Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold140
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: 3130556
ACGTcount: A:0.34, C:0.15, G:0.15, T:0.34
Warning! 82166 characters in sequence are not A, C, G, or T
File 12 of 20
Found at i:1797063 original size:18 final size:18
Alignment explanation
Indices: 1797037--1797071 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
1797027 TTAATGAATG
* *
1797037 TTTATAAAATTTTTATTT
1 TTTAAAAAATATTTATTT
1797055 TTTAAAAAATATTTATT
1 TTTAAAAAATATTTATT
1797072 AATCTAATTA
Statistics
Matches: 15, Mismatches: 2, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
18 15 1.00
ACGTcount: A:0.40, C:0.00, G:0.00, T:0.60
Consensus pattern (18 bp):
TTTAAAAAATATTTATTT
Found at i:1798066 original size:15 final size:14
Alignment explanation
Indices: 1798041--1798070 Score: 51
Period size: 15 Copynumber: 2.1 Consensus size: 14
1798031 TAGATAATAG
1798041 TTATTTTTATTTAA
1 TTATTTTTATTTAA
1798055 TTATTATTTATTTAA
1 TTATT-TTTATTTAA
1798070 T
1 T
1798071 ATCAGATTCA
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
14 5 0.33
15 10 0.67
ACGTcount: A:0.30, C:0.00, G:0.00, T:0.70
Consensus pattern (14 bp):
TTATTTTTATTTAA
Found at i:1798370 original size:29 final size:29
Alignment explanation
Indices: 1798330--1798385 Score: 85
Period size: 29 Copynumber: 1.9 Consensus size: 29
1798320 TTAAAGTAAA
* *
1798330 TTTTTAATTTATATTTAAATAAATTTTTT
1 TTTTTAATTTATACTCAAATAAATTTTTT
*
1798359 TTTTTGATTTATACTCAAATAAATTTT
1 TTTTTAATTTATACTCAAATAAATTTT
1798386 AATTTTCAGT
Statistics
Matches: 24, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
29 24 1.00
ACGTcount: A:0.34, C:0.04, G:0.02, T:0.61
Consensus pattern (29 bp):
TTTTTAATTTATACTCAAATAAATTTTTT
Found at i:1798391 original size:29 final size:29
Alignment explanation
Indices: 1798328--1798391 Score: 83
Period size: 29 Copynumber: 2.2 Consensus size: 29
1798318 TTTTAAAGTA
* *
1798328 AATTTTTAATTTATATTTAAATAAATTTT
1 AATTTTTAATTTATACTCAAATAAATTTT
** *
1798357 TTTTTTTGATTTATACTCAAATAAATTTT
1 AATTTTTAATTTATACTCAAATAAATTTT
1798386 AATTTT
1 AATTTT
1798392 CAGTGTAAGA
Statistics
Matches: 28, Mismatches: 7, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
29 28 1.00
ACGTcount: A:0.36, C:0.03, G:0.02, T:0.59
Consensus pattern (29 bp):
AATTTTTAATTTATACTCAAATAAATTTT
Found at i:1799307 original size:24 final size:22
Alignment explanation
Indices: 1799278--1799330 Score: 72
Period size: 21 Copynumber: 2.3 Consensus size: 22
1799268 TAAAAATGAC
1799278 ATATTAAATATATTTTTTAAATAAT
1 ATATTAAATA-A--TTTTAAATAAT
1799303 A-ATTAAATAATTTTAAATAAT
1 ATATTAAATAATTTTAAATAAT
1799324 ATATTAA
1 ATATTAA
1799331 TTAGATTCTT
Statistics
Matches: 27, Mismatches: 0, Indels: 5
0.84 0.00 0.16
Matches are distributed among these distances:
21 12 0.44
22 5 0.19
23 1 0.04
24 8 0.30
25 1 0.04
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (22 bp):
ATATTAAATAATTTTAAATAAT
Found at i:1799825 original size:17 final size:17
Alignment explanation
Indices: 1799803--1799861 Score: 72
Period size: 17 Copynumber: 3.6 Consensus size: 17
1799793 TATATTTAAA
1799803 AAATTTTAATTTTATAT
1 AAATTTTAATTTTATAT
1799820 AAATTTTAATATATTA-AT
1 AAATTTTAAT-T-TTATAT
1799838 -AA-TTT-ATTTTATAT
1 AAATTTTAATTTTATAT
1799852 AAATTTTAAT
1 AAATTTTAAT
1799862 ATGTTAATAT
Statistics
Matches: 36, Mismatches: 0, Indels: 12
0.75 0.00 0.25
Matches are distributed among these distances:
13 3 0.08
14 3 0.08
15 4 0.11
16 6 0.17
17 14 0.39
18 3 0.08
19 3 0.08
ACGTcount: A:0.44, C:0.00, G:0.00, T:0.56
Consensus pattern (17 bp):
AAATTTTAATTTTATAT
Found at i:1799848 original size:32 final size:33
Alignment explanation
Indices: 1799811--1799877 Score: 118
Period size: 32 Copynumber: 2.1 Consensus size: 33
1799801 AAAAATTTTA
1799811 ATTTTATATAAATTTTAATATATTAATA-ATTT
1 ATTTTATATAAATTTTAATATATTAATATATTT
*
1799843 ATTTTATATAAATTTTAATATGTTAATATATTT
1 ATTTTATATAAATTTTAATATATTAATATATTT
1799876 AT
1 AT
1799878 GTATTATTAT
Statistics
Matches: 33, Mismatches: 1, Indels: 1
0.94 0.03 0.03
Matches are distributed among these distances:
32 27 0.82
33 6 0.18
ACGTcount: A:0.42, C:0.00, G:0.01, T:0.57
Consensus pattern (33 bp):
ATTTTATATAAATTTTAATATATTAATATATTT
Found at i:1800028 original size:28 final size:30
Alignment explanation
Indices: 1799997--1800057 Score: 81
Period size: 28 Copynumber: 2.1 Consensus size: 30
1799987 AAATTTTAGT
*
1799997 TAAATCTTTATATTTT-ATTT-TATTTAAA
1 TAAATCTTTATATTTTAATTTATAATTAAA
* *
1800025 TAAATTTTTATTTTTTAATTTATAATTAAA
1 TAAATCTTTATATTTTAATTTATAATTAAA
1800055 TAA
1 TAA
1800058 TTTTTAATTT
Statistics
Matches: 28, Mismatches: 3, Indels: 2
0.85 0.09 0.06
Matches are distributed among these distances:
28 14 0.50
29 4 0.14
30 10 0.36
ACGTcount: A:0.39, C:0.02, G:0.00, T:0.59
Consensus pattern (30 bp):
TAAATCTTTATATTTTAATTTATAATTAAA
Found at i:1800060 original size:29 final size:30
Alignment explanation
Indices: 1799997--1800077 Score: 96
Period size: 29 Copynumber: 2.8 Consensus size: 30
1799987 AAATTTTAGT
* * *
1799997 TAAATCTTTATATTTT-ATTT-TATTTAAA
1 TAAATTTTTATTTTTTAATTTATAATTAAA
1800025 TAAATTTTTATTTTTTAATTTATAATTAAA
1 TAAATTTTTATTTTTTAATTTATAATTAAA
* *
1800055 T-AATTTTTAATTTTTAAATTATA
1 TAAATTTTTATTTTTTAATTTATA
1800078 CTCTCTTAGT
Statistics
Matches: 46, Mismatches: 5, Indels: 3
0.85 0.09 0.06
Matches are distributed among these distances:
28 14 0.30
29 24 0.52
30 8 0.17
ACGTcount: A:0.38, C:0.01, G:0.00, T:0.60
Consensus pattern (30 bp):
TAAATTTTTATTTTTTAATTTATAATTAAA
Found at i:1800865 original size:21 final size:20
Alignment explanation
Indices: 1800840--1800884 Score: 54
Period size: 21 Copynumber: 2.1 Consensus size: 20
1800830 TATTTATTTT
*
1800840 TATTTAATATAAATTATAAAA
1 TATTTAATATAAA-AATAAAA
*
1800861 TATTTTAAAATAAAAATAAAA
1 TA-TTTAATATAAAAATAAAA
1800882 TAT
1 TAT
1800885 ATTATTATAT
Statistics
Matches: 21, Mismatches: 2, Indels: 3
0.81 0.08 0.12
Matches are distributed among these distances:
20 1 0.05
21 10 0.48
22 10 0.48
ACGTcount: A:0.60, C:0.00, G:0.00, T:0.40
Consensus pattern (20 bp):
TATTTAATATAAAAATAAAA
Found at i:1801357 original size:19 final size:17
Alignment explanation
Indices: 1801333--1801367 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 17
1801323 TTATATAATT
1801333 TATATTATATAAATATTAA
1 TATATT-TATAAA-ATTAA
1801352 TATATTTATAAAATTA
1 TATATTTATAAAATTA
1801368 TTTTATATTT
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
17 4 0.25
18 6 0.38
19 6 0.38
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (17 bp):
TATATTTATAAAATTAA
Found at i:1801374 original size:19 final size:19
Alignment explanation
Indices: 1801331--1801381 Score: 61
Period size: 19 Copynumber: 2.7 Consensus size: 19
1801321 TTTTATATAA
1801331 TTTATA-TTATATAAATAT
1 TTTATATTTATATAAATAT
*
1801349 TAATATATTTATA-AAATTAT
1 T-TTATATTTATATAAA-TAT
1801369 TTTATATTTATAT
1 TTTATATTTATAT
1801382 TATATTTTCA
Statistics
Matches: 27, Mismatches: 2, Indels: 6
0.77 0.06 0.17
Matches are distributed among these distances:
18 1 0.04
19 17 0.63
20 9 0.33
ACGTcount: A:0.43, C:0.00, G:0.00, T:0.57
Consensus pattern (19 bp):
TTTATATTTATATAAATAT
Found at i:1801384 original size:11 final size:11
Alignment explanation
Indices: 1801316--1801428 Score: 60
Period size: 11 Copynumber: 10.5 Consensus size: 11
1801306 ATTAGATTTC
*
1801316 TATATTTTTA-
1 TATATTTATAT
1801326 TATAATTTATAT
1 TAT-ATTTATAT
**
1801338 TATATAAATAT
1 TATATTTATAT
1801349 TAATATATT-TA-
1 T-ATAT-TTATAT
* * *
1801360 TAAAATTATTT
1 TATATTTATAT
1801371 TATATTTATAT
1 TATATTTATAT
1801382 TATATTT-TCAT
1 TATATTTAT-AT
*
1801393 TATTTTTTATAT
1 TA-TATTTATAT
1801405 TATA--TA-AT
1 TATATTTATAT
*
1801413 TATAATTATAT
1 TATATTTATAT
1801424 TATAT
1 TATAT
1801429 CTGAAATTAT
Statistics
Matches: 77, Mismatches: 14, Indels: 23
0.68 0.12 0.20
Matches are distributed among these distances:
8 6 0.08
9 4 0.05
10 9 0.12
11 40 0.52
12 17 0.22
13 1 0.01
ACGTcount: A:0.40, C:0.01, G:0.00, T:0.59
Consensus pattern (11 bp):
TATATTTATAT
Found at i:1802841 original size:13 final size:14
Alignment explanation
Indices: 1802823--1802857 Score: 54
Period size: 13 Copynumber: 2.5 Consensus size: 14
1802813 TAATATATAA
1802823 TAAATTTAAAT-TT
1 TAAATTTAAATATT
1802836 TAAATTTAAATATT
1 TAAATTTAAATATT
1802850 TATAATTT
1 TA-AATTT
1802858 TTTTATATCT
Statistics
Matches: 20, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
13 11 0.55
14 4 0.20
15 5 0.25
ACGTcount: A:0.46, C:0.00, G:0.00, T:0.54
Consensus pattern (14 bp):
TAAATTTAAATATT
Found at i:1804878 original size:18 final size:17
Alignment explanation
Indices: 1804855--1804897 Score: 50
Period size: 18 Copynumber: 2.5 Consensus size: 17
1804845 TAACTTAAAC
*
1804855 ATAAATTTAATAAATAT
1 ATAAATTTAATAAACAT
**
1804872 AATAAATAGAATAAACAT
1 -ATAAATTTAATAAACAT
1804890 ATAAATTT
1 ATAAATTT
1804898 TTATTTTGAA
Statistics
Matches: 20, Mismatches: 5, Indels: 1
0.77 0.19 0.04
Matches are distributed among these distances:
17 6 0.30
18 14 0.70
ACGTcount: A:0.60, C:0.02, G:0.02, T:0.35
Consensus pattern (17 bp):
ATAAATTTAATAAACAT
Found at i:1805365 original size:25 final size:25
Alignment explanation
Indices: 1805310--1805368 Score: 73
Period size: 25 Copynumber: 2.4 Consensus size: 25
1805300 AAAAATAATT
* *
1805310 AATATAAAATATAAATATATTAAAA
1 AATATAAATTATAAATAAATTAAAA
** *
1805335 TTTATAAATTATTAATAAATTAAAA
1 AATATAAATTATAAATAAATTAAAA
1805360 AATATAAAT
1 AATATAAAT
1805369 ACATATTATT
Statistics
Matches: 27, Mismatches: 7, Indels: 0
0.79 0.21 0.00
Matches are distributed among these distances:
25 27 1.00
ACGTcount: A:0.63, C:0.00, G:0.00, T:0.37
Consensus pattern (25 bp):
AATATAAATTATAAATAAATTAAAA
Found at i:1807387 original size:13 final size:14
Alignment explanation
Indices: 1807352--1807412 Score: 63
Period size: 14 Copynumber: 4.4 Consensus size: 14
1807342 TATTCGTATA
*
1807352 ATTTTATATAAATT
1 ATTTTATTTAAATT
1807366 ATTTATATTTAAATT
1 ATTT-TATTTAAATT
*
1807381 -TTTTATTT-ATTT
1 ATTTTATTTAAATT
*
1807393 AATTTTATTTAAAAT
1 -ATTTTATTTAAATT
1807408 ATTTT
1 ATTTT
1807413 TATGTCATTG
Statistics
Matches: 39, Mismatches: 4, Indels: 8
0.76 0.08 0.16
Matches are distributed among these distances:
12 3 0.08
13 5 0.13
14 20 0.51
15 11 0.28
ACGTcount: A:0.36, C:0.00, G:0.00, T:0.64
Consensus pattern (14 bp):
ATTTTATTTAAATT
Found at i:1807413 original size:15 final size:14
Alignment explanation
Indices: 1807353--1807415 Score: 56
Period size: 15 Copynumber: 4.4 Consensus size: 14
1807343 ATTCGTATAA
*
1807353 TTTTATATAAATTAT
1 TTTTATTTAAA-TAT
*
1807368 TTATATTTAAAT-T
1 TTTTATTTAAATAT
** *
1807381 TTTTATTTATTTAA
1 TTTTATTTAAATAT
1807395 TTTTATTTAAAATAT
1 TTTTATTT-AAATAT
1807410 TTTTAT
1 TTTTAT
1807416 GTCATTGTAT
Statistics
Matches: 37, Mismatches: 9, Indels: 4
0.74 0.18 0.08
Matches are distributed among these distances:
13 10 0.27
14 9 0.24
15 18 0.49
ACGTcount: A:0.35, C:0.00, G:0.00, T:0.65
Consensus pattern (14 bp):
TTTTATTTAAATAT
Found at i:1807438 original size:30 final size:27
Alignment explanation
Indices: 1807368--1807439 Score: 74
Period size: 30 Copynumber: 2.5 Consensus size: 27
1807358 TATAAATTAT
*
1807368 TTATATTTAAAT-TTTTTATTTATTTAA
1 TTATATTTAAATATTTTTATTCATTT-A
*
1807395 TTTTATTTAAAATATTTTTATGTCATTGTA
1 TTATATTT-AAATATTTTTAT-TCATT-TA
1807425 TTCATATTTAAATAT
1 TT-ATATTTAAATAT
1807440 AATAATTTTT
Statistics
Matches: 37, Mismatches: 3, Indels: 7
0.79 0.06 0.15
Matches are distributed among these distances:
27 7 0.19
28 4 0.11
29 7 0.19
30 13 0.35
31 6 0.16
ACGTcount: A:0.33, C:0.03, G:0.03, T:0.61
Consensus pattern (27 bp):
TTATATTTAAATATTTTTATTCATTTA
Found at i:1807555 original size:15 final size:15
Alignment explanation
Indices: 1807528--1807595 Score: 57
Period size: 16 Copynumber: 4.2 Consensus size: 15
1807518 TTTAACGTAA
1807528 TTATATTTAATATATT
1 TTATATTT-ATATATT
1807544 TTATATTTATATAAATTT
1 TTATATTTATAT--A-TT
*
1807562 TTATATATTA-ATAAT
1 TTATAT-TTATATATT
*
1807577 TTATATTTTATAAATT
1 TTATA-TTTATATATT
1807593 TTA
1 TTA
1807596 AATATGTATT
Statistics
Matches: 43, Mismatches: 3, Indels: 12
0.74 0.05 0.21
Matches are distributed among these distances:
15 13 0.30
16 16 0.37
17 1 0.02
18 10 0.23
19 3 0.07
ACGTcount: A:0.40, C:0.00, G:0.00, T:0.60
Consensus pattern (15 bp):
TTATATTTATATATT
Found at i:1807608 original size:35 final size:33
Alignment explanation
Indices: 1807528--1807594 Score: 102
Period size: 32 Copynumber: 2.0 Consensus size: 33
1807518 TTTAACGTAA
1807528 TTATAT-TTAATATATTTTATATTTATATAAATTT
1 TTATATATTAATA-A-TTTATATTTATATAAATTT
1807562 TTATATATTAATAATTTATATTT-TATAAATTT
1 TTATATATTAATAATTTATATTTATATAAATTT
1807594 T
1 T
1807595 AAATATGTAT
Statistics
Matches: 32, Mismatches: 0, Indels: 4
0.89 0.00 0.11
Matches are distributed among these distances:
32 10 0.31
33 9 0.28
34 7 0.22
35 6 0.19
ACGTcount: A:0.39, C:0.00, G:0.00, T:0.61
Consensus pattern (33 bp):
TTATATATTAATAATTTATATTTATATAAATTT
Found at i:1807651 original size:20 final size:19
Alignment explanation
Indices: 1807530--1807644 Score: 63
Period size: 19 Copynumber: 6.4 Consensus size: 19
1807520 TAACGTAATT
1807530 ATATT-TAATATATTTTAT-
1 ATATTATAA-ATATTTTATC
1807548 AT-TTATATAA-ATTTT-T-
1 ATATTATA-AATATTTTATC
* *
1807564 ATA-TATTAATAATTTAT-
1 ATATTATAAATATTTTATC
* *
1807581 ATTTTAT-AA-ATTTTA-A
1 ATATTATAAATATTTTATC
*
1807597 ATATGTATTAATATTTTATC
1 ATAT-TATAAATATTTTATC
*
1807617 ATATTTTAAATATTTTATC
1 ATATTATAAATATTTTATC
1807636 TATATTATA
1 -ATATTATA
1807645 TTTATTTAAT
Statistics
Matches: 76, Mismatches: 9, Indels: 22
0.71 0.08 0.21
Matches are distributed among these distances:
15 2 0.03
16 18 0.24
17 15 0.20
18 10 0.13
19 20 0.26
20 11 0.14
ACGTcount: A:0.40, C:0.02, G:0.01, T:0.57
Consensus pattern (19 bp):
ATATTATAAATATTTTATC
Found at i:1816522 original size:21 final size:21
Alignment explanation
Indices: 1816493--1816561 Score: 65
Period size: 21 Copynumber: 3.4 Consensus size: 21
1816483 GAATCAAATT
* *
1816493 TATATAATAAATTATACAAAA
1 TATAAAATAAATTATAAAAAA
**
1816514 TATAAAATAAATTA-AATACGA
1 TATAAAATAAATTATAA-AAAA
1816535 TA-AAAATAAATT-TAAAAAA
1 TATAAAATAAATTATAAAAAA
1816554 T-TAAAATA
1 TATAAAATA
1816562 TAATATGATA
Statistics
Matches: 39, Mismatches: 6, Indels: 8
0.74 0.11 0.15
Matches are distributed among these distances:
19 9 0.23
20 13 0.33
21 17 0.44
ACGTcount: A:0.65, C:0.03, G:0.01, T:0.30
Consensus pattern (21 bp):
TATAAAATAAATTATAAAAAA
Found at i:1817174 original size:3 final size:3
Alignment explanation
Indices: 1817166--1817212 Score: 94
Period size: 3 Copynumber: 15.7 Consensus size: 3
1817156 TTTAAATTAA
1817166 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AA
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AA
1817213 AGATGTAGGC
Statistics
Matches: 44, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 44 1.00
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.32
Consensus pattern (3 bp):
AAT
Found at i:1819643 original size:7 final size:7
Alignment explanation
Indices: 1819633--1819672 Score: 53
Period size: 7 Copynumber: 5.7 Consensus size: 7
1819623 AATTATGCAT
1819633 TATATAA
1 TATATAA
1819640 TATATAA
1 TATATAA
*
1819647 TATAAAA
1 TATATAA
*
1819654 TATATAT
1 TATATAA
*
1819661 TATATTA
1 TATATAA
1819668 TATAT
1 TATAT
1819673 TTTTAAATTA
Statistics
Matches: 28, Mismatches: 5, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
7 28 1.00
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (7 bp):
TATATAA
Found at i:1819670 original size:14 final size:14
Alignment explanation
Indices: 1819631--1819724 Score: 70
Period size: 14 Copynumber: 6.8 Consensus size: 14
1819621 ATAATTATGC
1819631 ATTATATAATATAT
1 ATTATATAATATAT
* *
1819645 AATATAAAATATAT
1 ATTATATAATATAT
*
1819659 ATTATATTATATAT
1 ATTATATAATATAT
*
1819673 -TTTTA-AATTATTAT
1 ATTATATAA-TA-TAT
*
1819687 ATTGATATAAT-TTT
1 ATT-ATATAATATAT
*
1819701 ATT-TATATTATAT
1 ATTATATAATATAT
*
1819714 ATAATATAATA
1 ATTATATAATA
1819725 AAAATAAAAT
Statistics
Matches: 60, Mismatches: 13, Indels: 14
0.69 0.15 0.16
Matches are distributed among these distances:
12 6 0.10
13 10 0.17
14 37 0.62
15 2 0.03
16 3 0.05
17 2 0.03
ACGTcount: A:0.47, C:0.00, G:0.01, T:0.52
Consensus pattern (14 bp):
ATTATATAATATAT
Found at i:1819684 original size:23 final size:20
Alignment explanation
Indices: 1819656--1819715 Score: 68
Period size: 23 Copynumber: 2.9 Consensus size: 20
1819646 ATATAAAATA
1819656 TATATTATATTATATATTTT
1 TATATTATATTATATATTTT
*
1819676 TAAATTATTATATTGATATAATTT
1 T--A-TATTATATT-ATATATTTT
1819700 TAT-TTATATTATATAT
1 TATATTATATTATATAT
1819716 AATATAATAA
Statistics
Matches: 34, Mismatches: 2, Indels: 9
0.76 0.04 0.20
Matches are distributed among these distances:
19 5 0.15
20 8 0.24
21 1 0.03
22 2 0.06
23 9 0.26
24 9 0.26
ACGTcount: A:0.38, C:0.00, G:0.02, T:0.60
Consensus pattern (20 bp):
TATATTATATTATATATTTT
Found at i:1821139 original size:15 final size:15
Alignment explanation
Indices: 1821119--1821151 Score: 57
Period size: 15 Copynumber: 2.2 Consensus size: 15
1821109 CTTGAGTTGA
*
1821119 AAATAATTTAAATTT
1 AAATAATTTAAAATT
1821134 AAATAATTTAAAATT
1 AAATAATTTAAAATT
1821149 AAA
1 AAA
1821152 ATAAGTATAA
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 17 1.00
ACGTcount: A:0.61, C:0.00, G:0.00, T:0.39
Consensus pattern (15 bp):
AAATAATTTAAAATT
Found at i:1821153 original size:16 final size:15
Alignment explanation
Indices: 1821118--1821155 Score: 58
Period size: 16 Copynumber: 2.5 Consensus size: 15
1821108 ACTTGAGTTG
1821118 AAAATAATTTAAATT
1 AAAATAATTTAAATT
*
1821133 TAAATAATTTAAAATT
1 AAAATAATTT-AAATT
1821149 AAAATAA
1 AAAATAA
1821156 GTATAATTTT
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
15 9 0.45
16 11 0.55
ACGTcount: A:0.63, C:0.00, G:0.00, T:0.37
Consensus pattern (15 bp):
AAAATAATTTAAATT
Found at i:1825378 original size:2 final size:2
Alignment explanation
Indices: 1825371--1825423 Score: 97
Period size: 2 Copynumber: 26.5 Consensus size: 2
1825361 AGGCTTAAGT
*
1825371 TA TA TA TA TG TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1825413 TA TA TA TA TA T
1 TA TA TA TA TA T
1825424 TAATTTAAAA
Statistics
Matches: 49, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
2 49 1.00
ACGTcount: A:0.47, C:0.00, G:0.02, T:0.51
Consensus pattern (2 bp):
TA
Found at i:1830560 original size:19 final size:18
Alignment explanation
Indices: 1830514--1830561 Score: 51
Period size: 19 Copynumber: 2.5 Consensus size: 18
1830504 TTAATTTACC
*
1830514 ATATCCATATCATTCTCTA
1 ATATCCA-ATCATTATCTA
*
1830533 ATGATCCAATGATTATCTCA
1 AT-ATCCAATCATTATCT-A
1830553 ATATCCAAT
1 ATATCCAAT
1830562 AATTTTGCAA
Statistics
Matches: 25, Mismatches: 2, Indels: 4
0.81 0.06 0.13
Matches are distributed among these distances:
19 17 0.68
20 8 0.32
ACGTcount: A:0.35, C:0.23, G:0.04, T:0.38
Consensus pattern (18 bp):
ATATCCAATCATTATCTA
Found at i:1831219 original size:33 final size:33
Alignment explanation
Indices: 1831177--1831277 Score: 193
Period size: 33 Copynumber: 3.1 Consensus size: 33
1831167 TTATCTTTTC
1831177 TTATTTTAAGAATTTATGAAGTCAAAAATATAA
1 TTATTTTAAGAATTTATGAAGTCAAAAATATAA
1831210 TTATTTTAAGAATTTATGAAGTCAAAAATATAA
1 TTATTTTAAGAATTTATGAAGTCAAAAATATAA
*
1831243 TTATTTTCAGAATTTATGAAGTCAAAAATATAA
1 TTATTTTAAGAATTTATGAAGTCAAAAATATAA
1831276 TT
1 TT
1831278 TTTCTTCAAA
Statistics
Matches: 67, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
33 67 1.00
ACGTcount: A:0.47, C:0.04, G:0.09, T:0.41
Consensus pattern (33 bp):
TTATTTTAAGAATTTATGAAGTCAAAAATATAA
Found at i:1831638 original size:2 final size:2
Alignment explanation
Indices: 1831631--1831656 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
1831621 TATTTTAATA
1831631 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
1831657 TTGCATAATA
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 24 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:1832876 original size:12 final size:12
Alignment explanation
Indices: 1832859--1832919 Score: 70
Period size: 12 Copynumber: 5.1 Consensus size: 12
1832849 ACCAGATTTC
*
1832859 AATATACATATA
1 AATATATATATA
1832871 AATATATATATA
1 AATATATATATA
*
1832883 TATATATATATA
1 AATATATATATA
*
1832895 TATATATATATA
1 AATATATATATA
*
1832907 TATAGTA-ATATA
1 AATA-TATATATA
1832919 A
1 A
1832920 GCTGATTAAT
Statistics
Matches: 45, Mismatches: 3, Indels: 2
0.90 0.06 0.04
Matches are distributed among these distances:
12 43 0.96
13 2 0.04
ACGTcount: A:0.54, C:0.02, G:0.02, T:0.43
Consensus pattern (12 bp):
AATATATATATA
Found at i:1832879 original size:2 final size:2
Alignment explanation
Indices: 1832860--1832910 Score: 84
Period size: 2 Copynumber: 25.5 Consensus size: 2
1832850 CCAGATTTCA
* *
1832860 AT AT AC AT AT AA 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
1832902 AT AT AT AT A
1 AT AT AT AT A
1832911 GTAATATAAG
Statistics
Matches: 45, Mismatches: 4, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
2 45 1.00
ACGTcount: A:0.53, C:0.02, G:0.00, T:0.45
Consensus pattern (2 bp):
AT
Found at i:1833187 original size:3 final size:3
Alignment explanation
Indices: 1833179--1833214 Score: 72
Period size: 3 Copynumber: 12.0 Consensus size: 3
1833169 CCAGATTGAG
1833179 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
1833215 AATGAATTTT
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 33 1.00
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (3 bp):
TAA
Found at i:1834683 original size:2 final size:2
Alignment explanation
Indices: 1834676--1834719 Score: 88
Period size: 2 Copynumber: 22.0 Consensus size: 2
1834666 AACAATCTGC
1834676 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
1834718 AT
1 AT
1834720 CAGATTTTCT
Statistics
Matches: 42, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 42 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:1839395 original size:19 final size:19
Alignment explanation
Indices: 1839360--1839411 Score: 61
Period size: 19 Copynumber: 2.7 Consensus size: 19
1839350 TGATAAAAAA
*
1839360 ATTAAT-TTTTTAAAAATTT
1 ATTAATATTTTT-AAATTTT
1839379 ATTAATCATTTTTAAATTTT
1 ATTAAT-ATTTTTAAATTTT
*
1839399 TTTAATATTTTTA
1 ATTAATATTTTTA
1839412 CCGACGGATG
Statistics
Matches: 29, Mismatches: 2, Indels: 4
0.83 0.06 0.11
Matches are distributed among these distances:
19 13 0.45
20 11 0.38
21 5 0.17
ACGTcount: A:0.37, C:0.02, G:0.00, T:0.62
Consensus pattern (19 bp):
ATTAATATTTTTAAATTTT
Found at i:1843586 original size:2 final size:2
Alignment explanation
Indices: 1843574--1843609 Score: 54
Period size: 2 Copynumber: 18.0 Consensus size: 2
1843564 TCAAGAGTAA
* *
1843574 AT AT GT AT AT AT AT AT AT AT AT AT AT AT AG AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1843610 GGAAACTCAA
Statistics
Matches: 30, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
2 30 1.00
ACGTcount: A:0.47, C:0.00, G:0.06, T:0.47
Consensus pattern (2 bp):
AT
Found at i:1844273 original size:20 final size:19
Alignment explanation
Indices: 1844250--1844319 Score: 63
Period size: 20 Copynumber: 3.6 Consensus size: 19
1844240 CCATATGTAT
*
1844250 ATTTTTATTAATTATTTAAT
1 ATTTTTATTAA-TATTTAAA
*
1844270 ATTTAT-TTAATA-TTAAA
1 ATTTTTATTAATATTTAAA
*
1844287 ATTATTTTTTAAATATTTAAA
1 ATT-TTTATT-AATATTTAAA
1844308 ATTTTTAATTAA
1 ATTTTT-ATTAA
1844320 ATCAATTGAT
Statistics
Matches: 41, Mismatches: 4, Indels: 10
0.75 0.07 0.18
Matches are distributed among these distances:
17 7 0.17
18 4 0.10
19 6 0.15
20 14 0.34
21 10 0.24
ACGTcount: A:0.41, C:0.00, G:0.00, T:0.59
Consensus pattern (19 bp):
ATTTTTATTAATATTTAAA
Found at i:1844320 original size:21 final size:20
Alignment explanation
Indices: 1844250--1844321 Score: 69
Period size: 21 Copynumber: 3.6 Consensus size: 20
1844240 CCATATGTAT
*
1844250 ATTTTTATTAATTATTT--A
1 ATTTTTATTAAATATTTAAA
* *
1844268 ATATTTATTTAATA-TTAAA
1 ATTTTTATTAAATATTTAAA
*
1844287 ATTATTTTTTAAATATTTAAA
1 ATT-TTTATTAAATATTTAAA
1844308 ATTTTTAATTAAAT
1 ATTTTT-ATTAAAT
1844322 CAATTGATCT
Statistics
Matches: 42, Mismatches: 7, Indels: 7
0.75 0.12 0.12
Matches are distributed among these distances:
17 2 0.05
18 11 0.26
19 3 0.07
20 12 0.29
21 14 0.33
ACGTcount: A:0.42, C:0.00, G:0.00, T:0.58
Consensus pattern (20 bp):
ATTTTTATTAAATATTTAAA
Found at i:1845542 original size:2 final size:2
Alignment explanation
Indices: 1845535--1845559 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
1845525 AGATTCCCCG
1845535 AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT A
1845560 GAATCAATTT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:1845758 original size:85 final size:85
Alignment explanation
Indices: 1845615--1845784 Score: 304
Period size: 85 Copynumber: 2.0 Consensus size: 85
1845605 TTGATTTGGA
* *
1845615 TACATCCTTGATTTGAAATCTTTGTGACTTCATAGAGTTTGGGTATTGATGTTGTATTTAAAATT
1 TACATCCTTGATTTGAAATCTTTGTGACTTCATAGAGTTTGGGAATTAATGTTGTATTTAAAATT
1845680 AAAGAAATGCTTACTTGGCT
66 AAAGAAATGCTTACTTGGCT
*
1845700 TACATCCTTGATTTGAAATCTTTGTGAGTTCATAGAGTTTGGGAATTAATGTTGTATTTAAAATT
1 TACATCCTTGATTTGAAATCTTTGTGACTTCATAGAGTTTGGGAATTAATGTTGTATTTAAAATT
*
1845765 AAAGAAATGCTTGCTTGGCT
66 AAAGAAATGCTTACTTGGCT
1845785 CAATCAATCT
Statistics
Matches: 81, Mismatches: 4, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
85 81 1.00
ACGTcount: A:0.29, C:0.10, G:0.19, T:0.42
Consensus pattern (85 bp):
TACATCCTTGATTTGAAATCTTTGTGACTTCATAGAGTTTGGGAATTAATGTTGTATTTAAAATT
AAAGAAATGCTTACTTGGCT
Found at i:1847452 original size:3 final size:3
Alignment explanation
Indices: 1847446--1847480 Score: 70
Period size: 3 Copynumber: 11.7 Consensus size: 3
1847436 TCTTTTTTCT
1847446 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TT
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TT
1847481 CTCTCCAACC
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 32 1.00
ACGTcount: A:0.31, C:0.00, G:0.00, T:0.69
Consensus pattern (3 bp):
TTA
Found at i:1848509 original size:25 final size:26
Alignment explanation
Indices: 1848459--1848523 Score: 80
Period size: 25 Copynumber: 2.5 Consensus size: 26
1848449 CGGTTTATAA
*
1848459 ATTTATATATTATTAATAAATTAAATC
1 ATTTATAT-TTATTAATAAATAAAATC
*
1848486 ATATTAT-TTTATTAA-AAATAAAATT
1 AT-TTATATTTATTAATAAATAAAATC
1848511 ATTTATATTTATT
1 ATTTATATTTATT
1848524 TTTAAAAATA
Statistics
Matches: 34, Mismatches: 2, Indels: 6
0.81 0.05 0.14
Matches are distributed among these distances:
24 4 0.12
25 16 0.47
26 7 0.21
27 3 0.09
28 4 0.12
ACGTcount: A:0.46, C:0.02, G:0.00, T:0.52
Consensus pattern (26 bp):
ATTTATATTTATTAATAAATAAAATC
Found at i:1850533 original size:11 final size:11
Alignment explanation
Indices: 1850517--1850614 Score: 64
Period size: 11 Copynumber: 8.8 Consensus size: 11
1850507 GATAATAATT
1850517 TATTTATATTA
1 TATTTATATTA
*
1850528 TATTTATTTTA
1 TATTTATATTA
1850539 TTATGTTATAATTA
1 -TAT-TTAT-ATTA
*
1850553 TATTT-TA-AA
1 TATTTATATTA
1850562 TATTTTATATT-
1 TA-TTTATATTA
1850573 TATTTA-ATT-
1 TATTTATATTA
1850582 T-TTTAAATATATA
1 TATTT--ATAT-TA
*
1850595 TTTTTATATTA
1 TATTTATATTA
1850606 TATTTATAT
1 TATTTATAT
1850615 AATTATATTT
Statistics
Matches: 70, Mismatches: 5, Indels: 24
0.71 0.05 0.24
Matches are distributed among these distances:
8 3 0.04
9 7 0.10
10 9 0.13
11 27 0.39
12 10 0.14
13 8 0.11
14 6 0.09
ACGTcount: A:0.35, C:0.00, G:0.01, T:0.64
Consensus pattern (11 bp):
TATTTATATTA
Found at i:1850600 original size:26 final size:29
Alignment explanation
Indices: 1850555--1850610 Score: 73
Period size: 27 Copynumber: 2.0 Consensus size: 29
1850545 TATAATTATA
*
1850555 TTTTAAATATTTTATATTTAT-TTA-ATT
1 TTTTAAATATTATATATTTATATTATATT
*
1850582 TTTTAAATA-TATATTTTTATATTATATT
1 TTTTAAATATTATATATTTATATTATATT
1850610 T
1 T
1850611 ATATAATTAT
Statistics
Matches: 25, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
26 9 0.36
27 12 0.48
28 4 0.16
ACGTcount: A:0.34, C:0.00, G:0.00, T:0.66
Consensus pattern (29 bp):
TTTTAAATATTATATATTTATATTATATT
Found at i:1850625 original size:14 final size:14
Alignment explanation
Indices: 1850545--1850625 Score: 64
Period size: 14 Copynumber: 6.0 Consensus size: 14
1850535 TTTATTATGT
1850545 TATAATTATATTTTA
1 TATAATTATA-TTTA
* *
1850560 AATATTTTATATTTA
1 TATA-ATTATATTTA
*
1850575 TTTAATT-T-TTTA
1 TATAATTATATTTA
* *
1850587 AAT-A-TATATTTT
1 TATAATTATATTTA
1850599 TAT-ATTATATTTA
1 TATAATTATATTTA
1850612 TATAATTATATTTA
1 TATAATTATATTTA
1850626 ATATTATTAA
Statistics
Matches: 51, Mismatches: 10, Indels: 11
0.71 0.14 0.15
Matches are distributed among these distances:
10 1 0.02
11 2 0.04
12 11 0.22
13 11 0.22
14 12 0.24
15 9 0.18
16 5 0.10
ACGTcount: A:0.38, C:0.00, G:0.00, T:0.62
Consensus pattern (14 bp):
TATAATTATATTTA
Found at i:1852279 original size:13 final size:13
Alignment explanation
Indices: 1852261--1852287 Score: 54
Period size: 13 Copynumber: 2.1 Consensus size: 13
1852251 AAAAAGCAGT
1852261 TGTGAAGATTGAA
1 TGTGAAGATTGAA
1852274 TGTGAAGATTGAA
1 TGTGAAGATTGAA
1852287 T
1 T
1852288 AAGAACAAAA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 14 1.00
ACGTcount: A:0.37, C:0.00, G:0.30, T:0.33
Consensus pattern (13 bp):
TGTGAAGATTGAA
Found at i:1853320 original size:29 final size:27
Alignment explanation
Indices: 1853282--1853353 Score: 74
Period size: 29 Copynumber: 2.6 Consensus size: 27
1853272 TTTAAATTAA
*
1853282 ATTAAATTAAATATTTTAAAAAATAATTT
1 ATTATATTAAATATTTT-AAAAATAA-TT
* * *
1853311 ATTATTTTAAATAATATTAAAAATTATT
1 ATTATATTAAAT-ATTTTAAAAATAATT
1853339 ATTATATT-AATATTT
1 ATTATATTAAATATTT
1853354 ATAATTAAAT
Statistics
Matches: 36, Mismatches: 6, Indels: 5
0.77 0.13 0.11
Matches are distributed among these distances:
26 3 0.08
27 3 0.08
28 9 0.25
29 17 0.47
30 4 0.11
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (27 bp):
ATTATATTAAATATTTTAAAAATAATT
Found at i:1853727 original size:2 final size:2
Alignment explanation
Indices: 1853720--1853750 Score: 53
Period size: 2 Copynumber: 15.5 Consensus size: 2
1853710 TCCCTCTACA
*
1853720 TC TC TC TC TC TC TC TC TC TC TC TC TT TC TC T
1 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC T
1853751 TCCTCTGGCT
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:0.00, C:0.45, G:0.00, T:0.55
Consensus pattern (2 bp):
TC
Found at i:1864116 original size:24 final size:25
Alignment explanation
Indices: 1864076--1864139 Score: 76
Period size: 24 Copynumber: 2.6 Consensus size: 25
1864066 TTAAGAATTG
* *
1864076 AATATAAAGATATAATTTTTAAAAA
1 AATATAAAAATATAATTTATAAAAA
* *
1864101 ATTTTAAAAATA-AATTTATAAAAA
1 AATATAAAAATATAATTTATAAAAA
*
1864125 AATATAAAAAAATAA
1 AATATAAAAATATAA
1864140 ATTCATATTC
Statistics
Matches: 31, Mismatches: 7, Indels: 2
0.77 0.17 0.05
Matches are distributed among these distances:
24 20 0.65
25 11 0.35
ACGTcount: A:0.66, C:0.00, G:0.02, T:0.33
Consensus pattern (25 bp):
AATATAAAAATATAATTTATAAAAA
Found at i:1865824 original size:23 final size:20
Alignment explanation
Indices: 1865774--1865825 Score: 52
Period size: 21 Copynumber: 2.5 Consensus size: 20
1865764 ATATTAATTA
1865774 TTAAA-AAATATATATAAAT
1 TTAAACAAATATATATAAAT
*
1865793 ATAATACAAATATATATATATATT
1 TTAA-ACAAATATATATA-A-A-T
1865817 TTAAACAAA
1 TTAAACAAA
1865826 ATGAAAAATA
Statistics
Matches: 26, Mismatches: 2, Indels: 6
0.76 0.06 0.18
Matches are distributed among these distances:
19 3 0.12
20 1 0.04
21 11 0.42
22 1 0.04
23 6 0.23
24 4 0.15
ACGTcount: A:0.60, C:0.04, G:0.00, T:0.37
Consensus pattern (20 bp):
TTAAACAAATATATATAAAT
Found at i:1867052 original size:32 final size:32
Alignment explanation
Indices: 1867011--1867127 Score: 146
Period size: 32 Copynumber: 3.7 Consensus size: 32
1867001 GTTAGATAAG
*
1867011 ATATTTTATAATTTA-AGTAAAATTTGAGTAAA
1 ATATTTTATAATTTAGA-TTAAATTTGAGTAAA
* *
1867043 ATATTTTATAATTTAGATTGAGTTTGAGTAAA
1 ATATTTTATAATTTAGATTAAATTTGAGTAAA
* * * *
1867075 ATATTTTGTAGTTTTGATTAAATTTGAGGAAA
1 ATATTTTATAATTTAGATTAAATTTGAGTAAA
*
1867107 ATATTTTATAATTTAAATTAA
1 ATATTTTATAATTTAGATTAA
1867128 TCATATTCAA
Statistics
Matches: 71, Mismatches: 13, Indels: 2
0.83 0.15 0.02
Matches are distributed among these distances:
32 70 0.99
33 1 0.01
ACGTcount: A:0.41, C:0.00, G:0.12, T:0.47
Consensus pattern (32 bp):
ATATTTTATAATTTAGATTAAATTTGAGTAAA
Found at i:1868502 original size:2 final size:2
Alignment explanation
Indices: 1868495--1868528 Score: 68
Period size: 2 Copynumber: 17.0 Consensus size: 2
1868485 TTCTTTGTAC
1868495 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
1868529 GTATCATCAA
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 32 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:1869157 original size:2 final size:2
Alignment explanation
Indices: 1869150--1869186 Score: 74
Period size: 2 Copynumber: 18.5 Consensus size: 2
1869140 ATTCATGTTT
1869150 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
1869187 TGTAAACTGA
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:1869950 original size:18 final size:18
Alignment explanation
Indices: 1869929--1869981 Score: 56
Period size: 18 Copynumber: 2.9 Consensus size: 18
1869919 AAAATAAACC
1869929 AAAAGAGAAA-AAAAAAAA
1 AAAAGA-AAAGAAAAAAAA
*
1869947 AAAAGAAAAGAAAAGAAA
1 AAAAGAAAAGAAAAAAAA
*
1869965 AGAAG-AAAGAAAGAAAA
1 AAAAGAAAAGAAA-AAAA
1869982 CTAAACGAAA
Statistics
Matches: 30, Mismatches: 3, Indels: 4
0.81 0.08 0.11
Matches are distributed among these distances:
17 10 0.33
18 20 0.67
ACGTcount: A:0.83, C:0.00, G:0.17, T:0.00
Consensus pattern (18 bp):
AAAAGAAAAGAAAAAAAA
Found at i:1869966 original size:5 final size:5
Alignment explanation
Indices: 1869929--1869981 Score: 51
Period size: 5 Copynumber: 10.8 Consensus size: 5
1869919 AAAATAAACC
1869929 AAAAG AGAAA- AAAA- AAAA- AAAAG AAAAG AAAAG AAAAG AAGAA- AGAAAG
1 AAAAG A-AAAG AAAAG AAAAG AAAAG AAAAG AAAAG AAAAG AA-AAG A-AAAG
1869978 AAAA
1 AAAA
1869982 CTAAACGAAA
Statistics
Matches: 43, Mismatches: 0, Indels: 10
0.81 0.00 0.19
Matches are distributed among these distances:
4 11 0.26
5 25 0.58
6 7 0.16
ACGTcount: A:0.83, C:0.00, G:0.17, T:0.00
Consensus pattern (5 bp):
AAAAG
Found at i:1869977 original size:16 final size:16
Alignment explanation
Indices: 1869929--1869981 Score: 54
Period size: 16 Copynumber: 3.2 Consensus size: 16
1869919 AAAATAAACC
* *
1869929 AAAAG-AGAAAAAAAA
1 AAAAGAAGAAAGAAAG
*
1869944 AAAAAAAGAAAAGAAAAG
1 AAAAGAAG-AAAG-AAAG
1869962 AAAAGAAGAAAGAAAG
1 AAAAGAAGAAAGAAAG
1869978 AAAA
1 AAAA
1869982 CTAAACGAAA
Statistics
Matches: 31, Mismatches: 4, Indels: 5
0.77 0.10 0.12
Matches are distributed among these distances:
15 4 0.13
16 10 0.32
17 7 0.23
18 10 0.32
ACGTcount: A:0.83, C:0.00, G:0.17, T:0.00
Consensus pattern (16 bp):
AAAAGAAGAAAGAAAG
Found at i:1875906 original size:17 final size:16
Alignment explanation
Indices: 1875884--1875917 Score: 50
Period size: 16 Copynumber: 2.1 Consensus size: 16
1875874 TAATCACTTG
1875884 ATAAACAATAATATTTA
1 ATAAAC-ATAATATTTA
*
1875901 ATAAACTTAATATTTA
1 ATAAACATAATATTTA
1875917 A
1 A
1875918 ATTTTAATAT
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
16 10 0.62
17 6 0.38
ACGTcount: A:0.56, C:0.06, G:0.00, T:0.38
Consensus pattern (16 bp):
ATAAACATAATATTTA
Found at i:1879244 original size:6 final size:6
Alignment explanation
Indices: 1879233--1879301 Score: 63
Period size: 6 Copynumber: 11.3 Consensus size: 6
1879223 ATAATTGTAT
* *
1879233 AATATA AATAT- AATAT- AATAAA AATAATTA ATATAAA AATATA TAATATA
1 AATATA AATATA AATATA AATATA AAT-A-TA A-ATATA AATATA -AATATA
1879283 AATAT- AATATA AATATA AA
1 AATATA AATATA AATATA AA
1879302 AATGATCAAA
Statistics
Matches: 53, Mismatches: 4, Indels: 12
0.77 0.06 0.17
Matches are distributed among these distances:
5 14 0.26
6 25 0.47
7 9 0.17
8 3 0.06
9 2 0.04
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (6 bp):
AATATA
Found at i:1879246 original size:11 final size:11
Alignment explanation
Indices: 1879230--1879300 Score: 76
Period size: 11 Copynumber: 6.5 Consensus size: 11
1879220 GATATAATTG
1879230 TATAATATAAA
1 TATAATATAAA
1879241 TATAATAT-AA
1 TATAATATAAA
* *
1879251 TAAAAATAATTAA
1 T-ATAAT-ATAAA
1879264 TATAA-A-AATA
1 TATAATATAA-A
1879274 TATAATATAAA
1 TATAATATAAA
1879285 TATAATATAAA
1 TATAATATAAA
1879296 TATAA
1 TATAA
1879301 AAATGATCAA
Statistics
Matches: 51, Mismatches: 3, Indels: 12
0.77 0.05 0.18
Matches are distributed among these distances:
9 1 0.02
10 10 0.20
11 30 0.59
12 7 0.14
13 3 0.06
ACGTcount: A:0.65, C:0.00, G:0.00, T:0.35
Consensus pattern (11 bp):
TATAATATAAA
Found at i:1880847 original size:16 final size:17
Alignment explanation
Indices: 1880821--1880852 Score: 57
Period size: 16 Copynumber: 1.9 Consensus size: 17
1880811 AACACACATT
1880821 ATAATAATTAAATTTAA
1 ATAATAATTAAATTTAA
1880838 ATAA-AATTAAATTTA
1 ATAATAATTAAATTTA
1880853 TTAATTAAAT
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
16 11 0.73
17 4 0.27
ACGTcount: A:0.59, C:0.00, G:0.00, T:0.41
Consensus pattern (17 bp):
ATAATAATTAAATTTAA
Found at i:1881232 original size:16 final size:16
Alignment explanation
Indices: 1881181--1881234 Score: 51
Period size: 16 Copynumber: 3.5 Consensus size: 16
1881171 ATAAATATAT
*
1881181 ATAAATATTAAAA--A
1 ATAAAAATTAAAATTA
* *
1881195 ATAAAAATTATCATTTA
1 ATAAAAATTA-AAATTA
1881212 A-AAAAATTAAAATTA
1 ATAAAAATTAAAATTA
1881227 ATAAAAAT
1 ATAAAAAT
1881235 ATTTTTATTA
Statistics
Matches: 31, Mismatches: 5, Indels: 6
0.74 0.12 0.14
Matches are distributed among these distances:
14 9 0.29
15 6 0.19
16 14 0.45
17 2 0.06
ACGTcount: A:0.67, C:0.02, G:0.00, T:0.31
Consensus pattern (16 bp):
ATAAAAATTAAAATTA
Found at i:1882301 original size:2 final size:2
Alignment explanation
Indices: 1882294--1882334 Score: 82
Period size: 2 Copynumber: 20.5 Consensus size: 2
1882284 AGTGATGCGA
1882294 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
1882335 ACAGAACTAA
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:1883557 original size:2 final size:2
Alignment explanation
Indices: 1883550--1883589 Score: 80
Period size: 2 Copynumber: 20.0 Consensus size: 2
1883540 TGTTTTTATT
1883550 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC
1 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC
1883590 CTTTGATTTG
Statistics
Matches: 38, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 38 1.00
ACGTcount: A:0.00, C:0.50, G:0.00, T:0.50
Consensus pattern (2 bp):
TC
Found at i:1886824 original size:16 final size:16
Alignment explanation
Indices: 1886779--1886827 Score: 55
Period size: 16 Copynumber: 3.1 Consensus size: 16
1886769 ATAATTATAT
*
1886779 ATTTATATAAATTTTA
1 ATTTATATAAAATTTA
*
1886795 ATATAT-TAATAATTTA
1 ATTTATATAA-AATTTA
*
1886811 TTTTATATAAAATTTA
1 ATTTATATAAAATTTA
1886827 A
1 A
1886828 CACATATATA
Statistics
Matches: 26, Mismatches: 5, Indels: 4
0.74 0.14 0.11
Matches are distributed among these distances:
15 3 0.12
16 20 0.77
17 3 0.12
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (16 bp):
ATTTATATAAAATTTA
Found at i:1892638 original size:15 final size:15
Alignment explanation
Indices: 1892618--1892646 Score: 58
Period size: 15 Copynumber: 1.9 Consensus size: 15
1892608 AGCCATCTAA
1892618 AACAACAACAAGAAC
1 AACAACAACAAGAAC
1892633 AACAACAACAAGAA
1 AACAACAACAAGAA
1892647 ATTTAGAAAT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.69, C:0.24, G:0.07, T:0.00
Consensus pattern (15 bp):
AACAACAACAAGAAC
Found at i:1893164 original size:18 final size:19
Alignment explanation
Indices: 1893133--1893175 Score: 61
Period size: 18 Copynumber: 2.3 Consensus size: 19
1893123 ACACAGTTAG
1893133 ATAAAATATAATTATAATA
1 ATAAAATATAATTATAATA
**
1893152 ATAAAAT-TAATTATTTTA
1 ATAAAATATAATTATAATA
1893170 ATAAAA
1 ATAAAA
1893176 AAAAGTTTTG
Statistics
Matches: 22, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
18 15 0.68
19 7 0.32
ACGTcount: A:0.60, C:0.00, G:0.00, T:0.40
Consensus pattern (19 bp):
ATAAAATATAATTATAATA
Found at i:1893299 original size:17 final size:14
Alignment explanation
Indices: 1893258--1893310 Score: 54
Period size: 13 Copynumber: 3.6 Consensus size: 14
1893248 TAAGTTAACA
*
1893258 TAAAAATAAT-TAT
1 TAAAAATATTATAT
1893271 TAAAAATATTATAT
1 TAAAAATATTATAT
1893285 TAAAAAGTTATTTATAAT
1 TAAAAA--TA-TTAT-AT
1893303 TAAAAATA
1 TAAAAATA
1893311 ATATTTTTAT
Statistics
Matches: 34, Mismatches: 1, Indels: 7
0.81 0.02 0.17
Matches are distributed among these distances:
13 9 0.26
14 9 0.26
16 4 0.12
17 4 0.12
18 8 0.24
ACGTcount: A:0.58, C:0.00, G:0.02, T:0.40
Consensus pattern (14 bp):
TAAAAATATTATAT
Found at i:1893352 original size:16 final size:17
Alignment explanation
Indices: 1893305--1893353 Score: 55
Period size: 16 Copynumber: 2.9 Consensus size: 17
1893295 TTTATAATTA
1893305 AAAATAATATTTTTATAT
1 AAAATAATA-TTTTATAT
* * *
1893323 AAATTAAAACTTTA-AT
1 AAAATAATATTTTATAT
1893339 AAAATAATATTTTAT
1 AAAATAATATTTTAT
1893354 TCTTATTATC
Statistics
Matches: 24, Mismatches: 6, Indels: 3
0.73 0.18 0.09
Matches are distributed among these distances:
16 13 0.54
17 4 0.17
18 7 0.29
ACGTcount: A:0.53, C:0.02, G:0.00, T:0.45
Consensus pattern (17 bp):
AAAATAATATTTTATAT
Found at i:1894356 original size:2 final size:2
Alignment explanation
Indices: 1894349--1894387 Score: 78
Period size: 2 Copynumber: 19.5 Consensus size: 2
1894339 TATTTTTCAA
1894349 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1894388 AACTCATTTT
Statistics
Matches: 37, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 37 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:1895310 original size:11 final size:11
Alignment explanation
Indices: 1895294--1895330 Score: 56
Period size: 11 Copynumber: 3.3 Consensus size: 11
1895284 AATAAATATG
1895294 ATAATATAAAT
1 ATAATATAAAT
*
1895305 ATAATATAAAAA
1 ATAATAT-AAAT
1895317 ATAATATAAAT
1 ATAATATAAAT
1895328 ATA
1 ATA
1895331 TAAATATTTT
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
11 13 0.57
12 10 0.43
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.32
Consensus pattern (11 bp):
ATAATATAAAT
Found at i:1895310 original size:23 final size:23
Alignment explanation
Indices: 1895284--1895337 Score: 67
Period size: 23 Copynumber: 2.4 Consensus size: 23
1895274 ATGAAACTTG
*
1895284 AATAAATATGATAATATAAATAT
1 AATAAATATAATAATATAAATAT
*
1895307 AATATAA-AAAATAATATAAATAT
1 AATA-AATATAATAATATAAATAT
1895330 -ATAAATAT
1 AATAAATAT
1895338 TTTAAATTTT
Statistics
Matches: 26, Mismatches: 3, Indels: 5
0.76 0.09 0.15
Matches are distributed among these distances:
21 2 0.08
22 4 0.15
23 18 0.69
24 2 0.08
ACGTcount: A:0.65, C:0.00, G:0.02, T:0.33
Consensus pattern (23 bp):
AATAAATATAATAATATAAATAT
Found at i:1895337 original size:14 final size:12
Alignment explanation
Indices: 1895294--1895333 Score: 55
Period size: 12 Copynumber: 3.3 Consensus size: 12
1895284 AATAAATATG
1895294 ATAATAT-AAAT
1 ATAATATAAAAT
*
1895305 ATAATATAAAAA
1 ATAATATAAAAT
1895317 ATAATATAAATAT
1 ATAATATAAA-AT
1895330 ATAA
1 ATAA
1895334 ATATTTTAAA
Statistics
Matches: 25, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
11 7 0.28
12 13 0.52
13 5 0.20
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.33
Consensus pattern (12 bp):
ATAATATAAAAT
Found at i:1898970 original size:16 final size:16
Alignment explanation
Indices: 1898945--1898987 Score: 52
Period size: 16 Copynumber: 2.7 Consensus size: 16
1898935 AATAGAGTTT
*
1898945 AATATT-AAAATAATA
1 AATATTAAAAATAAAA
*
1898960 TATATTAAAAATAAAA
1 AATATTAAAAATAAAA
1898976 AATAATTAAAAA
1 AAT-ATTAAAAA
1898988 ATATGATAAT
Statistics
Matches: 23, Mismatches: 3, Indels: 2
0.82 0.11 0.07
Matches are distributed among these distances:
15 5 0.22
16 10 0.43
17 8 0.35
ACGTcount: A:0.70, C:0.00, G:0.00, T:0.30
Consensus pattern (16 bp):
AATATTAAAAATAAAA
Found at i:1899940 original size:6 final size:6
Alignment explanation
Indices: 1899929--1899953 Score: 50
Period size: 6 Copynumber: 4.2 Consensus size: 6
1899919 TTAAATAAAG
1899929 TTTATT TTTATT TTTATT TTTATT T
1 TTTATT TTTATT TTTATT TTTATT T
1899954 AAATAAATTA
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 19 1.00
ACGTcount: A:0.16, C:0.00, G:0.00, T:0.84
Consensus pattern (6 bp):
TTTATT
Found at i:1899943 original size:33 final size:34
Alignment explanation
Indices: 1899907--1899970 Score: 96
Period size: 33 Copynumber: 1.9 Consensus size: 34
1899897 CTGTCTTAGT
1899907 TTTTTA-TTATATTTAAATAAAGT-TTATTTTTA
1 TTTTTATTTATATTTAAATAAAGTATTATTTTTA
* *
1899939 TTTTTATTTTTATTTAAATAAATTATTATTTT
1 TTTTTATTTATATTTAAATAAAGTATTATTTT
1899971 AAATAAAATG
Statistics
Matches: 28, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
32 6 0.21
33 15 0.54
34 7 0.25
ACGTcount: A:0.33, C:0.00, G:0.02, T:0.66
Consensus pattern (34 bp):
TTTTTATTTATATTTAAATAAAGTATTATTTTTA
Found at i:1899967 original size:16 final size:15
Alignment explanation
Indices: 1899946--1900014 Score: 66
Period size: 16 Copynumber: 4.2 Consensus size: 15
1899936 TTATTTTTAT
1899946 TTTTATTTAAATAAA
1 TTTTATTTAAATAAA
1899961 TTATTATTTTAAATAAAA
1 TT-TTA-TTTAAAT-AAA
**
1899979 TGTTTATTTATGTAAGA
1 T-TTTATTTAAATAA-A
1899996 TTTTATTTAAATATAA
1 TTTTATTTAAATA-AA
1900012 TTT
1 TTT
1900015 AAAATAAAAA
Statistics
Matches: 44, Mismatches: 4, Indels: 11
0.75 0.07 0.19
Matches are distributed among these distances:
15 2 0.05
16 19 0.43
17 15 0.34
18 7 0.16
19 1 0.02
ACGTcount: A:0.41, C:0.00, G:0.04, T:0.55
Consensus pattern (15 bp):
TTTTATTTAAATAAA
Found at i:1899988 original size:17 final size:16
Alignment explanation
Indices: 1899946--1900034 Score: 71
Period size: 17 Copynumber: 5.6 Consensus size: 16
1899936 TTATTTTTAT
1899946 TTTTATTTAAAT-AAA
1 TTTTATTTAAATAAAA
1899961 TTATTATTTTAAATAAAA
1 TT-TTA-TTTAAATAAAA
** *
1899979 TGTTTATTTATGTAAGA
1 T-TTTATTTAAATAAAA
*
1899996 TTTTATTTAAATATAA
1 TTTTATTTAAATAAAA
1900012 -TTTA---AAATAAAAA
1 TTTTATTTAAAT-AAAA
1900025 TTTTATTTAA
1 TTTTATTTAA
1900035 TAATAAAATA
Statistics
Matches: 57, Mismatches: 8, Indels: 16
0.70 0.10 0.20
Matches are distributed among these distances:
12 4 0.07
13 3 0.05
14 4 0.07
15 6 0.11
16 14 0.25
17 18 0.32
18 7 0.12
19 1 0.02
ACGTcount: A:0.45, C:0.00, G:0.03, T:0.52
Consensus pattern (16 bp):
TTTTATTTAAATAAAA
Found at i:1900027 original size:29 final size:30
Alignment explanation
Indices: 1899995--1900065 Score: 83
Period size: 32 Copynumber: 2.4 Consensus size: 30
1899985 TTTATGTAAG
* *
1899995 ATTTTATTTAAATATAAT-TTAAAATAAAA
1 ATTTTATTTAAATAAAATAATAAAATAAAA
*
1900024 ATTTTATTTAATAATAAAATAATAAAATATAA
1 ATTTTATTT-A-AATAAAATAATAAAATAAAA
1900056 ATTTT-TTTAA
1 ATTTTATTTAA
1900066 TATTTTCACA
Statistics
Matches: 36, Mismatches: 3, Indels: 6
0.80 0.07 0.13
Matches are distributed among these distances:
29 10 0.28
30 2 0.06
31 10 0.28
32 14 0.39
ACGTcount: A:0.54, C:0.00, G:0.00, T:0.46
Consensus pattern (30 bp):
ATTTTATTTAAATAAAATAATAAAATAAAA
Found at i:1900229 original size:19 final size:19
Alignment explanation
Indices: 1900207--1900274 Score: 79
Period size: 19 Copynumber: 3.6 Consensus size: 19
1900197 TATAATTGAA
1900207 ATATTTATATATTTATATT
1 ATATTTATATATTTATATT
1900226 ATATTTATATATTT-TATT
1 ATATTTATATATTTATATT
**
1900244 ATA-TTATA-ATTATTATAAA
1 ATATTTATATA-T-TTATATT
1900263 ATATTTATATAT
1 ATATTTATATAT
1900275 AAAAATTTTA
Statistics
Matches: 42, Mismatches: 2, Indels: 9
0.79 0.04 0.17
Matches are distributed among these distances:
16 1 0.02
17 6 0.14
18 9 0.21
19 19 0.45
20 6 0.14
21 1 0.02
ACGTcount: A:0.41, C:0.00, G:0.00, T:0.59
Consensus pattern (19 bp):
ATATTTATATATTTATATT
Found at i:1900288 original size:16 final size:15
Alignment explanation
Indices: 1900260--1900316 Score: 53
Period size: 16 Copynumber: 3.6 Consensus size: 15
1900250 TAATTATTAT
1900260 AAAATATTTATATATA
1 AAAAT-TTTATATATA
1900276 AAAATTTTAATATATTA
1 AAAATTTT-ATATA-TA
**
1900293 TTAA-TTTATATTATA
1 AAAATTTTATA-TATA
1900308 AAAATTTTA
1 AAAATTTTA
1900317 AAATATATAT
Statistics
Matches: 33, Mismatches: 4, Indels: 8
0.73 0.09 0.18
Matches are distributed among these distances:
15 10 0.30
16 19 0.58
17 4 0.12
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (15 bp):
AAAATTTTATATATA
Found at i:1900338 original size:34 final size:32
Alignment explanation
Indices: 1900265--1900336 Score: 107
Period size: 32 Copynumber: 2.4 Consensus size: 32
1900255 ATTATAAAAT
*
1900265 ATTTATA-TATAAAAATTTTAATATATTATTA
1 ATTTATATTATAAAAATTTTAAAATATTATTA
1900296 ATTTATATTATAAAAATTTTAAAATA-TA-T-
1 ATTTATATTATAAAAATTTTAAAATATTATTA
1900325 ATTTATATTATA
1 ATTTATATTATA
1900337 TTTTATTATG
Statistics
Matches: 39, Mismatches: 1, Indels: 4
0.89 0.02 0.09
Matches are distributed among these distances:
29 12 0.31
30 1 0.03
31 9 0.23
32 17 0.44
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (32 bp):
ATTTATATTATAAAAATTTTAAAATATTATTA
Found at i:1901983 original size:15 final size:15
Alignment explanation
Indices: 1901958--1902278 Score: 89
Period size: 16 Copynumber: 20.3 Consensus size: 15
1901948 CAGCGAATCC
1901958 AATTAATTTTAAATTA
1 AATT-ATTTTAAATTA
*
1901974 AATTATTTTATATTTTTA
1 AATTATTTTA-A--ATTA
1901992 AATTTAAATTTTTAAATTTTA
1 AA-TT--A-TTTTAAA--TTA
*
1902013 TATTATTTTAAATTTA
1 AATTATTTTAAA-TTA
*
1902029 AATTATTTTAATTTTA
1 AATTATTTTAA-ATTA
* *
1902045 AATAATTTAAATTTATATA
1 AATTATTTTAA---AT-TA
*
1902064 AATTAAATTTAACATATA
1 AATT-ATTTTAA-AT-TA
*
1902082 AATTA-ATTAAATTCAA
1 AATTATTTTAAATT--A
** *
1902098 AAAAATTTTATATTCA
1 AATTATTTTAAATT-A
1902114 AATTATTTTAAA-TA
1 AATTATTTTAAATTA
*
1902128 AATTA-ATTAAATTTA
1 AATTATTTTAAA-TTA
1902143 AA--A-TTTAAATT-
1 AATTATTTTAAATTA
1902154 AATTAATTTTAAATT-
1 AATT-ATTTTAAATTA
1902169 AATTAATTTTAATATTTA
1 AATT-ATTTTAA-A-TTA
* * *
1902187 GATGTA--TCAAATTT
1 AAT-TATTTTAAATTA
1902201 AA-TATTTTAAATATA
1 AATTATTTTAAAT-TA
1902216 AATTATTTTAAATT-
1 AATTATTTTAAATTA
*
1902230 AATTA-GTTAAATT-
1 AATTATTTTAAATTA
*
1902243 -ATTAATTTTAAAAT-
1 AATT-ATTTTAAATTA
*
1902257 AATTAATTTTTTAATTA
1 AATT-A-TTTTAAATTA
1902274 AATTA
1 AATTA
1902279 AATTAAAATT
Statistics
Matches: 235, Mismatches: 34, Indels: 72
0.69 0.10 0.21
Matches are distributed among these distances:
11 2 0.01
12 7 0.03
13 19 0.08
14 27 0.11
15 43 0.18
16 71 0.30
17 20 0.09
18 20 0.09
19 8 0.03
20 7 0.03
21 6 0.03
22 5 0.02
ACGTcount: A:0.47, C:0.01, G:0.01, T:0.51
Consensus pattern (15 bp):
AATTATTTTAAATTA
Found at i:1902025 original size:31 final size:31
Alignment explanation
Indices: 1901978--1902073 Score: 115
Period size: 31 Copynumber: 3.1 Consensus size: 31
1901968 AAATTAAATT
1901978 ATTTTATAT-TTTTAAATTTAAATT-TTTAA
1 ATTTTATATATTTTAAATTTAAATTATTTAA
*
1902007 ATTTTATATTATTTTAAATTTAAATTATTTTA
1 ATTTTATA-TATTTTAAATTTAAATTATTTAA
* * * * *
1902039 ATTTTAAATAATTTAAATTTATATAAATTAA
1 ATTTTATATATTTTAAATTTAAATTATTTAA
1902070 ATTT
1 ATTT
1902074 AACATATAAA
Statistics
Matches: 57, Mismatches: 7, Indels: 4
0.84 0.10 0.06
Matches are distributed among these distances:
29 8 0.14
30 1 0.02
31 37 0.65
32 11 0.19
ACGTcount: A:0.42, C:0.00, G:0.00, T:0.58
Consensus pattern (31 bp):
ATTTTATATATTTTAAATTTAAATTATTTAA
Found at i:1902141 original size:36 final size:36
Alignment explanation
Indices: 1902082--1902184 Score: 86
Period size: 36 Copynumber: 2.8 Consensus size: 36
1902072 TTAACATATA
**
1902082 AATTAAT-TAAATTCAAAAAAATTTTATATTCAAATT
1 AATTAATATAAATT-AATTAAATTTTATATTCAAATT
* * * *
1902118 ATTTTAA-ATAAATTAATTAAATTTAAAATTTAAATT
1 A-ATTAATATAAATTAATTAAATTTTATATTCAAATT
*
1902154 AATTAATTTTAAATTAATT-AATTTTAATATT
1 AATTAA-TATAAATTAATTAAATTTT-ATATT
1902185 TAGATGTATC
Statistics
Matches: 52, Mismatches: 10, Indels: 9
0.73 0.14 0.13
Matches are distributed among these distances:
35 4 0.08
36 24 0.46
37 24 0.46
ACGTcount: A:0.50, C:0.02, G:0.00, T:0.48
Consensus pattern (36 bp):
AATTAATATAAATTAATTAAATTTTATATTCAAATT
Found at i:1902154 original size:22 final size:22
Alignment explanation
Indices: 1902048--1902166 Score: 77
Period size: 22 Copynumber: 5.4 Consensus size: 22
1902038 AATTTTAAAT
* *
1902048 AATTT-AAATTTATATAAATTA
1 AATTTAAAATTTAAATTAATTA
* *
1902069 AATTTAACATATAAATTAATTA
1 AATTTAAAATTTAAATTAATTA
* *
1902091 AATTCAAAAAAATTTTATATTCAAATT-
1 AATT---TAAAA-TTTAAATT--AATTA
*
1902118 -ATTTTAAA--TAAATTAATTA
1 AATTTAAAATTTAAATTAATTA
1902137 AATTTAAAATTTAAATTAATTA
1 AATTTAAAATTTAAATTAATTA
*
1902159 ATTTTAAA
1 AATTTAAA
1902167 TTAATTAATT
Statistics
Matches: 74, Mismatches: 13, Indels: 21
0.69 0.12 0.19
Matches are distributed among these distances:
18 4 0.05
20 12 0.16
21 5 0.07
22 34 0.46
23 3 0.04
25 3 0.04
26 9 0.12
28 4 0.05
ACGTcount: A:0.53, C:0.03, G:0.00, T:0.45
Consensus pattern (22 bp):
AATTTAAAATTTAAATTAATTA
Found at i:1902167 original size:37 final size:37
Alignment explanation
Indices: 1902126--1902301 Score: 126
Period size: 37 Copynumber: 4.9 Consensus size: 37
1902116 TTATTTTAAA
1902126 TAAATTAATTAAATTTAAAATTTAAATTAATTAATTT
1 TAAATTAATTAAATTTAAAATTTAAATTAATTAATTT
* * * * *
1902163 TAAATTAATTAATTTTAATATTTAGATGT-ATCAAATT
1 TAAATTAATTAAATTTAAAATTTAAAT-TAATTAATTT
* *
1902200 TAATATT--TTAAATATAAATTATTTTAAATTAATT-A-GT
1 TAA-ATTAATTAAATTTAAA--A-TTTAAATTAATTAATTT
*
1902237 TAAATT-ATTAATTTTAAAA--T-AATTAATT--TTT
1 TAAATTAATTAAATTTAAAATTTAAATTAATTAATTT
*
1902268 T-AATTAAATTAAA-TTAAAATTAAAATTAATTAAT
1 TAAATT-AATTAAATTTAAAATTTAAATTAATTAAT
1902302 AATTTTTTAA
Statistics
Matches: 108, Mismatches: 16, Indels: 31
0.70 0.10 0.20
Matches are distributed among these distances:
30 4 0.04
31 16 0.15
32 6 0.06
34 8 0.07
35 1 0.01
36 12 0.11
37 46 0.43
38 7 0.06
39 8 0.07
ACGTcount: A:0.49, C:0.01, G:0.02, T:0.49
Consensus pattern (37 bp):
TAAATTAATTAAATTTAAAATTTAAATTAATTAATTT
Found at i:1902186 original size:22 final size:22
Alignment explanation
Indices: 1902120--1902284 Score: 77
Period size: 22 Copynumber: 7.6 Consensus size: 22
1902110 TTCAAATTAT
*
1902120 TTTAAATAAATTAA--TTAA-A
1 TTTAAATTAATTAATTTTAATA
1902139 TTTAAAATTTAAATTAA--TTAAT-
1 TTT-AAA-TT-AATTAATTTTAATA
1902161 TTTAAATTAATTAATTTTAATA
1 TTTAAATTAATTAATTTTAATA
* * *
1902183 TTTAGATGT-ATCAAATTTAATA
1 TTTAAAT-TAATTAATTTTAATA
1902205 TTTTAAATATAAATT-ATTTTAA-A
1 -TTTAAAT-T-AATTAATTTTAATA
*
1902228 -TT-AATTAGTTAAATTATTAAT-
1 TTTAAATTAATT-AATT-TTAATA
* *
1902249 TTTAAAATAATTAATTTT-TTA
1 TTTAAATTAATTAATTTTAATA
*
1902270 ATTAAATTAAATTAA
1 TTTAAATT-AATTAA
1902285 AATTAAAATT
Statistics
Matches: 113, Mismatches: 14, Indels: 35
0.70 0.09 0.22
Matches are distributed among these distances:
18 3 0.03
19 10 0.09
20 12 0.11
21 23 0.20
22 42 0.37
23 15 0.13
24 6 0.05
25 2 0.02
ACGTcount: A:0.48, C:0.01, G:0.02, T:0.50
Consensus pattern (22 bp):
TTTAAATTAATTAATTTTAATA
Found at i:1902253 original size:14 final size:15
Alignment explanation
Indices: 1902204--1902266 Score: 53
Period size: 15 Copynumber: 4.3 Consensus size: 15
1902194 CAAATTTAAT
1902204 ATTTTAAATATAAATT-
1 ATTTTAAA-AT-AATTA
*
1902220 ATTTTAAATTAATT-
1 ATTTTAAAATAATTA
* *
1902234 A-GTT-AAATTATTA
1 ATTTTAAAATAATTA
1902247 ATTTTAAAATAATTA
1 ATTTTAAAATAATTA
1902262 ATTTT
1 ATTTT
1902267 TTAATTAAAT
Statistics
Matches: 38, Mismatches: 6, Indels: 7
0.75 0.12 0.14
Matches are distributed among these distances:
12 6 0.16
13 3 0.08
14 7 0.18
15 14 0.37
16 8 0.21
ACGTcount: A:0.46, C:0.00, G:0.02, T:0.52
Consensus pattern (15 bp):
ATTTTAAAATAATTA
Found at i:1902290 original size:16 final size:17
Alignment explanation
Indices: 1902268--1902305 Score: 53
Period size: 16 Copynumber: 2.3 Consensus size: 17
1902258 ATTAATTTTT
1902268 TAATT-AAATTAAATTAA
1 TAATTAAAATT-AATTAA
1902285 -AATTAAAATTAATTAA
1 TAATTAAAATTAATTAA
1902301 TAATT
1 TAATT
1902306 TTTTAAATTT
Statistics
Matches: 19, Mismatches: 0, Indels: 4
0.83 0.00 0.17
Matches are distributed among these distances:
16 10 0.53
17 9 0.47
ACGTcount: A:0.58, C:0.00, G:0.00, T:0.42
Consensus pattern (17 bp):
TAATTAAAATTAATTAA
Found at i:1902898 original size:14 final size:14
Alignment explanation
Indices: 1902879--1902906 Score: 56
Period size: 14 Copynumber: 2.0 Consensus size: 14
1902869 TTATATCTCT
1902879 TTTTCTTTTTTTTC
1 TTTTCTTTTTTTTC
1902893 TTTTCTTTTTTTTC
1 TTTTCTTTTTTTTC
1902907 AAGAATTGCT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 14 1.00
ACGTcount: A:0.00, C:0.14, G:0.00, T:0.86
Consensus pattern (14 bp):
TTTTCTTTTTTTTC
Found at i:1904404 original size:14 final size:15
Alignment explanation
Indices: 1904341--1904404 Score: 51
Period size: 16 Copynumber: 4.3 Consensus size: 15
1904331 GATTATAAAT
* *
1904341 ATAATAATTAATTATG
1 ATAA-AATTAATAATA
1904357 ATAAATATTAATAATA
1 ATAAA-ATTAATAATA
* *
1904373 AAAAAATTAA-AATC
1 ATAAAATTAATAATA
*
1904387 ATAAAA-TAATAATT
1 ATAAAATTAATAATA
1904401 ATAA
1 ATAA
1904405 TATCAAATTA
Statistics
Matches: 40, Mismatches: 6, Indels: 6
0.77 0.12 0.12
Matches are distributed among these distances:
13 3 0.08
14 15 0.38
15 6 0.15
16 16 0.40
ACGTcount: A:0.62, C:0.02, G:0.02, T:0.34
Consensus pattern (15 bp):
ATAAAATTAATAATA
Found at i:1909885 original size:2 final size:2
Alignment explanation
Indices: 1909878--1909902 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
1909868 TATTACATAC
1909878 AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT A
1909903 AACTGGCCAA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:1910044 original size:27 final size:29
Alignment explanation
Indices: 1910012--1910073 Score: 78
Period size: 26 Copynumber: 2.2 Consensus size: 29
1910002 TATAATTTAT
1910012 TAATTTTAAATT-TTAAATAAAT-TAAAAA
1 TAATTTT-AATTATTAAATAAATATAAAAA
*
1910040 T-A-TTTAATTATTAAATATATATAAAAA
1 TAATTTTAATTATTAAATAAATATAAAAA
1910067 TAATTTT
1 TAATTTT
1910074 TTAATTAAGA
Statistics
Matches: 29, Mismatches: 1, Indels: 7
0.78 0.03 0.19
Matches are distributed among these distances:
25 4 0.14
26 12 0.41
27 8 0.28
28 2 0.07
29 3 0.10
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (29 bp):
TAATTTTAATTATTAAATAAATATAAAAA
Found at i:1910511 original size:15 final size:15
Alignment explanation
Indices: 1910491--1910520 Score: 51
Period size: 15 Copynumber: 2.0 Consensus size: 15
1910481 TTATCATATT
1910491 AATTTTATTATTTAA
1 AATTTTATTATTTAA
*
1910506 AATTTTTTTATTTAA
1 AATTTTATTATTTAA
1910521 TTATATTAAT
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.37, C:0.00, G:0.00, T:0.63
Consensus pattern (15 bp):
AATTTTATTATTTAA
Found at i:1914420 original size:21 final size:21
Alignment explanation
Indices: 1914394--1914461 Score: 66
Period size: 21 Copynumber: 3.0 Consensus size: 21
1914384 TTTATAAAAT
1914394 ATTTTTATTATATTTAAATAA
1 ATTTTTATTATATTTAAATAA
* *
1914415 ATTTTTATTTTTAATTTATATTTAA
1 ATTTTTA-TTAT-ATTTA-A-ATAA
1914440 ATTATTTATTAT-TTTAAATAA
1 ATT-TTTATTATATTTAAATAA
1914461 A
1 A
1914462 AATTAATTTA
Statistics
Matches: 38, Mismatches: 4, Indels: 10
0.73 0.08 0.19
Matches are distributed among these distances:
21 11 0.29
22 4 0.11
23 9 0.24
24 1 0.03
25 9 0.24
26 4 0.11
ACGTcount: A:0.40, C:0.00, G:0.00, T:0.60
Consensus pattern (21 bp):
ATTTTTATTATATTTAAATAA
Found at i:1914437 original size:29 final size:27
Alignment explanation
Indices: 1914393--1914454 Score: 81
Period size: 29 Copynumber: 2.2 Consensus size: 27
1914383 ATTTATAAAA
1914393 TATTTTTATTATATTTAAATAAATTT-T
1 TATTTTTATTATATTTAAAT-AATTTAT
*
1914420 TATTTTTAATTTATATTTAAATTATTTAT
1 TATTTTT-A-TTATATTTAAATAATTTAT
1914449 TATTTT
1 TATTTT
1914455 AAATAAAAAT
Statistics
Matches: 31, Mismatches: 1, Indels: 4
0.86 0.03 0.11
Matches are distributed among these distances:
27 7 0.23
28 5 0.16
29 19 0.61
ACGTcount: A:0.34, C:0.00, G:0.00, T:0.66
Consensus pattern (27 bp):
TATTTTTATTATATTTAAATAATTTAT
Found at i:1914455 original size:28 final size:27
Alignment explanation
Indices: 1914393--1914456 Score: 76
Period size: 28 Copynumber: 2.3 Consensus size: 27
1914383 ATTTATAAAA
*
1914393 TATTTTTATTATATTTAAATAAATTTT
1 TATTTTAATTATATTTAAATAAATTTT
*
1914420 TATTTTTAATTTATATTTAAAT-TATTTAT
1 TA-TTTTAA-TTATATTTAAATAAATTT-T
1914449 TATTTTAA
1 TATTTTAA
1914457 ATAAAAATTA
Statistics
Matches: 32, Mismatches: 2, Indels: 5
0.82 0.05 0.13
Matches are distributed among these distances:
27 2 0.06
28 15 0.47
29 15 0.47
ACGTcount: A:0.36, C:0.00, G:0.00, T:0.64
Consensus pattern (27 bp):
TATTTTAATTATATTTAAATAAATTTT
Found at i:1914464 original size:23 final size:23
Alignment explanation
Indices: 1914387--1914472 Score: 68
Period size: 23 Copynumber: 3.7 Consensus size: 23
1914377 TACTGCATTT
1914387 ATAAAATATT-TTTATTATATTTAA
1 ATAAAA-ATTATTTATTAT-TTTAA
** * *
1914411 ATAAATTTTTATTT-TTAATTTAT
1 ATAAA-AATTATTTATTATTTTAA
**
1914434 ATTTAAATTATTTATTATTTTAA
1 ATAAAAATTATTTATTATTTTAA
1914457 ATAAAAATTAATTTAT
1 ATAAAAATT-ATTTAT
1914473 ATTAAAAATT
Statistics
Matches: 46, Mismatches: 12, Indels: 8
0.70 0.18 0.12
Matches are distributed among these distances:
22 6 0.13
23 21 0.46
24 16 0.35
25 3 0.07
ACGTcount: A:0.43, C:0.00, G:0.00, T:0.57
Consensus pattern (23 bp):
ATAAAAATTATTTATTATTTTAA
Found at i:1914466 original size:16 final size:17
Alignment explanation
Indices: 1914447--1914489 Score: 52
Period size: 16 Copynumber: 2.5 Consensus size: 17
1914437 TAAATTATTT
1914447 ATTATTTTA-AATAAAA
1 ATTATTTTATAATAAAA
* *
1914463 ATTAATTTATATTAAAA
1 ATTATTTTATAATAAAA
1914480 ATTTATTTTA
1 A-TTATTTTA
1914490 GTATAAATTA
Statistics
Matches: 22, Mismatches: 3, Indels: 2
0.81 0.11 0.07
Matches are distributed among these distances:
16 8 0.36
17 7 0.32
18 7 0.32
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (17 bp):
ATTATTTTATAATAAAA
Found at i:1914474 original size:39 final size:38
Alignment explanation
Indices: 1914425--1914558 Score: 118
Period size: 39 Copynumber: 3.5 Consensus size: 38
1914415 ATTTTTATTT
1914425 TTAATTTATATTTAAATTATTTATTATTTTAAATAAAAA
1 TTAATTTATATTTAAA-TATTTATTATTTTAAATAAAAA
*
1914464 TTAATTTATA-TTAAAAATTTATT-TTAGTATAAATTAAAAA
1 TTAATTTATATTTAAATATTTATTATT--T-TAAA-TAAAAA
* * *
1914504 TT-A-TGACTTATTTAAATA-TAATTATTTTAAATTAAAA
1 TTAATTTA--TATTTAAATATTTATTATTTTAAATAAAAA
*
1914541 TTAAATT-TATTTAAATAT
1 TTAATTTATATTTAAATAT
1914559 AATTAAAACT
Statistics
Matches: 78, Mismatches: 6, Indels: 24
0.72 0.06 0.22
Matches are distributed among these distances:
36 12 0.15
37 14 0.18
38 13 0.17
39 17 0.22
40 14 0.18
41 8 0.10
ACGTcount: A:0.47, C:0.01, G:0.01, T:0.51
Consensus pattern (38 bp):
TTAATTTATATTTAAATATTTATTATTTTAAATAAAAA
Found at i:1914481 original size:23 final size:23
Alignment explanation
Indices: 1914438--1914481 Score: 54
Period size: 23 Copynumber: 1.9 Consensus size: 23
1914428 ATTTATATTT
**
1914438 AAATTATTTATTATTTTAAATAA
1 AAATTATTTATTATTAAAAATAA
1914461 AAATTAATTTA-TATTAAAAAT
1 AAATT-ATTTATTATTAAAAAT
1914482 TTATTTTAGT
Statistics
Matches: 18, Mismatches: 2, Indels: 2
0.82 0.09 0.09
Matches are distributed among these distances:
23 13 0.72
24 5 0.28
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (23 bp):
AAATTATTTATTATTAAAAATAA
Found at i:1914496 original size:18 final size:16
Alignment explanation
Indices: 1914447--1914496 Score: 55
Period size: 18 Copynumber: 2.9 Consensus size: 16
1914437 TAAATTATTT
*
1914447 ATTATTTTAAATAAAA
1 ATTATTTTATATAAAA
*
1914463 ATTAATTTATATTAAAA
1 ATTATTTTATA-TAAAA
1914480 ATTTATTTTAGTATAAA
1 A-TTATTTTA-TATAAA
1914497 TTAAAAATTA
Statistics
Matches: 28, Mismatches: 3, Indels: 4
0.80 0.09 0.11
Matches are distributed among these distances:
16 9 0.32
17 6 0.21
18 11 0.39
19 2 0.07
ACGTcount: A:0.50, C:0.00, G:0.02, T:0.48
Consensus pattern (16 bp):
ATTATTTTATATAAAA
Found at i:1914547 original size:21 final size:20
Alignment explanation
Indices: 1914529--1914582 Score: 63
Period size: 21 Copynumber: 2.6 Consensus size: 20
1914519 ATATAATTAT
1914529 TTTAAATTAAAATTAAATTTA
1 TTTAAA-TAAAATTAAATTTA
* *
1914550 TTTAAATATAATTAAAACTTA
1 TTTAAATAAAATT-AAATTTA
*
1914571 TTTAGATAAAAT
1 TTTAAATAAAAT
1914583 AATAAAATTT
Statistics
Matches: 28, Mismatches: 4, Indels: 2
0.82 0.12 0.06
Matches are distributed among these distances:
20 6 0.21
21 22 0.79
ACGTcount: A:0.52, C:0.02, G:0.02, T:0.44
Consensus pattern (20 bp):
TTTAAATAAAATTAAATTTA
Found at i:1915111 original size:10 final size:10
Alignment explanation
Indices: 1915070--1915122 Score: 52
Period size: 10 Copynumber: 5.1 Consensus size: 10
1915060 TTTGAATTTT
1915070 TTAATTATTAA
1 TTAA-TATTAA
1915081 TTAATAGTTAA
1 TTAATA-TTAA
* * *
1915092 ATATTTTTAA
1 TTAATATTAA
1915102 TTAATATTAA
1 TTAATATTAA
*
1915112 TAAATATTAA
1 TTAATATTAA
1915122 T
1 T
1915123 ATAACTATAA
Statistics
Matches: 34, Mismatches: 7, Indels: 3
0.77 0.16 0.07
Matches are distributed among these distances:
10 23 0.68
11 11 0.32
ACGTcount: A:0.47, C:0.00, G:0.02, T:0.51
Consensus pattern (10 bp):
TTAATATTAA
Found at i:1915636 original size:3 final size:3
Alignment explanation
Indices: 1915628--1915666 Score: 69
Period size: 3 Copynumber: 13.0 Consensus size: 3
1915618 AATAATTAGC
*
1915628 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AGT AAT
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
1915667 CAACGGGCTT
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:0.64, C:0.00, G:0.03, T:0.33
Consensus pattern (3 bp):
AAT
Found at i:1915887 original size:11 final size:11
Alignment explanation
Indices: 1915867--1915917 Score: 59
Period size: 11 Copynumber: 4.5 Consensus size: 11
1915857 ATTTATTTAT
1915867 TATTTATAAATA
1 TATTT-TAAATA
1915879 TATTTTAAAT-
1 TATTTTAAATA
1915889 TATTTATAAATA
1 TATTT-TAAATA
* *
1915901 TAATTTAATTA
1 TATTTTAAATA
1915912 TATTTT
1 TATTTT
1915918 TTATTATAGT
Statistics
Matches: 34, Mismatches: 3, Indels: 5
0.81 0.07 0.12
Matches are distributed among these distances:
10 5 0.15
11 20 0.59
12 9 0.26
ACGTcount: A:0.43, C:0.00, G:0.00, T:0.57
Consensus pattern (11 bp):
TATTTTAAATA
Found at i:1915891 original size:22 final size:21
Alignment explanation
Indices: 1915861--1915912 Score: 79
Period size: 22 Copynumber: 2.5 Consensus size: 21
1915851 CTAATTATTT
1915861 ATTT-ATTATTTATAAATATA
1 ATTTAATTATTTATAAATATA
*
1915881 TTTTAAATTATTTATAAATATA
1 ATTT-AATTATTTATAAATATA
1915903 ATTTAATTAT
1 ATTTAATTAT
1915913 ATTTTTTATT
Statistics
Matches: 28, Mismatches: 2, Indels: 3
0.85 0.06 0.09
Matches are distributed among these distances:
20 3 0.11
21 6 0.21
22 19 0.68
ACGTcount: A:0.44, C:0.00, G:0.00, T:0.56
Consensus pattern (21 bp):
ATTTAATTATTTATAAATATA
Found at i:2001295 original size:2 final size:2
Alignment explanation
Indices: 2001288--2001316 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
2001278 ACAACACAAT
2001288 TC TC TC TC TC TC TC TC TC TC TC TC TC TC T
1 TC TC TC TC TC TC TC TC TC TC TC TC TC TC T
2001317 GGTGGAGCAG
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 27 1.00
ACGTcount: A:0.00, C:0.48, G:0.00, T:0.52
Consensus pattern (2 bp):
TC
Found at i:2002209 original size:2 final size:2
Alignment explanation
Indices: 2002202--2002233 Score: 64
Period size: 2 Copynumber: 16.0 Consensus size: 2
2002192 CTTGATAAGG
2002202 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
2002234 CCCCAAAAAA
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 30 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:2003839 original size:3 final size:3
Alignment explanation
Indices: 2003831--2003866 Score: 51
Period size: 3 Copynumber: 13.0 Consensus size: 3
2003821 TTCGATAGTA
2003831 AAT AAT AAT -AT AAT AA- AA- AAT AAT AAT AAT AAT AAT
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
2003867 GATCTGTTGT
Statistics
Matches: 31, Mismatches: 0, Indels: 4
0.89 0.00 0.11
Matches are distributed among these distances:
2 6 0.19
3 25 0.81
ACGTcount: A:0.69, C:0.00, G:0.00, T:0.31
Consensus pattern (3 bp):
AAT
Found at i:2003853 original size:18 final size:19
Alignment explanation
Indices: 2003830--2003865 Score: 65
Period size: 18 Copynumber: 1.9 Consensus size: 19
2003820 TTTCGATAGT
2003830 AAATAATAAT-ATAATAAA
1 AAATAATAATAATAATAAA
2003848 AAATAATAATAATAATAA
1 AAATAATAATAATAATAA
2003866 TGATCTGTTG
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
18 10 0.59
19 7 0.41
ACGTcount: A:0.72, C:0.00, G:0.00, T:0.28
Consensus pattern (19 bp):
AAATAATAATAATAATAAA
Found at i:2006335 original size:2 final size:2
Alignment explanation
Indices: 2006328--2006360 Score: 66
Period size: 2 Copynumber: 16.5 Consensus size: 2
2006318 GGTATAATTG
2006328 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
2006361 AACACAATTG
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 31 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:2007205 original size:15 final size:15
Alignment explanation
Indices: 2007197--2007238 Score: 57
Period size: 15 Copynumber: 2.7 Consensus size: 15
2007187 AATTTATTTT
2007197 TTATAAATTTAAATA
1 TTATAAATTTAAATA
2007212 TTATAAATTTAAAGTAA
1 TTATAAATTTAAA-T-A
*
2007229 ATATAAATTT
1 TTATAAATTT
2007239 TGATAATAAA
Statistics
Matches: 24, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
15 13 0.54
16 1 0.04
17 10 0.42
ACGTcount: A:0.52, C:0.00, G:0.02, T:0.45
Consensus pattern (15 bp):
TTATAAATTTAAATA
Found at i:2007470 original size:17 final size:18
Alignment explanation
Indices: 2007448--2007481 Score: 61
Period size: 17 Copynumber: 1.9 Consensus size: 18
2007438 AGTTATGTAT
2007448 TGAATTTAAAT-TTTTAG
1 TGAATTTAAATATTTTAG
2007465 TGAATTTAAATATTTTA
1 TGAATTTAAATATTTTA
2007482 CGAATAATAT
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
17 11 0.69
18 5 0.31
ACGTcount: A:0.38, C:0.00, G:0.09, T:0.53
Consensus pattern (18 bp):
TGAATTTAAATATTTTAG
Found at i:2007486 original size:17 final size:17
Alignment explanation
Indices: 2007449--2007486 Score: 51
Period size: 17 Copynumber: 2.2 Consensus size: 17
2007439 GTTATGTATT
*
2007449 GAATTTAAATTTTTAGT
1 GAATTTAAATTTTTAGC
2007466 GAATTTAAATATTTTA-C
1 GAATTTAAAT-TTTTAGC
2007483 GAAT
1 GAAT
2007487 AATATTATAT
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
17 14 0.74
18 5 0.26
ACGTcount: A:0.39, C:0.03, G:0.11, T:0.47
Consensus pattern (17 bp):
GAATTTAAATTTTTAGC
Found at i:2007599 original size:26 final size:28
Alignment explanation
Indices: 2007535--2007599 Score: 66
Period size: 26 Copynumber: 2.4 Consensus size: 28
2007525 TTTAATGTAG
2007535 ATAATAAATAAATTAAAATTTTAAAATATT
1 ATAA-AAA-AAATTAAAATTTTAAAATATT
* *
2007565 -T-ATATAAATTAAAA-TTTAAAA-ATT
1 ATAAAAAAAATTAAAATTTTAAAATATT
2007589 ATAAAAAAAAT
1 ATAAAAAAAAT
2007600 ACAAATATAT
Statistics
Matches: 29, Mismatches: 4, Indels: 8
0.71 0.10 0.20
Matches are distributed among these distances:
24 3 0.10
25 8 0.28
26 15 0.52
27 1 0.03
28 1 0.03
29 1 0.03
ACGTcount: A:0.63, C:0.00, G:0.00, T:0.37
Consensus pattern (28 bp):
ATAAAAAAAATTAAAATTTTAAAATATT
Found at i:2011816 original size:18 final size:18
Alignment explanation
Indices: 2011795--2011829 Score: 61
Period size: 18 Copynumber: 1.9 Consensus size: 18
2011785 TTTTACCTAC
2011795 ATGTAATTTTTATTTTTT
1 ATGTAATTTTTATTTTTT
*
2011813 ATGTTATTTTTATTTTT
1 ATGTAATTTTTATTTTT
2011830 AATTTTTTAA
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:0.20, C:0.00, G:0.06, T:0.74
Consensus pattern (18 bp):
ATGTAATTTTTATTTTTT
Done.