Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold57
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: 4071704
ACGTcount: A:0.34, C:0.15, G:0.15, T:0.34
Warning! 82236 characters in sequence are not A, C, G, or T
File 9 of 27
Found at i:1041386 original size:18 final size:18
Alignment explanation
Indices: 1041331--1041386 Score: 50
Period size: 18 Copynumber: 3.2 Consensus size: 18
1041321 TGTATTTATA
1041331 TTATATTTATAT--A-TT
1 TTATATTTATATAAATTT
1041346 TTATAATATT-TA-AAATATT
1 TTAT-AT-TTATATAAAT-TT
1041365 TTATATTTATATAAATTT
1 TTATATTTATATAAATTT
1041383 TTAT
1 TTAT
1041387 GATTATATTA
Statistics
Matches: 33, Mismatches: 0, Indels: 13
0.72 0.00 0.28
Matches are distributed among these distances:
15 4 0.12
16 4 0.12
17 5 0.15
18 10 0.30
19 10 0.30
ACGTcount: A:0.39, C:0.00, G:0.00, T:0.61
Consensus pattern (18 bp):
TTATATTTATATAAATTT
Found at i:1041394 original size:18 final size:19
Alignment explanation
Indices: 1041325--1041386 Score: 58
Period size: 19 Copynumber: 3.3 Consensus size: 19
1041315 TATTTATGTA
* *
1041325 TTTATATTATATTTATATAT
1 TTTATATT-TATATAAATAT
1041345 TTTATAATATT-TA-AAATAT
1 TTTAT-AT-TTATATAAATAT
1041364 TTTATATTTATATAAAT-T
1 TTTATATTTATATAAATAT
1041382 TTTAT
1 TTTAT
1041387 GATTATATTA
Statistics
Matches: 36, Mismatches: 2, Indels: 10
0.75 0.04 0.21
Matches are distributed among these distances:
17 2 0.06
18 10 0.28
19 14 0.39
20 6 0.17
21 3 0.08
22 1 0.03
ACGTcount: A:0.39, C:0.00, G:0.00, T:0.61
Consensus pattern (19 bp):
TTTATATTTATATAAATAT
Found at i:1041861 original size:13 final size:13
Alignment explanation
Indices: 1041831--1041863 Score: 50
Period size: 13 Copynumber: 2.5 Consensus size: 13
1041821 AAAAAAATTA
1041831 AAATTAGATCTATT
1 AAATTA-ATCTATT
1041845 -AATTAATCTATT
1 AAATTAATCTATT
1041857 AAATTAA
1 AAATTAA
1041864 AAATAGATAA
Statistics
Matches: 18, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
12 7 0.39
13 11 0.61
ACGTcount: A:0.48, C:0.06, G:0.03, T:0.42
Consensus pattern (13 bp):
AAATTAATCTATT
Found at i:1041970 original size:2 final size:2
Alignment explanation
Indices: 1041963--1042016 Score: 108
Period size: 2 Copynumber: 27.0 Consensus size: 2
1041953 TTTATATCAA
1041963 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1042005 AT AT AT AT AT AT
1 AT AT AT AT AT AT
1042017 TTCACGAAGT
Statistics
Matches: 52, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 52 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:1042231 original size:24 final size:22
Alignment explanation
Indices: 1042207--1042248 Score: 66
Period size: 22 Copynumber: 1.9 Consensus size: 22
1042197 TATTGAATAA
1042207 AAAATTACAATTTTTATAATCT
1 AAAATTACAATTTTTATAATCT
* *
1042229 AAAGTTACAATTTTTTTAAT
1 AAAATTACAATTTTTATAAT
1042249 TGGATATATC
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
22 18 1.00
ACGTcount: A:0.43, C:0.07, G:0.02, T:0.48
Consensus pattern (22 bp):
AAAATTACAATTTTTATAATCT
Found at i:1044248 original size:15 final size:16
Alignment explanation
Indices: 1044228--1044267 Score: 55
Period size: 15 Copynumber: 2.6 Consensus size: 16
1044218 AGATATTTGA
*
1044228 ATTTAATTTTAAATT-
1 ATTTAAATTTAAATTG
*
1044243 ATTTAAATTTAATTTG
1 ATTTAAATTTAAATTG
1044259 ATTTAAATT
1 ATTTAAATT
1044268 ATTGAGTAAG
Statistics
Matches: 22, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
15 13 0.59
16 9 0.41
ACGTcount: A:0.40, C:0.00, G:0.03, T:0.57
Consensus pattern (16 bp):
ATTTAAATTTAAATTG
Found at i:1045673 original size:16 final size:16
Alignment explanation
Indices: 1045652--1045690 Score: 60
Period size: 16 Copynumber: 2.4 Consensus size: 16
1045642 AAAATATATA
*
1045652 AAATATTTATTTTTTT
1 AAATATTTATATTTTT
1045668 AAATATTTATATTTTT
1 AAATATTTATATTTTT
*
1045684 AATTATT
1 AAATATT
1045691 AAATAATAAT
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
16 21 1.00
ACGTcount: A:0.36, C:0.00, G:0.00, T:0.64
Consensus pattern (16 bp):
AAATATTTATATTTTT
Found at i:1045723 original size:19 final size:19
Alignment explanation
Indices: 1045701--1045743 Score: 52
Period size: 19 Copynumber: 2.3 Consensus size: 19
1045691 AAATAATAAT
1045701 TTAAA-TCAAATTAAATTAA
1 TTAAACTCAAATTAAATT-A
**
1045720 TTAAACTCATTTTAAATTA
1 TTAAACTCAAATTAAATTA
1045739 TTAAA
1 TTAAA
1045744 ATTCACGCCC
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
19 11 0.52
20 10 0.48
ACGTcount: A:0.51, C:0.07, G:0.00, T:0.42
Consensus pattern (19 bp):
TTAAACTCAAATTAAATTA
Found at i:1045815 original size:20 final size:20
Alignment explanation
Indices: 1045785--1045836 Score: 61
Period size: 20 Copynumber: 2.5 Consensus size: 20
1045775 TAGAATAATT
1045785 AAAAATAAATTT-AATCGATAA
1 AAAAAT-AATTTAAATCGAT-A
**
1045806 AAAAATAATTTAAATTTATA
1 AAAAATAATTTAAATCGATA
1045826 AAAAATAATTT
1 AAAAATAATTT
1045837 TTTATTAAAA
Statistics
Matches: 28, Mismatches: 2, Indels: 3
0.85 0.06 0.09
Matches are distributed among these distances:
20 17 0.61
21 11 0.39
ACGTcount: A:0.62, C:0.02, G:0.02, T:0.35
Consensus pattern (20 bp):
AAAAATAATTTAAATCGATA
Found at i:1045846 original size:17 final size:18
Alignment explanation
Indices: 1045805--1045846 Score: 50
Period size: 20 Copynumber: 2.2 Consensus size: 18
1045795 TTAATCGATA
1045805 AAAAAATAATTTAAATTTAT
1 AAAAAATAATTT--ATTTAT
1045825 AAAAAATAATTT-TTTATT
1 AAAAAATAATTTATTTA-T
1045843 AAAA
1 AAAA
1045847 TGACATTAGA
Statistics
Matches: 21, Mismatches: 0, Indels: 4
0.84 0.00 0.16
Matches are distributed among these distances:
17 4 0.19
18 5 0.24
20 12 0.57
ACGTcount: A:0.60, C:0.00, G:0.00, T:0.40
Consensus pattern (18 bp):
AAAAAATAATTTATTTAT
Found at i:1046427 original size:10 final size:9
Alignment explanation
Indices: 1046414--1046501 Score: 51
Period size: 10 Copynumber: 9.8 Consensus size: 9
1046404 TAGATATTTG
1046414 TATATTATTA
1 TATATT-TTA
1046424 TATATTTATA
1 TATATTT-TA
*
1046434 TAAATTTTA
1 TATATTTTA
*
1046443 -ATATATTA
1 TATATTTTA
*
1046451 -ATAATTTA
1 TATATTTTA
*
1046459 -AT-TTATA
1 TATATTTTA
*
1046466 TAAATTTT-
1 TATATTTTA
1046474 TATATATTTA
1 TATAT-TTTA
1046484 TATATTTATA
1 TATATTT-TA
1046494 TTATATTT
1 -TATATTT
1046502 AATTTTTTTA
Statistics
Matches: 61, Mismatches: 10, Indels: 13
0.73 0.12 0.15
Matches are distributed among these distances:
7 3 0.05
8 19 0.31
9 11 0.18
10 21 0.34
11 7 0.11
ACGTcount: A:0.41, C:0.00, G:0.00, T:0.59
Consensus pattern (9 bp):
TATATTTTA
Found at i:1046432 original size:8 final size:8
Alignment explanation
Indices: 1046407--1046494 Score: 52
Period size: 8 Copynumber: 10.2 Consensus size: 8
1046397 GCTCCTGTAG
*
1046407 ATATTTGT
1 ATATTTAT
1046415 ATATTATTAT
1 ATA-T-TTAT
1046425 ATATTTAT
1 ATATTTAT
1046433 ATAAATTTTAAT
1 AT--A-TTT-AT
*
1046445 ATATTAAT
1 ATATTTAT
1046453 A-ATTTAAT
1 ATATTT-AT
* * *
1046461 TTATATAA
1 ATATTTAT
*
1046469 ATTTTTAT
1 ATATTTAT
1046477 ATATTTAT
1 ATATTTAT
1046485 ATATTTAT
1 ATATTTAT
1046493 AT
1 AT
1046495 TATATTTAAT
Statistics
Matches: 61, Mismatches: 11, Indels: 16
0.69 0.12 0.18
Matches are distributed among these distances:
7 3 0.05
8 36 0.59
9 7 0.11
10 8 0.13
11 3 0.05
12 4 0.07
ACGTcount: A:0.41, C:0.00, G:0.01, T:0.58
Consensus pattern (8 bp):
ATATTTAT
Found at i:1046448 original size:20 final size:19
Alignment explanation
Indices: 1046421--1046487 Score: 67
Period size: 20 Copynumber: 3.8 Consensus size: 19
1046411 TTGTATATTA
1046421 TTATATATTTATATAAATT
1 TTATATATTTATATAAATT
1046440 TTA-ATATATTA-AT-AA--
1 TTATATAT-TTATATAAATT
1046455 TT-TA-ATTTATATAAATTT
1 TTATATATTTATATAAA-TT
1046473 TTATATATTTATATA
1 TTATATATTTATATA
1046488 TTTATATTAT
Statistics
Matches: 39, Mismatches: 0, Indels: 17
0.70 0.00 0.30
Matches are distributed among these distances:
13 3 0.08
14 4 0.10
15 5 0.13
17 2 0.05
18 8 0.21
19 8 0.21
20 9 0.23
ACGTcount: A:0.43, C:0.00, G:0.00, T:0.57
Consensus pattern (19 bp):
TTATATATTTATATAAATT
Found at i:1046466 original size:32 final size:32
Alignment explanation
Indices: 1046414--1046499 Score: 106
Period size: 32 Copynumber: 2.7 Consensus size: 32
1046404 TAGATATTTG
*
1046414 TATATT-AT-TATATATTTATATAAATTTTAA
1 TATATTAATATATTTATTTATATAAATTTTAA
*
1046444 TATATTAATA-ATTTAATTTATATAAATTTTTA
1 TATATTAATATATTT-ATTTATATAAATTTTAA
*
1046476 TATATTTATATATTTATATTATAT
1 TATATTAATATATTTAT-TTATAT
1046500 TTAATTTTTT
Statistics
Matches: 48, Mismatches: 3, Indels: 7
0.83 0.05 0.12
Matches are distributed among these distances:
30 6 0.12
31 5 0.10
32 27 0.56
33 10 0.21
ACGTcount: A:0.42, C:0.00, G:0.00, T:0.58
Consensus pattern (32 bp):
TATATTAATATATTTATTTATATAAATTTTAA
Found at i:1046490 original size:18 final size:18
Alignment explanation
Indices: 1046407--1046511 Score: 69
Period size: 18 Copynumber: 5.9 Consensus size: 18
1046397 GCTCCTGTAG
* *
1046407 ATATTTGTATATTATTAT
1 ATATTTATATATTTTTAT
*
1046425 ATATTTATATAAATTTTA-
1 ATATTTATAT-ATTTTTAT
*
1046443 ATATATTA-ATA-ATTTA-
1 ATAT-TTATATATTTTTAT
*
1046459 AT-TTATATAAATTTTTAT
1 ATATT-TATATATTTTTAT
*
1046477 ATATTTATATATTTATATT
1 ATATTTATATATTTTTA-T
*
1046496 ATATTTA-ATTTTTTTA
1 ATATTTATATATTTTTA
1046512 ATTATATTAT
Statistics
Matches: 69, Mismatches: 10, Indels: 16
0.73 0.11 0.17
Matches are distributed among these distances:
14 1 0.01
15 3 0.04
16 8 0.12
17 5 0.07
18 34 0.49
19 18 0.26
ACGTcount: A:0.39, C:0.00, G:0.01, T:0.60
Consensus pattern (18 bp):
ATATTTATATATTTTTAT
Found at i:1046535 original size:34 final size:34
Alignment explanation
Indices: 1046438--1046538 Score: 93
Period size: 34 Copynumber: 2.9 Consensus size: 34
1046428 TTTATATAAA
*
1046438 TTTTAA-TATATTAATAATTT-AATTTATATAAATTT
1 TTTTAATTATATT-AT-ATTTAAATTTAT-TTAATTT
* *
1046473 TTATATATT-TA-TATATTTATATTATATTTAATTT
1 TTTTA-ATTATATTATATTTAAATT-TATTTAATTT
*
1046507 TTTTAATTATATTATATTTAAAATTATTTAAT
1 TTTTAATTATATTATATTTAAATTTATTTAAT
1046539 ATAATATGAG
Statistics
Matches: 54, Mismatches: 6, Indels: 13
0.74 0.08 0.18
Matches are distributed among these distances:
33 7 0.13
34 25 0.46
35 18 0.33
36 3 0.06
37 1 0.02
ACGTcount: A:0.40, C:0.00, G:0.00, T:0.60
Consensus pattern (34 bp):
TTTTAATTATATTATATTTAAATTTATTTAATTT
Found at i:1046540 original size:17 final size:17
Alignment explanation
Indices: 1046478--1046540 Score: 56
Period size: 17 Copynumber: 3.6 Consensus size: 17
1046468 AATTTTTATA
*
1046478 TATTTATATATTTATATT
1 TATTTA-ATATTTATAAT
* *
1046496 ATATTTAATTTTTTTAAT
1 -TATTTAATATTTATAAT
*
1046514 TATATT-ATATTTAAAAT
1 TAT-TTAATATTTATAAT
1046531 TATTTAATAT
1 TATTTAATAT
1046541 AATATGAGGA
Statistics
Matches: 36, Mismatches: 6, Indels: 6
0.75 0.12 0.12
Matches are distributed among these distances:
16 2 0.06
17 18 0.50
18 10 0.28
19 6 0.17
ACGTcount: A:0.38, C:0.00, G:0.00, T:0.62
Consensus pattern (17 bp):
TATTTAATATTTATAAT
Found at i:1046541 original size:24 final size:24
Alignment explanation
Indices: 1046489--1046538 Score: 73
Period size: 24 Copynumber: 2.0 Consensus size: 24
1046479 ATTTATATAT
* *
1046489 TTATATTATATTTAATTTTTTTAA
1 TTATATTATATTTAAATTATTTAA
1046513 TTATATTATATTTAAAATTATTTAA
1 TTATATTATATTT-AAATTATTTAA
1046538 T
1 T
1046539 ATAATATGAG
Statistics
Matches: 23, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
24 13 0.57
25 10 0.43
ACGTcount: A:0.38, C:0.00, G:0.00, T:0.62
Consensus pattern (24 bp):
TTATATTATATTTAAATTATTTAA
Found at i:1048760 original size:2 final size:2
Alignment explanation
Indices: 1048753--1048796 Score: 88
Period size: 2 Copynumber: 22.0 Consensus size: 2
1048743 AGATTCAATA
1048753 CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT
1 CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT
1048795 CT
1 CT
1048797 ATATATATAT
Statistics
Matches: 42, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 42 1.00
ACGTcount: A:0.00, C:0.50, G:0.00, T:0.50
Consensus pattern (2 bp):
CT
Found at i:1048843 original size:2 final size:2
Alignment explanation
Indices: 1048796--1048831 Score: 72
Period size: 2 Copynumber: 18.0 Consensus size: 2
1048786 TCTCTCTCTC
1048796 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1048832 ACAGATTATA
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 34 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:1049071 original size:12 final size:12
Alignment explanation
Indices: 1049054--1049079 Score: 52
Period size: 12 Copynumber: 2.2 Consensus size: 12
1049044 AAGATTTCTC
1049054 ATATATTTCATT
1 ATATATTTCATT
1049066 ATATATTTCATT
1 ATATATTTCATT
1049078 AT
1 AT
1049080 GTTATAGTTT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 14 1.00
ACGTcount: A:0.35, C:0.08, G:0.00, T:0.58
Consensus pattern (12 bp):
ATATATTTCATT
Found at i:1051469 original size:23 final size:24
Alignment explanation
Indices: 1051425--1051470 Score: 60
Period size: 24 Copynumber: 2.0 Consensus size: 24
1051415 AAATGTCTCT
*
1051425 AATTTATTTTATTATTATAATTTA
1 AATTTAATTTATTATTATAATTTA
1051449 AATTTAATTT-TTATGTA-AATTT
1 AATTTAATTTATTAT-TATAATTT
1051471 TTTAAAATGT
Statistics
Matches: 20, Mismatches: 1, Indels: 3
0.83 0.04 0.12
Matches are distributed among these distances:
23 9 0.45
24 11 0.55
ACGTcount: A:0.37, C:0.00, G:0.02, T:0.61
Consensus pattern (24 bp):
AATTTAATTTATTATTATAATTTA
Found at i:1051663 original size:3 final size:3
Alignment explanation
Indices: 1051657--1051689 Score: 57
Period size: 3 Copynumber: 11.0 Consensus size: 3
1051647 GATAGTATAG
*
1051657 ATT ATT ACT ATT ATT ATT ATT ATT ATT ATT ATT
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT
1051690 TTACCTCAAC
Statistics
Matches: 28, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
3 28 1.00
ACGTcount: A:0.33, C:0.03, G:0.00, T:0.64
Consensus pattern (3 bp):
ATT
Found at i:1052371 original size:4 final size:4
Alignment explanation
Indices: 1052364--1052390 Score: 54
Period size: 4 Copynumber: 6.8 Consensus size: 4
1052354 ATATATACAT
1052364 ATAC ATAC ATAC ATAC ATAC ATAC ATA
1 ATAC ATAC ATAC ATAC ATAC ATAC ATA
1052391 TGAATTTTAC
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 23 1.00
ACGTcount: A:0.52, C:0.22, G:0.00, T:0.26
Consensus pattern (4 bp):
ATAC
Found at i:1055230 original size:14 final size:15
Alignment explanation
Indices: 1055202--1055249 Score: 51
Period size: 15 Copynumber: 3.1 Consensus size: 15
1055192 TTTTAATTGA
1055202 TAAAAAATAAAAATT
1 TAAAAAATAAAAATT
* *
1055217 TAAAAAATATAATTT
1 TAAAAAATAAAAATT
*
1055232 TATAAAATTAAATAATT
1 TA-AAAAATAAA-AATT
1055249 T
1 T
1055250 TAATTTTAAT
Statistics
Matches: 26, Mismatches: 5, Indels: 2
0.79 0.15 0.06
Matches are distributed among these distances:
15 15 0.58
16 7 0.27
17 4 0.15
ACGTcount: A:0.62, C:0.00, G:0.00, T:0.38
Consensus pattern (15 bp):
TAAAAAATAAAAATT
Found at i:1055238 original size:24 final size:24
Alignment explanation
Indices: 1055211--1055257 Score: 60
Period size: 24 Copynumber: 2.0 Consensus size: 24
1055201 ATAAAAAATA
1055211 AAAATTTAAA-AAATATAATTTTAT
1 AAAA-TTAAATAAATATAATTTTAT
* *
1055235 AAAATTAAATAATTTTAATTTTA
1 AAAATTAAATAAATATAATTTTA
1055258 ATTTTAATTA
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
23 5 0.25
24 15 0.75
ACGTcount: A:0.55, C:0.00, G:0.00, T:0.45
Consensus pattern (24 bp):
AAAATTAAATAAATATAATTTTAT
Found at i:1055261 original size:12 final size:12
Alignment explanation
Indices: 1055243--1055272 Score: 51
Period size: 12 Copynumber: 2.5 Consensus size: 12
1055233 ATAAAATTAA
1055243 ATAATTTTAATT
1 ATAATTTTAATT
*
1055255 TTAATTTTAATT
1 ATAATTTTAATT
1055267 ATAATT
1 ATAATT
1055273 GTTTATCATA
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
12 16 1.00
ACGTcount: A:0.40, C:0.00, G:0.00, T:0.60
Consensus pattern (12 bp):
ATAATTTTAATT
Found at i:1057980 original size:17 final size:17
Alignment explanation
Indices: 1057940--1057987 Score: 62
Period size: 17 Copynumber: 2.9 Consensus size: 17
1057930 ATTTTTATAT
*
1057940 TAAATTTAAA-TAAAAA
1 TAAATTTAAATTATAAA
**
1057956 TATTTTTAAATTATAAA
1 TAAATTTAAATTATAAA
1057973 TAAATTTAAATTATA
1 TAAATTTAAATTATA
1057988 TGGATTTAAT
Statistics
Matches: 26, Mismatches: 5, Indels: 1
0.81 0.16 0.03
Matches are distributed among these distances:
16 8 0.31
17 18 0.69
ACGTcount: A:0.56, C:0.00, G:0.00, T:0.44
Consensus pattern (17 bp):
TAAATTTAAATTATAAA
Found at i:1058851 original size:2 final size:2
Alignment explanation
Indices: 1058844--1058874 Score: 62
Period size: 2 Copynumber: 15.5 Consensus size: 2
1058834 AAATGATGAT
1058844 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1058875 TTCATTATCC
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 29 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:1061155 original size:32 final size:32
Alignment explanation
Indices: 1061102--1061193 Score: 98
Period size: 32 Copynumber: 2.9 Consensus size: 32
1061092 TAAAAAAATA
* *
1061102 TAAATA-AAAATAAATCAAATTTAATATATCT
1 TAAATACAAAAAAAATTAAATTTAATATATCT
* *
1061133 TAAATACAAAAAAAATTAAATTTAAAATATTT
1 TAAATACAAAAAAAATTAAATTTAATATATCT
* * *
1061165 TACAT-CTAAAAAAATTATAATTAAATATA
1 TAAATACAAAAAAAATTA-AATTTAATATA
1061194 ATCCAAAAAA
Statistics
Matches: 51, Mismatches: 8, Indels: 3
0.82 0.13 0.05
Matches are distributed among these distances:
31 17 0.33
32 34 0.67
ACGTcount: A:0.60, C:0.05, G:0.00, T:0.35
Consensus pattern (32 bp):
TAAATACAAAAAAAATTAAATTTAATATATCT
Found at i:1063982 original size:20 final size:19
Alignment explanation
Indices: 1063928--1064000 Score: 74
Period size: 20 Copynumber: 3.5 Consensus size: 19
1063918 AATAAACTCA
1063928 TAATTTTTTTAAAAAATCAAT
1 TAATTTTTTTAAAAAA--AAT
1063949 TATTTATCTTTTTTAAAAAAAACT
1 TA---AT-TTTTTTAAAAAAAA-T
*
1063973 TGATTTTTTTAAAAAAAAT
1 TAATTTTTTTAAAAAAAAT
1063992 TAATTTTTT
1 TAATTTTTT
1064001 AAATTGTATA
Statistics
Matches: 45, Mismatches: 2, Indels: 12
0.76 0.03 0.20
Matches are distributed among these distances:
19 9 0.20
20 14 0.31
21 4 0.09
23 2 0.04
24 4 0.09
25 12 0.27
ACGTcount: A:0.42, C:0.04, G:0.01, T:0.52
Consensus pattern (19 bp):
TAATTTTTTTAAAAAAAAT
Found at i:1065443 original size:10 final size:10
Alignment explanation
Indices: 1065428--1065466 Score: 60
Period size: 10 Copynumber: 3.9 Consensus size: 10
1065418 CGAATTTAAT
1065428 ATTTAAATTA
1 ATTTAAATTA
*
1065438 ATTTAATTTA
1 ATTTAAATTA
1065448 ATTTAAATTA
1 ATTTAAATTA
*
1065458 TTTTAAATT
1 ATTTAAATT
1065467 TAAATCATAT
Statistics
Matches: 26, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
10 26 1.00
ACGTcount: A:0.44, C:0.00, G:0.00, T:0.56
Consensus pattern (10 bp):
ATTTAAATTA
Found at i:1065448 original size:15 final size:15
Alignment explanation
Indices: 1065428--1065471 Score: 52
Period size: 15 Copynumber: 2.9 Consensus size: 15
1065418 CGAATTTAAT
* *
1065428 ATTTAAATTAATTTA
1 ATTTAATTTAAATTA
1065443 ATTTAATTTAAATTA
1 ATTTAATTTAAATTA
*
1065458 TTTTAAATTTAAAT
1 ATTT-AATTTAAAT
1065472 CATATTGGGT
Statistics
Matches: 25, Mismatches: 3, Indels: 1
0.86 0.10 0.03
Matches are distributed among these distances:
15 16 0.64
16 9 0.36
ACGTcount: A:0.45, C:0.00, G:0.00, T:0.55
Consensus pattern (15 bp):
ATTTAATTTAAATTA
Found at i:1065731 original size:12 final size:13
Alignment explanation
Indices: 1065705--1065754 Score: 57
Period size: 13 Copynumber: 3.8 Consensus size: 13
1065695 TTTTATTTTT
1065705 AATTTAATTATTTA
1 AATTTAA-TATTTA
1065719 AATTTAA-ATTTA
1 AATTTAATATTTA
*
1065731 AAATTAATATTTA
1 AATTTAATATTTA
* *
1065744 TATTTATTATT
1 AATTTAATATT
1065755 AATATAAATT
Statistics
Matches: 31, Mismatches: 4, Indels: 3
0.82 0.11 0.08
Matches are distributed among these distances:
12 11 0.35
13 13 0.42
14 7 0.23
ACGTcount: A:0.44, C:0.00, G:0.00, T:0.56
Consensus pattern (13 bp):
AATTTAATATTTA
Found at i:1065742 original size:19 final size:19
Alignment explanation
Indices: 1065716--1065759 Score: 54
Period size: 19 Copynumber: 2.4 Consensus size: 19
1065706 ATTTAATTAT
1065716 TTAA-ATTTAAATTTAAAA
1 TTAATATTTAAATTTAAAA
* **
1065734 TTAATATTTATATTTATTA
1 TTAATATTTAAATTTAAAA
1065753 TTAATAT
1 TTAATAT
1065760 AAATTATGTG
Statistics
Matches: 22, Mismatches: 3, Indels: 1
0.85 0.12 0.04
Matches are distributed among these distances:
18 4 0.18
19 18 0.82
ACGTcount: A:0.45, C:0.00, G:0.00, T:0.55
Consensus pattern (19 bp):
TTAATATTTAAATTTAAAA
Found at i:1066286 original size:21 final size:22
Alignment explanation
Indices: 1066262--1066310 Score: 59
Period size: 19 Copynumber: 2.3 Consensus size: 22
1066252 AATTTTATTT
1066262 TTATTTAAAATAATTAA-AATA
1 TTATTTAAAATAATTAACAATA
*
1066283 TTA--TAAAATATTTAATCAATA
1 TTATTTAAAATAATTAA-CAATA
1066304 TTATTTA
1 TTATTTA
1066311 TATATTTTTA
Statistics
Matches: 23, Mismatches: 1, Indels: 6
0.77 0.03 0.20
Matches are distributed among these distances:
19 11 0.48
21 10 0.43
23 2 0.09
ACGTcount: A:0.51, C:0.02, G:0.00, T:0.47
Consensus pattern (22 bp):
TTATTTAAAATAATTAACAATA
Found at i:1066291 original size:10 final size:9
Alignment explanation
Indices: 1066263--1066297 Score: 52
Period size: 9 Copynumber: 3.8 Consensus size: 9
1066253 ATTTTATTTT
1066263 TATTTAAAA
1 TATTTAAAA
*
1066272 TAATTAAAA
1 TATTTAAAA
1066281 TATTATAAAA
1 TATT-TAAAA
1066291 TATTTAA
1 TATTTAA
1066298 TCAATATTAT
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
9 14 0.61
10 9 0.39
ACGTcount: A:0.57, C:0.00, G:0.00, T:0.43
Consensus pattern (9 bp):
TATTTAAAA
Found at i:1066546 original size:19 final size:19
Alignment explanation
Indices: 1066522--1066560 Score: 69
Period size: 19 Copynumber: 2.1 Consensus size: 19
1066512 ATATTTTAGC
1066522 TAAAATATTAAAAAAATAT
1 TAAAATATTAAAAAAATAT
*
1066541 TAAAATATTACAAAAATAT
1 TAAAATATTAAAAAAATAT
1066560 T
1 T
1066561 TATTTTTAAT
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
19 19 1.00
ACGTcount: A:0.64, C:0.03, G:0.00, T:0.33
Consensus pattern (19 bp):
TAAAATATTAAAAAAATAT
Found at i:1066606 original size:36 final size:36
Alignment explanation
Indices: 1066566--1066634 Score: 97
Period size: 36 Copynumber: 1.9 Consensus size: 36
1066556 ATATTTATTT
*
1066566 TTAATTTATATTTTAATAATTT-TTTAT-TTTAAATAA
1 TTAATTTATA--TTAAAAATTTATTTATATTTAAATAA
1066602 TTAATTTATATTAAAAATTTATTTATATTTAAA
1 TTAATTTATATTAAAAATTTATTTATATTTAAA
1066635 ATAAAGATTA
Statistics
Matches: 30, Mismatches: 1, Indels: 4
0.86 0.03 0.11
Matches are distributed among these distances:
34 9 0.30
35 5 0.17
36 16 0.53
ACGTcount: A:0.42, C:0.00, G:0.00, T:0.58
Consensus pattern (36 bp):
TTAATTTATATTAAAAATTTATTTATATTTAAATAA
Found at i:1066633 original size:18 final size:18
Alignment explanation
Indices: 1066569--1066635 Score: 77
Period size: 18 Copynumber: 3.8 Consensus size: 18
1066559 TTTATTTTTA
*
1066569 ATTTATATTTTAATAATTT
1 ATTTATA-TTTAAAAATTT
*
1066588 -TTTAT-TTTAAATAATTA
1 ATTTATATTTAAA-AATTT
1066605 ATTTATA-TTAAAAATTT
1 ATTTATATTTAAAAATTT
1066622 ATTTATATTTAAAA
1 ATTTATATTTAAAA
1066636 TAAAGATTAG
Statistics
Matches: 41, Mismatches: 3, Indels: 9
0.77 0.06 0.17
Matches are distributed among these distances:
16 5 0.12
17 15 0.37
18 21 0.51
ACGTcount: A:0.43, C:0.00, G:0.00, T:0.57
Consensus pattern (18 bp):
ATTTATATTTAAAAATTT
Found at i:1066636 original size:17 final size:18
Alignment explanation
Indices: 1066569--1066633 Score: 73
Period size: 17 Copynumber: 3.7 Consensus size: 18
1066559 TTTATTTTTA
1066569 ATTTATATTTTAATAATTT
1 ATTTATA-TTTAATAATTT
*
1066588 -TTTAT-TTTAAATAATTA
1 ATTTATATTT-AATAATTT
*
1066605 ATTTATA-TTAAAAATTT
1 ATTTATATTTAATAATTT
1066622 ATTTATATTTAA
1 ATTTATATTTAA
1066634 AATAAAGATT
Statistics
Matches: 39, Mismatches: 3, Indels: 9
0.76 0.06 0.18
Matches are distributed among these distances:
16 3 0.08
17 20 0.51
18 16 0.41
ACGTcount: A:0.42, C:0.00, G:0.00, T:0.58
Consensus pattern (18 bp):
ATTTATATTTAATAATTT
Found at i:1072386 original size:49 final size:49
Alignment explanation
Indices: 1072329--1072427 Score: 180
Period size: 49 Copynumber: 2.0 Consensus size: 49
1072319 CTTTCTTTCG
1072329 GGACATAACCTTAGTGGAATATTACAAAAAAGGTTGATTACGGTATAGA
1 GGACATAACCTTAGTGGAATATTACAAAAAAGGTTGATTACGGTATAGA
* *
1072378 GGACATAACCTTTGTGGAATATTCCAAAAAAGGTTGATTACGGTATAGA
1 GGACATAACCTTAGTGGAATATTACAAAAAAGGTTGATTACGGTATAGA
1072427 G
1 G
1072428 TATTTCCTCA
Statistics
Matches: 48, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
49 48 1.00
ACGTcount: A:0.38, C:0.11, G:0.23, T:0.27
Consensus pattern (49 bp):
GGACATAACCTTAGTGGAATATTACAAAAAAGGTTGATTACGGTATAGA
Found at i:1073710 original size:2 final size:2
Alignment explanation
Indices: 1073703--1073729 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
1073693 GTGCATCTAC
1073703 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
1073730 GTATTTGATG
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:1073837 original size:21 final size:19
Alignment explanation
Indices: 1073796--1073838 Score: 50
Period size: 21 Copynumber: 2.2 Consensus size: 19
1073786 GTCGATGTCT
**
1073796 TATTTTATTTTTTAATTAA
1 TATTTTATTTTTTAAAAAA
1073815 TATTTTATTATATTTAAAAAA
1 TATTTTATT-T-TTTAAAAAA
1073836 TAT
1 TAT
1073839 ATATCATTTA
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
19 9 0.45
20 1 0.05
21 10 0.50
ACGTcount: A:0.40, C:0.00, G:0.00, T:0.60
Consensus pattern (19 bp):
TATTTTATTTTTTAAAAAA
Found at i:1075324 original size:21 final size:20
Alignment explanation
Indices: 1075298--1075339 Score: 66
Period size: 21 Copynumber: 2.0 Consensus size: 20
1075288 AAAAATTAAC
1075298 TTTTAAATAAAAATTTTATTA
1 TTTTAAATAAAAATTTT-TTA
*
1075319 TTTTAAATAAATATTTTTTA
1 TTTTAAATAAAAATTTTTTA
1075339 T
1 T
1075340 ACATTTTATT
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
20 4 0.20
21 16 0.80
ACGTcount: A:0.43, C:0.00, G:0.00, T:0.57
Consensus pattern (20 bp):
TTTTAAATAAAAATTTTTTA
Found at i:1075699 original size:18 final size:17
Alignment explanation
Indices: 1075655--1075701 Score: 51
Period size: 18 Copynumber: 2.7 Consensus size: 17
1075645 TTAATATAAA
* *
1075655 TATATTTTACTAATTTT
1 TATATTTTATTAATATT
1075672 TAT-TTATTATTCAATATT
1 TATATT-TTATT-AATATT
1075690 TATATTTTATTA
1 TATATTTTATTA
1075702 TTTACTATAT
Statistics
Matches: 25, Mismatches: 2, Indels: 6
0.76 0.06 0.18
Matches are distributed among these distances:
16 2 0.08
17 8 0.32
18 13 0.52
19 2 0.08
ACGTcount: A:0.32, C:0.04, G:0.00, T:0.64
Consensus pattern (17 bp):
TATATTTTATTAATATT
Found at i:1075714 original size:21 final size:21
Alignment explanation
Indices: 1075673--1075719 Score: 58
Period size: 21 Copynumber: 2.2 Consensus size: 21
1075663 ACTAATTTTT
*
1075673 ATTTATTATTCAATATTTATA
1 ATTTATTATTCAATATATATA
* * *
1075694 TTTTATTATTTACTATATATA
1 ATTTATTATTCAATATATATA
1075715 ATTTA
1 ATTTA
1075720 ATTAAATAAT
Statistics
Matches: 21, Mismatches: 5, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
21 21 1.00
ACGTcount: A:0.36, C:0.04, G:0.00, T:0.60
Consensus pattern (21 bp):
ATTTATTATTCAATATATATA
Found at i:1076288 original size:3 final size:3
Alignment explanation
Indices: 1076280--1076319 Score: 80
Period size: 3 Copynumber: 13.3 Consensus size: 3
1076270 TTAAAATTTA
1076280 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT A
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT A
1076320 CTAAGTATTG
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:0.35, C:0.00, G:0.00, T:0.65
Consensus pattern (3 bp):
ATT
Found at i:1076501 original size:13 final size:13
Alignment explanation
Indices: 1076483--1076524 Score: 50
Period size: 13 Copynumber: 3.3 Consensus size: 13
1076473 AAAATTAAAT
*
1076483 ATATTTATATTTA
1 ATATTTATATATA
1076496 ATATTTATATATA
1 ATATTTATATATA
* *
1076509 A-ATTTAAATAAA
1 ATATTTATATATA
1076521 ATAT
1 ATAT
1076525 CATATTATTT
Statistics
Matches: 25, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
12 10 0.40
13 15 0.60
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (13 bp):
ATATTTATATATA
Found at i:1077532 original size:21 final size:22
Alignment explanation
Indices: 1077482--1077533 Score: 54
Period size: 21 Copynumber: 2.4 Consensus size: 22
1077472 GGTCTTAATT
* *
1077482 TGAATTATAATTTAAATATTTAA
1 TGAATTA-AATTTAAATAGTGAA
*
1077505 T-ATTTAAATTTAAA-AGTGAA
1 TGAATTAAATTTAAATAGTGAA
1077525 TGAATTAAA
1 TGAATTAAA
1077534 AATAAAAATA
Statistics
Matches: 24, Mismatches: 4, Indels: 4
0.75 0.12 0.12
Matches are distributed among these distances:
20 5 0.21
21 14 0.58
22 4 0.17
23 1 0.04
ACGTcount: A:0.50, C:0.00, G:0.08, T:0.42
Consensus pattern (22 bp):
TGAATTAAATTTAAATAGTGAA
Found at i:1077596 original size:14 final size:15
Alignment explanation
Indices: 1077574--1077615 Score: 52
Period size: 14 Copynumber: 2.9 Consensus size: 15
1077564 ATTTCATATC
*
1077574 AATATTTAAATATTA
1 AATAATTAAATATTA
1077589 AA-AATTAAATA-TA
1 AATAATTAAATATTA
1077602 AATAATTAATATAT
1 AATAATTAA-ATAT
1077616 GCTCATACTA
Statistics
Matches: 23, Mismatches: 1, Indels: 5
0.79 0.03 0.17
Matches are distributed among these distances:
13 4 0.17
14 14 0.61
15 5 0.22
ACGTcount: A:0.60, C:0.00, G:0.00, T:0.40
Consensus pattern (15 bp):
AATAATTAAATATTA
Found at i:1077710 original size:18 final size:18
Alignment explanation
Indices: 1077673--1077724 Score: 61
Period size: 17 Copynumber: 2.8 Consensus size: 18
1077663 GGTTTGTTTA
*
1077673 AATAATATTTGTAT-TTT
1 AATAATATTTTTATATTT
*
1077690 AATAAAATTTTTATATTT
1 AATAATATTTTTATATTT
1077708 AATCAATTATTTTTATA
1 AAT-AA-TATTTTTATA
1077725 GAGTTTAAAA
Statistics
Matches: 29, Mismatches: 3, Indels: 3
0.83 0.09 0.09
Matches are distributed among these distances:
17 12 0.41
18 6 0.21
19 2 0.07
20 9 0.31
ACGTcount: A:0.40, C:0.02, G:0.02, T:0.56
Consensus pattern (18 bp):
AATAATATTTTTATATTT
Found at i:1078584 original size:30 final size:28
Alignment explanation
Indices: 1078529--1078584 Score: 67
Period size: 30 Copynumber: 1.9 Consensus size: 28
1078519 ATAAAATATT
* *
1078529 ATATATATGTATAAATATATCAAATTAC
1 ATATATATGTATAAAAATATAAAATTAC
*
1078557 ATATATATTTATGCAAAAATATAAAATT
1 ATATATATGTAT--AAAAATATAAAATT
1078585 TTAAAATTAT
Statistics
Matches: 23, Mismatches: 3, Indels: 2
0.82 0.11 0.07
Matches are distributed among these distances:
28 11 0.48
30 12 0.52
ACGTcount: A:0.52, C:0.05, G:0.04, T:0.39
Consensus pattern (28 bp):
ATATATATGTATAAAAATATAAAATTAC
Found at i:1078668 original size:18 final size:18
Alignment explanation
Indices: 1078617--1078668 Score: 56
Period size: 18 Copynumber: 2.9 Consensus size: 18
1078607 TTTTTTAATC
*
1078617 ATAAATA-AATAAAATAA
1 ATAAATATAATAAATTAA
1078634 ATAAATATAA-AATATTAA
1 ATAAATATAATAA-ATTAA
1078652 A-AATATATAATAAATTA
1 ATAA-ATATAATAAATTA
1078669 TTATTGATTG
Statistics
Matches: 30, Mismatches: 1, Indels: 7
0.79 0.03 0.18
Matches are distributed among these distances:
17 11 0.37
18 17 0.57
19 2 0.07
ACGTcount: A:0.69, C:0.00, G:0.00, T:0.31
Consensus pattern (18 bp):
ATAAATATAATAAATTAA
Found at i:1078766 original size:9 final size:9
Alignment explanation
Indices: 1078716--1078796 Score: 53
Period size: 8 Copynumber: 9.1 Consensus size: 9
1078706 TATTTTATTG
1078716 TAAT-AAAA
1 TAATAAAAA
*
1078724 TTATAAAAA
1 TAATAAAAA
1078733 -AATAAAAA
1 TAATAAAAA
* * *
1078741 TTATTATAAC
1 -TAATAAAAA
1078751 T-ATAAAAA
1 TAATAAAAA
1078759 TAATAAAAA
1 TAATAAAAA
*
1078768 TTAATTAAAA
1 -TAATAAAAA
*
1078778 TAAT-TAAA
1 TAATAAAAA
1078786 TAAATAAAAA
1 T-AATAAAAA
1078796 T
1 T
1078797 TTTTTTAAAA
Statistics
Matches: 55, Mismatches: 11, Indels: 12
0.71 0.14 0.15
Matches are distributed among these distances:
8 19 0.35
9 19 0.35
10 17 0.31
ACGTcount: A:0.68, C:0.01, G:0.00, T:0.31
Consensus pattern (9 bp):
TAATAAAAA
Found at i:1078791 original size:28 final size:26
Alignment explanation
Indices: 1078719--1078797 Score: 81
Period size: 27 Copynumber: 2.9 Consensus size: 26
1078709 TTTATTGTAA
* *
1078719 TAAAATTATAAAAAAATAAAAATTAT
1 TAAAATAATAAATAAATAAAAATTAT
1078745 TATAACTATAA-AAAT-AATAAAAATTAAT
1 TA-AA--ATAATAAATAAATAAAAATT-AT
1078773 TAAAATAATTAAATAAATAAAAATT
1 TAAAATAA-TAAATAAATAAAAATT
1078798 TTTTTAAAAA
Statistics
Matches: 44, Mismatches: 2, Indels: 12
0.76 0.03 0.21
Matches are distributed among these distances:
25 4 0.09
26 2 0.05
27 18 0.41
28 17 0.39
29 3 0.07
ACGTcount: A:0.67, C:0.01, G:0.00, T:0.32
Consensus pattern (26 bp):
TAAAATAATAAATAAATAAAAATTAT
Found at i:1082891 original size:14 final size:14
Alignment explanation
Indices: 1082872--1082902 Score: 53
Period size: 14 Copynumber: 2.2 Consensus size: 14
1082862 TAAATCCTAC
*
1082872 CAAGCGTAATAAAT
1 CAAGCGTAACAAAT
1082886 CAAGCGTAACAAAT
1 CAAGCGTAACAAAT
1082900 CAA
1 CAA
1082903 ACTCCCACAT
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
14 16 1.00
ACGTcount: A:0.52, C:0.19, G:0.13, T:0.16
Consensus pattern (14 bp):
CAAGCGTAACAAAT
Found at i:1084178 original size:15 final size:15
Alignment explanation
Indices: 1084158--1084200 Score: 54
Period size: 16 Copynumber: 2.9 Consensus size: 15
1084148 TTTTATTTAT
1084158 TAATTATTATATTAA
1 TAATTATTATATTAA
1084173 TAATTATTTAATATTAA
1 TAATTA-TT-ATATTAA
1084190 -AATTA-TATATT
1 TAATTATTATATT
1084201 TGATATTTAA
Statistics
Matches: 26, Mismatches: 0, Indels: 6
0.81 0.00 0.19
Matches are distributed among these distances:
13 5 0.19
14 1 0.04
15 6 0.23
16 7 0.27
17 7 0.27
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (15 bp):
TAATTATTATATTAA
Found at i:1085122 original size:23 final size:24
Alignment explanation
Indices: 1085060--1085122 Score: 62
Period size: 24 Copynumber: 2.7 Consensus size: 24
1085050 TTTTAAAAAA
*
1085060 AAATTTTA-ATC-TTTTATTTTAT
1 AAATTTTATATCATTTTAATTTAT
1085082 AAATTTTACTAT-ACTTTTAATTTA-
1 AAATTTTA-TATCA-TTTTAATTTAT
*
1085106 AATTTTTATATCATTTT
1 AAATTTTATATCATTTT
1085123 TTATTTTTAT
Statistics
Matches: 34, Mismatches: 2, Indels: 9
0.76 0.04 0.20
Matches are distributed among these distances:
22 8 0.24
23 7 0.21
24 10 0.29
25 9 0.26
ACGTcount: A:0.33, C:0.06, G:0.00, T:0.60
Consensus pattern (24 bp):
AAATTTTATATCATTTTAATTTAT
Found at i:1087648 original size:13 final size:13
Alignment explanation
Indices: 1087630--1087662 Score: 57
Period size: 13 Copynumber: 2.5 Consensus size: 13
1087620 AAAAGTGCCT
1087630 TTTGTACCTTAGA
1 TTTGTACCTTAGA
1087643 TTTGTACCTTAGA
1 TTTGTACCTTAGA
1087656 TTCTGTA
1 TT-TGTA
1087663 TTTAATTAAT
Statistics
Matches: 19, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
13 15 0.79
14 4 0.21
ACGTcount: A:0.21, C:0.15, G:0.15, T:0.48
Consensus pattern (13 bp):
TTTGTACCTTAGA
Found at i:1091999 original size:19 final size:19
Alignment explanation
Indices: 1091977--1092031 Score: 58
Period size: 20 Copynumber: 2.9 Consensus size: 19
1091967 AAAAATAAAA
1091977 TATAAAATATAAAAATATT
1 TATAAAATATAAAAATATT
* *
1091996 TATATAATAATAAAAAAATT
1 TATAAAAT-ATAAAAATATT
* *
1092016 TA-AATATATGAAAATA
1 TATAAAATATAAAAATA
1092032 ATATATTTAT
Statistics
Matches: 29, Mismatches: 6, Indels: 3
0.76 0.16 0.08
Matches are distributed among these distances:
18 7 0.24
19 10 0.34
20 12 0.41
ACGTcount: A:0.64, C:0.00, G:0.02, T:0.35
Consensus pattern (19 bp):
TATAAAATATAAAAATATT
Found at i:1092000 original size:21 final size:20
Alignment explanation
Indices: 1091976--1092017 Score: 59
Period size: 21 Copynumber: 2.0 Consensus size: 20
1091966 TAAAAATAAA
1091976 ATATAA-AATATAAAAATATTT
1 ATATAATAATA-AAAAA-ATTT
1091997 ATATAATAATAAAAAAATTT
1 ATATAATAATAAAAAAATTT
1092017 A
1 A
1092018 AATATATGAA
Statistics
Matches: 20, Mismatches: 0, Indels: 3
0.87 0.00 0.13
Matches are distributed among these distances:
20 5 0.25
21 11 0.55
22 4 0.20
ACGTcount: A:0.64, C:0.00, G:0.00, T:0.36
Consensus pattern (20 bp):
ATATAATAATAAAAAAATTT
Found at i:1092037 original size:37 final size:36
Alignment explanation
Indices: 1091955--1092037 Score: 87
Period size: 37 Copynumber: 2.2 Consensus size: 36
1091945 GTTAAGTATT
*
1091955 TAATATTATTATAAAAATAAAATATAAAATATAAAAA
1 TAATA-TATAATAAAAATAAAATATAAAATATAAAAA
* * *
1091992 TATTTATATAATAATAAA-AAAATTTAAATATATGAAAA
1 TA-ATATATAATAA-AAATAAAATATAAA-ATATAAAAA
1092030 TAATATAT
1 TAATATAT
1092038 TTATTTTATT
Statistics
Matches: 38, Mismatches: 5, Indels: 6
0.78 0.10 0.12
Matches are distributed among these distances:
37 23 0.61
38 15 0.39
ACGTcount: A:0.63, C:0.00, G:0.01, T:0.36
Consensus pattern (36 bp):
TAATATATAATAAAAATAAAATATAAAATATAAAAA
Found at i:1093633 original size:18 final size:18
Alignment explanation
Indices: 1093610--1093647 Score: 51
Period size: 18 Copynumber: 2.1 Consensus size: 18
1093600 GTTGTGGTAT
1093610 CGCTTTCAG-CTCTTCCGG
1 CGCTTTCAGCCTCTT-CGG
*
1093628 CGCTTTCGGCCTCTTCGG
1 CGCTTTCAGCCTCTTCGG
1093646 CG
1 CG
1093648 ATTAGGCTGA
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
18 13 0.72
19 5 0.28
ACGTcount: A:0.03, C:0.39, G:0.26, T:0.32
Consensus pattern (18 bp):
CGCTTTCAGCCTCTTCGG
Found at i:1093779 original size:8 final size:9
Alignment explanation
Indices: 1093759--1093850 Score: 55
Period size: 9 Copynumber: 10.1 Consensus size: 9
1093749 TATGTCATCG
1093759 ATTAAATTA
1 ATTAAATTA
1093768 ATTAAA-TA
1 ATTAAATTA
** *
1093776 ATTATTTTTT
1 ATTA-AATTA
1093786 ATTAATATTA
1 ATTAA-ATTA
*
1093796 AAT-AATTA
1 ATTAAATTA
1093804 ATTAAATTAA
1 ATTAAATT-A
1093814 ATT-AATTA
1 ATTAAATTA
* *
1093822 ATTTAATAA
1 ATTAAATTA
* *
1093831 ATTTTAATAA
1 A-TTAAATTA
1093841 ATTAAATTA
1 ATTAAATTA
1093850 A
1 A
1093851 ATCTAGTTAA
Statistics
Matches: 65, Mismatches: 11, Indels: 14
0.72 0.12 0.16
Matches are distributed among these distances:
8 16 0.25
9 27 0.42
10 22 0.34
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (9 bp):
ATTAAATTA
Found at i:1093807 original size:18 final size:19
Alignment explanation
Indices: 1093786--1093866 Score: 73
Period size: 19 Copynumber: 4.4 Consensus size: 19
1093776 ATTATTTTTT
1093786 ATTAATATTAAA-TAATTA
1 ATTAATATTAAATTAATTA
1093804 ATTAA-ATTAAATTAATTA
1 ATTAATATTAAATTAATTA
* *
1093822 ATTTAATA--AATTTTAATAA
1 A-TTAATATTAA-ATTAATTA
*
1093841 ATTAA-ATTAAATCTAGTTA
1 ATTAATATTAAAT-TAATTA
1093860 ATTAATA
1 ATTAATA
1093867 GTTATCCTTA
Statistics
Matches: 50, Mismatches: 5, Indels: 14
0.72 0.07 0.20
Matches are distributed among these distances:
17 7 0.14
18 19 0.38
19 22 0.44
20 2 0.04
ACGTcount: A:0.53, C:0.01, G:0.01, T:0.44
Consensus pattern (19 bp):
ATTAATATTAAATTAATTA
Found at i:1093828 original size:23 final size:22
Alignment explanation
Indices: 1093759--1093824 Score: 59
Period size: 22 Copynumber: 3.1 Consensus size: 22
1093749 TATGTCATCG
*
1093759 ATTAAATTAATTAAA-TAATT-
1 ATTAATTTAATTAAATTAATTA
* *
1093779 ATT--TTTTATTAATATTAAATA
1 ATTAATTTAATTAA-ATTAATTA
*
1093800 ATTAATTAAATTAAATTAATTA
1 ATTAATTTAATTAAATTAATTA
1093822 ATT
1 ATT
1093825 TAATAAATTT
Statistics
Matches: 35, Mismatches: 6, Indels: 8
0.71 0.12 0.16
Matches are distributed among these distances:
18 7 0.20
19 1 0.03
20 7 0.20
21 3 0.09
22 10 0.29
23 7 0.20
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (22 bp):
ATTAATTTAATTAAATTAATTA
Found at i:1096925 original size:151 final size:151
Alignment explanation
Indices: 1096647--1096953 Score: 488
Period size: 151 Copynumber: 2.0 Consensus size: 151
1096637 TATGATAATT
1096647 GGTATCAAAACCAAGGTTGGTAGCGATTAAGAATAAAGGCCCCTAGTATGCCCTTTAGTGCTAAC
1 GGTATCAAAACCAAGGTTGGTAGCGATTAAGAATAAAGGCCCCTAGTATGCCCTTTAGTGCTAAC
* * * *
1096712 CGCGATAATACACTGTAATATGCATGTGGGCATGCTAAGTTATTGTTTGTGCTCATAGGCTAATG
66 CGCGATAATACACTGTAATATGCATATAGGCATGCTAAGTTATTGTTTATGCTCATAAGCTAATG
1096777 TGCCTCTTTGTAAGGCATATA
131 TGCCTCTTTGTAAGGCATATA
* * * * * *
1096798 GGTATCAAAACTAAGGTTGGTAGCGGTTGAGAATGAAGGCCCCTAGTATGCCTTTTAGTGCTAAG
1 GGTATCAAAACCAAGGTTGGTAGCGATTAAGAATAAAGGCCCCTAGTATGCCCTTTAGTGCTAAC
* * *
1096863 TGTGATAATACACTGTAATGTGCATATAGGCATGCTAAGTTATTGTTTATGCTCATAAGCTAATG
66 CGCGATAATACACTGTAATATGCATATAGGCATGCTAAGTTATTGTTTATGCTCATAAGCTAATG
*
1096928 TGCCTCTTTGTAAGGCATATT
131 TGCCTCTTTGTAAGGCATATA
1096949 GGTAT
1 GGTAT
1096954 GTTAGGTGCT
Statistics
Matches: 142, Mismatches: 14, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
151 142 1.00
ACGTcount: A:0.28, C:0.16, G:0.24, T:0.32
Consensus pattern (151 bp):
GGTATCAAAACCAAGGTTGGTAGCGATTAAGAATAAAGGCCCCTAGTATGCCCTTTAGTGCTAAC
CGCGATAATACACTGTAATATGCATATAGGCATGCTAAGTTATTGTTTATGCTCATAAGCTAATG
TGCCTCTTTGTAAGGCATATA
Found at i:1097595 original size:388 final size:388
Alignment explanation
Indices: 1096879--1097659 Score: 1427
Period size: 388 Copynumber: 2.0 Consensus size: 388
1096869 AATACACTGT
1096879 AATGTGCATATAGGCATGCTAAGTTATTGTTTATGCTCATAAGCTAATGTGCCTCTTTGTAAGGC
1 AATGTGCATATAGGCATGCTAAGTTATTGTTTATGCTCATAAGCTAATGTGCCTCTTTGTAAGGC
* * *
1096944 ATATTGGTATGTTAGGTGCTAATTGGTGCCTGAGATCGTATTGCTAGTATGTAATGGGTATGTAG
66 ATATAGGTATGCTAGGTGCTAATTGGTGCCTGAGATCGTACTGCTAGTATGTAATGGGTATGTAG
* * *
1097009 ATGATCAATGCTTTGTCATGCTTTATCGATAAAAGAGTGAGTTCTTAGGCCTTAATTTCGTGATT
131 ATGATCAATGCTTTGTCATGCTTTATCGATAAAAAAGTGAGTTCTTAAGCCTTAAATTCGTGATT
*
1097074 ACTAATGTGTATAGAAAGCATGGCACATGAGAGCTAATCATAAGTATTGAGAGAATAACAAGTAA
196 ACTAATGTGTATAGAAAGCATGGCACATGAAAGCTAATCATAAGTATTGAGAGAATAACAAGTAA
1097139 GAGCTAATCATAAAGCACGAGTGAAGTGCTAGAGTTTTGCACCCATAAATAAAGGAGGAAAGCTA
261 GAGCTAATCATAAAGCACGAGTGAAGTGCTAGAGTTTTGCACCCATAAATAAAGGAGGAAAGCTA
1097204 TGTGGAAAATCCGTAGACACCAGTTTAGCTGAGTGTAAAATAATTGTGGGAGAGTTGTAAGAA
326 TGTGGAAAATCCGTAGACACCAGTTTAGCTGAGTGTAAAATAATTGTGGGAGAGTTGTAAGAA
* *
1097267 AATGTGCGTATGGGCATGCTAAGTTATTGTTTATGCTCATAAGCTAATGTGCCTCTTTGTAAGGC
1 AATGTGCATATAGGCATGCTAAGTTATTGTTTATGCTCATAAGCTAATGTGCCTCTTTGTAAGGC
1097332 ATATAGGTATGCTAGGTGCTAATTGGTGCCTGAGATCGTACTGCTAGTATGTAATGGGTATGTAG
66 ATATAGGTATGCTAGGTGCTAATTGGTGCCTGAGATCGTACTGCTAGTATGTAATGGGTATGTAG
1097397 ATGATCAATGCTTTGTCATGCTTTATCGATAAAAAAGTGAGTTCTTAAGCCTTAAATTCGTGATT
131 ATGATCAATGCTTTGTCATGCTTTATCGATAAAAAAGTGAGTTCTTAAGCCTTAAATTCGTGATT
*
1097462 ACTAATGTGTATAGAAAGCATGGCACGTGAAAGCTAATCATAAGTATTGAGAGAATAACAAGTAA
196 ACTAATGTGTATAGAAAGCATGGCACATGAAAGCTAATCATAAGTATTGAGAGAATAACAAGTAA
*
1097527 GAGCTAATCATAAAGCACGAGTGAAGTGCTGGAGTTTTGCACCCATAAATAAAGGAGGAAAGCTA
261 GAGCTAATCATAAAGCACGAGTGAAGTGCTAGAGTTTTGCACCCATAAATAAAGGAGGAAAGCTA
* * * *
1097592 TGTGGATAATCCGTGGACACCTGTTTAGCTTAGTGTAAAATAATTGTGGGAGAGTTGTAAGAA
326 TGTGGAAAATCCGTAGACACCAGTTTAGCTGAGTGTAAAATAATTGTGGGAGAGTTGTAAGAA
1097655 AATGT
1 AATGT
1097660 TCAAAGACAC
Statistics
Matches: 378, Mismatches: 15, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
388 378 1.00
ACGTcount: A:0.32, C:0.12, G:0.25, T:0.31
Consensus pattern (388 bp):
AATGTGCATATAGGCATGCTAAGTTATTGTTTATGCTCATAAGCTAATGTGCCTCTTTGTAAGGC
ATATAGGTATGCTAGGTGCTAATTGGTGCCTGAGATCGTACTGCTAGTATGTAATGGGTATGTAG
ATGATCAATGCTTTGTCATGCTTTATCGATAAAAAAGTGAGTTCTTAAGCCTTAAATTCGTGATT
ACTAATGTGTATAGAAAGCATGGCACATGAAAGCTAATCATAAGTATTGAGAGAATAACAAGTAA
GAGCTAATCATAAAGCACGAGTGAAGTGCTAGAGTTTTGCACCCATAAATAAAGGAGGAAAGCTA
TGTGGAAAATCCGTAGACACCAGTTTAGCTGAGTGTAAAATAATTGTGGGAGAGTTGTAAGAA
Found at i:1102289 original size:71 final size:67
Alignment explanation
Indices: 1102151--1102293 Score: 205
Period size: 71 Copynumber: 2.1 Consensus size: 67
1102141 GACTTGAATT
* * *
1102151 TTATTGTAAACATCCACTTGCATCGTATATGTATCTTTTCTTCATATAAAAGTACTTTTCCTATG
1 TTATTGTAAACATCCACTTGCATCATATATGTATCTTTTCTTCAGATAAAAGGACTTTTCCTATG
1102216 TG
66 TG
* *
1102218 TTATTGTAAACATCCACTTGCATCCCATATGTATGTATCTTTTCTTCAGATCAAGGGACTTTTCC
1 TTATTGTAAACATCCACTTGCAT--CATA--TATGTATCTTTTCTTCAGATAAAAGGACTTTTCC
1102283 TATGTG
62 TATGTG
1102289 TTATT
1 TTATT
1102294 TTTCTAAAGC
Statistics
Matches: 67, Mismatches: 5, Indels: 4
0.88 0.07 0.05
Matches are distributed among these distances:
67 23 0.34
69 3 0.04
71 41 0.61
ACGTcount: A:0.25, C:0.19, G:0.12, T:0.44
Consensus pattern (67 bp):
TTATTGTAAACATCCACTTGCATCATATATGTATCTTTTCTTCAGATAAAAGGACTTTTCCTATG
TG
Found at i:1103505 original size:206 final size:206
Alignment explanation
Indices: 1103151--1103570 Score: 822
Period size: 206 Copynumber: 2.0 Consensus size: 206
1103141 ACTTATTAAA
1103151 TCTTTTTAGTGGAGTTTGGAAATTCAAAACTCTTGATGGCATTCTATTTATTAGATAAGTAGCAA
1 TCTTTTTAGTGGAGTTTGGAAATTCAAAACTCTTGATGGCATTCTATTTATTAGATAAGTAGCAA
1103216 TAAGAATAGCTTCTCTCTATAAGTATTTAAGTACTTTAGTTGTAAACCTTAAAGACTTGGTCACT
66 TAAGAATAGCTTCTCTCTATAAGTATTTAAGTACTTTAGTTGTAAACCTTAAAGACTTGGTCACT
1103281 TTTAAGAGGTGCTTATTTTTCTCTCTGCAACTCTTTTATGTTATAGTATGTCAATATAAGATCTT
131 TTTAAGAGGTGCTTATTTTTCTCTCTGCAACTCTTTTATGTTATAGTATGTCAATATAAGATCTT
1103346 TGATGAATTAT
196 TGATGAATTAT
1103357 TCTTTTTAGTGGAGTTTGGAAATTCAAAACTCTTGATGGCATTCTATTTATTAGATAAGTAGCAA
1 TCTTTTTAGTGGAGTTTGGAAATTCAAAACTCTTGATGGCATTCTATTTATTAGATAAGTAGCAA
1103422 TAAGAATAGCTTCTCTCTATAAGTATTTAAGTACTTTAGTTGTAAACCTTAAAGACTTGGTCACT
66 TAAGAATAGCTTCTCTCTATAAGTATTTAAGTACTTTAGTTGTAAACCTTAAAGACTTGGTCACT
*
1103487 TTTAAGAGGTGCTTATTTTTCTCTTTGCAACTCTTTTATGTTATAGTATGTCAATATAAGATCTT
131 TTTAAGAGGTGCTTATTTTTCTCTCTGCAACTCTTTTATGTTATAGTATGTCAATATAAGATCTT
1103552 TGATGAATTAT
196 TGATGAATTAT
1103563 TCTATTTT
1 TCT-TTTT
1103571 TCGAAAAAAA
Statistics
Matches: 212, Mismatches: 1, Indels: 1
0.99 0.00 0.00
Matches are distributed among these distances:
206 208 0.98
207 4 0.02
ACGTcount: A:0.29, C:0.12, G:0.15, T:0.43
Consensus pattern (206 bp):
TCTTTTTAGTGGAGTTTGGAAATTCAAAACTCTTGATGGCATTCTATTTATTAGATAAGTAGCAA
TAAGAATAGCTTCTCTCTATAAGTATTTAAGTACTTTAGTTGTAAACCTTAAAGACTTGGTCACT
TTTAAGAGGTGCTTATTTTTCTCTCTGCAACTCTTTTATGTTATAGTATGTCAATATAAGATCTT
TGATGAATTAT
Found at i:1106852 original size:30 final size:31
Alignment explanation
Indices: 1106818--1106890 Score: 89
Period size: 31 Copynumber: 2.4 Consensus size: 31
1106808 ATTTTTATTT
1106818 AAATTT-AATTATAAATTTT-AATAA-AAAATA
1 AAATTTAAATT-T-AATTTTAAATAATAAAATA
*
1106848 AAATTTAAATTTTATTTTAAATAATAAAATA
1 AAATTTAAATTTAATTTTAAATAATAAAATA
1106879 AAATTTTAAATT
1 AAA-TTTAAATT
1106891 AATCAAAATT
Statistics
Matches: 38, Mismatches: 1, Indels: 6
0.84 0.02 0.13
Matches are distributed among these distances:
29 5 0.13
30 12 0.32
31 13 0.34
32 8 0.21
ACGTcount: A:0.56, C:0.00, G:0.00, T:0.44
Consensus pattern (31 bp):
AAATTTAAATTTAATTTTAAATAATAAAATA
Found at i:1106854 original size:36 final size:36
Alignment explanation
Indices: 1106814--1106914 Score: 101
Period size: 36 Copynumber: 3.0 Consensus size: 36
1106804 TAATATTTTT
1106814 ATTTAAATTTAATTATAAATTTTAATAAAAAATAAA
1 ATTTAAATTTAATTATAAATTTTAATAAAAAATAAA
* *
1106850 ATTTAAATTTTATTTTAAA---TAAT--AAAATAAA
1 ATTTAAATTTAATTATAAATTTTAATAAAAAATAAA
* *
1106881 ATTTTAAA-TTAATCA-AAATTTTAA-AAAAATTAAA
1 A-TTTAAATTTAATTATAAATTTTAATAAAAAATAAA
1106915 TTCTTATCCA
Statistics
Matches: 53, Mismatches: 6, Indels: 14
0.73 0.08 0.19
Matches are distributed among these distances:
30 3 0.06
31 13 0.25
32 6 0.11
33 7 0.13
34 7 0.13
36 17 0.32
ACGTcount: A:0.57, C:0.01, G:0.00, T:0.42
Consensus pattern (36 bp):
ATTTAAATTTAATTATAAATTTTAATAAAAAATAAA
Found at i:1106880 original size:31 final size:30
Alignment explanation
Indices: 1106832--1106890 Score: 93
Period size: 31 Copynumber: 1.9 Consensus size: 30
1106822 TTAATTATAA
1106832 ATTTTAATAAAAAATAAAA-TTTAAATTTT
1 ATTTTAATAAAAAATAAAATTTTAAATTTT
1106861 ATTTTAAATAATAAAATAAAATTTTAAATT
1 ATTTT-AATAA-AAAATAAAATTTTAAATT
1106891 AATCAAAATT
Statistics
Matches: 27, Mismatches: 0, Indels: 3
0.90 0.00 0.10
Matches are distributed among these distances:
29 5 0.19
30 5 0.19
31 9 0.33
32 8 0.30
ACGTcount: A:0.56, C:0.00, G:0.00, T:0.44
Consensus pattern (30 bp):
ATTTTAATAAAAAATAAAATTTTAAATTTT
Found at i:1106892 original size:25 final size:26
Alignment explanation
Indices: 1106824--1106892 Score: 72
Period size: 25 Copynumber: 2.7 Consensus size: 26
1106814 ATTTAAATTT
1106824 AATTATAAATTTT-AA-TAAAAAATAA
1 AATTA-AAATTTTAAATTAAAAAATAA
* ** *
1106849 AATTTAAATTTTATTTTAAATAATAA
1 AATTAAAATTTTAAATTAAAAAATAA
1106875 AA-TAAAATTTTAAATTAA
1 AATTAAAATTTTAAATTAA
1106893 TCAAAATTTT
Statistics
Matches: 35, Mismatches: 7, Indels: 4
0.76 0.15 0.09
Matches are distributed among these distances:
24 7 0.20
25 17 0.49
26 11 0.31
ACGTcount: A:0.58, C:0.00, G:0.00, T:0.42
Consensus pattern (26 bp):
AATTAAAATTTTAAATTAAAAAATAA
Found at i:1111028 original size:2 final size:2
Alignment explanation
Indices: 1111021--1111058 Score: 67
Period size: 2 Copynumber: 19.0 Consensus size: 2
1111011 CGTATACTAC
*
1111021 AT AT AT AT AT AT AT AT AT AT AT AT AT AC 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
1111059 GTCCCCATGG
Statistics
Matches: 34, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
2 34 1.00
ACGTcount: A:0.50, C:0.03, G:0.00, T:0.47
Consensus pattern (2 bp):
AT
Found at i:1111491 original size:20 final size:19
Alignment explanation
Indices: 1111473--1111509 Score: 60
Period size: 19 Copynumber: 2.1 Consensus size: 19
1111463 GAATTAAATT
1111473 ATTTA-TTTA-ATTTAAAA
1 ATTTATTTTATATTTAAAA
1111490 ATTTATTTTATATTTAAAA
1 ATTTATTTTATATTTAAAA
1111509 A
1 A
1111510 AGTTTAAATA
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
17 5 0.28
18 4 0.22
19 9 0.50
ACGTcount: A:0.46, C:0.00, G:0.00, T:0.54
Consensus pattern (19 bp):
ATTTATTTTATATTTAAAA
Found at i:1111863 original size:173 final size:174
Alignment explanation
Indices: 1111430--1111896 Score: 512
Period size: 173 Copynumber: 2.7 Consensus size: 174
1111420 CGTTCAGATT
* *
1111430 ATGTAATTAAAAATTAAAATTAAAAGTATTTATGAATTAAATTATTTATTTAATTTAAAAATTTA
1 ATGTAATT-AAAATTAAAA-T-GAAGTATTTATGAATTAAGTTATTTATTTAATTTAAAAATTTA
* * * *
1111495 TTTTATATTTAAAAAAGTTTAAATAAAAATATCACGTTTAAAAAAAAAATTTGAGAAAAAATATA
63 TTTTATATTTAAGAAAGTTTAAATAAAAATATTATGTTT-AAAAAAAAATTTCA-AAAAAATATA
* * *
1111560 TTTCAAATCCTTAACAGAATAAGACCAACAAATAAAAAAAATTAATTGG
126 TTTCAAATCCTTAACAAAATAAGACCAACAAATAAAAAAAATCAATCGG
*
1111609 CTCG----T--AATTAAAA-G--G-ATTTATGAAGTTAAGTTATTTATTTAATTTAAAAATTTAT
1 AT-GTAATTAAAATTAAAATGAAGTATTTATGAA-TTAAGTTATTTATTTAATTTAAAAATTTAT
* *
1111664 TTTATATTTAAG-ATGATTTAAATAAAAATATTATGTTT-AAAAAAAATTTTAAAAAAATATA-T
64 TTTATATTTAAGAAAG-TTTAAATAAAAATATTATGTTTAAAAAAAAATTTCAAAAAAATATATT
* * * * * **
1111726 TCTGAATCCTTATCAAAATAAGATCAATAAAT-AGAAATGTCAATCGG
128 TC-AAATCCTTAACAAAATAAGACCAACAAATAAAAAAAATCAATCGG
* * *
1111773 ATGTAATTAAAAGTTAAAATGAAGTATTTATGAATTAGGTTATATATTTAATTTAAAAATTTATG
1 ATGTAATTAAAA-TTAAAATGAAGTATTTATGAATTAAGTTATTTATTTAATTTAAAAATTTATT
* * * *
1111838 TTATATTTAAGAAAGTTTGAATAAAAATTTTATGTTTGAAAAAAAAGTTCAAAAAAATA
65 TTATATTTAAGAAAGTTTAAATAAAAATATTATGTTTAAAAAAAAATTTCAAAAAAATA
1111897 GAACTTATTT
Statistics
Matches: 244, Mismatches: 27, Indels: 39
0.79 0.09 0.13
Matches are distributed among these distances:
163 1 0.00
164 14 0.06
165 34 0.14
166 12 0.05
167 12 0.05
168 61 0.25
169 2 0.01
170 6 0.02
171 1 0.00
173 68 0.28
174 30 0.12
176 1 0.00
179 1 0.00
180 1 0.00
ACGTcount: A:0.50, C:0.04, G:0.09, T:0.38
Consensus pattern (174 bp):
ATGTAATTAAAATTAAAATGAAGTATTTATGAATTAAGTTATTTATTTAATTTAAAAATTTATTT
TATATTTAAGAAAGTTTAAATAAAAATATTATGTTTAAAAAAAAATTTCAAAAAAATATATTTCA
AATCCTTAACAAAATAAGACCAACAAATAAAAAAAATCAATCGG
Found at i:1112003 original size:9 final size:9
Alignment explanation
Indices: 1111982--1112013 Score: 57
Period size: 9 Copynumber: 3.7 Consensus size: 9
1111972 ATATATTAAC
1111982 TTTATAT-T
1 TTTATATAT
1111990 TTTATATAT
1 TTTATATAT
1111999 TTTATATAT
1 TTTATATAT
1112008 TTTATA
1 TTTATA
1112014 ATATAAAAAA
Statistics
Matches: 23, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
8 7 0.30
9 16 0.70
ACGTcount: A:0.31, C:0.00, G:0.00, T:0.69
Consensus pattern (9 bp):
TTTATATAT
Found at i:1112099 original size:15 final size:15
Alignment explanation
Indices: 1112072--1112120 Score: 55
Period size: 15 Copynumber: 3.3 Consensus size: 15
1112062 AATTATTTAT
*
1112072 ATTAA-AAATATTAA
1 ATTAATAAAAATTAA
1112086 ATTAATAAAAATTAA
1 ATTAATAAAAATTAA
** *
1112101 ATTTTTAAAAAATAA
1 ATTAATAAAAATTAA
1112116 ATTAA
1 ATTAA
1112121 AAATAAAATA
Statistics
Matches: 28, Mismatches: 6, Indels: 1
0.80 0.17 0.03
Matches are distributed among these distances:
14 5 0.18
15 23 0.82
ACGTcount: A:0.63, C:0.00, G:0.00, T:0.37
Consensus pattern (15 bp):
ATTAATAAAAATTAA
Found at i:1113754 original size:21 final size:21
Alignment explanation
Indices: 1113743--1113782 Score: 71
Period size: 21 Copynumber: 1.9 Consensus size: 21
1113733 GATTAATTAT
*
1113743 TATAAGAATAAGATTAAAAAC
1 TATAAAAATAAGATTAAAAAC
1113764 TATAAAAATAAGATTAAAA
1 TATAAAAATAAGATTAAAA
1113783 TTAATAATAA
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
21 18 1.00
ACGTcount: A:0.65, C:0.03, G:0.07, T:0.25
Consensus pattern (21 bp):
TATAAAAATAAGATTAAAAAC
Found at i:1113789 original size:21 final size:20
Alignment explanation
Indices: 1113730--1113785 Score: 67
Period size: 21 Copynumber: 2.7 Consensus size: 20
1113720 ATGATAATAT
* *
1113730 TAAGATTAATTATTATAAGAA
1 TAAGATTAA-AATTATAAAAA
*
1113751 TAAGATTAAAAACTATAAAAA
1 TAAGATT-AAAATTATAAAAA
1113772 TAAGATTAAAATTA
1 TAAGATTAAAATTA
1113786 ATAATAAAAT
Statistics
Matches: 30, Mismatches: 4, Indels: 3
0.81 0.11 0.08
Matches are distributed among these distances:
20 6 0.20
21 22 0.73
22 2 0.07
ACGTcount: A:0.59, C:0.02, G:0.07, T:0.32
Consensus pattern (20 bp):
TAAGATTAAAATTATAAAAA
Found at i:1114520 original size:15 final size:15
Alignment explanation
Indices: 1114500--1114533 Score: 50
Period size: 15 Copynumber: 2.3 Consensus size: 15
1114490 ATTAGTTAAG
*
1114500 TTATCATTTAAATTA
1 TTATCAATTAAATTA
*
1114515 TTATCAATTAATTTA
1 TTATCAATTAAATTA
1114530 TTAT
1 TTAT
1114534 TTATATGAAT
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
15 17 1.00
ACGTcount: A:0.38, C:0.06, G:0.00, T:0.56
Consensus pattern (15 bp):
TTATCAATTAAATTA
Found at i:1115486 original size:19 final size:19
Alignment explanation
Indices: 1115436--1115486 Score: 59
Period size: 19 Copynumber: 2.7 Consensus size: 19
1115426 TTTGATATAA
*
1115436 TTTATACATAAA-ATAAAT
1 TTTATATATAAATATAAAT
* *
1115454 TTTATATGTTAATATAAAT
1 TTTATATATAAATATAAAT
*
1115473 TTTATTTATAAATA
1 TTTATATATAAATA
1115487 CTTTATTAAT
Statistics
Matches: 26, Mismatches: 6, Indels: 1
0.79 0.18 0.03
Matches are distributed among these distances:
18 9 0.35
19 17 0.65
ACGTcount: A:0.47, C:0.02, G:0.02, T:0.49
Consensus pattern (19 bp):
TTTATATATAAATATAAAT
Found at i:1115634 original size:17 final size:19
Alignment explanation
Indices: 1115602--1115642 Score: 59
Period size: 17 Copynumber: 2.3 Consensus size: 19
1115592 AAATAGTTAT
*
1115602 AAATATATTAATAAAATAA
1 AAATATATTAATAAAAGAA
1115621 AAAT-TATTAA-AAAAGAA
1 AAATATATTAATAAAAGAA
1115638 AAATA
1 AAATA
1115643 AAAAATTTTC
Statistics
Matches: 20, Mismatches: 1, Indels: 3
0.83 0.04 0.12
Matches are distributed among these distances:
17 10 0.50
18 6 0.30
19 4 0.20
ACGTcount: A:0.71, C:0.00, G:0.02, T:0.27
Consensus pattern (19 bp):
AAATATATTAATAAAAGAA
Found at i:1125128 original size:20 final size:20
Alignment explanation
Indices: 1125105--1125143 Score: 60
Period size: 20 Copynumber: 1.9 Consensus size: 20
1125095 AAAGAAACTA
*
1125105 AATTAAGAGTATAGAAAATT
1 AATTAAGAGCATAGAAAATT
*
1125125 AATTAAGAGCATAGGAAAT
1 AATTAAGAGCATAGAAAAT
1125144 ATACCAAGAA
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.54, C:0.03, G:0.18, T:0.26
Consensus pattern (20 bp):
AATTAAGAGCATAGAAAATT
Found at i:1129826 original size:20 final size:21
Alignment explanation
Indices: 1129785--1129847 Score: 69
Period size: 20 Copynumber: 3.0 Consensus size: 21
1129775 TTATTAAAAT
1129785 ATTATTTTTT-TAATTTTATA
1 ATTATTTTTTATAATTTTATA
1129805 ATTATTTTTTAT-ATATTT-TA
1 ATTATTTTTTATAAT-TTTATA
* *
1129825 ATTAATTTTTAAAATTTTTATA
1 ATTATTTTTTATAA-TTTTATA
1129847 A
1 A
1129848 AATTTTATTG
Statistics
Matches: 36, Mismatches: 2, Indels: 8
0.78 0.04 0.17
Matches are distributed among these distances:
20 24 0.67
21 8 0.22
22 4 0.11
ACGTcount: A:0.35, C:0.00, G:0.00, T:0.65
Consensus pattern (21 bp):
ATTATTTTTTATAATTTTATA
Found at i:1130020 original size:22 final size:21
Alignment explanation
Indices: 1129969--1130027 Score: 57
Period size: 23 Copynumber: 2.7 Consensus size: 21
1129959 AATCAAAATA
* *
1129969 AAATTTAATATAAATTTAAGT
1 AAATTAAATAAAAATTTAAGT
1129990 AAATGTAAATAAAAATTT-AGT
1 AAAT-TAAATAAAAATTTAAGT
1130011 CGAAATTAAAATAAAAA
1 --AAATT-AAATAAAAA
1130028 AACGATTTTA
Statistics
Matches: 32, Mismatches: 2, Indels: 6
0.80 0.05 0.15
Matches are distributed among these distances:
21 7 0.22
22 12 0.38
23 13 0.41
ACGTcount: A:0.59, C:0.02, G:0.07, T:0.32
Consensus pattern (21 bp):
AAATTAAATAAAAATTTAAGT
Found at i:1131754 original size:2 final size:2
Alignment explanation
Indices: 1131747--1131787 Score: 82
Period size: 2 Copynumber: 20.5 Consensus size: 2
1131737 GGGTTAAAAG
1131747 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1131788 CTTGGAAGGA
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:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:1134821 original size:2 final size:2
Alignment explanation
Indices: 1134814--1134841 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
1134804 AAATTGTGAC
1134814 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
1134842 CCAAGAAATT
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:1135253 original size:19 final size:19
Alignment explanation
Indices: 1135229--1135273 Score: 54
Period size: 19 Copynumber: 2.4 Consensus size: 19
1135219 AATTTTTAAG
* *
1135229 AAAAAATAAATAATTTTTT
1 AAAAAATAAATAACTTCTT
* *
1135248 AAAAAATTATTAACTTCTT
1 AAAAAATAAATAACTTCTT
1135267 AAAAAAT
1 AAAAAAT
1135274 TATAATTAAA
Statistics
Matches: 22, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
19 22 1.00
ACGTcount: A:0.58, C:0.04, G:0.00, T:0.38
Consensus pattern (19 bp):
AAAAAATAAATAACTTCTT
Found at i:1138945 original size:7 final size:7
Alignment explanation
Indices: 1138933--1138971 Score: 78
Period size: 7 Copynumber: 5.6 Consensus size: 7
1138923 ATGCACCTCT
1138933 CTTTTTC
1 CTTTTTC
1138940 CTTTTTC
1 CTTTTTC
1138947 CTTTTTC
1 CTTTTTC
1138954 CTTTTTC
1 CTTTTTC
1138961 CTTTTTC
1 CTTTTTC
1138968 CTTT
1 CTTT
1138972 CATTAGGAGG
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 32 1.00
ACGTcount: A:0.00, C:0.28, G:0.00, T:0.72
Consensus pattern (7 bp):
CTTTTTC
Found at i:1140418 original size:3 final size:3
Alignment explanation
Indices: 1140405--1140443 Score: 69
Period size: 3 Copynumber: 13.0 Consensus size: 3
1140395 AAGGAGACCA
*
1140405 ATG AGG ATG ATG ATG ATG ATG ATG ATG ATG ATG ATG ATG
1 ATG ATG ATG ATG ATG ATG ATG ATG ATG ATG ATG ATG ATG
1140444 TCACTGATGA
Statistics
Matches: 34, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
3 34 1.00
ACGTcount: A:0.33, C:0.00, G:0.36, T:0.31
Consensus pattern (3 bp):
ATG
Found at i:1146771 original size:2 final size:2
Alignment explanation
Indices: 1146764--1146800 Score: 74
Period size: 2 Copynumber: 18.5 Consensus size: 2
1146754 GTATTAATTT
1146764 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
1146801 GTCAGACTAT
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:1149366 original size:2 final size:2
Alignment explanation
Indices: 1149353--1149383 Score: 53
Period size: 2 Copynumber: 15.5 Consensus size: 2
1149343 GATTAGATAC
*
1149353 AT AT AC 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
1149384 AATAGACTTT
Statistics
Matches: 27, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
2 27 1.00
ACGTcount: A:0.52, C:0.03, G:0.00, T:0.45
Consensus pattern (2 bp):
AT
Found at i:1150354 original size:33 final size:33
Alignment explanation
Indices: 1150317--1150382 Score: 132
Period size: 33 Copynumber: 2.0 Consensus size: 33
1150307 ATTACTTTGA
1150317 GATAGTTTTTAATTATAATTATAGATAAATTAT
1 GATAGTTTTTAATTATAATTATAGATAAATTAT
1150350 GATAGTTTTTAATTATAATTATAGATAAATTAT
1 GATAGTTTTTAATTATAATTATAGATAAATTAT
1150383 AATGTTAGAT
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
33 33 1.00
ACGTcount: A:0.42, C:0.00, G:0.09, T:0.48
Consensus pattern (33 bp):
GATAGTTTTTAATTATAATTATAGATAAATTAT
Found at i:1150393 original size:17 final size:17
Alignment explanation
Indices: 1150327--1150385 Score: 59
Period size: 17 Copynumber: 3.5 Consensus size: 17
1150317 GATAGTTTTT
1150327 AATTATAATTATAGATA
1 AATTATAATTATAGATA
* ** *
1150344 AATTATGA-TAGT-TTTT
1 AATTATAATTA-TAGATA
1150360 AATTATAATTATAGATA
1 AATTATAATTATAGATA
1150377 AATTATAAT
1 AATTATAAT
1150386 GTTAGATATA
Statistics
Matches: 31, Mismatches: 8, Indels: 6
0.69 0.18 0.13
Matches are distributed among these distances:
16 11 0.35
17 20 0.65
ACGTcount: A:0.47, C:0.00, G:0.07, T:0.46
Consensus pattern (17 bp):
AATTATAATTATAGATA
Found at i:1150400 original size:33 final size:33
Alignment explanation
Indices: 1150326--1150393 Score: 93
Period size: 33 Copynumber: 2.1 Consensus size: 33
1150316 AGATAGTTTT
* **
1150326 TAATTATAATTATAGATAAATTATGATAGTTTT
1 TAATTATAATTATAGATAAATTATAATAGTTGA
1150359 TAATTATAATTATAGATAAATTATAAT-GTTAGA
1 TAATTATAATTATAGATAAATTATAATAGTT-GA
1150392 TA
1 TA
1150394 TATATAAATA
Statistics
Matches: 31, Mismatches: 3, Indels: 2
0.86 0.08 0.06
Matches are distributed among these distances:
32 3 0.10
33 28 0.90
ACGTcount: A:0.46, C:0.00, G:0.09, T:0.46
Consensus pattern (33 bp):
TAATTATAATTATAGATAAATTATAATAGTTGA
Found at i:1151668 original size:25 final size:24
Alignment explanation
Indices: 1151618--1151668 Score: 59
Period size: 25 Copynumber: 2.0 Consensus size: 24
1151608 AATCACCTAA
*
1151618 TTTATAAATAAATTTAATAATTATT
1 TTTAAAAATAAATTTAATAA-TATT
1151643 TTTAAAAATAATATTTTAATAA-ATT
1 TTTAAAAATAA-A-TTTAATAATATT
1151668 T
1 T
1151669 AAATTTAAAT
Statistics
Matches: 23, Mismatches: 1, Indels: 4
0.82 0.04 0.14
Matches are distributed among these distances:
25 14 0.61
26 1 0.04
27 8 0.35
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (24 bp):
TTTAAAAATAAATTTAATAATATT
Found at i:1152287 original size:23 final size:23
Alignment explanation
Indices: 1152261--1152313 Score: 56
Period size: 23 Copynumber: 2.3 Consensus size: 23
1152251 AAAATTTTTT
*
1152261 AATT-TTATTAAATAATTTTAAAA
1 AATTATTA-TAAATAATTTAAAAA
**
1152284 AATTATTATATTTAATTTAAAAA
1 AATTATTATAAATAATTTAAAAA
1152307 AA-TATTA
1 AATTATTA
1152314 ATATTAAAAA
Statistics
Matches: 26, Mismatches: 3, Indels: 3
0.81 0.09 0.09
Matches are distributed among these distances:
22 5 0.19
23 18 0.69
24 3 0.12
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (23 bp):
AATTATTATAAATAATTTAAAAA
Found at i:1152289 original size:21 final size:21
Alignment explanation
Indices: 1152265--1152317 Score: 63
Period size: 22 Copynumber: 2.5 Consensus size: 21
1152255 TTTTTTAATT
1152265 TTATTAA-ATAATTTTAAAAAA
1 TTATTAATATAA-TTTAAAAAA
*
1152286 TTATTATATTTAATTTAAAAAA
1 TTATTA-ATATAATTTAAAAAA
*
1152308 ATATTAATAT
1 TTATTAATAT
1152318 TAAAAAATAT
Statistics
Matches: 27, Mismatches: 3, Indels: 4
0.79 0.09 0.12
Matches are distributed among these distances:
21 9 0.33
22 15 0.56
23 3 0.11
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (21 bp):
TTATTAATATAATTTAAAAAA
Found at i:1152353 original size:15 final size:15
Alignment explanation
Indices: 1152303--1152354 Score: 54
Period size: 15 Copynumber: 3.4 Consensus size: 15
1152293 ATTTAATTTA
1152303 AAAAAATATTAATATT
1 AAAAAATA-TAATATT
1152319 AAAAAATATACATGA-T
1 AAAAAATATA-AT-ATT
*
1152335 -AAAATTATAATATT
1 AAAAAATATAATATT
1152349 AAAAAA
1 AAAAAA
1152355 ATTATAAATC
Statistics
Matches: 30, Mismatches: 2, Indels: 9
0.73 0.05 0.22
Matches are distributed among these distances:
13 1 0.03
14 3 0.10
15 14 0.47
16 11 0.37
17 1 0.03
ACGTcount: A:0.65, C:0.02, G:0.02, T:0.31
Consensus pattern (15 bp):
AAAAAATATAATATT
Found at i:1152354 original size:16 final size:16
Alignment explanation
Indices: 1152296--1152361 Score: 57
Period size: 17 Copynumber: 4.2 Consensus size: 16
1152286 TTATTATATT
*
1152296 TAAT-TTAAAAAAATA
1 TAATATTAAAAAATTA
1152311 TTAATATTAAAAAA-TA
1 -TAATATTAAAAAATTA
* * *
1152327 T-ACATGATAAAATTA
1 TAATATTAAAAAATTA
1152342 TAATATTAAAAAAATTA
1 TAATATT-AAAAAATTA
1152359 TAA
1 TAA
1152362 ATCATAAAAT
Statistics
Matches: 40, Mismatches: 6, Indels: 7
0.75 0.11 0.13
Matches are distributed among these distances:
14 8 0.20
15 4 0.10
16 9 0.22
17 19 0.47
ACGTcount: A:0.62, C:0.02, G:0.02, T:0.35
Consensus pattern (16 bp):
TAATATTAAAAAATTA
Found at i:1152369 original size:32 final size:30
Alignment explanation
Indices: 1152312--1152377 Score: 87
Period size: 32 Copynumber: 2.1 Consensus size: 30
1152302 AAAAAAATAT
* * *
1152312 TAATATTAAAAAATATACATGATAAAATTA
1 TAATATTAAAAAATATAAATCATAAAATCA
1152342 TAATATTAAAAAAATTATAAATCATAAAATCA
1 TAATATT-AAAAAA-TATAAATCATAAAATCA
1152374 TAAT
1 TAAT
1152378 TTTATTAGTT
Statistics
Matches: 31, Mismatches: 3, Indels: 2
0.86 0.08 0.06
Matches are distributed among these distances:
30 7 0.23
31 6 0.19
32 18 0.58
ACGTcount: A:0.61, C:0.05, G:0.02, T:0.33
Consensus pattern (30 bp):
TAATATTAAAAAATATAAATCATAAAATCA
Found at i:1152912 original size:3 final size:3
Alignment explanation
Indices: 1152904--1152943 Score: 71
Period size: 3 Copynumber: 13.3 Consensus size: 3
1152894 TTCACGTTAA
*
1152904 AAT AAT AAT AAT AAC AAT AAT AAT AAT AAT AAT AAT AAT A
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT A
1152944 TATTAAATTT
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:1153263 original size:26 final size:26
Alignment explanation
Indices: 1153213--1153273 Score: 72
Period size: 27 Copynumber: 2.3 Consensus size: 26
1153203 TTTATATATT
1153213 ATTATTTTATTAAATATAAATTTTTA
1 ATTATTTTATTAAATATAAATTTTTA
*
1153239 ATTATTTATATTATATCAT-AATTTTT-
1 ATTATTT-TATTAAAT-ATAAATTTTTA
*
1153265 TTTATTTTA
1 ATTATTTTA
1153274 ATTGATTAAA
Statistics
Matches: 31, Mismatches: 2, Indels: 5
0.82 0.05 0.13
Matches are distributed among these distances:
25 2 0.06
26 13 0.42
27 14 0.45
28 2 0.06
ACGTcount: A:0.36, C:0.02, G:0.00, T:0.62
Consensus pattern (26 bp):
ATTATTTTATTAAATATAAATTTTTA
Found at i:1153702 original size:11 final size:11
Alignment explanation
Indices: 1153688--1153769 Score: 58
Period size: 11 Copynumber: 6.7 Consensus size: 11
1153678 TTTTTTAAAA
1153688 ATTAATAATTT
1 ATTAATAATTT
1153699 ATTACAT-ATTAT
1 ATTA-ATAATT-T
*
1153711 ATTTAATAATTA
1 A-TTAATAATTT
*
1153723 AATAATAAATATTT
1 ATTAAT--A-ATTT
1153737 ATTAAAATAATTT
1 ATT--AATAATTT
1153750 ATTAATAATTT
1 ATTAATAATTT
1153761 ATATAATAA
1 AT-TAATAA
1153770 ATAATTATTT
Statistics
Matches: 57, Mismatches: 4, Indels: 19
0.71 0.05 0.24
Matches are distributed among these distances:
11 21 0.37
12 13 0.23
13 14 0.25
14 6 0.11
16 3 0.05
ACGTcount: A:0.51, C:0.01, G:0.00, T:0.48
Consensus pattern (11 bp):
ATTAATAATTT
Found at i:1153720 original size:27 final size:25
Alignment explanation
Indices: 1153690--1153775 Score: 77
Period size: 27 Copynumber: 3.3 Consensus size: 25
1153680 TTTTAAAAAT
1153690 TAATAATTTATTACATATTATATTTAA
1 TAATAATTTATTA-ATATT-TATTTAA
* * *
1153717 TAATTAAATAATAAATATTTA-TTAA
1 TAA-TAATTTATTAATATTTATTTAA
*
1153742 -AATAATTTATTAATAATTTATATAA
1 TAATAATTTATTAAT-ATTTATTTAA
1153767 TAAATAATT
1 T-AATAATT
1153776 ATTTTTAAAA
Statistics
Matches: 47, Mismatches: 7, Indels: 10
0.73 0.11 0.16
Matches are distributed among these distances:
23 9 0.19
24 7 0.15
25 7 0.15
26 2 0.04
27 15 0.32
28 7 0.15
ACGTcount: A:0.51, C:0.01, G:0.00, T:0.48
Consensus pattern (25 bp):
TAATAATTTATTAATATTTATTTAA
Found at i:1154156 original size:25 final size:24
Alignment explanation
Indices: 1154112--1154181 Score: 67
Period size: 24 Copynumber: 3.0 Consensus size: 24
1154102 TATATTGATG
*
1154112 TAAAATTAATTAATTTATATTTTT
1 TAAAATTAATTAATTAATATTTTT
1154136 TAAAATT-ATATATATTAATA-TTTT
1 TAAAATTAAT-TA-ATTAATATTTTT
*
1154160 AATAAATTAATT-ATTAA-ATTTT
1 TA-AAATTAATTAATTAATATTTT
1154182 AATAATATAA
Statistics
Matches: 39, Mismatches: 2, Indels: 11
0.75 0.04 0.21
Matches are distributed among these distances:
22 1 0.03
23 10 0.26
24 14 0.36
25 12 0.31
26 2 0.05
ACGTcount: A:0.46, C:0.00, G:0.00, T:0.54
Consensus pattern (24 bp):
TAAAATTAATTAATTAATATTTTT
Found at i:1154183 original size:22 final size:25
Alignment explanation
Indices: 1154138--1154186 Score: 77
Period size: 22 Copynumber: 2.1 Consensus size: 25
1154128 ATATTTTTTA
1154138 AAATTATATATATTAATATTTTAAT
1 AAATTATATATATTAATATTTTAAT
1154163 AAATTA-AT-TATTAA-ATTTTAAT
1 AAATTATATATATTAATATTTTAAT
1154185 AA
1 AA
1154187 TATAATAGTA
Statistics
Matches: 24, Mismatches: 0, Indels: 3
0.89 0.00 0.11
Matches are distributed among these distances:
22 10 0.42
23 6 0.25
24 2 0.08
25 6 0.25
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (25 bp):
AAATTATATATATTAATATTTTAAT
Found at i:1154192 original size:22 final size:23
Alignment explanation
Indices: 1154114--1154186 Score: 78
Period size: 25 Copynumber: 3.1 Consensus size: 23
1154104 TATTGATGTA
* *
1154114 AAATTAATTAATTTATATTTT-TT
1 AAATTAATT-ATTAATATTTTAAT
1154137 AAAATTATATATATTAATATTTTAAT
1 -AAATTA-AT-TATTAATATTTTAAT
1154163 AAATTAATTATTAA-ATTTTAAT
1 AAATTAATTATTAATATTTTAAT
1154185 AA
1 AA
1154187 TATAATAGTA
Statistics
Matches: 44, Mismatches: 2, Indels: 8
0.81 0.04 0.15
Matches are distributed among these distances:
22 10 0.23
23 6 0.14
24 8 0.18
25 18 0.41
26 2 0.05
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (23 bp):
AAATTAATTATTAATATTTTAAT
Found at i:1155519 original size:22 final size:21
Alignment explanation
Indices: 1155493--1155550 Score: 71
Period size: 23 Copynumber: 2.6 Consensus size: 21
1155483 TAACATTAGA
1155493 TATTTATAACTATAAAAAAAAT
1 TATTTATAA-TATAAAAAAAAT
*
1155515 TATTTATAATTTTTAAAAAAAAT
1 TATTTATAA--TATAAAAAAAAT
*
1155538 TATATATAATATA
1 TATTTATAATATA
1155551 TAATTTTTTA
Statistics
Matches: 31, Mismatches: 4, Indels: 3
0.82 0.11 0.08
Matches are distributed among these distances:
21 3 0.10
22 9 0.29
23 19 0.61
ACGTcount: A:0.55, C:0.02, G:0.00, T:0.43
Consensus pattern (21 bp):
TATTTATAATATAAAAAAAAT
Found at i:1156639 original size:2 final size:2
Alignment explanation
Indices: 1156595--1156621 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
1156585 ATCAGTCAGC
1156595 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
1156622 AAGAGAGAGA
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:1159092 original size:20 final size:19
Alignment explanation
Indices: 1159069--1159106 Score: 58
Period size: 20 Copynumber: 1.9 Consensus size: 19
1159059 TTATAATTTT
*
1159069 AATTTTTTTATTTTAAAATA
1 AATTTTTTT-TATTAAAATA
1159089 AATTTTTTTTATTAAAAT
1 AATTTTTTTTATTAAAAT
1159107 TTATTATTTA
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
19 8 0.47
20 9 0.53
ACGTcount: A:0.39, C:0.00, G:0.00, T:0.61
Consensus pattern (19 bp):
AATTTTTTTTATTAAAATA
Found at i:1159312 original size:20 final size:20
Alignment explanation
Indices: 1159279--1159316 Score: 58
Period size: 20 Copynumber: 1.9 Consensus size: 20
1159269 TGATAGTTTA
*
1159279 TTAATATAATTTTTAATTAT
1 TTAATATAAATTTTAATTAT
*
1159299 TTAATTTAAATTTTAATT
1 TTAATATAAATTTTAATT
1159317 CAAAACTTAA
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 16 1.00
ACGTcount: A:0.39, C:0.00, G:0.00, T:0.61
Consensus pattern (20 bp):
TTAATATAAATTTTAATTAT
Found at i:1160937 original size:13 final size:13
Alignment explanation
Indices: 1160919--1160950 Score: 64
Period size: 13 Copynumber: 2.5 Consensus size: 13
1160909 TTTTCATGTA
1160919 TTGGACATAGGTG
1 TTGGACATAGGTG
1160932 TTGGACATAGGTG
1 TTGGACATAGGTG
1160945 TTGGAC
1 TTGGAC
1160951 TAGTTTTTTT
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 19 1.00
ACGTcount: A:0.22, C:0.09, G:0.38, T:0.31
Consensus pattern (13 bp):
TTGGACATAGGTG
Found at i:1164172 original size:28 final size:28
Alignment explanation
Indices: 1164131--1164207 Score: 145
Period size: 28 Copynumber: 2.8 Consensus size: 28
1164121 TTTTGGAGAT
*
1164131 AATAACGGGGTTGGAGTATCCCTTTGAA
1 AATAACGGGATTGGAGTATCCCTTTGAA
1164159 AATAACGGGATTGGAGTATCCCTTTGAA
1 AATAACGGGATTGGAGTATCCCTTTGAA
1164187 AATAACGGGATTGGAGTATCC
1 AATAACGGGATTGGAGTATCC
1164208 TCGGTTGTGA
Statistics
Matches: 48, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
28 48 1.00
ACGTcount: A:0.31, C:0.14, G:0.27, T:0.27
Consensus pattern (28 bp):
AATAACGGGATTGGAGTATCCCTTTGAA
Found at i:1164258 original size:79 final size:77
Alignment explanation
Indices: 1164164--1164418 Score: 237
Period size: 79 Copynumber: 3.2 Consensus size: 77
1164154 TTGAAAATAA
* *
1164164 CGGGATTGGAGTATCCCTTTGAAAATAACGGGATTGGAGTATCCTCGGTTGTGAAAAATCGATGA
1 CGGGATTGGAGTATCCCTTTG-AAATAACGGG-TTGGAGTATCCTCGATTGTGAAAAATCAATGA
*
1164229 TTAGGAAATAAAAT
64 TTTGGAAATAAAAT
** * * * *
1164243 CGGGATTGGAGTATCCTCTCGGAAATAACGGGGTTGGAGTATCCCCAATTATGAGAAATCAAT-A
1 CGGGATTGGAGTATCC-CTTTGAAATAAC-GGGTTGGAGTATCCTCGATTGTGAAAAATCAATGA
* **
1164307 TTTTGGAAATACAGC
64 -TTTGGAAATAAAAT
* ** * *
1164322 CGGGGTTGGAGTATCCCCGATGAAATAACGAGGTTGGAGTATCCTTGATTGTGAAAAA-CTAGTG
1 CGGGATTGGAGTAT-CCCTTTGAAATAACG-GGTTGGAGTATCCTCGATTGTGAAAAATC-AATG
*
1164386 TTTTGGAAATAAAAT
63 ATTTGGAAATAAAAT
*
1164401 C-GGAGTTGGAATATCCCT
1 CGGGA-TTGGAGTATCCCT
1164419 GATTGTGGAG
Statistics
Matches: 139, Mismatches: 29, Indels: 17
0.75 0.16 0.09
Matches are distributed among these distances:
78 8 0.06
79 123 0.88
80 8 0.06
ACGTcount: A:0.32, C:0.14, G:0.27, T:0.28
Consensus pattern (77 bp):
CGGGATTGGAGTATCCCTTTGAAATAACGGGTTGGAGTATCCTCGATTGTGAAAAATCAATGATT
TGGAAATAAAAT
Found at i:1164416 original size:51 final size:51
Alignment explanation
Indices: 1164354--1164534 Score: 195
Period size: 51 Copynumber: 3.5 Consensus size: 51
1164344 AAATAACGAG
* * *
1164354 GTTGGAGTATCCTTGATTGTGAAAAACTAGTGTTTTGGAAATAAAATCGGA
1 GTTGGAGTATCCCTGATTGTGGAAAATTAGTGTTTTGGAAATAAAATCGGA
* * * * * *
1164405 GTTGGAATATCCCTGATTGTGGAGAATTGGTGTTTTGAAAATAAAACCGGG
1 GTTGGAGTATCCCTGATTGTGGAAAATTAGTGTTTTGGAAATAAAATCGGA
* * * *
1164456 GTTGTAGTATCCCCGATTGTGGAAAATTAGTGTTTTAGAAAAAAAATC-GA
1 GTTGGAGTATCCCTGATTGTGGAAAATTAGTGTTTTGGAAATAAAATCGGA
* *
1164506 GGTTGGAGTATCTCC-GATTATGAAAAATT
1 -GTTGGAGTATC-CCTGATTGTGGAAAATT
1164535 GAGAAACTTA
Statistics
Matches: 106, Mismatches: 22, Indels: 4
0.80 0.17 0.03
Matches are distributed among these distances:
50 1 0.01
51 103 0.97
52 2 0.02
ACGTcount: A:0.33, C:0.09, G:0.25, T:0.33
Consensus pattern (51 bp):
GTTGGAGTATCCCTGATTGTGGAAAATTAGTGTTTTGGAAATAAAATCGGA
Found at i:1166845 original size:20 final size:20
Alignment explanation
Indices: 1166820--1166962 Score: 98
Period size: 20 Copynumber: 7.8 Consensus size: 20
1166810 AAAATGCCTG
1166820 AATGTATCGATACATTGTA-A
1 AATGTATCGATACATTG-AGA
* *
1166840 AATGTATCGATACAATGAGC
1 AATGTATCGATACATTGAGA
1166860 AATGTATCGATACATT----
1 AATGTATCGATACATTGAGA
* *
1166876 --TGTATCGATACAATGAGC
1 AATGTATCGATACATTGAGA
1166894 AATGTATCGATACATT----
1 AATGTATCGATACATTGAGA
* * *
1166910 --TGCATCGATACAATGAGC
1 AATGTATCGATACATTGAGA
*
1166928 AATGTATCGATACAATGCA-A
1 AATGTATCGATACATTG-AGA
1166948 AATGTATCGATACAT
1 AATGTATCGATACAT
1166963 CTGGGTAAAC
Statistics
Matches: 99, Mismatches: 10, Indels: 28
0.72 0.07 0.20
Matches are distributed among these distances:
14 25 0.25
19 1 0.01
20 72 0.73
21 1 0.01
ACGTcount: A:0.38, C:0.15, G:0.17, T:0.30
Consensus pattern (20 bp):
AATGTATCGATACATTGAGA
Done.