Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01015307.1 Kokia drynarioides strain JFW-HI SEQ_130352, whole genome shotgun sequence
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: 395823
ACGTcount: A:0.34, C:0.16, G:0.16, T:0.34
Warning! 329 characters in sequence are not A, C, G, or T
Found at i:11758 original size:47 final size:47
Alignment explanation
Indices: 11665--11762 Score: 153
Period size: 47 Copynumber: 2.1 Consensus size: 47
11655 TTAGATGATT
* * *
11665 TCTGGATCAGGTTGTGTGTGATGAGTTGACGACTGAGCAGAGATGCC
1 TCTGGATCAGGTTGTGTGTGATGAGTTGACGACGGAGCACAAATGCC
11712 TCTGGATCAGGTTGTGTGTGATGAGTTGACGACGGA-CTACAAATGCC
1 TCTGGATCAGGTTGTGTGTGATGAGTTGACGACGGAGC-ACAAATGCC
11759 TCTG
1 TCTG
11763 CTACCGCATC
Statistics
Matches: 47, Mismatches: 3, Indels: 2
0.90 0.06 0.04
Matches are distributed among these distances:
46 1 0.02
47 46 0.98
ACGTcount: A:0.21, C:0.16, G:0.34, T:0.29
Consensus pattern (47 bp):
TCTGGATCAGGTTGTGTGTGATGAGTTGACGACGGAGCACAAATGCC
Found at i:15325 original size:14 final size:15
Alignment explanation
Indices: 15306--15336 Score: 55
Period size: 15 Copynumber: 2.1 Consensus size: 15
15296 AAAATTTTCA
15306 AAATTT-TCAAAATT
1 AAATTTATCAAAATT
15320 AAATTTATCAAAATT
1 AAATTTATCAAAATT
15335 AA
1 AA
15337 TTTCTGTAAT
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
14 6 0.38
15 10 0.62
ACGTcount: A:0.55, C:0.06, G:0.00, T:0.39
Consensus pattern (15 bp):
AAATTTATCAAAATT
Found at i:17704 original size:14 final size:15
Alignment explanation
Indices: 17687--17715 Score: 51
Period size: 14 Copynumber: 2.0 Consensus size: 15
17677 TAAAAGCATT
17687 TAATTAAT-TTAAAA
1 TAATTAATCTTAAAA
17701 TAATTAATCTTAAAA
1 TAATTAATCTTAAAA
17716 ATATTAAAAT
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
14 8 0.57
15 6 0.43
ACGTcount: A:0.55, C:0.03, G:0.00, T:0.41
Consensus pattern (15 bp):
TAATTAATCTTAAAA
Found at i:21581 original size:18 final size:18
Alignment explanation
Indices: 21558--21602 Score: 72
Period size: 18 Copynumber: 2.5 Consensus size: 18
21548 TTTTTAGAAG
21558 CACTTTTGACATGAAAAA
1 CACTTTTGACATGAAAAA
*
21576 CACTTTTAACATGAAAAA
1 CACTTTTGACATGAAAAA
*
21594 CATTTTTGA
1 CACTTTTGA
21603 AGCAAAAGAA
Statistics
Matches: 24, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
18 24 1.00
ACGTcount: A:0.42, C:0.16, G:0.09, T:0.33
Consensus pattern (18 bp):
CACTTTTGACATGAAAAA
Found at i:22913 original size:44 final size:44
Alignment explanation
Indices: 22841--22968 Score: 220
Period size: 44 Copynumber: 2.9 Consensus size: 44
22831 AATCCCGTGA
* *
22841 ATATATTAACTATGCACATGGAGTGGTCCGATGAAATAATCATC
1 ATATGTTACCTATGCACATGGAGTGGTCCGATGAAATAATCATC
22885 ATATGTTACCTATGCACATGGAGTGGTCCGATGAAATAATCATC
1 ATATGTTACCTATGCACATGGAGTGGTCCGATGAAATAATCATC
* *
22929 ATATGTTACCTATGCACATGGAGTGGTCCCATGGAATAAT
1 ATATGTTACCTATGCACATGGAGTGGTCCGATGAAATAAT
22969 AATATGCTCC
Statistics
Matches: 80, Mismatches: 4, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
44 80 1.00
ACGTcount: A:0.33, C:0.17, G:0.20, T:0.30
Consensus pattern (44 bp):
ATATGTTACCTATGCACATGGAGTGGTCCGATGAAATAATCATC
Found at i:41360 original size:15 final size:15
Alignment explanation
Indices: 41339--41380 Score: 50
Period size: 17 Copynumber: 2.7 Consensus size: 15
41329 TAATTCTTTA
41339 AAAATTATAAA-AAT
1 AAAATTATAAATAAT
41353 ATAAATTATTCAAATAAT
1 A-AAATTA-T-AAATAAT
41371 AAAATTATAA
1 AAAATTATAA
41381 TTTTTATTAT
Statistics
Matches: 24, Mismatches: 0, Indels: 7
0.77 0.00 0.23
Matches are distributed among these distances:
14 1 0.04
15 8 0.33
16 2 0.08
17 9 0.38
18 4 0.17
ACGTcount: A:0.64, C:0.02, G:0.00, T:0.33
Consensus pattern (15 bp):
AAAATTATAAATAAT
Found at i:41895 original size:17 final size:16
Alignment explanation
Indices: 41873--41914 Score: 59
Period size: 15 Copynumber: 2.6 Consensus size: 16
41863 AGAGTAAAAA
*
41873 TATAATTTTATTATTTT
1 TATAATTTTA-TATATT
41890 TATAA-TTTATATATT
1 TATAATTTTATATATT
41905 TATAATTTTA
1 TATAATTTTA
41915 AAGAATTAAA
Statistics
Matches: 23, Mismatches: 1, Indels: 3
0.85 0.04 0.11
Matches are distributed among these distances:
15 10 0.43
16 8 0.35
17 5 0.22
ACGTcount: A:0.36, C:0.00, G:0.00, T:0.64
Consensus pattern (16 bp):
TATAATTTTATATATT
Found at i:41966 original size:28 final size:28
Alignment explanation
Indices: 41902--41970 Score: 86
Period size: 28 Copynumber: 2.5 Consensus size: 28
41892 TAATTTATAT
* * *
41902 ATTTATAATTTTAAAGAATTAAATTAAA
1 ATTTATATTTTTAAAGAATCAAAATAAA
*
41930 TTTTATATTTTTAAAGGAATCAAAATAAA
1 ATTTATATTTTTAAA-GAATCAAAATAAA
41959 ATTT-TATTTTTA
1 ATTTATATTTTTA
41971 TTAATTTAAA
Statistics
Matches: 35, Mismatches: 5, Indels: 2
0.83 0.12 0.05
Matches are distributed among these distances:
28 21 0.60
29 14 0.40
ACGTcount: A:0.46, C:0.01, G:0.04, T:0.48
Consensus pattern (28 bp):
ATTTATATTTTTAAAGAATCAAAATAAA
Found at i:53154 original size:21 final size:22
Alignment explanation
Indices: 53120--53162 Score: 54
Period size: 20 Copynumber: 2.0 Consensus size: 22
53110 AAAGTAAGAA
*
53120 TTTTTACTTAAATATTATAAAAT
1 TTTTTACTTAAATAAT-TAAAAT
53143 TTTTTA-TT-AATAATTAAAAT
1 TTTTTACTTAAATAATTAAAAT
53163 GATATCCCAA
Statistics
Matches: 19, Mismatches: 1, Indels: 3
0.83 0.04 0.13
Matches are distributed among these distances:
20 6 0.32
21 5 0.26
22 2 0.11
23 6 0.32
ACGTcount: A:0.44, C:0.02, G:0.00, T:0.53
Consensus pattern (22 bp):
TTTTTACTTAAATAATTAAAAT
Found at i:53265 original size:8 final size:8
Alignment explanation
Indices: 53252--53276 Score: 50
Period size: 8 Copynumber: 3.1 Consensus size: 8
53242 TTTTGACACT
53252 TTTTTTTA
1 TTTTTTTA
53260 TTTTTTTA
1 TTTTTTTA
53268 TTTTTTTA
1 TTTTTTTA
53276 T
1 T
53277 ATATTTAAAA
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
8 17 1.00
ACGTcount: A:0.12, C:0.00, G:0.00, T:0.88
Consensus pattern (8 bp):
TTTTTTTA
Found at i:53630 original size:4 final size:4
Alignment explanation
Indices: 53617--53677 Score: 63
Period size: 4 Copynumber: 15.2 Consensus size: 4
53607 AAAATTGAAG
* *
53617 GAAA -AAA GAAA GAAA AAAGA GAAA GAAA GAAA GAAA GAAA G-AA GGAA
1 GAAA GAAA GAAA GAAA GAA-A GAAA GAAA GAAA GAAA GAAA GAAA GAAA
*
53664 GAAG GAGAA GAAA G
1 GAAA GA-AA GAAA G
53678 GGAAAAAGGA
Statistics
Matches: 48, Mismatches: 5, Indels: 8
0.79 0.08 0.13
Matches are distributed among these distances:
3 6 0.12
4 36 0.75
5 6 0.12
ACGTcount: A:0.70, C:0.00, G:0.30, T:0.00
Consensus pattern (4 bp):
GAAA
Found at i:53653 original size:25 final size:25
Alignment explanation
Indices: 53617--53695 Score: 83
Period size: 25 Copynumber: 3.2 Consensus size: 25
53607 AAAATTGAAG
53617 GAAA-AAAGAAAGAAAAAAGAGAAA
1 GAAAGAAAGAAAGAAAAAAGAGAAA
*
53641 GAAAGAAAGAAAGAAAGAAG-G-AA
1 GAAAGAAAGAAAGAAAAAAGAGAAA
* *
53664 GAAGGAGAAGAAAGGGAAAAAGGAGAAA
1 GAAAGA-AAGAAA--GAAAAAAGAGAAA
53692 GAAA
1 GAAA
53696 AAAAAGATAA
Statistics
Matches: 44, Mismatches: 5, Indels: 8
0.77 0.09 0.14
Matches are distributed among these distances:
23 7 0.16
24 11 0.25
25 14 0.32
26 6 0.14
27 1 0.02
28 5 0.11
ACGTcount: A:0.70, C:0.00, G:0.30, T:0.00
Consensus pattern (25 bp):
GAAAGAAAGAAAGAAAAAAGAGAAA
Found at i:53657 original size:12 final size:12
Alignment explanation
Indices: 53617--53677 Score: 63
Period size: 13 Copynumber: 5.1 Consensus size: 12
53607 AAAATTGAAG
53617 GAAA-AAAGAAA
1 GAAAGAAAGAAA
*
53628 GAAAAAAGAGAAA
1 GAAAGAA-AGAAA
53641 GAAAGAAAGAAA
1 GAAAGAAAGAAA
*
53653 GAAAG-AAGGAA
1 GAAAGAAAGAAA
*
53664 GAAGGAGAAGAAA
1 GAAAGA-AAGAAA
53677 G
1 G
53678 GGAAAAAGGA
Statistics
Matches: 42, Mismatches: 4, Indels: 6
0.81 0.08 0.12
Matches are distributed among these distances:
11 13 0.31
12 12 0.29
13 17 0.40
ACGTcount: A:0.70, C:0.00, G:0.30, T:0.00
Consensus pattern (12 bp):
GAAAGAAAGAAA
Found at i:53686 original size:18 final size:19
Alignment explanation
Indices: 53648--53695 Score: 62
Period size: 18 Copynumber: 2.5 Consensus size: 19
53638 AAAGAAAGAA
*
53648 AGAAAGAAAGAAGGAAGAAGG
1 AGAAAGAAAG--GGAAAAAGG
53669 AG-AAGAAAGGGAAAAAGG
1 AGAAAGAAAGGGAAAAAGG
53687 AGAAAGAAA
1 AGAAAGAAA
53696 AAAAAGATAA
Statistics
Matches: 25, Mismatches: 1, Indels: 4
0.83 0.03 0.13
Matches are distributed among these distances:
18 10 0.40
19 6 0.24
20 7 0.28
21 2 0.08
ACGTcount: A:0.65, C:0.00, G:0.35, T:0.00
Consensus pattern (19 bp):
AGAAAGAAAGGGAAAAAGG
Found at i:53886 original size:12 final size:12
Alignment explanation
Indices: 53869--53893 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
53859 TTAAGTTTGG
53869 TTAATTTTAAAA
1 TTAATTTTAAAA
53881 TTAATTTTAAAA
1 TTAATTTTAAAA
53893 T
1 T
53894 ATTTTAATTT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (12 bp):
TTAATTTTAAAA
Found at i:54081 original size:21 final size:20
Alignment explanation
Indices: 54048--54090 Score: 50
Period size: 21 Copynumber: 2.1 Consensus size: 20
54038 TAATTTACTT
*
54048 TAATTTAATTTTGCTAGTTAG
1 TAATTTAAGTTTG-TAGTTAG
* *
54069 TAATTTTAGTTTGTTGTTAG
1 TAATTTAAGTTTGTAGTTAG
54089 TA
1 TA
54091 GTAGTAAGTA
Statistics
Matches: 19, Mismatches: 3, Indels: 1
0.83 0.13 0.04
Matches are distributed among these distances:
20 8 0.42
21 11 0.58
ACGTcount: A:0.26, C:0.02, G:0.16, T:0.56
Consensus pattern (20 bp):
TAATTTAAGTTTGTAGTTAG
Found at i:54586 original size:14 final size:14
Alignment explanation
Indices: 54569--54608 Score: 57
Period size: 12 Copynumber: 3.0 Consensus size: 14
54559 CCTAACTAAT
54569 TAATTATCAAAATA
1 TAATTATCAAAATA
*
54583 TAA-TAT-AAAAAA
1 TAATTATCAAAATA
54595 TAATTATCAAAATA
1 TAATTATCAAAATA
54609 ATATCCTCAT
Statistics
Matches: 22, Mismatches: 2, Indels: 4
0.79 0.07 0.14
Matches are distributed among these distances:
12 8 0.36
13 6 0.27
14 8 0.36
ACGTcount: A:0.62, C:0.05, G:0.00, T:0.33
Consensus pattern (14 bp):
TAATTATCAAAATA
Found at i:56610 original size:45 final size:45
Alignment explanation
Indices: 56537--56671 Score: 189
Period size: 45 Copynumber: 3.0 Consensus size: 45
56527 GCATAGCTCA
* *
56537 TCAAGCCAAGGATATCAGCGTCAGTTTGACGAGCCACCGCAATAC
1 TCAAGCCAAGGATATCAGCCTCAATTTGACGAGCCACCGCAATAC
* *
56582 TCAAGCCAAGGATATCAACCTCAATTTGACGAGCCACTGCAATAC
1 TCAAGCCAAGGATATCAGCCTCAATTTGACGAGCCACCGCAATAC
** * * *
56627 TCAAGGGAAGGATATCAGGCTGAATTTGACGAGCCACCACAATAC
1 TCAAGCCAAGGATATCAGCCTCAATTTGACGAGCCACCGCAATAC
56672 CCTATTCCTC
Statistics
Matches: 79, Mismatches: 11, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
45 79 1.00
ACGTcount: A:0.34, C:0.27, G:0.21, T:0.19
Consensus pattern (45 bp):
TCAAGCCAAGGATATCAGCCTCAATTTGACGAGCCACCGCAATAC
Found at i:56960 original size:14 final size:14
Alignment explanation
Indices: 56938--56991 Score: 58
Period size: 14 Copynumber: 3.9 Consensus size: 14
56928 CATTAAACCC
56938 TAAAA-CCTAAACT
1 TAAAACCCTAAACT
56951 TAAAACCCTAAACT
1 TAAAACCCTAAACT
* *
56965 CT-AAACACTAGACT
1 -TAAAACCCTAAACT
*
56979 TAAAACTCTAAAC
1 TAAAACCCTAAAC
56992 CGTAAACACT
Statistics
Matches: 34, Mismatches: 4, Indels: 5
0.79 0.09 0.12
Matches are distributed among these distances:
13 6 0.18
14 27 0.79
15 1 0.03
ACGTcount: A:0.50, C:0.26, G:0.02, T:0.22
Consensus pattern (14 bp):
TAAAACCCTAAACT
Found at i:57003 original size:28 final size:27
Alignment explanation
Indices: 56931--57004 Score: 87
Period size: 28 Copynumber: 2.6 Consensus size: 27
56921 TTTATAACAT
*
56931 TAAACCCTAAA-ACCTAAACTTAAAACCC
1 TAAA-CCTAAACA-CTAGACTTAAAACCC
*
56959 TAAACTCTAAACACTAGACTTAAAACTC
1 TAAAC-CTAAACACTAGACTTAAAACCC
56987 TAAACCGTAAACACTAGA
1 TAAACC-TAAACACTAGA
57005 TTGATTAAGG
Statistics
Matches: 41, Mismatches: 2, Indels: 6
0.84 0.04 0.12
Matches are distributed among these distances:
27 2 0.05
28 38 0.93
29 1 0.02
ACGTcount: A:0.49, C:0.27, G:0.04, T:0.20
Consensus pattern (27 bp):
TAAACCTAAACACTAGACTTAAAACCC
Found at i:58608 original size:30 final size:30
Alignment explanation
Indices: 58572--58670 Score: 96
Period size: 30 Copynumber: 3.3 Consensus size: 30
58562 NNAACCTAGC
58572 TAATTAATTACCAAAATATAATATAAAAAA
1 TAATTAATTACCAAAATATAATATAAAAAA
* ****
58602 TAATTAATTATC-AAA-ATAATAT-CCCCA
1 TAATTAATTACCAAAATATAATATAAAAAA
* *
58629 TCATATTATTTACCAAAATTTAATATAAAAAA
1 T-A-ATTAATTACCAAAATATAATATAAAAAA
58661 TAATTAATTA
1 TAATTAATTA
58671 TGAAAATAAT
Statistics
Matches: 51, Mismatches: 13, Indels: 10
0.69 0.18 0.14
Matches are distributed among these distances:
27 2 0.04
28 8 0.16
29 11 0.22
30 21 0.41
31 7 0.14
32 2 0.04
ACGTcount: A:0.55, C:0.10, G:0.00, T:0.35
Consensus pattern (30 bp):
TAATTAATTACCAAAATATAATATAAAAAA
Found at i:58617 original size:16 final size:16
Alignment explanation
Indices: 58572--58621 Score: 52
Period size: 16 Copynumber: 3.2 Consensus size: 16
58562 NNAACCTAGC
*
58572 TAATTAATTACCAAAA
1 TAATTAATTATCAAAA
*
58588 T-A-TAA-TATAAAAAA
1 TAATTAATTAT-CAAAA
58602 TAATTAATTATCAAAA
1 TAATTAATTATCAAAA
58618 TAAT
1 TAAT
58622 ATCCCCATCA
Statistics
Matches: 27, Mismatches: 3, Indels: 8
0.71 0.08 0.21
Matches are distributed among these distances:
13 2 0.07
14 8 0.30
15 2 0.07
16 12 0.44
17 3 0.11
ACGTcount: A:0.60, C:0.06, G:0.00, T:0.34
Consensus pattern (16 bp):
TAATTAATTATCAAAA
Found at i:58645 original size:29 final size:28
Alignment explanation
Indices: 58604--58709 Score: 79
Period size: 29 Copynumber: 3.6 Consensus size: 28
58594 ATAAAAAATA
*
58604 ATTAATTATCAAAATAATATCCCCATCAT
1 ATTAATTACCAAAATAATAT-CCCATCAT
* ** **
58633 ATTATTTACCAAAATTTAATAT-AAAAAAT
1 ATTAATTACCAAAA--TAATATCCCATCAT
**
58662 AATTAATTATGAAAATAATATACCCATCAT
1 -ATTAATTACCAAAATAATAT-CCCATCAT
*
58692 ATTATTTACCAAAATAAT
1 ATTAATTACCAAAATAAT
58710 GGTGTGTGGA
Statistics
Matches: 56, Mismatches: 16, Indels: 10
0.68 0.20 0.12
Matches are distributed among these distances:
28 6 0.11
29 30 0.54
30 14 0.25
31 6 0.11
ACGTcount: A:0.50, C:0.13, G:0.01, T:0.36
Consensus pattern (28 bp):
ATTAATTACCAAAATAATATCCCATCAT
Found at i:58671 original size:59 final size:59
Alignment explanation
Indices: 58574--58707 Score: 232
Period size: 59 Copynumber: 2.3 Consensus size: 59
58564 AACCTAGCTA
* *
58574 ATTAATTACCAAAATATAATATAAAAAATAATTAATTATCAAAATAATATCCCCATCAT
1 ATTATTTACCAAAATATAATATAAAAAATAATTAATTATCAAAATAATATACCCATCAT
* *
58633 ATTATTTACCAAAATTTAATATAAAAAATAATTAATTATGAAAATAATATACCCATCAT
1 ATTATTTACCAAAATATAATATAAAAAATAATTAATTATCAAAATAATATACCCATCAT
58692 ATTATTTACCAAAATA
1 ATTATTTACCAAAATA
58708 ATGGTGTGTG
Statistics
Matches: 70, Mismatches: 5, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
59 70 1.00
ACGTcount: A:0.53, C:0.12, G:0.01, T:0.34
Consensus pattern (59 bp):
ATTATTTACCAAAATATAATATAAAAAATAATTAATTATCAAAATAATATACCCATCAT
Found at i:59091 original size:18 final size:18
Alignment explanation
Indices: 59064--59100 Score: 65
Period size: 18 Copynumber: 2.1 Consensus size: 18
59054 TGAGGGGTTG
59064 TGCACAGGGCCTTAAATT
1 TGCACAGGGCCTTAAATT
*
59082 TGCACGGGGCCTTAAATT
1 TGCACAGGGCCTTAAATT
59100 T
1 T
59101 CCCCCTCATG
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
18 18 1.00
ACGTcount: A:0.24, C:0.22, G:0.24, T:0.30
Consensus pattern (18 bp):
TGCACAGGGCCTTAAATT
Found at i:60037 original size:43 final size:43
Alignment explanation
Indices: 59955--60039 Score: 118
Period size: 43 Copynumber: 2.0 Consensus size: 43
59945 ATTAACATGT
* *
59955 TAAATTATATTACTTGACTCGTGTTAATATGGTTGCATGTTAC
1 TAAATTATATTACTTGACTCGTATTAATATGATTGCATGTTAC
* *
59998 TAAATTATATTACTTTACTCTTATTAATAT-ATTGACATGTTA
1 TAAATTATATTACTTGACTCGTATTAATATGATTG-CATGTTA
60040 TTAATTGTGC
Statistics
Matches: 37, Mismatches: 4, Indels: 2
0.86 0.09 0.05
Matches are distributed among these distances:
42 3 0.08
43 34 0.92
ACGTcount: A:0.32, C:0.11, G:0.11, T:0.47
Consensus pattern (43 bp):
TAAATTATATTACTTGACTCGTATTAATATGATTGCATGTTAC
Found at i:60748 original size:21 final size:21
Alignment explanation
Indices: 60722--60764 Score: 68
Period size: 21 Copynumber: 2.0 Consensus size: 21
60712 AGACATCGCG
* *
60722 ATACTCTATTCCTCTCGGGCA
1 ATACTCTACTCCTCTAGGGCA
60743 ATACTCTACTCCTCTAGGGCA
1 ATACTCTACTCCTCTAGGGCA
60764 A
1 A
60765 ATGGACCCTA
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
21 20 1.00
ACGTcount: A:0.23, C:0.33, G:0.14, T:0.30
Consensus pattern (21 bp):
ATACTCTACTCCTCTAGGGCA
Found at i:64112 original size:19 final size:20
Alignment explanation
Indices: 64071--64113 Score: 54
Period size: 19 Copynumber: 2.2 Consensus size: 20
64061 ATCCATCTTC
*
64071 AATAAATATGTTAAAAATTA
1 AATAAATATGTTAAAAATAA
64091 AATAAA-AT-TTAATAAATAA
1 AATAAATATGTTAA-AAATAA
64110 AATA
1 AATA
64114 CGATTTTAAA
Statistics
Matches: 21, Mismatches: 1, Indels: 3
0.84 0.04 0.12
Matches are distributed among these distances:
18 4 0.19
19 11 0.52
20 6 0.29
ACGTcount: A:0.65, C:0.00, G:0.02, T:0.33
Consensus pattern (20 bp):
AATAAATATGTTAAAAATAA
Found at i:64212 original size:4 final size:4
Alignment explanation
Indices: 64166--64234 Score: 59
Period size: 4 Copynumber: 17.0 Consensus size: 4
64156 ACACATTACA
* * * * * *
64166 TTTC TTTC CTTC -TTC TTTT TTTCC TTCC TCTC CTTC TTCC TTTC TTTC
1 TTTC TTTC TTTC TTTC TTTC TTT-C TTTC TTTC TTTC TTTC TTTC TTTC
64214 TTTC TTTTC TTTC TTTC TTTC
1 TTTC -TTTC TTTC TTTC TTTC
64235 CCGTTTATTT
Statistics
Matches: 51, Mismatches: 11, Indels: 6
0.75 0.16 0.09
Matches are distributed among these distances:
3 3 0.06
4 42 0.82
5 6 0.12
ACGTcount: A:0.00, C:0.32, G:0.00, T:0.68
Consensus pattern (4 bp):
TTTC
Found at i:64224 original size:13 final size:13
Alignment explanation
Indices: 64206--64233 Score: 56
Period size: 13 Copynumber: 2.2 Consensus size: 13
64196 TCCTTCTTCC
64206 TTTCTTTCTTTCT
1 TTTCTTTCTTTCT
64219 TTTCTTTCTTTCT
1 TTTCTTTCTTTCT
64232 TT
1 TT
64234 CCCGTTTATT
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:0.00, C:0.21, G:0.00, T:0.79
Consensus pattern (13 bp):
TTTCTTTCTTTCT
Found at i:67553 original size:2 final size:2
Alignment explanation
Indices: 67546--67585 Score: 80
Period size: 2 Copynumber: 20.0 Consensus size: 2
67536 TGGTGCACAA
67546 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
67586 TTACAATCTT
Statistics
Matches: 38, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 38 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:71453 original size:45 final size:43
Alignment explanation
Indices: 71375--71461 Score: 113
Period size: 45 Copynumber: 2.0 Consensus size: 43
71365 CAATGTATTT
71375 AAATTAATAAACAATTGCTATATCTACTAACTAACAAAATAAC
1 AAATTAATAAACAATTGCTATATCTACTAACTAACAAAATAAC
* * *
71418 AAATTGATAAACAACTT-CTAATTATCTGCTAACTAACATAATAA
1 AAATTAATAAACAA-TTGCT-A-TATCTACTAACTAACAAAATAA
71462 TTGATTGATT
Statistics
Matches: 38, Mismatches: 3, Indels: 4
0.84 0.07 0.09
Matches are distributed among these distances:
43 15 0.39
44 3 0.08
45 20 0.53
ACGTcount: A:0.51, C:0.16, G:0.03, T:0.30
Consensus pattern (43 bp):
AAATTAATAAACAATTGCTATATCTACTAACTAACAAAATAAC
Found at i:71724 original size:27 final size:25
Alignment explanation
Indices: 71667--71745 Score: 61
Period size: 27 Copynumber: 3.0 Consensus size: 25
71657 TTGTTTATAT
71667 AATTATATTTAATATAATATAATTTC
1 AATT-TATTTAATATAATATAATTTC
* *
71693 AATTTTTATTTAATATTATATGATTAT-
1 AA--TTTATTTAATATAATATAATT-TC
* *
71720 TATTTATTTAATCATATAAATAATTT
1 AATTTATTTAAT-ATA-ATATAATTT
71746 TAAAGGTAAA
Statistics
Matches: 42, Mismatches: 6, Indels: 10
0.72 0.10 0.17
Matches are distributed among these distances:
25 10 0.24
26 5 0.12
27 24 0.57
28 3 0.07
ACGTcount: A:0.42, C:0.03, G:0.01, T:0.54
Consensus pattern (25 bp):
AATTTATTTAATATAATATAATTTC
Found at i:72367 original size:18 final size:19
Alignment explanation
Indices: 72340--72378 Score: 53
Period size: 19 Copynumber: 2.1 Consensus size: 19
72330 ATTTGAAATT
* *
72340 TTTTATAAA-TATTTTGAA
1 TTTTAAAAATTATTTTCAA
72358 TTTTAAAAATTATTTTCAA
1 TTTTAAAAATTATTTTCAA
72377 TT
1 TT
72379 ATTTTTAATT
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
18 8 0.44
19 10 0.56
ACGTcount: A:0.38, C:0.03, G:0.03, T:0.56
Consensus pattern (19 bp):
TTTTAAAAATTATTTTCAA
Found at i:73236 original size:3 final size:3
Alignment explanation
Indices: 73228--73261 Score: 68
Period size: 3 Copynumber: 11.3 Consensus size: 3
73218 TGAGTGAGAG
73228 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA A
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA A
73262 CAAAAGAGAT
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 31 1.00
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.32
Consensus pattern (3 bp):
ATA
Found at i:79630 original size:28 final size:28
Alignment explanation
Indices: 79577--79631 Score: 83
Period size: 28 Copynumber: 2.0 Consensus size: 28
79567 AAATGAGCAT
**
79577 CATGACCTTTGGGTCAACACTTAGTAAG
1 CATGACCTTTGGGTCAACACGGAGTAAG
*
79605 CATGACCTTTGGGTCAACAGGGAGTAA
1 CATGACCTTTGGGTCAACACGGAGTAA
79632 ATCGAATATC
Statistics
Matches: 24, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
28 24 1.00
ACGTcount: A:0.29, C:0.20, G:0.25, T:0.25
Consensus pattern (28 bp):
CATGACCTTTGGGTCAACACGGAGTAAG
Found at i:82941 original size:27 final size:28
Alignment explanation
Indices: 82904--82972 Score: 74
Period size: 27 Copynumber: 2.6 Consensus size: 28
82894 GAATTGGAGC
*
82904 TATTTTTAAAAAAATTTATAAT-TTTTA
1 TATTTTAAAAAAAATTTATAATCTTTTA
* *
82931 TATTTTAAAAAATATTTTTTAATCTTTTA
1 TATTTTAAAAAA-AATTTATAATCTTTTA
82960 -A--TTAAAAAAAATT
1 TATTTTAAAAAAAATT
82973 AATTATTTGC
Statistics
Matches: 36, Mismatches: 4, Indels: 6
0.78 0.09 0.13
Matches are distributed among these distances:
25 3 0.08
26 8 0.22
27 11 0.31
28 9 0.25
29 5 0.14
ACGTcount: A:0.46, C:0.01, G:0.00, T:0.52
Consensus pattern (28 bp):
TATTTTAAAAAAAATTTATAATCTTTTA
Found at i:82953 original size:28 final size:27
Alignment explanation
Indices: 82907--82972 Score: 75
Period size: 26 Copynumber: 2.5 Consensus size: 27
82897 TTGGAGCTAT
82907 TTTTAAAAAAATTTATAAT-TTTTATA
1 TTTTAAAAAAATTTATAATCTTTTATA
*
82933 TTTTAAAAAATATTTTTTAATCTTTTA-A
1 TTTTAAAAAA-A-TTTATAATCTTTTATA
*
82961 -TTAAAAAAAATT
1 TTTTAAAAAAATT
82973 AATTATTTGC
Statistics
Matches: 35, Mismatches: 2, Indels: 7
0.80 0.05 0.16
Matches are distributed among these distances:
25 2 0.06
26 11 0.31
27 9 0.26
28 8 0.23
29 5 0.14
ACGTcount: A:0.47, C:0.02, G:0.00, T:0.52
Consensus pattern (27 bp):
TTTTAAAAAAATTTATAATCTTTTATA
Found at i:83666 original size:29 final size:28
Alignment explanation
Indices: 83633--83736 Score: 75
Period size: 29 Copynumber: 3.5 Consensus size: 28
83623 ACTTTTTCTT
83633 AATTTGGTACCTAAACTTTTTTTGGACTC
1 AATTTGGTACCTAAACTTTTTTT-GACTC
* * **
83662 AATTTGGTATCTGAACTTGACATTTTTTCCT-
1 AATTTGGTACCTAAACTT----TTTTTGACTC
* * * *
83693 AATTTGATACTTAAGCTTTTTTTAGATTC
1 AATTTGGTACCTAAACTTTTTTT-GACTC
83722 AATTTGGTACCTAAA
1 AATTTGGTACCTAAA
83737 TTTATTGAAT
Statistics
Matches: 54, Mismatches: 15, Indels: 12
0.67 0.19 0.15
Matches are distributed among these distances:
27 5 0.09
28 1 0.02
29 28 0.52
31 13 0.24
32 2 0.04
33 5 0.09
ACGTcount: A:0.27, C:0.14, G:0.12, T:0.46
Consensus pattern (28 bp):
AATTTGGTACCTAAACTTTTTTTGACTC
Found at i:83689 original size:60 final size:60
Alignment explanation
Indices: 83575--83731 Score: 176
Period size: 60 Copynumber: 2.6 Consensus size: 60
83565 TTAATATAAT
* * * *
83575 ATTTGGTATTTAAA--TTTTTTACGACTCAATTAGGTACTTGAATTTAACACTTTTTCTTA
1 ATTTGGTACTTAAACTTTTTTTA-GACTCAATTTGGTACTTGAACTTAACACTTTTTCCTA
* * * *
83634 ATTTGGTACCTAAACTTTTTTTGGACTCAATTTGGTA-TCTGAACTTGACATTTTTTCCTA
1 ATTTGGTACTTAAACTTTTTTTAGACTCAATTTGGTACT-TGAACTTAACACTTTTTCCTA
* * *
83694 ATTTGATACTTAAGCTTTTTTTAGATTCAATTTGGTAC
1 ATTTGGTACTTAAACTTTTTTTAGACTCAATTTGGTAC
83732 CTAAATTTAT
Statistics
Matches: 81, Mismatches: 13, Indels: 6
0.81 0.13 0.06
Matches are distributed among these distances:
59 13 0.16
60 62 0.77
61 6 0.07
ACGTcount: A:0.26, C:0.13, G:0.12, T:0.48
Consensus pattern (60 bp):
ATTTGGTACTTAAACTTTTTTTAGACTCAATTTGGTACTTGAACTTAACACTTTTTCCTA
Found at i:87555 original size:22 final size:24
Alignment explanation
Indices: 87530--87574 Score: 67
Period size: 24 Copynumber: 2.0 Consensus size: 24
87520 CACTAGTACA
*
87530 AAGAC-AATA-CAATTAGAAGTAT
1 AAGACAAATACCAATTAAAAGTAT
87552 AAGACAAATACCAATTAAAAGTA
1 AAGACAAATACCAATTAAAAGTA
87575 CAAATATATG
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
22 5 0.25
23 4 0.20
24 11 0.55
ACGTcount: A:0.58, C:0.11, G:0.11, T:0.20
Consensus pattern (24 bp):
AAGACAAATACCAATTAAAAGTAT
Found at i:91008 original size:24 final size:23
Alignment explanation
Indices: 90953--91017 Score: 69
Period size: 24 Copynumber: 2.7 Consensus size: 23
90943 AAATAAAATA
90953 TGCATAATAAAATTAAAATTTAT
1 TGCATAATAAAATTAAAATTTAT
* *
90976 GGAATTAATAAAA-TAAAATTCTAAT
1 TGCA-TAATAAAATTAAAATT-T-AT
*
91001 TGCATAATAAATTTAAA
1 TGCATAATAAAATTAAA
91018 GTTCTGTTCA
Statistics
Matches: 33, Mismatches: 5, Indels: 6
0.75 0.11 0.14
Matches are distributed among these distances:
23 9 0.27
24 16 0.48
25 8 0.24
ACGTcount: A:0.54, C:0.05, G:0.06, T:0.35
Consensus pattern (23 bp):
TGCATAATAAAATTAAAATTTAT
Found at i:95244 original size:7 final size:8
Alignment explanation
Indices: 95219--95287 Score: 52
Period size: 9 Copynumber: 8.0 Consensus size: 8
95209 CTTTAAAATG
95219 TTTTTATA
1 TTTTTATA
95227 --TTTATA
1 TTTTTATA
*
95233 TTTTTAATT
1 TTTTT-ATA
95242 TTTTTATAA
1 TTTTTAT-A
95251 TTTATATATA
1 TTT-T-TATA
95261 TTTTTAAATA
1 TTTTT--ATA
95271 TTTTTATAA
1 TTTTTAT-A
95280 TTTTTATA
1 TTTTTATA
95288 ATTAGGACTG
Statistics
Matches: 50, Mismatches: 2, Indels: 18
0.71 0.03 0.26
Matches are distributed among these distances:
6 6 0.12
8 9 0.18
9 19 0.38
10 13 0.26
11 3 0.06
ACGTcount: A:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (8 bp):
TTTTTATA
Found at i:95258 original size:9 final size:9
Alignment explanation
Indices: 95242--95290 Score: 62
Period size: 9 Copynumber: 5.2 Consensus size: 9
95232 ATTTTTAATT
95242 TTTTTATAA
1 TTTTTATAA
*
95251 TTTATATATA
1 TTTTTATA-A
*
95261 TTTTTAAATA
1 TTTTTATA-A
95271 TTTTTATAA
1 TTTTTATAA
95280 TTTTTATAA
1 TTTTTATAA
95289 TT
1 TT
95291 AGGACTGAAA
Statistics
Matches: 35, Mismatches: 4, Indels: 2
0.85 0.10 0.05
Matches are distributed among these distances:
9 19 0.54
10 16 0.46
ACGTcount: A:0.35, C:0.00, G:0.00, T:0.65
Consensus pattern (9 bp):
TTTTTATAA
Found at i:95275 original size:29 final size:28
Alignment explanation
Indices: 95229--95287 Score: 91
Period size: 29 Copynumber: 2.1 Consensus size: 28
95219 TTTTTATATT
*
95229 TATATTTTTAATTTTTTTATAATTTATA
1 TATATTTTTAATATTTTTATAATTTATA
*
95257 TATATTTTTAAATATTTTTATAATTTTTA
1 TATATTTTT-AATATTTTTATAATTTATA
95286 TA
1 TA
95288 ATTAGGACTG
Statistics
Matches: 28, Mismatches: 2, Indels: 1
0.90 0.06 0.03
Matches are distributed among these distances:
28 9 0.32
29 19 0.68
ACGTcount: A:0.34, C:0.00, G:0.00, T:0.66
Consensus pattern (28 bp):
TATATTTTTAATATTTTTATAATTTATA
Found at i:97773 original size:26 final size:26
Alignment explanation
Indices: 97743--97830 Score: 108
Period size: 26 Copynumber: 3.4 Consensus size: 26
97733 CTTCCAGAAA
*
97743 TTTAGCTCATATGAGCCCAAACAAAG
1 TTTAGCTCATATGAGCCCAGACAAAG
* *
97769 TTTAGCTCTTATAAGCCCAGACAAAG
1 TTTAGCTCATATGAGCCCAGACAAAG
*
97795 TTTAGCTCAT-TGAAGCCTAGACAGAA-
1 TTTAGCTCATATG-AGCCCAGACA-AAG
97821 TTTAGCTCAT
1 TTTAGCTCAT
97831 TCGAGCCATA
Statistics
Matches: 54, Mismatches: 6, Indels: 4
0.84 0.09 0.06
Matches are distributed among these distances:
25 1 0.02
26 51 0.94
27 2 0.04
ACGTcount: A:0.34, C:0.22, G:0.16, T:0.28
Consensus pattern (26 bp):
TTTAGCTCATATGAGCCCAGACAAAG
Found at i:101359 original size:24 final size:24
Alignment explanation
Indices: 101314--101359 Score: 58
Period size: 24 Copynumber: 1.9 Consensus size: 24
101304 TTGATAGCTC
* *
101314 CTCAATCTCATAATCGACAGTAGG
1 CTCAACCTCATAATAGACAGTAGG
101338 CTCAACCTCGATAATAGA-AGTA
1 CTCAACCTC-ATAATAGACAGTA
101360 AGTACAGAAG
Statistics
Matches: 19, Mismatches: 2, Indels: 2
0.83 0.09 0.09
Matches are distributed among these distances:
24 12 0.63
25 7 0.37
ACGTcount: A:0.37, C:0.24, G:0.15, T:0.24
Consensus pattern (24 bp):
CTCAACCTCATAATAGACAGTAGG
Found at i:107159 original size:95 final size:94
Alignment explanation
Indices: 106954--107159 Score: 218
Period size: 95 Copynumber: 2.2 Consensus size: 94
106944 GTGCTTCGTT
* * * * * * *
106954 TAAAAAAATGAGAACAACTTGTTATAGTGTTTCCTTAAAAAAGTGGGAACAAATAGGCAAAATGT
1 TAAAAAAATGAGAACAACTTATTAGAGTATTTCCCTAAAAAAGTGGGAACAAACAAGCAAAATAT
* *
107019 TTTCAGAATAACCAGTTATATTGTTTCAC
66 TTTCAGAATAACCAGTCATAGTGTTTCAC
* * * * * *
107048 TAAATAAATAAGGAACAATTTATTAGAGTATTTCCCTAAAAAAGTGGGAACAACCAAGTATAATA
1 TAAAAAAATGA-GAACAACTTATTAGAGTATTTCCCTAAAAAAGTGGGAACAAACAAGCAAAATA
*
107113 TTTTC-GAAATAACCTA-TCATAGTGTTTCCC
65 TTTTCAG-AATAACC-AGTCATAGTGTTTCAC
107143 TAAAAAAAGTGAGAACA
1 TAAAAAAA-TGAGAACA
107160 CTAAAGTATA
Statistics
Matches: 90, Mismatches: 18, Indels: 7
0.78 0.16 0.06
Matches are distributed among these distances:
94 10 0.11
95 77 0.86
96 3 0.03
ACGTcount: A:0.44, C:0.13, G:0.15, T:0.29
Consensus pattern (94 bp):
TAAAAAAATGAGAACAACTTATTAGAGTATTTCCCTAAAAAAGTGGGAACAAACAAGCAAAATAT
TTTCAGAATAACCAGTCATAGTGTTTCAC
Found at i:111461 original size:71 final size:71
Alignment explanation
Indices: 111341--111479 Score: 208
Period size: 71 Copynumber: 2.0 Consensus size: 71
111331 CCTTATTGAC
* **
111341 AGACTTGTCCAACAACAACATTCCTCTTACCATATAAAGCATTTTAGCTCTAACATATCGATCAA
1 AGACTTGTCCAACAACAACATTCATCTTACCATATAAAGCATTCAAGCTCTAACATATCGATCAA
111406 TCTTAT
66 TCTTAT
* * *
111412 AGACTTGTTCGAA-AACAACATTCATCTTACCATCTAAAGCATTCAAGCTCTAACATATTGATCA
1 AGACTTG-TCCAACAACAACATTCATCTTACCATATAAAGCATTCAAGCTCTAACATATCGATCA
111476 ATCT
65 ATCT
111480 CCTTCACAGT
Statistics
Matches: 61, Mismatches: 6, Indels: 2
0.88 0.09 0.03
Matches are distributed among these distances:
71 57 0.93
72 4 0.07
ACGTcount: A:0.36, C:0.24, G:0.08, T:0.32
Consensus pattern (71 bp):
AGACTTGTCCAACAACAACATTCATCTTACCATATAAAGCATTCAAGCTCTAACATATCGATCAA
TCTTAT
Found at i:111630 original size:76 final size:76
Alignment explanation
Indices: 111504--111655 Score: 232
Period size: 76 Copynumber: 2.0 Consensus size: 76
111494 TGTCGTGGAG
* * *
111504 GGGCCAATTTGACAAGTCTCTTAAACCATGTGCATTTCACCCGACTTCCACTTAATTTGTTCTCG
1 GGGCCAATTTGACAAGCCTCTCAAACCATGTGCATTTCACCCGACTTCCACTTAATTTGTTCTCA
111569 TCCTCAGACAA
66 TCCTCAGACAA
** * *
111580 GGGCCAATTTGGTAAGCCTCTCAAACCATGTGCATTTCACCTGACTTCCACTTAATTTTTTCTCA
1 GGGCCAATTTGACAAGCCTCTCAAACCATGTGCATTTCACCCGACTTCCACTTAATTTGTTCTCA
*
111645 TCCTTAGACAA
66 TCCTCAGACAA
111656 AATGACACCA
Statistics
Matches: 68, Mismatches: 8, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
76 68 1.00
ACGTcount: A:0.25, C:0.28, G:0.14, T:0.33
Consensus pattern (76 bp):
GGGCCAATTTGACAAGCCTCTCAAACCATGTGCATTTCACCCGACTTCCACTTAATTTGTTCTCA
TCCTCAGACAA
Found at i:119229 original size:18 final size:18
Alignment explanation
Indices: 119206--119260 Score: 65
Period size: 18 Copynumber: 3.1 Consensus size: 18
119196 AAAGCTCCCT
*
119206 AACCTGAATCCGAATCGG
1 AACCTGAATCCGAATCCG
* *
119224 AACCTGAACCCGAACCCG
1 AACCTGAATCCGAATCCG
* *
119242 AACCAGAATCGGAATCCG
1 AACCTGAATCCGAATCCG
119260 A
1 A
119261 TTTACGAGCG
Statistics
Matches: 30, Mismatches: 7, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
18 30 1.00
ACGTcount: A:0.36, C:0.33, G:0.20, T:0.11
Consensus pattern (18 bp):
AACCTGAATCCGAATCCG
Found at i:119736 original size:6 final size:6
Alignment explanation
Indices: 119727--119769 Score: 68
Period size: 6 Copynumber: 6.8 Consensus size: 6
119717 GAAATTAAAC
119727 AAAAGA AAAAGA AAAAGA AAAAGA AAAAGA AGGAAAGA AAAAG
1 AAAAGA AAAAGA AAAAGA AAAAGA AAAAGA A--AAAGA AAAAG
119770 CCGTTACCTT
Statistics
Matches: 35, Mismatches: 0, Indels: 4
0.90 0.00 0.10
Matches are distributed among these distances:
6 29 0.83
8 6 0.17
ACGTcount: A:0.79, C:0.00, G:0.21, T:0.00
Consensus pattern (6 bp):
AAAAGA
Found at i:124782 original size:27 final size:28
Alignment explanation
Indices: 124724--124782 Score: 68
Period size: 27 Copynumber: 2.1 Consensus size: 28
124714 ACTTTCATCA
* * *
124724 TTAAGCTTAATTAATTATATTTTTTTCT
1 TTAAGCTTAATTAATTACATTATTTTCC
124752 TTAA-CTTAATTAA-TACATTATTTTCAC
1 TTAAGCTTAATTAATTACATTATTTTC-C
124779 TTAA
1 TTAA
124783 ATATCATATC
Statistics
Matches: 27, Mismatches: 3, Indels: 3
0.82 0.09 0.09
Matches are distributed among these distances:
26 10 0.37
27 13 0.48
28 4 0.15
ACGTcount: A:0.34, C:0.10, G:0.02, T:0.54
Consensus pattern (28 bp):
TTAAGCTTAATTAATTACATTATTTTCC
Found at i:127543 original size:42 final size:42
Alignment explanation
Indices: 127431--127577 Score: 159
Period size: 42 Copynumber: 3.5 Consensus size: 42
127421 ACTGTCACAT
* * * *
127431 TGCTCCTAAGTACGAGCCTAAACAATTCATCCAAAATGTTGA
1 TGCTCCTAAGCATGAGCTTAAACAGTTCATCCAAAATGTTGA
** *
127473 TGCTCCTAAGCACAAGCCTAAACAGTTCATCCAAAATGTTGA
1 TGCTCCTAAGCATGAGCTTAAACAGTTCATCCAAAATGTTGA
* ** * * ***
127515 TGCTCCTAAACATGAGCTTAAAGTGTTCAACCCAAACAATGA
1 TGCTCCTAAGCATGAGCTTAAACAGTTCATCCAAAATGTTGA
127557 TGCTCCTAAGCATGAGCTTAA
1 TGCTCCTAAGCATGAGCTTAA
127578 CTAGCAGACC
Statistics
Matches: 90, Mismatches: 15, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
42 90 1.00
ACGTcount: A:0.35, C:0.24, G:0.15, T:0.25
Consensus pattern (42 bp):
TGCTCCTAAGCATGAGCTTAAACAGTTCATCCAAAATGTTGA
Found at i:134136 original size:19 final size:19
Alignment explanation
Indices: 134112--134174 Score: 58
Period size: 19 Copynumber: 3.3 Consensus size: 19
134102 TGCCTTAAGA
134112 ATTCAAACTTCCCTACAAC
1 ATTCAAACTTCCCTACAAC
* ** *
134131 ATTCAAGCCAACCTTA-AGA-
1 ATTCAA-ACTTCCCTACA-AC
134150 ATTCAAACTTCCCTACAAC
1 ATTCAAACTTCCCTACAAC
134169 ATTCAA
1 ATTCAA
134175 GCCAACTTCA
Statistics
Matches: 32, Mismatches: 8, Indels: 8
0.67 0.17 0.17
Matches are distributed among these distances:
18 6 0.19
19 20 0.62
20 6 0.19
ACGTcount: A:0.40, C:0.32, G:0.03, T:0.25
Consensus pattern (19 bp):
ATTCAAACTTCCCTACAAC
Found at i:134155 original size:38 final size:38
Alignment explanation
Indices: 134104--134180 Score: 154
Period size: 38 Copynumber: 2.0 Consensus size: 38
134094 CACTATAGTG
134104 CCTTAAGAATTCAAACTTCCCTACAACATTCAAGCCAA
1 CCTTAAGAATTCAAACTTCCCTACAACATTCAAGCCAA
134142 CCTTAAGAATTCAAACTTCCCTACAACATTCAAGCCAA
1 CCTTAAGAATTCAAACTTCCCTACAACATTCAAGCCAA
134180 C
1 C
134181 TTCAACATGA
Statistics
Matches: 39, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
38 39 1.00
ACGTcount: A:0.39, C:0.32, G:0.05, T:0.23
Consensus pattern (38 bp):
CCTTAAGAATTCAAACTTCCCTACAACATTCAAGCCAA
Found at i:147421 original size:14 final size:14
Alignment explanation
Indices: 147402--147436 Score: 52
Period size: 14 Copynumber: 2.5 Consensus size: 14
147392 TGTTTCACTG
*
147402 AAAATGATTTTTGA
1 AAAATGATTTCTGA
*
147416 AAAATGATTTCTGG
1 AAAATGATTTCTGA
147430 AAAATGA
1 AAAATGA
147437 CTTACTTTTT
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:0.46, C:0.03, G:0.17, T:0.34
Consensus pattern (14 bp):
AAAATGATTTCTGA
Found at i:147863 original size:19 final size:19
Alignment explanation
Indices: 147827--147865 Score: 51
Period size: 19 Copynumber: 2.1 Consensus size: 19
147817 TATTATTAAT
**
147827 ATATTTATAATTGTAATAA
1 ATATTTATAATTAAAATAA
*
147846 ATATTTATTATTAAAATAA
1 ATATTTATAATTAAAATAA
147865 A
1 A
147866 ATTAAAATAT
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:0.51, C:0.00, G:0.03, T:0.46
Consensus pattern (19 bp):
ATATTTATAATTAAAATAA
Found at i:149618 original size:20 final size:20
Alignment explanation
Indices: 149593--149654 Score: 74
Period size: 20 Copynumber: 3.2 Consensus size: 20
149583 AAAAAAAAAA
*
149593 AAAAATTCAAAATAATTTTT
1 AAAAATACAAAATAATTTTT
* *
149613 AAAAATAAAAAATAAATTTT
1 AAAAATACAAAATAATTTTT
*
149633 -AAAATACAAAAT-ATTTAT
1 AAAAATACAAAATAATTTTT
149651 AAAA
1 AAAA
149655 TTTTCAAATT
Statistics
Matches: 35, Mismatches: 6, Indels: 3
0.80 0.14 0.07
Matches are distributed among these distances:
18 4 0.11
19 14 0.40
20 17 0.49
ACGTcount: A:0.65, C:0.03, G:0.00, T:0.32
Consensus pattern (20 bp):
AAAAATACAAAATAATTTTT
Found at i:149636 original size:19 final size:20
Alignment explanation
Indices: 149601--149645 Score: 65
Period size: 19 Copynumber: 2.3 Consensus size: 20
149591 AAAAAAATTC
*
149601 AAAATAATTTTTAAAAATAA
1 AAAATAAATTTTAAAAATAA
*
149621 AAAATAAATTTT-AAAATAC
1 AAAATAAATTTTAAAAATAA
149640 AAAATA
1 AAAATA
149646 TTTATAAAAT
Statistics
Matches: 23, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
19 12 0.52
20 11 0.48
ACGTcount: A:0.67, C:0.02, G:0.00, T:0.31
Consensus pattern (20 bp):
AAAATAAATTTTAAAAATAA
Found at i:152860 original size:64 final size:61
Alignment explanation
Indices: 152690--152867 Score: 209
Period size: 64 Copynumber: 2.9 Consensus size: 61
152680 TTATTATAAT
* ** *
152690 ATTTGGTATCTAAACTTGACACTTTTTTTTTTTAATTTGATACCTAAA-TTCTTTTGACCCA
1 ATTTGGTACCTAAACTTGACA-TTTTTTTTCCTAATTTGATACCTAAACTTTTTTTGACCCA
* * *
152751 ATTTGATACTTGAACTTGACA--TTTTTTCCTAATTTGATACCTAAACTTTTTTTGGACCCA
1 ATTTGGTACCTAAACTTGACATTTTTTTTCCTAATTTGATACCTAAACTTTTTTT-GACCCA
* * *
152811 ATTTGGCACCTAAACTTGACATTTCCTTTTTCCTAATTTGGTACCTAAACTCTTTTT
1 ATTTGGTACCTAAACTTGACATTT--TTTTTCCTAATTTGATACCTAAACTTTTTTT
152868 AAGATTCAAT
Statistics
Matches: 98, Mismatches: 13, Indels: 9
0.82 0.11 0.08
Matches are distributed among these distances:
58 22 0.22
59 6 0.06
60 23 0.23
61 17 0.17
62 1 0.01
64 29 0.30
ACGTcount: A:0.25, C:0.19, G:0.09, T:0.47
Consensus pattern (61 bp):
ATTTGGTACCTAAACTTGACATTTTTTTTCCTAATTTGATACCTAAACTTTTTTTGACCCA
Found at i:153093 original size:29 final size:31
Alignment explanation
Indices: 153061--153136 Score: 84
Period size: 29 Copynumber: 2.5 Consensus size: 31
153051 GGACCTCAAA
*
153061 AAGTTTAAGTACAAACTTAA-AAAAA-TGTC
1 AAGTTTAAGTACAAAATTAAGAAAAAGTGTC
* * *
153090 AAGTTTAGGCACAAAATTAAGAAAAAGTTTC
1 AAGTTTAAGTACAAAATTAAGAAAAAGTGTC
*
153121 AAGTTTGAGTATCAAA
1 AAGTTTAAGTA-CAAA
153137 TTAGACCAAA
Statistics
Matches: 37, Mismatches: 7, Indels: 3
0.79 0.15 0.06
Matches are distributed among these distances:
29 17 0.46
30 5 0.14
31 11 0.30
32 4 0.11
ACGTcount: A:0.49, C:0.09, G:0.14, T:0.28
Consensus pattern (31 bp):
AAGTTTAAGTACAAAATTAAGAAAAAGTGTC
Found at i:153173 original size:88 final size:89
Alignment explanation
Indices: 153006--153187 Score: 201
Period size: 88 Copynumber: 2.1 Consensus size: 89
152996 TAAAAAAAAA
* * * * **
153006 TTAGGTACCAAATTAAGAAAAAGAGTCAAGTTCATGTACCAAATTGGACCTCAAAAAGTTTAAGT
1 TTAGGCACAAAATTAAGAAAAAGAGTCAAGTTCATGTACCAAATTAGACCTAAAAAAACTTAAGT
153071 ACAAACTTAAAAAAA-TGTCAAGT
66 ACAAACTTAAAAAAAGTGTCAAGT
** * *
153094 TTAGGCACAAAATTAAGAAAAAGTTTCAAGTTTGA-GTATCAAATTAGACC-AAAAAAACTTAAG
1 TTAGGCACAAAATTAAGAAAAAGAGTCAAG-TTCATGTACCAAATTAGACCTAAAAAAACTTAAG
* *
153157 TACCAAA-TTAGGAAAAAGTGTCATGT
65 TA-CAAACTTA-AAAAAAGTGTCAAGT
153183 TTAGG
1 TTAGG
153188 TGCCAAATAT
Statistics
Matches: 78, Mismatches: 12, Indels: 7
0.80 0.12 0.07
Matches are distributed among these distances:
87 15 0.19
88 48 0.62
89 15 0.19
ACGTcount: A:0.46, C:0.12, G:0.16, T:0.26
Consensus pattern (89 bp):
TTAGGCACAAAATTAAGAAAAAGAGTCAAGTTCATGTACCAAATTAGACCTAAAAAAACTTAAGT
ACAAACTTAAAAAAAGTGTCAAGT
Found at i:155939 original size:22 final size:21
Alignment explanation
Indices: 155892--155932 Score: 57
Period size: 21 Copynumber: 2.0 Consensus size: 21
155882 AAATTGATAA
*
155892 TTAAATTTTTATAATATTCAT
1 TTAAATTTTTATAATATTAAT
*
155913 TTAAATTTTTATTAT-TTAAT
1 TTAAATTTTTATAATATTAAT
155933 ATATAAAAAA
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
20 4 0.22
21 14 0.78
ACGTcount: A:0.37, C:0.02, G:0.00, T:0.61
Consensus pattern (21 bp):
TTAAATTTTTATAATATTAAT
Found at i:161472 original size:14 final size:14
Alignment explanation
Indices: 161453--161497 Score: 58
Period size: 14 Copynumber: 3.4 Consensus size: 14
161443 GTATATTCAA
161453 AATATATATGTTGT
1 AATATATATGTTGT
*
161467 AATATAT-T-TTTT
1 AATATATATGTTGT
*
161479 ATTATATATGTTGT
1 AATATATATGTTGT
161493 AATAT
1 AATAT
161498 TAACTCACAA
Statistics
Matches: 25, Mismatches: 4, Indels: 4
0.76 0.12 0.12
Matches are distributed among these distances:
12 9 0.36
13 2 0.08
14 14 0.56
ACGTcount: A:0.36, C:0.00, G:0.09, T:0.56
Consensus pattern (14 bp):
AATATATATGTTGT
Found at i:165410 original size:22 final size:22
Alignment explanation
Indices: 165370--165430 Score: 81
Period size: 22 Copynumber: 2.8 Consensus size: 22
165360 CGATCTAAGG
*
165370 AAAAATAAAAG-AAACAGAATT
1 AAAAATAAAAGAAAATAGAATT
165391 AAAAATAAAAGAAAATAGAATT
1 AAAAATAAAAGAAAATAGAATT
*
165413 AAAAGA-AATAGAAAATAG
1 AAAA-ATAAAAGAAAATAG
165431 GGAAGTCAAA
Statistics
Matches: 36, Mismatches: 2, Indels: 3
0.88 0.05 0.07
Matches are distributed among these distances:
21 11 0.31
22 24 0.67
23 1 0.03
ACGTcount: A:0.72, C:0.02, G:0.11, T:0.15
Consensus pattern (22 bp):
AAAAATAAAAGAAAATAGAATT
Found at i:165421 original size:15 final size:16
Alignment explanation
Indices: 165396--165425 Score: 53
Period size: 15 Copynumber: 1.9 Consensus size: 16
165386 GAATTAAAAA
165396 TAAAAGAAAATAGAAT
1 TAAAAGAAAATAGAAT
165412 TAAAAG-AAATAGAA
1 TAAAAGAAAATAGAA
165426 AATAGGGAAG
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 8 0.57
16 6 0.43
ACGTcount: A:0.70, C:0.00, G:0.13, T:0.17
Consensus pattern (16 bp):
TAAAAGAAAATAGAAT
Found at i:192451 original size:35 final size:37
Alignment explanation
Indices: 192405--192474 Score: 117
Period size: 37 Copynumber: 1.9 Consensus size: 37
192395 GGTTTGTAGA
192405 GATATTTGACAG-TAGAAAAGGATTCATT-TTTTAGG
1 GATATTTGACAGATAGAAAAGGATTCATTATTTTAGG
192440 GATATTTGACAGAATAGAAAAGGATTCATTATTTT
1 GATATTTGACAG-ATAGAAAAGGATTCATTATTTT
192475 TAGGCAGAAA
Statistics
Matches: 32, Mismatches: 0, Indels: 3
0.91 0.00 0.09
Matches are distributed among these distances:
35 12 0.38
37 16 0.50
38 4 0.12
ACGTcount: A:0.37, C:0.06, G:0.20, T:0.37
Consensus pattern (37 bp):
GATATTTGACAGATAGAAAAGGATTCATTATTTTAGG
Found at i:195580 original size:45 final size:45
Alignment explanation
Indices: 195529--195620 Score: 184
Period size: 45 Copynumber: 2.0 Consensus size: 45
195519 CTTTGACAGA
195529 GACTAAACTCTGTATCCATTGTTAGGCTTGAAAACACCAAAAGCG
1 GACTAAACTCTGTATCCATTGTTAGGCTTGAAAACACCAAAAGCG
195574 GACTAAACTCTGTATCCATTGTTAGGCTTGAAAACACCAAAAGCG
1 GACTAAACTCTGTATCCATTGTTAGGCTTGAAAACACCAAAAGCG
195619 GA
1 GA
195621 TGGATTGGTG
Statistics
Matches: 47, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
45 47 1.00
ACGTcount: A:0.36, C:0.22, G:0.18, T:0.24
Consensus pattern (45 bp):
GACTAAACTCTGTATCCATTGTTAGGCTTGAAAACACCAAAAGCG
Found at i:209782 original size:30 final size:31
Alignment explanation
Indices: 209742--209807 Score: 80
Period size: 30 Copynumber: 2.2 Consensus size: 31
209732 TTAGGCCCTT
*
209742 AACTTGGCAATTGTTCCAACATTGGGACCTA
1 AACTTGGCAATTGTTCCAACATTGGGACATA
* ** *
209773 AACTT-GCAATTTTTCCCTCATTGGGGCATA
1 AACTTGGCAATTGTTCCAACATTGGGACATA
209803 AACTT
1 AACTT
209808 TAGGATTTTA
Statistics
Matches: 30, Mismatches: 5, Indels: 1
0.83 0.14 0.03
Matches are distributed among these distances:
30 25 0.83
31 5 0.17
ACGTcount: A:0.27, C:0.23, G:0.17, T:0.33
Consensus pattern (31 bp):
AACTTGGCAATTGTTCCAACATTGGGACATA
Found at i:209917 original size:58 final size:59
Alignment explanation
Indices: 209832--209942 Score: 179
Period size: 58 Copynumber: 1.9 Consensus size: 59
209822 CTTGGACAAA
* * *
209832 AAAAAAATGTTCAAGCCCCAATGTGGGAACAATTGCCAAGTTCAGGGCCTAACCTGGAT
1 AAAAAAATGTTCAAACCCCAATATGGGAACAATTGCCAAGTTCAAGGCCTAACCTGGAT
*
209891 AAAAAAA-GTTTAAACCCCAATATGGGAACAATTGCCAAGTTCAAGGCCTAAC
1 AAAAAAATGTTCAAACCCCAATATGGGAACAATTGCCAAGTTCAAGGCCTAAC
209943 TTTAAAAAAG
Statistics
Matches: 48, Mismatches: 4, Indels: 1
0.91 0.08 0.02
Matches are distributed among these distances:
58 41 0.85
59 7 0.15
ACGTcount: A:0.40, C:0.22, G:0.19, T:0.20
Consensus pattern (59 bp):
AAAAAAATGTTCAAACCCCAATATGGGAACAATTGCCAAGTTCAAGGCCTAACCTGGAT
Found at i:214529 original size:2 final size:2
Alignment explanation
Indices: 214522--214579 Score: 107
Period size: 2 Copynumber: 29.0 Consensus size: 2
214512 TGAAAATTAA
214522 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG
1 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG
*
214564 AG AG AG AT AG AG AG AG
1 AG AG AG AG AG AG AG AG
214580 GAAAATCCTC
Statistics
Matches: 54, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
2 54 1.00
ACGTcount: A:0.50, C:0.00, G:0.48, T:0.02
Consensus pattern (2 bp):
AG
Found at i:219413 original size:32 final size:32
Alignment explanation
Indices: 219375--219436 Score: 124
Period size: 32 Copynumber: 1.9 Consensus size: 32
219365 AATTTCATCA
219375 AAAATCACTTTACAAAAAGGTTTAACCCAATC
1 AAAATCACTTTACAAAAAGGTTTAACCCAATC
219407 AAAATCACTTTACAAAAAGGTTTAACCCAA
1 AAAATCACTTTACAAAAAGGTTTAACCCAA
219437 GCATCAAACA
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
32 30 1.00
ACGTcount: A:0.48, C:0.21, G:0.06, T:0.24
Consensus pattern (32 bp):
AAAATCACTTTACAAAAAGGTTTAACCCAATC
Found at i:223570 original size:78 final size:78
Alignment explanation
Indices: 223486--223641 Score: 303
Period size: 78 Copynumber: 2.0 Consensus size: 78
223476 GGTATATCCT
223486 CCTCCTCCATCTAACTCCCTTTACATTGCCCATCATAATCCCAAAAACCATGTCTCATTTTACAA
1 CCTCCTCCATCTAACTCCCTTTACATTGCCCATCATAATCCCAAAAACCATGTCTCATTTTACAA
223551 CAATTAAAACAAA
66 CAATTAAAACAAA
*
223564 CCTCCTCCATCTAACTCCCTTTACATTGCCCATCATAATCCCAAAAGCCATGTCTCATTTTACAA
1 CCTCCTCCATCTAACTCCCTTTACATTGCCCATCATAATCCCAAAAACCATGTCTCATTTTACAA
223629 CAATTAAAACAAA
66 CAATTAAAACAAA
223642 AAATTGGCAG
Statistics
Matches: 77, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
78 77 1.00
ACGTcount: A:0.35, C:0.33, G:0.03, T:0.28
Consensus pattern (78 bp):
CCTCCTCCATCTAACTCCCTTTACATTGCCCATCATAATCCCAAAAACCATGTCTCATTTTACAA
CAATTAAAACAAA
Found at i:224835 original size:24 final size:24
Alignment explanation
Indices: 224789--224836 Score: 60
Period size: 24 Copynumber: 2.0 Consensus size: 24
224779 AAATTTATAC
* * *
224789 TATATATAATTATAAGAACATAAA
1 TATATAGAATTATAAAAAAATAAA
*
224813 TATATAGAATTTTAAAAAAATAAA
1 TATATAGAATTATAAAAAAATAAA
224837 AAAAATAACC
Statistics
Matches: 20, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
24 20 1.00
ACGTcount: A:0.60, C:0.02, G:0.04, T:0.33
Consensus pattern (24 bp):
TATATAGAATTATAAAAAAATAAA
Found at i:226041 original size:27 final size:27
Alignment explanation
Indices: 225990--226040 Score: 77
Period size: 27 Copynumber: 1.9 Consensus size: 27
225980 GATTACATAT
* *
225990 ATTTTTTAAAATATAAAATATAAAATC
1 ATTTTTTAAAATAGAAAATAAAAAATC
226017 ATTTTTTAAAAT-GAAAATAAAAAA
1 ATTTTTTAAAATAGAAAATAAAAAA
226041 AATTCAAATA
Statistics
Matches: 22, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
26 10 0.45
27 12 0.55
ACGTcount: A:0.59, C:0.02, G:0.02, T:0.37
Consensus pattern (27 bp):
ATTTTTTAAAATAGAAAATAAAAAATC
Found at i:237384 original size:27 final size:27
Alignment explanation
Indices: 237346--237409 Score: 92
Period size: 27 Copynumber: 2.4 Consensus size: 27
237336 TTTTTTTAAT
*
237346 ATAGGCATCATTGGTGCCGCCTACCCA
1 ATAGGCACCATTGGTGCCGCCTACCCA
* *
237373 ATAGGCACCATTGGTGCCGTCTACCCC
1 ATAGGCACCATTGGTGCCGCCTACCCA
*
237400 ATAGACACCA
1 ATAGGCACCA
237410 CTCGAAATTT
Statistics
Matches: 33, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
27 33 1.00
ACGTcount: A:0.25, C:0.34, G:0.20, T:0.20
Consensus pattern (27 bp):
ATAGGCACCATTGGTGCCGCCTACCCA
Found at i:237840 original size:14 final size:14
Alignment explanation
Indices: 237816--237852 Score: 58
Period size: 13 Copynumber: 2.7 Consensus size: 14
237806 TGTTTCACTA
*
237816 AAAATGATTTTT-G
1 AAAATAATTTTTAG
237829 AAAATAATTTTTAG
1 AAAATAATTTTTAG
237843 AAAATAATTT
1 AAAATAATTT
237853 ACTTTTTTGA
Statistics
Matches: 22, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
13 11 0.50
14 11 0.50
ACGTcount: A:0.49, C:0.00, G:0.08, T:0.43
Consensus pattern (14 bp):
AAAATAATTTTTAG
Found at i:238337 original size:15 final size:16
Alignment explanation
Indices: 238316--238362 Score: 51
Period size: 15 Copynumber: 2.8 Consensus size: 16
238306 TATACTACAA
238316 AATATTTATTATTAAT
1 AATATTTATTATTAAT
*
238332 -ATATTTATAATTGTAAT
1 AATATTTATTA-T-TAAT
238349 AAATATTTATTATT
1 -AATATTTATTATT
238363 GAAAATCTTC
Statistics
Matches: 25, Mismatches: 2, Indels: 7
0.74 0.06 0.21
Matches are distributed among these distances:
15 9 0.36
16 1 0.04
17 5 0.20
18 1 0.04
19 9 0.36
ACGTcount: A:0.43, C:0.00, G:0.02, T:0.55
Consensus pattern (16 bp):
AATATTTATTATTAAT
Found at i:238423 original size:16 final size:16
Alignment explanation
Indices: 238392--238428 Score: 58
Period size: 16 Copynumber: 2.3 Consensus size: 16
238382 ATGTTAATAA
238392 TATTATTTAAAATTAT
1 TATTATTTAAAATTAT
238408 TATT-TTTAAAATTTAT
1 TATTATTTAAAA-TTAT
238424 TATTA
1 TATTA
238429 AAATAAAATT
Statistics
Matches: 19, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
15 7 0.37
16 12 0.63
ACGTcount: A:0.41, C:0.00, G:0.00, T:0.59
Consensus pattern (16 bp):
TATTATTTAAAATTAT
Found at i:238461 original size:26 final size:25
Alignment explanation
Indices: 238432--238506 Score: 73
Period size: 26 Copynumber: 2.9 Consensus size: 25
238422 ATTATTAAAA
238432 TAAAATTGAAATATTAAATAATTTAT
1 TAAAATT-AAATATTAAATAATTTAT
*
238458 TAAAATAATAAATATT-ATTAATTTAT
1 TAAAAT--TAAATATTAAATAATTTAT
*
238484 TATATGATTAAATA-TAAATAATT
1 TA-A-AATTAAATATTAAATAATT
238507 AAATATGTAT
Statistics
Matches: 41, Mismatches: 3, Indels: 10
0.76 0.06 0.19
Matches are distributed among these distances:
25 1 0.02
26 29 0.71
27 8 0.20
28 3 0.07
ACGTcount: A:0.53, C:0.00, G:0.03, T:0.44
Consensus pattern (25 bp):
TAAAATTAAATATTAAATAATTTAT
Found at i:239268 original size:24 final size:26
Alignment explanation
Indices: 239241--239288 Score: 66
Period size: 24 Copynumber: 1.9 Consensus size: 26
239231 AGAGAAATGT
239241 AAATG-TGATATATGA-A-ATTATGAG
1 AAATGATGA-ATATGAGAGATTATGAG
239265 AAATGATGAATATGAGAGATTATG
1 AAATGATGAATATGAGAGATTATG
239289 CCCATGTAGA
Statistics
Matches: 21, Mismatches: 0, Indels: 4
0.84 0.00 0.16
Matches are distributed among these distances:
24 11 0.52
25 4 0.19
26 6 0.29
ACGTcount: A:0.46, C:0.00, G:0.23, T:0.31
Consensus pattern (26 bp):
AAATGATGAATATGAGAGATTATGAG
Found at i:239379 original size:23 final size:23
Alignment explanation
Indices: 239351--239521 Score: 136
Period size: 23 Copynumber: 7.3 Consensus size: 23
239341 ACGCTAGTGC
239351 GCTTACTG-TTCAGCACTGTGTGT
1 GCTTACTGATTC-GCACTGTGTGT
* *
239374 GCTTACTGTTTCGCACTTTGTGT
1 GCTTACTGATTCGCACTGTGTGT
* *
239397 GCTTACTGTTTCGCATCT-CGTGT
1 GCTTACTGATTCGCA-CTGTGTGT
* * ** * *
239420 GCCTACTGATTTGCGTTATGTGC
1 GCTTACTGATTCGCACTGTGTGT
*
239443 GCCTACTGATT-GCACTGTGTGT
1 GCTTACTGATTCGCACTGTGTGT
239465 GCTTACTGGATT-GCACTGTGTGT
1 GCTTACT-GATTCGCACTGTGTGT
*
239488 GCTTACTGTTTCCCCAGCACT-TGTGT
1 GCTTACTGATT---C-GCACTGTGTGT
239514 GCTTACTG
1 GCTTACTG
239522 TTAAGTACTT
Statistics
Matches: 124, Mismatches: 15, Indels: 15
0.81 0.10 0.10
Matches are distributed among these distances:
22 17 0.14
23 84 0.68
24 5 0.04
26 13 0.10
27 5 0.04
ACGTcount: A:0.12, C:0.23, G:0.25, T:0.40
Consensus pattern (23 bp):
GCTTACTGATTCGCACTGTGTGT
Found at i:241057 original size:3 final size:3
Alignment explanation
Indices: 241051--241115 Score: 121
Period size: 3 Copynumber: 21.3 Consensus size: 3
241041 TTATTATCAC
241051 ATT ATT ATT 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 ATT ATT ATT
241099 ATT ATT ATT ATTT ATT A
1 ATT ATT ATT A-TT ATT A
241116 ATTAAAACAT
Statistics
Matches: 61, Mismatches: 0, Indels: 2
0.97 0.00 0.03
Matches are distributed among these distances:
3 58 0.95
4 3 0.05
ACGTcount: A:0.34, C:0.00, G:0.00, T:0.66
Consensus pattern (3 bp):
ATT
Found at i:244807 original size:9 final size:8
Alignment explanation
Indices: 244769--244807 Score: 51
Period size: 8 Copynumber: 4.8 Consensus size: 8
244759 TTTTATCACC
244769 AAAAAAGA
1 AAAAAAGA
*
244777 AAAAAAGG
1 AAAAAAGA
*
244785 AAAAAGGA
1 AAAAAAGA
244793 AAAAAAGA
1 AAAAAAGA
244801 AATAAAA
1 AA-AAAA
244808 TAATATCAAG
Statistics
Matches: 26, Mismatches: 4, Indels: 1
0.84 0.13 0.03
Matches are distributed among these distances:
8 22 0.85
9 4 0.15
ACGTcount: A:0.82, C:0.00, G:0.15, T:0.03
Consensus pattern (8 bp):
AAAAAAGA
Found at i:244951 original size:27 final size:27
Alignment explanation
Indices: 244913--244967 Score: 92
Period size: 27 Copynumber: 2.0 Consensus size: 27
244903 TAAATTACAC
*
244913 ATTTTTTATTTTAAATACTTGAAATGA
1 ATTTTTTATTTTAAATACTTAAAATGA
*
244940 ATTTTTTATTTTAAATATTTAAAATGA
1 ATTTTTTATTTTAAATACTTAAAATGA
244967 A
1 A
244968 AAATATTGAT
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
27 26 1.00
ACGTcount: A:0.40, C:0.02, G:0.05, T:0.53
Consensus pattern (27 bp):
ATTTTTTATTTTAAATACTTAAAATGA
Found at i:259493 original size:32 final size:32
Alignment explanation
Indices: 259457--259558 Score: 75
Period size: 32 Copynumber: 3.2 Consensus size: 32
259447 GTACCCCTCT
259457 TGTGAACACTCAATAACATGCGCTATCTCACA
1 TGTGAACACTCAATAACATGCGCTATCTCACA
* * * * * *
259489 TGTGACCTCGCAA-AAGGATGCAGGTACATTTC-C-
1 TGTGAACACTCAATAA-CATGC-GCT--ATCTCACA
* *
259522 TGCGAACACTCAATACCATGCGCTATCTCACA
1 TGTGAACACTCAATAACATGCGCTATCTCACA
259554 TGTGA
1 TGTGA
259559 CTTCGCAAGA
Statistics
Matches: 48, Mismatches: 15, Indels: 14
0.62 0.19 0.18
Matches are distributed among these distances:
30 4 0.08
31 3 0.06
32 20 0.42
33 15 0.31
34 2 0.04
35 4 0.08
ACGTcount: A:0.30, C:0.27, G:0.18, T:0.25
Consensus pattern (32 bp):
TGTGAACACTCAATAACATGCGCTATCTCACA
Found at i:259588 original size:65 final size:65
Alignment explanation
Indices: 259416--259608 Score: 244
Period size: 65 Copynumber: 3.0 Consensus size: 65
259406 TTCATACGCG
* * * * *
259416 ATCTCACATGTGA-TCTCACAGGAGGATGTAAGTACCCCTCTTGTGAACACTCAATAACATGCGC
1 ATCTCACATGTGACT-TCGCAAGAGGATGTAAGTACCCCTCCTGCGAACACTCAATACCATGCGC
259480 T
65 T
* * * * ***
259481 ATCTCACATGTGACCTCGCAAAAGGATGCAGGTACATTTCCTGCGAACACTCAATACCATGCGCT
1 ATCTCACATGTGACTTCGCAAGAGGATGTAAGTACCCCTCCTGCGAACACTCAATACCATGCGCT
* *
259546 ATCTCACATGTGACTTCGCAAGAGGATGTAAGTACCCCTCCTGCAAAAACTCAATACCATGCG
1 ATCTCACATGTGACTTCGCAAGAGGATGTAAGTACCCCTCCTGCGAACACTCAATACCATGCG
259609 AGCTCGTTGC
Statistics
Matches: 106, Mismatches: 21, Indels: 2
0.82 0.16 0.02
Matches are distributed among these distances:
65 106 1.00
ACGTcount: A:0.30, C:0.28, G:0.18, T:0.24
Consensus pattern (65 bp):
ATCTCACATGTGACTTCGCAAGAGGATGTAAGTACCCCTCCTGCGAACACTCAATACCATGCGCT
Found at i:278563 original size:61 final size:61
Alignment explanation
Indices: 278468--278591 Score: 221
Period size: 61 Copynumber: 2.0 Consensus size: 61
278458 GGTCCGTGAC
*
278468 ACGATCCTCGACCCCAAAAACTAATTCCCATGAGAGTCCCTAATCACACCACCAACCAAAG
1 ACGATCCTCGACCCCAAAAACCAATTCCCATGAGAGTCCCTAATCACACCACCAACCAAAG
* *
278529 ACGATCCTCGACCCCAAAATCCAATTCCCATGAGAGTCTCTAATCACACCACCAACCAAAG
1 ACGATCCTCGACCCCAAAAACCAATTCCCATGAGAGTCCCTAATCACACCACCAACCAAAG
278590 AC
1 AC
278592 TACCCCTCAC
Statistics
Matches: 60, Mismatches: 3, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
61 60 1.00
ACGTcount: A:0.37, C:0.38, G:0.10, T:0.15
Consensus pattern (61 bp):
ACGATCCTCGACCCCAAAAACCAATTCCCATGAGAGTCCCTAATCACACCACCAACCAAAG
Found at i:287043 original size:80 final size:80
Alignment explanation
Indices: 286888--287043 Score: 172
Period size: 80 Copynumber: 1.9 Consensus size: 80
286878 GGGACAAGAG
* ** * * * *
286888 AAAAATTCAAGTACCAAATTGAACATTAAAGTTAAACTTAGTATTTATATTGTACAAAGAAAAAC
1 AAAAACTCAAGTACCAAATTGAACATTAAAACTAAACTAAGTATTCAAATTGGACAAAGAAAAAC
*
286953 TCAAGCATCAATCTA
66 TCAAACATCAATCTA
* * *
286968 AAAAACTCAATTACCAAATTGAACATTAAAACTAAACTCAAGTA-TCAAATTGAGACAAA-AGAT
1 AAAAACTCAAGTACCAAATTGAACATTAAAACTAAACT-AAGTATTCAAATTG-GACAAAGAAAA
*
287031 ACTCAAATATCAA
64 ACTCAAACATCAA
287044 ATTAAACATT
Statistics
Matches: 62, Mismatches: 12, Indels: 4
0.79 0.15 0.05
Matches are distributed among these distances:
80 53 0.85
81 9 0.15
ACGTcount: A:0.51, C:0.15, G:0.08, T:0.26
Consensus pattern (80 bp):
AAAAACTCAAGTACCAAATTGAACATTAAAACTAAACTAAGTATTCAAATTGGACAAAGAAAAAC
TCAAACATCAATCTA
Found at i:294922 original size:3 final size:3
Alignment explanation
Indices: 294916--294942 Score: 54
Period size: 3 Copynumber: 9.0 Consensus size: 3
294906 TAATAGGGTA
294916 AAT AAT AAT AAT AAT AAT AAT AAT AAT
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT
294943 TCTCAACGTT
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 24 1.00
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (3 bp):
AAT
Found at i:295119 original size:5 final size:5
Alignment explanation
Indices: 295109--295146 Score: 67
Period size: 5 Copynumber: 7.6 Consensus size: 5
295099 AACTTTAACA
*
295109 CTTCC CTTCC CTTCC CCTCC CTTCC CTTCC CTTCC CTT
1 CTTCC CTTCC CTTCC CTTCC CTTCC CTTCC CTTCC CTT
295147 TCTTATTTTT
Statistics
Matches: 31, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
5 31 1.00
ACGTcount: A:0.00, C:0.61, G:0.00, T:0.39
Consensus pattern (5 bp):
CTTCC
Found at i:297582 original size:24 final size:24
Alignment explanation
Indices: 297555--297612 Score: 107
Period size: 24 Copynumber: 2.4 Consensus size: 24
297545 GCCAAGCAAG
297555 AAGAAGCTGTCATTGAAGAAAACA
1 AAGAAGCTGTCATTGAAGAAAACA
297579 AAGAAGCTGTCATTGAAGAAAACA
1 AAGAAGCTGTCATTGAAGAAAACA
*
297603 AAGATGCTGT
1 AAGAAGCTGT
297613 TGGTGTTGAA
Statistics
Matches: 33, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
24 33 1.00
ACGTcount: A:0.47, C:0.12, G:0.22, T:0.19
Consensus pattern (24 bp):
AAGAAGCTGTCATTGAAGAAAACA
Found at i:301528 original size:2 final size:2
Alignment explanation
Indices: 301521--301553 Score: 66
Period size: 2 Copynumber: 16.5 Consensus size: 2
301511 CTATCTACAT
301521 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 T
301554 CGTTTTTCAT
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 31 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:303541 original size:14 final size:15
Alignment explanation
Indices: 303522--303554 Score: 50
Period size: 15 Copynumber: 2.3 Consensus size: 15
303512 ATACAATATT
*
303522 ATTAAAA-ATAGAAA
1 ATTAAAATATAAAAA
303536 ATTAAAATATAAAAA
1 ATTAAAATATAAAAA
303551 ATTA
1 ATTA
303555 CTAAAAAATT
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
14 7 0.41
15 10 0.59
ACGTcount: A:0.70, C:0.00, G:0.03, T:0.27
Consensus pattern (15 bp):
ATTAAAATATAAAAA
Found at i:303553 original size:15 final size:14
Alignment explanation
Indices: 303522--303571 Score: 52
Period size: 14 Copynumber: 3.7 Consensus size: 14
303512 ATACAATATT
*
303522 ATTAAAAATAGAAA
1 ATTAAAAATAAAAA
303536 ATTAAAATATAAAAA
1 ATTAAAA-ATAAAAA
*
303551 ATT---ACTAAAAA
1 ATTAAAAATAAAAA
303562 ATTAAAAATA
1 ATTAAAAATA
303572 TATTAGAAAT
Statistics
Matches: 29, Mismatches: 3, Indels: 8
0.73 0.08 0.20
Matches are distributed among these distances:
11 9 0.31
12 1 0.03
14 10 0.34
15 9 0.31
ACGTcount: A:0.70, C:0.02, G:0.02, T:0.26
Consensus pattern (14 bp):
ATTAAAAATAAAAA
Found at i:303602 original size:17 final size:17
Alignment explanation
Indices: 303568--303600 Score: 50
Period size: 16 Copynumber: 2.0 Consensus size: 17
303558 AAAAATTAAA
303568 AATATATTAGAAATTTT
1 AATATATTAGAAATTTT
*
303585 AATAT-TTATAAATTTT
1 AATATATTAGAAATTTT
303601 TATAAATCAC
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
16 10 0.67
17 5 0.33
ACGTcount: A:0.45, C:0.00, G:0.03, T:0.52
Consensus pattern (17 bp):
AATATATTAGAAATTTT
Found at i:307946 original size:4 final size:4
Alignment explanation
Indices: 307937--307964 Score: 56
Period size: 4 Copynumber: 7.0 Consensus size: 4
307927 TACAAATCCA
307937 TTTC TTTC TTTC TTTC TTTC TTTC TTTC
1 TTTC TTTC TTTC TTTC TTTC TTTC TTTC
307965 AGTATATAAA
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:0.00, C:0.25, G:0.00, T:0.75
Consensus pattern (4 bp):
TTTC
Found at i:310521 original size:31 final size:30
Alignment explanation
Indices: 310468--310529 Score: 72
Period size: 31 Copynumber: 2.0 Consensus size: 30
310458 AAATATTTGG
*
310468 TTTTCAAGAAAAATGAAAA-TTTTAGTTTTT
1 TTTTCAAAAAAAATGAAAATTTTTA-TTTTT
* *
310498 TTTTCTAAAAAAAATGGATATTTTTATTTTT
1 TTTTC-AAAAAAAATGAAAATTTTTATTTTT
310529 T
1 T
310530 ATAATTATTC
Statistics
Matches: 27, Mismatches: 3, Indels: 3
0.82 0.09 0.09
Matches are distributed among these distances:
30 5 0.19
31 17 0.63
32 5 0.19
ACGTcount: A:0.37, C:0.03, G:0.08, T:0.52
Consensus pattern (30 bp):
TTTTCAAAAAAAATGAAAATTTTTATTTTT
Found at i:318133 original size:23 final size:23
Alignment explanation
Indices: 318107--318150 Score: 70
Period size: 23 Copynumber: 1.9 Consensus size: 23
318097 AGCATTTTGG
318107 CACTTTAATGCGATTCATTCTGA
1 CACTTTAATGCGATTCATTCTGA
* *
318130 CACTTTAGTGGGATTCATTCT
1 CACTTTAATGCGATTCATTCT
318151 ATGGAGTGTT
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
23 19 1.00
ACGTcount: A:0.23, C:0.20, G:0.16, T:0.41
Consensus pattern (23 bp):
CACTTTAATGCGATTCATTCTGA
Found at i:318310 original size:25 final size:25
Alignment explanation
Indices: 318276--318335 Score: 66
Period size: 25 Copynumber: 2.4 Consensus size: 25
318266 AAAAGTAAAA
* *
318276 AATGACATGTAATTCTGATTTTGAT
1 AATGAAATGTAATTCTGATTCTGAT
* * *
318301 AATGAAATGTTATTTTGATTCTGGT
1 AATGAAATGTAATTCTGATTCTGAT
*
318326 AATCAAATGT
1 AATGAAATGT
318336 CATCTTGAAT
Statistics
Matches: 29, Mismatches: 6, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
25 29 1.00
ACGTcount: A:0.33, C:0.07, G:0.17, T:0.43
Consensus pattern (25 bp):
AATGAAATGTAATTCTGATTCTGAT
Found at i:318343 original size:25 final size:25
Alignment explanation
Indices: 318291--318343 Score: 61
Period size: 25 Copynumber: 2.1 Consensus size: 25
318281 CATGTAATTC
* * * *
318291 TGATTTTGATAATGAAATGTTATTT
1 TGATTCTGATAATCAAATGTCATCT
*
318316 TGATTCTGGTAATCAAATGTCATCT
1 TGATTCTGATAATCAAATGTCATCT
318341 TGA
1 TGA
318344 ATTTGAAAAT
Statistics
Matches: 23, Mismatches: 5, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
25 23 1.00
ACGTcount: A:0.30, C:0.08, G:0.17, T:0.45
Consensus pattern (25 bp):
TGATTCTGATAATCAAATGTCATCT
Found at i:323540 original size:21 final size:22
Alignment explanation
Indices: 323516--323569 Score: 58
Period size: 21 Copynumber: 2.5 Consensus size: 22
323506 AATCATCCTG
323516 AAGGCCATTGCT-TTCAATGTC
1 AAGGCCATTGCTCTTCAATGTC
** * *
323537 AAGGCTGTT-TTCTTCTATGTC
1 AAGGCCATTGCTCTTCAATGTC
323558 AAGGCCATTGCT
1 AAGGCCATTGCT
323570 GTCGATATCA
Statistics
Matches: 24, Mismatches: 7, Indels: 3
0.71 0.21 0.09
Matches are distributed among these distances:
20 1 0.04
21 22 0.92
22 1 0.04
ACGTcount: A:0.20, C:0.22, G:0.20, T:0.37
Consensus pattern (22 bp):
AAGGCCATTGCTCTTCAATGTC
Found at i:332746 original size:30 final size:30
Alignment explanation
Indices: 332712--332768 Score: 80
Period size: 30 Copynumber: 1.9 Consensus size: 30
332702 GTGATAAAAT
*
332712 TTTAATTCAGTAC-TTTAAAAATAATAATAA
1 TTTAATTCAAT-CTTTTAAAAATAATAATAA
*
332742 TTTAATTTAATCTTTTAAAAATAATAA
1 TTTAATTCAATCTTTTAAAAATAATAA
332769 ATATATAAAC
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
29 1 0.04
30 23 0.96
ACGTcount: A:0.49, C:0.05, G:0.02, T:0.44
Consensus pattern (30 bp):
TTTAATTCAATCTTTTAAAAATAATAATAA
Found at i:332873 original size:39 final size:39
Alignment explanation
Indices: 332816--332899 Score: 132
Period size: 39 Copynumber: 2.2 Consensus size: 39
332806 TTCTCCCAAT
* * *
332816 TTTTATCTTTCTTAATTTAATTTGAGATTAATGTATGGA
1 TTTTATCTTTCTTAATTTAATTTGAAATCAATGTAAGGA
*
332855 TTTTATCTTTCTTCATTTAATTTGAAATCAATGTAAGGA
1 TTTTATCTTTCTTAATTTAATTTGAAATCAATGTAAGGA
332894 TTTTAT
1 TTTTAT
332900 ATTGCCTAAT
Statistics
Matches: 41, Mismatches: 4, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
39 41 1.00
ACGTcount: A:0.29, C:0.07, G:0.11, T:0.54
Consensus pattern (39 bp):
TTTTATCTTTCTTAATTTAATTTGAAATCAATGTAAGGA
Found at i:352333 original size:8 final size:9
Alignment explanation
Indices: 352312--352337 Score: 52
Period size: 9 Copynumber: 2.9 Consensus size: 9
352302 CGTTTGAAAT
352312 TTTTTATTA
1 TTTTTATTA
352321 TTTTTATTA
1 TTTTTATTA
352330 TTTTTATT
1 TTTTTATT
352338 TACCTAATTG
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
9 17 1.00
ACGTcount: A:0.19, C:0.00, G:0.00, T:0.81
Consensus pattern (9 bp):
TTTTTATTA
Found at i:364214 original size:3 final size:3
Alignment explanation
Indices: 364196--364276 Score: 108
Period size: 3 Copynumber: 26.0 Consensus size: 3
364186 ATAAATATGG
364196 TAA TAAA TATA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
1 TAA T-AA TA-A TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
* * *
364243 TAA TAA TAA TAA TAA CAA GAA TAAA TAA AAA TAA
1 TAA TAA TAA TAA TAA TAA TAA T-AA TAA TAA TAA
364277 AAAGAGTTGA
Statistics
Matches: 70, Mismatches: 5, Indels: 6
0.86 0.06 0.07
Matches are distributed among these distances:
3 61 0.87
4 9 0.13
ACGTcount: A:0.68, C:0.01, G:0.01, T:0.30
Consensus pattern (3 bp):
TAA
Found at i:365618 original size:29 final size:28
Alignment explanation
Indices: 365585--365801 Score: 104
Period size: 29 Copynumber: 7.5 Consensus size: 28
365575 TGAACCTTCC
*
365585 AAAATTACCATTTTACCCCCGAATGTCT
1 AAAATTACCATTTTAACCCCGAATGTCT
* * *
365613 ATAAATT-CTATTTTTGA-CCCGAACCTTTC-
1 A-AAATTACCA-TTTTAACCCCGAA--TGTCT
*
365642 AAAATTACCATTTTAACCCCGGATGTCT
1 AAAATTACCATTTTAACCCCGAATGTCT
* ** * *
365670 AAAAATTTCGTTTTTAACCCCGAACTTTTCA
1 -AAAATTACCATTTTAACCCCGAA--TGTCT
*
365701 AAAATCACCATTTT-ACCCTCGAATGTCT
1 AAAATTACCATTTTAACCC-CGAATGTCT
* * * * *
365729 AAAATT-TCATTTTTGACTCCGAACTTTCCA
1 AAAATTACCA-TTTTAACCCCGAA-TGT-CT
* * *
365759 AAAATTACCATTTT-GCCCCTGAGTGTCC
1 AAAATTACCATTTTAACCCC-GAATGTCT
*
365787 AAAATTACCGTTTTA
1 AAAATTACCATTTTA
365802 CTCCCGGGCA
Statistics
Matches: 139, Mismatches: 32, Indels: 35
0.67 0.16 0.17
Matches are distributed among these distances:
27 5 0.04
28 49 0.35
29 50 0.36
30 30 0.22
31 5 0.04
ACGTcount: A:0.31, C:0.25, G:0.08, T:0.36
Consensus pattern (28 bp):
AAAATTACCATTTTAACCCCGAATGTCT
Found at i:365619 original size:114 final size:117
Alignment explanation
Indices: 365411--365631 Score: 261
Period size: 114 Copynumber: 1.9 Consensus size: 117
365401 TAAATTGCCC
** *
365411 AAAAATCACATTTTAACCCCTAAACTTTTCAAAAATTCCATTTTTAACCTAAAATTTTCTAAAAT
1 AAAAATCACATTTTAACCCCTAAACTTTTCAAAAATTCCATTTTTAACCTAAAACCTTCCAAAAT
** * *
365476 TACTTTTTTACCCCTAAACTTTCCAAAATTCCA-TTTTGACCTCAAATTTCT
66 TACCATTTTACCCCCAAACTGTCCAAAATTCCATTTTTGACCTCAAATTTCT
* * * * **
365527 AAAAATCACATTTT-ACCCTTAAA-TTTTCTAAAATTCCTTTTTTAATCTTGAACCTTCCAAAAT
1 AAAAATCACATTTTAACCCCTAAACTTTTCAAAAATTCCATTTTTAACCTAAAACCTTCCAAAAT
* * *
365590 TACCATTTTACCCCCGAA-TGTCTATAAATTCTATTTTTGACC
66 TACCATTTTACCCCCAAACTGTCCA-AAATTCCATTTTTGACC
365632 CGAACCTTTC
Statistics
Matches: 87, Mismatches: 16, Indels: 5
0.81 0.15 0.05
Matches are distributed among these distances:
113 4 0.05
114 53 0.61
115 16 0.18
116 14 0.16
ACGTcount: A:0.34, C:0.23, G:0.02, T:0.40
Consensus pattern (117 bp):
AAAAATCACATTTTAACCCCTAAACTTTTCAAAAATTCCATTTTTAACCTAAAACCTTCCAAAAT
TACCATTTTACCCCCAAACTGTCCAAAATTCCATTTTTGACCTCAAATTTCT
Found at i:365654 original size:57 final size:57
Alignment explanation
Indices: 365576--365792 Score: 244
Period size: 58 Copynumber: 3.8 Consensus size: 57
365566 TTTTAATCTT
*
365576 GAACC-TTCCAAAATTACCATTTTACCCCCGAATGTCTATAAA-TTCTATTTTTGACCC
1 GAACCTTTCAAAAATTACCATTTTACCCCCGAATGTCTA-AAATTTC-ATTTTTGACCC
* * * *
365633 GAACCTTTC-AAAATTACCATTTTAACCCCGGATGTCTAAAAATTTCGTTTTTAACCCC
1 GAACCTTTCAAAAATTACCATTTTACCCCCGAATGTCT-AAAATTTCATTTTTGA-CCC
* * *
365691 GAACTTTTCAAAAATCACCATTTTACCCTCGAATGTCTAAAATTTCATTTTTGACTCC
1 GAACCTTTCAAAAATTACCATTTTACCCCCGAATGTCTAAAATTTCATTTTTGAC-CC
* * * *
365749 GAA-CTTTCCAAAAATTACCATTTTGCCCCTGAGTGTCCAAAATT
1 GAACCTTT-CAAAAATTACCATTTTACCCCCGAATGTCTAAAATT
365793 ACCGTTTTAC
Statistics
Matches: 135, Mismatches: 18, Indels: 13
0.81 0.11 0.08
Matches are distributed among these distances:
57 44 0.33
58 67 0.50
59 24 0.18
ACGTcount: A:0.31, C:0.26, G:0.08, T:0.35
Consensus pattern (57 bp):
GAACCTTTCAAAAATTACCATTTTACCCCCGAATGTCTAAAATTTCATTTTTGACCC
Found at i:365715 original size:30 final size:29
Alignment explanation
Indices: 365410--365772 Score: 110
Period size: 29 Copynumber: 12.6 Consensus size: 29
365400 CTAAATTGCC
* *
365410 CAAAAATCA-CATTTTAACCCCTAAACTTTT
1 CAAAAATTACCATTTTAACCCC-GAAC-TTT
*** *
365440 CAAAAATT-CCATTTTTAACCTAAAATTTT
1 CAAAAATTACCA-TTTTAACCCCGAACTTT
* * * *
365469 CTAAAATTA-CTTTTTTACCCCTAAACTTT
1 CAAAAATTACCATTTTAACCCC-GAACTTT
* * * *
365498 CCAAAATT-CCATTTTGACCTC-AAATTT
1 CAAAAATTACCATTTTAACCCCGAACTTT
* ** *
365525 CTAAAAATCA-CATTTT-ACCCTTAAATTTT
1 C-AAAAATTACCATTTTAACCC-CGAACTTT
* * * ** *
365554 CTAAAATT-CCTTTTTTAATCTTGAACCTT
1 CAAAAATTACC-ATTTTAACCCCGAACTTT
* * *
365583 CCAAAATTACCATTTTACCCCCGAA-TGT
1 CAAAAATTACCATTTTAACCCCGAACTTT
* * *
365611 CTATAAATT-CTATTTTTGA-CCCGAACCTTT
1 C-AAAAATTACCA-TTTTAACCCCGAA-CTTT
* *
365641 C-AAAATTACCATTTTAACCCCGGA-TGT
1 CAAAAATTACCATTTTAACCCCGAACTTT
* **
365668 CTAAAAATTTCGTTTTTAACCCCGAACTTTT
1 C-AAAAATTACCATTTTAACCCCGAAC-TTT
* *
365699 CAAAAATCACCATTTT-ACCCTCGAA-TGT
1 CAAAAATTACCATTTTAACCC-CGAACTTT
* * * *
365727 CTAAAATT-TCATTTTTGACTCCGAACTTT
1 CAAAAATTACCA-TTTTAACCCCGAACTTT
365756 CCAAAAATTACCATTTT
1 -CAAAAATTACCATTTT
365773 GCCCCTGAGT
Statistics
Matches: 240, Mismatches: 64, Indels: 58
0.66 0.18 0.16
Matches are distributed among these distances:
27 14 0.06
28 60 0.25
29 108 0.45
30 45 0.19
31 13 0.05
ACGTcount: A:0.33, C:0.24, G:0.04, T:0.39
Consensus pattern (29 bp):
CAAAAATTACCATTTTAACCCCGAACTTT
Found at i:367635 original size:18 final size:18
Alignment explanation
Indices: 367614--367648 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
367604 GGGCAGCAGA
*
367614 AGAGTCTCGGGCAGAGGG
1 AGAGTCTCAGGCAGAGGG
*
367632 AGAGTCTTAGGCAGAGG
1 AGAGTCTCAGGCAGAGG
367649 AGTCAATGGT
Statistics
Matches: 15, Mismatches: 2, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
18 15 1.00
ACGTcount: A:0.26, C:0.14, G:0.46, T:0.14
Consensus pattern (18 bp):
AGAGTCTCAGGCAGAGGG
Found at i:367863 original size:15 final size:16
Alignment explanation
Indices: 367836--367865 Score: 53
Period size: 15 Copynumber: 1.9 Consensus size: 16
367826 TTTTATTTTA
367836 TTTATTATTTTTGGGT
1 TTTATTATTTTTGGGT
367852 TTTATT-TTTTTGGG
1 TTTATTATTTTTGGG
367866 CTCGATTAAA
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 8 0.57
16 6 0.43
ACGTcount: A:0.10, C:0.00, G:0.20, T:0.70
Consensus pattern (16 bp):
TTTATTATTTTTGGGT
Found at i:368751 original size:2 final size:2
Alignment explanation
Indices: 368744--368770 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
368734 AAATCTGTAA
368744 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
368771 AAGATTAAAT
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:369547 original size:2 final size:2
Alignment explanation
Indices: 369540--369569 Score: 60
Period size: 2 Copynumber: 15.0 Consensus size: 2
369530 ATATTTTCTC
369540 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
369570 GTTTGTTTGT
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:376079 original size:18 final size:20
Alignment explanation
Indices: 376046--376083 Score: 62
Period size: 18 Copynumber: 2.0 Consensus size: 20
376036 GGGTAAATAT
376046 TTTATTGTTTTATAATTTAA
1 TTTATTGTTTTATAATTTAA
376066 TTTATT-TTTT-TAATTTAA
1 TTTATTGTTTTATAATTTAA
376084 ATTTTTTTGC
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
18 8 0.44
19 4 0.22
20 6 0.33
ACGTcount: A:0.29, C:0.00, G:0.03, T:0.68
Consensus pattern (20 bp):
TTTATTGTTTTATAATTTAA
Done.