Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Chr13 ID=Chr13-JGI_221_v2.0
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: 58321163
ACGTcount: A:0.33, C:0.16, G:0.16, T:0.33
Warning! 747533 characters in sequence are not A, C, G, or T
File 57 of 199
Found at i:16751053 original size:134 final size:132
Alignment explanation
Indices: 16750809--16751429 Score: 531
Period size: 134 Copynumber: 4.7 Consensus size: 132
16750799 CAGTGAAAGC
* * * *
16750809 ACAAATCCTATCTCCATGAGGTTGCAGTGGAGCGGATTAAAGTTACAAGTCTTATCTCCCTGAAG
1 ACAAATCTTATCTCCCTGAAGTTGCAGTGGAGCAGATTAAAGTTACAAGTCTTATCTCCCTGAAG
* * * * * *
16750874 TTACAGTGGAACAGACTGAAG-AAAGCAAGTCTTAT-TCCCCTAAAGTTGCAGTAGG-GCAGACT
66 TTGCAGTGGAGCAGATTGAAGCCAA-TAA-TCCTATCT-CCCTAAAGTTGCAGT-GGAGCAGACT
*
16750936 GAAGAT
127 AAAGAT
* *
16750942 GACAAATCTTATCTCCTTGAAGTTGCAGTGGAGCGGATTAAAGTTACAAGTCTTATCTCCCTGAA
1 -ACAAATCTTATCTCCCTGAAGTTGCAGTGGAGCAGATTAAAGTTACAAGTCTTATCTCCCTGAA
* * *
16751007 GTTACAGTGGAGCAGATTGAAGCCAATAATCCTATCTCCCTAAAAGTTGCAGTGGAGCGGACTGA
65 GTTGCAGTGGAGCAGATTGAAGCCAATAATCCTATCTCCCT-AAAGTTGCAGTGGAGCAGACTAA
*
16751072 AGAA
129 AGAT
* * * * ** *
16751076 AGCAAGTCTTATC-CCCTTGAAGTTGCAGTGGGGCAGACTGAAGATGGCGAA-TCTCATCTCCCT
1 A-CAAATCTTATCTCCC-TGAAGTTGCAGTGGAGCAGATTAAAG-TTAC-AAGTCTTATCTCCCT
* ** * * * *
16751139 GAAGTTGCAGTGAAGCAGATCAAAGCCAATAATCCTATCTCCCTGAAGTTGCAGTGAAGCGGATT
62 GAAGTTGCAGTGGAGCAGATTGAAGCCAATAATCCTATCTCCCTAAAGTTGCAGTGGAGCAGACT
*
16751204 AAAGTT
127 AAAGAT
* * * * ** *
16751210 ACAAGTCTTATCTCCCTGAAGTTGCAGTGGAACAGACTGAAGAAAGCAAGTCTTATCCCCCTGAA
1 ACAAATCTTATCTCCCTGAAGTTGCAGTGGAGCAGATTAAAGTTA-CAAGTCTTATCTCCCTGAA
* * * * * * * * *
16751275 GTTGTAGTGGGGCAGACTAAAGATGGC-A-AATCTTATCTTCCTGAAGTTGCAGTGGAGCAGATT
65 GTTGCAGTGGAGCAGA-T--TGAAGCCAATAATCCTATCTCCCTAAAGTTGCAGTGGAGCAGACT
*
16751338 AAAGCT
127 AAAGAT
* * * * *
16751344 A-ATAATCCTATCTCCCTGAGGTTGCAGTGGAGCAGATTAAAGCTA-ATAATCCTATCTCCCTGA
1 ACA-AATCTTATCTCCCTGAAGTTGCAGTGGAGCAGATTAAAGTTACA-AGTCTTATCTCCCTGA
* *
16751407 GGTTGCAGTGGAGCAGACTGAAG
64 AGTTGCAGTGGAGCAGATTGAAG
16751430 ATAGCGAATC
Statistics
Matches: 406, Mismatches: 65, Indels: 36
0.80 0.13 0.07
Matches are distributed among these distances:
130 3 0.01
132 3 0.01
133 104 0.26
134 235 0.58
135 56 0.14
136 5 0.01
ACGTcount: A:0.31, C:0.20, G:0.24, T:0.25
Consensus pattern (132 bp):
ACAAATCTTATCTCCCTGAAGTTGCAGTGGAGCAGATTAAAGTTACAAGTCTTATCTCCCTGAAG
TTGCAGTGGAGCAGATTGAAGCCAATAATCCTATCTCCCTAAAGTTGCAGTGGAGCAGACTAAAG
AT
Found at i:16751286 original size:178 final size:178
Alignment explanation
Indices: 16750812--16751443 Score: 831
Period size: 178 Copynumber: 3.5 Consensus size: 178
16750802 TGAAAGCACA
* * * * * *
16750812 AATCCTATCTCCATGAGGTTGCAGTGGAGCGGATTAAAGTTACA-AGTCTTATCTCCCTGAAGTT
1 AATCCTATCTCCCTGAAGTTGCAGTGGAGCAGATTAAAGCTA-ATAATCCTATCTCCCTGAAGTT
* * * *
16750876 ACAGTGGAACAGACTGAAGAAAGCAAGTCTTATTCCCCTAAAGTTGCAGTAGGGCAGACTGAAGA
65 GCAGTGGAACAGACTGAAGAAAGCAAGTCTTATCCCCCTGAAGTTGCAGTGGGGCAGACTGAAGA
* * * *
16750941 TGACAAATCTTATCTCCTTGAAGTTGCAGTGGAGCGGATTAAAGTTACA-
130 TGGCAAATCTTATCTCCCTGAAGTTGCAGTGGAGCAGATTAAAGCTA-AT
* * * * * *
16750990 AGTCTTATCTCCCTGAAGTTACAGTGGAGCAGATTGAAGCCAATAATCCTATCTCCCTAAAAGTT
1 AATCCTATCTCCCTGAAGTTGCAGTGGAGCAGATTAAAGCTAATAATCCTATCTCCCT-GAAGTT
* * *
16751055 GCAGTGGAGCGGACTGAAGAAAGCAAGTCTTATCCCCTTGAAGTTGCAGTGGGGCAGACTGAAGA
65 GCAGTGGAACAGACTGAAGAAAGCAAGTCTTATCCCCCTGAAGTTGCAGTGGGGCAGACTGAAGA
* * * * *
16751120 TGGCGAATCTCATCTCCCTGAAGTTGCAGTGAAGCAGATCAAAGCCAAT
130 TGGCAAATCTTATCTCCCTGAAGTTGCAGTGGAGCAGATTAAAGCTAAT
* * * * *
16751169 AATCCTATCTCCCTGAAGTTGCAGTGAAGCGGATTAAAGTTACA-AGTCTTATCTCCCTGAAGTT
1 AATCCTATCTCCCTGAAGTTGCAGTGGAGCAGATTAAAGCTA-ATAATCCTATCTCCCTGAAGTT
* *
16751233 GCAGTGGAACAGACTGAAGAAAGCAAGTCTTATCCCCCTGAAGTTGTAGTGGGGCAGACTAAAGA
65 GCAGTGGAACAGACTGAAGAAAGCAAGTCTTATCCCCCTGAAGTTGCAGTGGGGCAGACTGAAGA
*
16751298 TGGCAAATCTTATCTTCCTGAAGTTGCAGTGGAGCAGATTAAAGCTAAT
130 TGGCAAATCTTATCTCCCTGAAGTTGCAGTGGAGCAGATTAAAGCTAAT
* *
16751347 AATCCTATCTCCCTGAGGTTGCAGTGGAGCAGATTAAAGCTAATAATCCTATCTCCCTGAGGTTG
1 AATCCTATCTCCCTGAAGTTGCAGTGGAGCAGATTAAAGCTAATAATCCTATCTCCCTGAAGTTG
* *
16751412 CAGTGGAGCAGACTGAAGATAGCGAA-TCTTAT
66 CAGTGGAACAGACTGAAGAAAGC-AAGTCTTAT
16751444 TTCCCTAGCG
Statistics
Matches: 389, Mismatches: 59, Indels: 12
0.85 0.13 0.03
Matches are distributed among these distances:
177 2 0.01
178 237 0.61
179 149 0.38
180 1 0.00
ACGTcount: A:0.31, C:0.20, G:0.24, T:0.26
Consensus pattern (178 bp):
AATCCTATCTCCCTGAAGTTGCAGTGGAGCAGATTAAAGCTAATAATCCTATCTCCCTGAAGTTG
CAGTGGAACAGACTGAAGAAAGCAAGTCTTATCCCCCTGAAGTTGCAGTGGGGCAGACTGAAGAT
GGCAAATCTTATCTCCCTGAAGTTGCAGTGGAGCAGATTAAAGCTAAT
Found at i:16751602 original size:45 final size:48
Alignment explanation
Indices: 16751551--16751645 Score: 115
Period size: 51 Copynumber: 2.0 Consensus size: 48
16751541 TCTCTTTGAA
*
16751551 GTTGCA-G-CAGAGCAGA-CTGAAGACAGCGAATCTTATTTCCCTAGT
1 GTTGCAGGACAGAGCAAAGCTGAAGACAGCGAATCTTATTTCCCTAGT
**
16751596 GTTGCAGTGGAACAGATTAAAGCTGAAGACAGCGAATCTTATTTCCCTAG
1 GTTGCA--GG-ACAGAGCAAAGCTGAAGACAGCGAATCTTATTTCCCTAG
16751646 CATTGCAGTA
Statistics
Matches: 41, Mismatches: 3, Indels: 6
0.82 0.06 0.12
Matches are distributed among these distances:
45 6 0.15
48 1 0.02
50 6 0.15
51 28 0.68
ACGTcount: A:0.31, C:0.20, G:0.24, T:0.25
Consensus pattern (48 bp):
GTTGCAGGACAGAGCAAAGCTGAAGACAGCGAATCTTATTTCCCTAGT
Found at i:16751612 original size:143 final size:143
Alignment explanation
Indices: 16751352--16751619 Score: 376
Period size: 143 Copynumber: 1.9 Consensus size: 143
16751342 CTAATAATCC
* * * * * **
16751352 TATCTCCCTGAGGTTGCAGTGGAGCAGATTAAAGCTAATAATCCTATCTCCCTGAGGTTGCAGTG
1 TATCTCCCTGAAGTTGCAATGGAGCAGATTAAAGCCAATAAGCCTATCTCCCTGAAGTTGCAGCA
* *
16751417 GAGCAGACTGAAGATAGCGAATCTTATTTCCCTAGCGTTGCAATGGAGCAGATTAAAGCTACAAA
66 GAGCAGACTGAAGACAGCGAATCTTATTTCCCTAGCGTTGCAATGGAACAGATTAAAGCTACAAA
16751482 TTATGGCGTATCT
131 TTATGGCGTATCT
* * * **
16751495 TATCTTCCTGAAGTTGCAATGGAGCAGATTGAAGCCACT-AGCCTTATCTCTTTGAAGTTGCAGC
1 TATCTCCCTGAAGTTGCAATGGAGCAGATTAAAGCCAATAAGCC-TATCTCCCTGAAGTTGCAGC
* *
16751559 AGAGCAGACTGAAGACAGCGAATCTTATTTCCCTAGTGTTGCAGTGGAACAGATTAAAGCT
65 AGAGCAGACTGAAGACAGCGAATCTTATTTCCCTAGCGTTGCAATGGAACAGATTAAAGCT
16751620 GAAGACAGCG
Statistics
Matches: 108, Mismatches: 16, Indels: 2
0.86 0.13 0.02
Matches are distributed among these distances:
142 3 0.03
143 105 0.97
ACGTcount: A:0.29, C:0.20, G:0.24, T:0.28
Consensus pattern (143 bp):
TATCTCCCTGAAGTTGCAATGGAGCAGATTAAAGCCAATAAGCCTATCTCCCTGAAGTTGCAGCA
GAGCAGACTGAAGACAGCGAATCTTATTTCCCTAGCGTTGCAATGGAACAGATTAAAGCTACAAA
TTATGGCGTATCT
Found at i:16751643 original size:51 final size:51
Alignment explanation
Indices: 16751567--16751670 Score: 163
Period size: 51 Copynumber: 2.0 Consensus size: 51
16751557 GCAGAGCAGA
** *
16751567 CTGAAGACAGCGAATCTTATTTCCCTAGTGTTGCAGTGGAACAGATTAAAG
1 CTGAAGACAGCGAATCTTATTTCCCTAGCATTGCAGTAGAACAGATTAAAG
**
16751618 CTGAAGACAGCGAATCTTATTTCCCTAGCATTGCAGTAGAGTAGATTAAAG
1 CTGAAGACAGCGAATCTTATTTCCCTAGCATTGCAGTAGAACAGATTAAAG
16751669 CT
1 CT
16751671 ACAAATTATG
Statistics
Matches: 48, Mismatches: 5, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
51 48 1.00
ACGTcount: A:0.32, C:0.18, G:0.22, T:0.28
Consensus pattern (51 bp):
CTGAAGACAGCGAATCTTATTTCCCTAGCATTGCAGTAGAACAGATTAAAG
Found at i:16751780 original size:194 final size:195
Alignment explanation
Indices: 16751304--16751785 Score: 551
Period size: 194 Copynumber: 2.5 Consensus size: 195
16751294 AAGATGGCAA
* * * * ** *
16751304 ATCTTATCTTCCTGAAGTTGCAGTGGAGCAGATTAAAGCTAATAATCC-TATCTCCCTGAGGTTG
1 ATCTTATCTTCCTGAAGTTACAATGGAGCAGATTGAAGCCACCAA-CCTTATCTCCCTGAAGTTG
** * * * * *
16751368 CAGTGGAGCAGATTAAAG-CTAA-TAATCCTATC-TCCCTGAG-GTTGCAGTGGAGCAG-----A
65 CAGCAGAGCAGACTGAAGAC-AACGAATCTTATCTTCCCT-AGTGTTGCAGTGGAACAGATTAAA
* * *
16751424 -CTGAAGATAGCGAATCTTATTTCCCTAGCGTTGCAATGGAGCAGATTAAAGCTACAAATTATGG
128 GCTGAAGACAGCGAATCTTATTTCCCTAGCATTGCAATAGAGCAGATTAAAGCTACAAATTATGG
*
16751488 CGT
193 CGG
* * * **
16751491 ATCTTATCTTCCTGAAGTTGCAATGGAGCAGATTGAAGCCACTAGCCTTATCTCTTTGAAGTTGC
1 ATCTTATCTTCCTGAAGTTACAATGGAGCAGATTGAAGCCACCAACCTTATCTCCCTGAAGTTGC
*
16751556 AGCAGAGCAGACTGAAGACAGCGAATCTTAT-TTCCCTAGTGTTGCAGTGGAACAGATTAAAGCT
66 AGCAGAGCAGACTGAAGACAACGAATCTTATCTTCCCTAGTGTTGCAGTGGAACAGATTAAAGCT
* *
16751620 GAAGACAGCGAATCTTATTTCCCTAGCATTGCAGTAGAGTAGATTAAAGCTACAAATTATGGCGG
131 GAAGACAGCGAATCTTATTTCCCTAGCATTGCAATAGAGCAGATTAAAGCTACAAATTATGGCGG
* *
16751685 ATCTTATCTTCCTGAAGTTACAATGGGGCA-AGTTGAAGCCACCAACCTTATCTCCCTGAATTTG
1 ATCTTATCTTCCTGAAGTTACAATGGAGCAGA-TTGAAGCCACCAACCTTATCTCCCTGAAGTTG
* *
16751749 CAGCAGAGCAGACTGATGATAAC-AGATCTTATCTTCC
65 CAGCAGAGCAGACTGAAGACAACGA-ATCTTATCTTCC
16751786 TGTATTGGCA
Statistics
Matches: 249, Mismatches: 32, Indels: 20
0.83 0.11 0.07
Matches are distributed among these distances:
186 2 0.01
187 70 0.28
188 27 0.11
193 3 0.01
194 143 0.57
195 4 0.02
ACGTcount: A:0.30, C:0.20, G:0.22, T:0.28
Consensus pattern (195 bp):
ATCTTATCTTCCTGAAGTTACAATGGAGCAGATTGAAGCCACCAACCTTATCTCCCTGAAGTTGC
AGCAGAGCAGACTGAAGACAACGAATCTTATCTTCCCTAGTGTTGCAGTGGAACAGATTAAAGCT
GAAGACAGCGAATCTTATTTCCCTAGCATTGCAATAGAGCAGATTAAAGCTACAAATTATGGCGG
Found at i:16751781 original size:45 final size:45
Alignment explanation
Indices: 16751731--16752161 Score: 136
Period size: 45 Copynumber: 9.7 Consensus size: 45
16751721 AGCCACCAAC
*
16751731 CTTATCTCCCTGAATTTGCAGCAGAGCAGACTGATGATAACAGAT
1 CTTATCTCCCTGAATTTGCAGCAGAGCAGACTGAAGATAACAGAT
* * * * * * *
16751776 CTTATCTTCCTGTATTGGCAGC-GAAGTAGA-TCGAAGACACCAG-C
1 CTTATCTCCCTGAATTTGCAGCAG-AGCAGACT-GAAGATAACAGAT
* * * *
16751820 CTTATCTCCTTGAATTTGCAGCAAAGCAAACTGACGATAACAGAT
1 CTTATCTCCCTGAATTTGCAGCAGAGCAGACTGAAGATAACAGAT
* * * * * *
16751865 CTTGTCTTCCT-ATATTGGCAGC-GAAGTAGATTGAA-A-ACACTAGCT
1 CTTATCTCCCTGA-ATTTGCAGCAG-AGCAGACTGAAGATA-AC-AGAT
** * ** * *
16751910 -TTGCCTCCCTGAGTTTGCAGTGGAGCAGACTAAAGATAACAAAT
1 CTTATCTCCCTGAATTTGCAGCAGAGCAGACTGAAGATAACAGAT
* * * * * * *
16751954 CTTGTCTTCCTGTATTGGCAGC-GAAGCAGA-TCAAAGA-CACTAG-C
1 CTTATCTCCCTGAATTTGCAGCAG-AGCAGACT-GAAGATAAC-AGAT
** * * *
16751998 CTTGCCTCCCTGAGTTTGCAGCAGAGCAAACTGAAGATAGCAGAT
1 CTTATCTCCCTGAATTTGCAGCAGAGCAGACTGAAGATAACAGAT
* *** * * * * * * *
16752043 CTTGTCTTTTTGTATTGGCAGCAAAGTAGA-TCGAAGACACCA-AC
1 CTTATCTCCCTGAATTTGCAGCAGAGCAGACT-GAAGATAACAGAT
** * * * *
16752087 CTTGCCTCCCTGAGTTTGCAGCGGAGCAGACTAAAGATAGCAGAT
1 CTTATCTCCCTGAATTTGCAGCAGAGCAGACTGAAGATAACAGAT
* * * *
16752132 CTTGTCTTCCTGTATTAGCAGC-GAAGCAGA
1 CTTATCTCCCTGAATTTGCAGCAG-AGCAGA
16752162 TCAAAGACAC
Statistics
Matches: 271, Mismatches: 90, Indels: 50
0.66 0.22 0.12
Matches are distributed among these distances:
43 1 0.00
44 122 0.45
45 147 0.54
46 1 0.00
ACGTcount: A:0.29, C:0.23, G:0.22, T:0.26
Consensus pattern (45 bp):
CTTATCTCCCTGAATTTGCAGCAGAGCAGACTGAAGATAACAGAT
Found at i:16751835 original size:89 final size:89
Alignment explanation
Indices: 16751736--16752290 Score: 633
Period size: 89 Copynumber: 6.2 Consensus size: 89
16751726 CCAACCTTAT
* * *
16751736 CTCCCTGAATTTGCAGCAGAGCAGACTGATGATAACAGATCTTATCTTCCTGTATTGGCAGCGAA
1 CTCCCTGAGTTTGCAGCAGAGCAGACTGAAGATAACAGATCTTGTCTTCCTGTATTGGCAGCGAA
**
16751801 GTAGATCGAAGACACCAGCCTTAT
66 GTAGATCGAAGACACCAGCCTTGC
* * * * * *
16751825 CTCCTTGAATTTGCAGCAAAGCAAACTGACGATAACAGATCTTGTCTTCCTATATTGGCAGCGAA
1 CTCCCTGAGTTTGCAGCAGAGCAGACTGAAGATAACAGATCTTGTCTTCCTGTATTGGCAGCGAA
* * * *
16751890 GTAGATTGAAAACACTAGCTTTGC
66 GTAGATCGAAGACACCAGCCTTGC
** * *
16751914 CTCCCTGAGTTTGCAGTGGAGCAGACTAAAGATAACAAATCTTGTCTTCCTGTATTGGCAGCGAA
1 CTCCCTGAGTTTGCAGCAGAGCAGACTGAAGATAACAGATCTTGTCTTCCTGTATTGGCAGCGAA
* * *
16751979 GCAGATCAAAGACACTAGCCTTGC
66 GTAGATCGAAGACACCAGCCTTGC
* * ** *
16752003 CTCCCTGAGTTTGCAGCAGAGCAAACTGAAGATAGCAGATCTTGTCTTTTTGTATTGGCAGCAAA
1 CTCCCTGAGTTTGCAGCAGAGCAGACTGAAGATAACAGATCTTGTCTTCCTGTATTGGCAGCGAA
*
16752068 GTAGATCGAAGACACCAACCTTGC
66 GTAGATCGAAGACACCAGCCTTGC
* * * *
16752092 CTCCCTGAGTTTGCAGCGGAGCAGACTAAAGATAGCAGATCTTGTCTTCCTGTATTAGCAGCGAA
1 CTCCCTGAGTTTGCAGCAGAGCAGACTGAAGATAACAGATCTTGTCTTCCTGTATTGGCAGCGAA
* * *
16752157 GCAGATCAAAGACACCAGTCTTGC
66 GTAGATCGAAGACACCAGCCTTGC
* * * * * ** * * * *
16752181 CTCTCTGAGTTAGCAGCGGAGTAGACTGAAAATAGTAGATCTTGTCTTCCTGTACTAGAAGTGAA
1 CTCCCTGAGTTTGCAGCAGAGCAGACTGAAGATAACAGATCTTGTCTTCCTGTATTGGCAGCGAA
** *
16752246 GTAGATAAAAAACACCAGCCTTGC
66 GTAGATCGAAGACACCAGCCTTGC
** * *
16752270 CTCTTTGAGTTTACAGTAGAG
1 CTCCCTGAGTTTGCAGCAGAG
16752291 TAGGTTGAAG
Statistics
Matches: 397, Mismatches: 69, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
89 397 1.00
ACGTcount: A:0.30, C:0.22, G:0.22, T:0.26
Consensus pattern (89 bp):
CTCCCTGAGTTTGCAGCAGAGCAGACTGAAGATAACAGATCTTGTCTTCCTGTATTGGCAGCGAA
GTAGATCGAAGACACCAGCCTTGC
Found at i:16752168 original size:45 final size:46
Alignment explanation
Indices: 16751933--16752234 Score: 159
Period size: 45 Copynumber: 6.8 Consensus size: 46
16751923 TTTGCAGTGG
* * *
16751933 AGCAGA-CTAAAGATAACAAATCTTGTCTTCCTGTA-TTGGCAGCGA
1 AGCAGATC-AAAGATAGCAGATCTTGTCTTCCTGTAGTTAGCAGCGA
* * * * *
16751978 AGCAGATCAAAGACA-CTAG-CCTTGCCTCCCTG-AGTTTGCAGC-A
1 AGCAGATCAAAGATAGC-AGATCTTGTCTTCCTGTAGTTAGCAGCGA
* * ** * *
16752021 GAGCA-AACTGAAGATAGCAGATCTTGTCTTTTTGTA-TTGGCAGCAA
1 -AGCAGATC-AAAGATAGCAGATCTTGTCTTCCTGTAGTTAGCAGCGA
* * * * * * * * *
16752067 AGTAGATCGAAGACACCA-ACCTTGCCTCCCTG-AGTTTGCAGCGG
1 AGCAGATCAAAGATAGCAGATCTTGTCTTCCTGTAGTTAGCAGCGA
16752111 AGCAGA-CTAAAGATAGCAGATCTTGTCTTCCTGTA-TTAGCAGCGA
1 AGCAGATC-AAAGATAGCAGATCTTGTCTTCCTGTAGTTAGCAGCGA
* * * *
16752156 AGCAGATCAAAGACACCAG-TCTTG-CCTCTCTG-AGTTAGCAGCGG
1 AGCAGATCAAAGATAGCAGATCTTGTCTTC-CTGTAGTTAGCAGCGA
* * *
16752200 AGTAGACTGAAA-ATAGTAGATCTTGTCTTCCTGTA
1 AGCAGA-TCAAAGATAGCAGATCTTGTCTTCCTGTA
16752235 CTAGAAGTGA
Statistics
Matches: 190, Mismatches: 46, Indels: 41
0.69 0.17 0.15
Matches are distributed among these distances:
43 10 0.05
44 83 0.44
45 86 0.45
46 11 0.06
ACGTcount: A:0.29, C:0.23, G:0.23, T:0.25
Consensus pattern (46 bp):
AGCAGATCAAAGATAGCAGATCTTGTCTTCCTGTAGTTAGCAGCGA
Found at i:16752196 original size:44 final size:44
Alignment explanation
Indices: 16751971--16752198 Score: 135
Period size: 44 Copynumber: 5.1 Consensus size: 44
16751961 TCCTGTATTG
* * * *
16751971 GCAGCGAAGCAGATCAAAGACACTAGCCTTGCCTCCCTGAGTTT
1 GCAGCGAAGCAGATCAAAGACACCAGTCTTGCCTCTCTGAGTTA
* * * * * * * *
16752015 GCAGC-AGAGCA-AACTGAAGATAGCAGATCTTGTCTTTTTGTA-TTG
1 GCAGCGA-AGCAGATC-AAAGACACCAG-TCTTGCCTCTCTG-AGTTA
* * * ** * *
16752060 GCAGCAAAGTAGATCGAAGACACCAACCTTGCCTCCCTGAGTTT
1 GCAGCGAAGCAGATCAAAGACACCAGTCTTGCCTCTCTGAGTTA
* * * *
16752104 GCAGCGGAGCAGA-CTAAAGATAGCAGATCTTGTCT-TCCTGTA-TTA
1 GCAGCGAAGCAGATC-AAAGACACCAG-TCTTGCCTCT-CTG-AGTTA
16752149 GCAGCGAAGCAGATCAAAGACACCAGTCTTGCCTCTCTGAGTTA
1 GCAGCGAAGCAGATCAAAGACACCAGTCTTGCCTCTCTGAGTTA
16752193 GCAGCG
1 GCAGCG
16752199 GAGTAGACTG
Statistics
Matches: 133, Mismatches: 37, Indels: 28
0.67 0.19 0.14
Matches are distributed among these distances:
43 6 0.05
44 62 0.47
45 59 0.44
46 6 0.05
ACGTcount: A:0.29, C:0.25, G:0.24, T:0.23
Consensus pattern (44 bp):
GCAGCGAAGCAGATCAAAGACACCAGTCTTGCCTCTCTGAGTTA
Found at i:16752443 original size:131 final size:133
Alignment explanation
Indices: 16752288--16752563 Score: 380
Period size: 131 Copynumber: 2.1 Consensus size: 133
16752278 GTTTACAGTA
* * * * *
16752288 GAGTAGGTTGAAGATTGTAGATCCTGTCTCCCTAAGCAGTAGTGAAGCAGATCGAAGACGGCGAA
1 GAGTAGGTTGAAGATTGTAGATCCTATCTCCCTAAACAGTAGTGAAGCAAATCAAAGACGACGAA
* *
16752353 TCTTATCTTCCCG-AGATAGTA-GGAAGCAGATTTAAGCCACTAGTCC-TATCTCCCTG-AGTAA
66 TCTTATCTT-CCGAAGATAGTAGGGAAGCAGAATTAAGCCACCAG-CCTTATCTCCCTGAAGTAA
16752414 TAGTG
129 TAGTG
* * *
16752419 GAGTAGGTTGAAGATTGTATATCCTATCTCCCTAAACAGTAGTGGAGCAAATCAAAGACGACGAG
1 GAGTAGGTTGAAGATTGTAGATCCTATCTCCCTAAACAGTAGTGAAGCAAATCAAAGACGACGAA
* **
16752484 TCTTATCTTCCGAAGGTAGTAGGGAAGCAGAATTAAGCCACCAGCCTTATCTCCCTGAAGTTGTA
66 TCTTATCTTCCGAAGATAGTAGGGAAGCAGAATTAAGCCACCAGCCTTATCTCCCTGAAGTAATA
16752549 GTG
131 GTG
*
16752552 GAGCAGGTTGAA
1 GAGTAGGTTGAA
16752564 ATTACCAATT
Statistics
Matches: 127, Mismatches: 14, Indels: 6
0.86 0.10 0.04
Matches are distributed among these distances:
130 3 0.02
131 75 0.59
132 30 0.24
133 19 0.15
ACGTcount: A:0.30, C:0.19, G:0.25, T:0.25
Consensus pattern (133 bp):
GAGTAGGTTGAAGATTGTAGATCCTATCTCCCTAAACAGTAGTGAAGCAAATCAAAGACGACGAA
TCTTATCTTCCGAAGATAGTAGGGAAGCAGAATTAAGCCACCAGCCTTATCTCCCTGAAGTAATA
GTG
Found at i:16756755 original size:11 final size:13
Alignment explanation
Indices: 16756735--16756766 Score: 50
Period size: 12 Copynumber: 2.6 Consensus size: 13
16756725 AATAAATTAA
16756735 TAAAATATCAT-T
1 TAAAATATCATAT
16756747 TAAAA-ATCATAT
1 TAAAATATCATAT
16756759 TAAAATAT
1 TAAAATAT
16756767 TAATAAACTA
Statistics
Matches: 18, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
11 5 0.28
12 11 0.61
13 2 0.11
ACGTcount: A:0.56, C:0.06, G:0.00, T:0.38
Consensus pattern (13 bp):
TAAAATATCATAT
Found at i:16758187 original size:17 final size:17
Alignment explanation
Indices: 16758140--16758187 Score: 51
Period size: 17 Copynumber: 2.7 Consensus size: 17
16758130 ACAAAACAAG
*
16758140 TTAATCAAATTAATTATAA
1 TTAATCAAA--AATTAAAA
*
16758159 TTAATCATAAATTAAAA
1 TTAATCAAAAATTAAAA
*
16758176 TTAATTAAAAAT
1 TTAATCAAAAAT
16758188 ATAATAAATA
Statistics
Matches: 25, Mismatches: 4, Indels: 2
0.81 0.13 0.06
Matches are distributed among these distances:
17 17 0.68
19 8 0.32
ACGTcount: A:0.56, C:0.04, G:0.00, T:0.40
Consensus pattern (17 bp):
TTAATCAAAAATTAAAA
Found at i:16758203 original size:27 final size:27
Alignment explanation
Indices: 16758146--16758215 Score: 70
Period size: 27 Copynumber: 2.5 Consensus size: 27
16758136 CAAGTTAATC
* * *
16758146 AAATTAATTATAATTAATCATAAATTA
1 AAATTAATTAAAAATAATAATAAATTA
16758173 AAATTAATTAAAAAT-ATAATAAATATGA
1 AAATTAATTAAAAATAATAATAAAT-T-A
*
16758201 AATATTAAGTAAAAA
1 AA-ATTAATTAAAAA
16758216 AACTTCCAAC
Statistics
Matches: 36, Mismatches: 4, Indels: 4
0.82 0.09 0.09
Matches are distributed among these distances:
26 8 0.22
27 14 0.39
28 3 0.08
29 11 0.31
ACGTcount: A:0.61, C:0.01, G:0.03, T:0.34
Consensus pattern (27 bp):
AAATTAATTAAAAATAATAATAAATTA
Found at i:16767572 original size:50 final size:50
Alignment explanation
Indices: 16767518--16767694 Score: 201
Period size: 50 Copynumber: 3.4 Consensus size: 50
16767508 TATCCTAAAT
** *
16767518 ATGGTCTTACATGGGAGTTCTCATATTGGTGCCCATGCCATGTCCCAGAC
1 ATGGTCTTACATGGGACCTCTCATATTGGTGCCAATGCCATGTCCCAGAC
** * *
16767568 ATGGTCTTACGGGGGACCTCTCATCTTGGTGCCAACGCCATGTCCCAGAC
1 ATGGTCTTACATGGGACCTCTCATATTGGTGCCAATGCCATGTCCCAGAC
* * *
16767618 TTGGTCTTACATGGGACCTCTCATAATCTCAATGATGCCAATGTCATGTCCCAGAC
1 ATGGTCTTACATGGGACCTCTCAT-A--T---TGGTGCCAATGCCATGTCCCAGAC
*
16767674 ATGGTCTTACATGGGATCTCT
1 ATGGTCTTACATGGGACCTCT
16767695 TTACCCAAAT
Statistics
Matches: 105, Mismatches: 16, Indels: 6
0.83 0.13 0.05
Matches are distributed among these distances:
50 64 0.61
53 1 0.01
56 40 0.38
ACGTcount: A:0.21, C:0.27, G:0.23, T:0.29
Consensus pattern (50 bp):
ATGGTCTTACATGGGACCTCTCATATTGGTGCCAATGCCATGTCCCAGAC
Found at i:16771468 original size:24 final size:25
Alignment explanation
Indices: 16771414--16771477 Score: 69
Period size: 24 Copynumber: 2.6 Consensus size: 25
16771404 CTGTAAGAAT
* *
16771414 CAAATAAAAGAAAA-ATTAAAATGTAA
1 CAAATAAAATAAAACA--AAAATATAA
*
16771440 CAAATAAATTAAAACAAAAATATAA
1 CAAATAAAATAAAACAAAAATATAA
16771465 -AAATAAAATAAAA
1 CAAATAAAATAAAA
16771478 ATAAATAAAT
Statistics
Matches: 33, Mismatches: 4, Indels: 4
0.80 0.10 0.10
Matches are distributed among these distances:
24 12 0.36
25 8 0.24
26 12 0.36
27 1 0.03
ACGTcount: A:0.73, C:0.05, G:0.03, T:0.19
Consensus pattern (25 bp):
CAAATAAAATAAAACAAAAATATAA
Found at i:16771478 original size:25 final size:26
Alignment explanation
Indices: 16771414--16771478 Score: 71
Period size: 25 Copynumber: 2.6 Consensus size: 26
16771404 CTGTAAGAAT
* ** *
16771414 CAAATAAAAGAAAAATTAAAATGTAA
1 CAAATAAAATAAAAACAAAAATATAA
*
16771440 CAAAT-AAATTAAAACAAAAATATAA
1 CAAATAAAATAAAAACAAAAATATAA
16771465 -AAATAAAATAAAAA
1 CAAATAAAATAAAAA
16771479 TAAATAAATT
Statistics
Matches: 32, Mismatches: 6, Indels: 3
0.78 0.15 0.07
Matches are distributed among these distances:
24 4 0.12
25 23 0.72
26 5 0.16
ACGTcount: A:0.74, C:0.05, G:0.03, T:0.18
Consensus pattern (26 bp):
CAAATAAAATAAAAACAAAAATATAA
Found at i:16773473 original size:50 final size:50
Alignment explanation
Indices: 16773348--16773580 Score: 238
Period size: 50 Copynumber: 4.7 Consensus size: 50
16773338 GAATATAACA
* * * ** *
16773348 TGCCAAAGCTATGTCCCAGACATAGTCTTACATGGGATGTTTCCAGTAT---
1 TGCCAATGCCATGTCCCAGACATGGTCTTACATGGGACCTCT-CA-TATCGG
* * **
16773397 TGCCAATGCCATATCCCAGATATGGTCTTACATGGGAGTTCTCATATCGG
1 TGCCAATGCCATGTCCCAGACATGGTCTTACATGGGACCTCTCATATCGG
* * ** *
16773447 TGCCCATGCCATGTCCAAGACATGGTCTTACGGGGGACCTCTCATCTCGG
1 TGCCAATGCCATGTCCCAGACATGGTCTTACATGGGACCTCTCATATCGG
* * *
16773497 TGCCAATGCCATGTCCCAGACATGATCTTACATGAGACCTCTCATCTCGG
1 TGCCAATGCCATGTCCCAGACATGGTCTTACATGGGACCTCTCATATCGG
* * *
16773547 TGCCAACGCCATGACCCCGACATGGTCTTACATG
1 TGCCAATGCCATGTCCCAGACATGGTCTTACATG
16773581 AGATCTCTTT
Statistics
Matches: 154, Mismatches: 27, Indels: 5
0.83 0.15 0.03
Matches are distributed among these distances:
47 3 0.02
48 2 0.01
49 34 0.22
50 115 0.75
ACGTcount: A:0.23, C:0.29, G:0.21, T:0.27
Consensus pattern (50 bp):
TGCCAATGCCATGTCCCAGACATGGTCTTACATGGGACCTCTCATATCGG
Found at i:16773581 original size:50 final size:50
Alignment explanation
Indices: 16773397--16773588 Score: 240
Period size: 50 Copynumber: 3.8 Consensus size: 50
16773387 TTTCCAGTAT
* * * ** *
16773397 TGCCAATGCCATATCCCAGATATGGTCTTACATGGGAGTTCTCATATCGG
1 TGCCAATGCCATGTCCCAGACATGGTCTTACATGAGACCTCTCATCTCGG
* * ** *
16773447 TGCCCATGCCATGTCCAAGACATGGTCTTACGGGGGACCTCTCATCTCGG
1 TGCCAATGCCATGTCCCAGACATGGTCTTACATGAGACCTCTCATCTCGG
*
16773497 TGCCAATGCCATGTCCCAGACATGATCTTACATGAGACCTCTCATCTCGG
1 TGCCAATGCCATGTCCCAGACATGGTCTTACATGAGACCTCTCATCTCGG
* * * *
16773547 TGCCAACGCCATGACCCCGACATGGTCTTACATGAGATCTCT
1 TGCCAATGCCATGTCCCAGACATGGTCTTACATGAGACCTCT
16773589 TTACCCAAAT
Statistics
Matches: 122, Mismatches: 20, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
50 122 1.00
ACGTcount: A:0.22, C:0.30, G:0.21, T:0.26
Consensus pattern (50 bp):
TGCCAATGCCATGTCCCAGACATGGTCTTACATGAGACCTCTCATCTCGG
Found at i:16776593 original size:14 final size:14
Alignment explanation
Indices: 16776574--16776600 Score: 54
Period size: 14 Copynumber: 1.9 Consensus size: 14
16776564 TGGCAGCTAG
16776574 CTCATGTAGCTTTT
1 CTCATGTAGCTTTT
16776588 CTCATGTAGCTTT
1 CTCATGTAGCTTT
16776601 AACTGTCTGG
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 13 1.00
ACGTcount: A:0.15, C:0.22, G:0.15, T:0.48
Consensus pattern (14 bp):
CTCATGTAGCTTTT
Found at i:16780214 original size:50 final size:50
Alignment explanation
Indices: 16780158--16780364 Score: 241
Period size: 50 Copynumber: 4.3 Consensus size: 50
16780148 GATCCTAGAT
* * *
16780158 ATGGTCTTACATGGGAGTTCTCATATCGGTGCCCATGCCATGTCCAAGAC
1 ATGGTCTTACATGGGAGCTCTCATATCGGTGCCAACGCCATGTCCAAGAC
** *
16780208 ATGGTCTTACGGGGGAGCTCTCATCTCGGTGCCAACGCCATGTCCCAA-AC
1 ATGGTCTTACATGGGAGCTCTCATATCGGTGCCAACGCCATGT-CCAAGAC
*
16780258 ATGGTCTTACATGGGA-C-CTC---TC-ATGCCAACGCCATGTCTC-AGAC
1 ATGGTCTTACATGGGAGCTCTCATATCGGTGCCAACGCCATGTC-CAAGAC
* * * *
16780302 ATGGTCTTACATAGGACCTCTCATATCGGTACCAACGCCATGTCCCAGAC
1 ATGGTCTTACATGGGAGCTCTCATATCGGTGCCAACGCCATGTCCAAGAC
16780352 ATGGTCTTACATG
1 ATGGTCTTACATG
16780365 AGATCTCTTT
Statistics
Matches: 134, Mismatches: 13, Indels: 20
0.80 0.08 0.12
Matches are distributed among these distances:
43 2 0.01
44 32 0.24
45 3 0.02
46 3 0.02
48 3 0.02
49 4 0.03
50 83 0.62
51 4 0.03
ACGTcount: A:0.23, C:0.29, G:0.22, T:0.26
Consensus pattern (50 bp):
ATGGTCTTACATGGGAGCTCTCATATCGGTGCCAACGCCATGTCCAAGAC
Found at i:16780304 original size:44 final size:45
Alignment explanation
Indices: 16780237--16780364 Score: 177
Period size: 44 Copynumber: 2.8 Consensus size: 45
16780227 CTCATCTCGG
*
16780237 TGCCAACGCCATGTCCCAAACATGGTCTTACATGGGACCTCTC-A
1 TGCCAACGCCATGTCCCAGACATGGTCTTACATGGGACCTCTCAA
* *
16780281 TGCCAACGCCATGTCTCAGACATGGTCTTACATAGGACCTCTCATA
1 TGCCAACGCCATGTCCCAGACATGGTCTTACATGGGACCTCTCA-A
16780327 TCGGTACCAACGCCATGTCCCAGACATGGTCTTACATG
1 T--G--CCAACGCCATGTCCCAGACATGGTCTTACATG
16780365 AGATCTCTTT
Statistics
Matches: 73, Mismatches: 5, Indels: 6
0.87 0.06 0.07
Matches are distributed among these distances:
44 40 0.55
46 2 0.03
48 1 0.01
50 30 0.41
ACGTcount: A:0.25, C:0.32, G:0.19, T:0.24
Consensus pattern (45 bp):
TGCCAACGCCATGTCCCAGACATGGTCTTACATGGGACCTCTCAA
Found at i:16780323 original size:94 final size:94
Alignment explanation
Indices: 16780194--16780364 Score: 263
Period size: 94 Copynumber: 1.8 Consensus size: 94
16780184 CGGTGCCCAT
* * * * *
16780194 GCCATGTCCAAGACATGGTCTTACGGGGGAGCTCTCATCTCGGTGCCAACGCCATGTCCCAAACA
1 GCCATGTCCAAGACATGGTCTTACAGAGGACCTCTCATATCGGTACCAACGCCATGTCCCAAACA
16780259 TGGTCTTACATGGGACCTCTCATGCCAAC
66 TGGTCTTACATGGGACCTCTCATGCCAAC
* *
16780288 GCCATGTCTC-AGACATGGTCTTACATAGGACCTCTCATATCGGTACCAACGCCATGTCCCAGAC
1 GCCATGTC-CAAGACATGGTCTTACAGAGGACCTCTCATATCGGTACCAACGCCATGTCCCAAAC
16780352 ATGGTCTTACATG
65 ATGGTCTTACATG
16780365 AGATCTCTTT
Statistics
Matches: 69, Mismatches: 7, Indels: 2
0.88 0.09 0.03
Matches are distributed among these distances:
94 68 0.99
95 1 0.01
ACGTcount: A:0.23, C:0.31, G:0.22, T:0.24
Consensus pattern (94 bp):
GCCATGTCCAAGACATGGTCTTACAGAGGACCTCTCATATCGGTACCAACGCCATGTCCCAAACA
TGGTCTTACATGGGACCTCTCATGCCAAC
Found at i:16789431 original size:30 final size:29
Alignment explanation
Indices: 16789375--16789431 Score: 71
Period size: 30 Copynumber: 1.9 Consensus size: 29
16789365 GTGTAATTGT
* *
16789375 ATACATGAATTTTGATTTTGTGCAATTTC
1 ATACATGAAATTTGATTTTGTCCAATTTC
16789404 ATACATGAAAATTTGA-TTTGATCCAATT
1 ATACATG-AAATTTGATTTTG-TCCAATT
16789432 CTTGTAAATT
Statistics
Matches: 24, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
29 11 0.46
30 13 0.54
ACGTcount: A:0.33, C:0.11, G:0.12, T:0.44
Consensus pattern (29 bp):
ATACATGAAATTTGATTTTGTCCAATTTC
Found at i:16790269 original size:126 final size:126
Alignment explanation
Indices: 16790091--16790387 Score: 382
Period size: 126 Copynumber: 2.4 Consensus size: 126
16790081 TTTTATTCAT
* * * * * * *
16790091 TCAGCCAAAGTATTGAAAAAAACTTCCAGCTAGACGCTCTTTTTCTAGAGTAGTTTCTGAAAAAA
1 TCAGCAAAAGTACTGAAAAAAGCTCCCACCTAGACGCTCTCTTTCCAGAGTAGTTTCTGAAAAAA
* * * *
16790156 TAATTTTGAGCAGA-TGATTCTGAAAAAATAGGGTCA-AAAACGCTTCAAGCAGGATGCACTG
66 TAATTTTGAGAAGATTG-TTCTAAAAAAATAGGGT-AGAAAAAGCTTCAAACAGGATGCACTG
* * * **
16790217 TCAGCAAAAGTACTGAAAAAAGCTCCCACCTCGATGCTCTCTTTCCATAGTAGTTTCTTTAAAAA
1 TCAGCAAAAGTACTGAAAAAAGCTCCCACCTAGACGCTCTCTTTCCAGAGTAGTTTCTGAAAAAA
16790282 TAATTTTGAGAAGATTGTTCTAAAAAAATAGGGTAGAAAAAGCTTCAAACAGGATGCACTG
66 TAATTTTGAGAAGATTGTTCTAAAAAAATAGGGTAGAAAAAGCTTCAAACAGGATGCACTG
* * * *
16790343 TCAACAAAAGTACTGAAAAAAGCTCCCACTTGGACGCTCTTTTTC
1 TCAGCAAAAGTACTGAAAAAAGCTCCCACCTAGACGCTCTCTTTC
16790388 TACAATACAT
Statistics
Matches: 148, Mismatches: 21, Indels: 4
0.86 0.12 0.02
Matches are distributed among these distances:
125 1 0.01
126 145 0.98
127 2 0.01
ACGTcount: A:0.37, C:0.19, G:0.17, T:0.27
Consensus pattern (126 bp):
TCAGCAAAAGTACTGAAAAAAGCTCCCACCTAGACGCTCTCTTTCCAGAGTAGTTTCTGAAAAAA
TAATTTTGAGAAGATTGTTCTAAAAAAATAGGGTAGAAAAAGCTTCAAACAGGATGCACTG
Found at i:16790491 original size:25 final size:25
Alignment explanation
Indices: 16790462--16790527 Score: 89
Period size: 25 Copynumber: 2.6 Consensus size: 25
16790452 TTACAACAAG
* *
16790462 AGAAATT-AGAGAAGTTTAGAAGAAT
1 AGAAATTGA-AGAAGTTCAGAAAAAT
16790487 AGAAATTGAAGAAGTTCAGAAAAAT
1 AGAAATTGAAGAAGTTCAGAAAAAT
*
16790512 ATAAATTGAAGAAGTT
1 AGAAATTGAAGAAGTT
16790528 GAAAAGGTAT
Statistics
Matches: 37, Mismatches: 3, Indels: 2
0.88 0.07 0.05
Matches are distributed among these distances:
25 36 0.97
26 1 0.03
ACGTcount: A:0.53, C:0.02, G:0.21, T:0.24
Consensus pattern (25 bp):
AGAAATTGAAGAAGTTCAGAAAAAT
Found at i:16797020 original size:30 final size:30
Alignment explanation
Indices: 16796984--16797044 Score: 122
Period size: 30 Copynumber: 2.0 Consensus size: 30
16796974 GATGCATGAG
16796984 TTGTCCAATTAAGTAAGCTACTTTCTTACT
1 TTGTCCAATTAAGTAAGCTACTTTCTTACT
16797014 TTGTCCAATTAAGTAAGCTACTTTCTTACT
1 TTGTCCAATTAAGTAAGCTACTTTCTTACT
16797044 T
1 T
16797045 CAATCCGTAG
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
30 31 1.00
ACGTcount: A:0.26, C:0.20, G:0.10, T:0.44
Consensus pattern (30 bp):
TTGTCCAATTAAGTAAGCTACTTTCTTACT
Found at i:16803504 original size:21 final size:21
Alignment explanation
Indices: 16803461--16803504 Score: 52
Period size: 21 Copynumber: 2.1 Consensus size: 21
16803451 TTTATATATT
* *
16803461 TTTACTATTATTATTTATCTA
1 TTTAATATTATTATTCATCTA
* *
16803482 TTTAATATTATTGTTCATTTA
1 TTTAATATTATTATTCATCTA
16803503 TT
1 TT
16803505 AATGCATGAT
Statistics
Matches: 19, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
21 19 1.00
ACGTcount: A:0.27, C:0.07, G:0.02, T:0.64
Consensus pattern (21 bp):
TTTAATATTATTATTCATCTA
Found at i:16808460 original size:1 final size:1
Alignment explanation
Indices: 16808454--16808551 Score: 52
Period size: 1 Copynumber: 98.0 Consensus size: 1
16808444 AAAGAATGTT
* * * * * * * * * *
16808454 AAAAAAAAAACAAACAAACAAACAAAAAAAAGAAGAAAAAGAAAAAGAAAAGAAAAAAAAAGAAA
1 AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA
* * * * * *
16808519 AGAAGAAAAATAAAAGAAAAAGAAAAAGAAAAA
1 AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA
16808552 GGAGAGGCCA
Statistics
Matches: 65, Mismatches: 32, Indels: 0
0.67 0.33 0.00
Matches are distributed among these distances:
1 65 1.00
ACGTcount: A:0.84, C:0.04, G:0.11, T:0.01
Consensus pattern (1 bp):
A
Found at i:16808497 original size:6 final size:6
Alignment explanation
Indices: 16808477--16808552 Score: 81
Period size: 6 Copynumber: 13.0 Consensus size: 6
16808467 ACAAACAAAC
16808477 AAAAA- AAAGAAG AAAAAG AAAAAG -AAAAG -AAAA- AAAAAG AAAAGAAG
1 AAAAAG AAA-AAG AAAAAG AAAAAG AAAAAG AAAAAG AAAAAG -AAA-AAG
*
16808524 AAAAA- TAAAAG AAAAAG AAAAAG AAAAAG
1 AAAAAG AAAAAG AAAAAG AAAAAG AAAAAG
16808553 GAGAGGCCAA
Statistics
Matches: 62, Mismatches: 2, Indels: 13
0.81 0.03 0.17
Matches are distributed among these distances:
5 20 0.32
6 30 0.48
7 9 0.15
8 3 0.05
ACGTcount: A:0.83, C:0.00, G:0.16, T:0.01
Consensus pattern (6 bp):
AAAAAG
Found at i:16808520 original size:35 final size:35
Alignment explanation
Indices: 16808454--16808551 Score: 112
Period size: 35 Copynumber: 2.8 Consensus size: 35
16808444 AAAGAATGTT
* * *
16808454 AAAAAAAAAACAAACAA-ACAAACAAAAAAAAGAAG
1 AAAAAAAAAAGAAA-AAGAAAAAGAAAAAAAAGAAG
16808489 AAAAAGAAAAAG-AAAAGAAAAA-AAAAGAAAAGAAG
1 AAAAA-AAAAAGAAAAAGAAAAAGAAAA-AAAAGAAG
*
16808524 AAAAATAAAAGAAAAAGAAAAAGAAAAA
1 AAAAAAAAAAGAAAAAGAAAAAGAAAAA
16808552 GGAGAGGCCA
Statistics
Matches: 55, Mismatches: 3, Indels: 10
0.81 0.04 0.15
Matches are distributed among these distances:
34 11 0.20
35 35 0.64
36 9 0.16
ACGTcount: A:0.84, C:0.04, G:0.11, T:0.01
Consensus pattern (35 bp):
AAAAAAAAAAGAAAAAGAAAAAGAAAAAAAAGAAG
Found at i:16808988 original size:97 final size:93
Alignment explanation
Indices: 16808835--16809019 Score: 289
Period size: 97 Copynumber: 1.9 Consensus size: 93
16808825 TTCATTTTTG
16808835 TATCTTAGCAAAATTTGCTATCTTGATTTATTCATTTCGAGCTGTGCTCTCAATAAAATTTCATC
1 TATCTTAGCAAAATTTGCTATCTTGATTTATTCATTTCGAGCTGTGCTCTCAATAAAATTTCATC
*
16808900 TTATCCATTGGGATAATCTTTTTCATCT
66 TTATACATTGGGATAATCTTTTTCATCT
* *
16808928 TATCTTAGCAAAATTTGCTATCTTGATTAATTTATTCATTTCGAGCTTTGTTCTCAATAAAATTT
1 TATCTTAGCAAAATTTGCTATCTTG----ATTTATTCATTTCGAGCTGTGCTCTCAATAAAATTT
* *
16808993 CATCTTGTACATTGTGATAATCTTTTT
62 CATCTTATACATTGGGATAATCTTTTT
16809020 TAAGCATTTT
Statistics
Matches: 83, Mismatches: 5, Indels: 4
0.90 0.05 0.04
Matches are distributed among these distances:
93 25 0.30
97 58 0.70
ACGTcount: A:0.26, C:0.16, G:0.10, T:0.47
Consensus pattern (93 bp):
TATCTTAGCAAAATTTGCTATCTTGATTTATTCATTTCGAGCTGTGCTCTCAATAAAATTTCATC
TTATACATTGGGATAATCTTTTTCATCT
Found at i:16809968 original size:44 final size:43
Alignment explanation
Indices: 16809902--16810520 Score: 324
Period size: 44 Copynumber: 14.2 Consensus size: 43
16809892 CATATCAAGC
* * * * * *
16809902 CTTATCTCCCTGAGCAGCAGTGGAGTAGGTTGAAGATTGTATAT
1 CTTATCTCCCTAAGCAGTAGTGGAGCAGATTGAAGACTGCA-AT
* *
16809946 CTTATCTCCCTAAGCAGTAGTGGAGCAGATCGAAGACGGCGAAT
1 CTTATCTCCCTAAGCAGTAGTGGAGCAGATTGAAGACTGC-AAT
* * * ** **
16809990 CTTATCTTCCTAAG--GTAGTAGGAAGCAGATTTAAGCCACCAGC
1 CTTATCTCCCTAAGCAGTAGT-GG-AGCAGATTGAAGACTGCAAT
* * * * *
16810033 CTTATCTCCCTGAGCAGCAGTGGAGTAGGTTGAAGATTGCAGAT
1 CTTATCTCCCTAAGCAGTAGTGGAGCAGATTGAAGACTGCA-AT
* * * *
16810077 CTTATCTCCCTAAGAAGTAGTGGAGCAGATCGAGGACGGCGAAT
1 CTTATCTCCCTAAGCAGTAGTGGAGCAGATTGAAGACTGC-AAT
* * * ** **
16810121 CTTATCTTCCTAAG--GTAGTAGGAAGCAGATTTAAGGCACCAGC
1 CTTATCTCCCTAAGCAGTAGT-GG-AGCAGATTGAAGACTGCAAT
* * * * *
16810164 CTTATCTCCCTGAGTAGCAGTGGAGTAGATTGAAGATTGCAGAT
1 CTTATCTCCCTAAGCAGTAGTGGAGCAGATTGAAGACTGCA-AT
* ** *
16810208 CTTATCTCCCTAACCAGTAGTGGAGCAGATCAAAGACGGCGAAT
1 CTTATCTCCCTAAGCAGTAGTGGAGCAGATTGAAGACTGC-AAT
* * ** **
16810252 CTTATCTCCCTAAG--GTAGTAGGAAGCAGATTTAAGGCACCAGC
1 CTTATCTCCCTAAGCAGTAGT-GG-AGCAGATTGAAGACTGCAAT
* * * * *
16810295 CTTATCTCCCTGAGCAGCAGTGGAGTAGGTTGAAGATTGCAGAT
1 CTTATCTCCCTAAGCAGTAGTGGAGCAGATTGAAGACTGCA-AT
* * *
16810339 CTTATCTCTCTAAGCAGTAGTGGAACAGATCGAAGACGGTG-AAT
1 CTTATCTCCCTAAGCAGTAGTGGAGCAGATTGAAGAC--TGCAAT
* * ** *
16810383 CTTATCTTCCTAAG--GTAGTAGGAAGCAGATTTAAG-CCACATGT
1 CTTATCTCCCTAAGCAGTAGT-GG-AGCAGATTGAAGACTGCA-AT
* * ** * * * **
16810426 CCTATC-CCCTTGAGCAACAGTGGAGTAGGTTGAAGATTAAAGAT
1 CTTATCTCCC-TAAGCAGTAGTGGAGCAGATTGAAGACTGCA-AT
* * * *
16810470 CCTGTCTCCCTAAGCAGTAGTGGAGCAGATCGAAGACAGCGAAT
1 CTTATCTCCCTAAGCAGTAGTGGAGCAGATTGAAGACTGC-AAT
16810514 CTTATCT
1 CTTATCT
16810521 TCCCAAGGTA
Statistics
Matches: 418, Mismatches: 127, Indels: 60
0.69 0.21 0.10
Matches are distributed among these distances:
42 23 0.06
43 101 0.24
44 269 0.64
45 23 0.06
46 2 0.00
ACGTcount: A:0.29, C:0.20, G:0.25, T:0.25
Consensus pattern (43 bp):
CTTATCTCCCTAAGCAGTAGTGGAGCAGATTGAAGACTGCAAT
Found at i:16810058 original size:131 final size:131
Alignment explanation
Indices: 16809899--16810604 Score: 1103
Period size: 131 Copynumber: 5.4 Consensus size: 131
16809889 CATCATATCA
* *
16809899 AGCCTTATCTCCCTGAGCAGCAGTGGAGTAGGTTGAAGATTGTATATCTTATCTCCCTAAGCAGT
1 AGCCTTATCTCCCTGAGCAGCAGTGGAGTAGGTTGAAGATTGCAGATCTTATCTCCCTAAGCAGT
16809964 AGTGGAGCAGATCGAAGACGGCGAATCTTATCTTCCTAAGGTAGTAGGAAGCAGATTTAAGCCAC
66 AGTGGAGCAGATCGAAGACGGCGAATCTTATCTTCCTAAGGTAGTAGGAAGCAGATTTAAGCCAC
16810029 C
131 C
*
16810030 AGCCTTATCTCCCTGAGCAGCAGTGGAGTAGGTTGAAGATTGCAGATCTTATCTCCCTAAGAAGT
1 AGCCTTATCTCCCTGAGCAGCAGTGGAGTAGGTTGAAGATTGCAGATCTTATCTCCCTAAGCAGT
* *
16810095 AGTGGAGCAGATCGAGGACGGCGAATCTTATCTTCCTAAGGTAGTAGGAAGCAGATTTAAGGCAC
66 AGTGGAGCAGATCGAAGACGGCGAATCTTATCTTCCTAAGGTAGTAGGAAGCAGATTTAAGCCAC
16810160 C
131 C
* * *
16810161 AGCCTTATCTCCCTGAGTAGCAGTGGAGTAGATTGAAGATTGCAGATCTTATCTCCCTAACCAGT
1 AGCCTTATCTCCCTGAGCAGCAGTGGAGTAGGTTGAAGATTGCAGATCTTATCTCCCTAAGCAGT
* * *
16810226 AGTGGAGCAGATCAAAGACGGCGAATCTTATCTCCCTAAGGTAGTAGGAAGCAGATTTAAGGCAC
66 AGTGGAGCAGATCGAAGACGGCGAATCTTATCTTCCTAAGGTAGTAGGAAGCAGATTTAAGCCAC
16810291 C
131 C
*
16810292 AGCCTTATCTCCCTGAGCAGCAGTGGAGTAGGTTGAAGATTGCAGATCTTATCTCTCTAAGCAGT
1 AGCCTTATCTCCCTGAGCAGCAGTGGAGTAGGTTGAAGATTGCAGATCTTATCTCCCTAAGCAGT
* *
16810357 AGTGGAACAGATCGAAGACGGTGAATCTTATCTTCCTAAGGTAGTAGGAAGCAGATTTAAGCCA-
66 AGTGGAGCAGATCGAAGACGGCGAATCTTATCTTCCTAAGGTAGTAGGAAGCAGATTTAAGCCAC
16810421 C
131 C
* ** * *
16810422 ATGTCC-TATC-CCCTTGAGCAACAGTGGAGTAGGTTGAAGATTAAAGATCCTGTCTCCCTAAGC
1 A-G-CCTTATCTCCC-TGAGCAGCAGTGGAGTAGGTTGAAGATTGCAGATCTTATCTCCCTAAGC
* * * *
16810485 AGTAGTGGAGCAGATCGAAGACAGCGAATCTTATCTTCCCAAGGTAGAAGGGAAGTAGATTTAAG
63 AGTAGTGGAGCAGATCGAAGACGGCGAATCTTATCTTCCTAAGGTAGTA-GGAAGCAGATTTAAG
*
16810550 CCACT
127 CCACC
* * * *
16810555 AGCCTTACCTCCCTGAGTAGCAGTGGAGTAGGTCGAAGATTGTAGATCTT
1 AGCCTTATCTCCCTGAGCAGCAGTGGAGTAGGTTGAAGATTGCAGATCTT
16810605 GTCTTCCTGT
Statistics
Matches: 527, Mismatches: 41, Indels: 13
0.91 0.07 0.02
Matches are distributed among these distances:
130 5 0.01
131 464 0.88
132 54 0.10
133 4 0.01
ACGTcount: A:0.29, C:0.20, G:0.26, T:0.25
Consensus pattern (131 bp):
AGCCTTATCTCCCTGAGCAGCAGTGGAGTAGGTTGAAGATTGCAGATCTTATCTCCCTAAGCAGT
AGTGGAGCAGATCGAAGACGGCGAATCTTATCTTCCTAAGGTAGTAGGAAGCAGATTTAAGCCAC
C
Found at i:16810341 original size:87 final size:87
Alignment explanation
Indices: 16809946--16810368 Score: 294
Period size: 87 Copynumber: 4.9 Consensus size: 87
16809936 GATTGTATAT
* *
16809946 CTTATCTCCCTAAGCAGTAGTGGAGCAGATCGAAGACGGC-GAATCTTATCTTCCTAAGGTAGTA
1 CTTATCTCCCTAAGCAGTAGTGGAGCAGATTGAAGACGGCAG-ATCTTATCTCCCTAAGGTAGTA
*
16810010 GGAAGCAGATTTAAGCCACCAGC
65 GGAAGCAGATTTAAGGCACCAGC
* * * * **
16810033 CTTATCTCCCTGAGCAGCAGTGGAGTAGGTTGAAGATTGCAGATCTTATCTCCCTAAGAAGTAGT
1 CTTATCTCCCTAAGCAGTAGTGGAGCAGATTGAAGACGGCAGATCTTATCTCCCTAAG--GTAGT
** **
16810098 -GG-AGCAGA-TCGAGG-ACGGCGAAT
64 AGGAAGCAGATTTAAGGCAC--C-AGC
* * * ** * * *
16810121 CTTATCTTCCTAAG--GTAGTAGGAAGCAGATTTAAGGCACCAG-CCTTATCTCCCTGA-GTAGC
1 CTTATCTCCCTAAGCAGTAGT-GG-AGCAGATTGAAGACGGCAGATCTTATCTCCCTAAGGTAGT
* * * **** *
16810182 AGTGGAGTAGATTGAAGATTGCAGAT
64 AG-GAAGCAGATTTAAGGCACCAG-C
* **
16810208 CTTATCTCCCTAACCAGTAGTGGAGCAGATCAAAGACGGC-GAATCTTATCTCCCTAAGGTAGTA
1 CTTATCTCCCTAAGCAGTAGTGGAGCAGATTGAAGACGGCAG-ATCTTATCTCCCTAAGGTAGTA
16810272 GGAAGCAGATTTAAGGCACCAGC
65 GGAAGCAGATTTAAGGCACCAGC
* * * * ** *
16810295 CTTATCTCCCTGAGCAGCAGTGGAGTAGGTTGAAGATTGCAGATCTTATCTCTCTAAGCAGTAGT
1 CTTATCTCCCTAAGCAGTAGTGGAGCAGATTGAAGACGGCAGATCTTATCTCCCTAAG--GTAGT
16810360 -GGAA-CAGAT
64 AGGAAGCAGAT
16810369 CGAAGACGGT
Statistics
Matches: 253, Mismatches: 61, Indels: 44
0.71 0.17 0.12
Matches are distributed among these distances:
84 4 0.02
85 3 0.01
86 10 0.04
87 151 0.60
88 64 0.25
89 21 0.08
ACGTcount: A:0.29, C:0.21, G:0.26, T:0.25
Consensus pattern (87 bp):
CTTATCTCCCTAAGCAGTAGTGGAGCAGATTGAAGACGGCAGATCTTATCTCCCTAAGGTAGTAG
GAAGCAGATTTAAGGCACCAGC
Found at i:16810628 original size:88 final size:88
Alignment explanation
Indices: 16810536--16810724 Score: 292
Period size: 88 Copynumber: 2.2 Consensus size: 88
16810526 AGGTAGAAGG
* ** * *
16810536 GAAGTAGATTTAAGCCACTAGCCTTACCTCCCTGAGTAGCAGTGGAGTA-GGTCGAAGATTGTAG
1 GAAGTAGATTAAAAACACCAGCCTTACCTCCCTGAGCAGCAGTGGAGTAGGGT-GAAGATTGTAG
16810600 ATCTTGTCTTCCTGTACTGGCAGT
65 ATCTTGTCTTCCTGTACTGGCAGT
*
16810624 GAAGTAGATTAAAAACACCAGCCTTATCTCCCTGAGCAGCAGTGGAGTAGGGTGAAGATTGTAGA
1 GAAGTAGATTAAAAACACCAGCCTTACCTCCCTGAGCAGCAGTGGAGTAGGGTGAAGATTGTAGA
16810689 TCTTGTCTTCCTGTACTGGCAGT
66 TCTTGTCTTCCTGTACTGGCAGT
*
16810712 GAAGCAGA-TAAAA
1 GAAGTAGATTAAAA
16810725 TAAAAAATAA
Statistics
Matches: 93, Mismatches: 7, Indels: 3
0.90 0.07 0.03
Matches are distributed among these distances:
87 5 0.05
88 85 0.91
89 3 0.03
ACGTcount: A:0.28, C:0.19, G:0.26, T:0.27
Consensus pattern (88 bp):
GAAGTAGATTAAAAACACCAGCCTTACCTCCCTGAGCAGCAGTGGAGTAGGGTGAAGATTGTAGA
TCTTGTCTTCCTGTACTGGCAGT
Found at i:16811050 original size:183 final size:183
Alignment explanation
Indices: 16810742--16811076 Score: 528
Period size: 183 Copynumber: 1.8 Consensus size: 183
16810732 TAAAATAAAA
* * * *
16810742 ACTAATCCTATCTCCCTAAAGTTGCAGTGGAGCGGATTAAAACGATGAATCTTATACCTTTGAAG
1 ACTAATCCTATCTCCCTAAAGTTGCAGTGGAGAGGATTAAAACGACGAATCCTATACCTTTGAAA
* * * *
16810807 TTACAGAGGGTCGGATTAAATCTAATCGTATCAAACCTTATCTCACTGAGGTCGCAGTGGAGCAG
66 TTACAGAGGGTCGGATTAAACCTAATCATATCAAACATTACCTCACTGAGGTCGCAGTGGAGCAG
16810872 GTTGAAG-ATACAAGTCTTATCTTCCTGAAGTTACAGTGAAGTAGGCTAAAGCG
131 GTTGAAGCA-ACAAGTCTTATCTTCCTGAAGTTACAGTGAAGTAGGCTAAAGCG
*
16810925 ACTAATCTTATCTCCCTAAAGTTGCAGTGGAGAGGATTAAAACGACGAATCCTATACCTTTGAAA
1 ACTAATCCTATCTCCCTAAAGTTGCAGTGGAGAGGATTAAAACGACGAATCCTATACCTTTGAAA
** * *
16810990 TTGTAGAGGGTCGGATTAAACCTTATCATATCAAACATTACCTCCCTGAGGTCGCAGTGGAGCAG
66 TTACAGAGGGTCGGATTAAACCTAATCATATCAAACATTACCTCACTGAGGTCGCAGTGGAGCAG
*
16811055 GTTGAGGCAACAAGTCTTATCT
131 GTTGAAGCAACAAGTCTTATCT
16811077 CCCTAACATT
Statistics
Matches: 137, Mismatches: 14, Indels: 2
0.90 0.09 0.01
Matches are distributed among these distances:
183 136 0.99
184 1 0.01
ACGTcount: A:0.31, C:0.19, G:0.22, T:0.28
Consensus pattern (183 bp):
ACTAATCCTATCTCCCTAAAGTTGCAGTGGAGAGGATTAAAACGACGAATCCTATACCTTTGAAA
TTACAGAGGGTCGGATTAAACCTAATCATATCAAACATTACCTCACTGAGGTCGCAGTGGAGCAG
GTTGAAGCAACAAGTCTTATCTTCCTGAAGTTACAGTGAAGTAGGCTAAAGCG
Found at i:16812485 original size:18 final size:18
Alignment explanation
Indices: 16812459--16812567 Score: 65
Period size: 18 Copynumber: 5.6 Consensus size: 18
16812449 TTTAATAATG
*
16812459 TTATCATTATTTTTACTA
1 TTATTATTATTTTTACTA
* *
16812477 TTATTATTATGTTTAATA
1 TTATTATTATTTTTACTA
* * * * *
16812495 CTGTTATTACTATTACCTTTT
1 TTATTATTATTTTTA-C--TA
16812516 TTATTTATATATTTTTACTA
1 TTA-TTAT-TATTTTTACTA
16812536 TTATTATTATTATTTATCTA
1 TTATTATTATT-TTTA-CTA
*
16812556 TTTAATATTATT
1 -TTATTATTATT
16812568 GTTCATTTAT
Statistics
Matches: 67, Mismatches: 16, Indels: 13
0.70 0.17 0.14
Matches are distributed among these distances:
18 29 0.43
19 8 0.12
20 7 0.10
21 12 0.18
22 5 0.07
23 6 0.09
ACGTcount: A:0.28, C:0.07, G:0.02, T:0.62
Consensus pattern (18 bp):
TTATTATTATTTTTACTA
Found at i:16812539 original size:20 final size:20
Alignment explanation
Indices: 16812520--16812567 Score: 55
Period size: 21 Copynumber: 2.4 Consensus size: 20
16812510 CCTTTTTTAT
16812520 TTATATATT-TTTA-CTATTA
1 TTAT-TATTATTTATCTATTA
16812539 TTATTATTATTTATCTATTTA
1 TTATTATTATTTATCTA-TTA
*
16812560 ATATTATT
1 TTATTATT
16812568 GTTCATTTAT
Statistics
Matches: 25, Mismatches: 1, Indels: 4
0.83 0.03 0.13
Matches are distributed among these distances:
18 4 0.16
19 8 0.32
20 3 0.12
21 10 0.40
ACGTcount: A:0.31, C:0.04, G:0.00, T:0.65
Consensus pattern (20 bp):
TTATTATTATTTATCTATTA
Found at i:16812577 original size:29 final size:29
Alignment explanation
Indices: 16812515--16812578 Score: 69
Period size: 29 Copynumber: 2.2 Consensus size: 29
16812505 TATTACCTTT
*
16812515 TTTATTTATATATTTTTACTATTATTATTA
1 TTTATTTATATA-TTTTAATATTATTATTA
* *
16812545 -TTATTTATCTA-TTTAATATTATTGTTCA
1 TTTATTTATATATTTTAATATTATTATT-A
16812573 TTTATT
1 TTTATT
16812579 AATGCATGAT
Statistics
Matches: 29, Mismatches: 3, Indels: 5
0.78 0.08 0.14
Matches are distributed among these distances:
27 13 0.45
28 1 0.03
29 15 0.52
ACGTcount: A:0.28, C:0.05, G:0.02, T:0.66
Consensus pattern (29 bp):
TTTATTTATATATTTTAATATTATTATTA
Found at i:16824635 original size:19 final size:19
Alignment explanation
Indices: 16824611--16824647 Score: 56
Period size: 19 Copynumber: 1.9 Consensus size: 19
16824601 ATTCTATATA
* *
16824611 TCTGTTCTTCTTATCTGAT
1 TCTGTTATTCGTATCTGAT
16824630 TCTGTTATTCGTATCTGA
1 TCTGTTATTCGTATCTGA
16824648 AATGGACTGA
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
19 16 1.00
ACGTcount: A:0.14, C:0.19, G:0.14, T:0.54
Consensus pattern (19 bp):
TCTGTTATTCGTATCTGAT
Found at i:16826885 original size:22 final size:22
Alignment explanation
Indices: 16826860--16826902 Score: 59
Period size: 22 Copynumber: 2.0 Consensus size: 22
16826850 ATAATAATAT
16826860 AATAATAAAATAACAACAAAAC
1 AATAATAAAATAACAACAAAAC
* * *
16826882 AATATTAAAATAGCAGCAAAA
1 AATAATAAAATAACAACAAAA
16826903 TAATGAAATT
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
22 18 1.00
ACGTcount: A:0.67, C:0.12, G:0.05, T:0.16
Consensus pattern (22 bp):
AATAATAAAATAACAACAAAAC
Found at i:16827235 original size:18 final size:18
Alignment explanation
Indices: 16827204--16827238 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
16827194 AAATTCTCAA
*
16827204 TTAAAAATAGTTTATTTT
1 TTAAAAATAATTTATTTT
*
16827222 TTAAACATAATTTATTT
1 TTAAAAATAATTTATTT
16827239 GTTTGAAATT
Statistics
Matches: 15, Mismatches: 2, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
18 15 1.00
ACGTcount: A:0.40, C:0.03, G:0.03, T:0.54
Consensus pattern (18 bp):
TTAAAAATAATTTATTTT
Found at i:16834307 original size:14 final size:13
Alignment explanation
Indices: 16834288--16834318 Score: 53
Period size: 14 Copynumber: 2.3 Consensus size: 13
16834278 GTGCAACGGT
16834288 CACAGGGCCAAGC
1 CACAGGGCCAAGC
16834301 ACACAGGGCCAAGC
1 -CACAGGGCCAAGC
16834315 CACA
1 CACA
16834319 TGCCCGTGTG
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
13 4 0.24
14 13 0.76
ACGTcount: A:0.35, C:0.39, G:0.26, T:0.00
Consensus pattern (13 bp):
CACAGGGCCAAGC
Found at i:16836516 original size:15 final size:15
Alignment explanation
Indices: 16836496--16836525 Score: 60
Period size: 15 Copynumber: 2.0 Consensus size: 15
16836486 ATAAAATGTG
16836496 CCGATTTAGTTAGTC
1 CCGATTTAGTTAGTC
16836511 CCGATTTAGTTAGTC
1 CCGATTTAGTTAGTC
16836526 TGTCAACAAT
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:0.20, C:0.20, G:0.20, T:0.40
Consensus pattern (15 bp):
CCGATTTAGTTAGTC
Found at i:16841399 original size:21 final size:21
Alignment explanation
Indices: 16841370--16841482 Score: 75
Period size: 21 Copynumber: 5.4 Consensus size: 21
16841360 CAGAAACCCG
* *
16841370 TAAGGGTTGAACGGAAGCTCA
1 TAAGAGTTGAACGGAAACTCA
*
16841391 TAAGAGTTGAACGGAAACCCA
1 TAAGAGTTGAACGGAAACTCA
* * * *
16841412 TAAGGGTTAAACTGAAGCTCA
1 TAAGAGTTGAACGGAAACTCA
* * * *
16841433 -AATGAGCTGAATGAAAACCCA
1 TAA-GAGTTGAACGGAAACTCA
* * *
16841454 TTAGGGTTGAACAGAAACTCA
1 TAAGAGTTGAACGGAAACTCA
*
16841475 TATGAGTT
1 TAAGAGTT
16841483 AACAGAAGCT
Statistics
Matches: 64, Mismatches: 26, Indels: 4
0.68 0.28 0.04
Matches are distributed among these distances:
20 2 0.03
21 61 0.95
22 1 0.02
ACGTcount: A:0.39, C:0.15, G:0.25, T:0.21
Consensus pattern (21 bp):
TAAGAGTTGAACGGAAACTCA
Found at i:16841408 original size:42 final size:42
Alignment explanation
Indices: 16841362--16841482 Score: 136
Period size: 42 Copynumber: 2.9 Consensus size: 42
16841352 GTACTAAACA
* *
16841362 GAAACCCGTAAGGGTTGAACGGAAGCTCATAAGAGTTGAACG
1 GAAACCCATAAGGGTTGAACAGAAGCTCATAAGAGTTGAACG
* * * *
16841404 GAAACCCATAAGGGTTAAACTGAAGCTCA-AATGAGCTGAATG
1 GAAACCCATAAGGGTTGAACAGAAGCTCATAA-GAGTTGAACG
* * * *
16841446 AAAACCCATTAGGGTTGAACAGAAACTCATATGAGTT
1 GAAACCCATAAGGGTTGAACAGAAGCTCATAAGAGTT
16841483 AACAGAAGCT
Statistics
Matches: 65, Mismatches: 12, Indels: 4
0.80 0.15 0.05
Matches are distributed among these distances:
41 2 0.03
42 62 0.95
43 1 0.02
ACGTcount: A:0.39, C:0.17, G:0.25, T:0.20
Consensus pattern (42 bp):
GAAACCCATAAGGGTTGAACAGAAGCTCATAAGAGTTGAACG
Found at i:16841500 original size:20 final size:21
Alignment explanation
Indices: 16841463--16841511 Score: 55
Period size: 20 Copynumber: 2.4 Consensus size: 21
16841453 ATTAGGGTTG
*
16841463 AACAGAAACTCATATGAG-TT
1 AACAGAAACTCATATGAGCTA
* * *
16841483 AACAGAAGCTCGTGTGAGCTA
1 AACAGAAACTCATATGAGCTA
16841504 AACAGAAA
1 AACAGAAA
16841512 GTAAATACGA
Statistics
Matches: 23, Mismatches: 5, Indels: 1
0.79 0.17 0.03
Matches are distributed among these distances:
20 15 0.65
21 8 0.35
ACGTcount: A:0.45, C:0.16, G:0.20, T:0.18
Consensus pattern (21 bp):
AACAGAAACTCATATGAGCTA
Found at i:16843396 original size:17 final size:17
Alignment explanation
Indices: 16843374--16843412 Score: 62
Period size: 17 Copynumber: 2.3 Consensus size: 17
16843364 ATTCTTTTTA
16843374 TCAAAA-CAAAATAATTT
1 TCAAAATCAAAAT-ATTT
16843391 TCAAAATCAAAATATTT
1 TCAAAATCAAAATATTT
16843408 TCAAA
1 TCAAA
16843413 CTTTCAAACT
Statistics
Matches: 21, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
17 15 0.71
18 6 0.29
ACGTcount: A:0.56, C:0.13, G:0.00, T:0.31
Consensus pattern (17 bp):
TCAAAATCAAAATATTT
Found at i:16844351 original size:17 final size:18
Alignment explanation
Indices: 16844306--16844351 Score: 51
Period size: 17 Copynumber: 2.6 Consensus size: 18
16844296 TTTCGGTAAA
16844306 ATATATTCAATTAATATTT
1 ATATATT-AATTAATATTT
* *
16844325 -TGTATGAATTAA-ATTT
1 ATATATTAATTAATATTT
16844341 ATATATTAATT
1 ATATATTAATT
16844352 TTATATATGT
Statistics
Matches: 22, Mismatches: 4, Indels: 4
0.73 0.13 0.13
Matches are distributed among these distances:
16 4 0.18
17 14 0.64
18 4 0.18
ACGTcount: A:0.41, C:0.02, G:0.04, T:0.52
Consensus pattern (18 bp):
ATATATTAATTAATATTT
Found at i:16859523 original size:20 final size:19
Alignment explanation
Indices: 16859498--16859536 Score: 60
Period size: 19 Copynumber: 2.0 Consensus size: 19
16859488 GATCTAAATG
*
16859498 ATATAATATATAATAATAGA
1 ATATAATAT-TAAAAATAGA
16859518 ATATAATATTAAAAATAGA
1 ATATAATATTAAAAATAGA
16859537 GTTGCATCAT
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
19 9 0.50
20 9 0.50
ACGTcount: A:0.62, C:0.00, G:0.05, T:0.33
Consensus pattern (19 bp):
ATATAATATTAAAAATAGA
Found at i:16861904 original size:20 final size:20
Alignment explanation
Indices: 16861873--16861934 Score: 61
Period size: 20 Copynumber: 3.1 Consensus size: 20
16861863 TGCAAATCAT
*
16861873 TTAAAATGATTTTAACTTGA
1 TTAAAATCATTTTAACTTGA
* * * *
16861893 TTGAAATCATTTTGACCTGG
1 TTAAAATCATTTTAACTTGA
**
16861913 TTAAAATCATTTGCACTTGA
1 TTAAAATCATTTTAACTTGA
16861933 TT
1 TT
16861935 TTAAATTGTT
Statistics
Matches: 32, Mismatches: 10, Indels: 0
0.76 0.24 0.00
Matches are distributed among these distances:
20 32 1.00
ACGTcount: A:0.32, C:0.11, G:0.13, T:0.44
Consensus pattern (20 bp):
TTAAAATCATTTTAACTTGA
Found at i:16885944 original size:26 final size:26
Alignment explanation
Indices: 16885876--16885945 Score: 86
Period size: 26 Copynumber: 2.7 Consensus size: 26
16885866 ACAAATCTTA
* *
16885876 AGAATCTAACAAATTAACTAACTTGG
1 AGAACCTAACAAATTAACTAACTAGG
* **
16885902 TGAACCTATTAAATTAACTAACTAGG
1 AGAACCTAACAAATTAACTAACTAGG
*
16885928 AGAACCTAACAAGTTAAC
1 AGAACCTAACAAATTAAC
16885946 AAACCTTGCA
Statistics
Matches: 35, Mismatches: 9, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
26 35 1.00
ACGTcount: A:0.46, C:0.17, G:0.11, T:0.26
Consensus pattern (26 bp):
AGAACCTAACAAATTAACTAACTAGG
Found at i:16891665 original size:17 final size:17
Alignment explanation
Indices: 16891643--16891678 Score: 72
Period size: 17 Copynumber: 2.1 Consensus size: 17
16891633 GAAGTACGCT
16891643 TATTTTGGAGAAAATGA
1 TATTTTGGAGAAAATGA
16891660 TATTTTGGAGAAAATGA
1 TATTTTGGAGAAAATGA
16891677 TA
1 TA
16891679 CATTGCCTAT
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 19 1.00
ACGTcount: A:0.42, C:0.00, G:0.22, T:0.36
Consensus pattern (17 bp):
TATTTTGGAGAAAATGA
Found at i:16907628 original size:23 final size:23
Alignment explanation
Indices: 16907602--16907647 Score: 92
Period size: 23 Copynumber: 2.0 Consensus size: 23
16907592 AAATTATCTT
16907602 AGCCTTCTTGATTTGTTGTCAAA
1 AGCCTTCTTGATTTGTTGTCAAA
16907625 AGCCTTCTTGATTTGTTGTCAAA
1 AGCCTTCTTGATTTGTTGTCAAA
16907648 CTTATCAATT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
23 23 1.00
ACGTcount: A:0.22, C:0.17, G:0.17, T:0.43
Consensus pattern (23 bp):
AGCCTTCTTGATTTGTTGTCAAA
Found at i:16908423 original size:29 final size:29
Alignment explanation
Indices: 16908381--16908439 Score: 100
Period size: 29 Copynumber: 2.0 Consensus size: 29
16908371 GCAACGTCGT
16908381 CATGACATACTGAGATAACCACGCCATGA
1 CATGACATACTGAGATAACCACGCCATGA
* *
16908410 CATGACATACTGAGATGACCACGTCATGA
1 CATGACATACTGAGATAACCACGCCATGA
16908439 C
1 C
16908440 GAAGTCGTGA
Statistics
Matches: 28, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
29 28 1.00
ACGTcount: A:0.36, C:0.27, G:0.19, T:0.19
Consensus pattern (29 bp):
CATGACATACTGAGATAACCACGCCATGA
Found at i:16925065 original size:30 final size:31
Alignment explanation
Indices: 16925031--16925098 Score: 84
Period size: 30 Copynumber: 2.2 Consensus size: 31
16925021 TTGCCCAAGA
** * **
16925031 GTAAATACTCAAAATTTGAGGGATTAA-AGT
1 GTAAATACGAAAAATTTGAAGGACCAATAGT
16925061 GTAAATACGAAAAATTTGAAGGACCAATAGT
1 GTAAATACGAAAAATTTGAAGGACCAATAGT
16925092 GTAAATA
1 GTAAATA
16925099 TTTTAAGGGT
Statistics
Matches: 32, Mismatches: 5, Indels: 1
0.84 0.13 0.03
Matches are distributed among these distances:
30 22 0.69
31 10 0.31
ACGTcount: A:0.47, C:0.07, G:0.19, T:0.26
Consensus pattern (31 bp):
GTAAATACGAAAAATTTGAAGGACCAATAGT
Found at i:16929158 original size:101 final size:101
Alignment explanation
Indices: 16929011--16929261 Score: 321
Period size: 101 Copynumber: 2.5 Consensus size: 101
16929001 CAAACATAAT
* * * *
16929011 ACCATGGTTGGACCATG-TAGTGTTTAAATGTAAGACCATAGTTGGGCTATGCCATTCCGATGAT
1 ACCATGGTTGGACCATGACAGTATTTATATGTAAGACCATAGTTGGGCTATGACATTCCGATGAT
* *
16929075 AAGACTATAACTGGGTTATGGCACTATGGATGCAAG
66 AAGACCATAACTGGGTTATGGCACTATGAATGCAAG
* ** *
16929111 ACCATGGTTGGACCATGACAGTATTTATATGTAAGACCATAGCTGGGCTATGACATTTTGATGGT
1 ACCATGGTTGGACCATGACAGTATTTATATGTAAGACCATAGTTGGGCTATGACATTCCGATGAT
*
16929176 AAGACCATAACTGGGTTATGGCACTATGAATGTAAG
66 AAGACCATAACTGGGTTATGGCACTATGAATGCAAG
** ** *
16929212 ACCATGGCAAGG-CCATGACA--ATGCATATGTAAGACCATAGTTGGACTATG
1 ACCATGG-TTGGACCATGACAGTATTTATATGTAAGACCATAGTTGGGCTATG
16929262 GCACAAATGA
Statistics
Matches: 132, Mismatches: 17, Indels: 5
0.86 0.11 0.03
Matches are distributed among these distances:
99 26 0.20
100 17 0.13
101 87 0.66
102 2 0.02
ACGTcount: A:0.31, C:0.16, G:0.25, T:0.28
Consensus pattern (101 bp):
ACCATGGTTGGACCATGACAGTATTTATATGTAAGACCATAGTTGGGCTATGACATTCCGATGAT
AAGACCATAACTGGGTTATGGCACTATGAATGCAAG
Found at i:16929211 original size:33 final size:33
Alignment explanation
Indices: 16929037--16929216 Score: 103
Period size: 33 Copynumber: 5.4 Consensus size: 33
16929027 GTAGTGTTTA
** * * **
16929037 AATGTAAGACCATAGTTGGGCTATGCCATTCCG
1 AATGTAAGACCATAACTGGGCTATGACACTATG
* * *
16929070 -ATGATAAGACTATAACTGGGTTATGGCACTATG
1 AATG-TAAGACCATAACTGGGCTATGACACTATG
* * *** * * * *
16929103 GATGCAAGACCATGGTTGGACCATGACAGTATTT
1 AATGTAAGACCATAACTGGGCTATGACACTA-TG
* * *
16929137 ATATGTAAGACCATAGCTGGGCTATGACATTTTG
1 A-ATGTAAGACCATAACTGGGCTATGACACTATG
* *
16929171 -ATGGTAAGACCATAACTGGGTTATGGCACTATG
1 AAT-GTAAGACCATAACTGGGCTATGACACTATG
16929204 AATGTAAGACCAT
1 AATGTAAGACCAT
16929217 GGCAAGGCCA
Statistics
Matches: 108, Mismatches: 33, Indels: 12
0.71 0.22 0.08
Matches are distributed among these distances:
32 5 0.05
33 73 0.68
34 7 0.06
35 23 0.21
ACGTcount: A:0.31, C:0.16, G:0.24, T:0.28
Consensus pattern (33 bp):
AATGTAAGACCATAACTGGGCTATGACACTATG
Found at i:16931384 original size:30 final size:31
Alignment explanation
Indices: 16931348--16931433 Score: 120
Period size: 31 Copynumber: 2.8 Consensus size: 31
16931338 GTATATGTTT
*
16931348 TATACATTGCCGAA-TTGATTTGTATATAGA
1 TATACATTGCCGAATTTGATTCGTATATAGA
* *
16931378 TATACATTGCTGAATTTGATTCGTATATGGA
1 TATACATTGCCGAATTTGATTCGTATATAGA
* *
16931409 TATATATCGCCGAATTTGATTCGTA
1 TATACATTGCCGAATTTGATTCGTA
16931434 CATGGATTTA
Statistics
Matches: 49, Mismatches: 6, Indels: 1
0.88 0.11 0.02
Matches are distributed among these distances:
30 13 0.27
31 36 0.73
ACGTcount: A:0.30, C:0.12, G:0.17, T:0.41
Consensus pattern (31 bp):
TATACATTGCCGAATTTGATTCGTATATAGA
Found at i:16931430 original size:31 final size:31
Alignment explanation
Indices: 16931356--16931446 Score: 112
Period size: 31 Copynumber: 3.0 Consensus size: 31
16931346 TTTATACATT
* * * *
16931356 GCCGAA-TTGATTTGTATATAGATATACATT
1 GCCGAATTTGATTCGTATATGGATATATATC
*
16931386 GCTGAATTTGATTCGTATATGGATATATATC
1 GCCGAATTTGATTCGTATATGGATATATATC
* *
16931417 GCCGAATTTGATTCGTACATGGATTTATAT
1 GCCGAATTTGATTCGTATATGGATATATAT
16931447 TGTTGAACTA
Statistics
Matches: 52, Mismatches: 8, Indels: 1
0.85 0.13 0.02
Matches are distributed among these distances:
30 5 0.10
31 47 0.90
ACGTcount: A:0.30, C:0.11, G:0.19, T:0.41
Consensus pattern (31 bp):
GCCGAATTTGATTCGTATATGGATATATATC
Found at i:16931647 original size:43 final size:43
Alignment explanation
Indices: 16931585--16931700 Score: 169
Period size: 43 Copynumber: 2.7 Consensus size: 43
16931575 TGTGATTTCA
* * * *
16931585 TGTAAAACCATGTCTGGGACATTTGCATCGAAGTGAGACAACG
1 TGTAAGACCATGTCTGGGACATTAGCATCGAAGAGAGAAAACG
* *
16931628 TGTAAGACCTTGTTTGGGACATTAGCATCGAAGAGAGAAAACG
1 TGTAAGACCATGTCTGGGACATTAGCATCGAAGAGAGAAAACG
*
16931671 TGTAAGACCATGTCTGGGACATTGGCATCG
1 TGTAAGACCATGTCTGGGACATTAGCATCG
16931701 TATATGATTC
Statistics
Matches: 64, Mismatches: 9, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
43 64 1.00
ACGTcount: A:0.31, C:0.17, G:0.28, T:0.24
Consensus pattern (43 bp):
TGTAAGACCATGTCTGGGACATTAGCATCGAAGAGAGAAAACG
Found at i:16959237 original size:75 final size:74
Alignment explanation
Indices: 16959065--16959326 Score: 242
Period size: 75 Copynumber: 3.5 Consensus size: 74
16959055 CATTTATAGT
* * * * * **
16959065 TGATATCTTTACGGTTTGCTGATTTAAAATCACGACCCTCGATTTTCTATTAGCTCGATGACCTA
1 TGATATATTTACGGTTCGCTGATTTAAGATCA-AACCCTCGAGTTTCTAACAGCTCGATGACCTA
* *
16959130 TATTCACATC
65 GATTCACAGC
* ** * * *
16959140 TGTTATATTTACTATTCACTGATTTAAGATCGAAACTCTCGAGTTTCTAACAGCTCAATGACCTA
1 TGATATATTTACGGTTCGCTGATTTAAGATC-AAACCCTCGAGTTTCTAACAGCTCGATGACCTA
16959205 GATTCACAGC
65 GATTCACAGC
* * * * *
16959215 TGATATCTTTACGG-TCTGCTGATTTAAGATCTCAACCCTCG-GTTTACTACCAACTCGATGACT
1 TGATATATTTACGGTTC-GCTGATTTAAGATC-AAACCCTCGAGTTT-CTAACAGCTCGATGACC
*
16959278 TATG-TTCATAGC
63 TA-GATTCACAGC
*
16959290 TGATATATTTATGGTTCGCTGATTTAAGATCACAACC
1 TGATATATTTACGGTTCGCTGATTTAAGATCA-AACC
16959327 TATCTATCTT
Statistics
Matches: 150, Mismatches: 31, Indels: 12
0.78 0.16 0.06
Matches are distributed among these distances:
74 6 0.04
75 140 0.93
76 4 0.03
ACGTcount: A:0.27, C:0.22, G:0.15, T:0.37
Consensus pattern (74 bp):
TGATATATTTACGGTTCGCTGATTTAAGATCAAACCCTCGAGTTTCTAACAGCTCGATGACCTAG
ATTCACAGC
Found at i:16959529 original size:105 final size:105
Alignment explanation
Indices: 16959309--16959535 Score: 256
Period size: 105 Copynumber: 2.2 Consensus size: 105
16959299 TATGGTTCGC
* * * * *
16959309 TGATTTAAGATCACAACCTATCTATCTTTAAGTTAGCTAATTTAAGATCGCAACTCCTAAACAAC
1 TGATTTAATATCGCAACCTATCTATCTTTAAGTTAGCTAATTTAAAATCACAACTCCTAAACAAA
** * *
16959374 TTGATGACCTACGTTAACAACTAATATTATAAAGGTTAGC
66 TCAATGACCTACGTTAACAAATAATATTATAAAGGTTAGA
** * * * ***
16959414 TGATCCAATATCGCAACCTATCTATCTTTGAGTTAGTTGATTTAAAATCATGGCTCCTAAACAAA
1 TGATTTAATATCGCAACCTATCTATCTTTAAGTTAGCTAATTTAAAATCACAACTCCTAAACAAA
* * * *
16959479 TCAATGACCTATGTTTACAAATGATATTATAAAGGTTGGA
66 TCAATGACCTACGTTAACAAATAATATTATAAAGGTTAGA
*
16959519 TGATTTAATATTGCAAC
1 TGATTTAATATCGCAAC
16959536 GCCTAAACAA
Statistics
Matches: 98, Mismatches: 24, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
105 98 1.00
ACGTcount: A:0.36, C:0.17, G:0.13, T:0.34
Consensus pattern (105 bp):
TGATTTAATATCGCAACCTATCTATCTTTAAGTTAGCTAATTTAAAATCACAACTCCTAAACAAA
TCAATGACCTACGTTAACAAATAATATTATAAAGGTTAGA
Found at i:16959661 original size:173 final size:173
Alignment explanation
Indices: 16959348--16959708 Score: 470
Period size: 173 Copynumber: 2.1 Consensus size: 173
16959338 AAGTTAGCTA
* * * *
16959348 ATTTAAGATCGCAACTCCTAAACAACTTGATGACCTACGTTAACAACTAATATTATAAAGGTTAG
1 ATTTAATATCGCAACGCCTAAACAACTCGATGAACTACGTTAACAACTAATATTATAAAGGTTAG
* **
16959413 CTGATCCAATATCGCAACCTATCTATCTTTGAGTTAGTTGATTTAAAATCATGGCTCCTAAACAA
66 CTGATCCAATATCGCAACCTATCTATCTTTGAGTTAGCTGATTTAAAATCACAGCTCCTAAACAA
** * * *
16959478 ATCAATGACCTATGTTTACAAATGATATTATAAAGGTTGGATG
131 ATCAATGACCTACATTCACAAATGATATTATAAAGGGTAGATG
* * * *
16959521 ATTTAATATTGCAACGCCTAAACAACTCGATGAACTACGTTCACAGCTGATATTATAAAGGTTAG
1 ATTTAATATCGCAACGCCTAAACAACTCGATGAACTACGTTAACAACTAATATTATAAAGGTTAG
** ** * *
16959586 CTGATTTAATATCTTAACCTATCTATCTTTGAGTTAGCTGATTTAATATCACAGCTCCTAAACAG
66 CTGATCCAATATCGCAACCTATCTATCTTTGAGTTAGCTGATTTAAAATCACAGCTCCTAAACAA
* * ** *
16959651 CTCGATGACCTACATTCACATCTGATATTATAAAGGGTAGCTG
131 ATCAATGACCTACATTCACAAATGATATTATAAAGGGTAGATG
*
16959694 ATTTAATATGGCAAC
1 ATTTAATATCGCAAC
16959709 CCATCTATCT
Statistics
Matches: 160, Mismatches: 28, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
173 160 1.00
ACGTcount: A:0.35, C:0.18, G:0.14, T:0.33
Consensus pattern (173 bp):
ATTTAATATCGCAACGCCTAAACAACTCGATGAACTACGTTAACAACTAATATTATAAAGGTTAG
CTGATCCAATATCGCAACCTATCTATCTTTGAGTTAGCTGATTTAAAATCACAGCTCCTAAACAA
ATCAATGACCTACATTCACAAATGATATTATAAAGGGTAGATG
Found at i:16959701 original size:105 final size:105
Alignment explanation
Indices: 16959519--16959950 Score: 426
Period size: 105 Copynumber: 4.1 Consensus size: 105
16959509 AAAGGTTGGA
* * * *
16959519 TGATTTAATATTGCAACGCCTAAACAACTCGATGAACTACGTTCACAGCTGATATTATAAAGGTT
1 TGATTTAATATCGCAACTCCTAAACAGCTCGATGACCTACGTTCACAGCTGATATTATAAAGGTT
** *
16959584 AGCTGATTTAATATCTTAACCTATCTATCTTTGAGTTAGC
66 AGCTGATTTAATATCACAACCTATCTATATTTGAGTTAGC
* * * * *
16959624 TGATTTAATATCACAGCTCCTAAACAGCTCGATGACCTACATTCACATCTGATATTATAAAGGGT
1 TGATTTAATATCGCAACTCCTAAACAGCTCGATGACCTACGTTCACAGCTGATATTATAAAGGTT
** * *
16959689 AGCTGATTTAATATGGCAACCCATCTATCTTTGAGTTAGC
66 AGCTGATTTAATATCACAACCTATCTATATTTGAGTTAGC
** * * * *
16959729 TGATTTACGATCGCAACTCCTAAATAGCTC-ATTGACCTACGTTCACGGCTAATGTTATAAAGGT
1 TGATTTAATATCGCAACTCCTAAACAGCTCGA-TGACCTACGTTCACAGCTGATATTATAAAGGT
* ** *
16959793 TATCTGATTTAAGT-TCACAACCTAAGTTTATTTGAGTTCA-C
65 TAGCTGATTTAA-TATCACAACCTATCTATATTTGAGTT-AGC
* * * * * ** * *
16959834 TAATTTAAGATCGCAACTCCT-AATAGCTTGCTGACCTACGTTCACAATTGATATTATTAAGGCT
1 TGATTTAATATCGCAACTCCTAAACAGCTCGATGACCTACGTTCACAGCTGATATTATAAAGGTT
* * * *
16959898 CGCTGATTTAAGATCAGAACC--TCTAATTATTTGAGTTAGT
66 AGCTGATTTAATATCACAACCTATCT-A-TATTTGAGTTAGC
16959938 TGATTTAATATCG
1 TGATTTAATATCG
16959951 TAATTCTGAA
Statistics
Matches: 266, Mismatches: 53, Indels: 17
0.79 0.16 0.05
Matches are distributed among these distances:
102 1 0.00
103 1 0.00
104 71 0.27
105 191 0.72
106 2 0.01
ACGTcount: A:0.31, C:0.19, G:0.15, T:0.35
Consensus pattern (105 bp):
TGATTTAATATCGCAACTCCTAAACAGCTCGATGACCTACGTTCACAGCTGATATTATAAAGGTT
AGCTGATTTAATATCACAACCTATCTATATTTGAGTTAGC
Found at i:16959789 original size:278 final size:278
Alignment explanation
Indices: 16959265--16959793 Score: 648
Period size: 278 Copynumber: 1.9 Consensus size: 278
16959255 GGTTTACTAC
* * * * *
16959265 CAACTCGATGACTTATGTTCATAGCTGATATATTTATGGTTCGCTGATTTAAGATCACAACCTAT
1 CAACTCGATGACTTACGTTCACAGCTGATATATTAAAGGTTAGCTGATTTAAGATCACAACCTAT
* * *
16959330 CTATCTTTAAGTTAGCTAATTTAAGATCGCAACTCCTAAACAACTTGATGACCTACGTTAACAAC
66 CTATCTTTAAGTTAGCTAATTTAAGATCACAACTCCTAAACAACTCGATGACCTACATTAACAAC
* * *
16959395 TAATATTATAAAGGTTAGCTGATCCAATATCGCAACCTATCTATCTTTGAGTTAGTTGATTTAAA
131 TAATATTATAAAGGGTAGCTGATCCAATATCGCAACCCATCTATCTTTGAGTTAGCTGATTTAAA
*** * * *
16959460 ATCATGGCTCCTAAACAAATCAATGACCTATGTTTACAAATGATATTATAAAGGTTGGATGATTT
196 ATCACAACTCCTAAACAAATCAATGACCTACGTTCACAAATAATATTATAAAGGTTGGATGATTT
16959525 AATATTGCAACGCCTAAA
261 AATATTGCAACGCCTAAA
* **
16959543 CAACTCGATGAAC-TACGTTCACAGCTGATAT-TATAAAGGTTAGCTGATTTAATATCTTAACCT
1 CAACTCGATG-ACTTACGTTCACAGCTGATATAT-TAAAGGTTAGCTGATTTAAGATCACAACCT
* * * * * *
16959606 ATCTATCTTTGAGTTAGCTGATTTAATATCACAGCTCCTAAACAGCTCGATGACCTACATTCACA
64 ATCTATCTTTAAGTTAGCTAATTTAAGATCACAACTCCTAAACAACTCGATGACCTACATTAACA
* * ** *
16959671 TCTGATATTATAAAGGGTAGCTGATTTAATATGGCAACCCATCTATCTTTGAGTTAGCTGATTTA
129 ACTAATATTATAAAGGGTAGCTGATCCAATATCGCAACCCATCTATCTTTGAGTTAGCTGATTTA
** * * ** * *** *
16959736 CGATCGCAACTCCTAAATAGCTCATTGACCTACGTTCACGGCTAATGTTATAAAGGTT
194 AAATCACAACTCCTAAACAAATCAATGACCTACGTTCACAAATAATATTATAAAGGTT
16959794 ATCTGATTTA
Statistics
Matches: 207, Mismatches: 42, Indels: 4
0.82 0.17 0.02
Matches are distributed among these distances:
277 1 0.00
278 204 0.99
279 2 0.01
ACGTcount: A:0.33, C:0.19, G:0.15, T:0.34
Consensus pattern (278 bp):
CAACTCGATGACTTACGTTCACAGCTGATATATTAAAGGTTAGCTGATTTAAGATCACAACCTAT
CTATCTTTAAGTTAGCTAATTTAAGATCACAACTCCTAAACAACTCGATGACCTACATTAACAAC
TAATATTATAAAGGGTAGCTGATCCAATATCGCAACCCATCTATCTTTGAGTTAGCTGATTTAAA
ATCACAACTCCTAAACAAATCAATGACCTACGTTCACAAATAATATTATAAAGGTTGGATGATTT
AATATTGCAACGCCTAAA
Found at i:16973938 original size:19 final size:20
Alignment explanation
Indices: 16973898--16973938 Score: 50
Period size: 20 Copynumber: 2.1 Consensus size: 20
16973888 TCCAAAATTC
*
16973898 AAATAATAAAAATAATGAGA
1 AAATAATAAAAATAAAGAGA
16973918 AAATAA-AAAAATTAAAG-GA
1 AAATAATAAAAA-TAAAGAGA
16973937 AA
1 AA
16973939 TTATATGACA
Statistics
Matches: 19, Mismatches: 1, Indels: 3
0.83 0.04 0.13
Matches are distributed among these distances:
19 9 0.47
20 10 0.53
ACGTcount: A:0.73, C:0.00, G:0.10, T:0.17
Consensus pattern (20 bp):
AAATAATAAAAATAAAGAGA
Found at i:16976176 original size:29 final size:26
Alignment explanation
Indices: 16976144--16976200 Score: 80
Period size: 25 Copynumber: 2.1 Consensus size: 26
16976134 TACATACGCA
16976144 TATTTTTTTAATATAATGTAATTATTTTT
1 TATTTTTTT--TAT-ATGTAATTATTTTT
16976173 TA-TTTTTTTATATGTAATTATTTTT
1 TATTTTTTTTATATGTAATTATTTTT
16976198 TAT
1 TAT
16976201 AATCTATATG
Statistics
Matches: 27, Mismatches: 0, Indels: 5
0.84 0.00 0.16
Matches are distributed among these distances:
25 16 0.59
26 3 0.11
28 6 0.22
29 2 0.07
ACGTcount: A:0.28, C:0.00, G:0.04, T:0.68
Consensus pattern (26 bp):
TATTTTTTTTATATGTAATTATTTTT
Found at i:16976208 original size:24 final size:24
Alignment explanation
Indices: 16976144--16976238 Score: 79
Period size: 25 Copynumber: 3.9 Consensus size: 24
16976134 TACATACGCA
16976144 TATTTTTT-TAATATA-ATGTAAT
1 TATTTTTTATAATATATATGTAAT
** *
16976166 TATTTTTTATTTTTTTATATGTAAT
1 TATTTTTTA-TAATATATATGTAAT
*
16976191 TATTTTTTATAATCTATATGT-AT
1 TATTTTTTATAATATATATGTAAT
* *
16976214 ATATTTATTTTTGTATATATATGTA
1 -TATTT-TTTAT-AATATATATGTA
16976239 TGTATACATA
Statistics
Matches: 57, Mismatches: 9, Indels: 9
0.76 0.12 0.12
Matches are distributed among these distances:
22 8 0.14
23 2 0.04
24 18 0.32
25 20 0.35
26 9 0.16
ACGTcount: A:0.31, C:0.01, G:0.05, T:0.63
Consensus pattern (24 bp):
TATTTTTTATAATATATATGTAAT
Found at i:16980985 original size:44 final size:44
Alignment explanation
Indices: 16980922--16981006 Score: 170
Period size: 44 Copynumber: 1.9 Consensus size: 44
16980912 GAAATATGAT
16980922 AATAAATTTGAATCTATCCTAATTGTGTTATGTATGTGTTCGAC
1 AATAAATTTGAATCTATCCTAATTGTGTTATGTATGTGTTCGAC
16980966 AATAAATTTGAATCTATCCTAATTGTGTTATGTATGTGTTC
1 AATAAATTTGAATCTATCCTAATTGTGTTATGTATGTGTTC
16981007 CACTAATGCT
Statistics
Matches: 41, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
44 41 1.00
ACGTcount: A:0.29, C:0.11, G:0.15, T:0.45
Consensus pattern (44 bp):
AATAAATTTGAATCTATCCTAATTGTGTTATGTATGTGTTCGAC
Found at i:16982926 original size:26 final size:26
Alignment explanation
Indices: 16982879--16982928 Score: 66
Period size: 26 Copynumber: 1.9 Consensus size: 26
16982869 AGAATCTAAC
* *
16982879 AAATTAACTAACTTCGTAAACCTATT
1 AAATTAACTAACTTAGGAAACCTATT
16982905 AAATTAACTAAC-TAGGAGAACCTA
1 AAATTAACTAACTTAGGA-AACCTA
16982929 ACAAGTTAAC
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
25 3 0.14
26 18 0.86
ACGTcount: A:0.46, C:0.18, G:0.08, T:0.28
Consensus pattern (26 bp):
AAATTAACTAACTTAGGAAACCTATT
Found at i:16991853 original size:3 final size:3
Alignment explanation
Indices: 16991845--16991906 Score: 88
Period size: 3 Copynumber: 20.7 Consensus size: 3
16991835 ACCTCATATG
* * *
16991845 AAT AAT AAT AAT AAT AAT AAT AAT AAT GAT AAT AAT AAT AGT AGT AAT
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
*
16991893 AAC AAT AAT AAT AA
1 AAT AAT AAT AAT AA
16991907 ACTAATTAAA
Statistics
Matches: 53, Mismatches: 6, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
3 53 1.00
ACGTcount: A:0.63, C:0.02, G:0.05, T:0.31
Consensus pattern (3 bp):
AAT
Found at i:17000158 original size:50 final size:50
Alignment explanation
Indices: 17000083--17000268 Score: 282
Period size: 50 Copynumber: 3.7 Consensus size: 50
17000073 ATTTGGGTAA
17000083 AGAGGTCCCATGTAAGACCATGTCTGGGACATGGCGTTGGCACCGAGATG
1 AGAGGTCCCATGTAAGACCATGTCTGGGACATGGCGTTGGCACCGAGATG
* *
17000133 AGAGGTCCCTTGTGAGACCATGTCTGGGACATGGCGTTGGCACCGAGATG
1 AGAGGTCCCATGTAAGACCATGTCTGGGACATGGCGTTGGCACCGAGATG
** * * *
17000183 AGAGGTCCCCCGTAAGACCATGTCTGGGACATGGCATGGGCACCGATATG
1 AGAGGTCCCATGTAAGACCATGTCTGGGACATGGCGTTGGCACCGAGATG
**
17000233 AGAACATCCCATGTAAGACCATGTCTGGGACATGGC
1 AG-AGGTCCCATGTAAGACCATGTCTGGGACATGGC
17000269 TTTTGCATGT
Statistics
Matches: 123, Mismatches: 12, Indels: 1
0.90 0.09 0.01
Matches are distributed among these distances:
50 94 0.76
51 29 0.24
ACGTcount: A:0.24, C:0.24, G:0.32, T:0.20
Consensus pattern (50 bp):
AGAGGTCCCATGTAAGACCATGTCTGGGACATGGCGTTGGCACCGAGATG
Found at i:17011227 original size:29 final size:29
Alignment explanation
Indices: 17011194--17011250 Score: 87
Period size: 29 Copynumber: 2.0 Consensus size: 29
17011184 CAACGTCATC
* *
17011194 ATGACATGCTGAGATGACCACGCCATGAT
1 ATGACATACTGAGATAACCACGCCATGAT
*
17011223 ATGACATACTGAGATAACCACGTCATGA
1 ATGACATACTGAGATAACCACGCCATGA
17011251 CGAAGTCGTG
Statistics
Matches: 25, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
29 25 1.00
ACGTcount: A:0.35, C:0.23, G:0.21, T:0.21
Consensus pattern (29 bp):
ATGACATACTGAGATAACCACGCCATGAT
Found at i:17018673 original size:22 final size:20
Alignment explanation
Indices: 17018632--17018668 Score: 58
Period size: 20 Copynumber: 1.9 Consensus size: 20
17018622 AAGGACAAAA
17018632 AATGTTATTTTCGTTGTTTT
1 AATGTTATTTTCGTTGTTTT
*
17018652 AATGTTATGTTC-TTGTT
1 AATGTTATTTTCGTTGTT
17018669 GTTTTCTCCC
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
19 5 0.31
20 11 0.69
ACGTcount: A:0.16, C:0.05, G:0.16, T:0.62
Consensus pattern (20 bp):
AATGTTATTTTCGTTGTTTT
Found at i:17030050 original size:33 final size:32
Alignment explanation
Indices: 17029906--17030084 Score: 115
Period size: 33 Copynumber: 5.4 Consensus size: 32
17029896 AAGTGTTTAA
* * **
17029906 ATGTAAGACCATAGTTGGGCTATGGGATTCCG
1 ATGTAAGACCATAGCTGGGCTATGGCATTTTG
* * * * *
17029938 ATGATAAGACTATAACTGGGTTATGGCACTATGG
1 ATG-TAAGACCATAGCTGGGCTATGGCA-TTTTG
* * * * * * *
17029972 ATGCAAGACCATGGTTGGACAATGACAGTATTTAT
1 ATGTAAGACCATAGCTGGGCTATGGCA-T-TTT-G
17030007 ATGTAAGACCATAGCTGGGCTATGGCATTTTG
1 ATGTAAGACCATAGCTGGGCTATGGCATTTTG
* * * *
17030039 ATGATAAGACCATAACTGGGTTATGGCACTATG
1 ATG-TAAGACCATAGCTGGGCTATGGCATTTTG
17030072 AATGTAAGACCAT
1 -ATGTAAGACCAT
17030085 GGCAGGGCCA
Statistics
Matches: 109, Mismatches: 32, Indels: 11
0.72 0.21 0.07
Matches are distributed among these distances:
32 6 0.06
33 72 0.66
34 10 0.09
35 21 0.19
ACGTcount: A:0.31, C:0.15, G:0.26, T:0.28
Consensus pattern (32 bp):
ATGTAAGACCATAGCTGGGCTATGGCATTTTG
Found at i:17030099 original size:101 final size:101
Alignment explanation
Indices: 17029874--17030086 Score: 320
Period size: 101 Copynumber: 2.1 Consensus size: 101
17029864 TATTCAAACA
* * *
17029874 TAAGACCATGGTTGGACCATGGA-AGTGTTTAAATGTAAGACCATAGTTGGGCTATGGGATTCCG
1 TAAGACCATGGTTGGACCAT-GACAGTATTTAAATGTAAGACCATAGCTGGGCTATGGCATTCCG
* *
17029938 ATGATAAGACTATAACTGGGTTATGGCACTATGGATG
65 ATGATAAGACCATAACTGGGTTATGGCACTATGAATG
* * * **
17029975 CAAGACCATGGTTGGACAATGACAGTATTTATATGTAAGACCATAGCTGGGCTATGGCATTTTGA
1 TAAGACCATGGTTGGACCATGACAGTATTTAAATGTAAGACCATAGCTGGGCTATGGCATTCCGA
17030040 TGATAAGACCATAACTGGGTTATGGCACTATGAATG
66 TGATAAGACCATAACTGGGTTATGGCACTATGAATG
17030076 TAAGACCATGG
1 TAAGACCATGG
17030087 CAGGGCCATG
Statistics
Matches: 100, Mismatches: 11, Indels: 2
0.88 0.10 0.02
Matches are distributed among these distances:
100 2 0.02
101 98 0.98
ACGTcount: A:0.31, C:0.14, G:0.27, T:0.28
Consensus pattern (101 bp):
TAAGACCATGGTTGGACCATGACAGTATTTAAATGTAAGACCATAGCTGGGCTATGGCATTCCGA
TGATAAGACCATAACTGGGTTATGGCACTATGAATG
Found at i:17030106 original size:13 final size:13
Alignment explanation
Indices: 17030088--17030113 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
17030078 AGACCATGGC
17030088 AGGGCCATGACAA
1 AGGGCCATGACAA
17030101 AGGGCCATGACAA
1 AGGGCCATGACAA
17030114 TGAATATGTA
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:0.38, C:0.23, G:0.31, T:0.08
Consensus pattern (13 bp):
AGGGCCATGACAA
Found at i:17032080 original size:30 final size:30
Alignment explanation
Indices: 17032044--17032185 Score: 124
Period size: 31 Copynumber: 4.7 Consensus size: 30
17032034 ATATGTTTTT
*
17032044 TACATTGCCGAATTGATTTGTATATAGATA
1 TACATTGCTGAATTGATTTGTATATAGATA
*
17032074 TACATTGTTGAATTGATTTGTATATAGATA
1 TACATTGCTGAATTGATTTGTATATAGATA
* * * *
17032104 TACATTACTAAATTTGATTCGTATATGGATA
1 TACATTGCTGAA-TTGATTTGTATATAGATA
* * *** *
17032135 TATAGTG-TCGAATTTGATTCAAATATGGATA
1 TACATTGCT-GAA-TTGATTTGTATATAGATA
* *
17032166 TATATTGTTGAATTGATTTG
1 TACATTGCTGAATTGATTTG
17032186 AGCATTGGAT
Statistics
Matches: 93, Mismatches: 16, Indels: 6
0.81 0.14 0.05
Matches are distributed among these distances:
30 44 0.47
31 48 0.52
32 1 0.01
ACGTcount: A:0.33, C:0.06, G:0.17, T:0.44
Consensus pattern (30 bp):
TACATTGCTGAATTGATTTGTATATAGATA
Found at i:17032128 original size:31 final size:30
Alignment explanation
Indices: 17032054--17032136 Score: 112
Period size: 30 Copynumber: 2.7 Consensus size: 30
17032044 TACATTGCCG
** *
17032054 AATTGATTTGTATATAGATATACATTGTTG
1 AATTGATTTGTATATAGATATACATTACTA
17032084 AATTGATTTGTATATAGATATACATTACTA
1 AATTGATTTGTATATAGATATACATTACTA
* *
17032114 AATTTGATTCGTATATGGATATA
1 AA-TTGATTTGTATATAGATATA
17032137 TAGTGTCGAA
Statistics
Matches: 47, Mismatches: 5, Indels: 1
0.89 0.09 0.02
Matches are distributed among these distances:
30 29 0.62
31 18 0.38
ACGTcount: A:0.36, C:0.05, G:0.14, T:0.45
Consensus pattern (30 bp):
AATTGATTTGTATATAGATATACATTACTA
Found at i:17050450 original size:13 final size:14
Alignment explanation
Indices: 17050426--17050452 Score: 54
Period size: 14 Copynumber: 1.9 Consensus size: 14
17050416 TTGAATTTTG
17050426 CATTTAAAAAAAAA
1 CATTTAAAAAAAAA
17050440 CATTTAAAAAAAA
1 CATTTAAAAAAAA
17050453 GGGTGGCAGA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 13 1.00
ACGTcount: A:0.70, C:0.07, G:0.00, T:0.22
Consensus pattern (14 bp):
CATTTAAAAAAAAA
Found at i:17076194 original size:26 final size:26
Alignment explanation
Indices: 17076125--17076188 Score: 74
Period size: 26 Copynumber: 2.5 Consensus size: 26
17076115 ATGAATCATA
* *
17076125 AGAATCTAACAAACTAACTAACTTGG
1 AGAACCTAACAAACTAACTAACTAGG
* ** *
17076151 CGAACCTATTAAATTAACTAACTAGG
1 AGAACCTAACAAACTAACTAACTAGG
17076177 AGAACCTAACAA
1 AGAACCTAACAA
17076189 GATAACCAAC
Statistics
Matches: 29, Mismatches: 9, Indels: 0
0.76 0.24 0.00
Matches are distributed among these distances:
26 29 1.00
ACGTcount: A:0.47, C:0.20, G:0.11, T:0.22
Consensus pattern (26 bp):
AGAACCTAACAAACTAACTAACTAGG
Found at i:17087590 original size:3 final size:3
Alignment explanation
Indices: 17087582--17087654 Score: 110
Period size: 3 Copynumber: 24.3 Consensus size: 3
17087572 TGTACTCTTG
*
17087582 TTA TTA TTA TCA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
* * *
17087630 TTA TTA TGA TTA CTA TTA CTA TTA T
1 TTA TTA TTA TTA TTA TTA TTA TTA T
17087655 ATTTTCATAT
Statistics
Matches: 62, Mismatches: 8, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
3 62 1.00
ACGTcount: A:0.33, C:0.04, G:0.01, T:0.62
Consensus pattern (3 bp):
TTA
Found at i:17087781 original size:20 final size:20
Alignment explanation
Indices: 17087731--17087789 Score: 54
Period size: 18 Copynumber: 3.1 Consensus size: 20
17087721 TTTTTATATT
*
17087731 ATTATATGTTAT-C-ATTTA
1 ATTATATATTATACTATTTA
* *
17087749 ATTTTATAATATACTATTTA
1 ATTATATATTATACTATTTA
*
17087769 ATTATATTTTATA-TA-TTA
1 ATTATATATTATACTATTTA
17087787 ATT
1 ATT
17087790 TAACATAATA
Statistics
Matches: 33, Mismatches: 6, Indels: 4
0.77 0.14 0.09
Matches are distributed among these distances:
18 15 0.45
19 3 0.09
20 15 0.45
ACGTcount: A:0.37, C:0.03, G:0.02, T:0.58
Consensus pattern (20 bp):
ATTATATATTATACTATTTA
Found at i:17094001 original size:9 final size:9
Alignment explanation
Indices: 17093987--17094021 Score: 61
Period size: 9 Copynumber: 3.8 Consensus size: 9
17093977 AGAGCCAATA
17093987 AAAAAATCC
1 AAAAAATCC
17093996 AAAAAAATCC
1 -AAAAAATCC
17094006 AAAAAATCC
1 AAAAAATCC
17094015 AAAAAAT
1 AAAAAAT
17094022 ATTTTTCAAA
Statistics
Matches: 25, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
9 16 0.64
10 9 0.36
ACGTcount: A:0.71, C:0.17, G:0.00, T:0.11
Consensus pattern (9 bp):
AAAAAATCC
Found at i:17094001 original size:10 final size:10
Alignment explanation
Indices: 17093986--17094020 Score: 63
Period size: 10 Copynumber: 3.6 Consensus size: 10
17093976 CAGAGCCAAT
17093986 AAAAAAATCC
1 AAAAAAATCC
17093996 AAAAAAATCC
1 AAAAAAATCC
17094006 -AAAAAATCC
1 AAAAAAATCC
17094015 AAAAAA
1 AAAAAA
17094021 TATTTTTCAA
Statistics
Matches: 24, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
9 9 0.38
10 15 0.62
ACGTcount: A:0.74, C:0.17, G:0.00, T:0.09
Consensus pattern (10 bp):
AAAAAAATCC
Found at i:17094045 original size:11 final size:10
Alignment explanation
Indices: 17094029--17094091 Score: 63
Period size: 11 Copynumber: 5.9 Consensus size: 10
17094019 AATATTTTTC
*
17094029 AAAAAAAAGG
1 AAAAAAAAGA
*
17094039 AAAAAAATGA
1 AAAAAAAAGA
*
17094049 TGAAAAAAAGA
1 -AAAAAAAAGA
17094060 AAAAGAAAAGA
1 AAAA-AAAAGA
17094071 AAAAGAAAAGA
1 AAAA-AAAAGA
17094082 AAAGAAAAAG
1 AAA-AAAAAG
17094092 GAGGGACCAA
Statistics
Matches: 45, Mismatches: 5, Indels: 5
0.82 0.09 0.09
Matches are distributed among these distances:
10 11 0.24
11 33 0.73
12 1 0.02
ACGTcount: A:0.79, C:0.00, G:0.17, T:0.03
Consensus pattern (10 bp):
AAAAAAAAGA
Found at i:17094062 original size:27 final size:27
Alignment explanation
Indices: 17094032--17094093 Score: 74
Period size: 27 Copynumber: 2.3 Consensus size: 27
17094022 ATTTTTCAAA
*
17094032 AAAAAGGAAA-AAAATGATGAAA-AAAAG
1 AAAAAGGAAAGAAAAAGA--AAAGAAAAG
*
17094059 AAAAAGAAAAGAAAAAGAAAAGAAAAG
1 AAAAAGGAAAGAAAAAGAAAAGAAAAG
17094086 AAAAAGGA
1 AAAAAGGA
17094094 GGGACCAAGG
Statistics
Matches: 30, Mismatches: 3, Indels: 4
0.81 0.08 0.11
Matches are distributed among these distances:
26 3 0.10
27 21 0.70
28 6 0.20
ACGTcount: A:0.77, C:0.00, G:0.19, T:0.03
Consensus pattern (27 bp):
AAAAAGGAAAGAAAAAGAAAAGAAAAG
Found at i:17094064 original size:6 final size:6
Alignment explanation
Indices: 17094053--17094091 Score: 57
Period size: 6 Copynumber: 7.0 Consensus size: 6
17094043 AAATGATGAA
17094053 AAAAAG AAAAAG -AAAAG AAAAAG -AAAAG -AAAAG AAAAAG
1 AAAAAG AAAAAG AAAAAG AAAAAG AAAAAG AAAAAG AAAAAG
17094092 GAGGGACCAA
Statistics
Matches: 31, Mismatches: 0, Indels: 4
0.89 0.00 0.11
Matches are distributed among these distances:
5 15 0.48
6 16 0.52
ACGTcount: A:0.82, C:0.00, G:0.18, T:0.00
Consensus pattern (6 bp):
AAAAAG
Found at i:17094068 original size:5 final size:5
Alignment explanation
Indices: 17094054--17094089 Score: 54
Period size: 5 Copynumber: 6.8 Consensus size: 5
17094044 AATGATGAAA
17094054 AAAAG AAAAAG AAAAG AAAAAG AAAAG AAAAG AAAA
1 AAAAG -AAAAG AAAAG -AAAAG AAAAG AAAAG AAAA
17094090 AGGAGGGACC
Statistics
Matches: 29, Mismatches: 0, Indels: 3
0.91 0.00 0.09
Matches are distributed among these distances:
5 19 0.66
6 10 0.34
ACGTcount: A:0.83, C:0.00, G:0.17, T:0.00
Consensus pattern (5 bp):
AAAAG
Found at i:17094185 original size:45 final size:45
Alignment explanation
Indices: 17094100--17094184 Score: 138
Period size: 44 Copynumber: 1.9 Consensus size: 45
17094090 AGGAGGGACC
*
17094100 AAGGTGAAAATCCGCAAAGGGGCGCTTTGAGTCCTAAAAAAGACT
1 AAGGTGAAAATCCGCAAAGGGGCGCTTTGAGTCATAAAAAAGACT
17094145 AAGGTGAAAA-CCTGCAAA-GGGCGCTTTGAGTCATAAAAAA
1 AAGGTGAAAATCC-GCAAAGGGGCGCTTTGAGTCATAAAAAA
17094185 ATAATAAGAA
Statistics
Matches: 38, Mismatches: 1, Indels: 3
0.90 0.02 0.07
Matches are distributed among these distances:
44 23 0.61
45 15 0.39
ACGTcount: A:0.40, C:0.16, G:0.26, T:0.18
Consensus pattern (45 bp):
AAGGTGAAAATCCGCAAAGGGGCGCTTTGAGTCATAAAAAAGACT
Found at i:17095536 original size:89 final size:89
Alignment explanation
Indices: 17095372--17096120 Score: 804
Period size: 89 Copynumber: 8.4 Consensus size: 89
17095362 AAGAAGATAA
* * * **
17095372 CAGAACTTGTCTTCCTGTATTGACAGCAAAATAGATCGAAGACACCAGCCTTGCCTCCCTGAGTT
1 CAGATCTTGTCTTCCTGTATTGGCAGCGAAGCAGATCGAAGACACCAGCCTTGCCTCCCTGAGTT
*
17095437 TGTAGCAGAGCAGACTGAAAATAG
66 TGCAGCAGAGCAGACTGAAAATAG
* * *
17095461 CAGATCTTGTCTTCCTATATTGGCAGCGAAGCAAATCGAAGACACCAGCCTTGCCTCCCTAAGTT
1 CAGATCTTGTCTTCCTGTATTGGCAGCGAAGCAGATCGAAGACACCAGCCTTGCCTCCCTGAGTT
*
17095526 TGCAGTAGAGCAGACTGAAAATAG
66 TGCAGCAGAGCAGACTGAAAATAG
* * * * **
17095550 CAGATCTTGTCTTCCTATACTAGCAGCGAAGCAGATCGAAGACACCAGTCTTATCTCCCTGAGTT
1 CAGATCTTGTCTTCCTGTATTGGCAGCGAAGCAGATCGAAGACACCAGCCTTGCCTCCCTGAGTT
* * * *
17095615 TGCAGCAGAACAGACTGACAACAT
66 TGCAGCAGAGCAGACTGAAAATAG
** * * * *
17095639 CAGATCTTACCTTCCTGTATTGGCAGCGAAGTAGATCAAAGACACCAGGCTTGCCTCCTTGAGTT
1 CAGATCTTGTCTTCCTGTATTGGCAGCGAAGCAGATCGAAGACACCAGCCTTGCCTCCCTGAGTT
*
17095704 TACAGCAGAGCAGACT-AAAA-ACG
66 TGCAGCAGAGCAGACTGAAAATA-G
* * * *
17095727 ACAGATCTTGTCTTCCTGTACTGGCAGCGAAGCAGATCGAAGATACCAGCC-TGACCTCCCTAAA
1 -CAGATCTTGTCTTCCTGTATTGGCAGCGAAGCAGATCGAAGACACCAGCCTTG-CCTCCCTGAG
* * * *
17095791 TTTACAGCGGAGTAGACTGAAGATAG
64 TTTGCAGCAGAGCAGACTGAAAATAG
* * * * * * ** *
17095817 TAGATCTTGTCTTCTTGTATTGGCAGTGAAGCAGATCCAAGACACTATCCTAACCTCCCTTAGTT
1 CAGATCTTGTCTTCCTGTATTGGCAGCGAAGCAGATCGAAGACACCAGCCTTGCCTCCCTGAGTT
* * * *
17095882 TGTAGCGGAGTAGACTGAAGATAG
66 TGCAGCAGAGCAGACTGAAAATAG
* * * *
17095906 CAGATCTTGTCTTCTTGTACTGGCAGCGCAGCAGATCGAAGACACCAGCC-TGACCTTCCTGAGT
1 CAGATCTTGTCTTCCTGTATTGGCAGCGAAGCAGATCGAAGACACCAGCCTTG-CCTCCCTGAGT
** * ** *
17095970 TTGCAGTGGAGCAAACTGAGGATAA
65 TTGCAGCAGAGCAGACTGAAAATAG
* ** * **
17095995 CAGATCTTGTCTTCCTGTATTGGCAGCGAAGTAGATTAAAGACACCATCCTTGCCTCTTTGAGTT
1 CAGATCTTGTCTTCCTGTATTGGCAGCGAAGCAGATCGAAGACACCAGCCTTGCCTCCCTGAGTT
* * * *
17096060 TGCAGCGGAGTAGACTAAAAACAG
66 TGCAGCAGAGCAGACTGAAAATAG
* *
17096084 CAAATCTTGTCTTCCTGTACTGGCAGCGAAGCAGATC
1 CAGATCTTGTCTTCCTGTATTGGCAGCGAAGCAGATC
17096121 AAAAGTATGT
Statistics
Matches: 549, Mismatches: 103, Indels: 16
0.82 0.15 0.02
Matches are distributed among these distances:
87 1 0.00
88 5 0.01
89 536 0.98
90 6 0.01
91 1 0.00
ACGTcount: A:0.29, C:0.24, G:0.22, T:0.25
Consensus pattern (89 bp):
CAGATCTTGTCTTCCTGTATTGGCAGCGAAGCAGATCGAAGACACCAGCCTTGCCTCCCTGAGTT
TGCAGCAGAGCAGACTGAAAATAG
Found at i:17096393 original size:51 final size:50
Alignment explanation
Indices: 17096317--17096475 Score: 155
Period size: 51 Copynumber: 3.2 Consensus size: 50
17096307 CGAAGAAAGT
* * *
17096317 GAATCTTATTTCCCTGGCATTGCAATGGAATAGATTAAAGCTTAAGGCAGC
1 GAATCTCATTTCCCTGGCGTTGCAATGG-ATAGATTAAAGCTAAAGGCAGC
* * * *
17096368 GAATCTCATTTCCTTGGCGTTGCAATGGAGCAGATTAAAGCTGAATGCAGC
1 GAATCTCATTTCCCTGGCGTTGCAATGGA-TAGATTAAAGCTAAAGGCAGC
* * * * *
17096419 AAATCTTATCTCCCTGGCGTCGC-A--G-TAGGTTAAAGCTAAAGGCAGC
1 GAATCTCATTTCCCTGGCGTTGCAATGGATAGATTAAAGCTAAAGGCAGC
*
17096465 GAGTCTCATTT
1 GAATCTCATTT
17096476 ACTTGGCATT
Statistics
Matches: 88, Mismatches: 19, Indels: 7
0.77 0.17 0.06
Matches are distributed among these distances:
46 24 0.27
48 1 0.01
50 2 0.02
51 61 0.69
ACGTcount: A:0.28, C:0.20, G:0.23, T:0.28
Consensus pattern (50 bp):
GAATCTCATTTCCCTGGCGTTGCAATGGATAGATTAAAGCTAAAGGCAGC
Found at i:17096464 original size:97 final size:96
Alignment explanation
Indices: 17096351--17096530 Score: 245
Period size: 97 Copynumber: 1.9 Consensus size: 96
17096341 ATGGAATAGA
* * * * *
17096351 TTAAAGCTTAAGGCAGCGAATCTCATTTCCTTGGCGTTGCAATGGAGCAGATTAAAGCTGAATG-
1 TTAAAGCTAAAGGCAGCGAATCTCATTTACTTGGCATTCCAATGGAGAAGATTAAAGCTGAA-GA
17096415 CAGCAAATCTTATCTCCCTGGCGTCGCAGTAGG
65 CA-CAAATCTTATCTCCCTGGCGTCGCAGTAGG
* ** *
17096448 TTAAAGCTAAAGGCAGCGAGTCTCATTTACTTGGCATTCCGGTGGAGAATATTAAAGCTGAAGAC
1 TTAAAGCTAAAGGCAGCGAATCTCATTTACTTGGCATTCCAATGGAGAAGATTAAAGCTGAAGAC
*
17096513 ACTAATCTTATCTCCCTG
66 ACAAATCTTATCTCCCTG
17096531 ACGTTAAGAT
Statistics
Matches: 72, Mismatches: 10, Indels: 3
0.85 0.12 0.04
Matches are distributed among these distances:
96 17 0.24
97 55 0.76
ACGTcount: A:0.28, C:0.21, G:0.23, T:0.28
Consensus pattern (96 bp):
TTAAAGCTAAAGGCAGCGAATCTCATTTACTTGGCATTCCAATGGAGAAGATTAAAGCTGAAGAC
ACAAATCTTATCTCCCTGGCGTCGCAGTAGG
Found at i:17096605 original size:44 final size:44
Alignment explanation
Indices: 17096541--17096627 Score: 129
Period size: 44 Copynumber: 2.0 Consensus size: 44
17096531 ACGTTAAGAT
* * *
17096541 TGAAGACACCAGTCTTATCTCCCTGAAGTTGCAGTGGAGCAGAC
1 TGAAGAAACCAATCCTATCTCCCTGAAGTTGCAGTGGAGCAGAC
* *
17096585 TGAAGAAACCAATCCTATCTCTCTGAAGTTGTAGTGGAGCAGA
1 TGAAGAAACCAATCCTATCTCCCTGAAGTTGCAGTGGAGCAGA
17096628 TTAAAATGAT
Statistics
Matches: 38, Mismatches: 5, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
44 38 1.00
ACGTcount: A:0.30, C:0.22, G:0.24, T:0.24
Consensus pattern (44 bp):
TGAAGAAACCAATCCTATCTCCCTGAAGTTGCAGTGGAGCAGAC
Found at i:17098167 original size:3 final size:3
Alignment explanation
Indices: 17098159--17098219 Score: 104
Period size: 3 Copynumber: 20.3 Consensus size: 3
17098149 TGTACTCTTG
* *
17098159 TTA TTA TTA TTA TCA TTA TTA TTA TCA TTA TTA TTA TTA TTA TTA TTA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
17098207 TTA TTA TTA TTA T
1 TTA TTA TTA TTA T
17098220 CACTATTATA
Statistics
Matches: 54, Mismatches: 4, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
3 54 1.00
ACGTcount: A:0.33, C:0.03, G:0.00, T:0.64
Consensus pattern (3 bp):
TTA
Found at i:17098178 original size:12 final size:12
Alignment explanation
Indices: 17098161--17098228 Score: 109
Period size: 12 Copynumber: 5.7 Consensus size: 12
17098151 TACTCTTGTT
17098161 ATTATTATTATC
1 ATTATTATTATC
17098173 ATTATTATTATC
1 ATTATTATTATC
*
17098185 ATTATTATTATT
1 ATTATTATTATC
*
17098197 ATTATTATTATT
1 ATTATTATTATC
17098209 ATTATTATTATC
1 ATTATTATTATC
*
17098221 ACTATTAT
1 ATTATTAT
17098229 ATTTTCATAT
Statistics
Matches: 53, Mismatches: 3, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
12 53 1.00
ACGTcount: A:0.34, C:0.06, G:0.00, T:0.60
Consensus pattern (12 bp):
ATTATTATTATC
Found at i:17098335 original size:25 final size:23
Alignment explanation
Indices: 17098303--17098360 Score: 55
Period size: 25 Copynumber: 2.4 Consensus size: 23
17098293 ATTTTTTACA
*
17098303 TTAT-TATATGTTATCATTTAATT
1 TTATATATATATT-TCATTTAATT
* *
17098326 TTATAATATAATATTTTATTTTATT
1 TTAT-ATAT-ATATTTCATTTAATT
17098351 TTATATATAT
1 TTATATATAT
17098361 TAATTCAACG
Statistics
Matches: 29, Mismatches: 3, Indels: 6
0.76 0.08 0.16
Matches are distributed among these distances:
23 6 0.21
24 4 0.14
25 15 0.52
26 4 0.14
ACGTcount: A:0.34, C:0.02, G:0.02, T:0.62
Consensus pattern (23 bp):
TTATATATATATTTCATTTAATT
Found at i:17098355 original size:20 final size:21
Alignment explanation
Indices: 17098318--17098365 Score: 55
Period size: 20 Copynumber: 2.4 Consensus size: 21
17098308 ATATGTTATC
17098318 ATTTAATTTTATAATATA-AT
1 ATTTAATTTTATAATATATAT
* **
17098338 ATTTTATTTTATTTTATATAT
1 ATTTAATTTTATAATATATAT
17098359 A-TTAATT
1 ATTTAATT
17098366 CAACGTAATA
Statistics
Matches: 23, Mismatches: 4, Indels: 2
0.79 0.14 0.07
Matches are distributed among these distances:
20 20 0.87
21 3 0.13
ACGTcount: A:0.38, C:0.00, G:0.00, T:0.62
Consensus pattern (21 bp):
ATTTAATTTTATAATATATAT
Found at i:17114077 original size:24 final size:24
Alignment explanation
Indices: 17114020--17114071 Score: 77
Period size: 24 Copynumber: 2.2 Consensus size: 24
17114010 TTTCTCGAAG
* * *
17114020 ATTTAGAATTTATTAATATAATAT
1 ATTTAGCATTTATTAACATAACAT
17114044 ATTTAGCATTTATTAACATAACAT
1 ATTTAGCATTTATTAACATAACAT
17114068 ATTT
1 ATTT
17114072 GACATTGATT
Statistics
Matches: 25, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
24 25 1.00
ACGTcount: A:0.42, C:0.06, G:0.04, T:0.48
Consensus pattern (24 bp):
ATTTAGCATTTATTAACATAACAT
Found at i:17114082 original size:24 final size:24
Alignment explanation
Indices: 17114020--17114082 Score: 65
Period size: 24 Copynumber: 2.6 Consensus size: 24
17114010 TTTCTCGAAG
* * * *
17114020 ATTTAGAATTTATTAATATAATAT
1 ATTTAGCATTGATTAACATAACAT
*
17114044 ATTTAGCATTTATTAACATAACAT
1 ATTTAGCATTGATTAACATAACAT
17114068 ATTT-GACATTGATTA
1 ATTTAG-CATTGATTA
17114083 TAATTAGATT
Statistics
Matches: 34, Mismatches: 4, Indels: 2
0.85 0.10 0.05
Matches are distributed among these distances:
23 1 0.03
24 33 0.97
ACGTcount: A:0.41, C:0.06, G:0.06, T:0.46
Consensus pattern (24 bp):
ATTTAGCATTGATTAACATAACAT
Found at i:17117922 original size:44 final size:44
Alignment explanation
Indices: 17117873--17117967 Score: 131
Period size: 44 Copynumber: 2.2 Consensus size: 44
17117863 GATAGATAAA
* *
17117873 ATATAA-ATTAATCTAAAATTTTAAATATATTTTAAATATTTAAT
1 ATATAATATTAATCT-AAATTTTAAATACATTTTAAATAATTAAT
* *
17117917 ATATAATATTAATCTAAATTTTATATCCATTTTAAATAATTAAT
1 ATATAATATTAATCTAAATTTTAAATACATTTTAAATAATTAAT
17117961 ATA-AATA
1 ATATAATA
17117968 AGATTATTTT
Statistics
Matches: 46, Mismatches: 4, Indels: 3
0.87 0.08 0.06
Matches are distributed among these distances:
43 4 0.09
44 34 0.74
45 8 0.17
ACGTcount: A:0.49, C:0.04, G:0.00, T:0.46
Consensus pattern (44 bp):
ATATAATATTAATCTAAATTTTAAATACATTTTAAATAATTAAT
Found at i:17121951 original size:17 final size:18
Alignment explanation
Indices: 17121919--17121953 Score: 54
Period size: 17 Copynumber: 2.0 Consensus size: 18
17121909 TTGATGTTCC
*
17121919 CCCGTGTGTTCCCACATG
1 CCCGTGTGTGCCCACATG
17121937 CCCGTGTG-GCCCACATG
1 CCCGTGTGTGCCCACATG
17121954 GCCGAAATTG
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
17 8 0.50
18 8 0.50
ACGTcount: A:0.11, C:0.40, G:0.26, T:0.23
Consensus pattern (18 bp):
CCCGTGTGTGCCCACATG
Found at i:17133669 original size:23 final size:23
Alignment explanation
Indices: 17133620--17133684 Score: 69
Period size: 23 Copynumber: 2.8 Consensus size: 23
17133610 GAAAAGACAA
* * *
17133620 ATGAATAGTGAAAAATCTCTGGC
1 ATGAACAGTGAAGATTCTCTGGC
17133643 ATGAACAGTGAAGATTCTCT-GC
1 ATGAACAGTGAAGATTCTCTGGC
* *
17133665 GATGAAGAATGAAGATTCTC
1 -ATGAACAGTGAAGATTCTC
17133685 CGAAAAAAAA
Statistics
Matches: 36, Mismatches: 5, Indels: 2
0.84 0.12 0.05
Matches are distributed among these distances:
22 2 0.06
23 34 0.94
ACGTcount: A:0.37, C:0.14, G:0.23, T:0.26
Consensus pattern (23 bp):
ATGAACAGTGAAGATTCTCTGGC
Found at i:17133951 original size:16 final size:17
Alignment explanation
Indices: 17133916--17133956 Score: 73
Period size: 17 Copynumber: 2.4 Consensus size: 17
17133906 TGTTTCTCTG
*
17133916 AAAATTTTTAGCTTTAA
1 AAAATTTCTAGCTTTAA
17133933 AAAATTTCTAGCTTTAA
1 AAAATTTCTAGCTTTAA
17133950 AAAATTT
1 AAAATTT
17133957 AAGTTTTTAA
Statistics
Matches: 23, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
17 23 1.00
ACGTcount: A:0.44, C:0.07, G:0.05, T:0.44
Consensus pattern (17 bp):
AAAATTTCTAGCTTTAA
Found at i:17134015 original size:14 final size:15
Alignment explanation
Indices: 17133974--17134006 Score: 50
Period size: 15 Copynumber: 2.2 Consensus size: 15
17133964 TAAAACAAAT
17133974 AAAA-TTTAAGTTTTC
1 AAAATTTTAA-TTTTC
17133989 AAAATTTTAATTTTC
1 AAAATTTTAATTTTC
17134004 AAA
1 AAA
17134007 TTATTATTTC
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
15 12 0.71
16 5 0.29
ACGTcount: A:0.45, C:0.06, G:0.03, T:0.45
Consensus pattern (15 bp):
AAAATTTTAATTTTC
Found at i:17137150 original size:28 final size:29
Alignment explanation
Indices: 17137094--17137151 Score: 84
Period size: 29 Copynumber: 2.0 Consensus size: 29
17137084 ATAAAAGCAC
17137094 CACAAAATCAGTCTAGGGCCTGTGCCCAT
1 CACAAAATCAGTCTAGGGCCTGTGCCCAT
*
17137123 CACAAAATCAGTTTA-GGCCT-TAGCCCAT
1 CACAAAATCAGTCTAGGGCCTGT-GCCCAT
17137151 C
1 C
17137152 CAGATACAGT
Statistics
Matches: 27, Mismatches: 1, Indels: 3
0.87 0.03 0.10
Matches are distributed among these distances:
27 1 0.04
28 12 0.44
29 14 0.52
ACGTcount: A:0.29, C:0.31, G:0.17, T:0.22
Consensus pattern (29 bp):
CACAAAATCAGTCTAGGGCCTGTGCCCAT
Found at i:17142925 original size:22 final size:21
Alignment explanation
Indices: 17142891--17142935 Score: 54
Period size: 22 Copynumber: 2.1 Consensus size: 21
17142881 TTTTATTTGC
*
17142891 AAAATCAAAATTTTCTTTTAAA
1 AAAATCAAAATTTT-TCTTAAA
**
17142913 AAAATCATTATTTTTCTTAAA
1 AAAATCAAAATTTTTCTTAAA
17142934 AA
1 AA
17142936 TCAAAACATT
Statistics
Matches: 20, Mismatches: 3, Indels: 1
0.83 0.12 0.04
Matches are distributed among these distances:
21 8 0.40
22 12 0.60
ACGTcount: A:0.49, C:0.09, G:0.00, T:0.42
Consensus pattern (21 bp):
AAAATCAAAATTTTTCTTAAA
Found at i:17143215 original size:51 final size:50
Alignment explanation
Indices: 17143146--17143372 Score: 128
Period size: 51 Copynumber: 4.5 Consensus size: 50
17143136 CAAAACTTTG
* *
17143146 TTTTAAAATTTTAAACTTTCCTTTAAAATGACTTAAAAAATAGATTTTTATT
1 TTTTAAAA-TCTAAACTTTCCTTTAAAA-GACTTAAAAAATAAATTTTTATT
* * * *
17143198 TTTTAAAATCTAAACTTTCTCCTCTTAGAA-A---AAAAAA-ACAGTATT-TT
1 TTTTAAAATCTAAAC-TT-TCCT-TTAAAAGACTTAAAAAATAAATTTTTATT
* ** * * **
17143245 TCTTAAAGAT-TAAAGCTTTTATTTTAAAGTAGTTAAAAAAATCAAAACTTTA-T
1 TTTTAAA-ATCTAAA-CTTTCCTTTAAAAG-ACTT-AAAAAAT-AAATTTTTATT
* * * * *
17143298 TTTAAAAATTTAAATTTTCCTTTAAAATAACTAAAAAAATAAATTTTTATT
1 TTTTAAAATCTAAACTTTCCTTTAAAA-GACTTAAAAAATAAATTTTTATT
17143349 TTTTAAAATCTAAACTTTCTCTTT
1 TTTTAAAATCTAAACTTTC-CTTT
17143373 TTTCTTAAAA
Statistics
Matches: 129, Mismatches: 28, Indels: 36
0.67 0.15 0.19
Matches are distributed among these distances:
45 4 0.03
46 2 0.02
47 15 0.12
48 8 0.06
49 6 0.05
50 7 0.05
51 36 0.28
52 28 0.22
53 18 0.14
54 5 0.04
ACGTcount: A:0.43, C:0.10, G:0.04, T:0.44
Consensus pattern (50 bp):
TTTTAAAATCTAAACTTTCCTTTAAAAGACTTAAAAAATAAATTTTTATT
Found at i:17143476 original size:152 final size:149
Alignment explanation
Indices: 17143112--17143552 Score: 566
Period size: 151 Copynumber: 2.9 Consensus size: 149
17143102 AATCAAAACG
* * *
17143112 TTATTTCGAAA-TAGTTAAAAAAATCAAAACTTTGTTTTAAAATTTTAAACTTTCCTTTAAAATG
1 TTATTT-GAAAGTAGTTAAAAAAATCAAAACTTTGTTTTAAAAATTTAATCTTTCCTTTAAAATA
* * * ***** *
17143176 ACTTAAAAAATAGATTTTTATTTTTTAAAATCTAAACTTTCTCCTCTTAGAAAAAAAAAACAGTA
65 ACTAAAAAAATAAATTTTTATTTTTTAAAATCTAAACTTTCTACT-TT-TTTTTAAAAAACACTA
17143241 TTTTTCTTAAAGATTAAAGCTT
128 TTTTTCTTAAAGATTAAAGCTT
* *
17143263 TTATTTTAAAGTAGTTAAAAAAATCAAAACTTTATTTTAAAAATTTAAAT-TTTCCTTTAAAATA
1 TTATTTGAAAGTAGTTAAAAAAATCAAAACTTTGTTTTAAAAATTT-AATCTTTCCTTTAAAATA
17143327 ACTAAAAAAATAAATTTTTATTTTTTAAAATCTAAACTTTCT-CTTTTTTCTTAAAAAACACTAT
65 ACTAAAAAAATAAATTTTTATTTTTTAAAATCTAAACTTTCTACTTTTTT-TTAAAAAACACTAT
17143391 TTTTCTTAAAGATTAAAGCTT
129 TTTTCTTAAAGATTAAAGCTT
17143412 TTACTTTGAAA-TAGTTGAAAAAAAAATCAAAACTTTGTTTTAAAAATTTAATCTTTCCTTTAAA
1 TTA-TTTGAAAGTAGTT---AAAAAAATCAAAACTTTGTTTTAAAAATTTAATCTTTCCTTTAAA
* * * *
17143476 ATAACTAAAAAAACCATATATTTATTTTTTTCAAAATCTAAAGTTTCTACTTTTTTTTAAAAAAA
62 ATAACTAAAAAAA-TAAATTTTTA-TTTTTT-AAAATCTAAACTTTCTACTTTTTTTT-AAAAAA
17143541 CCACTATTTTTC
123 -CACTATTTTTC
17143553 CCAAAATCAA
Statistics
Matches: 257, Mismatches: 19, Indels: 22
0.86 0.06 0.07
Matches are distributed among these distances:
149 42 0.16
150 11 0.04
151 95 0.37
152 55 0.21
153 7 0.03
154 6 0.02
155 17 0.07
156 13 0.05
157 11 0.04
ACGTcount: A:0.42, C:0.11, G:0.04, T:0.43
Consensus pattern (149 bp):
TTATTTGAAAGTAGTTAAAAAAATCAAAACTTTGTTTTAAAAATTTAATCTTTCCTTTAAAATAA
CTAAAAAAATAAATTTTTATTTTTTAAAATCTAAACTTTCTACTTTTTTTTAAAAAACACTATTT
TTCTTAAAGATTAAAGCTT
Found at i:17145060 original size:23 final size:23
Alignment explanation
Indices: 17145034--17145143 Score: 116
Period size: 23 Copynumber: 4.8 Consensus size: 23
17145024 AATATTTGGC
17145034 ATGAATAGTGAAGATT-TGCTACA
1 ATGAATAGTGAAGATTCT-CTACA
* *
17145057 ATGAATAGTAAAAATTCTCTGAC-
1 ATGAATAGTGAAGATTCTCT-ACA
* *
17145080 ATGAACAGTGAAGATTCTCTGCA
1 ATGAATAGTGAAGATTCTCTACA
* * * *
17145103 ATAAACAATGAAGATTCTCTACG
1 ATGAATAGTGAAGATTCTCTACA
17145126 ATGAATAGTGAAGATTCT
1 ATGAATAGTGAAGATTCT
17145144 TTGAAAAAAA
Statistics
Matches: 71, Mismatches: 13, Indels: 6
0.79 0.14 0.07
Matches are distributed among these distances:
22 1 0.01
23 67 0.94
24 3 0.04
ACGTcount: A:0.40, C:0.13, G:0.18, T:0.29
Consensus pattern (23 bp):
ATGAATAGTGAAGATTCTCTACA
Found at i:17145423 original size:16 final size:15
Alignment explanation
Indices: 17145399--17145432 Score: 50
Period size: 16 Copynumber: 2.2 Consensus size: 15
17145389 TTTAGCTTTA
17145399 AAAAATTTAATTTTTC
1 AAAAATTTAA-TTTTC
*
17145415 AAAATTTTAATTTTC
1 AAAAATTTAATTTTC
17145430 AAA
1 AAA
17145433 TTATTATCTC
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
15 8 0.47
16 9 0.53
ACGTcount: A:0.47, C:0.06, G:0.00, T:0.47
Consensus pattern (15 bp):
AAAAATTTAATTTTC
Found at i:17181737 original size:31 final size:31
Alignment explanation
Indices: 17181699--17181767 Score: 104
Period size: 31 Copynumber: 2.2 Consensus size: 31
17181689 TCACAAAATG
*
17181699 GTCACTAAACTATTGAAAAGTT-TTCATTCAA
1 GTCACTAAACTATTCAAAAGTTATT-ATTCAA
*
17181730 GTCACTAAACTATTCAAAAGTTATTATTTAA
1 GTCACTAAACTATTCAAAAGTTATTATTCAA
17181761 GTCACTA
1 GTCACTA
17181768 GGGTTTTAAG
Statistics
Matches: 35, Mismatches: 2, Indels: 2
0.90 0.05 0.05
Matches are distributed among these distances:
31 33 0.94
32 2 0.06
ACGTcount: A:0.39, C:0.16, G:0.09, T:0.36
Consensus pattern (31 bp):
GTCACTAAACTATTCAAAAGTTATTATTCAA
Found at i:17188049 original size:24 final size:24
Alignment explanation
Indices: 17188001--17188047 Score: 67
Period size: 24 Copynumber: 1.9 Consensus size: 24
17187991 ACTGATCATA
*
17188001 GAGAGAATTGAGGAGGGATATTTG
1 GAGAGAATTGAGGAGGAATATTTG
*
17188025 GAGAGATTTGAGGAGAGAATATT
1 GAGAGAATTGAGGAG-GAATATT
17188048 GGGATTTGGG
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
24 14 0.70
25 6 0.30
ACGTcount: A:0.36, C:0.00, G:0.38, T:0.26
Consensus pattern (24 bp):
GAGAGAATTGAGGAGGAATATTTG
Found at i:17188774 original size:27 final size:26
Alignment explanation
Indices: 17188737--17188869 Score: 160
Period size: 27 Copynumber: 5.0 Consensus size: 26
17188727 AGACCCCAAA
* * *
17188737 ATAGGTAAAATAACTGAAATACTCTC
1 ATAGGTAAAATGACTGAAATACCCCC
*
17188763 ATAGGATAAAATGACCGAAATACCCCC
1 ATAGG-TAAAATGACTGAAATACCCCC
17188790 ATAGGATAAAATGACTGAAATACCCCC
1 ATAGG-TAAAATGACTGAAATACCCCC
17188817 ATAAGGTAAAATGA-TCGAAATACCCCC
1 AT-AGGTAAAATGACT-GAAATACCCCC
**
17188844 ATAGGGTAAAATGACTGTTATACCCC
1 ATA-GGTAAAATGACTGAAATACCCC
17188870 TAGGAGATGA
Statistics
Matches: 95, Mismatches: 7, Indels: 9
0.86 0.06 0.08
Matches are distributed among these distances:
26 7 0.07
27 84 0.88
28 4 0.04
ACGTcount: A:0.43, C:0.21, G:0.15, T:0.21
Consensus pattern (26 bp):
ATAGGTAAAATGACTGAAATACCCCC
Found at i:17188807 original size:54 final size:53
Alignment explanation
Indices: 17188737--17188869 Score: 178
Period size: 54 Copynumber: 2.5 Consensus size: 53
17188727 AGACCCCAAA
* * *
17188737 ATAGGTAAAATAACTGAAATACTCTCAT-AGGATAAAATGACCGAAATACCCCC
1 ATAGGTAAAATGACTGAAATACCCCCATAAGG-TAAAATGACCGAAATACCCCC
*
17188790 ATAGGATAAAATGACTGAAATACCCCCATAAGGTAAAATGATCGAAATACCCCC
1 ATAGG-TAAAATGACTGAAATACCCCCATAAGGTAAAATGACCGAAATACCCCC
**
17188844 ATAGGGTAAAATGACTGTTATACCCC
1 ATA-GGTAAAATGACTGAAATACCCC
17188870 TAGGAGATGA
Statistics
Matches: 71, Mismatches: 6, Indels: 5
0.87 0.07 0.06
Matches are distributed among these distances:
53 5 0.07
54 61 0.86
55 5 0.07
ACGTcount: A:0.43, C:0.21, G:0.15, T:0.21
Consensus pattern (53 bp):
ATAGGTAAAATGACTGAAATACCCCCATAAGGTAAAATGACCGAAATACCCCC
Found at i:17188883 original size:54 final size:54
Alignment explanation
Indices: 17188737--17188885 Score: 165
Period size: 54 Copynumber: 2.8 Consensus size: 54
17188727 AGACCCCAAA
* * * * *
17188737 ATAGG-TAAAATAACTGAAATACTCTCATAGGATAAAATGACCGAAATACCCCC
1 ATAGGATAAAATGACTGAAATACCCCCAGAAGATAAAATGACCGAAATACCCCC
* * *
17188790 ATAGGATAAAATGACTGAAATACCCCCATAAGGTAAAATGATCGAAATACCCCC
1 ATAGGATAAAATGACTGAAATACCCCCAGAAGATAAAATGACCGAAATACCCCC
* ** * * *
17188844 ATAGGGTAAAATGACTGTTATACCCCTAGGAGATGAAATGAC
1 ATAGGATAAAATGACTGAAATACCCCCAGAAGATAAAATGAC
17188886 TGTTATGGTA
Statistics
Matches: 80, Mismatches: 15, Indels: 1
0.83 0.16 0.01
Matches are distributed among these distances:
53 5 0.06
54 75 0.94
ACGTcount: A:0.43, C:0.19, G:0.17, T:0.21
Consensus pattern (54 bp):
ATAGGATAAAATGACTGAAATACCCCCAGAAGATAAAATGACCGAAATACCCCC
Found at i:17193937 original size:18 final size:18
Alignment explanation
Indices: 17193914--17193948 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
17193904 TTCGAAACTT
*
17193914 TAGTGGAGAAGACTAAGG
1 TAGTGGAAAAGACTAAGG
*
17193932 TAGTGGAAAAGATTAAG
1 TAGTGGAAAAGACTAAG
17193949 CTCGTAGAAC
Statistics
Matches: 15, Mismatches: 2, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
18 15 1.00
ACGTcount: A:0.43, C:0.03, G:0.34, T:0.20
Consensus pattern (18 bp):
TAGTGGAAAAGACTAAGG
Found at i:17202646 original size:26 final size:27
Alignment explanation
Indices: 17202605--17202669 Score: 78
Period size: 26 Copynumber: 2.4 Consensus size: 27
17202595 TACAATGTAC
* * *
17202605 GCCACAAAAGCCATATATACAGAGTAT
1 GCCACAAAGGCTATATATACAGAGGAT
* *
17202632 -CCACCAAGGCTATATATAGAGAGGAT
1 GCCACAAAGGCTATATATACAGAGGAT
17202658 GCCACAAAGGCT
1 GCCACAAAGGCT
17202670 GACAGGATGC
Statistics
Matches: 31, Mismatches: 6, Indels: 2
0.79 0.15 0.05
Matches are distributed among these distances:
26 21 0.68
27 10 0.32
ACGTcount: A:0.40, C:0.23, G:0.20, T:0.17
Consensus pattern (27 bp):
GCCACAAAGGCTATATATACAGAGGAT
Done.