Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold221
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: 2539808
ACGTcount: A:0.35, C:0.15, G:0.15, T:0.35
File 4 of 19
Found at i:488820 original size:17 final size:18
Alignment explanation
Indices: 488788--488822 Score: 54
Period size: 17 Copynumber: 2.0 Consensus size: 18
488778 ATACAAATTA
488788 TAATAAAATAAAATACAC
1 TAATAAAATAAAATACAC
*
488806 TAATAATAT-AAATACAC
1 TAATAAAATAAAATACAC
488823 AAATGCACTT
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
17 8 0.50
18 8 0.50
ACGTcount: A:0.63, C:0.11, G:0.00, T:0.26
Consensus pattern (18 bp):
TAATAAAATAAAATACAC
Found at i:494009 original size:22 final size:20
Alignment explanation
Indices: 493981--494022 Score: 57
Period size: 20 Copynumber: 2.0 Consensus size: 20
493971 TTAAATATAA
493981 TTAATAAAAATATATATTAAAT
1 TTAAT-AAAATA-ATATTAAAT
*
494003 TTAATAATATAATATTAAAT
1 TTAATAAAATAATATTAAAT
494023 ATAAATTTAA
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
20 9 0.47
21 5 0.26
22 5 0.26
ACGTcount: A:0.57, C:0.00, G:0.00, T:0.43
Consensus pattern (20 bp):
TTAATAAAATAATATTAAAT
Found at i:494027 original size:26 final size:26
Alignment explanation
Indices: 493963--494037 Score: 76
Period size: 21 Copynumber: 3.2 Consensus size: 26
493953 TTTAATATTA
*
493963 AATAAAAT-TTAAATAT-AA-TTAAT
1 AATATAATATTAAATATAAATTTAAT
*
493986 AA-A-AATA-TATAT-TAAATTTAAT
1 AATATAATATTAAATATAAATTTAAT
494008 AATATAATATTAAATATAAATTTAA-
1 AATATAATATTAAATATAAATTTAAT
494033 AATAT
1 AATAT
494038 TAAAATTTTA
Statistics
Matches: 43, Mismatches: 2, Indels: 12
0.75 0.04 0.21
Matches are distributed among these distances:
20 1 0.02
21 9 0.21
22 8 0.19
23 3 0.07
24 4 0.09
25 9 0.21
26 9 0.21
ACGTcount: A:0.60, C:0.00, G:0.00, T:0.40
Consensus pattern (26 bp):
AATATAATATTAAATATAAATTTAAT
Found at i:494462 original size:20 final size:20
Alignment explanation
Indices: 494437--494494 Score: 66
Period size: 20 Copynumber: 2.9 Consensus size: 20
494427 ATATTATATC
*
494437 TAAATTTAATTTAATTTGAA
1 TAAATTTAATTTAATTTAAA
494457 TAAA-TTAA-TTAACTCTTAAA
1 TAAATTTAATTTAA-T-TTAAA
494477 TAAATTTATATTTAATTT
1 TAAATTTA-ATTTAATTT
494495 TTGTTACCAA
Statistics
Matches: 32, Mismatches: 1, Indels: 9
0.76 0.02 0.21
Matches are distributed among these distances:
18 4 0.12
19 5 0.16
20 12 0.38
21 5 0.16
22 2 0.06
23 4 0.12
ACGTcount: A:0.45, C:0.03, G:0.02, T:0.50
Consensus pattern (20 bp):
TAAATTTAATTTAATTTAAA
Found at i:494987 original size:21 final size:21
Alignment explanation
Indices: 494948--494992 Score: 56
Period size: 21 Copynumber: 2.1 Consensus size: 21
494938 CACTTAAATG
* *
494948 TTATTTAATTTAATTTATT-T
1 TTATTTAATCTAATATATTAT
494968 TTATTTAAATCTAATATATTAT
1 TTATTT-AATCTAATATATTAT
494990 TTA
1 TTA
494993 ATTGACTTTA
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
20 6 0.29
21 11 0.52
22 4 0.19
ACGTcount: A:0.36, C:0.02, G:0.00, T:0.62
Consensus pattern (21 bp):
TTATTTAATCTAATATATTAT
Found at i:495044 original size:14 final size:15
Alignment explanation
Indices: 495025--495057 Score: 50
Period size: 15 Copynumber: 2.3 Consensus size: 15
495015 GTATTAATTA
495025 TATTTT-ATAAATAT
1 TATTTTAATAAATAT
*
495039 TATTTTAATTAATAT
1 TATTTTAATAAATAT
495054 TATT
1 TATT
495058 AAATATTAAT
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
14 6 0.35
15 11 0.65
ACGTcount: A:0.39, C:0.00, G:0.00, T:0.61
Consensus pattern (15 bp):
TATTTTAATAAATAT
Found at i:495060 original size:25 final size:25
Alignment explanation
Indices: 495018--495065 Score: 71
Period size: 25 Copynumber: 1.9 Consensus size: 25
495008 AATTAATGTA
*
495018 TTAATTATATTTTATAAATATTATT
1 TTAATTATATTATATAAATATTATT
495043 TTAATTAATATTAT-TAAATATTA
1 TTAATT-ATATTATATAAATATTA
495066 ATTAATATAT
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
25 15 0.71
26 6 0.29
ACGTcount: A:0.44, C:0.00, G:0.00, T:0.56
Consensus pattern (25 bp):
TTAATTATATTATATAAATATTATT
Found at i:495068 original size:20 final size:20
Alignment explanation
Indices: 495043--495096 Score: 63
Period size: 21 Copynumber: 2.6 Consensus size: 20
495033 AAATATTATT
495043 TTAATTAATATTATTAAATA
1 TTAATTAATATTATTAAATA
* * *
495063 TTAATTAATATATTTTTACTA
1 TTAATTAATAT-TATTAAATA
*
495084 TAAATTAATATTA
1 TTAATTAATATTA
495097 AATATATTTT
Statistics
Matches: 28, Mismatches: 5, Indels: 2
0.80 0.14 0.06
Matches are distributed among these distances:
20 12 0.43
21 16 0.57
ACGTcount: A:0.46, C:0.02, G:0.00, T:0.52
Consensus pattern (20 bp):
TTAATTAATATTATTAAATA
Found at i:495227 original size:25 final size:25
Alignment explanation
Indices: 495194--495242 Score: 73
Period size: 25 Copynumber: 2.0 Consensus size: 25
495184 TTTAAAAAGT
*
495194 AAATTAAAATT-ATATAAATATAAAA
1 AAATAAAAATTAATAT-AATATAAAA
495219 AAATAAAAATTAATATAATATAAA
1 AAATAAAAATTAATATAATATAAA
495243 TATATAAATA
Statistics
Matches: 22, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
25 18 0.82
26 4 0.18
ACGTcount: A:0.69, C:0.00, G:0.00, T:0.31
Consensus pattern (25 bp):
AAATAAAAATTAATATAATATAAAA
Found at i:495249 original size:8 final size:8
Alignment explanation
Indices: 495204--495287 Score: 50
Period size: 8 Copynumber: 10.6 Consensus size: 8
495194 AAATTAAAAT
495204 TATATAAA
1 TATATAAA
495212 TATA-AAA
1 TATATAAA
*
495219 -AAATAAA
1 TATATAAA
*
495226 AAT-TAATA
1 TATATAA-A
495234 TAATATAAA
1 T-ATATAAA
495243 TATATAAA
1 TATATAAA
* * *
495251 TATTTTAT
1 TATATAAA
*
495259 TATTTAAA
1 TATATAAA
495267 TAATATAAA
1 T-ATATAAA
*
495276 T-TATTAA
1 TATATAAA
495283 TATAT
1 TATAT
495288 TAAAATTTAT
Statistics
Matches: 59, Mismatches: 10, Indels: 14
0.71 0.12 0.17
Matches are distributed among these distances:
6 2 0.03
7 15 0.25
8 28 0.47
9 11 0.19
10 3 0.05
ACGTcount: A:0.58, C:0.00, G:0.00, T:0.42
Consensus pattern (8 bp):
TATATAAA
Found at i:495249 original size:25 final size:25
Alignment explanation
Indices: 495199--495357 Score: 85
Period size: 25 Copynumber: 6.2 Consensus size: 25
495189 AAAGTAAATT
* *
495199 AAAATT-ATATAAATATAAAAAAATA
1 AAAATTAATAT-AATATAAATATATA
495224 AAAATTAATATAATATAAATATATA
1 AAAATTAATATAATATAAATATATA
* * * *
495249 AATATT-TTATTATTTAAATAATATA
1 AAAATTAATATAATATAAAT-ATATA
* *
495274 AATTATTAATATATTA-AAATTTATATA
1 AA-AATTAATATAATATAAA--TATATA
*
495301 ATAATTATAATATAAT-TATAATATA-A
1 A-AAAT-TAATATAATATA-AATATATA
* * ** *
495327 AAAATAAATATCACGTAAATATATG
1 AAAATTAATATAATATAAATATATA
495352 AAAATT
1 AAAATT
495358 TTGGTTTGAT
Statistics
Matches: 103, Mismatches: 19, Indels: 24
0.71 0.13 0.16
Matches are distributed among these distances:
24 22 0.21
25 40 0.39
26 13 0.13
27 15 0.15
28 11 0.11
29 2 0.02
ACGTcount: A:0.58, C:0.01, G:0.01, T:0.39
Consensus pattern (25 bp):
AAAATTAATATAATATAAATATATA
Found at i:495308 original size:11 final size:11
Alignment explanation
Indices: 495266--495326 Score: 53
Period size: 11 Copynumber: 5.8 Consensus size: 11
495256 TATTATTTAA
495266 ATAATATAAATT
1 ATAATAT-AATT
495278 ATTAATAT-ATT
1 A-TAATATAATT
495289 A-AA-AT--TT
1 ATAATATAATT
495296 AT-ATAATAATT
1 ATAAT-ATAATT
495307 ATAATATAATT
1 ATAATATAATT
495318 ATAATATAA
1 ATAATATAA
495327 AAAATAAATA
Statistics
Matches: 42, Mismatches: 0, Indels: 15
0.74 0.00 0.26
Matches are distributed among these distances:
7 4 0.10
8 2 0.05
9 4 0.10
11 23 0.55
12 3 0.07
13 6 0.14
ACGTcount: A:0.56, C:0.00, G:0.00, T:0.44
Consensus pattern (11 bp):
ATAATATAATT
Found at i:495332 original size:29 final size:29
Alignment explanation
Indices: 495274--495333 Score: 68
Period size: 29 Copynumber: 2.1 Consensus size: 29
495264 AAATAATATA
* * *
495274 AATTATTAATATATTAAAATTTATATAAT
1 AATTATTAATATATTAAAATATAAAAAAT
*
495303 AATTA-TAATATAATTATAATATAAAAAAT
1 AATTATTAATAT-ATTAAAATATAAAAAAT
495332 AA
1 AA
495334 ATATCACGTA
Statistics
Matches: 26, Mismatches: 4, Indels: 2
0.81 0.12 0.06
Matches are distributed among these distances:
28 6 0.23
29 20 0.77
ACGTcount: A:0.58, C:0.00, G:0.00, T:0.42
Consensus pattern (29 bp):
AATTATTAATATATTAAAATATAAAAAAT
Found at i:495950 original size:16 final size:17
Alignment explanation
Indices: 495911--495950 Score: 55
Period size: 19 Copynumber: 2.3 Consensus size: 17
495901 ATGAGTTAAA
495911 TTAAAATTATTATTTAT
1 TTAAAATTATTATTTAT
495928 TAATAAAATTATT-TTTAT
1 T--TAAAATTATTATTTAT
495946 TTAAA
1 TTAAA
495951 TTTAATTATA
Statistics
Matches: 21, Mismatches: 0, Indels: 5
0.81 0.00 0.19
Matches are distributed among these distances:
16 4 0.19
17 1 0.05
18 6 0.29
19 10 0.48
ACGTcount: A:0.45, C:0.00, G:0.00, T:0.55
Consensus pattern (17 bp):
TTAAAATTATTATTTAT
Found at i:495970 original size:20 final size:20
Alignment explanation
Indices: 495947--495984 Score: 60
Period size: 20 Copynumber: 1.9 Consensus size: 20
495937 TATTTTTATT
495947 TAAAT-TTAATTATAAAAATA
1 TAAATATTAA-TATAAAAATA
495967 TAAATATTAATATAAAAA
1 TAAATATTAATATAAAAA
495985 AAATTTTTAT
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
20 13 0.76
21 4 0.24
ACGTcount: A:0.63, C:0.00, G:0.00, T:0.37
Consensus pattern (20 bp):
TAAATATTAATATAAAAATA
Found at i:496505 original size:27 final size:27
Alignment explanation
Indices: 496475--496550 Score: 73
Period size: 27 Copynumber: 2.8 Consensus size: 27
496465 TTACAATCAT
496475 ATTTAAAATATTTTATATTCACATAAA
1 ATTTAAAATATTTTATATTCACATAAA
* * * * *
496502 ATTTAATA-AGTTAATAATTTATATAAA
1 ATTTAAAATATTTTAT-ATTCACATAAA
*
496529 TTTTAAAATATTTATATATTCA
1 ATTTAAAATATTT-TATATTCA
496551 TTTCATATTT
Statistics
Matches: 36, Mismatches: 10, Indels: 5
0.71 0.20 0.10
Matches are distributed among these distances:
26 5 0.14
27 22 0.61
28 7 0.19
29 2 0.06
ACGTcount: A:0.47, C:0.04, G:0.01, T:0.47
Consensus pattern (27 bp):
ATTTAAAATATTTTATATTCACATAAA
Found at i:496571 original size:25 final size:24
Alignment explanation
Indices: 496536--496626 Score: 75
Period size: 24 Copynumber: 3.9 Consensus size: 24
496526 AAATTTTAAA
*
496536 ATATTTATATATTCAT-TTCATATTT
1 ATATTTTTATATT-ATATT-ATATTT
496561 ATATTTTTATATTATATTATATTT
1 ATATTTTTATATTATATTATATTT
* *
496585 -TA-ATTT-T-TTATATCATATTT
1 ATATTTTTATATTATATTATATTT
* * *
496605 ATATTATAATATCATATTATAT
1 ATATTTTTATATTATATTATAT
496627 CTAATATTAT
Statistics
Matches: 53, Mismatches: 8, Indels: 11
0.74 0.11 0.15
Matches are distributed among these distances:
20 12 0.23
21 3 0.06
22 4 0.08
23 3 0.06
24 17 0.32
25 14 0.26
ACGTcount: A:0.35, C:0.04, G:0.00, T:0.60
Consensus pattern (24 bp):
ATATTTTTATATTATATTATATTT
Found at i:496577 original size:19 final size:19
Alignment explanation
Indices: 496536--496590 Score: 60
Period size: 19 Copynumber: 2.9 Consensus size: 19
496526 AAATTTTAAA
*
496536 ATATTTATATATTCATTTC
1 ATATTTATATTTTCATTTC
*
496555 ATATTTATATTTTTATATT-
1 ATATTTATATTTTCAT-TTC
*
496574 ATA-TTATATTTTAATTT
1 ATATTTATATTTTCATTT
496591 TTTATATCAT
Statistics
Matches: 32, Mismatches: 3, Indels: 4
0.82 0.08 0.10
Matches are distributed among these distances:
17 2 0.06
18 11 0.34
19 17 0.53
20 2 0.06
ACGTcount: A:0.33, C:0.04, G:0.00, T:0.64
Consensus pattern (19 bp):
ATATTTATATTTTCATTTC
Found at i:496582 original size:18 final size:18
Alignment explanation
Indices: 496559--496612 Score: 56
Period size: 18 Copynumber: 3.0 Consensus size: 18
496549 CATTTCATAT
496559 TTATATTTTTATATTATA
1 TTATATTTTTATATTATA
* * *
496577 TTATATTTTAATTTTTTA
1 TTATATTTTTATATTATA
*
496595 -TATCATATTTATATTATA
1 TTAT-ATTTTTATATTATA
496613 ATATCATATT
Statistics
Matches: 28, Mismatches: 7, Indels: 2
0.76 0.19 0.05
Matches are distributed among these distances:
17 3 0.11
18 25 0.89
ACGTcount: A:0.33, C:0.02, G:0.00, T:0.65
Consensus pattern (18 bp):
TTATATTTTTATATTATA
Found at i:497043 original size:15 final size:13
Alignment explanation
Indices: 497022--497053 Score: 50
Period size: 11 Copynumber: 2.6 Consensus size: 13
497012 AAATGCATGA
497022 AATATATA-ATAT
1 AATATATATATAT
497034 -ATATATATATAT
1 AATATATATATAT
497046 AATATATA
1 AATATATA
497054 AAAGTAAAAT
Statistics
Matches: 18, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
11 7 0.39
12 4 0.22
13 7 0.39
ACGTcount: A:0.56, C:0.00, G:0.00, T:0.44
Consensus pattern (13 bp):
AATATATATATAT
Found at i:497108 original size:25 final size:24
Alignment explanation
Indices: 497062--497123 Score: 74
Period size: 25 Copynumber: 2.6 Consensus size: 24
497052 TAAAAGTAAA
* *
497062 ATTTAAT-TA-TTTATATATTTAT
1 ATTTAATATATTTTTTATAATTAT
*
497084 ATTATATTATATTTTTTATAATTAT
1 ATT-TAATATATTTTTTATAATTAT
497109 ATTTAATATATTTTT
1 ATTTAATATATTTTT
497124 ATTTATATAA
Statistics
Matches: 33, Mismatches: 4, Indels: 4
0.80 0.10 0.10
Matches are distributed among these distances:
22 3 0.09
23 3 0.09
24 13 0.39
25 14 0.42
ACGTcount: A:0.35, C:0.00, G:0.00, T:0.65
Consensus pattern (24 bp):
ATTTAATATATTTTTTATAATTAT
Found at i:497118 original size:15 final size:14
Alignment explanation
Indices: 497075--497133 Score: 55
Period size: 15 Copynumber: 3.9 Consensus size: 14
497065 TAATTATTTA
497075 TATATTTATATTATAT
1 TATATTTATA-TA-AT
*
497091 TATATTTTTTATAAT
1 TATA-TTTATATAAT
*
497106 TATATTTAATATATT
1 TATATTT-ATATAAT
*
497121 TTTATTTATATAA
1 TATATTTATATAA
497134 ATTTTAATAT
Statistics
Matches: 36, Mismatches: 5, Indels: 6
0.77 0.11 0.13
Matches are distributed among these distances:
14 8 0.22
15 17 0.47
16 6 0.17
17 5 0.14
ACGTcount: A:0.37, C:0.00, G:0.00, T:0.63
Consensus pattern (14 bp):
TATATTTATATAAT
Found at i:497188 original size:50 final size:49
Alignment explanation
Indices: 497058--497235 Score: 139
Period size: 54 Copynumber: 3.5 Consensus size: 49
497048 TATATAAAAG
* *
497058 TAAAATTTAATTATTTATATATTTATATTATATTATATTTTTTATAATTATA
1 TAAAATTTAATTAATTATATATTT-TATTATATTA-ATTATTTA-AATTATA
* * *
497110 TTTAATATATTT--TTATTTATATAAATTTTAATATATTAATAATTTAAATTATA
1 --TAA-A-ATTTAATTAATTATAT--ATTTTATTATATTAATTATTTAAATTATA
*
497163 TAAAATTTAAATTAATTATATATTTTATTTTATTTAATTATTT-AATTATA
1 TAAAATTT-AATTAATTATATATTTTATTATA-TTAATTATTTAAATTATA
** *
497213 T-TTATTTAATTATATTAAATATT
1 TAAAATTTAATTA-ATTATATATT
497236 ATCAAGTATA
Statistics
Matches: 105, Mismatches: 10, Indels: 23
0.76 0.07 0.17
Matches are distributed among these distances:
48 5 0.05
49 17 0.16
50 18 0.17
51 12 0.11
52 9 0.09
53 7 0.07
54 19 0.18
55 10 0.10
56 8 0.08
ACGTcount: A:0.42, C:0.00, G:0.00, T:0.58
Consensus pattern (49 bp):
TAAAATTTAATTAATTATATATTTTATTATATTAATTATTTAAATTATA
Found at i:497192 original size:22 final size:22
Alignment explanation
Indices: 497174--497227 Score: 74
Period size: 22 Copynumber: 2.5 Consensus size: 22
497164 AAAATTTAAA
*
497174 TTAATTATAT-ATTTTATTTTAT
1 TTAATTATATAATTATA-TTTAT
*
497196 TTAATTATTTAATTATATTTAT
1 TTAATTATATAATTATATTTAT
497218 TTAATTATAT
1 TTAATTATAT
497228 TAAATATTAT
Statistics
Matches: 28, Mismatches: 3, Indels: 2
0.85 0.09 0.06
Matches are distributed among these distances:
22 23 0.82
23 5 0.18
ACGTcount: A:0.35, C:0.00, G:0.00, T:0.65
Consensus pattern (22 bp):
TTAATTATATAATTATATTTAT
Found at i:497219 original size:14 final size:14
Alignment explanation
Indices: 497181--497228 Score: 62
Period size: 14 Copynumber: 3.4 Consensus size: 14
497171 AAATTAATTA
*
497181 TATATTTTATTTTAT
1 TATA-TTTATTTAAT
*
497196 T-TAATTATTTAAT
1 TATATTTATTTAAT
497209 TATATTTATTTAAT
1 TATATTTATTTAAT
497223 TATATT
1 TATATT
497229 AAATATTATC
Statistics
Matches: 29, Mismatches: 3, Indels: 3
0.83 0.09 0.09
Matches are distributed among these distances:
13 9 0.31
14 19 0.66
15 1 0.03
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (14 bp):
TATATTTATTTAAT
Found at i:497529 original size:8 final size:8
Alignment explanation
Indices: 497513--497563 Score: 59
Period size: 8 Copynumber: 6.1 Consensus size: 8
497503 TATTCTTTTG
*
497513 ATTTTAAA
1 ATTTAAAA
497521 ATTTAAAA
1 ATTTAAAA
497529 ATTTAAAA
1 ATTTAAAA
497537 A-TTAAATA
1 ATTTAAA-A
497545 ATTTAATAAA
1 ATTT-A-AAA
497555 ATTTAAAA
1 ATTTAAAA
497563 A
1 A
497564 CTAATTAAAT
Statistics
Matches: 38, Mismatches: 1, Indels: 8
0.81 0.02 0.17
Matches are distributed among these distances:
7 5 0.13
8 22 0.58
9 3 0.08
10 6 0.16
11 2 0.05
ACGTcount: A:0.61, C:0.00, G:0.00, T:0.39
Consensus pattern (8 bp):
ATTTAAAA
Found at i:497535 original size:15 final size:16
Alignment explanation
Indices: 497515--497550 Score: 56
Period size: 15 Copynumber: 2.3 Consensus size: 16
497505 TTCTTTTGAT
*
497515 TTTAAAATTTAAA-AA
1 TTTAAAAATTAAATAA
497530 TTTAAAAATTAAATAA
1 TTTAAAAATTAAATAA
497546 TTTAA
1 TTTAA
497551 TAAAATTTAA
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
15 12 0.63
16 7 0.37
ACGTcount: A:0.58, C:0.00, G:0.00, T:0.42
Consensus pattern (16 bp):
TTTAAAAATTAAATAA
Found at i:497582 original size:26 final size:26
Alignment explanation
Indices: 497526--497583 Score: 71
Period size: 26 Copynumber: 2.2 Consensus size: 26
497516 TTAAAATTTA
* *
497526 AAAATTTAAAAATTAAATAATTTAAT
1 AAAATTTAAAAACTAAATAAATTAAT
* *
497552 AAAATTTAAAAACTAATTAAATTGAT
1 AAAATTTAAAAACTAAATAAATTAAT
*
497578 TAAATT
1 AAAATT
497584 AAATTAATTA
Statistics
Matches: 27, Mismatches: 5, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
26 27 1.00
ACGTcount: A:0.59, C:0.02, G:0.02, T:0.38
Consensus pattern (26 bp):
AAAATTTAAAAACTAAATAAATTAAT
Found at i:497598 original size:13 final size:13
Alignment explanation
Indices: 497565--497631 Score: 64
Period size: 13 Copynumber: 5.1 Consensus size: 13
497555 ATTTAAAAAC
*
497565 TAATTAAATTGAT
1 TAATTAAATTAAT
497578 TAAATTAAATTAAT
1 T-AATTAAATTAAT
*
497592 TAATTAAA-AAAT
1 TAATTAAATTAAT
**
497604 TAACTTAAATTTGT
1 TAA-TTAAATTAAT
*
497618 TACTTAAATTAAT
1 TAATTAAATTAAT
497631 T
1 T
497632 TAATCGATTT
Statistics
Matches: 43, Mismatches: 8, Indels: 6
0.75 0.14 0.11
Matches are distributed among these distances:
12 6 0.14
13 22 0.51
14 15 0.35
ACGTcount: A:0.49, C:0.03, G:0.03, T:0.45
Consensus pattern (13 bp):
TAATTAAATTAAT
Found at i:498046 original size:9 final size:9
Alignment explanation
Indices: 498034--498078 Score: 51
Period size: 9 Copynumber: 5.2 Consensus size: 9
498024 ATTTTATATT
498034 TTATATAAA
1 TTATATAAA
498043 TTATATAAA
1 TTATATAAA
498052 -TATA-AATA
1 TTATATAA-A
*
498060 TAATATAAA
1 TTATATAAA
498069 TTAT-TAAA
1 TTATATAAA
498077 TT
1 TT
498079 TATCAAAATT
Statistics
Matches: 31, Mismatches: 2, Indels: 7
0.77 0.05 0.17
Matches are distributed among these distances:
7 2 0.06
8 11 0.35
9 16 0.52
10 2 0.06
ACGTcount: A:0.56, C:0.00, G:0.00, T:0.44
Consensus pattern (9 bp):
TTATATAAA
Found at i:498056 original size:15 final size:17
Alignment explanation
Indices: 498036--498069 Score: 54
Period size: 15 Copynumber: 2.1 Consensus size: 17
498026 TTTATATTTT
498036 ATATAAAT-T-ATATAA
1 ATATAAATATAATATAA
498051 ATATAAATATAATATAA
1 ATATAAATATAATATAA
498068 AT
1 AT
498070 TATTAAATTT
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
15 8 0.47
16 1 0.06
17 8 0.47
ACGTcount: A:0.62, C:0.00, G:0.00, T:0.38
Consensus pattern (17 bp):
ATATAAATATAATATAA
Found at i:498628 original size:13 final size:13
Alignment explanation
Indices: 498610--498635 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
498600 AACATAATTA
498610 AATATTTAAATAT
1 AATATTTAAATAT
498623 AATATTTAAATAT
1 AATATTTAAATAT
498636 TAATTTTCCT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.54, C:0.00, G:0.00, T:0.46
Consensus pattern (13 bp):
AATATTTAAATAT
Found at i:499565 original size:15 final size:15
Alignment explanation
Indices: 499547--499597 Score: 50
Period size: 15 Copynumber: 3.1 Consensus size: 15
499537 AATATTTTTA
499547 AAATTTATATAATAT
1 AAATTTATATAATAT
499562 AAA-TTATTATAATATT
1 AAATTTA-TATAATA-T
499578 AAAATTTATAATAAATAT
1 -AAATTTAT-AT-AATAT
499596 AA
1 AA
499598 TTTTTTTAAA
Statistics
Matches: 30, Mismatches: 0, Indels: 10
0.75 0.00 0.25
Matches are distributed among these distances:
14 3 0.10
15 10 0.33
16 1 0.03
17 6 0.20
18 6 0.20
19 4 0.13
ACGTcount: A:0.57, C:0.00, G:0.00, T:0.43
Consensus pattern (15 bp):
AAATTTATATAATAT
Found at i:499591 original size:18 final size:17
Alignment explanation
Indices: 499544--499587 Score: 58
Period size: 15 Copynumber: 2.7 Consensus size: 17
499534 ATAAATATTT
499544 TTAAAATTTATATAATA
1 TTAAAATTTATATAATA
499561 -T-AAA-TTATTATAATA
1 TTAAAATTTA-TATAATA
499576 TTAAAATTTATA
1 TTAAAATTTATA
499588 ATAAATATAA
Statistics
Matches: 23, Mismatches: 0, Indels: 8
0.74 0.00 0.26
Matches are distributed among these distances:
14 3 0.13
15 10 0.43
16 2 0.09
17 5 0.22
18 3 0.13
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (17 bp):
TTAAAATTTATATAATA
Found at i:499622 original size:15 final size:15
Alignment explanation
Indices: 499583--499627 Score: 54
Period size: 15 Copynumber: 2.9 Consensus size: 15
499573 ATATTAAAAT
499583 TTATAATAAATATAA
1 TTATAATAAATATAA
* **
499598 TTTTTTTAAATATAA
1 TTATAATAAATATAA
499613 TTATAATAAAATATA
1 TTATAAT-AAATATA
499628 TGAATACTAA
Statistics
Matches: 23, Mismatches: 6, Indels: 1
0.77 0.20 0.03
Matches are distributed among these distances:
15 16 0.70
16 7 0.30
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (15 bp):
TTATAATAAATATAA
Found at i:502185 original size:2 final size:2
Alignment explanation
Indices: 502178--502202 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
502168 ATTGGAATGC
502178 AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT A
502203 ATTTGGCATG
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:503244 original size:12 final size:13
Alignment explanation
Indices: 503228--503269 Score: 54
Period size: 12 Copynumber: 3.4 Consensus size: 13
503218 ATATATATAA
503228 TAATTATAATTA-
1 TAATTATAATTAT
503240 TAATTAT-ATTAT
1 TAATTATAATTAT
503252 TAAATT-TAATTAT
1 T-AATTATAATTAT
503265 TAATT
1 TAATT
503270 TAAAAATATG
Statistics
Matches: 27, Mismatches: 0, Indels: 6
0.82 0.00 0.18
Matches are distributed among these distances:
11 4 0.15
12 13 0.48
13 10 0.37
ACGTcount: A:0.45, C:0.00, G:0.00, T:0.55
Consensus pattern (13 bp):
TAATTATAATTAT
Found at i:503247 original size:25 final size:24
Alignment explanation
Indices: 503210--503269 Score: 61
Period size: 25 Copynumber: 2.4 Consensus size: 24
503200 ATTGATTTAA
503210 AATTAT-ATATATATATAAT-AATTAT
1 AATTATAAT-TATAT-TAATAAATT-T
*
503235 AATTATAATTATATTATTAAATTT
1 AATTATAATTATATTAATAAATTT
503259 AATTATTAATT
1 AATTA-TAATT
503270 TAAAAATATG
Statistics
Matches: 31, Mismatches: 1, Indels: 6
0.82 0.03 0.16
Matches are distributed among these distances:
24 9 0.29
25 20 0.65
26 2 0.06
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (24 bp):
AATTATAATTATATTAATAAATTT
Found at i:503291 original size:25 final size:24
Alignment explanation
Indices: 503258--503305 Score: 62
Period size: 25 Copynumber: 2.0 Consensus size: 24
503248 TTATTAAATT
*
503258 TAATTATTA-ATTTAAAAATATGTA
1 TAATTATTATA-TAAAAAATATGTA
503282 TAATTAATTATATAAAAAATATGT
1 TAATT-ATTATATAAAAAATATGT
503306 GTATAAAATT
Statistics
Matches: 21, Mismatches: 1, Indels: 3
0.84 0.04 0.12
Matches are distributed among these distances:
24 5 0.24
25 15 0.71
26 1 0.05
ACGTcount: A:0.52, C:0.00, G:0.04, T:0.44
Consensus pattern (24 bp):
TAATTATTATATAAAAAATATGTA
Found at i:504208 original size:9 final size:9
Alignment explanation
Indices: 504194--504309 Score: 51
Period size: 9 Copynumber: 13.9 Consensus size: 9
504184 TGTAGATATG
504194 ATAATATTT
1 ATAATATTT
504203 ATAATA--T
1 ATAATATTT
*
504210 ATTATATTT
1 ATAATATTT
*
504219 ATATTATTT
1 ATAATATTT
504228 AT-ATATATT
1 ATAATAT-TT
504237 AT--T-TTT
1 ATAATATTT
*
504243 AAAAT-TTT
1 ATAATATTT
**
504251 AT-ATAAAT
1 ATAATATTT
504259 ATTAATATATT
1 A-TAATAT-TT
504270 A-AAT-TTT
1 ATAATATTT
504277 ATAAT-TTT
1 ATAATATTT
*
504285 ATAAAATTT
1 ATAATATTT
504294 A-ATATATTT
1 ATA-ATATTT
504303 AT-ATATT
1 ATAATATT
504310 CAATTTAAAT
Statistics
Matches: 82, Mismatches: 12, Indels: 27
0.68 0.10 0.22
Matches are distributed among these distances:
6 3 0.04
7 12 0.15
8 28 0.34
9 34 0.41
10 3 0.04
11 2 0.02
ACGTcount: A:0.44, C:0.00, G:0.00, T:0.56
Consensus pattern (9 bp):
ATAATATTT
Found at i:504216 original size:24 final size:24
Alignment explanation
Indices: 504192--504255 Score: 67
Period size: 24 Copynumber: 2.7 Consensus size: 24
504182 GATGTAGATA
504192 TGATAATATTTATAATATATTATAT
1 TGATAATATTTAT-ATATATTATAT
* * *
504217 TTATATTATTTATATATATTATTT
1 TGATAATATTTATATATATTATAT
* *
504241 TTAAAAT-TTTATATA
1 TGATAATATTTATATA
504256 AATATTAATA
Statistics
Matches: 34, Mismatches: 5, Indels: 2
0.83 0.12 0.05
Matches are distributed among these distances:
23 8 0.24
24 15 0.44
25 11 0.32
ACGTcount: A:0.41, C:0.00, G:0.02, T:0.58
Consensus pattern (24 bp):
TGATAATATTTATATATATTATAT
Found at i:504218 original size:16 final size:15
Alignment explanation
Indices: 504197--504231 Score: 52
Period size: 16 Copynumber: 2.3 Consensus size: 15
504187 AGATATGATA
504197 ATATTTATAATATATT
1 ATATTTATAATAT-TT
*
504213 ATATTTATATTATTT
1 ATATTTATAATATTT
504228 ATAT
1 ATAT
504232 ATATTATTTT
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
15 6 0.33
16 12 0.67
ACGTcount: A:0.40, C:0.00, G:0.00, T:0.60
Consensus pattern (15 bp):
ATATTTATAATATTT
Found at i:504222 original size:22 final size:24
Alignment explanation
Indices: 504197--504262 Score: 64
Period size: 25 Copynumber: 2.8 Consensus size: 24
504187 AGATATGATA
504197 ATATT-TATA-ATATATTATATTT
1 ATATTATATATATATATTATATTT
* *
504219 ATATTATTTATATATATTATTTTT
1 ATATTATATATATATATTATATTT
* * *
504243 AAAATTTTATATAAATATTA
1 -ATATTATATATATATATTA
504263 ATATATTAAA
Statistics
Matches: 35, Mismatches: 6, Indels: 3
0.80 0.14 0.07
Matches are distributed among these distances:
22 5 0.14
23 3 0.09
24 12 0.34
25 15 0.43
ACGTcount: A:0.42, C:0.00, G:0.00, T:0.58
Consensus pattern (24 bp):
ATATTATATATATATATTATATTT
Found at i:504234 original size:13 final size:13
Alignment explanation
Indices: 504198--504240 Score: 54
Period size: 13 Copynumber: 3.4 Consensus size: 13
504188 GATATGATAA
504198 TATTTATA-ATA-
1 TATTTATATATAT
*
504209 TATTATATTTATAT
1 TATT-TATATATAT
504223 TATTTATATATAT
1 TATTTATATATAT
504236 TATTT
1 TATTT
504241 TTAAAATTTT
Statistics
Matches: 27, Mismatches: 2, Indels: 4
0.82 0.06 0.12
Matches are distributed among these distances:
11 4 0.15
12 3 0.11
13 16 0.59
14 4 0.15
ACGTcount: A:0.37, C:0.00, G:0.00, T:0.63
Consensus pattern (13 bp):
TATTTATATATAT
Found at i:504283 original size:34 final size:31
Alignment explanation
Indices: 504224--504301 Score: 102
Period size: 34 Copynumber: 2.4 Consensus size: 31
504214 TATTTATATT
*
504224 ATTTATATATATTATTTTTAAAATTTTATATAA
1 ATTTA-ATATATTAATTTTAAAATTTTATA-AA
*
504257 ATATTAATATATTAAATTTTATAATTTTATAAA
1 AT-TTAATATATT-AATTTTAAAATTTTATAAA
504290 ATTTAATATATT
1 ATTTAATATATT
504302 TATATATTCA
Statistics
Matches: 41, Mismatches: 2, Indels: 5
0.85 0.04 0.10
Matches are distributed among these distances:
32 10 0.24
33 13 0.32
34 18 0.44
ACGTcount: A:0.45, C:0.00, G:0.00, T:0.55
Consensus pattern (31 bp):
ATTTAATATATTAATTTTAAAATTTTATAAA
Found at i:504315 original size:32 final size:34
Alignment explanation
Indices: 504245--504315 Score: 85
Period size: 32 Copynumber: 2.1 Consensus size: 34
504235 TTATTTTTAA
* *
504245 AATTTTATATAAATATTAATATATTAAATTTTAT
1 AATTTTATATAAATATTAATATATTAAATATTAC
*
504279 AATTTTATA-AAAT-TTAATATATTTATATATT-C
1 AATTTTATATAAATATTAATATA-TTAAATATTAC
504311 AATTT
1 AATTT
504316 AAATTAATAA
Statistics
Matches: 33, Mismatches: 3, Indels: 4
0.82 0.08 0.10
Matches are distributed among these distances:
32 13 0.39
33 11 0.33
34 9 0.27
ACGTcount: A:0.45, C:0.01, G:0.00, T:0.54
Consensus pattern (34 bp):
AATTTTATATAAATATTAATATATTAAATATTAC
Found at i:504700 original size:19 final size:19
Alignment explanation
Indices: 504673--504716 Score: 54
Period size: 20 Copynumber: 2.3 Consensus size: 19
504663 ATATTAAAAT
* *
504673 ATTAAAAATAGT-ATTTTA
1 ATTAAAAATAATAATTTAA
504691 ATTAATAAATAATAATTTAA
1 ATTAA-AAATAATAATTTAA
504711 ATTAAA
1 ATTAAA
504717 TTATAATTAA
Statistics
Matches: 22, Mismatches: 2, Indels: 3
0.81 0.07 0.11
Matches are distributed among these distances:
18 5 0.23
19 7 0.32
20 10 0.45
ACGTcount: A:0.57, C:0.00, G:0.02, T:0.41
Consensus pattern (19 bp):
ATTAAAAATAATAATTTAA
Found at i:504715 original size:24 final size:24
Alignment explanation
Indices: 504688--504748 Score: 63
Period size: 24 Copynumber: 2.5 Consensus size: 24
504678 AAATAGTATT
504688 TTAATTAATAAATAATAATTTA-AA
1 TTAATTAATAAATAAT-ATTTATAA
* *
504712 TTAAATT-ATAATTAATATTTATAT
1 TT-AATTAATAAATAATATTTATAA
*
504736 TTAATTATTAAAT
1 TTAATTAATAAAT
504749 GGATCTCCTC
Statistics
Matches: 30, Mismatches: 4, Indels: 6
0.75 0.10 0.15
Matches are distributed among these distances:
23 9 0.30
24 17 0.57
25 4 0.13
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (24 bp):
TTAATTAATAAATAATATTTATAA
Found at i:504990 original size:15 final size:16
Alignment explanation
Indices: 504967--505011 Score: 56
Period size: 16 Copynumber: 2.8 Consensus size: 16
504957 ATTAAAATAA
504967 TATATTTATAAAAATT
1 TATATTTATAAAAATT
*
504983 TA-ATTTATTAATAATT
1 TATATTTA-TAAAAATT
504999 TATATTATATAAA
1 TATATT-TATAAA
505012 TTTTAATATA
Statistics
Matches: 24, Mismatches: 2, Indels: 5
0.77 0.06 0.16
Matches are distributed among these distances:
15 5 0.21
16 11 0.46
17 6 0.25
18 2 0.08
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (16 bp):
TATATTTATAAAAATT
Found at i:505017 original size:32 final size:30
Alignment explanation
Indices: 504962--505023 Score: 79
Period size: 32 Copynumber: 2.0 Consensus size: 30
504952 TTATAATTAA
*
504962 AATAATATATTTATAAAAATTTAATTTATT
1 AATAATATATTTATAAAAATTTAATATATT
* *
504992 AATAATTTATATTATATAAATTTTAATATATT
1 AATAATATAT-TTATA-AAAATTTAATATATT
505024 TTATTTTTAT
Statistics
Matches: 27, Mismatches: 3, Indels: 2
0.84 0.09 0.06
Matches are distributed among these distances:
30 9 0.33
31 5 0.19
32 13 0.48
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (30 bp):
AATAATATATTTATAAAAATTTAATATATT
Found at i:505324 original size:20 final size:20
Alignment explanation
Indices: 505263--505327 Score: 58
Period size: 20 Copynumber: 3.2 Consensus size: 20
505253 TATATAAAAC
*
505263 TAATTTTATATTGGTTCAAT
1 TAATTTTATATTGATTCAAT
* ** *
505283 CTAATTTTTTATAAATTGAAT
1 -TAATTTTATATTGATTCAAT
* *
505304 TAATTTTGTATTGATTTAAT
1 TAATTTTATATTGATTCAAT
505324 TAAT
1 TAAT
505328 AATTAGTTTT
Statistics
Matches: 35, Mismatches: 9, Indels: 1
0.78 0.20 0.02
Matches are distributed among these distances:
20 20 0.57
21 15 0.43
ACGTcount: A:0.34, C:0.03, G:0.08, T:0.55
Consensus pattern (20 bp):
TAATTTTATATTGATTCAAT
Found at i:507151 original size:16 final size:17
Alignment explanation
Indices: 507130--507161 Score: 57
Period size: 16 Copynumber: 1.9 Consensus size: 17
507120 AATAAATATT
507130 TTTATATTT-TTATAAA
1 TTTATATTTATTATAAA
507146 TTTATATTTATTATAA
1 TTTATATTTATTATAA
507162 TAATAGATTA
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
16 9 0.60
17 6 0.40
ACGTcount: A:0.38, C:0.00, G:0.00, T:0.62
Consensus pattern (17 bp):
TTTATATTTATTATAAA
Found at i:507747 original size:20 final size:19
Alignment explanation
Indices: 507711--507749 Score: 51
Period size: 20 Copynumber: 2.0 Consensus size: 19
507701 AAATAATTAC
*
507711 ATTAATAATTATGAAATTT
1 ATTAATAAATATGAAATTT
*
507730 ATTAATAAAATATTAAATTT
1 ATTAAT-AAATATGAAATTT
507750 TCAATTTTTT
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
19 6 0.35
20 11 0.65
ACGTcount: A:0.51, C:0.00, G:0.03, T:0.46
Consensus pattern (19 bp):
ATTAATAAATATGAAATTT
Found at i:508526 original size:6 final size:6
Alignment explanation
Indices: 508517--508557 Score: 50
Period size: 6 Copynumber: 7.0 Consensus size: 6
508507 TAAATAATAA
*
508517 AAATTT AAA-TT AAATTT AAAATTT -GATTT AAATTT AAATTT
1 AAATTT AAATTT AAATTT -AAATTT AAATTT AAATTT AAATTT
508558 TATTAAATTT
Statistics
Matches: 30, Mismatches: 2, Indels: 6
0.79 0.05 0.16
Matches are distributed among these distances:
5 9 0.30
6 15 0.50
7 6 0.20
ACGTcount: A:0.49, C:0.00, G:0.02, T:0.49
Consensus pattern (6 bp):
AAATTT
Found at i:508533 original size:11 final size:11
Alignment explanation
Indices: 508517--508567 Score: 50
Period size: 12 Copynumber: 4.5 Consensus size: 11
508507 TAAATAATAA
508517 AAATTTAAATT
1 AAATTTAAATT
508528 AAATTTAAAATT
1 AAATTT-AAATT
**
508540 TGATTTAAATTT
1 AAATTTAAA-TT
*
508552 AAATTT-TATT
1 AAATTTAAATT
508562 AAATTT
1 AAATTT
508568 TATTTTTAAA
Statistics
Matches: 33, Mismatches: 5, Indels: 5
0.77 0.12 0.12
Matches are distributed among these distances:
10 8 0.24
11 10 0.30
12 15 0.45
ACGTcount: A:0.47, C:0.00, G:0.02, T:0.51
Consensus pattern (11 bp):
AAATTTAAATT
Found at i:508539 original size:18 final size:17
Alignment explanation
Indices: 508516--508567 Score: 61
Period size: 18 Copynumber: 3.0 Consensus size: 17
508506 TTAAATAATA
508516 AAAATTTAAATTAAATTT
1 AAAATTT-AATTAAATTT
*
508534 AAAATTTGATTTAAATTT
1 AAAATTT-AATTAAATTT
*
508552 -AAATTTTATTAAATTT
1 AAAATTTAATTAAATTT
508568 TATTTTTAAA
Statistics
Matches: 30, Mismatches: 4, Indels: 2
0.83 0.11 0.06
Matches are distributed among these distances:
16 8 0.27
17 6 0.20
18 16 0.53
ACGTcount: A:0.48, C:0.00, G:0.02, T:0.50
Consensus pattern (17 bp):
AAAATTTAATTAAATTT
Found at i:508557 original size:12 final size:12
Alignment explanation
Indices: 508517--508557 Score: 50
Period size: 11 Copynumber: 3.5 Consensus size: 12
508507 TAAATAATAA
508517 AAATTTAAA-TT
1 AAATTTAAATTT
508528 AAATTTAAAATTT
1 AAATTT-AAATTT
*
508541 -GATTTAAATTT
1 AAATTTAAATTT
508552 AAATTT
1 AAATTT
508558 TATTAAATTT
Statistics
Matches: 25, Mismatches: 2, Indels: 5
0.78 0.06 0.16
Matches are distributed among these distances:
11 12 0.48
12 11 0.44
13 2 0.08
ACGTcount: A:0.49, C:0.00, G:0.02, T:0.49
Consensus pattern (12 bp):
AAATTTAAATTT
Found at i:508557 original size:17 final size:17
Alignment explanation
Indices: 508525--508567 Score: 61
Period size: 16 Copynumber: 2.5 Consensus size: 17
508515 AAAAATTTAA
508525 ATTAAATTTAAAATTTG
1 ATTAAATTTAAAATTTG
*
508542 ATTTAAATTT-AAATTTT
1 A-TTAAATTTAAAATTTG
508559 ATTAAATTT
1 ATTAAATTT
508568 TATTTTTAAA
Statistics
Matches: 24, Mismatches: 1, Indels: 3
0.86 0.04 0.11
Matches are distributed among these distances:
16 8 0.33
17 8 0.33
18 8 0.33
ACGTcount: A:0.44, C:0.00, G:0.02, T:0.53
Consensus pattern (17 bp):
ATTAAATTTAAAATTTG
Found at i:508569 original size:17 final size:17
Alignment explanation
Indices: 508525--508569 Score: 56
Period size: 17 Copynumber: 2.6 Consensus size: 17
508515 AAAAATTTAA
*
508525 ATTAAATTTAAAATTTG
1 ATTAAATTTTAAATTTG
*
508542 ATTTAAA-TTTAAATTTT
1 A-TTAAATTTTAAATTTG
508559 ATTAAATTTTA
1 ATTAAATTTTA
508570 TTTTTAAAAT
Statistics
Matches: 24, Mismatches: 2, Indels: 4
0.80 0.07 0.13
Matches are distributed among these distances:
16 5 0.21
17 14 0.58
18 5 0.21
ACGTcount: A:0.44, C:0.00, G:0.02, T:0.53
Consensus pattern (17 bp):
ATTAAATTTTAAATTTG
Found at i:511153 original size:13 final size:13
Alignment explanation
Indices: 511135--511159 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
511125 CGAATATGCA
511135 TCGAACATAAATG
1 TCGAACATAAATG
511148 TCGAACATAAAT
1 TCGAACATAAAT
511160 ATTTTCAAAA
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:0.48, C:0.16, G:0.12, T:0.24
Consensus pattern (13 bp):
TCGAACATAAATG
Found at i:511355 original size:26 final size:26
Alignment explanation
Indices: 511323--511373 Score: 102
Period size: 26 Copynumber: 2.0 Consensus size: 26
511313 TGCCCACTAT
511323 TTCTATATTGTTCTAACTCTATTTTC
1 TTCTATATTGTTCTAACTCTATTTTC
511349 TTCTATATTGTTCTAACTCTATTTT
1 TTCTATATTGTTCTAACTCTATTTT
511374 TTTTAAGTAT
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
26 25 1.00
ACGTcount: A:0.20, C:0.18, G:0.04, T:0.59
Consensus pattern (26 bp):
TTCTATATTGTTCTAACTCTATTTTC
Found at i:511369 original size:16 final size:16
Alignment explanation
Indices: 511324--511370 Score: 52
Period size: 13 Copynumber: 3.3 Consensus size: 16
511314 GCCCACTATT
511324 TCTATATTGTTCTAAC
1 TCTATATTGTTCTAAC
511340 TC--TATT-TTCT---
1 TCTATATTGTTCTAAC
511350 TCTATATTGTTCTAAC
1 TCTATATTGTTCTAAC
511366 TCTAT
1 TCTAT
511371 TTTTTTTAAG
Statistics
Matches: 25, Mismatches: 0, Indels: 12
0.68 0.00 0.32
Matches are distributed among these distances:
10 2 0.08
12 4 0.16
13 8 0.32
14 4 0.16
16 7 0.28
ACGTcount: A:0.21, C:0.19, G:0.04, T:0.55
Consensus pattern (16 bp):
TCTATATTGTTCTAAC
Found at i:513597 original size:11 final size:12
Alignment explanation
Indices: 513571--513603 Score: 50
Period size: 11 Copynumber: 2.8 Consensus size: 12
513561 TATATTCTTA
513571 TTAATTATTATAT
1 TTAA-TATTATAT
513584 TTAATATT-TAT
1 TTAATATTATAT
513595 TTAATATTA
1 TTAATATTA
513604 AAATTACATA
Statistics
Matches: 19, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
11 11 0.58
12 4 0.21
13 4 0.21
ACGTcount: A:0.39, C:0.00, G:0.00, T:0.61
Consensus pattern (12 bp):
TTAATATTATAT
Found at i:514537 original size:15 final size:15
Alignment explanation
Indices: 514517--514581 Score: 71
Period size: 15 Copynumber: 4.5 Consensus size: 15
514507 TTTTTAAAAA
514517 ATTTATAATATATTT
1 ATTTATAATATATTT
* *
514532 ATTTATAAAATATTA
1 ATTTATAATATATTT
*
514547 ATTTAT-TTATATTT
1 ATTTATAATATATTT
**
514561 AAATA-AATATATTT
1 ATTTATAATATATTT
514575 ATTTATA
1 ATTTATA
514582 TTTAAATAAA
Statistics
Matches: 38, Mismatches: 10, Indels: 4
0.73 0.19 0.08
Matches are distributed among these distances:
14 18 0.47
15 20 0.53
ACGTcount: A:0.45, C:0.00, G:0.00, T:0.55
Consensus pattern (15 bp):
ATTTATAATATATTT
Found at i:514559 original size:25 final size:25
Alignment explanation
Indices: 514531--514663 Score: 157
Period size: 24 Copynumber: 5.3 Consensus size: 25
514521 ATAATATATT
*
514531 TATTTATA-AAATATTAATTTATTTA
1 TATTTAAATAAATA-TAATTTATTTA
514556 TATTTAAATAAATAT-ATTTATTTA
1 TATTTAAATAAATATAATTTATTTA
*
514580 TATTTAAATAAATATAGTTTATTTA
1 TATTTAAATAAATATAATTTATTTA
514605 -ATTTAAATAAATATATATTTATTTA
1 TATTTAAATAAATATA-ATTTATTTA
* *
514630 TATTTATAATATATATATAA-ATATATA
1 TATTTA-AATA-A-ATATAATTTATTTA
514657 TATTTAA
1 TATTTAA
514664 TTTATTTATT
Statistics
Matches: 96, Mismatches: 5, Indels: 13
0.84 0.04 0.11
Matches are distributed among these distances:
24 39 0.41
25 24 0.25
26 11 0.11
27 15 0.16
28 2 0.02
29 5 0.05
ACGTcount: A:0.47, C:0.00, G:0.01, T:0.53
Consensus pattern (25 bp):
TATTTAAATAAATATAATTTATTTA
Found at i:516054 original size:41 final size:42
Alignment explanation
Indices: 515988--516079 Score: 104
Period size: 41 Copynumber: 2.3 Consensus size: 42
515978 TTTATAATTT
* * *
515988 AAATTAATTTTATTTTATTTGAATTAT-TATTTTAATAATAAA
1 AAATTAATTTTATTTAATTTGAATTATAAATATTAAT-ATAAA
516030 AAATT-ATTTTATTTAAATTT-AATTATAAATATTAATAT-AA
1 AAATTAATTTTATTT-AATTTGAATTATAAATATTAATATAAA
516070 AAA-TAATTTT
1 AAATTAATTTT
516080 TAATATCTTT
Statistics
Matches: 44, Mismatches: 3, Indels: 8
0.80 0.05 0.15
Matches are distributed among these distances:
39 1 0.02
40 10 0.23
41 17 0.39
42 16 0.36
ACGTcount: A:0.47, C:0.00, G:0.01, T:0.52
Consensus pattern (42 bp):
AAATTAATTTTATTTAATTTGAATTATAAATATTAATATAAA
Found at i:521470 original size:20 final size:21
Alignment explanation
Indices: 521417--521470 Score: 60
Period size: 20 Copynumber: 2.6 Consensus size: 21
521407 TTGTTGATTT
*
521417 TTAATTAAAATAATTTTAAATA
1 TTAATT-AAGTAATTTTAAATA
521439 TTAA--AAGATAATTTT-AATA
1 TTAATTAAG-TAATTTTAAATA
521458 TTAATTAAGTAAT
1 TTAATTAAGTAAT
521471 CGATAAAAAT
Statistics
Matches: 28, Mismatches: 1, Indels: 8
0.76 0.03 0.22
Matches are distributed among these distances:
19 10 0.36
20 11 0.39
21 3 0.11
22 4 0.14
ACGTcount: A:0.52, C:0.00, G:0.04, T:0.44
Consensus pattern (21 bp):
TTAATTAAGTAATTTTAAATA
Found at i:522537 original size:22 final size:22
Alignment explanation
Indices: 522494--522537 Score: 63
Period size: 22 Copynumber: 2.0 Consensus size: 22
522484 AAATAATAAA
*
522494 ATATATTTTTATTTTAATATTT
1 ATATATTTTTATATTAATATTT
522516 ATATATTTTTATAATTAA-ATTT
1 ATATATTTTTAT-ATTAATATTT
522538 TAAAAATTTT
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
22 16 0.80
23 4 0.20
ACGTcount: A:0.36, C:0.00, G:0.00, T:0.64
Consensus pattern (22 bp):
ATATATTTTTATATTAATATTT
Found at i:524677 original size:14 final size:14
Alignment explanation
Indices: 524654--524713 Score: 58
Period size: 13 Copynumber: 4.6 Consensus size: 14
524644 AATAACAATC
524654 ATAA-TATTATATT
1 ATAATTATTATATT
*
524667 ATAATTATTATTTT
1 ATAATTATTATATT
524681 ATAATT-TTA-ATT
1 ATAATTATTATATT
* *
524693 -TATTTATTAT-TA
1 ATAATTATTATATT
524705 ATAATTATT
1 ATAATTATT
524714 TTAATAAATC
Statistics
Matches: 38, Mismatches: 5, Indels: 8
0.75 0.10 0.16
Matches are distributed among these distances:
11 4 0.11
12 6 0.16
13 14 0.37
14 14 0.37
ACGTcount: A:0.40, C:0.00, G:0.00, T:0.60
Consensus pattern (14 bp):
ATAATTATTATATT
Found at i:525867 original size:18 final size:17
Alignment explanation
Indices: 525826--525927 Score: 72
Period size: 18 Copynumber: 6.0 Consensus size: 17
525816 GAAAATATTT
525826 TAAAATTTATAT-AATA
1 TAAAATTTATATAAATA
525842 -AAAA-TTAT-TAACATA
1 TAAAATTTATATAA-ATA
525857 TTAAAATTTATATAAATA
1 -TAAAATTTATATAAATA
* *
525875 TAAAA-TAATTTAAATA
1 TAAAATTTATATAAATA
*
525891 TAATTATTTA-ATAAAATA
1 TAA-AATTTATAT-AAATA
*
525909 TATAAATATAATATAAATA
1 TA-AAAT-TTATATAAATA
525928 CATAAAATAT
Statistics
Matches: 67, Mismatches: 7, Indels: 21
0.71 0.07 0.22
Matches are distributed among these distances:
13 1 0.01
14 5 0.07
15 7 0.10
16 12 0.18
17 11 0.16
18 18 0.27
19 11 0.16
20 2 0.03
ACGTcount: A:0.59, C:0.01, G:0.00, T:0.40
Consensus pattern (17 bp):
TAAAATTTATATAAATA
Found at i:525886 original size:20 final size:20
Alignment explanation
Indices: 525861--525924 Score: 56
Period size: 20 Copynumber: 3.1 Consensus size: 20
525851 AACATATTAA
525861 AATTTATATAAATATAAAAT
1 AATTTATATAAATATAAAAT
* **
525881 AATTTAAATATAATTATTTAAT
1 AATTT--ATATAAATATAAAAT
** *
525903 AAAATATATAAATATAATAT
1 AATTTATATAAATATAAAAT
525923 AA
1 AA
525925 ATACATAAAA
Statistics
Matches: 33, Mismatches: 9, Indels: 4
0.72 0.20 0.09
Matches are distributed among these distances:
20 18 0.55
22 15 0.45
ACGTcount: A:0.59, C:0.00, G:0.00, T:0.41
Consensus pattern (20 bp):
AATTTATATAAATATAAAAT
Found at i:529549 original size:146 final size:147
Alignment explanation
Indices: 529358--529639 Score: 442
Period size: 146 Copynumber: 1.9 Consensus size: 147
529348 ATTCATAATG
*
529358 AATTGTTTTAGTTGAATTATCTAAAGCTCAAGTAGCTCAAATTCCTTTTGATCATCGTTCGTTTC
1 AATTGTTTTAGTTGAATTATCTAAAACTCAAGTAGCTCAAATTCCTTTTGATCATCGTTCGTTTC
* * * *
529423 TTCAGATTCAACTTTCATAGTTACTTA-ACATCATTAAGCTTAAATTCAAACTGAAATTAGGTCA
66 TTCAGATTCAACATTCACAGTTACTTATACATCATTAAACTCAAATTCAAACTGAAATTAGGTCA
529487 AAAAAGAGATCGTGATT
131 AAAAAGAGATCGTGATT
*
529504 AATTGTTTTAGTTGAGTCT-TCTAAAACTCAAGTAGCTCAAATTCCTTTTGATCATCGTTCGTTT
1 AATTGTTTTAGTTGAAT-TATCTAAAACTCAAGTAGCTCAAATTCCTTTTGATCATCGTTCGTTT
* *
529568 CTTCGGATTCAACATTCACGGTTACTTATCTGACATCATTAAACTCAAATTCAAACTGAAATTAG
65 CTTCAGATTCAACATTCACAGTTACTTA--T-ACATCATTAAACTCAAATTCAAACTGAAATTAG
529633 GTCAAAA
127 GTCAAAA
529640 TCAATCAAAT
Statistics
Matches: 123, Mismatches: 8, Indels: 6
0.90 0.06 0.04
Matches are distributed among these distances:
146 84 0.68
147 1 0.01
150 38 0.31
ACGTcount: A:0.33, C:0.17, G:0.13, T:0.37
Consensus pattern (147 bp):
AATTGTTTTAGTTGAATTATCTAAAACTCAAGTAGCTCAAATTCCTTTTGATCATCGTTCGTTTC
TTCAGATTCAACATTCACAGTTACTTATACATCATTAAACTCAAATTCAAACTGAAATTAGGTCA
AAAAAGAGATCGTGATT
Found at i:530895 original size:2 final size:2
Alignment explanation
Indices: 530888--530913 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
530878 CGCCTACTAG
530888 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
530914 TTAATGTTCA
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:531428 original size:23 final size:21
Alignment explanation
Indices: 531387--531428 Score: 57
Period size: 21 Copynumber: 1.9 Consensus size: 21
531377 GATAAATAGT
*
531387 ATAAATTTATTAAATTTAAAA
1 ATAAATTTAATAAATTTAAAA
531408 ATAAATTCTAATATAATTTAA
1 ATAAATT-TAATA-AATTTAA
531429 GTATTGCTCA
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
21 7 0.39
22 4 0.22
23 7 0.39
ACGTcount: A:0.55, C:0.02, G:0.00, T:0.43
Consensus pattern (21 bp):
ATAAATTTAATAAATTTAAAA
Found at i:533509 original size:63 final size:62
Alignment explanation
Indices: 533425--533553 Score: 188
Period size: 63 Copynumber: 2.1 Consensus size: 62
533415 TACAAAATAA
* * *
533425 TTAAAATATAATAAGATATAAAAAATAATATGAATACGATATTA-ATATATGAATTATTATAT
1 TTAAAATATAATAAAATATAAAAAATAATACGAATACGAT-TTAGATATATAAATTATTATAT
* *
533487 TTAACATATAATAAAAATATAAAAAATAATACGAATACGATTTAGATATATAAATTGTTATAT
1 TTAAAATATAAT-AAAATATAAAAAATAATACGAATACGATTTAGATATATAAATTATTATAT
533550 TTAA
1 TTAA
533554 TCACAATGAT
Statistics
Matches: 60, Mismatches: 5, Indels: 3
0.88 0.07 0.04
Matches are distributed among these distances:
62 14 0.23
63 46 0.77
ACGTcount: A:0.54, C:0.03, G:0.06, T:0.36
Consensus pattern (62 bp):
TTAAAATATAATAAAATATAAAAAATAATACGAATACGATTTAGATATATAAATTATTATAT
Found at i:536071 original size:17 final size:17
Alignment explanation
Indices: 536041--536073 Score: 50
Period size: 17 Copynumber: 1.9 Consensus size: 17
536031 GAAAAAATTG
536041 ATAATTATTATATTAAC
1 ATAATTATTATATTAAC
536058 ATAA-TATTATTATTAA
1 ATAATTATTA-TATTAA
536074 AAATTTATAT
Statistics
Matches: 15, Mismatches: 0, Indels: 2
0.88 0.00 0.12
Matches are distributed among these distances:
16 5 0.33
17 10 0.67
ACGTcount: A:0.48, C:0.03, G:0.00, T:0.48
Consensus pattern (17 bp):
ATAATTATTATATTAAC
Found at i:536843 original size:6 final size:6
Alignment explanation
Indices: 536832--536862 Score: 62
Period size: 6 Copynumber: 5.2 Consensus size: 6
536822 TCAACAGCCA
536832 TTGATT TTGATT TTGATT TTGATT TTGATT T
1 TTGATT TTGATT TTGATT TTGATT TTGATT T
536863 GCCCTTTTTG
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 25 1.00
ACGTcount: A:0.16, C:0.00, G:0.16, T:0.68
Consensus pattern (6 bp):
TTGATT
Found at i:537762 original size:2 final size:2
Alignment explanation
Indices: 537755--537793 Score: 78
Period size: 2 Copynumber: 19.5 Consensus size: 2
537745 GAGAAACTCA
537755 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 C
537794 AAAATACTTT
Statistics
Matches: 37, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 37 1.00
ACGTcount: A:0.00, C:0.51, G:0.00, T:0.49
Consensus pattern (2 bp):
CT
Found at i:538299 original size:19 final size:17
Alignment explanation
Indices: 538274--538322 Score: 57
Period size: 18 Copynumber: 2.9 Consensus size: 17
538264 TTGATCATTT
538274 TTATATTTATA-TTATAA
1 TTATATTTATATTTA-AA
*
538291 TTATATATTTTATTTAAA
1 TTATAT-TTATATTTAAA
538309 TTAT-TTTATATTTA
1 TTATATTTATATTTA
538323 TACCAATTTT
Statistics
Matches: 28, Mismatches: 2, Indels: 5
0.80 0.06 0.14
Matches are distributed among these distances:
16 8 0.29
17 7 0.25
18 10 0.36
19 3 0.11
ACGTcount: A:0.37, C:0.00, G:0.00, T:0.63
Consensus pattern (17 bp):
TTATATTTATATTTAAA
Found at i:543085 original size:7 final size:7
Alignment explanation
Indices: 543073--543097 Score: 50
Period size: 7 Copynumber: 3.6 Consensus size: 7
543063 ATTTACCATG
543073 AAAAAGA
1 AAAAAGA
543080 AAAAAGA
1 AAAAAGA
543087 AAAAAGA
1 AAAAAGA
543094 AAAA
1 AAAA
543098 GATTGATGAA
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 18 1.00
ACGTcount: A:0.88, C:0.00, G:0.12, T:0.00
Consensus pattern (7 bp):
AAAAAGA
Found at i:544199 original size:20 final size:18
Alignment explanation
Indices: 544174--544248 Score: 75
Period size: 17 Copynumber: 4.1 Consensus size: 18
544164 AATTAGAATG
544174 TATAATATAAAATATTAAAA
1 TATAATAT-AAATA-TAAAA
544194 TATAATAT-AATATAAAA
1 TATAATATAAATATAAAA
*
544211 -ATAATATAAATATCAAA
1 TATAATATAAATATAAAA
544228 TA-AATTATAAAATATTAAAA
1 TATAA-TAT-AAATA-TAAAA
544248 T
1 T
544249 TTATATAACA
Statistics
Matches: 48, Mismatches: 2, Indels: 10
0.80 0.03 0.17
Matches are distributed among these distances:
16 7 0.15
17 15 0.31
18 8 0.17
19 5 0.10
20 13 0.27
ACGTcount: A:0.64, C:0.01, G:0.00, T:0.35
Consensus pattern (18 bp):
TATAATATAAATATAAAA
Found at i:544216 original size:16 final size:18
Alignment explanation
Indices: 544174--544248 Score: 64
Period size: 20 Copynumber: 4.1 Consensus size: 18
544164 AATTAGAATG
544174 TATAATATAAAATATTAAAA
1 TATAATAT--AATATTAAAA
544194 TATAATATAATA-TAAAA
1 TATAATATAATATTAAAA
*
544211 -ATAATATAAATATCAAATA
1 TATAATAT-AATATTAAA-A
* * *
544230 AATTATAAAATATTAAAA
1 TATAATATAATATTAAAA
544248 T
1 T
544249 TTATATAACA
Statistics
Matches: 46, Mismatches: 5, Indels: 10
0.75 0.08 0.16
Matches are distributed among these distances:
16 7 0.15
17 9 0.20
18 8 0.17
19 9 0.20
20 13 0.28
ACGTcount: A:0.64, C:0.01, G:0.00, T:0.35
Consensus pattern (18 bp):
TATAATATAATATTAAAA
Found at i:544242 original size:36 final size:36
Alignment explanation
Indices: 544175--544248 Score: 87
Period size: 36 Copynumber: 2.1 Consensus size: 36
544165 ATTAGAATGT
* * *
544175 ATAATATAAAATATTAAAATATAATATAATATAAAA
1 ATAATATAAAATATCAAAAAATAATAAAATATAAAA
* *
544211 ATAATAT-AAATATCAAATAAATTATAAAATATTAAA
1 ATAATATAAAATATCAAA-AAATAATAAAATATAAAA
544247 AT
1 AT
544249 TTATATAACA
Statistics
Matches: 32, Mismatches: 5, Indels: 2
0.82 0.13 0.05
Matches are distributed among these distances:
35 9 0.28
36 23 0.72
ACGTcount: A:0.65, C:0.01, G:0.00, T:0.34
Consensus pattern (36 bp):
ATAATATAAAATATCAAAAAATAATAAAATATAAAA
Found at i:544248 original size:27 final size:25
Alignment explanation
Indices: 544174--544269 Score: 97
Period size: 27 Copynumber: 3.7 Consensus size: 25
544164 AATTAGAATG
544174 TATAATATAAAATATTAAAATATAA
1 TATAATATAAAATATTAAAATATAA
*
544199 TATAATATAAAAATAATATAAATATCAA
1 TATAATAT-AAAATATTA-AAATAT-AA
*
544227 -ATAAATTATAAAATATTAAAAT-TTA
1 TAT-AA-TATAAAATATTAAAATATAA
* *
544252 TATAACATAAATTATTAA
1 TATAATATAAAATATTAA
544270 TCTATCAAAA
Statistics
Matches: 60, Mismatches: 5, Indels: 13
0.77 0.06 0.17
Matches are distributed among these distances:
24 11 0.18
25 11 0.18
26 11 0.18
27 12 0.20
28 12 0.20
29 3 0.05
ACGTcount: A:0.61, C:0.02, G:0.00, T:0.36
Consensus pattern (25 bp):
TATAATATAAAATATTAAAATATAA
Found at i:544264 original size:31 final size:32
Alignment explanation
Indices: 544227--544288 Score: 90
Period size: 32 Copynumber: 2.0 Consensus size: 32
544217 TAAATATCAA
*
544227 ATAAATTA-TAAAATATTAAAATTTATATAAC
1 ATAAATTATTAAAATATCAAAATTTATATAAC
**
544258 ATAAATTATTAATCTATCAAAATTTATATAA
1 ATAAATTATTAAAATATCAAAATTTATATAA
544289 AAACATATAA
Statistics
Matches: 27, Mismatches: 3, Indels: 1
0.87 0.10 0.03
Matches are distributed among these distances:
31 8 0.30
32 19 0.70
ACGTcount: A:0.55, C:0.05, G:0.00, T:0.40
Consensus pattern (32 bp):
ATAAATTATTAAAATATCAAAATTTATATAAC
Found at i:545183 original size:30 final size:33
Alignment explanation
Indices: 545149--545234 Score: 108
Period size: 30 Copynumber: 2.7 Consensus size: 33
545139 GATTAGTTTG
*
545149 TTAAAATAAAATAAA-A-TAAATAA-TAATTCA
1 TTAAAATAAAATAAATATTAAATAATTAATTAA
*
545179 TTAAAATAAAATAAATATTATATAATTTAATTAA
1 TTAAAATAAAATAAATATTAAATAA-TTAATTAA
545213 TT-AAATAAAATAAATATCTAAA
1 TTAAAATAAAATAAATAT-TAAA
545235 AATATTAAAT
Statistics
Matches: 48, Mismatches: 3, Indels: 6
0.84 0.05 0.11
Matches are distributed among these distances:
30 15 0.31
31 1 0.02
32 6 0.12
33 15 0.31
34 11 0.23
ACGTcount: A:0.63, C:0.02, G:0.00, T:0.35
Consensus pattern (33 bp):
TTAAAATAAAATAAATATTAAATAATTAATTAA
Found at i:545363 original size:2 final size:2
Alignment explanation
Indices: 545356--545389 Score: 61
Period size: 2 Copynumber: 17.5 Consensus size: 2
545346 AGATCTTTTC
545356 AT AT AT AT AT AT AT AT AT AT AT AT AT AT -T AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
545390 ATCAAATCAA
Statistics
Matches: 31, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
1 1 0.03
2 30 0.97
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:545459 original size:19 final size:19
Alignment explanation
Indices: 545435--545473 Score: 60
Period size: 19 Copynumber: 2.1 Consensus size: 19
545425 TTTAGCTGTT
545435 AAAAAAAAAGAAAAAGAAA
1 AAAAAAAAAGAAAAAGAAA
* *
545454 AAAAAAAAAGGAAATGAAA
1 AAAAAAAAAGAAAAAGAAA
545473 A
1 A
545474 CATGAAGAAG
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
19 18 1.00
ACGTcount: A:0.85, C:0.00, G:0.13, T:0.03
Consensus pattern (19 bp):
AAAAAAAAAGAAAAAGAAA
Found at i:546043 original size:16 final size:16
Alignment explanation
Indices: 546024--546054 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
546014 ATTTTTTTTG
*
546024 AAATTAATTTATTTAA
1 AAATTAAATTATTTAA
546040 AAATTAAATTATTTA
1 AAATTAAATTATTTA
546055 CTTGACTTGA
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
16 14 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (16 bp):
AAATTAAATTATTTAA
Found at i:546148 original size:17 final size:17
Alignment explanation
Indices: 546121--546168 Score: 53
Period size: 16 Copynumber: 2.8 Consensus size: 17
546111 TATTATTTAA
*
546121 TAATAAAAATAATATTTT
1 TAAT-AAAATAATAATTT
*
546139 TATTAAAAT-ATAATTT
1 TAATAAAATAATAATTT
*
546155 TAATAATATAATAA
1 TAATAAAATAATAA
546169 AAATTAATAA
Statistics
Matches: 25, Mismatches: 4, Indels: 3
0.78 0.12 0.09
Matches are distributed among these distances:
16 13 0.52
17 9 0.36
18 3 0.12
ACGTcount: A:0.56, C:0.00, G:0.00, T:0.44
Consensus pattern (17 bp):
TAATAAAATAATAATTT
Found at i:546673 original size:28 final size:28
Alignment explanation
Indices: 546640--546701 Score: 79
Period size: 28 Copynumber: 2.2 Consensus size: 28
546630 ATTAAAATAT
* **
546640 TAAAAATTATTTTTATATTTAATTTTAAA
1 TAAAAATTATTTTT-TATTAAATAATAAA
*
546669 TAAAAATTATTTTTTATTAAATAATAAT
1 TAAAAATTATTTTTTATTAAATAATAAA
546697 TAAAA
1 TAAAA
546702 TTAAACTATA
Statistics
Matches: 29, Mismatches: 4, Indels: 1
0.85 0.12 0.03
Matches are distributed among these distances:
28 15 0.52
29 14 0.48
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (28 bp):
TAAAAATTATTTTTTATTAAATAATAAA
Found at i:547879 original size:18 final size:19
Alignment explanation
Indices: 547846--547881 Score: 56
Period size: 18 Copynumber: 1.9 Consensus size: 19
547836 TATAAAAGTA
547846 AATATAAAATAAATTTATT
1 AATATAAAATAAATTTATT
*
547865 AATATATAA-AAATTTAT
1 AATATAAAATAAATTTAT
547882 ATAAAATTAA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
18 8 0.50
19 8 0.50
ACGTcount: A:0.58, C:0.00, G:0.00, T:0.42
Consensus pattern (19 bp):
AATATAAAATAAATTTATT
Found at i:547884 original size:33 final size:30
Alignment explanation
Indices: 547847--547955 Score: 79
Period size: 30 Copynumber: 3.7 Consensus size: 30
547837 ATAAAAGTAA
547847 ATATAAAATAAATTTATTAATATATAAAAATTT
1 ATATAAAATAAA--TATT-ATATATAAAAATTT
* * *
547880 ATATAAAATTAATATTATATATTAAAATTA
1 ATATAAAATAAATATTATATATAAAAATTT
* *
547910 AT-TTATAT-AATATT-T-TA-AATAAA-TT
1 ATATAAAATAAATATTATATATAA-AAATTT
*
547935 ATATAAAATAAAAATT-TATAT
1 ATATAAAATAAATATTATATAT
547956 TAATAAAAAA
Statistics
Matches: 61, Mismatches: 10, Indels: 14
0.72 0.12 0.16
Matches are distributed among these distances:
25 4 0.07
26 9 0.15
27 7 0.11
28 8 0.13
29 4 0.07
30 14 0.23
31 4 0.07
33 11 0.18
ACGTcount: A:0.56, C:0.00, G:0.00, T:0.44
Consensus pattern (30 bp):
ATATAAAATAAATATTATATATAAAAATTT
Found at i:547899 original size:16 final size:16
Alignment explanation
Indices: 547877--547919 Score: 52
Period size: 19 Copynumber: 2.6 Consensus size: 16
547867 TATATAAAAA
547877 TTTATATAAAATTAAT
1 TTTATATAAAATTAAT
547893 ATTATATATTAAAATTAA-
1 -TT-TATA-TAAAATTAAT
547911 TTTATATAA
1 TTTATATAA
547920 TATTTTAAAT
Statistics
Matches: 24, Mismatches: 0, Indels: 6
0.80 0.00 0.20
Matches are distributed among these distances:
15 3 0.12
16 4 0.17
17 4 0.17
18 4 0.17
19 9 0.38
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (16 bp):
TTTATATAAAATTAAT
Found at i:547900 original size:18 final size:18
Alignment explanation
Indices: 547879--547918 Score: 64
Period size: 18 Copynumber: 2.2 Consensus size: 18
547869 TATAAAAATT
547879 TATA-TAAAATTAATATTA
1 TATATTAAAATTAAT-TTA
547897 TATATTAAAATTAATTTA
1 TATATTAAAATTAATTTA
547915 TATA
1 TATA
547919 ATATTTTAAA
Statistics
Matches: 21, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
18 11 0.52
19 10 0.48
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (18 bp):
TATATTAAAATTAATTTA
Found at i:547939 original size:23 final size:23
Alignment explanation
Indices: 547866--547944 Score: 63
Period size: 23 Copynumber: 3.4 Consensus size: 23
547856 AAATTTATTA
* * *
547866 ATATATAAAAATTTATATAAAATT
1 ATATATAATATTTTAAAT-AAATT
* * *
547890 A-ATATTATATATTAAAATTAATT
1 ATATATAATAT-TTTAAATAAATT
547913 -TATATAATATTTTAAATAAATT
1 ATATATAATATTTTAAATAAATT
*
547935 ATATAAAATA
1 ATATATAATA
547945 AAAATTTATA
Statistics
Matches: 42, Mismatches: 10, Indels: 7
0.71 0.17 0.12
Matches are distributed among these distances:
22 10 0.24
23 26 0.62
24 6 0.14
ACGTcount: A:0.56, C:0.00, G:0.00, T:0.44
Consensus pattern (23 bp):
ATATATAATATTTTAAATAAATT
Found at i:549846 original size:21 final size:20
Alignment explanation
Indices: 549803--549838 Score: 58
Period size: 18 Copynumber: 1.9 Consensus size: 20
549793 GTGTCATATA
549803 TTTTCTTTTTCTTTTTTTAG
1 TTTTCTTTTTCTTTTTTTAG
549823 TTTT-TTTTT-TTTTTTT
1 TTTTCTTTTTCTTTTTTT
549839 TCATGTTTCT
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
18 7 0.44
19 5 0.31
20 4 0.25
ACGTcount: A:0.03, C:0.06, G:0.03, T:0.89
Consensus pattern (20 bp):
TTTTCTTTTTCTTTTTTTAG
Found at i:550557 original size:22 final size:23
Alignment explanation
Indices: 550522--550567 Score: 69
Period size: 22 Copynumber: 2.0 Consensus size: 23
550512 TATTTTTATT
550522 TAAATTTAATTATAAAAA-AATA
1 TAAATTTAATTATAAAAATAATA
550544 TAAATATTAA-TATAAAAATAATA
1 TAAAT-TTAATTATAAAAATAATA
550567 T
1 T
550568 TTAAAATTTT
Statistics
Matches: 22, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
22 13 0.59
23 9 0.41
ACGTcount: A:0.63, C:0.00, G:0.00, T:0.37
Consensus pattern (23 bp):
TAAATTTAATTATAAAAATAATA
Found at i:552173 original size:21 final size:20
Alignment explanation
Indices: 552137--552179 Score: 52
Period size: 21 Copynumber: 2.1 Consensus size: 20
552127 TTAATTAAAA
*
552137 TATTTTTATTGATTTTTCAT
1 TATTTTTATTGATTTTTAAT
552157 TATTTTT-TTGAATTTTTTAAT
1 TATTTTTATTG-A-TTTTTAAT
552178 TA
1 TA
552180 CATTAAAATC
Statistics
Matches: 20, Mismatches: 1, Indels: 3
0.83 0.04 0.12
Matches are distributed among these distances:
19 3 0.15
20 8 0.40
21 9 0.45
ACGTcount: A:0.23, C:0.02, G:0.05, T:0.70
Consensus pattern (20 bp):
TATTTTTATTGATTTTTAAT
Found at i:558629 original size:15 final size:16
Alignment explanation
Indices: 558609--558638 Score: 53
Period size: 15 Copynumber: 1.9 Consensus size: 16
558599 ATATCATTAT
558609 TTTTCAAAA-ATTTTA
1 TTTTCAAAAGATTTTA
558624 TTTTCAAAAGATTTT
1 TTTTCAAAAGATTTT
558639 TTTATAAAAT
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 9 0.64
16 5 0.36
ACGTcount: A:0.37, C:0.07, G:0.03, T:0.53
Consensus pattern (16 bp):
TTTTCAAAAGATTTTA
Found at i:559807 original size:21 final size:22
Alignment explanation
Indices: 559769--559811 Score: 61
Period size: 21 Copynumber: 2.0 Consensus size: 22
559759 TTCATAAAAA
* *
559769 TTAAAATTATTTATATTTATTT
1 TTAAAAATATTTAAATTTATTT
559791 TTAAAAAT-TTTAAATTTATTT
1 TTAAAAATATTTAAATTTATTT
559812 GATCTATTAC
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
21 12 0.63
22 7 0.37
ACGTcount: A:0.40, C:0.00, G:0.00, T:0.60
Consensus pattern (22 bp):
TTAAAAATATTTAAATTTATTT
Found at i:560834 original size:5 final size:5
Alignment explanation
Indices: 560824--560889 Score: 50
Period size: 5 Copynumber: 13.6 Consensus size: 5
560814 ACGTTAATAG
* * *
560824 ATTAT ATTAT ATAAT TTTA- ATATAT TTTAT ATTAT ATTAT -TT-T ATTAT
1 ATTAT ATTAT ATTAT ATTAT AT-TAT ATTAT ATTAT ATTAT ATTAT ATTAT
*
560872 -TTTT AGTTAT ATTAT ATT
1 ATTAT A-TTAT ATTAT ATT
560890 TTTATTTTAA
Statistics
Matches: 47, Mismatches: 8, Indels: 12
0.70 0.12 0.18
Matches are distributed among these distances:
3 1 0.02
4 8 0.17
5 33 0.70
6 5 0.11
ACGTcount: A:0.35, C:0.00, G:0.02, T:0.64
Consensus pattern (5 bp):
ATTAT
Found at i:560872 original size:23 final size:23
Alignment explanation
Indices: 560825--560898 Score: 89
Period size: 23 Copynumber: 3.1 Consensus size: 23
560815 CGTTAATAGA
*
560825 TTATATTATATAATTTTAATATATT
1 TTATATTATATTATTTT-AT-TATT
560850 TTATATTATATTATTTTATTATT
1 TTATATTATATTATTTTATTATT
560873 TT-TAGTTATATTATATTT-TTATT
1 TTATA-TTATATTAT-TTTATTATT
560896 TTA
1 TTA
560899 ATATACTTTT
Statistics
Matches: 45, Mismatches: 1, Indels: 7
0.85 0.02 0.13
Matches are distributed among these distances:
22 2 0.04
23 22 0.49
24 5 0.11
25 16 0.36
ACGTcount: A:0.32, C:0.00, G:0.01, T:0.66
Consensus pattern (23 bp):
TTATATTATATTATTTTATTATT
Found at i:560881 original size:18 final size:17
Alignment explanation
Indices: 560825--560893 Score: 52
Period size: 17 Copynumber: 3.9 Consensus size: 17
560815 CGTTAATAGA
560825 TTATATTATATAATTTTA-
1 TTATATTATAT--TTTTAG
* * *
560843 ATATATTTTATATTATA-
1 TTATATTATAT-TTTTAG
*
560860 TTATTTTATTATTTTTAG
1 TTATATTA-TATTTTTAG
560878 TTATATTATATTTTTA
1 TTATATTATATTTTTA
560894 TTTTAATATA
Statistics
Matches: 41, Mismatches: 8, Indels: 5
0.76 0.15 0.09
Matches are distributed among these distances:
17 22 0.54
18 19 0.46
ACGTcount: A:0.33, C:0.00, G:0.01, T:0.65
Consensus pattern (17 bp):
TTATATTATATTTTTAG
Found at i:560903 original size:16 final size:16
Alignment explanation
Indices: 560860--560912 Score: 56
Period size: 16 Copynumber: 3.4 Consensus size: 16
560850 TTATATTATA
560860 TTATTTT-AT-TATTT
1 TTATTTTAATATATTT
* *
560874 TTAGTTATATTATATTT
1 TTA-TTTTAATATATTT
*
560891 TTATTTTAATATACTT
1 TTATTTTAATATATTT
560907 TTATTT
1 TTATTT
560913 ACTTTTCATT
Statistics
Matches: 31, Mismatches: 5, Indels: 4
0.77 0.12 0.10
Matches are distributed among these distances:
14 3 0.10
15 3 0.10
16 17 0.55
17 8 0.26
ACGTcount: A:0.26, C:0.02, G:0.02, T:0.70
Consensus pattern (16 bp):
TTATTTTAATATATTT
Found at i:560909 original size:33 final size:35
Alignment explanation
Indices: 560824--560909 Score: 90
Period size: 33 Copynumber: 2.5 Consensus size: 35
560814 ACGTTAATAG
* *
560824 ATTATATTATATAATTTTAATATATTTTATATTAT
1 ATTATTTTATATAATTTTAATATATATTATATTAT
* *
560859 ATTATTTTAT-TATTTTTAGT-TATATTATATT-T
1 ATTATTTTATATAATTTTAATATATATTATATTAT
*
560891 -TTATTTTAATATACTTTTA
1 ATTATTTT-ATATAATTTTA
560910 TTTACTTTTC
Statistics
Matches: 44, Mismatches: 5, Indels: 6
0.80 0.09 0.11
Matches are distributed among these distances:
31 7 0.16
32 3 0.07
33 17 0.39
34 8 0.18
35 9 0.20
ACGTcount: A:0.34, C:0.01, G:0.01, T:0.64
Consensus pattern (35 bp):
ATTATTTTATATAATTTTAATATATATTATATTAT
Found at i:561252 original size:14 final size:15
Alignment explanation
Indices: 561202--561250 Score: 55
Period size: 15 Copynumber: 3.1 Consensus size: 15
561192 GTAAATTTTA
561202 TTAATTTTAAAATTATTT
1 TTAATTTTAAAA--A-TT
561220 TTGAA-TTTAAAAATT
1 TT-AATTTTAAAAATT
561235 TTAATTTTAAAAATT
1 TTAATTTTAAAAATT
561250 T
1 T
561251 AAATAAAATT
Statistics
Matches: 29, Mismatches: 0, Indels: 7
0.81 0.00 0.19
Matches are distributed among these distances:
14 2 0.07
15 15 0.52
16 1 0.03
18 9 0.31
19 2 0.07
ACGTcount: A:0.43, C:0.00, G:0.02, T:0.55
Consensus pattern (15 bp):
TTAATTTTAAAAATT
Found at i:561517 original size:16 final size:18
Alignment explanation
Indices: 561496--561535 Score: 57
Period size: 18 Copynumber: 2.3 Consensus size: 18
561486 ACATAATTAT
*
561496 TATAATA-G-TAATAAAA
1 TATAATATGATAAAAAAA
561512 TATAATATGATAAAAAAA
1 TATAATATGATAAAAAAA
561530 TATAAT
1 TATAAT
561536 TACATTATAT
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
16 7 0.33
17 1 0.05
18 13 0.62
ACGTcount: A:0.62, C:0.00, G:0.05, T:0.33
Consensus pattern (18 bp):
TATAATATGATAAAAAAA
Found at i:562059 original size:14 final size:15
Alignment explanation
Indices: 562042--562074 Score: 59
Period size: 14 Copynumber: 2.3 Consensus size: 15
562032 GATTAATCAA
562042 AATTTTTTAA-TTTT
1 AATTTTTTAATTTTT
562056 AATTTTTTAATTTTT
1 AATTTTTTAATTTTT
562071 AATT
1 AATT
562075 AATATTAAAA
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
14 10 0.56
15 8 0.44
ACGTcount: A:0.30, C:0.00, G:0.00, T:0.70
Consensus pattern (15 bp):
AATTTTTTAATTTTT
Found at i:562304 original size:18 final size:19
Alignment explanation
Indices: 562274--562309 Score: 65
Period size: 18 Copynumber: 1.9 Consensus size: 19
562264 TTTGAATAAA
562274 ATTATTATTTATTTAAATC
1 ATTATTATTTATTTAAATC
562293 ATTATT-TTTATTTAAAT
1 ATTATTATTTATTTAAAT
562310 TTAATTATAA
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
18 11 0.65
19 6 0.35
ACGTcount: A:0.36, C:0.03, G:0.00, T:0.61
Consensus pattern (19 bp):
ATTATTATTTATTTAAATC
Found at i:562343 original size:22 final size:21
Alignment explanation
Indices: 562305--562355 Score: 63
Period size: 21 Copynumber: 2.5 Consensus size: 21
562295 TATTTTTATT
562305 TAAATTTAATTATAAAATATA
1 TAAATTTAATTATAAAATATA
562326 TAAATATTAA-TATAAAA-ATA
1 TAAAT-TTAATTATAAAATATA
*
562346 -ATATTTAATT
1 TAAATTTAATT
562356 TTTTAAATTA
Statistics
Matches: 27, Mismatches: 1, Indels: 6
0.79 0.03 0.18
Matches are distributed among these distances:
18 4 0.15
19 4 0.15
20 3 0.11
21 12 0.44
22 4 0.15
ACGTcount: A:0.57, C:0.00, G:0.00, T:0.43
Consensus pattern (21 bp):
TAAATTTAATTATAAAATATA
Found at i:563061 original size:20 final size:20
Alignment explanation
Indices: 563025--563062 Score: 51
Period size: 20 Copynumber: 1.9 Consensus size: 20
563015 AGAAAATAAT
*
563025 TTTTTATATTAGTATTTATA
1 TTTTTATATTAGAATTTATA
563045 TTTTTATAATTA-AATTTA
1 TTTTTAT-ATTAGAATTTA
563063 AATAAAAAAT
Statistics
Matches: 16, Mismatches: 1, Indels: 2
0.84 0.05 0.11
Matches are distributed among these distances:
20 12 0.75
21 4 0.25
ACGTcount: A:0.34, C:0.00, G:0.03, T:0.63
Consensus pattern (20 bp):
TTTTTATATTAGAATTTATA
Found at i:563505 original size:12 final size:11
Alignment explanation
Indices: 563486--563556 Score: 54
Period size: 12 Copynumber: 6.2 Consensus size: 11
563476 TAAATTCGTA
563486 TATTTATATTAT
1 TATTTATATT-T
*
563498 TTTTTATATTT
1 TATTTATATTT
**
563509 TATCGA-ATTT
1 TATTTATATTT
563519 ATATTTATATTAT
1 -TATTTATATT-T
*
563532 TTTTTATATTT
1 TATTTATATTT
*
563543 TATATCATATTT
1 TAT-TTATATTT
563555 TA
1 TA
563557 CTTTTTTTTT
Statistics
Matches: 46, Mismatches: 9, Indels: 8
0.73 0.14 0.13
Matches are distributed among these distances:
10 4 0.09
11 11 0.24
12 30 0.65
13 1 0.02
ACGTcount: A:0.30, C:0.03, G:0.01, T:0.66
Consensus pattern (11 bp):
TATTTATATTT
Found at i:563562 original size:19 final size:19
Alignment explanation
Indices: 563484--563556 Score: 59
Period size: 18 Copynumber: 4.1 Consensus size: 19
563474 AATAAATTCG
* *
563484 TATA-TTTATATTATTTTT
1 TATATTTTATATCATATTT
563502 TATA-TTT-TATCGA-A-TT
1 TATATTTTATATC-ATATTT
* *
563518 TATA-TTTATATTATTTTT
1 TATATTTTATATCATATTT
563536 TATATTTTATATCATATTT
1 TATATTTTATATCATATTT
563555 TA
1 TA
563557 CTTTTTTTTT
Statistics
Matches: 44, Mismatches: 6, Indels: 9
0.75 0.10 0.15
Matches are distributed among these distances:
16 10 0.23
17 6 0.14
18 14 0.32
19 14 0.32
ACGTcount: A:0.30, C:0.03, G:0.01, T:0.66
Consensus pattern (19 bp):
TATATTTTATATCATATTT
Found at i:564151 original size:22 final size:21
Alignment explanation
Indices: 564126--564166 Score: 55
Period size: 21 Copynumber: 1.9 Consensus size: 21
564116 TATAATATCA
*
564126 AATTAAGCATCAAATAAAAATT
1 AATTAAGAAT-AAATAAAAATT
*
564148 AATTAATAATAAATAAAAA
1 AATTAAGAATAAATAAAAA
564167 AATTTAATTT
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
21 9 0.53
22 8 0.47
ACGTcount: A:0.66, C:0.05, G:0.02, T:0.27
Consensus pattern (21 bp):
AATTAAGAATAAATAAAAATT
Found at i:564661 original size:26 final size:27
Alignment explanation
Indices: 564630--564730 Score: 77
Period size: 26 Copynumber: 3.8 Consensus size: 27
564620 TTTTAAAAAT
564630 AAATATAAATAATATT-ATTT-TTAATA
1 AAATATAAATAAT-TTAATTTATTAATA
*
564656 AAATAT-AATTATTTAATTTATTAATA
1 AAATATAAATAATTTAATTTATTAATA
* * * * *
564682 ATATATAAATTTATATAATATTAATATATC
1 AAATATAAA-TAATTTAAT-TTATTA-ATA
564712 AAATATAAAT-A-TTAATTTA
1 AAATATAAATAATTTAATTTA
564731 ATGTAAAAAA
Statistics
Matches: 62, Mismatches: 7, Indels: 12
0.77 0.09 0.15
Matches are distributed among these distances:
24 2 0.03
25 9 0.15
26 20 0.32
27 6 0.10
28 9 0.15
29 6 0.10
30 10 0.16
ACGTcount: A:0.52, C:0.01, G:0.00, T:0.47
Consensus pattern (27 bp):
AAATATAAATAATTTAATTTATTAATA
Found at i:564722 original size:21 final size:22
Alignment explanation
Indices: 564680--564727 Score: 64
Period size: 21 Copynumber: 2.2 Consensus size: 22
564670 AATTTATTAA
564680 TAATATATAAATTTATATAATAT
1 TAATATATAAA-TTATATAATAT
564703 TAATATATCAAA-TATA-AATAT
1 TAATATAT-AAATTATATAATAT
564724 TAAT
1 TAAT
564728 TTAATGTAAA
Statistics
Matches: 24, Mismatches: 0, Indels: 4
0.86 0.00 0.14
Matches are distributed among these distances:
21 9 0.38
22 4 0.17
23 8 0.33
24 3 0.12
ACGTcount: A:0.54, C:0.02, G:0.00, T:0.44
Consensus pattern (22 bp):
TAATATATAAATTATATAATAT
Found at i:566330 original size:20 final size:20
Alignment explanation
Indices: 566300--566345 Score: 65
Period size: 20 Copynumber: 2.2 Consensus size: 20
566290 TATATTTATT
566300 ATTTATTTAATATTTAAAATG
1 ATTT-TTTAATATTTAAAATG
* *
566321 ATTTTTTAATTTTTAAAATT
1 ATTTTTTAATATTTAAAATG
566341 ATTTT
1 ATTTT
566346 AATTTAAACC
Statistics
Matches: 23, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
20 19 0.83
21 4 0.17
ACGTcount: A:0.37, C:0.00, G:0.02, T:0.61
Consensus pattern (20 bp):
ATTTTTTAATATTTAAAATG
Found at i:568582 original size:2 final size:2
Alignment explanation
Indices: 568577--568606 Score: 51
Period size: 2 Copynumber: 15.0 Consensus size: 2
568567 TATATATATA
*
568577 TG TG TG TG TG TG TG TG TG TG TG TG TC TG TG
1 TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG
568607 AGATAATAGT
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.00, C:0.03, G:0.47, T:0.50
Consensus pattern (2 bp):
TG
Found at i:571538 original size:15 final size:14
Alignment explanation
Indices: 571498--571539 Score: 52
Period size: 13 Copynumber: 3.0 Consensus size: 14
571488 TAAAAGAATT
571498 AAAATATTTTTA-A
1 AAAATATTTTTATA
571511 AAAA-ATTTATTATA
1 AAAATATTT-TTATA
571525 AAAATTATTTTTATA
1 AAAA-TATTTTTATA
571540 TAAAGATCAT
Statistics
Matches: 25, Mismatches: 0, Indels: 6
0.81 0.00 0.19
Matches are distributed among these distances:
12 4 0.16
13 7 0.28
14 5 0.20
15 5 0.20
16 4 0.16
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (14 bp):
AAAATATTTTTATA
Done.