Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold142
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: 1427168
ACGTcount: A:0.34, C:0.16, G:0.16, T:0.33
Warning! 17476 characters in sequence are not A, C, G, or T
File 2 of 8
Found at i:289416 original size:6 final size:6
Alignment explanation
Indices: 289405--289439 Score: 61
Period size: 6 Copynumber: 5.7 Consensus size: 6
289395 AATTTCCACC
289405 TTTTAT TTTTAT TTTTAT TTTTAT TTTTAAT TTTT
1 TTTTAT TTTTAT TTTTAT TTTTAT TTTT-AT TTTT
289440 TGTCAAAAAA
Statistics
Matches: 28, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
6 22 0.79
7 6 0.21
ACGTcount: A:0.17, C:0.00, G:0.00, T:0.83
Consensus pattern (6 bp):
TTTTAT
Found at i:293768 original size:2 final size:2
Alignment explanation
Indices: 293761--293790 Score: 60
Period size: 2 Copynumber: 15.0 Consensus size: 2
293751 AATTCGGCTT
293761 CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA
1 CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA
293791 TTATATATAT
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:0.50, G:0.00, T:0.00
Consensus pattern (2 bp):
CA
Found at i:294737 original size:21 final size:21
Alignment explanation
Indices: 294712--294771 Score: 79
Period size: 20 Copynumber: 2.9 Consensus size: 21
294702 TTTTCTATTC
*
294712 TTTAAATATTTTAAATTTAAA
1 TTTAAATATTTTATATTTAAA
294733 TTTAAAT-TTATT-TATTTAAA
1 TTTAAATATT-TTATATTTAAA
*
294753 ATTAAATATTTTATATTTA
1 TTTAAATATTTTATATTTA
294772 TTCATTACAA
Statistics
Matches: 34, Mismatches: 2, Indels: 6
0.81 0.05 0.14
Matches are distributed among these distances:
20 17 0.50
21 17 0.50
ACGTcount: A:0.43, C:0.00, G:0.00, T:0.57
Consensus pattern (21 bp):
TTTAAATATTTTATATTTAAA
Found at i:294762 original size:14 final size:14
Alignment explanation
Indices: 294713--294802 Score: 51
Period size: 14 Copynumber: 6.5 Consensus size: 14
294703 TTTCTATTCT
*
294713 TTAAATATTTTAAA
1 TTAAATATTTAAAA
* *
294727 TTTAA-ATTTAAAT
1 TTAAATATTTAAAA
**
294740 TTATTTATTTAAAA
1 TTAAATATTTAAAA
* *
294754 TTAAATATTTTATA
1 TTAAATATTTAAAA
* * *
294768 TTTATTCA-TTACAA
1 TTAAAT-ATTTAAAA
294782 TTAAAT-TTATAAAA
1 TTAAATATT-TAAAA
294796 TTAAATA
1 TTAAATA
294803 AACATATTTA
Statistics
Matches: 52, Mismatches: 19, Indels: 9
0.65 0.24 0.11
Matches are distributed among these distances:
13 9 0.17
14 42 0.81
15 1 0.02
ACGTcount: A:0.47, C:0.02, G:0.00, T:0.51
Consensus pattern (14 bp):
TTAAATATTTAAAA
Found at i:294784 original size:28 final size:29
Alignment explanation
Indices: 294733--294787 Score: 76
Period size: 29 Copynumber: 1.9 Consensus size: 29
294723 TAAATTTAAA
*
294733 TTTAAATTTATTTATTTAAAATTAAATAT
1 TTTAAATTTATTCATTTAAAATTAAATAT
* *
294762 TTTATATTTATTCA-TTACAATTAAAT
1 TTTAAATTTATTCATTTAAAATTAAAT
294788 TTATAAAATT
Statistics
Matches: 23, Mismatches: 3, Indels: 1
0.85 0.11 0.04
Matches are distributed among these distances:
28 11 0.48
29 12 0.52
ACGTcount: A:0.42, C:0.04, G:0.00, T:0.55
Consensus pattern (29 bp):
TTTAAATTTATTCATTTAAAATTAAATAT
Found at i:294931 original size:37 final size:36
Alignment explanation
Indices: 294857--294948 Score: 93
Period size: 37 Copynumber: 2.6 Consensus size: 36
294847 AAATAAGTTG
* * *
294857 ATAAATAATAAATA-TA-TAAATATTTTTATTAATA
1 ATAAATTATAAATATTATTAAATATTTTAAATAATA
294891 ATAAATTATAAATATTATTAACATATTTATAAATAA-A
1 ATAAATTATAAATATTATTAA-ATATTT-TAAATAATA
*
294928 ATAAAATA-ATAATATTATTAA
1 ATAAATTATA-AATATTATTAA
294949 TTATATATAA
Statistics
Matches: 49, Mismatches: 4, Indels: 7
0.82 0.07 0.12
Matches are distributed among these distances:
34 13 0.27
35 2 0.04
36 4 0.08
37 25 0.51
38 5 0.10
ACGTcount: A:0.58, C:0.01, G:0.00, T:0.41
Consensus pattern (36 bp):
ATAAATTATAAATATTATTAAATATTTTAAATAATA
Found at i:295012 original size:16 final size:16
Alignment explanation
Indices: 294987--295049 Score: 65
Period size: 16 Copynumber: 3.9 Consensus size: 16
294977 AAAATTATTT
* *
294987 ATTATATAAAATTTAA
1 ATTATTTAAAATATAA
295003 ATTATTTAAAA-ATAA
1 ATTATTTAAAATATAA
295018 ATTTATTTATAAATATAA
1 A-TTATTTA-AAATATAA
* *
295036 ATAAATTAAAATAT
1 ATTATTTAAAATAT
295050 TATATTTTTA
Statistics
Matches: 40, Mismatches: 4, Indels: 6
0.80 0.08 0.12
Matches are distributed among these distances:
15 4 0.10
16 23 0.57
17 8 0.20
18 5 0.12
ACGTcount: A:0.57, C:0.00, G:0.00, T:0.43
Consensus pattern (16 bp):
ATTATTTAAAATATAA
Found at i:295072 original size:42 final size:41
Alignment explanation
Indices: 295026--295114 Score: 99
Period size: 42 Copynumber: 2.1 Consensus size: 41
295016 AAATTTATTT
* *
295026 ATAAATATAAATAAATTAAAATATTA-TATTTTTATTTAATAA
1 ATAAATATAAAAAAATTAAAAT-TTATTA-TTTAATTTAATAA
* * *
295068 ATAAATTTAAAAAAATTTAGATTTATTGATTTAATTTAATAA
1 ATAAATATAAAAAAATTAAAATTTATT-ATTTAATTTAATAA
295110 ATAAA
1 ATAAA
295115 AATTAAATTA
Statistics
Matches: 40, Mismatches: 5, Indels: 4
0.82 0.10 0.08
Matches are distributed among these distances:
41 3 0.08
42 36 0.90
43 1 0.03
ACGTcount: A:0.54, C:0.00, G:0.02, T:0.44
Consensus pattern (41 bp):
ATAAATATAAAAAAATTAAAATTTATTATTTAATTTAATAA
Found at i:313884 original size:11 final size:10
Alignment explanation
Indices: 313851--313885 Score: 52
Period size: 10 Copynumber: 3.4 Consensus size: 10
313841 AATAACTATT
313851 ATTAAATTTA
1 ATTAAATTTA
*
313861 TTTAAATTTA
1 ATTAAATTTA
313871 ATTAAATATTA
1 ATTAAAT-TTA
313882 ATTA
1 ATTA
313886 TAGTTTTATA
Statistics
Matches: 22, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
10 15 0.68
11 7 0.32
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (10 bp):
ATTAAATTTA
Found at i:314102 original size:2 final size:2
Alignment explanation
Indices: 314095--314121 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
314085 GTTAAGATGA
314095 AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT A
314122 ATTAATGCAT
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 25 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:320428 original size:32 final size:34
Alignment explanation
Indices: 320356--320434 Score: 92
Period size: 33 Copynumber: 2.4 Consensus size: 34
320346 TAAAAATTAA
**
320356 TTAAAATATTAAAAAAAAATAAATTTATAAGGAT
1 TTAAAATATTATTAAAAAATAAATTTATAAGGAT
* *
320390 TT-AAATATTATTAAAAAATTAATTT-TAA-TAT
1 TTAAAATATTATTAAAAAATAAATTTATAAGGAT
*
320421 TTAAAATATAATTA
1 TTAAAATATTATTA
320435 TTCACTAAAA
Statistics
Matches: 39, Mismatches: 5, Indels: 4
0.81 0.10 0.08
Matches are distributed among these distances:
31 4 0.10
32 13 0.33
33 20 0.51
34 2 0.05
ACGTcount: A:0.57, C:0.00, G:0.03, T:0.41
Consensus pattern (34 bp):
TTAAAATATTATTAAAAAATAAATTTATAAGGAT
Found at i:321546 original size:44 final size:44
Alignment explanation
Indices: 321482--321597 Score: 160
Period size: 44 Copynumber: 2.6 Consensus size: 44
321472 ATTTGAGTGG
* * *
321482 CTATGTCAATCTACGAAAAAATAAATAAATATGCAATTGGATGA
1 CTATGCCAATCAACGGAAAAATAAATAAATATGCAATTGGATGA
* * *
321526 CTATGCCAATCCACGGAAAAATAAATAAATATGTAATTGGGTGA
1 CTATGCCAATCAACGGAAAAATAAATAAATATGCAATTGGATGA
* *
321570 TTATGCCAATCAACAGAAAAATAAATAA
1 CTATGCCAATCAACGGAAAAATAAATAA
321598 TAAAAACACC
Statistics
Matches: 64, Mismatches: 8, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
44 64 1.00
ACGTcount: A:0.48, C:0.13, G:0.14, T:0.25
Consensus pattern (44 bp):
CTATGCCAATCAACGGAAAAATAAATAAATATGCAATTGGATGA
Found at i:321991 original size:14 final size:14
Alignment explanation
Indices: 321972--322044 Score: 73
Period size: 14 Copynumber: 5.4 Consensus size: 14
321962 TTGAATTTCA
321972 AAATTAACTATTTT
1 AAATTAACTATTTT
*
321986 AAATTAA--ATTTCA
1 AAATTAACTATTT-T
321999 AAATTAACTATTTT
1 AAATTAACTATTTT
322013 AAATTAA--ATTTT
1 AAATTAACTATTTT
* *
322025 AAAATTAACTGTTTC
1 -AAATTAACTATTTT
322040 AAATT
1 AAATT
322045 GATGATTTTC
Statistics
Matches: 49, Mismatches: 4, Indels: 12
0.75 0.06 0.18
Matches are distributed among these distances:
12 9 0.18
13 14 0.29
14 19 0.39
15 7 0.14
ACGTcount: A:0.47, C:0.07, G:0.01, T:0.45
Consensus pattern (14 bp):
AAATTAACTATTTT
Found at i:322004 original size:13 final size:12
Alignment explanation
Indices: 321959--322032 Score: 58
Period size: 13 Copynumber: 5.6 Consensus size: 12
321949 TCGCTGTTTT
*
321959 AAATTGAATTTCA
1 AAATTAAATTT-A
*
321972 AAATTAACTATTTT
1 AAATTAA--ATTTA
321986 AAATTAAATTTCA
1 AAATTAAATTT-A
*
321999 AAATTAACTATTTT
1 AAATTAA--ATTTA
322013 AAATTAAATTTTA
1 AAATTAAA-TTTA
322026 AAATTAA
1 AAATTAA
322033 CTGTTTCAAA
Statistics
Matches: 50, Mismatches: 5, Indels: 12
0.75 0.07 0.18
Matches are distributed among these distances:
12 5 0.10
13 23 0.46
14 14 0.28
15 8 0.16
ACGTcount: A:0.50, C:0.05, G:0.01, T:0.43
Consensus pattern (12 bp):
AAATTAAATTTA
Found at i:322020 original size:32 final size:27
Alignment explanation
Indices: 321955--322044 Score: 144
Period size: 27 Copynumber: 3.3 Consensus size: 27
321945 ACCTTCGCTG
*
321955 TTTTAAATTGAATTTCAAAATTAACTA
1 TTTTAAATTAAATTTCAAAATTAACTA
321982 TTTTAAATTAAATTTCAAAATTAACTA
1 TTTTAAATTAAATTTCAAAATTAACTA
* *
322009 TTTTAAATTAAATTTTAAAATTAACTG
1 TTTTAAATTAAATTTCAAAATTAACTA
*
322036 TTTCAAATT
1 TTTTAAATT
322045 GATGATTTTC
Statistics
Matches: 59, Mismatches: 4, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
27 59 1.00
ACGTcount: A:0.44, C:0.07, G:0.02, T:0.47
Consensus pattern (27 bp):
TTTTAAATTAAATTTCAAAATTAACTA
Found at i:322145 original size:6 final size:6
Alignment explanation
Indices: 322134--322168 Score: 52
Period size: 6 Copynumber: 5.8 Consensus size: 6
322124 TTGAACTGGA
* *
322134 AGAAGT AGAAGT AGCAGT TGAAGT AGAAGT AGAAG
1 AGAAGT AGAAGT AGAAGT AGAAGT AGAAGT AGAAG
322169 GTCAAGCCTC
Statistics
Matches: 25, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
6 25 1.00
ACGTcount: A:0.46, C:0.03, G:0.34, T:0.17
Consensus pattern (6 bp):
AGAAGT
Found at i:322543 original size:2 final size:2
Alignment explanation
Indices: 322536--322576 Score: 82
Period size: 2 Copynumber: 20.5 Consensus size: 2
322526 TATCAAGCAC
322536 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG A
1 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG A
322577 AGTACCTTAG
Statistics
Matches: 39, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 39 1.00
ACGTcount: A:0.51, C:0.00, G:0.49, T:0.00
Consensus pattern (2 bp):
AG
Found at i:340642 original size:13 final size:13
Alignment explanation
Indices: 340624--340649 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
340614 GACTGCAGCA
340624 AATAAATTTATCT
1 AATAAATTTATCT
340637 AATAAATTTATCT
1 AATAAATTTATCT
340650 CAACTACTGA
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:0.46, C:0.08, G:0.00, T:0.46
Consensus pattern (13 bp):
AATAAATTTATCT
Found at i:346786 original size:17 final size:17
Alignment explanation
Indices: 346764--346810 Score: 51
Period size: 16 Copynumber: 2.8 Consensus size: 17
346754 ATATTATTTT
346764 AATTAAAAATAATAATA
1 AATTAAAAATAATAATA
* * *
346781 AATTAAATAT-TTTATA
1 AATTAAAAATAATAATA
*
346797 AAATAAAAATAATA
1 AATTAAAAATAATA
346811 TTATAAAATA
Statistics
Matches: 22, Mismatches: 7, Indels: 2
0.71 0.23 0.06
Matches are distributed among these distances:
16 12 0.55
17 10 0.45
ACGTcount: A:0.66, C:0.00, G:0.00, T:0.34
Consensus pattern (17 bp):
AATTAAAAATAATAATA
Found at i:346860 original size:25 final size:25
Alignment explanation
Indices: 346831--346878 Score: 71
Period size: 25 Copynumber: 1.9 Consensus size: 25
346821 TATTTTTTTA
*
346831 ATTATTTTATTTAAAAAT-TATCACT
1 ATTATTTT-TTAAAAAATATATCACT
346856 ATTATTTTTTAAAAAATATATCA
1 ATTATTTTTTAAAAAATATATCA
346879 ATTTTTCAAA
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
24 8 0.38
25 13 0.62
ACGTcount: A:0.44, C:0.06, G:0.00, T:0.50
Consensus pattern (25 bp):
ATTATTTTTTAAAAAATATATCACT
Found at i:346902 original size:19 final size:19
Alignment explanation
Indices: 346855--346909 Score: 69
Period size: 20 Copynumber: 2.9 Consensus size: 19
346845 AAATTATCAC
346855 TATTATTTTTTAAAAAATA
1 TATTATTTTTTAAAAAATA
* *
346874 TATCAATTTTTCAAAAAAT-
1 TAT-TATTTTTTAAAAAATA
346893 TATTA-TTTTTAAAAAAT
1 TATTATTTTTTAAAAAAT
346910 CACAACTTCA
Statistics
Matches: 31, Mismatches: 4, Indels: 4
0.79 0.10 0.10
Matches are distributed among these distances:
17 11 0.35
18 1 0.03
19 6 0.19
20 13 0.42
ACGTcount: A:0.47, C:0.04, G:0.00, T:0.49
Consensus pattern (19 bp):
TATTATTTTTTAAAAAATA
Found at i:347864 original size:24 final size:22
Alignment explanation
Indices: 347816--347888 Score: 64
Period size: 24 Copynumber: 3.4 Consensus size: 22
347806 AAACTATACC
*
347816 ATAT-AAATAAAATATTAA--A
1 ATATAAAATAAAATATTAATTT
*
347835 AAATAAAATAAAATATTATATTTT
1 ATATAAAATAAAATATTA-A-TTT
* *
347859 ATATAATATAAATTATTAATTT
1 ATATAAAATAAAATATTAATTT
347881 AT-TAAAAT
1 ATATAAAAT
347889 TTATTTAATA
Statistics
Matches: 43, Mismatches: 6, Indels: 8
0.75 0.11 0.14
Matches are distributed among these distances:
19 3 0.07
20 13 0.30
21 6 0.14
22 5 0.12
23 1 0.02
24 15 0.35
ACGTcount: A:0.59, C:0.00, G:0.00, T:0.41
Consensus pattern (22 bp):
ATATAAAATAAAATATTAATTT
Found at i:347925 original size:37 final size:38
Alignment explanation
Indices: 347842--347925 Score: 91
Period size: 37 Copynumber: 2.2 Consensus size: 38
347832 AAAAAATAAA
* * * *
347842 ATAAAATATTATATTTTATATAATATAAATTATTAATTT
1 ATAAAA-ATTATATTTAATATAAAATAAATTATAAATAT
*
347881 ATTAAAATT-TATTTAATATAAAATATAATTA-AAATAT
1 ATAAAAATTATATTTAATATAAAATA-AATTATAAATAT
347918 ATAAAAAT
1 ATAAAAAT
347926 AAATAAATAA
Statistics
Matches: 38, Mismatches: 6, Indels: 4
0.79 0.12 0.08
Matches are distributed among these distances:
37 25 0.66
38 8 0.21
39 5 0.13
ACGTcount: A:0.55, C:0.00, G:0.00, T:0.45
Consensus pattern (38 bp):
ATAAAAATTATATTTAATATAAAATAAATTATAAATAT
Found at i:347942 original size:15 final size:14
Alignment explanation
Indices: 347912--347945 Score: 50
Period size: 14 Copynumber: 2.4 Consensus size: 14
347902 AATATAATTA
*
347912 AAATATATAAAAAT
1 AAATAAATAAAAAT
347926 AAATAAATAAAATAT
1 AAATAAATAAAA-AT
347941 AAATA
1 AAATA
347946 TTTTAATCAA
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
14 11 0.61
15 7 0.39
ACGTcount: A:0.74, C:0.00, G:0.00, T:0.26
Consensus pattern (14 bp):
AAATAAATAAAAAT
Found at i:347944 original size:11 final size:11
Alignment explanation
Indices: 347898--347945 Score: 53
Period size: 11 Copynumber: 4.3 Consensus size: 11
347888 TTTATTTAAT
347898 ATAAAATATAA
1 ATAAAATATAA
*
347909 TTAAAATATATA
1 ATAAAATATA-A
*
347921 A-AAATAAATAA
1 ATAAA-ATATAA
347932 ATAAAATATAA
1 ATAAAATATAA
347943 ATA
1 ATA
347946 TTTTAATCAA
Statistics
Matches: 30, Mismatches: 4, Indels: 6
0.75 0.10 0.15
Matches are distributed among these distances:
11 22 0.73
12 8 0.27
ACGTcount: A:0.71, C:0.00, G:0.00, T:0.29
Consensus pattern (11 bp):
ATAAAATATAA
Found at i:349972 original size:2 final size:2
Alignment explanation
Indices: 349967--350014 Score: 89
Period size: 2 Copynumber: 24.5 Consensus size: 2
349957 TCTCTCTATT
349967 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
350009 TA -A TA T
1 TA TA TA T
350015 TGAGCAACCA
Statistics
Matches: 45, Mismatches: 0, Indels: 2
0.96 0.00 0.04
Matches are distributed among these distances:
1 1 0.02
2 44 0.98
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:350380 original size:20 final size:19
Alignment explanation
Indices: 350355--350405 Score: 59
Period size: 20 Copynumber: 2.6 Consensus size: 19
350345 TATATTTAAA
*
350355 TAAAAATATAAAATTATTTT
1 TAAAAATATAAAA-AATTTT
350375 TAAAAATATATAAAAATTTT
1 TAAAAATATA-AAAAATTTT
*
350395 AAAAAAT-TAAA
1 TAAAAATATAAA
350406 TATGAAAAAA
Statistics
Matches: 28, Mismatches: 2, Indels: 4
0.82 0.06 0.12
Matches are distributed among these distances:
18 2 0.07
19 2 0.07
20 21 0.75
21 3 0.11
ACGTcount: A:0.63, C:0.00, G:0.00, T:0.37
Consensus pattern (19 bp):
TAAAAATATAAAAAATTTT
Found at i:360297 original size:23 final size:24
Alignment explanation
Indices: 360269--360314 Score: 67
Period size: 24 Copynumber: 2.0 Consensus size: 24
360259 TTTCCTAACC
360269 CTAATTTTGA-TTTTCAAATTTTG
1 CTAATTTTGATTTTTCAAATTTTG
* *
360292 CTAATTTTTATTTTTCAATTTTT
1 CTAATTTTGATTTTTCAAATTTT
360315 TTAAGCTTTG
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
23 9 0.45
24 11 0.55
ACGTcount: A:0.24, C:0.09, G:0.04, T:0.63
Consensus pattern (24 bp):
CTAATTTTGATTTTTCAAATTTTG
Found at i:360556 original size:17 final size:18
Alignment explanation
Indices: 360534--360581 Score: 55
Period size: 17 Copynumber: 2.8 Consensus size: 18
360524 TTTTTAAGTT
*
360534 ATTTT-ATATTTAAATAA
1 ATTTTAATATATAAATAA
360551 ATTTTAATATATAAAT-A
1 ATTTTAATATATAAATAA
* *
360568 ATTATATTATATAA
1 ATTTTAATATATAA
360582 CTAATTAAAA
Statistics
Matches: 27, Mismatches: 3, Indels: 2
0.84 0.09 0.06
Matches are distributed among these distances:
17 18 0.67
18 9 0.33
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (18 bp):
ATTTTAATATATAAATAA
Found at i:360646 original size:14 final size:12
Alignment explanation
Indices: 360605--360662 Score: 54
Period size: 11 Copynumber: 5.1 Consensus size: 12
360595 TCATATCTCT
*
360605 ATATTATATTTT
1 ATATTATATTTA
360617 A-ATTAT-TTT-
1 ATATTATATTTA
360626 -TATTATATTTA
1 ATATTATATTTA
360637 TATAATTATATTTA
1 -AT-ATTATATTTA
360651 ATATTAT-TTTA
1 ATATTATATTTA
360662 A
1 A
360663 AAAATATTAA
Statistics
Matches: 40, Mismatches: 0, Indels: 13
0.75 0.00 0.25
Matches are distributed among these distances:
9 5 0.12
10 6 0.15
11 10 0.25
12 6 0.15
13 3 0.08
14 10 0.25
ACGTcount: A:0.38, C:0.00, G:0.00, T:0.62
Consensus pattern (12 bp):
ATATTATATTTA
Found at i:361048 original size:82 final size:82
Alignment explanation
Indices: 360954--361119 Score: 332
Period size: 82 Copynumber: 2.0 Consensus size: 82
360944 CTCTCAAGCA
360954 ATCAAACTTCTTGGGAATCGTGATATGATTTACATAATAATAAGAACAACAAATTTTATATTGGA
1 ATCAAACTTCTTGGGAATCGTGATATGATTTACATAATAATAAGAACAACAAATTTTATATTGGA
361019 TATATATATATATATAT
66 TATATATATATATATAT
361036 ATCAAACTTCTTGGGAATCGTGATATGATTTACATAATAATAAGAACAACAAATTTTATATTGGA
1 ATCAAACTTCTTGGGAATCGTGATATGATTTACATAATAATAAGAACAACAAATTTTATATTGGA
361101 TATATATATATATATAT
66 TATATATATATATATAT
361118 AT
1 AT
361120 ATATAAATGC
Statistics
Matches: 84, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
82 84 1.00
ACGTcount: A:0.43, C:0.08, G:0.11, T:0.38
Consensus pattern (82 bp):
ATCAAACTTCTTGGGAATCGTGATATGATTTACATAATAATAAGAACAACAAATTTTATATTGGA
TATATATATATATATAT
Found at i:361107 original size:2 final size:2
Alignment explanation
Indices: 361100--361124 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
361090 TTTATATTGG
361100 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
361125 AATGCATGTC
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:366296 original size:19 final size:19
Alignment explanation
Indices: 366271--366307 Score: 56
Period size: 19 Copynumber: 1.9 Consensus size: 19
366261 ACGAAATAAT
*
366271 TTTTTTAGGAAAAAATCAA
1 TTTTTTAGAAAAAAATCAA
*
366290 TTTTTTATAAAAAAATCA
1 TTTTTTAGAAAAAAATCA
366308 TATAAATTTT
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
19 16 1.00
ACGTcount: A:0.49, C:0.05, G:0.05, T:0.41
Consensus pattern (19 bp):
TTTTTTAGAAAAAAATCAA
Found at i:373741 original size:19 final size:19
Alignment explanation
Indices: 373713--373750 Score: 67
Period size: 19 Copynumber: 2.0 Consensus size: 19
373703 GTGCTTTCAG
373713 TCAGACAGAGAGGAAGAGA
1 TCAGACAGAGAGGAAGAGA
*
373732 TCAGATAGAGAGGAAGAGA
1 TCAGACAGAGAGGAAGAGA
373751 GAGAGAGAGT
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
19 18 1.00
ACGTcount: A:0.47, C:0.08, G:0.37, T:0.08
Consensus pattern (19 bp):
TCAGACAGAGAGGAAGAGA
Found at i:374824 original size:20 final size:20
Alignment explanation
Indices: 374780--374826 Score: 60
Period size: 20 Copynumber: 2.4 Consensus size: 20
374770 TATGTCTTAA
374780 TATATTATTTAAAATTAATT
1 TATATTATTTAAAATTAATT
* *
374800 AATATTATTTATAA-TAATAT
1 TATATTATTTAAAATTAAT-T
374820 TATATTA
1 TATATTA
374827 AATGTAATAA
Statistics
Matches: 23, Mismatches: 3, Indels: 2
0.82 0.11 0.07
Matches are distributed among these distances:
19 4 0.17
20 19 0.83
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (20 bp):
TATATTATTTAAAATTAATT
Found at i:375851 original size:2 final size:2
Alignment explanation
Indices: 375844--375880 Score: 74
Period size: 2 Copynumber: 18.5 Consensus size: 2
375834 CAAGAAGAGA
375844 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
375881 AAGTTTGGGG
Statistics
Matches: 35, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 35 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:376946 original size:17 final size:19
Alignment explanation
Indices: 376920--376954 Score: 56
Period size: 18 Copynumber: 1.9 Consensus size: 19
376910 CATATTTTTT
376920 AAATTATTAATAT-TTATA
1 AAATTATTAATATATTATA
376938 AAATT-TTAATATATTAT
1 AAATTATTAATATATTAT
376955 TATATATTTA
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
17 7 0.44
18 9 0.56
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (19 bp):
AAATTATTAATATATTATA
Found at i:376964 original size:19 final size:19
Alignment explanation
Indices: 376942--377001 Score: 54
Period size: 19 Copynumber: 3.2 Consensus size: 19
376932 TTTATAAAAT
376942 TTTAATATATTATTATATA
1 TTTAATATATTATTATATA
376961 TTT-ATAT-TATACTTATATA
1 TTTAATATAT-TA-TTATATA
* *
376980 TTAAATTATATT-TTAAATA
1 TTTAA-TATATTATTATATA
376999 TTT
1 TTT
377002 TTTTATATTT
Statistics
Matches: 33, Mismatches: 3, Indels: 10
0.72 0.07 0.22
Matches are distributed among these distances:
17 1 0.03
18 6 0.18
19 20 0.61
20 1 0.03
21 4 0.12
22 1 0.03
ACGTcount: A:0.40, C:0.02, G:0.00, T:0.58
Consensus pattern (19 bp):
TTTAATATATTATTATATA
Found at i:377351 original size:23 final size:22
Alignment explanation
Indices: 377282--377347 Score: 62
Period size: 23 Copynumber: 2.8 Consensus size: 22
377272 ATTAAAATAT
*
377282 AATATAAATTATGATA-TAAAA
1 AATATAAATTATAATATTAAAA
377303 AATTTATAAATATATCAATATATAAAA
1 AA--TATAAAT-TAT-AATAT-TAAAA
*
377330 AATATAAATTATTATATT
1 AATATAAATTATAATATT
377348 TAAATCATAT
Statistics
Matches: 37, Mismatches: 2, Indels: 11
0.74 0.04 0.22
Matches are distributed among these distances:
21 2 0.05
22 1 0.03
23 11 0.30
24 6 0.16
25 10 0.27
27 7 0.19
ACGTcount: A:0.58, C:0.02, G:0.02, T:0.39
Consensus pattern (22 bp):
AATATAAATTATAATATTAAAA
Found at i:377888 original size:1 final size:1
Alignment explanation
Indices: 377882--377907 Score: 52
Period size: 1 Copynumber: 26.0 Consensus size: 1
377872 CCCGTTTCTC
377882 TTTTTTTTTTTTTTTTTTTTTTTTTT
1 TTTTTTTTTTTTTTTTTTTTTTTTTT
377908 ATTCTTGAGT
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
1 25 1.00
ACGTcount: A:0.00, C:0.00, G:0.00, T:1.00
Consensus pattern (1 bp):
T
Found at i:378839 original size:4 final size:4
Alignment explanation
Indices: 378830--378859 Score: 60
Period size: 4 Copynumber: 7.5 Consensus size: 4
378820 AGGACTTAAT
378830 TTTA TTTA TTTA TTTA TTTA TTTA TTTA TT
1 TTTA TTTA TTTA TTTA TTTA TTTA TTTA TT
378860 GCTTTGAATA
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 26 1.00
ACGTcount: A:0.23, C:0.00, G:0.00, T:0.77
Consensus pattern (4 bp):
TTTA
Found at i:379116 original size:15 final size:15
Alignment explanation
Indices: 379079--379119 Score: 50
Period size: 13 Copynumber: 2.9 Consensus size: 15
379069 TTTAAGTAAA
* *
379079 ATATAATAAAAAATT
1 ATATAATTAAAATTT
379094 A-A-AATTAAAATTT
1 ATATAATTAAAATTT
379107 ATATAATTAAAAT
1 ATATAATTAAAAT
379120 AATTAATATA
Statistics
Matches: 22, Mismatches: 2, Indels: 4
0.79 0.07 0.14
Matches are distributed among these distances:
13 10 0.45
14 2 0.09
15 10 0.45
ACGTcount: A:0.63, C:0.00, G:0.00, T:0.37
Consensus pattern (15 bp):
ATATAATTAAAATTT
Found at i:379140 original size:20 final size:22
Alignment explanation
Indices: 379117--379171 Score: 60
Period size: 20 Copynumber: 2.5 Consensus size: 22
379107 ATATAATTAA
379117 AATAATTAATATAT-TATAT-T
1 AATAATTAATATATATATATAT
* *
379137 AATACTTAAAATTATATATATAT
1 AATAATTAATA-TATATATATAT
*
379160 AATAATTTATAT
1 AATAATTAATAT
379172 CGTATTTATA
Statistics
Matches: 27, Mismatches: 5, Indels: 4
0.75 0.14 0.11
Matches are distributed among these distances:
20 9 0.33
21 3 0.11
22 6 0.22
23 9 0.33
ACGTcount: A:0.51, C:0.02, G:0.00, T:0.47
Consensus pattern (22 bp):
AATAATTAATATATATATATAT
Found at i:379895 original size:26 final size:26
Alignment explanation
Indices: 379847--379896 Score: 64
Period size: 26 Copynumber: 1.9 Consensus size: 26
379837 CAAATTTAAA
*
379847 TATTTATATTTATATATTCAAAATTT
1 TATTTATATTTATATATTAAAAATTT
* * *
379873 TATTTATTTTTATTTTTTAAAAAT
1 TATTTATATTTATATATTAAAAAT
379897 AAAATAAAAA
Statistics
Matches: 20, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
26 20 1.00
ACGTcount: A:0.36, C:0.02, G:0.00, T:0.62
Consensus pattern (26 bp):
TATTTATATTTATATATTAAAAATTT
Found at i:380370 original size:21 final size:22
Alignment explanation
Indices: 380346--380387 Score: 59
Period size: 21 Copynumber: 2.0 Consensus size: 22
380336 TTTATTAATA
*
380346 TTATTTATAAA-ATTTAAAATT
1 TTATTAATAAATATTTAAAATT
*
380367 TTATTAATAAATATTTTAAAT
1 TTATTAATAAATATTTAAAAT
380388 ATAATTTAAA
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
21 10 0.56
22 8 0.44
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (22 bp):
TTATTAATAAATATTTAAAATT
Found at i:380451 original size:41 final size:43
Alignment explanation
Indices: 380372--380451 Score: 101
Period size: 43 Copynumber: 1.9 Consensus size: 43
380362 AAATTTTATT
* *
380372 AATAAATATTTTAAATATAATTTAAAATAATTATATTAAGTAA
1 AATAAATATTTTAAATATAATTAAAAATAATTAAATTAAGTAA
* * *
380415 AATAATTATTTTTAATA-AATTAAAAAT-TTTAAATTAA
1 AATAAATATTTTAAATATAATTAAAAATAATTAAATTAA
380452 TTATTTTATT
Statistics
Matches: 32, Mismatches: 5, Indels: 2
0.82 0.13 0.05
Matches are distributed among these distances:
41 8 0.25
42 9 0.28
43 15 0.47
ACGTcount: A:0.55, C:0.00, G:0.01, T:0.44
Consensus pattern (43 bp):
AATAAATATTTTAAATATAATTAAAAATAATTAAATTAAGTAA
Found at i:382927 original size:22 final size:23
Alignment explanation
Indices: 382886--382928 Score: 61
Period size: 22 Copynumber: 1.9 Consensus size: 23
382876 CGGCCAACAA
* *
382886 TTTATAACTTAGCATGTTTTGAC
1 TTTATAACATAGCATATTTTGAC
382909 TTTATAACAT-GCATATTTTG
1 TTTATAACATAGCATATTTTG
382929 GATATAGTTT
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
22 9 0.50
23 9 0.50
ACGTcount: A:0.28, C:0.12, G:0.12, T:0.49
Consensus pattern (23 bp):
TTTATAACATAGCATATTTTGAC
Found at i:385762 original size:3 final size:3
Alignment explanation
Indices: 385754--385782 Score: 58
Period size: 3 Copynumber: 9.7 Consensus size: 3
385744 AAACTCCTTT
385754 TTC TTC TTC TTC TTC TTC TTC TTC TTC TT
1 TTC TTC TTC TTC TTC TTC TTC TTC TTC TT
385783 TGTATGGATC
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 26 1.00
ACGTcount: A:0.00, C:0.31, G:0.00, T:0.69
Consensus pattern (3 bp):
TTC
Found at i:391708 original size:2 final size:2
Alignment explanation
Indices: 391701--391725 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
391691 CTATTGAAAT
391701 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
391726 TAACCCTCTT
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:391883 original size:24 final size:24
Alignment explanation
Indices: 391828--391906 Score: 85
Period size: 24 Copynumber: 3.4 Consensus size: 24
391818 AATCTAACTT
*
391828 TTAAGAATTTATATTTA-ATA-TA
1 TTAATAATTTATATTTATATATTA
* *
391850 TTGATGATTTATATTTATATATTA
1 TTAATAATTTATATTTATATATTA
*
391874 TTAATAATTTATA-TTATTATTTTA
1 TTAATAATTTATATTTA-TATATTA
391898 TTAA-AATTT
1 TTAATAATTT
391907 TTAAAAATAA
Statistics
Matches: 48, Mismatches: 6, Indels: 5
0.81 0.10 0.08
Matches are distributed among these distances:
22 14 0.29
23 11 0.23
24 23 0.48
ACGTcount: A:0.39, C:0.00, G:0.04, T:0.57
Consensus pattern (24 bp):
TTAATAATTTATATTTATATATTA
Found at i:395331 original size:2 final size:2
Alignment explanation
Indices: 395324--395357 Score: 68
Period size: 2 Copynumber: 17.0 Consensus size: 2
395314 TCTATCTATC
395324 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
395358 ATGTACAGTC
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 32 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:399251 original size:14 final size:14
Alignment explanation
Indices: 399229--399263 Score: 52
Period size: 14 Copynumber: 2.5 Consensus size: 14
399219 TTTATTATAT
*
399229 TTTAAAAATATTAA
1 TTTATAAATATTAA
399243 TTTATAAATATTAA
1 TTTATAAATATTAA
*
399257 TTCATAA
1 TTTATAA
399264 GAAATTGATA
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
14 19 1.00
ACGTcount: A:0.51, C:0.03, G:0.00, T:0.46
Consensus pattern (14 bp):
TTTATAAATATTAA
Found at i:399712 original size:13 final size:13
Alignment explanation
Indices: 399694--399739 Score: 53
Period size: 13 Copynumber: 3.8 Consensus size: 13
399684 TTTAAATGTG
399694 ATATAAATATTTA
1 ATATAAATATTTA
*
399707 ATATAAATAATTA
1 ATATAAATATTTA
*
399720 AT-TAAA-ATATA
1 ATATAAATATTTA
399731 ATA-AAATAT
1 ATATAAATAT
399740 AAAAAATAAT
Statistics
Matches: 28, Mismatches: 3, Indels: 5
0.78 0.08 0.14
Matches are distributed among these distances:
11 8 0.29
12 6 0.21
13 14 0.50
ACGTcount: A:0.61, C:0.00, G:0.00, T:0.39
Consensus pattern (13 bp):
ATATAAATATTTA
Found at i:399761 original size:28 final size:29
Alignment explanation
Indices: 399706--399768 Score: 85
Period size: 28 Copynumber: 2.2 Consensus size: 29
399696 ATAAATATTT
* *
399706 AATATAAATAATTAATTAAAATATAATAA
1 AATATAAATAAATAATTAAAATAAAATAA
399735 AATATAAA-AAATAA-TATAAATAAAATAA
1 AATATAAATAAATAATTA-AAATAAAATAA
399763 AATATA
1 AATATA
399769 TTAAAATATT
Statistics
Matches: 31, Mismatches: 2, Indels: 3
0.86 0.06 0.08
Matches are distributed among these distances:
27 2 0.06
28 21 0.68
29 8 0.26
ACGTcount: A:0.70, C:0.00, G:0.00, T:0.30
Consensus pattern (29 bp):
AATATAAATAAATAATTAAAATAAAATAA
Found at i:399774 original size:38 final size:40
Alignment explanation
Indices: 399705--399791 Score: 115
Period size: 38 Copynumber: 2.2 Consensus size: 40
399695 TATAAATATT
399705 TAATATAAATAATTAATTAAAATATAATAAAATATAAAAAA
1 TAATATAAATAA-TAATTAAAATATAATAAAATATAAAAAA
* * *
399746 TAATATAAATAA-AA-TAAAATATATTAAAATATTAAAAT
1 TAATATAAATAATAATTAAAATATAATAAAATATAAAAAA
*
399784 TTATATAA
1 TAATATAA
399792 CATATATTAT
Statistics
Matches: 42, Mismatches: 4, Indels: 3
0.86 0.08 0.06
Matches are distributed among these distances:
38 28 0.67
39 2 0.05
41 12 0.29
ACGTcount: A:0.66, C:0.00, G:0.00, T:0.34
Consensus pattern (40 bp):
TAATATAAATAATAATTAAAATATAATAAAATATAAAAAA
Found at i:399783 original size:28 final size:27
Alignment explanation
Indices: 399706--399783 Score: 84
Period size: 28 Copynumber: 2.7 Consensus size: 27
399696 ATAAATATTT
* *
399706 AATATAAATAATTAATTAAAATATAATAA
1 AATATAAA-AAAT-ATTAAAATAAAATAA
*
399735 AATATAAAAAATAATATAAATAAAATAA
1 AATATAAAAAATATTA-AAATAAAATAA
*
399763 AATATATTAAAATATTAAAAT
1 AATATA-AAAAATATTAAAAT
399784 TTATATAACA
Statistics
Matches: 42, Mismatches: 5, Indels: 5
0.81 0.10 0.10
Matches are distributed among these distances:
27 3 0.07
28 23 0.55
29 16 0.38
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.32
Consensus pattern (27 bp):
AATATAAAAAATATTAAAATAAAATAA
Found at i:399811 original size:32 final size:31
Alignment explanation
Indices: 399764--399834 Score: 106
Period size: 32 Copynumber: 2.3 Consensus size: 31
399754 ATAAAATAAA
** *
399764 ATATATTAAAATATTAAAATTTATATAACAT
1 ATATATTAATGTATTAAAATTTATATAAAAT
399795 ATATTATTAATGTATTAAAATTTATATAAAAT
1 ATA-TATTAATGTATTAAAATTTATATAAAAT
399827 ATATATTA
1 ATATATTA
399835 CTTTAAATAT
Statistics
Matches: 36, Mismatches: 3, Indels: 2
0.88 0.07 0.05
Matches are distributed among these distances:
31 8 0.22
32 28 0.78
ACGTcount: A:0.52, C:0.01, G:0.01, T:0.45
Consensus pattern (31 bp):
ATATATTAATGTATTAAAATTTATATAAAAT
Found at i:399824 original size:11 final size:10
Alignment explanation
Indices: 399720--399830 Score: 70
Period size: 10 Copynumber: 11.2 Consensus size: 10
399710 TAAATAATTA
399720 ATTAAAATAT
1 ATTAAAATAT
*
399730 AATAAAATAT
1 ATTAAAATAT
399740 A--AAAA-AT
1 ATTAAAATAT
* *
399747 AATATAAATAA
1 ATTA-AAATAT
*
399758 AATAAAATAT
1 ATTAAAATAT
399768 ATT-AAA-AT
1 ATTAAAATAT
*
399776 ATTAAAATTT
1 ATTAAAATAT
*
399786 ATATAACATAT
1 AT-TAAAATAT
* *
399797 ATTATTAATGT
1 ATTA-AAATAT
*
399808 ATTAAAATTT
1 ATTAAAATAT
399818 ATATAAAATAT
1 AT-TAAAATAT
399829 AT
1 AT
399831 ATTACTTTAA
Statistics
Matches: 79, Mismatches: 13, Indels: 17
0.72 0.12 0.16
Matches are distributed among these distances:
7 3 0.04
8 9 0.11
9 7 0.09
10 31 0.39
11 29 0.37
ACGTcount: A:0.60, C:0.01, G:0.01, T:0.38
Consensus pattern (10 bp):
ATTAAAATAT
Found at i:399852 original size:34 final size:35
Alignment explanation
Indices: 399772--399852 Score: 89
Period size: 32 Copynumber: 2.4 Consensus size: 35
399762 AAATATATTA
*
399772 AAATATTAAAATTTATATAACATATATTATTAATGT
1 AAATA-TAAAATTTATATAAAATATATTATTAATGT
* *
399808 --AT-TAAAATTTATATAAAATATA-TATTACTTT
1 AAATATAAAATTTATATAAAATATATTATTAATGT
*
399839 AAATATAATATTTA
1 AAATATAAAATTTA
399853 AAATATTTAA
Statistics
Matches: 38, Mismatches: 4, Indels: 8
0.76 0.08 0.16
Matches are distributed among these distances:
31 7 0.18
32 19 0.50
33 2 0.05
34 10 0.26
ACGTcount: A:0.51, C:0.02, G:0.01, T:0.46
Consensus pattern (35 bp):
AAATATAAAATTTATATAAAATATATTATTAATGT
Found at i:399863 original size:22 final size:21
Alignment explanation
Indices: 399836--399892 Score: 64
Period size: 22 Copynumber: 2.7 Consensus size: 21
399826 TATATATTAC
399836 TTTAAATATAATATTTAAAATA
1 TTTAAATATAATATTT-AAATA
*
399858 TTTAAATATGATA--TAAATA
1 TTTAAATATAATATTTAAATA
*
399877 TATAAATTATAATATT
1 TTTAAA-TATAATATT
399893 ATTATTATTA
Statistics
Matches: 29, Mismatches: 3, Indels: 6
0.76 0.08 0.16
Matches are distributed among these distances:
19 10 0.34
20 7 0.24
22 12 0.41
ACGTcount: A:0.53, C:0.00, G:0.02, T:0.46
Consensus pattern (21 bp):
TTTAAATATAATATTTAAATA
Found at i:400204 original size:21 final size:20
Alignment explanation
Indices: 400158--400207 Score: 57
Period size: 21 Copynumber: 2.5 Consensus size: 20
400148 AAATTTTATG
* *
400158 TATAATTAATATATTAATAA
1 TATAATTATTAAATTAATAA
400178 -ATTAATTATTAAATTTAATAA
1 TA-TAATTATTAAA-TTAATAA
400199 TATAATTAT
1 TATAATTAT
400208 ACTCGTTATG
Statistics
Matches: 25, Mismatches: 2, Indels: 5
0.78 0.06 0.16
Matches are distributed among these distances:
19 1 0.04
20 9 0.36
21 14 0.56
22 1 0.04
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (20 bp):
TATAATTATTAAATTAATAA
Found at i:400555 original size:23 final size:23
Alignment explanation
Indices: 400514--400561 Score: 62
Period size: 23 Copynumber: 2.1 Consensus size: 23
400504 TTTAACACGT
*
400514 TTATTTATTTATGTCATATTCATA
1 TTATTTATTCATGTCATATT-ATA
*
400538 TTATTT-TTCATGTTATATTATA
1 TTATTTATTCATGTCATATTATA
400560 TT
1 TT
400562 TAAATTTTTT
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
22 5 0.23
23 11 0.50
24 6 0.27
ACGTcount: A:0.27, C:0.06, G:0.04, T:0.62
Consensus pattern (23 bp):
TTATTTATTCATGTCATATTATA
Found at i:400741 original size:14 final size:15
Alignment explanation
Indices: 400724--400776 Score: 58
Period size: 14 Copynumber: 3.7 Consensus size: 15
400714 TAAAATATAA
400724 ATATAATA-AAATTT
1 ATATAATATAAATTT
400738 ATATAATATAAA-TT
1 ATATAATATAAATTT
* *
400752 A-AAAATTTAAATTT
1 ATATAATATAAATTT
400766 ATATAAATATA
1 ATAT-AATATA
400777 TTAATTTTTA
Statistics
Matches: 31, Mismatches: 4, Indels: 6
0.76 0.10 0.15
Matches are distributed among these distances:
13 8 0.26
14 14 0.45
15 4 0.13
16 5 0.16
ACGTcount: A:0.58, C:0.00, G:0.00, T:0.42
Consensus pattern (15 bp):
ATATAATATAAATTT
Found at i:402479 original size:145 final size:145
Alignment explanation
Indices: 402191--402458 Score: 362
Period size: 145 Copynumber: 1.8 Consensus size: 145
402181 AAAGTTGCAG
* *
402191 AGGATAAAATACACTCACTTCGAAACGAATTTTTGAAACTCAAACTTTCAACCGAGTAGTGTGGT
1 AGGATAAAATACACTCACTTCGAAACGAAATTTTCAAACTCAAACTTTCAACCGAGTAGTGTGGT
* *
402256 GATTCCTAATTTTTCGAAGTGCTAAAAGTATTCTAAATTTAAAATTGCTGGTAATTTCCGTCCTT
66 GATTCCTAATTTCTCGAAGTGCTAAAAGTATTCTAAATTTAAAATTGCTCGTAATTTCCGTCCTT
402321 TAATCGCTGAGATTC
131 TAATCGCTGAGATTC
* * * * *
402336 AGGATGAAATATACTCACTTTGAAACGAAATTTTCAAATTCAAA-TTTCAACCGAGTAGTTTGGT
1 AGGATAAAATACACTCACTTCGAAACGAAATTTTCAAACTCAAACTTTCAACCGAGTAGTGTGGT
* * * * *
402400 GGTTTCCTAA-TTCTCAGAATTGCTAAAGGTATTTTAAAATTT-AAATTTCTCGTAATTTC
66 -GATTCCTAATTTCTC-GAAGTGCTAAAAGTATTCT-AAATTTAAAATTGCTCGTAATTTC
402459 TCTTTTTTAA
Statistics
Matches: 106, Mismatches: 14, Indels: 6
0.84 0.11 0.05
Matches are distributed among these distances:
144 23 0.22
145 77 0.73
146 6 0.06
ACGTcount: A:0.33, C:0.16, G:0.15, T:0.36
Consensus pattern (145 bp):
AGGATAAAATACACTCACTTCGAAACGAAATTTTCAAACTCAAACTTTCAACCGAGTAGTGTGGT
GATTCCTAATTTCTCGAAGTGCTAAAAGTATTCTAAATTTAAAATTGCTCGTAATTTCCGTCCTT
TAATCGCTGAGATTC
Found at i:402775 original size:24 final size:24
Alignment explanation
Indices: 402747--402792 Score: 92
Period size: 24 Copynumber: 1.9 Consensus size: 24
402737 GAGTTAAGTT
402747 AGCTTCTTTAATTCAGTAAGTATA
1 AGCTTCTTTAATTCAGTAAGTATA
402771 AGCTTCTTTAATTCAGTAAGTA
1 AGCTTCTTTAATTCAGTAAGTA
402793 ATTTCATTTA
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
24 22 1.00
ACGTcount: A:0.33, C:0.13, G:0.13, T:0.41
Consensus pattern (24 bp):
AGCTTCTTTAATTCAGTAAGTATA
Found at i:411362 original size:13 final size:13
Alignment explanation
Indices: 411344--411373 Score: 60
Period size: 13 Copynumber: 2.3 Consensus size: 13
411334 AAGTCTACAC
411344 TAAACCCCAAAGG
1 TAAACCCCAAAGG
411357 TAAACCCCAAAGG
1 TAAACCCCAAAGG
411370 TAAA
1 TAAA
411374 ACTAATAACA
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 17 1.00
ACGTcount: A:0.50, C:0.27, G:0.13, T:0.10
Consensus pattern (13 bp):
TAAACCCCAAAGG
Found at i:416705 original size:49 final size:49
Alignment explanation
Indices: 416651--416747 Score: 176
Period size: 49 Copynumber: 2.0 Consensus size: 49
416641 TGCTGGCATT
*
416651 CGCATTACTTTATAAATGTTATTAACTGCCATGGCCCTTCAGTTATAAC
1 CGCATTACTTTATAAATGTTATTAACTGCAATGGCCCTTCAGTTATAAC
*
416700 CGCATTACTTTATAAATGTTATTAACTGCAATGGTCCTTCAGTTATAA
1 CGCATTACTTTATAAATGTTATTAACTGCAATGGCCCTTCAGTTATAA
416748 ATAAGGGCTC
Statistics
Matches: 46, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
49 46 1.00
ACGTcount: A:0.30, C:0.20, G:0.12, T:0.38
Consensus pattern (49 bp):
CGCATTACTTTATAAATGTTATTAACTGCAATGGCCCTTCAGTTATAAC
Found at i:417037 original size:16 final size:16
Alignment explanation
Indices: 417016--417048 Score: 66
Period size: 16 Copynumber: 2.1 Consensus size: 16
417006 CTGTTCCTTA
417016 AAGGTTTTAACATATG
1 AAGGTTTTAACATATG
417032 AAGGTTTTAACATATG
1 AAGGTTTTAACATATG
417048 A
1 A
417049 GTGGTAAATA
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 17 1.00
ACGTcount: A:0.39, C:0.06, G:0.18, T:0.36
Consensus pattern (16 bp):
AAGGTTTTAACATATG
Found at i:424509 original size:20 final size:20
Alignment explanation
Indices: 424448--424510 Score: 51
Period size: 20 Copynumber: 3.3 Consensus size: 20
424438 CGAAAATTTG
*
424448 ATATTAAATTTACAAAA-T-
1 ATATTAAATTTAAAAAATTA
*** *
424466 -TATTAAATTTAATTGATGA
1 ATATTAAATTTAAAAAATTA
*
424485 CTATTAAATTTAAAAAATTA
1 ATATTAAATTTAAAAAATTA
424505 ATATTA
1 ATATTA
424511 TATATTTTAA
Statistics
Matches: 32, Mismatches: 10, Indels: 4
0.70 0.22 0.09
Matches are distributed among these distances:
17 12 0.38
20 20 0.62
ACGTcount: A:0.51, C:0.03, G:0.03, T:0.43
Consensus pattern (20 bp):
ATATTAAATTTAAAAAATTA
Found at i:425465 original size:33 final size:33
Alignment explanation
Indices: 425398--425463 Score: 82
Period size: 34 Copynumber: 2.0 Consensus size: 33
425388 ATCTGATCCA
*
425398 ATTTAAATTATTATTTATAAATAAAATATTTTT
1 ATTTAAATTATTATTAATAAATAAAATATTTTT
425431 ATTTAAATTTAATTA-TAATAATATAAAA-ATTTT
1 ATTTAAA-TT-ATTATTAATAA-ATAAAATATTTT
425464 ATATAAAATA
Statistics
Matches: 29, Mismatches: 1, Indels: 5
0.83 0.03 0.14
Matches are distributed among these distances:
33 7 0.24
34 12 0.41
35 10 0.34
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (33 bp):
ATTTAAATTATTATTAATAAATAAAATATTTTT
Found at i:426117 original size:2 final size:2
Alignment explanation
Indices: 426110--426146 Score: 74
Period size: 2 Copynumber: 18.5 Consensus size: 2
426100 CTTACTATGC
426110 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
426147 CATACACACA
Statistics
Matches: 35, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 35 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:426258 original size:2 final size:2
Alignment explanation
Indices: 426253--426291 Score: 78
Period size: 2 Copynumber: 19.5 Consensus size: 2
426243 TGTTAAAAAC
426253 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
426292 GTGCCCACGT
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:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:426757 original size:2 final size:2
Alignment explanation
Indices: 426750--426783 Score: 68
Period size: 2 Copynumber: 17.0 Consensus size: 2
426740 CCATCGTATT
426750 TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG
1 TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG
426784 CAATTTGATA
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 32 1.00
ACGTcount: A:0.00, C:0.00, G:0.50, T:0.50
Consensus pattern (2 bp):
TG
Found at i:427453 original size:2 final size:2
Alignment explanation
Indices: 427446--427473 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
427436 TTTACAAGTG
427446 TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA
427474 GAATAACTAA
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:430301 original size:13 final size:13
Alignment explanation
Indices: 430266--430303 Score: 60
Period size: 12 Copynumber: 3.0 Consensus size: 13
430256 GTTTATTAAA
430266 TTTTAATTAAATT
1 TTTTAATTAAATT
*
430279 TTTTTA-TAAATT
1 TTTTAATTAAATT
430291 TTTTAATTAAATT
1 TTTTAATTAAATT
430304 ATTATCACTT
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
12 11 0.50
13 11 0.50
ACGTcount: A:0.37, C:0.00, G:0.00, T:0.63
Consensus pattern (13 bp):
TTTTAATTAAATT
Found at i:430535 original size:17 final size:18
Alignment explanation
Indices: 430497--430536 Score: 57
Period size: 17 Copynumber: 2.3 Consensus size: 18
430487 TTAAAATAAT
*
430497 TAAATAAATATAACATAA
1 TAAATAAATATAACACAA
430515 -AAATAAATA-AACACAA
1 TAAATAAATATAACACAA
430531 TAAATA
1 TAAATA
430537 TAAAAATATA
Statistics
Matches: 20, Mismatches: 1, Indels: 3
0.83 0.04 0.12
Matches are distributed among these distances:
16 6 0.30
17 14 0.70
ACGTcount: A:0.70, C:0.07, G:0.00, T:0.23
Consensus pattern (18 bp):
TAAATAAATATAACACAA
Found at i:430646 original size:17 final size:16
Alignment explanation
Indices: 430588--430646 Score: 59
Period size: 16 Copynumber: 3.8 Consensus size: 16
430578 ATTAATTTGT
430588 TAAAATTTAT-ATAAA
1 TAAAATTTATAATAAA
** **
430603 TAAAAAATATTTTAAA
1 TAAAATTTATAATAAA
430619 TAAAA-TTATAATATAA
1 TAAAATTTATAATA-AA
430635 TAAAATTTATAA
1 TAAAATTTATAA
430647 AATAAACATA
Statistics
Matches: 35, Mismatches: 6, Indels: 4
0.78 0.13 0.09
Matches are distributed among these distances:
15 13 0.37
16 16 0.46
17 6 0.17
ACGTcount: A:0.61, C:0.00, G:0.00, T:0.39
Consensus pattern (16 bp):
TAAAATTTATAATAAA
Found at i:430651 original size:17 final size:16
Alignment explanation
Indices: 430617--430651 Score: 52
Period size: 17 Copynumber: 2.1 Consensus size: 16
430607 AAATATTTTA
*
430617 AATAAAATTATAATAT
1 AATAAAATTATAAAAT
430633 AATAAAATTTATAAAAT
1 AATAAAA-TTATAAAAT
430650 AA
1 AA
430652 ACATAATTAT
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
16 7 0.41
17 10 0.59
ACGTcount: A:0.66, C:0.00, G:0.00, T:0.34
Consensus pattern (16 bp):
AATAAAATTATAAAAT
Found at i:431290 original size:16 final size:17
Alignment explanation
Indices: 431269--431305 Score: 58
Period size: 16 Copynumber: 2.2 Consensus size: 17
431259 TTATTTTTTA
*
431269 AAAAAATAAATAAT-TT
1 AAAAAATAAAAAATATT
431285 AAAAAATAAAAAATATT
1 AAAAAATAAAAAATATT
431302 AAAA
1 AAAA
431306 CTTTTATTCT
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
16 13 0.68
17 6 0.32
ACGTcount: A:0.76, C:0.00, G:0.00, T:0.24
Consensus pattern (17 bp):
AAAAAATAAAAAATATT
Found at i:431582 original size:3 final size:3
Alignment explanation
Indices: 431574--431612 Score: 78
Period size: 3 Copynumber: 13.0 Consensus size: 3
431564 TAGATGTAAC
431574 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT
431613 TTTGAAAAAG
Statistics
Matches: 36, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 36 1.00
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (3 bp):
ATT
Found at i:434542 original size:15 final size:14
Alignment explanation
Indices: 434501--434552 Score: 52
Period size: 15 Copynumber: 3.7 Consensus size: 14
434491 TAATATAGTA
*
434501 TGATATTATA-TTA
1 TGATATTATATTTT
*
434514 TGATATTACATTTT
1 TGATATTATATTTT
*
434528 GTGATATTATTTTTT
1 -TGATATTATATTTT
*
434543 TAATATTATA
1 TGATATTATA
434553 AATTTAATTT
Statistics
Matches: 31, Mismatches: 6, Indels: 3
0.77 0.15 0.08
Matches are distributed among these distances:
13 9 0.29
14 10 0.32
15 12 0.39
ACGTcount: A:0.33, C:0.02, G:0.08, T:0.58
Consensus pattern (14 bp):
TGATATTATATTTT
Found at i:434623 original size:26 final size:28
Alignment explanation
Indices: 434580--434633 Score: 76
Period size: 26 Copynumber: 2.0 Consensus size: 28
434570 GTAAAAAAAA
*
434580 TTTAATTACTTTATATTTAAAATTTTAT
1 TTTAATCACTTTATATTTAAAATTTTAT
*
434608 TTTAATCA-TTTA-ATTTGAAATTTTAT
1 TTTAATCACTTTATATTTAAAATTTTAT
434634 ATTATTTTAA
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
26 13 0.54
27 4 0.17
28 7 0.29
ACGTcount: A:0.35, C:0.04, G:0.02, T:0.59
Consensus pattern (28 bp):
TTTAATCACTTTATATTTAAAATTTTAT
Found at i:435548 original size:36 final size:34
Alignment explanation
Indices: 435494--435574 Score: 83
Period size: 34 Copynumber: 2.3 Consensus size: 34
435484 ATTATAATTT
* *
435494 TTAAAAATTTTAAAAATTTATATTAATATTATT-AAA
1 TTAAAAATTATAAAAA-TT-T-TTAATATAATTAAAA
**
435530 TTAAAAATTATATCAATTTTTAATATAATTAAAA
1 TTAAAAATTATAAAAATTTTTAATATAATTAAAA
*
435564 TAAAAAATTAT
1 TTAAAAATTAT
435575 TTTATTTATC
Statistics
Matches: 39, Mismatches: 5, Indels: 4
0.81 0.10 0.08
Matches are distributed among these distances:
33 10 0.26
34 14 0.36
35 2 0.05
36 13 0.33
ACGTcount: A:0.54, C:0.01, G:0.00, T:0.44
Consensus pattern (34 bp):
TTAAAAATTATAAAAATTTTTAATATAATTAAAA
Found at i:435560 original size:28 final size:27
Alignment explanation
Indices: 435503--435563 Score: 70
Period size: 27 Copynumber: 2.2 Consensus size: 27
435493 TTTAAAAATT
* *
435503 TTAAAAATTTATATTAATATTATTAAA
1 TTAAAAATTTATATCAATATTAATAAA
*
435530 TTAAAAA-TTATATCAATTTTTAATATAA
1 TTAAAAATTTATATCAA-TATTAATA-AA
435558 TTAAAA
1 TTAAAA
435564 TAAAAAATTA
Statistics
Matches: 29, Mismatches: 3, Indels: 3
0.83 0.09 0.09
Matches are distributed among these distances:
26 8 0.28
27 13 0.45
28 8 0.28
ACGTcount: A:0.52, C:0.02, G:0.00, T:0.46
Consensus pattern (27 bp):
TTAAAAATTTATATCAATATTAATAAA
Found at i:436414 original size:13 final size:14
Alignment explanation
Indices: 436396--436438 Score: 52
Period size: 13 Copynumber: 3.1 Consensus size: 14
436386 TATTTATAAT
436396 ATAATAAAATA-TA
1 ATAATAAAATATTA
*
436409 ATAATATAATATTA
1 ATAATAAAATATTA
*
436423 ATACATAAAATCTTA
1 ATA-ATAAAATATTA
436438 A
1 A
436439 ATATATATTT
Statistics
Matches: 25, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
13 10 0.40
14 5 0.20
15 10 0.40
ACGTcount: A:0.60, C:0.05, G:0.00, T:0.35
Consensus pattern (14 bp):
ATAATAAAATATTA
Found at i:436875 original size:31 final size:29
Alignment explanation
Indices: 436823--436891 Score: 77
Period size: 31 Copynumber: 2.3 Consensus size: 29
436813 AAGTTTTTTA
436823 ATTTAAAATAAAATAAAAATAAATAAATT
1 ATTTAAAATAAAATAAAAATAAATAAATT
*
436852 ATTTAATAATTAAAA-AAATAATAATTAAATTT
1 ATTTAA-AA-TAAAATAAA-AATAAATAAA-TT
*
436884 ATATAAAA
1 ATTTAAAA
436892 ATATTTATAA
Statistics
Matches: 34, Mismatches: 2, Indels: 6
0.81 0.05 0.14
Matches are distributed among these distances:
29 6 0.18
30 5 0.15
31 16 0.47
32 7 0.21
ACGTcount: A:0.65, C:0.00, G:0.00, T:0.35
Consensus pattern (29 bp):
ATTTAAAATAAAATAAAAATAAATAAATT
Found at i:439668 original size:5 final size:5
Alignment explanation
Indices: 439654--439684 Score: 53
Period size: 5 Copynumber: 6.2 Consensus size: 5
439644 CTTCAAAATA
*
439654 TATAT GATAT TATAT TATAT TATAT TATAT T
1 TATAT TATAT TATAT TATAT TATAT TATAT T
439685 TGCCTAGTGG
Statistics
Matches: 24, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
5 24 1.00
ACGTcount: A:0.39, C:0.00, G:0.03, T:0.58
Consensus pattern (5 bp):
TATAT
Found at i:448047 original size:17 final size:17
Alignment explanation
Indices: 448015--448048 Score: 50
Period size: 17 Copynumber: 2.0 Consensus size: 17
448005 AATTTTGAAT
**
448015 ATACTCGTATTGGATAC
1 ATACTCGTATCCGATAC
448032 ATACTCGTATCCGATAC
1 ATACTCGTATCCGATAC
448049 CAACACTCAA
Statistics
Matches: 15, Mismatches: 2, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
17 15 1.00
ACGTcount: A:0.29, C:0.24, G:0.15, T:0.32
Consensus pattern (17 bp):
ATACTCGTATCCGATAC
Found at i:448994 original size:17 final size:17
Alignment explanation
Indices: 448939--449011 Score: 55
Period size: 17 Copynumber: 4.3 Consensus size: 17
448929 TTTAAAATTT
*
448939 ATTAAAT-ATTAATT-T
1 ATTAAATAATTAATTAA
448954 A-TAAATAATTATAATTAA
1 ATTAAATAA-T-TAATTAA
448972 CA-TAAATAATTAATTAA
1 -ATTAAATAATTAATTAA
* *
448989 ATTAAATTATAAATTAAA
1 ATTAAATAATTAATT-AA
449007 ATTAA
1 ATTAA
449012 TAGTAGCTTT
Statistics
Matches: 48, Mismatches: 3, Indels: 11
0.77 0.05 0.18
Matches are distributed among these distances:
14 5 0.10
15 2 0.04
16 2 0.04
17 23 0.48
18 8 0.17
19 8 0.17
ACGTcount: A:0.58, C:0.01, G:0.00, T:0.41
Consensus pattern (17 bp):
ATTAAATAATTAATTAA
Found at i:450930 original size:21 final size:22
Alignment explanation
Indices: 450894--450935 Score: 59
Period size: 21 Copynumber: 2.0 Consensus size: 22
450884 AGATAAAAAA
450894 AAATTGTAAATATATTAAATTT
1 AAATTGTAAATATATTAAATTT
* *
450916 AAATT-TAAATTTATTGAATT
1 AAATTGTAAATATATTAAATT
450936 GAATATCACT
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
21 13 0.72
22 5 0.28
ACGTcount: A:0.48, C:0.00, G:0.05, T:0.48
Consensus pattern (22 bp):
AAATTGTAAATATATTAAATTT
Found at i:451639 original size:2 final size:2
Alignment explanation
Indices: 451632--451665 Score: 59
Period size: 2 Copynumber: 17.0 Consensus size: 2
451622 CAGTAGAAGC
*
451632 AT AT AT AT AC AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
451666 GGAAAAACAA
Statistics
Matches: 30, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
2 30 1.00
ACGTcount: A:0.50, C:0.03, G:0.00, T:0.47
Consensus pattern (2 bp):
AT
Found at i:454075 original size:16 final size:16
Alignment explanation
Indices: 454056--454086 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
454046 TTTTTAATCT
454056 ATAAAAAAAATAATTC
1 ATAAAAAAAATAATTC
*
454072 ATAATAAAAATAATT
1 ATAAAAAAAATAATT
454087 TGATGATCTT
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:0.68, C:0.03, G:0.00, T:0.29
Consensus pattern (16 bp):
ATAAAAAAAATAATTC
Found at i:454372 original size:15 final size:15
Alignment explanation
Indices: 454354--454383 Score: 51
Period size: 15 Copynumber: 2.0 Consensus size: 15
454344 TGTTCAAAAA
*
454354 TAAATTTAATTATAT
1 TAAATATAATTATAT
454369 TAAATATAATTATAT
1 TAAATATAATTATAT
454384 GAATATAAAA
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (15 bp):
TAAATATAATTATAT
Found at i:455297 original size:24 final size:25
Alignment explanation
Indices: 455255--455304 Score: 66
Period size: 24 Copynumber: 2.0 Consensus size: 25
455245 AAAGTTTTTA
* *
455255 AGTAATTAGTAATCAAATTAA-AAT
1 AGTAATTAATAAACAAATTAACAAT
*
455279 AGTAATTAATAAACTAATTAACAAT
1 AGTAATTAATAAACAAATTAACAAT
455304 A
1 A
455305 CTTTGACACT
Statistics
Matches: 22, Mismatches: 3, Indels: 1
0.85 0.12 0.04
Matches are distributed among these distances:
24 18 0.82
25 4 0.18
ACGTcount: A:0.56, C:0.06, G:0.06, T:0.32
Consensus pattern (25 bp):
AGTAATTAATAAACAAATTAACAAT
Found at i:456240 original size:2 final size:2
Alignment explanation
Indices: 456233--456262 Score: 60
Period size: 2 Copynumber: 15.0 Consensus size: 2
456223 TGTTTGATAA
456233 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
456263 TTCAAACAAA
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:456940 original size:32 final size:32
Alignment explanation
Indices: 456897--456957 Score: 97
Period size: 32 Copynumber: 1.9 Consensus size: 32
456887 TCTTGATTAC
456897 GTAATAATTTCCCCATT-CACTTTCAAGTCTAT
1 GTAATAATTTCCCC-TTCCACTTTCAAGTCTAT
*
456929 GTAATACTTTCCCCTTCCACTTTCAAGTC
1 GTAATAATTTCCCCTTCCACTTTCAAGTC
456958 ACTACCTTGG
Statistics
Matches: 27, Mismatches: 1, Indels: 2
0.90 0.03 0.07
Matches are distributed among these distances:
31 2 0.07
32 25 0.93
ACGTcount: A:0.25, C:0.30, G:0.07, T:0.39
Consensus pattern (32 bp):
GTAATAATTTCCCCTTCCACTTTCAAGTCTAT
Found at i:462325 original size:29 final size:25
Alignment explanation
Indices: 462260--462323 Score: 74
Period size: 26 Copynumber: 2.4 Consensus size: 25
462250 TTTTTTTTAA
*
462260 AAAAATTATAATATTTTTTTAAATTT
1 AAAAA-TAAAATATTTTTTTAAATTT
*
462286 AAAAATAAAATATTTCTTTTACATTAT
1 AAAAATAAAATATTT-TTTTAAATT-T
462313 ATAAAATAAAA
1 A-AAAATAAAA
462324 ATTAATTAAA
Statistics
Matches: 33, Mismatches: 2, Indels: 4
0.85 0.05 0.10
Matches are distributed among these distances:
25 9 0.27
26 13 0.39
27 2 0.06
28 9 0.27
ACGTcount: A:0.53, C:0.03, G:0.00, T:0.44
Consensus pattern (25 bp):
AAAAATAAAATATTTTTTTAAATTT
Found at i:466922 original size:21 final size:21
Alignment explanation
Indices: 466871--466930 Score: 61
Period size: 20 Copynumber: 3.0 Consensus size: 21
466861 TAATAACTTA
* *
466871 AATTTAAAATTTTT-TTAATT
1 AATTTAAAATTTTTATTTATC
* *
466891 TATTT-AGATTTTTATTTATC
1 AATTTAAAATTTTTATTTATC
*
466911 AATTTAAAATTTTTAATTAT
1 AATTTAAAATTTTTATTTAT
466931 TTACGAATAT
Statistics
Matches: 31, Mismatches: 7, Indels: 3
0.76 0.17 0.07
Matches are distributed among these distances:
19 7 0.23
20 12 0.39
21 12 0.39
ACGTcount: A:0.37, C:0.02, G:0.02, T:0.60
Consensus pattern (21 bp):
AATTTAAAATTTTTATTTATC
Found at i:483196 original size:2 final size:2
Alignment explanation
Indices: 483189--483223 Score: 70
Period size: 2 Copynumber: 17.5 Consensus size: 2
483179 ACTATAATCT
483189 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
483224 TTTATACATA
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 33 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:483520 original size:21 final size:22
Alignment explanation
Indices: 483495--483539 Score: 74
Period size: 21 Copynumber: 2.1 Consensus size: 22
483485 TTTCACGTTA
*
483495 TTAATTTTTAA-AATTTTTTAT
1 TTAATTTTTAATAATTTTTAAT
483516 TTAATTTTTAATAATTTTTAAT
1 TTAATTTTTAATAATTTTTAAT
483538 TT
1 TT
483540 TTTTTCTTTT
Statistics
Matches: 22, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
21 11 0.50
22 11 0.50
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (22 bp):
TTAATTTTTAATAATTTTTAAT
Found at i:483544 original size:10 final size:10
Alignment explanation
Indices: 483496--483537 Score: 50
Period size: 10 Copynumber: 4.1 Consensus size: 10
483486 TTCACGTTAT
483496 TAATTTTTAA
1 TAATTTTTAA
*
483506 -AATTTTTTATT
1 TAA-TTTTTA-A
483517 TAATTTTTAA
1 TAATTTTTAA
483527 TAATTTTTAA
1 TAATTTTTAA
483537 T
1 T
483538 TTTTTTTCTT
Statistics
Matches: 27, Mismatches: 2, Indels: 6
0.77 0.06 0.17
Matches are distributed among these distances:
9 2 0.07
10 17 0.63
11 6 0.22
12 2 0.07
ACGTcount: A:0.36, C:0.00, G:0.00, T:0.64
Consensus pattern (10 bp):
TAATTTTTAA
Found at i:483767 original size:22 final size:20
Alignment explanation
Indices: 483739--483831 Score: 72
Period size: 19 Copynumber: 4.7 Consensus size: 20
483729 TTATATACGT
483739 AATATAAT--TATAAAATATA
1 AATATAATAATATAAAATA-A
*
483758 AATATAATAATAACAAACATAA
1 AATATAATAAT-ATAAA-ATAA
*
483780 AATATATTATAATATAAAA-AT
1 AATATA--ATAATATAAAATAA
483801 AATAT--TAATATAAAATAA
1 AATATAATAATATAAAATAA
483819 ATATATAA-AATAT
1 A-ATATAATAATAT
483832 TTAAATTTAT
Statistics
Matches: 60, Mismatches: 4, Indels: 19
0.72 0.05 0.23
Matches are distributed among these distances:
17 10 0.17
18 2 0.03
19 12 0.20
20 5 0.08
21 7 0.12
22 12 0.20
23 7 0.12
24 5 0.08
ACGTcount: A:0.65, C:0.02, G:0.00, T:0.33
Consensus pattern (20 bp):
AATATAATAATATAAAATAA
Found at i:483796 original size:17 final size:17
Alignment explanation
Indices: 483776--483869 Score: 61
Period size: 17 Copynumber: 5.4 Consensus size: 17
483766 AATAACAAAC
483776 ATAAAATATATTATAAT
1 ATAAAATATATTATAAT
*
483793 ATAAAA-ATAATATTAAT
1 ATAAAATATATTA-TAAT
*
483810 ATAAAATAAATATATAAAAT
1 ATAAAAT--ATAT-TATAAT
* *
483830 ATTTAAATTTA-TATAAT
1 A-TAAAATATATTATAAT
*
483847 AT-AAAT-TATTAAAAT
1 ATAAAATATATTATAAT
483862 ATTAAAAT
1 A-TAAAAT
483870 TTATATAAAT
Statistics
Matches: 61, Mismatches: 7, Indels: 18
0.71 0.08 0.21
Matches are distributed among these distances:
14 2 0.03
15 10 0.16
16 7 0.11
17 26 0.43
19 2 0.03
20 7 0.11
21 7 0.11
ACGTcount: A:0.61, C:0.00, G:0.00, T:0.39
Consensus pattern (17 bp):
ATAAAATATATTATAAT
Found at i:483851 original size:32 final size:32
Alignment explanation
Indices: 483808--483878 Score: 108
Period size: 32 Copynumber: 2.2 Consensus size: 32
483798 AATAATATTA
*
483808 ATATAAAATAAA-TATATAAAATATTTAAATTT
1 ATATAAAATAAATTAT-TAAAATATTAAAATTT
*
483840 ATATAATATAAATTATTAAAATATTAAAATTT
1 ATATAAAATAAATTATTAAAATATTAAAATTT
483872 ATATAAA
1 ATATAAA
483879 TTTTCATACC
Statistics
Matches: 35, Mismatches: 3, Indels: 2
0.88 0.08 0.05
Matches are distributed among these distances:
32 32 0.91
33 3 0.09
ACGTcount: A:0.59, C:0.00, G:0.00, T:0.41
Consensus pattern (32 bp):
ATATAAAATAAATTATTAAAATATTAAAATTT
Found at i:484169 original size:3 final size:3
Alignment explanation
Indices: 484161--484210 Score: 55
Period size: 3 Copynumber: 15.3 Consensus size: 3
484151 TCGACAGTCG
*
484161 ATA ATA ATA ATA ATA ATA ATA ATA AAA ATAA ATAA ATAA ATAA ATA ATA
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA AT-A AT-A AT-A AT-A ATA ATA
484210 A
1 A
484211 ACTTTATGAC
Statistics
Matches: 44, Mismatches: 2, Indels: 2
0.92 0.04 0.04
Matches are distributed among these distances:
3 29 0.66
4 15 0.34
ACGTcount: A:0.72, C:0.00, G:0.00, T:0.28
Consensus pattern (3 bp):
ATA
Found at i:485639 original size:23 final size:25
Alignment explanation
Indices: 485604--485649 Score: 60
Period size: 23 Copynumber: 1.9 Consensus size: 25
485594 AAACATAAAA
*
485604 ATAATATAAT-AAATAT-TATTAAT
1 ATAAAATAATAAAATATATATTAAT
*
485627 ATAAAATATTAAAATATATATTA
1 ATAAAATAATAAAATATATATTA
485650 TATTTTATAT
Statistics
Matches: 19, Mismatches: 2, Indels: 2
0.83 0.09 0.09
Matches are distributed among these distances:
23 8 0.42
24 6 0.32
25 5 0.26
ACGTcount: A:0.59, C:0.00, G:0.00, T:0.41
Consensus pattern (25 bp):
ATAAAATAATAAAATATATATTAAT
Found at i:485641 original size:24 final size:22
Alignment explanation
Indices: 485614--485683 Score: 68
Period size: 24 Copynumber: 3.0 Consensus size: 22
485604 ATAATATAAT
485614 AAATATTATTAATATAAAATATTA
1 AAATATTATT-ATAT-AAATATTA
**
485638 AAATATATATTATATTTTATATTTA
1 AAATAT-TATTATA-TAAATA-TTA
*
485663 AAATTTTATTATATAAATATT
1 AAATATTATTATATAAATATT
485684 TTATTATATT
Statistics
Matches: 38, Mismatches: 5, Indels: 8
0.75 0.10 0.16
Matches are distributed among these distances:
22 2 0.05
23 4 0.11
24 19 0.50
25 13 0.34
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (22 bp):
AAATATTATTATATAAATATTA
Found at i:485690 original size:16 final size:16
Alignment explanation
Indices: 485605--485700 Score: 81
Period size: 16 Copynumber: 6.0 Consensus size: 16
485595 AACATAAAAA
485605 TAATATAATAAATATTAT
1 TAATAT-ATAAATATT-T
*
485623 TAATATA-AAATATTA
1 TAATATATAAATATTT
* *
485638 AAATATATATTATATTT
1 TAATATATA-AATATTT
*
485655 T-ATATTTAAA-ATTT
1 TAATATATAAATATTT
*
485669 TATTATATAAATATTT
1 TAATATATAAATATTT
* *
485685 TATTATATTAATATTT
1 TAATATATAAATATTT
485701 ATATAATTAA
Statistics
Matches: 64, Mismatches: 10, Indels: 10
0.76 0.12 0.12
Matches are distributed among these distances:
14 5 0.08
15 14 0.22
16 33 0.52
17 6 0.09
18 6 0.09
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (16 bp):
TAATATATAAATATTT
Found at i:485705 original size:14 final size:15
Alignment explanation
Indices: 485641--485710 Score: 74
Period size: 16 Copynumber: 4.7 Consensus size: 15
485631 AATATTAAAA
485641 TATATATT-ATATTT
1 TATATATTAATATTT
*
485655 TATAT-TTAAAATTT
1 TATATATTAATATTT
*
485669 TATTATATAAATATTT
1 TA-TATATTAATATTT
485685 TATTATATTAATA-TT
1 TA-TATATTAATATTT
485700 TATATAATTAA
1 TATAT-ATTAA
485711 AAAAATATAA
Statistics
Matches: 48, Mismatches: 4, Indels: 7
0.81 0.07 0.12
Matches are distributed among these distances:
13 2 0.04
14 15 0.31
15 12 0.25
16 19 0.40
ACGTcount: A:0.43, C:0.00, G:0.00, T:0.57
Consensus pattern (15 bp):
TATATATTAATATTT
Found at i:490670 original size:60 final size:60
Alignment explanation
Indices: 490597--490714 Score: 184
Period size: 60 Copynumber: 2.0 Consensus size: 60
490587 TTATTTAGTT
* *
490597 TAACCCCAAATTCATCTGGAAAAGGTGGAAACATTCAAAAGCGACATACT-TTAGCTCCGC
1 TAACCCCAAATTCATCTGGAAAAGGTGGAAACATGCAAAAGCAACATA-TGTTAGCTCCGC
* *
490657 TAACCCCAGATTCATCTGGAAAAGGTGTAAACATGCAAAAGCAACATATGTTAGCTCC
1 TAACCCCAAATTCATCTGGAAAAGGTGGAAACATGCAAAAGCAACATATGTTAGCTCC
490715 TCAGACCAAT
Statistics
Matches: 53, Mismatches: 4, Indels: 2
0.90 0.07 0.03
Matches are distributed among these distances:
59 1 0.02
60 52 0.98
ACGTcount: A:0.37, C:0.24, G:0.17, T:0.22
Consensus pattern (60 bp):
TAACCCCAAATTCATCTGGAAAAGGTGGAAACATGCAAAAGCAACATATGTTAGCTCCGC
Found at i:493226 original size:7 final size:7
Alignment explanation
Indices: 493216--493242 Score: 54
Period size: 7 Copynumber: 3.9 Consensus size: 7
493206 GATATAAAAA
493216 AAAATTT
1 AAAATTT
493223 AAAATTT
1 AAAATTT
493230 AAAATTT
1 AAAATTT
493237 AAAATT
1 AAAATT
493243 ATTAAAATAT
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 20 1.00
ACGTcount: A:0.59, C:0.00, G:0.00, T:0.41
Consensus pattern (7 bp):
AAAATTT
Found at i:498581 original size:16 final size:16
Alignment explanation
Indices: 498562--498595 Score: 59
Period size: 16 Copynumber: 2.1 Consensus size: 16
498552 ATAATAAAAT
498562 TTTAAATTAATTTAAA
1 TTTAAATTAATTTAAA
*
498578 TTTAATTTAATTTAAA
1 TTTAAATTAATTTAAA
498594 TT
1 TT
498596 AAAAAAAATT
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 17 1.00
ACGTcount: A:0.44, C:0.00, G:0.00, T:0.56
Consensus pattern (16 bp):
TTTAAATTAATTTAAA
Found at i:498795 original size:11 final size:11
Alignment explanation
Indices: 498781--498833 Score: 51
Period size: 11 Copynumber: 5.0 Consensus size: 11
498771 AATATATTAT
498781 ATAAAAATATA
1 ATAAAAATATA
498792 ATAAAAATA-A
1 ATAAAAATATA
498802 ATAAAAA-ATTA
1 ATAAAAATA-TA
*
498813 AT-ATAATA-A
1 ATAAAAATATA
498822 ATAAAATATATA
1 ATAAAA-ATATA
498834 TGTATATGTA
Statistics
Matches: 34, Mismatches: 2, Indels: 11
0.72 0.04 0.23
Matches are distributed among these distances:
9 4 0.12
10 13 0.38
11 16 0.47
12 1 0.03
ACGTcount: A:0.72, C:0.00, G:0.00, T:0.28
Consensus pattern (11 bp):
ATAAAAATATA
Found at i:498807 original size:20 final size:19
Alignment explanation
Indices: 498784--498831 Score: 60
Period size: 20 Copynumber: 2.4 Consensus size: 19
498774 ATATTATATA
498784 AAAATATAATAAAAATAAAT
1 AAAATATAAT-AAAATAAAT
* *
498804 AAAAAATTAATATAATAAAT
1 AAAATA-TAATAAAATAAAT
498824 AAAATATA
1 AAAATATA
498832 TATGTATATG
Statistics
Matches: 24, Mismatches: 3, Indels: 3
0.80 0.10 0.10
Matches are distributed among these distances:
19 2 0.08
20 18 0.75
21 4 0.17
ACGTcount: A:0.73, C:0.00, G:0.00, T:0.27
Consensus pattern (19 bp):
AAAATATAATAAAATAAAT
Found at i:498807 original size:21 final size:20
Alignment explanation
Indices: 498781--498833 Score: 63
Period size: 21 Copynumber: 2.5 Consensus size: 20
498771 AATATATTAT
498781 ATAAAAATATAATAAAAATAA
1 ATAAAAATATAAT-AAAATAA
*
498802 ATAAAAA-ATTAATATAATAA
1 ATAAAAATA-TAATAAAATAA
498822 ATAAAATATATA
1 ATAAAA-ATATA
498834 TGTATATGTA
Statistics
Matches: 28, Mismatches: 1, Indels: 6
0.80 0.03 0.17
Matches are distributed among these distances:
20 13 0.46
21 14 0.50
22 1 0.04
ACGTcount: A:0.72, C:0.00, G:0.00, T:0.28
Consensus pattern (20 bp):
ATAAAAATATAATAAAATAA
Found at i:498873 original size:9 final size:9
Alignment explanation
Indices: 498859--498888 Score: 51
Period size: 9 Copynumber: 3.3 Consensus size: 9
498849 TGCTTAAATA
498859 TATTATATT
1 TATTATATT
*
498868 TATTATATA
1 TATTATATT
498877 TATTATATT
1 TATTATATT
498886 TAT
1 TAT
498889 ATTTAAAATT
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
9 19 1.00
ACGTcount: A:0.37, C:0.00, G:0.00, T:0.63
Consensus pattern (9 bp):
TATTATATT
Found at i:498889 original size:11 final size:11
Alignment explanation
Indices: 498857--498934 Score: 52
Period size: 11 Copynumber: 6.6 Consensus size: 11
498847 TATGCTTAAA
498857 TATATTATATT
1 TATATTATATT
498868 TAT-TATATATAT
1 TATAT-TATAT-T
498880 TATATTTATATT
1 TATA-TTATATT
* * *
498892 TAAAATTTTGATA
1 T-ATATTAT-ATT
498905 TA-ATTAATAATT
1 TATATT-AT-ATT
498917 TATATTATATT
1 TATATTATATT
498928 TATATTA
1 TATATTA
498935 AATAAATTTA
Statistics
Matches: 53, Mismatches: 6, Indels: 16
0.71 0.08 0.21
Matches are distributed among these distances:
10 1 0.02
11 21 0.40
12 17 0.32
13 13 0.25
14 1 0.02
ACGTcount: A:0.41, C:0.00, G:0.01, T:0.58
Consensus pattern (11 bp):
TATATTATATT
Found at i:498984 original size:48 final size:49
Alignment explanation
Indices: 498895--498991 Score: 117
Period size: 48 Copynumber: 2.0 Consensus size: 49
498885 TTATATTTAA
* * *
498895 AATTTTGATATAATTAATAATTTATATTATATTTATATTAAATAAATTT
1 AATTTTGATATAATTAATAATTTAAATAATATTAATATTAAATAAATTT
* * *
498944 AATTTTGATGTATTTAA-AATTTAAATAATATTAA-ATTTAAATTAATTT
1 AATTTTGATATAATTAATAATTTAAATAATATTAATA-TTAAATAAATTT
498992 TTTAAATAAT
Statistics
Matches: 41, Mismatches: 6, Indels: 3
0.82 0.12 0.06
Matches are distributed among these distances:
47 1 0.02
48 25 0.61
49 15 0.37
ACGTcount: A:0.45, C:0.00, G:0.03, T:0.52
Consensus pattern (49 bp):
AATTTTGATATAATTAATAATTTAAATAATATTAATATTAAATAAATTT
Found at i:503850 original size:21 final size:21
Alignment explanation
Indices: 503826--503898 Score: 67
Period size: 21 Copynumber: 3.4 Consensus size: 21
503816 CGGATATATT
503826 ATATATAAAAAAAAGTTTTAA
1 ATATATAAAAAAAAGTTTTAA
* *** *
503847 ATATATAAACAGGTGTGTTACA
1 ATATATAAAAAAAAGTTTTA-A
*
503869 CAT-TATAAAAAAAAATTTTAA
1 -ATATATAAAAAAAAGTTTTAA
503890 ATATATAAA
1 ATATATAAA
503899 CAGGTGTGTT
Statistics
Matches: 38, Mismatches: 11, Indels: 6
0.69 0.20 0.11
Matches are distributed among these distances:
20 2 0.05
21 22 0.58
22 12 0.32
23 2 0.05
ACGTcount: A:0.56, C:0.04, G:0.07, T:0.33
Consensus pattern (21 bp):
ATATATAAAAAAAAGTTTTAA
Found at i:503888 original size:43 final size:43
Alignment explanation
Indices: 503829--503914 Score: 163
Period size: 43 Copynumber: 2.0 Consensus size: 43
503819 ATATATTATA
*
503829 TATAAAAAAAAGTTTTAAATATATAAACAGGTGTGTTACACAT
1 TATAAAAAAAAATTTTAAATATATAAACAGGTGTGTTACACAT
503872 TATAAAAAAAAATTTTAAATATATAAACAGGTGTGTTACACAT
1 TATAAAAAAAAATTTTAAATATATAAACAGGTGTGTTACACAT
503915 CAGAAGAGTG
Statistics
Matches: 42, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
43 42 1.00
ACGTcount: A:0.50, C:0.07, G:0.10, T:0.33
Consensus pattern (43 bp):
TATAAAAAAAAATTTTAAATATATAAACAGGTGTGTTACACAT
Done.