Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold412
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: 4645160
ACGTcount: A:0.34, C:0.16, G:0.16, T:0.34
File 14 of 32
Found at i:1896419 original size:27 final size:28
Alignment explanation
Indices: 1896364--1896469 Score: 92
Period size: 27 Copynumber: 3.6 Consensus size: 28
1896354 ATGATAATTT
* *
1896364 TAAATATAATAAAATTA-TATAATATAATA
1 TAAA-ATAATAAAAATATTAT-ATAAAATA
1896393 -AAAATAATAAAAATATTATATAAAATA
1 TAAAATAATAAAAATATTATATAAAATA
*
1896420 TAAATTAATATAAAA-ATTAATATAAATATAA
1 TAAAATAATA-AAAATATT-ATATAAA-AT-A
1896451 TAAAATAAATTAAAAATAT
1 TAAAAT-AA-TAAAAATAT
1896470 AAAATTTTAT
Statistics
Matches: 64, Mismatches: 4, Indels: 14
0.78 0.05 0.17
Matches are distributed among these distances:
27 18 0.28
28 17 0.27
29 11 0.17
30 2 0.03
31 6 0.09
32 6 0.09
33 4 0.06
ACGTcount: A:0.66, C:0.00, G:0.00, T:0.34
Consensus pattern (28 bp):
TAAAATAATAAAAATATTATATAAAATA
Found at i:1896422 original size:20 final size:20
Alignment explanation
Indices: 1896365--1896471 Score: 82
Period size: 20 Copynumber: 5.4 Consensus size: 20
1896355 TGATAATTTT
*
1896365 AAATATAAT-AAAATTAT-A
1 AAATATAATAAAAATAATAA
*
1896383 TAATATAATAAAAATAATAA
1 AAATATAATAAAAATAATAA
*
1896403 AAATATTATATAAAAT-ATAA
1 AAATATAATA-AAAATAATAA
* *
1896423 ATTAATAT-A-AAAATTAATAT
1 A--AATATAATAAAAATAATAA
1896443 AAATATAAT-AAAATAAATTAA
1 AAATATAATAAAAAT-AA-TAA
1896464 AAATATAA
1 AAATATAA
1896472 AATTTTATAT
Statistics
Matches: 71, Mismatches: 8, Indels: 17
0.74 0.08 0.18
Matches are distributed among these distances:
18 13 0.18
19 16 0.23
20 21 0.30
21 16 0.23
22 5 0.07
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (20 bp):
AAATATAATAAAAATAATAA
Found at i:1896436 original size:12 final size:12
Alignment explanation
Indices: 1896421--1896463 Score: 52
Period size: 12 Copynumber: 3.6 Consensus size: 12
1896411 TATAAAATAT
1896421 AAATTAATATAA
1 AAATTAATATAA
1896433 AAATTAATATAA
1 AAATTAATATAA
* *
1896445 ATA-TAATAAAA
1 AAATTAATATAA
1896456 TAAATTAA
1 -AAATTAA
1896464 AAATATAAAA
Statistics
Matches: 26, Mismatches: 3, Indels: 3
0.81 0.09 0.09
Matches are distributed among these distances:
11 7 0.27
12 16 0.62
13 3 0.12
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (12 bp):
AAATTAATATAA
Found at i:1896511 original size:34 final size:33
Alignment explanation
Indices: 1896378--1896489 Score: 92
Period size: 30 Copynumber: 3.4 Consensus size: 33
1896368 TATAATAAAA
* * *
1896378 TTATATAATATAATAAA--AATAATA-AAAATA
1 TTATATAATAAAATAAATTAAAAATATAAAATT
* *
1896408 TTATATAA-AATATAAATT-AATATA-AAAATT
1 TTATATAATAAAATAAATTAAAAATATAAAATT
1896438 AATATAAATATAATAAAATAAATTAAAAATATAAAATT
1 --T-T--ATATAATAAAATAAATTAAAAATATAAAATT
1896476 TTATATAATAAAAT
1 TTATATAATAAAAT
1896490 TTACATAAAT
Statistics
Matches: 65, Mismatches: 7, Indels: 17
0.73 0.08 0.19
Matches are distributed among these distances:
29 6 0.09
30 17 0.26
32 1 0.02
33 13 0.20
35 7 0.11
36 10 0.15
37 5 0.08
38 6 0.09
ACGTcount: A:0.64, C:0.00, G:0.00, T:0.36
Consensus pattern (33 bp):
TTATATAATAAAATAAATTAAAAATATAAAATT
Found at i:1896732 original size:21 final size:23
Alignment explanation
Indices: 1896708--1896767 Score: 61
Period size: 25 Copynumber: 2.6 Consensus size: 23
1896698 TTGATTTGAC
* *
1896708 ATAATTTGA-TTATTTTA-TTAT
1 ATAATTTAATTTATTTAATTTAT
1896729 ATAATTTAATTTATTTAATTTAT
1 ATAATTTAATTTATTTAATTTAT
*
1896752 ATTAAATTAAATTTAT
1 A-T-AATTTAATTTAT
1896768 ATAAAAATTT
Statistics
Matches: 32, Mismatches: 3, Indels: 4
0.82 0.08 0.10
Matches are distributed among these distances:
21 8 0.25
22 7 0.22
23 5 0.16
24 1 0.03
25 11 0.34
ACGTcount: A:0.40, C:0.00, G:0.02, T:0.58
Consensus pattern (23 bp):
ATAATTTAATTTATTTAATTTAT
Found at i:1896816 original size:40 final size:41
Alignment explanation
Indices: 1896722--1896820 Score: 107
Period size: 40 Copynumber: 2.4 Consensus size: 41
1896712 TTTGATTATT
* *
1896722 TTATTATAT-AATTTAATTTATTTAATTTATATTAAATTAAA
1 TTATTATATAAATTTAA-TAATTTAATTCATATTAAATTAAA
* *
1896763 TT-TATATAAAAATTTAATAATTTAA-TCA-ATTTAATCTAAA
1 TTAT-TATATAAATTTAATAATTTAATTCATATTAAAT-TAAA
1896803 TTATTATATAAATTTAAT
1 TTATTATATAAATTTAAT
1896821 TATAAATTTT
Statistics
Matches: 49, Mismatches: 5, Indels: 9
0.78 0.08 0.14
Matches are distributed among these distances:
39 6 0.12
40 22 0.45
41 14 0.29
42 7 0.14
ACGTcount: A:0.46, C:0.02, G:0.00, T:0.52
Consensus pattern (41 bp):
TTATTATATAAATTTAATAATTTAATTCATATTAAATTAAA
Found at i:1899810 original size:17 final size:17
Alignment explanation
Indices: 1899751--1899808 Score: 55
Period size: 17 Copynumber: 3.4 Consensus size: 17
1899741 ATTTATACTC
*
1899751 AATAAAATCTTAATTTAA
1 AATAAAAT-TTTATTTAA
* ** *
1899769 ATTAATTTTTTGTTTAA
1 AATAAAATTTTATTTAA
1899786 AATAAAATTTTATTT-A
1 AATAAAATTTTATTTAA
1899802 AATAAAA
1 AATAAAA
1899809 ATCATAAGAT
Statistics
Matches: 31, Mismatches: 9, Indels: 2
0.74 0.21 0.05
Matches are distributed among these distances:
16 8 0.26
17 18 0.58
18 5 0.16
ACGTcount: A:0.50, C:0.02, G:0.02, T:0.47
Consensus pattern (17 bp):
AATAAAATTTTATTTAA
Found at i:1901210 original size:23 final size:24
Alignment explanation
Indices: 1901177--1901222 Score: 67
Period size: 23 Copynumber: 1.9 Consensus size: 24
1901167 AATATCTTAA
*
1901177 ATATAATTATAAC-AAAATAAAAT
1 ATATAAATATAACAAAAATAAAAT
1901200 ATATAAATATAACATAAAATAAA
1 ATATAAATATAACA-AAAATAAA
1901223 TCTAAAATTT
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
23 12 0.60
25 8 0.40
ACGTcount: A:0.67, C:0.04, G:0.00, T:0.28
Consensus pattern (24 bp):
ATATAAATATAACAAAAATAAAAT
Found at i:1901223 original size:29 final size:30
Alignment explanation
Indices: 1901163--1901223 Score: 72
Period size: 29 Copynumber: 2.1 Consensus size: 30
1901153 TTATATAAAT
* * *
1901163 ATAAAATATCTTAAATATAATTATAACAAA
1 ATAAAATATCATAAATATAATCATAAAAAA
1901193 ATAAAATAT-ATAAATATAA-CATAAAATAA
1 ATAAAATATCATAAATATAATCATAAAA-AA
1901222 AT
1 AT
1901224 CTAAAATTTA
Statistics
Matches: 27, Mismatches: 3, Indels: 3
0.82 0.09 0.09
Matches are distributed among these distances:
28 5 0.19
29 13 0.48
30 9 0.33
ACGTcount: A:0.64, C:0.05, G:0.00, T:0.31
Consensus pattern (30 bp):
ATAAAATATCATAAATATAATCATAAAAAA
Found at i:1904876 original size:15 final size:16
Alignment explanation
Indices: 1904853--1904907 Score: 60
Period size: 16 Copynumber: 3.4 Consensus size: 16
1904843 ATTTTAAAAA
1904853 AATTTAAATGATTTTT
1 AATTTAAATGATTTTT
*
1904869 AA-TTAAATTG-TTTGT
1 AATTTAAA-TGATTTTT
*
1904884 AATTTAAATAATTTTT
1 AATTTAAATGATTTTT
1904900 AAATTTAA
1 -AATTTAA
1904908 TTTATTTTAA
Statistics
Matches: 32, Mismatches: 3, Indels: 7
0.76 0.07 0.17
Matches are distributed among these distances:
15 12 0.38
16 13 0.41
17 7 0.22
ACGTcount: A:0.42, C:0.00, G:0.05, T:0.53
Consensus pattern (16 bp):
AATTTAAATGATTTTT
Found at i:1904890 original size:16 final size:17
Alignment explanation
Indices: 1904853--1904892 Score: 50
Period size: 15 Copynumber: 2.5 Consensus size: 17
1904843 ATTTTAAAAA
*
1904853 AATTTAAA-TGATTTTT
1 AATTTAAATTGATTTGT
1904869 AA-TTAAATTG-TTTGT
1 AATTTAAATTGATTTGT
1904884 AATTTAAAT
1 AATTTAAAT
1904893 AATTTTTAAA
Statistics
Matches: 21, Mismatches: 1, Indels: 4
0.81 0.04 0.15
Matches are distributed among these distances:
15 11 0.52
16 10 0.48
ACGTcount: A:0.40, C:0.00, G:0.07, T:0.53
Consensus pattern (17 bp):
AATTTAAATTGATTTGT
Found at i:1904917 original size:16 final size:16
Alignment explanation
Indices: 1904896--1905006 Score: 59
Period size: 16 Copynumber: 6.6 Consensus size: 16
1904886 TTTAAATAAT
1904896 TTTTAAATTTAATTTA
1 TTTTAAATTTAATTTA
*
1904912 TTTTAAATTATGAA-TAA
1 TTTTAAATT-T-AATTTA
1904929 TTTTAAATTTGAA--TA
1 TTTTAAATTT-AATTTA
* *
1904944 ATTTAAGTTTAATATATGAA
1 TTTTAAATTTAAT-T-T--A
* *
1904964 TTGTTTAAGTTTAAATTA
1 -T-TTTAAATTTAATTTA
*
1904982 TTTTAAATATAATTTA
1 TTTTAAATTTAATTTA
1904998 -TTTAAATTT
1 TTTTAAATTT
1905007 TAAAATTAAA
Statistics
Matches: 75, Mismatches: 10, Indels: 21
0.71 0.09 0.20
Matches are distributed among these distances:
14 2 0.03
15 17 0.23
16 25 0.33
17 13 0.17
18 4 0.05
20 2 0.03
21 1 0.01
22 11 0.15
ACGTcount: A:0.41, C:0.00, G:0.05, T:0.54
Consensus pattern (16 bp):
TTTTAAATTTAATTTA
Found at i:1904964 original size:22 final size:21
Alignment explanation
Indices: 1904930--1904979 Score: 64
Period size: 22 Copynumber: 2.3 Consensus size: 21
1904920 TATGAATAAT
*
1904930 TTTAAATTTGAATAATTTAAG
1 TTTAAATATGAATAATTTAAG
**
1904951 TTTAATATATGAATTGTTTAAG
1 TTTAA-ATATGAATAATTTAAG
1904973 TTTAAAT
1 TTTAAAT
1904980 TATTTTAAAT
Statistics
Matches: 25, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
21 7 0.28
22 18 0.72
ACGTcount: A:0.40, C:0.00, G:0.10, T:0.50
Consensus pattern (21 bp):
TTTAAATATGAATAATTTAAG
Found at i:1905009 original size:22 final size:23
Alignment explanation
Indices: 1904981--1905036 Score: 64
Period size: 22 Copynumber: 2.5 Consensus size: 23
1904971 AGTTTAAATT
* *
1904981 ATTTTAAATATAATTTAT-TTAA
1 ATTTTAAATATAAATCATATTAA
1905003 ATTTTAAA-ATTAAATCATATTAA
1 ATTTTAAATA-TAAATCATATTAA
1905026 A-TTTAAATATA
1 ATTTTAAATATA
1905037 TTATTTTAAT
Statistics
Matches: 29, Mismatches: 2, Indels: 6
0.78 0.05 0.16
Matches are distributed among these distances:
21 1 0.03
22 22 0.76
23 6 0.21
ACGTcount: A:0.50, C:0.02, G:0.00, T:0.48
Consensus pattern (23 bp):
ATTTTAAATATAAATCATATTAA
Found at i:1905031 original size:16 final size:15
Alignment explanation
Indices: 1905006--1905039 Score: 50
Period size: 16 Copynumber: 2.2 Consensus size: 15
1904996 TATTTAAATT
1905006 TTAAAATTAAATCATA
1 TTAAAATTAAAT-ATA
*
1905022 TTAAATTTAAATATA
1 TTAAAATTAAATATA
1905037 TTA
1 TTA
1905040 TTTTAATGAA
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
15 6 0.35
16 11 0.65
ACGTcount: A:0.53, C:0.03, G:0.00, T:0.44
Consensus pattern (15 bp):
TTAAAATTAAATATA
Found at i:1905037 original size:15 final size:15
Alignment explanation
Indices: 1904983--1905039 Score: 57
Period size: 15 Copynumber: 3.9 Consensus size: 15
1904973 TTTAAATTAT
*
1904983 TTTAAATATAATT-TA
1 TTTAAATAT-ATTAAA
1904998 TTTAAAT-T-TTAAA
1 TTTAAATATATTAAA
*
1905011 ATTAAATCATATTAAA
1 TTTAAAT-ATATTAAA
1905027 TTTAAATATATTA
1 TTTAAATATATTA
1905040 TTTTAATGAA
Statistics
Matches: 35, Mismatches: 3, Indels: 8
0.76 0.07 0.17
Matches are distributed among these distances:
12 2 0.06
13 7 0.20
14 1 0.03
15 14 0.40
16 11 0.31
ACGTcount: A:0.49, C:0.02, G:0.00, T:0.49
Consensus pattern (15 bp):
TTTAAATATATTAAA
Found at i:1905103 original size:21 final size:19
Alignment explanation
Indices: 1905079--1905118 Score: 53
Period size: 19 Copynumber: 2.0 Consensus size: 19
1905069 TATCAAGTAA
1905079 AAATAAATAATACTTAAAATT
1 AAATAAA-AATA-TTAAAATT
*
1905100 AAATAAAAATATTATAATT
1 AAATAAAAATATTAAAATT
1905119 TTTAAAAATA
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
19 7 0.39
20 4 0.22
21 7 0.39
ACGTcount: A:0.62, C:0.03, G:0.00, T:0.35
Consensus pattern (19 bp):
AAATAAAAATATTAAAATT
Found at i:1906273 original size:20 final size:22
Alignment explanation
Indices: 1906238--1906278 Score: 59
Period size: 21 Copynumber: 2.0 Consensus size: 22
1906228 ATTGGATTTT
1906238 AAAATTTTAAAATAT-ATATTA
1 AAAATTTTAAAATATAATATTA
*
1906259 AAAATTTT-AATTATAATATT
1 AAAATTTTAAAATATAATATT
1906279 TTTAAAATAT
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
20 5 0.28
21 13 0.72
ACGTcount: A:0.54, C:0.00, G:0.00, T:0.46
Consensus pattern (22 bp):
AAAATTTTAAAATATAATATTA
Found at i:1906305 original size:34 final size:35
Alignment explanation
Indices: 1906242--1906309 Score: 86
Period size: 36 Copynumber: 2.0 Consensus size: 35
1906232 GATTTTAAAA
**
1906242 TTTTAAAATATATATTAAAAATTTTAATTATAATAT
1 TTTTAAAATATATATTAAAAATTAAAATTA-AATAT
*
1906278 TTTTAAAATATAT-TT-TAAATTAAAATTAAATA
1 TTTTAAAATATATATTAAAAATTAAAATTAAATA
1906310 GAAATTTTAT
Statistics
Matches: 29, Mismatches: 3, Indels: 3
0.83 0.09 0.09
Matches are distributed among these distances:
33 4 0.14
34 10 0.34
35 2 0.07
36 13 0.45
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (35 bp):
TTTTAAAATATATATTAAAAATTAAAATTAAATAT
Found at i:1906318 original size:36 final size:34
Alignment explanation
Indices: 1906239--1906318 Score: 79
Period size: 36 Copynumber: 2.2 Consensus size: 34
1906229 TTGGATTTTA
** * *
1906239 AAATTTTAAAATATATATTAAAAATTTTAATTAT
1 AAATTTTAAAATATATATTAAAAAAATTAAATAG
*
1906273 AATATTTTTAAAATATATTTTAAATTAAAATTAAATAG
1 AA-A-TTTTAAAATATATATTAAA--AAAATTAAATAG
1906311 AAATTTTA
1 AAATTTTA
1906319 TTTTTACTAA
Statistics
Matches: 37, Mismatches: 5, Indels: 6
0.77 0.10 0.12
Matches are distributed among these distances:
34 2 0.05
35 1 0.03
36 23 0.62
37 1 0.03
38 10 0.27
ACGTcount: A:0.53, C:0.00, G:0.01, T:0.46
Consensus pattern (34 bp):
AAATTTTAAAATATATATTAAAAAAATTAAATAG
Found at i:1907761 original size:3 final size:3
Alignment explanation
Indices: 1907753--1907777 Score: 50
Period size: 3 Copynumber: 8.3 Consensus size: 3
1907743 TGATGTTCTT
1907753 TTA TTA TTA TTA TTA TTA TTA TTA T
1 TTA TTA TTA TTA TTA TTA TTA TTA T
1907778 GATTTATTTT
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 22 1.00
ACGTcount: A:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (3 bp):
TTA
Found at i:1908308 original size:2 final size:2
Alignment explanation
Indices: 1908301--1908349 Score: 59
Period size: 2 Copynumber: 26.0 Consensus size: 2
1908291 CGAAGTTCAT
* *
1908301 TA TA TA TA TA TA TA TA TA TA TA TA TA CA TA -A TA -A AA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1908341 TA TA T- TA TA
1 TA TA TA TA TA
1908350 AGATATTTAA
Statistics
Matches: 41, Mismatches: 3, Indels: 6
0.82 0.06 0.12
Matches are distributed among these distances:
1 3 0.07
2 38 0.93
ACGTcount: A:0.53, C:0.02, G:0.00, T:0.45
Consensus pattern (2 bp):
TA
Found at i:1908350 original size:16 final size:16
Alignment explanation
Indices: 1908302--1908355 Score: 54
Period size: 16 Copynumber: 3.2 Consensus size: 16
1908292 GAAGTTCATT
*
1908302 ATATATATATATATATAT
1 ATATATATAT-TATA-AA
* *
1908320 ATATATACATAATAAA
1 ATATATATATTATAAA
*
1908336 ATATATATATTATAAG
1 ATATATATATTATAAA
1908352 ATAT
1 ATAT
1908356 TTAAAGAGTT
Statistics
Matches: 30, Mismatches: 6, Indels: 2
0.79 0.16 0.05
Matches are distributed among these distances:
16 18 0.60
17 3 0.10
18 9 0.30
ACGTcount: A:0.54, C:0.02, G:0.02, T:0.43
Consensus pattern (16 bp):
ATATATATATTATAAA
Found at i:1913965 original size:17 final size:17
Alignment explanation
Indices: 1913943--1913977 Score: 54
Period size: 18 Copynumber: 2.1 Consensus size: 17
1913933 TATTATAAAT
1913943 TTAT-AAAAATTTTGATA
1 TTATAAAAAATTTT-ATA
1913960 TTATAAAAAATTTTATA
1 TTATAAAAAATTTTATA
1913977 T
1 T
1913978 CAATTTTAAT
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
17 8 0.47
18 9 0.53
ACGTcount: A:0.49, C:0.00, G:0.03, T:0.49
Consensus pattern (17 bp):
TTATAAAAAATTTTATA
Found at i:1914383 original size:22 final size:22
Alignment explanation
Indices: 1914339--1914422 Score: 82
Period size: 22 Copynumber: 3.7 Consensus size: 22
1914329 TTATGTTAAT
1914339 TATATTAAATATATATAATATAAA
1 TATATTAAATAT-TA-AATATAAA
*
1914363 T-TATTAAAATTTTAAATATAAA
1 TATATT-AAATATTAAATATAAA
* *
1914385 TATATTATATATTAAATAT-AT
1 TATATTAAATATTAAATATAAA
1914406 TATATTAATTATATTAA
1 TATATTAA--ATATTAA
1914423 TTGTATTTAA
Statistics
Matches: 51, Mismatches: 5, Indels: 9
0.78 0.08 0.14
Matches are distributed among these distances:
21 8 0.16
22 20 0.39
23 17 0.33
24 6 0.12
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (22 bp):
TATATTAAATATTAAATATAAA
Found at i:1914402 original size:16 final size:16
Alignment explanation
Indices: 1914334--1914410 Score: 63
Period size: 16 Copynumber: 4.9 Consensus size: 16
1914324 ATTTTTTATG
* *
1914334 TTAATTATATTAAATA
1 TTAAATATATTATATA
*
1914350 TATATAATATA-AAT-TA
1 T-TA-AATATATTATATA
* *
1914366 TTAAA-ATTTTAAATA
1 TTAAATATATTATATA
1914381 -TAAATATATTATATA
1 TTAAATATATTATATA
1914396 TTAAATATATTATAT
1 TTAAATATATTATAT
1914411 TAATTATATT
Statistics
Matches: 47, Mismatches: 8, Indels: 12
0.70 0.12 0.18
Matches are distributed among these distances:
13 2 0.04
14 7 0.15
15 12 0.26
16 18 0.38
17 3 0.06
18 5 0.11
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (16 bp):
TTAAATATATTATATA
Found at i:1914403 original size:9 final size:9
Alignment explanation
Indices: 1914334--1914407 Score: 51
Period size: 7 Copynumber: 9.3 Consensus size: 9
1914324 ATTTTTTATG
*
1914334 TTAATTATA
1 TTAAATATA
1914343 TTAAATATA
1 TTAAATATA
*
1914352 -TATA-ATA
1 TTAAATATA
1914359 -TAAAT-TA
1 TTAAATATA
1914366 TTAAA-AT-
1 TTAAATATA
*
1914373 TTTAA-ATA
1 TTAAATATA
1914381 -TAAATATA
1 TTAAATATA
1914389 TT--ATATA
1 TTAAATATA
1914396 TTAAATATA
1 TTAAATATA
1914405 TTA
1 TTA
1914408 TATTAATTAT
Statistics
Matches: 52, Mismatches: 5, Indels: 16
0.71 0.07 0.22
Matches are distributed among these distances:
7 24 0.46
8 11 0.21
9 17 0.33
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (9 bp):
TTAAATATA
Found at i:1914418 original size:14 final size:14
Alignment explanation
Indices: 1914337--1914421 Score: 56
Period size: 14 Copynumber: 6.3 Consensus size: 14
1914327 TTTTATGTTA
1914337 ATTATATTAAATAT
1 ATTATATTAAATAT
*
1914351 A-TATA--ATATA-
1 ATTATATTAAATAT
*
1914361 AAT-TATTAAA-AT
1 ATTATATTAAATAT
* *
1914373 TTTAAATATAAATAT
1 ATTATAT-TAAATAT
1914388 ATTATATATTAAATAT
1 A-T-TATATTAAATAT
*
1914404 ATTATATTAATTAT
1 ATTATATTAAATAT
1914418 ATTA
1 ATTA
1914422 ATTGTATTTA
Statistics
Matches: 54, Mismatches: 8, Indels: 18
0.68 0.10 0.22
Matches are distributed among these distances:
10 3 0.06
11 6 0.11
12 3 0.06
13 6 0.11
14 20 0.37
15 3 0.06
16 9 0.17
17 4 0.07
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (14 bp):
ATTATATTAAATAT
Found at i:1914441 original size:23 final size:22
Alignment explanation
Indices: 1914389--1914442 Score: 54
Period size: 23 Copynumber: 2.4 Consensus size: 22
1914379 TATAAATATA
*
1914389 TTATATATTAAATATATTATAT
1 TTATATATTAAATATATTAAAT
* * *
1914411 TAATTATATTAATTGTATTTAAAT
1 TTA-TATATTAAATATA-TTAAAT
1914435 TTATATAT
1 TTATATAT
1914443 AATATTTAAC
Statistics
Matches: 25, Mismatches: 5, Indels: 3
0.76 0.15 0.09
Matches are distributed among these distances:
22 2 0.08
23 16 0.64
24 7 0.28
ACGTcount: A:0.43, C:0.00, G:0.02, T:0.56
Consensus pattern (22 bp):
TTATATATTAAATATATTAAAT
Found at i:1914568 original size:15 final size:15
Alignment explanation
Indices: 1914548--1914595 Score: 51
Period size: 15 Copynumber: 3.0 Consensus size: 15
1914538 GAAAGGAGAT
1914548 ATAAAAAGAAAAAAA
1 ATAAAAAGAAAAAAA
*
1914563 ATAAAAGGAAAAGAAA
1 ATAAAAAGAAAA-AAA
*
1914579 AGTGAGAAAGAAAAAAA
1 A-T-AAAAAGAAAAAAA
1914596 TTATGTATTG
Statistics
Matches: 27, Mismatches: 3, Indels: 4
0.79 0.09 0.12
Matches are distributed among these distances:
15 11 0.41
16 4 0.15
17 4 0.15
18 8 0.30
ACGTcount: A:0.77, C:0.00, G:0.17, T:0.06
Consensus pattern (15 bp):
ATAAAAAGAAAAAAA
Found at i:1916321 original size:35 final size:35
Alignment explanation
Indices: 1916255--1916321 Score: 82
Period size: 35 Copynumber: 1.9 Consensus size: 35
1916245 TGAGTTTATA
* * * *
1916255 TTTAAGTTAAATTTTTTAATTTATTATTAATTAGT
1 TTTAAATTAAATTATTTAATATAATATTAATTAGT
1916290 TTTAAATTAAA-TATTTAATATAATATATAATT
1 TTTAAATTAAATTATTTAATATAATAT-TAATT
1916322 CAAAAATCAT
Statistics
Matches: 27, Mismatches: 4, Indels: 2
0.82 0.12 0.06
Matches are distributed among these distances:
34 12 0.44
35 15 0.56
ACGTcount: A:0.42, C:0.00, G:0.03, T:0.55
Consensus pattern (35 bp):
TTTAAATTAAATTATTTAATATAATATTAATTAGT
Found at i:1919355 original size:28 final size:30
Alignment explanation
Indices: 1919293--1919362 Score: 83
Period size: 28 Copynumber: 2.3 Consensus size: 30
1919283 TTTCATAAAC
1919293 GATATTAATAAAATAAAATAATTTTTTTGGAT
1 GATATTAA-AAAAT-AAATAATTTTTTTGGAT
*
1919325 GATATTAAAAAAT-AAT-ATTTTTATTTG-T
1 GATATTAAAAAATAAATAATTTTT-TTGGAT
1919353 GATATTAAAA
1 GATATTAAAA
1919363 TATTACATCA
Statistics
Matches: 36, Mismatches: 1, Indels: 6
0.84 0.02 0.14
Matches are distributed among these distances:
28 17 0.47
29 6 0.17
31 5 0.14
32 8 0.22
ACGTcount: A:0.47, C:0.00, G:0.09, T:0.44
Consensus pattern (30 bp):
GATATTAAAAAATAAATAATTTTTTTGGAT
Found at i:1920149 original size:13 final size:13
Alignment explanation
Indices: 1920131--1920155 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
1920121 GTGGGTCTTG
1920131 CCTTTTTTTTTTT
1 CCTTTTTTTTTTT
1920144 CCTTTTTTTTTT
1 CCTTTTTTTTTT
1920156 GAAGTTATCA
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.00, C:0.16, G:0.00, T:0.84
Consensus pattern (13 bp):
CCTTTTTTTTTTT
Found at i:1922832 original size:21 final size:20
Alignment explanation
Indices: 1922801--1922839 Score: 60
Period size: 21 Copynumber: 1.9 Consensus size: 20
1922791 TAATAATATA
*
1922801 ATAATTAATTTGATTAAATT
1 ATAATTAATTTAATTAAATT
1922821 ATAATATAATTTAATTAAA
1 ATAAT-TAATTTAATTAAA
1922840 ATAAAAAATT
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
20 5 0.29
21 12 0.71
ACGTcount: A:0.51, C:0.00, G:0.03, T:0.46
Consensus pattern (20 bp):
ATAATTAATTTAATTAAATT
Found at i:1926092 original size:20 final size:21
Alignment explanation
Indices: 1926056--1926094 Score: 62
Period size: 21 Copynumber: 1.9 Consensus size: 21
1926046 AAGAAAGGGC
1926056 AAAAAAATCAAACTAAAAAGA
1 AAAAAAATCAAACTAAAAAGA
*
1926077 AAAAAAATCAGA-TAAAAA
1 AAAAAAATCAAACTAAAAA
1926095 TTATATGGAA
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
20 6 0.35
21 11 0.65
ACGTcount: A:0.77, C:0.08, G:0.05, T:0.10
Consensus pattern (21 bp):
AAAAAAATCAAACTAAAAAGA
Found at i:1927827 original size:21 final size:21
Alignment explanation
Indices: 1927784--1927827 Score: 54
Period size: 21 Copynumber: 2.1 Consensus size: 21
1927774 TTATAAAATT
*
1927784 AAAATAAAAAATAAATTTTTA
1 AAAATAAAAAATAAATTTATA
*
1927805 AAAATAATAAAT-AATCTTATA
1 AAAATAAAAAATAAAT-TTATA
1927826 AA
1 AA
1927828 TATATTAAGT
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
20 3 0.15
21 17 0.85
ACGTcount: A:0.66, C:0.02, G:0.00, T:0.32
Consensus pattern (21 bp):
AAAATAAAAAATAAATTTATA
Found at i:1928138 original size:2 final size:2
Alignment explanation
Indices: 1928121--1928152 Score: 50
Period size: 2 Copynumber: 17.0 Consensus size: 2
1928111 TTTTTTAATC
1928121 TA TA T- TA TA T- 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
1928153 AAAGAGATTT
Statistics
Matches: 28, Mismatches: 0, Indels: 4
0.88 0.00 0.12
Matches are distributed among these distances:
1 2 0.07
2 26 0.93
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (2 bp):
TA
Found at i:1928486 original size:27 final size:26
Alignment explanation
Indices: 1928456--1928519 Score: 71
Period size: 27 Copynumber: 2.5 Consensus size: 26
1928446 TTTAATTAAA
1928456 ATTTAATTA-TAAATTAATATAATATAT
1 ATTTAATTATTAAATTAA-ATAATA-AT
*
1928483 ATTTAA-TATTAATTTAAATAATAAT
1 ATTTAATTATTAAATTAAATAATAAT
*
1928508 A-TTAATTTTTAA
1 ATTTAATTATTAA
1928520 GTCTACATAT
Statistics
Matches: 33, Mismatches: 2, Indels: 6
0.80 0.05 0.15
Matches are distributed among these distances:
24 4 0.12
25 8 0.24
26 8 0.24
27 13 0.39
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (26 bp):
ATTTAATTATTAAATTAAATAATAAT
Found at i:1929198 original size:42 final size:42
Alignment explanation
Indices: 1929152--1929283 Score: 119
Period size: 42 Copynumber: 3.2 Consensus size: 42
1929142 ATCCTTTTTC
*
1929152 TATTTGATTTTTAGTTATTTTTTTTTCTATTATGAGAATTTG
1 TATTTGATTTTCAGTTATTTTTTTTTCTATTATGAGAATTTG
* * * **** *
1929194 TATTTGAAATTCCA-TT-TTTTTTTTATGT-TTCAT-CCTTTTTC
1 TATTTG-ATTTTCAGTTATTTTTTTT-TCTATT-ATGAGAATTTG
*
1929235 TATTTAATTTTCAGTTATTTTTTTTTCTATTATGAGAATTTG
1 TATTTGATTTTCAGTTATTTTTTTTTCTATTATGAGAATTTG
1929277 TATTTGA
1 TATTTGA
1929284 AATTCTATTG
Statistics
Matches: 64, Mismatches: 19, Indels: 14
0.66 0.20 0.14
Matches are distributed among these distances:
40 5 0.08
41 24 0.38
42 31 0.48
43 4 0.06
ACGTcount: A:0.21, C:0.07, G:0.09, T:0.63
Consensus pattern (42 bp):
TATTTGATTTTCAGTTATTTTTTTTTCTATTATGAGAATTTG
Found at i:1929257 original size:83 final size:83
Alignment explanation
Indices: 1929118--1929288 Score: 306
Period size: 83 Copynumber: 2.1 Consensus size: 83
1929108 GGGTGCAATC
* *
1929118 AATTCCATTTCTTTTTGATGTTTCATCCTTTTTCTATTTGATTTTTAGTTATTTTTTTTTCTATT
1 AATTCCATTTCTTTTTGATGTTTCATCCTTTTTCTATTTAATTTTCAGTTATTTTTTTTTCTATT
1929183 ATGAGAATTTGTATTTGA
66 ATGAGAATTTGTATTTGA
* *
1929201 AATTCCATTTTTTTTTTATGTTTCATCCTTTTTCTATTTAATTTTCAGTTATTTTTTTTTCTATT
1 AATTCCATTTCTTTTTGATGTTTCATCCTTTTTCTATTTAATTTTCAGTTATTTTTTTTTCTATT
1929266 ATGAGAATTTGTATTTGA
66 ATGAGAATTTGTATTTGA
1929284 AATTC
1 AATTC
1929289 TATTGAAGAT
Statistics
Matches: 84, Mismatches: 4, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
83 84 1.00
ACGTcount: A:0.20, C:0.10, G:0.08, T:0.61
Consensus pattern (83 bp):
AATTCCATTTCTTTTTGATGTTTCATCCTTTTTCTATTTAATTTTCAGTTATTTTTTTTTCTATT
ATGAGAATTTGTATTTGA
Found at i:1932924 original size:2 final size:2
Alignment explanation
Indices: 1932917--1932950 Score: 68
Period size: 2 Copynumber: 17.0 Consensus size: 2
1932907 AGAGTATTTA
1932917 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
1932951 TCCCCCCCCC
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:0.00, C:0.50, G:0.00, T:0.50
Consensus pattern (2 bp):
CT
Found at i:1935526 original size:3 final size:3
Alignment explanation
Indices: 1935518--1935550 Score: 66
Period size: 3 Copynumber: 11.0 Consensus size: 3
1935508 AATATAAGTA
1935518 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
1935551 GTAAATATAT
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 30 1.00
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (3 bp):
AAT
Found at i:1935954 original size:4 final size:4
Alignment explanation
Indices: 1935947--1936000 Score: 81
Period size: 4 Copynumber: 13.5 Consensus size: 4
1935937 TATATATATA
* * *
1935947 TATG TATG TATG TATG TATG TATG TATT TATG TACG TACG TATG TATG
1 TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG
1935995 TATG TA
1 TATG TA
1936001 CATACCATTG
Statistics
Matches: 46, Mismatches: 4, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
4 46 1.00
ACGTcount: A:0.26, C:0.04, G:0.22, T:0.48
Consensus pattern (4 bp):
TATG
Found at i:1938548 original size:2 final size:2
Alignment explanation
Indices: 1938541--1938575 Score: 70
Period size: 2 Copynumber: 17.5 Consensus size: 2
1938531 TCTCTTATTT
1938541 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 T
1938576 GATTATTTAT
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 33 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:1938650 original size:32 final size:32
Alignment explanation
Indices: 1938614--1938674 Score: 79
Period size: 32 Copynumber: 1.9 Consensus size: 32
1938604 CTTAAATCTT
1938614 AAATAAACTT-AATAAAAAATAATTTAAATACA
1 AAAT-AACTTAAATAAAAAATAATTTAAATACA
* **
1938646 AAATAATTTAAATTTAAAATAATTTAAAT
1 AAATAACTTAAATAAAAAATAATTTAAAT
1938675 TTAAAATTAA
Statistics
Matches: 25, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
31 4 0.16
32 21 0.84
ACGTcount: A:0.62, C:0.03, G:0.00, T:0.34
Consensus pattern (32 bp):
AAATAACTTAAATAAAAAATAATTTAAATACA
Found at i:1938675 original size:16 final size:16
Alignment explanation
Indices: 1938629--1938681 Score: 88
Period size: 16 Copynumber: 3.3 Consensus size: 16
1938619 AACTTAATAA
**
1938629 AAAATAATTTAAATAC
1 AAAATAATTTAAATTT
1938645 AAAATAATTTAAATTT
1 AAAATAATTTAAATTT
1938661 AAAATAATTTAAATTT
1 AAAATAATTTAAATTT
1938677 AAAAT
1 AAAAT
1938682 TAATCCAAAC
Statistics
Matches: 35, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
16 35 1.00
ACGTcount: A:0.60, C:0.02, G:0.00, T:0.38
Consensus pattern (16 bp):
AAAATAATTTAAATTT
Found at i:1943695 original size:2 final size:2
Alignment explanation
Indices: 1943690--1943732 Score: 59
Period size: 2 Copynumber: 21.5 Consensus size: 2
1943680 AAAAGAGGAG
* * *
1943690 TA TA TA TA CA TA TG TA TA TA TA TA TA TA TA TA TA TA TT TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1943732 T
1 T
1943733 TTGTGTATAT
Statistics
Matches: 35, Mismatches: 6, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
2 35 1.00
ACGTcount: A:0.44, C:0.02, G:0.02, T:0.51
Consensus pattern (2 bp):
TA
Found at i:1945729 original size:16 final size:17
Alignment explanation
Indices: 1945692--1945727 Score: 54
Period size: 17 Copynumber: 2.1 Consensus size: 17
1945682 TCATGTTATG
*
1945692 TTTAAAATTTTAATTTA
1 TTTATAATTTTAATTTA
*
1945709 TTTATAATTTTATTTTA
1 TTTATAATTTTAATTTA
1945726 TT
1 TT
1945728 ATTTAAAAAC
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
17 17 1.00
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (17 bp):
TTTATAATTTTAATTTA
Found at i:1948314 original size:17 final size:18
Alignment explanation
Indices: 1948274--1948318 Score: 58
Period size: 17 Copynumber: 2.6 Consensus size: 18
1948264 ATCAAGATTT
1948274 AAATTATATATTTATTAG
1 AAATTATATATTTATTAG
*
1948292 ATATTATAT-TTTA-TAG
1 AAATTATATATTTATTAG
1948308 AAAATTATATA
1 -AAATTATATA
1948319 AGCTAATGAG
Statistics
Matches: 23, Mismatches: 2, Indels: 4
0.79 0.07 0.14
Matches are distributed among these distances:
16 3 0.13
17 12 0.52
18 8 0.35
ACGTcount: A:0.47, C:0.00, G:0.04, T:0.49
Consensus pattern (18 bp):
AAATTATATATTTATTAG
Found at i:1949626 original size:38 final size:40
Alignment explanation
Indices: 1949573--1949669 Score: 117
Period size: 38 Copynumber: 2.5 Consensus size: 40
1949563 TGTACAAATG
* * **
1949573 TATATTGAATATAAATATATTTAATTTTTAAATTT-TTTA
1 TATATTAAATATAAATATATTTAATATTTAAATTTGAATA
* * *
1949612 TATATTTAA-ATAAATATATTTTATATTTATATTTGAATA
1 TATATTAAATATAAATATATTTAATATTTAAATTTGAATA
1949651 TATATTAAATATAAATATA
1 TATATTAAATATAAATATA
1949670 AAATATAATA
Statistics
Matches: 49, Mismatches: 7, Indels: 3
0.83 0.12 0.05
Matches are distributed among these distances:
38 22 0.45
39 18 0.37
40 9 0.18
ACGTcount: A:0.45, C:0.00, G:0.02, T:0.53
Consensus pattern (40 bp):
TATATTAAATATAAATATATTTAATATTTAAATTTGAATA
Found at i:1950529 original size:2 final size:2
Alignment explanation
Indices: 1950522--1950552 Score: 55
Period size: 2 Copynumber: 16.0 Consensus size: 2
1950512 ATGATAGAAA
1950522 AT AT AT AT AT AT AT AT AT AT AT AT AT -T AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1950553 TCTTTTAGTT
Statistics
Matches: 28, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
1 1 0.04
2 27 0.96
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
AT
Found at i:1951157 original size:22 final size:21
Alignment explanation
Indices: 1951132--1951175 Score: 63
Period size: 22 Copynumber: 2.0 Consensus size: 21
1951122 AAAATATTAA
1951132 ATATATTTT-TATATTAATATTT
1 ATATATTTTATA-ATTAA-ATTT
1951154 ATATATTTTATAATTAAATTT
1 ATATATTTTATAATTAAATTT
1951175 A
1 A
1951176 AATAAAAATT
Statistics
Matches: 21, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
21 5 0.24
22 14 0.67
23 2 0.10
ACGTcount: A:0.41, C:0.00, G:0.00, T:0.59
Consensus pattern (21 bp):
ATATATTTTATAATTAAATTT
Found at i:1952201 original size:29 final size:29
Alignment explanation
Indices: 1952138--1952201 Score: 74
Period size: 29 Copynumber: 2.2 Consensus size: 29
1952128 TGCATCTCCA
* *
1952138 AACTTGAAGCTTTATTGAAGCTAATAACT
1 AACTTGAAGCTTTATTGAAGCTAAGAACC
** * *
1952167 TGCTTGCAGCTTTATTGAAGCTAAGAGCC
1 AACTTGAAGCTTTATTGAAGCTAAGAACC
1952196 AACTTG
1 AACTTG
1952202 TTAGCTCTTT
Statistics
Matches: 27, Mismatches: 8, Indels: 0
0.77 0.23 0.00
Matches are distributed among these distances:
29 27 1.00
ACGTcount: A:0.31, C:0.17, G:0.19, T:0.33
Consensus pattern (29 bp):
AACTTGAAGCTTTATTGAAGCTAAGAACC
Found at i:1953021 original size:19 final size:19
Alignment explanation
Indices: 1952974--1953064 Score: 77
Period size: 18 Copynumber: 5.0 Consensus size: 19
1952964 ACTAAAGTTA
1952974 AAATTTTAATATATTA-AT
1 AAATTTTAATATATTATAT
1952992 -AA-TTT-ATATATTATAT
1 AAATTTTAATATATTATAT
1953008 AAATTTTAATATATT-TAT
1 AAATTTTAATATATTATAT
* *
1953026 ATATTTATATTATATTTATAT
1 AAATTT-TAATATA-TTATAT
* * *
1953047 TATTTTTTA-ATATTATAT
1 AAATTTTAATATATTATAT
1953065 TTATTTTATC
Statistics
Matches: 59, Mismatches: 7, Indels: 14
0.74 0.09 0.17
Matches are distributed among these distances:
15 8 0.14
16 5 0.08
17 4 0.07
18 17 0.29
19 16 0.27
20 3 0.05
21 6 0.10
ACGTcount: A:0.42, C:0.00, G:0.00, T:0.58
Consensus pattern (19 bp):
AAATTTTAATATATTATAT
Found at i:1953039 original size:40 final size:40
Alignment explanation
Indices: 1952995--1953083 Score: 103
Period size: 40 Copynumber: 2.2 Consensus size: 40
1952985 TATTAATAAT
1952995 TTATATATTATA-TAAATTTTAATA-TAT-TTATATATTTATA
1 TTATAT-TTATATTAAATTTTAATATTATATT-TAT-TTTATA
** *
1953035 TTATATTTATATTATTTTTTAATATTATATTTATTTTATC
1 TTATATTTATATTAAATTTTAATATTATATTTATTTTATA
1953075 TTATATTTA
1 TTATATTTA
1953084 ATTTTTTATG
Statistics
Matches: 43, Mismatches: 3, Indels: 6
0.83 0.06 0.12
Matches are distributed among these distances:
39 5 0.12
40 30 0.70
41 6 0.14
42 2 0.05
ACGTcount: A:0.36, C:0.01, G:0.00, T:0.63
Consensus pattern (40 bp):
TTATATTTATATTAAATTTTAATATTATATTTATTTTATA
Found at i:1953041 original size:11 final size:11
Alignment explanation
Indices: 1953025--1953081 Score: 64
Period size: 11 Copynumber: 5.1 Consensus size: 11
1953015 AATATATTTA
1953025 TATATTTATAT
1 TATATTTATAT
1953036 TATATTTATAT
1 TATATTTATAT
*
1953047 TATTTTTTAATAT
1 TA-TATTT-ATAT
1953060 TATATTTAT-T
1 TATATTTATAT
1953070 T-TATCTTATAT
1 TATAT-TTATAT
1953081 T
1 T
1953082 TAATTTTTTA
Statistics
Matches: 40, Mismatches: 2, Indels: 8
0.80 0.04 0.16
Matches are distributed among these distances:
9 3 0.08
10 6 0.15
11 17 0.43
12 8 0.20
13 6 0.15
ACGTcount: A:0.32, C:0.02, G:0.00, T:0.67
Consensus pattern (11 bp):
TATATTTATAT
Found at i:1953083 original size:11 final size:10
Alignment explanation
Indices: 1953017--1953083 Score: 54
Period size: 11 Copynumber: 6.8 Consensus size: 10
1953007 TAAATTTTAA
1953017 TATATTTA--
1 TATATTTATT
1953025 TATATTTATAT
1 TATATTTAT-T
1953036 TATATTTATAT
1 TATATTTAT-T
1953047 TAT-TTT-TT
1 TATATTTATT
*
1953055 AATATTATATT
1 TATATT-TATT
1953066 TAT-TTTATCT
1 TATATTTAT-T
1953076 TATATTTA
1 TATATTTA
1953084 ATTTTTTATG
Statistics
Matches: 49, Mismatches: 2, Indels: 13
0.77 0.03 0.20
Matches are distributed among these distances:
8 11 0.22
9 6 0.12
10 10 0.20
11 22 0.45
ACGTcount: A:0.33, C:0.01, G:0.00, T:0.66
Consensus pattern (10 bp):
TATATTTATT
Found at i:1953089 original size:18 final size:19
Alignment explanation
Indices: 1953041--1953089 Score: 52
Period size: 16 Copynumber: 2.8 Consensus size: 19
1953031 TATATTATAT
*
1953041 TTATA-TTATTTTTTAATA
1 TTATATTTAATTTTTAATA
*
1953059 TTATATTT-A-TTTT-ATC
1 TTATATTTAATTTTTAATA
1953075 TTATATTTAATTTTT
1 TTATATTTAATTTTT
1953090 TATGTCGTAT
Statistics
Matches: 26, Mismatches: 2, Indels: 6
0.76 0.06 0.18
Matches are distributed among these distances:
16 10 0.38
17 5 0.19
18 9 0.35
19 2 0.08
ACGTcount: A:0.29, C:0.02, G:0.00, T:0.69
Consensus pattern (19 bp):
TTATATTTAATTTTTAATA
Found at i:1953983 original size:11 final size:11
Alignment explanation
Indices: 1953961--1954014 Score: 60
Period size: 12 Copynumber: 5.0 Consensus size: 11
1953951 TCATATTTTT
1953961 TATTTTTAAATA
1 TATTTTT-AATA
1953973 TATTTTTAATA
1 TATTTTTAATA
1953984 TAATTTTTAATA
1 T-ATTTTTAATA
*
1953996 -A--TTAAATA
1 TATTTTTAATA
1954004 TATTTTTAATA
1 TATTTTTAATA
1954015 AGCTCTATGT
Statistics
Matches: 36, Mismatches: 2, Indels: 9
0.77 0.04 0.19
Matches are distributed among these distances:
8 6 0.17
9 1 0.03
10 1 0.03
11 11 0.31
12 17 0.47
ACGTcount: A:0.43, C:0.00, G:0.00, T:0.57
Consensus pattern (11 bp):
TATTTTTAATA
Found at i:1954047 original size:24 final size:24
Alignment explanation
Indices: 1954002--1954047 Score: 56
Period size: 24 Copynumber: 1.9 Consensus size: 24
1953992 AATAATTAAA
* ** *
1954002 TATATTTTTAATAAGCTCTATGTT
1 TATATTTTTAAAAAAATATATGTT
1954026 TATATTTTTAAAAAAATATATG
1 TATATTTTTAAAAAAATATATG
1954048 GTATAAATTC
Statistics
Matches: 18, Mismatches: 4, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
24 18 1.00
ACGTcount: A:0.39, C:0.04, G:0.07, T:0.50
Consensus pattern (24 bp):
TATATTTTTAAAAAAATATATGTT
Found at i:1954145 original size:19 final size:20
Alignment explanation
Indices: 1954091--1954145 Score: 51
Period size: 21 Copynumber: 2.7 Consensus size: 20
1954081 AACTTGTAAA
1954091 ATAAAATTATTAA-TATTATT
1 ATAAAA-TATTAATTATTATT
**
1954111 ATAAAAATACAAAATTA-TATT
1 AT-AAAATA-TTAATTATTATT
1954132 ATAAAATATTAATT
1 ATAAAATATTAATT
1954146 TTGTTCAAAT
Statistics
Matches: 28, Mismatches: 4, Indels: 7
0.72 0.10 0.18
Matches are distributed among these distances:
19 4 0.14
20 10 0.36
21 12 0.43
22 2 0.07
ACGTcount: A:0.56, C:0.02, G:0.00, T:0.42
Consensus pattern (20 bp):
ATAAAATATTAATTATTATT
Found at i:1955022 original size:19 final size:18
Alignment explanation
Indices: 1954994--1955029 Score: 54
Period size: 19 Copynumber: 1.9 Consensus size: 18
1954984 AAAAATTATT
*
1954994 CTATTTTTAAAATCTAAAC
1 CTATTATTAAAAT-TAAAC
1955013 CTATTATTAAAATTAAA
1 CTATTATTAAAATTAAA
1955030 ATTTCAATTA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
18 4 0.25
19 12 0.75
ACGTcount: A:0.47, C:0.11, G:0.00, T:0.42
Consensus pattern (18 bp):
CTATTATTAAAATTAAAC
Found at i:1955371 original size:12 final size:12
Alignment explanation
Indices: 1955335--1955372 Score: 60
Period size: 12 Copynumber: 3.2 Consensus size: 12
1955325 ATCTTTGTGG
1955335 TATTTTTTATAT
1 TATTTTTTATAT
*
1955347 TATATTTTA-AT
1 TATTTTTTATAT
1955358 TATTTTTTATAT
1 TATTTTTTATAT
1955370 TAT
1 TAT
1955373 ATTCGTGTAA
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
11 10 0.43
12 13 0.57
ACGTcount: A:0.29, C:0.00, G:0.00, T:0.71
Consensus pattern (12 bp):
TATTTTTTATAT
Found at i:1955567 original size:2 final size:2
Alignment explanation
Indices: 1955560--1955585 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
1955550 TTGAGCTAAA
1955560 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
1955586 TTGTATTTTA
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:1956603 original size:18 final size:18
Alignment explanation
Indices: 1956570--1956604 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
1956560 TAAATATATT
*
1956570 ATTAAATTCATATTAAAA
1 ATTAAATTAATATTAAAA
*
1956588 ATTAAATTAATTTTAAA
1 ATTAAATTAATATTAAA
1956605 TCTAAATTTT
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:0.54, C:0.03, G:0.00, T:0.43
Consensus pattern (18 bp):
ATTAAATTAATATTAAAA
Found at i:1956739 original size:28 final size:30
Alignment explanation
Indices: 1956681--1956749 Score: 74
Period size: 28 Copynumber: 2.4 Consensus size: 30
1956671 ATTGATTTAT
* * *
1956681 TAAATTTA-AATAATATTTTAAATATATAA
1 TAAATATATAATAATAATATAAATATATAA
1956710 T-AATA-ATAATAATAATATAAATAT-TAAA
1 TAAATATATAATAATAATATAAATATAT-AA
1956738 TAAATATATAAT
1 TAAATATATAAT
1956750 TATTAAATTT
Statistics
Matches: 33, Mismatches: 3, Indels: 7
0.77 0.07 0.16
Matches are distributed among these distances:
27 2 0.06
28 21 0.64
29 5 0.15
30 5 0.15
ACGTcount: A:0.59, C:0.00, G:0.00, T:0.41
Consensus pattern (30 bp):
TAAATATATAATAATAATATAAATATATAA
Found at i:1960444 original size:14 final size:14
Alignment explanation
Indices: 1960387--1960444 Score: 55
Period size: 14 Copynumber: 4.1 Consensus size: 14
1960377 ATGTTAAAAA
*
1960387 TAAAT-AATTTAAT
1 TAAATAAATTAAAT
*
1960400 TGAATAAAATTAAAAT
1 TAAAT-AAATT-AAAT
*
1960416 CAAATAAATTAAAT
1 TAAATAAATTAAAT
*
1960430 TAAATTAATTAAAT
1 TAAATAAATTAAAT
1960444 T
1 T
1960445 TATCAATTTT
Statistics
Matches: 36, Mismatches: 6, Indels: 5
0.77 0.13 0.11
Matches are distributed among these distances:
13 4 0.11
14 17 0.47
15 9 0.25
16 6 0.17
ACGTcount: A:0.59, C:0.02, G:0.02, T:0.38
Consensus pattern (14 bp):
TAAATAAATTAAAT
Found at i:1964926 original size:10 final size:10
Alignment explanation
Indices: 1964888--1964933 Score: 56
Period size: 10 Copynumber: 4.6 Consensus size: 10
1964878 ACCTCCACCG
*
1964888 CTTCCTTCAC
1 CTTCCTTCCC
* * *
1964898 TTTCCTTTCA
1 CTTCCTTCCC
1964908 CTTCCTTCCC
1 CTTCCTTCCC
1964918 CTTCCTTCCC
1 CTTCCTTCCC
1964928 CTTCCT
1 CTTCCT
1964934 CCTTCTGCAA
Statistics
Matches: 29, Mismatches: 7, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
10 29 1.00
ACGTcount: A:0.04, C:0.50, G:0.00, T:0.46
Consensus pattern (10 bp):
CTTCCTTCCC
Found at i:1966468 original size:12 final size:13
Alignment explanation
Indices: 1966447--1966475 Score: 58
Period size: 13 Copynumber: 2.2 Consensus size: 13
1966437 TAATGATTTC
1966447 TTTTCTTTTTTTT
1 TTTTCTTTTTTTT
1966460 TTTTCTTTTTTTT
1 TTTTCTTTTTTTT
1966473 TTT
1 TTT
1966476 ACATTTTGAT
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 16 1.00
ACGTcount: A:0.00, C:0.07, G:0.00, T:0.93
Consensus pattern (13 bp):
TTTTCTTTTTTTT
Found at i:1968532 original size:15 final size:14
Alignment explanation
Indices: 1968496--1968534 Score: 51
Period size: 15 Copynumber: 2.6 Consensus size: 14
1968486 ACCCAATTTC
1968496 AATCCAAACTTAAA
1 AATCCAAACTTAAA
*
1968510 ACACCCAAACTTAAA
1 A-ATCCAAACTTAAA
1968525 TAATCCAAAC
1 -AATCCAAAC
1968535 CCCAAACAAT
Statistics
Matches: 21, Mismatches: 2, Indels: 3
0.81 0.08 0.12
Matches are distributed among these distances:
14 1 0.05
15 19 0.90
16 1 0.05
ACGTcount: A:0.54, C:0.28, G:0.00, T:0.18
Consensus pattern (14 bp):
AATCCAAACTTAAA
Found at i:1968958 original size:19 final size:19
Alignment explanation
Indices: 1968934--1969001 Score: 57
Period size: 19 Copynumber: 3.3 Consensus size: 19
1968924 GATTCAAAAA
1968934 ACACATCCTATTAAAATAC
1 ACACATCCTATTAAAATAC
* *
1968953 ACACAT-ATATTAGAAATTCAAAAA
1 ACACATCCTATTA-AAA-T----AC
1968977 ACACATCCTATTAAAATAC
1 ACACATCCTATTAAAATAC
1968996 ACACAT
1 ACACAT
1969002 ATATTAGTTA
Statistics
Matches: 38, Mismatches: 4, Indels: 14
0.68 0.07 0.25
Matches are distributed among these distances:
18 5 0.13
19 16 0.42
20 1 0.03
23 1 0.03
24 10 0.26
25 5 0.13
ACGTcount: A:0.51, C:0.22, G:0.01, T:0.25
Consensus pattern (19 bp):
ACACATCCTATTAAAATAC
Found at i:1968973 original size:43 final size:43
Alignment explanation
Indices: 1968925--1969008 Score: 168
Period size: 43 Copynumber: 2.0 Consensus size: 43
1968915 GTCAACGCAG
1968925 ATTCAAAAAACACATCCTATTAAAATACACACATATATTAGAA
1 ATTCAAAAAACACATCCTATTAAAATACACACATATATTAGAA
1968968 ATTCAAAAAACACATCCTATTAAAATACACACATATATTAG
1 ATTCAAAAAACACATCCTATTAAAATACACACATATATTAG
1969009 TTAAATACAC
Statistics
Matches: 41, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
43 41 1.00
ACGTcount: A:0.52, C:0.19, G:0.02, T:0.26
Consensus pattern (43 bp):
ATTCAAAAAACACATCCTATTAAAATACACACATATATTAGAA
Found at i:1969020 original size:2 final size:2
Alignment explanation
Indices: 1969015--1969065 Score: 88
Period size: 2 Copynumber: 26.5 Consensus size: 2
1969005 TTAGTTAAAT
1969015 AC AC AC AC AC AC AC AC AC AC A- AC AC AC AC AC AC AC AC AC A-
1 AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC
1969055 AC AC AC AC AC A
1 AC AC AC AC AC A
1969066 GAAGACAATT
Statistics
Matches: 47, Mismatches: 0, Indels: 4
0.92 0.00 0.08
Matches are distributed among these distances:
1 2 0.04
2 45 0.96
ACGTcount: A:0.53, C:0.47, G:0.00, T:0.00
Consensus pattern (2 bp):
AC
Found at i:1969041 original size:19 final size:19
Alignment explanation
Indices: 1969017--1969065 Score: 98
Period size: 19 Copynumber: 2.6 Consensus size: 19
1969007 AGTTAAATAC
1969017 ACACACACACACACACACA
1 ACACACACACACACACACA
1969036 ACACACACACACACACACA
1 ACACACACACACACACACA
1969055 ACACACACACA
1 ACACACACACA
1969066 GAAGACAATT
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 30 1.00
ACGTcount: A:0.53, C:0.47, G:0.00, T:0.00
Consensus pattern (19 bp):
ACACACACACACACACACA
Found at i:1969344 original size:2 final size:2
Alignment explanation
Indices: 1969337--1969391 Score: 101
Period size: 2 Copynumber: 27.5 Consensus size: 2
1969327 ATCCACAAAA
*
1969337 AG AG AG AG AA AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG
1 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG
1969379 AG AG AG AG AG AG A
1 AG AG AG AG AG AG A
1969392 AACAAAACAA
Statistics
Matches: 51, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
2 51 1.00
ACGTcount: A:0.53, C:0.00, G:0.47, T:0.00
Consensus pattern (2 bp):
AG
Found at i:1972542 original size:29 final size:30
Alignment explanation
Indices: 1972493--1972555 Score: 92
Period size: 29 Copynumber: 2.1 Consensus size: 30
1972483 ATACTTTCAT
* *
1972493 CTAACAATTTTGTATCATCTCAGTCAAACC
1 CTAACAATTTAGTATCATCTCAATCAAACC
*
1972523 CTAACAA-TTAGTATCGTCTCAATCAAACC
1 CTAACAATTTAGTATCATCTCAATCAAACC
1972552 CTAA
1 CTAA
1972556 GTTAGCTAGC
Statistics
Matches: 30, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
29 23 0.77
30 7 0.23
ACGTcount: A:0.37, C:0.27, G:0.06, T:0.30
Consensus pattern (30 bp):
CTAACAATTTAGTATCATCTCAATCAAACC
Found at i:1973954 original size:6 final size:6
Alignment explanation
Indices: 1973943--1973990 Score: 71
Period size: 6 Copynumber: 8.2 Consensus size: 6
1973933 AAAATTTTTT
* *
1973943 ATTTAA ATTTAA ATTTAA ATTTAA ATTT-A ATTTAA CTTTAA AATTAA
1 ATTTAA ATTTAA ATTTAA ATTTAA ATTTAA ATTTAA ATTTAA ATTTAA
1973990 A
1 A
1973991 ATTATTATTA
Statistics
Matches: 38, Mismatches: 3, Indels: 2
0.88 0.07 0.05
Matches are distributed among these distances:
5 5 0.13
6 33 0.87
ACGTcount: A:0.50, C:0.02, G:0.00, T:0.48
Consensus pattern (6 bp):
ATTTAA
Found at i:1973966 original size:18 final size:18
Alignment explanation
Indices: 1973943--1973990 Score: 71
Period size: 17 Copynumber: 2.7 Consensus size: 18
1973933 AAAATTTTTT
1973943 ATTTAAATTTAAATTTAA
1 ATTTAAATTTAAATTTAA
1973961 ATTTAAATTT-AATTTAA
1 ATTTAAATTTAAATTTAA
* *
1973978 CTTTAAAATTAAA
1 ATTTAAATTTAAA
1973991 ATTATTATTA
Statistics
Matches: 27, Mismatches: 2, Indels: 2
0.87 0.06 0.06
Matches are distributed among these distances:
17 15 0.56
18 12 0.44
ACGTcount: A:0.50, C:0.02, G:0.00, T:0.48
Consensus pattern (18 bp):
ATTTAAATTTAAATTTAA
Found at i:1974106 original size:27 final size:27
Alignment explanation
Indices: 1974059--1974113 Score: 67
Period size: 27 Copynumber: 2.0 Consensus size: 27
1974049 TTGAGTTAAA
*
1974059 TTAATTTATATTATTAAAAATAAAATT
1 TTAATTTATATTAATAAAAATAAAATT
* *
1974086 TTAATTTA-ATCTAATATAAATCAAATT
1 TTAATTTATAT-TAATAAAAATAAAATT
1974113 T
1 T
1974114 ATCAAATTAA
Statistics
Matches: 24, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
26 2 0.08
27 22 0.92
ACGTcount: A:0.49, C:0.04, G:0.00, T:0.47
Consensus pattern (27 bp):
TTAATTTATATTAATAAAAATAAAATT
Found at i:1974367 original size:79 final size:79
Alignment explanation
Indices: 1974236--1974392 Score: 314
Period size: 79 Copynumber: 2.0 Consensus size: 79
1974226 ATGCCATTAA
1974236 CTTCATCAATTCTTCTTGTACTTTGTTTTTAAATTTATAGACCGAATTGTTTTCATGTCCATTCA
1 CTTCATCAATTCTTCTTGTACTTTGTTTTTAAATTTATAGACCGAATTGTTTTCATGTCCATTCA
1974301 TTATTTATTTTATT
66 TTATTTATTTTATT
1974315 CTTCATCAATTCTTCTTGTACTTTGTTTTTAAATTTATAGACCGAATTGTTTTCATGTCCATTCA
1 CTTCATCAATTCTTCTTGTACTTTGTTTTTAAATTTATAGACCGAATTGTTTTCATGTCCATTCA
1974380 TTATTTATTTTAT
66 TTATTTATTTTAT
1974393 ATTTATATAT
Statistics
Matches: 78, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
79 78 1.00
ACGTcount: A:0.23, C:0.15, G:0.08, T:0.54
Consensus pattern (79 bp):
CTTCATCAATTCTTCTTGTACTTTGTTTTTAAATTTATAGACCGAATTGTTTTCATGTCCATTCA
TTATTTATTTTATT
Found at i:1974393 original size:40 final size:40
Alignment explanation
Indices: 1974269--1974393 Score: 98
Period size: 40 Copynumber: 3.1 Consensus size: 40
1974259 TGTTTTTAAA
1974269 TTTATAGACCGAATTGTTTTCATGTCCATTCATTATTTAT
1 TTTATAGACCGAATTGTTTTCATGTCCATTCATTATTTAT
** * * * * ** *
1974309 TTTATTCTTCATC-AA-T-TCTTCTTGTAC-TTTGTT-TTTAAA
1 TTTA---TAGACCGAATTGTTTTCATGTCCATTCATTATTT-AT
1974348 TTTATAGACCGAATTGTTTTCATGTCCATTCATTATTTAT
1 TTTATAGACCGAATTGTTTTCATGTCCATTCATTATTTAT
1974388 TTTATA
1 TTTATA
1974394 TTTATATATT
Statistics
Matches: 58, Mismatches: 18, Indels: 18
0.62 0.19 0.19
Matches are distributed among these distances:
36 3 0.05
37 2 0.03
38 4 0.07
39 17 0.29
40 23 0.40
41 4 0.07
42 2 0.03
43 3 0.05
ACGTcount: A:0.24, C:0.14, G:0.08, T:0.54
Consensus pattern (40 bp):
TTTATAGACCGAATTGTTTTCATGTCCATTCATTATTTAT
Found at i:1974403 original size:15 final size:15
Alignment explanation
Indices: 1974380--1974446 Score: 66
Period size: 15 Copynumber: 4.5 Consensus size: 15
1974370 TGTCCATTCA
*
1974380 TTATTTATTTTATAT
1 TTATATATTTTATAT
1974395 TTATATATTTTATA-
1 TTATATATTTTATAT
* *
1974409 ATATCATA-ATTATAT
1 TTAT-ATATTTTATAT
*
1974424 TTAAAATATTTTATAT
1 TT-ATATATTTTATAT
1974440 TTATATA
1 TTATATA
1974447 AAATTTGATA
Statistics
Matches: 41, Mismatches: 7, Indels: 8
0.73 0.12 0.14
Matches are distributed among these distances:
14 8 0.20
15 24 0.59
16 9 0.22
ACGTcount: A:0.39, C:0.01, G:0.00, T:0.60
Consensus pattern (15 bp):
TTATATATTTTATAT
Found at i:1974577 original size:33 final size:33
Alignment explanation
Indices: 1974515--1974577 Score: 85
Period size: 33 Copynumber: 1.9 Consensus size: 33
1974505 TTATATTTGT
*
1974515 ATTATTTTTTATTATATTTTAGATTTTATTTTA
1 ATTATTTTTTATTATATTTTAGATATTATTTTA
1974548 ATTATTTTTTA-TATCATATTTA-ATATTATT
1 ATTATTTTTTATTAT-AT-TTTAGATATTATT
1974578 AAATCTAATT
Statistics
Matches: 27, Mismatches: 1, Indels: 4
0.84 0.03 0.12
Matches are distributed among these distances:
32 3 0.11
33 20 0.74
34 4 0.15
ACGTcount: A:0.30, C:0.02, G:0.02, T:0.67
Consensus pattern (33 bp):
ATTATTTTTTATTATATTTTAGATATTATTTTA
Found at i:1974908 original size:17 final size:16
Alignment explanation
Indices: 1974886--1974937 Score: 54
Period size: 15 Copynumber: 3.2 Consensus size: 16
1974876 TTTAAGATAT
1974886 TTTATATTCATATAAAA
1 TTTATATT-ATATAAAA
*
1974903 TTTATATGT-TA-ATAA
1 TTTATAT-TATATAAAA
*
1974918 TTCATATTATATAAAA
1 TTTATATTATATAAAA
1974934 TTTA
1 TTTA
1974938 AAATATTTAT
Statistics
Matches: 28, Mismatches: 4, Indels: 7
0.72 0.10 0.18
Matches are distributed among these distances:
14 1 0.04
15 11 0.39
16 8 0.29
17 7 0.25
18 1 0.04
ACGTcount: A:0.44, C:0.04, G:0.02, T:0.50
Consensus pattern (16 bp):
TTTATATTATATAAAA
Found at i:1974978 original size:23 final size:21
Alignment explanation
Indices: 1974944--1975015 Score: 65
Period size: 23 Copynumber: 3.2 Consensus size: 21
1974934 TTTAAAATAT
1974944 TTATATATTTATATAATATTCATA
1 TTAT-TATTTATAT-ATATT-ATA
* *
1974968 TTATTTTTTATATTATATTTTAA
1 TTATTATTTATA-TATATTAT-A
1974991 TTATTATTTAT-TATATTTATA
1 TTATTATTTATATATA-TTATA
1975012 TTAT
1 TTAT
1975016 ATAATCATAT
Statistics
Matches: 41, Mismatches: 4, Indels: 9
0.76 0.07 0.17
Matches are distributed among these distances:
21 9 0.22
22 4 0.10
23 23 0.56
24 5 0.12
ACGTcount: A:0.35, C:0.01, G:0.00, T:0.64
Consensus pattern (21 bp):
TTATTATTTATATATATTATA
Found at i:1974982 original size:12 final size:12
Alignment explanation
Indices: 1974965--1975007 Score: 50
Period size: 12 Copynumber: 3.4 Consensus size: 12
1974955 TATAATATTC
1974965 ATATTATTTTTT
1 ATATTATTTTTT
*
1974977 ATATTATATTTTA
1 ATATTAT-TTTTT
*
1974990 ATTATTATTTATT
1 A-TATTATTTTTT
1975003 ATATT
1 ATATT
1975008 TATATTATAT
Statistics
Matches: 26, Mismatches: 3, Indels: 4
0.79 0.09 0.12
Matches are distributed among these distances:
12 11 0.42
13 9 0.35
14 6 0.23
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (12 bp):
ATATTATTTTTT
Found at i:1975014 original size:21 final size:20
Alignment explanation
Indices: 1974940--1975015 Score: 66
Period size: 21 Copynumber: 3.6 Consensus size: 20
1974930 AAAATTTAAA
* *
1974940 ATATTTATA-TATTTATATA
1 ATATTTATATTATTTTTATT
*
1974959 ATATTCATATTATTTTTTATATT
1 ATATTTATATTA--TTTT-TATT
1974982 ATATTT-TAATTATTATTTATT
1 ATATTTAT-ATTATT-TTTATT
1975003 ATATTTATATTAT
1 ATATTTATATTAT
1975016 ATAATCATAT
Statistics
Matches: 46, Mismatches: 4, Indels: 12
0.74 0.06 0.19
Matches are distributed among these distances:
19 8 0.17
20 2 0.04
21 17 0.37
22 7 0.15
23 12 0.26
ACGTcount: A:0.36, C:0.01, G:0.00, T:0.63
Consensus pattern (20 bp):
ATATTTATATTATTTTTATT
Found at i:1975016 original size:11 final size:11
Alignment explanation
Indices: 1974947--1975017 Score: 67
Period size: 11 Copynumber: 6.5 Consensus size: 11
1974937 AAAATATTTA
1974947 TATATTTATAT
1 TATATTTATAT
* *
1974958 AATATTCATAT
1 TATATTTATAT
*
1974969 TATTTTTTATAT
1 TA-TATTTATAT
1974981 TATATTT-TAAT
1 TATATTTAT-AT
1974992 TAT-TATT-TAT
1 TATAT-TTATAT
1975002 TATATTTATAT
1 TATATTTATAT
1975013 TATAT
1 TATAT
1975018 AATCATATTA
Statistics
Matches: 49, Mismatches: 6, Indels: 10
0.75 0.09 0.15
Matches are distributed among these distances:
10 9 0.18
11 31 0.63
12 9 0.18
ACGTcount: A:0.35, C:0.01, G:0.00, T:0.63
Consensus pattern (11 bp):
TATATTTATAT
Found at i:1975286 original size:23 final size:23
Alignment explanation
Indices: 1975238--1975303 Score: 71
Period size: 23 Copynumber: 2.9 Consensus size: 23
1975228 TAATAAAATA
* * *
1975238 TAAATTTAAACTCAAACCT-ATT
1 TAAATTTAAACTAAAAACTCATC
*
1975260 TAAATCTAAACTAAAAACTCATC
1 TAAATTTAAACTAAAAACTCATC
* *
1975283 TAAATTTAAATTAAAAGCTCA
1 TAAATTTAAACTAAAAACTCA
1975304 ATTAAAAAAA
Statistics
Matches: 36, Mismatches: 7, Indels: 1
0.82 0.16 0.02
Matches are distributed among these distances:
22 16 0.44
23 20 0.56
ACGTcount: A:0.50, C:0.17, G:0.02, T:0.32
Consensus pattern (23 bp):
TAAATTTAAACTAAAAACTCATC
Found at i:1975309 original size:23 final size:22
Alignment explanation
Indices: 1975259--1975309 Score: 57
Period size: 23 Copynumber: 2.2 Consensus size: 22
1975249 TCAAACCTAT
1975259 TTAAATCTAAACTAAAAACTCA
1 TTAAATCTAAACTAAAAACTCA
* * *
1975281 TCTAAATTTAAATTAAAAGCTCAA
1 T-TAAATCTAAACTAAAAACTC-A
1975305 TTAAA
1 TTAAA
1975310 AAAATAAAAT
Statistics
Matches: 24, Mismatches: 3, Indels: 3
0.80 0.10 0.10
Matches are distributed among these distances:
22 1 0.04
23 21 0.88
24 2 0.08
ACGTcount: A:0.53, C:0.14, G:0.02, T:0.31
Consensus pattern (22 bp):
TTAAATCTAAACTAAAAACTCA
Found at i:1975330 original size:27 final size:30
Alignment explanation
Indices: 1975294--1975357 Score: 89
Period size: 27 Copynumber: 2.2 Consensus size: 30
1975284 AAATTTAAAT
*
1975294 TAAAAGCTCAATTAAAA-AAATAAA-ATA-A
1 TAAAA-CTCAATTAAAATAAAAAAATATAGA
1975322 TAAAACTCAATTAAAATAAAAAAATATAGA
1 TAAAACTCAATTAAAATAAAAAAATATAGA
1975352 TAAAAC
1 TAAAAC
1975358 AAAATAAAAA
Statistics
Matches: 32, Mismatches: 1, Indels: 4
0.86 0.03 0.11
Matches are distributed among these distances:
27 11 0.34
28 11 0.34
29 3 0.09
30 7 0.22
ACGTcount: A:0.67, C:0.08, G:0.03, T:0.22
Consensus pattern (30 bp):
TAAAACTCAATTAAAATAAAAAAATATAGA
Found at i:1975380 original size:24 final size:25
Alignment explanation
Indices: 1975334--1975394 Score: 67
Period size: 24 Copynumber: 2.6 Consensus size: 25
1975324 AAACTCAATT
* *
1975334 AAAATAAAAA-AATATAGATAAAAC
1 AAAATAAAAATAATCTAGAAAAAAC
1975358 AAAATAAAAATAATCT-GAAAAAAC
1 AAAATAAAAATAATCTAGAAAAAAC
*
1975382 -TAA-AAAAATAATC
1 AAAATAAAAATAATC
1975395 AAACTGATCA
Statistics
Matches: 33, Mismatches: 3, Indels: 4
0.82 0.08 0.10
Matches are distributed among these distances:
22 10 0.30
23 2 0.06
24 17 0.52
25 4 0.12
ACGTcount: A:0.72, C:0.07, G:0.03, T:0.18
Consensus pattern (25 bp):
AAAATAAAAATAATCTAGAAAAAAC
Found at i:1975506 original size:9 final size:9
Alignment explanation
Indices: 1975449--1975483 Score: 70
Period size: 9 Copynumber: 3.9 Consensus size: 9
1975439 TTTAACATCG
1975449 ATTAATTTA
1 ATTAATTTA
1975458 ATTAATTTA
1 ATTAATTTA
1975467 ATTAATTTA
1 ATTAATTTA
1975476 ATTAATTT
1 ATTAATTT
1975484 TAATATTAAA
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
9 26 1.00
ACGTcount: A:0.43, C:0.00, G:0.00, T:0.57
Consensus pattern (9 bp):
ATTAATTTA
Found at i:1975508 original size:18 final size:17
Alignment explanation
Indices: 1975457--1975508 Score: 52
Period size: 18 Copynumber: 2.9 Consensus size: 17
1975447 CGATTAATTT
*
1975457 AATTAATTTAATTAATTT
1 AATTAATTTAATT-ATTA
1975475 AATTAATTTTAA-TATTAA
1 AATTAA-TTTAATTATT-A
*
1975493 AATTAATTAAATTATT
1 AATTAATTTAATTATT
1975509 TTTTTAATTT
Statistics
Matches: 29, Mismatches: 2, Indels: 6
0.78 0.05 0.16
Matches are distributed among these distances:
17 7 0.24
18 17 0.59
19 5 0.17
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (17 bp):
AATTAATTTAATTATTA
Found at i:1975522 original size:27 final size:25
Alignment explanation
Indices: 1975404--1975522 Score: 73
Period size: 27 Copynumber: 4.6 Consensus size: 25
1975394 CAAACTGATC
* * **
1975404 AATTTTAATATCAATTTAATTATTTT
1 AATTTTAAT-TTAAATTAATTAAATT
** *
1975430 AATTTTAAATTTAACATCGATTAATTT
1 AATTTT-AATTTAA-ATTAATTAAATT
*
1975457 AA--TTAATTT-AATTAATTTAATT
1 AATTTTAATTTAAATTAATTAAATT
1975479 AATTTTAATATTAAAATTAATTAAATT
1 AATTTTAAT-TT-AAATTAATTAAATT
*
1975506 ATTTTTTTAATTTAAAT
1 A--ATTTTAATTTAAAT
1975523 AAATCAAACT
Statistics
Matches: 73, Mismatches: 11, Indels: 17
0.72 0.11 0.17
Matches are distributed among these distances:
22 10 0.14
23 1 0.01
24 10 0.14
25 4 0.05
26 9 0.12
27 30 0.41
28 2 0.03
29 7 0.10
ACGTcount: A:0.43, C:0.03, G:0.01, T:0.54
Consensus pattern (25 bp):
AATTTTAATTTAAATTAATTAAATT
Found at i:1976211 original size:17 final size:17
Alignment explanation
Indices: 1976189--1976238 Score: 52
Period size: 17 Copynumber: 3.1 Consensus size: 17
1976179 ATATGTGAAT
1976189 ATATTAAAATTTATATA
1 ATATTAAAATTTATATA
*
1976206 ATATT--AA-TTATTATC
1 ATATTAAAATTTA-TATA
*
1976221 ATATCAAAATTTATATA
1 ATATTAAAATTTATATA
1976238 A
1 A
1976239 ATATATAATA
Statistics
Matches: 26, Mismatches: 3, Indels: 8
0.70 0.08 0.22
Matches are distributed among these distances:
14 3 0.12
15 9 0.35
17 11 0.42
18 3 0.12
ACGTcount: A:0.50, C:0.04, G:0.00, T:0.46
Consensus pattern (17 bp):
ATATTAAAATTTATATA
Found at i:1991379 original size:25 final size:26
Alignment explanation
Indices: 1991351--1991426 Score: 73
Period size: 27 Copynumber: 2.8 Consensus size: 26
1991341 GGATTCCATT
*
1991351 TTAATTTTTTTAAAAATTAAAT-AAA
1 TTAATTTTTTAAAAAATTAAATCAAA
*
1991376 TTAATTAAATTTAAAAAATATCAAATCAAA
1 TTAATT--TTTTAAAAAAT-T-AAATCAAA
* *
1991406 TAAATTTTATAAAAAATTAAA
1 TTAATTTTTTAAAAAATTAAA
1991427 ATAATAAATT
Statistics
Matches: 41, Mismatches: 5, Indels: 9
0.75 0.09 0.16
Matches are distributed among these distances:
25 6 0.15
26 3 0.07
27 10 0.24
28 10 0.24
29 4 0.10
30 8 0.20
ACGTcount: A:0.58, C:0.03, G:0.00, T:0.39
Consensus pattern (26 bp):
TTAATTTTTTAAAAAATTAAATCAAA
Found at i:1991414 original size:26 final size:24
Alignment explanation
Indices: 1991381--1991441 Score: 63
Period size: 25 Copynumber: 2.5 Consensus size: 24
1991371 ATAAATTAAT
1991381 TAAA-TTTAAAAAATATC-AAATCAAA
1 TAAATTTTAAAAAA-ATCAAAAT--AA
*
1991406 TAAATTTTATAAAAAATTAAAATAA
1 TAAATTTTA-AAAAAATCAAAATAA
1991431 TAAATTTTAAA
1 TAAATTTTAAA
1991442 TTAATTAAAA
Statistics
Matches: 32, Mismatches: 1, Indels: 7
0.80 0.03 0.17
Matches are distributed among these distances:
24 2 0.06
25 15 0.47
26 6 0.19
27 9 0.28
ACGTcount: A:0.62, C:0.03, G:0.00, T:0.34
Consensus pattern (24 bp):
TAAATTTTAAAAAAATCAAAATAA
Found at i:1991588 original size:14 final size:14
Alignment explanation
Indices: 1991569--1991608 Score: 53
Period size: 14 Copynumber: 2.9 Consensus size: 14
1991559 AATAAATCAA
*
1991569 TTAAATAAATTTAT
1 TTAAATAAATTTAC
*
1991583 TTAAATTAATTTAC
1 TTAAATAAATTTAC
*
1991597 TTAATTAAATTT
1 TTAAATAAATTT
1991609 TATCAAGATC
Statistics
Matches: 22, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
14 22 1.00
ACGTcount: A:0.45, C:0.03, G:0.00, T:0.53
Consensus pattern (14 bp):
TTAAATAAATTTAC
Found at i:1992491 original size:28 final size:28
Alignment explanation
Indices: 1992450--1992506 Score: 78
Period size: 28 Copynumber: 2.0 Consensus size: 28
1992440 TTTGAATCGA
*
1992450 ACTTGACTCTTTTTCAATTATATAATAT
1 ACTTGACTCGTTTTCAATTATATAATAT
* **
1992478 ACTTGATTCGTTTTTTATTATATAATAT
1 ACTTGACTCGTTTTCAATTATATAATAT
1992506 A
1 A
1992507 TATTAGTTTT
Statistics
Matches: 25, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
28 25 1.00
ACGTcount: A:0.32, C:0.11, G:0.05, T:0.53
Consensus pattern (28 bp):
ACTTGACTCGTTTTCAATTATATAATAT
Found at i:1992535 original size:26 final size:25
Alignment explanation
Indices: 1992466--1992528 Score: 72
Period size: 28 Copynumber: 2.4 Consensus size: 25
1992456 CTCTTTTTCA
* *
1992466 ATTATATAATATACTTGATTCGTTTTTT
1 ATTATATAATATA--T-ATTAGTTTTGT
1992494 ATTATATAATATATATTAGTTTTGT
1 ATTATATAATATATATTAGTTTTGT
1992519 ATATATATAA
1 AT-TATATAA
1992529 ATTATATAAT
Statistics
Matches: 32, Mismatches: 2, Indels: 4
0.84 0.05 0.11
Matches are distributed among these distances:
25 11 0.34
26 8 0.25
28 13 0.41
ACGTcount: A:0.37, C:0.03, G:0.06, T:0.54
Consensus pattern (25 bp):
ATTATATAATATATATTAGTTTTGT
Found at i:1992542 original size:26 final size:24
Alignment explanation
Indices: 1992488--1992551 Score: 60
Period size: 26 Copynumber: 2.6 Consensus size: 24
1992478 ACTTGATTCG
*
1992488 TTTTTTATTATATAATATATATTAG
1 TTTTTTATTATATAATATATA-TAA
*
1992513 TTTTGTATATATATAA-ATTATATAA
1 TTTTTTAT-TATATAATA-TATATAA
*
1992538 -TTTTTATTTTATAA
1 TTTTTTATTATATAA
1992552 AGTATAAATA
Statistics
Matches: 33, Mismatches: 4, Indels: 6
0.77 0.09 0.14
Matches are distributed among these distances:
23 6 0.18
24 6 0.18
25 10 0.30
26 11 0.33
ACGTcount: A:0.38, C:0.00, G:0.03, T:0.59
Consensus pattern (24 bp):
TTTTTTATTATATAATATATATAA
Found at i:1992557 original size:23 final size:23
Alignment explanation
Indices: 1992489--1992557 Score: 68
Period size: 25 Copynumber: 2.8 Consensus size: 23
1992479 CTTGATTCGT
*
1992489 TTTTTATTATATAATATATATTAG
1 TTTTTATTATATAA-ATATATTAA
1992513 TTTTGTATATATATAAAT-TATATAA
1 TTTT-TAT-TATATAAATATAT-TAA
*
1992538 TTTTTATTTTATAAAGTATA
1 TTTTTATTATATAAA-TATA
1992558 AATATATAAT
Statistics
Matches: 38, Mismatches: 2, Indels: 9
0.78 0.04 0.18
Matches are distributed among these distances:
23 7 0.18
24 11 0.29
25 13 0.34
26 7 0.18
ACGTcount: A:0.39, C:0.00, G:0.04, T:0.57
Consensus pattern (23 bp):
TTTTTATTATATAAATATATTAA
Found at i:1992893 original size:18 final size:18
Alignment explanation
Indices: 1992857--1992890 Score: 61
Period size: 18 Copynumber: 1.9 Consensus size: 18
1992847 TTTTTTTAAT
1992857 AAAAATTAATTTATTTTA
1 AAAAATTAATTTATTTTA
1992875 AAAAATTAA-TTATTTT
1 AAAAATTAATTTATTTT
1992891 TAAGAAAGAT
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
17 7 0.44
18 9 0.56
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (18 bp):
AAAAATTAATTTATTTTA
Found at i:1994588 original size:13 final size:13
Alignment explanation
Indices: 1994570--1994602 Score: 50
Period size: 12 Copynumber: 2.6 Consensus size: 13
1994560 AATTGTAAAA
*
1994570 AAATTTAAAATTT
1 AAATTTAAAACTT
1994583 AAATTT-AAACTT
1 AAATTTAAAACTT
1994595 AAATTTAA
1 AAATTTAA
1994603 TTTGATTGAG
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
12 11 0.61
13 7 0.39
ACGTcount: A:0.55, C:0.03, G:0.00, T:0.42
Consensus pattern (13 bp):
AAATTTAAAACTT
Found at i:1994675 original size:22 final size:22
Alignment explanation
Indices: 1994649--1994690 Score: 68
Period size: 22 Copynumber: 1.9 Consensus size: 22
1994639 TTTAAAAAAT
1994649 TATTTTTAT-ATTAATATTTATA
1 TATTTTTATAATTAA-ATTTATA
1994671 TATTTTTATAATTAAATTTA
1 TATTTTTATAATTAAATTTA
1994691 AAATAAATAT
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
22 14 0.74
23 5 0.26
ACGTcount: A:0.38, C:0.00, G:0.00, T:0.62
Consensus pattern (22 bp):
TATTTTTATAATTAAATTTATA
Found at i:1998209 original size:23 final size:23
Alignment explanation
Indices: 1998154--1998209 Score: 60
Period size: 23 Copynumber: 2.4 Consensus size: 23
1998144 TACTAATATT
*
1998154 TTTAAATTTTTTTTATATATTTA
1 TTTAAATATTTTTTATATATTTA
** *
1998177 AATAATTATTTTTTATAT-TTATA
1 TTTAAATATTTTTTATATATT-TA
1998200 TTTAAATATT
1 TTTAAATATT
1998210 AATCAAACAT
Statistics
Matches: 25, Mismatches: 7, Indels: 2
0.74 0.21 0.06
Matches are distributed among these distances:
22 2 0.08
23 23 0.92
ACGTcount: A:0.36, C:0.00, G:0.00, T:0.64
Consensus pattern (23 bp):
TTTAAATATTTTTTATATATTTA
Found at i:2000049 original size:17 final size:18
Alignment explanation
Indices: 2000029--2000062 Score: 52
Period size: 17 Copynumber: 1.9 Consensus size: 18
2000019 TTTTTAATTT
*
2000029 AATTAGTTTTT-ATAAAA
1 AATTAATTTTTAATAAAA
2000046 AATTAATTTTTAATAAA
1 AATTAATTTTTAATAAA
2000063 TTTAAATTTC
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 10 0.67
18 5 0.33
ACGTcount: A:0.50, C:0.00, G:0.03, T:0.47
Consensus pattern (18 bp):
AATTAATTTTTAATAAAA
Found at i:2001398 original size:15 final size:14
Alignment explanation
Indices: 2001339--2001398 Score: 54
Period size: 15 Copynumber: 4.4 Consensus size: 14
2001329 ATAATAAAAA
*
2001339 TATTTAAAATTTTT
1 TATTTAAAATTTAT
2001353 TATTT-AAATTTA-
1 TATTTAAAATTTAT
*
2001365 -ATTATAAAATATAT
1 TATT-TAAAATTTAT
*
2001379 AATTTAATAATTTAT
1 TATTTAA-AATTTAT
2001394 TATTT
1 TATTT
2001399 TATAAATAAT
Statistics
Matches: 37, Mismatches: 4, Indels: 9
0.74 0.08 0.18
Matches are distributed among these distances:
11 3 0.08
12 1 0.03
13 12 0.32
14 8 0.22
15 13 0.35
ACGTcount: A:0.43, C:0.00, G:0.00, T:0.57
Consensus pattern (14 bp):
TATTTAAAATTTAT
Found at i:2001425 original size:22 final size:22
Alignment explanation
Indices: 2001383--2001426 Score: 54
Period size: 22 Copynumber: 2.0 Consensus size: 22
2001373 ATATATAATT
* *
2001383 TAATAATTTATTATTTTATAAA
1 TAATAATTTATAATTTAATAAA
2001405 TAATAATTTA-AATTTAAATAAA
1 TAATAATTTATAATTT-AATAAA
2001427 AAAATTAAAA
Statistics
Matches: 19, Mismatches: 2, Indels: 2
0.83 0.09 0.09
Matches are distributed among these distances:
21 4 0.21
22 15 0.79
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (22 bp):
TAATAATTTATAATTTAATAAA
Found at i:2002165 original size:2 final size:2
Alignment explanation
Indices: 2002151--2002193 Score: 70
Period size: 2 Copynumber: 21.5 Consensus size: 2
2002141 TATGACTTCT
2002151 TA TA TA CTA -A 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
2002193 T
1 T
2002194 TCATAATTAA
Statistics
Matches: 39, Mismatches: 0, Indels: 4
0.91 0.00 0.09
Matches are distributed among these distances:
1 1 0.03
2 36 0.92
3 2 0.05
ACGTcount: A:0.49, C:0.02, G:0.00, T:0.49
Consensus pattern (2 bp):
TA
Found at i:2005428 original size:2 final size:2
Alignment explanation
Indices: 2005421--2005447 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
2005411 CACAATTAAT
2005421 TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA T
2005448 TGAGTTTCAT
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 25 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:2006316 original size:2 final size:2
Alignment explanation
Indices: 2006309--2006346 Score: 76
Period size: 2 Copynumber: 19.0 Consensus size: 2
2006299 AAAGAAGGGC
2006309 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
2006347 GAATTATTCA
Statistics
Matches: 36, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 36 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:2008334 original size:11 final size:11
Alignment explanation
Indices: 2008318--2008342 Score: 50
Period size: 11 Copynumber: 2.3 Consensus size: 11
2008308 ATTATATAAA
2008318 ATAATAAAAAT
1 ATAATAAAAAT
2008329 ATAATAAAAAT
1 ATAATAAAAAT
2008340 ATA
1 ATA
2008343 TCTATTGAAT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 14 1.00
ACGTcount: A:0.72, C:0.00, G:0.00, T:0.28
Consensus pattern (11 bp):
ATAATAAAAAT
Found at i:2008667 original size:2 final size:2
Alignment explanation
Indices: 2008660--2008687 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
2008650 CAAAATTAGG
2008660 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
2008688 TCCAAAAAGA
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:2011342 original size:2 final size:2
Alignment explanation
Indices: 2011335--2011369 Score: 63
Period size: 2 Copynumber: 18.0 Consensus size: 2
2011325 CATAAAAATA
2011335 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A- AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
2011370 GAATAAACAA
Statistics
Matches: 32, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
1 1 0.03
2 31 0.97
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:2011791 original size:2 final size:2
Alignment explanation
Indices: 2011778--2011822 Score: 81
Period size: 2 Copynumber: 22.5 Consensus size: 2
2011768 CTTATGTGTC
*
2011778 TA TA TA TC TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
2011820 TA T
1 TA T
2011823 GCTTTATTTA
Statistics
Matches: 41, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
2 41 1.00
ACGTcount: A:0.47, C:0.02, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:2012043 original size:2 final size:2
Alignment explanation
Indices: 2012036--2012062 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
2012026 TTATACATAC
2012036 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
2012063 ATTTAGAAAT
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:2012278 original size:121 final size:120
Alignment explanation
Indices: 2012064--2012292 Score: 386
Period size: 121 Copynumber: 1.9 Consensus size: 120
2012054 ATATATATAA
*
2012064 TTTAGAAATATGTGTTGATTAGATACTTCAAATTAAGATAAACATACATAGTTAGATTCCTTGCT
1 TTTAGAAATATGTGTTGATTAGATACTTCAAATTAAGATAAACATACATAGTTAAATTCCTTGCT
2012129 CAAATAATAATGAATGTAATATCATCAAAAAGGTTTTTAATTGTGTTAGATCGAAT
66 CAAATAATAATGAATGTAATATCATCAAAAA-GTTTTTAATTGTGTTAGATCGAAT
* * * *
2012185 TTTAGAAATATGTGTTGATTAGATACTTCAAGTTAGGATAAACATACATAGTTAAATTCTTTGTT
1 TTTAGAAATATGTGTTGATTAGATACTTCAAATTAAGATAAACATACATAGTTAAATTCCTTGCT
* *
2012250 CTAATAATAATGAATGTAATATGATCAAAAAGTTTTTAATTGT
66 CAAATAATAATGAATGTAATATCATCAAAAAGTTTTTAATTGT
2012293 AGTAGATTAA
Statistics
Matches: 101, Mismatches: 7, Indels: 1
0.93 0.06 0.01
Matches are distributed among these distances:
120 12 0.12
121 89 0.88
ACGTcount: A:0.39, C:0.08, G:0.14, T:0.39
Consensus pattern (120 bp):
TTTAGAAATATGTGTTGATTAGATACTTCAAATTAAGATAAACATACATAGTTAAATTCCTTGCT
CAAATAATAATGAATGTAATATCATCAAAAAGTTTTTAATTGTGTTAGATCGAAT
Found at i:2012762 original size:2 final size:2
Alignment explanation
Indices: 2012755--2012797 Score: 86
Period size: 2 Copynumber: 21.5 Consensus size: 2
2012745 GCTGGTGATT
2012755 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
2012797 T
1 T
2012798 TGCATTTGTG
Statistics
Matches: 41, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 41 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Done.