Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01011654.1 Kokia drynarioides strain JFW-HI SEQ_126646, whole genome shotgun sequence
Parameters: 2 7 7 80 10 50 1000
Pmatch=0.80,Pindel=0.10
tuple sizes 0,4,5,7
tuple distances 0, 29, 159, 1000
Length: 184726
ACGTcount: A:0.34, C:0.17, G:0.16, T:0.33
Warning! 66 characters in sequence are not A, C, G, or T
Found at i:749 original size:12 final size:12
Alignment explanation
Indices: 703--749 Score: 51
Period size: 12 Copynumber: 3.7 Consensus size: 12
693 AATAAATAGC
703 ATTAATAATAATGGT
1 ATTAATAATAA---T
718 ATTAATAATAAT
1 ATTAATAATAAT
730 ATCT-ATAATAAT
1 AT-TAATAATAAT
742 ATTAATAA
1 ATTAATAA
750 CATTAATAAT
Statistics
Matches: 30, Mismatches: 0, Indels: 7
0.81 0.00 0.19
Matches are distributed among these distances:
11 1 0.03
12 17 0.57
13 1 0.03
15 11 0.37
ACGTcount: A:0.53, C:0.02, G:0.04, T:0.40
Consensus pattern (12 bp):
ATTAATAATAAT
Found at i:831 original size:3 final size:3
Alignment explanation
Indices: 823--865 Score: 68
Period size: 3 Copynumber: 14.3 Consensus size: 3
813 ACTGCCTCAT
* *
823 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAT TAA TAT TAA T
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA T
866 TATTTTAATA
Statistics
Matches: 36, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
3 36 1.00
ACGTcount: A:0.60, C:0.00, G:0.00, T:0.40
Consensus pattern (3 bp):
TAA
Found at i:873 original size:15 final size:15
Alignment explanation
Indices: 826--876 Score: 66
Period size: 15 Copynumber: 3.4 Consensus size: 15
816 GCCTCATTAA
*
826 TAATAATAATAATAA
1 TAATAATAATAATAT
841 TAATAATAATAATAT
1 TAATAATAATAATAT
* * *
856 TAATATTAATTATTT
1 TAATAATAATAATAT
871 TAATAA
1 TAATAA
877 AAAAAAGAAT
Statistics
Matches: 31, Mismatches: 5, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
15 31 1.00
ACGTcount: A:0.57, C:0.00, G:0.00, T:0.43
Consensus pattern (15 bp):
TAATAATAATAATAT
Found at i:1901 original size:29 final size:29
Alignment explanation
Indices: 1868--2087 Score: 257
Period size: 29 Copynumber: 7.5 Consensus size: 29
1858 CTGAATTGTT
* *
1868 CAAAAATTCCATTTTTACCCCTGAGCTTC
1 CAAAAATTCCATTTTTACCCCTAAACTTC
* * *
1897 CAAAAATTACATTTTTGACCCCAAAACTTT
1 CAAAAATTCCATTTTT-ACCCCTAAACTTC
*
1927 CAAAAATTCCATTTTTA-CCCTCGAACTTC
1 CAAAAATTCCATTTTTACCCCT-AAACTTC
*
1956 CAAAAATTCCAGTTTTACCCCTAAACTTC
1 CAAAAATTCCATTTTTACCCCTAAACTTC
* *
1985 CAAGAATTCCATTTTTACCCCCAAACTTC
1 CAAAAATTCCATTTTTACCCCTAAACTTC
*
2014 CAAAAATTCCATTTTTGA-CCTTGAAACTTC
1 CAAAAATTCCATTTTT-ACCCCT-AAACTTC
* * *
2044 CAAAAATCCCATTTTTACCCCCAAACCTC
1 CAAAAATTCCATTTTTACCCCTAAACTTC
2073 C-AAAATCTCCATTTT
1 CAAAAAT-TCCATTTT
2088 CGACCTCGAA
Statistics
Matches: 162, Mismatches: 22, Indels: 14
0.82 0.11 0.07
Matches are distributed among these distances:
28 8 0.05
29 101 0.62
30 53 0.33
ACGTcount: A:0.33, C:0.30, G:0.04, T:0.33
Consensus pattern (29 bp):
CAAAAATTCCATTTTTACCCCTAAACTTC
Found at i:1958 original size:59 final size:59
Alignment explanation
Indices: 1866--2143 Score: 303
Period size: 59 Copynumber: 4.7 Consensus size: 59
1856 TCCTGAATTG
** * * *
1866 TTCAAAAATTCCATTTTTACCCCTGAGCTTCCAAAAATTACATTTTTGACCCCAAAACT
1 TTCAAAAATTCCATTTTTACCCCCAAACTTCCAAAAATTCCATTTTTGACCCCGAAACT
* * * *
1925 TTCAAAAATTCCATTTTTACCCTCGAACTTCCAAAAATTCCAGTTTT-ACCCCTAAACT
1 TTCAAAAATTCCATTTTTACCCCCAAACTTCCAAAAATTCCATTTTTGACCCCGAAACT
* * **
1983 TCCAAGAATTCCATTTTTACCCCCAAACTTCCAAAAATTCCATTTTTGACCTTGAAACT
1 TTCAAAAATTCCATTTTTACCCCCAAACTTCCAAAAATTCCATTTTTGACCCCGAAACT
* * * * *
2042 TCCAAAAATCCCATTTTTACCCCCAAACCTCC-AAAATCTCCATTTTCGACCTCGAAACT
1 TTCAAAAATTCCATTTTTACCCCCAAACTTCCAAAAAT-TCCATTTTTGACCCCGAAACT
* * ** *
2101 CTC-AAAATTACCA-TTTTGCCCCCAAAAATCCAAAATTTCCATT
1 TTCAAAAATT-CCATTTTTACCCCCAAACTTCCAAAAATTCCATT
2144 CTTCCCCCCG
Statistics
Matches: 189, Mismatches: 26, Indels: 9
0.84 0.12 0.04
Matches are distributed among these distances:
58 83 0.44
59 106 0.56
ACGTcount: A:0.33, C:0.31, G:0.04, T:0.32
Consensus pattern (59 bp):
TTCAAAAATTCCATTTTTACCCCCAAACTTCCAAAAATTCCATTTTTGACCCCGAAACT
Found at i:2042 original size:88 final size:87
Alignment explanation
Indices: 1868--2117 Score: 292
Period size: 88 Copynumber: 2.8 Consensus size: 87
1858 CTGAATTGTT
* * * *
1868 CAAAAATTCCATTTTTACCCCTGAGCTTCCAAAAATTACATTTTTGACCCCAAAACTTTCAAAAA
1 CAAAAATTCCATTTTTACCCCTAAACTTCC-AAAATTCCATTTTTGACCCCAAAACTTCCAAAAA
1933 TTCCATTTTTACCCTCGAACTTC
65 TTCCATTTTTACCCTCGAACTTC
* *
1956 CAAAAATTCCAGTTTTACCCCTAAACTTCCAAGAATTCCATTTTT-ACCCCCAAACTTCCAAAAA
1 CAAAAATTCCATTTTTACCCCTAAACTTCCAA-AATTCCATTTTTGACCCCAAAACTTCCAAAAA
*
2020 TTCCATTTTTGA-CCTTGAAACTTC
65 TTCCATTTTT-ACCCTCG-AACTTC
* * * * * *
2044 CAAAAATCCCATTTTTACCCCCAAACCTCCAAAATCTCCATTTTCGACCTCGAAAC-TCTC-AAA
1 CAAAAATTCCATTTTTACCCCTAAACTTCCAAAAT-TCCATTTTTGACCCCAAAACTTC-CAAAA
2107 ATTACCATTTT
64 ATT-CCATTTT
2118 GCCCCCAAAA
Statistics
Matches: 141, Mismatches: 14, Indels: 13
0.84 0.08 0.08
Matches are distributed among these distances:
87 36 0.26
88 89 0.63
89 16 0.11
ACGTcount: A:0.33, C:0.30, G:0.04, T:0.32
Consensus pattern (87 bp):
CAAAAATTCCATTTTTACCCCTAAACTTCCAAAATTCCATTTTTGACCCCAAAACTTCCAAAAAT
TCCATTTTTACCCTCGAACTTC
Found at i:2115 original size:30 final size:29
Alignment explanation
Indices: 1899--2118 Score: 141
Period size: 29 Copynumber: 7.5 Consensus size: 29
1889 TGAGCTTCCA
* * * * *
1899 AAAATTACATTTTTGACCCCAAAACTTTCA
1 AAAATTCCA-TTTTGACCTCGAAACTCTCC
*
1929 AAAATTCCATTTTTACCCTCG-AACT-TCC
1 AAAATTCCATTTTGA-CCTCGAAACTCTCC
* *
1957 AAAAATTCCAGTTTT-ACCCCTAAACT-TCC
1 -AAAATTCCA-TTTTGACCTCGAAACTCTCC
* * *
1986 AAGAATTCCATTTTTACCCCCAAACT-TCC
1 AA-AATTCCATTTTGACCTCGAAACTCTCC
*
2015 AAAAATTCCATTTTTGACCTTGAAACT-TCC
1 -AAAATTCCA-TTTTGACCTCGAAACTCTCC
* * * *
2045 AAAAATCCCATTTTTACCCCCAAAC-CTCC
1 -AAAATTCCATTTTGACCTCGAAACTCTCC
2074 AAAATCTCCATTTTCGACCTCGAAACTCT-C
1 AAAAT-TCCATTTT-GACCTCGAAACTCTCC
2104 AAAATTACCATTTTG
1 AAAATT-CCATTTTG
2119 CCCCCAAAAA
Statistics
Matches: 156, Mismatches: 21, Indels: 27
0.76 0.10 0.13
Matches are distributed among these distances:
28 16 0.10
29 76 0.49
30 62 0.40
31 2 0.01
ACGTcount: A:0.34, C:0.30, G:0.04, T:0.32
Consensus pattern (29 bp):
AAAATTCCATTTTGACCTCGAAACTCTCC
Found at i:2482 original size:96 final size:96
Alignment explanation
Indices: 2376--2562 Score: 238
Period size: 96 Copynumber: 1.9 Consensus size: 96
2366 AAAACTTTAA
* **
2376 AATCGAGGCAATA-TTCTTTTAT-TTCGAGTT-TCAAAAATTTGTGCATTAACTTACTAGGTGCA
1 AATCGAGGCAATATTTC-CTTATCTTCGA-TTCT-AAAAATTTGCACATTAACTTACTAGGTGCA
**
2438 ATTTTTCTTCAAATCGAA-ATAATCGAATACCCTT
63 ACCTTTCTTCAAATC-AAGATAATCGAATACCCTT
* * *
2472 AATCGAGGCAATGTTTCCTTATCTTCGATTCTGAAAATTTGCACCTTAACTTACTAGGTGCAACC
1 AATCGAGGCAATATTTCCTTATCTTCGATTCTAAAAATTTGCACATTAACTTACTAGGTGCAACC
2537 TTTCTTCAAATCAAGATAATCGAATA
66 TTTCTTCAAATCAAGATAATCGAATA
2563 TTCTTTTCCC
Statistics
Matches: 79, Mismatches: 8, Indels: 8
0.83 0.08 0.08
Matches are distributed among these distances:
95 2 0.03
96 68 0.86
97 9 0.11
ACGTcount: A:0.32, C:0.19, G:0.13, T:0.36
Consensus pattern (96 bp):
AATCGAGGCAATATTTCCTTATCTTCGATTCTAAAAATTTGCACATTAACTTACTAGGTGCAACC
TTTCTTCAAATCAAGATAATCGAATACCCTT
Found at i:3679 original size:29 final size:30
Alignment explanation
Indices: 3610--3681 Score: 83
Period size: 29 Copynumber: 2.4 Consensus size: 30
3600 TTTAAAATTG
*
3610 TACATGAATTATGATTTAATATGTAATTATA
1 TACATGAATTTTGATTT-ATATGTAATTATA
** *
3641 TATGTGAATTTTGATTT-TATGTAATTTTA
1 TACATGAATTTTGATTTATATGTAATTATA
*
3670 TACATAAATTTT
1 TACATGAATTTT
3682 TTATTTGATT
Statistics
Matches: 34, Mismatches: 7, Indels: 2
0.79 0.16 0.05
Matches are distributed among these distances:
29 20 0.59
31 14 0.41
ACGTcount: A:0.36, C:0.03, G:0.10, T:0.51
Consensus pattern (30 bp):
TACATGAATTTTGATTTATATGTAATTATA
Found at i:5848 original size:39 final size:40
Alignment explanation
Indices: 5794--5874 Score: 119
Period size: 39 Copynumber: 2.0 Consensus size: 40
5784 CAAGAGGTAT
*
5794 ATCCAATATGAAAAGGATTATGACTCTTCAATAGGTGTCC
1 ATCCAATATGAAAAGGATTATGACTCTTCAAAAGGTGTCC
* * *
5834 ATCCAATTTG-AAAGGGTTGTGACTCTTCAAAAGGTGTCC
1 ATCCAATATGAAAAGGATTATGACTCTTCAAAAGGTGTCC
5873 AT
1 AT
5875 TGAGTGCATA
Statistics
Matches: 37, Mismatches: 4, Indels: 1
0.88 0.10 0.02
Matches are distributed among these distances:
39 28 0.76
40 9 0.24
ACGTcount: A:0.32, C:0.17, G:0.20, T:0.31
Consensus pattern (40 bp):
ATCCAATATGAAAAGGATTATGACTCTTCAAAAGGTGTCC
Found at i:6246 original size:39 final size:40
Alignment explanation
Indices: 6192--6272 Score: 119
Period size: 39 Copynumber: 2.0 Consensus size: 40
6182 CAAGAGGTAT
*
6192 ATCCAATATGAAAAGGATTATGACTCTTCAATAGGTGTCC
1 ATCCAATATGAAAAGGATTATGACTCTTCAAAAGGTGTCC
* * *
6232 ATCCAATTTG-AAAGGGTTGTGACTCTTCAAAAGGTGTCC
1 ATCCAATATGAAAAGGATTATGACTCTTCAAAAGGTGTCC
6271 AT
1 AT
6273 TGAGTGCATA
Statistics
Matches: 37, Mismatches: 4, Indels: 1
0.88 0.10 0.02
Matches are distributed among these distances:
39 28 0.76
40 9 0.24
ACGTcount: A:0.32, C:0.17, G:0.20, T:0.31
Consensus pattern (40 bp):
ATCCAATATGAAAAGGATTATGACTCTTCAAAAGGTGTCC
Found at i:7977 original size:28 final size:28
Alignment explanation
Indices: 7945--8004 Score: 120
Period size: 28 Copynumber: 2.1 Consensus size: 28
7935 ATATGGAAAA
7945 GAATGGTTATATCAATCTAAGTAATGAT
1 GAATGGTTATATCAATCTAAGTAATGAT
7973 GAATGGTTATATCAATCTAAGTAATGAT
1 GAATGGTTATATCAATCTAAGTAATGAT
8001 GAAT
1 GAAT
8005 TTATAGATAA
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
28 32 1.00
ACGTcount: A:0.40, C:0.07, G:0.18, T:0.35
Consensus pattern (28 bp):
GAATGGTTATATCAATCTAAGTAATGAT
Found at i:11124 original size:39 final size:39
Alignment explanation
Indices: 11080--11163 Score: 91
Period size: 39 Copynumber: 2.2 Consensus size: 39
11070 TGGGACAAGT
*
11080 CTCTTCCAAGAGGTAT-GTCCAATATGAAAAGGATTGTGA
1 CTCTTCCAAGAGGTATCATCCAATATG-AAAGGATTGTGA
* * * *
11119 CTCTT-CAATAGGTGTCCATCCAATTTGAAAGGGTTGTGA
1 CTCTTCCAAGAGGTAT-CATCCAATATGAAAGGATTGTGA
11158 CTCTTC
1 CTCTTC
11164 AAAAGGTGTC
Statistics
Matches: 37, Mismatches: 5, Indels: 5
0.79 0.11 0.11
Matches are distributed among these distances:
38 8 0.22
39 21 0.57
40 8 0.22
ACGTcount: A:0.27, C:0.19, G:0.21, T:0.32
Consensus pattern (39 bp):
CTCTTCCAAGAGGTATCATCCAATATGAAAGGATTGTGA
Found at i:11164 original size:39 final size:40
Alignment explanation
Indices: 11097--11176 Score: 126
Period size: 39 Copynumber: 2.0 Consensus size: 40
11087 AAGAGGTATG
*
11097 TCCAATATGAAAAGGATTGTGACTCTTCAATAGGTGTCCA
1 TCCAATATGAAAAGGATTGTGACTCTTCAAAAGGTGTCCA
* *
11137 TCCAATTTG-AAAGGGTTGTGACTCTTCAAAAGGTGTCCA
1 TCCAATATGAAAAGGATTGTGACTCTTCAAAAGGTGTCCA
11176 T
1 T
11177 TGAGTGCATA
Statistics
Matches: 37, Mismatches: 3, Indels: 1
0.90 0.07 0.02
Matches are distributed among these distances:
39 29 0.78
40 8 0.22
ACGTcount: A:0.30, C:0.17, G:0.21, T:0.31
Consensus pattern (40 bp):
TCCAATATGAAAAGGATTGTGACTCTTCAAAAGGTGTCCA
Found at i:12352 original size:35 final size:35
Alignment explanation
Indices: 12270--12352 Score: 98
Period size: 35 Copynumber: 2.4 Consensus size: 35
12260 TTAAACTTCG
* *
12270 ATATTATAAATTTAAATTATCTCTTAATAAAAAAT
1 ATATTTTAAATTTAAATTATCTATTAATAAAAAAT
* * *
12305 ATATTTT-TATTTAAATGTTTTTATTAATAAAAAAT
1 ATATTTTAAATTTAAAT-TATCTATTAATAAAAAAT
12340 AT-TTTTAAATTTA
1 ATATTTTAAATTTA
12353 TTAAACTAAA
Statistics
Matches: 40, Mismatches: 6, Indels: 4
0.80 0.12 0.08
Matches are distributed among these distances:
34 12 0.30
35 28 0.70
ACGTcount: A:0.46, C:0.02, G:0.01, T:0.51
Consensus pattern (35 bp):
ATATTTTAAATTTAAATTATCTATTAATAAAAAAT
Found at i:12829 original size:12 final size:12
Alignment explanation
Indices: 12814--12839 Score: 52
Period size: 12 Copynumber: 2.2 Consensus size: 12
12804 ATACAATTAA
12814 AAATATTAAAAC
1 AAATATTAAAAC
12826 AAATATTAAAAC
1 AAATATTAAAAC
12838 AA
1 AA
12840 CAAACAAATT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 14 1.00
ACGTcount: A:0.69, C:0.08, G:0.00, T:0.23
Consensus pattern (12 bp):
AAATATTAAAAC
Found at i:12846 original size:19 final size:18
Alignment explanation
Indices: 12822--12857 Score: 54
Period size: 18 Copynumber: 1.9 Consensus size: 18
12812 AAAAATATTA
*
12822 AAACAAATATTAAAACAAC
1 AAACAAAT-TAAAAACAAC
12841 AAACAAATTAAAAACAA
1 AAACAAATTAAAAACAA
12858 TATTAAAATA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
18 8 0.50
19 8 0.50
ACGTcount: A:0.72, C:0.14, G:0.00, T:0.14
Consensus pattern (18 bp):
AAACAAATTAAAAACAAC
Found at i:13336 original size:20 final size:21
Alignment explanation
Indices: 13303--13342 Score: 55
Period size: 20 Copynumber: 2.0 Consensus size: 21
13293 AACAGCTTAT
*
13303 TATTACAAACAAAAA-AAAAG
1 TATTAAAAACAAAAATAAAAG
*
13323 TATTAAAAATAAAAATAAAA
1 TATTAAAAACAAAAATAAAA
13343 TCATTATTAT
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
20 13 0.76
21 4 0.24
ACGTcount: A:0.72, C:0.05, G:0.03, T:0.20
Consensus pattern (21 bp):
TATTAAAAACAAAAATAAAAG
Found at i:14154 original size:7 final size:7
Alignment explanation
Indices: 14142--14174 Score: 66
Period size: 7 Copynumber: 4.7 Consensus size: 7
14132 TTATAAGATA
14142 AAAATTT
1 AAAATTT
14149 AAAATTT
1 AAAATTT
14156 AAAATTT
1 AAAATTT
14163 AAAATTT
1 AAAATTT
14170 AAAAT
1 AAAAT
14175 CATTTTTATT
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 26 1.00
ACGTcount: A:0.61, C:0.00, G:0.00, T:0.39
Consensus pattern (7 bp):
AAAATTT
Found at i:16821 original size:29 final size:28
Alignment explanation
Indices: 16764--16821 Score: 80
Period size: 29 Copynumber: 2.0 Consensus size: 28
16754 GTTTATTAGA
**
16764 CTAAACCTTAAATCTTAAATCCTAAACC
1 CTAAACCAAAAATCTTAAATCCTAAACC
*
16792 CTAAACCAAAAATCCTTTAATCCTAAACC
1 CTAAACCAAAAAT-CTTAAATCCTAAACC
16821 C
1 C
16822 AAGTCGAGTA
Statistics
Matches: 26, Mismatches: 3, Indels: 1
0.87 0.10 0.03
Matches are distributed among these distances:
28 11 0.42
29 15 0.58
ACGTcount: A:0.43, C:0.31, G:0.00, T:0.26
Consensus pattern (28 bp):
CTAAACCAAAAATCTTAAATCCTAAACC
Found at i:17230 original size:43 final size:43
Alignment explanation
Indices: 17169--17308 Score: 262
Period size: 43 Copynumber: 3.3 Consensus size: 43
17159 AACTGCACAA
* *
17169 TTAATAACATGTCACGATATTAACAAGGGTCAAGTAATATAAT
1 TTAATAACATGCCACGATATTAACACGGGTCAAGTAATATAAT
17212 TTAATAACATGCCACGATATTAACACGGGTCAAGTAATATAAT
1 TTAATAACATGCCACGATATTAACACGGGTCAAGTAATATAAT
17255 TTAATAACATGCCACGATATTAACACGGGTCAAGTAATATAAT
1 TTAATAACATGCCACGATATTAACACGGGTCAAGTAATATAAT
17298 TTAATAACATG
1 TTAATAACATG
17309 TCAAGGAATA
Statistics
Matches: 95, Mismatches: 2, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
43 95 1.00
ACGTcount: A:0.43, C:0.14, G:0.14, T:0.29
Consensus pattern (43 bp):
TTAATAACATGCCACGATATTAACACGGGTCAAGTAATATAAT
Found at i:18424 original size:20 final size:20
Alignment explanation
Indices: 18373--18424 Score: 61
Period size: 20 Copynumber: 2.5 Consensus size: 20
18363 TGCAATTTAA
18373 AAAAAATTCAATTAATTCGGT
1 AAAAAATT-AATTAATTCGGT
* *
18394 ACATAAA-TAATTATTTCGGT
1 A-AAAAATTAATTAATTCGGT
18414 AAAAAATTAAT
1 AAAAAATTAAT
18425 AATAACCTAA
Statistics
Matches: 26, Mismatches: 3, Indels: 5
0.76 0.09 0.15
Matches are distributed among these distances:
19 4 0.15
20 16 0.62
21 2 0.08
22 4 0.15
ACGTcount: A:0.50, C:0.08, G:0.08, T:0.35
Consensus pattern (20 bp):
AAAAAATTAATTAATTCGGT
Found at i:19075 original size:31 final size:33
Alignment explanation
Indices: 19025--19086 Score: 101
Period size: 32 Copynumber: 1.9 Consensus size: 33
19015 TAATTACTAG
*
19025 TAACAAAATAACTTTAAAATAAC-AACAAAATT
1 TAACAAAATAAATTTAAAATAACAAACAAAATT
19057 TAACAAAA-AAATTTAAAATAACAAACAAAA
1 TAACAAAATAAATTTAAAATAACAAACAAAA
19087 CAATTATAAC
Statistics
Matches: 28, Mismatches: 1, Indels: 2
0.90 0.03 0.06
Matches are distributed among these distances:
31 13 0.46
32 15 0.54
ACGTcount: A:0.68, C:0.11, G:0.00, T:0.21
Consensus pattern (33 bp):
TAACAAAATAAATTTAAAATAACAAACAAAATT
Found at i:19083 original size:22 final size:23
Alignment explanation
Indices: 19058--19100 Score: 61
Period size: 22 Copynumber: 1.9 Consensus size: 23
19048 AACAAAATTT
19058 AACAAAAAAATT-TAAAATAACA
1 AACAAAAAAATTATAAAATAACA
* *
19080 AACAAAACAATTATAACATAA
1 AACAAAAAAATTATAAAATAA
19101 ACTAATTAAA
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
22 11 0.61
23 7 0.39
ACGTcount: A:0.70, C:0.12, G:0.00, T:0.19
Consensus pattern (23 bp):
AACAAAAAAATTATAAAATAACA
Found at i:20472 original size:24 final size:25
Alignment explanation
Indices: 20426--20478 Score: 74
Period size: 25 Copynumber: 2.2 Consensus size: 25
20416 AATTAGTAGC
*
20426 ATAAATAAAAATAATAGTAATGATA
1 ATAAATAAAAATAATACTAATGATA
20451 ATAAATAAAAAT-ATGACT-ATGATA
1 ATAAATAAAAATAAT-ACTAATGATA
20475 ATAA
1 ATAA
20479 CAATAAATAT
Statistics
Matches: 26, Mismatches: 1, Indels: 3
0.87 0.03 0.10
Matches are distributed among these distances:
24 12 0.46
25 14 0.54
ACGTcount: A:0.62, C:0.02, G:0.08, T:0.28
Consensus pattern (25 bp):
ATAAATAAAAATAATACTAATGATA
Found at i:20679 original size:18 final size:17
Alignment explanation
Indices: 20650--20684 Score: 61
Period size: 18 Copynumber: 2.0 Consensus size: 17
20640 AACCGAAACA
20650 AAATAAAATAAATAAAT
1 AAATAAAATAAATAAAT
20667 AAATAACAATAAATAAAT
1 AAATAA-AATAAATAAAT
20685 GCGAATATAA
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
17 6 0.35
18 11 0.65
ACGTcount: A:0.74, C:0.03, G:0.00, T:0.23
Consensus pattern (17 bp):
AAATAAAATAAATAAAT
Found at i:20698 original size:15 final size:13
Alignment explanation
Indices: 20660--20705 Score: 56
Period size: 14 Copynumber: 3.3 Consensus size: 13
20650 AAATAAAATA
*
20660 AATAAATAAATAAC
1 AATAAATAAAT-GC
20674 AATAAATAAATGC
1 AATAAATAAATGC
20687 GAATATAATAAATGC
1 -AATA-AATAAATGC
20702 AATA
1 AATA
20706 CAAATGATAA
Statistics
Matches: 29, Mismatches: 1, Indels: 4
0.85 0.03 0.12
Matches are distributed among these distances:
13 1 0.03
14 19 0.66
15 9 0.31
ACGTcount: A:0.63, C:0.07, G:0.07, T:0.24
Consensus pattern (13 bp):
AATAAATAAATGC
Found at i:22932 original size:101 final size:99
Alignment explanation
Indices: 22662--22958 Score: 320
Period size: 101 Copynumber: 3.0 Consensus size: 99
22652 AAAATAGGAC
* * * * *
22662 TTGTAGCTTTATCTTGCTTTACTGCAACTTTAGAGAGATAAGGATTTGCTTTCGTACCTTTAATT
1 TTGTAGC-TTATCTTGCTTTACTG-AACTTCAGAGAGATAAAGATTTGCTTTTGTAGCTTCAATT
* *
22727 CGATCCACTGCAACTTTAGGGATATAAGATTTAATG
64 CGATCCACTGCAACTTTAGGGATATAGGATTTGATG
* * * * * * *
22763 TCGTGACCTTATCTTGC--T-C--CAC-TCGGGGAGATAAATATTTGCTTTTATAGCTTCAATTC
1 TTGT-AGCTTATCTTGCTTTACTGAACTTCAGAGAGATAAAGATTTGCTTTTGTAGCTTCAATTC
* * *
22822 GATCCACTGCAACTTTAGGGGTATAGGATTTGGTT
65 GATCCACTGCAACTTTAGGGATATAGGATTTGATG
22857 TTGTAGCTTCATCTTGCTTTACTGTAACTTCAGAGAGATAAAGATTTGCTTTTGTAGCTTCAA-T
1 TTGTAGCTT-ATCTTGCTTTACTG-AACTTCAGAGAGATAAAGATTTGCTTTTGTAGCTTCAATT
* *
22921 CTGATCCACTGCAACTTCAGGAATATAGGATTTGATG
64 C-GATCCACTGCAACTTTAGGGATATAGGATTTGATG
22958 T
1 T
22959 CATAACTTCA
Statistics
Matches: 157, Mismatches: 29, Indels: 20
0.76 0.14 0.10
Matches are distributed among these distances:
93 4 0.03
94 68 0.43
95 2 0.01
96 1 0.01
97 1 0.01
98 1 0.01
99 1 0.01
100 4 0.03
101 73 0.46
102 2 0.01
ACGTcount: A:0.25, C:0.17, G:0.19, T:0.38
Consensus pattern (99 bp):
TTGTAGCTTATCTTGCTTTACTGAACTTCAGAGAGATAAAGATTTGCTTTTGTAGCTTCAATTCG
ATCCACTGCAACTTTAGGGATATAGGATTTGATG
Found at i:22937 original size:51 final size:50
Alignment explanation
Indices: 22789--22942 Score: 161
Period size: 51 Copynumber: 3.1 Consensus size: 50
22779 CTCCACTCGG
* * *
22789 GGAGATAAATATTTGCTTTTATAGCTTCAAT-TCGATCCACTGCAACTTTA
1 GGAGATAAAGATTTGCTTTTGTAGCTTCAATCT-GATCCACTGCAACTTCA
* * * * ** *
22839 GG-GGTATAGGATTTGGTTTTGTAGCTTC-ATCTTGCTTTACTGTAACTTCA
1 GGAGATA-AAGATTTGCTTTTGTAGCTTCAATC-TGATCCACTGCAACTTCA
22889 GAGAGATAAAGATTTGCTTTTGTAGCTTCAATCTGATCCACTGCAACTTCA
1 G-GAGATAAAGATTTGCTTTTGTAGCTTCAATCTGATCCACTGCAACTTCA
22940 GGA
1 GGA
22943 ATATAGGATT
Statistics
Matches: 81, Mismatches: 17, Indels: 12
0.74 0.15 0.11
Matches are distributed among these distances:
49 5 0.06
50 34 0.42
51 36 0.44
52 6 0.07
ACGTcount: A:0.26, C:0.17, G:0.19, T:0.38
Consensus pattern (50 bp):
GGAGATAAAGATTTGCTTTTGTAGCTTCAATCTGATCCACTGCAACTTCA
Found at i:22996 original size:101 final size:101
Alignment explanation
Indices: 22696--22996 Score: 237
Period size: 101 Copynumber: 3.0 Consensus size: 101
22686 CAACTTTAGA
* ** * * * * * *
22696 GAGATAAGGATTTGCTTTCGTACCTTTAATTCGATCCACTGCAACTTTAGGGATATAAGATTTAA
1 GAGATAAAGATTTGCTTTTATAGCTTCAATTCGATCCACTGCAACTTCAGGAATATAGGATTTGA
* * *
22761 TGTCGTGACCTT-ATCTTGC-T--C--C-AC-TCGGG
66 TGTCAT-AACTTCATCTTCCTTCACTACAACTTCGGG
* * ** *
22790 GAGATAAATATTTGCTTTTATAGCTTCAATTCGATCCACTGCAACTTTAGGGGTATAGGATTTGG
1 GAGATAAAGATTTGCTTTTATAGCTTCAATTCGATCCACTGCAACTTCAGGAATATAGGATTTGA
* ** * * * ** * *
22855 TTTTGTAGCTTCATCTTGCTTTACTGTAACTTCAGA
66 TGTCATAACTTCATCTTCCTTCACTACAACTTCGGG
*
22891 GAGATAAAGATTTGCTTTTGTAGCTTCAA-TCTGATCCACTGCAACTTCAGGAATATAGGATTTG
1 GAGATAAAGATTTGCTTTTATAGCTTCAATTC-GATCCACTGCAACTTCAGGAATATAGGATTTG
22955 ATGTCATAACTTCA-C-TCCATTACACTACAACTTCGGG
65 ATGTCATAACTTCATCTTCC-TT-CACTACAACTTCGGG
22992 GAGAT
1 GAGAT
22997 TGAGATCCGT
Statistics
Matches: 164, Mismatches: 32, Indels: 15
0.78 0.15 0.07
Matches are distributed among these distances:
93 4 0.02
94 66 0.40
95 1 0.01
97 1 0.01
99 2 0.01
100 7 0.04
101 83 0.51
ACGTcount: A:0.27, C:0.19, G:0.19, T:0.36
Consensus pattern (101 bp):
GAGATAAAGATTTGCTTTTATAGCTTCAATTCGATCCACTGCAACTTCAGGAATATAGGATTTGA
TGTCATAACTTCATCTTCCTTCACTACAACTTCGGG
Found at i:23661 original size:19 final size:20
Alignment explanation
Indices: 23614--23735 Score: 138
Period size: 20 Copynumber: 6.1 Consensus size: 20
23604 TAGCAATCAC
* * **
23614 TGGTCAAAAATGACAAATGT
1 TGGTAAAAAATGGCAAACAT
*
23634 TGGTAAAAAATGGAAAACAT
1 TGGTAAAAAATGGCAAACAT
*
23654 TGATAAAAAAATGGCAAACAT
1 TGGT-AAAAAATGGCAAACAT
* *
23675 TGGT-CAAAATTGCAAACAT
1 TGGTAAAAAATGGCAAACAT
*
23694 TGGTAAAAAATGGCAAATAT
1 TGGTAAAAAATGGCAAACAT
*
23714 TGGTAAAAAATAGCAAACAT
1 TGGTAAAAAATGGCAAACAT
23734 TG
1 TG
23736 ATCAAGAATT
Statistics
Matches: 85, Mismatches: 15, Indels: 4
0.82 0.14 0.04
Matches are distributed among these distances:
19 17 0.20
20 50 0.59
21 18 0.21
ACGTcount: A:0.50, C:0.09, G:0.18, T:0.23
Consensus pattern (20 bp):
TGGTAAAAAATGGCAAACAT
Found at i:23684 original size:40 final size:40
Alignment explanation
Indices: 23601--23737 Score: 141
Period size: 40 Copynumber: 3.4 Consensus size: 40
23591 AAAAGATTAG
* * * * * **
23601 AAATAGCAATCACTGGTCAAAAATGACAAATGTTGGTAAA
1 AAATAGCAAACATTGATAAAAAATGGCAAACATTGGTAAA
* * *
23641 AAATGGAAAACATTGATAAAAAAATGGCAAACATTGGT-CA
1 AAATAGCAAACATTGAT-AAAAAATGGCAAACATTGGTAAA
* * *
23681 AAATTGCAAACATTGGTAAAAAATGGCAAATATTGGTAAA
1 AAATAGCAAACATTGATAAAAAATGGCAAACATTGGTAAA
23721 AAATAGCAAACATTGAT
1 AAATAGCAAACATTGAT
23738 CAAGAATTGC
Statistics
Matches: 78, Mismatches: 17, Indels: 4
0.79 0.17 0.04
Matches are distributed among these distances:
39 19 0.24
40 43 0.55
41 16 0.21
ACGTcount: A:0.50, C:0.10, G:0.17, T:0.23
Consensus pattern (40 bp):
AAATAGCAAACATTGATAAAAAATGGCAAACATTGGTAAA
Found at i:34841 original size:27 final size:28
Alignment explanation
Indices: 34772--34842 Score: 99
Period size: 28 Copynumber: 2.6 Consensus size: 28
34762 TGCTCATACA
*
34772 AGCCAGAGTACAGAGTTACACTCTTACG
1 AGCCAGAATACAGAGTTACACTCTTACG
* *
34800 AGCCAGAATACAGAGTTACTCTCTTTCG
1 AGCCAGAATACAGAGTTACACTCTTACG
*
34828 A-CCAGAATATAGAGT
1 AGCCAGAATACAGAGT
34843 ATTTTCTAAG
Statistics
Matches: 39, Mismatches: 4, Indels: 1
0.89 0.09 0.02
Matches are distributed among these distances:
27 13 0.33
28 26 0.67
ACGTcount: A:0.34, C:0.23, G:0.20, T:0.24
Consensus pattern (28 bp):
AGCCAGAATACAGAGTTACACTCTTACG
Found at i:36938 original size:15 final size:13
Alignment explanation
Indices: 36900--36945 Score: 56
Period size: 14 Copynumber: 3.3 Consensus size: 13
36890 AGATAAGATA
*
36900 AATAAATAAATAAC
1 AATAAATAAAT-GC
36914 AATAAATAAATGC
1 AATAAATAAATGC
36927 GAATATAATAAATGC
1 -AATA-AATAAATGC
36942 AATA
1 AATA
36946 CAAATGATAA
Statistics
Matches: 29, Mismatches: 1, Indels: 4
0.85 0.03 0.12
Matches are distributed among these distances:
13 1 0.03
14 19 0.66
15 9 0.31
ACGTcount: A:0.63, C:0.07, G:0.07, T:0.24
Consensus pattern (13 bp):
AATAAATAAATGC
Found at i:39031 original size:16 final size:16
Alignment explanation
Indices: 39010--39042 Score: 66
Period size: 16 Copynumber: 2.1 Consensus size: 16
39000 AATTTTGAAA
39010 CCTTTAAAAGGGTATT
1 CCTTTAAAAGGGTATT
39026 CCTTTAAAAGGGTATT
1 CCTTTAAAAGGGTATT
39042 C
1 C
39043 GATTATTCTG
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 17 1.00
ACGTcount: A:0.30, C:0.15, G:0.18, T:0.36
Consensus pattern (16 bp):
CCTTTAAAAGGGTATT
Found at i:39456 original size:29 final size:29
Alignment explanation
Indices: 39423--39499 Score: 109
Period size: 29 Copynumber: 2.6 Consensus size: 29
39413 AGTTTTGGAG
*
39423 AATTTAGGGTTAAAATATAATTTTAGAAA
1 AATTTAAGGTTAAAATATAATTTTAGAAA
* *
39452 AATTTAAGGTTAAAATGTAATTTTAGGAA
1 AATTTAAGGTTAAAATATAATTTTAGAAA
*
39481 AGTTTGAAGGTTAAAATAT
1 AATTT-AAGGTTAAAATAT
39500 GGTTTTAGGA
Statistics
Matches: 42, Mismatches: 5, Indels: 1
0.88 0.10 0.02
Matches are distributed among these distances:
29 30 0.71
30 12 0.29
ACGTcount: A:0.45, C:0.00, G:0.17, T:0.38
Consensus pattern (29 bp):
AATTTAAGGTTAAAATATAATTTTAGAAA
Found at i:39493 original size:30 final size:30
Alignment explanation
Indices: 39430--39576 Score: 138
Period size: 30 Copynumber: 4.9 Consensus size: 30
39420 GAGAATTTAG
* * *
39430 GGTTAAAATATAATTTTAGAAAAATTT-AA
1 GGTTAAAATATGATTTTAGGAAAGTTTGAA
* *
39459 GGTTAAAATGTAATTTTAGGAAAGTTTGAA
1 GGTTAAAATATGATTTTAGGAAAGTTTGAA
* *
39489 GGTTAAAATATGGTTTTAGG-AAGTTTTTG-G
1 GGTTAAAATATGATTTTAGGAAAG--TTTGAA
* * *
39519 GGTCAAAATATGATTTTGGGAAAGTTTGAG
1 GGTTAAAATATGATTTTAGGAAAGTTTGAA
* * *
39549 GGTCAAAGTATGATTTTAAGAAAGTTTG
1 GGTTAAAATATGATTTTAGGAAAGTTTG
39577 GGGGTCAATT
Statistics
Matches: 100, Mismatches: 13, Indels: 9
0.82 0.11 0.07
Matches are distributed among these distances:
29 31 0.31
30 62 0.62
31 7 0.07
ACGTcount: A:0.37, C:0.01, G:0.24, T:0.37
Consensus pattern (30 bp):
GGTTAAAATATGATTTTAGGAAAGTTTGAA
Found at i:39582 original size:30 final size:30
Alignment explanation
Indices: 39428--39647 Score: 115
Period size: 30 Copynumber: 7.6 Consensus size: 30
39418 TGGAGAATTT
* * *
39428 AGGGTTAAAATATAATTTT-AGAAAAATTT-
1 AGGGTCAAAATATGATTTTAAG-AAAGTTTG
* * * * *
39457 AAGGTTAAAATGTAATTTTAGGAAAGTTTG
1 AGGGTCAAAATATGATTTTAAGAAAGTTTG
* * * *
39487 AAGGTTAAAATATGGTTTT-AGGAAGTTTTTG
1 AGGGTCAAAATATGATTTTAAGAAAG--TTTG
**
39518 -GGGTCAAAATATGATTTTGGGAAAGTTTG
1 AGGGTCAAAATATGATTTTAAGAAAGTTTG
*
39547 AGGGTCAAAGTATGATTTTAAGAAAGTTTG
1 AGGGTCAAAATATGATTTTAAGAAAGTTTG
* **
39577 GGGGTC-----A--ATTTGGA-AAAGTTT-
1 AGGGTCAAAATATGATTTTAAGAAAGTTTG
* * * *
39598 AGGGGTGAAAATATGATTTTAGGAAAATTTT
1 A-GGGTCAAAATATGATTTTAAGAAAGTTTG
39629 AGGGTCAAAATATGATTTT
1 AGGGTCAAAATATGATTTT
39648 GGAAAAGTTT
Statistics
Matches: 148, Mismatches: 27, Indels: 31
0.72 0.13 0.15
Matches are distributed among these distances:
22 11 0.07
23 5 0.03
25 1 0.01
27 1 0.01
29 35 0.24
30 86 0.58
31 9 0.06
ACGTcount: A:0.37, C:0.02, G:0.25, T:0.36
Consensus pattern (30 bp):
AGGGTCAAAATATGATTTTAAGAAAGTTTG
Found at i:39634 original size:52 final size:52
Alignment explanation
Indices: 39533--39636 Score: 129
Period size: 52 Copynumber: 2.0 Consensus size: 52
39523 AAAATATGAT
* * * *
39533 TTTGGGAAAGTTTGAGGGTCAAAGTATGATTTTAAGAAAGTTTGGGGGTCAA
1 TTTGGAAAAGTTTGAGGGTCAAAATATGATTTTAAGAAAATTTGAGGGTCAA
* * *
39585 TTTGGAAAAGTTT-AGGGGTGAAAATATGATTTTAGGAAAATTTTAGGGTCAA
1 TTTGGAAAAGTTTGA-GGGTCAAAATATGATTTTAAGAAAATTTGAGGGTCAA
39637 AATATGATTT
Statistics
Matches: 44, Mismatches: 7, Indels: 2
0.83 0.13 0.04
Matches are distributed among these distances:
51 1 0.02
52 43 0.98
ACGTcount: A:0.34, C:0.03, G:0.30, T:0.34
Consensus pattern (52 bp):
TTTGGAAAAGTTTGAGGGTCAAAATATGATTTTAAGAAAATTTGAGGGTCAA
Found at i:39655 original size:82 final size:84
Alignment explanation
Indices: 39517--39700 Score: 225
Period size: 82 Copynumber: 2.2 Consensus size: 84
39507 GGAAGTTTTT
* * *
39517 GGGGTCAAAATATGATTTTGGGAAAGTTTGAGGGTCAAAGTATGATTTTAAGAAAGTTT-GGGG-
1 GGGGTCAAAATATGATTTTAGGAAAATTTGAGGGTCAAAATATGATTTTAAGAAAGTTTAGGGGT
39580 GTCAA-TTTGGAAAAGTTTA
66 GT-AACTTTGGAAAAGTTTA
* * *
39599 GGGGTGAAAATATGATTTTAGGAAAATTTTAGGGTCAAAATATGATTTT-GGAAAAGTTTAGGGG
1 GGGGTCAAAATATGATTTTAGGAAAATTTGAGGGTCAAAATATGATTTTAAG-AAAGTTTAGGGG
*
39663 TGTAACTTTGGAAAA-ATTA
65 TGTAACTTTGGAAAAGTTTA
* * *
39682 AGAGTCAAAATGTGATTTT
1 GGGGTCAAAATATGATTTT
39701 TGAAAAGATT
Statistics
Matches: 87, Mismatches: 11, Indels: 7
0.83 0.10 0.07
Matches are distributed among these distances:
81 1 0.01
82 51 0.59
83 24 0.28
84 11 0.13
ACGTcount: A:0.35, C:0.03, G:0.28, T:0.34
Consensus pattern (84 bp):
GGGGTCAAAATATGATTTTAGGAAAATTTGAGGGTCAAAATATGATTTTAAGAAAGTTTAGGGGT
GTAACTTTGGAAAAGTTTA
Found at i:39713 original size:82 final size:82
Alignment explanation
Indices: 39520--39747 Score: 221
Period size: 83 Copynumber: 2.7 Consensus size: 82
39510 AGTTTTTGGG
* * *
39520 GTCAAAATATGATTTTGGGAAAGTTTGAGGGTCAAAGTATGATTTTAAGAAAGTTT-GGGG-GTC
1 GTCAAAATATGATTTTGGAAAAGTTT-AGGGTCAAAATATGATTTTGA-AAAGTTTAGGGGTGTC
* * *
39583 AATTTGGAAAAGTTTAGGG
64 AATTTGGAAAAGATTAAGA
* *
39602 GTGAAAATATGATTTTAGGAAAATTTTAGGGTCAAAATATGATTTTGGAAAAGTTTAGGGGTGT-
1 GTCAAAATATGATTTT-GGAAAAGTTTAGGGTCAAAATATGATTTT-GAAAAGTTTAGGGGTGTC
39666 AACTTTGGAAAA-ATTAAGA
64 AA-TTTGGAAAAGATTAAGA
* * * * * * **
39685 GTCAAAATGTGATTTTTGAAAAGATTAGGGATGAAAATGTAATTTTAGAAAAACTTAGGGGTG
1 GTCAAAATATGATTTTGGAAAAGTTTAGGG-TCAAAATATGATTTT-GAAAAGTTTAGGGGTG
39748 ATAATGTAAT
Statistics
Matches: 121, Mismatches: 19, Indels: 11
0.80 0.13 0.07
Matches are distributed among these distances:
82 51 0.42
83 59 0.49
84 11 0.09
ACGTcount: A:0.37, C:0.03, G:0.27, T:0.33
Consensus pattern (82 bp):
GTCAAAATATGATTTTGGAAAAGTTTAGGGTCAAAATATGATTTTGAAAAGTTTAGGGGTGTCAA
TTTGGAAAAGATTAAGA
Found at i:39722 original size:30 final size:29
Alignment explanation
Indices: 39589--39765 Score: 98
Period size: 30 Copynumber: 6.1 Consensus size: 29
39579 GGTCAATTTG
* * *
39589 GAAAAGTTTAGGGGTGAAAATATGATTTTA
1 GAAAAGATTA-GGGTGAAAATGTAATTTTA
** * * * *
39619 GGAAAATTTTAGGGTCAAAATATGATTTTG
1 -GAAAAGATTAGGGTGAAAATGTAATTTTA
* * *
39649 GAAAAGTTTAGGG-G----TGTAACTTTG
1 GAAAAGATTAGGGTGAAAATGTAATTTTA
* * * *
39673 GAAAA-ATTAAGAGTCAAAATGTGATTTTT
1 GAAAAGATT-AGGGTGAAAATGTAATTTTA
39702 GAAAAGATTAGGGATGAAAATGTAATTTTA
1 GAAAAGATTAGGG-TGAAAATGTAATTTTA
*
39732 GAAAA-ACTTAGGGGTGATAATGTAATTTTA
1 GAAAAGA-TTA-GGGTGAAAATGTAATTTTA
39762 GAAA
1 GAAA
39766 TGTTTGAGGG
Statistics
Matches: 117, Mismatches: 19, Indels: 21
0.75 0.12 0.13
Matches are distributed among these distances:
23 2 0.02
24 15 0.13
29 28 0.24
30 60 0.51
31 12 0.10
ACGTcount: A:0.41, C:0.02, G:0.24, T:0.33
Consensus pattern (29 bp):
GAAAAGATTAGGGTGAAAATGTAATTTTA
Found at i:41875 original size:84 final size:85
Alignment explanation
Indices: 41730--41896 Score: 219
Period size: 84 Copynumber: 2.0 Consensus size: 85
41720 TCGCGTCATT
* **
41730 GATTTAGTCTACTTCTCTGTATCTCATCAGGAAGATGACCGCTTCATTGATTTAATTCACTTCTC
1 GATTTAGTCTACTTCTCTGTATCTCATCAAGAAGATGACCGCTTCATTGATTTAACCCACTTCTC
41795 TATATCTCATCAGGAAGACG
66 TATATCTCATCAGGAAGACG
* * * * * * * *
41815 GATTTGGTTTACTT-TCTGTATCTCATCAAGAAGATGGCCTCTTTATTGCTTTGACCCACTTCTT
1 GATTTAGTCTACTTCTCTGTATCTCATCAAGAAGATGACCGCTTCATTGATTTAACCCACTTCTC
*
41879 TGTATCTCATCAGGAAGA
66 TATATCTCATCAGGAAGA
41897 TGAGGTTTAA
Statistics
Matches: 70, Mismatches: 12, Indels: 1
0.84 0.14 0.01
Matches are distributed among these distances:
84 58 0.83
85 12 0.17
ACGTcount: A:0.24, C:0.22, G:0.16, T:0.38
Consensus pattern (85 bp):
GATTTAGTCTACTTCTCTGTATCTCATCAAGAAGATGACCGCTTCATTGATTTAACCCACTTCTC
TATATCTCATCAGGAAGACG
Found at i:42029 original size:207 final size:208
Alignment explanation
Indices: 41662--42217 Score: 731
Period size: 207 Copynumber: 2.7 Consensus size: 208
41652 ATCTTTTGGT
* * * *
41662 CCACTTCTTTGTATCTCATCAGGAAGATAGGGGTTTGAAGTCTCACTCGTATTAAGCTTCGCGTC
1 CCACTTCTTTGTATCTCATCAGGAAGAT-GAGGTTTGAAGTCTCATTCGTATTGAGCTTCGCTTC
* * *
41727 ATTGATTTAGTCTACTTCTCTGTATCTCATCAGGAAGATGACCGCTTCATTGATTTAATTCACTT
65 ATTGATTTGGTCTACTTCTCTGTATCTTATCAGGAAGATGACCGCTTCATTGATTTAATCCACTT
* * ** ** *
41792 CTCTATATCTCATCAGGAAGACGGATTTGGTTTACTT-TCTGTATCTCATCAAGAAGATGGCCT-
130 CTCTGTATCTCATCAAGAAGACAAATTTGGTCCACTTCTCTGTATCTCATCAAGAAAATGG-CTG
*
41855 CTTTATTGCTTTGAC
194 CTTTATTGCCTTGAC
* *
41870 CCACTTCTTTGTATCTCATCAGGAAGATGAGGTTTAAAATCTCATTCGTATTGAGCTTCGCTTCA
1 CCACTTCTTTGTATCTCATCAGGAAGATGAGGTTTGAAGTCTCATTCGTATTGAGCTTCGCTTCA
* * * * * *
41935 TTGATTTGGTTTACTTCTTTGTATCTTATTAGGAAGATGACAGCTTTATTGATTTAATCCACTTT
66 TTGATTTGGTCTACTTCTCTGTATCTTATCAGGAAGATGACCGCTTCATTGATTTAATCCACTTC
* * * * *
42000 TTTGTATCTCATCAAGAAGGCAAATTTGGTCCACTTCTCTGTATCTTATTAGGAAAATGGCTGCT
131 TCTGTATCTCATCAAGAAGACAAATTTGGTCCACTTCTCTGTATCTCATCAAGAAAATGGCTGCT
42065 TTATTGCCTTGAC
196 TTATTGCCTTGAC
* * * * *
42078 CCACTTCTCTGTATCTCATCAAGAAGATAAGGGTTTGAAGTCTCATTCGTATTGAGCTTTGTTTC
1 CCACTTCTTTGTATCTCATCAGGAAGATGA-GGTTTGAAGTCTCATTCGTATTGAGCTTCGCTTC
* * *
42143 ATTGATTTGGTCTACTTCTCTGTAT-TTCATCAAGAAGATGACCGCCTCATTGTTTTAATCCACT
65 ATTGATTTGGTCTACTTCTCTGTATCTT-ATCAGGAAGATGACCGCTTCATTGATTTAATCCACT
42207 TCTCTGTATCT
129 TCTCTGTATCT
42218 TATTAGGAAG
Statistics
Matches: 299, Mismatches: 45, Indels: 7
0.85 0.13 0.02
Matches are distributed among these distances:
207 117 0.39
208 90 0.30
209 92 0.31
ACGTcount: A:0.23, C:0.20, G:0.17, T:0.40
Consensus pattern (208 bp):
CCACTTCTTTGTATCTCATCAGGAAGATGAGGTTTGAAGTCTCATTCGTATTGAGCTTCGCTTCA
TTGATTTGGTCTACTTCTCTGTATCTTATCAGGAAGATGACCGCTTCATTGATTTAATCCACTTC
TCTGTATCTCATCAAGAAGACAAATTTGGTCCACTTCTCTGTATCTCATCAAGAAAATGGCTGCT
TTATTGCCTTGAC
Found at i:42051 original size:85 final size:85
Alignment explanation
Indices: 41938--42103 Score: 224
Period size: 85 Copynumber: 2.0 Consensus size: 85
41928 CGCTTCATTG
** * * * * * *
41938 ATTTGGTTTACTTCTTTGTATCTTATTAGGAAGATGACAGCTTTATTGATTTAATCCACTTTTTT
1 ATTTGGTCCACTTCTCTGTATCTTATTAGGAAAATGACAGCTTTATTGACTTAACCCACTTCTCT
42003 GTATCTCATCAAGAAGGCAA
66 GTATCTCATCAAGAAGGCAA
* * * *
42023 ATTTGGTCCACTTCTCTGTATCTTATTAGGAAAATGGCTGCTTTATTGCCTTGACCCACTTCTCT
1 ATTTGGTCCACTTCTCTGTATCTTATTAGGAAAATGACAGCTTTATTGACTTAACCCACTTCTCT
42088 GTATCTCATCAAGAAG
66 GTATCTCATCAAGAAG
42104 ATAAGGGTTT
Statistics
Matches: 69, Mismatches: 12, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
85 69 1.00
ACGTcount: A:0.25, C:0.19, G:0.16, T:0.41
Consensus pattern (85 bp):
ATTTGGTCCACTTCTCTGTATCTTATTAGGAAAATGACAGCTTTATTGACTTAACCCACTTCTCT
GTATCTCATCAAGAAGGCAA
Found at i:42260 original size:124 final size:121
Alignment explanation
Indices: 42128--42351 Score: 313
Period size: 121 Copynumber: 1.8 Consensus size: 121
42118 TCTCATTCGT
* * * * * *
42128 ATTGAGCTTTGTTTCATTGATTTGGTCTACTTCTCTGTATTTCATCAAGAAGATGACCGCCTCAT
1 ATTGAGCTTCGCTTAATCGATTTGGTCTACTTCTCTGTATCTCATC-AG--GAAGACCGCCTCAT
* ** *
42193 TGTTTTAATCCACTTCTCTGTATCTTATTAGGAAGATGGGAGTTTAAAGTTTTACTCAC
63 TATTTTAATCCACTTCTCTGTATCAAATCAGGAAGATGGGAGTTTAAAGTTTTACTCAC
42252 ATTGAGCTTCGCTTAATCGATTTGGTCTACTTCTCTGTATCTCATCAGGAAGACCGCCTCATTAT
1 ATTGAGCTTCGCTTAATCGATTTGGTCTACTTCTCTGTATCTCATCAGGAAGACCGCCTCATTAT
* *
42317 TTTAATTCATTTCTCTGTATCAAATCAGGAAGATG
66 TTTAATCCACTTCTCTGTATCAAATCAGGAAGATG
42352 AATTTGATTC
Statistics
Matches: 88, Mismatches: 12, Indels: 3
0.85 0.12 0.03
Matches are distributed among these distances:
121 45 0.51
123 2 0.02
124 41 0.47
ACGTcount: A:0.24, C:0.19, G:0.17, T:0.40
Consensus pattern (121 bp):
ATTGAGCTTCGCTTAATCGATTTGGTCTACTTCTCTGTATCTCATCAGGAAGACCGCCTCATTAT
TTTAATCCACTTCTCTGTATCAAATCAGGAAGATGGGAGTTTAAAGTTTTACTCAC
Found at i:53708 original size:29 final size:29
Alignment explanation
Indices: 53650--53955 Score: 140
Period size: 29 Copynumber: 10.8 Consensus size: 29
53640 AAGGGGTTGA
*
53650 AAAATG-AAGTTTTGGAGAA-TTT-A-GTC
1 AAAATGTAA-TTTTGGAAAAGTTTAAGGTC
*
53676 AAAATGTAATTTTGGAAAACTTTAAGGTC
1 AAAATGTAATTTTGGAAAAGTTTAAGGTC
* *
53705 AAAATGTAATTTTAGG-AAAGTTTAGGGGTT
1 AAAATGTAATTTT-GGAAAAGTTTA-AGGTC
* ** *
53735 AAAATATGGTTTTAGG-AAAGTTTGAGGGGTC
1 AAAATGTAATTTT-GGAAAAGTTT-A-AGGTC
* * * *
53766 AAAGTATAATTTTGG-GAAGTTTAAGGTT
1 AAAATGTAATTTTGGAAAAGTTTAAGGTC
* * ** *
53794 AAAATGTGATTTTAGAAAAGTTTGGGGTG
1 AAAATGTAATTTTGGAAAAGTTTAAGGTC
53823 AAATATG--ATTTTGGAAAAGTTTAAGG--
1 AAA-ATGTAATTTTGGAAAAGTTTAAGGTC
* * * **
53849 ---GTGTAACTTTGGAAAAATTCGAGGTC
1 AAAATGTAATTTTGGAAAAGTTTAAGGTC
* * ** *
53875 AAAATATGATTTTGGAAAAG-TTGGGGATG
1 AAAATGTAATTTTGGAAAAGTTTAAGG-TC
*
53904 AAAATGTAATTTTGGAAAA-TTTAAGGGTG
1 AAAATGTAATTTTGGAAAAGTTTAA-GGTC
* **
53933 ATAATGTAATTTTAAAAAAGTTT
1 AAAATGTAATTTTGGAAAAGTTT
53956 GAGGGTTAAA
Statistics
Matches: 215, Mismatches: 45, Indels: 36
0.73 0.15 0.12
Matches are distributed among these distances:
22 2 0.01
24 15 0.07
26 15 0.07
27 5 0.02
28 35 0.16
29 86 0.40
30 41 0.19
31 16 0.07
ACGTcount: A:0.38, C:0.02, G:0.25, T:0.35
Consensus pattern (29 bp):
AAAATGTAATTTTGGAAAAGTTTAAGGTC
Found at i:53739 original size:30 final size:29
Alignment explanation
Indices: 53673--53989 Score: 131
Period size: 29 Copynumber: 11.0 Consensus size: 29
53663 GGAGAATTTA
* *
53673 GTCAAAATGTAATTTTGGAAAACTTTA-AG
1 GTCAAAATGTAATTTTGG-AAAGTTTAGGG
53702 GTCAAAATGTAATTTTAGGAAAGTTTAGGG
1 GTCAAAATGTAATTTT-GGAAAGTTTAGGG
* * **
53732 GTTAAAATATGGTTTTAGGAAAGTTTGAGGG
1 GTCAAAATGTAATTTT-GGAAAGTTT-AGGG
* * * *
53763 GTCAAAGTATAATTTTGGGAAGTTTA-AG
1 GTCAAAATGTAATTTTGGAAAGTTTAGGG
* * *
53791 GTTAAAATGTGATTTTAGAAAAGTTT-GGG
1 GTCAAAATGTAATTTT-GGAAAGTTTAGGG
* *
53820 GTGAAATATG--ATTTTGGAAAAGTTTAAGG
1 GTCAAA-ATGTAATTTTGG-AAAGTTTAGGG
* ** * *
53849 G------TGTAACTTTGGAAAAATTCGAG
1 GTCAAAATGTAATTTTGGAAAGTTTAGGG
* *
53872 GTCAAAATATGATTTTGGAAAAG-TT-GGG
1 GTCAAAATGTAATTTTGG-AAAGTTTAGGG
* * *
53900 GATGAAAATGTAATTTTGGAAAATTTAAGG
1 G-TCAAAATGTAATTTTGGAAAGTTTAGGG
* * **
53930 GTGATAATGTAATTTTAAAAAAGTTT-GAGG
1 GTCAAAATGTAATTTT-GGAAAGTTTAG-GG
* * * *
53960 GTTAAAATATGATTTTTGGAAAGTTCAGGG
1 GTCAAAATGT-AATTTTGGAAAGTTTAGGG
53990 ATCTTTTGAG
Statistics
Matches: 214, Mismatches: 50, Indels: 47
0.69 0.16 0.15
Matches are distributed among these distances:
22 2 0.01
23 7 0.03
24 6 0.03
27 1 0.00
28 31 0.14
29 80 0.37
30 65 0.30
31 22 0.10
ACGTcount: A:0.37, C:0.03, G:0.26, T:0.35
Consensus pattern (29 bp):
GTCAAAATGTAATTTTGGAAAGTTTAGGG
Found at i:55563 original size:17 final size:17
Alignment explanation
Indices: 55537--55569 Score: 50
Period size: 16 Copynumber: 1.9 Consensus size: 17
55527 TTTTTATCTA
55537 TTAATATGATTATTTTAT
1 TTAATATGATT-TTTTAT
55555 TTAAT-TGATTTTTTA
1 TTAATATGATTTTTTA
55570 AAGTAAACTT
Statistics
Matches: 15, Mismatches: 0, Indels: 2
0.88 0.00 0.12
Matches are distributed among these distances:
16 5 0.33
17 5 0.33
18 5 0.33
ACGTcount: A:0.30, C:0.00, G:0.06, T:0.64
Consensus pattern (17 bp):
TTAATATGATTTTTTAT
Found at i:61078 original size:25 final size:25
Alignment explanation
Indices: 61043--61229 Score: 212
Period size: 25 Copynumber: 7.4 Consensus size: 25
61033 TGGAATCAAA
*
61043 CTCGGAAGAGCAATATTCTGTCTGG
1 CTCGTAAGAGCAATATTCTGTCTGG
* * * *
61068 CTCATAAGAGCAACATTCTATTTGG
1 CTCGTAAGAGCAATATTCTGTCTGG
* *
61093 CTCGTAAGAGCCATATTCTATCTGG
1 CTCGTAAGAGCAATATTCTGTCTGG
*
61118 CTCGTAAGAGCAACATTCTGTCTGG
1 CTCGTAAGAGCAATATTCTGTCTGG
* * **
61143 TTCATAAGAGTGATATTCTGTCTGG
1 CTCGTAAGAGCAATATTCTGTCTGG
* *
61168 CTCATAAGAGCAATATTCTGTTTGG
1 CTCGTAAGAGCAATATTCTGTCTGG
* * *
61193 CTCGTAAAAGCGATATTCTGTCTAAG
1 CTCGTAAGAGCAATATTCTGTCT-GG
61219 CTCGTAAGAGC
1 CTCGTAAGAGC
61230 TAAACTCTAT
Statistics
Matches: 134, Mismatches: 27, Indels: 1
0.83 0.17 0.01
Matches are distributed among these distances:
25 123 0.92
26 11 0.08
ACGTcount: A:0.27, C:0.20, G:0.22, T:0.32
Consensus pattern (25 bp):
CTCGTAAGAGCAATATTCTGTCTGG
Found at i:63433 original size:24 final size:24
Alignment explanation
Indices: 63406--63497 Score: 112
Period size: 24 Copynumber: 3.8 Consensus size: 24
63396 CAGACAACAT
** * *
63406 TTAGCCCGCACAAGCCCAGAATGA
1 TTAGCCCTTACAAGCCCAAAATGG
* * *
63430 TTAGCTCTTACGAGCCCATAATGG
1 TTAGCCCTTACAAGCCCAAAATGG
*
63454 TTAGCTCTTACAAGCCCAAAATGG
1 TTAGCCCTTACAAGCCCAAAATGG
63478 TTAGCCCTTACAAGCCCAAA
1 TTAGCCCTTACAAGCCCAAA
63498 CAGAGTTTAA
Statistics
Matches: 59, Mismatches: 9, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
24 59 1.00
ACGTcount: A:0.32, C:0.29, G:0.17, T:0.22
Consensus pattern (24 bp):
TTAGCCCTTACAAGCCCAAAATGG
Found at i:71669 original size:13 final size:13
Alignment explanation
Indices: 71651--71675 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
71641 CCTCTTTTAA
71651 GAATTAAAATGTG
1 GAATTAAAATGTG
71664 GAATTAAAATGT
1 GAATTAAAATGT
71676 TTCAATTACA
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:0.48, C:0.00, G:0.20, T:0.32
Consensus pattern (13 bp):
GAATTAAAATGTG
Found at i:71862 original size:16 final size:18
Alignment explanation
Indices: 71841--71874 Score: 54
Period size: 16 Copynumber: 2.0 Consensus size: 18
71831 TTAATTTTTG
71841 AAAACAT-TTTAT-GTTT
1 AAAACATATTTATAGTTT
71857 AAAACATATTTATAGTTT
1 AAAACATATTTATAGTTT
71875 GTTTACTAAT
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
16 7 0.44
17 5 0.31
18 4 0.25
ACGTcount: A:0.41, C:0.06, G:0.06, T:0.47
Consensus pattern (18 bp):
AAAACATATTTATAGTTT
Found at i:72118 original size:14 final size:15
Alignment explanation
Indices: 72094--72136 Score: 52
Period size: 15 Copynumber: 2.9 Consensus size: 15
72084 AATATTTCAT
72094 TTTCTATTTTATTTTA
1 TTTC-ATTTTATTTTA
*
72110 -TTCATTTTATTCTA
1 TTTCATTTTATTTTA
*
72124 TTTCTTTTTATTT
1 TTTCATTTTATTT
72137 CTTTTTTTTC
Statistics
Matches: 23, Mismatches: 3, Indels: 3
0.79 0.10 0.10
Matches are distributed among these distances:
14 10 0.43
15 13 0.57
ACGTcount: A:0.16, C:0.09, G:0.00, T:0.74
Consensus pattern (15 bp):
TTTCATTTTATTTTA
Found at i:73275 original size:39 final size:39
Alignment explanation
Indices: 73219--73480 Score: 292
Period size: 39 Copynumber: 6.7 Consensus size: 39
73209 ATCAAATTAT
*
73219 TGAACTGGCAGTGACACTATAAACACCGCAATACAATAC
1 TGAACTGGCAGTGACACTATAAACACTGCAATACAATAC
* ** * * * *
73258 TAAACTGGTTGTAACACTAAAAAACACTGTAATATAATAC
1 TGAACTGGCAGTGACACT-ATAAACACTGCAATACAATAC
* *
73298 TGAACTGGCAGTGACACTGTAAACACTGCAATACAATAT
1 TGAACTGGCAGTGACACTATAAACACTGCAATACAATAC
*
73337 TGAACTGGCAGTGACACTATAAACATTGCAATACAATAC
1 TGAACTGGCAGTGACACTATAAACACTGCAATACAATAC
** *
73376 TGAACTGATAGTGACACTGTAAACACTGCAATACAATAC
1 TGAACTGGCAGTGACACTATAAACACTGCAATACAATAC
* * * * ***
73415 TAAACTGGCTGTAACACT-TAAATACCATAATACAATAC
1 TGAACTGGCAGTGACACTATAAACACTGCAATACAATAC
***
73453 TGAACTGATGGTGACACTATAAACACTG
1 TGAACTGGCAGTGACACTATAAACACTG
73481 TAATGCTATA
Statistics
Matches: 180, Mismatches: 41, Indels: 4
0.80 0.18 0.02
Matches are distributed among these distances:
38 29 0.16
39 120 0.67
40 31 0.17
ACGTcount: A:0.42, C:0.20, G:0.15, T:0.24
Consensus pattern (39 bp):
TGAACTGGCAGTGACACTATAAACACTGCAATACAATAC
Found at i:73397 original size:78 final size:78
Alignment explanation
Indices: 73219--73480 Score: 328
Period size: 78 Copynumber: 3.4 Consensus size: 78
73209 ATCAAATTAT
* * * *
73219 TGAACTGGCAGTGACACTATAAACACCGCAATACAATACTAAACTGGTTGTAACACTAAAAAACA
1 TGAACTGACAGTGACACTATAAACACTGCAATACAATACTAAACTGGCTGTAACACT-ATAAACA
*
73284 CTGTAATATAATAC
65 CTGTAATACAATAC
* * * * * * *
73298 TGAACTGGCAGTGACACTGTAAACACTGCAATACAATATTGAACTGGCAGTGACACTATAAACAT
1 TGAACTGACAGTGACACTATAAACACTGCAATACAATACTAAACTGGCTGTAACACTATAAACAC
*
73363 TGCAATACAATAC
66 TGTAATACAATAC
* * *
73376 TGAACTGATAGTGACACTGTAAACACTGCAATACAATACTAAACTGGCTGTAACACT-TAAATAC
1 TGAACTGACAGTGACACTATAAACACTGCAATACAATACTAAACTGGCTGTAACACTATAAACAC
**
73440 CATAATACAATAC
66 TGTAATACAATAC
**
73453 TGAACTGATGGTGACACTATAAACACTG
1 TGAACTGACAGTGACACTATAAACACTG
73481 TAATGCTATA
Statistics
Matches: 159, Mismatches: 24, Indels: 2
0.86 0.13 0.01
Matches are distributed among these distances:
77 41 0.26
78 68 0.43
79 50 0.31
ACGTcount: A:0.42, C:0.20, G:0.15, T:0.24
Consensus pattern (78 bp):
TGAACTGACAGTGACACTATAAACACTGCAATACAATACTAAACTGGCTGTAACACTATAAACAC
TGTAATACAATAC
Found at i:73506 original size:116 final size:117
Alignment explanation
Indices: 73219--73518 Score: 289
Period size: 116 Copynumber: 2.6 Consensus size: 117
73209 ATCAAATTAT
* * * * * * **
73219 TGAACTGGCAGTGACACTATAAACACCGCAATACAATACTAAACTGG-TTGTAACACTAAAAAAC
1 TGAACTGACAGTGACACTATAAACACTGCAATACAATAATGAAC-GGATAGTGACACT-GTAAAC
* * * * ** *
73283 ACTGTAATATAATACTGAACTGGCAGTGACACTGTAAACACTGCAATACAATAT
64 ACTGCAATACAATACTAAACTGGCAGTAACACTGTAAACACCACAATACAATAC
* * * *
73337 TGAACTGGCAGTGACACTATAAACATTGCAATACAATACTGAACTGATAGTGACACTGTAAACAC
1 TGAACTGACAGTGACACTATAAACACTGCAATACAATAATGAACGGATAGTGACACTGTAAACAC
* * *
73402 TGCAATACAATACTAAACTGGCTGTAACACT-TAAATACCATAATACAATAC
66 TGCAATACAATACTAAACTGGCAGTAACACTGTAAACACCACAATACAATAC
** * * * * * * *
73453 TGAACTGATGGTGACACTATAAACACTGTAATGCTATAATGAGCGGGTGGTGACATTGTAAACAC
1 TGAACTGACAGTGACACTATAAACACTGCAATACAATAATGAACGGATAGTGACACTGTAAACAC
73518 T
66 T
73519 ACCAGATGCT
Statistics
Matches: 150, Mismatches: 31, Indels: 4
0.81 0.17 0.02
Matches are distributed among these distances:
116 68 0.45
117 33 0.22
118 49 0.33
ACGTcount: A:0.40, C:0.19, G:0.16, T:0.24
Consensus pattern (117 bp):
TGAACTGACAGTGACACTATAAACACTGCAATACAATAATGAACGGATAGTGACACTGTAAACAC
TGCAATACAATACTAAACTGGCAGTAACACTGTAAACACCACAATACAATAC
Found at i:75345 original size:44 final size:44
Alignment explanation
Indices: 75282--75370 Score: 178
Period size: 44 Copynumber: 2.0 Consensus size: 44
75272 GAAAGTGCCA
75282 CCACCGCCACCTAAAGGTCGAGGCACCGGTCGAGTTAGTACTAT
1 CCACCGCCACCTAAAGGTCGAGGCACCGGTCGAGTTAGTACTAT
75326 CCACCGCCACCTAAAGGTCGAGGCACCGGTCGAGTTAGTACTAT
1 CCACCGCCACCTAAAGGTCGAGGCACCGGTCGAGTTAGTACTAT
75370 C
1 C
75371 TTTGGTAGGA
Statistics
Matches: 45, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
44 45 1.00
ACGTcount: A:0.25, C:0.33, G:0.25, T:0.18
Consensus pattern (44 bp):
CCACCGCCACCTAAAGGTCGAGGCACCGGTCGAGTTAGTACTAT
Found at i:80466 original size:39 final size:39
Alignment explanation
Indices: 80374--80480 Score: 133
Period size: 39 Copynumber: 2.7 Consensus size: 39
80364 CTGAACTAGT
* ** *
80374 AGTGATACTGTAAACACTGTAATACAATATTGAATTGAC
1 AGTGATACTGTAAACATTACAATACAATATTGAACTGAC
* * *
80413 AGTGAGATTGTAAACATTACAATACAATATTGAACTGAT
1 AGTGATACTGTAAACATTACAATACAATATTGAACTGAC
* *
80452 GGTGATACTATAAACATTACAATACAATA
1 AGTGATACTGTAAACATTACAATACAATA
80481 CTAAACTGGC
Statistics
Matches: 57, Mismatches: 11, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
39 57 1.00
ACGTcount: A:0.44, C:0.12, G:0.14, T:0.30
Consensus pattern (39 bp):
AGTGATACTGTAAACATTACAATACAATATTGAACTGAC
Found at i:80519 original size:31 final size:31
Alignment explanation
Indices: 80476--80547 Score: 117
Period size: 31 Copynumber: 2.3 Consensus size: 31
80466 CATTACAATA
*
80476 CAATACTAAACTGGCTATAAATACCGTAATG
1 CAATACTGAACTGGCTATAAATACCGTAATG
* *
80507 CAGTACTGAACTGGCTATAAATATCGTAATG
1 CAATACTGAACTGGCTATAAATACCGTAATG
80538 CAATACTGAA
1 CAATACTGAA
80548 GTGATGGTGA
Statistics
Matches: 37, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
31 37 1.00
ACGTcount: A:0.40, C:0.18, G:0.15, T:0.26
Consensus pattern (31 bp):
CAATACTGAACTGGCTATAAATACCGTAATG
Found at i:91554 original size:36 final size:36
Alignment explanation
Indices: 91514--91800 Score: 353
Period size: 36 Copynumber: 8.0 Consensus size: 36
91504 TCGAGCTATT
* *
91514 CATAGCATTACACTCTAACCAAGACATAAGCAATCA
1 CATAGCATTACACTCTAACCGAGACGTAAGCAATCA
* * *
91550 CATAGCACTACGCTCTAATCGAGACGTAAGCAATCA
1 CATAGCATTACACTCTAACCGAGACGTAAGCAATCA
* * * * *
91586 CATAGCATTACGCTATAATCGAGACATAAGCAATTA
1 CATAGCATTACACTCTAACCGAGACGTAAGCAATCA
* * * *
91622 CATAGCATTACACTTTAATCGAGACATAAACAATCA
1 CATAGCATTACACTCTAACCGAGACGTAAGCAATCA
91658 CATAGCATTACGA-TCTAACCGAGACGTAAGCAATCA
1 CATAGCATTAC-ACTCTAACCGAGACGTAAGCAATCA
*
91694 CATAGCATTA-AGCTCTAACTGAGACGTAAGCAATCA
1 CATAGCATTACA-CTCTAACCGAGACGTAAGCAATCA
* * *
91730 CATATCATTACGCTCTAACCGAGACGTAAACAATCA
1 CATAGCATTACACTCTAACCGAGACGTAAGCAATCA
* * *
91766 CATAGTATTACGCTCTAACCGAGATGTAAGCAATC
1 CATAGCATTACACTCTAACCGAGACGTAAGCAATC
91801 CATCGAAGTA
Statistics
Matches: 221, Mismatches: 26, Indels: 8
0.87 0.10 0.03
Matches are distributed among these distances:
34 1 0.00
36 219 0.99
37 1 0.00
ACGTcount: A:0.40, C:0.24, G:0.14, T:0.22
Consensus pattern (36 bp):
CATAGCATTACACTCTAACCGAGACGTAAGCAATCA
Found at i:91703 original size:108 final size:108
Alignment explanation
Indices: 91514--91800 Score: 414
Period size: 108 Copynumber: 2.7 Consensus size: 108
91504 TCGAGCTATT
* * * *
91514 CATAGCATTACACTCTAACCAAGACATAAGCAATCACATAGCACTACGCTCTAATCGAGACGTAA
1 CATAGCATTACACTCTAACCGAGACATAAACAATCACATAGCATTACGCTCTAACCGAGACGTAA
* *
91579 GCAATCACATAGCATTACGCTATAA-TCGAGACATAAGCAATTA
66 GCAATCACATAGCATTAAGCTATAACT-GAGACATAAGCAATCA
* * *
91622 CATAGCATTACACTTTAATCGAGACATAAACAATCACATAGCATTACGATCTAACCGAGACGTAA
1 CATAGCATTACACTCTAACCGAGACATAAACAATCACATAGCATTACGCTCTAACCGAGACGTAA
* *
91687 GCAATCACATAGCATTAAGCTCTAACTGAGACGTAAGCAATCA
66 GCAATCACATAGCATTAAGCTATAACTGAGACATAAGCAATCA
* * * * *
91730 CATATCATTACGCTCTAACCGAGACGTAAACAATCACATAGTATTACGCTCTAACCGAGATGTAA
1 CATAGCATTACACTCTAACCGAGACATAAACAATCACATAGCATTACGCTCTAACCGAGACGTAA
91795 GCAATC
66 GCAATC
91801 CATCGAAGTA
Statistics
Matches: 159, Mismatches: 19, Indels: 2
0.88 0.11 0.01
Matches are distributed among these distances:
108 158 0.99
109 1 0.01
ACGTcount: A:0.40, C:0.24, G:0.14, T:0.22
Consensus pattern (108 bp):
CATAGCATTACACTCTAACCGAGACATAAACAATCACATAGCATTACGCTCTAACCGAGACGTAA
GCAATCACATAGCATTAAGCTATAACTGAGACATAAGCAATCA
Found at i:99074 original size:43 final size:43
Alignment explanation
Indices: 98976--99190 Score: 331
Period size: 43 Copynumber: 5.0 Consensus size: 43
98966 TTTTGAATTG
* * *
98976 AATTAACCTTATGCTCTAACCGAGTCATAAGTTCTTCCATTTAC
1 AATTAATCTTATGCTCTAACCGAGACATAAG-TCTTCCATTTAT
* * *
99020 AAATAACCTTATGCTCTACCCGAGACATAAGTCTTCCATTTAT
1 AATTAATCTTATGCTCTAACCGAGACATAAGTCTTCCATTTAT
*
99063 AATTAATCTTATGCTCTAATCGAGACATAAGTCTTCCATTTAT
1 AATTAATCTTATGCTCTAACCGAGACATAAGTCTTCCATTTAT
** *
99106 AATTAATCTTATGCTCTAACTAAGACATAAGTCTTCTATTTAT
1 AATTAATCTTATGCTCTAACCGAGACATAAGTCTTCCATTTAT
99149 AATTAATCTTATGCTCTAACCGAGACATAAGTCTTCCATTTA
1 AATTAATCTTATGCTCTAACCGAGACATAAGTCTTCCATTTA
99191 GAGTCACCAA
Statistics
Matches: 156, Mismatches: 15, Indels: 1
0.91 0.09 0.01
Matches are distributed among these distances:
43 128 0.82
44 28 0.18
ACGTcount: A:0.33, C:0.21, G:0.09, T:0.37
Consensus pattern (43 bp):
AATTAATCTTATGCTCTAACCGAGACATAAGTCTTCCATTTAT
Found at i:102555 original size:18 final size:18
Alignment explanation
Indices: 102516--102560 Score: 56
Period size: 18 Copynumber: 2.5 Consensus size: 18
102506 ATAATAATTC
* *
102516 ATATTTTTATATTTTTTT
1 ATATTTTTATATTTTCTA
102534 ATATTATTT-TATTTTCTA
1 ATATT-TTTATATTTTCTA
102552 ATATTTTTA
1 ATATTTTTA
102561 ACTTGTGAAA
Statistics
Matches: 23, Mismatches: 2, Indels: 4
0.79 0.07 0.14
Matches are distributed among these distances:
17 3 0.13
18 17 0.74
19 3 0.13
ACGTcount: A:0.27, C:0.02, G:0.00, T:0.71
Consensus pattern (18 bp):
ATATTTTTATATTTTCTA
Found at i:104528 original size:43 final size:42
Alignment explanation
Indices: 104481--104563 Score: 105
Period size: 43 Copynumber: 2.0 Consensus size: 42
104471 TTATATTTCT
** *
104481 CTAGTTAGTTTAAATTAATTAAG-AGATAAATAATAAATTATCA
1 CTAGTTAAATTAAAATAATTAAGTA-AT-AATAATAAATTATCA
*
104524 CTAGTTAAATTAAAATAATTAAGTAATAATATTAAATTAT
1 CTAGTTAAATTAAAATAATTAAGTAATAATAATAAATTAT
104564 TATGTTTATC
Statistics
Matches: 35, Mismatches: 4, Indels: 3
0.83 0.10 0.07
Matches are distributed among these distances:
42 12 0.34
43 22 0.63
44 1 0.03
ACGTcount: A:0.51, C:0.04, G:0.07, T:0.39
Consensus pattern (42 bp):
CTAGTTAAATTAAAATAATTAAGTAATAATAATAAATTATCA
Found at i:110388 original size:94 final size:95
Alignment explanation
Indices: 110200--110403 Score: 245
Period size: 94 Copynumber: 2.1 Consensus size: 95
110190 AAAGTGATAG
* *
110200 AAATAAATAAATAAGCAAGGGACTAATTTGAAACTTAAAAGAAATTTAAAGGGGTAAAAATGTAA
1 AAATAAATAAATAAGCAAAGGACTAAATTGAAACTTAAAAGAAATTTAAAGGGG-AAAAATGTAA
*** * *
110265 ATATTTGAAAATAAAGGTGCTAGAAATAAAT
65 ATATAAAAAAATAAAGGTGCAAAAAATAAAT
* * * *
110296 AAATAAATAATTAAG-AAAGGACTAAATTGAAATTTAAATGAAATTT-AATGGGAGAAAATGTAA
1 AAATAAATAAATAAGCAAAGGACTAAATTGAAACTTAAAAGAAATTTAAAGGGGA-AAAATGTAA
110359 ATATAAAAAAAT-AAGAGTAG-AAAAAATAAAT
65 ATATAAAAAAATAAAG-GT-GCAAAAAATAAAT
110390 AAATAAATAAATAA
1 AAATAAATAAATAA
110404 TAAAATAAAA
Statistics
Matches: 93, Mismatches: 12, Indels: 8
0.82 0.11 0.07
Matches are distributed among these distances:
93 4 0.04
94 47 0.51
95 28 0.30
96 14 0.15
ACGTcount: A:0.59, C:0.02, G:0.14, T:0.25
Consensus pattern (95 bp):
AAATAAATAAATAAGCAAAGGACTAAATTGAAACTTAAAAGAAATTTAAAGGGGAAAAATGTAAA
TATAAAAAAATAAAGGTGCAAAAAATAAAT
Found at i:110391 original size:4 final size:4
Alignment explanation
Indices: 110382--110419 Score: 53
Period size: 4 Copynumber: 9.8 Consensus size: 4
110372 AGAGTAGAAA
110382 AAAT AAAT AAAT AAAT AAAT -AAT AAAAT AAA- AAAT AAA
1 AAAT AAAT AAAT AAAT AAAT AAAT -AAAT AAAT AAAT AAA
110420 ATGAATAAAA
Statistics
Matches: 31, Mismatches: 0, Indels: 6
0.84 0.00 0.16
Matches are distributed among these distances:
3 6 0.19
4 22 0.71
5 3 0.10
ACGTcount: A:0.79, C:0.00, G:0.00, T:0.21
Consensus pattern (4 bp):
AAAT
Found at i:110420 original size:12 final size:12
Alignment explanation
Indices: 110381--110432 Score: 61
Period size: 12 Copynumber: 4.2 Consensus size: 12
110371 AAGAGTAGAA
110381 AAAATAAATAAAT
1 AAAATAAA-AAAT
*
110394 -AAATAAATAAT
1 AAAATAAAAAAT
110405 AAAATAAAAAAT
1 AAAATAAAAAAT
110417 AAAATGAATAAAAT
1 AAAAT-AA-AAAAT
110431 AA
1 AA
110433 GTATGCAAAG
Statistics
Matches: 34, Mismatches: 2, Indels: 5
0.83 0.05 0.12
Matches are distributed among these distances:
11 3 0.09
12 22 0.65
13 2 0.06
14 7 0.21
ACGTcount: A:0.77, C:0.00, G:0.02, T:0.21
Consensus pattern (12 bp):
AAAATAAAAAAT
Found at i:112457 original size:100 final size:101
Alignment explanation
Indices: 112170--112979 Score: 492
Period size: 100 Copynumber: 8.0 Consensus size: 101
112160 GAGATAGGGC
* * ** * * * * *
112170 TTGCTAATGTAG-CTTTAATCCGATCCATTGTAACTTTAGGGATATAGGATTTGGTGTCT-T--C
1 TTGCTACTGTAGTCTTCAATCTAATCCACTGCAACTTCAGGGATATAAGATTTGATGT-TGTAGC
* * * *
112231 TTCATCTTACTCCACTTGCATCTTCAAAGAGATAAGAT
65 TTCATCTTGCTCTAC-TACATCTTCAGAGAGATAAGAT
* ** ** * * * * *
112269 TTGATTTTGTAG-CTTCAATCCGACCCACTACAACTTCA-AGAGTATATGATTTGATTTTGTAGC
1 TTGCTACTGTAGTCTTCAATCTAATCCACTGCAACTTCAGGGA-TATAAGATTTGATGTTGTAGC
*
112332 TTCATCTTGCTCTACTGCAAT-TTCAGAGAGATAAAGAT
65 TTCATCTTGCTCTACTAC-ATCTTCAGAGAGAT-AAGAT
* * ** *
112370 TTACAACTGTAGTCTT-AATCTAAT-CTTTGCAACTTCAGGGATATAGGATTTGATGTTGTAGCT
1 TTGCTACTGTAGTCTTCAATCTAATCCACTGCAACTTCAGGGATATAAGATTTGATGTTGTAGCT
* * * * *
112433 TCATCTTACTCCACTACGTCTTCAGGGAGATAAGAC
66 TCATCTTGCTCTACTACATCTTCAGAGAGATAAGAT
* * * * * * * *
112469 TTGCTTA-TGTA-ACTTCAATCTGACCCTCTACAATTTCAAAGG-TGTAAGATTTGATGTTGTAG
1 TTGC-TACTGTAGTCTTCAATCTAATCCACTGCAACTTC-AGGGATATAAGATTTGATGTTGTAG
* * * *
112531 CTTCATCTTGCTCTGCTGCAACTTCGGAGAGATAAAGAT
64 CTTCATCTTGCTCTACTACATCTTCAGAGAGAT-AAGAT
* * * * * *
112570 TTGCTACTATAGT-TTTAATTCGT--TCCACTGTAACTTCAGGGATATAAGGTTTGATGTCGTAA
1 TTGCTACTGTAGTCTTCAA-TC-TAATCCACTGCAACTTCAGGGATATAAGATTTGATGTTGTAG
* * * * *
112632 CTTCATCTTGCTCCACTACGTCTTTAGGGTGATAAGAT
64 CTTCATCTTGCTCTACTACATCTTCAGAGAGATAAGAT
* ** * * * * *
112670 TTTCTTTTATAG-CTTCAATTCGATCCATATCCATTGTAACTTTAGGGATATAGGATTT-ATGTT
1 TTGCTACTGTAGTCTTCAA-TC--T--A-ATCCACTGCAACTTCAGGGATATAAGATTTGATGTT
* * ** * * *
112733 ATAGCTTCATCTTGCTCCACTGTAACTTTAGGGAGATAAGAT
60 GTAGCTTCATCTTGCTCTACTACATCTTCAGAGAGATAAGAT
* ** * *
112775 TTGCTTCTGTAG-CTTCAATCCGATCCACTGCAATTTAAGGGATATAAGATTTGATGTTGTAGCT
1 TTGCTACTGTAGTCTTCAATCTAATCCACTGCAACTTCAGGGATATAAGATTTGATGTTGTAGCT
* * *
112839 TCATCTTGCTCTACTACAACTTCAAAGAAATAAAGAT
66 TCATCTTGCTCTACTACATCTTCAGAGAGAT-AAGAT
* * * * * *
112876 TTGTCGT-TTGAAAT-TTCATTCTTATCCACTGCAACTTTAGGGATATAAGATTTGATGTTGTAG
1 TTG-C-TACTGTAGTCTTCAATCTAATCCACTGCAACTTCAGGGATATAAGATTTGATGTTGTAG
* * *
112939 TTTCATCTTACTCTACTGCATCTTCA-AGGAGATAAGAT
64 CTTCATCTTGCTCTACTACATCTTCAGA-GAGATAAGAT
112977 TTG
1 TTG
112980 TTGTTTGTAA
Statistics
Matches: 553, Mismatches: 126, Indels: 62
0.75 0.17 0.08
Matches are distributed among these distances:
98 6 0.01
99 85 0.15
100 180 0.33
101 120 0.22
102 79 0.14
103 2 0.00
104 2 0.00
105 54 0.10
106 25 0.05
ACGTcount: A:0.27, C:0.18, G:0.17, T:0.38
Consensus pattern (101 bp):
TTGCTACTGTAGTCTTCAATCTAATCCACTGCAACTTCAGGGATATAAGATTTGATGTTGTAGCT
TCATCTTGCTCTACTACATCTTCAGAGAGATAAGAT
Found at i:112523 original size:200 final size:200
Alignment explanation
Indices: 112201--112978 Score: 553
Period size: 200 Copynumber: 3.9 Consensus size: 200
112191 GATCCATTGT
* * * * **
112201 AACTTTAGGGATATAGGATTTGGTGTCT-T-CTTCATCTTACTCCACTTGCATCTTCAAAGAGAT
1 AACTTCAGGGATATAGGATTTGATGT-TGTACTTCATCTTACTCCAC-TACGTCTTCAGGGAGAT
* * * * *
112264 AAGATTTGATTTTGTAGCTTCAATCCGACCCACTACAACTTCAAGAGTATATGATTTGATTTTGT
64 AAGACTTGATTATGTAACTTCAATCCGACCCACTACAACTTCAAGAGTATAAGATTTGATGTTGT
* *
112329 AGCTTCATCTTGCTCTACTGCAATTTCAGAGAGATAAAGATTTACAACTGTAGTCTTAA-TC-TA
129 AGCTTCATCTTGCTCTACTGCAACTTCAGAGAGATAAAGATTTACAACTATAGTCTTAATTCGT-
**
112392 AT-CTTTGC
193 -TCCACTGC
112400 AACTTCAGGGATATAGGATTTGATGTTGTAGCTTCATCTTACTCCACTACGTCTTCAGGGAGATA
1 AACTTCAGGGATATAGGATTTGATGTTGTA-CTTCATCTTACTCCACTACGTCTTCAGGGAGATA
* * * * *
112465 AGACTTGCTTATGTAACTTCAATCTGACCCTCTACAATTTCAA-AGGTGTAAGATTTGATGTTGT
65 AGACTTGATTATGTAACTTCAATCCGACCCACTACAACTTCAAGA-GTATAAGATTTGATGTTGT
* * * * *
112529 AGCTTCATCTTGCTCTGCTGCAACTTCGGAGAGATAAAGATTTGCTACTATAGTTTTAATTCGTT
129 AGCTTCATCTTGCTCTACTGCAACTTCAGAGAGATAAAGATTTACAACTATAGTCTTAATTCGTT
*
112594 CCACTGT
194 CCACTGC
* * * *
112601 AACTTCAGGGATATAAGG-TTTGATGTCGTAACTTCATCTTGCTCCACTACGTCTTTAGGGTGAT
1 AACTTCAGGGATAT-AGGATTTGATGTTGT-ACTTCATCTTACTCCACTACGTCTTCAGGGAGAT
* ** * * * * * * * *
112665 AAGATTTTCTTTTATAGCTTCAATTCGATCCA-TATCCATTGTAACTT-TAGGGATATAGGATTT
64 AAGACTTGATTATGTAACTTCAATCCGACCCACTA--C-----AACTTCAAGAG-TATAAGATTT
* * * * * * ** *
112728 -ATGTTATAGCTTCATCTTGCTCCACTGTAACTTTAGGGAGAT-AAGATTTGCTTCTGTAG-CTT
121 GATGTTGTAGCTTCATCTTGCTCTACTGCAACTTCAGAGAGATAAAGATTTACAACTATAGTCTT
* *
112790 CAATCCGATCCACTGC
186 -AATTCGTTCCACTGC
* * * * * ** ** *
112806 AATTTAAGGGATATAAGATTTGATGTTGTAGCTTCATCTTGCTCTACTACAACTTCAAAGAAATA
1 AACTTCAGGGATATAGGATTTGATGTTGTA-CTTCATCTTACTCCACTACGTCTTCAGGGAGAT-
* * * * * ** * * * *
112871 AAGATTTG-TCGTTTGAAATTTCATTCTTATCCACTGCAACTT-TAGGGATATAAGATTTGATGT
64 AAGACTTGAT--TATGTAACTTCAATCCGACCCACTACAACTTCAAGAG-TATAAGATTTGATGT
* * *
112934 TGTAGTTTCATCTTACTCTACTGCATCTTCA-AGGAGAT-AAGATTT
126 TGTAGCTTCATCTTGCTCTACTGCAACTTCAGA-GAGATAAAGATTT
112979 GTTGTTTGTA
Statistics
Matches: 464, Mismatches: 88, Indels: 51
0.77 0.15 0.08
Matches are distributed among these distances:
198 1 0.00
199 26 0.06
200 121 0.26
201 118 0.25
202 46 0.10
204 5 0.01
205 75 0.16
206 45 0.10
207 26 0.06
208 1 0.00
ACGTcount: A:0.27, C:0.18, G:0.17, T:0.38
Consensus pattern (200 bp):
AACTTCAGGGATATAGGATTTGATGTTGTACTTCATCTTACTCCACTACGTCTTCAGGGAGATAA
GACTTGATTATGTAACTTCAATCCGACCCACTACAACTTCAAGAGTATAAGATTTGATGTTGTAG
CTTCATCTTGCTCTACTGCAACTTCAGAGAGATAAAGATTTACAACTATAGTCTTAATTCGTTCC
ACTGC
Found at i:112926 original size:51 final size:50
Alignment explanation
Indices: 112748--113017 Score: 165
Period size: 50 Copynumber: 5.3 Consensus size: 50
112738 TTCATCTTGC
* * ** * **
112748 TCCACTGTAACTTTAGGGAGATAAGATTTGCT-TCTGTAGCTTCAATCCGA
1 TCCACTGCAACTTTAGGGAGATAAGATTTG-TGTTTGTAATTTCATTCTTA
* ** *
112798 TCCACTGCAA-TTTAAGGGATATAAGATTTGATG-TTGTAGCTTCA-TCTTGC
1 TCCACTGCAACTTT-AGGGAGATAAGATTTG-TGTTTGTAATTTCATTCTT-A
* * * ** * *
112848 TCTACTACAACTTCAAAGAAATAAAGATTTGTCGTTTGAAATTTCATTCTTA
1 TCCACTGCAACTTTAGGGAGAT-AAGATTTGT-GTTTGTAATTTCATTCTTA
* *
112900 TCCACTGCAACTTTAGGGATATAAGATTTGATG-TTGTAGTTTCA-TCTTA
1 TCCACTGCAACTTTAGGGAGATAAGATTTG-TGTTTGTAATTTCATTCTTA
* * * * **
112949 CTCTACTGCATCTTCAAGGAGATAAGATTTGTTGTTTGTAATTTCATTCCAA
1 -TCCACTGCAACTTTAGGGAGATAAGATTTG-TGTTTGTAATTTCATTCTTA
* *
113001 CCCACTACAACTTTAGG
1 TCCACTGCAACTTTAGG
113018 AGGACTGAAA
Statistics
Matches: 168, Mismatches: 40, Indels: 23
0.73 0.17 0.10
Matches are distributed among these distances:
49 10 0.06
50 85 0.51
51 41 0.24
52 28 0.17
53 4 0.02
ACGTcount: A:0.29, C:0.18, G:0.16, T:0.37
Consensus pattern (50 bp):
TCCACTGCAACTTTAGGGAGATAAGATTTGTGTTTGTAATTTCATTCTTA
Found at i:112957 original size:50 final size:50
Alignment explanation
Indices: 112201--112984 Score: 286
Period size: 50 Copynumber: 15.5 Consensus size: 50
112191 GATCCATTGT
* *
112201 AACTTTAGGGATATAGGATTTGGTGTCT-T--CTTCATCTTACTCCACTTGC
1 AACTTTAGGGATATAAGATTTGATGT-TGTAGCTTCATCTTACTCCAC-TGC
* * ** * * ** *
112250 ATCTTCAAAGAGATAAGATTTGATTTTGTAGCTTCAATCCGAC-CCACTAC
1 AACTTTAGGGATATAAGATTTGATGTTGTAGCTTC-ATCTTACTCCACTGC
* * * * * *
112300 AACTTCA-AGAGTATATGATTTGATTTTGTAGCTTCATCTTGCTCTACTGC
1 AACTTTAGGGA-TATAAGATTTGATGTTGTAGCTTCATCTTACTCCACTGC
*** * * **
112350 AA-TTTCAGAGAGATA-AAGATTT-ACAACTGTAGTCTTAATC-TAAT-CTTTGC
1 AACTTT-AG-G-GATATAAGATTTGA-TGTTGTAG-CTTCATCTTACTCCACTGC
* * *
112400 AACTTCAGGGATATAGGATTTGATGTTGTAGCTTCATCTTACTCCACTAC
1 AACTTTAGGGATATAAGATTTGATGTTGTAGCTTCATCTTACTCCACTGC
** * * * * * * * *
112450 GTCTTCAGGGAGATAAGACTTGCT-TATGTAACTTCAATCTGAC-CCTCTAC
1 AACTTTAGGGATATAAGATTTGATGT-TGTAGCTTC-ATCTTACTCCACTGC
* * * **
112500 AA-TTTCAAAGG-TGTAAGATTTGATGTTGTAGCTTCATCTTGCTCTGCTGC
1 AACTTT--AGGGATATAAGATTTGATGTTGTAGCTTCATCTTACTCCACTGC
* * * ** * * * * *
112550 AAC-TTCGGAGAGATAAAGATTTGCTACTATAGTTTTA-ATT-CGTTCCACTGT
1 AACTTTAGG-GATAT-AAGATTTGATGTTGTAGCTTCATCTTAC--TCCACTGC
* * * * * *
112601 AACTTCAGGGATATAAGGTTTGATGTCGTAACTTCATCTTGCTCCACTAC
1 AACTTTAGGGATATAAGATTTGATGTTGTAGCTTCATCTTACTCCACTGC
** ** * * * *
112651 GTCTTTAGGG-TGATAAGATTTTCTTTTATAGCTTCAATTCGATCCATA-TCCATTGT
1 AACTTTAGGGAT-ATAAGATTTGATGTTGTAGCTTC-A-TC--T---TACTCCACTGC
* * * *
112707 AACTTTAGGGATATAGGATTT-ATGTTATAGCTTCATCTTGCTCCACTGT
1 AACTTTAGGGATATAAGATTTGATGTTGTAGCTTCATCTTACTCCACTGC
* * **
112756 AACTTTAGGGAGATAAGATTTGCT-TCTGTAGCTTCAATCCGA-TCCACTGC
1 AACTTTAGGGATATAAGATTTGATGT-TGTAGCTTC-ATCTTACTCCACTGC
* * *
112806 AA-TTTAAGGGATATAAGATTTGATGTTGTAGCTTCATCTTGCTCTACTAC
1 AACTTT-AGGGATATAAGATTTGATGTTGTAGCTTCATCTTACTCCACTGC
* ** * * **
112856 AACTTCAAAGAAATAAAGATTTG-TCGTTTGAAATTTCATTCTTA-TCCACTGC
1 AACTTTAGGGATAT-AAGATTTGAT-G-TTGTAGCTTCA-TCTTACTCCACTGC
* *
112908 AACTTTAGGGATATAAGATTTGATGTTGTAGTTTCATCTTACTCTACTGC
1 AACTTTAGGGATATAAGATTTGATGTTGTAGCTTCATCTTACTCCACTGC
* * * * *
112958 ATCTTCAAGGAGATAAGATTTGTTGTT
1 AACTTTAGGGATATAAGATTTGATGTT
112985 TGTAATTTCA
Statistics
Matches: 529, Mismatches: 151, Indels: 109
0.67 0.19 0.14
Matches are distributed among these distances:
48 13 0.02
49 92 0.17
50 247 0.47
51 89 0.17
52 44 0.08
53 8 0.02
54 2 0.00
55 11 0.02
56 21 0.04
57 2 0.00
ACGTcount: A:0.27, C:0.18, G:0.17, T:0.38
Consensus pattern (50 bp):
AACTTTAGGGATATAAGATTTGATGTTGTAGCTTCATCTTACTCCACTGC
Found at i:118194 original size:3 final size:3
Alignment explanation
Indices: 118186--118220 Score: 70
Period size: 3 Copynumber: 11.7 Consensus size: 3
118176 TGATTTGACT
118186 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA AT
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA AT
118221 TAAAGGCAAT
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 32 1.00
ACGTcount: A:0.66, C:0.00, G:0.00, T:0.34
Consensus pattern (3 bp):
ATA
Found at i:120279 original size:19 final size:20
Alignment explanation
Indices: 120212--120271 Score: 79
Period size: 19 Copynumber: 3.0 Consensus size: 20
120202 ATATTAACAT
*
120212 AAATT-TTAATAAAATATTA
1 AAATTATTATTAAAATATTA
*
120231 AAATTATTTCTTAAAAT-TTA
1 AAATTA-TTATTAAAATATTA
120251 AAATTATTATTAAAATATTA
1 AAATTATTATTAAAATATTA
120271 A
1 A
120272 TTTATTATAA
Statistics
Matches: 35, Mismatches: 3, Indels: 5
0.81 0.07 0.12
Matches are distributed among these distances:
19 14 0.40
20 13 0.37
21 8 0.23
ACGTcount: A:0.53, C:0.02, G:0.00, T:0.45
Consensus pattern (20 bp):
AAATTATTATTAAAATATTA
Found at i:122288 original size:33 final size:33
Alignment explanation
Indices: 122246--122312 Score: 134
Period size: 33 Copynumber: 2.0 Consensus size: 33
122236 AAAAATTAAG
122246 ATAAAATTATCAATTATAATTGTTAATAATGTC
1 ATAAAATTATCAATTATAATTGTTAATAATGTC
122279 ATAAAATTATCAATTATAATTGTTAATAATGTC
1 ATAAAATTATCAATTATAATTGTTAATAATGTC
122312 A
1 A
122313 ACATTTTATT
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
33 34 1.00
ACGTcount: A:0.46, C:0.06, G:0.06, T:0.42
Consensus pattern (33 bp):
ATAAAATTATCAATTATAATTGTTAATAATGTC
Found at i:124940 original size:22 final size:20
Alignment explanation
Indices: 124905--124944 Score: 62
Period size: 22 Copynumber: 1.9 Consensus size: 20
124895 GAATGGAAAA
124905 TAAAAAAATAAAAGAAAAGT
1 TAAAAAAATAAAAGAAAAGT
124925 TAAAACAACATAAAAGAAAA
1 TAAAA-AA-ATAAAAGAAAA
124945 ACAATCAAAT
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
20 5 0.28
21 2 0.11
22 11 0.61
ACGTcount: A:0.75, C:0.05, G:0.07, T:0.12
Consensus pattern (20 bp):
TAAAAAAATAAAAGAAAAGT
Found at i:135863 original size:37 final size:37
Alignment explanation
Indices: 135808--135898 Score: 128
Period size: 37 Copynumber: 2.5 Consensus size: 37
135798 ATTATTGGAT
* * * *
135808 CACCGGCACAAAGTCTACTAGGCATATAGCCCGAATA
1 CACCGGCACAAAGCCTACTAGGCACAAAGCCCGAAAA
* *
135845 CACCGGCACAAGGCCTACTAGGCACAAAGCCTGAAAA
1 CACCGGCACAAAGCCTACTAGGCACAAAGCCCGAAAA
135882 CACCGGCACAAAGCCTA
1 CACCGGCACAAAGCCTA
135899 AAAACACCGG
Statistics
Matches: 47, Mismatches: 7, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
37 47 1.00
ACGTcount: A:0.36, C:0.33, G:0.20, T:0.11
Consensus pattern (37 bp):
CACCGGCACAAAGCCTACTAGGCACAAAGCCCGAAAA
Found at i:135891 original size:21 final size:21
Alignment explanation
Indices: 135865--135937 Score: 119
Period size: 21 Copynumber: 3.5 Consensus size: 21
135855 AGGCCTACTA
*
135865 GGCACAAAGCCTGAAAACACC
1 GGCACAAAGCCTAAAAACACC
135886 GGCACAAAGCCTAAAAACACC
1 GGCACAAAGCCTAAAAACACC
*
135907 GGCACAAAGCCTAAAAACACT
1 GGCACAAAGCCTAAAAACACC
*
135928 GGCGCAAAGC
1 GGCACAAAGC
135938 TTACTTGGCA
Statistics
Matches: 49, Mismatches: 3, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
21 49 1.00
ACGTcount: A:0.44, C:0.32, G:0.19, T:0.05
Consensus pattern (21 bp):
GGCACAAAGCCTAAAAACACC
Found at i:142706 original size:37 final size:37
Alignment explanation
Indices: 142649--142773 Score: 151
Period size: 37 Copynumber: 3.4 Consensus size: 37
142639 GTTATTGGAT
* * * *
142649 CACCGGCACAAAGCCTACTAGGCATATAGCCCGAATA
1 CACCGGCACAAAGCTTACTAGGCACAAAGCCCGAAAA
* * *
142686 CACTGGTACAAAGCTTACTAGGCACAAAGCCTGAAAA
1 CACCGGCACAAAGCTTACTAGGCACAAAGCCCGAAAA
**
142723 CACCGGCACAAAGCTTACTAGGCACAAAGCCTAAAAA
1 CACCGGCACAAAGCTTACTAGGCACAAAGCCCGAAAA
* *
142760 CACTGGCATAAAGC
1 CACCGGCACAAAGC
142774 CTGAATTTGT
Statistics
Matches: 76, Mismatches: 12, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
37 76 1.00
ACGTcount: A:0.39, C:0.29, G:0.18, T:0.14
Consensus pattern (37 bp):
CACCGGCACAAAGCTTACTAGGCACAAAGCCCGAAAA
Found at i:151978 original size:9 final size:9
Alignment explanation
Indices: 151966--151990 Score: 50
Period size: 9 Copynumber: 2.8 Consensus size: 9
151956 ATCAAATTTT
151966 TTTAATTAA
1 TTTAATTAA
151975 TTTAATTAA
1 TTTAATTAA
151984 TTTAATT
1 TTTAATT
151991 TTACTCGAAA
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
9 16 1.00
ACGTcount: A:0.40, C:0.00, G:0.00, T:0.60
Consensus pattern (9 bp):
TTTAATTAA
Found at i:155320 original size:16 final size:18
Alignment explanation
Indices: 155294--155326 Score: 52
Period size: 17 Copynumber: 1.9 Consensus size: 18
155284 TTAAATTAAC
155294 TAAATTAA-TTTCTCAAT
1 TAAATTAATTTTCTCAAT
155311 TAAA-TAATTTTCTCAA
1 TAAATTAATTTTCTCAA
155327 CCAACTTCTA
Statistics
Matches: 15, Mismatches: 0, Indels: 2
0.88 0.00 0.12
Matches are distributed among these distances:
16 3 0.20
17 12 0.80
ACGTcount: A:0.42, C:0.12, G:0.00, T:0.45
Consensus pattern (18 bp):
TAAATTAATTTTCTCAAT
Found at i:164367 original size:191 final size:192
Alignment explanation
Indices: 164029--164374 Score: 559
Period size: 191 Copynumber: 1.8 Consensus size: 192
164019 GAAACTGACG
* * * *
164029 CGATGGCTGAGGTACCGCATATATTGCGAGTCCTTGACAGCTCGTGTGAGCAGCATCGTGAGTTG
1 CGATGGCTGAGGTACCACATATATTACGAGTCCTCGACAGCTCGTGTGAGCAGCATCGTGAGTCG
* * *
164094 GAAAGAGATATGAAATCCTAAATGGATTATAGACCCTACGATGGCTGGGATTTATACTTGAATGC
66 AAAAAAGATATGAAATCCTAAATGGATTATAGACCCTACGACGGCTGGGATTTATACTTGAATGC
164159 ATATTCTCGACAGCTCGTGTGAGCAACATCGTTTGGGGACAGTTTACAAACAGACACCATAC
131 ATATTCTCGACAGCTCGTGTGAGCAACATCGTTTGGGGACAGTTTACAAACAGACACCATAC
* * * *
164221 CGATGG-TTAGGTACCACATATGTTACTAGTCCTCGACAGCTCGTGTGAGCAGCATTGTGAGTCG
1 CGATGGCTGAGGTACCACATATATTACGAGTCCTCGACAGCTCGTGTGAGCAGCATCGTGAGTCG
* *
164285 AAAAAATATATGAAATCCTAAATGGATTATAGACCCTACGACGGCTGGGATTTATGCTTGAATGC
66 AAAAAAGATATGAAATCCTAAATGGATTATAGACCCTACGACGGCTGGGATTTATACTTGAATGC
*
164350 ATATTCTCGATAGCTCGTGTGAGCA
131 ATATTCTCGACAGCTCGTGTGAGCA
164375 GGGGACAGTT
Statistics
Matches: 140, Mismatches: 14, Indels: 1
0.90 0.09 0.01
Matches are distributed among these distances:
191 134 0.96
192 6 0.04
ACGTcount: A:0.29, C:0.19, G:0.25, T:0.27
Consensus pattern (192 bp):
CGATGGCTGAGGTACCACATATATTACGAGTCCTCGACAGCTCGTGTGAGCAGCATCGTGAGTCG
AAAAAAGATATGAAATCCTAAATGGATTATAGACCCTACGACGGCTGGGATTTATACTTGAATGC
ATATTCTCGACAGCTCGTGTGAGCAACATCGTTTGGGGACAGTTTACAAACAGACACCATAC
Found at i:166854 original size:27 final size:27
Alignment explanation
Indices: 166822--166877 Score: 76
Period size: 27 Copynumber: 2.1 Consensus size: 27
166812 TAATTCAAAT
* *
166822 AACAAGATAATTAACAGAGTTCTTGTC
1 AACAAGATAATTAACAAAATTCTTGTC
* *
166849 AACAAGATTATTATCAAAATTCTTGTC
1 AACAAGATAATTAACAAAATTCTTGTC
166876 AA
1 AA
166878 TCACAGCTCA
Statistics
Matches: 25, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
27 25 1.00
ACGTcount: A:0.43, C:0.14, G:0.11, T:0.32
Consensus pattern (27 bp):
AACAAGATAATTAACAAAATTCTTGTC
Found at i:173155 original size:13 final size:13
Alignment explanation
Indices: 173123--173149 Score: 54
Period size: 13 Copynumber: 2.1 Consensus size: 13
173113 TTTCAGTCAC
173123 AATATCACATATT
1 AATATCACATATT
173136 AATATCACATATT
1 AATATCACATATT
173149 A
1 A
173150 TAATCATAAT
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:0.48, C:0.15, G:0.00, T:0.37
Consensus pattern (13 bp):
AATATCACATATT
Found at i:177058 original size:158 final size:158
Alignment explanation
Indices: 176831--177147 Score: 582
Period size: 158 Copynumber: 2.0 Consensus size: 158
176821 CATACTCGTC
*
176831 TTCCATTCTCGAATACTCTTGGGTGGCCTATTCTTCTTCCTCATCATCTCCTTCCTCCTCTTGCA
1 TTCCATTCCCGAATACTCTTGGGTGGCCTATTCTTCTTCCTCATCATCTCCTTCCTCCTCTTGCA
*
176896 CCTATTTTGATGGAAACATATTTTGGGGGTAGTTTGTTACT-CGAAGTCCATGCATCTTTGCGAA
66 CCTATTTTGATGGAAACATATTTTGGGGGTAGTTTGTT-CTGCGAAGTCCATGCATCTTCGCGAA
176960 TTCTGTGAGGATTGATCTCGTTTCTTGCA
130 TTCTGTGAGGATTGATCTCGTTTCTTGCA
176989 TTCCATTCCCGAATACTCTTGGGTGGCCTATTCTTCTTCCTCATCATCTCCTTCCTCCTCTTGCA
1 TTCCATTCCCGAATACTCTTGGGTGGCCTATTCTTCTTCCTCATCATCTCCTTCCTCCTCTTGCA
* *
177054 CCTATTTTGATGGAAACATATTTTGGGGGTAGTTTGTTGTGCGAAGTCCATGCATCTTCGTGAAT
66 CCTATTTTGATGGAAACATATTTTGGGGGTAGTTTGTTCTGCGAAGTCCATGCATCTTCGCGAAT
177119 TCTGTGAGGATTGATCTCGTTTCTTGCA
131 TCTGTGAGGATTGATCTCGTTTCTTGCA
177147 T
1 T
177148 CAATCGAATC
Statistics
Matches: 154, Mismatches: 4, Indels: 2
0.96 0.03 0.01
Matches are distributed among these distances:
157 1 0.01
158 153 0.99
ACGTcount: A:0.17, C:0.24, G:0.19, T:0.40
Consensus pattern (158 bp):
TTCCATTCCCGAATACTCTTGGGTGGCCTATTCTTCTTCCTCATCATCTCCTTCCTCCTCTTGCA
CCTATTTTGATGGAAACATATTTTGGGGGTAGTTTGTTCTGCGAAGTCCATGCATCTTCGCGAAT
TCTGTGAGGATTGATCTCGTTTCTTGCA
Found at i:178838 original size:24 final size:23
Alignment explanation
Indices: 178782--178864 Score: 85
Period size: 24 Copynumber: 3.4 Consensus size: 23
178772 ATAAATTTAT
*
178782 CTCATACGAGCCCAAACAAAATTAG
1 CTCATACGAGCCC-AA-ATAATTAG
* *
178807 GTCATACGAGCCCAGATAGATTAG
1 CTCATACGAGCCCAAATA-ATTAG
*
178831 CTCTTACGAGCCCAAATAAGTTAG
1 CTCATACGAGCCCAAATAA-TTAG
*
178855 CTCATTCGAG
1 CTCATACGAG
178865 TTCAGACAGA
Statistics
Matches: 48, Mismatches: 8, Indels: 5
0.79 0.13 0.08
Matches are distributed among these distances:
23 3 0.06
24 33 0.69
25 12 0.25
ACGTcount: A:0.35, C:0.25, G:0.18, T:0.22
Consensus pattern (23 bp):
CTCATACGAGCCCAAATAATTAG
Found at i:181325 original size:12 final size:12
Alignment explanation
Indices: 181310--181335 Score: 52
Period size: 12 Copynumber: 2.2 Consensus size: 12
181300 ATACACTTAA
181310 AAATATTAAAAC
1 AAATATTAAAAC
181322 AAATATTAAAAC
1 AAATATTAAAAC
181334 AA
1 AA
181336 CAAACAAATT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 14 1.00
ACGTcount: A:0.69, C:0.08, G:0.00, T:0.23
Consensus pattern (12 bp):
AAATATTAAAAC
Found at i:181373 original size:41 final size:41
Alignment explanation
Indices: 181312--181391 Score: 124
Period size: 41 Copynumber: 2.0 Consensus size: 41
181302 ACACTTAAAA
*
181312 ATATTAAAACAAATATTAAAACAACAAACAAATTAAAAACG
1 ATATTAAAACAAATAGTAAAACAACAAACAAATTAAAAACG
* * *
181353 ATATTAAAACAATTCGTAAAACAACAAACAAATTGAAAA
1 ATATTAAAACAAATAGTAAAACAACAAACAAATTAAAAA
181392 TACAATAAGC
Statistics
Matches: 35, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
41 35 1.00
ACGTcount: A:0.64, C:0.12, G:0.04, T:0.20
Consensus pattern (41 bp):
ATATTAAAACAAATAGTAAAACAACAAACAAATTAAAAACG
Found at i:183236 original size:19 final size:18
Alignment explanation
Indices: 183189--183237 Score: 71
Period size: 18 Copynumber: 2.7 Consensus size: 18
183179 TCGGCTTGTT
*
183189 AGAGCATATTGGCTCATA
1 AGAGCATACTGGCTCATA
*
183207 AGAGCATACTGGCTCGTA
1 AGAGCATACTGGCTCATA
183225 AGAGCAATACTGG
1 AGAGC-ATACTGG
183238 ATCGGAAGGA
Statistics
Matches: 28, Mismatches: 2, Indels: 1
0.90 0.06 0.03
Matches are distributed among these distances:
18 21 0.75
19 7 0.25
ACGTcount: A:0.33, C:0.18, G:0.27, T:0.22
Consensus pattern (18 bp):
AGAGCATACTGGCTCATA
Done.