Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold125
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: 3608436
ACGTcount: A:0.34, C:0.16, G:0.16, T:0.34
Warning! 25 characters in sequence are not A, C, G, or T
File 11 of 18
Found at i:1746720 original size:12 final size:12
Alignment explanation
Indices: 1746688--1746727 Score: 64
Period size: 12 Copynumber: 3.4 Consensus size: 12
1746678 AAAATAGATC
*
1746688 AGAGAGAGAGAG
1 AGAGAGAGGGAG
1746700 AGAGAGAGGGAG
1 AGAGAGAGGGAG
1746712 AGAGAGAGGGAG
1 AGAGAGAGGGAG
1746724 -GAGA
1 AGAGA
1746728 TCTGGAGAGG
Statistics
Matches: 27, Mismatches: 1, Indels: 1
0.93 0.03 0.03
Matches are distributed among these distances:
11 4 0.15
12 23 0.85
ACGTcount: A:0.45, C:0.00, G:0.55, T:0.00
Consensus pattern (12 bp):
AGAGAGAGGGAG
Found at i:1746912 original size:4 final size:4
Alignment explanation
Indices: 1746896--1746929 Score: 50
Period size: 4 Copynumber: 8.2 Consensus size: 4
1746886 AACGGTGCGT
*
1746896 TTCC TTGCC TTCC TTCC TTCC TTCC TTCC GTCC T
1 TTCC TT-CC TTCC TTCC TTCC TTCC TTCC TTCC T
1746930 CCTCATTCTC
Statistics
Matches: 27, Mismatches: 2, Indels: 2
0.87 0.06 0.06
Matches are distributed among these distances:
4 23 0.85
5 4 0.15
ACGTcount: A:0.00, C:0.47, G:0.06, T:0.47
Consensus pattern (4 bp):
TTCC
Found at i:1747010 original size:3 final size:3
Alignment explanation
Indices: 1746998--1747046 Score: 82
Period size: 3 Copynumber: 16.3 Consensus size: 3
1746988 TGGACTTTTC
1746998 TCT T-T TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT TCCT
1 TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT T-CT
1747043 TCT T
1 TCT T
1747047 GTAATTACTG
Statistics
Matches: 44, Mismatches: 0, Indels: 4
0.92 0.00 0.08
Matches are distributed among these distances:
2 2 0.05
3 39 0.89
4 3 0.07
ACGTcount: A:0.00, C:0.33, G:0.00, T:0.67
Consensus pattern (3 bp):
TCT
Found at i:1749156 original size:21 final size:19
Alignment explanation
Indices: 1749110--1749156 Score: 51
Period size: 21 Copynumber: 2.4 Consensus size: 19
1749100 TTGATAAGTG
1749110 TATA-TATATATTTTAAAT
1 TATATTATATATTTTAAAT
* *
1749128 TTTTTTATATATTTATAAAAT
1 TATATTATATATTT-T-AAAT
1749149 TATATTAT
1 TATATTAT
1749157 CATACTCTAG
Statistics
Matches: 22, Mismatches: 4, Indels: 3
0.76 0.14 0.10
Matches are distributed among these distances:
18 2 0.09
19 9 0.41
20 1 0.05
21 10 0.45
ACGTcount: A:0.40, C:0.00, G:0.00, T:0.60
Consensus pattern (19 bp):
TATATTATATATTTTAAAT
Found at i:1757890 original size:2 final size:2
Alignment explanation
Indices: 1757885--1757913 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
1757875 CGAGAGATCG
1757885 GA GA GA GA GA GA GA GA GA GA GA GA GA GA G
1 GA GA GA GA GA GA GA GA GA GA GA GA GA GA G
1757914 CGAAAACCTC
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:0.52, T:0.00
Consensus pattern (2 bp):
GA
Found at i:1758716 original size:43 final size:43
Alignment explanation
Indices: 1758669--1758754 Score: 106
Period size: 42 Copynumber: 2.0 Consensus size: 43
1758659 CTATACATGC
*
1758669 AATTATTTTAATATTTTT-TACTAT-TTTTAATT-TTTATTAATTT
1 AATTA-TTTAAT-TTTTTATA-TATAATTTAATTATTTATTAATTT
*
1758712 AATTATTTAATTTTTTATATATAATTTAATTATTTATTTATTT
1 AATTATTTAATTTTTTATATATAATTTAATTATTTATTAATTT
1758755 TACTCACATA
Statistics
Matches: 38, Mismatches: 2, Indels: 6
0.83 0.04 0.13
Matches are distributed among these distances:
41 8 0.21
42 15 0.39
43 15 0.39
ACGTcount: A:0.33, C:0.01, G:0.00, T:0.66
Consensus pattern (43 bp):
AATTATTTAATTTTTTATATATAATTTAATTATTTATTAATTT
Found at i:1758736 original size:27 final size:27
Alignment explanation
Indices: 1758698--1758756 Score: 86
Period size: 27 Copynumber: 2.2 Consensus size: 27
1758688 ACTATTTTTA
1758698 ATTTT-TATTAATTTAATTATTTAATT
1 ATTTTATATTAATTTAATTATTTAATT
*
1758724 -TTTTATATATAATTTAATTATTTATTT
1 ATTTTATAT-TAATTTAATTATTTAATT
1758751 ATTTTA
1 ATTTTA
1758757 CTCACATAGT
Statistics
Matches: 29, Mismatches: 1, Indels: 4
0.85 0.03 0.12
Matches are distributed among these distances:
25 4 0.14
26 3 0.10
27 17 0.59
28 5 0.17
ACGTcount: A:0.34, C:0.00, G:0.00, T:0.66
Consensus pattern (27 bp):
ATTTTATATTAATTTAATTATTTAATT
Found at i:1758746 original size:8 final size:8
Alignment explanation
Indices: 1758694--1758754 Score: 54
Period size: 8 Copynumber: 7.4 Consensus size: 8
1758684 TTTTACTATT
1758694 TTTAATT-
1 TTTAATTA
1758701 TTT-ATTAA
1 TTTAATT-A
1758709 TTTAATTA
1 TTTAATTA
*
1758717 TTTAATTT
1 TTTAATTA
1758725 TTTATATATAA
1 TTTA-AT-T-A
1758736 TTTAATTA
1 TTTAATTA
*
1758744 TTTATTTA
1 TTTAATTA
1758752 TTT
1 TTT
1758755 TACTCACATA
Statistics
Matches: 45, Mismatches: 3, Indels: 11
0.76 0.05 0.19
Matches are distributed among these distances:
6 3 0.07
7 3 0.07
8 26 0.58
9 6 0.13
10 3 0.07
11 4 0.09
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (8 bp):
TTTAATTA
Found at i:1761654 original size:21 final size:21
Alignment explanation
Indices: 1761629--1761689 Score: 77
Period size: 21 Copynumber: 2.9 Consensus size: 21
1761619 GATTGGCCGT
*
1761629 AGGAGTTAATGATGCGGCAGC
1 AGGAGTTAATGATGCAGCAGC
* *
1761650 AGGAGTTGATGATGCAGTAGC
1 AGGAGTTAATGATGCAGCAGC
* *
1761671 AGGAGTTGACGATGCAGCA
1 AGGAGTTAATGATGCAGCA
1761690 TCAGAGGGTG
Statistics
Matches: 35, Mismatches: 5, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
21 35 1.00
ACGTcount: A:0.30, C:0.13, G:0.38, T:0.20
Consensus pattern (21 bp):
AGGAGTTAATGATGCAGCAGC
Found at i:1762923 original size:2 final size:2
Alignment explanation
Indices: 1762910--1762947 Score: 67
Period size: 2 Copynumber: 19.0 Consensus size: 2
1762900 AATAATACTA
*
1762910 AT AT AT AG 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
1762948 TACAGTTAAT
Statistics
Matches: 34, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
2 34 1.00
ACGTcount: A:0.50, C:0.00, G:0.03, T:0.47
Consensus pattern (2 bp):
AT
Found at i:1781158 original size:17 final size:18
Alignment explanation
Indices: 1781119--1781159 Score: 57
Period size: 18 Copynumber: 2.3 Consensus size: 18
1781109 ATAATTCACT
*
1781119 TTAAATAAAAATTTTATA
1 TTAAATAAAAATTTGATA
*
1781137 TTAAATAATAATTTGA-A
1 TTAAATAAAAATTTGATA
1781154 TTAAAT
1 TTAAAT
1781160 TCAATTAATT
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
17 7 0.33
18 14 0.67
ACGTcount: A:0.54, C:0.00, G:0.02, T:0.44
Consensus pattern (18 bp):
TTAAATAAAAATTTGATA
Found at i:1785049 original size:28 final size:28
Alignment explanation
Indices: 1784987--1785049 Score: 67
Period size: 28 Copynumber: 2.2 Consensus size: 28
1784977 TAAACTAACT
* *
1784987 AAATTAAATTTTAAATTCATGTATATGA
1 AAATTAAATTATAAATTCATCTATATGA
*
1785015 AATTTAAATTATAAATGTACA-CTATAT-A
1 AAATTAAATTATAAAT-T-CATCTATATGA
1785043 AAATTAA
1 AAATTAA
1785050 TGAAGAAGAC
Statistics
Matches: 29, Mismatches: 4, Indels: 4
0.78 0.11 0.11
Matches are distributed among these distances:
28 21 0.72
29 6 0.21
30 2 0.07
ACGTcount: A:0.51, C:0.05, G:0.05, T:0.40
Consensus pattern (28 bp):
AAATTAAATTATAAATTCATCTATATGA
Found at i:1785247 original size:2 final size:2
Alignment explanation
Indices: 1785240--1785283 Score: 88
Period size: 2 Copynumber: 22.0 Consensus size: 2
1785230 GAAAATATTT
1785240 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
1785282 TA
1 TA
1785284 AAATTAAGCT
Statistics
Matches: 42, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 42 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:1787889 original size:20 final size:19
Alignment explanation
Indices: 1787845--1787903 Score: 54
Period size: 19 Copynumber: 3.2 Consensus size: 19
1787835 CGAGATTATA
1787845 ATATTAAAAA-ATA-AAAT
1 ATATTAAAAATATATAAAT
1787862 A-ATATAAATAATATATAAAT
1 ATAT-TAAA-AATATATAAAT
*
1787882 ATATTAAACAT-TATATAAT
1 ATATTAAAAATATATA-AAT
1787901 ATA
1 ATA
1787904 AATTTCAACA
Statistics
Matches: 35, Mismatches: 1, Indels: 10
0.76 0.02 0.22
Matches are distributed among these distances:
16 2 0.06
17 5 0.14
18 6 0.17
19 11 0.31
20 9 0.26
21 2 0.06
ACGTcount: A:0.63, C:0.02, G:0.00, T:0.36
Consensus pattern (19 bp):
ATATTAAAAATATATAAAT
Found at i:1787899 original size:27 final size:27
Alignment explanation
Indices: 1787869--1787974 Score: 76
Period size: 27 Copynumber: 3.8 Consensus size: 27
1787859 AATAATATAA
*
1787869 ATAATATATAAATATATTAAACATTAT
1 ATAATATATAAATATATTAAAAATTAT
1787896 ATAATATAAATTTCAACATAT-TTAAAAATTAT
1 ATAATAT--A--T-AA-ATATATTAAAAATTAT
* *
1787928 ATAATATAT--ATCATTTTAAATATTATT
1 ATAATATATAAAT-ATATTAAAAATTA-T
*
1787955 ATAATATA-AAATATAATAAA
1 ATAATATATAAATATATTAAA
1787975 TATATAAAAA
Statistics
Matches: 64, Mismatches: 4, Indels: 22
0.71 0.04 0.24
Matches are distributed among these distances:
24 2 0.03
25 2 0.03
26 9 0.14
27 22 0.34
28 3 0.05
29 1 0.02
30 1 0.02
31 1 0.02
32 19 0.30
33 4 0.06
ACGTcount: A:0.55, C:0.04, G:0.00, T:0.42
Consensus pattern (27 bp):
ATAATATATAAATATATTAAAAATTAT
Found at i:1787993 original size:19 final size:19
Alignment explanation
Indices: 1787955--1788002 Score: 64
Period size: 18 Copynumber: 2.5 Consensus size: 19
1787945 AAATATTATT
1787955 ATAATATAAAATATAATAA
1 ATAATATAAAATATAATAA
1787974 AT-ATATAAAA-ATAATTTAA
1 ATAATATAAAATATAA--TAA
1787993 ATAATATAAA
1 ATAATATAAA
1788003 GTGATATTTT
Statistics
Matches: 26, Mismatches: 0, Indels: 5
0.84 0.00 0.16
Matches are distributed among these distances:
17 4 0.15
18 8 0.31
19 7 0.27
20 7 0.27
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (19 bp):
ATAATATAAAATATAATAA
Found at i:1789798 original size:24 final size:23
Alignment explanation
Indices: 1789746--1789800 Score: 58
Period size: 24 Copynumber: 2.3 Consensus size: 23
1789736 AATGATGATT
**
1789746 TTTTATTTTATTTTAAATATTTT
1 TTTTATTTTATTTTAAATATTAA
1789769 TATTTATTTTATGATTTAAA-ATTAA
1 T-TTTATTTTAT--TTTAAATATTAA
1789794 TTTTATT
1 TTTTATT
1789801 AGAAAATTTG
Statistics
Matches: 27, Mismatches: 2, Indels: 5
0.79 0.06 0.15
Matches are distributed among these distances:
23 1 0.04
24 16 0.59
25 4 0.15
26 6 0.22
ACGTcount: A:0.31, C:0.00, G:0.02, T:0.67
Consensus pattern (23 bp):
TTTTATTTTATTTTAAATATTAA
Found at i:1792086 original size:20 final size:22
Alignment explanation
Indices: 1792037--1792086 Score: 61
Period size: 20 Copynumber: 2.4 Consensus size: 22
1792027 TTTAAAAATT
1792037 ATTAATAAAAATAATATATTAA
1 ATTAATAAAAATAATATATTAA
*
1792059 A-TATATAAAAAT-AT-TTTTAA
1 ATTA-ATAAAAATAATATATTAA
1792079 ATTAATAA
1 ATTAATAA
1792087 TTCAAATAAT
Statistics
Matches: 25, Mismatches: 1, Indels: 6
0.78 0.03 0.19
Matches are distributed among these distances:
20 10 0.40
21 6 0.24
22 9 0.36
ACGTcount: A:0.60, C:0.00, G:0.00, T:0.40
Consensus pattern (22 bp):
ATTAATAAAAATAATATATTAA
Found at i:1792449 original size:24 final size:24
Alignment explanation
Indices: 1792375--1792451 Score: 68
Period size: 24 Copynumber: 3.0 Consensus size: 24
1792365 CACATTTATA
*
1792375 TTTATAAAAAAATTAAAATT-T-AAT
1 TTTATATAAAAATT--AATTATAAAT
1792399 TTTATATAAATATATTAATAATCATAAAT
1 TTTATATAAA-A-ATTAAT--T-ATAAAT
1792428 TTTATATAAAAATTAATTATAAAT
1 TTTATATAAAAATTAATTATAAAT
1792452 ACTAAAACAA
Statistics
Matches: 45, Mismatches: 1, Indels: 14
0.75 0.02 0.23
Matches are distributed among these distances:
24 18 0.40
25 2 0.04
26 4 0.09
27 6 0.13
28 2 0.04
29 13 0.29
ACGTcount: A:0.55, C:0.01, G:0.00, T:0.44
Consensus pattern (24 bp):
TTTATATAAAAATTAATTATAAAT
Found at i:1795156 original size:2 final size:2
Alignment explanation
Indices: 1795149--1795180 Score: 64
Period size: 2 Copynumber: 16.0 Consensus size: 2
1795139 CAATAGCAAA
1795149 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
1795181 TACTACATGC
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):
AT
Found at i:1795365 original size:29 final size:30
Alignment explanation
Indices: 1795301--1795378 Score: 81
Period size: 29 Copynumber: 2.7 Consensus size: 30
1795291 TTTTTACTGT
* * **
1795301 ATAATTTTATACG-TTAAATTAGATAATTA
1 ATAATTTAATAAGTTTAAATTAGATAAAAA
*
1795330 ATTATTTAATAAGTTTAAATTA-ATAAAAA
1 ATAATTTAATAAGTTTAAATTAGATAAAAA
*
1795359 ATAATTTAATTA-TTTAAATT
1 ATAATTTAATAAGTTTAAATT
1795379 TTAATAGTTC
Statistics
Matches: 41, Mismatches: 7, Indels: 3
0.80 0.14 0.06
Matches are distributed among these distances:
28 8 0.20
29 25 0.61
30 8 0.20
ACGTcount: A:0.49, C:0.01, G:0.04, T:0.46
Consensus pattern (30 bp):
ATAATTTAATAAGTTTAAATTAGATAAAAA
Found at i:1797049 original size:35 final size:38
Alignment explanation
Indices: 1796989--1797064 Score: 97
Period size: 35 Copynumber: 2.1 Consensus size: 38
1796979 ATCTTTGTAT
* *
1796989 TTTTATTATCTTTATATATTTTAATAATATTTAAA-TTA
1 TTTTATTATCTTTATATATATTAATAAT-TTAAAATTTA
1797027 TTTTA-TAT-TTT-TATATATTAATAATTTAAAATTTA
1 TTTTATTATCTTTATATATATTAATAATTTAAAATTTA
1797062 TTT
1 TTT
1797065 ATTTATTTAA
Statistics
Matches: 35, Mismatches: 2, Indels: 5
0.83 0.05 0.12
Matches are distributed among these distances:
34 5 0.14
35 19 0.54
36 3 0.09
37 3 0.09
38 5 0.14
ACGTcount: A:0.37, C:0.01, G:0.00, T:0.62
Consensus pattern (38 bp):
TTTTATTATCTTTATATATATTAATAATTTAAAATTTA
Found at i:1801605 original size:21 final size:21
Alignment explanation
Indices: 1801581--1801620 Score: 55
Period size: 21 Copynumber: 1.9 Consensus size: 21
1801571 CTATCCTCTT
1801581 TCAT-TTTAAGTGTTTAAACTC
1 TCATATTT-AGTGTTTAAACTC
*
1801602 TCATATTTCGTGTTTAAAC
1 TCATATTTAGTGTTTAAAC
1801621 ACAAACTAGG
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
21 14 0.82
22 3 0.18
ACGTcount: A:0.28, C:0.15, G:0.10, T:0.47
Consensus pattern (21 bp):
TCATATTTAGTGTTTAAACTC
Found at i:1802303 original size:2 final size:2
Alignment explanation
Indices: 1802298--1802333 Score: 54
Period size: 2 Copynumber: 18.0 Consensus size: 2
1802288 GAGAGAATTC
* *
1802298 AG AG AG GG AG AG AG AG AG AG AG AG AG AG AC AG AG AG
1 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG
1802334 GGAAGGAAGG
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:0.47, C:0.03, G:0.50, T:0.00
Consensus pattern (2 bp):
AG
Found at i:1804210 original size:38 final size:40
Alignment explanation
Indices: 1804121--1804211 Score: 118
Period size: 38 Copynumber: 2.4 Consensus size: 40
1804111 TTTTAAGTAC
1804121 AAAATAATAAA-ACATTAGTATTATTAATTATATTATAAAT
1 AAAATAATAAATA-ATTAGTATTATTAATTATATTATAAAT
* *
1804161 AAAAT-ACAAATAA-TATTATTATTAATTATATTAT-AAT
1 AAAATAATAAATAATTAGTATTATTAATTATATTATAAAT
*
1804198 CAAATAATAAATAA
1 AAAATAATAAATAA
1804212 GTTTTAAACT
Statistics
Matches: 45, Mismatches: 4, Indels: 6
0.82 0.07 0.11
Matches are distributed among these distances:
37 7 0.16
38 27 0.60
39 5 0.11
40 6 0.13
ACGTcount: A:0.57, C:0.03, G:0.01, T:0.38
Consensus pattern (40 bp):
AAAATAATAAATAATTAGTATTATTAATTATATTATAAAT
Found at i:1804529 original size:11 final size:11
Alignment explanation
Indices: 1804502--1804552 Score: 54
Period size: 10 Copynumber: 4.9 Consensus size: 11
1804492 ATGTTATAAT
*
1804502 TATTTTTAAAA
1 TATTTATAAAA
1804513 TA-TTATAAAA
1 TATTTATAAAA
*
1804523 TATTTATATAA
1 TATTTATAAAA
*
1804534 -ATTT-TAATA
1 TATTTATAAAA
1804543 TATTTATAAA
1 TATTTATAAA
1804553 TTCACATTAT
Statistics
Matches: 32, Mismatches: 5, Indels: 6
0.74 0.12 0.14
Matches are distributed among these distances:
9 3 0.09
10 17 0.53
11 12 0.38
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (11 bp):
TATTTATAAAA
Found at i:1804574 original size:11 final size:11
Alignment explanation
Indices: 1804522--1804608 Score: 51
Period size: 11 Copynumber: 8.0 Consensus size: 11
1804512 ATATTATAAA
1804522 ATATTTATA-T
1 ATATTTATATT
* *
1804532 AAATTT-TAAT
1 ATATTTATATT
1804542 ATATTTATA--
1 ATATTTATATT
* *
1804551 A-ATTCACATT
1 ATATTTATATT
1804561 ATATTTATATT
1 ATATTTATATT
1804572 ATATTTTATCAAAATT
1 ATA-TTTAT----ATT
1804588 ATATTTATATT
1 ATATTTATATT
1804599 ATATTT-TATT
1 ATATTTATATT
1804609 GAGATGTTAT
Statistics
Matches: 61, Mismatches: 6, Indels: 20
0.70 0.07 0.23
Matches are distributed among these distances:
8 5 0.08
9 3 0.05
10 16 0.26
11 21 0.34
12 5 0.08
15 5 0.08
16 6 0.10
ACGTcount: A:0.40, C:0.03, G:0.00, T:0.56
Consensus pattern (11 bp):
ATATTTATATT
Found at i:1805288 original size:27 final size:27
Alignment explanation
Indices: 1805232--1805288 Score: 64
Period size: 27 Copynumber: 2.1 Consensus size: 27
1805222 TTTAATTTTT
*
1805232 AATAAAATTTTAAATTTATAATATAAA
1 AATAAAATTTTAAATTTAAAATATAAA
*
1805259 AATAAATATTTT-ATTTTAAAAT-TAATA
1 AATAAA-ATTTTAAATTTAAAATATAA-A
1805286 AAT
1 AAT
1805289 TTATTAAAAT
Statistics
Matches: 26, Mismatches: 2, Indels: 4
0.81 0.06 0.12
Matches are distributed among these distances:
26 3 0.12
27 18 0.69
28 5 0.19
ACGTcount: A:0.56, C:0.00, G:0.00, T:0.44
Consensus pattern (27 bp):
AATAAAATTTTAAATTTAAAATATAAA
Found at i:1805651 original size:13 final size:13
Alignment explanation
Indices: 1805633--1805658 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
1805623 AAGGATCCTT
1805633 CCCTTTGCCTTTA
1 CCCTTTGCCTTTA
1805646 CCCTTTGCCTTTA
1 CCCTTTGCCTTTA
1805659 TATTTCATCC
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:0.08, C:0.38, G:0.08, T:0.46
Consensus pattern (13 bp):
CCCTTTGCCTTTA
Found at i:1805925 original size:9 final size:8
Alignment explanation
Indices: 1805910--1805936 Score: 54
Period size: 8 Copynumber: 3.4 Consensus size: 8
1805900 AGTGAAAGGG
1805910 CTTTTTTT
1 CTTTTTTT
1805918 CTTTTTTT
1 CTTTTTTT
1805926 CTTTTTTT
1 CTTTTTTT
1805934 CTT
1 CTT
1805937 CTTTCTGGTA
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
8 19 1.00
ACGTcount: A:0.00, C:0.15, G:0.00, T:0.85
Consensus pattern (8 bp):
CTTTTTTT
Found at i:1809441 original size:35 final size:35
Alignment explanation
Indices: 1809402--1809470 Score: 138
Period size: 35 Copynumber: 2.0 Consensus size: 35
1809392 AAATGCATAG
1809402 AGCAAAGCAATCAGTGATGCCAGAATTGTTCAAAT
1 AGCAAAGCAATCAGTGATGCCAGAATTGTTCAAAT
1809437 AGCAAAGCAATCAGTGATGCCAGAATTGTTCAAA
1 AGCAAAGCAATCAGTGATGCCAGAATTGTTCAAA
1809471 ACTCAATTAA
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
35 34 1.00
ACGTcount: A:0.41, C:0.17, G:0.20, T:0.22
Consensus pattern (35 bp):
AGCAAAGCAATCAGTGATGCCAGAATTGTTCAAAT
Found at i:1813466 original size:16 final size:16
Alignment explanation
Indices: 1813431--1813464 Score: 52
Period size: 16 Copynumber: 2.2 Consensus size: 16
1813421 AATAATTTAT
*
1813431 AAATGATTTGGACTCA
1 AAATGATTTGGAATCA
1813447 AAATGATTT-GAATCA
1 AAATGATTTGGAATCA
1813462 AAA
1 AAA
1813465 ATAATTTTAA
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
15 8 0.47
16 9 0.53
ACGTcount: A:0.47, C:0.09, G:0.15, T:0.29
Consensus pattern (16 bp):
AAATGATTTGGAATCA
Found at i:1813498 original size:16 final size:17
Alignment explanation
Indices: 1813462--1813499 Score: 53
Period size: 16 Copynumber: 2.4 Consensus size: 17
1813452 ATTTGAATCA
*
1813462 AAAATAATTTTAACTCT
1 AAAATAATTTAAACTCT
1813479 -AAATAATTTAAACT-T
1 AAAATAATTTAAACTCT
1813494 AAAATA
1 AAAATA
1813500 GCTCAAATTT
Statistics
Matches: 19, Mismatches: 1, Indels: 3
0.83 0.04 0.13
Matches are distributed among these distances:
15 1 0.05
16 18 0.95
ACGTcount: A:0.55, C:0.08, G:0.00, T:0.37
Consensus pattern (17 bp):
AAAATAATTTAAACTCT
Found at i:1817839 original size:16 final size:17
Alignment explanation
Indices: 1817813--1817846 Score: 61
Period size: 16 Copynumber: 2.1 Consensus size: 17
1817803 ATTTTTATTA
1817813 ATTATTTAAAAATTTAT
1 ATTATTTAAAAATTTAT
1817830 ATTA-TTAAAAATTTAT
1 ATTATTTAAAAATTTAT
1817846 A
1 A
1817847 AAAAATAATA
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
16 13 0.76
17 4 0.24
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (17 bp):
ATTATTTAAAAATTTAT
Found at i:1823991 original size:15 final size:15
Alignment explanation
Indices: 1823973--1824004 Score: 55
Period size: 15 Copynumber: 2.1 Consensus size: 15
1823963 AGAGAGGTAA
*
1823973 AAACAGATGGGAGAG
1 AAACAGATCGGAGAG
1823988 AAACAGATCGGAGAG
1 AAACAGATCGGAGAG
1824003 AA
1 AA
1824005 TAGCTTTTTA
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:0.50, C:0.09, G:0.34, T:0.06
Consensus pattern (15 bp):
AAACAGATCGGAGAG
Found at i:1824270 original size:24 final size:25
Alignment explanation
Indices: 1824231--1824279 Score: 73
Period size: 24 Copynumber: 2.0 Consensus size: 25
1824221 AAAAAATCTA
* *
1824231 TTAAAAATCAAGAAAT-TTAAAAAT
1 TTAAAAATAAAAAAATGTTAAAAAT
1824255 TTAAAAATAAAAAAATGTTAAAAAT
1 TTAAAAATAAAAAAATGTTAAAAAT
1824280 CTAGAAATCT
Statistics
Matches: 22, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
24 14 0.64
25 8 0.36
ACGTcount: A:0.65, C:0.02, G:0.04, T:0.29
Consensus pattern (25 bp):
TTAAAAATAAAAAAATGTTAAAAAT
Found at i:1825838 original size:18 final size:18
Alignment explanation
Indices: 1825812--1825846 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
1825802 TGTAAAGCTT
*
1825812 TTTGTATACTAGTAAGAA
1 TTTGAATACTAGTAAGAA
*
1825830 TTTGAATACTATTAAGA
1 TTTGAATACTAGTAAGA
1825847 TTAGTAGTGA
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:0.40, C:0.06, G:0.14, T:0.40
Consensus pattern (18 bp):
TTTGAATACTAGTAAGAA
Found at i:1833276 original size:21 final size:21
Alignment explanation
Indices: 1833250--1833289 Score: 64
Period size: 21 Copynumber: 1.9 Consensus size: 21
1833240 TAAAAAATTT
1833250 TATATAAAT-TTAATTATAAAA
1 TATATAAATATTAA-TATAAAA
1833271 TATATAAATATTAATATAA
1 TATATAAATATTAATATAA
1833290 TACTTTTTTA
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
21 14 0.78
22 4 0.22
ACGTcount: A:0.57, C:0.00, G:0.00, T:0.42
Consensus pattern (21 bp):
TATATAAATATTAATATAAAA
Found at i:1839167 original size:20 final size:20
Alignment explanation
Indices: 1839142--1839185 Score: 88
Period size: 20 Copynumber: 2.2 Consensus size: 20
1839132 AGGCTTTTAA
1839142 ATATGAGAATATATATACCC
1 ATATGAGAATATATATACCC
1839162 ATATGAGAATATATATACCC
1 ATATGAGAATATATATACCC
1839182 ATAT
1 ATAT
1839186 AGTAATGGGC
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 24 1.00
ACGTcount: A:0.45, C:0.14, G:0.09, T:0.32
Consensus pattern (20 bp):
ATATGAGAATATATATACCC
Found at i:1843784 original size:64 final size:66
Alignment explanation
Indices: 1843668--1843789 Score: 164
Period size: 64 Copynumber: 1.9 Consensus size: 66
1843658 CTAACACACT
1843668 TTTTTATCAAATATATTTAAAAATAAGAAATAAATAAATAAATAATATATTTT-TTATTAATTTT
1 TTTTTATCAAATATATTTAAAAATAAGAAATAAATAAATAAATAATATATTTTATTATTAATTTT
1843732 A
66 A
* *
1843733 TTTTTAT-AAATATATTTAATAAATAA-ATAA-ACATATATAAGATAAT-TATTTTATTAT
1 TTTTTATCAAATATATTTAA-AAATAAGA-AATAAATAAATAA-ATAATATATTTTATTAT
1843790 GATTATTATT
Statistics
Matches: 51, Mismatches: 2, Indels: 8
0.84 0.03 0.13
Matches are distributed among these distances:
64 27 0.53
65 24 0.47
ACGTcount: A:0.50, C:0.02, G:0.02, T:0.47
Consensus pattern (66 bp):
TTTTTATCAAATATATTTAAAAATAAGAAATAAATAAATAAATAATATATTTTATTATTAATTTT
A
Found at i:1852200 original size:2 final size:2
Alignment explanation
Indices: 1852193--1852221 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
1852183 ACACATGAAA
1852193 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
1852222 AATTACTGGT
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:1853709 original size:2 final size:2
Alignment explanation
Indices: 1853702--1853729 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
1853692 GGCTTTTTAG
1853702 CT CT CT CT CT CT CT CT CT CT CT CT CT CT
1 CT CT CT CT CT CT CT CT CT CT CT CT CT CT
1853730 GGCTCGCATC
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.00, C:0.50, G:0.00, T:0.50
Consensus pattern (2 bp):
CT
Found at i:1854114 original size:2 final size:2
Alignment explanation
Indices: 1854107--1854141 Score: 70
Period size: 2 Copynumber: 17.5 Consensus size: 2
1854097 GCCCTTGTTG
1854107 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1854142 CACAACGTAC
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 33 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:1857436 original size:22 final size:22
Alignment explanation
Indices: 1857408--1857462 Score: 73
Period size: 22 Copynumber: 2.7 Consensus size: 22
1857398 ATATATATAT
1857408 ATATATAAATTTAATCTTTAAA
1 ATATATAAATTTAATCTTTAAA
*
1857430 ATATATAAA-ATAA-CTTTAAA
1 ATATATAAATTTAATCTTTAAA
1857450 A-A-ATAAATTTAAT
1 ATATATAAATTTAAT
1857463 TGTTTTAAAC
Statistics
Matches: 29, Mismatches: 2, Indels: 6
0.78 0.05 0.16
Matches are distributed among these distances:
18 5 0.17
19 4 0.14
20 8 0.28
21 3 0.10
22 9 0.31
ACGTcount: A:0.56, C:0.04, G:0.00, T:0.40
Consensus pattern (22 bp):
ATATATAAATTTAATCTTTAAA
Found at i:1862034 original size:16 final size:16
Alignment explanation
Indices: 1861992--1862034 Score: 50
Period size: 16 Copynumber: 2.7 Consensus size: 16
1861982 AATCAATTAC
* *
1861992 AAAAATATAAATTTTA
1 AAAAATATTATTTTTA
* *
1862008 AATAATTTTATTTTTA
1 AAAAATATTATTTTTA
1862024 AAAAATATTAT
1 AAAAATATTAT
1862035 ATATAAATCA
Statistics
Matches: 21, Mismatches: 6, Indels: 0
0.78 0.22 0.00
Matches are distributed among these distances:
16 21 1.00
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (16 bp):
AAAAATATTATTTTTA
Found at i:1864778 original size:2 final size:2
Alignment explanation
Indices: 1864771--1864803 Score: 66
Period size: 2 Copynumber: 16.5 Consensus size: 2
1864761 TTTAACCCAA
1864771 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1864804 ATACATCAAA
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:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:1868628 original size:3 final size:3
Alignment explanation
Indices: 1868620--1868644 Score: 50
Period size: 3 Copynumber: 8.3 Consensus size: 3
1868610 ACCTAGCAAT
1868620 ATA ATA ATA ATA ATA ATA ATA ATA A
1 ATA ATA ATA ATA ATA ATA ATA ATA A
1868645 ATTATCTCAT
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 22 1.00
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.32
Consensus pattern (3 bp):
ATA
Found at i:1870593 original size:2 final size:2
Alignment explanation
Indices: 1870588--1870626 Score: 71
Period size: 2 Copynumber: 20.0 Consensus size: 2
1870578 TGTGTGTGTG
1870588 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T- TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1870627 GTGGATATTG
Statistics
Matches: 36, Mismatches: 0, Indels: 2
0.95 0.00 0.05
Matches are distributed among these distances:
1 1 0.03
2 35 0.97
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:1872973 original size:22 final size:24
Alignment explanation
Indices: 1872923--1872988 Score: 82
Period size: 22 Copynumber: 2.8 Consensus size: 24
1872913 TTGCAAGTAA
* *
1872923 TAAAAATAAAATAACAAATATTTAT
1 TAAAAATAAATTAA-AAATATTTAC
1872948 TAAAAATAAATTAAAAAT-TTT-C
1 TAAAAATAAATTAAAAATATTTAC
*
1872970 TAAAAATTAATTAAAAATA
1 TAAAAATAAATTAAAAATA
1872989 AAACTATGAT
Statistics
Matches: 37, Mismatches: 3, Indels: 4
0.84 0.07 0.09
Matches are distributed among these distances:
22 17 0.46
23 3 0.08
24 4 0.11
25 13 0.35
ACGTcount: A:0.64, C:0.03, G:0.00, T:0.33
Consensus pattern (24 bp):
TAAAAATAAATTAAAAATATTTAC
Found at i:1873940 original size:24 final size:24
Alignment explanation
Indices: 1873913--1873959 Score: 67
Period size: 24 Copynumber: 2.0 Consensus size: 24
1873903 TATTATTTTT
* *
1873913 AAACTGAATTGAACAAATAAATTG
1 AAACTGAATTAAAAAAATAAATTG
*
1873937 AAACTTAATTAAAAAAATAAATT
1 AAACTGAATTAAAAAAATAAATT
1873960 ATTTTATTTT
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
24 20 1.00
ACGTcount: A:0.60, C:0.06, G:0.06, T:0.28
Consensus pattern (24 bp):
AAACTGAATTAAAAAAATAAATTG
Found at i:1875365 original size:10 final size:11
Alignment explanation
Indices: 1875345--1875383 Score: 62
Period size: 11 Copynumber: 3.6 Consensus size: 11
1875335 TTTCGTCTGA
1875345 TAAATTTAAAT
1 TAAATTTAAAT
1875356 TAAA-TTAAAT
1 TAAATTTAAAT
1875366 TAAATTTAAAT
1 TAAATTTAAAT
*
1875377 AAAATTT
1 TAAATTT
1875384 TTTAAAATAA
Statistics
Matches: 26, Mismatches: 1, Indels: 2
0.90 0.03 0.07
Matches are distributed among these distances:
10 10 0.38
11 16 0.62
ACGTcount: A:0.56, C:0.00, G:0.00, T:0.44
Consensus pattern (11 bp):
TAAATTTAAAT
Found at i:1878138 original size:2 final size:2
Alignment explanation
Indices: 1878131--1878169 Score: 78
Period size: 2 Copynumber: 19.5 Consensus size: 2
1878121 TTATGTTTGG
1878131 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1878170 AAATATTAAA
Statistics
Matches: 37, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 37 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:1883485 original size:2 final size:2
Alignment explanation
Indices: 1883478--1883509 Score: 64
Period size: 2 Copynumber: 16.0 Consensus size: 2
1883468 AATCCAGTTG
1883478 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
1883510 TCATAACTTG
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):
AT
Found at i:1886998 original size:32 final size:34
Alignment explanation
Indices: 1886962--1887024 Score: 94
Period size: 34 Copynumber: 1.9 Consensus size: 34
1886952 TTCTTTAAAT
*
1886962 TATAATTA-ATAAT-CAAAAATATTTTTTAAAAA
1 TATAATTATAAAATACAAAAATATTTTTTAAAAA
*
1886994 TATAATTATAAAATATAAAAATATTTTTTAA
1 TATAATTATAAAATACAAAAATATTTTTTAA
1887025 TATTTTATTA
Statistics
Matches: 27, Mismatches: 2, Indels: 2
0.87 0.06 0.06
Matches are distributed among these distances:
32 8 0.30
33 4 0.15
34 15 0.56
ACGTcount: A:0.56, C:0.02, G:0.00, T:0.43
Consensus pattern (34 bp):
TATAATTATAAAATACAAAAATATTTTTTAAAAA
Found at i:1891835 original size:17 final size:17
Alignment explanation
Indices: 1891813--1891852 Score: 53
Period size: 17 Copynumber: 2.4 Consensus size: 17
1891803 TTTTAATATA
1891813 TTAAAATAATAACTTAT
1 TTAAAATAATAACTTAT
* * *
1891830 TTAAAATCATAATTTTT
1 TTAAAATAATAACTTAT
1891847 TTAAAA
1 TTAAAA
1891853 ATACTTTAAA
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
17 20 1.00
ACGTcount: A:0.50, C:0.05, G:0.00, T:0.45
Consensus pattern (17 bp):
TTAAAATAATAACTTAT
Found at i:1891968 original size:2 final size:2
Alignment explanation
Indices: 1891961--1891990 Score: 60
Period size: 2 Copynumber: 15.0 Consensus size: 2
1891951 TATCTCATAC
1891961 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
1891991 TAAAATAATT
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 28 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:1892253 original size:23 final size:22
Alignment explanation
Indices: 1892227--1892272 Score: 65
Period size: 23 Copynumber: 2.0 Consensus size: 22
1892217 TTTTTTTGTA
*
1892227 ATATTTATCTTATAATATTATAT
1 ATATTTATCTTAT-ATATGATAT
*
1892250 ATATTTATTTTATATATGATAT
1 ATATTTATCTTATATATGATAT
1892272 A
1 A
1892273 AATTATAAAA
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
22 9 0.43
23 12 0.57
ACGTcount: A:0.39, C:0.02, G:0.02, T:0.57
Consensus pattern (22 bp):
ATATTTATCTTATATATGATAT
Found at i:1892299 original size:15 final size:16
Alignment explanation
Indices: 1892268--1892303 Score: 56
Period size: 15 Copynumber: 2.3 Consensus size: 16
1892258 TTTATATATG
*
1892268 ATATAAATTATAAAAT
1 ATATAAATTAAAAAAT
1892284 ATATAAA-TAAAAAAT
1 ATATAAATTAAAAAAT
1892299 ATATA
1 ATATA
1892304 TTATATAATT
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
15 12 0.63
16 7 0.37
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (16 bp):
ATATAAATTAAAAAAT
Found at i:1893002 original size:2 final size:2
Alignment explanation
Indices: 1892995--1893043 Score: 73
Period size: 2 Copynumber: 24.5 Consensus size: 2
1892985 CTGAAATCTG
*
1892995 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT GT A- AGT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A-T AT
1893037 AT AT AT A
1 AT AT AT A
1893044 AAAATTTAAC
Statistics
Matches: 43, Mismatches: 2, Indels: 4
0.88 0.04 0.08
Matches are distributed among these distances:
1 1 0.02
2 41 0.95
3 1 0.02
ACGTcount: A:0.49, C:0.00, G:0.04, T:0.47
Consensus pattern (2 bp):
AT
Found at i:1898164 original size:2 final size:2
Alignment explanation
Indices: 1898159--1898187 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
1898149 GCTAAAATTA
1898159 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
1898188 ATTTACACCA
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:1899606 original size:13 final size:13
Alignment explanation
Indices: 1899583--1899613 Score: 55
Period size: 13 Copynumber: 2.5 Consensus size: 13
1899573 CAATTGATAT
1899583 ATTAA-CCCTATA
1 ATTAATCCCTATA
1899595 ATTAATCCCTATA
1 ATTAATCCCTATA
1899608 ATTAAT
1 ATTAAT
1899614 GATGCAAAAA
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
12 5 0.28
13 13 0.72
ACGTcount: A:0.42, C:0.19, G:0.00, T:0.39
Consensus pattern (13 bp):
ATTAATCCCTATA
Found at i:1900740 original size:40 final size:40
Alignment explanation
Indices: 1900689--1900769 Score: 153
Period size: 40 Copynumber: 2.0 Consensus size: 40
1900679 ATATATATAT
*
1900689 ACAGAGCCGTATGTGTGTATGTATATATGGACGGATGGAA
1 ACAGAGACGTATGTGTGTATGTATATATGGACGGATGGAA
1900729 ACAGAGACGTATGTGTGTATGTATATATGGACGGATGGAA
1 ACAGAGACGTATGTGTGTATGTATATATGGACGGATGGAA
1900769 A
1 A
1900770 TGTTTTAAAA
Statistics
Matches: 40, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
40 40 1.00
ACGTcount: A:0.32, C:0.09, G:0.32, T:0.27
Consensus pattern (40 bp):
ACAGAGACGTATGTGTGTATGTATATATGGACGGATGGAA
Found at i:1900819 original size:22 final size:24
Alignment explanation
Indices: 1900794--1900838 Score: 76
Period size: 22 Copynumber: 2.0 Consensus size: 24
1900784 TGTATTTTTT
1900794 TAAAAAAATTATA-AT-TTAAAAA
1 TAAAAAAATTATATATATTAAAAA
1900816 TAAAAAAATTATATATATTAAAA
1 TAAAAAAATTATATATATTAAAA
1900839 TTTAAAATTT
Statistics
Matches: 21, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
22 13 0.62
23 2 0.10
24 6 0.29
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (24 bp):
TAAAAAAATTATATATATTAAAAA
Found at i:1909983 original size:2 final size:2
Alignment explanation
Indices: 1909976--1910017 Score: 84
Period size: 2 Copynumber: 21.0 Consensus size: 2
1909966 TGATTCTTTA
1909976 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC
1 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC
1910018 AGTTTCTTAT
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:0.00, C:0.50, G:0.00, T:0.50
Consensus pattern (2 bp):
TC
Found at i:1910198 original size:2 final size:2
Alignment explanation
Indices: 1910191--1910233 Score: 86
Period size: 2 Copynumber: 21.5 Consensus size: 2
1910181 AACAATTGTG
1910191 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
1910233 T
1 T
1910234 TTGGAATATT
Statistics
Matches: 41, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 41 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:1910733 original size:2 final size:2
Alignment explanation
Indices: 1910726--1910751 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
1910716 CTCCTTACAA
1910726 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
1910752 GCATGTATGT
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 24 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:1910962 original size:266 final size:268
Alignment explanation
Indices: 1910472--1910979 Score: 779
Period size: 266 Copynumber: 1.9 Consensus size: 268
1910462 ACAGATGAAT
* * * *
1910472 TATATATATATTATGTATGTATGTATGATAATGCATTGAAACTTGTATATTTATATGCTCTACCT
1 TATATATATATCATGTATGTATGTATAATAATGCATTGAAAATTGTATATCTATATGCTCTACCT
* * *
1910537 CAGAAGTAATAGTAGCATATTAATATTATTGCTGAAATACTGGTCATAGAATTTAAGATGCATGA
66 CAGAAG-AATAATAGCATATTAATATTAATGCTGAAATACTAGTCATAGAATTTAAGATGCATGA
* * ** *
1910602 ATGTCCAATGAACAAGATAGCATGTGAAATGCATTGATTGTGTTTTTCTTCCACTTTTTTTTTTC
130 ATGTACAATGAACAAGATAGCATGTGAAATGAATTGATTGTGCATTTCTTCCACTTTTTTTCTTC
*
1910667 CTCTTTGGCCACAGTAGTGGAGGAAAGTGTTTAATGATTAGACTCATATCTCCTTACAAATATAT
195 CTCTTTAGCCACAGTAGTGGAGGAAAGTGTTTAATGATTAGACTCATATCTCCTTACAAATATAT
1910732 ATATATATA
260 ATATATATA
* *
1910741 TATATATATATGCATGTATGTATGTATAATAATGCGTTGAAAATTGTATATCTGTATGCTCTACC
1 TATATATATAT-CATGTATGTATGTATAATAATGCATTGAAAATTGTATATCTATATGCTCTACC
* * * *
1910806 TCAGAA-AA-AATGGCATATTAA-ATTAATGTTGGAATACTAGTCATGGAATTTAAGATGCATGA
65 TCAGAAGAATAATAGCATATTAATATTAATGCTGAAATACTAGTCATAGAATTTAAGATGCATGA
1910868 ATGTACAATGAACAAGATAGCATGTGAAATGAATTGATTGTGCATTTCTTCCACTTTTTTTCTTC
130 ATGTACAATGAACAAGATAGCATGTGAAATGAATTGATTGTGCATTTCTTCCACTTTTTTTCTTC
* * *
1910933 CTCTTTAGTCACATTAGTGTAGGAAAGTGTTTAATGATTAGACTCAT
195 CTCTTTAGCCACAGTAGTGGAGGAAAGTGTTTAATGATTAGACTCAT
1910980 GGCTTCTTAC
Statistics
Matches: 216, Mismatches: 22, Indels: 5
0.89 0.09 0.02
Matches are distributed among these distances:
266 139 0.64
267 11 0.05
268 2 0.01
269 11 0.05
270 53 0.25
ACGTcount: A:0.33, C:0.12, G:0.16, T:0.39
Consensus pattern (268 bp):
TATATATATATCATGTATGTATGTATAATAATGCATTGAAAATTGTATATCTATATGCTCTACCT
CAGAAGAATAATAGCATATTAATATTAATGCTGAAATACTAGTCATAGAATTTAAGATGCATGAA
TGTACAATGAACAAGATAGCATGTGAAATGAATTGATTGTGCATTTCTTCCACTTTTTTTCTTCC
TCTTTAGCCACAGTAGTGGAGGAAAGTGTTTAATGATTAGACTCATATCTCCTTACAAATATATA
TATATATA
Found at i:1913701 original size:14 final size:15
Alignment explanation
Indices: 1913675--1913719 Score: 58
Period size: 15 Copynumber: 3.1 Consensus size: 15
1913665 TAAAAATAAA
1913675 AAAATTATAAATATT
1 AAAATTATAAATATT
1913690 AAAATT-TAAATA-T
1 AAAATTATAAATATT
*
1913703 AAATTTATTAAATATT
1 AAAATTA-TAAATATT
1913719 A
1 A
1913720 TATTTCAATA
Statistics
Matches: 26, Mismatches: 1, Indels: 5
0.81 0.03 0.16
Matches are distributed among these distances:
13 6 0.23
14 6 0.23
15 12 0.46
16 2 0.08
ACGTcount: A:0.58, C:0.00, G:0.00, T:0.42
Consensus pattern (15 bp):
AAAATTATAAATATT
Found at i:1913783 original size:16 final size:16
Alignment explanation
Indices: 1913762--1913795 Score: 68
Period size: 16 Copynumber: 2.1 Consensus size: 16
1913752 TTAATTTCAT
1913762 TTCGAGCTCATCAAGC
1 TTCGAGCTCATCAAGC
1913778 TTCGAGCTCATCAAGC
1 TTCGAGCTCATCAAGC
1913794 TT
1 TT
1913796 ACTGATGAGC
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 18 1.00
ACGTcount: A:0.24, C:0.29, G:0.18, T:0.29
Consensus pattern (16 bp):
TTCGAGCTCATCAAGC
Found at i:1914922 original size:2 final size:2
Alignment explanation
Indices: 1914915--1914944 Score: 60
Period size: 2 Copynumber: 15.0 Consensus size: 2
1914905 CAGTTCAGTT
1914915 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
1914945 AAATCAGGAG
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 28 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:1921501 original size:15 final size:15
Alignment explanation
Indices: 1921481--1921572 Score: 62
Period size: 17 Copynumber: 5.5 Consensus size: 15
1921471 ATTATTTATG
1921481 ATATAAATAAATATT
1 ATATAAATAAATATT
1921496 ATATAAAATAAAATATAAT
1 ATAT-AAAT-AAATAT--T
1921515 ATATAAAAATATAAATATT
1 ATAT---AA-ATAAATATT
1921534 ATAATAATATATAATATT
1 AT-ATAA-ATA-AATATT
*
1921552 -TA-AAATAAATATA
1 ATATAAATAAATATT
1921565 ATATAAAT
1 ATATAAAT
1921573 TATTAATATA
Statistics
Matches: 65, Mismatches: 1, Indels: 22
0.74 0.01 0.25
Matches are distributed among these distances:
13 5 0.08
14 5 0.08
15 10 0.15
16 5 0.08
17 13 0.20
18 6 0.09
19 8 0.12
20 2 0.03
21 9 0.14
22 2 0.03
ACGTcount: A:0.63, C:0.00, G:0.00, T:0.37
Consensus pattern (15 bp):
ATATAAATAAATATT
Found at i:1921509 original size:21 final size:21
Alignment explanation
Indices: 1921481--1921589 Score: 75
Period size: 21 Copynumber: 5.1 Consensus size: 21
1921471 ATTATTTATG
1921481 ATATAAATA-AATATTATATAAA
1 ATATAAATATAATA-TATA-AAA
1921503 ATA-AAATATAATATATAAAA
1 ATATAAATATAATATATAAAA
* *
1921523 ATATAAATATTATA-AT-AAT
1 ATATAAATATAATATATAAAA
* *
1921542 ATATAATATTTAAAATA-AATATA
1 ATATAA-ATATAATATATAA-A-A
*
1921565 ATATAAATTATTAATATATTAAA
1 ATATAAA-TA-TAATATATAAAA
1921588 AT
1 AT
1921590 TTATAATAAA
Statistics
Matches: 68, Mismatches: 9, Indels: 19
0.71 0.09 0.20
Matches are distributed among these distances:
19 8 0.12
20 13 0.19
21 20 0.29
22 9 0.13
23 10 0.15
24 7 0.10
25 1 0.01
ACGTcount: A:0.61, C:0.00, G:0.00, T:0.39
Consensus pattern (21 bp):
ATATAAATATAATATATAAAA
Found at i:1921516 original size:5 final size:5
Alignment explanation
Indices: 1921481--1921655 Score: 68
Period size: 5 Copynumber: 36.2 Consensus size: 5
1921471 ATTATTTATG
* * * *
1921481 ATATA A-ATA A-ATA TTAT- ATAAA ATAAA ATATA ATAT- ATAAAA ATATA
1 ATATA ATATA ATATA ATATA ATATA ATATA ATATA ATATA AT-ATA ATATA
* * * *
1921528 A-ATA TTATA ATA-A TATATA ATAT- TTAAA ATA-A ATATA ATATA A-ATT
1 ATATA ATATA ATATA -ATATA ATATA ATATA ATATA ATATA ATATA ATATA
* * * * * * *
1921574 AT-TA ATATA TTAAA ATTTATA ATAAA AAATA AAATA TTTTTA ATATA
1 ATATA ATATA ATATA A--TATA ATATA ATATA ATATA -ATATA ATATA
*
1921621 ATTATA ATATA ATAAA ATA-A ATA-A ATATA ATATA A
1 A-TATA ATATA ATATA ATATA ATATA ATATA ATATA A
1921656 AAAATCAATT
Statistics
Matches: 128, Mismatches: 26, Indels: 32
0.69 0.14 0.17
Matches are distributed among these distances:
4 35 0.27
5 79 0.62
6 10 0.08
7 4 0.03
ACGTcount: A:0.62, C:0.00, G:0.00, T:0.38
Consensus pattern (5 bp):
ATATA
Found at i:1921519 original size:19 final size:19
Alignment explanation
Indices: 1921495--1921569 Score: 79
Period size: 18 Copynumber: 4.2 Consensus size: 19
1921485 AAATAAATAT
1921495 TATATAAAATAAAATATAA
1 TATATAAAATAAAATATAA
*
1921514 TATAT-AAA-AATATA-AA
1 TATATAAAATAAAATATAA
* *
1921530 TAT-TATAATAATATATAA
1 TATATAAAATAAAATATAA
*
1921548 TATTTAAAAT-AAATATAA
1 TATATAAAATAAAATATAA
1921566 TATA
1 TATA
1921570 AATTATTAAT
Statistics
Matches: 47, Mismatches: 5, Indels: 9
0.77 0.08 0.15
Matches are distributed among these distances:
15 1 0.02
16 7 0.15
17 11 0.23
18 18 0.38
19 10 0.21
ACGTcount: A:0.63, C:0.00, G:0.00, T:0.37
Consensus pattern (19 bp):
TATATAAAATAAAATATAA
Found at i:1921519 original size:34 final size:34
Alignment explanation
Indices: 1921481--1921571 Score: 105
Period size: 34 Copynumber: 2.6 Consensus size: 34
1921471 ATTATTTATG
*
1921481 ATATAAATAAATATTATATAAAATAAAATATAAT
1 ATATAAATAAATATAATATAAAATAAAATATAAT
* *
1921515 ATAT-AA-AAATATAAATATTATAATAATATATAAT
1 ATATAAATAAATAT-AATA-TAAAATAAAATATAAT
*
1921549 ATTTAAAATAAATATAATATAAA
1 ATAT-AAATAAATATAATATAAA
1921572 TTATTAATAT
Statistics
Matches: 47, Mismatches: 5, Indels: 9
0.77 0.08 0.15
Matches are distributed among these distances:
32 6 0.13
33 5 0.11
34 21 0.45
35 3 0.06
36 6 0.13
37 6 0.13
ACGTcount: A:0.64, C:0.00, G:0.00, T:0.36
Consensus pattern (34 bp):
ATATAAATAAATATAATATAAAATAAAATATAAT
Found at i:1921526 original size:27 final size:26
Alignment explanation
Indices: 1921496--1921569 Score: 80
Period size: 27 Copynumber: 2.8 Consensus size: 26
1921486 AATAAATATT
1921496 ATATAAAATAAAATATAATATATAAA
1 ATATAAAATAAAATATAATATATAAA
** *
1921522 A-ATATAAATATTATAATAATATATAAT
1 ATATA-AAATAAAAT-ATAATATATAAA
*
1921549 ATTTAAAAT-AAATATAATATA
1 ATATAAAATAAAATATAATATA
1921570 AATTATTAAT
Statistics
Matches: 39, Mismatches: 6, Indels: 7
0.75 0.12 0.13
Matches are distributed among these distances:
25 11 0.28
26 10 0.26
27 16 0.41
28 2 0.05
ACGTcount: A:0.64, C:0.00, G:0.00, T:0.36
Consensus pattern (26 bp):
ATATAAAATAAAATATAATATATAAA
Found at i:1921563 original size:31 final size:31
Alignment explanation
Indices: 1921496--1921629 Score: 98
Period size: 30 Copynumber: 4.3 Consensus size: 31
1921486 AATAAATATT
*
1921496 ATATAA-AATAAAATATAATATATAAAAATATAA
1 ATATAATAAT-AAATATAATATAT-TAAA-ATAA
*
1921529 ATATTATAATAATATATAATAT-TTAAAATAA
1 ATATAATAATAA-ATATAATATATTAAAATAA
1921560 ATATAAT-ATAAATTATTAATATATTAAAAT--
1 ATATAATAATAAA-TA-TAATATATTAAAATAA
* * * * *
1921590 TTATAATAAAAAATAAAATATTTTTAATATAA
1 ATATAATAATAAATATAATA-TATTAAAATAA
*
1921622 TTATAATA
1 ATATAATA
1921630 TAATAAAATA
Statistics
Matches: 84, Mismatches: 8, Indels: 19
0.76 0.07 0.17
Matches are distributed among these distances:
29 5 0.06
30 21 0.25
31 20 0.24
32 18 0.21
33 8 0.10
34 12 0.14
ACGTcount: A:0.60, C:0.00, G:0.00, T:0.40
Consensus pattern (31 bp):
ATATAATAATAAATATAATATATTAAAATAA
Found at i:1921649 original size:23 final size:22
Alignment explanation
Indices: 1921618--1921660 Score: 68
Period size: 23 Copynumber: 1.9 Consensus size: 22
1921608 TATTTTTAAT
*
1921618 ATAATTATAATATAATAAAATAA
1 ATAAATATAATATAA-AAAATAA
1921641 ATAAATATAATATAAAAAAT
1 ATAAATATAATATAAAAAAT
1921661 CAATTACCAT
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
22 5 0.26
23 14 0.74
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (22 bp):
ATAAATATAATATAAAAAATAA
Found at i:1923296 original size:18 final size:19
Alignment explanation
Indices: 1923258--1923316 Score: 66
Period size: 19 Copynumber: 3.1 Consensus size: 19
1923248 TTAATATTTA
* *
1923258 AATATATAAATTATTAATTT
1 AATATATATATTATT-TTTT
*
1923278 AATATTTATA-TATTTTTT
1 AATATATATATTATTTTTT
*
1923296 ATTATATATATTATTTTTT
1 AATATATATATTATTTTTT
1923315 AA
1 AA
1923317 AATTAATATT
Statistics
Matches: 32, Mismatches: 6, Indels: 3
0.78 0.15 0.07
Matches are distributed among these distances:
18 11 0.34
19 13 0.41
20 8 0.25
ACGTcount: A:0.41, C:0.00, G:0.00, T:0.59
Consensus pattern (19 bp):
AATATATATATTATTTTTT
Found at i:1923305 original size:16 final size:16
Alignment explanation
Indices: 1923280--1923312 Score: 50
Period size: 16 Copynumber: 2.1 Consensus size: 16
1923270 ATTAATTTAA
1923280 TATTTATATATT-TTT
1 TATTTATATATTATTT
1923295 TATTATATATATTATTT
1 TATT-TATATATTATTT
1923312 T
1 T
1923313 TTAAAATTAA
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
15 4 0.25
16 8 0.50
17 4 0.25
ACGTcount: A:0.30, C:0.00, G:0.00, T:0.70
Consensus pattern (16 bp):
TATTTATATATTATTT
Found at i:1923395 original size:16 final size:16
Alignment explanation
Indices: 1923374--1923417 Score: 61
Period size: 19 Copynumber: 2.6 Consensus size: 16
1923364 AAAACTTAAT
1923374 ATGTCATAAAAATATA
1 ATGTCATAAAAATATA
1923390 ATGTCATAATAAAAATATA
1 ATGTC---ATAAAAATATA
1923409 ATGTCATAA
1 ATGTCATAA
1923418 TAAACATAAA
Statistics
Matches: 25, Mismatches: 0, Indels: 6
0.81 0.00 0.19
Matches are distributed among these distances:
16 9 0.36
19 16 0.64
ACGTcount: A:0.55, C:0.07, G:0.07, T:0.32
Consensus pattern (16 bp):
ATGTCATAAAAATATA
Found at i:1923401 original size:19 final size:19
Alignment explanation
Indices: 1923379--1923421 Score: 86
Period size: 19 Copynumber: 2.3 Consensus size: 19
1923369 TTAATATGTC
1923379 ATAAAAATATAATGTCATA
1 ATAAAAATATAATGTCATA
1923398 ATAAAAATATAATGTCATA
1 ATAAAAATATAATGTCATA
1923417 ATAAA
1 ATAAA
1923422 CATAAAAAAA
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 24 1.00
ACGTcount: A:0.60, C:0.05, G:0.05, T:0.30
Consensus pattern (19 bp):
ATAAAAATATAATGTCATA
Found at i:1923534 original size:24 final size:21
Alignment explanation
Indices: 1923503--1923546 Score: 61
Period size: 24 Copynumber: 2.0 Consensus size: 21
1923493 TATCAATTCA
1923503 AAAAATTAATATATATAATATAAT
1 AAAAATTAA-ATAT-TAA-ATAAT
1923527 AAAAATTAAATATTAAATAA
1 AAAAATTAAATATTAAATAA
1923547 ATATTTTTTA
Statistics
Matches: 20, Mismatches: 0, Indels: 3
0.87 0.00 0.13
Matches are distributed among these distances:
21 4 0.20
22 3 0.15
23 4 0.20
24 9 0.45
ACGTcount: A:0.66, C:0.00, G:0.00, T:0.34
Consensus pattern (21 bp):
AAAAATTAAATATTAAATAAT
Found at i:1923961 original size:12 final size:12
Alignment explanation
Indices: 1923944--1923980 Score: 51
Period size: 12 Copynumber: 3.2 Consensus size: 12
1923934 TTTAAATTTA
1923944 TATAATATAAAT
1 TATAATATAAAT
1923956 TATAATATAAA-
1 TATAATATAAAT
1923967 -ATAATATAATAT
1 TATAATATAA-AT
1923979 TA
1 TA
1923981 AAATTTAATA
Statistics
Matches: 22, Mismatches: 0, Indels: 5
0.81 0.00 0.19
Matches are distributed among these distances:
10 9 0.41
11 1 0.05
12 11 0.50
13 1 0.05
ACGTcount: A:0.59, C:0.00, G:0.00, T:0.41
Consensus pattern (12 bp):
TATAATATAAAT
Found at i:1923972 original size:10 final size:11
Alignment explanation
Indices: 1923943--1924002 Score: 51
Period size: 10 Copynumber: 5.9 Consensus size: 11
1923933 TTTTAAATTT
1923943 ATATAATATAA
1 ATATAATATAA
1923954 ATTATAATATAA
1 A-TATAATATAA
1923966 A-ATAATAT-A
1 ATATAATATAA
1923975 ATAT--TA-AA
1 ATATAATATAA
*
1923983 ATTTAATA-AA
1 ATATAATATAA
*
1923993 ATATTATATA
1 ATATAATATA
1924003 TATTTTTTAT
Statistics
Matches: 40, Mismatches: 3, Indels: 12
0.73 0.05 0.22
Matches are distributed among these distances:
8 6 0.15
9 2 0.05
10 19 0.47
11 2 0.05
12 11 0.28
ACGTcount: A:0.60, C:0.00, G:0.00, T:0.40
Consensus pattern (11 bp):
ATATAATATAA
Found at i:1931882 original size:32 final size:32
Alignment explanation
Indices: 1931845--1931907 Score: 126
Period size: 32 Copynumber: 2.0 Consensus size: 32
1931835 ATATATTAAG
1931845 GAATAAATTATTAATTTTACTTATAAAATTTT
1 GAATAAATTATTAATTTTACTTATAAAATTTT
1931877 GAATAAATTATTAATTTTACTTATAAAATTT
1 GAATAAATTATTAATTTTACTTATAAAATTT
1931908 AAAAATTTTG
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
32 31 1.00
ACGTcount: A:0.44, C:0.03, G:0.03, T:0.49
Consensus pattern (32 bp):
GAATAAATTATTAATTTTACTTATAAAATTTT
Found at i:1932464 original size:3 final size:3
Alignment explanation
Indices: 1932456--1932480 Score: 50
Period size: 3 Copynumber: 8.3 Consensus size: 3
1932446 TTATTTTGTA
1932456 AAT AAT AAT AAT AAT AAT AAT AAT A
1 AAT AAT AAT AAT AAT AAT AAT AAT A
1932481 GTTGTTTCTT
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 22 1.00
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.32
Consensus pattern (3 bp):
AAT
Found at i:1932871 original size:23 final size:24
Alignment explanation
Indices: 1932838--1932886 Score: 73
Period size: 23 Copynumber: 2.1 Consensus size: 24
1932828 TCTTAAAATT
* *
1932838 TAGTAAATATTAAAATTTATTATA
1 TAGTAAATATTAAAAATAATTATA
1932862 TAGT-AATATTAAAAATAATTATA
1 TAGTAAATATTAAAAATAATTATA
1932885 TA
1 TA
1932887 AATTAATTAA
Statistics
Matches: 23, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
23 19 0.83
24 4 0.17
ACGTcount: A:0.53, C:0.00, G:0.04, T:0.43
Consensus pattern (24 bp):
TAGTAAATATTAAAAATAATTATA
Found at i:1934345 original size:21 final size:21
Alignment explanation
Indices: 1934321--1934369 Score: 64
Period size: 21 Copynumber: 2.3 Consensus size: 21
1934311 ATATAAAAAA
1934321 ATTTAAAAAATAAATA-TAATT
1 ATTTAAAAAATAAATACTAA-T
* *
1934342 ATTTAAATAATATATACTAAT
1 ATTTAAAAAATAAATACTAAT
1934363 ATTTAAA
1 ATTTAAA
1934370 TTTAAACTTA
Statistics
Matches: 25, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
21 22 0.88
22 3 0.12
ACGTcount: A:0.57, C:0.02, G:0.00, T:0.41
Consensus pattern (21 bp):
ATTTAAAAAATAAATACTAAT
Found at i:1934370 original size:21 final size:19
Alignment explanation
Indices: 1934290--1934397 Score: 80
Period size: 18 Copynumber: 5.6 Consensus size: 19
1934280 GATGAATATG
*
1934290 ATAATATAATAATTTTTAA
1 ATAATATAATAATATTTAA
* *
1934309 AT-ATATAAAAAAATTTAA
1 ATAATATAATAATATTTAA
* *
1934327 AAAATAAATATAATTATTTAA
1 ATAATATA-ATAA-TATTTAA
1934348 ATAATATATACTAATATTTAA
1 ATAATATA-A-TAATATTTAA
*
1934369 AT-TTA-AACTTAA-ATTTAA
1 ATAATATAA--TAATATTTAA
1934387 ATAATATAATA
1 ATAATATAATA
1934398 TGGATAATTG
Statistics
Matches: 70, Mismatches: 12, Indels: 15
0.72 0.12 0.15
Matches are distributed among these distances:
18 25 0.36
19 12 0.17
20 7 0.10
21 23 0.33
22 3 0.04
ACGTcount: A:0.57, C:0.02, G:0.00, T:0.41
Consensus pattern (19 bp):
ATAATATAATAATATTTAA
Found at i:1948409 original size:17 final size:19
Alignment explanation
Indices: 1948377--1948423 Score: 62
Period size: 17 Copynumber: 2.5 Consensus size: 19
1948367 GCTTAAAAAA
1948377 ATAAATTAATTATTAAAT-TT
1 ATAAA-TAA-TATTAAATATT
1948397 AT-AATAATATTAAATATT
1 ATAAATAATATTAAATATT
1948415 ATAAATAAT
1 ATAAATAAT
1948424 TAACAAAAAT
Statistics
Matches: 25, Mismatches: 0, Indels: 5
0.83 0.00 0.17
Matches are distributed among these distances:
17 8 0.32
18 7 0.28
19 8 0.32
20 2 0.08
ACGTcount: A:0.55, C:0.00, G:0.00, T:0.45
Consensus pattern (19 bp):
ATAAATAATATTAAATATT
Found at i:1949316 original size:23 final size:24
Alignment explanation
Indices: 1949290--1949401 Score: 70
Period size: 24 Copynumber: 4.5 Consensus size: 24
1949280 AAACACAATA
*
1949290 TTAAAATTTAATA-AAAATAAAAT
1 TTAAAATATAATATAAAATAAAAT
*
1949313 TTAAAATATGATATAAAATAAAAATATT
1 TTAAAATATAATATAAAAT--AAA-A-T
* *
1949341 TTAAAAT-TTATATATAATTAAAAT
1 TTAAAATATAATATA-AAATAAAAT
* * *
1949365 TTTAATTA-AATATAATTATAATAA-
1 TTAAAATATAATATAA-AATAA-AAT
1949389 TTAAAATATAATA
1 TTAAAATATAATA
1949402 CGCGAATTAA
Statistics
Matches: 68, Mismatches: 11, Indels: 18
0.70 0.11 0.19
Matches are distributed among these distances:
23 12 0.18
24 25 0.37
25 7 0.10
26 6 0.09
27 7 0.10
28 11 0.16
ACGTcount: A:0.59, C:0.00, G:0.01, T:0.40
Consensus pattern (24 bp):
TTAAAATATAATATAAAATAAAAT
Found at i:1952427 original size:2 final size:2
Alignment explanation
Indices: 1952420--1952457 Score: 67
Period size: 2 Copynumber: 19.0 Consensus size: 2
1952410 AAGAAGAATC
*
1952420 AT AT AT AT GT 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
1952458 TTAATGAATA
Statistics
Matches: 34, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
2 34 1.00
ACGTcount: A:0.47, C:0.00, G:0.03, T:0.50
Consensus pattern (2 bp):
AT
Found at i:1957975 original size:22 final size:22
Alignment explanation
Indices: 1957898--1957982 Score: 91
Period size: 22 Copynumber: 3.6 Consensus size: 22
1957888 TAAATTAAAT
*
1957898 ATATAAATAAATTTAAAATTTA
1 ATATTAATAAATTTAAAATTTA
*
1957920 A-ATTAATTAATTTAAAAATTATAA
1 ATATTAATAAATTT-AAAATT-T-A
1957944 CCATATTTAATAAATTTAAAATTTA
1 --ATA-TTAATAAATTTAAAATTTA
1957969 ATATTAATAAATTT
1 ATATTAATAAATTT
1957983 TTTACAGCTC
Statistics
Matches: 53, Mismatches: 3, Indels: 14
0.76 0.04 0.20
Matches are distributed among these distances:
21 10 0.19
22 18 0.34
23 4 0.08
24 1 0.02
25 1 0.02
26 2 0.04
27 7 0.13
28 10 0.19
ACGTcount: A:0.54, C:0.02, G:0.00, T:0.44
Consensus pattern (22 bp):
ATATTAATAAATTTAAAATTTA
Found at i:1958756 original size:39 final size:38
Alignment explanation
Indices: 1958657--1958760 Score: 99
Period size: 39 Copynumber: 2.7 Consensus size: 38
1958647 GTATTTATAA
* * *
1958657 AATAAAAA-ATAAAATTAATATATTAATTTTAAAATTTT
1 AATAAAAATATTATATTAATATATT-ATTTTAAAATTAT
*
1958695 AATGAAAATATTATATTAAATATAATT-TTTTAAAATTAT
1 AATAAAAATATTATATT-AATAT-ATTATTTTAAAATTAT
1958734 AATAAATAATTATT-TATTAATAT-TTAT
1 AATAAA-AA-TATTATATTAATATATTAT
1958761 AAATTTTTTT
Statistics
Matches: 55, Mismatches: 5, Indels: 12
0.76 0.07 0.17
Matches are distributed among these distances:
37 2 0.04
38 8 0.15
39 27 0.49
40 11 0.20
41 7 0.13
ACGTcount: A:0.53, C:0.00, G:0.01, T:0.46
Consensus pattern (38 bp):
AATAAAAATATTATATTAATATATTATTTTAAAATTAT
Found at i:1958853 original size:21 final size:21
Alignment explanation
Indices: 1958806--1958853 Score: 69
Period size: 21 Copynumber: 2.3 Consensus size: 21
1958796 TAAGTTTTTT
*
1958806 AAAAAATTTAATTTTTAAAAT
1 AAAAAATTTAATTTTTAAAAA
**
1958827 TTAAAATTTAATTTTTAAAAA
1 AAAAAATTTAATTTTTAAAAA
1958848 AAAAAA
1 AAAAAA
1958854 AACTGTCCAA
Statistics
Matches: 22, Mismatches: 5, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
21 22 1.00
ACGTcount: A:0.60, C:0.00, G:0.00, T:0.40
Consensus pattern (21 bp):
AAAAAATTTAATTTTTAAAAA
Found at i:1959609 original size:19 final size:18
Alignment explanation
Indices: 1959567--1959602 Score: 54
Period size: 18 Copynumber: 1.9 Consensus size: 18
1959557 TATTTTTTTA
*
1959567 ATTAAATAAAAATAAGAT
1 ATTAAATAAAAATAAAAT
1959585 ATTAAATATAAAATAAAA
1 ATTAAATA-AAAATAAAA
1959603 ATTTAAAATG
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
18 8 0.50
19 8 0.50
ACGTcount: A:0.69, C:0.00, G:0.03, T:0.28
Consensus pattern (18 bp):
ATTAAATAAAAATAAAAT
Found at i:1959664 original size:27 final size:28
Alignment explanation
Indices: 1959602--1959661 Score: 95
Period size: 28 Copynumber: 2.1 Consensus size: 28
1959592 ATAAAATAAA
*
1959602 AATTTAAAATGATGATTAAATCATTATT
1 AATTTAAAATGATAATTAAATCATTATT
1959630 AATTTAAAATGATAATTAAAT-ATTAATT
1 AATTTAAAATGATAATTAAATCATT-ATT
1959658 AATT
1 AATT
1959662 AAACTCATAA
Statistics
Matches: 30, Mismatches: 1, Indels: 2
0.91 0.03 0.06
Matches are distributed among these distances:
27 3 0.10
28 27 0.90
ACGTcount: A:0.50, C:0.02, G:0.05, T:0.43
Consensus pattern (28 bp):
AATTTAAAATGATAATTAAATCATTATT
Found at i:1959671 original size:27 final size:28
Alignment explanation
Indices: 1959602--1959672 Score: 83
Period size: 28 Copynumber: 2.6 Consensus size: 28
1959592 ATAAAATAAA
* *
1959602 AATTTAAAATGATGATTAAATCATTATT
1 AATTTAAAATCATAATTAAATCATTATT
*
1959630 AATTTAAAATGATAATTAAAT-ATTAATT
1 AATTTAAAATCATAATTAAATCATT-ATT
*
1959658 AA-TTAAACTCATAAT
1 AATTTAAAATCATAAT
1959673 AATTTTATAT
Statistics
Matches: 39, Mismatches: 3, Indels: 3
0.87 0.07 0.07
Matches are distributed among these distances:
27 14 0.36
28 25 0.64
ACGTcount: A:0.51, C:0.04, G:0.04, T:0.41
Consensus pattern (28 bp):
AATTTAAAATCATAATTAAATCATTATT
Found at i:1967350 original size:6 final size:6
Alignment explanation
Indices: 1967339--1967364 Score: 52
Period size: 6 Copynumber: 4.3 Consensus size: 6
1967329 TTGCAAACAA
1967339 CCAAAG CCAAAG CCAAAG CCAAAG CC
1 CCAAAG CCAAAG CCAAAG CCAAAG CC
1967365 CCTCTCTCTC
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:0.46, C:0.38, G:0.15, T:0.00
Consensus pattern (6 bp):
CCAAAG
Found at i:1968893 original size:2 final size:2
Alignment explanation
Indices: 1968886--1968916 Score: 62
Period size: 2 Copynumber: 15.5 Consensus size: 2
1968876 GAGCTTGCAC
1968886 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG A
1 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG A
1968917 AGGGTTGCAT
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:0.52, C:0.00, G:0.48, T:0.00
Consensus pattern (2 bp):
AG
Found at i:1970383 original size:22 final size:23
Alignment explanation
Indices: 1970358--1970407 Score: 93
Period size: 23 Copynumber: 2.2 Consensus size: 23
1970348 ATTCATTCCT
1970358 AAATCTTGAAGA-TTGTCTAACC
1 AAATCTTGAAGATTTGTCTAACC
1970380 AAATCTTGAAGATTTGTCTAACC
1 AAATCTTGAAGATTTGTCTAACC
1970403 AAATC
1 AAATC
1970408 CCTCAATTTA
Statistics
Matches: 27, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
22 12 0.44
23 15 0.56
ACGTcount: A:0.38, C:0.18, G:0.12, T:0.32
Consensus pattern (23 bp):
AAATCTTGAAGATTTGTCTAACC
Found at i:1971108 original size:18 final size:19
Alignment explanation
Indices: 1971085--1971120 Score: 56
Period size: 18 Copynumber: 1.9 Consensus size: 19
1971075 ATTAGTTTAG
1971085 TTATTTAAAAATT-TTCAT
1 TTATTTAAAAATTGTTCAT
*
1971103 TTATTTTAAAATTGTTCA
1 TTATTTAAAAATTGTTCA
1971121 ATCCATTAAA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
18 12 0.75
19 4 0.25
ACGTcount: A:0.36, C:0.06, G:0.03, T:0.56
Consensus pattern (19 bp):
TTATTTAAAAATTGTTCAT
Found at i:1974141 original size:15 final size:16
Alignment explanation
Indices: 1974103--1974151 Score: 57
Period size: 15 Copynumber: 3.0 Consensus size: 16
1974093 TAATTTATGT
1974103 TTATATATTGTATTTATA
1 TTATATATTGT-TTT-TA
1974121 TATATATATT-TTTTTA
1 T-TATATATTGTTTTTA
1974137 TTATA-ATTGTTTTTA
1 TTATATATTGTTTTTA
1974152 AAACCTTATA
Statistics
Matches: 29, Mismatches: 0, Indels: 7
0.81 0.00 0.19
Matches are distributed among these distances:
14 3 0.10
15 10 0.34
16 3 0.10
17 3 0.10
18 2 0.07
19 8 0.28
ACGTcount: A:0.31, C:0.00, G:0.04, T:0.65
Consensus pattern (16 bp):
TTATATATTGTTTTTA
Found at i:1974199 original size:21 final size:22
Alignment explanation
Indices: 1974174--1974214 Score: 57
Period size: 21 Copynumber: 1.9 Consensus size: 22
1974164 TTGTAATATA
1974174 AATTTTAATA-AATTAATAAGT
1 AATTTTAATATAATTAATAAGT
* *
1974195 AATTTTCATATAATTTATAA
1 AATTTTAATATAATTAATAA
1974215 ATAAAATTAT
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
21 9 0.53
22 8 0.47
ACGTcount: A:0.49, C:0.02, G:0.02, T:0.46
Consensus pattern (22 bp):
AATTTTAATATAATTAATAAGT
Found at i:1974368 original size:15 final size:15
Alignment explanation
Indices: 1974348--1974376 Score: 58
Period size: 15 Copynumber: 1.9 Consensus size: 15
1974338 CTTGCCTTTC
1974348 TTTTTTATTTTTTAT
1 TTTTTTATTTTTTAT
1974363 TTTTTTATTTTTTA
1 TTTTTTATTTTTTA
1974377 AAAAAAACTT
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:0.14, C:0.00, G:0.00, T:0.86
Consensus pattern (15 bp):
TTTTTTATTTTTTAT
Found at i:1976700 original size:3 final size:3
Alignment explanation
Indices: 1976692--1976723 Score: 64
Period size: 3 Copynumber: 10.7 Consensus size: 3
1976682 ACCCTTTTCT
1976692 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TT
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TT
1976724 TTAATCATTG
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 29 1.00
ACGTcount: A:0.31, C:0.00, G:0.00, T:0.69
Consensus pattern (3 bp):
TTA
Found at i:1980458 original size:12 final size:11
Alignment explanation
Indices: 1980441--1980497 Score: 55
Period size: 12 Copynumber: 5.1 Consensus size: 11
1980431 GAAATTAGAG
1980441 TAAATTTTAAA
1 TAAATTTTAAA
1980452 TTAAATTTTAAA
1 -TAAATTTTAAA
*
1980464 TATAATATT-AA
1 TA-AATTTTAAA
*
1980475 TATATTTTAAA
1 TAAATTTTAAA
1980486 -AAATATTTAAA
1 TAAAT-TTTAAA
1980497 T
1 T
1980498 TTAATTTTTT
Statistics
Matches: 37, Mismatches: 4, Indels: 8
0.76 0.08 0.16
Matches are distributed among these distances:
10 7 0.19
11 14 0.38
12 16 0.43
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (11 bp):
TAAATTTTAAA
Found at i:1980622 original size:25 final size:24
Alignment explanation
Indices: 1980580--1980628 Score: 82
Period size: 24 Copynumber: 2.0 Consensus size: 24
1980570 TATTAATAAT
1980580 TATATTAAATATTATTTTTTAAAA
1 TATATTAAATATTATTTTTTAAAA
1980604 TATATATAAAT-TTATTTTTTAAAA
1 TATAT-TAAATATTATTTTTTAAAA
1980628 T
1 T
1980629 TTAAATTAAT
Statistics
Matches: 24, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
24 19 0.79
25 5 0.21
ACGTcount: A:0.45, C:0.00, G:0.00, T:0.55
Consensus pattern (24 bp):
TATATTAAATATTATTTTTTAAAA
Found at i:1980711 original size:20 final size:20
Alignment explanation
Indices: 1980686--1980760 Score: 66
Period size: 20 Copynumber: 3.7 Consensus size: 20
1980676 TTACGATAAA
1980686 TTTAATTAAATTTTAAATAT
1 TTTAATTAAATTTTAAATAT
* *
1980706 TTTAATTAAAATTTAATTTAT
1 TTTAATTAAATTTTAA-ATAT
*
1980727 TTAATAAATAAA-TTT-AATAT
1 TT--TAATTAAATTTTAAATAT
1980747 TTT-ATTAAAATTTT
1 TTTAATT-AAATTTT
1980761 TATAAATTTT
Statistics
Matches: 45, Mismatches: 5, Indels: 11
0.74 0.08 0.18
Matches are distributed among these distances:
17 2 0.04
18 4 0.09
19 3 0.07
20 20 0.44
21 6 0.13
22 3 0.07
23 7 0.16
ACGTcount: A:0.45, C:0.00, G:0.00, T:0.55
Consensus pattern (20 bp):
TTTAATTAAATTTTAAATAT
Found at i:1980757 original size:22 final size:22
Alignment explanation
Indices: 1980714--1980755 Score: 59
Period size: 22 Copynumber: 2.0 Consensus size: 22
1980704 ATTTTAATTA
*
1980714 AAATTTAATTTATTTAATAAAT
1 AAATTTAATATATTTAATAAAT
*
1980736 AAATTTAATAT-TTTATTAAA
1 AAATTTAATATATTTAATAAA
1980756 ATTTTTATAA
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
21 8 0.44
22 10 0.56
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (22 bp):
AAATTTAATATATTTAATAAAT
Found at i:1980762 original size:20 final size:20
Alignment explanation
Indices: 1980693--1980762 Score: 54
Period size: 19 Copynumber: 3.5 Consensus size: 20
1980683 AAATTTAATT
*
1980693 AAATTTTAAATATTTTAATTA
1 AAATTTTTAATATTTT-ATTA
* *
1980714 AAA--TTTAATTTATTTAATA
1 AAATTTTTAATAT-TTTATTA
**
1980733 AATAAATTTAATATTTTATTA
1 AA-ATTTTTAATATTTTATTA
1980754 AAATTTTTA
1 AAATTTTTA
1980763 TAAATTTTAA
Statistics
Matches: 38, Mismatches: 7, Indels: 9
0.70 0.13 0.17
Matches are distributed among these distances:
19 11 0.29
20 9 0.24
21 11 0.29
22 7 0.18
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (20 bp):
AAATTTTTAATATTTTATTA
Found at i:1981573 original size:25 final size:26
Alignment explanation
Indices: 1981539--1981587 Score: 73
Period size: 25 Copynumber: 1.9 Consensus size: 26
1981529 TTTAAAATTT
*
1981539 TATAATTAATAAATTA-ATTTTTTAA
1 TATAAATAATAAATTATATTTTTTAA
*
1981564 TATAAATAATATATTATATTTTTT
1 TATAAATAATAAATTATATTTTTT
1981588 TTAGATTATT
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
25 14 0.67
26 7 0.33
ACGTcount: A:0.45, C:0.00, G:0.00, T:0.55
Consensus pattern (26 bp):
TATAAATAATAAATTATATTTTTTAA
Found at i:1986376 original size:29 final size:29
Alignment explanation
Indices: 1986302--1986377 Score: 86
Period size: 28 Copynumber: 2.7 Consensus size: 29
1986292 TTAAACATAA
1986302 ATTAATAA-AAAATTTAAAATATTTTTAT
1 ATTAATAATAAAATTTAAAATATTTTTAT
* *
1986330 ATTTATAATTAAATTTAAAA-A-TTTTATT
1 ATTAATAATAAAATTTAAAATATTTTTA-T
*
1986358 ATTAATAATAATAAGTTAAA
1 ATTAATAATAA-AATTTAAA
1986378 TTAAATTAAT
Statistics
Matches: 40, Mismatches: 5, Indels: 5
0.80 0.10 0.10
Matches are distributed among these distances:
27 5 0.12
28 18 0.45
29 17 0.43
ACGTcount: A:0.53, C:0.00, G:0.01, T:0.46
Consensus pattern (29 bp):
ATTAATAATAAAATTTAAAATATTTTTAT
Found at i:1990654 original size:89 final size:88
Alignment explanation
Indices: 1990503--1990676 Score: 330
Period size: 89 Copynumber: 2.0 Consensus size: 88
1990493 TCTCAAATGC
1990503 AAAGCCATTGGACGGTAGACGGATTTTGGTTGAATTTTGTCTATATTAATTCATTTCTTTCCTTA
1 AAAGCCATTGGACGGTAGACGGATTTTGGTTGAATTTTGTCTATATTAATTCATTTCTTTCCTT-
1990568 ATTTTTTTCAAAGTTTGTCTGGGG
65 ATTTTTTTCAAAGTTTGTCTGGGG
*
1990592 AAAGCCATTGGATGGTAGACGGATTTTGGTTGAATTTTGTCTATATTAATTCATTTCTTTCCTTA
1 AAAGCCATTGGACGGTAGACGGATTTTGGTTGAATTTTGTCTATATTAATTCATTTCTTTCCTTA
1990657 TTTTTTTCAAAGTTTGTCTG
66 TTTTTTTCAAAGTTTGTCTG
1990677 CGGTAAAAAA
Statistics
Matches: 84, Mismatches: 1, Indels: 1
0.98 0.01 0.01
Matches are distributed among these distances:
88 21 0.25
89 63 0.75
ACGTcount: A:0.22, C:0.12, G:0.19, T:0.47
Consensus pattern (88 bp):
AAAGCCATTGGACGGTAGACGGATTTTGGTTGAATTTTGTCTATATTAATTCATTTCTTTCCTTA
TTTTTTTCAAAGTTTGTCTGGGG
Found at i:1994577 original size:19 final size:18
Alignment explanation
Indices: 1994529--1994600 Score: 90
Period size: 18 Copynumber: 3.9 Consensus size: 18
1994519 AATGCAGCCT
** *
1994529 CAGATGTTGCAACAGCCC
1 CAGATGTTGCCGCAGTCC
1994547 CAGATGTTGCCGCAGTCC
1 CAGATGTTGCCGCAGTCC
1994565 CAGATGCTTGCCGCAGTCC
1 CAGATG-TTGCCGCAGTCC
* *
1994584 CCGATGTTGCTGCAGTC
1 CAGATGTTGCCGCAGTC
1994601 TCAGGCTCAG
Statistics
Matches: 48, Mismatches: 5, Indels: 2
0.87 0.09 0.04
Matches are distributed among these distances:
18 31 0.65
19 17 0.35
ACGTcount: A:0.18, C:0.33, G:0.26, T:0.22
Consensus pattern (18 bp):
CAGATGTTGCCGCAGTCC
Found at i:2006005 original size:12 final size:12
Alignment explanation
Indices: 2005988--2006025 Score: 58
Period size: 12 Copynumber: 3.2 Consensus size: 12
2005978 CTTAAGATCA
*
2005988 AATGATAATGAT
1 AATGATAATAAT
2006000 AATGATAATAAT
1 AATGATAATAAT
*
2006012 AATAATAATAAT
1 AATGATAATAAT
2006024 AA
1 AA
2006026 AGTGATTGAT
Statistics
Matches: 24, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
12 24 1.00
ACGTcount: A:0.61, C:0.00, G:0.08, T:0.32
Consensus pattern (12 bp):
AATGATAATAAT
Found at i:2006012 original size:3 final size:3
Alignment explanation
Indices: 2005992--2006025 Score: 50
Period size: 3 Copynumber: 11.3 Consensus size: 3
2005982 AGATCAAATG
* *
2005992 ATA ATG ATA ATG ATA ATA ATA ATA ATA ATA ATA A
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA A
2006026 AGTGATTGAT
Statistics
Matches: 27, Mismatches: 4, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
3 27 1.00
ACGTcount: A:0.62, C:0.00, G:0.06, T:0.32
Consensus pattern (3 bp):
ATA
Found at i:2008354 original size:22 final size:23
Alignment explanation
Indices: 2008320--2008362 Score: 54
Period size: 22 Copynumber: 1.9 Consensus size: 23
2008310 TTTAAAAATA
2008320 AAAAATTATAAA-TATTTAAATTT
1 AAAAATTATAAATTA-TTAAATTT
*
2008343 AAAATTTA-AAATTATTAAAT
1 AAAAATTATAAATTATTAAAT
2008363 ATTATTTTTA
Statistics
Matches: 18, Mismatches: 1, Indels: 3
0.82 0.05 0.14
Matches are distributed among these distances:
22 9 0.50
23 9 0.50
ACGTcount: A:0.58, C:0.00, G:0.00, T:0.42
Consensus pattern (23 bp):
AAAAATTATAAATTATTAAATTT
Found at i:2009065 original size:20 final size:22
Alignment explanation
Indices: 2009039--2009091 Score: 76
Period size: 22 Copynumber: 2.5 Consensus size: 22
2009029 TATTAAAATA
2009039 ATATATAAAA-AATTTA-AAATC
1 ATATATAAAATAATTTATAAA-C
2009060 -TATATAAAATAATTTATAAAC
1 ATATATAAAATAATTTATAAAC
2009081 ATATATAAAAT
1 ATATATAAAAT
2009092 TATAATAGAT
Statistics
Matches: 29, Mismatches: 0, Indels: 5
0.85 0.00 0.15
Matches are distributed among these distances:
20 9 0.31
21 7 0.24
22 13 0.45
ACGTcount: A:0.60, C:0.04, G:0.00, T:0.36
Consensus pattern (22 bp):
ATATATAAAATAATTTATAAAC
Done.