Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold270
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: 409424
ACGTcount: A:0.37, C:0.14, G:0.14, T:0.36
File 2 of 4
Found at i:106785 original size:11 final size:12
Alignment explanation
Indices: 106769--106810 Score: 52
Period size: 11 Copynumber: 3.6 Consensus size: 12
106759 AAATTGAGAC
106769 ATAATAT-AAAT
1 ATAATATAAAAT
*
106780 ATAATATTAAAAA
1 ATAATA-TAAAAT
106793 ATAAT-TAAAAT
1 ATAATATAAAAT
106804 ATAATAT
1 ATAATAT
106811 GACACAAAAT
Statistics
Matches: 26, Mismatches: 2, Indels: 5
0.79 0.06 0.15
Matches are distributed among these distances:
11 16 0.62
12 2 0.08
13 8 0.31
ACGTcount: A:0.64, C:0.00, G:0.00, T:0.36
Consensus pattern (12 bp):
ATAATATAAAAT
Found at i:107121 original size:23 final size:23
Alignment explanation
Indices: 107069--107121 Score: 63
Period size: 23 Copynumber: 2.3 Consensus size: 23
107059 GAAACACGAA
* *
107069 ATGAACACAACATAGAAAATAAT
1 ATGAATACAACATAAAAAATAAT
*
107092 -TAAAATACAACATAAAAAATAAT
1 AT-GAATACAACATAAAAAATAAT
107115 ATGAATA
1 ATGAATA
107122 TAATACAAAT
Statistics
Matches: 24, Mismatches: 4, Indels: 4
0.75 0.12 0.12
Matches are distributed among these distances:
22 1 0.04
23 22 0.92
24 1 0.04
ACGTcount: A:0.64, C:0.09, G:0.06, T:0.21
Consensus pattern (23 bp):
ATGAATACAACATAAAAAATAAT
Found at i:107448 original size:24 final size:26
Alignment explanation
Indices: 107392--107452 Score: 71
Period size: 24 Copynumber: 2.6 Consensus size: 26
107382 TAATTGAGAT
*
107392 ATAATA-AAAACTCAACATATATAAA
1 ATAATATAAAACACAACATATATAAA
107417 A-AAT-TAAAACACAACATA-A-AAA
1 ATAATATAAAACACAACATATATAAA
107439 ATAATAT-AAACACA
1 ATAATATAAAACACA
107453 GTAAAAATAT
Statistics
Matches: 32, Mismatches: 1, Indels: 8
0.78 0.02 0.20
Matches are distributed among these distances:
22 4 0.12
23 11 0.34
24 16 0.50
25 1 0.03
ACGTcount: A:0.67, C:0.13, G:0.00, T:0.20
Consensus pattern (26 bp):
ATAATATAAAACACAACATATATAAA
Found at i:107977 original size:58 final size:59
Alignment explanation
Indices: 107898--108010 Score: 147
Period size: 59 Copynumber: 1.9 Consensus size: 59
107888 CAATTTTTTT
* * * * *
107898 AATTAAATCATTATAACAAATTATG-AAAAAATGTCACGAATTGAGATATGATACATTA
1 AATTAAATCATTAAAAAAAATTATGTAAAAAATGTCACAAATGGAGATACGATACATTA
* * *
107956 AATTAAATTATTAAAAAAAATTATGTAAAATATGTCATAAATGGAGATACGATAC
1 AATTAAATCATTAAAAAAAATTATGTAAAAAATGTCACAAATGGAGATACGATAC
108011 GAATATGACA
Statistics
Matches: 46, Mismatches: 8, Indels: 1
0.84 0.15 0.02
Matches are distributed among these distances:
58 22 0.48
59 24 0.52
ACGTcount: A:0.51, C:0.07, G:0.11, T:0.31
Consensus pattern (59 bp):
AATTAAATCATTAAAAAAAATTATGTAAAAAATGTCACAAATGGAGATACGATACATTA
Found at i:108760 original size:8 final size:8
Alignment explanation
Indices: 108747--108813 Score: 68
Period size: 8 Copynumber: 8.4 Consensus size: 8
108737 TAAATACAAA
108747 TTTTTTTC
1 TTTTTTTC
108755 TTTTTTTC
1 TTTTTTTC
108763 TTTTTTT-
1 TTTTTTTC
108770 TTCTCTTTTC
1 TT-T-TTTTC
108780 TTTATTTTC
1 TTT-TTTTC
108789 -TTTTTT-
1 TTTTTTTC
*
108795 TTTCTTTC
1 TTTTTTTC
*
108803 TTTCTTTC
1 TTTTTTTC
108811 TTT
1 TTT
108814 CTCTCTTGCC
Statistics
Matches: 52, Mismatches: 2, Indels: 10
0.81 0.03 0.16
Matches are distributed among these distances:
7 11 0.21
8 29 0.56
9 10 0.19
10 2 0.04
ACGTcount: A:0.01, C:0.15, G:0.00, T:0.84
Consensus pattern (8 bp):
TTTTTTTC
Found at i:108802 original size:4 final size:4
Alignment explanation
Indices: 108751--108820 Score: 60
Period size: 4 Copynumber: 18.5 Consensus size: 4
108741 TACAAATTTT
* * *
108751 TTTC TTTT TTTC TTT- TTT- TTTC TCT- TTTC TTTAT TTTC TTT- TTT-
1 TTTC TTTC TTTC TTTC TTTC TTTC TTTC TTTC TTT-C TTTC TTTC TTTC
*
108795 TTTC TTTC TTTC TTTC TTTC TCTC TT
1 TTTC TTTC TTTC TTTC TTTC TTTC TT
108821 GCCGAAAAAA
Statistics
Matches: 54, Mismatches: 8, Indels: 8
0.77 0.11 0.11
Matches are distributed among these distances:
3 14 0.26
4 37 0.69
5 3 0.06
ACGTcount: A:0.01, C:0.19, G:0.00, T:0.80
Consensus pattern (4 bp):
TTTC
Found at i:108814 original size:26 final size:25
Alignment explanation
Indices: 108750--108815 Score: 96
Period size: 26 Copynumber: 2.6 Consensus size: 25
108740 ATACAAATTT
108750 TTTTCTTTTTTTCTTTTTTTTTCTC
1 TTTTCTTTTTTTCTTTTTTTTTCTC
*
108775 TTTTCTTTATTTTCTTTTTTTTTCTT
1 TTTTCTTT-TTTTCTTTTTTTTTCTC
*
108801 TCTTTCTTTCTTTCT
1 T-TTTCTTTTTTTCT
108816 CTCTTGCCGA
Statistics
Matches: 37, Mismatches: 2, Indels: 3
0.88 0.05 0.07
Matches are distributed among these distances:
25 8 0.22
26 22 0.59
27 7 0.19
ACGTcount: A:0.02, C:0.17, G:0.00, T:0.82
Consensus pattern (25 bp):
TTTTCTTTTTTTCTTTTTTTTTCTC
Found at i:111407 original size:3 final size:3
Alignment explanation
Indices: 111399--111433 Score: 61
Period size: 3 Copynumber: 11.7 Consensus size: 3
111389 GAATGCTAAA
*
111399 AAT AAT AAT AAT AAT AAT AAT AAT AAT CAT AAT AA
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AA
111434 CAACAATAGT
Statistics
Matches: 30, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
3 30 1.00
ACGTcount: A:0.66, C:0.03, G:0.00, T:0.31
Consensus pattern (3 bp):
AAT
Found at i:111591 original size:32 final size:31
Alignment explanation
Indices: 111536--111595 Score: 86
Period size: 32 Copynumber: 1.9 Consensus size: 31
111526 AATTTTAAAA
*
111536 TTATTTTATTATTTATAATATTATTATAAATT
1 TTATTTTAATATTTATAATATTA-TATAAATT
111568 TTATTTTAATATTTAT-ATAATTATATAA
1 TTATTTTAATATTTATAAT-ATTATATAA
111596 TTAAATTTAA
Statistics
Matches: 26, Mismatches: 1, Indels: 3
0.87 0.03 0.10
Matches are distributed among these distances:
31 7 0.27
32 19 0.73
ACGTcount: A:0.40, C:0.00, G:0.00, T:0.60
Consensus pattern (31 bp):
TTATTTTAATATTTATAATATTATATAAATT
Found at i:111646 original size:32 final size:34
Alignment explanation
Indices: 111548--111647 Score: 84
Period size: 32 Copynumber: 3.0 Consensus size: 34
111538 ATTTTATTAT
* *
111548 TTATA-ATATTATTA-TAAATTTT-ATTTTAATA
1 TTATATATTTTATTATTAAATTTTAATTTAAATA
* * * **
111579 TTTATATAATTATATAATTAAATTTAAATAAAAATA
1 -TTATAT-ATTTTATTATTAAATTTTAATTTAAATA
111615 TTAT-T-TTTTATTATTAAATTTTAATTTAAATA
1 TTATATATTTTATTATTAAATTTTAATTTAAATA
111647 T
1 T
111648 AATTAAATAA
Statistics
Matches: 52, Mismatches: 12, Indels: 8
0.72 0.17 0.11
Matches are distributed among these distances:
32 28 0.54
34 7 0.13
35 11 0.21
36 6 0.12
ACGTcount: A:0.45, C:0.00, G:0.00, T:0.55
Consensus pattern (34 bp):
TTATATATTTTATTATTAAATTTTAATTTAAATA
Found at i:111677 original size:18 final size:20
Alignment explanation
Indices: 111637--111682 Score: 60
Period size: 18 Copynumber: 2.4 Consensus size: 20
111627 ATTAAATTTT
*
111637 AATTTAAATATAATTAAATA
1 AATTTAAATATAATTAAAAA
*
111657 AATTTAAAT-TTA-TAAAAA
1 AATTTAAATATAATTAAAAA
111675 AATTTAAA
1 AATTTAAA
111683 GTAAATCTGT
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
18 13 0.54
19 2 0.08
20 9 0.38
ACGTcount: A:0.61, C:0.00, G:0.00, T:0.39
Consensus pattern (20 bp):
AATTTAAATATAATTAAAAA
Found at i:112672 original size:18 final size:19
Alignment explanation
Indices: 112651--112699 Score: 55
Period size: 19 Copynumber: 2.5 Consensus size: 19
112641 TTAATATAAA
*
112651 AATAAATTTTTAATTTT-T
1 AATAAATTTTAAATTTTAT
*
112669 AATATTATTTTAAATTTTAT
1 AATA-AATTTTAAATTTTAT
112689 AATAAACTTTT
1 AATAAA-TTTT
112700 GATAGATTCA
Statistics
Matches: 25, Mismatches: 3, Indels: 4
0.78 0.09 0.12
Matches are distributed among these distances:
18 4 0.16
19 12 0.48
20 9 0.36
ACGTcount: A:0.41, C:0.02, G:0.00, T:0.57
Consensus pattern (19 bp):
AATAAATTTTAAATTTTAT
Found at i:115199 original size:110 final size:111
Alignment explanation
Indices: 114999--115228 Score: 306
Period size: 110 Copynumber: 2.1 Consensus size: 111
114989 CATCATTGAG
** * * *
114999 TCGAGCTCGCCGAATTAGAGTATCCTAATGCTTGATTCGAGTAATTCATGAACCTAATTGAGCTC
1 TCGAGCTCATCGAATTAGAGTATCCTAATGCTTGACTCGAGTAATCCACGAACCTAATTGAGCTC
115064 TTTTACTTTTAATTATTATTG-AAAAATCTCAATTAGAA-CTTGAAC
66 TTTTACTTTTAATTATTATTGAAAAAATCTCAATTAGAATC-TGAAC
* * * *
115109 TTGAGCTCATCGAATTTA-AGTATCCTAATGCTTGACTCGAGTAGTCCACGGACCTAGTTGAGCT
1 TCGAGCTCATCGAA-TTAGAGTATCCTAATGCTTGACTCGAGTAATCCACGAACCTAATTGAGCT
* *
115173 -TCTTTATTTTTAATTATTATTTAAAAAATCTCAATTAGAATCTGAAC
65 CT-TTTACTTTTAATTATTATTGAAAAAATCTCAATTAGAATCTGAAC
115220 TCGAGCTCA
1 TCGAGCTCA
115229 AACATAACAA
Statistics
Matches: 104, Mismatches: 12, Indels: 7
0.85 0.10 0.06
Matches are distributed among these distances:
109 1 0.01
110 69 0.66
111 33 0.32
112 1 0.01
ACGTcount: A:0.31, C:0.18, G:0.15, T:0.37
Consensus pattern (111 bp):
TCGAGCTCATCGAATTAGAGTATCCTAATGCTTGACTCGAGTAATCCACGAACCTAATTGAGCTC
TTTTACTTTTAATTATTATTGAAAAAATCTCAATTAGAATCTGAAC
Found at i:118428 original size:28 final size:29
Alignment explanation
Indices: 118374--118427 Score: 76
Period size: 28 Copynumber: 1.9 Consensus size: 29
118364 TAATCTGCGT
*
118374 GAAAGTAAAATCATAAACTTTTCTTTTAC
1 GAAAGTAAAATCATAAACTTTACTTTTAC
*
118403 GAAAGT-AAATTATAAA-TTTACTTTT
1 GAAAGTAAAATCATAAACTTTACTTTT
118428 TTATCTCAAA
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
27 8 0.35
28 9 0.39
29 6 0.26
ACGTcount: A:0.43, C:0.09, G:0.07, T:0.41
Consensus pattern (29 bp):
GAAAGTAAAATCATAAACTTTACTTTTAC
Found at i:118651 original size:18 final size:18
Alignment explanation
Indices: 118601--118653 Score: 63
Period size: 18 Copynumber: 3.0 Consensus size: 18
118591 TTTATATTAA
*
118601 AATTTATAA-TTAAATTT
1 AATTAATAATTTAAATTT
* **
118618 AAATAATAATAAAAATTT
1 AATTAATAATTTAAATTT
118636 AATTAATAATTTAAATTT
1 AATTAATAATTTAAATTT
118654 TACCGAATCA
Statistics
Matches: 28, Mismatches: 7, Indels: 1
0.78 0.19 0.03
Matches are distributed among these distances:
17 7 0.25
18 21 0.75
ACGTcount: A:0.55, C:0.00, G:0.00, T:0.45
Consensus pattern (18 bp):
AATTAATAATTTAAATTT
Found at i:119756 original size:39 final size:39
Alignment explanation
Indices: 119703--119810 Score: 182
Period size: 39 Copynumber: 2.8 Consensus size: 39
119693 TAATTTTTTG
*
119703 TTTCTGTCC-CTCCTCTCGATCTCACCCATTTTTCTTTA
1 TTTCTTTCCTCTCCTCTCGATCTCACCCATTTTTCTTTA
*
119741 TTTCTTTCCTCTCCTCTCGATCTCTCCCATTTTTCTTTA
1 TTTCTTTCCTCTCCTCTCGATCTCACCCATTTTTCTTTA
*
119780 TTTCTTCCCTCTCCTCTCGATCTCACCCATT
1 TTTCTTTCCTCTCCTCTCGATCTCACCCATT
119811 CCCACTTGTT
Statistics
Matches: 65, Mismatches: 4, Indels: 1
0.93 0.06 0.01
Matches are distributed among these distances:
38 8 0.12
39 57 0.88
ACGTcount: A:0.09, C:0.39, G:0.04, T:0.48
Consensus pattern (39 bp):
TTTCTTTCCTCTCCTCTCGATCTCACCCATTTTTCTTTA
Found at i:120604 original size:22 final size:23
Alignment explanation
Indices: 120565--120609 Score: 65
Period size: 22 Copynumber: 2.0 Consensus size: 23
120555 AAATTTTGAT
*
120565 ATAAATATTTATATATAATTTAA
1 ATAAATATTTATATATAAATTAA
*
120588 ATAAAT-TTTTTATATAAATTAA
1 ATAAATATTTATATATAAATTAA
120610 TAATTTAAAT
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
22 14 0.70
23 6 0.30
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (23 bp):
ATAAATATTTATATATAAATTAA
Found at i:120961 original size:15 final size:16
Alignment explanation
Indices: 120926--121004 Score: 62
Period size: 17 Copynumber: 5.2 Consensus size: 16
120916 GTATTTTTAG
*
120926 TTTATTATAATAATTAT
1 TTTATTAT-ATAATTAA
120943 TTTATTATA-AATTAA
1 TTTATTATATAATTAA
120958 TTTA--ATAT-ATT-A
1 TTTATTATATAATTAA
* *
120970 -TAATTATATAATTAT
1 TTTATTATATAATTAA
*
120985 TTTATTGAAATAATTAA
1 TTTATT-ATATAATTAA
121002 TTT
1 TTT
121005 TAATATTATT
Statistics
Matches: 49, Mismatches: 6, Indels: 14
0.71 0.09 0.20
Matches are distributed among these distances:
11 2 0.04
12 1 0.02
13 10 0.20
14 3 0.06
15 9 0.18
16 5 0.10
17 19 0.39
ACGTcount: A:0.43, C:0.00, G:0.01, T:0.56
Consensus pattern (16 bp):
TTTATTATATAATTAA
Found at i:121013 original size:37 final size:42
Alignment explanation
Indices: 120928--121027 Score: 107
Period size: 42 Copynumber: 2.3 Consensus size: 42
120918 ATTTTTAGTT
*
120928 TATTATAATAATTATTTTATTATAAATTAATTTAATATATTA
1 TATTATAATAATTATTTTATTAGAAATTAATTTAATATATTA
* *
120970 TAATTAT-ATAATTATTTTATTGAAATAATTAATTTTAATATTATTT
1 T-ATTATAATAATTATTTTATT-AGA-AATTAA-TTTAATA-TATTA
121016 TATT-TAA-AATTA
1 TATTATAATAATTA
121028 AAATAATTAT
Statistics
Matches: 50, Mismatches: 2, Indels: 10
0.81 0.03 0.16
Matches are distributed among these distances:
42 15 0.30
43 7 0.14
44 12 0.24
45 11 0.22
46 5 0.10
ACGTcount: A:0.44, C:0.00, G:0.01, T:0.55
Consensus pattern (42 bp):
TATTATAATAATTATTTTATTAGAAATTAATTTAATATATTA
Found at i:121159 original size:29 final size:29
Alignment explanation
Indices: 121086--121172 Score: 88
Period size: 30 Copynumber: 2.9 Consensus size: 29
121076 TAAAATATAA
121086 AATTATTTTAAAAATAAAATTTAAATTTAT
1 AATTATTTTAAAAATAAAA-TTAAATTTAT
* *
121116 AATAATTCTT-AAAATTAAATTAAATTTAT
1 AATTATT-TTAAAAATAAAATTAAATTTAT
*
121145 -TTTATTTTAATAAATCAAATATTAAATT
1 AATTATTTTAA-AAAT-AAA-ATTAAATT
121173 AAATTTATAT
Statistics
Matches: 47, Mismatches: 5, Indels: 9
0.77 0.08 0.15
Matches are distributed among these distances:
27 2 0.04
28 5 0.11
29 14 0.30
30 16 0.34
31 10 0.21
ACGTcount: A:0.51, C:0.02, G:0.00, T:0.47
Consensus pattern (29 bp):
AATTATTTTAAAAATAAAATTAAATTTAT
Found at i:130522 original size:107 final size:107
Alignment explanation
Indices: 130336--130550 Score: 403
Period size: 107 Copynumber: 2.0 Consensus size: 107
130326 GCTACAATGT
*
130336 ATAGTGATGTTCTTCATGTGTCATTGTGCCAATTGTGATTGTTGAATGTAGATTAATCTCAGCAT
1 ATAGTGATGTTCTTCATGTGTCATTGTGCAAATTGTGATTGTTGAATGTAGATTAATCTCAGCAT
* *
130401 GAATGACTGAACCCACATTTTCATTATAGTTGCCTTTGTGTC
66 GAATGACGGAACCCACATTTTCATTATAGTTGCCCTTGTGTC
130443 ATAGTGATGTTCTTCATGTGTCATTGTGCAAATTGTGATTGTTGAATGTAGATTAATCTCAGCAT
1 ATAGTGATGTTCTTCATGTGTCATTGTGCAAATTGTGATTGTTGAATGTAGATTAATCTCAGCAT
130508 GAATGACGGAACCCACATTTTCATTATAGTTGCCCTTGTGTC
66 GAATGACGGAACCCACATTTTCATTATAGTTGCCCTTGTGTC
130550 A
1 A
130551 AGGATTAGGG
Statistics
Matches: 105, Mismatches: 3, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
107 105 1.00
ACGTcount: A:0.25, C:0.16, G:0.20, T:0.39
Consensus pattern (107 bp):
ATAGTGATGTTCTTCATGTGTCATTGTGCAAATTGTGATTGTTGAATGTAGATTAATCTCAGCAT
GAATGACGGAACCCACATTTTCATTATAGTTGCCCTTGTGTC
Found at i:131571 original size:15 final size:16
Alignment explanation
Indices: 131548--131583 Score: 56
Period size: 15 Copynumber: 2.3 Consensus size: 16
131538 AACTTTGCAT
131548 TAAAATTAAAAATA-A
1 TAAAATTAAAAATACA
*
131563 TAAATTTAAAAATACA
1 TAAAATTAAAAATACA
131579 TAAAA
1 TAAAA
131584 CAAATTTGTA
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
15 13 0.72
16 5 0.28
ACGTcount: A:0.69, C:0.03, G:0.00, T:0.28
Consensus pattern (16 bp):
TAAAATTAAAAATACA
Found at i:136598 original size:16 final size:16
Alignment explanation
Indices: 136577--136609 Score: 50
Period size: 16 Copynumber: 2.1 Consensus size: 16
136567 AAAATTTAAT
136577 AATTT-ATTTATATTTA
1 AATTTAATTTA-ATTTA
136593 AATTTAATTTAATTTA
1 AATTTAATTTAATTTA
136609 A
1 A
136610 TAAAAAATTA
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
16 11 0.69
17 5 0.31
ACGTcount: A:0.42, C:0.00, G:0.00, T:0.58
Consensus pattern (16 bp):
AATTTAATTTAATTTA
Found at i:136651 original size:21 final size:21
Alignment explanation
Indices: 136622--136661 Score: 55
Period size: 21 Copynumber: 1.9 Consensus size: 21
136612 AAAAATTAAT
*
136622 AATTTAAAATT-TATTAAATCA
1 AATTCAAAATTAT-TTAAATCA
136643 AATTCAAAATTATTTAAAT
1 AATTCAAAATTATTTAAAT
136662 TTAAAATAAT
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
21 16 0.94
22 1 0.06
ACGTcount: A:0.53, C:0.05, G:0.00, T:0.42
Consensus pattern (21 bp):
AATTCAAAATTATTTAAATCA
Found at i:136667 original size:16 final size:16
Alignment explanation
Indices: 136642--136693 Score: 50
Period size: 16 Copynumber: 3.2 Consensus size: 16
136632 TTATTAAATC
*
136642 AAATTCAAAATTATTT
1 AAATTCAAAATAATTT
*
136658 AAATTTAAAATAATTT
1 AAATTCAAAATAATTT
* * *
136674 GAATTAAACAATAACTT
1 AAATTCAA-AATAATTT
136691 AAA
1 AAA
136694 ATTTATAAAA
Statistics
Matches: 29, Mismatches: 6, Indels: 1
0.81 0.17 0.03
Matches are distributed among these distances:
16 20 0.69
17 9 0.31
ACGTcount: A:0.56, C:0.06, G:0.02, T:0.37
Consensus pattern (16 bp):
AAATTCAAAATAATTT
Found at i:137306 original size:17 final size:17
Alignment explanation
Indices: 137281--137317 Score: 56
Period size: 17 Copynumber: 2.2 Consensus size: 17
137271 GGCTACCCGA
137281 AGACAAACAATATAAGG
1 AGACAAACAATATAAGG
* *
137298 AGACGAACACTATAAGG
1 AGACAAACAATATAAGG
137315 AGA
1 AGA
137318 ACATAGTTCC
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
17 18 1.00
ACGTcount: A:0.54, C:0.14, G:0.22, T:0.11
Consensus pattern (17 bp):
AGACAAACAATATAAGG
Found at i:142886 original size:13 final size:13
Alignment explanation
Indices: 142868--142892 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
142858 TACAAATATA
142868 ATAAATATTAATT
1 ATAAATATTAATT
142881 ATAAATATTAAT
1 ATAAATATTAAT
142893 AAAAGATAAA
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.56, C:0.00, G:0.00, T:0.44
Consensus pattern (13 bp):
ATAAATATTAATT
Found at i:143246 original size:21 final size:21
Alignment explanation
Indices: 143222--143264 Score: 52
Period size: 21 Copynumber: 2.0 Consensus size: 21
143212 ATTTTTTATG
143222 AAAA-TAATATTTAATATATTT
1 AAAATTAATATTTAAT-TATTT
* *
143243 AAAATTTATATTTTATTATTT
1 AAAATTAATATTTAATTATTT
143264 A
1 A
143265 TATTTTTTTT
Statistics
Matches: 19, Mismatches: 2, Indels: 2
0.83 0.09 0.09
Matches are distributed among these distances:
21 10 0.53
22 9 0.47
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (21 bp):
AAAATTAATATTTAATTATTT
Found at i:143663 original size:3 final size:3
Alignment explanation
Indices: 143655--143682 Score: 56
Period size: 3 Copynumber: 9.3 Consensus size: 3
143645 TGAGACCCTA
143655 TTC TTC TTC TTC TTC TTC TTC TTC TTC T
1 TTC TTC TTC TTC TTC TTC TTC TTC TTC T
143683 AGCTTTCCAC
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 25 1.00
ACGTcount: A:0.00, C:0.32, G:0.00, T:0.68
Consensus pattern (3 bp):
TTC
Found at i:144403 original size:13 final size:13
Alignment explanation
Indices: 144387--144414 Score: 56
Period size: 13 Copynumber: 2.2 Consensus size: 13
144377 AATGATATCG
144387 AATATAAATATTA
1 AATATAAATATTA
144400 AATATAAATATTA
1 AATATAAATATTA
144413 AA
1 AA
144415 AAAATTAAAA
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:0.64, C:0.00, G:0.00, T:0.36
Consensus pattern (13 bp):
AATATAAATATTA
Found at i:144655 original size:16 final size:18
Alignment explanation
Indices: 144612--144655 Score: 51
Period size: 16 Copynumber: 2.6 Consensus size: 18
144602 TTAGTATGAT
144612 TAATTATAATAAATATTAA
1 TAATTATAA-AAATATTAA
144631 TAA-TA-AAAAAT-TTAA
1 TAATTATAAAAATATTAA
144646 -AATTATAAAA
1 TAATTATAAAA
144656 TAATTATAAA
Statistics
Matches: 23, Mismatches: 0, Indels: 7
0.77 0.00 0.23
Matches are distributed among these distances:
14 2 0.09
15 6 0.26
16 8 0.35
17 2 0.09
18 2 0.09
19 3 0.13
ACGTcount: A:0.64, C:0.00, G:0.00, T:0.36
Consensus pattern (18 bp):
TAATTATAAAAATATTAA
Found at i:144655 original size:17 final size:19
Alignment explanation
Indices: 144633--144667 Score: 56
Period size: 17 Copynumber: 1.9 Consensus size: 19
144623 AATATTAATA
144633 ATAAAA-AATT-TAAAATT
1 ATAAAATAATTATAAAATT
144650 ATAAAATAATTATAAAAT
1 ATAAAATAATTATAAAAT
144668 GTAGTGCTGC
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
17 6 0.38
18 4 0.25
19 6 0.38
ACGTcount: A:0.66, C:0.00, G:0.00, T:0.34
Consensus pattern (19 bp):
ATAAAATAATTATAAAATT
Found at i:145198 original size:8 final size:8
Alignment explanation
Indices: 145185--145236 Score: 50
Period size: 8 Copynumber: 6.1 Consensus size: 8
145175 GCTTACTTAT
145185 ATATATAA
1 ATATATAA
145193 ATATATAA
1 ATATATAA
*
145201 ATATATAT
1 ATATATAA
*
145209 ATAAATAA
1 ATATATAA
*
145217 TTAAATATAA
1 --ATATATAA
145227 ATATGATAA
1 ATAT-ATAA
145236 A
1 A
145237 AAATAATTAA
Statistics
Matches: 35, Mismatches: 6, Indels: 5
0.76 0.13 0.11
Matches are distributed among these distances:
8 24 0.69
9 5 0.14
10 6 0.17
ACGTcount: A:0.62, C:0.00, G:0.02, T:0.37
Consensus pattern (8 bp):
ATATATAA
Found at i:145207 original size:20 final size:20
Alignment explanation
Indices: 145182--145230 Score: 73
Period size: 20 Copynumber: 2.5 Consensus size: 20
145172 AAAGCTTACT
145182 TATATATATAAAT-ATATAAA
1 TATATATATAAATAAT-TAAA
145202 TATATATATAAATAATTAAA
1 TATATATATAAATAATTAAA
*
145222 TATAAATAT
1 TATATATAT
145231 GATAAAAAAT
Statistics
Matches: 27, Mismatches: 1, Indels: 2
0.90 0.03 0.07
Matches are distributed among these distances:
20 25 0.93
21 2 0.07
ACGTcount: A:0.59, C:0.00, G:0.00, T:0.41
Consensus pattern (20 bp):
TATATATATAAATAATTAAA
Found at i:145224 original size:26 final size:26
Alignment explanation
Indices: 145195--145247 Score: 81
Period size: 26 Copynumber: 2.0 Consensus size: 26
145185 ATATATAAAT
*
145195 ATATAAATAT-ATATATAAATAATTAA
1 ATATAAATATGATA-AAAAATAATTAA
145221 ATATAAATATGATAAAAAATAATTAA
1 ATATAAATATGATAAAAAATAATTAA
145247 A
1 A
145248 AATTAAATTT
Statistics
Matches: 25, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
26 22 0.88
27 3 0.12
ACGTcount: A:0.64, C:0.00, G:0.02, T:0.34
Consensus pattern (26 bp):
ATATAAATATGATAAAAAATAATTAA
Found at i:145931 original size:25 final size:26
Alignment explanation
Indices: 145888--145942 Score: 69
Period size: 25 Copynumber: 2.2 Consensus size: 26
145878 TAATTAGTAA
* *
145888 ATTTATCAAAATATTAAA-T-AAAAT
1 ATTTATAAAAATATAAAATTAAAAAT
145912 ATTTATAACAAATATAAAATTAAAAAT
1 ATTTATAA-AAATATAAAATTAAAAAT
145939 ATTT
1 ATTT
145943 TATTTTAACT
Statistics
Matches: 26, Mismatches: 2, Indels: 3
0.84 0.06 0.10
Matches are distributed among these distances:
24 7 0.27
25 9 0.35
26 1 0.04
27 9 0.35
ACGTcount: A:0.58, C:0.04, G:0.00, T:0.38
Consensus pattern (26 bp):
ATTTATAAAAATATAAAATTAAAAAT
Found at i:146084 original size:17 final size:17
Alignment explanation
Indices: 146041--146086 Score: 58
Period size: 18 Copynumber: 2.6 Consensus size: 17
146031 ACAAGCTTAC
*
146041 TATATTATAATATTATT
1 TATATAATAATATTATT
146058 TATAATAATAATAATT-TT
1 TAT-ATAATAAT-ATTATT
146076 TATATAATAAT
1 TATATAATAAT
146087 TAATAACCAT
Statistics
Matches: 26, Mismatches: 1, Indels: 4
0.84 0.03 0.13
Matches are distributed among these distances:
17 11 0.42
18 12 0.46
19 3 0.12
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (17 bp):
TATATAATAATATTATT
Found at i:146548 original size:23 final size:23
Alignment explanation
Indices: 146503--146546 Score: 81
Period size: 22 Copynumber: 2.0 Consensus size: 23
146493 AAAATTATAA
146503 AATTAAATAATTGTTAAAAAAAT
1 AATTAAATAATTGTTAAAAAAAT
146526 AATTAAATAA-TGTTAAAAAAA
1 AATTAAATAATTGTTAAAAAAA
146547 ATTTATCTAT
Statistics
Matches: 21, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
22 11 0.52
23 10 0.48
ACGTcount: A:0.64, C:0.00, G:0.05, T:0.32
Consensus pattern (23 bp):
AATTAAATAATTGTTAAAAAAAT
Found at i:146663 original size:15 final size:15
Alignment explanation
Indices: 146624--146664 Score: 50
Period size: 15 Copynumber: 2.8 Consensus size: 15
146614 TTTATTTTTA
146624 AAAT-TAATTTTATT
1 AAATATAATTTTATT
146638 AAATA-ATATTTTATT
1 AAATATA-ATTTTATT
*
146653 AATTATAATTTT
1 AAATATAATTTT
146665 TAATATAAAC
Statistics
Matches: 23, Mismatches: 1, Indels: 5
0.79 0.03 0.17
Matches are distributed among these distances:
14 5 0.22
15 17 0.74
16 1 0.04
ACGTcount: A:0.44, C:0.00, G:0.00, T:0.56
Consensus pattern (15 bp):
AAATATAATTTTATT
Found at i:152838 original size:221 final size:221
Alignment explanation
Indices: 152455--152898 Score: 888
Period size: 221 Copynumber: 2.0 Consensus size: 221
152445 TTTGTCTTGC
152455 TTCATCACAATCAATTCTTTATTAGGAATAATAACATAATGAATATTTTCAATTCCTTAAATATT
1 TTCATCACAATCAATTCTTTATTAGGAATAATAACATAATGAATATTTTCAATTCCTTAAATATT
152520 TGAATTCCAATTTGTTTATTATTTAAATATTTTTATCTGAATCCAAATCCAAATTAGATAGTAAC
66 TGAATTCCAATTTGTTTATTATTTAAATATTTTTATCTGAATCCAAATCCAAATTAGATAGTAAC
152585 TAGTTATCATAATTTACTTATCTGAATTCTTGATAATAAAAGTTTGCATATGTCAAAGCTTTGTG
131 TAGTTATCATAATTTACTTATCTGAATTCTTGATAATAAAAGTTTGCATATGTCAAAGCTTTGTG
152650 CGAGTATAAAATTTTTTAATATTTTA
196 CGAGTATAAAATTTTTTAATATTTTA
152676 TTCATCACAATCAATTCTTTATTAGGAATAATAACATAATGAATATTTTCAATTCCTTAAATATT
1 TTCATCACAATCAATTCTTTATTAGGAATAATAACATAATGAATATTTTCAATTCCTTAAATATT
152741 TGAATTCCAATTTGTTTATTATTTAAATATTTTTATCTGAATCCAAATCCAAATTAGATAGTAAC
66 TGAATTCCAATTTGTTTATTATTTAAATATTTTTATCTGAATCCAAATCCAAATTAGATAGTAAC
152806 TAGTTATCATAATTTACTTATCTGAATTCTTGATAATAAAAGTTTGCATATGTCAAAGCTTTGTG
131 TAGTTATCATAATTTACTTATCTGAATTCTTGATAATAAAAGTTTGCATATGTCAAAGCTTTGTG
152871 CGAGTATAAAATTTTTTAATATTTTA
196 CGAGTATAAAATTTTTTAATATTTTA
152897 TT
1 TT
152899 TCTATTTGAA
Statistics
Matches: 223, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
221 223 1.00
ACGTcount: A:0.36, C:0.11, G:0.09, T:0.44
Consensus pattern (221 bp):
TTCATCACAATCAATTCTTTATTAGGAATAATAACATAATGAATATTTTCAATTCCTTAAATATT
TGAATTCCAATTTGTTTATTATTTAAATATTTTTATCTGAATCCAAATCCAAATTAGATAGTAAC
TAGTTATCATAATTTACTTATCTGAATTCTTGATAATAAAAGTTTGCATATGTCAAAGCTTTGTG
CGAGTATAAAATTTTTTAATATTTTA
Found at i:155859 original size:24 final size:24
Alignment explanation
Indices: 155813--155860 Score: 62
Period size: 24 Copynumber: 2.0 Consensus size: 24
155803 AAAAATATAT
**
155813 ATTATTTTTATTAAATTTTTAAAA
1 ATTATTTTTATTAAATTCATAAAA
155837 ATTATTTTTAATTAAA-TCATAAAA
1 ATTATTTTT-ATTAAATTCATAAAA
155861 TATTGATAAA
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
24 15 0.71
25 6 0.29
ACGTcount: A:0.46, C:0.02, G:0.00, T:0.52
Consensus pattern (24 bp):
ATTATTTTTATTAAATTCATAAAA
Found at i:155898 original size:25 final size:25
Alignment explanation
Indices: 155874--155928 Score: 67
Period size: 25 Copynumber: 2.2 Consensus size: 25
155864 TGATAAATTA
* * *
155874 ATATATTTTTTTTATT-TTTTTATT
1 ATATATTATATTTATTATTTATATT
155898 ATAATATTATATTTATTATTTATATT
1 AT-ATATTATATTTATTATTTATATT
155924 ATATA
1 ATATA
155929 AATTATAAAA
Statistics
Matches: 26, Mismatches: 3, Indels: 3
0.81 0.09 0.09
Matches are distributed among these distances:
24 2 0.08
25 15 0.58
26 9 0.35
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (25 bp):
ATATATTATATTTATTATTTATATT
Found at i:155924 original size:18 final size:17
Alignment explanation
Indices: 155892--155927 Score: 54
Period size: 18 Copynumber: 2.1 Consensus size: 17
155882 TTTTTATTTT
155892 TTTATTATAATATTATA
1 TTTATTATAATATTATA
*
155909 TTTATTATTTATATTATA
1 TTTATTA-TAATATTATA
155927 T
1 T
155928 AAATTATAAA
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
17 7 0.41
18 10 0.59
ACGTcount: A:0.36, C:0.00, G:0.00, T:0.64
Consensus pattern (17 bp):
TTTATTATAATATTATA
Found at i:158019 original size:26 final size:27
Alignment explanation
Indices: 157990--158043 Score: 74
Period size: 26 Copynumber: 2.0 Consensus size: 27
157980 TATTTATATA
*
157990 TTTTATAATTAAAT-TTAAATAAAATT
1 TTTTATAATTAAATAATAAATAAAATT
* *
158016 TTTTATTATTAAATAATAAGTAAAATT
1 TTTTATAATTAAATAATAAATAAAATT
158043 T
1 T
158044 AATTCACTTA
Statistics
Matches: 24, Mismatches: 3, Indels: 1
0.86 0.11 0.04
Matches are distributed among these distances:
26 13 0.54
27 11 0.46
ACGTcount: A:0.48, C:0.00, G:0.02, T:0.50
Consensus pattern (27 bp):
TTTTATAATTAAATAATAAATAAAATT
Found at i:158227 original size:18 final size:17
Alignment explanation
Indices: 158173--158238 Score: 61
Period size: 18 Copynumber: 4.0 Consensus size: 17
158163 AATTATTATT
158173 TAAATT-TATAT-TTAA
1 TAAATTATATATATTAA
*
158188 TATATTA-ATAATATT-A
1 TAAATTATAT-ATATTAA
158204 -AAATTATATATTATTAA
1 TAAATTATATA-TATTAA
158221 TAAATTATATCATATTAA
1 TAAATTATAT-ATATTAA
158239 CTCGTCATTT
Statistics
Matches: 41, Mismatches: 2, Indels: 13
0.73 0.04 0.23
Matches are distributed among these distances:
15 13 0.32
16 9 0.22
17 3 0.07
18 15 0.37
19 1 0.02
ACGTcount: A:0.50, C:0.02, G:0.00, T:0.48
Consensus pattern (17 bp):
TAAATTATATATATTAA
Found at i:158230 original size:29 final size:30
Alignment explanation
Indices: 158161--158230 Score: 72
Period size: 29 Copynumber: 2.3 Consensus size: 30
158151 AATAAAAAAT
*
158161 TAAATTATTATTTAAATTTATATTTAATATA
1 TAAATTA-TATTAAAATTTATATTTAATATA
* * *
158192 TTAATAATATTAAAA-TTATATATTATTA-A
1 TAAATTATATTAAAATTTATAT-TTAATATA
158221 TAAATTATAT
1 TAAATTATAT
158231 CATATTAACT
Statistics
Matches: 32, Mismatches: 6, Indels: 4
0.76 0.14 0.10
Matches are distributed among these distances:
29 15 0.47
30 12 0.38
31 5 0.16
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (30 bp):
TAAATTATATTAAAATTTATATTTAATATA
Found at i:160839 original size:16 final size:14
Alignment explanation
Indices: 160806--160833 Score: 56
Period size: 14 Copynumber: 2.0 Consensus size: 14
160796 TTAATTATAA
160806 AATATATAAATATT
1 AATATATAAATATT
160820 AATATATAAATATT
1 AATATATAAATATT
160834 TTAATAAAAA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 14 1.00
ACGTcount: A:0.57, C:0.00, G:0.00, T:0.43
Consensus pattern (14 bp):
AATATATAAATATT
Found at i:160894 original size:7 final size:7
Alignment explanation
Indices: 160876--160909 Score: 52
Period size: 7 Copynumber: 4.9 Consensus size: 7
160866 AAATTAAGTT
160876 AAATTT-
1 AAATTTA
160882 AAATTTA
1 AAATTTA
160889 AAATTTA
1 AAATTTA
160896 AAATTTTA
1 AAA-TTTA
160904 AAATTT
1 AAATTT
160910 TTAGATTGTC
Statistics
Matches: 26, Mismatches: 0, Indels: 3
0.90 0.00 0.10
Matches are distributed among these distances:
6 6 0.23
7 13 0.50
8 7 0.27
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (7 bp):
AAATTTA
Found at i:162914 original size:20 final size:20
Alignment explanation
Indices: 162875--162945 Score: 65
Period size: 20 Copynumber: 3.5 Consensus size: 20
162865 ATTAAGTTTA
* *
162875 TATTTATATTTTA-ATTTTT
1 TATTTAAATTTTATAATTTT
162894 TATTTTAAATTTTATAATTTT
1 TA-TTTAAATTTTATAATTTT
* * *
162915 TAGTTAAA-ATAATATATTTT
1 TATTTAAATTTTATA-ATTTT
162935 TATTTAAATTT
1 TATTTAAATTT
162946 AATTATATTA
Statistics
Matches: 41, Mismatches: 7, Indels: 6
0.76 0.13 0.11
Matches are distributed among these distances:
19 6 0.15
20 27 0.66
21 8 0.20
ACGTcount: A:0.35, C:0.00, G:0.01, T:0.63
Consensus pattern (20 bp):
TATTTAAATTTTATAATTTT
Found at i:162948 original size:21 final size:21
Alignment explanation
Indices: 162890--162976 Score: 79
Period size: 20 Copynumber: 4.0 Consensus size: 21
162880 ATATTTTAAT
*
162890 TTTTTATTTTAAATTTTATA-A
1 TTTTTA-TTTAAATTTAATATA
* *
162911 TTTTTAGTTAAA-ATAATATA
1 TTTTTATTTAAATTTAATATA
162931 TTTTTATTTAAATTTAATTATA
1 TTTTTATTTAAATTTAA-TATA
*
162953 TTATTTATATATAATATTAATATA
1 TT-TTTATTTA-AAT-TTAATATA
162977 AAAATAATTT
Statistics
Matches: 54, Mismatches: 6, Indels: 9
0.78 0.09 0.13
Matches are distributed among these distances:
19 4 0.07
20 17 0.31
21 9 0.17
22 6 0.11
23 7 0.13
24 7 0.13
25 4 0.07
ACGTcount: A:0.40, C:0.00, G:0.01, T:0.59
Consensus pattern (21 bp):
TTTTTATTTAAATTTAATATA
Found at i:162972 original size:25 final size:22
Alignment explanation
Indices: 162927--162973 Score: 58
Period size: 23 Copynumber: 2.0 Consensus size: 22
162917 GTTAAAATAA
*
162927 TATATTTTTATTTAAATTTAAT
1 TATATTTTTATATAAATTTAAT
162949 TATATTATTTATATATAATATTAAT
1 TATATT-TTTATATA-AAT-TTAAT
162974 ATAAAAATAA
Statistics
Matches: 21, Mismatches: 1, Indels: 3
0.84 0.04 0.12
Matches are distributed among these distances:
22 6 0.29
23 7 0.33
24 3 0.14
25 5 0.24
ACGTcount: A:0.40, C:0.00, G:0.00, T:0.60
Consensus pattern (22 bp):
TATATTTTTATATAAATTTAAT
Found at i:163926 original size:48 final size:45
Alignment explanation
Indices: 163873--163974 Score: 107
Period size: 49 Copynumber: 2.1 Consensus size: 45
163863 TTACACGTAA
* *
163873 ATTTAATAATTCATACTATATATTATTT-TTATATTTATAAATATTATT
1 ATTTAATAATTAATA-TAT-TATT-TTTATTAAATTTATAAATATTA-T
*
163921 ATTTAAAAATAATTAATATATTATTTTTATTAAATTTATAAATTTTAT
1 ATTT---AATAATTAATATATTATTTTTATTAAATTTATAAATATTAT
163969 ATTTAA
1 ATTTAA
163975 ATATTATTTT
Statistics
Matches: 47, Mismatches: 3, Indels: 11
0.77 0.05 0.18
Matches are distributed among these distances:
45 2 0.04
48 12 0.26
49 20 0.43
50 3 0.06
51 10 0.21
ACGTcount: A:0.43, C:0.02, G:0.00, T:0.55
Consensus pattern (45 bp):
ATTTAATAATTAATATATTATTTTTATTAAATTTATAAATATTAT
Found at i:164395 original size:26 final size:28
Alignment explanation
Indices: 164347--164413 Score: 73
Period size: 28 Copynumber: 2.3 Consensus size: 28
164337 TTGATAAATT
*
164347 ATTTTATTATATATTGATAATATTTAAA
1 ATTTTAATATATATTGATAATATTTAAA
*
164375 ATTTTAATATAT-TTTATATATTTATTTAAA
1 ATTTTAATATATATTGATA-A--TATTTAAA
164405 TATTTTAAT
1 -ATTTTAAT
164414 TGATTATCTA
Statistics
Matches: 33, Mismatches: 2, Indels: 5
0.82 0.05 0.12
Matches are distributed among these distances:
27 5 0.15
28 12 0.36
30 8 0.24
31 8 0.24
ACGTcount: A:0.40, C:0.00, G:0.01, T:0.58
Consensus pattern (28 bp):
ATTTTAATATATATTGATAATATTTAAA
Found at i:164963 original size:14 final size:15
Alignment explanation
Indices: 164944--164976 Score: 59
Period size: 14 Copynumber: 2.3 Consensus size: 15
164934 TACGTTATTC
164944 ATTTAATTT-AATAA
1 ATTTAATTTAAATAA
164958 ATTTAATTTAAATAA
1 ATTTAATTTAAATAA
164973 ATTT
1 ATTT
164977 TTTATAAATA
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
14 9 0.50
15 9 0.50
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (15 bp):
ATTTAATTTAAATAA
Found at i:164984 original size:15 final size:15
Alignment explanation
Indices: 164953--165003 Score: 50
Period size: 15 Copynumber: 3.3 Consensus size: 15
164943 CATTTAATTT
*
164953 AATAAATTTAATT-TA
1 AATAAATTT-TTTATA
164968 AATAAATTTTTTATA
1 AATAAATTTTTTATA
*
164983 AATAATAATTTTTTAAA
1 AAT-A-AATTTTTTATA
165000 AATA
1 AATA
165004 TAAGATGATA
Statistics
Matches: 31, Mismatches: 2, Indels: 5
0.82 0.05 0.13
Matches are distributed among these distances:
14 2 0.06
15 14 0.45
16 2 0.06
17 13 0.42
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (15 bp):
AATAAATTTTTTATA
Found at i:165212 original size:12 final size:11
Alignment explanation
Indices: 165174--165212 Score: 51
Period size: 12 Copynumber: 3.4 Consensus size: 11
165164 TAAATTTATT
165174 AATAATATATA
1 AATAATATATA
*
165185 AATTAATATATG
1 AA-TAATATATA
165197 AATAATATATTA
1 AATAATATA-TA
165209 AATA
1 AATA
165213 TAAATTTTAA
Statistics
Matches: 24, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
11 9 0.38
12 15 0.62
ACGTcount: A:0.59, C:0.00, G:0.03, T:0.38
Consensus pattern (11 bp):
AATAATATATA
Found at i:165538 original size:5 final size:5
Alignment explanation
Indices: 165498--165564 Score: 52
Period size: 5 Copynumber: 13.8 Consensus size: 5
165488 GATAGTTAAA
* * *
165498 TAATT T-ATT TGATT TAAAT TATATT AAATT TAAATT TAATT T--TT T-ATT
1 TAATT TAATT TAATT TAATT TA-ATT TAATT T-AATT TAATT TAATT TAATT
*
165546 TAAAT TAATT TAATT TAAT
1 TAATT TAATT TAATT TAAT
165565 GTGATTATTA
Statistics
Matches: 50, Mismatches: 7, Indels: 10
0.75 0.10 0.15
Matches are distributed among these distances:
3 3 0.06
4 7 0.14
5 32 0.64
6 8 0.16
ACGTcount: A:0.40, C:0.00, G:0.01, T:0.58
Consensus pattern (5 bp):
TAATT
Found at i:165547 original size:34 final size:35
Alignment explanation
Indices: 165498--165563 Score: 100
Period size: 33 Copynumber: 1.9 Consensus size: 35
165488 GATAGTTAAA
165498 TAATTTATTTGATTTAAATTATATTAAATTTAAATT
1 TAATTTATTTGATTTAAATTA-ATTAAATTTAAATT
*
165534 TAATTT-TTT-ATTTAAATTAATTTAATTTAA
1 TAATTTATTTGATTTAAATTAATTAAATTTAA
165564 TGTGATTATT
Statistics
Matches: 29, Mismatches: 1, Indels: 3
0.88 0.03 0.09
Matches are distributed among these distances:
33 10 0.34
34 10 0.34
35 3 0.10
36 6 0.21
ACGTcount: A:0.41, C:0.00, G:0.02, T:0.58
Consensus pattern (35 bp):
TAATTTATTTGATTTAAATTAATTAAATTTAAATT
Found at i:165677 original size:22 final size:22
Alignment explanation
Indices: 165630--165677 Score: 60
Period size: 22 Copynumber: 2.2 Consensus size: 22
165620 ATATAAATAT
* * *
165630 AATAATTTTATATAACATTTTT
1 AATAATTTTAAATAACAATTTA
*
165652 AATAATTTTAAATAATAATTTA
1 AATAATTTTAAATAACAATTTA
165674 AATA
1 AATA
165678 TATAAATCAA
Statistics
Matches: 22, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
22 22 1.00
ACGTcount: A:0.50, C:0.02, G:0.00, T:0.48
Consensus pattern (22 bp):
AATAATTTTAAATAACAATTTA
Found at i:165864 original size:17 final size:17
Alignment explanation
Indices: 165838--165872 Score: 61
Period size: 17 Copynumber: 2.1 Consensus size: 17
165828 ATATTAATTA
165838 AAATTAAAAAATTATAT
1 AAATTAAAAAATTATAT
*
165855 AAATTTAAAAATTATAT
1 AAATTAAAAAATTATAT
165872 A
1 A
165873 TTTATAAAAG
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
17 17 1.00
ACGTcount: A:0.63, C:0.00, G:0.00, T:0.37
Consensus pattern (17 bp):
AAATTAAAAAATTATAT
Found at i:165875 original size:15 final size:16
Alignment explanation
Indices: 165839--165881 Score: 52
Period size: 17 Copynumber: 2.6 Consensus size: 16
165829 TATTAATTAA
*
165839 AATTAAAAAATTATAT
1 AATTTAAAAATTATAT
165855 AAATTTAAAAATTATAT
1 -AATTTAAAAATTATAT
165872 -ATTTATAAAA
1 AATTTA-AAAA
165882 GAATTTATAT
Statistics
Matches: 24, Mismatches: 1, Indels: 3
0.86 0.04 0.11
Matches are distributed among these distances:
15 5 0.21
16 4 0.17
17 15 0.62
ACGTcount: A:0.60, C:0.00, G:0.00, T:0.40
Consensus pattern (16 bp):
AATTTAAAAATTATAT
Found at i:165880 original size:17 final size:18
Alignment explanation
Indices: 165842--165895 Score: 60
Period size: 18 Copynumber: 3.1 Consensus size: 18
165832 TAATTAAAAT
*
165842 TAAAAAATTATATAAATT-
1 TAAAAAATTATAT-ATTTA
165860 T-AAAAATTATATATTTA
1 TAAAAAATTATATATTTA
165877 TAAAAGAATT-TATATTTA
1 TAAAA-AATTATATATTTA
165895 T
1 T
165896 TAATTAAAAA
Statistics
Matches: 32, Mismatches: 1, Indels: 6
0.82 0.03 0.15
Matches are distributed among these distances:
16 3 0.09
17 12 0.38
18 13 0.41
19 4 0.12
ACGTcount: A:0.54, C:0.00, G:0.02, T:0.44
Consensus pattern (18 bp):
TAAAAAATTATATATTTA
Found at i:170428 original size:24 final size:26
Alignment explanation
Indices: 170384--170443 Score: 65
Period size: 24 Copynumber: 2.4 Consensus size: 26
170374 CATAAATTTT
170384 TAAAT-AAAATTAATTTCAAATTAAA-A
1 TAAATAAAAATT-ATTTCAAA-TAAAGA
170410 TAAATAAAAATT-TTT-AAATAAAGA
1 TAAATAAAAATTATTTCAAATAAAGA
*
170434 TAAAAAAAAA
1 TAAATAAAAA
170444 ATAATATCGA
Statistics
Matches: 31, Mismatches: 1, Indels: 6
0.82 0.03 0.16
Matches are distributed among these distances:
23 4 0.13
24 13 0.42
25 3 0.10
26 5 0.16
27 6 0.19
ACGTcount: A:0.67, C:0.02, G:0.02, T:0.30
Consensus pattern (26 bp):
TAAATAAAAATTATTTCAAATAAAGA
Found at i:170931 original size:19 final size:19
Alignment explanation
Indices: 170909--170977 Score: 63
Period size: 19 Copynumber: 3.6 Consensus size: 19
170899 TTTAAATTAT
170909 TATTTATTAATTAAAATAA
1 TATTTATTAATTAAAATAA
170928 TATTTAATT-A-TAAAATATA
1 TATTT-ATTAATTAAAATA-A
**
170947 TAAATATTAATATAAAATTAA
1 TATTTATTAAT-TAAAA-TAA
170968 TATTT-TTAAT
1 TATTTATTAAT
170978 ATTTTAATAT
Statistics
Matches: 40, Mismatches: 4, Indels: 11
0.73 0.07 0.20
Matches are distributed among these distances:
18 10 0.25
19 11 0.28
20 8 0.20
21 9 0.22
22 2 0.05
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (19 bp):
TATTTATTAATTAAAATAA
Found at i:170943 original size:18 final size:17
Alignment explanation
Indices: 170915--170972 Score: 55
Period size: 21 Copynumber: 3.1 Consensus size: 17
170905 TTATTATTTA
170915 TTAAT-TAAAATAATAT
1 TTAATATAAAATAATAT
170931 TTAATTATAAAATATATAAAT
1 TTAA-TATAAAATA-AT--AT
170952 ATTAATATAAAATTAATAT
1 -TTAATATAAAA-TAATAT
170971 TT
1 TT
170973 TTAATATTTT
Statistics
Matches: 35, Mismatches: 0, Indels: 12
0.74 0.00 0.26
Matches are distributed among these distances:
16 4 0.11
17 1 0.03
18 9 0.26
19 4 0.11
21 11 0.31
22 6 0.17
ACGTcount: A:0.55, C:0.00, G:0.00, T:0.45
Consensus pattern (17 bp):
TTAATATAAAATAATAT
Found at i:170970 original size:23 final size:24
Alignment explanation
Indices: 170917--170970 Score: 62
Period size: 22 Copynumber: 2.4 Consensus size: 24
170907 ATTATTTATT
*
170917 AATTAAAATAATATTTAATTATAA
1 AATTAATATAATATTTAATTATAA
170941 AA-T-ATATAA-ATATTAA-TATAA
1 AATTAATATAATAT-TTAATTATAA
170962 AATTAATAT
1 AATTAATAT
170971 TTTTAATATT
Statistics
Matches: 26, Mismatches: 1, Indels: 7
0.76 0.03 0.21
Matches are distributed among these distances:
21 9 0.35
22 10 0.38
23 5 0.19
24 2 0.08
ACGTcount: A:0.59, C:0.00, G:0.00, T:0.41
Consensus pattern (24 bp):
AATTAATATAATATTTAATTATAA
Found at i:170978 original size:20 final size:19
Alignment explanation
Indices: 170909--170979 Score: 58
Period size: 20 Copynumber: 3.6 Consensus size: 19
170899 TTTAAATTAT
170909 TATTTATTAAT-TAAAATAA
1 TATTT-TTAATATAAAATAA
170928 TA--TTTAATTATAAAATATA
1 TATTTTTAA-TATAAAATA-A
* *
170947 TAAATATTAATATAAAATTAA
1 T-ATTTTTAATATAAAA-TAA
170968 TATTTTTAATAT
1 TATTTTTAATAT
170980 TTTAATATAC
Statistics
Matches: 42, Mismatches: 3, Indels: 13
0.72 0.05 0.22
Matches are distributed among these distances:
16 4 0.10
17 2 0.05
18 7 0.17
19 4 0.10
20 10 0.24
21 9 0.21
22 6 0.14
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (19 bp):
TATTTTTAATATAAAATAA
Found at i:171409 original size:6 final size:6
Alignment explanation
Indices: 171401--171440 Score: 53
Period size: 6 Copynumber: 6.5 Consensus size: 6
171391 ATATTTTATT
* *
171401 TAAATT TAATTA TAAAATA TAAATA TAAATA TAAATA TAA
1 TAAATA TAAATA T-AAATA TAAATA TAAATA TAAATA TAA
171441 TTTTTTTAAT
Statistics
Matches: 30, Mismatches: 3, Indels: 2
0.86 0.09 0.06
Matches are distributed among these distances:
6 25 0.83
7 5 0.17
ACGTcount: A:0.62, C:0.00, G:0.00, T:0.38
Consensus pattern (6 bp):
TAAATA
Found at i:172118 original size:19 final size:20
Alignment explanation
Indices: 172084--172123 Score: 64
Period size: 19 Copynumber: 2.0 Consensus size: 20
172074 ACATTAAAAA
172084 AATTTAAATAATAAATAAAT
1 AATTTAAATAATAAATAAAT
*
172104 AATTTTAAT-ATAAATAAAT
1 AATTTAAATAATAAATAAAT
172123 A
1 A
172124 TTATATATAC
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
19 11 0.58
20 8 0.42
ACGTcount: A:0.62, C:0.00, G:0.00, T:0.38
Consensus pattern (20 bp):
AATTTAAATAATAAATAAAT
Found at i:184955 original size:9 final size:9
Alignment explanation
Indices: 184937--184970 Score: 52
Period size: 9 Copynumber: 3.8 Consensus size: 9
184927 TAATTTTTTT
184937 TAAAAA-AA
1 TAAAAATAA
184945 TAAAAATAA
1 TAAAAATAA
184954 TAAAAATATA
1 TAAAAATA-A
184964 TAAAAAT
1 TAAAAAT
184971 TTTAAAATAA
Statistics
Matches: 24, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
8 6 0.25
9 10 0.42
10 8 0.33
ACGTcount: A:0.76, C:0.00, G:0.00, T:0.24
Consensus pattern (9 bp):
TAAAAATAA
Found at i:184976 original size:19 final size:17
Alignment explanation
Indices: 184934--184983 Score: 55
Period size: 19 Copynumber: 2.8 Consensus size: 17
184924 TATTAATTTT
184934 TTTTAAAAAAATAAAAA
1 TTTTAAAAAAATAAAAA
**
184951 TAATAAAAATATATAAAAA
1 TTTTAAAAA-A-ATAAAAA
184970 TTTTAAAATAAATA
1 TTTTAAAA-AAATA
184984 TAATATAAAA
Statistics
Matches: 26, Mismatches: 4, Indels: 5
0.74 0.11 0.14
Matches are distributed among these distances:
17 7 0.27
18 4 0.15
19 14 0.54
20 1 0.04
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.32
Consensus pattern (17 bp):
TTTTAAAAAAATAAAAA
Found at i:187416 original size:24 final size:23
Alignment explanation
Indices: 187359--187416 Score: 57
Period size: 24 Copynumber: 2.5 Consensus size: 23
187349 AATCAAATAA
187359 TTAATT-AAA-TATAAAATATTT
1 TTAATTAAAATTATAAAATATTT
** *
187380 TTAAAAAATAATTATTAAATATTTT
1 TTAATTAA-AATTATAAAATA-TTT
187405 TTAATTAAAATT
1 TTAATTAAAATT
187417 TATAGATATC
Statistics
Matches: 28, Mismatches: 5, Indels: 5
0.74 0.13 0.13
Matches are distributed among these distances:
21 4 0.14
22 1 0.04
23 2 0.07
24 12 0.43
25 9 0.32
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (23 bp):
TTAATTAAAATTATAAAATATTT
Found at i:187680 original size:10 final size:10
Alignment explanation
Indices: 187665--187740 Score: 80
Period size: 10 Copynumber: 7.6 Consensus size: 10
187655 ATATTTATTA
187665 TTATATTAAT
1 TTATATTAAT
*
187675 TTATATTAAA
1 TTATATTAAT
*
187685 TTATTTTAAT
1 TTATATTAAT
* *
187695 TAATATTTAT
1 TTATATTAAT
187705 TTATATTAAT
1 TTATATTAAT
** *
187715 ACATATCAAT
1 TTATATTAAT
*
187725 TTATATTAGT
1 TTATATTAAT
187735 TTATAT
1 TTATAT
187741 AAAATTTTAG
Statistics
Matches: 51, Mismatches: 15, Indels: 0
0.77 0.23 0.00
Matches are distributed among these distances:
10 51 1.00
ACGTcount: A:0.39, C:0.03, G:0.01, T:0.57
Consensus pattern (10 bp):
TTATATTAAT
Found at i:187856 original size:14 final size:13
Alignment explanation
Indices: 187837--187867 Score: 53
Period size: 14 Copynumber: 2.3 Consensus size: 13
187827 TATTTAAAAA
187837 TAAATTATATTAAT
1 TAAATTATATT-AT
187851 TAAATTATATTAT
1 TAAATTATATTAT
187864 TAAA
1 TAAA
187868 CTTAGTTAAT
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
13 6 0.35
14 11 0.65
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (13 bp):
TAAATTATATTAT
Found at i:187950 original size:30 final size:30
Alignment explanation
Indices: 187893--187951 Score: 75
Period size: 30 Copynumber: 2.0 Consensus size: 30
187883 TTTATTGTAC
* **
187893 TTTTAAATATTTTTATAGTTATTTATTTAT
1 TTTTAAAAATTTTTATAGTTAAATATTTAT
187923 TTTTAAAAATTTTTAATA-TTAAATATTTA
1 TTTTAAAAATTTTT-ATAGTTAAATATTTA
187952 CAATTATAAA
Statistics
Matches: 25, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
30 22 0.88
31 3 0.12
ACGTcount: A:0.37, C:0.00, G:0.02, T:0.61
Consensus pattern (30 bp):
TTTTAAAAATTTTTATAGTTAAATATTTAT
Found at i:188591 original size:26 final size:26
Alignment explanation
Indices: 188562--188620 Score: 68
Period size: 26 Copynumber: 2.3 Consensus size: 26
188552 TCTTTATACG
188562 ATAAAAGTT-ATTTA-ATATATAAAAAT
1 ATAAAA-TTAATTTATAT-TATAAAAAT
* *
188588 ATAAAATTAATTTATATTATATAATT
1 ATAAAATTAATTTATATTATAAAAAT
188614 ATAAAAT
1 ATAAAAT
188621 GAGATGAATT
Statistics
Matches: 29, Mismatches: 2, Indels: 4
0.83 0.06 0.11
Matches are distributed among these distances:
25 2 0.07
26 25 0.86
27 2 0.07
ACGTcount: A:0.56, C:0.00, G:0.02, T:0.42
Consensus pattern (26 bp):
ATAAAATTAATTTATATTATAAAAAT
Found at i:189227 original size:30 final size:29
Alignment explanation
Indices: 189191--189265 Score: 89
Period size: 30 Copynumber: 2.5 Consensus size: 29
189181 AATATATTTA
*
189191 AATTTTAATTTATATAAAAATAAATTATT
1 AATTTTAATTTATACAAAAATAAATTATT
* *
189220 AACTTTTAACTTT-TACATAAATAAATTTTT
1 AA-TTTTAA-TTTATACAAAAATAAATTATT
189250 AATATTTAATTTATAC
1 AAT-TTTAATTTATAC
189266 TTTAAATTTT
Statistics
Matches: 39, Mismatches: 3, Indels: 7
0.80 0.06 0.14
Matches are distributed among these distances:
29 6 0.15
30 30 0.77
31 3 0.08
ACGTcount: A:0.45, C:0.05, G:0.00, T:0.49
Consensus pattern (29 bp):
AATTTTAATTTATACAAAAATAAATTATT
Found at i:189388 original size:12 final size:13
Alignment explanation
Indices: 189356--189386 Score: 53
Period size: 13 Copynumber: 2.4 Consensus size: 13
189346 AATGTAATAA
*
189356 AATTTTAAAAATT
1 AATTTTAAAAAAT
189369 AATTTTAAAAAAT
1 AATTTTAAAAAAT
189382 AATTT
1 AATTT
189387 AATATATATA
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
13 17 1.00
ACGTcount: A:0.55, C:0.00, G:0.00, T:0.45
Consensus pattern (13 bp):
AATTTTAAAAAAT
Found at i:189577 original size:2 final size:2
Alignment explanation
Indices: 189570--189608 Score: 78
Period size: 2 Copynumber: 19.5 Consensus size: 2
189560 CTTCTTTTGC
189570 AT 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 AT A
189609 CATTGATGTT
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:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:189647 original size:20 final size:22
Alignment explanation
Indices: 189622--189668 Score: 64
Period size: 19 Copynumber: 2.3 Consensus size: 22
189612 TGATGTTAAA
189622 ATAAAAAATAA-TT-AATAATG
1 ATAAAAAATAATTTAAATAATG
*
189642 AT-AAAAATAATTTAAATAATT
1 ATAAAAAATAATTTAAATAATG
189663 ATAAAA
1 ATAAAA
189669 TTATTAATGT
Statistics
Matches: 23, Mismatches: 1, Indels: 4
0.82 0.04 0.14
Matches are distributed among these distances:
19 8 0.35
20 4 0.17
21 8 0.35
22 3 0.13
ACGTcount: A:0.66, C:0.00, G:0.02, T:0.32
Consensus pattern (22 bp):
ATAAAAAATAATTTAAATAATG
Found at i:189649 original size:19 final size:21
Alignment explanation
Indices: 189625--189668 Score: 65
Period size: 21 Copynumber: 2.2 Consensus size: 21
189615 TGTTAAAATA
189625 AAAAATAA-TT-AATAATGAT
1 AAAAATAATTTAAATAATGAT
*
189644 AAAAATAATTTAAATAATTAT
1 AAAAATAATTTAAATAATGAT
189665 AAAA
1 AAAA
189669 TTATTAATGT
Statistics
Matches: 22, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
19 8 0.36
20 2 0.09
21 12 0.55
ACGTcount: A:0.66, C:0.00, G:0.02, T:0.32
Consensus pattern (21 bp):
AAAAATAATTTAAATAATGAT
Found at i:189823 original size:21 final size:20
Alignment explanation
Indices: 189765--189827 Score: 74
Period size: 21 Copynumber: 3.1 Consensus size: 20
189755 ATATGTTATA
*
189765 TAATATGTTAA-TATTTTTT
1 TAATATTTTAATTATTTTTT
* *
189784 TAATATTTAAATAAGTTTTTT
1 TAATATTTTAATTA-TTTTTT
189805 TAATATTATTAATTATTTTTT
1 TAATATT-TTAATTATTTTTT
189826 TA
1 TA
189828 TTATAATTTT
Statistics
Matches: 36, Mismatches: 5, Indels: 4
0.80 0.11 0.09
Matches are distributed among these distances:
19 9 0.25
20 1 0.03
21 21 0.58
22 5 0.14
ACGTcount: A:0.35, C:0.00, G:0.03, T:0.62
Consensus pattern (20 bp):
TAATATTTTAATTATTTTTT
Found at i:190106 original size:21 final size:20
Alignment explanation
Indices: 190080--190118 Score: 60
Period size: 21 Copynumber: 1.9 Consensus size: 20
190070 ATTAAAATAA
*
190080 AAATAATATTTTAATATTTTT
1 AAATAATAATTTAA-ATTTTT
190101 AAATAATAATTTAAATTT
1 AAATAATAATTTAAATTT
190119 AATGACTTGA
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
20 4 0.24
21 13 0.76
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (20 bp):
AAATAATAATTTAAATTTTT
Found at i:190192 original size:15 final size:17
Alignment explanation
Indices: 190158--190200 Score: 54
Period size: 15 Copynumber: 2.6 Consensus size: 17
190148 TATATATAGT
*
190158 TAAATATAATAATTTAA
1 TAAATATAATAATATAA
190175 TAAATATAA-AA-ATAA
1 TAAATATAATAATATAA
*
190190 TAAACATAATA
1 TAAATATAATA
190201 TGATTAAAAC
Statistics
Matches: 23, Mismatches: 2, Indels: 3
0.82 0.07 0.11
Matches are distributed among these distances:
15 11 0.48
16 3 0.13
17 9 0.39
ACGTcount: A:0.65, C:0.02, G:0.00, T:0.33
Consensus pattern (17 bp):
TAAATATAATAATATAA
Found at i:194571 original size:11 final size:11
Alignment explanation
Indices: 194557--194583 Score: 54
Period size: 11 Copynumber: 2.5 Consensus size: 11
194547 TATATTTAAA
194557 AAATAAAAAAT
1 AAATAAAAAAT
194568 AAATAAAAAAT
1 AAATAAAAAAT
194579 AAATA
1 AAATA
194584 GGATAAATGT
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 16 1.00
ACGTcount: A:0.81, C:0.00, G:0.00, T:0.19
Consensus pattern (11 bp):
AAATAAAAAAT
Found at i:195035 original size:14 final size:15
Alignment explanation
Indices: 195002--195036 Score: 54
Period size: 15 Copynumber: 2.4 Consensus size: 15
194992 TTATTTCAAT
*
195002 ATTTAAATTACTCTA
1 ATTTAAATTAATCTA
195017 ATTTAAATTAATC-A
1 ATTTAAATTAATCTA
195031 ATTTAA
1 ATTTAA
195037 CTTATTAAAT
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
14 7 0.37
15 12 0.63
ACGTcount: A:0.46, C:0.09, G:0.00, T:0.46
Consensus pattern (15 bp):
ATTTAAATTAATCTA
Found at i:195251 original size:18 final size:19
Alignment explanation
Indices: 195215--195255 Score: 66
Period size: 18 Copynumber: 2.2 Consensus size: 19
195205 AAAATAATAT
*
195215 TATTAAAATATTATTTTTA
1 TATTAAAATATTATATTTA
195234 TATTAAAA-ATTATATTTA
1 TATTAAAATATTATATTTA
195252 TATT
1 TATT
195256 TTATAATTAA
Statistics
Matches: 21, Mismatches: 1, Indels: 1
0.91 0.04 0.04
Matches are distributed among these distances:
18 13 0.62
19 8 0.38
ACGTcount: A:0.44, C:0.00, G:0.00, T:0.56
Consensus pattern (19 bp):
TATTAAAATATTATATTTA
Found at i:195606 original size:15 final size:14
Alignment explanation
Indices: 195586--195660 Score: 59
Period size: 13 Copynumber: 5.2 Consensus size: 14
195576 TATATATAAA
195586 ATATAAAATATTAT
1 ATATAAAATATTAT
195600 GATAT-AAATA-TAT
1 -ATATAAAATATTAT
*
195613 ATTTAAAAT-TTAT
1 ATATAAAATATTAT
195626 ATAATATAAATTATTAAT
1 AT-ATA-AAA-TATT-AT
195644 ATATTAAAAT-TTAT
1 ATA-TAAAATATTAT
195658 ATA
1 ATA
195661 AATATAAAAT
Statistics
Matches: 50, Mismatches: 2, Indels: 17
0.72 0.03 0.25
Matches are distributed among these distances:
12 3 0.06
13 12 0.24
14 12 0.24
15 9 0.18
16 2 0.04
17 6 0.12
18 6 0.12
ACGTcount: A:0.53, C:0.00, G:0.01, T:0.45
Consensus pattern (14 bp):
ATATAAAATATTAT
Found at i:195654 original size:32 final size:34
Alignment explanation
Indices: 195609--195673 Score: 107
Period size: 33 Copynumber: 2.0 Consensus size: 34
195599 TGATATAAAT
*
195609 ATATATTTAAAATTTATAT-AATATAAATTATTA
1 ATATATTTAAAATTTATATAAATATAAAATATTA
195642 ATATA-TTAAAATTTATATAAATATAAAATATT
1 ATATATTTAAAATTTATATAAATATAAAATATT
195674 TTAAATATAA
Statistics
Matches: 30, Mismatches: 1, Indels: 2
0.91 0.03 0.06
Matches are distributed among these distances:
32 13 0.43
33 17 0.57
ACGTcount: A:0.54, C:0.00, G:0.00, T:0.46
Consensus pattern (34 bp):
ATATATTTAAAATTTATATAAATATAAAATATTA
Found at i:195660 original size:49 final size:47
Alignment explanation
Indices: 195607--195711 Score: 113
Period size: 47 Copynumber: 2.2 Consensus size: 47
195597 TATGATATAA
* * *
195607 ATATATATTTAAAAT-TTATATAATATAAATTATTAATATATTAAAATTT
1 ATATATATATAAAATATTATA-AATAT-AATTA-TAATATAATAAAATAT
* * *
195656 ATATAAATATAAAATATTTTAAATATAATTATACTATAATAAAATAT
1 ATATATATATAAAATATTATAAATATAATTATAATATAATAAAATAT
*
195703 ATAAATATA
1 ATATATATA
195712 ATATGAATAT
Statistics
Matches: 47, Mismatches: 8, Indels: 4
0.80 0.14 0.07
Matches are distributed among these distances:
47 20 0.43
48 5 0.11
49 18 0.38
50 4 0.09
ACGTcount: A:0.55, C:0.01, G:0.00, T:0.44
Consensus pattern (47 bp):
ATATATATATAAAATATTATAAATATAATTATAATATAATAAAATAT
Found at i:195722 original size:29 final size:30
Alignment explanation
Indices: 195657--195723 Score: 79
Period size: 29 Copynumber: 2.3 Consensus size: 30
195647 TTAAAATTTA
*
195657 TATAA-AT-ATAAAATATTTTAAATATAAT
1 TATAATATAATAAAATATTATAAATATAAT
*
195685 TATACTATAATAAAATA-TATAAATATAA-
1 TATAATATAATAAAATATTATAAATATAAT
195713 TATGAATATAA
1 TAT-AATATAA
195724 AAATTACGAA
Statistics
Matches: 33, Mismatches: 3, Indels: 5
0.80 0.07 0.12
Matches are distributed among these distances:
28 7 0.21
29 18 0.55
30 8 0.24
ACGTcount: A:0.58, C:0.01, G:0.01, T:0.39
Consensus pattern (30 bp):
TATAATATAATAAAATATTATAAATATAAT
Found at i:195856 original size:3 final size:3
Alignment explanation
Indices: 195848--195890 Score: 86
Period size: 3 Copynumber: 14.3 Consensus size: 3
195838 ACTTTTTTAA
195848 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT A
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT A
195891 AAATTAAAAG
Statistics
Matches: 40, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 40 1.00
ACGTcount: A:0.35, C:0.00, G:0.00, T:0.65
Consensus pattern (3 bp):
ATT
Found at i:196700 original size:2 final size:2
Alignment explanation
Indices: 196689--196726 Score: 60
Period size: 2 Copynumber: 19.5 Consensus size: 2
196679 TTTAGGATAC
*
196689 TA TA TA -A TA TA TA TA TA TA TA TA TA TA TA TA TG TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
196727 TCATTAAAGA
Statistics
Matches: 33, Mismatches: 2, Indels: 2
0.89 0.05 0.05
Matches are distributed among these distances:
1 1 0.03
2 32 0.97
ACGTcount: A:0.47, C:0.00, G:0.03, T:0.50
Consensus pattern (2 bp):
TA
Found at i:196812 original size:12 final size:12
Alignment explanation
Indices: 196795--196820 Score: 52
Period size: 12 Copynumber: 2.2 Consensus size: 12
196785 AAAAGAGTTA
196795 TTTTATAATTTT
1 TTTTATAATTTT
196807 TTTTATAATTTT
1 TTTTATAATTTT
196819 TT
1 TT
196821 ATACGATTTA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 14 1.00
ACGTcount: A:0.23, C:0.00, G:0.00, T:0.77
Consensus pattern (12 bp):
TTTTATAATTTT
Found at i:196956 original size:25 final size:26
Alignment explanation
Indices: 196907--196962 Score: 73
Period size: 26 Copynumber: 2.2 Consensus size: 26
196897 ATTAAATTAA
196907 AAATATTTTATTATTTATATGATA-T
1 AAATATTTTATTATTTATATGATATT
196932 AAATATTTTTAATTATTTAT-T-ATATT
1 AAATA-TTTT-ATTATTTATATGATATT
196958 AAATA
1 AAATA
196963 AGATAATATT
Statistics
Matches: 28, Mismatches: 0, Indels: 5
0.85 0.00 0.15
Matches are distributed among these distances:
25 8 0.29
26 11 0.39
27 9 0.32
ACGTcount: A:0.43, C:0.00, G:0.02, T:0.55
Consensus pattern (26 bp):
AAATATTTTATTATTTATATGATATT
Found at i:197511 original size:16 final size:16
Alignment explanation
Indices: 197464--197511 Score: 53
Period size: 16 Copynumber: 2.9 Consensus size: 16
197454 TTCAAATTTT
197464 TTTTATTTTAAATAAAA
1 TTTTA-TTTAAATAAAA
* *
197481 -TTAATTTATATTAAAA
1 TTTTATTTA-AATAAAA
197497 TTTTATTTAAATAAA
1 TTTTATTTAAATAAA
197512 TTAAAAGTTA
Statistics
Matches: 25, Mismatches: 4, Indels: 5
0.74 0.12 0.15
Matches are distributed among these distances:
15 4 0.16
16 14 0.56
17 7 0.28
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (16 bp):
TTTTATTTAAATAAAA
Found at i:198930 original size:20 final size:19
Alignment explanation
Indices: 198905--198962 Score: 55
Period size: 20 Copynumber: 2.9 Consensus size: 19
198895 AAAATAATAT
198905 TTAAATTTATTTTAATAAAA
1 TTAAATTTATTTTAA-AAAA
**
198925 TTAAATATTAATAGCTAAAAAA
1 TTAAAT-TT-AT-TTTAAAAAA
198947 -TAAATTTATTTTAAAA
1 TTAAATTTATTTTAAAA
198963 TAAAATTTAA
Statistics
Matches: 31, Mismatches: 4, Indels: 8
0.72 0.09 0.19
Matches are distributed among these distances:
18 5 0.16
19 2 0.06
20 8 0.26
21 7 0.23
22 6 0.19
23 3 0.10
ACGTcount: A:0.53, C:0.02, G:0.02, T:0.43
Consensus pattern (19 bp):
TTAAATTTATTTTAAAAAA
Found at i:199667 original size:2 final size:2
Alignment explanation
Indices: 199660--199686 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
199650 GTGGATGATT
199660 TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA T
199687 TTTTAATCTA
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 25 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:200710 original size:22 final size:21
Alignment explanation
Indices: 200649--200713 Score: 69
Period size: 22 Copynumber: 3.1 Consensus size: 21
200639 TTATGTATAA
200649 TAATATTTTATATAATA-TAT
1 TAATATTTTATATAATATTAT
* ** * *
200669 TAAAATAATAAATAAAATTAT
1 TAATATTTTATATAATATTAT
200690 TAATTATTTTATATAATATTAT
1 TAA-TATTTTATATAATATTAT
200712 TA
1 TA
200714 TATAAATAAT
Statistics
Matches: 33, Mismatches: 10, Indels: 2
0.73 0.22 0.04
Matches are distributed among these distances:
20 12 0.36
21 6 0.18
22 15 0.45
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (21 bp):
TAATATTTTATATAATATTAT
Found at i:200714 original size:13 final size:13
Alignment explanation
Indices: 200637--200718 Score: 51
Period size: 12 Copynumber: 7.0 Consensus size: 13
200627 TATTTAAAGT
200637 TATTATGTATAATAA
1 TATTAT-TAT-ATAA
200652 TATT-TTATATAA
1 TATTATTATATAA
200664 TA-TATTA-A-AA
1 TATTATTATATAA
*
200674 TA--A-TAAATAA
1 TATTATTATATAA
*
200684 AATTATTA-AT--
1 TATTATTATATAA
200694 TATT-TTATATAA
1 TATTATTATATAA
200706 TATTATTATATAA
1 TATTATTATATAA
200719 ATAATATATT
Statistics
Matches: 55, Mismatches: 2, Indels: 22
0.70 0.03 0.28
Matches are distributed among these distances:
8 2 0.04
9 5 0.09
10 12 0.22
11 2 0.04
12 16 0.29
13 13 0.24
14 1 0.02
15 4 0.07
ACGTcount: A:0.50, C:0.00, G:0.01, T:0.49
Consensus pattern (13 bp):
TATTATTATATAA
Found at i:201123 original size:2 final size:2
Alignment explanation
Indices: 201116--201170 Score: 56
Period size: 2 Copynumber: 27.5 Consensus size: 2
201106 TTAAAAGTAC
* * * *
201116 AT AT AT AT AT AT AT AT TT AT GT GT AT AT AT AT AT AT AT GT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
* *
201158 AT TT AT AT TT AT A
1 AT AT AT AT AT AT A
201171 GTATGGTTAC
Statistics
Matches: 43, Mismatches: 10, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
2 43 1.00
ACGTcount: A:0.40, C:0.00, G:0.05, T:0.55
Consensus pattern (2 bp):
AT
Found at i:201144 original size:16 final size:16
Alignment explanation
Indices: 201121--201174 Score: 63
Period size: 16 Copynumber: 3.2 Consensus size: 16
201111 AGTACATATA
201121 TATATATATATTTATGTG
1 TATATATATATTTA--TG
*
201139 TATATATATATATATG
1 TATATATATATTTATG
*
201155 TATATTTATATTTATAG
1 TATATATATATTTAT-G
201172 TAT
1 TAT
201175 GGTTACTAGG
Statistics
Matches: 32, Mismatches: 3, Indels: 3
0.84 0.08 0.08
Matches are distributed among these distances:
16 15 0.47
17 4 0.12
18 13 0.41
ACGTcount: A:0.37, C:0.00, G:0.07, T:0.56
Consensus pattern (16 bp):
TATATATATATTTATG
Found at i:201144 original size:18 final size:18
Alignment explanation
Indices: 201116--201174 Score: 70
Period size: 18 Copynumber: 3.4 Consensus size: 18
201106 TTAAAAGTAC
*
201116 ATATATATATATATATTT
1 ATATGTATATATATATTT
*
201134 ATGTGTATATATATA--T
1 ATATGTATATATATATTT
*
201150 ATATGTATATTTATATTT
1 ATATGTATATATATATTT
201168 ATA-GTAT
1 ATATGTAT
201175 GGTTACTAGG
Statistics
Matches: 35, Mismatches: 4, Indels: 5
0.80 0.09 0.11
Matches are distributed among these distances:
16 14 0.40
17 4 0.11
18 17 0.49
ACGTcount: A:0.39, C:0.00, G:0.07, T:0.54
Consensus pattern (18 bp):
ATATGTATATATATATTT
Found at i:201323 original size:11 final size:11
Alignment explanation
Indices: 201307--201401 Score: 78
Period size: 11 Copynumber: 9.1 Consensus size: 11
201297 TAATTATTTA
201307 TATATTTATAT
1 TATATTTATAT
201318 TATATTTATAT
1 TATATTTATAT
*
201329 TATAATTATA-
1 TATATTTATAT
* *
201339 TAAATTT-TAA
1 TATATTTATAT
201349 TATA-TT-TA-
1 TATATTTATAT
*
201357 TATATTTATGT
1 TATATTTATAT
*
201368 TATATTAATAT
1 TATATTTATAT
201379 TAT-TTTAT-T
1 TATATTTATAT
201388 TAAATATTTATAT
1 T--ATATTTATAT
201401 T
1 T
201402 GGAGTTAAAA
Statistics
Matches: 68, Mismatches: 8, Indels: 14
0.76 0.09 0.16
Matches are distributed among these distances:
8 4 0.06
9 10 0.15
10 13 0.19
11 34 0.50
12 5 0.07
13 2 0.03
ACGTcount: A:0.39, C:0.00, G:0.01, T:0.60
Consensus pattern (11 bp):
TATATTTATAT
Found at i:201371 original size:33 final size:33
Alignment explanation
Indices: 201318--201401 Score: 91
Period size: 33 Copynumber: 2.6 Consensus size: 33
201308 ATATTTATAT
* *
201318 TATATTTATAT-TATA-ATTATATAAATTTTAA
1 TATATTTATATATTTATATTATATAAATATTAA
* * *
201349 TATATTTATATATTTATGTTATATTAATATTAT
1 TATATTTATATATTTATATTATATAAATATTAA
* *
201382 TTTATTTAAATATTTATATT
1 TATATTTATATATTTATATT
201402 GGAGTTAAAA
Statistics
Matches: 43, Mismatches: 8, Indels: 2
0.81 0.15 0.04
Matches are distributed among these distances:
31 11 0.26
32 3 0.07
33 29 0.67
ACGTcount: A:0.39, C:0.00, G:0.01, T:0.60
Consensus pattern (33 bp):
TATATTTATATATTTATATTATATAAATATTAA
Found at i:202591 original size:7 final size:6
Alignment explanation
Indices: 202564--202589 Score: 52
Period size: 6 Copynumber: 4.3 Consensus size: 6
202554 ATTTGGAAAT
202564 AATAAA AATAAA AATAAA AATAAA AA
1 AATAAA AATAAA AATAAA AATAAA AA
202590 ATGGTTTATC
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 20 1.00
ACGTcount: A:0.85, C:0.00, G:0.00, T:0.15
Consensus pattern (6 bp):
AATAAA
Found at i:205048 original size:27 final size:28
Alignment explanation
Indices: 204998--205103 Score: 92
Period size: 27 Copynumber: 3.6 Consensus size: 28
204988 TTTATGATTT
**
204998 ATATATTTATATTATA-ATTTATTTTAAA
1 ATATATTTATATTATATA-AAATTTTAAA
205026 ATAT-TTTATATT-TATATAAATTTTAATAA
1 ATATATTTATATTATATA-AAATTTT-A-AA
205055 ATTAATAATTTATATTATATAAAATTTTAAA
1 A-T-AT-ATTTATATTATATAAAATTTTAAA
*
205086 TATATATTTTTATTATAT
1 -ATATATTTATATTATAT
205104 TATATTCATT
Statistics
Matches: 66, Mismatches: 3, Indels: 17
0.77 0.03 0.20
Matches are distributed among these distances:
26 2 0.03
27 15 0.23
28 5 0.08
29 15 0.23
30 3 0.05
31 5 0.08
32 2 0.03
33 15 0.23
34 4 0.06
ACGTcount: A:0.44, C:0.00, G:0.00, T:0.56
Consensus pattern (28 bp):
ATATATTTATATTATATAAAATTTTAAA
Found at i:205765 original size:21 final size:20
Alignment explanation
Indices: 205724--205788 Score: 58
Period size: 21 Copynumber: 3.0 Consensus size: 20
205714 AATTTAAATT
* *
205724 ATTATTTAATTTATAAAATAA
1 ATTATTTAAATT-TAATATAA
205745 ATTATTTAAATTTAATTATAAA
1 ATTATTTAAATTTAA-TAT-AA
* *
205767 AATATATAAATTTTAATATAA
1 ATTATTTAAA-TTTAATATAA
205788 A
1 A
205789 AATATTTTTT
Statistics
Matches: 37, Mismatches: 4, Indels: 6
0.79 0.09 0.13
Matches are distributed among these distances:
20 3 0.08
21 16 0.43
22 13 0.35
23 5 0.14
ACGTcount: A:0.54, C:0.00, G:0.00, T:0.46
Consensus pattern (20 bp):
ATTATTTAAATTTAATATAA
Found at i:205776 original size:22 final size:22
Alignment explanation
Indices: 205751--205793 Score: 70
Period size: 22 Copynumber: 2.0 Consensus size: 22
205741 ATAAATTATT
205751 TAAA-TTTAATTATAAAAATATA
1 TAAATTTTAA-TATAAAAATATA
205773 TAAATTTTAATATAAAAATAT
1 TAAATTTTAATATAAAAATAT
205794 TTTTTAAATA
Statistics
Matches: 20, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
22 15 0.75
23 5 0.25
ACGTcount: A:0.58, C:0.00, G:0.00, T:0.42
Consensus pattern (22 bp):
TAAATTTTAATATAAAAATATA
Found at i:206261 original size:17 final size:18
Alignment explanation
Indices: 206241--206302 Score: 56
Period size: 17 Copynumber: 3.3 Consensus size: 18
206231 TTTAAATATG
206241 ATATAAAAATAATTAA-A
1 ATATAAAAATAATTAAGA
* *
206258 ATATAAAATAAAATTTAATATA
1 ATATAAAA-ATAA-TT-A-AGA
206280 ATATAAAAATAA-TAAGA
1 ATATAAAAATAATTAAGA
206297 ATATAA
1 ATATAA
206303 CAAAATTTAT
Statistics
Matches: 37, Mismatches: 3, Indels: 10
0.74 0.06 0.20
Matches are distributed among these distances:
17 16 0.43
18 4 0.11
19 3 0.08
20 1 0.03
21 4 0.11
22 9 0.24
ACGTcount: A:0.68, C:0.00, G:0.02, T:0.31
Consensus pattern (18 bp):
ATATAAAAATAATTAAGA
Found at i:206284 original size:39 final size:37
Alignment explanation
Indices: 206235--206322 Score: 117
Period size: 39 Copynumber: 2.4 Consensus size: 37
206225 GATAATTTTA
* *
206235 AATATGATATAAAAATAATTAA-AATATAAAATAAAATTT
1 AATATAATATAAAAATAA-TAAGAATAT--AACAAAATTT
206274 AATATAATATAAAAATAATAAGAATATAACAAAATTT
1 AATATAATATAAAAATAATAAGAATATAACAAAATTT
206311 -ATATAATATAAA
1 AATATAATATAAA
206323 TTATTAATGA
Statistics
Matches: 46, Mismatches: 2, Indels: 5
0.87 0.04 0.09
Matches are distributed among these distances:
36 12 0.26
37 9 0.20
38 3 0.07
39 22 0.48
ACGTcount: A:0.65, C:0.01, G:0.02, T:0.32
Consensus pattern (37 bp):
AATATAATATAAAAATAATAAGAATATAACAAAATTT
Found at i:206302 original size:22 final size:21
Alignment explanation
Indices: 206234--206302 Score: 65
Period size: 22 Copynumber: 3.4 Consensus size: 21
206224 AGATAATTTT
*
206234 AAATATGATATAAAAATAATTA
1 AAATATAATATAAAAATAA-TA
*
206256 AAATATAAAAT-AAAAT--T-
1 AAATATAATATAAAAATAATA
*
206273 TAATATAATATAAAAATAATA
1 AAATATAATATAAAAATAATA
206294 AGAATATAA
1 A-AATATAA
206303 CAAAATTTAT
Statistics
Matches: 37, Mismatches: 5, Indels: 10
0.71 0.10 0.19
Matches are distributed among these distances:
17 9 0.24
18 6 0.16
20 1 0.03
21 5 0.14
22 16 0.43
ACGTcount: A:0.67, C:0.00, G:0.03, T:0.30
Consensus pattern (21 bp):
AAATATAATATAAAAATAATA
Found at i:206318 original size:19 final size:18
Alignment explanation
Indices: 206267--206322 Score: 53
Period size: 19 Copynumber: 3.1 Consensus size: 18
206257 AATATAAAAT
206267 AAAATTTAATATAATAT-A
1 AAAATTT-ATATAATATAA
* *
206285 AAAA-TAATAAGAATATAA
1 AAAATTTAT-ATAATATAA
206303 CAAAATTTATATAATATAA
1 -AAAATTTATATAATATAA
206322 A
1 A
206323 TTATTAATGA
Statistics
Matches: 30, Mismatches: 4, Indels: 8
0.71 0.10 0.19
Matches are distributed among these distances:
16 2 0.07
17 7 0.23
18 6 0.20
19 12 0.40
20 3 0.10
ACGTcount: A:0.64, C:0.02, G:0.02, T:0.32
Consensus pattern (18 bp):
AAAATTTATATAATATAA
Found at i:207489 original size:23 final size:23
Alignment explanation
Indices: 207453--207504 Score: 61
Period size: 23 Copynumber: 2.3 Consensus size: 23
207443 TGTTATATTT
*
207453 TATAATTTAAATTAT-TATATGAA
1 TATAATTTAAATTATATATA-AAA
**
207476 TATAATTTTTATTATATATAAAA
1 TATAATTTAAATTATATATAAAA
207499 TATAAT
1 TATAAT
207505 GGAAAGAGTA
Statistics
Matches: 25, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
23 21 0.84
24 4 0.16
ACGTcount: A:0.48, C:0.00, G:0.02, T:0.50
Consensus pattern (23 bp):
TATAATTTAAATTATATATAAAA
Found at i:208986 original size:17 final size:17
Alignment explanation
Indices: 208954--208993 Score: 57
Period size: 16 Copynumber: 2.4 Consensus size: 17
208944 TATTTTTATT
208954 AAATA-TAATTATAAAA
1 AAATATTAATTATAAAA
208970 AAATATTAA-TATAAAA
1 AAATATTAATTATAAAA
208986 ATAATATT
1 A-AATATT
208994 TTAATATTAT
Statistics
Matches: 22, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
16 13 0.59
17 9 0.41
ACGTcount: A:0.65, C:0.00, G:0.00, T:0.35
Consensus pattern (17 bp):
AAATATTAATTATAAAA
Found at i:210553 original size:175 final size:176
Alignment explanation
Indices: 210218--210569 Score: 697
Period size: 175 Copynumber: 2.0 Consensus size: 176
210208 TTGTTCTATG
210218 GGTTTGTTTATCTAATTGTAGATTTGGGTAGCTGTTAATTTTTTATTTGTTTTGGAATTTTTTTC
1 GGTTTGTTTATCTAATTGTAGATTTGGGTAGCTGTTAATTTTTTATTTGTTTTGGAATTTTTTTC
210283 ATTACTGTTATATTTGATGTAAAATACGTATTTTTGTACCTAGCTTGAGTATATGTTTCGCAATT
66 ATTACTGTTATATTTGATGTAAAATACGTATTTTTGTACCTAGCTTGAGTATATGTTTCGCAATT
210348 TGAAGCATGTTGTTGTGGCTATCTTATGATGTTCTAGTTTTATGAT
131 TGAAGCATGTTGTTGTGGCTATCTTATGATGTTCTAGTTTTATGAT
210394 GGTTTGTTTATCTAATTGTAGATTTGGGTAGCTGTTAATTTTTTATTTGTTTTGGAATTTTTTTC
1 GGTTTGTTTATCTAATTGTAGATTTGGGTAGCTGTTAATTTTTTATTTGTTTTGGAATTTTTTTC
210459 ATTACTGTTATATTT-ATGTAAAATACGTATTTTTGTACCTAGCTTGAGTATATGTTTCGCAATT
66 ATTACTGTTATATTTGATGTAAAATACGTATTTTTGTACCTAGCTTGAGTATATGTTTCGCAATT
210523 TGAAGCATGTTGTTGTGGCTATCTTATGATGTTCTAGTTTTATGAT
131 TGAAGCATGTTGTTGTGGCTATCTTATGATGTTCTAGTTTTATGAT
210569 G
1 G
210570 AATATTCTGC
Statistics
Matches: 176, Mismatches: 0, Indels: 1
0.99 0.00 0.01
Matches are distributed among these distances:
175 96 0.55
176 80 0.45
ACGTcount: A:0.22, C:0.08, G:0.19, T:0.51
Consensus pattern (176 bp):
GGTTTGTTTATCTAATTGTAGATTTGGGTAGCTGTTAATTTTTTATTTGTTTTGGAATTTTTTTC
ATTACTGTTATATTTGATGTAAAATACGTATTTTTGTACCTAGCTTGAGTATATGTTTCGCAATT
TGAAGCATGTTGTTGTGGCTATCTTATGATGTTCTAGTTTTATGAT
Found at i:210869 original size:213 final size:213
Alignment explanation
Indices: 210497--210916 Score: 813
Period size: 213 Copynumber: 2.0 Consensus size: 213
210487 ATTTTTGTAC
210497 CTAGCTTGAGTATATGTTTCGCAATTTGAAGCATGTTGTTGTGGCTATCTTATGATGTTCTAGTT
1 CTAGCTTGAGTATATGTTTCGCAATTTGAAGCATGTTGTTGTGGCTATCTTATGATGTTCTAGTT
210562 TTATGATGAATATTCTGCTTTATTAATGATTATTAAGTAAAATTATACGGATTTTGCTAACAATT
66 TTATGATGAATATTCTGCTTTATTAATGATTATTAAGTAAAATTATACGGATTTTGCTAACAATT
*
210627 TCCTAATGATACTTTTTACATTTACCATATAGAGTAATATCTTTATCCGATGCATTGAAAATGGC
131 TCCTAAGGATACTTTTTACATTTACCATATAGAGTAATATCTTTATCCGATGCATTGAAAATGGC
210692 AAATAAAATTGCGATGTT
196 AAATAAAATTGCGATGTT
*
210710 CTAGTTTGAGTATATGTTTCGCAATTTGAAGCATGTTGTTGTGGCTATCTTATGATGTTCTAGTT
1 CTAGCTTGAGTATATGTTTCGCAATTTGAAGCATGTTGTTGTGGCTATCTTATGATGTTCTAGTT
210775 TTATGATGAATATTCTGCTTTATTAATGATTATTAAGTAAAATTATACGGATTTTGCTAACAATT
66 TTATGATGAATATTCTGCTTTATTAATGATTATTAAGTAAAATTATACGGATTTTGCTAACAATT
*
210840 TCCTAAGGATACTTTTTACATTTACCATATAGAGTAATGTCTTTATCCGATGCATTGAAAATGGC
131 TCCTAAGGATACTTTTTACATTTACCATATAGAGTAATATCTTTATCCGATGCATTGAAAATGGC
210905 AAATAAAATTGC
196 AAATAAAATTGC
210917 CAAATACTGC
Statistics
Matches: 204, Mismatches: 3, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
213 204 1.00
ACGTcount: A:0.30, C:0.12, G:0.16, T:0.42
Consensus pattern (213 bp):
CTAGCTTGAGTATATGTTTCGCAATTTGAAGCATGTTGTTGTGGCTATCTTATGATGTTCTAGTT
TTATGATGAATATTCTGCTTTATTAATGATTATTAAGTAAAATTATACGGATTTTGCTAACAATT
TCCTAAGGATACTTTTTACATTTACCATATAGAGTAATATCTTTATCCGATGCATTGAAAATGGC
AAATAAAATTGCGATGTT
Found at i:214657 original size:20 final size:21
Alignment explanation
Indices: 214622--214681 Score: 68
Period size: 21 Copynumber: 2.8 Consensus size: 21
214612 TGATTCAAAT
* *
214622 ATTGAAAAGCTTTAAAAT-TTA
1 ATTGAAAA-ATTTAAAATATGA
*
214643 ATTGAAAATTTTAAAATATGA
1 ATTGAAAAATTTAAAATATGA
214664 ATTGAAATAATTTAAAAT
1 ATTGAAA-AATTTAAAAT
214682 CAACCGGATT
Statistics
Matches: 34, Mismatches: 3, Indels: 3
0.85 0.08 0.08
Matches are distributed among these distances:
20 8 0.24
21 17 0.50
22 9 0.26
ACGTcount: A:0.52, C:0.02, G:0.08, T:0.38
Consensus pattern (21 bp):
ATTGAAAAATTTAAAATATGA
Found at i:216519 original size:15 final size:16
Alignment explanation
Indices: 216499--216532 Score: 52
Period size: 16 Copynumber: 2.2 Consensus size: 16
216489 ATTTTTCTTA
216499 TTTTTCTCT-CTTTTT
1 TTTTTCTCTGCTTTTT
*
216514 TTTTTCTTTGCTTTTT
1 TTTTTCTCTGCTTTTT
216530 TTT
1 TTT
216533 CTTTCTTTCT
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
15 8 0.47
16 9 0.53
ACGTcount: A:0.00, C:0.15, G:0.03, T:0.82
Consensus pattern (16 bp):
TTTTTCTCTGCTTTTT
Found at i:216528 original size:14 final size:13
Alignment explanation
Indices: 216492--216540 Score: 55
Period size: 14 Copynumber: 3.5 Consensus size: 13
216482 ACAAATAATT
216492 TTTCTTATTTTTCTC
1 TTTCTT-TTTTT-TC
216507 TCTT-TTTTTTTTC
1 T-TTCTTTTTTTTC
216520 TTTGCTTTTTTTTC
1 TTT-CTTTTTTTTC
216534 TTTCTTT
1 TTTCTTT
216541 CTTCCCCACC
Statistics
Matches: 31, Mismatches: 0, Indels: 8
0.79 0.00 0.21
Matches are distributed among these distances:
12 2 0.06
13 7 0.23
14 17 0.55
15 3 0.10
16 2 0.06
ACGTcount: A:0.02, C:0.16, G:0.02, T:0.80
Consensus pattern (13 bp):
TTTCTTTTTTTTC
Done.