Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold20
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: 3599867
ACGTcount: A:0.33, C:0.16, G:0.17, T:0.33
Warning! 51021 characters in sequence are not A, C, G, or T
File 16 of 25
Found at i:2271681 original size:22 final size:23
Alignment explanation
Indices: 2271656--2271716 Score: 54
Period size: 24 Copynumber: 2.5 Consensus size: 23
2271646 ATTTTTATGT
2271656 TTATTTTTTATTATTTA-AAATA
1 TTATTTTTTATTATTTATAAATA
2271678 TTATAATTTTATATAATATTTATAAATA
1 TTAT--TTTT-TAT--TATTTATAAATA
*
2271706 TT-TTTTATATT
1 TTATTTTTTATT
2271717 TATATATTTA
Statistics
Matches: 32, Mismatches: 1, Indels: 12
0.71 0.02 0.27
Matches are distributed among these distances:
22 5 0.16
24 7 0.22
25 6 0.19
27 7 0.22
28 7 0.22
ACGTcount: A:0.38, C:0.00, G:0.00, T:0.62
Consensus pattern (23 bp):
TTATTTTTTATTATTTATAAATA
Found at i:2271725 original size:17 final size:18
Alignment explanation
Indices: 2271678--2271736 Score: 57
Period size: 17 Copynumber: 3.2 Consensus size: 18
2271668 ATTTAAAATA
* *
2271678 TTATAATTTTATATAATAT
1 TTATAATATT-TATCATAT
* *
2271697 TTATAAATATTTTTTATAT
1 TTAT-AATATTTATCATAT
2271716 TTAT-ATATTTATCATAT
1 TTATAATATTTATCATAT
2271733 TTAT
1 TTAT
2271737 TTTTTGTATT
Statistics
Matches: 34, Mismatches: 5, Indels: 4
0.79 0.12 0.09
Matches are distributed among these distances:
17 15 0.44
19 14 0.41
20 5 0.15
ACGTcount: A:0.37, C:0.02, G:0.00, T:0.61
Consensus pattern (18 bp):
TTATAATATTTATCATAT
Found at i:2271867 original size:193 final size:197
Alignment explanation
Indices: 2271640--2271998 Score: 557
Period size: 193 Copynumber: 1.8 Consensus size: 197
2271630 TTTTTTGATA
* *
2271640 TTTATGATTTTTATGTTTATTTTTTATTATTTAAAATATTATAATTTTATATAATATTTATAAAT
1 TTTATAATTTTTATGTTTATTTTTTATTATTTAAAATATTATAAATTTATATAATATTTATAAAT
2271705 ATTTTTTATATTTATATATT-TATCATATTTA-TTTTTTGTATTATATTTTAATTAATTTTTAAT
66 ATTTTTTATATTTATATATTATATCATATTTATTTTTTTGTATTATATTTTAATTAATTTTTAAT
*** *
2271768 GTTATATTTGTGTTA-TTTTTATATATTTAAAGTAAAAGAGAGAAAAAAAGATAAAAAATTTAGG
131 ACCATATTTATGTTATTTTTTATATATTTAAAGTAAAAGAGAGAAAAAAAGATAAAAAATTTAGG
2271832 TT
196 TT
*
2271834 TTTATAATTTTTAT-TTGTA-TTTTTATTATTTAAAATATTATAAATTTGTATAATATTTATAAA
1 TTTATAATTTTTATGTT-TATTTTTTATTATTTAAAATATTATAAATTTATATAATATTTATAAA
* * * *
2271897 TATTTTTTATATTTGTATATTCATGTTATATTTATTTTTTTGTATTATTTTTTAATTAATTTTTA
65 TATTTTTTATATTTATATATT-ATATCATATTTATTTTTTTGTATTATATTTTAATTAATTTTTA
*
2271962 ATACCATATTTATGTTATTTTTTGTATATTTAAAGTA
129 ATACCATATTTATGTTATTTTTTATATATTTAAAGTA
2271999 TTAAAAATTT
Statistics
Matches: 148, Mismatches: 12, Indels: 7
0.89 0.07 0.04
Matches are distributed among these distances:
193 64 0.43
194 15 0.10
195 9 0.06
196 42 0.28
197 18 0.12
ACGTcount: A:0.35, C:0.01, G:0.06, T:0.58
Consensus pattern (197 bp):
TTTATAATTTTTATGTTTATTTTTTATTATTTAAAATATTATAAATTTATATAATATTTATAAAT
ATTTTTTATATTTATATATTATATCATATTTATTTTTTTGTATTATATTTTAATTAATTTTTAAT
ACCATATTTATGTTATTTTTTATATATTTAAAGTAAAAGAGAGAAAAAAAGATAAAAAATTTAGG
TT
Found at i:2273564 original size:34 final size:34
Alignment explanation
Indices: 2273526--2273626 Score: 139
Period size: 37 Copynumber: 2.9 Consensus size: 34
2273516 TTATTAAGTG
2273526 TGTTAGGTAAATATATTAGGTGTGTTAGGTGGTA
1 TGTTAGGTAAATATATTAGGTGTGTTAGGTGGTA
* *
2273560 TGTTAGGTAAGTAATATATTAAGTGTGTTAGGTGGTG
1 TGTTAGGT-A--AATATATTAGGTGTGTTAGGTGGTA
* *
2273597 TGTTAGGTAAACATATTAGGTGTGCTAGGT
1 TGTTAGGTAAATATATTAGGTGTGTTAGGT
2273627 AAACATATTA
Statistics
Matches: 59, Mismatches: 5, Indels: 6
0.84 0.07 0.09
Matches are distributed among these distances:
34 26 0.44
35 1 0.02
36 1 0.02
37 31 0.53
ACGTcount: A:0.27, C:0.02, G:0.32, T:0.40
Consensus pattern (34 bp):
TGTTAGGTAAATATATTAGGTGTGTTAGGTGGTA
Found at i:2273647 original size:22 final size:22
Alignment explanation
Indices: 2273594--2273648 Score: 83
Period size: 22 Copynumber: 2.5 Consensus size: 22
2273584 GTGTTAGGTG
*
2273594 GTGTGTTAGGTAAACATATTAG
1 GTGTGTTAGGTAAACATATTAA
*
2273616 GTGTGCTAGGTAAACATATTAA
1 GTGTGTTAGGTAAACATATTAA
*
2273638 GTGTATTAGGT
1 GTGTGTTAGGT
2273649 GAACTTATCT
Statistics
Matches: 29, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
22 29 1.00
ACGTcount: A:0.31, C:0.05, G:0.27, T:0.36
Consensus pattern (22 bp):
GTGTGTTAGGTAAACATATTAA
Found at i:2278235 original size:37 final size:34
Alignment explanation
Indices: 2278176--2278277 Score: 141
Period size: 37 Copynumber: 2.9 Consensus size: 34
2278166 TTATTAAATG
*
2278176 TGTTAGGTAAACTTATTAAGTGTGTTAGGTGGTA
1 TGTTAGGTAAACATATTAAGTGTGTTAGGTGGTA
* *
2278210 TGTTAGGTAAGTAATATATTAAGTGTGTTAGGTGGTG
1 TGTTAGGT-A--AACATATTAAGTGTGTTAGGTGGTA
*
2278247 TGTTAGGTAAACATATTAGGTGTGTTAGGTG
1 TGTTAGGTAAACATATTAAGTGTGTTAGGTG
2278278 AACTTATCTT
Statistics
Matches: 60, Mismatches: 5, Indels: 6
0.85 0.07 0.08
Matches are distributed among these distances:
34 28 0.47
35 1 0.02
36 1 0.02
37 30 0.50
ACGTcount: A:0.26, C:0.02, G:0.31, T:0.40
Consensus pattern (34 bp):
TGTTAGGTAAACATATTAAGTGTGTTAGGTGGTA
Found at i:2278392 original size:23 final size:24
Alignment explanation
Indices: 2278366--2278415 Score: 66
Period size: 23 Copynumber: 2.1 Consensus size: 24
2278356 AATCTCTCTC
* * *
2278366 TTTAATTATTTTTTTTAAAAT-TT
1 TTTAATTAATATTTTAAAAATATT
2278389 TTTAATTAATATTTTAAAAATATT
1 TTTAATTAATATTTTAAAAATATT
2278413 TTT
1 TTT
2278416 TAAAATTAAT
Statistics
Matches: 23, Mismatches: 3, Indels: 1
0.85 0.11 0.04
Matches are distributed among these distances:
23 18 0.78
24 5 0.22
ACGTcount: A:0.36, C:0.00, G:0.00, T:0.64
Consensus pattern (24 bp):
TTTAATTAATATTTTAAAAATATT
Found at i:2278760 original size:2 final size:2
Alignment explanation
Indices: 2278753--2278795 Score: 77
Period size: 2 Copynumber: 21.5 Consensus size: 2
2278743 GATAACAATC
*
2278753 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT GT 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
2278795 A
1 A
2278796 AAACCCCATG
Statistics
Matches: 39, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
2 39 1.00
ACGTcount: A:0.49, C:0.00, G:0.02, T:0.49
Consensus pattern (2 bp):
AT
Found at i:2280515 original size:9 final size:8
Alignment explanation
Indices: 2280488--2280523 Score: 54
Period size: 8 Copynumber: 4.5 Consensus size: 8
2280478 TATTGATTGT
2280488 AAAAAATA
1 AAAAAATA
*
2280496 AAATAATA
1 AAAAAATA
*
2280504 AAAAATTA
1 AAAAAATA
2280512 AAAAAATA
1 AAAAAATA
2280520 AAAA
1 AAAA
2280524 GAAAAGGGAG
Statistics
Matches: 24, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
8 24 1.00
ACGTcount: A:0.83, C:0.00, G:0.00, T:0.17
Consensus pattern (8 bp):
AAAAAATA
Found at i:2280757 original size:18 final size:17
Alignment explanation
Indices: 2280736--2280781 Score: 58
Period size: 17 Copynumber: 2.6 Consensus size: 17
2280726 ATAATATGAA
2280736 TTATTAATATATTAAAAT
1 TTATTAA-ATATTAAAAT
2280754 TTATATAAATA-TAAAAT
1 TTAT-TAAATATTAAAAT
*
2280771 TTTTTAAATAT
1 TTATTAAATAT
2280782 AATTATTATA
Statistics
Matches: 25, Mismatches: 1, Indels: 5
0.81 0.03 0.16
Matches are distributed among these distances:
16 6 0.24
17 9 0.36
18 7 0.28
19 3 0.12
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (17 bp):
TTATTAAATATTAAAAT
Found at i:2280780 original size:16 final size:17
Alignment explanation
Indices: 2280716--2280783 Score: 65
Period size: 16 Copynumber: 4.2 Consensus size: 17
2280706 ATAAATATTT
2280716 TAAAATTTATAT-AATA
1 TAAAATTTATATAAATA
*
2280732 T-GAA-TTAT-TAATATA
1 TAAAATTTATATAA-ATA
2280747 TTAAAATTTATATAAATA
1 -TAAAATTTATATAAATA
*
2280765 TAAAATTT-TTTAAATA
1 TAAAATTTATATAAATA
2280781 TAA
1 TAA
2280784 TTATTATATA
Statistics
Matches: 43, Mismatches: 3, Indels: 12
0.74 0.05 0.21
Matches are distributed among these distances:
13 1 0.02
14 5 0.12
15 5 0.12
16 12 0.28
17 10 0.23
18 7 0.16
19 3 0.07
ACGTcount: A:0.53, C:0.00, G:0.01, T:0.46
Consensus pattern (17 bp):
TAAAATTTATATAAATA
Found at i:2280796 original size:16 final size:16
Alignment explanation
Indices: 2280722--2280813 Score: 54
Period size: 14 Copynumber: 5.9 Consensus size: 16
2280712 ATTTTAAAAT
2280722 TTATATAATATGAATTA
1 TTATATAATAT-AATTA
* *
2280739 TTAATATATTA-AAAT-
1 TT-ATATAATATAATTA
2280754 TTATATAAATATAAAATT-
1 TTATAT-AATAT--AATTA
*
2280772 TTTTA-AATATAATTA
1 TTATATAATATAATTA
*
2280787 TTATATAATA-AAATA
1 TTATATAATATAATTA
2280802 -TATA-AATATAAT
1 TTATATAATATAAT
2280814 ATGAATATAT
Statistics
Matches: 59, Mismatches: 8, Indels: 19
0.69 0.09 0.22
Matches are distributed among these distances:
13 4 0.07
14 14 0.24
15 13 0.22
16 12 0.20
17 2 0.03
18 14 0.24
ACGTcount: A:0.53, C:0.00, G:0.01, T:0.46
Consensus pattern (16 bp):
TTATATAATATAATTA
Found at i:2280821 original size:29 final size:26
Alignment explanation
Indices: 2280775--2280838 Score: 67
Period size: 29 Copynumber: 2.3 Consensus size: 26
2280765 TAAAATTTTT
*
2280775 TAAATATAATTATTATATAATAAAATATA
1 TAAATATAATTATAATAT-AT-AAAT-TA
2280804 TAAATATAA-TATGAATATATAAATTA
1 TAAATATAATTAT-AATATATAAATTA
2280830 TAAGATATA
1 TAA-ATATA
2280839 TTTTATAAAA
Statistics
Matches: 32, Mismatches: 1, Indels: 6
0.82 0.03 0.15
Matches are distributed among these distances:
26 5 0.16
27 9 0.28
28 5 0.16
29 13 0.41
ACGTcount: A:0.58, C:0.00, G:0.03, T:0.39
Consensus pattern (26 bp):
TAAATATAATTATAATATATAAATTA
Found at i:2281462 original size:17 final size:16
Alignment explanation
Indices: 2281442--2281501 Score: 59
Period size: 17 Copynumber: 3.5 Consensus size: 16
2281432 AGCATAATCC
2281442 AATAAAAAAATAATATA
1 AATAAAAAAAT-ATATA
*
2281459 AATATAAAAAT-TATA
1 AATAAAAAAATATATA
2281474 AATACATAAAAATTTATATA
1 AATA-A-AAAAA--TATATA
2281494 AATAAAAA
1 AATAAAAA
2281502 TTATTAACAT
Statistics
Matches: 36, Mismatches: 2, Indels: 9
0.77 0.04 0.19
Matches are distributed among these distances:
15 8 0.22
17 15 0.42
18 3 0.08
19 2 0.06
20 8 0.22
ACGTcount: A:0.70, C:0.02, G:0.00, T:0.28
Consensus pattern (16 bp):
AATAAAAAAATATATA
Found at i:2281519 original size:33 final size:32
Alignment explanation
Indices: 2281447--2281525 Score: 86
Period size: 33 Copynumber: 2.4 Consensus size: 32
2281437 AATCCAATAA
* *
2281447 AAAAATAATATAAATATAAAAATTATAAATACAT
1 AAAAATTATAT-AA-ATAAAAATTATAAACACAT
* *
2281481 AAAAATTTATATAAATAAAAATTATTAACATAT
1 AAAAA-TTATATAAATAAAAATTATAAACACAT
*
2281514 TAAAATTATATA
1 AAAAATTATATA
2281526 CACATACGAT
Statistics
Matches: 39, Mismatches: 5, Indels: 4
0.81 0.10 0.08
Matches are distributed among these distances:
32 7 0.18
33 20 0.51
34 7 0.18
35 5 0.13
ACGTcount: A:0.63, C:0.03, G:0.00, T:0.34
Consensus pattern (32 bp):
AAAAATTATATAAATAAAAATTATAAACACAT
Found at i:2281766 original size:16 final size:17
Alignment explanation
Indices: 2281735--2281777 Score: 54
Period size: 16 Copynumber: 2.6 Consensus size: 17
2281725 TTTAATATTT
*
2281735 ATAAAATTTTTAATTAA
1 ATAAAATTTATAATTAA
2281752 ATAAAA-TTATAATT-A
1 ATAAAATTTATAATTAA
*
2281767 TTAAAATTTAT
1 ATAAAATTTAT
2281778 TTTAAAATAT
Statistics
Matches: 23, Mismatches: 2, Indels: 3
0.82 0.07 0.11
Matches are distributed among these distances:
15 6 0.26
16 11 0.48
17 6 0.26
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (17 bp):
ATAAAATTTATAATTAA
Found at i:2282761 original size:13 final size:13
Alignment explanation
Indices: 2282743--2282772 Score: 60
Period size: 13 Copynumber: 2.3 Consensus size: 13
2282733 TATTTTCAAT
2282743 AATAAAAAATATA
1 AATAAAAAATATA
2282756 AATAAAAAATATA
1 AATAAAAAATATA
2282769 AATA
1 AATA
2282773 CTTAAAATTT
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 17 1.00
ACGTcount: A:0.77, C:0.00, G:0.00, T:0.23
Consensus pattern (13 bp):
AATAAAAAATATA
Found at i:2282887 original size:14 final size:15
Alignment explanation
Indices: 2282870--2282900 Score: 55
Period size: 15 Copynumber: 2.1 Consensus size: 15
2282860 AAAATATAAT
2282870 AATT-TAAATACAAA
1 AATTATAAATACAAA
2282884 AATTATAAATACAAA
1 AATTATAAATACAAA
2282899 AA
1 AA
2282901 AAATTTCTTT
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
14 4 0.25
15 12 0.75
ACGTcount: A:0.68, C:0.06, G:0.00, T:0.26
Consensus pattern (15 bp):
AATTATAAATACAAA
Found at i:2283446 original size:11 final size:11
Alignment explanation
Indices: 2283438--2283467 Score: 51
Period size: 11 Copynumber: 2.6 Consensus size: 11
2283428 ATATATTATT
2283438 TAAAAATTAAA
1 TAAAAATTAAA
2283449 TAAAAATTAAA
1 TAAAAATTAAA
2283460 TATAAAAT
1 TA-AAAAT
2283468 ATTTAAAATG
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
11 13 0.72
12 5 0.28
ACGTcount: A:0.70, C:0.00, G:0.00, T:0.30
Consensus pattern (11 bp):
TAAAAATTAAA
Found at i:2283931 original size:6 final size:6
Alignment explanation
Indices: 2283910--2283944 Score: 52
Period size: 6 Copynumber: 5.7 Consensus size: 6
2283900 ATATTATTTT
*
2283910 AAAATA AAATTAA AAAATA AAAATA AAAATA AAAA
1 AAAATA AAAAT-A AAAATA AAAATA AAAATA AAAA
2283945 AATATTTTAA
Statistics
Matches: 26, Mismatches: 2, Indels: 2
0.87 0.07 0.07
Matches are distributed among these distances:
6 21 0.81
7 5 0.19
ACGTcount: A:0.83, C:0.00, G:0.00, T:0.17
Consensus pattern (6 bp):
AAAATA
Found at i:2284069 original size:15 final size:14
Alignment explanation
Indices: 2284051--2284081 Score: 53
Period size: 14 Copynumber: 2.1 Consensus size: 14
2284041 AAAATTTTAA
2284051 AAAAATACAAAACTT
1 AAAAATA-AAAACTT
2284066 AAAAATAAAAACTT
1 AAAAATAAAAACTT
2284080 AA
1 AA
2284082 CTAGTTTAGT
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
14 9 0.56
15 7 0.44
ACGTcount: A:0.71, C:0.10, G:0.00, T:0.19
Consensus pattern (14 bp):
AAAAATAAAAACTT
Found at i:2284187 original size:12 final size:11
Alignment explanation
Indices: 2284148--2284190 Score: 50
Period size: 11 Copynumber: 3.9 Consensus size: 11
2284138 CCTGTTTATT
* *
2284148 TATATAAATTA
1 TATAAAAATAA
2284159 TATAAAAATAA
1 TATAAAAATAA
*
2284170 TATAAAAATGA
1 TATAAAAATAA
*
2284181 TATTAAAATA
1 TATAAAAATA
2284191 TAAATTTATT
Statistics
Matches: 27, Mismatches: 5, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
11 27 1.00
ACGTcount: A:0.63, C:0.00, G:0.02, T:0.35
Consensus pattern (11 bp):
TATAAAAATAA
Found at i:2284266 original size:22 final size:23
Alignment explanation
Indices: 2284238--2284297 Score: 70
Period size: 22 Copynumber: 2.7 Consensus size: 23
2284228 ACATGATGTT
*
2284238 TATAAAAATATTTA-AAATATAA
1 TATAAAAATATATATAAATATAA
*
2284260 TATAAAAATA-ATATATATATAA
1 TATAAAAATATATATAAATATAA
* *
2284282 TATAAATATATGTATA
1 TATAAAAATATATATA
2284298 TATAAAAGTA
Statistics
Matches: 32, Mismatches: 4, Indels: 3
0.82 0.10 0.08
Matches are distributed among these distances:
21 2 0.06
22 26 0.81
23 4 0.12
ACGTcount: A:0.60, C:0.00, G:0.02, T:0.38
Consensus pattern (23 bp):
TATAAAAATATATATAAATATAA
Found at i:2284272 original size:11 final size:11
Alignment explanation
Indices: 2284238--2284287 Score: 57
Period size: 11 Copynumber: 4.5 Consensus size: 11
2284228 ACATGATGTT
2284238 TATAAAAAT-A
1 TATAAAAATAA
*
2284248 TTTAAAATATAA
1 TATAAAA-ATAA
2284260 TATAAAAATAA
1 TATAAAAATAA
* *
2284271 TATATATATAA
1 TATAAAAATAA
2284282 TATAAA
1 TATAAA
2284288 TATATGTATA
Statistics
Matches: 33, Mismatches: 5, Indels: 3
0.80 0.12 0.07
Matches are distributed among these distances:
10 6 0.18
11 20 0.61
12 7 0.21
ACGTcount: A:0.64, C:0.00, G:0.00, T:0.36
Consensus pattern (11 bp):
TATAAAAATAA
Found at i:2284281 original size:17 final size:17
Alignment explanation
Indices: 2284253--2284304 Score: 52
Period size: 21 Copynumber: 2.9 Consensus size: 17
2284243 AAATATTTAA
2284253 AATATA-ATATAAAAAT
1 AATATATATATAAAAAT
2284269 AATATATATATAATATAAAT
1 AATATATATAT-A-A-AAAT
*
2284289 ATATGTATATATAAAA
1 A-ATATATATATAAAA
2284305 GTATACATAA
Statistics
Matches: 30, Mismatches: 1, Indels: 8
0.77 0.03 0.21
Matches are distributed among these distances:
16 6 0.20
17 4 0.13
18 3 0.10
19 2 0.07
20 6 0.20
21 9 0.30
ACGTcount: A:0.62, C:0.00, G:0.02, T:0.37
Consensus pattern (17 bp):
AATATATATATAAAAAT
Found at i:2284290 original size:11 final size:11
Alignment explanation
Indices: 2284252--2284291 Score: 62
Period size: 11 Copynumber: 3.6 Consensus size: 11
2284242 AAAATATTTA
2284252 AAATATAATAT
1 AAATATAATAT
*
2284263 AAAAATAATAT
1 AAATATAATAT
*
2284274 ATATATAATAT
1 AAATATAATAT
2284285 AAATATA
1 AAATATA
2284292 TGTATATATA
Statistics
Matches: 25, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
11 25 1.00
ACGTcount: A:0.65, C:0.00, G:0.00, T:0.35
Consensus pattern (11 bp):
AAATATAATAT
Found at i:2284292 original size:13 final size:12
Alignment explanation
Indices: 2284238--2284323 Score: 56
Period size: 11 Copynumber: 7.2 Consensus size: 12
2284228 ACATGATGTT
2284238 TATAAAA-AT-A
1 TATAAAATATAA
*
2284248 TTTAAAATATAA
1 TATAAAATATAA
2284260 TATAAAA-ATAA
1 TATAAAATATAA
*
2284271 TAT-ATATATAA
1 TATAAAATATAA
2284282 TATAAATATATGTATA
1 TATAAA-ATA--TA-A
2284298 TATAAAAGTAT-A
1 TATAAAA-TATAA
* *
2284310 CATAAAATAGAA
1 TATAAAATATAA
2284322 TA
1 TA
2284324 AATTATGAAT
Statistics
Matches: 59, Mismatches: 7, Indels: 18
0.70 0.08 0.21
Matches are distributed among these distances:
10 8 0.14
11 18 0.31
12 17 0.29
13 3 0.05
14 1 0.02
15 3 0.05
16 9 0.15
ACGTcount: A:0.60, C:0.01, G:0.03, T:0.35
Consensus pattern (12 bp):
TATAAAATATAA
Found at i:2284425 original size:21 final size:20
Alignment explanation
Indices: 2284395--2284444 Score: 64
Period size: 20 Copynumber: 2.4 Consensus size: 20
2284385 TGTATAATTT
*
2284395 TTTTTCTTTTTTCTTTCTTTCC
1 TTTTT-TTTTCTCTTT-TTTCC
*
2284417 TTTTTTTTTCTCTTTTTTTC
1 TTTTTTTTTCTCTTTTTTCC
2284437 TTTTTTTT
1 TTTTTTTT
2284445 AACTTACTGA
Statistics
Matches: 26, Mismatches: 2, Indels: 2
0.87 0.07 0.07
Matches are distributed among these distances:
20 12 0.46
21 9 0.35
22 5 0.19
ACGTcount: A:0.00, C:0.16, G:0.00, T:0.84
Consensus pattern (20 bp):
TTTTTTTTTCTCTTTTTTCC
Found at i:2284430 original size:17 final size:16
Alignment explanation
Indices: 2284400--2284439 Score: 50
Period size: 13 Copynumber: 2.7 Consensus size: 16
2284390 AATTTTTTTT
2284400 CTTTTTTCTTTCTTTC
1 CTTTTTTCTTTCTTTC
2284416 CTTTTTT-TTTC--TC
1 CTTTTTTCTTTCTTTC
*
2284429 TTTTTTTCTTT
1 CTTTTTTCTTT
2284440 TTTTTAACTT
Statistics
Matches: 22, Mismatches: 1, Indels: 4
0.81 0.04 0.15
Matches are distributed among these distances:
13 8 0.36
14 3 0.14
15 4 0.18
16 7 0.32
ACGTcount: A:0.00, C:0.20, G:0.00, T:0.80
Consensus pattern (16 bp):
CTTTTTTCTTTCTTTC
Found at i:2284434 original size:10 final size:9
Alignment explanation
Indices: 2284392--2284444 Score: 56
Period size: 10 Copynumber: 5.9 Consensus size: 9
2284382 AAATGTATAA
2284392 TTTTTTTTC
1 TTTTTTTTC
2284401 --TTTTTTC
1 TTTTTTTTC
* *
2284408 TTTCTTTCC
1 TTTTTTTTC
2284417 TTTTTTTTTC
1 -TTTTTTTTC
2284427 TCTTTTTTTC
1 T-TTTTTTTC
2284437 TTTTTTTT
1 TTTTTTTT
2284445 AACTTACTGA
Statistics
Matches: 36, Mismatches: 4, Indels: 8
0.75 0.08 0.17
Matches are distributed among these distances:
7 7 0.19
9 13 0.36
10 16 0.44
ACGTcount: A:0.00, C:0.15, G:0.00, T:0.85
Consensus pattern (9 bp):
TTTTTTTTC
Found at i:2284977 original size:29 final size:31
Alignment explanation
Indices: 2284914--2284977 Score: 80
Period size: 29 Copynumber: 2.2 Consensus size: 31
2284904 AATTAATTTC
* *
2284914 ATTAAATTTAATAATTAAAAATATTTTTAAT
1 ATTAAATTTAATAATTAAAAATATTATAAAT
*
2284945 -TTAAATTTAATTA-TAAAAATA-TATAAAT
1 ATTAAATTTAATAATTAAAAATATTATAAAT
2284973 ATTAA
1 ATTAA
2284978 TATAAAATTT
Statistics
Matches: 29, Mismatches: 3, Indels: 4
0.81 0.08 0.11
Matches are distributed among these distances:
28 5 0.17
29 12 0.41
30 12 0.41
ACGTcount: A:0.55, C:0.00, G:0.00, T:0.45
Consensus pattern (31 bp):
ATTAAATTTAATAATTAAAAATATTATAAAT
Found at i:2289278 original size:26 final size:26
Alignment explanation
Indices: 2289249--2289321 Score: 83
Period size: 28 Copynumber: 2.7 Consensus size: 26
2289239 TTTAGGTTAG
2289249 ATAAATTTTTATTTTTATTAAAAATT
1 ATAAATTTTTATTTTTATTAAAAATT
* * *
2289275 ATAATTTTTTATATTTATTTTAAATATT
1 ATAAATTTTTAT-TTT-TATTAAAAATT
*
2289303 ATTAATTATTTATTTTTAT
1 ATAAATT-TTTATTTTTAT
2289322 ATTTTAATAA
Statistics
Matches: 38, Mismatches: 6, Indels: 5
0.78 0.12 0.10
Matches are distributed among these distances:
26 11 0.29
27 5 0.13
28 17 0.45
29 5 0.13
ACGTcount: A:0.37, C:0.00, G:0.00, T:0.63
Consensus pattern (26 bp):
ATAAATTTTTATTTTTATTAAAAATT
Found at i:2291052 original size:12 final size:13
Alignment explanation
Indices: 2291022--2291047 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
2291012 ATAAGAAATA
2291022 AAAAATTTATTAT
1 AAAAATTTATTAT
2291035 AAAAATTTATTAT
1 AAAAATTTATTAT
2291048 TAAATAATAA
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:0.54, C:0.00, G:0.00, T:0.46
Consensus pattern (13 bp):
AAAAATTTATTAT
Found at i:2291707 original size:27 final size:27
Alignment explanation
Indices: 2291646--2291723 Score: 77
Period size: 27 Copynumber: 2.9 Consensus size: 27
2291636 CCTAAGTTAA
* * *
2291646 AAATATATGTAATCTATGATATGTTTAT
1 AAATATA-ATAATCTATAATATATTTAT
**
2291674 ATTTATAATAATCTATAATATATTTAT
1 AAATATAATAATCTATAATATATTTAT
*
2291701 AAATAT-ATATATATATAATATAT
1 AAATATAATA-ATCTATAATATAT
2291724 AAAAGCACGA
Statistics
Matches: 41, Mismatches: 8, Indels: 3
0.79 0.15 0.06
Matches are distributed among these distances:
26 3 0.07
27 33 0.80
28 5 0.12
ACGTcount: A:0.46, C:0.03, G:0.04, T:0.47
Consensus pattern (27 bp):
AAATATAATAATCTATAATATATTTAT
Found at i:2291711 original size:21 final size:23
Alignment explanation
Indices: 2291671--2291726 Score: 64
Period size: 21 Copynumber: 2.5 Consensus size: 23
2291661 ATGATATGTT
*
2291671 TATATTTAT-AATAATCTATA-A
1 TATATTTATAAATAATATATATA
2291692 TATATTTATAAAT-ATATATATA
1 TATATTTATAAATAATATATATA
*
2291714 TATAATATATAAA
1 TAT-ATTTATAAA
2291727 AGCACGAATG
Statistics
Matches: 30, Mismatches: 2, Indels: 4
0.83 0.06 0.11
Matches are distributed among these distances:
21 15 0.50
22 7 0.23
23 8 0.27
ACGTcount: A:0.52, C:0.02, G:0.00, T:0.46
Consensus pattern (23 bp):
TATATTTATAAATAATATATATA
Found at i:2297840 original size:12 final size:12
Alignment explanation
Indices: 2297823--2297854 Score: 55
Period size: 12 Copynumber: 2.7 Consensus size: 12
2297813 GAAAACAAAG
2297823 GCTGCCAACTGT
1 GCTGCCAACTGT
2297835 GCTGCCAACTGT
1 GCTGCCAACTGT
*
2297847 GCCGCCAA
1 GCTGCCAA
2297855 TTTTGACATT
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
12 19 1.00
ACGTcount: A:0.19, C:0.38, G:0.25, T:0.19
Consensus pattern (12 bp):
GCTGCCAACTGT
Found at i:2298572 original size:2 final size:2
Alignment explanation
Indices: 2298565--2298609 Score: 83
Period size: 2 Copynumber: 23.0 Consensus size: 2
2298555 TCAAATCTTC
2298565 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT -T
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
2298606 AT AT
1 AT AT
2298610 TTTAAATTAC
Statistics
Matches: 42, Mismatches: 0, Indels: 2
0.95 0.00 0.05
Matches are distributed among these distances:
1 1 0.02
2 41 0.98
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
AT
Found at i:2304620 original size:57 final size:57
Alignment explanation
Indices: 2304532--2304644 Score: 208
Period size: 57 Copynumber: 2.0 Consensus size: 57
2304522 GATCATTAAT
2304532 GTGGTAATATTTGATGCAATTTTGTAATTTGGTAGTTAATCTTAATTATGTTCAAGA
1 GTGGTAATATTTGATGCAATTTTGTAATTTGGTAGTTAATCTTAATTATGTTCAAGA
* *
2304589 GTGGTAATATTTGATGTAATTTTGTAATTTGGTAGTTAGTCTTAATTATGTTCAAG
1 GTGGTAATATTTGATGCAATTTTGTAATTTGGTAGTTAATCTTAATTATGTTCAAG
2304645 TCTTTCATTA
Statistics
Matches: 54, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
57 54 1.00
ACGTcount: A:0.28, C:0.04, G:0.20, T:0.47
Consensus pattern (57 bp):
GTGGTAATATTTGATGCAATTTTGTAATTTGGTAGTTAATCTTAATTATGTTCAAGA
Found at i:2307319 original size:15 final size:16
Alignment explanation
Indices: 2307285--2307326 Score: 52
Period size: 15 Copynumber: 2.7 Consensus size: 16
2307275 TTGTATTACA
*
2307285 ATTTAATTATAA-TTT
1 ATTTTATTATAATTTT
2307300 ATTTTATTATAATTATT
1 ATTTTATTATAATT-TT
2307317 -TTTTATTATA
1 ATTTTATTATA
2307327 TGTGCATATT
Statistics
Matches: 24, Mismatches: 1, Indels: 3
0.86 0.04 0.11
Matches are distributed among these distances:
15 11 0.46
16 11 0.46
17 2 0.08
ACGTcount: A:0.36, C:0.00, G:0.00, T:0.64
Consensus pattern (16 bp):
ATTTTATTATAATTTT
Found at i:2307957 original size:18 final size:18
Alignment explanation
Indices: 2307934--2307968 Score: 61
Period size: 18 Copynumber: 1.9 Consensus size: 18
2307924 ACTTTGTTTA
*
2307934 AAAAAAATTATAACTTAC
1 AAAAAAACTATAACTTAC
2307952 AAAAAAACTATAACTTA
1 AAAAAAACTATAACTTA
2307969 TAATGTTTTC
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:0.63, C:0.11, G:0.00, T:0.26
Consensus pattern (18 bp):
AAAAAAACTATAACTTAC
Found at i:2309396 original size:32 final size:32
Alignment explanation
Indices: 2309355--2309427 Score: 103
Period size: 32 Copynumber: 2.3 Consensus size: 32
2309345 AGATTTAAGC
* *
2309355 AAAATATTAAA-CATATCAAATGAATTTAGACA
1 AAAATATTAAACCAAAT-AAATGAACTTAGACA
2309387 AAAATATTAAACCAAATAAATGAACTTAGACA
1 AAAATATTAAACCAAATAAATGAACTTAGACA
*
2309419 AAAACATTA
1 AAAATATTA
2309428 TACCTATTTT
Statistics
Matches: 37, Mismatches: 3, Indels: 2
0.88 0.07 0.05
Matches are distributed among these distances:
32 33 0.89
33 4 0.11
ACGTcount: A:0.59, C:0.11, G:0.05, T:0.25
Consensus pattern (32 bp):
AAAATATTAAACCAAATAAATGAACTTAGACA
Found at i:2310753 original size:30 final size:27
Alignment explanation
Indices: 2310718--2310776 Score: 73
Period size: 27 Copynumber: 2.1 Consensus size: 27
2310708 TCATTCATAA
2310718 TAATATTTTATATATATACATATATAATTT
1 TAATATTTT-T-TATATA-ATATATAATTT
* *
2310748 TAATATTTTTTATCTAATATATATTTT
1 TAATATTTTTTATATAATATATAATTT
2310775 TA
1 TA
2310777 GTATACATGT
Statistics
Matches: 27, Mismatches: 2, Indels: 3
0.84 0.06 0.09
Matches are distributed among these distances:
27 12 0.44
28 5 0.19
29 1 0.04
30 9 0.33
ACGTcount: A:0.39, C:0.03, G:0.00, T:0.58
Consensus pattern (27 bp):
TAATATTTTTTATATAATATATAATTT
Found at i:2315467 original size:16 final size:17
Alignment explanation
Indices: 2315426--2315468 Score: 52
Period size: 17 Copynumber: 2.5 Consensus size: 17
2315416 AAAATTTAAA
2315426 AAATTTAATTAATTCATTT
1 AAATTTAA--AATTCATTT
*
2315445 AAATTTAAAATTTATTT
1 AAATTTAAAATTCATTT
2315462 -AATTTAA
1 AAATTTAA
2315469 TTTAATTTAT
Statistics
Matches: 23, Mismatches: 1, Indels: 3
0.85 0.04 0.11
Matches are distributed among these distances:
16 7 0.30
17 8 0.35
19 8 0.35
ACGTcount: A:0.47, C:0.02, G:0.00, T:0.51
Consensus pattern (17 bp):
AAATTTAAAATTCATTT
Found at i:2315475 original size:26 final size:27
Alignment explanation
Indices: 2315425--2315497 Score: 80
Period size: 26 Copynumber: 2.8 Consensus size: 27
2315415 TAAAATTTAA
* *
2315425 AAAATTTAATTAA-TTCATTTAAATTT
1 AAAATTTATTTAATTTAATTTAAATTT
2315451 AAAATTTATTTAATTTAATTT-AATTT
1 AAAATTTATTTAATTTAATTTAAATTT
* *
2315477 -ATATTTATATTATTTTAATTT
1 AAAATTTAT-TTAATTTAATTT
2315498 TTATAATTTT
Statistics
Matches: 41, Mismatches: 4, Indels: 4
0.84 0.08 0.08
Matches are distributed among these distances:
25 7 0.17
26 28 0.68
27 6 0.15
ACGTcount: A:0.41, C:0.01, G:0.00, T:0.58
Consensus pattern (27 bp):
AAAATTTATTTAATTTAATTTAAATTT
Found at i:2315481 original size:21 final size:21
Alignment explanation
Indices: 2315457--2315497 Score: 57
Period size: 21 Copynumber: 2.0 Consensus size: 21
2315447 ATTTAAAATT
2315457 TATTTA-ATTTAATTTAATTTA
1 TATTTATA-TTAATTTAATTTA
*
2315478 TATTTATATTATTTTAATTT
1 TATTTATATTAATTTAATTT
2315498 TTATAATTTT
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
21 17 0.94
22 1 0.06
ACGTcount: A:0.34, C:0.00, G:0.00, T:0.66
Consensus pattern (21 bp):
TATTTATATTAATTTAATTTA
Found at i:2315498 original size:6 final size:5
Alignment explanation
Indices: 2315427--2315497 Score: 51
Period size: 5 Copynumber: 14.0 Consensus size: 5
2315417 AAATTTAAAA
*
2315427 AATTT AA-TT AA-TT CATTT AAATTT AAAATTT -ATTT AATTT AATTT
1 AATTT AATTT AATTT AATTT -AATTT --AATTT AATTT AATTT AATTT
*
2315472 AATTT ATATTT -ATATT ATTTT AATTT
1 AATTT A-ATTT AAT-TT AATTT AATTT
2315498 TTATAATTTT
Statistics
Matches: 55, Mismatches: 4, Indels: 14
0.75 0.05 0.19
Matches are distributed among these distances:
4 13 0.24
5 27 0.49
6 9 0.16
7 6 0.11
ACGTcount: A:0.39, C:0.01, G:0.00, T:0.59
Consensus pattern (5 bp):
AATTT
Found at i:2315502 original size:17 final size:17
Alignment explanation
Indices: 2315480--2315513 Score: 52
Period size: 17 Copynumber: 2.0 Consensus size: 17
2315470 TTAATTTATA
2315480 TTTAT-ATTATTTTAATT
1 TTTATAATT-TTTTAATT
2315497 TTTATAATTTTTTAATT
1 TTTATAATTTTTTAATT
2315514 AAATTGATAT
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
17 13 0.81
18 3 0.19
ACGTcount: A:0.29, C:0.00, G:0.00, T:0.71
Consensus pattern (17 bp):
TTTATAATTTTTTAATT
Found at i:2316145 original size:2 final size:2
Alignment explanation
Indices: 2316138--2316167 Score: 53
Period size: 2 Copynumber: 15.5 Consensus size: 2
2316128 CTTATTTTTG
2316138 TA TA TA TA TA TA TA TA TA TA TA TA T- TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
2316168 CCATATAAAT
Statistics
Matches: 27, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
1 1 0.04
2 26 0.96
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (2 bp):
TA
Found at i:2316666 original size:3 final size:3
Alignment explanation
Indices: 2316658--2316708 Score: 102
Period size: 3 Copynumber: 17.0 Consensus size: 3
2316648 GCTTTTTTAC
2316658 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT
2316706 ATT
1 ATT
2316709 TGTTTCAAAG
Statistics
Matches: 48, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 48 1.00
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (3 bp):
ATT
Found at i:2317390 original size:20 final size:21
Alignment explanation
Indices: 2317346--2317391 Score: 60
Period size: 19 Copynumber: 2.3 Consensus size: 21
2317336 TGATTACATT
*
2317346 TTAATATATCTTTTAAATACA
1 TTAATATATCTTTTAAATAAA
*
2317367 -TAATAT-TCTTTTTAATAAA
1 TTAATATATCTTTTAAATAAA
2317386 TTAATA
1 TTAATA
2317392 AATATTTGAT
Statistics
Matches: 22, Mismatches: 2, Indels: 3
0.81 0.07 0.11
Matches are distributed among these distances:
19 11 0.50
20 11 0.50
ACGTcount: A:0.43, C:0.07, G:0.00, T:0.50
Consensus pattern (21 bp):
TTAATATATCTTTTAAATAAA
Found at i:2318837 original size:11 final size:11
Alignment explanation
Indices: 2318799--2318841 Score: 50
Period size: 12 Copynumber: 3.5 Consensus size: 11
2318789 TTTATCTATA
2318799 AATTTATATTAT
1 AATTTA-ATTAT
2318811 AATTAATAATTAAT
1 AATT--TAATT-AT
2318825 AATTTAATTAT
1 AATTTAATTAT
2318836 AATTTA
1 AATTTA
2318842 TAGAGCAACA
Statistics
Matches: 28, Mismatches: 0, Indels: 7
0.80 0.00 0.20
Matches are distributed among these distances:
11 8 0.29
12 9 0.32
13 3 0.11
14 8 0.29
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (11 bp):
AATTTAATTAT
Found at i:2319128 original size:12 final size:12
Alignment explanation
Indices: 2319111--2319163 Score: 56
Period size: 12 Copynumber: 4.5 Consensus size: 12
2319101 TTTTATCACG
2319111 AATATAATATAA
1 AATATAATATAA
2319123 AATATAATATAA
1 AATATAATATAA
* *
2319135 TATA-AATACAA
1 AATATAATATAA
*
2319146 CATA-AATATATA
1 AATATAATATA-A
2319158 AATATA
1 AATATA
2319164 TAAAAATTTA
Statistics
Matches: 34, Mismatches: 5, Indels: 3
0.81 0.12 0.07
Matches are distributed among these distances:
11 14 0.41
12 19 0.56
13 1 0.03
ACGTcount: A:0.64, C:0.04, G:0.00, T:0.32
Consensus pattern (12 bp):
AATATAATATAA
Found at i:2319133 original size:17 final size:17
Alignment explanation
Indices: 2319111--2319248 Score: 65
Period size: 16 Copynumber: 8.9 Consensus size: 17
2319101 TTTTATCACG
2319111 AATATAATATAAAATAT
1 AATATAATATAAAATAT
*
2319128 AATATAATAT-AAATAC
1 AATATAATATAAAATAT
* *
2319144 AACATAA-AT-ATATA-
1 AATATAATATAAAATAT
2319158 AATAT-ATA-AAAAT-T
1 AATATAATATAAAATAT
* * *
2319172 TATATAATTTAAATTATT
1 AATATAATATAAAATA-T
2319190 AATA-AAT-TAAAAT-T
1 AATATAATATAAAATAT
* *
2319204 -TTA-AATAT-AATTAT
1 AATATAATATAAAATAT
2319218 AATAT-ATA-AAAACTAT
1 AATATAATATAAAA-TAT
2319234 GAATATAAT-TAAAAT
1 -AATATAATATAAAAT
2319249 TTAAGTTAAG
Statistics
Matches: 91, Mismatches: 14, Indels: 32
0.66 0.10 0.23
Matches are distributed among these distances:
13 9 0.10
14 15 0.16
15 15 0.16
16 23 0.25
17 19 0.21
18 10 0.11
ACGTcount: A:0.59, C:0.02, G:0.01, T:0.38
Consensus pattern (17 bp):
AATATAATATAAAATAT
Found at i:2319207 original size:16 final size:17
Alignment explanation
Indices: 2319164--2319216 Score: 56
Period size: 17 Copynumber: 3.1 Consensus size: 17
2319154 TATAAATATA
*
2319164 TAAAAATTT-ATATAAT
1 TAAAATTTTAATATAAT
*
2319180 TTAAATTATTAATA-AAT
1 TAAAATT-TTAATATAAT
2319197 TAAAATTTTAAATATAAT
1 TAAAATTTT-AATATAAT
2319215 TA
1 TA
2319217 TAATATATAA
Statistics
Matches: 30, Mismatches: 3, Indels: 6
0.77 0.08 0.15
Matches are distributed among these distances:
16 7 0.23
17 15 0.50
18 8 0.27
ACGTcount: A:0.55, C:0.00, G:0.00, T:0.45
Consensus pattern (17 bp):
TAAAATTTTAATATAAT
Found at i:2319220 original size:28 final size:29
Alignment explanation
Indices: 2319183--2319244 Score: 72
Period size: 28 Copynumber: 2.2 Consensus size: 29
2319173 ATATAATTTA
* * *
2319183 AATTATTAATAAATTAAAATTTTAAATAT
1 AATTATTAATAAATAAAAACTATAAATAT
* *
2319212 AATTA-TAATATATAAAAACTATGAATAT
1 AATTATTAATAAATAAAAACTATAAATAT
2319240 AATTA
1 AATTA
2319245 AAATTTAAGT
Statistics
Matches: 28, Mismatches: 5, Indels: 1
0.82 0.15 0.03
Matches are distributed among these distances:
28 23 0.82
29 5 0.18
ACGTcount: A:0.56, C:0.02, G:0.02, T:0.40
Consensus pattern (29 bp):
AATTATTAATAAATAAAAACTATAAATAT
Found at i:2319788 original size:29 final size:28
Alignment explanation
Indices: 2319750--2319828 Score: 104
Period size: 29 Copynumber: 2.8 Consensus size: 28
2319740 AAAGTTAAAG
*
2319750 TAAAGATTTATTTAAATATAATAAAAATA
1 TAAA-ATTTATTTAAATAAAATAAAAATA
*
2319779 TAATAATTTATTTAAATAAAATAAAAGTA
1 TAA-AATTTATTTAAATAAAATAAAAATA
* *
2319808 TAAAACTTATCTAAATAAAAT
1 TAAAATTTATTTAAATAAAAT
2319829 GATAGTTCAA
Statistics
Matches: 45, Mismatches: 4, Indels: 3
0.87 0.08 0.06
Matches are distributed among these distances:
28 16 0.36
29 28 0.62
30 1 0.02
ACGTcount: A:0.58, C:0.03, G:0.03, T:0.37
Consensus pattern (28 bp):
TAAAATTTATTTAAATAAAATAAAAATA
Found at i:2321014 original size:8 final size:8
Alignment explanation
Indices: 2321001--2321041 Score: 55
Period size: 8 Copynumber: 5.1 Consensus size: 8
2320991 TATGTAAAAA
2321001 TAAAAATT
1 TAAAAATT
2321009 TAAAAATT
1 TAAAAATT
*
2321017 TAAAAAGT
1 TAAAAATT
*
2321025 TAAAAAAT
1 TAAAAATT
*
2321033 TATAAATT
1 TAAAAATT
2321041 T
1 T
2321042 TTAAGTTTAT
Statistics
Matches: 29, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
8 29 1.00
ACGTcount: A:0.61, C:0.00, G:0.02, T:0.37
Consensus pattern (8 bp):
TAAAAATT
Found at i:2321022 original size:16 final size:16
Alignment explanation
Indices: 2320996--2321041 Score: 58
Period size: 16 Copynumber: 2.9 Consensus size: 16
2320986 ATTTATATGT
2320996 AAAAA-TAAAAATTTA
1 AAAAATTAAAAATTTA
* *
2321011 AAAATTTAAAAAGTTA
1 AAAAATTAAAAATTTA
*
2321027 AAAAATTATAAATTT
1 AAAAATTAAAAATTT
2321042 TTAAGTTTAT
Statistics
Matches: 25, Mismatches: 5, Indels: 1
0.81 0.16 0.03
Matches are distributed among these distances:
15 4 0.16
16 21 0.84
ACGTcount: A:0.65, C:0.00, G:0.02, T:0.33
Consensus pattern (16 bp):
AAAAATTAAAAATTTA
Found at i:2321030 original size:17 final size:17
Alignment explanation
Indices: 2321000--2321038 Score: 53
Period size: 17 Copynumber: 2.3 Consensus size: 17
2320990 ATATGTAAAA
*
2321000 ATAAAAATTTAAAAATT
1 ATAAAAATTAAAAAATT
2321017 -TAAAAAGTTAAAAAATT
1 ATAAAAA-TTAAAAAATT
2321034 ATAAA
1 ATAAA
2321039 TTTTTAAGTT
Statistics
Matches: 19, Mismatches: 1, Indels: 3
0.83 0.04 0.13
Matches are distributed among these distances:
16 6 0.32
17 9 0.47
18 4 0.21
ACGTcount: A:0.67, C:0.00, G:0.03, T:0.31
Consensus pattern (17 bp):
ATAAAAATTAAAAAATT
Found at i:2322017 original size:72 final size:72
Alignment explanation
Indices: 2321941--2322140 Score: 210
Period size: 74 Copynumber: 2.7 Consensus size: 72
2321931 TTTGTTTTAA
*
2321941 AAAATTTTTAAGTTACTATTTATCTTTATTTGTAAAAGTTTAAAT-T-TATTTTTGAGTATGAC-
1 AAAATTTTTAAG-TA-TATTTATCTTTATTTGTAAAAGTTTAAATGTGT-TTTTTGAGTA-CACT
*
2322003 TATATGAG-TT
62 TATATAAGTTT
* * **
2322013 AAAATTTTTAAAGTAAAATTTATCTTTATTTATAAAAGTTTAAATGTGTTTTTTGTTTACACTTA
1 AAAATTTTT-AAGT-ATATTTATCTTTATTTGTAAAAGTTTAAATGTGTTTTTTGAGTACACTTA
2322078 TATAAGTTT
64 TATAAGTTT
* * * *
2322087 AAATTTTTTATGGTATAATTTATTTTTATTTGTAAAAGTTTAAATATGTTTTTT
1 AAAATTTTTA-AGTAT-ATTTATCTTTATTTGTAAAAGTTTAAATGTGTTTTTT
2322141 TGGGGTATGA
Statistics
Matches: 108, Mismatches: 12, Indels: 14
0.81 0.09 0.10
Matches are distributed among these distances:
72 39 0.36
73 22 0.20
74 47 0.44
ACGTcount: A:0.34, C:0.03, G:0.10, T:0.54
Consensus pattern (72 bp):
AAAATTTTTAAGTATATTTATCTTTATTTGTAAAAGTTTAAATGTGTTTTTTGAGTACACTTATA
TAAGTTT
Found at i:2323486 original size:72 final size:72
Alignment explanation
Indices: 2323193--2323524 Score: 292
Period size: 72 Copynumber: 4.7 Consensus size: 72
2323183 ATTTAAATAA
* * * * *
2323193 AAATTTAAACTTTTACAAATAAAGATAAATAATA--TTCTAAAAATTTAAAAT--TAT-GTCA-A
1 AAATTTAAACTTTCACAAATAAAGATAAATTATACCATC-AAAAATTT-AACTCGTATAATCATA
2323252 CCCAAAAAT
64 CCCAAAAAT
* * * *
2323261 AAATTTAAA-TTTCTACAAATAAAAATAAATTATACGATCAAAAATATAAACTCGTATAATTATA
1 AAATTTAAACTTTC-ACAAATAAAGATAAATTATACCATCAAAAAT-TTAACTCGTATAATCATA
* *
2323325 TCCAAAACAC
64 CCCAAAA-AT
* * * * * * *
2323335 ACATTGAAACTTTTACAAA-AAA-ATAAATTATACCGTAAAAAAATTAAACTCATATAAGT-ATA
1 AAATTTAAACTTTCACAAATAAAGATAAATTATACCAT-CAAAAATTTAACTCGTATAA-TCATA
2323397 CCCAAAAAAT
64 CCC-AAAAAT
*
2323407 ACATTTAAACTTTCACAAATAAAGATAAATTATACCATCAAAAATTTAACTCGTATAATCATACC
1 AAATTTAAACTTTCACAAATAAAGATAAATTATACCATCAAAAATTTAACTCGTATAATCATACC
*
2323472 TAAAAAT
66 CAAAAAT
* * *
2323479 AAATTTAAAC-TTCTATAAATAAAGATAAATAATACC-TTAAAAATTT
1 AAATTTAAACTTTC-ACAAATAAAGATAAATTATACCATCAAAAATTT
2323525 TTTAATACAC
Statistics
Matches: 217, Mismatches: 30, Indels: 31
0.78 0.11 0.11
Matches are distributed among these distances:
67 3 0.01
68 27 0.12
69 9 0.04
70 3 0.01
71 15 0.07
72 85 0.39
73 46 0.21
74 26 0.12
75 3 0.01
ACGTcount: A:0.54, C:0.13, G:0.03, T:0.30
Consensus pattern (72 bp):
AAATTTAAACTTTCACAAATAAAGATAAATTATACCATCAAAAATTTAACTCGTATAATCATACC
CAAAAAT
Found at i:2323507 original size:146 final size:145
Alignment explanation
Indices: 2323251--2323521 Score: 361
Period size: 146 Copynumber: 1.9 Consensus size: 145
2323241 AATTATGTCA
*
2323251 ACCCAAAAATAAATTTAAATTTCTACAAATAAAAATAAATTATACGATCAAAAATATAAACTCGT
1 ACCCAAAAATAAATTTAAATTTCTACAAATAAAAATAAATTATACCATCAAAAATATAAACTCGT
* * * *
2323316 ATAATTATATCCAAAACACACATTGAAACTTTTACAAAAAAATAAATTATACCGTAAAAAAATTA
66 ATAATCATATCCAAAACACAAATTGAAACTTCTACAAAAAAATAAATAATACCGTAAAAAAATTA
2323381 AACTCATATAAGTAT
131 AACTCATATAAGTAT
* * *
2323396 ACCCAAAAAATACATTTAAACTTTC-ACAAATAAAGATAAATTATACCATCAAAAAT-TTAACTC
1 ACCC-AAAAATAAATTTAAA-TTTCTACAAATAAAAATAAATTATACCATCAAAAATATAAACTC
* * * *
2323459 GTATAATCATA-CCTAAAA-ATAAATTTAAACTTCTATAAATAAAGATAAATAATACCTTAAAAA
64 GTATAATCATATCC-AAAACACAAATTGAAACTTCTACAAA-AAA-ATAAATAATACCGTAAAAA
2323522 TTTTTTAATA
Statistics
Matches: 109, Mismatches: 12, Indels: 9
0.84 0.09 0.07
Matches are distributed among these distances:
144 18 0.17
145 27 0.25
146 60 0.55
147 4 0.04
ACGTcount: A:0.54, C:0.14, G:0.03, T:0.28
Consensus pattern (145 bp):
ACCCAAAAATAAATTTAAATTTCTACAAATAAAAATAAATTATACCATCAAAAATATAAACTCGT
ATAATCATATCCAAAACACAAATTGAAACTTCTACAAAAAAATAAATAATACCGTAAAAAAATTA
AACTCATATAAGTAT
Found at i:2323754 original size:28 final size:29
Alignment explanation
Indices: 2323723--2323781 Score: 70
Period size: 27 Copynumber: 2.1 Consensus size: 29
2323713 TTAGATAGCG
*
2323723 ATTTTTAAATAA-ATTTAT-AAAAAA-TT
1 ATTTTTAAAAAATATTTATCAAAAAATTT
*
2323749 ATATTTTAAAAAATATTTTTCAAAAAATTT
1 AT-TTTTAAAAAATATTTATCAAAAAATTT
2323779 ATT
1 ATT
2323782 ATTATTATAA
Statistics
Matches: 27, Mismatches: 2, Indels: 5
0.79 0.06 0.15
Matches are distributed among these distances:
26 2 0.07
27 9 0.33
28 5 0.19
29 7 0.26
30 4 0.15
ACGTcount: A:0.51, C:0.02, G:0.00, T:0.47
Consensus pattern (29 bp):
ATTTTTAAAAAATATTTATCAAAAAATTT
Found at i:2323773 original size:14 final size:14
Alignment explanation
Indices: 2323729--2323781 Score: 54
Period size: 15 Copynumber: 3.6 Consensus size: 14
2323719 AGCGATTTTT
*
2323729 AAATAAATTTATAAA
1 AAATATATTT-TAAA
2323744 AAATTATATTTTAAA
1 AAA-TATATTTTAAA
2323759 AAATAT-TTTTCAAA
1 AAATATATTTT-AAA
*
2323773 AAATTTATT
1 AAATATATT
2323782 ATTATTATAA
Statistics
Matches: 33, Mismatches: 2, Indels: 6
0.80 0.05 0.15
Matches are distributed among these distances:
13 4 0.12
14 11 0.33
15 12 0.36
16 6 0.18
ACGTcount: A:0.55, C:0.02, G:0.00, T:0.43
Consensus pattern (14 bp):
AAATATATTTTAAA
Found at i:2324680 original size:16 final size:16
Alignment explanation
Indices: 2324661--2324717 Score: 60
Period size: 16 Copynumber: 3.6 Consensus size: 16
2324651 ACCCGAACTT
*
2324661 GAAATAATCCAAACAC
1 GAAATAACCCAAACAC
*
2324677 GAAATAACCCAAACCC
1 GAAATAACCCAAACAC
* * *
2324693 GAAATGACCCGAACCC
1 GAAATAACCCAAACAC
*
2324709 AAAATAACC
1 GAAATAACC
2324718 TGAACCCAAA
Statistics
Matches: 35, Mismatches: 6, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
16 35 1.00
ACGTcount: A:0.51, C:0.32, G:0.09, T:0.09
Consensus pattern (16 bp):
GAAATAACCCAAACAC
Found at i:2324722 original size:16 final size:16
Alignment explanation
Indices: 2324678--2324735 Score: 71
Period size: 16 Copynumber: 3.6 Consensus size: 16
2324668 TCCAAACACG
* *
2324678 AAATAACCCAAACCCG
1 AAATAACCCGAACCCA
*
2324694 AAATGACCCGAACCCA
1 AAATAACCCGAACCCA
*
2324710 AAATAACCTGAACCCAA
1 AAATAACCCGAACCC-A
2324727 AAATAACCC
1 AAATAACCC
2324736 AAAAATTTTA
Statistics
Matches: 35, Mismatches: 6, Indels: 1
0.83 0.14 0.02
Matches are distributed among these distances:
16 26 0.74
17 9 0.26
ACGTcount: A:0.50, C:0.34, G:0.07, T:0.09
Consensus pattern (16 bp):
AAATAACCCGAACCCA
Found at i:2325945 original size:20 final size:20
Alignment explanation
Indices: 2325909--2325961 Score: 79
Period size: 20 Copynumber: 2.6 Consensus size: 20
2325899 TCTATAATTG
*
2325909 GTATCAATACAATAAGTTAAT
1 GTATCAATAC-ATAAGTGAAT
2325930 GTATCAATACATAAGTGAAT
1 GTATCAATACATAAGTGAAT
*
2325950 GTATCGATACAT
1 GTATCAATACAT
2325962 GCTTGAATTG
Statistics
Matches: 30, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
20 20 0.67
21 10 0.33
ACGTcount: A:0.43, C:0.11, G:0.13, T:0.32
Consensus pattern (20 bp):
GTATCAATACATAAGTGAAT
Found at i:2326086 original size:20 final size:20
Alignment explanation
Indices: 2326020--2326086 Score: 71
Period size: 20 Copynumber: 3.3 Consensus size: 20
2326010 CTGAAAAAAT
* *
2326020 TGTATCGATACATAAGTAAA
1 TGTATCGATACATAATTCAA
**
2326040 TGTATCGATACATGCTTGCAA
1 TGTATCGATACATAATT-CAA
* *
2326061 TGTATCGATACATTATTCAT
1 TGTATCGATACATAATTCAA
2326081 TGTATC
1 TGTATC
2326087 AATATATTTT
Statistics
Matches: 39, Mismatches: 7, Indels: 2
0.81 0.15 0.04
Matches are distributed among these distances:
20 22 0.56
21 17 0.44
ACGTcount: A:0.33, C:0.15, G:0.15, T:0.37
Consensus pattern (20 bp):
TGTATCGATACATAATTCAA
Found at i:2328727 original size:37 final size:37
Alignment explanation
Indices: 2328677--2328749 Score: 137
Period size: 37 Copynumber: 2.0 Consensus size: 37
2328667 TCCACGAGAA
*
2328677 TACTCCAACCTCTTCTTTCGAGGAGATACTCCAACCT
1 TACTCCAACCTCTTCTTTCGAGGAGACACTCCAACCT
2328714 TACTCCAACCTCTTCTTTCGAGGAGACACTCCAACC
1 TACTCCAACCTCTTCTTTCGAGGAGACACTCCAACC
2328750 CCATTTTTTA
Statistics
Matches: 35, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
37 35 1.00
ACGTcount: A:0.25, C:0.37, G:0.11, T:0.27
Consensus pattern (37 bp):
TACTCCAACCTCTTCTTTCGAGGAGACACTCCAACCT
Found at i:2341907 original size:51 final size:51
Alignment explanation
Indices: 2341843--2341953 Score: 186
Period size: 51 Copynumber: 2.2 Consensus size: 51
2341833 TTGTTTATGA
*
2341843 GATGGAAGTTGTATTACCTATCGAAATTGAGATCCCCTCTCTTAGAGTCTT
1 GATGGAAGCTGTATTACCTATCGAAATTGAGATCCCCTCTCTTAGAGTCTT
* * *
2341894 GATGGAAGCTGTATTACCTGTCGAAGTTGAGATCCCCTTTCTTAGAGTCTT
1 GATGGAAGCTGTATTACCTATCGAAATTGAGATCCCCTCTCTTAGAGTCTT
2341945 GATGGAAGC
1 GATGGAAGC
2341954 CAAACTTGAA
Statistics
Matches: 56, Mismatches: 4, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
51 56 1.00
ACGTcount: A:0.24, C:0.19, G:0.23, T:0.33
Consensus pattern (51 bp):
GATGGAAGCTGTATTACCTATCGAAATTGAGATCCCCTCTCTTAGAGTCTT
Found at i:2342357 original size:24 final size:22
Alignment explanation
Indices: 2342330--2342402 Score: 67
Period size: 21 Copynumber: 3.2 Consensus size: 22
2342320 TTCGTGCCAA
2342330 AAAAATAAAAAAAACCAAAAAAAC
1 AAAAA-AAAAAAAA-CAAAAAAAC
* * *
2342354 AAAACAAAAAAATAGAAAAAACC
1 AAAA-AAAAAAAAACAAAAAAAC
* *
2342377 AAAAACAAAAAAA-AAACAAAC
1 AAAAAAAAAAAAACAAAAAAAC
2342398 AAAAA
1 AAAAA
2342403 TGGGTCCATA
Statistics
Matches: 41, Mismatches: 7, Indels: 5
0.77 0.13 0.09
Matches are distributed among these distances:
21 11 0.27
22 7 0.17
23 11 0.27
24 11 0.27
25 1 0.02
ACGTcount: A:0.84, C:0.12, G:0.01, T:0.03
Consensus pattern (22 bp):
AAAAAAAAAAAAACAAAAAAAC
Found at i:2342362 original size:23 final size:23
Alignment explanation
Indices: 2342330--2342402 Score: 71
Period size: 23 Copynumber: 3.2 Consensus size: 23
2342320 TTCGTGCCAA
*
2342330 AAAAATAAAAAAAACCAAAAAAAC
1 AAAAACAAAAAAAA-CAAAAAAAC
* *
2342354 -AAAACAAAAAAATAGAAAAAACC
1 AAAAACAAAAAAA-ACAAAAAAAC
*
2342377 AAAAAC-AAAAAAA-AAACAAAC
1 AAAAACAAAAAAAACAAAAAAAC
2342398 AAAAA
1 AAAAA
2342403 TGGGTCCATA
Statistics
Matches: 42, Mismatches: 5, Indels: 7
0.78 0.09 0.13
Matches are distributed among these distances:
21 11 0.26
22 1 0.02
23 24 0.57
24 6 0.14
ACGTcount: A:0.84, C:0.12, G:0.01, T:0.03
Consensus pattern (23 bp):
AAAAACAAAAAAAACAAAAAAAC
Found at i:2342365 original size:31 final size:31
Alignment explanation
Indices: 2342327--2342402 Score: 102
Period size: 31 Copynumber: 2.5 Consensus size: 31
2342317 TCCTTCGTGC
2342327 CAAAAAAATAAAAAAAACCAAAAA-AACAAAA
1 CAAAAAAATAAAAAAAACCAAAAACAA-AAAA
*
2342358 CAAAAAAATAGAAAAAACCAAAAACAAAAAA
1 CAAAAAAATAAAAAAAACCAAAAACAAAAAA
*
2342389 -AAAACAAACAAAAA
1 CAAAA-AAATAAAAA
2342403 TGGGTCCATA
Statistics
Matches: 40, Mismatches: 3, Indels: 4
0.85 0.06 0.09
Matches are distributed among these distances:
30 4 0.10
31 34 0.85
32 2 0.05
ACGTcount: A:0.83, C:0.13, G:0.01, T:0.03
Consensus pattern (31 bp):
CAAAAAAATAAAAAAAACCAAAAACAAAAAA
Found at i:2343679 original size:28 final size:28
Alignment explanation
Indices: 2343648--2344002 Score: 319
Period size: 28 Copynumber: 12.5 Consensus size: 28
2343638 TATTCATCTC
2343648 TTCAAAGCCCACAAGTCAGTGGCATCCT
1 TTCAAAGCCCACAAGTCAGTGGCATCCT
2343676 TTCAAAGCCCACAAGTCAGTGGCAT-CT
1 TTCAAAGCCCACAAGTCAGTGGCATCCT
*
2343703 CTTCAAAAGCCCATAAGTCAGTGGCA-CCTT
1 -TTC-AAAGCCCACAAGTCAGTGGCATCC-T
* * *
2343733 TTCAAAGCCCATAAGTTAATGGCATACCCT
1 TTCAAAGCCCACAAGTCAGTGGCAT--CCT
* * * **
2343763 ATCAAAGCCCACACAAATCAGTAGCA-AAT
1 TTCAAAG-CC-CACAAGTCAGTGGCATCCT
* *
2343792 TCCAAAG--C-CAAGTCAGTGGCACCCT
1 TTCAAAGCCCACAAGTCAGTGGCATCCT
* * * *
2343817 TTCAAAGCACATAAGTCAATGGCACCCT
1 TTCAAAGCCCACAAGTCAGTGGCATCCT
* * *
2343845 TTCAAAGCACACAAGTCAGTGGTACCCT
1 TTCAAAGCCCACAAGTCAGTGGCATCCT
* * *
2343873 TTCAAAACCCACAAGTCAGTGGTATCCC
1 TTCAAAGCCCACAAGTCAGTGGCATCCT
2343901 TTCAAAGCCCACAAGTCAGTGGCATACCT
1 TTCAAAGCCCACAAGTCAGTGGCAT-CCT
*
2343930 TTCAAAGCCCACAAGTC-GATGGCACCCT
1 TTCAAAGCCCACAAGTCAG-TGGCATCCT
* * *
2343958 TTTAAAGCCCACACAAGTCGGTGGCAACTCTT
1 TTCAAAG-CC-CACAAGTCAGTGGC-A-TCCT
2343990 TTCAAAGCCCACA
1 TTCAAAGCCCACA
2344003 CAAGTTAGTG
Statistics
Matches: 272, Mismatches: 35, Indels: 38
0.79 0.10 0.11
Matches are distributed among these distances:
24 11 0.04
25 8 0.03
27 3 0.01
28 144 0.53
29 56 0.21
30 24 0.09
31 8 0.03
32 18 0.07
ACGTcount: A:0.32, C:0.31, G:0.16, T:0.21
Consensus pattern (28 bp):
TTCAAAGCCCACAAGTCAGTGGCATCCT
Found at i:2350803 original size:21 final size:21
Alignment explanation
Indices: 2350779--2350818 Score: 62
Period size: 21 Copynumber: 1.9 Consensus size: 21
2350769 GTTGGGAACT
*
2350779 TGTATCGATACATGGAAGACA
1 TGTATCAATACATGGAAGACA
*
2350800 TGTATCAATACATGTAAGA
1 TGTATCAATACATGGAAGA
2350819 AAAAATGTAA
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
21 17 1.00
ACGTcount: A:0.40, C:0.12, G:0.20, T:0.28
Consensus pattern (21 bp):
TGTATCAATACATGGAAGACA
Found at i:2352126 original size:11 final size:10
Alignment explanation
Indices: 2352104--2352133 Score: 51
Period size: 11 Copynumber: 2.9 Consensus size: 10
2352094 ATCGTATTCA
2352104 TATATTTAAT
1 TATATTTAAT
2352114 TATATTATAAT
1 TATATT-TAAT
2352125 TATATTTAA
1 TATATTTAA
2352134 AAATTTTATA
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
10 9 0.47
11 10 0.53
ACGTcount: A:0.43, C:0.00, G:0.00, T:0.57
Consensus pattern (10 bp):
TATATTTAAT
Found at i:2352142 original size:21 final size:21
Alignment explanation
Indices: 2352104--2352143 Score: 53
Period size: 21 Copynumber: 1.9 Consensus size: 21
2352094 ATCGTATTCA
**
2352104 TATATTTAATTATATTATAAT
1 TATATTTAAAAATATTATAAT
*
2352125 TATATTTAAAAATTTTATA
1 TATATTTAAAAATATTATA
2352144 TTTAAATAAA
Statistics
Matches: 16, Mismatches: 3, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
21 16 1.00
ACGTcount: A:0.45, C:0.00, G:0.00, T:0.55
Consensus pattern (21 bp):
TATATTTAAAAATATTATAAT
Found at i:2352169 original size:18 final size:18
Alignment explanation
Indices: 2352103--2352186 Score: 59
Period size: 18 Copynumber: 4.6 Consensus size: 18
2352093 TATCGTATTC
*
2352103 ATATATTTAATTATATTATA
1 ATATA-TTAATAAT-TTATA
*
2352123 ATTATATTTAAAAATTT-T-
1 A-TATA-TTAATAATTTATA
2352141 ATAT-TTAAATAAATTTA-A
1 ATATATT-AAT-AATTTATA
2352159 ATATATTAATAATTTATA
1 ATATATTAATAATTTATA
*
2352177 TTATATTAAT
1 ATATATTAAT
2352187 TTTAAAAAAC
Statistics
Matches: 53, Mismatches: 4, Indels: 16
0.73 0.05 0.22
Matches are distributed among these distances:
15 2 0.04
16 2 0.04
17 14 0.26
18 18 0.34
19 3 0.06
20 3 0.06
21 11 0.21
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (18 bp):
ATATATTAATAATTTATA
Found at i:2353816 original size:18 final size:20
Alignment explanation
Indices: 2353793--2353839 Score: 62
Period size: 18 Copynumber: 2.4 Consensus size: 20
2353783 AAAATTTGTA
2353793 TTTATATTT-ATATTAT-TT
1 TTTATATTTAATATTATATT
2353811 TTTATATTTAAAATATTATATT
1 TTTATATTT--AATATTATATT
2353833 TTTATAT
1 TTTATAT
2353840 AAATTTTTAT
Statistics
Matches: 25, Mismatches: 0, Indels: 4
0.86 0.00 0.14
Matches are distributed among these distances:
18 9 0.36
21 7 0.28
22 9 0.36
ACGTcount: A:0.34, C:0.00, G:0.00, T:0.66
Consensus pattern (20 bp):
TTTATATTTAATATTATATT
Found at i:2353847 original size:34 final size:35
Alignment explanation
Indices: 2353791--2353862 Score: 94
Period size: 34 Copynumber: 2.1 Consensus size: 35
2353781 AAAAAATTTG
* *
2353791 TATTTATATTTATATTATTTTTTATAT-TTAA-AA
1 TATTTATATTTATATAAATTTTTATATGTTAATAA
*
2353824 TATTATATTTTTATATAAATTTTTATATGTTAATAA
1 TATT-TATATTTATATAAATTTTTATATGTTAATAA
2353860 TAT
1 TAT
2353863 GTTTTATATC
Statistics
Matches: 33, Mismatches: 3, Indels: 3
0.85 0.08 0.08
Matches are distributed among these distances:
33 4 0.12
34 20 0.61
35 4 0.12
36 5 0.15
ACGTcount: A:0.38, C:0.00, G:0.01, T:0.61
Consensus pattern (35 bp):
TATTTATATTTATATAAATTTTTATATGTTAATAA
Found at i:2353911 original size:15 final size:15
Alignment explanation
Indices: 2353865--2353917 Score: 52
Period size: 15 Copynumber: 3.3 Consensus size: 15
2353855 AATAATATGT
*
2353865 TTTATATCATGTATA
1 TTTATATTATGTATA
**
2353880 TCTTTATATTACATATA
1 --TTTATATTATGTATA
2353897 TTTATATTATGTATA
1 TTTATATTATGTATA
2353912 TATTAT
1 T-TTAT
2353918 TTTAATATTA
Statistics
Matches: 30, Mismatches: 5, Indels: 3
0.79 0.13 0.08
Matches are distributed among these distances:
15 14 0.47
16 4 0.13
17 12 0.40
ACGTcount: A:0.34, C:0.06, G:0.04, T:0.57
Consensus pattern (15 bp):
TTTATATTATGTATA
Found at i:2353912 original size:17 final size:17
Alignment explanation
Indices: 2353865--2353915 Score: 61
Period size: 17 Copynumber: 3.1 Consensus size: 17
2353855 AATAATATGT
* *
2353865 TTTATATCATGTATATC
1 TTTATATTATGTATATA
*
2353882 TTTATATTA--CATATA
1 TTTATATTATGTATATA
2353897 TTTATATTATGTATATA
1 TTTATATTATGTATATA
2353914 TT
1 TT
2353916 ATTTTAATAT
Statistics
Matches: 28, Mismatches: 4, Indels: 4
0.78 0.11 0.11
Matches are distributed among these distances:
15 13 0.46
17 15 0.54
ACGTcount: A:0.33, C:0.06, G:0.04, T:0.57
Consensus pattern (17 bp):
TTTATATTATGTATATA
Found at i:2357218 original size:20 final size:21
Alignment explanation
Indices: 2357193--2357250 Score: 84
Period size: 20 Copynumber: 2.9 Consensus size: 21
2357183 GTAAAAAGAC
2357193 AGAATGTATCGATACATT-AG
1 AGAATGTATCGATACATTCAG
*
2357213 AGAATGTATCGATACATTCAT
1 AGAATGTATCGATACATTCAG
*
2357234 A-CATGTATCGATACATT
1 AGAATGTATCGATACATT
2357251 TTTTCAATGT
Statistics
Matches: 35, Mismatches: 2, Indels: 2
0.90 0.05 0.05
Matches are distributed among these distances:
20 33 0.94
21 2 0.06
ACGTcount: A:0.38, C:0.14, G:0.16, T:0.33
Consensus pattern (21 bp):
AGAATGTATCGATACATTCAG
Found at i:2358291 original size:20 final size:20
Alignment explanation
Indices: 2358263--2358308 Score: 65
Period size: 20 Copynumber: 2.2 Consensus size: 20
2358253 AGAAAGATGG
*
2358263 AAAAGAGAGAGAAACAAAGAAA
1 AAAAGAGA-ATAAA-AAAGAAA
2358285 AAAAGAGAATAAAAAAGAAA
1 AAAAGAGAATAAAAAAGAAA
2358305 AAAA
1 AAAA
2358309 AATTATATTC
Statistics
Matches: 23, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
20 11 0.48
21 4 0.17
22 8 0.35
ACGTcount: A:0.78, C:0.02, G:0.17, T:0.02
Consensus pattern (20 bp):
AAAAGAGAATAAAAAAGAAA
Found at i:2358889 original size:11 final size:11
Alignment explanation
Indices: 2358875--2358907 Score: 50
Period size: 11 Copynumber: 3.0 Consensus size: 11
2358865 TTGTATCATA
2358875 TTTATATTATT
1 TTTATATTATT
2358886 TTTATATTATGT
1 TTTATATTAT-T
2358898 TTTA-ATTATT
1 TTTATATTATT
2358908 CTATATGTTA
Statistics
Matches: 21, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
10 1 0.05
11 15 0.71
12 5 0.24
ACGTcount: A:0.27, C:0.00, G:0.03, T:0.70
Consensus pattern (11 bp):
TTTATATTATT
Found at i:2358918 original size:23 final size:23
Alignment explanation
Indices: 2358875--2358921 Score: 60
Period size: 23 Copynumber: 2.0 Consensus size: 23
2358865 TTGTATCATA
*
2358875 TTTATATTATTTTTATATTATGT
1 TTTATATTATTTATATATTATGT
*
2358898 TTTA-ATTATTCTATATGTTATGT
1 TTTATATTATT-TATATATTATGT
2358921 T
1 T
2358922 CGTATCGTGT
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
22 6 0.29
23 15 0.71
ACGTcount: A:0.26, C:0.02, G:0.06, T:0.66
Consensus pattern (23 bp):
TTTATATTATTTATATATTATGT
Found at i:2360976 original size:30 final size:29
Alignment explanation
Indices: 2360936--2361219 Score: 209
Period size: 30 Copynumber: 9.6 Consensus size: 29
2360926 TCACCCTTCA
* *
2360936 AAAGTCCACAAGTCAGTGGCATTTTTTTTC
1 AAAGCCCACAAGTCAGTGGCA-TCTTTTTC
*
2360966 AAAGCCCACAAGTCAGTGGCATTTTTTTC
1 AAAGCCCACAAGTCAGTGGCATCTTTTTC
* * *
2360995 AAAAGCCCACAAGTTAGTGGCAAC--CTTC
1 -AAAGCCCACAAGTCAGTGGCATCTTTTTC
* *
2361023 AAAGCCCACAAATCAGTGGCACCCTTTTTC
1 AAAGCCCACAAGTCAGTGGCA-TCTTTTTC
* * * * *
2361053 GAAGCCCACAAGTCGGCGGCCTCTTTTCC
1 AAAGCCCACAAGTCAGTGGCATCTTTTTC
* * *
2361082 AAAGCTCACAACTCTA-TAGCACTCTTTTTC
1 AAAGCCCACAAGTC-AGTGGCA-TCTTTTTC
* * * *
2361112 TTTTTAAGCCCACAAGTTAGTGGCACCCTTTTC
1 ----AAAGCCCACAAGTCAGTGGCATCTTTTTC
* * *
2361145 AAAAGCCCACAAGTCAGTGGCAAC-CTTTA
1 -AAAGCCCACAAGTCAGTGGCATCTTTTTC
* * *
2361174 AAAGCCCACAAGTCAGTGGCAAC-CTTTA
1 AAAGCCCACAAGTCAGTGGCATCTTTTTC
2361202 AAAGCCCACAAGTCAGTG
1 AAAGCCCACAAGTCAGTG
2361220 ATGCAAACCT
Statistics
Matches: 206, Mismatches: 37, Indels: 24
0.77 0.14 0.09
Matches are distributed among these distances:
27 19 0.09
28 50 0.24
29 30 0.15
30 86 0.42
33 7 0.03
34 14 0.07
ACGTcount: A:0.30, C:0.29, G:0.17, T:0.25
Consensus pattern (29 bp):
AAAGCCCACAAGTCAGTGGCATCTTTTTC
Found at i:2361185 original size:28 final size:28
Alignment explanation
Indices: 2361117--2361243 Score: 173
Period size: 28 Copynumber: 4.3 Consensus size: 28
2361107 TTTTCTTTTT
* *
2361117 AAGCCCACAAGTTAGTGGCACCCTTTTCAA
1 AAGCCCACAAGTCAGTGGCAACC-TTT-AA
2361147 AAGCCCACAAGTCAGTGGCAACCTTTAA
1 AAGCCCACAAGTCAGTGGCAACCTTTAA
2361175 AAGCCCACAAGTCAGTGGCAACCTTTAA
1 AAGCCCACAAGTCAGTGGCAACCTTTAA
*
2361203 AAGCCCACAAGTCAGTGATGCAAACCTCTCAA
1 AAGCCCACAAGTCAGTG--GC-AACCT-TTAA
2361235 AAGCCCACA
1 AAGCCCACA
2361244 CAAGTTGGTG
Statistics
Matches: 90, Mismatches: 3, Indels: 6
0.91 0.03 0.06
Matches are distributed among these distances:
28 47 0.52
29 3 0.03
30 23 0.26
31 5 0.06
32 12 0.13
ACGTcount: A:0.35, C:0.31, G:0.17, T:0.17
Consensus pattern (28 bp):
AAGCCCACAAGTCAGTGGCAACCTTTAA
Found at i:2361420 original size:21 final size:21
Alignment explanation
Indices: 2361353--2361420 Score: 52
Period size: 21 Copynumber: 3.2 Consensus size: 21
2361343 AATGTAGCTG
*
2361353 ACCTTGAATCAGCACATTGGC
1 ACCTTGAATCAGCATATTGGC
** *
2361374 ACCTT-AAGTCCAATATAGCTGG-
1 ACCTTGAA-T-CAGCATA-TTGGC
2361396 -CCTTGAATCAGCATATTGGC
1 ACCTTGAATCAGCATATTGGC
2361416 ACCTT
1 ACCTT
2361421 TTCCATCTTT
Statistics
Matches: 34, Mismatches: 7, Indels: 12
0.64 0.13 0.23
Matches are distributed among these distances:
19 3 0.09
20 7 0.21
21 15 0.44
22 6 0.18
23 3 0.09
ACGTcount: A:0.28, C:0.26, G:0.18, T:0.28
Consensus pattern (21 bp):
ACCTTGAATCAGCATATTGGC
Found at i:2361455 original size:52 final size:53
Alignment explanation
Indices: 2361377--2361528 Score: 173
Period size: 52 Copynumber: 2.8 Consensus size: 53
2361367 CATTGGCACC
2361377 TTAAGTCCAATATAGCTGGCCTTGAATCAGCATATTGGCACCTTTTC-CATCT
1 TTAAGTCCAATATAGCTGGCCTTGAATCAGCATATTGGCACCTTTTCTCATCT
* * ** *
2361429 TTAAGTTCAATGTAGCTGGCCTTGAATCAGCACGTTGACATCCTTTTTCTCATCT
1 TTAAGTCCAATATAGCTGGCCTTGAATCAGCATATTGGCA-CC-TTTTCTCATCT
* * * * *
2361484 TTAAG-CCTAATATCGTTGGCCATGAATCAACATATTGGCATCTTT
1 TTAAGTCC-AATATAGCTGGCCTTGAATCAGCATATTGGCACCTTT
2361529 ATCACTTTTC
Statistics
Matches: 81, Mismatches: 15, Indels: 7
0.79 0.15 0.07
Matches are distributed among these distances:
52 35 0.43
53 5 0.06
54 7 0.09
55 34 0.42
ACGTcount: A:0.25, C:0.23, G:0.16, T:0.36
Consensus pattern (53 bp):
TTAAGTCCAATATAGCTGGCCTTGAATCAGCATATTGGCACCTTTTCTCATCT
Found at i:2362432 original size:13 final size:13
Alignment explanation
Indices: 2362414--2362438 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
2362404 CATAAAGTGT
2362414 TGTATCGATACAA
1 TGTATCGATACAA
2362427 TGTATCGATACA
1 TGTATCGATACA
2362439 TATTTTTTTG
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:0.36, C:0.16, G:0.16, T:0.32
Consensus pattern (13 bp):
TGTATCGATACAA
Found at i:2362657 original size:1 final size:1
Alignment explanation
Indices: 2362651--2362706 Score: 85
Period size: 1 Copynumber: 56.0 Consensus size: 1
2362641 AAAGTGTTTG
***
2362651 AAAAAAAAAAAAATTGAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA
1 AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA
2362707 TTTAAATGTA
Statistics
Matches: 52, Mismatches: 3, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
1 52 1.00
ACGTcount: A:0.95, C:0.00, G:0.02, T:0.04
Consensus pattern (1 bp):
A
Found at i:2362735 original size:21 final size:21
Alignment explanation
Indices: 2362711--2362767 Score: 105
Period size: 21 Copynumber: 2.7 Consensus size: 21
2362701 AAAAAATTTA
2362711 AATGTATCGATACATTTGTAG
1 AATGTATCGATACATTTGTAG
*
2362732 AATGTATCGATACATTTGTGG
1 AATGTATCGATACATTTGTAG
2362753 AATGTATCGATACAT
1 AATGTATCGATACAT
2362768 CCTACAAATG
Statistics
Matches: 35, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
21 35 1.00
ACGTcount: A:0.33, C:0.11, G:0.19, T:0.37
Consensus pattern (21 bp):
AATGTATCGATACATTTGTAG
Found at i:2362847 original size:19 final size:19
Alignment explanation
Indices: 2362823--2362890 Score: 85
Period size: 19 Copynumber: 3.9 Consensus size: 19
2362813 AATTCAACAA
2362823 TTTGTATCGATACATAAGT
1 TTTGTATCGATACATAAGT
2362842 TTTGTATCGATAC--AA--
1 TTTGTATCGATACATAAGT
2362857 --TGTATCGATACATAAGT
1 TTTGTATCGATACATAAGT
*
2362874 ATTGTATCGATACATAA
1 TTTGTATCGATACATAA
2362891 TTAGCTACTG
Statistics
Matches: 43, Mismatches: 0, Indels: 12
0.78 0.00 0.22
Matches are distributed among these distances:
13 11 0.26
15 2 0.05
17 2 0.05
19 28 0.65
ACGTcount: A:0.35, C:0.12, G:0.15, T:0.38
Consensus pattern (19 bp):
TTTGTATCGATACATAAGT
Found at i:2362862 original size:13 final size:13
Alignment explanation
Indices: 2362844--2362868 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
2362834 ACATAAGTTT
2362844 TGTATCGATACAA
1 TGTATCGATACAA
2362857 TGTATCGATACA
1 TGTATCGATACA
2362869 TAAGTATTGT
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:0.36, C:0.16, G:0.16, T:0.32
Consensus pattern (13 bp):
TGTATCGATACAA
Found at i:2362866 original size:32 final size:32
Alignment explanation
Indices: 2362825--2362887 Score: 117
Period size: 32 Copynumber: 2.0 Consensus size: 32
2362815 TTCAACAATT
*
2362825 TGTATCGATACATAAGTTTTGTATCGATACAA
1 TGTATCGATACATAAGTATTGTATCGATACAA
2362857 TGTATCGATACATAAGTATTGTATCGATACA
1 TGTATCGATACATAAGTATTGTATCGATACA
2362888 TAATTAGCTA
Statistics
Matches: 30, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
32 30 1.00
ACGTcount: A:0.35, C:0.13, G:0.16, T:0.37
Consensus pattern (32 bp):
TGTATCGATACATAAGTATTGTATCGATACAA
Found at i:2362948 original size:13 final size:13
Alignment explanation
Indices: 2362930--2362955 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
2362920 CATTTTTCTG
2362930 TGTATCGATACAT
1 TGTATCGATACAT
2362943 TGTATCGATACAT
1 TGTATCGATACAT
2362956 GGATCTTTGT
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:0.31, C:0.15, G:0.15, T:0.38
Consensus pattern (13 bp):
TGTATCGATACAT
Found at i:2362952 original size:33 final size:33
Alignment explanation
Indices: 2362910--2362976 Score: 98
Period size: 33 Copynumber: 2.0 Consensus size: 33
2362900 GCCAAGGAAA
***
2362910 TGTATCGATACATTTTTCTGTGTATCGATACAT
1 TGTATCGATACATGGATCTGTGTATCGATACAT
*
2362943 TGTATCGATACATGGATCTTTGTATCGATACAT
1 TGTATCGATACATGGATCTGTGTATCGATACAT
2362976 T
1 T
2362977 TGGAAATTTT
Statistics
Matches: 30, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
33 30 1.00
ACGTcount: A:0.25, C:0.15, G:0.16, T:0.43
Consensus pattern (33 bp):
TGTATCGATACATGGATCTGTGTATCGATACAT
Found at i:2365436 original size:28 final size:28
Alignment explanation
Indices: 2365371--2365474 Score: 158
Period size: 28 Copynumber: 3.8 Consensus size: 28
2365361 TTTCTTCACA
* *
2365371 ATCGGGGACACTCCAACCCCGTTA-ATC
1 ATCGGGGATACTCCAACCCCGTTATTTC
2365398 ATCGGGGATACTCCAACCCCGTTATTTC
1 ATCGGGGATACTCCAACCCCGTTATTTC
2365426 ATCGGGGATACTCCAACCCCGTTATTTC
1 ATCGGGGATACTCCAACCCCGTTATTTC
*
2365454 -TGAGGGGATACTCCAACCCCG
1 AT-CGGGGATACTCCAACCCCG
2365475 ACTTTATTTT
Statistics
Matches: 72, Mismatches: 3, Indels: 3
0.92 0.04 0.04
Matches are distributed among these distances:
27 24 0.33
28 48 0.67
ACGTcount: A:0.23, C:0.34, G:0.20, T:0.23
Consensus pattern (28 bp):
ATCGGGGATACTCCAACCCCGTTATTTC
Found at i:2365525 original size:51 final size:51
Alignment explanation
Indices: 2365457--2365627 Score: 198
Period size: 51 Copynumber: 3.3 Consensus size: 51
2365447 TTATTTCTGA
* * *
2365457 GGGGATACTCCAACCCCGACTTTATTTTCAAAATATCGATTTTTCATAATC
1 GGGGATACTCCAACCCCGATTTTATTTTCAAAATACCAATTTTTCATAATC
* * * * *
2365508 GGGGATACTCCAACCCCGGTTTTATTTTCACAACACCAATTTCTCCTTTAATC
1 GGGGATACTCCAACCCCGATTTTATTTTCAAAATACCAATTT-TTC-ATAATC
** * *
2365561 GGGGATACTCCAATTCCGATTTTATTTCCAAAAATACCAATTTTTCACAATC
1 GGGGATACTCCAACCCCGATTTTATTTTC-AAAATACCAATTTTTCATAATC
*
2365613 GAGGATACTCCAACC
1 GGGGATACTCCAACC
2365628 TCGTTATTTC
Statistics
Matches: 97, Mismatches: 20, Indels: 5
0.80 0.16 0.04
Matches are distributed among these distances:
51 36 0.37
52 18 0.19
53 32 0.33
54 11 0.11
ACGTcount: A:0.29, C:0.26, G:0.12, T:0.33
Consensus pattern (51 bp):
GGGGATACTCCAACCCCGATTTTATTTTCAAAATACCAATTTTTCATAATC
Found at i:2365646 original size:28 final size:28
Alignment explanation
Indices: 2365610--2365691 Score: 96
Period size: 28 Copynumber: 2.9 Consensus size: 28
2365600 ATTTTTCACA
*
2365610 ATCGAGGATACTCCAACCTCGTTATTTC
1 ATCGGGGATACTCCAACCTCGTTATTTC
* *
2365638 ATCGGGGATACTCCAACCCCGTTACTTC
1 ATCGGGGATACTCCAACCTCGTTATTTC
*
2365666 --CGAGGGAACACTCCAACCTCGTTATT
1 ATCG-GGG-ATACTCCAACCTCGTTATT
2365692 ATCTCCAAAA
Statistics
Matches: 46, Mismatches: 6, Indels: 4
0.82 0.11 0.07
Matches are distributed among these distances:
26 2 0.04
27 3 0.07
28 41 0.89
ACGTcount: A:0.24, C:0.32, G:0.17, T:0.27
Consensus pattern (28 bp):
ATCGGGGATACTCCAACCTCGTTATTTC
Found at i:2382156 original size:15 final size:15
Alignment explanation
Indices: 2382136--2382199 Score: 67
Period size: 15 Copynumber: 4.3 Consensus size: 15
2382126 CCTTCTCTTC
2382136 AAAAAAAAAAAAGAA
1 AAAAAAAAAAAAGAA
2382151 AAAAAAAAACAAA-AA
1 AAAAAAAAA-AAAGAA
* *
2382166 AAACAAAACAAAGAA
1 AAAAAAAAAAAAGAA
* * *
2382181 AAAGAGAGAAAAGAA
1 AAAAAAAAAAAAGAA
2382196 AAAA
1 AAAA
2382200 CCTACTTAAG
Statistics
Matches: 40, Mismatches: 7, Indels: 4
0.78 0.14 0.08
Matches are distributed among these distances:
14 3 0.08
15 34 0.85
16 3 0.08
ACGTcount: A:0.86, C:0.05, G:0.09, T:0.00
Consensus pattern (15 bp):
AAAAAAAAAAAAGAA
Found at i:2382199 original size:1 final size:1
Alignment explanation
Indices: 2382136--2382183 Score: 51
Period size: 1 Copynumber: 48.0 Consensus size: 1
2382126 CCTTCTCTTC
* * * * *
2382136 AAAAAAAAAAAAGAAAAAAAAAAACAAAAAAAACAAAACAAAGAAAAA
1 AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA
2382184 GAGAGAAAAG
Statistics
Matches: 37, Mismatches: 10, Indels: 0
0.79 0.21 0.00
Matches are distributed among these distances:
1 37 1.00
ACGTcount: A:0.90, C:0.06, G:0.04, T:0.00
Consensus pattern (1 bp):
A
Found at i:2383249 original size:55 final size:55
Alignment explanation
Indices: 2383158--2383841 Score: 1028
Period size: 55 Copynumber: 12.4 Consensus size: 55
2383148 TCTCCTTCCG
* *
2383158 CTTTTTAGTCCTCAAAGAGCAGGACACGTTTCAAAGCCCACACAAGTTGGTGGCA
1 CTTTTCAGTCCTCAAAGAGCAGGACACCTTTCAAAGCCCACACAAGTTGGTGGCA
*
2383213 -TTTTCCAGTCCTCAAAGAGCAGGACACCTTTTAAAGCCCACACAAGTTGGTGGCA
1 CTTTT-CAGTCCTCAAAGAGCAGGACACCTTTCAAAGCCCACACAAGTTGGTGGCA
2383268 -TTTTCCAGTCCTCAAAGAGCAGGACACCTTTCAAAGCCCACACAAGTTGGTGGCA
1 CTTTT-CAGTCCTCAAAGAGCAGGACACCTTTCAAAGCCCACACAAGTTGGTGGCA
2383323 -TTTTCCAGTCCTCAAAGAGCAGGACACCTCTT-AAAGCCCACACAAGTTGGTGGCA
1 CTTTT-CAGTCCTCAAAGAGCAGGACACCT-TTCAAAGCCCACACAAGTTGGTGGCA
*
2383378 CCTTTCAGTCCTCAAAGAGCAGGACACCTTTCAAAGCCCACACAAGTTGGTGGCA
1 CTTTTCAGTCCTCAAAGAGCAGGACACCTTTCAAAGCCCACACAAGTTGGTGGCA
*
2383433 -TTGTCCAGTCCTCAAAGAGCAGGACACCTCTT-AAAGCCCACACAAGTTGGTGGCA
1 CTT-TTCAGTCCTCAAAGAGCAGGACACCT-TTCAAAGCCCACACAAGTTGGTGGCA
* *
2383488 CCTTTCAGTCCCCAAAGAGCAGGACACCTCTT-AAAGCCCACACAAGTTGGTGGCA
1 CTTTTCAGTCCTCAAAGAGCAGGACACCT-TTCAAAGCCCACACAAGTTGGTGGCA
*
2383543 CCTTTCAGTCCTCAAAGAGCAGGACACCTTTCAAAGCCCACACAAGTTGGTGGCA
1 CTTTTCAGTCCTCAAAGAGCAGGACACCTTTCAAAGCCCACACAAGTTGGTGGCA
*
2383598 -TTTTCCAGTCCTCAAAGAACAGGACACCTTTCAAAGCCCACACAAGTTGGTGGCA
1 CTTTT-CAGTCCTCAAAGAGCAGGACACCTTTCAAAGCCCACACAAGTTGGTGGCA
2383653 -TTTTCCAGTCCTCAAAGAGCAGGACACCTCTT-AAAGCCCACACAAGTTGGTGGCA
1 CTTTT-CAGTCCTCAAAGAGCAGGACACCT-TTCAAAGCCCACACAAGTTGGTGGCA
* * * * *
2383708 CCTTTCATTCCCCAAAGAGCAGGACACTTTTCAAAGCCCACACAAGTGGGTGGCA
1 CTTTTCAGTCCTCAAAGAGCAGGACACCTTTCAAAGCCCACACAAGTTGGTGGCA
* * *
2383763 CCTTTCAGTCCTCAAAGAGCAGGACGCCTTTCAAAGCCCACACGAGTTGGTGGCA
1 CTTTTCAGTCCTCAAAGAGCAGGACACCTTTCAAAGCCCACACAAGTTGGTGGCA
* * *
2383818 CTTTTTACTCCTCAATGAGCAGGA
1 CTTTTCAGTCCTCAAAGAGCAGGA
2383842 TACAACTTAT
Statistics
Matches: 588, Mismatches: 29, Indels: 24
0.92 0.05 0.04
Matches are distributed among these distances:
54 14 0.02
55 561 0.95
56 13 0.02
ACGTcount: A:0.29, C:0.29, G:0.20, T:0.21
Consensus pattern (55 bp):
CTTTTCAGTCCTCAAAGAGCAGGACACCTTTCAAAGCCCACACAAGTTGGTGGCA
Found at i:2384443 original size:1 final size:1
Alignment explanation
Indices: 2384437--2384489 Score: 79
Period size: 1 Copynumber: 53.0 Consensus size: 1
2384427 AAAGTGTTTG
***
2384437 AAAAAAAAAAAATTGAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA
1 AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA
2384490 TTTAAATGTA
Statistics
Matches: 49, Mismatches: 3, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
1 49 1.00
ACGTcount: A:0.94, C:0.00, G:0.02, T:0.04
Consensus pattern (1 bp):
A
Found at i:2384518 original size:21 final size:21
Alignment explanation
Indices: 2384494--2384550 Score: 105
Period size: 21 Copynumber: 2.7 Consensus size: 21
2384484 AAAAAATTTA
2384494 AATGTATCGATACATTTGTAG
1 AATGTATCGATACATTTGTAG
*
2384515 AATGTATCGATACATTTGTGG
1 AATGTATCGATACATTTGTAG
2384536 AATGTATCGATACAT
1 AATGTATCGATACAT
2384551 CCTACAAATG
Statistics
Matches: 35, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
21 35 1.00
ACGTcount: A:0.33, C:0.11, G:0.19, T:0.37
Consensus pattern (21 bp):
AATGTATCGATACATTTGTAG
Found at i:2384630 original size:19 final size:19
Alignment explanation
Indices: 2384606--2384673 Score: 85
Period size: 19 Copynumber: 3.9 Consensus size: 19
2384596 AATTCAACAA
2384606 TTTGTATCGATACATAAGT
1 TTTGTATCGATACATAAGT
2384625 TTTGTATCGATAC--AA--
1 TTTGTATCGATACATAAGT
2384640 --TGTATCGATACATAAGT
1 TTTGTATCGATACATAAGT
*
2384657 ATTGTATCGATACATAA
1 TTTGTATCGATACATAA
2384674 TTAGCTACTG
Statistics
Matches: 43, Mismatches: 0, Indels: 12
0.78 0.00 0.22
Matches are distributed among these distances:
13 11 0.26
15 2 0.05
17 2 0.05
19 28 0.65
ACGTcount: A:0.35, C:0.12, G:0.15, T:0.38
Consensus pattern (19 bp):
TTTGTATCGATACATAAGT
Found at i:2384645 original size:13 final size:13
Alignment explanation
Indices: 2384627--2384651 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
2384617 ACATAAGTTT
2384627 TGTATCGATACAA
1 TGTATCGATACAA
2384640 TGTATCGATACA
1 TGTATCGATACA
2384652 TAAGTATTGT
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:0.36, C:0.16, G:0.16, T:0.32
Consensus pattern (13 bp):
TGTATCGATACAA
Found at i:2384649 original size:32 final size:32
Alignment explanation
Indices: 2384608--2384670 Score: 117
Period size: 32 Copynumber: 2.0 Consensus size: 32
2384598 TTCAACAATT
*
2384608 TGTATCGATACATAAGTTTTGTATCGATACAA
1 TGTATCGATACATAAGTATTGTATCGATACAA
2384640 TGTATCGATACATAAGTATTGTATCGATACA
1 TGTATCGATACATAAGTATTGTATCGATACA
2384671 TAATTAGCTA
Statistics
Matches: 30, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
32 30 1.00
ACGTcount: A:0.35, C:0.13, G:0.16, T:0.37
Consensus pattern (32 bp):
TGTATCGATACATAAGTATTGTATCGATACAA
Found at i:2384731 original size:13 final size:13
Alignment explanation
Indices: 2384713--2384738 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
2384703 CATTTTTCTG
2384713 TGTATCGATACAT
1 TGTATCGATACAT
2384726 TGTATCGATACAT
1 TGTATCGATACAT
2384739 GGATCTTTGT
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:0.31, C:0.15, G:0.15, T:0.38
Consensus pattern (13 bp):
TGTATCGATACAT
Found at i:2384735 original size:33 final size:33
Alignment explanation
Indices: 2384693--2384759 Score: 98
Period size: 33 Copynumber: 2.0 Consensus size: 33
2384683 GCCAAGGAAA
***
2384693 TGTATCGATACATTTTTCTGTGTATCGATACAT
1 TGTATCGATACATGGATCTGTGTATCGATACAT
*
2384726 TGTATCGATACATGGATCTTTGTATCGATACAT
1 TGTATCGATACATGGATCTGTGTATCGATACAT
2384759 T
1 T
2384760 TGGAAATTTT
Statistics
Matches: 30, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
33 30 1.00
ACGTcount: A:0.25, C:0.15, G:0.16, T:0.43
Consensus pattern (33 bp):
TGTATCGATACATGGATCTGTGTATCGATACAT
Found at i:2387219 original size:28 final size:28
Alignment explanation
Indices: 2387154--2387257 Score: 158
Period size: 28 Copynumber: 3.8 Consensus size: 28
2387144 TTTCTTCACA
* *
2387154 ATCGGGGACACTCCAACCCCGTTA-ATC
1 ATCGGGGATACTCCAACCCCGTTATTTC
2387181 ATCGGGGATACTCCAACCCCGTTATTTC
1 ATCGGGGATACTCCAACCCCGTTATTTC
2387209 ATCGGGGATACTCCAACCCCGTTATTTC
1 ATCGGGGATACTCCAACCCCGTTATTTC
*
2387237 -TGAGGGGATACTCCAACCCCG
1 AT-CGGGGATACTCCAACCCCG
2387258 ACTTTATTTT
Statistics
Matches: 72, Mismatches: 3, Indels: 3
0.92 0.04 0.04
Matches are distributed among these distances:
27 24 0.33
28 48 0.67
ACGTcount: A:0.23, C:0.34, G:0.20, T:0.23
Consensus pattern (28 bp):
ATCGGGGATACTCCAACCCCGTTATTTC
Found at i:2387308 original size:51 final size:51
Alignment explanation
Indices: 2387240--2387410 Score: 198
Period size: 51 Copynumber: 3.3 Consensus size: 51
2387230 TTATTTCTGA
* * *
2387240 GGGGATACTCCAACCCCGACTTTATTTTCAAAATATCGATTTTTCATAATC
1 GGGGATACTCCAACCCCGATTTTATTTTCAAAATACCAATTTTTCATAATC
* * * * *
2387291 GGGGATACTCCAACCCCGGTTTTATTTTCACAACACCAATTTCTCCTTTAATC
1 GGGGATACTCCAACCCCGATTTTATTTTCAAAATACCAATTT-TTC-ATAATC
** * *
2387344 GGGGATACTCCAATTCCGATTTTATTTCCAAAAATACCAATTTTTCACAATC
1 GGGGATACTCCAACCCCGATTTTATTTTC-AAAATACCAATTTTTCATAATC
*
2387396 GAGGATACTCCAACC
1 GGGGATACTCCAACC
2387411 TCGTTATTTC
Statistics
Matches: 97, Mismatches: 20, Indels: 5
0.80 0.16 0.04
Matches are distributed among these distances:
51 36 0.37
52 18 0.19
53 32 0.33
54 11 0.11
ACGTcount: A:0.29, C:0.26, G:0.12, T:0.33
Consensus pattern (51 bp):
GGGGATACTCCAACCCCGATTTTATTTTCAAAATACCAATTTTTCATAATC
Found at i:2387429 original size:28 final size:28
Alignment explanation
Indices: 2387393--2387474 Score: 96
Period size: 28 Copynumber: 2.9 Consensus size: 28
2387383 ATTTTTCACA
*
2387393 ATCGAGGATACTCCAACCTCGTTATTTC
1 ATCGGGGATACTCCAACCTCGTTATTTC
* *
2387421 ATCGGGGATACTCCAACCCCGTTACTTC
1 ATCGGGGATACTCCAACCTCGTTATTTC
*
2387449 --CGAGGGAACACTCCAACCTCGTTATT
1 ATCG-GGG-ATACTCCAACCTCGTTATT
2387475 ATCTCCAAAA
Statistics
Matches: 46, Mismatches: 6, Indels: 4
0.82 0.11 0.07
Matches are distributed among these distances:
26 2 0.04
27 3 0.07
28 41 0.89
ACGTcount: A:0.24, C:0.32, G:0.17, T:0.27
Consensus pattern (28 bp):
ATCGGGGATACTCCAACCTCGTTATTTC
Found at i:2388512 original size:13 final size:13
Alignment explanation
Indices: 2388494--2388518 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
2388484 ATCACTTAAA
2388494 TGTATCGATACAT
1 TGTATCGATACAT
2388507 TGTATCGATACA
1 TGTATCGATACA
2388519 CTGATCTTTG
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:2391911 original size:2 final size:2
Alignment explanation
Indices: 2391904--2391930 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
2391894 GTGCTTTAGT
2391904 TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA T
2391931 GTGTGTGTAT
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 25 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:2392245 original size:22 final size:23
Alignment explanation
Indices: 2392218--2392280 Score: 67
Period size: 22 Copynumber: 2.8 Consensus size: 23
2392208 CGTTTACTTA
2392218 TTTATATTATATTCATATTATT-
1 TTTATATTATATTCATATTATTC
* *
2392240 TTTATACTATATT-TTAATTATTC
1 TTTATATTATATTCAT-ATTATTC
* *
2392263 TCTATGTTATATTCATAT
1 TTTATATTATATTCATAT
2392281 AGTATTTCAC
Statistics
Matches: 32, Mismatches: 6, Indels: 5
0.74 0.14 0.12
Matches are distributed among these distances:
21 1 0.03
22 18 0.56
23 12 0.38
24 1 0.03
ACGTcount: A:0.30, C:0.08, G:0.02, T:0.60
Consensus pattern (23 bp):
TTTATATTATATTCATATTATTC
Found at i:2392450 original size:59 final size:59
Alignment explanation
Indices: 2392363--2392483 Score: 140
Period size: 59 Copynumber: 2.1 Consensus size: 59
2392353 GTCATGTTCG
* *
2392363 TATCGTATCTCAATTCATGATATATTTTACATAATTTATCA-TAATAGTTTAA-TTTAAAA
1 TATCATATATCAATTCATGATATATTTTA-ATAATTTATCATTAATA-TTTAATTTTAAAA
* * * *
2392422 TATCATATATCAATTCATGACT-TTTTTTAATAATTTGTTATTATTATTTAATTTTAAAA
1 TATCATATATCAATTCATGA-TATATTTTAATAATTTATCATTAATATTTAATTTTAAAA
2392481 TAT
1 TAT
2392484 TATGTCTTTT
Statistics
Matches: 53, Mismatches: 6, Indels: 6
0.82 0.09 0.09
Matches are distributed among these distances:
58 14 0.26
59 38 0.72
60 1 0.02
ACGTcount: A:0.37, C:0.08, G:0.04, T:0.50
Consensus pattern (59 bp):
TATCATATATCAATTCATGATATATTTTAATAATTTATCATTAATATTTAATTTTAAAA
Found at i:2392611 original size:15 final size:15
Alignment explanation
Indices: 2392591--2392641 Score: 57
Period size: 17 Copynumber: 3.1 Consensus size: 15
2392581 CATATTCGTG
2392591 TATTTTTTATATTTA
1 TATTTTTTATATTTA
2392606 TATTTTTTTATCATATTA
1 TA-TTTTTTAT-AT-TTA
2392624 TATTTTAATTATATTTA
1 TATTTT--TTATATTTA
2392641 T
1 T
2392642 GTCATATCTT
Statistics
Matches: 31, Mismatches: 0, Indels: 8
0.79 0.00 0.21
Matches are distributed among these distances:
15 2 0.06
16 8 0.26
17 10 0.32
18 7 0.23
19 4 0.13
ACGTcount: A:0.29, C:0.02, G:0.00, T:0.69
Consensus pattern (15 bp):
TATTTTTTATATTTA
Found at i:2392624 original size:18 final size:16
Alignment explanation
Indices: 2392593--2392641 Score: 62
Period size: 18 Copynumber: 2.9 Consensus size: 16
2392583 TATTCGTGTA
2392593 TTTTTTATATTTATAT
1 TTTTTTATATTTATAT
2392609 TTTTTTATCATATTATAT
1 TTTTTTAT-AT-TTATAT
*
2392627 TTTAATTATATTTAT
1 TTT-TTTATATTTAT
2392642 GTCATATCTT
Statistics
Matches: 29, Mismatches: 1, Indels: 5
0.83 0.03 0.14
Matches are distributed among these distances:
16 8 0.28
17 6 0.21
18 11 0.38
19 4 0.14
ACGTcount: A:0.29, C:0.02, G:0.00, T:0.69
Consensus pattern (16 bp):
TTTTTTATATTTATAT
Done.