Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold148
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: 1464219
ACGTcount: A:0.32, C:0.15, G:0.15, T:0.32
Warning! 85296 characters in sequence are not A, C, G, or T
File 1 of 9
Found at i:1592 original size:2 final size:2
Alignment explanation
Indices: 1585--1610 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
1575 TTGATGACAA
1585 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
1611 TTGTTACATG
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 24 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:4183 original size:13 final size:13
Alignment explanation
Indices: 4165--4189 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
4155 ATTAACTTTT
4165 CTATTATATAATG
1 CTATTATATAATG
4178 CTATTATATAAT
1 CTATTATATAAT
4190 ATTGAAATTG
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:0.40, C:0.08, G:0.04, T:0.48
Consensus pattern (13 bp):
CTATTATATAATG
Found at i:4591 original size:13 final size:13
Alignment explanation
Indices: 4573--4597 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
4563 ACGATTAAAG
4573 CGTGTCATGTTTT
1 CGTGTCATGTTTT
4586 CGTGTCATGTTT
1 CGTGTCATGTTT
4598 AAAATTGCCA
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:0.08, C:0.16, G:0.24, T:0.52
Consensus pattern (13 bp):
CGTGTCATGTTTT
Found at i:8049 original size:23 final size:22
Alignment explanation
Indices: 8022--8064 Score: 59
Period size: 23 Copynumber: 1.9 Consensus size: 22
8012 ATATCGTATA
*
8022 TTTATATTATATTTTAATTATTT
1 TTTATATTAAATTTT-ATTATTT
*
8045 TTTATTTTAAATTTTATTAT
1 TTTATATTAAATTTTATTAT
8065 ATAATCAGAT
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
22 5 0.28
23 13 0.72
ACGTcount: A:0.30, C:0.00, G:0.00, T:0.70
Consensus pattern (22 bp):
TTTATATTAAATTTTATTATTT
Found at i:15927 original size:16 final size:16
Alignment explanation
Indices: 15906--15945 Score: 71
Period size: 16 Copynumber: 2.5 Consensus size: 16
15896 ATAGTTCATG
15906 TTCAAAACAATTTTTA
1 TTCAAAACAATTTTTA
15922 TTCAAAACAATTTTTA
1 TTCAAAACAATTTTTA
*
15938 TTTAAAAC
1 TTCAAAAC
15946 GACAAATTCA
Statistics
Matches: 23, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
16 23 1.00
ACGTcount: A:0.45, C:0.12, G:0.00, T:0.42
Consensus pattern (16 bp):
TTCAAAACAATTTTTA
Found at i:16945 original size:17 final size:17
Alignment explanation
Indices: 16923--16957 Score: 70
Period size: 17 Copynumber: 2.1 Consensus size: 17
16913 AAGGGAAGAA
16923 CTCAACCATCTTAATAC
1 CTCAACCATCTTAATAC
16940 CTCAACCATCTTAATAC
1 CTCAACCATCTTAATAC
16957 C
1 C
16958 ATCCTTTCAT
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 18 1.00
ACGTcount: A:0.34, C:0.37, G:0.00, T:0.29
Consensus pattern (17 bp):
CTCAACCATCTTAATAC
Found at i:19111 original size:19 final size:19
Alignment explanation
Indices: 19087--19123 Score: 74
Period size: 19 Copynumber: 1.9 Consensus size: 19
19077 TAACCATTCT
19087 TCTGTGTTGTAAAGAGATC
1 TCTGTGTTGTAAAGAGATC
19106 TCTGTGTTGTAAAGAGAT
1 TCTGTGTTGTAAAGAGAT
19124 TTTTGCCAAT
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 18 1.00
ACGTcount: A:0.27, C:0.08, G:0.27, T:0.38
Consensus pattern (19 bp):
TCTGTGTTGTAAAGAGATC
Found at i:19865 original size:57 final size:55
Alignment explanation
Indices: 19771--19888 Score: 129
Period size: 57 Copynumber: 2.1 Consensus size: 55
19761 TCTTAAAATT
* *
19771 TTTAGATTTATATAATTTTTAATTAAGTTAATCAAATTTGATAGTTAAATTATTTGAG
1 TTTAGATTTATATAATTTTTAATTAAGTAAATCAAATTT-A-A-ATAAATTATTTGAG
*
19829 TTTA-ATTTAT-TAATTTTATAATTAA-TAAGATTAAATTTAAATAAATTATTTGA-
1 TTTAGATTTATATAATTTT-TAATTAAGTAA-ATCAAATTTAAATAAATTATTTGAG
19882 -TTAGATT
1 TTTAGATT
19889 AAATTTAATT
Statistics
Matches: 54, Mismatches: 3, Indels: 11
0.79 0.04 0.16
Matches are distributed among these distances:
52 3 0.06
53 3 0.06
54 12 0.22
55 1 0.02
56 10 0.19
57 21 0.39
58 4 0.07
ACGTcount: A:0.41, C:0.01, G:0.08, T:0.51
Consensus pattern (55 bp):
TTTAGATTTATATAATTTTTAATTAAGTAAATCAAATTTAAATAAATTATTTGAG
Found at i:19926 original size:23 final size:23
Alignment explanation
Indices: 19900--19943 Score: 70
Period size: 23 Copynumber: 1.9 Consensus size: 23
19890 AATTTAATTA
* *
19900 AAATTATATTAAAAATAAATAAT
1 AAATAATATAAAAAATAAATAAT
19923 AAATAATATAAAAAATAAATA
1 AAATAATATAAAAAATAAATA
19944 TAGTAGTTGT
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:0.70, C:0.00, G:0.00, T:0.30
Consensus pattern (23 bp):
AAATAATATAAAAAATAAATAAT
Found at i:22935 original size:2 final size:2
Alignment explanation
Indices: 22928--22977 Score: 93
Period size: 2 Copynumber: 25.5 Consensus size: 2
22918 AAGCTTTTAC
22928 AT 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 AT
22970 AT AT -T AT A
1 AT AT AT AT A
22978 GATTATAGAT
Statistics
Matches: 47, Mismatches: 0, Indels: 2
0.96 0.00 0.04
Matches are distributed among these distances:
1 1 0.02
2 46 0.98
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:23122 original size:16 final size:17
Alignment explanation
Indices: 23086--23123 Score: 53
Period size: 16 Copynumber: 2.3 Consensus size: 17
23076 ACATGTTAAA
23086 AATTTAAATGTATATTT
1 AATTTAAATGTATATTT
23103 AATTT-AAT-TATATATT
1 AATTTAAATGTATAT-TT
23119 AATTT
1 AATTT
23124 TTAAATAAAT
Statistics
Matches: 20, Mismatches: 0, Indels: 3
0.87 0.00 0.13
Matches are distributed among these distances:
15 5 0.25
16 10 0.50
17 5 0.25
ACGTcount: A:0.42, C:0.00, G:0.03, T:0.55
Consensus pattern (17 bp):
AATTTAAATGTATATTT
Found at i:23170 original size:29 final size:29
Alignment explanation
Indices: 23123--23178 Score: 78
Period size: 30 Copynumber: 1.9 Consensus size: 29
23113 TATATTAATT
* *
23123 TTTAAATAAATTTA-TTAAATTATTTTTA
1 TTTAAATAAATTAAGTAAAATTATTTTTA
23151 TTTACAATAAATTAAGTAAAATTATTTT
1 TTTA-AATAAATTAAGTAAAATTATTTT
23179 AAAAATTTTA
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
28 4 0.17
29 9 0.38
30 11 0.46
ACGTcount: A:0.45, C:0.02, G:0.02, T:0.52
Consensus pattern (29 bp):
TTTAAATAAATTAAGTAAAATTATTTTTA
Found at i:23628 original size:13 final size:11
Alignment explanation
Indices: 23604--23642 Score: 53
Period size: 11 Copynumber: 3.5 Consensus size: 11
23594 TCATTAAAAT
*
23604 ATAATTTTATA
1 ATAATTTTAAA
23615 ATAA-TTTAAA
1 ATAATTTTAAA
23625 ATAATTTTAAA
1 ATAATTTTAAA
23636 ATTAATT
1 A-TAATT
23643 ATATATTATC
Statistics
Matches: 25, Mismatches: 1, Indels: 3
0.86 0.03 0.10
Matches are distributed among these distances:
10 9 0.36
11 11 0.44
12 5 0.20
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (11 bp):
ATAATTTTAAA
Found at i:24569 original size:12 final size:12
Alignment explanation
Indices: 24552--24576 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
24542 TTACTATCTA
24552 TTAAAAAAAAAT
1 TTAAAAAAAAAT
24564 TTAAAAAAAAAT
1 TTAAAAAAAAAT
24576 T
1 T
24577 CTTCCCTCAA
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:0.72, C:0.00, G:0.00, T:0.28
Consensus pattern (12 bp):
TTAAAAAAAAAT
Found at i:24922 original size:26 final size:26
Alignment explanation
Indices: 24886--24935 Score: 75
Period size: 26 Copynumber: 1.9 Consensus size: 26
24876 AGTATCCAAT
24886 TAGTTTCAGTTGATT-TCAATTCTTAA
1 TAGTTTCAGTTGATTAT-AATTCTTAA
*
24912 TAGTTTCAGTTTATTATAATTCTT
1 TAGTTTCAGTTGATTATAATTCTT
24936 CATTTCTTAA
Statistics
Matches: 22, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
26 21 0.95
27 1 0.05
ACGTcount: A:0.26, C:0.10, G:0.10, T:0.54
Consensus pattern (26 bp):
TAGTTTCAGTTGATTATAATTCTTAA
Found at i:34524 original size:2 final size:2
Alignment explanation
Indices: 34517--34552 Score: 72
Period size: 2 Copynumber: 18.0 Consensus size: 2
34507 TCTATCTCAT
34517 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
34553 AAAGAAATGT
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 34 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:34842 original size:36 final size:35
Alignment explanation
Indices: 34802--34913 Score: 92
Period size: 36 Copynumber: 3.3 Consensus size: 35
34792 TTATATTTAT
34802 ATTTTTATATATTTTAAATAATAAAAATTTACATAA
1 ATTTTTATATATTTTAAATAATAAAAATTTA-ATAA
** *
34838 A-TTTT-TATATTTT-AATAAT--TTATTTAGTAA
1 ATTTTTATATATTTTAAATAATAAAAATTTAATAA
* * *
34868 ATTTTAATATA-TTTAAAGTATTAAAAATTTTTATAA
1 ATTTTTATATATTTTAAA-TAATAAAAA-TTTAATAA
*
34904 AATTTTATAT
1 ATTTTTATAT
34914 TTAAATAATT
Statistics
Matches: 58, Mismatches: 11, Indels: 14
0.70 0.13 0.17
Matches are distributed among these distances:
30 4 0.07
31 11 0.19
32 6 0.10
33 9 0.16
34 8 0.14
35 5 0.09
36 15 0.26
ACGTcount: A:0.45, C:0.01, G:0.02, T:0.53
Consensus pattern (35 bp):
ATTTTTATATATTTTAAATAATAAAAATTTAATAA
Found at i:34893 original size:66 final size:64
Alignment explanation
Indices: 34779--34950 Score: 197
Period size: 66 Copynumber: 2.6 Consensus size: 64
34769 ATAAAAAAAA
* * *
34779 TTATATGTTAAT-ATTATATTTAT--ATTTTTATATATTTTAAATAATAAAAATTTACATAAATT
1 TTATATTTTAATAATT-TATTTATAAATTTTAATATA-TTTAAATAATAAAAATTTACATAAAAT
34841 T
64 T
* **
34842 TTATATTTTAATAATTTATTTAGTAAATTTTAATATATTTAAAGTATTAAAAATTTTTATAAAAT
1 TTATATTTTAATAATTTATTTA-TAAATTTTAATATATTTAAA-TAATAAAAATTTACATAAAAT
34907 T
64 T
*
34908 TTATATTTAAATAATTTATTTTATATAAATTTTAATATATTTA
1 TTATATTTTAATAATTTA--TT-TATAAATTTTAATATATTTA
34951 TGTATTTATA
Statistics
Matches: 94, Mismatches: 7, Indels: 11
0.84 0.06 0.10
Matches are distributed among these distances:
63 17 0.18
64 4 0.04
65 6 0.06
66 45 0.48
68 20 0.21
69 2 0.02
ACGTcount: A:0.43, C:0.01, G:0.02, T:0.55
Consensus pattern (64 bp):
TTATATTTTAATAATTTATTTATAAATTTTAATATATTTAAATAATAAAAATTTACATAAAATT
Found at i:34916 original size:16 final size:15
Alignment explanation
Indices: 34896--34941 Score: 51
Period size: 15 Copynumber: 3.0 Consensus size: 15
34886 TATTAAAAAT
34896 TTTTATAAAATTTTA
1 TTTTATAAAATTTTA
34911 TATTTA-AATAA-TTTA
1 T-TTTATAA-AATTTTA
34926 TTTTATATAAATTTTA
1 TTTTATA-AAATTTTA
34942 ATATATTTAT
Statistics
Matches: 26, Mismatches: 0, Indels: 9
0.74 0.00 0.26
Matches are distributed among these distances:
14 4 0.15
15 11 0.42
16 11 0.42
ACGTcount: A:0.41, C:0.00, G:0.00, T:0.59
Consensus pattern (15 bp):
TTTTATAAAATTTTA
Found at i:34968 original size:28 final size:28
Alignment explanation
Indices: 34927--35013 Score: 81
Period size: 28 Copynumber: 3.1 Consensus size: 28
34917 AATAATTTAT
* *
34927 TTTATATAAATTTTAATATATTTAT-GTA
1 TTTATAT-TATTTTTATATATTTATAGTA
34955 TTTATATTATTTTTATATTATTT-TAGTA
1 TTTATATTATTTTTATA-TATTTATAGTA
* *
34983 TTATGATATT-TTTTTATATGTTTAAAGTA
1 TT-T-ATATTATTTTTATATATTTATAGTA
35012 TT
1 TT
35014 ATAAATTTAT
Statistics
Matches: 50, Mismatches: 4, Indels: 9
0.79 0.06 0.14
Matches are distributed among these distances:
27 9 0.18
28 21 0.42
29 15 0.30
30 5 0.10
ACGTcount: A:0.32, C:0.00, G:0.06, T:0.62
Consensus pattern (28 bp):
TTTATATTATTTTTATATATTTATAGTA
Found at i:35001 original size:68 final size:68
Alignment explanation
Indices: 34802--34950 Score: 205
Period size: 66 Copynumber: 2.2 Consensus size: 68
34792 TTATATTTAT
* * ** * *
34802 ATTTTTATATATTTTAAA-TAATAAAAATTTACATAAATTTTTATATTTTAATAATTTA-TTTA-
1 ATTTTAATATA-TTTAAAGTATTAAAAATTTTTATAAAATTTTATATTTAAATAATTTATTTTAT
*
34864 GTAA
65 ATAA
34868 ATTTTAATATATTTAAAGTATTAAAAATTTTTATAAAATTTTATATTTAAATAATTTATTTTATA
1 ATTTTAATATATTTAAAGTATTAAAAATTTTTATAAAATTTTATATTTAAATAATTTATTTTATA
34933 TAA
66 TAA
34936 ATTTTAATATATTTA
1 ATTTTAATATATTTA
34951 TGTATTTATA
Statistics
Matches: 73, Mismatches: 7, Indels: 4
0.87 0.08 0.05
Matches are distributed among these distances:
65 6 0.08
66 45 0.62
67 4 0.05
68 18 0.25
ACGTcount: A:0.44, C:0.01, G:0.01, T:0.54
Consensus pattern (68 bp):
ATTTTAATATATTTAAAGTATTAAAAATTTTTATAAAATTTTATATTTAAATAATTTATTTTATA
TAA
Found at i:35089 original size:24 final size:22
Alignment explanation
Indices: 35060--35133 Score: 73
Period size: 22 Copynumber: 3.2 Consensus size: 22
35050 TTTTATGTGA
35060 ATTTTAATATATTTATATATTTAT
1 ATTTTAATATATTT-T-TATTTAT
35084 ATTTT-ATCATATTTTT-TTATAGT
1 ATTTTAAT-ATATTTTTATT-TA-T
35107 ATTTTAAT-TATTTTTATGTTAT
1 ATTTTAATATATTTTTAT-TTAT
35129 ATTTT
1 ATTTT
35134 TATCGTGTCA
Statistics
Matches: 44, Mismatches: 0, Indels: 14
0.76 0.00 0.24
Matches are distributed among these distances:
21 2 0.05
22 16 0.36
23 12 0.27
24 14 0.32
ACGTcount: A:0.30, C:0.01, G:0.03, T:0.66
Consensus pattern (22 bp):
ATTTTAATATATTTTTATTTAT
Found at i:35121 original size:124 final size:125
Alignment explanation
Indices: 34868--35123 Score: 315
Period size: 124 Copynumber: 2.1 Consensus size: 125
34858 TATTTAGTAA
* * * *
34868 ATTTTAATATATTTAAAGTATTAAAAATTTTTATAAAATTTTATATTTAAATAATTTATTTTATA
1 ATTTTTATATATTTAAAGTATTAAAAATTTATATAAAATTTTACATGTAAATAATTTATTTTATA
* * *
34933 TAAATTTTAATATATTTATGTATTTATATTATTTTTATATTATTTTAGTATTATGATATT
66 TAAATTTTAATATATTTATATATTTATATTATTATCATATTATTTTAGTATTATGATATT
* * * *
34993 -TTTTTATATGTTTAAAGTATTATAAATTTATATAGATTTTTACATAGTAAA-AATTTATTTTAT
1 ATTTTTATATATTTAAAGTATTAAAAATTTATATAAAATTTTACAT-GTAAATAATTTATTTTAT
* * * *
35056 GTGAATTTTAATATATTTATATATTTATATT-TTATCATATTTTTTTATAGTATT-TTA-ATT
65 ATAAATTTTAATATATTTATATATTTATATTATTATCATA-TTATTT-TAGTATTATGATATT
35116 ATTTTTAT
1 ATTTTTAT
35124 GTTATATTTT
Statistics
Matches: 112, Mismatches: 15, Indels: 9
0.82 0.11 0.07
Matches are distributed among these distances:
123 9 0.08
124 92 0.82
125 11 0.10
ACGTcount: A:0.37, C:0.01, G:0.04, T:0.58
Consensus pattern (125 bp):
ATTTTTATATATTTAAAGTATTAAAAATTTATATAAAATTTTACATGTAAATAATTTATTTTATA
TAAATTTTAATATATTTATATATTTATATTATTATCATATTATTTTAGTATTATGATATT
Found at i:36246 original size:18 final size:19
Alignment explanation
Indices: 36225--36262 Score: 51
Period size: 18 Copynumber: 2.1 Consensus size: 19
36215 AATTTATATT
36225 AAATTAAATTT-AAATTAA
1 AAATTAAATTTAAAATTAA
**
36243 AAATTTTATTTAAAATTAA
1 AAATTAAATTTAAAATTAA
36262 A
1 A
36263 TTTGAGTTAA
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
18 9 0.53
19 8 0.47
ACGTcount: A:0.58, C:0.00, G:0.00, T:0.42
Consensus pattern (19 bp):
AAATTAAATTTAAAATTAA
Found at i:36273 original size:30 final size:30
Alignment explanation
Indices: 36206--36265 Score: 88
Period size: 30 Copynumber: 2.0 Consensus size: 30
36196 ATTTTATTAA
*
36206 TAAATTAATAA-TTTATATTAAATTAAATT
1 TAAATTAAAAATTTTATATTAAATTAAATT
36235 TAAATTAAAAATTTTAT-TTAAAATTAAATT
1 TAAATTAAAAATTTTATATT-AAATTAAATT
36265 T
1 T
36266 GAGTTAAATT
Statistics
Matches: 28, Mismatches: 1, Indels: 3
0.88 0.03 0.09
Matches are distributed among these distances:
29 12 0.43
30 16 0.57
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (30 bp):
TAAATTAAAAATTTTATATTAAATTAAATT
Found at i:36350 original size:11 final size:11
Alignment explanation
Indices: 36326--36483 Score: 63
Period size: 11 Copynumber: 15.3 Consensus size: 11
36316 TAAATTTAAA
36326 ATTTA-ATT-T
1 ATTTATATTAT
36335 ATTTATATTAT
1 ATTTATATTAT
36346 ATTTATA-TAT
1 ATTTATATTAT
36356 ATTTATGTATTAT
1 ATTTA--TATTAT
* * *
36369 AATTAAATCTAA
1 ATTTATAT-TAT
* *
36381 AATAATA-TAT
1 ATTTATATTAT
*
36391 ATTTATA-TAA
1 ATTTATATTAT
*
36401 ATTT-TAATAT
1 ATTTATATTAT
* *
36411 ATTAATAATAT
1 ATTTATATTAT
36422 A-TTATA-TA-
1 ATTTATATTAT
* *
36430 ATTT-TA-AAA
1 ATTTATATTAT
36439 ATTT-TA-TAT
1 ATTTATATTAT
*
36448 ATTTTTATTAT
1 ATTTATATTAT
*
36459 TTTTATATTAT
1 ATTTATATTAT
* *
36470 TTTTATATTTT
1 ATTTATATTAT
36481 ATT
1 ATT
36484 ACGTCAGAGG
Statistics
Matches: 118, Mismatches: 19, Indels: 22
0.74 0.12 0.14
Matches are distributed among these distances:
8 4 0.03
9 22 0.19
10 35 0.30
11 41 0.35
12 9 0.08
13 7 0.06
ACGTcount: A:0.41, C:0.01, G:0.01, T:0.58
Consensus pattern (11 bp):
ATTTATATTAT
Found at i:36358 original size:10 final size:10
Alignment explanation
Indices: 36334--36482 Score: 60
Period size: 10 Copynumber: 14.7 Consensus size: 10
36324 AAATTTAATT
36334 TATTTATATTA
1 TATTTATA-TA
36345 TATTTATATA
1 TATTTATATA
36355 TATTTATGTATTA
1 TATTTA--TA-TA
* *
36368 TAATTAAATCTA
1 T-ATT-TATATA
* * *
36380 AAATAATATA
1 TATTTATATA
36390 TATTTATATA
1 TATTTATATA
*
36400 AATTT-TAATA
1 TATTTAT-ATA
*
36410 TATTAATA-A
1 TATTTATATA
36419 TATATTATATA
1 TAT-TTATATA
*
36430 -ATTT-TAAA
1 TATTTATATA
*
36438 AATTT-TATA
1 TATTTATATA
*
36447 TATTTTTAT-
1 TATTTATATA
*
36456 TATTTTTATA
1 TATTTATATA
*
36466 TTATTTTTATA
1 -TATTTATATA
36477 T-TTTAT
1 TATTTAT
36483 TACGTCAGAG
Statistics
Matches: 109, Mismatches: 16, Indels: 28
0.71 0.10 0.18
Matches are distributed among these distances:
8 3 0.03
9 31 0.28
10 41 0.38
11 22 0.20
12 4 0.04
13 4 0.04
14 3 0.03
15 1 0.01
ACGTcount: A:0.41, C:0.01, G:0.01, T:0.58
Consensus pattern (10 bp):
TATTTATATA
Found at i:36462 original size:19 final size:19
Alignment explanation
Indices: 36440--36480 Score: 66
Period size: 19 Copynumber: 2.2 Consensus size: 19
36430 ATTTTAAAAA
36440 TTTTATA-TATTTTTATTAT
1 TTTTATATTATTTTTA-TAT
36459 TTTTATATTATTTTTATAT
1 TTTTATATTATTTTTATAT
36478 TTT
1 TTT
36481 ATTACGTCAG
Statistics
Matches: 21, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
19 13 0.62
20 8 0.38
ACGTcount: A:0.24, C:0.00, G:0.00, T:0.76
Consensus pattern (19 bp):
TTTTATATTATTTTTATAT
Found at i:36719 original size:22 final size:22
Alignment explanation
Indices: 36691--36735 Score: 90
Period size: 22 Copynumber: 2.0 Consensus size: 22
36681 GTTTTCAATT
36691 GAAATTCTCTTATGTCAGTTTA
1 GAAATTCTCTTATGTCAGTTTA
36713 GAAATTCTCTTATGTCAGTTTA
1 GAAATTCTCTTATGTCAGTTTA
36735 G
1 G
36736 TCCATTTTTT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 23 1.00
ACGTcount: A:0.27, C:0.13, G:0.16, T:0.44
Consensus pattern (22 bp):
GAAATTCTCTTATGTCAGTTTA
Found at i:37671 original size:45 final size:45
Alignment explanation
Indices: 37564--37672 Score: 146
Period size: 45 Copynumber: 2.4 Consensus size: 45
37554 ATTACCTTAT
* * * *
37564 TGTGCTGTATTTAAGAGAGGTTCTCCAGTAAGATCATTGTTTGGT
1 TGTGCTGTATTTAAGAGACGTTCTCCAGCAAGAACATTGTTTGGA
* *
37609 TGTGCTGTACTTAAGAGACTTTCTCCAGCAAGAACATTGTTTGGA
1 TGTGCTGTATTTAAGAGACGTTCTCCAGCAAGAACATTGTTTGGA
* *
37654 TGTGCTCTATTTGAGAGAC
1 TGTGCTGTATTTAAGAGAC
37673 CATCTTCAGT
Statistics
Matches: 55, Mismatches: 9, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
45 55 1.00
ACGTcount: A:0.24, C:0.15, G:0.25, T:0.37
Consensus pattern (45 bp):
TGTGCTGTATTTAAGAGACGTTCTCCAGCAAGAACATTGTTTGGA
Found at i:47852 original size:2 final size:2
Alignment explanation
Indices: 47845--47882 Score: 76
Period size: 2 Copynumber: 19.0 Consensus size: 2
47835 CTACGCTCCA
47845 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
47883 TTGGATGAAG
Statistics
Matches: 36, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 36 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:55537 original size:16 final size:16
Alignment explanation
Indices: 55513--55546 Score: 50
Period size: 16 Copynumber: 2.1 Consensus size: 16
55503 AGGTATGCAA
*
55513 ATATCAAAGATATATT
1 ATATAAAAGATATATT
*
55529 ATATAAAAGATCTATT
1 ATATAAAAGATATATT
55545 AT
1 AT
55547 TTTCTTTTTA
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
16 16 1.00
ACGTcount: A:0.50, C:0.06, G:0.06, T:0.38
Consensus pattern (16 bp):
ATATAAAAGATATATT
Found at i:57098 original size:64 final size:64
Alignment explanation
Indices: 56981--57100 Score: 150
Period size: 64 Copynumber: 1.9 Consensus size: 64
56971 GTACGATTGA
* * * *
56981 CATTTTAACATATAAGTAAGTGACACAATCACCATACGCAGATGCTAAGAATGACCTTAATCTT
1 CATTTCAACATATAAGTAAGTGACACAATCACCATACGCACATACTAAAAATGACCTTAATCTT
* * * * * *
57045 CATTTCAACATATAAGTGAGTGATACAGTCACCATGCGTACTTACTAAAAATGACC
1 CATTTCAACATATAAGTAAGTGACACAATCACCATACGCACATACTAAAAATGACC
57101 ATAAAAGCCT
Statistics
Matches: 46, Mismatches: 10, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
64 46 1.00
ACGTcount: A:0.38, C:0.21, G:0.13, T:0.28
Consensus pattern (64 bp):
CATTTCAACATATAAGTAAGTGACACAATCACCATACGCACATACTAAAAATGACCTTAATCTT
Found at i:62028 original size:15 final size:15
Alignment explanation
Indices: 62008--62040 Score: 57
Period size: 15 Copynumber: 2.2 Consensus size: 15
61998 GAAGTTTAAA
*
62008 TTCATTTTTGAAATT
1 TTCATTTATGAAATT
62023 TTCATTTATGAAATT
1 TTCATTTATGAAATT
62038 TTC
1 TTC
62041 TTTCGAAAAG
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 17 1.00
ACGTcount: A:0.27, C:0.09, G:0.06, T:0.58
Consensus pattern (15 bp):
TTCATTTATGAAATT
Found at i:62517 original size:14 final size:13
Alignment explanation
Indices: 62494--62524 Score: 53
Period size: 14 Copynumber: 2.3 Consensus size: 13
62484 ATACTAAATA
62494 TTTTCTTATTTAT
1 TTTTCTTATTTAT
62507 TTTTACTTATTTAT
1 TTTT-CTTATTTAT
62521 TTTT
1 TTTT
62525 TATTGACTAA
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
13 4 0.24
14 13 0.76
ACGTcount: A:0.16, C:0.06, G:0.00, T:0.77
Consensus pattern (13 bp):
TTTTCTTATTTAT
Found at i:62893 original size:27 final size:27
Alignment explanation
Indices: 62863--62920 Score: 66
Period size: 28 Copynumber: 2.1 Consensus size: 27
62853 TTTTAATGAA
*
62863 AATTTT-ACATGAT-TAAATTTTTAATT
1 AATTTTGACAT-ATGTAAAATTTTAATT
*
62889 GAATTTTGTCATATGTAAAATTTTAATT
1 -AATTTTGACATATGTAAAATTTTAATT
62917 AATT
1 AATT
62921 CCTTGAGTAT
Statistics
Matches: 27, Mismatches: 2, Indels: 4
0.82 0.06 0.12
Matches are distributed among these distances:
27 12 0.44
28 15 0.56
ACGTcount: A:0.38, C:0.03, G:0.07, T:0.52
Consensus pattern (27 bp):
AATTTTGACATATGTAAAATTTTAATT
Found at i:63082 original size:207 final size:207
Alignment explanation
Indices: 62836--63232 Score: 616
Period size: 207 Copynumber: 1.9 Consensus size: 207
62826 TTGTAATTCA
62836 AAATTTTTCTTACAATATTTTAATGAAAATTTTACATGATTAAATTTTTAATTGAATTTTGTCAT
1 AAATTTTTCTTACAATATTTTAATGAAAATTTTACATGATTAAATTTTTAATTGAATTTTGTCAT
** * *
62901 ATGTAAAATTTTAATTAATTCCTTGAGTATAGAAATTT-TTTTCAATTTTTATTTGTTTCAATTT
66 ATGTAAAATTTTAATTAATTCCTTGAGTATAGAAATTTAAATCCAATTTTAATTTGTTTCAATTT
* *
62965 AGTCCTTGTATTTTAAATTGTTCAATGAATTTTCTTCAATTAATTTCCATTTCACATGGAACTAT
131 AGTCCTTGTAATTTAAATTGTTCAATGAATTTTCTTCAAATAATTTCCATTTCACATGGAACTAT
63030 CATGGCATATGT
196 CATGGCATATGT
** * * * *
63042 AAATTTTTCGTTATGATATTTTTATTAGAATTTTACATGATTAAATTTTTAATTGAATTTTTTCA
1 AAATTTTTC-TTACAATATTTTAATGAAAATTTTACATGATTAAATTTTTAATTGAATTTTGTCA
* * * *
63107 TATGTAAAATTTTGATTAATTCCTTGAGTATGGGAATTTAAATCCCATTTTAATTTGTTTCAATT
65 TATGTAAAATTTTAATTAATTCCTTGAGTATAGAAATTTAAATCCAATTTTAATTTGTTTCAATT
* *
63172 TAGTCTTTGTAATTTAAATTGTTCAATGAATTTTCTTTAAATAATTTCCATTTCACATGGA
130 TAGTCCTTGTAATTTAAATTGTTCAATGAATTTTCTTCAAATAATTTCCATTTCACATGGA
63233 GCTAATTTAG
Statistics
Matches: 171, Mismatches: 18, Indels: 2
0.90 0.09 0.01
Matches are distributed among these distances:
206 9 0.05
207 85 0.50
208 77 0.45
ACGTcount: A:0.32, C:0.09, G:0.09, T:0.50
Consensus pattern (207 bp):
AAATTTTTCTTACAATATTTTAATGAAAATTTTACATGATTAAATTTTTAATTGAATTTTGTCAT
ATGTAAAATTTTAATTAATTCCTTGAGTATAGAAATTTAAATCCAATTTTAATTTGTTTCAATTT
AGTCCTTGTAATTTAAATTGTTCAATGAATTTTCTTCAAATAATTTCCATTTCACATGGAACTAT
CATGGCATATGT
Found at i:66202 original size:2 final size:2
Alignment explanation
Indices: 66195--66228 Score: 68
Period size: 2 Copynumber: 17.0 Consensus size: 2
66185 TCTCATATTT
66195 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
66229 GTTAGTGCAT
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 32 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:67559 original size:33 final size:33
Alignment explanation
Indices: 67521--67603 Score: 112
Period size: 34 Copynumber: 2.5 Consensus size: 33
67511 GTGTGAGATC
*
67521 TGTTGATTAAATGGTGATTTAGTAGTTTACCAT
1 TGTTGATTAAATGGTGATTTAGTAGGTTACCAT
* * * *
67554 TGTTGACTAAATGGGAGATTTGGTAGGTTGCCAT
1 TGTTGATTAAAT-GGTGATTTAGTAGGTTACCAT
67588 TGTTGATTAAATGGTG
1 TGTTGATTAAATGGTG
67604 GTTTTTACCA
Statistics
Matches: 42, Mismatches: 7, Indels: 2
0.82 0.14 0.04
Matches are distributed among these distances:
33 14 0.33
34 28 0.67
ACGTcount: A:0.25, C:0.06, G:0.28, T:0.41
Consensus pattern (33 bp):
TGTTGATTAAATGGTGATTTAGTAGGTTACCAT
Found at i:72081 original size:34 final size:34
Alignment explanation
Indices: 72012--72229 Score: 278
Period size: 34 Copynumber: 6.5 Consensus size: 34
72002 AAGTGGGAGA
* * *
72012 ATTGTTGATTAAAT-GGTGATTTAGTAGTTTACC
1 ATTGTTGATTAAATGGGAGATTTGGTAGCTTACC
* * * * *
72045 ATTGTTGATTAAATGAGTGATTTGGTGGTTTGCC
1 ATTGTTGATTAAATGGGAGATTTGGTAGCTTACC
*
72079 ATTGTTGACTAAAT-GGAGATTTGGTAGCTTACC
1 ATTGTTGATTAAATGGGAGATTTGGTAGCTTACC
*
72112 ATTGTTGATTAAATGGGAAATTTGGTAGCTTACC
1 ATTGTTGATTAAATGGGAGATTTGGTAGCTTACC
* *
72146 ATTGTTGATTAAATGGGTGATTTGGTGGCTTACC
1 ATTGTTGATTAAATGGGAGATTTGGTAGCTTACC
* * * *
72180 ATTGTTGACTAAATGGGAGGTTTGGTAGGTTGCC
1 ATTGTTGATTAAATGGGAGATTTGGTAGCTTACC
72214 ATTGTTGATTAAATGG
1 ATTGTTGATTAAATGG
72230 TGGTTTTTAC
Statistics
Matches: 161, Mismatches: 22, Indels: 3
0.87 0.12 0.02
Matches are distributed among these distances:
33 41 0.25
34 120 0.75
ACGTcount: A:0.25, C:0.08, G:0.27, T:0.40
Consensus pattern (34 bp):
ATTGTTGATTAAATGGGAGATTTGGTAGCTTACC
Found at i:72193 original size:68 final size:67
Alignment explanation
Indices: 72012--72231 Score: 305
Period size: 67 Copynumber: 3.3 Consensus size: 67
72002 AAGTGGGAGA
* * * * * *
72012 ATTGTTGATTAAATGGTGATTTAGTAGTTTACCATTGTTGATTAAATGAGTGATTTGGTGGTTTG
1 ATTGTTGATTAAATGGTGATTTGGTAGCTTACCATTGTTGATTAAATGGGAGATTTGGTAGCTTG
72077 CC
66 CC
* * * *
72079 ATTGTTGACTAAATGGAGATTTGGTAGCTTACCATTGTTGATTAAATGGGAAATTTGGTAGCTTA
1 ATTGTTGATTAAATGGTGATTTGGTAGCTTACCATTGTTGATTAAATGGGAGATTTGGTAGCTTG
72144 CC
66 CC
* * * *
72146 ATTGTTGATTAAATGGGTGATTTGGTGGCTTACCATTGTTGACTAAATGGGAGGTTTGGTAGGTT
1 ATTGTTGATTAAAT-GGTGATTTGGTAGCTTACCATTGTTGATTAAATGGGAGATTTGGTAGCTT
72211 GCC
65 GCC
72214 ATTGTTGATTAAATGGTG
1 ATTGTTGATTAAATGGTG
72232 GTTTTTACCA
Statistics
Matches: 134, Mismatches: 18, Indels: 2
0.87 0.12 0.01
Matches are distributed among these distances:
67 74 0.55
68 60 0.45
ACGTcount: A:0.25, C:0.08, G:0.27, T:0.40
Consensus pattern (67 bp):
ATTGTTGATTAAATGGTGATTTGGTAGCTTACCATTGTTGATTAAATGGGAGATTTGGTAGCTTG
CC
Found at i:78287 original size:13 final size:13
Alignment explanation
Indices: 78269--78293 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
78259 CATAAAGTGT
78269 TGTATCGATACAA
1 TGTATCGATACAA
78282 TGTATCGATACA
1 TGTATCGATACA
78294 TATTTTTTTG
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:0.36, C:0.16, G:0.16, T:0.32
Consensus pattern (13 bp):
TGTATCGATACAA
Found at i:78291 original size:33 final size:33
Alignment explanation
Indices: 78249--78315 Score: 98
Period size: 33 Copynumber: 2.0 Consensus size: 33
78239 TTCAACGATT
78249 TGTATCGATACATAAAGTGTTGTATCGATACAA
1 TGTATCGATACATAAAGTGTTGTATCGATACAA
*** *
78282 TGTATCGATACATATTTTTTTGTATCGATACAA
1 TGTATCGATACATAAAGTGTTGTATCGATACAA
78315 T
1 T
78316 TTAAGCTACT
Statistics
Matches: 30, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
33 30 1.00
ACGTcount: A:0.33, C:0.12, G:0.15, T:0.40
Consensus pattern (33 bp):
TGTATCGATACATAAAGTGTTGTATCGATACAA
Found at i:78374 original size:13 final size:13
Alignment explanation
Indices: 78356--78380 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
78346 ATCACTTAAA
78356 TGTATCGATACAT
1 TGTATCGATACAT
78369 TGTATCGATACA
1 TGTATCGATACA
78381 CTGATCTTTG
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:0.32, C:0.16, G:0.16, T:0.36
Consensus pattern (13 bp):
TGTATCGATACAT
Found at i:78445 original size:52 final size:52
Alignment explanation
Indices: 78389--78517 Score: 222
Period size: 52 Copynumber: 2.5 Consensus size: 52
78379 CACTGATCTT
*
78389 TGTATCGATACATGCAGGCAAATTTGCCCAGATGTATCGATACATTATAAAA
1 TGTATCGATACATGCAGGCAAATTTGCCCAGATGTATCGATACACTATAAAA
* **
78441 TGTATCGATACATGCAGGCAAAATTGCCCAGATGTATCGATACACTATTCAA
1 TGTATCGATACATGCAGGCAAATTTGCCCAGATGTATCGATACACTATAAAA
78493 TGTATCGATACATGCAGGCAAATTT
1 TGTATCGATACATGCAGGCAAATTT
78518 TCATATTTCG
Statistics
Matches: 72, Mismatches: 5, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
52 72 1.00
ACGTcount: A:0.35, C:0.19, G:0.18, T:0.29
Consensus pattern (52 bp):
TGTATCGATACATGCAGGCAAATTTGCCCAGATGTATCGATACACTATAAAA
Found at i:84018 original size:12 final size:12
Alignment explanation
Indices: 84001--84025 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
83991 AAAACACGCA
84001 AAATTTTTTTAC
1 AAATTTTTTTAC
84013 AAATTTTTTTAC
1 AAATTTTTTTAC
84025 A
1 A
84026 TGTGTCCAAT
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:0.36, C:0.08, G:0.00, T:0.56
Consensus pattern (12 bp):
AAATTTTTTTAC
Found at i:84215 original size:241 final size:241
Alignment explanation
Indices: 83792--84266 Score: 950
Period size: 241 Copynumber: 2.0 Consensus size: 241
83782 TTATAGAACT
83792 AATATTATAGTAATTAATAATATATTATTACTATAAATTAGATTGTCTTGATGCCCAATTCAAAA
1 AATATTATAGTAATTAATAATATATTATTACTATAAATTAGATTGTCTTGATGCCCAATTCAAAA
83857 TTTTCTCAAATTAATATTTTAAAAACATTTAAATTTGCAAAAATTATGATATTTGAGTGTATATT
66 TTTTCTCAAATTAATATTTTAAAAACATTTAAATTTGCAAAAATTATGATATTTGAGTGTATATT
83922 ATATATATATATATACATATATATTATAGGGAGACATACATGTGTCCAATAAGTTGGACTAAACC
131 ATATATATATATATACATATATATTATAGGGAGACATACATGTGTCCAATAAGTTGGACTAAACC
83987 AGGCAAAACACGCAAAATTTTTTTACAAATTTTTTTACATGTGTCC
196 AGGCAAAACACGCAAAATTTTTTTACAAATTTTTTTACATGTGTCC
84033 AATATTATAGTAATTAATAATATATTATTACTATAAATTAGATTGTCTTGATGCCCAATTCAAAA
1 AATATTATAGTAATTAATAATATATTATTACTATAAATTAGATTGTCTTGATGCCCAATTCAAAA
84098 TTTTCTCAAATTAATATTTTAAAAACATTTAAATTTGCAAAAATTATGATATTTGAGTGTATATT
66 TTTTCTCAAATTAATATTTTAAAAACATTTAAATTTGCAAAAATTATGATATTTGAGTGTATATT
84163 ATATATATATATATACATATATATTATAGGGAGACATACATGTGTCCAATAAGTTGGACTAAACC
131 ATATATATATATATACATATATATTATAGGGAGACATACATGTGTCCAATAAGTTGGACTAAACC
84228 AGGCAAAACACGCAAAATTTTTTTACAAATTTTTTTACA
196 AGGCAAAACACGCAAAATTTTTTTACAAATTTTTTTACA
84267 AATTTTTATA
Statistics
Matches: 234, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
241 234 1.00
ACGTcount: A:0.41, C:0.11, G:0.10, T:0.39
Consensus pattern (241 bp):
AATATTATAGTAATTAATAATATATTATTACTATAAATTAGATTGTCTTGATGCCCAATTCAAAA
TTTTCTCAAATTAATATTTTAAAAACATTTAAATTTGCAAAAATTATGATATTTGAGTGTATATT
ATATATATATATATACATATATATTATAGGGAGACATACATGTGTCCAATAAGTTGGACTAAACC
AGGCAAAACACGCAAAATTTTTTTACAAATTTTTTTACATGTGTCC
Found at i:84262 original size:11 final size:12
Alignment explanation
Indices: 84242--84273 Score: 64
Period size: 12 Copynumber: 2.7 Consensus size: 12
84232 AAAACACGCA
84242 AAATTTTTTTAC
1 AAATTTTTTTAC
84254 AAATTTTTTTAC
1 AAATTTTTTTAC
84266 AAATTTTT
1 AAATTTTT
84274 ATAATAAGTT
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 20 1.00
ACGTcount: A:0.34, C:0.06, G:0.00, T:0.59
Consensus pattern (12 bp):
AAATTTTTTTAC
Found at i:84348 original size:2 final size:2
Alignment explanation
Indices: 84343--84386 Score: 88
Period size: 2 Copynumber: 22.0 Consensus size: 2
84333 TTTATTGATA
84343 AT 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 AT
84385 AT
1 AT
84387 TGAATTGATT
Statistics
Matches: 42, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 42 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:85274 original size:20 final size:21
Alignment explanation
Indices: 85239--85278 Score: 64
Period size: 20 Copynumber: 2.0 Consensus size: 21
85229 TAAGTAAAAA
85239 TTAACTATTAAATAAATAATT
1 TTAACTATTAAATAAATAATT
*
85260 TTAAC-ATTTAATAAATAAT
1 TTAACTATTAAATAAATAAT
85279 AAATATAGTA
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
20 13 0.72
21 5 0.28
ACGTcount: A:0.53, C:0.05, G:0.00, T:0.42
Consensus pattern (21 bp):
TTAACTATTAAATAAATAATT
Found at i:85993 original size:8 final size:8
Alignment explanation
Indices: 85973--86014 Score: 52
Period size: 8 Copynumber: 5.5 Consensus size: 8
85963 TTAAGAATAA
85973 AATA-TAT
1 AATATTAT
85980 AA-ATTAT
1 AATATTAT
85987 AATATTAT
1 AATATTAT
*
85995 AATATTTT
1 AATATTAT
*
86003 AATAATAT
1 AATATTAT
86011 AATA
1 AATA
86015 AAGTGAAATA
Statistics
Matches: 30, Mismatches: 3, Indels: 3
0.83 0.08 0.08
Matches are distributed among these distances:
6 1 0.03
7 7 0.23
8 22 0.73
ACGTcount: A:0.55, C:0.00, G:0.00, T:0.45
Consensus pattern (8 bp):
AATATTAT
Found at i:90667 original size:36 final size:36
Alignment explanation
Indices: 90627--90705 Score: 122
Period size: 36 Copynumber: 2.2 Consensus size: 36
90617 TTCCTCCTAG
90627 CCCTTTTCAGCAGCCACCAGCTCCAGTAATTCCAAA
1 CCCTTTTCAGCAGCCACCAGCTCCAGTAATTCCAAA
** **
90663 CCCTTTTGGGCCTCCACCAGCTCCAGTAATTCCAAA
1 CCCTTTTCAGCAGCCACCAGCTCCAGTAATTCCAAA
90699 CCCTTTT
1 CCCTTTT
90706 GGGCCTCCAC
Statistics
Matches: 39, Mismatches: 4, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
36 39 1.00
ACGTcount: A:0.23, C:0.39, G:0.11, T:0.27
Consensus pattern (36 bp):
CCCTTTTCAGCAGCCACCAGCTCCAGTAATTCCAAA
Found at i:90733 original size:36 final size:36
Alignment explanation
Indices: 90640--90722 Score: 166
Period size: 36 Copynumber: 2.3 Consensus size: 36
90630 TTTTCAGCAG
90640 CCACCAGCTCCAGTAATTCCAAACCCTTTTGGGCCT
1 CCACCAGCTCCAGTAATTCCAAACCCTTTTGGGCCT
90676 CCACCAGCTCCAGTAATTCCAAACCCTTTTGGGCCT
1 CCACCAGCTCCAGTAATTCCAAACCCTTTTGGGCCT
90712 CCACCAGCTCC
1 CCACCAGCTCC
90723 CCTAAATCCA
Statistics
Matches: 47, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
36 47 1.00
ACGTcount: A:0.22, C:0.42, G:0.13, T:0.23
Consensus pattern (36 bp):
CCACCAGCTCCAGTAATTCCAAACCCTTTTGGGCCT
Found at i:90748 original size:36 final size:36
Alignment explanation
Indices: 90640--90755 Score: 133
Period size: 36 Copynumber: 3.2 Consensus size: 36
90630 TTTTCAGCAG
* * *
90640 CCACCAGCTCCAGTAATTCCAAACCCTTTTGGGCCT
1 CCACCAGCTCCACTAATTCCAAACCCATTTCGGCCT
* * *
90676 CCACCAGCTCCAGTAATTCCAAACCCTTTTGGGCCT
1 CCACCAGCTCCACTAATTCCAAACCCATTTCGGCCT
* * * *
90712 CCACCAGCTCCCCTAAATCCAAGCCCATTTCTGCCT
1 CCACCAGCTCCACTAATTCCAAACCCATTTCGGCCT
*
90748 CCTCCAGC
1 CCACCAGC
90756 ACCTCAAGCT
Statistics
Matches: 72, Mismatches: 8, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
36 72 1.00
ACGTcount: A:0.22, C:0.43, G:0.12, T:0.23
Consensus pattern (36 bp):
CCACCAGCTCCACTAATTCCAAACCCATTTCGGCCT
Found at i:90781 original size:45 final size:45
Alignment explanation
Indices: 90717--90805 Score: 169
Period size: 45 Copynumber: 2.0 Consensus size: 45
90707 GGCCTCCACC
90717 AGCTCCCCTAAATCCAAGCCCATTTCTGCCTCCTCCAGCACCTCA
1 AGCTCCCCTAAATCCAAGCCCATTTCTGCCTCCTCCAGCACCTCA
*
90762 AGCTCCCCTAACTCCAAGCCCATTTCTGCCTCCTCCAGCACCTC
1 AGCTCCCCTAAATCCAAGCCCATTTCTGCCTCCTCCAGCACCTC
90806 TAGCACCATT
Statistics
Matches: 43, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
45 43 1.00
ACGTcount: A:0.20, C:0.48, G:0.09, T:0.22
Consensus pattern (45 bp):
AGCTCCCCTAAATCCAAGCCCATTTCTGCCTCCTCCAGCACCTCA
Found at i:90902 original size:15 final size:15
Alignment explanation
Indices: 90882--90910 Score: 58
Period size: 15 Copynumber: 1.9 Consensus size: 15
90872 CGCCAGACTT
90882 CCCATTTCCTTTCCC
1 CCCATTTCCTTTCCC
90897 CCCATTTCCTTTCC
1 CCCATTTCCTTTCC
90911 TACCTATGCC
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.07, C:0.52, G:0.00, T:0.41
Consensus pattern (15 bp):
CCCATTTCCTTTCCC
Found at i:91406 original size:15 final size:15
Alignment explanation
Indices: 91386--91419 Score: 50
Period size: 15 Copynumber: 2.3 Consensus size: 15
91376 AATTATTATA
91386 AATTTTTAATAATTT
1 AATTTTTAATAATTT
* *
91401 AATTTTTATTTATTT
1 AATTTTTAATAATTT
91416 AATT
1 AATT
91420 ATTTTATTTT
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
15 17 1.00
ACGTcount: A:0.35, C:0.00, G:0.00, T:0.65
Consensus pattern (15 bp):
AATTTTTAATAATTT
Found at i:93295 original size:33 final size:33
Alignment explanation
Indices: 93258--93328 Score: 81
Period size: 33 Copynumber: 2.2 Consensus size: 33
93248 AAAATTCAAT
*
93258 AAAATTAAAAAAATAAAAAAT-AAAAAAAAAGTA
1 AAAATTAAAAAAACAAAAAATCAAAAAAAAA-TA
** * *
93291 AAAATTTTAAAAACAAAAATTCAAAAAATAATA
1 AAAATTAAAAAAACAAAAAATCAAAAAAAAATA
93324 AAAAT
1 AAAAT
93329 CTATAAAATT
Statistics
Matches: 32, Mismatches: 5, Indels: 2
0.82 0.13 0.05
Matches are distributed among these distances:
33 24 0.75
34 8 0.25
ACGTcount: A:0.76, C:0.03, G:0.01, T:0.20
Consensus pattern (33 bp):
AAAATTAAAAAAACAAAAAATCAAAAAAAAATA
Found at i:93397 original size:7 final size:7
Alignment explanation
Indices: 93387--93427 Score: 82
Period size: 7 Copynumber: 5.9 Consensus size: 7
93377 TTAAAATATG
93387 TAAAAAA
1 TAAAAAA
93394 TAAAAAA
1 TAAAAAA
93401 TAAAAAA
1 TAAAAAA
93408 TAAAAAA
1 TAAAAAA
93415 TAAAAAA
1 TAAAAAA
93422 TAAAAA
1 TAAAAA
93428 TATACAATTA
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 34 1.00
ACGTcount: A:0.85, C:0.00, G:0.00, T:0.15
Consensus pattern (7 bp):
TAAAAAA
Found at i:93465 original size:7 final size:7
Alignment explanation
Indices: 93342--93465 Score: 52
Period size: 7 Copynumber: 16.7 Consensus size: 7
93332 TAAAATTCAA
93342 AAAAATT
1 AAAAATT
*
93349 AAAGCATAT
1 AAA-AAT-T
*
93358 AACAATT
1 AAAAATT
*
93365 CAAAATT
1 AAAAATT
**
93372 AATTATT
1 AAAAATT
93379 AAAATATGT
1 AAAA-AT-T
*
93388 AAAAAAT
1 AAAAATT
*
93395 AAAAAAT
1 AAAAATT
*
93402 AAAAAAT
1 AAAAATT
*
93409 AAAAAAT
1 AAAAATT
*
93416 AAAAAAT
1 AAAAATT
93423 AAAAA-T
1 AAAAATT
*
93429 ATACAATT
1 A-AAAATT
*
93437 AAAATTTGT
1 AAAA-AT-T
*
93446 AAGAAAAT
1 AA-AAATT
93454 AAAAATT
1 AAAAATT
93461 AAAAA
1 AAAAA
93466 ATATAAATCT
Statistics
Matches: 91, Mismatches: 17, Indels: 18
0.72 0.13 0.14
Matches are distributed among these distances:
6 2 0.02
7 63 0.69
8 13 0.14
9 11 0.12
10 2 0.02
ACGTcount: A:0.69, C:0.03, G:0.03, T:0.25
Consensus pattern (7 bp):
AAAAATT
Found at i:93468 original size:14 final size:14
Alignment explanation
Indices: 93387--93473 Score: 77
Period size: 14 Copynumber: 6.0 Consensus size: 14
93377 TTAAAATATG
*
93387 TAAAAAATAAAAAA
1 TAAAAAATAAAAAT
*
93401 TAAAAAATAAAAAA
1 TAAAAAATAAAAAT
93415 TAAAAAATAAAAA-
1 TAAAAAATAAAAAT
* * *
93428 TATACAATTAAAATTT
1 TA-AAAAATAAAA-AT
93444 GTAAGAAAATAAAAAT
1 -TAA-AAAATAAAAAT
*
93460 TAAAAAATATAAAT
1 TAAAAAATAAAAAT
93474 CTAGGAAAAC
Statistics
Matches: 61, Mismatches: 7, Indels: 10
0.78 0.09 0.13
Matches are distributed among these distances:
13 2 0.03
14 45 0.74
15 3 0.05
16 2 0.03
17 9 0.15
ACGTcount: A:0.74, C:0.01, G:0.02, T:0.23
Consensus pattern (14 bp):
TAAAAAATAAAAAT
Found at i:93472 original size:9 final size:8
Alignment explanation
Indices: 93240--93427 Score: 63
Period size: 7 Copynumber: 23.2 Consensus size: 8
93230 TATATTTTTT
93240 AAATTCAAA
1 AAATT-AAA
93249 AAATTCAATA
1 AAATT-AA-A
93259 AAATTAAA
1 AAATTAAA
*
93267 AAAATAAA
1 AAATTAAA
*
93275 AAATAAAAAA
1 AAAT--TAAA
*
93285 AAAGTAAA
1 AAATTAAA
* *
93293 AATTTTAA
1 AAATTAAA
*
93301 AAA--CAA
1 AAATTAAA
93307 AAATTCAAA
1 AAATT-AAA
*
93316 AAATAATAA
1 AAATTA-AA
*
93325 AAATCTATA
1 AAAT-TAAA
93334 AAATTCAAAA
1 AAATT--AAA
93344 AAATTAAA
1 AAATTAAA
**
93352 GCA-TATAA
1 AAATTA-AA
* *
93360 CAATT-CA
1 AAATTAAA
93367 AAATT-AA
1 AAATTAAA
**
93374 TTATTAAA
1 AAATTAAA
*
93382 ATATGTAAA
1 AAAT-TAAA
93391 AAA-TAAA
1 AAATTAAA
93398 AAA-TAAA
1 AAATTAAA
93405 AAA-TAAA
1 AAATTAAA
93412 AAA-TAAA
1 AAATTAAA
93419 AAA-TAAA
1 AAATTAAA
93426 AA
1 AA
93428 TATACAATTA
Statistics
Matches: 139, Mismatches: 26, Indels: 30
0.71 0.13 0.15
Matches are distributed among these distances:
6 5 0.04
7 45 0.32
8 35 0.25
9 34 0.24
10 20 0.14
ACGTcount: A:0.71, C:0.05, G:0.02, T:0.23
Consensus pattern (8 bp):
AAATTAAA
Found at i:93930 original size:14 final size:14
Alignment explanation
Indices: 93886--93919 Score: 50
Period size: 14 Copynumber: 2.4 Consensus size: 14
93876 CTTTATTCCT
* *
93886 TTTATTAAATTTAA
1 TTTATTATATTCAA
93900 TTTATTATATTCAA
1 TTTATTATATTCAA
93914 TTTATT
1 TTTATT
93920 TTTTCATATT
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
14 18 1.00
ACGTcount: A:0.35, C:0.03, G:0.00, T:0.62
Consensus pattern (14 bp):
TTTATTATATTCAA
Found at i:93987 original size:27 final size:26
Alignment explanation
Indices: 93951--94026 Score: 75
Period size: 26 Copynumber: 2.9 Consensus size: 26
93941 CTTTTAATTT
93951 TTTTA-ATTTTTTATAAATTTTTAAAA
1 TTTTAGATTTTTTATAAATTTTT-AAA
* * *
93977 TTTTAGGTTTTTTA-ATACTTTTTAGA
1 TTTTAGATTTTTTATA-AATTTTTAAA
*
94003 TTTTAGATTTTTTTTAAAGTTTTT
1 TTTTAGATTTTTTATAAA-TTTTT
94027 TTAACTTTGT
Statistics
Matches: 40, Mismatches: 6, Indels: 7
0.75 0.11 0.13
Matches are distributed among these distances:
26 21 0.52
27 19 0.47
ACGTcount: A:0.28, C:0.01, G:0.07, T:0.64
Consensus pattern (26 bp):
TTTTAGATTTTTTATAAATTTTTAAA
Found at i:94148 original size:18 final size:17
Alignment explanation
Indices: 94099--94149 Score: 57
Period size: 18 Copynumber: 2.9 Consensus size: 17
94089 TTTAATTAAA
*
94099 AATATTTTTATATTTTT
1 AATATTTTTAAATTTTT
* *
94116 AATTATATTTGAATTTTT
1 AA-TATTTTTAAATTTTT
94134 ATATATTTTTAAATTT
1 A-ATATTTTTAAATTT
94150 AACTTTTGTT
Statistics
Matches: 27, Mismatches: 5, Indels: 3
0.77 0.14 0.09
Matches are distributed among these distances:
17 2 0.07
18 24 0.89
19 1 0.04
ACGTcount: A:0.33, C:0.00, G:0.02, T:0.65
Consensus pattern (17 bp):
AATATTTTTAAATTTTT
Found at i:97965 original size:29 final size:29
Alignment explanation
Indices: 97929--98002 Score: 73
Period size: 29 Copynumber: 2.6 Consensus size: 29
97919 TAAATATAAA
97929 ATTT-TTAAAAATAAATA-AAAATAATTTT
1 ATTTATTAAAAATAAATATAAAATAA-TTT
* **
97957 ATTTATTAATAAAT-AATATTATTTAATTT
1 ATTTATTAA-AAATAAATATAAAATAATTT
*
97986 ATTTATTATAAATAAAT
1 ATTTATTAAAAATAAAT
98003 TTATACGCTA
Statistics
Matches: 38, Mismatches: 4, Indels: 7
0.78 0.08 0.14
Matches are distributed among these distances:
28 8 0.21
29 22 0.58
30 8 0.21
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (29 bp):
ATTTATTAAAAATAAATATAAAATAATTT
Found at i:97986 original size:25 final size:26
Alignment explanation
Indices: 97938--97988 Score: 68
Period size: 25 Copynumber: 2.0 Consensus size: 26
97928 AATTTTTAAA
*
97938 AATAAATAAAAATAATTTTATTTATT
1 AATAAATAAAAATAATTTAATTTATT
* *
97964 AATAAAT-AATATTATTTAATTTATT
1 AATAAATAAAAATAATTTAATTTATT
97989 TATTATAAAT
Statistics
Matches: 22, Mismatches: 3, Indels: 1
0.85 0.12 0.04
Matches are distributed among these distances:
25 15 0.68
26 7 0.32
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (26 bp):
AATAAATAAAAATAATTTAATTTATT
Found at i:98408 original size:2 final size:2
Alignment explanation
Indices: 98401--98426 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
98391 ATATTTAGCA
98401 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
98427 TATCATTTAA
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 24 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:99511 original size:60 final size:60
Alignment explanation
Indices: 99330--99514 Score: 175
Period size: 60 Copynumber: 3.1 Consensus size: 60
99320 AGTTACTAGA
* * *
99330 AAATCTTGACATAGCTTAATTATGATCACAAATTATTTTAATTTAAATATTTCAAAAACAT
1 AAAT-TTGACATAGCTTAATTATGATCACAAATTATTTTAGTTTAAATATTTTAAAAAGAT
* * ** * * * * *
99391 AATTTTAAC-T-TTTTTA-TATAAATC-TAAA-T-TTTTAGTTTAAATTTCAGTTTAAAAGGAT
1 AAATTTGACATAGCTTAATTAT-GATCACAAATTATTTTAGTTTAAA--T-ATTTTAAAAAGAT
99449 AAATTTGACATAGCTTAATTATGATCACAAATTATTTTAGTTTAAATATTTTAAAAAGAT
1 AAATTTGACATAGCTTAATTATGATCACAAATTATTTTAGTTTAAATATTTTAAAAAGAT
99509 AAATTT
1 AAATTT
99515 AACTTTTTTT
Statistics
Matches: 93, Mismatches: 21, Indels: 21
0.69 0.16 0.16
Matches are distributed among these distances:
55 11 0.12
56 1 0.01
57 7 0.08
58 22 0.24
59 2 0.02
60 27 0.29
61 10 0.11
62 1 0.01
63 12 0.13
ACGTcount: A:0.42, C:0.08, G:0.06, T:0.44
Consensus pattern (60 bp):
AAATTTGACATAGCTTAATTATGATCACAAATTATTTTAGTTTAAATATTTTAAAAAGAT
Found at i:100101 original size:13 final size:13
Alignment explanation
Indices: 100083--100156 Score: 51
Period size: 13 Copynumber: 5.5 Consensus size: 13
100073 TTAAAAAATA
100083 AAAAATTATTTTT
1 AAAAATTATTTTT
* *
100096 AAAAATT-TTAAAATA
1 AAAAATTATT---TTT
100111 AAAAATTATTTTT
1 AAAAATTATTTTT
*
100124 AATAATTATTTTT
1 AAAAATTATTTTT
* * *
100137 TAAAACTGTTTTT
1 AAAAATTATTTTT
*
100150 GAAAATT
1 AAAAATT
100157 TTAAAAATAA
Statistics
Matches: 46, Mismatches: 11, Indels: 8
0.71 0.17 0.12
Matches are distributed among these distances:
12 2 0.04
13 34 0.74
15 8 0.17
16 2 0.04
ACGTcount: A:0.47, C:0.01, G:0.03, T:0.49
Consensus pattern (13 bp):
AAAAATTATTTTT
Found at i:100141 original size:28 final size:28
Alignment explanation
Indices: 100077--100130 Score: 99
Period size: 28 Copynumber: 1.9 Consensus size: 28
100067 TTATCTTTAA
100077 AAAATAAAAAATTATTTTTAAAAATTTT
1 AAAATAAAAAATTATTTTTAAAAATTTT
*
100105 AAAATAAAAAATTATTTTTAATAATT
1 AAAATAAAAAATTATTTTTAAAAATT
100131 ATTTTTTAAA
Statistics
Matches: 25, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
28 25 1.00
ACGTcount: A:0.57, C:0.00, G:0.00, T:0.43
Consensus pattern (28 bp):
AAAATAAAAAATTATTTTTAAAAATTTT
Found at i:102277 original size:3 final size:3
Alignment explanation
Indices: 102264--102311 Score: 87
Period size: 3 Copynumber: 15.7 Consensus size: 3
102254 TGTAATGAAA
102264 AAT ATAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
1 AAT A-AT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
102310 AA
1 AA
102312 AAGTTATGAC
Statistics
Matches: 44, Mismatches: 0, Indels: 2
0.96 0.00 0.04
Matches are distributed among these distances:
3 41 0.93
4 3 0.07
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (3 bp):
AAT
Found at i:102855 original size:23 final size:23
Alignment explanation
Indices: 102820--102867 Score: 69
Period size: 23 Copynumber: 2.1 Consensus size: 23
102810 GGATCAAATA
* *
102820 CAGTGATCCCTCCATTTTCTTTC
1 CAGTCATCCCTCCATTTTCATTC
*
102843 CAGTCATCTCTCCATTTTCATTC
1 CAGTCATCCCTCCATTTTCATTC
102866 CA
1 CA
102868 TATTTTGTTG
Statistics
Matches: 22, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
23 22 1.00
ACGTcount: A:0.17, C:0.35, G:0.06, T:0.42
Consensus pattern (23 bp):
CAGTCATCCCTCCATTTTCATTC
Found at i:107389 original size:16 final size:16
Alignment explanation
Indices: 107324--107397 Score: 62
Period size: 16 Copynumber: 4.6 Consensus size: 16
107314 GCTCGAGTCC
*
107324 AAAATAATTTATATTT
1 AAAATAATTTACATTT
* * *
107340 AAAGTAGTTTGCA-TT
1 AAAATAATTTACATTT
* *
107355 CAAATAAACTTT-TATTT
1 AAAAT-AA-TTTACATTT
107372 AAAATAATTTACATTT
1 AAAATAATTTACATTT
107388 AAAATAATTT
1 AAAATAATTT
107398 CTGTTCAATC
Statistics
Matches: 44, Mismatches: 10, Indels: 8
0.71 0.16 0.13
Matches are distributed among these distances:
15 8 0.18
16 27 0.61
17 9 0.20
ACGTcount: A:0.46, C:0.05, G:0.04, T:0.45
Consensus pattern (16 bp):
AAAATAATTTACATTT
Found at i:115048 original size:17 final size:17
Alignment explanation
Indices: 115026--115060 Score: 70
Period size: 17 Copynumber: 2.1 Consensus size: 17
115016 TATTTTTTAA
115026 TATTTACACTATAATAT
1 TATTTACACTATAATAT
115043 TATTTACACTATAATAT
1 TATTTACACTATAATAT
115060 T
1 T
115061 CTTTTATGAC
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 18 1.00
ACGTcount: A:0.40, C:0.11, G:0.00, T:0.49
Consensus pattern (17 bp):
TATTTACACTATAATAT
Found at i:116421 original size:53 final size:51
Alignment explanation
Indices: 116307--116450 Score: 129
Period size: 53 Copynumber: 2.8 Consensus size: 51
116297 AAAACAATTC
*
116307 AATATAAATATTAA-AATTTTTTATTTATTATTAAATAAATCTATTTAACAA
1 AATATAAATA-AAATAATTTTTTATTTATTATTAAATAAATCTATTTAACAA
* *
116358 AATATTAAATAAAATTAATTTTTTATTTACTATTTTAAAT-ATTCTAATTTAA-AA
1 AATA-TAAATAAAA-TAATTTTTTATTTA-T-TATTAAATAAATCT-ATTTAACAA
* *
116412 TAATA-AAATAAAATAATTAGTATATTTATT-TTAAA-AAAT
1 -AATATAAATAAAATAATT-TTTTATTTATTATTAAATAAAT
116451 TTATAATTCC
Statistics
Matches: 78, Mismatches: 6, Indels: 19
0.76 0.06 0.18
Matches are distributed among these distances:
50 7 0.09
51 7 0.09
52 12 0.15
53 28 0.36
54 7 0.09
55 17 0.22
ACGTcount: A:0.50, C:0.03, G:0.01, T:0.47
Consensus pattern (51 bp):
AATATAAATAAAATAATTTTTTATTTATTATTAAATAAATCTATTTAACAA
Found at i:116680 original size:21 final size:22
Alignment explanation
Indices: 116648--116701 Score: 60
Period size: 21 Copynumber: 2.5 Consensus size: 22
116638 TTATTTATAA
*
116648 TTAAA-AAATTTAT-ATTAATAT
1 TTAAATAATTTTATAATTAA-AT
*
116669 TTATAT-ATTTTATAATTAAAT
1 TTAAATAATTTTATAATTAAAT
116690 TTAAATAATTTT
1 TTAAATAATTTT
116702 TTTAATTATT
Statistics
Matches: 27, Mismatches: 3, Indels: 5
0.77 0.09 0.14
Matches are distributed among these distances:
21 17 0.63
22 10 0.37
ACGTcount: A:0.46, C:0.00, G:0.00, T:0.54
Consensus pattern (22 bp):
TTAAATAATTTTATAATTAAAT
Found at i:117582 original size:29 final size:29
Alignment explanation
Indices: 117528--117585 Score: 71
Period size: 30 Copynumber: 2.0 Consensus size: 29
117518 TGATATTTAA
***
117528 TAATTAAAAAATATATTTTTATTTAAATT
1 TAATTAAAAAATATATAAATATTTAAATT
*
117557 TAATTATAAAAATATATAAATATTAAAAT
1 TAATTA-AAAAATATATAAATATTTAAAT
117586 AAAATTTTAT
Statistics
Matches: 24, Mismatches: 4, Indels: 1
0.83 0.14 0.03
Matches are distributed among these distances:
29 6 0.25
30 18 0.75
ACGTcount: A:0.55, C:0.00, G:0.00, T:0.45
Consensus pattern (29 bp):
TAATTAAAAAATATATAAATATTTAAATT
Found at i:118883 original size:32 final size:30
Alignment explanation
Indices: 118815--118886 Score: 76
Period size: 32 Copynumber: 2.3 Consensus size: 30
118805 AGTTTAATTT
*
118815 TTAAATT-TTTTTTATTATTTTAAAAAATT
1 TTAAATTATTTTTTATTATTTTAAAAAATA
*
118844 TTAAAATTATTTTTATATTAATATTT-ATAAATA
1 TT-AAATTATTTTT-TATT-AT-TTTAAAAAATA
118877 TTAAATTATT
1 TTAAATTATT
118887 CAAATCTGTC
Statistics
Matches: 36, Mismatches: 2, Indels: 7
0.80 0.04 0.16
Matches are distributed among these distances:
29 2 0.06
30 5 0.14
31 5 0.14
32 12 0.33
33 9 0.25
34 3 0.08
ACGTcount: A:0.42, C:0.00, G:0.00, T:0.58
Consensus pattern (30 bp):
TTAAATTATTTTTTATTATTTTAAAAAATA
Found at i:119633 original size:21 final size:23
Alignment explanation
Indices: 119588--119635 Score: 64
Period size: 25 Copynumber: 2.1 Consensus size: 23
119578 AAATAATATT
119588 TAAATTTTTTTATTATTAATTTAAA
1 TAAATTTTTTTATTA-TAA-TTAAA
119613 TAAATTTTTTTATTA-AA-TAAA
1 TAAATTTTTTTATTATAATTAAA
119634 TA
1 TA
119636 GTGATTCAGA
Statistics
Matches: 23, Mismatches: 0, Indels: 4
0.85 0.00 0.15
Matches are distributed among these distances:
21 6 0.26
23 2 0.09
25 15 0.65
ACGTcount: A:0.44, C:0.00, G:0.00, T:0.56
Consensus pattern (23 bp):
TAAATTTTTTTATTATAATTAAA
Found at i:120483 original size:5 final size:5
Alignment explanation
Indices: 120473--120523 Score: 88
Period size: 5 Copynumber: 10.6 Consensus size: 5
120463 GATGAAACCA
120473 TTCTT TTCTT TTCTT TTCTT TTCTT TTCTT TTCTT TTC-T TT-TT TTCTT
1 TTCTT TTCTT TTCTT TTCTT TTCTT TTCTT TTCTT TTCTT TTCTT TTCTT
120521 TTC
1 TTC
120524 CAAAGCTAAA
Statistics
Matches: 44, Mismatches: 0, Indels: 4
0.92 0.00 0.08
Matches are distributed among these distances:
4 6 0.14
5 38 0.86
ACGTcount: A:0.00, C:0.20, G:0.00, T:0.80
Consensus pattern (5 bp):
TTCTT
Found at i:120928 original size:33 final size:32
Alignment explanation
Indices: 120891--120994 Score: 97
Period size: 33 Copynumber: 3.2 Consensus size: 32
120881 AATAATATGA
120891 ATATAACATAAATATATAAATATTTTAAATTTT
1 ATATAA-ATAAATATATAAATATTTTAAATTTT
* * * *
120924 ATATAATACAAAT-TATTAATATTATCAAAATTT
1 ATATAA-ATAAATATATAAATATT-TTAAATTTT
* *
120957 ATA-AATTAAATATA-AAATATTTTAAATATT
1 ATATAAATAAATATATAAATATTTTAAATTTT
120987 ATTATAAA
1 A-TATAAA
120995 ATAATAAAAT
Statistics
Matches: 55, Mismatches: 12, Indels: 9
0.72 0.16 0.12
Matches are distributed among these distances:
30 7 0.13
31 12 0.22
32 15 0.27
33 21 0.38
ACGTcount: A:0.54, C:0.03, G:0.00, T:0.43
Consensus pattern (32 bp):
ATATAAATAAATATATAAATATTTTAAATTTT
Found at i:120964 original size:23 final size:23
Alignment explanation
Indices: 120938--120997 Score: 65
Period size: 21 Copynumber: 2.7 Consensus size: 23
120928 AATACAAATT
120938 ATTAATATTATCAAAAT-TTATAA
1 ATTAATATTAT-AAAATATTATAA
*
120961 ATTAA-A-TATAAAATATTTTAA
1 ATTAATATTATAAAATATTATAA
*
120982 A-TATTATTATAAAATA
1 ATTAATATTATAAAATA
120998 ATAAAATATA
Statistics
Matches: 32, Mismatches: 2, Indels: 7
0.78 0.05 0.17
Matches are distributed among these distances:
20 7 0.22
21 10 0.31
22 10 0.31
23 5 0.16
ACGTcount: A:0.55, C:0.02, G:0.00, T:0.43
Consensus pattern (23 bp):
ATTAATATTATAAAATATTATAA
Found at i:122357 original size:26 final size:25
Alignment explanation
Indices: 122315--122370 Score: 62
Period size: 26 Copynumber: 2.2 Consensus size: 25
122305 ATTACTGGTG
*
122315 TATTATTTTTAATTTTAATAAAAATT
1 TATTTTTTTTAATTTTAA-AAAAATT
*
122341 TATTTTTTTT-ATATTTAAAAATATT
1 TATTTTTTTTAAT-TTTAAAAAAATT
122366 T-TTTT
1 TATTTT
122371 AATAAATCTT
Statistics
Matches: 27, Mismatches: 2, Indels: 4
0.82 0.06 0.12
Matches are distributed among these distances:
24 4 0.15
25 9 0.33
26 14 0.52
ACGTcount: A:0.36, C:0.00, G:0.00, T:0.64
Consensus pattern (25 bp):
TATTTTTTTTAATTTTAAAAAAATT
Found at i:124995 original size:20 final size:21
Alignment explanation
Indices: 124972--125010 Score: 53
Period size: 21 Copynumber: 1.9 Consensus size: 21
124962 ATATCAAAAT
124972 TTAAA-TAAATATAAAATATC
1 TTAAACTAAATATAAAATATC
* *
124992 TTAAACTAATTATGAAATA
1 TTAAACTAAATATAAAATA
125011 ACAAAAAAAA
Statistics
Matches: 16, Mismatches: 2, Indels: 1
0.84 0.11 0.05
Matches are distributed among these distances:
20 5 0.31
21 11 0.69
ACGTcount: A:0.56, C:0.05, G:0.03, T:0.36
Consensus pattern (21 bp):
TTAAACTAAATATAAAATATC
Found at i:126708 original size:18 final size:18
Alignment explanation
Indices: 126685--126719 Score: 61
Period size: 18 Copynumber: 1.9 Consensus size: 18
126675 AAAATAGATT
*
126685 AAAATTAATTTAATTTAA
1 AAAATTAATTAAATTTAA
126703 AAAATTAATTAAATTTA
1 AAAATTAATTAAATTTA
126720 TTTTAATTAG
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
18 16 1.00
ACGTcount: A:0.57, C:0.00, G:0.00, T:0.43
Consensus pattern (18 bp):
AAAATTAATTAAATTTAA
Found at i:126713 original size:28 final size:28
Alignment explanation
Indices: 126674--126727 Score: 74
Period size: 28 Copynumber: 1.9 Consensus size: 28
126664 CCCCAAAAGT
126674 AAAAATAGATTAAAATTAATTTAATTTA
1 AAAAATAGATTAAAATTAATTTAATTTA
* *
126702 AAAAATTA-ATTAAATTTATTTTAATT
1 AAAAA-TAGATTAAAATTAATTTAATT
126728 AGTTTGATTA
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
28 21 0.91
29 2 0.09
ACGTcount: A:0.54, C:0.00, G:0.02, T:0.44
Consensus pattern (28 bp):
AAAAATAGATTAAAATTAATTTAATTTA
Found at i:126767 original size:17 final size:17
Alignment explanation
Indices: 126734--126772 Score: 53
Period size: 17 Copynumber: 2.3 Consensus size: 17
126724 AATTAGTTTG
126734 ATTAATTAAGTTTAAAT
1 ATTAATTAAGTTTAAAT
*
126751 TTTAATTAA-TTTAAAAT
1 ATTAATTAAGTTT-AAAT
126768 ATTAA
1 ATTAA
126773 GTGATTAATT
Statistics
Matches: 19, Mismatches: 2, Indels: 2
0.83 0.09 0.09
Matches are distributed among these distances:
16 3 0.16
17 16 0.84
ACGTcount: A:0.49, C:0.00, G:0.03, T:0.49
Consensus pattern (17 bp):
ATTAATTAAGTTTAAAT
Found at i:126837 original size:26 final size:25
Alignment explanation
Indices: 126799--126871 Score: 69
Period size: 26 Copynumber: 2.9 Consensus size: 25
126789 GTTTTTAATT
* *
126799 ATTAAAATATAAAATTAAATAAATAA
1 ATTAATATTTAAAA-TAAATAAATAA
* *
126825 ATTAATATTTAAAATATATTTAATAA
1 ATTAATATTTAAAATA-AATAAATAA
*
126851 AAT-ATATTTAAAATAAA-AAAT
1 ATTAATATTTAAAATAAATAAAT
126872 TTAATCGAAT
Statistics
Matches: 39, Mismatches: 7, Indels: 5
0.76 0.14 0.10
Matches are distributed among these distances:
23 3 0.08
24 1 0.03
25 14 0.36
26 21 0.54
ACGTcount: A:0.63, C:0.00, G:0.00, T:0.37
Consensus pattern (25 bp):
ATTAATATTTAAAATAAATAAATAA
Found at i:126875 original size:14 final size:16
Alignment explanation
Indices: 126834--126868 Score: 56
Period size: 14 Copynumber: 2.3 Consensus size: 16
126824 AATTAATATT
126834 TAAAATATATTT--AA
1 TAAAATATATTTAAAA
126848 TAAAATATATTTAAAA
1 TAAAATATATTTAAAA
126864 TAAAA
1 TAAAA
126869 AATTTAATCG
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
14 12 0.63
16 7 0.37
ACGTcount: A:0.63, C:0.00, G:0.00, T:0.37
Consensus pattern (16 bp):
TAAAATATATTTAAAA
Found at i:126970 original size:21 final size:21
Alignment explanation
Indices: 126946--126991 Score: 56
Period size: 21 Copynumber: 2.2 Consensus size: 21
126936 TCGATCAATT
* *
126946 TTAATATTAAATTTTATTAAA
1 TTAATATTAAATTTAAATAAA
* *
126967 TTAATTTTTAATTTAAATAAA
1 TTAATATTAAATTTAAATAAA
126988 TTAA
1 TTAA
126992 ATCACTTAAC
Statistics
Matches: 21, Mismatches: 4, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
21 21 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (21 bp):
TTAATATTAAATTTAAATAAA
Found at i:127289 original size:21 final size:23
Alignment explanation
Indices: 127265--127308 Score: 65
Period size: 21 Copynumber: 2.0 Consensus size: 23
127255 TTGAGTTTTT
*
127265 TATTTTTTTTA-TT-TTTTATCA
1 TATTTTCTTTATTTCTTTTATCA
127286 TATTTTCTTTATTTCTTTTATCA
1 TATTTTCTTTATTTCTTTTATCA
127309 GGAAATTCAA
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
21 10 0.50
22 2 0.10
23 8 0.40
ACGTcount: A:0.18, C:0.09, G:0.00, T:0.73
Consensus pattern (23 bp):
TATTTTCTTTATTTCTTTTATCA
Found at i:128074 original size:23 final size:24
Alignment explanation
Indices: 128045--128089 Score: 74
Period size: 24 Copynumber: 1.9 Consensus size: 24
128035 TAATTCAATT
128045 TTTTA-TTAAAAATAAAAAAATAA
1 TTTTATTTAAAAATAAAAAAATAA
*
128068 TTTTATTTAAAAATAAATAAAT
1 TTTTATTTAAAAATAAAAAAAT
128090 TTTAAAATTT
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
23 5 0.25
24 15 0.75
ACGTcount: A:0.60, C:0.00, G:0.00, T:0.40
Consensus pattern (24 bp):
TTTTATTTAAAAATAAAAAAATAA
Found at i:128255 original size:15 final size:14
Alignment explanation
Indices: 128218--128261 Score: 54
Period size: 15 Copynumber: 3.1 Consensus size: 14
128208 ATTAATATTT
128218 TATTATATAAA-AAA
1 TATTA-ATAAATAAA
*
128232 TATTTATAAATAAA
1 TATTAATAAATAAA
128246 TAGTTAATAAATAAA
1 TA-TTAATAAATAAA
128261 T
1 T
128262 TCATAAATAA
Statistics
Matches: 26, Mismatches: 2, Indels: 3
0.84 0.06 0.10
Matches are distributed among these distances:
13 5 0.19
14 9 0.35
15 12 0.46
ACGTcount: A:0.59, C:0.00, G:0.02, T:0.39
Consensus pattern (14 bp):
TATTAATAAATAAA
Found at i:128321 original size:5 final size:5
Alignment explanation
Indices: 128311--128338 Score: 56
Period size: 5 Copynumber: 5.6 Consensus size: 5
128301 TATATTTTCA
128311 TTTAT TTTAT TTTAT TTTAT TTTAT TTT
1 TTTAT TTTAT TTTAT TTTAT TTTAT TTT
128339 CTAAATTAGA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 23 1.00
ACGTcount: A:0.18, C:0.00, G:0.00, T:0.82
Consensus pattern (5 bp):
TTTAT
Found at i:128323 original size:15 final size:16
Alignment explanation
Indices: 128303--128339 Score: 60
Period size: 15 Copynumber: 2.4 Consensus size: 16
128293 TATATATATA
128303 TATTTTCA-TTTATTT
1 TATTTTCATTTTATTT
128318 TATTTT-ATTTTATTT
1 TATTTTCATTTTATTT
128333 TATTTTC
1 TATTTTC
128340 TAAATTAGAA
Statistics
Matches: 20, Mismatches: 0, Indels: 3
0.87 0.00 0.13
Matches are distributed among these distances:
14 1 0.05
15 19 0.95
ACGTcount: A:0.19, C:0.05, G:0.00, T:0.76
Consensus pattern (16 bp):
TATTTTCATTTTATTT
Found at i:128443 original size:18 final size:18
Alignment explanation
Indices: 128407--128444 Score: 51
Period size: 18 Copynumber: 2.1 Consensus size: 18
128397 ATCACAAATT
*
128407 AAAAGAAAAAAAATTAAA
1 AAAAGAAAAAAAATGAAA
128425 AAAAGAAAAGAAAA-GAAA
1 AAAAGAAAA-AAAATGAAA
128443 AA
1 AA
128445 GCAAAAGGCG
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
18 14 0.78
19 4 0.22
ACGTcount: A:0.84, C:0.00, G:0.11, T:0.05
Consensus pattern (18 bp):
AAAAGAAAAAAAATGAAA
Found at i:128982 original size:13 final size:13
Alignment explanation
Indices: 128964--128988 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
128954 AAAGTGTTCA
128964 TTTTTTCTTTTTC
1 TTTTTTCTTTTTC
128977 TTTTTTCTTTTT
1 TTTTTTCTTTTT
128989 TGAGTAAATA
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:0.00, C:0.12, G:0.00, T:0.88
Consensus pattern (13 bp):
TTTTTTCTTTTTC
Found at i:132905 original size:2 final size:2
Alignment explanation
Indices: 132898--132950 Score: 106
Period size: 2 Copynumber: 26.5 Consensus size: 2
132888 AGAATAAAGA
132898 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
132940 AG AG AG AG AG A
1 AG AG AG AG AG A
132951 ATTAGAATAA
Statistics
Matches: 51, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 51 1.00
ACGTcount: A:0.51, C:0.00, G:0.49, T:0.00
Consensus pattern (2 bp):
AG
Found at i:155272 original size:2 final size:2
Alignment explanation
Indices: 155265--155289 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
155255 TAGTTTAAGA
155265 AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT A
155290 ACTCTTTTAT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:156001 original size:14 final size:14
Alignment explanation
Indices: 155963--156002 Score: 62
Period size: 14 Copynumber: 2.9 Consensus size: 14
155953 AGCCAGCGCT
*
155963 TTGAAGCCTAACCG
1 TTGAAGCCTAGCCG
155977 TTGAAGCCTAGCCG
1 TTGAAGCCTAGCCG
*
155991 TTGGAGCCTAGC
1 TTGAAGCCTAGC
156003 AACTCAAACC
Statistics
Matches: 24, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
14 24 1.00
ACGTcount: A:0.23, C:0.28, G:0.28, T:0.23
Consensus pattern (14 bp):
TTGAAGCCTAGCCG
Found at i:156294 original size:13 final size:12
Alignment explanation
Indices: 156269--156306 Score: 51
Period size: 12 Copynumber: 3.2 Consensus size: 12
156259 TTTGAATTAA
156269 ATATTTATTTTT
1 ATATTTATTTTT
*
156281 ATATTTAGTTTT
1 ATATTTATTTTT
*
156293 -TATTTAATTTT
1 ATATTTATTTTT
156304 ATA
1 ATA
156307 AAAAAAATTT
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
11 10 0.43
12 13 0.57
ACGTcount: A:0.29, C:0.00, G:0.03, T:0.68
Consensus pattern (12 bp):
ATATTTATTTTT
Found at i:156640 original size:1 final size:1
Alignment explanation
Indices: 156630--156670 Score: 64
Period size: 1 Copynumber: 41.0 Consensus size: 1
156620 CCTTCACTCT
* *
156630 CCCCCTCCCCCCCCCCCCACCCCCCCCCCCCCCCCCCCCCC
1 CCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCC
156671 TTCTCCTTTC
Statistics
Matches: 36, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
1 36 1.00
ACGTcount: A:0.02, C:0.95, G:0.00, T:0.02
Consensus pattern (1 bp):
C
Found at i:158001 original size:3 final size:3
Alignment explanation
Indices: 157993--158021 Score: 58
Period size: 3 Copynumber: 9.7 Consensus size: 3
157983 CATTTCGATC
157993 ATG ATG ATG ATG ATG ATG ATG ATG ATG AT
1 ATG ATG ATG ATG ATG ATG ATG ATG ATG AT
158022 TATTCTTTCT
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 26 1.00
ACGTcount: A:0.34, C:0.00, G:0.31, T:0.34
Consensus pattern (3 bp):
ATG
Found at i:158805 original size:2 final size:2
Alignment explanation
Indices: 158800--158831 Score: 64
Period size: 2 Copynumber: 16.0 Consensus size: 2
158790 TTTAAAAAAC
158800 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
158832 AACTTTAGGA
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 30 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:159552 original size:22 final size:22
Alignment explanation
Indices: 159505--159557 Score: 63
Period size: 22 Copynumber: 2.4 Consensus size: 22
159495 TTTAAAATAG
* *
159505 ATTTAAATTTTTTTATTTTAAT
1 ATTTAAATATTTTTATGTTAAT
*
159527 ATTTATATATTTTTATAGTTAA-
1 ATTTAAATATTTTTAT-GTTAAT
159549 ATTTAAATA
1 ATTTAAATA
159558 AAATATTTTT
Statistics
Matches: 26, Mismatches: 4, Indels: 2
0.81 0.12 0.06
Matches are distributed among these distances:
22 22 0.85
23 4 0.15
ACGTcount: A:0.38, C:0.00, G:0.02, T:0.60
Consensus pattern (22 bp):
ATTTAAATATTTTTATGTTAAT
Found at i:161359 original size:28 final size:28
Alignment explanation
Indices: 161319--161376 Score: 107
Period size: 28 Copynumber: 2.1 Consensus size: 28
161309 ATTCCCCCAA
161319 AACTCATTCTTCCACCAAAAAGTAAGTT
1 AACTCATTCTTCCACCAAAAAGTAAGTT
*
161347 AACTCATTCTTCCGCCAAAAAGTAAGTT
1 AACTCATTCTTCCACCAAAAAGTAAGTT
161375 AA
1 AA
161377 GTTTCTTTGT
Statistics
Matches: 29, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
28 29 1.00
ACGTcount: A:0.40, C:0.24, G:0.09, T:0.28
Consensus pattern (28 bp):
AACTCATTCTTCCACCAAAAAGTAAGTT
Found at i:164572 original size:4 final size:4
Alignment explanation
Indices: 164565--164589 Score: 50
Period size: 4 Copynumber: 6.2 Consensus size: 4
164555 CTTGTTTCTT
164565 TTTA TTTA TTTA TTTA TTTA TTTA T
1 TTTA TTTA TTTA TTTA TTTA TTTA T
164590 CAATACCAAA
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 21 1.00
ACGTcount: A:0.24, C:0.00, G:0.00, T:0.76
Consensus pattern (4 bp):
TTTA
Found at i:165606 original size:18 final size:17
Alignment explanation
Indices: 165585--165657 Score: 53
Period size: 18 Copynumber: 4.2 Consensus size: 17
165575 TATTATGTTA
165585 ATTATATATATTTATTAT
1 ATTAT-TATATTTATTAT
*
165603 ATTATTTTTATTT-TTAT
1 ATTA-TTATATTTATTAT
* *
165620 -TT-TTATTTTTATTAA
1 ATTATTATATTTATTAT
165635 ATGTATTATATTCGTATTAT
1 AT-TATTATATT--TATTAT
165655 ATT
1 ATT
165658 TTAATATTAT
Statistics
Matches: 42, Mismatches: 6, Indels: 13
0.69 0.10 0.21
Matches are distributed among these distances:
14 6 0.14
15 3 0.07
16 3 0.07
17 5 0.12
18 16 0.38
19 2 0.05
20 7 0.17
ACGTcount: A:0.30, C:0.01, G:0.03, T:0.66
Consensus pattern (17 bp):
ATTATTATATTTATTAT
Found at i:165615 original size:6 final size:6
Alignment explanation
Indices: 165604--165632 Score: 58
Period size: 6 Copynumber: 4.8 Consensus size: 6
165594 ATTTATTATA
165604 TTATTT TTATTT TTATTT TTATTT TTATT
1 TTATTT TTATTT TTATTT TTATTT TTATT
165633 AAATGTATTA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 23 1.00
ACGTcount: A:0.17, C:0.00, G:0.00, T:0.83
Consensus pattern (6 bp):
TTATTT
Found at i:166376 original size:15 final size:14
Alignment explanation
Indices: 166356--166415 Score: 63
Period size: 15 Copynumber: 4.4 Consensus size: 14
166346 TATAAATGTT
166356 TTAAAATATAATATA
1 TTAAAATAT-ATATA
*
166371 TTAAAAT-TTTAT-
1 TTAAAATATATATA
166383 TTAAAA-ATATATA
1 TTAAAATATATATA
*
166396 TTAAAATATAACATA
1 TTAAAATAT-ATATA
166411 TTAAA
1 TTAAA
166416 TAATTTTAAA
Statistics
Matches: 38, Mismatches: 3, Indels: 8
0.78 0.06 0.16
Matches are distributed among these distances:
12 10 0.26
13 9 0.24
14 3 0.08
15 16 0.42
ACGTcount: A:0.57, C:0.02, G:0.00, T:0.42
Consensus pattern (14 bp):
TTAAAATATATATA
Found at i:166377 original size:25 final size:24
Alignment explanation
Indices: 166349--166402 Score: 65
Period size: 25 Copynumber: 2.2 Consensus size: 24
166339 TATTATTTAT
166349 AAATGT-TTTAAAATATAATATATTA
1 AAATGTATTTAAAA-AT-ATATATTA
*
166374 AAATTTTATTTAAAAATATATATTA
1 AAA-TGTATTTAAAAATATATATTA
166399 AAAT
1 AAAT
166403 ATAACATATT
Statistics
Matches: 26, Mismatches: 1, Indels: 5
0.81 0.03 0.16
Matches are distributed among these distances:
24 1 0.04
25 14 0.54
26 4 0.15
27 7 0.27
ACGTcount: A:0.54, C:0.00, G:0.02, T:0.44
Consensus pattern (24 bp):
AAATGTATTTAAAAATATATATTA
Found at i:166388 original size:12 final size:13
Alignment explanation
Indices: 166356--166402 Score: 51
Period size: 12 Copynumber: 3.5 Consensus size: 13
166346 TATAAATGTT
166356 TTAAAATATAATATA
1 TTAAAAT-T-ATATA
*
166371 TTAAAATTTTAT-
1 TTAAAATTATATA
*
166383 TTAAAAATATATA
1 TTAAAATTATATA
166396 TTAAAAT
1 TTAAAAT
166403 ATAACATATT
Statistics
Matches: 27, Mismatches: 4, Indels: 4
0.77 0.11 0.11
Matches are distributed among these distances:
12 10 0.37
13 9 0.33
14 1 0.04
15 7 0.26
ACGTcount: A:0.55, C:0.00, G:0.00, T:0.45
Consensus pattern (13 bp):
TTAAAATTATATA
Found at i:166898 original size:18 final size:21
Alignment explanation
Indices: 166877--166925 Score: 59
Period size: 21 Copynumber: 2.4 Consensus size: 21
166867 ATAAAAAAAT
166877 TTAAATTT-TAT-TTATAT-A
1 TTAAATTTATATATTATATAA
*
166895 TTAATATTTATATATTTTATAA
1 TTAA-ATTTATATATTATATAA
166917 TTAAATTTA
1 TTAAATTTA
166926 AATAAAATAT
Statistics
Matches: 26, Mismatches: 1, Indels: 5
0.81 0.03 0.16
Matches are distributed among these distances:
18 4 0.15
19 4 0.15
20 3 0.12
21 10 0.38
22 5 0.19
ACGTcount: A:0.41, C:0.00, G:0.00, T:0.59
Consensus pattern (21 bp):
TTAAATTTATATATTATATAA
Found at i:166935 original size:28 final size:29
Alignment explanation
Indices: 166904--166960 Score: 73
Period size: 28 Copynumber: 2.0 Consensus size: 29
166894 ATTAATATTT
166904 ATATATTTT-ATAATTAAAT-TTAAATAAA
1 ATAT-TTTTAATAATTAAATATTAAATAAA
* *
166932 ATATTTTTAATTATTAAATATTAATTAAA
1 ATATTTTTAATAATTAAATATTAAATAAA
166961 TAAAAATAAA
Statistics
Matches: 25, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
27 4 0.16
28 13 0.52
29 8 0.32
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (29 bp):
ATATTTTTAATAATTAAATATTAAATAAA
Found at i:166983 original size:39 final size:39
Alignment explanation
Indices: 166914--166988 Score: 89
Period size: 39 Copynumber: 1.9 Consensus size: 39
166904 ATATATTTTA
** * * *
166914 TAATTAAATTTAAATAAAATATTTTTAATTATTAAATAT
1 TAATTAAATAAAAATAAAATAGTTTAAATTAATAAATAT
166953 TAATTAAATAAAAAT-AAATAAGTTTAAATTAATAAA
1 TAATTAAATAAAAATAAAAT-AGTTTAAATTAATAAA
166989 AAACTTATTT
Statistics
Matches: 30, Mismatches: 5, Indels: 2
0.81 0.14 0.05
Matches are distributed among these distances:
38 4 0.13
39 26 0.87
ACGTcount: A:0.57, C:0.00, G:0.01, T:0.41
Consensus pattern (39 bp):
TAATTAAATAAAAATAAAATAGTTTAAATTAATAAATAT
Found at i:173217 original size:19 final size:20
Alignment explanation
Indices: 173174--173217 Score: 54
Period size: 19 Copynumber: 2.2 Consensus size: 20
173164 CATTCATAAA
173174 TTAAATTATTTATATAAAAT
1 TTAAATTATTTATATAAAAT
* * *
173194 ATAAA-TATTTATTTAATAT
1 TTAAATTATTTATATAAAAT
173213 TTAAA
1 TTAAA
173218 AAAATTAGAT
Statistics
Matches: 20, Mismatches: 4, Indels: 1
0.80 0.16 0.04
Matches are distributed among these distances:
19 16 0.80
20 4 0.20
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (20 bp):
TTAAATTATTTATATAAAAT
Found at i:173270 original size:22 final size:22
Alignment explanation
Indices: 173245--173292 Score: 53
Period size: 22 Copynumber: 2.2 Consensus size: 22
173235 TTAAATTAGA
*
173245 AAATAAATTTAAATAAA-AAATT
1 AAATAAATTTAAA-AAATAAATC
**
173267 AAATTCATTTAAAAAATAAATC
1 AAATAAATTTAAAAAATAAATC
173289 AAAT
1 AAAT
173293 CATAATTGTT
Statistics
Matches: 22, Mismatches: 3, Indels: 2
0.81 0.11 0.07
Matches are distributed among these distances:
21 3 0.14
22 19 0.86
ACGTcount: A:0.65, C:0.04, G:0.00, T:0.31
Consensus pattern (22 bp):
AAATAAATTTAAAAAATAAATC
Found at i:173353 original size:24 final size:24
Alignment explanation
Indices: 173326--173378 Score: 65
Period size: 24 Copynumber: 2.2 Consensus size: 24
173316 GACTTGATTT
173326 ATTTTATAATTATATA-ATATA-TTA
1 ATTTTAT-ATTATATATAT-TAGTTA
*
173350 ATTTTATATTTTATATATTAGTTA
1 ATTTTATATTATATATATTAGTTA
173374 ATTTT
1 ATTTT
173379 TATCATGTAA
Statistics
Matches: 26, Mismatches: 1, Indels: 4
0.84 0.03 0.13
Matches are distributed among these distances:
23 9 0.35
24 17 0.65
ACGTcount: A:0.38, C:0.00, G:0.02, T:0.60
Consensus pattern (24 bp):
ATTTTATATTATATATATTAGTTA
Found at i:173417 original size:30 final size:30
Alignment explanation
Indices: 173361--173417 Score: 71
Period size: 30 Copynumber: 1.9 Consensus size: 30
173351 TTTTATATTT
* *
173361 TATATATTAGTTAATTTTTATCATGTAAAA
1 TATATATTAGTTAATTATTATAATGTAAAA
*
173391 TATATATATATTTAA-TATTATAATGTA
1 TATATAT-TAGTTAATTATTATAATGTA
173418 CATTAAAAAA
Statistics
Matches: 23, Mismatches: 3, Indels: 2
0.82 0.11 0.07
Matches are distributed among these distances:
30 17 0.74
31 6 0.26
ACGTcount: A:0.42, C:0.02, G:0.05, T:0.51
Consensus pattern (30 bp):
TATATATTAGTTAATTATTATAATGTAAAA
Done.