Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: scaffold333
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: 1398653
ACGTcount: A:0.32, C:0.15, G:0.16, T:0.32
Warning! 76431 characters in sequence are not A, C, G, or T
File 1 of 5
Found at i:5109 original size:12 final size:12
Alignment explanation
Indices: 5083--5125 Score: 61
Period size: 12 Copynumber: 3.7 Consensus size: 12
5073 AATATAATAT
*
5083 AAAGAAAA-TAA
1 AAAGAAAACAAA
5094 AAAGAAAACAAA
1 AAAGAAAACAAA
*
5106 AAAGAAAACGAA
1 AAAGAAAACAAA
5118 AAAGAAAA
1 AAAGAAAA
5126 AGTGTCAATA
Statistics
Matches: 29, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
11 8 0.28
12 21 0.72
ACGTcount: A:0.81, C:0.05, G:0.12, T:0.02
Consensus pattern (12 bp):
AAAGAAAACAAA
Found at i:5346 original size:19 final size:19
Alignment explanation
Indices: 5318--5368 Score: 54
Period size: 19 Copynumber: 2.8 Consensus size: 19
5308 GAAAAAAAAC
* *
5318 TAAAACTAAATAATATTAA
1 TAAAAATAAATAATATGAA
5337 TAAAAATAAAATAA-ATGAA
1 TAAAAAT-AAATAATATGAA
5356 T-AAAAT-AATAATA
1 TAAAAATAAATAATA
5369 ACTAACAGAA
Statistics
Matches: 28, Mismatches: 2, Indels: 6
0.78 0.06 0.17
Matches are distributed among these distances:
16 5 0.18
17 1 0.04
18 5 0.18
19 11 0.39
20 6 0.21
ACGTcount: A:0.69, C:0.02, G:0.02, T:0.27
Consensus pattern (19 bp):
TAAAAATAAATAATATGAA
Found at i:5362 original size:24 final size:25
Alignment explanation
Indices: 5312--5369 Score: 66
Period size: 24 Copynumber: 2.3 Consensus size: 25
5302 TACTGTGAAA
*
5312 AAAAACTAAAACTAAATAATATTAAT
1 AAAAA-TAAAACTAAATAATATAAAT
5338 AAAAATAAAA-TAAATGAATA-AAAT
1 AAAAATAAAACTAAAT-AATATAAAT
*
5362 AATAATAA
1 AAAAATAA
5370 CTAACAGAAT
Statistics
Matches: 29, Mismatches: 2, Indels: 4
0.83 0.06 0.11
Matches are distributed among these distances:
24 15 0.52
25 9 0.31
26 5 0.17
ACGTcount: A:0.71, C:0.03, G:0.02, T:0.24
Consensus pattern (25 bp):
AAAAATAAAACTAAATAATATAAAT
Found at i:7248 original size:12 final size:12
Alignment explanation
Indices: 7231--7262 Score: 64
Period size: 12 Copynumber: 2.7 Consensus size: 12
7221 AATTGATTCT
7231 AATATTTACACA
1 AATATTTACACA
7243 AATATTTACACA
1 AATATTTACACA
7255 AATATTTA
1 AATATTTA
7263 ATTAGACAAT
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:0.50, C:0.12, G:0.00, T:0.38
Consensus pattern (12 bp):
AATATTTACACA
Found at i:10852 original size:18 final size:19
Alignment explanation
Indices: 10831--10868 Score: 53
Period size: 18 Copynumber: 2.1 Consensus size: 19
10821 TTAAATTCTA
10831 ATTTAACCCAA-AAT-ATTT
1 ATTT-ACCCAAGAATCATTT
10849 ATTTACCCAAGAATCATTT
1 ATTTACCCAAGAATCATTT
10868 A
1 A
10869 AAACTATAAA
Statistics
Matches: 18, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
17 6 0.33
18 7 0.39
19 5 0.28
ACGTcount: A:0.42, C:0.18, G:0.03, T:0.37
Consensus pattern (19 bp):
ATTTACCCAAGAATCATTT
Found at i:12376 original size:56 final size:59
Alignment explanation
Indices: 12302--12427 Score: 179
Period size: 56 Copynumber: 2.1 Consensus size: 59
12292 TCCAGGCTAA
12302 ATCCATTTTCCACATATTCTTCGGGAGGGCTATATC-A-A-GATCACCCGTCCGGGATAG
1 ATCC-TTTTCCACATATTCTTCGGGAGGGCTATATCGATAGGATCACCCGTCCGGGATAG
*
12359 AT-CTTTTCACACATATTCTTCGGGAGGGCTATATCAGGATAGGATCACCCGTCCGGGCTAG
1 ATCCTTTTC-CACATATTCTTCGGGAGGGCTATATC--GATAGGATCACCCGTCCGGGATAG
12420 ATCCTTTT
1 ATCCTTTT
12428 TACCGTCAAT
Statistics
Matches: 61, Mismatches: 1, Indels: 9
0.86 0.01 0.13
Matches are distributed among these distances:
55 5 0.08
56 27 0.44
57 2 0.03
59 1 0.02
60 1 0.02
61 20 0.33
62 5 0.08
ACGTcount: A:0.23, C:0.25, G:0.21, T:0.30
Consensus pattern (59 bp):
ATCCTTTTCCACATATTCTTCGGGAGGGCTATATCGATAGGATCACCCGTCCGGGATAG
Found at i:15808 original size:31 final size:30
Alignment explanation
Indices: 15772--15945 Score: 124
Period size: 31 Copynumber: 5.7 Consensus size: 30
15762 CCCATTTTTA
15772 TTTTAAAA-ATTTTAAAAAATTAAAAAAGTAT
1 TTTTAAAATATTTT-AAAAATTAAAAAA-TAT
15803 TTTTAAAATATTTT-AAAATTAAAAAAAGTAT
1 TTTTAAAATATTTTAAAAATT-AAAAAA-TAT
* *
15834 TTTAAAAATATTTT-AAAATTAAAAAAAAT
1 TTTTAAAATATTTTAAAAATTAAAAAATAT
*** ***
15863 TAAAAAAAGTATTTTAAAAATATTTTAAA-A-
1 TTTTAAAA-TATTTTAAAAAT-TAAAAAATAT
** *
15893 TTAAAAAATATTTTAAAAATATTTTAAAAATAT
1 TTTTAAAATATTTT-AAAA-A-TTAAAAAATAT
*
15926 TTTAAAAATATTTTAAAAAT
1 TTTTAAAATATTTTAAAAAT
15946 ATTTTAAAAT
Statistics
Matches: 122, Mismatches: 11, Indels: 21
0.79 0.07 0.14
Matches are distributed among these distances:
29 14 0.11
30 30 0.25
31 50 0.41
32 15 0.12
33 13 0.11
ACGTcount: A:0.58, C:0.00, G:0.02, T:0.40
Consensus pattern (30 bp):
TTTTAAAATATTTTAAAAATTAAAAAATAT
Found at i:15811 original size:30 final size:30
Alignment explanation
Indices: 15770--15881 Score: 138
Period size: 30 Copynumber: 3.7 Consensus size: 30
15760 GGCCCATTTT
*
15770 TATTTTAAAAAT-TTTAAAAAATTAAAAAAG
1 TATTTTAAAAATATTT-TAAAATTAAAAAAG
*
15800 TATTTTTAAAATATTTTAAAATTAAAAAAAG
1 TATTTTAAAAATATTTTAAAATT-AAAAAAG
15831 TATTTTAAAAATATTTTAAAATTAAAAAA-
1 TATTTTAAAAATATTTTAAAATTAAAAAAG
* **
15860 AATTAAAAAAAGTATTTTAAAA
1 TATTTTAAAAA-TATTTTAAAA
15882 ATATTTTAAA
Statistics
Matches: 73, Mismatches: 6, Indels: 6
0.86 0.07 0.07
Matches are distributed among these distances:
29 8 0.11
30 33 0.45
31 32 0.44
ACGTcount: A:0.59, C:0.00, G:0.03, T:0.38
Consensus pattern (30 bp):
TATTTTAAAAATATTTTAAAATTAAAAAAG
Found at i:15816 original size:11 final size:10
Alignment explanation
Indices: 15770--15955 Score: 114
Period size: 11 Copynumber: 18.1 Consensus size: 10
15760 GGCCCATTTT
15770 TATTTTAAAA
1 TATTTTAAAA
15780 -ATTTTAAAA
1 TATTTTAAAA
* **
15789 AATTAAAAAA
1 TATTTTAAAA
15799 GTATTTTTAAAA
1 -TA-TTTTAAAA
15811 TATTTTAAAA
1 TATTTTAAAA
***
15821 T-TAAAAAAA
1 TATTTTAAAA
15830 GTATTTTAAAAA
1 -TATTTT-AAAA
15842 TATTTT-AAA
1 TATTTTAAAA
**
15851 -ATTAAAAAA
1 TATTTTAAAA
* **
15860 AATTAAAAAAA
1 TATT-TTAAAA
15871 GTATTTTAAAAA
1 -TATTTT-AAAA
15883 TATTTT-AAA
1 TATTTTAAAA
**
15892 -ATTAAAAAA
1 TATTTTAAAA
15901 TATTTTAAAAA
1 TATTTT-AAAA
15912 TATTTTAAAAA
1 TATTTT-AAAA
15923 TATTTTAAAAA
1 TATTTT-AAAA
15934 TATTTTAAAAA
1 TATTTT-AAAA
15945 TATTTTAAAA
1 TATTTTAAAA
15955 T
1 T
15956 TAAAAAATAA
Statistics
Matches: 142, Mismatches: 20, Indels: 28
0.75 0.11 0.15
Matches are distributed among these distances:
8 6 0.04
9 26 0.18
10 28 0.20
11 65 0.46
12 17 0.12
ACGTcount: A:0.58, C:0.00, G:0.02, T:0.41
Consensus pattern (10 bp):
TATTTTAAAA
Found at i:15848 original size:41 final size:40
Alignment explanation
Indices: 15817--15932 Score: 189
Period size: 41 Copynumber: 2.9 Consensus size: 40
15807 AAAATATTTT
15817 AAAATTAAAAAAAGTATTTTAAAAATATTTTAAAATTAAAA
1 AAAATTAAAAAAAGTATTTTAAAAATATTTTAAAATT-AAA
15858 AAAATTAAAAAAAGTATTTTAAAAATATTTTAAAATTAAA
1 AAAATTAAAAAAAGTATTTTAAAAATATTTTAAAATTAAA
**
15898 AAATATTTTAAAAA-TATTTTAAAAATATTTTAAAA
1 AAA-ATTAAAAAAAGTATTTTAAAAATATTTTAAAA
15933 ATATTTTAAA
Statistics
Matches: 72, Mismatches: 2, Indels: 3
0.94 0.03 0.04
Matches are distributed among these distances:
40 27 0.38
41 45 0.62
ACGTcount: A:0.61, C:0.00, G:0.02, T:0.37
Consensus pattern (40 bp):
AAAATTAAAAAAAGTATTTTAAAAATATTTTAAAATTAAA
Found at i:15984 original size:62 final size:63
Alignment explanation
Indices: 15776--15986 Score: 202
Period size: 62 Copynumber: 3.3 Consensus size: 63
15766 TTTTTATTTT
*
15776 AAAA-ATTTT-AAAAA-ATT-AAAAAAGTATTTTTAAAATATTTTAAAATTAAAAAAAGTATTTT
1 AAAATATTTTAAAAAATATTAAAAAAAGTATTTTAAAAATATTTTAAAATT-AAAAAA-TA---T
15837 AAA
61 AAA
* * *
15840 AATATTTTAAAATTAAAAAAAATTAAAAAAAGTATTTTAAAAATATTTTAAAATTAAAAAATATT
1 AAAATATT----TTAAAAAATATTAAAAAAAGTATTTTAAAAATATTTTAAAATTAAAAAATA-T
**
15905 TTA
61 AAA
**
15908 AAAATATTTT-AAAAATATTTTAAAAA-TATTTTAAAAATATTTTAAAATTAAAAAATA-AAA
1 AAAATATTTTAAAAAATATTAAAAAAAGTATTTTAAAAATATTTTAAAATTAAAAAATATAAA
15968 AAAAGTATTTTAAAAAATA
1 AAAA-TATTTTAAAAAATA
15987 AATATATTTA
Statistics
Matches: 125, Mismatches: 12, Indels: 22
0.79 0.08 0.14
Matches are distributed among these distances:
60 5 0.04
61 6 0.05
62 38 0.30
63 13 0.10
64 5 0.04
65 2 0.02
68 9 0.07
69 2 0.02
70 7 0.06
71 9 0.07
72 29 0.23
ACGTcount: A:0.61, C:0.00, G:0.02, T:0.37
Consensus pattern (63 bp):
AAAATATTTTAAAAAATATTAAAAAAAGTATTTTAAAAATATTTTAAAATTAAAAAATATAAA
Found at i:27255 original size:12 final size:13
Alignment explanation
Indices: 27227--27255 Score: 51
Period size: 13 Copynumber: 2.3 Consensus size: 13
27217 TTCATTTTCA
27227 ATAAAATTCATAT
1 ATAAAATTCATAT
27240 ATAAAATTCA-AT
1 ATAAAATTCATAT
27252 ATAA
1 ATAA
27256 TCAAAAATAT
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
12 6 0.38
13 10 0.62
ACGTcount: A:0.59, C:0.07, G:0.00, T:0.34
Consensus pattern (13 bp):
ATAAAATTCATAT
Found at i:32225 original size:48 final size:50
Alignment explanation
Indices: 32163--32308 Score: 183
Period size: 54 Copynumber: 2.9 Consensus size: 50
32153 TAAATTATGG
*
32163 AGTTAGTTAAATATACAATAATTTACAAAAAAATCATGTAGCAATTCACA-T
1 AGTTA-TTAAATATACAATAATTTAC-AAAAAATCATGTAGCAATTCAAATT
*
32214 A-TT-TTAAATATACAATAATTTACAAAAAATCATGTAG-AATTTAAATT
1 AGTTATTAAATATACAATAATTTACAAAAAATCATGTAGCAATTCAAATT
32261 ATGGGGTTAGTTAAATATACAATAATTTACAAAAAATCATGTAGCAAT
1 A----GTTA-TTAAATATACAATAATTTACAAAAAATCATGTAGCAAT
32309 AATCGACAAT
Statistics
Matches: 84, Mismatches: 2, Indels: 14
0.84 0.02 0.14
Matches are distributed among these distances:
46 6 0.07
47 16 0.19
48 20 0.24
50 2 0.02
51 1 0.01
52 2 0.02
54 34 0.40
55 3 0.04
ACGTcount: A:0.49, C:0.09, G:0.09, T:0.34
Consensus pattern (50 bp):
AGTTATTAAATATACAATAATTTACAAAAAATCATGTAGCAATTCAAATT
Found at i:37057 original size:42 final size:42
Alignment explanation
Indices: 36982--37092 Score: 143
Period size: 42 Copynumber: 2.6 Consensus size: 42
36972 GTACATAAAT
* *
36982 GCTAAACGAAAACCCGTAAGGGTTAAATGGAAGCTCATAGGA
1 GCTAAACGAAAACCCGTAAGGGTTAAATGGAAGCTCAGAAGA
* * * *
37024 GCTGAACGGAAACCCGTAAGGGTTAATTTGAAGCTCAGAAGA
1 GCTAAACGAAAACCCGTAAGGGTTAAATGGAAGCTCAGAAGA
*
37066 GCTAAACTAAAACCCAG-AAGGGTTAAA
1 GCTAAACGAAAACCC-GTAAGGGTTAAA
37093 CTGAAACTCA
Statistics
Matches: 58, Mismatches: 10, Indels: 2
0.83 0.14 0.03
Matches are distributed among these distances:
42 57 0.98
43 1 0.02
ACGTcount: A:0.41, C:0.17, G:0.25, T:0.17
Consensus pattern (42 bp):
GCTAAACGAAAACCCGTAAGGGTTAAATGGAAGCTCAGAAGA
Found at i:37085 original size:21 final size:21
Alignment explanation
Indices: 37059--37099 Score: 55
Period size: 21 Copynumber: 2.0 Consensus size: 21
37049 ATTTGAAGCT
37059 CAGAAGAGCTAAACTAAAACC
1 CAGAAGAGCTAAACTAAAACC
* * *
37080 CAGAAGGGTTAAACTGAAAC
1 CAGAAGAGCTAAACTAAAAC
37100 TCATATGAGT
Statistics
Matches: 17, Mismatches: 3, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
21 17 1.00
ACGTcount: A:0.49, C:0.20, G:0.20, T:0.12
Consensus pattern (21 bp):
CAGAAGAGCTAAACTAAAACC
Found at i:38387 original size:20 final size:21
Alignment explanation
Indices: 38330--38397 Score: 111
Period size: 21 Copynumber: 3.3 Consensus size: 21
38320 ATATTTACAA
*
38330 CTCGATTTATAAAATTAAGGT
1 CTCGATTTATAAAATTGAGGT
*
38351 CTCAATTTATAAAATTGAGGT
1 CTCGATTTATAAAATTGAGGT
38372 CTCGATTTAT-AAATTGAGGT
1 CTCGATTTATAAAATTGAGGT
38392 CTCGAT
1 CTCGAT
38398 ACCCCGTTTT
Statistics
Matches: 44, Mismatches: 3, Indels: 1
0.92 0.06 0.02
Matches are distributed among these distances:
20 16 0.36
21 28 0.64
ACGTcount: A:0.34, C:0.12, G:0.16, T:0.38
Consensus pattern (21 bp):
CTCGATTTATAAAATTGAGGT
Found at i:41376 original size:17 final size:18
Alignment explanation
Indices: 41354--41387 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
41344 AAAATTGTAA
41354 TTTAAAT-TCTAATTATT
1 TTTAAATGTCTAATTATT
*
41371 TTTAAATGTGTAATTAT
1 TTTAAATGTCTAATTAT
41388 CTCAACTTCT
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 7 0.47
18 8 0.53
ACGTcount: A:0.35, C:0.03, G:0.06, T:0.56
Consensus pattern (18 bp):
TTTAAATGTCTAATTATT
Found at i:44140 original size:18 final size:18
Alignment explanation
Indices: 44117--44151 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
44107 TTACATATAA
44117 AAATAATAATTATATTTG
1 AAATAATAATTATATTTG
* *
44135 AAATAATTATTTTATTT
1 AAATAATAATTATATTT
44152 TATAATATTA
Statistics
Matches: 15, Mismatches: 2, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
18 15 1.00
ACGTcount: A:0.46, C:0.00, G:0.03, T:0.51
Consensus pattern (18 bp):
AAATAATAATTATATTTG
Found at i:48766 original size:21 final size:22
Alignment explanation
Indices: 48742--48784 Score: 61
Period size: 22 Copynumber: 2.0 Consensus size: 22
48732 AACAAATTTA
*
48742 AGTA-TGTTGCATTGCAAAAGC
1 AGTATTGTTGCACTGCAAAAGC
*
48763 AGTATTGTTGTACTGCAAAAGC
1 AGTATTGTTGCACTGCAAAAGC
48785 TGATTCTGTT
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
21 4 0.21
22 15 0.79
ACGTcount: A:0.33, C:0.14, G:0.23, T:0.30
Consensus pattern (22 bp):
AGTATTGTTGCACTGCAAAAGC
Found at i:52083 original size:39 final size:39
Alignment explanation
Indices: 52025--52104 Score: 142
Period size: 39 Copynumber: 2.1 Consensus size: 39
52015 ATCTGTGCCT
52025 AAATCTGAGGGAGAAGTTAATGTGGCAACTGATTCTTCA
1 AAATCTGAGGGAGAAGTTAATGTGGCAACTGATTCTTCA
* *
52064 AAATCTGATGGAGAGGTTAATGTGGCAACTGATTCTTCA
1 AAATCTGAGGGAGAAGTTAATGTGGCAACTGATTCTTCA
52103 AA
1 AA
52105 GGCTGCTGTT
Statistics
Matches: 39, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
39 39 1.00
ACGTcount: A:0.34, C:0.12, G:0.25, T:0.29
Consensus pattern (39 bp):
AAATCTGAGGGAGAAGTTAATGTGGCAACTGATTCTTCA
Found at i:62306 original size:30 final size:30
Alignment explanation
Indices: 62234--62319 Score: 86
Period size: 31 Copynumber: 2.9 Consensus size: 30
62224 GATTAAATTA
*
62234 AAATTAAAGTTTCAAGTATACATTTGAACC
1 AAATTAAAGTTTCAAGTATACAATTGAACC
* * * *
62264 ACAATTAGAGTTTCACGTATATAATT-ACATC
1 A-AATTAAAGTTTCAAGTATACAATTGA-ACC
*
62295 AAATTAAAGTTT-ATGTATACAATTG
1 AAATTAAAGTTTCAAGTATACAATTG
62320 CACATTAAAC
Statistics
Matches: 45, Mismatches: 8, Indels: 6
0.76 0.14 0.10
Matches are distributed among these distances:
29 10 0.22
30 12 0.27
31 23 0.51
ACGTcount: A:0.42, C:0.12, G:0.10, T:0.36
Consensus pattern (30 bp):
AAATTAAAGTTTCAAGTATACAATTGAACC
Found at i:62843 original size:3 final size:3
Alignment explanation
Indices: 62835--62888 Score: 99
Period size: 3 Copynumber: 18.0 Consensus size: 3
62825 CATAGTGAGA
*
62835 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AGT AAT AAT AAT
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
62883 AAT AAT
1 AAT AAT
62889 CTCTAGTTTC
Statistics
Matches: 49, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
3 49 1.00
ACGTcount: A:0.65, C:0.00, G:0.02, T:0.33
Consensus pattern (3 bp):
AAT
Found at i:69332 original size:25 final size:24
Alignment explanation
Indices: 69304--69356 Score: 88
Period size: 25 Copynumber: 2.2 Consensus size: 24
69294 ACATATCGCA
69304 GCTCTTTATGAGCGTCCTGATATAG
1 GCTCTTTATGAGCGTCCTGATAT-G
*
69329 GCTCTTTATGAGCTTCCTGATATG
1 GCTCTTTATGAGCGTCCTGATATG
69353 GCTC
1 GCTC
69357 GCTTGAACTT
Statistics
Matches: 27, Mismatches: 1, Indels: 1
0.93 0.03 0.03
Matches are distributed among these distances:
24 5 0.19
25 22 0.81
ACGTcount: A:0.17, C:0.23, G:0.23, T:0.38
Consensus pattern (24 bp):
GCTCTTTATGAGCGTCCTGATATG
Found at i:76311 original size:7 final size:7
Alignment explanation
Indices: 76301--76332 Score: 55
Period size: 7 Copynumber: 4.6 Consensus size: 7
76291 TGTTTCAAGT
*
76301 TTCATTC
1 TTCAATC
76308 TTCAATC
1 TTCAATC
76315 TTCAATC
1 TTCAATC
76322 TTCAATC
1 TTCAATC
76329 TTCA
1 TTCA
76333 TATTTAATTA
Statistics
Matches: 24, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
7 24 1.00
ACGTcount: A:0.25, C:0.28, G:0.00, T:0.47
Consensus pattern (7 bp):
TTCAATC
Found at i:88183 original size:31 final size:31
Alignment explanation
Indices: 88146--88211 Score: 100
Period size: 31 Copynumber: 2.1 Consensus size: 31
88136 TTTTTATTAG
88146 TATATGAATATTATGTTTGTTGATA-TATGA-A
1 TATATGAATATTATGTTTG--GATATTATGACA
88177 TATATGAATATTATGTTTGGATATTATGACA
1 TATATGAATATTATGTTTGGATATTATGACA
88208 TATA
1 TATA
88212 ACCTAATGAA
Statistics
Matches: 33, Mismatches: 0, Indels: 4
0.89 0.00 0.11
Matches are distributed among these distances:
29 4 0.12
30 5 0.15
31 24 0.73
ACGTcount: A:0.36, C:0.02, G:0.15, T:0.47
Consensus pattern (31 bp):
TATATGAATATTATGTTTGGATATTATGACA
Found at i:91339 original size:51 final size:48
Alignment explanation
Indices: 91270--91444 Score: 163
Period size: 50 Copynumber: 3.5 Consensus size: 48
91260 AGGGAAGCAT
* *
91270 GATTCGCTGTTGTGGCTTTAATCTGCTTCACTGCACTGACTGGGAATGTAA
1 GATTCGCTGTTGTAGCTTTAATCTG-TTCACTGCACTG-CTGGG-AGGTAA
* * * *
91321 GATTCGCTGTTGTAGCTTTAATCTTTTTAACTGCGA-TGTTAGGGAGGAAA
1 GATTCGCTGTTGTAGCTTTAATC-TGTTCACTGC-ACTGCT-GGGAGGTAA
* * * *
91371 GATTCACCGTTGTGGCTTTAATCTGTTCCACTACACTGCTTGGGAGGTAA
1 GATTCGCTGTTGTAGCTTTAATCTGTT-CACTGCACTGC-TGGGAGGTAA
**
91421 GATTCGCTACTGTAGCTTTAATCT
1 GATTCGCTGTTGTAGCTTTAATCT
91445 TTTTAACCGC
Statistics
Matches: 99, Mismatches: 19, Indels: 13
0.76 0.15 0.10
Matches are distributed among these distances:
49 4 0.04
50 58 0.59
51 35 0.35
52 2 0.02
ACGTcount: A:0.21, C:0.18, G:0.24, T:0.37
Consensus pattern (48 bp):
GATTCGCTGTTGTAGCTTTAATCTGTTCACTGCACTGCTGGGAGGTAA
Found at i:91389 original size:50 final size:48
Alignment explanation
Indices: 91319--91494 Score: 136
Period size: 50 Copynumber: 3.5 Consensus size: 48
91309 CTGGGAATGT
* *
91319 AAGATTCGCTGTTGTAGCTTTAATCTTTTTAACTGCGATGTTAGGGAGGA
1 AAGATTCACCGTTGTAGCTTTAATCTTTTTAACTGC-ATGTT-GGGAGGA
* * ** * *
91369 AAGATTCACCGTTGTGGCTTTAATCTGTTCCACTACACTGCTTGGGAGGT
1 AAGATTCACCGTTGTAGCTTTAATCTTTTTAACTGCA-TG-TTGGGAGGA
* *** * * * *
91419 AAGATTCGCTACTGTAGCTTTAATCTTTTTAACCGCAATGTCGGGGAAGC
1 AAGATTCACCGTTGTAGCTTTAATCTTTTTAACTGC-ATGT-TGGGAGGA
* *
91469 AAGATTCACCGATGTGGCTTTAATCT
1 AAGATTCACCGTTGTAGCTTTAATCT
91495 GTTCCACTAC
Statistics
Matches: 96, Mismatches: 26, Indels: 8
0.74 0.20 0.06
Matches are distributed among these distances:
49 2 0.02
50 91 0.95
51 3 0.03
ACGTcount: A:0.24, C:0.18, G:0.23, T:0.35
Consensus pattern (48 bp):
AAGATTCACCGTTGTAGCTTTAATCTTTTTAACTGCATGTTGGGAGGA
Found at i:91473 original size:100 final size:100
Alignment explanation
Indices: 91216--91523 Score: 361
Period size: 100 Copynumber: 3.1 Consensus size: 100
91206 CTTTTGGAAA
* * * * * * * * *
91216 GTAAGATTTGCCATTGTGGCTTTAATATTTTCAACTACAATGTCAGGGAAGCATGATTCGCTGTT
1 GTAAGATTCGCTATTGTAGCTTTAATCTTTTTAACTGCAATGTCAGGGAAGCAAGATTCACCGTT
* *
91281 GTGGCTTTAATCTGCTT-CACTGCACTGAC-TGGGAAT
66 GTGGCTTTAATCTG-TTCCACTACACTG-CTTGGG-AG
* * * * *
91317 GTAAGATTCGCTGTTGTAGCTTTAATCTTTTTAACTGCGATGTTAGGGAGGAAAGATTCACCGTT
1 GTAAGATTCGCTATTGTAGCTTTAATCTTTTTAACTGCAATGTCAGGGAAGCAAGATTCACCGTT
91382 GTGGCTTTAATCTGTTCCACTACACTGCTTGGGAG
66 GTGGCTTTAATCTGTTCCACTACACTGCTTGGGAG
* * * *
91417 GTAAGATTCGCTACTGTAGCTTTAATCTTTTTAACCGCAATGTCGGGGAAGCAAGATTCACCGAT
1 GTAAGATTCGCTATTGTAGCTTTAATCTTTTTAACTGCAATGTCAGGGAAGCAAGATTCACCGTT
*
91482 GTGGCTTTAATCTGTTCCACTACA-TCGTTTGGGAG
66 GTGGCTTTAATCTGTTCCACTACACT-GCTTGGGAG
*
91517 ATAAGAT
1 GTAAGAT
91524 CTGTAATTCT
Statistics
Matches: 177, Mismatches: 27, Indels: 7
0.84 0.13 0.03
Matches are distributed among these distances:
99 1 0.01
100 98 0.55
101 78 0.44
ACGTcount: A:0.24, C:0.18, G:0.23, T:0.35
Consensus pattern (100 bp):
GTAAGATTCGCTATTGTAGCTTTAATCTTTTTAACTGCAATGTCAGGGAAGCAAGATTCACCGTT
GTGGCTTTAATCTGTTCCACTACACTGCTTGGGAG
Found at i:91523 original size:50 final size:50
Alignment explanation
Indices: 91369--91523 Score: 120
Period size: 50 Copynumber: 3.1 Consensus size: 50
91359 TTAGGGAGGA
* * *
91369 AAGATTCACCGTTGTGGCTTTAATCTGTTCCACTACA-CTGCTTGGGAGGT
1 AAGATTCACCGATGTGGCTTTAATCTGTTCCACTACATC-GTTTGGGAGAT
* * * * ** ** ** *
91419 AAGATTC-GCTACTGTAGCTTTAATCTTTTTAACCGCAAT-GTCGGGGA-AGC
1 AAGATTCACCGA-TGTGGCTTTAATCTGTTCCACTAC-ATCGTTTGGGAGA-T
91469 AAGATTCACCGATGTGGCTTTAATCTGTTCCACTACATCGTTTGGGAGAT
1 AAGATTCACCGATGTGGCTTTAATCTGTTCCACTACATCGTTTGGGAGAT
91519 AAGAT
1 AAGAT
91524 CTGTAATTCT
Statistics
Matches: 73, Mismatches: 25, Indels: 14
0.65 0.22 0.12
Matches are distributed among these distances:
49 3 0.04
50 66 0.90
51 4 0.05
ACGTcount: A:0.25, C:0.20, G:0.23, T:0.33
Consensus pattern (50 bp):
AAGATTCACCGATGTGGCTTTAATCTGTTCCACTACATCGTTTGGGAGAT
Found at i:91797 original size:44 final size:44
Alignment explanation
Indices: 91749--92290 Score: 306
Period size: 44 Copynumber: 11.8 Consensus size: 44
91739 TCCTTATTTT
* *
91749 AATCTGCTCCACTGTAA-TCTCAGGGAGATAGGATTACTGGCCTC
1 AATCTGCTCCACTGTAACT-TCAGGGAGATAAGATTACTGGCTTC
* * **
91793 AATCTGCTCCGCTGCAACTTCAGGGAGATAAGATTTGTGGCTTC
1 AATCTGCTCCACTGTAACTTCAGGGAGATAAGATTACTGGCTTC
* * * *** *
91837 AATCTGATGCGATCTACTCTACTGTAACTTCAGAGAGATAAGATCATTTATTTT
1 AATC---T--G--CT-C-C-ACTGTAACTTCAGGGAGATAAGATTACTGGCTTC
* * *
91891 AATCCGCTCCACTGTAA-TCTCAGGGAGATAGGATTACTAGCTTC
1 AATCTGCTCCACTGTAACT-TCAGGGAGATAAGATTACTGGCTTC
* ** *
91935 AATCTGCTCCGCTGTAACTTCAGGGAGATAAGATTTGTGGCTTT
1 AATCTGCTCCACTGTAACTTCAGGGAGATAAGATTACTGGCTTC
* * * * *** *
91979 AATCTGATGCTCTACTGTAACTTTAGAGAGATAAGA-TCCTTTATTTT
1 AATC---TGCTCCACTGTAACTTCAGGGAGATAAGATTAC-TGGCTTC
* *
92026 AATCTGCTCCACTGTAA-TCTCAGGGAGATAGGATTACTGGCCTC
1 AATCTGCTCCACTGTAACT-TCAGGGAGATAAGATTACTGGCTTC
* * ** *
92070 AATCTGCTCCGCTGCAACTTCAGGGAGATAAGATTTGTGGATTC
1 AATCTGCTCCACTGTAACTTCAGGGAGATAAGATTACTGGCTTC
* * *** *
92114 AATCTGATGCGATCTACTCTACTGTAACTTCAGAGAGATAAGA-TCCTTTATTTT
1 AATC---T--G--CT-C-C-ACTGTAACTTCAGGGAGATAAGATTAC-TGGCTTC
* * * *
92168 AATCCGCTCCACTATAATCTT-AGGGAGATAGGATTACTAGCTTC
1 AATCTGCTCCACTGTAA-CTTCAGGGAGATAAGATTACTGGCTTC
* * *
92212 AATCTGCTCCGCTGTAA-TATTAGGGAGATAAGATTTCTGGCTTC
1 AATCTGCTCCACTGTAACT-TCAGGGAGATAAGATTACTGGCTTC
* * *
92256 AATCTGCTCTACTGTAACATCAAGGAGATAAGATT
1 AATCTGCTCCACTGTAACTTCAGGGAGATAAGATT
92291 CACCATTTTT
Statistics
Matches: 375, Mismatches: 87, Indels: 72
0.70 0.16 0.13
Matches are distributed among these distances:
42 1 0.00
43 3 0.01
44 249 0.66
45 12 0.03
46 3 0.01
47 39 0.10
49 4 0.01
51 4 0.01
52 2 0.01
53 3 0.01
54 55 0.15
ACGTcount: A:0.27, C:0.20, G:0.20, T:0.32
Consensus pattern (44 bp):
AATCTGCTCCACTGTAACTTCAGGGAGATAAGATTACTGGCTTC
Found at i:91967 original size:142 final size:142
Alignment explanation
Indices: 91711--92261 Score: 868
Period size: 142 Copynumber: 3.9 Consensus size: 142
91701 NNNNNNNNNN
* *
91711 CTCTACTGTAACTTTAGAGAGAATAAGATCC-TTATTTTAATCTGCTCCACTGTAATCTCAGGGA
1 CTCTACTGTAACTTCAGAGAG-ATAAGATCCTTTATTTTAATCCGCTCCACTGTAATCTCAGGGA
*
91775 GATAGGATTACTGGCCTCAATCTGCTCCGCTGCAACTTCAGGGAGATAAGATTTGTGGCTTCAAT
65 GATAGGATTACTAGCCTCAATCTGCTCCGCTGCAACTTCAGGGAGATAAGATTTGTGGCTTCAAT
91840 CTGATGCGATCTA
130 CTGATGCGATCTA
*
91853 CTCTACTGTAACTTCAGAGAGATAAGATCATTTATTTTAATCCGCTCCACTGTAATCTCAGGGAG
1 CTCTACTGTAACTTCAGAGAGATAAGATCCTTTATTTTAATCCGCTCCACTGTAATCTCAGGGAG
* * *
91918 ATAGGATTACTAGCTTCAATCTGCTCCGCTGTAACTTCAGGGAGATAAGATTTGTGGCTTTAATC
66 ATAGGATTACTAGCCTCAATCTGCTCCGCTGCAACTTCAGGGAGATAAGATTTGTGGCTTCAATC
91983 TGAT--G-----
131 TGATGCGATCTA
* *
91988 CTCTACTGTAACTTTAGAGAGATAAGATCCTTTATTTTAATCTGCTCCACTGTAATCTCAGGGAG
1 CTCTACTGTAACTTCAGAGAGATAAGATCCTTTATTTTAATCCGCTCCACTGTAATCTCAGGGAG
* *
92053 ATAGGATTACTGGCCTCAATCTGCTCCGCTGCAACTTCAGGGAGATAAGATTTGTGGATTCAATC
66 ATAGGATTACTAGCCTCAATCTGCTCCGCTGCAACTTCAGGGAGATAAGATTTGTGGCTTCAATC
92118 TGATGCGATCTA
131 TGATGCGATCTA
* *
92130 CTCTACTGTAACTTCAGAGAGATAAGATCCTTTATTTTAATCCGCTCCACTATAATCTTAGGGAG
1 CTCTACTGTAACTTCAGAGAGATAAGATCCTTTATTTTAATCCGCTCCACTGTAATCTCAGGGAG
* * * *
92195 ATAGGATTACTAGCTTCAATCTGCTCCGCTGTAA-TATTAGGGAGATAAGATTTCTGGCTTCAAT
66 ATAGGATTACTAGCCTCAATCTGCTCCGCTGCAACT-TCAGGGAGATAAGATTTGTGGCTTCAAT
92259 CTG
130 CTG
92262 CTCTACTGTA
Statistics
Matches: 375, Mismatches: 25, Indels: 18
0.90 0.06 0.04
Matches are distributed among these distances:
135 126 0.34
137 1 0.00
140 1 0.00
141 9 0.02
142 238 0.63
ACGTcount: A:0.27, C:0.20, G:0.20, T:0.33
Consensus pattern (142 bp):
CTCTACTGTAACTTCAGAGAGATAAGATCCTTTATTTTAATCCGCTCCACTGTAATCTCAGGGAG
ATAGGATTACTAGCCTCAATCTGCTCCGCTGCAACTTCAGGGAGATAAGATTTGTGGCTTCAATC
TGATGCGATCTA
Found at i:92094 original size:277 final size:273
Alignment explanation
Indices: 91570--92273 Score: 1040
Period size: 277 Copynumber: 2.6 Consensus size: 273
91560 GAGATAAGAC
* * * *
91570 CTGATGTGATCTACTCTACTATAACTTTAGAGAGATAAGATCATTTATTTTAATCCGTTCCACTG
1 CTGATGCGATCTACTCTACTGTAACTTCAGAGAGATAAGATCATTTATTTTAATCCGCTCCACTG
* * * * **
91635 TAATCTCATGGAGATAGGATTACTAGTTTCAATCTGCTCCACTGTAATCTCAGGGAGAT---ANN
66 TAATCTCAGGGAGATAGGATTACTAGCTTCAATCTGCTCCGCTGTAATATCAGGGAGATAAGATT
**************
91697 NNNNNNNNNNNNNNCTCTACTGTAACTTTAGAGAGAATAAGATCCTTATTTTAATCTGCTCCACT
131 TTGGCTTCAATCTGCTCTACTGTAACTTTAGAGAGAATAAGATCCTTATTTTAATCTGCTCCACT
91762 GTAATCTCAGGGAGATAGGATTACTGGCCTCAATCTGCTCCGCTGCAACTTCAGGGAGATAAGAT
196 GTAATCTCAGGGAGATAGGATTACTGGCCTCAATCTGCTCCGCTGCAACTTCAGGGAGATAAGAT
*
91827 TTGTGGCTTCAAT
261 TTGTGGATTCAAT
91840 CTGATGCGATCTACTCTACTGTAACTTCAGAGAGATAAGATCATTTATTTTAATCCGCTCCACTG
1 CTGATGCGATCTACTCTACTGTAACTTCAGAGAGATAAGATCATTTATTTTAATCCGCTCCACTG
91905 TAATCTCAGGGAGATAGGATTACTAGCTTCAATCTGCTCCGCTGTAACT-TCAGGGAGATAAGAT
66 TAATCTCAGGGAGATAGGATTACTAGCTTCAATCTGCTCCGCTGTAA-TATCAGGGAGATAAGAT
*
91969 TTGTGGCTTTAATCTGATGCTCTACTGTAACTTTAGAGAG-ATAAGATCCTTTATTTTAATCTGC
130 TT-TGGCTTCAATC---TGCTCTACTGTAACTTTAGAGAGAATAAGATCC-TTATTTTAATCTGC
92033 TCCACTGTAATCTCAGGGAGATAGGATTACTGGCCTCAATCTGCTCCGCTGCAACTTCAGGGAGA
190 TCCACTGTAATCTCAGGGAGATAGGATTACTGGCCTCAATCTGCTCCGCTGCAACTTCAGGGAGA
92098 TAAGATTTGTGGATTCAAT
255 TAAGATTTGTGGATTCAAT
* *
92117 CTGATGCGATCTACTCTACTGTAACTTCAGAGAGATAAGATCCTTTATTTTAATCCGCTCCACTA
1 CTGATGCGATCTACTCTACTGTAACTTCAGAGAGATAAGATCATTTATTTTAATCCGCTCCACTG
* *
92182 TAATCTTAGGGAGATAGGATTACTAGCTTCAATCTGCTCCGCTGTAATATTAGGGAGATAAGATT
66 TAATCTCAGGGAGATAGGATTACTAGCTTCAATCTGCTCCGCTGTAATATCAGGGAGATAAGATT
92247 TCTGGCTTCAATCTGCTCTACTGTAAC
131 T-TGGCTTCAATCTGCTCTACTGTAAC
92274 ATCAAGGAGA
Statistics
Matches: 394, Mismatches: 30, Indels: 16
0.90 0.07 0.04
Matches are distributed among these distances:
270 115 0.29
271 1 0.00
273 1 0.00
274 14 0.04
276 10 0.03
277 253 0.64
ACGTcount: A:0.27, C:0.20, G:0.19, T:0.33
Consensus pattern (273 bp):
CTGATGCGATCTACTCTACTGTAACTTCAGAGAGATAAGATCATTTATTTTAATCCGCTCCACTG
TAATCTCAGGGAGATAGGATTACTAGCTTCAATCTGCTCCGCTGTAATATCAGGGAGATAAGATT
TTGGCTTCAATCTGCTCTACTGTAACTTTAGAGAGAATAAGATCCTTATTTTAATCTGCTCCACT
GTAATCTCAGGGAGATAGGATTACTGGCCTCAATCTGCTCCGCTGCAACTTCAGGGAGATAAGAT
TTGTGGATTCAAT
Found at i:92864 original size:131 final size:130
Alignment explanation
Indices: 92379--92849 Score: 677
Period size: 131 Copynumber: 3.6 Consensus size: 130
92369 CCTTACACTT
** * * *
92379 GAAGATAAGATTTACCGTCTTCGATCTGCTCCGCTATTGCTTAGGGAGATAAGATCTGTAATTAT
1 GAAGATAAGATTCGCCGTCTTCGATCTGCTCCGCTACTGCTTAGGGAGACAAGATCTGCAATT-T
*
92444 -TAACCTATTCCACTGCTGGT------CATAGGACGTGTGGCTTAAATCTATTTCCCTACTCCTG
65 CCAACCTATTCCACTGCTGGTCAGGGACATAGGACGTGTGGCTTAAATCTATTTCCCTACTCCT-
92502 GG
129 GG
* * *
92504 GAAGATAAGATTCGCCGTCTTCGATCTGCTCCACTGCTGCTTAGGGAGACAAGATCTGTAATTTC
1 GAAGATAAGATTCGCCGTCTTCGATCTGCTCCGCTACTGCTTAGGGAGACAAGATCTGCAATTTC
* *
92569 CAACCTATTCCACTGCTGGTCAGGGACATAGGACGTGTGGCTTAAATCTGTTTCCCCACTCCTAG
66 CAACCTATTCCACTGCTGGTCAGGGACATAGGACGTGTGGCTTAAATCTATTTCCCTACTCCT-G
92634 G
130 G
* *
92635 GAAGATAAGATTCGTCGTCTTCGATCTGCTCCGCTACTGCTTAGGGAGACAAGATTTGCAATTTC
1 GAAGATAAGATTCGCCGTCTTCGATCTGCTCCGCTACTGCTTAGGGAGACAAGATCTGCAATTTC
*
92700 CAACCTATTCCACTGCTGGTCAGGGACATAGGACGTATGGCTTAAATCTATTTCCCTACTCCTGG
66 CAACCTATTCCACTGCTGGTCAGGGACATAGGACGTGTGGCTTAAATCTATTTCCCTACTCCTGG
* * * * * *
92765 AGAAGATAAGATTTGTCGTCTTTGATCTGCTCCGCTACTGCTCAGGGAAATAAGATCTGCAATTT
1 -GAAGATAAGATTCGCCGTCTTCGATCTGCTCCGCTACTGCTTAGGGAGACAAGATCTGCAATTT
92830 CCAACCTATTCCACTGCTGG
65 CCAACCTATTCCACTGCTGG
92850 CCAATGATAT
Statistics
Matches: 314, Mismatches: 24, Indels: 10
0.90 0.07 0.03
Matches are distributed among these distances:
124 1 0.00
125 76 0.24
130 2 0.01
131 235 0.75
ACGTcount: A:0.24, C:0.24, G:0.21, T:0.31
Consensus pattern (130 bp):
GAAGATAAGATTCGCCGTCTTCGATCTGCTCCGCTACTGCTTAGGGAGACAAGATCTGCAATTTC
CAACCTATTCCACTGCTGGTCAGGGACATAGGACGTGTGGCTTAAATCTATTTCCCTACTCCTGG
Found at i:93100 original size:87 final size:87
Alignment explanation
Indices: 92876--93135 Score: 388
Period size: 87 Copynumber: 3.1 Consensus size: 87
92866 TGTAATCTTT
* * *
92876 GATCTGCTTCACTGTCGACGCAGGAGGGCAAGATCTGCTATCTTTAACCAGCTCCACTGCAACCG
1 GATCTGCTTCGCTGTCAACGCAGGAAGGCAAGATCTGCTATCTTTAACCAGCTCCACTGCAACCG
*
92941 ATGGAGGCAA-GATTTGTTTTC
66 ATGGAGGCAAGGCTTTGTTTTC
*
92962 GATCTGC-T-G-T-T-AACGCAGGAAGGCAAGATCTGCTATCTTTAACCAGCTCCACTGCAACTG
1 GATCTGCTTCGCTGTCAACGCAGGAAGGCAAGATCTGCTATCTTTAACCAGCTCCACTGCAACCG
93022 ATGGAGGCAAGGCTTTGTTTTC
66 ATGGAGGCAAGGCTTTGTTTTC
* * * * *
93044 GATCTGCTTCGCTGTCAATGCATGAAGGCAAGATCTGCCATCTTTAACCAACTCCACTACAACCG
1 GATCTGCTTCGCTGTCAACGCAGGAAGGCAAGATCTGCTATCTTTAACCAGCTCCACTGCAACCG
93109 ATGGAGGCAAGGCTTTGTTTTC
66 ATGGAGGCAAGGCTTTGTTTTC
93131 GATCT
1 GATCT
93136 TCACTGATCT
Statistics
Matches: 157, Mismatches: 11, Indels: 11
0.88 0.06 0.06
Matches are distributed among these distances:
81 56 0.36
82 18 0.11
83 2 0.01
84 1 0.01
85 2 0.01
86 8 0.05
87 70 0.45
ACGTcount: A:0.24, C:0.25, G:0.23, T:0.28
Consensus pattern (87 bp):
GATCTGCTTCGCTGTCAACGCAGGAAGGCAAGATCTGCTATCTTTAACCAGCTCCACTGCAACCG
ATGGAGGCAAGGCTTTGTTTTC
Found at i:94677 original size:45 final size:44
Alignment explanation
Indices: 94587--94678 Score: 114
Period size: 44 Copynumber: 2.1 Consensus size: 44
94577 TTACAATATT
* **
94587 ATTCCATTCAACCAAACACAAGAATATTATTACAGTTCTATTCC
1 ATTCCATTCAACCAAACACAAGAATACTATTACACCTCTATTCC
* *
94631 ATTCCATTTAACCAAACA-ATTGAATTACTATTACACCTCTATTCC
1 ATTCCATTCAACCAAACACA-AGAA-TACTATTACACCTCTATTCC
94676 ATT
1 ATT
94679 ACAGCTCTAT
Statistics
Matches: 41, Mismatches: 5, Indels: 3
0.84 0.10 0.06
Matches are distributed among these distances:
43 1 0.02
44 20 0.49
45 20 0.49
ACGTcount: A:0.37, C:0.25, G:0.03, T:0.35
Consensus pattern (44 bp):
ATTCCATTCAACCAAACACAAGAATACTATTACACCTCTATTCC
Found at i:94681 original size:16 final size:16
Alignment explanation
Indices: 94660--94711 Score: 70
Period size: 16 Copynumber: 3.2 Consensus size: 16
94650 TTGAATTACT
*
94660 ATTACACCTCTATTCC
1 ATTACAGCTCTATTCC
94676 ATTACAGCTCTATT-C
1 ATTACAGCTCTATTCC
*
94691 AGTTACAGCTCTATTCT
1 A-TTACAGCTCTATTCC
94708 ATTA
1 ATTA
94712 TAGCGAACCA
Statistics
Matches: 32, Mismatches: 2, Indels: 4
0.84 0.05 0.11
Matches are distributed among these distances:
15 2 0.06
16 29 0.91
17 1 0.03
ACGTcount: A:0.27, C:0.27, G:0.06, T:0.40
Consensus pattern (16 bp):
ATTACAGCTCTATTCC
Found at i:105588 original size:44 final size:44
Alignment explanation
Indices: 105525--105616 Score: 175
Period size: 44 Copynumber: 2.1 Consensus size: 44
105515 ATTTGTAAAT
105525 GAATTTTTGAAGATAGCCTTGCCAATGACAAAGTTGTTGCATAA
1 GAATTTTTGAAGATAGCCTTGCCAATGACAAAGTTGTTGCATAA
*
105569 GAATTTTTTAAGATAGCCTTGCCAATGACAAAGTTGTTGCATAA
1 GAATTTTTGAAGATAGCCTTGCCAATGACAAAGTTGTTGCATAA
105613 GAAT
1 GAAT
105617 GTTCAGTTCG
Statistics
Matches: 47, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
44 47 1.00
ACGTcount: A:0.35, C:0.13, G:0.20, T:0.33
Consensus pattern (44 bp):
GAATTTTTGAAGATAGCCTTGCCAATGACAAAGTTGTTGCATAA
Found at i:108003 original size:24 final size:24
Alignment explanation
Indices: 107950--108021 Score: 76
Period size: 28 Copynumber: 2.8 Consensus size: 24
107940 AAGTAATAAA
107950 AAAAGAAAGAAAGAAAGAAGCCAAACG
1 AAAAGAAAGAAAGAAAGAA---AAACG
107977 AAACAGAAAGAAAGAAAGAAAAA-G
1 AAA-AGAAAGAAAGAAAGAAAAACG
108001 AAAAGGGAAAGAAAG-AAGAAA
1 AAAA--GAAAGAAAGAAAGAAA
108022 CGCAAAGTTT
Statistics
Matches: 42, Mismatches: 0, Indels: 9
0.82 0.00 0.18
Matches are distributed among these distances:
23 1 0.02
24 10 0.24
25 12 0.29
27 3 0.07
28 16 0.38
ACGTcount: A:0.71, C:0.06, G:0.24, T:0.00
Consensus pattern (24 bp):
AAAAGAAAGAAAGAAAGAAAAACG
Found at i:108452 original size:19 final size:20
Alignment explanation
Indices: 108428--108465 Score: 60
Period size: 19 Copynumber: 1.9 Consensus size: 20
108418 GAATTTAGGC
*
108428 AAATATTGAATA-AAAATTA
1 AAATATTCAATATAAAATTA
108447 AAATATTCAATATAAAATT
1 AAATATTCAATATAAAATT
108466 GAATTGTGTT
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
19 11 0.65
20 6 0.35
ACGTcount: A:0.61, C:0.03, G:0.03, T:0.34
Consensus pattern (20 bp):
AAATATTCAATATAAAATTA
Found at i:111093 original size:30 final size:30
Alignment explanation
Indices: 111053--111111 Score: 109
Period size: 30 Copynumber: 2.0 Consensus size: 30
111043 TTAACAATCA
111053 AAATGACTCTAAAATAATAACAAAATTAAT
1 AAATGACTCTAAAATAATAACAAAATTAAT
*
111083 AAATGCCTCTAAAATAATAACAAAATTAA
1 AAATGACTCTAAAATAATAACAAAATTAA
111112 CAATAAAACA
Statistics
Matches: 28, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
30 28 1.00
ACGTcount: A:0.59, C:0.12, G:0.03, T:0.25
Consensus pattern (30 bp):
AAATGACTCTAAAATAATAACAAAATTAAT
Found at i:111157 original size:11 final size:11
Alignment explanation
Indices: 111143--111190 Score: 51
Period size: 11 Copynumber: 4.4 Consensus size: 11
111133 ATATCCAAAC
*
111143 AATAATAACAA
1 AATAATAGCAA
*
111154 AATAGTAGCAA
1 AATAATAGCAA
* *
111165 CATAATAGTAA
1 AATAATAGCAA
*
111176 AATAGTAGCAA
1 AATAATAGCAA
111187 AATA
1 AATA
111191 GGGAGAAAAT
Statistics
Matches: 29, Mismatches: 8, Indels: 0
0.78 0.22 0.00
Matches are distributed among these distances:
11 29 1.00
ACGTcount: A:0.60, C:0.08, G:0.10, T:0.21
Consensus pattern (11 bp):
AATAATAGCAA
Found at i:111169 original size:22 final size:22
Alignment explanation
Indices: 111144--111186 Score: 68
Period size: 22 Copynumber: 2.0 Consensus size: 22
111134 TATCCAAACA
111144 ATAATAACAAAATAGTAGCAAC
1 ATAATAACAAAATAGTAGCAAC
**
111166 ATAATAGTAAAATAGTAGCAA
1 ATAATAACAAAATAGTAGCAA
111187 AATAGGGAGA
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
22 19 1.00
ACGTcount: A:0.58, C:0.09, G:0.12, T:0.21
Consensus pattern (22 bp):
ATAATAACAAAATAGTAGCAAC
Found at i:111191 original size:11 final size:11
Alignment explanation
Indices: 111151--111191 Score: 55
Period size: 11 Copynumber: 3.7 Consensus size: 11
111141 ACAATAATAA
111151 CAAAATAGTAG
1 CAAAATAGTAG
* *
111162 CAACATAATAG
1 CAAAATAGTAG
*
111173 TAAAATAGTAG
1 CAAAATAGTAG
111184 CAAAATAG
1 CAAAATAG
111192 GGAGAAAATA
Statistics
Matches: 24, Mismatches: 6, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
11 24 1.00
ACGTcount: A:0.56, C:0.10, G:0.15, T:0.20
Consensus pattern (11 bp):
CAAAATAGTAG
Found at i:112750 original size:793 final size:793
Alignment explanation
Indices: 111224--112809 Score: 3172
Period size: 793 Copynumber: 2.0 Consensus size: 793
111214 CATTAAAAAA
111224 GAGCAAATTTTTAAATGGGCCAAGCCCAGGCCAAAAATGCCTTACCCAAGGCCAAACGGGCCTTA
1 GAGCAAATTTTTAAATGGGCCAAGCCCAGGCCAAAAATGCCTTACCCAAGGCCAAACGGGCCTTA
111289 TTTTTTTGTCCAAGCCCATTTTTTGGGCCTATTTTTTTGCCCAAACCCTCTTACATTTCGGGCGG
66 TTTTTTTGTCCAAGCCCATTTTTTGGGCCTATTTTTTTGCCCAAACCCTCTTACATTTCGGGCGG
111354 GCCTTCGAGCCGGTCCGGGTGGCCCGACCCATGAACAGGTCTAGTCATATGCATTAAATGGATTG
131 GCCTTCGAGCCGGTCCGGGTGGCCCGACCCATGAACAGGTCTAGTCATATGCATTAAATGGATTG
111419 TTATAAAGTATTTGAGCTAATAATTGAAATAAATTACTATTTAGATCAAGAGTCAATAGATAATC
196 TTATAAAGTATTTGAGCTAATAATTGAAATAAATTACTATTTAGATCAAGAGTCAATAGATAATC
111484 GTGAAAAAGAGAATTTCTTATTAGTCCCTAACATTGTAATTTTTACTGTTTAGCCTTGGTAAGTT
261 GTGAAAAAGAGAATTTCTTATTAGTCCCTAACATTGTAATTTTTACTGTTTAGCCTTGGTAAGTT
111549 CATACGATATGTTTGTGTTAAATTGTTATGCATTTAAAATCATTATTTTAAACATGTTTAATTGA
326 CATACGATATGTTTGTGTTAAATTGTTATGCATTTAAAATCATTATTTTAAACATGTTTAATTGA
111614 AATTCTGATTGTTTACAATTCAGTACAAAAAGGTGAGATAAAATATTAAAATTGAACATAATTGA
391 AATTCTGATTGTTTACAATTCAGTACAAAAAGGTGAGATAAAATATTAAAATTGAACATAATTGA
111679 AGATAGTATAATTCGATAAATTAAGGAATTGACTTTTAATTGGACTGAAATAGGATATGTTATGT
456 AGATAGTATAATTCGATAAATTAAGGAATTGACTTTTAATTGGACTGAAATAGGATATGTTATGT
111744 GATAAAGTGATGATTTGATCAAAATAAGCTGAATTGATTCGATTTAAATTGGTTGTACATGAAAA
521 GATAAAGTGATGATTTGATCAAAATAAGCTGAATTGATTCGATTTAAATTGGTTGTACATGAAAA
111809 GAATTGAATTGATTTGAATTGAAAATATTAAATATTATTTGAAATGTGAGATTATACTAATGTGG
586 GAATTGAATTGATTTGAATTGAAAATATTAAATATTATTTGAAATGTGAGATTATACTAATGTGG
111874 TGATGAGCTATGATAAATATATATGTGGAATTCTTGATTTTTTTTGATTTAGATTACGATATTGA
651 TGATGAGCTATGATAAATATATATGTGGAATTCTTGATTTTTTTTGATTTAGATTACGATATTGA
111939 AATTGAGAATTGGTTTAAAATGAATATTAGAAACTTGTTACCCTATTAACTGTTCAAGCAATGTC
716 AATTGAGAATTGGTTTAAAATGAATATTAGAAACTTGTTACCCTATTAACTGTTCAAGCAATGTC
112004 GGGTATAATTAGC
781 GGGTATAATTAGC
112017 GAGCAAATTTTTAAATGGGCCAAGCCCAGGCCAAAAATGCCTTACCCAAGGCCAAACGGGCCTTA
1 GAGCAAATTTTTAAATGGGCCAAGCCCAGGCCAAAAATGCCTTACCCAAGGCCAAACGGGCCTTA
112082 TTTTTTTGTCCAAGCCCATTTTTTGGGCCTATTTTTTTGCCCAAACCCTCTTACATTTCGGGCGG
66 TTTTTTTGTCCAAGCCCATTTTTTGGGCCTATTTTTTTGCCCAAACCCTCTTACATTTCGGGCGG
112147 GCCTTCGAGCCGGTCCGGGTGGCCCGACCCATGAACAGGTCTAGTCATATGCATTAAATGGATTG
131 GCCTTCGAGCCGGTCCGGGTGGCCCGACCCATGAACAGGTCTAGTCATATGCATTAAATGGATTG
112212 TTATAAAGTATTTGAGCTAATAATTGAAATAAATTACTATTTAGATCAAGAGTCAATAGATAATC
196 TTATAAAGTATTTGAGCTAATAATTGAAATAAATTACTATTTAGATCAAGAGTCAATAGATAATC
112277 GTGAAAAAGAGAATTTCTTATTAGTCCCTAACATTGTAATTTTTACTGTTTAGCCTTGGTAAGTT
261 GTGAAAAAGAGAATTTCTTATTAGTCCCTAACATTGTAATTTTTACTGTTTAGCCTTGGTAAGTT
112342 CATACGATATGTTTGTGTTAAATTGTTATGCATTTAAAATCATTATTTTAAACATGTTTAATTGA
326 CATACGATATGTTTGTGTTAAATTGTTATGCATTTAAAATCATTATTTTAAACATGTTTAATTGA
112407 AATTCTGATTGTTTACAATTCAGTACAAAAAGGTGAGATAAAATATTAAAATTGAACATAATTGA
391 AATTCTGATTGTTTACAATTCAGTACAAAAAGGTGAGATAAAATATTAAAATTGAACATAATTGA
112472 AGATAGTATAATTCGATAAATTAAGGAATTGACTTTTAATTGGACTGAAATAGGATATGTTATGT
456 AGATAGTATAATTCGATAAATTAAGGAATTGACTTTTAATTGGACTGAAATAGGATATGTTATGT
112537 GATAAAGTGATGATTTGATCAAAATAAGCTGAATTGATTCGATTTAAATTGGTTGTACATGAAAA
521 GATAAAGTGATGATTTGATCAAAATAAGCTGAATTGATTCGATTTAAATTGGTTGTACATGAAAA
112602 GAATTGAATTGATTTGAATTGAAAATATTAAATATTATTTGAAATGTGAGATTATACTAATGTGG
586 GAATTGAATTGATTTGAATTGAAAATATTAAATATTATTTGAAATGTGAGATTATACTAATGTGG
112667 TGATGAGCTATGATAAATATATATGTGGAATTCTTGATTTTTTTTGATTTAGATTACGATATTGA
651 TGATGAGCTATGATAAATATATATGTGGAATTCTTGATTTTTTTTGATTTAGATTACGATATTGA
112732 AATTGAGAATTGGTTTAAAATGAATATTAGAAACTTGTTACCCTATTAACTGTTCAAGCAATGTC
716 AATTGAGAATTGGTTTAAAATGAATATTAGAAACTTGTTACCCTATTAACTGTTCAAGCAATGTC
112797 GGGTATAATTAGC
781 GGGTATAATTAGC
112810 ATGCCATATG
Statistics
Matches: 793, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
793 793 1.00
ACGTcount: A:0.34, C:0.12, G:0.18, T:0.36
Consensus pattern (793 bp):
GAGCAAATTTTTAAATGGGCCAAGCCCAGGCCAAAAATGCCTTACCCAAGGCCAAACGGGCCTTA
TTTTTTTGTCCAAGCCCATTTTTTGGGCCTATTTTTTTGCCCAAACCCTCTTACATTTCGGGCGG
GCCTTCGAGCCGGTCCGGGTGGCCCGACCCATGAACAGGTCTAGTCATATGCATTAAATGGATTG
TTATAAAGTATTTGAGCTAATAATTGAAATAAATTACTATTTAGATCAAGAGTCAATAGATAATC
GTGAAAAAGAGAATTTCTTATTAGTCCCTAACATTGTAATTTTTACTGTTTAGCCTTGGTAAGTT
CATACGATATGTTTGTGTTAAATTGTTATGCATTTAAAATCATTATTTTAAACATGTTTAATTGA
AATTCTGATTGTTTACAATTCAGTACAAAAAGGTGAGATAAAATATTAAAATTGAACATAATTGA
AGATAGTATAATTCGATAAATTAAGGAATTGACTTTTAATTGGACTGAAATAGGATATGTTATGT
GATAAAGTGATGATTTGATCAAAATAAGCTGAATTGATTCGATTTAAATTGGTTGTACATGAAAA
GAATTGAATTGATTTGAATTGAAAATATTAAATATTATTTGAAATGTGAGATTATACTAATGTGG
TGATGAGCTATGATAAATATATATGTGGAATTCTTGATTTTTTTTGATTTAGATTACGATATTGA
AATTGAGAATTGGTTTAAAATGAATATTAGAAACTTGTTACCCTATTAACTGTTCAAGCAATGTC
GGGTATAATTAGC
Found at i:120618 original size:32 final size:32
Alignment explanation
Indices: 120582--120656 Score: 109
Period size: 32 Copynumber: 2.3 Consensus size: 32
120572 ATATTATACC
120582 AGCCCAAACCCTTTTAC-CT-TATTTCCCTCCAA
1 AGCCCAAACCCTTTTACTCTAT-TTTCCC-CCAA
*
120614 AGCCCAAACCTTTTTACTCTATTTTCCCCCAA
1 AGCCCAAACCCTTTTACTCTATTTTCCCCCAA
120646 AGCCCAAACCC
1 AGCCCAAACCC
120657 CATCCCCCTC
Statistics
Matches: 39, Mismatches: 2, Indels: 4
0.87 0.04 0.09
Matches are distributed among these distances:
32 30 0.77
33 8 0.21
34 1 0.03
ACGTcount: A:0.27, C:0.41, G:0.04, T:0.28
Consensus pattern (32 bp):
AGCCCAAACCCTTTTACTCTATTTTCCCCCAA
Found at i:120783 original size:42 final size:42
Alignment explanation
Indices: 120737--120826 Score: 135
Period size: 42 Copynumber: 2.1 Consensus size: 42
120727 TTGTCTATCC
* ** *
120737 AAACCCCTAAATTTATGTTTCTTCTTCAAAAATCCTTAAATT
1 AAACCCCCAAATCCATGTTTCTTCTTCAAAAATCCCTAAATT
*
120779 AAACCCCCAAATCCATTTTTCTTCTTCAAAAATCCCTAAATT
1 AAACCCCCAAATCCATGTTTCTTCTTCAAAAATCCCTAAATT
120821 AAACCC
1 AAACCC
120827 TCTATTCTTC
Statistics
Matches: 43, Mismatches: 5, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
42 43 1.00
ACGTcount: A:0.37, C:0.28, G:0.01, T:0.34
Consensus pattern (42 bp):
AAACCCCCAAATCCATGTTTCTTCTTCAAAAATCCCTAAATT
Found at i:123890 original size:64 final size:66
Alignment explanation
Indices: 123757--123894 Score: 165
Period size: 64 Copynumber: 2.1 Consensus size: 66
123747 AGATGTCTCC
* * *
123757 TTCCCCTGCATAAAGATGACATAAAGATGACAAAGCAACATTTACACCTATGTTACCAAAAACTG
1 TTCCCCTGCATAAAGAT-AC--AAAGATGACAAAGCAACACTTACACCTATATTACCAAAAACTA
123822 CTAT
63 CTAT
* * *
123826 TTCCCCTGCATAAAGAT-C-AAGATGACAAAGCAACACTTACACTTCTATTACCATAAA-TCACT
1 TTCCCCTGCATAAAGATACAAAGATGACAAAGCAACACTTACACCTATATTACCAAAAACT-ACT
123888 AT
65 AT
123890 TTCCC
1 TTCCC
123895 TATCAATTTT
Statistics
Matches: 62, Mismatches: 6, Indels: 7
0.83 0.08 0.09
Matches are distributed among these distances:
63 1 0.02
64 43 0.69
67 1 0.02
69 17 0.27
ACGTcount: A:0.38, C:0.26, G:0.09, T:0.26
Consensus pattern (66 bp):
TTCCCCTGCATAAAGATACAAAGATGACAAAGCAACACTTACACCTATATTACCAAAAACTACTA
T
Found at i:128746 original size:31 final size:30
Alignment explanation
Indices: 128697--128782 Score: 75
Period size: 31 Copynumber: 2.8 Consensus size: 30
128687 AATATGTATG
* *
128697 ATTGAATCAAAATTAAAGTTTCATGTATACA
1 ATTGAA-CCAAATCAAAGTTTCATGTATACA
* * ** *
128728 TTTGAACCACAATCAAAGTTCCACATATATA
1 ATTGAACCA-AATCAAAGTTTCATGTATACA
*
128759 ATTGTACCAAATCAAAG-TTCATGT
1 ATTGAACCAAATCAAAGTTTCATGT
128783 GTAACACCCC
Statistics
Matches: 42, Mismatches: 12, Indels: 4
0.72 0.21 0.07
Matches are distributed among these distances:
29 4 0.10
30 10 0.24
31 28 0.67
ACGTcount: A:0.42, C:0.16, G:0.09, T:0.33
Consensus pattern (30 bp):
ATTGAACCAAATCAAAGTTTCATGTATACA
Found at i:131531 original size:45 final size:45
Alignment explanation
Indices: 131468--131556 Score: 142
Period size: 45 Copynumber: 2.0 Consensus size: 45
131458 GAATGATATT
*
131468 ATGTATTTAGTATATTGTTGAAAAATAGAACATTGTTAAATTATC
1 ATGTATTTAGCATATTGTTGAAAAATAGAACATTGTTAAATTATC
* * *
131513 ATGTATTTAGCATGTTGTTGAAAAATGGAATATTGTTAAATTAT
1 ATGTATTTAGCATATTGTTGAAAAATAGAACATTGTTAAATTAT
131557 GAAATTGAAT
Statistics
Matches: 40, Mismatches: 4, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
45 40 1.00
ACGTcount: A:0.38, C:0.03, G:0.16, T:0.43
Consensus pattern (45 bp):
ATGTATTTAGCATATTGTTGAAAAATAGAACATTGTTAAATTATC
Found at i:131735 original size:24 final size:24
Alignment explanation
Indices: 131616--131725 Score: 166
Period size: 24 Copynumber: 4.6 Consensus size: 24
131606 TCGTTCTGTG
*
131616 GCAAAGGATGAATTGATGGTAAAT
1 GCAAAGGATGAATTGACGGTAAAT
* *
131640 TCAAAGGATGAATTAACGGTAAAT
1 GCAAAGGATGAATTGACGGTAAAT
*
131664 GCAAAGGATGAATTGACAGTAAAT
1 GCAAAGGATGAATTGACGGTAAAT
* *
131688 GCAAAGGAAGAATTGGCGGTAAAT
1 GCAAAGGATGAATTGACGGTAAAT
131712 GCAAAGGATGAATT
1 GCAAAGGATGAATT
131726 AATGGCAAAT
Statistics
Matches: 76, Mismatches: 10, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
24 76 1.00
ACGTcount: A:0.44, C:0.07, G:0.27, T:0.22
Consensus pattern (24 bp):
GCAAAGGATGAATTGACGGTAAAT
Found at i:131849 original size:21 final size:21
Alignment explanation
Indices: 131820--132010 Score: 89
Period size: 21 Copynumber: 9.1 Consensus size: 21
131810 CATTAACTCA
131820 TATGAGTTTCCGTTCAACCCT
1 TATGAGTTTCCGTTCAACCCT
* **
131841 TATGGGTTTCCGTT-AAGCTTT
1 TATGAGTTTCCGTTCAA-CCCT
* * * ** *
131862 TTTAAGCTTCAATTTAACCCT
1 TATGAGTTTCCGTTCAACCCT
* * *
131883 TATGGGTTTCCGTTCAGCTCT
1 TATGAGTTTCCGTTCAACCCT
* * * *
131904 TTTGAGCTTCAGTTTAACCCT
1 TATGAGTTTCCGTTCAACCCT
* * * *
131925 TATGGGTTTCCATTCAGCTCT
1 TATGAGTTTCCGTTCAACCCT
* * * * *
131946 TTTCAGCTTCAGTTTAACCCT
1 TATGAGTTTCCGTTCAACCCT
* * *
131967 TATGGGTTTTCGTTCATCTCC-
1 TATGAGTTTCCGTTCAAC-CCT
*
131988 TATGAGCTTCCGTTCAACCCT
1 TATGAGTTTCCGTTCAACCCT
132009 TA
1 TA
132011 CGGGTTTCTA
Statistics
Matches: 110, Mismatches: 56, Indels: 8
0.63 0.32 0.05
Matches are distributed among these distances:
20 4 0.04
21 102 0.93
22 4 0.04
ACGTcount: A:0.17, C:0.25, G:0.16, T:0.42
Consensus pattern (21 bp):
TATGAGTTTCCGTTCAACCCT
Found at i:131894 original size:42 final size:42
Alignment explanation
Indices: 131835--132018 Score: 242
Period size: 42 Copynumber: 4.4 Consensus size: 42
131825 GTTTCCGTTC
* * *
131835 AACCCTTATGGGTTTCCGTTAAGCTTTTTTAAGCTTCAATTT
1 AACCCTTATGGGTTTCCGTTCAGCTCTTTTAAGCTTCAGTTT
*
131877 AACCCTTATGGGTTTCCGTTCAGCTCTTTTGAGCTTCAGTTT
1 AACCCTTATGGGTTTCCGTTCAGCTCTTTTAAGCTTCAGTTT
* *
131919 AACCCTTATGGGTTTCCATTCAGCTCTTTTCAGCTTCAGTTT
1 AACCCTTATGGGTTTCCGTTCAGCTCTTTTAAGCTTCAGTTT
* * * * * * *
131961 AACCCTTATGGGTTTTCGTTCATCTCCTATGAGCTTCCGTTC
1 AACCCTTATGGGTTTCCGTTCAGCTCTTTTAAGCTTCAGTTT
*
132003 AACCCTTACGGGTTTC
1 AACCCTTATGGGTTTC
132019 TAATTAGCAC
Statistics
Matches: 126, Mismatches: 16, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
42 126 1.00
ACGTcount: A:0.17, C:0.25, G:0.16, T:0.42
Consensus pattern (42 bp):
AACCCTTATGGGTTTCCGTTCAGCTCTTTTAAGCTTCAGTTT
Found at i:131981 original size:84 final size:84
Alignment explanation
Indices: 131820--132018 Score: 272
Period size: 84 Copynumber: 2.4 Consensus size: 84
131810 CATTAACTCA
* * * *
131820 TATGAGTTTCCGTTCAACCCTTATGGGTTTCCGTTAAGCTTTTTTAAGCTTCAATTTAACCCTTA
1 TATGAGCTTCAGTTCAACCCTTATGGGTTTCCATTAAGCTCTTTTAAGCTTCAATTTAACCCTTA
*
131885 TGGGTTTCCGTTCAGCTCT
66 TGGGTTTCCGTTCAGCTCC
* * * * *
131904 TTTGAGCTTCAGTTTAACCCTTATGGGTTTCCATTCAGCTCTTTTCAGCTTCAGTTTAACCCTTA
1 TATGAGCTTCAGTTCAACCCTTATGGGTTTCCATTAAGCTCTTTTAAGCTTCAATTTAACCCTTA
* *
131969 TGGGTTTTCGTTCATCTCC
66 TGGGTTTCCGTTCAGCTCC
* *
131988 TATGAGCTTCCGTTCAACCCTTACGGGTTTC
1 TATGAGCTTCAGTTCAACCCTTATGGGTTTC
132019 TAATTAGCAC
Statistics
Matches: 99, Mismatches: 16, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
84 99 1.00
ACGTcount: A:0.17, C:0.25, G:0.17, T:0.42
Consensus pattern (84 bp):
TATGAGCTTCAGTTCAACCCTTATGGGTTTCCATTAAGCTCTTTTAAGCTTCAATTTAACCCTTA
TGGGTTTCCGTTCAGCTCC
Found at i:132039 original size:84 final size:84
Alignment explanation
Indices: 131820--132045 Score: 229
Period size: 84 Copynumber: 2.7 Consensus size: 84
131810 CATTAACTCA
* * * ** * ** * * *
131820 TATGAGTTTCCGTTCAACCCTTATGGGTTTCCGTTAAGCTTTTTTAAGCTTCAATTTAACCCTTA
1 TATGAGCTTCAGTTCAACCCTTACGGGTTTCAATTCAGCACTTATCAGCTTCAGTTTAACCCTTA
*
131885 TGGGTTTCCGTTCAGCTCT
66 TGGGTTTCCGTTCAGCTCC
* * * * * *
131904 TTTGAGCTTCAGTTTAACCCTTATGGGTTTCCATTCAGCTCTTTTCAGCTTCAGTTTAACCCTTA
1 TATGAGCTTCAGTTCAACCCTTACGGGTTTCAATTCAGCACTTATCAGCTTCAGTTTAACCCTTA
* *
131969 TGGGTTTTCGTTCATCTCC
66 TGGGTTTCCGTTCAGCTCC
* **
131988 TATGAGCTTCCGTTCAACCCTTACGGGTTTCTAATT-AGCACTTATGTGCTTCAGTTTA
1 TATGAGCTTCAGTTCAACCCTTACGGGTTTC-AATTCAGCACTTATCAGCTTCAGTTTA
132046 GCCTTCAGGC
Statistics
Matches: 120, Mismatches: 21, Indels: 2
0.84 0.15 0.01
Matches are distributed among these distances:
84 117 0.98
85 3 0.03
ACGTcount: A:0.18, C:0.23, G:0.16, T:0.42
Consensus pattern (84 bp):
TATGAGCTTCAGTTCAACCCTTACGGGTTTCAATTCAGCACTTATCAGCTTCAGTTTAACCCTTA
TGGGTTTCCGTTCAGCTCC
Found at i:134221 original size:22 final size:22
Alignment explanation
Indices: 134186--134255 Score: 72
Period size: 22 Copynumber: 3.2 Consensus size: 22
134176 TATGCACAAG
*
134186 TAAACGGAGAGCACCAAGGTGC
1 TAAACAGAGAGCACCAAGGTGC
*
134208 TATAC-GAAGAGCA-CAAGCGTGC
1 TAAACAG-AGAGCACCAAG-GTGC
* *
134230 TAAACAGAGAGCACTAATGTGC
1 TAAACAGAGAGCACCAAGGTGC
134252 TAAA
1 TAAA
134256 AAATAAAGAG
Statistics
Matches: 40, Mismatches: 4, Indels: 8
0.77 0.08 0.15
Matches are distributed among these distances:
21 5 0.12
22 32 0.80
23 3 0.08
ACGTcount: A:0.40, C:0.20, G:0.26, T:0.14
Consensus pattern (22 bp):
TAAACAGAGAGCACCAAGGTGC
Found at i:135821 original size:25 final size:25
Alignment explanation
Indices: 135793--135902 Score: 82
Period size: 25 Copynumber: 4.4 Consensus size: 25
135783 TAGCTCTCTT
*
135793 GAGCTTCCCGATACT-TGGCTCGCAA
1 GAGCTTCCCGATA-TATAGCTCGCAA
* * * *
135818 GAGCTTTCTGATATATAGCTCGTAT
1 GAGCTTCCCGATATATAGCTCGCAA
* * *
135843 GAGCTTCCCGTTACT-TAGCTCACAT
1 GAGCTTCCCGATA-TATAGCTCGCAA
* *
135868 GAGCTTCCC-ATTATATGGCTCGGAA
1 GAGCTTCCCGA-TATATAGCTCGCAA
135893 GAGCTTCCCG
1 GAGCTTCCCG
135903 TTTACATGCT
Statistics
Matches: 65, Mismatches: 15, Indels: 9
0.73 0.17 0.10
Matches are distributed among these distances:
24 2 0.03
25 62 0.95
26 1 0.02
ACGTcount: A:0.21, C:0.27, G:0.22, T:0.30
Consensus pattern (25 bp):
GAGCTTCCCGATATATAGCTCGCAA
Found at i:135858 original size:50 final size:50
Alignment explanation
Indices: 135792--135904 Score: 129
Period size: 50 Copynumber: 2.3 Consensus size: 50
135782 ATAGCTCTCT
* * * ** *
135792 TGAGCTTCCCGATACTTGGCTCGCAAGAGCTTTCTGA-TATATAGCTCGTA
1 TGAGCTTCCCGTTACTTAGCTCACAAGAGC-TTCCCATTATATAGCTCGGA
* *
135842 TGAGCTTCCCGTTACTTAGCTCACATGAGCTTCCCATTATATGGCTCGGA
1 TGAGCTTCCCGTTACTTAGCTCACAAGAGCTTCCCATTATATAGCTCGGA
*
135892 AGAGCTTCCCGTT
1 TGAGCTTCCCGTT
135905 TACATGCTTG
Statistics
Matches: 53, Mismatches: 9, Indels: 2
0.83 0.14 0.03
Matches are distributed among these distances:
49 4 0.08
50 49 0.92
ACGTcount: A:0.20, C:0.27, G:0.21, T:0.32
Consensus pattern (50 bp):
TGAGCTTCCCGTTACTTAGCTCACAAGAGCTTCCCATTATATAGCTCGGA
Found at i:140425 original size:67 final size:67
Alignment explanation
Indices: 140317--140444 Score: 229
Period size: 67 Copynumber: 1.9 Consensus size: 67
140307 TTATATTACT
140317 GGGGATTTAGCCTGGACTGGAAATCCCGCTGTAAGAAATGAGATTCGCGGGAGTGTGCTCTCTTG
1 GGGGATTTAGCCTGGACTGGAAATCCCGCTGTAAGAAATGAGATTCGCGGGAGTGTGCTCTCTTG
140382 CA
66 CA
* * *
140384 GGGGATTTAGCCTGGACTGGTAATCCCGCTGTAAGAAATGAGGTTTGCGGGAGTGTGCTCT
1 GGGGATTTAGCCTGGACTGGAAATCCCGCTGTAAGAAATGAGATTCGCGGGAGTGTGCTCT
140445 TTGAATTGAA
Statistics
Matches: 58, Mismatches: 3, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
67 58 1.00
ACGTcount: A:0.21, C:0.18, G:0.34, T:0.27
Consensus pattern (67 bp):
GGGGATTTAGCCTGGACTGGAAATCCCGCTGTAAGAAATGAGATTCGCGGGAGTGTGCTCTCTTG
CA
Found at i:140637 original size:26 final size:27
Alignment explanation
Indices: 140570--140637 Score: 70
Period size: 26 Copynumber: 2.5 Consensus size: 27
140560 AAATGATAAG
140570 TACATAAAATCATGAAATTAAACTTGAAA
1 TACATAAAAT-ATGAAATT-AACTTGAAA
* *
140599 TACATAGAA-ATGATAATT-ACTTGATA
1 TACATAAAATATGA-AATTAACTTGAAA
140625 TAC-TAAAATATGA
1 TACATAAAATATGA
140638 CATGGAAAAT
Statistics
Matches: 34, Mismatches: 3, Indels: 7
0.77 0.07 0.16
Matches are distributed among these distances:
25 4 0.12
26 14 0.41
27 4 0.12
28 4 0.12
29 8 0.24
ACGTcount: A:0.51, C:0.09, G:0.09, T:0.31
Consensus pattern (27 bp):
TACATAAAATATGAAATTAACTTGAAA
Found at i:141733 original size:32 final size:32
Alignment explanation
Indices: 141656--141742 Score: 81
Period size: 32 Copynumber: 2.7 Consensus size: 32
141646 TTTAAAAAAT
* *
141656 AAAAAGTTATGAAAGACTAAAAAATTTAAACTTC
1 AAAAA-TTATAAAAAACTAAAAAATTT-AACTTC
*
141690 AAAAA-TA-AAAAAACTAAACAAATTT-ATTTC
1 AAAAATTATAAAAAACTAAA-AAATTTAACTTC
**
141720 AAAAATTATAAAAATTTAAAAAA
1 AAAAATTATAAAAAACTAAAAAA
141743 GTTTTAAAAA
Statistics
Matches: 45, Mismatches: 5, Indels: 9
0.76 0.08 0.15
Matches are distributed among these distances:
30 9 0.20
31 14 0.31
32 17 0.38
34 5 0.11
ACGTcount: A:0.63, C:0.07, G:0.03, T:0.26
Consensus pattern (32 bp):
AAAAATTATAAAAAACTAAAAAATTTAACTTC
Found at i:146807 original size:50 final size:50
Alignment explanation
Indices: 146683--146974 Score: 237
Period size: 50 Copynumber: 5.7 Consensus size: 50
146673 GGGAATGAGA
* * * *
146683 TCCCATGTAAGACCGTGTCTGGGACATGGCATTGGCATCAATAAGATTATGAGAGG
1 TCCCATGTAAGACCATGTCTGGGACATGGCGTTGGCA-C----CGA-GATGAGAGG
* *
146739 TCTCATGTAAGACCATGTCTGGGACATGGCGTTGGCACCGAGATGAGAGT
1 TCCCATGTAAGACCATGTCTGGGACATGGCGTTGGCACCGAGATGAGAGG
* *
146789 TCCCATGTAAGACTATGTCTGGGACATGGCGTTGGCACCGAGATAAGAGG
1 TCCCATGTAAGACCATGTCTGGGACATGGCGTTGGCACCGAGATGAGAGG
*** * * * * * **
146839 TCCCCCATAAGACCATGTCTGAGACATGGCATGGGCACCTATATGAGAAC
1 TCCCATGTAAGACCATGTCTGGGACATGGCGTTGGCACCGAGATGAGAGG
* * * ** * * * * **
146889 TCCCATGTAAGACCATATTTGGGATATGGTATTGG--CGGTACAGGAAACA
1 TCCCATGTAAGACCATGTCTGGGACATGGCGTTGGCACCG-AGATGAGAGG
*
146938 TCCCATGTAAGACCATGTCTGGGACATGGCTTTGGCA
1 TCCCATGTAAGACCATGTCTGGGACATGGCGTTGGCA
146975 TGTTATTATC
Statistics
Matches: 190, Mismatches: 43, Indels: 11
0.78 0.18 0.05
Matches are distributed among these distances:
48 1 0.01
49 35 0.18
50 117 0.62
51 2 0.01
55 1 0.01
56 34 0.18
ACGTcount: A:0.27, C:0.21, G:0.28, T:0.24
Consensus pattern (50 bp):
TCCCATGTAAGACCATGTCTGGGACATGGCGTTGGCACCGAGATGAGAGG
Found at i:155913 original size:6 final size:6
Alignment explanation
Indices: 155902--155931 Score: 60
Period size: 6 Copynumber: 5.0 Consensus size: 6
155892 CAATCTGGGA
155902 CTGATT CTGATT CTGATT CTGATT CTGATT
1 CTGATT CTGATT CTGATT CTGATT CTGATT
155932 GGGAGTAAGG
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 24 1.00
ACGTcount: A:0.17, C:0.17, G:0.17, T:0.50
Consensus pattern (6 bp):
CTGATT
Found at i:157230 original size:16 final size:16
Alignment explanation
Indices: 157205--157235 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
157195 TAACAAATGG
157205 ATAAGATTGGGGTGTT
1 ATAAGATTGGGGTGTT
*
157221 ATAAGGTTGGGGTGT
1 ATAAGATTGGGGTGT
157236 GTCTTGGGAG
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
16 14 1.00
ACGTcount: A:0.23, C:0.00, G:0.42, T:0.35
Consensus pattern (16 bp):
ATAAGATTGGGGTGTT
Found at i:161277 original size:3 final size:3
Alignment explanation
Indices: 161271--161323 Score: 97
Period size: 3 Copynumber: 17.7 Consensus size: 3
161261 TATCATTATT
*
161271 ATC ATC ATC ACC ATC ATC ATC ATC ATC ATC ATC ATC ATC ATC ATC ATC
1 ATC ATC ATC ATC ATC ATC ATC ATC ATC ATC ATC ATC ATC ATC ATC ATC
161319 ATC AT
1 ATC AT
161324 TGGCTCATTT
Statistics
Matches: 48, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
3 48 1.00
ACGTcount: A:0.34, C:0.34, G:0.00, T:0.32
Consensus pattern (3 bp):
ATC
Found at i:163946 original size:15 final size:15
Alignment explanation
Indices: 163926--163954 Score: 58
Period size: 15 Copynumber: 1.9 Consensus size: 15
163916 TGAGTATCAT
163926 CAAAACATGATATAA
1 CAAAACATGATATAA
163941 CAAAACATGATATA
1 CAAAACATGATATA
163955 GCCTCTTATA
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:0.59, C:0.14, G:0.07, T:0.21
Consensus pattern (15 bp):
CAAAACATGATATAA
Found at i:164449 original size:14 final size:14
Alignment explanation
Indices: 164430--164461 Score: 64
Period size: 14 Copynumber: 2.3 Consensus size: 14
164420 CTTTACTTTC
164430 CACAGTATCACTTG
1 CACAGTATCACTTG
164444 CACAGTATCACTTG
1 CACAGTATCACTTG
164458 CACA
1 CACA
164462 TATTACATAT
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 18 1.00
ACGTcount: A:0.31, C:0.31, G:0.12, T:0.25
Consensus pattern (14 bp):
CACAGTATCACTTG
Found at i:164484 original size:13 final size:13
Alignment explanation
Indices: 164466--164496 Score: 62
Period size: 13 Copynumber: 2.4 Consensus size: 13
164456 TGCACATATT
164466 ACATATAAATTCA
1 ACATATAAATTCA
164479 ACATATAAATTCA
1 ACATATAAATTCA
164492 ACATA
1 ACATA
164497 GATAAACTTA
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 18 1.00
ACGTcount: A:0.55, C:0.16, G:0.00, T:0.29
Consensus pattern (13 bp):
ACATATAAATTCA
Found at i:165252 original size:26 final size:25
Alignment explanation
Indices: 165173--165254 Score: 71
Period size: 26 Copynumber: 3.3 Consensus size: 25
165163 AAGTTAAAGC
*
165173 AAGCCA-T-ATCGGGAAGCTCCGGA
1 AAGCCATTAATCGGGAAGCTCCGAA
* * *
165196 GAGCCATTAATCAGGAAGC-CCACAA
1 AAGCCATTAATCGGGAAGCTCC-GAA
*
165221 AGAGCCTTTAATCGGGAAGCTCGCGAA
1 A-AGCCATTAATCGGGAAGCTC-CGAA
165248 AAGCCAT
1 AAGCCAT
165255 ATAACGAGAC
Statistics
Matches: 44, Mismatches: 9, Indels: 9
0.71 0.15 0.15
Matches are distributed among these distances:
23 5 0.11
24 3 0.07
25 10 0.23
26 21 0.48
27 4 0.09
28 1 0.02
ACGTcount: A:0.34, C:0.26, G:0.26, T:0.15
Consensus pattern (25 bp):
AAGCCATTAATCGGGAAGCTCCGAA
Found at i:169457 original size:7 final size:7
Alignment explanation
Indices: 169445--169479 Score: 70
Period size: 7 Copynumber: 5.0 Consensus size: 7
169435 GTATGCCTAC
169445 ATTTTTT
1 ATTTTTT
169452 ATTTTTT
1 ATTTTTT
169459 ATTTTTT
1 ATTTTTT
169466 ATTTTTT
1 ATTTTTT
169473 ATTTTTT
1 ATTTTTT
169480 TTTAAAAATG
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 28 1.00
ACGTcount: A:0.14, C:0.00, G:0.00, T:0.86
Consensus pattern (7 bp):
ATTTTTT
Found at i:172052 original size:39 final size:39
Alignment explanation
Indices: 172007--172124 Score: 121
Period size: 39 Copynumber: 3.3 Consensus size: 39
171997 AATTTATTAC
172007 TTATCTTAATAGTATTTTGTTCAGTTAATATTAAAGTGG
1 TTATCTTAATAGTATTTTGTTCAGTTAATATTAAAGTGG
* ** * *
172046 TTATCTTAATATTA-AAT-TT-AATT--TATT--A---C
1 TTATCTTAATAGTATTTTGTTCAGTTAATATTAAAGTGG
172075 TTATCTTAATAGTATTTTGTTCAGTTAATATTAAAGTGG
1 TTATCTTAATAGTATTTTGTTCAGTTAATATTAAAGTGG
172114 TTATCTTAATA
1 TTATCTTAATA
172125 TTAAATTTAA
Statistics
Matches: 59, Mismatches: 10, Indels: 20
0.66 0.11 0.22
Matches are distributed among these distances:
29 13 0.22
30 1 0.02
31 2 0.03
32 4 0.07
34 8 0.14
36 4 0.07
37 2 0.03
38 1 0.02
39 24 0.41
ACGTcount: A:0.33, C:0.06, G:0.10, T:0.51
Consensus pattern (39 bp):
TTATCTTAATAGTATTTTGTTCAGTTAATATTAAAGTGG
Found at i:172075 original size:68 final size:68
Alignment explanation
Indices: 171983--172181 Score: 317
Period size: 68 Copynumber: 2.9 Consensus size: 68
171973 TTTAATAGAT
171983 TTAATATTAAATTTAATTTATTACTTATCTTAATAGTATTTTGTTCAGTTAATATTAAAGTGGTT
1 TTAATATTAAATTTAATTTATTACTTATCTTAATAGTATTTTGTTCAGTTAATATTAAAGTGGTT
172048 ATC
66 ATC
172051 TTAATATTAAATTTAATTTATTACTTATCTTAATAGTATTTTGTTCAGTTAATATTAAAGTGGTT
1 TTAATATTAAATTTAATTTATTACTTATCTTAATAGTATTTTGTTCAGTTAATATTAAAGTGGTT
172116 ATC
66 ATC
* * * * * * * *
172119 TTAATATTAAATTTAATCTAATATTTATCTTGATAAGTATTATATTAATTTAATATTAAAGTG
1 TTAATATTAAATTTAATTTATTACTTATCTTAAT-AGTATTTTGTTCAGTTAATATTAAAGTG
172182 ATGAAGTTTA
Statistics
Matches: 122, Mismatches: 8, Indels: 1
0.93 0.06 0.01
Matches are distributed among these distances:
68 98 0.80
69 24 0.20
ACGTcount: A:0.36, C:0.05, G:0.08, T:0.51
Consensus pattern (68 bp):
TTAATATTAAATTTAATTTATTACTTATCTTAATAGTATTTTGTTCAGTTAATATTAAAGTGGTT
ATC
Found at i:173113 original size:36 final size:36
Alignment explanation
Indices: 173073--173160 Score: 104
Period size: 36 Copynumber: 2.4 Consensus size: 36
173063 TGAGCCTCCC
* * *
173073 CCCATGTGTGGGAGTAGGACCTCCCGTAAGCCTCAA
1 CCCATGTGAGGGAGCAGGACCTCCCGCAAGCCTCAA
* * **
173109 CCCATATGAGGGAGCAGGACCTCCTGCAAGCCTCTC
1 CCCATGTGAGGGAGCAGGACCTCCCGCAAGCCTCAA
*
173145 CCCATGTGCGGGAGCA
1 CCCATGTGAGGGAGCA
173161 ACACATTTGT
Statistics
Matches: 43, Mismatches: 9, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
36 43 1.00
ACGTcount: A:0.22, C:0.33, G:0.28, T:0.17
Consensus pattern (36 bp):
CCCATGTGAGGGAGCAGGACCTCCCGCAAGCCTCAA
Found at i:174828 original size:15 final size:15
Alignment explanation
Indices: 174808--174857 Score: 66
Period size: 15 Copynumber: 3.2 Consensus size: 15
174798 TGATAAATTT
174808 ATTGAATTTATATTG
1 ATTGAATTTATATTG
174823 ATTGAATTGGTATATAT-
1 ATTGAATT--TATAT-TG
174840 ATTGAATTTATATTG
1 ATTGAATTTATATTG
174855 ATT
1 ATT
174858 ATTTGAATTG
Statistics
Matches: 31, Mismatches: 0, Indels: 8
0.79 0.00 0.21
Matches are distributed among these distances:
14 1 0.03
15 16 0.52
17 13 0.42
18 1 0.03
ACGTcount: A:0.34, C:0.00, G:0.14, T:0.52
Consensus pattern (15 bp):
ATTGAATTTATATTG
Found at i:174861 original size:13 final size:11
Alignment explanation
Indices: 174807--174875 Score: 51
Period size: 11 Copynumber: 6.7 Consensus size: 11
174797 GTGATAAATT
174807 TATTGAATTTA
1 TATTGAATTTA
*
174818 TATTG-ATTGA
1 TATTGAATTTA
* *
174828 -ATTGGTATATA
1 TATT-GAATTTA
174839 TATTGAATTTA
1 TATTGAATTTA
174850 TATTG-A-TTA
1 TATTGAATTTA
*
174859 T-TTGAATTGA
1 TATTGAATTTA
174869 -ATTGAAT
1 TATTGAAT
174876 ATTGGTTGTG
Statistics
Matches: 46, Mismatches: 6, Indels: 13
0.71 0.09 0.20
Matches are distributed among these distances:
8 3 0.07
9 8 0.17
10 14 0.30
11 18 0.39
12 3 0.07
ACGTcount: A:0.35, C:0.00, G:0.14, T:0.51
Consensus pattern (11 bp):
TATTGAATTTA
Found at i:174872 original size:18 final size:19
Alignment explanation
Indices: 174836--174878 Score: 52
Period size: 18 Copynumber: 2.3 Consensus size: 19
174826 GAATTGGTAT
*
174836 ATATATTGAATTTATATTGA
1 ATAT-TTGAATTGATATTGA
*
174856 TTATTTGAATTGA-ATTGA
1 ATATTTGAATTGATATTGA
174874 ATATT
1 ATATT
174879 GGTTGTGTTT
Statistics
Matches: 20, Mismatches: 3, Indels: 2
0.80 0.12 0.08
Matches are distributed among these distances:
18 9 0.45
19 8 0.40
20 3 0.15
ACGTcount: A:0.37, C:0.00, G:0.12, T:0.51
Consensus pattern (19 bp):
ATATTTGAATTGATATTGA
Found at i:175034 original size:41 final size:40
Alignment explanation
Indices: 174990--175121 Score: 135
Period size: 41 Copynumber: 3.4 Consensus size: 40
174980 GACTTCGATT
*
174990 CGATGAGACACTGGGTGTCAATTTACTACTTCGGATTAATT
1 CGATGAGACACTGGGTGTCAATTTACTACTTCGGATT-ATC
* * * * *
175031 CGATGAGTCACTAGGTGCCAATTTAC-A--TCGGTTTAGC
1 CGATGAGACACTGGGTGTCAATTTACTACTTCGGATTATC
* * * *
175068 CGATGAGACACTGGGAGTCAATTTATTACTTTGAATTATC
1 CGATGAGACACTGGGTGTCAATTTACTACTTCGGATTATC
*
175108 CGATGAGGCACTGG
1 CGATGAGACACTGG
175122 ATGCCAAATT
Statistics
Matches: 72, Mismatches: 16, Indels: 7
0.76 0.17 0.07
Matches are distributed among these distances:
37 22 0.31
38 7 0.10
40 20 0.28
41 23 0.32
ACGTcount: A:0.27, C:0.18, G:0.24, T:0.31
Consensus pattern (40 bp):
CGATGAGACACTGGGTGTCAATTTACTACTTCGGATTATC
Found at i:175090 original size:37 final size:40
Alignment explanation
Indices: 174990--175097 Score: 114
Period size: 37 Copynumber: 2.8 Consensus size: 40
174980 GACTTCGATT
**
174990 CGATGAGACACTGGGTGTCAATTTACTACTTCGGATTAATT
1 CGATGAGACACTGGGTGTCAATTTACTAC-TCGGATTAAGC
* * * *
175031 CGATGAGTCACTAGGTGCCAATTTAC-A-TCGG-TTTAGC
1 CGATGAGACACTGGGTGTCAATTTACTACTCGGATTAAGC
* *
175068 CGATGAGACACTGGGAGTCAATTTATTACT
1 CGATGAGACACTGGGTGTCAATTTACTACT
175098 TTGAATTATC
Statistics
Matches: 54, Mismatches: 11, Indels: 6
0.76 0.15 0.08
Matches are distributed among these distances:
37 24 0.44
38 5 0.09
39 1 0.02
40 1 0.02
41 23 0.43
ACGTcount: A:0.27, C:0.19, G:0.23, T:0.31
Consensus pattern (40 bp):
CGATGAGACACTGGGTGTCAATTTACTACTCGGATTAAGC
Found at i:177291 original size:27 final size:29
Alignment explanation
Indices: 177238--177291 Score: 67
Period size: 27 Copynumber: 1.9 Consensus size: 29
177228 AAATTATAAA
* *
177238 TTTTATAAAAATTCAAAAAATTGAAAACT
1 TTTTATAAAAAATCAAAAAATTCAAAACT
*
177267 TTTTA-AAAAAATC-AAAATTTCAAAA
1 TTTTATAAAAAATCAAAAAATTCAAAA
177292 AATAACATAT
Statistics
Matches: 22, Mismatches: 3, Indels: 2
0.81 0.11 0.07
Matches are distributed among these distances:
27 10 0.45
28 7 0.32
29 5 0.23
ACGTcount: A:0.57, C:0.07, G:0.02, T:0.33
Consensus pattern (29 bp):
TTTTATAAAAAATCAAAAAATTCAAAACT
Found at i:191730 original size:16 final size:16
Alignment explanation
Indices: 191709--191742 Score: 59
Period size: 16 Copynumber: 2.1 Consensus size: 16
191699 AAACATTTTT
191709 TTATAAATGTTATATA
1 TTATAAATGTTATATA
*
191725 TTATAAATTTTATATA
1 TTATAAATGTTATATA
191741 TT
1 TT
191743 TTTGGCTTAA
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 17 1.00
ACGTcount: A:0.41, C:0.00, G:0.03, T:0.56
Consensus pattern (16 bp):
TTATAAATGTTATATA
Found at i:192481 original size:19 final size:21
Alignment explanation
Indices: 192457--192510 Score: 60
Period size: 21 Copynumber: 2.7 Consensus size: 21
192447 TTTTAGTATT
*
192457 TTGTAGCTCAAATT-AT-GTA
1 TTGTAGCTCAAATTCATAATA
*
192476 TTGTAG-TTAATATTCATAATA
1 TTGTAGCTCAA-ATTCATAATA
192497 TTGTAGCTCAAATT
1 TTGTAGCTCAAATT
192511 GTCAATCCGT
Statistics
Matches: 28, Mismatches: 3, Indels: 6
0.76 0.08 0.16
Matches are distributed among these distances:
18 3 0.11
19 9 0.32
20 2 0.07
21 11 0.39
22 3 0.11
ACGTcount: A:0.33, C:0.09, G:0.13, T:0.44
Consensus pattern (21 bp):
TTGTAGCTCAAATTCATAATA
Found at i:194462 original size:12 final size:12
Alignment explanation
Indices: 194445--194469 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
194435 CCACTTTATA
194445 AAAAAATCATTT
1 AAAAAATCATTT
194457 AAAAAATCATTT
1 AAAAAATCATTT
194469 A
1 A
194470 TGATAAAATA
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:0.60, C:0.08, G:0.00, T:0.32
Consensus pattern (12 bp):
AAAAAATCATTT
Found at i:194512 original size:20 final size:20
Alignment explanation
Indices: 194474--194519 Score: 58
Period size: 20 Copynumber: 2.2 Consensus size: 20
194464 CATTTATGAT
*
194474 AAAATACATAAGATTTTATA
1 AAAATACATAAGATATTATA
194494 AAAATACATACA-ATATTATA
1 AAAATACATA-AGATATTATA
194514 ATAAAT
1 A-AAAT
194520 GAATACCCAT
Statistics
Matches: 23, Mismatches: 1, Indels: 3
0.85 0.04 0.11
Matches are distributed among these distances:
20 18 0.78
21 5 0.22
ACGTcount: A:0.59, C:0.07, G:0.02, T:0.33
Consensus pattern (20 bp):
AAAATACATAAGATATTATA
Found at i:195108 original size:20 final size:20
Alignment explanation
Indices: 195085--195122 Score: 58
Period size: 20 Copynumber: 1.9 Consensus size: 20
195075 GGGTTTTCCT
* *
195085 TTTTTTTTATAAGATTATTA
1 TTTTATTTATAAAATTATTA
195105 TTTTATTTATAAAATTAT
1 TTTTATTTATAAAATTAT
195123 CATTATAATA
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 16 1.00
ACGTcount: A:0.34, C:0.00, G:0.03, T:0.63
Consensus pattern (20 bp):
TTTTATTTATAAAATTATTA
Found at i:195226 original size:22 final size:22
Alignment explanation
Indices: 195179--195236 Score: 57
Period size: 21 Copynumber: 2.7 Consensus size: 22
195169 ATCCATTTAT
* * *
195179 TTATAAATATTTTTA-ATAATTT
1 TTAT-AATATTTTTATAAAAATA
195201 TTATAATATTTTTATAAAAATA
1 TTATAATATTTTTATAAAAATA
*
195223 TTAT-GTATTTTTAT
1 TTATAATATTTTTAT
195237 TGAAAAATGA
Statistics
Matches: 31, Mismatches: 4, Indels: 3
0.82 0.11 0.08
Matches are distributed among these distances:
21 19 0.61
22 12 0.39
ACGTcount: A:0.40, C:0.00, G:0.02, T:0.59
Consensus pattern (22 bp):
TTATAATATTTTTATAAAAATA
Found at i:195278 original size:26 final size:27
Alignment explanation
Indices: 195247--195302 Score: 80
Period size: 26 Copynumber: 2.1 Consensus size: 27
195237 TGAAAAATGA
* *
195247 AATTTTTT-ATTTTTTATTTTTTTAA-
1 AATTTTTTAAATTTATATTTTTTTAAG
195272 AATTTTTTAAATTTATATTTTTTTAAG
1 AATTTTTTAAATTTATATTTTTTTAAG
195299 AATT
1 AATT
195303 AAGACTAAAT
Statistics
Matches: 27, Mismatches: 2, Indels: 2
0.87 0.06 0.06
Matches are distributed among these distances:
25 8 0.30
26 15 0.56
27 4 0.15
ACGTcount: A:0.30, C:0.00, G:0.02, T:0.68
Consensus pattern (27 bp):
AATTTTTTAAATTTATATTTTTTTAAG
Found at i:199296 original size:6 final size:6
Alignment explanation
Indices: 199285--199316 Score: 64
Period size: 6 Copynumber: 5.3 Consensus size: 6
199275 TTTGCTCAAA
199285 ATAAAT ATAAAT ATAAAT ATAAAT ATAAAT AT
1 ATAAAT ATAAAT ATAAAT ATAAAT ATAAAT AT
199317 TTTTATTTTT
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 26 1.00
ACGTcount: A:0.66, C:0.00, G:0.00, T:0.34
Consensus pattern (6 bp):
ATAAAT
Found at i:207407 original size:65 final size:65
Alignment explanation
Indices: 207303--207428 Score: 252
Period size: 65 Copynumber: 1.9 Consensus size: 65
207293 TGAGATTACG
207303 CTTTAACAAAGTTGACCTAAGGCTCTAAGAAGCTAAAGAAAGAACTCGACTCCAAAGGAAGAACT
1 CTTTAACAAAGTTGACCTAAGGCTCTAAGAAGCTAAAGAAAGAACTCGACTCCAAAGGAAGAACT
207368 CTTTAACAAAGTTGACCTAAGGCTCTAAGAAGCTAAAGAAAGAACTCGACTCCAAAGGAAG
1 CTTTAACAAAGTTGACCTAAGGCTCTAAGAAGCTAAAGAAAGAACTCGACTCCAAAGGAAG
207429 TAAGTTGCGC
Statistics
Matches: 61, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
65 61 1.00
ACGTcount: A:0.43, C:0.20, G:0.19, T:0.18
Consensus pattern (65 bp):
CTTTAACAAAGTTGACCTAAGGCTCTAAGAAGCTAAAGAAAGAACTCGACTCCAAAGGAAGAACT
Found at i:207725 original size:9 final size:9
Alignment explanation
Indices: 207711--207766 Score: 51
Period size: 9 Copynumber: 6.0 Consensus size: 9
207701 ATTTAACCCA
207711 TAATTTTTT
1 TAATTTTTT
207720 TAATTTTTT
1 TAATTTTTT
207729 T-ATCTTTTT
1 TAAT-TTTTT
* *
207738 CGAATTTTCT
1 -TAATTTTTT
*
207748 TGATTTTTGT
1 TAATTTTT-T
207758 TAATTTTTT
1 TAATTTTTT
207767 GTGGGAAATA
Statistics
Matches: 37, Mismatches: 6, Indels: 8
0.73 0.12 0.16
Matches are distributed among these distances:
8 2 0.05
9 21 0.57
10 12 0.32
11 2 0.05
ACGTcount: A:0.18, C:0.05, G:0.05, T:0.71
Consensus pattern (9 bp):
TAATTTTTT
Found at i:208861 original size:49 final size:49
Alignment explanation
Indices: 208804--208902 Score: 189
Period size: 49 Copynumber: 2.0 Consensus size: 49
208794 GATTCAAAGT
208804 ATGTTTCAAATTTAAAAGACAAATATTCAAACGCTATGCAGACATATCA
1 ATGTTTCAAATTTAAAAGACAAATATTCAAACGCTATGCAGACATATCA
*
208853 ATGTTTCAAATTTAAAAGACAGATATTCAAACGCTATGCAGACATATCA
1 ATGTTTCAAATTTAAAAGACAAATATTCAAACGCTATGCAGACATATCA
208902 A
1 A
208903 CCCAAAAATG
Statistics
Matches: 49, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
49 49 1.00
ACGTcount: A:0.44, C:0.16, G:0.11, T:0.28
Consensus pattern (49 bp):
ATGTTTCAAATTTAAAAGACAAATATTCAAACGCTATGCAGACATATCA
Found at i:209863 original size:13 final size:13
Alignment explanation
Indices: 209845--209882 Score: 67
Period size: 13 Copynumber: 2.9 Consensus size: 13
209835 AGTTCTTTAT
*
209845 TGCTTTTAAGAAG
1 TGCTTTTGAGAAG
209858 TGCTTTTGAGAAG
1 TGCTTTTGAGAAG
209871 TGCTTTTGAGAA
1 TGCTTTTGAGAA
209883 ATTTGGGTGT
Statistics
Matches: 24, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
13 24 1.00
ACGTcount: A:0.26, C:0.08, G:0.26, T:0.39
Consensus pattern (13 bp):
TGCTTTTGAGAAG
Found at i:210342 original size:12 final size:12
Alignment explanation
Indices: 210325--210354 Score: 60
Period size: 12 Copynumber: 2.5 Consensus size: 12
210315 GTCATTAACC
210325 CTAGATTATATT
1 CTAGATTATATT
210337 CTAGATTATATT
1 CTAGATTATATT
210349 CTAGAT
1 CTAGAT
210355 CCAAATCAAA
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 18 1.00
ACGTcount: A:0.33, C:0.10, G:0.10, T:0.47
Consensus pattern (12 bp):
CTAGATTATATT
Found at i:218022 original size:21 final size:18
Alignment explanation
Indices: 217997--218042 Score: 56
Period size: 18 Copynumber: 2.4 Consensus size: 18
217987 ATATGATTTT
217997 TTATTAAAATCTTAGTATTAA
1 TTATTAAAA--TTA-TATTAA
*
218018 TTATTTAAATTATATTAA
1 TTATTAAAATTATATTAA
218036 TTATTAA
1 TTATTAA
218043 GTAATTAAAA
Statistics
Matches: 23, Mismatches: 2, Indels: 3
0.82 0.07 0.11
Matches are distributed among these distances:
18 12 0.52
19 3 0.13
21 8 0.35
ACGTcount: A:0.43, C:0.02, G:0.02, T:0.52
Consensus pattern (18 bp):
TTATTAAAATTATATTAA
Found at i:218073 original size:14 final size:14
Alignment explanation
Indices: 218054--218083 Score: 60
Period size: 14 Copynumber: 2.1 Consensus size: 14
218044 TAATTAAAAC
218054 AATAAAGTAAATAA
1 AATAAAGTAAATAA
218068 AATAAAGTAAATAA
1 AATAAAGTAAATAA
218082 AA
1 AA
218084 GAAACTAAAG
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 16 1.00
ACGTcount: A:0.73, C:0.00, G:0.07, T:0.20
Consensus pattern (14 bp):
AATAAAGTAAATAA
Found at i:218110 original size:9 final size:9
Alignment explanation
Indices: 218080--218128 Score: 53
Period size: 9 Copynumber: 5.4 Consensus size: 9
218070 TAAAGTAAAT
218080 AAAAGAAAC
1 AAAAGAAAC
* *
218089 TAAAGAAAT
1 AAAAGAAAC
*
218098 AAAAGAAAG
1 AAAAGAAAC
**
218107 AAAAGAAGT
1 AAAAGAAAC
218116 AAAAGAAAC
1 AAAAGAAAC
218125 AAAA
1 AAAA
218129 AGAACAGCAG
Statistics
Matches: 32, Mismatches: 8, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
9 32 1.00
ACGTcount: A:0.76, C:0.04, G:0.14, T:0.06
Consensus pattern (9 bp):
AAAAGAAAC
Found at i:218128 original size:18 final size:18
Alignment explanation
Indices: 218071--218128 Score: 80
Period size: 18 Copynumber: 3.2 Consensus size: 18
218061 TAAATAAAAT
*
218071 AAAGTAAATAAAAGAAACT
1 AAAG-AAATAAAAGAAACA
*
218090 AAAGAAATAAAAGAAAGA
1 AAAGAAATAAAAGAAACA
*
218108 AAAGAAGTAAAAGAAACA
1 AAAGAAATAAAAGAAACA
218126 AAA
1 AAA
218129 AGAACAGCAG
Statistics
Matches: 35, Mismatches: 4, Indels: 1
0.88 0.10 0.03
Matches are distributed among these distances:
18 31 0.89
19 4 0.11
ACGTcount: A:0.74, C:0.03, G:0.14, T:0.09
Consensus pattern (18 bp):
AAAGAAATAAAAGAAACA
Found at i:218899 original size:18 final size:18
Alignment explanation
Indices: 218876--218913 Score: 51
Period size: 18 Copynumber: 2.1 Consensus size: 18
218866 GTATATTGAT
218876 TTGAAT-GTGAAATTGAAA
1 TTGAATAGTGAAATT-AAA
*
218894 TTGAATAGTGATATTAAA
1 TTGAATAGTGAAATTAAA
218912 TT
1 TT
218914 TGGTATGAAT
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
18 11 0.61
19 7 0.39
ACGTcount: A:0.42, C:0.00, G:0.18, T:0.39
Consensus pattern (18 bp):
TTGAATAGTGAAATTAAA
Found at i:219064 original size:23 final size:23
Alignment explanation
Indices: 219033--219143 Score: 97
Period size: 23 Copynumber: 5.0 Consensus size: 23
219023 GGTTTTGTCG
* *
219033 ATCAAGCACTTTATGTGTCGTAT
1 ATCAGGCACCTTATGTGTCGTAT
* *
219056 ATCAGGCACTTTATGTGCCGTAT
1 ATCAGGCACCTTATGTGTCGTAT
* **
219079 TTCAGGCACCTCGTGTGTCGTAT
1 ATCAGGCACCTTATGTGTCGTAT
**
219102 -T-AGGCACCTCGTGTGTCGT-T
1 ATCAGGCACCTTATGTGTCGTAT
*
219122 -TCAGGCA-CTTATGTATCGTAT
1 ATCAGGCACCTTATGTGTCGTAT
219143 A
1 A
219144 CTGATAAGGT
Statistics
Matches: 75, Mismatches: 10, Indels: 7
0.82 0.11 0.08
Matches are distributed among these distances:
20 11 0.15
21 24 0.32
22 1 0.01
23 39 0.52
ACGTcount: A:0.20, C:0.22, G:0.23, T:0.36
Consensus pattern (23 bp):
ATCAGGCACCTTATGTGTCGTAT
Found at i:219108 original size:21 final size:22
Alignment explanation
Indices: 219046--219129 Score: 100
Period size: 23 Copynumber: 3.8 Consensus size: 22
219036 AAGCACTTTA
* **
219046 TGTGTCGTATATCAGGCACTTTA
1 TGTGTCGTAT-TCAGGCACCTCG
*
219069 TGTGCCGTATTTCAGGCACCTCG
1 TGTGTCGTA-TTCAGGCACCTCG
219092 TGTGTCGTATT-AGGCACCTCG
1 TGTGTCGTATTCAGGCACCTCG
219113 TGTGTCGT-TTCAGGCAC
1 TGTGTCGTATTCAGGCAC
219130 TTATGTATCG
Statistics
Matches: 54, Mismatches: 5, Indels: 6
0.83 0.08 0.09
Matches are distributed among these distances:
20 2 0.04
21 24 0.44
22 2 0.04
23 25 0.46
24 1 0.02
ACGTcount: A:0.15, C:0.24, G:0.26, T:0.35
Consensus pattern (22 bp):
TGTGTCGTATTCAGGCACCTCG
Found at i:242863 original size:15 final size:17
Alignment explanation
Indices: 242845--242878 Score: 52
Period size: 17 Copynumber: 2.1 Consensus size: 17
242835 TATAGGTGAA
242845 CCCC-TATAAGCGAACC
1 CCCCATATAAGCGAACC
*
242861 CCCCATATATGCGAACC
1 CCCCATATAAGCGAACC
242878 C
1 C
242879 ATATGCAGAA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
16 4 0.25
17 12 0.75
ACGTcount: A:0.29, C:0.44, G:0.12, T:0.15
Consensus pattern (17 bp):
CCCCATATAAGCGAACC
Found at i:243016 original size:45 final size:45
Alignment explanation
Indices: 242967--243071 Score: 120
Period size: 45 Copynumber: 2.3 Consensus size: 45
242957 TATCTATTGA
*
242967 AATATGCAAACCCTATATGTTATTTACGCAAACCCTACATGTGGT
1 AATATGCAAACCCTATATGTCATTTACGCAAACCCTACATGTGGT
*** * * * * * *
243012 AATATATGAGCCTTATATGTCGTTTATGCGAACCCTATATGTGGT
1 AATATGCAAACCCTATATGTCATTTACGCAAACCCTACATGTGGT
243057 AATATGCAAACCCTA
1 AATATGCAAACCCTA
243072 ATTGTTTATA
Statistics
Matches: 45, Mismatches: 15, Indels: 0
0.75 0.25 0.00
Matches are distributed among these distances:
45 45 1.00
ACGTcount: A:0.32, C:0.20, G:0.15, T:0.32
Consensus pattern (45 bp):
AATATGCAAACCCTATATGTCATTTACGCAAACCCTACATGTGGT
Found at i:243050 original size:22 final size:23
Alignment explanation
Indices: 243025--243071 Score: 60
Period size: 23 Copynumber: 2.1 Consensus size: 23
243015 ATATGAGCCT
* *
243025 TATATGTCGT-TTATGCGAACCC
1 TATATGTCGTAATATGCAAACCC
*
243047 TATATGTGGTAATATGCAAACCC
1 TATATGTCGTAATATGCAAACCC
243070 TA
1 TA
243072 ATTGTTTATA
Statistics
Matches: 21, Mismatches: 3, Indels: 1
0.84 0.12 0.04
Matches are distributed among these distances:
22 9 0.43
23 12 0.57
ACGTcount: A:0.30, C:0.19, G:0.17, T:0.34
Consensus pattern (23 bp):
TATATGTCGTAATATGCAAACCC
Found at i:243068 original size:23 final size:23
Alignment explanation
Indices: 242967--243071 Score: 81
Period size: 22 Copynumber: 4.7 Consensus size: 23
242957 TATCTATTGA
242967 AATATGCAAACCCTATATGT--T
1 AATATGCAAACCCTATATGTGGT
* * *
242988 ATTTACGCAAACCCTACATGTGGT
1 A-ATATGCAAACCCTATATGTGGT
*** * * *
243012 AATATATGAGCCTTATATGTCGT
1 AATATGCAAACCCTATATGTGGT
* *
243035 -TTATGCGAACCCTATATGTGGT
1 AATATGCAAACCCTATATGTGGT
243057 AATATGCAAACCCTA
1 AATATGCAAACCCTA
243072 ATTGTTTATA
Statistics
Matches: 60, Mismatches: 20, Indels: 6
0.70 0.23 0.07
Matches are distributed among these distances:
21 1 0.02
22 32 0.53
23 25 0.42
24 2 0.03
ACGTcount: A:0.32, C:0.20, G:0.15, T:0.32
Consensus pattern (23 bp):
AATATGCAAACCCTATATGTGGT
Found at i:243120 original size:16 final size:16
Alignment explanation
Indices: 243099--243138 Score: 62
Period size: 16 Copynumber: 2.5 Consensus size: 16
243089 ACTCTATATG
243099 TGCAAACCCTAATGTA
1 TGCAAACCCTAATGTA
* *
243115 TGCAAACACTTATGTA
1 TGCAAACCCTAATGTA
243131 TGCAAACC
1 TGCAAACC
243139 TTAGGAATGC
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
16 21 1.00
ACGTcount: A:0.38, C:0.25, G:0.12, T:0.25
Consensus pattern (16 bp):
TGCAAACCCTAATGTA
Found at i:243148 original size:15 final size:16
Alignment explanation
Indices: 243114--243154 Score: 57
Period size: 15 Copynumber: 2.6 Consensus size: 16
243104 ACCCTAATGT
* *
243114 ATGCAAACACTTATGT
1 ATGCAAACACTTAGGA
243130 ATGCAAAC-CTTAGGA
1 ATGCAAACACTTAGGA
243145 ATGCAAACAC
1 ATGCAAACAC
243155 CTATGAACTT
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
15 13 0.59
16 9 0.41
ACGTcount: A:0.41, C:0.22, G:0.15, T:0.22
Consensus pattern (16 bp):
ATGCAAACACTTAGGA
Found at i:250461 original size:23 final size:23
Alignment explanation
Indices: 250434--250522 Score: 97
Period size: 23 Copynumber: 3.9 Consensus size: 23
250424 GAACGAACAG
250434 TGAACAATGAAGATTCTCTACGA
1 TGAACAATGAAGATTCTCTACGA
** * * *
250457 TGAACTGTGAAAATTTTCTACAA
1 TGAACAATGAAGATTCTCTACGA
*
250480 TGAACAATGAAGTTTCTCTACGA
1 TGAACAATGAAGATTCTCTACGA
* * *
250503 TTAACATTGAAGGTTCTCTA
1 TGAACAATGAAGATTCTCTA
250523 AAAAATACAA
Statistics
Matches: 52, Mismatches: 14, Indels: 0
0.79 0.21 0.00
Matches are distributed among these distances:
23 52 1.00
ACGTcount: A:0.36, C:0.16, G:0.16, T:0.33
Consensus pattern (23 bp):
TGAACAATGAAGATTCTCTACGA
Found at i:250810 original size:22 final size:22
Alignment explanation
Indices: 250768--250810 Score: 52
Period size: 23 Copynumber: 2.0 Consensus size: 22
250758 ATTTTCTAGA
* *
250768 TTTTAAAATTTTAAGTGTTTAC
1 TTTTAAAAATTTAAATGTTTAC
250790 TTTTAAAAAATTTAAAT-TTTA
1 TTTT-AAAAATTTAAATGTTTA
250811 AACAAATCAA
Statistics
Matches: 18, Mismatches: 2, Indels: 2
0.82 0.09 0.09
Matches are distributed among these distances:
22 8 0.44
23 10 0.56
ACGTcount: A:0.40, C:0.02, G:0.05, T:0.53
Consensus pattern (22 bp):
TTTTAAAAATTTAAATGTTTAC
Found at i:250837 original size:15 final size:15
Alignment explanation
Indices: 250819--250867 Score: 71
Period size: 15 Copynumber: 3.3 Consensus size: 15
250809 TAAACAAATC
250819 AATTAAGTTTTCAAA
1 AATTAAGTTTTCAAA
* *
250834 AATTTATTTTTCAAA
1 AATTAAGTTTTCAAA
*
250849 ATTTAAGTTTTCAAA
1 AATTAAGTTTTCAAA
250864 AATT
1 AATT
250868 TTTGCTTTAA
Statistics
Matches: 28, Mismatches: 6, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
15 28 1.00
ACGTcount: A:0.43, C:0.06, G:0.04, T:0.47
Consensus pattern (15 bp):
AATTAAGTTTTCAAA
Found at i:250897 original size:17 final size:16
Alignment explanation
Indices: 250827--250901 Score: 66
Period size: 15 Copynumber: 4.8 Consensus size: 16
250817 TCAATTAAGT
**
250827 TTTCAAAAA-TTTATT
1 TTTCAAAAATTTTAGC
* *
250842 TTTC-AAAATTTAAGT
1 TTTCAAAAATTTTAGC
*
250857 TTTCAAAAATTTTTGC
1 TTTCAAAAATTTTAGC
250873 TTT-AAAAAGTTTCTAGC
1 TTTCAAAAA-TTT-TAGC
250890 TTTCAAAAATTT
1 TTTCAAAAATTT
250902 AAGTTTTTAA
Statistics
Matches: 49, Mismatches: 6, Indels: 8
0.78 0.10 0.13
Matches are distributed among these distances:
14 4 0.08
15 17 0.35
16 14 0.29
17 9 0.18
18 5 0.10
ACGTcount: A:0.37, C:0.09, G:0.05, T:0.48
Consensus pattern (16 bp):
TTTCAAAAATTTTAGC
Found at i:254602 original size:17 final size:16
Alignment explanation
Indices: 254534--254604 Score: 88
Period size: 16 Copynumber: 4.4 Consensus size: 16
254524 AAAACAAATC
*
254534 AAATTTGAGCTTTCAA
1 AAATTTTAGCTTTCAA
* **
254550 AAATTTAAAATTTCAA
1 AAATTTTAGCTTTCAA
*
254566 AAATTTTAGCTTTAAA
1 AAATTTTAGCTTTCAA
254582 AAATTTCTAGCTTTCAA
1 AAATTT-TAGCTTTCAA
254599 AAATTT
1 AAATTT
254605 AAGTTTTTAA
Statistics
Matches: 46, Mismatches: 8, Indels: 1
0.84 0.15 0.02
Matches are distributed among these distances:
16 31 0.67
17 15 0.33
ACGTcount: A:0.44, C:0.10, G:0.06, T:0.41
Consensus pattern (16 bp):
AAATTTTAGCTTTCAA
Found at i:264297 original size:18 final size:18
Alignment explanation
Indices: 264274--264310 Score: 74
Period size: 18 Copynumber: 2.1 Consensus size: 18
264264 TTCAGAAAGT
264274 ACTAACTACAGTATTTCC
1 ACTAACTACAGTATTTCC
264292 ACTAACTACAGTATTTCC
1 ACTAACTACAGTATTTCC
264310 A
1 A
264311 GAGTATTCTA
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 19 1.00
ACGTcount: A:0.35, C:0.27, G:0.05, T:0.32
Consensus pattern (18 bp):
ACTAACTACAGTATTTCC
Found at i:265054 original size:6 final size:6
Alignment explanation
Indices: 265043--265077 Score: 61
Period size: 6 Copynumber: 5.7 Consensus size: 6
265033 ATGTCCATTT
265043 CAGATA CAGATA CAGATA CAGATA CAGATAA CAGA
1 CAGATA CAGATA CAGATA CAGATA CAGAT-A CAGA
265078 ATCATATATG
Statistics
Matches: 28, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
6 23 0.82
7 5 0.18
ACGTcount: A:0.51, C:0.17, G:0.17, T:0.14
Consensus pattern (6 bp):
CAGATA
Found at i:265548 original size:18 final size:18
Alignment explanation
Indices: 265521--265566 Score: 58
Period size: 18 Copynumber: 2.6 Consensus size: 18
265511 TTCAAAATTT
* *
265521 TGGGCTTACATGCCCGTG
1 TGGGCCTACACGCCCGTG
265539 TGGGCCTACACGCCCGTG
1 TGGGCCTACACGCCCGTG
*
265557 -CGGCCTACAC
1 TGGGCCTACAC
265567 ACCCAGATTG
Statistics
Matches: 25, Mismatches: 3, Indels: 1
0.86 0.10 0.03
Matches are distributed among these distances:
17 9 0.36
18 16 0.64
ACGTcount: A:0.13, C:0.37, G:0.30, T:0.20
Consensus pattern (18 bp):
TGGGCCTACACGCCCGTG
Found at i:267354 original size:16 final size:16
Alignment explanation
Indices: 267330--267363 Score: 50
Period size: 16 Copynumber: 2.1 Consensus size: 16
267320 TTGACTGAAC
267330 AATTAGAAAAAAGATA
1 AATTAGAAAAAAGATA
* *
267346 AATTCGAAAAAGGATA
1 AATTAGAAAAAAGATA
267362 AA
1 AA
267364 ACAAATTAAA
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:0.65, C:0.03, G:0.15, T:0.18
Consensus pattern (16 bp):
AATTAGAAAAAAGATA
Found at i:271101 original size:29 final size:29
Alignment explanation
Indices: 271038--271111 Score: 78
Period size: 29 Copynumber: 2.5 Consensus size: 29
271028 GGCATTGAAA
* * *
271038 TCCCTTAATTTTCTCCCCTATAGTTTTCG
1 TCCCTTGATTTCCTCCCCTATAGTGTTCG
271067 TCCCTTGATTTCCTCCCCTATAGGTGTT-G
1 TCCCTTGATTTCCTCCCCTATA-GTGTTCG
* *
271096 TTCCTTTGATTCCCTC
1 -TCCCTTGATTTCCTC
271112 AAGGTTGTTC
Statistics
Matches: 38, Mismatches: 5, Indels: 3
0.83 0.11 0.07
Matches are distributed among these distances:
29 21 0.55
30 17 0.45
ACGTcount: A:0.11, C:0.32, G:0.11, T:0.46
Consensus pattern (29 bp):
TCCCTTGATTTCCTCCCCTATAGTGTTCG
Found at i:272069 original size:19 final size:19
Alignment explanation
Indices: 272021--272060 Score: 57
Period size: 19 Copynumber: 2.2 Consensus size: 19
272011 GTACATTATC
272021 TATTATATA-T-TACATAA
1 TATTATATATTATACATAA
*
272038 TATTATATATTATACATAT
1 TATTATATATTATACATAA
272057 TATT
1 TATT
272061 GTTTATTATT
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
17 9 0.45
18 1 0.05
19 10 0.50
ACGTcount: A:0.42, C:0.05, G:0.00, T:0.53
Consensus pattern (19 bp):
TATTATATATTATACATAA
Found at i:272152 original size:15 final size:15
Alignment explanation
Indices: 272132--272163 Score: 55
Period size: 15 Copynumber: 2.1 Consensus size: 15
272122 TTAGCATTCC
*
272132 TACTATATTATATCA
1 TACTATATCATATCA
272147 TACTATATCATATCA
1 TACTATATCATATCA
272162 TA
1 TA
272164 TATTGATAGT
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 16 1.00
ACGTcount: A:0.41, C:0.16, G:0.00, T:0.44
Consensus pattern (15 bp):
TACTATATCATATCA
Found at i:273358 original size:11 final size:11
Alignment explanation
Indices: 273339--273374 Score: 56
Period size: 11 Copynumber: 3.4 Consensus size: 11
273329 GACGGTTTAG
273339 TTTTCGCTCGT
1 TTTTCGCTCGT
*
273350 TTTTTGCTCGT
1 TTTTCGCTCGT
273361 TTTTCGCTC-T
1 TTTTCGCTCGT
273371 TTTT
1 TTTT
273375 GCTTCCAAAT
Statistics
Matches: 23, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
10 5 0.22
11 18 0.78
ACGTcount: A:0.00, C:0.22, G:0.14, T:0.64
Consensus pattern (11 bp):
TTTTCGCTCGT
Found at i:276216 original size:13 final size:13
Alignment explanation
Indices: 276198--276224 Score: 54
Period size: 13 Copynumber: 2.1 Consensus size: 13
276188 TCTTAAGCCA
276198 CTACAATGTTATT
1 CTACAATGTTATT
276211 CTACAATGTTATT
1 CTACAATGTTATT
276224 C
1 C
276225 GTAATGTGAC
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 14 1.00
ACGTcount: A:0.30, C:0.19, G:0.07, T:0.44
Consensus pattern (13 bp):
CTACAATGTTATT
Found at i:277135 original size:36 final size:35
Alignment explanation
Indices: 277080--277150 Score: 108
Period size: 36 Copynumber: 2.0 Consensus size: 35
277070 CCATTGATTA
277080 CATTAATATCATCATCATCAAATCACAACTTCATT
1 CATTAATATCATCATCATCAAATCACAACTTCATT
*
277115 CATTACAT-TCATACATCATCAAATCGCAACTTCATT
1 CATTA-ATATCAT-CATCATCAAATCACAACTTCATT
277151 GCTGCCACCC
Statistics
Matches: 33, Mismatches: 1, Indels: 3
0.89 0.03 0.08
Matches are distributed among these distances:
35 9 0.27
36 24 0.73
ACGTcount: A:0.38, C:0.27, G:0.01, T:0.34
Consensus pattern (35 bp):
CATTAATATCATCATCATCAAATCACAACTTCATT
Found at i:284674 original size:30 final size:30
Alignment explanation
Indices: 284640--284715 Score: 89
Period size: 30 Copynumber: 2.5 Consensus size: 30
284630 CATAAGTTAG
*
284640 CTTGTGTGAGAAACTTTGATAAAATGACAA
1 CTTGTGTGAGCAACTTTGATAAAATGACAA
* ** * * *
284670 CTTGTATGAGCAACCCTGATATAATGTCAG
1 CTTGTGTGAGCAACTTTGATAAAATGACAA
284700 CTTGTGTGAGCAACTT
1 CTTGTGTGAGCAACTT
284716 ATTCACCCAT
Statistics
Matches: 36, Mismatches: 10, Indels: 0
0.78 0.22 0.00
Matches are distributed among these distances:
30 36 1.00
ACGTcount: A:0.32, C:0.16, G:0.21, T:0.32
Consensus pattern (30 bp):
CTTGTGTGAGCAACTTTGATAAAATGACAA
Done.