Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Chr01 113035596
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: 113035596
ACGTcount: A:0.32, C:0.17, G:0.18, T:0.33
Warning! 271 characters in sequence are not A, C, G, or T
File 6 of 378
Found at i:1836190 original size:18 final size:19
Alignment explanation
Indices: 1836164--1836203 Score: 55
Period size: 18 Copynumber: 2.2 Consensus size: 19
1836154 ATTTTTCATG
*
1836164 TCAACAAAAATTTAAAA-T
1 TCAAAAAAAATTTAAAAGT
*
1836182 TCAAAAAAATTTTAAAAGT
1 TCAAAAAAAATTTAAAAGT
1836201 TCA
1 TCA
1836204 CAAACTTTCA
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
18 15 0.79
19 4 0.21
ACGTcount: A:0.57, C:0.10, G:0.03, T:0.30
Consensus pattern (19 bp):
TCAAAAAAAATTTAAAAGT
Found at i:1839449 original size:10 final size:11
Alignment explanation
Indices: 1839427--1839460 Score: 52
Period size: 11 Copynumber: 3.2 Consensus size: 11
1839417 TCTATTTCTG
1839427 TTTTATATTTA
1 TTTTATATTTA
1839438 TTTTAT-TTTA
1 TTTTATATTTA
*
1839448 TTTTATAATTA
1 TTTTATATTTA
1839459 TT
1 TT
1839461 CTGACATATA
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
10 10 0.48
11 11 0.52
ACGTcount: A:0.26, C:0.00, G:0.00, T:0.74
Consensus pattern (11 bp):
TTTTATATTTA
Found at i:1839887 original size:16 final size:16
Alignment explanation
Indices: 1839866--1839915 Score: 54
Period size: 16 Copynumber: 3.3 Consensus size: 16
1839856 TAATTTCCTT
1839866 TAAAAATTATA-AAAA
1 TAAAAATTATATAAAA
*
1839881 GTAAAAATTTTATAAAA
1 -TAAAAATTATATAAAA
1839898 TAAAAA-TAT-TAAAA
1 TAAAAATTATATAAAA
1839912 -AAAA
1 TAAAA
1839916 TAAATTAAAT
Statistics
Matches: 31, Mismatches: 2, Indels: 5
0.82 0.05 0.13
Matches are distributed among these distances:
13 4 0.13
14 5 0.16
15 2 0.06
16 16 0.52
17 4 0.13
ACGTcount: A:0.70, C:0.00, G:0.02, T:0.28
Consensus pattern (16 bp):
TAAAAATTATATAAAA
Found at i:1839895 original size:18 final size:17
Alignment explanation
Indices: 1839867--1839919 Score: 56
Period size: 18 Copynumber: 3.1 Consensus size: 17
1839857 AATTTCCTTT
1839867 AAAA-ATTATAAAAAGTA
1 AAAATATTATAAAAA-TA
*
1839884 AAAATTTTAT-AAAATA
1 AAAATATTATAAAAATA
*
1839900 AAAATATTAAAAAAAATA
1 AAAATATT-ATAAAAATA
1839918 AA
1 AA
1839920 TTAAATTAGA
Statistics
Matches: 30, Mismatches: 3, Indels: 5
0.79 0.08 0.13
Matches are distributed among these distances:
16 9 0.30
17 9 0.30
18 12 0.40
ACGTcount: A:0.72, C:0.00, G:0.02, T:0.26
Consensus pattern (17 bp):
AAAATATTATAAAAATA
Found at i:1840991 original size:6 final size:6
Alignment explanation
Indices: 1840980--1841005 Score: 52
Period size: 6 Copynumber: 4.3 Consensus size: 6
1840970 AAATGACCTA
1840980 AAAAAT AAAAAT AAAAAT AAAAAT AA
1 AAAAAT AAAAAT AAAAAT AAAAAT AA
1841006 TAAAATAAAT
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 20 1.00
ACGTcount: A:0.85, C:0.00, G:0.00, T:0.15
Consensus pattern (6 bp):
AAAAAT
Found at i:1841265 original size:24 final size:23
Alignment explanation
Indices: 1841219--1841265 Score: 58
Period size: 24 Copynumber: 2.0 Consensus size: 23
1841209 TTTTTTTTTA
**
1841219 TTTTATTAAATAAATTATTAAAT
1 TTTTATTAAATAAATTAAAAAAT
*
1841242 TTTTATTAAAATATATTAAAAAAT
1 TTTTATT-AAATAAATTAAAAAAT
1841266 AAAAAAATTT
Statistics
Matches: 20, Mismatches: 3, Indels: 1
0.83 0.12 0.04
Matches are distributed among these distances:
23 7 0.35
24 13 0.65
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (23 bp):
TTTTATTAAATAAATTAAAAAAT
Found at i:1842965 original size:21 final size:22
Alignment explanation
Indices: 1842912--1842958 Score: 85
Period size: 22 Copynumber: 2.1 Consensus size: 22
1842902 TCGAGTTTAA
*
1842912 GCTCATGCTTGTCAATATTTGG
1 GCTCAAGCTTGTCAATATTTGG
1842934 GCTCAAGCTTGTCAATATTTGG
1 GCTCAAGCTTGTCAATATTTGG
1842956 GCT
1 GCT
1842959 TAGCTTGGCT
Statistics
Matches: 24, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
22 24 1.00
ACGTcount: A:0.19, C:0.19, G:0.23, T:0.38
Consensus pattern (22 bp):
GCTCAAGCTTGTCAATATTTGG
Found at i:1843061 original size:81 final size:81
Alignment explanation
Indices: 1842926--1843087 Score: 315
Period size: 81 Copynumber: 2.0 Consensus size: 81
1842916 ATGCTTGTCA
*
1842926 ATATTTGGGCTCAAGCTTGTCAATATTTGGGCTTAGCTTGGCTCAATTACACCCTTAAGAAGGAG
1 ATATTTGGGCTCAAGCTTGTCAATATTTAGGCTTAGCTTGGCTCAATTACACCCTTAAGAAGGAG
1842991 AAATGGGTTACAAACT
66 AAATGGGTTACAAACT
1843007 ATATTTGGGCTCAAGCTTGTCAATATTTAGGCTTAGCTTGGCTCAATTACACCCTTAAGAAGGAG
1 ATATTTGGGCTCAAGCTTGTCAATATTTAGGCTTAGCTTGGCTCAATTACACCCTTAAGAAGGAG
1843072 AAATGGGTTACAAACT
66 AAATGGGTTACAAACT
1843088 CAAGGTTTAA
Statistics
Matches: 80, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
81 80 1.00
ACGTcount: A:0.30, C:0.17, G:0.22, T:0.31
Consensus pattern (81 bp):
ATATTTGGGCTCAAGCTTGTCAATATTTAGGCTTAGCTTGGCTCAATTACACCCTTAAGAAGGAG
AAATGGGTTACAAACT
Found at i:1865741 original size:30 final size:31
Alignment explanation
Indices: 1865706--1865766 Score: 97
Period size: 31 Copynumber: 2.0 Consensus size: 31
1865696 CAACCTTATT
1865706 ACTTAAATAAAAA-ATTTAAATAATTCAATA
1 ACTTAAATAAAAACATTTAAATAATTCAATA
* *
1865736 ACTTAAATAAAAACTTTTAAATAATTTAATA
1 ACTTAAATAAAAACATTTAAATAATTCAATA
1865767 TTATACGCTT
Statistics
Matches: 28, Mismatches: 2, Indels: 1
0.90 0.06 0.03
Matches are distributed among these distances:
30 13 0.46
31 15 0.54
ACGTcount: A:0.57, C:0.07, G:0.00, T:0.36
Consensus pattern (31 bp):
ACTTAAATAAAAACATTTAAATAATTCAATA
Found at i:1873016 original size:31 final size:30
Alignment explanation
Indices: 1872976--1873060 Score: 93
Period size: 31 Copynumber: 2.8 Consensus size: 30
1872966 AAATGTGTAG
*
1872976 AATTAAATCAAAATCAAAGTTTCATGTATAT
1 AATTGAATCAAAATCAAA-TTTCATGTATAT
*
1873007 -ATATGAATCATAATTCAAATTTCATGTATAT
1 AAT-TGAATCA-AAATCAAATTTCATGTATAT
* *
1873038 AATTGTATC-AAATCAAAATTCAT
1 AATTGAATCAAAATCAAATTTCAT
1873061 CTATCAAATT
Statistics
Matches: 46, Mismatches: 5, Indels: 8
0.78 0.08 0.14
Matches are distributed among these distances:
29 12 0.26
30 2 0.04
31 23 0.50
32 9 0.20
ACGTcount: A:0.46, C:0.11, G:0.06, T:0.38
Consensus pattern (30 bp):
AATTGAATCAAAATCAAATTTCATGTATAT
Found at i:1874145 original size:47 final size:47
Alignment explanation
Indices: 1874083--1874208 Score: 137
Period size: 47 Copynumber: 2.7 Consensus size: 47
1874073 CTTTACATAA
* * *
1874083 TGATGCCATAGCCCAGCTATGGTATTACAC-GTAATCACATATCTCAC
1 TGATGCCATATCCCAGATATGGTATTACACAGTAAT-ACATATCGCAC
* * * * *
1874130 TGATGTCATATCCCAGATATGGTCTTATACAGTAGTATATATCGCAC
1 TGATGCCATATCCCAGATATGGTATTACACAGTAATACATATCGCAC
* * *
1874177 CGATGCCATATCCCAGATATGGTCTTATACAG
1 TGATGCCATATCCCAGATATGGTATTACACAG
1874209 AAATCACTTG
Statistics
Matches: 68, Mismatches: 10, Indels: 2
0.85 0.12 0.03
Matches are distributed among these distances:
47 64 0.94
48 4 0.06
ACGTcount: A:0.29, C:0.24, G:0.17, T:0.30
Consensus pattern (47 bp):
TGATGCCATATCCCAGATATGGTATTACACAGTAATACATATCGCAC
Found at i:1874232 original size:14 final size:14
Alignment explanation
Indices: 1874213--1874239 Score: 54
Period size: 14 Copynumber: 1.9 Consensus size: 14
1874203 ATACAGAAAT
1874213 CACTTGTCACTTGC
1 CACTTGTCACTTGC
1874227 CACTTGTCACTTG
1 CACTTGTCACTTG
1874240 TAGCCAAAGC
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:0.15, C:0.33, G:0.15, T:0.37
Consensus pattern (14 bp):
CACTTGTCACTTGC
Found at i:1874283 original size:31 final size:31
Alignment explanation
Indices: 1874246--1874478 Score: 349
Period size: 31 Copynumber: 7.5 Consensus size: 31
1874236 CTTGTAGCCA
*
1874246 AAGCTACCACTATTCACTGATCAGGTAGCTG
1 AAGCTACCACTTTTCACTGATCAGGTAGCTG
** *
1874277 GTGCTACCATTTTTCACTGATCAGGTAGCTG
1 AAGCTACCACTTTTCACTGATCAGGTAGCTG
** * *
1874308 GTGCTACCATTTTTCACTGATCAGGTAGCCG
1 AAGCTACCACTTTTCACTGATCAGGTAGCTG
* * *
1874339 GAGCTACCACTTTTCACTGATCAAGTAGCCG
1 AAGCTACCACTTTTCACTGATCAGGTAGCTG
*
1874370 AAGCTACCACTTTTCACTGATCAGGTAGCAG
1 AAGCTACCACTTTTCACTGATCAGGTAGCTG
1874401 AAGCTACCACTTTTCACTGATCAGGTAGCTG
1 AAGCTACCACTTTTCACTGATCAGGTAGCTG
*
1874432 AAACTACCACTTTTCACTGATCAGGTAGCTG
1 AAGCTACCACTTTTCACTGATCAGGTAGCTG
1874463 AAGCTACCACTTTTCA
1 AAGCTACCACTTTTCA
1874479 GTTGTCATTT
Statistics
Matches: 188, Mismatches: 14, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
31 188 1.00
ACGTcount: A:0.26, C:0.26, G:0.19, T:0.29
Consensus pattern (31 bp):
AAGCTACCACTTTTCACTGATCAGGTAGCTG
Found at i:1874562 original size:50 final size:50
Alignment explanation
Indices: 1874456--1874632 Score: 248
Period size: 50 Copynumber: 3.5 Consensus size: 50
1874446 CACTGATCAG
* * * *
1874456 GTAGCTGAAGCTACCACTTTTCAGTTGTCATTTG-CCATTGATCAGATAAGT
1 GTAGCCGAAGCTATCACTTATCACTT-TCATTTGTCC-TTGATCAGATAAGT
* *
1874507 GTAGCCGAAGCTATCACTTATCACTTTCACTTGTCCTTAATCAGATAAGT
1 GTAGCCGAAGCTATCACTTATCACTTTCATTTGTCCTTGATCAGATAAGT
* * *
1874557 GTAGCCGAAGTTATTACTTATCACTTTCATTTGTCATTGATCAGATAAGT
1 GTAGCCGAAGCTATCACTTATCACTTTCATTTGTCCTTGATCAGATAAGT
1874607 GTAGCCGAAGCTATCACTTATCACTT
1 GTAGCCGAAGCTATCACTTATCACTT
1874633 GTTTCCATGG
Statistics
Matches: 112, Mismatches: 13, Indels: 3
0.88 0.10 0.02
Matches are distributed among these distances:
50 88 0.79
51 24 0.21
ACGTcount: A:0.27, C:0.21, G:0.16, T:0.36
Consensus pattern (50 bp):
GTAGCCGAAGCTATCACTTATCACTTTCATTTGTCCTTGATCAGATAAGT
Found at i:1879825 original size:15 final size:16
Alignment explanation
Indices: 1879798--1879833 Score: 56
Period size: 15 Copynumber: 2.3 Consensus size: 16
1879788 TAAAAATATA
1879798 AATTTATTATTTTAAT
1 AATTTATTATTTTAAT
*
1879814 AATTTA-TATTTTTAT
1 AATTTATTATTTTAAT
1879829 AATTT
1 AATTT
1879834 TTAAAGGATT
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
15 13 0.68
16 6 0.32
ACGTcount: A:0.36, C:0.00, G:0.00, T:0.64
Consensus pattern (16 bp):
AATTTATTATTTTAAT
Found at i:1880874 original size:18 final size:18
Alignment explanation
Indices: 1880851--1880889 Score: 78
Period size: 18 Copynumber: 2.2 Consensus size: 18
1880841 ACTTGCAACC
1880851 AAATGTTTTTAATTAAAT
1 AAATGTTTTTAATTAAAT
1880869 AAATGTTTTTAATTAAAT
1 AAATGTTTTTAATTAAAT
1880887 AAA
1 AAA
1880890 AAAAGGTTGA
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 21 1.00
ACGTcount: A:0.49, C:0.00, G:0.05, T:0.46
Consensus pattern (18 bp):
AAATGTTTTTAATTAAAT
Found at i:1882896 original size:84 final size:84
Alignment explanation
Indices: 1882732--1882932 Score: 221
Period size: 84 Copynumber: 2.4 Consensus size: 84
1882722 TGAAGAAGAA
* **
1882732 GAAGAAGAAAAAGGGTTGTTCGAAGTGAAAGAAGTGATAACATCGGAAGCCGAGTCCGGAGAGGA
1 GAAGAAGAAAAAGGGTTGTTCGAAGTGAAAGAAGTCATAACATCGGAAGCCGACCCCGGAGAGGA
*
1882797 AGAACAAACACGTGAAGTT
66 AGAACAAACACGTGAAATT
* * *
1882816 GAAGAAGAAGAAGGGTCGTTCGAAGTGAAAGACA-TCATAACATC-GAAGGTCGACCCCTTGGA-
1 GAAGAAGAAAAAGGGTTGTTCGAAGTGAAAGA-AGTCATAACATCGGAA-GCCGACCCC--GGAG
* * *
1882878 A-GAGGAACGAACATGTGAAATT
62 AGGAAGAACAAACACGTGAAATT
* * *
1882900 AAAGAAGAAAAAGGGTTGATCGAAGTGCAAGAA
1 GAAGAAGAAAAAGGGTTGTTCGAAGTGAAAGAA
1882933 ACGAAAACAT
Statistics
Matches: 98, Mismatches: 15, Indels: 9
0.80 0.12 0.07
Matches are distributed among these distances:
83 4 0.04
84 89 0.91
85 2 0.02
86 3 0.03
ACGTcount: A:0.42, C:0.12, G:0.30, T:0.15
Consensus pattern (84 bp):
GAAGAAGAAAAAGGGTTGTTCGAAGTGAAAGAAGTCATAACATCGGAAGCCGACCCCGGAGAGGA
AGAACAAACACGTGAAATT
Found at i:1884636 original size:66 final size:66
Alignment explanation
Indices: 1884530--1884662 Score: 239
Period size: 66 Copynumber: 2.0 Consensus size: 66
1884520 GGATTAAATG
1884530 GTTCCTAGGTAACTCATGCCAGAGGGATAAACTGGAGATATGCAGGTAATCCAACAAAAGAGACT
1 GTTCCTAGGTAACTCATGCCAGAGGGATAAACTGGAGATATGCAGGTAATCCAACAAAAGAGACT
1884595 T
66 T
* * *
1884596 GTTCCTAGGTAAGTCATGGCAGAGGGATAAACTGGAGATATGCAGGTAATCCAACAAAAGCGACT
1 GTTCCTAGGTAACTCATGCCAGAGGGATAAACTGGAGATATGCAGGTAATCCAACAAAAGAGACT
1884661 T
66 T
1884662 G
1 G
1884663 AACTATAAAC
Statistics
Matches: 64, Mismatches: 3, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
66 64 1.00
ACGTcount: A:0.35, C:0.17, G:0.26, T:0.21
Consensus pattern (66 bp):
GTTCCTAGGTAACTCATGCCAGAGGGATAAACTGGAGATATGCAGGTAATCCAACAAAAGAGACT
T
Found at i:1888769 original size:17 final size:18
Alignment explanation
Indices: 1888738--1888771 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
1888728 CATATTAAGG
1888738 TTTTGATATATTTAATTA
1 TTTTGATATATTTAATTA
*
1888756 TTTTTATATA-TTAATT
1 TTTTGATATATTTAATT
1888772 TTTATATTAG
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 6 0.40
18 9 0.60
ACGTcount: A:0.32, C:0.00, G:0.03, T:0.65
Consensus pattern (18 bp):
TTTTGATATATTTAATTA
Found at i:1898342 original size:20 final size:20
Alignment explanation
Indices: 1898298--1898340 Score: 59
Period size: 20 Copynumber: 2.1 Consensus size: 20
1898288 TTATATTAAT
*
1898298 TTTATAAAATTAAAAATATA
1 TTTATAAAATTAAAAAGATA
*
1898318 TTTATAAAATTAAGATAGATA
1 TTTATAAAATTAA-AAAGATA
1898339 TT
1 TT
1898341 ATTAATTAAA
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
20 13 0.65
21 7 0.35
ACGTcount: A:0.53, C:0.00, G:0.05, T:0.42
Consensus pattern (20 bp):
TTTATAAAATTAAAAAGATA
Found at i:1901749 original size:17 final size:17
Alignment explanation
Indices: 1901716--1901749 Score: 50
Period size: 17 Copynumber: 2.0 Consensus size: 17
1901706 CTGATTTTAT
*
1901716 AATTTTTAAATATCTAA
1 AATTTTTAAATAACTAA
*
1901733 AATTTTTAATTAACTAA
1 AATTTTTAAATAACTAA
1901750 TTAATTAATT
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:0.47, C:0.06, G:0.00, T:0.47
Consensus pattern (17 bp):
AATTTTTAAATAACTAA
Found at i:1908410 original size:2 final size:2
Alignment explanation
Indices: 1908403--1908458 Score: 112
Period size: 2 Copynumber: 28.0 Consensus size: 2
1908393 TACATTATTA
1908403 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
1908445 AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT
1908459 GCACAATTGG
Statistics
Matches: 54, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 54 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:1908699 original size:18 final size:18
Alignment explanation
Indices: 1908676--1908710 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
1908666 TCGCCGATTG
1908676 AATTGACTTATAACATCT
1 AATTGACTTATAACATCT
* *
1908694 AATTGATTTATAGCATC
1 AATTGACTTATAACATC
1908711 AACTTAATTA
Statistics
Matches: 15, Mismatches: 2, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
18 15 1.00
ACGTcount: A:0.37, C:0.14, G:0.09, T:0.40
Consensus pattern (18 bp):
AATTGACTTATAACATCT
Found at i:1910059 original size:18 final size:18
Alignment explanation
Indices: 1910011--1910064 Score: 58
Period size: 18 Copynumber: 3.1 Consensus size: 18
1910001 TTATAATATA
1910011 TATTTTTATT-TTTATAAT
1 TATTTTTATTATTTA-AAT
** *
1910029 TAAATTTA-AATTTAAAT
1 TATTTTTATTATTTAAAT
1910046 TATTTTTATTATTTAAAT
1 TATTTTTATTATTTAAAT
1910064 T
1 T
1910065 GAATTTGAAT
Statistics
Matches: 28, Mismatches: 6, Indels: 4
0.74 0.16 0.11
Matches are distributed among these distances:
17 9 0.32
18 19 0.68
ACGTcount: A:0.37, C:0.00, G:0.00, T:0.63
Consensus pattern (18 bp):
TATTTTTATTATTTAAAT
Found at i:1915955 original size:20 final size:18
Alignment explanation
Indices: 1915930--1915988 Score: 55
Period size: 20 Copynumber: 2.9 Consensus size: 18
1915920 CGTGTGAATG
1915930 TTGACCAGTCAAAAACTGGA
1 TTGACCAGT-AAAAAC-GGA
*
1915950 TTGACCGGTATGAAAACGGA
1 TTGACCAGTA--AAAACGGA
1915970 TTGAACCAGTTAAAAACGG
1 TTG-ACCAG-TAAAAACGG
1915989 TTTTTTATTC
Statistics
Matches: 33, Mismatches: 2, Indels: 8
0.77 0.05 0.19
Matches are distributed among these distances:
19 1 0.03
20 21 0.64
21 9 0.27
22 2 0.06
ACGTcount: A:0.39, C:0.17, G:0.24, T:0.20
Consensus pattern (18 bp):
TTGACCAGTAAAAACGGA
Found at i:1921209 original size:4 final size:4
Alignment explanation
Indices: 1921200--1921230 Score: 55
Period size: 4 Copynumber: 8.0 Consensus size: 4
1921190 TAAAAAAATC
1921200 ATTA ATTA ATTA ATTA ATTA ATT- ATTA ATTA
1 ATTA ATTA ATTA ATTA ATTA ATTA ATTA ATTA
1921231 TTTTCAAATA
Statistics
Matches: 26, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
3 3 0.12
4 23 0.88
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (4 bp):
ATTA
Found at i:1925319 original size:19 final size:19
Alignment explanation
Indices: 1925291--1925338 Score: 80
Period size: 19 Copynumber: 2.6 Consensus size: 19
1925281 GTATATATTT
1925291 TAAA-TTTATTTAAGTAGA
1 TAAATTTTATTTAAGTAGA
*
1925309 TAAATTTTATTTACGTAGA
1 TAAATTTTATTTAAGTAGA
1925328 TAAATTTTATT
1 TAAATTTTATT
1925339 CATATTTTAT
Statistics
Matches: 28, Mismatches: 1, Indels: 1
0.93 0.03 0.03
Matches are distributed among these distances:
18 4 0.14
19 24 0.86
ACGTcount: A:0.40, C:0.02, G:0.08, T:0.50
Consensus pattern (19 bp):
TAAATTTTATTTAAGTAGA
Found at i:1928611 original size:47 final size:47
Alignment explanation
Indices: 1928547--1928657 Score: 145
Period size: 47 Copynumber: 2.4 Consensus size: 47
1928537 GACATTGAGT
*
1928547 CGATG-AGACACTATGTGT-CGACTACTGTTAAAGTTCCGGATTTATTC
1 CGATGAAG-CACTATGTGTACGA-TAATGTTAAAGTTCCGGATTTATTC
* * * *
1928594 CGATGAAGTACTTTGTGTACTATAATGTTAAAGTTCCGGATTTGTTC
1 CGATGAAGCACTATGTGTACGATAATGTTAAAGTTCCGGATTTATTC
1928641 CGATGAAGCACTATGTG
1 CGATGAAGCACTATGTG
1928658 CTTAACCTGG
Statistics
Matches: 55, Mismatches: 7, Indels: 4
0.83 0.11 0.06
Matches are distributed among these distances:
47 51 0.93
48 4 0.07
ACGTcount: A:0.26, C:0.16, G:0.23, T:0.35
Consensus pattern (47 bp):
CGATGAAGCACTATGTGTACGATAATGTTAAAGTTCCGGATTTATTC
Found at i:1930141 original size:47 final size:47
Alignment explanation
Indices: 1930090--1930266 Score: 202
Period size: 47 Copynumber: 3.8 Consensus size: 47
1930080 TGGTTGAACA
*
1930090 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGTGAAATG
1 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGTGAAACG
* * * *
1930137 TCCGAACTCGTTGAGTTGAGTCCAAGTTC-GTGA--GATGT-AATTAGGCA
1 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGTGAA--A--CG
*
1930184 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCG-AACG
1 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGTGAAACG
* * *
1930230 CCCGAGCTCATTGAGTTGAGTCCGAGTTCACTTATGG
1 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGG
1930267 GCGGGTTACA
Statistics
Matches: 109, Mismatches: 13, Indels: 17
0.78 0.09 0.12
Matches are distributed among these distances:
43 2 0.02
44 5 0.05
45 1 0.01
46 37 0.34
47 56 0.51
48 3 0.03
50 5 0.05
ACGTcount: A:0.23, C:0.20, G:0.28, T:0.30
Consensus pattern (47 bp):
TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGTGAAACG
Found at i:1935708 original size:47 final size:47
Alignment explanation
Indices: 1935556--1935732 Score: 213
Period size: 47 Copynumber: 3.8 Consensus size: 47
1935546 TGTAACCCGC
* *
1935556 CCATAAGTGAACTCGGACTCAACTCAACGAGCTT-GGGC-GTTCGCAT
1 CCATAAGTGAACTCGGACTCAACTCAACGAG-TTCGGACAGTTCACAT
*
1935602 CCATAAGTGAACTCGGACTCAACTCAATGAGTTCGGATGCCTAGTT-ACAT
1 CCATAAGTGAACTCGGACTCAACTCAACGAGTTCGGA---C-AGTTCACAT
* * *
1935652 -C-TCA-CGAACTCGGACTCAACTCAACGAGTTCGGACATTTCACAT
1 CCATAAGTGAACTCGGACTCAACTCAACGAGTTCGGACAGTTCACAT
1935696 CCATAAGTGAACTCGGACTCAACTCAACGAGTTCGGA
1 CCATAAGTGAACTCGGACTCAACTCAACGAGTTCGGA
1935733 TGTTCAACCA
Statistics
Matches: 112, Mismatches: 9, Indels: 19
0.80 0.06 0.14
Matches are distributed among these distances:
43 3 0.03
44 5 0.04
45 3 0.03
46 34 0.30
47 57 0.51
48 2 0.02
49 2 0.02
50 3 0.03
51 3 0.03
ACGTcount: A:0.29, C:0.28, G:0.20, T:0.23
Consensus pattern (47 bp):
CCATAAGTGAACTCGGACTCAACTCAACGAGTTCGGACAGTTCACAT
Found at i:1935728 original size:94 final size:93
Alignment explanation
Indices: 1935564--1935734 Score: 281
Period size: 94 Copynumber: 1.8 Consensus size: 93
1935554 GCCCATAAGT
* *
1935564 GAACTCGGACTCAACTCAACGAGCTTGGGCGTTCGCATCCATAAGTGAACTCGGACTCAACTCAA
1 GAACTCGGACTCAACTCAACGAGCTTGGACGTTCACATCCATAAGTGAACTCGGACTCAACTCAA
*
1935629 TGAGTTCGGATGCCTAGTTACATCTCAC
66 CGAGTTCGGATGCCTAGTTACATCTCAC
*
1935657 GAACTCGGACTCAACTCAACGAG-TTCGGACATTTCACATCCATAAGTGAACTCGGACTCAACTC
1 GAACTCGGACTCAACTCAACGAGCTT-GGAC-GTTCACATCCATAAGTGAACTCGGACTCAACTC
1935721 AACGAGTTCGGATG
64 AACGAGTTCGGATG
1935735 TTCAACCATC
Statistics
Matches: 72, Mismatches: 4, Indels: 3
0.91 0.05 0.04
Matches are distributed among these distances:
92 2 0.03
93 26 0.36
94 44 0.61
ACGTcount: A:0.29, C:0.27, G:0.21, T:0.23
Consensus pattern (93 bp):
GAACTCGGACTCAACTCAACGAGCTTGGACGTTCACATCCATAAGTGAACTCGGACTCAACTCAA
CGAGTTCGGATGCCTAGTTACATCTCAC
Found at i:1937281 original size:42 final size:42
Alignment explanation
Indices: 1937222--1937310 Score: 160
Period size: 42 Copynumber: 2.1 Consensus size: 42
1937212 TTAGGAATAT
*
1937222 TTTTATTTTATGTTTTAGTAGTTTATTAGAATAAGGGAACTA
1 TTTTATTTTATATTTTAGTAGTTTATTAGAATAAGGGAACTA
*
1937264 TTTTCTTTTATATTTTAGTAGTTTATTAGAATAAGGGAACTA
1 TTTTATTTTATATTTTAGTAGTTTATTAGAATAAGGGAACTA
1937306 TTTTA
1 TTTTA
1937311 CCAATTAGGA
Statistics
Matches: 44, Mismatches: 3, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
42 44 1.00
ACGTcount: A:0.30, C:0.03, G:0.15, T:0.52
Consensus pattern (42 bp):
TTTTATTTTATATTTTAGTAGTTTATTAGAATAAGGGAACTA
Found at i:1943793 original size:56 final size:57
Alignment explanation
Indices: 1943676--1943794 Score: 127
Period size: 56 Copynumber: 2.1 Consensus size: 57
1943666 TTAGTTATTA
* * * * *
1943676 ATTTTATTAAGTTTTCATTTGGGTTATCCATCACTAATTCAATATTATTGTACCATT
1 ATTTTAATAAGTTTTCATTTGAGTTATCCATCACTAATTCAAGATTATTATACCATC
* * *
1943733 ATTTTAATAAG-TTTCATTTTAGTTA-CCAGTCATTAATTCAAGGTTATTATA-CACTC
1 ATTTTAATAAGTTTTCATTTGAGTTATCCA-TCACTAATTCAAGATTATTATACCA-TC
1943789 ATTTTA
1 ATTTTA
1943795 GTGATAACTT
Statistics
Matches: 52, Mismatches: 8, Indels: 5
0.80 0.12 0.08
Matches are distributed among these distances:
55 5 0.10
56 37 0.71
57 10 0.19
ACGTcount: A:0.30, C:0.13, G:0.08, T:0.48
Consensus pattern (57 bp):
ATTTTAATAAGTTTTCATTTGAGTTATCCATCACTAATTCAAGATTATTATACCATC
Found at i:1944366 original size:21 final size:20
Alignment explanation
Indices: 1944343--1944380 Score: 67
Period size: 20 Copynumber: 1.9 Consensus size: 20
1944333 AATTAGGTTT
1944343 TTTTTAAAAAAATAAAATTA
1 TTTTTAAAAAAATAAAATTA
*
1944363 TTTTTGAAAAAATAAAAT
1 TTTTTAAAAAAATAAAAT
1944381 AAATAATTAA
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.58, C:0.00, G:0.03, T:0.39
Consensus pattern (20 bp):
TTTTTAAAAAAATAAAATTA
Found at i:1944679 original size:35 final size:35
Alignment explanation
Indices: 1944638--1944708 Score: 142
Period size: 35 Copynumber: 2.0 Consensus size: 35
1944628 ATATTTTTAC
1944638 TAATTTTAAAATAACAAAACAAAACAAATCATTTT
1 TAATTTTAAAATAACAAAACAAAACAAATCATTTT
1944673 TAATTTTAAAATAACAAAACAAAACAAATCATTTT
1 TAATTTTAAAATAACAAAACAAAACAAATCATTTT
1944708 T
1 T
1944709 CAAGCTACGC
Statistics
Matches: 36, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
35 36 1.00
ACGTcount: A:0.56, C:0.11, G:0.00, T:0.32
Consensus pattern (35 bp):
TAATTTTAAAATAACAAAACAAAACAAATCATTTT
Found at i:1944946 original size:25 final size:26
Alignment explanation
Indices: 1944904--1944961 Score: 66
Period size: 25 Copynumber: 2.3 Consensus size: 26
1944894 GTTACAATTT
* *
1944904 TATTATTAAATTACAAATA-ATTTAA
1 TATTATTTAAGTACAAATATATTTAA
* *
1944929 TATTATTTAAGTATAAATATTTTTAA
1 TATTATTTAAGTACAAATATATTTAA
1944955 T-TTATTT
1 TATTATTT
1944962 TTAATTTGTT
Statistics
Matches: 28, Mismatches: 4, Indels: 2
0.82 0.12 0.06
Matches are distributed among these distances:
25 22 0.79
26 6 0.21
ACGTcount: A:0.43, C:0.02, G:0.02, T:0.53
Consensus pattern (26 bp):
TATTATTTAAGTACAAATATATTTAA
Found at i:1958167 original size:20 final size:21
Alignment explanation
Indices: 1958144--1958183 Score: 55
Period size: 21 Copynumber: 2.0 Consensus size: 21
1958134 CTAAATTTCA
1958144 TAAATT-AAAAATAAAAAGAT
1 TAAATTCAAAAATAAAAAGAT
* *
1958164 TAAATTCCAAAATAAGAAGA
1 TAAATTCAAAAATAAAAAGA
1958184 ATAACGAGAC
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
20 6 0.35
21 11 0.65
ACGTcount: A:0.65, C:0.05, G:0.07, T:0.23
Consensus pattern (21 bp):
TAAATTCAAAAATAAAAAGAT
Found at i:1958596 original size:23 final size:23
Alignment explanation
Indices: 1958569--1958612 Score: 61
Period size: 23 Copynumber: 1.9 Consensus size: 23
1958559 AGTCTTTGTA
1958569 CTTTTACTTTTAAGAATTTAATT
1 CTTTTACTTTTAAGAATTTAATT
* * *
1958592 CTTTTGCTTTTCAGATTTTAA
1 CTTTTACTTTTAAGAATTTAA
1958613 AATGTAGGTC
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
23 18 1.00
ACGTcount: A:0.25, C:0.11, G:0.07, T:0.57
Consensus pattern (23 bp):
CTTTTACTTTTAAGAATTTAATT
Found at i:1970621 original size:2 final size:2
Alignment explanation
Indices: 1970614--1970643 Score: 51
Period size: 2 Copynumber: 15.0 Consensus size: 2
1970604 TTGAAGTTAA
*
1970614 AT AT AT AT AT AT AT AT AT AT AT AT GT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1970644 GTGCATTAAT
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.47, C:0.00, G:0.03, T:0.50
Consensus pattern (2 bp):
AT
Found at i:1977036 original size:32 final size:32
Alignment explanation
Indices: 1976993--1977056 Score: 110
Period size: 32 Copynumber: 2.0 Consensus size: 32
1976983 ATCCACAACT
1976993 AATAACATATCTTGAATCCATTAGATTACTTG
1 AATAACATATCTTGAATCCATTAGATTACTTG
* *
1977025 AATAACCTATCTTGAATCCATTAGATTGCTTG
1 AATAACATATCTTGAATCCATTAGATTACTTG
1977057 CTAATGATAT
Statistics
Matches: 30, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
32 30 1.00
ACGTcount: A:0.34, C:0.17, G:0.11, T:0.38
Consensus pattern (32 bp):
AATAACATATCTTGAATCCATTAGATTACTTG
Found at i:1980388 original size:11 final size:11
Alignment explanation
Indices: 1980346--1980386 Score: 55
Period size: 11 Copynumber: 3.7 Consensus size: 11
1980336 TATTTTCTCC
1980346 CTATTTTGCTA
1 CTATTTTGCTA
*
1980357 CTATTTTACTA
1 CTATTTTGCTA
* *
1980368 CTATGTTGTTA
1 CTATTTTGCTA
1980379 CTATTTTG
1 CTATTTTG
1980387 TTGTTATTGT
Statistics
Matches: 25, Mismatches: 5, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
11 25 1.00
ACGTcount: A:0.20, C:0.15, G:0.10, T:0.56
Consensus pattern (11 bp):
CTATTTTGCTA
Found at i:1980463 original size:30 final size:30
Alignment explanation
Indices: 1980427--1980487 Score: 95
Period size: 30 Copynumber: 2.0 Consensus size: 30
1980417 ATTTTATTGT
*
1980427 TAATTTTTTTATTATTTTAAAGACATTTGC
1 TAATTTTGTTATTATTTTAAAGACATTTGC
* *
1980457 TAATTTTGTTATTATTTTAGAGGCATTTGC
1 TAATTTTGTTATTATTTTAAAGACATTTGC
1980487 T
1 T
1980488 TATTAAGTTG
Statistics
Matches: 28, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
30 28 1.00
ACGTcount: A:0.26, C:0.07, G:0.11, T:0.56
Consensus pattern (30 bp):
TAATTTTGTTATTATTTTAAAGACATTTGC
Found at i:1980643 original size:2 final size:2
Alignment explanation
Indices: 1980597--1980629 Score: 66
Period size: 2 Copynumber: 16.5 Consensus size: 2
1980587 TTGATGGTTT
1980597 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1980630 TTTAAAATTA
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 31 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:1980648 original size:12 final size:12
Alignment explanation
Indices: 1980633--1980666 Score: 50
Period size: 12 Copynumber: 2.8 Consensus size: 12
1980623 TATATATTTT
*
1980633 AAAATTATATAA
1 AAAATAATATAA
1980645 AAAATAATATAA
1 AAAATAATATAA
*
1980657 AAATTAATAT
1 AAAATAATAT
1980667 GAGCGGACCA
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
12 20 1.00
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.32
Consensus pattern (12 bp):
AAAATAATATAA
Found at i:1981677 original size:11 final size:11
Alignment explanation
Indices: 1981663--1981703 Score: 55
Period size: 11 Copynumber: 3.7 Consensus size: 11
1981653 TGTTTTCTCC
1981663 CTATTTTGCTA
1 CTATTTTGCTA
*
1981674 CTATTTTACTA
1 CTATTTTGCTA
* *
1981685 TTATGTTGCTA
1 CTATTTTGCTA
1981696 CTATTTTG
1 CTATTTTG
1981704 TTGTTATTGT
Statistics
Matches: 24, Mismatches: 6, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
11 24 1.00
ACGTcount: A:0.20, C:0.15, G:0.10, T:0.56
Consensus pattern (11 bp):
CTATTTTGCTA
Found at i:1981790 original size:30 final size:27
Alignment explanation
Indices: 1981739--1981820 Score: 94
Period size: 26 Copynumber: 2.9 Consensus size: 27
1981729 AATTTATTTT
*
1981739 ATTGTTAATTTTTTATTATTATTTTAAACA
1 ATTGTTAA--TTTTGTTATTATTTTAAA-A
*
1981769 CATTTGTTAATTTTGTTATTATTTTAGAA
1 -A-TTGTTAATTTTGTTATTATTTTAAAA
1981798 A-TGTTAATTTTGTTATTATTTTA
1 ATTGTTAATTTTGTTATTATTTTA
1981821 GAAGAATTTG
Statistics
Matches: 48, Mismatches: 2, Indels: 7
0.84 0.04 0.12
Matches are distributed among these distances:
26 22 0.46
28 1 0.02
29 1 0.02
30 16 0.33
31 1 0.02
32 7 0.15
ACGTcount: A:0.29, C:0.02, G:0.07, T:0.61
Consensus pattern (27 bp):
ATTGTTAATTTTGTTATTATTTTAAAA
Found at i:1981803 original size:26 final size:26
Alignment explanation
Indices: 1981773--1981823 Score: 102
Period size: 26 Copynumber: 2.0 Consensus size: 26
1981763 TAAACACATT
1981773 TGTTAATTTTGTTATTATTTTAGAAA
1 TGTTAATTTTGTTATTATTTTAGAAA
1981799 TGTTAATTTTGTTATTATTTTAGAA
1 TGTTAATTTTGTTATTATTTTAGAA
1981824 GAATTTGCTT
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
26 25 1.00
ACGTcount: A:0.29, C:0.00, G:0.12, T:0.59
Consensus pattern (26 bp):
TGTTAATTTTGTTATTATTTTAGAAA
Found at i:1981975 original size:12 final size:12
Alignment explanation
Indices: 1981954--1981987 Score: 50
Period size: 12 Copynumber: 2.8 Consensus size: 12
1981944 TATATATTTT
*
1981954 AAAATTATATAA
1 AAAATAATATAA
1981966 AAAATAATATAA
1 AAAATAATATAA
*
1981978 AAATTAATAT
1 AAAATAATAT
1981988 GGGCGGGCCG
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
12 20 1.00
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.32
Consensus pattern (12 bp):
AAAATAATATAA
Found at i:1984742 original size:31 final size:31
Alignment explanation
Indices: 1984707--1984769 Score: 81
Period size: 31 Copynumber: 2.0 Consensus size: 31
1984697 AGTTACAAAA
* **
1984707 TGATCACCCAATTATTTGACTTTTTCTTTTT
1 TGATCACCCAACTATTTGAAATTTTCTTTTT
**
1984738 TGATCACTTAACTATTTGAAATTTTCTTTTT
1 TGATCACCCAACTATTTGAAATTTTCTTTTT
1984769 T
1 T
1984770 AGATTGTTAA
Statistics
Matches: 27, Mismatches: 5, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
31 27 1.00
ACGTcount: A:0.22, C:0.16, G:0.06, T:0.56
Consensus pattern (31 bp):
TGATCACCCAACTATTTGAAATTTTCTTTTT
Found at i:1985062 original size:2 final size:2
Alignment explanation
Indices: 1985055--1985079 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
1985045 ATTGAGGATT
1985055 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
1985080 TTGTAGTTTT
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:1986216 original size:14 final size:13
Alignment explanation
Indices: 1986197--1986228 Score: 55
Period size: 14 Copynumber: 2.4 Consensus size: 13
1986187 TGTGGGTTCA
1986197 TTTTTTGTATTTCT
1 TTTTTTGTATTT-T
1986211 TTTTTTGTATTTT
1 TTTTTTGTATTTT
1986224 TTTTT
1 TTTTT
1986229 ACTTCTCCTC
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
13 6 0.33
14 12 0.67
ACGTcount: A:0.06, C:0.03, G:0.06, T:0.84
Consensus pattern (13 bp):
TTTTTTGTATTTT
Found at i:2001145 original size:19 final size:19
Alignment explanation
Indices: 2001123--2001159 Score: 65
Period size: 19 Copynumber: 1.9 Consensus size: 19
2001113 CAACTTTTTC
2001123 ATATATTATAATATTTTAA
1 ATATATTATAATATTTTAA
*
2001142 ATATATTATTATATTTTA
1 ATATATTATAATATTTTA
2001160 GCATACCTTT
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
19 17 1.00
ACGTcount: A:0.43, C:0.00, G:0.00, T:0.57
Consensus pattern (19 bp):
ATATATTATAATATTTTAA
Found at i:2001266 original size:22 final size:20
Alignment explanation
Indices: 2001229--2001273 Score: 54
Period size: 20 Copynumber: 2.1 Consensus size: 20
2001219 TAAATTTAAT
*
2001229 AATTAATATATTATTTTTTA
1 AATTAATATATTATTTATTA
*
2001249 AATTAATATTTTAGATTTATTA
1 AATTAATATATT--ATTTATTA
2001271 AAT
1 AAT
2001274 ATATAACATA
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
20 11 0.52
22 10 0.48
ACGTcount: A:0.42, C:0.00, G:0.02, T:0.56
Consensus pattern (20 bp):
AATTAATATATTATTTATTA
Found at i:2005287 original size:40 final size:39
Alignment explanation
Indices: 2005216--2005294 Score: 99
Period size: 40 Copynumber: 2.0 Consensus size: 39
2005206 CTAAAGCTGA
*
2005216 AATGAACTTGAAATGACTCAAACCGAGAATGATTTGAAT
1 AATGAACTTGAAATGACTCAAACCGAGAATGATTAGAAT
*
2005255 AATGTAACTTGAAATGACGT-GAACCTGA-AATGATTAGAAT
1 AATG-AACTTGAAATGAC-TCAAACC-GAGAATGATTAGAAT
2005295 CCAAAATGAC
Statistics
Matches: 35, Mismatches: 2, Indels: 5
0.83 0.05 0.12
Matches are distributed among these distances:
39 4 0.11
40 28 0.80
41 3 0.09
ACGTcount: A:0.43, C:0.11, G:0.19, T:0.27
Consensus pattern (39 bp):
AATGAACTTGAAATGACTCAAACCGAGAATGATTAGAAT
Found at i:2010998 original size:201 final size:202
Alignment explanation
Indices: 2010595--2011109 Score: 610
Period size: 201 Copynumber: 2.5 Consensus size: 202
2010585 AATGTTCTAT
* * * * * *
2010595 GATAGTCTTTACCTATGTGAGTCAAATTCTTCATTTTTTTCCCAAAA-TATTGATGCTAGGCACT
1 GATAGTCTTTACCTATGTTACTCGAACTCTTCATATTTTT---AAAAGTATCGATGCTAGGCACT
* * * * * **
2010659 AGTTTCGAACATTTACGATCTGGCAAATATATG-AAAAAAAAAACCCAAAAAAAAGTTAAAAATT
63 AGTTTAGAACATGTATGATCT-CCAATTATATGAAAAAAAAAAAAACAAAAAAAAGTTAAAAATT
* * * *
2010723 GAGCACACCGGTGTCAAATACATGCACCTAACATATCCAACACCAACATTCGATTCCAATAGCAG
127 GAGCACACCAGTGTC-AAGACATGCACCTAACATATCCAACACCAACATTCAAGTCCAATAGCAG
2010788 ACAGCATACTAC
191 ACAGCATACTAC
* * *
2010800 GATAGTCTTTACCTATGTTACTTGAACTGTTCAT-TTTTCT-GAAGTATCGATGCTAGGCACTAG
1 GATAGTCTTTACCTATGTTACTCGAACTCTTCATATTTT-TAAAAGTATCGATGCTAGGCACTAG
**
2010863 TTTAGAACATGTATGATCCTCCAATTATATGAAAAAAAAAAAAACTCAAAAAAGTTAAAAATTGA
65 TTTAGAACATGTATGAT-CTCCAATTATATGAAAAAAAAAAAAACAAAAAAAAGTTAAAAATTGA
* * *
2010928 GCACACTAGTGTC-AGACATGCACCTAACATATCCAACACCCACATTCAAGTCCAATAGCAGACG
129 GCACACCAGTGTCAAGACATGCACCTAACATATCCAACACCAACATTCAAGTCCAATAGCAGACA
*
2010992 GCATACTAT
194 GCATACTAC
* * **
2011001 GGTAGTCTTTACCTATGTTACTCGAACTCTTCATATTTTTACAAAGTATCGACGCTAAACACTAG
1 GATAGTCTTTACCTATGTTACTCGAACTCTTCATATTTTTA-AAAGTATCGATGCTAGGCACTAG
* *
2011066 TTCAGAA-ATGTATGATGCTCCAATTTTATGAAAAAATAAAAAAA
65 TTTAGAACATGTATGAT-CTCCAATTATATGAAAAAA-AAAAAAA
2011110 ACCAAAATCA
Statistics
Matches: 267, Mismatches: 35, Indels: 18
0.83 0.11 0.06
Matches are distributed among these distances:
201 88 0.33
202 72 0.27
203 74 0.28
204 4 0.01
205 29 0.11
ACGTcount: A:0.38, C:0.20, G:0.13, T:0.29
Consensus pattern (202 bp):
GATAGTCTTTACCTATGTTACTCGAACTCTTCATATTTTTAAAAGTATCGATGCTAGGCACTAGT
TTAGAACATGTATGATCTCCAATTATATGAAAAAAAAAAAAACAAAAAAAAGTTAAAAATTGAGC
ACACCAGTGTCAAGACATGCACCTAACATATCCAACACCAACATTCAAGTCCAATAGCAGACAGC
ATACTAC
Found at i:2019149 original size:21 final size:21
Alignment explanation
Indices: 2019123--2019163 Score: 64
Period size: 21 Copynumber: 2.0 Consensus size: 21
2019113 AGACGAGCGA
* *
2019123 TACTCCACAGCAGGTGGAGTG
1 TACTCCAAAACAGGTGGAGTG
2019144 TACTCCAAAACAGGTGGAGT
1 TACTCCAAAACAGGTGGAGT
2019164 TTGAGCAGAT
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
21 18 1.00
ACGTcount: A:0.29, C:0.22, G:0.29, T:0.20
Consensus pattern (21 bp):
TACTCCAAAACAGGTGGAGTG
Found at i:2025603 original size:23 final size:25
Alignment explanation
Indices: 2025577--2025639 Score: 76
Period size: 24 Copynumber: 2.6 Consensus size: 25
2025567 TATTTTGTCA
2025577 TATTATTTTTATAAATAAAT-TAT-
1 TATTATTTTTATAAATAAATATATG
* **
2025600 TATTAATTTTTTTTTATAAATATATG
1 TATT-ATTTTTATAAATAAATATATG
2025626 TATTATTTTTATAA
1 TATTATTTTTATAA
2025640 TATATAGTAT
Statistics
Matches: 31, Mismatches: 6, Indels: 4
0.76 0.15 0.10
Matches are distributed among these distances:
23 4 0.13
24 13 0.42
25 10 0.32
26 4 0.13
ACGTcount: A:0.38, C:0.00, G:0.02, T:0.60
Consensus pattern (25 bp):
TATTATTTTTATAAATAAATATATG
Found at i:2025641 original size:20 final size:22
Alignment explanation
Indices: 2025610--2025649 Score: 66
Period size: 21 Copynumber: 1.9 Consensus size: 22
2025600 TATTAATTTT
2025610 TTTTTATAAATATAT-GTATTA
1 TTTTTATAAATATATAGTATTA
2025631 TTTTTAT-AATATATAGTAT
1 TTTTTATAAATATATAGTAT
2025650 GGACACTTAA
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
20 7 0.39
21 11 0.61
ACGTcount: A:0.38, C:0.00, G:0.05, T:0.57
Consensus pattern (22 bp):
TTTTTATAAATATATAGTATTA
Found at i:2027857 original size:197 final size:197
Alignment explanation
Indices: 2027522--2027912 Score: 622
Period size: 197 Copynumber: 2.0 Consensus size: 197
2027512 GATTATGATA
* * *
2027522 GTGGTATGCTATTGGATCACTATCTTCTTTGGTTGAATGCTCTTTATTCTTTTGAGCATATATCT
1 GTGGTATGCTATTAGATCACTATCATCTTTGGTTGAATGCTCTTTATGCTTTTGAGCATATATCT
* * *
2027587 GTATGTCTGTGTATTCTCAATGGTTATAATGTCTATCGAGGCTTTAGGTTGAATCCTTTATATAT
66 CTATGTCAGTGTATTCTCAATGGTTATAAAGTCTATCGAGGCTTTAGGTTGAATCCTTTATATAT
* * * *
2027652 TAAATCCAACATTGTCTCCAAAAACAATGAGTGATTAAATTGAATGG-CATGGTAAGAAGGTTGG
131 TAAATCCAACATTATCTCCAAAAACAATGAGTGATTAAATGGAATGGTC-TGATAAGAAGATTGG
2027716 GTT
195 GTT
* * * *
2027719 GTGGTATGCTTTTAGATCACTTTCATCTTTGGTTGAATGCTCTTTATGCTTTTGAGCATATGTTT
1 GTGGTATGCTATTAGATCACTATCATCTTTGGTTGAATGCTCTTTATGCTTTTGAGCATATATCT
* *
2027784 CTATGTCAGTGTATTCTCAATTGTTATAAAGTCTATCGAGGCTTTAGGTTGAATCCTTTATATGT
66 CTATGTCAGTGTATTCTCAATGGTTATAAAGTCTATCGAGGCTTTAGGTTGAATCCTTTATATAT
2027849 TAAATCCAACATTATCTCCAAAAACAATGAGTGATTAAATGGAATGGTCTGATAAGAAGATTGG
131 TAAATCCAACATTATCTCCAAAAACAATGAGTGATTAAATGGAATGGTCTGATAAGAAGATTGG
2027913 ATTGCATTCA
Statistics
Matches: 177, Mismatches: 16, Indels: 2
0.91 0.08 0.01
Matches are distributed among these distances:
197 176 0.99
198 1 0.01
ACGTcount: A:0.27, C:0.13, G:0.20, T:0.40
Consensus pattern (197 bp):
GTGGTATGCTATTAGATCACTATCATCTTTGGTTGAATGCTCTTTATGCTTTTGAGCATATATCT
CTATGTCAGTGTATTCTCAATGGTTATAAAGTCTATCGAGGCTTTAGGTTGAATCCTTTATATAT
TAAATCCAACATTATCTCCAAAAACAATGAGTGATTAAATGGAATGGTCTGATAAGAAGATTGGG
TT
Found at i:2036184 original size:17 final size:17
Alignment explanation
Indices: 2036162--2036194 Score: 57
Period size: 17 Copynumber: 1.9 Consensus size: 17
2036152 ACATCTTGGG
2036162 TTGTTTTTTAAATTTGT
1 TTGTTTTTTAAATTTGT
*
2036179 TTGTTTTTTAGATTTG
1 TTGTTTTTTAAATTTG
2036195 GGTTTTTATT
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
17 15 1.00
ACGTcount: A:0.15, C:0.00, G:0.15, T:0.70
Consensus pattern (17 bp):
TTGTTTTTTAAATTTGT
Found at i:2040596 original size:29 final size:31
Alignment explanation
Indices: 2040564--2040633 Score: 92
Period size: 31 Copynumber: 2.3 Consensus size: 31
2040554 TAATAATGAT
2040564 AAAATTATATTTTAA-TCTTT-AAAAATATA
1 AAAATTATATTTTAACTCTTTAAAAAATATA
*
2040593 AAAATT-TAATTTAACCTCTTTAAAAAATATA
1 AAAATTATATTTTAA-CTCTTTAAAAAATATA
*
2040624 AAAATAATAT
1 AAAATTATAT
2040634 ATTATTAAAT
Statistics
Matches: 34, Mismatches: 3, Indels: 5
0.81 0.07 0.12
Matches are distributed among these distances:
28 7 0.21
29 6 0.18
30 5 0.15
31 14 0.41
32 2 0.06
ACGTcount: A:0.54, C:0.06, G:0.00, T:0.40
Consensus pattern (31 bp):
AAAATTATATTTTAACTCTTTAAAAAATATA
Found at i:2041030 original size:16 final size:16
Alignment explanation
Indices: 2041009--2041043 Score: 54
Period size: 16 Copynumber: 2.2 Consensus size: 16
2040999 ATTTAGTTAA
2041009 TTTATATTATTATT-TT
1 TTTATATTA-TATTGTT
2041025 TTTATATTATATTGTT
1 TTTATATTATATTGTT
2041041 TTT
1 TTT
2041044 TACATAATTT
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
15 4 0.22
16 14 0.78
ACGTcount: A:0.23, C:0.00, G:0.03, T:0.74
Consensus pattern (16 bp):
TTTATATTATATTGTT
Found at i:2041131 original size:21 final size:20
Alignment explanation
Indices: 2041085--2041131 Score: 51
Period size: 21 Copynumber: 2.2 Consensus size: 20
2041075 TAAAAATATT
*
2041085 AAAATTATAAATATTTCTAA
1 AAAATTAAAAATATTTCTAA
2041105 ATAAATTAAAAATAAATTT-TAA
1 A-AAATTAAAAAT--ATTTCTAA
2041127 AAAAT
1 AAAAT
2041132 ATGTATATTT
Statistics
Matches: 23, Mismatches: 1, Indels: 5
0.79 0.03 0.17
Matches are distributed among these distances:
20 1 0.04
21 14 0.61
22 4 0.17
23 4 0.17
ACGTcount: A:0.62, C:0.02, G:0.00, T:0.36
Consensus pattern (20 bp):
AAAATTAAAAATATTTCTAA
Found at i:2045922 original size:17 final size:18
Alignment explanation
Indices: 2045890--2045926 Score: 58
Period size: 17 Copynumber: 2.1 Consensus size: 18
2045880 TATTTAAAAA
2045890 ATATTAAATGAATTATAT
1 ATATTAAATGAATTATAT
*
2045908 ATATTTAAT-AATTATAT
1 ATATTAAATGAATTATAT
2045925 AT
1 AT
2045927 TTATATATAT
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
17 10 0.56
18 8 0.44
ACGTcount: A:0.49, C:0.00, G:0.03, T:0.49
Consensus pattern (18 bp):
ATATTAAATGAATTATAT
Found at i:2047062 original size:9 final size:9
Alignment explanation
Indices: 2047050--2047074 Score: 50
Period size: 9 Copynumber: 2.8 Consensus size: 9
2047040 ATTATTAATC
2047050 AAATTAAAA
1 AAATTAAAA
2047059 AAATTAAAA
1 AAATTAAAA
2047068 AAATTAA
1 AAATTAA
2047075 TCGAACCGAA
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
9 16 1.00
ACGTcount: A:0.76, C:0.00, G:0.00, T:0.24
Consensus pattern (9 bp):
AAATTAAAA
Found at i:2049399 original size:25 final size:23
Alignment explanation
Indices: 2049352--2049404 Score: 72
Period size: 25 Copynumber: 2.2 Consensus size: 23
2049342 AAATAATGAA
2049352 AATTTTTATTTTAATTAATTTTT
1 AATTTTTATTTTAATTAATTTTT
2049375 AATTTTTATAATTTAATTTAA-TTTT
1 AATTTTTAT--TTTAA-TTAATTTTT
2049400 AATTT
1 AATTT
2049405 AAAAATATCA
Statistics
Matches: 27, Mismatches: 0, Indels: 4
0.87 0.00 0.13
Matches are distributed among these distances:
23 9 0.33
25 14 0.52
26 4 0.15
ACGTcount: A:0.34, C:0.00, G:0.00, T:0.66
Consensus pattern (23 bp):
AATTTTTATTTTAATTAATTTTT
Found at i:2050309 original size:22 final size:23
Alignment explanation
Indices: 2050265--2050310 Score: 76
Period size: 22 Copynumber: 2.0 Consensus size: 23
2050255 AATTTCAAAG
2050265 TCTAATAATTTAAATGAAAATTT
1 TCTAATAATTTAAATGAAAATTT
*
2050288 TCTAATAATTT-AATGAATATTT
1 TCTAATAATTTAAATGAAAATTT
2050310 T
1 T
2050311 GTTGTAAAAA
Statistics
Matches: 22, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
22 11 0.50
23 11 0.50
ACGTcount: A:0.43, C:0.04, G:0.04, T:0.48
Consensus pattern (23 bp):
TCTAATAATTTAAATGAAAATTT
Found at i:2050766 original size:37 final size:38
Alignment explanation
Indices: 2050715--2050790 Score: 120
Period size: 37 Copynumber: 2.0 Consensus size: 38
2050705 AATTAAATTA
2050715 AAATATTATTATTTTTAGGA-GGAGAAAAGTGGAATTTT
1 AAATATTATTATTTTTAGGAGGGA-AAAAGTGGAATTTT
*
2050753 AAAT-TTATTATTTTTAGGAGGGAAAAAGTGTAATTTT
1 AAATATTATTATTTTTAGGAGGGAAAAAGTGGAATTTT
2050790 A
1 A
2050791 CCATTGTTAA
Statistics
Matches: 36, Mismatches: 1, Indels: 3
0.90 0.03 0.08
Matches are distributed among these distances:
37 29 0.81
38 7 0.19
ACGTcount: A:0.39, C:0.00, G:0.20, T:0.41
Consensus pattern (38 bp):
AAATATTATTATTTTTAGGAGGGAAAAAGTGGAATTTT
Found at i:2054545 original size:12 final size:13
Alignment explanation
Indices: 2054528--2054559 Score: 57
Period size: 13 Copynumber: 2.5 Consensus size: 13
2054518 TTATTAATTT
2054528 AATTTAA-TTTAA
1 AATTTAATTTTAA
2054540 AATTTAATTTTAA
1 AATTTAATTTTAA
2054553 AATTTAA
1 AATTTAA
2054560 AAAAAAACTA
Statistics
Matches: 19, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
12 7 0.37
13 12 0.63
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (13 bp):
AATTTAATTTTAA
Found at i:2061359 original size:16 final size:17
Alignment explanation
Indices: 2061335--2061373 Score: 53
Period size: 16 Copynumber: 2.4 Consensus size: 17
2061325 AACTTTTAAT
*
2061335 ATTAGAAAAAAA-TAAA
1 ATTATAAAAAAAGTAAA
*
2061351 ATTATAAAAAAAGTTAA
1 ATTATAAAAAAAGTAAA
2061368 ATTATA
1 ATTATA
2061374 TATATGTAAA
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
16 11 0.55
17 9 0.45
ACGTcount: A:0.67, C:0.00, G:0.05, T:0.28
Consensus pattern (17 bp):
ATTATAAAAAAAGTAAA
Found at i:2061362 original size:17 final size:17
Alignment explanation
Indices: 2061340--2061373 Score: 50
Period size: 17 Copynumber: 2.0 Consensus size: 17
2061330 TTAATATTAG
2061340 AAAAAAATAAAATTATA
1 AAAAAAATAAAATTATA
* *
2061357 AAAAAAGTTAAATTATA
1 AAAAAAATAAAATTATA
2061374 TATATGTAAA
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:0.71, C:0.00, G:0.03, T:0.26
Consensus pattern (17 bp):
AAAAAAATAAAATTATA
Found at i:2068857 original size:47 final size:47
Alignment explanation
Indices: 2068749--2068850 Score: 134
Period size: 47 Copynumber: 2.2 Consensus size: 47
2068739 CGGGATAAGT
* * *
2068749 ACATAGTGCTTCATCGGAATAAATCCGGAACTTTAACATTATAGTAC
1 ACATAGTGCTTCATCAGAACAAATCCGGAACTTTAACAGTATAGTAC
* * *
2068796 ACAAAGTACTTCATCAGAACAAATCCGGAACTTTAACAGTAGTCG-AC
1 ACATAGTGCTTCATCAGAACAAATCCGGAACTTTAACAGTA-TAGTAC
2068843 ACATAGTG
1 ACATAGTG
2068851 TCTCATCGAC
Statistics
Matches: 46, Mismatches: 8, Indels: 2
0.82 0.14 0.04
Matches are distributed among these distances:
47 44 0.96
48 2 0.04
ACGTcount: A:0.38, C:0.21, G:0.16, T:0.25
Consensus pattern (47 bp):
ACATAGTGCTTCATCAGAACAAATCCGGAACTTTAACAGTATAGTAC
Found at i:2069494 original size:4 final size:4
Alignment explanation
Indices: 2069485--2069513 Score: 58
Period size: 4 Copynumber: 7.2 Consensus size: 4
2069475 AGCAAACGTG
2069485 AGAA AGAA AGAA AGAA AGAA AGAA AGAA A
1 AGAA AGAA AGAA AGAA AGAA AGAA AGAA A
2069514 TAGAAAAGGG
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 25 1.00
ACGTcount: A:0.76, C:0.00, G:0.24, T:0.00
Consensus pattern (4 bp):
AGAA
Found at i:2084444 original size:24 final size:24
Alignment explanation
Indices: 2084414--2084460 Score: 94
Period size: 24 Copynumber: 2.0 Consensus size: 24
2084404 TGTTTCCATG
2084414 AAAGAGGGTGACATATTCTTTGGT
1 AAAGAGGGTGACATATTCTTTGGT
2084438 AAAGAGGGTGACATATTCTTTGG
1 AAAGAGGGTGACATATTCTTTGG
2084461 ACTGGGCGGA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
24 23 1.00
ACGTcount: A:0.30, C:0.09, G:0.30, T:0.32
Consensus pattern (24 bp):
AAAGAGGGTGACATATTCTTTGGT
Found at i:2087093 original size:29 final size:29
Alignment explanation
Indices: 2087037--2087096 Score: 79
Period size: 29 Copynumber: 2.1 Consensus size: 29
2087027 AATGTTGAAT
*
2087037 TTTTTATAAATTTTAAATATATTCTTTAA
1 TTTTTATAAATTTTAAATATATTATTTAA
2087066 TTTTTATGAAATTTT-AAT-TAGTTATTTAA
1 TTTTTAT-AAATTTTAAATATA-TTATTTAA
2087095 TT
1 TT
2087097 ATTAAATTTT
Statistics
Matches: 28, Mismatches: 1, Indels: 4
0.85 0.03 0.12
Matches are distributed among these distances:
28 2 0.07
29 19 0.68
30 7 0.25
ACGTcount: A:0.35, C:0.02, G:0.03, T:0.60
Consensus pattern (29 bp):
TTTTTATAAATTTTAAATATATTATTTAA
Found at i:2087278 original size:2 final size:2
Alignment explanation
Indices: 2087271--2087297 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
2087261 GCTATTCATT
2087271 TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA T
2087298 TTAAAATGCG
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 25 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:2088796 original size:3 final size:3
Alignment explanation
Indices: 2088788--2088823 Score: 72
Period size: 3 Copynumber: 12.0 Consensus size: 3
2088778 TATGCTTATT
2088788 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
2088824 ATAACAAAGA
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 33 1.00
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (3 bp):
TAA
Found at i:2095286 original size:9 final size:9
Alignment explanation
Indices: 2095272--2095315 Score: 54
Period size: 9 Copynumber: 4.9 Consensus size: 9
2095262 TGTGTTTTTA
2095272 TATTTA-TT
1 TATTTATTT
2095280 TATTTTATTT
1 TA-TTTATTT
2095290 TATTTATTT
1 TATTTATTT
*
2095299 TACTTATTT
1 TATTTATTT
*
2095308 TTTTTATT
1 TATTTATT
2095316 AATTTTAAAA
Statistics
Matches: 31, Mismatches: 3, Indels: 3
0.84 0.08 0.08
Matches are distributed among these distances:
8 2 0.06
9 25 0.81
10 4 0.13
ACGTcount: A:0.20, C:0.02, G:0.00, T:0.77
Consensus pattern (9 bp):
TATTTATTT
Found at i:2095295 original size:18 final size:18
Alignment explanation
Indices: 2095272--2095322 Score: 59
Period size: 18 Copynumber: 2.8 Consensus size: 18
2095262 TGTGTTTTTA
2095272 TATTTATTTATTTTATTT
1 TATTTATTTATTTTATTT
*
2095290 TATTTATTT-TACTTATTT
1 TATTTATTTAT-TTTATTT
* *
2095308 TTTTTATTAATTTTA
1 TATTTATTTATTTTA
2095323 AAAATTTTGA
Statistics
Matches: 27, Mismatches: 4, Indels: 4
0.77 0.11 0.11
Matches are distributed among these distances:
17 1 0.04
18 25 0.93
19 1 0.04
ACGTcount: A:0.24, C:0.02, G:0.00, T:0.75
Consensus pattern (18 bp):
TATTTATTTATTTTATTT
Found at i:2095329 original size:22 final size:23
Alignment explanation
Indices: 2095281--2095330 Score: 57
Period size: 22 Copynumber: 2.2 Consensus size: 23
2095271 ATATTTATTT
* ***
2095281 ATTTTATTTTATTTATTTTACTT
1 ATTTTATTTTATTAATTTTAAAA
2095304 ATTTT-TTTTATTAATTTTAAAA
1 ATTTTATTTTATTAATTTTAAAA
2095326 ATTTT
1 ATTTT
2095331 GAAATATATA
Statistics
Matches: 23, Mismatches: 4, Indels: 1
0.82 0.14 0.04
Matches are distributed among these distances:
22 18 0.78
23 5 0.22
ACGTcount: A:0.28, C:0.02, G:0.00, T:0.70
Consensus pattern (23 bp):
ATTTTATTTTATTAATTTTAAAA
Found at i:2095352 original size:23 final size:22
Alignment explanation
Indices: 2095317--2095400 Score: 80
Period size: 23 Copynumber: 3.6 Consensus size: 22
2095307 TTTTTTATTA
* *
2095317 ATTTTAAAAATTTTGAAATATAT
1 ATTTGAAATATTTT-AAATATAT
2095340 ATTTGAAATATTTTATAATATAT
1 ATTTGAAATATTTTA-AATATAT
* *
2095363 ATTTTTAAA-ATTTAAATATATAT
1 A-TTTGAAATATTTTAA-ATATAT
2095386 ATTTGAAATTATTTT
1 ATTTGAAA-TATTTT
2095401 TAAAAATTTT
Statistics
Matches: 50, Mismatches: 6, Indels: 9
0.77 0.09 0.14
Matches are distributed among these distances:
22 8 0.16
23 32 0.64
24 10 0.20
ACGTcount: A:0.44, C:0.00, G:0.04, T:0.52
Consensus pattern (22 bp):
ATTTGAAATATTTTAAATATAT
Found at i:2095436 original size:13 final size:14
Alignment explanation
Indices: 2095407--2095443 Score: 51
Period size: 13 Copynumber: 2.7 Consensus size: 14
2095397 TTTTTAAAAA
2095407 TTTT-AAATATATAT
1 TTTTGAAAT-TATAT
2095421 TTTTGAAATTAT-T
1 TTTTGAAATTATAT
2095434 TTTTGAAATT
1 TTTTGAAATT
2095444 TTGAATATTA
Statistics
Matches: 22, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
13 11 0.50
14 7 0.32
15 4 0.18
ACGTcount: A:0.35, C:0.00, G:0.05, T:0.59
Consensus pattern (14 bp):
TTTTGAAATTATAT
Found at i:2095447 original size:21 final size:20
Alignment explanation
Indices: 2095421--2095482 Score: 72
Period size: 21 Copynumber: 3.0 Consensus size: 20
2095411 AAATATATAT
2095421 TTTTGAAATTATTTTTTGAAA
1 TTTTGAAATTATTTTTT-AAA
2095442 TTTTGAATATTATTTTTTAAA
1 TTTTGAA-ATTATTTTTTAAA
*
2095463 TATT-AAATATATATTTTTAA
1 TTTTGAAAT-TAT-TTTTTAA
2095483 TAATATAAAA
Statistics
Matches: 37, Mismatches: 1, Indels: 6
0.84 0.02 0.14
Matches are distributed among these distances:
19 2 0.05
20 5 0.14
21 20 0.54
22 10 0.27
ACGTcount: A:0.37, C:0.00, G:0.05, T:0.58
Consensus pattern (20 bp):
TTTTGAAATTATTTTTTAAA
Found at i:2095459 original size:35 final size:35
Alignment explanation
Indices: 2095362--2095463 Score: 138
Period size: 35 Copynumber: 3.0 Consensus size: 35
2095352 TTATAATATA
*
2095362 TATTTTT-AAAA-TTTAAATATATATATTTGAAAT
1 TATTTTTAAAAATTTTAAATATATATTTTTGAAAT
2095395 TATTTTTAAAAATTTTAAATATATATTTTTGAAAT
1 TATTTTTAAAAATTTTAAATATATATTTTTGAAAT
** * *
2095430 TATTTTTTGAAATTTTGAATAT-TATTTTTTAAAT
1 TATTTTTAAAAATTTTAAATATATATTTTTGAAAT
2095464 ATTAAATATA
Statistics
Matches: 62, Mismatches: 5, Indels: 3
0.89 0.07 0.04
Matches are distributed among these distances:
33 7 0.11
34 15 0.24
35 40 0.65
ACGTcount: A:0.40, C:0.00, G:0.04, T:0.56
Consensus pattern (35 bp):
TATTTTTAAAAATTTTAAATATATATTTTTGAAAT
Found at i:2095474 original size:23 final size:23
Alignment explanation
Indices: 2095447--2095495 Score: 66
Period size: 23 Copynumber: 2.2 Consensus size: 23
2095437 TGAAATTTTG
* *
2095447 AATAT-TATTTTTTA-AATATTA
1 AATATATATTTTTAATAATATAA
2095468 AATATATATTTTTAATAATATAA
1 AATATATATTTTTAATAATATAA
2095491 AATAT
1 AATAT
2095496 TTAAATATTT
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
21 5 0.21
22 8 0.33
23 11 0.46
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (23 bp):
AATATATATTTTTAATAATATAA
Found at i:2095495 original size:21 final size:21
Alignment explanation
Indices: 2095447--2095495 Score: 55
Period size: 22 Copynumber: 2.2 Consensus size: 21
2095437 TGAAATTTTG
*
2095447 AATATTATTTTTTAAATATTAA
1 AATA-TATTTTTAAAATATTAA
2095469 ATATATATTTTTAATAATA-TAA
1 A-ATATATTTTTAA-AATATTAA
2095491 AATAT
1 AATAT
2095496 TTAAATATTT
Statistics
Matches: 24, Mismatches: 1, Indels: 5
0.80 0.03 0.17
Matches are distributed among these distances:
21 4 0.17
22 13 0.54
23 7 0.29
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (21 bp):
AATATATTTTTAAAATATTAA
Found at i:2095594 original size:14 final size:15
Alignment explanation
Indices: 2095569--2095601 Score: 59
Period size: 14 Copynumber: 2.3 Consensus size: 15
2095559 TTAATTTGTT
2095569 TTATAATATTTTAAA
1 TTATAATATTTTAAA
2095584 TTATAAT-TTTTAAA
1 TTATAATATTTTAAA
2095598 TTAT
1 TTAT
2095602 TTTTAGAGAT
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
14 11 0.61
15 7 0.39
ACGTcount: A:0.42, C:0.00, G:0.00, T:0.58
Consensus pattern (15 bp):
TTATAATATTTTAAA
Found at i:2095963 original size:20 final size:21
Alignment explanation
Indices: 2095919--2095978 Score: 70
Period size: 21 Copynumber: 2.8 Consensus size: 21
2095909 AAATCTTTAA
2095919 AAATAAT-TTAAAAATCATAATT
1 AAATAATATTAAAAAT-A-AATT
*
2095941 TAA-AATATTATAAAATAAATT
1 AAATAATATTA-AAAATAAATT
2095962 AAATAATATTAAAAATA
1 AAATAATATTAAAAATA
2095979 TTAAAAAACT
Statistics
Matches: 33, Mismatches: 2, Indels: 7
0.79 0.05 0.17
Matches are distributed among these distances:
21 15 0.45
22 13 0.39
23 5 0.15
ACGTcount: A:0.63, C:0.02, G:0.00, T:0.35
Consensus pattern (21 bp):
AAATAATATTAAAAATAAATT
Found at i:2095981 original size:19 final size:21
Alignment explanation
Indices: 2095935--2095983 Score: 59
Period size: 21 Copynumber: 2.4 Consensus size: 21
2095925 TTTAAAAATC
*
2095935 ATAATTTAA-AATATTATAAA
1 ATAATTAAATAATATTATAAA
2095955 ATAAATTAAATAATATTA-AAA
1 AT-AATTAAATAATATTATAAA
2095976 AT-ATTAAA
1 ATAATTAAA
2095984 AAACTAATAA
Statistics
Matches: 26, Mismatches: 1, Indels: 5
0.81 0.03 0.16
Matches are distributed among these distances:
19 6 0.23
20 2 0.08
21 11 0.42
22 7 0.27
ACGTcount: A:0.63, C:0.00, G:0.00, T:0.37
Consensus pattern (21 bp):
ATAATTAAATAATATTATAAA
Found at i:2095984 original size:9 final size:9
Alignment explanation
Indices: 2095942--2095985 Score: 52
Period size: 9 Copynumber: 4.4 Consensus size: 9
2095932 ATCATAATTT
2095942 AAAATATTA
1 AAAATATTA
2095951 TAAAATAAATTA
1 -AAAAT--ATTA
2095963 AATAATATTA
1 AA-AATATTA
2095973 AAAATATTA
1 AAAATATTA
2095982 AAAA
1 AAAA
2095986 ACTAATAATA
Statistics
Matches: 31, Mismatches: 0, Indels: 7
0.82 0.00 0.18
Matches are distributed among these distances:
9 11 0.35
10 11 0.35
11 2 0.06
12 7 0.23
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.32
Consensus pattern (9 bp):
AAAATATTA
Found at i:2096067 original size:20 final size:20
Alignment explanation
Indices: 2096019--2096078 Score: 56
Period size: 20 Copynumber: 3.1 Consensus size: 20
2096009 GTATCTTTAA
2096019 AATATTT-AAATAT-T-TTAT
1 AATATTTAAAATATATATT-T
* *
2096037 ATTATTAAAAATATATATTT
1 AATATTTAAAATATATATTT
2096057 AATATTTAAAA-ATAATATTT
1 AATATTTAAAATAT-ATATTT
2096077 AA
1 AA
2096079 AAAATAATAT
Statistics
Matches: 34, Mismatches: 4, Indels: 6
0.77 0.09 0.14
Matches are distributed among these distances:
18 5 0.15
19 8 0.24
20 19 0.56
21 2 0.06
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (20 bp):
AATATTTAAAATATATATTT
Found at i:2096072 original size:13 final size:13
Alignment explanation
Indices: 2096056--2096094 Score: 60
Period size: 13 Copynumber: 2.9 Consensus size: 13
2096046 AATATATATT
2096056 TAATATTTAAAAA
1 TAATATTTAAAAA
2096069 TAATATTTAAAAAA
1 TAATATTT-AAAAA
*
2096083 TAATATTCAAAA
1 TAATATTTAAAA
2096095 TTTAAAAAAA
Statistics
Matches: 24, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
13 12 0.50
14 12 0.50
ACGTcount: A:0.62, C:0.03, G:0.00, T:0.36
Consensus pattern (13 bp):
TAATATTTAAAAA
Found at i:2096095 original size:12 final size:14
Alignment explanation
Indices: 2096056--2096094 Score: 62
Period size: 14 Copynumber: 2.9 Consensus size: 14
2096046 AATATATATT
2096056 TAATATTT-AAAAA
1 TAATATTTAAAAAA
2096069 TAATATTTAAAAAA
1 TAATATTTAAAAAA
*
2096083 TAATATTCAAAA
1 TAATATTTAAAA
2096095 TTTAAAAAAA
Statistics
Matches: 24, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
13 8 0.33
14 16 0.67
ACGTcount: A:0.62, C:0.03, G:0.00, T:0.36
Consensus pattern (14 bp):
TAATATTTAAAAAA
Found at i:2096134 original size:65 final size:66
Alignment explanation
Indices: 2096044--2096194 Score: 184
Period size: 66 Copynumber: 2.3 Consensus size: 66
2096034 TATATTATTA
* *
2096044 AAAATATATATTTAATA-TTTAAAAATAATATTTAAA-AAATA-ATATTCAAAATTTAAAAAAAT
1 AAAATATATATTTAAAATTTTAAAAATAAT-TTCAAATAAATATATATTCAAAATTTAAAAAAAT
2096106 TC
65 TC
* * * * *
2096108 AAAATATATATTTAAAATTTTAAAAATAGTTTCAAATATATATATATTTAAAATTTAAAATATTT
1 AAAATATATATTTAAAATTTTAAAAATAATTTCAAATAAATATATATTCAAAATTTAAAAAAATT
2096173 C
66 C
*
2096174 -AAATATACATTTTAAAATTTT
1 AAAATATATA-TTTAAAATTTT
2096195 TAAATTTTTT
Statistics
Matches: 75, Mismatches: 8, Indels: 6
0.84 0.09 0.07
Matches are distributed among these distances:
64 21 0.28
65 23 0.31
66 31 0.41
ACGTcount: A:0.54, C:0.03, G:0.01, T:0.42
Consensus pattern (66 bp):
AAAATATATATTTAAAATTTTAAAAATAATTTCAAATAAATATATATTCAAAATTTAAAAAAATT
C
Found at i:2100087 original size:31 final size:30
Alignment explanation
Indices: 2100050--2100122 Score: 83
Period size: 30 Copynumber: 2.4 Consensus size: 30
2100040 ATTAGTAATA
* * *
2100050 ATAAAATTATATTTTAACTTTTTTTTAAATG
1 ATAAAATTATAATTTAAC-TGTTTTAAAATG
* *
2100081 ATAAAATTTTAATTTAACTGTTTTAAAATT
1 ATAAAATTATAATTTAACTGTTTTAAAATG
*
2100111 ATAAAAATATAA
1 ATAAAATTATAA
2100123 ACTATTAAAA
Statistics
Matches: 35, Mismatches: 7, Indels: 1
0.81 0.16 0.02
Matches are distributed among these distances:
30 19 0.54
31 16 0.46
ACGTcount: A:0.47, C:0.03, G:0.03, T:0.48
Consensus pattern (30 bp):
ATAAAATTATAATTTAACTGTTTTAAAATG
Found at i:2100399 original size:30 final size:30
Alignment explanation
Indices: 2100365--2100434 Score: 86
Period size: 30 Copynumber: 2.3 Consensus size: 30
2100355 TTAATAAAAG
* *
2100365 TAAAATTATATTTTGACTCTTTAAAAATGA
1 TAAAATTATAATTTAACTCTTTAAAAATGA
* * *
2100395 TAAAATTTTAATTTAACTCTTTAAAATTTA
1 TAAAATTATAATTTAACTCTTTAAAAATGA
*
2100425 TAAAAATATA
1 TAAAATTATA
2100435 GGTCATTAAA
Statistics
Matches: 33, Mismatches: 7, Indels: 0
0.82 0.17 0.00
Matches are distributed among these distances:
30 33 1.00
ACGTcount: A:0.47, C:0.06, G:0.03, T:0.44
Consensus pattern (30 bp):
TAAAATTATAATTTAACTCTTTAAAAATGA
Found at i:2106791 original size:10 final size:11
Alignment explanation
Indices: 2106772--2106804 Score: 50
Period size: 11 Copynumber: 3.1 Consensus size: 11
2106762 TAATATATAT
2106772 TTATTTTTAAA
1 TTATTTTTAAA
2106783 TTA-TTTTAAA
1 TTATTTTTAAA
*
2106793 CTATTTTTAAA
1 TTATTTTTAAA
2106804 T
1 T
2106805 AAGTCAAATC
Statistics
Matches: 19, Mismatches: 2, Indels: 2
0.83 0.09 0.09
Matches are distributed among these distances:
10 9 0.47
11 10 0.53
ACGTcount: A:0.36, C:0.03, G:0.00, T:0.61
Consensus pattern (11 bp):
TTATTTTTAAA
Found at i:2112842 original size:5 final size:5
Alignment explanation
Indices: 2112826--2112866 Score: 57
Period size: 5 Copynumber: 8.2 Consensus size: 5
2112816 CCTAGAGTAG
*
2112826 TATTA T-TTA TATTA TATTA TATAA TATTTA TATTA TATTA T
1 TATTA TATTA TATTA TATTA TATTA TA-TTA TATTA TATTA T
2112867 TTTAATATTT
Statistics
Matches: 32, Mismatches: 2, Indels: 4
0.84 0.05 0.11
Matches are distributed among these distances:
4 4 0.12
5 24 0.75
6 4 0.12
ACGTcount: A:0.39, C:0.00, G:0.00, T:0.61
Consensus pattern (5 bp):
TATTA
Found at i:2112845 original size:14 final size:14
Alignment explanation
Indices: 2112826--2112868 Score: 52
Period size: 14 Copynumber: 2.9 Consensus size: 14
2112816 CCTAGAGTAG
2112826 TATTAT-TTATATTA
1 TATTATATTAT-TTA
2112840 TATTATATAATATTTA
1 TATTATAT--TATTTA
2112856 TATTATATTATTT
1 TATTATATTATTT
2112869 TAATATTTAA
Statistics
Matches: 26, Mismatches: 0, Indels: 6
0.81 0.00 0.19
Matches are distributed among these distances:
14 11 0.42
15 1 0.04
16 11 0.42
17 3 0.12
ACGTcount: A:0.37, C:0.00, G:0.00, T:0.63
Consensus pattern (14 bp):
TATTATATTATTTA
Found at i:2112855 original size:21 final size:22
Alignment explanation
Indices: 2112829--2112877 Score: 82
Period size: 21 Copynumber: 2.3 Consensus size: 22
2112819 AGAGTAGTAT
2112829 TATTTATATTATATTA-TATAA
1 TATTTATATTATATTATTATAA
*
2112850 TATTTATATTATATTATTTTAA
1 TATTTATATTATATTATTATAA
2112872 TATTTA
1 TATTTA
2112878 ATAATTTTAT
Statistics
Matches: 26, Mismatches: 1, Indels: 1
0.93 0.04 0.04
Matches are distributed among these distances:
21 16 0.62
22 10 0.38
ACGTcount: A:0.39, C:0.00, G:0.00, T:0.61
Consensus pattern (22 bp):
TATTTATATTATATTATTATAA
Found at i:2112858 original size:16 final size:15
Alignment explanation
Indices: 2112837--2112888 Score: 61
Period size: 16 Copynumber: 3.3 Consensus size: 15
2112827 ATTATTTATA
2112837 TTATATTATATAATAT
1 TTATATTATATAAT-T
*
2112853 TTATATTATATTATT
1 TTATATTATATAATT
2112868 TTAATATT-TAATAATT
1 TT-ATATTAT-ATAATT
2112884 TTATA
1 TTATA
2112889 CATTTTTATT
Statistics
Matches: 32, Mismatches: 2, Indels: 5
0.82 0.05 0.13
Matches are distributed among these distances:
15 7 0.22
16 25 0.78
ACGTcount: A:0.40, C:0.00, G:0.00, T:0.60
Consensus pattern (15 bp):
TTATATTATATAATT
Found at i:2114981 original size:14 final size:14
Alignment explanation
Indices: 2114962--2115001 Score: 53
Period size: 14 Copynumber: 2.7 Consensus size: 14
2114952 GCCTTTATCT
*
2114962 ATCTATTTATCTAA
1 ATCTATATATCTAA
2114976 ATCTATATATCTACA
1 ATCTATATATCTA-A
2114991 TATCTATATAT
1 -ATCTATATAT
2115002 ATATATAGAA
Statistics
Matches: 23, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
14 12 0.52
15 1 0.04
16 10 0.43
ACGTcount: A:0.38, C:0.15, G:0.00, T:0.47
Consensus pattern (14 bp):
ATCTATATATCTAA
Found at i:2114987 original size:8 final size:8
Alignment explanation
Indices: 2114961--2115008 Score: 55
Period size: 8 Copynumber: 6.2 Consensus size: 8
2114951 TGCCTTTATC
*
2114961 TATCTATT
1 TATCTATA
2114969 TATCTA-A
1 TATCTATA
2114976 -ATCTATA
1 TATCTATA
*
2114983 TATCTACA
1 TATCTATA
2114991 TATCTATA
1 TATCTATA
*
2114999 TATATATA
1 TATCTATA
2115007 TA
1 TA
2115009 GAAAAGTAAG
Statistics
Matches: 34, Mismatches: 4, Indels: 4
0.81 0.10 0.10
Matches are distributed among these distances:
6 5 0.15
7 1 0.03
8 28 0.82
ACGTcount: A:0.40, C:0.12, G:0.00, T:0.48
Consensus pattern (8 bp):
TATCTATA
Found at i:2115730 original size:12 final size:12
Alignment explanation
Indices: 2115709--2115748 Score: 53
Period size: 12 Copynumber: 3.3 Consensus size: 12
2115699 GGGCCTTTTA
*
2115709 CAAAAATAAACC
1 CAAAATTAAACC
2115721 CAAAATTAAACC
1 CAAAATTAAACC
* *
2115733 CAATATTACACC
1 CAAAATTAAACC
2115745 CAAA
1 CAAA
2115749 TCCAACAGAT
Statistics
Matches: 24, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
12 24 1.00
ACGTcount: A:0.57, C:0.28, G:0.00, T:0.15
Consensus pattern (12 bp):
CAAAATTAAACC
Found at i:2116914 original size:3 final size:3
Alignment explanation
Indices: 2116906--2117006 Score: 64
Period size: 3 Copynumber: 32.3 Consensus size: 3
2116896 AATTTTGCAA
* * *
2116906 TAT TAT TAT TATT TAT TGT TACT TAT TAT TAT TAT TGT TAT GTACA TAT
1 TAT TAT TAT TA-T TAT TAT TA-T TAT TAT TAT TAT TAT TAT -TA-T TAT
* * *
2116955 TAT T-T ATAC TA- TACT TAA TAT TAT TAT TAT TAT TA- TATT TAC TAT
1 TAT TAT -TAT TAT TA-T TAT TAT TAT TAT TAT TAT TAT TA-T TAT TAT
2117000 TAT TAT T
1 TAT TAT T
2117007 TATAAATATT
Statistics
Matches: 77, Mismatches: 11, Indels: 20
0.71 0.10 0.19
Matches are distributed among these distances:
2 5 0.06
3 58 0.75
4 14 0.18
ACGTcount: A:0.32, C:0.05, G:0.03, T:0.60
Consensus pattern (3 bp):
TAT
Found at i:2116918 original size:23 final size:23
Alignment explanation
Indices: 2116892--2116958 Score: 57
Period size: 23 Copynumber: 2.9 Consensus size: 23
2116882 GTATTTGTAA
*
2116892 TATTAATT-TTGCAATATTATTAT
1 TATTAATTGTTAC-ATATTATTAT
* *
2116915 TATTTATTGTTACTTATTATTAT
1 TATTAATTGTTACATATTATTAT
* *
2116938 TATT-GTTATGTACATATTATT
1 TATTAATTGT-TACATATTATT
2116959 TATACTATAC
Statistics
Matches: 36, Mismatches: 6, Indels: 4
0.78 0.13 0.09
Matches are distributed among these distances:
22 3 0.08
23 30 0.83
24 3 0.08
ACGTcount: A:0.30, C:0.04, G:0.06, T:0.60
Consensus pattern (23 bp):
TATTAATTGTTACATATTATTAT
Found at i:2116979 original size:24 final size:24
Alignment explanation
Indices: 2116952--2117010 Score: 75
Period size: 24 Copynumber: 2.5 Consensus size: 24
2116942 GTTATGTACA
2116952 TATTATTTATACTATACTTAATAT
1 TATTATTTATACTATACTTAATAT
* * *
2116976 TATTA-TTATTATTATATTTACTAT
1 TATTATTTA-TACTATACTTAATAT
2117000 TATTATTTATA
1 TATTATTTATA
2117011 AATATTAGTG
Statistics
Matches: 30, Mismatches: 3, Indels: 4
0.81 0.08 0.11
Matches are distributed among these distances:
23 3 0.10
24 24 0.80
25 3 0.10
ACGTcount: A:0.36, C:0.05, G:0.00, T:0.59
Consensus pattern (24 bp):
TATTATTTATACTATACTTAATAT
Found at i:2117185 original size:9 final size:9
Alignment explanation
Indices: 2117173--2117202 Score: 51
Period size: 9 Copynumber: 3.3 Consensus size: 9
2117163 GTATTTCTAC
2117173 TATTATTGT
1 TATTATTGT
*
2117182 TATTATTAT
1 TATTATTGT
2117191 TATTATTGT
1 TATTATTGT
2117200 TAT
1 TAT
2117203 ATCCAATTTT
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
9 19 1.00
ACGTcount: A:0.27, C:0.00, G:0.07, T:0.67
Consensus pattern (9 bp):
TATTATTGT
Found at i:2119067 original size:25 final size:24
Alignment explanation
Indices: 2119016--2119072 Score: 60
Period size: 25 Copynumber: 2.3 Consensus size: 24
2119006 AATACTAATG
* **
2119016 ATTTTAAATTACTTTATATTATTT
1 ATTTTAAATTACTTTATAGTACCT
*
2119040 ATTTTAAATTGCTCTTATAGTACCT
1 ATTTTAAATTACT-TTATAGTACCT
*
2119065 ATTCTAAA
1 ATTTTAAA
2119073 CCTTTATATA
Statistics
Matches: 27, Mismatches: 5, Indels: 1
0.82 0.15 0.03
Matches are distributed among these distances:
24 12 0.44
25 15 0.56
ACGTcount: A:0.33, C:0.11, G:0.04, T:0.53
Consensus pattern (24 bp):
ATTTTAAATTACTTTATAGTACCT
Found at i:2119084 original size:2 final size:2
Alignment explanation
Indices: 2119077--2119105 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
2119067 TCTAAACCTT
2119077 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
2119106 TATGTATTTA
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:2120062 original size:10 final size:11
Alignment explanation
Indices: 2120038--2120084 Score: 62
Period size: 11 Copynumber: 4.4 Consensus size: 11
2120028 GGTTTCGACA
2120038 ATTATTATATT
1 ATTATTATATT
2120049 ATTATTAT-TT
1 ATTATTATATT
2120059 ATTATTATATT
1 ATTATTATATT
*
2120070 -TATATAATATT
1 AT-TATTATATT
2120081 ATTA
1 ATTA
2120085 ATAGGTACTT
Statistics
Matches: 32, Mismatches: 1, Indels: 6
0.82 0.03 0.15
Matches are distributed among these distances:
10 11 0.34
11 20 0.62
12 1 0.03
ACGTcount: A:0.38, C:0.00, G:0.00, T:0.62
Consensus pattern (11 bp):
ATTATTATATT
Found at i:2120066 original size:16 final size:17
Alignment explanation
Indices: 2120044--2120084 Score: 50
Period size: 16 Copynumber: 2.5 Consensus size: 17
2120034 GACAATTATT
*
2120044 ATATTATTA-TTATTTA
1 ATATTATTATTTATATA
*
2120060 TTATTA-TATTTATATA
1 ATATTATTATTTATATA
2120076 ATATTATTA
1 ATATTATTA
2120085 ATAGGTACTT
Statistics
Matches: 20, Mismatches: 3, Indels: 3
0.77 0.12 0.12
Matches are distributed among these distances:
15 2 0.10
16 16 0.80
17 2 0.10
ACGTcount: A:0.39, C:0.00, G:0.00, T:0.61
Consensus pattern (17 bp):
ATATTATTATTTATATA
Found at i:2120218 original size:21 final size:20
Alignment explanation
Indices: 2120175--2120218 Score: 52
Period size: 21 Copynumber: 2.1 Consensus size: 20
2120165 AACGCCATAT
* * *
2120175 TATGTATATATTTTTAATGC
1 TATGTATACATTTGTAATAC
2120195 TATGTATACACTTTGTAATAC
1 TATGTATACA-TTTGTAATAC
2120216 TAT
1 TAT
2120219 TATTATGTAT
Statistics
Matches: 20, Mismatches: 3, Indels: 1
0.83 0.12 0.04
Matches are distributed among these distances:
20 9 0.45
21 11 0.55
ACGTcount: A:0.32, C:0.09, G:0.09, T:0.50
Consensus pattern (20 bp):
TATGTATACATTTGTAATAC
Found at i:2120245 original size:25 final size:28
Alignment explanation
Indices: 2120195--2120250 Score: 66
Period size: 25 Copynumber: 2.1 Consensus size: 28
2120185 TTTTTAATGC
2120195 TATGTATACACTTTGTAATACTATTA-T
1 TATGTATACACTTTGTAATACTATTAGT
*
2120222 TATGTATATA-TTT-TAATA-TCATTAGT
1 TATGTATACACTTTGTAATACT-ATTAGT
2120248 TAT
1 TAT
2120251 ACATTTTTGT
Statistics
Matches: 26, Mismatches: 1, Indels: 5
0.81 0.03 0.16
Matches are distributed among these distances:
24 1 0.04
25 9 0.35
26 7 0.27
27 9 0.35
ACGTcount: A:0.34, C:0.07, G:0.07, T:0.52
Consensus pattern (28 bp):
TATGTATACACTTTGTAATACTATTAGT
Found at i:2120362 original size:26 final size:27
Alignment explanation
Indices: 2120333--2120387 Score: 67
Period size: 28 Copynumber: 2.0 Consensus size: 27
2120323 TTATCATATG
**
2120333 TATA-TATACTCTCAATATTATATTTT
1 TATAGTATACTCTCAATACCATATTTT
*
2120359 TATATGTATACTCTTAATACCATATTTT
1 TATA-GTATACTCTCAATACCATATTTT
2120387 T
1 T
2120388 CTTATTATTT
Statistics
Matches: 24, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
26 4 0.17
28 20 0.83
ACGTcount: A:0.33, C:0.13, G:0.02, T:0.53
Consensus pattern (27 bp):
TATAGTATACTCTCAATACCATATTTT
Found at i:2120555 original size:11 final size:11
Alignment explanation
Indices: 2120531--2120561 Score: 53
Period size: 11 Copynumber: 2.7 Consensus size: 11
2120521 ATTTATTTTA
2120531 TATATATATATG
1 TATATAT-TATG
2120543 TATATATTATG
1 TATATATTATG
2120554 TATATATT
1 TATATATT
2120562 TTAACATTAC
Statistics
Matches: 19, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
11 12 0.63
12 7 0.37
ACGTcount: A:0.39, C:0.00, G:0.06, T:0.55
Consensus pattern (11 bp):
TATATATTATG
Found at i:2120617 original size:2 final size:2
Alignment explanation
Indices: 2120612--2120683 Score: 87
Period size: 2 Copynumber: 36.5 Consensus size: 2
2120602 CTTCAAACAC
* *
2120612 TA TA TA TA -A TA TA TT TA TA -A CA CTA T- TA CTA 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
2120653 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
2120684 TTTACGTACA
Statistics
Matches: 62, Mismatches: 3, Indels: 10
0.83 0.04 0.13
Matches are distributed among these distances:
1 3 0.05
2 56 0.90
3 3 0.05
ACGTcount: A:0.47, C:0.04, G:0.00, T:0.49
Consensus pattern (2 bp):
TA
Found at i:2123225 original size:31 final size:30
Alignment explanation
Indices: 2123190--2123250 Score: 77
Period size: 31 Copynumber: 2.0 Consensus size: 30
2123180 ATTCGGGTTT
* * *
2123190 TTTTTAAAAAGTTGATGATTAAATTTAACTA
1 TTTTTAAAAAGCTGAAG-TCAAATTTAACTA
*
2123221 TTTTTTAAAAGCTGAAGTCAAATTTAACTA
1 TTTTTAAAAAGCTGAAGTCAAATTTAACTA
2123251 AAAAAAAGGA
Statistics
Matches: 26, Mismatches: 4, Indels: 1
0.84 0.13 0.03
Matches are distributed among these distances:
30 12 0.46
31 14 0.54
ACGTcount: A:0.41, C:0.07, G:0.10, T:0.43
Consensus pattern (30 bp):
TTTTTAAAAAGCTGAAGTCAAATTTAACTA
Found at i:2123448 original size:23 final size:22
Alignment explanation
Indices: 2123402--2123444 Score: 70
Period size: 22 Copynumber: 2.0 Consensus size: 22
2123392 GAAATACTGA
2123402 TTAAAACATGTTGAATTGTTAT
1 TTAAAACATGTTGAATTGTTAT
2123424 TTAAAA-AGTGTTGAATTGTTA
1 TTAAAACA-TGTTGAATTGTTA
2123445 ATTTTTTAAC
Statistics
Matches: 20, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
21 1 0.05
22 19 0.95
ACGTcount: A:0.37, C:0.02, G:0.16, T:0.44
Consensus pattern (22 bp):
TTAAAACATGTTGAATTGTTAT
Found at i:2124199 original size:43 final size:43
Alignment explanation
Indices: 2124143--2124317 Score: 206
Period size: 43 Copynumber: 3.8 Consensus size: 43
2124133 TTATTGGAAA
2124143 AAAAACGCCGCTAAAGGTCAAGGCTTTTAGCGGCGTTTGTGGG
1 AAAAACGCCGCTAAAGGTCAAGGCTTTTAGCGGCGTTTGTGGG
*
2124186 AAAAACGCCGCTAAAGGTCCGTTAAAGGTTAAGGCTTTTAGCGGCGTTTGTGGA
1 AAAAACGCCGCTAAAGGT-C----------AAGGCTTTTAGCGGCGTTTGTGGG
* *
2124240 AAAAACGCCGCTAAAGGTCAAGGCTTTTAGCGGCATTTGTTGG
1 AAAAACGCCGCTAAAGGTCAAGGCTTTTAGCGGCGTTTGTGGG
* *
2124283 AAAAGCGCCGCCAAAGGTCAAGGCTTTTAGCGGCG
1 AAAAACGCCGCTAAAGGTCAAGGCTTTTAGCGGCG
2124318 CTTTTTCTAC
Statistics
Matches: 114, Mismatches: 7, Indels: 22
0.80 0.05 0.15
Matches are distributed among these distances:
43 71 0.62
44 1 0.01
53 1 0.01
54 41 0.36
ACGTcount: A:0.27, C:0.19, G:0.30, T:0.23
Consensus pattern (43 bp):
AAAAACGCCGCTAAAGGTCAAGGCTTTTAGCGGCGTTTGTGGG
Done.