Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: scaffold385
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: 592280
ACGTcount: A:0.31, C:0.16, G:0.16, T:0.32
Warning! 29825 characters in sequence are not A, C, G, or T
File 1 of 2
Found at i:10710 original size:44 final size:44
Alignment explanation
Indices: 10646--10768 Score: 138
Period size: 44 Copynumber: 2.7 Consensus size: 44
10636 CGGAGTAAGT
*
10646 TAAAAAGTAGCAGATCTTGTCTTCCTGTACTGGCAACAAAGTAGA
1 TAAAAA-TAGCAGATCTTGTCTTCCTATACTGGCAACAAAGTAGA
* * *** *
10691 TAAAAATAGCGGATCTTGTCTTCCCATACTGGTGGCGAAGTAGA
1 TAAAAATAGCAGATCTTGTCTTCCTATACTGGCAACAAAGTAGA
* *
10735 TCAGAAAATAGCAGATCTTATTTTCCTATACTGG
1 T-A-AAAATAGCAGATCTTGTCTTCCTATACTGG
10769 TGGCGAAGTA
Statistics
Matches: 65, Mismatches: 11, Indels: 3
0.82 0.14 0.04
Matches are distributed among these distances:
44 32 0.49
45 7 0.11
46 26 0.40
ACGTcount: A:0.33, C:0.18, G:0.20, T:0.29
Consensus pattern (44 bp):
TAAAAATAGCAGATCTTGTCTTCCTATACTGGCAACAAAGTAGA
Found at i:10766 original size:46 final size:45
Alignment explanation
Indices: 10647--10806 Score: 178
Period size: 46 Copynumber: 3.5 Consensus size: 45
10637 GGAGTAAGTT
* *** *
10647 AAAAAGTAGCAGATCTTGTCTTCCTGTACTGGCAACAAAGTAGAT-
1 AAAAA-TAGCAGATCTTGTCTTCCTATACTGGTGGCGAAGTAGATC
* *
10692 AAAAATAGCGGATCTTGTCTTCCCATACTGGTGGCGAAGTAGATC
1 AAAAATAGCAGATCTTGTCTTCCTATACTGGTGGCGAAGTAGATC
* *
10737 AGAAAATAGCAGATCTTATTTTCCTATACTGGTGGCGAAGTAGATC
1 A-AAAATAGCAGATCTTGTCTTCCTATACTGGTGGCGAAGTAGATC
* ** *
10783 GAAGGTAGCAAATCTTGTCTTCCT
1 AAAAATAGCAGATCTTGTCTTCCT
10807 GTATTGACAG
Statistics
Matches: 96, Mismatches: 17, Indels: 4
0.82 0.15 0.03
Matches are distributed among these distances:
44 32 0.33
45 24 0.25
46 40 0.42
ACGTcount: A:0.31, C:0.18, G:0.22, T:0.29
Consensus pattern (45 bp):
AAAAATAGCAGATCTTGTCTTCCTATACTGGTGGCGAAGTAGATC
Found at i:10933 original size:44 final size:43
Alignment explanation
Indices: 10885--11127 Score: 160
Period size: 44 Copynumber: 5.7 Consensus size: 43
10875 AAATCAATCC
*
10885 TATCTCCCTGAAGTTGCAGTGGAACGGATTAAAACCATAGATCT
1 TATCTCCCTGAAGTTGCAGTGGAGCGGATTAAAACCATAG-TCT
* * * *** *
10929 TATCTCTCTGAAGTTGCAGTAGAGCAGA-TCGCATC-TAGTCT
1 TATCTCCCTGAAGTTGCAGTGGAGCGGATTAAAACCATAGTCT
* * *
10970 TATTTCCCTGAAGTTGCAGTGGAGCAGGCA-GAGGAAACCA-ATTC-
1 TATCTCCCTGAAGTTGCAGTGGAGC-GG-ATTA--AAACCATAGTCT
* * *
11014 TATCTCCCTGAAGTT-CTAGTGGAGCGAATTAAAACTACAGATCT
1 TATCTCCCTGAAGTTGC-AGTGGAGCGGATTAAAACCATAG-TCT
** * * ***
11058 TATCTCTTTGAAGTTGCAGTAGAGCAGATCGCAA-C-TAGTCT
1 TATCTCCCTGAAGTTGCAGTGGAGCGGATTAAAACCATAGTCT
* *
11099 TATCTCCCTAAAGTTGCAGTGGAGTGGAT
1 TATCTCCCTGAAGTTGCAGTGGAGCGGAT
11128 CAGAATGATG
Statistics
Matches: 149, Mismatches: 39, Indels: 25
0.70 0.18 0.12
Matches are distributed among these distances:
41 56 0.38
42 8 0.05
43 9 0.06
44 70 0.47
45 6 0.04
ACGTcount: A:0.28, C:0.20, G:0.23, T:0.29
Consensus pattern (43 bp):
TATCTCCCTGAAGTTGCAGTGGAGCGGATTAAAACCATAGTCT
Found at i:11070 original size:129 final size:129
Alignment explanation
Indices: 10838--11122 Score: 437
Period size: 129 Copynumber: 2.2 Consensus size: 129
10828 GAAGATTTTT
* *
10838 TCTTATCTCCCTGAAGTAGCAGTGGAGCAGACAGAAGAAATCAATCCTATCTCCCTGAAGTTGCA
1 TCTTATCTCCCTGAAGTTGCAGTGGAGCAGACAGAAGAAACCAATCCTATCTCCCTGAAGTTGCA
* * *
10903 GTGGAACGGATTAAAACCATAGATCTTATCTCTCTGAAGTTGCAGTAGAGCAGATCGCATCTAG
66 GTGGAACGAATTAAAACCACAGATCTTATCTCTCTGAAGTTGCAGTAGAGCAGATCGCAACTAG
* * * *
10967 TCTTATTTCCCTGAAGTTGCAGTGGAGCAGGCAGAGGAAACCAATTCTATCTCCCTGAAGTT-CT
1 TCTTATCTCCCTGAAGTTGCAGTGGAGCAGACAGAAGAAACCAATCCTATCTCCCTGAAGTTGC-
* * *
11031 AGTGGAGCGAATTAAAACTACAGATCTTATCTCTTTGAAGTTGCAGTAGAGCAGATCGCAACTAG
65 AGTGGAACGAATTAAAACCACAGATCTTATCTCTCTGAAGTTGCAGTAGAGCAGATCGCAACTAG
*
11096 TCTTATCTCCCTAAAGTTGCAGTGGAG
1 TCTTATCTCCCTGAAGTTGCAGTGGAG
11123 TGGATCAGAA
Statistics
Matches: 141, Mismatches: 14, Indels: 2
0.90 0.09 0.01
Matches are distributed among these distances:
128 1 0.01
129 140 0.99
ACGTcount: A:0.29, C:0.21, G:0.22, T:0.27
Consensus pattern (129 bp):
TCTTATCTCCCTGAAGTTGCAGTGGAGCAGACAGAAGAAACCAATCCTATCTCCCTGAAGTTGCA
GTGGAACGAATTAAAACCACAGATCTTATCTCTCTGAAGTTGCAGTAGAGCAGATCGCAACTAG
Found at i:11113 original size:41 final size:41
Alignment explanation
Indices: 10838--11118 Score: 158
Period size: 44 Copynumber: 6.6 Consensus size: 41
10828 GAAGATTTTT
* * * *
10838 TCTTATCTCCCTGAAGTAGCAGTGGAGCAGA-CAGAAGAAATCAA
1 TCTTATCTCCCTGAAGTTGCAGTAGAGCAGATC-G-A-AACT-AG
* * * * **
10882 TCCTATCTCCCTGAAGTTGCAGTGGAACGGATTAAAACCATAG
1 TCTTATCTCCCTGAAGTTGCAGTAGAGCAGATCGAAA-C-TAG
* * *
10925 ATCTTATCTCTCTGAAGTTGCAGTAGAGCAGATCGCATCTAG
1 -TCTTATCTCCCTGAAGTTGCAGTAGAGCAGATCGAAACTAG
* * * *
10967 TCTTATTTCCCTGAAGTTGCAGTGGAGCAGGCAGA-GGAAACCAA
1 TCTTATCTCCCTGAAGTTGCAGT--AG-A-GCAGATCGAAACTAG
* **
11011 T-TCTATCTCCCTGAAGTT-CTAGTGGAGC-GAATTAAAACTACAG
1 TCT-TATCTCCCTGAAGTTGC-AGTAGAGCAG-ATCGAAACT--AG
** *
11054 ATCTTATCTCTTTGAAGTTGCAGTAGAGCAGATCGCAACTAG
1 -TCTTATCTCCCTGAAGTTGCAGTAGAGCAGATCGAAACTAG
*
11096 TCTTATCTCCCTAAAGTTGCAGT
1 TCTTATCTCCCTGAAGTTGCAGT
11119 GGAGTGGATC
Statistics
Matches: 180, Mismatches: 39, Indels: 39
0.70 0.15 0.15
Matches are distributed among these distances:
39 1 0.01
40 3 0.02
41 46 0.26
42 8 0.04
43 8 0.04
44 106 0.59
45 8 0.04
ACGTcount: A:0.30, C:0.21, G:0.21, T:0.28
Consensus pattern (41 bp):
TCTTATCTCCCTGAAGTTGCAGTAGAGCAGATCGAAACTAG
Found at i:13034 original size:19 final size:18
Alignment explanation
Indices: 13010--13045 Score: 54
Period size: 19 Copynumber: 1.9 Consensus size: 18
13000 TTTCAAAATT
*
13010 TATTTATGTATCATATTTA
1 TATTTATATA-CATATTTA
13029 TATTTATATACATATTT
1 TATTTATATACATATTT
13046 TGTAAACACA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
18 7 0.44
19 9 0.56
ACGTcount: A:0.33, C:0.06, G:0.03, T:0.58
Consensus pattern (18 bp):
TATTTATATACATATTTA
Found at i:16103 original size:11 final size:11
Alignment explanation
Indices: 16089--16114 Score: 52
Period size: 11 Copynumber: 2.4 Consensus size: 11
16079 AAATTAAAAA
16089 AAAAGTATTTT
1 AAAAGTATTTT
16100 AAAAGTATTTT
1 AAAAGTATTTT
16111 AAAA
1 AAAA
16115 TTAAAAAAAT
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 15 1.00
ACGTcount: A:0.54, C:0.00, G:0.08, T:0.38
Consensus pattern (11 bp):
AAAAGTATTTT
Found at i:16124 original size:42 final size:41
Alignment explanation
Indices: 15979--16131 Score: 184
Period size: 42 Copynumber: 3.7 Consensus size: 41
15969 ACCAAAAATT
15979 TATTTTAAAAATTAAAACAAA-AATTAAAAAAAGTATTTTAAAAA
1 TATTTT-AAAATTAAAA-AAATAA--AAAAAAAGTATTTTAAAAA
** * *
16023 TATTTTAAAATTAAAAAAA-ATTAAAGAAGTTTTTTAAAAA
1 TATTTTAAAATTAAAAAAATAAAAAAAAAGTATTTTAAAAA
* * *
16063 AATTTTAAAATTTAAAAAATTAAAAAAAAAGTATTTTAAAAG
1 TATTTTAAAA-TTAAAAAAATAAAAAAAAAGTATTTTAAAAA
16105 TATTTTAAAATTAAAAAAATAAAAAAA
1 TATTTTAAAATTAAAAAAATAAAAAAA
16132 TAAAAATATT
Statistics
Matches: 94, Mismatches: 13, Indels: 7
0.82 0.11 0.06
Matches are distributed among these distances:
40 25 0.27
41 24 0.26
42 29 0.31
43 10 0.11
44 6 0.06
ACGTcount: A:0.63, C:0.01, G:0.03, T:0.33
Consensus pattern (41 bp):
TATTTTAAAATTAAAAAAATAAAAAAAAAGTATTTTAAAAA
Found at i:16131 original size:41 final size:40
Alignment explanation
Indices: 15979--16131 Score: 180
Period size: 40 Copynumber: 3.7 Consensus size: 40
15969 ACCAAAAATT
15979 TATTTTAAAAATTAAAACAAAAATTAAAAAAAGTATTTTAAAAA
1 TATTTT-AAAATTAAAA-AAAAA--AAAAAAAGTATTTTAAAAA
** * *
16023 TATTTTAAAATTAAAAAAAATTAAAGAAGTTTTTTAAAAA
1 TATTTTAAAATTAAAAAAAAAAAAAAAAGTATTTTAAAAA
* * *
16063 AATTTTAAAATTTAAAAAATTAAAAAAAAAGTATTTTAAAAG
1 TATTTTAAAA-TTAAAAAA-AAAAAAAAAAGTATTTTAAAAA
*
16105 TATTTTAAAATTAAAAAAATAAAAAAA
1 TATTTTAAAATTAAAAAAAAAAAAAAA
16132 TAAAAATATT
Statistics
Matches: 93, Mismatches: 14, Indels: 8
0.81 0.12 0.07
Matches are distributed among these distances:
40 32 0.34
41 16 0.17
42 29 0.31
43 10 0.11
44 6 0.06
ACGTcount: A:0.63, C:0.01, G:0.03, T:0.33
Consensus pattern (40 bp):
TATTTTAAAATTAAAAAAAAAAAAAAAAGTATTTTAAAAA
Found at i:22957 original size:21 final size:21
Alignment explanation
Indices: 22924--22964 Score: 55
Period size: 21 Copynumber: 2.0 Consensus size: 21
22914 AGGATTGTTA
* *
22924 TGTGTTGCTGTTACGAGCATC
1 TGTGCTGCGGTTACGAGCATC
*
22945 TGTGCTGCGGTTATGAGCAT
1 TGTGCTGCGGTTACGAGCAT
22965 TTTTTGTTTA
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:0.15, C:0.17, G:0.32, T:0.37
Consensus pattern (21 bp):
TGTGCTGCGGTTACGAGCATC
Found at i:23365 original size:14 final size:14
Alignment explanation
Indices: 23346--23372 Score: 54
Period size: 14 Copynumber: 1.9 Consensus size: 14
23336 GAACCATTAC
23346 ATGATAAAAGACTG
1 ATGATAAAAGACTG
23360 ATGATAAAAGACT
1 ATGATAAAAGACT
23373 CCAGGCCATA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 13 1.00
ACGTcount: A:0.52, C:0.07, G:0.19, T:0.22
Consensus pattern (14 bp):
ATGATAAAAGACTG
Found at i:29753 original size:15 final size:16
Alignment explanation
Indices: 29735--29764 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
29725 AAATAGAAAA
29735 AAATA-AAAATTAAAG
1 AAATAGAAAATTAAAG
29750 AAATAGAAAATTAAA
1 AAATAGAAAATTAAA
29765 TTAAATTGGG
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 5 0.36
16 9 0.64
ACGTcount: A:0.73, C:0.00, G:0.07, T:0.20
Consensus pattern (16 bp):
AAATAGAAAATTAAAG
Found at i:30157 original size:24 final size:23
Alignment explanation
Indices: 30125--30189 Score: 80
Period size: 22 Copynumber: 2.9 Consensus size: 23
30115 CTTTTGAAGC
30125 AAAGAATCAATTTAAAACAAAAA
1 AAAGAATCAATTTAAAACAAAAA
* * *
30148 TAAAGAATCAA-TTCAAAGAAGAA
1 -AAAGAATCAATTTAAAACAAAAA
30171 AAA-AATCAATTTAAAACAA
1 AAAGAATCAATTTAAAACAA
30190 CAAACAATCG
Statistics
Matches: 35, Mismatches: 5, Indels: 4
0.80 0.11 0.09
Matches are distributed among these distances:
21 6 0.17
22 10 0.29
23 9 0.26
24 10 0.29
ACGTcount: A:0.66, C:0.09, G:0.06, T:0.18
Consensus pattern (23 bp):
AAAGAATCAATTTAAAACAAAAA
Found at i:30198 original size:21 final size:20
Alignment explanation
Indices: 30174--30332 Score: 70
Period size: 21 Copynumber: 7.5 Consensus size: 20
30164 AGAAGAAAAA
*
30174 AATCAATTTAAAACAACAAAC
1 AATCGATTTAAAA-AACAAAC
* * *
30195 AATCGATTCAAAGAACCAAAG
1 AATCGATTTAAA-AAACAAAC
* *
30216 AAACGA-TTAAAACAACAATAATG
1 AATCGATTTAAAA-AAC-A-AA-C
* * * *
30239 AATCAATTCAAAGAAGCAAAT
1 AATCGATTTAAA-AAACAAAC
*
30260 AATTGATTTAAAACAACAAAC
1 AATCGATTTAAAA-AACAAAC
* * *
30281 AATTGATTCAAAGAAGA-AAAG
1 AATCGATTTAAA-AA-ACAAAC
*
30302 AATCAATTTAAAATAACAAAC
1 AATCGATTTAAAA-AACAAAC
30323 AATCGATTTA
1 AATCGATTTA
30333 GGAAAAATAT
Statistics
Matches: 102, Mismatches: 24, Indels: 24
0.68 0.16 0.16
Matches are distributed among these distances:
19 1 0.01
20 9 0.09
21 72 0.71
22 7 0.07
23 6 0.06
24 6 0.06
25 1 0.01
ACGTcount: A:0.57, C:0.14, G:0.08, T:0.21
Consensus pattern (20 bp):
AATCGATTTAAAAAACAAAC
Found at i:30250 original size:44 final size:43
Alignment explanation
Indices: 30134--30278 Score: 143
Period size: 44 Copynumber: 3.3 Consensus size: 43
30124 CAAAGAATCA
* * *
30134 ATTTAAAACAAAAATAAAGAATCAATTCAAAGAAGAAAAAAATCA
1 ATTTAAAACAACAAT-AAGAATCAATTCAAAGAACAAAAAAA-CG
* * *
30179 ATTTAAAACAAC-A-AACAATCGATTCAAAGAACCAAAGAAACG
1 ATTTAAAACAACAATAAGAATCAATTCAAAGAA-CAAAAAAACG
* **
30221 A-TTAAAACAACAATAATGAATCAATTCAAAGAAGCAAATAATTG
1 ATTTAAAACAACAATAA-GAATCAATTCAAAGAA-CAAAAAAACG
30265 ATTTAAAACAACAA
1 ATTTAAAACAACAA
30279 ACAATTGATT
Statistics
Matches: 83, Mismatches: 12, Indels: 10
0.79 0.11 0.10
Matches are distributed among these distances:
41 10 0.12
42 19 0.23
43 8 0.10
44 23 0.28
45 23 0.28
ACGTcount: A:0.61, C:0.13, G:0.08, T:0.19
Consensus pattern (43 bp):
ATTTAAAACAACAATAAGAATCAATTCAAAGAACAAAAAAACG
Found at i:30281 original size:86 final size:86
Alignment explanation
Indices: 30136--30295 Score: 257
Period size: 86 Copynumber: 1.9 Consensus size: 86
30126 AAGAATCAAT
30136 TTAAAACAAAAATAAAGAATCAATTCAAAGAAGAAAAAAATCAATTTAAAACAACAAACAATCGA
1 TTAAAACAAAAATAAAGAATCAATTCAAAGAAGAAAAAAATCAATTTAAAACAACAAACAATCGA
30201 TTCAAAGAACCAAAGAAACGA
66 TTCAAAGAACCAAAGAAACGA
* * * * ** *
30222 TTAAAACAACAATAATGAATCAATTCAAAGAAGCAAATAATTGATTTAAAACAACAAACAATTGA
1 TTAAAACAAAAATAAAGAATCAATTCAAAGAAGAAAAAAATCAATTTAAAACAACAAACAATCGA
30287 TTCAAAGAA
66 TTCAAAGAA
30296 GAAAAGAATC
Statistics
Matches: 67, Mismatches: 7, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
86 67 1.00
ACGTcount: A:0.60, C:0.13, G:0.08, T:0.19
Consensus pattern (86 bp):
TTAAAACAAAAATAAAGAATCAATTCAAAGAAGAAAAAAATCAATTTAAAACAACAAACAATCGA
TTCAAAGAACCAAAGAAACGA
Found at i:30291 original size:42 final size:42
Alignment explanation
Indices: 30120--30330 Score: 208
Period size: 42 Copynumber: 4.9 Consensus size: 42
30110 ACGGGCTTTT
* * * *
30120 GAAGCAAAGAATCAATTTAAAACAAAAATAAAGAATCAATTCAAA
1 GAAGAAAAGAATCAATTTAAAAC---AACAAACAATCGATTCAAA
*
30165 GAAGAAAAAAATCAATTTAAAACAACAAACAATCGATTCAAA
1 GAAGAAAAGAATCAATTTAAAACAACAAACAATCGATTCAAA
** * * * *
30207 GAACCAAAGAAACGA-TTAAAACAACAATAATGAATCAATTCAAA
1 GAAGAAAAGAATCAATTTAAAACAAC-A-AA-CAATCGATTCAAA
* * ** *
30251 GAAGCAAATAATTGATTTAAAACAACAAACAATTGATTCAAA
1 GAAGAAAAGAATCAATTTAAAACAACAAACAATCGATTCAAA
*
30293 GAAGAAAAGAATCAATTTAAAATAACAAACAATCGATT
1 GAAGAAAAGAATCAATTTAAAACAACAAACAATCGATT
30331 TAGGAAAAAT
Statistics
Matches: 137, Mismatches: 25, Indels: 11
0.79 0.14 0.06
Matches are distributed among these distances:
41 10 0.07
42 69 0.50
43 4 0.03
44 23 0.17
45 31 0.23
ACGTcount: A:0.59, C:0.13, G:0.09, T:0.19
Consensus pattern (42 bp):
GAAGAAAAGAATCAATTTAAAACAACAAACAATCGATTCAAA
Found at i:31169 original size:42 final size:42
Alignment explanation
Indices: 31033--31420 Score: 418
Period size: 42 Copynumber: 9.0 Consensus size: 42
31023 CGAATCAATT
* * * * *
31033 AAAGAAGTAAATAATAGATTTAAAACAACAATAATAAATCGATTC
1 AAAGAAGCAAAGAATCGATTTAAAACAAC-A-AA-CAATTGATTC
* * *
31078 AAAGAAGCAAAGAATCTATTTAAAACAACAATAACGAATTGGTTT
1 AAAGAAGCAAAGAATCGATTTAAAACAAC-A-AAC-AATTGATTC
*
31123 AAAGAAGCCAAGAATCGATTTAAAACAACAAACAATTGATTC
1 AAAGAAGCAAAGAATCGATTTAAAACAACAAACAATTGATTC
* * * * *
31165 AAAGAAGAAAAGAATCAAATTAAAACAATAAGCAATTGATTC
1 AAAGAAGCAAAGAATCGATTTAAAACAACAAACAATTGATTC
* * *
31207 AAAGAAGCAAAGAATCTATTTAAAACAACAATAACGAATTGGTTT
1 AAAGAAGCAAAGAATCGATTTAAAACAAC-A-AAC-AATTGATTC
*
31252 AAAGAAGCCAAGAATCGATTTAAAACAACAAACAATTGATTC
1 AAAGAAGCAAAGAATCGATTTAAAACAACAAACAATTGATTC
* * * * *
31294 AAAGAAGAAAAGAATCAAATTAAAACAATAAGCAATTGATTC
1 AAAGAAGCAAAGAATCGATTTAAAACAACAAACAATTGATTC
* * *
31336 AAAGAAGCAAAGAATAGATTTAAAACAATAAACAATCGATTC
1 AAAGAAGCAAAGAATCGATTTAAAACAACAAACAATTGATTC
* * *
31378 AAAGAAGAAAAGAA-CTGATTTAAAACAATAAACAATCGATTC
1 AAAGAAGCAAAGAATC-GATTTAAAACAACAAACAATTGATTC
31420 A
1 A
31421 GCAAAAAAAA
Statistics
Matches: 295, Mismatches: 43, Indels: 13
0.84 0.12 0.04
Matches are distributed among these distances:
42 187 0.63
43 7 0.02
44 4 0.01
45 97 0.33
ACGTcount: A:0.55, C:0.12, G:0.12, T:0.21
Consensus pattern (42 bp):
AAAGAAGCAAAGAATCGATTTAAAACAACAAACAATTGATTC
Found at i:31224 original size:129 final size:129
Alignment explanation
Indices: 31059--31420 Score: 570
Period size: 129 Copynumber: 2.8 Consensus size: 129
31049 GATTTAAAAC
** *
31059 AACAATAATAAATCGATTCAAAGAAGCAAAGAATCTATTTAAAACAACAATAACGAATTGGTTTA
1 AACAATAAGCAATTGATTCAAAGAAGCAAAGAATCTATTTAAAACAACAATAACGAATTGGTTTA
31124 AAGAAGCCAAGAATCGATTTAAAACAACAAACAATTGATTCAAAGAAGAAAAGAATCAAATTAA
66 AAGAAGCCAAGAATCGATTTAAAACAACAAACAATTGATTCAAAGAAGAAAAGAATCAAATTAA
31188 AACAATAAGCAATTGATTCAAAGAAGCAAAGAATCTATTTAAAACAACAATAACGAATTGGTTTA
1 AACAATAAGCAATTGATTCAAAGAAGCAAAGAATCTATTTAAAACAACAATAACGAATTGGTTTA
31253 AAGAAGCCAAGAATCGATTTAAAACAACAAACAATTGATTCAAAGAAGAAAAGAATCAAATTAA
66 AAGAAGCCAAGAATCGATTTAAAACAACAAACAATTGATTCAAAGAAGAAAAGAATCAAATTAA
** * * * *
31317 AACAATAAGCAATTGATTCAAAGAAGCAAAGAATAGATTTAAAACAA-TA-AAC-AATCGATTCA
1 AACAATAAGCAATTGATTCAAAGAAGCAAAGAATCTATTTAAAACAACAATAACGAATTGGTTTA
** * *
31379 AAGAAGAAAAGAA-CTGATTTAAAACAATAAACAATCGATTCA
66 AAGAAGCCAAGAATC-GATTTAAAACAACAAACAATTGATTCA
31421 GCAAAAAAAA
Statistics
Matches: 219, Mismatches: 13, Indels: 5
0.92 0.05 0.02
Matches are distributed among these distances:
125 1 0.00
126 43 0.20
127 3 0.01
128 1 0.00
129 171 0.78
ACGTcount: A:0.55, C:0.12, G:0.12, T:0.21
Consensus pattern (129 bp):
AACAATAAGCAATTGATTCAAAGAAGCAAAGAATCTATTTAAAACAACAATAACGAATTGGTTTA
AAGAAGCCAAGAATCGATTTAAAACAACAAACAATTGATTCAAAGAAGAAAAGAATCAAATTAA
Found at i:34618 original size:35 final size:35
Alignment explanation
Indices: 34578--34667 Score: 110
Period size: 35 Copynumber: 2.5 Consensus size: 35
34568 GAAAAAAGGC
* *
34578 CTATCCTAACTTTTTTAAGGTTACCTTAGACAT-GT
1 CTATCCCAACTTTTTTAAGGTTACCATAGA-ATGGT
* **
34613 CTATCCCAACCTTTTTAAGGTTTGCATAGAATGGT
1 CTATCCCAACTTTTTTAAGGTTACCATAGAATGGT
34648 CTATCCCAACCTTTTTTAAG
1 CTATCCCAA-CTTTTTTAAG
34668 TTGATTTTGA
Statistics
Matches: 47, Mismatches: 6, Indels: 3
0.84 0.11 0.05
Matches are distributed among these distances:
34 2 0.04
35 36 0.77
36 9 0.19
ACGTcount: A:0.26, C:0.22, G:0.12, T:0.40
Consensus pattern (35 bp):
CTATCCCAACTTTTTTAAGGTTACCATAGAATGGT
Found at i:43180 original size:17 final size:17
Alignment explanation
Indices: 43158--43193 Score: 72
Period size: 17 Copynumber: 2.1 Consensus size: 17
43148 GGCCTTACAT
43158 AGTTAATAGATCCCATG
1 AGTTAATAGATCCCATG
43175 AGTTAATAGATCCCATG
1 AGTTAATAGATCCCATG
43192 AG
1 AG
43194 ACCATTGATC
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 19 1.00
ACGTcount: A:0.36, C:0.17, G:0.19, T:0.28
Consensus pattern (17 bp):
AGTTAATAGATCCCATG
Found at i:48039 original size:56 final size:57
Alignment explanation
Indices: 47937--48052 Score: 155
Period size: 56 Copynumber: 2.1 Consensus size: 57
47927 GAAATGGTGA
* * *
47937 AAATGGAGAAATGAGAAAGATTTGAAAATATTTATTGTTTTCTCCAAAATGAAAATG
1 AAATGGAGAAATGAGAAACATTTGAAAATAATTATGGTTTTCTCCAAAATGAAAATG
* * *
47994 AAATGGAGAAAT-AGAATCATTTGCAAATGAATT-TGGTTTTGTCCAAAATGAAAATG
1 AAATGGAGAAATGAGAAACATTTGAAAAT-AATTATGGTTTTCTCCAAAATGAAAATG
48050 AAA
1 AAA
48053 AATGACCTAG
Statistics
Matches: 52, Mismatches: 6, Indels: 3
0.85 0.10 0.05
Matches are distributed among these distances:
56 37 0.71
57 15 0.29
ACGTcount: A:0.46, C:0.06, G:0.18, T:0.30
Consensus pattern (57 bp):
AAATGGAGAAATGAGAAACATTTGAAAATAATTATGGTTTTCTCCAAAATGAAAATG
Found at i:50296 original size:38 final size:37
Alignment explanation
Indices: 50245--50368 Score: 167
Period size: 38 Copynumber: 3.3 Consensus size: 37
50235 GATTGGATGA
* * *
50245 AAATGTTTATCTACTGGCTCTTCGGAGCAAGACCATAG
1 AAATGGTTATCTACTGGCTCTTCGGAGCGACACCAT-G
* *
50283 AAATGGTTATCTACTGACTCTTCGAAGCGACACCATG
1 AAATGGTTATCTACTGGCTCTTCGGAGCGACACCATG
*
50320 AAAATGGTTATCTACTGGCTCTACGGAGCGACACCATGG
1 -AAATGGTTATCTACTGGCTCTTCGGAGCGACACCAT-G
50359 AAATGGTTAT
1 AAATGGTTAT
50369 TGACTCATTG
Statistics
Matches: 76, Mismatches: 8, Indels: 4
0.86 0.09 0.05
Matches are distributed among these distances:
37 1 0.01
38 74 0.97
39 1 0.01
ACGTcount: A:0.30, C:0.21, G:0.22, T:0.27
Consensus pattern (37 bp):
AAATGGTTATCTACTGGCTCTTCGGAGCGACACCATG
Found at i:54000 original size:20 final size:20
Alignment explanation
Indices: 53977--54028 Score: 68
Period size: 20 Copynumber: 2.6 Consensus size: 20
53967 ACTTCGATTC
53977 CTTTGTTTGCACTTTGGTGT
1 CTTTGTTTGCACTTTGGTGT
**
53997 CTTTGTTCACACTTTGGTGT
1 CTTTGTTTGCACTTTGGTGT
* *
54017 CTCTCTTTGCAC
1 CTTTGTTTGCAC
54029 CTCAATGCCT
Statistics
Matches: 26, Mismatches: 6, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
20 26 1.00
ACGTcount: A:0.08, C:0.23, G:0.19, T:0.50
Consensus pattern (20 bp):
CTTTGTTTGCACTTTGGTGT
Found at i:54217 original size:24 final size:24
Alignment explanation
Indices: 54187--54278 Score: 103
Period size: 24 Copynumber: 3.8 Consensus size: 24
54177 ATGCAAGTAC
*
54187 ACATGAATGATTTTGATTAAATAT
1 ACATGAATGATCTTGATTAAATAT
* * * *
54211 ACGTGAATGACCTTGAGTGAATAT
1 ACATGAATGATCTTGATTAAATAT
* * *
54235 ACATGACTGGTCTTGATTGAATAT
1 ACATGAATGATCTTGATTAAATAT
*
54259 ACATGAATGATCTTTATTAA
1 ACATGAATGATCTTGATTAA
54279 TTCTTGATGA
Statistics
Matches: 54, Mismatches: 14, Indels: 0
0.79 0.21 0.00
Matches are distributed among these distances:
24 54 1.00
ACGTcount: A:0.36, C:0.10, G:0.17, T:0.37
Consensus pattern (24 bp):
ACATGAATGATCTTGATTAAATAT
Found at i:57968 original size:19 final size:19
Alignment explanation
Indices: 57917--57969 Score: 53
Period size: 19 Copynumber: 3.0 Consensus size: 19
57907 TAATAATTTA
57917 TTATAAT-TACT-TTTAA-
1 TTATAATATACTGTTTAAT
*
57933 -TATAA-ATATTGTGTTAAT
1 TTATAATATACTGT-TTAAT
57951 TTATAATATACTGTTTAAT
1 TTATAATATACTGTTTAAT
57970 ATTGATATAA
Statistics
Matches: 29, Mismatches: 2, Indels: 9
0.73 0.05 0.22
Matches are distributed among these distances:
15 8 0.28
16 1 0.03
17 4 0.14
19 10 0.34
20 6 0.21
ACGTcount: A:0.38, C:0.04, G:0.06, T:0.53
Consensus pattern (19 bp):
TTATAATATACTGTTTAAT
Found at i:58544 original size:50 final size:50
Alignment explanation
Indices: 58484--58645 Score: 190
Period size: 50 Copynumber: 3.3 Consensus size: 50
58474 TTACAAATAT
58484 ATTTTAATAATCATATATTAAATAAATTAAATCAATCAATTTGATTACAA
1 ATTTTAATAATCATATATTAAATAAATTAAATCAATCAATTTGATTACAA
* ** * * * *
58534 ATTTTAATAATCA-ATAATT-GATCCATAAAATCAAATTAA-CTGA-CA-AA
1 ATTTTAATAATCATAT-ATTAAATAAATTAAATC-AATCAATTTGATTACAA
58581 TATATTTAATAATCATATATTAAATAAATTAAATCAATCAATTTGATTACAA
1 -AT-TTTAATAATCATATATTAAATAAATTAAATCAATCAATTTGATTACAA
58633 ATTTTAATAATCA
1 ATTTTAATAATCA
58646 ATAATTGATC
Statistics
Matches: 89, Mismatches: 14, Indels: 18
0.74 0.12 0.15
Matches are distributed among these distances:
47 2 0.02
48 3 0.03
49 33 0.37
50 46 0.52
51 3 0.03
52 2 0.02
ACGTcount: A:0.50, C:0.09, G:0.02, T:0.38
Consensus pattern (50 bp):
ATTTTAATAATCATATATTAAATAAATTAAATCAATCAATTTGATTACAA
Found at i:58590 original size:49 final size:49
Alignment explanation
Indices: 58525--58675 Score: 157
Period size: 49 Copynumber: 3.1 Consensus size: 49
58515 TCAATCAATT
*
58525 TGATTACAAATTTTAATAATCAATAATTGATCCATAAAATCAAATTAAC
1 TGATCACAAATTTTAATAATCAATAATTGATCCATAAAATCAAATTAAC
* ** * * *
58574 TGA-CA-AATATATTTAATAATC-ATATATTAAATAAATTAAATC-AATCAATT
1 TGATCACAA-AT-TTTAATAATCAATA-ATT-GATCCATAAAATCAAATTAA-C
*
58624 TGATTACAAATTTTAATAATCAATAATTGATCCATAAAATCAAATTAAC
1 TGATCACAAATTTTAATAATCAATAATTGATCCATAAAATCAAATTAAC
58673 TGA
1 TGA
58676 ATCTTTAATT
Statistics
Matches: 79, Mismatches: 14, Indels: 18
0.71 0.13 0.16
Matches are distributed among these distances:
47 2 0.03
48 6 0.08
49 33 0.42
50 30 0.38
51 6 0.08
52 2 0.03
ACGTcount: A:0.50, C:0.11, G:0.04, T:0.36
Consensus pattern (49 bp):
TGATCACAAATTTTAATAATCAATAATTGATCCATAAAATCAAATTAAC
Found at i:58598 original size:99 final size:100
Alignment explanation
Indices: 58476--58675 Score: 393
Period size: 99 Copynumber: 2.0 Consensus size: 100
58466 ATTGTATATT
58476 ACAAATATATTTTAATAATCATATATTAAATAAATTAAATCAATCAATTTGATTACAAATTTTAA
1 ACAAATATATTTTAATAATCATATATTAAATAAATTAAATCAATCAATTTGATTACAAATTTTAA
58541 TAATCAATAATTGATCCATAAAATCAAATTAACTG
66 TAATCAATAATTGATCCATAAAATCAAATTAACTG
58576 ACAAATATA-TTTAATAATCATATATTAAATAAATTAAATCAATCAATTTGATTACAAATTTTAA
1 ACAAATATATTTTAATAATCATATATTAAATAAATTAAATCAATCAATTTGATTACAAATTTTAA
58640 TAATCAATAATTGATCCATAAAATCAAATTAACTG
66 TAATCAATAATTGATCCATAAAATCAAATTAACTG
58675 A
1 A
58676 ATCTTTAATT
Statistics
Matches: 100, Mismatches: 0, Indels: 1
0.99 0.00 0.01
Matches are distributed among these distances:
99 91 0.91
100 9 0.09
ACGTcount: A:0.51, C:0.10, G:0.03, T:0.36
Consensus pattern (100 bp):
ACAAATATATTTTAATAATCATATATTAAATAAATTAAATCAATCAATTTGATTACAAATTTTAA
TAATCAATAATTGATCCATAAAATCAAATTAACTG
Found at i:66939 original size:26 final size:26
Alignment explanation
Indices: 66909--66962 Score: 108
Period size: 26 Copynumber: 2.1 Consensus size: 26
66899 AAGAAATTTT
66909 AATGTTTAAATAGTTAATTAAAGAAA
1 AATGTTTAAATAGTTAATTAAAGAAA
66935 AATGTTTAAATAGTTAATTAAAGAAA
1 AATGTTTAAATAGTTAATTAAAGAAA
66961 AA
1 AA
66963 GGACTAAATT
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
26 28 1.00
ACGTcount: A:0.56, C:0.00, G:0.11, T:0.33
Consensus pattern (26 bp):
AATGTTTAAATAGTTAATTAAAGAAA
Found at i:66970 original size:26 final size:26
Alignment explanation
Indices: 66915--66971 Score: 87
Period size: 26 Copynumber: 2.2 Consensus size: 26
66905 TTTTAATGTT
* **
66915 TAAATAGTTAATTAAAGAAAAATGTT
1 TAAATAGTTAATTAAAGAAAAAGGAC
66941 TAAATAGTTAATTAAAGAAAAAGGAC
1 TAAATAGTTAATTAAAGAAAAAGGAC
66967 TAAAT
1 TAAAT
66972 TGTAAAAAGT
Statistics
Matches: 28, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
26 28 1.00
ACGTcount: A:0.56, C:0.02, G:0.12, T:0.30
Consensus pattern (26 bp):
TAAATAGTTAATTAAAGAAAAAGGAC
Found at i:68213 original size:36 final size:37
Alignment explanation
Indices: 68105--68226 Score: 124
Period size: 37 Copynumber: 3.3 Consensus size: 37
68095 ACTCCCTATT
* * *
68105 TTGGCGTGTTTTCAATTGGACTAGCT-TTTTGAAGCAA
1 TTGGCGTGTTTTCAGTTGGATTAGCTCTTATG-AGCAA
* **
68142 TTGGCATGTTTTC-GATTGGATTAGCTCTTCCGAGCAA
1 TTGGCGTGTTTTCAG-TTGGATTAGCTCTTATGAGCAA
* *
68179 TTGGCGTG-TATCAGTTGGATTAGCTCTTATGAGCAT
1 TTGGCGTGTTTTCAGTTGGATTAGCTCTTATGAGCAA
*
68215 TTGGCATGTTTT
1 TTGGCGTGTTTT
68227 TGGATGGATT
Statistics
Matches: 69, Mismatches: 12, Indels: 8
0.78 0.13 0.09
Matches are distributed among these distances:
36 29 0.42
37 37 0.54
38 3 0.04
ACGTcount: A:0.19, C:0.15, G:0.25, T:0.41
Consensus pattern (37 bp):
TTGGCGTGTTTTCAGTTGGATTAGCTCTTATGAGCAA
Found at i:68800 original size:19 final size:19
Alignment explanation
Indices: 68768--68805 Score: 51
Period size: 19 Copynumber: 2.0 Consensus size: 19
68758 CCCGTAATAT
*
68768 AAAATCAAATCAAAACAAAA
1 AAAATCAAACCAAAA-AAAA
68788 AAAAT-AAACCAAAAAAAA
1 AAAATCAAACCAAAAAAAA
68806 TTAATAACAG
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
18 4 0.24
19 8 0.47
20 5 0.29
ACGTcount: A:0.79, C:0.13, G:0.00, T:0.08
Consensus pattern (19 bp):
AAAATCAAACCAAAAAAAA
Found at i:74778 original size:150 final size:150
Alignment explanation
Indices: 74507--74797 Score: 564
Period size: 150 Copynumber: 1.9 Consensus size: 150
74497 TGTTTAGACG
74507 GATCTCATGGCTTTGGAAATGACATAGATCGTAGCTTATCTCCGAACTTGTCGAGGATGGTAGAA
1 GATCTCATGGCTTTGGAAATGACATAGATCGTAGCTTATCTCCGAACTTGTCGAGGATGGTAGAA
*
74572 CAAGAGGATAAACAGATCCTACCTCTCAAGGAATTATAAAAAATTGTGAACTTGGTAAAGATTAA
66 CAAGAGGATAAACAGACCCTACCTCTCAAGGAATTATAAAAAATTGTGAACTTGGTAAAGATTAA
74637 AATTGACCTGAGGATAAACA
131 AATTGACCTGAGGATAAACA
74657 GATCTCATGGCTTTGGAAATGACATAGATCGTAGCTTATCTCCGAACTTGTCGAGGATGGTAGAA
1 GATCTCATGGCTTTGGAAATGACATAGATCGTAGCTTATCTCCGAACTTGTCGAGGATGGTAGAA
*
74722 CAAGAGGATAAACAGACCCTACCTCTCAAGGAATTATAAAAAATTGTGAGCTTGGTAAAGATTAA
66 CAAGAGGATAAACAGACCCTACCTCTCAAGGAATTATAAAAAATTGTGAACTTGGTAAAGATTAA
74787 AATTGACCTGA
131 AATTGACCTGA
74798 CCTCAAAGAT
Statistics
Matches: 139, Mismatches: 2, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
150 139 1.00
ACGTcount: A:0.36, C:0.16, G:0.22, T:0.26
Consensus pattern (150 bp):
GATCTCATGGCTTTGGAAATGACATAGATCGTAGCTTATCTCCGAACTTGTCGAGGATGGTAGAA
CAAGAGGATAAACAGACCCTACCTCTCAAGGAATTATAAAAAATTGTGAACTTGGTAAAGATTAA
AATTGACCTGAGGATAAACA
Found at i:75206 original size:12 final size:12
Alignment explanation
Indices: 75191--75224 Score: 52
Period size: 13 Copynumber: 2.8 Consensus size: 12
75181 GATTCAAAAA
75191 AAAAATCAAATC
1 AAAAATCAAATC
75203 AAAAATCAAAATC
1 AAAAATC-AAATC
75216 AAAAA-CAAA
1 AAAAATCAAA
75225 AAGAAAGACA
Statistics
Matches: 21, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
11 3 0.14
12 8 0.38
13 10 0.48
ACGTcount: A:0.74, C:0.15, G:0.00, T:0.12
Consensus pattern (12 bp):
AAAAATCAAATC
Found at i:75214 original size:13 final size:13
Alignment explanation
Indices: 75191--75225 Score: 56
Period size: 12 Copynumber: 2.8 Consensus size: 13
75181 GATTCAAAAA
75191 AAAAATC-AAATC
1 AAAAATCAAAATC
75203 AAAAATCAAAATC
1 AAAAATCAAAATC
75216 AAAAA-CAAAA
1 AAAAATCAAAA
75226 AGAAAGACAG
Statistics
Matches: 22, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
12 12 0.55
13 10 0.45
ACGTcount: A:0.74, C:0.14, G:0.00, T:0.11
Consensus pattern (13 bp):
AAAAATCAAAATC
Found at i:75683 original size:7 final size:7
Alignment explanation
Indices: 75671--75705 Score: 54
Period size: 7 Copynumber: 5.0 Consensus size: 7
75661 AAAAAAAGAG
75671 ATGAAAA
1 ATGAAAA
75678 ATG-AAA
1 ATGAAAA
75684 ATGAAAA
1 ATGAAAA
75691 ATGAAAAA
1 ATG-AAAA
75699 ATGAAAA
1 ATGAAAA
75706 GTAAAATAGA
Statistics
Matches: 26, Mismatches: 0, Indels: 4
0.87 0.00 0.13
Matches are distributed among these distances:
6 6 0.23
7 13 0.50
8 7 0.27
ACGTcount: A:0.71, C:0.00, G:0.14, T:0.14
Consensus pattern (7 bp):
ATGAAAA
Found at i:75687 original size:13 final size:13
Alignment explanation
Indices: 75671--75697 Score: 54
Period size: 13 Copynumber: 2.1 Consensus size: 13
75661 AAAAAAAGAG
75671 ATGAAAAATGAAA
1 ATGAAAAATGAAA
75684 ATGAAAAATGAAA
1 ATGAAAAATGAAA
75697 A
1 A
75698 AATGAAAAGT
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:0.70, C:0.00, G:0.15, T:0.15
Consensus pattern (13 bp):
ATGAAAAATGAAA
Found at i:77426 original size:87 final size:87
Alignment explanation
Indices: 76943--77416 Score: 714
Period size: 87 Copynumber: 5.4 Consensus size: 87
76933 GAAGATACAG
*
76943 GCCTTGCCTCCATCGGTTGTAGTGGAGCTGGTTAAAGATAGCAGATCTTGCCTTCCTGCGTAAAC
1 GCCTTGCCTCCATCGGTTGTAGTGGAGCTGGTTAAAGATAGCAGATCTTGCCTTCCTGCGTTAAC
*
77008 AGCGACGCAGATCGAAAACAAA
66 AGCGAAGCAGATCGAAAACAAA
* * *
77030 GCCTTACCTCCATCAGTTGTAGTGGAGCTGGTTAAAGATAACAGATCTTGCCTTCCTGCGTTAAC
1 GCCTTGCCTCCATCGGTTGTAGTGGAGCTGGTTAAAGATAGCAGATCTTGCCTTCCTGCGTTAAC
* *
77095 AGCGAAGCAGATTGAAAACAAG
66 AGCGAAGCAGATCGAAAACAAA
77117 GCCTTGCCTCCATCGGTTGTAGTGGAGCTGGTTAAAGATAGCAGATCTTGCCTTCCTGCGTTAAC
1 GCCTTGCCTCCATCGGTTGTAGTGGAGCTGGTTAAAGATAGCAGATCTTGCCTTCCTGCGTTAAC
*
77182 AGCGAAGCAGATCAAAAACAAA
66 AGCGAAGCAGATCGAAAACAAA
* * *** * *
77204 GCCTTGCCTCCATTGATTGTAGTGGAGCCAATTAAAGATAGCAGATCTTGCCTTCCTGCATTGAC
1 GCCTTGCCTCCATCGGTTGTAGTGGAGCTGGTTAAAGATAGCAGATCTTGCCTTCCTGCGTTAAC
* *
77269 AGCGAAGCAGATTGGAAACAAA
66 AGCGAAGCAGATCGAAAACAAA
* ** ***
77291 GCCTTGCCTCAATCGGTTACAGTGGAGCTGGTTAAAGATAGCAGATCTTGCCTTCCTATATTAAC
1 GCCTTGCCTCCATCGGTTGTAGTGGAGCTGGTTAAAGATAGCAGATCTTGCCTTCCTGCGTTAAC
* *
77356 AACGAAGCAGATCAAAAACAAA
66 AGCGAAGCAGATCGAAAACAAA
*
77378 GCCTTGCCTCCATCGGTTGCAGTGGAGCTGGTTAAAGAT
1 GCCTTGCCTCCATCGGTTGTAGTGGAGCTGGTTAAAGAT
77417 GACAAATCTT
Statistics
Matches: 347, Mismatches: 40, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
87 347 1.00
ACGTcount: A:0.29, C:0.23, G:0.24, T:0.25
Consensus pattern (87 bp):
GCCTTGCCTCCATCGGTTGTAGTGGAGCTGGTTAAAGATAGCAGATCTTGCCTTCCTGCGTTAAC
AGCGAAGCAGATCGAAAACAAA
Found at i:84276 original size:29 final size:29
Alignment explanation
Indices: 84205--84276 Score: 92
Period size: 29 Copynumber: 2.5 Consensus size: 29
84195 CACATGGCTG
*
84205 TGTGACCCACACGGTTTGCCACAAGACCA
1 TGTGACCCACATGGTTTGCCACAAGACCA
* *
84234 TGTGACCCATATGGTTTGCCACACAG-CCG
1 TGTGACCCACATGGTTTGCCACA-AGACCA
*
84263 TTTGACCCACATGG
1 TGTGACCCACATGG
84277 CCTAAAACAA
Statistics
Matches: 37, Mismatches: 5, Indels: 2
0.84 0.11 0.05
Matches are distributed among these distances:
29 35 0.95
30 2 0.05
ACGTcount: A:0.24, C:0.32, G:0.22, T:0.22
Consensus pattern (29 bp):
TGTGACCCACATGGTTTGCCACAAGACCA
Found at i:84380 original size:29 final size:29
Alignment explanation
Indices: 84328--84411 Score: 78
Period size: 29 Copynumber: 2.9 Consensus size: 29
84318 GGCACACGAT
* * * * *
84328 CGTGTGACCTACACGGCTTGCCACACAGT
1 CGTGTGACCCACATGGCCTACCACACAGC
* **
84357 TGTGTGACCCACATGGCCTACCACATGGC
1 CGTGTGACCCACATGGCCTACCACACAGC
* *
84386 CGTGTGATCCACATGACCTACCACAC
1 CGTGTGACCCACATGGCCTACCACAC
84412 GACTGTGTAA
Statistics
Matches: 43, Mismatches: 12, Indels: 0
0.78 0.22 0.00
Matches are distributed among these distances:
29 43 1.00
ACGTcount: A:0.23, C:0.36, G:0.21, T:0.20
Consensus pattern (29 bp):
CGTGTGACCCACATGGCCTACCACACAGC
Found at i:84419 original size:29 final size:29
Alignment explanation
Indices: 84357--84419 Score: 81
Period size: 29 Copynumber: 2.2 Consensus size: 29
84347 GCCACACAGT
* * *
84357 TGTGTGACCCACATGGCCTACCACATGGC
1 TGTGTGACCCACATGACCTACCACACGAC
* *
84386 CGTGTGATCCACATGACCTACCACACGAC
1 TGTGTGACCCACATGACCTACCACACGAC
84415 TGTGT
1 TGTGT
84420 AACGTCGATA
Statistics
Matches: 28, Mismatches: 6, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
29 28 1.00
ACGTcount: A:0.22, C:0.33, G:0.22, T:0.22
Consensus pattern (29 bp):
TGTGTGACCCACATGACCTACCACACGAC
Found at i:90175 original size:17 final size:17
Alignment explanation
Indices: 90155--90191 Score: 65
Period size: 17 Copynumber: 2.2 Consensus size: 17
90145 AATTTTTGAA
90155 TTAGTGAATTCTGTGAT
1 TTAGTGAATTCTGTGAT
*
90172 TTAGTGAATTTTGTGAT
1 TTAGTGAATTCTGTGAT
90189 TTA
1 TTA
90192 AAAAGAATTT
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
17 19 1.00
ACGTcount: A:0.24, C:0.03, G:0.22, T:0.51
Consensus pattern (17 bp):
TTAGTGAATTCTGTGAT
Found at i:91475 original size:46 final size:46
Alignment explanation
Indices: 91422--91604 Score: 271
Period size: 46 Copynumber: 4.0 Consensus size: 46
91412 CATGGAAAAA
*
91422 TTGTGAAAAGTAGGTATGGTATTTCAGTGAAGAAAGCCATACTAAG
1 TTGTGAAAAGTAGGTATGGTATTTCAGTGAAGAAAGCCATACTGAG
* *
91468 TTGTGAAAAGTAGGTATGGTGTTTCTGTGAAG-AAGACCATACTGAG
1 TTGTGAAAAGTAGGTATGGTATTTCAGTGAAGAAAG-CCATACTGAG
* * *
91514 TTGTGAAAAGCAGGTATGGTGTTTCAGTGAAGAAAACCATACTGAG
1 TTGTGAAAAGTAGGTATGGTATTTCAGTGAAGAAAGCCATACTGAG
*
91560 TTGTGAAAAGTAGGTATGATATTTCAGTGAAGGAAA-CCATACTGA
1 TTGTGAAAAGTAGGTATGGTATTTCAGTGAA-GAAAGCCATACTGA
91605 ATTATAGCAT
Statistics
Matches: 125, Mismatches: 9, Indels: 6
0.89 0.06 0.04
Matches are distributed among these distances:
45 3 0.02
46 116 0.93
47 6 0.05
ACGTcount: A:0.35, C:0.09, G:0.27, T:0.28
Consensus pattern (46 bp):
TTGTGAAAAGTAGGTATGGTATTTCAGTGAAGAAAGCCATACTGAG
Found at i:92585 original size:23 final size:25
Alignment explanation
Indices: 92545--92590 Score: 60
Period size: 23 Copynumber: 1.9 Consensus size: 25
92535 GTGGAAATTG
*
92545 AATTAGAATCTGAGTGAG-ATATGA
1 AATTAGAATCTGAATGAGTATATGA
*
92569 AATTA-AATTTGAATGAGTATAT
1 AATTAGAATCTGAATGAGTATAT
92591 TTTCACATGA
Statistics
Matches: 19, Mismatches: 2, Indels: 2
0.83 0.09 0.09
Matches are distributed among these distances:
23 10 0.53
24 9 0.47
ACGTcount: A:0.43, C:0.02, G:0.20, T:0.35
Consensus pattern (25 bp):
AATTAGAATCTGAATGAGTATATGA
Found at i:96261 original size:28 final size:28
Alignment explanation
Indices: 96229--96325 Score: 142
Period size: 28 Copynumber: 3.4 Consensus size: 28
96219 GAGCGGGGTG
96229 TTAGG-ATATTATTATTATGAGATATCTT
1 TTAGGAATA-TATTATTATGAGATATCTT
*
96257 TTAGGAATATATTATTATGATATATCTT
1 TTAGGAATATATTATTATGAGATATCTT
96285 TTAGGAATATATTATTATGAGATATTGTCTT
1 TTAGGAATATATTATTATGAGATA---TCTT
96316 TTAGGAATAT
1 TTAGGAATAT
96326 CTACATATAT
Statistics
Matches: 63, Mismatches: 2, Indels: 5
0.90 0.03 0.07
Matches are distributed among these distances:
28 46 0.73
29 3 0.05
31 14 0.22
ACGTcount: A:0.34, C:0.03, G:0.14, T:0.48
Consensus pattern (28 bp):
TTAGGAATATATTATTATGAGATATCTT
Found at i:96272 original size:31 final size:31
Alignment explanation
Indices: 96234--96358 Score: 120
Period size: 31 Copynumber: 4.2 Consensus size: 31
96224 GGGTGTTAGG
*
96234 ATATTATTATTATGAGATATCTTTTAGG-A-
1 ATATTATTATTATGATATATCTTTTAGGAAT
96263 ATA-TATTATTATGATATATCTTTTAGGAAT
1 ATATTATTATTATGATATATCTTTTAGGAAT
* *
96293 ATATTATTATGA-GATATTGTCTTTTAGGAAT
1 ATATTATTATTATGATA-TATCTTTTAGGAAT
* * *
96324 AT-CTA-CATATATTG-TATATCTTTTAGGTAT
1 ATATTATTAT-TA-TGATATATCTTTTAGGAAT
96354 ATATT
1 ATATT
96359 TAGGAATATA
Statistics
Matches: 79, Mismatches: 9, Indels: 14
0.77 0.09 0.14
Matches are distributed among these distances:
28 23 0.29
29 6 0.08
30 24 0.30
31 25 0.32
32 1 0.01
ACGTcount: A:0.34, C:0.05, G:0.12, T:0.50
Consensus pattern (31 bp):
ATATTATTATTATGATATATCTTTTAGGAAT
Found at i:96279 original size:13 final size:13
Alignment explanation
Indices: 96233--96310 Score: 57
Period size: 14 Copynumber: 5.6 Consensus size: 13
96223 GGGGTGTTAG
96233 GATATTATTATTAT
1 GATA-TATTATTAT
* * *
96247 GAGATATCTTTTAG
1 GATATAT-TATTAT
96261 GAATATATTATTAT
1 G-ATATATTATTAT
* *
96275 GATATATCTTTTAG
1 GATATAT-TATTAT
96289 GAATATATTATTAT
1 G-ATATATTATTAT
*
96303 GAGATATT
1 GATATATT
96311 GTCTTTTAGG
Statistics
Matches: 49, Mismatches: 11, Indels: 9
0.71 0.16 0.13
Matches are distributed among these distances:
13 15 0.31
14 23 0.47
15 11 0.22
ACGTcount: A:0.36, C:0.03, G:0.13, T:0.49
Consensus pattern (13 bp):
GATATATTATTAT
Found at i:96323 original size:59 final size:57
Alignment explanation
Indices: 96229--96358 Score: 158
Period size: 61 Copynumber: 2.2 Consensus size: 57
96219 GAGCGGGGTG
*
96229 TTAGGATATTATTATTATGAGATATCTTTTAGGAATATAT-TAT-TA-TGATATATCTT
1 TTAGGATA-TATTATTATGAGATATCTTTTAGGAATATATACATATATTG-TATATCTT
*
96285 TTAGGAATATATTATTATGAGATATTGTCTTTTAGGAATATCTACATATATTGTATATCTT
1 TTAGG-ATATATTATTATGAGATA---TCTTTTAGGAATATATACATATATTGTATATCTT
96346 TTAGGTATATATT
1 TTAGG-ATATATT
96359 TAGGAATATA
Statistics
Matches: 64, Mismatches: 3, Indels: 9
0.84 0.04 0.12
Matches are distributed among these distances:
56 20 0.31
57 3 0.05
59 15 0.23
60 2 0.03
61 22 0.34
62 2 0.03
ACGTcount: A:0.33, C:0.05, G:0.13, T:0.49
Consensus pattern (57 bp):
TTAGGATATATTATTATGAGATATCTTTTAGGAATATATACATATATTGTATATCTT
Found at i:96390 original size:31 final size:31
Alignment explanation
Indices: 96352--96417 Score: 107
Period size: 31 Copynumber: 2.2 Consensus size: 31
96342 TCTTTTAGGT
* *
96352 ATATATTTAGGAATATATTATGTATCTTTCC
1 ATATATTTAGGAATATATCATATATCTTTCC
96383 ATATATTTAGGAATATATCATATATCTTTCC
1 ATATATTTAGGAATATATCATATATCTTTCC
96414 -TATA
1 ATATA
96418 AATATTATGT
Statistics
Matches: 33, Mismatches: 2, Indels: 1
0.92 0.06 0.03
Matches are distributed among these distances:
30 4 0.12
31 29 0.88
ACGTcount: A:0.35, C:0.11, G:0.08, T:0.47
Consensus pattern (31 bp):
ATATATTTAGGAATATATCATATATCTTTCC
Found at i:96928 original size:17 final size:17
Alignment explanation
Indices: 96902--96942 Score: 64
Period size: 17 Copynumber: 2.4 Consensus size: 17
96892 TGAAACAACA
*
96902 TAAATAGGAAATTAAAT
1 TAAATTGGAAATTAAAT
96919 TAAATTGGAAATTAAAT
1 TAAATTGGAAATTAAAT
96936 TCAAATT
1 T-AAATT
96943 TTGTAATTAC
Statistics
Matches: 22, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
17 17 0.77
18 5 0.23
ACGTcount: A:0.54, C:0.02, G:0.10, T:0.34
Consensus pattern (17 bp):
TAAATTGGAAATTAAAT
Found at i:98575 original size:4 final size:4
Alignment explanation
Indices: 98566--98607 Score: 57
Period size: 4 Copynumber: 10.2 Consensus size: 4
98556 AACTTGAGCC
* *
98566 TTTA TTTA TTTA TTTA TTTT TTTGT TTTA TTTA TTTA TTTA T
1 TTTA TTTA TTTA TTTA TTTA TTT-A TTTA TTTA TTTA TTTA T
98608 GTACATTAAA
Statistics
Matches: 35, Mismatches: 2, Indels: 2
0.90 0.05 0.05
Matches are distributed among these distances:
4 31 0.89
5 4 0.11
ACGTcount: A:0.19, C:0.00, G:0.02, T:0.79
Consensus pattern (4 bp):
TTTA
Found at i:102913 original size:13 final size:13
Alignment explanation
Indices: 102894--102957 Score: 76
Period size: 13 Copynumber: 4.9 Consensus size: 13
102884 TTTGGCAATA
102894 CTTTTGAAAAGTG
1 CTTTTGAAAAGTG
*
102907 TTTTTGAAAAGTG
1 CTTTTGAAAAGTG
* *
102920 AC-ATGGAAAAGTG
1 -CTTTTGAAAAGTG
*
102933 CTTTTGAGAAGTG
1 CTTTTGAAAAGTG
102946 CTTTTGAAAAGT
1 CTTTTGAAAAGT
102958 TTGGTTTAAA
Statistics
Matches: 41, Mismatches: 8, Indels: 4
0.77 0.15 0.08
Matches are distributed among these distances:
12 1 0.02
13 40 0.98
ACGTcount: A:0.33, C:0.06, G:0.25, T:0.36
Consensus pattern (13 bp):
CTTTTGAAAAGTG
Found at i:109190 original size:36 final size:37
Alignment explanation
Indices: 109143--109215 Score: 130
Period size: 38 Copynumber: 2.0 Consensus size: 37
109133 TAAATAGAAG
109143 AAAGGAGATTG-ATTATAAACACTACTAGTATTGTGT
1 AAAGGAGATTGAATTATAAACACTACTAGTATTGTGT
109179 AAAGGAGATTGACATTATAAACACTACTAGTATTGTG
1 AAAGGAGATTGA-ATTATAAACACTACTAGTATTGTG
109216 CTTATCCCAA
Statistics
Matches: 35, Mismatches: 0, Indels: 2
0.95 0.00 0.05
Matches are distributed among these distances:
36 11 0.31
38 24 0.69
ACGTcount: A:0.40, C:0.10, G:0.19, T:0.32
Consensus pattern (37 bp):
AAAGGAGATTGAATTATAAACACTACTAGTATTGTGT
Found at i:109858 original size:22 final size:23
Alignment explanation
Indices: 109815--109862 Score: 64
Period size: 25 Copynumber: 2.1 Consensus size: 23
109805 TTAAATTGAT
109815 AAAGTTAATAAAATAAGGAAATAA
1 AAAGTTAATAAAATAA-GAAATAA
109839 AAAGTGTAATAAAAT-A-AAATAA
1 AAAGT-TAATAAAATAAGAAATAA
109861 AA
1 AA
109863 TAAGAATAGA
Statistics
Matches: 23, Mismatches: 0, Indels: 4
0.85 0.00 0.15
Matches are distributed among these distances:
22 8 0.35
24 6 0.26
25 9 0.39
ACGTcount: A:0.69, C:0.00, G:0.10, T:0.21
Consensus pattern (23 bp):
AAAGTTAATAAAATAAGAAATAA
Found at i:110496 original size:4 final size:4
Alignment explanation
Indices: 110487--110511 Score: 50
Period size: 4 Copynumber: 6.2 Consensus size: 4
110477 CTATTAGCAA
110487 ATTT ATTT ATTT ATTT ATTT ATTT A
1 ATTT ATTT ATTT ATTT ATTT ATTT A
110512 AACGAGTACT
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 21 1.00
ACGTcount: A:0.28, C:0.00, G:0.00, T:0.72
Consensus pattern (4 bp):
ATTT
Found at i:126717 original size:15 final size:15
Alignment explanation
Indices: 126697--126727 Score: 53
Period size: 15 Copynumber: 2.1 Consensus size: 15
126687 AAACCTGTAA
*
126697 AAATTAAATTAAACT
1 AAATTAAATAAAACT
126712 AAATTAAATAAAACT
1 AAATTAAATAAAACT
126727 A
1 A
126728 CTAAGTAAAA
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.65, C:0.06, G:0.00, T:0.29
Consensus pattern (15 bp):
AAATTAAATAAAACT
Found at i:128745 original size:51 final size:51
Alignment explanation
Indices: 128628--128807 Score: 168
Period size: 51 Copynumber: 3.5 Consensus size: 51
128618 GATGGTCACG
* * * * * **
128628 TGTGTAGTACTATGTGTAGGCTACTACGTGTACCGGA-A-TGATAGGTCGCA
1 TGTGTAGTACTATGTGCAGGCTACTATGCGTACCGGATAGTAATA-ATCAAA
* **
128678 TGTGTAGTACTATGTGCAGGCTACTATGCGTACCGGATAGT-TTCAATCACT
1 TGTGTAGTACTATGTGCAGGCTACTATGCGTACCGGATAGTAAT-AATCAAA
* * * * **
128729 TGTGTAGTACTATGTGCAGGCTACTACGTGTATCGGATGGTAATGGTCAAA
1 TGTGTAGTACTATGTGCAGGCTACTATGCGTACCGGATAGTAATAATCAAA
*
128780 TGTGTAGTAGTATGTGCAGGCTACTATG
1 TGTGTAGTACTATGTGCAGGCTACTATG
128808 TGAACCGAAC
Statistics
Matches: 108, Mismatches: 18, Indels: 7
0.81 0.14 0.05
Matches are distributed among these distances:
50 34 0.31
51 71 0.66
52 3 0.03
ACGTcount: A:0.24, C:0.16, G:0.28, T:0.32
Consensus pattern (51 bp):
TGTGTAGTACTATGTGCAGGCTACTATGCGTACCGGATAGTAATAATCAAA
Found at i:128867 original size:45 final size:45
Alignment explanation
Indices: 128816--128902 Score: 138
Period size: 45 Copynumber: 1.9 Consensus size: 45
128806 TGTGAACCGA
* * *
128816 ACATCATTGATTAGTAAGGTGGTTGCTATGTGCAGATTCCACCAG
1 ACATCATTGATTAATAAGGCGGTTGCTATGTGCAGAATCCACCAG
*
128861 ACATCATTGATTAATAAGGCGGTTGCTATGTGCTGAATCCAC
1 ACATCATTGATTAATAAGGCGGTTGCTATGTGCAGAATCCAC
128903 TGAGTTAGAA
Statistics
Matches: 38, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
45 38 1.00
ACGTcount: A:0.28, C:0.18, G:0.23, T:0.31
Consensus pattern (45 bp):
ACATCATTGATTAATAAGGCGGTTGCTATGTGCAGAATCCACCAG
Found at i:138098 original size:5 final size:5
Alignment explanation
Indices: 138090--138120 Score: 62
Period size: 5 Copynumber: 6.2 Consensus size: 5
138080 GCCCACATAC
138090 ATAAA ATAAA ATAAA ATAAA ATAAA ATAAA A
1 ATAAA ATAAA ATAAA ATAAA ATAAA ATAAA A
138121 CAAACCAAAT
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 26 1.00
ACGTcount: A:0.81, C:0.00, G:0.00, T:0.19
Consensus pattern (5 bp):
ATAAA
Found at i:139299 original size:16 final size:16
Alignment explanation
Indices: 139269--139306 Score: 51
Period size: 16 Copynumber: 2.4 Consensus size: 16
139259 AATTAATTGG
*
139269 TTTATT-GTTATTATT
1 TTTATTAGTCATTATT
139284 TTTATTAGTCATTATT
1 TTTATTAGTCATTATT
*
139300 ATTATTA
1 TTTATTA
139307 TTAGTCTTTT
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
15 6 0.30
16 14 0.70
ACGTcount: A:0.26, C:0.03, G:0.05, T:0.66
Consensus pattern (16 bp):
TTTATTAGTCATTATT
Found at i:139300 original size:19 final size:18
Alignment explanation
Indices: 139276--139322 Score: 67
Period size: 19 Copynumber: 2.6 Consensus size: 18
139266 TGGTTTATTG
139276 TTATTATTTTTATTAGTC
1 TTATTATTTTTATTAGTC
*
139294 ATTATTATTATTATTAGTC
1 -TTATTATTTTTATTAGTC
*
139313 TTTTTATTTT
1 TTATTATTTT
139323 ATTTTATACA
Statistics
Matches: 25, Mismatches: 3, Indels: 1
0.86 0.10 0.03
Matches are distributed among these distances:
18 8 0.32
19 17 0.68
ACGTcount: A:0.23, C:0.04, G:0.04, T:0.68
Consensus pattern (18 bp):
TTATTATTTTTATTAGTC
Found at i:140572 original size:73 final size:73
Alignment explanation
Indices: 140453--140601 Score: 253
Period size: 73 Copynumber: 2.0 Consensus size: 73
140443 TTTGAATCTT
*
140453 TTCAAAGTTTCGACACTAAGACAATAAACAATCAATTCGGTACCAATTTTGGGCGTCACGAGGGT
1 TTCAAAATTTCGACACTAAGACAATAAACAATCAATTCGGTACCAATTTTGGGCGTCACGAGGGT
140518 GCTAACCC
66 GCTAACCC
* * * *
140526 TTCAAAATTTCGACATTAAGACATTAAACAATCAATTTGGTACCAATTTTGGGCGTTACGAGGGT
1 TTCAAAATTTCGACACTAAGACAATAAACAATCAATTCGGTACCAATTTTGGGCGTCACGAGGGT
140591 GCTAACCC
66 GCTAACCC
140599 TTC
1 TTC
140602 CTCGTACGTA
Statistics
Matches: 71, Mismatches: 5, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
73 71 1.00
ACGTcount: A:0.32, C:0.21, G:0.18, T:0.28
Consensus pattern (73 bp):
TTCAAAATTTCGACACTAAGACAATAAACAATCAATTCGGTACCAATTTTGGGCGTCACGAGGGT
GCTAACCC
Found at i:146340 original size:13 final size:13
Alignment explanation
Indices: 146322--146348 Score: 54
Period size: 13 Copynumber: 2.1 Consensus size: 13
146312 ATGTGTATAC
146322 TTGCACATTCACA
1 TTGCACATTCACA
146335 TTGCACATTCACA
1 TTGCACATTCACA
146348 T
1 T
146349 ACGATAGGCT
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:0.30, G:0.07, T:0.33
Consensus pattern (13 bp):
TTGCACATTCACA
Found at i:150527 original size:51 final size:50
Alignment explanation
Indices: 150393--150585 Score: 237
Period size: 51 Copynumber: 3.8 Consensus size: 50
150383 ATTATTATCA
* *
150393 TTCGATACACGTAGTAGCCTTCACATAGTACTACATACGTGATC-AAGTT
1 TTCGATACACGTAGTAGCCTTCACATAGTACTACACACGTGACCAAAGTT
* * *
150442 TTACGGTCCACGTAGTAGCCTCCACATAGTACTACACACGTGACCAAAGCTT
1 TT-CGATACACGTAGTAGCCTTCACATAGTACTACACACGTGACCAAAG-TT
* * * * *
150494 TTCGGTACACATAGTAGCCTTCACTTAGTACTACACATGTGACCATTA-TT
1 TTCGATACACGTAGTAGCCTTCACATAGTACTACACACGTGACCA-AAGTT
*
150544 TATCGATACATGTAGTAGCCTTCACATAGTACTACACACGTG
1 T-TCGATACACGTAGTAGCCTTCACATAGTACTACACACGTG
150586 TTCATCGATA
Statistics
Matches: 123, Mismatches: 16, Indels: 8
0.84 0.11 0.05
Matches are distributed among these distances:
49 2 0.02
50 40 0.33
51 76 0.62
52 5 0.04
ACGTcount: A:0.30, C:0.25, G:0.16, T:0.29
Consensus pattern (50 bp):
TTCGATACACGTAGTAGCCTTCACATAGTACTACACACGTGACCAAAGTT
Found at i:155011 original size:18 final size:18
Alignment explanation
Indices: 154988--155025 Score: 67
Period size: 18 Copynumber: 2.1 Consensus size: 18
154978 CATTTGTTGC
154988 TCCACACAAAATTCTCAT
1 TCCACACAAAATTCTCAT
*
155006 TCCACACAAACTTCTCAT
1 TCCACACAAAATTCTCAT
155024 TC
1 TC
155026 TTTTTTAGTA
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
18 19 1.00
ACGTcount: A:0.34, C:0.37, G:0.00, T:0.29
Consensus pattern (18 bp):
TCCACACAAAATTCTCAT
Found at i:160717 original size:14 final size:14
Alignment explanation
Indices: 160674--160730 Score: 55
Period size: 14 Copynumber: 4.1 Consensus size: 14
160664 AATGTTAAGT
*
160674 AATTAAAGATAA-A
1 AATTAAAGAAAAGA
* *
160687 AATAATAAGAACA-A
1 AATTA-AAGAAAAGA
*
160701 AATTAAAGTAAAGA
1 AATTAAAGAAAAGA
160715 AATTAAAGAAAAGA
1 AATTAAAGAAAAGA
160729 AA
1 AA
160731 AATAGAAAAT
Statistics
Matches: 35, Mismatches: 7, Indels: 3
0.78 0.16 0.07
Matches are distributed among these distances:
13 9 0.26
14 26 0.74
ACGTcount: A:0.70, C:0.02, G:0.11, T:0.18
Consensus pattern (14 bp):
AATTAAAGAAAAGA
Found at i:178477 original size:15 final size:16
Alignment explanation
Indices: 178457--178489 Score: 50
Period size: 17 Copynumber: 2.1 Consensus size: 16
178447 ATTAAGGAAA
178457 AAAAT-ATCCCATAAT
1 AAAATAATCCCATAAT
178472 AAAATAAATCCCATAAT
1 AAAAT-AATCCCATAAT
178489 A
1 A
178490 TTCTCCCACT
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
15 5 0.31
17 11 0.69
ACGTcount: A:0.58, C:0.18, G:0.00, T:0.24
Consensus pattern (16 bp):
AAAATAATCCCATAAT
Found at i:181000 original size:20 final size:20
Alignment explanation
Indices: 180945--181038 Score: 75
Period size: 20 Copynumber: 4.7 Consensus size: 20
180935 TATAACAGGA
* *
180945 GCACCGAAGTGCAGACAGGG
1 GCACCGAAGTGCAAACAAGG
** *
180965 GCA-TAAATGTGAAAACAAGG
1 GCACCGAA-GTGCAAACAAGG
*
180985 GCACCGTAGTGCAAACAAGG
1 GCACCGAAGTGCAAACAAGG
* *
181005 GCACCGAAGTGTATAC-AGAG
1 GCACCGAAGTGCAAACAAG-G
*
181025 GCACCGAGGTGCAA
1 GCACCGAAGTGCAA
181039 GCATACTAAC
Statistics
Matches: 56, Mismatches: 15, Indels: 6
0.73 0.19 0.08
Matches are distributed among these distances:
19 4 0.07
20 51 0.91
21 1 0.02
ACGTcount: A:0.36, C:0.21, G:0.32, T:0.11
Consensus pattern (20 bp):
GCACCGAAGTGCAAACAAGG
Found at i:182809 original size:20 final size:21
Alignment explanation
Indices: 182770--182820 Score: 59
Period size: 20 Copynumber: 2.5 Consensus size: 21
182760 GATCATTAAG
182770 AAATTTTATTCATTAAAATA-
1 AAATTTTATTCATTAAAATAC
* **
182790 AAATTTTATTTATTTTAATAC
1 AAATTTTATTCATTAAAATAC
*
182811 AAATTCTATT
1 AAATTTTATT
182821 ACTACCTATA
Statistics
Matches: 26, Mismatches: 4, Indels: 1
0.84 0.13 0.03
Matches are distributed among these distances:
20 17 0.65
21 9 0.35
ACGTcount: A:0.43, C:0.06, G:0.00, T:0.51
Consensus pattern (21 bp):
AAATTTTATTCATTAAAATAC
Found at i:183661 original size:13 final size:13
Alignment explanation
Indices: 183641--183680 Score: 62
Period size: 13 Copynumber: 3.1 Consensus size: 13
183631 AGTTCTTCAT
183641 TACTTTTGAAAAG
1 TACTTTTGAAAAG
* *
183654 TGCTTTTGAGAAG
1 TACTTTTGAAAAG
183667 TACTTTTGAAAAG
1 TACTTTTGAAAAG
183680 T
1 T
183681 TTAGTTTAAA
Statistics
Matches: 23, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
13 23 1.00
ACGTcount: A:0.33, C:0.07, G:0.20, T:0.40
Consensus pattern (13 bp):
TACTTTTGAAAAG
Found at i:241055 original size:18 final size:18
Alignment explanation
Indices: 241034--241093 Score: 63
Period size: 18 Copynumber: 3.3 Consensus size: 18
241024 GTCATCAAAT
241034 TCATCAGATACAAGCTCA
1 TCATCAGATACAAGCTCA
*
241052 TCATCCAGATCATCAA-AT--
1 TCAT-CAGAT-A-CAAGCTCA
241070 TCATCAGATACAAGCTCA
1 TCATCAGATACAAGCTCA
241088 TCATCA
1 TCATCA
241094 TGGTCGTCAA
Statistics
Matches: 34, Mismatches: 2, Indels: 12
0.71 0.04 0.25
Matches are distributed among these distances:
15 3 0.09
16 2 0.06
17 5 0.15
18 14 0.41
19 5 0.15
20 2 0.06
21 3 0.09
ACGTcount: A:0.38, C:0.28, G:0.08, T:0.25
Consensus pattern (18 bp):
TCATCAGATACAAGCTCA
Found at i:241065 original size:36 final size:36
Alignment explanation
Indices: 241012--241117 Score: 151
Period size: 36 Copynumber: 2.9 Consensus size: 36
241002 CTTCATCAAA
* *
241012 CTCATCATCTTGGTCATCAAATTCATCAGATACAAG
1 CTCATCATCATGATCATCAAATTCATCAGATACAAG
241048 CTCATCATCCA-GATCATCAAATTCATCAGATACAAG
1 CTCATCAT-CATGATCATCAAATTCATCAGATACAAG
* * *
241084 CTCATCATCATGGTCGTCAACTTCATCAGATACA
1 CTCATCATCATGATCATCAAATTCATCAGATACA
241118 CTTTCCAATG
Statistics
Matches: 63, Mismatches: 5, Indels: 4
0.88 0.07 0.06
Matches are distributed among these distances:
35 2 0.03
36 60 0.95
37 1 0.02
ACGTcount: A:0.34, C:0.27, G:0.10, T:0.28
Consensus pattern (36 bp):
CTCATCATCATGATCATCAAATTCATCAGATACAAG
Found at i:249388 original size:18 final size:16
Alignment explanation
Indices: 249365--249409 Score: 54
Period size: 18 Copynumber: 2.7 Consensus size: 16
249355 ATCCAAACTT
249365 ATTCTCTCAATTCTCTTA
1 ATTCTCTCAATTCTC--A
*
249383 ATTCTCTAAATTCTCA
1 ATTCTCTCAATTCTCA
*
249399 ACTCTCTCAAT
1 ATTCTCTCAAT
249410 AATTTCGCTT
Statistics
Matches: 24, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
16 10 0.42
18 14 0.58
ACGTcount: A:0.27, C:0.29, G:0.00, T:0.44
Consensus pattern (16 bp):
ATTCTCTCAATTCTCA
Found at i:250318 original size:19 final size:18
Alignment explanation
Indices: 250278--250319 Score: 52
Period size: 17 Copynumber: 2.4 Consensus size: 18
250268 TGAAACCCTA
*
250278 GCGCCG-CACCTGCTCCT
1 GCGCCGCCACCTGCTACT
250295 G-GCCGCCACCTGCTACT
1 GCGCCGCCACCTGCTACT
250312 GACGCCGC
1 G-CGCCGC
250320 GTCACCTACT
Statistics
Matches: 21, Mismatches: 1, Indels: 4
0.81 0.04 0.15
Matches are distributed among these distances:
16 4 0.19
17 12 0.57
19 5 0.24
ACGTcount: A:0.10, C:0.50, G:0.26, T:0.14
Consensus pattern (18 bp):
GCGCCGCCACCTGCTACT
Found at i:251329 original size:3 final size:3
Alignment explanation
Indices: 251323--251356 Score: 68
Period size: 3 Copynumber: 11.3 Consensus size: 3
251313 AACTAATAAG
251323 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA T
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA T
251357 CTATATCTTG
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 31 1.00
ACGTcount: A:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (3 bp):
TTA
Found at i:254373 original size:18 final size:18
Alignment explanation
Indices: 254347--254389 Score: 77
Period size: 18 Copynumber: 2.4 Consensus size: 18
254337 AAAAGCTGTT
*
254347 TTTACATATATTAATAAA
1 TTTATATATATTAATAAA
254365 TTTATATATATTAATAAA
1 TTTATATATATTAATAAA
254383 TTTATAT
1 TTTATAT
254390 TTTGAATTTT
Statistics
Matches: 24, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
18 24 1.00
ACGTcount: A:0.47, C:0.02, G:0.00, T:0.51
Consensus pattern (18 bp):
TTTATATATATTAATAAA
Found at i:260065 original size:28 final size:28
Alignment explanation
Indices: 260034--260087 Score: 74
Period size: 28 Copynumber: 1.9 Consensus size: 28
260024 TTCCATTAAT
*
260034 TTATTTTA-CATTAATTAATTTAATTATG
1 TTATTTTAGCA-TAATTAATATAATTATG
*
260062 TTATTTTAGGATAATTAATATAATTA
1 TTATTTTAGCATAATTAATATAATTA
260088 GTTTAATTAA
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
28 22 0.96
29 1 0.04
ACGTcount: A:0.39, C:0.02, G:0.06, T:0.54
Consensus pattern (28 bp):
TTATTTTAGCATAATTAATATAATTATG
Found at i:264793 original size:87 final size:88
Alignment explanation
Indices: 264576--264843 Score: 333
Period size: 87 Copynumber: 3.1 Consensus size: 88
264566 GTGTGCTAAA
* * * * * * *
264576 CGATGGTCGTAAGCATCCCTTTTCATA-TTCGATGATTGTCACAATCCTTTTTCATATTTGATGG
1 CGATGGTCGTCACCATCCCTTTTCATAGTT-GATGGTTGTCACCATCCCTTTTCATAGTTGATAG
* *
264640 TCGAAACCATCTCTTTTCATTAAT
65 TCGAAACTATCCCTTTTCATTAAT
* *
264664 CGATGGTCGTCGCCATCCCTTTTAATAGTTGATGGTTGTCACCATCCCTTTTCATAGTTGATAGT
1 CGATGGTCGTCACCATCCCTTTTCATAGTTGATGGTTGTCACCATCCCTTTTCATAGTTGATAGT
*
264729 CGAAACTATCCCTTTTCA-TATT
66 CGAAACTATCCCTTTTCATTAAT
* ** * *
264751 TGATGGTCGTCACCATCCCTTTTCATAGTTGATGGTCATCACCATCCCTTTTCATAGTCGATAAT
1 CGATGGTCGTCACCATCCCTTTTCATAGTTGATGGTTGTCACCATCCCTTTTCATAGTTGATAGT
* *
264816 CAAAACTATCCCTTTTCTTTAAT
66 CGAAACTATCCCTTTTCATTAAT
*
264839 TGATG
1 CGATG
264844 CTTGTCGATA
Statistics
Matches: 156, Mismatches: 22, Indels: 4
0.86 0.12 0.02
Matches are distributed among these distances:
87 77 0.49
88 77 0.49
89 2 0.01
ACGTcount: A:0.23, C:0.24, G:0.14, T:0.40
Consensus pattern (88 bp):
CGATGGTCGTCACCATCCCTTTTCATAGTTGATGGTTGTCACCATCCCTTTTCATAGTTGATAGT
CGAAACTATCCCTTTTCATTAAT
Found at i:264807 original size:29 final size:29
Alignment explanation
Indices: 264577--264808 Score: 250
Period size: 29 Copynumber: 8.0 Consensus size: 29
264567 TGTGCTAAAC
* *
264577 GATGGTCGTAAGCATCCCTTTTCATA-TT
1 GATGGTCGTCACCATCCCTTTTCATAGTT
* * * * *
264605 CGATGATTGTCACAATCCTTTTTCATATTT
1 -GATGGTCGTCACCATCCCTTTTCATAGTT
** * * *
264635 GATGGTCGAAACCATCTCTTTTCATTAATC
1 GATGGTCGTCACCATCCCTTTTCA-TAGTT
* *
264665 GATGGTCGTCGCCATCCCTTTTAATAGTT
1 GATGGTCGTCACCATCCCTTTTCATAGTT
*
264694 GATGGTTGTCACCATCCCTTTTCATAGTT
1 GATGGTCGTCACCATCCCTTTTCATAGTT
* ** * *
264723 GATAGTCGAAACTATCCCTTTTCATATTT
1 GATGGTCGTCACCATCCCTTTTCATAGTT
264752 GATGGTCGTCACCATCCCTTTTCATAGTT
1 GATGGTCGTCACCATCCCTTTTCATAGTT
*
264781 GATGGTCATCACCATCCCTTTTCATAGT
1 GATGGTCGTCACCATCCCTTTTCATAGT
264809 CGATAATCAA
Statistics
Matches: 164, Mismatches: 37, Indels: 4
0.80 0.18 0.02
Matches are distributed among these distances:
29 140 0.85
30 24 0.15
ACGTcount: A:0.22, C:0.24, G:0.15, T:0.40
Consensus pattern (29 bp):
GATGGTCGTCACCATCCCTTTTCATAGTT
Found at i:264826 original size:29 final size:29
Alignment explanation
Indices: 264676--264832 Score: 143
Period size: 29 Copynumber: 5.4 Consensus size: 29
264666 ATGGTCGTCG
* * ****
264676 CCATCCCTTTTAATAGTTGATGGTTGTCA
1 CCATCCCTTTTCATAGTTGATAGTCAAAA
*
264705 CCATCCCTTTTCATAGTTGATAGTCGAAA
1 CCATCCCTTTTCATAGTTGATAGTCAAAA
* * * ***
264734 CTATCCCTTTTCATATTTGATGGTCGTCA
1 CCATCCCTTTTCATAGTTGATAGTCAAAA
* **
264763 CCATCCCTTTTCATAGTTGATGGTCATCA
1 CCATCCCTTTTCATAGTTGATAGTCAAAA
* *
264792 CCATCCCTTTTCATAGTCGATAATCAAAA
1 CCATCCCTTTTCATAGTTGATAGTCAAAA
*
264821 CTATCCCTTTTC
1 CCATCCCTTTTC
264833 TTTAATTGAT
Statistics
Matches: 109, Mismatches: 19, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
29 109 1.00
ACGTcount: A:0.23, C:0.26, G:0.12, T:0.39
Consensus pattern (29 bp):
CCATCCCTTTTCATAGTTGATAGTCAAAA
Found at i:266524 original size:16 final size:17
Alignment explanation
Indices: 266494--266526 Score: 50
Period size: 16 Copynumber: 2.0 Consensus size: 17
266484 TTTGGAATTA
*
266494 AAAAATATATTAAATGT
1 AAAAATATATAAAATGT
266511 AAAAAT-TATAAAATGT
1 AAAAATATATAAAATGT
266527 GAAATTTAAT
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
16 9 0.60
17 6 0.40
ACGTcount: A:0.61, C:0.00, G:0.06, T:0.33
Consensus pattern (17 bp):
AAAAATATATAAAATGT
Found at i:266815 original size:30 final size:31
Alignment explanation
Indices: 266776--266835 Score: 77
Period size: 30 Copynumber: 2.0 Consensus size: 31
266766 GGAGGTGGGA
*
266776 TGGGAAGGGAATAAAAGTTTTAAGGGAAAAG
1 TGGGAAGGGAATAAAAATTTTAAGGGAAAAG
* **
266807 TGGG-AGGGAGTAAAAATTTTGGGGGAAAA
1 TGGGAAGGGAATAAAAATTTTAAGGGAAAA
266836 TAAAAGCTTT
Statistics
Matches: 25, Mismatches: 4, Indels: 1
0.83 0.13 0.03
Matches are distributed among these distances:
30 21 0.84
31 4 0.16
ACGTcount: A:0.42, C:0.00, G:0.38, T:0.20
Consensus pattern (31 bp):
TGGGAAGGGAATAAAAATTTTAAGGGAAAAG
Found at i:269132 original size:22 final size:20
Alignment explanation
Indices: 269107--269146 Score: 53
Period size: 22 Copynumber: 1.9 Consensus size: 20
269097 AGCTAGCTGT
269107 GTACAGAGGTGCTGACGTGGAG
1 GTACAGAGGT--TGACGTGGAG
*
269129 GTACGGAGGTTGACGTGG
1 GTACAGAGGTTGACGTGG
269147 CGGTGGTGGC
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
20 8 0.47
22 9 0.53
ACGTcount: A:0.20, C:0.12, G:0.47, T:0.20
Consensus pattern (20 bp):
GTACAGAGGTTGACGTGGAG
Found at i:269675 original size:44 final size:44
Alignment explanation
Indices: 269575--270412 Score: 556
Period size: 44 Copynumber: 18.6 Consensus size: 44
269565 TTCGATCTAT
* * *
269575 TCCACTGCAACTT-TGGAGAGATAAGATTTGTTATCTTCAGTCTAC
1 TCCACTGCAACTTCAGG-GAGATAAGATTTG-TATCTTCAATCTGC
* * * *
269620 TCCACTACAACTTTAGAGAGATAAGACTTGTATCTTCAATCTGC
1 TCCACTGCAACTTCAGGGAGATAAGATTTGTATCTTCAATCTGC
* * * * * *
269664 CCCATTGCAACTTCAGGGAGATCTGATTGTAATTTGCAACCTT-AATCTGT
1 TCCACTGCAACTTCAGGGAGA--T-A-AG--ATTTG-TATCTTCAATCTGC
* * * * * *
269714 TGCACTGTAACTTCAGGGAAATAAGATTCGCTATCTTTAGTCTGC
1 TCCACTGCAACTTCAGGGAGATAAGATTTG-TATCTTCAATCTGC
* * * *
269759 TCCACTGCAACTTTAGGGAGATAAGACTTGTAACTTCAACCTGC
1 TCCACTGCAACTTCAGGGAGATAAGATTTGTATCTTCAATCTGC
* * * * * * * *
269803 TCCATTGCAACTTCAGAGAGATAAGGTTTATAGCTTTATTCTAC
1 TCCACTGCAACTTCAGGGAGATAAGATTTGTATCTTCAATCTGC
* * * **
269847 TCTACTGCAACTTCAGAGAGATAAGATTTGCTATCTTCAGTCTAT
1 TCCACTGCAACTTCAGGGAGATAAGATTTG-TATCTTCAATCTGC
** * * * * * *
269892 TCCACTAAAAATTTAGGGAGATAAGACTTGTAACTTCAACCTAC
1 TCCACTGCAACTTCAGGGAGATAAGATTTGTATCTTCAATCTGC
* * * * * *
269936 TCCACTGTAACTTCAGGGAGATAAGGTTTATAGCTTTATTCTGC
1 TCCACTGCAACTTCAGGGAGATAAGATTTGTATCTTCAATCTGC
* ** * **
269980 TCTACTGCAACTTCAAAGAGATAAGATTTGCTATCTTCAGTCTAT
1 TCCACTGCAACTTCAGGGAGATAAGATTTG-TATCTTCAATCTGC
* * *
270025 TCCACTACAACTTCAGGGAGATAAGACTTGTAACTTCAA-CATGC
1 TCCACTGCAACTTCAGGGAGATAAGATTTGTATCTTCAATC-TGC
* * * * *
270069 TCCACTGCAACTTCAGGGAGATAAGGTTTATAACTTTATTCTGC
1 TCCACTGCAACTTCAGGGAGATAAGATTTGTATCTTCAATCTGC
* * * **
270113 TCTACTGCAACTTCAGAGAGATAAGATTTGCTATCTTCAGTCTAT
1 TCCACTGCAACTTCAGGGAGATAAGATTTG-TATCTTCAATCTGC
* * *
270158 TCCACTACAACTTCAGGGAGATAAGACTTGTAACTT--ATACATGC
1 TCCACTGCAACTTCAGGGAGATAAGATTTGTATCTTCAAT-C-TGC
* * * *
270202 TCCACTGCAACTTCAGGGAGATAAGATTTATAGCTTTATTCTGC
1 TCCACTGCAACTTCAGGGAGATAAGATTTGTATCTTCAATCTGC
* * * **
270246 -CTTACTGCAACTTCAGAGAGATAAGATTTGCAATTTATAGCTTTAATCTAT
1 TC-CACTGCAACTTCAGGGAGATAAGATTTG-----TAT--CTTCAATCTGC
* * * * *
270297 TCCACTACAACTTTAGGGAAATAAGATTCGCTATCTTCAGTC-GC
1 TCCACTGCAACTTCAGGGAGATAAGATTTG-TATCTTCAATCTGC
* * * * ** *
270341 TTCACTGCAACTTTAGGGAGATAAGACTAGTGGCTTCAATATGC
1 TCCACTGCAACTTCAGGGAGATAAGATTTGTATCTTCAATCTGC
*
270385 TTCACTGCAACTTCAGGGAGATAAGATT
1 TCCACTGCAACTTCAGGGAGATAAGATT
270413 CACTATGATG
Statistics
Matches: 609, Mismatches: 156, Indels: 57
0.74 0.19 0.07
Matches are distributed among these distances:
42 1 0.00
43 10 0.02
44 361 0.59
45 163 0.27
46 4 0.01
47 5 0.01
48 2 0.00
49 2 0.00
50 26 0.04
51 34 0.06
52 1 0.00
ACGTcount: A:0.30, C:0.21, G:0.17, T:0.32
Consensus pattern (44 bp):
TCCACTGCAACTTCAGGGAGATAAGATTTGTATCTTCAATCTGC
Found at i:269913 original size:133 final size:133
Alignment explanation
Indices: 269578--270365 Score: 974
Period size: 133 Copynumber: 5.8 Consensus size: 133
269568 GATCTATTCC
** * * *
269578 ACTGCAACTTTGGAGAGATAAGATTTGTTATCTTCAGTCTACTCCACTACAACTTTAGAGAGATA
1 ACTGCAACTTCAGAGAGATAAGATTTGCTATCTTCAGTCTATTCCACTACAACTTTAGGGAGATA
* * * * ** * * *
269643 AGACTTGTATCTTCAATCTGCCCCATTGCAACTTCAGGGAGATCTGATTGTAATTTGCAACCTTA
66 AGACTTGTAACTTCAACCTGCTCCACTGCAACTTCAGGGAGATAAGGTT-T-A--T--AGCTTTA
* *
269708 ATCTGTTGC-
125 TTCTGCT-CT
* * * * * ** *
269717 ACTGTAACTTCAGGGAAATAAGATTCGCTATCTTTAGTCTGCTCCACTGCAACTTTAGGGAGATA
1 ACTGCAACTTCAGAGAGATAAGATTTGCTATCTTCAGTCTATTCCACTACAACTTTAGGGAGATA
* * *
269782 AGACTTGTAACTTCAACCTGCTCCATTGCAACTTCAGAGAGATAAGGTTTATAGCTTTATTCTAC
66 AGACTTGTAACTTCAACCTGCTCCACTGCAACTTCAGGGAGATAAGGTTTATAGCTTTATTCTGC
269847 TCT
131 TCT
* *
269850 ACTGCAACTTCAGAGAGATAAGATTTGCTATCTTCAGTCTATTCCACTAAAAATTTAGGGAGATA
1 ACTGCAACTTCAGAGAGATAAGATTTGCTATCTTCAGTCTATTCCACTACAACTTTAGGGAGATA
* *
269915 AGACTTGTAACTTCAACCTACTCCACTGTAACTTCAGGGAGATAAGGTTTATAGCTTTATTCTGC
66 AGACTTGTAACTTCAACCTGCTCCACTGCAACTTCAGGGAGATAAGGTTTATAGCTTTATTCTGC
269980 TCT
131 TCT
* *
269983 ACTGCAACTTCAAAGAGATAAGATTTGCTATCTTCAGTCTATTCCACTACAACTTCAGGGAGATA
1 ACTGCAACTTCAGAGAGATAAGATTTGCTATCTTCAGTCTATTCCACTACAACTTTAGGGAGATA
* *
270048 AGACTTGTAACTTCAACATGCTCCACTGCAACTTCAGGGAGATAAGGTTTATAACTTTATTCTGC
66 AGACTTGTAACTTCAACCTGCTCCACTGCAACTTCAGGGAGATAAGGTTTATAGCTTTATTCTGC
270113 TCT
131 TCT
*
270116 ACTGCAACTTCAGAGAGATAAGATTTGCTATCTTCAGTCTATTCCACTACAACTTCAGGGAGATA
1 ACTGCAACTTCAGAGAGATAAGATTTGCTATCTTCAGTCTATTCCACTACAACTTTAGGGAGATA
* *
270181 AGACTTGTAACTT-ATACATGCTCCACTGCAACTTCAGGGAGATAAGATTTATAGCTTTATTCTG
66 AGACTTGTAACTTCA-ACCTGCTCCACTGCAACTTCAGGGAGATAAGGTTTATAGCTTTATTCTG
270245 C-CTT
130 CTC-T
* *
270249 ACTGCAACTTCAGAGAGATAAGATTTGCAATTTATAGCTTTAATCTATTCCACTACAACTTTAGG
1 ACTGCAACTTCAGAGAGATAAGATTTGC----TAT--CTTCAGTCTATTCCACTACAACTTTAGG
* * ** * *
270314 GAAATAAGA-TTCGCTATCTTCAGTC-GCTTCACTGCAACTTTAGGGAGATAAG
60 GAGATAAGACTT-G-TAACTTCAACCTGCTCCACTGCAACTTCAGGGAGATAAG
270366 ACTAGTGGCT
Statistics
Matches: 578, Mismatches: 59, Indels: 24
0.87 0.09 0.04
Matches are distributed among these distances:
132 3 0.01
133 406 0.70
135 1 0.00
137 4 0.01
138 3 0.01
139 155 0.27
140 5 0.01
141 1 0.00
ACGTcount: A:0.30, C:0.21, G:0.17, T:0.33
Consensus pattern (133 bp):
ACTGCAACTTCAGAGAGATAAGATTTGCTATCTTCAGTCTATTCCACTACAACTTTAGGGAGATA
AGACTTGTAACTTCAACCTGCTCCACTGCAACTTCAGGGAGATAAGGTTTATAGCTTTATTCTGC
TCT
Found at i:269937 original size:89 final size:89
Alignment explanation
Indices: 269575--270412 Score: 442
Period size: 89 Copynumber: 9.3 Consensus size: 89
269565 TTCGATCTAT
* * * * *
269575 TCCACTGCAACTT-TGGAGAGATAAGATTTGTTATCTTCAGTCTACTCCACTACAACTTTAGAGA
1 TCCACTGCAACTTCAGG-GAGATAAGATTTGCTATCTTCAGTCTATTCCACTACAACTTCAGGGA
* * *
269639 GATAAGACTTGTATCTTCAATCTGC
65 GATAAGACTTGTAACTTCAACCTAC
* * * * * * * * **
269664 CCCATTGCAACTTCAGGGAGATCTGATTGTAATTTGCAACCTT-AATCTGTTGCACTGTAACTTC
1 TCCACTGCAACTTCAGGGAGA--T-A-AG--ATTTGCTATCTTCAGTCTATTCCACTACAACTTC
* * * ** *
269728 AGGGAAATAAGA-TTCGCTATCTTTAGTCTGC
60 AGGGAGATAAGACTT-G-TAACTTCAACCTAC
* * * ** ** * * *
269759 TCCACTGCAACTTTAGGGAGATAAGACTTG-TAACTTCAACCTGCTCCATTGCAACTTCAGAGAG
1 TCCACTGCAACTTCAGGGAGATAAGATTTGCTATCTTCAGTCTATTCCACTACAACTTCAGGGAG
** * * * **
269823 ATAAGGTTTATAGCTTTATTCTAC
66 ATAAGACTTGTAACTTCAACCTAC
* * * * *
269847 TCTACTGCAACTTCAGAGAGATAAGATTTGCTATCTTCAGTCTATTCCACTAAAAATTTAGGGAG
1 TCCACTGCAACTTCAGGGAGATAAGATTTGCTATCTTCAGTCTATTCCACTACAACTTCAGGGAG
269912 ATAAGACTTGTAACTTCAACCTAC
66 ATAAGACTTGTAACTTCAACCTAC
* * * * * * ** * * **
269936 TCCACTGTAACTTCAGGGAGATAAGGTTT-ATAGCTTTATTCTGCTCTACTGCAACTTCAAAGAG
1 TCCACTGCAACTTCAGGGAGATAAGATTTGCTATCTTCAGTCTATTCCACTACAACTTCAGGGAG
* * ** *
270000 ATAAGATTTGCTATCTTCAGTCTAT
66 ATAAGACTTG-TAACTTCAACCTAC
* * * * *
270025 TCCACTACAACTTCAGGGAGATAAGACTTG-TAACTTCA-AC-ATGCTCCACTGCAACTTCAGGG
1 TCCACTGCAACTTCAGGGAGATAAGATTTGCTATCTTCAGTCTAT--TCCACTACAACTTCAGGG
** * * ** *
270087 AGATAAGGTTTATAACTTTATTCTGC
64 AGATAAGACTTGTAACTTCAACCTAC
* *
270113 TCTACTGCAACTTCAGAGAGATAAGATTTGCTATCTTCAGTCTATTCCACTACAACTTCAGGGAG
1 TCCACTGCAACTTCAGGGAGATAAGATTTGCTATCTTCAGTCTATTCCACTACAACTTCAGGGAG
* *
270178 ATAAGACTTGTAACTT-ATACATGC
66 ATAAGACTTGTAACTTCA-ACCTAC
* * * * * * *
270202 TCCACTGCAACTTCAGGGAGATAAGATTT-ATAGCTTTA-T-TCTGCCTTACTGCAACTTCAGAG
1 TCCACTGCAACTTCAGGGAGATAAGATTTGCTATCTTCAGTCTATTCC--ACTACAACTTCAGGG
* * * *
270264 AGATAAGATTTGCAATTTATAGCTTTAATCTAT
64 AGATAAGACTTG-----TA-A-CTTCAACCTAC
* * * * ** * *
270297 TCCACTACAACTTTAGGGAAATAAGATTCGCTATCTTCAGTCGCTT-CACTGCAACTTTAGGGAG
1 TCCACTGCAACTTCAGGGAGATAAGATTTGCTATCTTCAGTCTATTCCACTACAACTTCAGGGAG
* ** ** *
270361 ATAAGACTAGTGGCTTCAATATGC
66 ATAAGACTTGTAACTTCAACCTAC
*
270385 TTCACTGCAACTTCAGGGAGATAAGATT
1 TCCACTGCAACTTCAGGGAGATAAGATT
270413 CACTATGATG
Statistics
Matches: 566, Mismatches: 150, Indels: 67
0.72 0.19 0.09
Matches are distributed among these distances:
86 4 0.01
87 1 0.00
88 170 0.30
89 244 0.43
90 6 0.01
91 4 0.01
92 2 0.00
93 6 0.01
94 26 0.05
95 92 0.16
96 7 0.01
97 2 0.00
98 2 0.00
ACGTcount: A:0.30, C:0.21, G:0.17, T:0.32
Consensus pattern (89 bp):
TCCACTGCAACTTCAGGGAGATAAGATTTGCTATCTTCAGTCTATTCCACTACAACTTCAGGGAG
ATAAGACTTGTAACTTCAACCTAC
Found at i:270428 original size:50 final size:48
Alignment explanation
Indices: 270027--270463 Score: 149
Period size: 44 Copynumber: 9.6 Consensus size: 48
270017 CAGTCTATTC
* * * *
270027 CACTACAACTTCAGGGAGATAAG---ACTTGTAACTTCAA-CATGCTC
1 CACTGCAACTTCAGGGAGATAAGATTACTAGTGACTTCAATCATGCTT
* * * *
270071 CACTGCAACTTCAGGGAGATAAGGTT--TA-TAACTTTATTC-TGC-T
1 CACTGCAACTTCAGGGAGATAAGATTACTAGTGACTTCAATCATGCTT
* * * *
270114 CTACTGCAACTTCAGAGAGATAAGATTTGCTA-T--CTTCAGTCTAT--TC
1 C-ACTGCAACTTCAGGGAGATAAGA-TTACTAGTGACTTCAATC-ATGCTT
* * * *
270160 CACTACAACTTCAGGGAGATAAG---ACTTGTAACTT--ATACATGCTC
1 CACTGCAACTTCAGGGAGATAAGATTACTAGTGACTTCAAT-CATGCTT
* *
270204 CACTGCAACTTCAGGGAGATAAGATT--TA-T-AGCTTTATTC-TGCCTT
1 CACTGCAACTTCAGGGAGATAAGATTACTAGTGA-CTTCAATCATG-CTT
* * * * * * *
270249 -ACTGCAACTTCAGAGAGATAAGATTTGCAATTTATAGCTTTAATCTAT--TC
1 CACTGCAACTTCAGGGAGATAAGA-TTACTA-GT-GA-CTTCAATC-ATGCTT
* * * * *
270299 CACTACAACTTTAGGGAAATAAGATTCGCTA-T--CTTCAGTC--GCTT
1 CACTGCAACTTCAGGGAGATAAGATT-ACTAGTGACTTCAATCATGCTT
* *
270343 CACTGCAACTTTAGGGAGATAAG---ACTAGTGGCTTCAAT-ATGCTT
1 CACTGCAACTTCAGGGAGATAAGATTACTAGTGACTTCAATCATGCTT
*
270387 CACTGCAACTTCAGGGAGATAAGATTCACTATGATGACTTCAATCCAT-C-C
1 CACTGCAACTTCAGGGAGATAAGATT-ACTA-G-TGACTTCAAT-CATGCTT
* *
270437 CACTGCAACTTCAGGGATATAGGATTA
1 CACTGCAACTTCAGGGAGATAAGATTA
270464 GTGGCTTCAT
Statistics
Matches: 303, Mismatches: 40, Indels: 95
0.69 0.09 0.22
Matches are distributed among these distances:
40 3 0.01
41 3 0.01
42 4 0.01
43 9 0.03
44 156 0.51
45 42 0.14
46 2 0.01
47 5 0.02
48 4 0.01
49 4 0.01
50 36 0.12
51 32 0.11
52 2 0.01
53 1 0.00
ACGTcount: A:0.31, C:0.21, G:0.17, T:0.31
Consensus pattern (48 bp):
CACTGCAACTTCAGGGAGATAAGATTACTAGTGACTTCAATCATGCTT
Found at i:277687 original size:14 final size:14
Alignment explanation
Indices: 277668--277695 Score: 56
Period size: 14 Copynumber: 2.0 Consensus size: 14
277658 GAACTTTGGA
277668 TTATTTAATTATTT
1 TTATTTAATTATTT
277682 TTATTTAATTATTT
1 TTATTTAATTATTT
277696 ATTTTTTGGT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 14 1.00
ACGTcount: A:0.29, C:0.00, G:0.00, T:0.71
Consensus pattern (14 bp):
TTATTTAATTATTT
Found at i:278724 original size:37 final size:37
Alignment explanation
Indices: 278683--278758 Score: 125
Period size: 37 Copynumber: 2.1 Consensus size: 37
278673 TTTTCGCAAA
278683 ATATCAAAAATTTTCCAAGGTGCAGGGGACACACACC
1 ATATCAAAAATTTTCCAAGGTGCAGGGGACACACACC
* * *
278720 ATATCAAAATTTTTCCAAGGTGTAGGGGACACACGCC
1 ATATCAAAAATTTTCCAAGGTGCAGGGGACACACACC
278757 AT
1 AT
278759 TGTGGCCAGG
Statistics
Matches: 36, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
37 36 1.00
ACGTcount: A:0.36, C:0.22, G:0.20, T:0.22
Consensus pattern (37 bp):
ATATCAAAAATTTTCCAAGGTGCAGGGGACACACACC
Found at i:281401 original size:27 final size:27
Alignment explanation
Indices: 281363--282022 Score: 929
Period size: 27 Copynumber: 24.6 Consensus size: 27
281353 CGAAAAGGTT
281363 GTAAAATGACCGTAATACCCCTGTAGG
1 GTAAAATGACCGTAATACCCCTGTAGG
*
281390 GTAAAATGACCGTAACACCCCTGTA-G
1 GTAAAATGACCGTAATACCCCTGTAGG
*
281416 GTAAACTGACCGTAATACCCCTGTAGG
1 GTAAAATGACCGTAATACCCCTGTAGG
* * *
281443 ATAAAATGATCGTAATACCTCTGTAGG
1 GTAAAATGACCGTAATACCCCTGTAGG
*
281470 ATAAAATGACCGTAATACCCCTGTAGG
1 GTAAAATGACCGTAATACCCCTGTAGG
* *
281497 GTAAAATGACCATAATACCTCTGTAGG
1 GTAAAATGACCGTAATACCCCTGTAGG
*
281524 GTAAAATGACCGTAATACCTCTGTAGG
1 GTAAAATGACCGTAATACCCCTGTAGG
*
281551 GTAAAATAACCGTAATA-CCCTGTAGG
1 GTAAAATGACCGTAATACCCCTGTAGG
* *
281577 GTAAAATGACCATAATACCTCTGTAGG
1 GTAAAATGACCGTAATACCCCTGTAGG
*
281604 GTAAAATGACCGTAATACCTCTGTAGG
1 GTAAAATGACCGTAATACCCCTGTAGG
*
281631 ATAAAATGACCGTAATACCCCTGTAGG
1 GTAAAATGACCGTAATACCCCTGTAGG
* *
281658 GTAAAATGACCATAATACCTCTGTAGG
1 GTAAAATGACCGTAATACCCCTGTAGG
* *
281685 GTAAAATGGACC-TAAT--CCCTATATCTG
1 GTAAAAT-GACCGTAATACCCCTGTA--GG
*
281712 GTAAAATAACCGTAATA-CCCTGTAGG
1 GTAAAATGACCGTAATACCCCTGTAGG
*
281738 GTAAAATGACCGTAATACCCCTATAGG
1 GTAAAATGACCGTAATACCCCTGTAGG
* *
281765 GTAGAATGACCGTAATGCCCCTGTAGG
1 GTAAAATGACCGTAATACCCCTGTAGG
* *
281792 GTAAAATAACCGTAATACCTCTGTAGG
1 GTAAAATGACCGTAATACCCCTGTAGG
* *
281819 ATAAAATGATCGTAATACCCCTGTAGG
1 GTAAAATGACCGTAATACCCCTGTAGG
* *
281846 GTAAAATGACCATAATACCTCTGTAGG
1 GTAAAATGACCGTAATACCCCTGTAGG
281873 GTAAAATGACCGTAATA-CCCTGTAGG
1 GTAAAATGACCGTAATACCCCTGTAGG
* *
281899 GTAAAATAACCGTAATACCCTTGTAGG
1 GTAAAATGACCGTAATACCCCTGTAGG
* *
281926 GTAGAATGACCGTAATGCCCCTGTAGG
1 GTAAAATGACCGTAATACCCCTGTAGG
*
281953 GTAAAATGACCGTAATACCCCTATAGG
1 GTAAAATGACCGTAATACCCCTGTAGG
* *
281980 GTAAAATAACCGTAATACCACTGTAGG
1 GTAAAATGACCGTAATACCCCTGTAGG
282007 GTAAAATGACCGTAAT
1 GTAAAATGACCGTAAT
282023 GCCCTAGTGG
Statistics
Matches: 562, Mismatches: 62, Indels: 18
0.88 0.10 0.03
Matches are distributed among these distances:
25 5 0.01
26 91 0.16
27 456 0.81
28 10 0.02
ACGTcount: A:0.35, C:0.20, G:0.20, T:0.24
Consensus pattern (27 bp):
GTAAAATGACCGTAATACCCCTGTAGG
Found at i:281603 original size:134 final size:135
Alignment explanation
Indices: 281363--282022 Score: 965
Period size: 134 Copynumber: 4.9 Consensus size: 135
281353 CGAAAAGGTT
* * *
281363 GTAAAATGACCGTAATACCCCTGTAGGGTAAAATGACCGTAACACCCCTGTA-GGTAAACTGACC
1 GTAAAATGACCGTAATACCCCTGTAGGGTAAAATGACCGTAATACCTCTGTAGGGTAAAATGACC
* * *
281427 GTAATACCCCTGTAGGATAAAATGATCGTAATACCTCTGTAGGATAAAATGACCGTAATACCCCT
66 GTAATACCCCTGTAGGGTAAAATGACCGTAATACCTCTGTAGGGTAAAATGACCGTAATACCCCT
281492 GTAGG
131 GTAGG
* * *
281497 GTAAAATGACCATAATACCTCTGTAGGGTAAAATGACCGTAATACCTCTGTAGGGTAAAATAACC
1 GTAAAATGACCGTAATACCCCTGTAGGGTAAAATGACCGTAATACCTCTGTAGGGTAAAATGACC
* *
281562 GTAATA-CCCTGTAGGGTAAAATGACCATAATACCTCTGTAGGGTAAAATGACCGTAATACCTCT
66 GTAATACCCCTGTAGGGTAAAATGACCGTAATACCTCTGTAGGGTAAAATGACCGTAATACCCCT
281626 GTAGG
131 GTAGG
* *
281631 ATAAAATGACCGTAATACCCCTGTAGGGTAAAATGACCATAATACCTCTGTAGGGTAAAATGGAC
1 GTAAAATGACCGTAATACCCCTGTAGGGTAAAATGACCGTAATACCTCTGTAGGGTAAAAT-GAC
* * *
281696 C-TAAT--CCCTATATCTGGTAAAATAACCGTAATACC-CTGTAGGGTAAAATGACCGTAATACC
65 CGTAATACCCCTGTA--GGGTAAAATGACCGTAATACCTCTGTAGGGTAAAATGACCGTAATACC
*
281757 CCTATAGG
128 CCTGTAGG
* * * * *
281765 GTAGAATGACCGTAATGCCCCTGTAGGGTAAAATAACCGTAATACCTCTGTAGGATAAAATGATC
1 GTAAAATGACCGTAATACCCCTGTAGGGTAAAATGACCGTAATACCTCTGTAGGGTAAAATGACC
*
281830 GTAATACCCCTGTAGGGTAAAATGACCATAATACCTCTGTAGGGTAAAATGACCGTAATA-CCCT
66 GTAATACCCCTGTAGGGTAAAATGACCGTAATACCTCTGTAGGGTAAAATGACCGTAATACCCCT
281894 GTAGG
131 GTAGG
* * * * *
281899 GTAAAATAACCGTAATACCCTTGTAGGGTAGAATGACCGTAATGCCCCTGTAGGGTAAAATGACC
1 GTAAAATGACCGTAATACCCCTGTAGGGTAAAATGACCGTAATACCTCTGTAGGGTAAAATGACC
* * *
281964 GTAATACCCCTATAGGGTAAAATAACCGTAATACCACTGTAGGGTAAAATGACCGTAAT
66 GTAATACCCCTGTAGGGTAAAATGACCGTAATACCTCTGTAGGGTAAAATGACCGTAAT
282023 GCCCTAGTGG
Statistics
Matches: 470, Mismatches: 48, Indels: 16
0.88 0.09 0.03
Matches are distributed among these distances:
133 9 0.02
134 394 0.84
135 61 0.13
136 6 0.01
ACGTcount: A:0.35, C:0.20, G:0.20, T:0.24
Consensus pattern (135 bp):
GTAAAATGACCGTAATACCCCTGTAGGGTAAAATGACCGTAATACCTCTGTAGGGTAAAATGACC
GTAATACCCCTGTAGGGTAAAATGACCGTAATACCTCTGTAGGGTAAAATGACCGTAATACCCCT
GTAGG
Found at i:281628 original size:161 final size:161
Alignment explanation
Indices: 281363--282022 Score: 964
Period size: 161 Copynumber: 4.1 Consensus size: 161
281353 CGAAAAGGTT
* * * *
281363 GTAAAATGACCGTAATACCCCTGTAGGGTAAAATGACCGTAACACCCCTGTA-GGTAAACTGACC
1 GTAAAATGACCGTAATACCTCTGTAGGGTAAAATAACCGTAATA-CCCTGTAGGGTAAAATGACC
* * *
281427 GTAATACCCCTGTAGGATAAAATGATCGTAATACCTCTGTAGGATAAAATGACCGTAATACCCCT
65 GTAATACCCCTGTAGGGTAAAATGACCGTAATACCCCTGTAGGATAAAATGACCGTAATACCCCT
281492 GTAGGGTAAAATGACCATAATACCTCTGTAGG
130 GTAGGGTAAAATGACCATAATACCTCTGTAGG
*
281524 GTAAAATGACCGTAATACCTCTGTAGGGTAAAATAACCGTAATACCCTGTAGGGTAAAATGACCA
1 GTAAAATGACCGTAATACCTCTGTAGGGTAAAATAACCGTAATACCCTGTAGGGTAAAATGACCG
* *
281589 TAATACCTCTGTAGGGTAAAATGACCGTAATACCTCTGTAGGATAAAATGACCGTAATACCCCTG
66 TAATACCCCTGTAGGGTAAAATGACCGTAATACCCCTGTAGGATAAAATGACCGTAATACCCCTG
281654 TAGGGTAAAATGACCATAATACCTCTGTAGG
131 TAGGGTAAAATGACCATAATACCTCTGTAGG
* * * **
281685 GTAAAATGGACC-TAATCCCTATATCTGGTAAAATAACCGTAATACCCTGTAGGGTAAAATGACC
1 GTAAAAT-GACCGTAATACCTCTGTAGGGTAAAATAACCGTAATACCCTGTAGGGTAAAATGACC
* * * * * *
281749 GTAATACCCCTATAGGGTAGAATGACCGTAATGCCCCTGTAGGGTAAAATAACCGTAATACCTCT
65 GTAATACCCCTGTAGGGTAAAATGACCGTAATACCCCTGTAGGATAAAATGACCGTAATACCCCT
* * * *
281814 GTAGGATAAAATGATCGTAATACCCCTGTAGG
130 GTAGGGTAAAATGACCATAATACCTCTGTAGG
* * *
281846 GTAAAATGACCATAATACCTCTGTAGGGTAAAATGACCGTAATACCCTGTAGGGTAAAATAACCG
1 GTAAAATGACCGTAATACCTCTGTAGGGTAAAATAACCGTAATACCCTGTAGGGTAAAATGACCG
* * * * *
281911 TAATACCCTTGTAGGGTAGAATGACCGTAATGCCCCTGTAGGGTAAAATGACCGTAATACCCCTA
66 TAATACCCCTGTAGGGTAAAATGACCGTAATACCCCTGTAGGATAAAATGACCGTAATACCCCTG
* * *
281976 TAGGGTAAAATAACCGTAATACCACTGTAGG
131 TAGGGTAAAATGACCATAATACCTCTGTAGG
282007 GTAAAATGACCGTAAT
1 GTAAAATGACCGTAAT
282023 GCCCTAGTGG
Statistics
Matches: 453, Mismatches: 43, Indels: 6
0.90 0.09 0.01
Matches are distributed among these distances:
160 11 0.02
161 438 0.97
162 4 0.01
ACGTcount: A:0.35, C:0.20, G:0.20, T:0.24
Consensus pattern (161 bp):
GTAAAATGACCGTAATACCTCTGTAGGGTAAAATAACCGTAATACCCTGTAGGGTAAAATGACCG
TAATACCCCTGTAGGGTAAAATGACCGTAATACCCCTGTAGGATAAAATGACCGTAATACCCCTG
TAGGGTAAAATGACCATAATACCTCTGTAGG
Found at i:282161 original size:24 final size:24
Alignment explanation
Indices: 282092--282156 Score: 112
Period size: 24 Copynumber: 2.7 Consensus size: 24
282082 TTAAATGGCA
282092 GATTTGTTTGTGTTTGGTATGATT
1 GATTTGTTTGTGTTTGGTATGATT
*
282116 GATTTGTCTGTGTTTGGTATGATT
1 GATTTGTTTGTGTTTGGTATGATT
282140 GATTTGTTTGTGATTTG
1 GATTTGTTTGTG-TTTG
282157 AATGACTAAT
Statistics
Matches: 38, Mismatches: 2, Indels: 1
0.93 0.05 0.02
Matches are distributed among these distances:
24 34 0.89
25 4 0.11
ACGTcount: A:0.12, C:0.02, G:0.29, T:0.57
Consensus pattern (24 bp):
GATTTGTTTGTGTTTGGTATGATT
Found at i:282278 original size:27 final size:27
Alignment explanation
Indices: 282235--282294 Score: 88
Period size: 27 Copynumber: 2.2 Consensus size: 27
282225 GGATGTACTG
282235 TACTGGTGGCTCTGCCACA-ATCACTAT
1 TACTGGTGGCTCTGCCACATAT-ACTAT
282262 TACTGGTGGCT-TGGCCACATATACTAT
1 TACTGGTGGCTCT-GCCACATATACTAT
282289 TACTGG
1 TACTGG
282295 CAGCTTTGTT
Statistics
Matches: 31, Mismatches: 0, Indels: 4
0.89 0.00 0.11
Matches are distributed among these distances:
26 1 0.03
27 28 0.90
28 2 0.06
ACGTcount: A:0.22, C:0.25, G:0.22, T:0.32
Consensus pattern (27 bp):
TACTGGTGGCTCTGCCACATATACTAT
Found at i:282300 original size:27 final size:27
Alignment explanation
Indices: 282248--282300 Score: 72
Period size: 27 Copynumber: 2.0 Consensus size: 27
282238 TGGTGGCTCT
**
282248 GCCACAATCACTATTACTGGTGGCTTG
1 GCCACAATCACTATTACTGGCAGCTTG
282275 GCCACATAT-ACTATTACTGGCAGCTT
1 GCCACA-ATCACTATTACTGGCAGCTT
282301 TGTTGTGATA
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
27 21 0.91
28 2 0.09
ACGTcount: A:0.25, C:0.26, G:0.19, T:0.30
Consensus pattern (27 bp):
GCCACAATCACTATTACTGGCAGCTTG
Found at i:282379 original size:32 final size:32
Alignment explanation
Indices: 282338--282508 Score: 191
Period size: 32 Copynumber: 5.4 Consensus size: 32
282328 GCTGCGATGC
282338 TACTGATGGCTTTGTGCCGATCATATTACCGT
1 TACTGATGGCTTTGTGCCGATCATATTACCGT
*
282370 TACTGATGGCTTTGTGTCGATCATATTACCGT
1 TACTGATGGCTTTGTGCCGATCATATTACCGT
* *
282402 TACTGATGGCTTTGTGCCGGTCATATTACCAT
1 TACTGATGGCTTTGTGCCGATCATATTACCGT
* * * * * * ** *
282434 TACTAATGACTGTGCGTCGATCATATCAATGC
1 TACTGATGGCTTTGTGCCGATCATATTACCGT
* * *
282466 TACTAATGGCTTTGTGCCAATCATATTACTG-
1 TACTGATGGCTTTGTGCCGATCATATTACCGT
*
282497 TACTTATGGCTT
1 TACTGATGGCTT
282509 GTAGCCATTC
Statistics
Matches: 116, Mismatches: 23, Indels: 1
0.83 0.16 0.01
Matches are distributed among these distances:
31 11 0.09
32 105 0.91
ACGTcount: A:0.22, C:0.20, G:0.20, T:0.38
Consensus pattern (32 bp):
TACTGATGGCTTTGTGCCGATCATATTACCGT
Found at i:282417 original size:64 final size:64
Alignment explanation
Indices: 282336--282508 Score: 213
Period size: 64 Copynumber: 2.7 Consensus size: 64
282326 TTGCTGCGAT
* * * *
282336 GCTACTGATGGCTTTGTGCCGATCATATTACCGTTACTGATGGCTTTGTGTCGATCATATTACC
1 GCTACTGATGGCTTTGTGCCGATCATATTACCGTTACTAATGGCTTTGCGTCGATCATATCAAC
* * * * * *
282400 GTTACTGATGGCTTTGTGCCGGTCATATTACCATTACTAATGACTGTGCGTCGATCATATCAAT
1 GCTACTGATGGCTTTGTGCCGATCATATTACCGTTACTAATGGCTTTGCGTCGATCATATCAAC
* * * *
282464 GCTACTAATGGCTTTGTGCCAATCATATTACTG-TACTTATGGCTT
1 GCTACTGATGGCTTTGTGCCGATCATATTACCGTTACTAATGGCTT
282509 GTAGCCATTC
Statistics
Matches: 90, Mismatches: 19, Indels: 1
0.82 0.17 0.01
Matches are distributed among these distances:
63 9 0.10
64 81 0.90
ACGTcount: A:0.21, C:0.21, G:0.20, T:0.38
Consensus pattern (64 bp):
GCTACTGATGGCTTTGTGCCGATCATATTACCGTTACTAATGGCTTTGCGTCGATCATATCAAC
Found at i:282525 original size:22 final size:21
Alignment explanation
Indices: 282500--282564 Score: 67
Period size: 22 Copynumber: 3.0 Consensus size: 21
282490 ATTACTGTAC
282500 TTATGGCTTGTAGCCATTCTGT
1 TTATGGCTT-TAGCCATTCTGT
* ** *
282522 TTATAGCTTATAGCTGTCCTGT
1 TTATGGCTT-TAGCCATTCTGT
282544 TTATGGCTCTTAGCCATTCTG
1 TTATGGCT-TTAGCCATTCTG
282565 GCTACTGGTA
Statistics
Matches: 33, Mismatches: 9, Indels: 2
0.75 0.20 0.05
Matches are distributed among these distances:
22 32 0.97
23 1 0.03
ACGTcount: A:0.15, C:0.20, G:0.20, T:0.45
Consensus pattern (21 bp):
TTATGGCTTTAGCCATTCTGT
Found at i:282723 original size:27 final size:27
Alignment explanation
Indices: 282693--282755 Score: 74
Period size: 27 Copynumber: 2.3 Consensus size: 27
282683 CTTGCACCAT
*
282693 ACTGATACTATATTGGGCTTAGG-CCAC
1 ACTG-TACTATATTGGGCTAAGGCCCAC
**
282720 ACTGTTTTTATATTGGGCTAAGGCCCAC
1 ACTG-TACTATATTGGGCTAAGGCCCAC
282748 ACTGTACT
1 ACTGTACT
282756 GTTACTGTTA
Statistics
Matches: 29, Mismatches: 6, Indels: 2
0.78 0.16 0.05
Matches are distributed among these distances:
27 21 0.72
28 8 0.28
ACGTcount: A:0.24, C:0.22, G:0.21, T:0.33
Consensus pattern (27 bp):
ACTGTACTATATTGGGCTAAGGCCCAC
Found at i:283808 original size:25 final size:25
Alignment explanation
Indices: 283779--283921 Score: 98
Period size: 25 Copynumber: 5.8 Consensus size: 25
283769 CAAGCACACA
*
283779 AACGGGAAGCTCATATGAGCCATAT
1 AACGGGAAGCTCATAAGAGCCATAT
***
283804 AACGGGAAGCTCCGGAGAGCCAT-T
1 AACGGGAAGCTCATAAGAGCCATAT
* *
283828 AACGAGAAGCTCATACGAGCCA-AT
1 AACGGGAAGCTCATAAGAGCCATAT
* * *
283852 ATCGGGAAGGTTCA-AGTGAGCCA-AT
1 AACGGGAA-GCTCATA-AGAGCCATAT
* *
283877 ATCGAGAAGCTCCA-AAGAGCCATAT
1 AACGGGAAGCT-CATAAGAGCCATAT
* * *
283902 ATCTGGATGCTCATAAGAGC
1 AACGGGAAGCTCATAAGAGC
283922 TACGGTGTGT
Statistics
Matches: 93, Mismatches: 19, Indels: 12
0.75 0.15 0.10
Matches are distributed among these distances:
24 36 0.39
25 57 0.61
ACGTcount: A:0.35, C:0.22, G:0.26, T:0.17
Consensus pattern (25 bp):
AACGGGAAGCTCATAAGAGCCATAT
Found at i:283873 original size:49 final size:49
Alignment explanation
Indices: 283779--283902 Score: 126
Period size: 49 Copynumber: 2.5 Consensus size: 49
283769 CAAGCACACA
* * ** *
283779 AACGGGAAGCTCATATGAGCCATATAACGGGAAGCTCCGGAGAGCCATT
1 AACGAGAAGCTCATACGAGCCATATAACGGGAAGCTCAAGAGAGCCAAT
* * *
283828 AACGAGAAGCTCATACGAGCCA-ATATCGGGAAGGTTCAAGTGAGCCAAT
1 AACGAGAAGCTCATACGAGCCATATAACGGGAA-GCTCAAGAGAGCCAAT
* *
283877 ATCGAGAAGCTCCA-AAGAGCCATATA
1 AACGAGAAGCT-CATACGAGCCATATA
283903 TCTGGATGCT
Statistics
Matches: 62, Mismatches: 10, Indels: 5
0.81 0.13 0.06
Matches are distributed among these distances:
48 9 0.15
49 48 0.77
50 5 0.08
ACGTcount: A:0.36, C:0.22, G:0.26, T:0.16
Consensus pattern (49 bp):
AACGAGAAGCTCATACGAGCCATATAACGGGAAGCTCAAGAGAGCCAAT
Found at i:286030 original size:15 final size:15
Alignment explanation
Indices: 286010--286040 Score: 62
Period size: 15 Copynumber: 2.1 Consensus size: 15
286000 GACTCATAAA
286010 TATTTAATTAAATAT
1 TATTTAATTAAATAT
286025 TATTTAATTAAATAT
1 TATTTAATTAAATAT
286040 T
1 T
286041 TATGAATTTA
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 16 1.00
ACGTcount: A:0.45, C:0.00, G:0.00, T:0.55
Consensus pattern (15 bp):
TATTTAATTAAATAT
Found at i:286328 original size:16 final size:18
Alignment explanation
Indices: 286296--286328 Score: 52
Period size: 16 Copynumber: 1.9 Consensus size: 18
286286 ATATATTATA
286296 ATAATTAAAATGAAAGAT
1 ATAATTAAAATGAAAGAT
286314 ATAA-TAAAA-GAAAGA
1 ATAATTAAAATGAAAGA
286329 AAAAGAGATG
Statistics
Matches: 15, Mismatches: 0, Indels: 2
0.88 0.00 0.12
Matches are distributed among these distances:
16 6 0.40
17 5 0.33
18 4 0.27
ACGTcount: A:0.67, C:0.00, G:0.12, T:0.21
Consensus pattern (18 bp):
ATAATTAAAATGAAAGAT
Found at i:287129 original size:25 final size:25
Alignment explanation
Indices: 287081--287129 Score: 62
Period size: 25 Copynumber: 2.0 Consensus size: 25
287071 CATAATTGAA
* * *
287081 ATGAAATGGATTGATTTTGTATATT
1 ATGAAATAGATTGATTATGAATATT
*
287106 ATGAAATATATTGATTATGAATAT
1 ATGAAATAGATTGATTATGAATAT
287130 ATGTGTATTG
Statistics
Matches: 20, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
25 20 1.00
ACGTcount: A:0.39, C:0.00, G:0.16, T:0.45
Consensus pattern (25 bp):
ATGAAATAGATTGATTATGAATATT
Found at i:287564 original size:43 final size:43
Alignment explanation
Indices: 287517--287598 Score: 119
Period size: 43 Copynumber: 1.9 Consensus size: 43
287507 TGATCGATAC
* **
287517 TGAAATAGAAAATTTGAGAAATGAATATTTGATGAGAAAATAT
1 TGAAATAGAAAATATGAGAAATGAATATGAGATGAGAAAATAT
* *
287560 TGAAATGGAAAATATGAGAAATGATTATGAGATGAGAAA
1 TGAAATAGAAAATATGAGAAATGAATATGAGATGAGAAA
287599 TCAAATATGA
Statistics
Matches: 34, Mismatches: 5, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
43 34 1.00
ACGTcount: A:0.51, C:0.00, G:0.22, T:0.27
Consensus pattern (43 bp):
TGAAATAGAAAATATGAGAAATGAATATGAGATGAGAAAATAT
Found at i:288747 original size:49 final size:49
Alignment explanation
Indices: 288675--288824 Score: 246
Period size: 49 Copynumber: 3.1 Consensus size: 49
288665 TCAAGAAGGG
* * *
288675 ATAAATATTGATAAGAATATAGACAGTGGAAGACTAAGTTTAGCAATGT
1 ATAAATAGTGATAAGAGTGTAGACAGTGGAAGACTAAGTTTAGCAATGT
*
288724 ATAAATAGTGATAAGAGTGTAGACAGTGAAAGACTAAGTTTAGCAATGT
1 ATAAATAGTGATAAGAGTGTAGACAGTGGAAGACTAAGTTTAGCAATGT
* *
288773 ATAAATAGTGATAAGAGTGTAGACAGTGGAAGACCAAGTTTAGCATTGT
1 ATAAATAGTGATAAGAGTGTAGACAGTGGAAGACTAAGTTTAGCAATGT
288822 ATA
1 ATA
288825 GCATGAATCA
Statistics
Matches: 94, Mismatches: 7, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
49 94 1.00
ACGTcount: A:0.43, C:0.07, G:0.23, T:0.27
Consensus pattern (49 bp):
ATAAATAGTGATAAGAGTGTAGACAGTGGAAGACTAAGTTTAGCAATGT
Found at i:289778 original size:14 final size:14
Alignment explanation
Indices: 289755--289785 Score: 53
Period size: 14 Copynumber: 2.2 Consensus size: 14
289745 TTCAGAAGAA
*
289755 ATTCTGGTTAATTC
1 ATTCTAGTTAATTC
289769 ATTCTAGTTAATTC
1 ATTCTAGTTAATTC
289783 ATT
1 ATT
289786 TATTAGATGC
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
14 16 1.00
ACGTcount: A:0.26, C:0.13, G:0.10, T:0.52
Consensus pattern (14 bp):
ATTCTAGTTAATTC
Found at i:295327 original size:12 final size:11
Alignment explanation
Indices: 295292--295323 Score: 64
Period size: 11 Copynumber: 2.9 Consensus size: 11
295282 ACAATAAAAA
295292 TTAAAAACAAT
1 TTAAAAACAAT
295303 TTAAAAACAAT
1 TTAAAAACAAT
295314 TTAAAAACAA
1 TTAAAAACAA
295324 ATTTCCTATG
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 21 1.00
ACGTcount: A:0.66, C:0.09, G:0.00, T:0.25
Consensus pattern (11 bp):
TTAAAAACAAT
Found at i:301791 original size:24 final size:25
Alignment explanation
Indices: 301754--301801 Score: 80
Period size: 24 Copynumber: 2.0 Consensus size: 25
301744 GCAATTTTAT
301754 TTTTATACTTTTTCGTTTATTTTTC
1 TTTTATACTTTTTCGTTTATTTTTC
*
301779 TTTT-TACTTTTTCGTTTGTTTTT
1 TTTTATACTTTTTCGTTTATTTTT
301802 TTGGTCAATA
Statistics
Matches: 22, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
24 18 0.82
25 4 0.18
ACGTcount: A:0.08, C:0.10, G:0.06, T:0.75
Consensus pattern (25 bp):
TTTTATACTTTTTCGTTTATTTTTC
Found at i:303809 original size:17 final size:17
Alignment explanation
Indices: 303787--303820 Score: 52
Period size: 17 Copynumber: 2.0 Consensus size: 17
303777 CAAGTTCTCC
303787 AAAGAAC-ACAAAATAAA
1 AAAGAACTA-AAAATAAA
303804 AAAGAACTAAAAATAAA
1 AAAGAACTAAAAATAAA
303821 CCTAAAGCCT
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
17 15 0.94
18 1 0.06
ACGTcount: A:0.76, C:0.09, G:0.06, T:0.09
Consensus pattern (17 bp):
AAAGAACTAAAAATAAA
Found at i:308942 original size:27 final size:27
Alignment explanation
Indices: 308911--308966 Score: 112
Period size: 27 Copynumber: 2.1 Consensus size: 27
308901 ATCATTGTAA
308911 AAATTATCCCATTTCTTCCTTCATACC
1 AAATTATCCCATTTCTTCCTTCATACC
308938 AAATTATCCCATTTCTTCCTTCATACC
1 AAATTATCCCATTTCTTCCTTCATACC
308965 AA
1 AA
308967 CTGTAATCAT
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
27 29 1.00
ACGTcount: A:0.29, C:0.32, G:0.00, T:0.39
Consensus pattern (27 bp):
AAATTATCCCATTTCTTCCTTCATACC
Found at i:309041 original size:17 final size:17
Alignment explanation
Indices: 309019--309082 Score: 51
Period size: 17 Copynumber: 3.7 Consensus size: 17
309009 TCAACAAGGG
309019 AAATAATAAAATAATAA
1 AAATAATAAAATAATAA
*
309036 AAATAATGAAA-AATGAA
1 AAATAATAAAATAAT-AA
* *
309053 AATTAAGCTGAAATAAT-A
1 AAATAA--TAAAATAATAA
*
309071 AATTAATAAAAT
1 AAATAATAAAAT
309083 TACCATACTA
Statistics
Matches: 40, Mismatches: 3, Indels: 9
0.77 0.06 0.17
Matches are distributed among these distances:
16 8 0.20
17 17 0.43
18 7 0.17
19 5 0.12
20 3 0.08
ACGTcount: A:0.67, C:0.02, G:0.06, T:0.25
Consensus pattern (17 bp):
AAATAATAAAATAATAA
Found at i:310100 original size:13 final size:13
Alignment explanation
Indices: 310079--310109 Score: 53
Period size: 13 Copynumber: 2.4 Consensus size: 13
310069 AATGAAAGAA
*
310079 AAACTTAAGAATC
1 AAACCTAAGAATC
310092 AAACCTAAGAATC
1 AAACCTAAGAATC
310105 AAACC
1 AAACC
310110 CTAAAAATTA
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
13 17 1.00
ACGTcount: A:0.55, C:0.23, G:0.06, T:0.16
Consensus pattern (13 bp):
AAACCTAAGAATC
Found at i:310595 original size:21 final size:22
Alignment explanation
Indices: 310571--310617 Score: 60
Period size: 22 Copynumber: 2.2 Consensus size: 22
310561 TTTTGCAACA
*
310571 TAGCAAC-CCTATGTTGAGATG
1 TAGCAACTCCTATGTTGAGACG
* *
310592 TAGCATCTTCTATGTTGAGACG
1 TAGCAACTCCTATGTTGAGACG
310614 TAGC
1 TAGC
310618 CTGAACATGA
Statistics
Matches: 22, Mismatches: 3, Indels: 1
0.85 0.12 0.04
Matches are distributed among these distances:
21 6 0.27
22 16 0.73
ACGTcount: A:0.26, C:0.19, G:0.23, T:0.32
Consensus pattern (22 bp):
TAGCAACTCCTATGTTGAGACG
Found at i:314839 original size:20 final size:20
Alignment explanation
Indices: 314796--314852 Score: 73
Period size: 20 Copynumber: 2.9 Consensus size: 20
314786 TATACGAGTA
* *
314796 TGCACTTCGGTGCC-CTGTT
1 TGCACTTTGGTGCCTCTGAT
314815 TGCACTTTGGTGCCTCTGAT
1 TGCACTTTGGTGCCTCTGAT
314835 TGCACATTT-GTGCCTCTG
1 TGCAC-TTTGGTGCCTCTG
314853 CCTAGACTTC
Statistics
Matches: 34, Mismatches: 2, Indels: 3
0.87 0.05 0.08
Matches are distributed among these distances:
19 13 0.38
20 18 0.53
21 3 0.09
ACGTcount: A:0.09, C:0.28, G:0.25, T:0.39
Consensus pattern (20 bp):
TGCACTTTGGTGCCTCTGAT
Found at i:328089 original size:20 final size:20
Alignment explanation
Indices: 328064--328103 Score: 64
Period size: 20 Copynumber: 2.0 Consensus size: 20
328054 TACTAAATTG
328064 CAAAACAATTCA-AAATTCAA
1 CAAAAC-ATTCATAAATTCAA
328084 CAAAACATTCATAAATTCAA
1 CAAAACATTCATAAATTCAA
328104 AATATAAAAT
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
19 5 0.26
20 14 0.74
ACGTcount: A:0.57, C:0.20, G:0.00, T:0.23
Consensus pattern (20 bp):
CAAAACATTCATAAATTCAA
Found at i:332434 original size:187 final size:187
Alignment explanation
Indices: 332114--332487 Score: 489
Period size: 187 Copynumber: 2.0 Consensus size: 187
332104 ACATAGGTAT
* * *
332114 CTAGACCACACCAGGTTGCTCATTAGAGTAGTAACTACACCGCACTAGGGCACCAAAGTGCAAAG
1 CTAGACCACACCAGGTTGCTCATTAGAGTAGTAACTACACCACACTAAGGCACCAAACTGCAAAG
* * ** * *
332179 CCTGTAGGCAACCATCTGTAAAATTGTATAACAATACGTCCCTAGACCACACTAGCATCTTTGTA
66 CCCGTAGACAACCATCTGTAAAATCATATAACAATACGTCCCTACACCACACTAGCATCTTCGTA
* **
332244 AAGATATTCAATACTCGATGGTCCACAACAAATGTTGGATCATTATATAATTTGTAA
131 AAGATATTCAATACTCGATGCTCCACAACAAATGTTGGATCACGATATAATTTGTAA
* * *
332301 CTAGACCACATCAGGTTGCTCGTTAGAGTAGTAACTACACCACACTAAGGCACCAAACTGCCAAG
1 CTAGACCACACCAGGTTGCTCATTAGAGTAGTAACTACACCACACTAAGGCACCAAACTGCAAAG
* * * ** * **
332366 CCCGTAGACAATCATTTGTAAAATCATATAACAATATGTCTTTCCACCACACTAGGGT-TTCCGT
66 CCCGTAGACAACCATCTGTAAAATCATATAACAATACGTCCCTACACCACACTAGCATCTT-CGT
* * * *
332430 AAAGATATTCAATACTCTATGCTCCGCAATAAATTTTGGATCACGATATAATTTGTAA
130 AAAGATATTCAATACTCGATGCTCCACAACAAATGTTGGATCACGATATAATTTGTAA
332488 AAGTTTCAGT
Statistics
Matches: 159, Mismatches: 27, Indels: 2
0.85 0.14 0.01
Matches are distributed among these distances:
186 2 0.01
187 157 0.99
ACGTcount: A:0.34, C:0.23, G:0.16, T:0.27
Consensus pattern (187 bp):
CTAGACCACACCAGGTTGCTCATTAGAGTAGTAACTACACCACACTAAGGCACCAAACTGCAAAG
CCCGTAGACAACCATCTGTAAAATCATATAACAATACGTCCCTACACCACACTAGCATCTTCGTA
AAGATATTCAATACTCGATGCTCCACAACAAATGTTGGATCACGATATAATTTGTAA
Found at i:343447 original size:22 final size:22
Alignment explanation
Indices: 343405--343471 Score: 68
Period size: 20 Copynumber: 3.0 Consensus size: 22
343395 AATCAAAATG
343405 AATA-AAAATTTTA-AAACATA
1 AATATAAAATTTTATAAACATA
*
343425 AA-ATAAAATTTTATAAATTATA
1 AATATAAAATTTTATAAA-CATA
343447 AATTATAATACATTTTATAAACATA
1 AA-TATAA-A-ATTTTATAAACATA
343472 TACATATATT
Statistics
Matches: 38, Mismatches: 2, Indels: 9
0.78 0.04 0.18
Matches are distributed among these distances:
19 1 0.03
20 11 0.29
21 3 0.08
22 5 0.13
24 4 0.11
25 4 0.11
26 10 0.26
ACGTcount: A:0.58, C:0.04, G:0.00, T:0.37
Consensus pattern (22 bp):
AATATAAAATTTTATAAACATA
Found at i:345448 original size:46 final size:46
Alignment explanation
Indices: 345398--345499 Score: 159
Period size: 46 Copynumber: 2.2 Consensus size: 46
345388 ACATTATCTG
* *
345398 GGAGATAAGGTCTGAAATTCTTTGGTCTATTCCACTGTAATCTCAA
1 GGAGATAAGATCTGAAATTCTTCGGTCTATTCCACTGTAATCTCAA
* **
345444 GGAGATAAGATCTGAAATTCTTCGGTCTATTCCATTGTAATCTCTG
1 GGAGATAAGATCTGAAATTCTTCGGTCTATTCCACTGTAATCTCAA
345490 GGAGATAAGA
1 GGAGATAAGA
345500 CCTAATGCGA
Statistics
Matches: 51, Mismatches: 5, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
46 51 1.00
ACGTcount: A:0.29, C:0.16, G:0.22, T:0.33
Consensus pattern (46 bp):
GGAGATAAGATCTGAAATTCTTCGGTCTATTCCACTGTAATCTCAA
Done.