAATAATATATTAATATCATTAATAAATATTT
Found at i:1885743 original size:19 final size:18
Alignment explanation
Indices: 1885701--1885765 Score: 51
Period size: 19 Copynumber: 3.4 Consensus size: 18
1885691 TCACATCAAA
* *
1885701 TAATATATTAATATATTAT
1 TAATAT-TTAATAAATTTT
* *
1885720 AAATATTTAAATAATTTTT
1 TAATATTT-AATAAATTTT
1885739 TAATATCATTAATAAATTTT
1 TAATAT--TTAATAAATTTT
1885759 T-ATATTT
1 TAATATTT
1885766 TTTTACAATT
Statistics
Matches: 37, Mismatches: 6, Indels: 8
0.73 0.12 0.16
Matches are distributed among these distances:
17 2 0.05
18 2 0.05
19 21 0.57
20 10 0.27
21 2 0.05
ACGTcount: A:0.45, C:0.02, G:0.00, T:0.54
Consensus pattern (18 bp):
TAATATTTAATAAATTTT
Found at i:1885799 original size:8 final size:8
Alignment explanation
Indices: 1885786--1885830 Score: 53
Period size: 8 Copynumber: 6.0 Consensus size: 8
1885776 TATAAAAATA
1885786 AAAATATT
1 AAAATATT
1885794 AAAATATT
1 AAAATATT
1885802 -AAAT-TT
1 AAAATATT
1885808 AATAATA-T
1 AA-AATATT
1885816 AAAA-ATT
1 AAAATATT
1885823 AAAATATT
1 AAAATATT
1885831 TTTTTATCAC
Statistics
Matches: 32, Mismatches: 0, Indels: 10
0.76 0.00 0.24
Matches are distributed among these distances:
6 3 0.09
7 12 0.38
8 17 0.53
ACGTcount: A:0.62, C:0.00, G:0.00, T:0.38
Consensus pattern (8 bp):
AAAATATT
Found at i:1885805 original size:15 final size:15
Alignment explanation
Indices: 1885787--1885830 Score: 56
Period size: 15 Copynumber: 3.0 Consensus size: 15
1885777 ATAAAAATAA
1885787 AAATATTAAAATATT
1 AAATATTAAAATATT
1885802 AAAT-TTAATAATA-T
1 AAATATTAA-AATATT
*
1885816 AAAAATTAAAATATT
1 AAATATTAAAATATT
1885831 TTTTTATCAC
Statistics
Matches: 25, Mismatches: 1, Indels: 6
0.78 0.03 0.19
Matches are distributed among these distances:
14 12 0.48
15 13 0.52
ACGTcount: A:0.61, C:0.00, G:0.00, T:0.39
Consensus pattern (15 bp):
AAATATTAAAATATT
Found at i:1886177 original size:12 final size:12
Alignment explanation
Indices: 1886149--1886210 Score: 74
Period size: 12 Copynumber: 5.2 Consensus size: 12
1886139 TTCAAACATG
*
1886149 ATAAAAAATAA-
1 ATAAAATATAAT
1886160 ATAAAATATAAT
1 ATAAAATATAAT
1886172 ATAAAATATAAT
1 ATAAAATATAAT
1886184 ATTAAAA-ATAAT
1 A-TAAAATATAAT
*
1886196 ATAATATAATAAT
1 ATAAAAT-ATAAT
1886209 AT
1 AT
1886211 TTATATGATA
Statistics
Matches: 45, Mismatches: 2, Indels: 6
0.85 0.04 0.11
Matches are distributed among these distances:
11 14 0.31
12 19 0.42
13 12 0.27
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.32
Consensus pattern (12 bp):
ATAAAATATAAT
Found at i:1886246 original size:15 final size:15
Alignment explanation
Indices: 1886166--1886284 Score: 60
Period size: 14 Copynumber: 8.3 Consensus size: 15
1886156 ATAAATAAAA
* *
1886166 TATAATATAAAATAT
1 TATATTATAATATAT
* * *
1886181 AATATTA-AAAATAA
1 TATATTATAATATAT
*
1886195 TATAATATAATA-A-
1 TATATTATAATATAT
1886208 TAT-TTAT-ATGATA-
1 TATATTATAAT-ATAT
*
1886221 TAAATTATTAATATAT
1 TATATTA-TAATATAT
*
1886237 TATATTTTAAT-TA-
1 TATATTATAATATAT
1886250 TA-ATTATAATAT-T
1 TATATTATAATATAT
1886263 TATATTATATATATAT
1 TATATTATA-ATATAT
1886279 ATATAT
1 -TATAT
1886285 ATGTGTAATA
Statistics
Matches: 80, Mismatches: 11, Indels: 24
0.70 0.10 0.21
Matches are distributed among these distances:
11 2 0.03
12 11 0.14
13 11 0.14
14 23 0.29
15 20 0.25
16 8 0.10
17 5 0.06
ACGTcount: A:0.51, C:0.00, G:0.01, T:0.48
Consensus pattern (15 bp):
TATATTATAATATAT
Found at i:1886845 original size:15 final size:15
Alignment explanation
Indices: 1886825--1886853 Score: 58
Period size: 15 Copynumber: 1.9 Consensus size: 15
1886815 AAATATATAA
1886825 TTTTATTTATTTATT
1 TTTTATTTATTTATT
1886840 TTTTATTTATTTAT
1 TTTTATTTATTTAT
1886854 CTGAAAGTAA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.21, C:0.00, G:0.00, T:0.79
Consensus pattern (15 bp):
TTTTATTTATTTATT
Found at i:1887051 original size:47 final size:45
Alignment explanation
Indices: 1886993--1887082 Score: 112
Period size: 47 Copynumber: 2.0 Consensus size: 45
1886983 GTTGGGATCA
*
1886993 ATTTAATTTAATT-TAAA-ATATTATATATTAATAAAAAATAATTTTTT
1 ATTTAAATTAATTATAAATATA-TA-ATATTAA-AAAAAA-AATTTTTT
*
1887040 ATTTAAATTAATTATAAATATATAATATTAAAATAAAAATTTT
1 ATTTAAATTAATTATAAATATATAATATTAAAAAAAAAATTTT
1887083 AATTTTTAAT
Statistics
Matches: 39, Mismatches: 2, Indels: 6
0.83 0.04 0.13
Matches are distributed among these distances:
45 6 0.15
46 5 0.13
47 19 0.49
48 6 0.15
49 3 0.08
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (45 bp):
ATTTAAATTAATTATAAATATATAATATTAAAAAAAAAATTTTTT
Found at i:1887098 original size:15 final size:15
Alignment explanation
Indices: 1887078--1887135 Score: 57
Period size: 15 Copynumber: 3.8 Consensus size: 15
1887068 TAAAATAAAA
1887078 ATTTTAATTTTTAAT
1 ATTTTAATTTTTAAT
*
1887093 ATTTTAATTTTAAAAT
1 ATTTTAATTTT-TAAT
*
1887109 ATACTT-ATTTTTAA-
1 AT-TTTAATTTTTAAT
1887123 ATTTTATATTTTT
1 ATTTTA-ATTTTT
1887136 TTAATATTAT
Statistics
Matches: 35, Mismatches: 4, Indels: 8
0.74 0.09 0.17
Matches are distributed among these distances:
13 2 0.06
14 2 0.06
15 19 0.54
16 10 0.29
17 2 0.06
ACGTcount: A:0.34, C:0.02, G:0.00, T:0.64
Consensus pattern (15 bp):
ATTTTAATTTTTAAT
Found at i:1887677 original size:23 final size:22
Alignment explanation
Indices: 1887640--1887700 Score: 72
Period size: 21 Copynumber: 2.8 Consensus size: 22
1887630 TATATTAAAT
**
1887640 TATTAATATAAATATTATTTTTA
1 TATTAATATTTATATTA-TTTTA
1887663 TATTAATATTTATA-TATTTTA
1 TATTAATATTTATATTATTTTA
1887684 TAATTAA-ATTTATATTA
1 T-ATTAATATTTATATTA
1887701 ATAATTTTTA
Statistics
Matches: 34, Mismatches: 2, Indels: 5
0.83 0.05 0.12
Matches are distributed among these distances:
21 13 0.38
22 9 0.26
23 12 0.35
ACGTcount: A:0.43, C:0.00, G:0.00, T:0.57
Consensus pattern (22 bp):
TATTAATATTTATATTATTTTA
Found at i:1887921 original size:19 final size:19
Alignment explanation
Indices: 1887876--1887925 Score: 64
Period size: 19 Copynumber: 2.6 Consensus size: 19
1887866 TTTGTTGAAA
*
1887876 GCAATATTTTAAAACCAAT
1 GCAATATTTTTAAACCAAT
* * *
1887895 GGATTATTTTTAAACCAGT
1 GCAATATTTTTAAACCAAT
1887914 GCAATATTTTTA
1 GCAATATTTTTA
1887926 TCTACAAATA
Statistics
Matches: 25, Mismatches: 6, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
19 25 1.00
ACGTcount: A:0.38, C:0.12, G:0.10, T:0.40
Consensus pattern (19 bp):
GCAATATTTTTAAACCAAT
Found at i:1888081 original size:19 final size:19
Alignment explanation
Indices: 1888053--1888089 Score: 56
Period size: 19 Copynumber: 1.9 Consensus size: 19
1888043 TTATCCTTAG
* *
1888053 GTAATGTTTTATGTAATTA
1 GTAATATTTTATATAATTA
1888072 GTAATATTTTATATAATT
1 GTAATATTTTATATAATT
1888090 CAATAAACAT
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
19 16 1.00
ACGTcount: A:0.35, C:0.00, G:0.11, T:0.54
Consensus pattern (19 bp):
GTAATATTTTATATAATTA
Found at i:1889050 original size:24 final size:25
Alignment explanation
Indices: 1889020--1889069 Score: 75
Period size: 24 Copynumber: 2.0 Consensus size: 25
1889010 AATAAATATA
*
1889020 TATAATATATTAA-TTTATGTAATT
1 TATAATATATAAACTTTATGTAATT
1889044 TATAATATATAAATCTTTATGTAATT
1 TATAATATATAAA-CTTTATGTAATT
1889070 CCTAACGTTA
Statistics
Matches: 23, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
24 12 0.52
26 11 0.48
ACGTcount: A:0.42, C:0.02, G:0.04, T:0.52
Consensus pattern (25 bp):
TATAATATATAAACTTTATGTAATT
Found at i:1893050 original size:15 final size:15
Alignment explanation
Indices: 1893030--1893075 Score: 74
Period size: 15 Copynumber: 3.1 Consensus size: 15
1893020 ACATCAGATC
*
1893030 CATCATCTGCATCAT
1 CATCATCTTCATCAT
1893045 CATCATCTTCATCAT
1 CATCATCTTCATCAT
*
1893060 CACCATCTTCATCAT
1 CATCATCTTCATCAT
1893075 C
1 C
1893076 TTTTGTACTC
Statistics
Matches: 29, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 29 1.00
ACGTcount: A:0.26, C:0.37, G:0.02, T:0.35
Consensus pattern (15 bp):
CATCATCTTCATCAT
Found at i:1895951 original size:23 final size:24
Alignment explanation
Indices: 1895916--1895969 Score: 78
Period size: 23 Copynumber: 2.3 Consensus size: 24
1895906 AATTTAAATA
1895916 ATTATTTATTTATATA-TATTAATT
1 ATTATTTATTTATATATTA-TAATT
1895940 ATTA-TTATTTATATATTATAATT
1 ATTATTTATTTATATATTATAATT
1895963 A-TATTTA
1 ATTATTTA
1895970 AAATATTATA
Statistics
Matches: 28, Mismatches: 0, Indels: 5
0.85 0.00 0.15
Matches are distributed among these distances:
22 2 0.07
23 20 0.71
24 6 0.21
ACGTcount: A:0.39, C:0.00, G:0.00, T:0.61
Consensus pattern (24 bp):
ATTATTTATTTATATATTATAATT
Found at i:1895958 original size:7 final size:7
Alignment explanation
Indices: 1895928--1895988 Score: 58
Period size: 7 Copynumber: 8.9 Consensus size: 7
1895918 TATTTATTTA
1895928 TATATAT
1 TATATAT
1895935 TA-ATTAT
1 TATA-TAT
1895942 TAT-TATT
1 TATATA-T
1895949 TATATAT
1 TATATAT
1895956 TATA-AT
1 TATATAT
1895962 TATAT-T
1 TATATAT
*
1895968 TAAAATAT
1 T-ATATAT
1895976 TATATAT
1 TATATAT
1895983 TATATA
1 TATATA
1895989 AATTTTAATA
Statistics
Matches: 45, Mismatches: 2, Indels: 14
0.74 0.03 0.23
Matches are distributed among these distances:
6 11 0.24
7 30 0.67
8 4 0.09
ACGTcount: A:0.44, C:0.00, G:0.00, T:0.56
Consensus pattern (7 bp):
TATATAT
Found at i:1896043 original size:18 final size:17
Alignment explanation
Indices: 1896016--1896079 Score: 58
Period size: 18 Copynumber: 3.6 Consensus size: 17
1896006 AATTTTTATT
* *
1896016 TTATAAATTTAAATAAAA
1 TTATATATTTAAAT-ATA
* *
1896034 TTATATATTTATATTATT
1 TTATATATTTA-AATATA
1896052 TTATATATTATAAATATA
1 TTATATATT-TAAATATA
1896070 TT-TATATTTA
1 TTATATATTTA
1896080 TATTACGTAA
Statistics
Matches: 38, Mismatches: 6, Indels: 6
0.76 0.12 0.12
Matches are distributed among these distances:
16 2 0.05
17 6 0.16
18 26 0.68
19 4 0.11
ACGTcount: A:0.45, C:0.00, G:0.00, T:0.55
Consensus pattern (17 bp):
TTATATATTTAAATATA
Found at i:1896046 original size:6 final size:6
Alignment explanation
Indices: 1896037--1896083 Score: 53
Period size: 6 Copynumber: 8.0 Consensus size: 6
1896027 AATAAAATTA
**
1896037 TATATT TATA-T TAT-TT TATATAT TATAAA TATATT TATATT TATATT
1 TATATT TATATT TATATT TATAT-T TATATT TATATT TATATT TATATT
1896084 ACGTAATTAT
Statistics
Matches: 34, Mismatches: 4, Indels: 6
0.77 0.09 0.14
Matches are distributed among these distances:
5 8 0.24
6 21 0.62
7 5 0.15
ACGTcount: A:0.38, C:0.00, G:0.00, T:0.62
Consensus pattern (6 bp):
TATATT
Found at i:1896079 original size:25 final size:25
Alignment explanation
Indices: 1896033--1896082 Score: 66
Period size: 25 Copynumber: 2.0 Consensus size: 25
1896023 TTTAAATAAA
* *
1896033 ATTATATATTTATATTATTTTATAT
1 ATTATAAATATATATTATTTTATAT
1896058 ATTATAAATATAT-TTATATTTATAT
1 ATTATAAATATATATTAT-TTTATAT
1896083 TACGTAATTA
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
24 4 0.18
25 18 0.82
ACGTcount: A:0.40, C:0.00, G:0.00, T:0.60
Consensus pattern (25 bp):
ATTATAAATATATATTATTTTATAT
Found at i:1896080 original size:61 final size:62
Alignment explanation
Indices: 1895903--1896081 Score: 154
Period size: 57 Copynumber: 3.0 Consensus size: 62
1895893 AAACAAAGAA
* ** *
1895903 ATAAATTTAAAT--AATTATTTATTTATATATATTAATTAT-TATTATTTATATA-TTATAATT
1 ATAAATTTAAATAAAATTATATATTTATATATATT--TTATATATTATAAATATATTTATATTT
* *
1895963 AT--ATTT-AA-AATATTATATA-TTATATAAATTTTA-ATACGTTA-ATAAT-T-TTTAT-TTT
1 ATAAATTTAAATAAAATTATATATTTATATATATTTTATATA--TTATA-AATATATTTATATTT
1896018 ATAAATTTAAATAAAATTATATATTTATAT-TATTTTATATATTATAAATATATTTATATTT
1 ATAAATTTAAATAAAATTATATATTTATATATATTTTATATATTATAAATATATTTATATTT
1896079 ATA
1 ATA
1896082 TTACGTAATT
Statistics
Matches: 94, Mismatches: 8, Indels: 33
0.70 0.06 0.24
Matches are distributed among these distances:
55 9 0.10
56 5 0.05
57 21 0.22
58 19 0.20
59 18 0.19
60 16 0.17
61 6 0.06
ACGTcount: A:0.44, C:0.01, G:0.01, T:0.55
Consensus pattern (62 bp):
ATAAATTTAAATAAAATTATATATTTATATATATTTTATATATTATAAATATATTTATATTT
Found at i:1896679 original size:18 final size:18
Alignment explanation
Indices: 1896654--1896730 Score: 63
Period size: 18 Copynumber: 4.3 Consensus size: 18
1896644 TATATATTTT
1896654 AAAT-TTAATATAATAAA
1 AAATATTAATATAATAAA
* *
1896671 AAATATTAAAATATTAAA
1 AAATATTAATATAATAAA
*
1896689 ATTTATATTAATAT-A-AAA
1 A--AATATTAATATAATAAA
1896707 AAAT-TTAAATATAATAAA
1 AAATATT-AATATAATAAA
*
1896725 ATATAT
1 AAATAT
1896731 GAACACCAAT
Statistics
Matches: 46, Mismatches: 7, Indels: 12
0.71 0.11 0.18
Matches are distributed among these distances:
15 2 0.04
16 7 0.15
17 5 0.11
18 22 0.48
19 1 0.02
20 9 0.20
ACGTcount: A:0.62, C:0.00, G:0.00, T:0.38
Consensus pattern (18 bp):
AAATATTAATATAATAAA
Found at i:1896696 original size:20 final size:20
Alignment explanation
Indices: 1896673--1896713 Score: 55
Period size: 20 Copynumber: 2.0 Consensus size: 20
1896663 ATAATAAAAA
**
1896673 ATATTAAAATATTAAAATTT
1 ATATTAAAATAAAAAAATTT
*
1896693 ATATTAATATAAAAAAATTT
1 ATATTAAAATAAAAAAATTT
1896713 A
1 A
1896714 AATATAATAA
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
20 18 1.00
ACGTcount: A:0.59, C:0.00, G:0.00, T:0.41
Consensus pattern (20 bp):
ATATTAAAATAAAAAAATTT
Found at i:1896727 original size:26 final size:26
Alignment explanation
Indices: 1896654--1896729 Score: 66
Period size: 27 Copynumber: 2.9 Consensus size: 26
1896644 TATATATTTT
* **
1896654 AAATTT-AATATAATAAAAAATATTA
1 AAATTTAAATATAATAAAATATAAAA
* *
1896679 AAATATTAAA-ATTTATATTAATATAAAA
1 AAAT-TTAAATA-TAATA-AAATATAAAA
1896707 AAATTTAAATATAATAAAATATA
1 AAATTTAAATATAATAAAATATA
1896730 TGAACACCAA
Statistics
Matches: 39, Mismatches: 7, Indels: 9
0.71 0.13 0.16
Matches are distributed among these distances:
25 4 0.10
26 9 0.23
27 15 0.38
28 11 0.28
ACGTcount: A:0.63, C:0.00, G:0.00, T:0.37
Consensus pattern (26 bp):
AAATTTAAATATAATAAAATATAAAA
Found at i:1897566 original size:15 final size:15
Alignment explanation
Indices: 1897546--1897601 Score: 51
Period size: 15 Copynumber: 3.7 Consensus size: 15
1897536 GGGTGTTTTT
1897546 ATTAAATTAATTTAA
1 ATTAAATTAATTTAA
*
1897561 ATTAAA-AAATTATAA
1 ATTAAATTAATT-TAA
* *
1897576 TTTAATTTAATTTAA
1 ATTAAATTAATTTAA
* *
1897591 TTTAATTTAAT
1 ATTAAATTAAT
1897602 GCAATTCCAA
Statistics
Matches: 35, Mismatches: 4, Indels: 4
0.81 0.09 0.09
Matches are distributed among these distances:
14 4 0.11
15 27 0.77
16 4 0.11
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (15 bp):
ATTAAATTAATTTAA
Found at i:1897598 original size:5 final size:5
Alignment explanation
Indices: 1897568--1897601 Score: 59
Period size: 5 Copynumber: 6.6 Consensus size: 5
1897558 TAAATTAAAA
1897568 AATTAT AATTT AATTT AATTT AATTT AATTT AAT
1 AATT-T AATTT AATTT AATTT AATTT AATTT AAT
1897602 GCAATTCCAA
Statistics
Matches: 28, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
5 24 0.86
6 4 0.14
ACGTcount: A:0.44, C:0.00, G:0.00, T:0.56
Consensus pattern (5 bp):
AATTT
Found at i:1897607 original size:15 final size:15
Alignment explanation
Indices: 1897574--1897607 Score: 50
Period size: 15 Copynumber: 2.3 Consensus size: 15
1897564 AAAAAATTAT
**
1897574 AATTTAATTTAATTT
1 AATTTAATTTAATGC
1897589 AATTTAATTTAATGC
1 AATTTAATTTAATGC
1897604 AATT
1 AATT
1897608 CCAACCAACT
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
15 17 1.00
ACGTcount: A:0.41, C:0.03, G:0.03, T:0.53
Consensus pattern (15 bp):
AATTTAATTTAATGC
Found at i:1903792 original size:2 final size:2
Alignment explanation
Indices: 1903780--1903809 Score: 53
Period size: 2 Copynumber: 15.5 Consensus size: 2
1903770 TCGCTTCCCT
1903780 TC TC T- TC TC TC TC TC TC TC TC TC TC TC TC T
1 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC T
1903810 GGGTTGAAAA
Statistics
Matches: 27, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
1 1 0.04
2 26 0.96
ACGTcount: A:0.00, C:0.47, G:0.00, T:0.53
Consensus pattern (2 bp):
TC
Found at i:1907869 original size:30 final size:30
Alignment explanation
Indices: 1907835--1907894 Score: 111
Period size: 30 Copynumber: 2.0 Consensus size: 30
1907825 TTGATGATCA
1907835 CACTCGAATTCAAATAACATAGAATAACAC
1 CACTCGAATTCAAATAACATAGAATAACAC
*
1907865 CACTCGAATTCAAGTAACATAGAATAACAC
1 CACTCGAATTCAAATAACATAGAATAACAC
1907895 TAGAGCTCTA
Statistics
Matches: 29, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
30 29 1.00
ACGTcount: A:0.48, C:0.23, G:0.08, T:0.20
Consensus pattern (30 bp):
CACTCGAATTCAAATAACATAGAATAACAC
Found at i:1909763 original size:3 final size:3
Alignment explanation
Indices: 1909755--1909787 Score: 66
Period size: 3 Copynumber: 11.0 Consensus size: 3
1909745 ATCAAACCTA
1909755 CTT CTT CTT CTT CTT CTT CTT CTT CTT CTT CTT
1 CTT CTT CTT CTT CTT CTT CTT CTT CTT CTT CTT
1909788 TTATCAATCT
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 30 1.00
ACGTcount: A:0.00, C:0.33, G:0.00, T:0.67
Consensus pattern (3 bp):
CTT
Found at i:1910173 original size:9 final size:9
Alignment explanation
Indices: 1910159--1910184 Score: 52
Period size: 9 Copynumber: 2.9 Consensus size: 9
1910149 AACTTCGTTT
1910159 TTTTTTTTG
1 TTTTTTTTG
1910168 TTTTTTTTG
1 TTTTTTTTG
1910177 TTTTTTTT
1 TTTTTTTT
1910185 TGGCGTGTTT
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
9 17 1.00
ACGTcount: A:0.00, C:0.00, G:0.08, T:0.92
Consensus pattern (9 bp):
TTTTTTTTG
Found at i:1910173 original size:10 final size:10
Alignment explanation
Indices: 1910158--1910186 Score: 51
Period size: 9 Copynumber: 3.0 Consensus size: 10
1910148 GAACTTCGTT
1910158 TTTTTTTTTG
1 TTTTTTTTTG
1910168 -TTTTTTTTG
1 TTTTTTTTTG
1910177 TTTTTTTTTG
1 TTTTTTTTTG
1910187 GCGTGTTTGG
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
9 9 0.50
10 9 0.50
ACGTcount: A:0.00, C:0.00, G:0.10, T:0.90
Consensus pattern (10 bp):
TTTTTTTTTG
Found at i:1915820 original size:64 final size:65
Alignment explanation
Indices: 1915711--1915844 Score: 180
Period size: 64 Copynumber: 2.1 Consensus size: 65
1915701 AAAGTTTTTG
* * * * *
1915711 AAATAATATTGGTCCCCAATATTGTTAAATTAAGAACGACGTTCATCCTAATACAACTAAAATCA
1 AAATAATATTGGTCCCCAACACTGATAAATTAAAAACGACATTCATCCTAATACAACTAAAATCA
* * * *
1915776 AAATAATATTGGTCCTCAACACT-ATAAATTAAAAACGACATTCATCCTAATATAATTCAAATCA
1 AAATAATATTGGTCCCCAACACTGATAAATTAAAAACGACATTCATCCTAATACAACTAAAATCA
1915840 AAATA
1 AAATA
1915845 GAAAAGATAT
Statistics
Matches: 60, Mismatches: 9, Indels: 1
0.86 0.13 0.01
Matches are distributed among these distances:
64 40 0.67
65 20 0.33
ACGTcount: A:0.46, C:0.18, G:0.07, T:0.29
Consensus pattern (65 bp):
AAATAATATTGGTCCCCAACACTGATAAATTAAAAACGACATTCATCCTAATACAACTAAAATCA
Found at i:1920396 original size:38 final size:38
Alignment explanation
Indices: 1920345--1920421 Score: 154
Period size: 38 Copynumber: 2.0 Consensus size: 38
1920335 TGGTCTGGTC
1920345 TTTAGTATAGTAATAAGAGGTTATGAGCTCAAATCTAA
1 TTTAGTATAGTAATAAGAGGTTATGAGCTCAAATCTAA
1920383 TTTAGTATAGTAATAAGAGGTTATGAGCTCAAATCTAA
1 TTTAGTATAGTAATAAGAGGTTATGAGCTCAAATCTAA
1920421 T
1 T
1920422 CACATACAGA
Statistics
Matches: 39, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
38 39 1.00
ACGTcount: A:0.39, C:0.08, G:0.18, T:0.35
Consensus pattern (38 bp):
TTTAGTATAGTAATAAGAGGTTATGAGCTCAAATCTAA
Found at i:1922558 original size:2 final size:2
Alignment explanation
Indices: 1922551--1922588 Score: 76
Period size: 2 Copynumber: 19.0 Consensus size: 2
1922541 AACTGAAAGG
1922551 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1922589 CAGTGTTGTC
Statistics
Matches: 36, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 36 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:1924763 original size:14 final size:14
Alignment explanation
Indices: 1924744--1924796 Score: 61
Period size: 14 Copynumber: 3.7 Consensus size: 14
1924734 ATTAAAAAAA
*
1924744 TATATTTTATTTTT
1 TATATTTTAATTTT
*
1924758 TATATTATTAAATTT
1 TATATT-TTAATTTT
*
1924773 AATATTTTAATTTT
1 TATATTTTAATTTT
*
1924787 TATAATTTAA
1 TATATTTTAA
1924797 AAATAATAAT
Statistics
Matches: 32, Mismatches: 6, Indels: 2
0.80 0.15 0.05
Matches are distributed among these distances:
14 21 0.66
15 11 0.34
ACGTcount: A:0.36, C:0.00, G:0.00, T:0.64
Consensus pattern (14 bp):
TATATTTTAATTTT
Found at i:1924768 original size:30 final size:30
Alignment explanation
Indices: 1924734--1924812 Score: 74
Period size: 29 Copynumber: 2.7 Consensus size: 30
1924724 TTTTTATTGC
* *
1924734 ATTAAAAAAATATATTTTATTTTTTATATT
1 ATTAAAAAAATATATTTTAATTTTTATAAT
***
1924764 ATTAAATTTA-ATATTTTAATTTTTATAAT
1 ATTAAAAAAATATATTTTAATTTTTATAAT
1924793 -TTAAAAATAATA-ATTATTAA
1 ATTAAAAA-AATATATT-TTAA
1924813 AAAATTATTA
Statistics
Matches: 38, Mismatches: 8, Indels: 6
0.73 0.15 0.12
Matches are distributed among these distances:
28 5 0.13
29 21 0.55
30 12 0.32
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (30 bp):
ATTAAAAAAATATATTTTAATTTTTATAAT
Found at i:1924780 original size:22 final size:22
Alignment explanation
Indices: 1924755--1924796 Score: 59
Period size: 22 Copynumber: 1.9 Consensus size: 22
1924745 ATATTTTATT
1924755 TTTTATATTATTA-AATTTAATA
1 TTTTA-ATTATTATAATTTAATA
*
1924777 TTTTAATTTTTATAATTTAA
1 TTTTAATTATTATAATTTAA
1924797 AAATAATAAT
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
21 6 0.33
22 12 0.67
ACGTcount: A:0.38, C:0.00, G:0.00, T:0.62
Consensus pattern (22 bp):
TTTTAATTATTATAATTTAATA
Found at i:1924803 original size:28 final size:29
Alignment explanation
Indices: 1924739--1924804 Score: 82
Period size: 29 Copynumber: 2.3 Consensus size: 29
1924729 ATTGCATTAA
* *
1924739 AAAAAT-ATATTTTATTTTTTATATTATT
1 AAAAATAATATTTTAATTTTTATAATATT
**
1924767 AAATTTAATATTTTAATTTTTATAAT-TT
1 AAAAATAATATTTTAATTTTTATAATATT
1924795 AAAAATAATA
1 AAAAATAATA
1924805 ATTATTAAAA
Statistics
Matches: 31, Mismatches: 6, Indels: 2
0.79 0.15 0.05
Matches are distributed among these distances:
28 14 0.45
29 17 0.55
ACGTcount: A:0.45, C:0.00, G:0.00, T:0.55
Consensus pattern (29 bp):
AAAAATAATATTTTAATTTTTATAATATT
Found at i:1924818 original size:11 final size:11
Alignment explanation
Indices: 1924804--1924835 Score: 50
Period size: 10 Copynumber: 3.1 Consensus size: 11
1924794 TAAAAATAAT
1924804 AATTATTAAAA
1 AATTATTAAAA
1924815 AATTATT-AAA
1 AATTATTAAAA
1924825 AATT-TTAAAA
1 AATTATTAAAA
1924835 A
1 A
1924836 TTTTATTTAA
Statistics
Matches: 20, Mismatches: 0, Indels: 3
0.87 0.00 0.13
Matches are distributed among these distances:
9 2 0.10
10 11 0.55
11 7 0.35
ACGTcount: A:0.62, C:0.00, G:0.00, T:0.38
Consensus pattern (11 bp):
AATTATTAAAA
Found at i:1924961 original size:24 final size:24
Alignment explanation
Indices: 1924933--1924987 Score: 67
Period size: 24 Copynumber: 2.3 Consensus size: 24
1924923 AGTTTGAATT
1924933 TTTATATAAAAT-TTAAAATTTTA
1 TTTATATAAAATATTAAAATTTTA
* * *
1924956 TATTATATGACATATTAATATTTTA
1 T-TTATATAAAATATTAAAATTTTA
1924981 TTTATAT
1 TTTATAT
1924988 TTAAATAAAT
Statistics
Matches: 27, Mismatches: 3, Indels: 3
0.82 0.09 0.09
Matches are distributed among these distances:
23 1 0.04
24 15 0.56
25 11 0.41
ACGTcount: A:0.42, C:0.02, G:0.02, T:0.55
Consensus pattern (24 bp):
TTTATATAAAATATTAAAATTTTA
Found at i:1925223 original size:26 final size:24
Alignment explanation
Indices: 1925179--1925227 Score: 71
Period size: 24 Copynumber: 2.0 Consensus size: 24
1925169 TTTGAAATGT
*
1925179 TATATTTTTATAATTATATGTTTA
1 TATATTTTTATAATAATATGTTTA
1925203 TATATTTTTATATATAAATATGTTT
1 TATATTTTTATA-AT-AATATGTTT
1925228 TAAGAATTAT
Statistics
Matches: 22, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
24 12 0.55
25 2 0.09
26 8 0.36
ACGTcount: A:0.35, C:0.00, G:0.04, T:0.61
Consensus pattern (24 bp):
TATATTTTTATAATAATATGTTTA
Found at i:1925491 original size:22 final size:23
Alignment explanation
Indices: 1925450--1925492 Score: 63
Period size: 22 Copynumber: 1.9 Consensus size: 23
1925440 TAAACTCGCA
1925450 TATTTATATTTTAAATAATTTTT
1 TATTTATATTTTAAATAATTTTT
1925473 TATTTA-ATCTTT-AATAATTT
1 TATTTATAT-TTTAAATAATTT
1925493 AATTTTTTAT
Statistics
Matches: 19, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
22 10 0.53
23 9 0.47
ACGTcount: A:0.35, C:0.02, G:0.00, T:0.63
Consensus pattern (23 bp):
TATTTATATTTTAAATAATTTTT
Found at i:1926148 original size:11 final size:11
Alignment explanation
Indices: 1926125--1926158 Score: 50
Period size: 11 Copynumber: 3.0 Consensus size: 11
1926115 AGTTTAAAAA
1926125 AAACTAATAAAT
1 AAACT-ATAAAT
*
1926137 AAACTTTAAAT
1 AAACTATAAAT
1926148 AAACTATAAAT
1 AAACTATAAAT
1926159 GAATTTATTC
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
11 15 0.75
12 5 0.25
ACGTcount: A:0.62, C:0.09, G:0.00, T:0.29
Consensus pattern (11 bp):
AAACTATAAAT
Found at i:1926955 original size:17 final size:17
Alignment explanation
Indices: 1926930--1926963 Score: 50
Period size: 17 Copynumber: 2.0 Consensus size: 17
1926920 ATTAAATAAT
1926930 AATTATTAATATTTTTA
1 AATTATTAATATTTTTA
* *
1926947 AATTCTTAATTTTTTTA
1 AATTATTAATATTTTTA
1926964 TCAAAAAAAG
Statistics
Matches: 15, Mismatches: 2, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
17 15 1.00
ACGTcount: A:0.35, C:0.03, G:0.00, T:0.62
Consensus pattern (17 bp):
AATTATTAATATTTTTA
Found at i:1928431 original size:6 final size:6
Alignment explanation
Indices: 1928420--1928453 Score: 50
Period size: 6 Copynumber: 5.5 Consensus size: 6
1928410 CTTACACCAT
*
1928420 ATATAA ATATAA ATATAA ATATAT ATATATA ATA
1 ATATAA ATATAA ATATAA ATATAA ATATA-A ATA
1928454 CAATTTCAAG
Statistics
Matches: 25, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
6 22 0.88
7 3 0.12
ACGTcount: A:0.62, C:0.00, G:0.00, T:0.38
Consensus pattern (6 bp):
ATATAA
Found at i:1929702 original size:4 final size:4
Alignment explanation
Indices: 1929687--1929723 Score: 51
Period size: 4 Copynumber: 9.5 Consensus size: 4
1929677 CAAATAAACT
1929687 TTTA TTTA --TA TTTA TTTA TTTA TTTA TTTAA TTTA TT
1 TTTA TTTA TTTA TTTA TTTA TTTA TTTA TTT-A TTTA TT
1929724 CGTGTTCGAT
Statistics
Matches: 30, Mismatches: 0, Indels: 6
0.83 0.00 0.17
Matches are distributed among these distances:
2 2 0.07
4 24 0.80
5 4 0.13
ACGTcount: A:0.27, C:0.00, G:0.00, T:0.73
Consensus pattern (4 bp):
TTTA
Found at i:1931291 original size:21 final size:21
Alignment explanation
Indices: 1931265--1931325 Score: 63
Period size: 20 Copynumber: 2.8 Consensus size: 21
1931255 ATATTTAAGT
1931265 TTTTTGTATTTTACAATTATTA
1 TTTTTGTATTTTA-AATTATTA
*
1931287 -TTTTGT-TATTAAAGTTATTA
1 TTTTTGTATTTTAAA-TTATTA
1931307 TTTTTTGTATTTTAGAATT
1 -TTTTTGTATTTTA-AATT
1931326 TATTCTTTAA
Statistics
Matches: 32, Mismatches: 2, Indels: 9
0.74 0.05 0.21
Matches are distributed among these distances:
19 2 0.06
20 10 0.31
21 6 0.19
22 6 0.19
23 6 0.19
24 2 0.06
ACGTcount: A:0.26, C:0.02, G:0.08, T:0.64
Consensus pattern (21 bp):
TTTTTGTATTTTAAATTATTA
Found at i:1931328 original size:21 final size:20
Alignment explanation
Indices: 1931264--1931329 Score: 55
Period size: 21 Copynumber: 3.1 Consensus size: 20
1931254 TATATTTAAG
1931264 TTTTTTGTATTTTACAA-TTA
1 TTTTTTGTATTTTA-AATTTA
*
1931284 TTATTTTGT-TATTAAAGTTATTA
1 TT-TTTTGTATTTTAAA--T-TTA
1931307 TTTTTTGTATTTTAGAATTTA
1 TTTTTTGTATTTTA-AATTTA
1931328 TT
1 TT
1931330 CTTTAATTAT
Statistics
Matches: 37, Mismatches: 2, Indels: 13
0.71 0.04 0.25
Matches are distributed among these distances:
19 2 0.05
20 6 0.16
21 11 0.30
22 7 0.19
23 9 0.24
24 2 0.05
ACGTcount: A:0.26, C:0.02, G:0.08, T:0.65
Consensus pattern (20 bp):
TTTTTTGTATTTTAAATTTA
Found at i:1931420 original size:25 final size:26
Alignment explanation
Indices: 1931376--1931441 Score: 78
Period size: 26 Copynumber: 2.4 Consensus size: 26
1931366 TTAATTTTAC
*
1931376 AAATTTAAATATTCAATAAATAATATTATT
1 AAATTTAAAT-TTAAAT-AATAATA-TA-T
*
1931406 TAATTTAAATTTAAATAATAATATAT
1 AAATTTAAATTTAAATAATAATATAT
1931432 AAATTTAAAT
1 AAATTTAAAT
1931442 GACTCTAAAT
Statistics
Matches: 33, Mismatches: 3, Indels: 4
0.82 0.08 0.10
Matches are distributed among these distances:
26 10 0.30
27 2 0.06
28 7 0.21
29 5 0.15
30 9 0.27
ACGTcount: A:0.55, C:0.02, G:0.00, T:0.44
Consensus pattern (26 bp):
AAATTTAAATTTAAATAATAATATAT
Found at i:1931489 original size:15 final size:15
Alignment explanation
Indices: 1931447--1931501 Score: 55
Period size: 14 Copynumber: 3.9 Consensus size: 15
1931437 TAAATGACTC
1931447 TAAATTT-TAAA--A
1 TAAATTTATAAATTA
*
1931459 TAATTTTATAAA-TA
1 TAAATTTATAAATTA
*
1931473 TAAATTTAAAAATTA
1 TAAATTTATAAATTA
1931488 TAAAATTTATAAAT
1 T-AAATTTATAAAT
1931502 ATCTAACTTG
Statistics
Matches: 35, Mismatches: 4, Indels: 4
0.81 0.09 0.09
Matches are distributed among these distances:
12 6 0.17
13 4 0.11
14 11 0.31
15 3 0.09
16 11 0.31
ACGTcount: A:0.56, C:0.00, G:0.00, T:0.44
Consensus pattern (15 bp):
TAAATTTATAAATTA
Found at i:1938185 original size:23 final size:25
Alignment explanation
Indices: 1938150--1938201 Score: 63
Period size: 24 Copynumber: 2.2 Consensus size: 25
1938140 TTTACTAAGT
* *
1938150 AAATAATAAATTT-TGTAAATTTTA
1 AAATAATAAATTTATATAAATTTGA
*
1938174 AAATAAT-TATTTATATAAATTTGA
1 AAATAATAAATTTATATAAATTTGA
1938198 AAAT
1 AAAT
1938202 TTTGTTAATA
Statistics
Matches: 24, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
23 4 0.17
24 20 0.83
ACGTcount: A:0.52, C:0.00, G:0.04, T:0.44
Consensus pattern (25 bp):
AAATAATAAATTTATATAAATTTGA
Found at i:1938384 original size:20 final size:20
Alignment explanation
Indices: 1938361--1938414 Score: 56
Period size: 20 Copynumber: 2.7 Consensus size: 20
1938351 ATAAATATTT
1938361 TTTATTAATAATATATATAA
1 TTTATTAATAATATATATAA
* * * *
1938381 TTTATAAATAAAAAATTTAA
1 TTTATTAATAATATATATAA
1938401 TTTGATTAA-AATAT
1 TTT-ATTAATAATAT
1938415 TTTATTAATG
Statistics
Matches: 26, Mismatches: 7, Indels: 2
0.74 0.20 0.06
Matches are distributed among these distances:
20 22 0.85
21 4 0.15
ACGTcount: A:0.52, C:0.00, G:0.02, T:0.46
Consensus pattern (20 bp):
TTTATTAATAATATATATAA
Found at i:1938898 original size:12 final size:12
Alignment explanation
Indices: 1938881--1938989 Score: 50
Period size: 12 Copynumber: 8.8 Consensus size: 12
1938871 TTATTATATC
1938881 ATATTTAAATAA
1 ATATTTAAATAA
1938893 ATATTTATAAT-A
1 ATATTTA-AATAA
**
1938905 ATATTTTAAATTT
1 ATA-TTTAAATAA
1938918 AT-TTTAAA-AA
1 ATATTTAAATAA
* *
1938928 A-ATTAAAAATTA
1 ATATT-TAAATAA
*
1938940 ATATTATAATATATT
1 ATATT-TAA-ATA-A
1938955 ATATTTAAA-ATA
1 ATATTTAAATA-A
1938967 ATATTTTAAATATA
1 ATA-TTTAAATA-A
1938981 AT-TTTAAAT
1 ATATTTAAAT
1938990 TATAATAATA
Statistics
Matches: 77, Mismatches: 9, Indels: 22
0.71 0.08 0.20
Matches are distributed among these distances:
10 3 0.04
11 9 0.12
12 28 0.36
13 22 0.29
14 10 0.13
15 5 0.06
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (12 bp):
ATATTTAAATAA
Found at i:1938984 original size:24 final size:24
Alignment explanation
Indices: 1938917--1938989 Score: 67
Period size: 24 Copynumber: 2.9 Consensus size: 24
1938907 ATTTTAAATT
* *
1938917 TATTTTAAA-AAAATTAAAAATTAA
1 TATTTTAAATATAATTTAAAA-TAA
*
1938941 TATTATAATATATTATATTTAAAATAA
1 TATTTTAA-ATA-TA-ATTTAAAATAA
*
1938968 TATTTTAAATATAATTTTAAAT
1 TATTTTAAATATAATTTAAAAT
1938990 TATAATAATA
Statistics
Matches: 40, Mismatches: 5, Indels: 8
0.75 0.09 0.15
Matches are distributed among these distances:
24 15 0.38
25 3 0.08
26 4 0.10
27 11 0.28
28 7 0.17
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (24 bp):
TATTTTAAATATAATTTAAAATAA
Found at i:1940311 original size:15 final size:15
Alignment explanation
Indices: 1940291--1940327 Score: 56
Period size: 15 Copynumber: 2.5 Consensus size: 15
1940281 TTAAAATTAA
1940291 ATTATTTTTTAAATT
1 ATTATTTTTTAAATT
* *
1940306 ATTATTATTTAATTT
1 ATTATTTTTTAAATT
1940321 ATTATTT
1 ATTATTT
1940328 ACATTAAAAA
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
15 19 1.00
ACGTcount: A:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (15 bp):
ATTATTTTTTAAATT
Found at i:1940892 original size:16 final size:16
Alignment explanation
Indices: 1940853--1940908 Score: 60
Period size: 17 Copynumber: 3.4 Consensus size: 16
1940843 ATTTTTTTTA
*
1940853 ATATATTTTATATCAT
1 ATATATTTTATATAAT
1940869 ATTATATTTTA-ATAAT
1 A-TATATTTTATATAAT
*
1940885 CATATATTATATATATAT
1 -ATATATTTTATATA-AT
1940903 ATATAT
1 ATATAT
1940909 ATAATCACAT
Statistics
Matches: 34, Mismatches: 2, Indels: 7
0.79 0.05 0.16
Matches are distributed among these distances:
16 13 0.38
17 19 0.56
18 2 0.06
ACGTcount: A:0.43, C:0.04, G:0.00, T:0.54
Consensus pattern (16 bp):
ATATATTTTATATAAT
Found at i:1940920 original size:31 final size:33
Alignment explanation
Indices: 1940853--1940921 Score: 81
Period size: 33 Copynumber: 2.2 Consensus size: 33
1940843 ATTTTTTTTA
* *
1940853 ATATATTTTATATCATATTATATTTTAATAATC
1 ATATATTATATATCATATTATATTATAATAATC
*
1940886 ATATATTATATAT-ATA-TATATATATAATCA-C
1 ATATATTATATATCATATTATAT-TATAATAATC
1940917 ATATA
1 ATATA
1940922 AAATTATTAA
Statistics
Matches: 32, Mismatches: 3, Indels: 4
0.82 0.08 0.10
Matches are distributed among these distances:
31 11 0.34
32 9 0.28
33 12 0.38
ACGTcount: A:0.45, C:0.06, G:0.00, T:0.49
Consensus pattern (33 bp):
ATATATTATATATCATATTATATTATAATAATC
Found at i:1941244 original size:33 final size:33
Alignment explanation
Indices: 1941178--1941244 Score: 80
Period size: 33 Copynumber: 2.0 Consensus size: 33
1941168 AGGCAGACAG
* **
1941178 AACAAACTTAACAAGTGTTGATTCATTTGTACA
1 AACAAACTTAACAAGCGTTGATTCATTCATACA
* * *
1941211 AACACACTTGACAAGCGTTGTTTCATTCATACA
1 AACAAACTTAACAAGCGTTGATTCATTCATACA
1941244 A
1 A
1941245 CCACTTTTTA
Statistics
Matches: 28, Mismatches: 6, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
33 28 1.00
ACGTcount: A:0.37, C:0.19, G:0.12, T:0.31
Consensus pattern (33 bp):
AACAAACTTAACAAGCGTTGATTCATTCATACA
Found at i:1944993 original size:17 final size:16
Alignment explanation
Indices: 1944967--1945034 Score: 52
Period size: 17 Copynumber: 4.1 Consensus size: 16
1944957 CATTCATAAG
1944967 ATTATTATAGTGATTTA
1 ATTA-TATAGTGATTTA
*
1944984 ATTATAATAGTGA-TAA
1 ATTAT-ATAGTGATTTA
1945000 GATTATCA-AGATGATTTA
1 -ATTAT-ATAG-TGATTTA
1945018 ATTAT-TAGTGATCTTA
1 ATTATATAGTGAT-TTA
1945034 A
1 A
1945035 ATCATTGTGT
Statistics
Matches: 42, Mismatches: 3, Indels: 13
0.72 0.05 0.22
Matches are distributed among these distances:
15 4 0.10
16 11 0.26
17 25 0.60
18 2 0.05
ACGTcount: A:0.40, C:0.03, G:0.13, T:0.44
Consensus pattern (16 bp):
ATTATATAGTGATTTA
Found at i:1945005 original size:34 final size:32
Alignment explanation
Indices: 1944962--1945029 Score: 93
Period size: 34 Copynumber: 2.1 Consensus size: 32
1944952 GGTATCATTC
*
1944962 ATAAGATTATTATAG-TGATTTAATTATAATAGTG
1 ATAAGATTATCA-AGATGATTTAATTAT--TAGTG
1944996 ATAAGATTATCAAGATGATTTAATTATTAGTG
1 ATAAGATTATCAAGATGATTTAATTATTAGTG
1945028 AT
1 AT
1945030 CTTAAATCAT
Statistics
Matches: 32, Mismatches: 1, Indels: 4
0.86 0.03 0.11
Matches are distributed among these distances:
32 7 0.22
33 2 0.06
34 23 0.72
ACGTcount: A:0.41, C:0.01, G:0.15, T:0.43
Consensus pattern (32 bp):
ATAAGATTATCAAGATGATTTAATTATTAGTG
Found at i:1946687 original size:2 final size:2
Alignment explanation
Indices: 1946680--1946704 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
1946670 TAAGACTGTT
1946680 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 T
1946705 GGAATTAGAT
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:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:1947428 original size:17 final size:17
Alignment explanation
Indices: 1947406--1947446 Score: 57
Period size: 18 Copynumber: 2.4 Consensus size: 17
1947396 CTATTATTTT
1947406 AAAAATT-TTAAAAATAA
1 AAAAATTATT-AAAATAA
1947423 AAAAATTGATTAAAATAA
1 AAAAATT-ATTAAAATAA
1947441 AAAAAT
1 AAAAAT
1947447 ATCTTTTATA
Statistics
Matches: 22, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
17 7 0.32
18 13 0.59
19 2 0.09
ACGTcount: A:0.71, C:0.00, G:0.02, T:0.27
Consensus pattern (17 bp):
AAAAATTATTAAAATAA
Found at i:1955326 original size:22 final size:22
Alignment explanation
Indices: 1955299--1955360 Score: 70
Period size: 23 Copynumber: 2.7 Consensus size: 22
1955289 TTTGAGAAAA
*
1955299 TTTTTTATTTTAATATTTATGTT
1 TTTTTTAATTT-ATATTTATGTT
*
1955322 TTTTTTAATTTATATTTATATT
1 TTTTTTAATTTATATTTATGTT
* *
1955344 TATATTATATTTATATT
1 TTTTTTA-ATTTATATT
1955361 ATTTTTAATT
Statistics
Matches: 34, Mismatches: 4, Indels: 2
0.85 0.10 0.05
Matches are distributed among these distances:
22 15 0.44
23 19 0.56
ACGTcount: A:0.27, C:0.00, G:0.02, T:0.71
Consensus pattern (22 bp):
TTTTTTAATTTATATTTATGTT
Found at i:1955339 original size:11 final size:12
Alignment explanation
Indices: 1955302--1955389 Score: 64
Period size: 11 Copynumber: 7.8 Consensus size: 12
1955292 GAGAAAATTT
1955302 TTTAT-TTTAATA
1 TTTATATTT-ATA
* *
1955314 TTTATGTTT-TT
1 TTTATATTTATA
1955325 TTTA-ATTTATA
1 TTTATATTTATA
1955336 TTTATATTTATA
1 TTTATATTTATA
1955348 -TTATATTTATA
1 TTTATATTTATA
*
1955359 -TTATTTTTA-A
1 TTTATATTTATA
* *
1955369 TTAAT-TTTTTA
1 TTTATATTTATA
1955380 TATTATATTT
1 T-TTATATTT
1955390 GTATCATATA
Statistics
Matches: 62, Mismatches: 7, Indels: 13
0.76 0.09 0.16
Matches are distributed among these distances:
10 7 0.11
11 34 0.55
12 15 0.24
13 6 0.10
ACGTcount: A:0.30, C:0.00, G:0.01, T:0.69
Consensus pattern (12 bp):
TTTATATTTATA
Found at i:1955354 original size:39 final size:34
Alignment explanation
Indices: 1955297--1955389 Score: 105
Period size: 39 Copynumber: 2.6 Consensus size: 34
1955287 AATTTGAGAA
* * *
1955297 AATTTTTTATTTTAATATTTATGTTTTTTTTAATTT
1 AATTTTTTATATT-ATATTTATATTATTTTTAA-TT
1955333 ATATTTATATTTATATTATATTTATATTATTTTTAATT
1 A-A-TT-T-TTTATATTATATTTATATTATTTTTAATT
1955371 AATTTTTTATATTATATTT
1 AATTTTTTATATTATATTT
1955390 GTATCATATA
Statistics
Matches: 50, Mismatches: 3, Indels: 10
0.79 0.05 0.16
Matches are distributed among these distances:
34 14 0.28
35 1 0.02
36 3 0.06
37 2 0.04
38 5 0.10
39 18 0.36
40 7 0.14
ACGTcount: A:0.30, C:0.00, G:0.01, T:0.69
Consensus pattern (34 bp):
AATTTTTTATATTATATTTATATTATTTTTAATT
Found at i:1955356 original size:28 final size:28
Alignment explanation
Indices: 1955302--1955365 Score: 69
Period size: 28 Copynumber: 2.3 Consensus size: 28
1955292 GAGAAAATTT
* * *
1955302 TTTATTTTAATATTTATGTTTTTTTTAA
1 TTTATTTTAATATTTATATTATATTTAA
1955330 TTTATATTT-ATATTTATATTATATTT-A
1 TTTAT-TTTAATATTTATATTATATTTAA
1955357 TATTATTTT
1 T-TTATTTT
1955366 TAATTAATTT
Statistics
Matches: 31, Mismatches: 3, Indels: 5
0.79 0.08 0.13
Matches are distributed among these distances:
27 5 0.16
28 23 0.74
29 3 0.10
ACGTcount: A:0.28, C:0.00, G:0.02, T:0.70
Consensus pattern (28 bp):
TTTATTTTAATATTTATATTATATTTAA
Found at i:1955379 original size:12 final size:14
Alignment explanation
Indices: 1955330--1955389 Score: 52
Period size: 17 Copynumber: 4.0 Consensus size: 14
1955320 TTTTTTTTAA
1955330 TTTATATTTATATTT
1 TTTATA-TTATATTT
1955345 ATATTATATTTATATTAT
1 -T-TTATA-TTATATT-T
1955363 TTT-TAATTA-ATTT
1 TTTAT-ATTATATTT
1955376 TTTATATTATATTT
1 TTTATATTATATTT
1955390 GTATCATATA
Statistics
Matches: 39, Mismatches: 0, Indels: 12
0.76 0.00 0.24
Matches are distributed among these distances:
13 8 0.21
14 8 0.21
15 4 0.10
16 4 0.10
17 14 0.36
18 1 0.03
ACGTcount: A:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (14 bp):
TTTATATTATATTT
Found at i:1955427 original size:26 final size:25
Alignment explanation
Indices: 1955380--1955428 Score: 62
Period size: 26 Copynumber: 1.9 Consensus size: 25
1955370 TAATTTTTTA
*
1955380 TATTATATTTGTATCATATATTAAT
1 TATTATATTTGTATAATATATTAAT
* *
1955405 TATTCATATTTTTATAATTTATTA
1 TATT-ATATTTGTATAATATATTA
1955429 TCGTGATTTA
Statistics
Matches: 20, Mismatches: 3, Indels: 1
0.83 0.12 0.04
Matches are distributed among these distances:
25 4 0.20
26 16 0.80
ACGTcount: A:0.35, C:0.04, G:0.02, T:0.59
Consensus pattern (25 bp):
TATTATATTTGTATAATATATTAAT
Found at i:1955518 original size:82 final size:80
Alignment explanation
Indices: 1955370--1955532 Score: 211
Period size: 82 Copynumber: 2.0 Consensus size: 80
1955360 TATTTTTAAT
* * **
1955370 TAATTTTTTATATTATATTTGTATCATATATTAATTATTCATATTTTTATAATTTATTATCGTGA
1 TAATTTTTTATATTATATTTGTATCATATATTAATTATACATATTTATATAATTTATTATAATGA
*
1955435 TTTAATTTTAAAAAA
66 TTTAATTTAAAAAAA
* * *
1955450 TAATATTTTTATATTATATTT-TATCATATCTTAATTTATGACATATTTATATAATTTTTTTTAA
1 TAAT-TTTTTATATTATATTTGTATCATATATTAA-TTAT-ACATATTTATATAATTTATTATAA
*
1955514 TGATTTGATTTAAAAAAA
63 TGATTTAATTTAAAAAAA
1955532 T
1 T
1955533 TGTACTCCTA
Statistics
Matches: 71, Mismatches: 9, Indels: 4
0.85 0.11 0.05
Matches are distributed among these distances:
80 16 0.23
81 20 0.28
82 35 0.49
ACGTcount: A:0.37, C:0.04, G:0.04, T:0.56
Consensus pattern (80 bp):
TAATTTTTTATATTATATTTGTATCATATATTAATTATACATATTTATATAATTTATTATAATGA
TTTAATTTAAAAAAA
Found at i:1956785 original size:21 final size:23
Alignment explanation
Indices: 1956755--1956806 Score: 63
Period size: 21 Copynumber: 2.3 Consensus size: 23
1956745 ATTACATAGT
*
1956755 ATATAATATATAATA-TT-AATG
1 ATATATTATATAATATTTGAATG
* *
1956776 ATATATTATATTATATTTGTATG
1 ATATATTATATAATATTTGAATG
1956799 ATATATTA
1 ATATATTA
1956807 AATATAATTA
Statistics
Matches: 26, Mismatches: 3, Indels: 2
0.84 0.10 0.06
Matches are distributed among these distances:
21 13 0.50
22 2 0.08
23 11 0.42
ACGTcount: A:0.44, C:0.00, G:0.06, T:0.50
Consensus pattern (23 bp):
ATATATTATATAATATTTGAATG
Found at i:1956786 original size:23 final size:25
Alignment explanation
Indices: 1956754--1956814 Score: 67
Period size: 23 Copynumber: 2.6 Consensus size: 25
1956744 TATTACATAG
*
1956754 TATATAATATATAATA-TT-AATGA
1 TATATTATATATAATATTTGAATGA
*
1956777 TATATTATAT-T-ATATTTGTATGA
1 TATATTATATATAATATTTGAATGA
*
1956800 TATATTAAATATAAT
1 TATATTATATATAAT
1956815 TAAAAATAAA
Statistics
Matches: 31, Mismatches: 3, Indels: 6
0.77 0.08 0.15
Matches are distributed among these distances:
21 3 0.10
22 3 0.10
23 22 0.71
24 1 0.03
25 2 0.06
ACGTcount: A:0.46, C:0.00, G:0.05, T:0.49
Consensus pattern (25 bp):
TATATTATATATAATATTTGAATGA
Found at i:1958116 original size:2 final size:2
Alignment explanation
Indices: 1958109--1958148 Score: 80
Period size: 2 Copynumber: 20.0 Consensus size: 2
1958099 TCTCGTAGCT
1958109 TA TA TA 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
1958149 GCTACTTATT
Statistics
Matches: 38, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 38 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:1960191 original size:2 final size:2
Alignment explanation
Indices: 1960184--1960214 Score: 62
Period size: 2 Copynumber: 15.5 Consensus size: 2
1960174 CTTATGATTT
1960184 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 T
1960215 CCATATTGTT
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 29 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:1960637 original size:2 final size:2
Alignment explanation
Indices: 1960630--1960666 Score: 74
Period size: 2 Copynumber: 18.5 Consensus size: 2
1960620 AATGTCTGCC
1960630 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
1960667 TCAAAAGTTT
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:1961709 original size:2 final size:2
Alignment explanation
Indices: 1961702--1961733 Score: 64
Period size: 2 Copynumber: 16.0 Consensus size: 2
1961692 TTTGAATCTT
1961702 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
1961734 AAGGTAATTC
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 30 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:1961925 original size:22 final size:22
Alignment explanation
Indices: 1961902--1961944 Score: 70
Period size: 22 Copynumber: 2.0 Consensus size: 22
1961892 TGACGGAGAT
*
1961902 TTTGATT-TTTAATTTAATTAA
1 TTTGATTGGTTAATTTAATTAA
1961923 TTTGATTGGTTAATTTAATTAA
1 TTTGATTGGTTAATTTAATTAA
1961945 GAGAAAAATT
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
21 7 0.35
22 13 0.65
ACGTcount: A:0.33, C:0.00, G:0.09, T:0.58
Consensus pattern (22 bp):
TTTGATTGGTTAATTTAATTAA
Found at i:1961989 original size:20 final size:20
Alignment explanation
Indices: 1961952--1961990 Score: 51
Period size: 20 Copynumber: 1.9 Consensus size: 20
1961942 TAAGAGAAAA
* *
1961952 ATTTTAATATTAATTATATG
1 ATTTTAATATGAAATATATG
*
1961972 ATTTTGATATGAAATATAT
1 ATTTTAATATGAAATATAT
1961991 ATTATATATA
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:0.41, C:0.00, G:0.08, T:0.51
Consensus pattern (20 bp):
ATTTTAATATGAAATATATG
Found at i:1963763 original size:12 final size:12
Alignment explanation
Indices: 1963746--1963772 Score: 54
Period size: 12 Copynumber: 2.2 Consensus size: 12
1963736 TATCTAAGAG
1963746 AGAAAGAAAAAA
1 AGAAAGAAAAAA
1963758 AGAAAGAAAAAA
1 AGAAAGAAAAAA
1963770 AGA
1 AGA
1963773 GGTTTGTATT
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 15 1.00
ACGTcount: A:0.81, C:0.00, G:0.19, T:0.00
Consensus pattern (12 bp):
AGAAAGAAAAAA
Found at i:1964899 original size:17 final size:18
Alignment explanation
Indices: 1964871--1964907 Score: 58
Period size: 17 Copynumber: 2.1 Consensus size: 18
1964861 AATTTTAAAA
1964871 AATTTAAATTTAAATTAT
1 AATTTAAATTTAAATTAT
*
1964889 AATTT-AATTTAATTTAT
1 AATTTAAATTTAAATTAT
1964906 AA
1 AA
1964908 ATATATGTAA
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
17 13 0.72
18 5 0.28
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (18 bp):
AATTTAAATTTAAATTAT
Found at i:1971933 original size:2 final size:2
Alignment explanation
Indices: 1971926--1971963 Score: 76
Period size: 2 Copynumber: 19.0 Consensus size: 2
1971916 TGCCATGAAC
1971926 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1971964 GGACATAATC
Statistics
Matches: 36, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 36 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:1977719 original size:2 final size:2
Alignment explanation
Indices: 1977712--1977740 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
1977702 GAAACAAACA
1977712 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 A
1977741 ATTTGTTTGT
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 27 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:1978025 original size:24 final size:24
Alignment explanation
Indices: 1977998--1978045 Score: 78
Period size: 24 Copynumber: 2.0 Consensus size: 24
1977988 GACACAAAAA
*
1977998 ATCCCAAGAGGAAATTGAAACAGG
1 ATCCCAAGAGGAAACTGAAACAGG
*
1978022 ATCCCAAGAGGAAGCTGAAACAGG
1 ATCCCAAGAGGAAACTGAAACAGG
1978046 GTTGTGTTTT
Statistics
Matches: 22, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
24 22 1.00
ACGTcount: A:0.44, C:0.19, G:0.27, T:0.10
Consensus pattern (24 bp):
ATCCCAAGAGGAAACTGAAACAGG
Found at i:1978761 original size:23 final size:22
Alignment explanation
Indices: 1978718--1978761 Score: 52
Period size: 23 Copynumber: 2.0 Consensus size: 22
1978708 TATATTATAT
*
1978718 TATTAATTTATTAAATTATTTA
1 TATTAATTTATTAAATAATTTA
* *
1978740 TATTCAATTTGTTACATAATTT
1 TATT-AATTTATTAAATAATTT
1978762 TAATAAAAAA
Statistics
Matches: 18, Mismatches: 3, Indels: 1
0.82 0.14 0.05
Matches are distributed among these distances:
22 4 0.22
23 14 0.78
ACGTcount: A:0.36, C:0.05, G:0.02, T:0.57
Consensus pattern (22 bp):
TATTAATTTATTAAATAATTTA
Found at i:1981835 original size:2 final size:2
Alignment explanation
Indices: 1981816--1981851 Score: 54
Period size: 2 Copynumber: 18.0 Consensus size: 2
1981806 CCAAGGACCC
* *
1981816 AT AT AT AC AT AT AC AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1981852 TTAGATCAAA
Statistics
Matches: 30, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
2 30 1.00
ACGTcount: A:0.50, C:0.06, G:0.00, T:0.44
Consensus pattern (2 bp):
AT
Found at i:1982075 original size:19 final size:19
Alignment explanation
Indices: 1982034--1982081 Score: 51
Period size: 19 Copynumber: 2.5 Consensus size: 19
1982024 AAATGAAAAT
* ***
1982034 AAATAAAATTAAAAATTCT
1 AAATAAAAATAAAAATAAA
1982053 AAATAAAAATAAAAATAAA
1 AAATAAAAATAAAAATAAA
1982072 AAATAGAAAA
1 AAATA-AAAA
1982082 ACAAATACAA
Statistics
Matches: 24, Mismatches: 4, Indels: 1
0.83 0.14 0.03
Matches are distributed among these distances:
19 20 0.83
20 4 0.17
ACGTcount: A:0.75, C:0.02, G:0.02, T:0.21
Consensus pattern (19 bp):
AAATAAAAATAAAAATAAA
Found at i:1983859 original size:21 final size:22
Alignment explanation
Indices: 1983820--1983871 Score: 72
Period size: 21 Copynumber: 2.5 Consensus size: 22
1983810 AAAATCATTT
* *
1983820 ATTAAA-TTATTATATAATTAA
1 ATTAAATTTAATATAAAATTAA
1983841 A-TAAATTTAATATAAAATTAA
1 ATTAAATTTAATATAAAATTAA
1983862 ATTAAATTTA
1 ATTAAATTTA
1983872 TAAATATTAA
Statistics
Matches: 27, Mismatches: 2, Indels: 3
0.84 0.06 0.09
Matches are distributed among these distances:
20 4 0.15
21 15 0.56
22 8 0.30
ACGTcount: A:0.56, C:0.00, G:0.00, T:0.44
Consensus pattern (22 bp):
ATTAAATTTAATATAAAATTAA
Found at i:1984619 original size:24 final size:23
Alignment explanation
Indices: 1984564--1984619 Score: 58
Period size: 24 Copynumber: 2.3 Consensus size: 23
1984554 TTTCCCCTCC
* *
1984564 TTTTGTGTTTGCATCAAGAGTAAA
1 TTTT-TGTTTGAATAAAGAGTAAA
*
1984588 TATATTGTTTGAATAAAGTAGTAAA
1 T-TTTTGTTTGAATAAAG-AGTAAA
1984613 TTTTTGT
1 TTTTTGT
1984620 GAAGTAACTC
Statistics
Matches: 26, Mismatches: 4, Indels: 4
0.76 0.12 0.12
Matches are distributed among these distances:
24 17 0.65
25 9 0.35
ACGTcount: A:0.32, C:0.04, G:0.18, T:0.46
Consensus pattern (23 bp):
TTTTTGTTTGAATAAAGAGTAAA
Found at i:1984689 original size:12 final size:12
Alignment explanation
Indices: 1984672--1984727 Score: 51
Period size: 12 Copynumber: 4.4 Consensus size: 12
1984662 TAGTGAAATA
1984672 ATTTTGTTATTT
1 ATTTTGTTATTT
1984684 ATTTTGGATTATTTT
1 ATTTT-G-TTA-TTT
* *
1984699 ATTATCTTATTT
1 ATTTTGTTATTT
1984711 ATTTAT-TTATTT
1 ATTT-TGTTATTT
1984723 ATTTT
1 ATTTT
1984728 ATAAAGTAAT
Statistics
Matches: 37, Mismatches: 3, Indels: 9
0.76 0.06 0.18
Matches are distributed among these distances:
11 1 0.03
12 21 0.57
13 5 0.14
14 3 0.08
15 7 0.19
ACGTcount: A:0.21, C:0.02, G:0.05, T:0.71
Consensus pattern (12 bp):
ATTTTGTTATTT
Found at i:1985738 original size:19 final size:20
Alignment explanation
Indices: 1985716--1985754 Score: 53
Period size: 19 Copynumber: 2.0 Consensus size: 20
1985706 ATATAATTAT
*
1985716 AATACTATAAAAT-AATAAA
1 AATAATATAAAATAAATAAA
*
1985735 AATAATATAATATAAATAAA
1 AATAATATAAAATAAATAAA
1985755 TATTTTAAAA
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
19 11 0.65
20 6 0.35
ACGTcount: A:0.69, C:0.03, G:0.00, T:0.28
Consensus pattern (20 bp):
AATAATATAAAATAAATAAA
Found at i:1985788 original size:31 final size:27
Alignment explanation
Indices: 1985750--1985880 Score: 94
Period size: 26 Copynumber: 4.7 Consensus size: 27
1985740 TATAATATAA
1985750 ATAAATATTTTAAAAATTTTGAATATAAATT
1 ATAAATATTTTAAAAA-TTT--ATATAAA-T
*
1985781 ATAAATATATT-AAAATTTATATAAAT
1 ATAAATATTTTAAAAATTTATATAAAT
*
1985807 ATAAATTTTTTAAAAAATATTATAATATAAT
1 ATAAATATTTT-AAAAAT-TTAT-ATA-AAT
* *
1985838 A-AAATA-TATAAAAA-TAATATAAAT
1 ATAAATATTTTAAAAATTTATATAAAT
*
1985862 ATATAA-ATTTT-CAAATTTA
1 ATA-AATATTTTAAAAATTTA
1985881 ATACAACATT
Statistics
Matches: 82, Mismatches: 9, Indels: 23
0.72 0.08 0.20
Matches are distributed among these distances:
24 4 0.05
25 8 0.10
26 19 0.23
27 7 0.09
28 10 0.12
29 9 0.11
30 11 0.13
31 14 0.17
ACGTcount: A:0.56, C:0.01, G:0.01, T:0.42
Consensus pattern (27 bp):
ATAAATATTTTAAAAATTTATATAAAT
Found at i:1985808 original size:18 final size:18
Alignment explanation
Indices: 1985787--1985868 Score: 51
Period size: 19 Copynumber: 4.4 Consensus size: 18
1985777 AATTATAAAT
1985787 ATATTAAAATTTATATAA
1 ATATTAAAATTTATATAA
* * *
1985805 ATA-TAAATTTTTTAAAAA
1 ATATTAAAATTTAT-ATAA
* *
1985823 ATATTATAATATA-ATAAA
1 ATATTAAAATTTATAT-AA
* *
1985841 ATATATAAAAATAATATAA
1 ATAT-TAAAATTTATATAA
1985860 ATATATAAA
1 ATAT-TAAA
1985869 TTTTCAAATT
Statistics
Matches: 47, Mismatches: 12, Indels: 9
0.69 0.18 0.13
Matches are distributed among these distances:
17 9 0.19
18 15 0.32
19 21 0.45
20 2 0.04
ACGTcount: A:0.61, C:0.00, G:0.00, T:0.39
Consensus pattern (18 bp):
ATATTAAAATTTATATAA
Found at i:1985808 original size:33 final size:31
Alignment explanation
Indices: 1985750--1985813 Score: 83
Period size: 31 Copynumber: 2.0 Consensus size: 31
1985740 TATAATATAA
* *
1985750 ATAAATATTTTAAAAATTTTGAATATAAATT
1 ATAAATATATTAAAAATTTTAAATATAAATT
*
1985781 ATAAATATATTAAAATTTATATAAATATAAATT
1 ATAAATATATTAAAAATT-T-TAAATATAAATT
1985814 TTTTAAAAAA
Statistics
Matches: 28, Mismatches: 3, Indels: 2
0.85 0.09 0.06
Matches are distributed among these distances:
31 16 0.57
32 1 0.04
33 11 0.39
ACGTcount: A:0.55, C:0.00, G:0.02, T:0.44
Consensus pattern (31 bp):
ATAAATATATTAAAAATTTTAAATATAAATT
Found at i:1985845 original size:10 final size:9
Alignment explanation
Indices: 1985772--1985868 Score: 51
Period size: 10 Copynumber: 10.8 Consensus size: 9
1985762 AAAATTTTGA
1985772 ATAT-AAAT
1 ATATAAAAT
1985780 -TAT-AAAT
1 ATATAAAAT
1985787 ATATTAAAAT
1 ATA-TAAAAT
* *
1985797 TTATATAA-
1 ATATAAAAT
*
1985805 ATATAAATT
1 ATATAAAAT
* * *
1985814 TTTTAAAAA
1 ATATAAAAT
*
1985823 ATATTATAAT
1 ATA-TAAAAT
1985833 ATAATAAAAT
1 AT-ATAAAAT
1985843 ATATAAAA-
1 ATATAAAAT
1985851 ATAATATAAAT
1 AT-ATA-AAAT
1985862 ATATAAA
1 ATATAAA
1985869 TTTTCAAATT
Statistics
Matches: 66, Mismatches: 14, Indels: 17
0.68 0.14 0.18
Matches are distributed among these distances:
7 7 0.11
8 9 0.14
9 22 0.33
10 25 0.38
11 3 0.05
ACGTcount: A:0.61, C:0.00, G:0.00, T:0.39
Consensus pattern (9 bp):
ATATAAAAT
Found at i:1985846 original size:20 final size:19
Alignment explanation
Indices: 1985817--1985865 Score: 55
Period size: 19 Copynumber: 2.5 Consensus size: 19
1985807 ATAAATTTTT
* *
1985817 TAAAAAATATTATAATATAA
1 TAAAATATATTA-AAAATAA
1985837 TAAAATATA-TAAAAATAA
1 TAAAATATATTAAAAATAA
1985855 TATAAATATAT
1 TA-AAATATAT
1985866 AAATTTTCAA
Statistics
Matches: 25, Mismatches: 2, Indels: 4
0.81 0.06 0.13
Matches are distributed among these distances:
18 8 0.32
19 9 0.36
20 8 0.32
ACGTcount: A:0.65, C:0.00, G:0.00, T:0.35
Consensus pattern (19 bp):
TAAAATATATTAAAAATAA
Found at i:1985863 original size:19 final size:18
Alignment explanation
Indices: 1985820--1985868 Score: 64
Period size: 18 Copynumber: 2.7 Consensus size: 18
1985810 AATTTTTTAA
*
1985820 AAAATAT-TATAATATAAT
1 AAAATATATA-AAAATAAT
1985838 AAAATATATAAAAATAAT
1 AAAATATATAAAAATAAT
1985856 ATAAATATATAAA
1 A-AAATATATAAA
1985869 TTTTCAAATT
Statistics
Matches: 28, Mismatches: 1, Indels: 3
0.88 0.03 0.09
Matches are distributed among these distances:
18 15 0.54
19 13 0.46
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (18 bp):
AAAATATATAAAAATAAT
Found at i:1985866 original size:57 final size:56
Alignment explanation
Indices: 1985711--1985872 Score: 174
Period size: 57 Copynumber: 2.9 Consensus size: 56
1985701 TGATTATATA
* *
1985711 ATTATAATACT-ATAAAATA-ATAAAAATAATATAATATAAATAAATATTTTAAAAAT
1 ATTATAATA-TAATAAAATATATAAAAATAATATAA-ATATATAAATTTTTTAAAAAT
* *
1985767 -TT-TGAATATAAATTATAAATATATTAAAAT-TTATATAA-ATATAAATTTTTTAAAAAAT
1 ATTAT-AATAT-AA-TA-AAATATATAAAAATAATATA-AATATATAAATTTTTT-AAAAAT
1985825 ATTATAATATAATAAAATATATAAAAATAATATAAATATATAAATTTT
1 ATTATAATATAATAAAATATATAAAAATAATATAAATATATAAATTTT
1985873 CAAATTTAAT
Statistics
Matches: 88, Mismatches: 6, Indels: 23
0.75 0.05 0.20
Matches are distributed among these distances:
54 2 0.02
55 6 0.07
56 16 0.18
57 30 0.34
58 18 0.20
59 15 0.17
60 1 0.01
ACGTcount: A:0.59, C:0.01, G:0.01, T:0.40
Consensus pattern (56 bp):
ATTATAATATAATAAAATATATAAAAATAATATAAATATATAAATTTTTTAAAAAT
Found at i:1986091 original size:46 final size:50
Alignment explanation
Indices: 1986041--1986138 Score: 114
Period size: 46 Copynumber: 2.0 Consensus size: 50
1986031 AGTGGTACGA
* * *
1986041 TATTTTTAAATTTTAA-AT-TTTTTTATAT-ATTTA-AAAATTAAATATT
1 TATTTTTAAATTTTAATATATATTTAATATAATATATAAAATTAAATATT
** *
1986087 TATTTTTGTATTTTAATATATATTTAATATAATATATAAATTTAAATATT
1 TATTTTTAAATTTTAATATATATTTAATATAATATATAAAATTAAATATT
1986137 TA
1 TA
1986139 AAAATATGAA
Statistics
Matches: 42, Mismatches: 6, Indels: 4
0.81 0.12 0.08
Matches are distributed among these distances:
46 14 0.33
47 2 0.05
48 8 0.19
49 4 0.10
50 14 0.33
ACGTcount: A:0.42, C:0.00, G:0.01, T:0.57
Consensus pattern (50 bp):
TATTTTTAAATTTTAATATATATTTAATATAATATATAAAATTAAATATT
Found at i:1986151 original size:26 final size:25
Alignment explanation
Indices: 1986106--1986164 Score: 61
Period size: 26 Copynumber: 2.3 Consensus size: 25
1986096 ATTTTAATAT
1986106 ATATTTAATATAATATATAA-ATTTAA
1 ATATTTAATATAATATATAATA-TT-A
1986132 ATATTTAA-A-AATATGAATAATATTA
1 ATATTTAATATAATAT--ATAATATTA
1986157 ATATTTAA
1 ATATTTAA
1986165 CAATTATCTA
Statistics
Matches: 30, Mismatches: 0, Indels: 7
0.81 0.00 0.19
Matches are distributed among these distances:
24 5 0.17
25 10 0.33
26 14 0.47
27 1 0.03
ACGTcount: A:0.54, C:0.00, G:0.02, T:0.44
Consensus pattern (25 bp):
ATATTTAATATAATATATAATATTA
Found at i:1987185 original size:2 final size:2
Alignment explanation
Indices: 1987178--1987206 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
1987168 AATGATTATT
1987178 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 T
1987207 TTAAACTTAT
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 27 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:1990445 original size:2 final size:2
Alignment explanation
Indices: 1990440--1990481 Score: 84
Period size: 2 Copynumber: 21.0 Consensus size: 2
1990430 TTTAAAAAAT
1990440 TA TA TA TA 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 TA
1990482 CATACACACA
Statistics
Matches: 40, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 40 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:1990921 original size:23 final size:22
Alignment explanation
Indices: 1990886--1990937 Score: 65
Period size: 22 Copynumber: 2.5 Consensus size: 22
1990876 TTAATAACAA
*
1990886 ATTAAATTT-TAT-TTTTTA-T
1 ATTAATTTTATATATTTTTATT
1990905 ATTAATATTTATATATTTTTATT
1 ATTAAT-TTTATATATTTTTATT
1990928 ATTAATTTTA
1 ATTAATTTTA
1990938 AATAAAAATA
Statistics
Matches: 28, Mismatches: 1, Indels: 5
0.82 0.03 0.15
Matches are distributed among these distances:
19 5 0.18
20 3 0.11
21 3 0.11
22 10 0.36
23 7 0.25
ACGTcount: A:0.35, C:0.00, G:0.00, T:0.65
Consensus pattern (22 bp):
ATTAATTTTATATATTTTTATT
Found at i:1992617 original size:23 final size:22
Alignment explanation
Indices: 1992594--1992674 Score: 72
Period size: 23 Copynumber: 3.5 Consensus size: 22
1992584 TTAATATTTA
*
1992594 TATTATTATTTTATGTCATATT
1 TATTATTATTTTATATCATATT
1992616 ATATTTTAATTATTTTATATCATATT
1 -TA--TT-ATTATTTTATATCATATT
* * *
1992642 TATTTTTATAATTATTTCATATT
1 TATTATTAT-TTTATATCATATT
*
1992665 TTTTATTATT
1 TATTATTATT
1992675 AAGTTTACTT
Statistics
Matches: 47, Mismatches: 7, Indels: 9
0.75 0.11 0.14
Matches are distributed among these distances:
22 4 0.09
23 22 0.47
25 4 0.09
26 17 0.36
ACGTcount: A:0.30, C:0.04, G:0.01, T:0.65
Consensus pattern (22 bp):
TATTATTATTTTATATCATATT
Found at i:1992627 original size:26 final size:28
Alignment explanation
Indices: 1992582--1992663 Score: 96
Period size: 26 Copynumber: 2.9 Consensus size: 28
1992572 GATATTTATG
* *
1992582 TATTAATATTTATATTATTATTTTATGTCA
1 TATTTATATTTATA--ATTATTTTATATCA
1992612 TA-TTATATTT-TAATTATTTTATATCA
1 TATTTATATTTATAATTATTTTATATCA
* *
1992638 TATTTATTTTTATAATTATTTCATAT
1 TATTTATATTTATAATTATTTTATAT
1992664 TTTTTATTAT
Statistics
Matches: 46, Mismatches: 4, Indels: 6
0.82 0.07 0.11
Matches are distributed among these distances:
26 15 0.33
27 7 0.15
28 15 0.33
29 7 0.15
30 2 0.04
ACGTcount: A:0.33, C:0.04, G:0.01, T:0.62
Consensus pattern (28 bp):
TATTTATATTTATAATTATTTTATATCA
Found at i:1995731 original size:2 final size:2
Alignment explanation
Indices: 1995724--1995774 Score: 102
Period size: 2 Copynumber: 25.5 Consensus size: 2
1995714 CAATTACTAC
1995724 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1995766 AT AT AT AT A
1 AT AT AT AT A
1995775 GGGGGGAAAT
Statistics
Matches: 49, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 49 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:1996257 original size:13 final size:13
Alignment explanation
Indices: 1996241--1996266 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
1996231 GGGAAAGTAT
1996241 GAGAATAAAGATA
1 GAGAATAAAGATA
1996254 GAGAATAAAGATA
1 GAGAATAAAGATA
1996267 ATAACCGTCT
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:0.62, C:0.00, G:0.23, T:0.15
Consensus pattern (13 bp):
GAGAATAAAGATA
Found at i:1996513 original size:22 final size:21
Alignment explanation
Indices: 1996488--1996541 Score: 56
Period size: 21 Copynumber: 2.5 Consensus size: 21
1996478 TATGCATTAC
*
1996488 ATATTTAATAAAAATATATATT
1 ATATTTAATAAAAAT-TATAAT
* *
1996510 ATATTT-ATATGAAATTTTAAT
1 ATATTTAATA-AAAATTATAAT
1996531 ATATTTAATAA
1 ATATTTAATAA
1996542 TTTATATTTA
Statistics
Matches: 26, Mismatches: 4, Indels: 5
0.74 0.11 0.14
Matches are distributed among these distances:
21 13 0.50
22 13 0.50
ACGTcount: A:0.50, C:0.00, G:0.02, T:0.48
Consensus pattern (21 bp):
ATATTTAATAAAAATTATAAT
Found at i:2001458 original size:24 final size:21
Alignment explanation
Indices: 2001390--2001453 Score: 92
Period size: 21 Copynumber: 3.0 Consensus size: 21
2001380 AAAGTCGCAT
* * *
2001390 TTTTTTAATCTAAAAAATACA
1 TTTTTTCATCCAAAAAATGCA
2001411 TTTTTTCATCCAAAAAATGCA
1 TTTTTTCATCCAAAAAATGCA
*
2001432 TTTTTTCATCCAACAAATGCA
1 TTTTTTCATCCAAAAAATGCA
2001453 T
1 T
2001454 CATTTCATTC
Statistics
Matches: 39, Mismatches: 4, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
21 39 1.00
ACGTcount: A:0.39, C:0.17, G:0.03, T:0.41
Consensus pattern (21 bp):
TTTTTTCATCCAAAAAATGCA
Done.