Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: D01
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: 64473564
ACGTcount: A:0.32, C:0.16, G:0.16, T:0.32
Warning! 1880000 characters in sequence are not A, C, G, or T
File 69 of 213
Found at i:18549974 original size:14 final size:14
Alignment explanation
Indices: 18549955--18549998 Score: 51
Period size: 14 Copynumber: 3.4 Consensus size: 14
18549945 TGGGAAGTCC
18549955 CTGTATTGTAAGGA
1 CTGTATTGTAAGGA
*
18549969 CTGTA-T-CAA--A
1 CTGTATTGTAAGGA
18549979 CTGTATTGTAAGGA
1 CTGTATTGTAAGGA
18549993 CTGTAT
1 CTGTAT
18549999 CAAATTAGTC
Statistics
Matches: 24, Mismatches: 2, Indels: 8
0.71 0.06 0.24
Matches are distributed among these distances:
10 6 0.25
11 1 0.04
12 4 0.17
13 1 0.04
14 12 0.50
ACGTcount: A:0.30, C:0.11, G:0.23, T:0.36
Consensus pattern (14 bp):
CTGTATTGTAAGGA
Found at i:18549982 original size:24 final size:24
Alignment explanation
Indices: 18549955--18550002 Score: 96
Period size: 24 Copynumber: 2.0 Consensus size: 24
18549945 TGGGAAGTCC
18549955 CTGTATTGTAAGGACTGTATCAAA
1 CTGTATTGTAAGGACTGTATCAAA
18549979 CTGTATTGTAAGGACTGTATCAAA
1 CTGTATTGTAAGGACTGTATCAAA
18550003 TTAGTCCCAT
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
24 24 1.00
ACGTcount: A:0.33, C:0.12, G:0.21, T:0.33
Consensus pattern (24 bp):
CTGTATTGTAAGGACTGTATCAAA
Found at i:18553831 original size:20 final size:19
Alignment explanation
Indices: 18553804--18553845 Score: 66
Period size: 20 Copynumber: 2.2 Consensus size: 19
18553794 CATTTTTTTA
*
18553804 TATATATTTTTACTATTAT
1 TATATATTATTACTATTAT
18553823 TATACTATTATTACTATTAT
1 TATA-TATTATTACTATTAT
18553843 TAT
1 TAT
18553846 GTTACATTGT
Statistics
Matches: 21, Mismatches: 1, Indels: 1
0.91 0.04 0.04
Matches are distributed among these distances:
19 4 0.19
20 17 0.81
ACGTcount: A:0.33, C:0.07, G:0.00, T:0.60
Consensus pattern (19 bp):
TATATATTATTACTATTAT
Found at i:18557740 original size:44 final size:44
Alignment explanation
Indices: 18557692--18557775 Score: 141
Period size: 44 Copynumber: 1.9 Consensus size: 44
18557682 GATCAAAGAC
*
18557692 AACAGATCTTGTCTTCCCATTCTGGTGGCGAAGTAGATTGGAAA
1 AACAGATCTTGTCTTCCCATACTGGTGGCGAAGTAGATTGGAAA
* *
18557736 AACAGATTTTGTCTTTCCATACTGGTGGCGAAGTAGATTG
1 AACAGATCTTGTCTTCCCATACTGGTGGCGAAGTAGATTG
18557776 AAGATTACAG
Statistics
Matches: 37, Mismatches: 3, Indels: 0
0.93 0.08 0.00
Matches are distributed among these distances:
44 37 1.00
ACGTcount: A:0.26, C:0.17, G:0.25, T:0.32
Consensus pattern (44 bp):
AACAGATCTTGTCTTCCCATACTGGTGGCGAAGTAGATTGGAAA
Found at i:18559550 original size:11 final size:11
Alignment explanation
Indices: 18559519--18559563 Score: 51
Period size: 11 Copynumber: 4.4 Consensus size: 11
18559509 TTCATTTTTT
*
18559519 TTATA-TATTT
1 TTATACTATTA
*
18559529 TTTTACTATTA
1 TTATACTATTA
18559540 TTATACTATTA
1 TTATACTATTA
18559551 -T-TACTATTA
1 TTATACTATTA
18559560 TTAT
1 TTAT
18559564 GTTACATTGT
Statistics
Matches: 29, Mismatches: 3, Indels: 5
0.78 0.08 0.14
Matches are distributed among these distances:
9 8 0.28
10 6 0.21
11 15 0.52
ACGTcount: A:0.31, C:0.07, G:0.00, T:0.62
Consensus pattern (11 bp):
TTATACTATTA
Found at i:18561917 original size:26 final size:28
Alignment explanation
Indices: 18561883--18561934 Score: 72
Period size: 26 Copynumber: 1.9 Consensus size: 28
18561873 TACTTTTATA
*
18561883 AAAAATATATGAAA-ATTTT-TAATTCC
1 AAAAATATATAAAATATTTTCTAATTCC
*
18561909 AAAATTATATAAAATATTTTCTAATT
1 AAAAATATATAAAATATTTTCTAATT
18561935 TTAAAATATT
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
26 12 0.55
27 5 0.23
28 5 0.23
ACGTcount: A:0.50, C:0.06, G:0.02, T:0.42
Consensus pattern (28 bp):
AAAAATATATAAAATATTTTCTAATTCC
Found at i:18562231 original size:19 final size:17
Alignment explanation
Indices: 18562198--18562263 Score: 64
Period size: 18 Copynumber: 3.7 Consensus size: 17
18562188 TTAAAATTAT
18562198 ATTTATATATGTTTTTTAA
1 ATTTATATA--TTTTTTAA
18562217 ATATTA-ATATATTTTTATA
1 AT-TTATATAT-TTTTTA-A
*
18562236 ATTTTTATATTTTTTAA
1 ATTTATATATTTTTTAA
18562253 ATTT-TATATTT
1 ATTTATATATTT
18562264 CTTATATATT
Statistics
Matches: 42, Mismatches: 1, Indels: 11
0.78 0.02 0.20
Matches are distributed among these distances:
16 7 0.17
17 6 0.14
18 14 0.33
19 12 0.29
20 3 0.07
ACGTcount: A:0.33, C:0.00, G:0.02, T:0.65
Consensus pattern (17 bp):
ATTTATATATTTTTTAA
Found at i:18562244 original size:17 final size:17
Alignment explanation
Indices: 18562224--18562269 Score: 67
Period size: 16 Copynumber: 2.7 Consensus size: 17
18562214 TAAATATTAA
*
18562224 TATATTTTTATAATTTT
1 TATATTTTTATAAATTT
18562241 TATATTTTT-TAAATTT
1 TATATTTTTATAAATTT
18562257 TATATTTCTTATA
1 TATATTT-TTATA
18562270 TATTCACTTT
Statistics
Matches: 26, Mismatches: 1, Indels: 3
0.87 0.03 0.10
Matches are distributed among these distances:
16 13 0.50
17 11 0.42
18 2 0.08
ACGTcount: A:0.30, C:0.02, G:0.00, T:0.67
Consensus pattern (17 bp):
TATATTTTTATAAATTT
Found at i:18562257 original size:16 final size:16
Alignment explanation
Indices: 18562209--18562263 Score: 65
Period size: 16 Copynumber: 3.2 Consensus size: 16
18562199 TTTATATATG
18562209 TTTTTTAAATATTAATATA
1 TTTTTTAAAT-TT--TATA
*
18562228 TTTTTATAATTTTTATA
1 TTTTT-TAAATTTTATA
18562245 TTTTTTAAATTTTATA
1 TTTTTTAAATTTTATA
18562261 TTT
1 TTT
18562264 CTTATATATT
Statistics
Matches: 33, Mismatches: 2, Indels: 5
0.82 0.05 0.12
Matches are distributed among these distances:
16 13 0.39
17 9 0.27
19 7 0.21
20 4 0.12
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (16 bp):
TTTTTTAAATTTTATA
Found at i:18562270 original size:9 final size:8
Alignment explanation
Indices: 18562224--18562270 Score: 51
Period size: 8 Copynumber: 5.6 Consensus size: 8
18562214 TAAATATTAA
18562224 TATATTTT
1 TATATTTT
18562232 TATAATTTT
1 TAT-ATTTT
18562241 TATATTTT
1 TATATTTT
*
18562249 T-TAAATTT
1 TAT-ATTTT
18562257 TATATTTCT
1 TATATTT-T
18562266 TATAT
1 TATAT
18562271 ATTCACTTTT
Statistics
Matches: 33, Mismatches: 2, Indels: 7
0.79 0.05 0.17
Matches are distributed among these distances:
7 1 0.03
8 17 0.52
9 15 0.45
ACGTcount: A:0.30, C:0.02, G:0.00, T:0.68
Consensus pattern (8 bp):
TATATTTT
Found at i:18563971 original size:18 final size:17
Alignment explanation
Indices: 18563948--18563982 Score: 61
Period size: 18 Copynumber: 2.0 Consensus size: 17
18563938 TTTCTAGACT
18563948 TTTAACTAACCCATATAA
1 TTTAACTAACCCA-ATAA
18563966 TTTAACTAACCCAATAA
1 TTTAACTAACCCAATAA
18563983 ACAATTTTTT
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
17 4 0.24
18 13 0.76
ACGTcount: A:0.46, C:0.23, G:0.00, T:0.31
Consensus pattern (17 bp):
TTTAACTAACCCAATAA
Found at i:18565373 original size:80 final size:80
Alignment explanation
Indices: 18565248--18565456 Score: 214
Period size: 80 Copynumber: 2.6 Consensus size: 80
18565238 TATAACAGTT
*
18565248 ATTTTACCC-TATGGAGGTATTT-TAGTAATTTTA-CCATTC-AGGGGTATTTC-GATAATTTTA
1 ATTTTACCCAT-TGG-GGTATTTCGA-TAATTTTACCCA-TCGA-GGGTATTTCAG-TAATTTTA
**
18565308 -CCATTCGGGGGTATTTCGGTA
60 CCCA-TCAAGGGTATTTCGGTA
*
18565329 ATTTTACCCATTGGGGTATTTCGATAATTTTACCCATCGAGGGTATTTCAGTCATTTTACCCATC
1 ATTTTACCCATTGGGGTATTTCGATAATTTTACCCATCGAGGGTATTTCAGTAATTTTACCCATC
*
18565394 AAGGGTATTTCGGTC
66 AAGGGTATTTCGGTA
* * * * *
18565409 ATTTTACACATTGAGGGTACTTCGATCATTTTACGCATAGAGGGTATT
1 ATTTTACCCATTG-GGGTATTTCGATAATTTTACCCATCGAGGGTATT
18565457 ACTGTCATTT
Statistics
Matches: 111, Mismatches: 10, Indels: 14
0.82 0.07 0.10
Matches are distributed among these distances:
80 59 0.53
81 51 0.46
82 1 0.01
ACGTcount: A:0.24, C:0.16, G:0.20, T:0.40
Consensus pattern (80 bp):
ATTTTACCCATTGGGGTATTTCGATAATTTTACCCATCGAGGGTATTTCAGTAATTTTACCCATC
AAGGGTATTTCGGTA
Found at i:18565391 original size:27 final size:26
Alignment explanation
Indices: 18565248--18565456 Score: 167
Period size: 27 Copynumber: 7.8 Consensus size: 26
18565238 TATAACAGTT
* *
18565248 ATTTTACCCTATGGA-GGTATTTTAGTA
1 ATTTTACCC-ATCGAGGGTA-TTTCGTA
18565275 ATTTTA-CCATTC-AGGGGTATTTCGATA
1 ATTTTACCCA-TCGA-GGGTATTTCG-TA
*
18565302 ATTTTA-CCATTCGGGGGTATTTCGGTA
1 ATTTTACCCA-TCGAGGGTATTTC-GTA
*
18565329 ATTTTACCCATTG-GGGTATTTCGATA
1 ATTTTACCCATCGAGGGTATTTCG-TA
*
18565355 ATTTTACCCATCGAGGGTATTTCAGTC
1 ATTTTACCCATCGAGGGTATTTC-GTA
* *
18565382 ATTTTACCCATCAAGGGTATTTCGGTC
1 ATTTTACCCATCGAGGGTATTTC-GTA
* * * *
18565409 ATTTTACACATTGAGGGTACTTCGATC
1 ATTTTACCCATCGAGGGTATTTCG-TA
* *
18565436 ATTTTACGCATAGAGGGTATT
1 ATTTTACCCATCGAGGGTATT
18565457 ACTGTCATTT
Statistics
Matches: 156, Mismatches: 15, Indels: 22
0.81 0.08 0.11
Matches are distributed among these distances:
25 3 0.02
26 31 0.20
27 117 0.75
28 5 0.03
ACGTcount: A:0.24, C:0.16, G:0.20, T:0.40
Consensus pattern (26 bp):
ATTTTACCCATCGAGGGTATTTCGTA
Found at i:18565425 original size:54 final size:53
Alignment explanation
Indices: 18565263--18565456 Score: 187
Period size: 54 Copynumber: 3.6 Consensus size: 53
18565253 ACCCTATGGA
* * *
18565263 GGTATTTTAGTAATTTTA-CCATTCAGGGGTATTTCGATAATTTTAC-CATTCGGG
1 GGTATTTCAGTAATTTTACCCA-T-AAGGGTATTTCGATAATTTTACACATT-GAG
* ** * *
18565317 GGTATTTCGGTAATTTTACCCATTGGGGTATTTCGATAATTTTACCCATCGAG
1 GGTATTTCAGTAATTTTACCCATAAGGGTATTTCGATAATTTTACACATTGAG
* * *
18565370 GGTATTTCAGTCATTTTACCCATCAAGGGTATTTCGGTCATTTTACACATTGAG
1 GGTATTTCAGTAATTTTACCCAT-AAGGGTATTTCGATAATTTTACACATTGAG
* * *
18565424 GGTACTTC-GATCATTTTACGCATAGAGGGTATT
1 GGTATTTCAG-TAATTTTACCCATA-AGGGTATT
18565457 ACTGTCATTT
Statistics
Matches: 120, Mismatches: 15, Indels: 10
0.83 0.10 0.07
Matches are distributed among these distances:
53 46 0.38
54 71 0.59
55 3 0.03
ACGTcount: A:0.24, C:0.16, G:0.21, T:0.40
Consensus pattern (53 bp):
GGTATTTCAGTAATTTTACCCATAAGGGTATTTCGATAATTTTACACATTGAG
Found at i:18565464 original size:81 final size:80
Alignment explanation
Indices: 18565316--18565466 Score: 221
Period size: 81 Copynumber: 1.9 Consensus size: 80
18565306 TACCATTCGG
* * * *
18565316 GGGTATTTCGGTAATTTTACCCATTGGGGTATTTCGATAATTTTACCCATCGAGGGTATTTCAGT
1 GGGTATTTCGGTAATTTTACACATTGGGGTACTTCGATAATTTTACCCATAGAGGGTATTACAGT
18565381 CATTTTACCCATCAA
66 CATTTTACCCATCAA
* * * *
18565396 GGGTATTTCGGTCATTTTACACATTGAGGGTACTTCGATCATTTTACGCATAGAGGGTATTACTG
1 GGGTATTTCGGTAATTTTACACATTG-GGGTACTTCGATAATTTTACCCATAGAGGGTATTACAG
18565461 TCATTT
65 TCATTT
18565467 AACAACATTT
Statistics
Matches: 62, Mismatches: 8, Indels: 1
0.87 0.11 0.01
Matches are distributed among these distances:
80 24 0.39
81 38 0.61
ACGTcount: A:0.23, C:0.17, G:0.21, T:0.39
Consensus pattern (80 bp):
GGGTATTTCGGTAATTTTACACATTGGGGTACTTCGATAATTTTACCCATAGAGGGTATTACAGT
CATTTTACCCATCAA
Found at i:18569730 original size:37 final size:37
Alignment explanation
Indices: 18569678--18569761 Score: 105
Period size: 37 Copynumber: 2.3 Consensus size: 37
18569668 CATGACCATA
* * * *
18569678 GCATAATCTAGGGAGGTCCACCAGATTTGCCTATATG
1 GCATAATCCAGGGAGGTCCACCAAATTCGCCTACATG
* **
18569715 GGATAATCCAGGGAGGTCTGCCAAATTCGCCTACATG
1 GCATAATCCAGGGAGGTCCACCAAATTCGCCTACATG
18569752 GCATAATCCA
1 GCATAATCCA
18569762 ACGGAGGCCT
Statistics
Matches: 39, Mismatches: 8, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
37 39 1.00
ACGTcount: A:0.29, C:0.24, G:0.24, T:0.24
Consensus pattern (37 bp):
GCATAATCCAGGGAGGTCCACCAAATTCGCCTACATG
Found at i:18576256 original size:4 final size:4
Alignment explanation
Indices: 18576247--18576319 Score: 64
Period size: 4 Copynumber: 17.8 Consensus size: 4
18576237 CAACCCAATT
18576247 TTTA TTTA TTTA TTTA TTTA -TTA TTTTA TTTA -TTA CTTTA TTTTA TTT-
1 TTTA TTTA TTTA TTTA TTTA TTTA -TTTA TTTA TTTA -TTTA -TTTA TTTA
18576295 TATTA TTTA -TTA CTTTA TTTTA TTT
1 T-TTA TTTA TTTA -TTTA -TTTA TTT
18576320 TAATAAATTT
Statistics
Matches: 59, Mismatches: 2, Indels: 16
0.77 0.03 0.21
Matches are distributed among these distances:
3 10 0.17
4 31 0.53
5 18 0.31
ACGTcount: A:0.23, C:0.03, G:0.00, T:0.74
Consensus pattern (4 bp):
TTTA
Found at i:18576264 original size:12 final size:12
Alignment explanation
Indices: 18576247--18576314 Score: 77
Period size: 12 Copynumber: 5.6 Consensus size: 12
18576237 CAACCCAATT
18576247 TTTATTTATTTA-
1 TTTATTTA-TTAC
*
18576259 TTTATTTATTAT
1 TTTATTTATTAC
18576271 TTTATTTATTAC
1 TTTATTTATTAC
*
18576283 TTTATTTTATT-T
1 TTTA-TTTATTAC
18576295 TATTATTTATTAC
1 T-TTATTTATTAC
18576308 TTTATTT
1 TTTATTT
18576315 TATTTTAATA
Statistics
Matches: 49, Mismatches: 3, Indels: 8
0.82 0.05 0.13
Matches are distributed among these distances:
11 3 0.06
12 36 0.73
13 10 0.20
ACGTcount: A:0.24, C:0.03, G:0.00, T:0.74
Consensus pattern (12 bp):
TTTATTTATTAC
Found at i:18576319 original size:25 final size:25
Alignment explanation
Indices: 18576248--18576321 Score: 109
Period size: 25 Copynumber: 3.0 Consensus size: 25
18576238 AACCCAATTT
18576248 TTATTTATTTA-TTTA-TTTATTATT-
1 TTATTTA-TTACTTTATTTTATT-TTA
18576272 TTATTTATTACTTTATTTTATTTTA
1 TTATTTATTACTTTATTTTATTTTA
18576297 TTATTTATTACTTTATTTTATTTTA
1 TTATTTATTACTTTATTTTATTTTA
18576322 ATAAATTTTT
Statistics
Matches: 47, Mismatches: 0, Indels: 5
0.90 0.00 0.10
Matches are distributed among these distances:
23 3 0.06
24 13 0.28
25 31 0.66
ACGTcount: A:0.24, C:0.03, G:0.00, T:0.73
Consensus pattern (25 bp):
TTATTTATTACTTTATTTTATTTTA
Found at i:18578016 original size:13 final size:13
Alignment explanation
Indices: 18578000--18578024 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
18577990 TATTAAAGAT
18578000 GATTTAATTTTAG
1 GATTTAATTTTAG
18578013 GATTTAATTTTA
1 GATTTAATTTTA
18578025 TTTATCTTTA
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.32, C:0.00, G:0.12, T:0.56
Consensus pattern (13 bp):
GATTTAATTTTAG
Found at i:18586866 original size:46 final size:46
Alignment explanation
Indices: 18586814--18586908 Score: 181
Period size: 46 Copynumber: 2.1 Consensus size: 46
18586804 AAAAAGATAG
*
18586814 AAACCAAAATATTATCTCCTAAACTTTAGTATCTAATCTCCTAATT
1 AAACCAAAATATTATCTCCTAAACTTTAGCATCTAATCTCCTAATT
18586860 AAACCAAAATATTATCTCCTAAACTTTAGCATCTAATCTCCTAATT
1 AAACCAAAATATTATCTCCTAAACTTTAGCATCTAATCTCCTAATT
18586906 AAA
1 AAA
18586909 AGAAAATAGA
Statistics
Matches: 48, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
46 48 1.00
ACGTcount: A:0.41, C:0.22, G:0.02, T:0.35
Consensus pattern (46 bp):
AAACCAAAATATTATCTCCTAAACTTTAGCATCTAATCTCCTAATT
Found at i:18590288 original size:33 final size:34
Alignment explanation
Indices: 18590205--18590294 Score: 128
Period size: 34 Copynumber: 2.7 Consensus size: 34
18590195 GGTTAACCAG
*
18590205 CCAGCACACCAAATGCTCATATGAGCCAGCCCAT
1 CCAGCACACCAAATGCTCATATGAGCCAACCCAT
* *
18590239 CCAGCACACCAGATGCTCATATGAGCCAATCCAT
1 CCAGCACACCAAATGCTCATATGAGCCAACCCAT
* *
18590273 -CAGTACACCAAATGCTCGTATG
1 CCAGCACACCAAATGCTCATATG
18590295 GCAAAATCCA
Statistics
Matches: 50, Mismatches: 6, Indels: 1
0.88 0.11 0.02
Matches are distributed among these distances:
33 19 0.38
34 31 0.62
ACGTcount: A:0.32, C:0.34, G:0.16, T:0.18
Consensus pattern (34 bp):
CCAGCACACCAAATGCTCATATGAGCCAACCCAT
Found at i:18590303 original size:33 final size:33
Alignment explanation
Indices: 18590206--18590306 Score: 114
Period size: 34 Copynumber: 3.0 Consensus size: 33
18590196 GTTAACCAGC
* **
18590206 CAGCACACCAAATGCTCATATGAGCCAGCCCAT
1 CAGCACACCAAATGCTCATATGAGCAAATCCAT
* *
18590239 CCAGCACACCAGATGCTCATATGAGCCAATCCAT
1 -CAGCACACCAAATGCTCATATGAGCAAATCCAT
* *
18590273 CAGTACACCAAATGCTCGTATG-GCAAAATCCAT
1 CAGCACACCAAATGCTCATATGAGC-AAATCCAT
18590306 C
1 C
18590307 CTTCACACCA
Statistics
Matches: 59, Mismatches: 7, Indels: 3
0.86 0.10 0.04
Matches are distributed among these distances:
32 2 0.03
33 27 0.46
34 30 0.51
ACGTcount: A:0.34, C:0.34, G:0.15, T:0.18
Consensus pattern (33 bp):
CAGCACACCAAATGCTCATATGAGCAAATCCAT
Found at i:18609282 original size:14 final size:16
Alignment explanation
Indices: 18609251--18609282 Score: 50
Period size: 14 Copynumber: 2.1 Consensus size: 16
18609241 AAAGGAAATC
18609251 AATGTAGAAAATTGTG
1 AATGTAGAAAATTGTG
18609267 AATGT-GAAAA-TGTG
1 AATGTAGAAAATTGTG
18609281 AA
1 AA
18609283 AAAAATGACC
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
14 6 0.38
15 5 0.31
16 5 0.31
ACGTcount: A:0.47, C:0.00, G:0.25, T:0.28
Consensus pattern (16 bp):
AATGTAGAAAATTGTG
Found at i:18611081 original size:12 final size:12
Alignment explanation
Indices: 18611064--18611089 Score: 52
Period size: 12 Copynumber: 2.2 Consensus size: 12
18611054 CCGTGTGGCT
18611064 CACATGGCCTAC
1 CACATGGCCTAC
18611076 CACATGGCCTAC
1 CACATGGCCTAC
18611088 CA
1 CA
18611090 TACGGTCATG
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 14 1.00
ACGTcount: A:0.27, C:0.42, G:0.15, T:0.15
Consensus pattern (12 bp):
CACATGGCCTAC
Found at i:18616855 original size:30 final size:29
Alignment explanation
Indices: 18616792--18617070 Score: 134
Period size: 30 Copynumber: 9.4 Consensus size: 29
18616782 TGGTTGACCC
* * * * *
18616792 ATCCCTTTTCGTAATTCGATAATTGAAATT
1 ATCCCTTTTCATAGTTCGATAGTCG-AACT
*
18616822 ATCCCTTTTCATAGTTCGACAGTCGAAGCT
1 ATCCCTTTTCATAGTTCGATAGTCGAA-CT
* * * * *
18616852 ATCCTTTTTCATAATTTGATAGTGGTCACT
1 ATCCCTTTTCATAGTTCGATAGTCG-AACT
* ** * * * *
18616882 ATCCCTTTTCATTGTTTAATGGTTGTCACC
1 ATCCCTTTTCATAGTTCGATAGTCG-AACT
* * * *
18616912 ATCCCTTTTCATAATTGGATAGCCGAAGCC
1 ATCCCTTTTCATAGTTCGATAGTCGAA-CT
* *
18616942 ATCCCTTTTCATAGTTCGATGGTC-ATCACC
1 ATCCCTTTTCATAGTTCGATAGTCGA--ACT
* * * * *
18616972 GTCCCTTTTCATTGTT-GATGGTCGTCACC
1 ATCCCTTTTCATAGTTCGATAGTCG-AACT
* *
18617001 ATCCCTTTTCATAATT-GACAGTCGAAGCT
1 ATCCCTTTTCATAGTTCGATAGTCGAA-CT
* * *
18617030 ATCCCCTTTCTTA-TTCGATAGTCAAAGCT
1 ATCCCTTTTCATAGTTCGATAGTCGAA-CT
18617059 ATCCCTTTTCAT
1 ATCCCTTTTCAT
18617071 TTGTTGATGA
Statistics
Matches: 193, Mismatches: 47, Indels: 19
0.75 0.18 0.07
Matches are distributed among these distances:
28 3 0.02
29 66 0.34
30 122 0.63
31 2 0.01
ACGTcount: A:0.22, C:0.25, G:0.14, T:0.39
Consensus pattern (29 bp):
ATCCCTTTTCATAGTTCGATAGTCGAACT
Found at i:18616921 original size:60 final size:60
Alignment explanation
Indices: 18616852--18617013 Score: 168
Period size: 60 Copynumber: 2.7 Consensus size: 60
18616842 AGTCGAAGCT
* * * * * **
18616852 ATCCTTTTTCATAATTTGATAGTGGTCACTATCCCTTTTCATTGTTTAATGGTTGTCACC
1 ATCCCTTTTCATAATTTGATAGTCGTCACCATCCCTTTTCATAGTTCAATGGTCATCACC
* * * *
18616912 ATCCCTTTTCATAATTGGATAGCCG-AAGCCATCCCTTTTCATAGTTCGATGGTCATCACC
1 ATCCCTTTTCATAATTTGATAGTCGTCA-CCATCCCTTTTCATAGTTCAATGGTCATCACC
* *
18616972 GTCCCTTTTCAT--TGTTGATGGTCGTCACCATCCCTTTTCATA
1 ATCCCTTTTCATAAT-TTGATAGTCGTCACCATCCCTTTTCATA
18617014 ATTGACAGTC
Statistics
Matches: 83, Mismatches: 16, Indels: 7
0.78 0.15 0.07
Matches are distributed among these distances:
58 1 0.01
59 23 0.28
60 59 0.71
ACGTcount: A:0.20, C:0.25, G:0.14, T:0.41
Consensus pattern (60 bp):
ATCCCTTTTCATAATTTGATAGTCGTCACCATCCCTTTTCATAGTTCAATGGTCATCACC
Found at i:18616951 original size:90 final size:88
Alignment explanation
Indices: 18616822--18617071 Score: 288
Period size: 90 Copynumber: 2.8 Consensus size: 88
18616812 AATTGAAATT
* * * ** *
18616822 ATCCCTTTTCATAGTTCGACAGTCGAAGCTATCCTTTTTCATAATTTGATAGTGGTCACTATCCC
1 ATCCCTTTTCATAATT-GACAGTCGAAGCTATCCCTTTTCATAATTCGATAGTCATCACCATCCC
*
18616887 TTTTCATTGTTTAATGGTTGTCACC
65 TTTTCATTG-TTAATGGTCGTCACC
* * * * * *
18616912 ATCCCTTTTCATAATTGGATAGCCGAAGCCATCCCTTTTCATAGTTCGATGGTCATCACCGTCCC
1 ATCCCTTTTCATAATT-GACAGTCGAAGCTATCCCTTTTCATAATTCGATAGTCATCACCATCCC
*
18616977 TTTTCATTGTTGATGGTCGTCACC
65 TTTTCATTGTTAATGGTCGTCACC
* * * *
18617001 ATCCCTTTTCATAATTGACAGTCGAAGCTATCCCCTTTC-TTATTCGATAGTCA-AAGCTATCCC
1 ATCCCTTTTCATAATTGACAGTCGAAGCTATCCCTTTTCATAATTCGATAGTCATCA-CCATCCC
18617064 TTTTCATT
65 TTTTCATT
18617072 TGTTGATGAT
Statistics
Matches: 134, Mismatches: 25, Indels: 5
0.82 0.15 0.03
Matches are distributed among these distances:
86 1 0.01
87 24 0.18
88 19 0.14
89 29 0.22
90 61 0.46
ACGTcount: A:0.21, C:0.26, G:0.14, T:0.39
Consensus pattern (88 bp):
ATCCCTTTTCATAATTGACAGTCGAAGCTATCCCTTTTCATAATTCGATAGTCATCACCATCCCT
TTTCATTGTTAATGGTCGTCACC
Found at i:18616999 original size:29 final size:30
Alignment explanation
Indices: 18616822--18617013 Score: 147
Period size: 30 Copynumber: 6.4 Consensus size: 30
18616812 AATTGAAATT
** * *
18616822 ATCCCTTTTCATAGTTCGACAGTCG-AAGCT
1 ATCCCTTTTCATAGTTCGATGGTCGTCA-CC
* * * * * *
18616852 ATCCTTTTTCATAATTTGATAGTGGTCACT
1 ATCCCTTTTCATAGTTCGATGGTCGTCACC
* ** *
18616882 ATCCCTTTTCATTGTTTAATGGTTGTCACC
1 ATCCCTTTTCATAGTTCGATGGTCGTCACC
* * * * *
18616912 ATCCCTTTTCATAATTGGATAGCCG-AAGCC
1 ATCCCTTTTCATAGTTCGATGGTCGTCA-CC
*
18616942 ATCCCTTTTCATAGTTCGATGGTCATCACC
1 ATCCCTTTTCATAGTTCGATGGTCGTCACC
* *
18616972 GTCCCTTTTCATTGTT-GATGGTCGTCACC
1 ATCCCTTTTCATAGTTCGATGGTCGTCACC
18617001 ATCCCTTTTCATA
1 ATCCCTTTTCATA
18617014 ATTGACAGTC
Statistics
Matches: 127, Mismatches: 32, Indels: 7
0.77 0.19 0.04
Matches are distributed among these distances:
29 24 0.19
30 101 0.80
31 2 0.02
ACGTcount: A:0.20, C:0.26, G:0.15, T:0.40
Consensus pattern (30 bp):
ATCCCTTTTCATAGTTCGATGGTCGTCACC
Found at i:18617033 original size:29 final size:30
Alignment explanation
Indices: 18617001--18617070 Score: 90
Period size: 29 Copynumber: 2.4 Consensus size: 30
18616991 GGTCGTCACC
*
18617001 ATCCCTTTTCATAATT-GACAGTCGAAGCT
1 ATCCCTTTTCATAATTCGACAGTCAAAGCT
* * *
18617030 ATCCCCTTTC-TTATTCGATAGTCAAAGCT
1 ATCCCTTTTCATAATTCGACAGTCAAAGCT
18617059 ATCCCTTTTCAT
1 ATCCCTTTTCAT
18617071 TTGTTGATGA
Statistics
Matches: 34, Mismatches: 5, Indels: 3
0.81 0.12 0.07
Matches are distributed among these distances:
28 4 0.12
29 29 0.85
30 1 0.03
ACGTcount: A:0.24, C:0.27, G:0.10, T:0.39
Consensus pattern (30 bp):
ATCCCTTTTCATAATTCGACAGTCAAAGCT
Found at i:18620158 original size:23 final size:23
Alignment explanation
Indices: 18620124--18620167 Score: 72
Period size: 23 Copynumber: 1.9 Consensus size: 23
18620114 GTCAATTATT
18620124 ATTTTAATAATATTTTATTTAAA
1 ATTTTAATAATATTTTATTTAAA
18620147 ATTTT-ATGAATATTTTATTTA
1 ATTTTAAT-AATATTTTATTTA
18620168 TTTAAAGTTA
Statistics
Matches: 20, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
22 2 0.10
23 18 0.90
ACGTcount: A:0.39, C:0.00, G:0.02, T:0.59
Consensus pattern (23 bp):
ATTTTAATAATATTTTATTTAAA
Found at i:18627953 original size:16 final size:17
Alignment explanation
Indices: 18627932--18627964 Score: 50
Period size: 17 Copynumber: 2.0 Consensus size: 17
18627922 AAGTAGTTGA
18627932 TTGAAT-GATGTTTTGG
1 TTGAATCGATGTTTTGG
*
18627948 TTGAATCTATGTTTTGG
1 TTGAATCGATGTTTTGG
18627965 AGTACTCGGA
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
16 6 0.40
17 9 0.60
ACGTcount: A:0.18, C:0.03, G:0.27, T:0.52
Consensus pattern (17 bp):
TTGAATCGATGTTTTGG
Found at i:18642046 original size:23 final size:22
Alignment explanation
Indices: 18642003--18642046 Score: 61
Period size: 23 Copynumber: 2.0 Consensus size: 22
18641993 AAATTATAAA
* *
18642003 ATATAAAAATATATATGTGTAC
1 ATATAAAAAAATATATATGTAC
18642025 ATATAAGAAAAATATATATGTA
1 ATATAA-AAAAATATATATGTA
18642047 TGTGAATTAT
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
22 6 0.32
23 13 0.68
ACGTcount: A:0.55, C:0.02, G:0.09, T:0.34
Consensus pattern (22 bp):
ATATAAAAAAATATATATGTAC
Found at i:18642816 original size:21 final size:21
Alignment explanation
Indices: 18642779--18642833 Score: 87
Period size: 21 Copynumber: 2.7 Consensus size: 21
18642769 AATCATATCT
18642779 TCTAAGATTGC--ATATCATA
1 TCTAAGATTGCATATATCATA
*
18642798 TTTAAGATTGCATATATCATA
1 TCTAAGATTGCATATATCATA
18642819 TCTAAGATTGCATAT
1 TCTAAGATTGCATAT
18642834 CCTTGAAGAT
Statistics
Matches: 32, Mismatches: 2, Indels: 2
0.89 0.06 0.06
Matches are distributed among these distances:
19 10 0.31
21 22 0.69
ACGTcount: A:0.36, C:0.13, G:0.11, T:0.40
Consensus pattern (21 bp):
TCTAAGATTGCATATATCATA
Found at i:18643648 original size:44 final size:45
Alignment explanation
Indices: 18643467--18643849 Score: 179
Period size: 44 Copynumber: 8.7 Consensus size: 45
18643457 GGATTATTGG
* * *
18643467 CTTCAATTTGCTCCACTACAACTTAGGGAGATAATATCT-GTAAT
1 CTTCAATCTGCTCCACTACTACTTAGGGAGATAAGATCTAGTAAT
* * * * * * **
18643511 TTTCAACCTACTCCACTGCTGCTCAGGGAGATAAGA-CTAGT-GG
1 CTTCAATCTGCTCCACTACTACTTAGGGAGATAAGATCTAGTAAT
* * ***
18643554 CTTAAATCTGCTTCC-CTACTACCTT-GGGAAGATAAGAT-TCGCCGT
1 CTTCAATCTGC-TCCACTACTA-CTTAGGG-AGATAAGATCTAGTAAT
* *
18643599 CTTCAATTTGCTCCACTACTACTTACGGAGATAAGATCT-GTAAT
1 CTTCAATCTGCTCCACTACTACTTAGGGAGATAAGATCTAGTAAT
* * * * * * *
18643643 TTTCAACCTACTCCACTGCTGCTTAGAGAGATAA-AGTCTA-CAAT
1 CTTCAATCTGCTCCACTACTACTTAGGGAGATAAGA-TCTAGTAAT
* ** * * * **
18643687 CTTCAACCT-CTCCACTGTTGCTCAGGGAGATAAG-GCTAGT-GG
1 CTTCAATCTGCTCCACTACTACTTAGGGAGATAAGATCTAGTAAT
* * ***
18643729 CTTAAATCTGCTTCC-CTACTACCTT-GGGAAGATAAGAT-TCGCCGT
1 CTTCAATCTGC-TCCACTACTA-CTTAGGG-AGATAAGATCTAGTAAT
* * *
18643774 CTTCGATCTGCTCCACTACTGCTTAGGGAGATAAGATCT-CTAAT
1 CTTCAATCTGCTCCACTACTACTTAGGGAGATAAGATCTAGTAAT
* * * *
18643818 -TTCAATCTACTCCACTGCTGCTCAGGGAGATA
1 CTTCAATCTGCTCCACTACTACTTAGGGAGATA
18643850 GGATTCAAAA
Statistics
Matches: 252, Mismatches: 65, Indels: 45
0.70 0.18 0.12
Matches are distributed among these distances:
42 10 0.04
43 73 0.29
44 131 0.52
45 38 0.15
ACGTcount: A:0.27, C:0.25, G:0.18, T:0.30
Consensus pattern (45 bp):
CTTCAATCTGCTCCACTACTACTTAGGGAGATAAGATCTAGTAAT
Found at i:18643711 original size:175 final size:175
Alignment explanation
Indices: 18643512--18643893 Score: 590
Period size: 175 Copynumber: 2.2 Consensus size: 175
18643502 ATCTGTAATT
18643512 TTCAACCTACTCCACTGCTGCTCAGGGAGATAAGACTAGTGGCTTAAATCTGCTTCCCTACTACC
1 TTCAACCTACTCCACTGCTGCTCAGGGAGATAAGACTAGTGGCTTAAATCTGCTTCCCTACTACC
* *
18643577 TTGGGAAGATAAGATTCGCCGTCTTCAATTTGCTCCACTACTACTTACGGAGATAAGATCTGTAA
66 TTGGGAAGATAAGATTCGCCGTCTTCAATCTGCTCCACTACTACTTACGGAGATAAGATCTCTAA
* *
18643642 TTTTCAACCTACTCCACTGCTGCTTAGAGAGATA-AAGTCTACAATC
131 -TTTCAACCTACTCCACTGCTGCTCAGAGAGATAGAAGTC-AAAATC
* *
18643688 TTCAACCT-CTCCACTGTTGCTCAGGGAGATAAGGCTAGTGGCTTAAATCTGCTTCCCTACTACC
1 TTCAACCTACTCCACTGCTGCTCAGGGAGATAAGACTAGTGGCTTAAATCTGCTTCCCTACTACC
* * *
18643752 TTGGGAAGATAAGATTCGCCGTCTTCGATCTGCTCCACTACTGCTTAGGGAGATAAGATCTCTAA
66 TTGGGAAGATAAGATTCGCCGTCTTCAATCTGCTCCACTACTACTTACGGAGATAAGATCTCTAA
* * * *
18643817 TTTCAATCTACTCCACTGCTGCTCAGGGAGATAGGATTCAAAATC
131 TTTCAACCTACTCCACTGCTGCTCAGAGAGATAGAAGTCAAAATC
*
18643862 TTCAACCTATTCCACTGCTGAC-CAGGGAGATA
1 TTCAACCTACTCCACTGCTG-CTCAGGGAGATA
18643894 GGATTCACAA
Statistics
Matches: 188, Mismatches: 15, Indels: 7
0.90 0.07 0.03
Matches are distributed among these distances:
174 43 0.23
175 136 0.72
176 9 0.05
ACGTcount: A:0.27, C:0.26, G:0.19, T:0.29
Consensus pattern (175 bp):
TTCAACCTACTCCACTGCTGCTCAGGGAGATAAGACTAGTGGCTTAAATCTGCTTCCCTACTACC
TTGGGAAGATAAGATTCGCCGTCTTCAATCTGCTCCACTACTACTTACGGAGATAAGATCTCTAA
TTTCAACCTACTCCACTGCTGCTCAGAGAGATAGAAGTCAAAATC
Found at i:18643880 original size:44 final size:44
Alignment explanation
Indices: 18643818--18644279 Score: 626
Period size: 44 Copynumber: 10.7 Consensus size: 44
18643808 GATCTCTAAT
* * *
18643818 TTCAATCTACTCCACTGCTG-CTCAGGGAGATAGGATTCAAAATC
1 TTCAACCTATTCCACTGCTGAC-CAGGGAGATAGGATTCACAATC
18643862 TTCAACCTATTCCACTGCTGACCAGGGAGATAGGATTCACAATC
1 TTCAACCTATTCCACTGCTGACCAGGGAGATAGGATTCACAATC
* * *
18643906 TTCAACCTATTCCACTGTTGACCTGGGAGATAGGACTCACAATC
1 TTCAACCTATTCCACTGCTGACCAGGGAGATAGGATTCACAATC
* *
18643950 TTCAACCTATTCCACTACTGACTAGGGAGATAGG-------A--
1 TTCAACCTATTCCACTGCTGACCAGGGAGATAGGATTCACAATC
18643985 TTC-ACCTATTCCACTGCTGACCAGGGAGATAGGACTT-ACAATC
1 TTCAACCTATTCCACTGCTGACCAGGGAGATAGGA-TTCACAATC
* *
18644028 TTCAACCTATTCCACTGCTGACCAGGGAGATAGAACTCACAATC
1 TTCAACCTATTCCACTGCTGACCAGGGAGATAGGATTCACAATC
* * *
18644072 TTCAACCTATTCCACCGTTGACCAGGGAGATAGGACTCACAATC
1 TTCAACCTATTCCACTGCTGACCAGGGAGATAGGATTCACAATC
*
18644116 TTCAACCTATTCCACTCCTGACCAGGGAGATAGGACTT-ACAATC
1 TTCAACCTATTCCACTGCTGACCAGGGAGATAGGA-TTCACAATC
* *
18644160 TTCAACCTATTTCACTGCTGACCAGGGAGATAGGACTCACAATC
1 TTCAACCTATTCCACTGCTGACCAGGGAGATAGGATTCACAATC
* *
18644204 TTCAACCTATTCCACTGCTGACCAGAGAGATAGGATTCACAATA
1 TTCAACCTATTCCACTGCTGACCAGGGAGATAGGATTCACAATC
* *
18644248 TTCAACCTATTCCATTGCTGACCAGGAAGATA
1 TTCAACCTATTCCACTGCTGACCAGGGAGATA
18644280 AAGCTTTGTG
Statistics
Matches: 373, Mismatches: 31, Indels: 28
0.86 0.07 0.06
Matches are distributed among these distances:
34 28 0.08
35 3 0.01
37 1 0.00
41 1 0.00
43 5 0.01
44 333 0.89
45 2 0.01
ACGTcount: A:0.30, C:0.27, G:0.18, T:0.25
Consensus pattern (44 bp):
TTCAACCTATTCCACTGCTGACCAGGGAGATAGGATTCACAATC
Found at i:18643997 original size:34 final size:34
Alignment explanation
Indices: 18643954--18644018 Score: 112
Period size: 34 Copynumber: 1.9 Consensus size: 34
18643944 ACAATCTTCA
*
18643954 ACCTATTCCACTACTGACTAGGGAGATAGGATTC
1 ACCTATTCCACTACTGACCAGGGAGATAGGATTC
*
18643988 ACCTATTCCACTGCTGACCAGGGAGATAGGA
1 ACCTATTCCACTACTGACCAGGGAGATAGGA
18644019 CTTACAATCT
Statistics
Matches: 29, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
34 29 1.00
ACGTcount: A:0.29, C:0.25, G:0.23, T:0.23
Consensus pattern (34 bp):
ACCTATTCCACTACTGACCAGGGAGATAGGATTC
Found at i:18645617 original size:21 final size:19
Alignment explanation
Indices: 18645593--18645636 Score: 61
Period size: 21 Copynumber: 2.2 Consensus size: 19
18645583 GATTTTTTTC
*
18645593 TTTTTTGGTTTTTTGTGTGTT
1 TTTTTTGGGTTTTT-T-TGTT
18645614 TTTTTTGGGTTTTTTTGTT
1 TTTTTTGGGTTTTTTTGTT
18645633 TTTT
1 TTTT
18645637 GAATTGGATC
Statistics
Matches: 22, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
19 8 0.36
20 1 0.05
21 13 0.59
ACGTcount: A:0.00, C:0.00, G:0.20, T:0.80
Consensus pattern (19 bp):
TTTTTTGGGTTTTTTTGTT
Found at i:18650833 original size:23 final size:22
Alignment explanation
Indices: 18650793--18650836 Score: 70
Period size: 23 Copynumber: 2.0 Consensus size: 22
18650783 AAATTATAAA
*
18650793 ATATAAAAATATATATATGTAC
1 ATATAAAAAAATATATATGTAC
18650815 ATATAAGAAAAATATATATGTA
1 ATATAA-AAAAATATATATGTA
18650837 TGTGAATTAT
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
22 6 0.30
23 14 0.70
ACGTcount: A:0.57, C:0.02, G:0.07, T:0.34
Consensus pattern (22 bp):
ATATAAAAAAATATATATGTAC
Found at i:18651554 original size:23 final size:22
Alignment explanation
Indices: 18651511--18651568 Score: 64
Period size: 22 Copynumber: 2.6 Consensus size: 22
18651501 AAAGGGTATC
* *
18651511 TACAAATTAAATC-TCTAAGAT
1 TACAAATCATATCTTCTAAGAT
18651532 TACAAAATCATATCTTCTAAGAT
1 TAC-AAATCATATCTTCTAAGAT
* *
18651555 TGCATATCATATCT
1 TACAAATCATATCT
18651569 AATATTGCAT
Statistics
Matches: 31, Mismatches: 4, Indels: 3
0.82 0.11 0.08
Matches are distributed among these distances:
21 3 0.10
22 18 0.58
23 10 0.32
ACGTcount: A:0.41, C:0.17, G:0.05, T:0.36
Consensus pattern (22 bp):
TACAAATCATATCTTCTAAGAT
Found at i:18664010 original size:28 final size:28
Alignment explanation
Indices: 18663978--18664033 Score: 103
Period size: 28 Copynumber: 2.0 Consensus size: 28
18663968 ATTTTGAGTA
18663978 AGATTAAGATAAGGATGATAAATTTTAT
1 AGATTAAGATAAGGATGATAAATTTTAT
*
18664006 AGATTAAGATAATGATGATAAATTTTAT
1 AGATTAAGATAAGGATGATAAATTTTAT
18664034 TGTAGGACTT
Statistics
Matches: 27, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
28 27 1.00
ACGTcount: A:0.46, C:0.00, G:0.16, T:0.38
Consensus pattern (28 bp):
AGATTAAGATAAGGATGATAAATTTTAT
Found at i:18665816 original size:21 final size:21
Alignment explanation
Indices: 18665790--18665837 Score: 87
Period size: 21 Copynumber: 2.2 Consensus size: 21
18665780 GATTGGGTCG
18665790 GGTAAGGGGTGTTACAATGTT
1 GGTAAGGGGTGTTACAATGTT
18665811 GGTAAGGGGTGTTACAATGTT
1 GGTAAGGGGTGTTACAATGTT
18665832 GTGTAA
1 G-GTAA
18665838 CAAGTTCATA
Statistics
Matches: 26, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
21 22 0.85
22 4 0.15
ACGTcount: A:0.25, C:0.04, G:0.38, T:0.33
Consensus pattern (21 bp):
GGTAAGGGGTGTTACAATGTT
Found at i:18679917 original size:132 final size:132
Alignment explanation
Indices: 18679768--18680821 Score: 1508
Period size: 132 Copynumber: 8.0 Consensus size: 132
18679758 TAACTTCAGG
* *
18679768 GAGATA-AGATTAGTGGCTTCAATGTACTCCACTGTAACCTCAGGGAGGTAAAATCCGCCATCTT
1 GAGATAGA-ATTACTGGCTTCAATGTACTCCACTGTAACCACAGGGAGGTAAAATCCGCCATCTT
* * * * * * *
18679832 CAATCTGCTCCACTACTGCTTAGGGAGATAAGATCTGTATTCTTCAATCTATTCCACTACTCCCC
65 CGATCTACTCCACTACTACTTAGGGAGGTAAGATCTGAAATCTTCAATCTATTCCACTGCTCCCC
18679897 AGA
130 AGA
* * *
18679900 GAGATAGAATTATTGGCTTCAATGTACTCCACTGTAATCACAGAGAGGTAAAATCCGCCATCTTC
1 GAGATAGAATTACTGGCTTCAATGTACTCCACTGTAACCACAGGGAGGTAAAATCCGCCATCTTC
*
18679965 GATCTACTCCACTACTACTTAGGGAGGTAAGATCTGAAATCTTCAATCTATTCCACTGC-CAACC
66 GATCTACTCCACTACTACTTAGGGAGGTAAGATCTGAAATCTTCAATCTATTCCACTGCTC-CCC
18680029 AGA
130 AGA
* *
18680032 GAGATATAATTACTGGCTTCAATGTACTCCACTGTAACCACAGGGAGGTAAAATCTGCCATCTTC
1 GAGATAGAATTACTGGCTTCAATGTACTCCACTGTAACCACAGGGAGGTAAAATCCGCCATCTTC
* * * * *
18680097 GATATACTCCACTACTACTTAGGGAGGTAAGATTTGAAATCTTCAATCTATTCAACTGCTGCTCA
66 GATCTACTCCACTACTACTTAGGGAGGTAAGATCTGAAATCTTCAATCTATTCCACTGCTCCCCA
*
18680162 GG
131 GA
* * *
18680164 GA-AGTAGAATTACTGGCTTCAATGTACTCCACTGTAATCATAGGGAGGTAAAATCTGCCATCTT
1 GAGA-TAGAATTACTGGCTTCAATGTACTCCACTGTAACCACAGGGAGGTAAAATCCGCCATCTT
* * * *
18680228 CGATCTACTCCACTACTACTTAGAGAGGTAAGATCTAAAATCTTCAATCGATTCCACTGCTGCCC
65 CGATCTACTCCACTACTACTTAGGGAGGTAAGATCTGAAATCTTCAATCTATTCCACTGCTCCCC
*
18680293 AGG
130 AGA
* ** *
18680296 GA-AGTAGAATTACTGGCTTCAATGTACTCCACTGTAATCACAGGGAGGTAAAATTTGCCATATT
1 GAGA-TAGAATTACTGGCTTCAATGTACTCCACTGTAACCACAGGGAGGTAAAATCCGCCATCTT
* ** *
18680360 CGATCTACTCCACTACTACTTAGGGAGGCAAGATCTGCTATCTTCAATCTATTCCACTACTCCCC
65 CGATCTACTCCACTACTACTTAGGGAGGTAAGATCTGAAATCTTCAATCTATTCCACTGCTCCCC
*
18680425 AAA
130 AGA
* * *
18680428 GAGATAGAATTATTGGCTTCAATGTACTCCACTGTAATCACAGAGAGGTAAAATCCGCCATCTTC
1 GAGATAGAATTACTGGCTTCAATGTACTCCACTGTAACCACAGGGAGGTAAAATCCGCCATCTTC
*
18680493 GATCTACTCCACTACTACTTAGGGAGGTAAGATCTGAAATCTTCAATCTATTCCACTGC-CAACC
66 GATCTACTCCACTACTACTTAGGGAGGTAAGATCTGAAATCTTCAATCTATTCCACTGCTC-CCC
18680557 AGA
130 AGA
* *
18680560 GAGATAGAATTACTGGCTTCAATGTACTCCACTGTAACAATAGGGAGGTAAAATCCGCCATCTTC
1 GAGATAGAATTACTGGCTTCAATGTACTCCACTGTAACCACAGGGAGGTAAAATCCGCCATCTTC
* * * * * *
18680625 GATATACTCCACTACTACTTAGGGAGGTAAGATTTGAAATCTTCAATTTATTCAACTGCTGCTCA
66 GATCTACTCCACTACTACTTAGGGAGGTAAGATCTGAAATCTTCAATCTATTCCACTGCTCCCCA
*
18680690 GG
131 GA
* *
18680692 GA-AGTAGAATTACTGGCTTCAATGTACTCCACTGTAATCACAGGGAGGTAAAATCTGCCATCTT
1 GAGA-TAGAATTACTGGCTTCAATGTACTCCACTGTAACCACAGGGAGGTAAAATCCGCCATCTT
* * *
18680756 CGATCTACTCCACTACTACTTAGAGAGGTAAGATCTAAAATCTTCAATCTATTCCACTGCTGCCC
65 CGATCTACTCCACTACTACTTAGGGAGGTAAGATCTGAAATCTTCAATCTATTCCACTGCTCCCC
18680821 A
130 A
18680822 TCAATGTACT
Statistics
Matches: 832, Mismatches: 82, Indels: 16
0.89 0.09 0.02
Matches are distributed among these distances:
131 4 0.00
132 826 0.99
133 2 0.00
ACGTcount: A:0.31, C:0.24, G:0.17, T:0.28
Consensus pattern (132 bp):
GAGATAGAATTACTGGCTTCAATGTACTCCACTGTAACCACAGGGAGGTAAAATCCGCCATCTTC
GATCTACTCCACTACTACTTAGGGAGGTAAGATCTGAAATCTTCAATCTATTCCACTGCTCCCCA
GA
Found at i:18680897 original size:44 final size:46
Alignment explanation
Indices: 18680845--18680959 Score: 117
Period size: 55 Copynumber: 2.3 Consensus size: 46
18680835 CTGTAATCAC
18680845 AGGGAGGTAAAATCTGC-C-ATATTCGATCTACTCCACTACTACTT
1 AGGGAGGTAAAATCTGCACTATATTCGATCTACTCCACTACTACTT
*
18680889 AGGGAGGTAAGATCTGAAATCTTCAATCTATATTCGATCTACTCCACTACTACTT
1 AGGGAGGT---A----AAATCTGC-A-CTATATTCGATCTACTCCACTACTACTT
*
18680944 AGGGAGGTAAGATCTG
1 AGGGAGGTAAAATCTG
18680960 AAATCTTCAA
Statistics
Matches: 57, Mismatches: 3, Indels: 18
0.73 0.04 0.23
Matches are distributed among these distances:
44 8 0.14
47 1 0.02
48 5 0.09
51 7 0.12
52 1 0.02
54 1 0.02
55 34 0.60
ACGTcount: A:0.30, C:0.21, G:0.19, T:0.30
Consensus pattern (46 bp):
AGGGAGGTAAAATCTGCACTATATTCGATCTACTCCACTACTACTT
Found at i:18680909 original size:112 final size:112
Alignment explanation
Indices: 18680710--18680919 Score: 393
Period size: 112 Copynumber: 1.9 Consensus size: 112
18680700 ATTACTGGCT
*
18680710 TCAATGTACTCCACTGTAATCACAGGGAGGTAAAATCTGCCATCTTCGATCTACTCCACTACTAC
1 TCAATGTACTCCACTGTAATCACAGGGAGGTAAAATCTGCCATATTCGATCTACTCCACTACTAC
18680775 TTAGAGAGGTAAGATCTAAAATCTTCAATCTATTCCACTGCTGCCCA
66 TTAGAGAGGTAAGATCTAAAATCTTCAATCTATTCCACTGCTGCCCA
18680822 TCAATGTACTCCACTGTAATCACAGGGAGGTAAAATCTGCCATATTCGATCTACTCCACTACTAC
1 TCAATGTACTCCACTGTAATCACAGGGAGGTAAAATCTGCCATATTCGATCTACTCCACTACTAC
* *
18680887 TTAGGGAGGTAAGATCTGAAATCTTCAATCTAT
66 TTAGAGAGGTAAGATCTAAAATCTTCAATCTAT
18680920 ATTCGATCTA
Statistics
Matches: 95, Mismatches: 3, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
112 95 1.00
ACGTcount: A:0.31, C:0.25, G:0.15, T:0.29
Consensus pattern (112 bp):
TCAATGTACTCCACTGTAATCACAGGGAGGTAAAATCTGCCATATTCGATCTACTCCACTACTAC
TTAGAGAGGTAAGATCTAAAATCTTCAATCTATTCCACTGCTGCCCA
Found at i:18680924 original size:55 final size:55
Alignment explanation
Indices: 18680863--18680974 Score: 224
Period size: 55 Copynumber: 2.0 Consensus size: 55
18680853 AAAATCTGCC
18680863 ATATTCGATCTACTCCACTACTACTTAGGGAGGTAAGATCTGAAATCTTCAATCT
1 ATATTCGATCTACTCCACTACTACTTAGGGAGGTAAGATCTGAAATCTTCAATCT
18680918 ATATTCGATCTACTCCACTACTACTTAGGGAGGTAAGATCTGAAATCTTCAATCT
1 ATATTCGATCTACTCCACTACTACTTAGGGAGGTAAGATCTGAAATCTTCAATCT
18680973 AT
1 AT
18680975 TCCACTGTTG
Statistics
Matches: 57, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
55 57 1.00
ACGTcount: A:0.31, C:0.21, G:0.14, T:0.33
Consensus pattern (55 bp):
ATATTCGATCTACTCCACTACTACTTAGGGAGGTAAGATCTGAAATCTTCAATCT
Found at i:18682400 original size:8 final size:8
Alignment explanation
Indices: 18682389--18682438 Score: 54
Period size: 7 Copynumber: 6.6 Consensus size: 8
18682379 CCCTTTTTAC
18682389 TTTTTCAT
1 TTTTTCAT
18682397 TTTTTCA-
1 TTTTTCAT
18682404 TTTTTCA-
1 TTTTTCAT
18682411 -TTTTCAT
1 TTTTTCAT
*
18682418 TTTTTC-C
1 TTTTTCAT
18682425 TTTTTCAT
1 TTTTTCAT
18682433 ATTTTT
1 -TTTTT
18682439 TCGACTTAAA
Statistics
Matches: 36, Mismatches: 2, Indels: 7
0.80 0.04 0.16
Matches are distributed among these distances:
6 6 0.17
7 13 0.36
8 12 0.33
9 5 0.14
ACGTcount: A:0.12, C:0.14, G:0.00, T:0.74
Consensus pattern (8 bp):
TTTTTCAT
Found at i:18682407 original size:15 final size:15
Alignment explanation
Indices: 18682389--18682438 Score: 59
Period size: 15 Copynumber: 3.3 Consensus size: 15
18682379 CCCTTTTTAC
18682389 TTTTTCATTTTTTCA-
1 TTTTTCA-TTTTTCAT
18682404 TTTTTCA-TTTTCAT
1 TTTTTCATTTTTCAT
*
18682418 TTTTTCCTTTTTCAT
1 TTTTTCATTTTTCAT
18682433 ATTTTT
1 -TTTTT
18682439 TCGACTTAAA
Statistics
Matches: 31, Mismatches: 1, Indels: 5
0.84 0.03 0.14
Matches are distributed among these distances:
13 6 0.19
14 6 0.19
15 14 0.45
16 5 0.16
ACGTcount: A:0.12, C:0.14, G:0.00, T:0.74
Consensus pattern (15 bp):
TTTTTCATTTTTCAT
Found at i:18682414 original size:21 final size:21
Alignment explanation
Indices: 18682390--18682432 Score: 77
Period size: 21 Copynumber: 2.0 Consensus size: 21
18682380 CCTTTTTACT
18682390 TTTTCATTTTTTCATTTTTCA
1 TTTTCATTTTTTCATTTTTCA
*
18682411 TTTTCATTTTTTCCTTTTTCA
1 TTTTCATTTTTTCATTTTTCA
18682432 T
1 T
18682433 ATTTTTTCGA
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
21 21 1.00
ACGTcount: A:0.12, C:0.16, G:0.00, T:0.72
Consensus pattern (21 bp):
TTTTCATTTTTTCATTTTTCA
Found at i:18683342 original size:13 final size:12
Alignment explanation
Indices: 18683294--18683342 Score: 62
Period size: 13 Copynumber: 3.8 Consensus size: 12
18683284 CTCCTTTTTC
*
18683294 TTTTTTCTTTAT
1 TTTTTTTTTTAT
18683306 TTTTATTTTTTAT
1 TTTT-TTTTTTAT
18683319 TTTATTTTTTTAT
1 TTT-TTTTTTTAT
18683332 TTTTTTCTTTT
1 TTTTTT-TTTT
18683343 GACTTTGATT
Statistics
Matches: 33, Mismatches: 1, Indels: 5
0.85 0.03 0.13
Matches are distributed among these distances:
12 7 0.21
13 25 0.76
14 1 0.03
ACGTcount: A:0.10, C:0.04, G:0.00, T:0.86
Consensus pattern (12 bp):
TTTTTTTTTTAT
Found at i:18683342 original size:27 final size:27
Alignment explanation
Indices: 18683296--18683381 Score: 88
Period size: 27 Copynumber: 3.1 Consensus size: 27
18683286 CCTTTTTCTT
18683296 TTTTCTTTATTTTTATT-TTTT-ATTTTA
1 TTTT-TTTATTTTT-TTCTTTTGATTTTA
*
18683323 TTTTTTTATTTTTTTCTTTTGACTTTGA
1 TTTTTTTATTTTTTTCTTTTGA-TTTTA
* *
18683351 TTTTTCT-TTTTCTTCTTTTGATTTTGA
1 TTTTTTTATTTTTTTCTTTTGATTTT-A
18683378 TTTT
1 TTTT
18683382 GATTTTTTTG
Statistics
Matches: 51, Mismatches: 4, Indels: 8
0.81 0.06 0.13
Matches are distributed among these distances:
25 2 0.04
26 16 0.31
27 23 0.45
28 10 0.20
ACGTcount: A:0.10, C:0.07, G:0.05, T:0.78
Consensus pattern (27 bp):
TTTTTTTATTTTTTTCTTTTGATTTTA
Found at i:18683387 original size:27 final size:26
Alignment explanation
Indices: 18683325--18683390 Score: 96
Period size: 27 Copynumber: 2.5 Consensus size: 26
18683315 TTATTTTATT
18683325 TTTTTATTTTTTTCTTTTGACTTTGA
1 TTTTTATTTTTTTCTTTTGACTTTGA
* *
18683351 TTTTTCTTTTTCTTCTTTTGATTTTGA
1 TTTTTATTTTT-TTCTTTTGACTTTGA
*
18683378 TTTTGATTTTTTT
1 TTTTTATTTTTTT
18683391 GATTGAATCT
Statistics
Matches: 35, Mismatches: 4, Indels: 2
0.85 0.10 0.05
Matches are distributed among these distances:
26 12 0.34
27 23 0.66
ACGTcount: A:0.09, C:0.08, G:0.08, T:0.76
Consensus pattern (26 bp):
TTTTTATTTTTTTCTTTTGACTTTGA
Found at i:18693519 original size:3 final size:3
Alignment explanation
Indices: 18693511--18693535 Score: 50
Period size: 3 Copynumber: 8.3 Consensus size: 3
18693501 TGCTTACTAT
18693511 TGA TGA TGA TGA TGA TGA TGA TGA T
1 TGA TGA TGA TGA TGA TGA TGA TGA T
18693536 TATGTGCCTC
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 22 1.00
ACGTcount: A:0.32, C:0.00, G:0.32, T:0.36
Consensus pattern (3 bp):
TGA
Found at i:18704301 original size:21 final size:23
Alignment explanation
Indices: 18704275--18704316 Score: 61
Period size: 23 Copynumber: 1.9 Consensus size: 23
18704265 AATGCATTCA
18704275 TATCA-TAA-AACACAATAATCT
1 TATCATTAAGAACACAATAATCT
*
18704296 TATCATTAAGCACACAATAAT
1 TATCATTAAGAACACAATAAT
18704317 GATATTTAAA
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
21 5 0.28
22 3 0.17
23 10 0.56
ACGTcount: A:0.50, C:0.19, G:0.02, T:0.29
Consensus pattern (23 bp):
TATCATTAAGAACACAATAATCT
Found at i:18707032 original size:18 final size:18
Alignment explanation
Indices: 18707009--18707043 Score: 54
Period size: 18 Copynumber: 1.9 Consensus size: 18
18706999 TATAAACTTT
18707009 AAAATTATATA-TTTTTTA
1 AAAATTA-ATACTTTTTTA
18707027 AAAATTAATACTTTTTT
1 AAAATTAATACTTTTTT
18707044 TCTTTTTCAT
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
17 3 0.19
18 13 0.81
ACGTcount: A:0.43, C:0.03, G:0.00, T:0.54
Consensus pattern (18 bp):
AAAATTAATACTTTTTTA
Found at i:18711445 original size:26 final size:26
Alignment explanation
Indices: 18711381--18711447 Score: 84
Period size: 25 Copynumber: 2.6 Consensus size: 26
18711371 TGTCGATTCT
18711381 CTGAAGCTAGTGTTAGCAACATCGAA
1 CTGAAGCTAGTGTTAGCAACATCGAA
* *
18711407 CT-AAGCTAGTGTTAGCAAC-CCTGAT
1 CTGAAGCTAGTGTTAGCAACATC-GAA
*
18711432 TTGAAGCTAGTGTTAG
1 CTGAAGCTAGTGTTAG
18711448 TAGCTCGGTA
Statistics
Matches: 36, Mismatches: 3, Indels: 4
0.84 0.07 0.09
Matches are distributed among these distances:
24 1 0.03
25 20 0.56
26 15 0.42
ACGTcount: A:0.30, C:0.18, G:0.24, T:0.28
Consensus pattern (26 bp):
CTGAAGCTAGTGTTAGCAACATCGAA
Found at i:18717711 original size:15 final size:16
Alignment explanation
Indices: 18717691--18717725 Score: 54
Period size: 16 Copynumber: 2.2 Consensus size: 16
18717681 AATTTTTTTC
18717691 AAATCA-AATCGAGTG
1 AAATCAGAATCGAGTG
*
18717706 AAATCAGATTCGAGTG
1 AAATCAGAATCGAGTG
18717722 AAAT
1 AAAT
18717726 TATTCTAGTT
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
15 6 0.33
16 12 0.67
ACGTcount: A:0.46, C:0.11, G:0.20, T:0.23
Consensus pattern (16 bp):
AAATCAGAATCGAGTG
Found at i:18717978 original size:29 final size:28
Alignment explanation
Indices: 18717914--18717982 Score: 93
Period size: 28 Copynumber: 2.4 Consensus size: 28
18717904 TTTTAGAAAA
18717914 TTTTAGAATTTTAACTTTCTTATCAAAT
1 TTTTAGAATTTTAACTTTCTTATCAAAT
* ** *
18717942 TTGTAGAATTTTAACTTTCTTTATTTATT
1 TTTTAGAATTTTAACTTTC-TTATCAAAT
18717971 TTTTAGAATTTT
1 TTTTAGAATTTT
18717983 TAAAATTTTT
Statistics
Matches: 35, Mismatches: 5, Indels: 1
0.85 0.12 0.02
Matches are distributed among these distances:
28 18 0.51
29 17 0.49
ACGTcount: A:0.28, C:0.07, G:0.06, T:0.59
Consensus pattern (28 bp):
TTTTAGAATTTTAACTTTCTTATCAAAT
Found at i:18717990 original size:19 final size:18
Alignment explanation
Indices: 18717968--18718052 Score: 54
Period size: 19 Copynumber: 4.7 Consensus size: 18
18717958 TTCTTTATTT
18717968 ATTTTTTAGAATTTTTAAA
1 ATTTTTT-GAATTTTTAAA
* *
18717987 ATTTTTTAAAATATTT---
1 ATTTTTT-GAATTTTTAAA
18718003 -TTTTTTGAAATTTTTATAA
1 ATTTTTTG-AATTTTTA-AA
*
18718022 ATATTTTGAA-TTTTAAA
1 ATTTTTTGAATTTTTAAA
18718039 ATTTATTTTGAATT
1 A-TT-TTTTGAATT
18718053 ATTTTGTAAT
Statistics
Matches: 51, Mismatches: 6, Indels: 17
0.69 0.08 0.23
Matches are distributed among these distances:
15 12 0.24
17 3 0.06
18 6 0.12
19 23 0.45
20 7 0.14
ACGTcount: A:0.35, C:0.00, G:0.05, T:0.60
Consensus pattern (18 bp):
ATTTTTTGAATTTTTAAA
Found at i:18718013 original size:25 final size:25
Alignment explanation
Indices: 18717979--18718042 Score: 76
Period size: 25 Copynumber: 2.5 Consensus size: 25
18717969 TTTTTTAGAA
18717979 TTTTTAAAATTTTT-TAAAATATTTT
1 TTTTTAAAATTTTTAT-AAATATTTT
*
18718004 TTTTTGAAATTTTTATAAATATTTT
1 TTTTTAAAATTTTTATAAATATTTT
*
18718029 GAATTTTAAAATTT
1 --TTTTTAAAATTT
18718043 ATTTTGAATT
Statistics
Matches: 33, Mismatches: 3, Indels: 4
0.82 0.08 0.10
Matches are distributed among these distances:
25 22 0.67
26 1 0.03
27 10 0.30
ACGTcount: A:0.36, C:0.00, G:0.03, T:0.61
Consensus pattern (25 bp):
TTTTTAAAATTTTTATAAATATTTT
Found at i:18735119 original size:15 final size:15
Alignment explanation
Indices: 18735084--18735135 Score: 56
Period size: 15 Copynumber: 3.6 Consensus size: 15
18735074 TTAAGAATTT
*
18735084 TATTAAATTAT-ATA
1 TATTTAATTATAATA
18735098 T-TTTAATTATAATA
1 TATTTAATTATAATA
*
18735112 TATTTAATAATAAT-
1 TATTTAATTATAATA
18735126 TATGTTAATT
1 TAT-TTAATT
18735136 TAAATTTTAT
Statistics
Matches: 32, Mismatches: 3, Indels: 5
0.80 0.08 0.12
Matches are distributed among these distances:
13 8 0.25
14 8 0.25
15 16 0.50
ACGTcount: A:0.44, C:0.00, G:0.02, T:0.54
Consensus pattern (15 bp):
TATTTAATTATAATA
Found at i:18735165 original size:120 final size:120
Alignment explanation
Indices: 18735033--18735251 Score: 420
Period size: 120 Copynumber: 1.8 Consensus size: 120
18735023 AACACGATTT
*
18735033 TATATTATGATTTGAGTAAATTCATATAAGAATATTAATTATTAAGAATTTTATTAAATTATATA
1 TATATTATGATTTGAGTAAATTCATATAAGAATACTAATTATTAAGAATTTTATTAAATTATATA
18735098 TTTTAATTATAATATATTTAATAATAATTATGTTAATTTAAATTTTATAGTATCA
66 TTTTAATTATAATATATTTAATAATAATTATGTTAATTTAAATTTTATAGTATCA
*
18735153 TATATTATGATTTGAGTAAATTCATATAAGAATACTGATTATTAAGAATTTTATTAAATTATATA
1 TATATTATGATTTGAGTAAATTCATATAAGAATACTAATTATTAAGAATTTTATTAAATTATATA
18735218 TTTTAATTATAATATATTTAATAATAATTATGTT
66 TTTTAATTATAATATATTTAATAATAATTATGTT
18735252 TAAATATGAT
Statistics
Matches: 97, Mismatches: 2, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
120 97 1.00
ACGTcount: A:0.43, C:0.02, G:0.06, T:0.49
Consensus pattern (120 bp):
TATATTATGATTTGAGTAAATTCATATAAGAATACTAATTATTAAGAATTTTATTAAATTATATA
TTTTAATTATAATATATTTAATAATAATTATGTTAATTTAAATTTTATAGTATCA
Found at i:18735217 original size:61 final size:60
Alignment explanation
Indices: 18735033--18735219 Score: 195
Period size: 61 Copynumber: 3.1 Consensus size: 60
18735023 AACACGATTT
*
18735033 TATATTATGATTTGAGTAAATTCATATAAGAATATTAATTATTAAGAATTTTATTAAATTA
1 TATATTATGATTTGAGTAAATTCATATAAGAATA-TGATTATTAAGAATTTTATTAAATTA
* * * * * * * * *
18735094 TATATTTTAATTAT-AATATATTTA-ATAATAATTATG-TTAATTTA-AATTTTA-TAGTATCA
1 TATATTATGATT-TGAGTAAATTCATATAAGAA-TATGATT-ATTAAGAATTTTATTA-AATTA
18735153 TATATTATGATTTGAGTAAATTCATATAAGAATACTGATTATTAAGAATTTTATTAAATTA
1 TATATTATGATTTGAGTAAATTCATATAAGAATA-TGATTATTAAGAATTTTATTAAATTA
18735214 TATATT
1 TATATT
18735220 TTAATTATAA
Statistics
Matches: 97, Mismatches: 19, Indels: 20
0.71 0.14 0.15
Matches are distributed among these distances:
58 3 0.03
59 31 0.32
60 23 0.24
61 37 0.38
62 3 0.03
ACGTcount: A:0.43, C:0.02, G:0.07, T:0.48
Consensus pattern (60 bp):
TATATTATGATTTGAGTAAATTCATATAAGAATATGATTATTAAGAATTTTATTAAATTA
Found at i:18735234 original size:16 final size:16
Alignment explanation
Indices: 18735213--18735254 Score: 52
Period size: 15 Copynumber: 2.7 Consensus size: 16
18735203 TTATTAAATT
*
18735213 ATATATTTTAATTATA
1 ATATATTTTAATAATA
18735229 ATATA-TTTAATAATA
1 ATATATTTTAATAATA
18735244 AT-TATGTTTAA
1 ATATAT-TTTAA
18735255 ATATGATTAA
Statistics
Matches: 23, Mismatches: 1, Indels: 4
0.82 0.04 0.14
Matches are distributed among these distances:
14 2 0.09
15 11 0.48
16 10 0.43
ACGTcount: A:0.45, C:0.00, G:0.02, T:0.52
Consensus pattern (16 bp):
ATATATTTTAATAATA
Found at i:18735239 original size:15 final size:15
Alignment explanation
Indices: 18735204--18735245 Score: 52
Period size: 15 Copynumber: 2.9 Consensus size: 15
18735194 TTAAGAATTT
*
18735204 TATTAAATTAT-ATA
1 TATTTAATTATAATA
18735218 T-TTTAATTATAATA
1 TATTTAATTATAATA
*
18735232 TATTTAATAATAAT
1 TATTTAATTATAAT
18735246 TATGTTTAAA
Statistics
Matches: 24, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
13 8 0.33
14 5 0.21
15 11 0.46
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (15 bp):
TATTTAATTATAATA
Found at i:18735489 original size:16 final size:16
Alignment explanation
Indices: 18735468--18735527 Score: 102
Period size: 16 Copynumber: 3.8 Consensus size: 16
18735458 TTGATTTGCT
18735468 ATTACACCTCTATTCC
1 ATTACACCTCTATTCC
*
18735484 ATTACACCTCTAATCC
1 ATTACACCTCTATTCC
18735500 ATTACACCTCTATTCC
1 ATTACACCTCTATTCC
*
18735516 ATTACGCCTCTA
1 ATTACACCTCTA
18735528 ATTCAATACA
Statistics
Matches: 41, Mismatches: 3, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
16 41 1.00
ACGTcount: A:0.27, C:0.37, G:0.02, T:0.35
Consensus pattern (16 bp):
ATTACACCTCTATTCC
Found at i:18735509 original size:32 final size:32
Alignment explanation
Indices: 18735468--18735529 Score: 115
Period size: 32 Copynumber: 1.9 Consensus size: 32
18735458 TTGATTTGCT
18735468 ATTACACCTCTATTCCATTACACCTCTAATCC
1 ATTACACCTCTATTCCATTACACCTCTAATCC
*
18735500 ATTACACCTCTATTCCATTACGCCTCTAAT
1 ATTACACCTCTATTCCATTACACCTCTAAT
18735530 TCAATACAGC
Statistics
Matches: 29, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
32 29 1.00
ACGTcount: A:0.27, C:0.35, G:0.02, T:0.35
Consensus pattern (32 bp):
ATTACACCTCTATTCCATTACACCTCTAATCC
Found at i:18737737 original size:20 final size:20
Alignment explanation
Indices: 18737696--18737738 Score: 52
Period size: 19 Copynumber: 2.1 Consensus size: 20
18737686 TAGATTGTTA
* *
18737696 ATATCAATATTTATATAAAT
1 ATATCAATATTTAAAGAAAT
18737716 ATAT-AATATTTAAAGAAGAT
1 ATATCAATATTTAAAGAA-AT
18737736 ATA
1 ATA
18737739 GTATATATAT
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
19 11 0.55
20 9 0.45
ACGTcount: A:0.53, C:0.02, G:0.05, T:0.40
Consensus pattern (20 bp):
ATATCAATATTTAAAGAAAT
Found at i:18739544 original size:3 final size:3
Alignment explanation
Indices: 18739538--18739585 Score: 60
Period size: 3 Copynumber: 16.0 Consensus size: 3
18739528 TCAGATTTTT
* * * *
18739538 TTA TTA TCA TTG TTA TTA TTA ATA TTA TTA TCA TTA TTA TTA TTA TTA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
18739586 CTTTTTTTTT
Statistics
Matches: 37, Mismatches: 8, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
3 37 1.00
ACGTcount: A:0.33, C:0.04, G:0.02, T:0.60
Consensus pattern (3 bp):
TTA
Found at i:18748651 original size:23 final size:21
Alignment explanation
Indices: 18748625--18748669 Score: 63
Period size: 22 Copynumber: 2.0 Consensus size: 21
18748615 ATTAATAAAA
18748625 ATAAAATTATTTATATTTATTAT
1 ATAAAA-TATTTATATTT-TTAT
*
18748648 ATAAAATATTTTTATTTTTAT
1 ATAAAATATTTATATTTTTAT
18748669 A
1 A
18748670 CATCCTAAAA
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
21 5 0.24
22 10 0.48
23 6 0.29
ACGTcount: A:0.42, C:0.00, G:0.00, T:0.58
Consensus pattern (21 bp):
ATAAAATATTTATATTTTTAT
Found at i:18748875 original size:20 final size:20
Alignment explanation
Indices: 18748833--18748913 Score: 76
Period size: 21 Copynumber: 4.0 Consensus size: 20
18748823 GATTTTATTA
* *
18748833 TTTT-TAAATTTATTTAATAT
1 TTTTATAAATTTA-TAAATTT
18748853 TTTTATAAATTT-TAATATTT
1 TTTTATAAATTTATAA-ATTT
*
18748873 TTTTACAAATTTATAAATTTT
1 TTTTATAAATTTATAAA-TTT
* *
18748894 TTTTAAAAATTTAAAAATTT
1 TTTTATAAATTTATAAATTT
18748914 AAATTTTTTA
Statistics
Matches: 52, Mismatches: 5, Indels: 8
0.80 0.08 0.12
Matches are distributed among these distances:
19 2 0.04
20 22 0.42
21 28 0.54
ACGTcount: A:0.40, C:0.01, G:0.00, T:0.59
Consensus pattern (20 bp):
TTTTATAAATTTATAAATTT
Found at i:18759247 original size:20 final size:19
Alignment explanation
Indices: 18759214--18759285 Score: 72
Period size: 20 Copynumber: 3.6 Consensus size: 19
18759204 GCATCATAGA
*
18759214 TGCATAACAGAGGCACTGAAG
1 TGCA-AACAAAGGCAC-GAAG
18759235 TGCAAACAAAGGCACGAACG
1 TGCAAACAAAGGCACGAA-G
* * *
18759255 TGCGATCAGAGGCACCGAAG
1 TGCAAACAAAGGCA-CGAAG
18759275 TGCAAACAAAG
1 TGCAAACAAAG
18759286 AGACCAAAGT
Statistics
Matches: 42, Mismatches: 7, Indels: 5
0.78 0.13 0.09
Matches are distributed among these distances:
19 3 0.07
20 31 0.74
21 8 0.19
ACGTcount: A:0.40, C:0.22, G:0.28, T:0.10
Consensus pattern (19 bp):
TGCAAACAAAGGCACGAAG
Found at i:18760722 original size:50 final size:50
Alignment explanation
Indices: 18760659--18760843 Score: 190
Period size: 50 Copynumber: 3.6 Consensus size: 50
18760649 CAATGTCATA
* ** * * *
18760659 TCCCAAATATGGTCTTACATGGGAGTTCTCATATCGGTGCCCATGTCATG
1 TCCCAAACATGGTCTTACATGGGACCTCTCATATCGGTGCCAACGCCATG
* * * * *
18760709 TCCTAGAGATGGTCTTACAGGGGACCTCTCATCTCGGTGCCAACGCCATG
1 TCCCAAACATGGTCTTACATGGGACCTCTCATATCGGTGCCAACGCCATG
* *
18760759 TCCCAAACATGGTCTTACATGGGACCTCTCATAACCTCAATGATGCCAATGCCATG
1 TCCCAAACATGGTCTTACATGGGACCTCTCAT-A--TC---GGTGCCAACGCCATG
*
18760815 TCCCAAACATGGTCTTACATGGGATCTCT
1 TCCCAAACATGGTCTTACATGGGACCTCT
18760844 TTACCCAAAT
Statistics
Matches: 111, Mismatches: 18, Indels: 6
0.82 0.13 0.04
Matches are distributed among these distances:
50 68 0.61
53 2 0.02
56 41 0.37
ACGTcount: A:0.24, C:0.28, G:0.21, T:0.28
Consensus pattern (50 bp):
TCCCAAACATGGTCTTACATGGGACCTCTCATATCGGTGCCAACGCCATG
Found at i:18765535 original size:278 final size:278
Alignment explanation
Indices: 18765038--18765600 Score: 1000
Period size: 278 Copynumber: 2.0 Consensus size: 278
18765028 ATAACAGAAA
*
18765038 TCATAGAGAGAGAACCATCTGACTCATTTGAATCAACCCGGATAATATCACCATTTTCACATTTC
1 TCATAGAGAGAGAACCATCTGACTCATCTGAATCAACCCGGATAATATCACCATTTTCACATTTC
* * **
18765103 AACTCCATGTATTTCTTTCTGCAATTTACTATCACATCATGGGCAGTCAACCAATCCATACCAAG
66 AACTCAATGTATTTATTTCCACAATTTACTATCACATCATGGGCAGTCAACCAATCCATACCAAG
* * *
18765168 AATCACATCAAACTCATCAAATGACAATAGCAAGAGATCGGTCGAAAAATAATGACCTCTAATCA
131 AATCACATCAAACTCATCAAACGACAATAGCAAGAGATCGGCCGAAAAACAATGACCTCTAATCA
*
18765233 TCAAAGGGTAACTCTTACATACTTTATCTACTAACACATACTGGCCTAATGGATTTGATACTTTA
196 TCAAAGGGCAACTCTTACATACTTTATCTACTAACACATACTGGCCTAATGGATTTGATACTTTA
18765298 ATTACAAATTCAGTGGAT
261 ATTACAAATTCAGTGGAT
18765316 TCATAGAGAGAGAACCATCTGACTCATCTGAATCAACCCGGATAATATCACCATTTTCACATTTC
1 TCATAGAGAGAGAACCATCTGACTCATCTGAATCAACCCGGATAATATCACCATTTTCACATTTC
18765381 AACTCAATGTATTTATTTCCACAATTTACTATCACATCATGGGCAGTCAACCAATCCATACCAAG
66 AACTCAATGTATTTATTTCCACAATTTACTATCACATCATGGGCAGTCAACCAATCCATACCAAG
* * * *
18765446 AATCACATTAAACTCATCAAACGGCAATAGCATGAGATTGGCCGAAAAACAATGACCTCTAATCA
131 AATCACATCAAACTCATCAAACGACAATAGCAAGAGATCGGCCGAAAAACAATGACCTCTAATCA
18765511 TCAAAGGGCAACTCTTACATACTTTATCTACTAACACATACTGGCCTAATGGATTTGATACTTTA
196 TCAAAGGGCAACTCTTACATACTTTATCTACTAACACATACTGGCCTAATGGATTTGATACTTTA
18765576 ATTACAAATTCAGTGGAT
261 ATTACAAATTCAGTGGAT
18765594 TCTATAG
1 TC-ATAG
18765601 GCATGTTCAT
Statistics
Matches: 271, Mismatches: 13, Indels: 1
0.95 0.05 0.00
Matches are distributed among these distances:
278 267 0.99
279 4 0.01
ACGTcount: A:0.36, C:0.23, G:0.12, T:0.29
Consensus pattern (278 bp):
TCATAGAGAGAGAACCATCTGACTCATCTGAATCAACCCGGATAATATCACCATTTTCACATTTC
AACTCAATGTATTTATTTCCACAATTTACTATCACATCATGGGCAGTCAACCAATCCATACCAAG
AATCACATCAAACTCATCAAACGACAATAGCAAGAGATCGGCCGAAAAACAATGACCTCTAATCA
TCAAAGGGCAACTCTTACATACTTTATCTACTAACACATACTGGCCTAATGGATTTGATACTTTA
ATTACAAATTCAGTGGAT
Found at i:18768713 original size:50 final size:51
Alignment explanation
Indices: 18768588--18768834 Score: 214
Period size: 50 Copynumber: 4.8 Consensus size: 51
18768578 GATAATAACA
* * ** * * *
18768588 TGCCAAAGCCATGTCCCAGACATGGTCTTACATGAGATGTTTCTTGTAC--
1 TGCCAATGCCATGTCCCAGACATGGTCTTACATGGGACCTCTCATATACGG
* * * * **
18768637 TACCAATGTCATATCCCAGATATGGTCTTACATGGGAGTTCTCATAT-CGG
1 TGCCAATGCCATGTCCCAGACATGGTCTTACATGGGACCTCTCATATACGG
* ** *
18768687 TGCCCATGCCATGTCCCAGACATGGTCTTACGGGGGACCTCTCATCT-CGG
1 TGCCAATGCCATGTCCCAGACATGGTCTTACATGGGACCTCTCATATACGG
* * * * *
18768737 TGCTAACGCCATGTCCCAAACATGGTCTTACATGGGACCTCTCATAACCTTAATGA
1 TGCCAATGCCATGTCCCAGACATGGTCTTACATGGGACCTCTCAT-A---T-ACGG
*
18768793 TGCCAATGCCATGTCCCAGACATGGTCTTACATGGGATCTCT
1 TGCCAATGCCATGTCCCAGACATGGTCTTACATGGGACCTCT
18768835 TTACCCAAAT
Statistics
Matches: 156, Mismatches: 34, Indels: 9
0.78 0.17 0.05
Matches are distributed among these distances:
48 1 0.01
49 36 0.23
50 79 0.51
54 1 0.01
56 39 0.25
ACGTcount: A:0.23, C:0.28, G:0.21, T:0.28
Consensus pattern (51 bp):
TGCCAATGCCATGTCCCAGACATGGTCTTACATGGGACCTCTCATATACGG
Found at i:18770067 original size:20 final size:20
Alignment explanation
Indices: 18770042--18770087 Score: 83
Period size: 20 Copynumber: 2.3 Consensus size: 20
18770032 TCGGGATGTT
*
18770042 ACAGAGGCATCGAAGTGCAG
1 ACAGAGGCATCGAAGTGCAA
18770062 ACAGAGGCATCGAAGTGCAA
1 ACAGAGGCATCGAAGTGCAA
18770082 ACAGAG
1 ACAGAG
18770088 AGACCAAAGT
Statistics
Matches: 25, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
20 25 1.00
ACGTcount: A:0.39, C:0.20, G:0.33, T:0.09
Consensus pattern (20 bp):
ACAGAGGCATCGAAGTGCAA
Found at i:18784025 original size:6 final size:6
Alignment explanation
Indices: 18784014--18784087 Score: 72
Period size: 6 Copynumber: 13.2 Consensus size: 6
18784004 GGGATCACTA
18784014 ACTAAT ACTAAT -CTAAT -CT-A- ACTAAT ACTAAT -CTAAT ACTAAT
1 ACTAAT ACTAAT ACTAAT ACTAAT ACTAAT ACTAAT ACTAAT ACTAAT
*
18784057 A-GAAT ACTAAT -CTAAT ACTCTAAT ACTAAT A
1 ACTAAT ACTAAT ACTAAT A--CTAAT ACTAAT A
18784088 GAATAGAAAA
Statistics
Matches: 58, Mismatches: 2, Indels: 16
0.76 0.03 0.21
Matches are distributed among these distances:
4 3 0.05
5 22 0.38
6 27 0.47
8 6 0.10
ACGTcount: A:0.47, C:0.18, G:0.01, T:0.34
Consensus pattern (6 bp):
ACTAAT
Found at i:18784031 original size:5 final size:5
Alignment explanation
Indices: 18784011--18784072 Score: 56
Period size: 5 Copynumber: 12.0 Consensus size: 5
18784001 GCCGGGATCA
18784011 CTAA- CTAAT ACTAAT CTAAT CTAA- CTAAT ACTAAT CTAAT ACTAAT
1 CTAAT CTAAT -CTAAT CTAAT CTAAT CTAAT -CTAAT CTAAT -CTAAT
**
18784057 AGAAT ACTAAT CTAAT
1 CTAAT -CTAAT CTAAT
18784073 ACTCTAATAC
Statistics
Matches: 48, Mismatches: 4, Indels: 11
0.76 0.06 0.17
Matches are distributed among these distances:
4 8 0.17
5 22 0.46
6 18 0.38
ACGTcount: A:0.47, C:0.18, G:0.02, T:0.34
Consensus pattern (5 bp):
CTAAT
Found at i:18784049 original size:11 final size:11
Alignment explanation
Indices: 18784010--18784086 Score: 94
Period size: 11 Copynumber: 7.5 Consensus size: 11
18784000 AGCCGGGATC
18784010 ACTAA-CTAAT
1 ACTAATCTAAT
18784020 ACTAATCTAAT
1 ACTAATCTAAT
18784031 -CTAA-CTAAT
1 ACTAATCTAAT
18784040 ACTAATCTAAT
1 ACTAATCTAAT
**
18784051 ACTAATAGAAT
1 ACTAATCTAAT
18784062 ACTAATCTAAT
1 ACTAATCTAAT
18784073 AC---TCTAAT
1 ACTAATCTAAT
18784081 ACTAAT
1 ACTAAT
18784087 AGAATAGAAA
Statistics
Matches: 57, Mismatches: 4, Indels: 11
0.79 0.06 0.15
Matches are distributed among these distances:
8 8 0.14
9 5 0.09
10 13 0.23
11 31 0.54
ACGTcount: A:0.47, C:0.18, G:0.01, T:0.34
Consensus pattern (11 bp):
ACTAATCTAAT
Found at i:18784065 original size:22 final size:21
Alignment explanation
Indices: 18784010--18784086 Score: 108
Period size: 20 Copynumber: 3.8 Consensus size: 21
18784000 AGCCGGGATC
18784010 ACTAACTAATACTAATCTAAT
1 ACTAACTAATACTAATCTAAT
18784031 -CTAACTAATACTAATCTAAT
1 ACTAACTAATACTAATCTAAT
18784051 ACTAA-TAGAATACTAATCTAAT
1 ACTAACT--AATACTAATCTAAT
18784073 ACT--CTAATACTAAT
1 ACTAACTAATACTAAT
18784087 AGAATAGAAA
Statistics
Matches: 52, Mismatches: 0, Indels: 10
0.84 0.00 0.16
Matches are distributed among these distances:
19 9 0.17
20 21 0.40
21 5 0.10
22 17 0.33
ACGTcount: A:0.47, C:0.18, G:0.01, T:0.34
Consensus pattern (21 bp):
ACTAACTAATACTAATCTAAT
Found at i:18784118 original size:13 final size:13
Alignment explanation
Indices: 18784084--18784110 Score: 54
Period size: 13 Copynumber: 2.1 Consensus size: 13
18784074 CTCTAATACT
18784084 AATAGAATAGAAA
1 AATAGAATAGAAA
18784097 AATAGAATAGAAA
1 AATAGAATAGAAA
18784110 A
1 A
18784111 TACTAATATA
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):
AATAGAATAGAAA
Found at i:18784118 original size:18 final size:18
Alignment explanation
Indices: 18784078--18784127 Score: 56
Period size: 18 Copynumber: 3.1 Consensus size: 18
18784068 CTAATACTCT
18784078 AATACTAATAGAATAG--
1 AATACTAATAGAATAGAA
18784094 AA-A--AATAGAATAGAA
1 AATACTAATAGAATAGAA
*
18784109 AATACTAATATAATAGAA
1 AATACTAATAGAATAGAA
18784127 A
1 A
18784128 GAACTGTCTT
Statistics
Matches: 28, Mismatches: 1, Indels: 8
0.76 0.03 0.22
Matches are distributed among these distances:
13 10 0.36
15 3 0.11
16 3 0.11
18 12 0.43
ACGTcount: A:0.64, C:0.04, G:0.10, T:0.22
Consensus pattern (18 bp):
AATACTAATAGAATAGAA
Found at i:18792436 original size:18 final size:18
Alignment explanation
Indices: 18792357--18792450 Score: 131
Period size: 18 Copynumber: 5.4 Consensus size: 18
18792347 CAAGGTCACG
*
18792357 ATCAATAGCGTCACTATC
1 ATCAATATCGTCACTATC
* *
18792375 ATCAATAGCGTCACTAGC
1 ATCAATATCGTCACTATC
*
18792393 ATCAATATCGTCACTAGC
1 ATCAATATCGTCACTATC
18792411 ATCAATATCGTCACTATC
1 ATCAATATCGTCACTATC
18792429 ATCAATATCG--A-TATC
1 ATCAATATCGTCACTATC
18792444 ATCAATA
1 ATCAATA
18792451 AGAAAACCTT
Statistics
Matches: 73, Mismatches: 3, Indels: 3
0.92 0.04 0.04
Matches are distributed among these distances:
15 11 0.15
16 1 0.01
18 61 0.84
ACGTcount: A:0.36, C:0.26, G:0.10, T:0.29
Consensus pattern (18 bp):
ATCAATATCGTCACTATC
Found at i:18792437 original size:9 final size:9
Alignment explanation
Indices: 18792357--18792437 Score: 54
Period size: 9 Copynumber: 9.0 Consensus size: 9
18792347 CAAGGTCACG
*
18792357 ATCAATAGC
1 ATCAATATC
* *
18792366 GTCACTATC
1 ATCAATATC
*
18792375 ATCAATAGC
1 ATCAATATC
* * *
18792384 GTCACTAGC
1 ATCAATATC
18792393 ATCAATATC
1 ATCAATATC
* * *
18792402 GTCACTAGC
1 ATCAATATC
18792411 ATCAATATC
1 ATCAATATC
* *
18792420 GTCACTATC
1 ATCAATATC
18792429 ATCAATATC
1 ATCAATATC
18792438 GATATCATCA
Statistics
Matches: 51, Mismatches: 21, Indels: 0
0.71 0.29 0.00
Matches are distributed among these distances:
9 51 1.00
ACGTcount: A:0.35, C:0.27, G:0.10, T:0.28
Consensus pattern (9 bp):
ATCAATATC
Found at i:18813375 original size:2 final size:2
Alignment explanation
Indices: 18813370--18813399 Score: 51
Period size: 2 Copynumber: 15.0 Consensus size: 2
18813360 TATATATATA
*
18813370 TG TG TG TG CG TG TG TG TG TG TG TG TG TG TG
1 TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG
18813400 ATATTTTCTT
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.00, C:0.03, G:0.50, T:0.47
Consensus pattern (2 bp):
TG
Found at i:18817129 original size:27 final size:27
Alignment explanation
Indices: 18817099--18817150 Score: 79
Period size: 27 Copynumber: 1.9 Consensus size: 27
18817089 AAGCATACTC
18817099 CAAACAAAAAGAGTAAA-AAAAAAGAGT
1 CAAACAAAAAGAG-AAACAAAAAAGAGT
*
18817126 CAAACAAATAGAGAAACAAAAAAGA
1 CAAACAAAAAGAGAAACAAAAAAGA
18817151 AAATAAATCA
Statistics
Matches: 23, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
26 3 0.13
27 20 0.87
ACGTcount: A:0.71, C:0.10, G:0.13, T:0.06
Consensus pattern (27 bp):
CAAACAAAAAGAGAAACAAAAAAGAGT
Found at i:18817138 original size:14 final size:14
Alignment explanation
Indices: 18817099--18817147 Score: 59
Period size: 13 Copynumber: 3.7 Consensus size: 14
18817089 AAGCATACTC
18817099 CAAACAAAAAGAGT
1 CAAACAAAAAGAGT
*
18817113 -AAAAAAAAAGAGT
1 CAAACAAAAAGAGT
*
18817126 CAAACAAATAGAG-
1 CAAACAAAAAGAGT
18817139 -AAACAAAAA
1 CAAACAAAAA
18817148 AGAAAATAAA
Statistics
Matches: 30, Mismatches: 4, Indels: 4
0.79 0.11 0.11
Matches are distributed among these distances:
12 8 0.27
13 12 0.40
14 10 0.33
ACGTcount: A:0.71, C:0.10, G:0.12, T:0.06
Consensus pattern (14 bp):
CAAACAAAAAGAGT
Found at i:18817867 original size:19 final size:19
Alignment explanation
Indices: 18817810--18817870 Score: 54
Period size: 19 Copynumber: 3.3 Consensus size: 19
18817800 GTTTTGTGTC
* *
18817810 ATAAGAATTAAAATAGAATA
1 ATAATAATTAAATTA-AATA
* **
18817830 A-AATAAAT-AATTAGTTA
1 ATAATAATTAAATTAAATA
18817847 ATAATAATTAAATTAAATA
1 ATAATAATTAAATTAAATA
18817866 ATAAT
1 ATAAT
18817871 GATATCAATA
Statistics
Matches: 31, Mismatches: 8, Indels: 5
0.70 0.18 0.11
Matches are distributed among these distances:
17 3 0.10
18 10 0.32
19 17 0.55
20 1 0.03
ACGTcount: A:0.62, C:0.00, G:0.05, T:0.33
Consensus pattern (19 bp):
ATAATAATTAAATTAAATA
Found at i:18822873 original size:18 final size:20
Alignment explanation
Indices: 18822847--18822889 Score: 63
Period size: 20 Copynumber: 2.2 Consensus size: 20
18822837 AGATGACACC
*
18822847 TTAACATTT-AAT-TAATTT
1 TTAAAATTTAAATATAATTT
18822865 TTAAAATTTAAATATAATTT
1 TTAAAATTTAAATATAATTT
18822885 TTAAA
1 TTAAA
18822890 TAATCTTAGT
Statistics
Matches: 22, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
18 8 0.36
19 3 0.14
20 11 0.50
ACGTcount: A:0.47, C:0.02, G:0.00, T:0.51
Consensus pattern (20 bp):
TTAAAATTTAAATATAATTT
Found at i:18823231 original size:28 final size:29
Alignment explanation
Indices: 18823200--18823261 Score: 74
Period size: 28 Copynumber: 2.1 Consensus size: 29
18823190 AATTCTTTTT
*
18823200 AAAATA-ATAAATTTTTTGTAAAAA-ATTA
1 AAAATATATAAA-ATTTTGTAAAAATATTA
*
18823228 AAAATATTTAAAATTTTGTAAAAATTATTA
1 AAAATATATAAAATTTTGTAAAAA-TATTA
18823258 AAAA
1 AAAA
18823262 CTCTAAAAAA
Statistics
Matches: 29, Mismatches: 2, Indels: 4
0.83 0.06 0.11
Matches are distributed among these distances:
28 17 0.59
29 4 0.14
30 8 0.28
ACGTcount: A:0.58, C:0.00, G:0.03, T:0.39
Consensus pattern (29 bp):
AAAATATATAAAATTTTGTAAAAATATTA
Found at i:18827985 original size:23 final size:23
Alignment explanation
Indices: 18827958--18828055 Score: 153
Period size: 23 Copynumber: 4.3 Consensus size: 23
18827948 AGTGTTATTG
*
18827958 ATCAGTGGTAACTTCGGCTACAT
1 ATCAGTGGTAGCTTCGGCTACAT
* *
18827981 TTCAGTGGTAGCTTTGGCTACAT
1 ATCAGTGGTAGCTTCGGCTACAT
*
18828004 -CCAGTGGTAGCTTCGGCTACAT
1 ATCAGTGGTAGCTTCGGCTACAT
18828026 ATCAGTGGTAGCTTCGGCTACAT
1 ATCAGTGGTAGCTTCGGCTACAT
18828049 ATCAGTG
1 ATCAGTG
18828056 TGGCACTTAT
Statistics
Matches: 68, Mismatches: 6, Indels: 2
0.89 0.08 0.03
Matches are distributed among these distances:
22 20 0.29
23 48 0.71
ACGTcount: A:0.21, C:0.21, G:0.26, T:0.32
Consensus pattern (23 bp):
ATCAGTGGTAGCTTCGGCTACAT
Found at i:18828024 original size:45 final size:45
Alignment explanation
Indices: 18827960--18828048 Score: 151
Period size: 45 Copynumber: 2.0 Consensus size: 45
18827950 TGTTATTGAT
* *
18827960 CAGTGGTAACTTCGGCTACATTTCAGTGGTAGCTTTGGCTACATC
1 CAGTGGTAACTTCGGCTACATATCAGTGGTAGCTTCGGCTACATC
*
18828005 CAGTGGTAGCTTCGGCTACATATCAGTGGTAGCTTCGGCTACAT
1 CAGTGGTAACTTCGGCTACATATCAGTGGTAGCTTCGGCTACAT
18828049 ATCAGTGTGG
Statistics
Matches: 41, Mismatches: 3, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
45 41 1.00
ACGTcount: A:0.20, C:0.22, G:0.26, T:0.31
Consensus pattern (45 bp):
CAGTGGTAACTTCGGCTACATATCAGTGGTAGCTTCGGCTACATC
Found at i:18833465 original size:23 final size:23
Alignment explanation
Indices: 18833438--18833535 Score: 153
Period size: 23 Copynumber: 4.3 Consensus size: 23
18833428 AGTGTTATTG
*
18833438 ATCAGTGGTAACTTCGGCTACAT
1 ATCAGTGGTAGCTTCGGCTACAT
* *
18833461 TTCAGTGGTAGCTTTGGCTACAT
1 ATCAGTGGTAGCTTCGGCTACAT
*
18833484 -CCAGTGGTAGCTTCGGCTACAT
1 ATCAGTGGTAGCTTCGGCTACAT
18833506 ATCAGTGGTAGCTTCGGCTACAT
1 ATCAGTGGTAGCTTCGGCTACAT
18833529 ATCAGTG
1 ATCAGTG
18833536 TGGCACTTAT
Statistics
Matches: 68, Mismatches: 6, Indels: 2
0.89 0.08 0.03
Matches are distributed among these distances:
22 20 0.29
23 48 0.71
ACGTcount: A:0.21, C:0.21, G:0.26, T:0.32
Consensus pattern (23 bp):
ATCAGTGGTAGCTTCGGCTACAT
Found at i:18833504 original size:45 final size:45
Alignment explanation
Indices: 18833440--18833528 Score: 151
Period size: 45 Copynumber: 2.0 Consensus size: 45
18833430 TGTTATTGAT
* *
18833440 CAGTGGTAACTTCGGCTACATTTCAGTGGTAGCTTTGGCTACATC
1 CAGTGGTAACTTCGGCTACATATCAGTGGTAGCTTCGGCTACATC
*
18833485 CAGTGGTAGCTTCGGCTACATATCAGTGGTAGCTTCGGCTACAT
1 CAGTGGTAACTTCGGCTACATATCAGTGGTAGCTTCGGCTACAT
18833529 ATCAGTGTGG
Statistics
Matches: 41, Mismatches: 3, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
45 41 1.00
ACGTcount: A:0.20, C:0.22, G:0.26, T:0.31
Consensus pattern (45 bp):
CAGTGGTAACTTCGGCTACATATCAGTGGTAGCTTCGGCTACATC
Found at i:18840507 original size:14 final size:14
Alignment explanation
Indices: 18840488--18840520 Score: 66
Period size: 14 Copynumber: 2.4 Consensus size: 14
18840478 TTTTAATTTT
18840488 AAAAAATAATAATA
1 AAAAAATAATAATA
18840502 AAAAAATAATAATA
1 AAAAAATAATAATA
18840516 AAAAA
1 AAAAA
18840521 GGAAAATCAG
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 19 1.00
ACGTcount: A:0.82, C:0.00, G:0.00, T:0.18
Consensus pattern (14 bp):
AAAAAATAATAATA
Found at i:18841304 original size:15 final size:15
Alignment explanation
Indices: 18841284--18841323 Score: 55
Period size: 15 Copynumber: 2.7 Consensus size: 15
18841274 AAGGCTAGAG
18841284 AGAAAAAAAAAAGAA
1 AGAAAAAAAAAAGAA
*
18841299 AGAAAAAAGAAAGAA
1 AGAAAAAAAAAAGAA
18841314 A-AAGAAAAAA
1 AGAA-AAAAAA
18841324 TAAAAATAAA
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
14 2 0.09
15 20 0.91
ACGTcount: A:0.85, C:0.00, G:0.15, T:0.00
Consensus pattern (15 bp):
AGAAAAAAAAAAGAA
Found at i:18841315 original size:10 final size:11
Alignment explanation
Indices: 18841284--18841320 Score: 58
Period size: 11 Copynumber: 3.5 Consensus size: 11
18841274 AAGGCTAGAG
*
18841284 AGAAAAAAAAA
1 AGAAAGAAAAA
18841295 AGAAAGAAAAA
1 AGAAAGAAAAA
18841306 AGAAAG-AAAA
1 AGAAAGAAAAA
18841316 AGAAA
1 AGAAA
18841321 AAATAAAAAT
Statistics
Matches: 25, Mismatches: 1, Indels: 1
0.93 0.04 0.04
Matches are distributed among these distances:
10 9 0.36
11 16 0.64
ACGTcount: A:0.84, C:0.00, G:0.16, T:0.00
Consensus pattern (11 bp):
AGAAAGAAAAA
Found at i:18848365 original size:291 final size:291
Alignment explanation
Indices: 18847793--18848667 Score: 1534
Period size: 291 Copynumber: 3.0 Consensus size: 291
18847783 AAGGTTATTA
* * * * *
18847793 AGTACAGTGAATATAACGTTGTTGAGTAATTAAACAAGCAGTCGGCGAGAATCTCGGTATTATCT
1 AGTACAGTGAATATAGCGTTGTGGAGTAATTAAACAAGTAGT-GGCGCGAATCTCGATATTATCT
*
18847858 CTATTGCTGAACTTAGAGCCACATCGAAACGTATTGCTAAAAGTGTTAAATCAAGCTTATGTGGC
65 CTATTGTTGAACTTAGAGCCACATCGAAACGTATTGCTAAAAGTGTTAAATCAAGCTTATGTGGC
* * *
18847923 AAGCAATGTATCTGTAGAAAAGCTCGATAGGTAGGTAAATAACCTGAATGCGGATAATTTTATCT
130 GAGCAATGTATCTGTAGAAAAGCTCGATAGGTGGGTAAATAACCTGAATGCGGATAATTTCATCT
18847988 GTTTTAGTGATGAGGAAATACCGCCGAATGGTAGGGGCTCTATAAAAACATTACACATCACAACC
195 GTTTTAGTGATGAGGAAATACCGCCGAATGGTAGGGGCTCTATAAAAACATTACACATCACAACC
*
18848053 AGTTGCAAGGGTTACATAGTACCGAATGTGCT
260 AGTTACAAGGGTTACATAGTACCGAATGTGCT
*
18848085 AGTACAGTGAATATAGCATTGTGGAGTAATTAAACAAGTAGTGGCGCGAATCTCGATATTATCTC
1 AGTACAGTGAATATAGCGTTGTGGAGTAATTAAACAAGTAGTGGCGCGAATCTCGATATTATCTC
18848150 TATTGTTGAACTTAGAGCCACATCGAAACGTATTGCTAAAAGTGTTAAATCAAGCTTATGTGGCG
66 TATTGTTGAACTTAGAGCCACATCGAAACGTATTGCTAAAAGTGTTAAATCAAGCTTATGTGGCG
*
18848215 AGCAATGTATCTGTAGAAAAGCTCGATAGGTGGGTAAATAACCTGAATGCGGATAATTTCATATG
131 AGCAATGTATCTGTAGAAAAGCTCGATAGGTGGGTAAATAACCTGAATGCGGATAATTTCATCTG
*
18848280 TTTTAGTGATGAGGAAATATCGCCGAATGGTAGGGGCTCTATAAAAACATTACACATCACAACCA
196 TTTTAGTGATGAGGAAATACCGCCGAATGGTAGGGGCTCTATAAAAACATTACACATCACAACCA
18848345 GTTACAAGGGTTACATAGTACCGAATGTGCT
261 GTTACAAGGGTTACATAGTACCGAATGTGCT
*
18848376 AGCACAGTGAATATAGCGTTGTGGAGTAATTAAACAAGTAGTTGGCGCGAATCTCGATATTATCT
1 AGTACAGTGAATATAGCGTTGTGGAGTAATTAAACAAGTAG-TGGCGCGAATCTCGATATTATCT
*
18848441 CTATTGTTGAACTTAGAGCCACATCGAAACGTATTGCTAAAAGTGTTAAATCAAGCTTATGTGAC
65 CTATTGTTGAACTTAGAGCCACATCGAAACGTATTGCTAAAAGTGTTAAATCAAGCTTATGTGGC
* * * *
18848506 GAGTAATGTATCTGTACAAAAGCTCGATAAGTGGGTAAATAACCTGAATGTGGATAATTTCATCT
130 GAGCAATGTATCTGTAGAAAAGCTCGATAGGTGGGTAAATAACCTGAATGCGGATAATTTCATCT
* * *
18848571 TTTTTAGTGATGACGAAATACCGCCGAATGGTAGGGGCTCTGTAAAAACATTACACATCACAACC
195 GTTTTAGTGATGAGGAAATACCGCCGAATGGTAGGGGCTCTATAAAAACATTACACATCACAACC
18848636 AGTTACAAGGGTTACATAGTACCGAATGTGCT
260 AGTTACAAGGGTTACATAGTACCGAATGTGCT
18848668 CATCGATAAC
Statistics
Matches: 557, Mismatches: 25, Indels: 2
0.95 0.04 0.00
Matches are distributed among these distances:
291 279 0.50
292 278 0.50
ACGTcount: A:0.34, C:0.16, G:0.22, T:0.28
Consensus pattern (291 bp):
AGTACAGTGAATATAGCGTTGTGGAGTAATTAAACAAGTAGTGGCGCGAATCTCGATATTATCTC
TATTGTTGAACTTAGAGCCACATCGAAACGTATTGCTAAAAGTGTTAAATCAAGCTTATGTGGCG
AGCAATGTATCTGTAGAAAAGCTCGATAGGTGGGTAAATAACCTGAATGCGGATAATTTCATCTG
TTTTAGTGATGAGGAAATACCGCCGAATGGTAGGGGCTCTATAAAAACATTACACATCACAACCA
GTTACAAGGGTTACATAGTACCGAATGTGCT
Found at i:18856288 original size:41 final size:41
Alignment explanation
Indices: 18856092--18856279 Score: 286
Period size: 41 Copynumber: 4.6 Consensus size: 41
18856082 ACCGGCAGTT
* * *
18856092 AGCCTGCTAGACATAAAGTCTGATATGTTTCACCGGCATCA
1 AGCCTGCTAGACATAATGTCTGGTATGTTTCACCAGCATCA
*
18856133 AGCCTGCTAGACATAAAGTCTGGTATGTTTCACCAGCATCA
1 AGCCTGCTAGACATAATGTCTGGTATGTTTCACCAGCATCA
* * * *
18856174 AGCCTGCTAGACGTAATGTCTAGTATGTTTCAACAACATCA
1 AGCCTGCTAGACATAATGTCTGGTATGTTTCACCAGCATCA
* *
18856215 AGCCTGCTAGACATAATGTCTAGTATGTTTCACCGGCATCA
1 AGCCTGCTAGACATAATGTCTGGTATGTTTCACCAGCATCA
18856256 AGCCTGCTAGACATAATGTCTGGT
1 AGCCTGCTAGACATAATGTCTGGT
18856280 TTACTTCACT
Statistics
Matches: 135, Mismatches: 12, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
41 135 1.00
ACGTcount: A:0.29, C:0.23, G:0.20, T:0.28
Consensus pattern (41 bp):
AGCCTGCTAGACATAATGTCTGGTATGTTTCACCAGCATCA
Found at i:18858997 original size:76 final size:76
Alignment explanation
Indices: 18858810--18859337 Score: 745
Period size: 76 Copynumber: 6.9 Consensus size: 76
18858800 ATCATTTCTT
* * * * *
18858810 TTTCTATTTTTTAAAAAATCAACTCATAATCCGATAGGTGAGTGGAGCATCGGGTCGCACGCCGA
1 TTTCTA-TTTTTCAAAGATCAACTCATAATCCGAGAGGTGAGTTGAGCCTCGGGTCGCACGCCGA
18858875 GGTA-TTTTCAA
65 GGTATTTTTCAA
* * * * *
18858886 TTTCTGTTTTTCAAATATCACCTCATAATCCGAGAGGTGAGTTGAGCCTCGAGTCGCACGCTGAG
1 TTTCTATTTTTCAAAGATCAACTCATAATCCGAGAGGTGAGTTGAGCCTCGGGTCGCACGCCGAG
*
18858951 GTGTTTTTCAA
66 GTATTTTTCAA
* ** *
18858962 TTTCTATTTTTCAAAGATCAAATCATAATTTGAGAGGTGAGTGGAGCCTCGGGTCGCACGCCGAG
1 TTTCTATTTTTCAAAGATCAACTCATAATCCGAGAGGTGAGTTGAGCCTCGGGTCGCACGCCGAG
18859027 GTATTTTTCAA
66 GTATTTTTCAA
* *
18859038 TTTCTGTTTTTCAAAGATCAACTCATAATCCGAGAGGTGAGTTGAGCCTCGGGTCGCACACCGAG
1 TTTCTATTTTTCAAAGATCAACTCATAATCCGAGAGGTGAGTTGAGCCTCGGGTCGCACGCCGAG
18859103 GTATTTTTCAA
66 GTATTTTTCAA
* * * * *
18859114 TTTCTATTTTTCAAATATCAACTCATAATCCGAGAGGCGAGTTAAGCCTTGCGTCGCACGCCGAG
1 TTTCTATTTTTCAAAGATCAACTCATAATCCGAGAGGTGAGTTGAGCCTCGGGTCGCACGCCGAG
*
18859179 GTATTTTTTAA
66 GTATTTTTCAA
*
18859190 TTTCTATTTTTCAAAGATCAACTCATAATCCGAGAGGTGAGTTGAGCCTCGAGTCGCACGCCGAG
1 TTTCTATTTTTCAAAGATCAACTCATAATCCGAGAGGTGAGTTGAGCCTCGGGTCGCACGCCGAG
18859255 GTATTTTTCAA
66 GTATTTTTCAA
* * * ** * *
18859266 TTTCTATTTTTCAAAGATTAACTCATAATCTGAGAGGTGA-TATGAGCTTTAGGCCGCACACCGA
1 TTTCTATTTTTCAAAGATCAACTCATAATCCGAGAGGTGAGT-TGAGCCTCGGGTCGCACGCCGA
18859330 GGTATTTT
65 GGTATTTT
18859338 AAATTTCAGT
Statistics
Matches: 402, Mismatches: 48, Indels: 4
0.89 0.11 0.01
Matches are distributed among these distances:
75 54 0.13
76 348 0.87
ACGTcount: A:0.26, C:0.20, G:0.21, T:0.33
Consensus pattern (76 bp):
TTTCTATTTTTCAAAGATCAACTCATAATCCGAGAGGTGAGTTGAGCCTCGGGTCGCACGCCGAG
GTATTTTTCAA
Found at i:18859935 original size:28 final size:29
Alignment explanation
Indices: 18859895--18859973 Score: 108
Period size: 28 Copynumber: 2.7 Consensus size: 29
18859885 TACAAAAATA
*
18859895 TACTAATTACATTTTGGCCCCTAA-TTTT
1 TACTAATTACATTTTAGCCCCTAACTTTT
*
18859923 TACTATTTACATTTTAGCCCCTAACTTTT
1 TACTAATTACATTTTAGCCCCTAACTTTT
18859952 T-CTAAAATTACATTTTAGCCCC
1 TACT--AATTACATTTTAGCCCC
18859974 GAGATTTTTG
Statistics
Matches: 45, Mismatches: 3, Indels: 4
0.87 0.06 0.08
Matches are distributed among these distances:
28 24 0.53
29 5 0.11
30 16 0.36
ACGTcount: A:0.27, C:0.24, G:0.05, T:0.44
Consensus pattern (29 bp):
TACTAATTACATTTTAGCCCCTAACTTTT
Found at i:18859965 original size:30 final size:28
Alignment explanation
Indices: 18859895--18859982 Score: 106
Period size: 28 Copynumber: 3.0 Consensus size: 28
18859885 TACAAAAATA
*
18859895 TACTAATTACATTTTGGCCCCTAATTTT
1 TACTAATTACATTTTAGCCCCTAATTTT
*
18859923 TACTATTTACATTTTAGCCCCTAACTTTT
1 TACTAATTACATTTTAGCCCCTAA-TTTT
*
18859952 T-CTAAAATTACATTTTAGCCCCGAGATTTT
1 TACT--AATTACATTTTAGCCCCTA-ATTTT
18859982 T
1 T
18859983 GCGTCTTCTA
Statistics
Matches: 52, Mismatches: 4, Indels: 6
0.84 0.06 0.10
Matches are distributed among these distances:
28 24 0.46
29 5 0.10
30 22 0.42
31 1 0.02
ACGTcount: A:0.26, C:0.22, G:0.07, T:0.45
Consensus pattern (28 bp):
TACTAATTACATTTTAGCCCCTAATTTT
Found at i:18860658 original size:20 final size:20
Alignment explanation
Indices: 18860635--18860678 Score: 63
Period size: 20 Copynumber: 2.2 Consensus size: 20
18860625 AGGGCTAGAG
* *
18860635 AAAAAATAG-AAGAAGAAGA
1 AAAAAAAAGAAAGAAAAAGA
18860654 AAAAAAAAGAAAGAAAAAGA
1 AAAAAAAAGAAAGAAAAAGA
18860674 AAAAA
1 AAAAA
18860679 TAAAATAAAA
Statistics
Matches: 22, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
19 8 0.36
20 14 0.64
ACGTcount: A:0.82, C:0.00, G:0.16, T:0.02
Consensus pattern (20 bp):
AAAAAAAAGAAAGAAAAAGA
Found at i:18860665 original size:10 final size:10
Alignment explanation
Indices: 18860650--18860693 Score: 54
Period size: 10 Copynumber: 4.5 Consensus size: 10
18860640 ATAGAAGAAG
18860650 AAGAAAAAAA
1 AAGAAAAAAA
*
18860660 AAGAAAGAAA
1 AAGAAAAAAA
*
18860670 AAGAAAAAAT
1 AAGAAAAAAA
*
18860680 AA-AATAAAA
1 AAGAAAAAAA
18860689 AAGAA
1 AAGAA
18860694 CAGTCGGGTT
Statistics
Matches: 28, Mismatches: 5, Indels: 2
0.80 0.14 0.06
Matches are distributed among these distances:
9 7 0.25
10 21 0.75
ACGTcount: A:0.84, C:0.00, G:0.11, T:0.05
Consensus pattern (10 bp):
AAGAAAAAAA
Found at i:18868593 original size:14 final size:14
Alignment explanation
Indices: 18868570--18868601 Score: 55
Period size: 14 Copynumber: 2.3 Consensus size: 14
18868560 TGTCGCGTTC
*
18868570 TTAGTTAATTTAGA
1 TTAGTAAATTTAGA
18868584 TTAGTAAATTTAGA
1 TTAGTAAATTTAGA
18868598 TTAG
1 TTAG
18868602 AACAATCATC
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
14 17 1.00
ACGTcount: A:0.38, C:0.00, G:0.16, T:0.47
Consensus pattern (14 bp):
TTAGTAAATTTAGA
Found at i:18868890 original size:20 final size:19
Alignment explanation
Indices: 18868842--18868890 Score: 62
Period size: 20 Copynumber: 2.5 Consensus size: 19
18868832 TTCTATTGCA
*
18868842 TTTTATTTTTGTTTTTAGT
1 TTTTATTTTTGTTTTTAAT
*
18868861 TTATTTTTTTTGTTTTCTAAT
1 TT-TTATTTTTGTTTT-TAAT
18868882 TTTTATTTT
1 TTTTATTTT
18868891 ATTTGTTTCT
Statistics
Matches: 25, Mismatches: 3, Indels: 3
0.81 0.10 0.10
Matches are distributed among these distances:
19 2 0.08
20 18 0.72
21 5 0.20
ACGTcount: A:0.12, C:0.02, G:0.06, T:0.80
Consensus pattern (19 bp):
TTTTATTTTTGTTTTTAAT
Found at i:18874355 original size:9 final size:8
Alignment explanation
Indices: 18874262--18874355 Score: 55
Period size: 9 Copynumber: 10.8 Consensus size: 8
18874252 CTTGTTCTTT
*
18874262 TTATTTTC
1 TTATTTTA
18874270 TTATTGTTA
1 TTATT-TTA
*
18874279 TTATATTA
1 TTATTTTA
*
18874287 TTATATTA
1 TTATTTTA
18874295 TTATTTCTTTA
1 TTA--T-TTTA
*
18874306 TTTATTCTAA
1 -TTATT-TTA
18874316 TTATTTTA
1 TTATTTTA
18874324 TT-TTTTA
1 TTATTTTA
18874331 TTAGTTTTA
1 TTA-TTTTA
*
18874340 CTGATTTTA
1 -TTATTTTA
18874349 TCTATTT
1 T-TATTT
18874356 CTTTATTTAT
Statistics
Matches: 69, Mismatches: 7, Indels: 19
0.73 0.07 0.20
Matches are distributed among these distances:
7 7 0.10
8 24 0.35
9 26 0.38
10 6 0.09
11 3 0.04
12 3 0.04
ACGTcount: A:0.23, C:0.05, G:0.03, T:0.68
Consensus pattern (8 bp):
TTATTTTA
Found at i:18876000 original size:6 final size:6
Alignment explanation
Indices: 18875984--18876021 Score: 60
Period size: 6 Copynumber: 6.5 Consensus size: 6
18875974 AGTCCATTTG
*
18875984 TTTTA- TTTTAT TTTTAT TTTTAT GTTTAT TTTTAT TTT
1 TTTTAT TTTTAT TTTTAT TTTTAT TTTTAT TTTTAT TTT
18876022 CTTAGACTTA
Statistics
Matches: 30, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
5 5 0.17
6 25 0.83
ACGTcount: A:0.16, C:0.00, G:0.03, T:0.82
Consensus pattern (6 bp):
TTTTAT
Found at i:18876013 original size:18 final size:17
Alignment explanation
Indices: 18875984--18876021 Score: 67
Period size: 18 Copynumber: 2.2 Consensus size: 17
18875974 AGTCCATTTG
18875984 TTTTATTTTATTTTTAT
1 TTTTATTTTATTTTTAT
18876001 TTTTATGTTTATTTTTAT
1 TTTTAT-TTTATTTTTAT
18876019 TTT
1 TTT
18876022 CTTAGACTTA
Statistics
Matches: 20, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
17 6 0.30
18 14 0.70
ACGTcount: A:0.16, C:0.00, G:0.03, T:0.82
Consensus pattern (17 bp):
TTTTATTTTATTTTTAT
Found at i:18878764 original size:14 final size:14
Alignment explanation
Indices: 18878741--18878772 Score: 55
Period size: 14 Copynumber: 2.3 Consensus size: 14
18878731 CGTCGCGTTC
*
18878741 TTAGTTAATTTAGA
1 TTAGTAAATTTAGA
18878755 TTAGTAAATTTAGA
1 TTAGTAAATTTAGA
18878769 TTAG
1 TTAG
18878773 AACAATCATC
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
14 17 1.00
ACGTcount: A:0.38, C:0.00, G:0.16, T:0.47
Consensus pattern (14 bp):
TTAGTAAATTTAGA
Found at i:18900468 original size:2 final size:2
Alignment explanation
Indices: 18900461--18900485 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
18900451 AACGTTAAAT
18900461 TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA T
18900486 GTACTTTTAT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:18923353 original size:17 final size:18
Alignment explanation
Indices: 18923331--18923364 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
18923321 GTCATGTTTT
*
18923331 GGTTTA-ACTATTTAAAG
1 GGTTTAGACTAATTAAAG
18923348 GGTTTAGACTAATTAAA
1 GGTTTAGACTAATTAAA
18923365 TTTTCAAGTA
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 6 0.40
18 9 0.60
ACGTcount: A:0.38, C:0.06, G:0.18, T:0.38
Consensus pattern (18 bp):
GGTTTAGACTAATTAAAG
Found at i:18925010 original size:21 final size:18
Alignment explanation
Indices: 18924984--18925026 Score: 50
Period size: 18 Copynumber: 2.2 Consensus size: 18
18924974 CTTGTATTGC
18924984 ATTTGAAGACATTTATGTTGT
1 ATTTG-AGACA-TTAT-TTGT
*
18925005 ATTTGATACATTATTTGT
1 ATTTGAGACATTATTTGT
18925023 ATTT
1 ATTT
18925027 AGATATTACG
Statistics
Matches: 21, Mismatches: 1, Indels: 3
0.84 0.04 0.12
Matches are distributed among these distances:
18 8 0.38
19 4 0.19
20 4 0.19
21 5 0.24
ACGTcount: A:0.28, C:0.05, G:0.14, T:0.53
Consensus pattern (18 bp):
ATTTGAGACATTATTTGT
Found at i:18931768 original size:16 final size:16
Alignment explanation
Indices: 18931735--18931768 Score: 50
Period size: 16 Copynumber: 2.1 Consensus size: 16
18931725 AGAACCTGTT
* *
18931735 AACATTAATGGGAGAC
1 AACATTAATGGAAAAC
18931751 AACATTAATGGAAAAC
1 AACATTAATGGAAAAC
18931767 AA
1 AA
18931769 TACAAAGTGG
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
16 16 1.00
ACGTcount: A:0.53, C:0.12, G:0.18, T:0.18
Consensus pattern (16 bp):
AACATTAATGGAAAAC
Found at i:18934733 original size:21 final size:21
Alignment explanation
Indices: 18934707--18934747 Score: 64
Period size: 21 Copynumber: 2.0 Consensus size: 21
18934697 AGACGAGCAA
* *
18934707 TACTCCACAGCAGGTGGAGTG
1 TACTCCAAAACAGGTGGAGTG
18934728 TACTCCAAAACAGGTGGAGT
1 TACTCCAAAACAGGTGGAGT
18934748 TTGAGCAGAT
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
21 18 1.00
ACGTcount: A:0.29, C:0.22, G:0.29, T:0.20
Consensus pattern (21 bp):
TACTCCAAAACAGGTGGAGTG
Found at i:18936686 original size:16 final size:16
Alignment explanation
Indices: 18936653--18936686 Score: 50
Period size: 16 Copynumber: 2.1 Consensus size: 16
18936643 GGAGATTGTT
* *
18936653 AACATTAATGGGAGAC
1 AACATTAATGGCAAAC
18936669 AACATTAATGGCAAAC
1 AACATTAATGGCAAAC
18936685 AA
1 AA
18936687 TACAAAGTGG
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
16 16 1.00
ACGTcount: A:0.50, C:0.15, G:0.18, T:0.18
Consensus pattern (16 bp):
AACATTAATGGCAAAC
Found at i:18938906 original size:44 final size:42
Alignment explanation
Indices: 18938843--18938956 Score: 142
Period size: 44 Copynumber: 2.6 Consensus size: 42
18938833 ATGTGTTATT
18938843 GTGTAAGACCACGTCTGGGACGTTGGCATCGACT-TGTGACTTAC
1 GTGTAAGACCACGTCTGGGACG-TGGCATCGA-TATGTGA-TTAC
18938887 GTGTAAGACC-CTGTCTGGGACAGTGGCATCGATATGTGATTAC
1 GTGTAAGACCAC-GTCTGGGAC-GTGGCATCGATATGTGATTAC
* *
18938930 ATGTAAGACCACGTCTGAGACGATGGC
1 GTGTAAGACCACGTCTGGGACG-TGGC
18938957 GTTGTACGAA
Statistics
Matches: 63, Mismatches: 2, Indels: 11
0.83 0.03 0.14
Matches are distributed among these distances:
42 1 0.02
43 27 0.43
44 34 0.54
45 1 0.02
ACGTcount: A:0.24, C:0.21, G:0.30, T:0.25
Consensus pattern (42 bp):
GTGTAAGACCACGTCTGGGACGTGGCATCGATATGTGATTAC
Found at i:18949317 original size:18 final size:19
Alignment explanation
Indices: 18949291--18949346 Score: 60
Period size: 20 Copynumber: 2.9 Consensus size: 19
18949281 AAAAATGTAA
*
18949291 AAGAGATAT-ATATATAAT
1 AAGACATATAATATATAAT
18949309 AAGACATATAAATATATAAT
1 AAGACATAT-AATATATAAT
* *
18949329 AAGATATAAAGATATATA
1 AAGACATATA-ATATATA
18949347 GATATAAGGT
Statistics
Matches: 32, Mismatches: 3, Indels: 4
0.82 0.08 0.10
Matches are distributed among these distances:
18 8 0.25
19 1 0.03
20 23 0.72
ACGTcount: A:0.59, C:0.02, G:0.09, T:0.30
Consensus pattern (19 bp):
AAGACATATAATATATAAT
Found at i:18949325 original size:20 final size:20
Alignment explanation
Indices: 18949300--18949346 Score: 69
Period size: 20 Copynumber: 2.4 Consensus size: 20
18949290 AAAGAGATAT
18949300 ATATATAATAAGACATATAA-
1 ATATATAATAAGACATA-AAG
*
18949320 ATATATAATAAGATATAAAG
1 ATATATAATAAGACATAAAG
18949340 ATATATA
1 ATATATA
18949347 GATATAAGGT
Statistics
Matches: 25, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
19 2 0.08
20 23 0.92
ACGTcount: A:0.60, C:0.02, G:0.06, T:0.32
Consensus pattern (20 bp):
ATATATAATAAGACATAAAG
Done.