Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold228
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: 4123243
ACGTcount: A:0.34, C:0.16, G:0.16, T:0.33
File 16 of 27
Found at i:2306391 original size:18 final size:18
Alignment explanation
Indices: 2306368--2306403 Score: 72
Period size: 18 Copynumber: 2.0 Consensus size: 18
2306358 ACATTTAAAT
2306368 TTTTTTTTTTTTTTTCAA
1 TTTTTTTTTTTTTTTCAA
2306386 TTTTTTTTTTTTTTTCAA
1 TTTTTTTTTTTTTTTCAA
2306404 ACACTTTATC
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 18 1.00
ACGTcount: A:0.11, C:0.06, G:0.00, T:0.83
Consensus pattern (18 bp):
TTTTTTTTTTTTTTTCAA
Found at i:2310996 original size:118 final size:117
Alignment explanation
Indices: 2310785--2311053 Score: 335
Period size: 118 Copynumber: 2.3 Consensus size: 117
2310775 CCCTTTCTAG
* * * *
2310785 GAGAATTCATTTTCACATTAATCACGTAGTACTTAGGCGCCAATATATTAACTTCGGGATAGGTT
1 GAGAATTCATTTTCACATTAATCACGTAGTACTCAGGCACCAATAGATTAACTTCAGGATAGGTT
* * *
2310850 GTCGGTCTTCCATTTAAAGTTGCAAAGAAGGCATATGAATGCCTTTTGTATAA
66 GTCAGTCTTCCATTTAAAGTTACAAAGAAGGCATATGAACGCCTTTTGTAT-A
* * *
2310903 GAGAATTCATTATT-A-AGTTAATCATGTAGTACTCAGGCACCAATAGATTAGCTTCAGTATAGG
1 GAGAATTCATT-TTCACA-TTAATCACGTAGTACTCAGGCACCAATAGATTAACTTCAGGATAGG
* * ** **
2310966 TTGTTAGTCTTCCATTTAGAGTTATGAAGAAGGTGTATGAACGCCTTTTGTATA
64 TTGTCAGTCTTCCATTTAAAGTTACAAAGAAGGCATATGAACGCCTTTTGTATA
*
2311020 GTAGAATTCATTTTCACATTAATCACATAGTACT
1 G-AGAATTCATTTTCACATTAATCACGTAGTACT
2311054 TAGTCACTAA
Statistics
Matches: 128, Mismatches: 18, Indels: 10
0.82 0.12 0.06
Matches are distributed among these distances:
117 5 0.04
118 120 0.94
119 3 0.02
ACGTcount: A:0.31, C:0.15, G:0.19, T:0.35
Consensus pattern (117 bp):
GAGAATTCATTTTCACATTAATCACGTAGTACTCAGGCACCAATAGATTAACTTCAGGATAGGTT
GTCAGTCTTCCATTTAAAGTTACAAAGAAGGCATATGAACGCCTTTTGTATA
Found at i:2320105 original size:3 final size:3
Alignment explanation
Indices: 2320097--2320139 Score: 86
Period size: 3 Copynumber: 14.3 Consensus size: 3
2320087 AATTAGGAAA
2320097 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT T
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT T
2320140 TTAGGGTAGA
Statistics
Matches: 40, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 40 1.00
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (3 bp):
TAT
Found at i:2320713 original size:158 final size:165
Alignment explanation
Indices: 2320346--2320763 Score: 426
Period size: 170 Copynumber: 2.5 Consensus size: 165
2320336 GGTTATGTTT
* *
2320346 ATTTTATTTCTTTTTCGAAAATATCATTTTGTACCTTAATGGAAA-CACGAAAAGATACGAAAAG
1 ATTTTATTTATTTTT-GAAAATATCATTTCGTACCTTAAT-GAAAGCACGAAAAGATACGAAAAG
* * *
2320410 TTTTTGAAATCTTTTATATCCCTACAAACTCCAATAGGAATATAAAAGATTAAAAAAAGAGAGTG
64 TTTTTGAAATCTTTTATACCCCTATAAACCCCAATAGGAATATAAAAGATT--AAAAAGAGAGTG
**
2320475 ATTAAAATTTATTTCAATCACGAAAGTGTTAGCCTAATTTA
127 ATTAAAATTTATAACAATCACGAAAG-GTTA-CCTAATTTA
* * * * * * *
2320516 ATTTTTGTTTATTTTCGTAAATATCATTTCGCATCTTAATGAAAGGC-CAAAAAGATATGAAAAG
1 A-TTTTATTTATTTTTGAAAATATCATTTCGTACCTTAATGAAA-GCACGAAAAGATACGAAAAG
** *
2320580 TTTTTGAAATCTTTTATACCCCTATGGACCCCTATAGGAATATAAAAGATT-AAAA-A-A-TGAT
64 TTTTTGAAATCTTTTATACCCCTATAAACCCCAATAGGAATATAAAAGATTAAAAAGAGAGTGAT
* * * *
2320641 TAAAATTTATAACGATTATGAAA-G-TA-TTAATTTA
129 TAAAATTTATAACAATCACGAAAGGTTACCTAATTTA
* * * *
2320675 ATTTAATTTATTTTTGAAAATA-CAATTTCGTACCTTAATGGAAGCTCGAAAAGATACAAAAAG-
1 ATTTTATTTATTTTTGAAAATATC-ATTTCGTACCTTAATGAAAGCACGAAAAGATACGAAAAGT
* *
2320738 TTTCGAAATATTTTCATACCCCTATA
65 TTTTGAAATCTTTT-ATACCCCTATA
2320764 GATGCCCATG
Statistics
Matches: 208, Mismatches: 34, Indels: 24
0.78 0.13 0.09
Matches are distributed among these distances:
157 15 0.07
158 57 0.27
159 8 0.04
161 2 0.01
162 1 0.00
164 22 0.11
165 1 0.00
166 1 0.00
167 4 0.02
169 4 0.02
170 81 0.39
171 12 0.06
ACGTcount: A:0.40, C:0.12, G:0.11, T:0.36
Consensus pattern (165 bp):
ATTTTATTTATTTTTGAAAATATCATTTCGTACCTTAATGAAAGCACGAAAAGATACGAAAAGTT
TTTGAAATCTTTTATACCCCTATAAACCCCAATAGGAATATAAAAGATTAAAAAGAGAGTGATTA
AAATTTATAACAATCACGAAAGGTTACCTAATTTA
Found at i:2322393 original size:166 final size:166
Alignment explanation
Indices: 2322221--2322655 Score: 536
Period size: 169 Copynumber: 2.6 Consensus size: 166
2322211 AAGAAAAAGG
* * * *
2322221 GAATTTCAAGGAAAGACTCAAAAACT-TATGAAAATGAATTAAATTTTGAAAATTGATTTAATAT
1 GAATTTCAAGAAAAAAATCAAAAA-TGAATGAAAATGAATTAAATTTTGAAAATTGATTTAATAT
* * * **
2322285 AAAATAAATAATAATATTTGATGAATTTTTAAAATTAAAAACCAAGAAAAAT-CCTTTGAAAAAA
65 GAATTAAATAATAATATTTGATGAATTTTAAAAATTAAAAACCAAGAAAAATCCCCCTGAAAAAA
* * *
2322349 TTTACGGAGTAGAAAACTCCTGTATATCGAAAATAGAA
130 TTTACGAAGTAAAAAACTCC-GTATATCGAAAATAAAA
* * *
2322387 GAATTTCAA-AAAAAAATAAAAAATGAATGAAAATGAA-TGAATTTATGAAAATTCAGTTTAATA
1 GAATTTCAAGAAAAAAATCAAAAATGAATGAAAATGAATTAAATTT-TGAAAATTGA-TTTAATA
*
2322450 TGAATTAAATAATAATATTTGATGAATTTAAAAAAAAATTAAAAACCAAGAAAAATCCCCCTGAA
64 TGAATTAAATAATAATATTTGATGAATTT---TAAAAATTAAAAACCAAGAAAAATCCCCCTGAA
* * * * * *
2322515 AATATTTATGAAGTAAAAAACTTCGTATTTTGGAAATAAAA
126 AAAATTTACGAAGTAAAAAACTCCGTATATCGAAAATAAAA
* * * *
2322556 GAATTTCAAGAAAAAAATCAAAAATGAATGAAAATGAATGAATTTTTGAAAAATGATTCAATATG
1 GAATTTCAAGAAAAAAATCAAAAATGAATGAAAATGAATTAAATTTTGAAAATTGATTTAATATG
*
2322621 AATTAAATAATATTATTTGATGAATTTTAAAAATT
66 AATTAAATAATAATATTTGATGAATTTTAAAAATT
2322656 TTAAACCCAT
Statistics
Matches: 229, Mismatches: 31, Indels: 18
0.82 0.11 0.06
Matches are distributed among these distances:
164 7 0.03
165 30 0.13
166 50 0.22
169 78 0.34
170 60 0.26
171 4 0.02
ACGTcount: A:0.52, C:0.06, G:0.11, T:0.31
Consensus pattern (166 bp):
GAATTTCAAGAAAAAAATCAAAAATGAATGAAAATGAATTAAATTTTGAAAATTGATTTAATATG
AATTAAATAATAATATTTGATGAATTTTAAAAATTAAAAACCAAGAAAAATCCCCCTGAAAAAAT
TTACGAAGTAAAAAACTCCGTATATCGAAAATAAAA
Found at i:2322978 original size:22 final size:23
Alignment explanation
Indices: 2322953--2322998 Score: 58
Period size: 22 Copynumber: 2.0 Consensus size: 23
2322943 CAAAGTATTG
* *
2322953 ATTTCTAAAATT-AGGAAAATAA
1 ATTTATAAAATTCACGAAAATAA
*
2322975 ATTTATACAATTCACGAAAATAA
1 ATTTATAAAATTCACGAAAATAA
2322998 A
1 A
2322999 ATTGAAAAAT
Statistics
Matches: 20, Mismatches: 3, Indels: 1
0.83 0.12 0.04
Matches are distributed among these distances:
22 10 0.50
23 10 0.50
ACGTcount: A:0.54, C:0.09, G:0.07, T:0.30
Consensus pattern (23 bp):
ATTTATAAAATTCACGAAAATAA
Found at i:2323768 original size:85 final size:85
Alignment explanation
Indices: 2323626--2323897 Score: 290
Period size: 85 Copynumber: 3.2 Consensus size: 85
2323616 TGGGCCAATG
* * * * * *
2323626 GGTAAATAATGAGATGGAGGTTGACC-GAAGACTAAGCTAAC-AGATCACCATAAGGGTAATGGG
1 GGTAAACAATGAGATGAAGGTTGACCAG-AGACTAAGTTGACAAG-TCAACATAGGGGTAATGGG
*
2323689 TTTACCGGGGA-CTGAGCCGATC-
64 TTTACCAGGGATC-GAGCCGA-CA
*
2323711 GGTAAACAATGAGATAAAGGTTGACCAGAGACTAAGTTGACAAGTCAACATAGGGGTAATGGGTT
1 GGTAAACAATGAGATGAAGGTTGACCAGAGACTAAGTTGACAAGTCAACATAGGGGTAATGGGTT
2323776 TACCAGGGATCGAGCCGACA
66 TACCAGGGATCGAGCCGACA
* * *
2323796 GGTAAACAATGAGATGAAGGTTGA-CAGGAGACTGAGTTGACAGGTC-ACTATAGAGGTAATGGG
1 GGTAAACAATGAGATGAAGGTTGACCA-GAGACTAAGTTGACAAGTCAAC-ATAGGGGTAATGGG
* *
2323859 TTTACTAGGGACTC-AGCTGACA
64 TTTACCAGGGA-TCGAGCCGACA
* *
2323881 AGTAAACAA-GGGATGAA
1 GGTAAACAATGAGATGAA
2323898 AAGTGATACC
Statistics
Matches: 164, Mismatches: 16, Indels: 15
0.84 0.08 0.08
Matches are distributed among these distances:
84 12 0.07
85 146 0.89
86 6 0.04
ACGTcount: A:0.35, C:0.14, G:0.31, T:0.20
Consensus pattern (85 bp):
GGTAAACAATGAGATGAAGGTTGACCAGAGACTAAGTTGACAAGTCAACATAGGGGTAATGGGTT
TACCAGGGATCGAGCCGACA
Found at i:2324052 original size:47 final size:47
Alignment explanation
Indices: 2323969--2324336 Score: 344
Period size: 47 Copynumber: 7.8 Consensus size: 47
2323959 ATGAGGATGA
* ** *
2323969 AAAGAGTTTGACTAGG-ACTAATGCCAATACAGTCAAACAAGGGTGG
1 AAAGAGTTTGACTAGGTCCTAACACCAATACAGTCAAACAAGAGTGG
* * * * *
2324015 AAAGAGTTTGATTAGGTCTTAACACTAATACAATCAAACGAGAGTGG
1 AAAGAGTTTGACTAGGTCCTAACACCAATACAGTCAAACAAGAGTGG
* * * *
2324062 AAAGAGTTTGACGAGGTCCTAACACTAATACAGTCAAACGAGAGTGA
1 AAAGAGTTTGACTAGGTCCTAACACCAATACAGTCAAACAAGAGTGG
* ** *
2324109 AAAGAGTTTAACTAGGTCCTAACACCAATGTAGTCAAACAAAAGTGG
1 AAAGAGTTTGACTAGGTCCTAACACCAATACAGTCAAACAAGAGTGG
* ** *
2324156 AAAGAGTTTGACTAGGTCTTAATGCCAATACAGTCAAACAAG-GATGA
1 AAAGAGTTTGACTAGGTCCTAACACCAATACAGTCAAACAAGAG-TGG
* * ** **
2324203 AAAGAGTTTGACCAGGTTCTAATGCCAATACAGTCAAATGAGAGTGG
1 AAAGAGTTTGACTAGGTCCTAACACCAATACAGTCAAACAAGAGTGG
* * * * * * *
2324250 AAAGAATGTCACTAGGTCCTAACGCCAACACAATCAAACGAGAGTGG
1 AAAGAGTTTGACTAGGTCCTAACACCAATACAGTCAAACAAGAGTGG
** * * **
2324297 ATTTGAGTTTGACCAGGTCTTAATGCCAATACAGTCAAAC
1 A-AAGAGTTTGACTAGGTCCTAACACCAATACAGTCAAAC
2324337 GTGGGTAAAA
Statistics
Matches: 263, Mismatches: 55, Indels: 6
0.81 0.17 0.02
Matches are distributed among these distances:
46 16 0.06
47 218 0.83
48 29 0.11
ACGTcount: A:0.39, C:0.17, G:0.22, T:0.22
Consensus pattern (47 bp):
AAAGAGTTTGACTAGGTCCTAACACCAATACAGTCAAACAAGAGTGG
Found at i:2324246 original size:141 final size:141
Alignment explanation
Indices: 2323958--2324336 Score: 431
Period size: 141 Copynumber: 2.7 Consensus size: 141
2323948 CATCATGTCG
* * * *
2323958 AATGAG-GATGAAAAGAGTTTGACTAGG-ACTAATGCCAATACAGTCAAACAAGGGTGGAAAGAG
1 AATGAGAG-TGAAAAGAGTTTAACTAGGTCCTAACGCCAATACAGTCAAACAAGAGTGGAAAGAG
* ** * * * * *
2324021 TTTGATTAGGTCTTAACACTAATACAATCAAACGAGAGTGGAAAGAGTTTGACGAGGTCCTAACA
65 TTTGACTAGGTCTTAATGCCAATACAGTCAAACAAGAGTGAAAAGAGTTTGACCAGGTCCTAACA
*
2324086 CTAATACAGTCA
130 CCAATACAGTCA
* * ** *
2324098 AACGAGAGTGAAAAGAGTTTAACTAGGTCCTAACACCAATGTAGTCAAACAAAAGTGGAAAGAGT
1 AATGAGAGTGAAAAGAGTTTAACTAGGTCCTAACGCCAATACAGTCAAACAAGAGTGGAAAGAGT
* **
2324163 TTGACTAGGTCTTAATGCCAATACAGTCAAACAAG-GATGAAAAGAGTTTGACCAGGTTCTAATG
66 TTGACTAGGTCTTAATGCCAATACAGTCAAACAAGAG-TGAAAAGAGTTTGACCAGGTCCTAACA
2324227 CCAATACAGTCA
130 CCAATACAGTCA
* * * * * * * **
2324239 AATGAGAGTGGAAAGAATGTCACTAGGTCCTAACGCCAACACAATCAAACGAGAGTGGATTTGAG
1 AATGAGAGTGAAAAGAGTTTAACTAGGTCCTAACGCCAATACAGTCAAACAAGAGTGGA-AAGAG
*
2324304 TTTGACCAGGTCTTAATGCCAATACAGTCAAAC
65 TTTGACTAGGTCTTAATGCCAATACAGTCAAAC
2324337 GTGGGTAAAA
Statistics
Matches: 199, Mismatches: 36, Indels: 6
0.83 0.15 0.02
Matches are distributed among these distances:
140 24 0.12
141 140 0.70
142 35 0.18
ACGTcount: A:0.39, C:0.16, G:0.22, T:0.22
Consensus pattern (141 bp):
AATGAGAGTGAAAAGAGTTTAACTAGGTCCTAACGCCAATACAGTCAAACAAGAGTGGAAAGAGT
TTGACTAGGTCTTAATGCCAATACAGTCAAACAAGAGTGAAAAGAGTTTGACCAGGTCCTAACAC
CAATACAGTCA
Found at i:2324474 original size:35 final size:35
Alignment explanation
Indices: 2324435--2324551 Score: 148
Period size: 35 Copynumber: 3.3 Consensus size: 35
2324425 TATGAAGGTG
*
2324435 GAAAGACTTTGACTAGATACAGTCAAACGATGATA
1 GAAAGAGTTTGACTAGATACAGTCAAACGATGATA
2324470 GAAAGAGTTTGA-TCAGATACAGTCAAACGATGATA
1 GAAAGAGTTTGACT-AGATACAGTCAAACGATGATA
* * * *
2324505 GAAAGAGTATGAC-AGGATATAGTCAAATGATGATG
1 GAAAGAGTTTGACTA-GATACAGTCAAACGATGATA
*
2324540 GAAAAAGTTTGA
1 GAAAGAGTTTGA
2324552 GAGAAAATTT
Statistics
Matches: 72, Mismatches: 7, Indels: 6
0.85 0.08 0.07
Matches are distributed among these distances:
34 2 0.03
35 70 0.97
ACGTcount: A:0.44, C:0.09, G:0.24, T:0.23
Consensus pattern (35 bp):
GAAAGAGTTTGACTAGATACAGTCAAACGATGATA
Found at i:2332627 original size:163 final size:164
Alignment explanation
Indices: 2332214--2332629 Score: 446
Period size: 169 Copynumber: 2.5 Consensus size: 164
2332204 AAATGAGATT
* * * * *
2332214 TATTTATTGTTATGTTTATTTTATTCTTTTTTTAAAAATATCATTTCATACTTTAATGAAAACCT
1 TATTAATT-TTAT-TTTATTTTATT-TATTTTTGAAAATA-CATTTCGTACCTTAATGAAAACCT
* *
2332279 GAAAAGATACGAAAAATTTTTGAAATCTTTTATACCCCTAAAGACCCTCATAAGAATATAAAATA
62 GAAAAGATACGAAAAGTTTTTGAAATCTTTTATACCCCTAAAGACCCTCATAAGAATATAAAAGA
*
2332344 TTAAAAAAAAGAATGATTAAAATTTATTTCAATCATGAAAG
127 TT---AAAAAGAATGATTAAAATTTATCTCAATCATGAAAG
* *** * * * *
2332385 TGTTAGCCTAATTTAATTTTTATTTATTTTCGTAAATACTATTTCGTACCTTAAT-AAAAGCCTG
1 TATTAATTTTATTTTA-TTTTATTTATTTTTGAAAATAC-ATTTCGTACCTTAATGAAAA-CCTG
* * * *
2332449 AAAAGATATGAAAAGTTTTTGAAATCTTTTATACCTCT-ATGCACTCC-CATAGGAATATAAAAG
63 AAAAGATACGAAAAGTTTTTGAAATCTTTTATACCCCTAAAG-AC-CCTCATAAGAATATAAAAG
** *
2332512 ATT-AAAA-AATGATTAAAATTTATCTCGGTTATGAAAG
126 ATTAAAAAGAATGATTAAAATTTATCTCAATCATGAAAG
* **
2332549 TATTAATTTTATTTTATTTTATTTATTTTTGAAAATACGATTTCGTACCTTAATGGAAACCCAAA
1 TATTAATTTTATTTTATTTTATTTATTTTTGAAAATAC-ATTTCGTACCTTAATGAAAACCTGAA
2332614 AAGATACGAAAAGTTT
65 AAGATACGAAAAGTTT
2332630 CAGAATATTT
Statistics
Matches: 203, Mismatches: 36, Indels: 20
0.78 0.14 0.08
Matches are distributed among these distances:
163 54 0.27
164 39 0.19
165 4 0.02
168 7 0.03
169 84 0.41
170 12 0.06
171 3 0.01
ACGTcount: A:0.40, C:0.11, G:0.10, T:0.40
Consensus pattern (164 bp):
TATTAATTTTATTTTATTTTATTTATTTTTGAAAATACATTTCGTACCTTAATGAAAACCTGAAA
AGATACGAAAAGTTTTTGAAATCTTTTATACCCCTAAAGACCCTCATAAGAATATAAAAGATTAA
AAAGAATGATTAAAATTTATCTCAATCATGAAAG
Found at i:2333875 original size:162 final size:160
Alignment explanation
Indices: 2333701--2334165 Score: 464
Period size: 162 Copynumber: 2.8 Consensus size: 160
2333691 AGATTCCTCT
* *
2333701 AAAAATATTTATGGA-AAAAAATTTAGT-TTTTTAAGAAAAGAGAAATTTCAAGAAAAAATAAAA
1 AAAAA-ATTTATGGAGAAAAAATCTAGTATTTTGAA-AAAAGAGAAATTTCAAGAAAAAATAAAA
* * *
2333764 AACTTATGAAATTGAATGAATTTTGAAAACTAATTTAATATGAAATAAATAATAATATTTGATGA
64 AA--TATGAAAATGAATGAATTTTGAAAAATAATTTAATATGAATTAAATAATAATATTTGATGA
* *
2333829 ATTTTGAAAATTAAAAACTAAGCAAAATC-CCCTTG
127 ATTTT-AAAATTAAAAACTAAGAAAAATCTCCC-CG
* *
2333864 AAGAAATTTATGGAGGAAAAAACTCCA-TATTTTGAAAATAAGA-AAATTTCAAG--AAAA-AAA
1 AAAAAATTTATGGA-GAAAAAA-TCTAGTATTTTGAAAA-AAGAGAAATTTCAAGAAAAAATAAA
** * * * * *
2333924 TGA-ATGAAAATGAATGAATTTCTGAAAATTGATTTATTATGAATTAAATAATAAAATTTGATAA
63 AAATATGAAAATGAATGAATTT-TGAAAAATAATTTAATATGAATTAAATAATAATATTTGATGA
*
2333988 ATTTAAAAAAAAATTAAAAACTAAGAAAAATCTCCCCG
127 ATTT----TAAAATTAAAAACTAAGAAAAATCTCCCCG
* * * *
2334026 AAAAAATTTATGGAGTAGAAAACTCT-GTATTTTGAAAATAGTGCAATTTCAAGAAAAAATTAAA
1 AAAAAATTTATGGAG-A-AAAAATCTAGTATTTTGAAAAAAGAGAAATTTCAAGAAAAAA-TAAA
* * *
2334090 AAATGAGTGAAAATGAGTGAATTTTTAAAAAATAATTTAATATGAATTAAATAATATTATTTGAT
63 AAAT-A-TGAAAATGAATGAA-TTTTGAAAAATAATTTAATATGAATTAAATAATAATATTTGAT
2334155 GAATTTTAAAA
125 GAATTTTAAAA
2334166 CTTTTAAACC
Statistics
Matches: 246, Mismatches: 33, Indels: 44
0.76 0.10 0.14
Matches are distributed among these distances:
158 17 0.07
159 40 0.16
161 7 0.03
162 72 0.29
163 11 0.04
164 23 0.09
165 16 0.07
166 4 0.02
168 1 0.00
169 52 0.21
170 3 0.01
ACGTcount: A:0.52, C:0.05, G:0.11, T:0.31
Consensus pattern (160 bp):
AAAAAATTTATGGAGAAAAAATCTAGTATTTTGAAAAAAGAGAAATTTCAAGAAAAAATAAAAAA
TATGAAAATGAATGAATTTTGAAAAATAATTTAATATGAATTAAATAATAATATTTGATGAATTT
TAAAATTAAAAACTAAGAAAAATCTCCCCG
Found at i:2334251 original size:169 final size:168
Alignment explanation
Indices: 2333730--2334233 Score: 400
Period size: 162 Copynumber: 3.1 Consensus size: 168
2333720 AATTTAGTTT
* * * *
2333730 TTTAAGAAA-AGAGAAATTTCAAGAAAAAA-TAAAAAACT-TATGAAATTGAATGAATTT-TGAA
1 TTTAA-AAATAGAGCAATTTCAAGAAAAAATTAAAAAA-TGAATGAAAATGAATGAATTTCTAAA
* * * * ** * *
2333791 AACTAATTTAATATGAAATAAATAATAATATTTGATGAATTT--TGAAAATTAAAAACTAAGCAA
64 AAATAATTTAATATGAATTAAATAATAAAATTTGATAAATTTAAAAAAAATTAAAAACCAAGAAA
* * * ** *
2333854 AATC-CCCTTGAAGAAATTTATGGAGGAA-AAAACTCCATAT
129 AATCTCCC-CGAAAAAATTTACGGA-GAAGAAAACTCTGTAA
* * *
2333894 TTTGAAAATA-AGAAAATTTCAAG-----A--AAAAAATGAATGAAAATGAATGAATTTCTGAAA
1 TTTAAAAATAGAG-CAATTTCAAGAAAAAATTAAAAAATGAATGAAAATGAATGAATTTCTAAAA
* * * *
2333951 ATTGATTTATTATGAATTAAATAATAAAATTTGATAAATTTAAAAAAAAATTAAAAACTAAGAAA
65 AATAATTTAATATGAATTAAATAATAAAATTTGATAAATTT-AAAAAAAATTAAAAACCAAGAAA
* * *
2334016 AATCTCCCCGAAAAAATTTATGGAGTAGAAAACTCTGTAT
129 AATCTCCCCGAAAAAATTTACGGAGAAGAAAACTCTGTAA
* * * * *
2334056 TTTGAAAATAGTGCAATTTCAAGAAAAAATTAAAAAATGAGTGAAAATGAGTGAATTTTTAAAAA
1 TTTAAAAATAGAGCAATTTCAAGAAAAAATTAAAAAATGAATGAAAATGAATGAATTTCTAAAAA
** * * ** * * *
2334121 ATAATTTAATATGAATTAAATAATATTATTTGATGAATTT-TAAAACTTTTAAACCCATG-AAAA
66 ATAATTTAATATGAATTAAATAATAAAATTTGATAAATTTAAAAAAAATTAAAAACCAAGAAAAA
* *
2334184 TCTTCTC-AAAAAATTTTACGGAGAAGAAAA-TCTCGTAA
131 TCTCCCCGAAAAAA-TTTACGGAGAAGAAAACTCT-GTAA
2334222 TTTAAAAATAGA
1 TTTAAAAATAGA
2334234 AAGAATTTCA
Statistics
Matches: 278, Mismatches: 43, Indels: 36
0.78 0.12 0.10
Matches are distributed among these distances:
157 1 0.00
158 23 0.08
159 41 0.15
161 2 0.01
162 65 0.23
163 9 0.03
164 15 0.05
165 9 0.03
166 36 0.13
167 13 0.05
169 64 0.23
ACGTcount: A:0.51, C:0.07, G:0.11, T:0.31
Consensus pattern (168 bp):
TTTAAAAATAGAGCAATTTCAAGAAAAAATTAAAAAATGAATGAAAATGAATGAATTTCTAAAAA
ATAATTTAATATGAATTAAATAATAAAATTTGATAAATTTAAAAAAAATTAAAAACCAAGAAAAA
TCTCCCCGAAAAAATTTACGGAGAAGAAAACTCTGTAA
Found at i:2337339 original size:2 final size:2
Alignment explanation
Indices: 2337332--2337369 Score: 53
Period size: 2 Copynumber: 19.5 Consensus size: 2
2337322 GAAACAATAC
2337332 AT AT AT AT AT AT AT AT A- AT AGT AT AT AT A- AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT A-T AT AT AT AT AT AT AT AT A
2337370 AACCAAAAAT
Statistics
Matches: 33, Mismatches: 0, Indels: 6
0.85 0.00 0.15
Matches are distributed among these distances:
1 2 0.06
2 29 0.88
3 2 0.06
ACGTcount: A:0.53, C:0.00, G:0.03, T:0.45
Consensus pattern (2 bp):
AT
Found at i:2337356 original size:12 final size:11
Alignment explanation
Indices: 2337327--2337369 Score: 61
Period size: 12 Copynumber: 3.9 Consensus size: 11
2337317 GAGTTGAAAC
*
2337327 AATACATATAT
1 AATATATATAT
2337338 -ATATATATAT
1 AATATATATAT
2337348 AATAGTATATAT
1 AATA-TATATAT
2337360 AATATATATA
1 AATATATATA
2337370 AACCAAAAAT
Statistics
Matches: 29, Mismatches: 1, Indels: 4
0.85 0.03 0.12
Matches are distributed among these distances:
10 9 0.31
11 9 0.31
12 11 0.38
ACGTcount: A:0.53, C:0.02, G:0.02, T:0.42
Consensus pattern (11 bp):
AATATATATAT
Found at i:2338143 original size:50 final size:51
Alignment explanation
Indices: 2338089--2338203 Score: 178
Period size: 51 Copynumber: 2.3 Consensus size: 51
2338079 TGAATAGTAC
2338089 ATGTATCGATACATTCT-GTTTTCTACCCAGATGTATCAATACATTTTTCA
1 ATGTATCGATACATTCTAGTTTTCTACCCAGATGTATCAATACATTTTTCA
* * * *
2338139 ATGTATCGATATATTCTATTTTTTTACCCAGATGTATCGATACATTTTTCA
1 ATGTATCGATACATTCTAGTTTTCTACCCAGATGTATCAATACATTTTTCA
*
2338190 ATGAATCGATACAT
1 ATGTATCGATACAT
2338204 ATAGTTAATT
Statistics
Matches: 58, Mismatches: 6, Indels: 1
0.89 0.09 0.02
Matches are distributed among these distances:
50 16 0.28
51 42 0.72
ACGTcount: A:0.30, C:0.17, G:0.10, T:0.43
Consensus pattern (51 bp):
ATGTATCGATACATTCTAGTTTTCTACCCAGATGTATCAATACATTTTTCA
Found at i:2344992 original size:23 final size:23
Alignment explanation
Indices: 2344966--2345013 Score: 87
Period size: 23 Copynumber: 2.1 Consensus size: 23
2344956 TATTAAACAT
2344966 AAATGTTAAGATTTTAATTATTA
1 AAATGTTAAGATTTTAATTATTA
*
2344989 AAATGTTAAGATTTTAATTGTTA
1 AAATGTTAAGATTTTAATTATTA
2345012 AA
1 AA
2345014 TTATTTCCTT
Statistics
Matches: 24, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
23 24 1.00
ACGTcount: A:0.44, C:0.00, G:0.10, T:0.46
Consensus pattern (23 bp):
AAATGTTAAGATTTTAATTATTA
Found at i:2348809 original size:41 final size:41
Alignment explanation
Indices: 2348764--2348880 Score: 144
Period size: 41 Copynumber: 2.9 Consensus size: 41
2348754 TCATAAAGCA
* * * *
2348764 TGCCCACATCTTATCAAACAAGAGTTTCTGTTTTCTTAACG
1 TGCCCACGTCTTATCAAACAAGAGTTTCTATTTTATTAACC
* *
2348805 TGCCCACGTCTTATCAAATAAGAGCTTCTATTTTATTAACC
1 TGCCCACGTCTTATCAAACAAGAGTTTCTATTTTATTAACC
* * * *
2348846 TACCCACGCCTTATCAAACTAGAGTTTCTAATTTA
1 TGCCCACGTCTTATCAAACAAGAGTTTCTATTTTA
2348881 AATTTGAATT
Statistics
Matches: 64, Mismatches: 12, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
41 64 1.00
ACGTcount: A:0.29, C:0.25, G:0.10, T:0.36
Consensus pattern (41 bp):
TGCCCACGTCTTATCAAACAAGAGTTTCTATTTTATTAACC
Found at i:2349888 original size:8 final size:7
Alignment explanation
Indices: 2349880--2349936 Score: 51
Period size: 8 Copynumber: 7.6 Consensus size: 7
2349870 AAATTAAAAG
2349880 AAAATAA
1 AAAATAA
*
2349887 GAAAATGA
1 -AAAATAA
*
2349895 AAAGTAA
1 AAAATAA
2349902 AAAATTAA
1 AAAA-TAA
2349910 AAAATTAA
1 AAAA-TAA
*
2349918 AAAATTA
1 AAAATAA
2349925 AAAATAGA
1 AAAATA-A
2349933 AAAA
1 AAAA
2349937 AAAGAAAAAA
Statistics
Matches: 41, Mismatches: 6, Indels: 4
0.80 0.12 0.08
Matches are distributed among these distances:
7 15 0.37
8 26 0.63
ACGTcount: A:0.75, C:0.00, G:0.07, T:0.18
Consensus pattern (7 bp):
AAAATAA
Found at i:2349918 original size:16 final size:16
Alignment explanation
Indices: 2349894--2349937 Score: 63
Period size: 16 Copynumber: 2.8 Consensus size: 16
2349884 TAAGAAAATG
2349894 AAAAGTAAAAAATTAA
1 AAAAGTAAAAAATTAA
*
2349910 AAAATTAAAAAATTAA
1 AAAAGTAAAAAATTAA
2349926 AAATAG-AAAAAA
1 AAA-AGTAAAAAA
2349938 AAGAAAAAAT
Statistics
Matches: 25, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
16 24 0.96
17 1 0.04
ACGTcount: A:0.77, C:0.00, G:0.05, T:0.18
Consensus pattern (16 bp):
AAAAGTAAAAAATTAA
Found at i:2349929 original size:7 final size:8
Alignment explanation
Indices: 2349894--2349928 Score: 61
Period size: 8 Copynumber: 4.4 Consensus size: 8
2349884 TAAGAAAATG
*
2349894 AAAAGTAA
1 AAAATTAA
2349902 AAAATTAA
1 AAAATTAA
2349910 AAAATTAA
1 AAAATTAA
2349918 AAAATTAA
1 AAAATTAA
2349926 AAA
1 AAA
2349929 TAGAAAAAAA
Statistics
Matches: 26, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
8 26 1.00
ACGTcount: A:0.77, C:0.00, G:0.03, T:0.20
Consensus pattern (8 bp):
AAAATTAA
Found at i:2349937 original size:18 final size:18
Alignment explanation
Indices: 2349924--2349964 Score: 64
Period size: 18 Copynumber: 2.3 Consensus size: 18
2349914 TTAAAAAATT
2349924 AAAAATAGAAAAAAAAGA
1 AAAAATAGAAAAAAAAGA
* *
2349942 AAAAATTGAAAAGAAAGA
1 AAAAATAGAAAAAAAAGA
2349960 AAAAA
1 AAAAA
2349965 ATTTTGAAAA
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
18 21 1.00
ACGTcount: A:0.80, C:0.00, G:0.12, T:0.07
Consensus pattern (18 bp):
AAAAATAGAAAAAAAAGA
Found at i:2349956 original size:23 final size:23
Alignment explanation
Indices: 2349856--2349962 Score: 67
Period size: 25 Copynumber: 4.3 Consensus size: 23
2349846 TATTTTCTTT
2349856 GAAAAAAAGAGAAAAAATTAAAA
1 GAAAAAAAGAGAAAAAATTAAAA
* * *
2349879 GAAAATAAGAAAATGAAAAGTAAAA
1 GAAAAAAAGAGAA--AAAATTAAAA
*
2349904 -AATTAAAAA-ATTAAAAAATTAAAAATA
1 GAA--AAAAAGA-GAAAAAATT--AAA-A
2349931 GAAAAAAA-AGAAAAAATTGAAAA
1 GAAAAAAAGAGAAAAAATT-AAAA
2349954 GAAAGAAAA
1 GAAA-AAAA
2349963 AAATTTTGAA
Statistics
Matches: 66, Mismatches: 8, Indels: 19
0.71 0.09 0.20
Matches are distributed among these distances:
23 16 0.24
24 14 0.21
25 18 0.27
26 15 0.23
27 1 0.02
28 2 0.03
ACGTcount: A:0.76, C:0.00, G:0.11, T:0.13
Consensus pattern (23 bp):
GAAAAAAAGAGAAAAAATTAAAA
Found at i:2353338 original size:20 final size:20
Alignment explanation
Indices: 2353313--2353358 Score: 56
Period size: 20 Copynumber: 2.3 Consensus size: 20
2353303 AAGAATTGAA
*
2353313 GAGGGATACAAGAGAGGGAT
1 GAGGGATACAAGAGAGGGAG
* **
2353333 GAGGGATGCTTGAGAGGGAG
1 GAGGGATACAAGAGAGGGAG
2353353 GAGGGA
1 GAGGGA
2353359 GCCTCTATTT
Statistics
Matches: 22, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
20 22 1.00
ACGTcount: A:0.33, C:0.04, G:0.52, T:0.11
Consensus pattern (20 bp):
GAGGGATACAAGAGAGGGAG
Found at i:2353428 original size:25 final size:25
Alignment explanation
Indices: 2353400--2353450 Score: 59
Period size: 25 Copynumber: 2.0 Consensus size: 25
2353390 TTTGTAATAA
*
2353400 AAATTAGCCATAAAT-TTTGACAAAT
1 AAATAAGCC-TAAATATTTGACAAAT
**
2353425 AAATAAGCCTCCATATTTGACAAAT
1 AAATAAGCCTAAATATTTGACAAAT
2353450 A
1 A
2353451 CAAAGGAAAC
Statistics
Matches: 22, Mismatches: 3, Indels: 2
0.81 0.11 0.07
Matches are distributed among these distances:
24 3 0.14
25 19 0.86
ACGTcount: A:0.47, C:0.16, G:0.08, T:0.29
Consensus pattern (25 bp):
AAATAAGCCTAAATATTTGACAAAT
Found at i:2353496 original size:27 final size:27
Alignment explanation
Indices: 2353425--2353505 Score: 101
Period size: 28 Copynumber: 2.9 Consensus size: 27
2353415 TTTGACAAAT
* * *
2353425 AAATAAGCCTCCATATTTGACAAATACA
1 AAATAA-CCACCATTTTTGACAAACACA
2353453 AAGGA-AACCACCATTTTTGACAAACACA
1 AA--ATAACCACCATTTTTGACAAACACA
2353481 AAATAACCACCATTTTTGACAAACA
1 AAATAACCACCATTTTTGACAAACA
2353506 AATGGGTGGC
Statistics
Matches: 47, Mismatches: 3, Indels: 7
0.82 0.05 0.12
Matches are distributed among these distances:
26 1 0.02
27 21 0.45
28 22 0.47
29 2 0.04
30 1 0.02
ACGTcount: A:0.47, C:0.23, G:0.07, T:0.22
Consensus pattern (27 bp):
AAATAACCACCATTTTTGACAAACACA
Found at i:2357996 original size:28 final size:27
Alignment explanation
Indices: 2357964--2358029 Score: 96
Period size: 27 Copynumber: 2.4 Consensus size: 27
2357954 AGCTTTCATA
*
2357964 TTTGATAAATACAAAAGAAACCACCATT
1 TTTGACAAATACAAAA-AAACCACCATT
* *
2357992 TTTGACAAACACAAAATAACCACCATT
1 TTTGACAAATACAAAAAAACCACCATT
2358019 TTTGACAAATA
1 TTTGACAAATA
2358030 AATGGGTGGC
Statistics
Matches: 34, Mismatches: 4, Indels: 1
0.87 0.10 0.03
Matches are distributed among these distances:
27 20 0.59
28 14 0.41
ACGTcount: A:0.48, C:0.20, G:0.06, T:0.26
Consensus pattern (27 bp):
TTTGACAAATACAAAAAAACCACCATT
Found at i:2359385 original size:17 final size:18
Alignment explanation
Indices: 2359358--2359396 Score: 53
Period size: 17 Copynumber: 2.2 Consensus size: 18
2359348 ATATATATAT
*
2359358 ATTTTTCTCTCTTTTAAC
1 ATTTTTCTCTCCTTTAAC
*
2359376 ATTTTT-TCTCCTTTAAT
1 ATTTTTCTCTCCTTTAAC
2359393 ATTT
1 ATTT
2359397 AATCTTTCTA
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
17 13 0.68
18 6 0.32
ACGTcount: A:0.18, C:0.18, G:0.00, T:0.64
Consensus pattern (18 bp):
ATTTTTCTCTCCTTTAAC
Found at i:2360975 original size:2 final size:2
Alignment explanation
Indices: 2360970--2360997 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
2360960 AACCCCAACA
2360970 AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT
2360998 TGAGAGCAAA
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:2362249 original size:32 final size:30
Alignment explanation
Indices: 2362193--2362278 Score: 77
Period size: 32 Copynumber: 2.8 Consensus size: 30
2362183 AAACTATTAA
*
2362193 AAAATTAAAGTAAA-AAATATATTTAAAAAAT
1 AAAA-TAAA-TAAATAAATAAATTTAAAAAAT
* * * *
2362224 AATATAATTAAACGTAAATAAATTTAGAATAT
1 AAAATAAATAAA--TAAATAAATTTAAAAAAT
2362256 AAAATAAATAAATAAA-AAATTTA
1 AAAATAAATAAATAAATAAATTTA
2362279 TATTTTAGAC
Statistics
Matches: 45, Mismatches: 7, Indels: 8
0.75 0.12 0.13
Matches are distributed among these distances:
29 11 0.24
30 7 0.16
31 3 0.07
32 24 0.53
ACGTcount: A:0.65, C:0.01, G:0.03, T:0.30
Consensus pattern (30 bp):
AAAATAAATAAATAAATAAATTTAAAAAAT
Found at i:2362589 original size:21 final size:20
Alignment explanation
Indices: 2362544--2362590 Score: 58
Period size: 21 Copynumber: 2.3 Consensus size: 20
2362534 TTAAAAATAG
* *
2362544 TTTTTGAAAAATATGAGTTT
1 TTTTTGAAAAATAAGAATTT
*
2362564 GTTTTGAAAAAATAAGAATTT
1 TTTTTG-AAAAATAAGAATTT
2362585 TTTTTG
1 TTTTTG
2362591 TTTAGACGAT
Statistics
Matches: 22, Mismatches: 4, Indels: 1
0.81 0.15 0.04
Matches are distributed among these distances:
20 5 0.23
21 17 0.77
ACGTcount: A:0.36, C:0.00, G:0.15, T:0.49
Consensus pattern (20 bp):
TTTTTGAAAAATAAGAATTT
Found at i:2362952 original size:21 final size:22
Alignment explanation
Indices: 2362934--2362981 Score: 71
Period size: 21 Copynumber: 2.2 Consensus size: 22
2362924 TCTATTTATA
* *
2362934 ATTAAACTATTAAT-TTTTAAT
1 ATTAAAATAATAATATTTTAAT
2362955 ATTAAAATAATAATATTTTAAT
1 ATTAAAATAATAATATTTTAAT
2362977 ATTAA
1 ATTAA
2362982 TATTTAATGT
Statistics
Matches: 24, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
21 12 0.50
22 12 0.50
ACGTcount: A:0.50, C:0.02, G:0.00, T:0.48
Consensus pattern (22 bp):
ATTAAAATAATAATATTTTAAT
Found at i:2362976 original size:22 final size:22
Alignment explanation
Indices: 2362906--2362989 Score: 82
Period size: 22 Copynumber: 3.8 Consensus size: 22
2362896 TATTGACATA
*
2362906 AATATTAAAATATTAAAATCTATT
1 AATATTAAAATATTAATAT-T-TT
* *
2362930 TATAATTAAACTATTAAT-TTTT
1 AAT-ATTAAAATATTAATATTTT
*
2362952 AATATTAAAATAATAATATTTT
1 AATATTAAAATATTAATATTTT
*
2362974 AATATTAATAT-TTAAT
1 AATATTAAAATATTAAT
2362990 GTTAAAATAT
Statistics
Matches: 50, Mismatches: 8, Indels: 7
0.77 0.12 0.11
Matches are distributed among these distances:
21 16 0.32
22 18 0.36
23 1 0.02
24 3 0.06
25 12 0.24
ACGTcount: A:0.50, C:0.02, G:0.00, T:0.48
Consensus pattern (22 bp):
AATATTAAAATATTAATATTTT
Found at i:2362986 original size:14 final size:14
Alignment explanation
Indices: 2362950--2363011 Score: 56
Period size: 13 Copynumber: 4.6 Consensus size: 14
2362940 CTATTAATTT
**
2362950 TTAATATTAAAATA
1 TTAATATTTTAATA
*
2362964 ATAATATTTTAATA
1 TTAATATTTTAATA
*
2362978 TTAATA-TTTAATG
1 TTAATATTTTAATA
* *
2362991 TTAAAATATT-ATA
1 TTAATATTTTAATA
2363004 TTAATATT
1 TTAATATT
2363012 AAATATATAA
Statistics
Matches: 37, Mismatches: 10, Indels: 3
0.74 0.20 0.06
Matches are distributed among these distances:
13 19 0.51
14 18 0.49
ACGTcount: A:0.48, C:0.00, G:0.02, T:0.50
Consensus pattern (14 bp):
TTAATATTTTAATA
Found at i:2362988 original size:35 final size:32
Alignment explanation
Indices: 2362914--2363013 Score: 92
Period size: 35 Copynumber: 2.8 Consensus size: 32
2362904 TAAATATTAA
*
2362914 AATATTAAAATCTATTTATAATTAAACTATTAATTTTT
1 AATATTAAAA--TA-TTAT-ATT-AA-TATTAATATTT
*
2362952 AATATTAAAATAATAATATTTTAATATTAATATTT
1 AATATTAAAAT-AT--TATATTAATATTAATATTT
*
2362987 AATGTTAAAATATTATATTAATATTAA
1 AATATTAAAATATTATATTAATATTAA
2363014 ATATATAAAA
Statistics
Matches: 55, Mismatches: 4, Indels: 12
0.77 0.06 0.17
Matches are distributed among these distances:
32 13 0.24
34 2 0.04
35 20 0.36
36 4 0.07
37 3 0.05
38 13 0.24
ACGTcount: A:0.49, C:0.02, G:0.01, T:0.48
Consensus pattern (32 bp):
AATATTAAAATATTATATTAATATTAATATTT
Found at i:2363010 original size:26 final size:27
Alignment explanation
Indices: 2362950--2363025 Score: 84
Period size: 26 Copynumber: 2.8 Consensus size: 27
2362940 CTATTAATTT
* *
2362950 TTAATATTAAA-ATAATAATATTTTAATA
1 TTAATATTAAATAT-ATAAAATATT-ATA
* *
2362978 TTAATATTTAATGT-TAAAATATTATA
1 TTAATATTAAATATATAAAATATTATA
2363004 TTAATATTAAATATATAAAATA
1 TTAATATTAAATATATAAAATA
2363026 ACACTCTTTA
Statistics
Matches: 40, Mismatches: 6, Indels: 5
0.78 0.12 0.10
Matches are distributed among these distances:
26 15 0.38
27 14 0.35
28 10 0.25
29 1 0.03
ACGTcount: A:0.53, C:0.00, G:0.01, T:0.46
Consensus pattern (27 bp):
TTAATATTAAATATATAAAATATTATA
Found at i:2363133 original size:22 final size:20
Alignment explanation
Indices: 2363108--2363169 Score: 52
Period size: 22 Copynumber: 2.8 Consensus size: 20
2363098 ATGTTATTTG
2363108 TATTGTATTTCTAATATTAAAA
1 TATT-TATTT-TAATATTAAAA
*
2363130 TATTCATATTTTTATATTAAAA
1 TATT--TATTTTAATATTAAAA
*
2363152 AATTTATTGTTAAATATT
1 TATTTATT-TT-AATATT
2363170 TATAAAGTAT
Statistics
Matches: 33, Mismatches: 4, Indels: 6
0.77 0.09 0.14
Matches are distributed among these distances:
20 4 0.12
21 2 0.06
22 22 0.67
23 5 0.15
ACGTcount: A:0.40, C:0.03, G:0.03, T:0.53
Consensus pattern (20 bp):
TATTTATTTTAATATTAAAA
Found at i:2363310 original size:16 final size:17
Alignment explanation
Indices: 2363291--2363330 Score: 64
Period size: 16 Copynumber: 2.4 Consensus size: 17
2363281 TTATTTAAAT
2363291 AATAATAGTTTTA-TTA
1 AATAATAGTTTTATTTA
*
2363307 AATAATATTTTTATTTA
1 AATAATAGTTTTATTTA
2363324 AATAATA
1 AATAATA
2363331 AATTATATTA
Statistics
Matches: 22, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
16 12 0.55
17 10 0.45
ACGTcount: A:0.47, C:0.00, G:0.03, T:0.50
Consensus pattern (17 bp):
AATAATAGTTTTATTTA
Found at i:2363324 original size:36 final size:35
Alignment explanation
Indices: 2363278--2363381 Score: 108
Period size: 36 Copynumber: 2.9 Consensus size: 35
2363268 ATGCTACGAC
2363278 TTATTATTTAAATAATAATAGTTTTATTAAATAATAT
1 TTATTATTTAAATAATAATAGTTTTATTAAAT--TAT
*
2363315 TT-TTATTTAAATAATAA-A-TTATATT-AATTAT
1 TTATTATTTAAATAATAATAGTTTTATTAAATTAT
* *
2363346 TTATTATTAAAATAAATAATATGATATTATTAAATT
1 TTATTATTTAAAT-AATAATA-G-TTTTATTAAATT
2363382 TTAAATATGT
Statistics
Matches: 56, Mismatches: 4, Indels: 13
0.77 0.05 0.18
Matches are distributed among these distances:
31 5 0.09
32 9 0.16
33 8 0.14
34 7 0.12
35 1 0.02
36 15 0.27
37 7 0.12
38 4 0.07
ACGTcount: A:0.47, C:0.00, G:0.02, T:0.51
Consensus pattern (35 bp):
TTATTATTTAAATAATAATAGTTTTATTAAATTAT
Found at i:2363336 original size:16 final size:17
Alignment explanation
Indices: 2363280--2363341 Score: 56
Period size: 17 Copynumber: 3.6 Consensus size: 17
2363270 GCTACGACTT
2363280 ATTAT-TTAAATAATAA
1 ATTATATTAAATAATAA
*
2363296 TAGTTTTATTAAATAAT-A
1 -A-TTATATTAAATAATAA
* *
2363314 TTTTTATTTAAATAATAA
1 ATTATA-TTAAATAATAA
2363332 ATTATATTAA
1 ATTATATTAA
2363342 TTATTTATTA
Statistics
Matches: 37, Mismatches: 4, Indels: 8
0.76 0.08 0.16
Matches are distributed among these distances:
16 5 0.14
17 14 0.38
18 9 0.24
19 9 0.24
ACGTcount: A:0.48, C:0.00, G:0.02, T:0.50
Consensus pattern (17 bp):
ATTATATTAAATAATAA
Found at i:2363348 original size:29 final size:30
Alignment explanation
Indices: 2363311--2363376 Score: 75
Period size: 29 Copynumber: 2.3 Consensus size: 30
2363301 TTATTAAATA
* *
2363311 ATATT-TTTATT-TAAATAATAAATTATATT
1 ATATTATTTATTATAAA-AATAAATAATATG
*
2363340 A-ATTATTTATTATTAAAATAAATAATATG
1 ATATTATTTATTATAAAAATAAATAATATG
2363369 ATATTATT
1 ATATTATT
2363377 AAATTTTAAA
Statistics
Matches: 31, Mismatches: 3, Indels: 5
0.79 0.08 0.13
Matches are distributed among these distances:
28 3 0.10
29 19 0.61
30 9 0.29
ACGTcount: A:0.47, C:0.00, G:0.02, T:0.52
Consensus pattern (30 bp):
ATATTATTTATTATAAAAATAAATAATATG
Found at i:2368619 original size:31 final size:31
Alignment explanation
Indices: 2368551--2368619 Score: 102
Period size: 31 Copynumber: 2.2 Consensus size: 31
2368541 ATTAAATTTG
* * **
2368551 GAATTTCCTAGCCGCCAGCCAAATCTTAATT
1 GAATTTGCTAGCAGCCAGCCAAATCCAAATT
2368582 GAATTTGCTAGCAGCCAGCCAAATCCAAATT
1 GAATTTGCTAGCAGCCAGCCAAATCCAAATT
2368613 GAATTTG
1 GAATTTG
2368620 ATTTGGCTCA
Statistics
Matches: 34, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
31 34 1.00
ACGTcount: A:0.32, C:0.25, G:0.16, T:0.28
Consensus pattern (31 bp):
GAATTTGCTAGCAGCCAGCCAAATCCAAATT
Found at i:2369128 original size:26 final size:26
Alignment explanation
Indices: 2369099--2369150 Score: 104
Period size: 26 Copynumber: 2.0 Consensus size: 26
2369089 CTCCTCACAA
2369099 TGTGTTTCCTCTAATAAAGACATTAG
1 TGTGTTTCCTCTAATAAAGACATTAG
2369125 TGTGTTTCCTCTAATAAAGACATTAG
1 TGTGTTTCCTCTAATAAAGACATTAG
2369151 AAGAGTAGCA
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
26 26 1.00
ACGTcount: A:0.31, C:0.15, G:0.15, T:0.38
Consensus pattern (26 bp):
TGTGTTTCCTCTAATAAAGACATTAG
Found at i:2369663 original size:21 final size:21
Alignment explanation
Indices: 2369639--2369680 Score: 57
Period size: 21 Copynumber: 2.0 Consensus size: 21
2369629 TGAAATGATG
*
2369639 CATTGGTTGGATGAAAGAATA
1 CATTGGTTGGATGAAAAAATA
**
2369660 CATTTTTTGGATGAAAAAATA
1 CATTGGTTGGATGAAAAAATA
2369681 TAACTTTTAA
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
21 18 1.00
ACGTcount: A:0.40, C:0.05, G:0.21, T:0.33
Consensus pattern (21 bp):
CATTGGTTGGATGAAAAAATA
Found at i:2369688 original size:21 final size:21
Alignment explanation
Indices: 2369645--2369688 Score: 52
Period size: 21 Copynumber: 2.1 Consensus size: 21
2369635 GATGCATTGG
* **
2369645 TTGGATGAAAGAATACATTTT
1 TTGGATGAAAAAATACAACTT
*
2369666 TTGGATGAAAAAATATAACTT
1 TTGGATGAAAAAATACAACTT
2369687 TT
1 TT
2369689 AATAACTAAA
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:0.41, C:0.05, G:0.16, T:0.39
Consensus pattern (21 bp):
TTGGATGAAAAAATACAACTT
Found at i:2373169 original size:19 final size:18
Alignment explanation
Indices: 2373136--2373172 Score: 56
Period size: 19 Copynumber: 2.0 Consensus size: 18
2373126 GTATTAATAC
2373136 AAAATAATATAAATTTAA
1 AAAATAATATAAATTTAA
*
2373154 AAAATATATATGAATTTAA
1 AAAATA-ATATAAATTTAA
2373173 TTTATTATAT
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
18 6 0.35
19 11 0.65
ACGTcount: A:0.62, C:0.00, G:0.03, T:0.35
Consensus pattern (18 bp):
AAAATAATATAAATTTAA
Found at i:2374520 original size:4 final size:4
Alignment explanation
Indices: 2374511--2374540 Score: 60
Period size: 4 Copynumber: 7.5 Consensus size: 4
2374501 GCTTTTTGAA
2374511 TTAT TTAT TTAT TTAT TTAT TTAT TTAT TT
1 TTAT TTAT TTAT TTAT TTAT TTAT TTAT TT
2374541 TTACGAATGA
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 26 1.00
ACGTcount: A:0.23, C:0.00, G:0.00, T:0.77
Consensus pattern (4 bp):
TTAT
Found at i:2374905 original size:2 final size:2
Alignment explanation
Indices: 2374900--2374933 Score: 68
Period size: 2 Copynumber: 17.0 Consensus size: 2
2374890 ACATACACAC
2374900 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
2374934 GCACTTTGAG
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 32 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:2375378 original size:12 final size:11
Alignment explanation
Indices: 2375353--2375390 Score: 51
Period size: 11 Copynumber: 3.4 Consensus size: 11
2375343 TTTCATAATG
2375353 AAAAAATGAAA
1 AAAAAATGAAA
2375364 AAAAAATGAACA
1 AAAAAATGAA-A
2375376 AAAAAA-GCAAA
1 AAAAAATG-AAA
2375387 AAAA
1 AAAA
2375391 GGGAGAAAAG
Statistics
Matches: 25, Mismatches: 0, Indels: 4
0.86 0.00 0.14
Matches are distributed among these distances:
11 16 0.64
12 9 0.36
ACGTcount: A:0.82, C:0.05, G:0.08, T:0.05
Consensus pattern (11 bp):
AAAAAATGAAA
Found at i:2377297 original size:20 final size:20
Alignment explanation
Indices: 2377272--2377322 Score: 75
Period size: 20 Copynumber: 2.5 Consensus size: 20
2377262 ACCCTCATTT
2377272 GTATCAATACAAGTTAAAAC
1 GTATCAATACAAGTTAAAAC
* * *
2377292 GTATCAATACAATTTACAAT
1 GTATCAATACAAGTTAAAAC
2377312 GTATCAATACA
1 GTATCAATACA
2377323 TTATATAAAT
Statistics
Matches: 28, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
20 28 1.00
ACGTcount: A:0.47, C:0.16, G:0.08, T:0.29
Consensus pattern (20 bp):
GTATCAATACAAGTTAAAAC
Found at i:2377415 original size:113 final size:111
Alignment explanation
Indices: 2377197--2377454 Score: 290
Period size: 113 Copynumber: 2.3 Consensus size: 111
2377187 TTCAGGATTG
* * *
2377197 AATGTATCGATACATCATATGAATGTATCGATTCATATGGTTGGCAGCAGCTAAGAAGCATTGAA
1 AATGTATCGATACATTATATAAATGTATCGATACATATGGTTGGCAGCAGCTAAGAA-CATTGAA
* **
2377262 ACCCTCATTTGTATCAATACAAGTTAAAACGTATCAATACAATTTAC
65 ACCCTCATTTGTATCAATACAAGTGAAAACGTATCAATACAATGCAC
* * * * * *
2377309 AATGTATCAATACATTATATAAATGTATTGATACATCTGGTTGGTAGTAGGTAAAGAA-ATTCTG
1 AATGTATCGATACATTATATAAATGTATCGATACATATGGTTGGCAGCAGCT-AAGAACA-T-TG
**
2377373 AAACCCTCATTTGTATCAATACACA-TGAAAATTTAT-AGATACAATGCAC
63 AAACCCTCATTTGTATCAATACA-AGTGAAAACGTATCA-ATACAATGCAC
* *
2377422 AATATATCGATACATT-CATAAATGTATCGATAC
1 AATGTATCGATACATTATATAAATGTATCGATAC
2377455 TTTGTGTTAT
Statistics
Matches: 123, Mismatches: 18, Indels: 10
0.81 0.12 0.07
Matches are distributed among these distances:
111 1 0.01
112 60 0.49
113 61 0.50
114 1 0.01
ACGTcount: A:0.39, C:0.15, G:0.14, T:0.32
Consensus pattern (111 bp):
AATGTATCGATACATTATATAAATGTATCGATACATATGGTTGGCAGCAGCTAAGAACATTGAAA
CCCTCATTTGTATCAATACAAGTGAAAACGTATCAATACAATGCAC
Found at i:2379466 original size:16 final size:16
Alignment explanation
Indices: 2379428--2379468 Score: 50
Period size: 16 Copynumber: 2.6 Consensus size: 16
2379418 GCATTGTTAC
2379428 TGAAAAAAGCTTGGAT
1 TGAAAAAAGCTTGGAT
2379444 T-AGAAAAAGCTTAGG-T
1 TGA-AAAAAGCTT-GGAT
2379460 TGAAAAAAG
1 TGAAAAAAG
2379469 TATGTTTGAA
Statistics
Matches: 22, Mismatches: 0, Indels: 6
0.79 0.00 0.21
Matches are distributed among these distances:
15 1 0.05
16 18 0.82
17 3 0.14
ACGTcount: A:0.49, C:0.05, G:0.24, T:0.22
Consensus pattern (16 bp):
TGAAAAAAGCTTGGAT
Found at i:2382793 original size:38 final size:39
Alignment explanation
Indices: 2382742--2382816 Score: 107
Period size: 38 Copynumber: 1.9 Consensus size: 39
2382732 CATGAAAGTG
* * *
2382742 CTAAAATAACTCTAAAGGCT-TATTTTAACTCAAAATTA
1 CTAAAACAACTCTAAAAGCTCGATTTTAACTCAAAATTA
*
2382780 CTAAAACAACTCTAAAAGCTCGATTTTGACTCAAAAT
1 CTAAAACAACTCTAAAAGCTCGATTTTAACTCAAAAT
2382817 AATTGAAATT
Statistics
Matches: 32, Mismatches: 4, Indels: 1
0.86 0.11 0.03
Matches are distributed among these distances:
38 18 0.56
39 14 0.44
ACGTcount: A:0.44, C:0.19, G:0.07, T:0.31
Consensus pattern (39 bp):
CTAAAACAACTCTAAAAGCTCGATTTTAACTCAAAATTA
Found at i:2383444 original size:21 final size:21
Alignment explanation
Indices: 2383420--2383460 Score: 57
Period size: 21 Copynumber: 2.0 Consensus size: 21
2383410 TTCTTTAATT
2383420 TTTTCCTT-TTTTTCTTCTTGG
1 TTTT-CTTCTTTTTCTTCTTGG
*
2383441 TTTTCTTCTTTTTGTTCTTG
1 TTTTCTTCTTTTTCTTCTTG
2383461 TAGAAAATGA
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
20 3 0.17
21 15 0.83
ACGTcount: A:0.00, C:0.17, G:0.10, T:0.73
Consensus pattern (21 bp):
TTTTCTTCTTTTTCTTCTTGG
Found at i:2386391 original size:26 final size:26
Alignment explanation
Indices: 2386346--2386415 Score: 88
Period size: 26 Copynumber: 2.6 Consensus size: 26
2386336 GGGTCATTAT
*
2386346 ATTTATTTAATTATTATATAATAAT-AA
1 ATTTATAT-ATTATTATATAA-AATAAA
2386373 ATTTATATATTATTATATAAAATAAA
1 ATTTATATATTATTATATAAAATAAA
*
2386399 ATTTATTATATAATTAT
1 ATTTA-TATATTATTAT
2386416 TTTGAAATTC
Statistics
Matches: 39, Mismatches: 2, Indels: 4
0.87 0.04 0.09
Matches are distributed among these distances:
25 3 0.08
26 19 0.49
27 17 0.44
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (26 bp):
ATTTATATATTATTATATAAAATAAA
Found at i:2392460 original size:3 final size:3
Alignment explanation
Indices: 2392454--2392483 Score: 60
Period size: 3 Copynumber: 10.0 Consensus size: 3
2392444 TTTTGCCTGA
2392454 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
2392484 AAAGAATTTA
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 27 1.00
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (3 bp):
TAT
Found at i:2394358 original size:2 final size:2
Alignment explanation
Indices: 2394351--2394377 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
2394341 TTGTCTGCAA
2394351 AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT A
2394378 CACACACATG
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 25 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:2394763 original size:2 final size:2
Alignment explanation
Indices: 2394756--2394790 Score: 52
Period size: 2 Copynumber: 17.5 Consensus size: 2
2394746 ATCCCTCCTT
* *
2394756 TA TA TA TA CA TA CA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
2394791 GCATAGTTTC
Statistics
Matches: 29, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
2 29 1.00
ACGTcount: A:0.49, C:0.06, G:0.00, T:0.46
Consensus pattern (2 bp):
TA
Found at i:2395081 original size:11 final size:12
Alignment explanation
Indices: 2395065--2395093 Score: 51
Period size: 11 Copynumber: 2.5 Consensus size: 12
2395055 TTGTAAAATC
2395065 AATATTTTCT-A
1 AATATTTTCTAA
2395076 AATATTTTCTAA
1 AATATTTTCTAA
2395088 AATATT
1 AATATT
2395094 AATGATATAA
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
11 10 0.59
12 7 0.41
ACGTcount: A:0.41, C:0.07, G:0.00, T:0.52
Consensus pattern (12 bp):
AATATTTTCTAA
Found at i:2396631 original size:23 final size:21
Alignment explanation
Indices: 2396580--2396632 Score: 52
Period size: 22 Copynumber: 2.4 Consensus size: 21
2396570 ATCATTTATT
* *
2396580 AGATAAAAATAACTTTTAAAA
1 AGATAAAAACAAATTTTAAAA
*
2396601 TGATTAAAAACAAATTTCGTAAAA
1 AGA-TAAAAACAAATTT--TAAAA
2396625 AGATAAAA
1 AGATAAAA
2396633 TTTCAAATTT
Statistics
Matches: 25, Mismatches: 4, Indels: 4
0.76 0.12 0.12
Matches are distributed among these distances:
21 2 0.08
22 11 0.44
23 5 0.20
24 7 0.28
ACGTcount: A:0.60, C:0.06, G:0.08, T:0.26
Consensus pattern (21 bp):
AGATAAAAACAAATTTTAAAA
Found at i:2400016 original size:6 final size:6
Alignment explanation
Indices: 2399982--2400044 Score: 76
Period size: 6 Copynumber: 10.8 Consensus size: 6
2399972 TACAAAAAGC
* * * *
2399982 CATATA CATACA TACATA CATAT- -ATATA CATATA CATATA CATACA
1 CATATA CATATA CATATA CATATA CATATA CATATA CATATA CATATA
2400028 CATATA CATATA CATAT
1 CATATA CATATA CATAT
2400045 TTATTATATG
Statistics
Matches: 47, Mismatches: 8, Indels: 4
0.80 0.14 0.07
Matches are distributed among these distances:
4 4 0.09
6 43 0.91
ACGTcount: A:0.49, C:0.19, G:0.00, T:0.32
Consensus pattern (6 bp):
CATATA
Found at i:2404211 original size:45 final size:44
Alignment explanation
Indices: 2404120--2404218 Score: 119
Period size: 45 Copynumber: 2.2 Consensus size: 44
2404110 ATTGCTGAAA
* *
2404120 TAAACATTATTATATATTATTATATTTATAATATATAGTGTAAAATT
1 TAAA-ATT-TTATATATCACTATATTTATAATATATAGTGTAAAA-T
* *
2404167 TAAAATTTTATATATCACTATATTTATAATATGGT-GTGTCAAAT
1 TAAAATTTTATATATCACTATATTTATAATAT-ATAGTGTAAAAT
2404211 TAAAATTT
1 TAAAATTT
2404219 AAAATTTCTT
Statistics
Matches: 47, Mismatches: 4, Indels: 5
0.84 0.07 0.09
Matches are distributed among these distances:
44 9 0.19
45 30 0.64
46 4 0.09
47 4 0.09
ACGTcount: A:0.42, C:0.04, G:0.06, T:0.47
Consensus pattern (44 bp):
TAAAATTTTATATATCACTATATTTATAATATATAGTGTAAAAT
Found at i:2405609 original size:28 final size:28
Alignment explanation
Indices: 2405499--2405605 Score: 187
Period size: 28 Copynumber: 3.8 Consensus size: 28
2405489 CAAATGCCAC
2405499 CCTTTGTATTTGTCAAATATGGTAGTTT
1 CCTTTGTATTTGTCAAATATGGTAGTTT
*
2405527 CCTTTGTATTTATCAAATATGGTAGTTT
1 CCTTTGTATTTGTCAAATATGGTAGTTT
*
2405555 CCTTTGTATTTGTCAAATATGGTGGTTT
1 CCTTTGTATTTGTCAAATATGGTAGTTT
*
2405583 CCTTTATATTTGTCAAATATGGT
1 CCTTTGTATTTGTCAAATATGGT
2405606 GGTTATTTTT
Statistics
Matches: 75, Mismatches: 4, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
28 75 1.00
ACGTcount: A:0.22, C:0.11, G:0.17, T:0.50
Consensus pattern (28 bp):
CCTTTGTATTTGTCAAATATGGTAGTTT
Found at i:2405735 original size:20 final size:20
Alignment explanation
Indices: 2405712--2405751 Score: 53
Period size: 20 Copynumber: 2.0 Consensus size: 20
2405702 AGGCTCCCAA
2405712 ATCCATCTCTAGCATCCCTC
1 ATCCATCTCTAGCATCCCTC
* * *
2405732 ATCCTTCTCTTGTATCCCTC
1 ATCCATCTCTAGCATCCCTC
2405752 TTCAATTCTT
Statistics
Matches: 17, Mismatches: 3, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.15, C:0.42, G:0.05, T:0.38
Consensus pattern (20 bp):
ATCCATCTCTAGCATCCCTC
Found at i:2410152 original size:28 final size:28
Alignment explanation
Indices: 2410120--2410197 Score: 122
Period size: 28 Copynumber: 2.8 Consensus size: 28
2410110 AATGCCACCC
2410120 TTTGTATTTGTCAAATATGGT-AGTTTCA
1 TTTGTATTTGTCAAATATGGTGA-TTTCA
*
2410148 TTTGTATTTGTCAAATATGGTGATTTCC
1 TTTGTATTTGTCAAATATGGTGATTTCA
*
2410176 TTTATATTTGTCAAATATGGTG
1 TTTGTATTTGTCAAATATGGTG
2410198 GTTATTTTTG
Statistics
Matches: 47, Mismatches: 2, Indels: 2
0.92 0.04 0.04
Matches are distributed among these distances:
28 46 0.98
29 1 0.02
ACGTcount: A:0.24, C:0.08, G:0.18, T:0.50
Consensus pattern (28 bp):
TTTGTATTTGTCAAATATGGTGATTTCA
Found at i:2410241 original size:24 final size:24
Alignment explanation
Indices: 2410205--2410250 Score: 83
Period size: 24 Copynumber: 1.9 Consensus size: 24
2410195 GTGGTTATTT
2410205 TTGTTTGTAAAAATTGGTGGCTTG
1 TTGTTTGTAAAAATTGGTGGCTTG
*
2410229 TTGTTTGTCAAAATTGGTGGCT
1 TTGTTTGTAAAAATTGGTGGCT
2410251 AATTTTTATT
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
24 21 1.00
ACGTcount: A:0.20, C:0.07, G:0.28, T:0.46
Consensus pattern (24 bp):
TTGTTTGTAAAAATTGGTGGCTTG
Found at i:2410327 original size:20 final size:20
Alignment explanation
Indices: 2410304--2410343 Score: 53
Period size: 20 Copynumber: 2.0 Consensus size: 20
2410294 AGGCTCCCAA
2410304 ATCCATCTCTAGCATCCCTC
1 ATCCATCTCTAGCATCCCTC
* * *
2410324 ATCCTTCTCTTGTATCCCTC
1 ATCCATCTCTAGCATCCCTC
2410344 TTCAATTCTT
Statistics
Matches: 17, Mismatches: 3, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.15, C:0.42, G:0.05, T:0.38
Consensus pattern (20 bp):
ATCCATCTCTAGCATCCCTC
Found at i:2414317 original size:25 final size:25
Alignment explanation
Indices: 2414261--2414309 Score: 66
Period size: 25 Copynumber: 2.0 Consensus size: 25
2414251 TAAAATACAA
* *
2414261 TTATTATATATGTTTATTTACTTCC
1 TTATTATATATATTTATTTACTTAC
2414286 TTATTATATATATTT-TTTA-TTAC
1 TTATTATATATATTTATTTACTTAC
2414309 T
1 T
2414310 ATAATTATTT
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
23 4 0.18
24 4 0.18
25 14 0.64
ACGTcount: A:0.27, C:0.08, G:0.02, T:0.63
Consensus pattern (25 bp):
TTATTATATATATTTATTTACTTAC
Found at i:2417065 original size:2 final size:2
Alignment explanation
Indices: 2417058--2417082 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
2417048 GGCAATGCAA
2417058 AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT A
2417083 CTATTATTAA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:2417453 original size:20 final size:20
Alignment explanation
Indices: 2417430--2417524 Score: 91
Period size: 20 Copynumber: 4.8 Consensus size: 20
2417420 CGACAGATAA
* *
2417430 TTGTAAAATATAACAAATAT
1 TTGTAAAAGATAACAAATAG
* ***
2417450 TTGTGATTTATAACAAATAG
1 TTGTAAAAGATAACAAATAG
* *
2417470 TTATAAAAGATAAAAAATAG
1 TTGTAAAAGATAACAAATAG
* *
2417490 TCGTAAAAGCTAACAAATAG
1 TTGTAAAAGATAACAAATAG
*
2417510 TTGTATAAGATAACA
1 TTGTAAAAGATAACA
2417525 TTGGTGATAA
Statistics
Matches: 58, Mismatches: 17, Indels: 0
0.77 0.23 0.00
Matches are distributed among these distances:
20 58 1.00
ACGTcount: A:0.52, C:0.06, G:0.12, T:0.31
Consensus pattern (20 bp):
TTGTAAAAGATAACAAATAG
Found at i:2417938 original size:20 final size:20
Alignment explanation
Indices: 2417902--2417952 Score: 86
Period size: 20 Copynumber: 2.6 Consensus size: 20
2417892 TAAAATAAAA
2417902 AAATTAAGTAA-TTAGTAAT
1 AAATTAAGTAATTTAGTAAT
*
2417921 AAGTTAAGTAATTTAGTAAT
1 AAATTAAGTAATTTAGTAAT
2417941 AAATTAAGTAAT
1 AAATTAAGTAAT
2417953 ATTTGAGAAT
Statistics
Matches: 29, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
19 10 0.34
20 19 0.66
ACGTcount: A:0.51, C:0.00, G:0.12, T:0.37
Consensus pattern (20 bp):
AAATTAAGTAATTTAGTAAT
Found at i:2418261 original size:3 final size:3
Alignment explanation
Indices: 2418255--2418287 Score: 66
Period size: 3 Copynumber: 11.0 Consensus size: 3
2418245 TATATTGTTG
2418255 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
2418288 AAAGGCTGTA
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 30 1.00
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (3 bp):
TTA
Found at i:2418923 original size:2 final size:2
Alignment explanation
Indices: 2418916--2418942 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
2418906 TAACTTAAAA
2418916 TG TG TG TG TG TG TG TG TG TG TG TG TG T
1 TG TG TG TG TG TG TG TG TG TG TG TG TG T
2418943 TTTTTTATTT
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 25 1.00
ACGTcount: A:0.00, C:0.00, G:0.48, T:0.52
Consensus pattern (2 bp):
TG
Found at i:2419043 original size:15 final size:15
Alignment explanation
Indices: 2419025--2419054 Score: 51
Period size: 15 Copynumber: 2.0 Consensus size: 15
2419015 ATTTAATTTT
2419025 AATTTAAAAATAAAA
1 AATTTAAAAATAAAA
*
2419040 AATTTAATAATAAAA
1 AATTTAAAAATAAAA
2419055 TTGTGCTTTC
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.70, C:0.00, G:0.00, T:0.30
Consensus pattern (15 bp):
AATTTAAAAATAAAA
Found at i:2421296 original size:18 final size:18
Alignment explanation
Indices: 2421275--2421316 Score: 75
Period size: 18 Copynumber: 2.3 Consensus size: 18
2421265 AATTTAATTA
*
2421275 TCATATTTCAAGTTCTAT
1 TCATATTTCAAATTCTAT
2421293 TCATATTTCAAATTCTAT
1 TCATATTTCAAATTCTAT
2421311 TCATAT
1 TCATAT
2421317 AGTTTTAAGT
Statistics
Matches: 23, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
18 23 1.00
ACGTcount: A:0.31, C:0.17, G:0.02, T:0.50
Consensus pattern (18 bp):
TCATATTTCAAATTCTAT
Found at i:2421469 original size:42 final size:42
Alignment explanation
Indices: 2421418--2421501 Score: 150
Period size: 42 Copynumber: 2.0 Consensus size: 42
2421408 CAACAATCGT
*
2421418 TTTTTAAAATTATATCTCTAAAAAATTTTAAAGATGATTATA
1 TTTTTAAAATTATATCTCTAAAAAATTTTAAAGATAATTATA
*
2421460 TTTTTAAAATTATATCTCTGAAAAATTTTAAAGATAATTATA
1 TTTTTAAAATTATATCTCTAAAAAATTTTAAAGATAATTATA
2421502 GACAATCGTC
Statistics
Matches: 40, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
42 40 1.00
ACGTcount: A:0.45, C:0.05, G:0.05, T:0.45
Consensus pattern (42 bp):
TTTTTAAAATTATATCTCTAAAAAATTTTAAAGATAATTATA
Found at i:2431979 original size:2 final size:2
Alignment explanation
Indices: 2431958--2432038 Score: 65
Period size: 2 Copynumber: 40.5 Consensus size: 2
2431948 ACAAAAAGTA
* * * * * *
2431958 AT AT AC AT AT AT AC AC AT AT AT GT AT AC AT AT AC AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
* * *
2432000 AT AT AT AT AT GT GA- AA AT AC AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT -AT AT AT AT AT AT AT AT AT AT AT AT AT A
2432039 CATACAAAAA
Statistics
Matches: 62, Mismatches: 15, Indels: 4
0.77 0.19 0.05
Matches are distributed among these distances:
1 1 0.02
2 61 0.98
ACGTcount: A:0.49, C:0.07, G:0.04, T:0.40
Consensus pattern (2 bp):
AT
Found at i:2432713 original size:38 final size:38
Alignment explanation
Indices: 2432671--2432763 Score: 125
Period size: 38 Copynumber: 2.4 Consensus size: 38
2432661 CCACCAATTA
*
2432671 AAAATAGTAGTTTTTGTATTGAACCATACCAAC-AGTTT
1 AAAATAGTAATTTTTGTATTGAACCATACCAACGAG-TT
* * * *
2432709 AAAATATTAATTTTTGTTTTGAACTATACCATCGAGTT
1 AAAATAGTAATTTTTGTATTGAACCATACCAACGAGTT
2432747 AAAATAGTAATTTTTGT
1 AAAATAGTAATTTTTGT
2432764 CCATAGCTTG
Statistics
Matches: 48, Mismatches: 6, Indels: 2
0.86 0.11 0.04
Matches are distributed among these distances:
38 46 0.96
39 2 0.04
ACGTcount: A:0.37, C:0.10, G:0.12, T:0.42
Consensus pattern (38 bp):
AAAATAGTAATTTTTGTATTGAACCATACCAACGAGTT
Found at i:2433761 original size:37 final size:36
Alignment explanation
Indices: 2433720--2433791 Score: 117
Period size: 37 Copynumber: 2.0 Consensus size: 36
2433710 TTAACCTTTA
**
2433720 TCTTGCATTTTGATTATCTTTTCATATAAAAAAATTT
1 TCTTGCATTTTGATTAGATTTTCATA-AAAAAAATTT
2433757 TCTTGCATTTTGATTAGATTTTCATAAAAAAAATT
1 TCTTGCATTTTGATTAGATTTTCATAAAAAAAATT
2433792 CAAGGTAAAG
Statistics
Matches: 33, Mismatches: 2, Indels: 1
0.92 0.06 0.03
Matches are distributed among these distances:
36 9 0.27
37 24 0.73
ACGTcount: A:0.35, C:0.10, G:0.07, T:0.49
Consensus pattern (36 bp):
TCTTGCATTTTGATTAGATTTTCATAAAAAAAATTT
Found at i:2434607 original size:21 final size:20
Alignment explanation
Indices: 2434583--2434621 Score: 51
Period size: 21 Copynumber: 1.9 Consensus size: 20
2434573 GGGTAATGAT
*
2434583 TTTTGGGTTAGGGTCTTTTTC
1 TTTTGCGTTAGGGT-TTTTTC
*
2434604 TTTTGCTTTAGGGTTTTT
1 TTTTGCGTTAGGGTTTTT
2434622 GAATTGATTT
Statistics
Matches: 16, Mismatches: 2, Indels: 1
0.84 0.11 0.05
Matches are distributed among these distances:
20 4 0.25
21 12 0.75
ACGTcount: A:0.05, C:0.08, G:0.26, T:0.62
Consensus pattern (20 bp):
TTTTGCGTTAGGGTTTTTTC
Found at i:2435819 original size:25 final size:23
Alignment explanation
Indices: 2435768--2435837 Score: 63
Period size: 22 Copynumber: 3.0 Consensus size: 23
2435758 TATATTTGTT
* *
2435768 GAAAAAGAAAG-AAAAAAATAGA
1 GAAAAAGAAAGAAAAAAAAAAAA
*
2435790 GAAAGAG-AAGAAAAAAAAAAAA
1 GAAAAAGAAAGAAAAAAAAAAAA
*
2435812 GAAAAAAGAAATAAAAAGAAACAAAA
1 G-AAAAAGAAAGAAAAA-AAA-AAAA
2435838 AAATTACAAG
Statistics
Matches: 38, Mismatches: 5, Indels: 6
0.78 0.10 0.12
Matches are distributed among these distances:
21 3 0.08
22 16 0.42
23 5 0.13
24 7 0.18
25 3 0.08
26 4 0.11
ACGTcount: A:0.80, C:0.01, G:0.16, T:0.03
Consensus pattern (23 bp):
GAAAAAGAAAGAAAAAAAAAAAA
Found at i:2435838 original size:34 final size:38
Alignment explanation
Indices: 2435769--2435840 Score: 98
Period size: 34 Copynumber: 2.0 Consensus size: 38
2435759 ATATTTGTTG
*
2435769 AAAAAGAAAGAAAAAAATAGAGAAAGAGAAGAAAAAAA
1 AAAAAGAAAGAAAAAAATAGAGAAAGAGAACAAAAAAA
*
2435807 AAAAAGAAA-AAAGAAATA-A-AAAGA-AACAAAAAAA
1 AAAAAGAAAGAAAAAAATAGAGAAAGAGAACAAAAAAA
2435841 TTACAAGGAA
Statistics
Matches: 32, Mismatches: 2, Indels: 4
0.84 0.05 0.11
Matches are distributed among these distances:
34 9 0.28
35 5 0.16
36 1 0.03
37 8 0.25
38 9 0.28
ACGTcount: A:0.82, C:0.01, G:0.14, T:0.03
Consensus pattern (38 bp):
AAAAAGAAAGAAAAAAATAGAGAAAGAGAACAAAAAAA
Found at i:2436111 original size:24 final size:24
Alignment explanation
Indices: 2436079--2436128 Score: 66
Period size: 24 Copynumber: 2.1 Consensus size: 24
2436069 TTGACAGTTA
2436079 ATTTATTCATATCGTATTTT-TATT
1 ATTTATTCATATCGT-TTTTGTATT
* *
2436103 ATTTTTTCATATTGTTTTTGTATT
1 ATTTATTCATATCGTTTTTGTATT
2436127 AT
1 AT
2436129 ATAATTATAT
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
23 4 0.17
24 19 0.83
ACGTcount: A:0.22, C:0.06, G:0.06, T:0.66
Consensus pattern (24 bp):
ATTTATTCATATCGTTTTTGTATT
Found at i:2438386 original size:38 final size:37
Alignment explanation
Indices: 2438325--2438493 Score: 142
Period size: 38 Copynumber: 4.4 Consensus size: 37
2438315 TAAGAACCAA
* * * *
2438325 TTTTGAATCGTGCCACCGATTAAAAATAATA-TTTTCT
1 TTTTGAACCATGCCACCAATTAAAAATAGTAGTTTT-T
*
2438362 TTTTCGAACCATGCCACCAATTAAAAATAGTGATTTTTT
1 TTTT-GAACCATGCCACCAATTAAAAATAGT-AGTTTTT
* * * *
2438401 GTTTTAAACCGTACTACCAATTAAAAATAGTAGTTTTT
1 -TTTTGAACCATGCCACCAATTAAAAATAGTAGTTTTT
* * * * *
2438439 GTATTGAACCATGCCACCAATTTAGAATATTAGTTTTCG
1 -TTTTGAACCATGCCACCAATTAAAAATAGTAGTTTT-T
*
2438478 TTTTGAACTATGCCAC
1 TTTTGAACCATGCCAC
2438494 TGGATTAGAA
Statistics
Matches: 107, Mismatches: 20, Indels: 9
0.79 0.15 0.07
Matches are distributed among these distances:
37 4 0.04
38 71 0.66
39 24 0.22
40 8 0.07
ACGTcount: A:0.33, C:0.17, G:0.12, T:0.38
Consensus pattern (37 bp):
TTTTGAACCATGCCACCAATTAAAAATAGTAGTTTTT
Found at i:2439035 original size:19 final size:20
Alignment explanation
Indices: 2439009--2439060 Score: 79
Period size: 19 Copynumber: 2.6 Consensus size: 20
2438999 CTGAAAAGAA
2439009 AATGTATCGATACATT-TTC
1 AATGTATCGATACATTCTTC
* *
2439028 ATTGTATCGATGCATTCTTC
1 AATGTATCGATACATTCTTC
2439048 AATGTATCGATAC
1 AATGTATCGATAC
2439061 TATAGACACC
Statistics
Matches: 28, Mismatches: 4, Indels: 1
0.85 0.12 0.03
Matches are distributed among these distances:
19 14 0.50
20 14 0.50
ACGTcount: A:0.29, C:0.17, G:0.13, T:0.40
Consensus pattern (20 bp):
AATGTATCGATACATTCTTC
Found at i:2439343 original size:8 final size:8
Alignment explanation
Indices: 2439330--2439470 Score: 81
Period size: 8 Copynumber: 17.1 Consensus size: 8
2439320 ATTTTCTTTG
2439330 ATAAAAAA
1 ATAAAAAA
2439338 ATAAAATAA
1 ATAAAA-AA
*
2439347 TTAAAAATA
1 ATAAAAA-A
2439356 ATAATAAAAA
1 AT-A-AAAAA
*
2439366 AGTCAAAAA
1 A-TAAAAAA
*
2439375 AT-ATAAA
1 ATAAAAAA
2439382 ATCAAAAAA
1 AT-AAAAAA
* *
2439391 ATCAAATA
1 ATAAAAAA
*
2439399 ATCAAAAA
1 ATAAAAAA
2439407 ATAAAAAA
1 ATAAAAAA
2439415 ATAAAAAA
1 ATAAAAAA
**
2439423 AT-TCAAA
1 ATAAAAAA
*
2439430 TTCAAAAAA
1 AT-AAAAAA
2439439 ATAAAAAA
1 ATAAAAAA
** *
2439447 AT-TTATA
1 ATAAAAAA
*
2439454 ATAAAAAT
1 ATAAAAAA
2439462 ATAAAAAA
1 ATAAAAAA
2439470 A
1 A
2439471 AAGTGAAATG
Statistics
Matches: 100, Mismatches: 23, Indels: 20
0.70 0.16 0.14
Matches are distributed among these distances:
7 14 0.14
8 53 0.53
9 25 0.25
10 3 0.03
11 5 0.05
ACGTcount: A:0.74, C:0.04, G:0.01, T:0.21
Consensus pattern (8 bp):
ATAAAAAA
Found at i:2439388 original size:24 final size:23
Alignment explanation
Indices: 2439330--2439470 Score: 108
Period size: 24 Copynumber: 6.0 Consensus size: 23
2439320 ATTTTCTTTG
2439330 ATAAAA-AAATAAAATAATTAAAAAT
1 ATAAAATAAA-AAAATAA--AAAAAT
* * *
2439355 A-ATAATAAAAAAGTCAAAAAAT
1 ATAAAATAAAAAAATAAAAAAAT
* *
2439377 ATAAAATCAAAAAAATCAAATAAT
1 ATAAAAT-AAAAAAATAAAAAAAT
*
2439401 CAAAAAATAAAAAAATAAAAAAAT
1 -ATAAAATAAAAAAATAAAAAAAT
*
2439425 -TCAAATTCAAAAAAATAAAAAAAT
1 AT-AAAAT-AAAAAAATAAAAAAAT
* * *
2439449 TTATAATAAAAATATAAAAAAA
1 ATAAAATAAAAAAATAAAAAAA
2439471 AAGTGAAATG
Statistics
Matches: 95, Mismatches: 14, Indels: 16
0.76 0.11 0.13
Matches are distributed among these distances:
22 7 0.07
23 22 0.23
24 55 0.58
25 11 0.12
ACGTcount: A:0.74, C:0.04, G:0.01, T:0.21
Consensus pattern (23 bp):
ATAAAATAAAAAAATAAAAAAAT
Found at i:2439445 original size:32 final size:32
Alignment explanation
Indices: 2439368--2439448 Score: 105
Period size: 32 Copynumber: 2.5 Consensus size: 32
2439358 AATAAAAAAG
*
2439368 TCAAAAAAT-ATAAAATCAAAAAAATCAAATAA
1 TCAAAAAATAAAAAAATCAAAAAAATCAAAT-A
2439400 TCAAAAAATAAAAAAAT-AAAAAAATTCAAAT-
1 TCAAAAAATAAAAAAATCAAAAAAA-TCAAATA
2439431 TCAAAAAAATAAAAAAAT
1 TC-AAAAAATAAAAAAAT
2439449 TTATAATAAA
Statistics
Matches: 45, Mismatches: 1, Indels: 6
0.87 0.02 0.12
Matches are distributed among these distances:
31 2 0.04
32 31 0.69
33 12 0.27
ACGTcount: A:0.74, C:0.07, G:0.00, T:0.19
Consensus pattern (32 bp):
TCAAAAAATAAAAAAATCAAAAAAATCAAATA
Found at i:2439447 original size:9 final size:9
Alignment explanation
Indices: 2439332--2439423 Score: 53
Period size: 9 Copynumber: 9.7 Consensus size: 9
2439322 TTTCTTTGAT
2439332 AAAAAAATA
1 AAAAAAATA
* *
2439341 AAATAATTA
1 AAAAAAATA
*
2439350 AAAATAATA
1 AAAAAAATA
2439359 ATAAAAAAGTCA
1 A-AAAAAA-T-A
*
2439371 AAAAATATA
1 AAAAAAATA
2439380 AAATCAAAA-A
1 AAA--AAAATA
**
2439390 AATCAAATA
1 AAAAAAATA
2439399 ATCAAAAAAT-
1 A--AAAAAATA
2439409 AAAAAAATA
1 AAAAAAATA
2439418 AAAAAA
1 AAAAAA
2439424 TTCAAATTCA
Statistics
Matches: 62, Mismatches: 12, Indels: 18
0.67 0.13 0.20
Matches are distributed among these distances:
8 10 0.16
9 26 0.42
10 10 0.16
11 14 0.23
12 2 0.03
ACGTcount: A:0.77, C:0.04, G:0.01, T:0.17
Consensus pattern (9 bp):
AAAAAAATA
Found at i:2439526 original size:20 final size:20
Alignment explanation
Indices: 2439501--2439540 Score: 80
Period size: 20 Copynumber: 2.0 Consensus size: 20
2439491 GAACATGCAT
2439501 GCAATGGGAGACAAAAGCAA
1 GCAATGGGAGACAAAAGCAA
2439521 GCAATGGGAGACAAAAGCAA
1 GCAATGGGAGACAAAAGCAA
2439541 ATGGAATGTG
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 20 1.00
ACGTcount: A:0.50, C:0.15, G:0.30, T:0.05
Consensus pattern (20 bp):
GCAATGGGAGACAAAAGCAA
Found at i:2439684 original size:17 final size:16
Alignment explanation
Indices: 2439657--2439688 Score: 55
Period size: 17 Copynumber: 1.9 Consensus size: 16
2439647 AGGTTGCCAG
2439657 CAAAGAAAGCAACGTT
1 CAAAGAAAGCAACGTT
2439673 CAAAGCAAAGCAACGT
1 CAAAG-AAAGCAACGT
2439689 GAAGCAGCAT
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
16 5 0.33
17 10 0.67
ACGTcount: A:0.50, C:0.22, G:0.19, T:0.09
Consensus pattern (16 bp):
CAAAGAAAGCAACGTT
Found at i:2440287 original size:43 final size:42
Alignment explanation
Indices: 2440220--2440300 Score: 110
Period size: 43 Copynumber: 1.9 Consensus size: 42
2440210 AACAGAAAAG
* *
2440220 AAGATAGCAGCAACGTGAAACTGCTGGAGGGGAAGAAGAGCGA
1 AAGACAGCAGCAACGTGAAACTGCTAG-GGGGAAGAAGAGCGA
*
2440263 AAGACAGCAGTAACGT-AAAGCTGCTAGGGGGAAGAAGA
1 AAGACAGCAGCAACGTGAAA-CTGCTAGGGGGAAGAAGA
2440301 CAGCAGCAAC
Statistics
Matches: 34, Mismatches: 3, Indels: 3
0.85 0.08 0.08
Matches are distributed among these distances:
42 14 0.41
43 20 0.59
ACGTcount: A:0.41, C:0.14, G:0.36, T:0.10
Consensus pattern (42 bp):
AAGACAGCAGCAACGTGAAACTGCTAGGGGGAAGAAGAGCGA
Found at i:2440306 original size:34 final size:34
Alignment explanation
Indices: 2440263--2440344 Score: 98
Period size: 34 Copynumber: 2.5 Consensus size: 34
2440253 AGAAGAGCGA
* *
2440263 AAGACAGCAGTAACGTAAAGCTGCTAGG-GGGAAG
1 AAGACAGCAGCAACGTAAAGCCGCT-GGAGGGAAG
* *
2440297 AAGACAGCAGCAACGTGAAGCCGCTGGAGGGAGG
1 AAGACAGCAGCAACGTAAAGCCGCTGGAGGGAAG
2440331 AAGA-A-CAGCAACGT
1 AAGACAGCAGCAACGT
2440345 GACAAGGGTA
Statistics
Matches: 43, Mismatches: 4, Indels: 4
0.84 0.08 0.08
Matches are distributed among these distances:
32 9 0.21
33 3 0.07
34 31 0.72
ACGTcount: A:0.38, C:0.18, G:0.35, T:0.09
Consensus pattern (34 bp):
AAGACAGCAGCAACGTAAAGCCGCTGGAGGGAAG
Found at i:2442285 original size:26 final size:26
Alignment explanation
Indices: 2442255--2442326 Score: 126
Period size: 26 Copynumber: 2.8 Consensus size: 26
2442245 TTTATTCATC
2442255 GGGGATACTCCAACCTCATTCCTCCG
1 GGGGATACTCCAACCTCATTCCTCCG
*
2442281 GGGGATACTCCAATCTCATTCCTCCG
1 GGGGATACTCCAACCTCATTCCTCCG
*
2442307 GGGGATACTCCAACCCCATT
1 GGGGATACTCCAACCTCATT
2442327 TTTAAAACTT
Statistics
Matches: 43, Mismatches: 3, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
26 43 1.00
ACGTcount: A:0.21, C:0.36, G:0.19, T:0.24
Consensus pattern (26 bp):
GGGGATACTCCAACCTCATTCCTCCG
Found at i:2449561 original size:36 final size:36
Alignment explanation
Indices: 2449520--2449590 Score: 133
Period size: 36 Copynumber: 2.0 Consensus size: 36
2449510 TATGGACTTA
2449520 ATAAATAGGGTTTTTAAACCTTACTTGGATAGATTG
1 ATAAATAGGGTTTTTAAACCTTACTTGGATAGATTG
*
2449556 ATAAATAGGGTTTTTAAACTTTACTTGGATAGATT
1 ATAAATAGGGTTTTTAAACCTTACTTGGATAGATT
2449591 TATGGTTATT
Statistics
Matches: 34, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
36 34 1.00
ACGTcount: A:0.34, C:0.07, G:0.18, T:0.41
Consensus pattern (36 bp):
ATAAATAGGGTTTTTAAACCTTACTTGGATAGATTG
Found at i:2455585 original size:99 final size:97
Alignment explanation
Indices: 2455387--2455597 Score: 271
Period size: 99 Copynumber: 2.2 Consensus size: 97
2455377 TATCGAGGAT
* * *
2455387 ACTCCAACCCTATTCTTCCGAGGGGATGCTCTAACTCTGTTTTTAAACTTGTCAAGATTTAAATC
1 ACTCCAACCCCATTCTTCCGAGGGGATACTCTAACTCTGTTTTTAAACTTATCAAGATTTAAATC
*
2455452 TTATTTTCATCTAAATTATCATCGCCGGGGAC
66 TTATTTTCATCTAAATTATCATCGCCGGGAAC
* * *
2455484 ACTCCAACCCCATTCTTCCGAGGGGATACTTTAATCTCGTTTTTTTAAACTTATCGAGATTTAAA
1 ACTCCAACCCCATTCTTCCGAGGGGATACTCTAA-CTC-TGTTTTTAAACTTATCAAGATTTAAA
* * * * *
2455549 TCTTATTTTC-TCTAGGATTGTTATTGTCGGGAAC
64 TCTTATTTTCATCTA-AATTATCATCGCCGGGAAC
*
2455583 ACTCTAACCCCATTC
1 ACTCCAACCCCATTC
2455598 CTCTAAGGAG
Statistics
Matches: 98, Mismatches: 13, Indels: 4
0.85 0.11 0.03
Matches are distributed among these distances:
97 31 0.32
98 7 0.07
99 60 0.61
ACGTcount: A:0.25, C:0.24, G:0.14, T:0.37
Consensus pattern (97 bp):
ACTCCAACCCCATTCTTCCGAGGGGATACTCTAACTCTGTTTTTAAACTTATCAAGATTTAAATC
TTATTTTCATCTAAATTATCATCGCCGGGAAC
Found at i:2455626 original size:99 final size:99
Alignment explanation
Indices: 2455387--2455626 Score: 218
Period size: 99 Copynumber: 2.4 Consensus size: 99
2455377 TATCGAGGAT
* * * * * * * *
2455387 ACTCCAACCCTATTCTTCCGAGGGGATGCTCTAA-CTC-TGTTTTTAAACTTGTCAAGATTTAAA
1 ACTCCAACCCCATTCCTCCAAGGAGATACTCCAACCTCATTTTTTTAAACTTATCAAGATTTAAA
*
2455450 TCTTATTTTCATCTAAATTATCATCGCCGGGGAC
66 TCTTATTTTCATCTAAATTATCATCGCCGGGAAC
* * * ** * * *
2455484 ACTCCAACCCCATTCTTCCGAGGGGATACTTTAATCTCGTTTTTTTAAACTTATCGAGATTTAAA
1 ACTCCAACCCCATTCCTCCAAGGAGATACTCCAACCTCATTTTTTTAAACTTATCAAGATTTAAA
* * * * *
2455549 TCTTATTTTC-TCTAGGATTGTTATTGTCGGGAAC
66 TCTTATTTTCATCTA-AATTATCATCGCCGGGAAC
* *
2455583 ACTCTAACCCCATTCCTCTAAGGAGATACTCCAACC-CTATTTTT
1 ACTCCAACCCCATTCCTCCAAGGAGATACTCCAACCTC-ATTTTT
2455627 CAACTAAAAT
Statistics
Matches: 118, Mismatches: 21, Indels: 6
0.81 0.14 0.04
Matches are distributed among these distances:
97 31 0.26
98 8 0.07
99 79 0.67
ACGTcount: A:0.25, C:0.24, G:0.13, T:0.37
Consensus pattern (99 bp):
ACTCCAACCCCATTCCTCCAAGGAGATACTCCAACCTCATTTTTTTAAACTTATCAAGATTTAAA
TCTTATTTTCATCTAAATTATCATCGCCGGGAAC
Found at i:2456631 original size:21 final size:22
Alignment explanation
Indices: 2456595--2456636 Score: 61
Period size: 21 Copynumber: 2.0 Consensus size: 22
2456585 ATTTTTCGCT
2456595 AAAATAATATATA-TTTAGTTA
1 AAAATAATATATATTTTAGTTA
2456616 AAAATAATAT-TAATTTTAGTT
1 AAAATAATATAT-ATTTTAGTT
2456637 TTATTAATTT
Statistics
Matches: 19, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
20 1 0.05
21 11 0.58
22 7 0.37
ACGTcount: A:0.50, C:0.00, G:0.05, T:0.45
Consensus pattern (22 bp):
AAAATAATATATATTTTAGTTA
Found at i:2457570 original size:38 final size:38
Alignment explanation
Indices: 2457503--2457577 Score: 105
Period size: 38 Copynumber: 2.0 Consensus size: 38
2457493 TTAGGATCTG
* * * *
2457503 GTTTCAAACCGTGTCACTAGTTAAGAATAGTAATTTTT
1 GTTTCAAACCGTGCCACCAATTAAAAATAGTAATTTTT
*
2457541 GTTTCAAACTGTGCCACCAATTAAAAATAGTAATTTT
1 GTTTCAAACCGTGCCACCAATTAAAAATAGTAATTTT
2457578 ATATTGAACT
Statistics
Matches: 32, Mismatches: 5, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
38 32 1.00
ACGTcount: A:0.35, C:0.15, G:0.13, T:0.37
Consensus pattern (38 bp):
GTTTCAAACCGTGCCACCAATTAAAAATAGTAATTTTT
Found at i:2458857 original size:20 final size:19
Alignment explanation
Indices: 2458829--2458866 Score: 58
Period size: 19 Copynumber: 1.9 Consensus size: 19
2458819 TTTAAATTAC
2458829 AATAATTTTAAATGTTAAAA
1 AATAATTTT-AATGTTAAAA
*
2458849 AATATTTTTAATGTTAAA
1 AATAATTTTAATGTTAAA
2458867 CAAAATATAA
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
19 9 0.53
20 8 0.47
ACGTcount: A:0.50, C:0.00, G:0.05, T:0.45
Consensus pattern (19 bp):
AATAATTTTAATGTTAAAA
Found at i:2462984 original size:30 final size:28
Alignment explanation
Indices: 2462943--2463014 Score: 92
Period size: 30 Copynumber: 2.5 Consensus size: 28
2462933 AATTTGCTCC
2462943 CAAATAAATTTTTA-TATTTAATTTATATT
1 CAAATAAATTTTTACT-TTTAATTTATA-T
*
2462972 CAAATAAAATTTTAACTTTTAATTTATAT
1 CAAAT-AAATTTTTACTTTTAATTTATAT
2463001 CTAAATAAATTTTT
1 C-AAATAAATTTTT
2463015 CACATAAATT
Statistics
Matches: 38, Mismatches: 2, Indels: 6
0.83 0.04 0.13
Matches are distributed among these distances:
29 14 0.37
30 23 0.61
31 1 0.03
ACGTcount: A:0.43, C:0.06, G:0.00, T:0.51
Consensus pattern (28 bp):
CAAATAAATTTTTACTTTTAATTTATAT
Found at i:2463024 original size:29 final size:28
Alignment explanation
Indices: 2462943--2463033 Score: 76
Period size: 30 Copynumber: 3.1 Consensus size: 28
2462933 AATTTGCTCC
*
2462943 CAAATAAATTTTTATATTTAATTTATATT
1 CAAATAAATTTTTACA-TTAATTTATATT
* *
2462972 CAAATAAAATTTTAACTTTTAATTTATA-T
1 CAAAT-AAATTTTTAC-ATTAATTTATATT
* *
2463001 CTAAATAAATTTTTCACATAAATTAATTATT
1 C-AAATAAATTTTT-ACATTAATTTA-TATT
2463032 CA
1 CA
2463034 TTTAAAATAA
Statistics
Matches: 49, Mismatches: 7, Indels: 11
0.73 0.10 0.16
Matches are distributed among these distances:
29 20 0.41
30 27 0.55
31 2 0.04
ACGTcount: A:0.44, C:0.08, G:0.00, T:0.48
Consensus pattern (28 bp):
CAAATAAATTTTTACATTAATTTATATT
Found at i:2463099 original size:30 final size:30
Alignment explanation
Indices: 2463039--2463099 Score: 79
Period size: 30 Copynumber: 2.0 Consensus size: 30
2463029 ATTCATTTAA
*
2463039 AATAAAAATTTATTTAAATTCATAATAAAT
1 AATAAAAATTTATTTAAATTAATAATAAAT
* *
2463069 AATAAAATTTTATTTAAGTATAATAA-AAAT
1 AATAAAAATTTATTTAAAT-TAATAATAAAT
2463099 A
1 A
2463100 TAATGATTTA
Statistics
Matches: 27, Mismatches: 3, Indels: 2
0.84 0.09 0.06
Matches are distributed among these distances:
30 22 0.81
31 5 0.19
ACGTcount: A:0.57, C:0.02, G:0.02, T:0.39
Consensus pattern (30 bp):
AATAAAAATTTATTTAAATTAATAATAAAT
Found at i:2463877 original size:3 final size:3
Alignment explanation
Indices: 2463869--2463895 Score: 54
Period size: 3 Copynumber: 9.0 Consensus size: 3
2463859 GGAGAGCGAG
2463869 AGA AGA AGA AGA AGA AGA AGA AGA AGA
1 AGA AGA AGA AGA AGA AGA AGA AGA AGA
2463896 GAAAAGAGAG
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 24 1.00
ACGTcount: A:0.67, C:0.00, G:0.33, T:0.00
Consensus pattern (3 bp):
AGA
Found at i:2463905 original size:9 final size:10
Alignment explanation
Indices: 2463866--2463906 Score: 52
Period size: 9 Copynumber: 4.4 Consensus size: 10
2463856 GAGGGAGAGC
2463866 GAGAGAAGAA
1 GAGAGAAGAA
2463876 GA-AGAAGAA
1 GAGAGAAGAA
2463885 GA-AGAAGAA
1 GAGAGAAGAA
*
2463894 GAGAAAAG-A
1 GAGAGAAGAA
2463903 GAGA
1 GAGA
2463907 CTGACCAGCT
Statistics
Matches: 29, Mismatches: 1, Indels: 3
0.88 0.03 0.09
Matches are distributed among these distances:
9 23 0.79
10 6 0.21
ACGTcount: A:0.63, C:0.00, G:0.37, T:0.00
Consensus pattern (10 bp):
GAGAGAAGAA
Found at i:2465144 original size:22 final size:22
Alignment explanation
Indices: 2465109--2465150 Score: 68
Period size: 22 Copynumber: 1.9 Consensus size: 22
2465099 TATTTTTATT
2465109 TAAATTTAATTATAAAAATATA
1 TAAATTTAATTATAAAAATATA
2465131 TAAATATTAA-TATAAAAATA
1 TAAAT-TTAATTATAAAAATA
2465151 ATATTTTAAT
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
22 15 0.79
23 4 0.21
ACGTcount: A:0.62, C:0.00, G:0.00, T:0.38
Consensus pattern (22 bp):
TAAATTTAATTATAAAAATATA
Found at i:2473004 original size:110 final size:110
Alignment explanation
Indices: 2472875--2473081 Score: 292
Period size: 110 Copynumber: 1.9 Consensus size: 110
2472865 AATTTACACG
* * *
2472875 AAAAATGAATTATCTTATATAAAAGGCATTCATATACCACTTTATGAC-CTTAGATGATGACCTA
1 AAAAATGAATTATCCTATATAAAAGGCATTCATATACCACTTTATGACTC-TAGACGATAACCTA
*
2472939 TTTCGGGGCAAATCTTTTGGT-CCTCGAATTTACGTAATTAACGCAA
65 TTTCGGGACAAATCTTTTGGTGCC-CGAATTTACGTAATTAACGCAA
* * * *
2472985 AAAAATGAATTATCCTATATAAATGGCGTTCGTATACCGCTTTATGACTCTAGACGATAACCTAT
1 AAAAATGAATTATCCTATATAAAAGGCATTCATATACCACTTTATGACTCTAGACGATAACCTAT
* *
2473050 TTTGGGACTAATCTTTTGGTGCCCGAATTTAC
66 TTCGGGACAAATCTTTTGGTGCCCGAATTTAC
2473082 ATATTGTAAA
Statistics
Matches: 85, Mismatches: 10, Indels: 4
0.86 0.10 0.04
Matches are distributed among these distances:
110 82 0.96
111 3 0.04
ACGTcount: A:0.32, C:0.18, G:0.15, T:0.34
Consensus pattern (110 bp):
AAAAATGAATTATCCTATATAAAAGGCATTCATATACCACTTTATGACTCTAGACGATAACCTAT
TTCGGGACAAATCTTTTGGTGCCCGAATTTACGTAATTAACGCAA
Found at i:2473728 original size:50 final size:51
Alignment explanation
Indices: 2473669--2473781 Score: 201
Period size: 51 Copynumber: 2.2 Consensus size: 51
2473659 TGAATAGTAC
*
2473669 ATGTATCGATACGTTCTG-TTTTTTACCCAGATGTATCGATACATTTTTCA
1 ATGTATCGATACCTTCTGTTTTTTTACCCAGATGTATCGATACATTTTTCA
*
2473719 ATGTATCGATACCTTCTGTTTTTTTACCTAGATGTATCGATACATTTTTCA
1 ATGTATCGATACCTTCTGTTTTTTTACCCAGATGTATCGATACATTTTTCA
2473770 ATGTATCGATAC
1 ATGTATCGATAC
2473782 ATCTAGTTTA
Statistics
Matches: 60, Mismatches: 2, Indels: 1
0.95 0.03 0.02
Matches are distributed among these distances:
50 17 0.28
51 43 0.72
ACGTcount: A:0.25, C:0.18, G:0.13, T:0.44
Consensus pattern (51 bp):
ATGTATCGATACCTTCTGTTTTTTTACCCAGATGTATCGATACATTTTTCA
Found at i:2473818 original size:31 final size:31
Alignment explanation
Indices: 2473783--2473846 Score: 110
Period size: 31 Copynumber: 2.1 Consensus size: 31
2473773 TATCGATACA
*
2473783 TCTAGTTTATTTTGAGCATTTTGAGCCATTT
1 TCTAGTTTATTTTGAGCATTTCGAGCCATTT
*
2473814 TCTAGTTTATTTTGAGCATTTCGGGCCATTT
1 TCTAGTTTATTTTGAGCATTTCGAGCCATTT
2473845 TC
1 TC
2473847 AACCTTGGCT
Statistics
Matches: 31, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
31 31 1.00
ACGTcount: A:0.17, C:0.16, G:0.17, T:0.50
Consensus pattern (31 bp):
TCTAGTTTATTTTGAGCATTTCGAGCCATTT
Found at i:2474727 original size:21 final size:21
Alignment explanation
Indices: 2474694--2474734 Score: 66
Period size: 21 Copynumber: 2.0 Consensus size: 21
2474684 TCATCTAAAC
2474694 AGCCGATGTCCATGCATTTTG
1 AGCCGATGTCCATGCATTTTG
2474715 AGCC-ATGTACCATGCATTTT
1 AGCCGATGT-CCATGCATTTT
2474735 AACATGTCCA
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
20 4 0.21
21 15 0.79
ACGTcount: A:0.22, C:0.24, G:0.20, T:0.34
Consensus pattern (21 bp):
AGCCGATGTCCATGCATTTTG
Found at i:2477210 original size:109 final size:109
Alignment explanation
Indices: 2477012--2477363 Score: 438
Period size: 109 Copynumber: 3.2 Consensus size: 109
2477002 CACATTGCGA
* * * * *** * *
2477012 TACATACTTAATGCAAAAAATGAATTATCCTATGTAAAGGGTATTTGTACATCGTTTTATGACTC
1 TACATAATTAATGC-AAAAATGAATTTTCCTATGTAAAGGGCATTCGTATGCCGCTTTACGACTC
*
2477077 TAGACAATGATTTATTTCGGGGCCAATCCCTTGGTGCTTGAAT-T
65 TAGACGATGATTTATTTCGGGGCCAATCCCTTGGTGCTTGAATAT
* * *
2477121 TACATAATTAATGCAAAAATGAATTTTCCTATGTAAAGGGCGTTCGTATGCCACTTTACGACTTT
1 TACATAATTAATGCAAAAATGAATTTTCCTATGTAAAGGGCATTCGTATGCCGCTTTACGACTCT
* * *
2477186 AGACGATTATTTTATTTCGAGGCCAATTCCTTGGTGCTTGAATAT
66 AGACGATGA-TTTATTTCGGGGCCAATCCCTTGGTGCTTGAATAT
** * * *
2477231 TATGTAATTAATGC-AAAATGAATTTTCCTATGTAGAGGGCATTCGTATGCTGCTTTACAACTCT
1 TACATAATTAATGCAAAAATGAATTTTCCTATGTAAAGGGCATTCGTATGCCGCTTTACGACTCT
**
2477295 AGACGATGATTTATTTCGGGGCCAATCCCTTGGTGCCCGAATAT
66 AGACGATGATTTATTTCGGGGCCAATCCCTTGGTGCTTGAATAT
** *
2477339 TATGTAATTGATGCAAAAATGAATT
1 TACATAATTAATGCAAAAATGAATT
2477364 CTAAATAGGC
Statistics
Matches: 210, Mismatches: 30, Indels: 6
0.85 0.12 0.02
Matches are distributed among these distances:
108 91 0.43
109 106 0.50
110 13 0.06
ACGTcount: A:0.30, C:0.16, G:0.18, T:0.36
Consensus pattern (109 bp):
TACATAATTAATGCAAAAATGAATTTTCCTATGTAAAGGGCATTCGTATGCCGCTTTACGACTCT
AGACGATGATTTATTTCGGGGCCAATCCCTTGGTGCTTGAATAT
Found at i:2477666 original size:54 final size:56
Alignment explanation
Indices: 2477567--2478058 Score: 400
Period size: 54 Copynumber: 8.9 Consensus size: 56
2477557 TGTCAACTAG
* * * * *
2477567 TGTGGGCTTTA-ACTTAGGTGCTAACGAATGTGGGCTTAGACTTATGTGCCAAGGAA
1 TGTGGGC-TTAGACTTATGTGCCAACTAATGTGGGCTTTGACTTATGTGCCAACGAA
* * * *
2477623 TGTGGCCTTTGAC-T-TGTGCCAACTAATGTGAGCTTTGACTTATGTGCCAGCGAA
1 TGTGGGCTTAGACTTATGTGCCAACTAATGTGGGCTTTGACTTATGTGCCAACGAA
* * * *
2477677 TGTGGGCTTAGACTT-T-TGCCAAC-AAGTGTGGACTTTAACTCA-GATGCCAACTAA
1 TGTGGGCTTAGACTTATGTGCCAACTAA-TGTGGGCTTTGACTTATG-TGCCAACGAA
* * * * *
2477731 TATGGGCTTAGACTTGTGTGCCAA-TGAGTGTGGACTTTGA-TT-TCTGCCAACGAA
1 TGTGGGCTTAGACTTATGTGCCAACT-AATGTGGGCTTTGACTTATGTGCCAACGAA
* * * * * * *
2477785 TGTGGGCTTTGACTTGTGTGCTAA-TGAATGTGGGCTTTAACTTGTGTGCCATCTAA
1 TGTGGGCTTAGACTTATGTGCCAACT-AATGTGGGCTTTGACTTATGTGCCAACGAA
* * ** ** * *
2477841 TGTGGGCTTTGA-TTCATATGCCAACTAGCGTGGATTTTGACTTGTGTGCCAATGAA
1 TGTGGGCTTAGACTT-ATGTGCCAACTAATGTGGGCTTTGACTTATGTGCCAACGAA
* * * * * * *
2477897 TATGGGCTTAGATTTCTATGCCAACGAATGTGGGCTATGACTTGTGTGCCAACGAA
1 TGTGGGCTTAGACTTATGTGCCAACTAATGTGGGCTTTGACTTATGTGCCAACGAA
* *
2477953 TGTGGGCTTAGACTTATGTGCCAACAAATGTGGGCTTTGA-GT-TGTGCCAACGAA
1 TGTGGGCTTAGACTTATGTGCCAACTAATGTGGGCTTTGACTTATGTGCCAACGAA
* * * * * *
2478007 TATGGGCTTTGACTTATGTGCCATCTAATGTAGGCTTTGACTCATATGCCAA
1 TGTGGGCTTAGACTTATGTGCCAACTAATGTGGGCTTTGACTTATGTGCCAA
2478059 ATAGCGTAGG
Statistics
Matches: 352, Mismatches: 68, Indels: 32
0.78 0.15 0.07
Matches are distributed among these distances:
53 3 0.01
54 175 0.50
55 12 0.03
56 158 0.45
57 4 0.01
ACGTcount: A:0.23, C:0.17, G:0.27, T:0.33
Consensus pattern (56 bp):
TGTGGGCTTAGACTTATGTGCCAACTAATGTGGGCTTTGACTTATGTGCCAACGAA
Found at i:2477677 original size:82 final size:84
Alignment explanation
Indices: 2477560--2478048 Score: 396
Period size: 82 Copynumber: 5.9 Consensus size: 84
2477550 ACTTAGATGT
* * * * *
2477560 CAACTAGTGTGGGCTTTAACTTAGGTGCTAACGAATGTGGGCTTAGACTTATGTGCCAAGGAATG
1 CAACTAATGTGGGCTTTGACTTATGTGCCAACGAATGTGGGCTTAGACTTATGTGCCAACGAATG
*
2477625 TGGCCTTTGAC-T-TGTGC
66 TGGACTTTGACTTGTGTGC
* *
2477642 CAACTAATGTGAGCTTTGACTTATGTGCCAGCGAATGTGGGCTTAGACTT-T-TGCCAAC-AAGT
1 CAACTAATGTGGGCTTTGACTTATGTGCCAACGAATGTGGGCTTAGACTTATGTGCCAACGAA-T
* * *
2477704 GTGGACTTTAACTCAG-ATGC
65 GTGGACTTTGACT-TGTGTGC
* * * * * * * *
2477724 CAACTAATATGGGCTTAGACTTGTGTGCCAATGAGTGTGGACTTTGA-TT-TCTGCCAACGAATG
1 CAACTAATGTGGGCTTTGACTTATGTGCCAACGAATGTGGGCTTAGACTTATGTGCCAACGAATG
*
2477787 TGGGCTTTGACTTGTGTGC
66 TGGACTTTGACTTGTGTGC
* * * * * * * * *
2477806 TAA-TGAATGTGGGCTTTAACTTGTGTGCCATCTAATGTGGGCTTTGA-TTCATATGCCAACTAG
1 CAACT-AATGTGGGCTTTGACTTATGTGCCAACGAATGTGGGCTTAGACTT-ATGTGCCAACGAA
* *
2477869 CGTGGATTTTGACTTGTGTGC
64 TGTGGACTTTGACTTGTGTGC
* * * * * *
2477890 CAA-TGAATATGGGCTTAGATTTCTATGCCAACGAATGTGGGC-TATGACTTGTGTGCCAACGAA
1 CAACT-AATGTGGGCTTTGACTTATGTGCCAACGAATGTGGGCTTA-GACTTATGTGCCAACGAA
* * *
2477953 TGTGGGCTTAGACTTATGTGC
64 TGTGGACTTTGACTTGTGTGC
* * * * * *
2477974 CAACAAATGTGGGCTTTGA-GT-TGTGCCAACGAATATGGGCTTTGACTTATGTGCCATCTAATG
1 CAACTAATGTGGGCTTTGACTTATGTGCCAACGAATGTGGGCTTAGACTTATGTGCCAACGAATG
2478037 TAGG-CTTTGACT
66 T-GGACTTTGACT
2478049 CATATGCCAA
Statistics
Matches: 323, Mismatches: 69, Indels: 30
0.77 0.16 0.07
Matches are distributed among these distances:
79 2 0.01
80 17 0.05
81 6 0.02
82 187 0.58
83 7 0.02
84 102 0.32
85 2 0.01
ACGTcount: A:0.23, C:0.17, G:0.27, T:0.33
Consensus pattern (84 bp):
CAACTAATGTGGGCTTTGACTTATGTGCCAACGAATGTGGGCTTAGACTTATGTGCCAACGAATG
TGGACTTTGACTTGTGTGC
Found at i:2478045 original size:28 final size:28
Alignment explanation
Indices: 2477567--2478058 Score: 412
Period size: 28 Copynumber: 17.9 Consensus size: 28
2477557 TGTCAACTAG
* * *
2477567 TGTGGGCTTTAACTTAGGTGCTAACGAA
1 TGTGGGCTTTGACTTATGTGCCAACGAA
* *
2477595 TGTGGGCTTAGACTTATGTGCCAAGGAA
1 TGTGGGCTTTGACTTATGTGCCAACGAA
* *
2477623 TGTGGCCTTTGAC-T-TGTGCCAACTAA
1 TGTGGGCTTTGACTTATGTGCCAACGAA
* *
2477649 TGTGAGCTTTGACTTATGTGCCAGCGAA
1 TGTGGGCTTTGACTTATGTGCCAACGAA
*
2477677 TGTGGGCTTAGACTT-T-TGCCAAC-AA
1 TGTGGGCTTTGACTTATGTGCCAACGAA
* * * *
2477702 GTGTGGACTTTAACTCA-GATGCCAACTAA
1 -TGTGGGCTTTGACTTATG-TGCCAACGAA
* * * * *
2477731 TATGGGCTTAGACTTGTGTGCCAATGAG
1 TGTGGGCTTTGACTTATGTGCCAACGAA
* *
2477759 TGTGGACTTTGA-TT-TCTGCCAACGAA
1 TGTGGGCTTTGACTTATGTGCCAACGAA
* * *
2477785 TGTGGGCTTTGACTTGTGTGCTAATGAA
1 TGTGGGCTTTGACTTATGTGCCAACGAA
* * * *
2477813 TGTGGGCTTTAACTTGTGTGCCATCTAA
1 TGTGGGCTTTGACTTATGTGCCAACGAA
* * *
2477841 TGTGGGCTTTGA-TTCATATGCCAACTAG
1 TGTGGGCTTTGACTT-ATGTGCCAACGAA
* ** * *
2477869 CGTGGATTTTGACTTGTGTGCCAATGAA
1 TGTGGGCTTTGACTTATGTGCCAACGAA
* * * * *
2477897 TATGGGCTTAGATTTCTATGCCAACGAA
1 TGTGGGCTTTGACTTATGTGCCAACGAA
* *
2477925 TGTGGGCTATGACTTGTGTGCCAACGAA
1 TGTGGGCTTTGACTTATGTGCCAACGAA
* *
2477953 TGTGGGCTTAGACTTATGTGCCAACAAA
1 TGTGGGCTTTGACTTATGTGCCAACGAA
*
2477981 TGTGGGCTTTGA-GT-TGTGCCAACGAA
1 TGTGGGCTTTGACTTATGTGCCAACGAA
* * *
2478007 TATGGGCTTTGACTTATGTGCCATCTAA
1 TGTGGGCTTTGACTTATGTGCCAACGAA
* * *
2478035 TGTAGGCTTTGACTCATATGCCAA
1 TGTGGGCTTTGACTTATGTGCCAA
2478059 ATAGCGTAGG
Statistics
Matches: 362, Mismatches: 88, Indels: 28
0.76 0.18 0.06
Matches are distributed among these distances:
25 2 0.01
26 80 0.22
27 11 0.03
28 264 0.73
29 5 0.01
ACGTcount: A:0.23, C:0.17, G:0.27, T:0.33
Consensus pattern (28 bp):
TGTGGGCTTTGACTTATGTGCCAACGAA
Found at i:2478071 original size:82 final size:82
Alignment explanation
Indices: 2477915--2478071 Score: 190
Period size: 82 Copynumber: 1.9 Consensus size: 82
2477905 TAGATTTCTA
* * * * *
2477915 TGCCAACGAATGTGGGCTATGACTTGTGTGCCAACGAATGTGGGCTTAGACTTATGTGCCAACAA
1 TGCCAACGAATATGGGCTATGACTTATGTGCCAACGAATGTAGGCTTAGACTCATATGCCAACAA
* *
2477980 ATGTGGGCTTTGAGTTG
66 ACGTAGGCTTTGAGTTG
* * * *
2477997 TGCCAACGAATATGGGCTTTGACTTATGTGCCATCTAATGTAGGCTTTGACTCATATGCCAA-AT
1 TGCCAACGAATATGGGCTATGACTTATGTGCCAACGAATGTAGGCTTAGACTCATATGCCAACA-
*
2478061 AGCGTAGGCTT
65 AACGTAGGCTT
2478072 CCTTTTGATA
Statistics
Matches: 62, Mismatches: 12, Indels: 2
0.82 0.16 0.03
Matches are distributed among these distances:
81 1 0.02
82 61 0.98
ACGTcount: A:0.24, C:0.18, G:0.27, T:0.31
Consensus pattern (82 bp):
TGCCAACGAATATGGGCTATGACTTATGTGCCAACGAATGTAGGCTTAGACTCATATGCCAACAA
ACGTAGGCTTTGAGTTG
Found at i:2484401 original size:20 final size:19
Alignment explanation
Indices: 2484376--2484426 Score: 66
Period size: 20 Copynumber: 2.6 Consensus size: 19
2484366 TTCAATAATT
*
2484376 TGTATCGATACAGCAGTAAA
1 TGTATCGATACAGAAGT-AA
* *
2484396 TGTATCGATACATAAGTGA
1 TGTATCGATACAGAAGTAA
2484415 TGTATCGATACA
1 TGTATCGATACA
2484427 ATGTATCGAT
Statistics
Matches: 28, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
19 13 0.46
20 15 0.54
ACGTcount: A:0.37, C:0.14, G:0.20, T:0.29
Consensus pattern (19 bp):
TGTATCGATACAGAAGTAA
Found at i:2484419 original size:19 final size:18
Alignment explanation
Indices: 2484376--2484458 Score: 68
Period size: 19 Copynumber: 4.7 Consensus size: 18
2484366 TTCAATAATT
**
2484376 TGTATCGATACAGCAGTAAA
1 TGTATCGATACATAAGT--A
2484396 TGTATCGATACATAAGTGA
1 TGTATCGATACATAAGT-A
2484415 TGTATCGATAC---A--A
1 TGTATCGATACATAAGTA
*
2484428 TGTATCGATACATAAGTTT
1 TGTATCGATACATAAG-TA
2484447 TGTATCGATACA
1 TGTATCGATACA
2484459 ATGTATCGCT
Statistics
Matches: 53, Mismatches: 4, Indels: 13
0.76 0.06 0.19
Matches are distributed among these distances:
13 12 0.23
16 2 0.04
19 24 0.45
20 15 0.28
ACGTcount: A:0.36, C:0.13, G:0.18, T:0.33
Consensus pattern (18 bp):
TGTATCGATACATAAGTA
Found at i:2484432 original size:13 final size:13
Alignment explanation
Indices: 2484414--2484472 Score: 55
Period size: 13 Copynumber: 4.1 Consensus size: 13
2484404 TACATAAGTG
2484414 ATGTATCGATACA
1 ATGTATCGATACA
2484427 ATGTATCGATACATA
1 ATGTATCGATAC--A
2484442 AGTTTTGTATCGATACA
1 A----TGTATCGATACA
*
2484459 ATGTATCGCTACA
1 ATGTATCGATACA
2484472 A
1 A
2484473 AGCTACTGCC
Statistics
Matches: 39, Mismatches: 1, Indels: 12
0.75 0.02 0.23
Matches are distributed among these distances:
13 24 0.62
15 2 0.05
17 2 0.05
19 11 0.28
ACGTcount: A:0.36, C:0.15, G:0.15, T:0.34
Consensus pattern (13 bp):
ATGTATCGATACA
Found at i:2484435 original size:32 final size:32
Alignment explanation
Indices: 2484394--2484471 Score: 129
Period size: 32 Copynumber: 2.4 Consensus size: 32
2484384 TACAGCAGTA
2484394 AATGTATCGATACATAAGTGATGTATCGATAC
1 AATGTATCGATACATAAGTGATGTATCGATAC
**
2484426 AATGTATCGATACATAAGTTTTGTATCGATAC
1 AATGTATCGATACATAAGTGATGTATCGATAC
*
2484458 AATGTATCGCTACA
1 AATGTATCGATACA
2484472 AAGCTACTGC
Statistics
Matches: 43, Mismatches: 3, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
32 43 1.00
ACGTcount: A:0.36, C:0.14, G:0.17, T:0.33
Consensus pattern (32 bp):
AATGTATCGATACATAAGTGATGTATCGATAC
Found at i:2486986 original size:75 final size:76
Alignment explanation
Indices: 2486902--2487085 Score: 273
Period size: 75 Copynumber: 2.4 Consensus size: 76
2486892 TTTTCATCTC
* *
2486902 GGGGATACTCCAACCCCGGTTTTATTTCTAAAACATCAATTTTTTATC-GGGATACTCTAACCCC
1 GGGGATACTCCAACCCCGGTTTTATTTCTAAAACATCAATTTTTCATCGGGGATACTCCAACCCC
*
2486966 GTTATTTTC-AA
66 ATTA-TTTCGAA
* *
2486977 GGGGATACTCTAACCCCGGTTTTATTTCTACAACATCAATTTTTCATCGGGGATACTCCAACCCC
1 GGGGATACTCCAACCCCGGTTTTATTTCTAAAACATCAATTTTTCATCGGGGATACTCCAACCCC
*
2487042 ATTATTTCGGA
66 ATTATTTCGAA
* *
2487053 GGGGATACTCCAACCCCGGCTTTATATCTAAAA
1 GGGGATACTCCAACCCCGGTTTTATTTCTAAAA
2487086 ATATTGTTTT
Statistics
Matches: 97, Mismatches: 10, Indels: 3
0.88 0.09 0.03
Matches are distributed among these distances:
75 49 0.51
76 48 0.49
ACGTcount: A:0.27, C:0.26, G:0.15, T:0.33
Consensus pattern (76 bp):
GGGGATACTCCAACCCCGGTTTTATTTCTAAAACATCAATTTTTCATCGGGGATACTCCAACCCC
ATTATTTCGAA
Done.