Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold5
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: 1536239
ACGTcount: A:0.33, C:0.13, G:0.13, T:0.33
Warning! 124408 characters in sequence are not A, C, G, or T
File 4 of 14
Found at i:487912 original size:17 final size:16
Alignment explanation
Indices: 487886--487918 Score: 57
Period size: 17 Copynumber: 2.0 Consensus size: 16
487876 CTCACTGTCC
487886 AAAAAAAATAAAAAAT
1 AAAAAAAATAAAAAAT
487902 AAAATAAAATAAAAAAT
1 AAAA-AAAATAAAAAAT
487919 TTGTACAAAC
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
16 4 0.25
17 12 0.75
ACGTcount: A:0.85, C:0.00, G:0.00, T:0.15
Consensus pattern (16 bp):
AAAAAAAATAAAAAAT
Found at i:488656 original size:18 final size:17
Alignment explanation
Indices: 488630--488664 Score: 52
Period size: 18 Copynumber: 2.0 Consensus size: 17
488620 ATTAAGTTTG
488630 TTTTACTCTTTTCTTTTT
1 TTTTACTCTTTT-TTTTT
*
488648 TTTTTCTCTTTTTTTTT
1 TTTTACTCTTTTTTTTT
488665 CATAAGAAAA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
17 5 0.31
18 11 0.69
ACGTcount: A:0.03, C:0.14, G:0.00, T:0.83
Consensus pattern (17 bp):
TTTTACTCTTTTTTTTT
Found at i:488796 original size:11 final size:12
Alignment explanation
Indices: 488772--488799 Score: 56
Period size: 12 Copynumber: 2.3 Consensus size: 12
488762 AAATTAATTC
488772 AATTGATAAAAA
1 AATTGATAAAAA
488784 AATTGATAAAAA
1 AATTGATAAAAA
488796 AATT
1 AATT
488800 TTGTTAATTT
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 16 1.00
ACGTcount: A:0.64, C:0.00, G:0.07, T:0.29
Consensus pattern (12 bp):
AATTGATAAAAA
Found at i:490114 original size:23 final size:22
Alignment explanation
Indices: 490078--490148 Score: 87
Period size: 23 Copynumber: 3.3 Consensus size: 22
490068 TAAATTTAAA
490078 TATATTTTTATTTATATTATGT
1 TATATTTTTATTTATATTATGT
490100 TCATATTATTT-TTTATATTATGT
1 T-ATATT-TTTATTTATATTATGT
490123 TATATTTTATATTT-T-TTAT-T
1 TATATTTT-TATTTATATTATGT
490143 TATATT
1 TATATT
490149 ATATCATATG
Statistics
Matches: 45, Mismatches: 0, Indels: 10
0.82 0.00 0.18
Matches are distributed among these distances:
20 7 0.16
21 6 0.13
22 8 0.18
23 21 0.47
24 3 0.07
ACGTcount: A:0.27, C:0.01, G:0.03, T:0.69
Consensus pattern (22 bp):
TATATTTTTATTTATATTATGT
Found at i:490151 original size:25 final size:26
Alignment explanation
Indices: 490077--490157 Score: 96
Period size: 25 Copynumber: 3.2 Consensus size: 26
490067 ATAAATTTAA
*
490077 ATATA-TTTTTATTTATATTATGTTC
1 ATATATTTTTTATTTATATTATATTC
*
490102 ATATTATTTTTTATATTATGTTATATT-
1 ATA-TATTTTTTAT-TTATATTATATTC
*
490129 TTATATTTTTTATTTATATTATA-TC
1 ATATATTTTTTATTTATATTATATTC
490154 ATAT
1 ATAT
490158 GGTTTACCAT
Statistics
Matches: 47, Mismatches: 5, Indels: 8
0.78 0.08 0.13
Matches are distributed among these distances:
24 1 0.02
25 15 0.32
26 12 0.26
27 9 0.19
28 10 0.21
ACGTcount: A:0.30, C:0.02, G:0.02, T:0.65
Consensus pattern (26 bp):
ATATATTTTTTATTTATATTATATTC
Found at i:492103 original size:17 final size:18
Alignment explanation
Indices: 492081--492116 Score: 56
Period size: 17 Copynumber: 2.1 Consensus size: 18
492071 CTTAATTTTT
*
492081 TATATTTTA-AATTTAAA
1 TATATTTTATAATTAAAA
492098 TATATTTTATAATTAAAA
1 TATATTTTATAATTAAAA
492116 T
1 T
492117 TTAAATAAAT
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
17 9 0.53
18 8 0.47
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (18 bp):
TATATTTTATAATTAAAA
Found at i:492105 original size:24 final size:24
Alignment explanation
Indices: 492078--492137 Score: 77
Period size: 24 Copynumber: 2.5 Consensus size: 24
492068 AAACTTAATT
*
492078 TTTTATATTTTAAATTTAAATATA
1 TTTTATATTTTAAATTTAAATAAA
* *
492102 TTTTATAATTAAAATTTAAATAAA
1 TTTTATATTTTAAATTTAAATAAA
*
492126 TATTAT-TTTTAA
1 TTTTATATTTTAA
492138 TTAAAAATAT
Statistics
Matches: 30, Mismatches: 6, Indels: 1
0.81 0.16 0.03
Matches are distributed among these distances:
23 4 0.13
24 26 0.87
ACGTcount: A:0.45, C:0.00, G:0.00, T:0.55
Consensus pattern (24 bp):
TTTTATATTTTAAATTTAAATAAA
Found at i:492154 original size:28 final size:28
Alignment explanation
Indices: 492094--492152 Score: 77
Period size: 28 Copynumber: 2.1 Consensus size: 28
492084 ATTTTAAATT
*
492094 TAAATATATTTTATAATTAAAATTTAAA
1 TAAATATATTTTATAATTAAAATATAAA
*
492122 TAAATATTATTTT-TAATTAAAA-ATATA
1 TAAATA-TATTTTATAATTAAAATATAAA
492149 TAAA
1 TAAA
492153 ATTAAATTTA
Statistics
Matches: 28, Mismatches: 2, Indels: 3
0.85 0.06 0.09
Matches are distributed among these distances:
27 7 0.25
28 15 0.54
29 6 0.21
ACGTcount: A:0.54, C:0.00, G:0.00, T:0.46
Consensus pattern (28 bp):
TAAATATATTTTATAATTAAAATATAAA
Found at i:492160 original size:21 final size:20
Alignment explanation
Indices: 492136--492174 Score: 51
Period size: 21 Copynumber: 1.9 Consensus size: 20
492126 TATTATTTTT
*
492136 AATTAAAAATATATAAAATTA
1 AATTAAAAAT-TAAAAAATTA
*
492157 AATTTAAAATTAAAAAAT
1 AATTAAAAATTAAAAAAT
492175 AATTTTTAAT
Statistics
Matches: 16, Mismatches: 2, Indels: 1
0.84 0.11 0.05
Matches are distributed among these distances:
20 7 0.44
21 9 0.56
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (20 bp):
AATTAAAAATTAAAAAATTA
Found at i:492725 original size:34 final size:35
Alignment explanation
Indices: 492683--492748 Score: 98
Period size: 35 Copynumber: 1.9 Consensus size: 35
492673 TTGATATAAA
* *
492683 AAAATTAAATT-AATATGTAATATTTTTATATTTT
1 AAAATTAAATTAAATATATAATATATTTATATTTT
*
492717 AAAATTAAATTAAATATATCATATATTTATAT
1 AAAATTAAATTAAATATATAATATATTTATAT
492749 ATGTGGATAT
Statistics
Matches: 28, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
34 11 0.39
35 17 0.61
ACGTcount: A:0.48, C:0.02, G:0.02, T:0.48
Consensus pattern (35 bp):
AAAATTAAATTAAATATATAATATATTTATATTTT
Found at i:492903 original size:17 final size:18
Alignment explanation
Indices: 492871--492904 Score: 52
Period size: 17 Copynumber: 1.9 Consensus size: 18
492861 TTATTTTTAT
492871 ATTAAGAAATTAAAATTA
1 ATTAAGAAATTAAAATTA
*
492889 ATTAA-AAATTTAAATT
1 ATTAAGAAATTAAAATT
492905 CAAATCAATT
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 10 0.67
18 5 0.33
ACGTcount: A:0.59, C:0.00, G:0.03, T:0.38
Consensus pattern (18 bp):
ATTAAGAAATTAAAATTA
Found at i:501063 original size:38 final size:38
Alignment explanation
Indices: 501021--501129 Score: 121
Period size: 38 Copynumber: 2.9 Consensus size: 38
501011 TAGCCACCGA
* **
501021 CCAATTTCAAATTAAATTCTCTAGTCGTCAGCCGCCAG
1 CCAATTTCAAATTGAATTCTCTAACCGTCAGCCGCCAG
* * *
501059 CCAA-TTCTAAATTGAATTTTTTAACCGTCAGCCGCTAG
1 CCAATTTC-AAATTGAATTCTCTAACCGTCAGCCGCCAG
* * *
501097 TCAATTTTAAATTGAATTCTCTAACTGTCAGCC
1 CCAATTTCAAATTGAATTCTCTAACCGTCAGCC
501130 AATTCAATTT
Statistics
Matches: 58, Mismatches: 11, Indels: 4
0.79 0.15 0.05
Matches are distributed among these distances:
37 3 0.05
38 53 0.91
39 2 0.03
ACGTcount: A:0.29, C:0.25, G:0.12, T:0.34
Consensus pattern (38 bp):
CCAATTTCAAATTGAATTCTCTAACCGTCAGCCGCCAG
Found at i:505798 original size:38 final size:38
Alignment explanation
Indices: 505730--505838 Score: 121
Period size: 38 Copynumber: 2.9 Consensus size: 38
505720 AGTCACCGAC
* * * ***
505730 CAATTCTAAATTAAATTCTCTAATTATCAGCTGTCAG-
1 CAATTCCAAATTAAATTCTCTAACTGTCAGCCACCAGT
* *
505767 CTAATTTCAAATTAAATTCTCTAACCGTCAGCCACCAGT
1 C-AATTCCAAATTAAATTCTCTAACTGTCAGCCACCAGT
*
505806 CAATTCCAAATTGAATTCTCTAACTGTCAGCCA
1 CAATTCCAAATTAAATTCTCTAACTGTCAGCCA
505839 ATTCAATTTG
Statistics
Matches: 59, Mismatches: 11, Indels: 3
0.81 0.15 0.04
Matches are distributed among these distances:
37 1 0.02
38 57 0.97
39 1 0.02
ACGTcount: A:0.34, C:0.25, G:0.08, T:0.33
Consensus pattern (38 bp):
CAATTCCAAATTAAATTCTCTAACTGTCAGCCACCAGT
Found at i:512454 original size:36 final size:36
Alignment explanation
Indices: 512411--512481 Score: 99
Period size: 35 Copynumber: 2.0 Consensus size: 36
512401 GTAAATATTA
* *
512411 AAAAATATTAAGCTATTTAAATTTTAAAAAT-TAATT
1 AAAAATATTAA-ATATTAAAATTTTAAAAATATAATT
*
512447 AAAAATATTAAATATTAAAATTTTACAAATATAAT
1 AAAAATATTAAATATTAAAATTTTAAAAATATAAT
512482 CAAACTTAAA
Statistics
Matches: 31, Mismatches: 3, Indels: 2
0.86 0.08 0.06
Matches are distributed among these distances:
35 16 0.52
36 15 0.48
ACGTcount: A:0.56, C:0.03, G:0.01, T:0.39
Consensus pattern (36 bp):
AAAAATATTAAATATTAAAATTTTAAAAATATAATT
Found at i:515351 original size:19 final size:19
Alignment explanation
Indices: 515296--515356 Score: 63
Period size: 19 Copynumber: 3.2 Consensus size: 19
515286 ATTAAATTAC
*
515296 AAATTAAAGAATATTA-ATT
1 AAATTAAA-AATATTATAAT
*
515315 TAATTAAAAATGTATTATAAT
1 AAATTAAAAA--TATTATAAT
515336 AAATTAAAAATATTAT-AT
1 AAATTAAAAATATTATAAT
515354 AAA
1 AAA
515357 AATATAAAAT
Statistics
Matches: 36, Mismatches: 3, Indels: 7
0.78 0.07 0.15
Matches are distributed among these distances:
18 7 0.19
19 13 0.36
20 5 0.14
21 11 0.31
ACGTcount: A:0.59, C:0.00, G:0.03, T:0.38
Consensus pattern (19 bp):
AAATTAAAAATATTATAAT
Found at i:515354 original size:21 final size:21
Alignment explanation
Indices: 515296--515365 Score: 60
Period size: 21 Copynumber: 3.4 Consensus size: 21
515286 ATTAAATTAC
515296 AAATTAAAGAATATTA-AT--T
1 AAATTAAA-AATATTATATAAT
* *
515315 TAATTAAAAAT-GTATTATAAT
1 AAATTAAAAATATTA-TATAAT
515336 AAATTAAAAATATTATATAA-
1 AAATTAAAAATATTATATAAT
515356 AAATATAAAA
1 AAAT-TAAAA
515366 TTAATTTTTT
Statistics
Matches: 41, Mismatches: 4, Indels: 10
0.75 0.07 0.18
Matches are distributed among these distances:
17 2 0.05
18 3 0.07
19 9 0.22
20 4 0.10
21 21 0.51
22 2 0.05
ACGTcount: A:0.61, C:0.00, G:0.03, T:0.36
Consensus pattern (21 bp):
AAATTAAAAATATTATATAAT
Found at i:515633 original size:39 final size:40
Alignment explanation
Indices: 515558--515638 Score: 119
Period size: 39 Copynumber: 2.0 Consensus size: 40
515548 ATTTTGGTGT
515558 TTTAATTTCTATATGAAAAAAAAATGTTTTAACTTTTTTTTC
1 TTTAATTTCTATATG--AAAAAAATGTTTTAACTTTTTTTTC
* *
515600 TTTAATTTTTATATG-AAAAAATGTTTTACCTTTTTTTTC
1 TTTAATTTCTATATGAAAAAAATGTTTTAACTTTTTTTTC
515639 GATTATAGAC
Statistics
Matches: 37, Mismatches: 2, Indels: 3
0.88 0.05 0.07
Matches are distributed among these distances:
39 23 0.62
42 14 0.38
ACGTcount: A:0.32, C:0.07, G:0.05, T:0.56
Consensus pattern (40 bp):
TTTAATTTCTATATGAAAAAAATGTTTTAACTTTTTTTTC
Found at i:515842 original size:4 final size:4
Alignment explanation
Indices: 515835--515869 Score: 70
Period size: 4 Copynumber: 8.8 Consensus size: 4
515825 TCCTCTCTCT
515835 TTTA TTTA TTTA TTTA TTTA TTTA TTTA TTTA TTT
1 TTTA TTTA TTTA TTTA TTTA TTTA TTTA TTTA TTT
515870 TTCTTTTAGT
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 31 1.00
ACGTcount: A:0.23, C:0.00, G:0.00, T:0.77
Consensus pattern (4 bp):
TTTA
Found at i:516005 original size:10 final size:10
Alignment explanation
Indices: 515990--516020 Score: 53
Period size: 10 Copynumber: 3.0 Consensus size: 10
515980 ATGTGACTTC
515990 TCTTTTTTTT
1 TCTTTTTTTT
516000 TCTTTTTTTTT
1 TC-TTTTTTTT
516011 TCTTTTTTTT
1 TCTTTTTTTT
516021 AAATTAAACT
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:0.00, C:0.10, G:0.00, T:0.90
Consensus pattern (10 bp):
TCTTTTTTTT
Found at i:516008 original size:11 final size:11
Alignment explanation
Indices: 515987--516020 Score: 59
Period size: 11 Copynumber: 3.0 Consensus size: 11
515977 TAAATGTGAC
515987 TTCTCTTTTTTT
1 TTCT-TTTTTTT
515999 TTCTTTTTTTT
1 TTCTTTTTTTT
516010 TTCTTTTTTTT
1 TTCTTTTTTTT
516021 AAATTAAACT
Statistics
Matches: 22, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
11 18 0.82
12 4 0.18
ACGTcount: A:0.00, C:0.12, G:0.00, T:0.88
Consensus pattern (11 bp):
TTCTTTTTTTT
Found at i:516757 original size:3 final size:3
Alignment explanation
Indices: 516745--516777 Score: 57
Period size: 3 Copynumber: 11.0 Consensus size: 3
516735 TAATAATAAT
*
516745 AAG AAA AAG AAG AAG AAG AAG AAG AAG AAG AAG
1 AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG
516778 GAAGTTATGG
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:0.70, C:0.00, G:0.30, T:0.00
Consensus pattern (3 bp):
AAG
Found at i:518492 original size:18 final size:19
Alignment explanation
Indices: 518463--518499 Score: 58
Period size: 18 Copynumber: 2.0 Consensus size: 19
518453 TCAATTAAAC
518463 AATATGATTAAGAATATCT
1 AATATGATTAAGAATATCT
*
518482 AATAT-ATTAAGTATATCT
1 AATATGATTAAGAATATCT
518500 TATGAAGTAA
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
18 12 0.71
19 5 0.29
ACGTcount: A:0.46, C:0.05, G:0.08, T:0.41
Consensus pattern (19 bp):
AATATGATTAAGAATATCT
Found at i:518656 original size:22 final size:22
Alignment explanation
Indices: 518631--518672 Score: 59
Period size: 22 Copynumber: 1.9 Consensus size: 22
518621 TTTTTTTTTT
518631 TAAAT-TTAATTATAAAAATATA
1 TAAATATT-ATTATAAAAATATA
*
518653 TAAATATTATTTTAAAAATA
1 TAAATATTATTATAAAAATA
518673 ATATTTTAAT
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
22 16 0.89
23 2 0.11
ACGTcount: A:0.57, C:0.00, G:0.00, T:0.43
Consensus pattern (22 bp):
TAAATATTATTATAAAAATATA
Found at i:520037 original size:20 final size:18
Alignment explanation
Indices: 520009--520047 Score: 51
Period size: 20 Copynumber: 2.1 Consensus size: 18
519999 TAGATTTAAT
*
520009 TATTTATATATTATATATCA
1 TATTCATATA-TAT-TATCA
520029 TATTCATATATATTATCA
1 TATTCATATATATTATCA
520047 T
1 T
520048 GTAATCGAAG
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
18 6 0.33
19 3 0.17
20 9 0.50
ACGTcount: A:0.38, C:0.08, G:0.00, T:0.54
Consensus pattern (18 bp):
TATTCATATATATTATCA
Found at i:520280 original size:32 final size:33
Alignment explanation
Indices: 520238--520312 Score: 95
Period size: 32 Copynumber: 2.4 Consensus size: 33
520228 TGAGATATTT
*
520238 TTTAT-TTATAT-AAATTTT-AATATTTTAATAA
1 TTTATATTATATAAAATTTTAAATATATTAAT-A
*
520269 TTTATATTATATAAAATTTTAAATATATTCATA
1 TTTATATTATATAAAATTTTAAATATATTAATA
520302 TTT-TATTATAT
1 TTTATATTATAT
520313 TTAATTATAT
Statistics
Matches: 39, Mismatches: 2, Indels: 5
0.85 0.04 0.11
Matches are distributed among these distances:
31 5 0.13
32 14 0.36
33 11 0.28
34 9 0.23
ACGTcount: A:0.41, C:0.01, G:0.00, T:0.57
Consensus pattern (33 bp):
TTTATATTATATAAAATTTTAAATATATTAATA
Found at i:520307 original size:34 final size:31
Alignment explanation
Indices: 520237--520312 Score: 91
Period size: 34 Copynumber: 2.4 Consensus size: 31
520227 TTGAGATATT
*
520237 TTTTATTTATATAAATTTTAATATTTTAATA
1 TTTTATTTATATAAATTTTAATATATTAATA
* *
520268 ATTTATATTATATAAAATTTTAAATATATTCATA
1 TTTTAT-TTATAT-AAATTTT-AATATATTAATA
520302 TTTTA-TTATAT
1 TTTTATTTATAT
520313 TTAATTATAT
Statistics
Matches: 38, Mismatches: 4, Indels: 5
0.81 0.09 0.11
Matches are distributed among these distances:
31 5 0.13
32 12 0.32
33 7 0.18
34 14 0.37
ACGTcount: A:0.41, C:0.01, G:0.00, T:0.58
Consensus pattern (31 bp):
TTTTATTTATATAAATTTTAATATATTAATA
Found at i:520620 original size:2 final size:2
Alignment explanation
Indices: 520613--520639 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
520603 TGTAAGACAT
520613 TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA T
520640 TTGGTATTTA
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 25 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:521509 original size:19 final size:19
Alignment explanation
Indices: 521472--521510 Score: 51
Period size: 19 Copynumber: 2.1 Consensus size: 19
521462 AATTTTACCA
* * *
521472 TATTATTTCATACTCAAAT
1 TATTATTTAATAATAAAAT
521491 TATTATTTAATAATAAAAT
1 TATTATTTAATAATAAAAT
521510 T
1 T
521511 TTTTTATTTA
Statistics
Matches: 17, Mismatches: 3, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
19 17 1.00
ACGTcount: A:0.44, C:0.08, G:0.00, T:0.49
Consensus pattern (19 bp):
TATTATTTAATAATAAAAT
Found at i:521588 original size:21 final size:20
Alignment explanation
Indices: 521558--521599 Score: 57
Period size: 21 Copynumber: 2.0 Consensus size: 20
521548 AATAAATTTT
* *
521558 TAATATTTTAATATTTTTAAA
1 TAATAATTTAA-ATTTATAAA
521579 TAATAATTTAAATTTATAAA
1 TAATAATTTAAATTTATAAA
521599 T
1 T
521600 TATATTAAAA
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
20 9 0.47
21 10 0.53
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (20 bp):
TAATAATTTAAATTTATAAA
Found at i:522319 original size:21 final size:21
Alignment explanation
Indices: 522285--522332 Score: 66
Period size: 21 Copynumber: 2.4 Consensus size: 21
522275 TATTTTAATT
522285 TAAAT-TTAATTATAAAATATA
1 TAAATATTAATTATAAAA-ATA
522306 TAAATATTAA-TATAAAAATA
1 TAAATATTAATTATAAAAATA
522326 -AAATATT
1 TAAATATT
522333 TTATTATTTT
Statistics
Matches: 26, Mismatches: 0, Indels: 4
0.87 0.00 0.13
Matches are distributed among these distances:
19 7 0.27
20 3 0.12
21 12 0.46
22 4 0.15
ACGTcount: A:0.60, C:0.00, G:0.00, T:0.40
Consensus pattern (21 bp):
TAAATATTAATTATAAAAATA
Found at i:522340 original size:27 final size:27
Alignment explanation
Indices: 522267--522340 Score: 69
Period size: 27 Copynumber: 2.7 Consensus size: 27
522257 ATTATTTATT
* *
522267 AAATAAAATATTTTAATT-TAAATTTAA
1 AAATAAAATATTTT-ATTATTAATATAA
** * * *
522294 TTATAAAATATATAAATATTAATATAA
1 AAATAAAATATTTTATTATTAATATAA
522321 AAATAAAATATTTTATTATT
1 AAATAAAATATTTTATTATT
522341 TTAATATATT
Statistics
Matches: 34, Mismatches: 12, Indels: 2
0.71 0.25 0.04
Matches are distributed among these distances:
26 2 0.06
27 32 0.94
ACGTcount: A:0.55, C:0.00, G:0.00, T:0.45
Consensus pattern (27 bp):
AAATAAAATATTTTATTATTAATATAA
Found at i:522391 original size:6 final size:6
Alignment explanation
Indices: 522380--522417 Score: 76
Period size: 6 Copynumber: 6.3 Consensus size: 6
522370 AATAAAATAA
522380 AATTTT AATTTT AATTTT AATTTT AATTTT AATTTT AA
1 AATTTT AATTTT AATTTT AATTTT AATTTT AATTTT AA
522418 AATTTCTTTA
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 32 1.00
ACGTcount: A:0.37, C:0.00, G:0.00, T:0.63
Consensus pattern (6 bp):
AATTTT
Found at i:522887 original size:42 final size:40
Alignment explanation
Indices: 522783--522875 Score: 108
Period size: 42 Copynumber: 2.4 Consensus size: 40
522773 TTAAAAATAA
522783 AAAATTAAA-TTAAAT-AA-AAA-TTA--ATTTTATAAAT
1 AAAATTAAACTTAAATAAATAAATTTATTATTTTATAAAT
* *
522817 AATATTAAATTTAAATAAATAAATTTATTATTTATATAAAT
1 AAAATTAAACTTAAATAAATAAATTTATTATTT-TATAAAT
522858 AAAAATTAAACTTAAATA
1 -AAAATTAAACTTAAATA
522876 TTTAATATTA
Statistics
Matches: 48, Mismatches: 3, Indels: 8
0.81 0.05 0.14
Matches are distributed among these distances:
34 8 0.17
35 6 0.12
36 2 0.04
37 3 0.06
38 3 0.06
40 4 0.08
41 7 0.15
42 15 0.31
ACGTcount: A:0.59, C:0.01, G:0.00, T:0.40
Consensus pattern (40 bp):
AAAATTAAACTTAAATAAATAAATTTATTATTTTATAAAT
Found at i:523558 original size:23 final size:21
Alignment explanation
Indices: 523524--523567 Score: 61
Period size: 23 Copynumber: 2.0 Consensus size: 21
523514 TAATATTTTA
523524 AATATAATTATATATAAAAAT
1 AATATAATTATATATAAAAAT
*
523545 AATATATATATATATATACAAAT
1 AATATA-AT-TATATATAAAAAT
523568 CTTTGTAAGT
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
21 6 0.30
22 2 0.10
23 12 0.60
ACGTcount: A:0.59, C:0.02, G:0.00, T:0.39
Consensus pattern (21 bp):
AATATAATTATATATAAAAAT
Found at i:523740 original size:15 final size:16
Alignment explanation
Indices: 523722--523785 Score: 76
Period size: 16 Copynumber: 4.1 Consensus size: 16
523712 AAATATATAT
523722 ATTAAATTTAAAA-AA
1 ATTAAATTTAAAATAA
523737 ATTAAATTTAAAATAA
1 ATTAAATTTAAAATAA
* *
523753 TTTTAATTTAAAATAA
1 ATTAAATTTAAAATAA
* * *
523769 TTTAAATCTGAAATAA
1 ATTAAATTTAAAATAA
523785 A
1 A
523786 ATAATTTTAT
Statistics
Matches: 42, Mismatches: 6, Indels: 1
0.86 0.12 0.02
Matches are distributed among these distances:
15 13 0.31
16 29 0.69
ACGTcount: A:0.58, C:0.02, G:0.02, T:0.39
Consensus pattern (16 bp):
ATTAAATTTAAAATAA
Found at i:523762 original size:16 final size:16
Alignment explanation
Indices: 523723--523775 Score: 81
Period size: 16 Copynumber: 3.4 Consensus size: 16
523713 AATATATATA
*
523723 TTAAATTTAAAA-AAA
1 TTAAATTTAAAATAAT
523738 TTAAATTTAAAATAAT
1 TTAAATTTAAAATAAT
*
523754 TTTAATTTAAAATAAT
1 TTAAATTTAAAATAAT
523770 TTAAAT
1 TTAAAT
523776 CTGAAATAAA
Statistics
Matches: 34, Mismatches: 3, Indels: 1
0.89 0.08 0.03
Matches are distributed among these distances:
15 12 0.35
16 22 0.65
ACGTcount: A:0.57, C:0.00, G:0.00, T:0.43
Consensus pattern (16 bp):
TTAAATTTAAAATAAT
Found at i:524884 original size:19 final size:20
Alignment explanation
Indices: 524850--524888 Score: 62
Period size: 19 Copynumber: 2.0 Consensus size: 20
524840 TATTATAAAA
524850 CATAATATTATAATTATTTT
1 CATAATATTATAATTATTTT
*
524870 CATAAT-TTTTAATTATTTT
1 CATAATATTATAATTATTTT
524889 AAAAAGTTTA
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
19 12 0.67
20 6 0.33
ACGTcount: A:0.36, C:0.05, G:0.00, T:0.59
Consensus pattern (20 bp):
CATAATATTATAATTATTTT
Found at i:525325 original size:21 final size:20
Alignment explanation
Indices: 525301--525339 Score: 60
Period size: 21 Copynumber: 1.9 Consensus size: 20
525291 ATAAAAAAAG
525301 AAATTATAAATATTAATAATT
1 AAATTATAAAT-TTAATAATT
*
525322 AAATTTTAAATTTAATAA
1 AAATTATAAATTTAATAA
525340 ATATTAATTT
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
20 7 0.41
21 10 0.59
ACGTcount: A:0.56, C:0.00, G:0.00, T:0.44
Consensus pattern (20 bp):
AAATTATAAATTTAATAATT
Found at i:525360 original size:15 final size:15
Alignment explanation
Indices: 525306--525356 Score: 54
Period size: 14 Copynumber: 3.5 Consensus size: 15
525296 AAAAGAAATT
525306 ATAAATATTAA--TA
1 ATAAATATTAATTTA
*
525319 ATTAAATTTTAAATTTA
1 A-TAAATATT-AATTTA
525336 ATAAATATTAATTTA
1 ATAAATATTAATTTA
525351 A-AAATA
1 ATAAATA
525357 ATTATATAAA
Statistics
Matches: 32, Mismatches: 2, Indels: 7
0.78 0.05 0.17
Matches are distributed among these distances:
13 1 0.03
14 12 0.38
15 9 0.28
16 7 0.22
17 3 0.09
ACGTcount: A:0.57, C:0.00, G:0.00, T:0.43
Consensus pattern (15 bp):
ATAAATATTAATTTA
Found at i:525788 original size:21 final size:20
Alignment explanation
Indices: 525764--525808 Score: 56
Period size: 20 Copynumber: 2.2 Consensus size: 20
525754 ATTTATATAA
* *
525764 ATTTAATAGATACAAATTATT
1 ATTTAATA-ATAAAAAATATT
525785 ATTTAATAATAAAAAATATT
1 ATTTAATAATAAAAAATATT
525805 -TTTA
1 ATTTA
525809 TTTAAATTTA
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
19 4 0.18
20 10 0.45
21 8 0.36
ACGTcount: A:0.51, C:0.02, G:0.02, T:0.44
Consensus pattern (20 bp):
ATTTAATAATAAAAAATATT
Found at i:525820 original size:33 final size:33
Alignment explanation
Indices: 525783--525862 Score: 135
Period size: 33 Copynumber: 2.4 Consensus size: 33
525773 ATACAAATTA
525783 TTATT-TAATAATAAAAAATATTTTTATTTAAAT
1 TTATTATAA-AATAAAAAATATTTTTATTTAAAT
*
525816 TTATTATAAAATATAAAATATTTTTATTTAAAT
1 TTATTATAAAATAAAAAATATTTTTATTTAAAT
525849 TTATTATAAAATAA
1 TTATTATAAAATAA
525863 TATAATAAAT
Statistics
Matches: 44, Mismatches: 2, Indels: 2
0.92 0.04 0.04
Matches are distributed among these distances:
33 41 0.93
34 3 0.07
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (33 bp):
TTATTATAAAATAAAAAATATTTTTATTTAAAT
Found at i:525937 original size:51 final size:50
Alignment explanation
Indices: 525866--525975 Score: 150
Period size: 51 Copynumber: 2.2 Consensus size: 50
525856 AAAATAATAT
* * * * *
525866 AATAAATAATAATATAAACTTTTAAATTAATTTAAATCTAA-TTAATTTCA
1 AATAAAAAATAAAATAAACTTTAAAATTAATTTAAATATAACTAAATTT-A
525916 AATAAAAAATTAAAATAAACTTTAAAATTAATTTAAATATAACTAAATTTA
1 AATAAAAAA-TAAAATAAACTTTAAAATTAATTTAAATATAACTAAATTTA
525967 AATAAAAAA
1 AATAAAAAA
525976 AAACTTTAAT
Statistics
Matches: 53, Mismatches: 5, Indels: 3
0.87 0.08 0.05
Matches are distributed among these distances:
50 8 0.15
51 39 0.74
52 6 0.11
ACGTcount: A:0.59, C:0.05, G:0.00, T:0.36
Consensus pattern (50 bp):
AATAAAAAATAAAATAAACTTTAAAATTAATTTAAATATAACTAAATTTA
Found at i:525952 original size:18 final size:17
Alignment explanation
Indices: 525875--525953 Score: 54
Period size: 18 Copynumber: 4.6 Consensus size: 17
525865 TAATAAATAA
* *
525875 TAATATAAACTTTTAAAT
1 TAATTTAAA-TTTAAAAT
*
525893 TAATTTAAATCT--AAT
1 TAATTTAAATTTAAAAT
**
525908 TAATTTCAAATAAAAAAT
1 TAATTT-AAATTTAAAAT
**
525926 TAAAATAAACTTTAAAAT
1 TAATTTAAA-TTTAAAAT
525944 TAATTTAAAT
1 TAATTTAAAT
525954 ATAACTAAAT
Statistics
Matches: 47, Mismatches: 10, Indels: 9
0.71 0.15 0.14
Matches are distributed among these distances:
15 9 0.19
16 4 0.09
17 6 0.13
18 28 0.60
ACGTcount: A:0.54, C:0.05, G:0.00, T:0.41
Consensus pattern (17 bp):
TAATTTAAATTTAAAAT
Found at i:526244 original size:17 final size:17
Alignment explanation
Indices: 526209--526256 Score: 55
Period size: 17 Copynumber: 2.9 Consensus size: 17
526199 CGATTTAAAT
* **
526209 TTAATAAGTTAAAAAAA
1 TTAATAATTTAAATTAA
526226 TTAATAATTTAAATTAA
1 TTAATAATTTAAATTAA
526243 TT-A-AATTTAAATTA
1 TTAATAATTTAAATTA
526257 TTATTTACAT
Statistics
Matches: 28, Mismatches: 3, Indels: 2
0.85 0.09 0.06
Matches are distributed among these distances:
15 11 0.39
16 1 0.04
17 16 0.57
ACGTcount: A:0.56, C:0.00, G:0.02, T:0.42
Consensus pattern (17 bp):
TTAATAATTTAAATTAA
Found at i:526251 original size:15 final size:13
Alignment explanation
Indices: 526223--526256 Score: 50
Period size: 15 Copynumber: 2.5 Consensus size: 13
526213 TAAGTTAAAA
526223 AAATTAATAATTT
1 AAATTAATAATTT
526236 AAATTAATTAAATTT
1 AAATTAA-T-AATTT
526251 AAATTA
1 AAATTA
526257 TTATTTACAT
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
13 7 0.37
14 1 0.05
15 11 0.58
ACGTcount: A:0.56, C:0.00, G:0.00, T:0.44
Consensus pattern (13 bp):
AAATTAATAATTT
Found at i:526951 original size:2 final size:2
Alignment explanation
Indices: 526944--526968 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
526934 TAGTGAGAAC
526944 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 T
526969 CTTTCTATAA
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:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:529199 original size:20 final size:20
Alignment explanation
Indices: 529158--529199 Score: 50
Period size: 20 Copynumber: 2.1 Consensus size: 20
529148 ATCATGATTA
*
529158 ATAAAATTTTACATAAATAT
1 ATAAAATTTTACATAAAAAT
*
529178 ATAATATTTTA-ATAATAAAT
1 ATAAAATTTTACATAA-AAAT
529198 AT
1 AT
529200 GATAATAACA
Statistics
Matches: 19, Mismatches: 2, Indels: 2
0.83 0.09 0.09
Matches are distributed among these distances:
19 4 0.21
20 15 0.79
ACGTcount: A:0.55, C:0.02, G:0.00, T:0.43
Consensus pattern (20 bp):
ATAAAATTTTACATAAAAAT
Found at i:529317 original size:4 final size:4
Alignment explanation
Indices: 529308--529335 Score: 56
Period size: 4 Copynumber: 7.0 Consensus size: 4
529298 CAGGTGGGGA
529308 AAAG AAAG AAAG AAAG AAAG AAAG AAAG
1 AAAG AAAG AAAG AAAG AAAG AAAG AAAG
529336 GAGAGAAGGT
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 24 1.00
ACGTcount: A:0.75, C:0.00, G:0.25, T:0.00
Consensus pattern (4 bp):
AAAG
Found at i:529501 original size:3 final size:3
Alignment explanation
Indices: 529493--529559 Score: 107
Period size: 3 Copynumber: 22.3 Consensus size: 3
529483 CTCTCTTCAT
* * *
529493 TTA TTA TTA CTA CTA CTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
529541 TTA TTA TTA TTA TTA TTA T
1 TTA TTA TTA TTA TTA TTA T
529560 GTGGTGTGTG
Statistics
Matches: 62, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
3 62 1.00
ACGTcount: A:0.33, C:0.04, G:0.00, T:0.63
Consensus pattern (3 bp):
TTA
Found at i:529867 original size:37 final size:36
Alignment explanation
Indices: 529800--529871 Score: 83
Period size: 37 Copynumber: 2.0 Consensus size: 36
529790 ATATAATTAA
* *
529800 ATTTAAATTATTATTTATATAATAAAATAATATTTTT
1 ATTTAAATTATAATTTAAATAATAAAATAAT-TTTTT
* *
529837 ATTTAAATT-TAATTATAAATATTAATATAATTTTT
1 ATTTAAATTATAATT-TAAATAATAAAATAATTTTT
529872 AAATAACAAA
Statistics
Matches: 30, Mismatches: 4, Indels: 3
0.81 0.11 0.08
Matches are distributed among these distances:
36 8 0.27
37 22 0.73
ACGTcount: A:0.46, C:0.00, G:0.00, T:0.54
Consensus pattern (36 bp):
ATTTAAATTATAATTTAAATAATAAAATAATTTTTT
Found at i:529954 original size:15 final size:14
Alignment explanation
Indices: 529925--529951 Score: 54
Period size: 14 Copynumber: 1.9 Consensus size: 14
529915 ATTTAAATTT
529925 AAATAAAAATTTTA
1 AAATAAAAATTTTA
529939 AAATAAAAATTTT
1 AAATAAAAATTTT
529952 TAATTTTAAT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 13 1.00
ACGTcount: A:0.63, C:0.00, G:0.00, T:0.37
Consensus pattern (14 bp):
AAATAAAAATTTTA
Found at i:529977 original size:19 final size:18
Alignment explanation
Indices: 529955--530019 Score: 80
Period size: 17 Copynumber: 3.7 Consensus size: 18
529945 AAATTTTTAA
529955 TTTTAATATATTAATATAT
1 TTTTAATATATT-ATATAT
*
529974 TTTTATTATATTA-ATAT
1 TTTTAATATATTATATAT
529991 TTTTAATAT-TTATATAT
1 TTTTAATATATTATATAT
* *
530008 TTATATTATATT
1 TTTTAATATATT
530020 GATTTTATAT
Statistics
Matches: 40, Mismatches: 4, Indels: 5
0.82 0.08 0.10
Matches are distributed among these distances:
16 3 0.08
17 23 0.57
18 3 0.08
19 11 0.28
ACGTcount: A:0.37, C:0.00, G:0.00, T:0.63
Consensus pattern (18 bp):
TTTTAATATATTATATAT
Found at i:533167 original size:13 final size:13
Alignment explanation
Indices: 533149--533173 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
533139 GTGATGACAA
533149 AAAAAATTAAAAT
1 AAAAAATTAAAAT
533162 AAAAAATTAAAA
1 AAAAAATTAAAA
533174 CGTCGTGATT
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:0.80, C:0.00, G:0.00, T:0.20
Consensus pattern (13 bp):
AAAAAATTAAAAT
Found at i:536962 original size:14 final size:14
Alignment explanation
Indices: 536940--536973 Score: 50
Period size: 14 Copynumber: 2.4 Consensus size: 14
536930 AAGTTTAATT
* *
536940 ATAAAAATATATAA
1 ATAATAATATAAAA
536954 ATAATAATATAAAA
1 ATAATAATATAAAA
536968 ATAATA
1 ATAATA
536974 TTATGTATAG
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
14 18 1.00
ACGTcount: A:0.71, C:0.00, G:0.00, T:0.29
Consensus pattern (14 bp):
ATAATAATATAAAA
Found at i:537800 original size:17 final size:17
Alignment explanation
Indices: 537757--537805 Score: 53
Period size: 17 Copynumber: 2.8 Consensus size: 17
537747 TAAATTACTG
* *
537757 TTTAAATAAAAATTTATT
1 TTTAATTAAAAA-TTATA
537775 TTATAATTAAAAATTATA
1 TT-TAATTAAAAATTATA
*
537793 TTTAATTATAAAT
1 TTTAATTAAAAAT
537806 ATAATATAAA
Statistics
Matches: 27, Mismatches: 3, Indels: 3
0.82 0.09 0.09
Matches are distributed among these distances:
17 10 0.37
18 8 0.30
19 9 0.33
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (17 bp):
TTTAATTAAAAATTATA
Found at i:537804 original size:19 final size:18
Alignment explanation
Indices: 537761--537804 Score: 52
Period size: 19 Copynumber: 2.3 Consensus size: 18
537751 TTACTGTTTA
*
537761 AATAAAAATTTATTTTAT
1 AATAAAAATTTATTTAAT
537779 AATTAAAAATTATATTTAAT
1 AA-TAAAAATT-TATTTAAT
*
537799 TATAAA
1 AATAAA
537805 TATAATATAA
Statistics
Matches: 22, Mismatches: 2, Indels: 3
0.81 0.07 0.11
Matches are distributed among these distances:
18 2 0.09
19 12 0.55
20 8 0.36
ACGTcount: A:0.55, C:0.00, G:0.00, T:0.45
Consensus pattern (18 bp):
AATAAAAATTTATTTAAT
Found at i:542297 original size:26 final size:28
Alignment explanation
Indices: 542251--542333 Score: 88
Period size: 26 Copynumber: 3.2 Consensus size: 28
542241 TAAATAATTT
*
542251 TAATA-TAAATTTATATATTTATAT-TA
1 TAATATTATATTTATATATTTATATATA
*
542277 TAATATTATATTTATGT-TTTATATATA
1 TAATATTATATTTATATATTTATATATA
**
542304 TAA-ATTATA-TTATATATAAATATATA
1 TAATATTATATTTATATATTTATATATA
542330 -AATA
1 TAATA
542334 ACATATATTA
Statistics
Matches: 48, Mismatches: 5, Indels: 8
0.79 0.08 0.13
Matches are distributed among these distances:
25 7 0.15
26 27 0.56
27 14 0.29
ACGTcount: A:0.47, C:0.00, G:0.01, T:0.52
Consensus pattern (28 bp):
TAATATTATATTTATATATTTATATATA
Found at i:542305 original size:19 final size:18
Alignment explanation
Indices: 542262--542321 Score: 59
Period size: 19 Copynumber: 3.2 Consensus size: 18
542252 AATATAAATT
542262 TATATATTTATATTATAA
1 TATATATTTATATTATAA
* *
542280 TATTATATTTATGTTTTATA
1 TA-TATATTTATATTATA-A
*
542300 TATATAAATTATATTAT-A
1 TATAT-ATTTATATTATAA
542318 TATA
1 TATA
542322 AATATATAAA
Statistics
Matches: 34, Mismatches: 5, Indels: 6
0.76 0.11 0.13
Matches are distributed among these distances:
18 7 0.21
19 16 0.47
20 11 0.32
ACGTcount: A:0.42, C:0.00, G:0.02, T:0.57
Consensus pattern (18 bp):
TATATATTTATATTATAA
Found at i:542319 original size:16 final size:15
Alignment explanation
Indices: 542298--542344 Score: 55
Period size: 16 Copynumber: 3.2 Consensus size: 15
542288 TTATGTTTTA
542298 TATATATAAATTATAT
1 TATATATAAA-TATAT
542314 TATATATAAATATA-
1 TATATATAAATATAT
542328 TA-A-ATAACATATAT
1 TATATATAA-ATATAT
542342 TAT
1 TAT
542345 TTAATTTAAA
Statistics
Matches: 28, Mismatches: 0, Indels: 7
0.80 0.00 0.20
Matches are distributed among these distances:
12 4 0.14
13 6 0.21
14 4 0.14
15 4 0.14
16 10 0.36
ACGTcount: A:0.53, C:0.02, G:0.00, T:0.45
Consensus pattern (15 bp):
TATATATAAATATAT
Found at i:542415 original size:29 final size:27
Alignment explanation
Indices: 542382--542446 Score: 69
Period size: 29 Copynumber: 2.3 Consensus size: 27
542372 AGTTTCCTAC
*
542382 TTTAAATATACAAGTAAAATTCATCTATT
1 TTTAAATATAAAAGTAAAATTCAT-T-TT
* *
542411 TTT-AATATTAAAAGTAATATTTATTTT
1 TTTAAATA-TAAAAGTAAAATTCATTTT
542438 TTTAAATAT
1 TTTAAATAT
542447 TTTTTTTATT
Statistics
Matches: 31, Mismatches: 3, Indels: 6
0.77 0.08 0.15
Matches are distributed among these distances:
27 6 0.19
28 9 0.29
29 16 0.52
ACGTcount: A:0.43, C:0.05, G:0.03, T:0.49
Consensus pattern (27 bp):
TTTAAATATAAAAGTAAAATTCATTTT
Found at i:542566 original size:17 final size:17
Alignment explanation
Indices: 542529--542563 Score: 54
Period size: 16 Copynumber: 2.1 Consensus size: 17
542519 TTAAATTAAT
*
542529 AATTTATATTTTAAATA
1 AATTTATATTATAAATA
542546 AATTTAT-TTATAAATA
1 AATTTATATTATAAATA
542562 AA
1 AA
542564 ATTAAAAATT
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
16 10 0.59
17 7 0.41
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (17 bp):
AATTTATATTATAAATA
Found at i:542798 original size:23 final size:22
Alignment explanation
Indices: 542771--542870 Score: 73
Period size: 21 Copynumber: 4.5 Consensus size: 22
542761 AATCTGATAA
542771 TATAATTATATAAATATAATATT
1 TATAATTATATAAATATAATA-T
* *
542794 TATAAAATTATAAAAATATGATAT
1 TAT--AATTATATAAATATAATAT
* * *
542818 AAT-ATCATATAAATATATTAT
1 TATAATTATATAAATATAATAT
*
542839 TA-AAATATATATAATATAA-AT
1 TATAATTATATA-AATATAATAT
542860 TATTAA-TATAT
1 TA-TAATTATAT
542871 CATAATTAAT
Statistics
Matches: 60, Mismatches: 11, Indels: 13
0.71 0.13 0.15
Matches are distributed among these distances:
21 25 0.42
22 11 0.18
23 5 0.08
24 3 0.05
25 16 0.27
ACGTcount: A:0.55, C:0.01, G:0.01, T:0.43
Consensus pattern (22 bp):
TATAATTATATAAATATAATAT
Found at i:542868 original size:35 final size:35
Alignment explanation
Indices: 542777--542875 Score: 93
Period size: 35 Copynumber: 2.9 Consensus size: 35
542767 ATAATATAAT
542777 TATATA-AATATAATATT-TATAA-A-ATTATAAAAA
1 TATATATAATATAA-ATTAT-TAATATATTATAAAAA
* * *
542810 TATGATATAATAT-CA-TATAAATATATTATTAAAA
1 TAT-ATATAATATAAATTATTAATATATTATAAAAA
*
542844 TATATATAATATAAATTATTAATATATCATAA
1 TATATATAATATAAATTATTAATATATTATAA
542876 TTAATAAAAA
Statistics
Matches: 52, Mismatches: 7, Indels: 12
0.73 0.10 0.17
Matches are distributed among these distances:
32 3 0.06
33 15 0.29
34 16 0.31
35 18 0.35
ACGTcount: A:0.56, C:0.02, G:0.01, T:0.41
Consensus pattern (35 bp):
TATATATAATATAAATTATTAATATATTATAAAAA
Found at i:542880 original size:27 final size:25
Alignment explanation
Indices: 542818--542895 Score: 83
Period size: 24 Copynumber: 3.2 Consensus size: 25
542808 AATATGATAT
*
542818 AATATCATATAA-ATATATTATTAA
1 AATATCATATAATATAAATTATTAA
542842 AATAT-ATATAATATAAATTATTAA
1 AATATCATATAATATAAATTATTAA
* *
542866 TATATCATAATTAATA-AAAATA-TAA
1 AATATCAT-A-TAATATAAATTATTAA
542891 AATAT
1 AATAT
542896 TTTAAATATA
Statistics
Matches: 46, Mismatches: 4, Indels: 7
0.81 0.07 0.12
Matches are distributed among these distances:
23 6 0.13
24 20 0.43
25 9 0.20
26 6 0.13
27 5 0.11
ACGTcount: A:0.58, C:0.03, G:0.00, T:0.40
Consensus pattern (25 bp):
AATATCATATAATATAAATTATTAA
Found at i:542889 original size:38 final size:37
Alignment explanation
Indices: 542830--542935 Score: 85
Period size: 38 Copynumber: 2.8 Consensus size: 37
542820 TATCATATAA
* *
542830 ATATATTATTAA-AATATATATAATATAAATTATTAAT
1 ATATATAATTAATAA-AAATATAATATAAATTATTAAT
*
542867 ATATCATAATTAATAAAAATATAA-A-ATATT-TTAAAT
1 ATAT-ATAATTAATAAAAATATAATATAAATTATT-AAT
542903 ATAATTATAATTTAATAAAATATATAAATATAA
1 AT-A-TATAA-TTAATAAAA-ATAT-AATATAA
542936 TATAAAAATA
Statistics
Matches: 55, Mismatches: 4, Indels: 15
0.74 0.05 0.20
Matches are distributed among these distances:
35 2 0.04
36 9 0.16
37 10 0.18
38 24 0.44
39 6 0.11
40 2 0.04
41 1 0.02
42 1 0.02
ACGTcount: A:0.58, C:0.01, G:0.00, T:0.42
Consensus pattern (37 bp):
ATATATAATTAATAAAAATATAATATAAATTATTAAT
Found at i:542895 original size:83 final size:79
Alignment explanation
Indices: 542767--542935 Score: 184
Period size: 83 Copynumber: 2.1 Consensus size: 79
542757 ATTAAATCTG
* * *
542767 ATAATAT-AATTATATAAATATAATATTTATAAAATTATAAAAATATGATATAATATCATATAAA
1 ATAATATAAATTATATAAATATAATATTAATAAAAATATAAAAATATGATA-AATATAAT-TAAA
*
542831 TATATTATTAAAATATAT
64 -AT-TTAATAAAATATAT
* ** *
542849 ATAATATAAATTAT-TAATATATCATAATTAATAAAAATAT-AAAATATTTTAAATATAATTATA
1 ATAATATAAATTATATAA-ATATAAT-ATTAATAAAAATATAAAAATATGATAAATATAATTAAA
542912 ATTTAATAAAATATAT
64 ATTTAATAAAATATAT
542928 A-AATATAA
1 ATAATATAA
542936 TATAAAAATA
Statistics
Matches: 76, Mismatches: 8, Indels: 10
0.81 0.09 0.11
Matches are distributed among these distances:
78 7 0.09
79 14 0.18
80 2 0.03
81 3 0.04
82 17 0.22
83 21 0.28
84 12 0.16
ACGTcount: A:0.57, C:0.01, G:0.01, T:0.41
Consensus pattern (79 bp):
ATAATATAAATTATATAAATATAATATTAATAAAAATATAAAAATATGATAAATATAATTAAAAT
TTAATAAAATATAT
Found at i:542945 original size:58 final size:60
Alignment explanation
Indices: 542778--542946 Score: 143
Period size: 55 Copynumber: 2.8 Consensus size: 60
542768 TAATATAATT
* * * *
542778 ATATAAATATAATATTTATAAAATTATAAAAATATGATATAATATCATATAAATATATTATTAAA
1 ATATAATTATAAT-TTAATAAAA-TATATAAATAT-ATATAA-A-AATATAAATATATTATTAAA
* * *
542843 ATATATATAATATAAATTATTAATATATCAT-AAT-TA-ATAAAAATATAAA-ATATT-TT-AA
1 ATATA-AT--TATAATTTAATAAAATAT-ATAAATATATATAAAAATATAAATATATTATTAAA
542901 ATATAATTATAATTTAATAAAATATATAAATATAATATAAAAATAT
1 ATATAATTATAATTTAATAAAATATATAAATAT-ATATAAAAATAT
542947 GAATTATCAG
Statistics
Matches: 86, Mismatches: 10, Indels: 23
0.72 0.08 0.19
Matches are distributed among these distances:
54 2 0.02
55 18 0.21
56 1 0.01
57 3 0.03
58 17 0.20
59 2 0.02
60 5 0.06
61 7 0.08
62 1 0.01
63 4 0.05
64 1 0.01
65 6 0.07
66 7 0.08
67 7 0.08
68 5 0.06
ACGTcount: A:0.58, C:0.01, G:0.01, T:0.40
Consensus pattern (60 bp):
ATATAATTATAATTTAATAAAATATATAAATATATATAAAAATATAAATATATTATTAAA
Found at i:543505 original size:12 final size:12
Alignment explanation
Indices: 543476--543513 Score: 53
Period size: 12 Copynumber: 3.3 Consensus size: 12
543466 ATAATATATA
*
543476 TATATATATATG
1 TATATATGTATG
543488 -A-ATATGTATG
1 TATATATGTATG
543498 TATATATGTATG
1 TATATATGTATG
543510 TATA
1 TATA
543514 CAATTTCAAA
Statistics
Matches: 23, Mismatches: 1, Indels: 4
0.82 0.04 0.14
Matches are distributed among these distances:
10 8 0.35
11 2 0.09
12 13 0.57
ACGTcount: A:0.39, C:0.00, G:0.13, T:0.47
Consensus pattern (12 bp):
TATATATGTATG
Found at i:555417 original size:19 final size:19
Alignment explanation
Indices: 555388--555439 Score: 58
Period size: 19 Copynumber: 2.9 Consensus size: 19
555378 AAATCCCATA
555388 ATTTA-ATATTAATATTTT
1 ATTTATATATTAATATTTT
* *
555406 ATTTATATATTATTATTGT
1 ATTTATATATTAATATTTT
555425 A-TTATA-ATT-ATATTT
1 ATTTATATATTAATATTT
555440 AAAATATTTT
Statistics
Matches: 29, Mismatches: 4, Indels: 4
0.78 0.11 0.11
Matches are distributed among these distances:
16 4 0.14
17 3 0.10
18 10 0.34
19 12 0.41
ACGTcount: A:0.37, C:0.00, G:0.02, T:0.62
Consensus pattern (19 bp):
ATTTATATATTAATATTTT
Found at i:555551 original size:61 final size:58
Alignment explanation
Indices: 555436--555562 Score: 141
Period size: 61 Copynumber: 2.1 Consensus size: 58
555426 TTATAATTAT
*
555436 ATTTAAAATATTTTATATTTATATAAATTTTAATAATATTAATAATTAAAATTATAAAA
1 ATTTAAAATATTTTATATTTATATAAATTTTAATAATATTAATAACTAAAATTAT-AAA
* * * * *
555495 ATTT-AAATATATTTATATTATATTATATATTTTAAT-TTCTTACATAACTAATATTATTAA
1 ATTTAAAATAT-TTTATATT-TA-TATAAATTTTAATAATATTA-ATAACTAAAATTATAAA
555555 ATTTAAAA
1 ATTTAAAA
555563 CAACTTATGG
Statistics
Matches: 57, Mismatches: 6, Indels: 8
0.80 0.08 0.11
Matches are distributed among these distances:
58 6 0.11
59 12 0.21
60 12 0.21
61 27 0.47
ACGTcount: A:0.48, C:0.02, G:0.00, T:0.50
Consensus pattern (58 bp):
ATTTAAAATATTTTATATTTATATAAATTTTAATAATATTAATAACTAAAATTATAAA
Found at i:556089 original size:11 final size:11
Alignment explanation
Indices: 556057--556170 Score: 50
Period size: 11 Copynumber: 10.7 Consensus size: 11
556047 TAAAAAATTA
*
556057 AAATATAACAT
1 AAATATAATAT
*
556068 AAAAAATAATAT
1 -AAATATAATAT
*
556080 TAATATAATAT
1 AAATATAATAT
556091 AAATAT-ATA-
1 AAATATAATAT
*
556100 AATATTTTAA-A-
1 AA-A-TATAATAT
556111 AAATATAATAT
1 AAATATAATAT
556122 AAAT-T-AT-T
1 AAATATAATAT
*
556130 -AATATATTA-
1 AAATATAATAT
*
556139 AAAT-TTATAT
1 AAATATAATAT
556149 AAATATATATTAT
1 AAATATA-A-TAT
556162 AAATTATAA
1 AAA-TATAA
556171 AATTATATAT
Statistics
Matches: 77, Mismatches: 11, Indels: 27
0.67 0.10 0.23
Matches are distributed among these distances:
7 3 0.04
8 2 0.03
9 12 0.16
10 14 0.18
11 24 0.31
12 11 0.14
13 7 0.09
14 4 0.05
ACGTcount: A:0.60, C:0.01, G:0.00, T:0.39
Consensus pattern (11 bp):
AAATATAATAT
Found at i:556140 original size:30 final size:31
Alignment explanation
Indices: 556081--556157 Score: 99
Period size: 31 Copynumber: 2.6 Consensus size: 31
556071 AAATAATATT
*
556081 AATATAATATAAATATATAAATATTTTAAAA
1 AATATAATATAAATATATAAATATATTAAAA
*
556112 AATATAATATAAAT-TATTAATATATT--AA
1 AATATAATATAAATATATAAATATATTAAAA
*
556140 AAT-TTATATAAATATATA
1 AATATAATATAAATATATA
556158 TTATAAATTA
Statistics
Matches: 41, Mismatches: 4, Indels: 5
0.82 0.08 0.10
Matches are distributed among these distances:
27 9 0.22
28 8 0.20
30 10 0.24
31 14 0.34
ACGTcount: A:0.58, C:0.00, G:0.00, T:0.42
Consensus pattern (31 bp):
AATATAATATAAATATATAAATATATTAAAA
Found at i:556159 original size:22 final size:22
Alignment explanation
Indices: 556131--556180 Score: 68
Period size: 22 Copynumber: 2.3 Consensus size: 22
556121 TAAATTATTA
556131 ATATATTA-AAATTTATATAAA-T
1 ATATATTATAAA-TTATA-AAATT
556153 ATATATTATAAATTATAAAATT
1 ATATATTATAAATTATAAAATT
556175 ATATAT
1 ATATAT
556181 ATATTTATAT
Statistics
Matches: 26, Mismatches: 0, Indels: 4
0.87 0.00 0.13
Matches are distributed among these distances:
21 3 0.12
22 20 0.77
23 3 0.12
ACGTcount: A:0.54, C:0.00, G:0.00, T:0.46
Consensus pattern (22 bp):
ATATATTATAAATTATAAAATT
Found at i:556160 original size:30 final size:29
Alignment explanation
Indices: 556076--556184 Score: 66
Period size: 30 Copynumber: 3.7 Consensus size: 29
556066 ATAAAAAATA
* *
556076 ATATTAATATAATATAAATATATA--AAT
1 ATATTAAAATTATATAAATATATATTAAT
* * *
556103 ATTTTAAAAAATATAATATAA-AT-TATTAAT
1 A-TATTAAAATTAT-ATA-AATATATATTAAT
556133 ATATTAAAATTTATATAAATATATATT-AT
1 ATATTAAAA-TTATATAAATATATATTAAT
* *
556162 AAATTATAAAATTATATATATAT
1 ATA-T-TAAAATTATATAAATAT
556185 TTATATATAT
Statistics
Matches: 62, Mismatches: 10, Indels: 17
0.70 0.11 0.19
Matches are distributed among these distances:
27 1 0.02
28 11 0.18
29 20 0.32
30 25 0.40
31 5 0.08
ACGTcount: A:0.56, C:0.00, G:0.00, T:0.44
Consensus pattern (29 bp):
ATATTAAAATTATATAAATATATATTAAT
Found at i:556169 original size:20 final size:20
Alignment explanation
Indices: 556071--556171 Score: 54
Period size: 18 Copynumber: 5.2 Consensus size: 20
556061 ATAACATAAA
556071 AAATA-ATATTAATATAA-TAT
1 AAATATATATT-ATA-AATTAT
* **
556091 AAATATATA-AATATTTTA-
1 AAATATATATTATAAATTAT
* *
556109 AAAAATATAATATAAATTAT
1 AAATATATATTATAAATTAT
*
556129 -TA-ATATATTA-AAATTTATAT
1 AAATATATATTATAAA--T-TAT
556149 AAATATATATTATAAATTAT
1 AAATATATATTATAAATTAT
556169 AAA
1 AAA
556172 ATTATATATA
Statistics
Matches: 61, Mismatches: 10, Indels: 20
0.67 0.11 0.22
Matches are distributed among these distances:
17 3 0.05
18 15 0.25
19 13 0.21
20 14 0.23
21 5 0.08
22 8 0.13
23 3 0.05
ACGTcount: A:0.58, C:0.00, G:0.00, T:0.42
Consensus pattern (20 bp):
AAATATATATTATAAATTAT
Found at i:556897 original size:60 final size:59
Alignment explanation
Indices: 556833--556958 Score: 225
Period size: 60 Copynumber: 2.1 Consensus size: 59
556823 GCCAACCAAA
* *
556833 TTAATATTTTATGTTTTACCATAAAATTCACGTTGTCTCCAATTATGGACCCATTTATAT
1 TTAATATTTTATGTTTTAACATAAAATTCACATTGTCTCCAATTATGGA-CCATTTATAT
556893 TTAATATTTTATGTTTTAACATAAAATTCACATTGTCTCCAATTATGGACCATTTATAT
1 TTAATATTTTATGTTTTAACATAAAATTCACATTGTCTCCAATTATGGACCATTTATAT
556952 TTAATAT
1 TTAATAT
556959 CTTACTTTCT
Statistics
Matches: 64, Mismatches: 2, Indels: 1
0.96 0.03 0.01
Matches are distributed among these distances:
59 17 0.27
60 47 0.73
ACGTcount: A:0.33, C:0.14, G:0.07, T:0.46
Consensus pattern (59 bp):
TTAATATTTTATGTTTTAACATAAAATTCACATTGTCTCCAATTATGGACCATTTATAT
Found at i:557391 original size:13 final size:13
Alignment explanation
Indices: 557373--557405 Score: 57
Period size: 13 Copynumber: 2.5 Consensus size: 13
557363 ACTCTTTGTC
557373 TTCTTTTTTTTTT
1 TTCTTTTTTTTTT
557386 TTCTTTTTTTTTT
1 TTCTTTTTTTTTT
*
557399 CTCTTTT
1 TTCTTTT
557406 GGTAAAAAAA
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
13 19 1.00
ACGTcount: A:0.00, C:0.12, G:0.00, T:0.88
Consensus pattern (13 bp):
TTCTTTTTTTTTT
Found at i:557544 original size:2 final size:2
Alignment explanation
Indices: 557537--557566 Score: 60
Period size: 2 Copynumber: 15.0 Consensus size: 2
557527 ATAATTGGGC
557537 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
557567 TTCTTTTATT
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 28 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:559164 original size:21 final size:21
Alignment explanation
Indices: 559112--559155 Score: 65
Period size: 21 Copynumber: 2.2 Consensus size: 21
559102 CTCAAATTTA
*
559112 ATTTAAAA-T-TTCAATTATT
1 ATTTAAAATTATTAAATTATT
559131 ATTTAAAATTATTAAATTATT
1 ATTTAAAATTATTAAATTATT
559152 ATTT
1 ATTT
559156 TTAAATATTT
Statistics
Matches: 22, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
19 8 0.36
20 1 0.05
21 13 0.59
ACGTcount: A:0.43, C:0.02, G:0.00, T:0.55
Consensus pattern (21 bp):
ATTTAAAATTATTAAATTATT
Found at i:559242 original size:33 final size:31
Alignment explanation
Indices: 559164--559244 Score: 76
Period size: 35 Copynumber: 2.5 Consensus size: 31
559154 TTTTAAATAT
*
559164 TTTATT-AA-TAAATAATAATTTAAATTAAA
1 TTTATTAAATTAAATAATAATATAAATTAAA
** *
559193 AATATATATATATAAATAATTTAATATAAATTAAA
1 TTTAT-TAAAT-TAAATAA--TAATATAAATTAAA
559228 TTTATTAAATTAAATAA
1 TTTATTAAATTAAATAA
559245 AAAATTAATT
Statistics
Matches: 39, Mismatches: 7, Indels: 8
0.72 0.13 0.15
Matches are distributed among these distances:
29 3 0.08
30 1 0.03
31 1 0.03
33 14 0.36
34 4 0.10
35 16 0.41
ACGTcount: A:0.57, C:0.00, G:0.00, T:0.43
Consensus pattern (31 bp):
TTTATTAAATTAAATAATAATATAAATTAAA
Found at i:561427 original size:15 final size:15
Alignment explanation
Indices: 561370--561427 Score: 55
Period size: 15 Copynumber: 3.9 Consensus size: 15
561360 TATCAAAATT
*
561370 TATATAAATATAAAA
1 TATATTAATATAAAA
* *
561385 TATTTTAA-ATATAAT
1 TATATTAATATA-AAA
* *
561400 TATAATAAAATAAAA
1 TATATTAATATAAAA
561415 TATATTAATATAA
1 TATATTAATATAA
561428 TCATATACAT
Statistics
Matches: 33, Mismatches: 8, Indels: 4
0.73 0.18 0.09
Matches are distributed among these distances:
14 3 0.09
15 27 0.82
16 3 0.09
ACGTcount: A:0.60, C:0.00, G:0.00, T:0.40
Consensus pattern (15 bp):
TATATTAATATAAAA
Found at i:561440 original size:32 final size:31
Alignment explanation
Indices: 561369--561428 Score: 90
Period size: 30 Copynumber: 2.0 Consensus size: 31
561359 ATATCAAAAT
*
561369 TTAT-ATAAATATAAAATATTTTAAATATAA
1 TTATAATAAATATAAAATATATTAAATATAA
561399 TTATAATAAA-ATAAAATATATT-AATATAA
1 TTATAATAAATATAAAATATATTAAATATAA
561428 T
1 T
561429 CATATACATA
Statistics
Matches: 28, Mismatches: 1, Indels: 3
0.88 0.03 0.09
Matches are distributed among these distances:
29 8 0.29
30 15 0.54
31 5 0.18
ACGTcount: A:0.58, C:0.00, G:0.00, T:0.42
Consensus pattern (31 bp):
TTATAATAAATATAAAATATATTAAATATAA
Found at i:561825 original size:4 final size:4
Alignment explanation
Indices: 561816--561877 Score: 74
Period size: 4 Copynumber: 15.5 Consensus size: 4
561806 TTTGGCTTGA
* *
561816 AAAG AAAG AAAG AAAG AAAG AAAG AAAAA AAAG AAAG AAAG AAAG -GAG
1 AAAG AAAG AAAG AAAG AAAG AAAG -AAAG AAAG AAAG AAAG AAAG AAAG
561864 AGAA- AAAG AAAG AA
1 A-AAG AAAG AAAG AA
561878 GCTTACTTGG
Statistics
Matches: 50, Mismatches: 4, Indels: 8
0.81 0.06 0.13
Matches are distributed among these distances:
3 4 0.08
4 42 0.84
5 4 0.08
ACGTcount: A:0.76, C:0.00, G:0.24, T:0.00
Consensus pattern (4 bp):
AAAG
Found at i:561848 original size:25 final size:26
Alignment explanation
Indices: 561814--561877 Score: 94
Period size: 25 Copynumber: 2.5 Consensus size: 26
561804 CGTTTGGCTT
*
561814 GAAAAGAAAGAAAGAAAGAAA-GAAA
1 GAAAAAAAAGAAAGAAAGAAAGGAAA
*
561839 GAAAAAAAAGAAAGAAAGAAAGGAGA
1 GAAAAAAAAGAAAGAAAGAAAGGAAA
561865 GAAAAAGAAAGAA
1 GAAAAA-AAAGAA
561878 GCTTACTTGG
Statistics
Matches: 35, Mismatches: 2, Indels: 2
0.90 0.05 0.05
Matches are distributed among these distances:
25 20 0.57
26 9 0.26
27 6 0.17
ACGTcount: A:0.75, C:0.00, G:0.25, T:0.00
Consensus pattern (26 bp):
GAAAAAAAAGAAAGAAAGAAAGGAAA
Found at i:561867 original size:17 final size:16
Alignment explanation
Indices: 561816--561877 Score: 74
Period size: 17 Copynumber: 3.9 Consensus size: 16
561806 TTTGGCTTGA
561816 AAAGAAAGAAAGAAAG
1 AAAGAAAGAAAGAAAG
*
561832 AAAGAAAGAAAAAAAAG
1 AAAGAAAG-AAAGAAAG
*
561849 AAAGAAAGAAAG-GAG
1 AAAGAAAGAAAGAAAG
561864 AGAA-AAAGAAAGAA
1 A-AAGAAAGAAAGAA
561878 GCTTACTTGG
Statistics
Matches: 39, Mismatches: 4, Indels: 6
0.80 0.08 0.12
Matches are distributed among these distances:
15 11 0.28
16 13 0.33
17 15 0.38
ACGTcount: A:0.76, C:0.00, G:0.24, T:0.00
Consensus pattern (16 bp):
AAAGAAAGAAAGAAAG
Found at i:562192 original size:16 final size:17
Alignment explanation
Indices: 562153--562193 Score: 50
Period size: 16 Copynumber: 2.5 Consensus size: 17
562143 TTTATACGTA
562153 TTTATATTCATTTTATG
1 TTTATATTCATTTTATG
*
562170 TTCATATT-ATTTTAT-
1 TTTATATTCATTTTATG
562185 TATTATATT
1 T-TTATATT
562194 TTAAATATTT
Statistics
Matches: 21, Mismatches: 2, Indels: 3
0.81 0.08 0.12
Matches are distributed among these distances:
15 1 0.05
16 13 0.62
17 7 0.33
ACGTcount: A:0.27, C:0.05, G:0.02, T:0.66
Consensus pattern (17 bp):
TTTATATTCATTTTATG
Found at i:562402 original size:19 final size:18
Alignment explanation
Indices: 562365--562413 Score: 59
Period size: 18 Copynumber: 2.8 Consensus size: 18
562355 ATGGGAAGAA
562365 AAAAAAAGAAAA--A-AG
1 AAAAAAAGAAAAGGAGAG
562380 AAAAGAAAGAAAAGGAGAG
1 AAAA-AAAGAAAAGGAGAG
*
562399 AAAAAAATAAAAGGA
1 AAAAAAAGAAAAGGA
562414 AAAGTTAATC
Statistics
Matches: 29, Mismatches: 1, Indels: 5
0.83 0.03 0.14
Matches are distributed among these distances:
15 4 0.14
16 8 0.28
18 11 0.38
19 6 0.21
ACGTcount: A:0.78, C:0.00, G:0.20, T:0.02
Consensus pattern (18 bp):
AAAAAAAGAAAAGGAGAG
Found at i:562974 original size:12 final size:11
Alignment explanation
Indices: 562949--562982 Score: 50
Period size: 11 Copynumber: 3.0 Consensus size: 11
562939 TTTATTTGAT
562949 AAAAAAGAAAA
1 AAAAAAGAAAA
562960 AAAAAAGAAAGA
1 AAAAAAGAAA-A
*
562972 AAAAGAGAAAA
1 AAAAAAGAAAA
562983 GATTTAGGCA
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
11 11 0.52
12 10 0.48
ACGTcount: A:0.85, C:0.00, G:0.15, T:0.00
Consensus pattern (11 bp):
AAAAAAGAAAA
Found at i:563743 original size:8 final size:9
Alignment explanation
Indices: 563726--563783 Score: 57
Period size: 9 Copynumber: 6.2 Consensus size: 9
563716 TGTTTATATT
563726 ATTT-TTTA
1 ATTTATTTA
563734 A-TTATTTA
1 ATTTATTTA
563742 ATTTATTATA
1 ATTTATT-TA
563752 TATTTATTTA
1 -ATTTATTTA
*
563762 ATATATTATA
1 ATTTATT-TA
563772 CATTTATTTA
1 -ATTTATTTA
563782 AT
1 AT
563784 ATTTTATACA
Statistics
Matches: 42, Mismatches: 2, Indels: 11
0.76 0.04 0.20
Matches are distributed among these distances:
7 2 0.05
8 6 0.14
9 13 0.31
10 8 0.19
11 13 0.31
ACGTcount: A:0.36, C:0.02, G:0.00, T:0.62
Consensus pattern (9 bp):
ATTTATTTA
Found at i:563752 original size:28 final size:30
Alignment explanation
Indices: 563719--563799 Score: 89
Period size: 31 Copynumber: 2.7 Consensus size: 30
563709 AGATTCGTGT
563719 TTATATTATTTTTTAAT-TATT-TA-ATTTA
1 TTATA-TATTTTTTAATATATTATACATTTA
563747 TTATATATTTATTTAATATATTATACATTTA
1 TTATATATTT-TTTAATATATTATACATTTA
*
563778 TT-TAATATTTTATACATATATT
1 TTAT-ATATTTTTTA-ATATATT
563800 TTATATATTA
Statistics
Matches: 46, Mismatches: 1, Indels: 9
0.82 0.02 0.16
Matches are distributed among these distances:
27 5 0.11
28 11 0.24
29 4 0.09
30 6 0.13
31 20 0.43
ACGTcount: A:0.36, C:0.02, G:0.00, T:0.62
Consensus pattern (30 bp):
TTATATATTTTTTAATATATTATACATTTA
Found at i:563784 original size:20 final size:20
Alignment explanation
Indices: 563735--563809 Score: 105
Period size: 20 Copynumber: 3.8 Consensus size: 20
563725 TATTTTTTAA
* *
563735 TTATTTAATTTATTATATAT
1 TTATTTAATATATTATACAT
563755 TTATTTAATATATTATACAT
1 TTATTTAATATATTATACAT
*
563775 TTATTTAATATTTTATACAT
1 TTATTTAATATATTATACAT
* *
563795 ATATTTTATATATTA
1 TTATTTAATATATTA
563810 ATATATTTTA
Statistics
Matches: 49, Mismatches: 6, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 49 1.00
ACGTcount: A:0.37, C:0.03, G:0.00, T:0.60
Consensus pattern (20 bp):
TTATTTAATATATTATACAT
Found at i:563807 original size:9 final size:9
Alignment explanation
Indices: 563793--563850 Score: 57
Period size: 9 Copynumber: 6.2 Consensus size: 9
563783 TATTTTATAC
563793 ATATATTTT
1 ATATATTTT
*
563802 ATATA-TTA
1 ATATATTTT
563810 ATATATTTT
1 ATATATTTT
563819 ATCATATTTAT
1 AT-ATATTT-T
563830 ATTATATTTT
1 A-TATATTTT
563840 A-ATTATTTT
1 ATA-TATTTT
563849 AT
1 AT
563851 GTTATATTCA
Statistics
Matches: 41, Mismatches: 2, Indels: 11
0.76 0.04 0.20
Matches are distributed among these distances:
8 8 0.20
9 16 0.39
10 8 0.20
11 8 0.20
12 1 0.02
ACGTcount: A:0.36, C:0.02, G:0.00, T:0.62
Consensus pattern (9 bp):
ATATATTTT
Found at i:563818 original size:30 final size:30
Alignment explanation
Indices: 563782--563850 Score: 88
Period size: 30 Copynumber: 2.3 Consensus size: 30
563772 CATTTATTTA
*
563782 ATATTTTATACATA-TATTTTATATATTAAT
1 ATATTTTAT-CATATTATATTATATATTAAT
*
563812 ATATTTTATCATATTTATATTATATTTTAAT
1 ATATTTTATCATA-TTATATTATATATTAAT
563843 -TATTTTAT
1 ATATTTTAT
563851 GTTATATTCA
Statistics
Matches: 35, Mismatches: 2, Indels: 4
0.85 0.05 0.10
Matches are distributed among these distances:
29 4 0.11
30 17 0.49
31 14 0.40
ACGTcount: A:0.36, C:0.03, G:0.00, T:0.61
Consensus pattern (30 bp):
ATATTTTATCATATTATATTATATATTAAT
Found at i:563845 original size:16 final size:16
Alignment explanation
Indices: 563719--563873 Score: 55
Period size: 15 Copynumber: 10.0 Consensus size: 16
563709 AGATTCGTGT
*
563719 TTATATTATTTTTTAA
1 TTATATTATATTTTAA
563735 TTAT-TTA-A-TTT-A
1 TTATATTATATTTTAA
*
563747 TTATA-TATTTATTTAA
1 TTATATTATAT-TTTAA
*
563763 -TATATTATACATTT-A
1 TTATATTATA-TTTTAA
*
563778 TT-TAATAT-TTTATACA
1 TTATATTATATTT-TA-A
* *
563794 TATATTTTATATATTAA
1 T-TATATTATATTTTAA
* ** *
563811 -TATATTTTATCATAT
1 TTATATTATATTTTAA
563826 TTATATTATATTTTAA
1 TTATATTATATTTTAA
*
563842 TTAT-TT-TATGTTATA
1 TTATATTATATTTTA-A
*
563857 TTCATATTATTTTTTAA
1 TT-ATATTATATTTTAA
563874 ATATTTAAAG
Statistics
Matches: 99, Mismatches: 21, Indels: 37
0.63 0.13 0.24
Matches are distributed among these distances:
12 7 0.07
13 5 0.05
14 7 0.07
15 31 0.31
16 31 0.31
17 5 0.05
18 11 0.11
19 2 0.02
ACGTcount: A:0.35, C:0.03, G:0.01, T:0.62
Consensus pattern (16 bp):
TTATATTATATTTTAA
Found at i:563864 original size:32 final size:30
Alignment explanation
Indices: 563778--563879 Score: 93
Period size: 32 Copynumber: 3.4 Consensus size: 30
563768 TATACATTTA
*
563778 TTTAA-TATTTTATACATA-T-ATTTTATAT
1 TTTAATTATTTTAT-CATATTCATATTATAT
* *
563806 ATTAATATATTTTATCATATTTATATTATAT
1 TTTAAT-TATTTTATCATATTCATATTATAT
* *
563837 TTTAATTATTTTATGTTATATTCATATTATTT
1 TTTAATTATTTTA--TCATATTCATATTATAT
*
563869 TTTAAATATTT
1 TTTAATTATTT
563880 AAAGTATTAT
Statistics
Matches: 61, Mismatches: 7, Indels: 8
0.80 0.09 0.11
Matches are distributed among these distances:
28 4 0.07
29 4 0.07
30 16 0.26
31 13 0.21
32 24 0.39
ACGTcount: A:0.34, C:0.03, G:0.01, T:0.62
Consensus pattern (30 bp):
TTTAATTATTTTATCATATTCATATTATAT
Found at i:564817 original size:18 final size:18
Alignment explanation
Indices: 564768--564817 Score: 66
Period size: 18 Copynumber: 2.7 Consensus size: 18
564758 ATGCATGCTA
564768 TTTATATACATTAAACTTT
1 TTTATATA-ATTAAACTTT
*
564787 TTTGATA-AGTTAAACTTT
1 TTT-ATATAATTAAACTTT
564805 TTTATATAATTAA
1 TTTATATAATTAA
564818 TTTCATAACT
Statistics
Matches: 27, Mismatches: 2, Indels: 5
0.79 0.06 0.15
Matches are distributed among these distances:
17 3 0.11
18 17 0.63
19 4 0.15
20 3 0.11
ACGTcount: A:0.38, C:0.06, G:0.04, T:0.52
Consensus pattern (18 bp):
TTTATATAATTAAACTTT
Found at i:565341 original size:39 final size:33
Alignment explanation
Indices: 565297--565363 Score: 116
Period size: 33 Copynumber: 2.0 Consensus size: 33
565287 ATATTTTTTA
*
565297 TTTTAATTTTAATTATATTAAAAATAAATATTAT
1 TTTTAA-TTTAATAATATTAAAAATAAATATTAT
565331 TTTTAATTTAATAATATTAAAAATAAATATTAT
1 TTTTAATTTAATAATATTAAAAATAAATATTAT
565364 ATAAGATAAA
Statistics
Matches: 32, Mismatches: 1, Indels: 1
0.94 0.03 0.03
Matches are distributed among these distances:
33 26 0.81
34 6 0.19
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (33 bp):
TTTTAATTTAATAATATTAAAAATAAATATTAT
Found at i:565407 original size:2 final size:2
Alignment explanation
Indices: 565402--565428 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
565392 AAAAATGGAT
565402 TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA T
565429 CTTTTAATAA
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 25 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:566742 original size:2 final size:2
Alignment explanation
Indices: 566735--566760 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
566725 TATTTTCTCC
566735 TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA
566761 AATTATTCCC
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):
TA
Found at i:566807 original size:13 final size:13
Alignment explanation
Indices: 566791--566818 Score: 56
Period size: 13 Copynumber: 2.2 Consensus size: 13
566781 GAGAATGTTA
566791 ATTATTATTATTT
1 ATTATTATTATTT
566804 ATTATTATTATTT
1 ATTATTATTATTT
566817 AT
1 AT
566819 AAATATATGT
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 15 1.00
ACGTcount: A:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (13 bp):
ATTATTATTATTT
Found at i:568299 original size:2 final size:2
Alignment explanation
Indices: 568292--568351 Score: 70
Period size: 2 Copynumber: 31.0 Consensus size: 2
568282 TTAAGCAAAC
* *
568292 AT AT AT AT AT AT AT AT AT AT GT -T GT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
* *
568333 AT AT AT -T GT AT GT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT
568352 GATTTTGTTA
Statistics
Matches: 51, Mismatches: 5, Indels: 4
0.85 0.08 0.07
Matches are distributed among these distances:
1 2 0.04
2 49 0.96
ACGTcount: A:0.42, C:0.00, G:0.07, T:0.52
Consensus pattern (2 bp):
AT
Found at i:568326 original size:25 final size:25
Alignment explanation
Indices: 568292--568351 Score: 102
Period size: 25 Copynumber: 2.4 Consensus size: 25
568282 TTAAGCAAAC
*
568292 ATATATATATATATATATATGTTGT
1 ATATATATATATATATATATATTGT
568317 ATATATATATATATATATATATTGT
1 ATATATATATATATATATATATTGT
*
568342 ATGTATATAT
1 ATATATATAT
568352 GATTTTGTTA
Statistics
Matches: 33, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
25 33 1.00
ACGTcount: A:0.42, C:0.00, G:0.07, T:0.52
Consensus pattern (25 bp):
ATATATATATATATATATATATTGT
Found at i:570376 original size:22 final size:23
Alignment explanation
Indices: 570331--570397 Score: 73
Period size: 22 Copynumber: 2.9 Consensus size: 23
570321 ATTTAAGATG
570331 AATATTAAATATAAATATATTTTT
1 AATA-TAAATATAAATATATTTTT
* *
570355 AATATGAATATATAT-TATTTTT
1 AATATAAATATAAATATATTTTT
* * *
570377 TATATAAATAAAAAAATATTT
1 AATATAAATATAAATATATTT
570398 ATATTTAAAA
Statistics
Matches: 35, Mismatches: 7, Indels: 3
0.78 0.16 0.07
Matches are distributed among these distances:
22 17 0.49
23 14 0.40
24 4 0.11
ACGTcount: A:0.51, C:0.00, G:0.01, T:0.48
Consensus pattern (23 bp):
AATATAAATATAAATATATTTTT
Found at i:570447 original size:22 final size:21
Alignment explanation
Indices: 570417--570457 Score: 57
Period size: 22 Copynumber: 1.9 Consensus size: 21
570407 AATTTATACC
570417 AAATAAAATAT-AAATAATAAA
1 AAATAAAAT-TCAAATAATAAA
570438 AAATATAAATTCAAATAATA
1 AAATA-AAATTCAAATAATA
570458 TAAGCTATTA
Statistics
Matches: 18, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
21 6 0.33
22 12 0.67
ACGTcount: A:0.71, C:0.02, G:0.00, T:0.27
Consensus pattern (21 bp):
AAATAAAATTCAAATAATAAA
Found at i:570967 original size:22 final size:23
Alignment explanation
Indices: 570934--570983 Score: 68
Period size: 22 Copynumber: 2.2 Consensus size: 23
570924 TAGAAGCTAG
*
570934 TATAAAATATAA-TACGAATAAAA
1 TATAAAATATAATTA-AAATAAAA
570957 TATAAAA-ATAATTAAAATAAAA
1 TATAAAATATAATTAAAATAAAA
570979 TATAA
1 TATAA
570984 TATAAATATA
Statistics
Matches: 25, Mismatches: 1, Indels: 3
0.86 0.03 0.10
Matches are distributed among these distances:
22 16 0.64
23 9 0.36
ACGTcount: A:0.68, C:0.02, G:0.02, T:0.28
Consensus pattern (23 bp):
TATAAAATATAATTAAAATAAAA
Found at i:570990 original size:16 final size:15
Alignment explanation
Indices: 570935--571001 Score: 64
Period size: 16 Copynumber: 4.3 Consensus size: 15
570925 AGAAGCTAGT
*
570935 ATAAAATATAATACGA
1 ATAAAATATAATA-TA
*
570951 ATAAAATATAAAAATA
1 ATAAAATAT-AATATA
*
570967 ATTAAAATAAAATATA
1 A-TAAAATATAATATA
570983 ATATAAATATAATA-A
1 ATA-AAATATAATATA
570998 ATAA
1 ATAA
571002 CGTGAATACA
Statistics
Matches: 43, Mismatches: 5, Indels: 8
0.77 0.09 0.14
Matches are distributed among these distances:
14 1 0.02
15 6 0.14
16 26 0.60
17 10 0.23
ACGTcount: A:0.69, C:0.01, G:0.01, T:0.28
Consensus pattern (15 bp):
ATAAAATATAATATA
Found at i:571106 original size:21 final size:20
Alignment explanation
Indices: 571080--571124 Score: 58
Period size: 19 Copynumber: 2.2 Consensus size: 20
571070 ATAATATTTT
571080 AAATAAAATTATAATAT-ATAA
1 AAATAAAA-TA-AATATAATAA
571101 AAAT-AAATAAATATAATAA
1 AAATAAAATAAATATAATAA
571120 AAATA
1 AAATA
571125 TATACATAAC
Statistics
Matches: 22, Mismatches: 0, Indels: 5
0.81 0.00 0.19
Matches are distributed among these distances:
18 5 0.23
19 10 0.45
20 3 0.14
21 4 0.18
ACGTcount: A:0.71, C:0.00, G:0.00, T:0.29
Consensus pattern (20 bp):
AAATAAAATAAATATAATAA
Found at i:572681 original size:15 final size:16
Alignment explanation
Indices: 572661--572697 Score: 53
Period size: 15 Copynumber: 2.5 Consensus size: 16
572651 TATTAAAATA
572661 ATTTATTTTAT-ATTT
1 ATTTATTTTATGATTT
572676 ATTTA-TTTATGATTT
1 ATTTATTTTATGATTT
572691 -TTTATTT
1 ATTTATTT
572698 AAATTCATTC
Statistics
Matches: 20, Mismatches: 0, Indels: 4
0.83 0.00 0.17
Matches are distributed among these distances:
14 9 0.45
15 11 0.55
ACGTcount: A:0.24, C:0.00, G:0.03, T:0.73
Consensus pattern (16 bp):
ATTTATTTTATGATTT
Found at i:572694 original size:14 final size:14
Alignment explanation
Indices: 572661--572698 Score: 51
Period size: 14 Copynumber: 2.6 Consensus size: 14
572651 TATTAAAATA
572661 ATTTATTTTATATTT
1 ATTTA-TTTATATTT
572676 ATTTATTTATGATTT
1 ATTTATTTAT-ATTT
572691 -TTTATTTA
1 ATTTATTTA
572699 AATTCATTCT
Statistics
Matches: 22, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
14 13 0.59
15 9 0.41
ACGTcount: A:0.26, C:0.00, G:0.03, T:0.71
Consensus pattern (14 bp):
ATTTATTTATATTT
Found at i:572902 original size:156 final size:156
Alignment explanation
Indices: 572728--573096 Score: 659
Period size: 157 Copynumber: 2.4 Consensus size: 156
572718 ATATTAATTG
*
572728 ATTTTAGATTTGATGTATTAATATTATTCATTAATAAAATAATTTATTTTCTAATACATATGAAA
1 ATTTTAGATTTGATGTATTAATATTATTCATTTATAAAATAATTTATTTTCTAATACATATGAAA
* *
572793 TTATTGAATTTGAGTTAGGC-AAAAAAAAATTTCTCTTCTTATTCTCTATTTTAGAGTTTTTTTT
66 TTATTGAATTTGAGTTAGGCAAAAAAAAAAATTCTCTTCTTATTCTCTATTTTAGA-ATTTTTTT
572857 TTTAAATAAGATTTTCATATTAACAAT
130 TTTAAATAAGATTTTCATATTAACAAT
572884 ATTTTAGATTTGATGTATTAATATTATTCATTTATAAAATAATTTATTTTCTAATACATATGAAA
1 ATTTTAGATTTGATGTATTAATATTATTCATTTATAAAATAATTTATTTTCTAATACATATGAAA
572949 TTATTGAATTTGAGTTAGGCAAAAAAAAAAAATTCTCTTCTTATTCTCTATTTTAGAATTTTTTT
66 TTATTGAATTTGAGTTAGGC-AAAAAAAAAAATTCTCTTCTTATTCTCTATTTTAGAATTTTTTT
573014 TTTAAATAAGATTTTCATATTAACAAT
130 TTTAAATAAGATTTTCATATTAACAAT
* * *
573041 ATTTTAGGTTTGATGTATTAATATTATTCATTTATAAATTATTTTATTTTCTAATA
1 ATTTTAGATTTGATGTATTAATATTATTCATTTATAAAATAATTTATTTTCTAATA
573097 TATTTCAATT
Statistics
Matches: 205, Mismatches: 6, Indels: 3
0.96 0.03 0.01
Matches are distributed among these distances:
156 84 0.41
157 87 0.42
158 34 0.17
ACGTcount: A:0.37, C:0.07, G:0.07, T:0.50
Consensus pattern (156 bp):
ATTTTAGATTTGATGTATTAATATTATTCATTTATAAAATAATTTATTTTCTAATACATATGAAA
TTATTGAATTTGAGTTAGGCAAAAAAAAAAATTCTCTTCTTATTCTCTATTTTAGAATTTTTTTT
TTAAATAAGATTTTCATATTAACAAT
Found at i:573924 original size:19 final size:19
Alignment explanation
Indices: 573902--573966 Score: 66
Period size: 18 Copynumber: 3.6 Consensus size: 19
573892 TCTATCTTTA
*
573902 ATTATTTAAATATAAAATT
1 ATTATATAAATATAAAATT
*
573921 ATTATATATAT-TAAAATT
1 ATTATATAAATATAAAATT
* *
573939 -TTAAATACATATAAAATT
1 ATTATATAAATATAAAATT
573957 A-TAT-TAAATA
1 ATTATATAAATA
573967 GTTTATGTTA
Statistics
Matches: 38, Mismatches: 6, Indels: 6
0.76 0.12 0.12
Matches are distributed among these distances:
17 13 0.34
18 16 0.42
19 9 0.24
ACGTcount: A:0.54, C:0.02, G:0.00, T:0.45
Consensus pattern (19 bp):
ATTATATAAATATAAAATT
Found at i:574292 original size:26 final size:28
Alignment explanation
Indices: 574253--574313 Score: 81
Period size: 28 Copynumber: 2.2 Consensus size: 28
574243 ACACAATAAA
*
574253 AAATATTAACAT-AAA-TTATTTTATTT
1 AAATATAAACATAAAATTTATTTTATTT
* *
574279 AAATATAAATATAAAATTTATTTTTTTT
1 AAATATAAACATAAAATTTATTTTATTT
574307 AAATATA
1 AAATATA
574314 TTTATATAAA
Statistics
Matches: 30, Mismatches: 3, Indels: 2
0.86 0.09 0.06
Matches are distributed among these distances:
26 10 0.33
27 3 0.10
28 17 0.57
ACGTcount: A:0.49, C:0.02, G:0.00, T:0.49
Consensus pattern (28 bp):
AAATATAAACATAAAATTTATTTTATTT
Found at i:574325 original size:15 final size:15
Alignment explanation
Indices: 574287--574344 Score: 62
Period size: 15 Copynumber: 3.7 Consensus size: 15
574277 TTAAATATAA
*
574287 ATATAAAATTTATTT
1 ATATAAAATATATTT
* * *
574302 TTTTTAAATATATTT
1 ATATAAAATATATTT
574317 ATATAAAATATATAATT
1 ATATAAAATATAT--TT
574334 ATATAAAATAT
1 ATATAAAATAT
574345 TTATTTACTC
Statistics
Matches: 34, Mismatches: 7, Indels: 2
0.79 0.16 0.05
Matches are distributed among these distances:
15 21 0.62
17 13 0.38
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (15 bp):
ATATAAAATATATTT
Found at i:574335 original size:17 final size:17
Alignment explanation
Indices: 574309--574344 Score: 63
Period size: 17 Copynumber: 2.1 Consensus size: 17
574299 TTTTTTTTAA
*
574309 ATATATTTATATAAAAT
1 ATATAATTATATAAAAT
574326 ATATAATTATATAAAAT
1 ATATAATTATATAAAAT
574343 AT
1 AT
574345 TTATTTACTC
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
17 18 1.00
ACGTcount: A:0.56, C:0.00, G:0.00, T:0.44
Consensus pattern (17 bp):
ATATAATTATATAAAAT
Found at i:574646 original size:27 final size:27
Alignment explanation
Indices: 574610--574663 Score: 74
Period size: 27 Copynumber: 2.0 Consensus size: 27
574600 TATAATTATA
*
574610 TTTAAAATATTATATATTTA-TATAAAT
1 TTTAAAATATTA-ATAATTATTATAAAT
*
574637 TTTAATATATTAATAATTATTATAAAT
1 TTTAAAATATTAATAATTATTATAAAT
574664 AAATGTTATT
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
26 6 0.25
27 18 0.75
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (27 bp):
TTTAAAATATTAATAATTATTATAAAT
Found at i:574803 original size:22 final size:22
Alignment explanation
Indices: 574767--574811 Score: 58
Period size: 22 Copynumber: 2.0 Consensus size: 22
574757 TTTTAAAATA
574767 ATTATATTTTAATTAAT-TTTTT
1 ATTATATTTTAATT-ATGTTTTT
574789 ATTATA-TTTATATTATGTTTTT
1 ATTATATTTTA-ATTATGTTTTT
574811 A
1 A
574812 GTCGTAAAAC
Statistics
Matches: 21, Mismatches: 0, Indels: 4
0.84 0.00 0.16
Matches are distributed among these distances:
21 6 0.29
22 15 0.71
ACGTcount: A:0.31, C:0.00, G:0.02, T:0.67
Consensus pattern (22 bp):
ATTATATTTTAATTATGTTTTT
Found at i:574902 original size:2 final size:2
Alignment explanation
Indices: 574895--574921 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
574885 GCAGAAAATG
574895 TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA T
574922 GAGGATATTC
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 25 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:575667 original size:29 final size:29
Alignment explanation
Indices: 575618--575681 Score: 78
Period size: 31 Copynumber: 2.2 Consensus size: 29
575608 ATATGAAATT
**
575618 AAAAT-TTTTTAATTTTTTAATT-TTTAA
1 AAAATATTTTTAATTTAGTAATTATTTAA
575645 AAAATATTTTTAATTTAAGTAATTAATTTAA
1 AAAATATTTTTAATTT-AGTAATT-ATTTAA
575676 AAAATA
1 AAAATA
575682 ATTACTAAAT
Statistics
Matches: 31, Mismatches: 2, Indels: 4
0.84 0.05 0.11
Matches are distributed among these distances:
27 5 0.16
28 10 0.32
29 5 0.16
31 11 0.35
ACGTcount: A:0.47, C:0.00, G:0.02, T:0.52
Consensus pattern (29 bp):
AAAATATTTTTAATTTAGTAATTATTTAA
Found at i:576448 original size:2 final size:2
Alignment explanation
Indices: 576443--576518 Score: 51
Period size: 2 Copynumber: 41.5 Consensus size: 2
576433 GGAAAAAAAT
* *
576443 TA TA TA TA AA TA TA T- TA TA TA T- TA -A TA T- TA TA T- TT TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
* *
576480 TA T- TA -A TT TT TA TA TA -A TA TCA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA T-A TA TA TA TA TA TA TA TA T
576519 TAATATTTAA
Statistics
Matches: 60, Mismatches: 5, Indels: 18
0.72 0.06 0.22
Matches are distributed among these distances:
1 8 0.13
2 50 0.83
3 2 0.03
ACGTcount: A:0.45, C:0.01, G:0.00, T:0.54
Consensus pattern (2 bp):
TA
Found at i:576484 original size:12 final size:12
Alignment explanation
Indices: 576453--576526 Score: 53
Period size: 12 Copynumber: 6.0 Consensus size: 12
576443 TATATATAAA
576453 TATATTATATATT
1 TATATTATAT-TT
*
576466 AATATTATATTT
1 TATATTATATTT
576478 TATATTA-ATTTT
1 TATATTATA-TTT
* **
576490 TATATAATATCA
1 TATATTATATTT
*
576502 TATA-TATATATA
1 TATATTATAT-TT
576514 TATATTAATATTT
1 TATATT-ATATTT
576527 AATAATTTTA
Statistics
Matches: 48, Mismatches: 8, Indels: 10
0.73 0.12 0.15
Matches are distributed among these distances:
11 5 0.10
12 27 0.56
13 12 0.25
14 4 0.08
ACGTcount: A:0.42, C:0.01, G:0.00, T:0.57
Consensus pattern (12 bp):
TATATTATATTT
Done.