Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold8
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: 6381039
ACGTcount: A:0.34, C:0.16, G:0.16, T:0.34
Warning! 22487 characters in sequence are not A, C, G, or T
File 14 of 33
Found at i:1882125 original size:30 final size:31
Alignment explanation
Indices: 1882089--1882215 Score: 103
Period size: 30 Copynumber: 4.3 Consensus size: 31
1882079 ATAAAATATA
1882089 ATATAATATAAAATATAAATATT-TTAAAAT
1 ATATAATATAAAATATAAATATTATTAAAAT
* * *
1882119 ATATAATATAAATTATTAAT-TTATTTAAAT
1 ATATAATATAAAATATAAATATTATTAAAAT
*
1882149 -T-T-ATAT-AAATATATAATATT-TTAATAT
1 ATATAATATAAAATATA-AATATTATTAAAAT
* *
1882176 AATTATAATATAAAA-AT-AATATTAATATAAT
1 -A-TATAATATAAAATATAAATATTATTAAAAT
1882207 AT-TAATATA
1 ATATAATATA
1882216 TTAATTATAA
Statistics
Matches: 77, Mismatches: 10, Indels: 22
0.71 0.09 0.20
Matches are distributed among these distances:
26 5 0.06
27 12 0.16
28 10 0.13
29 4 0.05
30 32 0.42
31 5 0.06
32 6 0.08
33 3 0.04
ACGTcount: A:0.55, C:0.00, G:0.00, T:0.45
Consensus pattern (31 bp):
ATATAATATAAAATATAAATATTATTAAAAT
Found at i:1882161 original size:8 final size:8
Alignment explanation
Indices: 1882039--1882226 Score: 61
Period size: 8 Copynumber: 22.9 Consensus size: 8
1882029 AGTGAATACA
1882039 ATATAAAT
1 ATATAAAT
*
1882047 ATATATAT
1 ATATAAAT
*
1882055 ATATATAT
1 ATATAAAT
*
1882063 ATAT-GAT
1 ATATAAAT
*
1882070 AT-TAAAA
1 ATATAAAT
*
1882077 AAATAAA-
1 ATATAAAT
1882084 ATATAATAT
1 ATATAA-AT
1882093 AATATAAA-
1 -ATATAAAT
1882101 ATATAAAT
1 ATATAAAT
*
1882109 ATTTTAAA-
1 A-TATAAAT
*
1882117 ATATATA-
1 ATATAAAT
1882124 ATATAAAT
1 ATATAAAT
*
1882132 -TATTAATTT
1 ATA-TAA-AT
*
1882141 ATTTAAATTT
1 ATATAAA--T
1882151 ATATAAAT
1 ATATAAAT
1882159 ATAT-AAT
1 ATATAAAT
* *
1882166 ATTTTAAT
1 ATATAAAT
1882174 ATAATTATAAT
1 AT-A-TA-AAT
*
1882185 ATAAAAAT
1 ATATAAAT
1882193 AATATTAATAT
1 -ATA-TAA-AT
*
1882204 AATATTAAT
1 -ATATAAAT
*
1882213 ATATTAAT
1 ATATAAAT
1882221 -TATAAA
1 ATATAAA
1882227 GTTGACTATC
Statistics
Matches: 139, Mismatches: 21, Indels: 41
0.69 0.10 0.20
Matches are distributed among these distances:
6 1 0.01
7 41 0.29
8 50 0.36
9 16 0.12
10 20 0.14
11 11 0.08
ACGTcount: A:0.56, C:0.00, G:0.01, T:0.43
Consensus pattern (8 bp):
ATATAAAT
Found at i:1889459 original size:6 final size:6
Alignment explanation
Indices: 1889448--1889497 Score: 52
Period size: 6 Copynumber: 8.7 Consensus size: 6
1889438 TATTATAATT
* *
1889448 TTTATA TTTATA -TTATA TTTATA TATTTTA -TTATA -TTATA ATTATA
1 TTTATA TTTATA TTTATA TTTATA T-TTATA TTTATA TTTATA TTTATA
1889494 TTTA
1 TTTA
1889498 AAATATTTTT
Statistics
Matches: 38, Mismatches: 3, Indels: 6
0.81 0.06 0.13
Matches are distributed among these distances:
5 14 0.37
6 20 0.53
7 4 0.11
ACGTcount: A:0.36, C:0.00, G:0.00, T:0.64
Consensus pattern (6 bp):
TTTATA
Found at i:1889465 original size:11 final size:11
Alignment explanation
Indices: 1889449--1889515 Score: 56
Period size: 11 Copynumber: 6.5 Consensus size: 11
1889439 ATTATAATTT
1889449 TTATATTTATA
1 TTATATTTATA
1889460 TTATA-TT-TA
1 TTATATTTATA
1889469 -TATATTT-TA
1 TTATATTTATA
1889478 TTATA-TTATAA
1 TTATATTTAT-A
*
1889489 TTATATTTAAA
1 TTATATTTATA
* *
1889500 ATATTTTTAT-
1 TTATATTTATA
1889510 TTATAT
1 TTATAT
1889516 AAATTTTGAT
Statistics
Matches: 45, Mismatches: 6, Indels: 11
0.73 0.10 0.18
Matches are distributed among these distances:
8 4 0.09
9 8 0.18
10 11 0.24
11 19 0.42
12 3 0.07
ACGTcount: A:0.37, C:0.00, G:0.00, T:0.63
Consensus pattern (11 bp):
TTATATTTATA
Found at i:1889469 original size:29 final size:29
Alignment explanation
Indices: 1889441--1889497 Score: 82
Period size: 29 Copynumber: 2.0 Consensus size: 29
1889431 TAATAATTAT
1889441 TATAATTT-TTATATT-TATATTATATTTA
1 TATAATTTATTATATTATA-ATTATATTTA
*
1889469 TATATTTTATTATATTATAATTATATTTA
1 TATAATTTATTATATTATAATTATATTTA
1889498 AAATATTTTT
Statistics
Matches: 26, Mismatches: 1, Indels: 3
0.87 0.03 0.10
Matches are distributed among these distances:
28 7 0.27
29 17 0.65
30 2 0.08
ACGTcount: A:0.37, C:0.00, G:0.00, T:0.63
Consensus pattern (29 bp):
TATAATTTATTATATTATAATTATATTTA
Found at i:1889484 original size:18 final size:18
Alignment explanation
Indices: 1889437--1889484 Score: 69
Period size: 19 Copynumber: 2.6 Consensus size: 18
1889427 GGTATAATAA
*
1889437 TTATTATAATTTTTATATT
1 TTATTAT-ATTTATATATT
1889456 TATATTATATTTATATATT
1 T-TATTATATTTATATATT
1889475 TTATTATATT
1 TTATTATATT
1889485 ATAATTATAT
Statistics
Matches: 27, Mismatches: 1, Indels: 3
0.87 0.03 0.10
Matches are distributed among these distances:
18 9 0.33
19 12 0.44
20 6 0.22
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (18 bp):
TTATTATATTTATATATT
Found at i:1889516 original size:29 final size:28
Alignment explanation
Indices: 1889445--1889517 Score: 80
Period size: 29 Copynumber: 2.6 Consensus size: 28
1889435 AATTATTATA
*
1889445 ATTTTTATATT-TAT-ATTATATTTATAT
1 ATTTTTAT-TTATATAATTATATTTAAAT
1889472 A-TTTTATTATATTATAATTATATTTAAAAT
1 ATTTTTATT-TA-TATAATTATATTT-AAAT
1889502 ATTTTTATTTATATAA
1 ATTTTTATTTATATAA
1889518 ATTTTGATAT
Statistics
Matches: 39, Mismatches: 1, Indels: 10
0.78 0.02 0.20
Matches are distributed among these distances:
25 1 0.03
26 7 0.18
27 1 0.03
28 3 0.08
29 14 0.36
30 6 0.15
31 7 0.18
ACGTcount: A:0.38, C:0.00, G:0.00, T:0.62
Consensus pattern (28 bp):
ATTTTTATTTATATAATTATATTTAAAT
Found at i:1899624 original size:2 final size:2
Alignment explanation
Indices: 1899617--1899647 Score: 62
Period size: 2 Copynumber: 15.5 Consensus size: 2
1899607 TCTGATTTAG
1899617 CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT C
1 CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT C
1899648 CCCGCGTGGT
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:0.00, C:0.52, G:0.00, T:0.48
Consensus pattern (2 bp):
CT
Found at i:1903031 original size:24 final size:25
Alignment explanation
Indices: 1903004--1903050 Score: 60
Period size: 25 Copynumber: 1.9 Consensus size: 25
1902994 CTTTATTAAT
*
1903004 TCATGTAAT-TATTTTTAAAAAGTA
1 TCATGTAATAAATTTTTAAAAAGTA
* *
1903028 TCATTTAATAAATTTTTACAAAG
1 TCATGTAATAAATTTTTAAAAAG
1903051 CAAACAGGTC
Statistics
Matches: 19, Mismatches: 3, Indels: 1
0.83 0.13 0.04
Matches are distributed among these distances:
24 8 0.42
25 11 0.58
ACGTcount: A:0.43, C:0.06, G:0.06, T:0.45
Consensus pattern (25 bp):
TCATGTAATAAATTTTTAAAAAGTA
Found at i:1903926 original size:29 final size:29
Alignment explanation
Indices: 1903891--1903950 Score: 77
Period size: 29 Copynumber: 2.1 Consensus size: 29
1903881 TTAAAAATTA
*
1903891 AATTATTAAATCA-AATAAATATTTTTATT
1 AATTATT-AATCATAATAAATATTTTGATT
* *
1903920 AATTATTAATTATATTAAATATTTTGATT
1 AATTATTAATCATAATAAATATTTTGATT
1903949 AA
1 AA
1903951 ATACTAATTC
Statistics
Matches: 27, Mismatches: 3, Indels: 2
0.84 0.09 0.06
Matches are distributed among these distances:
28 4 0.15
29 23 0.85
ACGTcount: A:0.47, C:0.02, G:0.02, T:0.50
Consensus pattern (29 bp):
AATTATTAATCATAATAAATATTTTGATT
Found at i:1906977 original size:20 final size:20
Alignment explanation
Indices: 1906952--1907010 Score: 55
Period size: 25 Copynumber: 2.7 Consensus size: 20
1906942 AGTCTGGTAG
*
1906952 AAAAGATTTATATAGTTCCC
1 AAAAGATTTATATAGTTACC
*
1906972 AAAAGAAATGAGTTATGTAGTTACC
1 AAAAG--AT---TTATATAGTTACC
1906997 AAAAGATTTATATA
1 AAAAGATTTATATA
1907011 TATATATATA
Statistics
Matches: 31, Mismatches: 3, Indels: 10
0.70 0.07 0.23
Matches are distributed among these distances:
20 11 0.35
22 2 0.06
23 2 0.06
25 16 0.52
ACGTcount: A:0.46, C:0.08, G:0.14, T:0.32
Consensus pattern (20 bp):
AAAAGATTTATATAGTTACC
Found at i:1906987 original size:25 final size:25
Alignment explanation
Indices: 1906950--1907002 Score: 70
Period size: 25 Copynumber: 2.1 Consensus size: 25
1906940 AAAGTCTGGT
* *
1906950 AGAAAAGATTTATATAGTTCCCAAA
1 AGAAAAGAGTTATATAGTTACCAAA
* *
1906975 AGAAATGAGTTATGTAGTTACCAAA
1 AGAAAAGAGTTATATAGTTACCAAA
1907000 AGA
1 AGA
1907003 TTTATATATA
Statistics
Matches: 24, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
25 24 1.00
ACGTcount: A:0.47, C:0.09, G:0.17, T:0.26
Consensus pattern (25 bp):
AGAAAAGAGTTATATAGTTACCAAA
Found at i:1907012 original size:2 final size:2
Alignment explanation
Indices: 1907005--1907034 Score: 60
Period size: 2 Copynumber: 15.0 Consensus size: 2
1906995 CCAAAAGATT
1907005 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
1907035 ATAACACCAG
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:1911637 original size:21 final size:21
Alignment explanation
Indices: 1911613--1911658 Score: 58
Period size: 20 Copynumber: 2.2 Consensus size: 21
1911603 GGAGTCTACT
1911613 AAAAAGGCAATGGAAAACCTG
1 AAAAAGGCAATGGAAAACCTG
* * *
1911634 -AAAAGGTAATGGAAAGCTTG
1 AAAAAGGCAATGGAAAACCTG
1911654 AAAAA
1 AAAAA
1911659 ATTAAATACT
Statistics
Matches: 21, Mismatches: 3, Indels: 2
0.81 0.12 0.08
Matches are distributed among these distances:
20 17 0.81
21 4 0.19
ACGTcount: A:0.54, C:0.09, G:0.24, T:0.13
Consensus pattern (21 bp):
AAAAAGGCAATGGAAAACCTG
Found at i:1914597 original size:24 final size:25
Alignment explanation
Indices: 1914571--1914629 Score: 77
Period size: 24 Copynumber: 2.4 Consensus size: 25
1914561 ATTTTAAAAT
*
1914571 AAATTTATTAAATTATTTTTATTTA
1 AAATTTATTAAATTATTATTATTTA
**
1914596 AAATAAATT-AATTATTATTATTTA
1 AAATTTATTAAATTATTATTATTTA
1914620 AAATTT-TTAA
1 AAATTTATTAA
1914630 TGACAAAGAA
Statistics
Matches: 28, Mismatches: 5, Indels: 3
0.78 0.14 0.08
Matches are distributed among these distances:
23 2 0.07
24 19 0.68
25 7 0.25
ACGTcount: A:0.46, C:0.00, G:0.00, T:0.54
Consensus pattern (25 bp):
AAATTTATTAAATTATTATTATTTA
Found at i:1918210 original size:52 final size:52
Alignment explanation
Indices: 1918132--1918260 Score: 222
Period size: 52 Copynumber: 2.5 Consensus size: 52
1918122 CGAAATATGA
* *
1918132 AAATTTGTCTACATGTATCGATACATTTAATAGTGTATCGATACATCTGACC
1 AAATTTGCCTGCATGTATCGATACATTTAATAGTGTATCGATACATCTGACC
* *
1918184 AAATTTGCCTGCATGTATCGATACATTTTATAGTGTATCGATACATCTGGCC
1 AAATTTGCCTGCATGTATCGATACATTTAATAGTGTATCGATACATCTGACC
1918236 AAATTTGCCTGCATGTATCGATACA
1 AAATTTGCCTGCATGTATCGATACA
1918261 AAGATCAGTA
Statistics
Matches: 73, Mismatches: 4, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
52 73 1.00
ACGTcount: A:0.30, C:0.19, G:0.16, T:0.36
Consensus pattern (52 bp):
AAATTTGCCTGCATGTATCGATACATTTAATAGTGTATCGATACATCTGACC
Found at i:1918374 original size:13 final size:13
Alignment explanation
Indices: 1918356--1918380 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
1918346 ACAAAACTTA
1918356 TGTATCGATACAT
1 TGTATCGATACAT
1918369 TGTATCGATACA
1 TGTATCGATACA
1918381 ACACTTTATG
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.32, C:0.16, G:0.16, T:0.36
Consensus pattern (13 bp):
TGTATCGATACAT
Found at i:1918377 original size:32 final size:33
Alignment explanation
Indices: 1918336--1918400 Score: 114
Period size: 32 Copynumber: 2.0 Consensus size: 33
1918326 GTAGCTTACT
1918336 TTGTATCGATACAAAAC-TTATGTATCGATACA
1 TTGTATCGATACAAAACTTTATGTATCGATACA
*
1918368 TTGTATCGATACAACACTTTATGTATCGATACA
1 TTGTATCGATACAAAACTTTATGTATCGATACA
1918401 AATCGTTGAA
Statistics
Matches: 31, Mismatches: 1, Indels: 1
0.94 0.03 0.03
Matches are distributed among these distances:
32 16 0.52
33 15 0.48
ACGTcount: A:0.35, C:0.17, G:0.12, T:0.35
Consensus pattern (33 bp):
TTGTATCGATACAAAACTTTATGTATCGATACA
Found at i:1919003 original size:15 final size:16
Alignment explanation
Indices: 1918964--1919003 Score: 55
Period size: 16 Copynumber: 2.6 Consensus size: 16
1918954 TAGATGCATT
*
1918964 AGAATAAAATTTAATC
1 AGAATTAAATTTAATC
1918980 AGAATTAAATTTAAT-
1 AGAATTAAATTTAATC
*
1918995 AGCATTAAA
1 AGAATTAAA
1919004 AAATTAAAAT
Statistics
Matches: 22, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
15 8 0.36
16 14 0.64
ACGTcount: A:0.55, C:0.05, G:0.07, T:0.33
Consensus pattern (16 bp):
AGAATTAAATTTAATC
Found at i:1922508 original size:106 final size:103
Alignment explanation
Indices: 1922306--1922601 Score: 409
Period size: 106 Copynumber: 2.9 Consensus size: 103
1922296 TCAGAATGAC
* *
1922306 GACCAAATGGAGATTAATAGTTGTAATGATCTACTCTTCTATTTTC--TTCTGATTTAATTTTTT
1 GACCAAATGGAGATTAATAGTTGTCATGATCTACTCTTTTATTTTCTTTTCTGATTTAA-TTTTT
* *
1922369 AGGCTTCCTAAAGCAAAAGGCTGCATTAACATGTAGGTG
65 AGGCTTCCTAAAGTAAAAGGCTGCATTAACATGTAAGTG
* * *
1922408 GACCAAATGGAGATTAATAGTTGTCATGCTCTACTCTATTTTTTTTTCTTATTCTCATTTAATTT
1 GACCAAATGGAGATTAATAGTTGTCATGATCTACTC--TTTTATTTTCTT-TTCTGATTTAATTT
* * **
1922473 TTAGGATTTCTAAAGTGGAAGGCTGCATTAACATGTAAGTG
63 TTAGGCTTCCTAAAGTAAAAGGCTGCATTAACATGTAAGTG
*
1922514 GACCAAATGGAGATTTATAGTTGTCATGATCTACTC-TTTATTTTCTTCTTCTGATTTAATTTTT
1 GACCAAATGGAGATTAATAGTTGTCATGATCTACTCTTTTATTTTCTT-TTCTGATTTAATTTTT
*
1922578 AGGCTTCCTAAAGTAAAAAGCTGC
65 AGGCTTCCTAAAGTAAAAGGCTGC
1922602 TTTGCATATT
Statistics
Matches: 168, Mismatches: 21, Indels: 9
0.85 0.11 0.05
Matches are distributed among these distances:
102 34 0.20
103 44 0.26
104 8 0.05
106 72 0.43
107 10 0.06
ACGTcount: A:0.28, C:0.15, G:0.17, T:0.41
Consensus pattern (103 bp):
GACCAAATGGAGATTAATAGTTGTCATGATCTACTCTTTTATTTTCTTTTCTGATTTAATTTTTA
GGCTTCCTAAAGTAAAAGGCTGCATTAACATGTAAGTG
Found at i:1930021 original size:31 final size:32
Alignment explanation
Indices: 1929961--1930023 Score: 119
Period size: 32 Copynumber: 2.0 Consensus size: 32
1929951 GAATGATCGG
1929961 CATACATTCTCCAGCTTGAGGAGGAGTGTAGA
1 CATACATTCTCCAGCTTGAGGAGGAGTGTAGA
1929993 CATACATTCTCCAGCTTGAGG-GGAGTGTAGA
1 CATACATTCTCCAGCTTGAGGAGGAGTGTAGA
1930024 TTTCCAGATT
Statistics
Matches: 31, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
31 10 0.32
32 21 0.68
ACGTcount: A:0.27, C:0.19, G:0.29, T:0.25
Consensus pattern (32 bp):
CATACATTCTCCAGCTTGAGGAGGAGTGTAGA
Found at i:1931517 original size:3 final size:3
Alignment explanation
Indices: 1931509--1931545 Score: 74
Period size: 3 Copynumber: 12.3 Consensus size: 3
1931499 TTGATTTTGG
1931509 TGA TGA TGA TGA TGA TGA TGA TGA TGA TGA TGA TGA T
1 TGA TGA TGA TGA TGA TGA TGA TGA TGA TGA TGA TGA T
1931546 TTCAAAGGTC
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 34 1.00
ACGTcount: A:0.32, C:0.00, G:0.32, T:0.35
Consensus pattern (3 bp):
TGA
Found at i:1937828 original size:3 final size:3
Alignment explanation
Indices: 1937820--1937859 Score: 71
Period size: 3 Copynumber: 13.3 Consensus size: 3
1937810 GTACCATAGA
*
1937820 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAC AAT AAT AAT A
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT A
1937860 CAAGAGAATA
Statistics
Matches: 35, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
3 35 1.00
ACGTcount: A:0.68, C:0.03, G:0.00, T:0.30
Consensus pattern (3 bp):
AAT
Found at i:1942387 original size:32 final size:31
Alignment explanation
Indices: 1942351--1942422 Score: 101
Period size: 30 Copynumber: 2.3 Consensus size: 31
1942341 AATTTTGTGT
*
1942351 ATTTTATTTAAATAAATTACTCATATCAAATA
1 ATTTT-TTTAAATAAATTACACATATCAAATA
*
1942383 A-TTTTTTAAATAATTTACACATATCAAATA
1 ATTTTTTTAAATAAATTACACATATCAAATA
1942413 ATATTTTTTA
1 AT-TTTTTTA
1942423 TTTTTTTATA
Statistics
Matches: 36, Mismatches: 2, Indels: 4
0.86 0.05 0.10
Matches are distributed among these distances:
30 25 0.69
31 3 0.08
32 8 0.22
ACGTcount: A:0.44, C:0.08, G:0.00, T:0.47
Consensus pattern (31 bp):
ATTTTTTTAAATAAATTACACATATCAAATA
Found at i:1942393 original size:30 final size:31
Alignment explanation
Indices: 1942357--1942420 Score: 103
Period size: 30 Copynumber: 2.1 Consensus size: 31
1942347 GTGTATTTTA
*
1942357 TTTAAATAAATTACTCATATCAAATAAT-TT
1 TTTAAATAAATTACACATATCAAATAATATT
*
1942387 TTTAAATAATTTACACATATCAAATAATATT
1 TTTAAATAAATTACACATATCAAATAATATT
1942418 TTT
1 TTT
1942421 TATTTTTTTA
Statistics
Matches: 31, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
30 26 0.84
31 5 0.16
ACGTcount: A:0.45, C:0.09, G:0.00, T:0.45
Consensus pattern (31 bp):
TTTAAATAAATTACACATATCAAATAATATT
Found at i:1942606 original size:23 final size:20
Alignment explanation
Indices: 1942568--1942617 Score: 66
Period size: 21 Copynumber: 2.5 Consensus size: 20
1942558 ATGTGAGTCT
1942568 ATAATTTTTTTAAAAAAATA
1 ATAATTTTTTTAAAAAAATA
*
1942588 ATAATTATTTTTAAGAAAA-A
1 ATAATT-TTTTTAAAAAAATA
1942608 ATATATTTTT
1 ATA-ATTTTT
1942618 ATATCATTTT
Statistics
Matches: 27, Mismatches: 1, Indels: 4
0.84 0.03 0.12
Matches are distributed among these distances:
20 13 0.48
21 14 0.52
ACGTcount: A:0.50, C:0.00, G:0.02, T:0.48
Consensus pattern (20 bp):
ATAATTTTTTTAAAAAAATA
Found at i:1953298 original size:2 final size:2
Alignment explanation
Indices: 1953293--1953329 Score: 74
Period size: 2 Copynumber: 18.5 Consensus size: 2
1953283 CCCTCTGTTT
1953293 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1953330 GTATTATCAA
Statistics
Matches: 35, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 35 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:1959044 original size:30 final size:29
Alignment explanation
Indices: 1958991--1959051 Score: 88
Period size: 30 Copynumber: 2.1 Consensus size: 29
1958981 ATATTTTTAT
*
1958991 ATATTTTTTTATAATTAAATTTAAATAAA
1 ATATTTTTTTATAATAAAATTTAAATAAA
1959020 ATATTTTTATTA-AATAATAATTTAAATAAA
1 ATATTTTT-TTATAATAA-AATTTAAATAAA
1959050 AT
1 AT
1959052 TAAACTACTT
Statistics
Matches: 29, Mismatches: 1, Indels: 3
0.88 0.03 0.09
Matches are distributed among these distances:
29 12 0.41
30 17 0.59
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (29 bp):
ATATTTTTTTATAATAAAATTTAAATAAA
Found at i:1959603 original size:14 final size:12
Alignment explanation
Indices: 1959546--1959604 Score: 55
Period size: 13 Copynumber: 4.3 Consensus size: 12
1959536 GTTTTATATA
1959546 TTAAAATTATATT
1 TTAAAATTA-ATT
1959559 TTAATTTAATTAATT
1 TTAA---AATTAATT
1959574 TATAAAATTAATT
1 T-TAAAATTAATT
1959587 TTAAAATATAATAT
1 TTAAAAT-TAAT-T
1959601 TTAA
1 TTAA
1959605 TAAAAATAAA
Statistics
Matches: 40, Mismatches: 0, Indels: 11
0.78 0.00 0.22
Matches are distributed among these distances:
12 6 0.15
13 17 0.43
14 5 0.12
15 4 0.10
16 8 0.20
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (12 bp):
TTAAAATTAATT
Found at i:1959997 original size:32 final size:31
Alignment explanation
Indices: 1959934--1960000 Score: 80
Period size: 32 Copynumber: 2.1 Consensus size: 31
1959924 ACCTATATAA
* **
1959934 AATTTTAAATTTAATTTTCATCCCTTAAAAT
1 AATTTTAAATTTAATTTTAATAACTTAAAAT
* *
1959965 AATTTTTAATTTACATTTTAATAACTTTAAAT
1 AATTTTAAATTTA-ATTTTAATAACTTAAAAT
1959997 AATT
1 AATT
1960001 ATATAAAGTA
Statistics
Matches: 30, Mismatches: 5, Indels: 1
0.83 0.14 0.03
Matches are distributed among these distances:
31 12 0.40
32 18 0.60
ACGTcount: A:0.40, C:0.09, G:0.00, T:0.51
Consensus pattern (31 bp):
AATTTTAAATTTAATTTTAATAACTTAAAAT
Found at i:1960085 original size:2 final size:2
Alignment explanation
Indices: 1960078--1960104 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
1960068 TGTGATTACA
1960078 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 A
1960105 AATAAAAGTG
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:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:1961739 original size:18 final size:18
Alignment explanation
Indices: 1961699--1961735 Score: 51
Period size: 17 Copynumber: 2.2 Consensus size: 18
1961689 TAAAATTAAT
*
1961699 TAATA-TATTATTTATAA
1 TAATATTATTATTTAAAA
1961716 TAATATTATTA-TTAAAA
1 TAATATTATTATTTAAAA
1961733 TAA
1 TAA
1961736 ATATAATAAT
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
17 13 0.72
18 5 0.28
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (18 bp):
TAATATTATTATTTAAAA
Found at i:1963607 original size:28 final size:28
Alignment explanation
Indices: 1963576--1963631 Score: 71
Period size: 28 Copynumber: 2.0 Consensus size: 28
1963566 TACATATAAT
1963576 AATTACATTAAATAATA-TT-ATTTTAAAA
1 AATTA-ATT-AATAATATTTAATTTTAAAA
*
1963604 AATTAATTAATTATATTTAATTTTAAAA
1 AATTAATTAATAATATTTAATTTTAAAA
1963632 TTTTGAATAA
Statistics
Matches: 25, Mismatches: 1, Indels: 4
0.83 0.03 0.13
Matches are distributed among these distances:
26 6 0.24
27 5 0.20
28 14 0.56
ACGTcount: A:0.52, C:0.02, G:0.00, T:0.46
Consensus pattern (28 bp):
AATTAATTAATAATATTTAATTTTAAAA
Found at i:1963692 original size:27 final size:28
Alignment explanation
Indices: 1963662--1963716 Score: 85
Period size: 27 Copynumber: 2.0 Consensus size: 28
1963652 TTAGATTTTA
*
1963662 ATATATTAATATTATAT-AAATATAAAT
1 ATATATTAATAATATATAAAATATAAAT
*
1963689 ATATATTATTAATATATAAAATATAAAT
1 ATATATTAATAATATATAAAATATAAAT
1963717 TTTTTATAGA
Statistics
Matches: 25, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
27 15 0.60
28 10 0.40
ACGTcount: A:0.56, C:0.00, G:0.00, T:0.44
Consensus pattern (28 bp):
ATATATTAATAATATATAAAATATAAAT
Found at i:1963694 original size:21 final size:20
Alignment explanation
Indices: 1963670--1963713 Score: 63
Period size: 21 Copynumber: 2.1 Consensus size: 20
1963660 TAATATATTA
1963670 ATATTATATAA-ATATAAATAT
1 ATATTAT-TAATATATAAA-AT
1963691 ATATTATTAATATATAAAAT
1 ATATTATTAATATATAAAAT
1963711 ATA
1 ATA
1963714 AATTTTTTAT
Statistics
Matches: 22, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
20 8 0.36
21 14 0.64
ACGTcount: A:0.57, C:0.00, G:0.00, T:0.43
Consensus pattern (20 bp):
ATATTATTAATATATAAAAT
Found at i:1964363 original size:19 final size:19
Alignment explanation
Indices: 1964339--1964387 Score: 64
Period size: 19 Copynumber: 2.6 Consensus size: 19
1964329 AAATTAAATC
*
1964339 ATATAAATTTAATAAAAAA
1 ATATAAATTAAATAAAAAA
* *
1964358 ATATAAAATAAATAATAAA
1 ATATAAATTAAATAAAAAA
1964377 ATA-AAATTAAA
1 ATATAAATTAAA
1964388 ATATTTTAAT
Statistics
Matches: 26, Mismatches: 4, Indels: 1
0.84 0.13 0.03
Matches are distributed among these distances:
18 7 0.27
19 19 0.73
ACGTcount: A:0.71, C:0.00, G:0.00, T:0.29
Consensus pattern (19 bp):
ATATAAATTAAATAAAAAA
Found at i:1964581 original size:9 final size:9
Alignment explanation
Indices: 1964536--1964610 Score: 53
Period size: 9 Copynumber: 7.9 Consensus size: 9
1964526 TAATTATATT
1964536 TAAAATT-A
1 TAAAATTAA
*
1964544 TAAATTTATA
1 TAAAATTA-A
1964554 TTAAAATTAAA
1 -TAAAATT-AA
*
1964565 TAATATTAA
1 TAAAATTAA
*
1964574 TATAATTAA
1 TAAAATTAA
1964583 TAAAATAATAA
1 TAAAAT--TAA
*
1964594 AAAAATTAA
1 TAAAATTAA
*
1964603 TATAATTA
1 TAAAATTA
1964611 TTTCGGGTGT
Statistics
Matches: 52, Mismatches: 9, Indels: 11
0.72 0.12 0.15
Matches are distributed among these distances:
8 6 0.12
9 23 0.44
10 7 0.13
11 15 0.29
12 1 0.02
ACGTcount: A:0.61, C:0.00, G:0.00, T:0.39
Consensus pattern (9 bp):
TAAAATTAA
Found at i:1965290 original size:61 final size:60
Alignment explanation
Indices: 1965186--1965397 Score: 320
Period size: 61 Copynumber: 3.5 Consensus size: 60
1965176 ATATTAAGTT
** * *
1965186 TAATATTAAATATAATTAATAAAAATATGTAT-T-TATCTTAAAGGTATAATCTTTATTTAA
1 TAATATTTGATATGATT-ATAAAAATATG-ATGTGTATCTTAAAGGTGTAATCTTTATTTAA
*
1965246 TAATATTTGATATGATTATAAAAATATGATGTGCTATCTTAAAGGTGTGATCTTTATTTAA
1 TAATATTTGATATGATTATAAAAATATGATGTG-TATCTTAAAGGTGTAATCTTTATTTAA
*
1965307 TAATATTTGATATGATTATAAAAATATGATGCGTTATCTTAAAGGTGTAATCTTTATTTAA
1 TAATATTTGATATGATTATAAAAATATGATGTG-TATCTTAAAGGTGTAATCTTTATTTAA
1965368 TAATATTTGATATGATTATAAAAATATGAT
1 TAATATTTGATATGATTATAAAAATATGAT
1965398 ACGCATAAAA
Statistics
Matches: 141, Mismatches: 8, Indels: 5
0.92 0.05 0.03
Matches are distributed among these distances:
58 2 0.01
59 12 0.09
60 14 0.10
61 113 0.80
ACGTcount: A:0.41, C:0.04, G:0.11, T:0.44
Consensus pattern (60 bp):
TAATATTTGATATGATTATAAAAATATGATGTGTATCTTAAAGGTGTAATCTTTATTTAA
Found at i:1965531 original size:29 final size:27
Alignment explanation
Indices: 1965495--1965556 Score: 70
Period size: 29 Copynumber: 2.2 Consensus size: 27
1965485 ATAAAATTTT
* **
1965495 TTAAATATAATCTTGATACGATAAAATA
1 TTAAATATAATATAAATAC-ATAAAATA
*
1965523 TATAAATATCATATAAATACATAAAATA
1 T-TAAATATAATATAAATACATAAAATA
1965551 TTAAAT
1 TTAAAT
1965557 TTTTATTAAT
Statistics
Matches: 29, Mismatches: 4, Indels: 3
0.81 0.11 0.08
Matches are distributed among these distances:
27 5 0.17
28 10 0.34
29 14 0.48
ACGTcount: A:0.55, C:0.06, G:0.03, T:0.35
Consensus pattern (27 bp):
TTAAATATAATATAAATACATAAAATA
Found at i:1966590 original size:5 final size:5
Alignment explanation
Indices: 1966560--1966593 Score: 50
Period size: 5 Copynumber: 6.6 Consensus size: 5
1966550 TCTATTTTGC
*
1966560 AAAAG AAAAAA AAAAG AAAAG AAAAG AAAAG AAA
1 AAAAG -AAAAG AAAAG AAAAG AAAAG AAAAG AAA
1966594 GATCAACCTG
Statistics
Matches: 26, Mismatches: 2, Indels: 1
0.90 0.07 0.03
Matches are distributed among these distances:
5 22 0.85
6 4 0.15
ACGTcount: A:0.85, C:0.00, G:0.15, T:0.00
Consensus pattern (5 bp):
AAAAG
Found at i:1970925 original size:12 final size:12
Alignment explanation
Indices: 1970910--1970934 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
1970900 TGCAAATGAC
1970910 AAAAAAACAAAA
1 AAAAAAACAAAA
1970922 AAAAAAACAAAA
1 AAAAAAACAAAA
1970934 A
1 A
1970935 CACAACATTT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.92, C:0.08, G:0.00, T:0.00
Consensus pattern (12 bp):
AAAAAAACAAAA
Found at i:1971384 original size:1 final size:1
Alignment explanation
Indices: 1971380--1971422 Score: 68
Period size: 1 Copynumber: 43.0 Consensus size: 1
1971370 ACCCCCACCA
**
1971380 CCCCCCCCATCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCC
1 CCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCC
1971423 GCGAAAACTC
Statistics
Matches: 39, Mismatches: 3, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
1 39 1.00
ACGTcount: A:0.02, C:0.95, G:0.00, T:0.02
Consensus pattern (1 bp):
C
Found at i:1971395 original size:9 final size:9
Alignment explanation
Indices: 1971370--1971421 Score: 65
Period size: 8 Copynumber: 6.0 Consensus size: 9
1971360 ACAAAATAAT
*
1971370 ACCCCCACC
1 ACCCCCCCC
1971379 ACCCCCCCC
1 ACCCCCCCC
1971388 ATCCCCCCCC
1 A-CCCCCCCC
1971398 -CCCCCCCC
1 ACCCCCCCC
1971406 -CCCCCCCC
1 ACCCCCCCC
1971414 -CCCCCCCC
1 ACCCCCCCC
1971422 CGCGAAAACT
Statistics
Matches: 41, Mismatches: 1, Indels: 3
0.91 0.02 0.07
Matches are distributed among these distances:
8 24 0.59
9 9 0.22
10 8 0.20
ACGTcount: A:0.08, C:0.90, G:0.00, T:0.02
Consensus pattern (9 bp):
ACCCCCCCC
Found at i:1978646 original size:3 final size:3
Alignment explanation
Indices: 1978640--1978671 Score: 64
Period size: 3 Copynumber: 10.7 Consensus size: 3
1978630 AATTTTTTTT
1978640 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TT
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TT
1978672 GCGTCAGATT
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:1979019 original size:38 final size:37
Alignment explanation
Indices: 1978976--1979058 Score: 112
Period size: 38 Copynumber: 2.2 Consensus size: 37
1978966 AGAGTTTTTA
* *
1978976 AATTTTATAAATAAAATTAGTTAAATAATACATATTT
1 AATTTTATAAATAAAATTACTAAAATAATACATATTT
* **
1979013 AGATTTTATAAGTAAAATTACTAAAATAATATTTATTT
1 A-ATTTTATAAATAAAATTACTAAAATAATACATATTT
1979051 AATTTTAT
1 AATTTTAT
1979059 GATATATTTT
Statistics
Matches: 40, Mismatches: 5, Indels: 2
0.85 0.11 0.04
Matches are distributed among these distances:
37 8 0.20
38 32 0.80
ACGTcount: A:0.48, C:0.02, G:0.04, T:0.46
Consensus pattern (37 bp):
AATTTTATAAATAAAATTACTAAAATAATACATATTT
Found at i:1979651 original size:23 final size:22
Alignment explanation
Indices: 1979625--1979686 Score: 63
Period size: 21 Copynumber: 2.7 Consensus size: 22
1979615 ATACATTTTT
1979625 ATATCATTTATAAATATAATATA
1 ATATCATTT-TAAATATAATATA
* *
1979648 ATAT-ATATTAAATATACTATA
1 ATATCATTTTAAATATAATATA
*
1979669 TTATTCATATTTAAATAT
1 ATA-TCAT-TTTAAATAT
1979687 TTTATATTTA
Statistics
Matches: 32, Mismatches: 4, Indels: 5
0.78 0.10 0.12
Matches are distributed among these distances:
21 14 0.44
22 4 0.12
23 6 0.19
24 8 0.25
ACGTcount: A:0.48, C:0.05, G:0.00, T:0.47
Consensus pattern (22 bp):
ATATCATTTTAAATATAATATA
Found at i:1981676 original size:4 final size:4
Alignment explanation
Indices: 1981661--1981718 Score: 66
Period size: 4 Copynumber: 14.2 Consensus size: 4
1981651 AATTAGTATC
*
1981661 ATAA ATTAA ATAA ATAA ATTA ATAA A-AA ATATA ATAA CATAA AT-A ATAA
1 ATAA A-TAA ATAA ATAA ATAA ATAA ATAA ATA-A ATAA -ATAA ATAA ATAA
1981710 ATAA ATAA A
1 ATAA ATAA A
1981719 ATATTTTAAT
Statistics
Matches: 47, Mismatches: 2, Indels: 10
0.80 0.03 0.17
Matches are distributed among these distances:
3 6 0.13
4 29 0.62
5 12 0.26
ACGTcount: A:0.71, C:0.02, G:0.00, T:0.28
Consensus pattern (4 bp):
ATAA
Found at i:1981694 original size:21 final size:21
Alignment explanation
Indices: 1981668--1981717 Score: 61
Period size: 21 Copynumber: 2.5 Consensus size: 21
1981658 ATCATAAATT
*
1981668 AAATA-AATAA-ATTAATAAA
1 AAATATAATAACATAAATAAA
*
1981687 AAATATAATAACATAAATAAT
1 AAATATAATAACATAAATAAA
1981708 AAATA-AATAA
1 AAATATAATAA
1981718 AATATTTTAA
Statistics
Matches: 27, Mismatches: 2, Indels: 3
0.84 0.06 0.09
Matches are distributed among these distances:
19 5 0.19
20 10 0.37
21 12 0.44
ACGTcount: A:0.72, C:0.02, G:0.00, T:0.26
Consensus pattern (21 bp):
AAATATAATAACATAAATAAA
Found at i:1981720 original size:9 final size:9
Alignment explanation
Indices: 1981661--1981721 Score: 50
Period size: 9 Copynumber: 6.3 Consensus size: 9
1981651 AATTAGTATC
*
1981661 ATAAATTAA
1 ATAAATAAA
1981670 ATAAATAAA
1 ATAAATAAA
* *
1981679 TTAATAAAAA
1 ATAA-ATAAA
*
1981689 ATATAATAAC
1 ATA-AATAAA
1981699 ATAAATAATAA
1 ATAAAT-A-AA
1981710 ATAAATAAA
1 ATAAATAAA
1981719 ATA
1 ATA
1981722 TTTTAATTTT
Statistics
Matches: 41, Mismatches: 7, Indels: 8
0.73 0.12 0.14
Matches are distributed among these distances:
9 19 0.46
10 14 0.34
11 8 0.20
ACGTcount: A:0.70, C:0.02, G:0.00, T:0.28
Consensus pattern (9 bp):
ATAAATAAA
Found at i:1981797 original size:12 final size:12
Alignment explanation
Indices: 1981773--1981811 Score: 60
Period size: 12 Copynumber: 3.2 Consensus size: 12
1981763 TAATGTTTGA
1981773 TATTTTAATATTT
1 TATTTT-ATATTT
1981786 TATTTTATATTT
1 TATTTTATATTT
*
1981798 TAATTTATATTT
1 TATTTTATATTT
1981810 TA
1 TA
1981812 AAAAACATAT
Statistics
Matches: 25, Mismatches: 1, Indels: 1
0.93 0.04 0.04
Matches are distributed among these distances:
12 19 0.76
13 6 0.24
ACGTcount: A:0.31, C:0.00, G:0.00, T:0.69
Consensus pattern (12 bp):
TATTTTATATTT
Found at i:1982680 original size:60 final size:61
Alignment explanation
Indices: 1982538--1982713 Score: 256
Period size: 61 Copynumber: 3.0 Consensus size: 61
1982528 ATATGTGTAT
* * *
1982538 TTATCTTAAAGGTAT-AATCTTTATTTA-ATACATTTGATATGATTATAACAAATATGATGTG
1 TTATCTTAAAGGTGTGAATCTTTATTTATA-ATATTTGATATGATTATAA-AAATATGATGCG
*
1982599 CTATCTTAAAGGTGTG-ATCTTTATTTATAATATTTGATATGATTATAAAAATATGATGCG
1 TTATCTTAAAGGTGTGAATCTTTATTTATAATATTTGATATGATTATAAAAATATGATGCG
1982659 TTATC-TAAAGGTGTGAATCTTTATTTATAATATTTGATA-GATT-TAAAAATATGAT
1 TTATCTTAAAGGTGTGAATCTTTATTTATAATATTTGATATGATTATAAAAATATGAT
1982714 ACGCATAAAA
Statistics
Matches: 107, Mismatches: 5, Indels: 9
0.88 0.04 0.07
Matches are distributed among these distances:
58 12 0.11
59 14 0.13
60 38 0.36
61 42 0.39
62 1 0.01
ACGTcount: A:0.37, C:0.06, G:0.13, T:0.44
Consensus pattern (61 bp):
TTATCTTAAAGGTGTGAATCTTTATTTATAATATTTGATATGATTATAAAAATATGATGCG
Found at i:1983867 original size:9 final size:9
Alignment explanation
Indices: 1983848--1983882 Score: 56
Period size: 9 Copynumber: 4.1 Consensus size: 9
1983838 ATCTATTTGC
1983848 AAAAGAAA-
1 AAAAGAAAG
1983856 AAAA-AAAG
1 AAAAGAAAG
1983864 AAAAGAAAG
1 AAAAGAAAG
1983873 AAAAGAAAG
1 AAAAGAAAG
1983882 A
1 A
1983883 TCAACCTGGC
Statistics
Matches: 25, Mismatches: 0, Indels: 3
0.89 0.00 0.11
Matches are distributed among these distances:
7 3 0.12
8 8 0.32
9 14 0.56
ACGTcount: A:0.83, C:0.00, G:0.17, T:0.00
Consensus pattern (9 bp):
AAAAGAAAG
Found at i:1988157 original size:11 final size:12
Alignment explanation
Indices: 1988141--1988165 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
1988131 TGCAAATGAC
1988141 AAAAAAAAACAA
1 AAAAAAAAACAA
1988153 AAAAAAAAACAA
1 AAAAAAAAACAA
1988165 A
1 A
1988166 CACAACATTT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.92, C:0.08, G:0.00, T:0.00
Consensus pattern (12 bp):
AAAAAAAAACAA
Found at i:1994537 original size:2 final size:2
Alignment explanation
Indices: 1994530--1994554 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
1994520 TGTGATTACA
1994530 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 A
1994555 AATAAAAGTG
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:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:1996182 original size:18 final size:18
Alignment explanation
Indices: 1996142--1996178 Score: 51
Period size: 17 Copynumber: 2.2 Consensus size: 18
1996132 TAAAATTAAT
*
1996142 TAATA-TATTATTTATAA
1 TAATATTATTATTTAAAA
1996159 TAATATTATTA-TTAAAA
1 TAATATTATTATTTAAAA
1996176 TAA
1 TAA
1996179 ATATAATAAT
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
17 13 0.72
18 5 0.28
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (18 bp):
TAATATTATTATTTAAAA
Found at i:1998046 original size:27 final size:27
Alignment explanation
Indices: 1998015--1998069 Score: 69
Period size: 27 Copynumber: 2.0 Consensus size: 27
1998005 TACATATAAT
1998015 AATTACATTAAATAATA-TT-ATTTTAAA
1 AATTA-ATT-AATAATATTTAATTTTAAA
*
1998042 AATTAATTAATTATATTTAATTTTAAA
1 AATTAATTAATAATATTTAATTTTAAA
1998069 A
1 A
1998070 TTTTGAATAA
Statistics
Matches: 25, Mismatches: 1, Indels: 4
0.83 0.03 0.13
Matches are distributed among these distances:
25 6 0.24
26 5 0.20
27 14 0.56
ACGTcount: A:0.51, C:0.02, G:0.00, T:0.47
Consensus pattern (27 bp):
AATTAATTAATAATATTTAATTTTAAA
Found at i:1998129 original size:21 final size:21
Alignment explanation
Indices: 1998105--1998145 Score: 66
Period size: 21 Copynumber: 2.0 Consensus size: 21
1998095 TTTTATATTA
1998105 ATATTATATAAAT-ATAAATAG
1 ATATTAT-TAAATAATAAATAG
1998126 ATATTATTAAATAATAAATA
1 ATATTATTAAATAATAAATA
1998146 TAAATTTTTT
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
20 5 0.26
21 14 0.74
ACGTcount: A:0.59, C:0.00, G:0.02, T:0.39
Consensus pattern (21 bp):
ATATTATTAAATAATAAATAG
Found at i:1998129 original size:27 final size:27
Alignment explanation
Indices: 1998099--1998150 Score: 70
Period size: 27 Copynumber: 1.9 Consensus size: 27
1998089 ATTAGATTTT
*
1998099 ATATTAAT-ATTATATAAATATAAATAG
1 ATATTAATAAATA-ATAAATATAAATAG
*
1998126 ATATTATTAAATAATAAATATAAAT
1 ATATTAATAAATAATAAATATAAAT
1998151 TTTTTATAGA
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
27 19 0.86
28 3 0.14
ACGTcount: A:0.58, C:0.00, G:0.02, T:0.40
Consensus pattern (27 bp):
ATATTAATAAATAATAAATATAAATAG
Found at i:1999131 original size:24 final size:24
Alignment explanation
Indices: 1999058--1999133 Score: 68
Period size: 23 Copynumber: 3.2 Consensus size: 24
1999048 AAGAAGTTAT
* *
1999058 TTATAAATTTTTTAAAAAAATAT-
1 TTATATATTTTTTTAAAAAATATA
* * *
1999081 TTAAATAATTATTTAATAAAA-A-A
1 TTATATATTTTTTTAA-AAAATATA
*
1999104 TTATGTATTTTTTTAAAAAATATA
1 TTATATATTTTTTTAAAAAATATA
1999128 TTATAT
1 TTATAT
1999134 TTAAATTTAA
Statistics
Matches: 39, Mismatches: 10, Indels: 7
0.70 0.18 0.12
Matches are distributed among these distances:
22 4 0.10
23 25 0.64
24 10 0.26
ACGTcount: A:0.50, C:0.00, G:0.01, T:0.49
Consensus pattern (24 bp):
TTATATATTTTTTTAAAAAATATA
Found at i:1999216 original size:19 final size:19
Alignment explanation
Indices: 1999192--1999240 Score: 64
Period size: 19 Copynumber: 2.6 Consensus size: 19
1999182 AAATTAAATC
*
1999192 ATATAAATTTAATAAAAAA
1 ATATAAATTAAATAAAAAA
* *
1999211 ATATAAAATAAATAATAAA
1 ATATAAATTAAATAAAAAA
1999230 ATA-AAATTAAA
1 ATATAAATTAAA
1999241 ATATTTTAAT
Statistics
Matches: 26, Mismatches: 4, Indels: 1
0.84 0.13 0.03
Matches are distributed among these distances:
18 7 0.27
19 19 0.73
ACGTcount: A:0.71, C:0.00, G:0.00, T:0.29
Consensus pattern (19 bp):
ATATAAATTAAATAAAAAA
Found at i:2000144 original size:61 final size:60
Alignment explanation
Indices: 2000040--2000251 Score: 329
Period size: 61 Copynumber: 3.5 Consensus size: 60
2000030 ATATTAAGTT
** * *
2000040 TAATATTAAATATAATTAATAAAAATATGTAT-T-TATCTTAAAGGTATAATCTTTATTTAA
1 TAATATTTGATATGATT-ATAAAAATATG-ATGTGTATCTTAAAGGTGTAATCTTTATTTAA
*
2000100 TAATATTTGATATGATTATAAAAATATGATGTGCTATCTTAAAGGTGTGATCTTTATTTAA
1 TAATATTTGATATGATTATAAAAATATGATGTG-TATCTTAAAGGTGTAATCTTTATTTAA
2000161 TAATATTTGATATGATTATAAAAATATGATGTGTTATCTTAAAGGTGTAATCTTTATTTAA
1 TAATATTTGATATGATTATAAAAATATGATGTG-TATCTTAAAGGTGTAATCTTTATTTAA
2000222 TAATATTTGATATGATTATAAAAATATGAT
1 TAATATTTGATATGATTATAAAAATATGAT
2000252 ACGCATAAAA
Statistics
Matches: 142, Mismatches: 7, Indels: 5
0.92 0.05 0.03
Matches are distributed among these distances:
58 2 0.01
59 12 0.08
60 14 0.10
61 114 0.80
ACGTcount: A:0.41, C:0.03, G:0.11, T:0.45
Consensus pattern (60 bp):
TAATATTTGATATGATTATAAAAATATGATGTGTATCTTAAAGGTGTAATCTTTATTTAA
Found at i:2000385 original size:29 final size:27
Alignment explanation
Indices: 2000349--2000410 Score: 70
Period size: 29 Copynumber: 2.2 Consensus size: 27
2000339 ATAAAATTTT
* **
2000349 TTAAATATAATCTTGATACGATAAAATA
1 TTAAATATAATATAAATAC-ATAAAATA
*
2000377 TATAAATATCATATAAATACATAAAATA
1 T-TAAATATAATATAAATACATAAAATA
2000405 TTAAAT
1 TTAAAT
2000411 TTTTATTAAT
Statistics
Matches: 29, Mismatches: 4, Indels: 3
0.81 0.11 0.08
Matches are distributed among these distances:
27 5 0.17
28 10 0.34
29 14 0.48
ACGTcount: A:0.55, C:0.06, G:0.03, T:0.35
Consensus pattern (27 bp):
TTAAATATAATATAAATACATAAAATA
Found at i:2005778 original size:12 final size:12
Alignment explanation
Indices: 2005763--2005787 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
2005753 TGCAAATGAC
2005763 AAAAAAACAAAA
1 AAAAAAACAAAA
2005775 AAAAAAACAAAA
1 AAAAAAACAAAA
2005787 A
1 A
2005788 CACAACATTT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.92, C:0.08, G:0.00, T:0.00
Consensus pattern (12 bp):
AAAAAAACAAAA
Found at i:2013476 original size:3 final size:3
Alignment explanation
Indices: 2013468--2013508 Score: 82
Period size: 3 Copynumber: 13.7 Consensus size: 3
2013458 CTCTTCAATT
2013468 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TT
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TT
2013509 GCGTCAGATT
Statistics
Matches: 38, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 38 1.00
ACGTcount: A:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (3 bp):
TTA
Found at i:2013894 original size:38 final size:37
Alignment explanation
Indices: 2013811--2013891 Score: 117
Period size: 38 Copynumber: 2.2 Consensus size: 37
2013801 AGAGTTTTTA
*
2013811 AATTTTATAAATAAAATTAGTTAAATAATACATATTT
1 AATTTTATAAATAAAATTAGTAAAATAATACATATTT
* **
2013848 AGATTTTATAAGTAAAATTAGTAAAATAATATTTATTT
1 A-ATTTTATAAATAAAATTAGTAAAATAATACATATTT
2013886 AATTTT
1 AATTTT
2013892 TATGATATAT
Statistics
Matches: 39, Mismatches: 4, Indels: 2
0.87 0.09 0.04
Matches are distributed among these distances:
37 6 0.15
38 33 0.85
ACGTcount: A:0.48, C:0.01, G:0.05, T:0.46
Consensus pattern (37 bp):
AATTTTATAAATAAAATTAGTAAAATAATACATATTT
Found at i:2014967 original size:2 final size:2
Alignment explanation
Indices: 2014960--2014992 Score: 66
Period size: 2 Copynumber: 16.5 Consensus size: 2
2014950 GCACTAGGAT
2014960 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
2014993 TTGAAGGTTT
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:2015093 original size:34 final size:34
Alignment explanation
Indices: 2015055--2015120 Score: 82
Period size: 34 Copynumber: 1.9 Consensus size: 34
2015045 TTTTTAAAAG
*
2015055 ATATAAAATAAT-TTAATTTATT-AATAATATATAA
1 ATAT-AAATAATATTAATATATTAAAT-ATATATAA
*
2015089 ATATATATAATATTAATATATTAAATATATAT
1 ATATAAATAATATTAATATATTAAATATATAT
2015121 TTTTAAGTTT
Statistics
Matches: 28, Mismatches: 2, Indels: 4
0.82 0.06 0.12
Matches are distributed among these distances:
33 6 0.21
34 19 0.68
35 3 0.11
ACGTcount: A:0.55, C:0.00, G:0.00, T:0.45
Consensus pattern (34 bp):
ATATAAATAATATTAATATATTAAATATATATAA
Found at i:2015099 original size:28 final size:25
Alignment explanation
Indices: 2015073--2015120 Score: 80
Period size: 24 Copynumber: 1.9 Consensus size: 25
2015063 TAATTTAATT
2015073 TATTAATAATATATAAATATATATAA
1 TATTAAT-ATATATAAATATATATAA
2015099 TATTAATATAT-TAAATATATAT
1 TATTAATATATATAAATATATAT
2015121 TTTTAAGTTT
Statistics
Matches: 22, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
24 11 0.50
25 4 0.18
26 7 0.32
ACGTcount: A:0.54, C:0.00, G:0.00, T:0.46
Consensus pattern (25 bp):
TATTAATATATATAAATATATATAA
Found at i:2015106 original size:15 final size:17
Alignment explanation
Indices: 2015078--2015119 Score: 54
Period size: 15 Copynumber: 2.6 Consensus size: 17
2015068 TAATTTATTA
2015078 ATAATATATAAATATAT
1 ATAATATATAAATATAT
2015095 ATAATAT-T-AATATAT
1 ATAATATATAAATATAT
2015110 -TAAATATATA
1 AT-AATATATA
2015120 TTTTTAAGTT
Statistics
Matches: 22, Mismatches: 0, Indels: 6
0.79 0.00 0.21
Matches are distributed among these distances:
14 1 0.05
15 12 0.55
16 2 0.09
17 7 0.32
ACGTcount: A:0.57, C:0.00, G:0.00, T:0.43
Consensus pattern (17 bp):
ATAATATATAAATATAT
Found at i:2015209 original size:30 final size:30
Alignment explanation
Indices: 2015148--2015210 Score: 74
Period size: 32 Copynumber: 2.1 Consensus size: 30
2015138 AAAATATCAT
2015148 AATTTAAAAATTTAAAAAATATTGATGTTAA
1 AATTTAAAAATTTAAAAAATATT-ATGTTAA
* * *
2015179 AATTTAAAATTATTAAATAATATT-TTTTAA
1 AATTTAAAAAT-TTAAAAAATATTATGTTAA
2015209 AA
1 AA
2015211 AATATTAAAT
Statistics
Matches: 28, Mismatches: 3, Indels: 3
0.82 0.09 0.09
Matches are distributed among these distances:
30 7 0.25
31 10 0.36
32 11 0.39
ACGTcount: A:0.54, C:0.00, G:0.03, T:0.43
Consensus pattern (30 bp):
AATTTAAAAATTTAAAAAATATTATGTTAA
Found at i:2015231 original size:23 final size:24
Alignment explanation
Indices: 2015179--2015232 Score: 65
Period size: 24 Copynumber: 2.3 Consensus size: 24
2015169 TTGATGTTAA
* *
2015179 AATTTAAAATTATTAAATAATATT
1 AATTAAAAAATATTAAATAATATT
**
2015203 TTTTAAAAAATATTAAATAA-ATT
1 AATTAAAAAATATTAAATAATATT
2015226 AATTAAA
1 AATTAAA
2015233 TTAAATTTTA
Statistics
Matches: 24, Mismatches: 6, Indels: 1
0.77 0.19 0.03
Matches are distributed among these distances:
23 8 0.33
24 16 0.67
ACGTcount: A:0.57, C:0.00, G:0.00, T:0.43
Consensus pattern (24 bp):
AATTAAAAAATATTAAATAATATT
Found at i:2015232 original size:13 final size:12
Alignment explanation
Indices: 2015185--2015245 Score: 56
Period size: 14 Copynumber: 5.0 Consensus size: 12
2015175 TTAAAATTTA
2015185 AAATTATTAAAT
1 AAATTATTAAAT
*
2015197 AATATTTTTTAAA-
1 AA-A-TTATTAAAT
2015210 AAA-TATTAAAT
1 AAATTATTAAAT
2015221 AAATTAATTAAATT
1 AAATT-ATTAAA-T
2015235 AAATT-TTAAAT
1 AAATTATTAAAT
2015246 TTACTGTAAT
Statistics
Matches: 41, Mismatches: 2, Indels: 13
0.73 0.04 0.23
Matches are distributed among these distances:
10 6 0.15
11 4 0.10
12 9 0.22
13 9 0.22
14 13 0.32
ACGTcount: A:0.56, C:0.00, G:0.00, T:0.44
Consensus pattern (12 bp):
AAATTATTAAAT
Found at i:2015244 original size:25 final size:24
Alignment explanation
Indices: 2015184--2015245 Score: 63
Period size: 25 Copynumber: 2.5 Consensus size: 24
2015174 GTTAAAATTT
**
2015184 AAAATTATTAAATAATATTTTTTAA
1 AAAATT-TTAAATAATATTAATTAA
*
2015209 AAAATATTAAATAA-ATTAATTAA
1 AAAATTTTAAATAATATTAATTAA
2015232 ATTAAATTTTAAAT
1 A--AAATTTTAAAT
2015246 TTACTGTAAT
Statistics
Matches: 31, Mismatches: 4, Indels: 4
0.79 0.10 0.10
Matches are distributed among these distances:
23 8 0.26
24 8 0.26
25 15 0.48
ACGTcount: A:0.56, C:0.00, G:0.00, T:0.44
Consensus pattern (24 bp):
AAAATTTTAAATAATATTAATTAA
Found at i:2016359 original size:23 final size:23
Alignment explanation
Indices: 2016294--2016360 Score: 68
Period size: 23 Copynumber: 3.0 Consensus size: 23
2016284 AAAATAATTA
*
2016294 TATTAAAT-ATTAATTATTATAT
1 TATTAAATAAATAATTATTATAT
* *
2016316 TA-AAAATATATATATTATTATATT
1 TATTAAATAAATA-ATTATTATA-T
2016340 TATTAAATAAATAATT-TTATA
1 TATTAAATAAATAATTATTATA
2016361 AATTGAATTT
Statistics
Matches: 36, Mismatches: 5, Indels: 7
0.75 0.10 0.15
Matches are distributed among these distances:
21 4 0.11
22 4 0.11
23 14 0.39
24 6 0.17
25 8 0.22
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (23 bp):
TATTAAATAAATAATTATTATAT
Found at i:2018446 original size:19 final size:19
Alignment explanation
Indices: 2018414--2018455 Score: 61
Period size: 19 Copynumber: 2.3 Consensus size: 19
2018404 ATTTGTTGTA
2018414 TAATTTTTATATAATTAAT
1 TAATTTTTATATAATTAAT
2018433 TAATATTTTA-ATAATTAA-
1 TAAT-TTTTATATAATTAAT
2018451 TAATT
1 TAATT
2018456 AAATTTAATT
Statistics
Matches: 22, Mismatches: 0, Indels: 4
0.85 0.00 0.15
Matches are distributed among these distances:
17 1 0.05
18 4 0.18
19 12 0.55
20 5 0.23
ACGTcount: A:0.45, C:0.00, G:0.00, T:0.55
Consensus pattern (19 bp):
TAATTTTTATATAATTAAT
Found at i:2019000 original size:2 final size:2
Alignment explanation
Indices: 2018983--2019030 Score: 78
Period size: 2 Copynumber: 24.0 Consensus size: 2
2018973 TAATCAGGAA
* *
2018983 AT AT TT AT AT AC 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
2019025 AT AT AT
1 AT AT AT
2019031 GACAAATGTG
Statistics
Matches: 42, Mismatches: 4, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
2 42 1.00
ACGTcount: A:0.48, C:0.02, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:2022939 original size:28 final size:28
Alignment explanation
Indices: 2022891--2022966 Score: 68
Period size: 28 Copynumber: 2.8 Consensus size: 28
2022881 TAAACTTTTA
2022891 TTATATAAT-TTTTGACA-TATTAATATAT
1 TTATATAATATTTT-A-ATTATTAATATAT
* ** *
2022919 TTATATAATATTTTTATTATTTTTTTAT
1 TTATATAATATTTTAATTATTAATATAT
*
2022947 TT-TATATTATTTTAATTATT
1 TTATATAATATTTTAATTATT
2022967 TTTTATTATG
Statistics
Matches: 40, Mismatches: 6, Indels: 5
0.78 0.12 0.10
Matches are distributed among these distances:
27 17 0.43
28 19 0.47
29 4 0.10
ACGTcount: A:0.33, C:0.01, G:0.01, T:0.64
Consensus pattern (28 bp):
TTATATAATATTTTAATTATTAATATAT
Found at i:2022964 original size:27 final size:28
Alignment explanation
Indices: 2022916--2022970 Score: 85
Period size: 27 Copynumber: 2.0 Consensus size: 28
2022906 CATATTAATA
*
2022916 TATTTATATAATATTTTTATTATTTTTT
1 TATTTATATAATATTTTAATTATTTTTT
*
2022944 TATTT-TATATTATTTTAATTATTTTTT
1 TATTTATATAATATTTTAATTATTTTTT
2022971 ATTATGTTCG
Statistics
Matches: 25, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
27 20 0.80
28 5 0.20
ACGTcount: A:0.27, C:0.00, G:0.00, T:0.73
Consensus pattern (28 bp):
TATTTATATAATATTTTAATTATTTTTT
Found at i:2023135 original size:18 final size:18
Alignment explanation
Indices: 2023114--2023148 Score: 61
Period size: 18 Copynumber: 1.9 Consensus size: 18
2023104 TTTTGCATGA
2023114 TTTTATATTTTAGTTATT
1 TTTTATATTTTAGTTATT
*
2023132 TTTTATATTTTATTTAT
1 TTTTATATTTTAGTTAT
2023149 GTTCGTGAGT
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
18 16 1.00
ACGTcount: A:0.23, C:0.00, G:0.03, T:0.74
Consensus pattern (18 bp):
TTTTATATTTTAGTTATT
Found at i:2023336 original size:40 final size:38
Alignment explanation
Indices: 2023292--2023410 Score: 104
Period size: 37 Copynumber: 3.1 Consensus size: 38
2023282 ATTTGACTCA
2023292 AATTATTGATTAAATAATAAAAATATTTTTATTTAAATTT
1 AATTATT-ATTAAATAATAAAAATATTTTTATTT-AATTT
* * *
2023332 AATTA-TA-TAAATATTAATATAATTTTTTTATTT--TTA
1 AATTATTATTAAATAATAA-A-AATATTTTTATTTAATTT
* *
2023368 ATATTATT-TTAAATAATAAAATATATTTTAAATTAATTT
1 A-ATTATTATTAAATAATAAAA-ATATTTTTATTTAATTT
2023407 AATT
1 AATT
2023411 TAAATTAAAT
Statistics
Matches: 63, Mismatches: 8, Indels: 18
0.71 0.09 0.20
Matches are distributed among these distances:
36 4 0.06
37 23 0.37
38 15 0.24
39 16 0.25
40 5 0.08
ACGTcount: A:0.46, C:0.00, G:0.01, T:0.53
Consensus pattern (38 bp):
AATTATTATTAAATAATAAAAATATTTTTATTTAATTT
Found at i:2026744 original size:2 final size:2
Alignment explanation
Indices: 2026737--2026777 Score: 82
Period size: 2 Copynumber: 20.5 Consensus size: 2
2026727 ACACTATCCT
2026737 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
2026778 GGTAGAAAAA
Statistics
Matches: 39, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 39 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:2027505 original size:14 final size:15
Alignment explanation
Indices: 2027488--2027528 Score: 50
Period size: 14 Copynumber: 2.9 Consensus size: 15
2027478 AAAAATATTT
*
2027488 TTATTTAAAT-TTAA
1 TTATATAAATATTAA
2027502 TTATATAAATATTAA
1 TTATATAAATATTAA
*
2027517 -TATAAAAATATT
1 TTATATAAATATT
2027529 TTTAATATTT
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
14 20 0.83
15 4 0.17
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (15 bp):
TTATATAAATATTAA
Found at i:2027570 original size:20 final size:19
Alignment explanation
Indices: 2027513--2027577 Score: 62
Period size: 20 Copynumber: 3.4 Consensus size: 19
2027503 TATATAAATA
2027513 TTAAT-ATAAAA-ATATTT
1 TTAATAATAAAATATATTT
* **
2027530 TTAATATTTTAATATTATTT
1 TTAATAATAAAATA-TATTT
*
2027550 TAAATAATAAAATATATTT
1 TTAATAATAAAATATATTT
2027569 TTGAATAAT
1 TT-AATAAT
2027578 CTAATTTAAA
Statistics
Matches: 36, Mismatches: 8, Indels: 5
0.73 0.16 0.10
Matches are distributed among these distances:
17 5 0.14
18 3 0.08
19 7 0.19
20 21 0.58
ACGTcount: A:0.48, C:0.00, G:0.02, T:0.51
Consensus pattern (19 bp):
TTAATAATAAAATATATTT
Found at i:2027592 original size:39 final size:38
Alignment explanation
Indices: 2027470--2027592 Score: 97
Period size: 39 Copynumber: 3.1 Consensus size: 38
2027460 GTTATTATTC
* *
2027470 AAATAATAAAAAATATTTTTATTTAAATTTAATTATATAAATAT
1 AAATAAT-AAAAATATTTTTA-AT-AATCTAA-TAT-TAAAT-T
* * * **
2027514 TAAT-ATAAAAATATTTTTAATATTTTAATATTATTTT
1 AAATAATAAAAATATTTTTAATAATCTAATATTAAATT
2027551 AAATAATAAAATATATTTTTGAATAATCTAAT-TTAAATT
1 AAATAATAAAA-ATATTTTT-AATAATCTAATATTAAATT
2027590 AAA
1 AAA
2027593 ATTTAAAAAT
Statistics
Matches: 66, Mismatches: 10, Indels: 11
0.76 0.11 0.13
Matches are distributed among these distances:
37 4 0.06
38 9 0.14
39 19 0.29
40 15 0.23
41 1 0.02
42 13 0.20
43 2 0.03
44 3 0.05
ACGTcount: A:0.51, C:0.01, G:0.01, T:0.47
Consensus pattern (38 bp):
AAATAATAAAAATATTTTTAATAATCTAATATTAAATT
Found at i:2032625 original size:23 final size:24
Alignment explanation
Indices: 2032583--2032627 Score: 65
Period size: 23 Copynumber: 1.9 Consensus size: 24
2032573 ATTTTTAAAA
*
2032583 TTAAAATATATATATTTAAATATT
1 TTAAAATATAAATATTTAAATATT
*
2032607 TTAAAA-ATAAATTTTTAAATA
1 TTAAAATATAAATATTTAAATA
2032628 AAATATGTTT
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
23 13 0.68
24 6 0.32
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (24 bp):
TTAAAATATAAATATTTAAATATT
Found at i:2035797 original size:4 final size:4
Alignment explanation
Indices: 2035790--2035832 Score: 86
Period size: 4 Copynumber: 10.8 Consensus size: 4
2035780 TATATATATA
2035790 TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG TAT
1 TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG TAT
2035833 TTAACAAACT
Statistics
Matches: 39, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 39 1.00
ACGTcount: A:0.26, C:0.00, G:0.23, T:0.51
Consensus pattern (4 bp):
TATG
Found at i:2036895 original size:12 final size:10
Alignment explanation
Indices: 2036856--2036906 Score: 52
Period size: 10 Copynumber: 5.0 Consensus size: 10
2036846 TGGTATGAAT
2036856 TTATTTTATTA
1 TTATTTTA-TA
*
2036867 TT-TGTTATA
1 TTATTTTATA
2036876 TTATTTTATA
1 TTATTTTATA
2036886 TTAATATTTATA
1 TT-AT-TTTATA
2036898 -TATTTTATA
1 TTATTTTATA
2036907 ATTAAATTTA
Statistics
Matches: 35, Mismatches: 2, Indels: 8
0.78 0.04 0.18
Matches are distributed among these distances:
9 10 0.29
10 14 0.40
11 5 0.14
12 6 0.17
ACGTcount: A:0.31, C:0.00, G:0.02, T:0.67
Consensus pattern (10 bp):
TTATTTTATA
Found at i:2036903 original size:21 final size:22
Alignment explanation
Indices: 2036871--2036916 Score: 69
Period size: 21 Copynumber: 2.1 Consensus size: 22
2036861 TTATTATTTG
2036871 TTATATTATTTTAT-ATTAATAT
1 TTATATTATTTTATAATTAA-AT
2036893 TTATA-TATTTTATAATTAAAT
1 TTATATTATTTTATAATTAAAT
2036914 TTA
1 TTA
2036917 AATAAAATAT
Statistics
Matches: 23, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
21 13 0.57
22 10 0.43
ACGTcount: A:0.39, C:0.00, G:0.00, T:0.61
Consensus pattern (22 bp):
TTATATTATTTTATAATTAAAT
Found at i:2037473 original size:17 final size:16
Alignment explanation
Indices: 2037462--2037506 Score: 54
Period size: 16 Copynumber: 2.7 Consensus size: 16
2037452 ATTTTCATAT
2037462 TTTTAAATTTTTATTA
1 TTTTAAATTTTTATTA
* *
2037478 TTTTAAATATATATTTA
1 TTTTAAATTTTTA-TTA
2037495 TTTTAAGATTTT
1 TTTTAA-ATTTT
2037507 AATTTCAATT
Statistics
Matches: 23, Mismatches: 4, Indels: 2
0.79 0.14 0.07
Matches are distributed among these distances:
16 11 0.48
17 9 0.39
18 3 0.13
ACGTcount: A:0.33, C:0.00, G:0.02, T:0.64
Consensus pattern (16 bp):
TTTTAAATTTTTATTA
Found at i:2037830 original size:14 final size:14
Alignment explanation
Indices: 2037797--2037864 Score: 55
Period size: 14 Copynumber: 4.4 Consensus size: 14
2037787 TTTTATTATT
*
2037797 ATATATAAGATATTA
1 ATATATAA-ATTTTA
2037812 TATATATAAATTTTA
1 -ATATATAAATTTTA
2037827 ATATATTAATAATTTATA
1 ATATA-T-A-AATTT-TA
*
2037845 TTATATAAATTTTA
1 ATATATAAATTTTA
*
2037859 ACATAT
1 ATATAT
2037865 TAATATATTC
Statistics
Matches: 44, Mismatches: 4, Indels: 10
0.76 0.07 0.17
Matches are distributed among these distances:
14 11 0.25
15 11 0.25
16 10 0.23
17 6 0.14
18 6 0.14
ACGTcount: A:0.49, C:0.01, G:0.01, T:0.49
Consensus pattern (14 bp):
ATATATAAATTTTA
Found at i:2037831 original size:18 final size:18
Alignment explanation
Indices: 2037810--2037864 Score: 57
Period size: 15 Copynumber: 3.3 Consensus size: 18
2037800 TATAAGATAT
2037810 TATATATATAAATTTTAA
1 TATATATATAAATTTTAA
2037828 TATAT-TA-ATAA-TTT-A
1 TATATATATA-AATTTTAA
2037843 TAT-TATATAAATTTTAA
1 TATATATATAAATTTTAA
*
2037860 CATAT
1 TATAT
2037865 TAATATATTC
Statistics
Matches: 30, Mismatches: 1, Indels: 12
0.70 0.02 0.28
Matches are distributed among these distances:
14 1 0.03
15 8 0.27
16 8 0.27
17 7 0.23
18 6 0.20
ACGTcount: A:0.47, C:0.02, G:0.00, T:0.51
Consensus pattern (18 bp):
TATATATATAAATTTTAA
Found at i:2037850 original size:32 final size:31
Alignment explanation
Indices: 2037809--2037869 Score: 104
Period size: 32 Copynumber: 1.9 Consensus size: 31
2037799 ATATAAGATA
*
2037809 TTATATATATAAATTTTAATATATTAATAAT
1 TTATATATATAAATTTTAACATATTAATAAT
2037840 TTATATTATATAAATTTTAACATATTAATA
1 TTATA-TATATAAATTTTAACATATTAATA
2037870 TATTCGTATT
Statistics
Matches: 28, Mismatches: 1, Indels: 1
0.93 0.03 0.03
Matches are distributed among these distances:
31 5 0.18
32 23 0.82
ACGTcount: A:0.48, C:0.02, G:0.00, T:0.51
Consensus pattern (31 bp):
TTATATATATAAATTTTAACATATTAATAAT
Found at i:2037858 original size:16 final size:16
Alignment explanation
Indices: 2037796--2037858 Score: 60
Period size: 16 Copynumber: 4.0 Consensus size: 16
2037786 GTTTTATTAT
*
2037796 TATATATAAGATATTA
1 TATATATAAGATTTTA
2037812 TATATATAA-ATTTTA
1 TATATATAAGATTTTA
* *
2037827 -ATATATTAATAATTTA
1 TATATA-TAAGATTTTA
2037843 TATTATATAA-ATTTTA
1 TA-TATATAAGATTTTA
2037859 ACATATTAAT
Statistics
Matches: 40, Mismatches: 3, Indels: 8
0.78 0.06 0.16
Matches are distributed among these distances:
14 5 0.12
15 8 0.20
16 19 0.47
17 4 0.10
18 4 0.10
ACGTcount: A:0.48, C:0.00, G:0.02, T:0.51
Consensus pattern (16 bp):
TATATATAAGATTTTA
Found at i:2037887 original size:14 final size:15
Alignment explanation
Indices: 2037868--2037908 Score: 50
Period size: 14 Copynumber: 2.9 Consensus size: 15
2037858 AACATATTAA
*
2037868 TATATTCGTATTATT
1 TATATTAGTATTATT
*
2037883 T-TATTATTATTATT
1 TATATTAGTATTATT
2037897 TATATTA-TATTA
1 TATATTAGTATTA
2037909 CGTTTTAATT
Statistics
Matches: 23, Mismatches: 2, Indels: 3
0.82 0.07 0.11
Matches are distributed among these distances:
14 17 0.74
15 6 0.26
ACGTcount: A:0.32, C:0.02, G:0.02, T:0.63
Consensus pattern (15 bp):
TATATTAGTATTATT
Found at i:2038074 original size:12 final size:11
Alignment explanation
Indices: 2038049--2038095 Score: 51
Period size: 11 Copynumber: 4.1 Consensus size: 11
2038039 ATTATGATAA
2038049 TTTATTTTTAT
1 TTTATTTTTAT
2038060 TTTATTTTATAT
1 TTTATTTT-TAT
*
2038072 TTTAGTTATT-T
1 TTTA-TTTTTAT
2038083 TTTATATTTTAT
1 TTTAT-TTTTAT
2038095 T
1 T
2038096 CTTGTTTTTG
Statistics
Matches: 30, Mismatches: 2, Indels: 7
0.77 0.05 0.18
Matches are distributed among these distances:
10 1 0.03
11 16 0.53
12 10 0.33
13 3 0.10
ACGTcount: A:0.21, C:0.00, G:0.02, T:0.77
Consensus pattern (11 bp):
TTTATTTTTAT
Found at i:2038103 original size:18 final size:16
Alignment explanation
Indices: 2038049--2038095 Score: 60
Period size: 18 Copynumber: 2.8 Consensus size: 16
2038039 ATTATGATAA
2038049 TTTAT-TTTTATTTTAT
1 TTTATATTTTATTTT-T
2038065 TTTATATTTTAGTTATTT
1 TTTATATTTTA-TT-TTT
2038083 TTTATATTTTATT
1 TTTATATTTTATT
2038096 CTTGTTTTTG
Statistics
Matches: 28, Mismatches: 0, Indels: 5
0.85 0.00 0.15
Matches are distributed among these distances:
16 5 0.18
17 7 0.25
18 14 0.50
19 2 0.07
ACGTcount: A:0.21, C:0.00, G:0.02, T:0.77
Consensus pattern (16 bp):
TTTATATTTTATTTTT
Found at i:2038356 original size:20 final size:20
Alignment explanation
Indices: 2038307--2038362 Score: 62
Period size: 20 Copynumber: 2.9 Consensus size: 20
2038297 ATATAAATAT
2038307 TAATATAAA-ATTATTTTAAA
1 TAATA-AAATATTATTTTAAA
* **
2038327 TATTTTAATATTATTTTAAA
1 TAATAAAATATTATTTTAAA
2038347 TAATAAAATA-TATTTT
1 TAATAAAATATTATTTT
2038363 TGAATCAATC
Statistics
Matches: 29, Mismatches: 6, Indels: 3
0.76 0.16 0.08
Matches are distributed among these distances:
19 8 0.28
20 21 0.72
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (20 bp):
TAATAAAATATTATTTTAAA
Found at i:2045410 original size:2 final size:2
Alignment explanation
Indices: 2045403--2045440 Score: 76
Period size: 2 Copynumber: 19.0 Consensus size: 2
2045393 TTGGTCAAGA
2045403 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
2045441 TCAATTTTAG
Statistics
Matches: 36, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 36 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:2047170 original size:23 final size:22
Alignment explanation
Indices: 2047144--2047190 Score: 60
Period size: 22 Copynumber: 2.1 Consensus size: 22
2047134 TAAATTTAAA
*
2047144 ATCTTAATATTTATAATTT-TTTT
1 ATCTTAAT-TTGA-AATTTCTTTT
2047167 ATCTTAATTTGAAATTTCTTTT
1 ATCTTAATTTGAAATTTCTTTT
2047189 AT
1 AT
2047191 AAAAAAAGTA
Statistics
Matches: 22, Mismatches: 1, Indels: 3
0.85 0.04 0.12
Matches are distributed among these distances:
21 5 0.23
22 9 0.41
23 8 0.36
ACGTcount: A:0.30, C:0.06, G:0.02, T:0.62
Consensus pattern (22 bp):
ATCTTAATTTGAAATTTCTTTT
Found at i:2050203 original size:27 final size:28
Alignment explanation
Indices: 2050141--2050219 Score: 72
Period size: 27 Copynumber: 2.8 Consensus size: 28
2050131 TCAATAAAAG
* * *
2050141 TTACTTTTTATGTTTATTAAAAATGATAA
1 TTACTTTGTA-GTTTGTCAAAAATGATAA
2050170 TTACTTTGTAG-TTGTCAAAAATGATAGA
1 TTACTTTGTAGTTTGTCAAAAATGATA-A
* * *
2050198 -TCCTTTTTTGTTTGTCAAAAAT
1 TTACTTTGTAGTTTGTCAAAAAT
2050220 TACGACTTAT
Statistics
Matches: 42, Mismatches: 6, Indels: 5
0.79 0.11 0.09
Matches are distributed among these distances:
27 20 0.48
28 13 0.31
29 9 0.21
ACGTcount: A:0.33, C:0.08, G:0.11, T:0.48
Consensus pattern (28 bp):
TTACTTTGTAGTTTGTCAAAAATGATAA
Found at i:2054729 original size:27 final size:25
Alignment explanation
Indices: 2054698--2054795 Score: 92
Period size: 27 Copynumber: 3.8 Consensus size: 25
2054688 AAAAACCACC
2054698 CTTTGTGTTTGTCAAAAATGGTGGTT
1 CTTTGTGTTTGTCAAAAATGGTGG-T
* *
2054724 ACTTTGTATTTGTCAAAAATGGTGAAT
1 -CTTTGTGTTTGTCAAAAATGGTG-GT
* *
2054751 CCTTTTTTGTTTGTCAAAAATTGTGG-
1 -C-TTTGTGTTTGTCAAAAATGGTGGT
2054777 C-TTGTTGTTTGTCAAAAAT
1 CTTTG-TGTTTGTCAAAAAT
2054796 TGGTAGCTAA
Statistics
Matches: 60, Mismatches: 8, Indels: 9
0.78 0.10 0.12
Matches are distributed among these distances:
23 2 0.03
24 14 0.23
25 1 0.02
27 24 0.40
28 19 0.32
ACGTcount: A:0.24, C:0.09, G:0.20, T:0.46
Consensus pattern (25 bp):
CTTTGTGTTTGTCAAAAATGGTGGT
Found at i:2054764 original size:28 final size:27
Alignment explanation
Indices: 2054698--2054771 Score: 94
Period size: 27 Copynumber: 2.7 Consensus size: 27
2054688 AAAAACCACC
**
2054698 CTTTGTGTTTGTCAAAAATGGTGGTTA
1 CTTTGTGTTTGTCAAAAATGGTGAATA
* *
2054725 CTTTGTATTTGTCAAAAATGGTGAATC
1 CTTTGTGTTTGTCAAAAATGGTGAATA
*
2054752 CTTTTTTGTTTGTCAAAAAT
1 C-TTTGTGTTTGTCAAAAAT
2054772 TGTGGCTTGT
Statistics
Matches: 40, Mismatches: 6, Indels: 1
0.85 0.13 0.02
Matches are distributed among these distances:
27 24 0.60
28 16 0.40
ACGTcount: A:0.26, C:0.09, G:0.19, T:0.46
Consensus pattern (27 bp):
CTTTGTGTTTGTCAAAAATGGTGAATA
Found at i:2059552 original size:2 final size:2
Alignment explanation
Indices: 2059545--2059575 Score: 62
Period size: 2 Copynumber: 15.5 Consensus size: 2
2059535 CCACCAAGAC
2059545 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 A
2059576 GACAAGAGCA
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:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:2069579 original size:15 final size:15
Alignment explanation
Indices: 2069561--2069592 Score: 55
Period size: 15 Copynumber: 2.1 Consensus size: 15
2069551 ATAATATTAG
*
2069561 ATACATATATATTTA
1 ATACAGATATATTTA
2069576 ATACAGATATATTTA
1 ATACAGATATATTTA
2069591 AT
1 AT
2069593 TTTTTAAATT
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 16 1.00
ACGTcount: A:0.47, C:0.06, G:0.03, T:0.44
Consensus pattern (15 bp):
ATACAGATATATTTA
Found at i:2070980 original size:19 final size:20
Alignment explanation
Indices: 2070944--2070985 Score: 50
Period size: 19 Copynumber: 2.1 Consensus size: 20
2070934 TCGACTCAAC
* *
2070944 TATTTTTCTATTACATAATA
1 TATTTTTCTATCACATAAAA
*
2070964 TATTTTT-TATCATATAAAA
1 TATTTTTCTATCACATAAAA
2070983 TAT
1 TAT
2070986 ATATAATATT
Statistics
Matches: 19, Mismatches: 3, Indels: 1
0.83 0.13 0.04
Matches are distributed among these distances:
19 12 0.63
20 7 0.37
ACGTcount: A:0.38, C:0.07, G:0.00, T:0.55
Consensus pattern (20 bp):
TATTTTTCTATCACATAAAA
Found at i:2073038 original size:9 final size:9
Alignment explanation
Indices: 2073024--2073077 Score: 51
Period size: 9 Copynumber: 6.1 Consensus size: 9
2073014 TCAAACGAGT
2073024 ATTTAATTA
1 ATTTAATTA
*
2073033 ATTTAATTG
1 ATTTAATTA
2073042 ATTTAATT-
1 ATTTAATTA
2073050 -TTTAAATATA
1 ATTT-AAT-TA
2073060 A-TTAATTA
1 ATTTAATTA
*
2073068 ATTAAATTA
1 ATTTAATTA
2073077 A
1 A
2073078 ATTATATTTT
Statistics
Matches: 38, Mismatches: 2, Indels: 10
0.76 0.04 0.20
Matches are distributed among these distances:
7 3 0.08
8 6 0.16
9 27 0.71
10 2 0.05
ACGTcount: A:0.46, C:0.00, G:0.02, T:0.52
Consensus pattern (9 bp):
ATTTAATTA
Found at i:2073199 original size:2 final size:2
Alignment explanation
Indices: 2073192--2073254 Score: 81
Period size: 2 Copynumber: 31.5 Consensus size: 2
2073182 ATACCTCATC
** * *
2073192 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA CG TG TG TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
*
2073234 TA TA TA TA TA TA TG TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA T
2073255 CGCAGCTAAG
Statistics
Matches: 55, Mismatches: 6, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
2 55 1.00
ACGTcount: A:0.43, C:0.02, G:0.06, T:0.49
Consensus pattern (2 bp):
TA
Found at i:2074393 original size:20 final size:20
Alignment explanation
Indices: 2074359--2074398 Score: 55
Period size: 20 Copynumber: 2.0 Consensus size: 20
2074349 AAAAAAATTA
*
2074359 ATAATAAATTATTATTAAAT
1 ATAATAAATTATTATAAAAT
2074379 ATAATAAA-TATTTATAAAAT
1 ATAATAAATTA-TTATAAAAT
2074399 TATATATTTA
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
19 2 0.11
20 16 0.89
ACGTcount: A:0.57, C:0.00, G:0.00, T:0.42
Consensus pattern (20 bp):
ATAATAAATTATTATAAAAT
Found at i:2074445 original size:28 final size:28
Alignment explanation
Indices: 2074414--2074467 Score: 83
Period size: 28 Copynumber: 1.9 Consensus size: 28
2074404 ATTTAATTTA
*
2074414 ATAT-ATAATTTTTAATATAAATTTTATT
1 ATATAATAATTTTT-ATAAAAATTTTATT
2074442 ATATAATAATTTTTATAAAAATTTTA
1 ATATAATAATTTTTATAAAAATTTTA
2074468 AAATTAATTT
Statistics
Matches: 24, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
28 15 0.62
29 9 0.38
ACGTcount: A:0.46, C:0.00, G:0.00, T:0.54
Consensus pattern (28 bp):
ATATAATAATTTTTATAAAAATTTTATT
Found at i:2074454 original size:16 final size:14
Alignment explanation
Indices: 2074410--2074456 Score: 60
Period size: 14 Copynumber: 3.3 Consensus size: 14
2074400 ATATATTTAA
2074410 TTTAATATATAATT
1 TTTAATATATAATT
2074424 TTTAATATA-AATT
1 TTTAATATATAATT
*
2074437 TTATTATATAATAATT
1 TT-TAATAT-ATAATT
2074453 TTTA
1 TTTA
2074457 TAAAAATTTT
Statistics
Matches: 28, Mismatches: 2, Indels: 5
0.80 0.06 0.14
Matches are distributed among these distances:
13 6 0.21
14 14 0.50
15 2 0.07
16 6 0.21
ACGTcount: A:0.43, C:0.00, G:0.00, T:0.57
Consensus pattern (14 bp):
TTTAATATATAATT
Found at i:2074457 original size:14 final size:13
Alignment explanation
Indices: 2074414--2074466 Score: 54
Period size: 14 Copynumber: 3.9 Consensus size: 13
2074404 ATTTAATTTA
*
2074414 ATATATAATTTTT
1 ATATAAAATTTTT
*
2074427 AATATAAATTTTATT
1 -ATATAAAATTT-TT
2074442 ATATAATAATTTTT
1 ATATAA-AATTTTT
2074456 ATA-AAAATTTT
1 ATATAAAATTTT
2074467 AAAATTAATT
Statistics
Matches: 34, Mismatches: 3, Indels: 6
0.79 0.07 0.14
Matches are distributed among these distances:
12 6 0.18
13 2 0.06
14 20 0.59
15 6 0.18
ACGTcount: A:0.45, C:0.00, G:0.00, T:0.55
Consensus pattern (13 bp):
ATATAAAATTTTT
Found at i:2075086 original size:20 final size:19
Alignment explanation
Indices: 2075061--2075121 Score: 61
Period size: 20 Copynumber: 3.2 Consensus size: 19
2075051 TTAGTTAATA
*
2075061 TTTTTATATACTTATATTAT
1 TTTTTAAATA-TTATATTAT
2075081 TTTTTAAAATATTATATTAT
1 TTTTT-AAATATTATATTAT
* * *
2075101 ATTTTAATTATT-TTTTAT
1 TTTTTAAATATTATATTAT
2075119 TTT
1 TTT
2075122 GATGATAAGA
Statistics
Matches: 35, Mismatches: 5, Indels: 4
0.80 0.11 0.09
Matches are distributed among these distances:
18 7 0.20
19 6 0.17
20 18 0.51
21 4 0.11
ACGTcount: A:0.31, C:0.02, G:0.00, T:0.67
Consensus pattern (19 bp):
TTTTTAAATATTATATTAT
Found at i:2076510 original size:20 final size:21
Alignment explanation
Indices: 2076469--2076510 Score: 59
Period size: 20 Copynumber: 2.0 Consensus size: 21
2076459 TTATTATTTA
*
2076469 TTATATTATTAAAATTATATT
1 TTATATTATTAAAATTAAATT
*
2076490 TTATATT-TTATAATTAAATT
1 TTATATTATTAAAATTAAATT
2076510 T
1 T
2076511 AAATAAAAAT
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
20 12 0.63
21 7 0.37
ACGTcount: A:0.40, C:0.00, G:0.00, T:0.60
Consensus pattern (21 bp):
TTATATTATTAAAATTAAATT
Found at i:2077197 original size:3 final size:3
Alignment explanation
Indices: 2077189--2077228 Score: 80
Period size: 3 Copynumber: 13.3 Consensus size: 3
2077179 AGTATCGTTG
2077189 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA T
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA T
2077229 ATTTGATTTG
Statistics
Matches: 37, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 37 1.00
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.68
Consensus pattern (3 bp):
TTA
Found at i:2077556 original size:20 final size:18
Alignment explanation
Indices: 2077517--2077560 Score: 54
Period size: 20 Copynumber: 2.4 Consensus size: 18
2077507 TAAAAGTAAT
*
2077517 TAATA-TATTATTTATAA
1 TAATATTATTATTTAAAA
2077534 TAATATTATTATATTAAATA
1 TAATATTATTAT-TTAAA-A
2077554 TAATATT
1 TAATATT
2077561 TAATAATTTT
Statistics
Matches: 23, Mismatches: 1, Indels: 3
0.85 0.04 0.11
Matches are distributed among these distances:
17 5 0.22
18 6 0.26
19 4 0.17
20 8 0.35
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (18 bp):
TAATATTATTATTTAAAA
Found at i:2077578 original size:33 final size:32
Alignment explanation
Indices: 2077518--2077612 Score: 100
Period size: 33 Copynumber: 2.9 Consensus size: 32
2077508 AAAAGTAATT
* *
2077518 AATATATTATTTATAATAATATTATTATATTA
1 AATATAATATTTATAATAATATCATTATATTA
** * *
2077550 AATATAATATTTAATAATTTTATCATTATTTTT
1 AATATAATATTT-ATAATAATATCATTATATTA
* * *
2077583 AATATAATATATATAAAAATATTATTATAT
1 AATATAATATTTATAATAATATCATTATAT
2077613 CCAATAACTT
Statistics
Matches: 50, Mismatches: 12, Indels: 2
0.78 0.19 0.03
Matches are distributed among these distances:
32 24 0.48
33 26 0.52
ACGTcount: A:0.47, C:0.01, G:0.00, T:0.52
Consensus pattern (32 bp):
AATATAATATTTATAATAATATCATTATATTA
Found at i:2078133 original size:24 final size:23
Alignment explanation
Indices: 2078090--2078138 Score: 57
Period size: 23 Copynumber: 2.1 Consensus size: 23
2078080 TTAATTAAAG
2078090 TAATATTTTAAAAAATAAAATTAA
1 TAATATTTTAAAAAATAAAA-TAA
2078114 TAAT-TTTTAAATTAAA-AAAATAA
1 TAATATTTTAAA--AAATAAAATAA
2078137 TA
1 TA
2078139 CATTAAATAT
Statistics
Matches: 23, Mismatches: 0, Indels: 5
0.82 0.00 0.18
Matches are distributed among these distances:
23 12 0.52
24 8 0.35
25 3 0.13
ACGTcount: A:0.61, C:0.00, G:0.00, T:0.39
Consensus pattern (23 bp):
TAATATTTTAAAAAATAAAATAA
Found at i:2078151 original size:22 final size:22
Alignment explanation
Indices: 2078120--2078179 Score: 59
Period size: 22 Copynumber: 2.7 Consensus size: 22
2078110 TTAATAATTT
2078120 TTAAAT-TAAAAAAATAATACA
1 TTAAATATAAAAAAATAATACA
* ** *
2078141 TTAAATATAAAACAATTCTATA
1 TTAAATATAAAAAAATAATACA
*
2078163 ATAAATTATAAAAAAAT
1 TTAAA-TATAAAAAAAT
2078180 TAATTTATAA
Statistics
Matches: 31, Mismatches: 6, Indels: 2
0.79 0.15 0.05
Matches are distributed among these distances:
21 6 0.19
22 15 0.48
23 10 0.32
ACGTcount: A:0.63, C:0.05, G:0.00, T:0.32
Consensus pattern (22 bp):
TTAAATATAAAAAAATAATACA
Found at i:2078163 original size:27 final size:26
Alignment explanation
Indices: 2078133--2078206 Score: 66
Period size: 27 Copynumber: 2.9 Consensus size: 26
2078123 AATTAAAAAA
*
2078133 ATAATACATTAAATATAAAACAATTCT
1 ATAATAAATTAAATATAAAACAATT-T
*
2078160 ATAATAAATTATAA-A-AAAATTAATTT
1 ATAATAAATTA-AATATAAAA-CAATTT
*
2078186 ATAAT-TA-TAAATATAAAACAA
1 ATAATAAATTAAATATAAAACAA
2078207 ATCTCTGAAA
Statistics
Matches: 39, Mismatches: 4, Indels: 11
0.72 0.07 0.20
Matches are distributed among these distances:
23 2 0.05
24 5 0.13
25 5 0.13
26 10 0.26
27 15 0.38
28 2 0.05
ACGTcount: A:0.61, C:0.05, G:0.00, T:0.34
Consensus pattern (26 bp):
ATAATAAATTAAATATAAAACAATTT
Found at i:2079682 original size:19 final size:20
Alignment explanation
Indices: 2079640--2079682 Score: 54
Period size: 19 Copynumber: 2.2 Consensus size: 20
2079630 TTGTGTTAAT
*
2079640 ATTA-TTTTTTATTATTTTA
1 ATTATTTTTTTATTATTATA
2079659 ATTATTTTTTTA-TATTATA
1 ATTATTTTTTTATTATTATA
*
2079678 TTTAT
1 ATTAT
2079683 ATCGTATCAA
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
19 14 0.67
20 7 0.33
ACGTcount: A:0.28, C:0.00, G:0.00, T:0.72
Consensus pattern (20 bp):
ATTATTTTTTTATTATTATA
Done.