Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold230
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: 2055625
ACGTcount: A:0.34, C:0.16, G:0.16, T:0.34
File 4 of 14
Found at i:332333 original size:26 final size:27
Alignment explanation
Indices: 332294--332351 Score: 68
Period size: 26 Copynumber: 2.2 Consensus size: 27
332284 ATTTATAATG
332294 TTTTATATTTTAT-ATAATTAT-ATTAT
1 TTTTATATTTTATAAT-ATTATAATTAT
*
332320 TTTTAT-TTTATATAATATTTTAATTAT
1 TTTTATATTT-TATAATATTATAATTAT
332347 TTTTA
1 TTTTA
332352 ACATCATAAT
Statistics
Matches: 28, Mismatches: 1, Indels: 5
0.82 0.03 0.15
Matches are distributed among these distances:
25 3 0.11
26 13 0.46
27 12 0.43
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (27 bp):
TTTTATATTTTATAATATTATAATTAT
Found at i:332537 original size:3 final size:3
Alignment explanation
Indices: 332529--332567 Score: 78
Period size: 3 Copynumber: 13.0 Consensus size: 3
332519 GGGTTAATGG
332529 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT
332568 GTTGTTGTTA
Statistics
Matches: 36, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 36 1.00
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (3 bp):
ATT
Found at i:333907 original size:14 final size:15
Alignment explanation
Indices: 333851--333912 Score: 54
Period size: 17 Copynumber: 3.9 Consensus size: 15
333841 TATAGTAATA
*
333851 TAAAATAAATATATTTT
1 TAAAATTAATATA--TT
*
333868 TAAAATTTATATATT
1 TAAAATTAATATATT
333883 ATAAATTATTAATATA-T
1 -TAAA--ATTAATATATT
333900 TAAAATTAATATA
1 TAAAATTAATATA
333913 AATATAAAAT
Statistics
Matches: 39, Mismatches: 3, Indels: 9
0.76 0.06 0.18
Matches are distributed among these distances:
14 9 0.23
15 2 0.05
16 8 0.21
17 12 0.31
18 8 0.21
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (15 bp):
TAAAATTAATATATT
Found at i:333916 original size:6 final size:6
Alignment explanation
Indices: 333907--333963 Score: 59
Period size: 6 Copynumber: 10.2 Consensus size: 6
333897 TATTAAAATT
* * *
333907 AATATA AATATA AA-ATA TAT-TA AATATA ATTAT- AATAT- AATAAA
1 AATATA AATATA AATATA AATATA AATATA AATATA AATATA AATATA
333951 AATATA AATATA A
1 AATATA AATATA A
333964 TATGAATTTT
Statistics
Matches: 42, Mismatches: 6, Indels: 6
0.78 0.11 0.11
Matches are distributed among these distances:
5 16 0.38
6 26 0.62
ACGTcount: A:0.65, C:0.00, G:0.00, T:0.35
Consensus pattern (6 bp):
AATATA
Found at i:333916 original size:20 final size:18
Alignment explanation
Indices: 333876--333941 Score: 59
Period size: 18 Copynumber: 3.6 Consensus size: 18
333866 TTTAAAATTT
333876 ATATATTATAAATTATTA
1 ATATATTATAAATTATTA
333894 ATATATTA-AAATTAATATA
1 ATATATTATAAATT-AT-TA
333913 A-ATA-TA-AAATATATTAA
1 ATATATTATAAAT-TATT-A
333930 ATATAATTATAA
1 ATAT-ATTATAA
333942 TATAATAAAA
Statistics
Matches: 40, Mismatches: 0, Indels: 13
0.75 0.00 0.25
Matches are distributed among these distances:
16 1 0.03
17 15 0.38
18 16 0.40
19 4 0.10
20 2 0.05
21 2 0.05
ACGTcount: A:0.58, C:0.00, G:0.00, T:0.42
Consensus pattern (18 bp):
ATATATTATAAATTATTA
Found at i:333936 original size:27 final size:27
Alignment explanation
Indices: 333876--333966 Score: 91
Period size: 27 Copynumber: 3.3 Consensus size: 27
333866 TTTAAAATTT
* *
333876 ATATATTATAAAT-TATTAATATATTAA
1 ATATAATATAAATATA-AAATATATTAA
333903 A-ATTAATATAAATATAAAATATATTAA
1 ATA-TAATATAAATATAAAATATATTAA
333930 ATATAATTATAATATAATAAAA-ATA-TAA
1 ATATAA-TATAA-AT-ATAAAATATATTAA
333958 ATATAATAT
1 ATATAATAT
333967 GAATTTTTTT
Statistics
Matches: 56, Mismatches: 2, Indels: 12
0.80 0.03 0.17
Matches are distributed among these distances:
26 1 0.02
27 27 0.48
28 17 0.30
29 5 0.09
30 6 0.11
ACGTcount: A:0.59, C:0.00, G:0.00, T:0.41
Consensus pattern (27 bp):
ATATAATATAAATATAAAATATATTAA
Found at i:333945 original size:11 final size:11
Alignment explanation
Indices: 333906--333971 Score: 62
Period size: 11 Copynumber: 5.9 Consensus size: 11
333896 ATATTAAAAT
*
333906 TAATATAAATA
1 TAATATAATTA
*
333917 TAAAATATATTA
1 TAATATA-ATTA
333929 -AATATAATTA
1 TAATATAATTA
*
333939 TAATATAATAA
1 TAATATAATTA
* *
333950 AAATATAAATA
1 TAATATAATTA
333961 TAATATGAATT
1 TAATAT-AATT
333972 TTTTTGTTAT
Statistics
Matches: 43, Mismatches: 9, Indels: 5
0.75 0.16 0.09
Matches are distributed among these distances:
10 4 0.09
11 33 0.77
12 6 0.14
ACGTcount: A:0.61, C:0.00, G:0.02, T:0.38
Consensus pattern (11 bp):
TAATATAATTA
Found at i:333964 original size:22 final size:22
Alignment explanation
Indices: 333907--333966 Score: 77
Period size: 22 Copynumber: 2.7 Consensus size: 22
333897 TATTAAAATT
* *
333907 AATATAAATATAAAATATATTA
1 AATATAAATATAATATATATAA
*
333929 AATATAATTATAATATA-ATAAA
1 AATATAAATATAATATATAT-AA
333951 AATATAAATATAATAT
1 AATATAAATATAATAT
333967 GAATTTTTTT
Statistics
Matches: 33, Mismatches: 4, Indels: 2
0.85 0.10 0.05
Matches are distributed among these distances:
21 2 0.06
22 31 0.94
ACGTcount: A:0.63, C:0.00, G:0.00, T:0.37
Consensus pattern (22 bp):
AATATAAATATAATATATATAA
Found at i:335590 original size:29 final size:30
Alignment explanation
Indices: 335558--335614 Score: 91
Period size: 29 Copynumber: 1.9 Consensus size: 30
335548 TTTATTAATT
335558 AAATAAATATAA-ATATAATAAA-ATTTTTA
1 AAATAAATATAATATATAA-AAATATTTTTA
335587 AAATAAATATAATATATAAAAATATTTT
1 AAATAAATATAATATATAAAAATATTTT
335615 ATATTAATCA
Statistics
Matches: 26, Mismatches: 0, Indels: 3
0.90 0.00 0.10
Matches are distributed among these distances:
29 15 0.58
30 11 0.42
ACGTcount: A:0.61, C:0.00, G:0.00, T:0.39
Consensus pattern (30 bp):
AAATAAATATAATATATAAAAATATTTTTA
Found at i:335685 original size:37 final size:37
Alignment explanation
Indices: 335605--335694 Score: 103
Period size: 37 Copynumber: 2.4 Consensus size: 37
335595 ATAATATATA
335605 AAAATATTTTATATTAATCATATTAATTATATTTAAAT
1 AAAATATTTTATATTAATCATATTAATTATATTT-AAT
* *
335643 AAAATATTTTATATT-ATTATATTACTTTTATATTT-AT
1 AAAATATTTTATATTAATCATATTA--ATTATATTTAAT
* *
335680 TAAATATATTATATT
1 AAAATATTTTATATT
335695 CAATTGGTGC
Statistics
Matches: 46, Mismatches: 4, Indels: 5
0.84 0.07 0.09
Matches are distributed among these distances:
37 23 0.50
38 15 0.33
39 8 0.17
ACGTcount: A:0.43, C:0.02, G:0.00, T:0.54
Consensus pattern (37 bp):
AAAATATTTTATATTAATCATATTAATTATATTTAAT
Found at i:337338 original size:21 final size:19
Alignment explanation
Indices: 337298--337338 Score: 55
Period size: 21 Copynumber: 2.1 Consensus size: 19
337288 ATTTAAAAAT
*
337298 TTTTATTTTTAAATTATAA
1 TTTTATTTTTAAAATATAA
337317 TTTTATTTATTAAAAATATAA
1 TTTTATTT-TT-AAAATATAA
337338 T
1 T
337339 CATTATTTTA
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
19 8 0.42
20 2 0.11
21 9 0.47
ACGTcount: A:0.41, C:0.00, G:0.00, T:0.59
Consensus pattern (19 bp):
TTTTATTTTTAAAATATAA
Found at i:338072 original size:27 final size:26
Alignment explanation
Indices: 338042--338109 Score: 63
Period size: 26 Copynumber: 2.7 Consensus size: 26
338032 ATAAATATTT
338042 TTATTTATTATATTTATATTTAAAATA
1 TTATTTATTATATTTATATTT-AAATA
* * * *
338069 TTATATATT-TATATAAATTTTAATA
1 TTATTTATTATATTTATATTTAAATA
338094 -TA-TT-TTATATTTATAT
1 TTATTTATTATATTTATAT
338110 ATTTCCATGA
Statistics
Matches: 33, Mismatches: 7, Indels: 6
0.72 0.15 0.13
Matches are distributed among these distances:
22 2 0.06
23 8 0.24
24 2 0.06
25 4 0.12
26 9 0.27
27 8 0.24
ACGTcount: A:0.40, C:0.00, G:0.00, T:0.60
Consensus pattern (26 bp):
TTATTTATTATATTTATATTTAAATA
Found at i:338078 original size:22 final size:23
Alignment explanation
Indices: 338050--338106 Score: 68
Period size: 22 Copynumber: 2.6 Consensus size: 23
338040 TTTTATTTAT
338050 TATATTTATATTTAAAATATT-A
1 TATATTTATATTTAAAATATTAA
*
338072 TATATTTATA--T-AAATTTTAA
1 TATATTTATATTTAAAATATTAA
338092 TATATTTTATATTTA
1 TATA-TTTATATTTA
338107 TATATTTCCA
Statistics
Matches: 29, Mismatches: 1, Indels: 8
0.76 0.03 0.21
Matches are distributed among these distances:
19 6 0.21
20 6 0.21
21 6 0.21
22 10 0.34
23 1 0.03
ACGTcount: A:0.42, C:0.00, G:0.00, T:0.58
Consensus pattern (23 bp):
TATATTTATATTTAAAATATTAA
Found at i:338111 original size:15 final size:15
Alignment explanation
Indices: 338022--338113 Score: 61
Period size: 15 Copynumber: 6.3 Consensus size: 15
338012 CTCCCTCATT
* * *
338022 TATTTTAAATATAAA
1 TATTTTATATTTATA
338037 TATTTT-TATTTAT-
1 TATTTTATATTTATA
*
338050 TATATTTATATTTAAAA
1 TAT-TTTATATTT-ATA
*
338067 TATTATATATTTATA
1 TATTTTATATTTATA
*
338082 TA---AAT-TTTAATA
1 TATTTTATATTT-ATA
338094 TATTTTATATTTATA
1 TATTTTATATTTATA
338109 TATTT
1 TATTT
338114 CCATGACTTC
Statistics
Matches: 60, Mismatches: 8, Indels: 18
0.70 0.09 0.21
Matches are distributed among these distances:
11 3 0.05
12 7 0.12
13 3 0.05
14 7 0.12
15 25 0.42
16 12 0.20
17 3 0.05
ACGTcount: A:0.40, C:0.00, G:0.00, T:0.60
Consensus pattern (15 bp):
TATTTTATATTTATA
Found at i:338438 original size:22 final size:21
Alignment explanation
Indices: 338413--338482 Score: 63
Period size: 22 Copynumber: 3.3 Consensus size: 21
338403 TTTAATTAAT
338413 AATTTAAAAAAATATAAATTTA
1 AATTTAAAAAAATATAAA-TTA
*
338435 AATTCAAATAAAA-AT-AATTA
1 AATTTAAA-AAAATATAAATTA
* * *
338455 ATTTTAAAATTAATATATATTA
1 AATTTAAAA-AAATATAAATTA
338477 AATTTA
1 AATTTA
338483 TTTTTTTTAG
Statistics
Matches: 38, Mismatches: 6, Indels: 8
0.73 0.12 0.15
Matches are distributed among these distances:
19 1 0.03
20 11 0.29
21 4 0.11
22 18 0.47
23 4 0.11
ACGTcount: A:0.59, C:0.01, G:0.00, T:0.40
Consensus pattern (21 bp):
AATTTAAAAAAATATAAATTA
Found at i:338645 original size:2 final size:2
Alignment explanation
Indices: 338638--338663 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
338628 GCTTCTGGTG
338638 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
338664 AAAATTATTT
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:0.00, C:0.50, G:0.00, T:0.50
Consensus pattern (2 bp):
CT
Found at i:339364 original size:2 final size:2
Alignment explanation
Indices: 339357--339391 Score: 70
Period size: 2 Copynumber: 17.5 Consensus size: 2
339347 ATACAGGTAA
339357 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 A
339392 AGTTTCTCTG
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:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:344952 original size:196 final size:196
Alignment explanation
Indices: 344618--344984 Score: 734
Period size: 196 Copynumber: 1.9 Consensus size: 196
344608 AAACTGTGAA
344618 AAAACAAGACAACAATTACCAAATTTATGAGAATATGCAAAGACTTTTTTCCATGAAAGAACAAA
1 AAAACAAGACAACAATTACCAAATTTATGAGAATATGCAAAGACTTTTTTCCATGAAAGAACAAA
344683 CTGATAAAACCGACTCTGCTAGGAGGACTTAGATTTCAACTTCTTTGTGCGTTTGACTAAAGGAT
66 CTGATAAAACCGACTCTGCTAGGAGGACTTAGATTTCAACTTCTTTGTGCGTTTGACTAAAGGAT
344748 ACATGCTCTTTATTACTTTCTTAACTTTCTTCGCAGATTTAAGAAAGTAATAAAGAGCAAACTGA
131 ACATGCTCTTTATTACTTTCTTAACTTTCTTCGCAGATTTAAGAAAGTAATAAAGAGCAAACTGA
344813 T
196 T
344814 AAAACAAGACAACAATTACCAAATTTATGAGAATATGCAAAGACTTTTTTCCATGAAAGAACAAA
1 AAAACAAGACAACAATTACCAAATTTATGAGAATATGCAAAGACTTTTTTCCATGAAAGAACAAA
344879 CTGATAAAACCGACTCTGCTAGGAGGACTTAGATTTCAACTTCTTTGTGCGTTTGACTAAAGGAT
66 CTGATAAAACCGACTCTGCTAGGAGGACTTAGATTTCAACTTCTTTGTGCGTTTGACTAAAGGAT
344944 ACATGCTCTTTATTACTTTCTTAACTTTCTTCGCAGATTTA
131 ACATGCTCTTTATTACTTTCTTAACTTTCTTCGCAGATTTA
344985 GCTTTCTTTA
Statistics
Matches: 171, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
196 171 1.00
ACGTcount: A:0.37, C:0.17, G:0.14, T:0.32
Consensus pattern (196 bp):
AAAACAAGACAACAATTACCAAATTTATGAGAATATGCAAAGACTTTTTTCCATGAAAGAACAAA
CTGATAAAACCGACTCTGCTAGGAGGACTTAGATTTCAACTTCTTTGTGCGTTTGACTAAAGGAT
ACATGCTCTTTATTACTTTCTTAACTTTCTTCGCAGATTTAAGAAAGTAATAAAGAGCAAACTGA
T
Found at i:346913 original size:11 final size:11
Alignment explanation
Indices: 346899--346931 Score: 50
Period size: 11 Copynumber: 3.1 Consensus size: 11
346889 ATTACATAAT
346899 ATATATATTAA
1 ATATATATTAA
346910 ATATATATTAA
1 ATATATATTAA
*
346921 AT-TATTTTAA
1 ATATATATTAA
346931 A
1 A
346932 ATAAAATTAT
Statistics
Matches: 21, Mismatches: 1, Indels: 1
0.91 0.04 0.04
Matches are distributed among these distances:
10 8 0.38
11 13 0.62
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (11 bp):
ATATATATTAA
Found at i:346938 original size:16 final size:16
Alignment explanation
Indices: 346919--346951 Score: 57
Period size: 16 Copynumber: 2.1 Consensus size: 16
346909 AATATATATT
*
346919 AAATTATTTTAAAATA
1 AAATTATTTAAAAATA
346935 AAATTATTTAAAAATA
1 AAATTATTTAAAAATA
346951 A
1 A
346952 TACTTGAAAA
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 16 1.00
ACGTcount: A:0.61, C:0.00, G:0.00, T:0.39
Consensus pattern (16 bp):
AAATTATTTAAAAATA
Found at i:347085 original size:22 final size:23
Alignment explanation
Indices: 347060--347118 Score: 68
Period size: 22 Copynumber: 2.7 Consensus size: 23
347050 ATTTAATAAA
347060 TAAAATT-TTATAAATTAATTAT
1 TAAAATTATTATAAATTAATTAT
* *
347082 TAAAATTATTTTAAATT-ATTTT
1 TAAAATTATTATAAATTAATTAT
* *
347104 TTAAATTATGATAAA
1 TAAAATTATTATAAA
347119 AAAGTAATAA
Statistics
Matches: 31, Mismatches: 5, Indels: 2
0.82 0.13 0.05
Matches are distributed among these distances:
22 23 0.74
23 8 0.26
ACGTcount: A:0.47, C:0.00, G:0.02, T:0.51
Consensus pattern (23 bp):
TAAAATTATTATAAATTAATTAT
Found at i:347096 original size:23 final size:23
Alignment explanation
Indices: 347046--347112 Score: 66
Period size: 22 Copynumber: 3.0 Consensus size: 23
347036 ATTTTTAAAA
* * *
347046 TTTAATTTAATAAATAAAATT-T
1 TTTAAATTAATTATTAAAATTAT
*
347068 TATAAATTAATTATTAAAATTAT
1 TTTAAATTAATTATTAAAATTAT
* *
347091 TTTAAATT-ATTTTTTAAATTAT
1 TTTAAATTAATTATTAAAATTAT
347113 GATAAAAAAG
Statistics
Matches: 37, Mismatches: 7, Indels: 2
0.80 0.15 0.04
Matches are distributed among these distances:
22 29 0.78
23 8 0.22
ACGTcount: A:0.46, C:0.00, G:0.00, T:0.54
Consensus pattern (23 bp):
TTTAAATTAATTATTAAAATTAT
Found at i:347461 original size:2 final size:2
Alignment explanation
Indices: 347454--347494 Score: 82
Period size: 2 Copynumber: 20.5 Consensus size: 2
347444 CAGTAACCTC
347454 CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT C
1 CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT C
347495 CCCTCCATTC
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:0.00, C:0.51, G:0.00, T:0.49
Consensus pattern (2 bp):
CT
Found at i:347641 original size:16 final size:17
Alignment explanation
Indices: 347600--347641 Score: 54
Period size: 16 Copynumber: 2.6 Consensus size: 17
347590 CTCTCTCCTC
347600 TCATT-TCATCTCTTAT
1 TCATTCTCATCTCTTAT
347616 TC-TCTCTCATCTCTT-T
1 TCAT-TCTCATCTCTTAT
347632 TCATTCTCAT
1 TCATTCTCAT
347642 ATCACACCAC
Statistics
Matches: 23, Mismatches: 0, Indels: 6
0.79 0.00 0.21
Matches are distributed among these distances:
15 1 0.04
16 12 0.52
17 10 0.43
ACGTcount: A:0.14, C:0.31, G:0.00, T:0.55
Consensus pattern (17 bp):
TCATTCTCATCTCTTAT
Found at i:347701 original size:18 final size:18
Alignment explanation
Indices: 347675--347737 Score: 53
Period size: 18 Copynumber: 3.6 Consensus size: 18
347665 TAACTTATAT
*
347675 TATATATTTTATTATTTA
1 TATAAATTTTATTATTTA
*
347693 TATAAATTTTAATATATTA
1 TATAAATTTTATTAT-TTA
347712 -AT-AA-TTTATATATTT-
1 TATAAATTTTAT-TATTTA
*
347727 CATAAATTTTA
1 TATAAATTTTA
347738 AAATATTAAA
Statistics
Matches: 37, Mismatches: 3, Indels: 10
0.74 0.06 0.20
Matches are distributed among these distances:
16 8 0.22
17 7 0.19
18 19 0.51
19 3 0.08
ACGTcount: A:0.41, C:0.02, G:0.00, T:0.57
Consensus pattern (18 bp):
TATAAATTTTATTATTTA
Found at i:347732 original size:34 final size:35
Alignment explanation
Indices: 347670--347757 Score: 108
Period size: 34 Copynumber: 2.5 Consensus size: 35
347660 TTACATAACT
* *
347670 TATATTATATATTTTAT-TATTTATATAAATTTTAA
1 TATATTA-ATAATTTATATATTTACATAAATTTTAA
347705 TATATTAATAATTTATATATTT-CATAAATTTTAA
1 TATATTAATAATTTATATATTTACATAAATTTTAA
* *
347739 AATATTAAAATATTTATAT
1 TATATTAATA-ATTTATAT
347758 TATATTTTAA
Statistics
Matches: 47, Mismatches: 4, Indels: 4
0.85 0.07 0.07
Matches are distributed among these distances:
34 27 0.57
35 20 0.43
ACGTcount: A:0.44, C:0.01, G:0.00, T:0.55
Consensus pattern (35 bp):
TATATTAATAATTTATATATTTACATAAATTTTAA
Found at i:351757 original size:85 final size:84
Alignment explanation
Indices: 351657--351819 Score: 224
Period size: 85 Copynumber: 1.9 Consensus size: 84
351647 AAATAAAATT
* *
351657 ATTTTTTATTAATTTAATTTAATATTTTTGA-TTAAACAGA-TT-TATTAGTTTAATTAATAAAT
1 ATTTTTTATTAATTTAATTTAAAATTTTT-ATTTAAACA-ATTTATATTAATTTAATTAAT-AAT
351719 TAATTTTTAATATATATTAAACC
63 TAA-TTTTAATATATATTAAACC
* **
351742 ATTTTTTATTTATTTAATTTAAAATTTTTATTTAATTAATTTATATTAATTTAATTAATAATTAA
1 ATTTTTTATTAATTTAATTTAAAATTTTTATTTAAACAATTTATATTAATTTAATTAATAATTAA
351807 TTTTAATATATAT
66 TTTTAATATATAT
351820 CAATAGATTC
Statistics
Matches: 70, Mismatches: 5, Indels: 7
0.85 0.06 0.09
Matches are distributed among these distances:
84 15 0.21
85 40 0.57
86 15 0.21
ACGTcount: A:0.40, C:0.02, G:0.02, T:0.56
Consensus pattern (84 bp):
ATTTTTTATTAATTTAATTTAAAATTTTTATTTAAACAATTTATATTAATTTAATTAATAATTAA
TTTTAATATATATTAAACC
Found at i:351813 original size:10 final size:9
Alignment explanation
Indices: 351771--351809 Score: 55
Period size: 9 Copynumber: 4.4 Consensus size: 9
351761 TAAAATTTTT
351771 ATTTAATTA
1 ATTTAATTA
351780 ATTTATATTA
1 ATTTA-ATTA
351790 ATTTAATTA
1 ATTTAATTA
351799 A--TAATTA
1 ATTTAATTA
351806 ATTT
1 ATTT
351810 TAATATATAT
Statistics
Matches: 27, Mismatches: 0, Indels: 6
0.82 0.00 0.18
Matches are distributed among these distances:
7 7 0.26
9 11 0.41
10 9 0.33
ACGTcount: A:0.44, C:0.00, G:0.00, T:0.56
Consensus pattern (9 bp):
ATTTAATTA
Found at i:354190 original size:13 final size:14
Alignment explanation
Indices: 354167--354213 Score: 51
Period size: 14 Copynumber: 3.1 Consensus size: 14
354157 ATTTATTAAT
354167 AATTATTTTAT-TTA
1 AATT-TTTTATATTA
354181 AATTTTTTATATTA
1 AATTTTTTATATTA
354195 ATATTTTGTATATATTA
1 A-ATTTT-T-TATATTA
354212 AA
1 AA
354214 ACATAAATAT
Statistics
Matches: 29, Mismatches: 0, Indels: 6
0.83 0.00 0.17
Matches are distributed among these distances:
13 6 0.21
14 8 0.28
15 5 0.17
16 2 0.07
17 8 0.28
ACGTcount: A:0.38, C:0.00, G:0.02, T:0.60
Consensus pattern (14 bp):
AATTTTTTATATTA
Found at i:354200 original size:15 final size:15
Alignment explanation
Indices: 354160--354212 Score: 56
Period size: 17 Copynumber: 3.4 Consensus size: 15
354150 AGAGTATATT
354160 TATTAATAATTATTTTA
1 TATTAAT-ATT-TTTTA
354177 T-TTAA-ATTTTTTA
1 TATTAATATTTTTTA
354190 TATTAATATTTTGTATA
1 TATTAATATTTT-T-TA
354207 TATTAA
1 TATTAA
354213 AACATAAATA
Statistics
Matches: 32, Mismatches: 0, Indels: 8
0.80 0.00 0.20
Matches are distributed among these distances:
13 6 0.19
14 7 0.22
15 5 0.16
16 5 0.16
17 9 0.28
ACGTcount: A:0.38, C:0.00, G:0.02, T:0.60
Consensus pattern (15 bp):
TATTAATATTTTTTA
Found at i:354273 original size:17 final size:18
Alignment explanation
Indices: 354244--354281 Score: 60
Period size: 17 Copynumber: 2.2 Consensus size: 18
354234 TCATCAATTC
354244 TTTAAATAAATAAAAAAA
1 TTTAAATAAATAAAAAAA
*
354262 TTTAAA-AAATAAAAATA
1 TTTAAATAAATAAAAAAA
354279 TTT
1 TTT
354282 TTATTCTAAA
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
17 13 0.68
18 6 0.32
ACGTcount: A:0.66, C:0.00, G:0.00, T:0.34
Consensus pattern (18 bp):
TTTAAATAAATAAAAAAA
Found at i:357148 original size:17 final size:17
Alignment explanation
Indices: 357126--357160 Score: 70
Period size: 17 Copynumber: 2.1 Consensus size: 17
357116 TATTGTTGCT
357126 CAGTGTTGTGATTTTTG
1 CAGTGTTGTGATTTTTG
357143 CAGTGTTGTGATTTTTG
1 CAGTGTTGTGATTTTTG
357160 C
1 C
357161 TTACATATTG
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 18 1.00
ACGTcount: A:0.11, C:0.09, G:0.29, T:0.51
Consensus pattern (17 bp):
CAGTGTTGTGATTTTTG
Found at i:364281 original size:6 final size:6
Alignment explanation
Indices: 364270--364343 Score: 52
Period size: 6 Copynumber: 12.7 Consensus size: 6
364260 GGCTAAAAAG
* *
364270 GAGAAA GAG-AA -AG-AA GAGAAA GAGAGAA G-GAAA GAGAAG GAGAAG
1 GAGAAA GAGAAA GAGAAA GAGAAA GAGA-AA GAGAAA GAGAAA GAGAAA
364315 GAGAAGGA GAGAAA G-GAGAA G-GAAA GAGA
1 GAGAA--A GAGAAA GAGA-AA GAGAAA GAGA
364344 TCGTGAAAGG
Statistics
Matches: 58, Mismatches: 2, Indels: 16
0.76 0.03 0.21
Matches are distributed among these distances:
4 4 0.07
5 12 0.21
6 34 0.59
7 3 0.05
8 5 0.09
ACGTcount: A:0.58, C:0.00, G:0.42, T:0.00
Consensus pattern (6 bp):
GAGAAA
Found at i:364307 original size:27 final size:29
Alignment explanation
Indices: 364272--364341 Score: 83
Period size: 30 Copynumber: 2.4 Consensus size: 29
364262 CTAAAAAGGA
364272 GAAAGAGAAAGAA-GAGAAAGAGAG-AAG
1 GAAAGAGAAAGAAGGAGAAAGAGAGAAAG
*
364299 GAAAGAGAAGGAGAAGGAGAAGGAGAGAAAG
1 GAAAGAGAA--AGAAGGAGAAAGAGAGAAAG
364330 GAGAAG-GAAAGA
1 GA-AAGAGAAAGA
364342 GATCGTGAAA
Statistics
Matches: 37, Mismatches: 1, Indels: 8
0.80 0.02 0.17
Matches are distributed among these distances:
27 9 0.24
29 7 0.19
30 10 0.27
31 8 0.22
32 3 0.08
ACGTcount: A:0.59, C:0.00, G:0.41, T:0.00
Consensus pattern (29 bp):
GAAAGAGAAAGAAGGAGAAAGAGAGAAAG
Found at i:364310 original size:39 final size:37
Alignment explanation
Indices: 364267--364343 Score: 118
Period size: 37 Copynumber: 2.0 Consensus size: 37
364257 GCAGGCTAAA
364267 AAGGAGAAAGAGAAAGAAGAGAAAGAGAGAAGGAAAGAG
1 AAGGAGAAAGAG-AAGAAGAGAAAG-GAGAAGGAAAGAG
* *
364306 AAGGAGAAGGAGAAGGAGAGAAAGGAGAAGGAAAGAG
1 AAGGAGAAAGAGAAGAAGAGAAAGGAGAAGGAAAGAG
364343 A
1 A
364344 TCGTGAAAGG
Statistics
Matches: 36, Mismatches: 2, Indels: 2
0.90 0.05 0.05
Matches are distributed among these distances:
37 14 0.39
38 11 0.31
39 11 0.31
ACGTcount: A:0.58, C:0.00, G:0.42, T:0.00
Consensus pattern (37 bp):
AAGGAGAAAGAGAAGAAGAGAAAGGAGAAGGAAAGAG
Found at i:365764 original size:24 final size:23
Alignment explanation
Indices: 365737--365800 Score: 67
Period size: 22 Copynumber: 2.7 Consensus size: 23
365727 TTAACGTATA
*
365737 AATAATTTTTATTATATTAATTTT
1 AATAA-TTTTATTATATTAATATT
* *
365761 AATAAATTTA-TATATTTATATT
1 AATAATTTTATTATATTAATATT
*
365783 ATATAATTATATTATATT
1 A-ATAATTTTATTATATT
365801 TAACGCAAGA
Statistics
Matches: 33, Mismatches: 5, Indels: 4
0.79 0.12 0.10
Matches are distributed among these distances:
22 11 0.33
23 11 0.33
24 11 0.33
ACGTcount: A:0.42, C:0.00, G:0.00, T:0.58
Consensus pattern (23 bp):
AATAATTTTATTATATTAATATT
Found at i:365786 original size:13 final size:13
Alignment explanation
Indices: 365768--365799 Score: 55
Period size: 13 Copynumber: 2.5 Consensus size: 13
365758 TTTAATAAAT
*
365768 TTATATATTTATA
1 TTATATAATTATA
365781 TTATATAATTATA
1 TTATATAATTATA
365794 TTATAT
1 TTATAT
365800 TTAACGCAAG
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
13 18 1.00
ACGTcount: A:0.41, C:0.00, G:0.00, T:0.59
Consensus pattern (13 bp):
TTATATAATTATA
Found at i:367871 original size:23 final size:22
Alignment explanation
Indices: 367827--367878 Score: 59
Period size: 23 Copynumber: 2.3 Consensus size: 22
367817 GGATATTATG
* ** *
367827 ATTAGATTTTAAATTTATTAAA
1 ATTATATTTTAAAAATAATAAA
367849 TATTATATTTTAAAAATAATAAA
1 -ATTATATTTTAAAAATAATAAA
367872 ATTATAT
1 ATTATAT
367879 ATATACTATT
Statistics
Matches: 25, Mismatches: 4, Indels: 1
0.83 0.13 0.03
Matches are distributed among these distances:
22 7 0.28
23 18 0.72
ACGTcount: A:0.50, C:0.00, G:0.02, T:0.48
Consensus pattern (22 bp):
ATTATATTTTAAAAATAATAAA
Found at i:368105 original size:114 final size:115
Alignment explanation
Indices: 367886--368102 Score: 287
Period size: 114 Copynumber: 1.9 Consensus size: 115
367876 TATATATACT
* * * * *
367886 ATTAAGTTAAATTTTAAAATTTTTATTATTCATCTTTACTTTCAGATTTTAATATTTTAAGTAAA
1 ATTAAGTTAAATTTTAAAATTTTTATTATTCACCGTTACTTTCAAACTTTAATATCTTAAGTAAA
* * *
367951 ATTTAATTTTAAATTTTATTAAATATTATTTATTAAAAATAATTTTATAA
66 ATTTAATCTTAAAATCTATTAAATATTATTTATTAAAAATAATTTTATAA
* * *
368001 ATTAA-TTAAATTTT-AAATTCTTTATTATTCGCCGTTACTTTCAAACTTTGATATCTTAATTAA
1 ATTAAGTTAAATTTTAAAATT-TTTATTATTCACCGTTACTTTCAAACTTTAATATCTTAAGTAA
* *
368064 AATTTGATCTTAAAATCTATTAAATTTTATTT-TTAAAAA
65 AATTTAATCTTAAAATCTATTAAATATTATTTATTAAAAA
368103 ATATACAAAT
Statistics
Matches: 88, Mismatches: 13, Indels: 4
0.84 0.12 0.04
Matches are distributed among these distances:
113 12 0.14
114 71 0.81
115 5 0.06
ACGTcount: A:0.39, C:0.06, G:0.03, T:0.51
Consensus pattern (115 bp):
ATTAAGTTAAATTTTAAAATTTTTATTATTCACCGTTACTTTCAAACTTTAATATCTTAAGTAAA
ATTTAATCTTAAAATCTATTAAATATTATTTATTAAAAATAATTTTATAA
Found at i:368118 original size:114 final size:113
Alignment explanation
Indices: 367886--368138 Score: 276
Period size: 114 Copynumber: 2.2 Consensus size: 113
367876 TATATATACT
* * * * *
367886 ATTAAGTTAAATTTTAAAATTTTTATTATTCATCTTTACTTTCAGATTTTAATATTTTAAGTAAA
1 ATTAA-TTAAATTTT-AAATTTTTATTATTCACCGTTACTTTCAAACTTTAATATCTTAAGTAAA
* * * ***
367951 ATTTAATTTTAAATTTTATTAAATATTATTTATTAAAAATAATTTTATAA
64 ATTTAATCTTAAAATCTATTAAATATTATTTATTAAAAATAATCAAATAA
* * *
368001 ATTAATTAAATTTTAAATTCTTTATTATTCGCCGTTACTTTCAAACTTTGATATCTTAATTAAAA
1 ATTAATTAAATTTTAAATT-TTTATTATTCACCGTTACTTTCAAACTTTAATATCTTAAGTAAAA
* * *
368066 TTTGATCTTAAAATCTATTAAATTTTATTT-TTAAAAA-ATATACAAATCA
65 TTTAATCTTAAAATCTATTAAATATTATTTATTAAAAATA-AT-CAAATAA
*
368115 ATTAAATTAAATTTTTAATTTTTA
1 ATT-AATTAAATTTTAAATTTTTA
368139 ATTTCTTGAT
Statistics
Matches: 116, Mismatches: 18, Indels: 9
0.81 0.13 0.06
Matches are distributed among these distances:
112 1 0.01
113 14 0.12
114 81 0.70
115 20 0.17
ACGTcount: A:0.40, C:0.06, G:0.03, T:0.51
Consensus pattern (113 bp):
ATTAATTAAATTTTAAATTTTTATTATTCACCGTTACTTTCAAACTTTAATATCTTAAGTAAAAT
TTAATCTTAAAATCTATTAAATATTATTTATTAAAAATAATCAAATAA
Found at i:369392 original size:19 final size:18
Alignment explanation
Indices: 369340--369393 Score: 54
Period size: 19 Copynumber: 2.9 Consensus size: 18
369330 TAAGTTTAAC
* *
369340 TTTATTCAAATTACTATT
1 TTTATTTAAATTAATATT
* *
369358 TTTATAATAAAATAATATT
1 TTTAT-TTAAATTAATATT
369377 TTTATTTAAATTTAATA
1 TTTATTTAAA-TTAATA
369394 ATAAATATTA
Statistics
Matches: 28, Mismatches: 6, Indels: 3
0.76 0.16 0.08
Matches are distributed among these distances:
18 9 0.32
19 19 0.68
ACGTcount: A:0.43, C:0.04, G:0.00, T:0.54
Consensus pattern (18 bp):
TTTATTTAAATTAATATT
Found at i:370461 original size:22 final size:22
Alignment explanation
Indices: 370398--370461 Score: 58
Period size: 22 Copynumber: 2.9 Consensus size: 22
370388 TTTTTTTAAA
370398 AAAATATAAAAATTTTTAAATTT
1 AAAAT-TAAAAATTTTTAAATTT
* * *
370421 AAAATTACAAATATCTAAATTT
1 AAAATTAAAAATTTTTAAATTT
* *
370443 -CATTTAAAAAATTTTTAAA
1 AAAATT-AAAAATTTTTAAA
370462 ATTATTAAGC
Statistics
Matches: 32, Mismatches: 8, Indels: 3
0.74 0.19 0.07
Matches are distributed among these distances:
21 3 0.09
22 24 0.75
23 5 0.16
ACGTcount: A:0.55, C:0.05, G:0.00, T:0.41
Consensus pattern (22 bp):
AAAATTAAAAATTTTTAAATTT
Found at i:370817 original size:2 final size:2
Alignment explanation
Indices: 370810--370849 Score: 80
Period size: 2 Copynumber: 20.0 Consensus size: 2
370800 TTTTTACTCC
370810 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
370850 TTGAGATTAT
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:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:372071 original size:17 final size:19
Alignment explanation
Indices: 372026--372071 Score: 53
Period size: 17 Copynumber: 2.6 Consensus size: 19
372016 TATTTAATAC
372026 AAATATATTT-TTTTAATT
1 AAATATATTTATTTTAATT
*
372044 AAATATTTTTATTTT-A-T
1 AAATATATTTATTTTAATT
*
372061 AATTATATTTA
1 AAATATATTTA
372072 AATATATATA
Statistics
Matches: 24, Mismatches: 3, Indels: 3
0.80 0.10 0.10
Matches are distributed among these distances:
17 10 0.42
18 10 0.42
19 4 0.17
ACGTcount: A:0.39, C:0.00, G:0.00, T:0.61
Consensus pattern (19 bp):
AAATATATTTATTTTAATT
Found at i:375774 original size:19 final size:20
Alignment explanation
Indices: 375733--375774 Score: 50
Period size: 20 Copynumber: 2.1 Consensus size: 20
375723 TCACTAACAA
* * *
375733 AAAGGAAAATAAAAAAGACG
1 AAAGAAAAAGAAAAAAGAAG
375753 AAAGAAAAAGAAAAAA-AAG
1 AAAGAAAAAGAAAAAAGAAG
375772 AAA
1 AAA
375775 AGACGAGGGT
Statistics
Matches: 19, Mismatches: 3, Indels: 1
0.83 0.13 0.04
Matches are distributed among these distances:
19 5 0.26
20 14 0.74
ACGTcount: A:0.79, C:0.02, G:0.17, T:0.02
Consensus pattern (20 bp):
AAAGAAAAAGAAAAAAGAAG
Found at i:375939 original size:34 final size:34
Alignment explanation
Indices: 375891--375974 Score: 93
Period size: 34 Copynumber: 2.5 Consensus size: 34
375881 TTAATTAAAA
* *
375891 ATAAT-ATTAAATAATCTTATATACT-ATATAATT
1 ATAATAATTAAATAATATTAAATA-TAATATAATT
*
375924 ATAATAATTTAATAATATTAAATATAATATAATT
1 ATAATAATTAAATAATATTAAATATAATATAATT
*
375958 A-AATAATATAAAAAATA
1 ATAATAAT-TAAATAATA
375975 AAATTTATAT
Statistics
Matches: 43, Mismatches: 5, Indels: 5
0.81 0.09 0.09
Matches are distributed among these distances:
33 12 0.28
34 31 0.72
ACGTcount: A:0.57, C:0.02, G:0.00, T:0.40
Consensus pattern (34 bp):
ATAATAATTAAATAATATTAAATATAATATAATT
Found at i:375962 original size:25 final size:25
Alignment explanation
Indices: 375927--375975 Score: 71
Period size: 25 Copynumber: 2.0 Consensus size: 25
375917 TATAATTATA
* * *
375927 ATAATTTAATAATATTAAATATAAT
1 ATAATTAAATAATATAAAAAATAAT
375952 ATAATTAAATAATATAAAAAATAA
1 ATAATTAAATAATATAAAAAATAA
375976 AATTTATATG
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
25 21 1.00
ACGTcount: A:0.63, C:0.00, G:0.00, T:0.37
Consensus pattern (25 bp):
ATAATTAAATAATATAAAAAATAAT
Found at i:377658 original size:19 final size:20
Alignment explanation
Indices: 377635--377679 Score: 56
Period size: 19 Copynumber: 2.3 Consensus size: 20
377625 TCATTCATTA
*
377635 AATTTATGAAAATATTAATT
1 AATTTATAAAAATATTAATT
* *
377655 -ATTTTTAAAAATTTTAATT
1 AATTTATAAAAATATTAATT
377674 AATTTA
1 AATTTA
377680 AGTTACTTAA
Statistics
Matches: 20, Mismatches: 4, Indels: 2
0.77 0.15 0.08
Matches are distributed among these distances:
19 16 0.80
20 4 0.20
ACGTcount: A:0.47, C:0.00, G:0.02, T:0.51
Consensus pattern (20 bp):
AATTTATAAAAATATTAATT
Found at i:380051 original size:22 final size:23
Alignment explanation
Indices: 380002--380054 Score: 65
Period size: 22 Copynumber: 2.3 Consensus size: 23
379992 AAATATTTTT
380002 TAATTTTATCTTTAGTAATTTAA
1 TAATTTTATCTTTAGTAATTTAA
* *
380025 TAATTTTAT-TTTATTAAGTTTCA
1 TAATTTTATCTTTAGTAA-TTTAA
380048 -AATTTTA
1 TAATTTTA
380055 AATAATTTAA
Statistics
Matches: 27, Mismatches: 2, Indels: 3
0.84 0.06 0.09
Matches are distributed among these distances:
22 14 0.52
23 13 0.48
ACGTcount: A:0.34, C:0.04, G:0.04, T:0.58
Consensus pattern (23 bp):
TAATTTTATCTTTAGTAATTTAA
Found at i:380670 original size:18 final size:19
Alignment explanation
Indices: 380635--380676 Score: 50
Period size: 19 Copynumber: 2.3 Consensus size: 19
380625 TAATTTTTAT
* *
380635 TTAAATTTAATTATATATA
1 TTAATTTTAAATATATATA
*
380654 TTAATTTTAAATA-ATATT
1 TTAATTTTAAATATATATA
380672 TTAAT
1 TTAAT
380677 AATTTAGCGA
Statistics
Matches: 20, Mismatches: 3, Indels: 1
0.83 0.12 0.04
Matches are distributed among these distances:
18 9 0.45
19 11 0.55
ACGTcount: A:0.45, C:0.00, G:0.00, T:0.55
Consensus pattern (19 bp):
TTAATTTTAAATATATATA
Found at i:381999 original size:3 final size:3
Alignment explanation
Indices: 381991--382023 Score: 57
Period size: 3 Copynumber: 11.0 Consensus size: 3
381981 CTTTTTCTTA
*
381991 ATT ATT ATT ATG ATT ATT ATT ATT ATT ATT ATT
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT
382024 TTCATGGGAA
Statistics
Matches: 28, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
3 28 1.00
ACGTcount: A:0.33, C:0.00, G:0.03, T:0.64
Consensus pattern (3 bp):
ATT
Found at i:382593 original size:37 final size:37
Alignment explanation
Indices: 382531--382602 Score: 85
Period size: 37 Copynumber: 1.9 Consensus size: 37
382521 TTTTATGTAT
*
382531 TTTATTATATTATAATTATAATTTAAAT-ATTTTATA
1 TTTATTAAATTATAATTATAATTTAAATAATTTTATA
* *
382567 TTTATATAAATTATAA-TATATTTTTAATTAATTTTA
1 TTTAT-TAAATTATAATTATA-ATTTAAATAATTTTA
382603 ATAAAAAAAT
Statistics
Matches: 30, Mismatches: 3, Indels: 4
0.81 0.08 0.11
Matches are distributed among these distances:
36 9 0.30
37 15 0.50
38 6 0.20
ACGTcount: A:0.42, C:0.00, G:0.00, T:0.58
Consensus pattern (37 bp):
TTTATTAAATTATAATTATAATTTAAATAATTTTATA
Found at i:383001 original size:11 final size:11
Alignment explanation
Indices: 382981--383035 Score: 60
Period size: 11 Copynumber: 5.2 Consensus size: 11
382971 AAATATTCAC
382981 ATATTTATATT
1 ATATTTATATT
*
382992 ATATTCATATT
1 ATATTTATATT
*
383003 ATTTTTATATT
1 ATATTTATATT
383014 AT-TTT-TATT
1 ATATTTATATT
* *
383023 ATAATTATTTT
1 ATATTTATATT
383034 AT
1 AT
383036 TTCGTATCAA
Statistics
Matches: 37, Mismatches: 5, Indels: 4
0.80 0.11 0.09
Matches are distributed among these distances:
9 6 0.16
10 5 0.14
11 26 0.70
ACGTcount: A:0.33, C:0.02, G:0.00, T:0.65
Consensus pattern (11 bp):
ATATTTATATT
Found at i:383036 original size:14 final size:14
Alignment explanation
Indices: 382982--383033 Score: 50
Period size: 15 Copynumber: 3.4 Consensus size: 14
382972 AATATTCACA
*
382982 TATTTATATTATAT
1 TATTTTTATTATAT
*
382996 TCATATTATTTTTATAT
1 T-AT-TT-TTATTATAT
383013 TATTTTTATTATAAT
1 TATTTTTATTAT-AT
383028 TATTTT
1 TATTTT
383034 ATTTCGTATC
Statistics
Matches: 31, Mismatches: 3, Indels: 7
0.76 0.07 0.17
Matches are distributed among these distances:
14 7 0.23
15 12 0.39
16 4 0.13
17 8 0.26
ACGTcount: A:0.31, C:0.02, G:0.00, T:0.67
Consensus pattern (14 bp):
TATTTTTATTATAT
Found at i:384654 original size:2 final size:2
Alignment explanation
Indices: 384647--384691 Score: 72
Period size: 2 Copynumber: 22.5 Consensus size: 2
384637 TCAGTGGAGC
* *
384647 CT CT CT CT CT CT CC CT CT CT CT CT CT CT CT CT CT TT CT CT CT
1 CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT
384689 CT C
1 CT C
384692 CCCCATGTGC
Statistics
Matches: 39, Mismatches: 4, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
2 39 1.00
ACGTcount: A:0.00, C:0.51, G:0.00, T:0.49
Consensus pattern (2 bp):
CT
Found at i:389401 original size:2 final size:2
Alignment explanation
Indices: 389394--389452 Score: 109
Period size: 2 Copynumber: 29.5 Consensus size: 2
389384 TTGAAAGGGA
*
389394 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AG AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
389436 AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT A
389453 ATGAAATAAA
Statistics
Matches: 55, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
2 55 1.00
ACGTcount: A:0.51, C:0.00, G:0.02, T:0.47
Consensus pattern (2 bp):
AT
Found at i:393514 original size:108 final size:108
Alignment explanation
Indices: 393325--393541 Score: 362
Period size: 108 Copynumber: 2.0 Consensus size: 108
393315 ATGATCCAAC
* * *
393325 ATTGTCAAAGACTTTTAACAACAGAATCAATGGCTTACATAATAAACTAAGAAAATAATGGAAAT
1 ATTGTCAAAGACCTTCAACAACAGAATCAATGGATTACATAATAAACTAAGAAAATAATGGAAAT
* *
393390 ATACATTTGGCAAATTTTACATACAGTAAAGGTTTGAATTCAA
66 ATAAATTTGGCAAATTTTACATAAAGTAAAGGTTTGAATTCAA
* * *
393433 ATTGTCAAAGACCTTCAACAACAGAATCAATTGATTACATAATAAACTAAGAAAATAATGGTAGT
1 ATTGTCAAAGACCTTCAACAACAGAATCAATGGATTACATAATAAACTAAGAAAATAATGGAAAT
393498 ATAAATTTGGCAAATTTTACATAAAGTAAAGGTTTGAATTCAA
66 ATAAATTTGGCAAATTTTACATAAAGTAAAGGTTTGAATTCAA
393541 A
1 A
393542 CGATTCAGTA
Statistics
Matches: 101, Mismatches: 8, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
108 101 1.00
ACGTcount: A:0.46, C:0.12, G:0.13, T:0.29
Consensus pattern (108 bp):
ATTGTCAAAGACCTTCAACAACAGAATCAATGGATTACATAATAAACTAAGAAAATAATGGAAAT
ATAAATTTGGCAAATTTTACATAAAGTAAAGGTTTGAATTCAA
Found at i:394635 original size:14 final size:14
Alignment explanation
Indices: 394616--394654 Score: 53
Period size: 14 Copynumber: 2.8 Consensus size: 14
394606 ATGAGTAATT
394616 TTATTTTATTTAAA
1 TTATTTTATTTAAA
*
394630 TTATTTTATATTATA
1 TTATTTTAT-TTAAA
394645 -TATTTTATTT
1 TTATTTTATTT
394655 TTAAAATATA
Statistics
Matches: 23, Mismatches: 1, Indels: 3
0.85 0.04 0.11
Matches are distributed among these distances:
13 2 0.09
14 17 0.74
15 4 0.17
ACGTcount: A:0.31, C:0.00, G:0.00, T:0.69
Consensus pattern (14 bp):
TTATTTTATTTAAA
Found at i:394668 original size:13 final size:13
Alignment explanation
Indices: 394650--394715 Score: 50
Period size: 12 Copynumber: 5.2 Consensus size: 13
394640 TTATATATTT
394650 TATTTTTAAAATA
1 TATTTTTAAAATA
**
394663 TATTTTTAAGTTA
1 TATTTTTAAAATA
394676 -ATTTTTAATAA-A
1 TATTTTTAA-AATA
*
394688 T-TTTTTATTAATA
1 TATTTTTA-AAATA
*
394701 T-TTTTTAAAAAA
1 TATTTTTAAAATA
394713 TAT
1 TAT
394716 ATGATATAAT
Statistics
Matches: 41, Mismatches: 7, Indels: 10
0.71 0.12 0.17
Matches are distributed among these distances:
12 21 0.51
13 20 0.49
ACGTcount: A:0.41, C:0.00, G:0.02, T:0.58
Consensus pattern (13 bp):
TATTTTTAAAATA
Found at i:394778 original size:23 final size:24
Alignment explanation
Indices: 394752--394804 Score: 74
Period size: 23 Copynumber: 2.2 Consensus size: 24
394742 TTTAATAAAT
394752 TATTATTAATATAATA-A-AATTA
1 TATTATTAATATAATATATAATTA
*
394774 CTATTATTATTATAATATATAATTA
1 -TATTATTAATATAATATATAATTA
394799 TATTAT
1 TATTAT
394805 ACAATATTAA
Statistics
Matches: 27, Mismatches: 1, Indels: 3
0.87 0.03 0.10
Matches are distributed among these distances:
23 15 0.56
24 7 0.26
25 5 0.19
ACGTcount: A:0.47, C:0.02, G:0.00, T:0.51
Consensus pattern (24 bp):
TATTATTAATATAATATATAATTA
Found at i:394942 original size:16 final size:17
Alignment explanation
Indices: 394921--394965 Score: 56
Period size: 16 Copynumber: 2.6 Consensus size: 17
394911 TATAAAAAAA
*
394921 TAAATATTTTAAATT-T
1 TAAATATTATAAATTAT
*
394937 TAAATAATATAAATTAT
1 TAAATATTATAAATTAT
394954 TAACATATTATA
1 TAA-ATATTATA
394966 TTTTACAAAT
Statistics
Matches: 24, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
16 13 0.54
17 4 0.17
18 7 0.29
ACGTcount: A:0.51, C:0.02, G:0.00, T:0.47
Consensus pattern (17 bp):
TAAATATTATAAATTAT
Found at i:395309 original size:2 final size:2
Alignment explanation
Indices: 395302--395345 Score: 81
Period size: 2 Copynumber: 22.5 Consensus size: 2
395292 TTTATTGGTG
395302 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA -A
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
395343 TA T
1 TA T
395346 TTTCTTTTTC
Statistics
Matches: 41, Mismatches: 0, Indels: 2
0.95 0.00 0.05
Matches are distributed among these distances:
1 1 0.02
2 40 0.98
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:395852 original size:6 final size:6
Alignment explanation
Indices: 395841--395909 Score: 65
Period size: 6 Copynumber: 12.0 Consensus size: 6
395831 AATTTTAATA
* * *
395841 TATATT TATATT TATA-T TATATT TATA-A TATATT TCGTATC T-TATT
1 TATATT TATATT TATATT TATATT TATATT TATATT T-ATATT TATATT
*
395887 TAAATT TATATT TATA-T TATATT
1 TATATT TATATT TATATT TATATT
395910 CATAAAAATT
Statistics
Matches: 51, Mismatches: 7, Indels: 10
0.75 0.10 0.15
Matches are distributed among these distances:
5 18 0.35
6 29 0.57
7 4 0.08
ACGTcount: A:0.35, C:0.03, G:0.01, T:0.61
Consensus pattern (6 bp):
TATATT
Found at i:395854 original size:17 final size:17
Alignment explanation
Indices: 395841--395909 Score: 70
Period size: 17 Copynumber: 4.0 Consensus size: 17
395831 AATTTTAATA
395841 TATATTTATATT-TATAT
1 TATATTTATATTATAT-T
*
395858 TATATTTATAATATATT
1 TATATTTATATTATATT
* *
395875 TCGTATCTTAT-TTAAATT
1 T-ATAT-TTATATTATATT
395893 TATATTTATATTATATT
1 TATATTTATATTATATT
395910 CATAAAAATT
Statistics
Matches: 42, Mismatches: 6, Indels: 8
0.75 0.11 0.14
Matches are distributed among these distances:
16 4 0.10
17 22 0.52
18 12 0.29
19 4 0.10
ACGTcount: A:0.35, C:0.03, G:0.01, T:0.61
Consensus pattern (17 bp):
TATATTTATATTATATT
Found at i:395860 original size:11 final size:11
Alignment explanation
Indices: 395817--395909 Score: 73
Period size: 11 Copynumber: 8.3 Consensus size: 11
395807 TATGTTAATA
395817 ATTTATATTAT
1 ATTTATATTAT
** *
395828 ATAAATTTTA-
1 ATTTATATTAT
*
395838 ATATATATTTAT
1 ATTTATA-TTAT
395850 ATTTATATTAT
1 ATTTATATTAT
*
395861 ATTTATAATAT
1 ATTTATATTAT
*
395872 ATTTCGTATCT-T
1 ATTT-ATAT-TAT
*
395884 ATTTAAATTTAT
1 ATTTATA-TTAT
395896 ATTTATATTAT
1 ATTTATATTAT
395907 ATT
1 ATT
395910 CATAAAAATT
Statistics
Matches: 64, Mismatches: 12, Indels: 12
0.73 0.14 0.14
Matches are distributed among these distances:
10 5 0.08
11 37 0.58
12 21 0.33
13 1 0.02
ACGTcount: A:0.38, C:0.02, G:0.01, T:0.59
Consensus pattern (11 bp):
ATTTATATTAT
Found at i:396790 original size:2 final size:2
Alignment explanation
Indices: 396778--396810 Score: 57
Period size: 2 Copynumber: 16.5 Consensus size: 2
396768 TATTTTCTCT
*
396778 TA TA AA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
396811 GTGAAAAGTA
Statistics
Matches: 29, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
2 29 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
TA
Found at i:399052 original size:24 final size:25
Alignment explanation
Indices: 399025--399111 Score: 83
Period size: 24 Copynumber: 3.4 Consensus size: 25
399015 CGTATTATTT
*
399025 ATTTTATATTATATTATATTTAA-A
1 ATTTTATATTATTTTATATTTAATA
*
399049 ATTTTAT-TAATTTTAATATATTAATA
1 ATTTTATATTATTTT-ATAT-TTAATA
399075 A-TTTATATT-TTTTATATTTTAATA
1 ATTTTATATTATTTTATA-TTTAATA
399099 CATTTATATATTA
1 -ATTT-TATATTA
399112 ATATCTTATT
Statistics
Matches: 51, Mismatches: 3, Indels: 14
0.75 0.04 0.21
Matches are distributed among these distances:
23 5 0.10
24 20 0.39
25 15 0.29
26 5 0.10
27 6 0.12
ACGTcount: A:0.39, C:0.01, G:0.00, T:0.60
Consensus pattern (25 bp):
ATTTTATATTATTTTATATTTAATA
Found at i:399079 original size:33 final size:30
Alignment explanation
Indices: 399019--399121 Score: 82
Period size: 32 Copynumber: 3.2 Consensus size: 30
399009 CGTATTCGTA
*
399019 TTATTTATTTTATATTATATTATATTTAAAATT
1 TTATTAATTTTA-A-TATATTATATTT-AAATT
*
399052 TTATTAATTTTAATATATTAATAATTTATATT
1 TTATTAATTTTAATATATT-AT-ATTTAAATT
* *
399084 TT-TTATATTTTAATACATTTATATATTAATATC
1 TTATTA-ATTTTAATATA-TTATAT-TTAA-ATT
399117 TTATT
1 TTATT
399122 CGTATTATCT
Statistics
Matches: 58, Mismatches: 5, Indels: 13
0.76 0.07 0.17
Matches are distributed among these distances:
31 11 0.19
32 24 0.41
33 21 0.36
34 2 0.03
ACGTcount: A:0.37, C:0.02, G:0.00, T:0.61
Consensus pattern (30 bp):
TTATTAATTTTAATATATTATATTTAAATT
Found at i:409737 original size:28 final size:28
Alignment explanation
Indices: 409679--409740 Score: 74
Period size: 28 Copynumber: 2.2 Consensus size: 28
409669 ATTTTTATTT
*
409679 AATTTTTAATTTTTATAATATAGAAATA
1 AATTTTTAATTTTTATAATATAGAAAGA
*
409707 AATTTTTTATTTTTA-AAT-TAGTATAAGA
1 AATTTTTAATTTTTATAATATAG-A-AAGA
409735 AATTTT
1 AATTTT
409741 AAAATACTGT
Statistics
Matches: 30, Mismatches: 2, Indels: 4
0.83 0.06 0.11
Matches are distributed among these distances:
26 3 0.10
27 4 0.13
28 23 0.77
ACGTcount: A:0.42, C:0.00, G:0.05, T:0.53
Consensus pattern (28 bp):
AATTTTTAATTTTTATAATATAGAAAGA
Found at i:416433 original size:14 final size:16
Alignment explanation
Indices: 416406--416437 Score: 50
Period size: 14 Copynumber: 2.1 Consensus size: 16
416396 TTTTCCTATT
416406 TATTATATTATTAATA
1 TATTATATTATTAATA
416422 TATTAT-TT-TTAATA
1 TATTATATTATTAATA
416436 TA
1 TA
416438 AAATATGTTT
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
14 8 0.50
15 2 0.12
16 6 0.38
ACGTcount: A:0.41, C:0.00, G:0.00, T:0.59
Consensus pattern (16 bp):
TATTATATTATTAATA
Found at i:419238 original size:51 final size:51
Alignment explanation
Indices: 419162--419268 Score: 196
Period size: 51 Copynumber: 2.1 Consensus size: 51
419152 AACCCAGAAA
*
419162 ACAAATTCAGGAAAAAAAAACCAGAATATAAATGAGAAACAATCAATCAAG
1 ACAAATTCAGGAAAAAAAAAACAGAATATAAATGAGAAACAATCAATCAAG
*
419213 ACAAATTCAGGAAAAAAAAAACAGAATATATATGAGAAACAATCAATCAAG
1 ACAAATTCAGGAAAAAAAAAACAGAATATAAATGAGAAACAATCAATCAAG
419264 ACAAA
1 ACAAA
419269 CTTAAAAGAA
Statistics
Matches: 54, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
51 54 1.00
ACGTcount: A:0.62, C:0.13, G:0.11, T:0.14
Consensus pattern (51 bp):
ACAAATTCAGGAAAAAAAAAACAGAATATAAATGAGAAACAATCAATCAAG
Found at i:420730 original size:3 final size:3
Alignment explanation
Indices: 420722--420765 Score: 88
Period size: 3 Copynumber: 14.7 Consensus size: 3
420712 AAATATTTAA
420722 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 AA
420766 ACTGAAAAAA
Statistics
Matches: 41, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 41 1.00
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.32
Consensus pattern (3 bp):
AAT
Found at i:421006 original size:14 final size:15
Alignment explanation
Indices: 420987--421023 Score: 58
Period size: 15 Copynumber: 2.5 Consensus size: 15
420977 TAACTATTAA
420987 CTTTTTT-AAAAAAT
1 CTTTTTTAAAAAAAT
421001 CTTTTTTAAAAAAAT
1 CTTTTTTAAAAAAAT
421016 CATTTTTT
1 C-TTTTTT
421024 CACTCACATT
Statistics
Matches: 21, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
14 7 0.33
15 8 0.38
16 6 0.29
ACGTcount: A:0.38, C:0.08, G:0.00, T:0.54
Consensus pattern (15 bp):
CTTTTTTAAAAAAAT
Found at i:421372 original size:17 final size:17
Alignment explanation
Indices: 421320--421373 Score: 53
Period size: 17 Copynumber: 3.3 Consensus size: 17
421310 CGAATATTTC
*
421320 AAAATTTATATAA-CAT
1 AAAATTTATATAATTAT
421336 -AAA-TTAT-TAATGTAT
1 AAAATTTATATAAT-TAT
421351 CAAAATTTATATAATTAT
1 -AAAATTTATATAATTAT
421369 AAAAT
1 AAAAT
421374 ATTTTAAACT
Statistics
Matches: 31, Mismatches: 1, Indels: 11
0.72 0.02 0.26
Matches are distributed among these distances:
13 3 0.10
14 4 0.13
15 5 0.16
17 8 0.26
18 7 0.23
19 4 0.13
ACGTcount: A:0.54, C:0.04, G:0.02, T:0.41
Consensus pattern (17 bp):
AAAATTTATATAATTAT
Found at i:424178 original size:33 final size:35
Alignment explanation
Indices: 424140--424209 Score: 110
Period size: 33 Copynumber: 2.1 Consensus size: 35
424130 AAAAATAAAA
424140 TATATAATATAAA-TATATAAA-TA-TATTAAAATT
1 TATATAATATAAATTAT-TAAATTATTATTAAAATT
424173 TATATAATATAAATTATTAAATTATTATTAAAATT
1 TATATAATATAAATTATTAAATTATTATTAAAATT
424208 TA
1 TA
424210 CGAACATAAA
Statistics
Matches: 34, Mismatches: 0, Indels: 4
0.89 0.00 0.11
Matches are distributed among these distances:
33 17 0.50
34 5 0.15
35 12 0.35
ACGTcount: A:0.54, C:0.00, G:0.00, T:0.46
Consensus pattern (35 bp):
TATATAATATAAATTATTAAATTATTATTAAAATT
Found at i:426208 original size:29 final size:30
Alignment explanation
Indices: 426106--426209 Score: 101
Period size: 29 Copynumber: 3.5 Consensus size: 30
426096 GGTTAAATTA
426106 TTAAA-AAATTTTTAAATTTTATAATTT-TAT
1 TTAAATAAATTTTT-AATTTT-TAATTTCTAT
* * *
426136 TTAAGTAAATTTTTATATTTTT-AGTAC-AT
1 TTAAATAAATTTTTA-ATTTTTAATTTCTAT
* *
426165 TAAAATAAATCTTTAATTTTTAATTTCTAT
1 TTAAATAAATTTTTAATTTTTAATTTCTAT
426195 TTAAAT-AATTTTTAA
1 TTAAATAAATTTTTAA
426210 AACTTAAATT
Statistics
Matches: 59, Mismatches: 10, Indels: 11
0.74 0.12 0.14
Matches are distributed among these distances:
28 6 0.10
29 27 0.46
30 13 0.22
31 13 0.22
ACGTcount: A:0.40, C:0.03, G:0.02, T:0.55
Consensus pattern (30 bp):
TTAAATAAATTTTTAATTTTTAATTTCTAT
Found at i:426331 original size:25 final size:24
Alignment explanation
Indices: 426303--426354 Score: 61
Period size: 24 Copynumber: 2.1 Consensus size: 24
426293 ATAAAATTTT
*
426303 ATTTAAATATAATAAAGA-TATAAAA
1 ATTTAAATA-AACAAA-ATTATAAAA
*
426328 ATTTACATAAACAAAATTATAAAA
1 ATTTAAATAAACAAAATTATAAAA
426352 ATT
1 ATT
426355 AAAAAAAATT
Statistics
Matches: 24, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
23 1 0.04
24 15 0.62
25 8 0.33
ACGTcount: A:0.62, C:0.04, G:0.02, T:0.33
Consensus pattern (24 bp):
ATTTAAATAAACAAAATTATAAAA
Found at i:426332 original size:29 final size:29
Alignment explanation
Indices: 426255--426332 Score: 77
Period size: 29 Copynumber: 2.7 Consensus size: 29
426245 TTTTTTATTT
** * *
426255 AATAAAAAATATTAATTAAATTTAAATGTA
1 AATAAAAAATAAAAATT-TATTTAAATATA
*
426285 AATAAAAAATAAAATTTTATTTAAATAT-
1 AATAAAAAATAAAAATTTATTTAAATATA
*
426313 AATAAAGATATAAAAATTTA
1 AATAAA-AAATAAAAATTTA
426333 CATAAACAAA
Statistics
Matches: 40, Mismatches: 7, Indels: 3
0.80 0.14 0.06
Matches are distributed among these distances:
28 6 0.15
29 20 0.50
30 14 0.35
ACGTcount: A:0.62, C:0.00, G:0.03, T:0.36
Consensus pattern (29 bp):
AATAAAAAATAAAAATTTATTTAAATATA
Found at i:426774 original size:10 final size:10
Alignment explanation
Indices: 426761--426794 Score: 59
Period size: 10 Copynumber: 3.4 Consensus size: 10
426751 TTTTTAATAT
*
426761 AATATAATTA
1 AATAGAATTA
426771 AATAGAATTA
1 AATAGAATTA
426781 AATAGAATTA
1 AATAGAATTA
426791 AATA
1 AATA
426795 ATTAAAATAA
Statistics
Matches: 23, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
10 23 1.00
ACGTcount: A:0.62, C:0.00, G:0.06, T:0.32
Consensus pattern (10 bp):
AATAGAATTA
Found at i:427459 original size:20 final size:20
Alignment explanation
Indices: 427423--427460 Score: 51
Period size: 20 Copynumber: 1.9 Consensus size: 20
427413 AATAGAATAT
*
427423 TAAATTTTTAATATTAAAAA
1 TAAATTTTAAATATTAAAAA
427443 TAAATATTTAAAT-TTAAA
1 TAAAT-TTTAAATATTAAA
427461 CAACTTTAAA
Statistics
Matches: 16, Mismatches: 1, Indels: 2
0.84 0.05 0.11
Matches are distributed among these distances:
20 10 0.62
21 6 0.38
ACGTcount: A:0.55, C:0.00, G:0.00, T:0.45
Consensus pattern (20 bp):
TAAATTTTAAATATTAAAAA
Found at i:427722 original size:2 final size:2
Alignment explanation
Indices: 427717--427754 Score: 76
Period size: 2 Copynumber: 19.0 Consensus size: 2
427707 TATATAGCTC
427717 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
427755 TGTCATGAAA
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:428704 original size:29 final size:30
Alignment explanation
Indices: 428672--428730 Score: 84
Period size: 29 Copynumber: 2.0 Consensus size: 30
428662 TAATGAAAAA
**
428672 AATATTTTGGTTTTTATATTATTA-AATTT
1 AATATTTTAATTTTTATATTATTAGAATTT
*
428701 AATATTTTAATTTTTATATTTTTAGAATTT
1 AATATTTTAATTTTTATATTATTAGAATTT
428731 TAACAAATAA
Statistics
Matches: 26, Mismatches: 3, Indels: 1
0.87 0.10 0.03
Matches are distributed among these distances:
29 21 0.81
30 5 0.19
ACGTcount: A:0.32, C:0.00, G:0.05, T:0.63
Consensus pattern (30 bp):
AATATTTTAATTTTTATATTATTAGAATTT
Found at i:431025 original size:18 final size:19
Alignment explanation
Indices: 431004--431039 Score: 56
Period size: 19 Copynumber: 1.9 Consensus size: 19
430994 TTAAATTGTG
431004 ATTT-CTTTTAAAAAATTA
1 ATTTGCTTTTAAAAAATTA
*
431022 ATTTGCTTTTAAATAATT
1 ATTTGCTTTTAAAAAATT
431040 GATTCAGTGA
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:0.39, C:0.06, G:0.03, T:0.53
Consensus pattern (19 bp):
ATTTGCTTTTAAAAAATTA
Found at i:431840 original size:11 final size:10
Alignment explanation
Indices: 431824--431854 Score: 53
Period size: 10 Copynumber: 3.0 Consensus size: 10
431814 AATTTTCTAT
431824 TTTATTATTA
1 TTTATTATTA
431834 TTATATTATTA
1 TT-TATTATTA
431845 TTTATTATTA
1 TTTATTATTA
431855 AATTTTTTTA
Statistics
Matches: 20, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
10 10 0.50
11 10 0.50
ACGTcount: A:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (10 bp):
TTTATTATTA
Found at i:431851 original size:18 final size:16
Alignment explanation
Indices: 431822--431866 Score: 54
Period size: 18 Copynumber: 2.7 Consensus size: 16
431812 TAAATTTTCT
* *
431822 ATTTTATTATTATTAT
1 ATTTTTTTATTATTAA
431838 ATTATTATTTATTATTAA
1 ATT-TT-TTTATTATTAA
431856 ATTTTTTTATT
1 ATTTTTTTATT
431867 TTTTTATAAA
Statistics
Matches: 25, Mismatches: 2, Indels: 4
0.81 0.06 0.13
Matches are distributed among these distances:
16 9 0.36
17 4 0.16
18 12 0.48
ACGTcount: A:0.31, C:0.00, G:0.00, T:0.69
Consensus pattern (16 bp):
ATTTTTTTATTATTAA
Found at i:431873 original size:21 final size:23
Alignment explanation
Indices: 431839--431882 Score: 65
Period size: 21 Copynumber: 2.0 Consensus size: 23
431829 TATTATTATA
*
431839 TTATTATTTATTATTAAATTTTT
1 TTATTATTTATTATAAAATTTTT
431862 TTATT-TTT-TTATAAAATTTTT
1 TTATTATTTATTATAAAATTTTT
431883 AGAATTTATT
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
21 12 0.60
22 3 0.15
23 5 0.25
ACGTcount: A:0.30, C:0.00, G:0.00, T:0.70
Consensus pattern (23 bp):
TTATTATTTATTATAAAATTTTT
Found at i:432220 original size:15 final size:15
Alignment explanation
Indices: 432187--432256 Score: 54
Period size: 15 Copynumber: 4.6 Consensus size: 15
432177 GAATTAAAAA
* **
432187 AATTATATACATTAA
1 AATTATTTACATTTT
432202 AATTATATTA-ATTTT
1 AATTAT-TTACATTTT
432217 AATTATTTACATTTTT
1 AATTATTTACA-TTTT
*
432233 AAATT-TTTAAATTTT
1 -AATTATTTACATTTT
*
432248 AATTTTTTA
1 AATTATTTA
432257 TAATTTAAAT
Statistics
Matches: 46, Mismatches: 4, Indels: 10
0.77 0.07 0.17
Matches are distributed among these distances:
14 7 0.15
15 24 0.52
16 11 0.24
17 4 0.09
ACGTcount: A:0.40, C:0.03, G:0.00, T:0.57
Consensus pattern (15 bp):
AATTATTTACATTTT
Found at i:432233 original size:8 final size:8
Alignment explanation
Indices: 432213--432262 Score: 50
Period size: 8 Copynumber: 6.2 Consensus size: 8
432203 ATTATATTAA
432213 TTTT-AAT
1 TTTTAAAT
*
432220 TATTTACAT
1 T-TTTAAAT
432229 TTTTAAAT
1 TTTTAAAT
432237 TTTTAAA-
1 TTTTAAAT
*
432244 TTTTAATT
1 TTTTAAAT
432252 TTTTATAAT
1 TTTTA-AAT
432261 TT
1 TT
432263 AAATAAGTAT
Statistics
Matches: 35, Mismatches: 4, Indels: 6
0.78 0.09 0.13
Matches are distributed among these distances:
7 7 0.20
8 21 0.60
9 7 0.20
ACGTcount: A:0.32, C:0.02, G:0.00, T:0.66
Consensus pattern (8 bp):
TTTTAAAT
Found at i:432261 original size:16 final size:16
Alignment explanation
Indices: 432210--432262 Score: 63
Period size: 16 Copynumber: 3.4 Consensus size: 16
432200 AAAATTATAT
*
432210 TAATTTTAATTATTTA
1 TAATTTTAATTTTTTA
* * *
432226 CATTTTTAAATTTTTA
1 TAATTTTAATTTTTTA
432242 -AATTTTAATTTTTTA
1 TAATTTTAATTTTTTA
432257 TAATTT
1 TAATTT
432263 AAATAAGTAT
Statistics
Matches: 30, Mismatches: 6, Indels: 2
0.79 0.16 0.05
Matches are distributed among these distances:
15 13 0.43
16 17 0.57
ACGTcount: A:0.34, C:0.02, G:0.00, T:0.64
Consensus pattern (16 bp):
TAATTTTAATTTTTTA
Found at i:432263 original size:15 final size:15
Alignment explanation
Indices: 432211--432266 Score: 53
Period size: 15 Copynumber: 3.7 Consensus size: 15
432201 AAATTATATT
432211 AATTTT-AATTATTTA
1 AATTTTAAATT-TTTA
*
432226 CATTTTTAAATTTTTA
1 -AATTTTAAATTTTTA
*
432242 AATTTTAATTTTTTA
1 AATTTTAAATTTTTA
432257 TAA-TTTAAAT
1 -AATTTTAAAT
432267 AAGTATAATC
Statistics
Matches: 34, Mismatches: 4, Indels: 5
0.79 0.09 0.12
Matches are distributed among these distances:
15 19 0.56
16 11 0.32
17 4 0.12
ACGTcount: A:0.38, C:0.02, G:0.00, T:0.61
Consensus pattern (15 bp):
AATTTTAAATTTTTA
Found at i:433658 original size:3 final size:3
Alignment explanation
Indices: 433650--433686 Score: 65
Period size: 3 Copynumber: 12.3 Consensus size: 3
433640 AAAAATAAAT
*
433650 TTA TTA TTA TTA TTA TTA TTA TTA TTG TTA TTA TTA T
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA T
433687 AAGACAAATA
Statistics
Matches: 32, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
3 32 1.00
ACGTcount: A:0.30, C:0.00, G:0.03, T:0.68
Consensus pattern (3 bp):
TTA
Found at i:434318 original size:9 final size:9
Alignment explanation
Indices: 434304--434345 Score: 50
Period size: 9 Copynumber: 4.6 Consensus size: 9
434294 TATTTATATT
434304 TTAAATTTA
1 TTAAATTTA
434313 TTAAATATTAA
1 TTAAAT-TT-A
434324 TT-AATTTA
1 TTAAATTTA
*
434332 TTAAATTAA
1 TTAAATTTA
434341 TTAAA
1 TTAAA
434346 CTAAGCTTTG
Statistics
Matches: 29, Mismatches: 1, Indels: 6
0.81 0.03 0.17
Matches are distributed among these distances:
8 3 0.10
9 18 0.62
10 5 0.17
11 3 0.10
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (9 bp):
TTAAATTTA
Found at i:434800 original size:26 final size:26
Alignment explanation
Indices: 434753--434802 Score: 66
Period size: 26 Copynumber: 1.9 Consensus size: 26
434743 ATTTAGATGA
* *
434753 AAATATAAAATATGTAATAATATTTT
1 AAATATAAAAAATGTAAAAATATTTT
434779 AAATATAAGAAAATG-AAAAATATT
1 AAATATAA-AAAATGTAAAAATATT
434803 AATTTTAAAT
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
26 16 0.76
27 5 0.24
ACGTcount: A:0.60, C:0.00, G:0.06, T:0.34
Consensus pattern (26 bp):
AAATATAAAAAATGTAAAAATATTTT
Found at i:435792 original size:2 final size:2
Alignment explanation
Indices: 435785--435812 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
435775 AGCCTCTTTG
435785 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
435813 AACTCGAAAG
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:0.00, C:0.50, G:0.00, T:0.50
Consensus pattern (2 bp):
TC
Found at i:437640 original size:28 final size:29
Alignment explanation
Indices: 437598--437654 Score: 107
Period size: 28 Copynumber: 2.0 Consensus size: 29
437588 TGTAATAACT
437598 TAATTAAAAAGTAAAGTGAACTCGATTAA
1 TAATTAAAAAGTAAAGTGAACTCGATTAA
437627 TAATT-AAAAGTAAAGTGAACTCGATTAA
1 TAATTAAAAAGTAAAGTGAACTCGATTAA
437655 GCAAAGTGAA
Statistics
Matches: 28, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
28 23 0.82
29 5 0.18
ACGTcount: A:0.51, C:0.07, G:0.14, T:0.28
Consensus pattern (29 bp):
TAATTAAAAAGTAAAGTGAACTCGATTAA
Found at i:439569 original size:13 final size:12
Alignment explanation
Indices: 439551--439587 Score: 58
Period size: 11 Copynumber: 3.1 Consensus size: 12
439541 AATATTAAAC
439551 ATAATATAATTAT
1 ATAATATAA-TAT
439564 ATAATATAA-AT
1 ATAATATAATAT
439575 ATAATATAATAT
1 ATAATATAATAT
439587 A
1 A
439588 AAAATTAAAC
Statistics
Matches: 23, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
11 11 0.48
12 3 0.13
13 9 0.39
ACGTcount: A:0.59, C:0.00, G:0.00, T:0.41
Consensus pattern (12 bp):
ATAATATAATAT
Found at i:439570 original size:5 final size:5
Alignment explanation
Indices: 439551--439588 Score: 53
Period size: 5 Copynumber: 7.8 Consensus size: 5
439541 AATATTAAAC
439551 ATAAT ATAAT -T-AT ATAAT ATAAAT ATAAT ATAAT ATAA
1 ATAAT ATAAT ATAAT ATAAT AT-AAT ATAAT ATAAT ATAA
439589 AAATTAAACT
Statistics
Matches: 30, Mismatches: 0, Indels: 6
0.83 0.00 0.17
Matches are distributed among these distances:
3 2 0.07
4 2 0.07
5 21 0.70
6 5 0.17
ACGTcount: A:0.61, C:0.00, G:0.00, T:0.39
Consensus pattern (5 bp):
ATAAT
Found at i:439583 original size:16 final size:14
Alignment explanation
Indices: 439551--439589 Score: 53
Period size: 16 Copynumber: 2.7 Consensus size: 14
439541 AATATTAAAC
439551 ATAATAT-AATTAT
1 ATAATATAAATTAT
439564 ATAATATAAATATAAT
1 ATAATATAAAT-T-AT
439580 ATAATATAAA
1 ATAATATAAA
439590 AATTAAACTA
Statistics
Matches: 23, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
13 7 0.30
14 3 0.13
15 1 0.04
16 12 0.52
ACGTcount: A:0.62, C:0.00, G:0.00, T:0.38
Consensus pattern (14 bp):
ATAATATAAATTAT
Found at i:439601 original size:24 final size:24
Alignment explanation
Indices: 439539--439607 Score: 72
Period size: 24 Copynumber: 2.9 Consensus size: 24
439529 GCATCATCAA
*
439539 ATAATATTAAAC-ATAATATAATT
1 ATAAAATTAAACTATAATATAATT
*
439562 ATATAATATAAA-TATAATATAA-T
1 ATAAAAT-TAAACTATAATATAATT
*
439585 ATAAAAATTAAACTATAAAATAA
1 AT-AAAATTAAACTATAATATAA
439608 AATATATAAA
Statistics
Matches: 38, Mismatches: 4, Indels: 7
0.78 0.08 0.14
Matches are distributed among these distances:
23 12 0.32
24 26 0.68
ACGTcount: A:0.62, C:0.03, G:0.00, T:0.35
Consensus pattern (24 bp):
ATAAAATTAAACTATAATATAATT
Found at i:439637 original size:30 final size:29
Alignment explanation
Indices: 439603--439681 Score: 85
Period size: 30 Copynumber: 2.8 Consensus size: 29
439593 TAAACTATAA
439603 AATAAAATATATAAATATTTTAAAATTTAT
1 AATAAAATAT-TAAATATTTTAAAATTTAT
* *
439633 AATAAAAGTATT-AATATAATAAAAATTTAT
1 AATAAAA-TATTAAATAT-TTTAAAATTTAT
439663 -AT-AAATATTAAAT-TTTTAA
1 AATAAAATATTAAATATTTTAA
439682 TTATAATAAT
Statistics
Matches: 42, Mismatches: 4, Indels: 10
0.75 0.07 0.18
Matches are distributed among these distances:
26 3 0.07
27 5 0.12
28 6 0.14
29 7 0.17
30 18 0.43
31 3 0.07
ACGTcount: A:0.57, C:0.00, G:0.01, T:0.42
Consensus pattern (29 bp):
AATAAAATATTAAATATTTTAAAATTTAT
Found at i:440672 original size:30 final size:30
Alignment explanation
Indices: 440621--440703 Score: 80
Period size: 30 Copynumber: 2.8 Consensus size: 30
440611 AACCTGTAGT
** *
440621 TTATA-CATAAATAAATTTTTAATTTTTAAA
1 TTATATCA-AAATAAACCTTTAACTTTTAAA
* **
440651 TTATACTC-AAATAAGCCTTTAACTTTTAGT
1 TTATA-TCAAAATAAACCTTTAACTTTTAAA
440681 TTATATCAAAATAAACCTTTAAC
1 TTATATCAAAATAAACCTTTAAC
440704 ATAAATCAAT
Statistics
Matches: 43, Mismatches: 7, Indels: 6
0.77 0.12 0.11
Matches are distributed among these distances:
29 2 0.05
30 40 0.93
32 1 0.02
ACGTcount: A:0.42, C:0.12, G:0.02, T:0.43
Consensus pattern (30 bp):
TTATATCAAAATAAACCTTTAACTTTTAAA
Found at i:440791 original size:51 final size:52
Alignment explanation
Indices: 440725--440823 Score: 130
Period size: 51 Copynumber: 1.9 Consensus size: 52
440715 TTTTATTTGA
* * *
440725 AATAAAAACTTATTTAGATATAATTTAAAT-GAT-AAAAATTTATTTAAGTAC
1 AATAAAAAATTATTTAGATA-AAATAAAATGGATCAAAAATTTATTTAAGTAC
* *
440776 AATAAAAAATTATTTATATAAAATAAAATGGTTCAAAAATTTATTTAA
1 AATAAAAAATTATTTAGATAAAATAAAATGGATCAAAAATTTATTTAA
440824 ATAAAAATAA
Statistics
Matches: 41, Mismatches: 5, Indels: 3
0.84 0.10 0.06
Matches are distributed among these distances:
50 7 0.17
51 20 0.49
52 14 0.34
ACGTcount: A:0.54, C:0.03, G:0.05, T:0.38
Consensus pattern (52 bp):
AATAAAAAATTATTTAGATAAAATAAAATGGATCAAAAATTTATTTAAGTAC
Found at i:440800 original size:21 final size:21
Alignment explanation
Indices: 440756--440803 Score: 62
Period size: 21 Copynumber: 2.3 Consensus size: 21
440746 AATTTAAATG
* *
440756 ATAAAAATTTATTTAAGTACA
1 ATAAAAAATTATTTAAGTAAA
440777 ATAAAAAATTATTTATA-TAAA
1 ATAAAAAATTATTTA-AGTAAA
440798 ATAAAA
1 ATAAAA
440804 TGGTTCAAAA
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
21 23 0.96
22 1 0.04
ACGTcount: A:0.60, C:0.02, G:0.02, T:0.35
Consensus pattern (21 bp):
ATAAAAAATTATTTAAGTAAA
Found at i:441390 original size:22 final size:22
Alignment explanation
Indices: 441355--441399 Score: 65
Period size: 22 Copynumber: 2.0 Consensus size: 22
441345 TATTTAAATT
441355 TAAATTTAATTATAAAAATATA
1 TAAATTTAATTATAAAAATATA
*
441377 TAAATATTAA-TATAAAATTATA
1 TAAAT-TTAATTATAAAAATATA
441399 T
1 T
441400 TTTAAAATAA
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
22 17 0.81
23 4 0.19
ACGTcount: A:0.58, C:0.00, G:0.00, T:0.42
Consensus pattern (22 bp):
TAAATTTAATTATAAAAATATA
Found at i:441932 original size:20 final size:21
Alignment explanation
Indices: 441898--441942 Score: 67
Period size: 19 Copynumber: 2.2 Consensus size: 21
441888 AACAAAAAAA
441898 AAATTATATTAATATTTTATTT
1 AAATTATATTAATA-TTTATTT
441920 AAATTAT-TT-ATATTTATTT
1 AAATTATATTAATATTTATTT
441939 AAAT
1 AAAT
441943 ATCTTGAAAA
Statistics
Matches: 23, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
19 11 0.48
20 3 0.13
21 2 0.09
22 7 0.30
ACGTcount: A:0.42, C:0.00, G:0.00, T:0.58
Consensus pattern (21 bp):
AAATTATATTAATATTTATTT
Found at i:442385 original size:6 final size:6
Alignment explanation
Indices: 442374--442401 Score: 56
Period size: 6 Copynumber: 4.7 Consensus size: 6
442364 AATTGAGTTG
442374 ATTTAA ATTTAA ATTTAA ATTTAA ATTT
1 ATTTAA ATTTAA ATTTAA ATTTAA ATTT
442402 TTATTTTTTT
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 22 1.00
ACGTcount: A:0.46, C:0.00, G:0.00, T:0.54
Consensus pattern (6 bp):
ATTTAA
Found at i:442476 original size:21 final size:21
Alignment explanation
Indices: 442435--442477 Score: 61
Period size: 21 Copynumber: 2.0 Consensus size: 21
442425 TAAAAATAAA
*
442435 ATATATTTTATGTTAATATTT
1 ATATATTTTATATTAATATTT
442456 ATATATTTTATTATTAA-ATTT
1 ATATATTTTA-TATTAATATTT
442477 A
1 A
442478 AATAAAAAAT
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
21 15 0.75
22 5 0.25
ACGTcount: A:0.37, C:0.00, G:0.02, T:0.60
Consensus pattern (21 bp):
ATATATTTTATATTAATATTT
Found at i:442625 original size:16 final size:16
Alignment explanation
Indices: 442587--442627 Score: 66
Period size: 17 Copynumber: 2.6 Consensus size: 16
442577 AAACTGAATA
442587 AATA-ATTTAATTTAT
1 AATATATTTAATTTAT
442602 AGATATATTTAATTTAT
1 A-ATATATTTAATTTAT
442619 AATATATTT
1 AATATATTT
442628 CTTTCGGTAT
Statistics
Matches: 24, Mismatches: 0, Indels: 3
0.89 0.00 0.11
Matches are distributed among these distances:
15 1 0.04
16 11 0.46
17 12 0.50
ACGTcount: A:0.44, C:0.00, G:0.02, T:0.54
Consensus pattern (16 bp):
AATATATTTAATTTAT
Found at i:442649 original size:29 final size:29
Alignment explanation
Indices: 442617--442702 Score: 76
Period size: 29 Copynumber: 3.1 Consensus size: 29
442607 TATTTAATTT
442617 ATAATATATTTCTTTCGGTATATTAAATC
1 ATAATATATTTCTTTCGGTATATTAAATC
* ****
442646 ATAAGATAAAAGTTT---T-T-TTAATAT-
1 ATAATATATTTCTTTCGGTATATTAA-ATC
442670 ATAATATATTTCTTTCGGTATATTAAATC
1 ATAATATATTTCTTTCGGTATATTAAATC
442699 ATAA
1 ATAA
442703 GATAAAATTT
Statistics
Matches: 40, Mismatches: 10, Indels: 14
0.62 0.16 0.22
Matches are distributed among these distances:
24 14 0.35
25 3 0.08
26 1 0.03
27 1 0.03
28 3 0.08
29 18 0.45
ACGTcount: A:0.40, C:0.07, G:0.07, T:0.47
Consensus pattern (29 bp):
ATAATATATTTCTTTCGGTATATTAAATC
Found at i:442673 original size:53 final size:53
Alignment explanation
Indices: 442609--442709 Score: 193
Period size: 53 Copynumber: 1.9 Consensus size: 53
442599 TATAGATATA
*
442609 TTTAATTTATAATATATTTCTTTCGGTATATTAAATCATAAGATAAAAGTTTT
1 TTTAATATATAATATATTTCTTTCGGTATATTAAATCATAAGATAAAAGTTTT
442662 TTTAATATATAATATATTTCTTTCGGTATATTAAATCATAAGATAAAA
1 TTTAATATATAATATATTTCTTTCGGTATATTAAATCATAAGATAAAA
442710 TTTCATCTTT
Statistics
Matches: 47, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
53 47 1.00
ACGTcount: A:0.41, C:0.06, G:0.07, T:0.47
Consensus pattern (53 bp):
TTTAATATATAATATATTTCTTTCGGTATATTAAATCATAAGATAAAAGTTTT
Found at i:443876 original size:30 final size:30
Alignment explanation
Indices: 443842--443903 Score: 97
Period size: 30 Copynumber: 2.1 Consensus size: 30
443832 AATTTAAATT
*
443842 AAAGTTTATTTAAGTACAAATTAAAAGTTA
1 AAAGTTTATTTAAGTAAAAATTAAAAGTTA
* *
443872 AAAGTTTATTTGAGTAAAAATTAAAATTTA
1 AAAGTTTATTTAAGTAAAAATTAAAAGTTA
443902 AA
1 AA
443904 GACTTATTTA
Statistics
Matches: 29, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
30 29 1.00
ACGTcount: A:0.52, C:0.02, G:0.10, T:0.37
Consensus pattern (30 bp):
AAAGTTTATTTAAGTAAAAATTAAAAGTTA
Found at i:443911 original size:30 final size:30
Alignment explanation
Indices: 443842--443914 Score: 85
Period size: 30 Copynumber: 2.4 Consensus size: 30
443832 AATTTAAATT
* *
443842 AAAGTTTATTTAAGTACAAATTAAAAGTTA
1 AAAGCTTATTTAAGTAAAAATTAAAAGTTA
* * *
443872 AAAGTTTATTTGAGTAAAAATTAAAA-TTT
1 AAAGCTTATTTAAGTAAAAATTAAAAGTTA
443901 AAAGACTTATTTAA
1 AAAG-CTTATTTAA
443915 CTTTAATAAC
Statistics
Matches: 37, Mismatches: 5, Indels: 2
0.84 0.11 0.05
Matches are distributed among these distances:
29 6 0.16
30 31 0.84
ACGTcount: A:0.49, C:0.03, G:0.10, T:0.38
Consensus pattern (30 bp):
AAAGCTTATTTAAGTAAAAATTAAAAGTTA
Found at i:444778 original size:7 final size:7
Alignment explanation
Indices: 444762--444793 Score: 55
Period size: 7 Copynumber: 4.6 Consensus size: 7
444752 TACAAAGTAC
*
444762 TAGATTA
1 TAGATCA
444769 TAGATCA
1 TAGATCA
444776 TAGATCA
1 TAGATCA
444783 TAGATCA
1 TAGATCA
444790 TAGA
1 TAGA
444794 AGCACGGCAA
Statistics
Matches: 24, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
7 24 1.00
ACGTcount: A:0.44, C:0.09, G:0.16, T:0.31
Consensus pattern (7 bp):
TAGATCA
Found at i:445529 original size:24 final size:23
Alignment explanation
Indices: 445474--445558 Score: 88
Period size: 22 Copynumber: 3.7 Consensus size: 23
445464 AAACTATTAC
445474 TTAATAATAA-AAATAAAATTTAAA
1 TTAAT-ATAATAAATAAAA-TTAAA
*
445498 TTTA-ATAATAAA-AAATATTAATA
1 TTAATATAATAAATAAA-ATTAA-A
*
445521 TTAATATAA-AAATAAAATTTAA
1 TTAATATAATAAATAAAATTAAA
445543 TTAATATAATAAATAA
1 TTAATATAATAAATAA
445559 TGAAATAAAC
Statistics
Matches: 52, Mismatches: 3, Indels: 13
0.76 0.04 0.19
Matches are distributed among these distances:
22 21 0.40
23 21 0.40
24 10 0.19
ACGTcount: A:0.64, C:0.00, G:0.00, T:0.36
Consensus pattern (23 bp):
TTAATATAATAAATAAAATTAAA
Found at i:446413 original size:3 final size:3
Alignment explanation
Indices: 446400--446431 Score: 55
Period size: 3 Copynumber: 10.7 Consensus size: 3
446390 TATTCTCCTC
*
446400 CTT CTT ATT CTT CTT CTT CTT CTT CTT CTT CT
1 CTT CTT CTT CTT CTT CTT CTT CTT CTT CTT CT
446432 CGTCTTGCAA
Statistics
Matches: 27, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
3 27 1.00
ACGTcount: A:0.03, C:0.31, G:0.00, T:0.66
Consensus pattern (3 bp):
CTT
Found at i:448168 original size:11 final size:11
Alignment explanation
Indices: 448152--448179 Score: 56
Period size: 11 Copynumber: 2.5 Consensus size: 11
448142 TGAAAGAAAT
448152 AATAAATTAAA
1 AATAAATTAAA
448163 AATAAATTAAA
1 AATAAATTAAA
448174 AATAAA
1 AATAAA
448180 GATTGATATT
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 17 1.00
ACGTcount: A:0.75, C:0.00, G:0.00, T:0.25
Consensus pattern (11 bp):
AATAAATTAAA
Found at i:448342 original size:25 final size:25
Alignment explanation
Indices: 448286--448343 Score: 62
Period size: 25 Copynumber: 2.3 Consensus size: 25
448276 ATATAAAAAT
* * *
448286 ATTTTTAATTTTATATTTATTATAA
1 ATTTTTTATTTGAAATTTATTATAA
** *
448311 AAATTTTATTTGAAATTTTTTATAA
1 ATTTTTTATTTGAAATTTATTATAA
448336 ATTTTTTA
1 ATTTTTTA
448344 ATAAAATTAA
Statistics
Matches: 25, Mismatches: 8, Indels: 0
0.76 0.24 0.00
Matches are distributed among these distances:
25 25 1.00
ACGTcount: A:0.36, C:0.00, G:0.02, T:0.62
Consensus pattern (25 bp):
ATTTTTTATTTGAAATTTATTATAA
Found at i:448757 original size:16 final size:16
Alignment explanation
Indices: 448716--448758 Score: 50
Period size: 16 Copynumber: 2.6 Consensus size: 16
448706 ATTTTTTAAA
* *
448716 TATAATAATAATCATTT
1 TATAATAA-AATAATTG
*
448733 TAAAATAAAATAATTG
1 TATAATAAAATAATTG
448749 TATAATAAAA
1 TATAATAAAA
448759 AATAAATAAT
Statistics
Matches: 22, Mismatches: 4, Indels: 1
0.81 0.15 0.04
Matches are distributed among these distances:
16 15 0.68
17 7 0.32
ACGTcount: A:0.58, C:0.02, G:0.02, T:0.37
Consensus pattern (16 bp):
TATAATAAAATAATTG
Found at i:448776 original size:22 final size:23
Alignment explanation
Indices: 448734--448776 Score: 54
Period size: 22 Copynumber: 1.9 Consensus size: 23
448724 TAATCATTTT
*
448734 AAAATAAAATAATTGTATAATAA
1 AAAATAAAATAATTATATAATAA
448757 AAAAT-AAATAA-TATACTAAT
1 AAAATAAAATAATTATA-TAAT
448777 GCACTTTAGT
Statistics
Matches: 18, Mismatches: 1, Indels: 3
0.82 0.05 0.14
Matches are distributed among these distances:
21 3 0.17
22 10 0.56
23 5 0.28
ACGTcount: A:0.65, C:0.02, G:0.02, T:0.30
Consensus pattern (23 bp):
AAAATAAAATAATTATATAATAA
Found at i:457338 original size:21 final size:21
Alignment explanation
Indices: 457310--457371 Score: 58
Period size: 21 Copynumber: 2.9 Consensus size: 21
457300 GAATATAATA
457310 TTAA-TTAATAAAAATATTTT
1 TTAATTTAATAAAAATATTTT
457330 TTAATTTAATAACATAAT-TTTT
1 TTAATTTAATAA-A-AATATTTT
*
457352 TATAAATATAA-AAAAATATT
1 T-T-AATTTAATAAAAATATT
457372 ATCAAACATA
Statistics
Matches: 35, Mismatches: 1, Indels: 10
0.76 0.02 0.22
Matches are distributed among these distances:
20 4 0.11
21 10 0.29
22 9 0.26
23 6 0.17
24 6 0.17
ACGTcount: A:0.52, C:0.02, G:0.00, T:0.47
Consensus pattern (21 bp):
TTAATTTAATAAAAATATTTT
Done.