Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: D12
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: 63843421
ACGTcount: A:0.32, C:0.16, G:0.16, T:0.32
Warning! 1690000 characters in sequence are not A, C, G, or T
File 71 of 214
Found at i:20293462 original size:2 final size:2
Alignment explanation
Indices: 20293457--20293481 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
20293447 AAAGTAAAAT
20293457 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
20293482 GAGAAAGCAT
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:20301312 original size:332 final size:334
Alignment explanation
Indices: 20300702--20301351 Score: 1043
Period size: 332 Copynumber: 1.9 Consensus size: 334
20300692 GTAGGCCCAA
*
20300702 ATTTTAGAATTTTTCCCTAAGGTCGTACATGTTGTCCCGATCGACTGTGGGCCTTCCGTGAGGTC
1 ATTTTAGAATTTTTCCCTAAGGTCGTACATGTTGTCCAGATCGACTGTGGGCCTTCCGTGAGGTC
* *
20300767 GGTATGTGTTATATAAGCTTTAAAGTATGAAGTCTACTGATCTATTTGTATGAATTGGACATAAA
66 GGTATGTGTTATATAAGCTTTAAAGTATGAACTCTACTGATCTATTTGTACGAATTGGACATAAA
* *
20300832 TAATGCCTAAATGCATGTAATGTGATGTGATAGGTTTGATCTGTTATGTATAAGCATGTTCAATA
131 TAATGCCTAAATGCATCTAATGTGATGCGATAGGTTTGATCTGTTATGTATAAGCATGTTCAATA
* * *
20300897 TCTGTTATACGAGCATGCATGATATATATATTCTGGAATCTGTTATTCTATTATATCTGGTATTC
196 TCTATTATACGAGCATGCATGATATATATATTCTGGAATCTATTATTCTATTATATCTGCTATTC
* *
20300962 TGTTTGTATCTGGCTAT-GGTATGTATTATGTGGAGGAAGTGTTCTGTGTGAGGCGTTAACTAGC
261 TGTTTGTATCTAGCTATGGGTATGTATTATGTGGAGGAAATGTTCTGTGTGAGGCGTTAACTAGC
20301026 AATTTTACT
326 AATTTTACT
* * * *
20301035 ATTTTAGAATTTTTCCCTACGGTTGTACATGTTGTCCAGTTCGACTGTGGGCCTTCCG-GTGGTC
1 ATTTTAGAATTTTTCCCTAAGGTCGTACATGTTGTCCAGATCGACTGTGGGCCTTCCGTGAGGTC
* * *
20301099 GGTATGTGTTATATAAGCTTTAAAGTATGAACTCTGCTGATCTGTTTGTACGAATTGGACGTAAA
66 GGTATGTGTTATATAAGCTTTAAAGTATGAACTCTACTGATCTATTTGTACGAATTGGACATAAA
*
20301164 TAATGCCTAAATGCATCTAATGTGATGCGATATGTTTGATCTGTTATGTATAAGCATGTTCAATA
131 TAATGCCTAAATGCATCTAATGTGATGCGATAGGTTTGATCTGTTATGTATAAGCATGTTCAATA
* * *
20301229 TCTATTATACGAGCATGCATGATATATATATTCTGGTATCTATTATTTTGTTATATCTGCTATTC
196 TCTATTATACGAGCATGCATGATATATATATTCTGGAATCTATTATTCTATTATATCTGCTATTC
20301294 TGTTTGTATCTAGCTATGGGGCAGGGTATGTATTATGTGGAGGAAATGTTCTGTGTGA
261 TGTTTGTATCTAGCTAT------GGGTATGTATTATGTGGAGGAAATGTTCTGTGTGA
20301352 CGTTTGGTAA
Statistics
Matches: 289, Mismatches: 21, Indels: 8
0.91 0.07 0.03
Matches are distributed among these distances:
332 202 0.70
333 54 0.19
339 33 0.11
ACGTcount: A:0.25, C:0.13, G:0.22, T:0.40
Consensus pattern (334 bp):
ATTTTAGAATTTTTCCCTAAGGTCGTACATGTTGTCCAGATCGACTGTGGGCCTTCCGTGAGGTC
GGTATGTGTTATATAAGCTTTAAAGTATGAACTCTACTGATCTATTTGTACGAATTGGACATAAA
TAATGCCTAAATGCATCTAATGTGATGCGATAGGTTTGATCTGTTATGTATAAGCATGTTCAATA
TCTATTATACGAGCATGCATGATATATATATTCTGGAATCTATTATTCTATTATATCTGCTATTC
TGTTTGTATCTAGCTATGGGTATGTATTATGTGGAGGAAATGTTCTGTGTGAGGCGTTAACTAGC
AATTTTACT
Found at i:20303109 original size:18 final size:18
Alignment explanation
Indices: 20303082--20303119 Score: 58
Period size: 18 Copynumber: 2.1 Consensus size: 18
20303072 TATAAGAGAA
20303082 TTCACATTTCAAGGACTC
1 TTCACATTTCAAGGACTC
* *
20303100 TTCACTTTTCAAGGGCTC
1 TTCACATTTCAAGGACTC
20303118 TT
1 TT
20303120 AAAGCCTTTT
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
18 18 1.00
ACGTcount: A:0.21, C:0.26, G:0.13, T:0.39
Consensus pattern (18 bp):
TTCACATTTCAAGGACTC
Found at i:20304151 original size:3 final size:3
Alignment explanation
Indices: 20304143--20304241 Score: 198
Period size: 3 Copynumber: 33.0 Consensus size: 3
20304133 AAAAATCTCT
20304143 TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC
1 TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC
20304191 TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC
1 TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC
20304239 TTC
1 TTC
20304242 CATTTAAAAT
Statistics
Matches: 96, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 96 1.00
ACGTcount: A:0.00, C:0.33, G:0.00, T:0.67
Consensus pattern (3 bp):
TTC
Found at i:20305757 original size:17 final size:17
Alignment explanation
Indices: 20305737--20305795 Score: 57
Period size: 17 Copynumber: 3.4 Consensus size: 17
20305727 TCAATATGAT
20305737 TAAATAATTCAATAATA
1 TAAATAATTCAATAATA
* *
20305754 TAAATAGTACAA-AATA
1 TAAATAATTCAATAATA
*
20305770 TGAAATTTAATTTAATAATA
1 T-AAA--TAATTCAATAATA
20305790 TAAATA
1 TAAATA
20305796 GTAGAATATA
Statistics
Matches: 33, Mismatches: 5, Indels: 8
0.72 0.11 0.17
Matches are distributed among these distances:
16 5 0.15
17 15 0.45
19 8 0.24
20 5 0.15
ACGTcount: A:0.58, C:0.03, G:0.03, T:0.36
Consensus pattern (17 bp):
TAAATAATTCAATAATA
Found at i:20318790 original size:19 final size:17
Alignment explanation
Indices: 20318735--20318819 Score: 64
Period size: 18 Copynumber: 4.6 Consensus size: 17
20318725 ATAATTATTT
20318735 TAAATTATAT-TTTATAG
1 TAAATTATATATTT-TAG
*
20318752 TATTATATATTATGATTTTAG
1 TA-AAT-TA-TAT-ATTTTAG
*
20318773 TAAATTTCATATATTTTAT
1 TAAA-TT-ATATATTTTAG
*
20318792 TAAATTATATATTTTTAT
1 TAAATTATATA-TTTTAG
20318810 TAAATTATAT
1 TAAATTATAT
20318820 TTAATAATAA
Statistics
Matches: 57, Mismatches: 3, Indels: 15
0.76 0.04 0.20
Matches are distributed among these distances:
17 7 0.12
18 20 0.35
19 12 0.21
20 8 0.14
21 7 0.12
22 3 0.05
ACGTcount: A:0.39, C:0.01, G:0.04, T:0.56
Consensus pattern (17 bp):
TAAATTATATATTTTAG
Found at i:20319057 original size:46 final size:44
Alignment explanation
Indices: 20318971--20319064 Score: 120
Period size: 46 Copynumber: 2.1 Consensus size: 44
20318961 ATTACAATAT
*
20318971 CATTCCATTCAACCAAATATAAAAATACTATTACAGTTCTATTC
1 CATTCCATTCAACCAAACATAAAAATACTATTACAGTTCTATTC
*
20319015 CATTTCATTCAACCAAACA-AAAAGATTACCTATTAC-GCTTCTATTC
1 CATTCCATTCAACCAAACATAAAA-A-TA-CTATTACAG-TTCTATTC
20319061 CATT
1 CATT
20319065 AAGCCTCTAT
Statistics
Matches: 44, Mismatches: 2, Indels: 6
0.85 0.04 0.12
Matches are distributed among these distances:
43 4 0.09
44 18 0.41
45 3 0.07
46 19 0.43
ACGTcount: A:0.38, C:0.24, G:0.03, T:0.34
Consensus pattern (44 bp):
CATTCCATTCAACCAAACATAAAAATACTATTACAGTTCTATTC
Found at i:20334738 original size:16 final size:16
Alignment explanation
Indices: 20334705--20334738 Score: 50
Period size: 16 Copynumber: 2.1 Consensus size: 16
20334695 TTTTAATTTC
*
20334705 TATTTATCTACTTATT
1 TATTTATCTAATTATT
*
20334721 TATTTATCTAATTTTT
1 TATTTATCTAATTATT
20334737 TA
1 TA
20334739 AAATTATTTA
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:0.26, C:0.09, G:0.00, T:0.65
Consensus pattern (16 bp):
TATTTATCTAATTATT
Found at i:20336161 original size:21 final size:22
Alignment explanation
Indices: 20336105--20336214 Score: 89
Period size: 22 Copynumber: 5.0 Consensus size: 22
20336095 TGAGTATACT
20336105 CAAATTAATCCCTCAAGGGATA
1 CAAATTAATCCCTCAAGGGATA
* * * *
20336127 TAACTCAATCCC-CTAGGGGATA
1 CAAATTAATCCCTC-AAGGGATA
* *
20336149 CAAATTAATCCCTCATGGTATA
1 CAAATTAATCCCTCAAGGGATA
* * * *
20336171 TAACA-CAATCCCTCAAAGCATA
1 CAA-ATTAATCCCTCAAGGGATA
*
20336193 CGAATTAATCCCTCAAGGGATA
1 CAAATTAATCCCTCAAGGGATA
20336215 TAAAAAATCT
Statistics
Matches: 65, Mismatches: 19, Indels: 8
0.71 0.21 0.09
Matches are distributed among these distances:
21 2 0.03
22 61 0.94
23 2 0.03
ACGTcount: A:0.38, C:0.25, G:0.13, T:0.24
Consensus pattern (22 bp):
CAAATTAATCCCTCAAGGGATA
Found at i:20336172 original size:44 final size:44
Alignment explanation
Indices: 20336105--20336217 Score: 147
Period size: 44 Copynumber: 2.6 Consensus size: 44
20336095 TGAGTATACT
* ** *
20336105 CAAATTAATCCCTCAAGGGATATAACTCAATCCC-CTAGGGGATA
1 CAAATTAATCCCTCAAGGGATATAACACAATCCCTC-AAAGCATA
* *
20336149 CAAATTAATCCCTCATGGTATATAACACAATCCCTCAAAGCATA
1 CAAATTAATCCCTCAAGGGATATAACACAATCCCTCAAAGCATA
*
20336193 CGAATTAATCCCTCAAGGGATATAA
1 CAAATTAATCCCTCAAGGGATATAA
20336218 AAAATCTGCA
Statistics
Matches: 59, Mismatches: 9, Indels: 2
0.84 0.13 0.03
Matches are distributed among these distances:
44 58 0.98
45 1 0.02
ACGTcount: A:0.39, C:0.25, G:0.12, T:0.24
Consensus pattern (44 bp):
CAAATTAATCCCTCAAGGGATATAACACAATCCCTCAAAGCATA
Found at i:20344163 original size:29 final size:29
Alignment explanation
Indices: 20344119--20344330 Score: 177
Period size: 29 Copynumber: 7.3 Consensus size: 29
20344109 ACCTCAGATA
*
20344119 ATGAAAAGGGATAGCTTCTACTATCGAAT
1 ATGAAAAGGGATAGCTTCGACTATCGAAT
*
20344148 ACGAAAAGGGATAGCTTCTG-CTATCGAAT
1 ATGAAAAGGGATAGCTTC-GACTATCGAAT
* * *
20344177 GTGAAAAGTGATAACTTC-AGCTATC-AATT
1 ATGAAAAGGGATAGCTTCGA-CTATCGAA-T
* * * *
20344206 ATGAGAAGGGAT-GGTGACGACCATC-AATT
1 ATGAAAAGGGATAGCT-TCGACTATCGAA-T
* *
20344235 ATGAAAAGGGAT-GGTGAT-GACCATCGAAT
1 ATGAAAAGGGATAGCT--TCGACTATCGAAT
*
20344264 ATGAAAAGGGATAGCTTCGGCTATCGAAT
1 ATGAAAAGGGATAGCTTCGACTATCGAAT
* * *
20344293 GTGAAAAGGGATAACTTCGACTATCGATT
1 ATGAAAAGGGATAGCTTCGACTATCGAAT
20344322 ATGAAAAGG
1 ATGAAAAGG
20344331 CATGGTGATA
Statistics
Matches: 149, Mismatches: 24, Indels: 20
0.77 0.12 0.10
Matches are distributed among these distances:
28 4 0.03
29 140 0.94
30 5 0.03
ACGTcount: A:0.37, C:0.13, G:0.25, T:0.25
Consensus pattern (29 bp):
ATGAAAAGGGATAGCTTCGACTATCGAAT
Found at i:20344287 original size:87 final size:87
Alignment explanation
Indices: 20344170--20344362 Score: 212
Period size: 87 Copynumber: 2.2 Consensus size: 87
20344160 AGCTTCTGCT
* * * **
20344170 ATCGAATGTGAAAAGTGATAACTTCAGCTATC-AATTATGAGAAGGGAT-GGTGACGACCATCAA
1 ATCGAATATGAAAAGGGATAACTTCAGCTATCGAA-TATGAAAAGGGATAACT-ACGACCATCAA
* *
20344233 TTATGAAAAGGGATGGTGATGACC
64 TTATGAAAAGGCATGGTGATAACC
* * * * * *
20344257 ATCGAATATGAAAAGGGATAGCTTCGGCTATCGAATGTGAAAAGGGATAACTTCGACTATCGATT
1 ATCGAATATGAAAAGGGATAACTTCAGCTATCGAATATGAAAAGGGATAACTACGACCATCAATT
20344322 ATGAAAAGGCATGGTGATAACC
66 ATGAAAAGGCATGGTGATAACC
*
20344344 ATC-AGCTATGAAAAGGGAT
1 ATCGA-ATATGAAAAGGGAT
20344363 GGTGACGACC
Statistics
Matches: 89, Mismatches: 14, Indels: 6
0.82 0.13 0.06
Matches are distributed among these distances:
86 1 0.01
87 85 0.96
88 3 0.03
ACGTcount: A:0.37, C:0.13, G:0.26, T:0.24
Consensus pattern (87 bp):
ATCGAATATGAAAAGGGATAACTTCAGCTATCGAATATGAAAAGGGATAACTACGACCATCAATT
ATGAAAAGGCATGGTGATAACC
Found at i:20344323 original size:116 final size:116
Alignment explanation
Indices: 20344141--20344419 Score: 371
Period size: 116 Copynumber: 2.4 Consensus size: 116
20344131 AGCTTCTACT
* * *
20344141 ATCGAATACGAAAAGGGATAGCTTCTGCTATCGAATGTGAAAAGTGATAACTTCAGCTATCAATT
1 ATCGAATATGAAAAGGGATAGCTTCAGCTATCGAATGTGAAAAGGGATAACTTCAGCTATCAATT
* * * * *
20344206 ATGAGAAGGGATGGTGACGACCATCAATTATGAAAAGGGATGGTGATGACC
66 ATGAAAAGGCATGGTGACAACCATCAACTATGAAAAGGGATGGTGACGACC
* *
20344257 ATCGAATATGAAAAGGGATAGCTTCGGCTATCGAATGTGAAAAGGGATAACTTC-GACTATCGAT
1 ATCGAATATGAAAAGGGATAGCTTCAGCTATCGAATGTGAAAAGGGATAACTTCAG-CTATCAAT
* *
20344321 TATGAAAAGGCATGGTGATAACCATCAGCTATGAAAAGGGATGGTGACGACC
65 TATGAAAAGGCATGGTGACAACCATCAACTATGAAAAGGGATGGTGACGACC
* * * * * *
20344373 ATCGATTAATGAAAAGGGATGGTTTCAACCATCGAATATGAAAAGGG
1 ATCGAAT-ATGAAAAGGGATAGCTTCAGCTATCGAATGTGAAAAGGG
20344420 GCGGTTACAA
Statistics
Matches: 143, Mismatches: 18, Indels: 3
0.87 0.11 0.02
Matches are distributed among these distances:
115 1 0.01
116 109 0.76
117 33 0.23
ACGTcount: A:0.37, C:0.14, G:0.26, T:0.23
Consensus pattern (116 bp):
ATCGAATATGAAAAGGGATAGCTTCAGCTATCGAATGTGAAAAGGGATAACTTCAGCTATCAATT
ATGAAAAGGCATGGTGACAACCATCAACTATGAAAAGGGATGGTGACGACC
Found at i:20344373 original size:29 final size:29
Alignment explanation
Indices: 20344203--20344419 Score: 179
Period size: 29 Copynumber: 7.4 Consensus size: 29
20344193 TCAGCTATCA
* *
20344203 ATTATGAGAAGGGATGGTGACGACCATCA
1 ATTATGAAAAGGGATGGTGACGACCATCG
*
20344232 ATTATGAAAAGGGATGGTGATGACCATCG
1 ATTATGAAAAGGGATGGTGACGACCATCG
* * * * *
20344261 AATATGAAAAGGGATAGCT-TCGGCTATCG
1 ATTATGAAAAGGGAT-GGTGACGACCATCG
* * ** * *
20344290 AATGTGAAAAGGGATAACT-TCGACTATCG
1 ATTATGAAAAGGGAT-GGTGACGACCATCG
* **
20344319 ATTATGAAAAGGCATGGTGATAACCATC-
1 ATTATGAAAAGGGATGGTGACGACCATCG
*
20344347 AGCTATGAAAAGGGATGGTGACGACCATCG
1 A-TTATGAAAAGGGATGGTGACGACCATCG
** *
20344377 ATTAATGAAAAGGGATGGTTTCAACCATCG
1 ATT-ATGAAAAGGGATGGTGACGACCATCG
*
20344407 AATATGAAAAGGG
1 ATTATGAAAAGGG
20344420 GCGGTTACAA
Statistics
Matches: 153, Mismatches: 30, Indels: 10
0.79 0.16 0.05
Matches are distributed among these distances:
28 2 0.01
29 123 0.80
30 28 0.18
ACGTcount: A:0.37, C:0.13, G:0.28, T:0.23
Consensus pattern (29 bp):
ATTATGAAAAGGGATGGTGACGACCATCG
Found at i:20344377 original size:87 final size:88
Alignment explanation
Indices: 20344223--20344418 Score: 202
Period size: 87 Copynumber: 2.2 Consensus size: 88
20344213 GGGATGGTGA
* * * * *
20344223 CGACCATCAATTATGAAAAGGGATGGTGATGACCATCGAATATGAAAAGGGATAGCTTCGGCTAT
1 CGACCATCAATTATGAAAAGGCATGGTGATAACCATCGAATATGAAAAGGGATAGCTACGACCAT
*
20344288 CGAAT-GTGAAAAGGGATAACTT
66 CGAATAATGAAAAGGGATAACTT
* * * *
20344310 CGACTATCGATTATGAAAAGGCATGGTGATAACCATC-AGCTATGAAAAGGGAT-GGTGACGACC
1 CGACCATCAATTATGAAAAGGCATGGTGATAACCATCGA-ATATGAAAAGGGATAGCT-ACGACC
* ***
20344373 ATCGATTAATGAAAAGGGATGGTTT
64 ATCGAATAATGAAAAGGGATAACTT
*
20344398 CAACCATCGAA-TATGAAAAGG
1 CGACCATC-AATTATGAAAAGG
20344419 GGCGGTTACA
Statistics
Matches: 88, Mismatches: 17, Indels: 7
0.79 0.15 0.06
Matches are distributed among these distances:
86 3 0.03
87 55 0.62
88 29 0.33
89 1 0.01
ACGTcount: A:0.37, C:0.14, G:0.26, T:0.22
Consensus pattern (88 bp):
CGACCATCAATTATGAAAAGGCATGGTGATAACCATCGAATATGAAAAGGGATAGCTACGACCAT
CGAATAATGAAAAGGGATAACTT
Found at i:20344425 original size:29 final size:30
Alignment explanation
Indices: 20344351--20344435 Score: 100
Period size: 30 Copynumber: 2.9 Consensus size: 30
20344341 ACCATCAGCT
* * * *
20344351 ATGAAAAGGGATGGTGACGACCATCGATTA
1 ATGAAAAGGGACGGTTACAACCATCGAATA
* *
20344381 ATGAAAAGGGATGGTTTCAACCATCGAAT-
1 ATGAAAAGGGACGGTTACAACCATCGAATA
*
20344410 ATGAAAAGGGGCGGTTACAACCATCG
1 ATGAAAAGGGACGGTTACAACCATCG
20344436 TTTAGCACAC
Statistics
Matches: 48, Mismatches: 7, Indels: 1
0.86 0.12 0.02
Matches are distributed among these distances:
29 23 0.48
30 25 0.52
ACGTcount: A:0.36, C:0.15, G:0.28, T:0.20
Consensus pattern (30 bp):
ATGAAAAGGGACGGTTACAACCATCGAATA
Found at i:20344433 original size:59 final size:58
Alignment explanation
Indices: 20344315--20344435 Score: 138
Period size: 59 Copynumber: 2.1 Consensus size: 58
20344305 AACTTCGACT
* * *
20344315 ATCGATTATGAAAAGGCATGGTGATAACCATCAGCTATGAAAAGGGATGGTGACGACC
1 ATCGATTATGAAAAGGCATGGTGATAACCATCAGATATGAAAAGGGACGGTGACAACC
* * * *
20344373 ATCGATTAATGAAAAGGGATGGT-TTCAACCATC-GAATATGAAAAGGGGCGGTTACAACC
1 ATCGATT-ATGAAAAGGCATGGTGAT-AACCATCAG-ATATGAAAAGGGACGGTGACAACC
20344432 ATCG
1 ATCG
20344436 TTTAGCACAC
Statistics
Matches: 53, Mismatches: 7, Indels: 5
0.82 0.11 0.08
Matches are distributed among these distances:
58 9 0.17
59 44 0.83
ACGTcount: A:0.36, C:0.16, G:0.26, T:0.21
Consensus pattern (58 bp):
ATCGATTATGAAAAGGCATGGTGATAACCATCAGATATGAAAAGGGACGGTGACAACC
Found at i:20352876 original size:16 final size:16
Alignment explanation
Indices: 20352857--20352891 Score: 61
Period size: 16 Copynumber: 2.2 Consensus size: 16
20352847 ATGATGAGAC
*
20352857 TGTTAAATTTGTTTTT
1 TGTTAAATTTGTTGTT
20352873 TGTTAAATTTGTTGTT
1 TGTTAAATTTGTTGTT
20352889 TGT
1 TGT
20352892 GCATACTATC
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
16 18 1.00
ACGTcount: A:0.17, C:0.00, G:0.17, T:0.66
Consensus pattern (16 bp):
TGTTAAATTTGTTGTT
Found at i:20354882 original size:18 final size:19
Alignment explanation
Indices: 20354856--20354897 Score: 59
Period size: 20 Copynumber: 2.2 Consensus size: 19
20354846 AAAAATGTAA
*
20354856 AAGAGATAT-ATATATAAT
1 AAGACATATAATATATAAT
20354874 AAGACATATAGATATATAAT
1 AAGACATATA-ATATATAAT
20354894 AAGA
1 AAGA
20354898 TAAAAAGATA
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
18 8 0.38
20 13 0.62
ACGTcount: A:0.57, C:0.02, G:0.12, T:0.29
Consensus pattern (19 bp):
AAGACATATAATATATAAT
Found at i:20354890 original size:20 final size:20
Alignment explanation
Indices: 20354865--20354911 Score: 67
Period size: 20 Copynumber: 2.4 Consensus size: 20
20354855 AAAGAGATAT
* *
20354865 ATATATAATAAGACATATAG
1 ATATATAATAAGACAAAAAG
*
20354885 ATATATAATAAGATAAAAAG
1 ATATATAATAAGACAAAAAG
20354905 ATATATA
1 ATATATA
20354912 GATATAAGGT
Statistics
Matches: 24, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 24 1.00
ACGTcount: A:0.60, C:0.02, G:0.09, T:0.30
Consensus pattern (20 bp):
ATATATAATAAGACAAAAAG
Found at i:20356770 original size:44 final size:44
Alignment explanation
Indices: 20356705--20357031 Score: 120
Period size: 44 Copynumber: 7.5 Consensus size: 44
20356695 GATCTGCTCT
* * * *
20356705 ACTGGAACCTCAGGGAAATAAGATTTGCTTCT-TCACTCTGCCCC
1 ACTGTAACTTCAGGGAGATAAGACTTG-TTCTCTCACTCTGCCCC
* * * * *
20356749 ACTGTGACTTCAGGGGGATAAGACTTGTTTTCTCAGTCTGCTCC
1 ACTGTAACTTCAGGGAGATAAGACTTGTTCTCTCACTCTGCCCC
* ** * * * *
20356793 GCTGTAACTTCAGGGAGATAAGACCCGAT-GC-GA-TCTGCTCC
1 ACTGTAACTTCAGGGAGATAAGACTTGTTCTCTCACTCTGCCCC
* * * * * * * * *
20356834 ACTACT-GCTT-AGGGAGATAAGA-TATATTGTTTTAATCCGCTCC
1 ACT-GTAACTTCAGGGAGATAAGACT-TGTTCTCTCACTCTGCCCC
* * * ** * *
20356877 ACTGCAACTTCAGGGAGATAGGA-TTCATT-TCTTCTGTATGCTCC
1 ACTGTAACTTCAGGGAGATAAGACTT-GTTCTC-TCACTCTGCCCC
* * *
20356921 ACTACT-GCTT-AGGGAGATAAGACTTGCTTCT-TCAGTCTGCCCC
1 ACT-GTAACTTCAGGGAGATAAGACTTG-TTCTCTCACTCTGCCCC
* * * * *
20356964 ACTGTGACTTCAGGGGGATAAGACTTGTTTTCTCAGTCTGCTCC
1 ACTGTAACTTCAGGGAGATAAGACTTGTTCTCTCACTCTGCCCC
* * *
20357008 GCTGCAACTCCAGGGAGATAAGAC
1 ACTGTAACTTCAGGGAGATAAGAC
20357032 CCGACACGAT
Statistics
Matches: 210, Mismatches: 56, Indels: 34
0.70 0.19 0.11
Matches are distributed among these distances:
40 13 0.06
41 13 0.06
42 4 0.02
43 48 0.23
44 131 0.62
45 1 0.00
ACGTcount: A:0.23, C:0.24, G:0.23, T:0.30
Consensus pattern (44 bp):
ACTGTAACTTCAGGGAGATAAGACTTGTTCTCTCACTCTGCCCC
Found at i:20356952 original size:43 final size:44
Alignment explanation
Indices: 20356883--20356990 Score: 107
Period size: 43 Copynumber: 2.5 Consensus size: 44
20356873 CTCCACTGCA
* * *
20356883 ACTTCAGGGAGATAGGA-TT-CATTTCTTCTGTATGCTCCACTACTG
1 ACTTCAGGGAGATAAGACTTGC--TTCTTCAGTATGCCCCACT-CTG
* *
20356928 -CTT-AGGGAGATAAGACTTGCTTCTTCAGTCTGCCCCACTGTG
1 ACTTCAGGGAGATAAGACTTGCTTCTTCAGTATGCCCCACTCTG
*
20356970 ACTTCAGGGGGATAAGACTTG
1 ACTTCAGGGAGATAAGACTTG
20356991 TTTTCTCAGT
Statistics
Matches: 53, Mismatches: 6, Indels: 9
0.78 0.09 0.13
Matches are distributed among these distances:
42 2 0.04
43 30 0.57
44 20 0.38
45 1 0.02
ACGTcount: A:0.22, C:0.22, G:0.24, T:0.31
Consensus pattern (44 bp):
ACTTCAGGGAGATAAGACTTGCTTCTTCAGTATGCCCCACTCTG
Found at i:20357006 original size:87 final size:86
Alignment explanation
Indices: 20356826--20357007 Score: 190
Period size: 87 Copynumber: 2.1 Consensus size: 86
20356816 CCCGATGCGA
*
20356826 TCTGCTCCACTACTGCTTAGGGAGATAAGATATATTGTTTTAATCCGCTCCACTGCAACTTCAGG
1 TCTGCTCCACTACTGCTTAGGGAGATAAGA-ATATTGTTTTAATCCGCCCCACTGCAACTTCAGG
* *
20356891 GAGATAGGATTCATTTCTTCTG
65 GAGATAAGATTCATTTCTTCAG
* * * * **
20356913 TATGCTCCACTACTGCTTAGGGAGATAAG-A-CTTGCTTCTTCAGTCTGCCCCACTGTGACTTCA
1 TCTGCTCCACTACTGCTTAGGGAGATAAGAATATTG-TT-TT-AATCCGCCCCACTGCAACTTCA
* **
20356976 GGGGGATAAGACTTGTTTTC-TCAG
63 GGGAGATAAGA-TTCATTTCTTCAG
20357000 TCTGCTCC
1 TCTGCTCC
20357008 GCTGCAACTC
Statistics
Matches: 78, Mismatches: 13, Indels: 8
0.79 0.13 0.08
Matches are distributed among these distances:
84 3 0.04
85 3 0.04
86 2 0.03
87 64 0.82
88 6 0.08
ACGTcount: A:0.21, C:0.24, G:0.21, T:0.34
Consensus pattern (86 bp):
TCTGCTCCACTACTGCTTAGGGAGATAAGAATATTGTTTTAATCCGCCCCACTGCAACTTCAGGG
AGATAAGATTCATTTCTTCAG
Found at i:20357273 original size:87 final size:87
Alignment explanation
Indices: 20357124--20357474 Score: 515
Period size: 87 Copynumber: 4.0 Consensus size: 87
20357114 ACTTGTAATC
* ** * * *
20357124 TTCGATCTGCTTCACTATCGACGCAGGAGGGCAAGATTTGCTATCTTTAACCAGCTCCACTGCAA
1 TTCGATCTGCTTCACTGTTAACGCAGGAAGGCAAGATCTGTTATCTTTAACCAGCTCCACTGCAA
*
20357189 CCGATGGAGGTAAGGCTTTGTT
66 CCGATGGAGGCAAGGCTTTGTT
* ** *
20357211 TTTGATCTGCTTCGTTGTTAACGCAGGAAGGCAATATCTGTTATCTTTAACCAGCTCCACTGCAA
1 TTCGATCTGCTTCACTGTTAACGCAGGAAGGCAAGATCTGTTATCTTTAACCAGCTCCACTGCAA
20357276 CCGATGGAGGCAAGGCTTTGTT
66 CCGATGGAGGCAAGGCTTTGTT
*
20357298 TTCGATCTGCTTCACTGTTAACGCAAGAAGGCAAGATCTGTTATCTTTAACCAGCTCCACTGCAA
1 TTCGATCTGCTTCACTGTTAACGCAGGAAGGCAAGATCTGTTATCTTTAACCAGCTCCACTGCAA
*
20357363 CCGATAGAGGCAAGGCTTTGTT
66 CCGATGGAGGCAAGGCTTTGTT
* * *
20357385 TTCGGTCTGCTTCACTGTTAACGTAGGAATGG-AAGATCTTTTATCTTTAACCAGCTCCAACTGC
1 TTCGATCTGCTTCACTGTTAACGCAGGAA-GGCAAGATCTGTTATCTTTAACCAGCTCC-ACTGC
* *
20357449 AATCGATGGAGGTAAGGCTTTGTT
64 AACCGATGGAGGCAAGGCTTTGTT
20357473 TT
1 TT
20357475 TTATCTTCAC
Statistics
Matches: 238, Mismatches: 24, Indels: 3
0.90 0.09 0.01
Matches are distributed among these distances:
87 208 0.87
88 30 0.13
ACGTcount: A:0.24, C:0.22, G:0.23, T:0.31
Consensus pattern (87 bp):
TTCGATCTGCTTCACTGTTAACGCAGGAAGGCAAGATCTGTTATCTTTAACCAGCTCCACTGCAA
CCGATGGAGGCAAGGCTTTGTT
Found at i:20357376 original size:44 final size:44
Alignment explanation
Indices: 20357239--20357376 Score: 124
Period size: 44 Copynumber: 3.2 Consensus size: 44
20357229 TAACGCAGGA
* *
20357239 AGGCAATATCTGTTATCTTTAACCAGCTCCACTGCAACCGATGG
1 AGGCAAGATCTGTTATCTTTAACCAGCTCCACTGCAACCGATAG
* * * * * * *
20357283 AGGCAAG-GCT-TTGT-TTTCGATCTGCTTCACTGTTAA-CGCA-AG
1 AGGCAAGATCTGTTATCTTT-AACCAGCTCCACTG-CAACCG-ATAG
20357325 AAGGCAAGATCTGTTATCTTTAACCAGCTCCACTGCAACCGATAG
1 -AGGCAAGATCTGTTATCTTTAACCAGCTCCACTGCAACCGATAG
20357370 AGGCAAG
1 AGGCAAG
20357377 GCTTTGTTTT
Statistics
Matches: 69, Mismatches: 16, Indels: 18
0.67 0.16 0.17
Matches are distributed among these distances:
41 3 0.04
42 16 0.23
43 12 0.17
44 18 0.26
45 17 0.25
46 3 0.04
ACGTcount: A:0.28, C:0.25, G:0.21, T:0.27
Consensus pattern (44 bp):
AGGCAAGATCTGTTATCTTTAACCAGCTCCACTGCAACCGATAG
Found at i:20366018 original size:31 final size:29
Alignment explanation
Indices: 20365961--20366037 Score: 82
Period size: 31 Copynumber: 2.5 Consensus size: 29
20365951 TTATATTTTA
20365961 TTTGACTTTGATTGATTTCTCTTTTTTTGCT
1 TTTGACTTTGATT--TTTCTCTTTTTTTGCT
* *
20365992 TTTGACTTTGATTTTTCTTTTCTTTTTTGTT
1 TTTGACTTTGATTTTTC-TCT-TTTTTTGCT
* *
20366023 TTTTATTTTGATTTT
1 TTTGACTTTGATTTT
20366038 GATTTTTTTT
Statistics
Matches: 40, Mismatches: 4, Indels: 4
0.83 0.08 0.08
Matches are distributed among these distances:
29 4 0.10
30 2 0.05
31 34 0.85
ACGTcount: A:0.09, C:0.09, G:0.10, T:0.71
Consensus pattern (29 bp):
TTTGACTTTGATTTTTCTCTTTTTTTGCT
Found at i:20366020 original size:19 final size:18
Alignment explanation
Indices: 20365991--20366044 Score: 54
Period size: 18 Copynumber: 2.9 Consensus size: 18
20365981 CTTTTTTTGC
* *
20365991 TTTTGACTTTGATTTTTC
1 TTTTGATTTTGATTTTTA
** *
20366009 TTTTCTTTTTTGTTTTTTA
1 TTTT-GATTTTGATTTTTA
20366028 TTTTGATTTTGATTTTT
1 TTTTGATTTTGATTTTT
20366045 TTTGAATCTG
Statistics
Matches: 27, Mismatches: 8, Indels: 2
0.73 0.22 0.05
Matches are distributed among these distances:
18 14 0.52
19 13 0.48
ACGTcount: A:0.09, C:0.06, G:0.09, T:0.76
Consensus pattern (18 bp):
TTTTGATTTTGATTTTTA
Found at i:20370601 original size:20 final size:20
Alignment explanation
Indices: 20370576--20370622 Score: 67
Period size: 20 Copynumber: 2.4 Consensus size: 20
20370566 TAAAAGATAT
* *
20370576 ATATATAATAAGACATATAG
1 ATATATAATAAGACAAAAAG
*
20370596 ATATATAATAAGATAAAAAG
1 ATATATAATAAGACAAAAAG
20370616 ATATATA
1 ATATATA
20370623 GATATAAGGT
Statistics
Matches: 24, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 24 1.00
ACGTcount: A:0.60, C:0.02, G:0.09, T:0.30
Consensus pattern (20 bp):
ATATATAATAAGACAAAAAG
Found at i:20372255 original size:24 final size:23
Alignment explanation
Indices: 20372206--20372255 Score: 57
Period size: 24 Copynumber: 2.1 Consensus size: 23
20372196 TAAAGTAGGT
* *
20372206 TATATATTATTTTTATAATATTA
1 TATATATGATTTTTATAATATCA
20372229 TATATTATGATTTTTATTAAT-TCA
1 TATA-TATGATTTTTA-TAATATCA
20372253 TAT
1 TAT
20372256 TTTTAATAAT
Statistics
Matches: 23, Mismatches: 2, Indels: 3
0.82 0.07 0.11
Matches are distributed among these distances:
23 4 0.17
24 15 0.65
25 4 0.17
ACGTcount: A:0.36, C:0.02, G:0.02, T:0.60
Consensus pattern (23 bp):
TATATATGATTTTTATAATATCA
Found at i:20372287 original size:17 final size:19
Alignment explanation
Indices: 20372265--20372311 Score: 53
Period size: 20 Copynumber: 2.5 Consensus size: 19
20372255 TTTTTAATAA
20372265 TTATTATATTA-AGA-ATT
1 TTATTATATTATAGATATT
* *
20372282 TTATTAAATTATATATTATT
1 TTATTATATTATAGA-TATT
20372302 TTATTATATT
1 TTATTATATT
20372312 GTATTTAATA
Statistics
Matches: 24, Mismatches: 3, Indels: 3
0.80 0.10 0.10
Matches are distributed among these distances:
17 10 0.42
18 2 0.08
20 12 0.50
ACGTcount: A:0.38, C:0.00, G:0.02, T:0.60
Consensus pattern (19 bp):
TTATTATATTATAGATATT
Found at i:20372367 original size:61 final size:58
Alignment explanation
Indices: 20372240--20372395 Score: 156
Period size: 61 Copynumber: 2.6 Consensus size: 58
20372230 ATATTATGAT
* *
20372240 TTTTATT-AATTCATATTTTTAATAATTATTATATTAAGAATTTTATTAAATTATATATTA
1 TTTTATTAAATT-ATA--TTTAATAATAATTATATTAAGAATATTATTAAATTATATATTA
* * * *
20372300 TTTTATTATATTGTATTTAATAATAATTATGTTAA-AATATTATTAAATTATTTGTTATTA
1 TTTTATTAAATTATATTTAATAATAATTATATTAAGAATATTATTAAATTA--T-ATATTA
*
20372360 TTTTTATTAAATTATATATAATAATAATCT-TATTAA
1 -TTTTATTAAATTATATTTAATAATAAT-TATATTAA
20372396 AACTTAATAA
Statistics
Matches: 80, Mismatches: 10, Indels: 11
0.79 0.10 0.11
Matches are distributed among these distances:
57 14 0.17
58 18 0.22
59 1 0.01
60 14 0.17
61 32 0.40
62 1 0.01
ACGTcount: A:0.40, C:0.01, G:0.03, T:0.56
Consensus pattern (58 bp):
TTTTATTAAATTATATTTAATAATAATTATATTAAGAATATTATTAAATTATATATTA
Found at i:20375578 original size:19 final size:19
Alignment explanation
Indices: 20375556--20375615 Score: 86
Period size: 19 Copynumber: 3.2 Consensus size: 19
20375546 CTTCAAAAAG
*
20375556 AATTTTAAAAAAATATTAA
1 AATTTTAAAAAAATATAAA
*
20375575 AATTTTAAAAAGATATAAA
1 AATTTTAAAAAAATATAAA
*
20375594 AAATTTAAAAAAATA-AAA
1 AATTTTAAAAAAATATAAA
20375612 AATT
1 AATT
20375616 AATTGTTGAC
Statistics
Matches: 36, Mismatches: 5, Indels: 1
0.86 0.12 0.02
Matches are distributed among these distances:
18 6 0.17
19 30 0.83
ACGTcount: A:0.67, C:0.00, G:0.02, T:0.32
Consensus pattern (19 bp):
AATTTTAAAAAAATATAAA
Found at i:20375593 original size:10 final size:9
Alignment explanation
Indices: 20375563--20375614 Score: 52
Period size: 9 Copynumber: 5.8 Consensus size: 9
20375553 AAGAATTTTA
20375563 AAAAAATAT
1 AAAAAATAT
* * *
20375572 TAAAATTTT
1 AAAAAATAT
20375581 AAAAAGATAT
1 AAAAA-ATAT
*
20375591 AAAAAATTT
1 AAAAAATAT
20375600 AAAAAA-AT
1 AAAAAATAT
20375608 AAAAAAT
1 AAAAAAT
20375615 TAATTGTTGA
Statistics
Matches: 33, Mismatches: 8, Indels: 4
0.73 0.18 0.09
Matches are distributed among these distances:
8 7 0.21
9 19 0.58
10 7 0.21
ACGTcount: A:0.71, C:0.00, G:0.02, T:0.27
Consensus pattern (9 bp):
AAAAAATAT
Found at i:20375955 original size:30 final size:30
Alignment explanation
Indices: 20375921--20375981 Score: 86
Period size: 30 Copynumber: 2.0 Consensus size: 30
20375911 ATACTTAAAA
* *
20375921 ATATTCAAATAAACTCTTAAATTTTAATTG
1 ATATTCAAATAAACCCTTAAAATTTAATTG
* *
20375951 ATATTCAAGTGAACCCTTAAAATTTAATTG
1 ATATTCAAATAAACCCTTAAAATTTAATTG
20375981 A
1 A
20375982 CGCTCAAATA
Statistics
Matches: 27, Mismatches: 4, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
30 27 1.00
ACGTcount: A:0.43, C:0.11, G:0.07, T:0.39
Consensus pattern (30 bp):
ATATTCAAATAAACCCTTAAAATTTAATTG
Found at i:20377706 original size:77 final size:77
Alignment explanation
Indices: 20377525--20377740 Score: 310
Period size: 77 Copynumber: 2.8 Consensus size: 77
20377515 AGTGTTAGTG
** * *
20377525 CAAATGTACTAAATTACACGTGACAAAATATAAGTTCAAATGATATCAACTAAAT-AAAAAATAA
1 CAAATGTACTAAATTGTA--TGACAGAATATAAGTTCAGATGATATCAACTAAATAAAAAAATAA
20377589 AAATCAAACAAATA
64 AAATCAAACAAATA
* * *
20377603 CGAATGTACTAAATTGTGTGACAGAATATAAGTTCAGATGATATCAACTAATTAAAAAAATAAAA
1 CAAATGTACTAAATTGTATGACAGAATATAAGTTCAGATGATATCAACTAAATAAAAAAATAAAA
*
20377668 ATCAAATAAATA
66 ATCAAACAAATA
*
20377680 CAAATGTACTAAATTGTATGATAGAATATAAGTTCATG-TGATATCAACTAAATAAAAAAAT
1 CAAATGTACTAAATTGTATGACAGAATATAAGTTCA-GATGATATCAACTAAATAAAAAAAT
20377741 GAAATAAATA
Statistics
Matches: 124, Mismatches: 12, Indels: 5
0.88 0.09 0.04
Matches are distributed among these distances:
76 32 0.26
77 77 0.62
78 15 0.12
ACGTcount: A:0.53, C:0.10, G:0.10, T:0.27
Consensus pattern (77 bp):
CAAATGTACTAAATTGTATGACAGAATATAAGTTCAGATGATATCAACTAAATAAAAAAATAAAA
ATCAAACAAATA
Found at i:20378528 original size:24 final size:24
Alignment explanation
Indices: 20378501--20378547 Score: 67
Period size: 24 Copynumber: 2.0 Consensus size: 24
20378491 CTAAATCGGG
* *
20378501 TATCTTTTTCTAGTTAAACTCTAT
1 TATCTTTTCCCAGTTAAACTCTAT
*
20378525 TATCTTTTCCCAGTTGAACTCTA
1 TATCTTTTCCCAGTTAAACTCTA
20378548 ATAACTCTAG
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
24 20 1.00
ACGTcount: A:0.23, C:0.21, G:0.06, T:0.49
Consensus pattern (24 bp):
TATCTTTTCCCAGTTAAACTCTAT
Found at i:20380333 original size:16 final size:16
Alignment explanation
Indices: 20380312--20380345 Score: 59
Period size: 16 Copynumber: 2.1 Consensus size: 16
20380302 TAGGATTGAT
20380312 TTTTAAAATTTCAAAG
1 TTTTAAAATTTCAAAG
*
20380328 TTTTAAAATTTTAAAG
1 TTTTAAAATTTCAAAG
20380344 TT
1 TT
20380346 GGCATCAATA
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 17 1.00
ACGTcount: A:0.41, C:0.03, G:0.06, T:0.50
Consensus pattern (16 bp):
TTTTAAAATTTCAAAG
Found at i:20381479 original size:12 final size:11
Alignment explanation
Indices: 20381447--20381489 Score: 50
Period size: 12 Copynumber: 3.7 Consensus size: 11
20381437 ACAAGAAAAT
* *
20381447 AAACTATTTTA
1 AAACTAATTAA
20381458 AAACTGAATTAA
1 AAACT-AATTAA
20381470 AAACCTAATTAA
1 AAA-CTAATTAA
20381482 AAACTAAT
1 AAACTAAT
20381490 GGCCTTCTAG
Statistics
Matches: 28, Mismatches: 2, Indels: 4
0.82 0.06 0.12
Matches are distributed among these distances:
11 10 0.36
12 16 0.57
13 2 0.07
ACGTcount: A:0.56, C:0.12, G:0.02, T:0.30
Consensus pattern (11 bp):
AAACTAATTAA
Found at i:20382199 original size:35 final size:35
Alignment explanation
Indices: 20382157--20382232 Score: 125
Period size: 35 Copynumber: 2.2 Consensus size: 35
20382147 ATGACTTGAG
* *
20382157 AATTAATTTATAATTTTTTAAATTATTAGTTAATT
1 AATTAATTTATAATTCTTTAAATTATTAATTAATT
*
20382192 AATTAATTTATAATTCTTTGAATTATTAATTAATT
1 AATTAATTTATAATTCTTTAAATTATTAATTAATT
20382227 AATTAA
1 AATTAA
20382233 ATTTCAAAAT
Statistics
Matches: 38, Mismatches: 3, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
35 38 1.00
ACGTcount: A:0.42, C:0.01, G:0.03, T:0.54
Consensus pattern (35 bp):
AATTAATTTATAATTCTTTAAATTATTAATTAATT
Found at i:20382231 original size:15 final size:15
Alignment explanation
Indices: 20382177--20382231 Score: 51
Period size: 15 Copynumber: 3.6 Consensus size: 15
20382167 TAATTTTTTA
20382177 AATT-ATTAGTTAATT
1 AATTAATTA-TTAATT
20382192 AATTAATT-TATAATT
1 AATTAATTAT-TAATT
**
20382207 CTTTGAATTATTAATT
1 AATT-AATTATTAATT
20382223 AATTAATTA
1 AATTAATTA
20382232 AATTTCAAAA
Statistics
Matches: 32, Mismatches: 4, Indels: 8
0.73 0.09 0.18
Matches are distributed among these distances:
14 1 0.03
15 16 0.50
16 14 0.44
17 1 0.03
ACGTcount: A:0.42, C:0.02, G:0.04, T:0.53
Consensus pattern (15 bp):
AATTAATTATTAATT
Found at i:20383779 original size:17 final size:17
Alignment explanation
Indices: 20383749--20383807 Score: 52
Period size: 17 Copynumber: 3.5 Consensus size: 17
20383739 ACATTAAATT
20383749 TAATAATTTTATTAAAA
1 TAATAATTTTATTAAAA
*
20383766 TAAT-ATTTTAATTAAGA
1 TAATAATTTT-ATTAAAA
*
20383783 TAAT--TTTCATTAATAA
1 TAATAATTTTATTAA-AA
20383799 TTAATAATT
1 -TAATAATT
20383808 AATAGGTTTG
Statistics
Matches: 34, Mismatches: 3, Indels: 8
0.76 0.07 0.18
Matches are distributed among these distances:
15 5 0.15
16 9 0.26
17 18 0.53
19 2 0.06
ACGTcount: A:0.47, C:0.02, G:0.02, T:0.49
Consensus pattern (17 bp):
TAATAATTTTATTAAAA
Found at i:20386863 original size:18 final size:18
Alignment explanation
Indices: 20386840--20386876 Score: 74
Period size: 18 Copynumber: 2.1 Consensus size: 18
20386830 CTGAAGTGTA
20386840 TATTAATACTATATTATT
1 TATTAATACTATATTATT
20386858 TATTAATACTATATTATT
1 TATTAATACTATATTATT
20386876 T
1 T
20386877 GTAATTGAAA
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 19 1.00
ACGTcount: A:0.38, C:0.05, G:0.00, T:0.57
Consensus pattern (18 bp):
TATTAATACTATATTATT
Found at i:20395219 original size:15 final size:15
Alignment explanation
Indices: 20395199--20395231 Score: 66
Period size: 15 Copynumber: 2.2 Consensus size: 15
20395189 ACTGTTATAC
20395199 TAATAAATTAAAATT
1 TAATAAATTAAAATT
20395214 TAATAAATTAAAATT
1 TAATAAATTAAAATT
20395229 TAA
1 TAA
20395232 ATAGTTCAGT
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 18 1.00
ACGTcount: A:0.61, C:0.00, G:0.00, T:0.39
Consensus pattern (15 bp):
TAATAAATTAAAATT
Found at i:20395674 original size:44 final size:44
Alignment explanation
Indices: 20395623--20395709 Score: 174
Period size: 44 Copynumber: 2.0 Consensus size: 44
20395613 AGTTTGCTTA
20395623 GCCAAGAAAATTGGACTTAAAAACTTCAACCAAGTTTGCTCTTT
1 GCCAAGAAAATTGGACTTAAAAACTTCAACCAAGTTTGCTCTTT
20395667 GCCAAGAAAATTGGACTTAAAAACTTCAACCAAGTTTGCTCTT
1 GCCAAGAAAATTGGACTTAAAAACTTCAACCAAGTTTGCTCTT
20395710 ACAAAACAAA
Statistics
Matches: 43, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
44 43 1.00
ACGTcount: A:0.37, C:0.21, G:0.14, T:0.29
Consensus pattern (44 bp):
GCCAAGAAAATTGGACTTAAAAACTTCAACCAAGTTTGCTCTTT
Found at i:20402377 original size:36 final size:35
Alignment explanation
Indices: 20402337--20402732 Score: 123
Period size: 33 Copynumber: 11.2 Consensus size: 35
20402327 GGATAAATTT
20402337 ATTTAAAGGAATAAATTTAAATTTTAAAACAATTGA
1 ATTTAAAGGAATAAATTTAAATTTTAAAA-AATTGA
** * *
20402373 ATTTAATTAAAAAATAAATAATTAAA---TGATAAATT-A
1 ATTT-A--AAGGAATAAAT--TTAAATTTTAAAAAATTGA
20402409 ATTTAAAGGAATAAATTTAAATTTTTAAAAAATTGA
1 ATTTAAAGGAATAAATTTAAA-TTTTAAAAAATTGA
** ** * * *
20402445 ATTT-AATTAA-AAA-AGAAATAATTAAAGGATAAATCA
1 ATTTAAAGGAATAAATTTAAAT-TTTAAA--A-AATTGA
20402481 ATTTAAAGGAATAAATTTAAA--TTAAAAAATTGA
1 ATTTAAAGGAATAAATTTAAATTTTAAAAAATTGA
** * ** *
20402514 ATTT-AATTAAAAAATAAAAAAATTTAAGGATAAATT-A
1 ATTTAAAGGAATAAAT-TTAAATTTTAA--A-AAATTGA
*
20402551 ATTTAAAGGATTAAATTTAAA-TTTAAAAAATAT-A
1 ATTTAAAGGAATAAATTTAAATTTTAAAAAAT-TGA
** *** *
20402585 ATTT-AATTAA-AAAAAGAAATAATTAAAGGATAAATT-A
1 ATTTAAAGGAATAAATTTAAAT--TTTAA--A-AAATTGA
* *
20402622 ATTTTAAGGAAAAAATTTAAATTTT-AAAAATTGA
1 ATTTAAAGGAATAAATTTAAATTTTAAAAAATTGA
** *
20402656 ATTT-AATTAA-AAA-ATAAATAATTTAAGGATAAATT-A
1 ATTTAAAGGAATAAATTTAAAT--TTTAA--A-AAATTGA
* * *
20402692 ATTTAGAGGAATAAATTTAAATTTAAAAAAATAGA
1 ATTTAAAGGAATAAATTTAAATTTTAAAAAATTGA
20402727 ATTTAA
1 ATTTAA
20402733 TTAAAAAAGA
Statistics
Matches: 261, Mismatches: 55, Indels: 89
0.64 0.14 0.22
Matches are distributed among these distances:
31 10 0.04
32 18 0.07
33 47 0.18
34 22 0.08
35 28 0.11
36 39 0.15
37 39 0.15
38 29 0.11
39 24 0.09
41 5 0.02
ACGTcount: A:0.58, C:0.01, G:0.07, T:0.35
Consensus pattern (35 bp):
ATTTAAAGGAATAAATTTAAATTTTAAAAAATTGA
Found at i:20402397 original size:72 final size:71
Alignment explanation
Indices: 20402253--20402749 Score: 716
Period size: 72 Copynumber: 7.0 Consensus size: 71
20402243 GTTAATGTGC
* **
20402253 GGATAAATCAATTTAAAGGAATAAATTTAAATTTTTTAAAAAAATAAAATTTAATTAAAAAAGAA
1 GGATAAATTAATTTAAAGGAATAAATTTAAA--TTTT-AAAAAATTGAATTTAATTAAAAAAGAA
20402318 ATAATTAAA
63 ATAATTAAA
* *
20402327 GGATAAATTTATTTAAAGGAATAAATTTAAATTTTAAAACAATTGAATTTAATTAAAAAATAAAT
1 GGATAAATTAATTTAAAGGAATAAATTTAAATTTTAAAA-AATTGAATTTAATTAAAAAAGAAAT
20402392 AATTAAA
65 AATTAAA
*
20402399 TGATAAATTAATTTAAAGGAATAAATTTAAATTTTTAAAAAATTGAATTTAATTAAAAAAGAAAT
1 GGATAAATTAATTTAAAGGAATAAATTTAAA-TTTTAAAAAATTGAATTTAATTAAAAAAGAAAT
20402464 AATTAAA
65 AATTAAA
* * *
20402471 GGATAAATCAATTTAAAGGAATAAATTTAAA--TTAAAAAATTGAATTTAATTAAAAAATAAAAA
1 GGATAAATTAATTTAAAGGAATAAATTTAAATTTTAAAAAATTGAATTTAATTAAAAAA-GAAAT
*
20402534 AATTTAA
65 AATTAAA
*
20402541 GGATAAATTAATTTAAAGGATTAAATTTAAA-TTTAAAAAATAT-AATTTAATTAAAAAAAGAAA
1 GGATAAATTAATTTAAAGGAATAAATTTAAATTTTAAAAAAT-TGAATTTAATT-AAAAAAGAAA
20402604 TAATTAAA
64 TAATTAAA
* * *
20402612 GGATAAATTAATTTTAAGGAAAAAATTTAAATTTT-AAAAATTGAATTTAATTAAAAAATAAATA
1 GGATAAATTAATTTAAAGGAATAAATTTAAATTTTAAAAAATTGAATTTAATTAAAAAAGAAATA
*
20402676 ATTTAA
66 ATTAAA
* * * *
20402682 GGATAAATTAATTTAGAGGAATAAATTTAAATTTAAAAAAATAGAATTTAATTAAAAAAGAAAAA
1 GGATAAATTAATTTAAAGGAATAAATTTAAATTTTAAAAAATTGAATTTAATTAAAAAAGAAATA
20402747 ATT
66 ATT
20402750 TAAGAAAAGA
Statistics
Matches: 384, Mismatches: 30, Indels: 21
0.88 0.07 0.05
Matches are distributed among these distances:
69 26 0.07
70 86 0.22
71 103 0.27
72 132 0.34
73 8 0.02
74 29 0.08
ACGTcount: A:0.58, C:0.01, G:0.07, T:0.34
Consensus pattern (71 bp):
GGATAAATTAATTTAAAGGAATAAATTTAAATTTTAAAAAATTGAATTTAATTAAAAAAGAAATA
ATTAAA
Found at i:20402404 original size:15 final size:16
Alignment explanation
Indices: 20402291--20402740 Score: 102
Period size: 18 Copynumber: 25.4 Consensus size: 16
20402281 AAATTTTTTA
20402291 AAAAAATAAAATTTAATT
1 AAAAAAT-AAA-TTAATT
*
20402309 AAAAAAGAAA-TAATT
1 AAAAAATAAATTAATT
** *
20402324 AAAGGATAAATTTATTT
1 AAAAAATAAA-TTAATT
*
20402341 AAAGGAATAAATTTAAATTTT
1 AAA-AAATAAA-TT-AA--TT
*
20402362 AAAACAATTGAATTTAATT
1 AAAA-AA-T-AAATTAATT
20402381 AAAAAATAAA-TAATT
1 AAAAAATAAATTAATT
**
20402396 AAATGATAAATTAATTT
1 AAAAAATAAATTAA-TT
*
20402413 AAAGGAATAAATTTAAATTTTT
1 AAA-AAATAAA-TT-AA---TT
*
20402435 AAAAAATTGAATTTAATT
1 AAAAAA-T-AAATTAATT
*
20402453 AAAAAAGAAA-TAATT
1 AAAAAATAAATTAATT
** *
20402468 AAAGGATAAATCAATTT
1 AAAAAATAAATTAA-TT
*
20402485 AAAGGAATAAATTTAAATT
1 AAA-AAATAAA-TT-AATT
*
20402504 AAAAAATTGAATTTAATT
1 AAAAAA-T-AAATTAATT
**
20402522 AAAAAATAAAAAAATT
1 AAAAAATAAATTAATT
* **
20402538 TAAGGATAAATTAATTT
1 AAAAAATAAATTAA-TT
* *
20402555 AAAGGATTAAATTTAAATTT
1 AAA-AAATAAA-TT-AA-TT
20402575 AAAAAATATAATTTAATT
1 AAAAAATA-AA-TTAATT
*
20402593 AAAAAA-AGAAATAATT
1 AAAAAATA-AATTAATT
**
20402609 AAAGGATAAATTAATTTT
1 AAAAAATAAATTAA--TT
*
20402627 AAGGAAAA-AATTTAAATTTT
1 AA--AAAATAAATT-AA--TT
* *
20402647 AAAAATTGAATTTAATT
1 AAAAAAT-AAATTAATT
20402664 AAAAAATAAA-TAATT
1 AAAAAATAAATTAATT
* **
20402679 TAAGGATAAATTAATTT
1 AAAAAATAAATTAA-TT
**
20402696 AGAGGAATAAATTTAAATTT
1 A-AAAAATAAA-TT-AA-TT
20402716 AAAAAAATAGAATTTAATT
1 -AAAAAATA-AA-TTAATT
20402735 AAAAAA
1 AAAAAA
20402741 GAAAAAATTT
Statistics
Matches: 329, Mismatches: 58, Indels: 90
0.69 0.12 0.19
Matches are distributed among these distances:
15 49 0.15
16 43 0.13
17 40 0.12
18 81 0.25
19 35 0.11
20 46 0.14
21 19 0.06
22 12 0.04
23 4 0.01
ACGTcount: A:0.59, C:0.00, G:0.07, T:0.34
Consensus pattern (16 bp):
AAAAAATAAATTAATT
Found at i:20402625 original size:141 final size:142
Alignment explanation
Indices: 20402253--20402749 Score: 761
Period size: 141 Copynumber: 3.5 Consensus size: 142
20402243 GTTAATGTGC
* *
20402253 GGATAAATCAATTTAAAGGAATAAATTTAAATTTTTTAAAAAAATAAAATTTAATTAAAAAAGAA
1 GGATAAATTAATTTAAAGGAATAAATTTAAA--TTTTAAAAAAATATAATTTAATTAAAAAAGAA
*
20402318 ATAATTAAAGGATAAATTTATTTAAAGGAATAAATTTAAATTTTAAAACAATTGAATTTAATTAA
64 ATAATTAAAGGATAAATTAATTTAAAGGAATAAATTTAAA-TTTAAAA-AATTGAATTTAATTAA
*
20402383 AAAATAAATAATTAAA
127 AAAATAAATAATTTAA
* *
20402399 TGATAAATTAATTTAAAGGAATAAATTTAAATTTTTAAAAAAT-TGAATTTAATTAAAAAAGAAA
1 GGATAAATTAATTTAAAGGAATAAATTTAAATTTTAAAAAAATAT-AATTTAATTAAAAAAGAAA
*
20402463 TAATTAAAGGATAAATCAATTTAAAGGAATAAATTTAAA-TTAAAAAATTGAATTTAATTAAAAA
65 TAATTAAAGGATAAATTAATTTAAAGGAATAAATTTAAATTTAAAAAATTGAATTTAATTAAAAA
*
20402527 ATAAAAAAATTTAA
130 AT-AAATAATTTAA
*
20402541 GGATAAATTAATTTAAAGGATTAAATTTAAA-TTT-AAAAAATATAATTTAATTAAAAAAAGAAA
1 GGATAAATTAATTTAAAGGAATAAATTTAAATTTTAAAAAAATATAATTTAATT-AAAAAAGAAA
* * *
20402604 TAATTAAAGGATAAATTAATTTTAAGGAAAAAATTTAAATTTTAAAAATTGAATTTAATTAAAAA
65 TAATTAAAGGATAAATTAATTTAAAGGAATAAATTTAAATTTAAAAAATTGAATTTAATTAAAAA
20402669 ATAAATAATTTAA
130 ATAAATAATTTAA
* * *
20402682 GGATAAATTAATTTAGAGGAATAAATTTAAA-TTTAAAAAAATAGAATTTAATTAAAAAAGAAAA
1 GGATAAATTAATTTAAAGGAATAAATTTAAATTTTAAAAAAATATAATTTAATTAAAAAAGAAAT
20402746 AATT
66 AATT
20402750 TAAGAAAAGA
Statistics
Matches: 326, Mismatches: 19, Indels: 17
0.90 0.05 0.05
Matches are distributed among these distances:
140 16 0.05
141 127 0.39
142 87 0.27
144 67 0.21
146 29 0.09
ACGTcount: A:0.58, C:0.01, G:0.07, T:0.34
Consensus pattern (142 bp):
GGATAAATTAATTTAAAGGAATAAATTTAAATTTTAAAAAAATATAATTTAATTAAAAAAGAAAT
AATTAAAGGATAAATTAATTTAAAGGAATAAATTTAAATTTAAAAAATTGAATTTAATTAAAAAA
TAAATAATTTAA
Found at i:20402693 original size:16 final size:18
Alignment explanation
Indices: 20402668--20402708 Score: 61
Period size: 16 Copynumber: 2.4 Consensus size: 18
20402658 TTAATTAAAA
20402668 AATAAA-TAATTTA-AGG
1 AATAAATTAATTTAGAGG
20402684 -ATAAATTAATTTAGAGG
1 AATAAATTAATTTAGAGG
20402701 AATAAATT
1 AATAAATT
20402709 TAAATTTAAA
Statistics
Matches: 22, Mismatches: 0, Indels: 4
0.85 0.00 0.15
Matches are distributed among these distances:
15 5 0.23
16 7 0.32
17 3 0.14
18 7 0.32
ACGTcount: A:0.54, C:0.00, G:0.12, T:0.34
Consensus pattern (18 bp):
AATAAATTAATTTAGAGG
Found at i:20402759 original size:5 final size:5
Alignment explanation
Indices: 20402751--20402795 Score: 65
Period size: 5 Copynumber: 8.8 Consensus size: 5
20402741 GAAAAAATTT
20402751 AAGAA AAGAA AAGAA AAGAA AAGAA GAA-AA GAAGAA AAGAA AAGA
1 AAGAA AAGAA AAGAA AAGAA AAGAA -AAGAA -AAGAA AAGAA AAGA
20402796 GGATCGAACT
Statistics
Matches: 38, Mismatches: 0, Indels: 4
0.90 0.00 0.10
Matches are distributed among these distances:
5 34 0.89
6 4 0.11
ACGTcount: A:0.78, C:0.00, G:0.22, T:0.00
Consensus pattern (5 bp):
AAGAA
Found at i:20402779 original size:8 final size:8
Alignment explanation
Indices: 20402751--20402791 Score: 59
Period size: 8 Copynumber: 5.2 Consensus size: 8
20402741 GAAAAAATTT
20402751 AAGAAAAG
1 AAGAAAAG
20402759 AA-AAGAA-
1 AAGAA-AAG
20402766 AAGAAAAG
1 AAGAAAAG
20402774 AAGAAAAG
1 AAGAAAAG
20402782 AAGAAAAG
1 AAGAAAAG
20402790 AA
1 AA
20402792 AAGAGGATCG
Statistics
Matches: 30, Mismatches: 0, Indels: 6
0.83 0.00 0.17
Matches are distributed among these distances:
7 6 0.20
8 24 0.80
ACGTcount: A:0.78, C:0.00, G:0.22, T:0.00
Consensus pattern (8 bp):
AAGAAAAG
Found at i:20402779 original size:13 final size:13
Alignment explanation
Indices: 20402756--20402795 Score: 64
Period size: 13 Copynumber: 3.1 Consensus size: 13
20402746 AATTTAAGAA
20402756 AAGAAAAGAAAAG
1 AAGAAAAGAAAAG
20402769 AA-AAGAAGAAAAG
1 AAGAA-AAGAAAAG
20402782 AAGAAAAGAAAAG
1 AAGAAAAGAAAAG
20402795 A
1 A
20402796 GGATCGAACT
Statistics
Matches: 25, Mismatches: 0, Indels: 4
0.86 0.00 0.14
Matches are distributed among these distances:
12 2 0.08
13 21 0.84
14 2 0.08
ACGTcount: A:0.78, C:0.00, G:0.23, T:0.00
Consensus pattern (13 bp):
AAGAAAAGAAAAG
Found at i:20407305 original size:40 final size:39
Alignment explanation
Indices: 20407207--20407429 Score: 198
Period size: 40 Copynumber: 5.6 Consensus size: 39
20407197 TCCTCGTTCA
* * * ** * *
20407207 AATGCCTTCGGGACATAGCCCGGTTTTAGTAACTCACAC
1 AATGCCTTCGGGACTTAACCCGGATTTAACAATTCGCAC
*
20407246 AATGCCTTCGGGACATAACCCGGATTTAACAATTCGCAC
1 AATGCCTTCGGGACTTAACCCGGATTTAACAATTCGCAC
* *
20407285 GAATGCCTTCGGGACTTAACCCGGATTTAACAACTCACAC
1 -AATGCCTTCGGGACTTAACCCGGATTTAACAATTCGCAC
**
20407325 GAATGCCTTCGGGACTTAACCCGGATTT-AGTATCTCGCAC
1 -AATGCCTTCGGGACTTAACCCGGATTTAACAAT-TCGCAC
* * * * * *
20407365 AAAGGCCTTC-GGATCTTAATCCGGATATATTCACTTAGCAC
1 -AATGCCTTCGGGA-CTTAACCCGGATTTA-ACAATTCGCAC
* *
20407406 AAAGCCTTCGGGACTTAGCCCGGA
1 AATGCCTTCGGGACTTAACCCGGA
20407430 CAGCATTCAA
Statistics
Matches: 153, Mismatches: 25, Indels: 11
0.81 0.13 0.06
Matches are distributed among these distances:
39 38 0.25
40 106 0.69
41 8 0.05
42 1 0.01
ACGTcount: A:0.27, C:0.28, G:0.20, T:0.25
Consensus pattern (39 bp):
AATGCCTTCGGGACTTAACCCGGATTTAACAATTCGCAC
Found at i:20407308 original size:79 final size:80
Alignment explanation
Indices: 20407207--20407353 Score: 233
Period size: 79 Copynumber: 1.9 Consensus size: 80
20407197 TCCTCGTTCA
* * **
20407207 AATGCCTTCGGGACATAGCCCGGTTTTAGTAACTCACAC-AATGCCTTCGGGACATAACCCGGAT
1 AATGCCTTCGGGACATAACCCGGATTTAACAACTCACACGAATGCCTTCGGGACATAACCCGGAT
20407271 TTAACAATTCGCACG
66 TTAACAATTCGCACG
* *
20407286 AATGCCTTCGGGACTTAACCCGGATTTAACAACTCACACGAATGCCTTCGGGACTTAACCCGGAT
1 AATGCCTTCGGGACATAACCCGGATTTAACAACTCACACGAATGCCTTCGGGACATAACCCGGAT
20407351 TTA
66 TTA
20407354 GTATCTCGCA
Statistics
Matches: 61, Mismatches: 6, Indels: 1
0.90 0.09 0.01
Matches are distributed among these distances:
79 34 0.56
80 27 0.44
ACGTcount: A:0.28, C:0.28, G:0.20, T:0.24
Consensus pattern (80 bp):
AATGCCTTCGGGACATAACCCGGATTTAACAACTCACACGAATGCCTTCGGGACATAACCCGGAT
TTAACAATTCGCACG
Found at i:20407363 original size:80 final size:79
Alignment explanation
Indices: 20407205--20407429 Score: 240
Period size: 80 Copynumber: 2.8 Consensus size: 79
20407195 GCTCCTCGTT
* * * ** *
20407205 CAAATGCCTTCGGGACATAGCCCGGTTTTAGTAACTCACACAATGCCTTCGGGACATAACCCGGA
1 CAAATGCCTTCGGGACTTAACCCGGATTTAACAACTCACACAATGCCTTCGGGACTTAACCCGGA
20407270 TTTAACAATTCGCA
66 TTTAACAATTCGCA
*
20407284 CGAATGCCTTCGGGACTTAACCCGGATTTAACAACTCACACGAATGCCTTCGGGACTTAACCCGG
1 CAAATGCCTTCGGGACTTAACCCGGATTTAACAACTCACAC-AATGCCTTCGGGACTTAACCCGG
**
20407349 ATTT-AGTATCTCGCA
65 ATTTAACAAT-TCGCA
* * * * * * *
20407364 CAAAGGCCTTC-GGATCTTAATCCGGATATATTC-ACTTAGCACAAAGCCTTCGGGACTTAGCCC
1 CAAATGCCTTCGGGA-CTTAACCCGGATTTA-ACAACTCA-CACAATGCCTTCGGGACTTAACCC
20407427 GGA
63 GGA
20407430 CAGCATTCAA
Statistics
Matches: 124, Mismatches: 17, Indels: 9
0.83 0.11 0.06
Matches are distributed among these distances:
79 41 0.33
80 79 0.64
81 4 0.03
ACGTcount: A:0.28, C:0.28, G:0.20, T:0.24
Consensus pattern (79 bp):
CAAATGCCTTCGGGACTTAACCCGGATTTAACAACTCACACAATGCCTTCGGGACTTAACCCGGA
TTTAACAATTCGCA
Found at i:20407429 original size:120 final size:119
Alignment explanation
Indices: 20407207--20407429 Score: 279
Period size: 120 Copynumber: 1.9 Consensus size: 119
20407197 TCCTCGTTCA
* * * *
20407207 AATGCCTTCGGGACATAGCCCGGTTTTAGTAACTCACACAATGCCTTCGGGACATAACCCGGATT
1 AATGCCTTCGGGACATAACCCGGATTTAGTAACTCACACAAGGCCTTCGGGACATAACCCGGATA
* *
20407272 TAACAATTCGCACGAATGCCTTCGGGACTTAACCCGGATTTAACAACTCACACG
66 TAACAATTAGCACGAAAGCCTTCGGGACTTAACCCGGATTTAACAACTCACACG
* * * * *
20407326 AATGCCTTCGGGACTTAACCCGGATTTAGTATCTCGCACAAAGGCCTTC-GGATCTTAATCCGGA
1 AATGCCTTCGGGACATAACCCGGATTTAGTAACTCACAC-AAGGCCTTCGGGA-CATAACCCGGA
* * *
20407390 TATATTCACTTAGCAC-AAAGCCTTCGGGACTTAGCCCGGA
64 TATA-ACAATTAGCACGAAAGCCTTCGGGACTTAACCCGGA
20407430 CAGCATTCAA
Statistics
Matches: 87, Mismatches: 14, Indels: 5
0.82 0.13 0.05
Matches are distributed among these distances:
119 37 0.43
120 42 0.48
121 8 0.09
ACGTcount: A:0.27, C:0.28, G:0.20, T:0.25
Consensus pattern (119 bp):
AATGCCTTCGGGACATAACCCGGATTTAGTAACTCACACAAGGCCTTCGGGACATAACCCGGATA
TAACAATTAGCACGAAAGCCTTCGGGACTTAACCCGGATTTAACAACTCACACG
Found at i:20425838 original size:39 final size:40
Alignment explanation
Indices: 20425737--20425921 Score: 191
Period size: 40 Copynumber: 4.7 Consensus size: 40
20425727 TTGAATGATG
* * *
20425737 TCCGGGCTAAGTCCCGAAGGC-TTTGTGCTAAGTGAC-CAT
1 TCCGGGCTAAGTCCCGAAGGCATTTGTGC-GAGTTACTAAT
* * *
20425776 ATCCGGACTAAGAT-CCGAAGGCATTTGTCCGAGATACTAAT
1 -TCCGGGCTAAG-TCCCGAAGGCATTTGTGCGAGTTACTAAT
*
20425817 TCCGGGCTAAG-CCCGAAGGCATTTGTGCGAGTTACTAAA
1 TCCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTAAT
* * *
20425856 TCCGGGTTAAGTCCCGAAGGTAATTGTGCGAGTTACT-AT
1 TCCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTAAT
* *
20425895 AACCGGGCTATGTCCCGAAGGCATTTG
1 -TCCGGGCTAAGTCCCGAAGGCATTTG
20425922 AACGAGTAGC
Statistics
Matches: 120, Mismatches: 19, Indels: 12
0.79 0.13 0.08
Matches are distributed among these distances:
39 35 0.29
40 76 0.63
41 9 0.08
ACGTcount: A:0.25, C:0.23, G:0.27, T:0.25
Consensus pattern (40 bp):
TCCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTAAT
Found at i:20425873 original size:79 final size:81
Alignment explanation
Indices: 20425737--20425921 Score: 209
Period size: 79 Copynumber: 2.3 Consensus size: 81
20425727 TTGAATGATG
* *
20425737 TCCGGGCTAAGTCCCGAAGGC-TTTGTGCTAAGTGACCATATCCGGACTAAGATCCGAAGGCATT
1 TCCGGGCTAAGTCCCGAAGGCATTTGTGCTAAGTGACCAAATCCGGACTAAGATCCGAAGGCAAT
20425801 TGTCCGAGATACTA-A
66 TGTCCGAGATACTATA
* * * ** *
20425816 TTCCGGGCTAAG-CCCGAAGGCATTTGTGC-GAGTTACTAAATCCGGGTTAAG-TCCCGAAGGTA
1 -TCCGGGCTAAGTCCCGAAGGCATTTGTGCTAAGTGACCAAATCCGGACTAAGAT-CCGAAGGCA
* *
20425878 ATTGTGCGAGTTACTATA
64 ATTGTCCGAGATACTATA
* *
20425896 ACCGGGCTATGTCCCGAAGGCATTTG
1 TCCGGGCTAAGTCCCGAAGGCATTTG
20425922 AACGAGTAGC
Statistics
Matches: 89, Mismatches: 12, Indels: 8
0.82 0.11 0.07
Matches are distributed among these distances:
78 1 0.01
79 55 0.62
80 33 0.37
ACGTcount: A:0.25, C:0.23, G:0.27, T:0.25
Consensus pattern (81 bp):
TCCGGGCTAAGTCCCGAAGGCATTTGTGCTAAGTGACCAAATCCGGACTAAGATCCGAAGGCAAT
TGTCCGAGATACTATA
Found at i:20433745 original size:39 final size:39
Alignment explanation
Indices: 20433657--20433898 Score: 230
Period size: 39 Copynumber: 6.1 Consensus size: 39
20433647 TTGAATGATG
* *
20433657 TCCGGGCTAAGTCCCGAAGGC-TTTGTGCTAAGTGAC-CATA
1 TCCGGGCTAAGT-CCGAAGGCATTTGTGC-GAGT-ACTAATA
*
20433697 TCCGGACTAAGATCCGAAGGCATTTGTGCGA-TACTAATA
1 TCCGGGCTAAG-TCCGAAGGCATTTGTGCGAGTACTAATA
*
20433736 TCCGGACTAAGATCCGAAGGCATTTGTGCGAGTTACTAA-A
1 TCCGGGCTAAG-TCCGAAGGCATTTGTGCGAG-TACTAATA
* *
20433776 TCCGGGTTAAGCCCGAAGGCATTTGTGCGAGTTACTAA-A
1 TCCGGGCTAAGTCCGAAGGCATTTGTGCGAG-TACTAATA
*
20433815 TCCGGGTTAAGTCCCGAAGGCA-TTGTGCGAGTTACT-ATA
1 TCCGGGCTAAGT-CCGAAGGCATTTGTGCGAG-TACTAATA
* * **
20433854 ACCGGGCTATGTCCCGAAGGCATTTGAACGAGTAGCT-ATA
1 TCCGGGCTAAGT-CCGAAGGCATTTGTGCGAGTA-CTAATA
20433894 TCCGG
1 TCCGG
20433899 TTAAATTCCA
Statistics
Matches: 180, Mismatches: 13, Indels: 18
0.85 0.06 0.09
Matches are distributed among these distances:
38 3 0.02
39 109 0.61
40 54 0.30
41 14 0.08
ACGTcount: A:0.26, C:0.22, G:0.27, T:0.25
Consensus pattern (39 bp):
TCCGGGCTAAGTCCGAAGGCATTTGTGCGAGTACTAATA
Found at i:20433871 original size:118 final size:119
Alignment explanation
Indices: 20433657--20433879 Score: 269
Period size: 118 Copynumber: 1.9 Consensus size: 119
20433647 TTGAATGATG
*
20433657 TCCGGGCTAAGTCCCGAAGGCTTTGTGCTAAGTGACCATATCCGGACTAAGATCCGAAGGCATTT
1 TCCGGGCTAAGTCCCGAAGGCTTTGTGCTAAGTGACCAAATCCGGACTAAGATCCGAAGGCATTT
*
20433722 GTGCGATACTAATATCCGGACTAAGATCCGAAGGCATTTGTGCGAGTTACTAAA
66 GTGCGATACTAATAACCGGACTAAGATCCGAAGGCATTTGTGCGAGTTACTAAA
* * * * **
20433776 TCCGGGTTAAG-CCCGAAGGCATTTGTGC-GAGTTACTAAATCCGGGTTAAG-TCCCGAAGGCA-
1 TCCGGGCTAAGTCCCGAAGGC-TTTGTGCTAAGTGACCAAATCCGGACTAAGAT-CCGAAGGCAT
* *
20433837 TTGTGCGAGTTACT-ATAACCGGGCTATG-TCCCGAAGGCATTTG
64 TTGTGCGA--TACTAATAACCGGACTAAGAT-CCGAAGGCATTTG
20433880 AACGAGTAGC
Statistics
Matches: 89, Mismatches: 10, Indels: 11
0.81 0.09 0.10
Matches are distributed among these distances:
117 10 0.11
118 58 0.65
119 21 0.24
ACGTcount: A:0.26, C:0.22, G:0.27, T:0.26
Consensus pattern (119 bp):
TCCGGGCTAAGTCCCGAAGGCTTTGTGCTAAGTGACCAAATCCGGACTAAGATCCGAAGGCATTT
GTGCGATACTAATAACCGGACTAAGATCCGAAGGCATTTGTGCGAGTTACTAAA
Found at i:20433886 original size:79 final size:78
Alignment explanation
Indices: 20433657--20433898 Score: 260
Period size: 79 Copynumber: 3.1 Consensus size: 78
20433647 TTGAATGATG
* * * * * *
20433657 TCCGGGCTAAGTCCCGAAGGCTTTGTGCTAAGTGACCATATCCGGACTAAGAT-CCGAAGGCATT
1 TCCGGGCTAAGTCCCGAAGGCATTGTGC-GAGTTACTATAACCGGGCTAAG-TCCCGAAGGCATT
20433721 TGTGCGA-TACTAATA
64 TGTGCGAGTACTAA-A
* *
20433736 TCCGGACTAAGAT-CCGAAGGCATTTGTGCGAGTTACTA-AATCCGGGTTAAG-CCCGAAGGCAT
1 TCCGGGCTAAG-TCCCGAAGGCA-TTGTGCGAGTTACTATAA-CCGGGCTAAGTCCCGAAGGCAT
20433798 TTGTGCGAGTTACTAAA
63 TTGTGCGAG-TACTAAA
* *
20433815 TCCGGGTTAAGTCCCGAAGGCATTGTGCGAGTTACTATAACCGGGCTATGTCCCGAAGGCATTTG
1 TCCGGGCTAAGTCCCGAAGGCATTGTGCGAGTTACTATAACCGGGCTAAGTCCCGAAGGCATTTG
** *
20433880 AACGAGTAGCTATA
66 TGCGAGTA-CTAAA
20433894 TCCGG
1 TCCGG
20433899 TTAAATTCCA
Statistics
Matches: 138, Mismatches: 15, Indels: 20
0.80 0.09 0.12
Matches are distributed among these distances:
78 45 0.33
79 80 0.58
80 13 0.09
ACGTcount: A:0.26, C:0.22, G:0.27, T:0.25
Consensus pattern (78 bp):
TCCGGGCTAAGTCCCGAAGGCATTGTGCGAGTTACTATAACCGGGCTAAGTCCCGAAGGCATTTG
TGCGAGTACTAAA
Found at i:20437661 original size:13 final size:13
Alignment explanation
Indices: 20437643--20437668 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
20437633 CACCCCAAAC
20437643 ACAAATACAAAAT
1 ACAAATACAAAAT
20437656 ACAAATACAAAAT
1 ACAAATACAAAAT
20437669 TAAGGGATTT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.69, C:0.15, G:0.00, T:0.15
Consensus pattern (13 bp):
ACAAATACAAAAT
Found at i:20460364 original size:27 final size:27
Alignment explanation
Indices: 20460334--20460385 Score: 77
Period size: 27 Copynumber: 1.9 Consensus size: 27
20460324 TTTCAATTCC
*
20460334 TAGGGGTATAACAATCATTTTACCCTA
1 TAGGGGTATAACAATAATTTTACCCTA
**
20460361 TAGGGGTATTTCAATAATTTTACCC
1 TAGGGGTATAACAATAATTTTACCC
20460386 ATCGAGGATA
Statistics
Matches: 22, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
27 22 1.00
ACGTcount: A:0.31, C:0.17, G:0.15, T:0.37
Consensus pattern (27 bp):
TAGGGGTATAACAATAATTTTACCCTA
Found at i:20460397 original size:27 final size:27
Alignment explanation
Indices: 20460345--20460541 Score: 218
Period size: 27 Copynumber: 7.3 Consensus size: 27
20460335 AGGGGTATAA
* *
20460345 CAATCATTTTACCCTATAG-GGGTATTT
1 CAATAATTTTACCC-ATCGAGGGTATTT
*
20460372 CAATAATTTTACCCATCGAGGATATTT
1 CAATAATTTTACCCATCGAGGGTATTT
*
20460399 CAGTAATTTTACCCATCGAGGGTATTT
1 CAATAATTTTACCCATCGAGGGTATTT
** **
20460426 TGATAATTTTACCCATTAAGGGTATTT
1 CAATAATTTTACCCATCGAGGGTATTT
* *
20460453 CAATAATTTTACCTAT-TAGGGTATTT
1 CAATAATTTTACCCATCGAGGGTATTT
* * *
20460479 CGATCATTTTACCCTTCGAGGGTATTT
1 CAATAATTTTACCCATCGAGGGTATTT
* * *
20460506 TAGTAATTTTACCCTTCGAGGGTATTT
1 CAATAATTTTACCCATCGAGGGTATTT
*
20460533 CAGTAATTT
1 CAATAATTT
20460542 AACAACCTTT
Statistics
Matches: 144, Mismatches: 24, Indels: 4
0.84 0.14 0.02
Matches are distributed among these distances:
26 24 0.17
27 120 0.83
ACGTcount: A:0.27, C:0.16, G:0.15, T:0.42
Consensus pattern (27 bp):
CAATAATTTTACCCATCGAGGGTATTT
Found at i:20460540 original size:107 final size:108
Alignment explanation
Indices: 20460345--20460541 Score: 283
Period size: 107 Copynumber: 1.8 Consensus size: 108
20460335 AGGGGTATAA
*
20460345 CAATCATTTTACCCTATAGGGGTATTTCAATAATTTTACCCATCGAGGATATTTCAGTAATTTTA
1 CAATAATTTTACCCTATAGGGGTATTTCAATAATTTTACCCATCGAGGATATTTCAGTAATTTTA
*
20460410 CCCATCGAGGGTATTTTGATAATTTTACCCATTAAGGGTATTT
66 CCCATCGAGGGTATTTAGATAATTTTACCCATTAAGGGTATTT
* * * * *
20460453 CAATAATTTTA-CCTATTA-GGGTATTTCGATCATTTTACCCTTCGAGGGTATTTTAGTAATTTT
1 CAATAATTTTACCCTA-TAGGGGTATTTCAATAATTTTACCCATCGAGGATATTTCAGTAATTTT
*
20460516 ACCCTTCGAGGGTATTTCAG-TAATTT
65 ACCCATCGAGGGTATTT-AGATAATTT
20460542 AACAACCTTT
Statistics
Matches: 79, Mismatches: 8, Indels: 5
0.86 0.09 0.05
Matches are distributed among these distances:
107 66 0.84
108 13 0.16
ACGTcount: A:0.27, C:0.16, G:0.15, T:0.42
Consensus pattern (108 bp):
CAATAATTTTACCCTATAGGGGTATTTCAATAATTTTACCCATCGAGGATATTTCAGTAATTTTA
CCCATCGAGGGTATTTAGATAATTTTACCCATTAAGGGTATTT
Found at i:20462076 original size:25 final size:25
Alignment explanation
Indices: 20462039--20462092 Score: 90
Period size: 25 Copynumber: 2.2 Consensus size: 25
20462029 TGAACCTCTG
20462039 ACCTCCTTACCACACCTGTGACACC
1 ACCTCCTTACCACACCTGTGACACC
* *
20462064 ACCTCCTTGCCACACCTGTGTCACC
1 ACCTCCTTACCACACCTGTGACACC
20462089 ACCT
1 ACCT
20462093 TGCCACTACA
Statistics
Matches: 27, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
25 27 1.00
ACGTcount: A:0.20, C:0.48, G:0.09, T:0.22
Consensus pattern (25 bp):
ACCTCCTTACCACACCTGTGACACC
Found at i:20462093 original size:22 final size:23
Alignment explanation
Indices: 20462043--20462098 Score: 69
Period size: 25 Copynumber: 2.4 Consensus size: 23
20462033 CCTCTGACCT
*
20462043 CCTTACCACACCTGTGACACCACC
1 CCTTGCCACACCTGTGACACCA-C
*
20462067 TCCTTGCCACACCTGTGTCACCA-
1 -CCTTGCCACACCTGTGACACCAC
20462090 CCTTGCCAC
1 CCTTGCCAC
20462099 TACACCATAG
Statistics
Matches: 29, Mismatches: 2, Indels: 3
0.85 0.06 0.09
Matches are distributed among these distances:
22 9 0.31
25 20 0.69
ACGTcount: A:0.20, C:0.48, G:0.11, T:0.21
Consensus pattern (23 bp):
CCTTGCCACACCTGTGACACCAC
Found at i:20465179 original size:266 final size:266
Alignment explanation
Indices: 20464702--20465237 Score: 930
Period size: 266 Copynumber: 2.0 Consensus size: 266
20464692 GTTTAAGCTC
20464702 ATCAAACCAAGTGCACCACATACGACCTCGAAAGGCCCATCCAACCCTACACACCATGTATGTGG
1 ATCAAACCAAGTGCACCACATACGACCTCGAAAGGCCCATCCAACCCTACACACCATGTATGTGG
* * * *
20464767 GCTAAGTCACTCAGATAATAATACGCAATAAGGCTAGCGTATATGCAGTACAGTGCATTGCGGTA
66 ACTAAGCCACTCAGATAATAATACGCAACAAGGCTAGCATATATGCAGTACAGTGCATTGCGGTA
*
20464832 AACCATTGTACAGACATGTTGCAGTTTAAACTGCCAGATAAAATAATAGTATGCAACAAAGTTAA
131 AACCATTGTACAGACATGTTGCAGTTTAAACTGCCAGATAAAATAATAGTACGCAACAAAGTTAA
* * *
20464897 CGTACATGTAGTGCAGTGCGGTAAACCACTGTACCGATAAGTTTGTAGTTAAACTGCCAGATCAG
196 CGTACATGCAGTGCAGTGCGGTAAACCACTGTACCGATAAGTTTGTAATTAAACTGCAAGATCAG
20464962 ATCAGA
261 ATCAGA
* *
20464968 ATCAAACCAAGCT-CACCACATAGGACCTCGAAAGGCCCATCCAACCCTACATACCATGTATGTG
1 ATCAAACCAAG-TGCACCACATACGACCTCGAAAGGCCCATCCAACCCTACACACCATGTATGTG
*
20465032 GACTAAGCCACTCAGATAATAATACGCAGCAAGGCTAGCATATATGCAGTACAGTGCATTGCGGT
65 GACTAAGCCACTCAGATAATAATACGCAACAAGGCTAGCATATATGCAGTACAGTGCATTGCGGT
*
20465097 AAACCATTGTACAGACATGTTGCAGTTTAAACTGCCAGATAAAATAATAGTACGCAACAAAGTTG
130 AAACCATTGTACAGACATGTTGCAGTTTAAACTGCCAGATAAAATAATAGTACGCAACAAAGTTA
* *
20465162 ACGTACATGCGGTGCAGTGTGGTAAACCACTGTACCGATAAGTTTGTAATTAAACTGCAAGATCA
195 ACGTACATGCAGTGCAGTGCGGTAAACCACTGTACCGATAAGTTTGTAATTAAACTGCAAGATCA
20465227 GATCAGA
260 GATCAGA
20465234 ATCA
1 ATCA
20465238 GTCTTCCTTC
Statistics
Matches: 255, Mismatches: 14, Indels: 2
0.94 0.05 0.01
Matches are distributed among these distances:
266 254 1.00
267 1 0.00
ACGTcount: A:0.36, C:0.22, G:0.19, T:0.23
Consensus pattern (266 bp):
ATCAAACCAAGTGCACCACATACGACCTCGAAAGGCCCATCCAACCCTACACACCATGTATGTGG
ACTAAGCCACTCAGATAATAATACGCAACAAGGCTAGCATATATGCAGTACAGTGCATTGCGGTA
AACCATTGTACAGACATGTTGCAGTTTAAACTGCCAGATAAAATAATAGTACGCAACAAAGTTAA
CGTACATGCAGTGCAGTGCGGTAAACCACTGTACCGATAAGTTTGTAATTAAACTGCAAGATCAG
ATCAGA
Found at i:20469726 original size:25 final size:26
Alignment explanation
Indices: 20469685--20469735 Score: 70
Period size: 25 Copynumber: 2.0 Consensus size: 26
20469675 TAGCCTACAC
20469685 TAATAAAAGTTTAAGT-GTGAAACTAA
1 TAATAAAAGTTTAAGTGGT-AAACTAA
*
20469711 TAAT-AAATTTTAAGTGGTAAACTAA
1 TAATAAAAGTTTAAGTGGTAAACTAA
20469736 AAACAGAGTT
Statistics
Matches: 23, Mismatches: 1, Indels: 3
0.85 0.04 0.11
Matches are distributed among these distances:
25 17 0.74
26 6 0.26
ACGTcount: A:0.49, C:0.04, G:0.14, T:0.33
Consensus pattern (26 bp):
TAATAAAAGTTTAAGTGGTAAACTAA
Found at i:20469747 original size:25 final size:25
Alignment explanation
Indices: 20469690--20469747 Score: 64
Period size: 25 Copynumber: 2.3 Consensus size: 25
20469680 TACACTAATA
* *
20469690 AAAGTTTAAGTGTGAAACTAATAAT
1 AAAGTTTAAGTGTGAAACTAAAAAC
*
20469715 AAATTTTAAGTG-GTAAACTAAAAAC
1 AAAGTTTAAGTGTG-AAACTAAAAAC
*
20469740 AGAGTTTA
1 AAAGTTTA
20469748 GCTGGGAGAA
Statistics
Matches: 27, Mismatches: 5, Indels: 2
0.79 0.15 0.06
Matches are distributed among these distances:
24 1 0.04
25 26 0.96
ACGTcount: A:0.48, C:0.05, G:0.16, T:0.31
Consensus pattern (25 bp):
AAAGTTTAAGTGTGAAACTAAAAAC
Found at i:20474130 original size:94 final size:93
Alignment explanation
Indices: 20474021--20474194 Score: 267
Period size: 94 Copynumber: 1.9 Consensus size: 93
20474011 GTTAAAAAGG
* * *
20474021 GGATTTGATATATTCCTTATCAAATATGGAAATATAATTTAATTATTATTTAAAAGAGTTTTAAA
1 GGATTTGATATATTCCTTATCAAATAAGGAAATATAATTTAATTATTATTTAAAACACTTTTAAA
20474086 GAAATAATAATTAAATTTCAAAATCGAAA
66 -AAATAATAATTAAATTTCAAAATCGAAA
* * * *
20474115 GGATTTGATATATTCCTTATGAGATAAGGAAATATAATTTAGTTATTATTTAAAACTCTTTTAAA
1 GGATTTGATATATTCCTTATCAAATAAGGAAATATAATTTAATTATTATTTAAAACACTTTTAAA
*
20474180 TAATAATAATTAAAT
66 AAATAATAATTAAAT
20474195 AATAAAATTT
Statistics
Matches: 72, Mismatches: 8, Indels: 1
0.89 0.10 0.01
Matches are distributed among these distances:
93 14 0.19
94 58 0.81
ACGTcount: A:0.45, C:0.05, G:0.10, T:0.40
Consensus pattern (93 bp):
GGATTTGATATATTCCTTATCAAATAAGGAAATATAATTTAATTATTATTTAAAACACTTTTAAA
AAATAATAATTAAATTTCAAAATCGAAA
Found at i:20477077 original size:32 final size:32
Alignment explanation
Indices: 20477016--20477093 Score: 104
Period size: 32 Copynumber: 2.5 Consensus size: 32
20477006 GAATGGCAAC
* *
20477016 AAGCCATAAGTA-CAGTAATATGATTGGCACA
1 AAGCCATCAGTAGCAGTAATATGATCGGCACA
*
20477047 AAGCCATCAGTAGCAGTGATATGATCGGCACA
1 AAGCCATCAGTAGCAGTAATATGATCGGCACA
* *
20477079 CAGCCATCAATAGCA
1 AAGCCATCAGTAGCA
20477094 TCGCAGCAAA
Statistics
Matches: 41, Mismatches: 5, Indels: 1
0.87 0.11 0.02
Matches are distributed among these distances:
31 11 0.27
32 30 0.73
ACGTcount: A:0.38, C:0.22, G:0.21, T:0.19
Consensus pattern (32 bp):
AAGCCATCAGTAGCAGTAATATGATCGGCACA
Found at i:20477282 original size:24 final size:24
Alignment explanation
Indices: 20477240--20477293 Score: 81
Period size: 24 Copynumber: 2.2 Consensus size: 24
20477230 GCTCAGAATA
*
20477240 AGTCATACAAATCAGAGACAAACC
1 AGTCATACAAATCACAGACAAACC
* *
20477264 AGTCATACCAGTCACAGACAAACC
1 AGTCATACAAATCACAGACAAACC
20477288 AGTCAT
1 AGTCAT
20477294 TTACATCATG
Statistics
Matches: 27, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
24 27 1.00
ACGTcount: A:0.44, C:0.28, G:0.13, T:0.15
Consensus pattern (24 bp):
AGTCATACAAATCACAGACAAACC
Found at i:20477426 original size:27 final size:27
Alignment explanation
Indices: 20477352--20477697 Score: 352
Period size: 27 Copynumber: 12.9 Consensus size: 27
20477342 ATTTACTGTC
* * *
20477352 CAGGGGCATTACGGTTATTTAACCTTA
1 CAGGGGCATTACGGTCATTTTACCCTA
* ** * *
20477379 CAGGGGGATTTTGATCATTTAACCCTA
1 CAGGGGCATTACGGTCATTTTACCCTA
* *
20477406 TA-AGGCATTACGGTCATTTTACCCTA
1 CAGGGGCATTACGGTCATTTTACCCTA
* * *
20477432 TAAGGACATTACGGTCATTTTACCCTA
1 CAGGGGCATTACGGTCATTTTACCCTA
*
20477459 CAGGGGCATTACGATCATTTTACCCTA
1 CAGGGGCATTACGGTCATTTTACCCTA
* * * * *
20477486 CAGGGCCATTATGATCATTTTATCGTA
1 CAGGGGCATTACGGTCATTTTACCCTA
20477513 CAGGGGCATTACGGTCATTTTACCCTA
1 CAGGGGCATTACGGTCATTTTACCCTA
*** *
20477540 CAAAAGCATTACAGTCATTTTACCCTA
1 CAGGGGCATTACGGTCATTTTACCCTA
* **
20477567 TAGGGGCATTACAATCATTTTACCCTA
1 CAGGGGCATTACGGTCATTTTACCCTA
* *
20477594 TAGGGGCATTATGGTCATTTTACCCTA
1 CAGGGGCATTACGGTCATTTTACCCTA
* *
20477621 CAGGGGCATTACAGTCATTTTACCCTG
1 CAGGGGCATTACGGTCATTTTACCCTA
* * *
20477648 CAGGGGCATTACAGTCATATTATCCTA
1 CAGGGGCATTACGGTCATTTTACCCTA
* * * *
20477675 CAGGAGTATTATGATCATTTTAC
1 CAGGGGCATTACGGTCATTTTAC
20477698 GGCCTAAGCC
Statistics
Matches: 264, Mismatches: 54, Indels: 2
0.82 0.17 0.01
Matches are distributed among these distances:
26 20 0.08
27 244 0.92
ACGTcount: A:0.27, C:0.22, G:0.18, T:0.33
Consensus pattern (27 bp):
CAGGGGCATTACGGTCATTTTACCCTA
Found at i:20480657 original size:22 final size:21
Alignment explanation
Indices: 20480604--20480663 Score: 59
Period size: 22 Copynumber: 2.7 Consensus size: 21
20480594 GCCAGTAACT
20480604 AGAATGGCTAAGAGCCGTAAAC
1 AGAATGGCTAA-AGCCGTAAAC
* *
20480626 AGGATAGCTATAAGCTC-TAAAC
1 AGAATGGCTA-AAGC-CGTAAAC
20480648 AGAATGGCTACAAGCC
1 AGAATGGCTA-AAGCC
20480664 ATCAGTAGTA
Statistics
Matches: 31, Mismatches: 5, Indels: 5
0.76 0.12 0.12
Matches are distributed among these distances:
21 1 0.03
22 28 0.90
23 2 0.06
ACGTcount: A:0.40, C:0.20, G:0.23, T:0.17
Consensus pattern (21 bp):
AGAATGGCTAAAGCCGTAAAC
Found at i:20480701 original size:32 final size:32
Alignment explanation
Indices: 20480660--20480767 Score: 123
Period size: 32 Copynumber: 3.4 Consensus size: 32
20480650 AATGGCTACA
20480660 AGCCATCAGTAGTAGTGATATGATCGACACAC
1 AGCCATCAGTAGTAGTGATATGATCGACACAC
** *
20480692 AGCCATCAGTA--ACGACAATATGATC-AGCACAA
1 AGCCATCAGTAGTA-G-TGATATGATCGA-CACAC
* *
20480724 AGCCATCAGTAGTAGTGATATGACCGGCACAC
1 AGCCATCAGTAGTAGTGATATGATCGACACAC
20480756 AGCCATCAGTAG
1 AGCCATCAGTAG
20480768 CATCGCAGCA
Statistics
Matches: 62, Mismatches: 8, Indels: 12
0.76 0.10 0.15
Matches are distributed among these distances:
30 1 0.02
31 2 0.03
32 57 0.92
33 1 0.02
34 1 0.02
ACGTcount: A:0.36, C:0.24, G:0.21, T:0.19
Consensus pattern (32 bp):
AGCCATCAGTAGTAGTGATATGATCGACACAC
Found at i:20480798 original size:26 final size:26
Alignment explanation
Indices: 20480769--20480822 Score: 81
Period size: 26 Copynumber: 2.1 Consensus size: 26
20480759 CATCAGTAGC
* *
20480769 ATCGCAGCAAAGCTGCCAGTAACAGT
1 ATCGCAGCAAAGCTACCAGTAAAAGT
*
20480795 ATCGCAGCAAAGCTACCGGTAAAAGT
1 ATCGCAGCAAAGCTACCAGTAAAAGT
20480821 AT
1 AT
20480823 ATGTGACCAA
Statistics
Matches: 25, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
26 25 1.00
ACGTcount: A:0.37, C:0.24, G:0.22, T:0.17
Consensus pattern (26 bp):
ATCGCAGCAAAGCTACCAGTAAAAGT
Found at i:20480968 original size:24 final size:24
Alignment explanation
Indices: 20480941--20480995 Score: 65
Period size: 24 Copynumber: 2.3 Consensus size: 24
20480931 TGCTCAGAAT
*
20480941 CAGTCATACAAATCACAGACAAAC
1 CAGTCATACAAATCACAAACAAAC
** *
20480965 CAGTCATTTACATCACAAACAAAC
1 CAGTCATACAAATCACAAACAAAC
*
20480989 CAATCAT
1 CAGTCAT
20480996 TTACACTCGA
Statistics
Matches: 26, Mismatches: 5, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
24 26 1.00
ACGTcount: A:0.47, C:0.29, G:0.05, T:0.18
Consensus pattern (24 bp):
CAGTCATACAAATCACAAACAAAC
Found at i:20480996 original size:24 final size:24
Alignment explanation
Indices: 20480952--20481000 Score: 80
Period size: 24 Copynumber: 2.0 Consensus size: 24
20480942 AGTCATACAA
* *
20480952 ATCACAGACAAACCAGTCATTTAC
1 ATCACAAACAAACCAATCATTTAC
20480976 ATCACAAACAAACCAATCATTTAC
1 ATCACAAACAAACCAATCATTTAC
20481000 A
1 A
20481001 CTCGAGGGGC
Statistics
Matches: 23, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
24 23 1.00
ACGTcount: A:0.47, C:0.29, G:0.04, T:0.20
Consensus pattern (24 bp):
ATCACAAACAAACCAATCATTTAC
Found at i:20481103 original size:27 final size:27
Alignment explanation
Indices: 20481021--20481294 Score: 223
Period size: 27 Copynumber: 10.2 Consensus size: 27
20481011 AAAATACTCA
* * * *
20481021 TTTACCCTCTAGAGGCATTACGGTTAT
1 TTTACCCTATAGGGGCATTACGATCAT
* * * *
20481048 TTAACCTTACAGGGGTACTT-CGATC-T
1 TTTACCCTATAGGGGCA-TTACGATCAT
**
20481074 TTTAACCCTAT-GGGGCATTATAATCAT
1 TTT-ACCCTATAGGGGCATTACGATCAT
*
20481101 TTTACACTATAGGGGCATTACGATCAT
1 TTTACCCTATAGGGGCATTACGATCAT
* * * *
20481128 TTTACCTTACAAGGGCATTACGGTCAT
1 TTTACCCTATAGGGGCATTACGATCAT
*
20481155 TTTACCCTATAGGGGCATTAC-AGTCGT
1 TTTACCCTATAGGGGCATTACGA-TCAT
* * * * *
20481182 TTTATCGTACAGGGGCATTACTATTAT
1 TTTACCCTATAGGGGCATTACGATCAT
* *
20481209 TTTACCCTAGAAGGGCATTACGATCAT
1 TTTACCCTATAGGGGCATTACGATCAT
* * * *
20481236 TTTACCTTACAAGGGTATTACGATCAT
1 TTTACCCTATAGGGGCATTACGATCAT
* * *
20481263 ATTACCCTATAGGAGCATTACGGTCAT
1 TTTACCCTATAGGGGCATTACGATCAT
20481290 TTTAC
1 TTTAC
20481295 AGCCCAAGCC
Statistics
Matches: 191, Mismatches: 49, Indels: 14
0.75 0.19 0.06
Matches are distributed among these distances:
25 2 0.01
26 17 0.09
27 169 0.88
28 3 0.02
ACGTcount: A:0.27, C:0.20, G:0.18, T:0.35
Consensus pattern (27 bp):
TTTACCCTATAGGGGCATTACGATCAT
Found at i:20481146 original size:54 final size:54
Alignment explanation
Indices: 20481086--20481294 Score: 258
Period size: 54 Copynumber: 3.9 Consensus size: 54
20481076 TAACCCTATG
** *
20481086 GGGCATTATAATCATTTTACACTATAGGGGCATTACGATCATTTTACCTTACAA
1 GGGCATTACGATCATTTTACCCTATAGGGGCATTACGATCATTTTACCTTACAA
* * * * *
20481140 GGGCATTACGGTCATTTTACCCTATAGGGGCATTAC-AGTCGTTTTATCGTACAG
1 GGGCATTACGATCATTTTACCCTATAGGGGCATTACGA-TCATTTTACCTTACAA
* * * *
20481194 GGGCATTACTATTATTTTACCCTAGAAGGGCATTACGATCATTTTACCTTACAA
1 GGGCATTACGATCATTTTACCCTATAGGGGCATTACGATCATTTTACCTTACAA
* * * *
20481248 GGGTATTACGATCATATTACCCTATAGGAGCATTACGGTCATTTTAC
1 GGGCATTACGATCATTTTACCCTATAGGGGCATTACGATCATTTTAC
20481295 AGCCCAAGCC
Statistics
Matches: 128, Mismatches: 25, Indels: 4
0.82 0.16 0.03
Matches are distributed among these distances:
53 1 0.01
54 126 0.98
55 1 0.01
ACGTcount: A:0.28, C:0.20, G:0.18, T:0.34
Consensus pattern (54 bp):
GGGCATTACGATCATTTTACCCTATAGGGGCATTACGATCATTTTACCTTACAA
Found at i:20481225 original size:108 final size:108
Alignment explanation
Indices: 20481085--20481293 Score: 312
Period size: 108 Copynumber: 1.9 Consensus size: 108
20481075 TTAACCCTAT
* *
20481085 GGGGCATTATAATCATTTTACACTATAGGGGCATTACGATCATTTTACCTTACAAGGGCATTACG
1 GGGGCATTATAATCATTTTACACTAGAAGGGCATTACGATCATTTTACCTTACAAGGGCATTACG
* * * *
20481150 GTCATTTTACCCTATAGGGGCATTACAGTCGTTTTATCGTACA
66 ATCATATTACCCTATAGGAGCATTACAGTCATTTTATCGTACA
* * *
20481193 GGGGCATTACT-ATTATTTTACCCTAGAAGGGCATTACGATCATTTTACCTTACAAGGGTATTAC
1 GGGGCATTA-TAATCATTTTACACTAGAAGGGCATTACGATCATTTTACCTTACAAGGGCATTAC
*
20481257 GATCATATTACCCTATAGGAGCATTACGGTCATTTTA
65 GATCATATTACCCTATAGGAGCATTACAGTCATTTTA
20481294 CAGCCCAAGC
Statistics
Matches: 90, Mismatches: 10, Indels: 2
0.88 0.10 0.02
Matches are distributed among these distances:
108 89 0.99
109 1 0.01
ACGTcount: A:0.28, C:0.19, G:0.19, T:0.34
Consensus pattern (108 bp):
GGGGCATTATAATCATTTTACACTAGAAGGGCATTACGATCATTTTACCTTACAAGGGCATTACG
ATCATATTACCCTATAGGAGCATTACAGTCATTTTATCGTACA
Found at i:20483172 original size:15 final size:15
Alignment explanation
Indices: 20483152--20483187 Score: 54
Period size: 15 Copynumber: 2.4 Consensus size: 15
20483142 GGAATGAATG
20483152 GTCTTTGATTGTGGT
1 GTCTTTGATTGTGGT
*
20483167 GTCTTTGGTTGTGGT
1 GTCTTTGATTGTGGT
*
20483182 GCCTTT
1 GTCTTT
20483188 AAATGGCATA
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
15 19 1.00
ACGTcount: A:0.03, C:0.11, G:0.33, T:0.53
Consensus pattern (15 bp):
GTCTTTGATTGTGGT
Found at i:20494315 original size:39 final size:39
Alignment explanation
Indices: 20494256--20494338 Score: 148
Period size: 39 Copynumber: 2.1 Consensus size: 39
20494246 CTTTCTTGGT
* *
20494256 GATAAGAATATTCTCCCAGTTATTGTCTCTGCAACACTG
1 GATATGAATATTCTCCCAGTTATTGTCTCTACAACACTG
20494295 GATATGAATATTCTCCCAGTTATTGTCTCTACAACACTG
1 GATATGAATATTCTCCCAGTTATTGTCTCTACAACACTG
20494334 GATAT
1 GATAT
20494339 AACTCAAGAA
Statistics
Matches: 42, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
39 42 1.00
ACGTcount: A:0.29, C:0.22, G:0.14, T:0.35
Consensus pattern (39 bp):
GATATGAATATTCTCCCAGTTATTGTCTCTACAACACTG
Found at i:20495958 original size:15 final size:15
Alignment explanation
Indices: 20495938--20495967 Score: 60
Period size: 15 Copynumber: 2.0 Consensus size: 15
20495928 TGAACGAATC
20495938 GTATTTATTCAAGGT
1 GTATTTATTCAAGGT
20495953 GTATTTATTCAAGGT
1 GTATTTATTCAAGGT
20495968 ATGCAAAGAC
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.27, C:0.07, G:0.20, T:0.47
Consensus pattern (15 bp):
GTATTTATTCAAGGT
Found at i:20501611 original size:12 final size:12
Alignment explanation
Indices: 20501594--20501618 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
20501584 CTGTAGGTTT
20501594 ACACGGCCTAGC
1 ACACGGCCTAGC
20501606 ACACGGCCTAGC
1 ACACGGCCTAGC
20501618 A
1 A
20501619 AGCAATCCTA
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:0.28, C:0.40, G:0.24, T:0.08
Consensus pattern (12 bp):
ACACGGCCTAGC
Found at i:20503246 original size:49 final size:52
Alignment explanation
Indices: 20503126--20503316 Score: 176
Period size: 49 Copynumber: 3.7 Consensus size: 52
20503116 GTAAAGAGAC
* * *
20503126 CCCATGTAAGACCATGTATGGGACATGGCATTGGCATCATTGAGATTATGAGAGGT
1 CCCACGTAAGACCATGTCTGGGACATGGCATTGGCACCA-T-AG--TATGAGAGGT
* *
20503182 CCCATGTAAGACCATGTCTGGGACATGGCGTTGGCACCA-AG-ATGAG-GGT
1 CCCACGTAAGACCATGTCTGGGACATGGCATTGGCACCATAGTATGAGAGGT
* * * * **
20503231 CCCCCGTAAGACCATGTCTGGGACATGGCCTGGGCACC-GA-TATGAGAACT
1 CCCACGTAAGACCATGTCTGGGACATGGCATTGGCACCATAGTATGAGAGGT
* * * *
20503281 CCCATGTAAGACCATATCTGAGATATGGCATTGGCA
1 CCCACGTAAGACCATGTCTGGGACATGGCATTGGCA
20503317 GTACAAGAAA
Statistics
Matches: 116, Mismatches: 16, Indels: 12
0.81 0.11 0.08
Matches are distributed among these distances:
49 43 0.37
50 35 0.30
53 2 0.02
56 36 0.31
ACGTcount: A:0.27, C:0.23, G:0.28, T:0.23
Consensus pattern (52 bp):
CCCACGTAAGACCATGTCTGGGACATGGCATTGGCACCATAGTATGAGAGGT
Found at i:20507881 original size:33 final size:33
Alignment explanation
Indices: 20507842--20508124 Score: 136
Period size: 33 Copynumber: 8.6 Consensus size: 33
20507832 ATGATACAGT
20507842 GGAATCAGCACTTAGCAACCACCAATGAATCGG
1 GGAATCAGCACTTAGCAACCACCAATGAATCGG
* * * *
20507875 AGAATCAACACTTAGAAACC-CC--T---TGGG
1 GGAATCAGCACTTAGCAACCACCAATGAATCGG
* *
20507902 GGAATCAGCACTTAGCAACCCCCTTCACATTTAAAATACGG
1 GGAATCAGCACTTAGCAA-CCAC--CA-A--T-GAAT-CGG
* * *
20507943 TGGAATCAGCACTTAGAAACCACCAATGAATAGA
1 -GGAATCAGCACTTAGCAACCACCAATGAATCGG
*
20507977 GGAATCAGCACTTAGCAACC-CC--T---TGGG
1 GGAATCAGCACTTAGCAACCACCAATGAATCGG
* *
20508004 GGAATCAGCACTTAGCAACCCCCTTCACATTTAAAATACGG
1 GGAATCAGCACTTAGCAA-CCAC--CA-A--T-GAAT-CGG
* *
20508045 TGGAATCAACACTTAGCAACCACCAATGAATTGG
1 -GGAATCAGCACTTAGCAACCACCAATGAATCGG
*
20508079 GGAATCAACACTTAGCAACC-CC--T---T-GG
1 GGAATCAGCACTTAGCAACCACCAATGAATCGG
20508105 GGAATCAGCACTTAGCAACC
1 GGAATCAGCACTTAGCAACC
20508125 CCCTTTATAT
Statistics
Matches: 198, Mismatches: 22, Indels: 67
0.69 0.08 0.23
Matches are distributed among these distances:
26 21 0.11
27 39 0.20
28 4 0.02
29 2 0.01
30 3 0.02
31 2 0.01
32 6 0.03
33 56 0.28
34 3 0.02
35 6 0.03
36 4 0.02
38 2 0.01
39 4 0.02
40 2 0.01
41 10 0.05
42 34 0.17
ACGTcount: A:0.35, C:0.27, G:0.18, T:0.19
Consensus pattern (33 bp):
GGAATCAGCACTTAGCAACCACCAATGAATCGG
Found at i:20507982 original size:102 final size:101
Alignment explanation
Indices: 20507797--20508129 Score: 533
Period size: 102 Copynumber: 3.3 Consensus size: 101
20507787 CCAGTGATTC
* * * *
20507797 GGGGAATCAGCACTTAGCAACCCCTTTCACATTCAATGATACAGTGGAATCAGCACTTAGCAACC
1 GGGGAATCAGCACTTAGCAACCCCCTTCACATTTAA-AATACGGTGGAATCAGCACTTAGCAACC
* *
20507862 ACCAATGAATCGGAGAATCAACACTTAGAAACCCCTTG
65 ACCAATGAATAGG-GAATCAACACTTAGCAACCCCTTG
*
20507900 GGGGAATCAGCACTTAGCAACCCCCTTCACATTTAAAATACGGTGGAATCAGCACTTAGAAACCA
1 GGGGAATCAGCACTTAGCAACCCCCTTCACATTTAAAATACGGTGGAATCAGCACTTAGCAACCA
*
20507965 CCAATGAATAGAGGAATCAGCACTTAGCAACCCCTTG
66 CCAATGAATAG-GGAATCAACACTTAGCAACCCCTTG
*
20508002 GGGGAATCAGCACTTAGCAACCCCCTTCACATTTAAAATACGGTGGAATCAACACTTAGCAACCA
1 GGGGAATCAGCACTTAGCAACCCCCTTCACATTTAAAATACGGTGGAATCAGCACTTAGCAACCA
*
20508067 CCAATGAATTGGGGAATCAACACTTAGCAACCCCTT-
66 CCAATGAA-TAGGGAATCAACACTTAGCAACCCCTTG
20508103 GGGGAATCAGCACTTAGCAACCCCCTT
1 GGGGAATCAGCACTTAGCAACCCCCTT
20508130 TATATTCAAA
Statistics
Matches: 216, Mismatches: 12, Indels: 6
0.92 0.05 0.03
Matches are distributed among these distances:
101 27 0.12
102 152 0.70
103 37 0.17
ACGTcount: A:0.34, C:0.28, G:0.18, T:0.20
Consensus pattern (101 bp):
GGGGAATCAGCACTTAGCAACCCCCTTCACATTTAAAATACGGTGGAATCAGCACTTAGCAACCA
CCAATGAATAGGGAATCAACACTTAGCAACCCCTTG
Found at i:20508104 original size:26 final size:26
Alignment explanation
Indices: 20508075--20508126 Score: 95
Period size: 26 Copynumber: 2.0 Consensus size: 26
20508065 CACCAATGAA
20508075 TTGGGGAATCAACACTTAGCAACCCC
1 TTGGGGAATCAACACTTAGCAACCCC
*
20508101 TTGGGGAATCAGCACTTAGCAACCCC
1 TTGGGGAATCAACACTTAGCAACCCC
20508127 CTTTATATTC
Statistics
Matches: 25, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
26 25 1.00
ACGTcount: A:0.29, C:0.31, G:0.21, T:0.19
Consensus pattern (26 bp):
TTGGGGAATCAACACTTAGCAACCCC
Found at i:20508228 original size:51 final size:51
Alignment explanation
Indices: 20508152--20508281 Score: 215
Period size: 51 Copynumber: 2.5 Consensus size: 51
20508142 TACCGGTTCA
* *
20508152 CATAGTAGCCTGGACATGGTACTACACACGTGATCGAAGCTATCCAGTATG
1 CATAGTAGCCTGCACATAGTACTACACACGTGATCGAAGCTATCCAGTATG
**
20508203 CATAGTAGCCTGCACATAGTACTACACACGTGATCGAAGCTATCTGGTATG
1 CATAGTAGCCTGCACATAGTACTACACACGTGATCGAAGCTATCCAGTATG
*
20508254 CATAATAGCCTGCACATAGTACTACACA
1 CATAGTAGCCTGCACATAGTACTACACA
20508282 TGCGACCTAT
Statistics
Matches: 74, Mismatches: 5, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
51 74 1.00
ACGTcount: A:0.32, C:0.25, G:0.20, T:0.24
Consensus pattern (51 bp):
CATAGTAGCCTGCACATAGTACTACACACGTGATCGAAGCTATCCAGTATG
Found at i:20515041 original size:376 final size:375
Alignment explanation
Indices: 20514346--20515104 Score: 1446
Period size: 376 Copynumber: 2.0 Consensus size: 375
20514336 AGGGTCATAT
20514346 GTTAGTGTCTGAATATGAACGAGAATTTGTTCGATTAAGTAAATATGCTCAAGAGTGCATTTTGA
1 GTTAGTGTCTGAATATGAACGAGAATTTGTTCGATTAAGTAAATATGCTCAAGAGTGCATTTTGA
20514411 CTGAGACTGCAATGTGTAAACGATTTGAAGATGGATTAAATGAAGATATAAAGCTATTAGTCGGG
66 CTGAGACTGCAATGTGTAAACGATTTGAAGATGGATTAAATGAAGATATAAAGCTATTAGTCGGG
* *
20514476 ATCCTTGAGTTGAAAGAAATTATTGTACTAGTTGATCGAGCACATAAAGGCGAAGAGCTGAGTAA
131 ATCCTTGAGTTGAAAGAAATTATTGTACTAGTTGATCGAGCACATAAAGCCGAAGAGCTAAGTAA
20514541 AAAGAAAAGACACGCTGAATTTGAAGCTAAAGATTTGAGAAAGAGATTGACGAGAAAGTCATATC
196 AAAGAAAAGACACGCTGAATTTGAAGCTAAAGATTTGAGAAAGAGATTGACGAGAAAGTCATATC
*
20514606 AGTCAACATCGAAAAAATCTAAAGAACATCACTACCGTTCTACTACTTCTGTGGGAGATTCTAAT
261 AGTCAACATCGAAAAAATCTAAAGAACATCACTACCGTTCTACTACTTCTGTAGGAGATTCTAAT
20514671 AGAGATAGAGATGCGAGAGGCTTGAATCCTAAACCCCAGGCTACATCTGTA
326 AGAGATAGAGATGCGAGAGGCTTGAATCCTAAA-CCCAGGCTACATCTGTA
20514722 GTTAGTGTCTGAATATGAACGAGAATTTGTTCGATTAAGTAAATATGCTCAAGAGTGCATTTTGA
1 GTTAGTGTCTGAATATGAACGAGAATTTGTTCGATTAAGTAAATATGCTCAAGAGTGCATTTTGA
20514787 CTGAGACTGCAATGTGTAAACGATTTGAAGATGGATTAAATGAAGATATAAAGCTATTAGTCGGG
66 CTGAGACTGCAATGTGTAAACGATTTGAAGATGGATTAAATGAAGATATAAAGCTATTAGTCGGG
**
20514852 ATCCTTGAGTTGAAAGAAATTATTGTACTAGTTGATCGAGCGTATAAAGCCGAAGAGCTAAGTAA
131 ATCCTTGAGTTGAAAGAAATTATTGTACTAGTTGATCGAGCACATAAAGCCGAAGAGCTAAGTAA
*
20514917 AAAGAAAAGACACGCTGAATTTGAAGCTAAAGATTTTAGAAAGAGATTGACGAGAAAGTCATATC
196 AAAGAAAAGACACGCTGAATTTGAAGCTAAAGATTTGAGAAAGAGATTGACGAGAAAGTCATATC
20514982 AGTCAACATCGAAAAAATCTAAAGAACATCACTACCGTTCTACTACTTCTGTAGGAGATTCTAAT
261 AGTCAACATCGAAAAAATCTAAAGAACATCACTACCGTTCTACTACTTCTGTAGGAGATTCTAAT
20515047 AGAGATAGAGATGCGAGAGGCTTGAATCCTAAACCCAGGCTACATCTGTA
326 AGAGATAGAGATGCGAGAGGCTTGAATCCTAAACCCAGGCTACATCTGTA
*
20515097 GTGAGTGT
1 GTTAGTGT
20515105 GTTTAGTGTT
Statistics
Matches: 376, Mismatches: 7, Indels: 1
0.98 0.02 0.00
Matches are distributed among these distances:
375 24 0.06
376 352 0.94
ACGTcount: A:0.37, C:0.14, G:0.23, T:0.27
Consensus pattern (375 bp):
GTTAGTGTCTGAATATGAACGAGAATTTGTTCGATTAAGTAAATATGCTCAAGAGTGCATTTTGA
CTGAGACTGCAATGTGTAAACGATTTGAAGATGGATTAAATGAAGATATAAAGCTATTAGTCGGG
ATCCTTGAGTTGAAAGAAATTATTGTACTAGTTGATCGAGCACATAAAGCCGAAGAGCTAAGTAA
AAAGAAAAGACACGCTGAATTTGAAGCTAAAGATTTGAGAAAGAGATTGACGAGAAAGTCATATC
AGTCAACATCGAAAAAATCTAAAGAACATCACTACCGTTCTACTACTTCTGTAGGAGATTCTAAT
AGAGATAGAGATGCGAGAGGCTTGAATCCTAAACCCAGGCTACATCTGTA
Found at i:20521525 original size:25 final size:25
Alignment explanation
Indices: 20521497--20521552 Score: 67
Period size: 25 Copynumber: 2.2 Consensus size: 25
20521487 GTTATCGATT
* *
20521497 TCAGCTCTTCTAAGCTTACCGATAG
1 TCAGCTCGTATAAGCTTACCGATAG
* * *
20521522 TCAGCTCGTATGAGCTTACCGTTAT
1 TCAGCTCGTATAAGCTTACCGATAG
20521547 TCAGCT
1 TCAGCT
20521553 TGGAGGAGCT
Statistics
Matches: 26, Mismatches: 5, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
25 26 1.00
ACGTcount: A:0.21, C:0.27, G:0.18, T:0.34
Consensus pattern (25 bp):
TCAGCTCGTATAAGCTTACCGATAG
Found at i:20521561 original size:25 final size:25
Alignment explanation
Indices: 20521509--20521565 Score: 69
Period size: 25 Copynumber: 2.3 Consensus size: 25
20521499 AGCTCTTCTA
* *
20521509 AGCTTACCGATAGTCAGCTCGTATG
1 AGCTTACCGATAGTCAGCTCGGAGG
* * *
20521534 AGCTTACCGTTATTCAGCTTGGAGG
1 AGCTTACCGATAGTCAGCTCGGAGG
20521559 AGCTTAC
1 AGCTTAC
20521566 ACTTTACAGC
Statistics
Matches: 27, Mismatches: 5, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
25 27 1.00
ACGTcount: A:0.23, C:0.23, G:0.25, T:0.30
Consensus pattern (25 bp):
AGCTTACCGATAGTCAGCTCGGAGG
Found at i:20532616 original size:14 final size:15
Alignment explanation
Indices: 20532593--20532626 Score: 52
Period size: 14 Copynumber: 2.3 Consensus size: 15
20532583 TAGTCAAAAA
20532593 AAATTAATTATTATG
1 AAATTAATTATTATG
20532608 AAATT-ATTATTATG
1 AAATTAATTATTATG
*
20532622 TAATT
1 AAATT
20532627 CTATTTTACT
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
14 13 0.72
15 5 0.28
ACGTcount: A:0.44, C:0.00, G:0.06, T:0.50
Consensus pattern (15 bp):
AAATTAATTATTATG
Found at i:20534933 original size:17 final size:17
Alignment explanation
Indices: 20534911--20534957 Score: 60
Period size: 16 Copynumber: 2.8 Consensus size: 17
20534901 GTTAGTGAAC
*
20534911 ATTGTCGTTGCATTTTT
1 ATTGTCATTGCATTTTT
20534928 ATTGTCATTGCA-TTTT
1 ATTGTCATTGCATTTTT
* *
20534944 AATGTCACTGCATT
1 ATTGTCATTGCATT
20534958 GGGGACAATG
Statistics
Matches: 26, Mismatches: 3, Indels: 2
0.84 0.10 0.06
Matches are distributed among these distances:
16 14 0.54
17 12 0.46
ACGTcount: A:0.19, C:0.15, G:0.15, T:0.51
Consensus pattern (17 bp):
ATTGTCATTGCATTTTT
Found at i:20540913 original size:17 final size:17
Alignment explanation
Indices: 20540891--20540923 Score: 57
Period size: 17 Copynumber: 1.9 Consensus size: 17
20540881 GACCATGTGG
20540891 CCAGGCCGTGTGACTCC
1 CCAGGCCGTGTGACTCC
*
20540908 CCAGGCTGTGTGACTC
1 CCAGGCCGTGTGACTC
20540924 ACATGGCTAA
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
17 15 1.00
ACGTcount: A:0.12, C:0.36, G:0.30, T:0.21
Consensus pattern (17 bp):
CCAGGCCGTGTGACTCC
Found at i:20543249 original size:138 final size:137
Alignment explanation
Indices: 20542993--20543251 Score: 324
Period size: 138 Copynumber: 1.9 Consensus size: 137
20542983 GCAATAAATG
* *
20542993 GGTCTGCTTACACAAGCTGACGGTTGAAATGTAGCTACACGATGCCGCTCACACAAGTTGATGAG
1 GGTCTGCTCACACAAGCTGACGGTTGAAATGTAGCTACACGATACCGCTCACACAAGTTGATGAG
* ** * * *
20543058 TATTTGTAAAAAATGTTAGAACTCAACCATCAATAGGACATTCAGTACTAGCACCCTGAACATGG
66 TATCTACAAAAAATGTTAGAACTCAACCATCAATAGAACATTCAGGACCAGCACCCTGAACATGG
20543123 TAACCTA
131 TAACCTA
* * *
20543130 GGTCTGCTCACACAAGTTGACGGTTGGAATGTAAGCTACTA-GATACTGCTCACACAAGTTGATG
1 GGTCTGCTCACACAAGCTGACGGTTGAAATGT-AGCTAC-ACGATACCGCTCACACAAGTTGATG
* * * ** *
20543194 AGTATCTACAAAAAAT-TTCGGACCTCAGCCATCGGTAGAACATTTAGGACCAGCACCC
64 AGTATCTACAAAAAATGTT-AGAACTCAACCATCAATAGAACATTCAGGACCAGCACCC
20543252 AAAACATGAA
Statistics
Matches: 102, Mismatches: 17, Indels: 5
0.82 0.14 0.04
Matches are distributed among these distances:
137 31 0.30
138 70 0.69
139 1 0.01
ACGTcount: A:0.32, C:0.23, G:0.20, T:0.24
Consensus pattern (137 bp):
GGTCTGCTCACACAAGCTGACGGTTGAAATGTAGCTACACGATACCGCTCACACAAGTTGATGAG
TATCTACAAAAAATGTTAGAACTCAACCATCAATAGAACATTCAGGACCAGCACCCTGAACATGG
TAACCTA
Found at i:20549583 original size:4 final size:4
Alignment explanation
Indices: 20549574--20549603 Score: 60
Period size: 4 Copynumber: 7.5 Consensus size: 4
20549564 TGATTTCTCA
20549574 TTAT TTAT TTAT TTAT TTAT TTAT TTAT TT
1 TTAT TTAT TTAT TTAT TTAT TTAT TTAT TT
20549604 TCTTTTTATT
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 26 1.00
ACGTcount: A:0.23, C:0.00, G:0.00, T:0.77
Consensus pattern (4 bp):
TTAT
Found at i:20551453 original size:20 final size:20
Alignment explanation
Indices: 20551417--20551455 Score: 60
Period size: 20 Copynumber: 1.9 Consensus size: 20
20551407 TCGCTTCTTC
**
20551417 TTTACTTACTTTCTTACTTG
1 TTTACTTACTTGATTACTTG
20551437 TTTACTTACTTGATTACTT
1 TTTACTTACTTGATTACTT
20551456 AGATAAATCA
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.18, C:0.18, G:0.05, T:0.59
Consensus pattern (20 bp):
TTTACTTACTTGATTACTTG
Found at i:20551729 original size:50 final size:50
Alignment explanation
Indices: 20551658--20551859 Score: 206
Period size: 50 Copynumber: 3.9 Consensus size: 50
20551648 GATAATAACA
* **
20551658 TGCCAAAGCCATGTCCCAGACATGGTCTTACATGGGAGTTCTCATATCGG
1 TGCCAACGCCATGTCCCAGACATGGTCTTACATGGGACCTCTCATATCGG
* * * ** *
20551708 TGCCCATGCCATGTCCTAGACATGGTCTTACGGGGGACCTCTCATCTCGG
1 TGCCAACGCCATGTCCCAGACATGGTCTTACATGGGACCTCTCATATCGG
* **
20551758 TGCCAACGCCATGTCCCAGACATGGTCTTACATGAGACCTCTCATAACCTCAA
1 TGCCAACGCCATGTCCCAGACATGGTCTTACATGGGACCTCTCAT-A--TCGG
* * * *
20551811 TAACGCCAATGTCATATCCTAGACATGGTCTTACATGGGACCTCTCATA
1 T---GCCAACGCCATGTCCCAGACATGGTCTTACATGGGACCTCTCATA
20551860 ACCTCAATAA
Statistics
Matches: 124, Mismatches: 22, Indels: 7
0.81 0.14 0.05
Matches are distributed among these distances:
50 81 0.65
53 3 0.02
55 1 0.01
56 39 0.31
ACGTcount: A:0.24, C:0.30, G:0.20, T:0.26
Consensus pattern (50 bp):
TGCCAACGCCATGTCCCAGACATGGTCTTACATGGGACCTCTCATATCGG
Found at i:20551904 original size:56 final size:56
Alignment explanation
Indices: 20551659--20551906 Score: 241
Period size: 56 Copynumber: 4.6 Consensus size: 56
20551649 ATAATAACAT
* * ** **
20551659 GCCAAAGCCATGTCCCAGACATGGTCTTACATGGGAGTTCTCAT-A--TCGGT---
1 GCCAATGCCATGTCCTAGACATGGTCTTACATGGGACCTCTCATAACCTCAATAAC
* ** **
20551709 GCCCATGCCATGTCCTAGACATGGTCTTACGGGGGACCTCTCAT---CTCGGT---
1 GCCAATGCCATGTCCTAGACATGGTCTTACATGGGACCTCTCATAACCTCAATAAC
* * *
20551759 GCCAACGCCATGTCCCAGACATGGTCTTACATGAGACCTCTCATAACCTCAATAAC
1 GCCAATGCCATGTCCTAGACATGGTCTTACATGGGACCTCTCATAACCTCAATAAC
* * *
20551815 GCCAATGTCATATCCTAGACATGGTCTTACATGGGACCTCTCATAACCTCAATAAT
1 GCCAATGCCATGTCCTAGACATGGTCTTACATGGGACCTCTCATAACCTCAATAAC
* *
20551871 TCCAATGCCATGTCCTAAACATGGTCTTACATGGGA
1 GCCAATGCCATGTCCTAGACATGGTCTTACATGGGA
20551907 TCTCATTCCT
Statistics
Matches: 166, Mismatches: 25, Indels: 8
0.83 0.13 0.04
Matches are distributed among these distances:
50 80 0.48
53 4 0.02
56 82 0.49
ACGTcount: A:0.26, C:0.29, G:0.19, T:0.26
Consensus pattern (56 bp):
GCCAATGCCATGTCCTAGACATGGTCTTACATGGGACCTCTCATAACCTCAATAAC
Found at i:20555894 original size:40 final size:40
Alignment explanation
Indices: 20555747--20555897 Score: 169
Period size: 40 Copynumber: 3.8 Consensus size: 40
20555737 TGCATATGCC
* * * *
20555747 TGCCCCTATTTGTACTTCGATGCC-CATAAATGAACATACA
1 TGCCCCTATTTGTACTTTGGTACCTC-TAAATGCACATACA
* * *
20555787 TGCCCTTATTTGTACTTTGGTACCCCTGAATGCACATACA
1 TGCCCCTATTTGTACTTTGGTACCTCTAAATGCACATACA
* * * *
20555827 TCCCCCTGTTTGTACTTTGGTACCTCTAAATGCCCATACG
1 TGCCCCTATTTGTACTTTGGTACCTCTAAATGCACATACA
* *
20555867 TGCCCCTATTTGTACTTTGGCAACTCTAAAT
1 TGCCCCTATTTGTACTTTGGTACCTCTAAAT
20555898 CAAATAGTAT
Statistics
Matches: 93, Mismatches: 17, Indels: 2
0.83 0.15 0.02
Matches are distributed among these distances:
40 92 0.99
41 1 0.01
ACGTcount: A:0.23, C:0.28, G:0.14, T:0.34
Consensus pattern (40 bp):
TGCCCCTATTTGTACTTTGGTACCTCTAAATGCACATACA
Found at i:20562460 original size:20 final size:20
Alignment explanation
Indices: 20562380--20562462 Score: 62
Period size: 20 Copynumber: 4.2 Consensus size: 20
20562370 ATAATTAGTG
* *
20562380 CTGAATGCACACATGTGCCC
1 CTGAATGCACATACGTGCCC
*
20562400 CTGAATGCACATACATGCCC
1 CTGAATGCACATACGTGCCC
* * * * *
20562420 CT-ATTTGTA-GTTCGGTACCC
1 CTGA-ATGCACATAC-GTGCCC
20562440 CTGAATGCACATACGTGCCC
1 CTGAATGCACATACGTGCCC
20562460 CTG
1 CTG
20562463 TTTGTACTCT
Statistics
Matches: 45, Mismatches: 14, Indels: 8
0.67 0.21 0.12
Matches are distributed among these distances:
19 3 0.07
20 39 0.87
21 3 0.07
ACGTcount: A:0.23, C:0.33, G:0.19, T:0.25
Consensus pattern (20 bp):
CTGAATGCACATACGTGCCC
Found at i:20562484 original size:40 final size:40
Alignment explanation
Indices: 20562398--20562485 Score: 115
Period size: 40 Copynumber: 2.2 Consensus size: 40
20562388 ACACATGTGC
* *
20562398 CCCTGAATGCACATACATGCCCCTATTTGTAGTTCGGTAC
1 CCCTGAATGCACATACATGCCCCTATTTGTACTTCGGTAA
* *
20562438 CCCTGAATGCACATACGTGCCCCTGTTTGTAC-TCTGGTAA
1 CCCTGAATGCACATACATGCCCCTATTTGTACTTC-GGTAA
*
20562478 CTCTGAAT
1 CCCTGAAT
20562486 CAAATAGTAT
Statistics
Matches: 42, Mismatches: 5, Indels: 2
0.86 0.10 0.04
Matches are distributed among these distances:
39 2 0.05
40 40 0.95
ACGTcount: A:0.22, C:0.30, G:0.18, T:0.31
Consensus pattern (40 bp):
CCCTGAATGCACATACATGCCCCTATTTGTACTTCGGTAA
Found at i:20578925 original size:31 final size:31
Alignment explanation
Indices: 20578890--20578948 Score: 84
Period size: 31 Copynumber: 1.9 Consensus size: 31
20578880 GAAAAAAAGA
20578890 AGAAACAGA-AGACGCAAATCGGCAGAAACTG
1 AGAAACAGAGAGA-GCAAATCGGCAGAAACTG
* *
20578921 AGAAATAGAGGGAGCAAATCGGCAGAAA
1 AGAAACAGAGAGAGCAAATCGGCAGAAA
20578949 AGAAAAGAAA
Statistics
Matches: 25, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
31 23 0.92
32 2 0.08
ACGTcount: A:0.49, C:0.15, G:0.29, T:0.07
Consensus pattern (31 bp):
AGAAACAGAGAGAGCAAATCGGCAGAAACTG
Found at i:20585881 original size:39 final size:39
Alignment explanation
Indices: 20585827--20585905 Score: 158
Period size: 39 Copynumber: 2.0 Consensus size: 39
20585817 AGCGGTGAAG
20585827 AATTTAGACTAATTTGATCTCTTTCCACCTCCTAAACTA
1 AATTTAGACTAATTTGATCTCTTTCCACCTCCTAAACTA
20585866 AATTTAGACTAATTTGATCTCTTTCCACCTCCTAAACTA
1 AATTTAGACTAATTTGATCTCTTTCCACCTCCTAAACTA
20585905 A
1 A
20585906 CCTATTGAAT
Statistics
Matches: 40, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
39 40 1.00
ACGTcount: A:0.32, C:0.25, G:0.05, T:0.38
Consensus pattern (39 bp):
AATTTAGACTAATTTGATCTCTTTCCACCTCCTAAACTA
Found at i:20590149 original size:121 final size:121
Alignment explanation
Indices: 20589935--20590176 Score: 475
Period size: 121 Copynumber: 2.0 Consensus size: 121
20589925 AGAAGCTCAC
*
20589935 ACATCCCTGAATTCCTGGTCACGGTAGTGGTAATGGCCCCTCATCATGCAAACCACTCTAGCTGG
1 ACATCCCTGAATTCCTGGTCACGGTAGTGGTAATGGCCCCTCATCATGCAAACCACTCGAGCTGG
20590000 CAATCTAGAGGCAAGTACACAGTTTCTTTTGTCCTATTTGTTCAAATAATAGTATT
66 CAATCTAGAGGCAAGTACACAGTTTCTTTTGTCCTATTTGTTCAAATAATAGTATT
20590056 ACATCCCTGAATTCCTGGTCACGGTAGTGGTAATGGCCCCTCATCATGCAAACCACTCGAGCTGG
1 ACATCCCTGAATTCCTGGTCACGGTAGTGGTAATGGCCCCTCATCATGCAAACCACTCGAGCTGG
20590121 CAATCTAGAGGCAAGTACACAGTTTCTTTTGTCCTATTTGTTCAAATAATAGTATT
66 CAATCTAGAGGCAAGTACACAGTTTCTTTTGTCCTATTTGTTCAAATAATAGTATT
20590177 TTTGAGCTCT
Statistics
Matches: 120, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
121 120 1.00
ACGTcount: A:0.26, C:0.24, G:0.19, T:0.31
Consensus pattern (121 bp):
ACATCCCTGAATTCCTGGTCACGGTAGTGGTAATGGCCCCTCATCATGCAAACCACTCGAGCTGG
CAATCTAGAGGCAAGTACACAGTTTCTTTTGTCCTATTTGTTCAAATAATAGTATT
Found at i:20592666 original size:18 final size:19
Alignment explanation
Indices: 20592643--20592686 Score: 56
Period size: 18 Copynumber: 2.3 Consensus size: 19
20592633 TTAAAGCTTT
20592643 ATTTTAATATTT-TTA-TAC
1 ATTTTAAT-TTTATTAGTAC
20592661 ATTTTAATTTTATTATGTAC
1 ATTTTAATTTTATTA-GTAC
20592681 ATTTTA
1 ATTTTA
20592687 TTTCTTTCAT
Statistics
Matches: 23, Mismatches: 0, Indels: 4
0.85 0.00 0.15
Matches are distributed among these distances:
17 3 0.13
18 11 0.48
20 9 0.39
ACGTcount: A:0.32, C:0.05, G:0.02, T:0.61
Consensus pattern (19 bp):
ATTTTAATTTTATTAGTAC
Found at i:20598889 original size:29 final size:29
Alignment explanation
Indices: 20598842--20599005 Score: 129
Period size: 29 Copynumber: 5.7 Consensus size: 29
20598832 GTTTGTCACC
* *
20598842 AGGCATTCCTT-TAATAGAGGTAGCCACAA
1 AGGCA-TCCTTATAACAGAGATAGCCACAA
20598871 AGGCATCCTTATAACAGAGATAGCCACAA
1 AGGCATCCTTATAACAGAGATAGCCACAA
*
20598900 AGGCATCCTTATAACAAAGATAG--ACAA
1 AGGCATCCTTATAACAGAGATAGCCACAA
* ** ** * *
20598927 AGACATTTTTATAGTAGAGATCGCCATAA
1 AGGCATCCTTATAACAGAGATAGCCACAA
* * ** *
20598956 ATGCTTTTTTATAACAGAGATCA-CCATAA
1 AGGCATCCTTATAACAGAGAT-AGCCACAA
* *
20598985 AGGCTTTCTTATAACAGAGAT
1 AGGCATCCTTATAACAGAGAT
20599006 CACCACCGAG
Statistics
Matches: 112, Mismatches: 19, Indels: 8
0.81 0.14 0.06
Matches are distributed among these distances:
27 20 0.18
28 5 0.04
29 87 0.78
ACGTcount: A:0.39, C:0.18, G:0.16, T:0.26
Consensus pattern (29 bp):
AGGCATCCTTATAACAGAGATAGCCACAA
Found at i:20599006 original size:29 final size:29
Alignment explanation
Indices: 20598865--20599025 Score: 123
Period size: 29 Copynumber: 5.6 Consensus size: 29
20598855 ATAGAGGTAG
* *
20598865 CCACAAAGGCATCCTTATAACAGAGAT-A
1 CCACAAAGGCTTTCTTATAACAGAGATCA
* * *
20598893 GCCACAAAGGCATCCTTATAACAAAGAT-A
1 -CCACAAAGGCTTTCTTATAACAGAGATCA
* * ** *
20598922 -GACAAAGACATTT-TTATAGTAGAGATCG
1 CCACAAAGGC-TTTCTTATAACAGAGATCA
* * *
20598950 CCATAAATGCTTTTTTATAACAGAGATCA
1 CCACAAAGGCTTTCTTATAACAGAGATCA
*
20598979 CCATAAAGGCTTTCTTATAACAGAGATCA
1 CCACAAAGGCTTTCTTATAACAGAGATCA
** *
20599008 CCACCGAGGGTTTCTTAT
1 CCACAAAGGCTTTCTTAT
20599026 GAAAACTGCT
Statistics
Matches: 106, Mismatches: 22, Indels: 8
0.78 0.16 0.06
Matches are distributed among these distances:
27 17 0.16
28 4 0.04
29 85 0.80
ACGTcount: A:0.38, C:0.20, G:0.16, T:0.26
Consensus pattern (29 bp):
CCACAAAGGCTTTCTTATAACAGAGATCA
Found at i:20599080 original size:29 final size:28
Alignment explanation
Indices: 20599048--20599124 Score: 81
Period size: 29 Copynumber: 2.8 Consensus size: 28
20599038 AAAGACACTT
20599048 TTTTAATAGAAATAGCCACAAAGGC-TCAC
1 TTTTAATAG-AATAGCCACAAAGGCATC-C
20599077 TTTTAACT-GAGATAGCCACAAAGGCATCC
1 TTTTAA-TAGA-ATAGCCACAAAGGCATCC
*
20599106 TTTCAA-AG-ATAGCCACAAA
1 TTTTAATAGAATAGCCACAAA
20599125 AGGTTCCATT
Statistics
Matches: 43, Mismatches: 1, Indels: 11
0.78 0.02 0.20
Matches are distributed among these distances:
26 11 0.26
28 2 0.05
29 27 0.63
30 3 0.07
ACGTcount: A:0.40, C:0.22, G:0.14, T:0.23
Consensus pattern (28 bp):
TTTTAATAGAATAGCCACAAAGGCATCC
Found at i:20599122 original size:26 final size:27
Alignment explanation
Indices: 20599059--20599124 Score: 82
Period size: 29 Copynumber: 2.4 Consensus size: 27
20599049 TTTAATAGAA
*
20599059 ATAGCCACAAAGGCTCACTTTTAACTGAG
1 ATAGCCACAAAGGCTCACTTTCAAC--AG
20599088 ATAGCCACAAAGGCATC-CTTTCAA-AG
1 ATAGCCACAAAGGC-TCACTTTCAACAG
20599114 ATAGCCACAAA
1 ATAGCCACAAA
20599125 AGGTTCCATT
Statistics
Matches: 35, Mismatches: 1, Indels: 5
0.85 0.02 0.12
Matches are distributed among these distances:
26 13 0.37
29 20 0.57
30 2 0.06
ACGTcount: A:0.39, C:0.26, G:0.15, T:0.20
Consensus pattern (27 bp):
ATAGCCACAAAGGCTCACTTTCAACAG
Found at i:20604774 original size:25 final size:25
Alignment explanation
Indices: 20604729--20604906 Score: 107
Period size: 25 Copynumber: 7.2 Consensus size: 25
20604719 AAGCTCATAC
* * *
20604729 GAGCCAGTAA-CGGGTAGCTCCGAA
1 GAGCCATTAATCGGGAAGCTCCAAA
* **
20604753 GAGCCATTAATCAGGAAGCTCCGGA
1 GAGCCATTAATCGGGAAGCTCCAAA
* * * *
20604778 TAGTCA-TATATCGGGAAG-TTCAAGC
1 GAGCCATTA-ATCGGGAAGCTCCAA-A
* *
20604803 GAGCCA-T-ATCGGGAAGCTCTAGA
1 GAGCCATTAATCGGGAAGCTCCAAA
*
20604826 GAGCCATTAATCAGGAAGCTCACAAA
1 GAGCCATTAATCGGGAAGCTC-CAAA
**
20604852 GAGCTTTTAATCGGGAAGCTCACAAA
1 GAGCCATTAATCGGGAAGCTC-CAAA
* * *
20604878 GAGCCA-TATATCGAGATGCTCAAAA
1 GAGCCATTA-ATCGGGAAGCTCCAAA
20604903 GAGC
1 GAGC
20604907 TGCGGTGTGC
Statistics
Matches: 118, Mismatches: 28, Indels: 15
0.73 0.17 0.09
Matches are distributed among these distances:
23 15 0.13
24 16 0.14
25 48 0.41
26 39 0.33
ACGTcount: A:0.34, C:0.21, G:0.26, T:0.19
Consensus pattern (25 bp):
GAGCCATTAATCGGGAAGCTCCAAA
Found at i:20604783 original size:73 final size:73
Alignment explanation
Indices: 20604706--20604846 Score: 189
Period size: 73 Copynumber: 1.9 Consensus size: 73
20604696 AACTCATAAA
*
20604706 AGTCATAT-TCAGGAAGCTCATA-CGAGCCAGTAACGGGTAGCTCCGA-AGAGCCATTAATCAGG
1 AGTCATATATCAGGAAGCTCA-AGCGAGCCA-TAACGGGAAGCT-CGAGAGAGCCATTAATCAGG
20604768 AAGCTCCGGAT
63 AAGCTCCGGAT
* * * *
20604779 AGTCATATATCGGGAAGTTCAAGCGAGCCATATCGGGAAGCTCTAGAGAGCCATTAATCAGGAAG
1 AGTCATATATCAGGAAGCTCAAGCGAGCCATAACGGGAAGCTCGAGAGAGCCATTAATCAGGAAG
20604844 CTC
66 CTC
20604847 ACAAAGAGCT
Statistics
Matches: 60, Mismatches: 5, Indels: 6
0.85 0.07 0.08
Matches are distributed among these distances:
72 2 0.03
73 41 0.68
74 17 0.28
ACGTcount: A:0.32, C:0.22, G:0.26, T:0.20
Consensus pattern (73 bp):
AGTCATATATCAGGAAGCTCAAGCGAGCCATAACGGGAAGCTCGAGAGAGCCATTAATCAGGAAG
CTCCGGAT
Found at i:20604815 original size:23 final size:23
Alignment explanation
Indices: 20604785--20604886 Score: 78
Period size: 26 Copynumber: 4.2 Consensus size: 23
20604775 GGATAGTCAT
* *
20604785 ATATCGGGAAGTTCAAGCGAGCC
1 ATATCGGGAAGCTCAAGAGAGCC
*
20604808 ATATCGGGAAGCTCTAGAGAGCC
1 ATATCGGGAAGCTCAAGAGAGCC
* * *
20604831 ATTAATCAGGAAGCTCACAAAGAGCTT
1 A-T-ATCGGGAAGCTCA-AGAGAGC-C
* *
20604858 TTAATCGGGAAGCTCACAAAGAGCC
1 AT-ATCGGGAAGCTCA-AGAGAGCC
20604883 ATAT
1 ATAT
20604887 ATCGAGATGC
Statistics
Matches: 64, Mismatches: 11, Indels: 7
0.78 0.13 0.09
Matches are distributed among these distances:
23 21 0.33
24 3 0.05
25 12 0.19
26 28 0.44
ACGTcount: A:0.35, C:0.21, G:0.25, T:0.20
Consensus pattern (23 bp):
ATATCGGGAAGCTCAAGAGAGCC
Found at i:20604861 original size:26 final size:26
Alignment explanation
Indices: 20604832--20604881 Score: 91
Period size: 26 Copynumber: 1.9 Consensus size: 26
20604822 TAGAGAGCCA
20604832 TTAATCAGGAAGCTCACAAAGAGCTT
1 TTAATCAGGAAGCTCACAAAGAGCTT
*
20604858 TTAATCGGGAAGCTCACAAAGAGC
1 TTAATCAGGAAGCTCACAAAGAGC
20604882 CATATATCGA
Statistics
Matches: 23, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
26 23 1.00
ACGTcount: A:0.38, C:0.20, G:0.22, T:0.20
Consensus pattern (26 bp):
TTAATCAGGAAGCTCACAAAGAGCTT
Found at i:20604890 original size:26 final size:26
Alignment explanation
Indices: 20604682--20604906 Score: 93
Period size: 25 Copynumber: 9.1 Consensus size: 26
20604672 AGCTTATCCG
* * *
20604682 GCCATATAGCGGGAAACTCATAAA-A
1 GCCATATATCGGGAAGCTCACAAAGA
* * * *
20604707 GTCATAT-TCAGGAAGCTCA-TACGA
1 GCCATATATCGGGAAGCTCACAAAGA
* *
20604731 GCCAGTA-A-CGGGTAGCTC-CGAAGA
1 GCCA-TATATCGGGAAGCTCACAAAGA
* ** *
20604755 GCCAT-TAATCAGGAAGCTC-CGGATA
1 GCCATAT-ATCGGGAAGCTCACAAAGA
* * **
20604780 GTCATATATCGGGAAGTTCA-AGCGA
1 GCCATATATCGGGAAGCTCACAAAGA
* *
20604805 GCC--ATATCGGGAAGCTC-TAGAGA
1 GCCATATATCGGGAAGCTCACAAAGA
*
20604828 GCCAT-TAATCAGGAAGCTCACAAAGA
1 GCCATAT-ATCGGGAAGCTCACAAAGA
* *
20604854 G-CTTTTAATCGGGAAGCTCACAAAGA
1 GCCATAT-ATCGGGAAGCTCACAAAGA
* *
20604880 GCCATATATCGAGATGCTCA-AAAGA
1 GCCATATATCGGGAAGCTCACAAAGA
20604905 GC
1 GC
20604907 TGCGGTGTGC
Statistics
Matches: 151, Mismatches: 33, Indels: 32
0.70 0.15 0.15
Matches are distributed among these distances:
23 22 0.15
24 30 0.20
25 58 0.38
26 38 0.25
27 3 0.02
ACGTcount: A:0.35, C:0.21, G:0.24, T:0.19
Consensus pattern (26 bp):
GCCATATATCGGGAAGCTCACAAAGA
Found at i:20606814 original size:25 final size:26
Alignment explanation
Indices: 20606762--20606819 Score: 66
Period size: 25 Copynumber: 2.3 Consensus size: 26
20606752 CATTATAATC
* * * *
20606762 AACCT-TTCACCTTTCATCTTCTTTT
1 AACCTCTTCACATTTCACCTCCTTAT
20606787 AA-CTCTTCACATTTCACCTCCTTAT
1 AACCTCTTCACATTTCACCTCCTTAT
20606812 AACCTCTT
1 AACCTCTT
20606820 TACTATTTAT
Statistics
Matches: 27, Mismatches: 4, Indels: 3
0.79 0.12 0.09
Matches are distributed among these distances:
24 2 0.07
25 20 0.74
26 5 0.19
ACGTcount: A:0.21, C:0.34, G:0.00, T:0.45
Consensus pattern (26 bp):
AACCTCTTCACATTTCACCTCCTTAT
Found at i:20614134 original size:18 final size:17
Alignment explanation
Indices: 20614098--20614136 Score: 51
Period size: 17 Copynumber: 2.2 Consensus size: 17
20614088 TTATTAGTTT
20614098 TTATCAAAAAAATTAAA
1 TTATCAAAAAAATTAAA
* *
20614115 TTATCTAAATAATATAAA
1 TTATCAAAAAAAT-TAAA
20614133 TTAT
1 TTAT
20614137 TTCAAATATG
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
17 11 0.58
18 8 0.42
ACGTcount: A:0.56, C:0.05, G:0.00, T:0.38
Consensus pattern (17 bp):
TTATCAAAAAAATTAAA
Done.