Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Chr01 113035596
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: 113035596
ACGTcount: A:0.32, C:0.17, G:0.18, T:0.33
Warning! 271 characters in sequence are not A, C, G, or T
File 342 of 378
Found at i:103322514 original size:140 final size:141
Alignment explanation
Indices: 103322210--103322725 Score: 391
Period size: 141 Copynumber: 3.7 Consensus size: 141
103322200 ATAGGAAGAA
* * * *
103322210 CTAAGGCTCCCAATTATGATCTTAAGGCTCGCAGGTTTAATACCACAGCCTCTAAAATAGTTAGC
1 CTAAGGCTCCCAACTATGATATTAAGGCTCGCAAGTTTAACACCACAGCCTCTAAAATAGTTAGC
* * * * * *
103322275 AAGAGTTCAAGCTCTAAGCTGTGATCTTAGGGCTTGCAGTTTTAATACCGTAGCCCCCAAAAATA
66 AAGAGCTCAAGCTCCAAGCTGTAATCTTAGGGCCTGCAGGTTCAATACCGTAGCCCCCAAAAATA
103322340 GTTAACGAAAG
131 GTTAACGAAAG
* * * * *
103322351 CTAAAGCTCCCAGCTAT-AGTATTAAGGCTTGTAAGTTTAACACCATAGCCTCTAAAATAGTTAG
1 CTAAGGCTCCCAACTATGA-TATTAAGGCTCGCAAGTTTAACACCACAGCCTCTAAAATAGTTAG
* * * *
103322415 CTAGAGCT-AAGCTCCCAGCTGTAATCTTGGGGCCCT-CAGGTTCAGTATCC-TAGCCCCCAAAA
65 CAAGAGCTCAAGCTCCAAGCTGTAATCTTAGGG-CCTGCAGGTTCAATA-CCGTAGCCCCCAAAA
* **
103322477 ATAGTTAATGAGGG
128 ATAGTTAACGAAAG
* * * * * * * * * * * *
103322491 TTAAGGCTCTCAACTATGATATTAATGCTAGCAGGTTTAATATCGCAACCCCGAAAAATAGTTAA
1 CTAAGGCTCCCAACTATGATATTAAGGCTCGCAAGTTTAACACCACAGCCTC-TAAAATAGTTAG
*** * * * * * * * *
103322556 CAAGAGCT-AAGGCTTTTAGTTTTGATCTTAAGG-CTCGCAGGTTCAATACTGTA-TCCTCTAAA
65 CAAGAGCTCAA-GCTCCAAGCTGTAATCTTAGGGCCT-GCAGGTTCAATACCGTAGCCCCCAAAA
* * *
103322618 ACAGTTAGCGAGAG
128 ATAGTTAACGAAAG
* * * * * * **
103322632 TTAAGGCTCCCAACTATGATCTTAAGGCTCGTAGGTTCAATACCGTAGCCTCTAAAATAGTTAGC
1 CTAAGGCTCCCAACTATGATATTAAGGCTCGCAAGTTTAACACCACAGCCTCTAAAATAGTTAGC
* *
103322697 GAGAGCTCAAGCTCTC-AGCTGTGATCTTA
66 AAGAGCTCAAGCTC-CAAGCTGTAATCTTA
103322726 AGGTTTGTAG
Statistics
Matches: 291, Mismatches: 73, Indels: 23
0.75 0.19 0.06
Matches are distributed among these distances:
140 121 0.42
141 144 0.49
142 26 0.09
ACGTcount: A:0.31, C:0.22, G:0.20, T:0.28
Consensus pattern (141 bp):
CTAAGGCTCCCAACTATGATATTAAGGCTCGCAAGTTTAACACCACAGCCTCTAAAATAGTTAGC
AAGAGCTCAAGCTCCAAGCTGTAATCTTAGGGCCTGCAGGTTCAATACCGTAGCCCCCAAAAATA
GTTAACGAAAG
Found at i:103322691 original size:211 final size:209
Alignment explanation
Indices: 103322157--103322728 Score: 517
Period size: 211 Copynumber: 2.7 Consensus size: 209
103322147 CTCCCATTGT
* * *
103322157 TATCTTAAGGCTCGCAAGTTCAATACCACATCCTCTAAAATAGATAG-GAAGAACTAAGGCTCCC
1 TATCTTAAGGCTCGCAAGTTCAATACCATATCCTCTAAAATAGTTAGCG-AGAGCTAAGGCTCCC
* * * * *
103322221 AATTATGATCTTAAGGCTCGCAGGTTTAATACCACAGCCTCTAAAATAGTTAGCAAGAGTTCAAG
65 AACTATGATCTTAAGGCTCGTAGGTTCAATACC-TAGCCTCTAAAATAGTTAACAAGAGTTCAAG
* * * * * * *
103322286 CTCTAAGCTGTGATCTTAGGGCTTGCAGTTTTAATACCGTAGCCCCCAAAAATAGTTAACGAAAG
129 CTCTAAGCTATGATATTAAGGCTAGCAGGTTTAATACCGCAACCCCCAAAAATAGTTAACGAAAG
103322351 CTAAAGCTCCCAGCTA
194 CTAAAGCTCCCAGCTA
* * * * * * *
103322367 TAGTATTAAGGCTTGTAAGTTTAACACCATAGCCTCTAAAATAGTTAGCTAGAGCTAA-GCTCCC
1 TA-TCTTAAGGCTCGCAAGTTCAATACCATATCCTCTAAAATAGTTAGCGAGAGCTAAGGCTCCC
* * * ** * * * * ** *
103322431 AGCTGTAATCTTGGGGC-CCTCAGGTTCAGTATCCTAGCCCCCAAAAATAGTTAATGAGGGTT-A
65 AACTATGATCTTAAGGCTCGT-AGGTTCAATA-CCTAG-CCTCTAAAATAGTTAACAAGAGTTCA
* * *
103322494 AGGCTCTCAA-CTATGATATTAATGCTAGCAGGTTTAATATCGCAACCCCGAAAAATAGTTAAC-
127 A-GCTCT-AAGCTATGATATTAAGGCTAGCAGGTTTAATACCGCAACCCCCAAAAATAGTTAACG
* *** * *
103322557 AAGAGCTAAGGCTTTTAGTTT
190 AA-AGCTAAAGCTCCCAGCTA
* ** * *
103322578 TGATCTTAAGGCTCGCAGGTTCAATACTGTATCCTCTAAAACAGTTAGCGAGAGTTAAGGCTCCC
1 T-ATCTTAAGGCTCGCAAGTTCAATACCATATCCTCTAAAATAGTTAGCGAGAGCTAAGGCTCCC
* * *
103322643 AACTATGATCTTAAGGCTCGTAGGTTCAATACCGTAGCCTCTAAAATAGTTAGCGAGAGCTCAAG
65 AACTATGATCTTAAGGCTCGTAGGTTCAATACC-TAGCCTCTAAAATAGTTAACAAGAGTTCAAG
* * *
103322708 CTCTCAGCTGTGATCTTAAGG
129 CTCTAAGCTATGATATTAAGG
103322729 TTTGTAGGAT
Statistics
Matches: 276, Mismatches: 72, Indels: 27
0.74 0.19 0.07
Matches are distributed among these distances:
209 1 0.00
210 34 0.12
211 204 0.74
212 35 0.13
213 2 0.01
ACGTcount: A:0.32, C:0.22, G:0.19, T:0.27
Consensus pattern (209 bp):
TATCTTAAGGCTCGCAAGTTCAATACCATATCCTCTAAAATAGTTAGCGAGAGCTAAGGCTCCCA
ACTATGATCTTAAGGCTCGTAGGTTCAATACCTAGCCTCTAAAATAGTTAACAAGAGTTCAAGCT
CTAAGCTATGATATTAAGGCTAGCAGGTTTAATACCGCAACCCCCAAAAATAGTTAACGAAAGCT
AAAGCTCCCAGCTA
Found at i:103322742 original size:140 final size:141
Alignment explanation
Indices: 103322211--103322834 Score: 485
Period size: 140 Copynumber: 4.4 Consensus size: 141
103322201 TAGGAAGAAC
* *
103322211 TAAGGCTCCCAATTATGATCTTAAGGCTCGCAGGTTTAATACCACAGCCTCTAAAATAGTTAGCA
1 TAAGGCTCCCAACTATGATCTTAAGGCTCGTAGGTTTAATACCACAGCCTCTAAAATAGTTAGCA
* * * * * *
103322276 AGAGTTCAAGCTCTAAGCTGTGATCTTAGGGCTTGCAGTTTTAATAC-CGTAGCCCCCAAAAATA
66 AGAGCT-AAGCTCTCAGCTGTGATCTTAAGGCTTGCAGGTTCAATACTCGTAGCCCCCAAAAACA
* *
103322340 GTTAACGAAAGC
130 GTTAACGAGAGT
* * * * * * *
103322352 TAAAGCTCCCAGCTAT-AGTATTAAGGCTTGTAAGTTTAACACCATAGCCTCTAAAATAGTTAGC
1 TAAGGCTCCCAACTATGA-TCTTAAGGCTCGTAGGTTTAATACCACAGCCTCTAAAATAGTTAGC
* * * ** * * * *
103322416 TAGAGCTAAGCTCCCAGCTGTAATCTTGGGGCCCT-CAGGTTCAGTA-TCCTAGCCCCCAAAAAT
65 AAGAGCTAAGCTCTCAGCTGTGATCTTAAGG-CTTGCAGGTTCAATACTCGTAGCCCCCAAAAAC
* *
103322479 AGTTAATGAGGGT
129 AGTTAACGAGAGT
* * * * * * * * * * *
103322492 TAAGGCTCTCAACTATGATATTAATGCTAGCAGGTTTAATATCGCAACCCCGAAAAATAGTTAAC
1 TAAGGCTCCCAACTATGATCTTAAGGCTCGTAGGTTTAATACCACAGCCTC-TAAAATAGTTAGC
* * * * * * * *
103322557 AAGAGCTAAGGCTTTTAGTTTTGATCTTAAGGCTCGCAGGTTCAATACT-GTA-TCCTCTAAAAC
65 AAGAGCTAA-GCTCTCAGCTGTGATCTTAAGGCTTGCAGGTTCAATACTCGTAGCCCCCAAAAAC
*
103322620 AGTTAGCGAGAGT
129 AGTTAACGAGAGT
* ** *
103322633 TAAGGCTCCCAACTATGATCTTAAGGCTCGTAGGTTCAATACCGTAGCCTCTAAAATAGTTAGCG
1 TAAGGCTCCCAACTATGATCTTAAGGCTCGTAGGTTTAATACCACAGCCTCTAAAATAGTTAGCA
* * * * * * * *
103322698 AGAGCTCAAGCTCTCAGCTGTGATCTTAAGGTTTGTAGGATCAAT-GTCGCAG-CCTCTAAAACT
66 AGAGCT-AAGCTCTCAGCTGTGATCTTAAGGCTTGCAGGTTCAATACTCGTAGCCCCCAAAAACA
*
103322761 GTTAGCGAGAGCT
130 GTTAACGAGAG-T
* ** * * * * *
103322774 CAA-GCT-CTTACTTGTGATCTTAAGGCTCATAGGTTCAACACCACAGCCTCTAAAACAGTTA
1 TAAGGCTCCCAAC-TATGATCTTAAGGCTCGTAGGTTTAATACCACAGCCTCTAAAATAGTTA
103322835 TTGTAAGCTG
Statistics
Matches: 378, Mismatches: 92, Indels: 27
0.76 0.19 0.05
Matches are distributed among these distances:
139 4 0.01
140 203 0.54
141 144 0.38
142 26 0.07
143 1 0.00
ACGTcount: A:0.31, C:0.22, G:0.20, T:0.28
Consensus pattern (141 bp):
TAAGGCTCCCAACTATGATCTTAAGGCTCGTAGGTTTAATACCACAGCCTCTAAAATAGTTAGCA
AGAGCTAAGCTCTCAGCTGTGATCTTAAGGCTTGCAGGTTCAATACTCGTAGCCCCCAAAAACAG
TTAACGAGAGT
Found at i:103323928 original size:24 final size:24
Alignment explanation
Indices: 103323875--103323928 Score: 63
Period size: 24 Copynumber: 2.2 Consensus size: 24
103323865 GGTGACACAG
* * *
103323875 AGCTAGCTTACCATTGTTTTTAGC
1 AGCTAGCTCACCACTGTTTTCAGC
* *
103323899 AACTAGCTCACCACTGTTTTCAGT
1 AGCTAGCTCACCACTGTTTTCAGC
103323923 AGCTAG
1 AGCTAG
103323929 TTCCCTAGCG
Statistics
Matches: 24, Mismatches: 6, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
24 24 1.00
ACGTcount: A:0.24, C:0.24, G:0.17, T:0.35
Consensus pattern (24 bp):
AGCTAGCTCACCACTGTTTTCAGC
Found at i:103325817 original size:33 final size:33
Alignment explanation
Indices: 103325772--103325844 Score: 94
Period size: 33 Copynumber: 2.2 Consensus size: 33
103325762 GGATAGTTAG
* **
103325772 GGGAGCTTGCGATATCGGCTCACGGGAGTTGAA
1 GGGAGCTTGCGATATCAGCTCACAAGAGTTGAA
*
103325805 GGGAG-TTCGCGATATCAGCTCGCAAGAGTTGAA
1 GGGAGCTT-GCGATATCAGCTCACAAGAGTTGAA
103325838 GGGAGCT
1 GGGAGCT
103325845 CATAGCATCA
Statistics
Matches: 34, Mismatches: 4, Indels: 3
0.83 0.10 0.07
Matches are distributed among these distances:
32 2 0.06
33 31 0.91
34 1 0.03
ACGTcount: A:0.23, C:0.18, G:0.38, T:0.21
Consensus pattern (33 bp):
GGGAGCTTGCGATATCAGCTCACAAGAGTTGAA
Found at i:103326244 original size:21 final size:19
Alignment explanation
Indices: 103326220--103326258 Score: 60
Period size: 19 Copynumber: 1.9 Consensus size: 19
103326210 GAAACAAAGC
103326220 AGGGAAAGAAAGAAAGAAAAA
1 AGGGAAAG-AA-AAAGAAAAA
103326241 AGGGAAAGAAAAAGAAAA
1 AGGGAAAGAAAAAGAAAA
103326259 GGAAAATTTA
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
19 8 0.44
20 2 0.11
21 8 0.44
ACGTcount: A:0.72, C:0.00, G:0.28, T:0.00
Consensus pattern (19 bp):
AGGGAAAGAAAAAGAAAAA
Found at i:103326247 original size:17 final size:17
Alignment explanation
Indices: 103326227--103326260 Score: 52
Period size: 17 Copynumber: 2.0 Consensus size: 17
103326217 AGCAGGGAAA
103326227 GAAAGAAAGAA-AAAAGG
1 GAAAGAAA-AAGAAAAGG
103326244 GAAAGAAAAAGAAAAGG
1 GAAAGAAAAAGAAAAGG
103326261 AAAATTTAGG
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
16 2 0.12
17 14 0.88
ACGTcount: A:0.71, C:0.00, G:0.29, T:0.00
Consensus pattern (17 bp):
GAAAGAAAAAGAAAAGG
Found at i:103327047 original size:20 final size:20
Alignment explanation
Indices: 103327032--103327090 Score: 118
Period size: 20 Copynumber: 3.0 Consensus size: 20
103327022 TGTGTCCATA
103327032 AGACACTATATGTGTCGACG
1 AGACACTATATGTGTCGACG
103327052 AGACACTATATGTGTCGACG
1 AGACACTATATGTGTCGACG
103327072 AGACACTATATGTGTCGAC
1 AGACACTATATGTGTCGAC
103327091 TACTGTGACT
Statistics
Matches: 39, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 39 1.00
ACGTcount: A:0.31, C:0.20, G:0.24, T:0.25
Consensus pattern (20 bp):
AGACACTATATGTGTCGACG
Found at i:103329523 original size:3 final size:3
Alignment explanation
Indices: 103329515--103329539 Score: 50
Period size: 3 Copynumber: 8.3 Consensus size: 3
103329505 TGTTGAAGAA
103329515 TCT TCT TCT TCT TCT TCT TCT TCT T
1 TCT TCT TCT TCT TCT TCT TCT TCT T
103329540 TTATGCTTTA
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:0.00, C:0.32, G:0.00, T:0.68
Consensus pattern (3 bp):
TCT
Found at i:103331957 original size:22 final size:22
Alignment explanation
Indices: 103331914--103331957 Score: 54
Period size: 22 Copynumber: 2.0 Consensus size: 22
103331904 TAAAATATTT
* *
103331914 TTTTACAATTTAAAGTATTTAA
1 TTTTACAATTTAAAATAATTAA
103331936 TTTTA-AATTTTAAAATAATTAA
1 TTTTACAA-TTTAAAATAATTAA
103331958 GTCCAAAAAT
Statistics
Matches: 19, Mismatches: 2, Indels: 2
0.83 0.09 0.09
Matches are distributed among these distances:
21 2 0.11
22 17 0.89
ACGTcount: A:0.45, C:0.02, G:0.02, T:0.50
Consensus pattern (22 bp):
TTTTACAATTTAAAATAATTAA
Found at i:103333104 original size:27 final size:27
Alignment explanation
Indices: 103333072--103333136 Score: 96
Period size: 27 Copynumber: 2.4 Consensus size: 27
103333062 AGATACAGAT
103333072 AGAGCCACCAGAACAGAT-ATATGTGGC
1 AGAGCCACCAGAACAGATAAT-TGTGGC
*
103333099 AGAGCCACCAGATCAGATAATTGTGGC
1 AGAGCCACCAGAACAGATAATTGTGGC
*
103333126 ATAGCCACCAG
1 AGAGCCACCAG
103333137 GACGCTTCCT
Statistics
Matches: 35, Mismatches: 2, Indels: 2
0.90 0.05 0.05
Matches are distributed among these distances:
27 33 0.94
28 2 0.06
ACGTcount: A:0.35, C:0.25, G:0.25, T:0.15
Consensus pattern (27 bp):
AGAGCCACCAGAACAGATAATTGTGGC
Found at i:103334781 original size:26 final size:26
Alignment explanation
Indices: 103334746--103334855 Score: 168
Period size: 26 Copynumber: 4.2 Consensus size: 26
103334736 CATGAAATTC
*
103334746 TTATTATGAAACATTTACCTAACCCA
1 TTATCATGAAACATTTACCTAACCCA
103334772 TTATCATGAAACATTTACCTAACCCA
1 TTATCATGAAACATTTACCTAACCCA
* *
103334798 TTATCATGGAACATTTACCTAACCTA
1 TTATCATGAAACATTTACCTAACCCA
*
103334824 TTATCATTG-AACATTTACCTAACCTA
1 TTATCA-TGAAACATTTACCTAACCCA
103334850 TTATCA
1 TTATCA
103334856 ATTTGTATCA
Statistics
Matches: 80, Mismatches: 3, Indels: 2
0.94 0.04 0.02
Matches are distributed among these distances:
26 78 0.98
27 2 0.03
ACGTcount: A:0.36, C:0.24, G:0.05, T:0.35
Consensus pattern (26 bp):
TTATCATGAAACATTTACCTAACCCA
Found at i:103338200 original size:26 final size:26
Alignment explanation
Indices: 103338164--103338216 Score: 97
Period size: 26 Copynumber: 2.0 Consensus size: 26
103338154 TGACCTTCTT
*
103338164 TTGGCTTTTCTTTATATTTCTTTTAA
1 TTGGCTTTTCTTTATATTTCTTATAA
103338190 TTGGCTTTTCTTTATATTTCTTATAA
1 TTGGCTTTTCTTTATATTTCTTATAA
103338216 T
1 T
103338217 CATTCTTTAT
Statistics
Matches: 26, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
26 26 1.00
ACGTcount: A:0.17, C:0.11, G:0.08, T:0.64
Consensus pattern (26 bp):
TTGGCTTTTCTTTATATTTCTTATAA
Found at i:103346602 original size:32 final size:32
Alignment explanation
Indices: 103346563--103346658 Score: 138
Period size: 32 Copynumber: 3.0 Consensus size: 32
103346553 TTAGATATTG
*
103346563 ATTATGTTTTAAACTTGTTAGATATTAAATTT
1 ATTATGTTTTAAACTTGTTGGATATTAAATTT
* **
103346595 ATTATGTTTTAAGCTTGTTGGATATCGAATTT
1 ATTATGTTTTAAACTTGTTGGATATTAAATTT
*
103346627 ATTATGTTTCAAACTTGTTGGATATTGAAATT
1 ATTATGTTTTAAACTTGTTGGATATT-AAATT
103346659 GACAATGACA
Statistics
Matches: 55, Mismatches: 8, Indels: 1
0.86 0.12 0.02
Matches are distributed among these distances:
32 51 0.93
33 4 0.07
ACGTcount: A:0.30, C:0.05, G:0.15, T:0.50
Consensus pattern (32 bp):
ATTATGTTTTAAACTTGTTGGATATTAAATTT
Found at i:103347647 original size:29 final size:29
Alignment explanation
Indices: 103347608--103347667 Score: 120
Period size: 29 Copynumber: 2.1 Consensus size: 29
103347598 TTTTAATGTG
103347608 GTGTAATATTAGTTATGCACTTGGACAAT
1 GTGTAATATTAGTTATGCACTTGGACAAT
103347637 GTGTAATATTAGTTATGCACTTGGACAAT
1 GTGTAATATTAGTTATGCACTTGGACAAT
103347666 GT
1 GT
103347668 TGTTATTATT
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
29 31 1.00
ACGTcount: A:0.30, C:0.10, G:0.22, T:0.38
Consensus pattern (29 bp):
GTGTAATATTAGTTATGCACTTGGACAAT
Found at i:103347953 original size:20 final size:20
Alignment explanation
Indices: 103347930--103347969 Score: 71
Period size: 20 Copynumber: 2.0 Consensus size: 20
103347920 ACAATTTAAA
103347930 ATATAAATTTATTAATATAT
1 ATATAAATTTATTAATATAT
*
103347950 ATATAAATTTATTTATATAT
1 ATATAAATTTATTAATATAT
103347970 CTAAAAATAG
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
20 19 1.00
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (20 bp):
ATATAAATTTATTAATATAT
Found at i:103347977 original size:20 final size:20
Alignment explanation
Indices: 103347934--103347977 Score: 61
Period size: 20 Copynumber: 2.2 Consensus size: 20
103347924 TTTAAAATAT
*
103347934 AAATTTATTAATATATATAT
1 AAATTTATTAATATATATAA
* *
103347954 AAATTTATTTATATATCTAA
1 AAATTTATTAATATATATAA
103347974 AAAT
1 AAAT
103347978 AGCTTTTTCG
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
20 21 1.00
ACGTcount: A:0.50, C:0.02, G:0.00, T:0.48
Consensus pattern (20 bp):
AAATTTATTAATATATATAA
Found at i:103348078 original size:19 final size:20
Alignment explanation
Indices: 103348054--103348094 Score: 66
Period size: 19 Copynumber: 2.1 Consensus size: 20
103348044 CAAACACCAC
*
103348054 AAAGTAAATTA-TTTCCAGA
1 AAAGTAAATCATTTTCCAGA
103348073 AAAGTAAATCATTTTCCAGA
1 AAAGTAAATCATTTTCCAGA
103348093 AA
1 AA
103348095 TCATTTTCTG
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
19 10 0.50
20 10 0.50
ACGTcount: A:0.49, C:0.12, G:0.10, T:0.29
Consensus pattern (20 bp):
AAAGTAAATCATTTTCCAGA
Found at i:103348108 original size:14 final size:14
Alignment explanation
Indices: 103348078--103348123 Score: 56
Period size: 14 Copynumber: 3.2 Consensus size: 14
103348068 CCAGAAAAGT
**
103348078 AAATCATTTTCCAG
1 AAATCATTTTCTGG
103348092 AAATCATTTTCTGG
1 AAATCATTTTCTGG
*
103348106 AAAACATTTTACTGG
1 AAATCATTTT-CTGG
103348121 AAA
1 AAA
103348124 ACAAACAGAC
Statistics
Matches: 28, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
14 21 0.75
15 7 0.25
ACGTcount: A:0.39, C:0.15, G:0.11, T:0.35
Consensus pattern (14 bp):
AAATCATTTTCTGG
Found at i:103363077 original size:104 final size:104
Alignment explanation
Indices: 103362937--103363146 Score: 357
Period size: 104 Copynumber: 2.0 Consensus size: 104
103362927 TGTTGCTCTA
*
103362937 ATACAAATGTTATTATAGTACTACTCTAATTTGTTTCCTCAAGTGTGTTTTTTTGTTGTTGTAAT
1 ATACAAATGTTATTATAGTACTACTCTAATTTGTTTCCTCAAGTGTGCTTTTTTGTTGTTGTAAT
* *
103363002 AAACCATGTTATGAATAGTTAGTATGCTTTTAATTGTGC
66 AAACCATGTTATGAAGAGTTAGTATGCTTTGAATTGTGC
* *
103363041 ATACAGATGTTATTATAGTACTACTCTAATTTGTTTCCTCAAGTGTGCTTTTTTGTTGTTGTACT
1 ATACAAATGTTATTATAGTACTACTCTAATTTGTTTCCTCAAGTGTGCTTTTTTGTTGTTGTAAT
* *
103363106 GAAGCATGTTATGAAGAGTTAGTATGCTTTGAATTGTGC
66 AAACCATGTTATGAAGAGTTAGTATGCTTTGAATTGTGC
103363145 AT
1 AT
103363147 TTGTATATAG
Statistics
Matches: 99, Mismatches: 7, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
104 99 1.00
ACGTcount: A:0.26, C:0.11, G:0.18, T:0.46
Consensus pattern (104 bp):
ATACAAATGTTATTATAGTACTACTCTAATTTGTTTCCTCAAGTGTGCTTTTTTGTTGTTGTAAT
AAACCATGTTATGAAGAGTTAGTATGCTTTGAATTGTGC
Found at i:103380387 original size:6 final size:6
Alignment explanation
Indices: 103380376--103380414 Score: 78
Period size: 6 Copynumber: 6.5 Consensus size: 6
103380366 TATACACAAT
103380376 TGCATG TGCATG TGCATG TGCATG TGCATG TGCATG TGC
1 TGCATG TGCATG TGCATG TGCATG TGCATG TGCATG TGC
103380415 CTGGCCTTAA
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 33 1.00
ACGTcount: A:0.15, C:0.18, G:0.33, T:0.33
Consensus pattern (6 bp):
TGCATG
Found at i:103382208 original size:28 final size:29
Alignment explanation
Indices: 103382150--103382209 Score: 68
Period size: 28 Copynumber: 2.1 Consensus size: 29
103382140 AAACAATTTT
* * * *
103382150 TTTTTTTACTTTTAACCCTTATACTTTAA
1 TTTTTTTACTTTTAACCCATAAAATTGAA
*
103382179 TTTTTTTA-TTTTAATCCATAAAATTGAA
1 TTTTTTTACTTTTAACCCATAAAATTGAA
103382207 TTT
1 TTT
103382210 CTGATAGTAG
Statistics
Matches: 26, Mismatches: 5, Indels: 1
0.81 0.16 0.03
Matches are distributed among these distances:
28 18 0.69
29 8 0.31
ACGTcount: A:0.28, C:0.12, G:0.02, T:0.58
Consensus pattern (29 bp):
TTTTTTTACTTTTAACCCATAAAATTGAA
Found at i:103387069 original size:127 final size:127
Alignment explanation
Indices: 103386917--103387173 Score: 338
Period size: 127 Copynumber: 2.0 Consensus size: 127
103386907 AAAGTGGAAA
* * *
103386917 AACTCCTCAATAGAAGATAAGAAACTACAGACAAAAGGAGATTTCACTATAATCAATAAGAGTAC
1 AACTCCTCAAAAGAAGATAAAAAACTACAGACAAAAGGAGATTTCACTATAATAAATAAGAGTAC
* * *
103386982 AAAATAT-AGAGAAAATTAAAAGAAAAACTCGAAA-CCCACAAGAAAAACCCTTTGAAACAAAG
66 AAAAGATGA-AGAAAATTAAAA-AAAAACTCAAAACCCCACAAGAAAAACCCTTCGAAACAAAG
* * * ** *
103387044 AACTCCTTAAAAGAGGATAAAAAACTACGGACAAAAGGAGATTTTGCTATAATAAATTAGAGTAC
1 AACTCCTCAAAAGAAGATAAAAAACTACAGACAAAAGGAGATTTCACTATAATAAATAAGAGTAC
** * *
103387109 AAAAGATGAAGAGGATTAAAAAAAAACTCAAAACCCCATAAGAAAAATCCTTCGAAACAAAG
66 AAAAGATGAAGAAAATTAAAAAAAAACTCAAAACCCCACAAGAAAAACCCTTCGAAACAAAG
103387171 AAC
1 AAC
103387174 GAAATTCTCT
Statistics
Matches: 112, Mismatches: 16, Indels: 4
0.85 0.12 0.03
Matches are distributed among these distances:
126 11 0.10
127 100 0.89
128 1 0.01
ACGTcount: A:0.54, C:0.16, G:0.14, T:0.17
Consensus pattern (127 bp):
AACTCCTCAAAAGAAGATAAAAAACTACAGACAAAAGGAGATTTCACTATAATAAATAAGAGTAC
AAAAGATGAAGAAAATTAAAAAAAAACTCAAAACCCCACAAGAAAAACCCTTCGAAACAAAG
Found at i:103389577 original size:5 final size:5
Alignment explanation
Indices: 103389567--103389600 Score: 52
Period size: 5 Copynumber: 7.0 Consensus size: 5
103389557 AAATTCATCG
*
103389567 AATTA AATTA AATTA AATT- AATTA GATTA AATTA
1 AATTA AATTA AATTA AATTA AATTA AATTA AATTA
103389601 TCTTTTTAAT
Statistics
Matches: 26, Mismatches: 2, Indels: 2
0.87 0.07 0.07
Matches are distributed among these distances:
4 4 0.15
5 22 0.85
ACGTcount: A:0.56, C:0.00, G:0.03, T:0.41
Consensus pattern (5 bp):
AATTA
Found at i:103389589 original size:14 final size:14
Alignment explanation
Indices: 103389567--103389600 Score: 50
Period size: 14 Copynumber: 2.4 Consensus size: 14
103389557 AAATTCATCG
103389567 AATTAAATTAAATTA
1 AATT-AATTAAATTA
*
103389582 AATTAATTAGATTA
1 AATTAATTAAATTA
103389596 AATTA
1 AATTA
103389601 TCTTTTTAAT
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
14 14 0.78
15 4 0.22
ACGTcount: A:0.56, C:0.00, G:0.03, T:0.41
Consensus pattern (14 bp):
AATTAATTAAATTA
Found at i:103390070 original size:1 final size:1
Alignment explanation
Indices: 103390066--103390090 Score: 50
Period size: 1 Copynumber: 25.0 Consensus size: 1
103390056 TTTTATTTCC
103390066 TTTTTTTTTTTTTTTTTTTTTTTTT
1 TTTTTTTTTTTTTTTTTTTTTTTTT
103390091 GGTTTAAGCG
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
1 24 1.00
ACGTcount: A:0.00, C:0.00, G:0.00, T:1.00
Consensus pattern (1 bp):
T
Found at i:103393302 original size:31 final size:31
Alignment explanation
Indices: 103393242--103393302 Score: 77
Period size: 31 Copynumber: 2.0 Consensus size: 31
103393232 GAGAAATTAT
* * **
103393242 TTTTACTCTCTTAATTAATTAATGTAAAATA
1 TTTTAATCTCTTAATAAATTAATAAAAAATA
*
103393273 TTTTAATCTCTTACTAAATTAATAAAAAAT
1 TTTTAATCTCTTAATAAATTAATAAAAAAT
103393303 GTCTTTTTTT
Statistics
Matches: 25, Mismatches: 5, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
31 25 1.00
ACGTcount: A:0.43, C:0.10, G:0.02, T:0.46
Consensus pattern (31 bp):
TTTTAATCTCTTAATAAATTAATAAAAAATA
Found at i:103403108 original size:20 final size:22
Alignment explanation
Indices: 103403066--103403110 Score: 58
Period size: 20 Copynumber: 2.1 Consensus size: 22
103403056 ATAACTTGAG
*
103403066 TTTTATTATATATAAATTTTAT
1 TTTTATTATATATAAATTGTAT
*
103403088 TTTTATT-TAT-TTAATTGTAT
1 TTTTATTATATATAAATTGTAT
103403108 TTT
1 TTT
103403111 GTAATGATTA
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
20 11 0.52
21 3 0.14
22 7 0.33
ACGTcount: A:0.29, C:0.00, G:0.02, T:0.69
Consensus pattern (22 bp):
TTTTATTATATATAAATTGTAT
Found at i:103403616 original size:37 final size:36
Alignment explanation
Indices: 103403546--103403618 Score: 87
Period size: 36 Copynumber: 2.0 Consensus size: 36
103403536 GTTGCTACCA
* *
103403546 TTTTGTTGTTAATGTTTGAATATTGTATAACATTTG
1 TTTTATTGTTAATGTTTGAATATTGTAGAACATTTG
103403582 TTTTATTGTTAAT-TTTGCTAATATT-TAGAGACATTTG
1 TTTTATTGTTAATGTTTG--AATATTGTAGA-ACATTTG
103403619 CTTGTTAAAT
Statistics
Matches: 32, Mismatches: 2, Indels: 5
0.82 0.05 0.13
Matches are distributed among these distances:
35 4 0.12
36 15 0.47
37 13 0.41
ACGTcount: A:0.26, C:0.04, G:0.15, T:0.55
Consensus pattern (36 bp):
TTTTATTGTTAATGTTTGAATATTGTAGAACATTTG
Found at i:103409765 original size:51 final size:51
Alignment explanation
Indices: 103409701--103409836 Score: 148
Period size: 51 Copynumber: 2.7 Consensus size: 51
103409691 TGGAAACATG
*
103409701 ATCTTAAAAGATATGATATTATAGTCTTAGAGATCTTAGATATGATATGGA
1 ATCTTAAAAGATATGATATTATAGTCTTAGAGATCTTAGATAAGATATGGA
* * * * * * ** *
103409752 ATCTTATAAGATATTATTTTATAAG-ATTACATATCTTATCTAAGATATGTA
1 ATCTTAAAAGATATGATATTAT-AGTCTTAGAGATCTTAGATAAGATATGGA
* *
103409803 ATCTTAGAAGATATGATATTATATTCTTAGAGAT
1 ATCTTAAAAGATATGATATTATAGTCTTAGAGAT
103409837 TTGGTGGTAG
Statistics
Matches: 66, Mismatches: 17, Indels: 4
0.76 0.20 0.05
Matches are distributed among these distances:
50 1 0.02
51 63 0.95
52 2 0.03
ACGTcount: A:0.39, C:0.07, G:0.13, T:0.41
Consensus pattern (51 bp):
ATCTTAAAAGATATGATATTATAGTCTTAGAGATCTTAGATAAGATATGGA
Found at i:103413231 original size:12 final size:12
Alignment explanation
Indices: 103413214--103413238 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
103413204 AATTTAGATT
103413214 AAATAATTTTAA
1 AAATAATTTTAA
103413226 AAATAATTTTAA
1 AAATAATTTTAA
103413238 A
1 A
103413239 TATATTAATG
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.60, C:0.00, G:0.00, T:0.40
Consensus pattern (12 bp):
AAATAATTTTAA
Found at i:103417953 original size:29 final size:31
Alignment explanation
Indices: 103417920--103417985 Score: 84
Period size: 31 Copynumber: 2.2 Consensus size: 31
103417910 TTTAAATTAC
*
103417920 GTTTTGATCATTGAAC-TT-T-AATTTGTTAT
1 GTTTTGATCATT-AACATTATCAATTTGTAAT
*
103417949 GTTTTGGTCATTAACATTATCAATTTGTAAT
1 GTTTTGATCATTAACATTATCAATTTGTAAT
103417980 GTTTTG
1 GTTTTG
103417986 GTCACTCTGC
Statistics
Matches: 32, Mismatches: 2, Indels: 4
0.84 0.05 0.11
Matches are distributed among these distances:
28 3 0.09
29 13 0.41
30 1 0.03
31 15 0.47
ACGTcount: A:0.24, C:0.08, G:0.15, T:0.53
Consensus pattern (31 bp):
GTTTTGATCATTAACATTATCAATTTGTAAT
Found at i:103426828 original size:4 final size:4
Alignment explanation
Indices: 103426815--103426843 Score: 51
Period size: 4 Copynumber: 7.5 Consensus size: 4
103426805 TGGTTTTTCA
103426815 AATT -ATT AATT AATT AATT AATT AATT AA
1 AATT AATT AATT AATT AATT AATT AATT AA
103426844 AGTTCAAAAA
Statistics
Matches: 24, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
3 3 0.12
4 21 0.88
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (4 bp):
AATT
Found at i:103429486 original size:17 final size:16
Alignment explanation
Indices: 103429452--103429486 Score: 52
Period size: 16 Copynumber: 2.1 Consensus size: 16
103429442 AAAAAATAAG
*
103429452 GAAAAAAAATGAACGA
1 GAAAAAAAATGAAAGA
103429468 GAAAAAAAATAGAAAGA
1 GAAAAAAAAT-GAAAGA
103429485 GA
1 GA
103429487 CCAAAGAGGA
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
16 10 0.59
17 7 0.41
ACGTcount: A:0.71, C:0.03, G:0.20, T:0.06
Consensus pattern (16 bp):
GAAAAAAAATGAAAGA
Found at i:103429541 original size:15 final size:16
Alignment explanation
Indices: 103429523--103429552 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
103429513 ATAATAGAAA
103429523 AAAATA-GAAAAAAAT
1 AAAATAGGAAAAAAAT
103429538 AAAATAGGAAAAAAA
1 AAAATAGGAAAAAAA
103429553 AAGGAAAGAG
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 6 0.43
16 8 0.57
ACGTcount: A:0.80, C:0.00, G:0.10, T:0.10
Consensus pattern (16 bp):
AAAATAGGAAAAAAAT
Found at i:103429552 original size:11 final size:10
Alignment explanation
Indices: 103429509--103429538 Score: 51
Period size: 10 Copynumber: 3.0 Consensus size: 10
103429499 GAAAAGAAAG
*
103429509 GAAAATAATA
1 GAAAAAAATA
103429519 GAAAAAAATA
1 GAAAAAAATA
103429529 GAAAAAAATA
1 GAAAAAAATA
103429539 AAATAGGAAA
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
10 19 1.00
ACGTcount: A:0.77, C:0.00, G:0.10, T:0.13
Consensus pattern (10 bp):
GAAAAAAATA
Found at i:103432093 original size:21 final size:21
Alignment explanation
Indices: 103432067--103432107 Score: 55
Period size: 21 Copynumber: 2.0 Consensus size: 21
103432057 AACAAACAAT
* *
103432067 AAAAATAATAAATAAATAAAC
1 AAAAATAAGAAAAAAATAAAC
*
103432088 AAAAATTAGAAAAAAATAAA
1 AAAAATAAGAAAAAAATAAA
103432108 GTGAAAGATG
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:0.78, C:0.02, G:0.02, T:0.17
Consensus pattern (21 bp):
AAAAATAAGAAAAAAATAAAC
Found at i:103436052 original size:20 final size:20
Alignment explanation
Indices: 103436027--103436064 Score: 67
Period size: 20 Copynumber: 1.9 Consensus size: 20
103436017 AAGTATTATT
*
103436027 AGATATTTATTATTTAAAAA
1 AGATATTTATTAATTAAAAA
103436047 AGATATTTATTAATTAAA
1 AGATATTTATTAATTAAA
103436065 TAATTATATT
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.50, C:0.00, G:0.05, T:0.45
Consensus pattern (20 bp):
AGATATTTATTAATTAAAAA
Found at i:103437510 original size:18 final size:18
Alignment explanation
Indices: 103437489--103437535 Score: 58
Period size: 18 Copynumber: 2.6 Consensus size: 18
103437479 ATTGACTATT
103437489 AATAAACGATTGATACTG
1 AATAAACGATTGATACTG
* *
103437507 AATAAATGATTGTTACTG
1 AATAAACGATTGATACTG
* *
103437525 ATTAACCGATT
1 AATAAACGATT
103437536 ATTACTGTTG
Statistics
Matches: 24, Mismatches: 5, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
18 24 1.00
ACGTcount: A:0.40, C:0.11, G:0.15, T:0.34
Consensus pattern (18 bp):
AATAAACGATTGATACTG
Found at i:103444974 original size:27 final size:26
Alignment explanation
Indices: 103444929--103444983 Score: 65
Period size: 27 Copynumber: 2.1 Consensus size: 26
103444919 CTCATAATAG
* *
103444929 TTACAATTTCATCAATTTTTACGACTT
1 TTACAATTTAATCAATTTTCAC-ACTT
**
103444956 TTACAATTTAATCTTTTTTCACACTT
1 TTACAATTTAATCAATTTTCACACTT
103444982 TT
1 TT
103444984 CTTTCACCTT
Statistics
Matches: 24, Mismatches: 4, Indels: 1
0.83 0.14 0.03
Matches are distributed among these distances:
26 6 0.25
27 18 0.75
ACGTcount: A:0.27, C:0.18, G:0.02, T:0.53
Consensus pattern (26 bp):
TTACAATTTAATCAATTTTCACACTT
Found at i:103456924 original size:19 final size:19
Alignment explanation
Indices: 103456872--103456928 Score: 55
Period size: 19 Copynumber: 3.0 Consensus size: 19
103456862 TTATTAAAAG
103456872 TAAAGATTATAAATTTAAA
1 TAAAGATTATAAATTTAAA
* * *
103456891 AAAAAATTGA-GAATTGT-AA
1 TAAAGATT-ATAAATT-TAAA
103456910 TAAAGATTATAAATTTAAA
1 TAAAGATTATAAATTTAAA
103456929 AAAAATTGAG
Statistics
Matches: 28, Mismatches: 6, Indels: 8
0.67 0.14 0.19
Matches are distributed among these distances:
18 2 0.07
19 24 0.86
20 2 0.07
ACGTcount: A:0.58, C:0.00, G:0.09, T:0.33
Consensus pattern (19 bp):
TAAAGATTATAAATTTAAA
Found at i:103456939 original size:37 final size:38
Alignment explanation
Indices: 103456872--103456946 Score: 143
Period size: 37 Copynumber: 2.0 Consensus size: 38
103456862 TTATTAAAAG
103456872 TAAAGATTATAAATTTAAAAAAAAATTGAGAATTGTAA
1 TAAAGATTATAAATTTAAAAAAAAATTGAGAATTGTAA
103456910 TAAAGATTATAAATTT-AAAAAAAATTGAGAATTGTAA
1 TAAAGATTATAAATTTAAAAAAAAATTGAGAATTGTAA
103456947 AAAAAAAACT
Statistics
Matches: 37, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
37 21 0.57
38 16 0.43
ACGTcount: A:0.57, C:0.00, G:0.11, T:0.32
Consensus pattern (38 bp):
TAAAGATTATAAATTTAAAAAAAAATTGAGAATTGTAA
Found at i:103456948 original size:18 final size:18
Alignment explanation
Indices: 103456890--103456951 Score: 65
Period size: 18 Copynumber: 3.4 Consensus size: 18
103456880 ATAAATTTAA
103456890 AAAAAAATTGAGAATTGT
1 AAAAAAATTGAGAATTGT
* *
103456908 AATAAAGATT-ATAAATT-T
1 AA-AAAAATTGA-GAATTGT
103456926 AAAAAAAATTGAGAATTGT
1 -AAAAAAATTGAGAATTGT
103456945 AAAAAAA
1 AAAAAAA
103456952 AAACTTAAAT
Statistics
Matches: 35, Mismatches: 4, Indels: 10
0.71 0.08 0.20
Matches are distributed among these distances:
18 21 0.60
19 14 0.40
ACGTcount: A:0.61, C:0.00, G:0.11, T:0.27
Consensus pattern (18 bp):
AAAAAAATTGAGAATTGT
Found at i:103456949 original size:19 final size:19
Alignment explanation
Indices: 103456889--103456952 Score: 78
Period size: 19 Copynumber: 3.4 Consensus size: 19
103456879 TATAAATTTA
103456889 AAAAAAAATTGAGAATTGT
1 AAAAAAAATTGAGAATTGT
* * *
103456908 AATAAAGATT-ATAAATT-T
1 AAAAAAAATTGA-GAATTGT
103456926 AAAAAAAATTGAGAATTGT
1 AAAAAAAATTGAGAATTGT
103456945 AAAAAAAA
1 AAAAAAAA
103456953 AACTTAAATA
Statistics
Matches: 36, Mismatches: 6, Indels: 6
0.75 0.12 0.12
Matches are distributed among these distances:
18 14 0.39
19 22 0.61
ACGTcount: A:0.62, C:0.00, G:0.11, T:0.27
Consensus pattern (19 bp):
AAAAAAAATTGAGAATTGT
Found at i:103457193 original size:5 final size:5
Alignment explanation
Indices: 103457183--103457227 Score: 54
Period size: 5 Copynumber: 8.8 Consensus size: 5
103457173 AATTTTTTTA
* * *
103457183 AAAAT AAAAT AAAAT AAAAAT AAAAG AAAAT TAAAT AAAGT AAAA
1 AAAAT AAAAT AAAAT -AAAAT AAAAT AAAAT AAAAT AAAAT AAAA
103457228 AGTTATTTTT
Statistics
Matches: 33, Mismatches: 6, Indels: 2
0.80 0.15 0.05
Matches are distributed among these distances:
5 28 0.85
6 5 0.15
ACGTcount: A:0.78, C:0.00, G:0.04, T:0.18
Consensus pattern (5 bp):
AAAAT
Found at i:103457200 original size:16 final size:16
Alignment explanation
Indices: 103457181--103457227 Score: 60
Period size: 16 Copynumber: 3.0 Consensus size: 16
103457171 ATAATTTTTT
103457181 TAAAAATAAAATAAAA
1 TAAAAATAAAATAAAA
*
103457197 TAAAAATAAAAGAAAA
1 TAAAAATAAAATAAAA
* *
103457213 T-TAAATAAAGTAAAA
1 TAAAAATAAAATAAAA
103457228 AGTTATTTTT
Statistics
Matches: 27, Mismatches: 4, Indels: 1
0.84 0.12 0.03
Matches are distributed among these distances:
15 11 0.41
16 16 0.59
ACGTcount: A:0.77, C:0.00, G:0.04, T:0.19
Consensus pattern (16 bp):
TAAAAATAAAATAAAA
Found at i:103458102 original size:14 final size:16
Alignment explanation
Indices: 103458083--103458115 Score: 52
Period size: 16 Copynumber: 2.2 Consensus size: 16
103458073 CACAAAAATC
103458083 CTTATA-TTT-TTAAT
1 CTTATAGTTTATTAAT
103458097 CTTATAGTTTATTAAT
1 CTTATAGTTTATTAAT
103458113 CTT
1 CTT
103458116 TTAAGTTTCA
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
14 6 0.35
15 3 0.18
16 8 0.47
ACGTcount: A:0.27, C:0.09, G:0.03, T:0.61
Consensus pattern (16 bp):
CTTATAGTTTATTAAT
Found at i:103460434 original size:41 final size:41
Alignment explanation
Indices: 103460378--103460508 Score: 167
Period size: 41 Copynumber: 3.2 Consensus size: 41
103460368 TCAACATAGT
*
103460378 TTTGGCTATATATGGCATTTTGTGTGCGAGATTGAGATAAC
1 TTTGGCTATATATGGCACTTTGTGTGCGAGATTGAGATAAC
* * *
103460419 TTTGTCTATATATGGCACTTTGTATGCGAGATTGAGATAGC
1 TTTGGCTATATATGGCACTTTGTGTGCGAGATTGAGATAAC
* * *
103460460 TTCGGCTATATATGGCACTTAGTGTGC-A-ATTTGAGATAGC
1 TTTGGCTATATATGGCACTTTGTGTGCGAGA-TTGAGATAAC
*
103460500 TTCGGCTAT
1 TTTGGCTAT
103460509 GTACGACACT
Statistics
Matches: 81, Mismatches: 8, Indels: 3
0.88 0.09 0.03
Matches are distributed among these distances:
39 1 0.01
40 20 0.25
41 60 0.74
ACGTcount: A:0.24, C:0.13, G:0.25, T:0.38
Consensus pattern (41 bp):
TTTGGCTATATATGGCACTTTGTGTGCGAGATTGAGATAAC
Found at i:103460504 original size:40 final size:39
Alignment explanation
Indices: 103460343--103460528 Score: 165
Period size: 41 Copynumber: 4.6 Consensus size: 39
103460333 GACAAATCAA
* * * * * *
103460343 CTATATGTGGCACTTAGTGTGCGATTCAACATAGTTTTGG
1 CTATATATGGCACTTAGTGTGCAATT-GAGATAGCTTCGG
* * * * *
103460383 CTATATATGGCATTTTGTGTGCGAGATTGAGATAACTTTGT
1 CTATATATGGCACTTAGTGTGC-A-ATTGAGATAGCTTCGG
* *
103460424 CTATATATGGCACTTTGTATGCGAGATTGAGATAGCTTCGG
1 CTATATATGGCACTTAGTGTGC-A-ATTGAGATAGCTTCGG
103460465 CTATATATGGCACTTAGTGTGCAATTTGAGATAGCTTCGG
1 CTATATATGGCACTTAGTGTGCAA-TTGAGATAGCTTCGG
* * * *
103460505 CTATGTACGACACTTAATGTGCAA
1 CTATATATGGCACTTAGTGTGCAA
103460529 GATATCGAGT
Statistics
Matches: 123, Mismatches: 20, Indels: 6
0.83 0.13 0.04
Matches are distributed among these distances:
39 1 0.01
40 55 0.45
41 64 0.52
42 3 0.02
ACGTcount: A:0.25, C:0.15, G:0.24, T:0.36
Consensus pattern (39 bp):
CTATATATGGCACTTAGTGTGCAATTGAGATAGCTTCGG
Found at i:103464152 original size:18 final size:19
Alignment explanation
Indices: 103464129--103464167 Score: 53
Period size: 19 Copynumber: 2.1 Consensus size: 19
103464119 TACAAATACA
*
103464129 AACATT-ACATAATTATTT
1 AACATTCACATAATAATTT
*
103464147 AACATTCACATCATAATTT
1 AACATTCACATAATAATTT
103464166 AA
1 AA
103464168 TCATATCGTT
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
18 6 0.33
19 12 0.67
ACGTcount: A:0.46, C:0.15, G:0.00, T:0.38
Consensus pattern (19 bp):
AACATTCACATAATAATTT
Found at i:103464824 original size:22 final size:22
Alignment explanation
Indices: 103464787--103464855 Score: 84
Period size: 22 Copynumber: 3.1 Consensus size: 22
103464777 TATGCACTAT
* *
103464787 TAAATAGAGAGCACTAAAGTGT
1 TAAACAGAGAGCACTAAAGTGC
* * *
103464809 TATACAGATAGCACTAATGTGC
1 TAAACAGAGAGCACTAAAGTGC
*
103464831 TAAACAGAGAGCACTAACGTGC
1 TAAACAGAGAGCACTAAAGTGC
103464853 TAA
1 TAA
103464856 TAATCAGAGA
Statistics
Matches: 39, Mismatches: 8, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
22 39 1.00
ACGTcount: A:0.42, C:0.16, G:0.20, T:0.22
Consensus pattern (22 bp):
TAAACAGAGAGCACTAAAGTGC
Found at i:103467207 original size:67 final size:66
Alignment explanation
Indices: 103467006--103467213 Score: 176
Period size: 67 Copynumber: 3.2 Consensus size: 66
103466996 ATCAACTGTA
* * * * *
103467006 ATATTAAATCAGCGAGCTATTTGGAGTTGTGATTTTAAATCATTTAAGTCAAATAAGATTGTTCA
1 ATATTAAATCAACGAGCT-TTTGGAGTTGTGATATTAAATCAATTAACTCAAATAAGATTGTTTA
103467071 TG
65 TG
* * * * * * * * *
103467073 ATATTAAATCAAATGAAC--TTAG-GTTGTGATCTTAAATC-ATAGAAC-CTTAACAATATCAG-
1 ATATTAAATC-AACGAGCTTTTGGAGTTGTGATATTAAATCAAT-TAACTC-AAATAAGAT-TGT
*
103467132 TTGTG
62 TTATG
*
103467137 ATATTAAATCAACGAGCTGTTTGGAGTTGCGATATTAAATCAATTAACTCAAATAAGATTGTTTA
1 ATATTAAATCAACGAGCT-TTTGGAGTTGTGATATTAAATCAATTAACTCAAATAAGATTGTTTA
103467202 TG
65 TG
103467204 ATATTAAATC
1 ATATTAAATC
103467214 GAATGAACTT
Statistics
Matches: 105, Mismatches: 25, Indels: 22
0.69 0.16 0.14
Matches are distributed among these distances:
63 7 0.07
64 36 0.34
65 4 0.04
66 4 0.04
67 47 0.45
68 7 0.07
ACGTcount: A:0.38, C:0.11, G:0.15, T:0.37
Consensus pattern (66 bp):
ATATTAAATCAACGAGCTTTTGGAGTTGTGATATTAAATCAATTAACTCAAATAAGATTGTTTAT
G
Found at i:103467253 original size:131 final size:131
Alignment explanation
Indices: 103466788--103467240 Score: 577
Period size: 131 Copynumber: 3.5 Consensus size: 131
103466778 GAAAATTAGC
* * * *
103466788 TAACACAAATGAA-ATTGTTCATGATATTAAATCGAATGAACTTAGATTACGAAATTAAATCAAC
1 TAACTCAAAT-AAGATTGTTCATGATATTAAATCGAATGAACTTAGGTTGCGATATTAAATCAAC
* * * * * * * *
103466852 GAACCTTAACGATATCAATTGCAATTTTTAATCAGCGAGTTGTTTGGAGATGCGATCTTAAATTA
65 GAACCTTAACAATATCAATTGTAATATTAAATCAGCGAGCTGTTTGGAGTTGCGATATTAAATCA
**
103466917 GC
130 AT
* * *
103466919 TAAATCAAATATGATTGTTCATGATGTTAAATCGAATGAACTTAGGTTGCGATATTAAATCAACG
1 TAACTCAAATAAGATTGTTCATGATATTAAATCGAATGAACTTAGGTTGCGATATTAAATCAACG
* ** * * * * *
103466984 AACCTCAATGATATCAACTGTAATATTAAATCAGCGAGCTATTTGGAGTTGTGATTTTAAATCAT
66 AACCTTAACAATATCAATTGTAATATTAAATCAGCGAGCTGTTTGGAGTTGCGATATTAAATCAA
103467049 T
131 T
* * * *
103467050 TAAGTCAAATAAGATTGTTCATGATATTAAATCAAATGAACTTAGGTTGTGATCTTAAATCATA-
1 TAACTCAAATAAGATTGTTCATGATATTAAATCGAATGAACTTAGGTTGCGATATTAAATCA-AC
* * *
103467114 GAACCTTAACAATATCAGTTGTGATATTAAATCAACGAGCTGTTTGGAGTTGCGATATTAAATCA
65 GAACCTTAACAATATCAATTGTAATATTAAATCAGCGAGCTGTTTGGAGTTGCGATATTAAATCA
103467179 AT
130 AT
*
103467181 TAACTCAAATAAGATTGTTTATGATATTAAATCGAATGAACTTAGGTTGCGATATTAAAT
1 TAACTCAAATAAGATTGTTCATGATATTAAATCGAATGAACTTAGGTTGCGATATTAAAT
103467241 TAGCAAACCT
Statistics
Matches: 277, Mismatches: 43, Indels: 4
0.85 0.13 0.01
Matches are distributed among these distances:
130 1 0.00
131 275 0.99
132 1 0.00
ACGTcount: A:0.38, C:0.12, G:0.16, T:0.34
Consensus pattern (131 bp):
TAACTCAAATAAGATTGTTCATGATATTAAATCGAATGAACTTAGGTTGCGATATTAAATCAACG
AACCTTAACAATATCAATTGTAATATTAAATCAGCGAGCTGTTTGGAGTTGCGATATTAAATCAA
T
Found at i:103476000 original size:1 final size:1
Alignment explanation
Indices: 103475994--103476028 Score: 52
Period size: 1 Copynumber: 35.0 Consensus size: 1
103475984 TGTTGAAATT
* *
103475994 AAAAAAAAAAAAAAAAAAAAAAAAAGAAAGAAAAA
1 AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA
103476029 TTTATTAGAA
Statistics
Matches: 30, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
1 30 1.00
ACGTcount: A:0.94, C:0.00, G:0.06, T:0.00
Consensus pattern (1 bp):
A
Found at i:103478042 original size:19 final size:20
Alignment explanation
Indices: 103477999--103478049 Score: 63
Period size: 19 Copynumber: 2.7 Consensus size: 20
103477989 GAAAAAAATT
103477999 ATAAAAATAATAAATTTTAG
1 ATAAAAATAATAAATTTTAG
* *
103478019 A-AAAATTATTAAATTTTA-
1 ATAAAAATAATAAATTTTAG
103478037 ATAAAAAT-ATAAA
1 ATAAAAATAATAAA
103478050 AAATTAAAAT
Statistics
Matches: 26, Mismatches: 4, Indels: 4
0.76 0.12 0.12
Matches are distributed among these distances:
18 5 0.19
19 20 0.77
20 1 0.04
ACGTcount: A:0.63, C:0.00, G:0.02, T:0.35
Consensus pattern (20 bp):
ATAAAAATAATAAATTTTAG
Found at i:103478368 original size:46 final size:49
Alignment explanation
Indices: 103478288--103478394 Score: 141
Period size: 47 Copynumber: 2.3 Consensus size: 49
103478278 GTAAAAAATG
* *
103478288 TTATGAAATTTT-TATTTCTTTACATTTTGTATAATTTTCTTACGA-CT
1 TTATAAAATTTTATATTTCTATACATTTTGTATAATTTTCTTACGATCT
* * *
103478335 TTATAAAATTTTATATTTCTATATA-TTT-TATAATTTTTTTACGATTT
1 TTATAAAATTTTATATTTCTATACATTTTGTATAATTTTCTTACGATCT
103478382 TTATAAAATTTTA
1 TTATAAAATTTTA
103478395 CAATTTTTTA
Statistics
Matches: 53, Mismatches: 5, Indels: 4
0.85 0.08 0.06
Matches are distributed among these distances:
46 15 0.28
47 28 0.53
48 10 0.19
ACGTcount: A:0.31, C:0.07, G:0.04, T:0.59
Consensus pattern (49 bp):
TTATAAAATTTTATATTTCTATACATTTTGTATAATTTTCTTACGATCT
Found at i:103478385 original size:20 final size:20
Alignment explanation
Indices: 103478360--103478433 Score: 71
Period size: 20 Copynumber: 3.7 Consensus size: 20
103478350 TTTCTATATA
*
103478360 TTTTATAATTTTTTTACGAT
1 TTTTATAATTTTTTTACAAT
**
103478380 TTTTATAA-AATTTTACAAT
1 TTTTATAATTTTTTTACAAT
* *
103478399 TTTT-TATATTGTTTCACAAT
1 TTTTATA-ATTTTTTTACAAT
103478419 TTTTAATAATTTTTT
1 TTTT-ATAATTTTTT
103478434 AATATTTAAA
Statistics
Matches: 43, Mismatches: 7, Indels: 7
0.75 0.12 0.12
Matches are distributed among these distances:
18 2 0.05
19 13 0.30
20 20 0.47
21 6 0.14
22 2 0.05
ACGTcount: A:0.30, C:0.05, G:0.03, T:0.62
Consensus pattern (20 bp):
TTTTATAATTTTTTTACAAT
Found at i:103478407 original size:47 final size:46
Alignment explanation
Indices: 103478317--103478408 Score: 123
Period size: 47 Copynumber: 2.0 Consensus size: 46
103478307 TTACATTTTG
*
103478317 TATAATTTTCTTACGACTTTATAAAATTTTATATTTCTATATATTT
1 TATAATTTTCTTACGACTTTATAAAATTTTAAATTTCTATATATTT
* * *
103478363 TATAATTTTTTTACGATTTTTATAAAATTTTACAATTT-TTTATATT
1 TATAATTTTCTTACGA-CTTTATAAAATTTTA-AATTTCTATATATT
103478409 GTTTCACAAT
Statistics
Matches: 40, Mismatches: 4, Indels: 3
0.85 0.09 0.06
Matches are distributed among these distances:
46 15 0.38
47 21 0.52
48 4 0.10
ACGTcount: A:0.33, C:0.07, G:0.02, T:0.59
Consensus pattern (46 bp):
TATAATTTTCTTACGACTTTATAAAATTTTAAATTTCTATATATTT
Found at i:103478689 original size:88 final size:90
Alignment explanation
Indices: 103478509--103478729 Score: 243
Period size: 88 Copynumber: 2.5 Consensus size: 90
103478499 AACTTTTAAT
* * * * *
103478509 AAAAGTAAGGGCTTATTTGATTTTTCTGAAAAAAAATTGAGGGTCTTTTTAATACATTTTGAAAG
1 AAAAGTAAGGGCTTAATTGCTTTTTTTG-AAAAAATTTGAGGGTCTTTTTAATACATTTTGAAAC
* * *
103478574 TTCAAGTACCCAATTGAGTAC-AAAA
65 TTCAAGTACCCAAATAAATACAAAAA
* ** * **
103478599 AAAATTAAGGGCTTAATTGCTTTTTTTGAAAAGGTTTGAGGGTC-TTTTGATGTATTTTGAAACT
1 AAAAGTAAGGGCTTAATTGCTTTTTTTGAAAAAATTTGAGGGTCTTTTTAATACATTTTGAAACT
*
103478663 TCAAGTACTCAAATAAATA-AATAAA
66 TCAAGTACCCAAATAAATACAA-AAA
* *
103478688 AAAAGCAA-GGCTTAATTGCATTTTTTGAAAAAATTTGAGGGT
1 AAAAGTAAGGGCTTAATTGCTTTTTTTGAAAAAATTTGAGGGT
103478730 TATTTTTGCA
Statistics
Matches: 109, Mismatches: 20, Indels: 6
0.81 0.15 0.04
Matches are distributed among these distances:
88 63 0.58
89 22 0.20
90 24 0.22
ACGTcount: A:0.38, C:0.09, G:0.18, T:0.36
Consensus pattern (90 bp):
AAAAGTAAGGGCTTAATTGCTTTTTTTGAAAAAATTTGAGGGTCTTTTTAATACATTTTGAAACT
TCAAGTACCCAAATAAATACAAAAA
Found at i:103486620 original size:16 final size:15
Alignment explanation
Indices: 103486593--103486649 Score: 66
Period size: 16 Copynumber: 3.9 Consensus size: 15
103486583 TATCATTTAA
103486593 ATATATAATTTAAAT
1 ATATATAATTTAAAT
103486608 ATATATAAATTTAAAT
1 ATATAT-AATTTAAAT
103486624 ATAT-TAA--TAATAT
1 ATATATAATTTAA-AT
*
103486637 ATAAATAATTTAA
1 ATATATAATTTAA
103486650 CAATATAATA
Statistics
Matches: 36, Mismatches: 1, Indels: 9
0.78 0.02 0.20
Matches are distributed among these distances:
12 3 0.08
13 5 0.14
14 5 0.14
15 7 0.19
16 16 0.44
ACGTcount: A:0.56, C:0.00, G:0.00, T:0.44
Consensus pattern (15 bp):
ATATATAATTTAAAT
Found at i:103486638 original size:29 final size:27
Alignment explanation
Indices: 103486587--103486668 Score: 96
Period size: 29 Copynumber: 2.9 Consensus size: 27
103486577 ACTATTTATC
*
103486587 ATTTAAATATATAATTTAA-ATATATATAA
1 ATTTAAATATATAA--TAATATATAAAT-A
103486616 ATTTAAATATATTAATAATATATAAATA
1 ATTTAAATATA-TAATAATATATAAATA
103486644 ATTTAACA-ATATAATAATATATAAA
1 ATTTAA-ATATATAATAATATATAAA
103486669 GAAATATGCG
Statistics
Matches: 49, Mismatches: 1, Indels: 8
0.84 0.02 0.14
Matches are distributed among these distances:
27 14 0.29
28 13 0.27
29 19 0.39
30 3 0.06
ACGTcount: A:0.57, C:0.01, G:0.00, T:0.41
Consensus pattern (27 bp):
ATTTAAATATATAATAATATATAAATA
Found at i:103486643 original size:19 final size:19
Alignment explanation
Indices: 103486603--103486665 Score: 55
Period size: 19 Copynumber: 3.5 Consensus size: 19
103486593 ATATATAATT
*
103486603 TAAATATA-T-ATAA-ATT
1 TAAATATATTAATAATATA
103486619 TAAATATATTAATAATATA
1 TAAATATATTAATAATATA
*
103486638 TAAATA-ATTTAACAATATA
1 TAAATATA-TTAATAATATA
103486657 -ATAATATAT
1 TA-AATATAT
103486666 AAAGAAATAT
Statistics
Matches: 39, Mismatches: 2, Indels: 9
0.78 0.04 0.18
Matches are distributed among these distances:
16 8 0.21
17 1 0.03
18 6 0.15
19 23 0.59
20 1 0.03
ACGTcount: A:0.57, C:0.02, G:0.00, T:0.41
Consensus pattern (19 bp):
TAAATATATTAATAATATA
Found at i:103490468 original size:21 final size:21
Alignment explanation
Indices: 103490442--103490482 Score: 64
Period size: 21 Copynumber: 2.0 Consensus size: 21
103490432 ATCTGATCAA
* *
103490442 ACTCCACCTGTTTTGGAGTAC
1 ACTCCACCTGCTGTGGAGTAC
103490463 ACTCCACCTGCTGTGGAGTA
1 ACTCCACCTGCTGTGGAGTA
103490483 TCGCTCGTCT
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:0.20, C:0.29, G:0.22, T:0.29
Consensus pattern (21 bp):
ACTCCACCTGCTGTGGAGTAC
Found at i:103495530 original size:46 final size:44
Alignment explanation
Indices: 103495430--103495537 Score: 135
Period size: 44 Copynumber: 2.4 Consensus size: 44
103495420 TGTCTTTGAC
** * * * *
103495430 ATGGACTTACATGAATTATTCCTGTCTCCAATGCCATATATAAT
1 ATGGACTTACATGGCTCAATCCTATCTCCAAAGCCATATATAAT
*
103495474 ATGGACTTACATGGCTCAATCCTATCTCCAAAGCCATATTTCTAAT
1 ATGGACTTACATGGCTCAATCCTATCTCCAAAGCCATA--TATAAT
103495520 ATGGACTTACATGGCTCA
1 ATGGACTTACATGGCTCA
103495538 TTTCTGTTCT
Statistics
Matches: 55, Mismatches: 7, Indels: 2
0.86 0.11 0.03
Matches are distributed among these distances:
44 32 0.58
46 23 0.42
ACGTcount: A:0.31, C:0.23, G:0.13, T:0.33
Consensus pattern (44 bp):
ATGGACTTACATGGCTCAATCCTATCTCCAAAGCCATATATAAT
Found at i:103497461 original size:31 final size:32
Alignment explanation
Indices: 103497423--103497488 Score: 82
Period size: 31 Copynumber: 2.1 Consensus size: 32
103497413 TGATTTTTTA
*
103497423 ATTTAAAAAGTTACAATTT-GGTCAC-TAAATT
1 ATTTAAAAAGTTAC-ATTTAAGTCACTTAAATT
* *
103497454 ATTTAAAAATTTTCATTTAAGTCACTTAAATT
1 ATTTAAAAAGTTACATTTAAGTCACTTAAATT
103497486 ATT
1 ATT
103497489 AAATTTGTTG
Statistics
Matches: 30, Mismatches: 3, Indels: 3
0.83 0.08 0.08
Matches are distributed among these distances:
30 4 0.13
31 17 0.57
32 9 0.30
ACGTcount: A:0.41, C:0.09, G:0.06, T:0.44
Consensus pattern (32 bp):
ATTTAAAAAGTTACATTTAAGTCACTTAAATT
Found at i:103508027 original size:2 final size:2
Alignment explanation
Indices: 103508020--103508046 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
103508010 TCAGGTTAAA
103508020 AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT A
103508047 CTTAAATGAA
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 25 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:103508708 original size:9 final size:9
Alignment explanation
Indices: 103508694--103508728 Score: 61
Period size: 9 Copynumber: 3.9 Consensus size: 9
103508684 CCCAAATAGT
*
103508694 CTTCTTCGC
1 CTTCTTCTC
103508703 CTTCTTCTC
1 CTTCTTCTC
103508712 CTTCTTCTC
1 CTTCTTCTC
103508721 CTTCTTCT
1 CTTCTTCT
103508729 TTTATCTTCT
Statistics
Matches: 25, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
9 25 1.00
ACGTcount: A:0.00, C:0.43, G:0.03, T:0.54
Consensus pattern (9 bp):
CTTCTTCTC
Found at i:103508709 original size:3 final size:3
Alignment explanation
Indices: 103508693--103508749 Score: 53
Period size: 3 Copynumber: 19.0 Consensus size: 3
103508683 ACCCAAATAG
* * * * *
103508693 TCT TCT TCG CCT TCT TCT CCT TCT TCT CCT TCT TCT TTT ATCT TCT
1 TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT -TCT TCT
103508739 T-T TCT TCT TCT
1 TCT TCT TCT TCT
103508750 AGAAGAAGAT
Statistics
Matches: 42, Mismatches: 10, Indels: 4
0.75 0.18 0.07
Matches are distributed among these distances:
2 2 0.05
3 38 0.90
4 2 0.05
ACGTcount: A:0.02, C:0.35, G:0.02, T:0.61
Consensus pattern (3 bp):
TCT
Found at i:103509491 original size:19 final size:18
Alignment explanation
Indices: 103509462--103509503 Score: 57
Period size: 19 Copynumber: 2.3 Consensus size: 18
103509452 GTGTTGATCC
*
103509462 AATTGTAATTTTTGTTTT
1 AATTTTAATTTTTGTTTT
*
103509480 ATATTTTAATTTTTTTTTT
1 A-ATTTTAATTTTTGTTTT
103509499 AATTT
1 AATTT
103509504 CTTTGGCAGA
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
18 5 0.24
19 16 0.76
ACGTcount: A:0.24, C:0.00, G:0.05, T:0.71
Consensus pattern (18 bp):
AATTTTAATTTTTGTTTT
Found at i:103512689 original size:17 final size:19
Alignment explanation
Indices: 103512652--103512689 Score: 53
Period size: 19 Copynumber: 2.1 Consensus size: 19
103512642 TAATACTTCA
103512652 AAAAATACATTGTTAATAT
1 AAAAATACATTGTTAATAT
*
103512671 AAAAATATATT-TT-ATAT
1 AAAAATACATTGTTAATAT
103512688 AA
1 AA
103512690 TATATTATTT
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
17 6 0.33
18 2 0.11
19 10 0.56
ACGTcount: A:0.55, C:0.03, G:0.03, T:0.39
Consensus pattern (19 bp):
AAAAATACATTGTTAATAT
Found at i:103515112 original size:12 final size:11
Alignment explanation
Indices: 103515079--103515103 Score: 50
Period size: 11 Copynumber: 2.3 Consensus size: 11
103515069 AGTTAGGAGC
103515079 AAAATGAGCAA
1 AAAATGAGCAA
103515090 AAAATGAGCAA
1 AAAATGAGCAA
103515101 AAA
1 AAA
103515104 TTGGAGCAAG
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 14 1.00
ACGTcount: A:0.68, C:0.08, G:0.16, T:0.08
Consensus pattern (11 bp):
AAAATGAGCAA
Found at i:103517501 original size:46 final size:46
Alignment explanation
Indices: 103517442--103517671 Score: 309
Period size: 46 Copynumber: 5.0 Consensus size: 46
103517432 TTATCTTTGA
* * * * *
103517442 CATGATGCCATAGTGTCTTTCAACTATGGTCTTACTCATTTTC-TGT
1 CATGTTGCCATGGTATCTTTCAACCATGGTCTTACTCA-TTTCATAT
* *
103517488 CATGTTGCCATAGTATCTTTCAACCATGGTCTTATTCATTTCATAT
1 CATGTTGCCATGGTATCTTTCAACCATGGTCTTACTCATTTCATAT
* * *
103517534 CATGTTGCCATGGTATCTTTCAACCATGGTTTTATTCATTCCATAT
1 CATGTTGCCATGGTATCTTTCAACCATGGTCTTACTCATTTCATAT
* * *
103517580 CACGTTGCCATGGCATCTTTCAACCATGGTCTTACACATTTCATAT
1 CATGTTGCCATGGTATCTTTCAACCATGGTCTTACTCATTTCATAT
* *
103517626 CAGGTTGCCATGGTATCTTTCAACCATGGTCTTACACATTTCATAT
1 CATGTTGCCATGGTATCTTTCAACCATGGTCTTACTCATTTCATAT
103517672 TAGAGAGCAC
Statistics
Matches: 167, Mismatches: 16, Indels: 2
0.90 0.09 0.01
Matches are distributed among these distances:
45 4 0.02
46 163 0.98
ACGTcount: A:0.23, C:0.23, G:0.13, T:0.40
Consensus pattern (46 bp):
CATGTTGCCATGGTATCTTTCAACCATGGTCTTACTCATTTCATAT
Found at i:103519116 original size:10 final size:11
Alignment explanation
Indices: 103519090--103519122 Score: 50
Period size: 11 Copynumber: 3.1 Consensus size: 11
103519080 TTCTACACTA
103519090 TTTCTCTTCAC
1 TTTCTCTTCAC
*
103519101 TTTCTCTT-AT
1 TTTCTCTTCAC
103519111 TTTCTCTTCAC
1 TTTCTCTTCAC
103519122 T
1 T
103519123 AACATGACAA
Statistics
Matches: 19, Mismatches: 2, Indels: 2
0.83 0.09 0.09
Matches are distributed among these distances:
10 9 0.47
11 10 0.53
ACGTcount: A:0.09, C:0.30, G:0.00, T:0.61
Consensus pattern (11 bp):
TTTCTCTTCAC
Found at i:103520776 original size:13 final size:13
Alignment explanation
Indices: 103520744--103520776 Score: 57
Period size: 13 Copynumber: 2.5 Consensus size: 13
103520734 ATCGTTGGAT
*
103520744 ACACGAATAGTAC
1 ACACGAGTAGTAC
103520757 ACACGAGTAGTAC
1 ACACGAGTAGTAC
103520770 ACACGAG
1 ACACGAG
103520777 GTATACTGAA
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
13 19 1.00
ACGTcount: A:0.42, C:0.24, G:0.21, T:0.12
Consensus pattern (13 bp):
ACACGAGTAGTAC
Found at i:103520877 original size:25 final size:25
Alignment explanation
Indices: 103520849--103520918 Score: 113
Period size: 25 Copynumber: 2.8 Consensus size: 25
103520839 AGCTCCACCA
*
103520849 AGCTGAATAACGGTAAGTTCCTTCG
1 AGCTGAATAACGGTAAGCTCCTTCG
*
103520874 AGCTAAATAACGGTAAGCTCCTTCG
1 AGCTGAATAACGGTAAGCTCCTTCG
*
103520899 ATCTGAATAACGGTAAGCTC
1 AGCTGAATAACGGTAAGCTC
103520919 ATAGCTGAGT
Statistics
Matches: 41, Mismatches: 4, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
25 41 1.00
ACGTcount: A:0.31, C:0.21, G:0.21, T:0.26
Consensus pattern (25 bp):
AGCTGAATAACGGTAAGCTCCTTCG
Found at i:103525387 original size:6 final size:6
Alignment explanation
Indices: 103525339--103525399 Score: 50
Period size: 6 Copynumber: 9.5 Consensus size: 6
103525329 AAAAAGTTTA
* * * *
103525339 AAAACAT AACAAT AAACAT AAAAAT AGAAAT AAAACTAA AAAAAT AAAAAT
1 AAAA-AT AAAAAT AAAAAT AAAAAT AAAAAT AAAA--AT AAAAAT AAAAAT
103525390 AAATAAT AAA
1 AAA-AAT AAA
103525400 TAGACTCAAT
Statistics
Matches: 43, Mismatches: 8, Indels: 6
0.75 0.14 0.11
Matches are distributed among these distances:
6 29 0.67
7 9 0.21
8 5 0.12
ACGTcount: A:0.75, C:0.07, G:0.02, T:0.16
Consensus pattern (6 bp):
AAAAAT
Found at i:103540274 original size:40 final size:40
Alignment explanation
Indices: 103540049--103540246 Score: 276
Period size: 40 Copynumber: 5.0 Consensus size: 40
103540039 TCGAATGATG
* * * *
103540049 TCCGGGCTAAG-TCCCGAAGGC-TTTGTGCTAAGTGACTATA
1 TCCGGACTAAGAT-CCGAAGGCATTTGTGC-GAGTTACTAAA
103540089 TCCGGACTAAGATCCGAAGGCATTTGTGCGAGTTACTAAA
1 TCCGGACTAAGATCCGAAGGCATTTGTGCGAGTTACTAAA
103540129 TCCGGACTAAGATCCGAAGGCATTTGTGCGAGTTACTAAA
1 TCCGGACTAAGATCCGAAGGCATTTGTGCGAGTTACTAAA
103540169 TCCGGACTAAGATCCGAAGGCATTTGTGCGAGTTACTAAA
1 TCCGGACTAAGATCCGAAGGCATTTGTGCGAGTTACTAAA
** * *
103540209 TCCGGGTTAAG-TCCCGAAGGTATTTGTGCGAGCTACTA
1 TCCGGACTAAGAT-CCGAAGGCATTTGTGCGAGTTACTA
103540247 TAACCGGGCT
Statistics
Matches: 147, Mismatches: 8, Indels: 6
0.91 0.05 0.04
Matches are distributed among these distances:
39 1 0.01
40 138 0.94
41 8 0.05
ACGTcount: A:0.27, C:0.21, G:0.26, T:0.26
Consensus pattern (40 bp):
TCCGGACTAAGATCCGAAGGCATTTGTGCGAGTTACTAAA
Found at i:103540288 original size:40 final size:40
Alignment explanation
Indices: 103540083--103540293 Score: 121
Period size: 40 Copynumber: 5.3 Consensus size: 40
103540073 GTGCTAAGTG
* * * ** *
103540083 ACTATATCCGGACTAAGAT-CCGAAGGCATTTGTGCGAGTT
1 ACTATAACCGGGCTAAG-TCCCGAAGGTATTTGAACGAGCT
* * ** *
103540123 ACTA-AATCCGGACTAAGAT-CCGAAGGCATTTGTGCGAGTT
1 ACTATAA-CCGGGCTAAG-TCCCGAAGGTATTTGAACGAGCT
* * ** *
103540163 ACTA-AATCCGGACTAAGAT-CCGAAGGCATTTGTGCGAGTT
1 ACTATAA-CCGGGCTAAG-TCCCGAAGGTATTTGAACGAGCT
* **
103540203 ACTA-AATCCGGGTTAAGTCCCGAAGGTATTTGTGCGAGCT
1 ACTATAA-CCGGGCTAAGTCCCGAAGGTATTTGAACGAGCT
*
103540243 ACTATAACCGGGCTATGTCCCGAAGGTATTTGAACGAG-T
1 ACTATAACCGGGCTAAGTCCCGAAGGTATTTGAACGAGCT
*
103540282 AGCTATATCCGG
1 A-CTATAACCGG
103540294 TTAAACTCCG
Statistics
Matches: 157, Mismatches: 10, Indels: 8
0.90 0.06 0.05
Matches are distributed among these distances:
39 4 0.03
40 151 0.96
41 2 0.01
ACGTcount: A:0.28, C:0.20, G:0.26, T:0.26
Consensus pattern (40 bp):
ACTATAACCGGGCTAAGTCCCGAAGGTATTTGAACGAGCT
Found at i:103540292 original size:80 final size:79
Alignment explanation
Indices: 103540083--103540310 Score: 241
Period size: 80 Copynumber: 2.9 Consensus size: 79
103540073 GTGCTAAGTG
* ** *
103540083 ACTATATCCGGACTAAGATCCGAAGGCATTTGTGCGAGTTACTAAATCCGGACTAAGA-TCCGAA
1 ACTAAATCCGGACTAAGATCCGAAGGCATTTGAACGAGTTACTAAATCCGG-TTAA-ACTCCGAA
* *
103540147 GGCATTTGTGCGAGTT
64 GGTATTTGTGCGAGCT
** *
103540163 ACTAAATCCGGACTAAGATCCGAAGGCATTTGTGCGAGTTACTAAATCCGGGTT-AAGTCCCGAA
1 ACTAAATCCGGACTAAGATCCGAAGGCATTTGAACGAGTTACTAAATCC-GGTTAAACT-CCGAA
103540227 GGTATTTGTGCGAGCT
64 GGTATTTGTGCGAGCT
* * * *
103540243 ACTATAA-CCGGGCTATG-TCCCGAAGGTATTTGAACGAG-TAGCTATATCCGGTTAAACTCCGA
1 ACTA-AATCCGGACTAAGAT-CCGAAGGCATTTGAACGAGTTA-CTAAATCCGGTTAAACTCCGA
103540305 AGGTAT
63 AGGTAT
103540311 GTGATTCGGG
Statistics
Matches: 130, Mismatches: 11, Indels: 15
0.83 0.07 0.10
Matches are distributed among these distances:
78 1 0.01
79 19 0.15
80 106 0.82
81 4 0.03
ACGTcount: A:0.29, C:0.20, G:0.25, T:0.26
Consensus pattern (79 bp):
ACTAAATCCGGACTAAGATCCGAAGGCATTTGAACGAGTTACTAAATCCGGTTAAACTCCGAAGG
TATTTGTGCGAGCT
Found at i:103540293 original size:120 final size:120
Alignment explanation
Indices: 103540049--103540281 Score: 269
Period size: 120 Copynumber: 1.9 Consensus size: 120
103540039 TCGAATGATG
* *
103540049 TCCGGGCTAAGTCCCGAAGGCTTTGTGCTAAGTGACTATATCCGGACTAAGATCCGAAGGCATTT
1 TCCGGACTAAGTCCCGAAGGCTTTGTGCTAAGTGACTAAATCCGGACTAAGATCCGAAGGCATTT
* **
103540114 GTGCGAGTTACTAAATCCGGACTAAGATCCGAAGGCATTTGTGCGAGTTACTAAA
66 GTGCGAGCTACTAAATCCGGACTAAGATCCGAAGGCATTTGAACGAGTTACTAAA
* * ** *
103540169 TCCGGACTAAGAT-CCGAAGGCATTTGTGC-GAGTTACTAAATCCGGGTTAAG-TCCCGAAGGTA
1 TCCGGACTAAG-TCCCGAAGGC-TTTGTGCTAAGTGACTAAATCCGGACTAAGAT-CCGAAGGCA
* * *
103540231 TTTGTGCGAGCTACTATAA-CCGGGCTATG-TCCCGAAGGTATTTGAACGAGT
63 TTTGTGCGAGCTACTA-AATCCGGACTAAGAT-CCGAAGGCATTTGAACGAGT
103540282 AGCTATATCC
Statistics
Matches: 95, Mismatches: 13, Indels: 10
0.81 0.11 0.08
Matches are distributed among these distances:
119 2 0.02
120 83 0.87
121 10 0.11
ACGTcount: A:0.27, C:0.21, G:0.27, T:0.26
Consensus pattern (120 bp):
TCCGGACTAAGTCCCGAAGGCTTTGTGCTAAGTGACTAAATCCGGACTAAGATCCGAAGGCATTT
GTGCGAGCTACTAAATCCGGACTAAGATCCGAAGGCATTTGAACGAGTTACTAAA
Found at i:103548395 original size:39 final size:40
Alignment explanation
Indices: 103548172--103548367 Score: 281
Period size: 40 Copynumber: 4.9 Consensus size: 40
103548162 TCGAATGATG
* * * * *
103548172 TCCGGTCTAAG-TCCCGAAGGC-TTTGTACTAAGTGACTATA
1 TCCGGACTAAGAT-CCGAAGGCATTTGTGC-GAGTTACTAAA
103548212 TCCGGACTAAGATCCGAAGGCATTTGTGCGAGTTACTAAA
1 TCCGGACTAAGATCCGAAGGCATTTGTGCGAGTTACTAAA
103548252 TCCGGACTAAGATCCGAAGGCATTTGTGCGAGTTACTAAA
1 TCCGGACTAAGATCCGAAGGCATTTGTGCGAGTTACTAAA
103548292 TCCGGACTAAGATCCGAAGGCATTTGTGCGAGTTACTAAA
1 TCCGGACTAAGATCCGAAGGCATTTGTGCGAGTTACTAAA
** *
103548332 TCCGGGTTAAG-TCCGAAGGCATTTGTGCGAGCTACT
1 TCCGGACTAAGATCCGAAGGCATTTGTGCGAGTTACT
103548368 TAACCGGGCT
Statistics
Matches: 146, Mismatches: 8, Indels: 5
0.92 0.05 0.03
Matches are distributed among these distances:
39 24 0.16
40 115 0.79
41 7 0.05
ACGTcount: A:0.27, C:0.21, G:0.26, T:0.27
Consensus pattern (40 bp):
TCCGGACTAAGATCCGAAGGCATTTGTGCGAGTTACTAAA
Found at i:103548428 original size:78 final size:79
Alignment explanation
Indices: 103548206--103548428 Score: 238
Period size: 80 Copynumber: 2.8 Consensus size: 79
103548196 GTACTAAGTG
* ** ** *
103548206 ACTATATCCGGACTAAGATCCGAAGGCATTTGTGCGAGTTACTAAATCCGGACTAAGATCCGAAG
1 ACTAAATCCGGACTAAGATCCGAAGGCATTTGAACGAGTTACTAAATCCGGGTTAA-CTCCGAAG
*
103548271 GCATTTGTGCGAGTT
65 GCATTTGTGCGAGCT
** *
103548286 ACTAAATCCGGACTAAGATCCGAAGGCATTTGTGCGAGTTACTAAATCCGGGTTAAGTCCGAAGG
1 ACTAAATCCGGACTAAGATCCGAAGGCATTTGAACGAGTTACTAAATCCGGGTTAACTCCGAAGG
103548351 CATTTGTGCGAGCT
66 CATTTGTGCGAGCT
* * * * * *
103548365 ACTTAA-CCGGGCTATG-TCCCGAAGGTATTTGAACGAG-TAGCTATATCC-GGTTAAACTCTGA
1 ACTAAATCCGGACTAAGAT-CCGAAGGCATTTGAACGAGTTA-CTAAATCCGGGTT-AACTCCGA
103548426 AGG
63 AGG
103548429 TATGTGATTC
Statistics
Matches: 126, Mismatches: 14, Indels: 8
0.85 0.09 0.05
Matches are distributed among these distances:
77 7 0.06
78 40 0.32
79 26 0.21
80 53 0.42
ACGTcount: A:0.28, C:0.20, G:0.26, T:0.26
Consensus pattern (79 bp):
ACTAAATCCGGACTAAGATCCGAAGGCATTTGAACGAGTTACTAAATCCGGGTTAACTCCGAAGG
CATTTGTGCGAGCT
Found at i:103552115 original size:14 final size:15
Alignment explanation
Indices: 103552096--103552125 Score: 53
Period size: 15 Copynumber: 2.1 Consensus size: 15
103552086 TTTACTTTCC
103552096 AGAGA-GTAGAAAAG
1 AGAGAGGTAGAAAAG
103552110 AGAGAGGTAGAAAAG
1 AGAGAGGTAGAAAAG
103552125 A
1 A
103552126 AAATCTGGAA
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
14 5 0.33
15 10 0.67
ACGTcount: A:0.57, C:0.00, G:0.37, T:0.07
Consensus pattern (15 bp):
AGAGAGGTAGAAAAG
Found at i:103560888 original size:204 final size:205
Alignment explanation
Indices: 103560031--103561023 Score: 1708
Period size: 205 Copynumber: 4.9 Consensus size: 205
103560021 GTAATAGGCC
*
103560031 ACACATAGCAGATCTCGCCTTCAGATG-TTTATGCTGAAGC-GATCCAAGATGGTTTGGCATCCT
1 ACACATAGCAGATCTCGCCTTCAGATGATTT-CGCTGAAGCAGATCCAAGATGGTTTGGCATCCT
103560094 TGTGTTTACAAGGAGCAAATCGAAGACATAGCTGATTTGGCTTTCACGTGATTACGATGAAGCAA
65 TGTGTTTACAAGGAGCAAATCGAAGACATAGCTGATTTGGCTTTCACGTGATTACGATGAAGCAA
*
103560159 ATCTAAGATGATTTGTCGTCTCTGTATCGTCAGAGAACGAATCGAAGTTTGGCATCTTCACTTTG
130 ATCTAAGATGATTTGTCGTCTCTGTATTGTCAGAGAACGAATCGAAGTTTGGCATCTTCACTTTG
103560224 ATGGAGAGCAG
195 ATGGAGAGCAG
*
103560235 ACACATAGCAGATCTCACCTTCAGATGATTTCGCTGAAGCAGATCCAAGATGGTTTGGCATCCTT
1 ACACATAGCAGATCTCGCCTTCAGATGATTTCGCTGAAGCAGATCCAAGATGGTTTGGCATCCTT
103560300 GTGTTTACAAGGAGCAAATCGAAGACATAGCTGATTTGGCTTTCACGTGATTACGATGAAGCAAA
66 GTGTTTACAAGGAGCAAATCGAAGACATAGCTGATTTGGCTTTCACGTGATTACGATGAAGCAAA
103560365 TCTAAGATGATTTGTCGTCTCTGTATTGTCAGAGAACGAATCGAAGTTTGGCATCTTCACTTTGA
131 TCTAAGATGATTTGTCGTCTCTGTATTGTCAGAGAACGAATCGAAGTTTGGCATCTTCACTTTGA
103560430 TGGAGAGCAG
196 TGGAGAGCAG
*
103560440 ACACATAGCAGATCTCGCCTTCAGATGATTTCACTGAAGCAGATCCAAGATGGTTTGGCATCCTT
1 ACACATAGCAGATCTCGCCTTCAGATGATTTCGCTGAAGCAGATCCAAGATGGTTTGGCATCCTT
*
103560505 GTGTTTACAAGGAACAAATCGAAGACATAGCTGATTTGGCTTTCACGTGATTACGATGAAGCAAA
66 GTGTTTACAAGGAGCAAATCGAAGACATAGCTGATTTGGCTTTCACGTGATTACGATGAAGCAAA
103560570 TCTAAGATGATTTGTCGTCTCTGTATTGTCAGAGAACGAATCGAAGTTTGGCATCTTCACTTTGA
131 TCTAAGATGATTTGTCGTCTCTGTATTGTCAGAGAACGAATCGAAGTTTGGCATCTTCACTTTGA
103560635 TGGAGAGCAG
196 TGGAGAGCAG
* * *
103560645 ACACATAGCAGATCTCGCCTTCAGACGATTTCACTGAAGCAAATCCAAGATGGTTTGGCATCCTT
1 ACACATAGCAGATCTCGCCTTCAGATGATTTCGCTGAAGCAGATCCAAGATGGTTTGGCATCCTT
* *
103560710 GTGTTTACAAGGAACAAATCGAAGACATAGTTGATTTGGCTTTCACGTGATTACGA-GAAGCAAA
66 GTGTTTACAAGGAGCAAATCGAAGACATAGCTGATTTGGCTTTCACGTGATTACGATGAAGCAAA
*
103560774 TCTAAGATGATTTGTCGTCTCTGTATCGTCAGAGAACGAATCGAAGTTTGGCATCTTCACTTTGA
131 TCTAAGATGATTTGTCGTCTCTGTATTGTCAGAGAACGAATCGAAGTTTGGCATCTTCACTTTGA
103560839 TGGAGAGCAG
196 TGGAGAGCAG
* * *
103560849 ACACATAGCAGATCTCACCTTCGGATG-TTTACGCTGAAGCGGATCCAAGATGGTTTGGCATCCT
1 ACACATAGCAGATCTCGCCTTCAGATGATTT-CGCTGAAGCAGATCCAAGATGGTTTGGCATCCT
* * * * * * *
103560913 TATGCTTACAAGGAGCAAATCGAA-TCATAGTTGATTTGGCTTTCACGTGCTTACGTTAAAGCAA
65 TGTGTTTACAAGGAGCAAATCGAAGACATAGCTGATTTGGCTTTCACGTGATTACGATGAAGCAA
* * * *
103560977 ATCTAAGATGATTTGGCATCTCTGTATTGTCAGGGAACAAATCGAAG
130 ATCTAAGATGATTTGTCGTCTCTGTATTGTCAGAGAACGAATCGAAG
103561024 AAATAGATCT
Statistics
Matches: 757, Mismatches: 28, Indels: 8
0.95 0.04 0.01
Matches are distributed among these distances:
203 32 0.04
204 239 0.32
205 486 0.64
ACGTcount: A:0.29, C:0.19, G:0.23, T:0.29
Consensus pattern (205 bp):
ACACATAGCAGATCTCGCCTTCAGATGATTTCGCTGAAGCAGATCCAAGATGGTTTGGCATCCTT
GTGTTTACAAGGAGCAAATCGAAGACATAGCTGATTTGGCTTTCACGTGATTACGATGAAGCAAA
TCTAAGATGATTTGTCGTCTCTGTATTGTCAGAGAACGAATCGAAGTTTGGCATCTTCACTTTGA
TGGAGAGCAG
Found at i:103561125 original size:44 final size:43
Alignment explanation
Indices: 103561077--103561162 Score: 129
Period size: 44 Copynumber: 2.0 Consensus size: 43
103561067 GATTTCAGCA
*
103561077 TGGCATCCCTGTGTTTATAAGGAACA-AGTTGAAGACAGCAGATT
1 TGGCATCCCTGTGTTTATAAGGAACAGA-TCGAAGA-AGCAGATT
*
103561121 TGGCATCCCTGTGTTTATAGGGAACAGATCGAAGAAGCAGAT
1 TGGCATCCCTGTGTTTATAAGGAACAGATCGAAGAAGCAGAT
103561163 CAAGAACTCA
Statistics
Matches: 39, Mismatches: 2, Indels: 3
0.89 0.05 0.07
Matches are distributed among these distances:
43 7 0.18
44 31 0.79
45 1 0.03
ACGTcount: A:0.31, C:0.16, G:0.27, T:0.26
Consensus pattern (43 bp):
TGGCATCCCTGTGTTTATAAGGAACAGATCGAAGAAGCAGATT
Found at i:103561609 original size:21 final size:23
Alignment explanation
Indices: 103561583--103561630 Score: 64
Period size: 24 Copynumber: 2.1 Consensus size: 23
103561573 TATTTTGGAG
103561583 AGAAGA-A-ATTTTTGAGATTCA
1 AGAAGAGATATTTTTGAGATTCA
*
103561604 AGAAGAGATTTTTTTTGAGATTCA
1 AGAAGAGA-TATTTTTGAGATTCA
103561628 AGA
1 AGA
103561631 GGGGATTTTT
Statistics
Matches: 23, Mismatches: 1, Indels: 3
0.85 0.04 0.11
Matches are distributed among these distances:
21 6 0.26
22 1 0.04
24 16 0.70
ACGTcount: A:0.40, C:0.04, G:0.21, T:0.35
Consensus pattern (23 bp):
AGAAGAGATATTTTTGAGATTCA
Found at i:103561623 original size:24 final size:24
Alignment explanation
Indices: 103561591--103561640 Score: 82
Period size: 24 Copynumber: 2.1 Consensus size: 24
103561581 AGAGAAGAAA
103561591 TTTTTGAGATTCAAGAAGAGATTT
1 TTTTTGAGATTCAAGAAGAGATTT
* *
103561615 TTTTTGAGATTCAAGAGGGGATTT
1 TTTTTGAGATTCAAGAAGAGATTT
103561639 TT
1 TT
103561641 CTTTTTTTTA
Statistics
Matches: 24, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
24 24 1.00
ACGTcount: A:0.28, C:0.04, G:0.24, T:0.44
Consensus pattern (24 bp):
TTTTTGAGATTCAAGAAGAGATTT
Found at i:103561639 original size:21 final size:21
Alignment explanation
Indices: 103561583--103561640 Score: 62
Period size: 24 Copynumber: 2.6 Consensus size: 21
103561573 TATTTTGGAG
*
103561583 AGAAGAAATTTTTGAGATTCA
1 AGAAGAGATTTTTGAGATTCA
103561604 AGAAGAGATTTTTTTTGAGATTCA
1 AGAAGAGA---TTTTTGAGATTCA
* *
103561628 AGAGGGGATTTTT
1 AGAAGAGATTTTT
103561641 CTTTTTTTTA
Statistics
Matches: 31, Mismatches: 3, Indels: 6
0.77 0.08 0.15
Matches are distributed among these distances:
21 12 0.39
24 19 0.61
ACGTcount: A:0.34, C:0.03, G:0.24, T:0.38
Consensus pattern (21 bp):
AGAAGAGATTTTTGAGATTCA
Found at i:103562121 original size:3 final size:3
Alignment explanation
Indices: 103562113--103562149 Score: 67
Period size: 3 Copynumber: 12.7 Consensus size: 3
103562103 TGCATTTTAA
103562113 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TA- TAT TA
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TA
103562150 GTGTATATTT
Statistics
Matches: 33, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
2 2 0.06
3 31 0.94
ACGTcount: A:0.35, C:0.00, G:0.00, T:0.65
Consensus pattern (3 bp):
TAT
Found at i:103562252 original size:3 final size:3
Alignment explanation
Indices: 103562244--103562276 Score: 66
Period size: 3 Copynumber: 11.0 Consensus size: 3
103562234 TGTATTTCTA
103562244 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
103562277 AATATGGTAG
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 30 1.00
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (3 bp):
TAT
Found at i:103562405 original size:16 final size:15
Alignment explanation
Indices: 103562374--103562416 Score: 59
Period size: 16 Copynumber: 2.8 Consensus size: 15
103562364 CCTTCATTCC
*
103562374 ATTATTATTATTACT
1 ATTATTATTTTTACT
103562389 ATTATTATATTTTACT
1 ATTATTAT-TTTTACT
*
103562405 ATCATTATTTTT
1 ATTATTATTTTT
103562417 CATACGTATA
Statistics
Matches: 25, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
15 12 0.48
16 13 0.52
ACGTcount: A:0.30, C:0.07, G:0.00, T:0.63
Consensus pattern (15 bp):
ATTATTATTTTTACT
Found at i:103562540 original size:16 final size:16
Alignment explanation
Indices: 103562519--103562550 Score: 55
Period size: 16 Copynumber: 2.0 Consensus size: 16
103562509 CTATTGTTAC
103562519 TGTTATTATCATCACT
1 TGTTATTATCATCACT
*
103562535 TGTTATTCTCATCACT
1 TGTTATTATCATCACT
103562551 ATTATTATAA
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 15 1.00
ACGTcount: A:0.22, C:0.22, G:0.06, T:0.50
Consensus pattern (16 bp):
TGTTATTATCATCACT
Found at i:103562592 original size:11 final size:13
Alignment explanation
Indices: 103562562--103562593 Score: 50
Period size: 13 Copynumber: 2.6 Consensus size: 13
103562552 TTATTATAAT
103562562 TTATTATTGTTAC
1 TTATTATTGTTAC
103562575 TTATTATT-TTAC
1 TTATTATTGTTAC
103562587 -TATTATT
1 TTATTATT
103562594 ATCTAATATA
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
11 7 0.37
12 4 0.21
13 8 0.42
ACGTcount: A:0.25, C:0.06, G:0.03, T:0.66
Consensus pattern (13 bp):
TTATTATTGTTAC
Found at i:103562698 original size:12 final size:13
Alignment explanation
Indices: 103562663--103562700 Score: 53
Period size: 12 Copynumber: 3.1 Consensus size: 13
103562653 TAGCACTACT
103562663 TTTATTACTATTA
1 TTTATTACTATTA
*
103562676 TTTAATA-TATTA
1 TTTATTACTATTA
103562688 TTT-TTACTATTA
1 TTTATTACTATTA
103562700 T
1 T
103562701 CGTCATATTG
Statistics
Matches: 22, Mismatches: 2, Indels: 3
0.81 0.07 0.11
Matches are distributed among these distances:
11 2 0.09
12 14 0.64
13 6 0.27
ACGTcount: A:0.32, C:0.05, G:0.00, T:0.63
Consensus pattern (13 bp):
TTTATTACTATTA
Found at i:103562769 original size:22 final size:22
Alignment explanation
Indices: 103562732--103562798 Score: 66
Period size: 22 Copynumber: 3.0 Consensus size: 22
103562722 TATTATGTTA
103562732 TTATATCTTTTACTATTATTATTG
1 TTATAT-TTTT-CTATTATTATTG
* * *
103562756 TTGTATTTTTCTATTATTGTTA
1 TTATATTTTTCTATTATTATTG
*
103562778 TTATA-TTTTCT-TTATTTTTG
1 TTATATTTTTCTATTATTATTG
103562798 T
1 T
103562799 ATTTACTTAT
Statistics
Matches: 37, Mismatches: 6, Indels: 4
0.79 0.13 0.09
Matches are distributed among these distances:
20 8 0.22
21 6 0.16
22 14 0.38
23 4 0.11
24 5 0.14
ACGTcount: A:0.19, C:0.06, G:0.06, T:0.69
Consensus pattern (22 bp):
TTATATTTTTCTATTATTATTG
Found at i:103564294 original size:57 final size:57
Alignment explanation
Indices: 103564228--103564337 Score: 202
Period size: 57 Copynumber: 1.9 Consensus size: 57
103564218 AAGAGTAGTT
*
103564228 ATTAAATGTAAAGAATAACCATTAAATTTGACATCAATGAACATGAGTATAAGAGTC
1 ATTAAATGTAAAGAATAACCATTAAATTTGACATCAACGAACATGAGTATAAGAGTC
*
103564285 ATTAAATGTAAAGAGTAACCATTAAATTTGACATCAACGAACATGAGTATAAG
1 ATTAAATGTAAAGAATAACCATTAAATTTGACATCAACGAACATGAGTATAAG
103564338 GGTATATACA
Statistics
Matches: 51, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
57 51 1.00
ACGTcount: A:0.47, C:0.11, G:0.15, T:0.27
Consensus pattern (57 bp):
ATTAAATGTAAAGAATAACCATTAAATTTGACATCAACGAACATGAGTATAAGAGTC
Found at i:103565527 original size:4 final size:4
Alignment explanation
Indices: 103565482--103565507 Score: 52
Period size: 4 Copynumber: 6.5 Consensus size: 4
103565472 ATAAATACTT
103565482 AATA AATA AATA AATA AATA AATA AA
1 AATA AATA AATA AATA AATA AATA AA
103565508 AGCAACTAAA
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 22 1.00
ACGTcount: A:0.77, C:0.00, G:0.00, T:0.23
Consensus pattern (4 bp):
AATA
Found at i:103566023 original size:22 final size:21
Alignment explanation
Indices: 103565998--103566052 Score: 65
Period size: 22 Copynumber: 2.5 Consensus size: 21
103565988 ATTAAAGTTG
* *
103565998 AATATATATATATAATATATAA
1 AATATATATAAATAA-AAATAA
103566020 AATATATATTAAATAAAAATAA
1 AATATATA-TAAATAAAAATAA
*
103566042 AATTTATATAA
1 AATATATATAA
103566053 TTACTAAATA
Statistics
Matches: 29, Mismatches: 3, Indels: 3
0.83 0.09 0.09
Matches are distributed among these distances:
21 3 0.10
22 20 0.69
23 6 0.21
ACGTcount: A:0.62, C:0.00, G:0.00, T:0.38
Consensus pattern (21 bp):
AATATATATAAATAAAAATAA
Found at i:103567084 original size:20 final size:20
Alignment explanation
Indices: 103567055--103567092 Score: 58
Period size: 20 Copynumber: 1.9 Consensus size: 20
103567045 TTAAAAATAT
*
103567055 ATATAGAAATTTATAAAAGA
1 ATATAGAAATATATAAAAGA
*
103567075 ATATATAAATATATAAAA
1 ATATAGAAATATATAAAA
103567093 TTGAGAAACG
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 16 1.00
ACGTcount: A:0.63, C:0.00, G:0.05, T:0.32
Consensus pattern (20 bp):
ATATAGAAATATATAAAAGA
Found at i:103570484 original size:40 final size:40
Alignment explanation
Indices: 103570421--103570534 Score: 151
Period size: 40 Copynumber: 2.9 Consensus size: 40
103570411 ATTTGATGTG
* *
103570421 TATCCGGGCTTAAAGACCTGCAGGCTTCGTGCTGGTAAAA
1 TATCCGGGCTTAAAAACCCGCAGGCTTCGTGCTGGTAAAA
*
103570461 TATCCGGGCTTAAAAACCCGCAGGCTTCATGCTGGTAAAA
1 TATCCGGGCTTAAAAACCCGCAGGCTTCGTGCTGGTAAAA
* * * *
103570501 TATACGGG-TT-AAATCTCGCAGGCTTGGTGCTGGT
1 TATCCGGGCTTAAAAACCCGCAGGCTTCGTGCTGGT
103570535 GATGTATATT
Statistics
Matches: 66, Mismatches: 8, Indels: 2
0.87 0.11 0.03
Matches are distributed among these distances:
38 20 0.30
39 2 0.03
40 44 0.67
ACGTcount: A:0.25, C:0.22, G:0.27, T:0.26
Consensus pattern (40 bp):
TATCCGGGCTTAAAAACCCGCAGGCTTCGTGCTGGTAAAA
Found at i:103570571 original size:16 final size:16
Alignment explanation
Indices: 103570545--103570606 Score: 106
Period size: 16 Copynumber: 3.8 Consensus size: 16
103570535 GATGTATATT
103570545 CAGGCCTTCGTGCCTAG
1 CAGG-CTTCGTGCCTAG
103570562 CAGGCTTCGTGCCTAG
1 CAGGCTTCGTGCCTAG
*
103570578 TAGGCTTCGTGCCTAG
1 CAGGCTTCGTGCCTAG
103570594 CAGGCTTCGTGCC
1 CAGGCTTCGTGCC
103570607 GGTGATGTGT
Statistics
Matches: 43, Mismatches: 2, Indels: 1
0.93 0.04 0.02
Matches are distributed among these distances:
16 39 0.91
17 4 0.09
ACGTcount: A:0.11, C:0.32, G:0.31, T:0.26
Consensus pattern (16 bp):
CAGGCTTCGTGCCTAG
Found at i:103570736 original size:86 final size:86
Alignment explanation
Indices: 103570582--103570740 Score: 273
Period size: 86 Copynumber: 1.8 Consensus size: 86
103570572 GCCTAGTAGG
* * **
103570582 CTTCGTGCCTAGCAGGCTTCGTGCCGGTGATGTGTATTCGGGCCTTCGTGCCTAGTAGGCTTCGT
1 CTTCGTGCCTAGCAGGCTTCGTGCCGGTGATGTGTATTCGGGCCTTCGTGCCTAGCAGGCATAAT
103570647 GCCGGTGATGTGTTTTCGGGC
66 GCCGGTGATGTGTTTTCGGGC
*
103570668 CTTCGTGCCTAGCAGGCTTCGTGCCGGTGATGTGTATTCGGGCCTTCGTGCCTAGCATGCATAAT
1 CTTCGTGCCTAGCAGGCTTCGTGCCGGTGATGTGTATTCGGGCCTTCGTGCCTAGCAGGCATAAT
103570733 GCCGGTGA
66 GCCGGTGA
103570741 AATGATATGT
Statistics
Matches: 68, Mismatches: 5, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
86 68 1.00
ACGTcount: A:0.11, C:0.25, G:0.33, T:0.31
Consensus pattern (86 bp):
CTTCGTGCCTAGCAGGCTTCGTGCCGGTGATGTGTATTCGGGCCTTCGTGCCTAGCAGGCATAAT
GCCGGTGATGTGTTTTCGGGC
Found at i:103570740 original size:43 final size:43
Alignment explanation
Indices: 103570582--103570724 Score: 268
Period size: 43 Copynumber: 3.3 Consensus size: 43
103570572 GCCTAGTAGG
103570582 CTTCGTGCCTAGCAGGCTTCGTGCCGGTGATGTGTATTCGGGC
1 CTTCGTGCCTAGCAGGCTTCGTGCCGGTGATGTGTATTCGGGC
* *
103570625 CTTCGTGCCTAGTAGGCTTCGTGCCGGTGATGTGTTTTCGGGC
1 CTTCGTGCCTAGCAGGCTTCGTGCCGGTGATGTGTATTCGGGC
103570668 CTTCGTGCCTAGCAGGCTTCGTGCCGGTGATGTGTATTCGGGC
1 CTTCGTGCCTAGCAGGCTTCGTGCCGGTGATGTGTATTCGGGC
103570711 CTTCGTGCCTAGCA
1 CTTCGTGCCTAGCA
103570725 TGCATAATGC
Statistics
Matches: 96, Mismatches: 4, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
43 96 1.00
ACGTcount: A:0.09, C:0.26, G:0.34, T:0.31
Consensus pattern (43 bp):
CTTCGTGCCTAGCAGGCTTCGTGCCGGTGATGTGTATTCGGGC
Found at i:103573154 original size:6 final size:6
Alignment explanation
Indices: 103573120--103573152 Score: 59
Period size: 6 Copynumber: 5.7 Consensus size: 6
103573110 ATTTGTGATC
103573120 TTTTCT TTTTCT TTTTCT TTTTCT TTTT-T TTTT
1 TTTTCT TTTTCT TTTTCT TTTTCT TTTTCT TTTT
103573153 TTATGTTATA
Statistics
Matches: 27, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
5 5 0.19
6 22 0.81
ACGTcount: A:0.00, C:0.12, G:0.00, T:0.88
Consensus pattern (6 bp):
TTTTCT
Found at i:103578871 original size:26 final size:26
Alignment explanation
Indices: 103578842--103578951 Score: 184
Period size: 26 Copynumber: 4.2 Consensus size: 26
103578832 TGATACAAAT
*
103578842 TGATAATGGGTTAGGTAAATGTTCCA
1 TGATAATGGGTTAGGTAAATGTTTCA
* *
103578868 TGATAATGGATTAGGTAAATATTTCA
1 TGATAATGGGTTAGGTAAATGTTTCA
103578894 TGATAATGGGTTAGGTAAATGTTTCA
1 TGATAATGGGTTAGGTAAATGTTTCA
*
103578920 TGATAATGGTTTAGGTAAATGTTTCA
1 TGATAATGGGTTAGGTAAATGTTTCA
103578946 TGATAA
1 TGATAA
103578952 GAAATTCATG
Statistics
Matches: 78, Mismatches: 6, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
26 78 1.00
ACGTcount: A:0.34, C:0.05, G:0.24, T:0.38
Consensus pattern (26 bp):
TGATAATGGGTTAGGTAAATGTTTCA
Found at i:103579055 original size:10 final size:10
Alignment explanation
Indices: 103579036--103579065 Score: 51
Period size: 10 Copynumber: 3.0 Consensus size: 10
103579026 AGAACAAAGT
*
103579036 TTTGTCCATC
1 TTTGTTCATC
103579046 TTTGTTCATC
1 TTTGTTCATC
103579056 TTTGTTCATC
1 TTTGTTCATC
103579066 ATAGCTGAAA
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
10 19 1.00
ACGTcount: A:0.10, C:0.23, G:0.10, T:0.57
Consensus pattern (10 bp):
TTTGTTCATC
Found at i:103583352 original size:48 final size:48
Alignment explanation
Indices: 103583269--103583500 Score: 208
Period size: 48 Copynumber: 4.9 Consensus size: 48
103583259 CATTGGTTTG
* * * * * *
103583269 ATGAGATCCCGTATAAGACCTTATCTAGGATATGGCATCGGCATCGAT
1 ATGAGATCCCATGTAAGACCATGTCTAGGACATGGCATTGGCATCGAT
* * * *
103583317 GTGAGATCCCATGTAAGACCATGTCTGGGACATGGCTTTGGCATCGTT
1 ATGAGATCCCATGTAAGACCATGTCTAGGACATGGCATTGGCATCGAT
*
103583365 ATGTGATCCCATGTAAGACCATGTCTAGGACATGGCATTGGCATCGAT
1 ATGAGATCCCATGTAAGACCATGTCTAGGACATGGCATTGGCATCGAT
* * * *
103583413 ATGAGA-CATCGTGTAAGACCATAG-CT-GGGCTATCGGC-TTCG-AT--AT
1 ATGAGATC-CCATGTAAGACCAT-GTCTAGGAC-AT-GGCATTGGCATCGAT
* * * *
103583458 ATGTGATCCCATGTAAGACCATATCTCGGATATGGCATTGGCA
1 ATGAGATCCCATGTAAGACCATGTCTAGGACATGGCATTGGCA
103583501 CCTTACCATG
Statistics
Matches: 148, Mismatches: 27, Indels: 20
0.76 0.14 0.10
Matches are distributed among these distances:
44 3 0.02
45 26 0.18
46 4 0.03
47 6 0.04
48 105 0.71
49 4 0.03
ACGTcount: A:0.26, C:0.21, G:0.25, T:0.28
Consensus pattern (48 bp):
ATGAGATCCCATGTAAGACCATGTCTAGGACATGGCATTGGCATCGAT
Found at i:103583498 original size:93 final size:95
Alignment explanation
Indices: 103583273--103583500 Score: 261
Period size: 96 Copynumber: 2.4 Consensus size: 95
103583263 GGTTTGATGA
* * * * *
103583273 GATCCCGTATAAGACCTTATCTAGGATATGGCATCGGCATCGATGTGAGATCCCATGTAAGACCA
1 GATCCCATGTAAGACCATATCTAGGATATGGCATTGGCATCGATATGAGATCCCATGTAAGACCA
* *
103583338 TGTCTGGGACATGGCTTTGGCATCGTTATGT
66 TGTCTGGGACATGGCTTTCGCATC-ATATGT
* * * *
103583369 GATCCCATGTAAGACCATGTCTAGGACATGGCATTGGCATCGATATGAGA-CATCGTGTAAGACC
1 GATCCCATGTAAGACCATATCTAGGATATGGCATTGGCATCGATATGAGATC-CCATGTAAGACC
103583433 ATAG-CTGGG-CTATCGGC-TTCG-AT-ATATGT
65 AT-GTCTGGGAC-AT-GGCTTTCGCATCATATGT
*
103583462 GATCCCATGTAAGACCATATCTCGGATATGGCATTGGCA
1 GATCCCATGTAAGACCATATCTAGGATATGGCATTGGCA
103583501 CCTTACCATG
Statistics
Matches: 114, Mismatches: 14, Indels: 11
0.82 0.10 0.08
Matches are distributed among these distances:
93 41 0.36
95 4 0.04
96 65 0.57
97 4 0.04
ACGTcount: A:0.26, C:0.21, G:0.25, T:0.28
Consensus pattern (95 bp):
GATCCCATGTAAGACCATATCTAGGATATGGCATTGGCATCGATATGAGATCCCATGTAAGACCA
TGTCTGGGACATGGCTTTCGCATCATATGT
Found at i:103586472 original size:20 final size:21
Alignment explanation
Indices: 103586447--103586486 Score: 64
Period size: 21 Copynumber: 2.0 Consensus size: 21
103586437 CTCTTGTAAC
*
103586447 AGGGC-ACACGCTCGTGTGGA
1 AGGGCAACACGCCCGTGTGGA
103586467 AGGGCAACACGCCCGTGTGG
1 AGGGCAACACGCCCGTGTGG
103586487 TCATTATAAC
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
20 5 0.28
21 13 0.72
ACGTcount: A:0.20, C:0.28, G:0.40, T:0.12
Consensus pattern (21 bp):
AGGGCAACACGCCCGTGTGGA
Found at i:103587810 original size:48 final size:47
Alignment explanation
Indices: 103587739--103587951 Score: 198
Period size: 46 Copynumber: 4.5 Consensus size: 47
103587729 AAGCTAACGC
* * * *
103587739 CATGTCCCAGATAGGCCTTACACTAGCTTGTATATCGCGAGGCCGATG
1 CATGTCCCAGACATGTCTTACACTAGCTT-TATATCTCGAGGCCGATG
** * *
103587787 CATGTCCCAGACATGTCTTACACTAGCTTT-CGTCTCAATGCCGATG
1 CATGTCCCAGACATGTCTTACACTAGCTTTATATCTCGAGGCCGATG
* * * **
103587833 CATGTCCCAGACATGTCTCACACTGGCTTAAATATCTCGAGGCTAATG
1 CATGTCCCAGACATGTCTTACACTAGCTT-TATATCTCGAGGCCGATG
* * ***
103587881 CATGTCCCAGACATGTCTTACACTGGCTCTTATA-CT-GTGATTGATG
1 CATGTCCCAGACATGTCTTACACTAGCT-TTATATCTCGAGGCCGATG
* *
103587927 CATGTCCCAGATATTTCTTACACTA
1 CATGTCCCAGACATGTCTTACACTA
103587952 TCACACATAT
Statistics
Matches: 136, Mismatches: 26, Indels: 8
0.80 0.15 0.05
Matches are distributed among these distances:
46 66 0.49
47 3 0.02
48 66 0.49
49 1 0.01
ACGTcount: A:0.24, C:0.27, G:0.19, T:0.30
Consensus pattern (47 bp):
CATGTCCCAGACATGTCTTACACTAGCTTTATATCTCGAGGCCGATG
Found at i:103587845 original size:46 final size:46
Alignment explanation
Indices: 103587739--103587904 Score: 172
Period size: 48 Copynumber: 3.5 Consensus size: 46
103587729 AAGCTAACGC
* * * * *
103587739 CATGTCCCAGATAGGCCTTACACTAGCTTGTATATCGCGAGGCCGATG
1 CATGTCCCAGACATGTCTTACACTAGC-T-TATATCTCAAGGCCGATG
* *
103587787 CATGTCCCAGACATGTCTTACACTAGCTT-TCGTCTCAATGCCGATG
1 CATGTCCCAGACATGTCTTACACTAGCTTAT-ATCTCAAGGCCGATG
* * * **
103587833 CATGTCCCAGACATGTCTCACACTGGCTTAAATATCTCGAGGCTAATG
1 CATGTCCCAGACATGTCTTACACTAGCTT--ATATCTCAAGGCCGATG
103587881 CATGTCCCAGACATGTCTTACACT
1 CATGTCCCAGACATGTCTTACACT
103587905 GGCTCTTATA
Statistics
Matches: 99, Mismatches: 15, Indels: 8
0.81 0.12 0.07
Matches are distributed among these distances:
45 1 0.01
46 39 0.39
47 1 0.01
48 57 0.58
49 1 0.01
ACGTcount: A:0.24, C:0.29, G:0.19, T:0.28
Consensus pattern (46 bp):
CATGTCCCAGACATGTCTTACACTAGCTTATATCTCAAGGCCGATG
Found at i:103587950 original size:94 final size:93
Alignment explanation
Indices: 103587739--103587951 Score: 232
Period size: 94 Copynumber: 2.3 Consensus size: 93
103587729 AAGCTAACGC
* * ** *
103587739 CATGTCCCAGATAGGCCTTACACTAGCTTGTATATCGCGAGGCCGATGCATGTCCCAGACATGTC
1 CATGTCCCAGATATGTCTTACACTAGCTTAAATATCGCGAGGCCAATGCATGTCCCAGACATGTC
*
103587804 TTACACTAGCTTTCGTCTCAATGCCGATG
66 TTACACTAGCTTTCATCT-AATGCCGATG
* * * * *
103587833 CATGTCCCAGACATGTCTCACACTGGCTTAAATATCTCGAGGCTAATGCATGTCCCAGACATGTC
1 CATGTCCCAGATATGTCTTACACTAGCTTAAATATCGCGAGGCCAATGCATGTCCCAGACATGTC
* * **
103587898 TTACACTGGCTCTT-ATACT-GTGATTGATG
66 TTACACTAGCT-TTCAT-CTAATG-CCGATG
*
103587927 CATGTCCCAGATATTTCTTACACTA
1 CATGTCCCAGATATGTCTTACACTA
103587952 TCACACATAT
Statistics
Matches: 97, Mismatches: 19, Indels: 6
0.80 0.16 0.05
Matches are distributed among these distances:
93 2 0.02
94 91 0.94
95 4 0.04
ACGTcount: A:0.24, C:0.27, G:0.19, T:0.30
Consensus pattern (93 bp):
CATGTCCCAGATATGTCTTACACTAGCTTAAATATCGCGAGGCCAATGCATGTCCCAGACATGTC
TTACACTAGCTTTCATCTAATGCCGATG
Found at i:103592867 original size:96 final size:96
Alignment explanation
Indices: 103592700--103592891 Score: 366
Period size: 96 Copynumber: 2.0 Consensus size: 96
103592690 AGGTCAAAGC
*
103592700 TGTCAAATAGCAGAACATGGAAAAATTTGAAGATTTACTATACTTATTGGCTAAACTATAAATTC
1 TGTCAAACAGCAGAACATGGAAAAATTTGAAGATTTACTATACTTATTGGCTAAACTATAAATTC
103592765 TAAAAATTTTATGGTAGAAATATATGTGAGT
66 TAAAAATTTTATGGTAGAAATATATGTGAGT
103592796 TGTCAAACAGCAGAACATGGAAAAATTTGAAGATTTACTATACTTATTGGCTAAACTATAAATTC
1 TGTCAAACAGCAGAACATGGAAAAATTTGAAGATTTACTATACTTATTGGCTAAACTATAAATTC
*
103592861 TGAAAATTTTATGGTAGAAATATATGTGAGT
66 TAAAAATTTTATGGTAGAAATATATGTGAGT
103592892 CTAGTTTCTA
Statistics
Matches: 94, Mismatches: 2, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
96 94 1.00
ACGTcount: A:0.41, C:0.09, G:0.16, T:0.34
Consensus pattern (96 bp):
TGTCAAACAGCAGAACATGGAAAAATTTGAAGATTTACTATACTTATTGGCTAAACTATAAATTC
TAAAAATTTTATGGTAGAAATATATGTGAGT
Found at i:103593047 original size:2 final size:2
Alignment explanation
Indices: 103593042--103593099 Score: 107
Period size: 2 Copynumber: 29.0 Consensus size: 2
103593032 GGAAGAAAAA
*
103593042 AT AT AT AT AT AT AT AT TT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
103593084 AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT
103593100 GAATATTCAT
Statistics
Matches: 54, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
2 54 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
AT
Found at i:103593909 original size:64 final size:64
Alignment explanation
Indices: 103593784--103593911 Score: 211
Period size: 64 Copynumber: 2.0 Consensus size: 64
103593774 TAGAGCATAT
* * *
103593784 GTTACAGACAGGATTTAGCCTGGACTAGTAATCCTGCTGTATGATATGTGGCTCGAGAATGTGC
1 GTTACAGACAGGATTTAGCCTGGACTAGTAATCCTGCAGTATGATATGTGGCTCAAAAATGTGC
* *
103593848 GTTACAGACAGGATTTAGCCTGGACTGGTAATCCTGCAGTATGATATGTGGCTTAAAAATGTGC
1 GTTACAGACAGGATTTAGCCTGGACTAGTAATCCTGCAGTATGATATGTGGCTCAAAAATGTGC
103593912 TCTCAGAATA
Statistics
Matches: 59, Mismatches: 5, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
64 59 1.00
ACGTcount: A:0.27, C:0.16, G:0.27, T:0.30
Consensus pattern (64 bp):
GTTACAGACAGGATTTAGCCTGGACTAGTAATCCTGCAGTATGATATGTGGCTCAAAAATGTGC
Found at i:103594864 original size:16 final size:16
Alignment explanation
Indices: 103594843--103594879 Score: 56
Period size: 16 Copynumber: 2.3 Consensus size: 16
103594833 AATCCCTAAC
* *
103594843 AATCTTCAAGTCCCTA
1 AATCTTCAAATACCTA
103594859 AATCTTCAAATACCTA
1 AATCTTCAAATACCTA
103594875 AATCT
1 AATCT
103594880 ATAGCATTCC
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
16 19 1.00
ACGTcount: A:0.38, C:0.27, G:0.03, T:0.32
Consensus pattern (16 bp):
AATCTTCAAATACCTA
Found at i:103596186 original size:39 final size:39
Alignment explanation
Indices: 103596100--103596277 Score: 143
Period size: 39 Copynumber: 4.6 Consensus size: 39
103596090 ACTTGAAACC
* *
103596100 AATTACCAGCAC-AAGCCTGCGGGAATTTAAACCCGG-TAT
1 AATT-CCAGCACGAAGCCTGCGGGACTTT-AGCCCGGATAT
* * *
103596139 AATACCAGCTCGAAGCCTGCGGGACTTTAGCCCGGACAT
1 AATTCCAGCACGAAGCCTGCGGGACTTTAGCCCGGATAT
* * * * *
103596178 ATTTCCAGCACGTAGCCGGC-GGACCTTAAGTCCGGATAT
1 AATTCCAGCACGAAGCCTGCGGGA-CTTTAGCCCGGATAT
* * *
103596217 AATTCCAGCAC-ATAGCCTGC-GGACCCTAAGTCCGGATAT
1 AATTCCAGCACGA-AGCCTGCGGGA-CTTTAGCCCGGATAT
103596256 AATTCCAGCAC-ATAGCCTGCGG
1 AATTCCAGCACGA-AGCCTGCGG
103596278 ACCCTAAGTC
Statistics
Matches: 117, Mismatches: 17, Indels: 9
0.82 0.12 0.06
Matches are distributed among these distances:
38 15 0.13
39 101 0.86
40 1 0.01
ACGTcount: A:0.28, C:0.29, G:0.23, T:0.20
Consensus pattern (39 bp):
AATTCCAGCACGAAGCCTGCGGGACTTTAGCCCGGATAT
Found at i:103596278 original size:39 final size:39
Alignment explanation
Indices: 103596170--103596295 Score: 207
Period size: 39 Copynumber: 3.2 Consensus size: 39
103596160 GGACTTTAGC
* * * * *
103596170 CCGGACATATTTCCAGCACGTAGCCGGCGGACCTTAAGT
1 CCGGATATAATTCCAGCACATAGCCTGCGGACCCTAAGT
103596209 CCGGATATAATTCCAGCACATAGCCTGCGGACCCTAAGT
1 CCGGATATAATTCCAGCACATAGCCTGCGGACCCTAAGT
103596248 CCGGATATAATTCCAGCACATAGCCTGCGGACCCTAAGT
1 CCGGATATAATTCCAGCACATAGCCTGCGGACCCTAAGT
103596287 CCGGATATA
1 CCGGATATA
103596296 CATCACTGAA
Statistics
Matches: 82, Mismatches: 5, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
39 82 1.00
ACGTcount: A:0.27, C:0.30, G:0.22, T:0.21
Consensus pattern (39 bp):
CCGGATATAATTCCAGCACATAGCCTGCGGACCCTAAGT
Found at i:103599078 original size:22 final size:22
Alignment explanation
Indices: 103599048--103599092 Score: 72
Period size: 22 Copynumber: 2.0 Consensus size: 22
103599038 TAAGCATATG
*
103599048 ATTTGGATAAATGTACTTTACA
1 ATTTCGATAAATGTACTTTACA
*
103599070 ATTTCGATAAGTGTACTTTACA
1 ATTTCGATAAATGTACTTTACA
103599092 A
1 A
103599093 AAGCATATGA
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
22 21 1.00
ACGTcount: A:0.36, C:0.11, G:0.13, T:0.40
Consensus pattern (22 bp):
ATTTCGATAAATGTACTTTACA
Found at i:103601877 original size:51 final size:52
Alignment explanation
Indices: 103601817--103601969 Score: 206
Period size: 51 Copynumber: 3.0 Consensus size: 52
103601807 CTACGTGTAG
* *
103601817 CAGCAACATTATCTAGTCCATTTGATGTTGCAAAGTCA-TAAGCATATTCAT
1 CAGCAACATTATCTACTCCATTTGATGTTGCAAAATCACTAAGCATATTCAT
* * *
103601868 CAGCAACATTAT-TCACTCTATCTGATGTTGCAAAATCACCAA-CATATTCAT
1 CAGCAACATTATCT-ACTCCATTTGATGTTGCAAAATCACTAAGCATATTCAT
* *
103601919 CAGCAACATTATCCACTCCATTTGATGTTTCAAAATCACT-AGCATATTCAT
1 CAGCAACATTATCTACTCCATTTGATGTTGCAAAATCACTAAGCATATTCAT
103601970 TACCAGAAAC
Statistics
Matches: 88, Mismatches: 10, Indels: 8
0.83 0.09 0.08
Matches are distributed among these distances:
50 2 0.02
51 84 0.95
52 2 0.02
ACGTcount: A:0.34, C:0.24, G:0.10, T:0.33
Consensus pattern (52 bp):
CAGCAACATTATCTACTCCATTTGATGTTGCAAAATCACTAAGCATATTCAT
Done.